Yeo Lab

Degrees

Ph.D., Chemistry and Biochemistry, University of Colorado, Boulder, 2003

Summary

Stefan is an RNA biochemist, neuroscientist and stem cell biologist. Among his many responsibilities in the lab, he is the project coordinator for an NIH-funded U19 academic/industrial collaboration dubbed Copacabana (Collaboration On Preclinical Autism Cellular Assays, Biosignatures And Network Analyses), which is led by the Yeo lab and includes four other labs at UCSD and the Salk Institute, as well as Fluidigm and Allele Biotech as the industrial partners.

Stefan received his PhD in Chemistry and Biochemistry from the University of Colorado at Boulder. In his thesis work in the lab of Tom Cech, he elucidated the role of p43, a protein subunit of telomerase from the ciliated model organism Euplotes. As a postdoctoral fellow of the Damon Runyon Cancer Research Foundation, Stefan joined the lab of Fred Gage at the Salk Institute to study transcriptional and post-transcriptional gene regulation in embryonic and adult neurogenesis. After brief but highly productive venture into the pharma industry, which led Stefan to Roche in Basel (Switzerland) to establish genome-editing based models of neurodevelopmental disorders, Stefan joined the Yeo lab as an Associate Project Scientist.

Publications

Okholm TLH, Sathe S, Park SS, Kamstrup AB, Rasmussen AM, Shankar A, Chua ZM, Fristrup N, Nielsen MM, Vang S, Dyrskjor L, Aigner S, Damgaard CK, Yeo GW, Pedersen JS. Transcriptome-wide profiles of circular RNA and RNA-binding protein interactions review effects on circular RNA biogenesis and cancer pathway expression. Genome Medicine, 2020.

Donsbach P, Yee BA, Sanchez-Hevia D, Berenguer J, Aigner S, Yeo GW, Klostermeier D. The Thermus thermophilus DEAD-box protein Hera is a general RNA binding protein and plays a key role in tRNA metabolism. RNA, 2020.

Lasman L, Krupalnik V, Viukov S, Mor N, Aguilera-Castrejon A, Schneir D, Bayerl J, Mizrahi O, Peles S, Tawil S, Sathe S, Nachshon A, Shani T, Zerbib M, Kilimnik I, Aigner S, Shankar A, Mueller JR, Schwartz S, Stern-Ginossar N, Yeo GW, Geula S, Novershtern N, Hanna JH. Context-dependent functional compensation between Ythdf m6a reader proteins. Genes & Dev, 2020.

Batra R, Nelles DA, Roth DM, Krach F, Nutter CA, Tadokoro T, Thomas JD, Sznajder L, Blue SM, Gutierrez H, Liu P, Aigner S, Platoshyn O, Miyanohara A, Marsala M, Swanson MS, Yeo GW. The sustained expression of Cas9 targeting toxic RNAs reverses disease phenotypes in mouse models of myotonic dystrophy type 1. Nature Biomedical Engineering, 2020.

Tavares CDJ§, Aigner S§, Sharabi K, Sathe S, Mutli B, Yeo GW, Puigserver P. Transcriptome-wide analysis of PGC-1a-binding RNAs identifies genes linked to glucagon metabolic action. PNAS. 2020 July 23. (co-first author)

Coyne A, Zaepfel B, Hayes L, Fitchman B, Salzberg Y, Luo EC, Bowen K, Trost H, Aigner S, Rigo F, Yeo GW, Harel A, Svendsen CN, Sareen D, Rothstein JD. G4C2 Repeat RNA Initiates a POM121-Mediated Reduction in Specific Nucleoporins in C9orf72 ALS/FTD. Neuron. 2020 Sept 23.

Luo EC, Nathanson JL, Tan FE, Schwartz JL, Schmok JC, Shankar A, Markmiller S, Yee BA, Sathe S, Pratt GA, Scaletta DB, Ha Y, Hill DE, Aigner S, Yeo GW. Large-scale tethered function assays identify factors that regulate mRNA stability and translation. Nature Structural and Molecular Biology. 2020 Aug 17.

Van Nostrand EL, Freese P, Pratt GA, Wang X, Wei X, Xiao R, Blue SM, Chen J-Y, Cody NAL, Dominguez D, Olson S, Sundararaman B, Zhan L, Bazile C, Bouvrette LPB, Bergalet J, Duff MO, Garcia KE, Gelboin-Burkhart C, Hochman M, Lambert NJ, Li H, Nguyen TB, Palden T, Rabano I, Sathe S, Stanton R, Su A, Wang R, Yee BA, Zhou B, Louie AL, Aigner S, Fu X-D, Lécuyer E, Burge CB, Graveley BR, Yeo GW. A large-scale binding and functional map of human RNA-binding proteins. Nature. 2020 Jul 29. doi: 10.1038/s41586-020-2077-3

Di Stefano B, Luo EC, Haggerty C, Aigner S, Charlton J, Brumbaugh J, Ji F, Rabano Jiménez I, Clowers KJ, Huebner AJ, Clement K, Lipchina I, de Kort MAC,Anselmo A, Pulice J, Gerli MFM, Gu H, Gygi SP, Sadreyev RI, Meissner A, Yeo GW, Hochedlinger K. The RNA Helicase DDX6 Controls Cellular Plasticity by Modulating P-Body Homeostasis. Cell Stem Cell. 2019 Sep 27. doi: 10.1016/j.stem.2019.08.018.

Kathuria A, Nowosiad P, Jagasia R, Aigner S, Taylor RD, Andreae LC, Gatford NJF, Lucchesi W, Srivastava DP, Price J. Stem cell-derived neurons from autistic individuals with SHANK3 mutation show morphogenetic abnormalities during early development. Mol Psychiatry. 2017 Sep 26. doi: 10.1038/mp.2017.185.

Batra R, Nelles DA, Pirie E, Blue SM, Marina RJ, Wang H, Chaim IA, Thomas JD, Zhang N, Nguyen V, Aigner S, Markmiller S, Xia G, Corbett KD, Swanson MS, Yeo GW. Elimination of Toxic Microsatellite Repeat Expansion RNA by RNA-Targeting Cas9. Cell. 2017 Aug 10. doi: 10.1016/j.cell.2017.07.010.

Gündner AL, Meyer CA, Aigner S, Christensen K, Patsch C, Jagasia R, Baumann K, Burcin M. Generation of a homozygous GBA deletion human embryonic stem cell line. Stem Cell Research. 2017 Jul 11. doi: 10.1016/j.scr.2017.07.009.

Lugert S, Kremer T, Jagasia R, Herrmann A, Aigner S, Giachino C, Mendez-David I, Gardier AM, Carralot JP, Meistermann H, Augustin A, Saxe MD, Lamerz J,Duran-Pacheco G, Ducret A, Taylor V, David DJ, Czech C. Glypican-2 levels incerebrospinal fluid predict the status of adult hippocampal neurogenesis. SciRep. 2017 Apr 25. doi: 10.1038/srep46543. PMID: 28440309

Kakaradov B, Arsenio J, Widjaja CE, He Z, Aigner S, Metz PJ, Yu B, Wehrens EJ,Lopez J, Kim SH, Zuniga EI, Goldrath AW, Chang JT, Yeo GW. Early transcriptional and epigenetic regulation of CD8(+) T cell differentiation revealed by single-cell RNA sequencing. Nat Immunol. 2017 Feb 20. doi: 10.1038/ni.3688.PMID: 28218746.

Batra R, Stark TJ, Clark E, Belzile JP, Wheeler EC, Yee BA, Huang H, Gelboin-Burkhart C, Huelga SC, Aigner S, Roberts BT, Bos TJ, Sathe S, Donohue JP, Rigo F, Ares M Jr, Spector DH, Yeo GW. RNA-binding protein CPEB1 remodels host and viral RNA landscapes. Nat Struct Mol Biol. 2016 Oct 24. doi:10.1038/nsmb.3310. PMID: 27775709.

Grabole N, Zhang JD, Aigner S, Ruderisch N, Costa V, Weber FC, Theron M, Berntenis N, Spleiss O, Ebeling M, Yeo GW, Jagasia R, Kiialainen A. Genomic analysis of the molecular neuropathology of tuberous sclerosis using a human stem cell model. Genome Med. 2016 Sep 21;8(1):94. PMID: 27655340

Conway AE, Van Nostrand EL, Pratt GA, Aigner S, Wilbert ML, Sundararaman B, Freese P, Lambert NJ, Sathe S, Liang TY, Essex A, Landais S, Burge CB, Jones DL, Yeo GW. Enhanced CLIP Uncovers IMP Protein-RNA Targets in Human Pluripotent Stem Cells Important for Cell Adhesion and Survival. Cell Rep. 2016; 15(3):666-79. PMID: 27068461

Costa V * , Aigner S * , Vukcevic M *, Sauter E, Behr K, Ebeling M, Dunkley T, Friedlein A, Zoffmann S, Meyer CA, Knoflach F, Lugert S, Patsch C, Fjeldskaar F, Chicha-Gaudimier L, Kiialainen A, Piraino P, Bedoucha M, Graf M, Jessberger S, Ghosh A, Bischofberger J, Jagasia R. mTORC1 Inhibition Corrects Neurodevelopmental and Synaptic Alterations in a Human Stem Cell Model of Tuberous Sclerosis. Cell Rep. 2016; 15(1):86-95. PMID: 27052171 ( * Co-first authors)

Bos TJ, Nussbacher JK, Aigner S, Yeo GW. Tethered Function Assays as Tools to Elucidate the Molecular Roles of RNA-Binding Proteins. Adv Exp Med Biol. 2016; 907:61-88. PMID: 27256382

Dunkley T, Costa V, Friedlein A, Lugert S, Aigner S, Ebeling M, Miller MT, Patsch C, Piraino P, Cutler P, Jagasia R. Characterization of a human pluripotent stem cell-derived model of neuronal development using multiplexed targeted proteomics.Proteomics Clin. Appl. 2015; 9(7-8):684-94. PMID: 25684324

Nelles DA, Fang MY, Aigner S, Yeo GW. Applications of Cas9 as an RNA-programmed RNA-binding protein. BioEssays. 2015; 37(7):732-9. PMID: 25880497

Havlicek S, Kohl Z, Mishra HK, Prots I, Eberhardt E, Denguir N, Wend H, Plötz S, Boyer L, Marchetto MC, Aigner S, Sticht H, Groemer TW, Hehr U, Lampert A, Schlötzer-Schrehardt U, Winkler J, Gage FH, Winner B. Gene dosage-dependent rescue of HSP neurite defects in SPG4 patients’ neurons. Hum. Mol. Genet. 2014; 23(10):2527-41. PMID: 24381312

Aigner S, Heckel T, Zhang JD, Andreae LC, Jagasia R. Human pluripotent stem cell models of autism spectrum disorder: emerging frontiers, opportunities, and challenges towards neuronal networks in a dish. Psychopharmacology. 2014; 231(6):1089-104. PMID: 24232378

Vorstman JA, Spooren W, Persico AM, Collier DA, Aigner S, Jagasia R, Glennon JC, Buitelaar JK. Using genetic findings in autism for the development of new pharmaceutical compounds. Psychopharmacology. 2014; 231(6):1063-78. PMID: 24292384

Urich E, Patsch C, Aigner S, Graf M, Iacone R, Freskgård PO. Multicellular self-assembled spheroidal model of the blood brain barrier. Sci. Rep. 2013; 3:1500. PMID: 23511305

Bracko O, Singer T, Aigner S, Knobloch M, Winner B, Ray J, Clemenson GD Jr, Suh H, Couillard-Despres S, Aigner L, Gage FH, Jessberger S. Gene expression profiling of neural stem cells and their neuronal progeny reveals IGF2 as a regulator of adult hippocampal neurogenesis. J. Neurosci. 2012; 32(10):3376-87. PMID: 22399759

Winner B, Jappelli R, Maji SK, Desplats PA, Boyer L, Aigner S, Hetzer C, Loher T, Vilar M, Campioni S, Tzitzilonis C, Soragni A, Jessberger S, Mira H, Consiglio A, Pham E, Masliah E, Gage FH, Riek R. In vivo demonstration that alpha-synuclein oligomers are toxic. Proc Natl Acad Sci U S A. 2011; 108(10):4194-9. PMID: 21325059

Lu YC, Smielewska M, Palakodeti D, Lovci MT, Aigner S, Yeo GW, Graveley BR. Deep sequencing identifies new and regulated microRNAs in Schmidtea mediterranea. RNA. 2009; 15(8):1483-91. PMID: 19553344

Thuret S, Toni N, Aigner S, Yeo GW, Gage FH. Hippocampus-dependent learning is associated with adult neurogenesis in MRL/MpJ mice. Hippocampus. 2009; 19(7):658-69. PMID: 19140178

Jessberger S, Aigner S, Clemenson GD Jr, Toni N, Lie DC, Karalay O, Overall R, Kempermann G, Gage FH. Cdk5 regulates accurate maturation of newborn granule cells in the adult hippocampus. PLoS Biol. 2008; 6(11):e272. PMID: 18998770

Yeo GW, Coufal N, Aigner S, Winner B, Scolnick JA, Marchetto MC, Muotri AR, Carson C, Gage FH. Multiple layers of molecular controls modulate self-renewal and neuronal lineage specification of embryonic stem cells. Hum Mol Genet. 2008; 17(R1):R67-75. PMID: 18632700

Aigner S, Denli AM, Gage FH. A novel model for an older remodeler: the BAF swap in neurogenesis. Neuron. 2007; 55(2):171-3. PMID: 17640518

Carson CT, Aigner S, Gage FH. Stem cells: the good, bad and barely in control. Nat. Med. 2006; 12(11):1237-8. PMID: 17088886

Aigner S, Gage FH. A small gem with great powers: geminin keeps neural progenitors thriving. Dev. Cell. 2005; 9(2):171-2. PMID: 16054024

Aigner S, Cech TR. The Euplotes telomerase subunit p43 stimulates enzymatic activity and processivity in vitro. RNA. 2004; 10(7):1108-18. PMID: 15208446

Aigner S, Postberg J, Lipps HJ, Cech TR. The Euplotes La motif protein p43 has properties of a telomerase-specific subunit. Biochemistry. 2003; 42(19):5736-47. PMID: 12741831

Aigner S, Lingner J, Goodrich KJ, Grosshans CA, Shevchenko A, Mann M, Cech TR. Euplotes telomerase contains an La motif protein produced by apparent translational frameshifting. EMBO J. 2000; 19(22):6230-9. PMID: 11080168, PMCID: PMC305813

Seiwert SD, Stines Nahreini T, Aigner S, Ahn NG, Uhlenbeck OC. RNA aptamers as pathway-specific MAP kinase inhibitors. Chem Biol. 2000; 7(11):833-43. PMID: 11094337

Jabri E, Aigner S, Cech TR. Kinetic and secondary structure analysis of Naegleria andersoni GIR1, a group I ribozyme whose putative biological function is site-specific hydrolysis. Biochemistry. 1997; 36(51):16345-54. PMID: 9405070