Studying and Fighting pathogenic bacteria with CRISPR David Bikard - PowerPoint PPT Presentation

Studying and Fighting pathogenic bacteria with CRISPR David Bikard Synthetic Biology Group

History of CRISPR: first observation (1987) Direct Repeats (29 pb) Variable region = spacers (32-33 pb)

History of CRISPR: weird repeats in the genomes of bacterial and archaea (1987-2002) DVR (Direct Variable Repeats), TREP (Tandem Repeats), LTRR (Long Tandemly Repeated Repetitive Sequences), SRSR (Short Regularly Spaced Repeats), LCTR (Large Clusters of Tandem Repeats), SPIDR (Spacer Interspersed Direct Repeats) CRISPR Clustered Regularly Interspaced Short Palindromic Repeats Jansen et al., molecular microbiology 2002

History of CRISPR: Spacers sequences match foreign DNA (2005) Mojica, F. J., Diez-Villasenor, C., Garcia-Martinez, J. & Soria, E. J. Mol. Evol. 2005 Pourcel, C., Salvignol, G. & Vergnaud, G. Microbiology 2005 Bolotin, A., Quinquis, B., Sorokin, A. & Ehrlich, S. D. Microbiology 2005

History of CRISPR: Experimental evidence (2007)

CRISPR Marraffini, Nature 2015

The diversity of CRISPR-Cas system Class 1 Class 2 Koonin & al., Current Opinion in Microbiology 2017

S. pyogenes CRISPR02 tracrRNA Jinek & al., Science 2012 Garneau & al., Nature 2010 Gasiunas & al., PNAS 2012 Sapranauskas & al., PNAS 2011 Sternberg & al., Nature 2014 Deltcheva & al., Nature 2011

CRISPR as a biotechnological tool Cas9 Homologous Point mutation Recombination Gene insertion etc. NHEJ Small indels No repair Cell death

Genome Editing • S. pneumoniae (Jiang, Bikard et al , 2013 , Nat. Biotechnol. ) • E. coli (Jiang, Bikard et al , 2013 , Nature Biotechnol. ) • Human cells (Le Cong et al. , 2013 , Science ) • Monkeys (Niu et al. , 2014 , Cell ) • Livestocks (Tan et al. , 2013 , PNAS) • Mice (Wang et al. , 2013 , Cell ) • Frogs (Blitz et al. and Nakayama et al. , 2013 , Genetics ) • Zebrafish (Hwang et al. , 2013 , Nature Biotechnol. ) • Insects ( Wang et al. , 2013 , Cell. Res. ) • Plants (Li et al. , Shan et al. , 2013 , Nature Biotechnol. ): • Flies (Gratz et al. , 2013 , Genetics ) • Nematodes (Lo et al. , 2013 , Genetics ) • Yeast (DiCarlo et al. , 2013 , NAR)

CRISPR as a biotechnological tool Cas9 Homologous Point mutation Recombination Gene insertion etc. NHEJ Small indels No repair Cell death

Sequence specific killing with Cas9 Bikard & al., Nat Biotech, 2014

Competition with non-targeted strain 1.8 40000 KanR 1.6 35000 1.4 30000 KanS OD (600nm) 1.2 25000 1 GFP 20000 0.8 15000 0.6 10000 0.4 5000 0.2 0 0 0 200 400 600 800 1000 Time (min) Bikard & al., Nat Biotech, 2014

Competition with non-targeted strain 1.8 40000 KanR 1.6 35000 1.4 30000 KanS OD (600nm) 1.2 25000 1 GFP 20000 0.8 15000 0.6 10000 0.4 5000 0.2 0 0 0 200 400 600 800 1000 Time (min) Bikard & al., Nat Biotech, 2014

Competition with non-targeted strain 1.8 40000 KanR 1.6 35000 1.4 30000 KanS OD (600nm) 1.2 25000 1 GFP 20000 0.8 15000 0.6 10000 0.4 5000 0.2 0 0 0 200 400 600 800 1000 Time (min) Bikard & al., Nat Biotech, 2014

Competition with non-targeted strain KanR 1.8 40000 1.6 35000 1.4 30000 KanS OD (600nm) 1.2 25000 GFP 1 20000 0.8 15000 0.6 10000 0.4 5000 0.2 0 0 0 200 400 600 800 1000 Time (min) Bikard & al., Nat Biotech, 2014

Plasmid curing: re-sensitizing bacteria to antibiotics 10 5 Selection 10 4 Ø Cm 10 3 CFU/ul Tet 10 2 10 1 10 0 Ø 1 2 1+2 Target: pUSA C 1 2 3 4 5 6 7 8 - 1kb - 0.5kb pUSA01 - 1kb - 0.5kb pUSA02

Specific decolonization of antibiotic resistant S. aureus on the mouse skin Chad Euler, Rockefeller Vince Fischetti, Rockefeller

CRISPR diagnostics

The diversity of CRISPR-Cas system Class 1 Class 2 Koonin & al., Current Opinion in Microbiology 2017

Cas9 Cas12 Cas13

The Synthetic Biology Group Team Collaborations • • Florence Depardieu Engineer Eduardo Rocha, Institut Pasteur • • Baptiste Saudemont Engineer Sven van Teeffelen, Institut Pasteur • • Theophile Grebert Postdoc Bruno Dupuy, Institut Pasteur • • Constanze Hoffmann Postdoc Sylvain Brisse, Institut Pasteur • • Justen Russell Postdoc Chase Beisel, Helmholtz HIRI • • Alicia Calvo Villamanan PhD Raffaele Ieva, IBCG • • Francois Rousset PhD Alvaro san Millan, IRYCIS, Madrid • • Antoine Vigouroux PhD Fernando de la Cruz, Cantabria University Funding LabEx IBEID