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Wegner M, Kaulich M. ReCo: automated NGS read-counting of single and combinatorial CRISPR gRNAs. Bioinformatics 2023; 39:btad448. [PMID: 37481709 PMCID: PMC10400375 DOI: 10.1093/bioinformatics/btad448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 07/04/2023] [Accepted: 07/21/2023] [Indexed: 07/24/2023] Open
Abstract
SUMMARY CRISPR screens are increasingly performed to associate genotypes with genotypes. So far, however, their analysis required specialized computational knowledge to transform high-throughput next-generation sequencing (NGS) data into sequence formats amenable for downstream analysis. We developed ReCo, a stand-alone and user-friendly analytics tool for generating read-count tables of single and combinatorial CRISPR library and screen-based NGS data. Together with cutadapt and bowtie2 for rapid sequence trimming and alignment, ReCo enables the automated generation of read count tables from staggered NGS reads for the downstream identification of gRNA-induced phenotypes. AVAILABILITY AND IMPLEMENTATION ReCo is published under the MIT license and available at: https://github.com/KaulichLab/ReCo.
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Affiliation(s)
- Martin Wegner
- Goethe University Frankfurt, University Hospital, Institute of Biochemistry II, 60590, Frankfurt am Main, Germany
| | - Manuel Kaulich
- Goethe University Frankfurt, University Hospital, Institute of Biochemistry II, 60590, Frankfurt am Main, Germany
- Frankfurt Cancer Institute, Frankfurt am Main, Germany
- Cardio-Pulmonary Institute, Frankfurt am Main, Germany
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Elcocks H, Brazel AJ, McCarron KR, Kaulich M, Husnjak K, Mortiboys H, Clague MJ, Urbé S. FBXL4 ubiquitin ligase deficiency promotes mitophagy by elevating NIX levels. EMBO J 2023; 42:e112799. [PMID: 37102372 PMCID: PMC10308357 DOI: 10.15252/embj.2022112799] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 03/17/2023] [Accepted: 04/09/2023] [Indexed: 04/28/2023] Open
Abstract
Selective autophagy of mitochondria, mitophagy, is linked to mitochondrial quality control and as such is critical to a healthy organism. We have used a CRISPR/Cas9 approach to screen human E3 ubiquitin ligases for influence on mitophagy under both basal cell culture conditions and upon acute mitochondrial depolarization. We identify two cullin-RING ligase substrate receptors, VHL and FBXL4, as the most profound negative regulators of basal mitophagy. We show that these converge, albeit via different mechanisms, on control of the mitophagy adaptors BNIP3 and BNIP3L/NIX. FBXL4 restricts NIX and BNIP3 levels via direct interaction and protein destabilization, while VHL acts through suppression of HIF1α-mediated transcription of BNIP3 and NIX. Depletion of NIX but not BNIP3 is sufficient to restore mitophagy levels. Our study contributes to an understanding of the aetiology of early-onset mitochondrial encephalomyopathy that is supported by analysis of a disease-associated mutation. We further show that the compound MLN4924, which globally interferes with cullin-RING ligase activity, is a strong inducer of mitophagy, thus providing a research tool in this context and a candidate therapeutic agent for conditions linked to mitochondrial dysfunction.
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Affiliation(s)
- Hannah Elcocks
- Molecular Physiology and Cell Signalling, Institute of Systems, Molecular and Integrative BiologyUniversity of LiverpoolLiverpoolUK
| | - Ailbhe J Brazel
- Molecular Physiology and Cell Signalling, Institute of Systems, Molecular and Integrative BiologyUniversity of LiverpoolLiverpoolUK
- Present address:
Department of BiologyMaynooth UniversityMaynoothIreland
| | - Katy R McCarron
- Molecular Physiology and Cell Signalling, Institute of Systems, Molecular and Integrative BiologyUniversity of LiverpoolLiverpoolUK
| | - Manuel Kaulich
- Institute of Biochemistry IIGoethe University, Medical Faculty, University HospitalFrankfurt am MainGermany
- Frankfurt Cancer InstituteFrankfurt am MainGermany
| | - Koraljka Husnjak
- Institute of Biochemistry IIGoethe University, Medical Faculty, University HospitalFrankfurt am MainGermany
| | - Heather Mortiboys
- Sheffield Institute for Translational Neuroscience (SITraN)University of SheffieldSheffieldUK
| | - Michael J Clague
- Molecular Physiology and Cell Signalling, Institute of Systems, Molecular and Integrative BiologyUniversity of LiverpoolLiverpoolUK
| | - Sylvie Urbé
- Molecular Physiology and Cell Signalling, Institute of Systems, Molecular and Integrative BiologyUniversity of LiverpoolLiverpoolUK
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Cetin R, Wegner M, Luwisch L, Saud S, Achmedov T, Süsser S, Vera-Guapi A, Müller K, Matthess Y, Quandt E, Schaubeck S, Beisel CL, Kaulich M. Optimized metrics for orthogonal combinatorial CRISPR screens. Sci Rep 2023; 13:7405. [PMID: 37149686 PMCID: PMC10164157 DOI: 10.1038/s41598-023-34597-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 05/04/2023] [Indexed: 05/08/2023] Open
Abstract
CRISPR-based gene perturbation enables unbiased investigations of single and combinatorial genotype-to-phenotype associations. In light of efforts to map combinatorial gene dependencies at scale, choosing an efficient and robust CRISPR-associated (Cas) nuclease is of utmost importance. Even though SpCas9 and AsCas12a are widely used for single, combinatorial, and orthogonal screenings, side-by-side comparisons remain sparse. Here, we systematically compared combinatorial SpCas9, AsCas12a, and CHyMErA in hTERT-immortalized retinal pigment epithelial cells and extracted performance-critical parameters for combinatorial and orthogonal CRISPR screens. Our analyses identified SpCas9 to be superior to enhanced and optimized AsCas12a, with CHyMErA being largely inactive in the tested conditions. Since AsCas12a contains RNA processing activity, we used arrayed dual-gRNAs to improve AsCas12a and CHyMErA applications. While this negatively influenced the effect size range of combinatorial AsCas12a applications, it enhanced the performance of CHyMErA. This improved performance, however, was limited to AsCas12a dual-gRNAs, as SpCas9 gRNAs remained largely inactive. To avoid the use of hybrid gRNAs for orthogonal applications, we engineered the multiplex SpCas9-enAsCas12a approach (multiSPAS) that avoids RNA processing for efficient orthogonal gene editing.
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Affiliation(s)
- Ronay Cetin
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany
| | - Martin Wegner
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany
| | - Leah Luwisch
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany
| | - Sarada Saud
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany
| | - Tatjana Achmedov
- Helmholtz-Centre for Infection Research (HZI), Helmholtz Institute for RNA-Based Infection Research (HIRI), 97080, Würzburg, Germany
| | - Sebastian Süsser
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany
| | - Antonella Vera-Guapi
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany
| | - Konstantin Müller
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany
| | - Yves Matthess
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany
| | - Eva Quandt
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany
- Faculty of Medicine and Health Sciences, Universitat Internacional de Catalunya, 08195, Barcelona, Spain
| | - Simone Schaubeck
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany
| | - Chase L Beisel
- Helmholtz-Centre for Infection Research (HZI), Helmholtz Institute for RNA-Based Infection Research (HIRI), 97080, Würzburg, Germany
- Medical Faculty, University of Würzburg, 97080, Würzburg, Germany
| | - Manuel Kaulich
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany.
- Frankfurt Cancer Institute, 60596, Frankfurt am Main, Germany.
- Cardio-Pulmonary Institute, 60590, Frankfurt am Main, Germany.
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Diehl V, Wegner M, Grumati P, Husnjak K, Schaubeck S, Gubas A, Shah V, Polat I, Langschied F, Prieto-Garcia C, Müller K, Kalousi A, Ebersberger I, Brandts C, Dikic I, Kaulich M. Minimized combinatorial CRISPR screens identify genetic interactions in autophagy. Nucleic Acids Res 2021; 49:5684-5704. [PMID: 33956155 PMCID: PMC8191801 DOI: 10.1093/nar/gkab309] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 04/01/2021] [Accepted: 04/14/2021] [Indexed: 12/13/2022] Open
Abstract
Combinatorial CRISPR-Cas screens have advanced the mapping of genetic interactions, but their experimental scale limits the number of targetable gene combinations. Here, we describe 3Cs multiplexing, a rapid and scalable method to generate highly diverse and uniformly distributed combinatorial CRISPR libraries. We demonstrate that the library distribution skew is the critical determinant of its required screening coverage. By circumventing iterative cloning of PCR-amplified oligonucleotides, 3Cs multiplexing facilitates the generation of combinatorial CRISPR libraries with low distribution skews. We show that combinatorial 3Cs libraries can be screened with minimal coverages, reducing associated efforts and costs at least 10-fold. We apply a 3Cs multiplexing library targeting 12,736 autophagy gene combinations with 247,032 paired gRNAs in viability and reporter-based enrichment screens. In the viability screen, we identify, among others, the synthetic lethal WDR45B-PIK3R4 and the proliferation-enhancing ATG7-KEAP1 genetic interactions. In the reporter-based screen, we identify over 1,570 essential genetic interactions for autophagy flux, including interactions among paralogous genes, namely ATG2A-ATG2B, GABARAP-MAP1LC3B and GABARAP-GABARAPL2. However, we only observe few genetic interactions within paralogous gene families of more than two members, indicating functional compensation between them. This work establishes 3Cs multiplexing as a platform for genetic interaction screens at scale.
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Affiliation(s)
- Valentina Diehl
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
| | - Martin Wegner
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
| | - Paolo Grumati
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
| | - Koraljka Husnjak
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
| | - Simone Schaubeck
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
| | - Andrea Gubas
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
| | - Varun Jayeshkumar Shah
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
| | - Ibrahim H Polat
- Department of Medicine, Hematology/Oncology, University Hospital, Goethe University, 60590 Frankfurt am Main, Germany
| | - Felix Langschied
- Applied Bioinformatics Group, Institute of Cell Biology and Neuroscience, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Cristian Prieto-Garcia
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
| | - Konstantin Müller
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
| | - Alkmini Kalousi
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
| | - Ingo Ebersberger
- Applied Bioinformatics Group, Institute of Cell Biology and Neuroscience, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
- Senckenberg Biodiversity and Climate Research Centre (S-BIK-F), Frankfurt am Main, Germany
- LOEWE Centre for Translational Biodiversity Genomics (TBG), Frankfurt am Main, Germany
| | - Christian H Brandts
- Department of Medicine, Hematology/Oncology, University Hospital, Goethe University, 60590 Frankfurt am Main, Germany
- Frankfurt Cancer Institute, 60596 Frankfurt am Main, Germany
- University Cancer Center Frankfurt (UCT), University Hospital, Goethe University, Frankfurt, Germany
| | - Ivan Dikic
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
- Frankfurt Cancer Institute, 60596 Frankfurt am Main, Germany
- Cardio-Pulmonary Institute, 60590 Frankfurt am Main, Germany
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Manuel Kaulich
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
- Frankfurt Cancer Institute, 60596 Frankfurt am Main, Germany
- Cardio-Pulmonary Institute, 60590 Frankfurt am Main, Germany
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