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Application of CRISPR-Cas9 Screening Technologies to Study Mitochondrial Biology in Healthy and Disease States

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Part of the book series: Advances in Experimental Medicine and Biology ((AEMB,volume 1158))

Abstract

Mitochondria play a central role in maintaining normal cellular homeostasis as well as contributing to the pathogenesis of numerous disease states. The advent of CRISPR-Cas9 screening technologies has greatly accelerated the study of mitochondrial biology. In this chapter, we review the various CRISPR-Cas9 screening platforms that are currently available and prior studies that leveraged this technology to identify genes involved in mitochondrial biology in both healthy and disease states. In addition, we discuss the challenges associated with current CRISPR-Cas9 platforms and potential solutions to further enhance this promising technology.

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References

  1. Liberti MV, Locasale JW (2016) The Warburg effect: how does it benefit cancer cells? Trends Biochem Sci 41(3):211–218

    Article  CAS  Google Scholar 

  2. Hanahan D, Weinberg RA (2011) Hallmarks of cancer: the next generation. Cell 144(5):646–674

    Article  CAS  Google Scholar 

  3. Hanahan D, Weinberg RA (2000) The hallmarks of cancer. Cell 100(1):57–70

    Article  CAS  Google Scholar 

  4. Pilie PG, Tang C, Mills GB, Yap TA (2018) State-of-the-art strategies for targeting the DNA damage response in cancer. Nat Rev Clin Oncol

    Google Scholar 

  5. Calvo SE, Clauser KR, Mootha VK (2016) MitoCarta2.0: an updated inventory of mammalian mitochondrial proteins. Nucleic Acids Res 44(D1):D1251–D1257

    Article  CAS  Google Scholar 

  6. Jiang D, Zhao L, Clapham DE (2009) Genome-wide RNAi screen identifies Letm1 as a mitochondrial Ca2+/H+ antiporter. Science 326(5949):144–147

    Article  CAS  Google Scholar 

  7. Lanning NJ, Looyenga BD, Kauffman AL, Niemi NM, Sudderth J, DeBerardinis RJ et al (2014) A mitochondrial RNAi screen defines cellular bioenergetic determinants and identifies an adenylate kinase as a key regulator of ATP levels. Cell Rep 7(3):907–917

    Article  CAS  Google Scholar 

  8. Doudna JA, Charpentier E (2014) Genome editing. The new frontier of genome engineering with CRISPR-Cas9. Science 346(6213):1258096

    Article  Google Scholar 

  9. Smith I, Greenside PG, Natoli T, Lahr DL, Wadden D, Tirosh I et al (2017) Evaluation of RNAi and CRISPR technologies by large-scale gene expression profiling in the Connectivity Map. PLoS Biol 15(11):e2003213

    Article  Google Scholar 

  10. Doench JG, Fusi N, Sullender M, Hegde M, Vaimberg EW, Donovan KF et al (2016) Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR-Cas9. Nat Biotechnol 34(2):184–191

    Article  CAS  Google Scholar 

  11. Doench JG, Hartenian E, Graham DB, Tothova Z, Hegde M, Smith I et al (2014) Rational design of highly active sgRNAs for CRISPR-Cas9-mediated gene inactivation. Nat Biotechnol 32(12):1262–1267

    Article  CAS  Google Scholar 

  12. Hart T, Tong AHY, Chan K, Van Leeuwen J, Seetharaman A, Aregger M et al (2017) Evaluation and design of genome-wide CRISPR/SpCas9 knockout screens. G3 (Bethesda) 7(8):2719–2727

    Article  CAS  Google Scholar 

  13. Wang T, Birsoy K, Hughes NW, Krupczak KM, Post Y, Wei JJ et al (2015) Identification and characterization of essential genes in the human genome. Science 350(6264):1096–1101

    Article  CAS  Google Scholar 

  14. Sanjana NE, Shalem O, Zhang F (2014) Improved vectors and genome-wide libraries for CRISPR screening. Nat Methods 11(8):783–784

    Article  CAS  Google Scholar 

  15. Hart T, Chandrashekhar M, Aregger M, Steinhart Z, Brown KR, MacLeod G et al (2015) High-resolution CRISPR screens reveal fitness genes and genotype-specific cancer liabilities. Cell 163(6):1515–1526

    Article  CAS  Google Scholar 

  16. Jinek M, Chylinski K, Fonfara I, Hauer M, Doudna JA, Charpentier E (2012) A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science 337(6096):816–821

    Article  CAS  Google Scholar 

  17. Birsoy K, Wang T, Chen WW, Freinkman E, Abu-Remaileh M, Sabatini DM (2015) An essential role of the mitochondrial electron transport chain in cell proliferation is to enable aspartate synthesis. Cell 162(3):540–551

    Article  CAS  Google Scholar 

  18. Jain IH, Zazzeron L, Goli R, Alexa K, Schatzman-Bone S, Dhillon H et al (2016) Hypoxia as a therapy for mitochondrial disease. Science 352(6281):54–61

    Article  CAS  Google Scholar 

  19. Haase VH (2009) The VHL tumor suppressor: master regulator of HIF. Curr Pharm Des 15(33):3895–3903

    Article  CAS  Google Scholar 

  20. Martin TD, Cook DR, Choi MY, Li MZ, Haigis KM, Elledge SJ (2017) A role for mitochondrial translation in promotion of viability in K-Ras mutant cells. Cell Rep 20(2):427–438

    Article  CAS  Google Scholar 

  21. Ashton TM, McKenna WG, Kunz-Schughart LA, Higgins GS (2018) Oxidative phosphorylation as an emerging target in cancer therapy. Clin Cancer Res 24(11):2482–2490

    Article  CAS  Google Scholar 

  22. Barrow JJ, Balsa E, Verdeguer F, Tavares CD, Soustek MS, Hollingsworth LR et al (2016) Bromodomain inhibitors correct bioenergetic deficiency caused by mitochondrial disease complex I mutations. Mol Cell 64(1):163–175

    Article  CAS  Google Scholar 

  23. Simon DK, Friedman J, Breakefield XO, Jankovic J, Brin MF, Provias J et al (2003) A heteroplasmic mitochondrial complex I gene mutation in adult-onset dystonia. Neurogenetics 4(4):199–205

    Article  CAS  Google Scholar 

  24. Doroshow DB, Eder JP, LoRusso PM (2017) BET inhibitors: a novel epigenetic approach. Ann Oncol Off J Eur Soc Med Oncol 28(8):1776–1787

    Article  CAS  Google Scholar 

  25. Abedin SM, Boddy CS, Munshi HG (2016) BET inhibitors in the treatment of hematologic malignancies: current insights and future prospects. Oncotarget Ther 9:5943–5953

    Article  CAS  Google Scholar 

  26. Scarpulla RC (2011) Metabolic control of mitochondrial biogenesis through the PGC-1 family regulatory network. Biochim Biophys Acta 1813(7):1269–1278

    Article  CAS  Google Scholar 

  27. Santidrian AF, Matsuno-Yagi A, Ritland M, Seo BB, LeBoeuf SE, Gay LJ et al (2013) Mitochondrial complex I activity and NAD+/NADH balance regulate breast cancer progression. J Clin Invest 123(3):1068–1081

    Article  CAS  Google Scholar 

  28. Arroyo JD, Jourdain AA, Calvo SE, Ballarano CA, Doench JG, Root DE et al (2016) A genome-wide CRISPR death screen identifies genes essential for oxidative phosphorylation. Cell Metab 24(6):875–885

    Article  CAS  Google Scholar 

  29. Horlbeck MA, Xu A, Wang M, Bennett NK, Park CY, Bogdanoff D et al (2018) Mapping the genetic landscape of human cells. Cell 174(4):953–67 e22

    Article  CAS  Google Scholar 

  30. Marin TL, Gongol B, Zhang F, Martin M, Johnson DA, Xiao H et al (2017) AMPK promotes mitochondrial biogenesis and function by phosphorylating the epigenetic factors DNMT1, RBBP7, and HAT1. Sci Signal 10(464)

    Article  Google Scholar 

  31. Wang T, Yu H, Hughes NW, Liu B, Kendirli A, Klein K et al (2017) Gene essentiality profiling reveals gene networks and synthetic lethal interactions with oncogenic Ras. Cell 168(5):890–903 e15

    Article  CAS  Google Scholar 

  32. Haapaniemi E, Botla S, Persson J, Schmierer B, Taipale J (2018) CRISPR-Cas9 genome editing induces a p53-mediated DNA damage response. Nat Med 24(7):927–930

    Article  CAS  Google Scholar 

  33. Ihry RJ, Worringer KA, Salick MR, Frias E, Ho D, Theriault K et al (2018) p53 inhibits CRISPR-Cas9 engineering in human pluripotent stem cells. Nat Med 24(7):939–946

    Article  CAS  Google Scholar 

  34. Aguirre AJ, Meyers RM, Weir BA, Vazquez F, Zhang CZ, Ben-David U et al (2016) Genomic copy number dictates a gene-independent cell response to CRISPR/Cas9 targeting. Cancer Discov 6(8):914–929

    Article  CAS  Google Scholar 

  35. Munoz DM, Cassiani PJ, Li L, Billy E, Korn JM, Jones MD et al (2016) CRISPR screens provide a comprehensive assessment of cancer vulnerabilities but generate false-positive hits for highly amplified genomic regions. Cancer Discov 6(8):900–913

    Article  CAS  Google Scholar 

  36. Iorio F, Behan FM, Goncalves E, Bhosle SG, Chen E, Shepherd R et al (2018) Unsupervised correction of gene-independent cell responses to CRISPR-Cas9 targeting. BMC Genomics 19(1):604

    Article  Google Scholar 

  37. Maeder ML, Linder SJ, Cascio VM, Fu Y, Ho QH, Joung JK (2013) CRISPR RNA-guided activation of endogenous human genes. Nat Methods 10(10):977–979

    Article  CAS  Google Scholar 

  38. Yeo NC, Chavez A, Lance-Byrne A, Chan Y, Menn D, Milanova D et al (2018) An enhanced CRISPR repressor for targeted mammalian gene regulation. Nat Methods 15(8):611–616

    Article  CAS  Google Scholar 

  39. Gilbert LA, Larson MH, Morsut L, Liu Z, Brar GA, Torres SE et al (2013) CRISPR-mediated modular RNA-guided regulation of transcription in eukaryotes. Cell 154(2):442–451

    Article  CAS  Google Scholar 

  40. Xu X, Tao Y, Gao X, Zhang L, Li X, Zou W et al (2016) A CRISPR-based approach for targeted DNA demethylation. Cell Discov 2:16009

    Article  CAS  Google Scholar 

  41. Gilbert LA, Horlbeck MA, Adamson B, Villalta JE, Chen Y, Whitehead EH et al (2014) Genome-scale CRISPR-mediated control of gene repression and activation. Cell 159(3):647–661

    Article  CAS  Google Scholar 

  42. Stojic L, Lun ATL, Mangei J, Mascalchi P, Quarantotti V, Barr AR et al (2018) Specificity of RNAi, LNA and CRISPRi as loss-of-function methods in transcriptional analysis. Nucleic Acids Res 46(12):5950–5966

    Article  CAS  Google Scholar 

  43. Gaudelli NM, Komor AC, Rees HA, Packer MS, Badran AH, Bryson DI et al (2017) Programmable base editing of A∗T to G∗C in genomic DNA without DNA cleavage. Nature 551(7681):464–471

    Article  CAS  Google Scholar 

  44. Komor AC, Kim YB, Packer MS, Zuris JA, Liu DR (2016) Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage. Nature 533(7603):420–424

    Article  CAS  Google Scholar 

  45. Billon P, Bryant EE, Joseph SA, Nambiar TS, Hayward SB, Rothstein R et al (2017) CRISPR-mediated base editing enables efficient disruption of eukaryotic genes through induction of STOP codons. Mol Cell 67(6):1068–79 e4

    Article  CAS  Google Scholar 

  46. Kuscu C, Parlak M, Tufan T, Yang J, Szlachta K, Wei X et al (2017) CRISPR-STOP: gene silencing through base-editing-induced nonsense mutations. Nat Methods 14(7):710–712

    Article  CAS  Google Scholar 

  47. Morita K, Hama Y, Izume T, Tamura N, Ueno T, Yamashita Y et al (2018) Genome-wide CRISPR screen identifies TMEM41B as a gene required for autophagosome formation. J Cell Biol 217:3817–3828

    Article  CAS  Google Scholar 

  48. Imamura H, Nhat KP, Togawa H, Saito K, Iino R, Kato-Yamada Y et al (2009) Visualization of ATP levels inside single living cells with fluorescence resonance energy transfer-based genetically encoded indicators. Proc Natl Acad Sci U S A 106(37):15651–15656

    Article  CAS  Google Scholar 

  49. Hernandez G, Thornton C, Stotland A, Lui D, Sin J, Ramil J et al (2013) MitoTimer: a novel tool for monitoring mitochondrial turnover. Autophagy 9(11):1852–1861

    Article  CAS  Google Scholar 

  50. Katayama H, Kogure T, Mizushima N, Yoshimori T, Miyawaki A (2011) A sensitive and quantitative technique for detecting autophagic events based on lysosomal delivery. Chem Biol 18(8):1042–1052

    Article  CAS  Google Scholar 

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Correspondence to Steven M. Chan .

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Sharon, D., Chan, S.M. (2019). Application of CRISPR-Cas9 Screening Technologies to Study Mitochondrial Biology in Healthy and Disease States. In: Urbani, A., Babu, M. (eds) Mitochondria in Health and in Sickness. Advances in Experimental Medicine and Biology, vol 1158. Springer, Singapore. https://doi.org/10.1007/978-981-13-8367-0_15

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