Skip to main content

Monitoring the Clearance of Apoptotic and Necrotic Cells in the Nematode Caenorhabditis elegans

  • Protocol
  • First Online:
Necrosis

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1004))

Abstract

The nematode Caenorhabditis elegans is an excellent model organism for studying the mechanisms ­controlling cell death, including apoptosis, a cell suicide event, and necrosis, pathological cell deaths caused by environmental insults or genetic alterations. C. elegans has also been established as a model for understanding how dying cells are cleared from animal bodies. In particular, the transparent nature of worm bodies and eggshells make C. elegans particularly amenable for live-cell microscopy. Here we describe methods for identifying apoptotic and necrotic cells in living C. elegans embryos, larvae, and adults and for monitoring their clearance during development. We further discuss specific methods to distinguish engulfed from unengulfed apoptotic cells, and methods to monitor cellular and molecular events occurring during phagosome maturation. These methods are based on Differential Interference Contrast (DIC) microscopy or fluorescence microscopy using GFP-based reporters.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 79.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 99.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 109.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Savill J, Fadok V (2000) Corpse clearance defines the meaning of cell death. Nature 407(6805):784–788

    Article  CAS  Google Scholar 

  2. Jacobson MD, Weil M, Raff MC (1997) Programmed cell death in animal development. Cell 88(3):347–354

    Article  CAS  Google Scholar 

  3. Elliott MR, Ravichandran KS (2010) Clearance of apoptotic cells: implications in health and disease. J Cell Biol 189(7):1059–1070

    Article  CAS  Google Scholar 

  4. Golstein P, Kroemer G (2007) Cell death by necrosis: towards a molecular definition. Trends Biochem Sci 32(1):37–43

    Article  CAS  Google Scholar 

  5. Kroemer G, Galluzzi L, Vandenabeele P, Abrams J, Alnemri ES, Baehrecke EH, Blagosklonny MV, El-Deiry WS, Golstein P, Green DR, Hengartner M, Knight RA, Kumar S, Lipton SA, Malorni W, Nunez G, Peter ME, Tschopp J, Yuan J, Piacentini M, Zhivotovsky B, Melino G (2009) Classification of cell death: recommendations of the Nomenclature Committee on Cell Death 2009. Cell Death Differ 16(1):3–11

    Article  CAS  Google Scholar 

  6. Jacobson MD, Bergeron L (2002) Cell death in the nervous system. In: Jacobson MD, McCarthy N (eds) Apoptosis, the molecular biology of programmed cell death. Oxford University Press, Oxford, pp 278–301

    Google Scholar 

  7. Yamashima T (2004) Ca2+-dependent proteases in ischemic neuronal death: a conserved ‘calpain-cathepsin cascade’ from nematodes to primates. Cell Calcium 36(3–4):285–293

    Article  CAS  Google Scholar 

  8. Noch E, Khalili K (2009) Molecular mechanisms of necrosis in glioblastoma: the role of glutamate excitotoxicity. Cancer Biol Ther 8(19):1791–1797

    Article  CAS  Google Scholar 

  9. Challa S, Chan FK (2010) Going up in flames: necrotic cell injury and inflammatory diseases. Cell Mol Life Sci 67(19):3241–3253

    Article  CAS  Google Scholar 

  10. Fujimoto K, Chen Y, Polonsky KS, Dorn GW II (2010) Targeting cyclophilin D and the mitochondrial permeability transition enhances beta-cell survival and prevents diabetes in Pdx1 deficiency. Proc Natl Acad Sci U S A 107(22):10214–10219

    Article  CAS  Google Scholar 

  11. Whelan RS, Kaplinskiy V, Kitsis RN (2010) Cell death in the pathogenesis of heart disease: mechanisms and significance. Annu Rev Physiol 72:19–44

    Article  CAS  Google Scholar 

  12. Christofferson DE, Yuan J (2010) Necroptosis as an alternative form of programmed cell death. Curr Opin Cell Biol 22(2):263–268

    Article  CAS  Google Scholar 

  13. McCall K (2010) Genetic control of necrosis—another type of programmed cell death. Curr Opin Cell Biol 22(6):882–888

    Article  CAS  Google Scholar 

  14. Moquin D, Chan FK (2010) The molecular regulation of programmed necrotic cell injury. Trends Biochem Sci 35(8):434–441

    Article  CAS  Google Scholar 

  15. Vlachos M, Tavernarakis N (2010) Non-apoptotic cell death in Caenorhabditis elegans. Dev Dyn 239(5):1337–1351

    Article  CAS  Google Scholar 

  16. Krysko DV, D’Herde K, Vandenabeele P (2006) Clearance of apoptotic and necrotic cells and its immunological consequences. Apoptosis 11(10):1709–1726

    Article  Google Scholar 

  17. Poon IK, Hulett MD, Parish CR (2010) Molecular mechanisms of late apoptotic/necrotic cell clearance. Cell Death Differ 17(3):381–397

    Article  CAS  Google Scholar 

  18. Metzstein MM, Stanfield GM, Horvitz HR (1998) Genetics of programmed cell death in C. elegans: past, present and future. Trends Genet 14:410–416

    Article  CAS  Google Scholar 

  19. Reddien PW, Horvitz HR (2004) The engulfment process of programmed cell death in Caenorhabditis elegans. Annu Rev Cell Dev Biol 20:193–221

    Article  CAS  Google Scholar 

  20. Sulston JE, Horvitz HR (1977) Post-embryonic cell lineages of the nematode, Caenorhabditis elegans. Dev Biol 56(1):110–156

    Article  CAS  Google Scholar 

  21. Sulston JE, Schierenberg E, White JG, Thomson JN (1983) The embryonic cell lineage of the nematode Caenorhabditis elegans. Dev Biol 100(1):64–119

    Article  CAS  Google Scholar 

  22. Gumienny TL, Lambie E, Hartwieg E, Horvitz HR, Hengartner MO (1999) Genetic control of programmed cell death in the Caenorhabditis elegans hermaphrodite germline. Development 126:1011–1022

    CAS  PubMed  Google Scholar 

  23. Zhou Z, Hartwieg E, Horvitz HR (2001) CED-1 is a transmembrane receptor that mediates cell corpse engulfment in C. elegans. Cell 104(1):43–56

    Article  CAS  Google Scholar 

  24. Zhou Z, Mangahas PM, Yu X (2004) The genetics of hiding the corpse: engulfment and degradation of apoptotic cells in C. elegans and D. melanogaster. Curr Top Dev Biol 63:91–143

    Article  CAS  Google Scholar 

  25. Driscoll M, Chalfie M (1991) The mec-4 gene is a member of a family of Caenorhabditis elegans genes that can mutate to induce neuronal degeneration. Nature 349(6310):588–593

    Article  CAS  Google Scholar 

  26. Driscoll M, Gerstbrein B (2003) Dying for a cause: invertebrate genetics takes on human neurodegeneration. Nat Rev Genet 4(3):181–194

    Article  CAS  Google Scholar 

  27. Bianchi L, Gerstbrein B, Frokjaer-Jensen C, Royal DC, Mukherjee G, Royal MA, Xue J, Schafer WR, Driscoll M (2004) The ­neurotoxic MEC-4(d) DEG/ENaC sodium channel conducts calcium: implications for necrosis initiation. Nat Neurosci 7(12):1337–1344

    Article  CAS  Google Scholar 

  28. Treinin M, Chalfie M (1995) A mutated acetylcholine receptor subunit causes neuronal degeneration in C. elegans. Neuron 14(4):871–877

    Article  CAS  Google Scholar 

  29. Hall DH, Gu G, Garcia-Anoveros J, Gong L, Chalfie M, Driscoll M (1997) Neuropathology of degenerative cell death in Caenorhabditis elegans. J Neurosci 17(3):1033–1045

    Article  CAS  Google Scholar 

  30. Xu K, Tavernarakis N, Driscoll M (2001) Necrotic cell death in C. elegans requires the function of calreticulin and regulators of Ca(2+) release from the endoplasmic reticulum. Neuron 31(6):957–971

    Article  CAS  Google Scholar 

  31. Chung S, Gumienny TL, Hengartner MO, Driscoll M (2000) A common set of engulfment genes mediates removal of both apoptotic and necrotic cell corpses in C. elegans. Nat Cell Biol 2(12):931–937

    Article  CAS  Google Scholar 

  32. Schwartz HT (2007) A protocol describing pharynx counts and a review of other assays of apoptotic cell death in the nematode worm Caenorhabditis elegans. Nat Protoc 2(3):705–714

    Article  Google Scholar 

  33. Venegas V, Zhou Z (2007) Two alternative mechanisms that regulate the presentation of apoptotic cell engulfment signal in Caenorhabditis elegans. Mol Biol Cell 18(8):3180–3192

    Article  CAS  Google Scholar 

  34. Wang X, Wang J, Gengyo-Ando K, Gu L, Sun CL, Yang C, Shi Y, Kobayashi T, Mitani S, Xie XS, Xue D (2007) C. elegans mitochondrial factor WAH-1 promotes phosphatidylserine externalization in apoptotic cells through phospholipid scramblase SCRM-1. Nat Cell Biol 9(5):541–549

    Article  CAS  Google Scholar 

  35. Zullig S, Neukomm LJ, Jovanovic M, Charette SJ, Lyssenko NN, Halleck MS, Reutelingsperger CP, Schlegel RA, Hengartner MO (2007) Aminophospholipid translocase TAT-1 promotes phosphatidylserine exposure during C. elegans apoptosis. Curr Biol 17(11):994–999

    Article  Google Scholar 

  36. Ooi SL, Priess JR, Henikoff S (2006) Histone H3.3 variant dynamics in the germline of Caenorhabditis elegans. PLoS Genet 2(6):e97

    Article  Google Scholar 

  37. Mangahas PM, Yu X, Miller KG, Zhou Z (2008) The small GTPase Rab2 functions in the removal of apoptotic cells in Caenorhabditis elegans. J Cell Biol 180(2):357–373

    Article  CAS  Google Scholar 

  38. Yu X, Odera S, Chuang CH, Lu N, Zhou Z (2006) C. elegans Dynamin mediates the signaling of phagocytic receptor CED-1 for the engulfment and degradation of apoptotic cells. Dev Cell 10(6):743–757

    Article  CAS  Google Scholar 

  39. Yu X, Lu N, Zhou Z (2008) Phagocytic receptor CED-1 initiates a signaling pathway for degrading engulfed apoptotic cells. PLoS Biol 6(3):e61

    Article  Google Scholar 

  40. He B, Yu X, Margolis M, Liu X, Leng X, Etzion Y, Zheng F, Lu N, Quiocho FA, Danino D, Zhou Z (2010) Live-cell imaging in Caenorhabditis elegans reveals the distinct roles of dynamin self-assembly and guanosine triphosphate hydrolysis in the removal of apoptotic cells. Mol Biol Cell 21(4):610–629

    Article  CAS  Google Scholar 

  41. Lu N, Shen Q, Mahoney TR, Liu X, Zhou Z (2011) Three sorting nexins drive the degradation of apoptotic cells in response to PtdIns(3)P signaling. Mol Biol Cell 22(3):354–374

    Article  CAS  Google Scholar 

  42. Lu N, Shen Q, Mahoney TR, Neukomm LJ, Wang Y, Zhou Z (2012) Two PI 3-kinases and one PI 3-phosphatase together establish the cyclic waves of phagosomal PtdIns(3)P critical for the degradation of apoptotic cells. PLoS Biol 10(1):e1001245

    Article  CAS  Google Scholar 

  43. Ellis RE, Jacobson DM, Horvitz HR (1991) Genes required for the engulfment of cell corpses during programmed cell death in Caenorhabditis elegans. Genetics 129(1):79–94

    CAS  PubMed  PubMed Central  Google Scholar 

  44. Zhou Z, Caron E, Hartwieg E, Hall A, Horvitz HR (2001) The C. elegans PH domain ­protein CED-12 regulates cytoskeletal ­reorganization via a Rho/Rac GTPase ­signaling pathway. Dev Cell 1(4):477–489

    Article  CAS  Google Scholar 

  45. Hamelin M, Scott IM, Way JC, Culotti JG (1992) The mec-7 beta-tubulin gene of Caenorhabditis elegans is expressed primarily in the touch receptor neurons. EMBO J 11(8):2885–2893

    Article  CAS  Google Scholar 

  46. Wood WB, Researchers of the C. elegans Community (1988) The nematode Caenorhabditis elegans. Cold Spring Harbor Laboratory, Cold Spring Harbor, NY

    Google Scholar 

  47. Shaham S (2005) Methods in cell biology, WormBook. In: C. elegans (ed) Research Community, WormBook, doi/10.1895/wormbook.1.7.1, http://www.wormbook.org

  48. Lu N, Zhou Z (2012) Membrane trafficking and phagosome maturation during the clearance of apoptotic cells. Int Rev Cell Mol Biol 293:269–309

    Article  CAS  Google Scholar 

  49. Gartner A, Milstein S, Ahmed S, Hodgkin J, Hengartner MO (2000) A conserved checkpoint pathway mediates DNA damage-induced apoptosis and cell cycle arrest in C. elegans. Mol Cell 5(3):435–443

    Article  CAS  Google Scholar 

  50. Sibarita JB (2005) Deconvolution microscopy. Adv Biochem Eng Biotechnol 95:201–243

    PubMed  Google Scholar 

Download references

Acknowledgments

Z. Z. was supported by NIH (GM067848) and the March of Dimes Foundation (1-FY10-434). X. H. was supported by NIH (GM068676).

Author information

Authors and Affiliations

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2013 Springer Science+Business Media, LLC

About this protocol

Cite this protocol

Li, Z., Lu, N., He, X., Zhou, Z. (2013). Monitoring the Clearance of Apoptotic and Necrotic Cells in the Nematode Caenorhabditis elegans. In: McCall, K., Klein, C. (eds) Necrosis. Methods in Molecular Biology, vol 1004. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-383-1_14

Download citation

  • DOI: https://doi.org/10.1007/978-1-62703-383-1_14

  • Published:

  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-62703-382-4

  • Online ISBN: 978-1-62703-383-1

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics