Image - Barts and The London logo and link to home page Image - divider Image - divider
  Institute of Cell and Molecular Science
Flow Cytometry Core Facility equipment, images used with permission by BD
  Flow Cytometry Core Facility
  link Home link Instruments available link Flow cytometry link Uses of flow cytometry link Flow sorting link Links link Contacts



Type II Cell Death

Macroautophagy or autophagy translates as 'self eating' which is an apoptotic process in response to nutrient starvation, protein aggregation, Endoplasmic Reticulum (ER) stress, calcium overload, hypoxia, removal of damaged organelles and proteasome impairment. Autophagy can be triggered as a cell survival mechanism and hence may prevent cell death and thus it is integral to human health in terms of organism development, cell homeostasis and is involved in a wide range of diseases including cancer, neurodegeneration, aging and the innate immune response to pathogens.

Autophagy was first fully described in 1963 by Christian de Duve who observed cytoplasmic material such as mitochondria and endoplasmic reticulum being engulfed by double-membrane vesicles or autophagosomes and after fusion with lysosomes digestion by lysosomal enzymes in the newly formed auto-lysosome.

Autophagy can be characterized morphologically in a similar manner to that of other forms of cell death by cell shrinkage, formation of autophagosomes and degradation of cell organelles. There are numerous signalling routes that regulate autophagy, these include mTOR and JNK signalling. Autophagy can be induced by nutrient starvation, formation of cytosolic protein aggregates, ER stress, calcium overload and damaged organelles.

There are numerous methods of inducing autophagy including serum and total nutrient starvation and rapamycin which both inhibit mTOR signalling. Chloroquine can also induce autophagy as well as ER-ATPase inhibitor, Thapsigargin which causesreticulophagy of the ER.

Morphological Changes

  • Cell shrinkage
  • Double membrane vesicles or autophagosomes
  • Degradation of organelles
Functional/Biochemical Regulators
  • mTOR
  • PI3 kinases
  • UPR stress sensors
  • Kinases - JNK
  • Bcl-2
  • IP3-receptor


  • Nutrient starvation
  • Protein aggregation
  • Ischemia
  • Hypoxia
  • Calcium overload
  • ER Stress
  • Damaged organelles
  • Proteasome impairment

Model of Autophagy

Figure by SA Tooze, The orgin of the autophagosomal membrane, Nature Cell Biology, 12, (9), p831-835, 2010.


D Bergamaschi, A Vossenkaemper, WYJ Lee, P Wang, E Bochukova, G Warnes. Simultaneous polchromatic flow cytometric detection of multiple forms of regulated cell death. Apoptosis, 2019. (DOI: 10.1007/s10495-019-01528-w)

A Popat, AA Patel, G WarnesA flow cytometric study of ER Stress and autophagy, Cytometry A, DOI: 10.1002/cyto.a.23665, 2018.

G Warnes. Flow cytometric assays for the study of autophagy. Methods,doi:10.1016/j.ymeth.2015.03.027, 2015.

A Chikh, P Sanza, C Raimondi, O Akinduro, G Warnes, G Chiorino, C Byrne, CA Harwood, and D Bergamaschi. IASPP is a novel autophagy inhibitor in keratinocytes. Journal of Cell Science Apr28, 2014.

G Warnes. Measurement of autophagy by flow cytometry, Studies of Cell Function. Curr Protoc Cytom. Apr 1;68:9.45.1-9.45.10, 2014.

S Chikte, N Panchal, G Warnes. Use of LysoTracker dyes: A flow cytometric study of autophagy. Cytometry A Feb, 85(2), 169-178, 2014

A Want, S Cohen, G Warnes. Cell suicide is not painless for the flow cytometrist: New Assays to measure cell death. Meeting report of the flow cytometry Euroscicon meeting in UK 7th November 2012. Kindle Edition, Amazon, Honnao Publishing, June 2013.

N Panchal, S Chikte, BR Wilbourn, UC Meier, G Warnes. Flow cytometric measurement of cell organelle autophagy. Autophagy - A Double-Edged Sword - Cell Survival or Death? Ed, Y. Bailly. InTech Open Access Publisher ISBN 978-953-51-1062-0, April 2013.

A Rosello, G Warnes, UC Meir. Cell death pathways and autophagy in the central nervous system and its involvement in neurodegeneration, immunity and CNS infection:  to die or not to die - that is the question. Clinical & Experimental Immunology Apr, 162(1), 52-7, 2012.

by Gary Warnes. © Queen Mary, University of London 2007
Institute of Cell and Molecular Science, The Blizard Building, Barts and The London School of Medicine and Dentistry, 4 Newark Street, London E1 2AT, UK Tel: +44 (0)20 7882 2483, Fax: +44 (0)20 7882 2200