Autophagy Research Update: What a difference a year makes!

By Christina Towers, PhD

Over the last two decades the field of autophagy has exploded! Innovative techniques, comprehensive analysis and disease-relevant models have yielded basic and clinical discoveries of consequence. The Nobel Prize for Physiology or Medicine was awarded to Dr. Yoshinori Ohsumi in 2016, for his ground-breaking work in yeast to identify many of the core autophagy proteins. Since then, the field has only expanded. In just the past year, the field has produced numerous high-profile studies with broad application in the fields of selective autophagy, aging, and cancer – just to name a few.

Selective Autophagy

Autophagy is no longer considered a bulk degradation pathway, but instead a network of highly coordinated signaling pathways that mediate selective autophagic degradation of targeted proteins/organelles. In the past year there have been new advances in selective autophagy of the endoplasmic reticulum¹ (ER-phagy), mitochondria² (mitophagy), peroxisomes² (pexophagy), ribosomes³ (ribophagy) and bacteria⁴ (xenophagy). In particular, one recent study identified a mechanism of cooperation between autophagy receptors, including NDP52 and TBK1, and ULK1 to better characterize how selective autophagy is initiated independent of nutrient-sensing pathways² . Another study created a reporter termed “Ribo-Keima” and discovered that ribophagy can occur independent of LC3-conjugation, but still dependent of upstream autophagic machinery including VPS34 and Beclin1³.

TBK1 immunostaining with Mouse Monoclonal Antibody TBK1 (108A429) [NB100-56705] in HeLa cells fixed (10 minutes with 10% formalin) and permeabilized (5 minutes with 1X PBS + 0.05% Triton X-100). TBK1 antibody was used at 20 ug/ml overnight at 4°C. For detection, secondary antibody anti-mouse DyLight 488 (Green) was used at a 1:500 dilution. Phalloidin 568 (Red) was used to detect Actin at a 1:200 dilution. Nuclei were counterstained with DAPI (Blue).

Autophagy and Aging

Autophagy has been associated with longevity and increased life span in multiple organisms⁵. However, the exact contexts for which this is true are largely unknown. In 2019, headway was made when Dr. Alexander Soukas   ’ group showed that low mitochondrial permeability is necessary for autophagy-dependent lifespan expansion in both worms and mice⁶. Fernández et al    also published an elegant knock-in mouse model with a Beclin1 mutation which disrupts the interaction between Beclin1 and the negative regulator, BCL2⁷. The Becn1^F121A/F121A mice showed increased autophagic flux and a corresponding increase in lifespan and overall health. Other recent advances in this field have implicated the autophagy adaptor protein p62/SQSTM1 and the autophagophore interacting protein, WIPI2B, in autophagy-dependent longevity^8,9.

p62/SQSTM1 immunostaining with Rabbit Polyclonal Antibody p62/SQSTM1 [NBP1-48320] in HeLa cells treated overnight with 50uM Chloroquine  , fixed (10 minutes with 10% formalin), and permeabilized (5 minutes with 1X TBS + 0.5% Triton X-100). p62/SQSTM1 antibody was used at 1:200 dilution overnight at 4°C. For detection, secondary anti-rabbit Dylight 488 was used (Green). HeLa cells were co-stained with Mouse Monoclonal Alpha tubulin (DM1A) NB100-690 used at a 1:1000 dilution and detected with secondary anti-mouse DyLight 550 (Red). Nuclei were counterstained with DAPI (Blue).

Autophagy and Cancer

Autophagy plays a complex role in cancer where it can have tumor suppressive functions during early stages of tumorigenesis but can be pro-tumorigenic in established tumors. The exact contexts and mechanisms behind this conclusion have been hotly debated. This year, additional evidence was found implicating autophagy as a tumor suppressive process important for replicative crisis in fibroblasts¹⁰ and downstream of a tumor suppressive PTEN signaling cascade in lung cancer¹¹. There were also recent advances regarding the tumor-promotional role of autophagy, and back-to-back publications in Nature Medicine showed convincing data that combined targeting of autophagy inhibition and the RAS/RAF/MEK/ERK pathway caused synergistic tumor regression of pancreatic ductal carcinoma in mice^12,13. Moreover, recent work from Dr. Eileen White’s    and Dr. Alec Kimmelman’s    groups showed autophagy can be pro-tumorigenic via non-cell autonomous mechanisms^14,15.

The past year has been a productive season for the field of autophagy, and still the field is far from saturated with much left to learn about the signaling pathways, mechanisms, and clinical implications of the pathway.

Learn more about Autophagy

Christina Towers, PhD   
University of Colorado (AMC)
Dr. Towers studies the roles of autophagy, apoptosis and cell death in cancer.

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2. Vargas, J. N. S., Wang, C., Bunker, E., Hao, L., Maric, D., Schiavo, G., … Youle, R. J. (2019). Spatiotemporal Control of ULK1 Activation by NDP52 and TBK1 during Selective Autophagy. Molecular Cell. https://doi.org/10.1016/j.molcel.2019.02.010
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9. Stavoe, A. K. H., Gopal, P. P., Gubas, A., Tooze, S. A., & Holzbaur, E. L. F. (2019). Expression of WIPI2B counteracts age-related decline in autophagosome biogenesis in neurons. ELife. https://doi.org/10.7554/eLife.44219
10. Nassour, J., Radford, R., Correia, A., Fusté, J. M., Schoell, B., Jauch, A., … Karlseder, J. (2019). Autophagic cell death restricts chromosomal instability during replicative crisis. Nature. https://doi.org/10.1038/s41586-019-0885-0
11. Cai, J., Li, R., Xu, X., Zhang, L., Lian, R., Fang, L., … Li, M. (2018). CK1α suppresses lung tumour growth by stabilizing PTEN and inducing autophagy. Nature Cell Biology. https://doi.org/10.1038/s41556-018-0065-8
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13. Kinsey, C. G., Camolotto, S. A., Boespflug, A. M., Guillen, K. P., Foth, M., Truong, A., … McMahon, M. (2019). Protective autophagy elicited by RAF→MEK→ERK inhibition suggests a treatment strategy for RAS-driven cancers. Nature Medicine. https://doi.org/10.1038/s41591-019-0367-9