Vojo Deretic

Vojo Peter Deretic received his undergraduate, graduate and postdoctoral education in Belgrade, Paris, and Chicago. He was a faculty member at the University of Texas, University of Michigan, and joined University of New Mexico Health Sciences Center in 2001.

Vojo Deretic's main contributions to science come from studies by his team on the role of autophagy in infection and immunity.{{cite journal |last1=Deretic |first1=Vojo |last2=Saitoh |first2=Tatsuya |last3=Akira |first3=Shizuo |title=Autophagy in infection, inflammation and immunity |journal=Nature Reviews Immunology |date=October 2013 |volume=13 |issue=10 |pages=722–737 |doi=10.1038/nri3532 |pmid=24064518 |pmc=5340150 }} Autophagy is a cytoplasmic pathway with quality control and metabolic roles.{{cite journal |last1=Deretic |first1=Vojo |last2=Kroemer |first2=Guido |title=Autophagy in metabolism and quality control: opposing, complementary or interlinked functions? |journal=Autophagy |date=22 June 2021 |volume=18 |issue=2 |pages=283–292 |doi=10.1080/15548627.2021.1933742 |pmid=34036900 |pmc=8942406 |s2cid=235199344 }} Autophagic removal of damaged or surplus organelles, has been implicated in cancer, neurodegeneration such as Alzheimer's disease, Huntington's disease and Parkinson's disease, diabetes, development, and aging. Deretic's group is one of those that made the discovery{{cite journal | last1 = Gutierrez | first1 = M. G. | last2 = Master | first2 = S. S. | last3 = Singh | first3 = S. B. | last4 = Taylor | first4 = G. A. | last5 = Colombo | first5 = M. I. | last6 = Deretic | first6 = V. | year = 2004 | title = Autophagy is a defense mechanism inhibiting BCG and Mycobacterium tuberculosis survival in infected macrophages | journal = Cell | volume = 119 | issue = 6| pages = 1–20 | doi = 10.1016/j.cell.2004.11.038 | pmid=15607973| citeseerx = 10.1.1.495.3789 | s2cid = 16651183 }} that autophagic degradation is a major effector of innate and possibly adaptive immunity mechanisms for direct elimination of intracellular microbes (such as Mycobacterium tuberculosis{{cite journal | last1 = Castillo | first1 = E. F. | last2 = Dekonenko | first2 = A. | last3 = Arko-Mensah | first3 = J. | last4 = Mandell | first4 = M.A. | last5 = Dupont | first5 = N. | last6 = Jiang | first6 = S. | last7 = Delgado-Vargas | first7 = M. | last8 = Timmins | first8 = G.S. | last9 = Bhattacharya | first9 = D. | last10 = Yang | first10 = H. | last11 = Hutt | first11 = J. | last12 = Lyons | first12 = C. | last13 = Dobos | first13 = K. M. | last14 = Deretic | first14 = V. | year = 2012 | title = Autophagy protects against active tuberculosis by suppressing bacterial burden and inflammation | journal = Proc. Natl. Acad. Sci. USA | volume = 109 | issue = 46| pages = E3168–3176 | doi = 10.1073/pnas.1210500109 | pmid = 23093667 | pmc = 3503152 | doi-access = free }}{{cite journal | last1 = Deretic | first1 = V | last2 = Kimura | first2 = T | last3 = Timmins | first3 = G | last4 = Moseley | first4 = P | last5 = Chauhan | first5 = S | last6 = Mandell | first6 = M | date = Jan 2015 | title = Immunologic manifestations of autophagy | journal = J Clin Invest | volume = 125 | issue = 1| pages = 75–84 | doi = 10.1172/JCI73945 | pmid = 25654553 | pmc = 4350422 }}{{Cite journal |last1=Deretic |first1=Vojo |last2=Wang |first2=Fulong |date=2023-05-04 |title=Autophagy is part of the answer to tuberculosis |journal=Nature Microbiology |language=en |volume=8 |issue=5 |pages=762–763 |doi=10.1038/s41564-023-01373-3 |pmid=37142685 |issn=2058-5276|doi-access=free |pmc=10636698 }}). This has placed immunity and infection on the repertoire of autophagy's sphere of influence.{{cite journal |last1=Deretic |first1=Vojo |title=Autophagy in inflammation, infection, and immunometabolism |journal=Immunity |date=March 2021 |volume=54 |issue=3 |pages=437–453 |doi=10.1016/j.immuni.2021.01.018 |pmid=33691134 |pmc=8026106 }}

Studies in the Deretic laboratory have contributed to our understanding of the basic mechanisms of autophagy in mammalian and human cells applicable to generic, i.e. metabolic and quality control autophagy, as well as to autophagy processes specializing in immune functions. The work by Deretic and colleagues has shown how autophagosomes form in mammalian cells, identifying HyPAS (hybrid pre-autophagosomal structure) prophagophores as direct precursors to autophagosomes in mammalian cells. The HyPAS prophagophores are formed through a membrane fusion between endosomes endowed with the E3 ligase ATG16L1 and the cis-Golgi derived FIP200 vesicles and cisternae. By subsequent atg8ylation, a nascent prophagophore converts into an LC3-positive phagophore. LC3B is one of the six major mammalian ATG8 proteins, which modify membranes in a process referred to as atg8ylation, analogous to the process of protein modification via ubiquitylation. Autophagosomal phagophores expand through lipid transfer processes dependent on ATG9A and ATG2A/B whereas mATG8s play multiple roles, one of which is to serve as adaptors for autophagic receptors thus sequestering cargo into the autophagosomal lumen. The latest findings form Dr. Deretic's laboratory show that atg8ylation and mATG8s play a role in recruiting ESCRT machinery to seal open phagophores, thus generating double membrane autophagosomes,{{Cite journal |last1=Javed |first1=Ruheena |last2=Jain |first2=Ashish |last3=Duque |first3=Thabata |last4=Hendrix |first4=Emily |last5=Paddar |first5=Masroor Ahmad |last6=Khan |first6=Sajjad |last7=Claude-Taupin |first7=Aurore |last8=Jia |first8=Jingyue |last9=Allers |first9=Lee |last10=Wang |first10=Fulong |last11=Mudd |first11=Michal |last12=Timmins |first12=Graham |last13=Lidke |first13=Keith |last14=Rusten |first14=Tor Erik |last15=Akepati |first15=Prithvi Reddy |date=2023-06-05 |title=Mammalian ATG8 proteins maintain autophagosomal membrane integrity through ESCRTs |journal=The EMBO Journal |volume=42 |issue=14 |pages=e112845 |language=en |doi=10.15252/embj.2022112845 |pmid=37272163 |pmc=10350836 |issn=0261-4189 }} and to maintain autophagosomal membranes in a sealed and impermeable, i.e. nonporous state so that digestion of the captured material can take place.

The tight relationship between autophagy as a quality control and metabolic process on the one hand, and as innate immunity process on the other hand, probably harks back to the bacterial endosymbiotic origins of mitochondria.{{Cite journal|last=Deretic|first=Vojo|date=2010-06-23|title=Autophagy of intracellular microbes and mitochondria: two sides of the same coin?|journal=F1000 Biology Reports|volume=2|doi=10.3410/B2-45|pmc=2950027|pmid=20948788 |doi-access=free }} From bacteria to viruses, autophagy and autophagy-related processes, often referred to as non-canonical autophagy, recently categorized as different manifestations of membrane atg8ylation, play roles in controlling microbes or are targeted by pathogens. For example, as shown in a study {{Cite journal|last1=Kumar|first1=Suresh|last2=Javed|first2=Ruheena|last3=Mudd|first3=Michal|last4=Pallikkuth|first4=Sandeep|last5=Lidke|first5=Keith A.|last6=Jain|first6=Ashish|last7=Tangavelou|first7=Karthikeyan|last8=Gudmundsson|first8=Sigurdur Runar|last9=Ye|first9=Chunyan|last10=Rusten|first10=Tor Erik|last11=Anonsen|first11=Jan Haug|date=November 2021|title=Mammalian hybrid pre-autophagosomal structure HyPAS generates autophagosomes|journal=Cell|volume=184|issue=24|language=en|pages=5950–5969.e22|doi=10.1016/j.cell.2021.10.017|pmid=34741801|pmc=8616855}} from the Deretic laboratory, SARS-CoV-2 inhibits the earliest stage of autophagosome formation in human cells known as the prophagophore or HyPAS.

Deretic's laboratory has linked autophagy with several families of innate immunity proteins. This includes TLRs,{{cite journal |last1=Delgado |first1=Mónica A |last2=Elmaoued |first2=Rasha A |last3=Davis |first3=Alexander S |last4=Kyei |first4=George |last5=Deretic |first5=Vojo |title=Toll-like receptors control autophagy |journal=The EMBO Journal |date=9 April 2008 |volume=27 |issue=7 |pages=1110–1121 |doi=10.1038/emboj.2008.31 |pmid=18337753 |pmc=2323261 }} TBK1,{{cite journal |last1=Pilli |first1=Manohar |last2=Arko-Mensah |first2=John |last3=Ponpuak |first3=Marisa |last4=Roberts |first4=Esteban |last5=Master |first5=Sharon |last6=Mandell |first6=Michael A. |last7=Dupont |first7=Nicolas |last8=Ornatowski |first8=Wojciech |last9=Jiang |first9=Shanya |last10=Bradfute |first10=Steven B. |last11=Bruun |first11=Jack-Ansgar |last12=Hansen |first12=Tom Egil |last13=Johansen |first13=Terje |last14=Deretic |first14=Vojo |title=TBK-1 Promotes Autophagy-Mediated Antimicrobial Defense by Controlling Autophagosome Maturation |journal=Immunity |date=August 2012 |volume=37 |issue=2 |pages=223–234 |doi=10.1016/j.immuni.2012.04.015 |pmid=22921120 |pmc=3428731 }} immunity related GTPases such as IRGM and TRIMs, such as TRIM5 (implicated in HIV restriction), TRIM16{{cite journal |last1=Chauhan |first1=Santosh |last2=Kumar |first2=Suresh |last3=Jain |first3=Ashish |last4=Ponpuak |first4=Marisa |last5=Mudd |first5=Michal H. |last6=Kimura |first6=Tomonori |last7=Choi |first7=Seong Won |last8=Peters |first8=Ryan |last9=Mandell |first9=Michael |last10=Bruun |first10=Jack-Ansgar |last11=Johansen |first11=Terje |last12=Deretic |first12=Vojo |title=TRIMs and Galectins Globally Cooperate and TRIM16 and Galectin-3 Co-direct Autophagy in Endomembrane Damage Homeostasis |journal=Developmental Cell |date=October 2016 |volume=39 |issue=1 |pages=13–27 |doi=10.1016/j.devcel.2016.08.003 |pmid=27693506 |pmc=5104201 }} and PYRIN/TRIM20 (implicated in inflammasome regulation), and TRIM21 (implicated in Type I Interferon responses) etc.{{Cite journal|last1=Kimura|first1=Tomonori|last2=Mandell|first2=Michael|last3=Deretic|first3=Vojo|date=2016-03-01|title=Precision autophagy directed by receptor regulators – emerging examples within the TRIM family|journal=Journal of Cell Science|volume=129|issue=5|pages=881–891|doi=10.1242/jcs.163758|issn=1477-9137|pmid=26906420|pmc=6518167}} TRIMs play immune and other roles but with incompletely understood function(s), and the above cited work shows that they act as autophagic receptor-regulators in mammalian cells.{{Cite journal|last1=Kimura|first1=Tomonori|last2=Jia|first2=Jingyue|last3=Kumar|first3=Suresh|last4=Choi|first4=Seong Won|last5=Gu|first5=Yuexi|last6=Mudd|first6=Michal|last7=Dupont|first7=Nicolas|last8=Jiang|first8=Shanya|last9=Peters|first9=Ryan|date=4 January 2017|title=Dedicated SNAREs and specialized TRIM cargo receptors mediate secretory autophagy|journal=The EMBO Journal|volume=36|issue=1|pages=42–60|doi=10.15252/embj.201695081|issn=1460-2075|pmc=5210154|pmid=27932448}}{{cite journal | last1 = Mandell | first1 = M | last2 = Jain | first2 = A. | last3 = Arko-Mensah | first3 = J. | last4 = Chauhan | first4 = S. | last5 = Kimura | first5 = T. | last6 = Dinkins | first6 = C. | last7 = Silvestri | first7 = G | last8 = Münch | first8 = J. | last9 = Kirchhoff | first9 = F. | last10 = Simonsen | first10 = A. | last11 = Wei | first11 = Y. | last12 = Levine | first12 = B. | last13 = Johansen | first13 = T. | last14 = Deretic | first14 = V. | year = 2014 | title = TRIM Proteins Regulate Autophagy and Can Target Autophagic Substrates by Direct Recognition | journal = Developmental Cell | volume = 30 | issue = 4| pages = 394–409 | doi = 10.1016/j.devcel.2014.06.013 | pmid = 25127057 | pmc = 4146662 }}{{cite journal | last1 = Kimura | first1 = A. Jain A | last2 = Choi | first2 = S.W. | last3 = Mandell | first3 = M.A. | last4 = Schroder | first4 = K. | last5 = Johansen | first5 = T. | last6 = Deretic | first6 = V. | year = 2015 | title = TRIM-mediated precision autophagy targets cytoplasmic regulators of innate immunity | journal = J. Cell Biol. | volume = 210 | issue = 6| pages = 973–989 | doi = 10.1083/jcb.201503023 | pmid = 26347139 | pmc = 4576868 }}{{Cite journal|last1=Chauhan|first1=Santosh |last2=Kumar|first2=Suresh |last3=Jain|first3=Ashish |last4=Ponpuak|first4=Marisa |last5=Mudd|first5=Michal H. |last6=Kimura|first6=Tomonori |last7=Choi|first7=Seong Won |last8=Peters|first8=Ryan |last9=Mandell|first9=Michael |date=10 October 2016 |title=TRIMs and Galectins Globally Cooperate and TRIM16 and Galectin-3 Co-direct Autophagy in Endomembrane Damage Homeostasis|journal=Developmental Cell |volume=39 |issue=1 |pages=13–27 |doi=10.1016/j.devcel.2016.08.003 |issn=1878-1551|pmc=5104201|pmid=27693506}} A series of studies{{cite journal | last1 = Singh | first1 = S.B. | last2 = Davis | first2 = A. | last3 = Taylor | first3 = G. A. | last4 = Deretic | first4 = V. | year = 2006 | title = Human IRGM Induces Autophagy to Eliminate Intracellular Mycobacteria | journal = Science | volume = 313| issue = 5792| pages = 1438–1441| doi = 10.1126/science.1129577 | pmid=16888103| bibcode = 2006Sci...313.1438S | s2cid = 2274272 }}{{cite journal | last1 = Singh | first1 = S. B. | last2 = Ornatowski | first2 = W. | last3 = Vergne | first3 = I. | last4 = Naylor | first4 = J. | last5 = Delgado | first5 = M. | last6 = Roberts | first6 = E. | last7 = Ponpuak | first7 = M. | last8 = Master | first8 = S. | last9 = Pilli | first9 = M. | last10 = White | first10 = E. | last11 = Komatsu | first11 = M. | last12 = Deretic | first12 = V. | year = 2010 | title = Human IRGM regulates autophagy and cell-autonomous immunity functions through mitochondria | journal = Nat Cell Biol | volume = 12 | issue = 12| pages = 1154–1165 | doi = 10.1038/ncb2119 | pmid = 21102437 | pmc=2996476}}{{cite journal | last1 = Chauhan | first1 = S. | last2 = Mandell | first2 = M. | last3 = Deretic | first3 = V. | year = 2015| title = IRGM Governs the Core Autophagy Machinery to Conduct Antimicrobial Defense | journal = Molecular Cell | volume = 58| issue = 3| pages = 507–521| doi = 10.1016/j.molcel.2015.03.020 | pmid = 25891078 | pmc = 4427528}}{{Cite journal|last1=Kumar|first1=Suresh|last2=Jain|first2=Ashish|last3=Farzam|first3=Farzin|last4=Jia|first4=Jingyue|last5=Gu|first5=Yuexi|last6=Choi|first6=Seong Won|last7=Mudd|first7=Michal H.|last8=Claude-Taupin|first8=Aurore|last9=Wester|first9=Michael J.|date=2018-02-02|title=Mechanism of Stx17 recruitment to autophagosomes via IRGM and mammalian Atg8 proteins|journal=The Journal of Cell Biology|volume=217|issue=3|pages=997–1013|doi=10.1083/jcb.201708039|issn=1540-8140|pmid=29420192|pmc=5839791}} from Deretic's group shows how the human immunity related GTPase IRGM works in autophagy by demonstrating IRGM's direct interactions with the core autophagy (ATG) factors, and their assembly and activation downstream of PRRs: NOD1, NOD2, TLRs, RIG-I and inflammasome components, enabling them to carry out antimicrobial and anti-inflammatory autophagic functions of significance in tuberculosis and Crohn's disease. A related line of studies shows that IRGM helps recruit a SNARE Syntaxin 17, which is also a target for phosphorylation and control by TBK1{{cite journal |last1=Kumar |first1=Suresh |last2=Gu |first2=Yuexi |last3=Abudu |first3=Yakubu Princely |last4=Bruun |first4=Jack-Ansgar |last5=Jain |first5=Ashish |last6=Farzam |first6=Farzin |last7=Mudd |first7=Michal |last8=Anonsen |first8=Jan Haug |last9=Rusten |first9=Tor Erik |last10=Kasof |first10=Gary |last11=Ktistakis |first11=Nicholas |last12=Lidke |first12=Keith A. |last13=Johansen |first13=Terje |last14=Deretic |first14=Vojo |title=Phosphorylation of Syntaxin 17 by TBK1 Controls Autophagy Initiation |journal=Developmental Cell |date=April 2019 |volume=49 |issue=1 |pages=130–144.e6 |doi=10.1016/j.devcel.2019.01.027 |pmid=30827897 |pmc=6907693}} and plays a role in both autophagy initiation and maturation. Both IRGM and Syntaxin 17 bind mammalian ATG8s such as MAP1LC3B (LC3s) and GABARAPs. A recent study{{cite journal |last1=Kumar |first1=Suresh |last2=Jain |first2=Ashish |last3=Choi |first3=Seong Won |last4=da Silva |first4=Gustavo Peixoto Duarte |last5=Allers |first5=Lee |last6=Mudd |first6=Michal H. |last7=Peters |first7=Ryan Scott |last8=Anonsen |first8=Jan Haug |last9=Rusten |first9=Tor-Erik |last10=Lazarou |first10=Michael |last11=Deretic |first11=Vojo |title=Mammalian Atg8 proteins and the autophagy factor IRGM control mTOR and TFEB at a regulatory node critical for responses to pathogens |journal=Nature Cell Biology |date=August 2020 |volume=22 |issue=8 |pages=973–985 |doi=10.1038/s41556-020-0549-1 |pmid=32753672 |s2cid=220966510 |pmc=7482486}} shows that IRGM controls lysosomal biogenesis though binding to and controlling TFEB, the key transcriptional regulator of lysosomal genes. Moreover, mammalian ATG8s, which interact with IRGM, are upstream of lysosomal biogenesis and control both mTOR and TFEB.

A recent review {{cite journal |last1=Kumar |first1=Suresh |last2=Jia |first2=Jingyue |last3=Deretic |first3=Vojo |title=Atg8ylation as a general membrane stress and remodeling response |journal=Cell Stress |date=13 September 2021 |volume=5 |issue=9 |pages=128–142 |doi=10.15698/cst2021.09.255 |pmid=34527862 |pmc=8404385}} by Deretic and colleagues proposes the principle of "atg8ylation" as a general membrane stress response mirroring what ubiquitylation does for stressed proteins. Furthermore, the mammalian ATG8s association with SNAREs has proven to be far more general than originally anticipated. It has recently been expanded to a large number of other SNAREs, with one specific subset characterized as driving lysosome biogenesis via a TGN-lysosome trafficking route.{{Cite journal|last1=Gu|first1=Yuexi|last2=Princely Abudu |first2=Yakubu |last3=Kumar|first3=Suresh |last4=Bissa|first4=Bhawana| last5=Choi|first5=Seong Won |last6=Jia|first6=Jingyue |last7=Lazarou|first7=Michael |last8=Eskelinen|first8=Eeva-Liisa |last9=Johansen|first9=Terje |last10=Deretic|first10=Vojo |date=2019-10-18|title=Mammalian Atg8 proteins regulate lysosome and autolysosome biogenesis through SNAREs |journal=The EMBO Journal |volume=38 |issue=22 |pages=e101994 |doi=10.15252/embj.2019101994 |issn=0261-4189|pmc=6856626|pmid=31625181}} These studies have led to an unanticipated alternative model for how mammalian ATG8s work – by broadly interacting with and modulating SNAREs to redirect general intracellular membrane flow toward the organelles that converge upon the lysosomal-autolysosomal system. Moreover, recent studies show that mammalian ATG8s actually regulate lysosomal biogenesis, expanding or potentially revising their function that was originally restricted to be autophagosomal formation. As mentioned above, atg8ylation and specific mATG8s (curiously, excluding LC3B) direct ESCRTs to complete autophagosmal closure and to maintain autophagic membranes in a sealed state. The concept of atg8ylation posits that mATG8s and atg8ylation represent to membranes what ubiquitin and ubiquitylation represent to proteins, and that, paralleling manifestations of ubiquitylation, atg8ylation of stressed or remodeling membranes has a plethora of biological consequences, only one of which is autophagy, as reviewed in June 2022 by Deretic and Lazarou.{{Cite journal |last1=Deretic |first1=Vojo |last2=Lazarou |first2=Michael |date=2022-06-14 |title=A guide to membrane atg8ylation and autophagy with reflections on immunity |url=https://doi.org/10.1083/jcb.202203083 |journal=Journal of Cell Biology |volume=221 |issue=7 |pages=e202203083 |doi=10.1083/jcb.202203083 |pmid=35699692 |pmc=9202678 |s2cid=249644004 |issn=0021-9525}} Membrane atg8ylation controls many functions, and has recently been shown to elicit and coordinate during lysosomal membrane stress multiple effector mechanisms: mTOR inactivation, stress granule formation, inhibition of general protein translation via IF2α phosphorylation, and integrated stress response via ATF4.{{Cite journal |last1=Jia |first1=Jingyue |last2=Wang |first2=Fulong |last3=Bhujabal |first3=Zambarlal |last4=Peters |first4=Ryan |last5=Mudd |first5=Michal |last6=Duque |first6=Thabata |last7=Allers |first7=Lee |last8=Javed |first8=Ruheena |last9=Salemi |first9=Michelle |last10=Behrends |first10=Christian |last11=Phinney |first11=Brett |last12=Johansen |first12=Terje |last13=Deretic |first13=Vojo |date=2022-11-07 |title=Stress granules and mTOR are regulated by membrane atg8ylation during lysosomal damage |url=https://rupress.org/jcb/article/221/11/e202207091/213514/Stress-granules-and-mTOR-are-regulated-by-membrane |journal=Journal of Cell Biology |language=en |volume=221 |issue=11 |pages=e202207091 |doi=10.1083/jcb.202207091 |issn=0021-9525 |pmc=9533235 |pmid=36179369|hdl=10037/28759 }}

Studies by Deretic's group from the AIM center for autophagy, inflammation and metabolism studies, provide insight into how cells detect endomembrane and plasma membrane damage and what systems are deployed to help repair or eliminate/replace such membranes. In a paper in Molecular Cell,{{Cite journal|last1=Jia|first1=Jingyue |last2=Abudu|first2=Yakubu Princely |last3=Claude-Taupin|first3=Aurore |last4=Gu|first4=Yuexi |last5=Kumar|first5=Suresh |last6=Choi|first6=Seong Won |last7=Peters|first7=Ryan |last8=Mudd|first8=Michal H. |last9=Allers|first9=Lee |date=2018-04-05|title=Galectins Control mTOR in Response to Endomembrane Damage|journal=Molecular Cell |volume=70 |issue=1 |pages=120–135.e8 |doi=10.1016/j.molcel.2018.03.009 |issn=1097-4164 |pmid=29625033|pmc=5911935}} this group has shown that a novel system termed GALTOR, based on Galectin-8, interacts with the mTOR regulatory system composed of SLC38A9, Ragulator, RagA/B, RagCD. Following lysosomal damage, GALTOR inhibits mTOR causing its dissociation from damaged lysosomes. The key to GALTOR's action are galectins, sugar-binding cytosolic proteins, which can detect glycoconjugates exposed on the lumenal (exofacial) side of the lysosomal membrane upon membrane damage, thus transducing the breach of the membrane to mTOR. The physiological consequences of mTOR inhibition following endomembrane damage are many including induction of autophagy and metabolic switching. The functional roles of galectins in cellular response to membrane damage are rapidly expanding and Deretic's group has recently shown{{Cite journal|last1=Jia|first1=Jingyue|last2=Claude-Taupin|first2=Aurore|last3=Gu|first3=Yuexi|last4=Choi|first4=Seong Won|last5=Peters|first5=Ryan|last6=Bissa|first6=Bhawana|last7=Mudd|first7=Michal H.|last8=Allers|first8=Lee|last9=Pallikkuth|first9=Sandeep|last10=Lidke|first10=Keith A.|last11=Salemi|first11=Michelle|date=December 2019|title=Galectin-3 Coordinates a Cellular System for Lysosomal Repair and Removal|journal=Developmental Cell|volume=52|issue=1|pages=69–87.e8|doi=10.1016/j.devcel.2019.10.025|issn=1534-5807|pmc=6997950|pmid=31813797}} that Galectin-3 recruits ESCRTs to damaged lysosomes so that lysosomes can be repaired. Most recent findings show that Galectin-9 responds to lysosomal damage by activating AMPK, a central regulator of metabolism and autophagy.{{cite journal |last1=Jia |first1=Jingyue |last2=Bissa |first2=Bhawana |last3=Brecht |first3=Lukas |last4=Allers |first4=Lee |last5=Choi |first5=Seong Won |last6=Gu |first6=Yuexi |last7=Zbinden |first7=Mark |last8=Burge |first8=Mark R. |last9=Timmins |first9=Graham |last10=Hallows |first10=Kenneth |last11=Behrends |first11=Christian |last12=Deretic |first12=Vojo |title=AMPK, a Regulator of Metabolism and Autophagy, Is Activated by Lysosomal Damage via a Novel Galectin-Directed Ubiquitin Signal Transduction System |journal=Molecular Cell |date=March 2020 |volume=77 |issue=5 |pages=951–969.e9 |doi=10.1016/j.molcel.2019.12.028 |pmid=31995728 |pmc=7785494 }} This occurs by Galectin-9-dependent activation of the ubiquitination systems on damaged lysosomes resulting in K63-ubiqutination of TAK1, an upstream kinase that phosphorylates and activates AMPK. Continuing the theme of homeostatic responses to membrane damage, Deretic's group has recently shown that ATG9A, primarily considered to be a core autophagy gene and one of the few that are membrane integral proteins, organizes the ESCRT machinery along with a Ca²⁺ responsive protein IQGAP1 to protect plasma membrane from damage, and programmed or incidental permeabilization.{{cite journal |last1=Claude-Taupin |first1=Aurore |last2=Jia |first2=Jingyue |last3=Bhujabal |first3=Zambarlal |last4=Garfa-Traoré |first4=Meriem |last5=Kumar |first5=Suresh |last6=da Silva |first6=Gustavo Peixoto Duarte |last7=Javed |first7=Ruheena |last8=Gu |first8=Yuexi |last9=Allers |first9=Lee |last10=Peters |first10=Ryan |last11=Wang |first11=Fulong |last12=da Costa |first12=Luciana Jesus |last13=Pallikkuth |first13=Sandeep |last14=Lidke |first14=Keith A. |last15=Mauthe |first15=Mario |last16=Verlhac |first16=Pauline |last17=Uchiyama |first17=Yasuo |last18=Salemi |first18=Michelle |last19=Phinney |first19=Brett |last20=Tooze |first20=Sharon A. |last21=Mari |first21=Muriel C. |last22=Johansen |first22=Terje |last23=Reggiori |first23=Fulvio |last24=Deretic |first24=Vojo |title=ATG9A protects the plasma membrane from programmed and incidental permeabilization |journal=Nature Cell Biology |date=August 2021 |volume=23 |issue=8 |pages=846–858 |doi=10.1038/s41556-021-00706-w |pmid=34257406 |pmc=8276549 }} ATG9A marshals ESCRT proteins to repair pores on plasma membrane introduced by gasdermin (GSDMD) during pyroptosis, by MLKL during necroptosis, by Mycobacterium tuberculosis during infection of host cells, and by SARS-CoV-2 ORF3a's MLKL-like action at the plama membrane. A recent study shows further specialization of atg8ylation factors in membrane protection, uncovering unique effects of ATG5 on the maintenance of lysosomal membrane integrity via effects on ESCRT mobilization and additional interactors. This series of studies expands the scope of the membrane homeostatic roles of autophagy proteins beyond the process of canonical autophagy.

The Deretic laboratory has shown that autophagy in mammalian cells plays not only a degradative role but that it also carries the task of unconventional secretion of cytoplasmic proteins.{{cite journal|last1=Dupont|first1=N|last2=Jiang|first2=S|last3=Pilli|first3=M|last4=Ornatowski|first4=W|last5=Bhattacharya|first5=D|last6=Deretic|first6=V|date=Nov 2011|title=Autophagy-based unconventional secretory pathway for extracellular delivery of IL-1β.|journal=EMBO J.|volume=30|issue=23|pages=4701–11|doi=10.1038/emboj.2011.398|pmc=3243609|pmid=22068051}} This has led to the term "secretory autophagy".{{Cite journal|last1=Ponpuak|first1=Marisa|last2=Mandell|first2=Michael A.|last3=Kimura|first3=Tomonori|last4=Chauhan|first4=Santosh|last5=Cleyrat|first5=Cédric|last6=Deretic|first6=Vojo|date=August 2015|title=Secretory autophagy|journal=Current Opinion in Cell Biology|volume=35|pages=106–116|doi=10.1016/j.ceb.2015.04.016|issn=1879-0410|pmc=4529791|pmid=25988755}}{{Cite journal|last1=Claude-Taupin|first1=Aurore|last2=Jia|first2=Jingyue|last3=Mudd|first3=Michal|last4=Deretic|first4=Vojo|date=2017-12-12|title=Autophagy's secret life: secretion instead of degradation|journal=Essays in Biochemistry|volume=61|issue=6|pages=637–647|doi=10.1042/EBC20170024|issn=1744-1358|pmid=29233874}} This work, along with the work by others in yeast, extends the influence sphere of autophagy from its canonical roles inside the cell and the confines of the intracellular space to the extracellular space, affecting cell-cell interactions, inflammation, tissue organization, function, and remodeling.

Autophagy and coronavirus biology are intertwined. SARS-CoV-2 inhibits autophagosomal prophagophore (HyPAS) formation, likely to divert cellular membranes for the formation of protrusion-type viral-replication and viral assembly compartments or to protect the coronavirus. Another example is that ATG9A protein protects cells against plasma membrane damage caused by SARS-CoV-2 ORF3a. Deretic's group has previously shown how chloroquine works by functions in respiratory epithelial cells including suppressing inflammation and drivers of fibrosis that can lead to lung damage and loss of function,{{Cite journal|last1=Poschet|first1=J. F.|last2=Boucher|first2=J. C.|last3=Tatterson|first3=L.|last4=Skidmore|first4=J.|last5=Van Dyke|first5=R. W.|last6=Deretic|first6=V.|date=2001-11-20|title=Molecular basis for defective glycosylation and Pseudomonas pathogenesis in cystic fibrosis lung|journal=Proceedings of the National Academy of Sciences of the United States of America|volume=98|issue=24|pages=13972–13977|doi=10.1073/pnas.241182598|issn=0027-8424|pmc=61151|pmid=11717455|bibcode=2001PNAS...9813972P|doi-access=free}}{{Cite journal|last1=Ornatowski|first1=Wojciech|last2=Poschet|first2=Jens F.|last3=Perkett|first3=Elizabeth|last4=Taylor-Cousar|first4=Jennifer L.|last5=Deretic|first5=Vojo|date=November 2007|title=Elevated furin levels in human cystic fibrosis cells result in hypersusceptibility to exotoxin A-induced cytotoxicity|journal=The Journal of Clinical Investigation|volume=117|issue=11|pages=3489–3497|doi=10.1172/JCI31499|issn=0021-9738|pmc=2030457|pmid=17948127}}{{Cite journal|last1=Perkett|first1=Elizabeth A.|last2=Ornatowski|first2=Wojciech|last3=Poschet|first3=Jens F.|last4=Deretic|first4=Vojo|date=August 2006|title=Chloroquine normalizes aberrant transforming growth factor beta activity in cystic fibrosis bronchial epithelial cells|journal=Pediatric Pulmonology|volume=41|issue=8|pages=771–778|doi=10.1002/ppul.20452|issn=8755-6863|pmid=16779853|s2cid=42376196}} and recently put that in the context of how chloroquine, azithromycin and ciprofloxacin may help with the covid19 pandemic crisis.{{cite bioRxiv |last1=Poschet |first1=Jens F. |last2=Perkett |first2=Elizabeth A. |last3=Timmins |first3=Graham S. |last4=Deretic |first4=Vojo |title=Azithromycin and ciprofloxacin have a chloroquine-like effect on respiratory epithelial cells |date=31 March 2020 |biorxiv=10.1101/2020.03.29.008631 }} A follow-up study{{cite bioRxiv |last1=Bradfute |first1=Steven B |last2=Ye |first2=Chunyan |last3=Clarke |first3=Elizabeth C |last4=Kumar |first4=Suresh |last5=Timmins |first5=Graham S |last6=Deretic |first6=Vojo |title=Ambroxol and Ciprofloxacin Show Activity Against SARS-CoV2 in Vero E6 Cells at Clinically-Relevant Concentrations |date=11 August 2020 |biorxiv=10.1101/2020.08.11.245100 }} indicates that ciprofloxacin has potent effects on inhibiting SARS-CoV-2 in Vero E6 cells as measured by reduced cytopathic effects, quantitative RT-PCR and plaque forming units. Ambroxol is another drug that has beneficial effects in Vero E6 cells.

A comprehensive review with over 1,500 citations by Deretic and colleagues summarizes the role of autophagy in immunity and inflammation: A more recent review by Deretic in the Cell Press journal Immunity summarizes the role of autophagy in inflammation and how it affects various diseases, from autoimmunity to cancer, infections (including COVID-19), cardiovascular and liver diseases, neurodegeneration, diabetes and metabolic disorders.

Some of the early publications (the original discovery that autophagy acts against intracellular microbes with >2,000 citations) include: Cell{{cite journal |last1=Gutierrez |first1=Maximiliano G. |last2=Master |first2=Sharon S. |last3=Singh |first3=Sudha B. |last4=Taylor |first4=Gregory A. |last5=Colombo |first5=Maria I. |last6=Deretic |first6=Vojo |title=Autophagy Is a Defense Mechanism Inhibiting BCG and Mycobacterium tuberculosis Survival in Infected Macrophages |journal=Cell |date=December 2004 |volume=119 |issue=6 |pages=753–766 |doi=10.1016/j.cell.2004.11.038 |pmid=15607973 |doi-access=free }} and in Science.{{cite journal |last1=Singh |first1=S. B. |last2=Davis |first2=A. S. |last3=Taylor |first3=G. A. |last4=Deretic |first4=V. |title=Human IRGM Induces Autophagy to Eliminate Intracellular Mycobacteria |journal=Science |date=8 September 2006 |volume=313 |issue=5792 |pages=1438–1441 |doi=10.1126/science.1129577 |pmid=16888103 |bibcode=2006Sci...313.1438S |s2cid=2274272 }}

Several more recent primary publications include reports in Cell Molecular Cell,{{cite journal |last1=Jia |first1=Jingyue |last2=Abudu |first2=Yakubu Princely |last3=Claude-Taupin |first3=Aurore |last4=Gu |first4=Yuexi |last5=Kumar |first5=Suresh |last6=Choi |first6=Seong Won |last7=Peters |first7=Ryan |last8=Mudd |first8=Michal H. |last9=Allers |first9=Lee |last10=Salemi |first10=Michelle |last11=Phinney |first11=Brett |last12=Johansen |first12=Terje |last13=Deretic |first13=Vojo |title=Galectins Control mTOR in Response to Endomembrane Damage |journal=Molecular Cell |date=April 2018 |volume=70 |issue=1 |pages=120–135.e8 |doi=10.1016/j.molcel.2018.03.009 |pmid=29625033 |pmc=5911935 }} Developmental Cell,{{Cite journal |last1=Wang |first1=Fulong |last2=Peters |first2=Ryan |last3=Jia |first3=Jingyue |last4=Mudd |first4=Michal |last5=Salemi |first5=Michelle |last6=Allers |first6=Lee |last7=Javed |first7=Ruheena |last8=Duque |first8=Thabata L.A. |last9=Paddar |first9=Masroor A. |last10=Trosdal |first10=Einar S. |last11=Phinney |first11=Brett |last12=Deretic |first12=Vojo |date=April 2023 |title=ATG5 provides host protection acting as a switch in the atg8ylation cascade between autophagy and secretion |journal=Developmental Cell |volume=58 |issue=10 |language=en |pages=866–884.e8 |doi=10.1016/j.devcel.2023.03.014|pmid=37054706 |pmc=10205698 }} Journal of Cell Biology and Nature Cell Biology.

• Autophagy Inflammation and Metabolism (AIM) Center

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