LC3-dependent extracellular vesicle loading and secretion (LDELS)

ABSTRACT

Accumulating evidence implicates various autophagy-related (ATG) proteins in cellular secretion. Recently, we identified a new secretory autophagy pathway in which components of LC3 conjugation machinery specify the incorporation of RNA binding proteins (RBPs) and small non-coding RNAs into extracellular vesicles (EVs), resulting in their secretion outside of cells. We term this process LC3-Dependent EV Loading and Secretion (LDELS). Importantly, LDELS is distinct from classical macroautophagy/autophagy because it requires components of the LC3 conjugation machinery, but not other ATGs involved in autophagosome formation. Because EVs have emerged as mediators of intracellular communication, our results provide new insight into how the autophagy machinery may influence the non-cell autonomous exchange of information between cells.

Although autophagy is classically viewed as a lysosomal degradation pathway, increasing evidence implicates ATGs in processes distinct from classical autophagy, such as cellular secretion. Indeed, genetic loss-of-function studies have revealed ATGs are required for the efficient secretion of inflammatory cytokines, extracellular release of bactericidal enzymes and tissue repair factors, EV production and unconventional secretion of proteins lacking amino-terminal leader sequences. To gain insight into the mechanisms and targets of secretory autophagy, we developed a proximity biotinylation (BioID) strategy to label proteins released by this pathway [1]. We created a recombinant probe combining the mutant BirA biotin ligase (BirA*) with MAP1LC3B/LC3, which robustly biotinylates proteins that interact with the autophagy machinery and subsequently are secreted outside cells. In contrast to genetic loss-of-function approaches targeting ATGs, we hypothesized that this experimental strategy facilitates the labeling and identification of direct targets of secretory autophagy. Quantitative proteomics revealed that the BirA*-LC3-labeled secretome is enriched in RNA-binding proteins (RBPs) and proteins detected in EVs, and also highlighted that lipidated LC3 (LC3-II) itself is released extracellularly. Together, these proteomic data suggest that LC3 and the autophagy machinery specifies proteins for secretion in EVs.

EVs are small membrane-bound organelles containing select proteins, RNAs, and lipids that are released from cells through regulated pathways. Nevertheless, the mechanisms that specify cargo for secretion in EVs remain poorly understood. To test whether LC3 and the autophagy machinery are involved in cargo selection, we first examined whether LC3 is secreted within EVs. Indeed, EVs isolated from conditioned culture media and subject to fractionation protocols or affinity purification contain LC3-II along with established EV marker proteins such as TSG101 and CD9. Protease protection assays further corroborate that LC3-II resides within the lumen of EVs. Utilizing cells expressing a constitutively active form of RAB5 (RAB5^Q79L) to trap endocytic vesicular intermediates, or cell expressing an ascorbate peroxidase-LC3 (APEX-LC3) recombinant fusion protein, we corroborated that LC3 is present at the endocytic limiting membrane and within intralumenal vesicles (ILVs) of multivesicular bodies (MVBs), an organelle implicated in EV biogenesis. Interestingly, LC3 is only present in a subset of ILVs, reinforcing the emerging concept that EVs represent a heterogeneous collection of vesicles derived from multiple different biogenesis pathways, including a subpopulation that is LC3-mediated.

To ascertain how the genetic loss of ATGs affects EV cargo selection and secretion, we performed quantitative proteomics and RNA profiling of EVs isolated from wild-type cells and cells deficient for ATG7 or ATG12. This screen identified 815 proteins and 88 non-coding RNAs, including small nucleolar RNAs (snoRNAs) and microRNAs (miRNAs), that required the LC3-conjugation machinery for secretion in EV fractions. Additionally, similar to the BirA*-LC3 secretome, this ATG7- and ATG12-dependent EV secretome was enriched in RBPs and proteins that interact with LC3 and other Atg8-family members. Among the RBPs found in these orthogonal datasets are SAFB (scaffold attachment factor B) and HNRNPK (heterogenous nuclear ribonucleoprotein K). Experiments confirmed that SAFB and HNRNPK interact with LC3-II, are released within EVs, and are not degraded via classical autophagy. We also interrogated the broader role of the autophagy biogenesis machinery in LC3-II and LC3-binding RBP secretion. These analyses revealed that cells deficient for the LC3-conjugation components ATG7 or ATG12 produce fewer EVs and are completely impaired for secretion of LC3, SAFB and HNRNPK. In contrast, the disruption of the other autophagy initiation components, such as ATG14 or RB1CC1, negligibly affected EV production and cargo loading. Finally, our studies revealed that LC3 and RBP secretion requires SMPD3, a neutral sphingomyelinase that drives EV biogenesis via ceramide production, and LC3-dependent recruitment of NSMAF, a known regulator of SMPD3. Collectively, these analyses reveal a novel autophagy-related pathway that specifies proteins for secretion within EVs. We have termed this process LC3-dependent EV loading and secretion (LDELS) (Figure 1). Because EVs serve as couriers for the intercellular transfer of important biomolecules from one cell to nearby and distant cells, scrutinizing how LDELS influences intracellular communication in vivo remains an important topic for future study.

Figure 1.

Proposed model for LC3-dependent extracellular vesicle loading and secretion (LDELS). In addition to its functions in classical autophagy, LC3 specifies the secretion of proteins and RNAs in extracellular vesicles (EVs). During LDELS, LC3 and cargo delivered to the limiting membrane of multivesicular bodies (MVBs) undergo intralumenal budding and are released as extracellular vesicles upon fusion of the MVB with the plasma membrane. This novel autophagy-related secretory pathway requires the LC3-conjugation machinery, SMPD3 and LC3-dependent recruitment of NSMAF, which may locally drive ceramide production at the MVB membranes to facilitate EV biogenesis.

LDELS bears similarities to a number of recently identified autophagy-related pathways including LC3-associated endocytosis (LANDO), LC3-associated phagocytosis (LAP) and endosomal microautophagy (eMI). Similar to LAP and LANDO, LDELS requires the delivery of LC3 to single-membrane organelles of the endolysosomal system through mechanisms requiring LC3-conjugation machinery but distinct from classical autophagy. Nevertheless, the function and fate of LC3-II within these pathways dramatically differs. During LANDO and LAP, LC3 coats the surface of endosomes and phagosomes, respectively, regulating the trafficking and lysosomal clearance of engulfed extracellular material. In contrast, LC3 is localized to subdomains at the limiting membrane of MVBs during LDELS, which subsequently undergo intralumenal budding to deliver LC3 into the cisternae of these organelles in the form of ILVs. Furthermore, during eMI, cytosolic cargoes are captured at the late endosome limiting membrane via ESCRT-dependent intralumenal budding pathways. Despite these striking topological similarities between LDELS and eMI, LDELS results in the secretion of LC3 and RBPs via EVs, whereas endosomal microautophagy primarily results in cargo degradation. Undoubtedly, understanding how these diverse functions of the autophagy machinery components cooperate to regulate cellular function will reveal new roles for these autophagy-related pathways in normal physiology and disease, and the best strategies to target ATGs for therapeutic benefit.

Funding Statement

Grant support to JD includes the NIH (CA201849, CA126792, CA201849, CA213775, AG057462), the DOD BCRP (W81XWH-11-1-0130), Samuel Waxman Cancer Research Foundation, and UCSF QB3 Calico Longevity Fellowship (to JD and AML). Fellowship support to AML includes a Banting Postdoctoral Fellowship from the Government of Canada (201409BPF-335868) and Cancer Research Society Scholarship for Next Generation of Scientists (22805).

Disclosure statement

J.D. is on the Scientific Advisory Board of Vescor Therapeutics, LLC.