dismutase1(SOD1)G93A ALSmiceoriginatefromastrocytes andneuronsandcarrymisfoldedSOD1 › content ›...

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CNS-derived extracellular vesicles from superoxide dismutase 1 (SOD1) G93A ALS mice originate from astrocytes and neurons and carry misfolded SOD1 Received for publication, July 10, 2018, and in revised form, January 2, 2019 Published, Papers in Press, January 11, 2019, DOI 10.1074/jbc.RA118.004825 Judith M. Silverman , Darren Christy , Chih Cheih Shyu , Kyung-Mee Moon § , Sarah Fernando , Zoe Gidden , Catherine M. Cowan , Yuxin Ban , R. Greg Stacey § , Leslie I. Grad , Luke McAlary ‡¶ , Ian R. Mackenzie , X Leonard J. Foster § , and X Neil R. Cashman ‡1 From the Centre for Brain Health, Department of Medicine, University of British Columbia, Vancouver, British Columbia V6T 1B5, Canada, the § Centre for High-throughput Biology, University of British Columbia, Vancouver, British Columbia V6T 1B5, Canada, the Department of Physics and Astronomy, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada, and the Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia V6T 1B5, Canada Edited by Phyllis I. Hanson Extracellular vesicles (EVs) are secreted by myriad cells in cul- ture and also by unicellular organisms, and their identification in mammalian fluids suggests that EV release also occurs at the organism level. However, although it is clearly important to bet- ter understand EVs’ roles in organismal biology, EVs in solid tissues have received little attention. Here, we modified a proto- col for EV isolation from primary neural cell culture to collect EVs from frozen whole murine and human neural tissues by serial centrifugation and purification on a sucrose gradient. Quantitative proteomics comparing brain-derived EVs from nontransgenic (NTg) and a transgenic amyotrophic lateral scle- rosis (ALS) mouse model, superoxide dismutase 1 (SOD1) G93A , revealed that these EVs contain canonical exosomal markers and are enriched in synaptic and RNA-binding proteins. The com- piled brain EV proteome contained numerous proteins implicated in ALS, and EVs from SOD1 G93A mice were significantly depleted in myelin-oligodendrocyte glycoprotein compared with those from NTg animals. We observed that brain- and spinal cord– derived EVs, from NTg and SOD1 G93A mice, are positive for the astrocyte marker GLAST and the synaptic marker SNAP25, whereas CD11b, a microglial marker, was largely absent. EVs from brains and spinal cords of the SOD1 G93A ALS mouse model, as well as from human SOD1 familial ALS patient spinal cord, contained abundant misfolded and nonnative dis- ulfide-cross-linked aggregated SOD1. Our results indicate that CNS-derived EVs from an ALS animal model contain patho- genic disease-causing proteins and suggest that brain astrocytes and neurons, but not microglia, are the main EV source. Amyotrophic lateral sclerosis (ALS) 2 is a fatal neurodegen- erative disease resulting in the progressive loss of motor neu- rons in the brain, brainstem, and spinal cord. The disease is characterized by progressive propagation of pathology spread- ing from the CNS foci in which symptoms first appear (1). Neu- roanatomical propagation may occur by two distinct pathways: 1) contiguous propagation, which occurs side-to-side region- ally through the extracellular matrix independent of synaptic connection and 2) network propagation, which occurs end-to- end, dependent on synaptic connections and axonal transmis- sion in connected neural networks (1). The molecular mecha- nisms responsible for the above observations are the subject of intense study, among which prion-like propagated protein mis- folding has emerged as a prominent candidate. Discovery of dominant mutations resulting in the ALS syndrome has impli- cated a number of proteins responsible for cellular toxicity and perhaps also spreading of pathology in ALS. Whereas the vast majority of clinical ALS cases are sporadic, mutations in human copper-zinc superoxide dismutase (SOD1) cause about 20% of inherited cases of ALS, with mutations in other genes such as TARDBP (encoding the protein TDP-43), FUS, and C9ORF72 (reviewed in Ref. 2), each accounting for a sizable percentage of cases. At the moment, there is experimental evidence in vitro supporting propagation of pathological conformations in both SOD1 (3–6) and TDP-43 (7, 8). These proteins have been shown to induce a pathologic conformation on their natively folded counterparts in a template-directed manner. Our previ- ous work with transfected immortalized cell lines suggests that misfolded SOD1 protein can be transferred from cell to cell via both exosome-dependent and -independent routes (6). How- ever, cell culture studies in vitro may not recapitulate the per- tinent mechanisms in a living organism. All of the cells of the nervous system, including neurons (9), oligodendrocytes (10), astrocytes (11), and microglia (12), have been shown to release membrane-bound vesicles into the extracellular milieu. Such vesicles have the same membrane topology as the cell and range in diameter from 30 to 2000 nm. This work was supported by a Bernice Ramsay ALS Canada grant, along with funding from the Paul Heller Memorial Fund (to J. M. S.). N. R. C. is the Chief Scientific Officer of ProMIS Neurosciences, which has licensed the 3H1 mis- folded SOD1–specific antibody technology. This article contains Figs. S1 and S2 and Tables S1–S9. 1 To whom correspondence should be addressed: Dept. of Medicine, Univer- sity of British Columbia, Vancouver, British Columbia V6T 1B5, Canada. Tel.: 604-822-2135; E-mail: [email protected]. 2 The abbreviations used are: ALS, amyotrophic lateral sclerosis; CNS, central nervous system; SOD1, superoxide dismutase 1; EV, extracellular vesicle; MV, microvesicle; EX, exosome; AD, Alzheimer’s disease; NTg, nontrans- genic; RBP, RNA-binding protein; PrP, prion protein; BDEX, brain-derived EX; BDEV, brain-derived EV; BDMV, brain-derived MV; BisTris, 2-[bis(2-hy- droxyethyl)amino]-2-(hydroxymethyl)propane-1,3-diol; TEM, transmis- sion EM; GO, gene ontology; ANOVA, analysis of variance. cro ARTICLE 3744 J. Biol. Chem. (2019) 294(10) 3744 –3759 © 2019 Silverman et al. Published under exclusive license by The American Society for Biochemistry and Molecular Biology, Inc. by guest on July 4, 2020 http://www.jbc.org/ Downloaded from

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CNS-derived extracellular vesicles from superoxidedismutase 1 (SOD1)G93A ALS mice originate from astrocytesand neurons and carry misfolded SOD1Received for publication, July 10, 2018, and in revised form, January 2, 2019 Published, Papers in Press, January 11, 2019, DOI 10.1074/jbc.RA118.004825

Judith M. Silverman‡, Darren Christy‡, Chih Cheih Shyu‡, Kyung-Mee Moon§, Sarah Fernando‡, Zoe Gidden‡,Catherine M. Cowan‡, Yuxin Ban‡, R. Greg Stacey§, Leslie I. Grad‡, Luke McAlary‡¶, Ian R. Mackenzie�,X Leonard J. Foster§, and X Neil R. Cashman‡1

From the ‡Centre for Brain Health, Department of Medicine, University of British Columbia, Vancouver, British Columbia V6T 1B5,Canada, the §Centre for High-throughput Biology, University of British Columbia, Vancouver, British Columbia V6T 1B5, Canada,the ¶Department of Physics and Astronomy, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada, and the�Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia V6T 1B5, Canada

Edited by Phyllis I. Hanson

Extracellular vesicles (EVs) are secreted by myriad cells in cul-ture and also by unicellular organisms, and their identificationin mammalian fluids suggests that EV release also occurs at theorganism level. However, although it is clearly important to bet-ter understand EVs’ roles in organismal biology, EVs in solidtissues have received little attention. Here, we modified a proto-col for EV isolation from primary neural cell culture to collectEVs from frozen whole murine and human neural tissues byserial centrifugation and purification on a sucrose gradient.Quantitative proteomics comparing brain-derived EVs fromnontransgenic (NTg) and a transgenic amyotrophic lateral scle-rosis (ALS) mouse model, superoxide dismutase 1 (SOD1)G93A,revealed that these EVs contain canonical exosomal markersand are enriched in synaptic and RNA-binding proteins. The com-piled brain EV proteome contained numerous proteins implicatedin ALS, and EVs from SOD1G93A mice were significantly depletedin myelin-oligodendrocyte glycoprotein compared withthose from NTg animals. We observed that brain- and spinalcord– derived EVs, from NTg and SOD1G93A mice, are positivefor the astrocyte marker GLAST and the synaptic markerSNAP25, whereas CD11b, a microglial marker, was largelyabsent. EVs from brains and spinal cords of the SOD1G93A ALSmouse model, as well as from human SOD1 familial ALS patientspinal cord, contained abundant misfolded and nonnative dis-ulfide-cross-linked aggregated SOD1. Our results indicate thatCNS-derived EVs from an ALS animal model contain patho-genic disease-causing proteins and suggest that brain astrocytesand neurons, but not microglia, are the main EV source.

Amyotrophic lateral sclerosis (ALS)2 is a fatal neurodegen-erative disease resulting in the progressive loss of motor neu-

rons in the brain, brainstem, and spinal cord. The disease ischaracterized by progressive propagation of pathology spread-ing from the CNS foci in which symptoms first appear (1). Neu-roanatomical propagation may occur by two distinct pathways:1) contiguous propagation, which occurs side-to-side region-ally through the extracellular matrix independent of synapticconnection and 2) network propagation, which occurs end-to-end, dependent on synaptic connections and axonal transmis-sion in connected neural networks (1). The molecular mecha-nisms responsible for the above observations are the subject ofintense study, among which prion-like propagated protein mis-folding has emerged as a prominent candidate. Discovery ofdominant mutations resulting in the ALS syndrome has impli-cated a number of proteins responsible for cellular toxicity andperhaps also spreading of pathology in ALS. Whereas the vastmajority of clinical ALS cases are sporadic, mutations in humancopper-zinc superoxide dismutase (SOD1) cause about 20% ofinherited cases of ALS, with mutations in other genes such asTARDBP (encoding the protein TDP-43), FUS, and C9ORF72(reviewed in Ref. 2), each accounting for a sizable percentage ofcases. At the moment, there is experimental evidence in vitrosupporting propagation of pathological conformations in bothSOD1 (3–6) and TDP-43 (7, 8). These proteins have beenshown to induce a pathologic conformation on their nativelyfolded counterparts in a template-directed manner. Our previ-ous work with transfected immortalized cell lines suggests thatmisfolded SOD1 protein can be transferred from cell to cell viaboth exosome-dependent and -independent routes (6). How-ever, cell culture studies in vitro may not recapitulate the per-tinent mechanisms in a living organism.

All of the cells of the nervous system, including neurons (9),oligodendrocytes (10), astrocytes (11), and microglia (12), havebeen shown to release membrane-bound vesicles into theextracellular milieu. Such vesicles have the same membranetopology as the cell and range in diameter from 30 to 2000 nm.

This work was supported by a Bernice Ramsay ALS Canada grant, along withfunding from the Paul Heller Memorial Fund (to J. M. S.). N. R. C. is the ChiefScientific Officer of ProMIS Neurosciences, which has licensed the 3H1 mis-folded SOD1–specific antibody technology.

This article contains Figs. S1 and S2 and Tables S1–S9.1 To whom correspondence should be addressed: Dept. of Medicine, Univer-

sity of British Columbia, Vancouver, British Columbia V6T 1B5, Canada. Tel.:604-822-2135; E-mail: [email protected].

2 The abbreviations used are: ALS, amyotrophic lateral sclerosis; CNS, centralnervous system; SOD1, superoxide dismutase 1; EV, extracellular vesicle;

MV, microvesicle; EX, exosome; AD, Alzheimer’s disease; NTg, nontrans-genic; RBP, RNA-binding protein; PrP, prion protein; BDEX, brain-derivedEX; BDEV, brain-derived EV; BDMV, brain-derived MV; BisTris, 2-[bis(2-hy-droxyethyl)amino]-2-(hydroxymethyl)propane-1,3-diol; TEM, transmis-sion EM; GO, gene ontology; ANOVA, analysis of variance.

croARTICLE

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These extracellular vesicles (EVs), neuronal and otherwise, arecurrently the subjects of intense functional study worldwide.EVs mediate the secretion of an assortment of macromolecularcargo, including mRNAs, miRNAs, lipids, and proteins (13–16); interact with neighboring cells; and transmit their cargofrom cell to cell (17–19). Likewise, an increasing body of workhas demonstrated a functional role in health and disease of EVs(20 –23), which are released by virtually all mammalian cells, aswell as nonmammalian and bacterial cells (16).

Exosomes (EXs) and microvesicles (MVs) are the two mainclasses of EVs, characterized in part, and for the purpose of thisstudy, by the centrifugation parameters at which they pellet,100,000 � g and 15,000 � g, respectively. The most currentstudies, using nanoparticle tracking analysis, show these twovesicle pellets to be dominated by vesicles of the same size,�100 nm in diameter, whereas the MV population has a largersize range, up to 2 �m, and contains more large (0.5–2-�m)vesicles (24, 25). The mechanisms of vesicle biogenesis are notsettled, with evidence for both direct budding from the plasmamembrane (26) and release of vesicles from multivesicularendosomes (27). For recent comprehensive reviews of the var-ious types of vesicles secreted by cells, see Refs. 16, 28, and 29).

In the past 5 years, investigations of EVs have been expandedfrom cell lines and mixed primary cell cultures to the collectionof vesicles from the extracellular spaces within tissues (30, 31).These studies have focused on the EV population in Alzhei-mer’s disease (AD), deriving either from human brains or ADmouse model brains. Few publications have examined themolecular mechanisms responsible for ALS and its spreadingpathology from the tissue-derived EV perspective (32, 33).

To better understand the role of EVs in an ALS-affectedcentral nervous system, we employed a method of whole-tissue vesicle isolation (30). Herein, we establish a pheno-typic profile of vesicles from whole mouse brains and spinalcords and investigate how model motor neuron disease mod-ifies this phenotype.

Results

Extracellular vesicles were collected from mouse brain andspinal cord tissues

In 2012, Perez-Gonzalez et al. (30) showed that it was possible tocollect vesicles from the extracellular space of whole mouse brainsand, by extension, from human brain tissue. We tested this tech-nique on brains from the ALS mouse model overexpressinghuman SOD1 with the G93A mutation (SOD1G93A) and non-transgenic (NTg) littermates. NTg vesicles that had been pelletedat 100,000 � g (EX) floated through a sucrose gradient as canonicalexosomes, primarily floating to �30% sucrose fractions (Fig. 1A).This fraction contained classic exosomal markers (34), includingprion protein (PrP) and SOD1 (Fig. 1A). To test for contaminationfrom intracellular vesicles released by the isolation procedure, weexamined markers of the Golgi apparatus (GM130) and Bcl-2, amarker of the mitochondria as well as apoptotic cells and vesicles(35). We also compared known protein amounts of purified vesiclelysates with equal and higher protein amounts of whole-brainhomogenates. Whereas exosome markers were detected in the

vesicle sample (GRP78, PrP, and SOD1), the markers of contami-nation were only evident in the brain homogenates (Fig. 1B).

EM confirmed a vesicular morphology of the 30% sucrose-purified vesicles (Fig. 1C). Vesicles were then floated throughan iodixanol gradient for greater fractionation. For both NTgand SOD1G93A samples, the exosomal marker PrP was found inthe center of the gradient, focused in and around fractions 5 and6 (Fig. 1D). SOD1 showed a wider distribution, with strongsignals in fractions 2 and 3 as well as 5–7, for both genotypes(Fig. 1D). In the SOD1G93A samples, two SOD1-reactive bandswere evident (Fig. 1D, bottom), suggesting that both the humantransgene and endogenous mouse SOD1 are present in the ves-icles. Notably, SOD1 and PrP were also detected at the bottomof the gradient, in fraction 11 (Fig. 1D), which may representdense debris from the digestion and extraction.

In ALS and mice transgenic for human mutant SOD1(e.g. SOD1G93A), both upper and lower motor neurons wereaffected, with maximal pathology and motor neuron deathoccurring in the spinal cord (1, 36). We applied the methods forextracting brain-derived EXs (BDEXs) to mouse spinal cords,with the important modification that five spinal cords werepooled for every vesicle isolation. Moreover, we expanded ourinvestigation to the sucrose gradient–purified MV as well, fromboth brains and spinal cords, to generate a comprehensiveunderstanding of the CNS EV population. As can be seen in Fig.1E, both brain and spinal cord– derived 100,000 � g (EX) and15,000 � g (MV) pellets contained spherical structures withevident bilayers and morphology consistent with vesicles.

Immunoblotting of spinal cord MVs (Fig. S1) revealed a pat-tern of protein expression similar to that found in the BDEX(Fig. 1B), where vesicle markers SOD1, PrP, actin, GRP78/Bip,and CD9 were clearly represented, whereas contaminationmarkers such as GM130, Bcl-2, and the neuronal nuclear pro-tein NeuN were absent (Fig. S1).

Proteomic profiling describes a distinct vesicle surfaceproteome and demonstrates a loss of myelin oligodendrocyteglycoprotein in BDEX from SOD1G93A transgenic mice

To further characterize the BDEXs and potentially identifynovel EV-associated proteins involved in SOD1-ALS, we per-formed advanced quantitative proteomics. Using a trilabeltechnique, we compared 1) the relative expression of proteinsidentified in the 100,000 � g pelleted and sucrose gradient–purified surface-depleted BDEXs from SOD1G93A and NTgmice (Fig. 2A); 2) proteins expressed on the surface of BDEXsfrom SOD1G93A and NTg mice (Fig. 2B); 3) the relative expres-sion of proteins on the surface versus the BDEX for NTg mice(Fig. 2C); and 4) the relative expression of proteins on the sur-face of SOD1G93A vesicles versus NTg BDEXs (Fig. 2D). Therelative quantitation is calculated as a ratio of expression foreach protein and provided as the log2 -fold difference (1e-1).Significant enrichments of the ratios were calculated using a ttest with false discovery rate corrections.

Approximately 1200 proteins were identified in the BDEXproteome (Table S1). Due to the remaining presence of trans-membrane proteins, and likely incomplete surface trypsindigestion, these surface-depleted BDEX preparations wereassumed to retain a signal from the majority of surface proteins,

CNS tissues contain diverse extracellular vesicles

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an assumption supported by our results (Fig. 2E). Of the 1200BDEX proteins, 268 were assigned a ratio in at least six of eightexperiments (Table S2). Human SOD1G93A did not receive aquantifiable ratio owing to its complete absence from the NTgsample. Only one protein was found to be significantly enrichedafter the false discovery rate corrections; myelin-oligodendro-cyte glycoprotein (MOG) was significantly enriched in the NTgvesicles (Fig. 2A), at a NTg/SOD1G93A ratio of �1.29, prior tothe log2 transform. This slight (�30%) although significantenrichment is consistent with studies demonstrating that oli-gogendrocytes are lost in neurodegeneration (37). Some otherproteins approached significance, including the enrichment ofprotein-disulfide isomerase in SOD1G93A BDEX, which hasbeen linked to ALS pathologies (38, 39), and SNAP25 in NTgBDEX. SNAP25 mediates axonal repair, calcium signaling, andvesicle fusion and recycling (40, 41) and therefore has an impact

on at least three processes critical to ALS pathogenesis. How-ever, the absence of a large significantly enriched protein pop-ulation in the transgenic vesicles suggests that the SOD1G93A

genotype has little effect on the BDEX proteome, at least at 3months of age, the age of disease onset in this animal model.

In neither SOD1G93A nor NTg BDEX did we find the ALS-associated protein TDP-43 or the dipeptide repeated sequencesof C9orf72 (Table S1). TDP-43 inclusions have been shown in97% of sporadic (but not SOD1 familial) ALS (42, 43), and thehexanucleotide repeat expansion-prone C9orf72 (44) is themost common genetic determinant of TDP-43 pathology. How-ever, the ALS-associated RNA-binding protein (RBP) MATR3 andcandidate genes hnRNPU and SRSF2 (45, 46) were identified inboth SOD1G93A and nontransgenic vesicles (Table S1); RBM6, apredicted but not yet validated ALS-associated RBP, was alsoidentified.

Figure 1. Intact EVs are isolated from the extracellular spaces of whole mouse brains with minimal contamination. A, EVs were collected from wholebrains from NTg animals, and 100,000 � g pellets were floated through a stepwise sucrose gradient (fraction 1 � 0%, fraction 6 � 60% sucrose). B, NTg-purifiedBDEVs were compared directly with equal and increasing amounts of NTg brain homogenate prepared with a wand homogenizer. GRP78, PrP, and SOD1exposure was for 30 s; Bcl-2 and GM130 exposure was for 300 s. C, electron micrographs of BDEVs (100,000 � g pellets) from NTg– and human SOD1G93A–overexpressing animals show vesicular structures with canonical exosome morphology. Scale bar, 100 nm. D, BDEV 100,000 � g pellets were fractionated in an11-step iodixanol gradient (fraction 1 � 0%, fraction 11 � 60%). E, electron micrographs of purified tissue-derived MVs, isolated at 15,000 � g, and EXs isolatedat 100,000 � g. Brain MV scale bar � 200 nm. Brain EX, Spinal Cord MV and EX, and Brain and Spinal Cord MV inset scale bars, 100 nm.

CNS tissues contain diverse extracellular vesicles

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The vesicle surface proteome showed a similar pattern ofenrichment to the BDEX proteome. Approximately 800 pro-teins were identified in the surface protein preparations (TableS3). We observed significant overlap between the BDEX pro-teome and the surface proteome; �50% of the BDEX proteinswere also identified on the surface (Fig. 2E). Of the 202 uniquesurface protein identifications (Fig. 2E), these were likely attrib-utable to the surface-depleted nature of the BDEX sample.

Of these proteins, only 184 had quantifiable ratios in at leastsix of eight experiments (Fig. 2B and Table S4). None of theseproteins displayed significant concentrations in vesicles fromeither transgenic or nontransgenic mice. We can conclude thatthe expression of human SOD1G93A does not globally modifythe BDEX surface proteome.

Examination of the relative expression of vesicle proteins onthe surface versus the whole vesicle (Fig. 2, C and D) clearlyidentified groups of significantly enriched proteins (Table S5(SOD1G93A surface versus NTg vesicle) and Table S6 (NTg sur-face versus NTg vesicle)). In these comparisons, �150 proteinshad quantifiable ratios in at least seven of eight experiments(Tables S5 and S6).

In both surface versus vesicle comparisons, �60 proteinswere relatively enriched on the vesicle surface. These includedknown membrane proteins such as cadherin-13 and trans-membrane proteins like alastin-1. Perhaps surprisingly, manyof the surface-enriched proteins were ribosomal subunits(Tables S5 and S6). In fact, after gene ontology and KEGG anno-tation of the data, a one-dimensional annotation enrichmenttest showed significant enrichment of the KEGG term “ribo-some” with the surface of SOD1G93A BDEX (Fig. 2D and TableS7). This term did not reach significant enrichment on the sur-face of NTg vesicles.

Whereas 60 proteins were enriched on the vesicle surface,only eight (Fig. 2C) and six (Fig. 2D) proteins were more con-centrated in the NTg vesicle proteome. This may seem surpris-ingly low but is almost certainly because many proteins that areexclusively luminal (absent from the surface) cannot be ana-lyzed by ratio analysis and are thus automatically excluded fromthe quantitative analysis. Interestingly, SNAP25 and synapto-physin were found to be enriched in the vesicle proteome inboth comparisons (Fig. 2, C and D). This orientation is partic-ularly meaningful; SNAP25 and synaptophysin coat the inner

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RibosomePhagosomePhagosomeFigure 2. Quantitative identification of BDEX and surface proteomes. A–D, quantitative proteomics data were analyzed using Perseus (89, 90). Data are presentedas the -fold difference on the x axis and the negative log of the p values on the y axis. For each plot, proteins are marked with a different color and shape according tothe significance of the enrichment in either sample. Pink squares, significant p values after applying Benjamin–Hochberg correction for false discovery rate; bluetriangles, not significant with false discovery correction but have p values� 0.01; green diamonds, p values between 0.01 and 1. Select proteins are labeled. Significantlyenriched KEGG terms, when present, are listed below the graphs. A, SOD1G93A BDEX over NTg BDEX. B, surface proteins from SOD1G93A BDEX over surface proteins fromNTg BDEX. C, the relative abundance ratios for surface versus whole vesicles, where all of the proteins are from NTg samples. D, relative abundance ratios for SOD1G93A

vesicle surface proteins versus NTg whole vesicles. E, Venn diagram of overlap between surface-depleted BDEX proteome and surface proteome. F, Venn diagramsshowing overlap between mouse BDEX and vesicles found in human CSF (49) and vesicles secreted by human SH-SY5Y neuroblastoma cell line (50).

CNS tissues contain diverse extracellular vesicles

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leaflet cytoplasmic side of the plasma membrane (47). Con-versely, these proteins decorate the outer membrane surface ofintracellular synaptic vesicles (47). Likewise, the concentrationof SNAP25 and synaptophysin in the vesicle fraction militatesagainst the possibility that the vesicles harvested by our tech-nique represent synaptic vesicles released during tissue pro-cessing. Furthermore, the KEGG terms “phagosome,” “cyto-plasmic vesicle,” and “rheumatoid arthritis” were statisticallyenriched in the NTg vesicles (Fig. 2, C and D and Table S7).

Many exosome proteomes have been published, and lists ofcommon exosomal proteins have been compiled (48). TheBDEX proteome contained 71% of the published top 100 exo-some proteins. Previous work has described the proteomes ofvesicles secreted by other CNS cell types, although the majorityof these are from immortalized cell lines. A whole mouse braincontains blood and CSF, and we can assume that some of thevesicles collected in brain isolation would come from these bio-fluids as well as from the extracellular spaces between cells.Unfortunately, no proteomic analysis of mouse blood or CSFexosomes has been published; however, a detailed human CSFexosome proteome is available (49). The BDEX had 340 pro-teins in common with human CSF extracellular vesicles (Fig.2F). SH-SY5Y cells are an immortalized human neuroblastomacell line and are often used as neuronal surrogates in vitro. Aproteomic description of exosomes secreted by SH-SY5Y cells(50) had 413 proteins in common with the mouse BDEX pro-teome (Fig. 2F). Together, the high percentage of overlap withpreviously published extracellular vesicle proteomes providesadditional support for characterization of the vesicles collectedform whole brains as extracellular.

Additionally, when we performed a gene ontology analysis ofthe BDEX proteome and surface proteome, the most overrep-resented term, compared with the mouse genome, was “extra-cellular exosome” (Fig. 3). Many terms were found to be over-represented (Tables S8 and S9), including RNA binding,ribosome, neuron part, and synapse (Fig. 3). The proteomicanalysis suggested that these vesicles are similar to previouslydescribed exosomes, that they are of a neural origin, and thatthe expression of human SOD1G93A had a minimal impact onthe wider vesicle proteome.

Brain- and spinal cord– derived extracellular vesicles areprimarily of astrocyte and neuronal origin

One of the goals of these studies was to determine the relativeproportion of BDEXs that were derived from various CNScell types (i.e. neurons, astrocytes, microglia, and oligodendro-cytes). Due to differences in published proteome depth andlimited information from primary cells, the proteomic compar-isons did not provide significant insight into this question. Flowcytometry is often used to differentiate individual cell type con-tributions to a mixed cell population, such as whole blood.Whereas exosomes, at �100 nm in diameter, are below thelowest level of detection by a forward scatter laser for the cur-rently available flow cytometers, fluorescent labeling of smallerparticles is detectable (51, 52). We examined the proportion ofvesicles that were positive for various CNS cell type markers.We used the astrocyte marker GLAST, also known as excitatoryamino acid transporter 2 (EAAT2), the neuron marker NCAM/

CD56, the microglia marker CD11b, the exosome markerCD81, and the synaptic protein SNAP25. Fig. 4A includes for-ward (FSC) and side scatter (SSC) plots illustrating the noiseand how the BDEX and BDMV populations were affected bylysis; the left panels show 0.1-�m-filtered PBS, the middle pan-els show unlabeled vesicles purified after 100,000 � g (EX) or15,000 � g (MV) centrifugation; and the right panels show thesame after the vesicles had been lysed with 1.0% Nonidet P-40.After lysis, the events from side scatter 104-105 essentially dis-appeared, suggesting that these are true vesicles (Fig. 4A). Sim-ilar results are seen with spinal cord EVs (Fig. S2A). However,events that disappear with lysis appear as low as 103 in SSC;these events cannot be isolated from noise by gating on thescatter plot. As such, for calculation of the proportion of posi-tive events for each marker, first we analyzed all of the events,including noise, and subtracted the events that were positiveeven after lysis. We performed additional confirmation that themarkers were associated with bona fide vesicles by immuno-TEM (Fig. S2B). We found vesicular structures labeled withthe canonical vesicle markers CD63 and CD81, the astrocytemarker GLAST, and the synaptic markers SNAP25 and VGAT(Fig. S2B).

When analyzing the EVs for cell type marker expression byflow cytometry, we saw little difference in the marker percent-

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Figure 3. BDEXs and surface proteomes have significantly enriched geneontology annotations that reflect their neuronal and vesicular origin.Enrichment of GO annotations in the BDEX proteome or the BDEX surface pro-teome, compared with the entire mouse genome, was performed using ErmineJ(91, 92). False discovery rate correction was used to determine significant enrich-ments. A, Venn diagram of the overlap in GO annotations between the BDEX andthe surface proteome. B, a selection of significantly overrepresented GO terms isshown; the full list can be found in Tables S8 and S9.

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ages between SOD1G93A and NTg BDEVs (Fig. 4, B and C).Moreover, no significant effect of genotype was found for vesi-cles harvested from spinal cords (Fig. 4, E and F). Within eachvesicle population, the majority of markers existed at about thesame level in the population (15– 40% EX, 40 – 65% MV), withCD11b as the exception and at a much lower expression level(2–5%; Fig. 4, B–G). CD11b is a marker of microglia, and its lowrepresentation suggests that the brain and spinal cord EV pop-ulations, under these specific conditions, are primarily derived

from neurons and astrocytes. The contribution of oligodendro-cytes is yet to be determined.

A comparison of marker expression between MV and EXsamples and between brain and spinal cord samples generatedsome interesting observations. We observed a statistically sig-nificant reduction in positive events in brain-derived EX sam-ples compared with MV samples (Fig. 4D), likely correspondingto the smaller size of the EX compared with MVs. The largerMVs will have a greater number of fluorochrome-conjugated

Figure 4. Flow cytometric analysis suggests that the majority of BDMV may be of astrocyte origin. A, forward-side scatter plots of BDEX and MVs beforeand after lysis in 1% Nonidet P-40 shows separation of vesicle signal from noise. Percentage of total events within an arbitrary gate is shown for illustrativepurpose only. B and C, the percentage positive of total events (including noise) for an astrocyte marker (GLAST), neuronal marker NCAM (CD56), exo-some marker (CD81), synaptic vesicle marker (SNAP25), and microglia marker (CD11b). The number of positive events found after lysis was subtracted. Datawere analyzed by two-way ANOVA. No difference between G93A and NTg BDMV (B, p � 0.4012) or BDEX (C, p � 0.8095) marker expression was found. Thepercentage positive of all events collected, after subtraction of positive events in the lysed sample, is shown. Data are from 4 –5 identical experiments. D,significant decreases in the percentage of positive events in NTg brain EXs for most markers are observed compared with NTg brain MVs. Data were analyzedby two-way ANOVA with Sidak’s multiple-comparison test: p � 0.0002 (interaction), p � 0.0001 (marker), and p � 0.0001 (vesicle). E and F, the percentagepositive of total events (including noise) after lysis subtraction in vesicles collected from spinal cords. Data were analyzed by two-way ANOVA. No differencebetween G93A and NTg spinal cord MV (E, p � 0.6218) and EX (F, p � 0.4530) marker expression was found. G, when spinal cord MVs are compared directly withthe EXs by two-way ANOVA, p � 0.0007 (interaction), p � 0.0001 (marker), and p � 0.0321 (vesicle). Sidak’s multiple-comparison test showed some significantdifferences within individual markers. H and I, comparison of percentage positive MV (H) and EX (I) events between brains and spinal cords (Sp. Cord). Data wereanalyzed by two-way ANOVA with Sidak’s multiple-comparison test: for MVs (H), p � 0.0001 (interaction), p � 0.0001 (marker), and p � 0.0001 (tissue); for EXs(I), p � 0.0001 (interaction), p � 0.0001 (marker), and p � 0.7523 (tissue). Error bars, S.E.

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antibodies bound and as such will have a greater signal. Thespinal cord EVs showed a slightly different pattern; only CD81had a significant decrease in EX samples, and SNAP25 demon-strated a significant increase in the smaller EXs (Fig. 4G).

A similar pattern was observed when we compared brain andspinal cord MVs or EXs. For MVs, the brain-derived vesicleshad significantly higher marker expression across all measuredmarkers, excepting CD11b (Fig. 4H). In contrast, the EX vesi-cles from brains and spinal cords had equal levels of CD81 andCD56/NCAM, whereas spinal cord EXs had less GLASTexpression and more SNAP25 expression than the brain EXs(Fig. 4I). The equivalent levels of CD81 suggested that the totalnumber of vesicles is the same in brain and spinal cord EXsamples. The reduction in GLAST and increase in SNAP25 sug-gests that fewer of the vesicles are derived from astrocytes andperhaps more are derived from neurons.

Mouse BDEVs reflect neurodegeneration occurring over time

The data presented thus far were derived from animals sac-rificed at 3 months of age, the age of disease onset in humanSOD1G93A-expressing mice. We hypothesized that as the ani-mal ages and the disease progressed, the vesicle populationwould change along with the tissue. However, we did notobserve clear evidence of this in the brain-derived EVs. Weexamined brain MVs from animals sacrificed at 2 and 5 monthsof age to determine whether the cell type marker phenotype isage-dependent. We found no effect of age on MVs from NTganimals within this range (Fig. 5, A–D). However, the GLASTMV population from SOD1G93A animals did have a significantdecrease at 5 months, and CD11b was increased from 2 to 5months of age (Fig. 5, A and B). The percentage of CD11b-positive vesicles remained below 5%, so the impact of thisincrease was minimal; however, the data do indicate that overthe course of the disease, the MV population may be modified.

Brain and spinal cord EVs from mice overexpressing humanSOD1G93A contain and are decorated by misfolded SOD1

We have previously shown misfolded SOD1 to be involved inintermolecular and intercellular prion-like template-directedmisfolding (3, 6). As part of that investigation, we showed thatexosomes secreted by a mouse motor neuron–like cell (NSC34)after transfection with various human SOD1 mutations weresurface-decorated with misfolded SOD1 (6). The CNS–tissuevesicle isolations allowed us to determine ex vivo whether mis-folded SOD1 associates with extracellular vesicles within neuraltissues of ALS model mice.

We utilized antibodies specifically designed to bind only mis-folded SOD1 (3, 53) to assay the association of misfolded SOD1with tissue-derived EVs. Whole EXs harvested from brains andspinal cords of SOD1G93A and NTg mice were immunoprecipi-tated with the SOD1-misfolded antibodies 3H1 and 10C12 (Fig.6A). Vesicles from both brains and (Fig. 6B) spinal cords (Fig.6C) of SOD1G93A mice had significantly more misfolded SOD1on the vesicle surface than NTg littermate mice. This finding isin agreement with our findings from exosomes secreted by cellsin culture.

Misfolded SOD1 on vesicle surfaces is surprising, consider-ing the cytosolic nature of SOD1 and the established topologyof EVs, which recapitulate the cell of origin, with cytosolic com-ponents in the vesicle lumen and plasma membrane outerleaflet components exposed on the outer leaf of the vesiclemembrane (19). Moving from immunoprecipitation to ELISA,we found that lysates of brain- and spinal cord– derived EXsfrom SOD1G93A mice were significantly enriched in misfoldedSOD1, compared with vesicles from NTg animals (Fig. 6D).Moreover, we found that brain and spinal cord MVs (Fig. 6D)displayed a similar pattern, although they appeared to havelower total levels of misfolded SOD1 than the smaller EXs. No

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Figure 5. Mouse brain EVs reflect neurodegeneration occurring over time. Brain microvesicles from mice sacrificed at 2 and 5 months of age (MOA) wereprobed with antibodies against GLAST (A), CD11b (B), CD56 (C), and CD81 (D), and the number of positive vesicles was determined by flow cytometry. Positiveevents are reported as the percentage of the total positive population (including noise) minus the percentage of positive events after vesicle lysis. Data wereanalyzed by two-way ANOVA with a Sidak multiple-comparison test for the effect of genotype and age: Glast (A), p � 0.0007 (interaction), p � 0.0511 (age), andp � 0.0206 (genotype); CD11b (B), p � 0.3539 (interaction), p � 0.0001 (age), and p � 0.03779 (genotype). C and D, results not significant. Error bars, S.E.

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difference in misfolded SOD1 load is seen in the vesicles har-vested from brains compared with spinal cords.

Vesicles from human spinal cord tissues from SOD1 FALSpatients and control patients showed a similar pattern. Whenvesicles were immunoprecipitated, both misfolded SOD1-spe-cific antibodies (3H1 and 10C12) had an increased signal fromFALS patient vesicles compared with controls (Fig. 6E, 3H1(p � 0.0496) and 10C12 (p � 0.0219)). Similar results wereobserved when vesicle lysates were subjected to ELISA (Fig. 6F);unfortunately, access to patient spinal cord tissue was limited,and only two samples were obtained, resulting in a clear trend

toward increased misfolded SOD1 in the vesicles, but lacking instatistical significance (p � 0.1003).

Differential aggregation profiles of mutant SOD1 in mouseand human CNS EVs

We have previously demonstrated the prion-like capabilityof mutant human SOD1G127X to convert human WT SOD1(HuWTSOD1) into a misfolded conformation and the subse-quent spreading of this misfolded conformation from cell cul-ture to cell culture successively (3, 6). SOD1-induced motorneuron disease has also been demonstrated in vivo using the

Figure 6. Brain and spinal cord EVs from mice overexpressing human SOD1G93A contain and are decorated by misfolded SOD1. A, intact EXsimmunoprecipitate with misfolded SOD1-specific antibodies 3H1 and 10C12 (3, 53). B and C, quantitation of the signal from three immunoprecipitationexperiments: brain (B), Student’s t test, p � 0.0447 (3H1) and p � 0.0170 (10C12); Spinal cord (C), Student’s t test, p � 0.0070 (3H1) and p � 0.0159(10C12). D, purified vesicle lysates from 100,000 � g pellet (EX) and 15,000 � g pellet (MV) from brains and spinal cords were assayed for misfolded SOD1in a chemiluminescent ELISA. Anti-misfolded SOD1 antibody 3H1 was used as the capture antibody. Data are provided as raw luminescence units (RLU),as no standards of misfolded SOD1 were available for comparison. Data were analyzed by paired Student’s t test. E, intact EXs from human spinal cordtissues, four each of control and SOD1 FALS (n � 3 SOD1-A4V, n � 1 SOD1-N139K), immunoprecipitated with misfolded SOD1-specific antibodies 3H1and 10C12 (3, 53). Quantitation of the signal, normalized to the weight of source tissue, from four immunoprecipitation experiments is shown.Differences were determined by a Kruskal–Wallis nonparametric ANOVA (p � 0.0009) with Dunn’s multiple-comparison test (p � 0.0496 for 3H1, p �0.0219 for 10C12). F, purified MV lysates from human spinal cords, three control and two SOD1A4V FALS tissues, were assayed for misfolded SOD1 byELISA. Anti-misfolded SOD1 antibody 3H1 was used as the capture antibody. Data were analyzed by Student’s t test (p � 0.1003). IP, immunoprecipi-tation; IB, immunoblotting; error bars, S.E.

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spinal cord homogenate from mutant SOD1G93A as the seed(5). Under native cytosolic conditions, HuWTSOD1 forms astable homodimer that does not aggregate. HuSOD1G93A isthought to be indistinguishable from HuWTSOD1 until late indisease progression (�120 days in mice), at which point aggre-gates (54) and oligomers (55) have been observed. Conversely,the molecular state of SOD1G127X in cytosol is unclear, consid-ering 1) the SOD1G127X truncation mutation, which results inthe loss of � strand 8, a critical portion of the homodimer inter-face; 2) lack of Cys-146, which forms a monomer-stabilizingdisulfide bond with Cys-57 required for native homodimer for-mation; and 3) lack of stoichiometric metal binding, which con-tributes significantly to stabilization. HuSOD1G127X has beenshown to form intracellular aggregates (56), likely due to non-native interchain disulfide bonds (57).

To identify the quaternary structure of the propagation-competent species of HuSOD1G127X and HuSOD1G93A in theCNS EVs, brain MVs from NTg mice with endogenous mouseSOD1 (mSOD1), HuSOD1G127X transgenic mice, SOD1 knock-out mice (mSOD1�/�), mSOD1�/�/HuSOD1G127X crossesand HuSOD1G93A transgenic mice were subjected to SDS-PAGE under reducing and nonreducing conditions with andwithout iodoacetamide to block artifactual formation of disul-fide bonds (Fig. 7A). HuSOD1G127X is a truncation mutation,and the truncation results in the loss of epitope for the mis-folded SOD1-specific antibody used in the immunoprecipita-tions and ELISAs in Fig. 6 (3, 58). For this reason, nonreducingPAGE could produce the most information regarding theaggregation profile of mutant SOD1 in EVs.

The vesicles were collected at symptom onset, 90 days forHuSOD1G93A and 150 days for HuSOD1G127X. Under reduc-ing conditions, all species of SOD1, mouse WT and humanG127X and G93A, appeared as monomer bands around 17kDa (Fig. 7A). However, under nonreducing conditions,where disulfide bonds were maintained, higher-order aggre-gates of HuSOD1G93A and, more robustly, HuSOD1G127X

appeared in the very top of the gel, which included the stack-ing gel (Fig. 7A). Artifactual aggregation was observed inHuSOD1G93A without iodoacetamide. The bona fide disul-fide-mediated aggregates were restricted to the expressionof HuSOD1, as no such aggregates were observed in the NTgand no SOD1 bands were detected in the mSOD1�/� vesicles(Fig. 7A). Moreover, HuSOD1G127X expression was found tobe relatively low; twice as much protein per well wasrequired from the mSOD1�/�/HuSOD1G127X sample tovisualize a clear signal (Fig. 7A). Volumetric quantitation ofthe SOD1 monomer band (Fig. 7B) and aggregate bands/smears (Fig. 7C) from replicate immunoblot analyses con-firmed that EV SOD1G93A is predominantly monomericunder nonreducing conditions, in contrast to SOD1G127X,which takes the form of insoluble aggregates under theseconditions. We can conclude that SOD1G127X mouse CNSEVs contain large insoluble aggregates of SOD1G127X as wellas native mSOD1. In contrast, SOD1G93A mice at 3 monthsof age have fewer and lower-order aggregates of SOD1 inbrain-derived EVs.

We confirmed these findings with EVs harvested fromhuman spinal cords. Under reducing conditions, SOD1 signal

was restricted to the monomeric range, as well as some lower-molecular weight degradation products, in EVs from controland FALS patients (Fig. 7D). However, FALS SOD1A4V

patient–specific SOD1 aggregates at �70 and �140 kDa wereobserved under nonreducing conditions (Fig. 7D). After volu-metric quantitation of replicate experiments with additionalpatient material, we observed that the monomeric SOD1 isequivalent in the control and FALS patients (Fig. 7E). Con-versely, under nonreducing conditions, the FALS patient EVsshow a concentration of aggregated SOD1 (Fig. 7F). In conclu-sion, both human ALS and mouse ALS-model CNS EVs con-tain aggregated SOD1 cargo.

Discussion

We developed methods to investigate the intra-organ extra-cellular vesicle population of the mouse brain and spinal cord(Figs. 1–7). At the onset of motor neuron disease in SOD1G93A

mice, the vesicle proteome is largely unchanged comparedwith nontransgenic mice, except for the presence of humanSOD1G93A on the surface and in the lumen of vesicles (Figs.2–5). Microglia contribute little to the EV population, with themajority of vesicles likely being secreted by astrocytes and neu-rons (Figs. 4 and 5).

Understanding the cellular mechanisms of prion-like proteinmisfolding and neuroanatomical pathology propagation is essen-tial for a comprehensive understanding of the etiology of neurode-generative diseases and for effective therapeutic development.Using mouse models of disease, descriptions of brain EV seeding ofTau pathology in AD (31) and �-synuclein pathology in dementiawith Lewy body disease (59) are demonstrating, ex vivo, a role forEVs in propagation of proteopathy. In this work, we show evi-dence that CNS-derived extracellular vesicles isolated from theSOD1G93A ALS mouse model and human SOD1-FALS neural tis-sues carry misfolded and aggregated SOD1 cargo. This findingindicates that mutant/misfolded SOD1 within EVs might be suffi-cient to induce misfolding of full-length WT protein in recipientcells, representing a potential mechanism for systematic spread ofALS pathogenesis. Follow-on functional studies are needed to fullyelucidate the role of EVs in disease.

SOD1-induced motor neuron disease has been demon-strated in vivo using spinal cord homogenate from paralyzedSOD1G93A mice (5). We have demonstrated the ability ofSOD1G127X to seed conversion of HuWTSOD1 into a mis-folded conformation and the subsequent spreading of this mis-folded conformation in cell cultures (3, 6). It is thought thatboth vesicles and free aggregates of pathogenic proteins may beinvolved in releasing SOD1 “seeds” from affected cells (6), con-sistent with contiguous propagation of clinical symptoms.However, it remains to be determined which mechanism, if any,is responsible for the spread of proteopathy. Moreover, as bothSOD1 and TDP43 mutant-associated ALS have been shown tobe non-cell-autonomous (60 –63), the question of which cell isreleasing the misfolded protein species and which cell is therecipient remains unclear.

Our data suggesting an overrepresentation of astrocyte-de-rived EVs in the brain are evocative of the large body of litera-ture describing a toxic role of astrocytes in the context ofSOD1-ALS (63–65). Additionally, mutant SOD1-expressing

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actrocytes have been found to increase exosome release andcause SOD1 pathology in naive recipient neurons (65). The lowerlevels of GLAST vesicles in the spinal cord compared with brain,and the increased SNAP25 surface decoration of EXs in the spinalcord, point to differing populations in these two tissues, the phe-notypic effect of which is not yet understood.

In cell culture systems, we have previously reported that mis-folded SOD1 aggregates are released from dead and dying cells,whereas EVs were released primarily from live cells early in thedegenerating process (6). Here, we showed that mouse ALS-model CNS vesicles carry soluble mutant SOD1 as well as insol-uble aggregates (Fig. 7, A–C) and confirmed those findings with

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Figure 7. Differential aggregation profiles of mutant SOD1 in mice and human brain EVs. The protein cargo of microvesicles harvested from NTg andmultiple ALS model mice (A–C) or human spinal cord tissue (D–F) was analyzed by reducing and nonreducing SDS-PAGE followed by SOD1 immunoblot. Forrepresentative immunoblots (A and D), reducing lanes include �-mercaptoethanol (�-merc.). Iodoacetamide (iodoact.) was included to block artifactualdisulfide bonds from forming during sample processing. -mon., monomer band (�17 kDa); *, aggregate band(s). B and C, quantitation of volume intensity ofimmunoblots from n � 2– 4 brain MV samples per genotype normalized to the amount of protein analyzed. ��-merc./-iodoact., reducing lanes; ��-merc./�iodoact., nonreducing lanes. B, HuSOD1G93A reported on right y axis; C, aggregate; *, band at top of gel. Mean and S.E. (error bars) are shown. Differences weredetermined by two-way ANOVA with Sidak’s multiple-comparison test. B, p � 0.2667 (interaction), p � 0.0001 (genotype), and p � 0.0140 (reduction). C, p �0.2003 (interaction), p � 0.0031 (genotype), and p � 0.4553 (reduction). E and F, quantitation of volume intensity of immunoblots from n � 4 FALS A4V samplesand n � 4 control samples, normalized to the amount of protein analyzed. Mean and S.E. are shown. Aggregate signal (F) is the sum of the volume intensitiesfor bands marked with an asterisk in D. ��-merc./�iodoact., reducing lanes; ��-merc./�iodoact., nonreducing lanes. Differences were determined by two-wayANOVA with Sidak’s multiple-comparison test. E, p � 0.4012 (interaction), p � 0.5241 (disease status), and p � 0.0184 (reduction). F, p � 0.2204 (interaction),p � 0.0466 (disease status), and p � 0.0761 (reduction). Error bars, S.E.

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human spinal cord EVs (Fig. 7, D–F). The age of the animal mayalso be relevant to the packing of EVs with aggregated SOD1;aggregates of SOD1G93A have previously been observed in dis-ease-affected animals of �120 days of age, whereas little aggre-gation was seen in younger animals, in agreement with our find-ings (54, 55). In the context of the literature, our results suggestthat astrocytes are primarily secreting vesicles carrying toxiccargo, including aggregated and soluble mutant SOD1, whereasfree protein aggregates are also released from dead and dyingneurons. One might speculate that both mechanisms play sig-nificant roles during disease, perhaps at different times, orsimultaneously but in dynamic ratios.

Recent work has suggested that, in the context of the synapse,the release of vesicles packed with misfolded proteins is a pro-teostatic protective cellular function mediated by neuron-spe-cific cysteine string protein (CSP�, DnaJC5) (32, 66). We iden-tified this protein in the mouse brain– derived EXs, and itappears in similar levels in the SOD1G93A and NTg samples. Inlight of the demonstrated role for DnaJC5 in vesicle secretion ofunfolded proteins (32), the lack of concentration of DnaJC5 inthe SOD1G93A vesicles, which we know to be enriched in themutant and misfolded SOD1 (Figs. 1, 2, and 6), supports ourconclusion that perhaps the majority of these vesicles arederived from astrocytes.

The role of protein supersaturation in triggering toxicity andperhaps propagated misfolding has been investigated (67). Inthis elegant computational study, SOD1 and TDP-43 are shownto have orders of magnitude higher supersaturation values inmotor neurons, compared with other cellular proteins. Theauthors suggest that supersaturation is responsible for proteinaggregation or co-aggregation and gain of toxic function. Wecompared the list of supersaturated proteins found in humanand mouse SOD1 inclusions with our mouse brain EX pro-teome and found relatively little overlap: 23 of the 77 humanSOD1 inclusion proteins and 12 of the 58 mouse SOD1 inclu-sion proteins. This indicates that key proteins may dominatedisease progression, rather than co-aggregation of multipleproteins, most consistent with a prion-like propagated misfold-ing mechanism of spreading.

SOD1 is widely thought to play an important role only infamilial cases of ALS where SOD1 mutations occur, less than2% of all ALS cases (68), although some literature supports arole for WT human SOD1 in sporadic ALS (69). In this light, itis interesting that SOD1 is a common EV marker, and futureCNS vesicle studies in sporadic ALS may reveal misfoldedSOD1, perhaps concentrated as a protective proteostatic cellu-lar function. Our current findings on the baseline phenotype ofmouse brain and spinal cord EVs may have bearing on the widerspectrum of ALS (70). The apparent significant enrichment ofribosome-associated proteins on the surface of only the ALSmouse model BDEV is reminiscent of the emerging consensusthat dysregulation of translation is a hallmark of ALS andother neurodegenerative diseases like FTD (71, 72). RBPs likeTDP-43 and FUS, as well as a growing list of others, are recog-nized as pathogenic markers of disease, although the exactmechanisms of pathogenicity are under intense investigation(73). A growing body of work is linking RBP and EVs to disease(8, 32, 74), and RNA and RBP cargo of exosomes is a well-

established phenomenon (23). What remains to be determinedis the interplay between RBP, stress granules, protein aggrega-tion, vesicle release, and their summated toxicity. Our worksupports the conclusion that RBPs are constitutively secreted inassociation with brain and spinal cord vesicles but that themouse RBPs are not recruited to the vesicles by mutant SOD1.Additionally, the enrichment of synaptic and synaptic vesicleproteins in the brain EVs suggests a role for these vesicles inregulation of synaptic transmission, supported by a small bodyof literature (75, 76).

Only one protein, besides human SOD1G93A, had signifi-cantly modified representation in the SOD1G93A BDEXs, MOG(Fig. 2A). Antibodies targeting MOG are thought to play a rolein some demyelinating diseases (77). The biological signifi-cance of MOG’s reduced abundance in the SOD1G93A vesiclesis unclear and may simply reflect the process of neurodegenera-tion occurring in the transgenic mice (78). However, it is tempt-ing to speculate that effective therapies would protect againstthe loss of this protein, and as such, it may have value as abiomarker for therapeutic efficacy. The field of cancer diagno-sis has turned to vesicles as potent and plentiful markers ofmigrating tumor cells and, by screening for multiple disease-associated proteins, has been able to drastically improve diag-nostic potential for prostate and breast cancer (79). Our workhas identified at least one attractive candidate protein (and,including protein-disulfide isomerase, perhaps two) for similarsorting of patients with early signs of ALS or neurologicdysfunction.

In conclusion, extracellular vesicles collected from whole tis-sues provide an ex vivo platform for the investigation of intra-organ intercellular communication. It is of great interest to per-form additional characterization studies on vesicles fromhuman tissue to assess the baseline phenotype of tissue EVs andthe complex modifications that occur in disease.

Experimental procedures

Animals

Animals used in this study, C57 BL/6 and HuSOD1G93A,mSOD1�/� (strains: B6SJL, Cg-Tg(Sod1-G93A)1Gur/JB6, andB6;129S-Sod1tm1Leb/J purchased from Jackson Laboratories (BarHarbor,ME)),andHuSOD1G127X mice(Tg(SOD1*G127X)716Mrkl;a gift from Stefan Marklund) (80 –82) were housed in accreditedfacilities in accordance with University of British Columbia andinternational animal ethics guidelines. All animals were sacri-ficed early in disease onset to avoid unnecessary suffering:HumanWTSOD1 mice and G93A mice and WT littermates at 3months of age, G127X mice and WT littermates at 5 months ofage. The studies were reviewed and approved by the Universityof British Columbia Animal Care Committee.

Human tissue

The human tissues used in this study were obtained frombrain banks affiliated with the University of British Columbiaand the Target ALS–Johns Hopkins School of Medicine. Con-sent for autopsy was obtained from the legal representative inaccordance with local institutional review boards. The studieswere reviewed and approved by the University of BritishColumbia Ethics Board and are in accordance with the Decla-

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ration of Helsinki principles. Cases included nonneurodegen-erative control patients (n � 4) and cases with FALS with con-firmed SOD1 mutations (n � 6). Sequencing of SOD1 hadpreviously been performed at each of these centers using meth-ods described elsewhere (42).

Vesicle isolation

The isolation of vesicles from whole tissues was adopted andmodified from Ref. 30. Frozen tissue, brain, and spinal cordfrom SOD1-G93A and NTg littermates and human spinalcords were first weighed. Whole mouse brains (0.4 – 0.6 g) wereused. Five murine spinal cords, �100 mg/cord, were pooled forthe isolation. 0.3– 0.75 g of human spinal cord tissue wasemployed for each isolation. The tissue was sliced minimally inHibernate A solution (Brain Bits, Springfield, IL) and treatedwith papain (20 units/ml) or collagenase III (75–125 units/ml)at 37 °C for 15 min to digest connective tissue. Tissue was fur-ther disassociated by up-and-down aspiration in 2 volumes ofcold Hibernate A solution plus protease inhibitor (Roche, Mis-sissauga, Canada). The disassociated tissue was then sequen-tially centrifuged at 2000 � g to separate cell debris and collectextracellular material and at 15,000 � g to collect large vesicles,such as microvesicles. EVs were collected by centrifugation at100,000 � g for 1 h.

Sucrose gradients

The EV pellet was purified by density gradient centrifugationin a sucrose step gradient, with concentrations ranging from 2.0M (�60% sucrose) to 0.25 M (�7.5% sucrose) in 0.35 M incre-ments and centrifuged at 200,000 � g for 16 h at 4 °C in aBeckman L90 Ultracentrifuge (Beckman Coulter, Mississauga,Canada). Fractions of equal volume are collected, diluted inPBS, and centrifuged again at 100,000 � g for 70 min at 4 °C.Sucrose gradient fraction pellets were resuspended in PBS andstored at �80 °C. Where appropriate, protease inhibitors wereadded to storage buffer.

OptiPrep gradients

BDEVs were purified on OptiPrepTM density gradient fol-lowing previously published protocols (35, 83). Briefly, a dis-continuous iodixanol (OptiPrepTM, MilliporeSigma, Oakville,Canada) gradient was prepared by diluting stock solutions ofOptiPrepTM (60% (w/v) aqueous iodixanol) with 0.25 M sucrose,10 mM Tris, pH 7.5. The 100,000 � g pellet was overlaid ontothe top of the gradient and centrifuged at 100,000 � g for 18 h at4 °C. 0.6-ml gradient fractions were collected manually fromthe top (with increasing density). Fractions were diluted withPBS and centrifuged at 100,000 � g for 3 h at 4 °C, washed inPBS, and resuspended in PBS and stored at �80 °C until furtheruse.

Sucrose cushion

For quantitative proteomics and flow cytometric studies,BDEVs were purified using a sucrose cushion system. A cush-ion of 0.5 ml of 2 M sucrose overlaid with 0.25 ml of 1 M sucrosefollowed by 0.6 ml of PBS was constructed in 1.5-ml ultracen-trifuge tubes. Resuspended EV pellets (0.2– 0.4 ml) were layeredon top of the gradient followed by ultracentrifugation at

150,000 � g at 4 °C for 2 h in a Hitachi CX 150NS Micro Ultra-centrifuge. 0.7 ml was removed from the top of the gradient anddiscarded. 0.4 ml, including the �1 M EV fraction was removedand resuspended in PBS followed by additional ultracentrifuga-tion, 100,000 � g 4 °C for 1 h. Pellets were resuspended in PBSand stored at �80 °C until further use.

Immunoblotting

Equal volumes of either sucrose or OptiPrep fraction sampleswere boiled in SDS sample buffer containing 1% �-mercapto-ethanol and subjected to SDS-PAGE, followed by immunode-tection with a pan-SOD1 rabbit polyclonal antibody (SOD100;ENZO Life Sciences, Plymouth Meeting, PA), prion protein(PrP 6D11; Santa Cruz Biotechnology, Inc., Dallas, TX), CD9(clone EPR2949, Abcam Inc., Cambridge, MA), or GRP78/BiP(clone 40/BiP, BD Biosciences, Mississauga, Canada) to confirmthe presence of exosome vesicles. Fractions were also blotted formarkers of other organellar membranes, such as Bcl-2 (clone7/Bcl-2) and GM-130 (clone 35/GM130), all purchased from BDBiosciences, to assess the purity of the EV pellets. Vesicles werealso blotted for GLAST (clone ACSA-1, Miltenyi Biotech, Auburn,CA), SNAP25 (clone SMI 81, BioLegend, San Diego, CA), NeuN(clone A60, MilliporeSigma), GFAP (polyclonal, ab7260; Abcam),and synaptophysin (clone YE269; Abcam).

Electron microscopy

Transmission EM of sucrose-purified EVs was performedessentially as described (84). Briefly, EVs were fixed in 2%glutaraldehyde and 4% paraformaldehyde in 0.1 M cacodylatebuffer for 2 h at room temperature. Vesicles were collected byultracentrifugation and washed in 0.1 M cacodylate buffer.Fixed vesicles were absorbed onto Formvar-coated 200-meshnickel grids (Electron Microscopy Sciences, Hatfield, PA). Forimmunoelectron microscopy, grids were blocked with 1% milkin PBS followed by probing with primary antibodies overnightin blocking buffer. After washing, grids were incubated withsecondary antibodies in 1% milk and 0.5% PEG. All grids werenegatively stained with 0.5% aqueous uranyl acetate for 30 s andviewed on a FEI Tecnai G2 Spirit transmission electronmicroscope.

Antibodies were purchased from the following sources:mouse anti-CD63 (clone H5C6) and mouse anti-SNAP25 bothfrom BioLegend; mouse anti-GLAST (clone ACSA-1) andhamster anti-CD81-biotinylated (clone EAT2) both fromMiltenyi; guinea pig anti-VGAT (Synaptic Systems, GoettingenGermany); all secondary antibodies (anti-mouse 15-nm gold,anti-biotin 25-nm gold, anti-guinea pig 10-nm gold) from Elec-tron Microscopy Sciences.

Immunoprecipitation

Quantitative immunoprecipitation of misfolded SOD1 wasperformed as described previously (3, 6) using the resuspendedpellet fractions in PBS alone so as not to disrupt vesicles; pull-down of misfolded SOD1 therefore only occurred if it presentedon the vesicle surface. The following antibodies were coupled tomagnetic Dynabeads (Invitrogen) following the manufacturer’sinstructions: mouse IgG2A isotype control (Abcam Inc.),SOD100, and misfolded SOD1-specific antibodies 3H1 and

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10C12 (3). An equal amount of EV sample, 10 –20 �g, wasadded to each antibody bead combination and incubated for24 h at 4 °C with constant rotation, followed by three briefwashes in PBS. Samples were boiled in SDS sample buffer con-taining 1% �-mercaptoethanol and subjected to SDS-PAGE,followed by immunodetection with a pan-SOD1 rabbit poly-clonal antibody (SOD100).

ELISA

96-well Nunc ELISA plates (Thermo Fisher Scientific) werecoated with 7.38 �g/well of the anti-misfolded SOD1 mAb 3H1overnight at 4 °C. Plates were washed with TBS containing 0.1%Tween 20 and blocked with filtered PBS � 0.1% Tween 20 with3% normal goat serum (MilliporeSigma) overnight at 4 °C andwashed again. Samples were prepared by measuring total pro-tein concentration using the Pierce BCA assay kit (ThermoFisher Scientific). Equal protein amounts (MV and EX � 0.05�g/�l) of EV lysates, lysed in 1% Triton X-100 for 20 min on ice,were incubated with the captured 3H1 antibody for 1 h at roomtemperature. Plates were washed and incubated with 2 �g/mlrabbit polyclonal SOD100 antibody at room temperature for1 h. Finally, the plate was washed and incubated with HRP-linked anti-rabbit IgG (GE Healthcare) diluted 1:5000 for 1 h atroom temperature, followed by five final washes. The plateswere incubated with SupersignalTM ELISA Femto substrate(Thermo Fisher Scientific) for 5 min at room temperature.Total chemiluminescence at all wavelengths was read on aSpectraMax M2 Molecular Devices instrument.

Quantitative proteomics

When isolating BDEX for proteomics, TBS was substitutedfor PBS at all steps, and at the final pelleting step, vesicles wereresuspended in TBS without protease inhibitor. Protein con-centration was determined using a Pierce BCA kit (ThermoFisher Scientific).

To remove surface proteins from BDEX for separate analysis,it was assumed that the surface protein content was 1% of totalvesicle protein content, as is generally assumed for eukaryoticcells (48). Trypsin (Promega, Madison, WI) was added to BDEXat a 1:50 protein ratio in TBS and incubated at 37 °C for 4 h, afterwhich vesicles were acidified to pH 2 with 10% acetic acid to killtrypsin activity. TBS was added to the trypsinized BDEX fol-lowed by ultracentrifugation at 100,000 � g at 4 °C for 1 h.Tryptic peptides from surface proteins remained in the super-natant while intact vesicles were pelleted and resuspended in 50mM ammonium bicarbonate, 1% sodium deoxycholate andstored at �80 °C.

The resulting surface-depleted vesicle pellet and surface pep-tide preparations were reduced and alkylated as per (85) andfurther digested with trypsin at 37 °C overnight. Peptide sam-ples were purified by solid-phase extraction on C-18 STop AndGo Extraction (STAGE) tips (86), and each treatment waschemically labeled by reductive demethylation using formalde-hyde isotopologues (87). The final product was purified againby C-18 STAGE tips and run on a Bruker Impact II Q-TOFcoupled to an Easy-Nano LC 1000 HPLC (Thermo Fisher Sci-entific) (88).

MaxQuant was used to assign peptide and protein identifica-tions and relative abundance ratios (89). Perseus was usedto analyze relative abundance ratios and determine signifi-cantly enriched proteins (90). ErmineJ was used to determinestatically enriched gene ontology (GO) annotations in theBDEX and surface proteomes compared with the entire mousegenome (91, 92).

Flow cytometry

Flow cytometry analysis of 15,000 � g and 100,000 � g pelletswas performed with modifications following published proto-cols (51, 52, 93, 94). All buffers are passaged through a 0.1-�mpolyvinylidene difluoride filter (Corning Life Sciences, Tewks-bury MA) prior to use. BDEVs and BDMVs were resuspendedin 0.4% BSA in PBS. EVs and MVs were probed with the follow-ing antibodies at the manufacturer’s recommended concentra-tion. Anti-GLAST (phycoerythrin and allophycocyanine, cloneACSA-1), anti-CD81 (phycoerythrin, clone EAT2), and anti-CD11b (FITC, clone M1/70.15.11.5) were purchased fromMiltenyi Biotech. Anti-CD56/NCAM (allophycocyanine, cloneFAB7820A) was purchased from R&D Systems (Minneapolis,MN). All isotype control antibodies and anti-SNAP25 werepurchased from Biolegend. Anti-mouse Alexa-488 secondaryantibody was purchased from Life Technologies (ThermoFisher Scientific). Antibodies were centrifuged at 20,000 � g for20 min prior to incubation with vesicles for 1 h at room tem-perature in the dark. Unbound antibody was removed fromvesicles after resuspension in 1 ml of PBS by ultracentrifugationat either 15,000 � g for 30 min or 100,000 � g for 1 h for BDMVand BDEX, respectively. Vesicle pellets were resuspended in100 –500 �l of PBS and then diluted further to 1:250 for BDMVand 1:10 for BDEV in PBS and PBS � 1.0% Nonidet P-40. Ves-icles were analyzed on a MACSQuant analyzer (Miltenyi Bio-tech) after thorough washing of the machine with 1% bleach.Samples were collected on the lowest flow setting for 2 mineach. Between each sample, PBS was run on the high flow set-ting. Data were analyzed with FlowJo (Ashland, OR). Statisticalanalysis was performed with GraphPad Prism versions 5–7.

Nonreducing SDS-PAGE

Purified vesicles were thawed on ice, and the total proteinconcentration was measured using the Pierce BCA assay kit.Reducing and nonreducing SDS-PAGE was carried out using15 �g of protein from mouse MVs (30 �g for mSOD1�/�/HuSOD1G127X MVs) and 5 �g from human MVs, with andwithout the presence of 100 mM iodoacetamide. The vesicleswere mixed with 5 �l of 1� NuPAGE sample buffer (ThermoFisher Scientific) with one of four possible treatments andbuffered with PBS (pH 7.4) to a total volume of 15 �l. Thetreatments were as follows: 2.5% �-mercaptoethanol, 2.5%�-mercaptoethanol with 100 mM iodoacetamide, 100 mM

iodoacetamide, and no treatment. Samples were heated for 5min at 95 °C and electrophoresed on NuPAGE 4 –12% Bis-Tris gels (Thermo Fisher Scientific) before being transferredonto polyvinylidene difluoride membranes. After transfer,the membranes were probed with rabbit polyclonal SOD100antibody followed by horseradish peroxidase anti-rabbit IgG (GEHealthcare). Membranes were exposed to SupersignalTM West

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Femto substrate (Thermo Fisher Scientific), and the chemilu-minescence was measured using a ChemiDoc system (Bio-Rad). The relative intensity of the bands was measured usingImageLab, and the percentage of aggregate signal comparedwith the total band signal was calculated.

Author contributions—J. M. S. proposed the hypothesis, designedand performed experiments, and drafted the manuscript. D. C.,C. C. S., Y. B., S. F., Z. G., and L. M. contributed to optimization andperformed vesicle collection and immunoblotting, proteomics, flowcytometric, and ELISA experiments. K. M. M. performed quantita-tive mass spectrometry, and R. G. S. assisted in quantitative pro-teomics analysis. L. I. G. contributed to experimental design andperformed immunoprecipitation experiments. Z. G. and C. M. C.performed TEM experiments. I. R. M. contributed to experimen-tal design and provided human ALS tissue. L. J. F. and N. R. C.contributed to the hypothesis, experimental design, and manu-script drafting.

Acknowledgments—We thank Dr. Lyle Ostrow (Target ALS–JohnsHopkins School of Medicine) for human patient tissue. We thank Dr.Andy Hill and Dr. Laura Jayne Vella for technical assistance andthoughtful scientific discussions. We thank Dr. Wayne Vogle for tech-nical TEM assistance. We thank Andy Johnson and Justin Wong (Uni-versity of British Columbia Flow Core) for technical assistance andsupport with flow cytometry. We thank Dr. Emma Guns for criticalreading of the manuscript.

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CNS tissues contain diverse extracellular vesicles

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Grad, Luke McAlary, Ian R. Mackenzie, Leonard J. Foster and Neil R. CashmanFernando, Zoe Gidden, Catherine M. Cowan, Yuxin Ban, R. Greg Stacey, Leslie I. Judith M. Silverman, Darren Christy, Chih Cheih Shyu, Kyung-Mee Moon, Sarah

mice originate from astrocytes and neurons and carry misfolded SOD1 ALSG93ACNS-derived extracellular vesicles from superoxide dismutase 1 (SOD1)

doi: 10.1074/jbc.RA118.004825 originally published online January 11, 20192019, 294:3744-3759.J. Biol. Chem. 

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