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Details	EV-TRACK ID	Experiment nr.	Species	Sample type	Separation protocol	First author	Year	EV-METRIC
	EV190053	1/2	Homo sapiens	THP-1-derived macrophages	SEC SEC (non-commercial) UF	Benet, Susana	2021	0%
Study summary Full title Dissemination of Mycobacterium tuberculosis is associated to a SIGLEC1 null variant that limits antigen exchange via trafficking extracellular vesicles All authors Susana Benet, Cristina Gálvez, Francis Drobniewski, Irina Kontsevaya, Lilibeth Arias, Marta Monguió‐Tortajada, Itziar Erkizia, Victor Urrea, Ruo‐Yan Ong, Marina Luquin, Maeva Dupont, Jakub Chojnacki, Judith Dalmau, Paula Cardona, Olivier Neyrolles, Geanncarlo Lugo‐Villarino, Christel Vérollet, Esther Julián, Hansjakob Furrer, Huldrych F. Günthard, Paul R. Crocker, Gustavo Tapia, Francesc E. Borràs, Jacques Fellay, Paul J. McLaren, Amalio Telenti, Pere‐Joan Cardona, Bonaventura Clotet, Cristina Vilaplana, Javier Martinez‐Picado, Nuria Izquierdo‐Useros Journal J Extracell Vesicles Abstract The identification of individuals with null alleles enables studying how the loss of gene function a (show more...)The identification of individuals with null alleles enables studying how the loss of gene function affects infection. We previously described a non‐functional variant in SIGLEC1, which encodes the myeloid‐cell receptor Siglec‐1/CD169 implicated in HIV‐1 cell‐to‐cell transmission. Here we report a significant association between the SIGLEC1 null variant and extrapulmonary dissemination of Mycobacterium tuberculosis (Mtb) in two clinical cohorts comprising 6,256 individuals. Local spread of bacteria within the lung is apparent in Mtb‐infected Siglec‐1 knockout mice which, despite having similar bacterial load, developed more extensive lesions compared to wild type mice. We find that Siglec‐1 is necessary to induce antigen presentation through extracellular vesicle uptake. We postulate that lack of Siglec‐1 delays the onset of protective immunity against Mtb by limiting antigen exchange via extracellular vesicles, allowing for an early local spread of mycobacteria that increases the risk for extrapulmonary dissemination. (hide) EV-METRIC 0% (median: 14% of all experiments on the same sample type) Reported Not reported Not applicable EV-enriched proteins Protein analysis: analysis of three or more EV-enriched proteins non EV-enriched protein Protein analysis: assessment of a non-EV-enriched protein qualitative and quantitative analysis Particle analysis: implementation of both qualitative and quantitative methods. For the quantitative method, the reporting of measured EV concentration is expected. electron microscopy images Particle analysis: inclusion of a widefield and close-up electron microscopy image density gradient Separation method: density gradient, at least as validation of results attributed to EVs EV density Separation method: reporting of obtained EV density ultracentrifugation specifics Separation method: reporting of g-forces, duration and rotor type of ultracentrifugation steps antibody specifics Protein analysis: antibody clone/reference number and dilution lysate preparation Protein analysis: lysis buffer composition Study data Sample type Cell culture supernatant Sample origin Control condition Focus vesicles extracellular vesicle Separation protocol Separation protocol Gives a short, non-chronological overview of the different steps of the separation protocol. dUC = (Differential) (ultra)centrifugation DG = density gradient UF = ultrafiltration SEC = size-exclusion chromatography IAF = immuno-affinity capture SEC Size-exclusion chromatography (non-commercial) UF Protein markers EV: CD63/ CD9 non-EV: Proteomics no Show all info Study aim Function/Mechanism of uptake/transfer Sample Species Homo sapiens Sample Type Cell culture supernatant EV-producing cells THP-1-derived macrophages EV-harvesting Medium EV-depleted medium Preparation of EDS overnight (16h) at >=100,000g Separation Method Ultra filtration Cut-off size (kDa) 100 Membrane type Regenerated cellulose Size-exclusion chromatography Total column volume (mL) 12 Sample volume/column (mL) 0.25 Resin type Sepharose CL-2B Other Name other separation method Protein Concentration Method Nanodrop Absorbance at 280nm Flow cytometry aspecific beads Antibody details provided? No Detected EV-associated proteins CD9/ CD63 Other 1 Flow cytometry (after non-specific association of vesicles to beads) Characterization: Lipid analysis No

	EV190053	2/2	Homo sapiens	THP-1-derived macrophages	SEC SEC (non-commercial) UF	Benet, Susana	2021	0%
Study summary Full title Dissemination of Mycobacterium tuberculosis is associated to a SIGLEC1 null variant that limits antigen exchange via trafficking extracellular vesicles All authors Susana Benet, Cristina Gálvez, Francis Drobniewski, Irina Kontsevaya, Lilibeth Arias, Marta Monguió‐Tortajada, Itziar Erkizia, Victor Urrea, Ruo‐Yan Ong, Marina Luquin, Maeva Dupont, Jakub Chojnacki, Judith Dalmau, Paula Cardona, Olivier Neyrolles, Geanncarlo Lugo‐Villarino, Christel Vérollet, Esther Julián, Hansjakob Furrer, Huldrych F. Günthard, Paul R. Crocker, Gustavo Tapia, Francesc E. Borràs, Jacques Fellay, Paul J. McLaren, Amalio Telenti, Pere‐Joan Cardona, Bonaventura Clotet, Cristina Vilaplana, Javier Martinez‐Picado, Nuria Izquierdo‐Useros Journal J Extracell Vesicles Abstract The identification of individuals with null alleles enables studying how the loss of gene function a (show more...)The identification of individuals with null alleles enables studying how the loss of gene function affects infection. We previously described a non‐functional variant in SIGLEC1, which encodes the myeloid‐cell receptor Siglec‐1/CD169 implicated in HIV‐1 cell‐to‐cell transmission. Here we report a significant association between the SIGLEC1 null variant and extrapulmonary dissemination of Mycobacterium tuberculosis (Mtb) in two clinical cohorts comprising 6,256 individuals. Local spread of bacteria within the lung is apparent in Mtb‐infected Siglec‐1 knockout mice which, despite having similar bacterial load, developed more extensive lesions compared to wild type mice. We find that Siglec‐1 is necessary to induce antigen presentation through extracellular vesicle uptake. We postulate that lack of Siglec‐1 delays the onset of protective immunity against Mtb by limiting antigen exchange via extracellular vesicles, allowing for an early local spread of mycobacteria that increases the risk for extrapulmonary dissemination. (hide) EV-METRIC 0% (median: 14% of all experiments on the same sample type) Reported Not reported Not applicable EV-enriched proteins Protein analysis: analysis of three or more EV-enriched proteins non EV-enriched protein Protein analysis: assessment of a non-EV-enriched protein qualitative and quantitative analysis Particle analysis: implementation of both qualitative and quantitative methods. For the quantitative method, the reporting of measured EV concentration is expected. electron microscopy images Particle analysis: inclusion of a widefield and close-up electron microscopy image density gradient Separation method: density gradient, at least as validation of results attributed to EVs EV density Separation method: reporting of obtained EV density ultracentrifugation specifics Separation method: reporting of g-forces, duration and rotor type of ultracentrifugation steps antibody specifics Protein analysis: antibody clone/reference number and dilution lysate preparation Protein analysis: lysis buffer composition Study data Sample type Cell culture supernatant Sample origin Mycobacterium tuberculosis infection Focus vesicles extracellular vesicle Separation protocol Separation protocol Gives a short, non-chronological overview of the different steps of the separation protocol. dUC = (Differential) (ultra)centrifugation DG = density gradient UF = ultrafiltration SEC = size-exclusion chromatography IAF = immuno-affinity capture SEC Size-exclusion chromatography (non-commercial) UF Protein markers EV: CD63/ CD9 non-EV: Proteomics no Show all info Study aim Function/Mechanism of uptake/transfer Sample Species Homo sapiens Sample Type Cell culture supernatant EV-producing cells THP-1-derived macrophages EV-harvesting Medium EV-depleted medium Preparation of EDS overnight (16h) at >=100,000g Separation Method Ultra filtration Cut-off size (kDa) 100 Membrane type Regenerated cellulose Size-exclusion chromatography Total column volume (mL) 12 Sample volume/column (mL) 0.25 Resin type Sepharose CL-2B Other Name other separation method Protein Concentration Method Nanodrop Absorbance 280nm Flow cytometry aspecific beads Antibody details provided? No Detected EV-associated proteins CD9/ CD63 Other 1 Flow cytometry (after non-specific association of vesicles to beads) Characterization: Lipid analysis No

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EV-TRACK ID	EV190053
species	Homo sapiens
sample type	Cell culture
cell type	THP-1-derived macrophages
condition	Control condition	Mycobacterium tuberculosis infection
separation protocol	SEC Size-exclusion chromatography (non-commercial) UF	SEC Size-exclusion chromatography (non-commercial) UF
Exp. nr.	1	2
EV-METRIC %	0	0