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Status |
Public on Apr 12, 2021 |
Title |
Molecular tracking devices quantify antigen distribution and archiving in the lymph node. |
Organism |
Mus musculus |
Experiment type |
Expression profiling by high throughput sequencing Other
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Summary |
Live, attenuated vaccines generate humoral and cellular immune memory, increasing the duration of protective immune memory. We previously found that antigens derived from vaccination or viral infection persist beyond infection clearance via acquisition and retention (“archiving”) in lymphatic endothelial cells (LECs). Archived antigen maintains an effector-like pool of antigen-specific memory T cells, enhancing clearance of subsequent infections. Technical limitations of fluorescent labeling have precluded a complete picture of antigen archiving across cell types in lymph tissue. We developed a “molecular tracking device” to follow the distribution, acquisition, and retention of antigen in the lymph node. We immunized mice with an antigen conjugated to a nuclease-resistant DNA tag and used single-cell mRNA sequencing to quantify its abundance across major cell types in the lymph node two weeks later, validating its acquisition by migratory dendritic cells and durable retention by LECs and unexpected stromal cell types. Variable antigen levels in LECs enabled the identification and validation of caveolar endocytosis as a mechanism of antigen acquisition. Molecular tracking devices enable new approaches to study dynamic tis-sue dissemination at cellular resolution in vivo.
We developed a 'molecular tracking device' to follow the distribution, acquisition, and retention of antigen across cell types in the lymph node. We immunized mice with an antigen conjugated to a nuclease-resistant DNA tag and used single-cell mRNA sequencing to quantify its abundance in immune and stromal cell types two weeks later, validating its retention by LECs and transfer to migratory dendritic cells and defining new reservoirs of archived antigen in stromal cells. Molecular tracking devices broadly enable new approaches to study molecular dissemination and retention in live animals.
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Overall design |
Single-cell mRNA sequencing libraries and matching antigen-tracking libraries generated from the 10X Genomics system.
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Web link |
https://github.com/rnabioco/antigen-tracking
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Contributor(s) |
Hesselberth JR |
Citation(s) |
33843587 |
NIH grant(s) |
Grant ID |
Grant title |
Affiliation |
Name |
T32 AI007405 |
Training Program in Immunology |
UNIVERSITY OF COLORADO DENVER |
Raul Martin Torres |
R35 GM119550 |
Coordination of RNA cleavage with end modification and processing |
UNIVERSITY OF COLORADO DENVER |
Jay R Hesselberth |
R01 AI121209 |
Cooperation between lymphatic stroma and hematopoietic cells shapes protective immunity |
UNIVERSITY OF COLORADO DENVER |
Beth Ann Tamburini |
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Submission date |
May 17, 2020 |
Last update date |
Apr 13, 2021 |
Contact name |
Jay R. Hesselberth |
E-mail(s) |
jay.hesselberth@cuanschutz.edu
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Organization name |
University of Colorado School of Medicine
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Department |
Biochemistry and Molecular Gentetics
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Lab |
Jay Hesselberth
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Street address |
12801 E 17TH AVE
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City |
Aurora |
State/province |
CO |
ZIP/Postal code |
80045 |
Country |
USA |
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Platforms (1) |
GPL24247 |
Illumina NovaSeq 6000 (Mus musculus) |
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Samples (8)
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Relations |
BioProject |
PRJNA633370 |
SRA |
SRP262039 |
Supplementary file |
Size |
Download |
File type/resource |
GSE150719_CD45neg_d14_barcodes.tsv.gz |
33.2 Kb |
(ftp)(http) |
TSV |
GSE150719_CD45neg_d14_features.tsv.gz |
274.4 Kb |
(ftp)(http) |
TSV |
GSE150719_CD45neg_d14_matrix.mtx.gz |
44.3 Mb |
(ftp)(http) |
MTX |
GSE150719_CD45neg_d2_barcodes.tsv.gz |
6.0 Kb |
(ftp)(http) |
TSV |
GSE150719_CD45neg_d2_features.tsv.gz |
274.4 Kb |
(ftp)(http) |
TSV |
GSE150719_CD45neg_d2_matrix.mtx.gz |
10.1 Mb |
(ftp)(http) |
MTX |
GSE150719_CD45pos_d14_barcodes.tsv.gz |
25.8 Kb |
(ftp)(http) |
TSV |
GSE150719_CD45pos_d14_features.tsv.gz |
274.4 Kb |
(ftp)(http) |
TSV |
GSE150719_CD45pos_d14_matrix.mtx.gz |
34.5 Mb |
(ftp)(http) |
MTX |
GSE150719_CD45pos_d2_barcodes.tsv.gz |
41.7 Kb |
(ftp)(http) |
TSV |
GSE150719_CD45pos_d2_features.tsv.gz |
274.4 Kb |
(ftp)(http) |
TSV |
GSE150719_CD45pos_d2_matrix.mtx.gz |
56.7 Mb |
(ftp)(http) |
MTX |
GSE150719_d14_DC_count_matrix.tsv.gz |
9.5 Mb |
(ftp)(http) |
TSV |
GSE150719_d14_DC_metadata.tsv.gz |
292.3 Kb |
(ftp)(http) |
TSV |
GSE150719_d14_FRC_count_matrix.tsv.gz |
5.0 Mb |
(ftp)(http) |
TSV |
GSE150719_d14_FRC_metadata.tsv.gz |
147.0 Kb |
(ftp)(http) |
TSV |
GSE150719_d14_LEC_count_matrix.tsv.gz |
8.8 Mb |
(ftp)(http) |
TSV |
GSE150719_d14_LEC_metadata.tsv.gz |
275.3 Kb |
(ftp)(http) |
TSV |
GSE150719_d2_DC_count_matrix.tsv.gz |
15.6 Mb |
(ftp)(http) |
TSV |
GSE150719_d2_DC_metadata.tsv.gz |
494.5 Kb |
(ftp)(http) |
TSV |
GSE150719_d2_FRC_count_matrix.tsv.gz |
1.2 Mb |
(ftp)(http) |
TSV |
GSE150719_d2_FRC_metadata.tsv.gz |
25.3 Kb |
(ftp)(http) |
TSV |
GSE150719_d2_LEC_count_matrix.tsv.gz |
1.5 Mb |
(ftp)(http) |
TSV |
GSE150719_d2_LEC_metadata.tsv.gz |
33.5 Kb |
(ftp)(http) |
TSV |
GSE150719_walsh_d14_DC_metadata.tsv.gz |
324.7 Kb |
(ftp)(http) |
TSV |
GSE150719_walsh_d14_FRC_metadata.tsv.gz |
163.8 Kb |
(ftp)(http) |
TSV |
GSE150719_walsh_d14_LEC_metadata.tsv.gz |
311.0 Kb |
(ftp)(http) |
TSV |
GSE150719_walsh_d2_DC_metadata.tsv.gz |
553.9 Kb |
(ftp)(http) |
TSV |
GSE150719_walsh_d2_FRC_metadata.tsv.gz |
28.2 Kb |
(ftp)(http) |
TSV |
GSE150719_walsh_d2_LEC_metadata.tsv.gz |
37.4 Kb |
(ftp)(http) |
TSV |
SRA Run Selector |
Raw data are available in SRA |
Processed data are available on Series record |