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| Status |
Public on Oct 13, 2017 |
| Title |
Gene signature profiles in respiratory epithelium infected with nontuberculous mycobacteria |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
The incidence of pulmonary nontuberculous mycobacterial (PNTM) disease is increasing, but host susceptibility factors are not fully understood. We infected air-liquid interface (ALI) primary respiratory epithelial cell cultures with Mycobacterium avium complex (MAC) or Mycobacterium abscessus (MAB) and performed transcriptome sequencing (RNA-Seq) to identify relevant gene expression differences. We used cells from 4 different donors in order to try to obtain generalizable data. The differentiated respiratory epithelial cells in ALI were infected with MAC or MAB at MOI of 100:1 or 1000:1, and RNA-seq was performed at 1 and 3 days after infection. We found downregulation of ciliary genes, including several identified with polymorphisms in previous PNTM cohorts. The cytokine IL-32, the superpathway of cholesterol biosynthesis and downstream targets within the IL-17 signaling pathway were all elevated. The integrin signaling pathway was more upregulated by MAB than MAC infection. Working with primary respiratory epithelial cells infected with nontuberculous mycobacteria at ALI, we identified ciliary function, cholesterol biosynthesis, chemokine production and the IL-17 pathway as major targets of host responses to infection. Some of these pathways may be amenable to therapeutic manipulation.
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| Overall design |
44 strand-specific RNA libraries for high-throughput sequencing were prepared (samples from 4 different donors, 57F, 75M, 69F, and 42F, for each condition) using the TruSeq Stranded mRNA Sample Preparation Kit with 750ng of total RNA according to manufacturer’s instructions.
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| Contributor(s) |
Matsuyama M, Martins AJ, Tsang JS, Holland SM |
| Citation(s) |
28915071 |
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| Submission date |
Jan 11, 2017 |
| Last update date |
Sep 05, 2023 |
| Contact name |
Andrew Martins |
| E-mail(s) |
andrew.martins@yale.edu
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| Organization name |
Yale School of Medicine
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| Department |
Immunobiology
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| Street address |
100 College Street Rm 1155
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| City |
New Haven |
| State/province |
Connecticut |
| ZIP/Postal code |
06510 |
| Country |
USA |
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| Platforms (1) |
| GPL11154 |
Illumina HiSeq 2000 (Homo sapiens) |
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| Samples (44)
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| GSM2454165 |
57F,uninfected control,at 0 day after infection |
| GSM2454166 |
57F,uninfected control,at 1 day after infection |
| GSM2454167 |
57F,MAB at MOI of 100:1,at 1 day after infection |
| GSM2454168 |
57F,MAB at MOI of 1000:1,at 1 day after infection |
| GSM2454169 |
57F,MAC at MOI of 100:1,at 1 day after infection |
| GSM2454170 |
57F,MAC at MOI of 1000:1,at 1 day after infection |
| GSM2454171 |
57F,uninfected control,at 3 days after infection |
| GSM2454172 |
57F,MAB at MOI of 100:1,at 3 days after infection |
| GSM2454173 |
57F,MAB at MOI of 1000:1,at 3 days after infection |
| GSM2454174 |
57F,MAC at MOI of 100:1,at 3 days after infection |
| GSM2454175 |
57F,MAC at MOI of 1000:1,at 3 days after infection |
| GSM2454176 |
75M,uninfected control,at 0 day after infection |
| GSM2454177 |
75M,uninfected control,at 1 day after infection |
| GSM2454178 |
75M,MAB at MOI of 100:1,at 1 day after infection |
| GSM2454179 |
75M,MAB at MOI of 1000:1,at 1 day after infection |
| GSM2454180 |
75M,MAC at MOI of 100:1,at 1 day after infection |
| GSM2454181 |
75M,MAC at MOI of 1000:1,at 1 day after infection |
| GSM2454182 |
75M,uninfected control,at 3 days after infection |
| GSM2454183 |
75M,MAB at MOI of 100:1,at 3 days after infection |
| GSM2454184 |
75M,MAB at MOI of 1000:1,at 3 days after infection |
| GSM2454185 |
75M,MAC at MOI of 100:1,at 3 days after infection |
| GSM2454186 |
75M,MAC at MOI of 1000:1,at 3 days after infection |
| GSM2454187 |
69F,uninfected control,at 0 day after infection |
| GSM2454188 |
69F,uninfected control,at 1 day after infection |
| GSM2454189 |
69F,MAB at MOI of 100:1,at 1 day after infection |
| GSM2454190 |
69F,MAB at MOI of 1000:1,at 1 day after infection |
| GSM2454191 |
69F,MAC at MOI of 100:1,at 1 day after infection |
| GSM2454192 |
69F,MAC at MOI of 1000:1,at 1 day after infection |
| GSM2454193 |
69F,uninfected control,at 3 days after infection |
| GSM2454194 |
69F,MAB at MOI of 100:1,at 3 days after infection |
| GSM2454195 |
69F,MAB at MOI of 1000:1,at 3 days after infection |
| GSM2454196 |
69F,MAC at MOI of 100:1,at 3 days after infection |
| GSM2454197 |
69F,MAC at MOI of 1000:1,at 3 days after infection |
| GSM2454198 |
42F,uninfected control,at 0 day after infection |
| GSM2454199 |
42F,uninfected control,at 1 day after infection |
| GSM2454200 |
42F,MAB at MOI of 100:1,at 1 day after infection |
| GSM2454201 |
42F,MAB at MOI of 1000:1,at 1 day after infection |
| GSM2454202 |
42F,MAC at MOI of 100:1,at 1 day after infection |
| GSM2454203 |
42F,MAC at MOI of 1000:1,at 1 day after infection |
| GSM2454204 |
42F,uninfected control,at 3 days after infection |
| GSM2454205 |
42F,MAB at MOI of 100:1,at 3 days after infection |
| GSM2454206 |
42F,MAB at MOI of 1000:1,at 3 days after infection |
| GSM2454207 |
42F,MAC at MOI of 100:1,at 3 days after infection |
| GSM2454208 |
42F,MAC at MOI of 1000:1,at 3 days after infection |
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| Relations |
| BioProject |
PRJNA360991 |
| SRA |
SRP096589 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE93526_DESeq2results_D1_1000_MAB.csv.gz |
1.5 Mb |
(ftp)(http) |
CSV |
| GSE93526_DESeq2results_D1_1000_MAC.csv.gz |
1.4 Mb |
(ftp)(http) |
CSV |
| GSE93526_DESeq2results_D1_1000_MACvsMAB.csv.gz |
1.2 Mb |
(ftp)(http) |
CSV |
| GSE93526_DESeq2results_D1_100_MAB.csv.gz |
1.4 Mb |
(ftp)(http) |
CSV |
| GSE93526_DESeq2results_D1_100_MAC.csv.gz |
1.4 Mb |
(ftp)(http) |
CSV |
| GSE93526_DESeq2results_D3_1000_MAB.csv.gz |
1.4 Mb |
(ftp)(http) |
CSV |
| GSE93526_DESeq2results_D3_1000_MAC.csv.gz |
1.4 Mb |
(ftp)(http) |
CSV |
| GSE93526_DESeq2results_D3_1000_MACvsMAB.csv.gz |
1.1 Mb |
(ftp)(http) |
CSV |
| GSE93526_DESeq2results_D3_100_MAB.csv.gz |
1.5 Mb |
(ftp)(http) |
CSV |
| GSE93526_DESeq2results_D3_100_MAC.csv.gz |
1.4 Mb |
(ftp)(http) |
CSV |
| GSE93526_RAW.tar |
108.7 Mb |
(http)(custom) |
TAR (of TXT) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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