Differentially expressed transcript isoforms associate with resistance to tuberculin skin test and interferon gamma release assay conversion.
<h4>Background</h4>A mechanistic understanding of uncommon immune outcomes such as resistance to infection has led to the development of novel therapies. Using gene level analytic methods, we previously found distinct monocyte transcriptional responses associated with resistance to Mycob...
Saved in:
| Main Authors: | , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2023-01-01
|
| Series: | PLoS ONE |
| Online Access: | https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0284498&type=printable |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1823856803184640000 |
|---|---|
| author | Jason D Simmons R Max Segnitz Kimberly A Dill-McFarland Catherine M Stein Glenna J Peterson Harriet Mayanja-Kizza W Henry Boom Thomas R Hawn |
| author_facet | Jason D Simmons R Max Segnitz Kimberly A Dill-McFarland Catherine M Stein Glenna J Peterson Harriet Mayanja-Kizza W Henry Boom Thomas R Hawn |
| author_sort | Jason D Simmons |
| collection | DOAJ |
| description | <h4>Background</h4>A mechanistic understanding of uncommon immune outcomes such as resistance to infection has led to the development of novel therapies. Using gene level analytic methods, we previously found distinct monocyte transcriptional responses associated with resistance to Mycobacterium tuberculosis (Mtb) infection defined as persistently negative tuberculin skin test (TST) and interferon gamma release assay (IGRA) reactivity among highly exposed contacts (RSTR phenotype).<h4>Objective</h4>Using transcript isoform analyses, we aimed to identify novel RSTR-associated genes hypothesizing that previous gene-level differential expression analysis obscures isoform-specific differences that contribute to phenotype.<h4>Materials and methods</h4>Monocytes from 49 RSTR versus 52 subjects with latent Mtb infection (LTBI) were infected with M. tuberculosis (H37Rv) or left unstimulated (media) prior to RNA isolation and sequencing. RSTR-associated gene expression was then identified using differential transcript isoform analysis.<h4>Results</h4>We identified 81 differentially expressed transcripts (DETs) in 70 genes (FDR <0.05) comparing RSTR and LTBI phenotypes with the majority (n = 79 DETs) identified under Mtb-stimulated conditions. Seventeen of these genes were previously identified with gene-level bulk RNAseq analyses including genes in the IFNγ response that had increased expression among LTBI subjects, findings consistent with a clinical phenotype based on IGRA reactivity. Among the subset of 23 genes with positive differential expression among Mtb-infected RSTR monocytes, 13 were not previously identified. These novel DET genes included PDE4A and ZEB2, which each had multiple DETs with higher expression among RSTR subjects, and ACSL4 and GAPDH that each had a single transcript isoform associated with RSTR.<h4>Conclusion and limitations</h4>Transcript isoform-specific analyses identify transcriptional associations, such as those associated with resistance to TST/IGRA conversion, that are obscured when using gene-level approaches. These findings should be validated with additional RSTR cohorts and whether the newly identified candidate resistance genes directly influence the monocyte Mtb response requires functional study. |
| format | Article |
| id | doaj-art-18e905409be14fb8b0a6884e0c8d5dbf |
| institution | Kabale University |
| issn | 1932-6203 |
| language | English |
| publishDate | 2023-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj-art-18e905409be14fb8b0a6884e0c8d5dbf2025-02-12T05:31:02ZengPublic Library of Science (PLoS)PLoS ONE1932-62032023-01-01184e028449810.1371/journal.pone.0284498Differentially expressed transcript isoforms associate with resistance to tuberculin skin test and interferon gamma release assay conversion.Jason D SimmonsR Max SegnitzKimberly A Dill-McFarlandCatherine M SteinGlenna J PetersonHarriet Mayanja-KizzaW Henry BoomThomas R Hawn<h4>Background</h4>A mechanistic understanding of uncommon immune outcomes such as resistance to infection has led to the development of novel therapies. Using gene level analytic methods, we previously found distinct monocyte transcriptional responses associated with resistance to Mycobacterium tuberculosis (Mtb) infection defined as persistently negative tuberculin skin test (TST) and interferon gamma release assay (IGRA) reactivity among highly exposed contacts (RSTR phenotype).<h4>Objective</h4>Using transcript isoform analyses, we aimed to identify novel RSTR-associated genes hypothesizing that previous gene-level differential expression analysis obscures isoform-specific differences that contribute to phenotype.<h4>Materials and methods</h4>Monocytes from 49 RSTR versus 52 subjects with latent Mtb infection (LTBI) were infected with M. tuberculosis (H37Rv) or left unstimulated (media) prior to RNA isolation and sequencing. RSTR-associated gene expression was then identified using differential transcript isoform analysis.<h4>Results</h4>We identified 81 differentially expressed transcripts (DETs) in 70 genes (FDR <0.05) comparing RSTR and LTBI phenotypes with the majority (n = 79 DETs) identified under Mtb-stimulated conditions. Seventeen of these genes were previously identified with gene-level bulk RNAseq analyses including genes in the IFNγ response that had increased expression among LTBI subjects, findings consistent with a clinical phenotype based on IGRA reactivity. Among the subset of 23 genes with positive differential expression among Mtb-infected RSTR monocytes, 13 were not previously identified. These novel DET genes included PDE4A and ZEB2, which each had multiple DETs with higher expression among RSTR subjects, and ACSL4 and GAPDH that each had a single transcript isoform associated with RSTR.<h4>Conclusion and limitations</h4>Transcript isoform-specific analyses identify transcriptional associations, such as those associated with resistance to TST/IGRA conversion, that are obscured when using gene-level approaches. These findings should be validated with additional RSTR cohorts and whether the newly identified candidate resistance genes directly influence the monocyte Mtb response requires functional study.https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0284498&type=printable |
| spellingShingle | Jason D Simmons R Max Segnitz Kimberly A Dill-McFarland Catherine M Stein Glenna J Peterson Harriet Mayanja-Kizza W Henry Boom Thomas R Hawn Differentially expressed transcript isoforms associate with resistance to tuberculin skin test and interferon gamma release assay conversion. PLoS ONE |
| title | Differentially expressed transcript isoforms associate with resistance to tuberculin skin test and interferon gamma release assay conversion. |
| title_full | Differentially expressed transcript isoforms associate with resistance to tuberculin skin test and interferon gamma release assay conversion. |
| title_fullStr | Differentially expressed transcript isoforms associate with resistance to tuberculin skin test and interferon gamma release assay conversion. |
| title_full_unstemmed | Differentially expressed transcript isoforms associate with resistance to tuberculin skin test and interferon gamma release assay conversion. |
| title_short | Differentially expressed transcript isoforms associate with resistance to tuberculin skin test and interferon gamma release assay conversion. |
| title_sort | differentially expressed transcript isoforms associate with resistance to tuberculin skin test and interferon gamma release assay conversion |
| url | https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0284498&type=printable |
| work_keys_str_mv | AT jasondsimmons differentiallyexpressedtranscriptisoformsassociatewithresistancetotuberculinskintestandinterferongammareleaseassayconversion AT rmaxsegnitz differentiallyexpressedtranscriptisoformsassociatewithresistancetotuberculinskintestandinterferongammareleaseassayconversion AT kimberlyadillmcfarland differentiallyexpressedtranscriptisoformsassociatewithresistancetotuberculinskintestandinterferongammareleaseassayconversion AT catherinemstein differentiallyexpressedtranscriptisoformsassociatewithresistancetotuberculinskintestandinterferongammareleaseassayconversion AT glennajpeterson differentiallyexpressedtranscriptisoformsassociatewithresistancetotuberculinskintestandinterferongammareleaseassayconversion AT harrietmayanjakizza differentiallyexpressedtranscriptisoformsassociatewithresistancetotuberculinskintestandinterferongammareleaseassayconversion AT whenryboom differentiallyexpressedtranscriptisoformsassociatewithresistancetotuberculinskintestandinterferongammareleaseassayconversion AT thomasrhawn differentiallyexpressedtranscriptisoformsassociatewithresistancetotuberculinskintestandinterferongammareleaseassayconversion |