An interspecies translation model implicates integrin signaling in infliximab-resistant inflammatory bowel disease
© 2020 American Association for the Advancement of Science. All rights reserved. Anti-tumor necrosis factor (anti-TNF) therapy resistance is a major clinical challenge in inflammatory bowel disease (IBD), due, in part, to insufficient understanding of disease-site, protein-level mechanisms. Although...
| Main Authors: | , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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American Association for the Advancement of Science (AAAS)
2021
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| Online Access: | https://hdl.handle.net/1721.1/136133 |
| _version_ | 1811081836096389120 |
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| author | Brubaker, Douglas K Kumar, Manu P Chiswick, Evan L Gregg, Cecil Starchenko, Alina Vega, Paige N Southard-Smith, Austin N Simmons, Alan J Scoville, Elizabeth A Coburn, Lori A Wilson, Keith T Lau, Ken S Lauffenburger, Douglas A |
| author_facet | Brubaker, Douglas K Kumar, Manu P Chiswick, Evan L Gregg, Cecil Starchenko, Alina Vega, Paige N Southard-Smith, Austin N Simmons, Alan J Scoville, Elizabeth A Coburn, Lori A Wilson, Keith T Lau, Ken S Lauffenburger, Douglas A |
| author_sort | Brubaker, Douglas K |
| collection | MIT |
| description | © 2020 American Association for the Advancement of Science. All rights reserved. Anti-tumor necrosis factor (anti-TNF) therapy resistance is a major clinical challenge in inflammatory bowel disease (IBD), due, in part, to insufficient understanding of disease-site, protein-level mechanisms. Although proteomics data from IBD mouse models exist, data and phenotype discrepancies contribute to confounding translation from preclinical animal models of disease to clinical cohorts. We developed an approach called translatable components regression (TransComp-R) to overcome interspecies and trans-omic discrepancies between mouse models and human subjects. TransComp-R combines mouse proteomic data with patient pretreatment transcriptomic data to identify molecular features discernable in the mouse data that are predictive of patient response to therapy. Interrogating the TransComp-R models revealed activated integrin pathway signaling in patients with anti-TNF-resistant colonic Crohn's disease (cCD) and ulcerative colitis (UC). As a step toward validation, we performed single-cell RNA sequencing (scRNA-seq) on biopsies from a patient with cCD and analyzed publicly available immune cell proteomics data to characterize the immune and intestinal cell types contributing to anti-TNF resistance. We found that ITGA1 was expressed in T cells and that interactions between these cells and intestinal cell types were associated with resistance to anti-TNF therapy. We experimentally showed that the ?1 integrin subunit mediated the effectiveness of anti-TNF therapy in human immune cells. Thus, TransComp-R identified an integrin signaling mechanism with potential therapeutic implications for overcoming anti-TNF therapy resistance. We suggest that TransComp-R is a generalizable framework for addressing species, molecular, and phenotypic discrepancies between model systems and patients to translationally deliver relevant biological insights. |
| first_indexed | 2024-09-23T11:52:55Z |
| format | Article |
| id | mit-1721.1/136133 |
| institution | Massachusetts Institute of Technology |
| language | English |
| last_indexed | 2024-09-23T11:52:55Z |
| publishDate | 2021 |
| publisher | American Association for the Advancement of Science (AAAS) |
| record_format | dspace |
| spelling | mit-1721.1/1361332021-10-28T04:10:00Z An interspecies translation model implicates integrin signaling in infliximab-resistant inflammatory bowel disease Brubaker, Douglas K Kumar, Manu P Chiswick, Evan L Gregg, Cecil Starchenko, Alina Vega, Paige N Southard-Smith, Austin N Simmons, Alan J Scoville, Elizabeth A Coburn, Lori A Wilson, Keith T Lau, Ken S Lauffenburger, Douglas A © 2020 American Association for the Advancement of Science. All rights reserved. Anti-tumor necrosis factor (anti-TNF) therapy resistance is a major clinical challenge in inflammatory bowel disease (IBD), due, in part, to insufficient understanding of disease-site, protein-level mechanisms. Although proteomics data from IBD mouse models exist, data and phenotype discrepancies contribute to confounding translation from preclinical animal models of disease to clinical cohorts. We developed an approach called translatable components regression (TransComp-R) to overcome interspecies and trans-omic discrepancies between mouse models and human subjects. TransComp-R combines mouse proteomic data with patient pretreatment transcriptomic data to identify molecular features discernable in the mouse data that are predictive of patient response to therapy. Interrogating the TransComp-R models revealed activated integrin pathway signaling in patients with anti-TNF-resistant colonic Crohn's disease (cCD) and ulcerative colitis (UC). As a step toward validation, we performed single-cell RNA sequencing (scRNA-seq) on biopsies from a patient with cCD and analyzed publicly available immune cell proteomics data to characterize the immune and intestinal cell types contributing to anti-TNF resistance. We found that ITGA1 was expressed in T cells and that interactions between these cells and intestinal cell types were associated with resistance to anti-TNF therapy. We experimentally showed that the ?1 integrin subunit mediated the effectiveness of anti-TNF therapy in human immune cells. Thus, TransComp-R identified an integrin signaling mechanism with potential therapeutic implications for overcoming anti-TNF therapy resistance. We suggest that TransComp-R is a generalizable framework for addressing species, molecular, and phenotypic discrepancies between model systems and patients to translationally deliver relevant biological insights. 2021-10-27T20:30:58Z 2021-10-27T20:30:58Z 2020 2021-09-07T15:37:08Z Article http://purl.org/eprint/type/JournalArticle https://hdl.handle.net/1721.1/136133 en 10.1126/SCISIGNAL.AAY3258 Science Signaling Creative Commons Attribution-Noncommercial-Share Alike http://creativecommons.org/licenses/by-nc-sa/4.0/ application/pdf American Association for the Advancement of Science (AAAS) PMC |
| spellingShingle | Brubaker, Douglas K Kumar, Manu P Chiswick, Evan L Gregg, Cecil Starchenko, Alina Vega, Paige N Southard-Smith, Austin N Simmons, Alan J Scoville, Elizabeth A Coburn, Lori A Wilson, Keith T Lau, Ken S Lauffenburger, Douglas A An interspecies translation model implicates integrin signaling in infliximab-resistant inflammatory bowel disease |
| title | An interspecies translation model implicates integrin signaling in infliximab-resistant inflammatory bowel disease |
| title_full | An interspecies translation model implicates integrin signaling in infliximab-resistant inflammatory bowel disease |
| title_fullStr | An interspecies translation model implicates integrin signaling in infliximab-resistant inflammatory bowel disease |
| title_full_unstemmed | An interspecies translation model implicates integrin signaling in infliximab-resistant inflammatory bowel disease |
| title_short | An interspecies translation model implicates integrin signaling in infliximab-resistant inflammatory bowel disease |
| title_sort | interspecies translation model implicates integrin signaling in infliximab resistant inflammatory bowel disease |
| url | https://hdl.handle.net/1721.1/136133 |
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