Integrated in vivo multiomics analysis identifies p21-activated kinase signaling as a driver of colitis

Lyons, Jesse; Brubaker, Douglas K.; Ghazi, Phaedra C.; Baldwin, Katherine; Edwards, Amanda; Boukhali, Myriam; Strasser, Samantha Dale; Suárez-López, Lucía; Lin, Yu‐Ju; Yajnik, Vijay; Kissil, Joseph L.; Haas, Wilhelm; Lauffenburger, Douglas A.; Haigis, Kevin M.

doi:10.1126/scisignal.aan3580

Cited by 35 publications

(41 citation statements)

References 53 publications

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“…For inference of kinase activity, we performed GSEA on phosphoproteomic data with custom gene sets constructed of kinases and their respective species-specific substrate sites, termed substrate site sets, assembled from data sets available from PhosphoSite (49). A preranked enrichment was conducted as described above, using scaled phosphopeptide data.…”

Section: Analysis Of Ms Datamentioning

confidence: 99%

Tissue-Specific Oncogenic Activity of KRASA146T

et al. 2019

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KRAS is the most frequently mutated oncogene. The incidence of specifi c KRAS alleles varies between cancers from different sites, but it is unclear whether allelic selection results from biological selection for specifi c mutant KRAS proteins. We used a crossdisciplinary approach to compare KRAS G12D , a common mutant form, and KRAS A146T , a mutant that occurs only in selected cancers. Biochemical and structural studies demonstrated that KRAS A146T exhibits a marked extension of switch 1 away from the protein body and nucleotide binding site, which activates KRAS by promoting a high rate of intrinsic and guanine nucleotide exchange factorinduced nucleotide exchange. Using mice genetically engineered to express either allele, we found that KRAS G12D and KRAS A146T exhibit distinct tissue-specifi c effects on homeostasis that mirror mutational frequencies in human cancers. These tissue-specifi c phenotypes result from allele-specifi c signaling properties, demonstrating that context-dependent variations in signaling downstream of different KRAS mutants drive the KRAS mutational pattern seen in cancer. SIGNIFICANCE: Although epidemiologic and clinical studies have suggested allele-specifi c behaviors for KRAS , experimental evidence for allele-specifi c biological properties is limited. We combined structural biology, mass spectrometry, and mouse modeling to demonstrate that the selection for specifi c KRAS mutants in human cancers from different tissues is due to their distinct signaling properties.

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Section: Analysis Of Ms Datamentioning

confidence: 99%

Tissue-Specific Oncogenic Activity of KRASA146T

et al. 2019

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“…Proteomic and phosphoproteomic data from a TCT mouse model were described and generated previously (MassIVE, accession no. MSV000081198) [25]. TNFΔARE tissue samples were collected and processed as in Lyons et al [25], however from the ileum rather than the colon.…”

Section: Collection Of Ms Datasetsmentioning

confidence: 99%

“…MSV000081198) [25]. TNFΔARE tissue samples were collected and processed as in Lyons et al [25], however from the ileum rather than the colon. Sample processing and MS measurements were performed as described in previous work [25].…”

Section: Collection Of Ms Datasetsmentioning

confidence: 99%

“…Targeted and global proteomic and phosphoproteomic data from a mouse model of colitis indicate that p21-activated kinase (PAK) and mechanistic target of rapamycin (mTOR) promote gastrointestinal inflammation [24,25]. Here, we have further developed a userfriendly GSEA-based approach to infer changes in kinase activity from global phosphoproteomic data.…”

Section: Introductionmentioning

confidence: 99%

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Substrate-based kinase activity inference identifies MK2 as driver of colitis

Strasser

Ghazi

Starchenko

et al. 2019

Integrative Biology

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Inflammatory bowel disease (IBD) is a chronic and debilitating disorder that has few treatment options due to a lack of comprehensive understanding of its molecular pathogenesis. We used multiplexed mass spectrometry to collect high-content information on protein phosphorylation in two different mouse models of IBD. Because the biological function of the vast majority of phosphorylation sites remains unknown, we developed Substrate-based Kinase Activity Inference (SKAI), a methodology to infer kinase activity from phosphoproteomic data. This approach draws upon prior knowledge of kinase-substrate interactions to construct custom lists of kinases and their respective substrate sites, termed kinase-substrate sets that employ prior knowledge across organisms. This expansion as much as triples the amount of prior knowledge available. We then used these sets within the Gene Set Enrichment Analysis framework to infer kinase activity based on increased or decreased phosphorylation of its substrates in a dataset. When applied to the phosphoproteomic datasets from the two mouse models, SKAI predicted largely non-overlapping kinase activation profiles. These results suggest that chronic inflammation may arise through activation of largely divergent signaling networks. However, the one kinase inferred to be activated in both mouse models was mitogen-activated protein kinase-activated protein kinase 2 (MAPKAPK2 or MK2), a serine/threonine kinase that functions downstream of p38 stress-activated mitogen-activated protein kinase. Treatment of mice with active colitis with ATI450, an orally bioavailable small molecule inhibitor of the MK2 pathway, reduced inflammatory signaling in the colon and alleviated the clinical and histological features of inflammation. These studies establish MK2 as a therapeutic target in IBD and identify ATI450 as a potential therapy for the disease.

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“…The available proteomic studies in CD have principally been serum-based and do not provide direct measurements of Infliximab resistance signaling from the site of disease (18)(19)(20). We have previously conducted high throughput proteomic measurements from two mouse models of IBD, the Adoptive T-cell Transfer (TCT) and Tumor Necrosis Factor Delta-ARE (TNF-ARE) models in inflamed and un-inflamed conditions (8,9). However, no therapeutic stimuli were studied in these mice, which potentially limits the applicability of these datasets for understanding Infliximab resistance in patients.…”

Section: Translatable Components Regression Predicts Proteomic Dysregmentioning

confidence: 99%

An Inter-Species Translation Model Implicates Integrin Signaling in Infliximab-Resistant Colonic Crohn’s Disease

Brubaker

Kumar

Vega

et al. 2019

Preprint

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One Sentence Summary: Brubaker et al. implicate dysregulated collagen-binding integrin signaling in resistance to anti-TNF therapy in Crohn's Disease by developing a mouse-proteomic to human-transcriptomic translation model and confirm the associated inter-cellular signaling network using single-cell RNA sequencing. AbstractAnti-TNF therapy resistance is a major clinical challenge in Crohn's Disease (CD), partly due to insufficient understanding of disease-site, protein-level mechanisms of CD and anti-TNF treatment resistance. Although some proteomics data from CD mouse models exists, data type and phenotype discrepancies contribute to confounding attempts to translate between preclinical animal models of disease and human clinical cohorts. To meet this important challenge, we develop and demonstrate here an approach called Translatable Components Regression (TransComp-R) to overcome inter-species and trans-omic discrepancies between CD mouse models and human subjects. TransComp-R combines CD mouse model proteomic data with patient pre-treatment transcriptomic data to identify molecular features discernable in the mouse data predictive of patient response to anti-TNF therapy. Interrogating the TransComp-R models predominantly revealed upregulated integrin pathway signaling via collagen-binding integrin ITGA1 in anti-TNF resistant colonic CD (cCD) patients. Toward validation, we performed single-cell RNA sequencing on biopsies from a cCD patient 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 is indeed expressed in colonic T-cell populations and that interactions between collagen-binding integrins on T-cells and colonic cell types expressing secreted collagens are associated with anti-TNF therapy resistance. Biologically, TransComp-R linked previously disparate observations about collagen and ITGA1 signaling to a potential therapeutic avenue for overcoming anti-TNF therapy resistance in cCD. Methodologically, TransComp-R provides a flexible, generalizable framework for addressing inter-species, interomic, and inter-phenotypic discrepancies between animal models and patients to deliver translationally relevant biological insights.

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Integrated in vivo multiomics analysis identifies p21-activated kinase signaling as a driver of colitis

Cited by 35 publications

References 53 publications

Tissue-Specific Oncogenic Activity of KRASA146T

Tissue-Specific Oncogenic Activity of KRASA146T

Substrate-based kinase activity inference identifies MK2 as driver of colitis

An Inter-Species Translation Model Implicates Integrin Signaling in Infliximab-Resistant Colonic Crohn’s Disease

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