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Ran R, Muñoz Briones J, Jena S, Anderson NL, Olson MR, Green LN, Brubaker DK. Detailed survey of an in vitro intestinal epithelium model by single-cell transcriptomics. iScience 2024; 27:109383. [PMID: 38523788 PMCID: PMC10959667 DOI: 10.1016/j.isci.2024.109383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 12/01/2023] [Accepted: 02/27/2024] [Indexed: 03/26/2024] Open
Abstract
The co-culture of two adult human colorectal cancer cell lines, Caco-2 and HT29, on Transwell is commonly used as an in vitro gut mimic, yet the translatability of insights from such a system to adult human physiological contexts is not fully characterized. Here, we used single-cell RNA sequencing on the co-culture to obtain a detailed survey of cell type heterogeneity in the system and conducted a holistic comparison with human physiology. We identified the intestinal stem cell-, transit amplifying-, enterocyte-, goblet cell-, and enteroendocrine-like cells in the system. In general, the co-culture was fetal intestine-like, with less variety of gene expression compared to the adult human gut. Transporters for major types of nutrients were found in the majority of the enterocytes-like cells in the system. TLR 4 was not expressed in the sample, indicating that the co-culture model is incapable of mimicking the innate immune aspect of the human epithelium.
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Affiliation(s)
- Ran Ran
- Center for Global Health and Diseases, Department of Pathology, Case Western Reserve University, Cleveland, OH, USA
| | - Javier Muñoz Briones
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA
- Purdue Interdisciplinary Life Science Program, West Lafayette, IN, USA
| | - Smrutiti Jena
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA
| | - Nicole L. Anderson
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Matthew R. Olson
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Leopold N. Green
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA
| | - Douglas K. Brubaker
- Center for Global Health and Diseases, Department of Pathology, Case Western Reserve University, Cleveland, OH, USA
- The Blood, Heart, Lung, and Immunology Research Center, Case Western Reserve University, University Hospitals of Cleveland, Cleveland, OH, USA
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2
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Ball BK, Kuhn MK, Fleeman RM, Proctor EA, Brubaker DK. Differential responses of primary neuron-secreted MCP-1 and IL-9 to type 2 diabetes and Alzheimer's disease-associated metabolites. bioRxiv 2023:2023.11.17.567595. [PMID: 38014333 PMCID: PMC10680853 DOI: 10.1101/2023.11.17.567595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Type 2 diabetes (T2D) is implicated as a risk factor for Alzheimer's disease (AD), the most common form of dementia. In this work, we investigated neuroinflammatory responses of primary neurons to potentially circulating, blood-brain barrier (BBB) permeable metabolites associated with AD, T2D, or both. We identified nine metabolites associated with protective or detrimental properties of AD and T2D in literature (lauric acid, asparagine, fructose, arachidonic acid, aminoadipic acid, sorbitol, retinol, tryptophan, niacinamide) and stimulated primary mouse neuron cultures with each metabolite before quantifying cytokine secretion via Luminex. We employed unsupervised clustering, inferential statistics, and partial least squares discriminant analysis to identify relationships between cytokine concentration and disease-associations of metabolites. We identified MCP-1, a cytokine associated with monocyte recruitment, as differentially abundant between neurons stimulated by metabolites associated with protective and detrimental properties of AD and T2D. We also identified IL-9, a cytokine that promotes mast cell growth, to be differentially associated with T2D. Indeed, cytokines, such as MCP-1 and IL-9, released from neurons in response to BBB-permeable metabolites associated with T2D may contribute to AD development by downstream effects of neuroinflammation.
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Affiliation(s)
- Brendan K. Ball
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA
| | - Madison K. Kuhn
- Department of Neurosurgery, Penn State College of Medicine, Hershey, PA, USA
- Department of Pharmacology, Penn State College of Medicine, Hershey, PA, USA
- Department of Biomedical Engineering, Penn State University, State College, PA, USA
- Center for Neural Engineering, Penn State University, State College, PA, USA
| | - Rebecca M. Fleeman
- Department of Neurosurgery, Penn State College of Medicine, Hershey, PA, USA
- Department of Pharmacology, Penn State College of Medicine, Hershey, PA, USA
| | - Elizabeth A. Proctor
- Department of Neurosurgery, Penn State College of Medicine, Hershey, PA, USA
- Department of Pharmacology, Penn State College of Medicine, Hershey, PA, USA
- Department of Biomedical Engineering, Penn State University, State College, PA, USA
- Center for Neural Engineering, Penn State University, State College, PA, USA
- Department of Engineering Science & Mechanics, Penn State University, State College, PA, USA
| | - Douglas K. Brubaker
- Center for Global Health & Diseases, Department of Pathology, School of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, USA
- Blood Heart Lung Immunology Research Center, University Hospitals, Cleveland, OH, USA
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3
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Ran R, Brubaker DK. Enhanced annotation of CD45RA to distinguish T cell subsets in single-cell RNA-seq via machine learning. Bioinform Adv 2023; 3:vbad159. [PMID: 38023329 PMCID: PMC10676521 DOI: 10.1093/bioadv/vbad159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Revised: 10/20/2023] [Accepted: 11/03/2023] [Indexed: 12/01/2023]
Abstract
Motivation T cell heterogeneity presents a challenge for accurate cell identification, understanding their inherent plasticity, and characterizing their critical role in adaptive immunity. Immunologists have traditionally employed techniques such as flow cytometry to identify T cell subtypes based on a well-established set of surface protein markers. With the advent of single-cell RNA sequencing (scRNA-seq), researchers can now investigate the gene expression profiles of these surface proteins at the single-cell level. The insights gleaned from these profiles offer valuable clues and a deeper understanding of cell identity. However, CD45RA, the isoform of CD45 which distinguishes between naive/central memory T cells and effector memory/effector memory cells re-expressing CD45RA T cells, cannot be well profiled by scRNA-seq due to the difficulty in mapping short reads to genes. Results In order to facilitate cell-type annotation in T cell scRNA-seq analysis, we employed machine learning and trained a CD 45 RA + / - classifier on single-cell mRNA count data annotated with known CD45RA antibody levels provided by cellular indexing of transcriptomes and epitopes sequencing data. Among all the algorithms we tested, the trained support vector machine with a radial basis function kernel with optimized hyperparameters achieved a 99.96% accuracy on an unseen dataset. The multilayer perceptron classifier, the second most predictive method overall, also achieved a decent accuracy of 99.74%. Our simple yet robust machine learning approach provides a valid inference on the CD45RA level, assisting the cell identity annotation and further exploring the heterogeneity within human T cells. Based on the overall performance, we chose the support vector machine with a radial basis function kernel as the model implemented in our Python package scCD45RA. Availability and implementation The resultant package scCD45RA can be found at https://github.com/BrubakerLab/ScCD45RA and can be installed from the Python Package Index (PyPI) using the command "pip install sccd45ra."
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Affiliation(s)
- Ran Ran
- Department of Pathology, Center for Global Health and Diseases, Case Western Reserve University School of Medicine, Cleveland, OH 44106, United States
| | - Douglas K Brubaker
- Department of Pathology, Center for Global Health and Diseases, Case Western Reserve University School of Medicine, Cleveland, OH 44106, United States
- The Blood, Heart, Lung, and Immunology Research Center, Case Western Reserve University, University Hospitals of Cleveland, Cleveland, OH 44106, United States
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4
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Berard AR, Brubaker DK, Birse K, Lamont A, Mackelprang RD, Noël-Romas L, Perner M, Hou X, Irungu E, Mugo N, Knodel S, Muwonge TR, Katabira E, Hughes SM, Levy C, Calienes FL, Lauffenburger DA, Baeten JM, Celum C, Hladik F, Lingappa J, Burgener AD. Vaginal epithelial dysfunction is mediated by the microbiome, metabolome, and mTOR signaling. Cell Rep 2023; 42:112474. [PMID: 37149863 DOI: 10.1016/j.celrep.2023.112474] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 03/15/2023] [Accepted: 04/19/2023] [Indexed: 05/09/2023] Open
Abstract
Bacterial vaginosis (BV) is characterized by depletion of Lactobacillus and overgrowth of anaerobic and facultative bacteria, leading to increased mucosal inflammation, epithelial disruption, and poor reproductive health outcomes. However, the molecular mediators contributing to vaginal epithelial dysfunction are poorly understood. Here we utilize proteomic, transcriptomic, and metabolomic analyses to characterize biological features underlying BV in 405 African women and explore functional mechanisms in vitro. We identify five major vaginal microbiome groups: L. crispatus (21%), L. iners (18%), Lactobacillus (9%), Gardnerella (30%), and polymicrobial (22%). Using multi-omics we show that BV-associated epithelial disruption and mucosal inflammation link to the mammalian target of rapamycin (mTOR) pathway and associate with Gardnerella, M. mulieris, and specific metabolites including imidazole propionate. Experiments in vitro confirm that type strain G. vaginalis and M. mulieris supernatants and imidazole propionate directly affect epithelial barrier function and activation of mTOR pathways. These results find that the microbiome-mTOR axis is a central feature of epithelial dysfunction in BV.
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Affiliation(s)
- Alicia R Berard
- Department of Obstetrics & Gynecology, University of Manitoba, Winnipeg, MB R3E 3P5, Canada; Center for Global Health and Diseases, Department of Pathology, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Douglas K Brubaker
- Weldon School of Biomedical Engineering and Regenstrief Center for Healthcare Engineering, Purdue University, West Lafayette, IN 47907, USA
| | - Kenzie Birse
- Department of Obstetrics & Gynecology, University of Manitoba, Winnipeg, MB R3E 3P5, Canada; Center for Global Health and Diseases, Department of Pathology, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Alana Lamont
- Department of Obstetrics & Gynecology, University of Manitoba, Winnipeg, MB R3E 3P5, Canada
| | - Romel D Mackelprang
- Department of Global Health, University of Washington, Seattle, WA 98105, USA
| | - Laura Noël-Romas
- Department of Obstetrics & Gynecology, University of Manitoba, Winnipeg, MB R3E 3P5, Canada; Center for Global Health and Diseases, Department of Pathology, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Michelle Perner
- Medical Microbiology and Infectious Disease University of Manitoba, Winnipeg, MB R3E 0J9, Canada
| | - Xuanlin Hou
- Department of Global Health, University of Washington, Seattle, WA 98105, USA
| | - Elizabeth Irungu
- Partners in Health Research and Development, Kenya Medical Research Institute, Mbagathi Road, Nairobi, Kenya
| | - Nelly Mugo
- Department of Global Health, University of Washington, Seattle, WA 98105, USA; Partners in Health Research and Development, Kenya Medical Research Institute, Mbagathi Road, Nairobi, Kenya
| | - Samantha Knodel
- Department of Obstetrics & Gynecology, University of Manitoba, Winnipeg, MB R3E 3P5, Canada; Center for Global Health and Diseases, Department of Pathology, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Timothy R Muwonge
- Infectious Disease Institute, Makerere University, Makerere, Kampala, Uganda
| | - Elly Katabira
- Infectious Disease Institute, Makerere University, Makerere, Kampala, Uganda
| | - Sean M Hughes
- Department of Obstetrics and Gynecology, University of Washington, Seattle, WA 98195, USA
| | - Claire Levy
- Department of Obstetrics and Gynecology, University of Washington, Seattle, WA 98195, USA
| | | | | | - Jared M Baeten
- Department of Global Health, University of Washington, Seattle, WA 98105, USA; Department of Medicine, University of Washington, Seattle, WA 98195, USA; Department of Epidemiology, University of Washington, Seattle, WA 98195, USA; Gilead Sciences, Foster City, CA 94404, USA
| | - Connie Celum
- Department of Global Health, University of Washington, Seattle, WA 98105, USA; Department of Medicine, University of Washington, Seattle, WA 98195, USA; Department of Epidemiology, University of Washington, Seattle, WA 98195, USA
| | - Florian Hladik
- Department of Obstetrics and Gynecology, University of Washington, Seattle, WA 98195, USA; Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Jairam Lingappa
- Department of Global Health, University of Washington, Seattle, WA 98105, USA; Department of Medicine, University of Washington, Seattle, WA 98195, USA; Department of Pediatrics, University of Washington, Seattle, WA 98195, USA
| | - Adam D Burgener
- Department of Obstetrics & Gynecology, University of Manitoba, Winnipeg, MB R3E 3P5, Canada; Center for Global Health and Diseases, Department of Pathology, Case Western Reserve University, Cleveland, OH 44106, USA; Department of Medicine Solna, Karolinska Institutet, Framstegsgatan, 171 64 Solna, Sweden.
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5
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Pendyala M, Woods PS, Brubaker DK, Blaber EA, Schmidt TA, Chan DD. Endogenous production of hyaluronan, PRG4, and cytokines is sensitive to cyclic loading in synoviocytes. PLoS One 2022; 17:e0267921. [PMID: 36576921 PMCID: PMC9797074 DOI: 10.1371/journal.pone.0267921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 12/09/2022] [Indexed: 12/29/2022] Open
Abstract
Synovial fluid is composed of hyaluronan and proteoglycan-4 (PRG4 or lubricin), which work synergistically to maintain joint lubrication. In diseases like osteoarthritis, hyaluronan and PRG4 concentrations can be altered, resulting in lowered synovial fluid viscosity, and pro-inflammatory cytokine concentrations within the synovial fluid increase. Synovial fibroblasts within the synovium are responsible for contributing to synovial fluid and can be targeted to improve endogenous production of hyaluronan and PRG4 and to alter the cytokine profile. We cyclically loaded SW982 synoviocytes to 0%, 5%, 10%, or 20% strain for three hours at 1 Hz. To assess the impact of substrate stiffness, we compared the 0% strain group to cells grown on tissue culture plastic. We measured the expression of hyaluronan turnover genes, hyaluronan localization within the cell layer, hyaluronan concentration, PRG4 concentration, and the cytokine profile within the media. Our results show that the addition of cyclic loading increased HAS3 expression, but not in a magnitude-dependent response. Hyaluronidase expression was impacted by strain magnitude, which is exemplified by the decrease in hyaluronan concentration due to cyclic loading. We also show that PRG4 concentration is increased at 5% strain, while higher strain magnitude decreases overall PRG4 concentration. Finally, 10% and 20% strain show a distinct, more pro-inflammatory cytokine profile when compared to the unloaded group. Multivariate analysis showed distinct separation between certain strain groups in being able to predict strain group, hyaluronan concentration, and PRG4 concentration from gene expression or cytokine concentration data, highlighting the complexity of the system. Overall, this study shows that cyclic loading can be used tool to modulate the endogenous production of hyaluronan, PRG4, and cytokines from synovial fibroblasts.
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Affiliation(s)
- Meghana Pendyala
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, Troy, New York, United States of America
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York, United States of America
| | - Paige S Woods
- Department of Biomedical Engineering, University of Connecticut Health Center, Farmington, Connecticut, United States of America
| | - Douglas K Brubaker
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, Indiana, United States of America
- Regenstrief Center for Healthcare Engineering, Purdue University, West Lafayette, Indiana, United States of America
| | - Elizabeth A Blaber
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, Troy, New York, United States of America
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York, United States of America
- Blue Marble Space Institute of Science at NASA Ames Research Center, Moffett Field, California, United States of America
| | - Tannin A Schmidt
- Department of Biomedical Engineering, University of Connecticut Health Center, Farmington, Connecticut, United States of America
| | - Deva D Chan
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, Troy, New York, United States of America
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York, United States of America
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, Indiana, United States of America
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6
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Suarez-Lopez L, Shui B, Brubaker DK, Hill M, Bergendorf A, Changelian PS, Laguna A, Starchenko A, Lauffenburger DA, Haigis KM. Cross-species transcriptomic signatures predict response to MK2 inhibition in mouse models of chronic inflammation. iScience 2021; 24:103406. [PMID: 34849469 PMCID: PMC8609096 DOI: 10.1016/j.isci.2021.103406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 06/28/2021] [Accepted: 11/03/2021] [Indexed: 11/30/2022] Open
Abstract
Inflammatory bowel diseases (IBDs) are genetically complex and exhibit significant inter-patient heterogeneity in disease presentation and therapeutic response. Here, we show that mouse models of IBD exhibit variable responses to inhibition of MK2, a pro-inflammatory serine/threonine kinase, and that MK2 inhibition suppresses inflammation by targeting inflammatory monocytes and neutrophils in murine models. Using a computational approach (TransComp-R) that allows for cross-species comparison of transcriptomic features, we identified an IBD patient subgroup that is predicted to respond to MK2 inhibition, and an independent preclinical model of chronic intestinal inflammation predicted to be non-responsive, which we validated experimentally. Thus, cross-species mouse-human translation approaches can help to identify patient subpopulations in which to deploy new therapies. MK2 kinase inhibition shows variable efficacy in different IBD mouse models TCT and TNFΔARE mice express distinct inflammatory and MK2-responsive genes “Response to MK2i” signature is enriched in monocytes and neutrophils Cross-species modeling identifies patient groups potentially responsive to MK2i
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Affiliation(s)
- Lucia Suarez-Lopez
- Department of Cancer Biology, Dana Farber Cancer Institute, Boston, MA 02215, USA
- Department of Medicine, Brigham & Women's Hospital and Harvard Medical School, Boston, MA 02215, USA
| | - Bing Shui
- Department of Cancer Biology, Dana Farber Cancer Institute, Boston, MA 02215, USA
- Department of Medicine, Brigham & Women's Hospital and Harvard Medical School, Boston, MA 02215, USA
| | - Douglas K. Brubaker
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN 47906, USA
- Regenstrief Center for Healthcare Engineering, Purdue University, West Lafayette, IN 47906, USA
| | - Marza Hill
- Department of Cancer Biology, Dana Farber Cancer Institute, Boston, MA 02215, USA
| | - Alexander Bergendorf
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN 47906, USA
| | - Paul S. Changelian
- Aclaris Therapeutics, Inc., 4320 Forest Park Avenue, St. Louis, MO 63108, USA
| | - Aisha Laguna
- Department of Cancer Biology, Dana Farber Cancer Institute, Boston, MA 02215, USA
| | - Alina Starchenko
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Douglas A. Lauffenburger
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Kevin M. Haigis
- Department of Cancer Biology, Dana Farber Cancer Institute, Boston, MA 02215, USA
- Department of Medicine, Brigham & Women's Hospital and Harvard Medical School, Boston, MA 02215, USA
- Corresponding author
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7
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Lee MJ, Wang C, Carroll MJ, Brubaker DK, Hyman BT, Lauffenburger DA. Computational Interspecies Translation Between Alzheimer's Disease Mouse Models and Human Subjects Identifies Innate Immune Complement, TYROBP, and TAM Receptor Agonist Signatures, Distinct From Influences of Aging. Front Neurosci 2021; 15:727784. [PMID: 34658769 PMCID: PMC8515135 DOI: 10.3389/fnins.2021.727784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Accepted: 09/03/2021] [Indexed: 11/30/2022] Open
Abstract
Mouse models are vital for preclinical research on Alzheimer’s disease (AD) pathobiology. Many traditional models are driven by autosomal dominant mutations identified from early onset AD genetics whereas late onset and sporadic forms of the disease are predominant among human patients. Alongside ongoing experimental efforts to improve fidelity of mouse model representation of late onset AD, a computational framework termed Translatable Components Regression (TransComp-R) offers a complementary approach to leverage human and mouse datasets concurrently to enhance translation capabilities. We employ TransComp-R to integratively analyze transcriptomic data from human postmortem and traditional amyloid mouse model hippocampi to identify pathway-level signatures present in human patient samples yet predictive of mouse model disease status. This method allows concomitant evaluation of datasets across different species beyond observational seeking of direct commonalities between the species. Additional linear modeling focuses on decoupling disease signatures from effects of aging. Our results elucidated mouse-to-human translatable signatures associated with disease: excitatory synapses, inflammatory cytokine signaling, and complement cascade- and TYROBP-based innate immune activity; these signatures all find validation in previous literature. Additionally, we identified agonists of the Tyro3 / Axl / MerTK (TAM) receptor family as significant contributors to the cross-species innate immune signature; the mechanistic roles of the TAM receptor family in AD merit further dedicated study. We have demonstrated that TransComp-R can enhance translational understanding of relationships between AD mouse model data and human data, thus aiding generation of biological hypotheses concerning AD progression and holding promise for improved preclinical evaluation of therapies.
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Affiliation(s)
- Meelim J Lee
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Chuangqi Wang
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Molly J Carroll
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Douglas K Brubaker
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, United States.,Regenstrief Center for Healthcare Engineering, Purdue University, West Lafayette, IN, United States
| | - Bradley T Hyman
- MassGeneral Institute for Neurodegenerative Disease, Massachusetts General Hospital, Boston, MA, United States
| | - Douglas A Lauffenburger
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
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8
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Brubaker DK, Kumar MP, Chiswick EL, Gregg C, Starchenko A, Vega PN, Southard-Smith AN, Simmons AJ, Scoville EA, Coburn LA, Wilson KT, Lau KS, Lauffenburger DA. An interspecies translation model implicates integrin signaling in infliximab-resistant inflammatory bowel disease. Sci Signal 2020; 13:13/643/eaay3258. [PMID: 32753478 DOI: 10.1126/scisignal.aay3258] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
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 α1 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.
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Affiliation(s)
- Douglas K Brubaker
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Department of Biomedical Engineering, Purdue University, West Lafayette, IN 47906, USA.,Regenstrief Center for Healthcare Engineering, Purdue University, West Lafayette, IN 47906, USA
| | - Manu P Kumar
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Evan L Chiswick
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Cecil Gregg
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Alina Starchenko
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Paige N Vega
- Epithelial Biology Center, Vanderbilt University School of Medicine, Nashville, TN 37232, USA.,Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Austin N Southard-Smith
- Epithelial Biology Center, Vanderbilt University School of Medicine, Nashville, TN 37232, USA.,Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Alan J Simmons
- Epithelial Biology Center, Vanderbilt University School of Medicine, Nashville, TN 37232, USA.,Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Elizabeth A Scoville
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA.,Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Lori A Coburn
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA.,Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center, Nashville, TN 37232, USA.,Veterans Affairs Tennessee Valley Healthcare System, Nashville, TN 37212, USA
| | - Keith T Wilson
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA.,Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center, Nashville, TN 37232, USA.,Veterans Affairs Tennessee Valley Healthcare System, Nashville, TN 37212, USA.,Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Ken S Lau
- Epithelial Biology Center, Vanderbilt University School of Medicine, Nashville, TN 37232, USA.,Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37232, USA.,Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Douglas A Lauffenburger
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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9
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Proctor EA, Dineen SM, Van Nostrand SC, Kuhn MK, Barrett CD, Brubaker DK, Yaffe MB, Lauffenburger DA, Leon LR. Coagulopathy signature precedes and predicts severity of end-organ heat stroke pathology in a mouse model. J Thromb Haemost 2020; 18:1900-1910. [PMID: 32367690 PMCID: PMC7496969 DOI: 10.1111/jth.14875] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 03/05/2020] [Accepted: 04/23/2020] [Indexed: 12/25/2022]
Abstract
BACKGROUND Immune challenge is known to increase heat stroke risk, although the mechanism of this increased risk is unclear. OBJECTIVES We sought to understand the effect of immune challenge on heat stroke pathology. PATIENTS/METHODS Using a mouse model of classic heat stroke, we examined the impact of prior viral or bacterial infection on hematological aspects of recovery. Mice were exposed to heat either 48 or 72 hours following polyinosinic:polycytidylic acid (poly I:C) or lipopolysaccharide injection, time points when symptoms of illness (fever, lethargy, anorexia) were minimized or completely absent. RESULTS Employing multivariate supervised machine learning to identify patterns of molecular and cellular markers associated with heat stroke, we found that prior viral infection simulated with poly I:C injection resulted in heat stroke presenting with high levels of factors indicating coagulopathy. Despite a decreased number of platelets in the blood, platelets are large and non-uniform in size, suggesting younger, more active platelets. Levels of D-dimer and soluble thrombomodulin were increased in more severe heat stroke, and in cases of the highest level of organ damage markers D-dimer levels dropped, indicating potential fibrinolysis-resistant thrombosis. Genes corresponding to immune response, coagulation, hypoxia, and vessel repair were up-regulated in kidneys of heat-challenged animals; these correlated with both viral treatment and distal organ damage while appearing before discernible tissue damage to the kidney itself. CONCLUSIONS Heat stroke-induced coagulopathy may be a driving mechanistic force in heat stroke pathology, especially when exacerbated by prior infection. Coagulation markers may serve as accessible biomarkers for heat stroke severity and therapeutic strategies.
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Affiliation(s)
- Elizabeth A. Proctor
- Department of Biological EngineeringMassachusetts Institute of TechnologyCambridgeMAUSA
- Departments of Neurosurgery and PharmacologyPenn State College of MedicineHersheyPAUSA
- Departments of Biomedical Engineering and Engineering Science & Mechanics and Center for Neural EngineeringPennsylvania State UniversityUniversity ParkPAUSA
| | - Shauna M. Dineen
- Thermal and Mountain Medicine DivisionUnited States Army Research Institute of Environmental MedicineNatickMAUSA
| | | | - Madison K. Kuhn
- Departments of Neurosurgery and PharmacologyPenn State College of MedicineHersheyPAUSA
- Departments of Biomedical Engineering and Engineering Science & Mechanics and Center for Neural EngineeringPennsylvania State UniversityUniversity ParkPAUSA
| | - Christopher D. Barrett
- Department of BiologyMassachusetts Institute of TechnologyCambridgeMAUSA
- Department of SurgeryBeth Israel Deaconess Medical Center and Harvard Medical SchoolBostonMAUSA
- Koch Institute for Integrative Cancer ResearchCambridgeMAUSA
| | - Douglas K. Brubaker
- Department of Biological EngineeringMassachusetts Institute of TechnologyCambridgeMAUSA
| | - Michael B. Yaffe
- Department of Biological EngineeringMassachusetts Institute of TechnologyCambridgeMAUSA
- Department of BiologyMassachusetts Institute of TechnologyCambridgeMAUSA
- Department of SurgeryBeth Israel Deaconess Medical Center and Harvard Medical SchoolBostonMAUSA
- Koch Institute for Integrative Cancer ResearchCambridgeMAUSA
| | - Douglas A. Lauffenburger
- Department of Biological EngineeringMassachusetts Institute of TechnologyCambridgeMAUSA
- Koch Institute for Integrative Cancer ResearchCambridgeMAUSA
| | - Lisa R. Leon
- Thermal and Mountain Medicine DivisionUnited States Army Research Institute of Environmental MedicineNatickMAUSA
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10
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Strasser SD, Ghazi PC, Starchenko A, Boukhali M, Edwards A, Suarez-Lopez L, Lyons J, Changelian PS, Monahan JB, Jacobsen J, Brubaker DK, Joughin BA, Yaffe MB, Haas W, Lauffenburger DA, Haigis KM. Substrate-based kinase activity inference identifies MK2 as driver of colitis. Integr Biol (Camb) 2020; 11:301-314. [PMID: 31617572 DOI: 10.1093/intbio/zyz025] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2019] [Revised: 07/19/2019] [Accepted: 07/28/2019] [Indexed: 12/30/2022]
Abstract
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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Affiliation(s)
- Samantha Dale Strasser
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA.,Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA.,Cancer Research Institute and Division of Genetics, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA 02215, USA.,Department of Medicine, Harvard Medical School, 25 Shattuck Street, Boston, MA 02115, USA
| | - Phaedra C Ghazi
- Cancer Research Institute and Division of Genetics, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA 02215, USA.,Department of Medicine, Harvard Medical School, 25 Shattuck Street, Boston, MA 02115, USA
| | - Alina Starchenko
- Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA.,Cancer Research Institute and Division of Genetics, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA 02215, USA.,Department of Medicine, Harvard Medical School, 25 Shattuck Street, Boston, MA 02115, USA
| | - Myriam Boukhali
- Department of Medicine, Harvard Medical School, 25 Shattuck Street, Boston, MA 02115, USA.,Center for Cancer Research, Massachusetts General Hospital, 55 Fruit Street, Boston, MA 02114, USA
| | - Amanda Edwards
- Department of Medicine, Harvard Medical School, 25 Shattuck Street, Boston, MA 02115, USA.,Center for Cancer Research, Massachusetts General Hospital, 55 Fruit Street, Boston, MA 02114, USA
| | - Lucia Suarez-Lopez
- Cancer Research Institute and Division of Genetics, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA 02215, USA.,Department of Medicine, Harvard Medical School, 25 Shattuck Street, Boston, MA 02115, USA.,David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Jesse Lyons
- Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA.,Cancer Research Institute and Division of Genetics, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA 02215, USA.,Department of Medicine, Harvard Medical School, 25 Shattuck Street, Boston, MA 02115, USA
| | - Paul S Changelian
- Aclaris Therapeutics, Inc., 4320 Forest Park Avenue, St. Louis, MO 63108, USA
| | - Joseph B Monahan
- Aclaris Therapeutics, Inc., 4320 Forest Park Avenue, St. Louis, MO 63108, USA
| | - Jon Jacobsen
- Aclaris Therapeutics, Inc., 4320 Forest Park Avenue, St. Louis, MO 63108, USA
| | - Douglas K Brubaker
- Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA.,Cancer Research Institute and Division of Genetics, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA 02215, USA.,Department of Medicine, Harvard Medical School, 25 Shattuck Street, Boston, MA 02115, USA
| | - Brian A Joughin
- Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA.,David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Michael B Yaffe
- Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA.,David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Wilhelm Haas
- Department of Medicine, Harvard Medical School, 25 Shattuck Street, Boston, MA 02115, USA.,Center for Cancer Research, Massachusetts General Hospital, 55 Fruit Street, Boston, MA 02114, USA
| | - Douglas A Lauffenburger
- Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA.,David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Kevin M Haigis
- Cancer Research Institute and Division of Genetics, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA 02215, USA.,Department of Medicine, Harvard Medical School, 25 Shattuck Street, Boston, MA 02115, USA.,Harvard Digestive Disease Center, Harvard Medical School, 320 Longwood Avenue, Boston, MA 02115, USA
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11
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Abstract
Computational models for cross-species translation could improve drug development
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Affiliation(s)
- Douglas K Brubaker
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Douglas A Lauffenburger
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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12
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Brubaker DK, Paulo JA, Sheth S, Poulin EJ, Popow O, Joughin BA, Strasser SD, Starchenko A, Gygi SP, Lauffenburger DA, Haigis KM. Proteogenomic Network Analysis of Context-Specific KRAS Signaling in Mouse-to-Human Cross-Species Translation. Cell Syst 2019; 9:258-270.e6. [PMID: 31521603 PMCID: PMC6816257 DOI: 10.1016/j.cels.2019.07.006] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2018] [Revised: 06/01/2019] [Accepted: 07/15/2019] [Indexed: 12/21/2022]
Abstract
The highest frequencies of KRAS mutations occur in colorectal carcinoma (CRC) and pancreatic ductal adenocarcinoma (PDAC). The ability to target downstream pathways mediating KRAS oncogenicity is limited by an incomplete understanding of the contextual cues modulating the signaling output of activated K-RAS. We performed mass spectrometry on mouse tissues expressing wild-type or mutant Kras to determine how tissue context and genetic background modulate oncogenic signaling. Mutant Kras dramatically altered the proteomes and phosphoproteomes of preneoplastic and neoplastic colons and pancreases in a context-specific manner. We developed an approach to statistically humanize the mouse networks with data from human cancer and identified genes within the humanized CRC and PDAC networks synthetically lethal with mutant KRAS. Our studies demonstrate the context-dependent plasticity of oncogenic signaling, identify non-canonical mediators of KRAS oncogenicity within the KRAS-regulated signaling network, and demonstrate how statistical integration of mouse and human datasets can reveal cross-species therapeutic insights.
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Affiliation(s)
- Douglas K Brubaker
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Cancer Research Institute, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Joao A Paulo
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Shikha Sheth
- Cancer Research Institute, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Emily J Poulin
- Cancer Research Institute, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Olesja Popow
- Cancer Research Institute, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Brian A Joughin
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Samantha Dale Strasser
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Cancer Research Institute, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Alina Starchenko
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Cancer Research Institute, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Douglas A Lauffenburger
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
| | - Kevin M Haigis
- Cancer Research Institute, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; Harvard Digestive Disease Center, Harvard Medical School, Boston, MA 02115, USA.
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13
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Poulin EJ, Bera AK, Lu J, Lin YJ, Strasser SD, Paulo JA, Huang TQ, Morales C, Yan W, Cook J, Nowak JA, Brubaker DK, Joughin BA, Johnson CW, DeStefanis RA, Ghazi PC, Gondi S, Wales TE, Iacob RE, Bogdanova L, Gierut JJ, Li Y, Engen JR, Perez-Mancera PA, Braun BS, Gygi SP, Lauffenburger DA, Westover KD, Haigis KM. Tissue-Specific Oncogenic Activity of KRAS A146T. Cancer Discov 2019; 9:738-755. [PMID: 30952657 PMCID: PMC6548671 DOI: 10.1158/2159-8290.cd-18-1220] [Citation(s) in RCA: 119] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 03/06/2019] [Accepted: 04/02/2019] [Indexed: 12/16/2022]
Abstract
KRAS is the most frequently mutated oncogene. The incidence of specific KRAS alleles varies between cancers from different sites, but it is unclear whether allelic selection results from biological selection for specific mutant KRAS proteins. We used a cross-disciplinary approach to compare KRASG12D, a common mutant form, and KRASA146T, a mutant that occurs only in selected cancers. Biochemical and structural studies demonstrated that KRASA146T 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 factor-induced nucleotide exchange. Using mice genetically engineered to express either allele, we found that KRASG12D and KRASA146T exhibit distinct tissue-specific effects on homeostasis that mirror mutational frequencies in human cancers. These tissue-specific phenotypes result from allele-specific 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-specific behaviors for KRAS, experimental evidence for allele-specific biological properties is limited. We combined structural biology, mass spectrometry, and mouse modeling to demonstrate that the selection for specific KRAS mutants in human cancers from different tissues is due to their distinct signaling properties.See related commentary by Hobbs and Der, p. 696.This article is highlighted in the In This Issue feature, p. 681.
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Affiliation(s)
- Emily J Poulin
- Cancer Research Institute, Beth Israel Deaconess Medical Center, Boston, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Asim K Bera
- Departments of Biochemistry and Radiation Oncology, The University of Texas Southwestern Medical Center at Dallas, Dallas, Texas
| | - Jia Lu
- Departments of Biochemistry and Radiation Oncology, The University of Texas Southwestern Medical Center at Dallas, Dallas, Texas
| | - Yi-Jang Lin
- Cancer Research Institute, Beth Israel Deaconess Medical Center, Boston, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Samantha Dale Strasser
- Cancer Research Institute, Beth Israel Deaconess Medical Center, Boston, Massachusetts
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Joao A Paulo
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts
| | - Tannie Q Huang
- Department of Pediatrics and Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California
| | - Carolina Morales
- Department of Pediatrics and Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California
| | - Wei Yan
- Departments of Biochemistry and Radiation Oncology, The University of Texas Southwestern Medical Center at Dallas, Dallas, Texas
| | - Joshua Cook
- Cancer Research Institute, Beth Israel Deaconess Medical Center, Boston, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Jonathan A Nowak
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts
| | - Douglas K Brubaker
- Cancer Research Institute, Beth Israel Deaconess Medical Center, Boston, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Brian A Joughin
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Christian W Johnson
- Cancer Research Institute, Beth Israel Deaconess Medical Center, Boston, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Rebecca A DeStefanis
- Cancer Research Institute, Beth Israel Deaconess Medical Center, Boston, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Phaedra C Ghazi
- Cancer Research Institute, Beth Israel Deaconess Medical Center, Boston, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Sudershan Gondi
- Departments of Biochemistry and Radiation Oncology, The University of Texas Southwestern Medical Center at Dallas, Dallas, Texas
| | - Thomas E Wales
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts
| | - Roxana E Iacob
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts
| | - Lana Bogdanova
- Department of Pediatrics and Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California
| | - Jessica J Gierut
- Cancer Research Institute, Beth Israel Deaconess Medical Center, Boston, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Yina Li
- Cancer Research Institute, Beth Israel Deaconess Medical Center, Boston, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - John R Engen
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts
| | - Pedro A Perez-Mancera
- Department of Molecular and Clinical Cancer Medicine, Institute of Translational Medicine, University of Liverpool, Liverpool, UK
| | - Benjamin S Braun
- Department of Pediatrics and Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts
| | - Douglas A Lauffenburger
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Kenneth D Westover
- Departments of Biochemistry and Radiation Oncology, The University of Texas Southwestern Medical Center at Dallas, Dallas, Texas.
| | - Kevin M Haigis
- Cancer Research Institute, Beth Israel Deaconess Medical Center, Boston, Massachusetts.
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
- Harvard Digestive Disease Center, Harvard Medical School, Boston, Massachusetts
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14
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Lyons J, Brubaker DK, Ghazi PC, Baldwin KR, Edwards A, Boukhali M, Strasser SD, Suarez-Lopez L, Lin YJ, Yajnik V, Kissil JL, Haas W, Lauffenburger DA, Haigis KM. Integrated in vivo multiomics analysis identifies p21-activated kinase signaling as a driver of colitis. Sci Signal 2018; 11:11/519/eaan3580. [PMID: 29487189 DOI: 10.1126/scisignal.aan3580] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Inflammatory bowel disease (IBD) is a chronic disorder of the gastrointestinal tract that has limited treatment options. To gain insight into the pathogenesis of chronic colonic inflammation (colitis), we performed a multiomics analysis that integrated RNA microarray, total protein mass spectrometry (MS), and phosphoprotein MS measurements from a mouse model of the disease. Because we collected all three types of data from individual samples, we tracked information flow from RNA to protein to phosphoprotein and identified signaling molecules that were coordinately or discordantly regulated and pathways that had complex regulation in vivo. For example, the genes encoding acute-phase proteins were expressed in the liver, but the proteins were detected by MS in the colon during inflammation. We also ascertained the types of data that best described particular facets of chronic inflammation. Using gene set enrichment analysis and trans-omics coexpression network analysis, we found that each data set provided a distinct viewpoint on the molecular pathogenesis of colitis. Combining human transcriptomic data with the mouse multiomics data implicated increased p21-activated kinase (Pak) signaling as a driver of colitis. Chemical inhibition of Pak1 and Pak2 with FRAX597 suppressed active colitis in mice. These studies provide translational insights into the mechanisms contributing to colitis and identify Pak as a potential therapeutic target in IBD.
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Affiliation(s)
- Jesse Lyons
- Cancer Research Institute and Department of Medicine, Beth-Israel Deaconess Medical Center, Boston, MA 02215, USA.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Douglas K Brubaker
- Cancer Research Institute and Department of Medicine, Beth-Israel Deaconess Medical Center, Boston, MA 02215, USA.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Phaedra C Ghazi
- Cancer Research Institute and Department of Medicine, Beth-Israel Deaconess Medical Center, Boston, MA 02215, USA
| | - Katherine R Baldwin
- Cancer Research Institute and Department of Medicine, Beth-Israel Deaconess Medical Center, Boston, MA 02215, USA.,Department of Pediatric Gastroenterology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Amanda Edwards
- Center for Cancer Research, Massachusetts General Hospital, Boston, MA 02114, USA.,Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Myriam Boukhali
- Center for Cancer Research, Massachusetts General Hospital, Boston, MA 02114, USA.,Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Samantha Dale Strasser
- Cancer Research Institute and Department of Medicine, Beth-Israel Deaconess Medical Center, Boston, MA 02215, USA.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Lucia Suarez-Lopez
- Cancer Research Institute and Department of Medicine, Beth-Israel Deaconess Medical Center, Boston, MA 02215, USA.,David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Yi-Jang Lin
- Cancer Research Institute and Department of Medicine, Beth-Israel Deaconess Medical Center, Boston, MA 02215, USA
| | - Vijay Yajnik
- Department of Medicine, Division of Gastroenterology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Joseph L Kissil
- Department of Cancer Biology, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Wilhelm Haas
- Center for Cancer Research, Massachusetts General Hospital, Boston, MA 02114, USA.,Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Douglas A Lauffenburger
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Kevin M Haigis
- Cancer Research Institute and Department of Medicine, Beth-Israel Deaconess Medical Center, Boston, MA 02215, USA. .,Department of Medicine, Harvard Medical School, Boston, MA 02115, USA.,Harvard Digestive Disease Center, Harvard Medical School, Boston, MA 02115, USA
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15
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Kuo K, Amini P, Brubaker DK, Tan H, Yi L, Mesiano S. 500: Differential phosphorylation of connexin-43 in human myometrium: a key regulator of labor progress. Am J Obstet Gynecol 2016. [DOI: 10.1016/j.ajog.2015.10.543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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