1
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Deng R, Cui C, Remedios LW, Bao S, Womick RM, Chiron S, Li J, Roland JT, Lau KS, Liu Q, Wilson KT, Wang Y, Coburn LA, Landman BA, Huo Y. Cross-scale multi-instance learning for pathological image diagnosis. Med Image Anal 2024; 94:103124. [PMID: 38428271 PMCID: PMC11016375 DOI: 10.1016/j.media.2024.103124] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 02/16/2024] [Accepted: 02/26/2024] [Indexed: 03/03/2024]
Abstract
Analyzing high resolution whole slide images (WSIs) with regard to information across multiple scales poses a significant challenge in digital pathology. Multi-instance learning (MIL) is a common solution for working with high resolution images by classifying bags of objects (i.e. sets of smaller image patches). However, such processing is typically performed at a single scale (e.g., 20× magnification) of WSIs, disregarding the vital inter-scale information that is key to diagnoses by human pathologists. In this study, we propose a novel cross-scale MIL algorithm to explicitly aggregate inter-scale relationships into a single MIL network for pathological image diagnosis. The contribution of this paper is three-fold: (1) A novel cross-scale MIL (CS-MIL) algorithm that integrates the multi-scale information and the inter-scale relationships is proposed; (2) A toy dataset with scale-specific morphological features is created and released to examine and visualize differential cross-scale attention; (3) Superior performance on both in-house and public datasets is demonstrated by our simple cross-scale MIL strategy. The official implementation is publicly available at https://github.com/hrlblab/CS-MIL.
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Affiliation(s)
| | - Can Cui
- Vanderbilt University, Nashville, TN 37215, USA
| | | | | | - R Michael Womick
- The University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
| | - Sophie Chiron
- Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Jia Li
- Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Joseph T Roland
- Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Ken S Lau
- Vanderbilt University, Nashville, TN 37215, USA
| | - Qi Liu
- Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Keith T Wilson
- Vanderbilt University Medical Center, Nashville, TN 37232, USA; Veterans Affairs Tennessee Valley Healthcare System, Nashville, TN 37212, USA
| | - Yaohong Wang
- Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Lori A Coburn
- Vanderbilt University Medical Center, Nashville, TN 37232, USA; Veterans Affairs Tennessee Valley Healthcare System, Nashville, TN 37212, USA
| | - Bennett A Landman
- Vanderbilt University, Nashville, TN 37215, USA; Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Yuankai Huo
- Vanderbilt University, Nashville, TN 37215, USA.
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2
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Lunger C, Shen Z, Holcombe H, Mannion AJ, Dzink-Fox J, Kurnick S, Feng Y, Muthupalani S, Carrasco SE, Wilson KT, Peek RM, Piazuelo MB, Morgan DR, Armijo AL, Mammoliti M, Wang TC, Fox JG. Gastric coinfection with thiopeptide-positive Cutibacterium acnes decreases FOXM1 and pro-inflammatory biomarker expression in a murine model of Helicobacter pylori-induced gastric cancer. Microbiol Spectr 2024; 12:e0345023. [PMID: 38014984 PMCID: PMC10783005 DOI: 10.1128/spectrum.03450-23] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 10/19/2023] [Indexed: 11/29/2023] Open
Abstract
IMPORTANCE H. pylori infects half of the world population and is the leading cause of gastric cancer. We previously demonstrated that gastric cancer risk is associated with gastric microbiota. Specifically, gastric urease-positive Staphylococcus epidermidis and Streptococcus salivarius had contrasting effects on H. pylori-associated gastric pathology and immune responses in germ-free INS-GAS mice. As gastritis progresses to gastric cancer, the oncogenic transcription factor Foxm1 becomes increasingly expressed. In this study, we evaluated the gastric commensal C. acnes, certain strains of which produce thiopeptides that directly inhibit FOXM1. Thiopeptide-positive C. acnes was isolated from Nicaraguan patient gastric biopsies and inoculated into germ-free INS-GAS mice with H. pylori. We, therefore, asked whether coinfection with C. acnes expressing thiopeptide and H. pylori would decrease gastric Foxm1 expression and pro-inflammatory cytokine mRNA and protein levels. Our study supports the growing literature that specific non-H. pylori gastric bacteria affect inflammatory and cancer biomarkers in H. pylori pathogenesis.
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Affiliation(s)
- Courtney Lunger
- Division of Comparative Medicine, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Zeli Shen
- Division of Comparative Medicine, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Hilda Holcombe
- Division of Comparative Medicine, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Anthony J. Mannion
- Division of Comparative Medicine, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - JoAnn Dzink-Fox
- Division of Comparative Medicine, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Susanna Kurnick
- Division of Comparative Medicine, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Yan Feng
- Division of Comparative Medicine, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Sureshkumar Muthupalani
- Division of Comparative Medicine, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Sebastian E. Carrasco
- Division of Comparative Medicine, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Keith T. Wilson
- Division of Gastroenterology, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Richard M. Peek
- Division of Gastroenterology, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - M. Blanca Piazuelo
- Division of Gastroenterology, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Douglas R. Morgan
- Division of Gastroenterology and Hepatology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Amanda L. Armijo
- Division of Comparative Medicine, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Melissa Mammoliti
- Division of Comparative Medicine, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Timothy C. Wang
- Division of Gastroenterology and Irvine Cancer Research Center, Columbia University, New York, New York, USA
| | - James G. Fox
- Division of Comparative Medicine, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
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3
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Latour YL, McNamara KM, Allaman MM, Barry DP, Smith TM, Asim M, Williams KJ, Hawkins CV, Jacobse J, Goettel JA, Delgado AG, Piazuelo MB, Washington MK, Gobert AP, Wilson KT. Myeloid deletion of talin-1 reduces mucosal macrophages and protects mice from colonic inflammation. Sci Rep 2023; 13:22368. [PMID: 38102166 PMCID: PMC10724268 DOI: 10.1038/s41598-023-49614-z] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 12/10/2023] [Indexed: 12/17/2023] Open
Abstract
The intestinal immune response is crucial in maintaining a healthy gut, but the enhanced migration of macrophages in response to pathogens is a major contributor to disease pathogenesis. Integrins are ubiquitously expressed cellular receptors that are highly involved in immune cell adhesion to endothelial cells while in the circulation and help facilitate extravasation into tissues. Here we show that specific deletion of the Tln1 gene encoding the protein talin-1, an integrin-activating scaffold protein, from cells of the myeloid lineage using the Lyz2-cre driver mouse reduces epithelial damage, attenuates colitis, downregulates the expression of macrophage markers, decreases the number of differentiated colonic mucosal macrophages, and diminishes the presence of CD68-positive cells in the colonic mucosa of mice infected with the enteric pathogen Citrobacter rodentium. Bone marrow-derived macrophages lacking expression of Tln1 did not exhibit a cell-autonomous phenotype; there was no impaired proinflammatory gene expression, nitric oxide production, phagocytic ability, or surface expression of CD11b, CD86, or major histocompatibility complex II in response to C. rodentium. Thus, we demonstrate that talin-1 plays a role in the manifestation of infectious colitis by increasing mucosal macrophages, with an effect that is independent of macrophage activation.
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Affiliation(s)
- Yvonne L Latour
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, 2215B Garland Ave., 1030C MRB IV, Nashville, TN, 37232-0252, USA
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Kara M McNamara
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Program in Cancer Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Margaret M Allaman
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Daniel P Barry
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Thaddeus M Smith
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Mohammad Asim
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Kamery J Williams
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Caroline V Hawkins
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Justin Jacobse
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, 2215B Garland Ave., 1030C MRB IV, Nashville, TN, 37232-0252, USA
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jeremy A Goettel
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, 2215B Garland Ave., 1030C MRB IV, Nashville, TN, 37232-0252, USA
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Program in Cancer Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
- Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Alberto G Delgado
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - M Blanca Piazuelo
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center, Nashville, TN, USA
| | - M Kay Washington
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, 2215B Garland Ave., 1030C MRB IV, Nashville, TN, 37232-0252, USA
- Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Alain P Gobert
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Keith T Wilson
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, 2215B Garland Ave., 1030C MRB IV, Nashville, TN, 37232-0252, USA.
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA.
- Program in Cancer Biology, Vanderbilt University School of Medicine, Nashville, TN, USA.
- Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center, Nashville, TN, USA.
- Veterans Affairs Tennessee Valley Healthcare System, Nashville, TN, USA.
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4
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Hoek KL, McClanahan KG, Latour YL, Shealy N, Piazuelo MB, Vallance BA, Byndloss MX, Wilson KT, Olivares-Villagómez D. Turicibacterales protect mice from severe Citrobacter rodentium infection. Infect Immun 2023; 91:e0032223. [PMID: 37800916 PMCID: PMC10652940 DOI: 10.1128/iai.00322-23] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 08/21/2023] [Indexed: 10/07/2023] Open
Abstract
One of the major contributors to child mortality in the world is diarrheal diseases, with an estimated 800,000 deaths per year. Many pathogens are causative agents of these illnesses, including the enteropathogenic or enterohemorrhagic forms of Escherichia coli. These bacteria are characterized by their ability to cause attaching and effacing lesions in the gut mucosa. Although much has been learned about the pathogenicity of these organisms and the immune response against them, the role of the intestinal microbiota during these infections is not well characterized. Infection of mice with E. coli requires pre-treatment with antibiotics in most mouse models, which hinders the study of the microbiota in an undisturbed environment. Using Citrobacter rodentium as a murine model for attaching and effacing bacteria, we show that C57BL/6 mice deficient in granzyme B expression are highly susceptible to severe disease caused by C. rodentium infection. Although a previous publication from our group shows that granzyme B-deficient CD4+ T cells are partially responsible for this phenotype, in this report, we present data demonstrating that the microbiota, in particular members of the order Turicibacterales, have an important role in conferring resistance. Mice deficient in Turicibacter sanguinis have increased susceptibility to severe disease. However, when these mice are co-housed with resistant mice or colonized with T. sanguinis, susceptibility to severe infection is reduced. These results clearly suggest a critical role for this commensal in the protection against enteropathogens.
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Affiliation(s)
- Kristen L. Hoek
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Kathleen G. McClanahan
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Yvonne L. Latour
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Nicolas Shealy
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - M. Blanca Piazuelo
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Bruce A. Vallance
- Department of Pediatrics, BC Children’s Hospital, University of British Columbia, Vancouver, British Columbia, Canada
| | - Mariana X. Byndloss
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Vanderbilt Institute of Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Vanderbilt Microbiome Innovation Center, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Keith T. Wilson
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Veternas Affairs Tennessee Valley Healthcare System, Nashville, Tennessee, USA
| | - Danyvid Olivares-Villagómez
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Vanderbilt Institute of Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, Tennessee, USA
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5
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Modi N, Chen Y, Dong X, Hu X, Lau GW, Wilson KT, Peek RM, Chen LF. BRD4 Regulates Glycolysis-Dependent Nos2 Expression in Macrophages Upon H pylori Infection. Cell Mol Gastroenterol Hepatol 2023; 17:292-308.e1. [PMID: 37820788 PMCID: PMC10829522 DOI: 10.1016/j.jcmgh.2023.10.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 10/03/2023] [Accepted: 10/04/2023] [Indexed: 10/13/2023]
Abstract
BACKGROUND & AIMS Metabolic reprogramming is essential for the activation and functions of macrophages, including bacterial killing and cytokine production. Bromodomain-containing protein 4 (BRD4) has emerged as a critical regulator of innate immune response. However, the potential role of BRD4 in the metabolic reprogramming of macrophage activation upon Helicobacter pylori infection remains unclear. METHODS Bone marrow-derived macrophages (BMDMs) from wild-type (WT) and Brd4-myeloid deletion conditional knockout (Brd4-CKO) mice were infected with H pylori. RNA sequencing was performed to evaluate the differential gene expression between WT and Brd4-deficient BMDMs upon infection. An in vivo model of H pylori infection using WT and Brd4-CKO mice was used to confirm the role of BRD4 in innate immune response to infection. RESULTS Depletion of Brd4 in BMDMs showed impaired H pylori-induced glycolysis. In addition, H pylori-induced expression of glycolytic genes, including Slc2a1 and Hk2, was decreased in Brd4-deficient BMDMs. BRD4 was recruited to the promoters of Slc2a1 and Hk2 via hypoxia-inducible factor-1α, facilitating their expression. BRD4-mediated glycolysis stabilized H pylori-induced nitric oxide synthase (Nos2) messenger RNA to produce nitric oxide. The NO-mediated killing of H pylori decreased in Brd4-deficient BMDMs, which was rescued by pyruvate. Furthermore, Brd4-CKO mice infected with H pylori showed reduced gastric inflammation and increased H pylori colonization with reduced inducible NO synthase expression in gastric macrophages. CONCLUSIONS Our study identified BRD4 as a key regulator of hypoxia-inducible factor-1α-dependent glycolysis and macrophage activation. Furthermore, we show a novel regulatory role of BRD4 in innate immunity through glycolysis to stabilize Nos2 messenger RNA for NO production to eliminate H pylori infection.
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Affiliation(s)
- Nikita Modi
- Department of Biochemistry, College of Liberal Arts & Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Yanheng Chen
- Department of Biochemistry, College of Liberal Arts & Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Xingchen Dong
- Department of Biochemistry, College of Liberal Arts & Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Xiangming Hu
- Department of Biochemistry, College of Liberal Arts & Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Gee W Lau
- Department of Pathobiology, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Keith T Wilson
- Division of Gastroenterology, Hepatology, and Nutrition, Vanderbilt University Medical Center, Nashville, Tennessee; Veterans Affairs Tennessee Valley Healthcare System, Nashville, Tennessee
| | - Richard M Peek
- Division of Gastroenterology, Hepatology, and Nutrition, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Lin-Feng Chen
- Department of Biochemistry, College of Liberal Arts & Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois; Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois.
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6
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Li J, Simmons AJ, Chiron S, Ramirez-Solano MA, Tasneem N, Kaur H, Xu Y, Revetta F, Vega PN, Bao S, Cui C, Tyree RN, Raber LW, Conner AN, Beaulieu DB, Dalal RL, Horst SN, Pabla BS, Huo Y, Landman BA, Roland JT, Scoville EA, Schwartz DA, Washington MK, Shyr Y, Wilson KT, Coburn LA, Lau KS, Liu Q. A Specialized Epithelial Cell Type Regulating Mucosal Immunity and Driving Human Crohn's Disease. bioRxiv 2023:2023.09.30.560293. [PMID: 37873404 PMCID: PMC10592875 DOI: 10.1101/2023.09.30.560293] [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: 10/25/2023]
Abstract
Crohn's disease (CD) is a complex chronic inflammatory disorder that may affect any part of gastrointestinal tract with extra-intestinal manifestations and associated immune dysregulation. To characterize heterogeneity in CD, we profiled single-cell transcriptomics of 170 samples from 65 CD patients and 18 non-inflammatory bowel disease (IBD) controls in both the terminal ileum (TI) and ascending colon (AC). Analysis of 202,359 cells identified a novel epithelial cell type in both TI and AC, featuring high expression of LCN2, NOS2, and DUOX2, and thus is named LND. LND cells, confirmed by high-resolution in-situ RNA imaging, were rarely found in non-IBD controls, but expanded significantly in active CD. Compared to other epithelial cells, genes defining LND cells were enriched in antimicrobial response and immunoregulation. Moreover, multiplexed protein imaging demonstrated that LND cell abundance was associated with immune infiltration. Cross-talk between LND and immune cells was explored by ligand-receptor interactions and further evidenced by their spatial colocalization. LND cells showed significant enrichment of expression specificity of IBD/CD susceptibility genes, revealing its role in immunopathogenesis of CD. Investigating lineage relationships of epithelial cells detected two LND cell subpopulations with different origins and developmental potential, early and late LND. The ratio of the late to early LND cells was related to anti-TNF response. These findings emphasize the pathogenic role of the specialized LND cell type in both Crohn's ileitis and Crohn's colitis and identify novel biomarkers associated with disease activity and treatment response.
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Affiliation(s)
- Jia Li
- Center for Quantitative Sciences, Vanderbilt Univerity Medical Center, Nashville, TN, USA
- Department of Biostatistics, Vanderbilt Univerity Medical Center, Nashville, TN, USA
| | - Alan J. Simmons
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Sophie Chiron
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Marisol A. Ramirez-Solano
- Center for Quantitative Sciences, Vanderbilt Univerity Medical Center, Nashville, TN, USA
- Department of Biostatistics, Vanderbilt Univerity Medical Center, Nashville, TN, USA
| | - Naila Tasneem
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Harsimran Kaur
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, USA
- Program in Chemical and Physical Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Yanwen Xu
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Frank Revetta
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Paige N. Vega
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Shunxing Bao
- Department of Electrical and Computer Engineering, Vanderbilt University, Nashville, TN, USA
- Department of Computer Science, Vanderbilt University, Nashville, TN, USA
| | - Can Cui
- Department of Electrical and Computer Engineering, Vanderbilt University, Nashville, TN, USA
- Department of Computer Science, Vanderbilt University, Nashville, TN, USA
| | - Regina N. Tyree
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Larry W. Raber
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Anna N. Conner
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Dawn B. Beaulieu
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Robin L. Dalal
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Sara N. Horst
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Baldeep S. Pabla
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Yuankai Huo
- Department of Electrical and Computer Engineering, Vanderbilt University, Nashville, TN, USA
- Department of Computer Science, Vanderbilt University, Nashville, TN, USA
| | - Bennett A. Landman
- Department of Electrical and Computer Engineering, Vanderbilt University, Nashville, TN, USA
- Department of Computer Science, Vanderbilt University, Nashville, TN, USA
| | - Joseph T. Roland
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Surgery, Vanderbilt University Medical Center, Nashville TN, USA
| | - Elizabeth A. Scoville
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center; Nashville, TN, USA
| | - David A. Schwartz
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - M. Kay Washington
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
- Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center; Nashville, TN, USA
| | - Yu Shyr
- Center for Quantitative Sciences, Vanderbilt Univerity Medical Center, Nashville, TN, USA
- Department of Biostatistics, Vanderbilt Univerity Medical Center, Nashville, TN, USA
| | - Keith T. Wilson
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
- Veterans Affairs Tennessee Valley Healthcare System, Nashville, TN, USA
- Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center; Nashville, TN, USA
| | - Lori A. Coburn
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Veterans Affairs Tennessee Valley Healthcare System, Nashville, TN, USA
- Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center; Nashville, TN, USA
| | - Ken S. Lau
- Center for Quantitative Sciences, Vanderbilt Univerity Medical Center, Nashville, TN, USA
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
- Program in Chemical and Physical Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
- Department of Surgery, Vanderbilt University Medical Center, Nashville TN, USA
- Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center; Nashville, TN, USA
| | - Qi Liu
- Center for Quantitative Sciences, Vanderbilt Univerity Medical Center, Nashville, TN, USA
- Department of Biostatistics, Vanderbilt Univerity Medical Center, Nashville, TN, USA
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7
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Cui C, Wang Y, Bao S, Tang Y, Deng R, Remedios LW, Asad Z, Roland JT, Lau KS, Liu Q, Coburn LA, Wilson KT, Landman BA, Huo Y. Feasibility of Universal Anomaly Detection without Knowing the Abnormality in Medical Images. Med Image Learn Ltd Noisy Data (2023) 2023; 14307:82-92. [PMID: 38523773 PMCID: PMC10959499 DOI: 10.1007/978-3-031-44917-8_8] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/26/2024]
Abstract
Many anomaly detection approaches, especially deep learning methods, have been recently developed to identify abnormal image morphology by only employing normal images during training. Unfortunately, many prior anomaly detection methods were optimized for a specific "known" abnormality (e.g., brain tumor, bone fraction, cell types). Moreover, even though only the normal images were used in the training process, the abnormal images were often employed during the validation process (e.g., epoch selection, hyper-parameter tuning), which might leak the supposed "unknown" abnormality unintentionally. In this study, we investigated these two essential aspects regarding universal anomaly detection in medical images by (1) comparing various anomaly detection methods across four medical datasets, (2) investigating the inevitable but often neglected issues on how to unbiasedly select the optimal anomaly detection model during the validation phase using only normal images, and (3) proposing a simple decision-level ensemble method to leverage the advantage of different kinds of anomaly detection without knowing the abnormality. The results of our experiments indicate that none of the evaluated methods consistently achieved the best performance across all datasets. Our proposed method enhanced the robustness of performance in general (average AUC 0.956).
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Affiliation(s)
- Can Cui
- Vanderbilt University, Nashville TN 37235, USA
| | - Yaohong Wang
- Vanderbilt University Medical Center, Nashville TN 37215, USA
| | | | - Yucheng Tang
- NVIDIA Corporation, Santa Clara and Bethesda, USA
| | | | | | - Zuhayr Asad
- Vanderbilt University, Nashville TN 37235, USA
| | - Joseph T Roland
- Vanderbilt University Medical Center, Nashville TN 37215, USA
| | - Ken S Lau
- Vanderbilt University Medical Center, Nashville TN 37215, USA
| | - Qi Liu
- Vanderbilt University Medical Center, Nashville TN 37215, USA
| | - Lori A Coburn
- Vanderbilt University Medical Center, Nashville TN 37215, USA
| | - Keith T Wilson
- Vanderbilt University Medical Center, Nashville TN 37215, USA
| | | | - Yuankai Huo
- Vanderbilt University, Nashville TN 37235, USA
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8
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Zilbauer M, James KR, Kaur M, Pott S, Li Z, Burger A, Thiagarajah JR, Burclaff J, Jahnsen FL, Perrone F, Ross AD, Matteoli G, Stakenborg N, Sujino T, Moor A, Bartolome-Casado R, Bækkevold ES, Zhou R, Xie B, Lau KS, Din S, Magness ST, Yao Q, Beyaz S, Arends M, Denadai-Souza A, Coburn LA, Gaublomme JT, Baldock R, Papatheodorou I, Ordovas-Montanes J, Boeckxstaens G, Hupalowska A, Teichmann SA, Regev A, Xavier RJ, Simmons A, Snyder MP, Wilson KT. A Roadmap for the Human Gut Cell Atlas. Nat Rev Gastroenterol Hepatol 2023; 20:597-614. [PMID: 37258747 PMCID: PMC10527367 DOI: 10.1038/s41575-023-00784-1] [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] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/14/2023] [Indexed: 06/02/2023]
Abstract
The number of studies investigating the human gastrointestinal tract using various single-cell profiling methods has increased substantially in the past few years. Although this increase provides a unique opportunity for the generation of the first comprehensive Human Gut Cell Atlas (HGCA), there remains a range of major challenges ahead. Above all, the ultimate success will largely depend on a structured and coordinated approach that aligns global efforts undertaken by a large number of research groups. In this Roadmap, we discuss a comprehensive forward-thinking direction for the generation of the HGCA on behalf of the Gut Biological Network of the Human Cell Atlas. Based on the consensus opinion of experts from across the globe, we outline the main requirements for the first complete HGCA by summarizing existing data sets and highlighting anatomical regions and/or tissues with limited coverage. We provide recommendations for future studies and discuss key methodologies and the importance of integrating the healthy gut atlas with related diseases and gut organoids. Importantly, we critically overview the computational tools available and provide recommendations to overcome key challenges.
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Affiliation(s)
- Matthias Zilbauer
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK.
- University Department of Paediatrics, University of Cambridge, Cambridge, UK.
- Department of Paediatric Gastroenterology, Hepatology and Nutrition, Cambridge University Hospitals, Cambridge, UK.
| | - Kylie R James
- Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
- School of Biomedical Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Mandeep Kaur
- School of Molecular and Cell Biology, University of the Witwatersrand, Johannesburg, South Africa
| | - Sebastian Pott
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Zhixin Li
- Dana-Farber Cancer Institute, Boston, MA, USA
| | - Albert Burger
- Department of Computer Science, Heriot-watt University, Edinburgh, UK
| | - Jay R Thiagarajah
- Division of Gastroenterology, Hepatology and Nutrition, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Joseph Burclaff
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill and North Carolina State University', Chapel Hill, NC, USA
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Frode L Jahnsen
- Department of Pathology, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Francesca Perrone
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- University Department of Paediatrics, University of Cambridge, Cambridge, UK
| | - Alexander D Ross
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- University Department of Paediatrics, University of Cambridge, Cambridge, UK
- University Department of Medical Genetics, University of Cambridge, Cambridge, UK
| | - Gianluca Matteoli
- Translational Research Center for Gastrointestinal Disorders (TARGID), Department of Chronic Diseases, Metabolism and Ageing, KU Leuven, Leuven, Belgium
| | - Nathalie Stakenborg
- Translational Research Center for Gastrointestinal Disorders (TARGID), Department of Chronic Diseases, Metabolism and Ageing, KU Leuven, Leuven, Belgium
| | - Tomohisa Sujino
- Center for the Diagnostic and Therapeutic Endoscopy, School of Medicine, Keio University, Tokyo, Japan
| | - Andreas Moor
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Raquel Bartolome-Casado
- Department of Pathology, Oslo University Hospital and University of Oslo, Oslo, Norway
- Wellcome Sanger Institute, Hinxton, UK
| | - Espen S Bækkevold
- Department of Pathology, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Ran Zhou
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Bingqing Xie
- Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Ken S Lau
- Epithelial Biology Center and Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Shahida Din
- Edinburgh IBD Unit, Western General Hospital, NHS Lothian, Edinburgh, UK
| | - Scott T Magness
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill and North Carolina State University', Chapel Hill, NC, USA
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Qiuming Yao
- Department of Computer Science and Engineering, University of Nebraska Lincoln, Lincoln, NE, USA
| | - Semir Beyaz
- Cold Spring Harbour Laboratory, Cold Spring Harbour, New York, NY, USA
| | - Mark Arends
- Division of Pathology, Centre for Comparative Pathology, Cancer Research UK Edinburgh Centre, Institute of Cancer and Genetics, University of Edinburgh, Edinburgh, UK
| | - Alexandre Denadai-Souza
- Laboratory of Mucosal Biology, Department of Chronic Diseases, Metabolism and Ageing, KU Leuven, Leuven, Belgium
| | - Lori A Coburn
- Vanderbilt University Medical Center, Nashville, TN, USA
- Veterans Affairs Tennessee Valley Healthcare System, Nashville, TN, USA
| | | | | | - Irene Papatheodorou
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Wellcome Genome Campus, Hinxton, UK
| | - Jose Ordovas-Montanes
- Division of Gastroenterology, Hepatology and Nutrition, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Guy Boeckxstaens
- Translational Research Center for Gastrointestinal Disorders (TARGID), Department of Chronic Diseases, Metabolism and Ageing, KU Leuven, Leuven, Belgium
| | | | - Sarah A Teichmann
- Wellcome Sanger Institute, Hinxton, UK
- Theory of Condensed Matter Group, Cavendish Laboratory/Department of Physics, University of Cambridge, Cambridge, UK
| | - Aviv Regev
- Genentech, San Francisco, CA, USA
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Ramnik J Xavier
- Broad Institute and Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Alison Simmons
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | | | - Keith T Wilson
- Vanderbilt University Medical Center, Nashville, TN, USA
- Veterans Affairs Tennessee Valley Healthcare System, Nashville, TN, USA
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9
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Gobert AP, Smith TM, Latour YL, Asim M, Barry DP, Allaman MM, Williams KJ, McNamara KM, Delgado AG, Short SP, Mirmira RG, Rose KL, Schey KL, Zagol-Ikapitte I, Coleman JS, Boutaud O, Zhao S, Piazuelo MB, Washington MK, Coburn LA, Wilson KT. Hypusination Maintains Intestinal Homeostasis and Prevents Colitis and Carcinogenesis by Enhancing Aldehyde Detoxification. Gastroenterology 2023; 165:656-669.e8. [PMID: 37271289 PMCID: PMC10527201 DOI: 10.1053/j.gastro.2023.05.041] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 04/19/2023] [Accepted: 05/25/2023] [Indexed: 06/06/2023]
Abstract
BACKGROUND & AIMS The amino acid hypusine, synthesized from the polyamine spermidine by the enzyme deoxyhypusine synthase (DHPS), is essential for the activity of eukaryotic translation initiation factor 5A (EIF5A). The role of hypusinated EIF5A (EIF5AHyp) remains unknown in intestinal homeostasis. Our aim was to investigate EIF5AHyp in the gut epithelium in inflammation and carcinogenesis. METHODS We used human colon tissue messenger RNA samples and publicly available transcriptomic datasets, tissue microarrays, and patient-derived colon organoids. Mice with intestinal epithelial-specific deletion of Dhps were investigated at baseline and in models of colitis and colon carcinogenesis. RESULTS We found that patients with ulcerative colitis and Crohn's disease exhibit reduced colon levels of DHPS messenger RNA and DHPS protein and reduced levels of EIF5AHyp. Similarly, colonic organoids from colitis patients also show down-regulated DHPS expression. Mice with intestinal epithelial-specific deletion of Dhps develop spontaneous colon hyperplasia, epithelial proliferation, crypt distortion, and inflammation. Furthermore, these mice are highly susceptible to experimental colitis and show exacerbated colon tumorigenesis when treated with a carcinogen. Transcriptomic and proteomic analysis on colonic epithelial cells demonstrated that loss of hypusination induces multiple pathways related to cancer and immune response. Moreover, we found that hypusination enhances translation of numerous enzymes involved in aldehyde detoxification, including glutathione S-transferases and aldehyde dehydrogenases. Accordingly, hypusination-deficient mice exhibit increased levels of aldehyde adducts in the colon, and their treatment with a scavenger of electrophiles reduces colitis. CONCLUSIONS Hypusination in intestinal epithelial cells has a key role in the prevention of colitis and colorectal cancer, and enhancement of this pathway via supplementation of spermidine could have a therapeutic impact.
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Affiliation(s)
- Alain P Gobert
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee; Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center, Nashville, Tennessee; Program in Cancer Biology, Vanderbilt University Medical Center, Nashville, Tennessee.
| | - Thaddeus M Smith
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Yvonne L Latour
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee; Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Mohammad Asim
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Daniel P Barry
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Margaret M Allaman
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Kamery J Williams
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Kara M McNamara
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee; Program in Cancer Biology, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Alberto G Delgado
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Sarah P Short
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee; Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Raghavendra G Mirmira
- Kovler Diabetes Center, Department of Medicine, The University of Chicago, Chicago, Illinois
| | - Kristie L Rose
- Department of Biochemistry, Mass Spectrometry Research Center, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Kevin L Schey
- Department of Biochemistry, Mass Spectrometry Research Center, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Irene Zagol-Ikapitte
- Warren Center for Neuroscience Drug Discovery, Vanderbilt University, Nashville, Tennessee; Department of Pharmacology, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Jeremy S Coleman
- Warren Center for Neuroscience Drug Discovery, Vanderbilt University, Nashville, Tennessee; Department of Pharmacology, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Olivier Boutaud
- Warren Center for Neuroscience Drug Discovery, Vanderbilt University, Nashville, Tennessee; Department of Pharmacology, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Shilin Zhao
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - M Blanca Piazuelo
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee; Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center, Nashville, Tennessee
| | - M Kay Washington
- Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center, Nashville, Tennessee; Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Lori A Coburn
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee; Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center, Nashville, Tennessee; Program in Cancer Biology, Vanderbilt University Medical Center, Nashville, Tennessee; Veterans Affairs Tennessee Valley Healthcare System, Nashville, Tennessee
| | - Keith T Wilson
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee; Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center, Nashville, Tennessee; Program in Cancer Biology, Vanderbilt University Medical Center, Nashville, Tennessee; Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee; Veterans Affairs Tennessee Valley Healthcare System, Nashville, Tennessee.
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10
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Spears E, Stanley JE, Shou M, Yin L, Li X, Dai C, Bradley A, Sellick K, Poffenberger G, Coate KC, Shrestha S, Jenkins R, Sloop KW, Wilson KT, Attie AD, Keller MP, Chen W, Powers AC, Dean ED. Pancreatic islet α cell function and proliferation requires the arginine transporter SLC7A2. bioRxiv 2023:2023.08.10.552656. [PMID: 37645716 PMCID: PMC10461917 DOI: 10.1101/2023.08.10.552656] [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: 08/31/2023]
Abstract
Interrupting glucagon signaling decreases gluconeogenesis and the fractional extraction of amino acids by liver from blood resulting in lower glycemia. The resulting hyperaminoacidemia stimulates α cell proliferation and glucagon secretion via a liver-α cell axis. We hypothesized that α cells detect and respond to circulating amino acids levels via a unique amino acid transporter repertoire. We found that Slc7a2ISLC7A2 is the most highly expressed cationic amino acid transporter in α cells with its expression being three-fold greater in α than β cells in both mouse and human. Employing cell culture, zebrafish, and knockout mouse models, we found that the cationic amino acid arginine and SLC7A2 are required for α cell proliferation in response to interrupted glucagon signaling. Ex vivo and in vivo assessment of islet function in Slc7a2-/- mice showed decreased arginine-stimulated glucagon and insulin secretion. We found that arginine activation of mTOR signaling and induction of the glutamine transporter SLC38A5 was dependent on SLC7A2, showing that both's role in α cell proliferation is dependent on arginine transport and SLC7A2. Finally, we identified single nucleotide polymorphisms in SLC7A2 associated with HbA1c. Together, these data indicate a central role for SLC7A2 in amino acid-stimulated α cell proliferation and islet hormone secretion.
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Affiliation(s)
- Erick Spears
- Division of Diabetes, Endocrinology, and Metabolism, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
- Department of Biology, Belmont University, Nashville, TN
| | - Jade E. Stanley
- Division of Diabetes, Endocrinology, and Metabolism, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
- Department of Molecular Physiology & Biophysics, Vanderbilt University, Nashville, TN
| | - Matthew Shou
- Division of Diabetes, Endocrinology, and Metabolism, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - Linlin Yin
- Department of Molecular Physiology & Biophysics, Vanderbilt University, Nashville, TN
| | - Xuan Li
- Department of Molecular Physiology & Biophysics, Vanderbilt University, Nashville, TN
| | - Chunhua Dai
- Division of Diabetes, Endocrinology, and Metabolism, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - Amber Bradley
- Division of Diabetes, Endocrinology, and Metabolism, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - Katelyn Sellick
- Division of Diabetes, Endocrinology, and Metabolism, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - Greg Poffenberger
- Division of Diabetes, Endocrinology, and Metabolism, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - Katie C. Coate
- Division of Diabetes, Endocrinology, and Metabolism, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - Shristi Shrestha
- Division of Diabetes, Endocrinology, and Metabolism, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - Regina Jenkins
- Division of Diabetes, Endocrinology, and Metabolism, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - Kyle W. Sloop
- Diabetes and Complications, Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN
| | - Keith T. Wilson
- Division of Gastroenterology, Hepatology and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN
- Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center, Nashville, TN
- Program in Cancer Biology, Vanderbilt University School of Medicine, Nashville, TN
- Veterans Affairs Tennessee Valley Healthcare System, Nashville, TN
| | - Alan D. Attie
- Department of Biochemistry, University of Wisconsin, Madison, WI
| | - Mark P. Keller
- Department of Biochemistry, University of Wisconsin, Madison, WI
| | - Wenbiao Chen
- Department of Molecular Physiology & Biophysics, Vanderbilt University, Nashville, TN
| | - Alvin C. Powers
- Division of Diabetes, Endocrinology, and Metabolism, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
- Department of Molecular Physiology & Biophysics, Vanderbilt University, Nashville, TN
- Veterans Affairs Tennessee Valley Healthcare System, Nashville, TN
| | - E. Danielle Dean
- Division of Diabetes, Endocrinology, and Metabolism, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
- Department of Molecular Physiology & Biophysics, Vanderbilt University, Nashville, TN
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11
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Gobert AP, Asim M, Smith TM, Williams KJ, Barry DP, Allaman MM, McNamara KM, Hawkins CV, Delgado AG, Zhao S, Piazuelo MB, Washington MK, Coburn LA, Rathmacher JA, Wilson KT. Electrophilic reactive aldehydes as a therapeutic target in colorectal cancer prevention and treatment. Oncogene 2023; 42:1685-1691. [PMID: 37037901 PMCID: PMC10182918 DOI: 10.1038/s41388-023-02691-w] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 03/28/2023] [Accepted: 03/29/2023] [Indexed: 04/12/2023]
Abstract
Colorectal cancer (CRC) is a major health problem worldwide. Dicarbonyl electrophiles, such as isolevuglandins (isoLGs), are generated from lipid peroxidation and form covalent adducts with amine-containing macromolecules. We have shown high levels of adducts of isoLGs in colonic epithelial cells of patients with CRC. We thus investigated the role of these reactive aldehydes in colorectal cancer development. We found that 2-hydroxybenzylamine (2-HOBA), a natural compound derived from buckwheat seeds that acts as a potent scavenger of electrophiles, is bioavailable in the colon of mice after supplementation in the drinking water and does not affect the colonic microbiome. 2-HOBA reduced the level of isoLG adducts to lysine as well as tumorigenesis in models of colitis-associated carcinogenesis and of sporadic CRC driven by specific deletion of the adenomatous polyposis coli gene in colonic epithelial cells. In parallel, we found that oncogenic NRF2 activation and signaling were decreased in the colon of 2-HOBA-treated mice. Additionally, the growth of xenografted human HCT116 CRC cells in nude mice was significantly attenuated by 2-HOBA supplementation. In conclusion, 2-HOBA represents a promising natural compound for the prevention and treatment of CRC.
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Affiliation(s)
- Alain P Gobert
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Mohammad Asim
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Thaddeus M Smith
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Kamery J Williams
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Daniel P Barry
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Margaret M Allaman
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Kara M McNamara
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Program in Cancer Biology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Caroline V Hawkins
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Alberto G Delgado
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Shilin Zhao
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - M Blanca Piazuelo
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center, Nashville, TN, USA
| | - M Kay Washington
- Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Lori A Coburn
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center, Nashville, TN, USA
- Program in Cancer Biology, Vanderbilt University Medical Center, Nashville, TN, USA
- Veterans Affairs Tennessee Valley Healthcare System, Nashville, TN, USA
| | - John A Rathmacher
- MTI BioTech Inc., Iowa State University Research Park, Ames, IA, USA
- Department of Animal Science, Iowa State University, Ames, IA, USA
| | - Keith T Wilson
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA.
- Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center, Nashville, TN, USA.
- Program in Cancer Biology, Vanderbilt University Medical Center, Nashville, TN, USA.
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA.
- Veterans Affairs Tennessee Valley Healthcare System, Nashville, TN, USA.
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12
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Hoek KL, McClanahan KG, Latour YL, Shealy N, Piazuelo MB, Vallance BA, Byndloss MX, Wilson KT, Olivares-Villagómez D. Turicibacterales protect mice from severe Citrobacter rodentium infection. bioRxiv 2023:2023.04.25.538270. [PMID: 37163036 PMCID: PMC10168287 DOI: 10.1101/2023.04.25.538270] [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: 05/11/2023]
Abstract
One of the major contributors to child mortality in the world is diarrheal diseases, with an estimated 800,000 deaths per year. Many pathogens are causative agents of these illnesses, including the enteropathogenic (EPEC) or enterohemorrhagic (EHEC) forms of Escherichia coli. These bacteria are characterized by their ability to cause attaching and effacing lesions in the gut mucosa. Although much has been learned about the pathogenicity of these organisms and the immune response against them, the role of the intestinal microbiota during these infections is not well characterized. Infection of mice with E. coli requires pre-treatment with antibiotics in most mouse models, which hinders the study of the microbiota in an undisturbed environment. Using Citrobacter rodentium as a murine model for attaching and effacing bacteria, we show that C57BL/6 mice deficient in granzyme B expression are highly susceptible to severe disease caused by C. rodentium infection. Although a previous publication from our group shows that granzyme B-deficient CD4+ T cells are partially responsible for this phenotype, in this report we present data demonstrating that the microbiota, in particular members of the order Turicibacterales, have an important role in conferring resistance. Mice deficient in Turicibacter sanguinis have increased susceptibility to severe disease. However, when these mice are co-housed with resistant mice, or colonized with T. sanguinis, susceptibility to severe infection is reduced. These results clearly suggest a critical role for this commensal in the protection against entero-pathogens.
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Affiliation(s)
- Kristen L. Hoek
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Kathleen G. McClanahan
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Yvonne L. Latour
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Nicolas Shealy
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - M. Blanca Piazuelo
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Bruce A. Vallance
- Department of Pediatrics, BC Children’s Hospital, University of British Columbia, Vancouver, BC, Canada
| | - Mariana X. Byndloss
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
- Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt Institute of Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt Microbiome Innovation Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Keith T. Wilson
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center, Nashville, TN, USA
- Veternas Affairs Tennessee Valley Healthcare System, Nashville, TN, USA
| | - Danyvid Olivares-Villagómez
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
- Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt Institute of Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, TN, USA
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13
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Cui C, Yang H, Wang Y, Zhao S, Asad Z, Coburn LA, Wilson KT, Landman BA, Huo Y. Deep multimodal fusion of image and non-image data in disease diagnosis and prognosis: a review. Prog Biomed Eng (Bristol) 2023; 5:10.1088/2516-1091/acc2fe. [PMID: 37360402 PMCID: PMC10288577 DOI: 10.1088/2516-1091/acc2fe] [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] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/28/2023]
Abstract
The rapid development of diagnostic technologies in healthcare is leading to higher requirements for physicians to handle and integrate the heterogeneous, yet complementary data that are produced during routine practice. For instance, the personalized diagnosis and treatment planning for a single cancer patient relies on various images (e.g. radiology, pathology and camera images) and non-image data (e.g. clinical data and genomic data). However, such decision-making procedures can be subjective, qualitative, and have large inter-subject variabilities. With the recent advances in multimodal deep learning technologies, an increasingly large number of efforts have been devoted to a key question: how do we extract and aggregate multimodal information to ultimately provide more objective, quantitative computer-aided clinical decision making? This paper reviews the recent studies on dealing with such a question. Briefly, this review will include the (a) overview of current multimodal learning workflows, (b) summarization of multimodal fusion methods, (c) discussion of the performance, (d) applications in disease diagnosis and prognosis, and (e) challenges and future directions.
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Affiliation(s)
- Can Cui
- Department of Computer Science, Vanderbilt University, Nashville, TN 37235, United States of America
| | - Haichun Yang
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN 37215, United States of America
| | - Yaohong Wang
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN 37215, United States of America
| | - Shilin Zhao
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN 37215, United States of America
| | - Zuhayr Asad
- Department of Computer Science, Vanderbilt University, Nashville, TN 37235, United States of America
| | - Lori A Coburn
- Division of Gastroenterology Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, United States of America
- Veterans Affairs Tennessee Valley Healthcare System, Nashville, TN 37212, United States of America
| | - Keith T Wilson
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN 37215, United States of America
- Division of Gastroenterology Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, United States of America
- Veterans Affairs Tennessee Valley Healthcare System, Nashville, TN 37212, United States of America
| | - Bennett A Landman
- Department of Computer Science, Vanderbilt University, Nashville, TN 37235, United States of America
- Department of Electrical and Computer Engineering, Vanderbilt University, Nashville, TN 37235, United States of America
| | - Yuankai Huo
- Department of Computer Science, Vanderbilt University, Nashville, TN 37235, United States of America
- Department of Electrical and Computer Engineering, Vanderbilt University, Nashville, TN 37235, United States of America
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14
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Jacobse J, Brown RE, Li J, Pilat JM, Pham L, Short SP, Peek CT, Rolong A, Washington MK, Martinez-Barricarte R, Byndloss MX, Shelton C, Markle JG, Latour YL, Allaman MM, Cassat JE, Wilson KT, Choksi YA, Williams CS, Lau KS, Flynn CR, Casanova JL, Rings EHHM, Samsom JN, Goettel JA. Interleukin-23 receptor signaling impairs the stability and function of colonic regulatory T cells. Cell Rep 2023; 42:112128. [PMID: 36807140 PMCID: PMC10432575 DOI: 10.1016/j.celrep.2023.112128] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 12/29/2022] [Accepted: 01/31/2023] [Indexed: 02/19/2023] Open
Abstract
The cytokine interleukin-23 (IL-23) is involved in the pathogenesis of inflammatory and autoimmune conditions including inflammatory bowel disease (IBD). IL23R is enriched in intestinal Tregs, yet whether IL-23 modulates intestinal Tregs remains unknown. Here, investigating IL-23R signaling in Tregs specifically, we show that colonic Tregs highly express Il23r compared with Tregs from other compartments and their frequency is reduced upon IL-23 administration and impairs Treg suppressive function. Similarly, colonic Treg frequency is increased in mice lacking Il23r specifically in Tregs and exhibits a competitive advantage over IL-23R-sufficient Tregs during inflammation. Finally, IL-23 antagonizes liver X receptor pathway, cellular cholesterol transporter Abca1, and increases Treg apoptosis. Our results show that IL-23R signaling regulates intestinal Tregs by increasing cell turnover, antagonizing suppression, and decreasing cholesterol efflux. These results suggest that IL-23 negatively regulates Tregs in the intestine with potential implications for promoting chronic inflammation in patients with IBD.
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Affiliation(s)
- Justin Jacobse
- Department of Medicine, Division of Gastroenterology, Hepatology and Nutrition, Vanderbilt University Medical Center, 2215 Garland Avenue, 1075J MRB IV, Nashville, TN 37232, USA; Willem-Alexander Children's Hospital, Department of Pediatrics, Leiden University Medical Center, Leiden, the Netherlands; Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA; Veterans Affairs Tennessee Valley Healthcare System, Nashville, TN 37212, USA
| | - Rachel E Brown
- Program in Cancer Biology, Vanderbilt University School of Medicine, Nashville, TN, USA; Medical Scientist Training Program, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Jing Li
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jennifer M Pilat
- Program in Cancer Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Ly Pham
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Sarah P Short
- Department of Medicine, Division of Gastroenterology, Hepatology and Nutrition, Vanderbilt University Medical Center, 2215 Garland Avenue, 1075J MRB IV, Nashville, TN 37232, USA; Program in Cancer Biology, Vanderbilt University School of Medicine, Nashville, TN, USA; Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Christopher T Peek
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA; Medical Scientist Training Program, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Andrea Rolong
- Department of Cell and Developmental Biology and Epithelial Biology Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - M Kay Washington
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA; Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Ruben Martinez-Barricarte
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA; Department of Medicine, Division of Genetic Medicine, Vanderbilt University Medical Center, Nashville, TN, USA; Vanderbilt Institute for Infection, Immunology and Inflammation, Vanderbilt University Medical Center, Nashville, TN, USA; Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Mariana X Byndloss
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA; Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center, Nashville, TN, USA; Vanderbilt Institute for Infection, Immunology and Inflammation, Vanderbilt University Medical Center, Nashville, TN, USA; Vanderbilt Center for Immunobiology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Catherine Shelton
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Janet G Markle
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA; Department of Medicine, Division of Genetic Medicine, Vanderbilt University Medical Center, Nashville, TN, USA; Vanderbilt Institute for Infection, Immunology and Inflammation, Vanderbilt University Medical Center, Nashville, TN, USA; Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Yvonne L Latour
- Department of Medicine, Division of Gastroenterology, Hepatology and Nutrition, Vanderbilt University Medical Center, 2215 Garland Avenue, 1075J MRB IV, Nashville, TN 37232, USA; Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Margaret M Allaman
- Department of Medicine, Division of Gastroenterology, Hepatology and Nutrition, Vanderbilt University Medical Center, 2215 Garland Avenue, 1075J MRB IV, Nashville, TN 37232, USA
| | - James E Cassat
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA; Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center, Nashville, TN, USA; Vanderbilt Institute for Infection, Immunology and Inflammation, Vanderbilt University Medical Center, Nashville, TN, USA; Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA; Department of Pediatrics, Division of Pediatric Infectious Diseases, Vanderbilt University Medical Center, Nashville, TN, USA; Vanderbilt Center for Immunobiology, Vanderbilt University Medical Center, Nashville, TN, USA; Vanderbilt Center for Bone Biology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Keith T Wilson
- Department of Medicine, Division of Gastroenterology, Hepatology and Nutrition, Vanderbilt University Medical Center, 2215 Garland Avenue, 1075J MRB IV, Nashville, TN 37232, USA; Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA; Veterans Affairs Tennessee Valley Healthcare System, Nashville, TN 37212, USA; Program in Cancer Biology, Vanderbilt University School of Medicine, Nashville, TN, USA; Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center, Nashville, TN, USA; Vanderbilt Institute for Infection, Immunology and Inflammation, Vanderbilt University Medical Center, Nashville, TN, USA; Vanderbilt Center for Immunobiology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Yash A Choksi
- Department of Medicine, Division of Gastroenterology, Hepatology and Nutrition, Vanderbilt University Medical Center, 2215 Garland Avenue, 1075J MRB IV, Nashville, TN 37232, USA; Veterans Affairs Tennessee Valley Healthcare System, Nashville, TN 37212, USA; Program in Cancer Biology, Vanderbilt University School of Medicine, Nashville, TN, USA; Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Christopher S Williams
- Department of Medicine, Division of Gastroenterology, Hepatology and Nutrition, Vanderbilt University Medical Center, 2215 Garland Avenue, 1075J MRB IV, Nashville, TN 37232, USA; Program in Cancer Biology, Vanderbilt University School of Medicine, Nashville, TN, USA; Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Ken S Lau
- Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center, Nashville, TN, USA; Department of Cell and Developmental Biology and Epithelial Biology Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Charles R Flynn
- Department of Surgery, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jean-Laurent Casanova
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA; Laboratory of Human Genetics of Infectious Diseases, Necker Branch, Institut National de la Santé et de la Recherche Médicale (INSERM) U1163, Necker Hospital for Sick Children, Paris, France; The Center for Stem Cell Biology, Sloan-Kettering Institute for Cancer Research, New York, NY, USA; Developmental Biology Program, Sloan-Kettering Institute for Cancer Research, 1275 York Avenue, New York, NY, USA; Howard Hughes Medical Institute, New York, NY, USA
| | - Edmond H H M Rings
- Willem-Alexander Children's Hospital, Department of Pediatrics, Leiden University Medical Center, Leiden, the Netherlands; Sophia Children's Hospital, Department of Pediatrics, Erasmus University, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Janneke N Samsom
- Laboratory of Pediatrics, Division of Gastroenterology and Nutrition, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Jeremy A Goettel
- Department of Medicine, Division of Gastroenterology, Hepatology and Nutrition, Vanderbilt University Medical Center, 2215 Garland Avenue, 1075J MRB IV, Nashville, TN 37232, USA; Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA; Program in Cancer Biology, Vanderbilt University School of Medicine, Nashville, TN, USA; Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center, Nashville, TN, USA; Vanderbilt Institute for Infection, Immunology and Inflammation, Vanderbilt University Medical Center, Nashville, TN, USA.
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15
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Cui C, Bao S, Li J, Deng R, Remedios LW, Asad Z, Chiron S, Lau KS, Wang Y, Coburn LA, Wilson KT, Roland JT, Landman BA, Liu Q, Huo Y. Influence of Cell-type Ratio on Spatially Resolved Single-cell Transcriptomes using the Tangram Algorithm: Based on Implementation on Single-Cell and MxIF Data. Proc SPIE Int Soc Opt Eng 2023; 12471:124710A. [PMID: 37324550 PMCID: PMC10270698] [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] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
The Tangram algorithm is a benchmarking method of aligning single-cell (sc/snRNA-seq) data to various forms of spatial data collected from the same region. With this data alignment, the annotation of the single-cell data can be projected to spatial data. However, the cell composition (cell-type ratio) of the single-cell data and spatial data might be different because of heterogeneous cell distribution. Whether the Tangram algorithm can be adapted when the two data have different cell-type ratios has not been discussed in previous works. In our practical application that maps the cell-type classification results of single-cell data to the Multiplex immunofluorescence (MxIF) spatial data, cell-type ratios were different, though they were sampled from adjacent areas. In this work, both simulation and empirical validation were conducted to quantitatively explore the impact of the mismatched cell-type ratio on the Tangram mapping in different situations. Results show that the cell-type difference has a negative influence on classification accuracy.
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Affiliation(s)
- Can Cui
- Vanderbilt University, Nashville TN 37215, USA
| | | | - Jia Li
- Vanderbilt University Medical Center, Nashville TN 37232, USA
| | | | | | - Zuhayr Asad
- Vanderbilt University, Nashville TN 37215, USA
| | - Sophie Chiron
- Vanderbilt University Medical Center, Nashville TN 37232, USA
| | - Ken S Lau
- Vanderbilt University, Nashville TN 37215, USA
| | - Yaohong Wang
- Vanderbilt University Medical Center, Nashville TN 37232, USA
| | - Lori A Coburn
- Vanderbilt University Medical Center, Nashville TN 37232, USA; Veterans Affairs Tennessee Valley Healthcare System, Nashville, TN, 37212, USA
| | - Keith T Wilson
- Vanderbilt University Medical Center, Nashville TN 37232, USA; Veterans Affairs Tennessee Valley Healthcare System, Nashville, TN, 37212, USA
| | - Joseph T Roland
- Vanderbilt University Medical Center, Nashville TN 37232, USA
| | | | - Qi Liu
- Vanderbilt University Medical Center, Nashville TN 37232, USA
| | - Yuankai Huo
- Vanderbilt University, Nashville TN 37215, USA
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16
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Remedios LW, Bao S, Kerley CI, Cai LY, Rheault F, Deng R, Cui C, Chiron S, Lau KS, Roland JT, Washington MK, Coburn LA, Wilson KT, Huo Y, Landman BA. Predicting Crohn's disease severity in the colon using mixed cell nucleus density from pseudo labels. Proc SPIE Int Soc Opt Eng 2023; 12471:1247116. [PMID: 37465840 PMCID: PMC10353830 DOI: 10.1117/12.2653918] [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] [Subscribe] [Scholar Register] [Indexed: 07/20/2023]
Abstract
Crohn's disease (CD) is a debilitating inflammatory bowel disease with no known cure. Computational analysis of hematoxylin and eosin (H&E) stained colon biopsy whole slide images (WSIs) from CD patients provides the opportunity to discover unknown and complex relationships between tissue cellular features and disease severity. While there have been works using cell nuclei-derived features for predicting slide-level traits, this has not been performed on CD H&E WSIs for classifying normal tissue from CD patients vs active CD and assessing slide label-predictive performance while using both separate and combined information from pseudo-segmentation labels of nuclei from neutrophils, eosinophils, epithelial cells, lymphocytes, plasma cells, and connective cells. We used 413 WSIs of CD patient biopsies and calculated normalized histograms of nucleus density for the six cell classes for each WSI. We used a support vector machine to classify the truncated singular value decomposition representations of the normalized histograms as normal or active CD with four-fold cross-validation in rounds where nucleus types were first compared individually, the best was selected, and further types were added each round. We found that neutrophils were the most predictive individual nucleus type, with an AUC of 0.92 ± 0.0003 on the withheld test set. Adding information improved cross-validation performance for the first two rounds and on the withheld test set for the first three rounds, though performance metrics did not increase substantially beyond when neutrophils were used alone.
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Affiliation(s)
- Lucas W Remedios
- Department of Computer Science, Vanderbilt University, Nashville, TN, USA
| | - Shunxing Bao
- Department of Electrical and Computer Engineering, Vanderbilt University, Nashville, TN, USA
| | - Cailey I Kerley
- Department of Electrical and Computer Engineering, Vanderbilt University, Nashville, TN, USA
| | - Leon Y Cai
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA
| | - François Rheault
- Department of Electrical and Computer Engineering, Vanderbilt University, Nashville, TN, USA
- Department of Computer Science, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Ruining Deng
- Department of Computer Science, Vanderbilt University, Nashville, TN, USA
| | - Can Cui
- Department of Computer Science, Vanderbilt University, Nashville, TN, USA
| | - Sophie Chiron
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Ken S Lau
- Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, TN, USA
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Joseph T Roland
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Mary K Washington
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Lori A Coburn
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center, Nashville, TN, USA
- Program in Cancer Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
- Veterans Affairs Tennessee Valley Healthcare System, Nashville, TN, USA
| | - Keith T Wilson
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center, Nashville, TN, USA
- Program in Cancer Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
- Veterans Affairs Tennessee Valley Healthcare System, Nashville, TN, USA
| | - Yuankai Huo
- Department of Computer Science, Vanderbilt University, Nashville, TN, USA
- Department of Electrical and Computer Engineering, Vanderbilt University, Nashville, TN, USA
| | - Bennett A Landman
- Department of Computer Science, Vanderbilt University, Nashville, TN, USA
- Department of Electrical and Computer Engineering, Vanderbilt University, Nashville, TN, USA
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA
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17
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Gobert AP, Asim M, Smith TM, Williams KJ, Barry DP, Allaman MM, McNamara KM, Hawkins CV, Delgado AG, Piazuelo MB, Rathmacher JA, Wilson KT. The nutraceutical electrophile scavenger 2-hydroxybenzylamine (2-HOBA) attenuates gastric cancer development caused by Helicobacter pylori. Biomed Pharmacother 2023; 158:114092. [PMID: 36493697 PMCID: PMC9879697 DOI: 10.1016/j.biopha.2022.114092] [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: 10/08/2022] [Revised: 11/22/2022] [Accepted: 12/04/2022] [Indexed: 12/12/2022] Open
Abstract
Stomach cancer is a leading cause of cancer death. Helicobacter pylori is a bacterial gastric pathogen that is the primary risk factor for carcinogenesis, associated with its induction of inflammation and DNA damage. Dicarbonyl electrophiles are generated from lipid peroxidation during the inflammatory response and form covalent adducts with amine-containing macromolecules. 2-hydroxybenzylamine (2-HOBA) is a natural compound derived from buckwheat seeds and acts as a potent scavenger of reactive aldehydes. Our goal was to investigate the effect of 2-HOBA on the pathogenesis of H. pylori infection. We used transgenic FVB/N insulin-gastrin (INS-GAS) mice as a model of gastric cancer. First, we found that 2-HOBA is bioavailable in the gastric tissues of these mice after supplementation in the drinking water. Moreover, 2-HOBA reduced the development of gastritis in H. pylori-infected INS-GAS mice without affecting the bacterial colonization level in the stomach. Further, we show that the development of gastric dysplasia and carcinoma was significantly reduced by 2-HOBA. Concomitantly, DNA damage were also inhibited by 2-HOBA treatment in H. pylori-infected mice. In parallel, DNA damage was inhibited by 2-HOBA in H. pylori-infected gastric epithelial cells in vitro. In conclusion, 2-HOBA, which has been shown to be safe in human clinical trials, represents a promising nutritional compound for the chemoprevention of the more severe effects of H. pylori infection.
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Affiliation(s)
- Alain P. Gobert
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA,Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Mohammad Asim
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Thaddeus M. Smith
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Kamery J. Williams
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Daniel P. Barry
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Margaret M. Allaman
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Kara M. McNamara
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA,Program in Cancer Biology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Caroline V. Hawkins
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Alberto G. Delgado
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - M. Blanca Piazuelo
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA,Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center, Nashville, TN, USA
| | - John A. Rathmacher
- MTI BioTech, Iowa State University Research Park, Ames, IA, USA,Department of Animal Science, Iowa State University, Ames, IA, USA
| | - Keith T. Wilson
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA,Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center, Nashville, TN, USA,Program in Cancer Biology, Vanderbilt University Medical Center, Nashville, TN, USA,Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA,Veterans Affairs Tennessee Valley Healthcare System, Nashville, TN, USA,Correspondence to: Vanderbilt University Medical Center, 2215B Garland Ave., 1030C MRB IV, Nashville, TN 37232-0252, USA. (K.T. Wilson)
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18
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Bao S, Cui C, Li J, Tang Y, Lee HH, Deng R, Remedios LW, Yu X, Yang Q, Chiron S, Patterson NH, Lau KS, Liu Q, Roland JT, Coburn LA, Wilson KT, Landman BA, Huo Y. Topological-Preserving Membrane Skeleton Segmentation in Multiplex Immunofluorescence Imaging. Proc SPIE Int Soc Opt Eng 2023; 12471:124710B. [PMID: 37786583 PMCID: PMC10545297 DOI: 10.1117/12.2654087] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
Multiplex immunofluorescence (MxIF) is an emerging imaging technology whose downstream molecular analytics highly rely upon the effectiveness of cell segmentation. In practice, multiple membrane markers (e.g., NaKATPase, PanCK and β-catenin) are employed to stain membranes for different cell types, so as to achieve a more comprehensive cell segmentation since no single marker fits all cell types. However, prevalent watershed-based image processing might yield inferior capability for modeling complicated relationships between markers. For example, some markers can be misleading due to questionable stain quality. In this paper, we propose a deep learning based membrane segmentation method to aggregate complementary information that is uniquely provided by large scale MxIF markers. We aim to segment tubular membrane structure in MxIF data using global (membrane markers z-stack projection image) and local (separate individual markers) information to maximize topology preservation with deep learning. Specifically, we investigate the feasibility of four SOTA 2D deep networks and four volumetric-based loss functions. We conducted a comprehensive ablation study to assess the sensitivity of the proposed method with various combinations of input channels. Beyond using adjusted rand index (ARI) as the evaluation metric, which was inspired by the clDice, we propose a novel volumetric metric that is specific for skeletal structure, denoted as c l D i c e S K E L . In total, 80 membrane MxIF images were manually traced for 5-fold cross-validation. Our model outperforms the baseline with a 20.2% and 41.3% increase in c l D i c e S K E L and ARI performance, which is significant (p<0.05) using the Wilcoxon signed rank test. Our work explores a promising direction for advancing MxIF imaging cell segmentation with deep learning membrane segmentation. Tools are available at https://github.com/MASILab/MxIF_Membrane_Segmentation.
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Affiliation(s)
- Shunxing Bao
- Dept. of Electrical and Computer Engineering, Vanderbilt University, Nashville, TN, USA
| | - Can Cui
- Dept. of Computer Science, Vanderbilt University, Nashville, TN, USA
| | - Jia Li
- Dept. of Biostatistics, Vanderbilt University Medical center, Nashville, TN, USA
| | - Yucheng Tang
- Dept. of Electrical and Computer Engineering, Vanderbilt University, Nashville, TN, USA
| | - Ho Hin Lee
- Dept. of Computer Science, Vanderbilt University, Nashville, TN, USA
| | - Ruining Deng
- Dept. of Computer Science, Vanderbilt University, Nashville, TN, USA
| | - Lucas W Remedios
- Dept. of Computer Science, Vanderbilt University, Nashville, TN, USA
| | - Xin Yu
- Dept. of Computer Science, Vanderbilt University, Nashville, TN, USA
| | - Qi Yang
- Dept. of Computer Science, Vanderbilt University, Nashville, TN, USA
| | - Sophie Chiron
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Nathan Heath Patterson
- Dept. of Biochemistry, Vanderbilt University
- Mass Spectrometry Research Center, Vanderbilt University
| | - Ken S Lau
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, USA
- Dept. of Cell and Developmental Biology, Vanderbilt University School of Medicine
- Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Qi Liu
- Dept. of Biostatistics, Vanderbilt University Medical center, Nashville, TN, USA
- Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Joseph T Roland
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Lori A Coburn
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center, Nashville, TN, USA
- Program in Cancer Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
- Veterans Affairs Tennessee Valley Healthcare System, Nashville, TN, USA
| | - Keith T Wilson
- Dept. of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center, Nashville, TN, USA
- Program in Cancer Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
- Veterans Affairs Tennessee Valley Healthcare System, Nashville, TN, USA
| | - Bennett A Landman
- Dept. of Electrical and Computer Engineering, Vanderbilt University, Nashville, TN, USA
- Dept. of Computer Science, Vanderbilt University, Nashville, TN, USA
- Dept. of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA
- Department of Radiology and Radiological Sciences, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Yuankai Huo
- Dept. of Electrical and Computer Engineering, Vanderbilt University, Nashville, TN, USA
- Dept. of Computer Science, Vanderbilt University, Nashville, TN, USA
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19
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Latour YL, Allaman MM, Barry DP, Smith TM, Williams KJ, McNamara KM, Jacobse J, Goettel JA, Delgado AG, Piazuelo MB, Zhao S, Gobert AP, Wilson KT. Epithelial talin-1 protects mice from citrobacter rodentium-induced colitis by restricting bacterial crypt intrusion and enhancing t cell immunity. Gut Microbes 2023; 15:2192623. [PMID: 36951501 PMCID: PMC10038039 DOI: 10.1080/19490976.2023.2192623] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/24/2023] Open
Abstract
Pathogenic enteric Escherichia coli present a significant burden to global health. Food-borne enteropathogenic E. coli (EPEC) and Shiga toxin-producing E. coli (STEC) utilize attaching and effacing (A/E) lesions and actin-dense pedestal formation to colonize the gastrointestinal tract. Talin-1 is a large structural protein that links the actin cytoskeleton to the extracellular matrix though direct influence on integrins. Here we show that mice lacking talin-1 in intestinal epithelial cells (Tln1Δepi) have heightened susceptibility to colonic disease caused by the A/E murine pathogen Citrobacter rodentium. Tln1Δepi mice exhibit decreased survival, and increased colonization, colon weight, and histologic colitis compared to littermate Tln1fl/fl controls. These findings were associated with decreased actin polymerization and increased infiltration of innate myeloperoxidase-expressing immune cells, confirmed as neutrophils by flow cytometry, but more bacterial dissemination deep into colonic crypts. Further evaluation of the immune population recruited to the mucosa in response to C. rodentium revealed that loss of Tln1 in colonic epithelial cells (CECs) results in impaired recruitment and activation of T cells. C. rodentium infection-induced colonic mucosal hyperplasia was exacerbated in Tln1Δepi mice compared to littermate controls. We demonstrate that this is associated with decreased CEC apoptosis and crowding of proliferating cells in the base of the glands. Taken together, talin-1 expression by CECs is important in the regulation of both epithelial renewal and the inflammatory T cell response in the setting of colitis caused by C. rodentium, suggesting that this protein functions in CECs to limit, rather than contribute to the pathogenesis of this enteric infection.
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Affiliation(s)
- Yvonne L Latour
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Margaret M Allaman
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Daniel P Barry
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Thaddeus M Smith
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Kamery J Williams
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Kara M McNamara
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Program in Cancer Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Justin Jacobse
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jeremy A Goettel
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Alberto G Delgado
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - M Blanca Piazuelo
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Shilin Zhao
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Alain P Gobert
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Keith T Wilson
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Program in Cancer Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
- Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center, Nashville, TN, USA
- Medical Service, Veterans Affairs Tennessee Valley Healthcare System, Nashville, TN, USA
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20
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Mannion A, Sheh A, Shen Z, Dzink-Fox J, Piazuelo MB, Wilson KT, Peek R, Fox JG. Shotgun Metagenomics of Gastric Biopsies Reveals Compositional and Functional Microbiome Shifts in High- and Low-Gastric-Cancer-Risk Populations from Colombia, South America. Gut Microbes 2023; 15:2186677. [PMID: 36907988 PMCID: PMC10026914 DOI: 10.1080/19490976.2023.2186677] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 02/27/2023] [Indexed: 03/14/2023] Open
Abstract
Along with Helicobacter pylori infection, the gastric microbiota is hypothesized to modulate stomach cancer risk in susceptible individuals. Whole metagenomic shotgun sequencing (WMS) is a sequencing approach to characterize the microbiome with advantages over traditional culture and 16S rRNA sequencing including identification of bacterial and non-bacterial taxa, species/strain resolution, and functional characterization of the microbiota. In this study, we used WMS to survey the microbiome in extracted DNA from antral gastric biopsy samples from Colombian patients residing in the high-risk gastric cancer town Túquerres (n = 10, H. pylori-positive = 7) and low-risk town of Tumaco (n = 10, H. pylori-positive = 6). Kraken2/Bracken was used for taxonomic classification and abundance. Functional gene profiles were inferred by InterProScan and KEGG analysis of assembled contigs and gene annotation. The most abundant taxa represented bacteria, non-human eukaryota, and viral genera found in skin, oral, food, and plant/soil environments including Staphylococus, Streptococcus, Bacillus, Aspergillus, and Siphoviridae. H. pylori was the predominant taxa present in H. pylori-positive samples. Beta diversity was significantly different based on H. pylori-status, risk group, and sex. WMS detected more bacterial taxa than 16S rRNA sequencing and aerobic, anaerobic, and microaerobic culture performed on the same gastric biopsy samples. WMS identified significant differences in functional profiles found between H. pylori-status, but not risk or sex groups. H. pylori-positive samples were significantly enriched for H. pylori-specific genes including virulence factors such as vacA, cagA, and urease, while carbohydrate and amino acid metabolism genes were enriched in H. pylori-negative samples. This study shows WMS has the potential to characterize the taxonomy and function of the gastric microbiome as risk factors for H. pylori-associated gastric disease. Future studies will be needed to compare and validate WMS versus traditional culture and 16S rRNA sequencing approaches for characterization of the gastric microbiome.
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Affiliation(s)
- Anthony Mannion
- Division of Comparative Medicine, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Alexander Sheh
- Division of Comparative Medicine, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Zeli Shen
- Division of Comparative Medicine, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - JoAnn Dzink-Fox
- Division of Comparative Medicine, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - M. Blanca Piazuelo
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Keith T Wilson
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Richard Peek
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - James G. Fox
- Division of Comparative Medicine, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
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21
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Deng R, Cui C, Remedios LW, Bao S, Womick RM, Chiron S, Li J, Roland JT, Lau KS, Liu Q, Wilson KT, Wang Y, Coburn LA, Landman BA, Huo Y. Cross-scale Attention Guided Multi-instance Learning for Crohn's Disease Diagnosis with Pathological Images. Multiscale Multimodal Med Imaging (2022) 2022; 13594:24-33. [PMID: 36331283 PMCID: PMC9628695 DOI: 10.1007/978-3-031-18814-5_3] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Multi-instance learning (MIL) is widely used in the computer-aided interpretation of pathological Whole Slide Images (WSIs) to solve the lack of pixel-wise or patch-wise annotations. Often, this approach directly applies "natural image driven" MIL algorithms which overlook the multi-scale (i.e. pyramidal) nature of WSIs. Off-the-shelf MIL algorithms are typically deployed on a single-scale of WSIs (e.g., 20× magnification), while human pathologists usually aggregate the global and local patterns in a multi-scale manner (e.g., by zooming in and out between different magnifications). In this study, we propose a novel cross-scale attention mechanism to explicitly aggregate inter-scale interactions into a single MIL network for Crohn's Disease (CD), which is a form of inflammatory bowel disease. The contribution of this paper is two-fold: (1) a cross-scale attention mechanism is proposed to aggregate features from different resolutions with multi-scale interaction; and (2) differential multi-scale attention visualizations are generated to localize explainable lesion patterns. By training ~250,000 H&E-stained Ascending Colon (AC) patches from 20 CD patient and 30 healthy control samples at different scales, our approach achieved a superior Area under the Curve (AUC) score of 0.8924 compared with baseline models. The official implementation is publicly available at https://github.com/hrlblab/CS-MIL.
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Affiliation(s)
| | - Can Cui
- Vanderbilt University, Nashville TN 37215, USA
| | | | | | - R Michael Womick
- The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27514, USA
| | - Sophie Chiron
- Vanderbilt University Medical Center, Nashville TN 37232, USA
| | - Jia Li
- Vanderbilt University Medical Center, Nashville TN 37232, USA
| | - Joseph T Roland
- Vanderbilt University Medical Center, Nashville TN 37232, USA
| | - Ken S Lau
- Vanderbilt University, Nashville TN 37215, USA
| | - Qi Liu
- Vanderbilt University Medical Center, Nashville TN 37232, USA
| | - Keith T Wilson
- Vanderbilt University Medical Center, Nashville TN 37232, USA
- Veterans Affairs Tennessee Valley Healthcare System, Nashville, TN, 37212, USA
| | - Yaohong Wang
- Vanderbilt University Medical Center, Nashville TN 37232, USA
| | - Lori A Coburn
- Vanderbilt University Medical Center, Nashville TN 37232, USA
- Veterans Affairs Tennessee Valley Healthcare System, Nashville, TN, 37212, USA
| | | | - Yuankai Huo
- Vanderbilt University, Nashville TN 37215, USA
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22
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Latour YL, Sierra JC, McNamara KM, Smith TM, Luis PB, Schneider C, Delgado AG, Barry DP, Allaman MM, Calcutt MW, Schey KL, Piazuelo MB, Gobert AP, Wilson KT. Ornithine Decarboxylase in Gastric Epithelial Cells Promotes the Immunopathogenesis of Helicobacter pylori Infection. J Immunol 2022; 209:796-805. [PMID: 35896340 PMCID: PMC9378675 DOI: 10.4049/jimmunol.2100795] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 06/06/2022] [Indexed: 01/04/2023]
Abstract
Colonization by Helicobacter pylori is associated with gastric diseases, ranging from superficial gastritis to more severe pathologies, including intestinal metaplasia and adenocarcinoma. The interplay of the host response and the pathogen affect the outcome of disease. One major component of the mucosal response to H. pylori is the activation of a strong but inefficient immune response that fails to control the infection and frequently causes tissue damage. We have shown that polyamines can regulate H. pylori-induced inflammation. Chemical inhibition of ornithine decarboxylase (ODC), which generates the polyamine putrescine from l-ornithine, reduces gastritis in mice and adenocarcinoma incidence in gerbils infected with H. pylori However, we have also demonstrated that Odc deletion in myeloid cells enhances M1 macrophage activation and gastritis. Here we used a genetic approach to assess the specific role of gastric epithelial ODC during H. pylori infection. Specific deletion of the gene encoding for ODC in gastric epithelial cells reduces gastritis, attenuates epithelial proliferation, alters the metabolome, and downregulates the expression of immune mediators induced by H. pylori Inhibition of ODC activity or ODC knockdown in human gastric epithelial cells dampens H. pylori-induced NF-κB activation, CXCL8 mRNA expression, and IL-8 production. Chronic inflammation is a major risk factor for the progression to more severe pathologies associated with H. pylori infection, and we now show that epithelial ODC plays an important role in mediating this inflammatory response.
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Affiliation(s)
- Yvonne L Latour
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University School of Medicine, Nashville, TN
| | - Johanna C Sierra
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
- Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center, Nashville, TN
| | - Kara M McNamara
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
- Program in Cancer Biology, Vanderbilt University School of Medicine, Nashville, TN
| | - Thaddeus M Smith
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - Paula B Luis
- Department of Pharmacology, Vanderbilt University School of Medicine, Nashville, TN
| | - Claus Schneider
- Department of Pharmacology, Vanderbilt University School of Medicine, Nashville, TN
| | - Alberto G Delgado
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - Daniel P Barry
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - Margaret M Allaman
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - M Wade Calcutt
- Department of Biochemistry, Mass Spectrometry Research Center, Vanderbilt University School of Medicine, Nashville, TN; and
| | - Kevin L Schey
- Department of Biochemistry, Mass Spectrometry Research Center, Vanderbilt University School of Medicine, Nashville, TN; and
| | - M Blanca Piazuelo
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
- Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center, Nashville, TN
| | - Alain P Gobert
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
- Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center, Nashville, TN
| | - Keith T Wilson
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN;
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University School of Medicine, Nashville, TN
- Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center, Nashville, TN
- Program in Cancer Biology, Vanderbilt University School of Medicine, Nashville, TN
- Veterans Affairs Tennessee Valley Healthcare System, Nashville, TN
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23
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Peek CT, Ford CA, Eichelberger KR, Jacobse J, Torres TP, Maseda D, Latour YL, Piazuelo MB, Johnson JR, Byndloss MX, Wilson KT, Rathmell JC, Goettel JA, Cassat JE. Intestinal Inflammation Promotes MDL-1 + Osteoclast Precursor Expansion to Trigger Osteoclastogenesis and Bone Loss. Cell Mol Gastroenterol Hepatol 2022; 14:731-750. [PMID: 35835390 PMCID: PMC9420375 DOI: 10.1016/j.jcmgh.2022.07.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Revised: 07/01/2022] [Accepted: 07/05/2022] [Indexed: 12/13/2022]
Abstract
BACKGROUND & AIMS Inflammatory bowel disease (IBD) is characterized by severe gastrointestinal inflammation, but many patients experience extra-intestinal disease. Bone loss is one common extra-intestinal manifestation of IBD that occurs through dysregulated interactions between osteoclasts and osteoblasts. Systemic inflammation has been postulated to contribute to bone loss, but the specific pathologic mechanisms have not yet been fully elucidated. We hypothesized that intestinal inflammation leads to bone loss through increased abundance and altered function of osteoclast progenitors. METHODS We used chemical, T cell driven, and infectious models of intestinal inflammation to determine the impact of intestinal inflammation on bone volume, the skeletal cytokine environment, and the cellular changes to pre-osteoclast populations within bone marrow. Additionally, we evaluated the potential for monoclonal antibody treatment against an inflammation-induced osteoclast co-receptor, myeloid DNAX activation protein 12-associating lectin-1 (MDL-1) to reduce bone loss during colitis. RESULTS We observed significant bone loss across all models of intestinal inflammation. Bone loss was associated with an increase in pro-osteoclastogenic cytokines within the bone and an expansion of a specific Cd11b-/loLy6Chi osteoclast precursor (OCP) population. Intestinal inflammation led to altered OCP expression of surface receptors involved in osteoclast differentiation and function, including the pro-osteoclastogenic co-receptor MDL-1. OCPs isolated from mice with intestinal inflammation demonstrated enhanced osteoclast differentiation ex vivo compared to controls, which was abrogated by anti-MDL-1 antibody treatment. Importantly, in vivo anti-MDL-1 antibody treatment ameliorated bone loss during intestinal inflammation. CONCLUSIONS Collectively, these data implicate the pathologic expansion and altered function of OCPs expressing MDL-1 in bone loss during IBD.
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Affiliation(s)
- Christopher T. Peek
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Caleb A. Ford
- Department of Biomedical Engineering, Vanderbilt University, Nashville, Tennessee
| | - Kara R. Eichelberger
- Department of Pediatrics, Division of Pediatric Infectious Diseases, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Justin Jacobse
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee,Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Teresa P. Torres
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Damian Maseda
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee,Department of Dermatology, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Yvonne L. Latour
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee
| | - M. Blanca Piazuelo
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee,Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Joshua R. Johnson
- Vanderbilt Center for Bone Biology, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Mariana X. Byndloss
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee,Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Keith T. Wilson
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee,Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee,Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, Tennessee,Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center, Nashville, Tennessee,Veterans Affairs Tennessee Valley Healthcare System, Nashville, Tennessee
| | - Jeffrey C. Rathmell
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee,Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, Tennessee,Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center, Nashville, Tennessee,Vanderbilt Center for Immunobiology, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Jeremy A. Goettel
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee,Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee,Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, Tennessee,Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center, Nashville, Tennessee
| | - James E. Cassat
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee,Department of Biomedical Engineering, Vanderbilt University, Nashville, Tennessee,Department of Pediatrics, Division of Pediatric Infectious Diseases, Vanderbilt University Medical Center, Nashville, Tennessee,Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, Tennessee,Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center, Nashville, Tennessee,Vanderbilt Center for Immunobiology, Vanderbilt University Medical Center, Nashville, Tennessee,Vanderbilt Center for Bone Biology, Vanderbilt University Medical Center, Nashville, Tennessee,Correspondence Address correspondence to: Dr Jim Cassat, Division of Pediatric Infectious Diseases, Department of Pediatrics, Vanderbilt University Medical Center, 1035 Light Hall, 2215-B Garland Ave, Nashville, TN, 37232. tel: (615) 936-6494.
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24
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Latour YL, Sierra JC, Finley JL, Asim M, Barry DP, Allaman MM, Smith TM, McNamara KM, Luis PB, Schneider C, Jacobse J, Goettel JA, Calcutt MW, Rose KL, Schey KL, Milne GL, Delgado AG, Piazuelo MB, Paul BD, Snyder S, Gobert AP, Wilson KT. CTH exacerbates Helicobacter pylori immunopathogenesis by promoting macrophage metabolic remodeling and activation. JCI Insight 2022; 7:155338. [PMID: 35579952 DOI: 10.1172/jci.insight.155338] [Citation(s) in RCA: 6] [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: 09/28/2021] [Accepted: 05/10/2022] [Indexed: 11/17/2022] Open
Abstract
Macrophages play a crucial role in the inflammatory response to the human stomach pathogen Helicobacter pylori, which infects half of the world's population and causes gastric cancer. Recent studies have highlighted the importance of macrophage immunometabolism in their activation state and function. We have demonstrated that the cysteine-producing enzyme, cystathionine g-lyase (CTH), is upregulated in humans and mice with H. pylori infection. Here we show that induction of CTH in macrophages by H. pylori promotes persistent inflammation. Cth-/- mice have reduced macrophage and T-cell activation in H. pylori-infected tissues, an altered metabolome, and decreased enrichment of immune-associated gene networks, culminating in decreased H. pylori-induced-gastritis. CTH is downstream of the proposed anti-inflammatory molecule, S-adenosylmethionine (SAM). While Cth-/- mice exhibit gastric SAM accumulation, WT mice treated with SAM did not display protection against H. pylori-induced inflammation. Instead, we demonstrate that Cth-deficient macrophages exhibit alterations in the proteome, decreased NF-kB activation, diminished expression of macrophage activation markers, and impaired oxidative phosphorylation and glycolysis. Thus, through altering cellular respiration, CTH is a key enhancer of macrophage activation contributing to a pathogenic inflammatory response that is the universal precursor for the development of H. pylori-induced gastric disease.
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Affiliation(s)
- Yvonne L Latour
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University School of Medicine, Nashville, United States of America
| | - Johanna C Sierra
- Department of Medicine, Vanderbilt University Medical Center, Nashville, United States of America
| | - Jordan L Finley
- Department of Medicine, Vanderbilt University Medical Center, Nashville, United States of America
| | - Mohammad Asim
- Department of Medicine, Vanderbilt University Medical Center, Nashville, United States of America
| | - Daniel P Barry
- Department of Medicine, Vanderbilt Univeristy Medical Center, Nashville, United States of America
| | - Margaret M Allaman
- Department of Medicine, Vanderbilt University Medical Center, Nashville, United States of America
| | - Thaddeus M Smith
- Department of Medicine, Vanderbilt University Medical Center, Nashville, United States of America
| | - Kara M McNamara
- Program in Cancer Biology, Vanderbilt University School of Medicine, Nashville, United States of America
| | - Paula B Luis
- Department of Pharmacology, Vanderbilt University School of Medicine, Nashville, United States of America
| | - Claus Schneider
- Department of Pharmacology, Vanderbilt University School of Medicine, Nashville, United States of America
| | - Justin Jacobse
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University School of Medicine, Nashville, United States of America
| | - Jeremy A Goettel
- Department of Medicine, Vanderbilt University Medical Center, Nashville, United States of America
| | - M Wade Calcutt
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, United States of America
| | - Kristie L Rose
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, United States of America
| | - Kevin L Schey
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, United States of America
| | - Ginger L Milne
- Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University Medical Center, Nashville, United States of America
| | - Alberto G Delgado
- Department of Medicine, Vanderbilt University Medical Center, Nashville, United States of America
| | - M Blanca Piazuelo
- Department of Medicine, Vanderbilt University Medical Center, Nashville, United States of America
| | - Bindu D Paul
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, United States of America
| | - Solomon Snyder
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, United States of America
| | - Alain P Gobert
- Department of Medicine, Vandebilt University Medical Center, Nashville, United States of America
| | - Keith T Wilson
- Department of Medicine, Vanderbilt University Medical Center, Nashville, United States of America
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25
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Noto JM, Piazuelo MB, Shah SC, Romero-Gallo J, Hart JL, Di C, Carmichael JD, Delgado AG, Halvorson AE, Greevy RA, Wroblewski LE, Sharma A, Newton AB, Allaman MM, Wilson KT, Washington MK, Calcutt MW, Schey KL, Cummings BP, Flynn CR, Zackular JP, Peek RM. Iron deficiency linked to altered bile acid metabolism promotes Helicobacter pylori-induced inflammation-driven gastric carcinogenesis. J Clin Invest 2022; 132:e147822. [PMID: 35316215 PMCID: PMC9106351 DOI: 10.1172/jci147822] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [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: 01/19/2021] [Accepted: 03/16/2022] [Indexed: 12/24/2022] Open
Abstract
Gastric carcinogenesis is mediated by complex interactions among Helicobacter pylori, host, and environmental factors. Here, we demonstrate that H. pylori augmented gastric injury in INS-GAS mice under iron-deficient conditions. Mechanistically, these phenotypes were not driven by alterations in the gastric microbiota; however, discovery-based and targeted metabolomics revealed that bile acids were significantly altered in H. pylori-infected mice with iron deficiency, with significant upregulation of deoxycholic acid (DCA), a carcinogenic bile acid. The severity of gastric injury was further augmented when H. pylori-infected mice were treated with DCA, and, in vitro, DCA increased translocation of the H. pylori oncoprotein CagA into host cells. Conversely, bile acid sequestration attenuated H. pylori-induced injury under conditions of iron deficiency. To translate these findings to human populations, we evaluated the association between bile acid sequestrant use and gastric cancer risk in a large human cohort. Among 416,885 individuals, a significant dose-dependent reduction in risk was associated with cumulative bile acid sequestrant use. Further, expression of the bile acid receptor transmembrane G protein-coupled bile acid receptor 5 (TGR5) paralleled the severity of carcinogenic lesions in humans. These data demonstrate that increased H. pylori-induced injury within the context of iron deficiency is tightly linked to altered bile acid metabolism, which may promote gastric carcinogenesis.
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Affiliation(s)
- Jennifer M Noto
- Division of Gastroenterology, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - M Blanca Piazuelo
- Division of Gastroenterology, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Shailja C Shah
- Division of Gastroenterology, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Judith Romero-Gallo
- Division of Gastroenterology, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | | | - Chao Di
- Division of Protective Immunity, and
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - James D Carmichael
- Department of Biochemistry, Mass Spectrometry Research Center Laboratory, Vanderbilt University, Nashville, Tennessee, USA
| | - Alberto G Delgado
- Division of Gastroenterology, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Alese E Halvorson
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Robert A Greevy
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Lydia E Wroblewski
- Division of Gastroenterology, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Ayushi Sharma
- Creighton University School of Medicine, Omaha, Nebraska, USA
| | | | - Margaret M Allaman
- Division of Gastroenterology, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Keith T Wilson
- Division of Gastroenterology, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Department of Veterans Affairs, Tennessee Valley Healthcare System, Nashville, Tennessee, USA
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - M Kay Washington
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - M Wade Calcutt
- Department of Biochemistry, Mass Spectrometry Research Center Laboratory, Vanderbilt University, Nashville, Tennessee, USA
| | - Kevin L Schey
- Department of Biochemistry, Mass Spectrometry Research Center Laboratory, Vanderbilt University, Nashville, Tennessee, USA
| | - Bethany P Cummings
- Department of Surgery, University of California, Davis, Davis, California, USA
| | - Charles R Flynn
- Department of Surgery, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Joseph P Zackular
- Division of Protective Immunity, and
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Richard M Peek
- Division of Gastroenterology, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
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26
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Gobert AP, Latour YL, Asim M, Barry DP, Allaman MM, Finley JL, Smith TM, McNamara KM, Singh K, Sierra JC, Delgado AG, Luis PB, Schneider C, Washington MK, Piazuelo MB, Zhao S, Coburn LA, Wilson KT. Protective Role of Spermidine in Colitis and Colon Carcinogenesis. Gastroenterology 2022; 162:813-827.e8. [PMID: 34767785 PMCID: PMC8881368 DOI: 10.1053/j.gastro.2021.11.005] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 10/27/2021] [Accepted: 11/02/2021] [Indexed: 12/15/2022]
Abstract
BACKGROUND & AIMS Because inflammatory bowel disease is increasing worldwide and can lead to colitis-associated carcinoma (CAC), new interventions are needed. We have shown that spermine oxidase (SMOX), which generates spermidine (Spd), regulates colitis. Here we determined whether Spd treatment reduces colitis and carcinogenesis. METHODS SMOX was quantified in human colitis and associated dysplasia using quantitative reverse-transcription polymerase chain reaction and immunohistochemistry. We used wild-type (WT) and Smox-/- C57BL/6 mice treated with dextran sulfate sodium (DSS) or azoxymethane (AOM)-DSS as models of colitis and CAC, respectively. Mice with epithelial-specific deletion of Apc were used as a model of sporadic colon cancer. Animals were supplemented or not with Spd in the drinking water. Colonic polyamines, inflammation, tumorigenesis, transcriptomes, and microbiomes were assessed. RESULTS SMOX messenger RNA levels were decreased in human ulcerative colitis tissues and inversely correlated with disease activity, and SMOX protein was reduced in colitis-associated dysplasia. DSS colitis and AOM-DSS-induced dysplasia and tumorigenesis were worsened in Smox-/- vs WT mice and improved in both genotypes with Spd. Tumor development caused by Apc deletion was also reduced by Spd. Smox deletion and AOM-DSS treatment were both strongly associated with increased expression of α-defensins, which was reduced by Spd. A shift in the microbiome, with reduced abundance of Prevotella and increased Proteobacteria and Deferribacteres, occurred in Smox-/- mice and was reversed with Spd. CONCLUSIONS Loss of SMOX is associated with exacerbated colitis and CAC, increased α-defensin expression, and dysbiosis of the microbiome. Spd supplementation reverses these phenotypes, indicating that it has potential as an adjunctive treatment for colitis and chemopreventive for colon carcinogenesis.
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Affiliation(s)
- Alain P Gobert
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee; Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center, Nashville, Tennessee; Program in Cancer Biolog Vanderbilt University Medical Center, Nashville, Tennessee
| | - Yvonne L Latour
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee; Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Mohammad Asim
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Daniel P Barry
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Margaret M Allaman
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Jordan L Finley
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Thaddeus M Smith
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Kara M McNamara
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee; Program in Cancer Biolog Vanderbilt University Medical Center, Nashville, Tennessee
| | - Kshipra Singh
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee; Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Johanna C Sierra
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee; Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Alberto G Delgado
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Paula B Luis
- Department of Pharmacology, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Claus Schneider
- Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center, Nashville, Tennessee; Department of Pharmacology, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - M Kay Washington
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee
| | - M Blanca Piazuelo
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee; Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Shilin Zhao
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Lori A Coburn
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee; Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center, Nashville, Tennessee; Program in Cancer Biolog Vanderbilt University Medical Center, Nashville, Tennessee; Veterans Affairs Tennessee Valley Healthcare System, Nashville, Tennessee
| | - Keith T Wilson
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee; Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center, Nashville, Tennessee; Program in Cancer Biolog Vanderbilt University Medical Center, Nashville, Tennessee; Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee; Veterans Affairs Tennessee Valley Healthcare System, Nashville, Tennessee.
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27
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Gobert AP, Wilson KT. Induction and Regulation of the Innate Immune Response in Helicobacter pylori Infection. Cell Mol Gastroenterol Hepatol 2022; 13:1347-1363. [PMID: 35124288 PMCID: PMC8933844 DOI: 10.1016/j.jcmgh.2022.01.022] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 01/25/2022] [Accepted: 01/25/2022] [Indexed: 12/30/2022]
Abstract
Gastric cancer (GC) is the fifth most common cancer and the fourth most common cause of cancer-related death worldwide. The intestinal type of GC progresses from acute to chronic gastritis, multifocal atrophic gastritis, intestinal metaplasia, dysplasia, and carcinoma. Infection of the stomach by Helicobacter pylori, a Gram-negative bacterium that infects approximately 50% of the world's population, is the causal determinant that initiates the gastric inflammation and then disease progression. In this context, the induction of the innate immune response of gastric epithelial cells and myeloid cells by H. pylori effectors plays a critical role in the outcome of the infection. However, only 1% to 3% of infected patients develop gastric adenocarcinoma, emphasizing that other mechanisms regulate the localized non-specific response, including the gastric microbiota and genetic factors. This review summarizes studies describing the factors that induce and regulate the mucosal innate immune response during H. pylori infection.
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Affiliation(s)
- Alain P Gobert
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Nashville, Tennessee; Center for Mucosal Inflammation and Cancer, Nashville, Tennessee; Program in Cancer Biology, Nashville, Tennessee.
| | - Keith T Wilson
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Nashville, Tennessee; Center for Mucosal Inflammation and Cancer, Nashville, Tennessee; Program in Cancer Biology, Nashville, Tennessee; Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee; Veterans Affairs Tennessee Valley Healthcare System, Nashville, Tennessee.
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28
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Cui C, Asad Z, Dean WF, Smith IT, Madden C, Bao S, Landman BA, Roland JT, Coburn LA, Wilson KT, Zwerner JP, Zhao S, Wheless LE, Huo Y. Multi-modal Learning with Missing Data for Cancer Diagnosis Using Histopathological and Genomic Data. Proc SPIE Int Soc Opt Eng 2022; 12033:120331D. [PMID: 36304178 PMCID: PMC9605813 DOI: 10.1117/12.2612318] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Multi-modal learning (e.g., integrating pathological images with genomic features) tends to improve the accuracy of cancer diagnosis and prognosis as compared to learning with a single modality. However, missing data is a common problem in clinical practice, i.e., not every patient has all modalities available. Most of the previous works directly discarded samples with missing modalities, which might lose information in these data and increase the likelihood of overfitting. In this work, we generalize the multi-modal learning in cancer diagnosis with the capacity of dealing with missing data using histological images and genomic data. Our integrated model can utilize all available data from patients with both complete and partial modalities. The experiments on the public TCGA-GBM and TCGA-LGG datasets show that the data with missing modalities can contribute to multi-modal learning, which improves the model performance in grade classification of glioma cancer.
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Affiliation(s)
- Can Cui
- Department of Computer Science, Vanderbilt University, Nashville, TN 37235, USA
| | - Zuhayr Asad
- Department of Computer Science, Vanderbilt University, Nashville, TN 37235, USA
| | - William F Dean
- College of Arts and Science, Vanderbilt University, Nashville, TN 37235, USA
| | - Isabelle T Smith
- College of Arts and Science, Vanderbilt University, Nashville, TN 37235, USA
| | - Christopher Madden
- College of Medicine, SUNY Downstate Health Science University, Brooklyn, NY 11203, USA
| | - Shunxing Bao
- Department of Electrical and Computer Engineering, Vanderbilt University, Nashville, TN 37235, USA
| | - Bennett A Landman
- Department of Electrical and Computer Engineering, Vanderbilt University, Nashville, TN 37235, USA
- Department of Computer Science, Vanderbilt University, Nashville, TN 37235, USA
| | - Joseph T Roland
- Department of Surgery, Vanderbilt University Medical Center, Nashville, TN 37215, USA
| | - Lori A Coburn
- Division of Gastroenterology Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37215, USA
| | - Keith T Wilson
- Division of Gastroenterology Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37215, USA
| | - Jeffrey P Zwerner
- Department of Dermatology, Vanderbilt University Medical Center, Nashville, TN 37215, USA
| | - Shilin Zhao
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN 37215, USA
| | - Lee E Wheless
- Department of Dermatology, Vanderbilt University Medical Center, Nashville, TN 37215, USA
| | - Yuankai Huo
- Department of Computer Science, Vanderbilt University, Nashville, TN 37235, USA
- Department of Electrical and Computer Engineering, Vanderbilt University, Nashville, TN 37235, USA
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29
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Bao S, Tang Y, Lee HH, Gao R, Yang Q, Yu X, Chiron S, Coburn LA, Wilson KT, Roland JT, Landman BA, Huo Y. Inpainting Missing Tissue in Multiplexed Immunofluorescence Imaging. Proc SPIE Int Soc Opt Eng 2022; 12039:120390K. [PMID: 35531320 PMCID: PMC9070577 DOI: 10.1117/12.2611827] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Multiplex immunofluorescence (MxIF) is an emerging technique that allows for staining multiple cellular and histological markers to stain simultaneously on a single tissue section. However, with multiple rounds of staining and bleaching, it is inevitable that the scarce tissue may be physically depleted. Thus, a digital way of synthesizing such missing tissue would be appealing since it would increase the useable areas for the downstream single-cell analysis. In this work, we investigate the feasibility of employing generative adversarial network (GAN) approaches to synthesize missing tissues using 11 MxIF structural molecular markers (i.e., epithelial and stromal). Briefly, we integrate a multi-channel high-resolution image synthesis approach to synthesize the missing tissue from the remaining markers. The performance of different methods is quantitatively evaluated via the downstream cell membrane segmentation task. Our contribution is that we, for the first time, assess the feasibility of synthesizing missing tissues in MxIF via quantitative segmentation. The proposed synthesis method has comparable reproducibility with the baseline method on performance for the missing tissue region reconstruction only, but it improves 40% on whole tissue synthesis that is crucial for practical application. We conclude that GANs are a promising direction of advancing MxIF imaging with deep image synthesis.
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Affiliation(s)
- Shunxing Bao
- Dept. of Electrical and Computer Engineering, Vanderbilt University, Nashville, TN, USA
- Dept. of Computer Science, Vanderbilt University, Nashville, TN, USA
| | - Yucheng Tang
- Dept. of Computer Science, Vanderbilt University, Nashville, TN, USA
| | - Ho Hin Lee
- Dept. of Electrical and Computer Engineering, Vanderbilt University, Nashville, TN, USA
| | - Riqiang Gao
- Dept. of Electrical and Computer Engineering, Vanderbilt University, Nashville, TN, USA
| | - Qi Yang
- Dept. of Computer Science, Vanderbilt University, Nashville, TN, USA
| | - Xin Yu
- Dept. of Computer Science, Vanderbilt University, Nashville, TN, USA
| | - Sophie Chiron
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Lori A Coburn
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt Center for Mucosal Inflammation and Cancer, Nashville, TN, USA
- Dept. of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
- Veterans Affairs Tennessee Valley Healthcare System, Nashville, TN, USA
| | - Keith T Wilson
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt Center for Mucosal Inflammation and Cancer, Nashville, TN, USA
- Program in Cancer Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
- Dept. of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
- Veterans Affairs Tennessee Valley Healthcare System, Nashville, TN, USA
| | - Joseph T Roland
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Bennett A Landman
- Dept. of Electrical and Computer Engineering, Vanderbilt University, Nashville, TN, USA
- Dept. of Computer Science, Vanderbilt University, Nashville, TN, USA
| | - Yuankai Huo
- Dept. of Electrical and Computer Engineering, Vanderbilt University, Nashville, TN, USA
- Dept. of Computer Science, Vanderbilt University, Nashville, TN, USA
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30
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Ray AK, Luis PB, Mishra SK, Barry DP, Asim M, Pandey A, Chaturvedi M, Gupta J, Gupta S, Mahant S, Das R, Kumar P, Shalimar, Wilson KT, Schneider C, Chaturvedi R. Curcumin Oxidation Is Required for Inhibition of Helicobacter pylori Growth, Translocation and Phosphorylation of Cag A. Front Cell Infect Microbiol 2022; 11:765842. [PMID: 35004346 PMCID: PMC8740292 DOI: 10.3389/fcimb.2021.765842] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [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: 08/27/2021] [Accepted: 12/02/2021] [Indexed: 01/22/2023] Open
Abstract
Curcumin is a potential natural remedy for preventing Helicobacter pylori-associated gastric inflammation and cancer. Here, we analyzed the effect of a phospholipid formulation of curcumin on H. pylori growth, translocation and phosphorylation of the virulence factor CagA and host protein kinase Src in vitro and in an in vivo mouse model of H. pylori infection. Growth of H. pylori was inhibited dose-dependently by curcumin in vitro. H. pylori was unable to metabolically reduce curcumin, whereas two enterobacteria, E. coli and Citrobacter rodentium, which efficiently reduced curcumin to the tetra- and hexahydro metabolites, evaded growth inhibition. Oxidative metabolism of curcumin was required for the growth inhibition of H. pylori and the translocation and phosphorylation of CagA and cSrc, since acetal- and diacetal-curcumin that do not undergo oxidative transformation were ineffective. Curcumin attenuated mRNA expression of the H. pylori virulence genes cagE and cagF in a dose-dependent manner and inhibited translocation and phosphorylation of CagA in gastric epithelial cells. H. pylori strains isolated from dietary curcumin-treated mice showed attenuated ability to induce cSrc phosphorylation and the mRNA expression of the gene encoding for IL-8, suggesting long-lasting effects of curcumin on the virulence of H. pylori. Our work provides mechanistic evidence that encourages testing of curcumin as a dietary approach to inhibit the virulence of CagA.
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Affiliation(s)
- Ashwini Kumar Ray
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, India.,Department of Microbiology, Saheed Rajguru College of Applied Sciences for Women, University of Delhi, New Delhi, India.,Department of Environmental Studies, University of Delhi, New Delhi, India
| | - Paula B Luis
- Department of Pharmacology and Vanderbilt Institute of Chemical Biology, Vanderbilt University School of Medicine, Nashville, TN, United States
| | | | - Daniel P Barry
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Mohammad Asim
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Achyut Pandey
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | - Maya Chaturvedi
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | - Jyoti Gupta
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | - Shilpi Gupta
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | - Shweta Mahant
- Centre for Medical Biotechnology, Amity Institute of Biotechnology, Amity University, Noida, India
| | - Rajashree Das
- Centre for Medical Biotechnology, Amity Institute of Biotechnology, Amity University, Noida, India
| | - Pramod Kumar
- Department of Chemistry, Sri Aurobindo College, University of Delhi, New Delhi, India
| | - Shalimar
- Department of Gastroenterology and Human Nutrition Unit, All India Institute of Medical Sciences, New Delhi, India
| | - Keith T Wilson
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, United States.,Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center, Nashville, TN, United States.,Veterans Affairs Tennessee Valley Healthcare System, Nashville, TN, United States
| | - Claus Schneider
- Department of Pharmacology and Vanderbilt Institute of Chemical Biology, Vanderbilt University School of Medicine, Nashville, TN, United States
| | - Rupesh Chaturvedi
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
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31
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Bao S, Chiron S, Tang Y, Heiser CN, Southard-Smith AN, Lee HH, Ramirez MA, Huo Y, Washington MK, Scoville EA, Roland JT, Liu Q, Lau KS, Wilson KT, Coburn LA, Landman BA. A cross-platform informatics system for the Gut Cell Atlas: integrating clinical, anatomical and histological data. Proc SPIE Int Soc Opt Eng 2021; 11601. [PMID: 34539029 DOI: 10.1117/12.2581074] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
The Gut Cell Atlas (GCA), an initiative funded by the Helmsley Charitable Trust, seeks to create a reference platform to understand the human gut, with a specific focus on Crohn's disease. Although a primary focus of the GCA is on focusing on single-cell profiling, we seek to provide a framework to integrate other analyses on multi-modality data such as electronic health record data, radiological images, and histology tissues/images. Herein, we use the research electronic data capture (REDCap) system as the central tool for a secure web application that supports protected health information (PHI) restricted access. Our innovations focus on addressing the challenges with tracking all specimens and biopsies, validating manual data entry at scale, and sharing organizational data across the group. We present a scalable, cross-platform barcode printing/record system that integrates with REDCap. The central informatics infrastructure to support our design is a tuple table to track longitudinal data entry and sample tracking. The current data collection (by December 2020) is illustrated with types and formats of the data that the system collects. We estimate that one terabyte is needed for data storage per patient study. Our proposed data sharing informatics system addresses the challenges with integrating physical sample tracking, large files, and manual data entry with REDCap.
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Affiliation(s)
- Shunxing Bao
- Dept. of Electrical Engineering and Computer Science, Vanderbilt University, Nashville, TN, USA
| | - Sophie Chiron
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Yucheng Tang
- Dept. of Electrical Engineering and Computer Science, Vanderbilt University, Nashville, TN, USA
| | - Cody N Heiser
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, USA.,Chemical and Physical Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Austin N Southard-Smith
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, USA.,Dept. of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Ho Hin Lee
- Dept. of Electrical Engineering and Computer Science, Vanderbilt University, Nashville, TN, USA
| | - Marisol A Ramirez
- Dept. of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA.,Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Yuankai Huo
- Dept. of Electrical Engineering and Computer Science, Vanderbilt University, Nashville, TN, USA.,Data science institute, Vanderbilt University, Nashville, TN, USA
| | - Mary K Washington
- Dept. of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Elizabeth A Scoville
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Joseph T Roland
- Dept. of Surgery, Vanderbilt University Medical Center, Nashville TN, USA.,Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Qi Liu
- Dept. of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA.,Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Ken S Lau
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, USA.,Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, TN, USA.,Dept. of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Keith T Wilson
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA.,Vanderbilt Center for Mucosal Inflammation and Cancer, Nashville, TN, USA.,Dept. of Cancer Biology, Vanderbilt University School of Medicine, Nashville, TN, USA.,Dept. of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA.,Veterans Affairs Tennessee Valley Healthcare System, Nashville, TN, USA
| | - Lori A Coburn
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA.,Vanderbilt Center for Mucosal Inflammation and Cancer, Nashville, TN, USA.,Dept. of Cancer Biology, Vanderbilt University School of Medicine, Nashville, TN, USA.,Veterans Affairs Tennessee Valley Healthcare System, Nashville, TN, USA
| | - Bennett A Landman
- Dept. of Electrical Engineering and Computer Science, Vanderbilt University, Nashville, TN, USA.,Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA.,Institute of Image Science, Vanderbilt University Medical Center, Nashville, TN, USA
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32
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Bao S, Tang Y, Lee HH, Gao R, Chiron S, Lyu I, Coburn LA, Wilson KT, Roland JT, Landman BA, Huo Y. Random Multi-Channel Image Synthesis for Multiplexed Immunofluorescence Imaging. Proc Mach Learn Res 2021; 156:36-46. [PMID: 34993490 PMCID: PMC8730359] [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] [Grants] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
Abstract
Multiplex immunofluorescence (MxIF) is an emerging imaging technique that produces the high sensitivity and specificity of single-cell mapping. With a tenet of "seeing is believing", MxIF enables iterative staining and imaging extensive antibodies, which provides comprehensive biomarkers to segment and group different cells on a single tissue section. However, considerable depletion of the scarce tissue is inevitable from extensive rounds of staining and bleaching ("missing tissue"). Moreover, the immunofluorescence (IF) imaging can globally fail for particular rounds ("missing stain"). In this work, we focus on the "missing stain" issue. It would be appealing to develop digital image synthesis approaches to restore missing stain images without losing more tissue physically. Herein, we aim to develop image synthesis approaches for eleven MxIF structural molecular markers (i.e., epithelial and stromal) on real samples. We propose a novel multi-channel high-resolution image synthesis approach, called pixN2N-HD, to tackle possible missing stain scenarios via a high-resolution generative adversarial network (GAN). Our contribution is three-fold: (1) a single deep network framework is proposed to tackle missing stain in MxIF; (2) the proposed "N-to-N" strategy reduces theoretical four years of computational time to 20 hours when covering all possible missing stains scenarios, with up to five missing stains (e.g., "(N-1)-to-1", "(N-2)-to-2"); and (3) this work is the first comprehensive experimental study of investigating cross-stain synthesis in MxIF. Our results elucidate a promising direction of advancing MxIF imaging with deep image synthesis.
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Affiliation(s)
- Shunxing Bao
- Dept. of Computer Science, Vanderbilt University, USA
| | - Yucheng Tang
- Dept. of Electrical and Computer Engineering, Vanderbilt University, USA
| | - Ho Hin Lee
- Dept. of Computer Science, Vanderbilt University, USA
| | - Riqiang Gao
- Dept. of Computer Science, Vanderbilt University, USA
| | - Sophie Chiron
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, USA
| | - Ilwoo Lyu
- Computer Science & Engineering, Ulsan National Institute of Science and Technology, South Korea
| | - Lori A Coburn
- Division of Gastroenterology, Hepatology, and Nutrition, Dept. of Medicine, Vanderbilt University Medical Center, USA
| | - Keith T Wilson
- Division of Gastroenterology, Hepatology, and Nutrition, Dept. of Medicine, Vanderbilt University Medical Center, USA
| | - Joseph T Roland
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Bennett A Landman
- Dept. of Electrical and Computer Engineering, Vanderbilt University, USA
| | - Yuankai Huo
- Dept. of Computer Science, Vanderbilt University, USA
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McNamara KM, Gobert AP, Wilson KT. The role of polyamines in gastric cancer. Oncogene 2021; 40:4399-4412. [PMID: 34108618 PMCID: PMC8262120 DOI: 10.1038/s41388-021-01862-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 05/07/2021] [Accepted: 05/24/2021] [Indexed: 02/05/2023]
Abstract
Advancements in our understanding of polyamine molecular and cellular functions have led to increased interest in targeting polyamine metabolism for anticancer therapeutic benefits. The polyamines putrescine, spermidine, and spermine are polycationic alkylamines commonly found in all living cells and are essential for cellular growth and survival. This review summarizes the existing research on polyamine metabolism and function, specifically the role of polyamines in gastric immune cell and epithelial cell function. Polyamines have been implicated in a multitude of cancers, but in this review, we focus on the role of polyamine dysregulation in the context of Helicobacter pylori-induced gastritis and subsequent progression to gastric cancer. Due to the emerging implication of polyamines in cancer development, there is an increasing number of promising clinical trials using agents to target the polyamine metabolic pathway for potential chemoprevention and anticancer therapy.
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Affiliation(s)
- Kara M. McNamara
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA,Program in Cancer Biology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Alain P. Gobert
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA,Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Keith T. Wilson
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA,Program in Cancer Biology, Vanderbilt University Medical Center, Nashville, TN, USA,Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center, Nashville, TN, USA,Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA,Veterans Affairs Tennessee Valley Healthcare System, Nashville, TN, USA
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Mannion A, Dzink-Fox J, Shen Z, Piazuelo MB, Wilson KT, Correa P, Peek RM, Camargo MC, Fox JG. Helicobacter pylori Antimicrobial Resistance and Gene Variants in High- and Low-Gastric-Cancer-Risk Populations. J Clin Microbiol 2021; 59:e03203-20. [PMID: 33692136 PMCID: PMC8091839 DOI: 10.1128/jcm.03203-20] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [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: 12/23/2020] [Accepted: 02/28/2021] [Indexed: 02/07/2023] Open
Abstract
Colombia, South America has one of the world's highest burdens of Helicobacter pylori infection and gastric cancer. While multidrug antibiotic regimens can effectively eradicate H. pylori, treatment efficacy is being jeopardized by the emergence of antibiotic-resistant H. pylori strains. Moreover, the spectrum of and genetic mechanisms for antibiotic resistance in Colombia is underreported. In this study, 28 H. pylori strains isolated from gastric biopsy specimens from a high-gastric-cancer-risk (HGCR) population living in the Andes Mountains in Túquerres, Colombia and 31 strains from a low-gastric-cancer-risk (LGCR) population residing on the Pacific coast in Tumaco, Colombia were subjected to antibiotic susceptibility testing for amoxicillin, clarithromycin, levofloxacin, metronidazole, rifampin, and tetracycline. Resistance-associated genes were amplified by PCR for all isolates, and 29 isolates were whole-genome sequenced (WGS). No strains were resistant to amoxicillin, clarithromycin, or rifampin. One strain was resistant to tetracycline and had an A926G mutation in its 16S rRNA gene. Levofloxacin resistance was observed in 12/59 isolates and was significantly associated with N87I/K and/or D91G/Y mutations in gyrA Most isolates were resistant to metronidazole; this resistance was significantly higher in the LGCR (31/31) group compared to the HGCR (24/28) group. Truncations in rdxA and frxA were present in nearly all metronidazole-resistant strains. There was no association between phylogenetic relationship and resistance profiles based on WGS analysis. Our results indicate H. pylori isolates from Colombians exhibit multidrug antibiotic resistance. Continued surveillance of H. pylori antibiotic resistance in Colombia is warranted in order to establish appropriate eradication treatment regimens for this population.
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Affiliation(s)
- Anthony Mannion
- Division of Comparative Medicine, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - JoAnn Dzink-Fox
- Division of Comparative Medicine, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Zeli Shen
- Division of Comparative Medicine, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | | | | | | | | | - M Constanza Camargo
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland, USA
| | - James G Fox
- Division of Comparative Medicine, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
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Short SP, Pilat JM, Barrett CW, Reddy VK, Haberman Y, Hendren JR, Marsh BJ, Keating CE, Motley AK, Hill KE, Zemper AE, Washington MK, Shi C, Chen X, Wilson KT, Hyams JS, Denson LA, Burk RF, Rosen MJ, Williams CS. Colonic Epithelial-Derived Selenoprotein P Is the Source for Antioxidant-Mediated Protection in Colitis-Associated Cancer. Gastroenterology 2021; 160:1694-1708.e3. [PMID: 33388316 PMCID: PMC8035252 DOI: 10.1053/j.gastro.2020.12.059] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 12/07/2020] [Accepted: 12/23/2020] [Indexed: 02/07/2023]
Abstract
BACKGROUND & AIMS Patients with inflammatory bowel disease (IBD) demonstrate nutritional selenium deficiencies and are at greater risk of developing colon cancer. Previously, we determined that global reduction of the secreted antioxidant selenium-containing protein, selenoprotein P (SELENOP), substantially increased tumor development in an experimental colitis-associated cancer (CAC) model. We next sought to delineate tissue-specific contributions of SELENOP to intestinal inflammatory carcinogenesis and define clinical context. METHODS Selenop floxed mice crossed with Cre driver lines to delete Selenop from the liver, myeloid lineages, or intestinal epithelium were placed on an azoxymethane/dextran sodium sulfate experimental CAC protocol. SELENOP loss was assessed in human ulcerative colitis (UC) organoids, and expression was queried in human and adult UC samples. RESULTS Although large sources of SELENOP, both liver- and myeloid-specific Selenop deletion failed to modify azoxymethane/dextran sodium sulfate-mediated tumorigenesis. Instead, epithelial-specific deletion increased CAC tumorigenesis, likely due to elevated oxidative stress with a resulting increase in genomic instability and augmented tumor initiation. SELENOP was down-regulated in UC colon biopsies and levels were inversely correlated with endoscopic disease severity and tissue S100A8 (calprotectin) gene expression. CONCLUSIONS Although global selenium status is typically assessed by measuring liver-derived plasma SELENOP levels, our results indicate that the peripheral SELENOP pool is dispensable for CAC. Colonic epithelial SELENOP is the main contributor to local antioxidant capabilities. Thus, colonic SELENOP is the most informative means to assess selenium levels and activity in IBD patients and may serve as a novel biomarker for UC disease severity and identify patients most predisposed to CAC development.
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Affiliation(s)
- Sarah P Short
- Department of Medicine, Division of Gastroenterology, Vanderbilt University Medical Center, Nashville, Tennessee; Program in Cancer Biology, Vanderbilt University, Nashville, Tennessee; Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Jennifer M Pilat
- Department of Medicine, Division of Gastroenterology, Vanderbilt University Medical Center, Nashville, Tennessee; Program in Cancer Biology, Vanderbilt University, Nashville, Tennessee
| | - Caitlyn W Barrett
- Department of Medicine, Division of Gastroenterology, Vanderbilt University Medical Center, Nashville, Tennessee; Program in Cancer Biology, Vanderbilt University, Nashville, Tennessee
| | - Vishruth K Reddy
- Department of Medicine, Division of Gastroenterology, Vanderbilt University Medical Center, Nashville, Tennessee; Program in Cancer Biology, Vanderbilt University, Nashville, Tennessee; Department of Radiation Oncology, Perelman School of Medicine of the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Yael Haberman
- Division of Gastroenterology, Hepatology and Nutrition, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio; Sheba Medical Center, Tel Hashomer, affiliated with the Tel Aviv University, Tel Aviv, Israel
| | - Jared R Hendren
- Department of Medicine, Division of Gastroenterology, Vanderbilt University Medical Center, Nashville, Tennessee; School of Medicine, Southern Illinois University, Springfield, Illinois
| | - Benjamin J Marsh
- Department of Medicine, Division of Gastroenterology, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Cody E Keating
- Department of Medicine, Division of Gastroenterology, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Amy K Motley
- Department of Medicine, Division of Gastroenterology, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Kristina E Hill
- Department of Medicine, Division of Gastroenterology, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Anne E Zemper
- Department of Biology, University of Oregon, Eugene, Oregon; Institute of Molecular Biology, University of Oregon, Eugene, Oregon
| | - M Kay Washington
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Chanjuan Shi
- Department of Pathology, Duke University School of Medicine, Durham, North Carolina
| | - Xi Chen
- Department of Public Health Sciences and the Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, Florida
| | - Keith T Wilson
- Department of Medicine, Division of Gastroenterology, Vanderbilt University Medical Center, Nashville, Tennessee; Program in Cancer Biology, Vanderbilt University, Nashville, Tennessee; Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center, Nashville, Tennessee; Veterans Affairs Tennessee Valley Health Care System, Nashville, Tennessee; Vanderbilt Ingram Cancer Center, Nashville, Tennessee
| | - Jeffrey S Hyams
- Connecticut Children's Medical Center, Hartford, Connecticut
| | - Lee A Denson
- Division of Gastroenterology, Hepatology and Nutrition, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - Raymond F Burk
- Department of Medicine, Division of Gastroenterology, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Michael J Rosen
- Division of Gastroenterology, Hepatology and Nutrition, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - Christopher S Williams
- Department of Medicine, Division of Gastroenterology, Vanderbilt University Medical Center, Nashville, Tennessee; Program in Cancer Biology, Vanderbilt University, Nashville, Tennessee; Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center, Nashville, Tennessee; Veterans Affairs Tennessee Valley Health Care System, Nashville, Tennessee; Vanderbilt Ingram Cancer Center, Nashville, Tennessee.
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Gobert AP, Boutaud O, Asim M, Zagol-Ikapitte IA, Delgado AG, Latour YL, Finley JL, Singh K, Verriere TG, Allaman MM, Barry DP, McNamara KM, Sierra JC, Amarnath V, Tantawy MN, Bimczok D, Piazuelo MB, Washington MK, Zhao S, Coburn LA, Wilson KT. Dicarbonyl Electrophiles Mediate Inflammation-Induced Gastrointestinal Carcinogenesis. Gastroenterology 2021; 160:1256-1268.e9. [PMID: 33189701 PMCID: PMC7956217 DOI: 10.1053/j.gastro.2020.11.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 10/23/2020] [Accepted: 11/06/2020] [Indexed: 02/08/2023]
Abstract
BACKGROUND & AIMS Inflammation in the gastrointestinal tract may lead to the development of cancer. Dicarbonyl electrophiles, such as isolevuglandins (isoLGs), are generated from lipid peroxidation during the inflammatory response and form covalent adducts with amine-containing macromolecules. Thus, we sought to determine the role of dicarbonyl electrophiles in inflammation-associated carcinogenesis. METHODS The formation of isoLG adducts was analyzed in the gastric tissues of patients infected with Helicobacter pylori from gastritis to precancerous intestinal metaplasia, in human gastric organoids, and in patients with colitis and colitis-associated carcinoma (CAC). The effect on cancer development of a potent scavenger of dicarbonyl electrophiles, 5-ethyl-2-hydroxybenzylamine (EtHOBA), was determined in transgenic FVB/N insulin-gastrin (INS-GAS) mice and Mongolian gerbils as models of H pylori-induced carcinogenesis and in C57BL/6 mice treated with azoxymethane-dextran sulfate sodium as a model of CAC. The effect of EtHOBA on mutations in gastric epithelial cells of H pylori-infected INS-GAS mice was assessed by whole-exome sequencing. RESULTS We show increased isoLG adducts in gastric epithelial cell nuclei in patients with gastritis and intestinal metaplasia and in human gastric organoids infected with H pylori. EtHOBA inhibited gastric carcinoma in infected INS-GAS mice and gerbils and attenuated isoLG adducts, DNA damage, and somatic mutation frequency. Additionally, isoLG adducts were elevated in tissues from patients with colitis, colitis-associated dysplasia, and CAC as well as in dysplastic tumors of C57BL/6 mice treated with azoxymethane-dextran sulfate sodium. In this model, EtHOBA significantly reduced adduct formation, tumorigenesis, and dysplasia severity. CONCLUSIONS Dicarbonyl electrophiles represent a link between inflammation and somatic genomic alterations and are thus key targets for cancer chemoprevention.
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Affiliation(s)
- Alain P. Gobert
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA.,Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Olivier Boutaud
- Department of Pharmacology, Vanderbilt University School of Medicine, Nashville, Tennessee.
| | - Mohammad Asim
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Irene A. Zagol-Ikapitte
- Department of Biochemistry, Mass Spectrometry Research Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Alberto G. Delgado
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Yvonne L. Latour
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA.,Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jordan L. Finley
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Kshipra Singh
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA.,Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Thomas G. Verriere
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Margaret M. Allaman
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Daniel P. Barry
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Kara M. McNamara
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Johanna C. Sierra
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA.,Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Venkataraman Amarnath
- Department of Pharmacology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Mohammed N. Tantawy
- Vanderbilt University Institute of Imaging Science, Vanderbilt University Medical Center, Nashville, TN, USA.,Department of Radiology and Radiological Sciences, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Diane Bimczok
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, USA
| | - M. Blanca Piazuelo
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA.,Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center, Nashville, TN, USA
| | - M. Kay Washington
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA.,Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center, Nashville, TN, USA.,Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Shilin Zhao
- Department of Biostatistics, 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, USA.,Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center, Nashville, TN, USA.,Veterans Affairs Tennessee Valley Healthcare System, Nashville, TN, USA
| | - Keith T. Wilson
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA.,Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center, Nashville, TN, USA.,Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA.,Veterans Affairs Tennessee Valley Healthcare System, Nashville, TN, USA
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Piazuelo MB, Bravo LE, Mera RM, Camargo MC, Bravo JC, Delgado AG, Washington MK, Rosero A, Garcia LS, Realpe JL, Cifuentes SP, Morgan DR, Peek RM, Correa P, Wilson KT. The Colombian Chemoprevention Trial: 20-Year Follow-Up of a Cohort of Patients With Gastric Precancerous Lesions. Gastroenterology 2021; 160:1106-1117.e3. [PMID: 33220252 PMCID: PMC7956231 DOI: 10.1053/j.gastro.2020.11.017] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 11/10/2020] [Accepted: 11/12/2020] [Indexed: 02/08/2023]
Abstract
BACKGROUND & AIMS Helicobacter pylori eradication and endoscopic surveillance of gastric precancerous lesions are strategies to reduce gastric cancer (GC) risk. To our knowledge, this study is the longest prospective cohort of an H pylori eradication trial in a Hispanic population. METHODS A total of 800 adults with precancerous lesions were randomized to anti-H pylori treatment or placebo. Gastric biopsy samples taken at baseline and 3, 6, 12, 16, and 20 years were assessed by our Correa histopathology score. A generalized linear mixed model with a participant-level random intercept was used to estimate the effect of H pylori status on the score over time. Logistic regression models were used to estimate progression by baseline diagnosis and to estimate GC risk by intestinal metaplasia (IM) subtype and anatomic location. RESULTS Overall, 356 individuals completed 20 years of follow-up. Anti-H pylori therapy (intention-to-treat) reduced progression of the Correa score (odds ratio [OR], 0.59; 95% confidence interval [CI], 0.38-0.93). H pylori-negative status had a beneficial effect on the score over time (P = .036). Among individuals with IM (including indefinite for dysplasia) at baseline, incidence rates per 100 person-years were 1.09 (95% CI, 0.85-1.33) for low-grade/high-grade dysplasia and 0.14 (95% CI, 0.06-0.22) for GC. Incomplete-type (vs complete-type) IM at baseline presented higher GC risk (OR, 13.4; 95% CI, 1.8-103.8). Individuals with corpus (vs antrum-restricted) IM showed an OR of 2.1 (95% CI, 0.7-6.6) for GC. CONCLUSIONS In a high-GC-risk Hispanic population, anti-H pylori therapy had a long-term beneficial effect against histologic progression. Incomplete IM is a strong predictor of GC risk.
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Affiliation(s)
- M. Blanca Piazuelo
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA,Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Luis E. Bravo
- Department of Pathology, Universidad del Valle School of Medicine, Cali, Valle del Cauca, Colombia
| | - Robertino M. Mera
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - M. Constanza Camargo
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Juan C. Bravo
- Department of Pathology, Universidad del Valle School of Medicine, Cali, Valle del Cauca, Colombia
| | - Alberto G. Delgado
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - M. Kay Washington
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | | | - Luz S. Garcia
- Department of Pathology, Universidad del Valle School of Medicine, Cali, Valle del Cauca, Colombia
| | | | | | - Douglas R. Morgan
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA,Division of Gastroenterology, Department of Medicine, University of Alabama, Birmingham, AL, USA
| | - Richard M. Peek
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA,Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center, Nashville, TN, USA,Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Pelayo Correa
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Keith T. Wilson
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA,Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center, Nashville, TN, USA,Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA,Veterans Affairs Tennessee Valley Healthcare System, Nashville, TN, USA
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Palrasu M, Zaika E, El-Rifai W, Garcia-Buitrago M, Piazuelo MB, Wilson KT, Peek RM, Zaika AI. Bacterial CagA protein compromises tumor suppressor mechanisms in gastric epithelial cells. J Clin Invest 2021; 130:2422-2434. [PMID: 32250340 DOI: 10.1172/jci130015] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [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: 05/03/2019] [Accepted: 01/22/2020] [Indexed: 01/01/2023] Open
Abstract
Approximately half of the world's population is infected with the stomach pathogen Helicobacter pylori. Infection with H. pylori is the main risk factor for distal gastric cancer. Bacterial virulence factors, such as the oncoprotein CagA, augment cancer risk. Yet despite high infection rates, only a fraction of H. pylori-infected individuals develop gastric cancer. This raises the question of defining the specific host and bacterial factors responsible for gastric tumorigenesis. To investigate the tumorigenic determinants, we analyzed gastric tissues from human subjects and animals infected with H. pylori bacteria harboring different CagA status. For laboratory studies, well-defined H. pylori strain B128 and its cancerogenic derivative strain 7.13, as well as various bacterial isogenic mutants were employed. We found that H. pylori compromises key tumor suppressor mechanisms: the host stress and apoptotic responses. Our studies showed that CagA induces phosphorylation of XIAP E3 ubiquitin ligase, which enhances ubiquitination and proteasomal degradation of the host proapoptotic factor Siva1. This process is mediated by the PI3K/Akt pathway. Inhibition of Siva1 by H. pylori increases survival of human cells with damaged DNA. It occurs in a strain-specific manner and is associated with the ability to induce gastric tumor.
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Affiliation(s)
- Manikandan Palrasu
- Department of Surgery, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Elena Zaika
- Department of Surgery, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Wael El-Rifai
- Department of Surgery, University of Miami Miller School of Medicine, Miami, Florida, USA.,Department of Veterans Affairs, Miami VA Healthcare System, Miami, Florida, USA
| | - Monica Garcia-Buitrago
- Department of Pathology, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Maria Blanca Piazuelo
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Keith T Wilson
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA.,Department of Veterans Affairs, VA Tennessee Valley Health Care System, Nashville, Tennessee, USA
| | - Richard M Peek
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Alexander I Zaika
- Department of Surgery, University of Miami Miller School of Medicine, Miami, Florida, USA.,Department of Veterans Affairs, Miami VA Healthcare System, Miami, Florida, USA
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Tyagi RK, Jacobse J, Li J, Allaman MM, Otipoby KL, Sampson ER, Wilson KT, Goettel JA. HLA-Restriction of Human Treg Cells Is Not Required for Therapeutic Efficacy of Low-Dose IL-2 in Humanized Mice. Front Immunol 2021; 12:630204. [PMID: 33717161 PMCID: PMC7945590 DOI: 10.3389/fimmu.2021.630204] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [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: 11/16/2020] [Accepted: 01/15/2021] [Indexed: 02/05/2023] Open
Abstract
Regulatory T (Treg) cells are essential to maintain immune homeostasis in the intestine and Treg cell dysfunction is associated with several inflammatory and autoimmune disorders including inflammatory bowel disease (IBD). Efforts using low-dose (LD) interleukin-2 (IL-2) to expand autologous Treg cells show therapeutic efficacy for several inflammatory conditions. Whether LD IL-2 is an effective strategy for treating patients with IBD is unknown. Recently, we demonstrated that LD IL-2 was protective against experimental colitis in immune humanized mice in which human CD4+ T cells were restricted to human leukocyte antigen (HLA). Whether HLA restriction is required for human Treg cells to ameliorate colitis following LD IL-2 therapy has not been demonstrated. Here, we show that treatment with LD IL-2 reduced 2,4,6-trinitrobenzensulfonic acid (TNBS) colitis severity in NOD.PrkdcscidIl2rg-/- (NSG) mice reconstituted with human CD34+ hematopoietic stem cells. These data demonstrate the utility of standard immune humanized NSG mice as a pre-clinical model system to evaluate therapeutics targeting human Treg cells to treat IBD.
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Affiliation(s)
- Rajeev K. Tyagi
- Division of Gastroenterology, Hepatology and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Justin Jacobse
- Division of Gastroenterology, Hepatology and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, United States
- Willem-Alexander Children’s Hospital, Department of Pediatrics, Leiden University Medical Center, Leiden, Netherlands
| | - Jing Li
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Margret M. Allaman
- Division of Gastroenterology, Hepatology and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Kevin L. Otipoby
- Pandion Therapeutics, Immunology Department, Watertown, MA, United States
| | - Erik R. Sampson
- Pandion Therapeutics, Immunology Department, Watertown, MA, United States
| | - Keith T. Wilson
- Division of Gastroenterology, Hepatology and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, United States
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, United States
- Program in Cancer Biology, Vanderbilt University School of Medicine, Nashville, TN, United States
- Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, TN, United States
- Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center, Nashville, TN, United States
- Veterans Affairs Tennessee Valley Healthcare System, Nashville, TN, United States
| | - Jeremy A. Goettel
- Division of Gastroenterology, Hepatology and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, United States
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, United States
- Program in Cancer Biology, Vanderbilt University School of Medicine, Nashville, TN, United States
- Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, TN, United States
- Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center, Nashville, TN, United States
- *Correspondence: Jeremy A. Goettel,
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Banerjee A, Herring CA, Chen B, Kim H, Simmons AJ, Southard-Smith AN, Allaman MM, White JR, Macedonia MC, Mckinley ET, Solano MAR, Scoville EA, Liu Q, Wilson KT, Coffey RJ, Washington MK, Goettel JA, Lau KS. Succinate Produced by Intestinal Microbes Promotes Specification of Tuft Cells to Suppress Ileal Inflammation. Gastroenterology 2020; 159:2101-2115.e5. [PMID: 32828819 PMCID: PMC7725941 DOI: 10.1053/j.gastro.2020.08.029] [Citation(s) in RCA: 98] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 08/12/2020] [Accepted: 08/15/2020] [Indexed: 12/20/2022]
Abstract
BACKGROUND & AIMS Countries endemic for parasitic infestations have a lower incidence of Crohn's disease (CD) than nonendemic countries, and there have been anecdotal reports of the beneficial effects of helminths in CD patients. Tuft cells in the small intestine sense and direct the immune response against eukaryotic parasites. We investigated the activities of tuft cells in patients with CD and mouse models of intestinal inflammation. METHODS We used microscopy to quantify tuft cells in intestinal specimens from patients with ileal CD (n = 19), healthy individuals (n = 14), and TNFΔARE/+ mice, which develop Crohn's-like ileitis. We performed single-cell RNA sequencing, mass spectrometry, and microbiome profiling of intestinal tissues from wild-type and Atoh1-knockout mice, which have expansion of tuft cells, to study interactions between microbes and tuft cell populations. We assessed microbe dependence of tuft cell populations using microbiome depletion, organoids, and microbe transplant experiments. We used multiplex imaging and cytokine assays to assess alterations in inflammatory response following expansion of tuft cells with succinate administration in TNFΔARE/+ and anti-CD3E CD mouse models. RESULTS Inflamed ileal tissues from patients and mice had reduced numbers of tuft cells, compared with healthy individuals or wild-type mice. Expansion of tuft cells was associated with increased expression of genes that regulate the tricarboxylic acid cycle, which resulted from microbe production of the metabolite succinate. Experiments in which we manipulated the intestinal microbiota of mice revealed the existence of an ATOH1-independent population of tuft cells that was sensitive to metabolites produced by microbes. Administration of succinate to mice expanded tuft cells and reduced intestinal inflammation in TNFΔARE/+ mice and anti-CD3E-treated mice, increased GATA3+ cells and type 2 cytokines (IL22, IL25, IL13), and decreased RORGT+ cells and type 17 cytokines (IL23) in a tuft cell-dependent manner. CONCLUSIONS We found that tuft cell expansion reduced chronic intestinal inflammation in mice. Strategies to expand tuft cells might be developed for treatment of CD.
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Affiliation(s)
- Amrita Banerjee
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA,Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Charles A. Herring
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA,Program in Chemical and Physical Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Bob Chen
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA,Program in Chemical and Physical Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Hyeyon Kim
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Alan J. Simmons
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA,Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Austin N. Southard-Smith
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA,Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Margaret M. Allaman
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA,Center Mucosal Inflammation and Cancer, Vanderbilt University Medical Center Nashville, TN 37232, USA
| | | | - Mary C. Macedonia
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA,Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Eliot T. Mckinley
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA,Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Marisol A. Ramirez Solano
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN 37232, USA,Center for Quantitative Sciences, Vanderbilt University School of Medicine, 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 Mucosal Inflammation and Cancer, Vanderbilt University Medical Center Nashville, TN 37232, USA
| | - Qi Liu
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN 37232, USA,Center for Quantitative Sciences, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Keith T. Wilson
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA,Center Mucosal Inflammation and Cancer, Vanderbilt University Medical Center Nashville, TN 37232, USA,Veterans Affairs Medical Center, Tennessee Valley Healthcare System, Nashville, TN,Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Robert J. Coffey
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA,Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - M. Kay Washington
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Jeremy A. Goettel
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA,Center Mucosal Inflammation and Cancer, Vanderbilt University Medical Center Nashville, TN 37232, USA,Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Ken S. Lau
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA,Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA,Program in Chemical and Physical Biology, Vanderbilt University, Nashville, TN 37232, USA,Center Mucosal Inflammation and Cancer, Vanderbilt University Medical Center Nashville, TN 37232, USA,Center for Quantitative Sciences, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
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41
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Gobert AP, Finley JL, Latour YL, Asim M, Smith TM, Verriere TG, Barry DP, Allaman MM, Delagado AG, Rose KL, Calcutt MW, Schey KL, Sierra JC, Piazuelo MB, Mirmira RG, Wilson KT. Hypusination Orchestrates the Antimicrobial Response of Macrophages. Cell Rep 2020; 33:108510. [PMID: 33326776 PMCID: PMC7812972 DOI: 10.1016/j.celrep.2020.108510] [Citation(s) in RCA: 20] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 10/28/2020] [Accepted: 11/18/2020] [Indexed: 12/21/2022] Open
Abstract
Innate responses of myeloid cells defend against pathogenic bacteria via inducible effectors. Deoxyhypusine synthase (DHPS) catalyzes the transfer of the N-moiety of spermidine to the lysine-50 residue of eukaryotic translation initiation factor 5A (EIF5A) to form the amino acid hypusine. Hypusinated EIF5A (EIF5AHyp) transports specific mRNAs to ribosomes for translation. We show that DHPS is induced in macrophages by two gastrointestinal pathogens, Helicobacter pylori and Citrobacter rodentium, resulting in enhanced hypusination of EIF5A. EIF5AHyp was also increased in gastric macrophages from patients with H. pylori gastritis. Furthermore, we identify the bacteria-induced immune effectors regulated by hypusination. This set of proteins includes essential constituents of antimicrobial response and autophagy. Mice with myeloid cell-specific deletion of Dhps exhibit reduced EIF5AHyp in macrophages and increased bacterial burden and inflammation. Thus, regulation of translation through hypusination is a critical hallmark of the defense of eukaryotic hosts against pathogenic bacteria. Gobert et al. demonstrate that hypusination, a specific mechanism regulating translation, is induced in macrophages by bacteria. Hypusination is required for the translation of inducible antimicrobial effectors. Mice that specifically lack hypusination in macrophages are highly susceptible to Helicobacter pylori and Citrobacter rodentium, two pathogens of the gastrointestinal tract.
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Affiliation(s)
- Alain P Gobert
- 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.
| | - Jordan L Finley
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Yvonne L Latour
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Department of Pathology, Microbiology, and Immunology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Mohammad Asim
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Thaddeus M Smith
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Thomas G Verriere
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Daniel P Barry
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Margaret M Allaman
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Alberto G Delagado
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Kristie L Rose
- Department of Biochemistry, Mass Spectrometry Research Center, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - M Wade Calcutt
- Department of Biochemistry, Mass Spectrometry Research Center, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Kevin L Schey
- Department of Biochemistry, Mass Spectrometry Research Center, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Johanna C Sierra
- 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
| | - M Blanca Piazuelo
- 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
| | - Raghavendra G Mirmira
- Translational Research Center, Department of Medicine, The University of Chicago, Chicago, IL 60637, 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; Department of Pathology, Microbiology, and Immunology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; Veterans Affairs Tennessee Valley Healthcare System, Nashville, TN 37232, USA.
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42
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Huang RJ, Koh H, Hwang JH, Abnet CC, Alarid-Escudero F, Amieva MR, Bruce MG, Camargo MC, Chan AT, Choi IJ, Corvalan A, Davis JL, Deapen D, Epplein M, Greenwald DA, Hamashima C, Hur C, Inadomi JM, Ji HP, Jung HY, Lee E, Lin B, Palaniappan LP, Parsonnet J, Peek RM, Piazuelo MB, Rabkin CS, Shah SC, Smith A, So S, Stoffel EM, Umar A, Wilson KT, Woo Y, Yeoh KG. A Summary of the 2020 Gastric Cancer Summit at Stanford University. Gastroenterology 2020; 159:1221-1226. [PMID: 32707045 PMCID: PMC7577947 DOI: 10.1053/j.gastro.2020.05.100] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 05/04/2020] [Indexed: 02/06/2023]
Abstract
There exists no coherent national strategy for the early detection or prevention of gastric cancer in the United States (US), even among identified high-risk groups such as Asian Americans, African Americans, Hispanic Americans, and Alaska Native/American Indian peoples. As a result, patients with gastric cancer in the US are diagnosed at later stages and demonstrate worse overall survival compared to nations of East Asia with established screening programs (Table 1). The under-recognition of gastric cancer risk within minority communities is a significant unaddressed healthcare disparity.
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Affiliation(s)
- Robert J. Huang
- Division of Gastroenterology and Hepatology, Department of Medicine, Stanford University, Stanford, CA
| | - Howard Koh
- Harvard TH Chan School of Public Health, Boston, MA
| | - Joo Ha Hwang
- Division of Gastroenterology and Hepatology, Department of Medicine, Stanford University, Stanford, California.
| | | | - Christian C. Abnet
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, Rockville, MD
| | - Fernando Alarid-Escudero
- Division of Public Administration, Center for Research and Teaching in Economics, Aguascalientes, Mexico
| | - Manuel R. Amieva
- Division of Infectious Diseases, Department of Pediatrics, Stanford University
| | - Michael G. Bruce
- Arctic Investigations Program, Centers for Disease Control and Prevention, Anchorage, AK
| | - M. Constanza Camargo
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, Rockville, MD
| | - Andrew T. Chan
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital, Boston, MA
| | - Il Ju Choi
- Center for Gastric Cancer, National Cancer Center, Goyang, South Korea
| | - Alejandro Corvalan
- Advanced Center for Chronic Diseases (ACCDiS), Pontificia Universidad Catolica de Chile, Santiago, Chile
| | - Jeremy L. Davis
- Center for Cancer Research, National Cancer Institute, Bethesda, MD
| | - Dennis Deapen
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA
| | - Meira Epplein
- Department of Population Health Sciences, Duke University, and Cancer Control and Population Sciences Program, Duke Cancer Institute, Durham, NC
| | - David A. Greenwald
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | | | - Chin Hur
- Division of Digestive & Liver Diseases, Columbia University, New York, NY
| | - John M. Inadomi
- Division of Gastroenterology, University of Washington, Seattle, WA
| | - Hanlee P. Ji
- Division of Hematology and Oncology, Department of Medicine, Stanford University
| | - Hwoon-Yong Jung
- Department of Gastroenterology, University of Ulsan College of Medicine, Asan Medical Center, Seoul, South Korea
| | - Eunjung Lee
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA
| | - Bryant Lin
- Division of Primary Care and Population Health, Department of Medicine, Stanford University
| | - Latha P. Palaniappan
- Division of Primary Care and Population Health, Department of Medicine, Stanford University
| | - Julie Parsonnet
- Division of Infectious Diseases, Department of Medicine, Stanford University
| | - Richard M. Peek
- Division of Gastroenterology, Hepatology, and Nutrition, Vanderbilt University Medical Center, Nashville, TN
| | - M. Blanca Piazuelo
- Division of Gastroenterology, Hepatology, and Nutrition, Vanderbilt University Medical Center, Nashville, TN
| | - Charles S. Rabkin
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, Rockville, MD
| | - Shailja C. Shah
- Division of Gastroenterology, Hepatology, and Nutrition, Vanderbilt University Medical Center, Nashville, TN,Department of Veterans Affairs, Tennessee Valley Healthcare System, Nashville, TN
| | - Aki Smith
- Hope for Stomach Cancer, Marina Del Rey, CA
| | - Samuel So
- The Asian Liver Center, Stanford University
| | - Elena M. Stoffel
- Division of Gastroenterology and Hepatology, University of Michigan, Ann Arbor, MI
| | - Asad Umar
- Division of Cancer Prevention, National Cancer Institute, Rockville, MD
| | - Keith T. Wilson
- Division of Gastroenterology, Hepatology, and Nutrition, Vanderbilt University Medical Center, Nashville, TN,Department of Veterans Affairs, Tennessee Valley Healthcare System, Nashville, TN
| | - Yanghee Woo
- Division of Surgical Oncology, Department of Surgery, City of Hope National Comprehensive Cancer Center, Duarte, CA
| | - Khay Guan Yeoh
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
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43
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Wang S, Raybuck A, Shiuan E, Cho SH, Wang Q, Brantley-Sieders DM, Edwards D, Allaman MM, Nathan J, Wilson KT, DeNardo D, Zhang S, Cook R, Boothby M, Chen J. Selective inhibition of mTORC1 in tumor vessels increases antitumor immunity. JCI Insight 2020; 5:139237. [PMID: 32759497 PMCID: PMC7455083 DOI: 10.1172/jci.insight.139237] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [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: 04/17/2020] [Accepted: 07/01/2020] [Indexed: 02/06/2023] Open
Abstract
A tumor blood vessel is a key regulator of tissue perfusion, immune cell trafficking, cancer metastasis, and therapeutic responsiveness. mTORC1 is a signaling node downstream of multiple angiogenic factors in the endothelium. However, mTORC1 inhibitors have limited efficacy in most solid tumors, in part due to inhibition of immune function at high doses used in oncology patients and compensatory PI3K signaling triggered by mTORC1 inhibition in tumor cells. Here we show that low-dose RAD001/everolimus, an mTORC1 inhibitor, selectively targets mTORC1 signaling in endothelial cells (ECs) without affecting tumor cells or immune cells, resulting in tumor vessel normalization and increased antitumor immunity. Notably, this phenotype was recapitulated upon targeted inducible gene ablation of the mTORC1 component Raptor in tumor ECs (RaptorECKO). Tumors grown in RaptorECKO mice displayed a robust increase in tumor-infiltrating lymphocytes due to GM-CSF-mediated activation of CD103+ dendritic cells and displayed decreased tumor growth and metastasis. GM-CSF neutralization restored tumor growth and metastasis, as did T cell depletion. Importantly, analyses of human tumor data sets support our animal studies. Collectively, these findings demonstrate that endothelial mTORC1 is an actionable target for tumor vessel normalization, which could be leveraged to enhance antitumor immune therapies.
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Affiliation(s)
- Shan Wang
- Veterans Affairs Medical Center, Tennessee Valley Healthcare System, Nashville, Tennessee, USA.,Division of Rheumatology and Immunology and
| | - Ariel Raybuck
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Eileen Shiuan
- Program in Cancer Biology, School of Medicine, Vanderbilt University, Nashville, Tennessee, USA
| | - Sung Hoon Cho
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Qingfei Wang
- Department of Biological Sciences, Harper Cancer Research Institute, University of Notre Dame, South Bend, Indiana, USA
| | | | | | - Margaret M Allaman
- Division of Gastroenterology, Hepatology, and Nutrition, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - James Nathan
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Keith T Wilson
- Veterans Affairs Medical Center, Tennessee Valley Healthcare System, Nashville, Tennessee, USA.,Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA.,Program in Cancer Biology, School of Medicine, Vanderbilt University, Nashville, Tennessee, USA.,Vanderbilt-Ingram Cancer Center and.,Division of Gastroenterology, Hepatology, and Nutrition, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - David DeNardo
- Department of Medicine, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
| | - Siyuan Zhang
- Department of Biological Sciences, Harper Cancer Research Institute, University of Notre Dame, South Bend, Indiana, USA
| | - Rebecca Cook
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA.,Division of Gastroenterology, Hepatology, and Nutrition, Vanderbilt University Medical Center, Nashville, Tennessee, USA.,Department of Cell and Developmental Biology, School of Medicine, Vanderbilt University, Nashville, Tennessee, USA
| | - Mark Boothby
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA.,Program in Cancer Biology, School of Medicine, Vanderbilt University, Nashville, Tennessee, USA.,Vanderbilt-Ingram Cancer Center and
| | - Jin Chen
- Veterans Affairs Medical Center, Tennessee Valley Healthcare System, Nashville, Tennessee, USA.,Division of Rheumatology and Immunology and.,Program in Cancer Biology, School of Medicine, Vanderbilt University, Nashville, Tennessee, USA.,Vanderbilt-Ingram Cancer Center and.,Department of Cell and Developmental Biology, School of Medicine, Vanderbilt University, Nashville, Tennessee, USA
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44
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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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Whary MT, Avenia JMR, Bravo LE, Lofgren JL, Lertpiriyapong K, Mera-Giler R, Piazuelo MB, Correa P, Peek RM, Wilson KT, Fox JG. Contrasting serum biomarker profiles in two Colombian populations with different risks for progression of premalignant gastric lesions during chronic Helicobacter pylori infection. Cancer Epidemiol 2020; 67:101726. [PMID: 32447242 DOI: 10.1016/j.canep.2020.101726] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 04/24/2020] [Accepted: 04/27/2020] [Indexed: 11/26/2022]
Abstract
BACKGROUND Colombians in coastal Tumaco have a lower incidence of Helicobacter pylori-associated gastric cancer compared to individuals from Tuquerres in the high Andes. This is despite nearly universal prevalence of H. pylori infection and chronic gastritis. METHODS H. pylori infection was confirmed by Steiner stain and serology using African and European-origin strains. Gastric histology and serum inflammatory biomarkers in dyspeptic Tumaco or Tuquerres patients were evaluated to predict progression of gastric lesions. RESULTS H. pylori infection was nearly universal by Steiner stain and serology. IgG response to European-origin H. pylori strains were greater than African-origin. High gastric cancer-risk Tuquerres patients, compared to low-risk Tumaco, had significant odds ratios for lesion progression associated with serum IL-5, trefoil factor 3 (TFF3), and low pepsinogen I/II ratio. Sensitivity and specificity for these parameters was 63.8% and 67.9%, respectively, with correctly classifying patients at 66.7%. Most odds ratios for 26 other biomarkers were significant for the town of residency, indicating an environmental impact on Tumaco patients associated with decreased lesion progression. CONCLUSION An IL-5 association with progression of gastric lesions is novel and could be evaluated in addition to TFF3 and pepsinogen I/II ratio as a non-invasive prognostic screen. Results suggest Tumaco patients were exposed to infectious diseases beyond H. pylori such as the documented high incidence of helminthiasis and toxoplasmosis. IMPACT Results support a prior recommendation to evaluate TFF3 and pepsinogen I/II together to predict aggressive gastric histology. Our data indicate IL-5 should be further evaluated as prognostic parameter.
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Affiliation(s)
- Mark T Whary
- Division of Comparative Medicine, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | - Luis E Bravo
- Department of Pathology, Universidad Del Valle, Cali, Colombia
| | - Jennifer L Lofgren
- Division of Comparative Medicine, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Kvin Lertpiriyapong
- Division of Comparative Medicine, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Robertino Mera-Giler
- Division of Gastroenterology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - M Blanca Piazuelo
- Division of Gastroenterology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Pelayo Correa
- Division of Gastroenterology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Richard M Peek
- Division of Gastroenterology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA; Veterans Affairs Tennessee Valley Healthcare System, Nashville, TN, USA; Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Keith T Wilson
- Division of Gastroenterology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA; Veterans Affairs Tennessee Valley Healthcare System, Nashville, TN, USA; Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - James G Fox
- Division of Comparative Medicine, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
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Sierra JC, Piazuelo MB, Luis PB, Barry DP, Allaman MM, Asim M, Sebrell TA, Finley JL, Rose KL, Hill S, Holshouser SL, Casero RA, Cleveland JL, Woster PM, Schey KL, Bimczok D, Schneider C, Gobert AP, Wilson KT. Spermine oxidase mediates Helicobacter pylori-induced gastric inflammation, DNA damage, and carcinogenic signaling. Oncogene 2020; 39:4465-4474. [PMID: 32350444 PMCID: PMC7260102 DOI: 10.1038/s41388-020-1304-6] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 04/14/2020] [Accepted: 04/16/2020] [Indexed: 01/05/2023]
Abstract
Helicobacter pylori infection is the main risk factor for the development of gastric cancer, the third leading cause of cancer death worldwide. H. pylori colonizes the human gastric mucosa and persists for decades. The inflammatory response is ineffective in clearing the infection, leading to disease progression that may result in gastric adenocarcinoma. We have shown that polyamines are regulators of the host response to H. pylori, and that spermine oxidase (SMOX), which metabolizes the polyamine spermine into spermidine plus H2O2, is associated with increased human gastric cancer risk. We now used a molecular approach to directly address the role of SMOX, and demonstrate that Smox-deficient mice exhibit significant reductions of gastric spermidine levels and H. pylori-induced inflammation. Proteomic analysis revealed that cancer was the most significantly altered functional pathway in Smox-/- gastric organoids. Moreover, there was also less DNA damage and β-catenin activation in H. pylori-infected Smox-/- mice or gastric organoids, compared to infected wild-type animals or gastroids. The link between SMOX and β-catenin activation was confirmed in human gastric organoids that were treated with a novel SMOX inhibitor. These findings indicate that SMOX promotes H. pylori-induced carcinogenesis by causing inflammation, DNA damage, and activation of β-catenin signaling.
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Affiliation(s)
- Johanna C Sierra
- 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
| | - M Blanca Piazuelo
- 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
| | - Paula B Luis
- Department of Pharmacology, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA
| | - Daniel P Barry
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Margaret M Allaman
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Mohammad Asim
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Thomas A Sebrell
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, 59717, USA
| | - Jordan L Finley
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Kristie L Rose
- Department of Biochemistry, Mass Spectrometry Research Center, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Salisha Hill
- Department of Biochemistry, Mass Spectrometry Research Center, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Steven L Holshouser
- Department of Drug Discovery and Biomedical Sciences, Medical University of South Carolina, Charleston, SC, 29425, USA
| | - Robert A Casero
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, 21287, USA
| | - John L Cleveland
- Department of Tumor Biology, Moffitt Cancer Center and Research Institute, Tampa, FL, 33612, USA
| | - Patrick M Woster
- Department of Drug Discovery and Biomedical Sciences, Medical University of South Carolina, Charleston, SC, 29425, USA
| | - Kevin L Schey
- Department of Biochemistry, Mass Spectrometry Research Center, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Diane Bimczok
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, 59717, USA
| | - Claus Schneider
- Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
- Department of Pharmacology, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA
| | - Alain P Gobert
- 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
| | - 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.
- Department of Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA.
- Veterans Affairs Tennessee Valley Healthcare System, Nashville, TN, 37232, USA.
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Gobert AP, Latour YL, Finley JK, Asim M, barry DP, Allaman MM, Lindsey-Rose KK, Piazuelo MB, Sierra JC, Wilson KT. Hypusination regulates the antibacterial response of macrophages. The Journal of Immunology 2020. [DOI: 10.4049/jimmunol.204.supp.227.5] [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] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Abstract
Introduction
Hypusine is an amino acid found only in the eukaryotic translation initiation factor 5A (EIF5A). Hypusine is synthesized by the enzyme deoxyhypusine synthase (DHPS) that transfers the N-moiety of spermidine to a lysine residue in EIF5A. This post-translational modification (hypusination) is essential to binding specific mRNAs. The EIF5AHyp/mRNA complex is translocated to the cytoplasm, reaches ribosomes, and allows for translation. We analyzed the role of hypusination in the innate response of macrophages.
Results
The gastric pathogen Helicobacter pylori stimulated DHPS expression and hypusination in murine bone marrow-derived macrophages (BMmacs). We generated myeloid-specific Dhps knockout mice (DhpsΔmye) by crossing Dhpsfl/fl mice to Lyz2-cre mice. By iTRAQ proteomics, 29 of the proteins induced by H. pylori in BMmacs from Dhpsfl/fl mice were significantly less expressed in infected DhpsΔmye mice. These included antibacterial effectors (IRG1, NOS2), cytokines (TNF-α, IL-1β), and mediators of autophagy (SQSTM, IRGM1). These findings were confirmed by Western blot. DhpsΔmye mice infected with H. pylori exhibited increased colonization (p<0.01) and gastritis (p<0.05) compared to Dhpsfl/fl mice. DhpsΔmye mice were also more colonized by the intestinal pathogen Citrobacter rodentium than Dhpsfl/fl mice (p<0.05). EIF5AHyp and NOS2 were more expressed in gastric and colonic CD68+ macrophages from H. pylori- and C. rodentium-infected Dhpsfl/fl mice versus uninfected animals, respectively. The staining for EIF5AHyp and NOS2 was markedly reduced in infected DhpsΔmye mice.
Conclusions
Hypusination in myeloid cells is critical for host innate immunity to limit the infectivity of pathogenic bacteria.
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Ortiz V, Estevez-Ordonez D, Montalvan-Sanchez E, Urrutia-Argueta S, Israel D, Krishna US, Romero-Gallo J, Wilson KT, Peek RM, Dominguez R, Morgan DR. Helicobacter pylori antimicrobial resistance and antibiotic consumption in the low-resource Central America setting. Helicobacter 2019; 24:e12595. [PMID: 31111610 PMCID: PMC6619433 DOI: 10.1111/hel.12595] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/13/2019] [Revised: 04/20/2019] [Accepted: 04/22/2019] [Indexed: 12/31/2022]
Abstract
BACKGROUND Antimicrobial resistance is a global public health problem, particularly in low- and middle-income countries (LMICs), where antibiotics are often obtained without a prescription. H. pylori antimicrobial resistance patterns are informative for patient care and gastric cancer prevention programs, have been shown to correlate with general antimicrobial consumption, and may guide antimicrobial stewardship programs in LMICs. We report H. pylori resistance and antimicrobial utilization patterns for western Honduras, representative of rural Central America. METHODS In the context of the western Honduras gastric cancer epidemiology initiative, gastric biopsies from 189 patients were studied for culture and resistance patterns. Antimicrobial utilization was investigated for common H. pylori treatment regimens from regional public (7 antimicrobials) and national private (4 antimicrobials) data, analyzed in accordance with WHO anatomical therapeutic chemical defined daily doses (DDD) method and expressed as DDD/1000 inhabitants per day (DID) and per year (DIY). RESULTS H. pylori was successfully cultured from 116 patients (56% males, mean age: 54), and nearly all strains were cagA+ and vacAs1m1+ positive (99% and 90.4%, respectively). Unexpectedly, high resistance was noted for levofloxacin (20.9%) and amoxicillin (10.7%), while metronidazole (67.9%) and clarithromycin (11.2%) were similar to data from Latin America. Significant associations with age, gender, or histology were not noted, with the exception of levofloxacin (28%, P = 0.01) in those with histology limited to non-atrophic gastritis. Total antimicrobial usage in western Honduras of amoxicillin (17.3 DID) and the quinolones had the highest relative utilizations compared with other representative nations. CONCLUSIONS We observed significant H. pylori resistance to amoxicillin and levofloxacin in the context of high community antimicrobial utilization. This has implications in Central America for H. pylori treatment guidelines as well as antimicrobial stewardship programs.
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Affiliation(s)
- Vivian Ortiz
- Department of Internal Medicine, Yale University
| | - Dagoberto Estevez-Ordonez
- The Vanderbilt Division of Gastroenterology, Hepatology, and Nutrition, Vanderbilt University Medical Center;,School of Medicine, University of Alabama at Birmingham
| | | | | | - Dawn Israel
- The Vanderbilt Division of Gastroenterology, Hepatology, and Nutrition, Vanderbilt University Medical Center
| | - Uma S. Krishna
- The Vanderbilt Division of Gastroenterology, Hepatology, and Nutrition, Vanderbilt University Medical Center
| | - Judith Romero-Gallo
- The Vanderbilt Division of Gastroenterology, Hepatology, and Nutrition, Vanderbilt University Medical Center
| | - Keith T. Wilson
- The Vanderbilt Division of Gastroenterology, Hepatology, and Nutrition, Vanderbilt University Medical Center
| | - Richard M. Peek
- The Vanderbilt Division of Gastroenterology, Hepatology, and Nutrition, Vanderbilt University Medical Center
| | | | - Douglas R. Morgan
- The Vanderbilt Division of Gastroenterology, Hepatology, and Nutrition, Vanderbilt University Medical Center;,School of Medicine, University of Alabama at Birmingham
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Wilson KT. Preventing Gastric Cancer Development by Inhibiting the Virulence of H. pylori Infection. Oncology (Williston Park) 2019; 33:227-231. [PMID: 31219607 PMCID: PMC6685684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
In this interview with ONCOLOGY, Keith Wilson, MD, discusses a drug that may help prevent gastric cancer. Dr. Wilson and his colleagues recently published a study showing that a chemopreventive drug can also act directly on Helicobacter pylori (H. pylori), a bacterium that is the primary cause of gastric cancer.[1]
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50
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Dominguez RL, Cherry CB, Estevez-Ordonez D, Mera R, Escamilla V, Pawlita M, Waterboer T, Wilson KT, Peek RM, Tavera G, Williams SM, Gulley ML, Emch M, Morgan DR. Geospatial analyses identify regional hot spots of diffuse gastric cancer in rural Central America. BMC Cancer 2019; 19:545. [PMID: 31174492 PMCID: PMC6554991 DOI: 10.1186/s12885-019-5726-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [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: 05/04/2018] [Accepted: 05/16/2019] [Indexed: 12/12/2022] Open
Abstract
Background Geospatial technology has facilitated the discovery of disease distributions and etiology and helped target prevention programs. Globally, gastric cancer is the leading infection-associated cancer, and third leading cause of cancer mortality worldwide, with marked geographic variation. Central and South America have a significant burden, particularly in the mountainous regions. In the context of an ongoing population-based case-control study in Central America, our aim was to examine the spatial epidemiology of gastric cancer subtypes and H. pylori virulence factors. Methods Patients diagnosed with gastric cancer from 2002 to 2013 in western Honduras were identified in the prospective gastric cancer registry at the principal district hospital. Diagnosis was based on endoscopy and confirmatory histopathology. Geospatial methods were applied using the ArcGIS v10.3.1 and SaTScan v9.4.2 platforms to examine regional distributions of the gastric cancer histologic subtypes (Lauren classification), and the H. pylori CagA virulence factor. Getis-Ord-Gi hot spot and Discrete Poisson SaTScan statistics, respectively, were used to explore spatial clustering at the village level (30–50 rural households), with standardization by each village’s population. H. pylori and CagA serologic status was determined using the novel H. pylori multiplex assay (DKFZ, Germany). Results Three hundred seventy-eight incident cases met the inclusion criteria (mean age 63.7, male 66.3%). Areas of higher gastric cancer incidence were identified. Significant spatial clustering of diffuse histology adenocarcinoma was revealed both by the Getis-Ord-GI* hot spot analysis (P-value < 0.0015; range 0.00003–0.0014; 99%CI), and by the SaTScan statistic (P-value < 0.006; range 0.0026–0.0054). The intestinal subtype was randomly distributed. H. pylori CagA had significant spatial clustering only in association with the diffuse histology cancer hot spot (Getis-Ord-Gi* P value ≤0.001; range 0.0001–0.0010; SaTScan statistic P value 0.0085). In the diffuse gastric cancer hot spot, the lowest age quartile range was 21–46 years, significantly lower than the intestinal cancers (P = 0.024). Conclusions Geospatial methods have identified a significant cluster of incident diffuse type adenocarcinoma cases in rural Central America, suggest of a germline genetic association. Further genomic and geospatial analyses to identify potential spatial patterns of genetic, bacterial, and environmental risk factors may be informative.
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Affiliation(s)
| | - Charlotte B Cherry
- Office of Public Health Informatics & Analytics, Tennessee Department of Public Health, Nashville, TN, USA
| | - Dago Estevez-Ordonez
- Vanderbilt Ingram Cancer Center (VICC), Vanderbilt University Medical Center, Nashville, USA
| | - Robertino Mera
- Division of Gastroenterology, Hepatology, and Nutrition, Vanderbilt University Medical Center, Nashville, USA
| | - Veronica Escamilla
- Carolina Population Center, University of North Carolina, Chapel Hill, USA
| | - Michael Pawlita
- Division of Molecular Diagnostics of Oncogenic Infections, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Tim Waterboer
- Division of Molecular Diagnostics of Oncogenic Infections, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Keith T Wilson
- Division of Gastroenterology, Hepatology, and Nutrition, Vanderbilt University Medical Center, Nashville, USA
| | - Richard M Peek
- Division of Gastroenterology, Hepatology, and Nutrition, Vanderbilt University Medical Center, Nashville, USA
| | - Gloria Tavera
- Department of Population and Quantitative Health Sciences and Institute of Computational Biology, Case Western Reserve University, Cleveland, USA
| | - Scott M Williams
- Department of Population and Quantitative Health Sciences and Institute of Computational Biology, Case Western Reserve University, Cleveland, USA
| | - Margaret L Gulley
- Department of Pathology, University of North Carolina, Chapel Hill, USA
| | - Michael Emch
- Department of Geography, University of North Carolina, Chapel Hill, USA
| | - Douglas R Morgan
- Vanderbilt Ingram Cancer Center (VICC), Vanderbilt University Medical Center, Nashville, USA. .,Division of Gastroenterology, Hepatology, and Nutrition, Vanderbilt University Medical Center, Nashville, USA. .,Division of Gastroenterology and Hepatology, The University of Alabama at Birmingham (UAB), 1808 7th Avenue South, BDB 373, Birmingham, AL, 35233, USA.
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