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McKinley ET, Shao J, Ellis ST, Heiser CN, Roland JT, Macedonia MC, Vega PN, Shin S, Coffey RJ, Lau KS. MIRIAM: A machine and deep learning single-cell segmentation and quantification pipeline for multi-dimensional tissue images. Cytometry A 2022; 101:521-528. [PMID: 35084791 PMCID: PMC9167255 DOI: 10.1002/cyto.a.24541] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 12/16/2021] [Accepted: 01/17/2022] [Indexed: 11/25/2022]
Abstract
Increasingly, highly multiplexed tissue imaging methods are used to profile protein expression at the single‐cell level. However, a critical limitation is the lack of robust cell segmentation tools for tissue sections. We present Multiplexed Image Resegmentation of Internal Aberrant Membranes (MIRIAM) that combines (a) a pipeline for cell segmentation and quantification that incorporates machine learning‐based pixel classification to define cellular compartments, (b) a novel method for extending incomplete cell membranes, and (c) a deep learning‐based cell shape descriptor. Using human colonic adenomas as an example, we show that MIRIAM is superior to widely utilized segmentation methods and provides a pipeline that is broadly applicable to different imaging platforms and tissue types.
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Affiliation(s)
- Eliot T McKinley
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, USA.,Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Justin Shao
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, USA.,Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Samuel T Ellis
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Cody N Heiser
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, USA.,Program in Chemical & Physical Biology, Vanderbilt University School of Medicine, 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
| | - Mary C Macedonia
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, USA.,Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, 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
| | - Susie Shin
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, USA.,Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Robert J Coffey
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, USA.,Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Ken S Lau
- 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 & Physical Biology, Vanderbilt University School of Medicine, Nashville, TN, USA.,Department of Surgery, Vanderbilt University Medical Center, Nashville, TN, USA
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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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