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Populin LC, Rajala AZ, Matkowskyj KA, Saha S, Zeng W, Christian B, McVea A, Tay EX, Mueller EM, Malone ME, Brust-Mascher I, McMillan AB, Ludwig KA, Suminski AJ, Reardon C, Furness JB. Characterization of idiopathic chronic diarrhea and associated intestinal inflammation and preliminary observations of effects of vagal nerve stimulation in a non-human primate. Neurogastroenterol Motil 2024; 36:e14876. [PMID: 39072841 PMCID: PMC11321913 DOI: 10.1111/nmo.14876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 05/26/2024] [Accepted: 07/11/2024] [Indexed: 07/30/2024]
Abstract
BACKGROUND Diarrhea is commonly associated with irritable bowel syndrome, inflammatory bowel disease, microscopic colitis, and other gastrointestinal dysfunctions. Spontaneously occurring idiopathic chronic diarrhea is frequent in rhesus macaques, but has not been used as a model for the investigation of diarrhea or its treatment. We characterized this condition and present preliminary data demonstrating that left vagal nerve stimulation provides relief. METHODS Stool consistency scores were followed for up to 12 years. Inflammation was assessed by plasma C-reactive protein, [18F]fluorodeoxyglucose (FDG) uptake, measured by positron emission tomography (PET), multiplex T cell localization, endoscopy and histology. The vagus was stimulated for 9 weeks in conscious macaques, using fully implanted electrodes, under wireless control. KEY RESULTS Macaques exhibited recurrent periods of diarrhea for up to 12 years, and signs of inflammation: elevated plasma C-reactive protein, increased bowel FDG uptake and increased mucosal T helper1 T-cells. The colon and distal ileum were endoscopically normal, and histology revealed mild colonic inflammation. Application of vagal nerve stimulation to conscious macaques (10 Hz, 30 s every 3 h; 24 h a day for 9 weeks) significantly reduced severity of diarrhea and also reduced inflammation, as measured by FDG uptake and C-reactive protein. CONCLUSIONS AND INFERENCES These macaques exhibit spontaneously occurring diarrhea with intestinal inflammation that can be reduced by VNS. The data demonstrate the utility of this naturally occurring primate model to study the physiology and treatments for chronic diarrhea and the neural control circuits influencing diarrhea and inflammation that are not accessible in human subjects.
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Affiliation(s)
- Luis C Populin
- Department of Neuroscience, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI
| | - Abigail Z Rajala
- Department of Neuroscience, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI
| | - Kristina A Matkowskyj
- Department of Pathology & Laboratory Medicine, University of Wisconsin-Madison, Madison, WI
| | - Sumona Saha
- Division of Gastroenterology and Hepatology, University of Wisconsin School of Medicine and Public Health, Madison, WI
| | - Weifeng Zeng
- Department of Surgery, Dental and Plastic Surgery, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI
| | - Bradley Christian
- Department of Medical Physics, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI
| | - Andrew McVea
- Department of Medical Physics, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI
| | - Emmy Xue Tay
- Department of Anatomy, Physiology and Cell Biology, UC Davis
| | - Ellie M Mueller
- Department of Neuroscience, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI
| | - Margaret E Malone
- Department of Neuroscience, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI
| | | | - Alan B McMillan
- Department of Medical Physics, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI
- Department of Radiology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI
| | - Kip A Ludwig
- Department of Neurological Surgery, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI
| | - Aaron J Suminski
- Department of Neurological Surgery, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI
| | - Colin Reardon
- Department of Anatomy, Physiology and Cell Biology, UC Davis
| | - John B Furness
- Department of Anatomy & Physiology, University of Melbourne, Parkville, VIC 3010, Australia
- Florey Institute of Neuroscience and Mental Health, Parkville, VIC 3010, Australia
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2
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Werid GM, Miller D, Hemmatzadeh F, Messele YE, Petrovski K. An overview of the detection of bovine respiratory disease complex pathogens using immunohistochemistry: emerging trends and opportunities. J Vet Diagn Invest 2024; 36:12-23. [PMID: 37982437 PMCID: PMC10734592 DOI: 10.1177/10406387231210489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2023] Open
Abstract
The bovine respiratory disease complex (BRDC) is caused by a variety of pathogens, as well as contributing environmental and host-related risk factors. BRDC is the costliest disease for feedlot cattle globally. Immunohistochemistry (IHC) is a valuable tool for enhancing our understanding of BRDC given its specificity, sensitivity, cost-effectiveness, and capacity to provide information on antigen localization and immune response. Emerging trends in IHC include the use of multiplex IHC for the detection of coinfections, the use of digital imaging and automation, improved detection systems using enhanced fluorescent dyes, and the integration of IHC with spatial transcriptomics. Overall, identifying biomarkers for early detection, utilizing high-throughput IHC for large-scale studies, developing standardized protocols and reagents, and integrating IHC with other technologies are some of the opportunities to enhance the accuracy and applicability of IHC. We summarize here the various techniques and protocols used in IHC and highlight their current and potential role in BRDC research.
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Affiliation(s)
- Gebremeskel Mamu Werid
- Davies Livestock Research Centre, School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy, SA, Australia
| | - Darren Miller
- Davies Livestock Research Centre, School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy, SA, Australia
| | - Farhid Hemmatzadeh
- Australian Centre for Antimicrobial Resistance Ecology, School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy, SA, Australia
| | - Yohannes E. Messele
- Davies Livestock Research Centre, School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy, SA, Australia
| | - Kiro Petrovski
- Australian Centre for Antimicrobial Resistance Ecology, School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy, SA, Australia
- Davies Livestock Research Centre, School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy, SA, Australia
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3
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Speranza E. Understanding virus-host interactions in tissues. Nat Microbiol 2023; 8:1397-1407. [PMID: 37488255 DOI: 10.1038/s41564-023-01434-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 06/20/2023] [Indexed: 07/26/2023]
Abstract
Although virus-host interactions are usually studied in a single cell type using in vitro assays in immortalized cell lines or isolated cell populations, it is important to remember that what is happening inside one infected cell does not translate to understanding how an infected cell behaves in a tissue, organ or whole organism. Infections occur in complex tissue environments, which contain a host of factors that can alter the course of the infection, including immune cells, non-immune cells and extracellular-matrix components. These factors affect how the host responds to the virus and form the basis of the protective response. To understand virus infection, tools are needed that can profile the tissue environment. This Review highlights methods to study virus-host interactions in the infection microenvironment.
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Affiliation(s)
- Emily Speranza
- Cleveland Clinic Lerner Research Institute, Port Saint Lucie, FL, USA.
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4
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Feng Y, Yang T, Zhu J, Li M, Doyle M, Ozcoban V, Bass GT, Pizzolla A, Cain L, Weng S, Pasam A, Kocovski N, Huang YK, Keam SP, Speed TP, Neeson PJ, Pearson RB, Sandhu S, Goode DL, Trigos AS. Spatial analysis with SPIAT and spaSim to characterize and simulate tissue microenvironments. Nat Commun 2023; 14:2697. [PMID: 37188662 DOI: 10.1038/s41467-023-37822-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 03/30/2023] [Indexed: 05/17/2023] Open
Abstract
Spatial proteomics technologies have revealed an underappreciated link between the location of cells in tissue microenvironments and the underlying biology and clinical features, but there is significant lag in the development of downstream analysis methods and benchmarking tools. Here we present SPIAT (spatial image analysis of tissues), a spatial-platform agnostic toolkit with a suite of spatial analysis algorithms, and spaSim (spatial simulator), a simulator of tissue spatial data. SPIAT includes multiple colocalization, neighborhood and spatial heterogeneity metrics to characterize the spatial patterns of cells. Ten spatial metrics of SPIAT are benchmarked using simulated data generated with spaSim. We show how SPIAT can uncover cancer immune subtypes correlated with prognosis in cancer and characterize cell dysfunction in diabetes. Our results suggest SPIAT and spaSim as useful tools for quantifying spatial patterns, identifying and validating correlates of clinical outcomes and supporting method development.
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Affiliation(s)
- Yuzhou Feng
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Tianpei Yang
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - John Zhu
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Mabel Li
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Maria Doyle
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Volkan Ozcoban
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Greg T Bass
- Research & Development, CSL Innovation, Parkville, VIC, Australia
| | - Angela Pizzolla
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- The Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, VIC, Australia
| | - Lachlan Cain
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Sirui Weng
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- The Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, VIC, Australia
| | - Anupama Pasam
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | | | - Yu-Kuan Huang
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- The Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, VIC, Australia
| | - Simon P Keam
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- The Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, VIC, Australia
| | - Terence P Speed
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Paul J Neeson
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- The Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, VIC, Australia
| | - Richard B Pearson
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- The Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, VIC, Australia
| | - Shahneen Sandhu
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- The Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, VIC, Australia
| | - David L Goode
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- The Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, VIC, Australia
| | - Anna S Trigos
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia.
- The Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, VIC, Australia.
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5
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Kuswanto W, Nolan G, Lu G. Highly multiplexed spatial profiling with CODEX: bioinformatic analysis and application in human disease. Semin Immunopathol 2023; 45:145-157. [PMID: 36414691 PMCID: PMC9684921 DOI: 10.1007/s00281-022-00974-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 11/06/2022] [Indexed: 11/23/2022]
Abstract
Multiplexed imaging, which enables spatial localization of proteins and RNA to cells within tissues, complements existing multi-omic technologies and has deepened our understanding of health and disease. CODEX, a multiplexed single-cell imaging technology, utilizes a microfluidics system that incorporates DNA barcoded antibodies to visualize 50 + cellular markers at the single-cell level. Here, we discuss the latest applications of CODEX to studies of cancer, autoimmunity, and infection as well as current bioinformatics approaches for analysis of multiplexed imaging data from preprocessing to cell segmentation and marker quantification to spatial analysis techniques. We conclude with a commentary on the challenges and future developments for multiplexed spatial profiling.
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Affiliation(s)
- Wilson Kuswanto
- Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, CA, 94304, USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, 94304, USA
| | - Garry Nolan
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, 94304, USA
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, 94304, USA
| | - Guolan Lu
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, 94304, USA.
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, 94304, USA.
- Department of Otolaryngology, Stanford University School of Medicine, Stanford, CA, 94304, USA.
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6
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Cheng Y, Burrack RK, Li Q. Spatially Resolved and Highly Multiplexed Protein and RNA In Situ Detection by Combining CODEX With RNAscope In Situ Hybridization. J Histochem Cytochem 2022; 70:571-581. [PMID: 35848523 PMCID: PMC9393509 DOI: 10.1369/00221554221114174] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Highly multiplexed protein and RNA in situ detection on a single tissue section concurrently is highly desirable for both basic and applied biomedical research. CO-detection by inDEXing (CODEX) is a new and powerful platform to visualize up to 60 protein biomarkers in situ, and RNAscope in situ hybridization (RNAscope) is a novel RNA detection system with high sensitivity and unprecedent specificity at a single-cell level. Nevertheless, to our knowledge, the combination of CODEX and RNAscope remained unreported until this study. Here, we report a simple and reproducible combination of CODEX and RNAscope. We also determined the cross-reactivities of CODEX anti-human antibodies to rhesus macaques, a widely used animal model of human disease.
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Affiliation(s)
- Yilun Cheng
- Nebraska Center for Virology, School of Biological Sciences, University of Nebraska–Lincoln, Lincoln, Nebraska
| | - Rachel K. Burrack
- Nebraska Center for Virology, School of Biological Sciences, University of Nebraska–Lincoln, Lincoln, Nebraska
| | - Qingsheng Li
- Nebraska Center for Virology, School of Biological Sciences, University of Nebraska–Lincoln, Lincoln, Nebraska
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7
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Jiang S, Chan CN, Rovira-Clavé X, Chen H, Bai Y, Zhu B, McCaffrey E, Greenwald NF, Liu C, Barlow GL, Weirather JL, Oliveria JP, Nakayama T, Lee IT, Matter MS, Carlisle AE, Philips D, Vazquez G, Mukherjee N, Busman-Sahay K, Nekorchuk M, Terry M, Younger S, Bosse M, Demeter J, Rodig SJ, Tzankov A, Goltsev Y, McIlwain DR, Angelo M, Estes JD, Nolan GP. Combined protein and nucleic acid imaging reveals virus-dependent B cell and macrophage immunosuppression of tissue microenvironments. Immunity 2022; 55:1118-1134.e8. [PMID: 35447093 PMCID: PMC9220319 DOI: 10.1016/j.immuni.2022.03.020] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 10/13/2021] [Accepted: 03/25/2022] [Indexed: 12/12/2022]
Abstract
Understanding the mechanisms of HIV tissue persistence necessitates the ability to visualize tissue microenvironments where infected cells reside; however, technological barriers limit our ability to dissect the cellular components of these HIV reservoirs. Here, we developed protein and nucleic acid in situ imaging (PANINI) to simultaneously quantify DNA, RNA, and protein levels within these tissue compartments. By coupling PANINI with multiplexed ion beam imaging (MIBI), we measured over 30 parameters simultaneously across archival lymphoid tissues from healthy or simian immunodeficiency virus (SIV)-infected nonhuman primates. PANINI enabled the spatial dissection of cellular phenotypes, functional markers, and viral events resulting from infection. SIV infection induced IL-10 expression in lymphoid B cells, which correlated with local macrophage M2 polarization. This highlights a potential viral mechanism for conditioning an immunosuppressive tissue environment for virion production. The spatial multimodal framework here can be extended to decipher tissue responses in other infectious diseases and tumor biology.
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Affiliation(s)
- Sizun Jiang
- Department of Pathology, Stanford University, Stanford, CA, USA; Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA.
| | - Chi Ngai Chan
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR, USA
| | | | - Han Chen
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Yunhao Bai
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Bokai Zhu
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Erin McCaffrey
- Department of Pathology, Stanford University, Stanford, CA, USA
| | | | - Candace Liu
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Graham L Barlow
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Jason L Weirather
- Center of Immuno-Oncology, Dana-Faber Cancer Institute, Boston, MA, USA
| | - John Paul Oliveria
- Department of Pathology, Stanford University, Stanford, CA, USA; Department of Medicine, McMaster University, Hamilton, ON, Canada
| | - Tsuguhisa Nakayama
- Department of Pathology, Stanford University, Stanford, CA, USA; Department of Otorhinolaryngology, Jikei University School of Medicine, Tokyo, Japan
| | - Ivan T Lee
- Department of Pathology, Stanford University, Stanford, CA, USA; Division of Allergy, Immunology, and Rheumatology, Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Matthias S Matter
- Pathology, Institute of Medical Genetics and Pathology, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Anne E Carlisle
- Center of Immuno-Oncology, Dana-Faber Cancer Institute, Boston, MA, USA
| | - Darci Philips
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Gustavo Vazquez
- Department of Pathology, Stanford University, Stanford, CA, USA
| | | | - Kathleen Busman-Sahay
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR, USA
| | - Michael Nekorchuk
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR, USA
| | - Margaret Terry
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR, USA
| | - Skyler Younger
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR, USA
| | - Marc Bosse
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Janos Demeter
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Scott J Rodig
- Department of Pathology, Brigham & Women's Hospital, Boston, MA, USA
| | - Alexandar Tzankov
- Pathology, Institute of Medical Genetics and Pathology, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Yury Goltsev
- Department of Pathology, Stanford University, Stanford, CA, USA
| | | | - Michael Angelo
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Jacob D Estes
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR, USA; Division of Pathobiology & Immunology, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR, USA.
| | - Garry P Nolan
- Department of Pathology, Stanford University, Stanford, CA, USA.
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