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Thapa S, Rathnaiah G, Zinniel DK, Barletta RG, Bannantine JP, Huebner M, Sreevatsan S. The Fur-like regulatory protein MAP3773c modulates key metabolic pathways in Mycobacterium avium subsp. paratuberculosis under in-vitro iron starvation. Sci Rep 2024; 14:8941. [PMID: 38637716 PMCID: PMC11026511 DOI: 10.1038/s41598-024-59691-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Accepted: 04/14/2024] [Indexed: 04/20/2024] Open
Abstract
Johne's disease (JD) is a chronic enteric infection of dairy cattle worldwide. Mycobacterium avium subsp. paratuberculosis (MAP), the causative agent of JD, is fastidious often requiring eight to sixteen weeks to produce colonies in culture-a major hurdle in the diagnosis and therefore in implementation of optimal JD control measures. A significant gap in knowledge is the comprehensive understanding of the metabolic networks deployed by MAP to regulate iron both in-vitro and in-vivo. The genome of MAP carries MAP3773c, a putative metal regulator, which is absent in all other mycobacteria. The role of MAP3773c in intracellular iron regulation is poorly understood. In the current study, a field isolate (K-10) and an in-frame MAP3773c deletion mutant (ΔMAP3773c) derived from K-10, were exposed to iron starvation for 5, 30, 60, and 90 min and RNA-Seq was performed. A comparison of transcriptional profiles between K-10 and ΔMAP3773c showed 425 differentially expressed genes (DEGs) at 30 min time post-iron restriction. Functional analysis of DEGs in ΔMAP3773c revealed that pantothenate (Pan) biosynthesis, polysaccharide biosynthesis and sugar metabolism genes were downregulated at 30 min post-iron starvation whereas ATP-binding cassette (ABC) type metal transporters, putative siderophore biosynthesis, PPE and PE family genes were upregulated. Pathway analysis revealed that the MAP3773c knockout has an impairment in Pan and Coenzyme A (CoA) biosynthesis pathways suggesting that the absence of those pathways likely affect overall metabolic processes and cellular functions, which have consequences on MAP survival and pathogenesis.
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Affiliation(s)
- Sajani Thapa
- Department of Pathobiology and Diagnostic Investigation, College of Veterinary Medicine, Michigan State University, 784 Wilson Road, STEG300, East Lansing, MI, 48824, USA
| | - Govardhan Rathnaiah
- School of Veterinary Medicine and Biomedical Sciences, University of Nebraska, Lincoln, USA
- University Of Nebraska, Eppley Institute for Cancer Research, Lincoln, USA
| | - Denise K Zinniel
- School of Veterinary Medicine and Biomedical Sciences, University of Nebraska, Lincoln, USA
| | - Raul G Barletta
- School of Veterinary Medicine and Biomedical Sciences, University of Nebraska, Lincoln, USA
| | | | - Marianne Huebner
- Department of Statistics and Probability, Michigan State University, East Lansing, MI, USA
| | - Srinand Sreevatsan
- Department of Pathobiology and Diagnostic Investigation, College of Veterinary Medicine, Michigan State University, 784 Wilson Road, STEG300, East Lansing, MI, 48824, USA.
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Dinarvand M, Koch FC, Al Mouiee D, Vuong K, Vijayan A, Tanzim AF, Azad AKM, Penesyan A, Castaño-Rodríguez N, Vafaee F. dRNASb: a systems biology approach to decipher dynamics of host-pathogen interactions using temporal dual RNA-seq data. Microb Genom 2022; 8. [PMID: 36136078 DOI: 10.1099/mgen.0.000862] [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: 11/18/2022] Open
Abstract
Infection triggers a dynamic cascade of reciprocal events between host and pathogen wherein the host activates complex mechanisms to recognise and kill pathogens while the pathogen often adjusts its virulence and fitness to avoid eradication by the host. The interaction between the pathogen and the host results in large-scale changes in gene expression in both organisms. Dual RNA-seq, the simultaneous detection of host and pathogen transcripts, has become a leading approach to unravelling complex molecular interactions between the host and the pathogen and is particularly informative for intracellular organisms. The amount of in vitro and in vivo dual RNA-seq data is rapidly growing, which demands computational pipelines to effectively analyse such data. In particular, holistic, systems-level, and temporal analyses of dual RNA-seq data are essential to enable further insights into the host-pathogen transcriptional dynamics and potential interactions. Here, we developed an integrative network-driven bioinformatics pipeline, dRNASb, a systems biology-based computational pipeline to analyse temporal transcriptional clusters, incorporate molecular interaction networks (e.g. protein-protein interactions), identify topologically and functionally key transcripts in host and pathogen, and associate host and pathogen temporal transcriptome to decipher potential between-species interactions. The pipeline is applicable to various dual RNA-seq data from different species and experimental conditions. As a case study, we applied dRNASb to analyse temporal dual RNA-seq data of Salmonella-infected human cells, which enabled us to uncover genes contributing to the infection process and their potential functions and to identify putative associations between host and pathogen genes during infection. Overall, dRNASb has the potential to identify key genes involved in bacterial growth or host defence mechanisms for future uses as therapeutic targets.
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Affiliation(s)
- Mojdeh Dinarvand
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Forrest C Koch
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Daniel Al Mouiee
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
- Ingham Institute for Applied Medical Research, Liverpool, NSW, Australia
- UNSW Data Science Hub, University of New South Wales, Sydney, NSW, Australia
| | - Kaylee Vuong
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Abhishek Vijayan
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Afia Fariha Tanzim
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - A K M Azad
- ProCan®, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW, Australia
| | - Anahit Penesyan
- School of Natural Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, NSW, Australia
| | - Natalia Castaño-Rodríguez
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Fatemeh Vafaee
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
- UNSW Data Science Hub, University of New South Wales, Sydney, NSW, Australia
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Song Q, Nasri U, Zeng D. Steroid-Refractory Gut Graft-Versus-Host Disease: What We Have Learned From Basic Immunology and Experimental Mouse Model. Front Immunol 2022; 13:844271. [PMID: 35251043 PMCID: PMC8894323 DOI: 10.3389/fimmu.2022.844271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Accepted: 01/26/2022] [Indexed: 11/23/2022] Open
Abstract
Intestinal graft-versus-host disease (Gut-GVHD) is one of the major causes of mortality after allogeneic hematopoietic stem cell transplantation (allo-HSCT). While systemic glucocorticoids (GCs) comprise the first-line treatment option, the response rate for GCs varies from 30% to 50%. The prognosis for patients with steroid-refractory acute Gut-GVHD (SR-Gut-aGVHD) remains dismal. The mechanisms underlying steroid resistance are unclear, and apart from ruxolitinib, there are no approved treatments for SR-Gut-aGVHD. In this review, we provide an overview of the current biological understanding of experimental SR-Gut-aGVHD pathogenesis, the advanced technology that can be applied to the human SR-Gut-aGVHD studies, and the potential novel therapeutic options for patients with SR-Gut-aGVHD.
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Affiliation(s)
- Qingxiao Song
- Arthur D. Riggs Diabetes and Metabolism Research Institute, The Beckman Research Institute, City of Hope National Medical Center, Duarte, CA, United States
- Hematologic Malignancies and Stem Cell Transplantation Institute, City of Hope National Medical Center, Duarte, CA, United States
- Fujian Medical University Center of Translational Hematology, Fujian Institute of Hematology, and Fujian Medical University Union Hospital, Fuzhou, China
- *Correspondence: Qingxiao Song,
| | - Ubaydah Nasri
- Arthur D. Riggs Diabetes and Metabolism Research Institute, The Beckman Research Institute, City of Hope National Medical Center, Duarte, CA, United States
- Hematologic Malignancies and Stem Cell Transplantation Institute, City of Hope National Medical Center, Duarte, CA, United States
| | - Defu Zeng
- Arthur D. Riggs Diabetes and Metabolism Research Institute, The Beckman Research Institute, City of Hope National Medical Center, Duarte, CA, United States
- Hematologic Malignancies and Stem Cell Transplantation Institute, City of Hope National Medical Center, Duarte, CA, United States
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Jacob C, Velásquez AC, Josh NA, Settles M, He SY, Melotto M. Dual transcriptomic analysis reveals metabolic changes associated with differential persistence of human pathogenic bacteria in leaves of Arabidopsis and lettuce. G3 (BETHESDA, MD.) 2021; 11:jkab331. [PMID: 34550367 PMCID: PMC8664426 DOI: 10.1093/g3journal/jkab331] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 09/09/2021] [Indexed: 11/14/2022]
Abstract
Understanding the molecular determinants underlying the interaction between the leaf and human pathogenic bacteria is key to provide the foundation to develop science-based strategies to prevent or decrease the pathogen contamination of leafy greens. In this study, we conducted a dual RNA-sequencing analysis to simultaneously define changes in the transcriptomic profiles of the plant and the bacterium when they come in contact. We used an economically relevant vegetable crop, lettuce (Lactuca sativa L. cultivar Salinas), and a model plant, Arabidopsis thaliana Col-0, as well as two pathogenic bacterial strains that cause disease outbreaks associated with fresh produce, Escherichia coli O157:H7 and Salmonella enterica serovar Typhimurium 14028s (STm 14028s). We observed commonalities and specificities in the modulation of biological processes between Arabidopsis and lettuce and between O157:H7 and STm 14028s during early stages of the interaction. We detected a larger alteration of gene expression at the whole transcriptome level in lettuce and Arabidopsis at 24 h post inoculation with STm 14028s compared to that with O157:H7. In addition, bacterial transcriptomic adjustments were substantially larger in Arabidopsis than in lettuce. Bacterial transcriptome was affected at a larger extent in the first 4 h compared to the subsequent 20 h after inoculation. Overall, we gained valuable knowledge about the responses and counter-responses of both bacterial pathogen and plant host when these bacteria are residing in the leaf intercellular space. These findings and the public genomic resources generated in this study are valuable for additional data mining.
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Affiliation(s)
- Cristián Jacob
- Department of Plant Sciences, University of California, Davis, Davis, CA 95616, USA
- Department of Plant Sciences, Horticulture and Agronomy Graduate Group, University of California, Davis, Davis, CA 95616, USA
- Departamento de Ciencias Vegetales, Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile
| | - André C Velásquez
- Department of Biology, Howard Hughes Medical Institute, Duke University, Durham, NC 27708, USA
| | - Nikhil A Josh
- Bioinformatics Core Facility in the Genome Center, University of California, Davis, Davis, CA 95616, USA
| | - Matthew Settles
- Bioinformatics Core Facility in the Genome Center, University of California, Davis, Davis, CA 95616, USA
| | - Sheng Yang He
- Department of Biology, Howard Hughes Medical Institute, Duke University, Durham, NC 27708, USA
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - Maeli Melotto
- Department of Plant Sciences, University of California, Davis, Davis, CA 95616, USA
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5
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Molecular insights into the mechanisms of susceptibility of Labeo rohita against oomycete Aphanomyces invadans. Sci Rep 2020; 10:19531. [PMID: 33177569 PMCID: PMC7658212 DOI: 10.1038/s41598-020-76278-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 10/20/2020] [Indexed: 01/22/2023] Open
Abstract
Aphanomyces invadans, the causative agent of epizootic ulcerative syndrome, is one of the most destructive pathogens of freshwater fishes. To date, the disease has been reported from over 160 fish species in 20 countries and notably, this is the first non-salmonid disease that has resulted in major impacts globally. In particular, Indian major carps (IMCs) are highly susceptible to this disease. To increase our knowledge particularly with regards to host immune response against A. invadans infection in a susceptible host, the gene expression profile in head kidney of A. invadans-infected and control rohu, Labeo rohita was investigated using RNA sequencing. Time course analysis of RNA-Seq data revealed 5608 differentially expressed genes, involved among others in Antigen processing and presentation, Leukocyte transendothelial migration, IL-17 signaling, Chemokine signaling, C-type lectin receptor signaling and Toll-like receptor signaling pathways. In the affected pathways, a number of immune genes were found to be downregulated, suggesting an immune evasion strategy of A. invadans in establishing the infection. The information generated in this study offers first systematic mechanistic understanding of the host–pathogen interaction that might underpin the development of new management strategies for this economically devastating fish-pathogenic oomycete A. invadans.
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Hayward RJ, Marsh JW, Humphrys MS, Huston WM, Myers GSA. Early Transcriptional Landscapes of Chlamydia trachomatis-Infected Epithelial Cells at Single Cell Resolution. Front Cell Infect Microbiol 2019; 9:392. [PMID: 31803632 PMCID: PMC6877545 DOI: 10.3389/fcimb.2019.00392] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 11/01/2019] [Indexed: 12/22/2022] Open
Abstract
Chlamydia are Gram-negative obligate intracellular bacterial pathogens responsible for a variety of disease in humans and animals worldwide. Chlamydia trachomatis causes trachoma in disadvantaged populations, and is the most common bacterial sexually transmitted infection in humans, causing reproductive tract disease. Antibiotic therapy successfully treats diagnosed chlamydial infections, however asymptomatic infections are common. High-throughput transcriptomic approaches have explored chlamydial gene expression and infected host cell gene expression. However, these were performed on large cell populations, averaging gene expression profiles across all cells sampled and potentially obscuring biologically relevant subsets of cells. We generated a pilot dataset, applying single cell RNA-Seq (scRNA-Seq) to C. trachomatis infected and mock-infected epithelial cells to assess the utility, pitfalls and challenges of single cell approaches applied to chlamydial biology, and to potentially identify early host cell biomarkers of chlamydial infection. Two hundred sixty-four time-matched C. trachomatis-infected and mock-infected HEp-2 cells were collected and subjected to scRNA-Seq. After quality control, 200 cells were retained for analysis. Two distinct clusters distinguished 3-h cells from 6- and 12-h. Pseudotime analysis identified a possible infection-specific cellular trajectory for Chlamydia-infected cells, while differential expression analyses found temporal expression of metallothioneins and genes involved with cell cycle regulation, innate immune responses, cytoskeletal components, lipid biosynthesis and cellular stress. We find that changes to the host cell transcriptome at early times of C. trachomatis infection are readily discernible by scRNA-Seq, supporting the utility of single cell approaches to identify host cell biomarkers of chlamydial infection, and to further deconvolute the complex host response to infection.
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Affiliation(s)
- Regan J. Hayward
- Faculty of Science, School of Life Sciences, The ithree Institute, University of Technology Sydney, Ultimo, NSW, Australia
| | - James W. Marsh
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Michael S. Humphrys
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Wilhelmina M. Huston
- Faculty of Science, School of Life Sciences, University of Technology Sydney, Ultimo, NSW, Australia
| | - Garry S. A. Myers
- Faculty of Science, School of Life Sciences, The ithree Institute, University of Technology Sydney, Ultimo, NSW, Australia
- Faculty of Science, School of Life Sciences, University of Technology Sydney, Ultimo, NSW, Australia
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Holtan SG, Shabaneh A, Betts BC, Rashidi A, MacMillan ML, Ustun C, Amin K, Vaughn BP, Howard J, Khoruts A, Arora M, DeFor TE, Johnson D, Blazar BR, Weisdorf DJ, Wang J. Stress responses, M2 macrophages, and a distinct microbial signature in fatal intestinal acute graft-versus-host disease. JCI Insight 2019; 5:129762. [PMID: 31393854 DOI: 10.1172/jci.insight.129762] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Steroid-refractory intestinal acute graft-versus-host disease (aGVHD) is a frequently fatal condition with little known about mechanisms driving failed steroid responses in gut mucosa. To uncover novel molecular insights in steroid-refractory aGVHD, we compared gene expression profiles of rectosigmoid biopsies from patients at diagnosis of clinical stage 3-4 lower intestinal aGVHD (N=22), to repeat biopsies when the patients became steroid refractory (N=22), and normal controls (N=10). We also performed single gene analyses of factors associated with tolerance (programmed death ligand-1 [PDL1], indoleamine 2,3 dioxygenase [IDO1], and T cell immunoreceptor with Ig and ITIM domains [TIGIT]) and found that significantly higher expression levels of these aGVHD inhibitory genes (PDL1, IDO1, TIGIT) at aGVHD onset became decreased in the steroid-refractory state. We examined genes triggered by microbial ligands to stimulate gut repair, amphiregulin (AREG) and the aryl hydrocarbon receptor (AhR), and found that both AREG and AhR gene expression levels were increased at aGVHD onset and remained elevated in steroid-refractory aGVHD. We also identified higher expression levels of metallothioneines, metal-binding enzymes induced in stress responses, and M2 macrophage genes in steroid-refractory aGVHD. We observed no differences in T-cell subsets between onset and steroid-refractory aGVHD. Patients with a rapidly fatal course showed greater DNA damage and a distinct microbial signature at aGVHD onset, whereas patients with more prolonged survival exhibited a gene expression profile consistent with activation of Smoothened. Our results extend the paradigm beyond T cell-centric therapies for steroid-refractory GI aGVHD and highlight new mechanisms for therapeutic exploration.
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Affiliation(s)
| | | | - Brian C Betts
- Blood and Marrow Transplant Program, Department of Medicine
| | - Armin Rashidi
- Blood and Marrow Transplant Program, Department of Medicine
| | - Margaret L MacMillan
- Blood and Marrow Transplant Program, Department of Pediatrics, University of Minnesota, Minneapolis, Minnesota, USA
| | - Celalletin Ustun
- Rush University Blood and Marrow Transplant Program, Chicago, Illinois, USA
| | | | | | - Justin Howard
- Division of Gastroenterology, Department of Medicine
| | | | - Mukta Arora
- Blood and Marrow Transplant Program, Department of Medicine
| | | | | | - Bruce R Blazar
- Blood and Marrow Transplant Program, Department of Pediatrics, University of Minnesota, Minneapolis, Minnesota, USA
| | | | - Jinhua Wang
- Cancer Bioinformatics, Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA
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Marsh JW, Hayward RJ, Shetty A, Mahurkar A, Humphrys MS, Myers GSA. Dual RNA-Seq of Chlamydia and Host Cells. Methods Mol Biol 2019; 2042:123-135. [PMID: 31385273 DOI: 10.1007/978-1-4939-9694-0_9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
During the infection of a host cell by a bacterial pathogen, a cascading series of gene expression changes occurs as each organism manipulates or responds to the other via defense or survival strategies. Unraveling this complex interplay is key for our understanding of bacterial virulence and host response pathways for the development of novel therapeutics. Dual RNA sequencing (dual RNA-Seq) has recently been developed to simultaneously capture host and bacterial transcriptomes from an infected cell. Leveraging the sensitivity and resolution allowed by RNA-seq, dual RNA-Seq can be applied to any bacteria-eukaryotic host interaction. We pioneered dual RNA-Seq to simultaneously capture Chlamydia and host expression profiles during an in vitro infection as proof of principle. Here we provide a detailed laboratory protocol and bioinformatics analysis guidelines for dual RNA-seq experiments focusing on Chlamydia as the organism of interest.
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Affiliation(s)
- James W Marsh
- The iThree Institute, University of Technology Sydney, Ultimo, NSW, Australia
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Regan J Hayward
- The iThree Institute, University of Technology Sydney, Ultimo, NSW, Australia
| | - Amol Shetty
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MA, USA
| | - Anup Mahurkar
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MA, USA
| | - Michael S Humphrys
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MA, USA
| | - Garry S A Myers
- The iThree Institute, University of Technology Sydney, Ultimo, NSW, Australia.
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Afify HM, Al-Masni MA. Taxonomy metagenomic analysis for microbial sequences in three domains system via machine learning approaches. INFORMATICS IN MEDICINE UNLOCKED 2018. [DOI: 10.1016/j.imu.2018.05.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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10
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Marsh JW, Humphrys MS, Myers GSA. A Laboratory Methodology for Dual RNA-Sequencing of Bacteria and their Host Cells In Vitro. Front Microbiol 2017; 8:1830. [PMID: 28983295 PMCID: PMC5613115 DOI: 10.3389/fmicb.2017.01830] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Accepted: 09/06/2017] [Indexed: 12/15/2022] Open
Abstract
Dual RNA-Sequencing leverages established next-generation sequencing (NGS)-enabled RNA-Seq approaches to measure genome-wide transcriptional changes of both an infecting bacteria and host cells. By simultaneously investigating both organisms from the same biological sample, dual RNA-Seq can provide unique insight into bacterial infection processes and reciprocal host responses at once. However, the difficulties involved in handling both prokaryotic and eukaryotic material require distinct, optimized procedures. We previously developed and applied dual RNA-Seq to measure prokaryotic and eukaryotic expression profiles of human cells infected with bacteria, using in vitro Chlamydia-infected epithelial cells as proof of principle. Here we provide a detailed laboratory protocol for in vitro dual RNA-Seq that is readily adaptable to any host-bacteria system of interest.
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Affiliation(s)
- James W Marsh
- School of Life Sciences, The ithree institute, University of Technology SydneyUltimo, NSW, Australia
| | - Michael S Humphrys
- Institute for Genome Sciences, University of Maryland School of MedicineBaltimore, MD, United States
| | - Garry S A Myers
- School of Life Sciences, The ithree institute, University of Technology SydneyUltimo, NSW, Australia
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