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He J, Ganesamoorthy D, Chang JJY, Zhang J, Trevor SL, Gibbons KS, McPherson SJ, Kling JC, Schlapbach LJ, Blumenthal A, Coin LJM. Utilizing Nanopore direct RNA sequencing of blood from patients with sepsis for discovery of co- and post-transcriptional disease biomarkers. BMC Infect Dis 2025; 25:692. [PMID: 40355874 PMCID: PMC12070577 DOI: 10.1186/s12879-025-11078-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2025] [Accepted: 05/02/2025] [Indexed: 05/15/2025] Open
Abstract
BACKGROUND RNA sequencing of whole blood has been increasingly employed to find transcriptomic signatures of disease states. These studies traditionally utilize short-read sequencing of cDNA, missing important aspects of RNA expression such as differential isoform abundance and poly(A) tail length variation. METHODS We used Oxford Nanopore Technologies sequencing to sequence native mRNA extracted from whole blood from 12 patients with definite bacterial and viral sepsis and compared with results from matching Illumina short-read cDNA sequencing data. Additionally, we explored poly(A) tail length variation, novel transcript identification, and differential transcript usage. RESULTS The correlation of gene count data between Illumina cDNA- and Nanopore RNA-sequencing strongly depended on the choice of analysis pipeline; NanoCount for Nanopore and Kallisto for Illumina data yielded the highest mean Pearson's correlation of 0.927 at the gene level and 0.736 at the transcript isoform level. We identified 2 genes with differential polyadenylation, 9 genes with differential expression and 4 genes with differential transcript usage between bacterial and viral infection. Gene ontology gene set enrichment analysis of poly(A) tail length revealed enrichment of long tails in mRNA of genes involved in signaling and short tails in oxidoreductase molecular functions. Additionally, we detected 240 non-artifactual novel transcript isoforms. CONCLUSIONS Nanopore RNA- and Illumina cDNA-gene counts are strongly correlated, indicating that both platforms are suitable for discovery and validation of gene count biomarkers. Nanopore direct RNA-seq provides additional advantages by uncovering additional post- and co-transcriptional biomarkers, such as poly(A) tail length variation and transcript isoform usage.
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Affiliation(s)
- Jingni He
- Department of Clinical Pathology, The University of Melbourne, Parkville, Australia
| | - Devika Ganesamoorthy
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
- Children's Intensive Care Research Program, Child Health Research Centre, The University of Queensland, Brisbane, Australia
| | - Jessie J-Y Chang
- Department of Microbiology and Immunology, The University of Melbourne, Parkville, Australia
| | - Jianshu Zhang
- Department of Microbiology and Immunology, The University of Melbourne, Parkville, Australia
| | - Sharon L Trevor
- Department of Microbiology and Immunology, The University of Melbourne, Parkville, Australia
| | - Kristen S Gibbons
- Children's Intensive Care Research Program, Child Health Research Centre, The University of Queensland, Brisbane, Australia
| | | | - Jessica C Kling
- Frazer Institute, The University of Queensland, Brisbane, Australia
| | - Luregn J Schlapbach
- Children's Intensive Care Research Program, Child Health Research Centre, The University of Queensland, Brisbane, Australia
- Department of Intensive Care and Neonatology, and Children's Research Center, University Children's Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Antje Blumenthal
- Frazer Institute, The University of Queensland, Brisbane, Australia
| | - Lachlan J M Coin
- Department of Clinical Pathology, The University of Melbourne, Parkville, Australia.
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia.
- Department of Microbiology and Immunology, The University of Melbourne, Parkville, Australia.
- Department of Infectious Disease, Imperial College London, London, UK.
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2
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Nilaweera KN, Nychyk O, McCarthy W, Moreira LPD, Alabedallat QM, Purfied D, Doyle J, Cormican P, Santos A, Yin X, Tobin J, Speakman JR, Berry D, Brennan L, Cotter PD. The Sex Dependent and Independent Effects of Dietary Whey Proteins Are Passed from the Mother to the Offspring. Mol Nutr Food Res 2024; 68:e2400584. [PMID: 39491812 DOI: 10.1002/mnfr.202400584] [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] [Received: 07/26/2024] [Revised: 10/11/2024] [Indexed: 11/05/2024]
Abstract
SCOPE The study assesses the metabolic impact of dietary whey proteins across generations. METHOD AND RESULTS Virgin females are fed 20% energy whey proteins with 70% energy carbohydrates, which reduces body weight gain and visceral adipose compared to controls fed dietary casein. In contrast, the males are unresponsive. The effect is accentuated in reproductive females that also have reduced plasma levels of glucose. The responsive females have increased cecal levels of pyruvic and lactic acid, suggesting a greater catabolism of carbohydrates in the gut. While the male and female offspring born to mothers on whey proteins continue to reduce body weight gain, the female offspring further decreases the visceral and subcutaneous tissues and increases the gut capacity to breakdown dietary carbohydrates and proteins, whereas the male offspring are able to only decrease the visceral and increase protein catabolism in the gut. The ileum of male mice responded by reducing the gene expression for fibroblast growth factor 15 and increasing the expression of chymotrypsinogen B1. CONCLUSION The effect of whey proteins on growth can be passed from the mother to the offspring without a sex preference, whereas the transmission of gut activity and adiposity are dependent on the sex of the offspring.
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Affiliation(s)
- Kanishka N Nilaweera
- Food Bioscience Department, Teagasc Food Research Centre, Moorepark, County Cork, Fermoy, P61 C996, Ireland
- VistaMilk Research Centre, Teagasc, Moorepark, County Cork, Fermoy, P61 C996, Ireland
| | - Oleksandr Nychyk
- Food Bioscience Department, Teagasc Food Research Centre, Moorepark, County Cork, Fermoy, P61 C996, Ireland
| | - William McCarthy
- VistaMilk Research Centre, Teagasc, Moorepark, County Cork, Fermoy, P61 C996, Ireland
- Food Chemistry and Technology Department, Teagasc Food Research Centre, Moorepark, County Cork, Fermoy, P61 C996, Ireland
| | - Luiza P D Moreira
- Food Bioscience Department, Teagasc Food Research Centre, Moorepark, County Cork, Fermoy, P61 C996, Ireland
- VistaMilk Research Centre, Teagasc, Moorepark, County Cork, Fermoy, P61 C996, Ireland
| | - Qusai M Alabedallat
- Food Bioscience Department, Teagasc Food Research Centre, Moorepark, County Cork, Fermoy, P61 C996, Ireland
- VistaMilk Research Centre, Teagasc, Moorepark, County Cork, Fermoy, P61 C996, Ireland
| | - Deirdre Purfied
- Animal Bioscience Department, Teagasc Food Research Centre, Moorepark, County Cork, Fermoy, P61 C996, Ireland
| | - Jennifer Doyle
- Animal Bioscience Department, Teagasc Food Research Centre, Moorepark, County Cork, Fermoy, P61 C996, Ireland
| | - Paul Cormican
- Animal and Grassland Research and Innovation Centre, Teagasc, Grange, County Meath, Dunsany, C15 PW93, Ireland
| | - Antonia Santos
- Teagasc Food Research Centre, Ashtown, Dublin, D15 DY05, Ireland
| | - Xiaofei Yin
- School of Agriculture and Food Science, Institute of Food and Health and Conway Institute, University College Dublin, Dublin, D04 C1P1, Ireland
| | - John Tobin
- VistaMilk Research Centre, Teagasc, Moorepark, County Cork, Fermoy, P61 C996, Ireland
- Food Chemistry and Technology Department, Teagasc Food Research Centre, Moorepark, County Cork, Fermoy, P61 C996, Ireland
| | - John R Speakman
- School of Biological Sciences, University of Aberdeen, Aberdeen, AB24 2TZ, UK
| | - Donagh Berry
- VistaMilk Research Centre, Teagasc, Moorepark, County Cork, Fermoy, P61 C996, Ireland
- Animal Bioscience Department, Teagasc Food Research Centre, Moorepark, County Cork, Fermoy, P61 C996, Ireland
| | - Lorraine Brennan
- VistaMilk Research Centre, Teagasc, Moorepark, County Cork, Fermoy, P61 C996, Ireland
- School of Agriculture and Food Science, Institute of Food and Health and Conway Institute, University College Dublin, Dublin, D04 C1P1, Ireland
| | - Paul D Cotter
- Food Bioscience Department, Teagasc Food Research Centre, Moorepark, County Cork, Fermoy, P61 C996, Ireland
- VistaMilk Research Centre, Teagasc, Moorepark, County Cork, Fermoy, P61 C996, Ireland
- APC Microbiome Ireland, University College Cork, Cork T12 YT20, Ireland
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Trionfetti F, Montaldo C, Caiello I, Bontempi G, Terri M, Tiberi M, Marchant V, Domenici A, Menè P, Cordani M, Zwergel C, Prencipe G, Ruiz-Ortega M, Valente S, Mai A, Tripodi M, Strippoli R. Mechanisms of mesothelial cell response to viral infections: HDAC1-3 inhibition blocks poly(I:C)-induced type I interferon response and modulates the mesenchymal/inflammatory phenotype. Front Cell Infect Microbiol 2024; 14:1308362. [PMID: 38476167 PMCID: PMC10927979 DOI: 10.3389/fcimb.2024.1308362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 01/24/2024] [Indexed: 03/14/2024] Open
Abstract
Infectious peritonitis is a leading cause of peritoneal functional impairment and a primary factor for therapy discontinuation in peritoneal dialysis (PD) patients. Although bacterial infections are a common cause of peritonitis episodes, emerging evidence suggests a role for viral pathogens. Toll-like receptors (TLRs) specifically recognize conserved pathogen-associated molecular patterns (PAMPs) from bacteria, viruses, and fungi, thereby orchestrating the ensuing inflammatory/immune responses. Among TLRs, TLR3 recognizes viral dsRNA and triggers antiviral response cascades upon activation. Epigenetic regulation, mediated by histone deacetylase (HDAC), has been demonstrated to control several cellular functions in response to various extracellular stimuli. Employing epigenetic target modulators, such as epidrugs, is a current therapeutic option in several cancers and holds promise in treating viral diseases. This study aims to elucidate the impact of TLR3 stimulation on the plasticity of human mesothelial cells (MCs) in PD patients and to investigate the effects of HDAC1-3 inhibition. Treatment of MCs from PD patients with the TLR3 agonist polyinosinic:polycytidylic acid (Poly(I:C)), led to the acquisition of a bona fide mesothelial-to-mesenchymal transition (MMT) characterized by the upregulation of mesenchymal genes and loss of epithelial-like features. Moreover, Poly(I:C) modulated the expression of several inflammatory cytokines and chemokines. A quantitative proteomic analysis of MCs treated with MS-275, an HDAC1-3 inhibitor, unveiled altered expression of several proteins, including inflammatory cytokines/chemokines and interferon-stimulated genes (ISGs). Treatment with MS-275 facilitated MMT reversal and inhibited the interferon signature, which was associated with reduced STAT1 phosphorylation. However, the modulation of inflammatory cytokine/chemokine production was not univocal, as IL-6 and CXCL8 were augmented while TNF-α and CXCL10 were decreased. Collectively, our findings underline the significance of viral infections in acquiring a mesenchymal-like phenotype by MCs and the potential consequences of virus-associated peritonitis episodes for PD patients. The observed promotion of MMT reversal and interferon response inhibition by an HDAC1-3 inhibitor, albeit without a general impact on inflammatory cytokine production, has translational implications deserving further analysis.
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Affiliation(s)
- Flavia Trionfetti
- Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
- Gene Expression Laboratory, National Institute for Infectious Diseases, Lazzaro Spallanzani IRCCS, Rome, Italy
| | - Claudia Montaldo
- Gene Expression Laboratory, National Institute for Infectious Diseases, Lazzaro Spallanzani IRCCS, Rome, Italy
| | - Ivan Caiello
- Division of Rheumatology, Ospedale Pediatrico Bambino Gesù IRCCS, Rome, Italy
| | - Giulio Bontempi
- Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
- Gene Expression Laboratory, National Institute for Infectious Diseases, Lazzaro Spallanzani IRCCS, Rome, Italy
| | - Michela Terri
- Gene Expression Laboratory, National Institute for Infectious Diseases, Lazzaro Spallanzani IRCCS, Rome, Italy
| | - Marta Tiberi
- Gene Expression Laboratory, National Institute for Infectious Diseases, Lazzaro Spallanzani IRCCS, Rome, Italy
| | - Vanessa Marchant
- Cellular Biology in Renal Diseases Laboratory, IIS-Fundación Jiménez Díaz-Universidad Autónoma Madrid, Madrid, Spain
- 15 REDINREN/RICORS2040, Madrid, Spain
| | - Alessandro Domenici
- Renal Unit, Department of Clinical and Molecular Medicine, Sant’Andrea University Hospital, Sapienza University of Rome, Rome, Italy
| | - Paolo Menè
- Renal Unit, Department of Clinical and Molecular Medicine, Sant’Andrea University Hospital, Sapienza University of Rome, Rome, Italy
| | - Marco Cordani
- Department of Biochemistry and Molecular Biology, Faculty of Biology, Complutense University of Madrid, Madrid, Spain
- Instituto de Investigaciones Sanitarias San Carlos (IdISSC), Madrid, Spain
| | - Clemens Zwergel
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, Rome, Italy
| | - Giusi Prencipe
- Division of Rheumatology, Ospedale Pediatrico Bambino Gesù IRCCS, Rome, Italy
| | - Marta Ruiz-Ortega
- Cellular Biology in Renal Diseases Laboratory, IIS-Fundación Jiménez Díaz-Universidad Autónoma Madrid, Madrid, Spain
- 15 REDINREN/RICORS2040, Madrid, Spain
| | - Sergio Valente
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, Rome, Italy
| | - Antonello Mai
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, Rome, Italy
| | - Marco Tripodi
- Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
- Gene Expression Laboratory, National Institute for Infectious Diseases, Lazzaro Spallanzani IRCCS, Rome, Italy
| | - Raffaele Strippoli
- Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
- Gene Expression Laboratory, National Institute for Infectious Diseases, Lazzaro Spallanzani IRCCS, Rome, Italy
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Vuletić A, Mirjačić Martinović K, Spasić J. Role of Histone Deacetylase 6 and Histone Deacetylase 6 Inhibition in Colorectal Cancer. Pharmaceutics 2023; 16:54. [PMID: 38258065 PMCID: PMC10818982 DOI: 10.3390/pharmaceutics16010054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 12/22/2023] [Accepted: 12/27/2023] [Indexed: 01/24/2024] Open
Abstract
Histone deacetylase 6 (HDAC6), by deacetylation of multiple substrates and association with interacting proteins, regulates many physiological processes that are involved in cancer development and invasiveness such as cell proliferation, apoptosis, motility, epithelial to mesenchymal transition, and angiogenesis. Due to its ability to remove misfolded proteins, induce autophagy, and regulate unfolded protein response, HDAC6 plays a protective role in responses to stress and enables tumor cell survival. The scope of this review is to discuss the roles of HDCA6 and its implications for the therapy of colorectal cancer (CRC). As HDAC6 is overexpressed in CRC, correlates with poor disease prognosis, and is not essential for normal mammalian development, it represents a good therapeutic target. Selective inhibition of HDAC6 impairs growth and progression without inducing major adverse events in experimental animals. In CRC, HDAC6 inhibitors have shown the potential to reduce tumor progression and enhance the therapeutic effect of other drugs. As HDAC6 is involved in the regulation of immune responses, HDAC6 inhibitors have shown the potential to improve antitumor immunity by increasing the immunogenicity of tumor cells, augmenting immune cell activity, and alleviating immunosuppression in the tumor microenvironment. Therefore, HDAC6 inhibitors may represent promising candidates to improve the effect of and overcome resistance to immunotherapy.
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Affiliation(s)
- Ana Vuletić
- Department of Experimental Oncology, Institute of Oncology and Radiology of Serbia, Pasterova 14, 11000 Belgrade, Serbia;
| | - Katarina Mirjačić Martinović
- Department of Experimental Oncology, Institute of Oncology and Radiology of Serbia, Pasterova 14, 11000 Belgrade, Serbia;
| | - Jelena Spasić
- Clinic for Medical Oncology, Institute of Oncology and Radiology of Serbia, Pasterova 14, 11000 Belgrade, Serbia;
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Rodríguez Mesa XM, Contreras Bolaños LA, Modesti Costa G, Mejia AL, Santander González SP. A Bidens pilosa L. Non-Polar Extract Modulates the Polarization of Human Macrophages and Dendritic Cells into an Anti-Inflammatory Phenotype. Molecules 2023; 28:7094. [PMID: 37894572 PMCID: PMC10608814 DOI: 10.3390/molecules28207094] [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] [Received: 08/28/2023] [Revised: 10/03/2023] [Accepted: 10/10/2023] [Indexed: 10/29/2023] Open
Abstract
Different communities around the world traditionally use Bidens pilosa L. for medicinal purposes, mainly for its anti-inflammatory, antinociceptive, and antioxidant properties; it is used as an ingredient in teas or herbal medicines for the treatment of pain, inflammation, and immunological disorders. Several studies have been conducted that prove the immunomodulatory properties of this plant; however, it is not known whether the immunomodulatory properties of B. pilosa are mediated by its ability to modulate antigen-presenting cells (APCs) such as macrophages (MØs) and dendritic cells (DCs) (through polarization or the maturation state, respectively). Different polar and non-polar extracts and fractions were prepared from the aerial part of B. pilosa. Their cytotoxic and immunomodulatory effects were first tested on human peripheral blood mononuclear cells (PBMCs) and phytohemagglutinin (PHA)-stimulated PBMCs, respectively, via an MTT assay. Then, the non-cytotoxic plant extracts and fractions that showed the highest immunomodulatory activity were selected to evaluate their effects on human MØ polarization and DC maturation (cell surface phenotype and cytokine secretion) through multiparametric flow cytometry. Finally, the chemical compounds of the B. pilosa extract that showed the most significant immunomodulatory effects on human APCs were identified using gas chromatography coupled with mass spectrometry. The petroleum ether extract and the ethyl acetate and hydroalcoholic fractions obtained from B. pilosa showed low cytotoxicity and modulated the PHA-stimulated proliferation of PBMCs. Furthermore, the B. pilosa petroleum ether extract induced M2 polarization or a hybrid M1/M2 phenotype in MØs and a semi-mature status in DCs, regardless of exposure to a maturation stimulus. The immunomodulatory activity of the non-polar (petroleum ether) extract of B. pilosa on human PBMC proliferation, M2 polarization of MØs, and semi-mature status in DCs might be attributed to the low-medium polarity components in the extract, such as phytosterol terpenes and fatty acid esters.
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Affiliation(s)
| | | | - Geison Modesti Costa
- Phytochemistry Research Group (GIFUJ), Pontificia Universidad Javeriana, Bogotá 110231, Colombia
| | - Antonio Luis Mejia
- Phytoimmunomodulation Research Group, Juan N. Corpas University Foundation, Bogotá 111161, Colombia
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de Souza-Silva GA, Sulczewski FB, Boscardin SB. Recombinant antigen delivery to dendritic cells as a way to improve vaccine design. Exp Biol Med (Maywood) 2023; 248:1616-1623. [PMID: 37750021 PMCID: PMC10723026 DOI: 10.1177/15353702231191185] [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] [Indexed: 09/27/2023] Open
Abstract
Dendritic cells are central to the development of immunity, as they are specialized in initiating antigen-specific immune responses. In this review, we briefly present the existing knowledge on dendritic cell biology and how their division in different dendritic cell subsets may impact the development of immune responses. In addition, we explore the use of chimeric monoclonal antibodies that bind to dendritic cell surface receptors, with an emphasis on the C-type lectin family of endocytic receptors, to deliver antigens directly to these cells. Promising preclinical studies have shown that it is possible to modulate the development of immune responses to different pathogens when monoclonal antibodies fused to pathogen-derived antigens are used to deliver the antigen to different subsets of dendritic cells. This approach can be used to improve the efficacy of vaccines against different pathogens.
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Affiliation(s)
| | - Fernando Bandeira Sulczewski
- Departamento de Parasitologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, 05508-000, Brazil
| | - Silvia Beatriz Boscardin
- Departamento de Parasitologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, 05508-000, Brazil
- Instituto de Investigação em Imunologia (iii), Instituto Nacional de Ciência e Tecnologia, São Paulo, 05401-350, Brazil
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