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Brideau G, Cheval L, Griveau C, Ling WME, Lievre L, Crambert G, Müller D, Broćić J, Cherchame E, Houillier P, Prot-Bertoye C. Claudin-10 Expression and the Gene Expression Pattern of Thick Ascending Limb Cells. Int J Mol Sci 2024; 25:4008. [PMID: 38612818 PMCID: PMC11011785 DOI: 10.3390/ijms25074008] [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: 01/31/2024] [Revised: 03/16/2024] [Accepted: 03/27/2024] [Indexed: 04/14/2024] Open
Abstract
Many genomic, anatomical and functional differences exist between the medullary (MTAL) and the cortical thick ascending limb of the loop of Henle (CTAL), including a higher expression of claudin-10 (CLDN10) in the MTAL than in the CTAL. Therefore, we assessed to what extent the Cldn10 gene expression is a determinant of differential gene expression between MTAL and CTAL. RNAs extracted from CTAL and MTAL microdissected from wild type (WT) and Cldn10 knock out mice (cKO) were analyzed by RNAseq. Differential and enrichment analyses (GSEA) were performed with interactive R Shiny software. Between WT and cKO MTAL, 637 genes were differentially expressed, whereas only 76 were differentially expressed between WT and cKO CTAL. Gene expression patterns and GSEA analyses in all replicates showed that WT MTAL did not cluster with the other replicates; no hierarchical clustering could be found between WT CTAL, cKO CTAL and cKO MTAL. Compared to WT replicates, cKO replicates were enriched in Cldn16, Cldn19, Pth1r, (parathyroid hormone receptor type 1), Casr (calcium sensing receptor) and Vdr (Vitamin D Receptor) mRNA in both the cortex and medulla. Cldn10 is associated with gene expression patterns, including genes specifically involved in divalent cations reabsorption in the TAL.
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Affiliation(s)
- Gaelle Brideau
- Centre de Recherche des Cordeliers, Institut National de la Santé et de la Recherche Médicale, Sorbonne Université, Université Paris Cité, F-75006 Paris, France; (G.B.); (L.C.); (C.G.); (W.-M.E.L.); (L.L.); (G.C.)
- Centre National de la Recherche Scientifique, Equipe Mixte de Recherche 8228-Laboratoire de Physiologie Rénale et Tubulopathies, F-75006 Paris, France
| | - Lydie Cheval
- Centre de Recherche des Cordeliers, Institut National de la Santé et de la Recherche Médicale, Sorbonne Université, Université Paris Cité, F-75006 Paris, France; (G.B.); (L.C.); (C.G.); (W.-M.E.L.); (L.L.); (G.C.)
- Centre National de la Recherche Scientifique, Equipe Mixte de Recherche 8228-Laboratoire de Physiologie Rénale et Tubulopathies, F-75006 Paris, France
| | - Camille Griveau
- Centre de Recherche des Cordeliers, Institut National de la Santé et de la Recherche Médicale, Sorbonne Université, Université Paris Cité, F-75006 Paris, France; (G.B.); (L.C.); (C.G.); (W.-M.E.L.); (L.L.); (G.C.)
- Centre National de la Recherche Scientifique, Equipe Mixte de Recherche 8228-Laboratoire de Physiologie Rénale et Tubulopathies, F-75006 Paris, France
| | - Wung-Man Evelyne Ling
- Centre de Recherche des Cordeliers, Institut National de la Santé et de la Recherche Médicale, Sorbonne Université, Université Paris Cité, F-75006 Paris, France; (G.B.); (L.C.); (C.G.); (W.-M.E.L.); (L.L.); (G.C.)
- Centre National de la Recherche Scientifique, Equipe Mixte de Recherche 8228-Laboratoire de Physiologie Rénale et Tubulopathies, F-75006 Paris, France
| | - Loïc Lievre
- Centre de Recherche des Cordeliers, Institut National de la Santé et de la Recherche Médicale, Sorbonne Université, Université Paris Cité, F-75006 Paris, France; (G.B.); (L.C.); (C.G.); (W.-M.E.L.); (L.L.); (G.C.)
- Centre National de la Recherche Scientifique, Equipe Mixte de Recherche 8228-Laboratoire de Physiologie Rénale et Tubulopathies, F-75006 Paris, France
| | - Gilles Crambert
- Centre de Recherche des Cordeliers, Institut National de la Santé et de la Recherche Médicale, Sorbonne Université, Université Paris Cité, F-75006 Paris, France; (G.B.); (L.C.); (C.G.); (W.-M.E.L.); (L.L.); (G.C.)
- Centre National de la Recherche Scientifique, Equipe Mixte de Recherche 8228-Laboratoire de Physiologie Rénale et Tubulopathies, F-75006 Paris, France
| | - Dominik Müller
- Department of Pediatrics, Division of Gastroenterology, Nephrology and Metabolic Diseases, Charité-Universitätsmedizin Berlin, DE-13353 Berlin, Germany;
| | - Jovana Broćić
- Paris Brain Institute (ICM), Hôpital Pitié-Salpêtrière, Inserm U 1127, CNRS UMR 7225, Sorbonne Université, Data Analysis Core Platform, F-75013 Paris, France; (J.B.); (E.C.)
| | - Emeline Cherchame
- Paris Brain Institute (ICM), Hôpital Pitié-Salpêtrière, Inserm U 1127, CNRS UMR 7225, Sorbonne Université, Data Analysis Core Platform, F-75013 Paris, France; (J.B.); (E.C.)
| | - Pascal Houillier
- Centre de Recherche des Cordeliers, Institut National de la Santé et de la Recherche Médicale, Sorbonne Université, Université Paris Cité, F-75006 Paris, France; (G.B.); (L.C.); (C.G.); (W.-M.E.L.); (L.L.); (G.C.)
- Centre National de la Recherche Scientifique, Equipe Mixte de Recherche 8228-Laboratoire de Physiologie Rénale et Tubulopathies, F-75006 Paris, France
- Assistance Publique-Hôpitaux de Paris, Hôpital Européen Georges Pompidou, Service de Physiologie, F-75015 Paris, France
- Centre de Référence des Maladies Rénales Héréditaires de l’Enfant et de l’Adulte (MARHEA), The European Rare Kidney Disease Reference Network (ERKNet), F-75015 Paris, France
- Centre de Référence des Maladies Rares du Calcium et du Phosphate, The European Reference Network on Rare Endocrine Conditions (Endo-ERN), F-75015 Paris, France
- Faculté de Médecine, Université Paris Cité, F-75006 Paris, France
| | - Caroline Prot-Bertoye
- Centre de Recherche des Cordeliers, Institut National de la Santé et de la Recherche Médicale, Sorbonne Université, Université Paris Cité, F-75006 Paris, France; (G.B.); (L.C.); (C.G.); (W.-M.E.L.); (L.L.); (G.C.)
- Centre National de la Recherche Scientifique, Equipe Mixte de Recherche 8228-Laboratoire de Physiologie Rénale et Tubulopathies, F-75006 Paris, France
- Assistance Publique-Hôpitaux de Paris, Hôpital Européen Georges Pompidou, Service de Physiologie, F-75015 Paris, France
- Centre de Référence des Maladies Rénales Héréditaires de l’Enfant et de l’Adulte (MARHEA), The European Rare Kidney Disease Reference Network (ERKNet), F-75015 Paris, France
- Centre de Référence des Maladies Rares du Calcium et du Phosphate, The European Reference Network on Rare Endocrine Conditions (Endo-ERN), F-75015 Paris, France
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Land ES, Sheppard J, Doherty CJ, Perera IY. Conserved plant transcriptional responses to microgravity from two consecutive spaceflight experiments. Front Plant Sci 2024; 14:1308713. [PMID: 38259952 PMCID: PMC10800490 DOI: 10.3389/fpls.2023.1308713] [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] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Accepted: 12/12/2023] [Indexed: 01/24/2024]
Abstract
Introduction Understanding how plants adapt to the space environment is essential, as plants will be a valuable component of long duration space missions. Several spaceflight experiments have focused on transcriptional profiling as a means of understanding plant adaptation to microgravity. However, there is limited overlap between results from different experiments. Differences in experimental conditions and hardware make it difficult to find a consistent response across experiments and to distinguish the primary effects of microgravity from other spaceflight effects. Methods Plant Signaling (PS) and Plant RNA Regulation (PRR) were two separate spaceflight experiments conducted on the International Space Station utilizing the European Modular Cultivation System (EMCS). The EMCS provided a lighted environment for plant growth with centrifugal capabilities providing an onboard 1 g control. Results and discussion An RNA-Seq analysis of shoot samples from PS and PRR revealed a significant overlap of genes differentially expressed in microgravity between the two experiments. Relative to onboard 1 g controls, genes involved in transcriptional regulation, shoot development, and response to auxin and light were upregulated in microgravity in both experiments. Conversely, genes involved in defense response, abiotic stress, Ca++ signaling, and cell wall modification were commonly downregulated in both datasets. The downregulation of stress responses in microgravity in these two experiments is interesting as these pathways have been previously observed as upregulated in spaceflight compared to ground controls. Similarly, we have observed many stress response genes to be upregulated in the 1 g onboard control compared to ground reference controls; however these genes were specifically downregulated in microgravity. In addition, we analyzed the sRNA landscape of the 1 g and microgravity (μ g) shoot samples from PRR. We identified three miRNAs (miR319c, miR398b, and miR8683) which were upregulated in microgravity, while several of their corresponding target genes were found to be downregulated in microgravity. Interestingly, the downregulated target genes are enriched in those encoding chloroplast-localized enzymes and proteins. These results uncover microgravity unique transcriptional changes and highlight the validity and importance of an onboard 1 g control.
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Affiliation(s)
- Eric S. Land
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States
| | - James Sheppard
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC, United States
| | - Colleen J. Doherty
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC, United States
| | - Imara Y. Perera
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States
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Silver KI, Patkar S, Mazcko C, Berger EP, Beck JA, LeBlanc AK. Patterns of metastatic progression and association with clinical outcomes in canine osteosarcoma: A necropsy study of 83 dogs. Vet Comp Oncol 2023; 21:646-655. [PMID: 37592810 PMCID: PMC10842475 DOI: 10.1111/vco.12927] [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: 03/13/2023] [Revised: 07/17/2023] [Accepted: 07/18/2023] [Indexed: 08/19/2023]
Abstract
Osteosarcoma is a highly metastatic primary bone tumour that occurs spontaneously in both pet dogs and humans. Patterns of metastasis to organs beyond the most common site (lung) are poorly characterised and it is unknown whether specific associations between patterns of metastatic progression and patient features exist. This retrospective study characterised the necropsy findings of 83 dogs receiving standardised therapy and clinical monitoring in a prospective clinical trial setting to document patterns of metastasis and correlate outcomes with these patterns and other patient and tumour-specific factors. A total of 20 different sites of metastasis were documented, with lung as the most common site, followed by bone, kidney, liver, and heart. Two distinct clusters of dogs were identified based on patterns of metastasis. There was no significant association between site of enrollment, trial arm, sex, serum alkaline phosphatase (ALP) activity, or tumour location and clinical outcomes. A second cancer type was identified at necropsy in 10 dogs (10/83; 12%). These data showcase the extensive nature of osteosarcoma metastasis beyond the lung and provide a benchmark for clinical monitoring of the disease. Further, this study provides insight into transcriptional features of primary tumours that may relate to a propensity for osteosarcoma metastasis to specific organs and tissues.
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Affiliation(s)
- K I Silver
- Comparative Oncology Program, Molecular Imaging Branch, National Cancer Institute, NIH, Bethesda, Maryland, USA
| | - S Patkar
- Artificial Intelligence Resource, Molecular Imaging Branch, National Cancer Institute, NIH, Bethesda, Maryland, USA
| | - C Mazcko
- Comparative Oncology Program, Molecular Imaging Branch, National Cancer Institute, NIH, Bethesda, Maryland, USA
| | - E P Berger
- Frederick National Laboratory for Cancer Research in the Comparative Oncology Program, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - J A Beck
- Comparative Oncology Program, Molecular Imaging Branch, National Cancer Institute, NIH, Bethesda, Maryland, USA
| | - A K LeBlanc
- Comparative Oncology Program, Molecular Imaging Branch, National Cancer Institute, NIH, Bethesda, Maryland, USA
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Yoshimura Y, Muto Y, Omachi K, Miner JH, Humphreys BD. Elucidating the Proximal Tubule HNF4A Gene Regulatory Network in Human Kidney Organoids. J Am Soc Nephrol 2023; 34:1672-1686. [PMID: 37488681 PMCID: PMC10561821 DOI: 10.1681/asn.0000000000000197] [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: 03/07/2023] [Accepted: 07/08/2023] [Indexed: 07/26/2023] Open
Abstract
SIGNIFICANCE STATEMENT HNF4 genes promote proximal tubule differentiation in mice, but their function in human nephrogenesis is not fully defined. This study uses human pluripotent stem cell (PSC)-derived kidney organoids as a model to investigate HNF4A and HNF4G functions. The loss of HNF4A , but not HNF4G , impaired reabsorption-related molecule expression and microvilli formation in human proximal tubules. Cleavage under targets and release using nuclease (CUT&RUN) sequencing and CRISPR-mediated transcriptional activation (CRISPRa) further confirm that HNF4A directly regulates its target genes. Human kidney organoids provide a good model for studying transcriptional regulation in human kidney development. BACKGROUND The proximal tubule plays a major role in electrolyte homeostasis. Previous studies have shown that HNF4A regulates reabsorption-related genes and promotes proximal tubule differentiation during murine kidney development. However, the functions and gene regulatory mechanisms of HNF4 family genes in human nephrogenesis have not yet been investigated. METHODS We generated HNF4A -knock out (KO), HNF4G -KO, and HNF4A/4G -double KO human pluripotent stem cell lines, differentiated each into kidney organoids, and used immunofluorescence analysis, electron microscopy, and RNA-seq to analyze them. We probed HNF4A-binding sites genome-wide by cleavage under targets and release using nuclease sequencing in both human adult kidneys and kidney organoid-derived proximal tubular cells. Clustered Regularly Interspaced Short Palindromic Repeats-mediated transcriptional activation validated HNF4A and HNF4G function in proximal tubules during kidney organoid differentiation. RESULTS Organoids lacking HNF4A , but not HNF4G , showed reduced expression of transport-related, endocytosis-related, and brush border-related genes, as well as disorganized brush border structure in the apical lumen of the organoid proximal tubule. Cleavage under targets and release using nuclease revealed that HNF4A primarily bound promoters and enhancers of genes that were downregulated in HNF4A -KO, suggesting direct regulation. Induced expression of HNF4A or HNF4G by CRISPR-mediated transcriptional activation drove increased expression of selected target genes during kidney organoid differentiation. CONCLUSIONS This study reveals regulatory mechanisms of HNF4A and HNF4G during human proximal tubule differentiation. The experimental strategy can be applied more broadly to investigate transcriptional regulation in human kidney development.
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Affiliation(s)
- Yasuhiro Yoshimura
- Division of Nephrology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, Missouri
| | - Yoshiharu Muto
- Division of Nephrology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, Missouri
| | - Kohei Omachi
- Division of Nephrology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, Missouri
| | - Jeffrey H. Miner
- Division of Nephrology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, Missouri
| | - Benjamin D. Humphreys
- Division of Nephrology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, Missouri
- Department of Developmental Biology, Washington University in St. Louis School of Medicine, St. Louis, Missouri
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Choudhary S, Mundodi V, Smith AD, Kadosh D. Genome-wide translational response of Candida albicans to fluconazole treatment. Microbiol Spectr 2023; 11:e0257223. [PMID: 37610232 PMCID: PMC10580883 DOI: 10.1128/spectrum.02572-23] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Accepted: 07/05/2023] [Indexed: 08/24/2023] Open
Abstract
Azoles are commonly used for the treatment of fungal infections, and the ability of human fungal pathogens to rapidly respond to azole treatment is critical for the development of antifungal resistance. While the roles of genetic mutations, chromosomal rearrangements, and transcriptional mechanisms in azole resistance have been well-characterized, very little is known about post-transcriptional and translational mechanisms that drive this process. In addition, most previous genome-wide studies have focused on transcriptional responses to azole treatment and likely serve as inaccurate proxies for changes in protein expression due to extensive post-transcriptional and translational regulation. In this study, we use ribosome profiling to provide the first picture of the global translational response of a major human fungal pathogen, Candida albicans, to treatment with fluconazole (Flu), one of the most widely used azole drugs. We identify sets of genes showing significantly altered translational efficiency, including genes associated with a variety of biological processes such as the cell cycle, DNA repair, cell wall/cell membrane biosynthesis, transport, signaling, DNA- and RNA-binding activities, and protein synthesis. We observe both similarities and differences among the most highly represented gene categories (as defined by gene ontology) that are regulated by fluconazole at the translational vs transcriptional levels. Importantly, however, very few genes that are translationally regulated by fluconazole are also controlled transcriptionally under this condition. Our findings suggest that C. albicans possesses distinct translational mechanisms that are important for the response to antifungal treatment, which could eventually be targeted by novel antifungal therapies. IMPORTANCE Azoles are one of the most commonly used drug classes to treat human fungal pathogens. While point mutations, chromosomal rearrangements, and transcriptional mechanisms that drive azole resistance have been well-characterized, we know very little about the role of translational mechanisms. In this study, we determined the global translational profile of genes that are expressed in the major human fungal pathogen Candida albicans in response to fluconazole, one of the most widely used azole drugs. We find both similarities and differences among the most highly represented categories of genes regulated by fluconazole at the transcriptional and translational levels. Interestingly, however, many of the specific genes that are regulated by fluconazole at the translational level do not appear to be controlled by transcriptional mechanisms under this condition. Our results suggest that distinct C. albicans translational mechanisms control the response to antifungals and could eventually be targeted in the development of new therapies.
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Affiliation(s)
- Saket Choudhary
- Quantitative and Computational Biology, University of Southern California, Los Angeles, California, USA
| | - Vasanthakrishna Mundodi
- Department of Microbiology, Immunology, and Molecular Genetics, University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA
| | - Andrew D. Smith
- Quantitative and Computational Biology, University of Southern California, Los Angeles, California, USA
| | - David Kadosh
- Department of Microbiology, Immunology, and Molecular Genetics, University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA
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Killick R, Elliott C, Ribe E, Broadstock M, Ballard C, Aarsland D, Williams G. Neurodegenerative Disease Associated Pathways in the Brains of Triple Transgenic Alzheimer's Model Mice Are Reversed Following Two Weeks of Peripheral Administration of Fasudil. Int J Mol Sci 2023; 24:11219. [PMID: 37446396 PMCID: PMC10342807 DOI: 10.3390/ijms241311219] [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: 06/06/2023] [Revised: 06/30/2023] [Accepted: 07/04/2023] [Indexed: 07/15/2023] Open
Abstract
The pan Rho-associated coiled-coil-containing protein kinase (ROCK) inhibitor fasudil acts as a vasodilator and has been used as a medication for post-cerebral stroke for the past 29 years in Japan and China. More recently, based on the involvement of ROCK inhibition in synaptic function, neuronal survival, and processes associated with neuroinflammation, it has been suggested that the drug may be repurposed for neurodegenerative diseases. Indeed, fasudil has demonstrated preclinical efficacy in many neurodegenerative disease models. To facilitate an understanding of the wider biological processes at play due to ROCK inhibition in the context of neurodegeneration, we performed a global gene expression analysis on the brains of Alzheimer's disease model mice treated with fasudil via peripheral IP injection. We then performed a comparative analysis of the fasudil-driven transcriptional profile with profiles generated from a meta-analysis of multiple neurodegenerative diseases. Our results show that fasudil tends to drive gene expression in a reverse sense to that seen in brains with post-mortem neurodegenerative disease. The results are most striking in terms of pathway enrichment analysis, where pathways perturbed in Alzheimer's and Parkinson's diseases are overwhelmingly driven in the opposite direction by fasudil treatment. Thus, our results bolster the repurposing potential of fasudil by demonstrating an anti-neurodegenerative phenotype in a disease context and highlight the potential of in vivo transcriptional profiling of drug activity.
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Affiliation(s)
- Richard Killick
- Institute of Psychiatry, Psychology and Neuroscience, King’s College London, Denmark Hill, London SE5 8AF, UK; (R.K.); (E.R.); (D.A.)
- College of Medicine and Health, University of Exeter, Exeter EX1 2UL, UK;
| | - Christina Elliott
- Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK;
| | - Elena Ribe
- Institute of Psychiatry, Psychology and Neuroscience, King’s College London, Denmark Hill, London SE5 8AF, UK; (R.K.); (E.R.); (D.A.)
| | - Martin Broadstock
- Wolfson CARD, King’s College London, London Bridge, London SE1 1UL, UK;
| | - Clive Ballard
- College of Medicine and Health, University of Exeter, Exeter EX1 2UL, UK;
| | - Dag Aarsland
- Institute of Psychiatry, Psychology and Neuroscience, King’s College London, Denmark Hill, London SE5 8AF, UK; (R.K.); (E.R.); (D.A.)
| | - Gareth Williams
- Wolfson CARD, King’s College London, London Bridge, London SE1 1UL, UK;
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Li Y, Liu P, Zhou Y, Maekawa H, Silva JB, Ansari MJ, Boubes K, Alia Y, Deb DK, Thomson BR, Jin J, Quaggin SE. Activation of Angiopoietin-Tie2 Signaling Protects the Kidney from Ischemic Injury by Modulation of Endothelial-Specific Pathways. J Am Soc Nephrol 2023; 34:969-987. [PMID: 36787763 PMCID: PMC10278803 DOI: 10.1681/asn.0000000000000098] [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: 12/04/2021] [Accepted: 01/19/2023] [Indexed: 02/16/2023] Open
Abstract
SIGNIFICANCE STATEMENT Ischemia-reperfusion AKI (IR-AKI) is common and causes significant morbidity. Effective treatments are lacking. However, preclinical studies suggest that inhibition of angiopoietin-Tie2 vascular signaling promotes injury, whereas activation of Tie2 is protective. We show that kidney ischemia leads to increased levels of the endothelial-specific phosphatase vascular endothelial protein tyrosine phosphatase (VE-PTP; PTPRB), which inactivates Tie2. Activation of Tie2 through VE-PTP deletion, or delivery of a novel angiopoietin mimetic (Hepta-ANG1), abrogated IR-AKI in mice. Single-cell RNAseq analysis showed Tie2 activation promotes increased Entpd1 expression, downregulation of FOXO1 target genes in the kidney vasculature, and emergence of a new subpopulation of glomerular endothelial cells. Our data provide a molecular basis and identify a candidate therapeutic to improve endothelial integrity and kidney function after IR-AKI. BACKGROUND Ischemia-reperfusion AKI (IR-AKI) is estimated to affect 2%-7% of all hospitalized patients. The significant morbidity and mortality associated with AKI indicates urgent need for effective treatments. Previous studies have shown activation of the vascular angiopoietin-Tie2 tyrosine kinase signaling pathway abrogates ischemia-reperfusion injury (IRI). We extended previous studies to (1) determine the molecular mechanism(s) underlying kidney injury and protection related to decreased or increased activation of Tie2, respectively, and (2) to test the hypothesis that deletion of the Tie2 inhibitory phosphatase vascular endothelial protein tyrosine phosphatase (VE-PTP) or injection of a new angiopoietin mimetic protects the kidney from IRI by common molecular mechanism(s). METHODS Bilateral IR-AKI was performed in VE-PTP wild-type or knockout mice and in C57BL/6J mice treated with Hepta-ANG1 or vehicle. Histologic, immunostaining, and single-cell RNA sequencing analyses were performed. RESULTS The phosphatase VE-PTP, which negatively regulates the angiopoietin-Tie2 pathway, was upregulated in kidney endothelial cells after IRI, and genetic deletion of VE-PTP in mice protected the kidney from IR-AKI. Injection of Hepta-ANG1 potently activated Tie2 and protected the mouse kidney from IRI. Single-cell RNAseq analysis of kidneys from Hepta-ANG1-treated and vehicle-treated mice identified endothelial-specific gene signatures and emergence of a new glomerular endothelial subpopulation associated with improved kidney function. Overlap was found between endothelial-specific genes upregulated by Hepta-ANG1 treatment and those downregulated in HUVECs with constitutive FOXO1 activation, including Entpd1 / ENTPD1 that modulates purinergic receptor signaling. CONCLUSIONS Our data support a key role of the endothelium in the development of IR-AKI, introduce Hepta-ANG1 as a putative new therapeutic biologic, and report a model to explain how IRI reduces Tie2 signaling and how Tie2 activation protects the kidney. PODCAST This article contains a podcast at https://dts.podtrac.com/redirect.mp3/www.asn-online.org/media/podcast/JASN/2023_05_23_JSN_Ang_EP23_052323.mp3.
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Affiliation(s)
- Yanyang Li
- Division of Nephrology and Hypertension, Northwestern University Feinberg School of Medicine, Chicago, Illinois
- The Feinberg Cardiovascular and Renal Research Institute, Chicago, Illinois
| | - Pan Liu
- Division of Nephrology and Hypertension, Northwestern University Feinberg School of Medicine, Chicago, Illinois
- The Feinberg Cardiovascular and Renal Research Institute, Chicago, Illinois
| | - Yalu Zhou
- Division of Nephrology and Hypertension, Northwestern University Feinberg School of Medicine, Chicago, Illinois
- The Feinberg Cardiovascular and Renal Research Institute, Chicago, Illinois
| | - Hiroshi Maekawa
- Division of Nephrology and Hypertension, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - John B. Silva
- Division of Nephrology and Hypertension, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Mohammed Javeed Ansari
- Division of Nephrology and Hypertension, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Khaled Boubes
- Division of Nephrology and Hypertension, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Yazan Alia
- Division of Nephrology and Hypertension, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Dilip K. Deb
- Division of Nephrology and Hypertension, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | | | - Jing Jin
- Division of Nephrology and Hypertension, Northwestern University Feinberg School of Medicine, Chicago, Illinois
- The Feinberg Cardiovascular and Renal Research Institute, Chicago, Illinois
| | - Susan E. Quaggin
- Division of Nephrology and Hypertension, Northwestern University Feinberg School of Medicine, Chicago, Illinois
- The Feinberg Cardiovascular and Renal Research Institute, Chicago, Illinois
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Yu AD, Rosbash M. Butt-seq: a new method for facile profiling of transcription. Genes Dev 2023:gad.350434.123. [PMID: 37164645 DOI: 10.1101/gad.350434.123] [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: 01/14/2023] [Accepted: 04/20/2023] [Indexed: 05/12/2023]
Abstract
A wide range of sequencing methods has been developed to assess nascent RNA transcription and resolve the single-nucleotide position of RNA polymerase genome-wide. These techniques are often burdened with high input material requirements and lengthy protocols. We leveraged the template-switching properties of thermostable group II intron reverse transcriptase (TGIRT) and developed Butt-seq (bulk analysis of nascent transcript termini sequencing), which can produce libraries from purified nascent RNA in 6 h and from as few as 10,000 cells-an improvement of at least 10-fold over existing techniques. Butt-seq shows that inhibition of the superelongation complex (SEC) causes promoter-proximal pausing to move upstream in a fashion correlated with subnucleosomal fragments. To address transcriptional regulation in a tissue, Butt-seq was used to measure the circadian regulation of transcription from fly heads. All the results indicate that Butt-seq is a simple and powerful technique to analyze transcription at a high level of resolution.
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Affiliation(s)
- Albert D Yu
- Department of Biology, Howard Hughes Medical Institute, National Center for Behavioral Genomics, Brandeis University, Waltham, Massachusetts 02453, USA
| | - Michael Rosbash
- Department of Biology, Howard Hughes Medical Institute, National Center for Behavioral Genomics, Brandeis University, Waltham, Massachusetts 02453, USA
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9
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Gerhardt LM, Koppitch K, van Gestel J, Guo J, Cho S, Wu H, Kirita Y, Humphreys BD, McMahon AP. Lineage Tracing and Single-Nucleus Multiomics Reveal Novel Features of Adaptive and Maladaptive Repair after Acute Kidney Injury. J Am Soc Nephrol 2023; 34:554-571. [PMID: 36735940 PMCID: PMC10103206 DOI: 10.1681/asn.0000000000000057] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [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: 07/26/2022] [Accepted: 11/17/2022] [Indexed: 01/22/2023] Open
Abstract
SIGNIFICANCE STATEMENT Understanding the mechanisms underlying adaptive and maladaptive renal repair after AKI and their long-term consequences is critical to kidney health. The authors used lineage tracing of cycling cells and single-nucleus multiomics (profiling transcriptome and chromatin accessibility) after AKI. They demonstrated that AKI triggers a cell-cycle response in most epithelial and nonepithelial kidney cell types. They also showed that maladaptive proinflammatory proximal tubule cells (PTCs) persist until 6 months post-AKI, although they decreased in abundance over time, in part, through cell death. Single-nucleus multiomics of lineage-traced cells revealed regulatory features of adaptive and maladaptive repair. These included activation of cell state-specific transcription factors and cis-regulatory elements, and effects in PTCs even after adaptive repair, weeks after the injury event. BACKGROUND AKI triggers a proliferative response as part of an intrinsic cellular repair program, which can lead to adaptive renal repair, restoring kidney structure and function, or maladaptive repair with the persistence of injured proximal tubule cells (PTCs) and an altered kidney structure. However, the cellular and molecular understanding of these repair programs is limited. METHODS To examine chromatin and transcriptional responses in the same cell upon ischemia-reperfusion injury (IRI), we combined genetic fate mapping of cycling ( Ki67+ ) cells labeled early after IRI with single-nucleus multiomics-profiling transcriptome and chromatin accessibility in the same nucleus-and generated a dataset of 83,315 nuclei. RESULTS AKI triggered a broad cell cycle response preceded by cell type-specific and global transcriptional changes in the nephron, the collecting and vascular systems, and stromal and immune cell types. We observed a heterogeneous population of maladaptive PTCs throughout proximal tubule segments 6 months post-AKI, with a marked loss of maladaptive cells from 4 weeks to 6 months. Gene expression and chromatin accessibility profiling in the same nuclei highlighted differences between adaptive and maladaptive PTCs in the activity of cis-regulatory elements and transcription factors, accompanied by corresponding changes in target gene expression. Adaptive repair was associated with reduced expression of genes encoding transmembrane transport proteins essential to kidney function. CONCLUSIONS Analysis of genome organization and gene activity with single-cell resolution using lineage tracing and single-nucleus multiomics offers new insight into the regulation of renal injury repair. Weeks to months after mild-to-moderate IRI, maladaptive PTCs persist with an aberrant epigenetic landscape, and PTCs exhibit an altered transcriptional profile even following adaptive repair.
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Affiliation(s)
- Louisa M.S. Gerhardt
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, Keck School of Medicine of the University of Southern California, Los Angeles, California
| | - Kari Koppitch
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, Keck School of Medicine of the University of Southern California, Los Angeles, California
| | - Jordi van Gestel
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, California
- Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Jinjin Guo
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, Keck School of Medicine of the University of Southern California, Los Angeles, California
| | - Sam Cho
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, Keck School of Medicine of the University of Southern California, Los Angeles, California
| | - Haojia Wu
- Division of Nephrology, Department of Medicine, Washington University in St. Louis, St. Louis, Missouri
| | - Yuhei Kirita
- Department of Nephrology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Benjamin D. Humphreys
- Division of Nephrology, Department of Medicine, Washington University in St. Louis, St. Louis, Missouri
- Department of Developmental Biology, Washington University in St. Louis, St. Louis, Missouri
| | - Andrew P. McMahon
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, Keck School of Medicine of the University of Southern California, Los Angeles, California
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Medina Rangel PX, Tian X. Understanding Nephrotic Syndrome Using Kidney Transcriptome Profiling and Computational Studies. Kidney360 2023; 4:e431-e433. [PMID: 37103957 PMCID: PMC10371383 DOI: 10.34067/kid.0000000000000117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/28/2023]
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11
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Martini P, Mingardi J, Carini G, Mattevi S, Ndoj E, La Via L, Magri C, Gennarelli M, Russo I, Popoli M, Musazzi L, Barbon A. Transcriptional Profiling of Rat Prefrontal Cortex after Acute Inescapable Footshock Stress. Genes (Basel) 2023; 14:genes14030740. [PMID: 36981011 PMCID: PMC10048409 DOI: 10.3390/genes14030740] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 01/31/2023] [Accepted: 03/16/2023] [Indexed: 03/30/2023] Open
Abstract
Stress is a primary risk factor for psychiatric disorders such as Major Depressive Disorder (MDD) and Post Traumatic Stress Disorder (PTSD). The response to stress involves the regulation of transcriptional programs, which is supposed to play a role in coping with stress. To evaluate transcriptional processes implemented after exposure to unavoidable traumatic stress, we applied microarray expression analysis to the PFC of rats exposed to acute footshock (FS) stress that were sacrificed immediately after the 40 min session or 2 h or 24 h after. While no substantial changes were observed at the single gene level immediately after the stress session, gene set enrichment analysis showed alterations in neuronal pathways associated with glia development, glia-neuron networking, and synaptic function. Furthermore, we found alterations in the expression of gene sets regulated by specific transcription factors that could represent master regulators of the acute stress response. Of note, these pathways and transcriptional programs are activated during the early stress response (immediately after FS) and are already turned off after 2 h-while at 24 h, the transcriptional profile is largely unaffected. Overall, our analysis provided a transcriptional landscape of the early changes triggered by acute unavoidable FS stress in the PFC of rats, suggesting that the transcriptional wave is fast and mild, but probably enough to activate a cellular response to acute stress.
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Affiliation(s)
- Paolo Martini
- Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy
| | - Jessica Mingardi
- Department of Medicine and Surgery, University of Milano-Bicocca, 20900 Monza, Italy
| | - Giulia Carini
- Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy
- Genetics Unit, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, 25123 Brescia, Italy
| | - Stefania Mattevi
- Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy
| | - Elona Ndoj
- Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy
| | - Luca La Via
- Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy
| | - Chiara Magri
- Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy
| | - Massimo Gennarelli
- Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy
- Genetics Unit, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, 25123 Brescia, Italy
| | - Isabella Russo
- Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy
- Genetics Unit, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, 25123 Brescia, Italy
| | - Maurizio Popoli
- Department of Pharmaceutical Sciences, University of Milan, 20133 Milan, Italy
| | - Laura Musazzi
- Department of Medicine and Surgery, University of Milano-Bicocca, 20900 Monza, Italy
| | - Alessandro Barbon
- Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy
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Oszwald A, Mejía-Pedroza RA, Schachner H, Aigner C, Rees A, Kain R. Digital Spatial Profiling of Glomerular Gene Expression in Pauci-Immune Focal Necrotizing Glomerulonephritis. Kidney360 2023; 4:83-91. [PMID: 36700908 PMCID: PMC10101620 DOI: 10.34067/kid.000461202] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 11/09/2022] [Indexed: 01/27/2023]
Abstract
Pauci-immune focal necrotizing glomerulonephritis (piFNGN) involves asynchronous onset and progression of injurious lesions in biopsies. Pathologists can describe this heterogeneity within a biopsy, but translating the information into prognostic or expression analyses is challenging. Understanding the underlying molecular processes could improve treatment; however, bulk or single-cell transcriptomic analyses of dissociated tissue disregard the heterogeneity of glomerular injury. We characterize protein and mRNA expression of individual glomeruli in 20 biopsies from 18 patients with antineutrophil cytoplasmic antibody-associated piFNGN using the NanoString digital spatial profiling (DSP) platform. For this purpose, circular annotations of glomeruli were analyzed using protein, immuno-oncology RNA, and Cancer Transcriptome Atlas panels (n=120, 72, and 48 glomeruli, respectively). Histologic evaluation of glomerular patterns of injury was performed in adjacent serial sections. Expression data were processed by log2 transformation, quantile normalization, and batch adjustment. DSP revealed distinct but overlapping gene expression profiles relating to the morphological evolution of injurious lesions, including dynamic expression of various immune checkpoint regulators. Enrichment analysis indicated deregulated pathways that underline known and highlight novel potential mechanisms of disease. Moreover, by capturing individual glomeruli, DSP describes heterogeneity between and within biopsies. We demonstrate the benefit of spatial profiling for characterization of heterogeneous glomerular injury, indicating novel molecular correlates of glomerular injury in piFNGN.
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Affiliation(s)
- André Oszwald
- Department of Pathology, Medical University of Vienna, Vienna, Austria
| | | | - Helga Schachner
- Department of Pathology, Medical University of Vienna, Vienna, Austria
| | - Christof Aigner
- Internal Medicine III, Medical University of Vienna, Vienna, Austria
| | - Andrew Rees
- Department of Pathology, Medical University of Vienna, Vienna, Austria
| | - Renate Kain
- Department of Pathology, Medical University of Vienna, Vienna, Austria
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Alam F, Blair JMA, Hall RA. Transcriptional profiling of Pseudomonas aeruginosa mature single- and dual-species biofilms in response to meropenem. Microbiology (Reading) 2023; 169:001271. [PMID: 36748572 PMCID: PMC9993114 DOI: 10.1099/mic.0.001271] [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: 01/24/2023]
Abstract
Pseudomonas aeruginosa is a Gram-negative opportunistic pathogen frequently isolated from chronic infections of the cystic fibrosis lung and burn wounds, and is a major cause of antimicrobial-resistant nosocomial infections. P. aeruginosa is frequently co-isolated with the opportunistic fungal pathogen Candida albicans, with the presence of C. albicans in dual-species biofilms promoting tolerance to meropenem. Here, transcription profiling of mature P. aeruginosa single- or dual-species biofilms was carried out to understand the molecular mechanism(s) by which C. albicans enhances meropenem tolerance. C. albicans appeared to have a mild impact on the transcriptome of P. aeruginosa mature biofilms, with most differentially regulated genes being involved in interkingdom interactions (i.e. quorum sensing and phenazine biosynthesis). The addition of meropenem to mature single- or dual-species biofilms resulted in a significant bacterial transcriptional response, including the induction of the beta-lactamase, ampC, genes involved in biofilm formation. P. aeruginosa elicited a similar transcriptional response to meropenem in the presence of C. albicans, but C. albicans promoted the expression of additional efflux pumps, which could play roles in increasing the tolerance of P. aeruginosa to meropenem.
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Affiliation(s)
- Farhana Alam
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Jessica M A Blair
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Rebecca A Hall
- Kent Fungal Group, Division of Natural Sciences, School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK
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14
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Zheng X, Higdon L, Gaudet A, Shah M, Balistieri A, Li C, Nadai P, Palaniappan L, Yang X, Santo B, Ginley B, Wang XX, Myakala K, Nallagatla P, Levi M, Sarder P, Rosenberg A, Maltzman JS, de Freitas Caires N, Bhalla V. Endothelial Cell-Specific Molecule-1 Inhibits Albuminuria in Diabetic Mice. Kidney360 2022; 3:2059-2076. [PMID: 36591362 PMCID: PMC9802554 DOI: 10.34067/kid.0001712022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 07/19/2022] [Indexed: 01/13/2023]
Abstract
Background Diabetic kidney disease (DKD) is the most common cause of kidney failure in the world, and novel predictive biomarkers and molecular mechanisms of disease are needed. Endothelial cell-specific molecule-1 (Esm-1) is a secreted proteoglycan that attenuates inflammation. We previously identified that a glomerular deficiency of Esm-1 associates with more pronounced albuminuria and glomerular inflammation in DKD-susceptible relative to DKD-resistant mice, but its contribution to DKD remains unexplored. Methods Using hydrodynamic tail-vein injection, we overexpress Esm-1 in DKD-susceptible DBA/2 mice and delete Esm-1 in DKD-resistant C57BL/6 mice to study the contribution of Esm-1 to DKD. We analyze clinical indices of DKD, leukocyte infiltration, podocytopenia, and extracellular matrix production. We also study transcriptomic changes to assess potential mechanisms of Esm-1 in glomeruli. Results In DKD-susceptible mice, Esm-1 inversely correlates with albuminuria and glomerular leukocyte infiltration. We show that overexpression of Esm-1 reduces albuminuria and diabetes-induced podocyte injury, independent of changes in leukocyte infiltration. Using a complementary approach, we find that constitutive deletion of Esm-1 in DKD-resistant mice modestly increases the degree of diabetes-induced albuminuria versus wild-type controls. By glomerular RNAseq, we identify that Esm-1 attenuates expression of kidney disease-promoting and interferon (IFN)-related genes, including Ackr2 and Cxcl11. Conclusions We demonstrate that, in DKD-susceptible mice, Esm-1 protects against diabetes-induced albuminuria and podocytopathy, possibly through select IFN signaling. Companion studies in patients with diabetes suggest a role of Esm-1 in human DKD.
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Affiliation(s)
- Xiaoyi Zheng
- Division of Nephrology, Department of Medicine, Stanford University School of Medicine, Stanford, California
| | - Lauren Higdon
- Division of Nephrology, Department of Medicine, Stanford University School of Medicine, Stanford, California
- Veterans Affairs Palo Alto Heath Care System, Palo Alto, California
| | - Alexandre Gaudet
- Division of Nephrology, Department of Medicine, Stanford University School of Medicine, Stanford, California
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1019-UMR9017-Center for Infection & Immunity of Lille, Pasteur Institute of Lille, University of Lille, Lille, France
| | - Manav Shah
- Division of Nephrology, Department of Medicine, Stanford University School of Medicine, Stanford, California
| | - Angela Balistieri
- Division of Nephrology, Department of Medicine, Stanford University School of Medicine, Stanford, California
| | - Catherine Li
- Division of Nephrology, Department of Medicine, Stanford University School of Medicine, Stanford, California
| | - Patricia Nadai
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1019-UMR9017-Center for Infection & Immunity of Lille, Pasteur Institute of Lille, University of Lille, Lille, France
| | - Latha Palaniappan
- Division of Primary Care and Population Health, Stanford University School of Medicine, Stanford, California
| | - Xiaoping Yang
- Division of Kidney-Urologic Pathology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Briana Santo
- Department of Pathology and Anatomical Sciences, University at Buffalo–The State University of New York, Buffalo, New York
| | - Brandon Ginley
- Department of Pathology and Anatomical Sciences, University at Buffalo–The State University of New York, Buffalo, New York
| | - Xiaoxin X. Wang
- Department of Biochemistry, Molecular and Cellular Biology, Georgetown University Medical Center, Washington, DC
| | - Komuraiah Myakala
- Department of Biochemistry, Molecular and Cellular Biology, Georgetown University Medical Center, Washington, DC
| | | | - Moshe Levi
- Department of Biochemistry, Molecular and Cellular Biology, Georgetown University Medical Center, Washington, DC
| | - Pinaki Sarder
- Department of Pathology and Anatomical Sciences, University at Buffalo–The State University of New York, Buffalo, New York
| | - Avi Rosenberg
- Division of Kidney-Urologic Pathology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Jonathan S. Maltzman
- Division of Nephrology, Department of Medicine, Stanford University School of Medicine, Stanford, California
- Veterans Affairs Palo Alto Heath Care System, Palo Alto, California
| | - Nathalie de Freitas Caires
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1019-UMR9017-Center for Infection & Immunity of Lille, Pasteur Institute of Lille, University of Lille, Lille, France
- Biothelis, Lille, France
| | - Vivek Bhalla
- Division of Nephrology, Department of Medicine, Stanford University School of Medicine, Stanford, California
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15
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Naciff JM, Shan YK, Wang X, Daston GP. Article title: Transcriptional profiling efficacy to define biological activity similarity for cosmetic ingredients' safety assessment based on next-generation read-across. Front Toxicol 2022; 4:1082222. [PMID: 36618549 PMCID: PMC9811170 DOI: 10.3389/ftox.2022.1082222] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 12/05/2022] [Indexed: 12/24/2022] Open
Abstract
The objective of this work was to use transcriptional profiling to assess the biological activity of structurally related chemicals to define their biological similarity and with that, substantiate the validity of a read-across approach usable in risk assessment. Two case studies are presented, one with 4 short alkyl chain parabens: methyl (MP), ethyl (EP), butyl (BP), and propylparaben (PP), as well as their main metabolite, p-hydroxybenzoic acid (pHBA) with the assumption that propylparaben was the target chemical; and a second one with caffeine and its main metabolites theophylline, theobromine and paraxanthine where CA was the target chemical. The comprehensive transcriptional response of MCF7, HepG2, A549 and ICell cardiomyocytes was evaluated (TempO-Seq) after exposure to vehicle-control, each paraben or pHBA, CA or its metabolites, at 3 non-cytotoxic concentrations, for 6 h. Differentially expressed genes (FDR ≥0.05, and fold change ±1.2≥) were identified for each chemical, at each concentration, and used to determine similarities. Each of the chemicals is able to elicit changes in the expression of a number of genes, as compared to controls. Importantly, the transcriptional profile elicited by each of the parabens shares a high degree of similarity across the group. The highest number of genes commonly affected was between butylparaben and PP. The transcriptional profile of the parabens is similar to the one elicited by estrogen receptor agonists, with BP being the closest structural and biological analogue for PP. In the CA case, the transcriptional profile elicited of all four methylxanthines had a high degree of similarity across the cell types, with CA and theophylline being the most active. The most robust response was obtained in the cardiomyocytes with the highest transcriptional profile similarity between CA and TP. The transcriptional profile of the methylxanthines is similar to the one elicited by inhibitors of phosphatidylinositol 3-kinase as well as other kinase inhibitors. Overall, our results support the approach of incorporating transcriptional profiling in well-designed in vitro tests as one robust stream of data to support biological similarity driven read-across procedures and strengthening the traditional structure-based approaches useful in risk assessment.
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Sealfon R, Mariani L, Kretzler M, Beck LH. Authors' Reply: In Silico-Based Approach to the Discovery of New Antigens in Membranous Nephropathy. J Am Soc Nephrol 2022; 33:2322-2323. [PMID: 36175144 PMCID: PMC9731634 DOI: 10.1681/asn.2022080921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Affiliation(s)
- Rachel Sealfon
- Center for Computational Biology, Flatiron Institute, New York, New York
- Princeton University, Princeton, New Jersey
| | - Laura Mariani
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
| | - Matthias Kretzler
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
| | - Laurence H. Beck
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan
- School of Medicine, Boston University, Boston, Massachusetts
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Sinigaglia C, Almazán A, Lebel M, Sémon M, Gillet B, Hughes S, Edsinger E, Averof M, Paris M. Distinct gene expression dynamics in developing and regenerating crustacean limbs. Proc Natl Acad Sci U S A 2022; 119:e2119297119. [PMID: 35776546 DOI: 10.1073/pnas.2119297119] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Regenerating animals have the ability to reproduce body parts that were originally made in the embryo and subsequently lost due to injury. Understanding whether regeneration mirrors development is an open question in most regenerative species. Here, we take a transcriptomics approach to examine whether leg regeneration shows similar temporal patterns of gene expression as leg development in the embryo, in the crustacean Parhyale hawaiensis. We find that leg development in the embryo shows stereotypic temporal patterns of gene expression. In contrast, the dynamics of gene expression during leg regeneration show a higher degree of variation related to the physiology of individual animals. A major driver of this variation is the molting cycle. We dissect the transcriptional signals of individual physiology and regeneration to obtain clearer temporal signals marking distinct phases of leg regeneration. Comparing the transcriptional dynamics of development and regeneration we find that, although the two processes use similar sets of genes, the temporal patterns in which these genes are deployed are different and cannot be systematically aligned.
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Yan L, Li Y, Qing Y, Tao X, Wang H, Lai X, Zhang Y. Integrative Analysis of Genes Involved in the Global Response to Potato Wart Formation. Front Plant Sci 2022; 13:865716. [PMID: 35845669 PMCID: PMC9277394 DOI: 10.3389/fpls.2022.865716] [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] [Received: 01/30/2022] [Accepted: 05/17/2022] [Indexed: 06/15/2023]
Abstract
Synchytrium endobioticum, the causal agent of potato wart disease, poses a major threat to commercial potato production. Understanding the roles of transcriptionally regulated genes following pathogen infection is necessary for understanding the system-level host response to pathogen. Although some understanding of defense mechanisms against S. endobioticum infection has been gained for incompatible interactions, the genes and signaling pathways involved in the compatible interaction remain unclear. Based on the collection of wart diseased tubers of a susceptible cultivar, we performed phenotypic and dual RNA-Seq analyses of wart lesions in seven stages of disease progression. We totally detected 5,052 differentially expressed genes (DEGs) by comparing the different stages of infection to uninfected controls. The tendency toward differential gene expression was active rather than suppressed under attack by the pathogen. The number of DEGs step-up along with the development of the disease and the first, third and seventh of the disease stages showed substantially increase of DEGs in comparison of the previous stage. The important functional groups identified via Gene ontology (GO) and KEGG enrichment were those responsible for plant-pathogen interaction, fatty acid elongation and phenylpropanoid biosynthesis. Gene coexpression networks, composed of 17 distinct gene modules that contained between 25 and 813 genes, revealed high interconnectivity of the induced response and led to the identification of a number of hub genes enriched at different stages of infection. These results provide a comprehensive perspective on the global response of potato to S. endobioticum infection and identify a potential transcriptional regulatory network underlying this susceptible response, which contribute to a better understanding of the potato-S. endobioticum pathosystem.
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Affiliation(s)
- Lang Yan
- Panxi Crops Research and Utilization Key Laboratory of Sichuan Province, College of Agricultural Science, Xichang University, Liangshan, China
| | - Yan Li
- College of Life Sciences, Sichuan Normal University, Chengdu, China
| | - Yuan Qing
- Panxi Crops Research and Utilization Key Laboratory of Sichuan Province, College of Agricultural Science, Xichang University, Liangshan, China
| | - Xiang Tao
- College of Life Sciences, Sichuan Normal University, Chengdu, China
| | - Haiyan Wang
- Sichuan Key Laboratory of Molecular Biology and Biotechnology, College of Life Sciences, Sichuan University, Chengdu, China
| | - Xianjun Lai
- Panxi Crops Research and Utilization Key Laboratory of Sichuan Province, College of Agricultural Science, Xichang University, Liangshan, China
| | - Yizheng Zhang
- Sichuan Key Laboratory of Molecular Biology and Biotechnology, College of Life Sciences, Sichuan University, Chengdu, China
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Demars F, Todorova R, Makdah G, Forestier A, Krebs MO, Godsil BP, Jay TM, Wiener SI, Pompili MN. Post-trauma behavioral phenotype predicts the degree of vulnerability to fear relapse after extinction in male rats. Curr Biol 2022; 32:3180-3188.e4. [PMID: 35705096 DOI: 10.1016/j.cub.2022.05.050] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 04/19/2022] [Accepted: 05/18/2022] [Indexed: 11/30/2022]
Abstract
Current treatments for trauma-related disorders remain ineffective for many patients.1,2 Fear extinction deficiency is a prominent feature of these diseases,3 and many behavioral treatments rely on extinction training.4,5 However, in many patients, therapy is followed by a relapse of symptoms, and the underpinnings of such interindividual variations in vulnerability to relapse remain unknown.6-8 Here, we modeled interindividual differences in post-therapy fear relapse with an ethologically relevant trauma recovery paradigm. After fear conditioning, male rats underwent fear extinction while foraging in a large enriched arena, permitting the expression of a wide spectrum of behaviors. An automated multidimensional behavioral assessment revealed that post-conditioning fear response profiles clustered into two groups: some animals expressed fear by freezing more, whereas others darted more, as if fleeing from danger. Remarkably, the tendency of an animal to dart or to freeze after CS presentation during the first extinction session was, respectively, associated with stronger or weaker fear renewal. Moreover, genome-wide transcriptional profiling revealed that these groups differentially regulated specific sets of genes, some of which were previously implicated in anxiety and trauma-related disorders. Our results suggest that post-trauma behavioral phenotypes and the associated gene expression landscapes can serve as markers of fear relapse susceptibility and thus may be instrumental for future development of more effective treatments for psychiatric patients.
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Affiliation(s)
- Fanny Demars
- Institut de Psychiatrie et Neurosciences de Paris (IPNP)-INSERM U1266, Institut de Psychiatrie-CNRS GDR3557, GHU Psychiatrie Neurosciences, Université Paris Cité, 102-108 Rue de la Santé, 75014 Paris, France
| | - Ralitsa Todorova
- Centre Interdisciplinaire de Recherche en Biologie (CIRB)-CNRS UMR 7241-INSERM U1050, Collège de France, Université PSL, 11 place Marcelin Berthelot, 75005 Paris, France
| | - Gabriel Makdah
- Centre Interdisciplinaire de Recherche en Biologie (CIRB)-CNRS UMR 7241-INSERM U1050, Collège de France, Université PSL, 11 place Marcelin Berthelot, 75005 Paris, France; Hospices Civils de Lyon, Faculté de Médecine Lyon Est, Université Claude Bernard, Lyon, France
| | - Antonin Forestier
- Institut de Psychiatrie et Neurosciences de Paris (IPNP)-INSERM U1266, Institut de Psychiatrie-CNRS GDR3557, GHU Psychiatrie Neurosciences, Université Paris Cité, 102-108 Rue de la Santé, 75014 Paris, France; Ecole Nationale Vétérinaire d'Alfort, Maisons-Alfort, France
| | - Marie-Odile Krebs
- Institut de Psychiatrie et Neurosciences de Paris (IPNP)-INSERM U1266, Institut de Psychiatrie-CNRS GDR3557, GHU Psychiatrie Neurosciences, Université Paris Cité, 102-108 Rue de la Santé, 75014 Paris, France
| | - Bill P Godsil
- Institut de Psychiatrie et Neurosciences de Paris (IPNP)-INSERM U1266, Institut de Psychiatrie-CNRS GDR3557, GHU Psychiatrie Neurosciences, Université Paris Cité, 102-108 Rue de la Santé, 75014 Paris, France
| | - Thérèse M Jay
- Institut de Psychiatrie et Neurosciences de Paris (IPNP)-INSERM U1266, Institut de Psychiatrie-CNRS GDR3557, GHU Psychiatrie Neurosciences, Université Paris Cité, 102-108 Rue de la Santé, 75014 Paris, France
| | - Sidney I Wiener
- Centre Interdisciplinaire de Recherche en Biologie (CIRB)-CNRS UMR 7241-INSERM U1050, Collège de France, Université PSL, 11 place Marcelin Berthelot, 75005 Paris, France
| | - Marco N Pompili
- Institut de Psychiatrie et Neurosciences de Paris (IPNP)-INSERM U1266, Institut de Psychiatrie-CNRS GDR3557, GHU Psychiatrie Neurosciences, Université Paris Cité, 102-108 Rue de la Santé, 75014 Paris, France; Centre Interdisciplinaire de Recherche en Biologie (CIRB)-CNRS UMR 7241-INSERM U1050, Collège de France, Université PSL, 11 place Marcelin Berthelot, 75005 Paris, France.
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20
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Sealfon R, Mariani L, Avila-Casado C, Nair V, Menon R, Funk J, Wong A, Lerner G, Hayashi N, Troyanskaya O, Kretzler M, Beck LH. Molecular Characterization of Membranous Nephropathy. J Am Soc Nephrol 2022; 33:1208-1221. [PMID: 35477557 PMCID: PMC9161788 DOI: 10.1681/asn.2021060784] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [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: 06/11/2021] [Accepted: 03/21/2022] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Molecular characterization of nephropathies may facilitate pathophysiologic insight, development of targeted therapeutics, and transcriptome-based disease classification. Although membranous nephropathy (MN) is a common cause of adult-onset nephrotic syndrome, the molecular pathways of kidney damage in MN require further definition. METHODS We applied a machine-learning framework to predict diagnosis on the basis of gene expression from the microdissected kidney tissue of participants in the Nephrotic Syndrome Study Network (NEPTUNE) cohort. We sought to identify differentially expressed genes between participants with MN versus those of other glomerulonephropathies across the NEPTUNE and European Renal cDNA Bank (ERCB) cohorts, to find MN-specific gene modules in a kidney-specific functional network, and to identify cell-type specificity of MN-specific genes using single-cell sequencing data from reference nephrectomy tissue. RESULTS Glomerular gene expression alone accurately separated participants with MN from those with other nephrotic syndrome etiologies. The top predictive classifier genes from NEPTUNE participants were also differentially expressed in the ERCB participants with MN. We identified a signature of 158 genes that are significantly differentially expressed in MN across both cohorts, finding 120 of these in a validation cohort. This signature is enriched in targets of transcription factor NF-κB. Clustering these MN-specific genes in a kidney-specific functional network uncovered modules with functional enrichments, including in ion transport, cell projection morphogenesis, regulation of adhesion, and wounding response. Expression data from reference nephrectomy tissue indicated 43% of these genes are most highly expressed by podocytes. CONCLUSIONS These results suggest that, relative to other glomerulonephropathies, MN has a distinctive molecular signature that includes upregulation of many podocyte-expressed genes, provides a molecular snapshot of MN, and facilitates insight into MN's underlying pathophysiology.
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Affiliation(s)
- Rachel Sealfon
- Center for Computational Biology, Flatiron Institute, New York, New York,Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey
| | - Laura Mariani
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
| | | | - Viji Nair
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
| | - Rajasree Menon
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
| | - Julien Funk
- Center for Computational Biology, Flatiron Institute, New York, New York
| | - Aaron Wong
- Center for Computational Biology, Flatiron Institute, New York, New York,Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey
| | - Gabriel Lerner
- Department of Medicine, Boston Medical Center and Boston University School of Medicine, Boston, Massachusetts
| | - Norifumi Hayashi
- Department of Medicine, Boston Medical Center and Boston University School of Medicine, Boston, Massachusetts,Division of Nephrology, Kanazawa Medical University, Uchinada, Ishikawa, Japan
| | - Olga Troyanskaya
- Center for Computational Biology, Flatiron Institute, New York, New York,Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey,Department of Computer Science, Princeton University, Princeton, New Jersey
| | - Matthias Kretzler
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan,Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan
| | - Laurence H. Beck
- Department of Medicine, Boston Medical Center and Boston University School of Medicine, Boston, Massachusetts
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21
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Allert S, Schulz D, Kämmer P, Großmann P, Wolf T, Schäuble S, Panagiotou G, Brunke S, Hube B. From environmental adaptation to host survival: Attributes that mediate pathogenicity of Candida auris. Virulence 2022; 13:191-214. [PMID: 35142597 PMCID: PMC8837256 DOI: 10.1080/21505594.2022.2026037] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [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] [Indexed: 01/08/2023] Open
Abstract
Candida species are a major cause of invasive fungal infections. While Candida albicans, C. glabrata, C. parapsilosis, and C. tropicalis are the most dominant species causing life-threatening candidiasis, C. auris recently emerged as a new species causing invasive infections with high rates of clinical treatment failures. To mimic initial phases of systemic Candida infections with dissemination via the bloodstream and to elucidate the pathogenic potential of C. auris, we used an ex vivo whole blood infection model. Similar to other clinically relevant Candida spp., C. auris is efficiently killed in human blood, but showed characteristic patterns of immune cell association, survival rates, and cytokine induction. Dual-species transcriptional profiling of C. auris-infected blood revealed a unique C. auris gene expression program during infection, while the host response proofed similar and conserved compared to other Candida species. C. auris-specific responses included adaptation and survival strategies, such as counteracting oxidative burst of immune cells, but also expression of potential virulence factors, (drug) transporters, and cell surface-associated genes. Despite comparable pathogenicity to other Candida species in our model, C. auris-specific transcriptional adaptations as well as its increased stress resistance and long-term environmental survival, likely contribute to the high risk of contamination and distribution in a nosocomial setting. Moreover, infections of neutrophils with pre-starved C. auris cells suggest that environmental preconditioning can have modulatory effects on the early host interaction. In summary, we present novel insights into C. auris pathogenicity, revealing adaptations to human blood and environmental niches distinctive from other Candida species.
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Affiliation(s)
- Stefanie Allert
- Department of Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology, Hans-Knoell-Institute, Jena, Germany
| | - Daniela Schulz
- Department of Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology, Hans-Knoell-Institute, Jena, Germany
| | - Philipp Kämmer
- Department of Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology, Hans-Knoell-Institute, Jena, Germany
| | - Peter Großmann
- Systems Biology and Bioinformatics Unit, Leibniz Institute for Natural Product Research and Infection Biology, Hans-Knoell-Institute, Jena, Germany
| | - Thomas Wolf
- Systems Biology and Bioinformatics Unit, Leibniz Institute for Natural Product Research and Infection Biology, Hans-Knoell-Institute, Jena, Germany
| | - Sascha Schäuble
- Systems Biology and Bioinformatics Unit, Leibniz Institute for Natural Product Research and Infection Biology, Hans-Knoell-Institute, Jena, Germany
| | - Gianni Panagiotou
- Systems Biology and Bioinformatics Unit, Leibniz Institute for Natural Product Research and Infection Biology, Hans-Knoell-Institute, Jena, Germany.,Department of Medicine and State Key Laboratory of Pharmaceutical Biotechnology, University of Hong Kong, Hong Kong, China
| | - Sascha Brunke
- Department of Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology, Hans-Knoell-Institute, Jena, Germany
| | - Bernhard Hube
- Department of Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology, Hans-Knoell-Institute, Jena, Germany.,Institute of Microbiology, Friedrich-Schiller-University, Jena, Germany
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22
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Morgan MB, Ross J, Ellwanger J, Phrommala RM, Youngblood H, Qualley D, Williams J. Sea Anemones Responding to Sex Hormones, Oxybenzone, and Benzyl Butyl Phthalate: Transcriptional Profiling and in Silico Modelling Provide Clues to Decipher Endocrine Disruption in Cnidarians. Front Genet 2022; 12:793306. [PMID: 35087572 PMCID: PMC8787064 DOI: 10.3389/fgene.2021.793306] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 10/25/2021] [Accepted: 12/24/2021] [Indexed: 01/09/2023] Open
Abstract
Endocrine disruption is suspected in cnidarians, but questions remain how occurs. Steroid sex hormones are detected in corals and sea anemones even though these animals do not have estrogen receptors and their repertoire of steroidogenic enzymes appears to be incomplete. Pathways associated with sex hormone biosynthesis and sterol signaling are an understudied area in cnidarian biology. The objective of this study was to identify a suite of genes that can be linked to exposure of endocrine disruptors. Exaiptasia diaphana were exposed to nominal 20ppb concentrations of estradiol (E2), testosterone (T), cholesterol, oxybenzone (BP-3), or benzyl butyl phthalate (BBP) for 4 h. Eleven genes of interest (GOIs) were chosen from a previously generated EST library. The GOIs are 17β-hydroxysteroid dehydrogenases type 14 (17β HSD14) and type 12 (17β HSD12), Niemann-Pick C type 2 (NPC2), Equistatin (EI), Complement component C3 (C3), Cathepsin L (CTSL), Patched domain-containing protein 3 (PTCH3), Smoothened (SMO), Desert Hedgehog (DHH), Zinc finger protein GLI2 (GLI2), and Vitellogenin (VTG). These GOIs were selected because of functional associations with steroid hormone biosynthesis; cholesterol binding/transport; immunity; phagocytosis; or Hedgehog signaling. Quantitative Real-Time PCR quantified expression of GOIs. In silico modelling utilized protein structures from Protein Data Bank as well as creating protein structures with SWISS-MODEL. Results show transcription of steroidogenic enzymes, and cholesterol binding/transport proteins have similar transcription profiles for E2, T, and cholesterol treatments, but different profiles when BP-3 or BBP is present. C3 expression can differentiate between exposures to BP-3 versus BBP as well as exposure to cholesterol versus sex hormones. In silico modelling revealed all ligands (E2, T, cholesterol, BBP, and BP-3) have favorable binding affinities with 17β HSD14, 17β HSD12, NPC2, SMO, and PTCH proteins. VTG expression was down-regulated in the sterol treatments but up-regulated in BP-3 and BBP treatments. In summary, these eleven GOIs collectively generate unique transcriptional profiles capable of discriminating between the five chemical exposures used in this investigation. This suite of GOIs are candidate biomarkers for detecting transcriptional changes in steroidogenesis, gametogenesis, sterol transport, and Hedgehog signaling. Detection of disruptions in these pathways offers new insight into endocrine disruption in cnidarians.
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Affiliation(s)
- Michael B Morgan
- Department of Biology, Berry College, Mount Berry, GA, United States.,Department of Chemistry and Biochemistry, Berry College, Mount Berry, GA, United States
| | - James Ross
- Department of Biology, Berry College, Mount Berry, GA, United States.,Department of Chemistry and Biochemistry, Berry College, Mount Berry, GA, United States.,Department of Microbiology and Immunology, Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA, United States
| | - Joseph Ellwanger
- Department of Biology, Berry College, Mount Berry, GA, United States
| | | | - Hannah Youngblood
- Department of Biology, Berry College, Mount Berry, GA, United States.,Department of Chemistry and Biochemistry, Berry College, Mount Berry, GA, United States.,Department of Cellular Biology and Anatomy, Augusta University, Augusta, GA, United States
| | - Dominic Qualley
- Department of Chemistry and Biochemistry, Berry College, Mount Berry, GA, United States
| | - Jacob Williams
- Department of Biology, Berry College, Mount Berry, GA, United States
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23
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Long KR, Rbaibi Y, Bondi CD, Ford BR, Poholek AC, Boyd-Shiwarski CR, Tan RJ, Locker JD, Weisz OA. Cubilin-, megalin-, and Dab2-dependent transcription revealed by CRISPR/Cas9 knockout in kidney proximal tubule cells. Am J Physiol Renal Physiol 2022; 322:F14-F26. [PMID: 34747197 PMCID: PMC8698540 DOI: 10.1152/ajprenal.00259.2021] [Citation(s) in RCA: 4] [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: 07/08/2021] [Revised: 11/01/2021] [Accepted: 11/01/2021] [Indexed: 01/03/2023] Open
Abstract
The multiligand receptors megalin (Lrp2) and cubilin (Cubn) and their endocytic adaptor protein Dab2 (Dab2) play essential roles in maintaining the integrity of the apical endocytic pathway of proximal tubule (PT) cells and have complex and poorly understood roles in the development of chronic kidney disease. Here, we used RNA-sequencing and CRISPR/Cas9 knockout (KO) technology in a well-differentiated cell culture model to identify PT-specific transcriptional changes that are directly consequent to the loss of megalin, cubilin, or Dab2 expression. KO of Lrp2 had the greatest transcriptional effect, and nearly all genes whose expression was affected in Cubn KO and Dab2 KO cells were also changed in Lrp2 KO cells. Pathway analysis and more granular inspection of the altered gene profiles suggested changes in pathways with immunomodulatory functions that might trigger the pathological changes observed in KO mice and patients with Donnai-Barrow syndrome. In addition, differences in transcription patterns between Lrp2 and Dab2 KO cells suggested the possibility that altered spatial signaling by aberrantly localized receptors contributes to transcriptional changes upon the disruption of PT endocytic function. A reduction in transcripts encoding sodium-glucose cotransporter isoform 2 was confirmed in Lrp2 KO mouse kidney lysates by quantitative PCR analysis. Our results highlight the role of megalin as a master regulator and coordinator of ion transport, metabolism, and endocytosis in the PT. Compared with the studies in animal models, this approach provides a means to identify PT-specific transcriptional changes that are directly consequent to the loss of these target genes.NEW & NOTEWORTHY Megalin and cubilin receptors together with their adaptor protein Dab2 represent major components of the endocytic machinery responsible for efficient uptake of filtered proteins by the proximal tubule (PT). Dab2 and megalin expression have been implicated as both positive and negative modulators of kidney disease. We used RNA sequencing to knock out CRISPR/Cas9 cubilin, megalin, and Dab2 in highly differentiated PT cells to identify PT-specific changes that are directly consequent to knockout of each component.
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MESH Headings
- Adaptor Proteins, Signal Transducing/genetics
- Adaptor Proteins, Signal Transducing/metabolism
- Agenesis of Corpus Callosum/genetics
- Agenesis of Corpus Callosum/metabolism
- Agenesis of Corpus Callosum/pathology
- Animals
- Apoptosis Regulatory Proteins/genetics
- Apoptosis Regulatory Proteins/metabolism
- CRISPR-Associated Protein 9/genetics
- CRISPR-Cas Systems
- Cells, Cultured
- Databases, Genetic
- Gene Knockout Techniques
- Gene Regulatory Networks
- Hearing Loss, Sensorineural/genetics
- Hearing Loss, Sensorineural/metabolism
- Hearing Loss, Sensorineural/pathology
- Hernias, Diaphragmatic, Congenital/genetics
- Hernias, Diaphragmatic, Congenital/metabolism
- Hernias, Diaphragmatic, Congenital/pathology
- Humans
- Kidney Tubules, Proximal/metabolism
- Kidney Tubules, Proximal/pathology
- Low Density Lipoprotein Receptor-Related Protein-2/genetics
- Low Density Lipoprotein Receptor-Related Protein-2/metabolism
- Male
- Mice, Knockout
- Monodelphis
- Myopia/genetics
- Myopia/metabolism
- Myopia/pathology
- Proteinuria/genetics
- Proteinuria/metabolism
- Proteinuria/pathology
- Receptors, Cell Surface/genetics
- Receptors, Cell Surface/metabolism
- Renal Tubular Transport, Inborn Errors/genetics
- Renal Tubular Transport, Inborn Errors/metabolism
- Renal Tubular Transport, Inborn Errors/pathology
- Transcription, Genetic
- Mice
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Affiliation(s)
- Kimberly R Long
- Renal Electrolyte Division, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Youssef Rbaibi
- Renal Electrolyte Division, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Corry D Bondi
- Renal Electrolyte Division, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - B Rhodes Ford
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Amanda C Poholek
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Cary R Boyd-Shiwarski
- Renal Electrolyte Division, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Roderick J Tan
- Renal Electrolyte Division, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Joseph D Locker
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Ora A Weisz
- Renal Electrolyte Division, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
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24
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Chen W, Sun Q, Yan Z, Zhou Q, Cao Y, Chen F, Wei X. Transcriptional profiling of the chicken tracheal and splenic response to virulent Mycoplasma synoviae. Poult Sci 2021; 101:101660. [PMID: 35077920 DOI: 10.1016/j.psj.2021.101660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 12/01/2021] [Accepted: 12/01/2021] [Indexed: 10/25/2022] Open
Abstract
Mycoplasma synoviae (MS), an important avian pathogen, can cause chronic respiratory disease, eggshell apex abnormalities, infectious synovitis, and arthritis in avian species, leading serious economic losses in the global poultry industry. To date, studies have shown significant different transcript profiles using various chicken cells after MS infection. However, in vitro cell models cannot fully represent the complex in vivo regulations after adventitious infection. The objective of this study was to explore the nature of the host-pathogen interaction during MS infection. The tracheal and spleen tissues of chickens were collected at d 0, 1, 3, and 5 postinoculation, and samples were analyzed for differential gene expression using Illumina RNA sequencing. A lot of significantly differentially expressed genes (DEGs) were observed in this analysis, and 861 DEGs were observed in trachea tissues and 753 DEGs were observed in spleen samples. Many of DEGs in trachea tissues participate in a variety of cellular activities, especially cellular metabolism. Immune-related DEGs were mainly enriched at d 3, and 5 postinfection in trachea tissues. While, DEGs in spleen tissues were significantly and mainly enriched into immune-related pathways. The results of this study show the direct interactions between MS and the chicken trachea and spleen for the first time. Early dysregulation of tissue-wide gene expression as observed here set the stage for persistent infection of MS.
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25
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Olschok K, Han L, de Toledo MAS, Böhnke J, Graßhoff M, Costa IG, Theocharides A, Maurer A, Schüler HM, Buhl EM, Pannen K, Baumeister J, Kalmer M, Gupta S, Boor P, Gezer D, Brümmendorf TH, Zenke M, Chatain N, Koschmieder S. CALR frameshift mutations in MPN patient-derived iPSCs accelerate maturation of megakaryocytes. Stem Cell Reports 2021; 16:2768-2783. [PMID: 34678208 PMCID: PMC8581168 DOI: 10.1016/j.stemcr.2021.09.019] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [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: 07/15/2019] [Revised: 09/24/2021] [Accepted: 09/27/2021] [Indexed: 12/13/2022] Open
Abstract
Calreticulin (CALR) mutations are driver mutations in myeloproliferative neoplasms (MPNs), leading to activation of the thrombopoietin receptor and causing abnormal megakaryopoiesis. Here, we generated patient-derived CALRins5- or CALRdel52-positive induced pluripotent stem cells (iPSCs) to establish an MPN disease model for molecular and mechanistic studies. We demonstrated myeloperoxidase deficiency in granulocytic cells derived from homozygous CALR mutant iPSCs, rescued by repairing the mutation using CRISPR/Cas9. iPSC-derived megakaryocytes showed characteristics of primary megakaryocytes such as formation of demarcation membrane system and cytoplasmic pro-platelet protrusions. Importantly, CALR mutations led to enhanced megakaryopoiesis and accelerated megakaryocytic development in a thrombopoietin-independent manner. Mechanistically, our study identified differentially regulated pathways in mutated versus unmutated megakaryocytes, such as hypoxia signaling, which represents a potential target for therapeutic intervention. Altogether, we demonstrate key aspects of mutated CALR-driven pathogenesis dependent on its zygosity, and found novel therapeutic targets, making our model a valuable tool for clinical drug screening in MPNs. CALR-mutated iPSCs allow efficient modeling of human MPN disease CRISPR-mediated repair of CALR mutations rescues normal iPSC function Megakaryopoiesis in CALR-mutated iPSCs is hyperplastic and accelerated Transcriptome screen of mutated megakaryocytes identifies novel therapeutic options
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Affiliation(s)
- Kathrin Olschok
- Department of Hematology, Oncology, Hemostaseology, and Stem Cell Transplantation, Faculty of Medicine, RWTH Aachen University, Pauwelsstraße 30, 52074 Aachen, Germany; Center for Integrated Oncology Aachen Bonn Cologne Düsseldorf (CIO ABCD), Aachen, Germany
| | - Lijuan Han
- Department of Hematology, Oncology, Hemostaseology, and Stem Cell Transplantation, Faculty of Medicine, RWTH Aachen University, Pauwelsstraße 30, 52074 Aachen, Germany; Center for Integrated Oncology Aachen Bonn Cologne Düsseldorf (CIO ABCD), Aachen, Germany; Department of Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Marcelo A S de Toledo
- Department of Hematology, Oncology, Hemostaseology, and Stem Cell Transplantation, Faculty of Medicine, RWTH Aachen University, Pauwelsstraße 30, 52074 Aachen, Germany; Center for Integrated Oncology Aachen Bonn Cologne Düsseldorf (CIO ABCD), Aachen, Germany
| | - Janik Böhnke
- Institute for Biomedical Engineering, Department of Cell Biology, Faculty of Medicine, RWTH Aachen University, Aachen, Germany; Helmholtz Institute for Biomedical Engineering, RWTH Aachen University, Aachen, Germany
| | - Martin Graßhoff
- Institute for Computational Genomics Joint Research Center for Computational Biomedicine, Faculty of Medicine, RWTH Aachen University, Aachen, Germany
| | - Ivan G Costa
- Institute for Computational Genomics Joint Research Center for Computational Biomedicine, Faculty of Medicine, RWTH Aachen University, Aachen, Germany
| | - Alexandre Theocharides
- Division of Hematology, University Hospital Zurich and University of Zurich, Zurich, Switzerland
| | - Angela Maurer
- Department of Hematology, Oncology, Hemostaseology, and Stem Cell Transplantation, Faculty of Medicine, RWTH Aachen University, Pauwelsstraße 30, 52074 Aachen, Germany; Center for Integrated Oncology Aachen Bonn Cologne Düsseldorf (CIO ABCD), Aachen, Germany
| | - Herdit M Schüler
- Institute for Human Genetics, Faculty of Medicine, RWTH Aachen University, Aachen, Germany
| | - Eva Miriam Buhl
- Institute for Pathology, Electron Microscopy Facility, Faculty of Medicine, RWTH Aachen University, Aachen, Germany
| | - Kristina Pannen
- Department of Hematology, Oncology, Hemostaseology, and Stem Cell Transplantation, Faculty of Medicine, RWTH Aachen University, Pauwelsstraße 30, 52074 Aachen, Germany; Center for Integrated Oncology Aachen Bonn Cologne Düsseldorf (CIO ABCD), Aachen, Germany
| | - Julian Baumeister
- Department of Hematology, Oncology, Hemostaseology, and Stem Cell Transplantation, Faculty of Medicine, RWTH Aachen University, Pauwelsstraße 30, 52074 Aachen, Germany; Center for Integrated Oncology Aachen Bonn Cologne Düsseldorf (CIO ABCD), Aachen, Germany
| | - Milena Kalmer
- Department of Hematology, Oncology, Hemostaseology, and Stem Cell Transplantation, Faculty of Medicine, RWTH Aachen University, Pauwelsstraße 30, 52074 Aachen, Germany; Center for Integrated Oncology Aachen Bonn Cologne Düsseldorf (CIO ABCD), Aachen, Germany
| | - Siddharth Gupta
- Department of Hematology, Oncology, Hemostaseology, and Stem Cell Transplantation, Faculty of Medicine, RWTH Aachen University, Pauwelsstraße 30, 52074 Aachen, Germany; Center for Integrated Oncology Aachen Bonn Cologne Düsseldorf (CIO ABCD), Aachen, Germany
| | - Peter Boor
- Institute for Pathology, Electron Microscopy Facility, Faculty of Medicine, RWTH Aachen University, Aachen, Germany
| | - Deniz Gezer
- Department of Hematology, Oncology, Hemostaseology, and Stem Cell Transplantation, Faculty of Medicine, RWTH Aachen University, Pauwelsstraße 30, 52074 Aachen, Germany; Center for Integrated Oncology Aachen Bonn Cologne Düsseldorf (CIO ABCD), Aachen, Germany
| | - Tim H Brümmendorf
- Department of Hematology, Oncology, Hemostaseology, and Stem Cell Transplantation, Faculty of Medicine, RWTH Aachen University, Pauwelsstraße 30, 52074 Aachen, Germany; Center for Integrated Oncology Aachen Bonn Cologne Düsseldorf (CIO ABCD), Aachen, Germany
| | - Martin Zenke
- Institute for Biomedical Engineering, Department of Cell Biology, Faculty of Medicine, RWTH Aachen University, Aachen, Germany; Helmholtz Institute for Biomedical Engineering, RWTH Aachen University, Aachen, Germany
| | - Nicolas Chatain
- Department of Hematology, Oncology, Hemostaseology, and Stem Cell Transplantation, Faculty of Medicine, RWTH Aachen University, Pauwelsstraße 30, 52074 Aachen, Germany; Center for Integrated Oncology Aachen Bonn Cologne Düsseldorf (CIO ABCD), Aachen, Germany
| | - Steffen Koschmieder
- Department of Hematology, Oncology, Hemostaseology, and Stem Cell Transplantation, Faculty of Medicine, RWTH Aachen University, Pauwelsstraße 30, 52074 Aachen, Germany; Center for Integrated Oncology Aachen Bonn Cologne Düsseldorf (CIO ABCD), Aachen, Germany.
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26
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Łastowska M, Matyja E, Sobocińska A, Wojtaś B, Niemira M, Szałkowska A, Krętowski A, Karkucińska‐Więckowska A, Kaleta M, Ejmont M, Tarasińska M, Perek‐Polnik M, Dembowska‐Bagińska B, Pronicki M, Grajkowska W, Trubicka J. Transcriptional profiling of paediatric ependymomas identifies prognostically significant groups. J Pathol Clin Res 2021; 7:565-576. [PMID: 34314101 PMCID: PMC8503892 DOI: 10.1002/cjp2.236] [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] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 06/29/2021] [Accepted: 07/02/2021] [Indexed: 11/21/2022]
Abstract
The majority of supratentorial ependymomas in children contain oncogenic fusions, such as ZFTA-RELA or YAP1-MAMLD1. In contrast, posterior fossa (PF) ependymomas lack recurrent somatic mutations and are classified based on gene expression or methylation profiling into group A (PFA) and group B (PFB). We have applied a novel method, NanoString nCounter Technology, to identify four molecular groups among 16 supratentorial and 50 PF paediatric ependymomas, using 4-5 group-specific signature genes. Clustering analysis of 16 supratentorial ependymomas revealed 9 tumours with a RELA fusion-positive signature (RELA+), 1 tumour with a YAP1 fusion-positive signature (YAP1+), and 6 not-classified tumours. Additionally, we identified one RELA+ tumour among historically diagnosed CNS primitive neuroectodermal tumour samples. Overall, 9 of 10 tumours with the RELA+ signature possessed the ZFTA-RELA fusion as detected by next-generation sequencing (p = 0.005). Similarly, the only tumour with a YAP1+ signature exhibited the YAP1-MAMLD1 fusion. Among the remaining unclassified ependymomas, which did not exhibit the ZFTA-RELA fusion, the ZFTA-MAML2 fusion was detected in one case. Notably, among nine ependymoma patients with the RELA+ signature, eight survived at least 5 years after diagnosis. Clustering analysis of PF tumours revealed 42 samples with PFA signatures and 7 samples with PFB signatures. Clinical characteristics of patients with PFA and PFB ependymomas corroborated the previous findings. In conclusion, we confirm here that the NanoString method is a useful single tool for the diagnosis of all four main molecular groups of ependymoma. The differences in reported survival rates warrant further clinical investigation of patients with the ZFTA-RELA fusion.
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Affiliation(s)
- Maria Łastowska
- Department of PathomorphologyThe Children's Memorial Health InstituteWarsawPoland
| | - Ewa Matyja
- Department of Experimental and Clinical NeuropathologyMossakowski Medical Research Institute, Polish Academy of SciencesWarsawPoland
| | - Anna Sobocińska
- Department of Experimental and Clinical NeuropathologyMossakowski Medical Research Institute, Polish Academy of SciencesWarsawPoland
| | - Bartosz Wojtaś
- Neurobiology CenterNencki Institute of Experimental BiologyWarsawPoland
| | - Magdalena Niemira
- Clinical Research CentreMedical University of BiałystokBiałystokPoland
| | - Anna Szałkowska
- Clinical Research CentreMedical University of BiałystokBiałystokPoland
| | - Adam Krętowski
- Clinical Research CentreMedical University of BiałystokBiałystokPoland
| | | | - Magdalena Kaleta
- Department of PathomorphologyThe Children's Memorial Health InstituteWarsawPoland
| | - Maria Ejmont
- Department of PathomorphologyThe Children's Memorial Health InstituteWarsawPoland
| | | | | | | | - Maciej Pronicki
- Department of PathomorphologyThe Children's Memorial Health InstituteWarsawPoland
| | - Wiesława Grajkowska
- Department of PathomorphologyThe Children's Memorial Health InstituteWarsawPoland
| | - Joanna Trubicka
- Department of PathomorphologyThe Children's Memorial Health InstituteWarsawPoland
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Huberman LB, Wu VW, Lee J, Daum C, O'Malley RC, Glass NL. Aspects of the Neurospora crassa Sulfur Starvation Response Are Revealed by Transcriptional Profiling and DNA Affinity Purification Sequencing. mSphere 2021; 6:e0056421. [PMID: 34523983 DOI: 10.1128/mSphere.00564-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Accurate nutrient sensing is important for rapid fungal growth and exploitation of available resources. Sulfur is an important nutrient source found in a number of biological macromolecules, including proteins and lipids. The model filamentous fungus Neurospora crassa is capable of utilizing sulfur found in a variety of sources from amino acids to sulfate. During sulfur starvation, the transcription factor CYS-3 is responsible for upregulation of genes involved in sulfur uptake and assimilation. Using a combination of RNA sequencing and DNA affinity purification sequencing, we performed a global survey of the N. crassa sulfur starvation response and the role of CYS-3 in regulating sulfur-responsive genes. The CYS-3 transcription factor bound the promoters and regulated genes involved in sulfur metabolism. Additionally, CYS-3 directly activated the expression of a number of uncharacterized transporter genes, suggesting that regulation of sulfur import is an important aspect of regulation by CYS-3. CYS-3 also directly regulated the expression of genes involved in mitochondrial electron transfer. During sulfur starvation, genes involved in nitrogen metabolism, such as amino acid and nucleic acid metabolic pathways, along with genes encoding proteases and nucleases that are necessary for scavenging nitrogen, were activated. Sulfur starvation also caused changes in the expression of genes involved in carbohydrate metabolism, such as those encoding glycosyl hydrolases. Thus, our data suggest a connection between sulfur metabolism and other aspects of cellular metabolism. IMPORTANCE Identification of nutrients present in the environment is a challenge common to all organisms. Sulfur is an important nutrient source found in proteins, lipids, and electron carriers that are required for the survival of filamentous fungi such as Neurospora crassa. Here, we transcriptionally profiled the response of N. crassa to characterize the global response to sulfur starvation. We also used DNA affinity purification sequencing to identify the direct downstream targets of the transcription factor responsible for regulating genes involved in sulfur uptake and assimilation. Along with genes involved in sulfur metabolism, this transcription factor regulated a number of uncharacterized transporter genes and genes involved in mitochondrial electron transfer. Our data also suggest a connection between sulfur, nitrogen, and carbon metabolism, indicating that the regulation of a number of metabolic pathways is intertwined.
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28
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Gómez I, Thomas MC, Palacios G, Egui A, Carrilero B, Simón M, Valladares B, Segovia M, Carmelo E, López MC. Differential Expression of Immune Response Genes in Asymptomatic Chronic Chagas Disease Patients Versus Healthy Subjects. Front Cell Infect Microbiol 2021; 11:722984. [PMID: 34552885 PMCID: PMC8450343 DOI: 10.3389/fcimb.2021.722984] [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: 06/09/2021] [Accepted: 08/12/2021] [Indexed: 11/30/2022] Open
Abstract
Infection by the Trypanosoma cruzi parasite causes Chagas disease and triggers multiple immune mechanisms in the host to combat the pathogen. Chagas disease has a variable clinical presentation and progression, producing in the chronic phase a fragile balance between the host immune response and parasite replication that keeps patients in a clinically silent asymptomatic stage for years. Since the parasite is intracellular and replicates within cells, the cell-mediated response of the host adaptive immunity plays a critical role. This function is mainly orchestrated by T lymphocytes, which recognize parasite antigens and promote specific functions to control the infection. However, little is known about the immunological markers associated with this asymptomatic stage of the disease. In this large-scale analysis, the differential expression of 106 immune system-related genes has been analyzed using high-throughput qPCR in T. cruzi antigen-stimulated PBMC from chronic Chagas disease patients with indeterminate form (IND) and healthy donors (HD) from endemic and non-endemic areas of Chagas disease. This analysis revealed that there were no differences in the expression level of most genes under study between healthy donors from endemic and non-endemic areas determined by PCA and differential gene expression analysis. Instead, PCA revealed the existence of different expression profiles between IND patients and HD (p < 0.0001), dependent on the 32 genes included in PC1. Differential gene expression analysis also revealed 23 upregulated genes (expression fold change > 2) and 11 downregulated genes (expression fold change < 0.5) in IND patients versus HD. Enrichment analysis showed that several upregulated genes in IND patients participate in relevant immunological pathways such as antigen-dependent B cell activation, stress induction of HSP regulation, NO2-dependent IL12 pathway in NK cells, and cytokine-inflammatory response. The antigen-specific differential gene expression profile detected in these patients and the relevant immunological pathways that seem to be activated could represent potential biomarkers of the asymptomatic form of Chagas disease, helpful to diagnosis and infection control.
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Affiliation(s)
- Inmaculada Gómez
- Instituto de Parasitología y Biomedicina López-Neyra, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - M Carmen Thomas
- Instituto de Parasitología y Biomedicina López-Neyra, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Génesis Palacios
- Instituto Universitario de Enfermedades Tropicales y Salud Pública de Canarias, Universidad de La Laguna, La Laguna, Spain
| | - Adriana Egui
- Instituto de Parasitología y Biomedicina López-Neyra, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Bartolomé Carrilero
- Unidad Regional de Medicina Tropical, Hospital Universitario Virgen de la Arrixaca, Murcia, Spain
| | - Marina Simón
- Unidad Regional de Medicina Tropical, Hospital Universitario Virgen de la Arrixaca, Murcia, Spain
| | - Basilio Valladares
- Instituto Universitario de Enfermedades Tropicales y Salud Pública de Canarias, Universidad de La Laguna, La Laguna, Spain.,Departamento de Obstetricia y Ginecología, Pediatría, Medicina Preventiva y Salud Pública, Toxicología, Medicina Legal y Forense y Parasitología, Universidad de La Laguna, La Laguna, Spain
| | - Manuel Segovia
- Unidad Regional de Medicina Tropical, Hospital Universitario Virgen de la Arrixaca, Murcia, Spain
| | - Emma Carmelo
- Instituto Universitario de Enfermedades Tropicales y Salud Pública de Canarias, Universidad de La Laguna, La Laguna, Spain.,Departamento de Obstetricia y Ginecología, Pediatría, Medicina Preventiva y Salud Pública, Toxicología, Medicina Legal y Forense y Parasitología, Universidad de La Laguna, La Laguna, Spain
| | - Manuel Carlos López
- Instituto de Parasitología y Biomedicina López-Neyra, Consejo Superior de Investigaciones Científicas, Granada, Spain
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29
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Huberman LB. Developing Functional Genomics Platforms for Fungi. mSystems 2021; 6:e0073021. [PMID: 34427501 DOI: 10.1128/mSystems.00730-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Fungi are responsible for diseases that result in the deaths of over a million individuals each year and devastating crop infestations that threaten global food supplies. However, outside of a select few model organisms, the majority of fungal genes are uncharacterized. The roles of these genes in the biology of the organism, pathogenesis, and mediating interactions with the environment and other microbes are unknown. Historically, fungal gene characterization has primarily relied on classical genetic screens. However, advances in sequencing technology have enabled more rapid methods of gene functional characterization. Large-scale transcriptional profiling projects are one solution to generating hypotheses about fungal gene function. Together with other 'omics techniques and newer tools that enable massively parallel mutant screens, knowledge of fungal gene function will be substantially improved. Understanding the function of fungal genes will be instrumental in increasing global food security, protecting ecosystems, and improving health outcomes.
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30
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Karami H, Derakhshani A, Ghasemigol M, Fereidouni M, Miri-Moghaddam E, Baradaran B, Tabrizi NJ, Najafi S, Solimando AG, Marsh LM, Silvestris N, De Summa S, Paradiso AV, Racanelli V, Safarpour H. Weighted Gene Co-Expression Network Analysis Combined with Machine Learning Validation to Identify Key Modules and Hub Genes Associated with SARS-CoV-2 Infection. J Clin Med 2021; 10:3567. [PMID: 34441862 PMCID: PMC8397209 DOI: 10.3390/jcm10163567] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [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: 06/22/2021] [Revised: 07/25/2021] [Accepted: 08/03/2021] [Indexed: 02/06/2023] Open
Abstract
The coronavirus disease-2019 (COVID-19) pandemic has caused an enormous loss of lives. Various clinical trials of vaccines and drugs are being conducted worldwide; nevertheless, as of today, no effective drug exists for COVID-19. The identification of key genes and pathways in this disease may lead to finding potential drug targets and biomarkers. Here, we applied weighted gene co-expression network analysis and LIME as an explainable artificial intelligence algorithm to comprehensively characterize transcriptional changes in bronchial epithelium cells (primary human lung epithelium (NHBE) and transformed lung alveolar (A549) cells) during severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Our study detected a network that significantly correlated to the pathogenicity of COVID-19 infection based on identified hub genes in each cell line separately. The novel hub gene signature that was detected in our study, including PGLYRP4 and HEPHL1, may shed light on the pathogenesis of COVID-19, holding promise for future prognostic and therapeutic approaches. The enrichment analysis of hub genes showed that the most relevant biological process and KEGG pathways were the type I interferon signaling pathway, IL-17 signaling pathway, cytokine-mediated signaling pathway, and defense response to virus categories, all of which play significant roles in restricting viral infection. Moreover, according to the drug-target network, we identified 17 novel FDA-approved candidate drugs, which could potentially be used to treat COVID-19 patients through the regulation of four hub genes of the co-expression network. In conclusion, the aforementioned hub genes might play potential roles in translational medicine and might become promising therapeutic targets. Further in vitro and in vivo experimental studies are needed to evaluate the role of these hub genes in COVID-19.
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Affiliation(s)
- Hassan Karami
- Student Research Committee, Birjand University of Medical Sciences, Birjand 9717853577, Iran;
| | - Afshin Derakhshani
- Laboratory of Experimental Pharmacology, IRCCS-Istituto Tumori Giovanni Paolo II, 70124 Bari, Italy;
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz 516615731, Iran; (B.B.); (N.J.T.); (S.N.)
| | - Mohammad Ghasemigol
- Department of Computer Engineering, University of Birjand, Birjand 9717434765, Iran;
| | - Mohammad Fereidouni
- Cellular and Molecular Research Center, Birjand University of Medical Sciences, Birjand 9717853577, Iran;
| | - Ebrahim Miri-Moghaddam
- Cardiovascular Diseases Research Center & Department of Molecular Medicine, School of Medicine, Birjand University of Medical Sciences, Birjand 9717853577, Iran;
| | - Behzad Baradaran
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz 516615731, Iran; (B.B.); (N.J.T.); (S.N.)
- Pharmaceutical Analysis Research Center, Tabriz University of Medical Sciences, Tabriz 516615731, Iran
| | - Neda Jalili Tabrizi
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz 516615731, Iran; (B.B.); (N.J.T.); (S.N.)
| | - Souzan Najafi
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz 516615731, Iran; (B.B.); (N.J.T.); (S.N.)
| | - Antonio Giovanni Solimando
- Department of Biomedical Sciences and Human Oncology, University of Bari “Aldo Moro”, 70121 Bari, Italy; (A.G.S.); (N.S.)
| | - Leigh M. Marsh
- Ludwig Boltzmann Institute for Lung Vascular Research, Neue Stiftingtalstraße 6/VI, 8010 Graz, Austria;
| | - Nicola Silvestris
- Department of Biomedical Sciences and Human Oncology, University of Bari “Aldo Moro”, 70121 Bari, Italy; (A.G.S.); (N.S.)
- Medical Oncology Unit, IRCCS-Istituto Tumori “Giovanni Paolo II” of Bari, 70124 Bari, Italy
| | - Simona De Summa
- Molecular Diagnostics and Pharmacogenetics Unit, IRCCS-Istituto Tumori ‘Giovanni Paolo II’, 70124 Bari, Italy;
| | | | - Vito Racanelli
- Department of Biomedical Sciences and Human Oncology, University of Bari “Aldo Moro”, 70121 Bari, Italy; (A.G.S.); (N.S.)
| | - Hossein Safarpour
- Cellular and Molecular Research Center, Birjand University of Medical Sciences, Birjand 9717853577, Iran;
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31
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Buscher K, Heitplatz B, van Marck V, Song J, Loismann S, Rixen R, Hüchtmann B, Kurian S, Ehinger E, Wolf D, Ley K, Pavenstädt H, Reuter S. Data-Driven Kidney Transplant Phenotyping as a Histology-Independent Framework for Biomarker Discovery. J Am Soc Nephrol 2021; 32:1933-1945. [PMID: 34078665 PMCID: PMC8455252 DOI: 10.1681/asn.2020121685] [Citation(s) in RCA: 3] [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] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 03/15/2021] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND In transplant medicine, clinical decision making largely relies on histology of biopsy specimens. However, histology suffers from low specificity, sensitivity, and reproducibility, leading to suboptimal stratification of patients. We developed a histology-independent immune framework of kidney graft homeostasis and rejection. METHODS We applied tailored RNA deconvolution for leukocyte enumeration and coregulated gene network analysis to published bulk human kidney transplant RNA transcriptomes as input for unsupervised, high-dimensional phenotype clustering. We used framework-based graft survival analysis to identify a biomarker that was subsequently characterized in independent transplant biopsy specimens. RESULTS We found seven immune phenotypes that confirm known rejection types and uncovered novel signatures. The molecular phenotypes allow for improved graft survival analysis compared with histology, and identify a high-risk group in nonrejecting transplants. Two fibrosis-related phenotypes with distinct immune features emerged with reduced graft survival. We identified lysyl oxidase-like 2 (LOXL2)-expressing peritubular CD68+ macrophages as a framework-derived biomarker of impaired allograft function. These cells precede graft fibrosis, as demonstrated in longitudinal biopsy specimens, and may be clinically useful as a biomarker for early fibrogenesis. CONCLUSIONS This study provides a comprehensive, data-driven atlas of human kidney transplant phenotypes and demonstrates its utility to identify novel clinical biomarkers.
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Affiliation(s)
- Konrad Buscher
- Division of General Internal Medicine, Nephrology and Rheumatology, Department of Medicine D, University Hospital of Muenster, Muenster, Germany,Division of Inflammation Biology, La Jolla Institute for Immunology, La Jolla, California
| | - Barbara Heitplatz
- Institute of Pathology, University Hospital Muenster, Muenster, Germany
| | - Veerle van Marck
- Institute of Pathology, University Hospital Muenster, Muenster, Germany
| | - Jian Song
- Institute of Physiological Chemistry and Pathobiochemistry, University of Muenster, Muenster, Germany,Cells-in-Motion Cluster of Excellence, University of Muenster, Muenster, Germany
| | - Sophie Loismann
- Institute of Physiological Chemistry and Pathobiochemistry, University of Muenster, Muenster, Germany,Cells-in-Motion Cluster of Excellence, University of Muenster, Muenster, Germany
| | - Rebecca Rixen
- Division of General Internal Medicine, Nephrology and Rheumatology, Department of Medicine D, University Hospital of Muenster, Muenster, Germany
| | - Birte Hüchtmann
- Division of General Internal Medicine, Nephrology and Rheumatology, Department of Medicine D, University Hospital of Muenster, Muenster, Germany
| | - Sunil Kurian
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, California
| | - Erik Ehinger
- Division of Signaling and Gene Expression, La Jolla Institute for Immunology, La Jolla, California
| | - Dennis Wolf
- Division of Inflammation Biology, La Jolla Institute for Immunology, La Jolla, California,Department of Cardiology and Angiology I, University Heart Center, and Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Klaus Ley
- Division of Inflammation Biology, La Jolla Institute for Immunology, La Jolla, California
| | - Hermann Pavenstädt
- Division of General Internal Medicine, Nephrology and Rheumatology, Department of Medicine D, University Hospital of Muenster, Muenster, Germany
| | - Stefan Reuter
- Division of General Internal Medicine, Nephrology and Rheumatology, Department of Medicine D, University Hospital of Muenster, Muenster, Germany
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Fletcher EJR, Kaminski T, Williams G, Duty S. Drug repurposing strategies of relevance for Parkinson's disease. Pharmacol Res Perspect 2021; 9:e00841. [PMID: 34309236 PMCID: PMC8311732 DOI: 10.1002/prp2.841] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 04/15/2021] [Accepted: 06/29/2021] [Indexed: 01/01/2023] Open
Abstract
Parkinson's disease is a highly disabling, progressive neurodegenerative disease that manifests as a mix of motor and non-motor signs. Although we are equipped with some symptomatic treatments, especially for the motor signs of the disease, there are still no established disease-modifying drugs so the disease progresses unchecked. Standard drug discovery programs for disease-modifying therapies have provided key insights into the pathogenesis of Parkinson's disease but, of the many positive candidates identified in pre-clinical studies, none has yet translated into a successful clinically efficacious drug. Given the huge cost of drug discovery programs, it is not surprising that much attention has turned toward repurposing strategies. The trialing of an established therapeutic has the advantage of bypassing the need for preclinical safety testing and formulation optimization, thereby cutting both time and costs involved in getting a treatment to the clinic. Additional reduced failure rates for repurposed drugs are also a potential bonus. Many different strategies for drug repurposing are open to researchers in the Parkinson's disease field. Some of these have already proven effective in identifying suitable drugs for clinical trials, lending support to such approaches. In this review, we present a summary of the different strategies for drug repurposing, from large-scale epidemiological correlation analysis through to single-gene transcriptional approaches. We provide examples of past or ongoing studies adopting each strategy, where these exist. For strategies that have yet to be applied to Parkinson's disease, their utility is illustrated using examples taken from other disorders.
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Affiliation(s)
- Edward J. R. Fletcher
- King’s College LondonInstitute of Psychiatry, Psychology & NeuroscienceWolfson Centre for Age‐Related DiseasesLondonUK
| | - Thomas Kaminski
- King’s College LondonInstitute of Psychiatry, Psychology & NeuroscienceWolfson Centre for Age‐Related DiseasesLondonUK
| | - Gareth Williams
- King’s College LondonInstitute of Psychiatry, Psychology & NeuroscienceWolfson Centre for Age‐Related DiseasesLondonUK
| | - Susan Duty
- King’s College LondonInstitute of Psychiatry, Psychology & NeuroscienceWolfson Centre for Age‐Related DiseasesLondonUK
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Deleersnijder D, Callemeyn J, Arijs I, Naesens M, Van Craenenbroeck AH, Lambrechts D, Sprangers B. Current Methodological Challenges of Single-Cell and Single-Nucleus RNA-Sequencing in Glomerular Diseases. J Am Soc Nephrol 2021; 32:1838-1852. [PMID: 34140401 PMCID: PMC8455274 DOI: 10.1681/asn.2021020157] [Citation(s) in RCA: 15] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Single-cell RNA sequencing (scRNA-seq) and single-nucleus RNA-seq (snRNA-seq) allow transcriptomic profiling of thousands of cells from a renal biopsy specimen at a single-cell resolution. Both methods are promising tools to unravel the underlying pathophysiology of glomerular diseases. This review provides an overview of the technical challenges that should be addressed when designing single-cell transcriptomics experiments that focus on glomerulopathies. The isolation of glomerular cells from core needle biopsy specimens for single-cell transcriptomics remains difficult and depends upon five major factors. First, core needle biopsies generate little tissue material, and several samples are required to identify glomerular cells. Second, both fresh and frozen tissue samples may yield glomerular cells, although every experimental pipeline has different (dis)advantages. Third, enrichment for glomerular cells in human tissue before single-cell analysis is challenging because no effective standardized pipelines are available. Fourth, the current warm cell-dissociation protocols may damage glomerular cells and induce transcriptional artifacts, which can be minimized by using cold dissociation techniques at the cost of less efficient cell dissociation. Finally, snRNA-seq methods may be superior to scRNA-seq in isolating glomerular cells; however, the efficacy of snRNA-seq on core needle biopsy specimens remains to be proven. The field of single-cell omics is rapidly evolving, and the integration of these techniques in multiomics assays will undoubtedly create new insights in the complex pathophysiology of glomerular diseases.
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Affiliation(s)
- Dries Deleersnijder
- Department of Microbiology, Immunology and Transplantation, Laboratory of Molecular Immunology, Rega Institute, KU Leuven, Leuven, Belgium,Division of Nephrology, University Hospitals Leuven, Leuven, Belgium
| | - Jasper Callemeyn
- Division of Nephrology, University Hospitals Leuven, Leuven, Belgium,Department of Microbiology, Immunology and Transplantation, Nephrology and Renal Transplantation Research Group, KU Leuven, Leuven, Belgium
| | - Ingrid Arijs
- Laboratory for Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium,Vlaams Instituut voor Biotechnologie Center for Cancer Biology, Leuven, Belgium
| | - Maarten Naesens
- Division of Nephrology, University Hospitals Leuven, Leuven, Belgium,Department of Microbiology, Immunology and Transplantation, Nephrology and Renal Transplantation Research Group, KU Leuven, Leuven, Belgium
| | - Amaryllis H. Van Craenenbroeck
- Division of Nephrology, University Hospitals Leuven, Leuven, Belgium,Department of Microbiology, Immunology and Transplantation, Nephrology and Renal Transplantation Research Group, KU Leuven, Leuven, Belgium
| | - Diether Lambrechts
- Laboratory for Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium,Vlaams Instituut voor Biotechnologie Center for Cancer Biology, Leuven, Belgium
| | - Ben Sprangers
- Department of Microbiology, Immunology and Transplantation, Laboratory of Molecular Immunology, Rega Institute, KU Leuven, Leuven, Belgium,Division of Nephrology, University Hospitals Leuven, Leuven, Belgium,Correspondence: Prof. Ben Sprangers, Department of Microbiology, Immunology and Transplantation, Laboratory of Molecular Immunology (Rega Institute), KU Leuven, Herestraat 49, Leuven 3000, Belgium.
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34
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Palacios G, Diaz-Solano R, Valladares B, Dorta-Guerra R, Carmelo E. Early Transcriptional Liver Signatures in Experimental Visceral Leishmaniasis. Int J Mol Sci 2021; 22:7161. [PMID: 34281214 PMCID: PMC8267970 DOI: 10.3390/ijms22137161] [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] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 06/28/2021] [Accepted: 06/28/2021] [Indexed: 01/01/2023] Open
Abstract
Transcriptional analysis of complex biological scenarios has been used extensively, even though sometimes the results of such analysis may prove imprecise or difficult to interpret due to an overwhelming amount of information. In this study, a large-scale real-time qPCR experiment was coupled to multivariate statistical analysis in order to describe the main immunological events underlying the early L. infantum infection in livers of BALB/c mice. High-throughput qPCR was used to evaluate the expression of 223 genes related to immunological response and metabolism 1, 3, 5, and 10 days post infection. This integrative analysis showed strikingly different gene signatures at 1 and 10 days post infection, revealing the progression of infection in the experimental model based on the upregulation of particular immunological response patterns and mediators. The gene signature 1 day post infection was not only characterized by the upregulation of mediators involved in interferon signaling and cell chemotaxis, but also the upregulation of some inhibitory markers. In contrast, at 10 days post infection, the upregulation of many inflammatory and Th1 markers characterized a more defined gene signature with the upregulation of mediators in the IL-12 signaling pathway. Our results reveal a significant connection between the expression of innate immune response and metabolic and inhibitory markers in early L. infantum infection of the liver.
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Affiliation(s)
- Génesis Palacios
- Instituto Universitario de Enfermedades Tropicales y Salud Pública de Canarias (IUESTPC), Universidad de la Laguna (ULL), Avenida Astrofísico Francisco Sánchez s/n, 38200 La Laguna (Tenerife), Spain; (G.P.); (R.D.-S.); (B.V.); (R.D.-G.)
| | - Raquel Diaz-Solano
- Instituto Universitario de Enfermedades Tropicales y Salud Pública de Canarias (IUESTPC), Universidad de la Laguna (ULL), Avenida Astrofísico Francisco Sánchez s/n, 38200 La Laguna (Tenerife), Spain; (G.P.); (R.D.-S.); (B.V.); (R.D.-G.)
| | - Basilio Valladares
- Instituto Universitario de Enfermedades Tropicales y Salud Pública de Canarias (IUESTPC), Universidad de la Laguna (ULL), Avenida Astrofísico Francisco Sánchez s/n, 38200 La Laguna (Tenerife), Spain; (G.P.); (R.D.-S.); (B.V.); (R.D.-G.)
- Departamento de Obstetricia y Ginecología, Pediatría, Medicina Preventiva y Salud Pública, Toxicología, Medicina Legal y Forense y Parasitología, Universidad de La Laguna, Avda. Astrofísico F. Sánchez s/n, 38200 La Laguna (Tenerife), Spain
- Red de Investigación Colaborativa en Enfermedades Tropicales (RICET)
| | - Roberto Dorta-Guerra
- Instituto Universitario de Enfermedades Tropicales y Salud Pública de Canarias (IUESTPC), Universidad de la Laguna (ULL), Avenida Astrofísico Francisco Sánchez s/n, 38200 La Laguna (Tenerife), Spain; (G.P.); (R.D.-S.); (B.V.); (R.D.-G.)
- Departamento de Matemáticas, Estadística e Investigación Operativa, Facultad de Ciencias, Universidad de La Laguna, 38200 La Laguna (Tenerife), Spain
| | - Emma Carmelo
- Instituto Universitario de Enfermedades Tropicales y Salud Pública de Canarias (IUESTPC), Universidad de la Laguna (ULL), Avenida Astrofísico Francisco Sánchez s/n, 38200 La Laguna (Tenerife), Spain; (G.P.); (R.D.-S.); (B.V.); (R.D.-G.)
- Departamento de Obstetricia y Ginecología, Pediatría, Medicina Preventiva y Salud Pública, Toxicología, Medicina Legal y Forense y Parasitología, Universidad de La Laguna, Avda. Astrofísico F. Sánchez s/n, 38200 La Laguna (Tenerife), Spain
- Departamento de Matemáticas, Estadística e Investigación Operativa, Facultad de Ciencias, Universidad de La Laguna, 38200 La Laguna (Tenerife), Spain
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Sivakumaran D, Blatner G, Bakken R, Hokey D, Ritz C, Jenum S, Grewal HMS. A 2-Dose AERAS-402 Regimen Boosts CD8 + Polyfunctionality in HIV-Negative, BCG-Vaccinated Recipients. Front Immunol 2021; 12:673532. [PMID: 34177914 PMCID: PMC8231292 DOI: 10.3389/fimmu.2021.673532] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [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: 02/27/2021] [Accepted: 05/18/2021] [Indexed: 11/20/2022] Open
Abstract
Despite the widespread use of BCG, tuberculosis (TB) remains a global threat. Existing vaccine candidates in clinical trials are designed to replace or boost BCG which does not provide satisfying long-term protection. AERAS-402 is a replication-deficient Ad35 vaccine encoding a fusion protein of the M. tuberculosis (Mtb) antigens 85A, 85B, and TB10.4. The present phase I trial assessed the safety and immunogenicity of AERAS-402 in participants living in India – a highly TB-endemic area. Healthy male participants aged 18–45 years with a negative QuantiFERON-TB Gold in-tube test (QFT) were recruited. Enrolled participants (n=12) were randomized 2:1 to receive two intramuscular injections of either AERAS-402 (3 x 1010 viral particles [vp]); (n=8) or placebo (n=4) on study days 0 and 28. Safety and immunogenicity parameters were evaluated for up to 182 days post the second injection. Immunogenicity was assessed by a flow cytometry-based intracellular cytokine staining (ICS) assay and transcriptional profiling. The latter was examined using dual-color-Reverse-Transcriptase-Multiplex-Ligation-dependent-Probe-Amplification (dc-RT MLPA) assay. AERAS-402 was well tolerated, and no vaccine-related serious adverse events were recorded. The vaccine-induced CD8+ T-cell responses were dominated by cells co-expressing IFN-γ, TNF-α, and IL-2 (“polyfunctional” cells) and were more robust than CD4+ T-cell responses. Five genes (CXCL10, GNLY, IFI35, IL1B and PTPRCv2) were differentially expressed between the AERAS-402-group and the placebo group, suggesting vaccine-induced responses. Further, compared to pre-vaccination, three genes (CLEC7A, PTPRCv1 and TAGAP) were consistently up-regulated following two doses of vaccination in the AERAS-402-group. No safety concerns were observed for AERAS-402 in healthy Indian adult males. The vaccine-induced predominantly polyfunctional CD8+ T cells in response to Ag85B, humoral immunity, and altered gene expression profiles in peripheral blood mononuclear cells (PBMCs) indicative of activation of various immunologically relevant biological pathways.
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Affiliation(s)
- Dhanasekaran Sivakumaran
- Department of Clinical Science, Bergen Integrated Diagnostic Stewardship Cluster, Faculty of Medicine, University of Bergen, Bergen, Norway.,Department of Microbiology, Haukeland University Hospital, University of Bergen, Bergen, Norway
| | - Gretta Blatner
- Biomedical Advanced Research and Development Authority (BARDA), Department of Health and Human Services, Washington, DC, United States.,Aeras Global TB Vaccine Foundation, Rockville, MD, United States
| | - Rasmus Bakken
- Department of Clinical Science, Bergen Integrated Diagnostic Stewardship Cluster, Faculty of Medicine, University of Bergen, Bergen, Norway.,Department of Microbiology, Haukeland University Hospital, University of Bergen, Bergen, Norway
| | - David Hokey
- Aeras Global TB Vaccine Foundation, Rockville, MD, United States
| | - Christian Ritz
- Department of Clinical Science, Bergen Integrated Diagnostic Stewardship Cluster, Faculty of Medicine, University of Bergen, Bergen, Norway.,Department of Nutrition, Exercise and Sports, University of Copenhagen, Copenhagen, Denmark
| | - Synne Jenum
- Department of Infectious Diseases, Oslo University Hospital, Oslo, Norway
| | - Harleen M S Grewal
- Department of Clinical Science, Bergen Integrated Diagnostic Stewardship Cluster, Faculty of Medicine, University of Bergen, Bergen, Norway.,Department of Microbiology, Haukeland University Hospital, University of Bergen, Bergen, Norway
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Ma J, Liu Y, Guo Y, Ma Q, Ji C, Zhao L. Transcriptional Profiling of Aflatoxin B1-Induced Oxidative Stress and Inflammatory Response in Macrophages. Toxins (Basel) 2021; 13:401. [PMID: 34199697 PMCID: PMC8228812 DOI: 10.3390/toxins13060401] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [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: 05/05/2021] [Revised: 05/28/2021] [Accepted: 05/28/2021] [Indexed: 12/12/2022] Open
Abstract
Aflatoxin B1 (AFB1) is a highly toxic mycotoxin that causes severe suppression of the immune system of humans and animals, as well as enhances reactive oxygen species (ROS) formation, causing oxidative damage. However, the mechanisms underlying the ROS formation and immunotoxicity of AFB1 are poorly understood. This study used the mouse macrophage RAW264.7 cell line and whole-transcriptome sequencing (RNA-Seq) technology to address this knowledge-gap. The results show that AFB1 induced the decrease of cell viability in a dose- and time-dependent manner. AFB1 also significantly increased intracellular productions of ROS and malondialdehyde and decreased glutathione levels. These changes correlated with increased mRNA expression of NOS2, TNF-α and CXCL2 and decreased expression of CD86. In total, 783 differentially expressed genes (DEGs) were identified via RNA-Seq technology. KEGG analysis of the oxidative phosphorylation pathway revealed that mRNA levels of ND1, ND2, ND3, ND4, ND4L, ND5, ND6, Cyt b, COX2, ATPeF0A and ATPeF08 were higher in AFB1-treated cells than control cells, whereas 14 DEGs were downregulated in the AFB1 group. Furthermore, seven immune regulatory pathways mediated by oxidative stress were identified by KEGG analysis. Altogether, these data suggest that AFB1 induces oxidative stress in macrophages via affecting the respiratory chain, which leads to the activation of several signaling pathways related to the inflammatory response.
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Affiliation(s)
| | | | | | | | | | - Lihong Zhao
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (J.M.); (Y.L.); (Y.G.); (Q.M.); (C.J.)
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Strano A, Tuck E, Stubbs VE, Livesey FJ. Variable Outcomes in Neural Differentiation of Human PSCs Arise from Intrinsic Differences in Developmental Signaling Pathways. Cell Rep 2021; 31:107732. [PMID: 32521257 PMCID: PMC7296348 DOI: 10.1016/j.celrep.2020.107732] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 03/09/2020] [Accepted: 05/14/2020] [Indexed: 12/12/2022] Open
Abstract
Directed differentiation of human pluripotent stem cells varies in specificity and efficiency. Stochastic, genetic, intracellular, and environmental factors affect maintenance of pluripotency and differentiation into early embryonic lineages. However, factors affecting variation in in vitro differentiation to defined cell types are not well understood. To address this, we focused on a well-established differentiation process to cerebral cortex neural progenitor cells and their neuronal progeny from human pluripotent stem cells. Analysis of 162 differentiation outcomes of 61 stem cell lines derived from 37 individuals showed that most variation occurs along gene expression axes reflecting dorsoventral and rostrocaudal spatial expression during in vivo brain development. Line-independent and line-dependent variations occur, with the latter driven largely by differences in endogenous Wnt signaling activity. Tuning Wnt signaling during a specific phase early in the differentiation process reduces variability, demonstrating that cell-line/genome-specific differentiation outcome biases can be corrected by controlling extracellular signaling. Analysis of 162 iPSC neural differentiation quantifies sources of variability Variation in outcomes occurs along developmental brain spatial and regional axes Variation depends on iPSC-line-specific differences in Wnt/β-catenin signaling Effects of signaling differences can be rescued by exogenous pathway activation
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Affiliation(s)
- Alessio Strano
- The Wellcome Trust/Cancer Research UK Gurdon Institute & Department of Biochemistry, University of Cambridge, Cambridge, UK; UCL Great Ormond Street Institute of Child Health, Zayed Centre for Research into Rare Disease in Children, University College London, 20 Guilford Street, London WC1N 1DZ, UK
| | - Eleanor Tuck
- UCL Great Ormond Street Institute of Child Health, Zayed Centre for Research into Rare Disease in Children, University College London, 20 Guilford Street, London WC1N 1DZ, UK
| | - Victoria E Stubbs
- The Wellcome Trust/Cancer Research UK Gurdon Institute & Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Frederick J Livesey
- UCL Great Ormond Street Institute of Child Health, Zayed Centre for Research into Rare Disease in Children, University College London, 20 Guilford Street, London WC1N 1DZ, UK.
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Lecluze E, Rolland AD, Filis P, Evrard B, Leverrier-Penna S, Maamar MB, Coiffec I, Lavoué V, Fowler PA, Mazaud-Guittot S, Jégou B, Chalmel F. Dynamics of the transcriptional landscape during human fetal testis and ovary development. Hum Reprod 2021; 35:1099-1119. [PMID: 32412604 DOI: 10.1093/humrep/deaa041] [Citation(s) in RCA: 12] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 02/10/2020] [Indexed: 12/17/2022] Open
Abstract
STUDY QUESTION Which transcriptional program triggers sex differentiation in bipotential gonads and downstream cellular events governing fetal testis and ovary development in humans? SUMMARY ANSWER The characterization of a dynamically regulated protein-coding and non-coding transcriptional landscape in developing human gonads of both sexes highlights a large number of potential key regulators that show an early sexually dimorphic expression pattern. WHAT IS KNOWN ALREADY Gonadal sex differentiation is orchestrated by a sexually dimorphic gene expression program in XX and XY developing fetal gonads. A comprehensive characterization of its non-coding counterpart offers promising perspectives for deciphering the molecular events underpinning gonad development and for a complete understanding of the etiology of disorders of sex development in humans. STUDY DESIGN, SIZE, DURATION To further investigate the protein-coding and non-coding transcriptional landscape during gonad differentiation, we used RNA-sequencing (RNA-seq) and characterized the RNA content of human fetal testis (N = 24) and ovaries (N = 24) from 6 to 17 postconceptional week (PCW), a key period in sex determination and gonad development. PARTICIPANTS/MATERIALS, SETTING, METHODS First trimester fetuses (6-12 PCW) and second trimester fetuses (13-14 and 17 PCW) were obtained from legally induced normally progressing terminations of pregnancy. Total RNA was extracted from whole human fetal gonads and sequenced as paired-end 2 × 50 base reads. Resulting sequences were mapped to the human genome, allowing for the assembly and quantification of corresponding transcripts. MAIN RESULTS AND THE ROLE OF CHANCE This RNA-seq analysis of human fetal testes and ovaries at seven key developmental stages led to the reconstruction of 22 080 transcripts differentially expressed during testicular and/or ovarian development. In addition to 8935 transcripts displaying sex-independent differential expression during gonad development, the comparison of testes and ovaries enabled the discrimination of 13 145 transcripts that show a sexually dimorphic expression profile. The latter include 1479 transcripts differentially expressed as early as 6 PCW, including 39 transcription factors, 40 long non-coding RNAs and 20 novel genes. Despite the use of stringent filtration criteria (expression cut-off of at least 1 fragment per kilobase of exon model per million reads mapped, fold change of at least 2 and false discovery rate adjusted P values of less than <1%), the possibility of assembly artifacts and of false-positive differentially expressed transcripts cannot be fully ruled out. LARGE-SCALE DATA Raw data files (fastq) and a searchable table (.xlss) containing information on genomic features and expression data for all refined transcripts have been submitted to the NCBI GEO under accession number GSE116278. LIMITATIONS, REASONS FOR CAUTION The intrinsic nature of this bulk analysis, i.e. the sequencing of transcripts from whole gonads, does not allow direct identification of the cellular origin(s) of the transcripts characterized. Potential cellular dilution effects (e.g. as a result of distinct proliferation rates in XX and XY gonads) may account for a few of the expression profiles identified as being sexually dimorphic. Finally, transcriptome alterations that would result from exposure to pre-abortive drugs cannot be completely excluded. Although we demonstrated the high quality of the sorted cell populations used for experimental validations using quantitative RT-PCR, it cannot be totally excluded that some germline expression may correspond to cell contamination by, for example, macrophages. WIDER IMPLICATIONS OF THE FINDINGS For the first time, this study has led to the identification of 1000 protein-coding and non-coding candidate genes showing an early, sexually dimorphic, expression pattern that have not previously been associated with sex differentiation. Collectively, these results increase our understanding of gonad development in humans, and contribute significantly to the identification of new candidate genes involved in fetal gonad differentiation. The results also provide a unique resource that may improve our understanding of the fetal origin of testicular and ovarian dysgenesis syndromes, including cryptorchidism and testicular cancers. STUDY FUNDING/COMPETING INTEREST(S) This work was supported by the French National Institute of Health and Medical Research (Inserm), the University of Rennes 1, the French School of Public Health (EHESP), the Swiss National Science Foundation [SNF n° CRS115_171007 to B.J.], the French National Research Agency [ANR n° 16-CE14-0017-02 and n° 18-CE14-0038-02 to F.C.], the Medical Research Council [MR/L010011/1 to P.A.F.] and the European Community's Seventh Framework Programme (FP7/2007-2013) [under grant agreement no 212885 to P.A.F.] and from the European Union's Horizon 2020 Research and Innovation Programme [under grant agreement no 825100 to P.A.F. and S.M.G.]. There are no competing interests related to this study.
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Affiliation(s)
- Estelle Lecluze
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, F-35000 Rennes, France
| | - Antoine D Rolland
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, F-35000 Rennes, France
| | - Panagiotis Filis
- Institute of Medical Sciences, School of Medicine, Medical Sciences & Nutrition, University of Aberdeen, Foresterhill, Aberdeen, AB25 2ZD, UK
| | - Bertrand Evrard
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, F-35000 Rennes, France
| | - Sabrina Leverrier-Penna
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, F-35000 Rennes, France.,Univ Poitiers, STIM, CNRS ERL7003, Poitiers Cedex 9, CNRS ERL7003, France
| | - Millissia Ben Maamar
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, F-35000 Rennes, France
| | - Isabelle Coiffec
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, F-35000 Rennes, France
| | - Vincent Lavoué
- Service Gynécologie et Obstétrique, CHU Rennes, F-35000 Rennes, France
| | - Paul A Fowler
- Institute of Medical Sciences, School of Medicine, Medical Sciences & Nutrition, University of Aberdeen, Foresterhill, Aberdeen, AB25 2ZD, UK
| | - Séverine Mazaud-Guittot
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, F-35000 Rennes, France
| | - Bernard Jégou
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, F-35000 Rennes, France
| | - Frédéric Chalmel
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, F-35000 Rennes, France
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Rosin JM, Sinha S, Biernaskie J, Kurrasch DM. A subpopulation of embryonic microglia respond to maternal stress and influence nearby neural progenitors. Dev Cell 2021; 56:1326-1345.e6. [PMID: 33887203 DOI: 10.1016/j.devcel.2021.03.018] [Citation(s) in RCA: 9] [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: 07/08/2020] [Revised: 01/21/2021] [Accepted: 03/11/2021] [Indexed: 12/31/2022]
Abstract
The interplay between hypothalamic neurons and microglia as they integrate stressors to regulate homeostasis is of growing interest. We asked if microglia in the embryonic hypothalamus were likewise stress responsive and, if so, whether their precocious activation perturbs nearby neural stem cell (NSC) programs. We performed single-cell transcriptomics to define embryonic hypothalamic microglia heterogeneity and identified four microglial subsets, including a subpopulation adjacent to NSCs that was responsive to gestational cold stress. Stress exposure elevated CCL3 and CCL4 secretion, but only in male brains, and ex vivo CCL4 treatment of hypothalamic NSCs altered proliferation and differentiation. Concomitantly, gestational stress decreased PVN oxytocin neurons only in male embryos, which was reversed by microglia depletion. Adult offspring exposed to gestational stress displayed altered social behaviors, which was likewise microglia dependent, but only in males. Collectively, immature hypothalamic microglia play an unappreciated role in translating maternal stressors to sexually dimorphic perturbation of neurodevelopmental programs.
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Affiliation(s)
- Jessica M Rosin
- Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada; Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB T2N 4N1, Canada; Hotchkiss Brain Institute, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Sarthak Sinha
- Department of Comparative Biology and Experimental Medicine, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada; Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB T2N 4N1, Canada; Hotchkiss Brain Institute, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Jeff Biernaskie
- Department of Comparative Biology and Experimental Medicine, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada; Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB T2N 4N1, Canada; Hotchkiss Brain Institute, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Deborah M Kurrasch
- Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada; Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB T2N 4N1, Canada; Hotchkiss Brain Institute, University of Calgary, Calgary, AB T2N 4N1, Canada.
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40
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Jenull S, Tscherner M, Kashko N, Shivarathri R, Stoiber A, Chauhan M, Petryshyn A, Chauhan N, Kuchler K. Transcriptome Signatures Predict Phenotypic Variations of Candida auris. Front Cell Infect Microbiol 2021; 11:662563. [PMID: 33937102 PMCID: PMC8079977 DOI: 10.3389/fcimb.2021.662563] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [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: 02/01/2021] [Accepted: 03/23/2021] [Indexed: 12/13/2022] Open
Abstract
Health care facilities are facing serious threats by the recently emerging human fungal pathogen Candida auris owing to its pronounced antifungal multidrug resistance and poor diagnostic tools. Distinct C. auris clades evolved seemingly simultaneously at independent geographical locations and display both genetic and phenotypic diversity. Although comparative genomics and phenotypic profiling studies are increasing, we still lack mechanistic knowledge about the C. auris species diversification and clinical heterogeneity. Since gene expression variability impacts phenotypic plasticity, we aimed to characterize transcriptomic signatures of C. auris patient isolates with distinct antifungal susceptibility profiles in this study. First, we employed an antifungal susceptibility screening of clinical C. auris isolates to identify divergent intra-clade responses to antifungal treatments. Interestingly, comparative transcriptional profiling reveals large gene expression differences between clade I isolates and one clade II strain, irrespective of their antifungal susceptibilities. However, comparisons at the clade levels demonstrate that minor changes in gene expression suffice to drive divergent drug responses. Finally, we functionally validate transcriptional signatures reflecting phenotypic divergence of clinical isolates. Thus, our results suggest that large-scale transcriptional profiling allows for predicting phenotypic diversities of patient isolates, which may help choosing suitable antifungal therapies of multidrug-resistant C. auris.
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Affiliation(s)
- Sabrina Jenull
- Max Perutz Labs Vienna, Department of Medical Biochemistry, Medical University of Vienna, Vienna, Austria
| | - Michael Tscherner
- Max Perutz Labs Vienna, Department of Medical Biochemistry, Medical University of Vienna, Vienna, Austria
| | - Nataliya Kashko
- Max Perutz Labs Vienna, Department of Medical Biochemistry, Medical University of Vienna, Vienna, Austria
| | - Raju Shivarathri
- Public Health Research Institute & Department of Microbiology, Biochemistry and Molecular Genetics, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ, United States
| | - Anton Stoiber
- Max Perutz Labs Vienna, Department of Medical Biochemistry, Medical University of Vienna, Vienna, Austria
| | - Manju Chauhan
- Public Health Research Institute & Department of Microbiology, Biochemistry and Molecular Genetics, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ, United States
| | - Andriy Petryshyn
- Max Perutz Labs Vienna, Department of Medical Biochemistry, Medical University of Vienna, Vienna, Austria
| | - Neeraj Chauhan
- Public Health Research Institute & Department of Microbiology, Biochemistry and Molecular Genetics, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ, United States
| | - Karl Kuchler
- Max Perutz Labs Vienna, Department of Medical Biochemistry, Medical University of Vienna, Vienna, Austria
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41
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Affiliation(s)
- David H Ellison
- Department of Medicine Oregon Health & Science University, Portland, Oregon
- Veterans Affairs Portland Health Care System, Portland, Oregon
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42
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Hung CF, Holton S, Chow YH, Liles WC, Gharib SA, Altemeier WA. Pericyte-like cells undergo transcriptional reprogramming and distinct functional adaptations in acute lung injury. FASEB J 2021; 35:e21323. [PMID: 33710674 PMCID: PMC10115144 DOI: 10.1096/fj.201903192rr] [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] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 12/08/2020] [Accepted: 12/14/2020] [Indexed: 11/11/2022]
Abstract
We previously reported on the role of pericyte-like cells as functional sentinel immune cells in lung injury. However, much about the biological role of pericytes in lung injury remains unknown. Lung pericyte-like cells are well-positioned to sense disruption to the epithelial barrier and coordinate local inflammatory responses due to their anatomic niche within the alveoli. In this report, we characterized transcriptional responses and functional changes in pericyte-like cells following activation by alveolar components from injured and uninjured lungs in a mouse model of acute lung injury (ALI). Purified pericyte-like cells from lung digests using PDGFRβ as a selection marker were expanded in culture as previously described (1). We induced sterile acute lung injury in mice with recombinant human Fas ligand (rhFasL) instillation followed by mechanical ventilation (1). We then collected bronchoalveolar lavage fluid (BALF) from injured and uninjured mice. Purified pericyte-like cells in culture were exposed to growth media only (control), BALF from uninjured mice, and BALF from injured mice for 6 and 24 hours. RNA collected from these treatment conditions were processed for RNAseq. Targets of interest identified by pathway analysis were validated using in vitro and in vivo assays. We observed robust global transcriptional changes in pericyte-like cells following treatment with uninjured and injured BALF at 6 hours, but this response persisted for 24 hours only after exposure to injured BALF. Functional enrichment analysis of pericytes treated with injured BALF revealed the activation of pro-inflammatory, cell migration, and angiogenesis-related pathways, whereas processes associated with tissue development and cell differentiation were down-regulated. We validated select upregulated targets in the inflammatory, angiogenic, and cell migratory pathways using functional biological assays in vitro and in vivo. We conclude that lung pericyte-like cells are highly responsive to alveolar compartment content from both uninjured and injured lungs, but injured BALF elicits a more sustained response. The inflammatory, angiogenic, and migratory changes exhibited by activated pericyte-like cells underscore the phenotypic plasticity of these specialized stromal cells in the setting of acute lung injury.
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Affiliation(s)
- Chi F Hung
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, University of Washington, Seattle, WA, USA.,Center for Lung Biology, University of Washington, Seattle, WA, USA
| | - Sarah Holton
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, University of Washington, Seattle, WA, USA.,Center for Lung Biology, University of Washington, Seattle, WA, USA
| | - Yu-Hua Chow
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, University of Washington, Seattle, WA, USA.,Center for Lung Biology, University of Washington, Seattle, WA, USA
| | - Wayne Conrad Liles
- Center for Lung Biology, University of Washington, Seattle, WA, USA.,Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Sina A Gharib
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, University of Washington, Seattle, WA, USA.,Center for Lung Biology, University of Washington, Seattle, WA, USA
| | - William A Altemeier
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, University of Washington, Seattle, WA, USA.,Center for Lung Biology, University of Washington, Seattle, WA, USA
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Zhang C, Balbo B, Ma M, Zhao J, Tian X, Kluger Y, Somlo S. Cyclin-Dependent Kinase 1 Activity Is a Driver of Cyst Growth in Polycystic Kidney Disease. J Am Soc Nephrol 2021; 32:41-51. [PMID: 33046531 PMCID: PMC7894654 DOI: 10.1681/asn.2020040511] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [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: 05/04/2020] [Accepted: 09/03/2020] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND Mutations in PKD1 and PKD2, which encode the transmembrane proteins polycystin-1 and polycystin-2, respectively, cause autosomal dominant polycystic kidney disease (ADPKD). Polycystins are expressed in the primary cilium, and disrupting cilia structure significantly slows ADPKD progression following inactivation of polycystins. The cellular mechanisms of polycystin- and cilia-dependent cyst progression in ADPKD remain incompletely understood. METHODS Unbiased transcriptional profiling in an adult-onset Pkd2 mouse model before cysts formed revealed significant differentially expressed genes (DEGs) in Pkd2 single-knockout kidneys, which were used to identify candidate pathways dysregulated in kidneys destined to form cysts. In vivo studies validated the role of the candidate pathway in the progression of ADPKD. Wild-type and Pkd2/Ift88 double-knockout mice that are protected from cyst growth served as controls. RESULTS The RNASeq data identified cell proliferation as the most dysregulated pathway, with 15 of 241 DEGs related to cell cycle functions. Cdk1 appeared as a central component in this analysis. Cdk1 expression was similarly dysregulated in Pkd1 models of ADPKD, and conditional inactivation of Cdk1 with Pkd1 markedly improved the cystic phenotype and kidney function compared with inactivation of Pkd1 alone. The Pkd1/Cdk1 double knockout blocked cyst cell proliferation that otherwise accompanied Pkd1 inactivation alone. CONCLUSIONS Dysregulation of Cdk1 is an early driver of cyst cell proliferation in ADPKD due to Pkd1 inactivation. Selective targeting of cyst cell proliferation is an effective means of slowing ADPKD progression caused by inactivation of Pkd1.
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Affiliation(s)
- Chao Zhang
- Department of Internal Medicine, Yale University, New Haven, Connecticut
| | - Bruno Balbo
- Department of Internal Medicine, Yale University, New Haven, Connecticut
| | - Ming Ma
- Department of Internal Medicine, Yale University, New Haven, Connecticut
| | - Jun Zhao
- Department of Pathology, Yale University, New Haven, Connecticut,Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut
| | - Xin Tian
- Department of Internal Medicine, Yale University, New Haven, Connecticut
| | - Yuval Kluger
- Department of Pathology, Yale University, New Haven, Connecticut,Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut,Program in Applied Mathematics, Yale University, New Haven, Connecticut
| | - Stefan Somlo
- Department of Internal Medicine, Yale University, New Haven, Connecticut,Department of Genetics, Yale University, New Haven, Connecticut
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Ye H, Qiao L, Guo H, Guo L, Ren F, Bai J, Wang Y. Genome-Wide Identification of Wheat WRKY Gene Family Reveals That TaWRKY75-A Is Referred to Drought and Salt Resistances. Front Plant Sci 2021; 12:663118. [PMID: 34149760 PMCID: PMC8212938 DOI: 10.3389/fpls.2021.663118] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 04/12/2021] [Indexed: 05/14/2023]
Abstract
It is well known that WRKY transcription factors play essential roles in plants' response to diverse stress responses, especially to drought and salt stresses. However, a full comprehensive analysis of this family in wheat is still missing. Here we used in silico analysis and identified 124 WRKY genes, including 294 homeologous copies from a high-quality reference genome of wheat (Triticum aestivum). We also found that the TaWRKY gene family did not undergo gene duplication rather than gene loss during the evolutionary process. The TaWRKY family members displayed different expression profiles under several abiotic stresses, indicating their unique functions in the mediation of particular responses. Furthermore, TaWRKY75-A was highly induced after polyethylene glycol and salt treatments. The ectopic expression of TaWRKY75-A in Arabidopsis enhanced drought and salt tolerance. A comparative transcriptome analysis demonstrated that TaWRKY75-A integrated jasmonic acid biosynthetic pathway and other potential metabolic pathways to increase drought and salt resistances in transgenic Arabidopsis. Our study provides valuable insights into the WRKY family in wheat and will generate a useful genetic resource for improving wheat breeding.
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Affiliation(s)
- Hong Ye
- Division of Biological Science, Nara Institute of Science and Technology, Ikoma, Japan
| | - Linyi Qiao
- College of Agriculture, Shanxi Agricultural University, Taiyuan, Shanxi, China
| | - Haoyu Guo
- College of Life Science, Capital Normal University, Beijing, China
| | - Liping Guo
- College of Horticulture, Northwest A&F University, Yangling, China
| | - Fei Ren
- School of Agricultural Science and Engineering, Shaoguan University, Shaoguan, China
| | - Jianfang Bai
- Beijing Engineering Research Center for Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- *Correspondence: Jianfang Bai,
| | - Yukun Wang
- Division of Biological Science, Nara Institute of Science and Technology, Ikoma, Japan
- *Correspondence: Jianfang Bai,
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45
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Nicolas de Lamballerie C, Pizzorno A, Fouret J, Szpiro L, Padey B, Dubois J, Julien T, Traversier A, Dulière V, Brun P, Lina B, Rosa-Calatrava M, Terrier O. Transcriptional Profiling of Immune and Inflammatory Responses in the Context of SARS-CoV-2 Fungal Superinfection in a Human Airway Epithelial Model. Microorganisms 2020; 8:microorganisms8121974. [PMID: 33322535 PMCID: PMC7764715 DOI: 10.3390/microorganisms8121974] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [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: 11/03/2020] [Revised: 12/06/2020] [Accepted: 12/10/2020] [Indexed: 01/08/2023] Open
Abstract
An increasing amount of evidence indicates a relatively high prevalence of superinfections associated with coronavirus disease 2019 (COVID-19), including invasive aspergillosis, but the underlying mechanisms remain to be characterized. In the present study, to better understand the biological impact of superinfection, we determine and compare the host transcriptional response to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) versus Aspergillus superinfection, using a model of reconstituted human airway epithelium. Our analyses reveal that both simple infection and superinfection induce strong deregulation of core components of innate immune and inflammatory responses, with a stronger response to superinfection in the bronchial epithelial model compared to its nasal counterpart. Our results also highlight unique transcriptional footprints of SARS-CoV-2 Aspergillus superinfection, such as an imbalanced type I/type III IFN, and an induction of several monocyte and neutrophil associated chemokines, that could be useful for the understanding of Aspergillus-associated COVID-19 and also the management of severe forms of aspergillosis in this specific context.
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Affiliation(s)
- Claire Nicolas de Lamballerie
- CIRI, Centre International de Recherche en Infectiologie, (Team VirPath), Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France; (C.N.d.L.); (A.P.); (L.S.); (B.P.); (J.D.); (T.J.); (A.T.); (V.D.); (P.B.); (B.L.); (M.R.-C.)
| | - Andrés Pizzorno
- CIRI, Centre International de Recherche en Infectiologie, (Team VirPath), Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France; (C.N.d.L.); (A.P.); (L.S.); (B.P.); (J.D.); (T.J.); (A.T.); (V.D.); (P.B.); (B.L.); (M.R.-C.)
| | | | - Lea Szpiro
- CIRI, Centre International de Recherche en Infectiologie, (Team VirPath), Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France; (C.N.d.L.); (A.P.); (L.S.); (B.P.); (J.D.); (T.J.); (A.T.); (V.D.); (P.B.); (B.L.); (M.R.-C.)
| | - Blandine Padey
- CIRI, Centre International de Recherche en Infectiologie, (Team VirPath), Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France; (C.N.d.L.); (A.P.); (L.S.); (B.P.); (J.D.); (T.J.); (A.T.); (V.D.); (P.B.); (B.L.); (M.R.-C.)
- Signia Therapeutics SAS, F-69008 Lyon, France;
| | - Julia Dubois
- CIRI, Centre International de Recherche en Infectiologie, (Team VirPath), Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France; (C.N.d.L.); (A.P.); (L.S.); (B.P.); (J.D.); (T.J.); (A.T.); (V.D.); (P.B.); (B.L.); (M.R.-C.)
| | - Thomas Julien
- CIRI, Centre International de Recherche en Infectiologie, (Team VirPath), Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France; (C.N.d.L.); (A.P.); (L.S.); (B.P.); (J.D.); (T.J.); (A.T.); (V.D.); (P.B.); (B.L.); (M.R.-C.)
- VirNext, Faculté de Médecine RTH Laennec, Université Claude Bernard Lyon 1, Université de Lyon, F-69008 Lyon, France
| | - Aurélien Traversier
- CIRI, Centre International de Recherche en Infectiologie, (Team VirPath), Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France; (C.N.d.L.); (A.P.); (L.S.); (B.P.); (J.D.); (T.J.); (A.T.); (V.D.); (P.B.); (B.L.); (M.R.-C.)
| | - Victoria Dulière
- CIRI, Centre International de Recherche en Infectiologie, (Team VirPath), Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France; (C.N.d.L.); (A.P.); (L.S.); (B.P.); (J.D.); (T.J.); (A.T.); (V.D.); (P.B.); (B.L.); (M.R.-C.)
- VirNext, Faculté de Médecine RTH Laennec, Université Claude Bernard Lyon 1, Université de Lyon, F-69008 Lyon, France
| | - Pauline Brun
- CIRI, Centre International de Recherche en Infectiologie, (Team VirPath), Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France; (C.N.d.L.); (A.P.); (L.S.); (B.P.); (J.D.); (T.J.); (A.T.); (V.D.); (P.B.); (B.L.); (M.R.-C.)
- VirNext, Faculté de Médecine RTH Laennec, Université Claude Bernard Lyon 1, Université de Lyon, F-69008 Lyon, France
| | - Bruno Lina
- CIRI, Centre International de Recherche en Infectiologie, (Team VirPath), Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France; (C.N.d.L.); (A.P.); (L.S.); (B.P.); (J.D.); (T.J.); (A.T.); (V.D.); (P.B.); (B.L.); (M.R.-C.)
- Laboratoire de Virologie, Centre National de Référence des virus Influenza Sud, Institut des Agents Infectieux, Groupement Hospitalier Nord, Hospices Civils de Lyon, F-69004 Lyon, France
| | - Manuel Rosa-Calatrava
- CIRI, Centre International de Recherche en Infectiologie, (Team VirPath), Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France; (C.N.d.L.); (A.P.); (L.S.); (B.P.); (J.D.); (T.J.); (A.T.); (V.D.); (P.B.); (B.L.); (M.R.-C.)
- VirNext, Faculté de Médecine RTH Laennec, Université Claude Bernard Lyon 1, Université de Lyon, F-69008 Lyon, France
| | - Olivier Terrier
- CIRI, Centre International de Recherche en Infectiologie, (Team VirPath), Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France; (C.N.d.L.); (A.P.); (L.S.); (B.P.); (J.D.); (T.J.); (A.T.); (V.D.); (P.B.); (B.L.); (M.R.-C.)
- Correspondence:
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Boroughs AC, Larson RC, Marjanovic ND, Gosik K, Castano AP, Porter CBM, Lorrey SJ, Ashenberg O, Jerby L, Hofree M, Smith-Rosario G, Morris R, Gould J, Riley LS, Berger TR, Riesenfeld SJ, Rozenblatt-Rosen O, Choi BD, Regev A, Maus MV. A Distinct Transcriptional Program in Human CAR T Cells Bearing the 4-1BB Signaling Domain Revealed by scRNA-Seq. Mol Ther 2020; 28:2577-2592. [PMID: 32755564 PMCID: PMC7704462 DOI: 10.1016/j.ymthe.2020.07.023] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [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: 04/28/2020] [Revised: 06/26/2020] [Accepted: 07/21/2020] [Indexed: 01/22/2023] Open
Abstract
T cells engineered to express chimeric antigen receptors (CARs) targeting CD19 have produced impressive outcomes for the treatment of B cell malignancies, but different products vary in kinetics, persistence, and toxicity profiles based on the co-stimulatory domains included in the CAR. In this study, we performed transcriptional profiling of bulk CAR T cell populations and single cells to characterize the transcriptional states of human T cells transduced with CD3ζ, 4-1BB-CD3ζ (BBζ), or CD28-CD3ζ (28ζ) co-stimulatory domains at rest and after activation by triggering their CAR or their endogenous T cell receptor (TCR). We identified a transcriptional signature common across CARs with the CD3ζ signaling domain, as well as a distinct program associated with the 4-1BB co-stimulatory domain at rest and after activation. CAR T cells bearing BBζ had increased expression of human leukocyte antigen (HLA) class II genes, ENPP2, and interleukin (IL)-21 axis genes, and decreased PD1 compared to 28ζ CAR T cells. Similar to previous studies, we also found BBζ CAR CD8 T cells to be enriched in a central memory cell phenotype and fatty acid metabolism genes. Our data uncovered transcriptional signatures related to costimulatory domains and demonstrated that signaling domains included in CARs uniquely shape the transcriptional programs of T cells.
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Affiliation(s)
- Angela C Boroughs
- Cellular Immunotherapy Program and Cancer Center, Massachusetts General Hospital, Charlestown, MA 02129, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Rebecca C Larson
- Cellular Immunotherapy Program and Cancer Center, Massachusetts General Hospital, Charlestown, MA 02129, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Nemanja D Marjanovic
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
| | - Kirk Gosik
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
| | - Ana P Castano
- Cellular Immunotherapy Program and Cancer Center, Massachusetts General Hospital, Charlestown, MA 02129, USA
| | - Caroline B M Porter
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
| | - Selena J Lorrey
- Cellular Immunotherapy Program and Cancer Center, Massachusetts General Hospital, Charlestown, MA 02129, USA
| | - Orr Ashenberg
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
| | - Livnat Jerby
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
| | - Matan Hofree
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
| | | | - Robert Morris
- Howard Hughes Medical Institute, Koch Institute of Integrative Cancer Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02140, USA
| | - Joshua Gould
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
| | - Lauren S Riley
- Cellular Immunotherapy Program and Cancer Center, Massachusetts General Hospital, Charlestown, MA 02129, USA
| | - Trisha R Berger
- Cellular Immunotherapy Program and Cancer Center, Massachusetts General Hospital, Charlestown, MA 02129, USA
| | - Samantha J Riesenfeld
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
| | - Orit Rozenblatt-Rosen
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
| | - Bryan D Choi
- Cellular Immunotherapy Program and Cancer Center, Massachusetts General Hospital, Charlestown, MA 02129, USA
| | - Aviv Regev
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Koch Institute of Integrative Cancer Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02140, USA.
| | - Marcela V Maus
- Cellular Immunotherapy Program and Cancer Center, Massachusetts General Hospital, Charlestown, MA 02129, USA; Harvard Medical School, Boston, MA 02115, USA; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA; Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA.
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47
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Blackwell JM, Fakiola M, Singh OP. Genetics, Transcriptomics and Meta-Taxonomics in Visceral Leishmaniasis. Front Cell Infect Microbiol 2020; 10:590888. [PMID: 33324576 PMCID: PMC7723821 DOI: 10.3389/fcimb.2020.590888] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [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: 08/03/2020] [Accepted: 10/20/2020] [Indexed: 12/26/2022] Open
Abstract
Visceral leishmaniasis (VL) caused by parasites of the Leishmania donovani complex can be fatal in susceptible individuals. Understanding the interactions between host and pathogen is one way to obtain leads to develop better drugs and for vaccine development. In recent years multiple omics-based approaches have assisted researchers to gain a more global picture of this interaction in leishmaniasis. Here we review results from studies using three omics-based approaches to study VL caused by L. donovani in India: (i) chip-based analysis of single nucleotide variants in the first genome-wide association study of host genetic risk factors for VL, followed by analysis of epitope binding to HLA DRB1 risk versus protective alleles; (ii) transcriptional profiling demonstrating pathways important in Amphotericin B treated compared to active VL cases, including demonstration that anti-interleukin-10 unleashes a storm of chemokines and cytokines in whole blood responses to soluble leishmania antigen in active cases; and (iii) a meta-taxonomic approach based on sequencing amplicons derived from regions of 16S ribosomal RNA (16S rRNA) and 18S rRNA genes that allowed us to determine composition of both prokaryotic and eukaryotic gut microflora in VL cases compared to endemic controls. Overall, our omics-based approaches demonstrate that global analyses of genetic risk factors, host responses to infection, and the interaction between host, parasite and the microbiome can point to the most critical factors that determine the outcome of infection.
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Affiliation(s)
- Jenefer M. Blackwell
- Telethon Kids Institute, The University of Western Australia, Nedlands, WA, Australia
| | | | - Om Prakash Singh
- Department of Medicine, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
- Department of Biochemistry, Institute of Science, Banaras Hindu University, Varanasi, India
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48
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Louis K, Macedo C, Bailly E, Lau L, Ramaswami B, Marrari M, Landsittel D, Chang A, Chandran U, Fadakar P, Yamada M, Chalasani G, Randhawa P, Zeevi A, Singh H, Lefaucheur C, Metes D. Coordinated Circulating T Follicular Helper and Activated B Cell Responses Underlie the Onset of Antibody-Mediated Rejection in Kidney Transplantation. J Am Soc Nephrol 2020; 31:2457-2474. [PMID: 32723838 DOI: 10.1681/asn.2020030320] [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] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 05/31/2020] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Although antibody-mediated rejection (ABMR) has been long recognized as a leading cause of allograft failure after kidney transplantation, the cellular and molecular processes underlying the induction of deleterious donor-specific antibody (DSA) responses remain poorly understood. METHODS Using high-dimensional flow cytometry, in vitro assays, and RNA sequencing, we concomitantly investigated the role of T follicular helper (TFH) cells and B cells during ABMR in 105 kidney transplant recipients. RESULTS There were 54 patients without DSAs; of those with DSAs, ABMR emerged in 20 patients, but not in 31 patients. We identified proliferating populations of circulating TFH cells and activated B cells emerging in blood of patients undergoing ABMR. Although these circulating TFH cells comprised heterogeneous phenotypes, they were dominated by activated (ICOS+PD-1+) and early memory precursor (CCR7+CD127+) subsets, and were enriched for the transcription factors IRF4 and c-Maf. These circulating TFH cells produced large amounts of IL-21 upon stimulation with donor antigen and induced B cells to differentiate into antibody-secreting cells that produced DSAs. Combined analysis of the matched circulating TFH cell and activated B cell RNA-sequencing profiles identified highly coordinated transcriptional programs in circulating TFH cells and B cells among patients with ABMR, which markedly differed from those of patients who did not develop DSAs or ABMR. The timing of expansion of the distinctive circulating TFH cells and activated B cells paralleled emergence of DSAs in blood, and their magnitude was predictive of IgG3 DSA generation, more severe allograft injury, and higher rate of allograft loss. CONCLUSIONS Patients undergoing ABMR may benefit from monitoring and therapeutic targeting of TFH cell-B cell interactions.
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Affiliation(s)
- Kevin Louis
- Department of Surgery, Thomas E. Starzl Transplantation Institute, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania.,Human Immunology and Immunopathology, Institut National de la Santé et de la Recherche Médicale, Unité Mixte de Recherche 976, Université de Paris, Paris, France
| | - Camila Macedo
- Department of Surgery, Thomas E. Starzl Transplantation Institute, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - Elodie Bailly
- Department of Surgery, Thomas E. Starzl Transplantation Institute, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania.,Human Immunology and Immunopathology, Institut National de la Santé et de la Recherche Médicale, Unité Mixte de Recherche 976, Université de Paris, Paris, France
| | - Louis Lau
- Center for Systems Immunology, Department of Immunology, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Bala Ramaswami
- Department of Surgery, Thomas E. Starzl Transplantation Institute, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - Marilyn Marrari
- Department of Surgery, Thomas E. Starzl Transplantation Institute, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania.,Department of Pathology, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Douglas Landsittel
- Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Alexander Chang
- Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Uma Chandran
- Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Paul Fadakar
- Department of Surgery, Thomas E. Starzl Transplantation Institute, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - Masaki Yamada
- Department of Surgery, Thomas E. Starzl Transplantation Institute, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - Geetha Chalasani
- Department of Surgery, Thomas E. Starzl Transplantation Institute, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania.,Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania.,Department of Immunology, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Parmjeet Randhawa
- Department of Surgery, Thomas E. Starzl Transplantation Institute, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania.,Department of Pathology, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Adriana Zeevi
- Department of Surgery, Thomas E. Starzl Transplantation Institute, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania.,Department of Pathology, University of Pittsburgh, Pittsburgh, Pennsylvania.,Department of Immunology, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Harinder Singh
- Center for Systems Immunology, Department of Immunology, University of Pittsburgh, Pittsburgh, Pennsylvania.,Department of Immunology, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Carmen Lefaucheur
- Paris Translational Research Center for Organ Transplantation, Inserm UMR S970, Université de Paris, Paris, France
| | - Diana Metes
- Department of Surgery, Thomas E. Starzl Transplantation Institute, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania .,Department of Immunology, University of Pittsburgh, Pittsburgh, Pennsylvania
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49
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Malone AF, Wu H, Fronick C, Fulton R, Gaut JP, Humphreys BD. Harnessing Expressed Single Nucleotide Variation and Single Cell RNA Sequencing To Define Immune Cell Chimerism in the Rejecting Kidney Transplant. J Am Soc Nephrol 2020; 31:1977-1986. [PMID: 32669324 DOI: 10.1681/asn.2020030326] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [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: 03/19/2020] [Accepted: 06/10/2020] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND In solid organ transplantation, donor-derived immune cells are assumed to decline with time after surgery. Whether donor leukocytes persist within kidney transplants or play any role in rejection is unknown, however, in part because of limited techniques for distinguishing recipient from donor cells. METHODS Whole-exome sequencing of donor and recipient DNA and single-cell RNA sequencing (scRNA-seq) of five human kidney transplant biopsy cores distinguished immune cell contributions from both participants. DNA-sequence comparisons used single nucleotide variants (SNVs) identified in the exome sequences across all samples. RESULTS Analysis of expressed SNVs in the scRNA-seq data set distinguished recipient versus donor origin for all 81,139 cells examined. The leukocyte donor/recipient ratio varied with rejection status for macrophages and with time post-transplant for lymphocytes. Recipient macrophages displayed inflammatory activation whereas donor macrophages demonstrated antigen presentation and complement signaling. Recipient-origin T cells expressed cytotoxic and proinflammatory genes consistent with an effector cell phenotype, whereas donor-origin T cells appeared quiescent, expressing oxidative phosphorylation genes. Finally, both donor and recipient T cell clones within the rejecting kidney suggested lymphoid aggregation. The results indicate that donor-origin macrophages and T cells have distinct transcriptional profiles compared with their recipient counterparts, and that donor macrophages can persist for years post-transplantation. CONCLUSIONS Analysis of single nucleotide variants and their expression in single cells provides a powerful novel approach to accurately define leukocyte chimerism in a complex organ such as a transplanted kidney, coupled with the ability to examine transcriptional profiles at single-cell resolution.
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Affiliation(s)
- Andrew F Malone
- Division of Nephrology, Department of Medicine, Washington University School of Medicine in St. Louis, St. Louis, Missouri
| | - Haojia Wu
- Division of Nephrology, Department of Medicine, Washington University School of Medicine in St. Louis, St. Louis, Missouri
| | - Catrina Fronick
- McDonnell Genome Institute, Washington University School of Medicine in St. Louis, St. Louis, Missouri
| | - Robert Fulton
- McDonnell Genome Institute, Washington University School of Medicine in St. Louis, St. Louis, Missouri
| | - Joseph P Gaut
- Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, Missouri
| | - Benjamin D Humphreys
- Division of Nephrology, Department of Medicine, Washington University School of Medicine in St. Louis, St. Louis, Missouri .,Department of Developmental Biology, Washington University School of Medicine in St. Louis, St. Louis, Missouri
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50
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Greene CL, Jaatinen KJ, Wang H, Koyano TK, Bilbao MS, Woo YJ. Transcriptional Profiling of Normal, Stenotic, and Regurgitant Human Aortic Valves. Genes (Basel) 2020; 11:genes11070789. [PMID: 32674273 PMCID: PMC7397246 DOI: 10.3390/genes11070789] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [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: 05/30/2020] [Revised: 07/01/2020] [Accepted: 07/08/2020] [Indexed: 12/26/2022] Open
Abstract
The genetic mechanisms underlying aortic stenosis (AS) and aortic insufficiency (AI) disease progression remain unclear. We hypothesized that normal aortic valves and those with AS or AI all exhibit unique transcriptional profiles. Normal control (NC) aortic valves were collected from non-matched donor hearts that were otherwise acceptable for transplantation (n = 5). Valves with AS or AI (n = 5, each) were collected from patients undergoing surgical aortic valve replacement. High-throughput sequencing of total RNA revealed 6438 differentially expressed genes (DEGs) for AS vs. NC, 4994 DEGs for AI vs. NC, and 2771 DEGs for AS vs. AI. Among 21 DEGs of interest, APCDD1L, CDH6, COL10A1, HBB, IBSP, KRT14, PLEKHS1, PRSS35, and TDO2 were upregulated in both AS and AI compared to NC, whereas ALDH1L1, EPHB1, GPX3, HIF3A, and KCNT1 were downregulated in both AS and AI (p < 0.05). COL11A1, H19, HIF1A, KCNJ6, PRND, and SPP1 were upregulated only in AS, and NPY was downregulated only in AS (p < 0.05). The functional network for AS clustered around ion regulation, immune regulation, and lipid homeostasis, and that for AI clustered around ERK1/2 regulation. Overall, we report transcriptional profiling data for normal human aortic valves from non-matched donor hearts that were acceptable for transplantation and demonstrated that valves with AS and AI possess unique genetic signatures. These data create a roadmap for the development of novel therapeutics to treat AS and AI.
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Affiliation(s)
- Christina L. Greene
- Department of Cardiothoracic Surgery, Stanford University, Stanford, CA 94305, USA; (C.L.G.); (K.J.J.); (H.W.); (T.K.K.); (M.S.B.)
| | - Kevin J. Jaatinen
- Department of Cardiothoracic Surgery, Stanford University, Stanford, CA 94305, USA; (C.L.G.); (K.J.J.); (H.W.); (T.K.K.); (M.S.B.)
| | - Hanjay Wang
- Department of Cardiothoracic Surgery, Stanford University, Stanford, CA 94305, USA; (C.L.G.); (K.J.J.); (H.W.); (T.K.K.); (M.S.B.)
- Stanford Cardiovascular Institute, Stanford University, Stanford, CA 94305, USA
| | - Tiffany K. Koyano
- Department of Cardiothoracic Surgery, Stanford University, Stanford, CA 94305, USA; (C.L.G.); (K.J.J.); (H.W.); (T.K.K.); (M.S.B.)
| | - Mary S. Bilbao
- Department of Cardiothoracic Surgery, Stanford University, Stanford, CA 94305, USA; (C.L.G.); (K.J.J.); (H.W.); (T.K.K.); (M.S.B.)
| | - Y. Joseph Woo
- Department of Cardiothoracic Surgery, Stanford University, Stanford, CA 94305, USA; (C.L.G.); (K.J.J.); (H.W.); (T.K.K.); (M.S.B.)
- Stanford Cardiovascular Institute, Stanford University, Stanford, CA 94305, USA
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
- Correspondence: ; Tel.: +1-650-725-3828
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