1
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Watson KJ, Bromley RE, Sparklin BC, Gasser MT, Bhattacharya T, Lebov JF, Tyson T, Dai N, Teigen LE, Graf KT, Foster JM, Michalski M, Bruno VM, Lindsey AR, Corrêa IR, Hardy RW, Newton IL, Dunning Hotopp JC. Common analysis of direct RNA sequencinG CUrrently leads to misidentification of m 5C at GCU motifs. Life Sci Alliance 2024; 7:e202302201. [PMID: 38030223 PMCID: PMC10687253 DOI: 10.26508/lsa.202302201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 11/16/2023] [Accepted: 11/20/2023] [Indexed: 12/01/2023] Open
Abstract
RNA modifications, such as methylation, can be detected with Oxford Nanopore Technologies direct RNA sequencing. One commonly used tool for detecting 5-methylcytosine (m5C) modifications is Tombo, which uses an "Alternative Model" to detect putative modifications from a single sample. We examined direct RNA sequencing data from diverse taxa including viruses, bacteria, fungi, and animals. The algorithm consistently identified a m5C at the central position of a GCU motif. However, it also identified a m5C in the same motif in fully unmodified in vitro transcribed RNA, suggesting that this is a frequent false prediction. In the absence of further validation, several published predictions of m5C in a GCU context should be reconsidered, including those from human coronavirus and human cerebral organoid samples.
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Affiliation(s)
- Kaylee J Watson
- https://ror.org/04rq5mt64 Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Robin E Bromley
- https://ror.org/04rq5mt64 Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Benjamin C Sparklin
- https://ror.org/04rq5mt64 Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Mark T Gasser
- https://ror.org/04rq5mt64 Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Tamanash Bhattacharya
- https://ror.org/01kg8sb98 Department of Biology, Indiana University, Bloomington, IN, USA
| | - Jarrett F Lebov
- https://ror.org/04rq5mt64 Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Tyonna Tyson
- https://ror.org/04rq5mt64 Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Nan Dai
- https://ror.org/04ywg3445 New England Biolabs, Ipswich, MA, USA
| | - Laura E Teigen
- https://ror.org/05w22af52 Department of Biology, University of Wisconsin Oshkosh, Oshkosh, WI, USA
| | - Karen T Graf
- https://ror.org/04rq5mt64 Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Jeremy M Foster
- https://ror.org/04ywg3445 New England Biolabs, Ipswich, MA, USA
| | - Michelle Michalski
- https://ror.org/05w22af52 Department of Biology, University of Wisconsin Oshkosh, Oshkosh, WI, USA
| | - Vincent M Bruno
- https://ror.org/04rq5mt64 Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
- https://ror.org/04rq5mt64 Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Amelia Ri Lindsey
- https://ror.org/01kg8sb98 Department of Biology, Indiana University, Bloomington, IN, USA
| | - Ivan R Corrêa
- https://ror.org/04ywg3445 New England Biolabs, Ipswich, MA, USA
| | - Richard W Hardy
- https://ror.org/01kg8sb98 Department of Biology, Indiana University, Bloomington, IN, USA
| | - Irene Lg Newton
- https://ror.org/01kg8sb98 Department of Biology, Indiana University, Bloomington, IN, USA
| | - Julie C Dunning Hotopp
- https://ror.org/04rq5mt64 Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
- https://ror.org/04rq5mt64 Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA
- https://ror.org/04rq5mt64 Greenebaum Cancer Center, University of Maryland School of Medicine, Baltimore, MD, USA
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2
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Watson KJ, Bromley RE, Sparklin BC, Gasser MT, Bhattacharya T, Lebov JF, Tyson T, Teigen LE, Graf KT, Michalski M, Bruno VM, Lindsey ARI, Hardy RW, Newton ILG, Hotopp JCD. Common Analysis of Direct RNA SequencinG CUrrently Leads to Misidentification of 5-Methylcytosine Modifications at GCU Motifs. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.03.539298. [PMID: 37205495 PMCID: PMC10187288 DOI: 10.1101/2023.05.03.539298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
RNA modifications, such as méthylation, can be detected with Oxford Nanopore Technologies direct RNA sequencing. One commonly used tool for detecting 5-methylcytosine (m5C) modifications is Tombo, which uses an "Alternative Model" to detect putative modifications from a single sample. We examined direct RNA sequencing data from diverse taxa including virus, bacteria, fungi, and animals. The algorithm consistently identified a 5-methylcytosine at the central position of a GCU motif. However, it also identified a 5-methylcytosine in the same motif in fully unmodified in vitro transcribed RNA, suggesting that this a frequent false prediction. In the absence of further validation, several published predictions of 5-methylcytosine in human coronavirus and human cerebral organoid RNA in a GCU context should be reconsidered.
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Affiliation(s)
- Kaylee J. Watson
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Robin E. Bromley
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Benjamin C. Sparklin
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Mark T. Gasser
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | | | - Jarrett F. Lebov
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Tyonna Tyson
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Laura E. Teigen
- Department of Biology, University of Wisconsin Oshkosh, Oshkosh, WI, USA
| | - Karen T. Graf
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Michelle Michalski
- Department of Biology, University of Wisconsin Oshkosh, Oshkosh, WI, USA
| | - Vincent M. Bruno
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
- Department of Microbiology & Immunology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | | | | | | | - Julie C. Dunning Hotopp
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
- Department of Microbiology & Immunology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
- Greenebaum Cancer Center, University of Maryland School of Medicine, Baltimore, MD 21201, USA
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3
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Xu D, Tang L, Kapranov P. Complexities of mammalian transcriptome revealed by targeted RNA enrichment techniques. Trends Genet 2023; 39:320-333. [PMID: 36681580 DOI: 10.1016/j.tig.2022.12.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 12/27/2022] [Accepted: 12/30/2022] [Indexed: 01/21/2023]
Abstract
Studies using highly sensitive targeted RNA enrichment methods have shown that a large portion of the human transcriptome remains to be discovered and that most of the genome is transcribed in a complex, interleaved fashion characterized by a complex web of transcripts emanating from protein coding and noncoding loci. These results resonate with those from single-cell transcriptome profiling endeavors that reveal the existence of multiple novel, cell type-specific transcripts and clearly demonstrate that our understanding of the complexities of the human transcriptome is far from being complete. Here, we review the current status of the targeted RNA enrichment techniques, their application to the discovery of novel cell type-specific transcripts, and their impact on our understanding of the human genome and transcriptome.
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Affiliation(s)
- Dongyang Xu
- Institute of Genomics, School of Medicine, Huaqiao University, 668 Jimei Road, Xiamen 361021, China
| | - Lu Tang
- Institute of Genomics, School of Medicine, Huaqiao University, 668 Jimei Road, Xiamen 361021, China
| | - Philipp Kapranov
- Institute of Genomics, School of Medicine, Huaqiao University, 668 Jimei Road, Xiamen 361021, China.
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4
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Hovhannisyan H, Rodríguez A, Saus E, Vaneechoutte M, Gabaldón T. Multiplexed target enrichment of coding and non-coding transcriptomes enables studying Candida spp. infections from human derived samples. Front Cell Infect Microbiol 2023; 13:1093178. [PMID: 36761895 PMCID: PMC9902369 DOI: 10.3389/fcimb.2023.1093178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 01/03/2023] [Indexed: 01/26/2023] Open
Abstract
The study of transcriptomic interactions between host and pathogens in in vivo conditions is challenged by the low relative amounts of the pathogen RNA. Yeast opportunistic pathogens of the genus Candida can cause life-threatening systemic infections in immunocompromised patients, and are of growing medical concern. Four phylogenetically diverse species account for over 90% of Candida infections, and their specific interactions with various human tissues are still poorly understood. To enable in vivo transcriptomic analysis in these species, we designed and validated pan-Candida target capture probes to enrich protein-coding and non-coding transcriptomes. The probe-based enrichment approach outperformed enrichment based on differential lysis of host cells, and showed similar enrichment performance as an existing capture design, yet achieving better fidelity of expression levels, enabling species multiplexing and capturing of lncRNAs. In addition, we show that our probe-based enrichment strategy allows robust genotype-based identification of the infecting strain present in the sample.
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Affiliation(s)
- Hrant Hovhannisyan
- Life Sciences Department, Barcelona Supercomputing Center (BSC), Barcelona, Spain,Mechanisms of Disease Department, Institute for Research in Biomedicine (IRB), Barcelona, Spain
| | - Antonio Rodríguez
- Laboratory Bacteriology Research, Department of Diagnostic Sciences, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Ester Saus
- Life Sciences Department, Barcelona Supercomputing Center (BSC), Barcelona, Spain,Mechanisms of Disease Department, Institute for Research in Biomedicine (IRB), Barcelona, Spain
| | - Mario Vaneechoutte
- Laboratory Bacteriology Research, Department of Diagnostic Sciences, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Toni Gabaldón
- Life Sciences Department, Barcelona Supercomputing Center (BSC), Barcelona, Spain,Mechanisms of Disease Department, Institute for Research in Biomedicine (IRB), Barcelona, Spain,Department of Biomedicine and Life Sciences, Universitat Pompeu Fabra (UPF), Barcelona, Spain,Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys 23, Barcelona, Spain,*Correspondence: Toni Gabaldón,
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5
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Schrevens S, Durandau E, Tran VDT, Sanglard D. Using in vivo transcriptomics and RNA enrichment to identify genes involved in virulence of Candida glabrata. Virulence 2022; 13:1285-1303. [PMID: 35795910 PMCID: PMC9348041 DOI: 10.1080/21505594.2022.2095716] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Candida species are the most commonly isolated opportunistic fungal pathogens in humans. Candida albicans causes most of the diagnosed infections, closely followed by Candida glabrata. C. albicans is well studied, and many genes have been shown to be important for infection and colonization of the host. It is however less clear how C. glabrata infects the host. With the help of fungal RNA enrichment, we here investigated for the first time the transcriptomic profile of C. glabrata during urinary tract infection (UTI) in mice. In the UTI model, bladders and kidneys are major target organs and therefore fungal transcriptomes were addressed in these organs. Our results showed that, next to adhesins and proteases, nitrogen metabolism and regulation play a vital role during C. glabrata UTI. Genes involved in nitrogen metabolism were upregulated and among them we show that DUR1,2 (urea amidolyase) and GAP1 (amino acid permease) were important for virulence. Furthermore, we confirmed the importance of the glyoxylate cycle in the host and identified MLS1 (malate synthase) as an important gene necessary for C. glabrata virulence. In conclusion, our study shows with the support of in vivo transcriptomics how C. glabrata adapts to host conditions.
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Affiliation(s)
- Sanne Schrevens
- Institute of Microbiology, University of Lausanne and University Hospital, CH-1011 Lausanne, Switzerland
| | - Eric Durandau
- Institute of Microbiology, University of Lausanne and University Hospital, CH-1011 Lausanne, Switzerland
| | - Van Du T Tran
- Vital-IT Group, SIB Swiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland
| | - Dominique Sanglard
- Institute of Microbiology, University of Lausanne and University Hospital, CH-1011 Lausanne, Switzerland
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6
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Chung M, Bruno VM, Rasko DA, Cuomo CA, Muñoz JF, Livny J, Shetty AC, Mahurkar A, Dunning Hotopp JC. Best practices on the differential expression analysis of multi-species RNA-seq. Genome Biol 2021; 22:121. [PMID: 33926528 PMCID: PMC8082843 DOI: 10.1186/s13059-021-02337-8] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 04/01/2021] [Indexed: 02/07/2023] Open
Abstract
Advances in transcriptome sequencing allow for simultaneous interrogation of differentially expressed genes from multiple species originating from a single RNA sample, termed dual or multi-species transcriptomics. Compared to single-species differential expression analysis, the design of multi-species differential expression experiments must account for the relative abundances of each organism of interest within the sample, often requiring enrichment methods and yielding differences in total read counts across samples. The analysis of multi-species transcriptomics datasets requires modifications to the alignment, quantification, and downstream analysis steps compared to the single-species analysis pipelines. We describe best practices for multi-species transcriptomics and differential gene expression.
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Affiliation(s)
- Matthew Chung
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.,Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Vincent M Bruno
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.,Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - David A Rasko
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.,Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Christina A Cuomo
- Infectious Disease and Microbiome Program, Broad Institute, Cambridge, MA, 02142, USA
| | - José F Muñoz
- Infectious Disease and Microbiome Program, Broad Institute, Cambridge, MA, 02142, USA
| | - Jonathan Livny
- Infectious Disease and Microbiome Program, Broad Institute, Cambridge, MA, 02142, USA
| | - Amol C Shetty
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Anup Mahurkar
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Julie C Dunning Hotopp
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201, USA. .,Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA. .,Greenebaum Cancer Center, University of Maryland, Baltimore, MD, 21201, USA.
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7
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Long-read RNA sequencing of human and animal filarial parasites improves gene models and discovers operons. PLoS Negl Trop Dis 2020; 14:e0008869. [PMID: 33196647 PMCID: PMC7704054 DOI: 10.1371/journal.pntd.0008869] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 11/30/2020] [Accepted: 10/09/2020] [Indexed: 01/01/2023] Open
Abstract
Filarial parasitic nematodes (Filarioidea) cause substantial disease burden to humans and animals around the world. Recently there has been a coordinated global effort to generate, annotate, and curate genomic data from nematode species of medical and veterinary importance. This has resulted in two chromosome-level assemblies (Brugia malayi and Onchocerca volvulus) and 11 additional draft genomes from Filarioidea. These reference assemblies facilitate comparative genomics to explore basic helminth biology and prioritize new drug and vaccine targets. While the continual improvement of genome contiguity and completeness advances these goals, experimental functional annotation of genes is often hindered by poor gene models. Short-read RNA sequencing data and expressed sequence tags, in cooperation with ab initio prediction algorithms, are employed for gene prediction, but these can result in missing clade-specific genes, fragmented models, imperfect mapping of gene ends, and lack of isoform resolution. Long-read RNA sequencing can overcome these drawbacks and greatly improve gene model quality. Here, we present Iso-Seq data for B. malayi and Dirofilaria immitis, etiological agents of lymphatic filariasis and canine heartworm disease, respectively. These data cover approximately half of the known coding genomes and substantially improve gene models by extending untranslated regions, cataloging novel splice junctions from novel isoforms, and correcting mispredicted junctions. Furthermore, we validated computationally predicted operons, manually curated new operons, and merged fragmented gene models. We carried out analyses of poly(A) tails in both species, leading to the identification of non-canonical poly(A) signals. Finally, we prioritized and assessed known and putative anthelmintic targets, correcting or validating gene models for molecular cloning and target-based anthelmintic screening efforts. Overall, these data significantly improve the catalog of gene models for two important parasites, and they demonstrate how long-read RNA sequencing should be prioritized for ongoing improvement of parasitic nematode genome assemblies. Filarial parasitic nematodes are vector-borne parasites that infect humans and animals. Brugia malayi and Dirofilaria immitis are transmitted by mosquitoes and cause human lymphatic filariasis and canine heartworm disease, respectively. Recent years have seen a dramatic increase in genomic and transcriptomic data sets and the concomitant increase in innovative strategies for drug target identification, validation, and screening. However, while the completeness of genome assemblies of filarial parasitic nematodes has seen steady improvements, the reliability of gene models has not kept pace, hindering cloning efforts. Long-read RNA sequencing technologies are uniquely able to improve gene models, but have not been widely used for the causative agents of neglected tropical diseases. Here, we report the improvement of gene models in both B. malayi and D. immitis by long-read RNA sequencing. We identified novel operons, deprecated false positive operons, identified dozens of novel genes, and described the parameters of polyadenylation. We also focused on putative anthelmintic targets, identifying novel isoforms and correcting gene models. These data substantially increase the trustworthiness of gene models in these two species and demonstrate how long-read sequencing approaches should be prioritized in the continued improvement of genome assemblies and their gene annotations.
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8
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A Meta-Analysis of Wolbachia Transcriptomics Reveals a Stage-Specific Wolbachia Transcriptional Response Shared Across Different Hosts. G3-GENES GENOMES GENETICS 2020; 10:3243-3260. [PMID: 32718933 PMCID: PMC7467002 DOI: 10.1534/g3.120.401534] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Wolbachia is a genus containing obligate, intracellular endosymbionts with arthropod and nematode hosts. Numerous studies have identified differentially expressed transcripts in Wolbachia endosymbionts that potentially inform the biological interplay between these endosymbionts and their hosts, albeit with discordant results. Here, we re-analyze previously published Wolbachia RNA-Seq transcriptomics data sets using a single workflow consisting of the most up-to-date algorithms and techniques, with the aim of identifying trends or patterns in the pan-Wolbachia transcriptional response. We find that data from one of the early studies in filarial nematodes did not allow for robust conclusions about Wolbachia differential expression with these methods, suggesting the original interpretations should be reconsidered. Across datasets analyzed with this unified workflow, there is a general lack of global gene regulation with the exception of a weak transcriptional response resulting in the upregulation of ribosomal proteins in early larval stages. This weak response is observed across diverse Wolbachia strains from both nematode and insect hosts suggesting a potential pan-Wolbachia transcriptional response during host development that diverged more than 700 million years ago.
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9
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Soare AY, Watkins TN, Bruno VM. Understanding Mucormycoses in the Age of "omics". Front Genet 2020; 11:699. [PMID: 32695145 PMCID: PMC7339291 DOI: 10.3389/fgene.2020.00699] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 06/09/2020] [Indexed: 12/14/2022] Open
Abstract
Mucormycoses are deadly invasive infections caused by several fungal species belonging to the subphylum Mucoromycotina, order Mucorales. Hallmarks of disease progression include angioinvasion and tissue necrosis that aid in fungal dissemination through the blood stream, causing deeper infections and resulting in poor penetration of antifungal agents to the site of infection. In the absence of surgical removal of the infected focus, antifungal therapy alone is rarely curative. Even when surgical debridement is combined with high-dose antifungal therapy, the mortality associated with mucormycoses is >50%. The unacceptably high mortality rate, limited options for therapy and the extreme morbidity of highly disfiguring surgical therapy provide a clear mandate to understand the molecular mechanisms that govern pathogenesis with the hopes of developing alternative strategies to treat and prevent mucormycoses. In the absence of robust forward and reverse genetic systems available for this taxonomic group of fungi, unbiased next generation sequence (NGS)-based approaches have provided much needed insights into our understanding of many aspects of Mucormycoses, including genome structure, drug resistance, diagnostic development, and fungus-host interactions. Here, we will discuss the specific contributions that NGS-based approaches have made to the field and discuss open questions that can be addressed using similar approaches.
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Affiliation(s)
- Alexandra Y Soare
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, United States
- Institute of Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Tonya N Watkins
- Institute of Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Vincent M Bruno
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, United States
- Institute of Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, United States
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10
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Drug Repurposing of Bromodomain Inhibitors as Potential Novel Therapeutic Leads for Lymphatic Filariasis Guided by Multispecies Transcriptomics. mSystems 2019; 4:4/6/e00596-19. [PMID: 31796568 PMCID: PMC6890932 DOI: 10.1128/msystems.00596-19] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The current treatment regimen for lymphatic filariasis is mostly microfilaricidal. In an effort to identify new drug candidates for lymphatic filariasis, we conducted a three-way transcriptomics/systems biology study of one of the causative agents of lymphatic filariasis, Brugia malayi, its Wolbachia endosymbiont wBm, and its vector host Aedes aegypti at 16 distinct B. malayi life stages. B. malayi upregulates the expression of bromodomain-containing proteins in the adult female, embryo, and microfilaria stages. In vitro, we find that the existing cancer therapeutic JQ1(+), which is a bromodomain and extraterminal protein inhibitor, has adulticidal activity in B. malayi. To better understand the transcriptomic interplay of organisms associated with lymphatic filariasis, we conducted multispecies transcriptome sequencing (RNA-Seq) on the filarial nematode Brugia malayi, its Wolbachia endosymbiont wBm, and its laboratory vector Aedes aegypti across the entire B. malayi life cycle. In wBm, transcription of the noncoding 6S RNA suggests that it may be a regulator of bacterial cell growth, as its transcript levels correlate with bacterial replication rates. For A. aegypti, the transcriptional response reflects the stress that B. malayi infection exerts on the mosquito with indicators of increased energy demand. In B. malayi, expression modules associated with adult female samples consistently contained an overrepresentation of genes involved in chromatin remodeling, such as the bromodomain-containing proteins. All bromodomain-containing proteins encoded by B. malayi were observed to be upregulated in the adult female, embryo, and microfilaria life stages, including 2 members of the bromodomain and extraterminal (BET) protein family. The BET inhibitor JQ1(+), originally developed as a cancer therapeutic, caused lethality of adult worms in vitro, suggesting that it may be a potential therapeutic that can be repurposed for treating lymphatic filariasis. IMPORTANCE The current treatment regimen for lymphatic filariasis is mostly microfilaricidal. In an effort to identify new drug candidates for lymphatic filariasis, we conducted a three-way transcriptomics/systems biology study of one of the causative agents of lymphatic filariasis, Brugia malayi, its Wolbachia endosymbiont wBm, and its vector host Aedes aegypti at 16 distinct B. malayi life stages. B. malayi upregulates the expression of bromodomain-containing proteins in the adult female, embryo, and microfilaria stages. In vitro, we find that the existing cancer therapeutic JQ1(+), which is a bromodomain and extraterminal protein inhibitor, has adulticidal activity in B. malayi.
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11
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Rodríguez A, Guillemyn B, Coucke P, Vaneechoutte M. Nucleic acids enrichment of fungal pathogens to study host-pathogen interactions. Sci Rep 2019; 9:18037. [PMID: 31792282 PMCID: PMC6889467 DOI: 10.1038/s41598-019-54608-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 11/15/2019] [Indexed: 12/11/2022] Open
Abstract
Fungal infections, ranging from superficial to life-threatening infections, represent a major public health problem that affects 25% of the worldwide population. In this context, the study of host-pathogen interactions within the host is crucial to advance antifungal therapy. However, since fungal cells are usually outnumbered by host cells, the fungal transcriptome frequently remains uncovered. We compared three different methods to selectively lyse human cells from in vitro mixes, composed of Candida cells and peripheral blood mononuclear cells. In order to prevent transcriptional modification, the mixes were stored in RNAlater. We evaluated the enrichment of fungal cells through cell counting using microscopy and aimed to further enrich fungal nucleic acids by centrifugation and by reducing contaminant nucleic acids from the host. We verified the enrichment of fungal DNA and RNA through qPCR and RT-qPCR respectively and confirmed that the resulting RNA has high integrity scores, suitable for downstream applications. The enrichment method provided here, i.e., lysis with Buffer RLT followed by centrifugation, may contribute to increase the proportion of nucleic acids from fungi in clinical samples, thus promoting more comprehensive analysis of fungal transcriptional profiles. Although we focused on C. albicans, the enrichment may be applicable to other fungal pathogens.
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Affiliation(s)
- Antonio Rodríguez
- Laboratory Bacteriology Research, Department of Diagnostic Sciences, Faculty of Medicine and Health Sciences, Ghent University, Ghent, 9000, Belgium.
| | - Brecht Guillemyn
- Center for Medical Genetics Ghent, Ghent University Hospital, Department of Biomolecular Medicine, Ghent, 9000, Belgium
| | - Paul Coucke
- Center for Medical Genetics Ghent, Ghent University Hospital, Department of Biomolecular Medicine, Ghent, 9000, Belgium
| | - Mario Vaneechoutte
- Laboratory Bacteriology Research, Department of Diagnostic Sciences, Faculty of Medicine and Health Sciences, Ghent University, Ghent, 9000, Belgium
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12
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O'Connell CM, Brochu H, Girardi J, Harrell E, Jones A, Darville T, Seña AC, Peng X. Simultaneous profiling of sexually transmitted bacterial pathogens, microbiome, and concordant host response in cervical samples using whole transcriptome sequencing analysis. MICROBIAL CELL 2019; 6:177-183. [PMID: 30854394 PMCID: PMC6402362 DOI: 10.15698/mic2019.03.672] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Pelvic inflammatory disease (PID) is a female upper genital tract inflammatory disorder that arises after sexually transmitted bacterial infections (STI). Factors modulating risk for reproductive sequelae include co-infection, microbiota, host genetics and physiology. In a pilot study of cervical samples obtained from women at high risk for STIs, we examined the potential for unbiased characterization of host, pathogen and microbiome interactions using whole transcriptome sequencing analysis of ribosomal RNA-depleted total RNAs (Total RNA-Seq). Only samples from women with STI infection contained pathogen-specific sequences (3 to 38% transcriptome coverage). Simultaneously, we identified and quantified their active microbial communities. After integration with host-derived reads from the same data, we detected clustering of host transcriptional profiles that reflected microbiome differences and STI infection. Together, our study suggests that total RNA profiling will advance understanding of the interplay of pathogen, host and microbiota during natural infection and may reveal novel, outcome-relevant biomarkers.
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Affiliation(s)
- Catherine M O'Connell
- Department of Pediatrics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Hayden Brochu
- Department of Molecular Biomedical Sciences, North Carolina State University, Raleigh, North Carolina, USA
| | - Jenna Girardi
- Department of Pediatrics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Erin Harrell
- Department of Molecular Biomedical Sciences, North Carolina State University, Raleigh, North Carolina, USA
| | - Aiden Jones
- Department of Molecular Biomedical Sciences, North Carolina State University, Raleigh, North Carolina, USA
| | - Toni Darville
- Department of Pediatrics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Arlene C Seña
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Xinxia Peng
- Department of Molecular Biomedical Sciences, North Carolina State University, Raleigh, North Carolina, USA.,Bioinformatics Research Center, North Carolina State University, Raleigh, North Carolina, USA
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Multispecies Transcriptomics Data Set of Brugia malayi, Its Wolbachia Endosymbiont wBm, and Aedes aegypti across the B. malayi Life Cycle. Microbiol Resour Announc 2018; 7:MRA01306-18. [PMID: 30533772 PMCID: PMC6256537 DOI: 10.1128/mra.01306-18] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 10/15/2018] [Indexed: 02/05/2023] Open
Abstract
Here, we present a comprehensive transcriptomics data set of Brugia malayi, its Wolbachia endosymbiont wBm, and its vector host. This study samples from 16 stages across the entire B. malayi life cycle, including stage 1 through 4 larvae, adult males and females, embryos, immature microfilariae, and mature microfilariae. Here, we present a comprehensive transcriptomics data set of Brugia malayi, its Wolbachia endosymbiont wBm, and its vector host. This study samples from 16 stages across the entire B. malayi life cycle, including stage 1 through 4 larvae, adult males and females, embryos, immature microfilariae, and mature microfilariae.
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