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Lee CN, Hall BA, Sanford L, Molehin AJ. Molecular Characterization and Functional Analysis of a Schistosoma mansoni Serine Protease Inhibitor, Smserpin-p46. Microorganisms 2024; 12:1164. [PMID: 38930546 PMCID: PMC11205507 DOI: 10.3390/microorganisms12061164] [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: 05/10/2024] [Revised: 05/30/2024] [Accepted: 06/05/2024] [Indexed: 06/28/2024] Open
Abstract
Serine protease inhibitors are a superfamily of proteins that regulate various physiological processes including fibrinolysis, inflammation and immune responses. In parasite systems, serpins are believed to play important roles in parasite colonization, inhibition of host immune serine proteases and penetration of defensive barriers. However, serpins are less well characterized in schistosomes. In this study, a Schistosoma mansoni serpin (Smserpin-p46) containing a 1360 base pair open reading frame, was cloned, expressed and functionally characterized. Bioinformatics analysis revealed that Smserpin-p46 contains the key residues, structural domains and motifs characteristic of inhibitory serpins. Gene expression profiling demonstrated stage-specific expression of Smserpin-p46 with the highest expression in adult male worms. Recombinant Smserpin-p46 (rSmserpin-p46) inhibited both human neutrophil cathepsin G and elastase, key serine proteases involved in NETosis, a program for the formation of neutrophil extracellular traps. Using specific rabbit antiserum, Smserpin-p46 was detected in soluble worm antigen preparation and was localized to the adult worm tegument. Cumulatively, the expression of Smserpin-p46 on the parasite tegument and its ability to inhibit proteases involved in NETosis highlights the importance of this serpin in parasite-host interactions and encourages its further investigation as a candidate vaccine antigen for the control of schistosomiasis.
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Affiliation(s)
- Christine N. Lee
- Biomedical Sciences Program, College of Graduate Studies, Midwestern University, Glendale, AZ 85308, USA;
| | - Brooke Ashlyn Hall
- Department of Microbiology and Immunology, College of Graduate Studies, Midwestern University, Glendale, AZ 85308, USA;
| | - Leah Sanford
- Arizona College of Osteopathic Medicine, Midwestern University, Glendale, AZ 85308, USA;
| | - Adebayo J. Molehin
- Department of Microbiology and Immunology, College of Graduate Studies, Midwestern University, Glendale, AZ 85308, USA;
- Arizona College of Osteopathic Medicine, Midwestern University, Glendale, AZ 85308, USA;
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2
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Jardim Poli P, Fischer-Carvalho A, Tahira AC, Chan JD, Verjovski-Almeida S, Sena Amaral M. Long Non-Coding RNA Levels Are Modulated in Schistosoma mansoni following In Vivo Praziquantel Exposure. Noncoding RNA 2024; 10:27. [PMID: 38668385 PMCID: PMC11053911 DOI: 10.3390/ncrna10020027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 04/05/2024] [Accepted: 04/13/2024] [Indexed: 04/29/2024] Open
Abstract
Schistosomiasis is a disease caused by trematodes of the genus Schistosoma that affects over 200 million people worldwide. For decades, praziquantel (PZQ) has been the only available drug to treat the disease. Despite recent discoveries that identified a transient receptor ion channel as the target of PZQ, schistosome response to this drug remains incompletely understood, since effectiveness relies on other factors that may trigger a complex regulation of parasite gene expression. Long non-coding RNAs (lncRNAs) are transcripts longer than 200 nucleotides with low or no protein-coding potential that play important roles in S. mansoni homeostasis, reproduction, and fertility. Here, we show that in vivo PZQ treatment modulates lncRNA levels in S. mansoni. We re-analyzed public RNA-Seq data from mature and immature S. mansoni worms treated in vivo with PZQ and detected hundreds of lncRNAs differentially expressed following drug exposure, many of which are shared among mature and immature worms. Through RT-qPCR, seven out of ten selected lncRNAs were validated as differentially expressed; interestingly, we show that these lncRNAs are not adult worm stage-specific and are co-expressed with PZQ-modulated protein-coding genes. By demonstrating that parasite lncRNA expression levels alter in response to PZQ, this study unravels an important step toward elucidating the complex mechanisms of S. mansoni response to PZQ.
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Affiliation(s)
- Pedro Jardim Poli
- Laboratório de Ciclo Celular, Instituto Butantan, São Paulo 05503-900, SP, Brazil; (P.J.P.); (A.F.-C.); (A.C.T.); (S.V.-A.)
| | - Agatha Fischer-Carvalho
- Laboratório de Ciclo Celular, Instituto Butantan, São Paulo 05503-900, SP, Brazil; (P.J.P.); (A.F.-C.); (A.C.T.); (S.V.-A.)
| | - Ana Carolina Tahira
- Laboratório de Ciclo Celular, Instituto Butantan, São Paulo 05503-900, SP, Brazil; (P.J.P.); (A.F.-C.); (A.C.T.); (S.V.-A.)
| | - John D. Chan
- Global Health Institute, University of Wisconsin-Madison, Madison, WI 53792, USA;
| | - Sergio Verjovski-Almeida
- Laboratório de Ciclo Celular, Instituto Butantan, São Paulo 05503-900, SP, Brazil; (P.J.P.); (A.F.-C.); (A.C.T.); (S.V.-A.)
- Instituto de Química, Universidade de São Paulo, São Paulo 05508-900, SP, Brazil
| | - Murilo Sena Amaral
- Laboratório de Ciclo Celular, Instituto Butantan, São Paulo 05503-900, SP, Brazil; (P.J.P.); (A.F.-C.); (A.C.T.); (S.V.-A.)
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3
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Steinacher C, Rieder D, Turner JE, Solanky N, Nishio SY, Usami SI, Hausott B, Schrott-Fischer A, Dudas J. Validation of RNA Extraction Methods and Suitable Reference Genes for Gene Expression Studies in Developing Fetal Human Inner Ear Tissue. Int J Mol Sci 2024; 25:2907. [PMID: 38474154 DOI: 10.3390/ijms25052907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 02/21/2024] [Accepted: 02/28/2024] [Indexed: 03/14/2024] Open
Abstract
A comprehensive gene expression investigation requires high-quality RNA extraction, in sufficient amounts for real-time quantitative polymerase chain reaction and next-generation sequencing. In this work, we compared different RNA extraction methods and evaluated different reference genes for gene expression studies in the fetal human inner ear. We compared the RNA extracted from formalin-fixed paraffin-embedded tissue with fresh tissue stored at -80 °C in RNAlater solution and validated the expression stability of 12 reference genes (from gestational week 11 to 19). The RNA from fresh tissue in RNAlater resulted in higher amounts and a better quality of RNA than that from the paraffin-embedded tissue. The reference gene evaluation exhibited four stably expressed reference genes (B2M, HPRT1, GAPDH and GUSB). The selected reference genes were then used to examine the effect on the expression outcome of target genes (OTOF and TECTA), which are known to be regulated during inner ear development. The selected reference genes displayed no differences in the expression profile of OTOF and TECTA, which was confirmed by immunostaining. The results underline the importance of the choice of the RNA extraction method and reference genes used in gene expression studies.
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Affiliation(s)
- Claudia Steinacher
- Department of Otorhinolaryngology, Medical University Innsbruck, 6020 Innsbruck, Austria
| | - Dietmar Rieder
- Institute of Bioinformatics, Medical University Innsbruck, 6020 Innsbruck, Austria
| | - Jasmin E Turner
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE1 4EP, UK
| | - Nita Solanky
- UCL Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK
| | - Shin-Ya Nishio
- Department of Hearing Implant Sciences, Shinshu University School of Medicine, Matsumoto 3-1-1 Asahi, Nagano 390-8621, Japan
| | - Shin-Ichi Usami
- Department of Hearing Implant Sciences, Shinshu University School of Medicine, Matsumoto 3-1-1 Asahi, Nagano 390-8621, Japan
| | - Barbara Hausott
- Institute of Neuroanatomy, Medical University Innsbruck, 6020 Innsbruck, Austria
| | | | - Jozsef Dudas
- Department of Otorhinolaryngology, Medical University Innsbruck, 6020 Innsbruck, Austria
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4
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de Sousa PRC, da Silva ASM, de Ponte CGG, Nogueira LL, Frota CC, Antas PRZ. Commentary: Identification of optimal reference genes for gene expression normalization in human osteosarcoma cell lines under proliferative conditions. Front Genet 2024; 15:1342447. [PMID: 38333617 PMCID: PMC10850317 DOI: 10.3389/fgene.2024.1342447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 01/02/2024] [Indexed: 02/10/2024] Open
Affiliation(s)
- Paulo R. C. de Sousa
- Programa de Pós-Graduação em Patologia, Universidade Federal do Ceará, Fortaleza, Brazil
| | | | | | - Lucas L. Nogueira
- Programa de Pós-Graduação em Patologia, Universidade Federal do Ceará, Fortaleza, Brazil
| | - Cristiane C. Frota
- Programa de Pós-Graduação em Patologia, Universidade Federal do Ceará, Fortaleza, Brazil
| | - Paulo R. Z. Antas
- Programa de Pós-Graduação em Patologia, Universidade Federal do Ceará, Fortaleza, Brazil
- Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
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5
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Guo W, Yang Y, Ma B, Wang W, Hu Z, Leng P. Selection and Validation of Reference Genes for Gene Expression Studies in Euonymus japonicus Based on RNA Sequencing. Genes (Basel) 2024; 15:131. [PMID: 38275612 PMCID: PMC10815735 DOI: 10.3390/genes15010131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 01/13/2024] [Accepted: 01/19/2024] [Indexed: 01/27/2024] Open
Abstract
Euonymus japonicus is one of the most low-temperature-tolerant evergreen broad-leaved tree species in the world and is widely used in urban greening. However, there are very few molecular biology studies on its low-temperature tolerance mechanism. So far, no researcher has selected and reported on its reference genes. In this study, 21 candidate reference genes (12 traditional housekeeping genes and 9 other genes) were initially selected based on gene expression and coefficient of variation (CV) through RNA-Seq (unpublished data), and qRT-PCR was used to detect the expression levels of candidate reference genes in three different groups of samples (leaves under different temperature stresses, leaves of plants at different growth stages, and different organs). After further evaluating the expression stability of these genes using geNorm, NormFinder, Bestkeeper, and RefFind, the results show that the traditional housekeeping gene eIF5A and the new reference gene RTNLB1 have good stability in the three different groups of samples, so they are reference genes with universality. In addition, we used eIF5A and RTNLB1 as reference genes to calibrate the expression pattern of the target gene EjMAH1, which confirmed this view. This article is the first to select and report on the reference gene of E. japonicus, laying the foundation for its low-temperature tolerance mechanism and other molecular biology research.
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Affiliation(s)
- Wei Guo
- College of Landscape Architecture, Beijing University of Agriculture, Beijing 102206, China; (W.G.); (B.M.); (W.W.)
| | - Yihui Yang
- College of Landscape Architecture, Beijing University of Agriculture, Beijing 102206, China; (W.G.); (B.M.); (W.W.)
| | - Bo Ma
- College of Landscape Architecture, Beijing University of Agriculture, Beijing 102206, China; (W.G.); (B.M.); (W.W.)
| | - Wenbo Wang
- College of Landscape Architecture, Beijing University of Agriculture, Beijing 102206, China; (W.G.); (B.M.); (W.W.)
| | - Zenghui Hu
- Engineering Research Center for Ancient Tree Health and Ancient Tree Culture of National Forestry and Grassland Administration, Beijing 102206, China
| | - Pingsheng Leng
- College of Landscape Architecture, Beijing University of Agriculture, Beijing 102206, China; (W.G.); (B.M.); (W.W.)
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Silveira GO, Coelho HS, Pereira ASA, Miyasato PA, Santos DW, Maciel LF, Olberg GGG, Tahira AC, Nakano E, Oliveira MLS, Amaral MS, Verjovski-Almeida S. Long non-coding RNAs are essential for Schistosoma mansoni pairing-dependent adult worm homeostasis and fertility. PLoS Pathog 2023; 19:e1011369. [PMID: 37146077 DOI: 10.1371/journal.ppat.1011369] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 05/17/2023] [Accepted: 04/18/2023] [Indexed: 05/07/2023] Open
Abstract
The trematode parasite Schistosoma mansoni causes schistosomiasis, which affects over 200 million people worldwide. Schistosomes are dioecious, with egg laying depending on the females' obligatory pairing with males. Long non-coding RNAs (lncRNAs) are transcripts longer than 200 nucleotides with low or no protein-coding potential that have been involved in other species with reproduction, stem cell maintenance, and drug resistance. In S. mansoni, we recently showed that the knockdown of one lncRNA affects the pairing status of these parasites. Here, we re-analyzed public RNA-Seq data from paired and unpaired adult male and female worms and their gonads, obtained from mixed-sex or single-sex cercariae infections, and found thousands of differentially expressed pairing-dependent lncRNAs among the 23 biological samples that were compared. The expression levels of selected lncRNAs were validated by RT-qPCR using an in vitro unpairing model. In addition, the in vitro silencing of three selected lncRNAs showed that knockdown of these pairing-dependent lncRNAs reduced cell proliferation in adult worms and their gonads, and are essential for female vitellaria maintenance, reproduction, and/or egg development. Remarkably, in vivo silencing of each of the three selected lncRNAs significantly reduced worm burden in infected mice by 26 to 35%. Whole mount in situ hybridization experiments showed that these pairing-dependent lncRNAs are expressed in reproductive tissues. These results show that lncRNAs are key components intervening in S. mansoni adult worm homeostasis, which affects pairing status and survival in the mammalian host, thus presenting great potential as new therapeutic target candidates.
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Affiliation(s)
- Gilbert O Silveira
- Laboratório de Ciclo Celular, Instituto Butantan, São Paulo, São Paulo, Brazil
- Instituto de Química, Universidade de São Paulo, São Paulo, São Paulo, Brazil
| | - Helena S Coelho
- Laboratório de Ciclo Celular, Instituto Butantan, São Paulo, São Paulo, Brazil
| | - Adriana S A Pereira
- Laboratório de Ciclo Celular, Instituto Butantan, São Paulo, São Paulo, Brazil
- Instituto de Química, Universidade de São Paulo, São Paulo, São Paulo, Brazil
| | - Patrícia A Miyasato
- Laboratório de Parasitologia, Instituto Butantan, São Paulo, São Paulo, Brazil
| | - Daisy W Santos
- Laboratório de Ciclo Celular, Instituto Butantan, São Paulo, São Paulo, Brazil
- Instituto de Química, Universidade de São Paulo, São Paulo, São Paulo, Brazil
| | - Lucas F Maciel
- Laboratório de Ciclo Celular, Instituto Butantan, São Paulo, São Paulo, Brazil
| | - Giovanna G G Olberg
- Laboratório de Ciclo Celular, Instituto Butantan, São Paulo, São Paulo, Brazil
| | - Ana C Tahira
- Laboratório de Ciclo Celular, Instituto Butantan, São Paulo, São Paulo, Brazil
| | - Eliana Nakano
- Laboratório de Parasitologia, Instituto Butantan, São Paulo, São Paulo, Brazil
| | | | - Murilo S Amaral
- Laboratório de Ciclo Celular, Instituto Butantan, São Paulo, São Paulo, Brazil
| | - Sergio Verjovski-Almeida
- Laboratório de Ciclo Celular, Instituto Butantan, São Paulo, São Paulo, Brazil
- Instituto de Química, Universidade de São Paulo, São Paulo, São Paulo, Brazil
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7
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Morales-Vicente DA, Zhao L, Silveira GO, Tahira AC, Amaral MS, Collins JJ, Verjovski-Almeida S. Single-cell RNA-seq analyses show that long non-coding RNAs are conspicuously expressed in Schistosoma mansoni gamete and tegument progenitor cell populations. Front Genet 2022; 13:924877. [PMID: 36204320 PMCID: PMC9531161 DOI: 10.3389/fgene.2022.924877] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 08/24/2022] [Indexed: 11/17/2022] Open
Abstract
Schistosoma mansoni is a flatworm that causes schistosomiasis, a neglected tropical disease that affects over 200 million people worldwide. New therapeutic targets are needed with only one drug available for treatment and no vaccine. Long non-coding RNAs (lncRNAs) are transcripts longer than 200 nucleotides with low or no protein-coding potential. In other organisms, they have been shown as involved with reproduction, stem cell maintenance and drug resistance, and they tend to exhibit tissue-specific expression patterns. S. mansoni expresses thousands of lncRNA genes; however, the cell type expression patterns of lncRNAs in the parasite remain uncharacterized. Here, we have re-analyzed publicly available single-cell RNA-sequencing (scRNA-seq) data obtained from adult S. mansoni to identify the lncRNAs signature of adult schistosome cell types. A total of 8023 lncRNAs (79% of all lncRNAs) were detected. Analyses of the lncRNAs expression profiles in the cells using statistically stringent criteria were performed to identify 74 lncRNA gene markers of cell clusters. Male gamete and tegument progenitor lineages clusters contained most of the cluster-specific lncRNA markers. We also identified lncRNA markers of specific neural clusters. Whole-mount in situ hybridization (WISH) and double fluorescence in situ hybridization were used to validate the cluster-specific expression of 13 out of 16 selected lncRNA genes (81%) in the male and female adult parasite tissues; for one of these 16 gene loci, probes for two different lncRNA isoforms were used, which showed differential isoform expression in testis and ovary. An atlas of the expression profiles across the cell clusters of all lncRNAs detected in our analysis is available as a public website resource (http://verjolab.usp.br:8081). The results presented here give strong support to a tissue-specific expression and to a regulated expression program of lncRNAs in S. mansoni. This will be the basis for further exploration of lncRNA genes as potential therapeutic targets.
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Affiliation(s)
- David A. Morales-Vicente
- Laboratório de Parasitologia, Instituto Butantan, São Paulo, Brazil
- Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Lu Zhao
- Department of Pharmacology, UT Southwestern Medical Center, Dallas, TX, United States
| | - Gilbert O. Silveira
- Laboratório de Parasitologia, Instituto Butantan, São Paulo, Brazil
- Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Ana C. Tahira
- Laboratório de Parasitologia, Instituto Butantan, São Paulo, Brazil
| | - Murilo S. Amaral
- Laboratório de Parasitologia, Instituto Butantan, São Paulo, Brazil
| | - James J. Collins
- Department of Pharmacology, UT Southwestern Medical Center, Dallas, TX, United States
| | - Sergio Verjovski-Almeida
- Laboratório de Parasitologia, Instituto Butantan, São Paulo, Brazil
- Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
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8
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Pirovich DB, Da'dara AA, Skelly PJ. Schistosoma mansoni phosphoglycerate mutase: a glycolytic ectoenzyme with thrombolytic potential. PARASITE (PARIS, FRANCE) 2022; 29:41. [PMID: 36083036 PMCID: PMC9461710 DOI: 10.1051/parasite/2022042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 08/28/2022] [Indexed: 11/14/2022]
Abstract
Schistosomiasis is a debilitating parasitic disease caused by intravascular flatworms called schistosomes (blood flukes) that affects >200 million people worldwide. Proteomic analysis has revealed the surprising presence of classical glycolytic enzymes – typically cytosolic proteins – located on the extracellular surface of the parasite tegument (skin). Immunolocalization experiments show that phosphoglycerate mutase (PGM) is widely expressed in parasite tissues and is highly expressed in the tegument. We demonstrate that live Schistosoma mansoni parasites express enzymatically active PGM on their tegumental surface. Suppression of PGM using RNA interference (RNAi) diminishes S. mansoni PGM (SmPGM) gene expression, protein levels, and surface enzyme activity. Sequence comparisons place SmPGM in the cofactor (2,3-bisphosphoglycerate)-dependent PGM (dPGM) family. We have produced recombinant SmPGM (rSmPGM) in an enzymatically active form in Escherichia coli. The Michaelis-Menten constant (Km) of rSmPGM for its glycolytic substrate (3-phosphoglycerate) is 0.85 mM ± 0.02. rSmPGM activity is inhibited by the dPGM-specific inhibitor vanadate. Here, we show that rSmPGM not only binds to plasminogen but also promotes its conversion to an active form (plasmin) in vitro. This supports the hypothesis that host-interactive tegumental proteins (such as SmPGM), by enhancing plasmin formation, may help degrade blood clots around the worms in the vascular microenvironment and thus promote parasite survival in vivo.
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Affiliation(s)
- David B Pirovich
- Molecular Helminthology Laboratory, Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine, Tufts University, 200 Westboro Road, North Grafton, MA 01536, USA
| | - Akram A Da'dara
- Molecular Helminthology Laboratory, Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine, Tufts University, 200 Westboro Road, North Grafton, MA 01536, USA
| | - Patrick J Skelly
- Molecular Helminthology Laboratory, Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine, Tufts University, 200 Westboro Road, North Grafton, MA 01536, USA
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Li J, Fu N, Ren L, Luo Y. Identification and Validation of Reference Genes for Gene Expression Analysis in Monochamus saltuarius Under Bursaphelenchus xylophilus Treatment. Front Physiol 2022; 13:882792. [PMID: 35547586 PMCID: PMC9082747 DOI: 10.3389/fphys.2022.882792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 03/21/2022] [Indexed: 11/13/2022] Open
Abstract
A special mutual relationship exists between the pine wood nematode (PWN) Bursaphelenchus xylophilus and its vector beetles of genus Monochamus, which enables PWN to spread, at the same time provides longhorned beetles with more weak hosts. PWN are attracted to the pupal chambers and then carried inside the trachea of beetle adults, which is a necessary part to complete the B. xylophilus infection cycle. The growth and immune responses of the vector beetle will affect this carrying process, however, they were rarely studied in Monochamus saltuarius. Real-time quantitative polymerase chain reaction (RT-qPCR), one of the most common methods for quantitative gene expression analysis, was performed to explore the key genes and pathways involved in the growth, development and immune responses of M. saltuarius at different developmental stages associated with infection of PWN and PWN treatment conditions. To enhance the accuracy of RT-qPCR data, the expression of target genes needs to be normalized with reference genes, which are stably expressed under varied experimental conditions. In our study, the stability of 14 candidate reference genes in M. saltuarius samples at different developmental stages associated with infection of PWN or PWN treatment conditions was evaluated using delta Ct, geNorm, NormFinder, BestKeeper and RefFinder algorithms. Moreover, KLF gene was used to validate the stability of the selected reference genes. Under experimental conditions of this study, RPL7 and TER were suitable reference genes at different developmental stages associated with infection of PWN. RPL7 and RPS5 were considered the most stable reference genes in the pupae treated with PWN. RPS5 and SNX6 could be used as reference genes in the adults treated with PWN. RPL7, EF1-γ, and RPS5 could be used as stable reference genes in all the samples. This work is the first to evaluate reference genes in M. saltuarius, laying a foundation for further gene expression experimental procedures and understanding the phoretic relationship between M. saltuarius and B. xylophilus.
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Affiliation(s)
- Jiaxing Li
- Beijing Key Laboratory for Forest Pest Control, Beijing Forestry University, Beijing, China
| | - Ningning Fu
- Beijing Key Laboratory for Forest Pest Control, Beijing Forestry University, Beijing, China
| | - Lili Ren
- Beijing Key Laboratory for Forest Pest Control, Beijing Forestry University, Beijing, China
| | - Youqing Luo
- Beijing Key Laboratory for Forest Pest Control, Beijing Forestry University, Beijing, China
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Grätz C, Bui MLU, Thaqi G, Kirchner B, Loewe RP, Pfaffl MW. Obtaining Reliable RT-qPCR Results in Molecular Diagnostics—MIQE Goals and Pitfalls for Transcriptional Biomarker Discovery. Life (Basel) 2022; 12:life12030386. [PMID: 35330136 PMCID: PMC8953338 DOI: 10.3390/life12030386] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 02/15/2022] [Accepted: 03/02/2022] [Indexed: 11/16/2022] Open
Abstract
In this review, we discuss the development pipeline for transcriptional biomarkers in molecular diagnostics and stress the importance of a reliable gene transcript quantification strategy. Hence, a further focus is put on the MIQE guidelines and how to adapt them for biomarker discovery, from signature validation up to routine diagnostic applications. First, the advantages and pitfalls of the holistic RNA sequencing for biomarker development will be described to establish a candidate biomarker signature. Sequentially, the RT-qPCR confirmation process will be discussed to validate the discovered biomarker signature. Examples for the successful application of RT-qPCR as a fast and reproducible quantification method in routinemolecular diagnostics are provided. Based on the MIQE guidelines, the importance of “key steps” in RT-qPCR is accurately described, e.g., reverse transcription, proper reference gene selection and, finally, the application of automated RT-qPCR data analysis software. In conclusion, RT-qPCR proves to be a valuable tool in the establishment of a disease-specific transcriptional biomarker signature and will have a great future in molecular diagnostics or personalized medicine.
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Affiliation(s)
- Christian Grätz
- Department of Animal Physiology and Immunology, School of Life Sciences, Technical University of Munich, Weihenstephaner Berg 3, 85354 Freising, Germany; (C.G.); (M.L.U.B.); (G.T.); (B.K.)
- GeneSurge GmbH, Ottostr. 3, 80333 München, Germany;
| | - Maria L. U. Bui
- Department of Animal Physiology and Immunology, School of Life Sciences, Technical University of Munich, Weihenstephaner Berg 3, 85354 Freising, Germany; (C.G.); (M.L.U.B.); (G.T.); (B.K.)
- GeneSurge GmbH, Ottostr. 3, 80333 München, Germany;
| | - Granit Thaqi
- Department of Animal Physiology and Immunology, School of Life Sciences, Technical University of Munich, Weihenstephaner Berg 3, 85354 Freising, Germany; (C.G.); (M.L.U.B.); (G.T.); (B.K.)
| | - Benedikt Kirchner
- Department of Animal Physiology and Immunology, School of Life Sciences, Technical University of Munich, Weihenstephaner Berg 3, 85354 Freising, Germany; (C.G.); (M.L.U.B.); (G.T.); (B.K.)
- GeneSurge GmbH, Ottostr. 3, 80333 München, Germany;
| | | | - Michael W. Pfaffl
- Department of Animal Physiology and Immunology, School of Life Sciences, Technical University of Munich, Weihenstephaner Berg 3, 85354 Freising, Germany; (C.G.); (M.L.U.B.); (G.T.); (B.K.)
- Correspondence: or
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