201
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Chandler AC, Yakoub M, Fujiwara T, Donlin LT, Purdue PE, Healey JH. Neoplastic synovial lining cells that coexpress podoplanin and CD90 overproduce CSF-1, driving tenosynovial giant cell tumor. J Orthop Res 2022; 40:1918-1925. [PMID: 34855235 PMCID: PMC9160208 DOI: 10.1002/jor.25216] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 10/07/2021] [Accepted: 11/09/2021] [Indexed: 02/04/2023]
Abstract
Tenosynovial giant cell tumor (TCGT) is a rare neoplasm affecting the synovium of joints, bursae, and tendon sheaths. The overproduction of colony-stimulating factor-1 (CSF-1) by a minority of the tumor population works in a paracrine fashion to drive tumor growth. Pathology of the reactive, monocytic component has been well elucidated, whereas the populations of neoplastic cells and all the sources of CSF-1 overproduction are incompletely characterized. Podoplanin (PDPN), or gp38, is a cell surface glycoprotein that is expressed on fibroblast-like synovial cells and upregulated in rheumatoid arthritis and many cancers; it governs cell mobility, epithelial-mesenchymal transition, and other functions and is associated with lymphangiogenesis and poor prognosis in many solid tumors, which underscores its local and possible systemic effects. We found higher PDPN expression in TGCT than in internal controls of patients' healthy synovium. Flow cytometry partitioned PDPNhigh cells into PDPNhigh CD90+ and PDPNhigh CD14+ populations. Quantitative real-time polymerase chain reaction analysis of the PDPNhigh CD90+ cells revealed that CSF-1 expression was 10-fold higher than in PDPNhigh CD14+ cells. Therefore, we conclude that the lining fibroblast-like synovial cells, which express PDPNhigh CD90+ , are responsible for the overproduction of CSF-1 and for driving tumor growth.
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Affiliation(s)
- Andrew C. Chandler
- Department of Surgery, Orthopaedic Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Touro College of Osteopathic Medicine, New York, NY, USA
| | - Mohamed Yakoub
- Department of Surgery, Orthopaedic Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Tomohiro Fujiwara
- Department of Surgery, Orthopaedic Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | | | - John H. Healey
- Department of Surgery, Orthopaedic Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Hospital for Special Surgery, New York, NY, USA
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202
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Kandoi D, Ruhil K, Govindjee G, Tripathy BC. Overexpression of cytoplasmic C 4 Flaveria bidentis carbonic anhydrase in C 3 Arabidopsis thaliana increases amino acids, photosynthetic potential, and biomass. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:1518-1532. [PMID: 35467074 PMCID: PMC9342616 DOI: 10.1111/pbi.13830] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 04/15/2022] [Accepted: 04/18/2022] [Indexed: 05/20/2023]
Abstract
An important method to improve photosynthesis in C3 crops, such as rice and wheat, is to transfer efficient C4 characters to them. Here, cytosolic carbonic anhydrase (CA: βCA3) of the C4 Flaveria bidentis (Fb) was overexpressed under the control of 35 S promoter in Arabidopsis thaliana, a C3 plant, to enhance its photosynthetic efficiency. Overexpression of CA resulted in a better supply of the substrate HCO3- for the endogenous phosphoenolpyruvate carboxylase in the cytosol of the overexpressers, and increased its activity for generating malate that feeds into the tricarboxylic acid cycle. This provided additional carbon skeleton for increased synthesis of amino acids aspartate, asparagine, glutamate, and glutamine. Increased amino acids contributed to higher protein content in the transgenics. Furthermore, expression of FbβCA3 in Arabidopsis led to a better growth due to expression of several genes leading to higher chlorophyll content, electron transport, and photosynthetic carbon assimilation in the transformants. Enhanced CO2 assimilation resulted in increased sugar and starch content, and plant dry weight. In addition, transgenic plants had lower stomatal conductance, reduced transpiration rate, and higher water-use efficiency. These results, taken together, show that expression of C4 CA in the cytosol of a C3 plant can indeed improve its photosynthetic capacity with enhanced water-use efficiency.
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Affiliation(s)
- Deepika Kandoi
- School of Life SciencesJawaharlal Nehru UniversityNew DelhiIndia
| | - Kamal Ruhil
- School of Life SciencesJawaharlal Nehru UniversityNew DelhiIndia
| | - Govindjee Govindjee
- Department of Plant BiologyDepartment of Biochemistry, and Center of Biophysics & Quantitative BiologyUniversity of Illinois at Urbana‐ChampaignUrbanaILUSA
| | - Baishnab C. Tripathy
- School of Life SciencesJawaharlal Nehru UniversityNew DelhiIndia
- Department of BiotechnologySharda UniversityGreater NoidaUPIndia
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203
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Cao X, Mao Y, Gu Y, Ge S, Lu W, Gu Y, Li Z. Highly sensitive and simultaneous detection of ctDNAs related to non-small cell lung cancer in serum using a catalytic hairpin assembly strategy in a SERS microfluidic chip. J Mater Chem B 2022; 10:6194-6206. [PMID: 35904034 DOI: 10.1039/d2tb01024k] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Circulating tumor DNA (ctDNA) is an ideal biomarker for cancer diagnosis based on liquid biopsy, so there is an urgent need for developing an efficient, rapid, and ultrasensitive detection method to meet clinical needs. In this paper, a novel surface-enhanced Raman scattering (SERS) microfluidic chip combined with a catalytic hairpin assembly (CHA) was proposed to detect two non-small cell lung cancer (NSCLC)-related ctDNA (TP53 and PIK3CA-Q546K) simultaneously. The chip consists of six channels for parallel detection. In the reaction region, the CHA reaction between HP1 of the SERS probe and HP2 of the capture substrate was triggered by ctDNAs to form HP1-HP2 duplexes. As the reaction proceeds, more and more SERS probes are captured on the substrate. The gathered reaction products continuously form a lot of hot spots, which greatly enhance the SERS signal. This reaction was completed within 5 minutes. Through this method, the detection limits of TP53 and PIK3CA-Q546K in human serum were as low as 2.26 aM and 2.34 aM, respectively. The microfluidic chip also exhibited high specificity, reproducibility and stability. The clinical feasibility of the SERS microfluidic chip was verified by analyzing the serum samples of healthy subjects and NSCLC patients. The reliability of the experimental results was verified by the qRT-PCR test. The constructed SERS-based analytical micro-platform has great potential in dynamic monitoring of cancer staging and could be used as a clinical tool for early cancer screening.
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Affiliation(s)
- Xiaowei Cao
- Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou, 225001, P. R. China. .,Jiangsu Key Laboratory of Integrated Traditional Chinese and Western Medicine for Prevention and Treatment of Senile Diseases, Yangzhou University, Yangzhou, 225001, P. R. China.,Jiangsu Key Laboratory of Experimental & Translational Noncoding RNA Research, Medical College, Yangzhou University, Yangzhou, 225001, P. R. China
| | - Yu Mao
- Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou, 225001, P. R. China. .,Jiangsu Key Laboratory of Integrated Traditional Chinese and Western Medicine for Prevention and Treatment of Senile Diseases, Yangzhou University, Yangzhou, 225001, P. R. China.,Jiangsu Key Laboratory of Experimental & Translational Noncoding RNA Research, Medical College, Yangzhou University, Yangzhou, 225001, P. R. China
| | - Yuexing Gu
- Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou, 225001, P. R. China. .,Jiangsu Key Laboratory of Integrated Traditional Chinese and Western Medicine for Prevention and Treatment of Senile Diseases, Yangzhou University, Yangzhou, 225001, P. R. China.,Jiangsu Key Laboratory of Experimental & Translational Noncoding RNA Research, Medical College, Yangzhou University, Yangzhou, 225001, P. R. China
| | - Shengjie Ge
- Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou, 225001, P. R. China. .,Jiangsu Key Laboratory of Integrated Traditional Chinese and Western Medicine for Prevention and Treatment of Senile Diseases, Yangzhou University, Yangzhou, 225001, P. R. China.,Jiangsu Key Laboratory of Experimental & Translational Noncoding RNA Research, Medical College, Yangzhou University, Yangzhou, 225001, P. R. China
| | - Wenbo Lu
- Shanxi Normal University, College of Chemistry and Material Science, Linfen, 041004, P. R. China
| | - Yingyan Gu
- Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou, 225001, P. R. China. .,Jiangsu Key Laboratory of Integrated Traditional Chinese and Western Medicine for Prevention and Treatment of Senile Diseases, Yangzhou University, Yangzhou, 225001, P. R. China.,Jiangsu Key Laboratory of Experimental & Translational Noncoding RNA Research, Medical College, Yangzhou University, Yangzhou, 225001, P. R. China
| | - Zhiyue Li
- The First Clinical College, Dalian Medical University, Dalian, 116000, P. R. China
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204
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Kot M, Mazurkiewicz E, Wiktor M, Wiertelak W, Mazur AJ, Rahalevich A, Olczak M, Maszczak-Seneczko D. SLC35A2 Deficiency Promotes an Epithelial-to-Mesenchymal Transition-like Phenotype in Madin–Darby Canine Kidney Cells. Cells 2022; 11:cells11152273. [PMID: 35892570 PMCID: PMC9331475 DOI: 10.3390/cells11152273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 07/15/2022] [Accepted: 07/20/2022] [Indexed: 11/16/2022] Open
Abstract
In mammalian cells, SLC35A2 delivers UDP–galactose for galactosylation reactions that take place predominantly in the Golgi lumen. Mutations in the corresponding gene cause a subtype of a congenital disorder of glycosylation (SLC35A2-CDG). Although more and more patients are diagnosed with SLC35A2-CDG, the link between defective galactosylation and disease symptoms is not fully understood. According to a number of reports, impaired glycosylation may trigger the process of epithelial-to-mesenchymal transition (EMT). We therefore examined whether the loss of SLC35A2 activity would promote EMT in a non-malignant epithelial cell line. For this purpose, we knocked out the SLC35A2 gene in Madin–Darby canine kidney (MDCK) cells. The resulting clones adopted an elongated, spindle-shaped morphology and showed impaired cell–cell adhesion. Using qPCR and western blotting, we revealed down-regulation of E-cadherin in the knockouts, while the fibronectin and vimentin levels were elevated. Moreover, the knockout cells displayed reorganization of vimentin intermediate filaments and altered subcellular distribution of a vimentin-binding protein, formiminotransferase cyclodeaminase (FTCD). Furthermore, depletion of SLC35A2 triggered Golgi compaction. Finally, the SLC35A2 knockouts displayed increased motility and invasiveness. In conclusion, SLC35A2-deficient MDCK cells showed several hallmarks of EMT. Our findings point to a novel role for SLC35A2 as a gatekeeper of the epithelial phenotype.
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Affiliation(s)
- Magdalena Kot
- Department of Cell Pathology, Faculty of Biotechnology, University of Wroclaw, 14A F. Joliot-Curie St., 50-383 Wroclaw, Poland; (M.K.); (E.M.); (A.J.M.)
| | - Ewa Mazurkiewicz
- Department of Cell Pathology, Faculty of Biotechnology, University of Wroclaw, 14A F. Joliot-Curie St., 50-383 Wroclaw, Poland; (M.K.); (E.M.); (A.J.M.)
| | - Maciej Wiktor
- Department of Biochemistry, Faculty of Biotechnology, University of Wroclaw, 14A F. Joliot-Curie St., 50-383 Wroclaw, Poland; (M.W.); (W.W.); (A.R.); (M.O.)
| | - Wojciech Wiertelak
- Department of Biochemistry, Faculty of Biotechnology, University of Wroclaw, 14A F. Joliot-Curie St., 50-383 Wroclaw, Poland; (M.W.); (W.W.); (A.R.); (M.O.)
| | - Antonina Joanna Mazur
- Department of Cell Pathology, Faculty of Biotechnology, University of Wroclaw, 14A F. Joliot-Curie St., 50-383 Wroclaw, Poland; (M.K.); (E.M.); (A.J.M.)
| | - Andrei Rahalevich
- Department of Biochemistry, Faculty of Biotechnology, University of Wroclaw, 14A F. Joliot-Curie St., 50-383 Wroclaw, Poland; (M.W.); (W.W.); (A.R.); (M.O.)
| | - Mariusz Olczak
- Department of Biochemistry, Faculty of Biotechnology, University of Wroclaw, 14A F. Joliot-Curie St., 50-383 Wroclaw, Poland; (M.W.); (W.W.); (A.R.); (M.O.)
| | - Dorota Maszczak-Seneczko
- Department of Biochemistry, Faculty of Biotechnology, University of Wroclaw, 14A F. Joliot-Curie St., 50-383 Wroclaw, Poland; (M.W.); (W.W.); (A.R.); (M.O.)
- Correspondence:
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205
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Crobeddu B, Jutras-Carignan A, Kolasa É, Mounier C, Robaire B, Plante I. Gestational and lactational exposure to the emergent alternative plasticizer 1,2-cyclohexane dicarboxylic acid diisononyl ester (DINCH) impairs lipid metabolism to a greater extent than the commonly used Di(2-ethylhexyl) phthalate (DEHP) in the adult rat mammary gland. Toxicol Sci 2022; 189:268-286. [PMID: 35861430 DOI: 10.1093/toxsci/kfac076] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Due to their endocrine disruption properties, phthalate plasticizers such as di(2-ethylhexyl) phthalate (DEHP) can affect the hormone-dependent development of the mammary gland. Over the past few years, DEHP has been partially replaced by 1,2-cyclohexane dicarboxylic acid diisononyl ester (DINCH) which also have potential endocrine disrupting properties. The goal of the present study is to understand the impact of a gestational and lactational exposure to DEHP and DINCH on mammary gland development using Sprague-Dawley rats. Both plasticizers altered the adipocytes of the mammary gland fat pad of adult progeny, as demonstrated by a decrease in their size, folding of their membrane and modulations of the lipid profiles. DEHP treatments decreased the expression of Rxrα and Scd1 at the low and high dose, respectively, but did not affect any of the other genes studied. DINCH modulation of lipid metabolism could be observed at puberty by a decreased expression of genes implicated in triglyceride synthesis, lipid transport and lipolysis, but by an increased expression of genes of the β-oxidation pathway and of genes involved in lipid storage and fatty acid synthesis at adulthood, compared to control and DEHP-treated rats. A strong upregulation of different inflammatory markers was observed following DINCH exposure only. Together, our results indicate that a gestational and lactational exposure to DINCH has earlier and more significant effects on lipid homeostasis, adipogenesis and the inflammatory state of the adult mammary gland than DEHP exposure. The long-term consequence of these effects on mammary gland health remained to be determined.
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Affiliation(s)
- Bélinda Crobeddu
- INRS-Centre Armand-Frappier Santé Biotechnologie, 531 boul. des Prairies, Laval, Québec, H7V 1B7, Canada
| | - Antoine Jutras-Carignan
- Laboratoire du métabolisme des lipides, CERMO-FC, Département des sciences biologiques, Université du Québec à Montréal, Case postale 8888, succursale Centre-Ville, Montréal, Québec, H3C 3P8, Canada
| | - Élise Kolasa
- INRS-Centre Armand-Frappier Santé Biotechnologie, 531 boul. des Prairies, Laval, Québec, H7V 1B7, Canada
| | - Catherine Mounier
- Laboratoire du métabolisme des lipides, CERMO-FC, Département des sciences biologiques, Université du Québec à Montréal, Case postale 8888, succursale Centre-Ville, Montréal, Québec, H3C 3P8, Canada
| | - Bernard Robaire
- Department of Pharmacology & Therapeutics, McGill University, Montreal, Quebec, H3G 1Y6, Canada.,Department of Obstetrics & Gynecology, McGill University, Montreal, Quebec, H4A 3J1, Canada
| | - Isabelle Plante
- INRS-Centre Armand-Frappier Santé Biotechnologie, 531 boul. des Prairies, Laval, Québec, H7V 1B7, Canada
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206
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Flatschacher D, Speckbacher V, Zeilinger S. qRAT: an R-based stand-alone application for relative expression analysis of RT-qPCR data. BMC Bioinformatics 2022; 23:286. [PMID: 35854213 PMCID: PMC9297597 DOI: 10.1186/s12859-022-04823-7] [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] [Received: 12/15/2021] [Accepted: 07/06/2022] [Indexed: 11/10/2022] Open
Abstract
Background Reverse transcription quantitative real-time PCR (RT-qPCR) is a well-established method for analysing gene expression. Most RT-qPCR experiments in the field of microbiology aim for the detection of transcriptional changes by relative quantification, which means the comparison of the expression level of a specific gene between different samples by the application of a calibration condition and internal reference genes. Due to the numerous data processing procedures and factors that can influence the final result, relative expression analysis and interpretation of RT-qPCR data are still not trivial and often necessitate the use of multiple separate software packages capable of performing specific functions. Results Here we present qRAT, a stand-alone desktop application based on R that automatically processes raw output data from any qPCR machine using well-established and state-of-the-art statistical and graphical techniques. The ability of qRAT to analyse RT-qPCR data was evaluated using two example datasets generated in our laboratory. The tool successfully completed the procedure in both cases, returning the expected results. The current implementation includes functionalities for parsing, filtering, normalizing and visualisation of relative RT-qPCR data, like the determination of the relative quantity and the fold change of differentially expressed genes as well as the correction of inter-plate variation for multiple-plate experiments. Conclusion qRAT provides a comprehensive, straightforward, and easy-to-use solution for the relative quantification of RT-qPCR data that requires no programming knowledge or additional software installation. All application features are available for free and without requiring a login or registration. Supplementary Information The online version contains supplementary material available at 10.1186/s12859-022-04823-7.
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Affiliation(s)
| | | | - Susanne Zeilinger
- Department of Microbiology, University of Innsbruck, Innsbruck, Austria
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207
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Ahmed W, Bivins A, Metcalfe S, Smith WJM, Ziels R, Korajkic A, McMinn B, Graber TE, Simpson SL. RT-qPCR and ATOPlex sequencing for the sensitive detection of SARS-CoV-2 RNA for wastewater surveillance. WATER RESEARCH 2022; 220:118621. [PMID: 35665675 PMCID: PMC9109001 DOI: 10.1016/j.watres.2022.118621] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Revised: 05/07/2022] [Accepted: 05/13/2022] [Indexed: 05/27/2023]
Abstract
During the coronavirus disease 2019 (COVID-19) pandemic, wastewater surveillance has become an important tool for monitoring the spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) within communities. In particular, reverse transcription-quantitative PCR (RT-qPCR) has been used to detect and quantify SARS-CoV-2 RNA in wastewater, while monitoring viral genome mutations requires separate approaches such as deep sequencing. A high throughput sequencing platform (ATOPlex) that uses a multiplex tiled PCR-based enrichment technique has shown promise in detecting variants of concern (VOC) while also providing virus quantitation data. However, detection sensitivities of both RT-qPCR and sequencing can be impacted through losses occurring during sample handling, virus concentration, nucleic acid extraction, and RT-qPCR. Therefore, process limit of detection (PLOD) assessments are required to estimate the gene copies of target molecule to attain specific probability of detection. In this study, we compare the PLOD of four RT-qPCR assays (US CDC N1 and N2, China CDC N and ORF1ab) for detection of SARS-CoV-2 to that of ATOPlex sequencing by seeding known concentrations of gamma-irradiated SARS-CoV-2 into wastewater. Results suggest that among the RT-qPCR assays, US CDC N1 was the most sensitive, especially at lower SARS-CoV-2 seed levels. However, when results from all RT-qPCR assays were combined, it resulted in greater detection rates than individual assays, suggesting that application of multiple assays is better suited for the trace detection of SARS-CoV-2 from wastewater samples. Furthermore, while ATOPlex offers a promising approach to SARS-CoV-2 wastewater surveillance, this approach appears to be less sensitive compared to RT-qPCR under the experimental conditions of this study, and may require further refinements. Nonetheless, the combination of RT-qPCR and ATOPlex may be a powerful tool to simultaneously detect/quantify SARS-CoV-2 RNA and monitor emerging VOC in wastewater samples.
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Affiliation(s)
- Warish Ahmed
- CSIRO Land and Water, Ecosciences Precinct, 41 Boggo Road, Dutton Park, QLD 4102, Australia.
| | - Aaron Bivins
- Department of Civil & Environmental Engineering, Louisiana State University, LA, USA
| | - Suzanne Metcalfe
- CSIRO Land and Water, Ecosciences Precinct, 41 Boggo Road, Dutton Park, QLD 4102, Australia
| | - Wendy J M Smith
- CSIRO Land and Water, Ecosciences Precinct, 41 Boggo Road, Dutton Park, QLD 4102, Australia
| | - Ryan Ziels
- Department of Civil Engineering, University of British Columbia, Vancouver, Canada
| | - Asja Korajkic
- United States Environmental Protection Agency, 26 W Martin Luther King Jr. Drive, Cincinnati, OH 45268, USA
| | - Brian McMinn
- United States Environmental Protection Agency, 26 W Martin Luther King Jr. Drive, Cincinnati, OH 45268, USA
| | - Tyson E Graber
- Children's Hospital of Eastern Ontario Research Institute, Ottawa K1H 8L1, Canada
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208
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Zhang X, Tian C, Tian C, Cheng J, Mao W, Li M, Chen M. LTBP2 inhibits prostate cancer progression and metastasis via the PI3K/AKT signaling pathway. Exp Ther Med 2022; 24:563. [PMID: 36034756 PMCID: PMC9400130 DOI: 10.3892/etm.2022.11500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 05/11/2022] [Indexed: 12/02/2022] Open
Abstract
Biochemical recurrence (BCR) is a cause of concern in advanced prostate cancer (PCa). Thus, novel diagnostic biomarkers are required to improve clinical care. However, research on PCa immunotherapy is also scarce. Hence, the present study aimed to explore promising BCR-related diagnostic biomarkers, and their expression pattern, prognostic value, immune response effects, biological functions, and possible molecular mechanisms were evaluated. GEO datasets (GSE46602, GSE70768, and GSE116918) were downloaded and merged as the training cohort, and differential expression analysis was performed. Lasso regression and SVM-RFE algorithm, as well as PPI analysis and MCODE algorithm, were then applied to filter BCR-related biomarker genes. The CIBERSORT and estimation of stromal and immune cells in malignant tumor tissues using expression data (ESTIMATE) methods were used to calculate the fractions of tumor-infiltrating immune cells. GO/DO enrichment analyses were used to identify the biological functions. The expression of latent transforming growth factor β-binding protein 2 (LTBP2) was determined by RT-qPCR and western blotting. The role of LTBP2 in PCa was determined by CCK-8, Transwell, and the potential mechanism was investigated by KEGG and GSEA and confirmed by western blotting. In total, 44 BCR-related differentially expressed genes (DEGs) in the training cohort were screened. LTBP2 was found to be a diagnostic biomarker of BCR in PCa and was associated with CD4+ T-cell infiltration and response to anti-PD-1/PD-L1 immunotherapy. Subsequently, using the ESTIMATE algorithm, it was identified that LTBP2 was associated with the tumor microenvironment and could be a predictor of the clinical benefit of immune checkpoint blockade. Finally, the expression and biological function of LTBP2 were evaluated via cellular experiments. The results showed that LTBP2 was downregulated in PCa cells and inhibited PCa proliferation and metastasis via the PI3K/AKT signaling pathway in vitro. In conclusion, LTBP2 was a promising diagnostic biomarker of BCR of PCa and had an important role in CD4+ T-cell recruitment. Moreover, it was associated with immunotherapy in patients with PCa who developed BCR, and it inhibited PCa proliferation and metastasis via the PI3K/AKT signaling pathway in vitro.
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Affiliation(s)
- Xiaowen Zhang
- Department of Urology, Affiliated Zhongda Hospital of South‑East University, Nanjing, Jiangsu 210009, P.R. China
| | - Chuanjie Tian
- Department of Urology, Langxi County People's Hospital, Xuancheng, Anhui 242100, P.R. China
| | - Chuanjie Tian
- Department of Urology, Langxi County People's Hospital, Xuancheng, Anhui 242100, P.R. China
| | - Jianbin Cheng
- Department of Urology Surgery, Heqiao Hospital, Yixing, Jiangsu 214200, P.R. China
| | - Weipu Mao
- Department of Urology, Affiliated Zhongda Hospital of South‑East University, Nanjing, Jiangsu 210009, P.R. China
| | - Menglan Li
- NHC Contraceptives Adverse Reaction Surveillance Center, Jiangsu Health Development Research Center, Nanjing, Jiangsu 210036, P.R. China
| | - Ming Chen
- Department of Urology, Affiliated Zhongda Hospital of South‑East University, Nanjing, Jiangsu 210009, P.R. China
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209
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Jurickova I, Bonkowski E, Angerman E, Novak E, Huron A, Akers, G, Iwasawa K, Braun T, Hadar R, Hooker M, Han S, Cutler DJ, Okou DT, Kugathasan S, Jegga A, Wells J, Takebe T, Mollen KP, Haberman Y, Denson LA. Eicosatetraynoic Acid and Butyrate Regulate Human Intestinal Organoid Mitochondrial and Extracellular Matrix Pathways Implicated in Crohn's Disease Strictures. Inflamm Bowel Dis 2022; 28:988-1003. [PMID: 35259271 PMCID: PMC9247849 DOI: 10.1093/ibd/izac037] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Indexed: 12/19/2022]
Abstract
BACKGROUND Perturbagen analysis of Crohn's disease (CD) ileal gene expression data identified small molecules including eicosatetraynoic acid (ETYA), which may exert an antifibrotic effect. We developed a patient-specific human intestinal organoid (HIO) model system to test small molecule regulation of mitochondrial and wound-healing functions implicated in stricturing behavior. METHODS HIOs were made from CD induced pluripotent stem cells with and without a loss-of-function haplotype in the DUOX2 gene implicated in ileal homeostasis and characterized under basal conditions and following exposure to butyrate and ETYA using RNA sequencing, flow cytometry, and immunofluorescent and polarized light microscopy. Mitochondrial activity was measured using high-resolution respirometry and tissue stiffness using atomic force microscopy. RESULTS HIOs expressed core mitochondrial and extracellular matrix (ECM) genes and enriched biologic functions implicated in CD ileal strictures; ECM gene expression was suppressed by both butyrate and ETYA, with butyrate also suppressing genes regulating epithelial proliferation. Consistent with this, butyrate, but not ETYA, exerted a profound effect on HIO epithelial mitochondrial function, reactive oxygen species production, and cellular abundance. Butyrate and ETYA suppressed HIO expression of alpha smooth muscle actin expressed by myofibroblasts, type I collagen, and collagen protein abundance. HIOs exhibited tissue stiffness comparable to normal human ileum; this was reduced by chronic ETYA exposure in HIOs carrying the DUOX2 loss-of-function haplotype. CONCLUSIONS ETYA regulates ECM genes implicated in strictures and suppresses collagen content and tissue stiffness in an HIO model. HIOs provide a platform to test personalized therapeutics, including small molecules prioritized by perturbagen analysis.
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Affiliation(s)
- Ingrid Jurickova
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Cincinnati Children’s Hospital Medical Center, the University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Erin Bonkowski
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Cincinnati Children’s Hospital Medical Center, the University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Elizabeth Angerman
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Cincinnati Children’s Hospital Medical Center, the University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Elizabeth Novak
- Division of General and Thoracic Surgery, UPMC Children’s Hospital of Pittsburgh, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Alex Huron
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Cincinnati Children’s Hospital Medical Center, the University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Grayce Akers,
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Cincinnati Children’s Hospital Medical Center, the University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Kentaro Iwasawa
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Cincinnati Children’s Hospital Medical Center, the University of Cincinnati College of Medicine, Cincinnati, OH, USA
- Division of Biomedical Informatics, Department of Pediatrics, Cincinnati Children’s Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Tzipi Braun
- Department of Pediatrics, Sheba Medical Center, Tel-Aviv University, Tel-HaShomer, Israel
| | - Rotem Hadar
- Department of Pediatrics, Sheba Medical Center, Tel-Aviv University, Tel-HaShomer, Israel
| | - Maria Hooker
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Cincinnati Children’s Hospital Medical Center, the University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Sarah Han
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Cincinnati Children’s Hospital Medical Center, the University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - David J Cutler
- Department of Human Genetics, Emory University, Atlanta, GA, USA
| | - David T Okou
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Emory University, Atlanta, GA, USA
| | - Subra Kugathasan
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Emory University, Atlanta, GA, USA
| | - Anil Jegga
- Division of Biomedical Informatics, Department of Pediatrics, Cincinnati Children’s Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - James Wells
- Division of Developmental Biology, Department of Pediatrics, Cincinnati Children’s Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Takanori Takebe
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Cincinnati Children’s Hospital Medical Center, the University of Cincinnati College of Medicine, Cincinnati, OH, USA
- Division of Developmental Biology, Department of Pediatrics, Cincinnati Children’s Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH, USA
- Institute of Research, Tokyo Medical and Dental University, Japan
| | - Kevin P Mollen
- Division of General and Thoracic Surgery, UPMC Children’s Hospital of Pittsburgh, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Yael Haberman
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Cincinnati Children’s Hospital Medical Center, the University of Cincinnati College of Medicine, Cincinnati, OH, USA
- Department of Pediatrics, Sheba Medical Center, Tel-Aviv University, Tel-HaShomer, Israel
| | - Lee A Denson
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Cincinnati Children’s Hospital Medical Center, the University of Cincinnati College of Medicine, Cincinnati, OH, USA
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210
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Byrne DJ, Lipovsek M, Crespo A, Grubb MS. Brief sensory deprivation triggers plasticity of dopamine-synthesising enzyme expression in genetically labelled olfactory bulb dopaminergic neurons. Eur J Neurosci 2022; 56:3591-3612. [PMID: 35510299 PMCID: PMC9540594 DOI: 10.1111/ejn.15684] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 04/25/2022] [Indexed: 11/30/2022]
Abstract
In the glomerular layer of the olfactory bulb, local dopaminergic interneurons play a key role in regulating the flow of sensory information from nose to cortex. These dual dopamine- and GABA-releasing cells are capable of marked experience-dependent changes in the expression of neurotransmitter-synthesising enzymes, including tyrosine hydroxylase (TH). However, such plasticity has most commonly been studied in cell populations identified by their expression of the enzyme being studied and after long periods of sensory deprivation. Here, instead, we used brief 1- or 3-day manipulations of olfactory experience in juvenile mice, coupled with a conditional genetic approach that labelled neurons contingent upon their expression of the dopamine transporter (DAT-tdTomato). This enabled us to evaluate the potential for rapid changes in neurotransmitter-synthesising enzyme expression in an independently identified neuronal population. Our labelling strategy showed good specificity for olfactory bulb dopaminergic neurons, while revealing a minority sub-population of non-dopaminergic DAT-tdTomato cells that expressed the calcium-binding protein calretinin. Crucially, the proportions of these neuronal subtypes were not affected by brief alterations in sensory experience. Short-term olfactory manipulations also produced no significant changes in immunofluorescence or whole-bulb mRNA for the GABA-synthesising enzyme GAD67/Gad1. However, in bulbar DAT-tdTomato neurons, brief sensory deprivation was accompanied by a transient, small drop in immunofluorescence for the dopamine-synthesising enzyme dopa decarboxylase (DDC) and a sustained decrease for TH. Deprivation also produced a sustained decrease in whole-bulb Th mRNA. Careful characterisation of an independently identified, genetically labelled neuronal population therefore enabled us to uncover rapid experience-dependent changes in dopamine-synthesising enzyme expression.
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Affiliation(s)
- Darren J. Byrne
- Centre for Developmental Neurobiology, Institute of Psychiatry, Psychology and Neuroscience (IoPPN)King's College LondonLondonUK
| | - Marcela Lipovsek
- Centre for Developmental Neurobiology, Institute of Psychiatry, Psychology and Neuroscience (IoPPN)King's College LondonLondonUK
- Ear InstituteUniversity College LondonLondonUK
| | - Andres Crespo
- Centre for Developmental Neurobiology, Institute of Psychiatry, Psychology and Neuroscience (IoPPN)King's College LondonLondonUK
| | - Matthew S. Grubb
- Centre for Developmental Neurobiology, Institute of Psychiatry, Psychology and Neuroscience (IoPPN)King's College LondonLondonUK
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211
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Amelioration for an ignored pitfall in reference gene selection by considering the mean expression and standard deviation of target genes. Sci Rep 2022; 12:11129. [PMID: 35778437 PMCID: PMC9249883 DOI: 10.1038/s41598-022-15277-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Accepted: 06/21/2022] [Indexed: 11/08/2022] Open
Abstract
Routine tissue-specific reference genes are often used in expression studies, but target genes are not taken into account. Using the relative RT-qPCR approach, we evaluated the expression of three target genes. At the same time, meta-analyses were conducted in various ethnic groups, genders, and thyroid cancer subtypes. When eight common reference genes were examined, it was discovered that some of them not only lacked consistent expression but also had considerable expression variance. It is worth noting that while choosing a reference gene, the mean gene expression and its standard deviation should be carefully addressed. An equation was developed based on this, and it was used to perform statistical analysis on over 25,000 genes. According to the subtype of thyroid cancer and, of course, the target genes in this investigation, appropriate reference genes were proposed. The intuitive choice of GAPDH as a common reference gene caused a major shift in the quantitative expression data of target genes, inverting the relative expression values. As a result, choosing the appropriate reference gene(s) for quantification of transcription data, and especially for relative studies of the expression of target gene(s), is critical and should be carefully considered during the study design.
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212
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Liu F, Kambakam S, Almeida MP, Ming Z, Welker JM, Wierson WA, Schultz-Rogers LE, Ekker SC, Clark KJ, Essner JJ, McGrail M. Cre/ lox regulated conditional rescue and inactivation with zebrafish UFlip alleles generated by CRISPR-Cas9 targeted integration. eLife 2022; 11:71478. [PMID: 35713402 PMCID: PMC9270027 DOI: 10.7554/elife.71478] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Accepted: 06/16/2022] [Indexed: 11/13/2022] Open
Abstract
The ability to regulate gene activity spatially and temporally is essential to investigate cell type-specific gene function during development and in postembryonic processes and disease models. The Cre/lox system has been widely used for performing cell and tissue-specific conditional analysis of gene function in zebrafish. However, simple and efficient methods for isolation of stable, Cre/lox regulated zebrafish alleles are lacking. Here we applied our GeneWeld CRISPR-Cas9 targeted integration strategy to generate floxed alleles that provide robust conditional inactivation and rescue. A universal targeting vector, UFlip, with sites for cloning short homology arms flanking a floxed 2A-mRFP gene trap, was integrated into an intron in rbbp4 and rb1. rbbp4off and rb1off integration alleles resulted in strong mRFP expression, >99% reduction of endogenous gene expression, and recapitulated known indel loss of function phenotypes. Introduction of Cre led to stable inversion of the floxed cassette, loss of mRFP expression, and phenotypic rescue. rbbp4on and rb1on integration alleles did not cause phenotypes in combination with a loss of function mutation. Addition of Cre led to conditional inactivation by stable inversion of the cassette, gene trapping and mRFP expression, and the expected mutant phenotype. Neural progenitor Cre drivers were used for conditional inactivation and phenotypic rescue to showcase how this approach can be used in specific cell populations. Together these results validate a simplified approach for efficient isolation of Cre/lox responsive conditional alleles in zebrafish. Our strategy provides a new toolkit for generating genetic mosaics and represents a significant advance in zebrafish genetics.
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Affiliation(s)
- Fang Liu
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, United States
| | - Sekhar Kambakam
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, United States
| | - Maira P Almeida
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, United States
| | - Zhitao Ming
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, United States
| | - Jordan M Welker
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, United States
| | - Wesley A Wierson
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, United States
| | - Laura E Schultz-Rogers
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, United States
| | - Stephen C Ekker
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, United States
| | - Karl J Clark
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, United States
| | - Jeffrey J Essner
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, United States
| | - Maura McGrail
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, United States
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213
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Schüle S, Ostheim P, Port M, Abend M. Identifying radiation responsive exon-regions of genes often used for biodosimetry and acute radiation syndrome prediction. Sci Rep 2022; 12:9545. [PMID: 35680903 PMCID: PMC9184472 DOI: 10.1038/s41598-022-13577-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 05/17/2022] [Indexed: 11/12/2022] Open
Abstract
Gene expression (GE) analysis of FDXR, DDB2, WNT3 and POU2AF1 is a promising approach for identification of clinically relevant groups (unexposed, low- and high exposed) after radiological/nuclear events. However, results from international biodosimetry exercises have shown differences in dose estimates based on radiation-induced GE of the four genes. Also, differences in GE using next-generation-sequening (NGS) and validation with quantitative real-time polymerase chain reaction (qRT-PCR) was reported. These discrepancies could be caused by radiation-responsive differences among exons of the same gene. We performed GE analysis with qRT-PCR using TaqMan-assays covering all exon-regions of FDXR, DDB2, WNT3 and POU2AF1. Peripheral whole blood from three healthy donors was X-irradiated with 0, 0.5 and 4 Gy. After 24 and 48 h a dose-dependent up-regulation across almost all exon-regions for FDXR and DDB2 (4–42-fold) was found. A down-regulation for POU2AF1 (two- to threefold) and WNT3 (< sevenfold) at the 3’-end was found at 4 Gy irradiation only. Hence, this confirms our hypothesis for radiation-responsive exon-regions for WNT3 and POU2AF1, but not for FDXR and DDB2. Finally, we identified the most promising TaqMan-assays for FDXR (e.g. AR7DTG3, Hs00244586_m1), DDB2 (AR47X6H, Hs03044951_m1), WNT3 (Hs00902258_m1, Hs00902257_m1) and POU2AF1 (Hs01573370_g1, Hs01573371_m1) for biodosimetry purposes and acute radiation syndrome prediction, considering several criteria (detection limit, dose dependency, time persistency, inter-individual variability).
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Affiliation(s)
- Simone Schüle
- Bundeswehr Institute of Radiobiology Affiliated to the University Ulm, Neuherbergstr. 11, 80937, Munich, Germany
| | - Patrick Ostheim
- Bundeswehr Institute of Radiobiology Affiliated to the University Ulm, Neuherbergstr. 11, 80937, Munich, Germany
| | - Matthias Port
- Bundeswehr Institute of Radiobiology Affiliated to the University Ulm, Neuherbergstr. 11, 80937, Munich, Germany
| | - Michael Abend
- Bundeswehr Institute of Radiobiology Affiliated to the University Ulm, Neuherbergstr. 11, 80937, Munich, Germany.
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214
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Ngouth N, Monaco MC, Walker L, Corey S, Ikpeama I, Fahle G, Cortese I, Das S, Jacobson S. Comparison of qPCR with ddPCR for the Quantification of JC Polyomavirus in CSF from Patients with Progressive Multifocal Leukoencephalopathy. Viruses 2022; 14:v14061246. [PMID: 35746716 PMCID: PMC9229850 DOI: 10.3390/v14061246] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 06/02/2022] [Accepted: 06/03/2022] [Indexed: 02/01/2023] Open
Abstract
Background: Lytic infection of oligodendrocytes by the human JC polyomavirus (JCPyV) results in the demyelinating disease called progressive multifocal leukoencephalopathy (PML). The detection of viral DNA in the cerebrospinal fluid (CSF) by PCR is an important diagnostic tool and, in conjunction with defined radiological and clinical features, can provide diagnosis of definite PML, avoiding the need for brain biopsy. The main aim of this study is to compare the droplet digital PCR (ddPCR) assay with the gold standard quantitative PCR (qPCR) for the quantification of JC viral loads in clinical samples. Methods: A total of 62 CSF samples from 31 patients with PML were analyzed to compare the qPCR gold standard technique with ddPCR to detect conserved viral DNA sequences in the JCPyV genome. As part of the validation process, ddPCR results were compared to qPCR data obtained in 42 different laboratories around the world. In addition, the characterization of a novel triplex ddPCR to detect viral DNA sequence from both prototype and archetype variants and a cellular housekeeping reference gene is described. Triplex ddPCR was used to analyze the serum from six PML patients and from three additional cohorts, including 20 healthy controls (HC), 20 patients with multiple sclerosis (MS) who had never been treated with natalizumab (no-NTZ-treated), and 14 patients with MS who were being treated with natalizumab (NTZ-treated); three from this last group seroconverted during the course of treatment with natalizumab. Results: JCPyV DNA was detected only by ddPCR for 5 of the 62 CSF samples (8%), while remaining undetected by qPCR. For nine CSF samples (15%), JCPyV DNA was at the lower limit of quantification for qPCR, set at <250 copies/mL, and therefore no relative quantitation could be determined. By contrast, exact copies of JCPyV for each of these samples were quantified by ddPCR. No differences were observed between qPCR and ddPCR when five standardized plasma samples were analyzed for JCPyV in 42 laboratories in the United States and Europe. JCPyV-DNA was undetected in all the sera from HC and MS cohorts tested by triplex ddPCR, while serum samples from six patients with PML tested positive for JCPyV. Conclusion: This study shows strong correlation between ddPCR and qPCR with increased sensitivity of the ddPCR assay. Further work will be needed to determine whether multiplex ddPCR can be useful to determine PML risk in natalizumab-treated MS patients.
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Affiliation(s)
- Nyater Ngouth
- Viral Immunology Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health (NIH), Bethesda, MD 20892, USA; (N.N.); (M.C.M.)
| | - Maria Chiara Monaco
- Viral Immunology Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health (NIH), Bethesda, MD 20892, USA; (N.N.); (M.C.M.)
| | - Lorenzo Walker
- Department of Laboratory Medicine, National Institutes of Health (NIH), Bethesda, MD 20892, USA; (L.W.); (I.I.); (G.F.); (S.D.)
| | - Sydney Corey
- Neuroimmunology Clinic, National Institute of Neurological Disorders and Stroke, National Institutes of Health (NIH), Bethesda, MD 20892, USA; (S.C.); (I.C.)
| | - Ijeoma Ikpeama
- Department of Laboratory Medicine, National Institutes of Health (NIH), Bethesda, MD 20892, USA; (L.W.); (I.I.); (G.F.); (S.D.)
| | - Gary Fahle
- Department of Laboratory Medicine, National Institutes of Health (NIH), Bethesda, MD 20892, USA; (L.W.); (I.I.); (G.F.); (S.D.)
| | - Irene Cortese
- Neuroimmunology Clinic, National Institute of Neurological Disorders and Stroke, National Institutes of Health (NIH), Bethesda, MD 20892, USA; (S.C.); (I.C.)
| | - Sanchita Das
- Department of Laboratory Medicine, National Institutes of Health (NIH), Bethesda, MD 20892, USA; (L.W.); (I.I.); (G.F.); (S.D.)
| | - Steven Jacobson
- Viral Immunology Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health (NIH), Bethesda, MD 20892, USA; (N.N.); (M.C.M.)
- Correspondence:
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215
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Medeiros-Furquim T, Ayoub S, Johnson LJ, Aprico A, Nwoke E, Binder MD, Kilpatrick TJ. Cladribine Treatment for MS Preserves the Differentiative Capacity of Subsequently Generated Monocytes, Whereas Its Administration In Vitro Acutely Influences Monocyte Differentiation but Not Microglial Activation. Front Immunol 2022; 13:678817. [PMID: 35734180 PMCID: PMC9207174 DOI: 10.3389/fimmu.2022.678817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 03/31/2022] [Indexed: 12/04/2022] Open
Abstract
Cladribine (2-chlorodeoxyadenosine, 2CdA) is one of the most effective disease-modifying drugs for multiple sclerosis (MS). Cladribine is a synthetic purine nucleoside analog that induces cell death of lymphocytes and oral cladribine treatment leads to a long-lasting disease stabilization, potentially attributable to immune reconstitution. In addition to its effects on lymphocytes, cladribine has been shown to have immunomodulatory effects on innate immune cells, including dendritic cells and monocytes, which could also contribute to its therapeutic efficacy. However, whether cladribine can modulate human macrophage/microglial activation or monocyte differentiation is currently unknown. The aim of this study was to determine the immunomodulatory effects of cladribine upon monocytes, monocyte-derived macrophages (MDMs) and microglia. We analyzed the phenotype and differentiation of monocytes from MS patients receiving their first course of oral cladribine both before and three weeks after the start of treatment. Flow cytometric analysis of monocytes from MS patients undergoing cladribine treatment revealed that the number and composition of CD14/CD16 monocyte subsets remained unchanged after treatment. Furthermore, after differentiation with M-CSF, such MDMs from treated MS patients showed no difference in gene expression of the inflammatory markers compared to baseline. We further investigated the direct effects of cladribine in vitro using human adult primary MDMs and microglia. GM-CSF-derived MDMs were more sensitive to cell death than M-CSF-derived MDMs. In addition, MDMs treated with cladribine showed increased expression of costimulatory molecules CD80 and CD40, as well as expression of anti-inflammatory, pro-trophic genes IL10 and MERTK, depending on the differentiation condition. Cladribine treatment in vitro did not modulate the expression of activation markers in human microglia. Our study shows that cladribine treatment in vitro affects the differentiation of monocytes into macrophages by modulating the expression of activation markers, which might occur similarly in tissue after their infiltration in the CNS during MS.
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Affiliation(s)
- Tiago Medeiros-Furquim
- Department of Biomedical Sciences of Cells and Systems, Section Molecular Neurobiology, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
- The Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville, VIC, Australia
| | - Sinan Ayoub
- The Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville, VIC, Australia
| | - Laura J. Johnson
- The Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville, VIC, Australia
| | - Andrea Aprico
- The Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville, VIC, Australia
| | - Eze Nwoke
- The Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville, VIC, Australia
| | - Michele D. Binder
- The Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville, VIC, Australia
- Department of Neuroscience and Physiology, University of Melbourne, Parkville, VIC, Australia
| | - Trevor J. Kilpatrick
- The Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville, VIC, Australia
- Florey Department of Neuroscience and Mental Health, University of Melbourne, Parkville, VIC, Australia
- *Correspondence: Trevor J. Kilpatrick,
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216
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Renault C, Bolloré K, Pisoni A, Motto-Ros C, Van de Perre P, Reynes J, Tuaillon E. Accuracy of real-time PCR and digital PCR for the monitoring of total HIV DNA under prolonged antiretroviral therapy. Sci Rep 2022; 12:9323. [PMID: 35665775 PMCID: PMC9167282 DOI: 10.1038/s41598-022-13581-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Accepted: 04/21/2022] [Indexed: 12/16/2022] Open
Abstract
Total HIV DNA is a standard marker to monitor the HIV reservoir in people living with HIV. We investigated HIV DNA quantification accuracy by a real-time PCR kit (qPCR) and digital PCR (dPCR) method within the same set of primers and probes. Among 48 aviremic patients followed for up to 7 years with qPCR, the mean coefficient of variation of total HIV DNA between two successive measurements was 77% (± 0.42log10 HIVDNA copies/106 PBMC). The total HIV DNA quantified by the two PCR methods has a high correlation (0.99 and 0.83, for 8E5 and PLHIV samples, respectively), but we observed better repeatability and reproducibility of the dPCR compared to the qPCR (CV of 11.9% vs. 24.7% for qPCR, p-value = 0.024). Furthermore, we highlighted a decay of the number of HIV copies in the 8E5 cell line qPCR standard over time (from 0.73 to 0.43 copies per cell), contributing to variations of HIV DNA results in patients whose HIV reservoir should be theoretically stabilized. Our study highlighted that absolute quantification of total HIV DNA by dPCR allows more accurate monitoring of the HIV reservoir than qPCR in patients under prolonged antiretroviral therapy.
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Affiliation(s)
- Constance Renault
- Pathogenesis and Control of Chronic and Emerging Infections, University of Montpellier, INSERM, Etablissement Français du Sang, Antilles University, Montpellier, France
| | - Karine Bolloré
- Pathogenesis and Control of Chronic and Emerging Infections, University of Montpellier, INSERM, Etablissement Français du Sang, Antilles University, Montpellier, France
| | - Amandine Pisoni
- Pathogenesis and Control of Chronic and Emerging Infections, University of Montpellier, INSERM, Etablissement Français du Sang, Antilles University, Montpellier, France.,CHU de Montpellier, Montpellier, France
| | - Camille Motto-Ros
- Pathogenesis and Control of Chronic and Emerging Infections, University of Montpellier, INSERM, Etablissement Français du Sang, Antilles University, Montpellier, France
| | - Philippe Van de Perre
- Pathogenesis and Control of Chronic and Emerging Infections, University of Montpellier, INSERM, Etablissement Français du Sang, Antilles University, Montpellier, France.,CHU de Montpellier, Montpellier, France
| | - Jacques Reynes
- IRD UMI 233, INSERM U1175, Montpellier University, Montpellier, France.,Infectious Diseases Department, CHU de Montpellier, Montpellier, France
| | - Edouard Tuaillon
- Pathogenesis and Control of Chronic and Emerging Infections, University of Montpellier, INSERM, Etablissement Français du Sang, Antilles University, Montpellier, France. .,CHU de Montpellier, Montpellier, France.
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217
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Zhang X, Li Z, Liu X, Qin X, Luo J, Zhang W, Liu B, Wei Y. ZPI prevents ox-LDL-mediated endothelial injury leading to inhibition of EndMT, inflammation, apoptosis, and oxidative stress through activating Pi3k/Akt signal pathway. Drug Dev Res 2022; 83:1212-1225. [PMID: 35656597 DOI: 10.1002/ddr.21952] [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: 11/24/2021] [Revised: 03/31/2022] [Accepted: 05/02/2022] [Indexed: 11/09/2022]
Abstract
Oxidized low-density lipoprotein (ox-LDL)-mediated endothelial dysfunction exerts an essential role in the development of atherosclerosis. Protein Z-dependent protease inhibitor (ZPI), a member of the serine protease inhibitor superfamily, could inhibit the function of activated coagulation factor X (FXa) via interaction with protein Z (PZ). Studies have pointed out that ZPI was statistically related to atherosclerotic diseases, which may have a robust cardiovascular protective effect. However, the underlying mechanism of ZPI on ox-LDL-mediated endothelial injury requires further elucidation. Human umbilical vein endothelial cells (HUVECs) were treated with ox-LDL (100 μg/ml) and ZPI (10 μg/ml). Cell viability was measured by the Cell Counting Kit-8 (CCK-8) assay. Cell apoptosis, oxidative stress, and endothelial-to-mesenchymal transition (EndMT) were analyzed by immunofluorescence (IF). Cell migration was measured using a wound-healing assay. Quantitative real-time polymerase chain reaction and western blot analysis were performed to determine messenger RNA and protein expression. Ox-LDL (100 μg/ml, 48 h) significantly reduced cell viability and migration, increased EndMT, inflammation, apoptosis, and oxidative stress. The related protein expression of phosphatidylinositol 3 kinase/protein kinase B (Pi3k/Akt) signal pathway in HUVECs was also simultaneously decreased. We also discovered that ZPI treatment could prevent ox-LDL-mediated endothelial injury through the improvement of cell viability and alleviation of apoptosis, oxidative stress, EndMT, and inflammation. Thus, the protective effect of ZPI on HUVECs may be mediated by activation of the Pi3k/Akt signal pathway. ZPI may exert an important protective role in HUVECs dysfunction triggered by ox-LDL via activation of the Pi3k/Akt signal pathway. Therefore, ZPI may possess potential therapeutic effects on atherosclerotic endothelial injury-related diseases.
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Affiliation(s)
- Xingxu Zhang
- Department of Cardiology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Zhiqiang Li
- Department of Cardiology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Xiangdong Liu
- Department of Cardiology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Xiaoming Qin
- Department of Cardiology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Jiachen Luo
- Department of Cardiology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Wenming Zhang
- Department of Cardiology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Baoxin Liu
- Department of Cardiology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Yidong Wei
- Department of Cardiology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
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218
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Alsing S, Doktor TK, Askou AL, Jensen EG, Ahmadov U, Kristensen LS, Andresen BS, Aagaard L, Corydon TJ. VEGFA-targeting miR-agshRNAs combine efficacy with specificity and safety for retinal gene therapy. MOLECULAR THERAPY - NUCLEIC ACIDS 2022; 28:58-76. [PMID: 35356684 PMCID: PMC8933642 DOI: 10.1016/j.omtn.2022.02.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 02/25/2022] [Indexed: 11/09/2022]
Abstract
Retinal gene therapy using RNA interference (RNAi) to silence targeted genes requires both efficacy and safety. Short hairpin RNAs (shRNAs) are useful for RNAi, but high expression levels and activity from the co-delivered passenger strand may cause undesirable cellular responses. Ago2-dependent shRNAs (agshRNAs) produce no passenger strand activity. To enhance efficacy and to investigate improvements in safety, we have generated VEGFA-targeting agshRNAs and microRNA (miRNA)-embedded agshRNAs (miR-agshRNAs) and inserted these RNAi effectors in Pol II/III-driven expression cassettes and lentiviral vectors (LVs). Compared with corresponding shRNAs, agshRNAs and miR-agshRNAs increased specificity and safety, while retaining a high knockdown efficacy and abolishing passenger strand activity. The agshRNAs also caused significantly smaller reductions in cell viability and reduced competition with the processing of endogenous miR21 compared with their shRNA counterparts. RNA sequencing (RNA-seq) analysis of LV-transduced ARPE19 cells revealed that expression of shRNAs in general leads to more changes in gene expression levels compared with their agshRNA counterparts and activation of immune-related pathways. In mice, subretinal delivery of LVs encoding tissue-specific miR-agshRNAs resulted in retinal pigment epithelium (RPE)-restricted expression and significant knockdown of Vegfa in transduced RPE cells. Collectively, our data suggest that agshRNAs and miR-agshRNA possess important advantages over shRNAs, thereby posing a clinically relevant approach with respect to efficacy, specificity, and safety.
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219
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Puris E, Jalkanen A, Auriola S, Loppi S, Korhonen P, Kanninen KM, Malm T, Koistinaho J, Gynther M. Systemic inflammation elevates cytosolic prolyl oligopeptidase protein expression but not peptidase activity in the cerebral cortices of familial Alzheimer`s disease modeling mice. BRAIN DISORDERS 2022. [DOI: 10.1016/j.dscb.2022.100035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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220
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Rakpenthai A, Apodiakou A, Whitcomb SJ, Hoefgen R. In silico analysis of cis-elements and identification of transcription factors putatively involved in the regulation of the OAS cluster genes SDI1 and SDI2. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 110:1286-1304. [PMID: 35315155 DOI: 10.1111/tpj.15735] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 02/09/2022] [Accepted: 03/01/2022] [Indexed: 06/14/2023]
Abstract
Arabidopsis thaliana sulfur deficiency-induced 1 and sulfur deficiency-induced 2 (SDI1 and SDI2) are involved in partitioning sulfur among metabolite pools during sulfur deficiency, and their transcript levels strongly increase in this condition. However, little is currently known about the cis- and trans-factors that regulate SDI expression. We aimed at identifying DNA sequence elements (cis-elements) and transcription factors (TFs) involved in regulating expression of the SDI genes. We performed in silico analysis of their promoter sequences cataloging known cis-elements and identifying conserved sequence motifs. We screened by yeast-one-hybrid an arrayed library of Arabidopsis TFs for binding to the SDI1 and SDI2 promoters. In total, 14 candidate TFs were identified. Direct association between particular cis-elements in the proximal SDI promoter regions and specific TFs was established via electrophoretic mobility shift assays: sulfur limitation 1 (SLIM1) was shown to bind SURE cis-element(s), the basic domain/leucine zipper (bZIP) core cis-element was shown to be important for HY5-homolog (HYH) binding, and G-box binding factor 1 (GBF1) was shown to bind the E box. Functional analysis of GBF1 and HYH using mutant and over-expressing lines indicated that these TFs promote a higher transcript level of SDI1 in vivo. Additionally, we performed a meta-analysis of expression changes of the 14 TF candidates in a variety of conditions that alter SDI expression. The presented results expand our understanding of sulfur pool regulation by SDI genes.
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Affiliation(s)
- Apidet Rakpenthai
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Anastasia Apodiakou
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Sarah J Whitcomb
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Rainer Hoefgen
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
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221
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Skurska E, Szulc B, Maszczak-Seneczko D, Wiktor M, Wiertelak W, Makowiecka A, Olczak M. Incorporation of fucose into glycans independent of the GDP-fucose transporter SLC35C1 preferentially utilizes salvaged over de novo GDP-fucose. J Biol Chem 2022; 298:102206. [PMID: 35772493 PMCID: PMC9304781 DOI: 10.1016/j.jbc.2022.102206] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 06/22/2022] [Accepted: 06/23/2022] [Indexed: 11/29/2022] Open
Abstract
Mutations in the SLC35C1 gene encoding the Golgi GDP-fucose transporter are known to cause leukocyte adhesion deficiency II. However, improvement of fucosylation in leukocyte adhesion deficiency II patients treated with exogenous fucose suggests the existence of an SLC35C1-independent route of GDP-fucose transport, which remains a mystery. To investigate this phenomenon, we developed and characterized a human cell–based model deficient in SLC35C1 activity. The resulting cells were cultured in the presence/absence of exogenous fucose and mannose, followed by examination of fucosylation potential and nucleotide sugar levels. We found that cells displayed low but detectable levels of fucosylation in the absence of SLC35C1. Strikingly, we show that defects in fucosylation were almost completely reversed upon treatment with millimolar concentrations of fucose. Furthermore, we show that even if fucose was supplemented at nanomolar concentrations, it was still incorporated into glycans by these knockout cells. We also found that the SLC35C1-independent transport preferentially utilized GDP-fucose from the salvage pathway over the de novo biogenesis pathway as a source of this substrate. Taken together, our results imply that the Golgi systems of GDP-fucose transport discriminate between substrate pools obtained from different metabolic pathways, which suggests a functional connection between nucleotide sugar transporters and nucleotide sugar synthases.
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Affiliation(s)
- Edyta Skurska
- Faculty of Biotechnology, University of Wroclaw, Poland, Wrocław, Poland
| | - Bożena Szulc
- Faculty of Biotechnology, University of Wroclaw, Poland, Wrocław, Poland
| | | | - Maciej Wiktor
- Faculty of Biotechnology, University of Wroclaw, Poland, Wrocław, Poland
| | - Wojciech Wiertelak
- Faculty of Biotechnology, University of Wroclaw, Poland, Wrocław, Poland
| | | | - Mariusz Olczak
- Faculty of Biotechnology, University of Wroclaw, Poland, Wrocław, Poland.
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222
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Kong WL, Machida RJ. Development of transcriptomics-based growth rate indices in two model eukaryotes and relevance to metatranscriptomic datasets. Mol Ecol Resour 2022; 22:2627-2639. [PMID: 35620942 PMCID: PMC9545445 DOI: 10.1111/1755-0998.13652] [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: 10/24/2021] [Accepted: 05/17/2022] [Indexed: 11/29/2022]
Abstract
Growth rate estimation is important to understand the flow of energy and nutrient elements in an ecosystem, but it has remained challenging, especially on microscopic organisms. In this study, we propose four growth rate indices that use mRNA abundance ratios between nuclear and mitochondrial genes: (1) total nuclear and mitochondrial mRNA ratio (Nuc:Mito‐TmRNA); (2) nuclear and mitochondrial ribosomal protein mRNA ratio (Nuc:Mito‐RPmRNA); (3) gene ontology (GO) terms and total mitochondrial mRNA ratios; and (4) nuclear and mitochondrial specific gene mRNA ratio. We examine these proposed ratios using RNA‐Seq datasets of Daphnia magna, and Saccharomyces cerevisiae retrieved from the NCBI Short Read Archive. The results showed that both Nuc:Mito‐TmRNA and Nuc:Mito‐RPmRNA ratio indices showed significant correlations with the growth rate for both species. A large number of GO terms mRNA ratios showed significant correlations with the growth rate of S. cerevisiae. Lastly, we identified mRNA ratios of several specific nuclear and mitochondrial gene pairs that showed significant correlations. We foresee future implications for the proposed mRNA ratios used in metatranscriptome analyses to estimate the growth rate of communities and species.
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Affiliation(s)
- Wye-Lup Kong
- Biodiversity Program, International Graduate Program, Academia Sinica and National Taiwan Normal University, Taipei, Taiwan.,Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
| | - Ryuji J Machida
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
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223
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Fischer F, Benner C, Goyala A, Grigolon G, Vitiello D, Wu J, Zarse K, Ewald CY, Ristow M. Ingestion of single guide RNAs induces gene overexpression and extends lifespan in Caenorhabditis elegans via CRISPR activation. J Biol Chem 2022; 298:102085. [PMID: 35636511 PMCID: PMC9243178 DOI: 10.1016/j.jbc.2022.102085] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 05/17/2022] [Accepted: 05/18/2022] [Indexed: 11/21/2022] Open
Abstract
Inhibition of gene expression in Caenorhabditis elegans, a versatile model organism for studying the genetics of development and aging, is achievable by feeding nematodes with bacteria expressing specific dsRNAs. Overexpression of hypoxia-inducible factor 1 (hif-1) or heat-shock factor 1 (hsf-1) by conventional transgenesis has previously been shown to promote nematodal longevity. However, it is unclear whether other methods of gene overexpression are feasible, particularly with the advent of CRISPR-based techniques. Here, we show that feeding C. elegans engineered to stably express a Cas9-derived synthetic transcription factor with bacteria expressing promoter-specific single guide RNAs (sgRNAs) also allows activation of gene expression. We demonstrate that CRISPR activation via ingested sgRNAs specific for the respective promoter regions of hif-1 or hsf-1 increases gene expression and extends lifespan of C. elegans. Furthermore, and as an in silico resource for future studies aiming to use CRISPR activation in C. elegans, we provide predicted promoter-specific sgRNA target sequences for >13,000 C. elegans genes with experimentally defined transcription start sites. We anticipate that the approach and components described herein will help to facilitate genome-wide gene overexpression studies, for example, to identify modulators of aging or other phenotypes of interest, by enabling induction of transcription by feeding of sgRNA-expressing bacteria to nematodes.
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Affiliation(s)
- Fabian Fischer
- Energy Metabolism Laboratory, Department of Health Sciences and Technology, Institute of Translational Medicine, Swiss Federal Institute of Technology (ETH) Zurich, Schwerzenbach, Switzerland.
| | - Christoph Benner
- Energy Metabolism Laboratory, Department of Health Sciences and Technology, Institute of Translational Medicine, Swiss Federal Institute of Technology (ETH) Zurich, Schwerzenbach, Switzerland; Science and Policy Program, Life Science Zurich Graduate School, Zurich, Switzerland
| | - Anita Goyala
- Extracellular Matrix Regeneration Laboratory, Department of Health Sciences and Technology, Institute of Translational Medicine, Swiss Federal Institute of Technology (ETH) Zurich, Schwerzenbach, Switzerland
| | - Giovanna Grigolon
- Energy Metabolism Laboratory, Department of Health Sciences and Technology, Institute of Translational Medicine, Swiss Federal Institute of Technology (ETH) Zurich, Schwerzenbach, Switzerland
| | - Davide Vitiello
- Energy Metabolism Laboratory, Department of Health Sciences and Technology, Institute of Translational Medicine, Swiss Federal Institute of Technology (ETH) Zurich, Schwerzenbach, Switzerland
| | - JiaYee Wu
- Energy Metabolism Laboratory, Department of Health Sciences and Technology, Institute of Translational Medicine, Swiss Federal Institute of Technology (ETH) Zurich, Schwerzenbach, Switzerland
| | - Kim Zarse
- Energy Metabolism Laboratory, Department of Health Sciences and Technology, Institute of Translational Medicine, Swiss Federal Institute of Technology (ETH) Zurich, Schwerzenbach, Switzerland; Charité - Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Experimental Endocrinology and Diabetology, Berlin, Germany
| | - Collin Y Ewald
- Extracellular Matrix Regeneration Laboratory, Department of Health Sciences and Technology, Institute of Translational Medicine, Swiss Federal Institute of Technology (ETH) Zurich, Schwerzenbach, Switzerland
| | - Michael Ristow
- Energy Metabolism Laboratory, Department of Health Sciences and Technology, Institute of Translational Medicine, Swiss Federal Institute of Technology (ETH) Zurich, Schwerzenbach, Switzerland; Charité - Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Experimental Endocrinology and Diabetology, Berlin, Germany.
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224
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Lopes-Junior EH, Bertevello CR, de Oliveira Silveira G, Guedes CB, Rodrigues GD, Ribeiro VS, Amaral MS, Kanamura CT, Pinto PLS, Krüger RF, Verjovski-Almeida S, Oliveira KC. Human tumor necrosis factor alpha affects the egg-laying dynamics and glucose metabolism of Schistosoma mansoni adult worms in vitro. Parasit Vectors 2022; 15:176. [PMID: 35610661 PMCID: PMC9128126 DOI: 10.1186/s13071-022-05278-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 04/08/2022] [Indexed: 11/10/2022] Open
Abstract
Several studies have described the effects of human tumor necrosis factor alpha (hTNF-α) on Schistosoma mansoni. hTNF-α affects the worm’s development, metabolism, egg-laying, gene expression and protein phosphorylation. The available data on the influence of hTNF-α on egg-laying in S. mansoni are controversial, but understanding the mechanism of egg-laying regulation in this species is essential in combating schistosomiasis. We characterized the effects of in vitro treatment of S. mansoni adult worms with different doses of hTNF-α (5, 20 and 40 ng/ml) for 5 days. We explored the effects on egg-laying rate, glucose levels, ATP metabolism, and messenger RNA (mRNA) expression levels of lactate dehydrogenase, glucose transporters and the parasite gene which acts as an hTNF-α receptor, SmTNFR. hTNF-α influenced egg-laying in a time- and dose-dependent manner: at a dose of 40 ng/ml, egg-laying increased on day 2 and decreased on days 3 and 4; at 20 ng/ml, egg-laying decreased on day 3; while at 5 ng/ml, egg-laying decreased on day 4. The total number of eggs produced was not affected by the different treatments, but the egg-laying dynamics were: the median egg-laying time decreased significantly with treatment, and egg developmental stages and size were also affected. At 5 and 20 ng/ml hTNF-α, lactate production diminished on day 3 up to day 5, while glucose uptake increased on day 5. At 40 ng/ml, glucose uptake diminished on day 1 up to day 3, while ATP accumulation was detected on day 5. No significant changes in mRNA expression were detected in any of the treatments. We found that crosstalk involving hTNF-α and parasite signaling plays a role in the fine-scale regulation of the worm’s metabolism and physiology, and points to new strategies for disease control.
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Affiliation(s)
- Ednilson Hilário Lopes-Junior
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Claudio Romero Bertevello
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Gilbert de Oliveira Silveira
- Laboratório de Parasitologia, Instituto Butantan, São Paulo, Brazil.,Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Camila Banca Guedes
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Gratchela Dutra Rodrigues
- Departamento de Microbiologia e Parasitologia, Instituto de Biologia, Universidade Federal de Pelotas, Pelotas, Brazil
| | - Viviane Sousa Ribeiro
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | | | | | | | - Rodrigo Ferreira Krüger
- Departamento de Microbiologia e Parasitologia, Instituto de Biologia, Universidade Federal de Pelotas, Pelotas, Brazil
| | - Sergio Verjovski-Almeida
- Laboratório de Parasitologia, Instituto Butantan, São Paulo, Brazil.,Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Katia Cristina Oliveira
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil.
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225
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Jiang LY, Sun HZ, Guan RW, Shi F, Zhao FQ, Liu JX. Formation of Blood Neutrophil Extracellular Traps Increases the Mastitis Risk of Dairy Cows During the Transition Period. Front Immunol 2022; 13:880578. [PMID: 35572521 PMCID: PMC9092530 DOI: 10.3389/fimmu.2022.880578] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 03/31/2022] [Indexed: 11/30/2022] Open
Abstract
The current study was conducted to analyze the functions of blood neutrophils in transition cows and their association with postpartum mastitis risk as indicated by somatic cell counts (SCCs) in milk. Seventy-six healthy Holstein dairy cows were monitored from Week 4 prepartum to Week 4 postpartum. Five dairy cows with low SCCs (38 ± 6.0 × 103/mL) and five with high SCCs (3,753 ± 570.0 × 103/mL) were selected based on milk SCCs during the first three weeks of lactation. At Week 1 pre- and postpartum, serum samples were obtained from each cow to measure neutrophil extracellular trap (NET)-related variables, and blood neutrophils were collected for transcriptome analysis by RNA sequencing. The serum concentration of NETs was significantly higher (P < 0.05) in cows with high SCCs than in cows with low SCCs (36.5 ± 2.92 vs. 18.4 ± 1.73 ng/mL). The transcriptomic analysis revealed that the transcriptome differences in neutrophils between high- and low-SCC cows were mainly in cell cycle-related pathways (42.6%), including the cell cycle, DNA damage, and chromosomal conformation, at Week 1 prepartum. The hub genes of these pathways were mainly involved in both the cell cycle and NETosis. These results indicated that the formation of NETs in the blood of transition dairy cows was different between cows with low and high SCCs, which may be used as a potential indicator for the prognosis of postpartum mastitis risk and management strategies of perinatal dairy cows.
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Affiliation(s)
- Lu-Yi Jiang
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Hui-Zeng Sun
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Ruo-Wei Guan
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Fushan Shi
- Department of Veterinary Science, College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Feng-Qi Zhao
- Department of Animal & Veterinary Sciences, University of Vermont, Burlington, MA, United States
| | - Jian-Xin Liu
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou, China
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226
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Yang J, Li D, Wang J, Zhang R, Li J. Design, optimization, and application of multiplex rRT-PCR in the detection of respiratory viruses. Crit Rev Clin Lab Sci 2022:1-18. [PMID: 35559711 DOI: 10.1080/10408363.2022.2072467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Viral respiratory infections are common and serious diseases. Because there is no effective treatment method or vaccine for respiratory tract infection, early diagnosis is vital to identify the pathogen so as to determine the infectivity of the patient and to quickly take measures to curb the spread of the virus, if warranted, to avoid serious public health problems. Real-time reverse transcriptase PCR (rRT-PCR), which has high sensitivity and specificity, is the best approach for early diagnosis. Among rRT-PCR methods, multiplex rRT-PCR can resolve issues arising from various types of viruses, high mutation frequency, coinfection, and low concentrations of virus. However, the design, optimization, and validation of multiplex rRT-PCR are more complicated than singleplex rRT-PCR, and comprehensive research on multiplex rRT-PCR methodology is lacking. This review summarizes recent progress in multiplex rRT-PCR methodology, outlines the principles of design, optimization and validation, and describes a scheme to help diagnostic companies to design and optimize their multiplex rRT-PCR detection panel and to assist laboratory staff to solve problems in their daily work. In addition, the analytical validity, clinical validity and clinical utility of multiplex rRT-PCR in viral respiratory tract infection diagnosis are assessed to provide theoretical guidance and useful information for physicians to understand the test results.
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Affiliation(s)
- Jing Yang
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/ National Center of Gerontology, P.R. China.,Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, P.R. China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, P.R. China
| | - Dandan Li
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/ National Center of Gerontology, P.R. China.,Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, P.R. China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, P.R. China
| | - Jie Wang
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/ National Center of Gerontology, P.R. China.,Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, P.R. China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, P.R. China
| | - Rui Zhang
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/ National Center of Gerontology, P.R. China.,Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, P.R. China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, P.R. China
| | - Jinming Li
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/ National Center of Gerontology, P.R. China.,Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, P.R. China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, P.R. China
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227
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Serra I, Stravs A, Osório C, Oyaga MR, Schonewille M, Tudorache C, Badura A. Tsc1 Haploinsufficiency Leads to Pax2 Dysregulation in the Developing Murine Cerebellum. Front Mol Neurosci 2022; 15:831687. [PMID: 35645731 PMCID: PMC9137405 DOI: 10.3389/fnmol.2022.831687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 04/04/2022] [Indexed: 12/03/2022] Open
Abstract
Tuberous sclerosis complex 1 (TSC1) is a tumor suppressor that promotes the inhibition of mechanistic target of rapamycin (mTOR) pathway, and mutations in TSC1 lead to a rare complex disorder of the same name. Despite phenotype heterogeneity, up to 50% of TSC patients present with autism spectrum disorder (ASD). Consequently, TSC models are often used to probe molecular and behavioral mechanisms of ASD development. Amongst the different brain areas proposed to play a role in the development of ASD, the cerebellum is commonly reported to be altered, and cerebellar-specific deletion of Tsc1 in mice is sufficient to induce ASD-like phenotypes. However, despite these functional changes, whether Tsc1 haploinsufficiency affects cerebellar development is still largely unknown. Given that the mTOR pathway is a master regulator of cell replication and migration, we hypothesized that dysregulation of this pathway would also disrupt the development of cell populations during critical periods of cerebellar development. Here, we used a mouse model of TSC to investigate gene and protein expression during embryonic and early postnatal periods of cerebellar development. We found that, at E18 and P7, mRNA levels of the cerebellar inhibitory interneuron marker paired box gene 2 (Pax2) were dysregulated. This dysregulation was accompanied by changes in the expression of mTOR pathway-related genes and downstream phosphorylation of S6. Differential gene correlation analysis revealed dynamic changes in correlated gene pairs across development, with an overall loss of correlation between mTOR- and cerebellar-related genes in Tsc1 mutants compared to controls. We corroborated the genetic findings by characterizing the mTOR pathway and cerebellar development on protein and cellular levels with Western blot and immunohistochemistry. We found that Pax2-expressing cells were largely unchanged at E18 and P1, while at P7, their number was increased and maturation into parvalbumin-expressing cells delayed. Our findings indicate that, in mice, Tsc1 haploinsufficiency leads to altered cerebellar development and that cerebellar interneuron precursors are particularly susceptible to mTOR pathway dysregulation.
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Affiliation(s)
- Ines Serra
- Department of Neuroscience, Erasmus MC, Rotterdam, Netherlands
| | - Ana Stravs
- Department of Neuroscience, Erasmus MC, Rotterdam, Netherlands
- Institute of Biology Leiden, Leiden University, Leiden, Netherlands
| | - Catarina Osório
- Department of Neuroscience, Erasmus MC, Rotterdam, Netherlands
| | - Maria Roa Oyaga
- Department of Neuroscience, Erasmus MC, Rotterdam, Netherlands
| | | | | | - Aleksandra Badura
- Department of Neuroscience, Erasmus MC, Rotterdam, Netherlands
- *Correspondence: Aleksandra Badura,
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228
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Savarese AM, Grigsby KB, Jensen BE, Borrego MB, Finn DA, Crabbe JC, Ozburn AR. Corticosterone Levels and Glucocorticoid Receptor Gene Expression in High Drinking in the Dark Mice and Their Heterogeneous Stock (HS/NPT) Founder Line. Front Behav Neurosci 2022; 16:821859. [PMID: 35645743 PMCID: PMC9135139 DOI: 10.3389/fnbeh.2022.821859] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 03/28/2022] [Indexed: 12/02/2022] Open
Abstract
The High Drinking in the Dark (HDID-1) line of mice has been selectively bred for achieving high blood alcohol levels (BALs) in the Drinking in the Dark task, a model of binge-like drinking. Recently, we determined that glucocorticoid receptor (GR) antagonism with either mifepristone or CORT113176 (a selective GR antagonist) reduced binge-like ethanol intake in the HDID-1 mice, but not in their founder line, HS/NPT. Here, we examined whether the selection process may have altered glucocorticoid functioning by measuring (1) plasma corticosterone levels and (2) expression of the genes encoding GR (Nr3c1) and two of its chaperone proteins FKBP51 and FKBP52 (Fkbp5 and Fkbp4) in the brains (nucleus accumbens, NAc) of HDID-1 and HS/NPT mice. We observed no genotype differences in baseline circulating corticosterone levels. However, HDID-1 mice exhibited a greater stimulated peak corticosterone response to an IP injection (of either ethanol or saline) relative to their founder line. We further observed reduced basal expression of Fkbp4 and Nr3c1 in the NAc of HDID-1 mice relative to HS/NPT mice. Finally, HDID-1 mice exhibited reduced Fkbp5 expression in the NAc relative to HS/NPT mice following an injection of 2 g/kg ethanol. Together, these data suggest that selective breeding for high BALs may have altered stress signaling in the HDID-1 mice, which may contribute to the observed selective efficacy of GR antagonism in reducing binge-like ethanol intake in HDID-1, but not HS/NPT mice. These data have important implications for the role that stress signaling plays in the genetic risk for binge drinking.
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Affiliation(s)
- Antonia M. Savarese
- Portland Alcohol Research Center, Department of Behavioral Neuroscience, Oregon Health & Science University, Portland, OR, United States
- *Correspondence: Antonia M. Savarese,
| | - Kolter B. Grigsby
- Portland Alcohol Research Center, Department of Behavioral Neuroscience, Oregon Health & Science University, Portland, OR, United States
| | - Bryan E. Jensen
- Portland Alcohol Research Center, Department of Behavioral Neuroscience, Oregon Health & Science University, Portland, OR, United States
- VA Portland Health Care System, Portland, OR, United States
| | - Marissa B. Borrego
- Portland Alcohol Research Center, Department of Behavioral Neuroscience, Oregon Health & Science University, Portland, OR, United States
- VA Portland Health Care System, Portland, OR, United States
| | - Deborah A. Finn
- Portland Alcohol Research Center, Department of Behavioral Neuroscience, Oregon Health & Science University, Portland, OR, United States
- VA Portland Health Care System, Portland, OR, United States
| | - John C. Crabbe
- Portland Alcohol Research Center, Department of Behavioral Neuroscience, Oregon Health & Science University, Portland, OR, United States
- VA Portland Health Care System, Portland, OR, United States
| | - Angela R. Ozburn
- Portland Alcohol Research Center, Department of Behavioral Neuroscience, Oregon Health & Science University, Portland, OR, United States
- VA Portland Health Care System, Portland, OR, United States
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229
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Transcriptomes of testis and pituitary from male Nile tilapia (O. niloticus L.) in the context of social status. PLoS One 2022; 17:e0268140. [PMID: 35544481 PMCID: PMC9094562 DOI: 10.1371/journal.pone.0268140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 04/22/2022] [Indexed: 11/19/2022] Open
Abstract
African cichlids are well established models for studying social hierarchies in teleosts and elucidating the effects social dominance has on gene expression. Ascension in the social hierarchy has been found to increase plasma levels of steroid hormones, follicle stimulating hormone (Fsh) and luteinizing hormone (Lh) as well as gonadosomatic index (GSI). Furthermore, the expression of genes related to gonadotropins and steroidogenesis and signaling along the brain-pituitary-gonad axis (BPG-axis) is affected by changes of an animal’s social status. In this study, we use RNA-sequencing to obtain an in-depth look at the transcriptomes of testes and pituitaries from dominant and subordinate male Nile tilapia living in long-term stable social hierarchies. This allows us to draw conclusions about factors along the brain-pituitary-gonad axis that are involved in maintaining dominance over weeks or even months. We identify a number of genes that are differentially regulated between dominant and subordinate males and show that in high-ranking fish this subset of genes is generally upregulated. Genes differentially expressed between the two social groups comprise growth factors, related binding proteins and receptors, components of Wnt-, Tgfβ- and retinoic acid-signaling pathway, gonadotropin signaling and steroidogenesis pathways. The latter is backed up by elevated levels of 11-ketotestosterone, testosterone and estradiol in dominant males. Luteinizing hormone (Lh) is found in higher concentration in the plasma of long-term dominant males than in subordinate animals. Our results both strengthen the existing models and propose new candidates for functional studies to expand our understanding of social phenomena in teleost fish.
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230
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Graça AL, Gómez-Florit M, Osório H, Rodrigues MT, Domingues RMA, Reis RL, Gomes ME. Controlling the fate of regenerative cells with engineered platelet-derived extracellular vesicles. NANOSCALE 2022; 14:6543-6556. [PMID: 35420605 DOI: 10.1039/d1nr08108j] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Extracellular vesicles (EVs) have emerged as cell-free nanotherapeutic agents for the potential treatment of multiple diseases and for tissue engineering and regenerative medicine strategies. Nevertheless, the field has typically relied on EVs derived from stem cells, the production of which in high quantities and high reproducibility is still under debate. Platelet-derived EVs were produced by a freeze-thaw method of platelet concentrates, a highly available clinical waste material. The aim of this study was to produce and thoroughly characterize platelet-derived EVs and understand their effects in adipose-tissue derived stem cells (hASCs), endothelial cells (HUVECs) and macrophages. Two different EV populations were obtained after differential centrifugation, namely small EVs (sEVs) and medium EVs (mEVs), which showed different size distributions and unique proteomic signatures. EV interaction with hASCs resulted in the modulation of the gene expression of markers related to their commitment toward different lineages. Moreover, mEVs showed higher angiogenic potential than sEVs, in a tube formation assay with HUVECs. Also, the EVs were able to modulate macrophage polarization. Altogether, these results suggest that platelet-derived EVs are promising candidates to be used as biochemical signals or therapeutic tools in tissue engineering and regenerative medicine approaches.
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Affiliation(s)
- Ana L Graça
- 3B's Research Group, I3Bs - Research Institute on Biomaterials, Biodegradables and Biomimetics, University of Minho, Headquarters of the European Institute of Excellence on Tissue Engineering and Regenerative Medicine, AvePark, Parque de Ciência e Tecnologia, Zona Industrial da Gandra, 4805-017 Barco, Guimarães, Portugal.
- ICVS/3B's-PT Government Associate Laboratory, Braga, Guimarães, Portugal
| | - Manuel Gómez-Florit
- 3B's Research Group, I3Bs - Research Institute on Biomaterials, Biodegradables and Biomimetics, University of Minho, Headquarters of the European Institute of Excellence on Tissue Engineering and Regenerative Medicine, AvePark, Parque de Ciência e Tecnologia, Zona Industrial da Gandra, 4805-017 Barco, Guimarães, Portugal.
- ICVS/3B's-PT Government Associate Laboratory, Braga, Guimarães, Portugal
| | - Hugo Osório
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal
| | - Márcia T Rodrigues
- 3B's Research Group, I3Bs - Research Institute on Biomaterials, Biodegradables and Biomimetics, University of Minho, Headquarters of the European Institute of Excellence on Tissue Engineering and Regenerative Medicine, AvePark, Parque de Ciência e Tecnologia, Zona Industrial da Gandra, 4805-017 Barco, Guimarães, Portugal.
- ICVS/3B's-PT Government Associate Laboratory, Braga, Guimarães, Portugal
| | - Rui M A Domingues
- 3B's Research Group, I3Bs - Research Institute on Biomaterials, Biodegradables and Biomimetics, University of Minho, Headquarters of the European Institute of Excellence on Tissue Engineering and Regenerative Medicine, AvePark, Parque de Ciência e Tecnologia, Zona Industrial da Gandra, 4805-017 Barco, Guimarães, Portugal.
- ICVS/3B's-PT Government Associate Laboratory, Braga, Guimarães, Portugal
| | - Rui L Reis
- 3B's Research Group, I3Bs - Research Institute on Biomaterials, Biodegradables and Biomimetics, University of Minho, Headquarters of the European Institute of Excellence on Tissue Engineering and Regenerative Medicine, AvePark, Parque de Ciência e Tecnologia, Zona Industrial da Gandra, 4805-017 Barco, Guimarães, Portugal.
- ICVS/3B's-PT Government Associate Laboratory, Braga, Guimarães, Portugal
| | - Manuela E Gomes
- 3B's Research Group, I3Bs - Research Institute on Biomaterials, Biodegradables and Biomimetics, University of Minho, Headquarters of the European Institute of Excellence on Tissue Engineering and Regenerative Medicine, AvePark, Parque de Ciência e Tecnologia, Zona Industrial da Gandra, 4805-017 Barco, Guimarães, Portugal.
- ICVS/3B's-PT Government Associate Laboratory, Braga, Guimarães, Portugal
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231
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A “notch” in the cellular communication network in response to anoxia by wood frog (Rana sylvatica). Cell Signal 2022; 93:110305. [DOI: 10.1016/j.cellsig.2022.110305] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 03/06/2022] [Accepted: 03/07/2022] [Indexed: 12/12/2022]
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232
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Ahmed W, Bivins A, Metcalfe S, Smith WJM, Verbyla ME, Symonds EM, Simpson SL. Evaluation of process limit of detection and quantification variation of SARS-CoV-2 RT-qPCR and RT-dPCR assays for wastewater surveillance. WATER RESEARCH 2022; 213:118132. [PMID: 35152136 PMCID: PMC8812148 DOI: 10.1016/j.watres.2022.118132] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 01/21/2022] [Accepted: 01/29/2022] [Indexed: 05/21/2023]
Abstract
Effective wastewater surveillance of SARS-CoV-2 RNA requires the rigorous characterization of the limit of detection resulting from the entire sampling process - the process limit of detection (PLOD). Yet to date, no studies have gone beyond quantifying the assay limit of detection (ALOD) for RT-qPCR or RT-dPCR assays. While the ALOD is the lowest number of gene copies (GC) associated with a 95% probability of detection in a single PCR reaction, the PLOD represents the sensitivity of the method after considering the efficiency of all processing steps (e.g., sample handling, concentration, nucleic acid extraction, and PCR assays) to determine the number of GC in the wastewater sample matrix with a specific probability of detection. The primary objective of this study was to estimate the PLOD resulting from the combination of primary concentration and extraction with six SARS-CoV-2 assays: five RT-qPCR assays (US CDC N1 and N2, China CDC N and ORF1ab (CCDC N and CCDC ORF1ab), and E_Sarbeco RT-qPCR, and one RT-dPCR assay (US CDC N1 RT-dPCR) using two models (exponential survival and cumulative Gaussian). An adsorption extraction (AE) concentration method (i.e., virus adsorption on membrane and the RNA extraction from the membrane) was used to concentrate gamma-irradiated SARS-CoV-2 seeded into 36 wastewater samples. Overall, the US CDC N1 RT-dPCR and RT-qPCR assays had the lowest ALODs (< 10 GC/reaction) and PLODs (<3,954 GC/50 mL; 95% probability of detection) regardless of the seeding level and model used. Nevertheless, consistent amplification and detection rates decreased when seeding levels were < 2.32 × 103 GC/50 mL even for US CDC N1 RT-qPCR and RT-dPCR assays. Consequently, when SARS-CoV-2 RNA concentrations are expected to be low, it may be necessary to improve the positive detection rates of wastewater surveillance by analyzing additional field and RT-PCR replicates. To the best of our knowledge, this is the first study to assess the SARS-CoV-2 PLOD for wastewater and provides important insights on the analytical limitations for trace detection of SARS-CoV-2 RNA in wastewater.
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Affiliation(s)
- Warish Ahmed
- CSIRO Land and Water, Ecosciences Precinct, 41 Boggo Road, Dutton Park, QLD 4102, Australia.
| | - Aaron Bivins
- Department of Civil & Environmental Engineering & Earth Science, University of Notre Dame, 156 Fitzpatrick Hall, Notre Dame, IN, 46556, USA
| | - Suzanne Metcalfe
- CSIRO Land and Water, Ecosciences Precinct, 41 Boggo Road, Dutton Park, QLD 4102, Australia
| | - Wendy J M Smith
- CSIRO Land and Water, Ecosciences Precinct, 41 Boggo Road, Dutton Park, QLD 4102, Australia
| | - Matthew E Verbyla
- Department of Civil, Construction and Environmental Engineering, San Diego State University, San Diego, CA, USA
| | - Erin M Symonds
- Department of Anthropology, Southern Methodist University, Dallas, Texas, USA
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233
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Green TJ, Yin Walker C, Leduc S, Michalchuk T, McAllister J, Roth M, Janes JK, Krogh ET. Spatial and Temporal Pattern of Norovirus Dispersal in an Oyster Growing Region in the Northeast Pacific. Viruses 2022; 14:v14040762. [PMID: 35458492 PMCID: PMC9024690 DOI: 10.3390/v14040762] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 03/30/2022] [Accepted: 04/02/2022] [Indexed: 02/01/2023] Open
Abstract
Contamination of Pacific oysters, Crassostrea gigas, by human norovirus (HuNoV) is a major constraint to sustainable shellfish farming in coastal waters of the Northeast Pacific. HuNoV is not a marine virus and must originate from a human source. A barrier to effective management is a paucity of data regarding HuNoV dispersal in the marine environment. The main objective of this study was to identify the spatial distribution and persistence of HuNoV in an active shellfish farming region in the Northeast Pacific. Market-size C. gigas were sequentially deployed for two-week intervals at 12 sites during the 2020 winter risk period from January to April. Detection of HuNoV quantification was performed by reverse transcription real-time PCR (RTqPCR) according to method ISO 15216-1:2017, with modifications. RTqPCR did not detect GI HuNoV. The estimated prevalence of GII HuNoV in oyster digestive tissue was 0.8 ± 0.2%. Spatiotemporal analysis revealed that contamination of oysters with GII HuNoV changed through time and space during the surveillance period. A single cluster of oysters contaminated with GII.2 HuNoV was detected in a small craft harbor on 23 April. There was no significant increase in the proportion of positive pools in the next nearest sampling station, indicating that HuNoV is likely to disperse less than 7 km from this non-point source of contamination. Results from this study indicate that HuNoV contamination of coastal waters from non-point sources, such as small craft harbors and urban settings, can pose a significant localised risk to shellfish farming operations in the region.
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Affiliation(s)
- Timothy J. Green
- Faculty of Science and Technology, Vancouver Island University, Nanaimo, BC V9R 5S5, Canada; (C.Y.W.); (S.L.); (T.M.); (J.M.); (J.K.J.); (E.T.K.)
- Correspondence:
| | - Chen Yin Walker
- Faculty of Science and Technology, Vancouver Island University, Nanaimo, BC V9R 5S5, Canada; (C.Y.W.); (S.L.); (T.M.); (J.M.); (J.K.J.); (E.T.K.)
| | - Sarah Leduc
- Faculty of Science and Technology, Vancouver Island University, Nanaimo, BC V9R 5S5, Canada; (C.Y.W.); (S.L.); (T.M.); (J.M.); (J.K.J.); (E.T.K.)
| | - Trevor Michalchuk
- Faculty of Science and Technology, Vancouver Island University, Nanaimo, BC V9R 5S5, Canada; (C.Y.W.); (S.L.); (T.M.); (J.M.); (J.K.J.); (E.T.K.)
| | - Joe McAllister
- Faculty of Science and Technology, Vancouver Island University, Nanaimo, BC V9R 5S5, Canada; (C.Y.W.); (S.L.); (T.M.); (J.M.); (J.K.J.); (E.T.K.)
| | - Myron Roth
- BC Ministry of Agriculture, Food & Fisheries, P.O. Box 9120, Victoria, BC V8W 9B4, Canada;
| | - Jasmine K. Janes
- Faculty of Science and Technology, Vancouver Island University, Nanaimo, BC V9R 5S5, Canada; (C.Y.W.); (S.L.); (T.M.); (J.M.); (J.K.J.); (E.T.K.)
- Department of Ecosystem Science and Management, University of Northern British Columbia, Prince George, BC V2N 4Z9, Canada
| | - Erik T. Krogh
- Faculty of Science and Technology, Vancouver Island University, Nanaimo, BC V9R 5S5, Canada; (C.Y.W.); (S.L.); (T.M.); (J.M.); (J.K.J.); (E.T.K.)
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234
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Pantaleón García J, Kulkarni VV, Reese TC, Wali S, Wase SJ, Zhang J, Singh R, Caetano MS, Kadara H, Moghaddam S, Johnson FM, Wang J, Wang Y, Evans S. OBIF: an omics-based interaction framework to reveal molecular drivers of synergy. NAR Genom Bioinform 2022; 4:lqac028. [PMID: 35387383 PMCID: PMC8982434 DOI: 10.1093/nargab/lqac028] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 02/28/2022] [Accepted: 03/10/2022] [Indexed: 01/08/2023] Open
Abstract
Bioactive molecule library screening may empirically identify effective combination therapies, but molecular mechanisms underlying favorable drug–drug interactions often remain unclear, precluding further rational design. In the absence of an accepted systems theory to interrogate synergistic responses, we introduce Omics-Based Interaction Framework (OBIF) to reveal molecular drivers of synergy through integration of statistical and biological interactions in synergistic biological responses. OBIF performs full factorial analysis of feature expression data from single versus dual exposures to identify molecular clusters that reveal synergy-mediating pathways, functions and regulators. As a practical demonstration, OBIF analyzed transcriptomic and proteomic data of a dyad of immunostimulatory molecules that induces synergistic protection against influenza A and revealed unanticipated NF-κB/AP-1 cooperation that is required for antiviral protection. To demonstrate generalizability, OBIF analyzed data from a diverse array of Omics platforms and experimental conditions, successfully identifying the molecular clusters driving their synergistic responses. Hence, unlike existing synergy quantification and prediction methods, OBIF is a phenotype-driven systems model that supports multiplatform interrogation of synergy mechanisms.
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Affiliation(s)
- Jezreel Pantaleón García
- Department of Pulmonary Medicine, University of Texas MD Anderson Cancer Center, HoustonTX 77030, USA
| | - Vikram V Kulkarni
- Department of Pulmonary Medicine, University of Texas MD Anderson Cancer Center, HoustonTX 77030, USA
- MD Anderson Cancer Center UT Health Graduate School of Biomedical Sciences, Houston, TX 77030, USA
| | - Tanner C Reese
- Department of Pulmonary Medicine, University of Texas MD Anderson Cancer Center, HoustonTX 77030, USA
- Rice University, Houston, TX 77005, USA
| | - Shradha Wali
- Department of Pulmonary Medicine, University of Texas MD Anderson Cancer Center, HoustonTX 77030, USA
- MD Anderson Cancer Center UT Health Graduate School of Biomedical Sciences, Houston, TX 77030, USA
| | - Saima J Wase
- Department of Pulmonary Medicine, University of Texas MD Anderson Cancer Center, HoustonTX 77030, USA
| | - Jiexin Zhang
- Department of Bioinformatics and Computational Biology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Ratnakar Singh
- Department of Thoracic, Head and Neck Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Department of Comparative Biosciences, University of Illinois at Urbana-Champaign, Urbana, IL 61802, USA
| | - Mauricio S Caetano
- Department of Pulmonary Medicine, University of Texas MD Anderson Cancer Center, HoustonTX 77030, USA
| | - Humam Kadara
- Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Seyed Javad Moghaddam
- Department of Pulmonary Medicine, University of Texas MD Anderson Cancer Center, HoustonTX 77030, USA
- MD Anderson Cancer Center UT Health Graduate School of Biomedical Sciences, Houston, TX 77030, USA
| | - Faye M Johnson
- Department of Thoracic, Head and Neck Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jing Wang
- Department of Bioinformatics and Computational Biology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yongxing Wang
- Department of Pulmonary Medicine, University of Texas MD Anderson Cancer Center, HoustonTX 77030, USA
| | - Scott E Evans
- Department of Pulmonary Medicine, University of Texas MD Anderson Cancer Center, HoustonTX 77030, USA
- MD Anderson Cancer Center UT Health Graduate School of Biomedical Sciences, Houston, TX 77030, USA
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235
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Chalmers RM, Katzer F, La Carbona S, Lalle M, Razakandrainibe R, Robertson LJ, Robinson G, Šoba B, Temesgen T, Mayer-Scholl A. A guide to standardise artificial contamination procedures with protozoan parasite oocysts or cysts during method evaluation, using Cryptosporidium and leafy greens as models. Food Control 2022. [DOI: 10.1016/j.foodcont.2021.108678] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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236
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Altered protein expression of membrane transporters in isolated cerebral microvessels and brain cortex of a rat Alzheimer's disease model. Neurobiol Dis 2022; 169:105741. [DOI: 10.1016/j.nbd.2022.105741] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 03/25/2022] [Accepted: 04/20/2022] [Indexed: 01/28/2023] Open
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237
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Donath S, Angerstein L, Gentemann L, Müller D, Seidler AE, Jesinghaus C, Bleich A, Heisterkamp A, Buettner M, Kalies S. Investigation of Colonic Regeneration via Precise Damage Application Using Femtosecond Laser-Based Nanosurgery. Cells 2022; 11:1143. [PMID: 35406708 PMCID: PMC8998079 DOI: 10.3390/cells11071143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 03/21/2022] [Accepted: 03/23/2022] [Indexed: 11/23/2022] Open
Abstract
Organoids represent the cellular composition of natural tissue. So called colonoids, organoids derived from colon tissue, are a good model for understanding regeneration. However, next to the cellular composition, the surrounding matrix, the cell-cell interactions, and environmental factors have to be considered. This requires new approaches for the manipulation of a colonoid. Of key interest is the precise application of localized damage and the following cellular reaction. We have established multiphoton imaging in combination with femtosecond laser-based cellular nanosurgery in colonoids to ablate single cells in the colonoids' crypts, the proliferative zones, and the differentiated zones. We observed that half of the colonoids recovered within six hours after manipulation. An invagination of the damaged cell and closing of the structure was observed. In about a third of the cases of targeted crypt damage, it caused a stop in crypt proliferation. In the majority of colonoids ablated in the crypt, the damage led to an increase in Wnt signalling, indicated via a fluorescent lentiviral biosensor. qRT-PCR analysis showed increased expression of various proliferation and Wnt-associated genes in response to damage. Our new model of probing colonoid regeneration paves the way to better understand organoid dynamics on a single cell level.
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Affiliation(s)
- Sören Donath
- Institute of Quantum Optics, Leibniz University Hannover, 30167 Hannover, Germany; (L.A.); (L.G.); (D.M.); (A.E.S.); (C.J.); (A.H.); (S.K.)
- Lower Saxony Center for Biomedical Engineering, Implant Research and Development (NIFE), 30625 Hannover, Germany; (A.B.); (M.B.)
| | - Leon Angerstein
- Institute of Quantum Optics, Leibniz University Hannover, 30167 Hannover, Germany; (L.A.); (L.G.); (D.M.); (A.E.S.); (C.J.); (A.H.); (S.K.)
- Lower Saxony Center for Biomedical Engineering, Implant Research and Development (NIFE), 30625 Hannover, Germany; (A.B.); (M.B.)
| | - Lara Gentemann
- Institute of Quantum Optics, Leibniz University Hannover, 30167 Hannover, Germany; (L.A.); (L.G.); (D.M.); (A.E.S.); (C.J.); (A.H.); (S.K.)
- Lower Saxony Center for Biomedical Engineering, Implant Research and Development (NIFE), 30625 Hannover, Germany; (A.B.); (M.B.)
| | - Dominik Müller
- Institute of Quantum Optics, Leibniz University Hannover, 30167 Hannover, Germany; (L.A.); (L.G.); (D.M.); (A.E.S.); (C.J.); (A.H.); (S.K.)
- Lower Saxony Center for Biomedical Engineering, Implant Research and Development (NIFE), 30625 Hannover, Germany; (A.B.); (M.B.)
- REBIRTH Research Center for Translational Regenerative Medicine, 30625 Hannover, Germany
| | - Anna E. Seidler
- Institute of Quantum Optics, Leibniz University Hannover, 30167 Hannover, Germany; (L.A.); (L.G.); (D.M.); (A.E.S.); (C.J.); (A.H.); (S.K.)
- Lower Saxony Center for Biomedical Engineering, Implant Research and Development (NIFE), 30625 Hannover, Germany; (A.B.); (M.B.)
| | - Christian Jesinghaus
- Institute of Quantum Optics, Leibniz University Hannover, 30167 Hannover, Germany; (L.A.); (L.G.); (D.M.); (A.E.S.); (C.J.); (A.H.); (S.K.)
- Lower Saxony Center for Biomedical Engineering, Implant Research and Development (NIFE), 30625 Hannover, Germany; (A.B.); (M.B.)
| | - André Bleich
- Lower Saxony Center for Biomedical Engineering, Implant Research and Development (NIFE), 30625 Hannover, Germany; (A.B.); (M.B.)
- REBIRTH Research Center for Translational Regenerative Medicine, 30625 Hannover, Germany
- Institute for Laboratory Animal Science, Hannover Medical School, 30625 Hannover, Germany
| | - Alexander Heisterkamp
- Institute of Quantum Optics, Leibniz University Hannover, 30167 Hannover, Germany; (L.A.); (L.G.); (D.M.); (A.E.S.); (C.J.); (A.H.); (S.K.)
- Lower Saxony Center for Biomedical Engineering, Implant Research and Development (NIFE), 30625 Hannover, Germany; (A.B.); (M.B.)
| | - Manuela Buettner
- Lower Saxony Center for Biomedical Engineering, Implant Research and Development (NIFE), 30625 Hannover, Germany; (A.B.); (M.B.)
- REBIRTH Research Center for Translational Regenerative Medicine, 30625 Hannover, Germany
- Institute for Laboratory Animal Science, Hannover Medical School, 30625 Hannover, Germany
| | - Stefan Kalies
- Institute of Quantum Optics, Leibniz University Hannover, 30167 Hannover, Germany; (L.A.); (L.G.); (D.M.); (A.E.S.); (C.J.); (A.H.); (S.K.)
- Lower Saxony Center for Biomedical Engineering, Implant Research and Development (NIFE), 30625 Hannover, Germany; (A.B.); (M.B.)
- REBIRTH Research Center for Translational Regenerative Medicine, 30625 Hannover, Germany
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238
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Therapeutic Effects of Platelet-Derived Extracellular Vesicles in a Bioengineered Tendon Disease Model. Int J Mol Sci 2022; 23:ijms23062948. [PMID: 35328370 PMCID: PMC8954460 DOI: 10.3390/ijms23062948] [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: 02/03/2022] [Revised: 03/03/2022] [Accepted: 03/07/2022] [Indexed: 11/17/2022] Open
Abstract
Tendon injuries represent over 30–50% of musculoskeletal disorders worldwide, yet the available therapies do not provide complete tendon repair/regeneration and full functionality restoring. Extracellular vesicles (EVs), membrane-enclosed nanoparticles, have emerged as the next breakthrough in tissue engineering and regenerative medicine to promote endogenous tissue regeneration. Here, we developed a 3D human in vitro model mimicking the signature of pathological tendon and used it to evaluate the influence that different platelet-derived EVs might have in tendon tissue repair mechanisms. For this, different EV populations isolated from platelets, small EVs (sEVs) and medium EVs (mEVs), were added to the culture media of human tendon-derived cells (hTDCs) cultured on isotropic nanofibrous scaffolds. The platelet-derived EVs increased the expression of tenogenic markers, promoted a healthy extracellular matrix (ECM) remodeling, and the synthesis of anti-inflammatory mediators. These findings suggest that platelet EVs provided relevant biochemical cues that potentiated a recovery of hTDCs phenotype from a diseased to a healthy state. Thus, this study opens new perspectives for the translation of platelet-derived EVs as therapeutics.
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239
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Quach ABV, Little SR, Shih SCC. Viral Generation, Packaging, and Transduction on a Digital Microfluidic Platform. Anal Chem 2022; 94:4039-4047. [PMID: 35192339 DOI: 10.1021/acs.analchem.1c05227] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Viral-based systems are a popular delivery method for introducing exogenous genetic material into mammalian cells. Unfortunately, the preparation of lentiviruses containing the machinery to edit the cells is labor-intensive, with steps requiring optimization and sensitive handling. To mitigate these challenges, we introduce the first microfluidic method that integrates lentiviral generation, packaging, and transduction. The new method allows the production of viral titers between 106 and 107 (similar to macroscale production) and high transduction efficiency for hard-to-transfect cell lines. We extend the technique for gene editing applications and show how this technique can be used to knock out and knock down estrogen receptor gene─a gene prominently responsible for 70% of breast cancer cases. This new technique is automated with multiplexing capabilities, which have the potential to standardize the methods for viral-based genome engineering.
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Affiliation(s)
- Angela B V Quach
- Department of Biology, Concordia University, 7141 Sherbrooke Street West, Montréal, Québec H4B 1R6, Canada.,Centre for Applied Synthetic Biology, Concordia University, 7141 Sherbrooke Street West, Montréal, Québec H4B 1R6, Canada
| | - Samuel R Little
- Centre for Applied Synthetic Biology, Concordia University, 7141 Sherbrooke Street West, Montréal, Québec H4B 1R6, Canada.,Department of Electrical and Computer Engineering, Concordia University, 1455 de Maisonneuve Blvd. West, Montréal, Québec H3G 1M8, Canada
| | - Steve C C Shih
- Department of Biology, Concordia University, 7141 Sherbrooke Street West, Montréal, Québec H4B 1R6, Canada.,Centre for Applied Synthetic Biology, Concordia University, 7141 Sherbrooke Street West, Montréal, Québec H4B 1R6, Canada.,Department of Electrical and Computer Engineering, Concordia University, 1455 de Maisonneuve Blvd. West, Montréal, Québec H3G 1M8, Canada
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240
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Yamkasem J, Tattiyapong P, Surachetpong W. Development and application of TaqMan probe-based quantitative PCR assays for the detection of tilapia parvovirus. JOURNAL OF FISH DISEASES 2022; 45:379-386. [PMID: 34871459 DOI: 10.1111/jfd.13565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 11/12/2021] [Accepted: 11/18/2021] [Indexed: 06/13/2023]
Abstract
Tilapia parvovirus (TiPV) is a novel parvovirus associated with high mortality in Nile tilapia and red hybrid tilapia, leading to severe economic losses for tilapia aquaculture. It is critical to develop a sensitive and accurate assay to detect TiPV in fish tissues. In this study, new TaqMan probe-based quantitative PCR (qPCR) assays targeting the non-structural (NS) and viral protein (VP) genes of TiPV were developed. The standard curves of the assays were 95.64%-98.96% over a wide linear range of 109 -101 copies of the corresponding standard DNA per reaction. The intra- and inter-assay coefficients of variation were in the ranges 0.54%-2.50% and 0.13%-1.17%, respectively, which suggests good repeatability and reproducibility. The detection limit of the TaqMan TiPV assays was 10 copies/µl. The application of the TaqMan qPCR assays to field samples revealed that they had comparable sensitivity to a previously developed SYBR Green qPCR, but more sensitive than the conventional PCR. No cross-reactivity of the TaqMan TiPV assays was found with the samples infected with other viruses and bacteria. Overall, the assays offered high sensitivity and specificity in the detection of low concentrations of TiPV DNA in infected tilapia samples. These new TaqMan qPCR assays could provide a valuable diagnostic tool for the reliable and specific detection of TiPV in experimental and field samples.
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Affiliation(s)
- Jidapa Yamkasem
- Department of Veterinary Microbiology and Immunology, Faculty of Veterinary Medicine, Kasetsart University, Bangkok, Thailand
| | - Puntanat Tattiyapong
- Department of Veterinary Microbiology and Immunology, Faculty of Veterinary Medicine, Kasetsart University, Bangkok, Thailand
| | - Win Surachetpong
- Department of Veterinary Microbiology and Immunology, Faculty of Veterinary Medicine, Kasetsart University, Bangkok, Thailand
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241
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Qi W, Wang S, Wang L, Xi X, Wu S, Li Y, Liao M, Lin J. A portable viable Salmonella detection device based on microfluidic chip and recombinase aided amplification. CHINESE CHEM LETT 2022. [DOI: 10.1016/j.cclet.2022.03.083] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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242
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Fan Y, Chen J, Liu M, Xu X, Zhang Y, Yue P, Cao W, Ji Z, Su X, Wen S, Kong J, Zhou G, Li B, Dong Y, Liu A, Bao F. Application of Droplet Digital PCR to Detection of Mycobacterium tuberculosis and Mycobacterium leprae Infections: A Narrative Review. Infect Drug Resist 2022; 15:1067-1076. [PMID: 35313727 PMCID: PMC8934166 DOI: 10.2147/idr.s349607] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 01/25/2022] [Indexed: 12/15/2022] Open
Abstract
Tuberculosis (TB) is a chronic infectious disease caused by Mycobacterium tuberculosis (MTB) infection, which has seriously endangered human health for many years. With the emergence of multidrug-resistant and extensively drug-resistant MTB, the prevention and treatment of TB has become a pressing need. Early diagnosis, drug resistance monitoring, and control of disease transmission are critical aspects in the prevention and treatment of TB. However, the currently available diagnostic technologies and drug sensitivity tests are time consuming, and thus, it is difficult to achieve the goal of early diagnosis and detection drug sensitivity, which results in limited control of disease transmission. The development of molecular testing technology has gradually achieved the vision of rapid and accurate diagnosis of TB. Droplet digital PCR (ddPCR) is an excellent nucleic acid quantification method with high sensitivity and no need for a calibration curve. Herein, we review the application of ddPCR in TB diagnosis and drug resistance detection and transmission monitoring.
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Affiliation(s)
- Yuxin Fan
- The Institute for Tropical Medicine, Faculty of Basic Medical Sciences, Kunming Medical University, Kunming, 650500, People’s Republic of China
- Department of Microbiology and Immunology, Kunming Medical University, Kunming, 650030, People’s Republic of China
- Yunnan Province Key Laboratory of Children’s Major Diseases Research, The Affiliated Children Hospital, Kunming Medical University, Kunming, 650030, People’s Republic of China
| | - Jingjing Chen
- The Institute for Tropical Medicine, Faculty of Basic Medical Sciences, Kunming Medical University, Kunming, 650500, People’s Republic of China
- Department of Biochemistry and Molecular Biology, Kunming Medical University, Kunming, 650030, People’s Republic of China
| | - Meixiao Liu
- The Institute for Tropical Medicine, Faculty of Basic Medical Sciences, Kunming Medical University, Kunming, 650500, People’s Republic of China
- Department of Microbiology and Immunology, Kunming Medical University, Kunming, 650030, People’s Republic of China
| | - Xin Xu
- The Institute for Tropical Medicine, Faculty of Basic Medical Sciences, Kunming Medical University, Kunming, 650500, People’s Republic of China
- Department of Microbiology and Immunology, Kunming Medical University, Kunming, 650030, People’s Republic of China
| | - Yu Zhang
- The Institute for Tropical Medicine, Faculty of Basic Medical Sciences, Kunming Medical University, Kunming, 650500, People’s Republic of China
- Department of Microbiology and Immunology, Kunming Medical University, Kunming, 650030, People’s Republic of China
- Yunnan Province Key Laboratory of Children’s Major Diseases Research, The Affiliated Children Hospital, Kunming Medical University, Kunming, 650030, People’s Republic of China
| | - Peng Yue
- The Institute for Tropical Medicine, Faculty of Basic Medical Sciences, Kunming Medical University, Kunming, 650500, People’s Republic of China
- Department of Biochemistry and Molecular Biology, Kunming Medical University, Kunming, 650030, People’s Republic of China
| | - Wenjing Cao
- The Institute for Tropical Medicine, Faculty of Basic Medical Sciences, Kunming Medical University, Kunming, 650500, People’s Republic of China
- Department of Biochemistry and Molecular Biology, Kunming Medical University, Kunming, 650030, People’s Republic of China
| | - Zhenhua Ji
- The Institute for Tropical Medicine, Faculty of Basic Medical Sciences, Kunming Medical University, Kunming, 650500, People’s Republic of China
- Department of Microbiology and Immunology, Kunming Medical University, Kunming, 650030, People’s Republic of China
| | - Xuan Su
- The Institute for Tropical Medicine, Faculty of Basic Medical Sciences, Kunming Medical University, Kunming, 650500, People’s Republic of China
- Department of Microbiology and Immunology, Kunming Medical University, Kunming, 650030, People’s Republic of China
| | - Shiyuan Wen
- The Institute for Tropical Medicine, Faculty of Basic Medical Sciences, Kunming Medical University, Kunming, 650500, People’s Republic of China
- Department of Microbiology and Immunology, Kunming Medical University, Kunming, 650030, People’s Republic of China
- Yunnan Province Key Laboratory of Children’s Major Diseases Research, The Affiliated Children Hospital, Kunming Medical University, Kunming, 650030, People’s Republic of China
| | - Jing Kong
- The Institute for Tropical Medicine, Faculty of Basic Medical Sciences, Kunming Medical University, Kunming, 650500, People’s Republic of China
- Department of Microbiology and Immunology, Kunming Medical University, Kunming, 650030, People’s Republic of China
| | - Guozhong Zhou
- The Institute for Tropical Medicine, Faculty of Basic Medical Sciences, Kunming Medical University, Kunming, 650500, People’s Republic of China
- Department of Microbiology and Immunology, Kunming Medical University, Kunming, 650030, People’s Republic of China
| | - Bingxue Li
- The Institute for Tropical Medicine, Faculty of Basic Medical Sciences, Kunming Medical University, Kunming, 650500, People’s Republic of China
- Department of Microbiology and Immunology, Kunming Medical University, Kunming, 650030, People’s Republic of China
| | - Yan Dong
- The Institute for Tropical Medicine, Faculty of Basic Medical Sciences, Kunming Medical University, Kunming, 650500, People’s Republic of China
- Department of Microbiology and Immunology, Kunming Medical University, Kunming, 650030, People’s Republic of China
| | - Aihua Liu
- The Institute for Tropical Medicine, Faculty of Basic Medical Sciences, Kunming Medical University, Kunming, 650500, People’s Republic of China
- Yunnan Province Key Laboratory of Children’s Major Diseases Research, The Affiliated Children Hospital, Kunming Medical University, Kunming, 650030, People’s Republic of China
- Department of Biochemistry and Molecular Biology, Kunming Medical University, Kunming, 650030, People’s Republic of China
- Correspondence: Aihua Liu; Fukai Bao, The Institute for Tropical Medicine, Faculty of Basic Medical Sciences, Kunming Medical University, Kunming, 650500, People’s Republic of China, Email ;
| | - Fukai Bao
- The Institute for Tropical Medicine, Faculty of Basic Medical Sciences, Kunming Medical University, Kunming, 650500, People’s Republic of China
- Department of Microbiology and Immunology, Kunming Medical University, Kunming, 650030, People’s Republic of China
- Yunnan Province Key Laboratory of Children’s Major Diseases Research, The Affiliated Children Hospital, Kunming Medical University, Kunming, 650030, People’s Republic of China
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243
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Regon P, Dey S, Rehman M, Pradhan AK, Chowra U, Tanti B, Talukdar AD, Panda SK. Transcriptomic Analysis Revealed Reactive Oxygen Species Scavenging Mechanisms Associated With Ferrous Iron Toxicity in Aromatic Keteki Joha Rice. FRONTIERS IN PLANT SCIENCE 2022; 13:798580. [PMID: 35283928 PMCID: PMC8913046 DOI: 10.3389/fpls.2022.798580] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 01/21/2022] [Indexed: 06/14/2023]
Abstract
Lowland acidic soils with water-logged regions are often affected by ferrous iron (Fe2+) toxicity, a major yield-limiting factor of rice production. Under severe Fe2+ toxicity, reactive oxygen species (ROS) are crucial, although molecular mechanisms and associated ROS homeostasis genes are still unknown. In this study, a comparative RNA-Seq based transcriptome analysis was conducted to understand the Fe2+ toxicity tolerance mechanism in aromatic Keteki Joha. About 69 Fe homeostasis related genes and their homologs were identified, where most of the genes were downregulated. Under severe Fe2+ toxicity, the biosynthesis of amino acids, RNA degradation, and glutathione metabolism were induced, whereas phenylpropanoid biosynthesis, photosynthesis, and fatty acid elongation were inhibited. The mitochondrial iron transporter (OsMIT), vacuolar iron transporter 2 (OsVIT2), ferritin (OsFER), vacuolar mugineic acid transporter (OsVMT), phenolic efflux zero1 (OsPEZ1), root meander curling (OsRMC), and nicotianamine synthase (OsNAS3) were upregulated in different tissues, suggesting the importance of Fe retention and sequestration for detoxification. However, several antioxidants, ROS scavenging genes and abiotic stress-responsive transcription factors indicate ROS homeostasis as one of the most important defense mechanisms under severe Fe2+ toxicity. Catalase (CAT), glutathione (GSH), ascorbate peroxidase (APX), monodehydroascorbate reductase (MDHAR), dehydroascorbate reductase (DHAR), and glutathione reductase (GR) were upregulated. Moreover, abiotic stress-responsive transcription factors, no apical meristem (NAC), myeloblastosis (MYB), auxin response factor (ARF), basic helix-loop-helix (bZIP), WRKY, and C2H2-zinc finger protein (C2H2-ZFP) were also upregulated. Accordingly, ROS homeostasis has been proposed as an essential defense mechanism under such conditions. Thus, the current study may enrich the understanding of Fe-homeostasis in rice.
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Affiliation(s)
- Preetom Regon
- Department of Life Science and Bioinformatics, Assam University, Silchar, India
- Plant Molecular Biology Laboratory, Department of Botany, Gauhati University, Guwahati, India
| | - Sangita Dey
- Department of Life Science and Bioinformatics, Assam University, Silchar, India
| | - Mehzabin Rehman
- Plant Molecular Biology Laboratory, Department of Botany, Gauhati University, Guwahati, India
| | - Amit Kumar Pradhan
- Plant Molecular Biology Laboratory, Department of Botany, Gauhati University, Guwahati, India
- Department of Botany, Pragjyotish College, Guwahati, India
| | | | - Bhaben Tanti
- Plant Molecular Biology Laboratory, Department of Botany, Gauhati University, Guwahati, India
| | - Anupam Das Talukdar
- Department of Life Science and Bioinformatics, Assam University, Silchar, India
| | - Sanjib Kumar Panda
- Department of Biochemistry, Central University of Rajasthan, Ajmer, India
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244
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Raven N, Klaassen M, Madsen T, Thomas F, Hamede R, Ujvari B. Transmissible cancer influences immune gene expression in an endangered marsupial, the Tasmanian devil (Sarcophilus harrisii). Mol Ecol 2022; 31:2293-2311. [PMID: 35202488 PMCID: PMC9310804 DOI: 10.1111/mec.16408] [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: 11/13/2020] [Accepted: 02/14/2022] [Indexed: 11/28/2022]
Abstract
Understanding the effects of wildlife diseases on populations requires insight into local environmental conditions, host defence mechanisms, host life‐history trade‐offs, pathogen population dynamics, and their interactions. The survival of Tasmanian devils (Sarcophilus harrisii) is challenged by a novel, fitness limiting pathogen, Tasmanian devil facial tumour disease (DFTD), a clonally transmissible, contagious cancer. In order to understand the devils’ capacity to respond to DFTD, it is crucial to gain information on factors influencing the devils’ immune system. By using RT‐qPCR, we investigated how DFTD infection in association with intrinsic (sex and age) and environmental (season) factors influences the expression of 10 immune genes in Tasmanian devil blood. Our study showed that the expression of immune genes (both innate and adaptive) differed across seasons, a pattern that was altered when infected with DFTD. The expression of immunogbulins IgE and IgM:IgG showed downregulation in colder months in DFTD infected animals. We also observed strong positive association between the expression of an innate immune gene, CD16, and DFTD infection. Our results demonstrate that sampling across seasons, age groups and environmental conditions are beneficial when deciphering the complex ecoevolutionary interactions of not only conventional host‐parasite systems, but also of host and diseases with high mortality rates, such as transmissible cancers.
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Affiliation(s)
- N Raven
- Deakin University, Geelong, School of Life and Environmental Sciences, Centre for Integrative Ecology, Waurn Ponds, Vic, 3216, Australia
| | - M Klaassen
- Deakin University, Geelong, School of Life and Environmental Sciences, Centre for Integrative Ecology, Waurn Ponds, Vic, 3216, Australia
| | - T Madsen
- Deakin University, Geelong, School of Life and Environmental Sciences, Centre for Integrative Ecology, Waurn Ponds, Vic, 3216, Australia
| | - F Thomas
- CREEC/CANECEV (CREES), Montpellier, France.,MIVEGEC, Université de Montpellier, CNRS, IRD, Montpellier, France
| | - R Hamede
- Deakin University, Geelong, School of Life and Environmental Sciences, Centre for Integrative Ecology, Waurn Ponds, Vic, 3216, Australia.,School of Natural Sciences, University of Tasmania, Private Bag 55, Hobart, Tasmania, 7001, Australia
| | - B Ujvari
- Deakin University, Geelong, School of Life and Environmental Sciences, Centre for Integrative Ecology, Waurn Ponds, Vic, 3216, Australia
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245
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Wade MJ, Lo Jacomo A, Armenise E, Brown MR, Bunce JT, Cameron GJ, Fang Z, Farkas K, Gilpin DF, Graham DW, Grimsley JMS, Hart A, Hoffmann T, Jackson KJ, Jones DL, Lilley CJ, McGrath JW, McKinley JM, McSparron C, Nejad BF, Morvan M, Quintela-Baluja M, Roberts AMI, Singer AC, Souque C, Speight VL, Sweetapple C, Walker D, Watts G, Weightman A, Kasprzyk-Hordern B. Understanding and managing uncertainty and variability for wastewater monitoring beyond the pandemic: Lessons learned from the United Kingdom national COVID-19 surveillance programmes. JOURNAL OF HAZARDOUS MATERIALS 2022; 424:127456. [PMID: 34655869 PMCID: PMC8498793 DOI: 10.1016/j.jhazmat.2021.127456] [Citation(s) in RCA: 81] [Impact Index Per Article: 40.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 09/23/2021] [Accepted: 10/05/2021] [Indexed: 05/18/2023]
Abstract
The COVID-19 pandemic has put unprecedented pressure on public health resources around the world. From adversity, opportunities have arisen to measure the state and dynamics of human disease at a scale not seen before. In the United Kingdom, the evidence that wastewater could be used to monitor the SARS-CoV-2 virus prompted the development of National wastewater surveillance programmes. The scale and pace of this work has proven to be unique in monitoring of virus dynamics at a national level, demonstrating the importance of wastewater-based epidemiology (WBE) for public health protection. Beyond COVID-19, it can provide additional value for monitoring and informing on a range of biological and chemical markers of human health. A discussion of measurement uncertainty associated with surveillance of wastewater, focusing on lessons-learned from the UK programmes monitoring COVID-19 is presented, showing that sources of uncertainty impacting measurement quality and interpretation of data for public health decision-making, are varied and complex. While some factors remain poorly understood, we present approaches taken by the UK programmes to manage and mitigate the more tractable sources of uncertainty. This work provides a platform to integrate uncertainty management into WBE activities as part of global One Health initiatives beyond the pandemic.
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Affiliation(s)
- Matthew J Wade
- UK Health Security Agency, Environmental Monitoring for Health Protection, Windsor House, Victoria Street, London SW1H 0TL, UK; Newcastle University, School of Engineering, Cassie Building, Newcastle-upon-Tyne NE1 7RU, UK.
| | - Anna Lo Jacomo
- UK Health Security Agency, Environmental Monitoring for Health Protection, Windsor House, Victoria Street, London SW1H 0TL, UK; Bristol University, Department of Engineering Mathematics, Bristol BS8 1TW, UK
| | - Elena Armenise
- Environment Agency, Research, Horizon House, Deanery Road, Bristol BS1 5AH, UK
| | - Mathew R Brown
- UK Health Security Agency, Environmental Monitoring for Health Protection, Windsor House, Victoria Street, London SW1H 0TL, UK; Newcastle University, School of Engineering, Cassie Building, Newcastle-upon-Tyne NE1 7RU, UK
| | - Joshua T Bunce
- UK Health Security Agency, Environmental Monitoring for Health Protection, Windsor House, Victoria Street, London SW1H 0TL, UK; Newcastle University, School of Engineering, Cassie Building, Newcastle-upon-Tyne NE1 7RU, UK; Department for Environment, Food and Rural Affairs, Seacole Building, 2 Marsham Street, London SW1P 4DF, UK
| | - Graeme J Cameron
- Scottish Environment Protection Agency, Strathallan House, Stirling FK9 4TZ, UK
| | - Zhou Fang
- Biomathematics and Statistics Scotland, James Clerk Maxwell Building, Peter Guthrie Tait Road, Edinburgh EH9 3FD, UK
| | - Kata Farkas
- Bangor University, School of Natural Sciences, Deiniol Road, Bangor LL57 2UW, UK
| | - Deidre F Gilpin
- Queen's University Belfast, School of Pharmacy, Lisburn Road, Belfast BT9 7BL, UK
| | - David W Graham
- Newcastle University, School of Engineering, Cassie Building, Newcastle-upon-Tyne NE1 7RU, UK
| | - Jasmine M S Grimsley
- UK Health Security Agency, Environmental Monitoring for Health Protection, Windsor House, Victoria Street, London SW1H 0TL, UK
| | - Alwyn Hart
- Environment Agency, Research, Horizon House, Deanery Road, Bristol BS1 5AH, UK
| | - Till Hoffmann
- UK Health Security Agency, Environmental Monitoring for Health Protection, Windsor House, Victoria Street, London SW1H 0TL, UK; Imperial College London, Department of Mathematics, London SW7 2AZ, UK
| | - Katherine J Jackson
- Environment Agency, Research, Horizon House, Deanery Road, Bristol BS1 5AH, UK
| | - David L Jones
- Bangor University, School of Natural Sciences, Deiniol Road, Bangor LL57 2UW, UK; The University of Western Australia, UWA School of Agriculture and Environment, Perth, WA 6009, Australia
| | - Chris J Lilley
- UK Health Security Agency, Environmental Monitoring for Health Protection, Windsor House, Victoria Street, London SW1H 0TL, UK
| | - John W McGrath
- Queen's University Belfast, School of Biological Sciences, Chlorine Gardens, Belfast BT9 5DL, UK
| | - Jennifer M McKinley
- Queen's University Belfast, School of Natural and Built Environment, Stranmills Road, Belfast BT9 5AG, UK
| | - Cormac McSparron
- Queen's University Belfast, School of Natural and Built Environment, Stranmills Road, Belfast BT9 5AG, UK
| | - Behnam F Nejad
- Queen's University Belfast, School of Natural and Built Environment, Stranmills Road, Belfast BT9 5AG, UK
| | - Mario Morvan
- UK Health Security Agency, Environmental Monitoring for Health Protection, Windsor House, Victoria Street, London SW1H 0TL, UK; University College London, Department of Physics and Astronomy, Gower Street, London WC1E 6BT, UK
| | - Marcos Quintela-Baluja
- Newcastle University, School of Engineering, Cassie Building, Newcastle-upon-Tyne NE1 7RU, UK
| | - Adrian M I Roberts
- Biomathematics and Statistics Scotland, James Clerk Maxwell Building, Peter Guthrie Tait Road, Edinburgh EH9 3FD, UK
| | - Andrew C Singer
- UK Centre for Ecology and Hydrology, Benson Lane, Wallingford OX10 8BB, UK
| | - Célia Souque
- UK Health Security Agency, Environmental Monitoring for Health Protection, Windsor House, Victoria Street, London SW1H 0TL, UK; University of Oxford, Department of Zoology, Mansfield Road, Oxford OX1 3SZ, UK
| | - Vanessa L Speight
- University of Sheffield, Department of Civil and Structural Engineering, Mappin Street, Sheffield S1 3JD, UK
| | - Chris Sweetapple
- UK Health Security Agency, Environmental Monitoring for Health Protection, Windsor House, Victoria Street, London SW1H 0TL, UK; University of Exeter, Centre for Water Systems, College of Engineering, Mathematics and Physical Sciences, Exeter EX4 4QF, UK
| | - David Walker
- Centre for Environment, Fisheries and Aquaculture Science, Barrack Road, Weymouth DT4 8UB, UK
| | - Glenn Watts
- Environment Agency, Research, Horizon House, Deanery Road, Bristol BS1 5AH, UK
| | - Andrew Weightman
- Cardiff University, Cardiff School of Biosciences, The Sir Martin Evans Building, Museum Avenue, Cardiff CF10 3AX, UK
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246
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In Vivo Evaluation of Mechanically Processed Stromal Vascular Fraction in a Chamber Vascularized by an Arteriovenous Shunt. Pharmaceutics 2022; 14:pharmaceutics14020417. [PMID: 35214149 PMCID: PMC8880586 DOI: 10.3390/pharmaceutics14020417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 02/01/2022] [Accepted: 02/07/2022] [Indexed: 11/16/2022] Open
Abstract
Mechanically processed stromal vascular fraction (mSVF) is a promising source for regenerative purposes. To study the in vivo fate of the mSVF, we herein used a vascularized tissue engineering chamber that insulates the target mSVF from the surrounding environment. In contrast to previous models, we propose an arteriovenous (AV) shunt between saphenous vessels in rats without a venous graft. Mechanical SVF was processed from the fat pads of male Sprague Dawley rats, mixed with a fibrin hydrogel and implanted into an inguinal tissue engineering chamber. An arteriovenous shunt was established between saphenous artery and vein. On the contralateral side, an mSVF-fibrin hydrogel mix without vascular axis served as a non-vascularized control. After two and six weeks, rats were sacrificed for further analysis. Mechanical SVF showed significant numbers of mesenchymal stromal cells. Vascularized mSVF explants gained weight over time. Perilipin and CD31 expression were significantly higher in the mSVF explants after six weeks while no difference in DAPI positive cells, collagen deposition and FABP4 expression was observed. Morphologically, no differentiated adipocytes but a dense cell-rich tissue with perilipin-positive cells was found after six weeks. The phosphorylation of ERK1/2 was significantly enhanced after six weeks while Akt activation remained unaltered. Finally, mSVF explants stably expressed and released VEGF, bFGF and TGFb. Vascularized mSVF is able to proliferate and express adipocyte-specific markers. The AV shunt model is a valuable refinement of currently existing AV loop models in the rat which contributes to the fundamental 3R principles of animal research.
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247
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Evaluation of stable reference genes for qPCR normalization in circadian studies related to lung inflammation and injury in mouse model. Sci Rep 2022; 12:1764. [PMID: 35110670 PMCID: PMC8810972 DOI: 10.1038/s41598-022-05836-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 01/05/2022] [Indexed: 12/21/2022] Open
Abstract
Circadian rhythms have a profound effect on lung function and immune-inflammatory response in chronic airway diseases. Thus, understanding the molecular mechanisms of circadian gene expression of core clock-controlled genes (CCGs) may help better understand how it contributes to the physiology and pathology of lung diseases. Ongoing studies have been analyzing gene expression levels of CCGs in mouse lungs using quantitative real-time PCR (qRT-PCR). However, to date, there are no reports on the most stable reference gene in the mouse lung for circadian studies. Herein, we utilized an acute house dust mite (HDM)-sensitization mouse model to evaluate the stability of 10 reference genes commonly used for qRT-PCR normalization using 5 unique algorithms: GeNorm, NormFinder, BestKeeper, RefFinder and Qbase+. Rn18s was determined as the most stable reference gene across all samples evaluated, and Actb, the least stable reference gene. Furthermore, CircWave analysis showed no diurnal variation in the expression pattern for Rn18s but Actb showed strong diurnal changes in the lungs of both PBS (control) and HDM groups. We demonstrate systematically how using Actb as a housekeeping gene offsets the diurnal expression patterns of the CCGs and leads to statistically significant results which may not be the true reflection of the qRT-PCR analysis.
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248
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Ahmed W, Simpson SL, Bertsch PM, Bibby K, Bivins A, Blackall LL, Bofill-Mas S, Bosch A, Brandão J, Choi PM, Ciesielski M, Donner E, D'Souza N, Farnleitner AH, Gerrity D, Gonzalez R, Griffith JF, Gyawali P, Haas CN, Hamilton KA, Hapuarachchi HC, Harwood VJ, Haque R, Jackson G, Khan SJ, Khan W, Kitajima M, Korajkic A, La Rosa G, Layton BA, Lipp E, McLellan SL, McMinn B, Medema G, Metcalfe S, Meijer WG, Mueller JF, Murphy H, Naughton CC, Noble RT, Payyappat S, Petterson S, Pitkänen T, Rajal VB, Reyneke B, Roman FA, Rose JB, Rusiñol M, Sadowsky MJ, Sala-Comorera L, Setoh YX, Sherchan SP, Sirikanchana K, Smith W, Steele JA, Sabburg R, Symonds EM, Thai P, Thomas KV, Tynan J, Toze S, Thompson J, Whiteley AS, Wong JCC, Sano D, Wuertz S, Xagoraraki I, Zhang Q, Zimmer-Faust AG, Shanks OC. Minimizing errors in RT-PCR detection and quantification of SARS-CoV-2 RNA for wastewater surveillance. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 805:149877. [PMID: 34818780 PMCID: PMC8386095 DOI: 10.1016/j.scitotenv.2021.149877] [Citation(s) in RCA: 123] [Impact Index Per Article: 61.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 08/20/2021] [Accepted: 08/20/2021] [Indexed: 05/18/2023]
Abstract
Wastewater surveillance for pathogens using reverse transcription-polymerase chain reaction (RT-PCR) is an effective and resource-efficient tool for gathering community-level public health information, including the incidence of coronavirus disease-19 (COVID-19). Surveillance of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) in wastewater can potentially provide an early warning signal of COVID-19 infections in a community. The capacity of the world's environmental microbiology and virology laboratories for SARS-CoV-2 RNA characterization in wastewater is increasing rapidly. However, there are no standardized protocols or harmonized quality assurance and quality control (QA/QC) procedures for SARS-CoV-2 wastewater surveillance. This paper is a technical review of factors that can cause false-positive and false-negative errors in the surveillance of SARS-CoV-2 RNA in wastewater, culminating in recommended strategies that can be implemented to identify and mitigate some of these errors. Recommendations include stringent QA/QC measures, representative sampling approaches, effective virus concentration and efficient RNA extraction, PCR inhibition assessment, inclusion of sample processing controls, and considerations for RT-PCR assay selection and data interpretation. Clear data interpretation guidelines (e.g., determination of positive and negative samples) are critical, particularly when the incidence of SARS-CoV-2 in wastewater is low. Corrective and confirmatory actions must be in place for inconclusive results or results diverging from current trends (e.g., initial onset or reemergence of COVID-19 in a community). It is also prudent to perform interlaboratory comparisons to ensure results' reliability and interpretability for prospective and retrospective analyses. The strategies that are recommended in this review aim to improve SARS-CoV-2 characterization and detection for wastewater surveillance applications. A silver lining of the COVID-19 pandemic is that the efficacy of wastewater surveillance continues to be demonstrated during this global crisis. In the future, wastewater should also play an important role in the surveillance of a range of other communicable diseases.
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Affiliation(s)
- Warish Ahmed
- CSIRO Land and Water, Ecosciences Precinct, 41 Boggo Road, QLD 4102, Australia.
| | | | - Paul M Bertsch
- CSIRO Land and Water, Ecosciences Precinct, 41 Boggo Road, QLD 4102, Australia
| | - Kyle Bibby
- Department of Civil & Environmental Engineering & Earth Science, University of Notre Dame, 156 Fitzpatrick Hall, Notre Dame, IN 46556, USA
| | - Aaron Bivins
- Department of Civil & Environmental Engineering & Earth Science, University of Notre Dame, 156 Fitzpatrick Hall, Notre Dame, IN 46556, USA
| | - Linda L Blackall
- School of BioSciences, The University of Melbourne, Melbourne, VIC, Australia
| | - Sílvia Bofill-Mas
- Laboratory of Virus Contaminants of Water and Food, Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, 08028 Barcelona, Spain
| | - Albert Bosch
- Enteric Virus Laboratory, Department of Genetics, Microbiology and Statistics, University of Barcelona, Avda. Diagonal 643, 08028 Barcelona, Spain
| | - João Brandão
- Department of Environmental Health, National Institute of Health Dr. Ricardo Jorge, Lisboa, Portugal
| | - Phil M Choi
- Water Unit, Health Protection Branch, Prevention Division, Queensland Health, QLD, Australia; The University of Queensland, Queensland Alliance for Environmental Health Sciences, QLD, Australia
| | - Mark Ciesielski
- University of North Carolina at Chapel Hill, Institute of Marine Sciences, Morehead City, NC, United States
| | - Erica Donner
- Future Industries Institute, University of South Australia, University Boulevard, Mawson Lakes, SA 5095, Australia
| | - Nishita D'Souza
- Department of Fisheries and Wildlife, Michigan State University, E. Lansing, MI, USA
| | - Andreas H Farnleitner
- Institute of Chemical, Environmental & Bioscience Engineering, Research Group Environmental Microbiology and Molecular Diagnostic, 166/5/3, Technische Universität Wien, Vienna, Austria; Research Division Water Quality and Health, Department Pharmacology, Physiology and Microbiology, Karl Landsteiner University of Health Sciences, Dr. Karl-Dorrek-Straβe 30, 3500 Krems an der Donau, Austria
| | - Daniel Gerrity
- Southern Nevada Water Authority, P.O. Box 99954, Las Vegas, NV 89193, USA
| | - Raul Gonzalez
- Hampton Roads Sanitation District, 1434 Air Rail Avenue, Virginia Beach, VA 23455, USA
| | - John F Griffith
- Southern California Coastal Water Research Project, Costa Mesa, CA 92626, USA
| | - Pradip Gyawali
- Institute of Environmental Science and Research Ltd (ESR), Porirua 5240, New Zealand
| | | | - Kerry A Hamilton
- School of Sustainable Engineering and the Built Environment and The Biodesign Institute Center for Environmental Health Engineering, Arizona State University, Tempe, AZ 85287, USA
| | | | - Valerie J Harwood
- Department of Integrative Biology, University of South Florida, Tampa, FL, USA
| | - Rehnuma Haque
- Environmental Interventions Unit, Icddr,b, 68 Shaheed Tajuddin Ahmed Sarani, Mohakhali, Dhaka 1212, Bangladesh
| | - Greg Jackson
- Water Unit, Health Protection Branch, Prevention Division, Queensland Health, QLD, Australia
| | - Stuart J Khan
- Water Research Centre, School of Civil and Environmental Engineering, University of New South Wales, NSW 2052, Australia
| | - Wesaal Khan
- Department of Microbiology, Faculty of Science, Stellenbosch University, Private Bag X1, Stellenbosch 7602, South Africa
| | - Masaaki Kitajima
- Division of Environmental Engineering, Faculty of Engineering, Hokkaido University, North 13 West 8, Kita-ku, Sapporo, Hokkaido 060-8628, Japan
| | - Asja Korajkic
- United States Environmental Protection Agency, Office of Research and Development, 26W Martin Luther King Jr. Drive, Cincinnati, OH 45268, USA
| | - Giuseppina La Rosa
- Department of Environment and Health, Istituto Superiore di Sanità, Rome, Italy
| | - Blythe A Layton
- Department of Research & Innovation, Clean Water Services, Hillsboro, OR, USA
| | - Erin Lipp
- Environmental Health Sciences Department, University of Georgia, Athens, GA 30602, USA
| | - Sandra L McLellan
- School of Freshwater Sciences, University of Wisconsin-Milwaukee, WI, USA
| | - Brian McMinn
- United States Environmental Protection Agency, Office of Research and Development, 26W Martin Luther King Jr. Drive, Cincinnati, OH 45268, USA
| | - Gertjan Medema
- KWR Water Research Institute, Groningenhaven 7, 3433 PE Nieuwegein, the Netherlands
| | - Suzanne Metcalfe
- CSIRO Land and Water, Ecosciences Precinct, 41 Boggo Road, QLD 4102, Australia
| | - Wim G Meijer
- UCD School of Biomolecular and Biomedical Science, University College Dublin, Dublin, Ireland
| | - Jochen F Mueller
- The University of Queensland, Queensland Alliance for Environmental Health Sciences, QLD, Australia
| | - Heather Murphy
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, ON, Canada
| | - Coleen C Naughton
- University of California Merced, Department of Civil and Environmental Engineering, 5200 N. Lake Rd., Merced, CA 95343, USA
| | - Rachel T Noble
- University of North Carolina at Chapel Hill, Institute of Marine Sciences, Morehead City, NC, United States
| | - Sudhi Payyappat
- Sydney Water, 1 Smith Street, Parramatta, NSW 2150, Australia
| | - Susan Petterson
- Water and Health Pty Ltd., 13 Lord St, North Sydney, NSW 2060, Australia; School of Medicine, Griffith University, Parklands Drive, Gold Coast, Australia
| | - Tarja Pitkänen
- Finnish Institute for Health and Welfare, Expert Microbiology Unit, P.O. Box 95, FI-70701 Kuopio, Finland; University of Helsinki, Faculty of Veterinary Medicine, Department of Food Hygiene and Environmental Health, P.O. Box 66, FI-00014, Finland
| | - Veronica B Rajal
- Facultad de Ingeniería and Instituto de Investigaciones para la Industria Química (INIQUI) - CONICET and Universidad Nacional de Salta, Av. Bolivia 5150, Salta, Argentina
| | - Brandon Reyneke
- Department of Microbiology, Faculty of Science, Stellenbosch University, Private Bag X1, Stellenbosch 7602, South Africa
| | - Fernando A Roman
- University of California Merced, Department of Civil and Environmental Engineering, 5200 N. Lake Rd., Merced, CA 95343, USA
| | - Joan B Rose
- Department of Fisheries and Wildlife, Michigan State University, E. Lansing, MI, USA
| | - Marta Rusiñol
- Institute of Environmental Assessment & Water Research (IDAEA), CSIC, Barcelona, Spain
| | - Michael J Sadowsky
- Biotechnology Institute and Department of Soil, Water, and Climate, University of Minnesota, St. Paul, MN, USA
| | - Laura Sala-Comorera
- UCD School of Biomolecular and Biomedical Science, University College Dublin, Dublin, Ireland
| | - Yin Xiang Setoh
- Environmental Health Institute, National Environment Agency, Singapore
| | - Samendra P Sherchan
- Department of Environmental Health Sciences, Tulane University, 1440 Canal Street, New Orleans, LA 70112, USA
| | - Kwanrawee Sirikanchana
- Research Laboratory of Biotechnology, Chulabhorn Research Institute, 54 Kampangpetch 6 Road, Laksi, Bangkok 10210, Thailand
| | - Wendy Smith
- CSIRO Land and Water, Ecosciences Precinct, 41 Boggo Road, QLD 4102, Australia
| | - Joshua A Steele
- Southern California Coastal Water Research Project, Costa Mesa, CA 92626, USA
| | - Rosalie Sabburg
- CSIRO Agriculture and Food, Bioscience Precinct, St Lucia, QLD 4067, Australia
| | - Erin M Symonds
- College of Marine Science, University of South Florida, St. Petersburg, FL, USA
| | - Phong Thai
- The University of Queensland, Queensland Alliance for Environmental Health Sciences, QLD, Australia
| | - Kevin V Thomas
- The University of Queensland, Queensland Alliance for Environmental Health Sciences, QLD, Australia
| | - Josh Tynan
- The University of Queensland, Queensland Alliance for Environmental Health Sciences, QLD, Australia
| | - Simon Toze
- CSIRO Land and Water, Ecosciences Precinct, 41 Boggo Road, QLD 4102, Australia
| | - Janelle Thompson
- Asian School of the Environment, Nanyang Technological University, Singapore 639798, Singapore; Singapore Centre for Environmental Life Sciences Engineering (SCELSE) Singapore 637551
| | | | | | - Daisuke Sano
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, Aoba 6-6-06, Aramaki, Aoba-Ku, Sendai, Miyagi 980-8597, Japan
| | - Stefan Wuertz
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE) Singapore 637551; School of Civil and Environmental Engineering, Nanyang Technological University, Singapore 639798
| | - Irene Xagoraraki
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI 48824, USA
| | - Qian Zhang
- Biotechnology Institute and Department of Soil, Water, and Climate, University of Minnesota, St. Paul, MN, USA
| | | | - Orin C Shanks
- United States Environmental Protection Agency, Office of Research and Development, 26W Martin Luther King Jr. Drive, Cincinnati, OH 45268, USA
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249
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Custódio N, Savisaar R, Carvalho C, Bak-Gordon P, Ribeiro MI, Tavares J, Nunes PB, Peixoto A, Pinto C, Escudeiro C, Teixeira MR, Carmo-Fonseca M. Expression Profiling in Ovarian Cancer Reveals Coordinated Regulation of BRCA1/2 and Homologous Recombination Genes. Biomedicines 2022; 10:biomedicines10020199. [PMID: 35203410 PMCID: PMC8868827 DOI: 10.3390/biomedicines10020199] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 01/09/2022] [Accepted: 01/13/2022] [Indexed: 02/04/2023] Open
Abstract
Predictive biomarkers are crucial in clarifying the best strategy to use poly(ADP-ribose) polymerase inhibitors (PARPi) for the greatest benefit to ovarian cancer patients. PARPi are specifically lethal to cancer cells that cannot repair DNA damage by homologous recombination (HR), and HR deficiency is frequently associated with BRCA1/2 mutations. Genetic tests for BRCA1/2 mutations are currently used in the clinic, but results can be inconclusive due to the high prevalence of rare DNA sequence variants of unknown significance. Most tests also fail to detect epigenetic modifications and mutations located deep within introns that may alter the mRNA. The aim of this study was to investigate whether quantitation of BRCA1/2 mRNAs in ovarian cancer can provide information beyond the DNA tests. Using the nCounter assay from NanoString Technologies, we analyzed RNA isolated from 38 ovarian cancer specimens and 11 normal fallopian tube samples. We found that BRCA1/2 expression was highly variable among tumors. We further observed that tumors with lower levels of BRCA1/2 mRNA showed downregulated expression of 12 additional HR genes. Analysis of 299 ovarian cancer samples from The Cancer Genome Atlas (TCGA) confirmed the coordinated expression of BRCA1/2 and HR genes. To facilitate the routine analysis of BRCA1/2 mRNA in the clinical setting, we developed a targeted droplet digital PCR approach that can be used with FFPE samples. In conclusion, this study underscores the potential clinical benefit of measuring mRNA levels in tumors when BRCA1/2 DNA tests are negative or inconclusive.
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Affiliation(s)
- Noélia Custódio
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal; (R.S.); (C.C.); (P.B.-G.); (M.I.R.); (M.C.-F.)
- Correspondence: ; Tel.: +35-121-799-9411
| | - Rosina Savisaar
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal; (R.S.); (C.C.); (P.B.-G.); (M.I.R.); (M.C.-F.)
| | - Célia Carvalho
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal; (R.S.); (C.C.); (P.B.-G.); (M.I.R.); (M.C.-F.)
| | - Pedro Bak-Gordon
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal; (R.S.); (C.C.); (P.B.-G.); (M.I.R.); (M.C.-F.)
| | - Maria I. Ribeiro
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal; (R.S.); (C.C.); (P.B.-G.); (M.I.R.); (M.C.-F.)
| | - Joana Tavares
- Serviço de Anatomia Patológica, Hospital de Santa Maria, Centro Hospitalar Universitário Lisboa Norte, 1649-028 Lisboa, Portugal;
| | - Paula B. Nunes
- Hospital CUF Descobertas, 1998-018 Lisboa, Portugal;
- Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal
| | - Ana Peixoto
- Serviço de Genética, Instituto Português de Oncologia do Porto Francisco Gentil, 4200-072 Porto, Portugal; (A.P.); (C.P.); (C.E.); (M.R.T.)
| | - Carla Pinto
- Serviço de Genética, Instituto Português de Oncologia do Porto Francisco Gentil, 4200-072 Porto, Portugal; (A.P.); (C.P.); (C.E.); (M.R.T.)
| | - Carla Escudeiro
- Serviço de Genética, Instituto Português de Oncologia do Porto Francisco Gentil, 4200-072 Porto, Portugal; (A.P.); (C.P.); (C.E.); (M.R.T.)
| | - Manuel R. Teixeira
- Serviço de Genética, Instituto Português de Oncologia do Porto Francisco Gentil, 4200-072 Porto, Portugal; (A.P.); (C.P.); (C.E.); (M.R.T.)
| | - Maria Carmo-Fonseca
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal; (R.S.); (C.C.); (P.B.-G.); (M.I.R.); (M.C.-F.)
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250
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Protective Effects of Honey-Processed Astragalus on Liver Injury and Gut Microbiota in Mice Induced by Chronic Alcohol Intake. J FOOD QUALITY 2022. [DOI: 10.1155/2022/5333691] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Honey-processed Astragalus (HPA) is a mixture of Astragalus and honey, which is a processed product of Chinese medicine. It has the active ingredients of Astragalus and the unique effects of honey. However, the mechanism of HPA for improving alcoholic liver disease (ALD) is not clear. The purpose of this study is to explore the ameliorating effect and mechanism of HPA (4 and 8 g/kg bw) on alcoholic liver injury. Two doses of HPA were orally administered to alcohol-treated mice for four weeks. The results showed that HPA could effectively reduce triglycerides (TG) by 59% and free fat acid (FFA) and total cholesterol (TC) in serum and hepatic were reduced by least 25.9%. HPA could cause a decrease in serum low-density lipoprotein cholesterol (LDL-C) from 0.145 mM to 0.117 mM, and the serum high-density lipoprotein cholesterol (HDL-C) was increased. After alcohol-treated mice were supplemented with HPA, antioxidant markers (superoxide dismutase (SOD), catalase (CAT), glutathione (GSH), and Glutathione peroxidase (GSH-Px)), liver function index (alanine aminotransferase (ALT), aspartate aminotransferase (AST), and alkaline phosphatase (ALP)), proinflammatory cytokines (tumor necrosis factor-α (TNF-α), interleukin-6 (IL-6), and interleukin-1β (IL-1β)), and liver tissue were all significantly improved. This is related to the fact that HPA can promote the expression of oxidative stress-related genes and inhibit the expression of inflammation-related genes. In addition, HPA could also regulate the disturbance of the intestinal microflora. In general, HPA could significantly improve the accumulation of serum and liver lipids caused by alcohol and the imbalance of intestinal flora in mice. It could also improve liver function, oxidative stress, and inflammation.
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