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Chen B, Zhen L, Yang Z, Liu T, Yang S, Mu W, Xiao X, Chen J. miRNA-mRNA integrated analysis reveals candidate genes associated with salt stress response in Halophytic Sonneratia apetala. RNA Biol 2025; 22:1-13. [PMID: 40296366 PMCID: PMC12045576 DOI: 10.1080/15476286.2025.2496097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 01/20/2025] [Accepted: 04/01/2025] [Indexed: 04/30/2025] Open
Abstract
Sonneratia apetala is a pioneering species of mangrove plants, which has evolved various mechanisms to tolerate salt-stress due to their long-term exposure to a salinized environment as compared to the of terrestrial freshwater plants. However, limited attempt has been made to uncover the underlying molecular mechanism of their saline adaptation. Here, we integrated mRNA and microRNA (miRNA) sequencing to identify the genes and pathways that may be involved in salt stress-response in the roots of S. apetala. A comprehensive full‑length transcriptome containing 295,501 high‑quality unigenes was obtained by PacBio sequencing technology. Of these, 6,686 genes exhibited significantly differential accumulation after salt stress treatment (p < 0.001, Q < 0.01). They were mainly implicated in plant signal transduction and diverse metabolic pathways, such as those involving phenylpropanoid biosynthesis, plant-pathogen interaction and protein processing. Also, our results identified the regulatory interaction between miRNA-target counterparts during salt stress. Taken together, we present the first global overview of the transcriptome of S. apetala roots, and identify potentially important genes and pathways associated with salt tolerance for further investigation. This study is expected to deliver novel insights in understanding the regulatory mechanism in S. apetala response to salt stress.
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Affiliation(s)
- Beibei Chen
- Guangdong Engineering Technology Research Center of Tropical Crops High Efficient Production, College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, PR, China
| | - Lishan Zhen
- Guangdong Engineering Technology Research Center of Tropical Crops High Efficient Production, College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, PR, China
| | - Zhuanying Yang
- Guangdong Engineering Technology Research Center of Tropical Crops High Efficient Production, College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, PR, China
| | - Tingting Liu
- Guangdong Engineering Technology Research Center of Tropical Crops High Efficient Production, College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, PR, China
| | - Shaoxia Yang
- Guangdong Engineering Technology Research Center of Tropical Crops High Efficient Production, College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, PR, China
| | - Wei Mu
- Guangdong Engineering Technology Research Center of Tropical Crops High Efficient Production, College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, PR, China
| | - Xiao Xiao
- School of Chemistry and Environment, Guangdong Ocean University, Zhanjiang, PR, China
| | - Jinhui Chen
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya, PR, China
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2
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Osman A, Andrus PS, Zhu X, Dong Z, Guo Y, Nour BYM, Zhou X, Zhao L. Comparative Mitochondrial Genome Analysis of the Intestinal Schistosomiasis Snail Host Biomphalaria pfeifferi from Multiple Populations in Gezira State, Sudan. Int J Mol Sci 2025; 26:4756. [PMID: 40429898 DOI: 10.3390/ijms26104756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2025] [Revised: 05/07/2025] [Accepted: 05/09/2025] [Indexed: 05/29/2025] Open
Abstract
Biomphalaria pfeifferi is a key intermediate host for Schistosoma mansoni transmission in Sudan. In total, 27 complete mitochondrial genomes from seven B. pfeifferi populations in Gezira State, Sudan, were sequenced for the first time to investigate their population structure and phylogenetic relationships. This involved comparing the nucleotide composition, codon usage, rRNAs, and tRNAs of the East Gezira (EG), South Gezira (SG), Hasahisa (HA), Greater Wad Medani (GW), Managil (MA), and North Umelgura (NU1, NU3) populations. All 27 mitogenomes (13,688-13,696 bp) contained 37 genes with conserved AT/GC content (76.7/23.4%). Phylogenetic analysis revealed that although samples clustered within the same clade, B. pfeifferi from EG, SG, NU1, and NU3 grouped closely with B. pfeifferi from Kenya, whereas HA and GW samples formed distinct ancestral lineages. The MA population exhibited unique genetic characteristics, supported by phylogenetic trees and nucleotide/amino acid identity, suggesting the potential presence of a distinct B. pfeifferi subspecies that warrants further investigation. All protein-coding genes evolved under negative selection, with the amino acids of nad1 and nad6 being highly conserved, while nad3 exhibited some variation. Further research on the mitogenomic diversity of B. pfeifferi and other Biomphalaria species in Sudan and across Africa is needed in order to better understand the population structure and evolutionary history of Biomphalaria.
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Affiliation(s)
- Arwa Osman
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
- Blue Nile National Institute for Communicable Diseases, University of Gezira, P.O. Box 20, Wad Madani 5118 40466, Sudan
| | - Peter S Andrus
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention (Chinese Center for Tropical Diseases Research), Shanghai 200025, China
- School of Global Health, Chinese Centre for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Xianglu Zhu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Zhaoyang Dong
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Yunhai Guo
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention (Chinese Center for Tropical Diseases Research), Shanghai 200025, China
| | - Bakri Y M Nour
- Faculty of Medical Laboratories, University of Gezira, P.O. Box 20, Wad Madani 5118 40466, Sudan
| | - Xiaonong Zhou
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention (Chinese Center for Tropical Diseases Research), Shanghai 200025, China
- School of Global Health, Chinese Centre for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Liming Zhao
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
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3
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Ruppeka Rupeika E, D’Huys L, Leen V, Hofkens J. Sequencing and Optical Genome Mapping for the Adventurous Chemist. CHEMICAL & BIOMEDICAL IMAGING 2024; 2:784-807. [PMID: 39735829 PMCID: PMC11673194 DOI: 10.1021/cbmi.4c00060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/14/2024] [Revised: 10/03/2024] [Accepted: 10/04/2024] [Indexed: 12/31/2024]
Abstract
This review provides a comprehensive overview of the chemistries and workflows of the sequencing methods that have been or are currently commercially available, providing a very brief historical introduction to each method. The main optical genome mapping approaches are introduced in the same manner, although only a subset of these are or have ever been commercially available. The review comes with a deck of slides containing all of the figures for ease of access and consultation.
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Affiliation(s)
| | - Laurens D’Huys
- Faculty
of Science, Chemistry, KU Leuven, Celestijnenlaan 200F, Leuven, Flanders 3001, Belgium
| | - Volker Leen
- Perseus
Biomics B.V., Industriepark
6 bus 3, Tienen 3300, Belgium
| | - Johan Hofkens
- Faculty
of Science, Chemistry, KU Leuven, Celestijnenlaan 200F, Leuven, Flanders 3001, Belgium
- Max
Planck Institute for Polymer Research, Mainz, Rheinland-Pfalz 55128, Germany
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4
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Liu X, Pang Y, Shan J, Wang Y, Zheng Y, Xue Y, Zhou X, Wang W, Sun Y, Yan X, Shi J, Wang X, Gu H, Zhang F. Beyond the base pairs: comparative genome-wide DNA methylation profiling across sequencing technologies. Brief Bioinform 2024; 25:bbae440. [PMID: 39256199 PMCID: PMC11387064 DOI: 10.1093/bib/bbae440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 07/28/2024] [Accepted: 08/21/2024] [Indexed: 09/12/2024] Open
Abstract
Deoxyribonucleic acid (DNA) methylation plays a key role in gene regulation and is critical for development and human disease. Techniques such as whole-genome bisulfite sequencing (WGBS) and reduced representation bisulfite sequencing (RRBS) allow DNA methylation analysis at the genome scale, with Illumina NovaSeq 6000 and MGI Tech DNBSEQ-T7 being popular due to their efficiency and affordability. However, detailed comparative studies of their performance are not available. In this study, we constructed 60 WGBS and RRBS libraries for two platforms using different types of clinical samples and generated approximately 2.8 terabases of sequencing data. We systematically compared quality control metrics, genomic coverage, CpG methylation levels, intra- and interplatform correlations, and performance in detecting differentially methylated positions. Our results revealed that the DNBSEQ platform exhibited better raw read quality, although base quality recalibration indicated potential overestimation of base quality. The DNBSEQ platform also showed lower sequencing depth and less coverage uniformity in GC-rich regions than did the NovaSeq platform and tended to enrich methylated regions. Overall, both platforms demonstrated robust intra- and interplatform reproducibility for RRBS and WGBS, with NovaSeq performing better for WGBS, highlighting the importance of considering these factors when selecting a platform for bisulfite sequencing.
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Affiliation(s)
- Xin Liu
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui Province 230031, China
- Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei, Anhui Province 230031, China
| | - Yu Pang
- Department of Bacteriology and Immunology, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing 101149, China
| | - Junqi Shan
- Department of Gastrointestinal Surgery, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong 250117, China
| | - Yunfei Wang
- Hangzhou ShengTing Biotech Co. Ltd, Hangzhou, Zhejiang Province 310018, China
| | - Yanhua Zheng
- Department of Hematology, The First Hospital of China Medical University, Shenyang, Liaoning, Shenyang, Liaoning province 110001, China
| | - Yuhang Xue
- Department of Hematology, The First Hospital of China Medical University, Shenyang, Liaoning, Shenyang, Liaoning province 110001, China
| | - Xuerong Zhou
- Department of Hematology, The First Hospital of China Medical University, Shenyang, Liaoning, Shenyang, Liaoning province 110001, China
| | - Wenjun Wang
- Hangzhou ShengTing Biotech Co. Ltd, Hangzhou, Zhejiang Province 310018, China
| | - Yanlai Sun
- Department of Gastrointestinal Surgery, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong 250117, China
| | - Xiaojing Yan
- Department of Hematology, The First Hospital of China Medical University, Shenyang, Liaoning, Shenyang, Liaoning province 110001, China
| | - Jiantao Shi
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
| | - Xiaoxue Wang
- Department of Hematology, The First Hospital of China Medical University, Shenyang, Liaoning, Shenyang, Liaoning province 110001, China
| | - Hongcang Gu
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui Province 230031, China
- Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei, Anhui Province 230031, China
| | - Fan Zhang
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui Province 230031, China
- Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei, Anhui Province 230031, China
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5
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Chaudhari JK, Pant S, Jha R, Pathak RK, Singh DB. Biological big-data sources, problems of storage, computational issues, and applications: a comprehensive review. Knowl Inf Syst 2024; 66:3159-3209. [DOI: 10.1007/s10115-023-02049-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 09/12/2023] [Accepted: 12/11/2023] [Indexed: 01/03/2025]
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Linck Moroni J, Tsoi S, Wenger II, Plastow GS, Dyck MK. Placental Transcriptome Analysis in Connection with Low Litter Birth Weight Phenotype (LBWP) Sows. Genes (Basel) 2024; 15:703. [PMID: 38927639 PMCID: PMC11203121 DOI: 10.3390/genes15060703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2024] [Revised: 05/16/2024] [Accepted: 05/21/2024] [Indexed: 06/28/2024] Open
Abstract
It is possible to identify sub-populations of sows in every pig herd that consistently give birth to low birth weight (BW) piglets, irrespective of the litter size. A previous study from our group demonstrated that placental development is a main factor affecting the litter birth weight phenotype (LBWP) in sows, thereby impacting the BW of entire litters, but the biological and molecular pathways behind this phenomenon are largely unknown. The aim of this study was to investigate the differential gene expression in placental tissues at day 30 of gestation between low LBWP (LLBWP) vs. high LBWP (HLBWP) sows from a purebred Large White maternal line. Using mRNA sequencing, we found 45 differentially expressed genes (DEGs) in placental tissues of LLBWP and HLBWP sows. Furthermore, (GO) enrichment of upregulated DEGs predicted that there were two biological processes significantly related to cornification and regulation of cell population proliferation. To better understand the molecular interaction between cell proliferation and cornification, we conducted transcriptional factor binding site (TFBS) prediction analysis. The results indicated that a highly significant TFBS was located at the 5' upstream of all four upregulated genes (CDSN, DSG3, KLK14, KRT17), recognized by transcription factors EGR4 and FOSL1. Our findings provide novel insight into how transcriptional regulation of two different biological processes interact in placental tissues of LLBWP sows.
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Affiliation(s)
| | | | | | | | - Michael K. Dyck
- Department of Agricultural, Food & Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada; (J.L.M.); (S.T.); (I.I.W.); (G.S.P.)
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7
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Piryaei F, Mehta P, Mozdarani H, Hamzehlooy F, Barati M, Piryaei Z, Gilani MAS, Alemi M, Singh R. Testicular piRNA Analysis Identified Dysregulated piRNAs in Non-obstructive Azoospermia. Reprod Sci 2024; 31:1246-1255. [PMID: 38133767 DOI: 10.1007/s43032-023-01433-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 12/12/2023] [Indexed: 12/23/2023]
Abstract
Male infertility has remained idiopathic in a remarkable proportion of all cases. Gonadal expression of PIWI-interacting RNAs (piRNAs) has been shown to be vital to normal spermatogenesis, as they are expressed in almost all types of testicular germ cells. These molecules and their related Piwi proteins strictly regulate transposable elements' activity and gene expression. We aimed to identify dysregulated piRNAs in idiopathic non-obstructive azoospermic (NOA) testis by global expression analysis. Testis tissue samples from 18 azoospermic patients (ten NOA and eight OA) were studied by small RNA sequencing. To validate high-throughput sequencing data, quantitative real-time polymerase chain reactions for two differentially altered piRNAs were performed. Bioinformatics analyses were undertaken to identify pathways affected by piRNA dysregulation. In the NOA group, 1328 piRNAs were identified to be differentially expressed, of which 1322 were downregulated and 6 were upregulated. Bioinformatics analysis corroborated the involvement of dysregulated piRNA in spermatogenesis. We also identified 64 clusters of differentially expressed piRNAs, of which 42 clusters had a minimum of ten absolute piRNA hits. Our study suggests that piRNAs show significant dysregulation in infertility. Their target genes play a role in their self-biogenesis, probably by regulating their own production through a feedback mechanism. The downregulated piRNAs may find value as biomarkers for the presence of spermatozoa in the testis of azoospermic individuals, while the upregulated piRNAs are great candidates for further investigation of their precise functions in spermatogenesis.
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Affiliation(s)
- Fahimeh Piryaei
- Research Center for Molecular Medicine, Hamadan University of Medical Sciences, Hamadan, Iran.
| | - Poonam Mehta
- Male Reproductive Biology Laboratory, Central Drug Research Institute, Lucknow, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Hossein Mozdarani
- Department of Medical Genetics, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Fatemeh Hamzehlooy
- Department of Medical Biotechnology, Faculty of Allied Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Mahmoud Barati
- Department of Medical Biotechnology, Faculty of Allied Medicine, Iran University of Medical Sciences, Tehran, Iran
- Cellular and Molecular Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Zeynab Piryaei
- Department of Bioinformatics, Kish International Campus, University of Tehran, Kish, Iran
| | - Mohammad Ali Sadighi Gilani
- Department of Andrology, Reproductive Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACECR, Tehran, Iran
| | - Mohsen Alemi
- Urology and Nephrology Research Center, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Rajender Singh
- Male Reproductive Biology Laboratory, Central Drug Research Institute, Lucknow, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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8
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Póliska S, Fareh C, Lengyel A, Göczi L, Tőzsér J, Szatmari I. Comparative transcriptomic analysis of Illumina and MGI next-generation sequencing platforms using RUNX3- and ZBTB46-instructed embryonic stem cells. Front Genet 2024; 14:1275383. [PMID: 38250572 PMCID: PMC10796612 DOI: 10.3389/fgene.2023.1275383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 12/11/2023] [Indexed: 01/23/2024] Open
Abstract
Introduction: We have previously observed phenotypic and developmental changes upon the ectopic expression of the RUNX3 or the ZBTB46 transcription factors in mouse embryonic stem cell (ESC) derived progenitors. In this study, we evaluated the gene expression profiles of the RUNX3- and the ZBTB46-instructed murine ESCs with RNA-seq testing two next-generation sequencing technologies. Methods: We compared the DNA nanoball-based DNBSEQ G400 sequencer (MGI) with the bridge-PCR-based NextSeq 500 instrument (Illumina) for RNA sequencing. Moreover, we also compared two types of MGI sequencing reagents (Standard versus Hot-massive parallel sequencing (MPS)) with the DNBSEQ G400. Results: We observed that both sequencing platforms showed comparable levels of quality, sequencing uniformity, and gene expression profiles. For example, highly overlapping RUNX3- and ZBTB46-regulated gene lists were obtained from both sequencing datasets. Moreover, we observed that the Standard and the Hot-MPS-derived RUNX3- and ZBTB46-regulated gene lists were also considerably overlapped. This transcriptome analysis also helped us to identify differently expressed genes in the presence of the transgenic RUNX3 or ZBTB46. For example, we found that Gzmb, Gzmd, Gzme, Gdf6, and Ccr7 genes were robustly upregulated upon the forced expression of Runx3; on the other hand, Gpx2, Tdpoz4, and Arg2 were induced alongside the ectopic expression of Zbtb46. Discussion: Similar gene expression profile and greatly overlapping RUNX3- and ZBTB46-regulated gene sets were detected with both DNA sequencing platforms. Our analyses demonstrate that both sequencing technologies are suitable for transcriptome profiling and target gene selection. These findings suggest that DNBSEQ G400 represents a cost-effective alternative sequencing platform for gene expression monitoring. Moreover, this analysis provides a resource for exploration of the RUNX3- and ZBTB46-dependent gene regulatory networks.
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Affiliation(s)
- Szilárd Póliska
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Chahra Fareh
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
- Doctoral School of Molecular Cell and Immune Biology, University of Debrecen, Debrecen, Hungary
| | - Adél Lengyel
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
- Doctoral School of Molecular Cell and Immune Biology, University of Debrecen, Debrecen, Hungary
| | - Loránd Göczi
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
- Department of Human Genetics, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - József Tőzsér
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Istvan Szatmari
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
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9
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Penkova A, Kuziakova O, Gulaia V, Tiasto V, Goncharov NV, Lanskikh D, Zhmenia V, Baklanov I, Farniev V, Kumeiko V. Comprehensive clinical assays for molecular diagnostics of gliomas: the current state and future prospects. Front Mol Biosci 2023; 10:1216102. [PMID: 37908227 PMCID: PMC10613994 DOI: 10.3389/fmolb.2023.1216102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 09/04/2023] [Indexed: 11/02/2023] Open
Abstract
Glioma is one of the most intractable types of cancer, due to delayed diagnosis at advanced stages. The clinical symptoms of glioma are unclear and due to a variety of glioma subtypes, available low-invasive testing is not effective enough to be introduced into routine medical laboratory practice. Therefore, recent advances in the clinical diagnosis of glioma have focused on liquid biopsy approaches that utilize a wide range of techniques such as next-generation sequencing (NGS), droplet-digital polymerase chain reaction (ddPCR), and quantitative PCR (qPCR). Among all techniques, NGS is the most advantageous diagnostic method. Despite the rapid cheapening of NGS experiments, the cost of such diagnostics remains high. Moreover, high-throughput diagnostics are not appropriate for molecular profiling of gliomas since patients with gliomas exhibit only a few diagnostic markers. In this review, we highlighted all available assays for glioma diagnosing for main pathogenic glioma DNA sequence alterations. In the present study, we reviewed the possibility of integrating routine molecular methods into the diagnosis of gliomas. We state that the development of an affordable assay covering all glioma genetic aberrations could enable early detection and improve patient outcomes. Moreover, the development of such molecular diagnostic kits could potentially be a good alternative to expensive NGS-based approaches.
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Affiliation(s)
- Alina Penkova
- Institute of Life Sciences and Biomedicine, Far Eastern Federal University, Vladivostok, Russia
| | - Olga Kuziakova
- Institute of Life Sciences and Biomedicine, Far Eastern Federal University, Vladivostok, Russia
| | - Valeriia Gulaia
- Institute of Life Sciences and Biomedicine, Far Eastern Federal University, Vladivostok, Russia
| | - Vladlena Tiasto
- Institute of Life Sciences and Biomedicine, Far Eastern Federal University, Vladivostok, Russia
| | - Nikolay V. Goncharov
- Institute of Life Sciences and Biomedicine, Far Eastern Federal University, Vladivostok, Russia
- A. V. Zhirmunsky National Scientific Center of Marine Biology, FEB RAS, Vladivostok, Russia
| | - Daria Lanskikh
- Institute of Life Sciences and Biomedicine, Far Eastern Federal University, Vladivostok, Russia
| | - Valeriia Zhmenia
- Institute of Life Sciences and Biomedicine, Far Eastern Federal University, Vladivostok, Russia
| | - Ivan Baklanov
- Institute of Life Sciences and Biomedicine, Far Eastern Federal University, Vladivostok, Russia
- A. V. Zhirmunsky National Scientific Center of Marine Biology, FEB RAS, Vladivostok, Russia
| | - Vladislav Farniev
- Institute of Life Sciences and Biomedicine, Far Eastern Federal University, Vladivostok, Russia
| | - Vadim Kumeiko
- Institute of Life Sciences and Biomedicine, Far Eastern Federal University, Vladivostok, Russia
- A. V. Zhirmunsky National Scientific Center of Marine Biology, FEB RAS, Vladivostok, Russia
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10
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Kurt S, Kaymaz Y, Ateş D, Tanyolaç MB. Complete chloroplast genome of Lens lamottei reveals intraspecies variation among with Lens culinaris. Sci Rep 2023; 13:14959. [PMID: 37696838 PMCID: PMC10495401 DOI: 10.1038/s41598-023-41287-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Accepted: 08/24/2023] [Indexed: 09/13/2023] Open
Abstract
Lens lamottei is a member of the Fabaceae family and the second gene pool of the genus Lens. The environmental factors that drove the divergence among wild and cultivated species have been studied extensively. Recent research has focused on genomic signatures associated with various phenotypes with the acceleration of next-generation techniques in molecular profiling. Therefore, in this study, we provide the complete sequence of the chloroplast genome sequence in the wild Lens species L. lamottei with a deep coverage of 713 × next-generation sequencing (NGS) data for the first time. Compared to the cultivated species, Lens culinaris, we identified synonymous, and nonsynonymous changes in the protein-coding regions of the genes ndhB, ndhF, ndhH, petA, rpoA, rpoC2, rps3, and ycf2 in L. lamottei. Phylogenetic analysis of chloroplast genomes of various plants under Leguminosae revealed that L. lamottei and L. culinaris are closest to one another than to other species. The complete chloroplast genome of L. lamottei also allowed us to reanalyze previously published transcriptomic data, which showed high levels of gene expression for ATP-synthase, rubisco, and photosystem genes. Overall, this study provides a deeper insight into the diversity of Lens species and the agricultural importance of these plants through their chloroplast genomes.
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Affiliation(s)
- Selda Kurt
- Faculty of Engineering, Department of Bioengineering, Ege University, Izmir, Turkey
| | - Yasin Kaymaz
- Faculty of Engineering, Department of Bioengineering, Ege University, Izmir, Turkey
| | - Duygu Ateş
- Faculty of Engineering, Department of Bioengineering, Ege University, Izmir, Turkey
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11
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Guo Y, Wang Y, Zang X, Luo C, Huang C, Cong K, Guo X. Transcriptomic analysis of Amaranthus retroflex resistant to PPO-inhibitory herbicides. PLoS One 2023; 18:e0288775. [PMID: 37616256 PMCID: PMC10449157 DOI: 10.1371/journal.pone.0288775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Accepted: 07/04/2023] [Indexed: 08/26/2023] Open
Abstract
Amaranthus retroflexus L. is one of the malignant weeds which can cause a reduction in the soybean yield. We found a population of A. retroflexus (R-Q) resistant to fomesafen through the initial screening of whole-plant dose response bioassay in the research. The resistance index of the population (R-Q) was 183 times of the sensitive population (S-N). The resistant and sensitive populations were used as experimental materials in the paper. Strand-specific RNA-Seq analyses of R‒Q and S‒N populations obtained from herbicide-treated and mock-treated leaf samples after treatment were conducted to generate a full-length transcriptome database. We analyzed differentially expressed genes (DEGs) among the R-Q and S‒N A. retroflexus populations treated with recommended dose and mock-treated on the 1st (24 h) and 3rd (72 h) days to identify genes involved in fomesafen resistance. All 82,287 unigenes were annotated by Blastx search with E-value < 0.00001 from 7 databases. A total of 94,815 DEGs among the three group comparisons were identified. Two nuclear genes encoding PPO (PPX1 and PPX2) and five unigenes belonging to the AP2-EREBP, GRAS, NAC, bHLH and bZIP families exhibited different expression patterns between individuals of S‒N and R-Q populations. The A. retroflexus transcriptome and specific transcription factor families which can respond to fomesafen in resistant and susceptible genotypes were reported in this paper. The PPX1 and PPX2 genes of the target enzyme were identified. The study establishes the foundation for future research and provides opportunities to manage resistant weeds better.
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Affiliation(s)
- Yulian Guo
- Institute of Plant Protection, Heilongjiang Academy of Agricultural Sciences, Harbin, Heilongjiang Province, China
| | - Yu Wang
- Institute of Plant Protection, Heilongjiang Academy of Agricultural Sciences, Harbin, Heilongjiang Province, China
| | - Xiangyun Zang
- Institute of Plant Protection, Heilongjiang Academy of Agricultural Sciences, Harbin, Heilongjiang Province, China
| | - Chan Luo
- Institute of Plant Protection, Heilongjiang Academy of Agricultural Sciences, Harbin, Heilongjiang Province, China
| | - Chunyan Huang
- Institute of Plant Protection, Heilongjiang Academy of Agricultural Sciences, Harbin, Heilongjiang Province, China
| | - Keqiang Cong
- Institute of Plant Protection, Heilongjiang Academy of Agricultural Sciences, Harbin, Heilongjiang Province, China
| | - Xiaotong Guo
- Institute of Plant Protection, Heilongjiang Academy of Agricultural Sciences, Harbin, Heilongjiang Province, China
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12
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Sun J, Su M, Ma J, Xu M, Ma C, Li W, Liu R, He Q, Su Z. Cross-platform comparisons for targeted bisulfite sequencing of MGISEQ-2000 and NovaSeq6000. Clin Epigenetics 2023; 15:130. [PMID: 37582783 PMCID: PMC10426093 DOI: 10.1186/s13148-023-01543-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 07/28/2023] [Indexed: 08/17/2023] Open
Abstract
BACKGROUND An accurate and reproducible next-generation sequencing platform is essential to identify malignancy-related abnormal DNA methylation changes and translate them into clinical applications including cancer detection, prognosis, and surveillance. However, high-quality DNA methylation sequencing has been challenging because poor sequence diversity of the bisulfite-converted libraries severely impairs sequencing quality and yield. In this study, we tested MGISEQ-2000 Sequencer's capability of DNA methylation sequencing with a published non-invasive pancreatic cancer detection assay, using NovaSeq6000 as the benchmark. RESULTS We sequenced a series of synthetic cell-free DNA (cfDNA) samples with different tumor fractions and found MGISEQ-2000 yielded data with similar quality as NovaSeq6000. The methylation levels measured by MGISEQ-2000 demonstrated high consistency with NovaSeq6000. Moreover, MGISEQ-2000 showed a comparable analytic sensitivity with NovaSeq6000, suggesting its potential for clinical detection. As to evaluate the clinical performance of MGISEQ-2000, we sequenced 24 clinical samples and predicted the pathology of the samples with a clinical diagnosis model, PDACatch classifier. The clinical model performance of MGISEQ-2000's data was highly consistent with that of NovaSeq6000's data, with the area under the curve of 1. We also tested the model's robustness with MGISEQ-2000's data when reducing the sequencing depth. The results showed that MGISEQ-2000's data showed matching robustness of the PDACatch classifier with NovaSeq6000's data. CONCLUSIONS Taken together, MGISEQ-2000 demonstrated similar data quality, consistency of the methylation levels, comparable analytic sensitivity, and matching clinical performance, supporting its application in future non-invasive early cancer detection investigations by detecting distinct methylation patterns of cfDNAs.
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Affiliation(s)
- Jin Sun
- Singlera Genomics (Shanghai) Ltd., No. 500, Furonghua Road, Shanghai, 201203, China
| | - Mingyang Su
- Singlera Genomics (Shanghai) Ltd., No. 500, Furonghua Road, Shanghai, 201203, China
| | - Jianhua Ma
- Singlera Genomics (Shanghai) Ltd., No. 500, Furonghua Road, Shanghai, 201203, China
| | - Minjie Xu
- Singlera Genomics (Shanghai) Ltd., No. 500, Furonghua Road, Shanghai, 201203, China
| | - Chengcheng Ma
- Singlera Genomics (Shanghai) Ltd., No. 500, Furonghua Road, Shanghai, 201203, China
| | - Wei Li
- Singlera Genomics (Shanghai) Ltd., No. 500, Furonghua Road, Shanghai, 201203, China
| | - Rui Liu
- Singlera Genomics (Shanghai) Ltd., No. 500, Furonghua Road, Shanghai, 201203, China
| | - Qiye He
- Singlera Genomics (Shanghai) Ltd., No. 500, Furonghua Road, Shanghai, 201203, China.
| | - Zhixi Su
- Singlera Genomics (Shanghai) Ltd., No. 500, Furonghua Road, Shanghai, 201203, China.
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13
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Gryaznova M, Smirnova Y, Burakova I, Morozova P, Nesterova E, Gladkikh M, Mikhaylov E, Syromyatnikov M. Characteristics of the Fecal Microbiome of Piglets with Diarrhea Identified Using Shotgun Metagenomics Sequencing. Animals (Basel) 2023; 13:2303. [PMID: 37508080 PMCID: PMC10376196 DOI: 10.3390/ani13142303] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 07/05/2023] [Accepted: 07/12/2023] [Indexed: 07/30/2023] Open
Abstract
Diarrhea in piglets is one of the most common diseases leading to high mortality and, as a result, to economic losses. Shotgun metagenomic sequencing was performed on the DNBSEQ-G50, MGI system to study the role of the fecal microbiome in the development of diarrhea in newborn piglets. Analysis of the study data showed that the composition of the fecal microbiome at the level of bacteria and fungi did not differ in piglets with diarrhea from the healthy group. Bacteria belonging to the phyla Firmicutes, Bacteroidetes, Proteobacteria, Actinobacteria, and Fusobacteria were the most abundant. However, a higher level of bacterial alpha diversity was observed in the group of piglets with diarrhea, which may be due to dysbacteriosis and inflammation. The study of the virome showed the difference between the two types of phages: Bacteroides B40-8 prevailed in diseased piglets, while Escherichia virus BP4 was found in greater numbers in healthy piglets. The results of our study suggest that the association between the fecal microbiome and susceptibility to diarrhea in suckling piglets may have been previously overestimated.
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Affiliation(s)
- Mariya Gryaznova
- Laboratory of Metagenomics and Food Biotechnology, Voronezh State University of Engineering Technologies, 394036 Voronezh, Russia
- Department of Genetics, Cytology and Bioengineering, Voronezh State University, 394018 Voronezh, Russia
| | - Yuliya Smirnova
- Laboratory of Metagenomics and Food Biotechnology, Voronezh State University of Engineering Technologies, 394036 Voronezh, Russia
- Department of Genetics, Cytology and Bioengineering, Voronezh State University, 394018 Voronezh, Russia
| | - Inna Burakova
- Laboratory of Metagenomics and Food Biotechnology, Voronezh State University of Engineering Technologies, 394036 Voronezh, Russia
| | - Polina Morozova
- Laboratory of Metagenomics and Food Biotechnology, Voronezh State University of Engineering Technologies, 394036 Voronezh, Russia
- Department of Genetics, Cytology and Bioengineering, Voronezh State University, 394018 Voronezh, Russia
| | - Ekaterina Nesterova
- Laboratory of Metagenomics and Food Biotechnology, Voronezh State University of Engineering Technologies, 394036 Voronezh, Russia
- Department of Genetics, Cytology and Bioengineering, Voronezh State University, 394018 Voronezh, Russia
| | - Mariya Gladkikh
- Laboratory of Metagenomics and Food Biotechnology, Voronezh State University of Engineering Technologies, 394036 Voronezh, Russia
| | - Evgeny Mikhaylov
- FSBSI All-Russian Veterinary Research Institute of Pathology, Pharmacology and Therapy, 394061 Voronezh, Russia
| | - Mikhail Syromyatnikov
- Laboratory of Metagenomics and Food Biotechnology, Voronezh State University of Engineering Technologies, 394036 Voronezh, Russia
- Department of Genetics, Cytology and Bioengineering, Voronezh State University, 394018 Voronezh, Russia
- FSBSI All-Russian Veterinary Research Institute of Pathology, Pharmacology and Therapy, 394061 Voronezh, Russia
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14
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Rayford KJ, Cooley A, Strode AW, Osi I, Arun A, Lima MF, Misra S, Pratap S, Nde PN. Trypanosoma cruzi dysregulates expression profile of piRNAs in primary human cardiac fibroblasts during early infection phase. Front Cell Infect Microbiol 2023; 13:1083379. [PMID: 36936778 PMCID: PMC10017870 DOI: 10.3389/fcimb.2023.1083379] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 02/13/2023] [Indexed: 03/06/2023] Open
Abstract
Trypanosoma cruzi, the etiological agent of Chagas Disease, causes severe morbidity, mortality, and economic burden worldwide. Though originally endemic to Central and South America, globalization has led to increased parasite presence in most industrialized countries. About 40% of infected individuals will develop cardiovascular, neurological, and/or gastrointestinal pathologies. Accumulating evidence suggests that the parasite induces alterations in host gene expression profiles in order to facilitate infection and pathogenesis. The role of regulatory gene expression machinery during T. cruzi infection, particularly small noncoding RNAs, has yet to be elucidated. In this study, we aim to evaluate dysregulation of a class of sncRNAs called piRNAs during early phase of T. cruzi infection in primary human cardiac fibroblasts by RNA-Seq. We subsequently performed in silico analysis to predict piRNA-mRNA interactions. We validated the expression of these selected piRNAs and their targets during early parasite infection phase by stem loop qPCR and qPCR, respectively. We found about 26,496,863 clean reads (92.72%) which mapped to the human reference genome. During parasite challenge, 441 unique piRNAs were differentially expressed. Of these differentially expressed piRNAs, 29 were known and 412 were novel. In silico analysis showed several of these piRNAs were computationally predicted to target and potentially regulate expression of genes including SMAD2, EGR1, ICAM1, CX3CL1, and CXCR2, which have been implicated in parasite infection, pathogenesis, and various cardiomyopathies. Further evaluation of the function of these individual piRNAs in gene regulation and expression will enhance our understanding of early molecular mechanisms contributing to infection and pathogenesis. Our findings here suggest that piRNAs play important roles in infectious disease pathogenesis and can serve as potential biomarkers and therapeutic targets.
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Affiliation(s)
- Kayla J. Rayford
- Department of Microbiology, Immunology, and Physiology, Meharry Medical College, Nashville, TN, United States
| | - Ayorinde Cooley
- Department of Microbiology, Immunology, and Physiology, Meharry Medical College, Nashville, TN, United States
| | - Anthony W. Strode
- Department of Microbiology, Immunology, and Physiology, Meharry Medical College, Nashville, TN, United States
| | - Inmar Osi
- Department of Microbiology, Immunology, and Physiology, Meharry Medical College, Nashville, TN, United States
| | - Ashutosh Arun
- Department of Microbiology, Immunology, and Physiology, Meharry Medical College, Nashville, TN, United States
| | - Maria F. Lima
- Biomedical Sciences, School of Medicine, City College of New York, New York, NY, United States
| | - Smita Misra
- School of Graduate Studies and Research, Meharry Medical College, Nashville, TN, United States
| | - Siddharth Pratap
- Department of Microbiology, Immunology, and Physiology, Meharry Medical College, Nashville, TN, United States
- Bioinformatics Core, School of Graduate Studies and Research, Meharry Medical College, Nashville, TN, United States
| | - Pius N. Nde
- Department of Microbiology, Immunology, and Physiology, Meharry Medical College, Nashville, TN, United States
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15
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Henriques DG, Miranda RL, Dezonne RS, Wildemberg LE, Camacho AHDS, Chimelli L, Kasuki L, Lamback EB, Guterres A, Gadelha MR. miR-383-5p, miR-181a-5p, and miR-181b-5p as Predictors of Response to First-Generation Somatostatin Receptor Ligands in Acromegaly. Int J Mol Sci 2023; 24:ijms24032875. [PMID: 36769196 PMCID: PMC9918086 DOI: 10.3390/ijms24032875] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 01/19/2023] [Accepted: 01/24/2023] [Indexed: 02/05/2023] Open
Abstract
Acromegaly is a chronic systemic disease caused in the vast majority of cases by growth hormone (GH)-secreting adenoma, with surgery being the first-line treatment. When a cure is not attained with surgery, first-generation somatostatin receptor ligands (fg-SRLs) are the most common medication prescribed. Predictors of response to fg-SRLs have been studied; however, they cannot fully predict the response to fg-SRL. MicroRNAs are small RNAs, the main role of which is messenger RNA (mRNA) post-transcriptional regulation. This study aimed to identify the microRNAs involved in resistance to treatment with fg-SRLs in acromegaly. Ten patients with acromegaly undergoing treatment with fg-SRLs were selected to undergo miRNA sequencing: five controlled and five uncontrolled with treatment. Bioinformatic analysis was performed to detect differentially expressed miRNAs. Then, the same 10 samples were used for validation by qPCR and an additional 22 samples were analyzed, totaling 32 samples. e We found 59 differentially expressed miRNAs in the first analysis. miR-181a-5p and miR-181b-5p were downregulated, and miR-383-5p was upregulated in the uncontrolled group. Receiver operating characteristic (ROC) curve analysis of miR-383-5p showed an NPV of 84.3% and a PPV of 84.5%. In summary, miR-181a-5p, miR-181b-5p, and miR-383-5p are biomarkers of response to fg-SRLs, and they can be used individually or included in prediction models as tools to guide clinical decisions.
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Affiliation(s)
- Daniel G. Henriques
- Endocrine Unit and Neuroendocrinology Research Center, Medical School and Hospital Universitário Clementino Fraga Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-617, Brazil
| | - Renan Lyra Miranda
- Neuropathology and Molecular Genetics Laboratory, Instituto Estadual do Cérebro Paulo Niemeyer, Rio de Janeiro 20231-092, Brazil
| | - Rômulo Sperduto Dezonne
- Neuropathology and Molecular Genetics Laboratory, Instituto Estadual do Cérebro Paulo Niemeyer, Rio de Janeiro 20231-092, Brazil
| | - Luiz Eduardo Wildemberg
- Endocrine Unit and Neuroendocrinology Research Center, Medical School and Hospital Universitário Clementino Fraga Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-617, Brazil
- Neuroendocrinology Division, Instituto Estadual do Cérebro Paulo Niemeyer, Rio de Janeiro 20231-092, Brazil
| | - Aline Helen da Silva Camacho
- Neuropathology and Molecular Genetics Laboratory, Instituto Estadual do Cérebro Paulo Niemeyer, Rio de Janeiro 20231-092, Brazil
| | - Leila Chimelli
- Neuropathology and Molecular Genetics Laboratory, Instituto Estadual do Cérebro Paulo Niemeyer, Rio de Janeiro 20231-092, Brazil
| | - Leandro Kasuki
- Endocrine Unit and Neuroendocrinology Research Center, Medical School and Hospital Universitário Clementino Fraga Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-617, Brazil
- Neuroendocrinology Division, Instituto Estadual do Cérebro Paulo Niemeyer, Rio de Janeiro 20231-092, Brazil
- Endocrinology Division, Hospital Federal de Bonsucesso, Rio de Janeiro 21041-020, Brazil
| | - Elisa B. Lamback
- Endocrine Unit and Neuroendocrinology Research Center, Medical School and Hospital Universitário Clementino Fraga Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-617, Brazil
- Neuropathology and Molecular Genetics Laboratory, Instituto Estadual do Cérebro Paulo Niemeyer, Rio de Janeiro 20231-092, Brazil
- Neuroendocrinology Division, Instituto Estadual do Cérebro Paulo Niemeyer, Rio de Janeiro 20231-092, Brazil
| | - Alexandro Guterres
- Neuropathology and Molecular Genetics Laboratory, Instituto Estadual do Cérebro Paulo Niemeyer, Rio de Janeiro 20231-092, Brazil
| | - Monica R. Gadelha
- Endocrine Unit and Neuroendocrinology Research Center, Medical School and Hospital Universitário Clementino Fraga Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-617, Brazil
- Neuropathology and Molecular Genetics Laboratory, Instituto Estadual do Cérebro Paulo Niemeyer, Rio de Janeiro 20231-092, Brazil
- Neuroendocrinology Division, Instituto Estadual do Cérebro Paulo Niemeyer, Rio de Janeiro 20231-092, Brazil
- Correspondence:
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16
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Xie SC, Zhou CX, Zhai BT, Zheng WB, Liu GH, Zhu XQ. A combined miRNA-piRNA signature in the serum and urine of rabbits infected with Toxoplasma gondii oocysts. Parasit Vectors 2022; 15:490. [PMID: 36572911 PMCID: PMC9793633 DOI: 10.1186/s13071-022-05620-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 12/15/2022] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Increasing evidence has shown that non-coding RNA (ncRNA) molecules play fundamental roles in cells, and many are stable in body fluids as circulating RNAs. Study on these ncRNAs will provide insights into toxoplasmosis pathophysiology and/or help reveal diagnostic biomarkers. METHODS We performed a high-throughput RNA-Seq study to comprehensively profile the microRNAs (miRNAs) and PIWI-interacting RNAs (piRNAs) in rabbit serum and urine after infection with Toxoplasma gondii oocysts during the whole infection process. RESULTS Total RNA extracted from serum and urine samples of acutely infected [8 days post-infection (DPI)], chronically infected (70 DPI) and uninfected rabbits were subjected to genome-wide small RNA sequencing. We identified 2089 miRNAs and 2224 novel piRNAs from the rabbit sera associated with T. gondii infection. Meanwhile, a total of 518 miRNAs and 4182 novel piRNAs were identified in the rabbit urine associated with T. gondii infection. Of these identified small ncRNAs, 1178 and 1317 serum miRNAs and 311 and 294 urine miRNAs were identified as differentially expressed (DE) miRNAs in the acute and chronic stages of infections, respectively. A total of 1748 and 1814 serum piRNAs and 597 and 708 urine piRNAs were found in the acute and chronic infection stages, respectively. Of these dysregulated ncRNAs, a total of 88 common DE miRNAs and 120 DE novel piRNAs were found in both serum and urine samples of infected rabbits. CONCLUSIONS These findings provide valuable data for revealing the physiology of herbivore toxoplasmosis caused by oocyst infection. Circulating ncRNAs identified in this study are potential novel diagnostic biomarkers for the detection/diagnosis of toxoplasmosis in herbivorous animals.
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Affiliation(s)
- Shi-Chen Xie
- grid.257160.70000 0004 1761 0331Research Center for Parasites and Vectors, College of Veterinary Medicine, Hunan Agricultural University, Changsha, 410128 Hunan Province People’s Republic of China ,grid.412545.30000 0004 1798 1300Laboratory of Parasitic Diseases, College of Veterinary Medicine, Shanxi Agricultural University, Taigu, 030801 Shanxi Province People’s Republic of China
| | - Chun-Xue Zhou
- grid.27255.370000 0004 1761 1174Department of Pathogen Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, 250012 Shandong Province People’s Republic of China
| | - Bin-Tao Zhai
- grid.410727.70000 0001 0526 1937Key Laboratory of Veterinary Pharmaceutical Development, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Lanzhou, 730050 Gansu Province People’s Republic of China ,grid.410727.70000 0001 0526 1937State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046 Gansu Province People’s Republic of China
| | - Wen-Bin Zheng
- grid.412545.30000 0004 1798 1300Laboratory of Parasitic Diseases, College of Veterinary Medicine, Shanxi Agricultural University, Taigu, 030801 Shanxi Province People’s Republic of China
| | - Guo-Hua Liu
- grid.257160.70000 0004 1761 0331Research Center for Parasites and Vectors, College of Veterinary Medicine, Hunan Agricultural University, Changsha, 410128 Hunan Province People’s Republic of China
| | - Xing-Quan Zhu
- grid.257160.70000 0004 1761 0331Research Center for Parasites and Vectors, College of Veterinary Medicine, Hunan Agricultural University, Changsha, 410128 Hunan Province People’s Republic of China ,grid.412545.30000 0004 1798 1300Laboratory of Parasitic Diseases, College of Veterinary Medicine, Shanxi Agricultural University, Taigu, 030801 Shanxi Province People’s Republic of China
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17
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Zhu M, Tao L, Zhang J, Liu R, Tian H, Hu C, Zhu Y, Li M, Wei Z, Yi J, Li J, Gou X. The type-B response regulators ARR10, ARR12, and ARR18 specify the central cell in Arabidopsis. THE PLANT CELL 2022; 34:4714-4737. [PMID: 36130292 PMCID: PMC9709988 DOI: 10.1093/plcell/koac285] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 09/15/2022] [Indexed: 06/15/2023]
Abstract
In Arabidopsis thaliana, the female gametophyte consists of two synergid cells, an egg cell, a diploid central cell, and three antipodal cells. CYTOKININ INDEPENDENT 1 (CKI1), a histidine kinase constitutively activating the cytokinin signaling pathway, specifies the central cell and restricts the egg cell. However, the mechanism regulating CKI1-dependent central cell specification is largely unknown. Here, we showed that the type-B ARABIDOPSIS RESPONSE REGULATORS10, 12, and 18 (ARR10/12/18) localize at the chalazal pole of the female gametophyte. Phenotypic analysis showed that the arr10 12 18 triple mutant is female sterile. We examined the expression patterns of embryo sac marker genes and found that the embryo sac of arr10 12 18 plants had lost central cell identity, a phenotype similar to that of the Arabidopsis cki1 mutant. Genetic analyses demonstrated that ARR10/12/18, CKI1, and ARABIDOPSIS HISTIDINE PHOSPHOTRANSFER PROTEIN2, 3, and 5 (AHP2/3/5) function in a common pathway to regulate female gametophyte development. In addition, constitutively activated ARR10/12/18 in the cki1 embryo sac partially restored the fertility of cki1. Results of transcriptomic analysis supported the conclusion that ARR10/12/18 and CKI1 function together to regulate the identity of the central cell. Our results demonstrated that ARR10/12/18 function downstream of CKI1-AHP2/3/5 as core factors to determine cell fate of the female gametophyte.
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Affiliation(s)
- Mingsong Zhu
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Liang Tao
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Jinghua Zhang
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Ruini Liu
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Hongai Tian
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Chong Hu
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Yafen Zhu
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Meizhen Li
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Zhuoyun Wei
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Jing Yi
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Jia Li
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Xiaoping Gou
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
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18
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Xuan R, Qiu W, Zhou Y, Magnuson JT, Luo S, Greer JB, Xu B, Liu J, Xu EG, Schlenk D, Zheng C. Parental transfer of an antibiotic mixture induces cardiotoxicity in early life-stage zebrafish: A cross-generational study. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 849:157726. [PMID: 35914592 DOI: 10.1016/j.scitotenv.2022.157726] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 07/26/2022] [Accepted: 07/26/2022] [Indexed: 06/15/2023]
Abstract
Antibiotic residues in the aquatic environment have been shown to induce significant adverse effects on the early-life stage development of aquatic organisms, though the underlying molecular mechanisms of these effects have not been well characterized. In this study, we performed global mRNA-miRNA sequencing, canonical pathway analyses, morphological, physiological, immunohistochemical, and behavioral analyses to comprehensively assess the cross-generational cardiotoxicity and mechanisms of antibiotic mixtures in zebrafish. Following parental treatment to 1 and 100 μg/L antibiotic mixtures (15 of the most commonly detected antibiotics) for 150 days, all 15 assessed antibiotics were detected in the F1 eggs, indicating the cross-generational transfer of antibiotics. Global mRNA-miRNA sequencing functional analysis predicted cardiotoxicity in the F1 generation by using the F1 whole fish. Consistent with canonical pathway analyses, significant cardiotoxicity was observed in F1 larvae, as well as the apoptosis of cardiac cells. Furthermore, let-7a-5p regulated the cardiac hypertrophy signaling pathway, suggesting mechanisms of miRNA of let-7 family mediating cross-generational cardiotoxicity of antibiotics in zebrafish. This study lays some groundwork for developing interventions to prevent parental exposure to environmental pollutants such as antibiotics from adversely affecting offspring development.
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Affiliation(s)
- Rongrong Xuan
- The Affiliated Hospital of Medical School, Ningbo University, Ningbo 315020, China
| | - Wenhui Qiu
- School of Public Health and Emergency Management, Southern University of Science and Technology, Shenzhen 518055, China; State Environmental Protection Key Laboratory of Integrated Surface Water-Groundwater Pollution Control, Guangdong Provincial Key Laboratory of Soil and Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, China.
| | - Yuping Zhou
- The Affiliated Hospital of Medical School, Ningbo University, Ningbo 315020, China
| | - Jason T Magnuson
- Department of Environmental Sciences, University of California, Riverside, CA 92521, United States
| | - Shusheng Luo
- State Environmental Protection Key Laboratory of Integrated Surface Water-Groundwater Pollution Control, Guangdong Provincial Key Laboratory of Soil and Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Justin B Greer
- Department of Environmental Sciences, University of California, Riverside, CA 92521, United States
| | - Bentuo Xu
- School of Life and Environmental Science, Wenzhou University, Wenzhou 325035, China
| | - Jingyu Liu
- State Environmental Protection Key Laboratory of Integrated Surface Water-Groundwater Pollution Control, Guangdong Provincial Key Laboratory of Soil and Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Elvis Genbo Xu
- Department of Biology, University of Southern Denmark, Odense 5230, Denmark
| | - Daniel Schlenk
- Department of Environmental Sciences, University of California, Riverside, CA 92521, United States
| | - Chunmiao Zheng
- State Environmental Protection Key Laboratory of Integrated Surface Water-Groundwater Pollution Control, Guangdong Provincial Key Laboratory of Soil and Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, China
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Relationship between CYP2C19 Polymorphism and Clopidogrel Resistance in Patients with Coronary Heart Disease and Ischemic Stroke in China. Genet Res (Camb) 2022; 2022:1901256. [PMID: 36325266 PMCID: PMC9616677 DOI: 10.1155/2022/1901256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 10/15/2022] [Indexed: 11/25/2022] Open
Abstract
Objective Clopidogrel is widely used for preventing ischemic complications related to cardiovascular diseases. However, many patients experience clopidogrel resistance (CR). The polymorphisms of CYP2C19 have been implicated in CR, but CYP2C19 polymorphism considerably varies with both ethnic group and geographical location. This study aimed to investigate the association between CYP2C19 polymorphisms and clopidogrel resistance (CR) in patients with coronary heart disease and ischemic stroke among Han and Tibetan populations in Qinghai Province, China. Methods From June 2019 to January 2020, patients who were diagnosed with coronary heart disease or cerebral infarction in internal medicine of Qinghai Provincial People's Hospital and had taken dual antiplatelet drugs were included in this study. Blood was collected and routine items were completed. Whole exome sequencing was performed for CYP2C19 genetic polymorphisms of CYP2C19∗2 (rs4244285), CYP2C19∗3 (rs4986893), and CYP2C19∗17 (rs12248560). Results A total of 91 patients with coronary heart disease or cerebral infarction (67 Han people (65.99 ± 12.25 years old) and 24 Tibetan (63.6324 Tib years old)) including 52 cases with CR and 39 cases with non-CR were enrolled in this study. For the Han population, the differences in age, glycosylated hemoglobin, activated partial thromboplastin time (APTT), gender, aspirin resistance, and diabetes were significant between the CR and non-CR groups. For the Tibetan population, the two groups showed no significant difference in all indicators. There was no significant difference between CR and non-CR groups for all genotypes (CYP2C19 ∗2, ∗3, and ∗17) in either Han or Tibetan populations. For the Han populations, age, APTT, and aspirin resistance were significantly correlated with CR. Conclusion The present study indicated that CYP2C19∗2, CYP2C19∗3, and CYP2C19∗17 alleles were not correlated with CR for both Han and Tibetan populations in Qinghai Province, while age, APTT, and aspirin resistance were independent risk factors of CR in this region.
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20
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A Comprehensive Characterization of Small RNA Profiles by Massively Parallel Sequencing in Six Forensic Body Fluids/Tissue. Genes (Basel) 2022; 13:genes13091530. [PMID: 36140698 PMCID: PMC9498867 DOI: 10.3390/genes13091530] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 08/15/2022] [Accepted: 08/22/2022] [Indexed: 11/25/2022] Open
Abstract
Body fluids/tissue identification (BFID) is an essential procedure in forensic practice, and RNA profiling has become one of the most important methods. Small non-coding RNAs, being expressed in high copy numbers and resistant to degradation, have great potential in BFID but have not been comprehensively characterized in common forensic stains. In this study, the miRNA, piRNA, snoRNA, and snRNA were sequenced in 30 forensic relevant samples (menstrual blood, saliva, semen, skin, venous blood, and vaginal secretion) using the BGI platform. Based on small RNA profiles, relative specific markers (RSM) and absolute specific markers (ASM) were defined, which can be used to identify a specific body fluid/tissue out of two or six, respectively. A total of 5204 small RNAs were discovered including 1394 miRNAs (including 236 novel miRNA), 3157 piRNAs, 636 snoRNAs, and 17 snRNAs. RSMs for 15 pairwise body fluid/tissue groups were discovered by differential RNA analysis. In addition, 90 ASMs that were specifically expressed in a certain type of body fluid/tissue were screened, among them, snoRNAs were reported first in forensic genetics. In brief, our study deepened the understanding of small RNA profiles in forensic stains and offered potential BFID markers that can be applied in different forensic scenarios.
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21
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Yang Z, Zhang Y, Stubbe-Espejel A, Zhao Y, Liu M, Li J, Zhao Y, Tong G, Liu N, Qi L, Hutchins A, Lin S, Li Y. Vaginal microbiota and personal risk factors associated with HPV status conversion—A new approach to reduce the risk of cervical cancer? PLoS One 2022; 17:e0270521. [PMID: 35944043 PMCID: PMC9362946 DOI: 10.1371/journal.pone.0270521] [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: 12/14/2021] [Accepted: 06/11/2022] [Indexed: 11/19/2022] Open
Abstract
Vaginal microbiota (VMB) is associated with changes in Human papilloma virus (HPV) status, which consequently influences the risk of cervical cancer. This association was often confounded by personal risk factors. This pilot research aimed to explore the relationship between vaginal microbiota, personal risk factors and their interactions with HPV status conversion to identify the vaginal microbiota that was associated with HPV clearance under heterogeneous personal risk factors. A total of 38 women participated by self-collecting a cervicovaginal mucus (CVM) sample that was sent for metagenomics sequencing. Most of the participants also filled in personal risk factors questionnaire through an eHealth platform and authorized the use of their previous HPV genotyping results stored in this eHealth platform. Based on the two HPV results, the participants were grouped into three cohorts, namely HPV negative, HPV persistent infection, and HPV status conversion. The relative abundance of VMB and personal factors were compared among these three cohorts. A correlation investigation was performed between VMB and the significant personal factors to characterize a robustness of the panel for HPV status change using R programming. At baseline, 12 participants were HPV-negative, and 22 were HPV-positive. Within one year, 18 women remained HPV-positive, 12 were HPV-negative and 4 participants showed HPV clearance. The factors in the eHealth questionnaire were systematically evaluated which identified several factors significantly associated with persistent HPV infection, including age, salary, history of reproductive tract infection, and the total number of sexual partners. Concurrent vaginal microbiome samples suggest that a candidate biomarker panel consisting of Lactobacillus gasseri, Streptococcus agalactiae, and Timona prevotella bacteria, which may be associated with HPV clearance. This pilot study indicates a stable HPV status-related vaginal microbe environment. To establish a robust biomarker panel for clinical use, larger cohorts will be recruited into follow-up studies.
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Affiliation(s)
| | - Ye Zhang
- Department of Traditional Chinese Medicine, Women & Children Health Institute Futian Shenzhen, Shenzhen, China
| | | | - Yumei Zhao
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - Mengping Liu
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Jianjun Li
- Department of Traditional Chinese Medicine, Women & Children Health Institute Futian Shenzhen, Shenzhen, China
| | - Yanping Zhao
- BGI-Shenzhen, Shenzhen Key Laboratory of Unknown Pathogen, Shenzhen, China
| | - Guoqing Tong
- Shouguang Hospital of Traditional Chinese Medicine, Reproduction Medicine Center Shanghai, China
| | - Na Liu
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - Le Qi
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - Andrew Hutchins
- Department of Biology, Southern University of Science and Technology, Xueyuan Lu, Shenzhen, China
| | - Songqing Lin
- Department of Traditional Chinese Medicine, Women & Children Health Institute Futian Shenzhen, Shenzhen, China
| | - Yantao Li
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
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22
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Chen B, Ding Z, Zhou X, Wang Y, Huang F, Sun J, Chen J, Han W. Integrated Full-Length Transcriptome and MicroRNA Sequencing Approaches Provide Insights Into Salt Tolerance in Mangrove ( Sonneratia apetala Buch.-Ham.). Front Genet 2022; 13:932832. [PMID: 35899202 PMCID: PMC9310009 DOI: 10.3389/fgene.2022.932832] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 06/08/2022] [Indexed: 11/13/2022] Open
Abstract
MicroRNAs (miRNAs) are small RNA molecules that serve as key players in plant stress responses. Although stress-regulated miRNAs have been explored in various plants, they are not well studied in mangroves. Herein, we combined PacBio isoform sequencing (Iso-Seq) with BGISEQ short-read RNA-seq to probe the role of miRNAs in the salt stress response of the mangrove plant, Sonneratia apetala Buch.-Ham. A total of 1,702,463 circular consensus sequencing reads were generated that produced 295,501 nonredundant full-length transcripts from the leaves of a 1-year-old S. apetala. After sequencing nine small RNA libraries constructed from control and 1- and 28-day 300 mM NaCl treatments, we identified 143 miRNAs (114 known and 29 novel) from a total of >261 million short reads. With the criteria of |log2FC| ≥ 1 and q-value < 0.05, 42 and 70 miRNAs were differentially accumulated after 1- and 28-day salt treatments, respectively. These differential accumulated miRNAs potentially targeted salt-responsive genes encoding transcription factors, ion homeostasis, osmotic protection, and detoxificant-related proteins, reminiscent of their responsibility for salinity adaptation in S. apetala. Particularly, 62 miRNAs were Sonneratia specific under salt stress, of which 34 were co-expressed with their 131 predicted targets, thus producing 140 miRNA-target interactions. Of these, 82 miRNA-target pairs exhibited negative correlations. Eighteen miRNA targets were categorized for the 'environmental information processing' during KEGG analysis and were related to plant hormone signal transduction (ko04075), MAPK signaling pathway-plant (ko04016), and ABC transporters (ko02010). These results underscored miRNAs as possible contributors to mangrove success in severe environments and offer insights into an miRNA-mediated regulatory mechanism of salt response in S. apetala.
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Affiliation(s)
- Beibei Chen
- College of Coastal Agricultural Science, Guangdong Ocean University, Zhanjiang, China
| | - Zeyi Ding
- College of Coastal Agricultural Science, Guangdong Ocean University, Zhanjiang, China
| | - Xiang Zhou
- College of Coastal Agricultural Science, Guangdong Ocean University, Zhanjiang, China
| | - Yue Wang
- Hainan Yazhou Bay Seed Laboratory, Sanya Nanfan Research Institute of Hainan University, Sanya, China
| | - Fei Huang
- College of Coastal Agricultural Science, Guangdong Ocean University, Zhanjiang, China
| | - Jiaxin Sun
- College of Coastal Agricultural Science, Guangdong Ocean University, Zhanjiang, China
| | - Jinhui Chen
- Hainan Yazhou Bay Seed Laboratory, Sanya Nanfan Research Institute of Hainan University, Sanya, China
| | - Weidong Han
- College of Coastal Agricultural Science, Guangdong Ocean University, Zhanjiang, China
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23
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Naval-Sanchez M, Deshpande N, Tran M, Zhang J, Alhomrani M, Alsanie W, Nguyen Q, Nefzger CM. Benchmarking of ATAC Sequencing Data From BGI's Low-Cost DNBSEQ-G400 Instrument for Identification of Open and Occupied Chromatin Regions. Front Mol Biosci 2022; 9:900323. [PMID: 35874611 PMCID: PMC9302965 DOI: 10.3389/fmolb.2022.900323] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Accepted: 05/18/2022] [Indexed: 11/17/2022] Open
Abstract
Background: Chromatin falls into one of two major subtypes: closed heterochromatin and euchromatin which is accessible, transcriptionally active, and occupied by transcription factors (TFs). The most widely used approach to interrogate differences in the chromatin state landscape is the Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq). While library generation is relatively inexpensive, sequencing depth requirements can make this assay cost-prohibitive for some laboratories. Findings: Here, we benchmark data from Beijing Genomics Institute's (BGI) DNBSEQ-G400 low-cost sequencer against data from a standard Illumina instrument (HiSeqX10). For comparisons, the same bulk ATAC-seq libraries generated from pluripotent stem cells (PSCs) and fibroblasts were sequenced on both platforms. Both instruments generate sequencing reads with comparable mapping rates and genomic context. However, DNBSEQ-G400 data contained a significantly higher number of small, sub-nucleosomal reads (>30% increase) and a reduced number of bi-nucleosomal reads (>75% decrease), which resulted in narrower peak bases and improved peak calling, enabling the identification of 4% more differentially accessible regions between PSCs and fibroblasts. The ability to identify master TFs that underpin the PSC state relative to fibroblasts (via HOMER, HINT-ATAC, TOBIAS), namely, foot-printing capacity, were highly similar between data generated on both platforms. Integrative analysis with transcriptional data equally enabled direct recovery of three published 3-factor combinations that have been shown to induce pluripotency. Conclusion: Other than a small increase in peak calling sensitivity for DNBSEQ-G400 data (BGI), both platforms enable comparable levels of open chromatin identification for ATAC-seq library sequencing, yielding similar analytical outcomes, albeit at low-data generation costs in the case of the BGI instrument.
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Affiliation(s)
- Marina Naval-Sanchez
- Institute for Molecular Bioscience, University of Queensland, St Lucia, QLD, Australia
| | - Nikita Deshpande
- Institute for Molecular Bioscience, University of Queensland, St Lucia, QLD, Australia
| | - Minh Tran
- Institute for Molecular Bioscience, University of Queensland, St Lucia, QLD, Australia
| | - Jingyu Zhang
- Institute for Molecular Bioscience, University of Queensland, St Lucia, QLD, Australia
| | - Majid Alhomrani
- Department of Clinical Laboratories Sciences, Faculty of Applied Medical Sciences, Taif University, Taif, Saudi Arabia
- Centre of Biomedical Sciences Research (CBSR), Deanship of Scientific Research, Taif University, Taif, Saudi Arabia
| | - Walaa Alsanie
- Department of Clinical Laboratories Sciences, Faculty of Applied Medical Sciences, Taif University, Taif, Saudi Arabia
- Centre of Biomedical Sciences Research (CBSR), Deanship of Scientific Research, Taif University, Taif, Saudi Arabia
| | - Quan Nguyen
- Institute for Molecular Bioscience, University of Queensland, St Lucia, QLD, Australia
| | - Christian M. Nefzger
- Institute for Molecular Bioscience, University of Queensland, St Lucia, QLD, Australia
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24
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Lang J, Sun J, Yang Z, He L, He Y, Chen Y, Huang L, Li P, Li J, Qin L. Nano2NGS-Muta: a framework for converting nanopore sequencing data to NGS-liked sequencing data for hotspot mutation detection. NAR Genom Bioinform 2022; 4:lqac033. [PMID: 35464239 PMCID: PMC9022462 DOI: 10.1093/nargab/lqac033] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Revised: 03/30/2022] [Accepted: 04/13/2022] [Indexed: 12/12/2022] Open
Abstract
Nanopore sequencing, also known as single-molecule real-time sequencing, is a third/fourth generation sequencing technology that enables deciphering single DNA/RNA molecules without the polymerase chain reaction. Although nanopore sequencing has made significant progress in scientific research and clinical practice, its application has been limited compared with next-generation sequencing (NGS) due to specific design principle and data characteristics, especially in hotspot mutation detection. Therefore, we developed Nano2NGS-Muta as a data analysis framework for hotspot mutation detection based on long reads from nanopore sequencing. Nano2NGS-Muta is characterized by applying nanopore sequencing data to NGS-liked data analysis pipelines. Long reads can be converted into short reads and then processed through existing NGS analysis pipelines in combination with statistical methods for hotspot mutation detection. Nano2NGS-Muta not only effectively avoids false positive/negative results caused by non-random errors and unexpected insertions-deletions (indels) of nanopore sequencing data, improves the detection accuracy of hotspot mutations compared to conventional nanopore sequencing data analysis algorithms but also breaks the barriers of data analysis methods between short-read sequencing and long-read sequencing. We hope Nano2NGS-Muta can serves as a reference method for nanopore sequencing data and promotes higher application scope of nanopore sequencing technology in scientific research and clinical practice.
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Affiliation(s)
- Jidong Lang
- Bioinformatics and Product Development Department, Qitan Technology (Beijing) Co., Ltd, Beijing 100192, China
| | - Jiguo Sun
- Bioinformatics and Product Development Department, Qitan Technology (Beijing) Co., Ltd, Beijing 100192, China
| | - Zhi Yang
- Bioinformatics and Product Development Department, Qitan Technology (Beijing) Co., Ltd, Beijing 100192, China
| | - Lei He
- Bioinformatics and Product Development Department, Qitan Technology (Beijing) Co., Ltd, Beijing 100192, China
| | - Yu He
- Bioinformatics and Product Development Department, Qitan Technology (Beijing) Co., Ltd, Beijing 100192, China
| | - Yanmei Chen
- Bioinformatics and Product Development Department, Qitan Technology (Beijing) Co., Ltd, Beijing 100192, China
| | - Lei Huang
- Bioinformatics and Product Development Department, Qitan Technology (Beijing) Co., Ltd, Beijing 100192, China
| | - Ping Li
- Bioinformatics and Product Development Department, Qitan Technology (Beijing) Co., Ltd, Beijing 100192, China
| | - Jialin Li
- Bioinformatics and Product Development Department, Qitan Technology (Beijing) Co., Ltd, Beijing 100192, China
| | - Liu Qin
- Bioinformatics and Product Development Department, Qitan Technology (Beijing) Co., Ltd, Beijing 100192, China
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25
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Chu C, Poore RC, Bolton MD, Fugate KK. Mechanism of Sugarbeet Seed Germination Enhanced by Hydrogen Peroxide. FRONTIERS IN PLANT SCIENCE 2022; 13:888519. [PMID: 35548268 PMCID: PMC9082935 DOI: 10.3389/fpls.2022.888519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 03/28/2022] [Indexed: 06/15/2023]
Abstract
Seed germination is a critical first stage of plant development but can be arrested by factors including dormancy and environmental conditions. Strategies to enhance germination are of interest to plant breeders to ensure the ability to utilize the genetic potential residing inside a dormant seed. In this study, seed germination in two sugarbeet (Beta vulgaris ssp. vulgaris L.) lines F1004 and F1015 through incubating seeds in hydrogen peroxide (H2O2) solution was improved over 70% relative to germinating seeds through water incubation. It was further found that low germination from water incubation was caused by physical dormancy in F1015 seeds with initial seed imbibition blocked by the seed pericarp, and physiological dormancy in F1004 seeds with germination compromised due to the physiological condition of the embryo. To identify genes that are differentially expressed in response to cellular activities promoted by H2O2 during overcoming different type of dormancies, an RNA-Seq study was carried out and found H2O2 treatment during germination accelerated the degradation of seed stored mRNAs that were synthesized before or during seed storage to provide protections and maintain the dormant state. Comparison of transcripts in H2O2-treated seeds between the two sugarbeet lines identified differentially expressed genes (DEGs) that were higher in F1004 for alleviating physiological dormancy were known to relative to gene expression regulation. The research established that H2O2 overcomes both physical and physiological dormancies by hastening the transition of seeds from dormancy into germination. More DEGs related to gene expression regulation were involved in relieving physiological dormancy which provides new knowledge about the role of exogenous H2O2 as a signaling molecule for regulating gene activities during germination. Moreover, the protocol using H2O2 to promote germination will be useful for rescuing plant germplasms with poor germination.
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26
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Kong J, Qiang W, Jiang J, Hu X, Chen Y, Guo Y, Liu H, Sun S, Gao H, Zhang Y, Gao Y, Liu X, Liu X, Li H. Safflower oil body nanoparticles deliver hFGF10 to hair follicles and reduce microinflammation to accelerate hair regeneration in androgenetic alopecia. Int J Pharm 2022; 616:121537. [PMID: 35150848 DOI: 10.1016/j.ijpharm.2022.121537] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 01/19/2022] [Accepted: 01/29/2022] [Indexed: 12/19/2022]
Abstract
Androgenetic alopecia (AGA) affects physical and mental health with limited therapeutic options. Novel materials and delivery methods have considerable potential to improve the current paradigm of treatment. In this study, we used a novel plant nanoparticle of safflower oil body (SOB) loaded with human fibroblast growth factor 10 (hFGF10) to target hair follicles and accelerate hair regeneration in AGA mice with few adverse effects. Our data revealed that the average particle size of SOB-hFGF10 was 226.73 ± 9.98 nm, with a spherical and uniform structure, and that SOB-hFGF10 was quicker to preferentially penetrate into hair follicles than hFGF2 alone. Using a mouse model of AGA, SOB-hFGF10 was found to significantly improve hair regeneration without any significant toxicity. Furthermore, SOB-hFGF10 inhibited dihydrotestosterone (DHT)-induced TNF-α, IL-1β, and IL-6 overproduction in macrophages in relation to hair follicle microinflammation, thereby enhancing the proliferation of dermal papilla cells. Overall, this study provides an applicable therapeutic method through targeting hair follicles and reducing microinflammation to accelerate hair regeneration in AGA.
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Affiliation(s)
- Jie Kong
- College of Life Science, Engineering Research Center of the Chinese Ministry of Education for Bioreactor and Pharmaceutical Development, Jilin Agricultural University, Changchun 130118, China
| | - Weidong Qiang
- College of Life Science, Engineering Research Center of the Chinese Ministry of Education for Bioreactor and Pharmaceutical Development, Jilin Agricultural University, Changchun 130118, China
| | - Jingyi Jiang
- College of Life Science, Engineering Research Center of the Chinese Ministry of Education for Bioreactor and Pharmaceutical Development, Jilin Agricultural University, Changchun 130118, China
| | - Xingli Hu
- College of Life Science, Engineering Research Center of the Chinese Ministry of Education for Bioreactor and Pharmaceutical Development, Jilin Agricultural University, Changchun 130118, China
| | - Yining Chen
- College of Life Science, Engineering Research Center of the Chinese Ministry of Education for Bioreactor and Pharmaceutical Development, Jilin Agricultural University, Changchun 130118, China
| | - YongXin Guo
- College of Life Science, Engineering Research Center of the Chinese Ministry of Education for Bioreactor and Pharmaceutical Development, Jilin Agricultural University, Changchun 130118, China
| | - Hongxiang Liu
- College of Life Science, Engineering Research Center of the Chinese Ministry of Education for Bioreactor and Pharmaceutical Development, Jilin Agricultural University, Changchun 130118, China
| | - Siming Sun
- College of Life Science, Engineering Research Center of the Chinese Ministry of Education for Bioreactor and Pharmaceutical Development, Jilin Agricultural University, Changchun 130118, China
| | - Hongtao Gao
- College of Tropical Crops, Hainan University, Haikou, China
| | - Yuan Zhang
- College of Life Science, Engineering Research Center of the Chinese Ministry of Education for Bioreactor and Pharmaceutical Development, Jilin Agricultural University, Changchun 130118, China
| | - Yanyan Gao
- College of Life Science, Engineering Research Center of the Chinese Ministry of Education for Bioreactor and Pharmaceutical Development, Jilin Agricultural University, Changchun 130118, China
| | - Xiuming Liu
- College of Life Science, Engineering Research Center of the Chinese Ministry of Education for Bioreactor and Pharmaceutical Development, Jilin Agricultural University, Changchun 130118, China
| | - Xin Liu
- College of Life Science, Engineering Research Center of the Chinese Ministry of Education for Bioreactor and Pharmaceutical Development, Jilin Agricultural University, Changchun 130118, China.
| | - Haiyan Li
- College of Life Science, Engineering Research Center of the Chinese Ministry of Education for Bioreactor and Pharmaceutical Development, Jilin Agricultural University, Changchun 130118, China; College of Tropical Crops, Hainan University, Haikou, China.
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27
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Belova V, Pavlova A, Afasizhev R, Moskalenko V, Korzhanova M, Krivoy A, Cheranev V, Nikashin B, Bulusheva I, Rebrikov D, Korostin D. System analysis of the sequencing quality of human whole exome samples on BGI NGS platform. Sci Rep 2022; 12:609. [PMID: 35022470 PMCID: PMC8755732 DOI: 10.1038/s41598-021-04526-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 12/16/2021] [Indexed: 12/05/2022] Open
Abstract
Human exome sequencing is a classical method used in most medical genetic applications. The leaders in the field are the manufacturers of enrichment kits based on hybridization of cRNA or cDNA biotinylated probes specific for a genomic region of interest. Recently, the platforms manufactured by the Chinese company MGI Tech have become widespread in Europe and Asia. The reliability and quality of the obtained data are already beyond any doubt. However, only a few kits compatible with these sequencers can be used for such specific tasks as exome sequencing. We developed our own solution for library pre-capture pooling and exome enrichment with Agilent probes. In this work, using a set of the standard benchmark samples from the Platinum Genome collection, we demonstrate that the qualitative and quantitative parameters of our protocol which we called "RSMU_exome" exceed those of the MGI Tech kit. Our protocol allows for identifying more SNV and indels, generates fewer PCR duplicates, enables pooling of more samples in a single enrichment procedure, and requires less raw data to obtain results comparable with the MGI Tech's protocol. The cost of our protocol is also lower than that of MGI Tech's solution.
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Affiliation(s)
- Vera Belova
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Medical University, Ostovityanova str. 1, Moscow, Russian Federation, 117997.
| | - Anna Pavlova
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Medical University, Ostovityanova str. 1, Moscow, Russian Federation, 117997
| | - Robert Afasizhev
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Medical University, Ostovityanova str. 1, Moscow, Russian Federation, 117997
| | - Viktoriya Moskalenko
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Medical University, Ostovityanova str. 1, Moscow, Russian Federation, 117997
| | - Margarita Korzhanova
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Medical University, Ostovityanova str. 1, Moscow, Russian Federation, 117997
| | - Andrey Krivoy
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Medical University, Ostovityanova str. 1, Moscow, Russian Federation, 117997
| | - Valery Cheranev
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Medical University, Ostovityanova str. 1, Moscow, Russian Federation, 117997
| | - Boris Nikashin
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Medical University, Ostovityanova str. 1, Moscow, Russian Federation, 117997
| | - Irina Bulusheva
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Medical University, Ostovityanova str. 1, Moscow, Russian Federation, 117997
| | - Denis Rebrikov
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Medical University, Ostovityanova str. 1, Moscow, Russian Federation, 117997
| | - Dmitriy Korostin
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Medical University, Ostovityanova str. 1, Moscow, Russian Federation, 117997
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28
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Lang J, Zhu R, Sun X, Zhu S, Li T, Shi X, Sun Y, Yang Z, Wang W, Bing P, He B, Tian G. Evaluation of the MGISEQ-2000 Sequencing Platform for Illumina Target Capture Sequencing Libraries. Front Genet 2021; 12:730519. [PMID: 34777467 PMCID: PMC8578046 DOI: 10.3389/fgene.2021.730519] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 09/24/2021] [Indexed: 01/19/2023] Open
Abstract
Illumina is the leading sequencing platform in the next-generation sequencing (NGS) market globally. In recent years, MGI Tech has presented a series of new sequencers, including DNBSEQ-T7, MGISEQ-2000 and MGISEQ-200. As a complex application of NGS, cancer-detecting panels pose increasing demands for the high accuracy and sensitivity of sequencing and data analysis. In this study, we used the same capture DNA libraries constructed based on the Illumina protocol to evaluate the performance of the Illumina Nextseq500 and MGISEQ-2000 sequencing platforms. We found that the two platforms had high consistency in the results of hotspot mutation analysis; more importantly, we found that there was a significant loss of fragments in the 101-133 bp size range on the MGISEQ-2000 sequencing platform for Illumina libraries, but not for the capture DNA libraries prepared based on the MGISEQ protocol. This phenomenon may indicate fragment selection or low fragment ligation efficiency during the DNA circularization step, which is a unique step of the MGISEQ-2000 sequence platform. In conclusion, these different sequencing libraries and corresponding sequencing platforms are compatible with each other, but protocol and platform selection need to be carefully evaluated in combination with research purpose.
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Affiliation(s)
- Jidong Lang
- Bioinformatics and R and D Department, Geneis (Beijing) Co. Ltd., Beijing, China.,Qingdao Geneis Institute of Big Data Mining and Precision Medicine, Qingdao, China.,Academician Workstation, Changsha Medical University, Changsha, China
| | - Rongrong Zhu
- Vascular Surgery Department, Tsinghua University Affiliated Beijing Tsinghua Changgung Hospital, Beijing, China
| | - Xue Sun
- Bioinformatics and R and D Department, Geneis (Beijing) Co. Ltd., Beijing, China
| | - Siyu Zhu
- Department of Medicine, School of Medicine, University of California at San Diego, La Jolla, CA, United States
| | - Tianbao Li
- Bioinformatics and R and D Department, Geneis (Beijing) Co. Ltd., Beijing, China.,Qingdao Geneis Institute of Big Data Mining and Precision Medicine, Qingdao, China
| | - Xiaoli Shi
- Bioinformatics and R and D Department, Geneis (Beijing) Co. Ltd., Beijing, China
| | - Yanqi Sun
- Bioinformatics and R and D Department, Geneis (Beijing) Co. Ltd., Beijing, China
| | - Zhou Yang
- Bioinformatics and R and D Department, Geneis (Beijing) Co. Ltd., Beijing, China
| | - Weiwei Wang
- Bioinformatics and R and D Department, Geneis (Beijing) Co. Ltd., Beijing, China.,Qingdao Geneis Institute of Big Data Mining and Precision Medicine, Qingdao, China
| | - Pingping Bing
- Academician Workstation, Changsha Medical University, Changsha, China
| | - Binsheng He
- Academician Workstation, Changsha Medical University, Changsha, China
| | - Geng Tian
- Bioinformatics and R and D Department, Geneis (Beijing) Co. Ltd., Beijing, China.,Qingdao Geneis Institute of Big Data Mining and Precision Medicine, Qingdao, China
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29
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Wang JS, Kamath T, Mazur CM, Mirzamohammadi F, Rotter D, Hojo H, Castro CD, Tokavanich N, Patel R, Govea N, Enishi T, Wu Y, da Silva Martins J, Bruce M, Brooks DJ, Bouxsein ML, Tokarz D, Lin CP, Abdul A, Macosko EZ, Fiscaletti M, Munns CF, Ryder P, Kost-Alimova M, Byrne P, Cimini B, Fujiwara M, Kronenberg HM, Wein MN. Control of osteocyte dendrite formation by Sp7 and its target gene osteocrin. Nat Commun 2021; 12:6271. [PMID: 34725346 PMCID: PMC8560803 DOI: 10.1038/s41467-021-26571-7] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 10/12/2021] [Indexed: 02/05/2023] Open
Abstract
Some osteoblasts embed within bone matrix, change shape, and become dendrite-bearing osteocytes. The circuitry that drives dendrite formation during "osteocytogenesis" is poorly understood. Here we show that deletion of Sp7 in osteoblasts and osteocytes causes defects in osteocyte dendrites. Profiling of Sp7 target genes and binding sites reveals unexpected repurposing of this transcription factor to drive dendrite formation. Osteocrin is a Sp7 target gene that promotes osteocyte dendrite formation and rescues defects in Sp7-deficient mice. Single-cell RNA-sequencing demonstrates defects in osteocyte maturation in the absence of Sp7. Sp7-dependent osteocyte gene networks are associated with human skeletal diseases. Moreover, humans with a SP7R316C mutation show defective osteocyte morphology. Sp7-dependent genes that mark osteocytes are enriched in neurons, highlighting shared features between osteocytic and neuronal connectivity. These findings reveal a role for Sp7 and its target gene Osteocrin in osteocytogenesis, revealing that pathways that control osteocyte development influence human bone diseases.
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Affiliation(s)
- Jialiang S Wang
- Endocrine Unit, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Tushar Kamath
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Courtney M Mazur
- Endocrine Unit, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Fatemeh Mirzamohammadi
- Endocrine Unit, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Plastic and Reconstructive Surgery, Wright State University, Dayton, OH, USA
| | - Daniel Rotter
- Endocrine Unit, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- University of Applied Sciences Technikum Wien, Vienna, Austria
| | - Hironori Hojo
- Center for Disease Biology and Integrative Medicine, The University of Tokyo Graduate School of Medicine, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Christian D Castro
- Endocrine Unit, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Nicha Tokavanich
- Endocrine Unit, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Rushi Patel
- Endocrine Unit, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Nicolas Govea
- Endocrine Unit, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Anesthesiology, Weill Cornell Medical School, New York, NY, USA
| | - Tetsuya Enishi
- Endocrine Unit, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Orthopedic Surgery, Tokushima Municipal Hospital, Tokushima, Japan
| | - Yunshu Wu
- Endocrine Unit, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | | | - Michael Bruce
- Endocrine Unit, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Daniel J Brooks
- Endocrine Unit, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Center for Advanced Orthopedic Studies, Department of Orthopedic Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MaA, USA
| | - Mary L Bouxsein
- Endocrine Unit, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Center for Advanced Orthopedic Studies, Department of Orthopedic Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MaA, USA
| | - Danielle Tokarz
- Advanced Microscopy Program, Center for Systems Biology and Wellman Center for Photomedicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Chemistry, Saint Mary's University, Halifax, Canada
| | - Charles P Lin
- Advanced Microscopy Program, Center for Systems Biology and Wellman Center for Photomedicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Abdul Abdul
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Evan Z Macosko
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Psychiatry, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Melissa Fiscaletti
- Pediatric Department, Sainte-Justine University Hospital Centre, Montreal, Canada
| | - Craig F Munns
- Institute of Endocrinology and Diabetes, The Children's Hospital at Westmead, Sydney, NSW, Australia
- Discipline of Paediatrics & Child Health, University of Sydney, Sydney, 2006, Australia
| | - Pearl Ryder
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Broad Institute of Harvard and MIT, Imaging Platform, Cambridge, MA, USA
| | - Maria Kost-Alimova
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Broad Institute of Harvard and MIT, Center for the Development of Therapeutics, Cambridge, MA, USA
| | - Patrick Byrne
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Broad Institute of Harvard and MIT, Center for the Development of Therapeutics, Cambridge, MA, USA
| | - Beth Cimini
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Broad Institute of Harvard and MIT, Imaging Platform, Cambridge, MA, USA
| | - Makoto Fujiwara
- Department of Pediatrics, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Henry M Kronenberg
- Endocrine Unit, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Marc N Wein
- Endocrine Unit, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Harvard Stem Cell Institute, Cambridge, MA, USA.
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30
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Shan S, Wang SN, Song X, Khashaveh A, Lu ZY, Dhiloo KH, Li RJ, Gao XW, Zhang YJ. Characterization and target gene analysis of microRNAs in the antennae of the parasitoid wasp Microplitis mediator. INSECT SCIENCE 2021; 28:1033-1048. [PMID: 32496619 DOI: 10.1111/1744-7917.12832] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 05/14/2020] [Accepted: 05/26/2020] [Indexed: 06/11/2023]
Abstract
MicroRNAs (miRNAs), a class of non-coding single-strand RNA molecules encoded by endogenous genes, are about 21-24 nucleotides long and are involved in the post-transcriptional regulation of gene expression in plants and animals. Generally, the types and quantities of miRNAs in the different tissues of an organism are diverse, and these divergences may be related to their specific functions. Here we have identified 296 known miRNAs and 46 novel miRNAs in the antennae of the parasitoid wasp Microplitis mediator by high-throughput sequencing. Thirty-three miRNAs were predicted to target olfactory-associated genes, including odorant binding proteins (OBPs), chemosensory proteins, odorant receptors (ORs), ionotropic receptors (IRs) and gustatory receptors. Among these, 17 miRNAs were significantly highly expressed in the antennae, four miRNAs were highly expressed both in the antennae and head or wings, while the remaining 12 miRNAs were mainly expressed in the head, thorax, abdomen, legs and wings. Notably, miR-9a-5p and miR-2525-3p were highly expressed in male antennae, whereas miR-1000-5p and novel-miR-13 were enriched in female antennae. The 17 miRNAs highly expressed in antennae are likely to be associated with olfaction, and were predicted to target one OBP (targeted by miR-3751-3p), one IR (targeted by miR-7-5p) and 14 ORs (targeted by 15 miRNAs including miR-6-3p, miR-9a-5p, miR-9b-5p, miR-29-5p, miR-71-5p, miR-275-3p, miR-1000-5p, miR-1000-3p, miR-2525-3p, miR-6012-3p, miR-9719-3p, novel-miR-10, novel-miR-13, novel-miR-14 and novel-miR-28). These candidate olfactory-associated miRNAs are all likely to be involved in chemoreception through the regulation of chemosensory gene expression in the antennae of M. mediator.
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Affiliation(s)
- Shuang Shan
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shan-Ning Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
- Institute of Plant and Environment Protection, Beijing Academy of Agricultural and Forestry Sciences, Beijing, China
| | - Xuan Song
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
- College of Plant Protection, China Agricultural University, Beijing, China
| | - Adel Khashaveh
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zi-Yun Lu
- IPM Center of Hebei Province, Key Laboratory of Integrated Pest Management on Crops in Northern Region of North China, Ministry of Agriculture, Plant Protection Institute, Hebei Academy of Agricultural and Forestry Sciences, Baoding, Hebei, China
| | - Khalid Hussain Dhiloo
- Department of Entomology, Faculty of Crop Protection, Sindh Agriculture University, Tandojam, Pakistan
| | - Rui-Jun Li
- College of Plant Protection, Agricultural University of Hebei, Baoding, Hebei, China
| | - Xi-Wu Gao
- College of Plant Protection, China Agricultural University, Beijing, China
| | - Yong-Jun Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
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31
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Luo X, Jean-Toussaint R, Sacan A, Ajit SK. Differential RNA packaging into small extracellular vesicles by neurons and astrocytes. Cell Commun Signal 2021; 19:75. [PMID: 34246289 PMCID: PMC8272329 DOI: 10.1186/s12964-021-00757-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Accepted: 06/03/2021] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Small extracellular vesicles (sEVs) mediate intercellular communication by transferring RNA, proteins, and lipids to recipient cells. These cargo molecules are selectively loaded into sEVs and mirror the physiological state of the donor cells. Given that sEVs can cross the blood-brain barrier and their composition can change in neurological disorders, the molecular signatures of sEVs in circulation can be potential disease biomarkers. Characterizing the molecular composition of sEVs from different cell types is an important first step in determining which donor cells contribute to the circulating sEVs. METHODS Cell culture supernatants from primary mouse cortical neurons and astrocytes were used to purify sEVs by differential ultracentrifugation and sEVs were characterized using nanoparticle tracking analysis, transmission electron microscopy and western blot. RNA sequencing was used to determine differential expression and loading patterns of miRNAs in sEVs released by primary neurons and astrocytes. Motif analysis was conducted on enriched miRNAs in sEVs and their respective donor cells. RESULTS Sequencing total cellular RNA, and miRNAs from sEVs isolated from culture media of postnatal mouse cortical neurons and astrocytes revealed a distinct profile between sEVs and their corresponding cells. Though the total number of detected miRNAs in astrocytes was greater than neurons, neurons expressed more sEV-associated miRNAs than astrocytes. Only 20.7% of astrocytic miRNAs were loaded into sEVs, while 41.0% of neuronal miRNAs were loaded into sEVs, suggesting differences in the cellular sorting mechanisms. We identified short RNA sequence motifs, or EXOmotifs, on the miRNAs that were differentially loaded or excluded from sEVs. A sequence motif GUAC was enriched in astrocytic sEVs. miRNAs preferably retained in neurons or astrocytes had a similar RNA motif CACACA, suggesting a cell-type-independent mechanism to maintain cellular miRNAs. mRNAs of five RNA-binding proteins associated with passive or active RNA sorting into sEVs were differentially expressed between neurons and astrocytes, one of which, major vault protein was higher in astrocytes than in neurons and detected in astrocytic sEVs. CONCLUSIONS Our studies suggest differences in RNA sorting into sEVs. These differences in miRNA signatures can be used for determining the cellular sources of sEVs altered in neurological disorders. Video abstract.
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Affiliation(s)
- Xuan Luo
- Department of Pharmacology and Physiology, Drexel University College of Medicine, 245 North 15th Street, Philadelphia, PA 19102 USA
| | - Renée Jean-Toussaint
- Department of Pharmacology and Physiology, Drexel University College of Medicine, 245 North 15th Street, Philadelphia, PA 19102 USA
| | - Ahmet Sacan
- School of Biomedical Engineering, Science and Health Systems, Drexel University, 3141 Chestnut Street, Philadelphia, PA 19104 USA
| | - Seena K. Ajit
- Department of Pharmacology and Physiology, Drexel University College of Medicine, 245 North 15th Street, Philadelphia, PA 19102 USA
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32
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Zhang L, Lv D, Pan J, Zhang K, Wen H, Chen Y, Du H, He H, Cai R, Pan J, Wang G. A SNP of HD-ZIP I transcription factor leads to distortion of trichome morphology in cucumber (Cucumis sativus L.). BMC PLANT BIOLOGY 2021; 21:182. [PMID: 33863289 PMCID: PMC8052656 DOI: 10.1186/s12870-021-02955-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 03/24/2021] [Indexed: 05/23/2023]
Abstract
BACKGROUND Trichomes are excellent model systems for the analysis of cell differentiation and play essential roles in plant protection. From cucumber inbred line 'WD1', we identified an EMS-induced trichome abnormally developing mutant, nps, which exhibited smaller, denser and no pyramid-shaped head trichomes. RESULTS Using F2 and BC1 populations constructed from a cross between nps and '9930', the genetic analysis showed that the nps trait is controlled by a single recessive nuclear gene. We identified CsNps by map-based cloning with 576 individuals of the F2 population generated from the cross of nps and inbred line '9930'. The CsNps was located at a 13.4-kb genomic region on chromosome 3, which region contains three predicted genes. Sequence analysis showed that only one single nucleotide mutation (C → T) between 9930 and nps was found in the second exon of Csa3G748220, a plant-specific class I HD-Zip gene. The result of allelism test also indicated that nps is a novel allelic mutant of Mict (Micro-trichome). Thus, nps was renamed mict-L130F. By comparing the transcriptome of mict-L130F vs WD1 and 06-2 (mict) vs 06-1 (wildtype, near-isogenic line of 06-2), several potential target genes that may be related to trichome development were identified. CONCLUSIONS Our results demonstrate that Mict-L130F is involved in the morphogenesis of trichomes. Map-based cloning of the Mict-L130F gene could promote the study of trichome development in cucumber.
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Affiliation(s)
- Leyu Zhang
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Duo Lv
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jian Pan
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Keyan Zhang
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Haifan Wen
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yue Chen
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Hui Du
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Huanle He
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Run Cai
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
- State Key Laboratory of Vegetable Germplasm Innovation, Tianjin, 300384, China
| | - Junsong Pan
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China.
| | - Gang Wang
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China.
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33
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Papasavva PL, Papaioannou NY, Patsali P, Kurita R, Nakamura Y, Sitarou M, Christou S, Kleanthous M, Lederer CW. Distinct miRNA Signatures and Networks Discern Fetal from Adult Erythroid Differentiation and Primary from Immortalized Erythroid Cells. Int J Mol Sci 2021; 22:3626. [PMID: 33807258 PMCID: PMC8037168 DOI: 10.3390/ijms22073626] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 03/23/2021] [Accepted: 03/24/2021] [Indexed: 01/22/2023] Open
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs crucial for post-transcriptional and translational regulation of cellular and developmental pathways. The study of miRNAs in erythropoiesis elucidates underlying regulatory mechanisms and facilitates related diagnostic and therapy development. Here, we used DNA Nanoball (DNB) small RNA sequencing to comprehensively characterize miRNAs in human erythroid cell cultures. Based on primary human peripheral-blood-derived CD34+ (hCD34+) cells and two influential erythroid cell lines with adult and fetal hemoglobin expression patterns, HUDEP-2 and HUDEP-1, respectively, our study links differential miRNA expression to erythroid differentiation, cell type, and hemoglobin expression profile. Sequencing results validated by reverse-transcription quantitative PCR (RT-qPCR) of selected miRNAs indicate shared differentiation signatures in primary and immortalized cells, characterized by reduced overall miRNA expression and reciprocal expression increases for individual lineage-specific miRNAs in late-stage erythropoiesis. Despite the high similarity of same-stage hCD34+ and HUDEP-2 cells, differential expression of several miRNAs highlighted informative discrepancies between both cell types. Moreover, a comparison between HUDEP-2 and HUDEP-1 cells displayed changes in miRNAs, transcription factors (TFs), target genes, and pathways associated with globin switching. In resulting TF-miRNA co-regulatory networks, major therapeutically relevant regulators of globin expression were targeted by many co-expressed miRNAs, outlining intricate combinatorial miRNA regulation of globin expression in erythroid cells.
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Affiliation(s)
- Panayiota L. Papasavva
- Department of Molecular Genetics Thalassemia, The Cyprus Institute of Neurology and Genetics, Nicosia 2371, Cyprus; (P.L.P.); (N.Y.P.); (P.P.); (M.K.)
- Cyprus School of Molecular Medicine, Nicosia 2371, Cyprus
| | - Nikoletta Y. Papaioannou
- Department of Molecular Genetics Thalassemia, The Cyprus Institute of Neurology and Genetics, Nicosia 2371, Cyprus; (P.L.P.); (N.Y.P.); (P.P.); (M.K.)
- Cyprus School of Molecular Medicine, Nicosia 2371, Cyprus
| | - Petros Patsali
- Department of Molecular Genetics Thalassemia, The Cyprus Institute of Neurology and Genetics, Nicosia 2371, Cyprus; (P.L.P.); (N.Y.P.); (P.P.); (M.K.)
- Cyprus School of Molecular Medicine, Nicosia 2371, Cyprus
| | - Ryo Kurita
- Cell Engineering Division, RIKEN BioResource Center, Tsukuba, Ibaraki 305-0074, Japan; (R.K.); (Y.N.)
| | - Yukio Nakamura
- Cell Engineering Division, RIKEN BioResource Center, Tsukuba, Ibaraki 305-0074, Japan; (R.K.); (Y.N.)
| | - Maria Sitarou
- Thalassemia Clinic Larnaca, Larnaca General Hospital, Larnaca 6301, Cyprus;
| | - Soteroulla Christou
- Thalassemia Clinic Nicosia, Archbishop Makarios III Hospital, Nicosia 1474, Cyprus;
| | - Marina Kleanthous
- Department of Molecular Genetics Thalassemia, The Cyprus Institute of Neurology and Genetics, Nicosia 2371, Cyprus; (P.L.P.); (N.Y.P.); (P.P.); (M.K.)
- Cyprus School of Molecular Medicine, Nicosia 2371, Cyprus
| | - Carsten W. Lederer
- Department of Molecular Genetics Thalassemia, The Cyprus Institute of Neurology and Genetics, Nicosia 2371, Cyprus; (P.L.P.); (N.Y.P.); (P.P.); (M.K.)
- Cyprus School of Molecular Medicine, Nicosia 2371, Cyprus
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34
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Qu S, Zhang Y, Yang X, Tan Y, Li M, Yang X, Zhou L, Chen D, Chen Y, Yan M, Wang Q, Yu T, Sun N, Jiang H, Su F, Di Y, Lin G, Yuan Y, Chen F, Mu F, Huang J. The Setup and Application of Reference Material in Sequencing-Based Noninvasive Prenatal Testing. Gynecol Obstet Invest 2021; 86:123-131. [PMID: 33784691 DOI: 10.1159/000513472] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 11/30/2020] [Indexed: 11/19/2022]
Abstract
INTRODUCTION The sequencing-based noninvasive prenatal testing (NIPT) has been successfully integrated into clinical practice and facilitated the early detection of fetal chromosomal anomalies. However, a comprehensive reference material to evaluate and quality control NIPT services from different NIPT providers remains unavailable. METHODS In this study, we established a set of NIPT reference material consisting of 192 simulated samples. Most of the potential factors influencing the accuracy of NIPT, such as fetal fraction, mosaicism, and interfering substances, were included in the reference material. We compared the performance of chromosomal abnormalities detection on 3 widely used sequencers (NextSeq 500, BGISEQ-500, and Ion Proton) based on the reference material. RESULTS All 3 sequencers provided highly accurate and reliable results to samples with ≥3.5% fetal fractions and high percentage of mosaicism. CONCLUSIONS The established reference material can serve as a universal standard quality control for the current and new-coming NIPT providers based on various sequencers.
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Affiliation(s)
- Shoufang Qu
- National Institutes for Food and Drug Control (NIFDC), Beijing, China
| | | | - Xin Yang
- Yantai Yuhuangding Hospital, Yantai, China
| | - Yueqiu Tan
- Institute of Reproductive and Stem Cell Engineering, Central South University, Changsha, China.,Key Laboratory of Stem Cell and Reproductive Engineering, Ministry of Health, Changsha, China
| | - Ming Li
- Guangzhou Darui Biotechnology Co., Ltd., Guangzhou, China
| | - Xuexi Yang
- R&D, Southern Medical University, Guangzhou, China
| | - Lijun Zhou
- BGI-Genomics, BGI-Shenzhen, Shenzhen, China
| | - Di Chen
- Berry Genomics Corporation, Beijing, China
| | | | | | | | - Ting Yu
- National Institutes for Food and Drug Control (NIFDC), Beijing, China
| | - Nan Sun
- National Institutes for Food and Drug Control (NIFDC), Beijing, China
| | | | | | - Yufen Di
- Institute of Reproductive and Stem Cell Engineering, Central South University, Changsha, China.,Key Laboratory of Stem Cell and Reproductive Engineering, Ministry of Health, Changsha, China
| | - Ge Lin
- Key Laboratory of Stem Cell and Reproductive Engineering, Ministry of Health, Changsha, China
| | | | | | - Feng Mu
- BGI-Shenzhen, Shenzhen, China
| | - Jie Huang
- National Institutes for Food and Drug Control (NIFDC), Beijing, China
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35
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Sun X, Hu YH, Wang J, Fang C, Li J, Han M, Wei X, Zheng H, Luo X, Jia Y, Gong M, Xiao L, Song Z. Efficient and stable metabarcoding sequencing data using a DNBSEQ-G400 sequencer validated by comprehensive community analyses. GIGABYTE 2021; 2021:gigabyte16. [PMID: 36824325 PMCID: PMC9632034 DOI: 10.46471/gigabyte.16] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 03/18/2021] [Indexed: 11/09/2022] Open
Abstract
Metabarcoding is a widely used method for fast characterization of microbial communities in complex environmental samples. However, the selction of sequencing platform can have a noticeable effect on the estimated community composition. Here, we evaluated the metabarcoding performance of a DNBSEQ-G400 sequencer developed by MGI Tech using 16S and internal transcribed spacer (ITS) markers to investigate bacterial and fungal mock communities, as well as the ITS2 marker to investigate the fungal community of 1144 soil samples, with additional technical replicates. We show that highly accurate sequencing of bacterial and fungal communities is achievable using DNBSEQ-G400. Measures of diversity and correlation from soil metabarcoding showed that the results correlated highly with those of different machines of the same model, as well as between different sequencing modes (single-end 400 bp and paired-end 200 bp). Moderate, but significant differences were observed between results produced with different sequencing platforms (DNBSEQ-G400 and MiSeq); however, the highest differences can be caused by selecting different primer pairs for PCR amplification of taxonomic markers. These differences suggested that care is needed while jointly analyzing metabarcoding data from differenet experiments. This study demonstrated the high performance and accuracy of DNBSEQ-G400 for short-read metabarcoding of microbial communities. Our study also produced datasets to allow further investigation of microbial diversity.
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Affiliation(s)
| | - Yue-Hua Hu
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla 666303, China
| | | | - Chao Fang
- BGI-Shenzhen, Shenzhen 518083, China
- Shenzhen Key Laboratory of Human Commensal Microorganisms and Health Research, BGI-Shenzhen, Shenzhen 518083, China
| | - Jiguang Li
- MGI, BGI-Shenzhen, Shenzhen 518083, China
| | - Mo Han
- BGI-Shenzhen, Shenzhen 518083, China
| | | | - Haotian Zheng
- BGI-Shenzhen, Shenzhen 518083, China
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China
| | - Xiaoqing Luo
- BGI-Shenzhen, Shenzhen 518083, China
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
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36
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Juan CX, Mao Y, Cao Q, Chen Y, Zhou LB, Li S, Chen H, Chen JH, Zhou GP, Jin R. Exosome-mediated pyroptosis of miR-93-TXNIP-NLRP3 leads to functional difference between M1 and M2 macrophages in sepsis-induced acute kidney injury. J Cell Mol Med 2021; 25:4786-4799. [PMID: 33745232 PMCID: PMC8107088 DOI: 10.1111/jcmm.16449] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 02/22/2021] [Accepted: 02/25/2021] [Indexed: 02/06/2023] Open
Abstract
Sepsis is a systemic inflammatory response syndrome caused by infection, resulting in organ dysfunction. Sepsis-induced acute kidney injury (AKI) is one of the most common potential complications. Increasing reports have shown that M1 and M2 macrophages both take part in the progress of AKI by influencing the level of inflammatory factors and the cell death, including pyroptosis. However, whether M1 and M2 macrophages regulate AKI by secreting exosome remains unknown. In the present study, we isolated the exosomes from M1 and M2 macrophages and used Western blot and enzyme-linked immunosorbent assay (ELISA) to investigate the effect of M1 and M2 exosomes on cell pyroptosis. miRNA sequencing was used to identify the different miRNA in M1 and M2 exosomes. Luciferase reporter assay was used to verify the target gene of miRNA. We confirmed that exosomes excreted by macrophages regulated cell pyroptosis in vitro by using Western blot and ELISA. miRNA sequencing revealed the differentially expressed level of miRNAs in M1 and M2 exosomes, among which miR-93-5p was involved in the regulation of pyroptosis. By using bioinformatics predictions and luciferase reporter assay, we found that thioredoxin-interacting protein (TXNIP) was a direct target of miR-93-5p. Further in vitro and in vivo experiments indicated that exosomal miR-93-5p regulated the TXNIP directly to influence the pyroptosis in renal epithelial cells, which explained the functional difference between different phenotypes of macrophages. This study might provide new targets for the treatment of sepsis-induced AKI.
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Affiliation(s)
- Chen-Xia Juan
- Department of Pediatrics, the First Affiliated Hospital, Nanjing Medical University, Nanjing, China.,Department of Nephrology, Affiliated Hospital of Nanjing University of Chinese Medicine, Jiangsu Province Hospital of Chinese Medicine, Nanjing, China
| | - Yan Mao
- Department of Pediatrics, the First Affiliated Hospital, Nanjing Medical University, Nanjing, China
| | - Qian Cao
- Department of Pediatrics, the First Affiliated Hospital, Nanjing Medical University, Nanjing, China
| | - Yan Chen
- Department of Nephrology, Affiliated Geriatric Hospital, Nanjing Medical University, Nanjing, China
| | - Lan-Bo Zhou
- Department of Dermatology, the First Affiliated Hospital, Nanjing Medical University, Nanjing, China
| | - Sheng Li
- Department of Pediatrics, Yancheng Maternity and Child Health Care Hospital, Yancheng, China
| | - Hao Chen
- Department of Urology, the First Affiliated Hospital, Nanjing Medical University, Nanjing, China
| | - Jia-He Chen
- Department of Pediatrics, the First Affiliated Hospital, Nanjing Medical University, Nanjing, China
| | - Guo-Ping Zhou
- Department of Pediatrics, the First Affiliated Hospital, Nanjing Medical University, Nanjing, China
| | - Rui Jin
- Department of Pediatrics, the First Affiliated Hospital, Nanjing Medical University, Nanjing, China
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Li R, Shen X, Chen H, Peng D, Wu R, Sun H. Developmental validation of the MGIEasy Signature Identification Library Prep Kit, an all-in-one multiplex system for forensic applications. Int J Legal Med 2021; 135:739-753. [PMID: 33523251 DOI: 10.1007/s00414-021-02507-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 01/08/2021] [Indexed: 01/23/2023]
Abstract
Analyzing genetic markers in nuclear and mitochondrial genomes is helpful in various forensic applications, such as individual identifications and kinship analyses. However, most commercial kits detect these markers separately, which is time-consuming, laborious, and more error-prone (mislabelling, contamination, ...). The MGIEasy Signature Identification Library Prep Kit (hereinafter "MGIEasy identification system"; MGI Tech, Shenzhen, China) has been designed to provide a simple, fast, and robust way to detect appropriate markers in one multiplex PCR reaction: 52 autosomal STRs, 27 X-chromosomal STRs, 48 Y-chromosomal STRs, 145 identity-informative SNPs, 53 ancestry-informative SNPs, 29 phenotype-informative SNPs, and the hypervariable regions of mitochondrial DNA (mtDNA). Here, we validated the performance of MGIEasy identification system following the guidelines of the Scientific Working Group on DNA Analysis Methods (SWGDAM), assessing species specificity, sensitivity, mixture identification, stability under non-optimal conditions (degraded samples, inhibitor contamination, and various substrates), repeatability, and concordance. Libraries prepared using MGIEasy identification system were sequenced on a MGISEQ-2000 instrument (MGI Tech). MGIEasy-derived STR, SNP, and mtDNA genotypes were highly concordant with CE-based STR genotypes (99.79%), MiSeq FGx-based SNP genotypes (99.78%), and Sanger-based mtDNA genotypes (100%), respectively. This system was strongly human-specific, resistant to four common PCR inhibitors, and reliably amplified both low quantities of DNA (as low as 0.125 ng) and degraded DNA (~ 150 nt). Most of the unique alleles from the minor contributor were detected in 1:10 male-female and male-male mixtures; some minor Y-STR alleles were even detected in 1:1000 male-female mixtures. MGIEasy also successfully directly amplified markers from blood stains on FTA cards, filter papers, and swabs. Thus, our results demonstrated that MGIEasy identification system was suitable for use in forensic analyses due to its robust and reliable performance on samples of varying quality and quantity.
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Affiliation(s)
- Ran Li
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, People's Republic of China.,Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, No. 74 Zhongshan Road II, Guangzhou, 510080, Guangdong, People's Republic of China
| | - Xuefeng Shen
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, People's Republic of China.,Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, No. 74 Zhongshan Road II, Guangzhou, 510080, Guangdong, People's Republic of China
| | - Hui Chen
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, People's Republic of China.,Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, No. 74 Zhongshan Road II, Guangzhou, 510080, Guangdong, People's Republic of China
| | - Dan Peng
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, People's Republic of China.,Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, No. 74 Zhongshan Road II, Guangzhou, 510080, Guangdong, People's Republic of China
| | - Riga Wu
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, People's Republic of China.,Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, No. 74 Zhongshan Road II, Guangzhou, 510080, Guangdong, People's Republic of China
| | - Hongyu Sun
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, People's Republic of China. .,Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, No. 74 Zhongshan Road II, Guangzhou, 510080, Guangdong, People's Republic of China.
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Lee JH, Kweon S, Park YR. Sharing genetic variants with the NGS pipeline is essential for effective genomic data sharing and reproducibility in health information exchange. Sci Rep 2021; 11:2268. [PMID: 33500538 PMCID: PMC7838410 DOI: 10.1038/s41598-021-82006-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 01/07/2021] [Indexed: 11/09/2022] Open
Abstract
Genetic variants causing underlying pharmacogenetic and disease phenotypes have been used as the basis for clinical decision-making. However, due to the lack of standards for next-generation sequencing (NGS) pipelines, reproducing genetic variants among institutions is still difficult. The aim of this study is to show how many important variants for clinical decisions can be individually detected using different pipelines. Genetic variants were derived from 105 breast cancer patient target DNA sequences via three different variant-calling pipelines. HaplotypeCaller, Mutect2 tumor-only mode in the Genome Analysis ToolKit (GATK), and VarScan were used in variant calling from the sequence read data processed by the same NGS preprocessing tools using Variant Effect Predictor. GATK HaplotypeCaller, VarScan, and MuTect2 found 25,130, 16,972, and 4232 variants, comprising 1491, 1400, and 321 annotated variants with ClinVar significance, respectively. The average number of ClinVar significant variants in the patients was 769.43, 16.50% of the variants were detected by only one variant caller. Despite variants with significant impact on clinical decision-making, the detected variants are different for each algorithm. To utilize genetic variants in the clinical field, a strict standard for NGS pipelines is essential.
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Affiliation(s)
- Jeong Hoon Lee
- Lunit Inc., 175 Yeoksamro, Gangnam-gu, Seoul, Republic of Korea
- Department of Biomedical Systems Informatics, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Solbi Kweon
- Department of Biomedical Systems Informatics, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Yu Rang Park
- Department of Biomedical Systems Informatics, Yonsei University College of Medicine, Seoul, Republic of Korea.
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Li Y, Fehlmann T, Borcherding A, Drmanac S, Liu S, Groeger L, Xu C, Callow M, Villarosa C, Jorjorian A, Kern F, Grammes N, Meese E, Jiang H, Drmanac R, Ludwig N, Keller A. CoolMPS: evaluation of antibody labeling based massively parallel non-coding RNA sequencing. Nucleic Acids Res 2021; 49:e10. [PMID: 33290507 PMCID: PMC7826284 DOI: 10.1093/nar/gkaa1122] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 10/02/2020] [Accepted: 11/26/2020] [Indexed: 12/16/2022] Open
Abstract
Results of massive parallel sequencing-by-synthesis vary depending on the sequencing approach. CoolMPS™ is a new sequencing chemistry that incorporates bases by labeled antibodies. To evaluate the performance, we sequenced 240 human non-coding RNA samples (dementia patients and controls) with and without CoolMPS. The Q30 value as indicator of the per base sequencing quality increased from 91.8 to 94%. The higher quality was reached across the whole read length. Likewise, the percentage of reads mapping to the human genome increased from 84.9 to 86.2%. For both technologies, we computed similar distributions between different RNA classes (miRNA, piRNA, tRNA, snoRNA and yRNA) and within the classes. While standard sequencing-by-synthesis allowed to recover more annotated miRNAs, CoolMPS yielded more novel miRNAs. The correlation between the two methods was 0.97. Evaluating the diagnostic performance, we observed lower minimal P-values for CoolMPS (adjusted P-value of 0.0006 versus 0.0004) and larger effect sizes (Cohen's d of 0.878 versus 0.9). Validating 19 miRNAs resulted in a correlation of 0.852 between CoolMPS and reverse transcriptase-quantitative polymerase chain reaction. Comparison to data generated with Illumina technology confirmed a known shift in the overall RNA composition. With CoolMPS we evaluated a novel sequencing-by-synthesis technology showing high performance for the analysis of non-coding RNAs.
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Affiliation(s)
- Yongping Li
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
- MGI, BGI-Shenzhen, Shenzhen 518083, China
| | - Tobias Fehlmann
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | | | | | - Sophie Liu
- Complete Genomics Incorporated, San Jose, CA 95134, USA
| | - Laura Groeger
- Department of Human Genetics, Saarland University, 66421 Homburg, Germany
| | - Chongjun Xu
- MGI, BGI-Shenzhen, Shenzhen 518083, China
- Complete Genomics Incorporated, San Jose, CA 95134, USA
- BGI-Shenzhen, Shenzhen 518083, China
- China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | | | | | | | - Fabian Kern
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Nadja Grammes
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Eckart Meese
- Department of Human Genetics, Saarland University, 66421 Homburg, Germany
| | - Hui Jiang
- MGI, BGI-Shenzhen, Shenzhen 518083, China
| | - Radoje Drmanac
- MGI, BGI-Shenzhen, Shenzhen 518083, China
- Complete Genomics Incorporated, San Jose, CA 95134, USA
- BGI-Shenzhen, Shenzhen 518083, China
- China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Nicole Ludwig
- Department of Human Genetics, Saarland University, 66421 Homburg, Germany
| | - Andreas Keller
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
- Department of Neurology and Neurological Sciences, Stanford UniversitySchool of Medicine, Stanford, CA 94304, USA
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Trypanosoma cruzi Modulates PIWI-Interacting RNA Expression in Primary Human Cardiac Myocytes during the Early Phase of Infection. Int J Mol Sci 2020; 21:ijms21249439. [PMID: 33322418 PMCID: PMC7764157 DOI: 10.3390/ijms21249439] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 11/28/2020] [Accepted: 12/10/2020] [Indexed: 02/07/2023] Open
Abstract
Trypanosoma cruzi dysregulates the gene expression profile of primary human cardiomyocytes (PHCM) during the early phase of infection through a mechanism which remains to be elucidated. The role that small non-coding RNAs (sncRNA) including PIWI-interacting RNA (piRNA) play in regulating gene expression during the early phase of infection is unknown. To understand how T. cruzi dysregulate gene expression in the heart, we challenged PHCM with T. cruzi trypomastigotes and analyzed sncRNA, especially piRNA, by RNA-sequencing. The parasite induced significant differential expression of host piRNAs, which can target and regulate the genes which are important during the early infection phase. An average of 21,595,866 (88.40%) of clean reads mapped to the human reference genome. The parasite induced 217 unique piRNAs that were significantly differentially expressed (q ≥ 0.8). Of these differentially expressed piRNAs, 6 were known and 211 were novel piRNAs. In silico analysis showed that some of the dysregulated known and novel piRNAs could target and potentially regulate the expression of genes including NFATC2, FOS and TGF-β1, reported to play important roles during T. cruzi infection. Further evaluation of the specific functions of the piRNAs in the regulation of gene expression during the early phase of infection will enhance our understanding of the molecular mechanism of T. cruzi pathogenesis. Our novel findings constitute the first report that T. cruzi can induce differential expression of piRNAs in PHCM, advancing our knowledge about the involvement of piRNAs in an infectious disease model, which can be exploited for biomarker and therapeutic development.
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Li J, Tan Y, Sheng Z, Zhou P, Liu C, Zhao H, Song L, Zhou J, Chen R, Chen Y, Yan H. RNA-seq identifies circulating miRNAs as potential biomarkers for plaque rupture in patients with ST-segment elevation myocardial infarction. Genomics 2020; 113:1-10. [PMID: 33253792 DOI: 10.1016/j.ygeno.2020.11.019] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 11/02/2020] [Accepted: 11/22/2020] [Indexed: 11/19/2022]
Abstract
BACKGROUND Plaque rupture (PR) and plaque erosion (PE) are the two major pathological phenotypes in acute coronary syndrome. Since microRNAs have been found to be involved in the mechanisms of PR and PE, we investigated the diagnostic utility of microRNAs in differentiating between patients with PR and patients with PE. METHODS MicroRNA sequencing was performed on plasma from 21 patients with PR, 20 patients with PE and 17 healthy control subjects (HCs). 24 miRNAs were selected for validation in 20 PR patients and 20 PE patients and 8 miRNAs were further validated in an independent replication cohort (82 patients with PR, 84 patients with PE and 59 HCs) by applying quantitative real-time polymerase chain reaction. Then we analyzed pathways associated with significant miRNAs in PR. RESULTS MiR-744-3p, miR-324-3p and miR-330-3p were significantly upregulated in the PR group compared with the PE group (Log10miR-744-3p: 0.26[--0.28-1.57] versus -0.41[-0.83--0.03], padj < 0.001; Log10miR-324-3p: 0.40[-0.09-0.84] versus -0.12[-0.53-0.29], padj < 0.001; Log10miR-330-3p: 0.34[0.08-0.93] versus -0.07[-0.65-0.22], padj < 0.001), The area under the receiver operating characteristic curve for the combination of these three miRNAs in distinguishing between PR from PE in training and test set was 0.764 (0.679-0.850, sensitivity = 86.2%, specificity = 54.4%, P < 0.001) and 0.768 (0.637-0.898, sensitivity,65.4%, specificity:80.0%, P = 0.001), respectively. CONCLUSION A set of circulating microRNAs (miR-744-3p, miR-330-3p, and miR-324-3p) is associated with PR and has clinical utility as a diagnostic marker for distinguishing the plaque phenotype in STEMI patients.
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Affiliation(s)
- Jiannan Li
- Department of Cardiology, Fuwai Hospital, National Center for Cardiovascular Diseases, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing, China
| | - Yu Tan
- Department of Cardiology, Fuwai Hospital, National Center for Cardiovascular Diseases, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing, China; Xiamen cardiovascular hospital, Xiamen university, Fujian, China
| | - Zhaoxue Sheng
- Department of Cardiology, Fuwai Hospital, National Center for Cardiovascular Diseases, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing, China
| | - Peng Zhou
- Department of Cardiology, Fuwai Hospital, National Center for Cardiovascular Diseases, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing, China
| | - Chen Liu
- Department of Cardiology, Fuwai Hospital, National Center for Cardiovascular Diseases, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing, China
| | - Hanjun Zhao
- Department of Cardiology, Fuwai Hospital, National Center for Cardiovascular Diseases, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing, China
| | - Li Song
- Department of Cardiology, Fuwai Hospital, National Center for Cardiovascular Diseases, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing, China
| | - Jinying Zhou
- Department of Cardiology, Fuwai Hospital, National Center for Cardiovascular Diseases, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing, China
| | - Runzhen Chen
- Department of Cardiology, Fuwai Hospital, National Center for Cardiovascular Diseases, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing, China
| | - Yi Chen
- Department of Cardiology, Fuwai Hospital, National Center for Cardiovascular Diseases, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing, China
| | - Hongbing Yan
- Department of Cardiology, Fuwai Hospital, National Center for Cardiovascular Diseases, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing, China; Fuwai Hospital, Chinese Academy of Medical Sciences, Shenzhen, China.
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Fehlmann T, Lehallier B, Schaum N, Hahn O, Kahraman M, Li Y, Grammes N, Geffers L, Backes C, Balling R, Kern F, Krüger R, Lammert F, Ludwig N, Meder B, Fromm B, Maetzler W, Berg D, Brockmann K, Deuschle C, von Thaler AK, Eschweiler GW, Milman S, Barziliai N, Reichert M, Wyss-Coray T, Meese E, Keller A. Common diseases alter the physiological age-related blood microRNA profile. Nat Commun 2020; 11:5958. [PMID: 33235214 PMCID: PMC7686493 DOI: 10.1038/s41467-020-19665-1] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 10/16/2020] [Indexed: 02/07/2023] Open
Abstract
Aging is a key risk factor for chronic diseases of the elderly. MicroRNAs regulate post-transcriptional gene silencing through base-pair binding on their target mRNAs. We identified nonlinear changes in age-related microRNAs by analyzing whole blood from 1334 healthy individuals. We observed a larger influence of the age as compared to the sex and provide evidence for a shift to the 5' mature form of miRNAs in healthy aging. The addition of 3059 diseased patients uncovered pan-disease and disease-specific alterations in aging profiles. Disease biomarker sets for all diseases were different between young and old patients. Computational deconvolution of whole-blood miRNAs into blood cell types suggests that cell intrinsic gene expression changes may impart greater significance than cell abundance changes to the whole blood miRNA profile. Altogether, these data provide a foundation for understanding the relationship between healthy aging and disease, and for the development of age-specific disease biomarkers.
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Affiliation(s)
- Tobias Fehlmann
- Chair for Clinical Bioinformatics, Saarland University, 66123, Saarbrücken, Germany
| | - Benoit Lehallier
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, 94305, USA
| | - Nicholas Schaum
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, 94305, USA
| | - Oliver Hahn
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, 94305, USA
| | - Mustafa Kahraman
- Chair for Clinical Bioinformatics, Saarland University, 66123, Saarbrücken, Germany
| | - Yongping Li
- Chair for Clinical Bioinformatics, Saarland University, 66123, Saarbrücken, Germany
| | - Nadja Grammes
- Chair for Clinical Bioinformatics, Saarland University, 66123, Saarbrücken, Germany
| | - Lars Geffers
- Luxembourg Center for Systems Biomedicine, 4362, Esch-sur-Alzette, Luxemburg
| | - Christina Backes
- Chair for Clinical Bioinformatics, Saarland University, 66123, Saarbrücken, Germany
| | - Rudi Balling
- Luxembourg Center for Systems Biomedicine, 4362, Esch-sur-Alzette, Luxemburg
- Transversal Translational Medicine, Luxembourg Institute of Health (LIH), 1445, Strassen, Luxemburg
- Parkinson Research Clinic, Centre Hospitalier de Luxembourg, 1210, Luxembourg, Luxemburg
| | - Fabian Kern
- Chair for Clinical Bioinformatics, Saarland University, 66123, Saarbrücken, Germany
| | - Rejko Krüger
- Luxembourg Center for Systems Biomedicine, 4362, Esch-sur-Alzette, Luxemburg
- Transversal Translational Medicine, Luxembourg Institute of Health (LIH), 1445, Strassen, Luxemburg
- Parkinson Research Clinic, Centre Hospitalier de Luxembourg, 1210, Luxembourg, Luxemburg
| | - Frank Lammert
- Internal Medicine, Saarland University, 66421, Homburg, Germany
| | - Nicole Ludwig
- Human Genetics, Saarland University, 66421, Homburg, Germany
| | - Benjamin Meder
- Internal Medicine, University Hospital Heidelberg, 69120, Heidelberg, Germany
| | - Bastian Fromm
- Department of Molecular Biosciences, Stockholm University, 11418, Stockholm, Sweden
| | - Walter Maetzler
- Department of Neurology, Christian-Albrechts-Universität zu Kiel, 24105, Kiel, Germany
| | - Daniela Berg
- Department of Neurology, Christian-Albrechts-Universität zu Kiel, 24105, Kiel, Germany
| | | | | | | | - Gerhard W Eschweiler
- Geriatric Center and the Department of Psychiatry and Psychotherapy, University Hospital Tübingen, 72076, Tübingen, Germany
| | - Sofiya Milman
- The Institute for Aging Research, Albert Einstein College of Medicine, New York, NY, 10461, USA
| | - Nir Barziliai
- The Institute for Aging Research, Albert Einstein College of Medicine, New York, NY, 10461, USA
| | | | - Tony Wyss-Coray
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, 94305, USA
| | - Eckart Meese
- Human Genetics, Saarland University, 66421, Homburg, Germany
| | - Andreas Keller
- Chair for Clinical Bioinformatics, Saarland University, 66123, Saarbrücken, Germany.
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, 94305, USA.
- Center for Bioinformatics, Saarland Informatics Campus, Saarland University, 66123, Saarbrücken, Germany.
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Čermák V, Tyč D, Přibylová A, Fischer L. Unexpected variations in posttranscriptional gene silencing induced by differentially produced dsRNAs in tobacco cells. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2020; 1863:194647. [PMID: 33127485 DOI: 10.1016/j.bbagrm.2020.194647] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 10/15/2020] [Accepted: 10/19/2020] [Indexed: 11/17/2022]
Abstract
In plants, posttranscriptional gene silencing (PTGS) is induced by small RNAs (sRNAs) generated from various dsRNA precursors. To assess the impact of dsRNA origin, we compared downregulation of GFP expression triggered by inverted repeat (IR), antisense (AS) and unterminated sense (UT) transcripts transiently expressed from the estradiol-inducible promoter. The use of homogeneously responding tobacco BY-2 cell lines allowed monitoring the onset of silencing and its reversibility. In this system, IR induced the strongest and fastest silencing accompanied by dense DNA methylation. At low induction, silencing in individual cells was binary (either strong or missing), suggesting that a certain threshold sRNA level had to be exceeded. The AS variant specifically showed a deviated sRNA-strand ratio shifted in favor of antisense orientation. In AS lines and weakly induced IR lines, only the silencer DNA was methylated, but the same target GFP sequence was not, showing that DNA methylation accompanying PTGS was influenced both by the level and origin of sRNAs, and possibly also by the epigenetic state of the locus. UT silencing appeared to be the least effective and resembled classical sense PTGS. The best responding UT lines behaved relatively heterogeneously possibly due to complexly arranged T-DNA insertions. Unlike IR and AS variants that fully restored GFP expression upon removal of the inducer, only partial reactivation was observed in some UT lines. Our results pointed out several not yet described phenomena and differences between the long-known silencer variants that may direct further research and affect selection of proper silencer variants for specific applications.
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Affiliation(s)
- Vojtěch Čermák
- Charles University, Faculty of Science, Department of Experimental Plant Biology, Viničná 5, Prague 2 128 44, Czech Republic
| | - Dimitrij Tyč
- Charles University, Faculty of Science, Department of Experimental Plant Biology, Viničná 5, Prague 2 128 44, Czech Republic
| | - Adéla Přibylová
- Charles University, Faculty of Science, Department of Experimental Plant Biology, Viničná 5, Prague 2 128 44, Czech Republic
| | - Lukáš Fischer
- Charles University, Faculty of Science, Department of Experimental Plant Biology, Viničná 5, Prague 2 128 44, Czech Republic.
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Kanzi AM, San JE, Chimukangara B, Wilkinson E, Fish M, Ramsuran V, de Oliveira T. Next Generation Sequencing and Bioinformatics Analysis of Family Genetic Inheritance. Front Genet 2020; 11:544162. [PMID: 33193618 PMCID: PMC7649788 DOI: 10.3389/fgene.2020.544162] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 09/21/2020] [Indexed: 12/29/2022] Open
Abstract
Mendelian and complex genetic trait diseases continue to burden and affect society both socially and economically. The lack of effective tests has hampered diagnosis thus, the affected lack proper prognosis. Mendelian diseases are caused by genetic mutations in a singular gene while complex trait diseases are caused by the accumulation of mutations in either linked or unlinked genomic regions. Significant advances have been made in identifying novel diseases associated mutations especially with the introduction of next generation and third generation sequencing. Regardless, some diseases are still without diagnosis as most tests rely on SNP genotyping panels developed from population based genetic analyses. Analysis of family genetic inheritance using whole genomes, whole exomes or a panel of genes has been shown to be effective in identifying disease-causing mutations. In this review, we discuss next generation and third generation sequencing platforms, bioinformatic tools and genetic resources commonly used to analyze family based genomic data with a focus on identifying inherited or novel disease-causing mutations. Additionally, we also highlight the analytical, ethical and regulatory challenges associated with analyzing personal genomes which constitute the data used for family genetic inheritance.
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Affiliation(s)
- Aquillah M. Kanzi
- Kwazulu-Natal Research and Innovation Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
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Kern F, Amand J, Senatorov I, Isakova A, Backes C, Meese E, Keller A, Fehlmann T. miRSwitch: detecting microRNA arm shift and switch events. Nucleic Acids Res 2020; 48:W268-W274. [PMID: 32356893 PMCID: PMC7319450 DOI: 10.1093/nar/gkaa323] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 04/15/2020] [Accepted: 04/22/2020] [Indexed: 12/27/2022] Open
Abstract
Arm selection, the preferential expression of a 3′ or 5′ mature microRNA (miRNA), is a highly dynamic and tissue-specific process. Time-dependent expression shifts or switches between the arms are also relevant for human diseases. We present miRSwitch, a web server to facilitate the analysis and interpretation of arm selection events. Our species-independent tool evaluates pre-processed small non-coding RNA sequencing (sncRNA-seq) data, i.e. expression matrices or output files from miRNA quantification tools (miRDeep2, miRMaster, sRNAbench). miRSwitch highlights potential changes in the distribution of mature miRNAs from the same precursor. Group comparisons from one or several user-provided annotations (e.g. disease states) are possible. Results can be dynamically adjusted by choosing from a continuous range of highly specific to very sensitive parameters. Users can compare potential arm shifts in the provided data to a human reference map of pre-computed arm shift frequencies. We created this map from 46 tissues and 30 521 samples. As case studies we present novel arm shift information in a Alzheimer’s disease biomarker data set and from a comparison of tissues in Homo sapiens and Mus musculus. In summary, miRSwitch offers a broad range of customized arm switch analyses along with comprehensive visualizations, and is freely available at: https://www.ccb.uni-saarland.de/mirswitch/.
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Affiliation(s)
- Fabian Kern
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Jeremy Amand
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Ilya Senatorov
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Alina Isakova
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Christina Backes
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Eckart Meese
- Department of Human Genetics, Saarland University, 66421 Homburg, Germany
| | - Andreas Keller
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany.,School of Medicine Office, Stanford University, Stanford, CA 94305, USA.,Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA 94304, USA
| | - Tobias Fehlmann
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
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Zhou H, Liu J, Sun W, Ding R, Li X, Shangguan A, Zhou Y, Worku T, Hao X, Khan FA, Yang L, Zhang S. Differences in small noncoding RNAs profile between bull X and Y sperm. PeerJ 2020; 8:e9822. [PMID: 32999759 PMCID: PMC7505075 DOI: 10.7717/peerj.9822] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 08/05/2020] [Indexed: 12/21/2022] Open
Abstract
The differences in small noncoding RNAs (sncRNAs), including miRNAs, piRNAs, and tRNA-derived fragments (tsRNAs), between X and Y sperm of mammals remain unclear. Here, we employed high-throughput sequencing to systematically compare the sncRNA profiles of X and Y sperm from bulls (n = 3), which may have a wider implication for the whole mammalian class. For the comparison of miRNA profiles, we found that the abundance of bta-miR-652 and bta-miR-378 were significantly higher in X sperm, while nine miRNAs, including bta-miR-204 and bta-miR-3432a, had greater abundance in Y sperm (p < 0.05). qPCR was then used to further validate their abundances. Subsequent functional analysis revealed that their targeted genes in sperm were significantly involved in nucleosome binding and nucleosomal DNA binding. In contrast, their targeted genes in mature oocyte were significantly enriched in 11 catabolic processes, indicating that these differentially abundant miRNAs may trigger a series of catabolic processes for the catabolization of different X and Y sperm components during fertilization. Furthermore, we found that X and Y sperm showed differences in piRNA clusters distributed in the genome as well as piRNA and tsRNA abundance, two tsRNAs (tRNA-Ser-AGA and tRNA-Ser-TGA) had lower abundance in X sperm than Y sperm (p < 0.05). Overall, our work describes the different sncRNA profiles of X and Y sperm in cattle and enhances our understanding of their potential roles in the regulation of sex differences in sperm and early embryonic development.
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Affiliation(s)
- Hao Zhou
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Education Ministry of China, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China.,Inner Mongolia Saikexing Institute of Breeding and Reproductive Biotechnology in Domestic Animal, Hohhot, China
| | - Jiajia Liu
- School of Biological Science and Technology, University of Jinan, Jinan, China
| | - Wei Sun
- Inner Mongolia Saikexing Institute of Breeding and Reproductive Biotechnology in Domestic Animal, Hohhot, China
| | - Rui Ding
- Inner Mongolia Saikexing Institute of Breeding and Reproductive Biotechnology in Domestic Animal, Hohhot, China
| | - Xihe Li
- Inner Mongolia Saikexing Institute of Breeding and Reproductive Biotechnology in Domestic Animal, Hohhot, China
| | - Aishao Shangguan
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Education Ministry of China, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Yang Zhou
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Education Ministry of China, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Tesfaye Worku
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Education Ministry of China, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Xingjie Hao
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Education Ministry of China, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Faheem Ahmed Khan
- Department of Zoology, University of Central Punjab, Lahore, Pakistan
| | - Liguo Yang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Education Ministry of China, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Shujun Zhang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Education Ministry of China, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
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Miao X, Shen Y, Gong X, Yu H, Li B, Chang L, Wang Y, Fan J, Liang Z, Tan B, Li S, Zhang B. A novel forensic panel of 186-plex SNPs and 123-plex STR loci based on massively parallel sequencing. Int J Legal Med 2020; 135:709-718. [PMID: 32851473 DOI: 10.1007/s00414-020-02403-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 08/21/2020] [Indexed: 01/23/2023]
Abstract
The MiSeq® FGX Forensic system and the HID-Ion AmpliSeq Panel were previously developed for massively parallel sequencing (MPS) for forensic casework. Among the three major sequencing platforms, BGISEQ-500TM, which is based on multiple PCRs, is still lacking in forensics. Here, a novel forensic panel was constructed to detect 186 single-nucleotide polymorphisms (SNPs) and 123 short tandem repeats (STRs) with MPS technology on the BGISEQ-500™ platform. First, the library preparation, sequencing process, and data analysis were performed, focusing on the average depth of coverage and heterozygote balance. We calculated the allelic frequencies and forensic parameters of STR and SNP loci in 73 unrelated Chinese Han individuals. In addition, performance was evaluated with accuracy, uniformity, sensitivity, PCR inhibitor, repeatability and reproducibility, mixtures, degraded samples, case-type samples, and pedigree analyses. The results showed that 100% accurate and concordant genotypes can be obtained, and the loci with an abundance in the interquartile range accounted for 92.90% of the total, suggesting reliable uniformity in this panel. We obtained a locus detection rate that was higher than 98.78% from 78 pg of input DNA, and the optimal amount was 1.25-10 ng. The maximum concentrations of hematin and humic acid were 200 and 100 μM, respectively (the ratios of detected loci were 96.52% and 92.41%), in this panel. As a mixture, compared with those of SNPs, minor-contributor alleles of STRs could be detected at higher levels. For the degraded sample, the ratio of detected loci was 98.41%, and most profiles from case-type samples were not significantly different in abundance in our studies. As a whole, this panel showed high-performance, reliable, robust, repeatable, and reproducible results, which are sufficient for paternity testing, individual identification, and use for potentially degraded samples in forensic science.
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Affiliation(s)
- Xinyao Miao
- College of Forensic Medicine, Health Science Center, Xi'an Jiaotong University, Xi'an, People's Republic of China
| | - Yuesheng Shen
- School of Life Science, Northwest A&F University, Yangling, People's Republic of China
| | - Xiaojuan Gong
- College of Forensic Medicine, Health Science Center, Xi'an Jiaotong University, Xi'an, People's Republic of China
- School of Health Science Center, Xi'an Jiaotong University, Xi'an, People's Republic of China
| | - Huiyun Yu
- School of Life Science, Northwest A&F University, Yangling, People's Republic of China
| | - Bowen Li
- School of Life Science, Sichuan University, Chengdu, People's Republic of China
| | - Liao Chang
- College of Forensic Medicine, Health Science Center, Xi'an Jiaotong University, Xi'an, People's Republic of China
| | - Yinan Wang
- College of Forensic Medicine, Health Science Center, Xi'an Jiaotong University, Xi'an, People's Republic of China
| | - Jingna Fan
- College of Forensic Medicine, Health Science Center, Xi'an Jiaotong University, Xi'an, People's Republic of China
| | - Zuhuan Liang
- Forensic Genomics International, The Beijing Genomics Institute (BGI), Shenzhen, People's Republic of China
| | - Bowen Tan
- School of Computer Science, City University of Hong Kong, Hong Kong, People's Republic of China
| | - Shengbin Li
- College of Forensic Medicine, Health Science Center, Xi'an Jiaotong University, Xi'an, People's Republic of China
| | - Bao Zhang
- College of Forensic Medicine, Health Science Center, Xi'an Jiaotong University, Xi'an, People's Republic of China.
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Liu PJ, Harris JM, Marchi E, D'Arienzo V, Michler T, Wing PAC, Magri A, Ortega-Prieto AM, van de Klundert M, Wettengel J, Durantel D, Dorner M, Klenerman P, Protzer U, Giotis ES, McKeating JA. Hypoxic gene expression in chronic hepatitis B virus infected patients is not observed in state-of-the-art in vitro and mouse infection models. Sci Rep 2020; 10:14101. [PMID: 32839523 PMCID: PMC7445281 DOI: 10.1038/s41598-020-70865-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 07/31/2020] [Indexed: 02/07/2023] Open
Abstract
Hepatitis B virus (HBV) is the leading cause of hepatocellular carcinoma (HCC) worldwide. The prolyl hydroxylase domain (PHD)-hypoxia inducible factor (HIF) pathway is a key mammalian oxygen sensing pathway and is frequently perturbed by pathological states including infection and inflammation. We discovered a significant upregulation of hypoxia regulated gene transcripts in patients with chronic hepatitis B (CHB) in the absence of liver cirrhosis. We used state-of-the-art in vitro and in vivo HBV infection models to evaluate a role for HBV infection and the viral regulatory protein HBx to drive HIF-signalling. HBx had no significant impact on HIF expression or associated transcriptional activity under normoxic or hypoxic conditions. Furthermore, we found no evidence of hypoxia gene expression in HBV de novo infection, HBV infected human liver chimeric mice or transgenic mice with integrated HBV genome. Collectively, our data show clear evidence of hypoxia gene induction in CHB that is not recapitulated in existing models for acute HBV infection, suggesting a role for inflammatory mediators in promoting hypoxia gene expression.
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Affiliation(s)
- Peter Jianrui Liu
- Nuffield Department of Medicine Research Building, University of Oxford, Oxford, OX3 7LF, UK
| | - James M Harris
- Nuffield Department of Medicine Research Building, University of Oxford, Oxford, OX3 7LF, UK
| | - Emanuele Marchi
- Medawar Building, University of Oxford, South Parks Road, Oxford, OX1 3SY, UK
| | - Valentina D'Arienzo
- Nuffield Department of Medicine Research Building, University of Oxford, Oxford, OX3 7LF, UK
| | - Thomas Michler
- Institute of Virology, Technical University of Munich/Helmholtz Zentrum München, Trogerstrasse 30, 81675, Munich, Germany
| | - Peter A C Wing
- Nuffield Department of Medicine Research Building, University of Oxford, Oxford, OX3 7LF, UK
| | - Andrea Magri
- Nuffield Department of Medicine Research Building, University of Oxford, Oxford, OX3 7LF, UK
| | - Ana Maria Ortega-Prieto
- Section of Molecular Virology, Department of Infectious Diseases, Imperial College London, London, W2 1PG, UK
| | - Maarten van de Klundert
- Institute of Virology, Technical University of Munich/Helmholtz Zentrum München, Trogerstrasse 30, 81675, Munich, Germany
| | - Jochen Wettengel
- Institute of Virology, Technical University of Munich/Helmholtz Zentrum München, Trogerstrasse 30, 81675, Munich, Germany
| | - David Durantel
- Cancer Research Center of Lyon (CRCL), INSERM U1052, and University of Lyon (UCBL1), Lyon, France
| | - Marcus Dorner
- Section of Molecular Virology, Department of Infectious Diseases, Imperial College London, London, W2 1PG, UK
| | - Paul Klenerman
- Medawar Building, University of Oxford, South Parks Road, Oxford, OX1 3SY, UK
| | - Ulrike Protzer
- Institute of Virology, Technical University of Munich/Helmholtz Zentrum München, Trogerstrasse 30, 81675, Munich, Germany
| | - Efstathios S Giotis
- Section of Molecular Virology, Department of Infectious Diseases, Imperial College London, London, W2 1PG, UK
- School of Life Sciences, University of Essex, Colchester, C04 3SQ, UK
| | - Jane A McKeating
- Nuffield Department of Medicine Research Building, University of Oxford, Oxford, OX3 7LF, UK.
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Wang M, Chen L, Liang Z, He X, Liu W, Jiang B, Yan J, Sun P, Cao Z, Peng Q, Lin Y. Metabolome and transcriptome analyses reveal chlorophyll and anthocyanin metabolism pathway associated with cucumber fruit skin color. BMC PLANT BIOLOGY 2020; 20:386. [PMID: 32831013 PMCID: PMC7444041 DOI: 10.1186/s12870-020-02597-9] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 08/12/2020] [Indexed: 05/21/2023]
Abstract
BACKGROUND Fruit skin color play important role in commercial value of cucumber, which is mainly determined by the content and composition of chlorophyll and anthocyanins. Therefore, understanding the related genes and metabolomics involved in composition of fruit skin color is essential for cucumber quality and commodity value. RESULTS The results showed that chlorophyll a, chlorophyll b and carotenoid content in fruit skin were higher in Lv (dark green skin) than Bai (light green skin) on fruit skin. Cytological observation showed more chloroplast existed in fruit skin cells of Lv. A total of 162 significantly different metabolites were found between the fruit skin of the two genotypes by metabolome analysis, including 40 flavones, 9 flavanones, 8 flavonols, 6 anthocyanins, and other compounds. Crucial anthocyanins and flavonols for fruit skin color, were detected significantly decreased in fruit skin of Bai compared with Lv. By RNA-seq assay, 4516 differentially expressed genes (DEGs) were identified between two cultivars. Further analyses suggested that low expression level of chlorophyll biosynthetic genes, such as chlM, por and NOL caused less chlorophylls or chloroplast in fruit skin of Bai. Meanwhile, a predicted regulatory network of anthocyanin biosynthesis was established to illustrate involving many DEGs, especially 4CL, CHS and UFGT. CONCLUSIONS This study uncovered significant differences between two cucumber genotypes with different fruit color using metabolome and RNA-seq analysis. We lay a foundation to understand molecular regulation mechanism on formation of cucumber skin color, by exploring valuable genes, which is helpful for cucumber breeding and improvement on fruit skin color.
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Affiliation(s)
- Min Wang
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
- Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou, 510640, China
| | - Lin Chen
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
- Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou, 510640, China
| | - Zhaojun Liang
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
- Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou, 510640, China
| | - Xiaoming He
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
- Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou, 510640, China
| | - Wenrui Liu
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
- Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou, 510640, China
| | - Biao Jiang
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
- Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou, 510640, China
| | - Jinqiang Yan
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
- Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou, 510640, China
| | - Piaoyun Sun
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
- Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou, 510640, China
| | - Zhenqiang Cao
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
- Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou, 510640, China
| | - Qingwu Peng
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China.
- Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou, 510640, China.
| | - Yu'e Lin
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China.
- Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou, 510640, China.
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50
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Mapping a mammalian adult adrenal gland hierarchy across species by microwell-seq. CELL REGENERATION (LONDON, ENGLAND) 2020; 9:11. [PMID: 32743779 PMCID: PMC7396412 DOI: 10.1186/s13619-020-00042-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Accepted: 03/27/2020] [Indexed: 01/21/2023]
Abstract
Recently, single-cell RNA-seq technologies have been rapidly updated, leading to a revolution in biology. We previously developed Microwell-seq, a cost-effective and high-throughput single cell RNA sequencing(scRNA-seq) method with a very simple device. Most cDNA libraries are sequenced using an expensive Illumina platform. Here, we present the first report showing combined Microwell-seq and BGI MGISEQ2000, a less expensive sequencing platform, to profile the whole transcriptome of 11,883 individual mouse adult adrenal gland cells and identify 18 transcriptionally distinct clusters. Moreover, we performed a single-cell comparative analysis of human and mouse adult adrenal glands to reveal the conserved genetic networks in these mammalian systems. These results provide new insights into the sophisticated adrenal gland hierarchy and provide a benchmark, low-cost strategy for high-throughput single-cell RNA study.
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