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Marković V, Cvrčková F, Potocký M, Kulich I, Pejchar P, Kollárová E, Synek L, Žárský V. EXO70A2 Is Critical for Exocyst Complex Function in Pollen Development. PLANT PHYSIOLOGY 2020; 184:1823-1839. [PMID: 33051268 PMCID: PMC7723085 DOI: 10.1104/pp.19.01340] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 10/01/2020] [Indexed: 05/15/2023]
Abstract
Pollen development, pollen grain germination, and pollen tube elongation are crucial biological processes in angiosperm plants that need precise regulation to deliver sperm cells to ovules for fertilization. Highly polarized secretion at a growing pollen tube tip requires the exocyst tethering complex responsible for specific targeting of secretory vesicles to the plasma membrane. Here, we demonstrate that Arabidopsis (Arabidopsis thaliana) EXO70A2 (At5g52340) is the main exocyst EXO70 isoform in the male gametophyte, governing the conventional secretory function of the exocyst, analogous to EXO70A1 (At5g03540) in the sporophyte. Our analysis of a CRISPR-generated exo70a2 mutant revealed that EXO70A2 is essential for efficient pollen maturation, pollen grain germination, and pollen tube growth. GFP:EXO70A2 was localized to the nucleus and cytoplasm in developing pollen grains and later to the apical domain in growing pollen tube tips characterized by intensive exocytosis. Moreover, EXO70A2 could substitute for EXO70A1 function in the sporophyte, but not vice versa, indicating partial functional redundancy of these two closely related isoforms and higher specificity of EXO70A2 for pollen development-related processes. Phylogenetic analysis revealed that the ancient duplication of EXO70A, one of which is always highly expressed in pollen, occurred independently in monocots and dicots. In summary, EXO70A2 is a crucial component of the exocyst complex in Arabidopsis pollen that is required for efficient plant sexual reproduction.
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Affiliation(s)
- Vedrana Marković
- Department of Experimental Plant Biology, Faculty of Science, Charles University, 12844 Prague 2, Czech Republic
- Institute of Experimental Botany, Czech Academy of Sciences, 16502 Prague 6, Czech Republic
| | - Fatima Cvrčková
- Department of Experimental Plant Biology, Faculty of Science, Charles University, 12844 Prague 2, Czech Republic
| | - Martin Potocký
- Department of Experimental Plant Biology, Faculty of Science, Charles University, 12844 Prague 2, Czech Republic
- Institute of Experimental Botany, Czech Academy of Sciences, 16502 Prague 6, Czech Republic
| | - Ivan Kulich
- Department of Experimental Plant Biology, Faculty of Science, Charles University, 12844 Prague 2, Czech Republic
| | - Přemysl Pejchar
- Institute of Experimental Botany, Czech Academy of Sciences, 16502 Prague 6, Czech Republic
| | - Eva Kollárová
- Department of Experimental Plant Biology, Faculty of Science, Charles University, 12844 Prague 2, Czech Republic
| | - Lukáš Synek
- Institute of Experimental Botany, Czech Academy of Sciences, 16502 Prague 6, Czech Republic
| | - Viktor Žárský
- Department of Experimental Plant Biology, Faculty of Science, Charles University, 12844 Prague 2, Czech Republic
- Institute of Experimental Botany, Czech Academy of Sciences, 16502 Prague 6, Czech Republic
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Li W, Chung CYL, Wang CC, Chan TF, Leung MBW, Chan OK, Wu L, Appiah K, Chaemsaithong P, Cheng YKY, Poon LCY, Leung TY. Monochorionic twins with selective fetal growth restriction: insight from placental whole-transcriptome analysis. Am J Obstet Gynecol 2020; 223:749.e1-749.e16. [PMID: 32437666 DOI: 10.1016/j.ajog.2020.05.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 04/24/2020] [Accepted: 05/05/2020] [Indexed: 11/29/2022]
Abstract
BACKGROUND The underlying pathomechanism in placenta-related selective fetal growth restriction in monochorionic diamniotic twin pregnancy is not known. OBJECTIVE This study aimed to investigate any differences in placental transcriptomic profile between the selectively growth-restricted twins and the normally grown cotwins in monochorionic diamniotic twin pregnancies. STUDY DESIGN This was a prospective study of monochorionic diamniotic twin pregnancies complicated by selective fetal growth restriction. Placental biopsy specimens were obtained from the subjects in the delivery suite. The placental transcriptome of the selectively growth-restricted twin was compared with that of the normally grown cotwin. This study was divided into 2 stages: (1) gene discovery phase in which placental tissues from 5 monochorionic diamniotic twin pregnancies complicated by selective fetal growth restriction plus 2 control twin pregnancies underwent transcriptome profiling, and transcriptome profiling was carried out using whole-genome RNA sequencing; and (2) validation phase in which placental tissues from 13 monochorionic diamniotic twin pregnancies with selective fetal growth restriction underwent RNA and protein validation. RNA and protein expression levels of candidate genes were determined using quantitative real-time polymerase chain reaction and immunohistochemistry staining. RESULTS A total of 1429 transcripts were differentially expressed in the placentae of selectively growth-restricted twin pairs, where 610 were up-regulated and 819 were down-regulated. Endoplasmic reticulum lectin and mannose 6-phosphate receptor were consistently differentially up-regulated in all placentae of selectively growth-restricted twins. Quantitative real-time polymerase chain reaction and immunohistochemistry staining were used to validate the results (P<.05). CONCLUSION The expression of endoplasmic reticulum lectin and mannose 6-phosphate receptor, which are important for angiogenesis and fetal growth, was significantly increased in the placentae of selectively growth-restricted twin of a monochorionic twin pair.
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Affiliation(s)
- Wei Li
- Department of Obstetrics and Gynaecology, Faculty of Medicine, the Chinese University of Hong Kong, Shatin, Hong Kong
| | - Claire Yik Lok Chung
- School of Life Sciences, the Chinese University of Hong Kong, Shatin, Hong Kong; Hong Kong Bioinformatics Centre, the Chinese University of Hong Kong, Shatin, Hong Kong
| | - Chi Chiu Wang
- Department of Obstetrics and Gynaecology, Faculty of Medicine, the Chinese University of Hong Kong, Shatin, Hong Kong; Department of Reproduction and Development, Li Ka Shing Institute of Health Sciences, the Chinese University of Hong Kong, Shatin, Hong Kong; School of Biomedical Sciences, the Chinese University of Hong Kong, Shatin, Hong Kong
| | - Ting Fung Chan
- School of Life Sciences, the Chinese University of Hong Kong, Shatin, Hong Kong
| | - Maran Bo Wah Leung
- Department of Obstetrics and Gynaecology, Faculty of Medicine, the Chinese University of Hong Kong, Shatin, Hong Kong
| | - Oi Ka Chan
- Department of Obstetrics and Gynaecology, Faculty of Medicine, the Chinese University of Hong Kong, Shatin, Hong Kong; Hong Kong Bioinformatics Centre, the Chinese University of Hong Kong, Shatin, Hong Kong
| | - Ling Wu
- Department of Obstetrics and Gynaecology, Faculty of Medicine, the Chinese University of Hong Kong, Shatin, Hong Kong
| | - Kubi Appiah
- Department of Obstetrics and Gynaecology, Faculty of Medicine, the Chinese University of Hong Kong, Shatin, Hong Kong
| | - Piya Chaemsaithong
- Department of Obstetrics and Gynaecology, Faculty of Medicine, the Chinese University of Hong Kong, Shatin, Hong Kong
| | - Yvonne Kwun Yue Cheng
- Department of Obstetrics and Gynaecology, Faculty of Medicine, the Chinese University of Hong Kong, Shatin, Hong Kong
| | - Liona Chiu Yee Poon
- Department of Obstetrics and Gynaecology, Faculty of Medicine, the Chinese University of Hong Kong, Shatin, Hong Kong
| | - Tak Yeung Leung
- Department of Obstetrics and Gynaecology, Faculty of Medicine, the Chinese University of Hong Kong, Shatin, Hong Kong.
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Liu Y, Wang F, Zhang Y, Jia J, Yan T. ST6Gal1 is up-regulated and associated with aberrant IgA1 glycosylation in IgA nephropathy: An integrated analysis of the transcriptome. J Cell Mol Med 2020; 24:10493-10500. [PMID: 32677771 PMCID: PMC7521275 DOI: 10.1111/jcmm.15664] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Revised: 06/17/2020] [Accepted: 06/23/2020] [Indexed: 11/28/2022] Open
Abstract
Galactose-deficient IgA1 (Gd-IgA1) plays a crucial role in the development of Immunoglobulin A nephropathy (IgAN), however, the underlying pathogenic mechanisms driving Gd-IgA1 production in B cells are not well understood. In this study, RNA-seq analysis identified 337 down-regulated and 405 up-regulated genes in B cells from 17 patients with IgAN and 6 healthy controls. Among them, ST6Gal1, which was associated with IgAN in a previous genome-wide association study (GWAS), was up-regulated in IgAN and significantly positive correlated with elevated Gd-IgA1. In addition, we identified increased plasma ST6Gal1 levels in 100 patients with IgAN, which were associated with higher levels of proteinuria, plasma IgA, Gd-IgA1 levels, greater degrees of systemic complement activation including C3a, Bb, C4d, MAC and a lower proportion classified as C2 grade (crescent proportion ≥25%). Interesting, in vitro, recombinant ST6Gal1 (rST6Gal1) exposure reduced the production of Gd-IgA1 in cultured peripheral blood mononuclear cells from IgAN patients. rST6Gal1 stimuli also increased expression of C1GALT1, which were well-known proportional to the decrease in galactose deficiency of IgA1. In conclusions, we identified increased plasma ST6Gal1 levels and the association of ST6Gal1 with disease severity of IgAN. Additionally, rST6Gal1 administration in vitro increased expression of C1GALT1 and reduced the production of Gd-IgA1.
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Affiliation(s)
- Youxia Liu
- Department of Nephrology, Tianjin Medical University General Hospital, Tianjin, China
| | - Fanghao Wang
- Department of Nephrology, Tianjin Medical University General Hospital, Tianjin, China
| | - Yaru Zhang
- Department of Nephrology, Hunan Second People's Hospital, Hunan, China
| | - Junya Jia
- Department of Nephrology, Tianjin Medical University General Hospital, Tianjin, China
| | - Tiekun Yan
- Department of Nephrology, Tianjin Medical University General Hospital, Tianjin, China
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Pejchar P, Sekereš J, Novotný O, Žárský V, Potocký M. Functional analysis of phospholipase Dδ family in tobacco pollen tubes. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 103:212-226. [PMID: 32064689 DOI: 10.1111/tpj.14720] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 01/17/2020] [Accepted: 02/04/2020] [Indexed: 06/10/2023]
Abstract
Phosphatidic acid (PA), an important signalling and metabolic phospholipid, is predominantly localized in the subapical plasma membrane (PM) of growing pollen tubes. PA can be produced from structural phospholipids by phospholipase D (PLD), but the isoforms responsible for production of PM PA were not identified yet and their functional roles remain unknown. Following genome-wide bioinformatic analysis of the PLD family in tobacco, we focused on the pollen-overrepresented PLDδ class. Combining live-cell imaging, gene overexpression, lipid-binding and structural bioinformatics, we characterized five NtPLDδ isoforms. Distinct PLDδ isoforms preferentially localize to the cytoplasm or subapical PM. Using fluorescence recovery after photobleaching, domain deletion and swapping analyses we show that membrane-bound PLDδs are tightly bound to PM, primarily via the central catalytic domain. Overexpression analyses suggested isoform PLDδ3 as the most important member of the PLDδ subfamily active in pollen tubes. Moreover, only PLDδ3 shows significant constitutive PLD activity in vivo and, in turn, PA promotes binding of PLDδ3 to the PM. This forms a positive feedback loop leading to PA accumulation and the formation of massive PM invaginations. Tightly controlled production of PA generated by PLDδ3 at the PM is important for maintaining the balance between various membrane trafficking processes that are crucial for plant cell tip growth.
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Affiliation(s)
- Přemysl Pejchar
- Institute of Experimental Botany of the Czech Academy of Sciences, 16502, Prague 6, Czech Republic
| | - Juraj Sekereš
- Institute of Experimental Botany of the Czech Academy of Sciences, 16502, Prague 6, Czech Republic
| | - Ondřej Novotný
- Institute of Experimental Botany of the Czech Academy of Sciences, 16502, Prague 6, Czech Republic
- Department of Biochemistry and Microbiology, University of Chemistry and Technology Prague, 16628, Prague 6, Czech Republic
| | - Viktor Žárský
- Institute of Experimental Botany of the Czech Academy of Sciences, 16502, Prague 6, Czech Republic
- Department of Experimental Plant Biology, Charles University, 128 44, Prague 2, Czech Republic
| | - Martin Potocký
- Institute of Experimental Botany of the Czech Academy of Sciences, 16502, Prague 6, Czech Republic
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Wu J, Mamidi TKK, Zhang L, Hicks C. Unraveling the Genomic-Epigenomic Interaction Landscape in Triple Negative and Non-Triple Negative Breast Cancer. Cancers (Basel) 2020; 12:cancers12061559. [PMID: 32545594 PMCID: PMC7352267 DOI: 10.3390/cancers12061559] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 06/03/2020] [Accepted: 06/05/2020] [Indexed: 01/01/2023] Open
Abstract
Background: The recent surge of next generation sequencing of breast cancer genomes has enabled development of comprehensive catalogues of somatic mutations and expanded the molecular classification of subtypes of breast cancer. However, somatic mutations and gene expression data have not been leveraged and integrated with epigenomic data to unravel the genomic-epigenomic interaction landscape of triple negative breast cancer (TNBC) and non-triple negative breast cancer (non-TNBC). Methods: We performed integrative data analysis combining somatic mutation, epigenomic and gene expression data from The Cancer Genome Atlas (TCGA) to unravel the possible oncogenic interactions between genomic and epigenomic variation in TNBC and non-TNBC. We hypothesized that within breast cancers, there are differences in somatic mutation, DNA methylation and gene expression signatures between TNBC and non-TNBC. We further hypothesized that genomic and epigenomic alterations affect gene regulatory networks and signaling pathways driving the two types of breast cancer. Results: The investigation revealed somatic mutated, epigenomic and gene expression signatures unique to TNBC and non-TNBC and signatures distinguishing the two types of breast cancer. In addition, the investigation revealed molecular networks and signaling pathways enriched for somatic mutations and epigenomic changes unique to each type of breast cancer. The most significant pathways for TNBC were: retinal biosynthesis, BAG2, LXR/RXR, EIF2 and P2Y purigenic receptor signaling pathways. The most significant pathways for non-TNBC were: UVB-induced MAPK, PCP, Apelin endothelial, Endoplasmatic reticulum stress and mechanisms of viral exit from host signaling Pathways. Conclusion: The investigation revealed integrated genomic, epigenomic and gene expression signatures and signing pathways unique to TNBC and non-TNBC, and a gene signature distinguishing the two types of breast cancer. The study demonstrates that integrative analysis of multi-omics data is a powerful approach for unravelling the genomic-epigenomic interaction landscape in TNBC and non-TNBC.
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Affiliation(s)
- Jiande Wu
- Health Sciences Center, Department of Genetic, Louisiana State University School of Medicine, 533 Bolivar Street, New Orleans, LA 70112, USA;
| | - Tarun Karthik Kumar Mamidi
- Center for Computational Genomics and Data Science, Departments of Pediatrics and Pathology, University of Alabama–Birmingham School of Medicine, Birmingham, AL 35233, USA;
| | - Lu Zhang
- Department of Public Health Sciences, Clemson University, 513 Edwards Hall, Clemson, SC 29634, USA;
| | - Chindo Hicks
- Health Sciences Center, Department of Genetic, Louisiana State University School of Medicine, 533 Bolivar Street, New Orleans, LA 70112, USA;
- Correspondence: ; Tel.: +1-504-568-2657
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Zhao Z, Dai Y, Zhang C, Mathé E, Wei L, Wang K. The International Conference on Intelligent Biology and Medicine (ICIBM) 2019: bioinformatics methods and applications for human diseases. BMC Bioinformatics 2019; 20:676. [PMID: 31861973 PMCID: PMC6924135 DOI: 10.1186/s12859-019-3240-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Between June 9-11, 2019, the International Conference on Intelligent Biology and Medicine (ICIBM 2019) was held in Columbus, Ohio, USA. The conference included 12 scientific sessions, five tutorials or workshops, one poster session, four keynote talks and four eminent scholar talks that covered a wide range of topics in bioinformatics, medical informatics, systems biology and intelligent computing. Here, we describe 13 high quality research articles selected for publishing in BMC Bioinformatics.
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Affiliation(s)
- Zhongming Zhao
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030 USA
| | - Yulin Dai
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030 USA
| | - Chi Zhang
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202 USA
| | - Ewy Mathé
- Department of Biomedical Informatics, The Ohio State University College of Medicine, Columbus, OH 43214 USA
| | - Lai Wei
- Department of Biomedical Informatics, The Ohio State University College of Medicine, Columbus, OH 43214 USA
| | - Kai Wang
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104 USA
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