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Wan L, Huo J, Huang Q, Ji X, Song L, Zhang Z, Pan L, Fu J, Abd Elhamid MA, Soaud SA, Heakel RMY, Gao J, Wei S, El-Sappah AH. Genetics and metabolic responses of Artemisia annua L to the lake of phosphorus under the sparingly soluble phosphorus fertilizer: evidence from transcriptomics analysis. Funct Integr Genomics 2024; 24:26. [PMID: 38329581 DOI: 10.1007/s10142-024-01301-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 01/14/2024] [Accepted: 01/16/2024] [Indexed: 02/09/2024]
Abstract
The medicinal herb Artemisia annua L. is prized for its capacity to generate artemisinin, which is used to cure malaria. Potentially influencing the biomass and secondary metabolite synthesis of A. annua is plant nutrition, particularly phosphorus (P). However, most soil P exist as insoluble inorganic and organic phosphates, which results to low P availability limiting plant growth and development. Although plants have developed several adaptation strategies to low P levels, genetics and metabolic responses to P status remain largely unknown. In a controlled greenhouse experiment, the sparingly soluble P form, hydroxyapatite (Ca5OH(PO4)3/CaP) was used to simulate calcareous soils with low P availability. In contrast, the soluble P form KH2PO4/KP was used as a control. A. annua's morphological traits, growth, and artemisinin concentration were determined, and RNA sequencing was used to identify the differentially expressed genes (DEGs) under two different P forms. Total biomass, plant height, leaf number, and stem diameter, as well as leaf area, decreased by 64.83%, 27.49%, 30.47%, 38.70%, and 54.64% in CaP compared to KP; however, LC-MS tests showed an outstanding 37.97% rise in artemisinin content per unit biomass in CaP contrary to KP. Transcriptome analysis showed 2015 DEGs (1084 up-regulated and 931 down-regulated) between two P forms, including 39 transcription factor (TF) families. Further analysis showed that DEGs were mainly enriched in carbohydrate metabolism, secondary metabolites biosynthesis, enzyme catalytic activity, signal transduction, and so on, such as tricarboxylic acid (TCA) cycle, glycolysis, starch and sucrose metabolism, flavonoid biosynthesis, P metabolism, and plant hormone signal transduction. Meanwhile, several artemisinin biosynthesis genes were up-regulated, including DXS, GPPS, GGPS, MVD, and ALDH, potentially increasing artemisinin accumulation. Furthermore, 21 TF families, including WRKY, MYB, bHLH, and ERF, were up-regulated in reaction to CaP, confirming their importance in P absorption, internal P cycling, and artemisinin biosynthesis regulation. Our results will enable us to comprehend how low P availability impacts the parallel transcriptional control of plant development, growth, and artemisinin production in A. annua. This study could lay the groundwork for future research into the molecular mechanisms underlying A. annua's low P adaptation.
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Affiliation(s)
- Lingyun Wan
- Guangxi Key Laboratory of High-Quality Formation and Utilization of Dao-di Herbs, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Juan Huo
- Guangxi Key Laboratory of High-Quality Formation and Utilization of Dao-di Herbs, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Qiulan Huang
- Faculty of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, China
| | - Xiaowen Ji
- Guangxi Key Laboratory of High-Quality Formation and Utilization of Dao-di Herbs, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Lisha Song
- Guangxi Key Laboratory of High-Quality Formation and Utilization of Dao-di Herbs, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Zhanjiang Zhang
- Guangxi Key Laboratory of High-Quality Formation and Utilization of Dao-di Herbs, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Limei Pan
- Guangxi Key Laboratory of High-Quality Formation and Utilization of Dao-di Herbs, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Jine Fu
- Guangxi Key Laboratory of High-Quality Formation and Utilization of Dao-di Herbs, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | | | - Salma A Soaud
- Genetics Department, Faculty of Agriculture, Zagazig University, Zagazig, Egypt
| | - Rania M Y Heakel
- Genetics Department, Faculty of Agriculture, Zagazig University, Zagazig, Egypt
| | - Jihai Gao
- School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Shugen Wei
- Guangxi Key Laboratory of High-Quality Formation and Utilization of Dao-di Herbs, Guangxi Botanical Garden of Medicinal Plants, Nanning, China.
| | - Ahmed H El-Sappah
- Faculty of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, China.
- Genetics Department, Faculty of Agriculture, Zagazig University, Zagazig, Egypt.
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Hu Y, Li C, Zhou R, Song Y, Lv Z, Wang Q, Dong X, Liu S, Feng C, Zhou Y, Zeng X, Zhang L, Wang Z, Di H. The Transcription Factor ZmNAC89 Gene Is Involved in Salt Tolerance in Maize ( Zea mays L.). Int J Mol Sci 2023; 24:15099. [PMID: 37894780 PMCID: PMC10606073 DOI: 10.3390/ijms242015099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 10/03/2023] [Accepted: 10/10/2023] [Indexed: 10/29/2023] Open
Abstract
The NAC gene family has transcription factors specific to plants, which are involved in development and stress response and adaptation. In this study, ZmNAC89, an NAC gene in maize that plays a role in saline-alkaline tolerance, was isolated and characterized. ZmNAC89 was localized in the nucleus and had transcriptional activation activity during in vitro experiments. The expression of ZmNAC89 was strongly upregulated under saline-alkaline, drought and ABA treatments. Overexpression of the ZmNAC89 gene in transgenic Arabidopsis and maize enhanced salt tolerance at the seedling stage. Differentially expressed genes (DEGs) were then confirmed via RNA-sequencing analysis with the transgenic maize line. GO analyses showed that oxidation-reduction process-regulated genes were involved in ZmNAC89-mediated salt-alkaline stress. ZmNAC89 may regulate maize saline-alkali tolerance through the REDOX pathway and ABA signal transduction pathway. From 140 inbred maize lines, 20 haplotypes and 16 SNPs were found in the coding region of the ZmNAC89 gene, including the excellent haplotype HAP20. These results contribute to a better understanding of the response mechanism of maize to salt-alkali stress and marker-assisted selection during maize breeding.
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Affiliation(s)
- Yingying Hu
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Engineering Technology Research Center of Maize Germplasm Resources Innovation on Cold land of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, China; (Y.H.); (C.L.); (R.Z.); (Y.S.); (Z.L.); (Q.W.); (X.D.); (S.L.); (C.F.); (Y.Z.); (X.Z.); (L.Z.)
| | - Chunxiang Li
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Engineering Technology Research Center of Maize Germplasm Resources Innovation on Cold land of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, China; (Y.H.); (C.L.); (R.Z.); (Y.S.); (Z.L.); (Q.W.); (X.D.); (S.L.); (C.F.); (Y.Z.); (X.Z.); (L.Z.)
| | - Runyu Zhou
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Engineering Technology Research Center of Maize Germplasm Resources Innovation on Cold land of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, China; (Y.H.); (C.L.); (R.Z.); (Y.S.); (Z.L.); (Q.W.); (X.D.); (S.L.); (C.F.); (Y.Z.); (X.Z.); (L.Z.)
| | - Yongfeng Song
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Engineering Technology Research Center of Maize Germplasm Resources Innovation on Cold land of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, China; (Y.H.); (C.L.); (R.Z.); (Y.S.); (Z.L.); (Q.W.); (X.D.); (S.L.); (C.F.); (Y.Z.); (X.Z.); (L.Z.)
| | - Zhichao Lv
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Engineering Technology Research Center of Maize Germplasm Resources Innovation on Cold land of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, China; (Y.H.); (C.L.); (R.Z.); (Y.S.); (Z.L.); (Q.W.); (X.D.); (S.L.); (C.F.); (Y.Z.); (X.Z.); (L.Z.)
| | - Qi Wang
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Engineering Technology Research Center of Maize Germplasm Resources Innovation on Cold land of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, China; (Y.H.); (C.L.); (R.Z.); (Y.S.); (Z.L.); (Q.W.); (X.D.); (S.L.); (C.F.); (Y.Z.); (X.Z.); (L.Z.)
| | - Xiaojie Dong
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Engineering Technology Research Center of Maize Germplasm Resources Innovation on Cold land of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, China; (Y.H.); (C.L.); (R.Z.); (Y.S.); (Z.L.); (Q.W.); (X.D.); (S.L.); (C.F.); (Y.Z.); (X.Z.); (L.Z.)
- Institute of Crop Resources Research, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China
| | - Shan Liu
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Engineering Technology Research Center of Maize Germplasm Resources Innovation on Cold land of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, China; (Y.H.); (C.L.); (R.Z.); (Y.S.); (Z.L.); (Q.W.); (X.D.); (S.L.); (C.F.); (Y.Z.); (X.Z.); (L.Z.)
| | - Chenchen Feng
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Engineering Technology Research Center of Maize Germplasm Resources Innovation on Cold land of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, China; (Y.H.); (C.L.); (R.Z.); (Y.S.); (Z.L.); (Q.W.); (X.D.); (S.L.); (C.F.); (Y.Z.); (X.Z.); (L.Z.)
| | - Yu Zhou
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Engineering Technology Research Center of Maize Germplasm Resources Innovation on Cold land of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, China; (Y.H.); (C.L.); (R.Z.); (Y.S.); (Z.L.); (Q.W.); (X.D.); (S.L.); (C.F.); (Y.Z.); (X.Z.); (L.Z.)
| | - Xing Zeng
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Engineering Technology Research Center of Maize Germplasm Resources Innovation on Cold land of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, China; (Y.H.); (C.L.); (R.Z.); (Y.S.); (Z.L.); (Q.W.); (X.D.); (S.L.); (C.F.); (Y.Z.); (X.Z.); (L.Z.)
| | - Lin Zhang
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Engineering Technology Research Center of Maize Germplasm Resources Innovation on Cold land of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, China; (Y.H.); (C.L.); (R.Z.); (Y.S.); (Z.L.); (Q.W.); (X.D.); (S.L.); (C.F.); (Y.Z.); (X.Z.); (L.Z.)
| | - Zhenhua Wang
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Engineering Technology Research Center of Maize Germplasm Resources Innovation on Cold land of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, China; (Y.H.); (C.L.); (R.Z.); (Y.S.); (Z.L.); (Q.W.); (X.D.); (S.L.); (C.F.); (Y.Z.); (X.Z.); (L.Z.)
| | - Hong Di
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Engineering Technology Research Center of Maize Germplasm Resources Innovation on Cold land of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, China; (Y.H.); (C.L.); (R.Z.); (Y.S.); (Z.L.); (Q.W.); (X.D.); (S.L.); (C.F.); (Y.Z.); (X.Z.); (L.Z.)
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Yehezkel AS, Abudi N, Nevo Y, Benyamini H, Elgavish S, Weinstock M, Abramovitch R. AN1284 attenuates steatosis, lipogenesis, and fibrosis in mice with pre-existing non-alcoholic steatohepatitis and directly affects aryl hydrocarbon receptor in a hepatic cell line. Front Endocrinol (Lausanne) 2023; 14:1226808. [PMID: 37664863 PMCID: PMC10469006 DOI: 10.3389/fendo.2023.1226808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 07/19/2023] [Indexed: 09/05/2023] Open
Abstract
Non-alcoholic steatohepatitis (NASH) is an aggressive form of fatty liver disease with hepatic inflammation and fibrosis for which there is currently no drug treatment. This study determined whether an indoline derivative, AN1284, which significantly reduced damage in a model of acute liver disease, can reverse steatosis and fibrosis in mice with pre-existing NASH and explore its mechanism of action. The mouse model of dietary-induced NASH reproduces most of the liver pathology seen in human subjects. This was confirmed by RNA-sequencing analysis. The Western diet, given for 4 months, caused steatosis, inflammation, and liver fibrosis. AN1284 (1 mg or 5 mg/kg/day) was administered for the last 2 months of the diet by micro-osmotic-pumps (mps). Both doses significantly decreased hepatic damage, liver weight, hepatic fat content, triglyceride, serum alanine transaminase, and fibrosis. AN1284 (1 mg/kg/day) given by mps or in the drinking fluid significantly reduced fibrosis produced by carbon tetrachloride injections. In human HUH7 hepatoma cells incubated with palmitic acid, AN1284 (2.1 and 6.3 ng/ml), concentrations compatible with those in the liver of mice treated with AN1284, decreased lipid formation by causing nuclear translocation of the aryl hydrocarbon receptor (AhR). AN1284 downregulated fatty acid synthase (FASN) and sterol regulatory element-binding protein 1c (SREBP-1c) and upregulated Acyl-CoA Oxidase 1 and Cytochrome P450-a1, genes involved in lipid metabolism. In conclusion, chronic treatment with AN1284 (1mg/kg/day) reduced pre-existing steatosis and fibrosis through AhR, which affects several contributors to the development of fatty liver disease. Additional pathways are also influenced by AN1284 treatment.
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Affiliation(s)
- Adi S. Yehezkel
- The Goldyne Savad Institute of Gene Therapy, Hadassah Medical Center, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
- The Wohl Institute for Translational Medicine, Hadassah Medical Center, Jerusalem, Israel
| | - Nathalie Abudi
- The Goldyne Savad Institute of Gene Therapy, Hadassah Medical Center, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
- The Wohl Institute for Translational Medicine, Hadassah Medical Center, Jerusalem, Israel
| | - Yuval Nevo
- Info-CORE, Bioinformatics Unit of the I-CORE at the Hebrew University of Jerusalem, Jerusalem, Israel
| | - Hadar Benyamini
- Info-CORE, Bioinformatics Unit of the I-CORE at the Hebrew University of Jerusalem, Jerusalem, Israel
| | - Sharona Elgavish
- Info-CORE, Bioinformatics Unit of the I-CORE at the Hebrew University of Jerusalem, Jerusalem, Israel
| | - Marta Weinstock
- Faculty of Medicine, School of Pharmacy, Institute for Drug Research, Hebrew University, Jerusalem, Israel
| | - Rinat Abramovitch
- The Goldyne Savad Institute of Gene Therapy, Hadassah Medical Center, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
- The Wohl Institute for Translational Medicine, Hadassah Medical Center, Jerusalem, Israel
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Zhang M, Fu YH, Luo YW, Gou MR, Zhang L, Fei Z, Gao DK. d-allose protects brain microvascular endothelial cells from hypoxic/reoxygenated injury by inhibiting endoplasmic reticulum stress. Neurosci Lett 2023; 793:137000. [PMID: 36473686 DOI: 10.1016/j.neulet.2022.137000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 11/17/2022] [Accepted: 11/30/2022] [Indexed: 12/12/2022]
Abstract
Ischemic stroke is an acute brain disease with a high mortality rate. Currently, the only effective method is to restore the blood supply. But the inflammation and oxidative stress induced by this approach can damage the integrity of the endothelial system, which hampers the patient's outcome. d-allose has the biological activity to protect against ischemia-reperfusion injury, however, the underlying mechanism remains unclear. Here, brain microvascular endothelial cells (RBMECs) were used as the study material to establish an IR-injury model. Cell viability of RBMECs was suppressed after hypoxia/reoxygenation (H/R) treatment and significantly increased after d-allose supplementation. RNAseq results showed 180 differentially expressed genes (DEGs) between the therapy group (H/R + Dal) and the model group (H/R), of which 151 DEGs were restored to control levels by d-allose. Enrichment analysis revealed that DEGs were mainly involved in protein processing in endoplasmic reticulum. 6 DEGs in the unfolded protein response (UPR) pathway were verified by qRT-PCR. All of them were significantly down-regulated by d-allose, indicating that endoplasmic reticulum stress (ERS) was relieved. In addition, d-allose significantly inhibited the phosphorylation level of eIF2α, a marker of ERS. The downstream molecules of Phosphorylation of eIF2α, Gadd45a and Chac1, which trigger cycle arrest and apoptosis, respectively, were also significantly inhibited by d-allose. Thus, we conclude that d-allose inhibits the UPR pathway, attenuates eIF2α phosphorylation and ERS, restores the cell cycle, inhibits apoptosis, and thus enhances endothelial cell tolerance to H/R injury.
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Fu D, Li J, Yang X, Li W, Zhou Z, Xiao S, Xue C. Iron redistribution induces oxidative burst and resistance in maize against Curvularia lunata. Planta 2022; 256:46. [PMID: 35867182 DOI: 10.1007/s00425-022-03963-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 07/14/2022] [Indexed: 06/15/2023]
Abstract
ΔClnps6 induced iron redistribution in maize B73 leaf cells and resulted in reactive oxygen species (ROS) burst to enhance plant resistance against Curvularia lunata. Iron is an indispensable co-factor of various crucial enzymes that are involved in cellular metabolic processes and energy metabolism in eukaryotes. For this reason, plants and pathogens compete for iron to maintain their iron homeostasis, respectively. In our previous study, ΔClnps6, the extracellular siderophore biosynthesis deletion mutant of Curvularia lunata, was sensitive to exogenous hydrogen peroxide and virulence reduction. However, the mechanism was not studied. Here, we report that maize B73 displayed highly resistance to ΔClnps6. The plants recruited more iron at cell wall appositions (CWAs) to cause ROS bursts. Intracellular iron deficiency induced by iron redistribution originated form up-regulated expression of genes involved in intracellular iron consumption in leaves and absorption in roots. The RNA-sequencing data also showed that the expression of respiratory burst oxidase homologue (ZmRBOH4) and NADP-dependent malic enzyme 4 (ZmNADP-ME4) involved in ROS production was up-regulated in maize B73 after ΔClnps6 infection. Simultaneously, jasmonic acid (JA) biosynthesis genes lipoxygenase (ZmLOX), allene oxide synthase (ZmAOS), GA degradation gene gibberellin 2-beta-dioxygenase (ZmGA2OX6) and ABA degradation genes abscisic acid hydroxylase (ZmABH1, ZmABH2) involved in iron homeostasis were up-regulated expression. Ferritin1 (ZmFER1) positive regulated maize resistance against C. lunata via ROS burst under Fe-limiting conditions. Overall, our results showed that iron played vital roles in activating maize resistance in B73-C. lunata interaction.
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Affiliation(s)
- Dandan Fu
- College of Plant Protection, Shenyang Agricultural University, Shenyang, 110866, China
| | - Jiayang Li
- College of Plant Protection, Shenyang Agricultural University, Shenyang, 110866, China
| | - Xue Yang
- College of Plant Protection, Shenyang Agricultural University, Shenyang, 110866, China
| | - Wenling Li
- College of Plant Protection, Shenyang Agricultural University, Shenyang, 110866, China
| | - Zengran Zhou
- College of Plant Protection, Shenyang Agricultural University, Shenyang, 110866, China
| | - Shuqin Xiao
- College of Plant Protection, Shenyang Agricultural University, Shenyang, 110866, China.
| | - Chunsheng Xue
- College of Plant Protection, Shenyang Agricultural University, Shenyang, 110866, China.
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Ou SM, Tsai MT, Chen HY, Li FA, Tseng WC, Lee KH, Chang FP, Lin YP, Yang RB, Tarng DC. Identification of Galectin-3 as Potential Biomarkers for Renal Fibrosis by RNA-Sequencing and Clinicopathologic Findings of Kidney Biopsy. Front Med (Lausanne) 2021; 8:748225. [PMID: 34869439 PMCID: PMC8633540 DOI: 10.3389/fmed.2021.748225] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 10/13/2021] [Indexed: 12/16/2022] Open
Abstract
Background: Galectin-3 (Gal-3) is a multifunctional glycan-binding protein shown to be linked to chronic inflammation and fibrogenesis. Plasma Gal-3 is associated with proteinuria and renal dysfunction, but its role has never been confirmed with kidney biopsy results. In our study, we aimed to explore the expression of Gal-3 in biopsy-proven patients, and we tested the hypothesis that chronic kidney disease (CKD) leads to upregulation of plasma Gal-3 expression in corresponding biopsy findings and RNA sequencing analysis. Method: In 249 patients (male/female: 155/94, age: 57.2 ± 16.3 years) who underwent kidney biopsy, plasma levels of Gal-3 were measured to estimate the association of renal fibrosis. Relationships between plasma Gal-3 levels, estimated glomerular filtration rate (eGFR) and renal histology findings were also assessed. We further examined the gene expression of Gal-3 in RNA-sequencing analysis in biopsy-proven patients. Results: Compared to patients without CKD, CKD patients had higher levels of plasma Gal-3 (1,016.3 ± 628.1 pg/mL vs. 811.6 ± 369.6 pg/ml; P = 0.010). Plasma Gal-3 was inversely correlated with eGFR (P = 0.005) but not with proteinuria. Higher Gal-3 levels were associated with interstitial fibrosis, tubular atrophy and vascular intimal fibrosis. RNA-sequencing analysis showed the upregulation of Gal-3 in fibrotic kidney biopsy samples, and the differentially expressed genes were mainly enhanced in immune cell activation and the regulation of cell-cell adhesion. Conclusions: Plasma Gal-3 levels are inverse correlated with eGFR but positively correlated with renal fibrosis, which may be involved in the immune response and associated pathways. These findings support the role of Gal-3 as a predictive marker of renal fibrosis.
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Affiliation(s)
- Shuo-Ming Ou
- Division of Nephrology, Department of Medicine, Taipei Veterans General Hospital, Taipei, Taiwan.,School of Medicine, National Yang-Ming University, Taipei, Taiwan.,School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan.,Institute of Clinical Medicine, National Yang-Ming University, Taipei, Taiwan.,Institute of Clinical Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan.,Center for Intelligent Drug Systems and Smart Bio-devices (IDS2B), National Yang Ming Chiao Tung University, Hsinchu, Taiwan
| | - Ming-Tsun Tsai
- Division of Nephrology, Department of Medicine, Taipei Veterans General Hospital, Taipei, Taiwan.,School of Medicine, National Yang-Ming University, Taipei, Taiwan.,School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan.,Institute of Clinical Medicine, National Yang-Ming University, Taipei, Taiwan.,Institute of Clinical Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan.,Center for Intelligent Drug Systems and Smart Bio-devices (IDS2B), National Yang Ming Chiao Tung University, Hsinchu, Taiwan
| | - Huan-Yuan Chen
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Fu-An Li
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Wei-Cheng Tseng
- Division of Nephrology, Department of Medicine, Taipei Veterans General Hospital, Taipei, Taiwan.,School of Medicine, National Yang-Ming University, Taipei, Taiwan.,School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan.,Institute of Clinical Medicine, National Yang-Ming University, Taipei, Taiwan.,Institute of Clinical Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan.,Center for Intelligent Drug Systems and Smart Bio-devices (IDS2B), National Yang Ming Chiao Tung University, Hsinchu, Taiwan
| | - Kuo-Hua Lee
- Division of Nephrology, Department of Medicine, Taipei Veterans General Hospital, Taipei, Taiwan.,School of Medicine, National Yang-Ming University, Taipei, Taiwan.,School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan.,Institute of Clinical Medicine, National Yang-Ming University, Taipei, Taiwan.,Institute of Clinical Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan.,Center for Intelligent Drug Systems and Smart Bio-devices (IDS2B), National Yang Ming Chiao Tung University, Hsinchu, Taiwan
| | - Fu-Pang Chang
- Department of Pathology and Laboratory Medicine, Taipei Veterans General Hospital, Taipei, Taiwan.,Inflammation and Immunity Research Center, National Yang-Ming University, Taipei, Taiwan
| | - Yao-Ping Lin
- Division of Nephrology, Department of Medicine, Taipei Veterans General Hospital, Taipei, Taiwan.,School of Medicine, National Yang-Ming University, Taipei, Taiwan.,School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan.,Institute of Clinical Medicine, National Yang-Ming University, Taipei, Taiwan.,Institute of Clinical Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan.,Center for Intelligent Drug Systems and Smart Bio-devices (IDS2B), National Yang Ming Chiao Tung University, Hsinchu, Taiwan
| | - Ruey-Bing Yang
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Der-Cherng Tarng
- Division of Nephrology, Department of Medicine, Taipei Veterans General Hospital, Taipei, Taiwan.,School of Medicine, National Yang-Ming University, Taipei, Taiwan.,School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan.,Institute of Clinical Medicine, National Yang-Ming University, Taipei, Taiwan.,Institute of Clinical Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan.,Center for Intelligent Drug Systems and Smart Bio-devices (IDS2B), National Yang Ming Chiao Tung University, Hsinchu, Taiwan.,Department and Institute of Physiology, National Yang-Ming University, Taipei, Taiwan.,Department and Institute of Physiology, National Yang Ming Chiao Tung University, Taipei, Taiwan
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Zhou N, Yao Y, Wu N, Du H, Xu M, Zhao Y, Tu Y. VF-4 and DR-8 Derived from Salted Egg White Inhibit Inflammatory Activity via NF-κB/PI3K-Akt/MAPK Signal Transduction Pathways in HT-29 Cells Induced by TNF-α. Mol Nutr Food Res 2021; 66:e2100682. [PMID: 34821458 DOI: 10.1002/mnfr.202100682] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 10/04/2021] [Indexed: 12/11/2022]
Abstract
SCOPE Inflammation is the pathological basis of many chronic diseases, and persistent intestinal inflammation is a key factor in the further development of colon cancer. Egg-derived peptides have been proven to have anti-intestinal inflammation activity. Egg white treated with salt contains a lot of rich protein, whether its peptides have anti-inflammatory activity and how their mechanism of action is still unclear. METHODS AND RESULTS In this study, ELISA is used to determine the anti-inflammatory activity of the peptides (VF-4 and DR-8 from salted egg white), and then RNA-seq is used to explore the mechanism of their anti-inflammatory activity, and then verified by western blotting and inhibitors. The results show that VF-4 and DR-8 significantly inhibit TNF-α-induced IL-8 secretion in HT-29 cells in a concentration-dependent manner, and VF-4 show a more significant anti-inflammatory effect than DR-8. The anti-inflammatory mechanism of VF-4 and DR-8 is through inhibiting the activation of Nuclear factor kappa B (NF-κB), mitogen-activated protein kinase (MAPK), and phosphatidylinositol 3' -kinase(PI3K)-Akt pathways, reducing the production of inflammatory mediators. CONCLUSION VF-4 and DR-8 have obvious anti-inflammatory activity, which can reduce intestinal inflammation and inhibit its further development into colon cancer.
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Affiliation(s)
- Na Zhou
- Jiangxi Key Laboratory of Natural Products and Functional Food, Jiangxi Agricultural University, Nanchang, 330045, China.,Agricultural Products Processing and Quality Control Engineering Laboratory of Jiangxi, Jiangxi Agricultural University, Nan Chang, 330045, China
| | - Yao Yao
- Jiangxi Key Laboratory of Natural Products and Functional Food, Jiangxi Agricultural University, Nanchang, 330045, China.,Agricultural Products Processing and Quality Control Engineering Laboratory of Jiangxi, Jiangxi Agricultural University, Nan Chang, 330045, China
| | - Na Wu
- Jiangxi Key Laboratory of Natural Products and Functional Food, Jiangxi Agricultural University, Nanchang, 330045, China.,Agricultural Products Processing and Quality Control Engineering Laboratory of Jiangxi, Jiangxi Agricultural University, Nan Chang, 330045, China
| | - Huaying Du
- Jiangxi Key Laboratory of Natural Products and Functional Food, Jiangxi Agricultural University, Nanchang, 330045, China.,Agricultural Products Processing and Quality Control Engineering Laboratory of Jiangxi, Jiangxi Agricultural University, Nan Chang, 330045, China
| | - Mingsheng Xu
- Jiangxi Key Laboratory of Natural Products and Functional Food, Jiangxi Agricultural University, Nanchang, 330045, China.,Agricultural Products Processing and Quality Control Engineering Laboratory of Jiangxi, Jiangxi Agricultural University, Nan Chang, 330045, China
| | - Yan Zhao
- Jiangxi Key Laboratory of Natural Products and Functional Food, Jiangxi Agricultural University, Nanchang, 330045, China.,Agricultural Products Processing and Quality Control Engineering Laboratory of Jiangxi, Jiangxi Agricultural University, Nan Chang, 330045, China
| | - Yonggang Tu
- Jiangxi Key Laboratory of Natural Products and Functional Food, Jiangxi Agricultural University, Nanchang, 330045, China.,Agricultural Products Processing and Quality Control Engineering Laboratory of Jiangxi, Jiangxi Agricultural University, Nan Chang, 330045, China
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8
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Cochran KR, Veeraraghavan K, Kundu G, Mazan-Mamczarz K, Coletta C, Thambisetty M, Gorospe M, De S. Systematic Identification of circRNAs in Alzheimer's Disease. Genes (Basel) 2021; 12:1258. [PMID: 34440432 DOI: 10.3390/genes12081258] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 07/25/2021] [Accepted: 08/10/2021] [Indexed: 12/13/2022] Open
Abstract
Mammalian circRNAs are covalently closed circular RNAs often generated through backsplicing of precursor linear RNAs. Although their functions are largely unknown, they have been found to influence gene expression at different levels and in a wide range of biological processes. Here, we investigated if some circRNAs may be differentially abundant in Alzheimer’s Disease (AD). We identified and analyzed publicly available RNA-sequencing data from the frontal lobe, temporal cortex, hippocampus, and plasma samples reported from persons with AD and persons who were cognitively normal, focusing on circRNAs shared across these datasets. We identified an overlap of significantly changed circRNAs among AD individuals in the various brain datasets, including circRNAs originating from genes strongly linked to AD pathology such as DOCK1, NTRK2, APC (implicated in synaptic plasticity and neuronal survival) and DGL1/SAP97, TRAPPC9, and KIF1B (implicated in vesicular traffic). We further predicted the presence of circRNA isoforms in AD using specialized statistical analysis packages to create approximations of entire circRNAs. We propose that the catalog of differentially abundant circRNAs can guide future investigation on the expression and splicing of the host transcripts, as well as the possible roles of these circRNAs in AD pathogenesis.
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9
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Son SH, Lee MK, Son YE, Park HS. HbxB Is a Key Regulator for Stress Response and β-Glucan Biogenesis in Aspergillus nidulans. Microorganisms 2021; 9:microorganisms9010144. [PMID: 33440846 PMCID: PMC7827800 DOI: 10.3390/microorganisms9010144] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 01/06/2021] [Accepted: 01/08/2021] [Indexed: 01/16/2023] Open
Abstract
Homeobox transcription factors are conserved in eukaryotes and act as multi-functional transcription factors in filamentous fungi. Previously, it was demonstrated that HbxB governs fungal development and spore viability in Aspergillus nidulans. Here, the role of HbxB in A. nidulans was further characterized. RNA-sequencing revealed that HbxB affects the transcriptomic levels of genes associated with trehalose biosynthesis and response to thermal, oxidative, and radiation stresses in asexual spores called conidia. A phenotypic analysis found that hbxB deletion mutant conidia were more sensitive to ultraviolet stress. The loss of hbxB increased the mRNA expression of genes associated with β-glucan degradation and decreased the amount of β-glucan in conidia. In addition, hbxB deletion affected the expression of the sterigmatocystin gene cluster and the amount of sterigmatocystin. Overall, these results indicated that HbxB is a key transcription factor regulating trehalose biosynthesis, stress tolerance, β-glucan degradation, and sterigmatocystin production in A.nidulans conidia.
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Affiliation(s)
- Sung-Hun Son
- School of Food Science and Biotechnology Kyungpook National University, Daegu 41566, Korea; (S.-H.S.); (Y.-E.S.)
| | - Mi-Kyung Lee
- Biological Resource Center (BRC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup-si 56212, Korea;
| | - Ye-Eun Son
- School of Food Science and Biotechnology Kyungpook National University, Daegu 41566, Korea; (S.-H.S.); (Y.-E.S.)
| | - Hee-Soo Park
- School of Food Science and Biotechnology Kyungpook National University, Daegu 41566, Korea; (S.-H.S.); (Y.-E.S.)
- Department of Integrative Biology, Kyungpook National University, Daegu 41566, Korea
- Correspondence: ; Tel.: +82-53-950-5751
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10
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Li BN, Tang QD, Tan YL, Yan L, Sun L, Guo WB, Qian MY, Chen A, Luo YJ, Zheng ZX, Zhang ZW, Jia HL, Liu C. Key Regulatory Differentially Expressed Genes in the Blood of Atrial Septal Defect Children Treated With Occlusion Devices. Front Genet 2021; 12:790426. [PMID: 34956331 PMCID: PMC8692776 DOI: 10.3389/fgene.2021.790426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 11/10/2021] [Indexed: 02/05/2023] Open
Abstract
Atrial septal defects (ASDs) are the most common types of cardiac septal defects in congenital heart defects. In addition to traditional therapy, interventional closure has become the main treatment method. However, the molecular events and mechanisms underlying the repair progress by occlusion device remain unknown. In this study, we aimed to characterize differentially expressed genes (DEGs) in the blood of patients treated with occlusion devices (metal or poly-L-lactic acid devices) using RNA-sequencing, and further validated them by qRT-PCR analysis to finally determine the expression of key mediating genes after closure of ASD treatment. The result showed that total 1,045 genes and 1,523 genes were expressed differently with significance in metal and poly-L-lactic acid devices treatment, respectively. The 115 overlap genes from the different sub-analyses are illustrated. The similarities and differences in gene expression reflect that the body response process involved after interventional therapy for ASDs has both different parts that do not overlap and the same part that crosses. The same portion of body response regulatory genes are key regulatory genes expressed in the blood of patients with ASDs treated with closure devices. The gene ontology enrichment analysis showed that biological processes affected in metal device therapy are immune response with CXCR4 genes and poly-L-lactic acid device treatment, and the key pathways are nuclear-transcribed mRNA catabolic process and proteins targeting endoplasmic reticulum process with ribosomal proteins (such as RPS26). We confirmed that CXCR4, TOB1, and DDIT4 gene expression are significantly downregulated toward the pre-therapy level after the post-treatment in both therapy groups by qRT-PCR. Our study suggests that the potential role of CXCR4, DDIT4, and TOB1 may be key regulatory genes in the process of endothelialization in the repair progress of ASDs, providing molecular insights into this progress for future studies.
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Affiliation(s)
- Bo-Ning Li
- The Department of Cardiology, Shenzhen Children’s Hospital, Shenzhen, China
| | - Quan-Dong Tang
- Department of Pathophysiology, The Key Immunopathology Laboratory of Guangdong Province, Shantou University Medical College, Shantou, China
| | - Yan-Lian Tan
- Department of Medical Biochemistry and Molecular Biology, School of Medicine, Jinan University, Guangzhou, China
| | - Liang Yan
- Department of Medical Biochemistry and Molecular Biology, School of Medicine, Jinan University, Guangzhou, China
| | - Ling Sun
- Guangdong Cardiovascular Institute, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Wei-Bing Guo
- Guangdong Cardiovascular Institute, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
- The Department of Cardiology, Zhong Shan Affiliated Hospital of Xiamen University, Xiamen, China
| | - Ming-Yang Qian
- Guangdong Cardiovascular Institute, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Allen Chen
- Guangzhou Mendel Genomics and Medical Technology Co., Guangzhou, China
| | - Ying-Jun Luo
- Guangzhou Mendel Genomics and Medical Technology Co., Guangzhou, China
| | - Zhou-Xia Zheng
- Guangzhou Mendel Genomics and Medical Technology Co., Guangzhou, China
| | - Zhi-Wei Zhang
- Guangdong Cardiovascular Institute, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
- *Correspondence: Zhi-Wei Zhang, ; Hong-Ling Jia, ; Cong Liu,
| | - Hong-Ling Jia
- Department of Medical Biochemistry and Molecular Biology, School of Medicine, Jinan University, Guangzhou, China
- *Correspondence: Zhi-Wei Zhang, ; Hong-Ling Jia, ; Cong Liu,
| | - Cong Liu
- The Department of Cardiology, Shenzhen Children’s Hospital, Shenzhen, China
- *Correspondence: Zhi-Wei Zhang, ; Hong-Ling Jia, ; Cong Liu,
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11
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Gao Y, Zhang X, Ren G, Wu C, Qin P, Yao Y. Peptides from Extruded Lupin ( Lupinus albus L.) Regulate Inflammatory Activity via the p38 MAPK Signal Transduction Pathway in RAW 264.7 Cells. J Agric Food Chem 2020; 68:11702-11709. [PMID: 32869636 DOI: 10.1021/acs.jafc.0c02476] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
In this study, protein was extracted from extruded lupin and submitted to gastroduodenal digests to obtain lupin peptides, which were characterized using ultraperformance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS). After this, IQDKEGIPPDQQR (IQD), the lupine peptide monomer characterized after UPLC-MS/MS, was screened out by macrophage inflammatory cytokine production assay. RNA-sequencing analysis was performed to explore the mechanisms underlying the anti-inflammatory activity associated with this peptide. The results indicated that lupin peptides effectively inhibited the lipopolysaccharide-induced overproduction of proinflammatory mediators. IQD inhibited the production of tumor necrosis factor-α, interleukin (IL)-6, IL-1β, and monocyte chemoattractant protein-1 by 51.20, 38.52, 44.70, and 40.43%, respectively. RNA-sequencing results showed that IQD inhibited the inflammatory response by regulating the gene expression of the p38 mitogen-activated protein kinase pathway and inhibiting downstream inflammatory cytokines. These bioactive peptides may be used to develop new ingredients for anti-inflammatory nutritional supplements.
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Affiliation(s)
- Yue Gao
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, No. 80 South Xueyuan Road, Haidian District, Beijing 100081, China
| | - Xuna Zhang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, No. 80 South Xueyuan Road, Haidian District, Beijing 100081, China
| | - Guixing Ren
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, No. 80 South Xueyuan Road, Haidian District, Beijing 100081, China
| | - Caie Wu
- College of Light Industry and Food Engineering, Nanjing Forestry University, Nanjing 210037, Jiangsu Province, China
| | - Peiyou Qin
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, No. 80 South Xueyuan Road, Haidian District, Beijing 100081, China
| | - Yang Yao
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, No. 80 South Xueyuan Road, Haidian District, Beijing 100081, China
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12
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Chen HL, Kasuya J, Lansdon P, Kaas G, Tang H, Sodders M, Kitamoto T. Reduced Function of the Glutathione S-Transferase S1 Suppresses Behavioral Hyperexcitability in Drosophila Expressing Mutant Voltage-Gated Sodium Channels. G3 (Bethesda) 2020; 10:1327-40. [PMID: 32054635 DOI: 10.1534/g3.119.401025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Voltage-gated sodium (Nav) channels play a central role in the generation and propagation of action potentials in excitable cells such as neurons and muscles. To determine how the phenotypes of Nav-channel mutants are affected by other genes, we performed a forward genetic screen for dominant modifiers of the seizure-prone, gain-of-function Drosophila melanogaster Nav-channel mutant, paraShu. Our analyses using chromosome deficiencies, gene-specific RNA interference, and single-gene mutants revealed that a null allele of glutathione S-transferase S1 (GstS1) dominantly suppresses paraShu phenotypes. Reduced GstS1 function also suppressed phenotypes of other seizure-prone Nav-channel mutants, paraGEFS+ and parabss. Notably, paraShu mutants expressed 50% less GstS1 than wild-type flies, further supporting the notion that paraShu and GstS1 interact functionally. Introduction of a loss-of-function GstS1 mutation into a paraShu background led to up- and down-regulation of various genes, with those encoding cytochrome P450 (CYP) enzymes most significantly over-represented in this group. Because GstS1 is a fly ortholog of mammalian hematopoietic prostaglandin D synthase, and in mammals CYPs are involved in the oxygenation of polyunsaturated fatty acids including prostaglandins, our results raise the intriguing possibility that bioactive lipids play a role in GstS1-mediated suppression of paraShu phenotypes.
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13
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Gokulnath P, de Cristofaro T, Manipur I, Di Palma T, Soriano AA, Guarracino MR, Zannini M. Long Non-Coding RNA MAGI2-AS3 is a New Player with a Tumor Suppressive Role in High Grade Serous Ovarian Carcinoma. Cancers (Basel) 2019; 11:cancers11122008. [PMID: 31842477 PMCID: PMC6966615 DOI: 10.3390/cancers11122008] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 12/03/2019] [Accepted: 12/06/2019] [Indexed: 12/24/2022] Open
Abstract
High-Grade Serous Ovarian Carcinoma (HGSC) is the most incidental and lethal subtype of epithelial ovarian cancer (EOC) with a high mortality rate of nearly 65%. Recent findings aimed at understanding the pathogenesis of HGSC have attributed its principal source as the Fallopian Tube (FT). To further comprehend the exact mechanism of carcinogenesis, which is still less known, we performed a transcriptome analysis comparing FT and HGSC. Our study aims at exploring new players involved in the development of HGSC from FT, along with their signaling network, and we chose to focus on non-coding RNAs. Non-coding RNAs (ncRNAs) are increasingly observed to be the major regulators of several cellular processes and could have key functions as biological markers, as well as even a therapeutic approach. The most physiologically relevant and significantly dysregulated non-coding RNAs were identified bioinformatically. After analyzing the trend in HGSC and other cancers, MAGI2-AS3 was observed to be an important player in EOC. We assessed its tumor-suppressive role in EOC by means of various assays. Further, we mapped its signaling pathway using its role as a miRNA sponge to predict the miRNAs binding to MAGI2AS3 and showed it experimentally. We conclude that MAGI2-AS3 acts as a tumor suppressor in EOC, specifically in HGSC by sponging miR-15-5p, miR-374a-5p and miR-374b-5p, and altering downstream signaling of certain mRNAs through a ceRNA network.
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Affiliation(s)
- Priyanka Gokulnath
- IEOS - Institute of Experimental Endocrinology and Oncology ‘G. Salvatore’, National Research Council, via S. Pansini 5, 80131 Napoli, Italy; (P.G.)
- Dpt. Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania “Luigi Vanvitelli”, 81100 Caserta, Italy
| | - Tiziana de Cristofaro
- IEOS - Institute of Experimental Endocrinology and Oncology ‘G. Salvatore’, National Research Council, via S. Pansini 5, 80131 Napoli, Italy; (P.G.)
| | - Ichcha Manipur
- High Performance Computing and Networking Institute, National Research Council, via P. Castellino 111, 80131 Napoli, Italy
| | - Tina Di Palma
- IEOS - Institute of Experimental Endocrinology and Oncology ‘G. Salvatore’, National Research Council, via S. Pansini 5, 80131 Napoli, Italy; (P.G.)
| | - Amata Amy Soriano
- IEOS - Institute of Experimental Endocrinology and Oncology ‘G. Salvatore’, National Research Council, via S. Pansini 5, 80131 Napoli, Italy; (P.G.)
- Present affiliation: IRCCS Casa Sollievo della Sofferenza, Cancer Stem Cells Unit, ISReMIT, 71013 San Giovanni Rotondo FG, Italy
| | - Mario Rosario Guarracino
- Dpt. Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania “Luigi Vanvitelli”, 81100 Caserta, Italy
| | - Mariastella Zannini
- IEOS - Institute of Experimental Endocrinology and Oncology ‘G. Salvatore’, National Research Council, via S. Pansini 5, 80131 Napoli, Italy; (P.G.)
- Correspondence:
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14
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Bang JS, Choi NY, Lee M, Ko K, Park YS, Ko K. Reprogramming of Cancer Cells into Induced Pluripotent Stem Cells Questioned. Int J Stem Cells 2019; 12:430-439. [PMID: 31474029 PMCID: PMC6881048 DOI: 10.15283/ijsc19067] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 07/26/2019] [Accepted: 07/27/2019] [Indexed: 12/20/2022] Open
Abstract
Background and Objectives Several recent studies have claimed that cancer cells can be reprogrammed into induced pluripotent stem cells (iPSCs). However, in most cases, cancer cells seem to be resistant to cellular reprogramming. Furthermore, the underlying mechanisms of limited reprogramming in cancer cells are largely unknown. Here, we identified the candidate barrier genes and their target genes at the early stage of reprogramming for investigating cancer reprogramming. Methods We tried induction of pluripotency in normal human fibroblasts (BJ) and both human benign (MCF10A) and malignant (MCF7) breast cancer cell lines using a classical retroviral reprogramming method. We conducted RNA-sequencing analysis to compare the transcriptome of the three cell lines at early stage of reprogramming. Results We could generate iPSCs from BJ, whereas we were unable to obtain iPSCs from cancer cell lines. To address the underlying mechanism of limited reprogramming in cancer cells, we identified 29 the candidate barrier genes based on RNA-sequencing data. In addition, we found 40 their target genes using Cytoscape software. Conclusions Our data suggest that these genes might one of the roadblock for cancer cell reprogramming. Furthermore, we provide new insights into application of iPSCs technology in cancer cell field for therapeutic purposes.
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Affiliation(s)
- Jin Seok Bang
- Department of Stem Cell Biology, Konkuk University School of Medicine, Seoul, Korea.,Center for Stem Cell Research, Institute of Advanced Biomedical Science, Konkuk University, Seoul, Korea
| | - Na Young Choi
- Department of Stem Cell Biology, Konkuk University School of Medicine, Seoul, Korea.,Center for Stem Cell Research, Institute of Advanced Biomedical Science, Konkuk University, Seoul, Korea
| | - Minseong Lee
- Department of Stem Cell Biology, Konkuk University School of Medicine, Seoul, Korea.,Center for Stem Cell Research, Institute of Advanced Biomedical Science, Konkuk University, Seoul, Korea
| | - Kisung Ko
- Department of Medicine, College of Medicine, Chung-Ang University, Seoul, Korea
| | - Yo Seph Park
- Department of Stem Cell Biology, Konkuk University School of Medicine, Seoul, Korea.,Center for Stem Cell Research, Institute of Advanced Biomedical Science, Konkuk University, Seoul, Korea
| | - Kinarm Ko
- Department of Stem Cell Biology, Konkuk University School of Medicine, Seoul, Korea.,Center for Stem Cell Research, Institute of Advanced Biomedical Science, Konkuk University, Seoul, Korea.,Research Institute of Medical Science, Konkuk University, Seoul, Korea
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15
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Goldstein O, Meyer K, Greenshpan Y, Bujanover N, Feigin M, Ner-Gaon H, Shay T, Gazit R. Mapping Whole-Transcriptome Splicing in Mouse Hematopoietic Stem Cells. Stem Cell Reports 2016; 8:163-176. [PMID: 28041879 PMCID: PMC5233452 DOI: 10.1016/j.stemcr.2016.12.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Revised: 12/01/2016] [Accepted: 12/01/2016] [Indexed: 10/31/2022] Open
Abstract
Hematopoietic stem cells (HSCs) are rare cells that generate all the various types of blood and immune cells. High-quality transcriptome data have enabled the identification of significant genes for HSCs. However, most genes are expressed in various forms by alternative splicing (AS), extending transcriptome complexity. Here, we delineate AS to determine which isoforms are expressed in mouse HSCs. Our analysis of microarray and RNA-sequencing data includes differential expression of splicing factors that may regulate AS, and a complete map of splicing isoforms. Multiple types of isoforms for known HSC genes and unannotated splicing that may alter gene function are presented. Transcriptome-wide identification of genes and their respective isoforms in mouse HSCs will open another dimension for adult stem cells.
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Affiliation(s)
- Oron Goldstein
- The Shraga Segal Department for Microbiology, Immunology and Genetics, Faculty of Health Science, Ben-Gurion University of the Negev, Be'er Sheva 84105, Israel; The National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Be'er Sheva 84105, Israel
| | - Karin Meyer
- The Shraga Segal Department for Microbiology, Immunology and Genetics, Faculty of Health Science, Ben-Gurion University of the Negev, Be'er Sheva 84105, Israel
| | - Yariv Greenshpan
- The Shraga Segal Department for Microbiology, Immunology and Genetics, Faculty of Health Science, Ben-Gurion University of the Negev, Be'er Sheva 84105, Israel; The National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Be'er Sheva 84105, Israel
| | - Nir Bujanover
- The Shraga Segal Department for Microbiology, Immunology and Genetics, Faculty of Health Science, Ben-Gurion University of the Negev, Be'er Sheva 84105, Israel; The National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Be'er Sheva 84105, Israel
| | - Mili Feigin
- The Shraga Segal Department for Microbiology, Immunology and Genetics, Faculty of Health Science, Ben-Gurion University of the Negev, Be'er Sheva 84105, Israel
| | - Hadas Ner-Gaon
- Department of Life Sciences, Ben-Gurion University of the Negev, Be'er Sheva 84105, Israel
| | - Tal Shay
- Department of Life Sciences, Ben-Gurion University of the Negev, Be'er Sheva 84105, Israel
| | - Roi Gazit
- The Shraga Segal Department for Microbiology, Immunology and Genetics, Faculty of Health Science, Ben-Gurion University of the Negev, Be'er Sheva 84105, Israel; The National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Be'er Sheva 84105, Israel; Regenerative Medicine and Stem Cell (RMSC) Research Center, Ben-Gurion University of the Negev, Be'er Sheva 84105, Israel.
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16
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Shi W, Man K, Smyth GK, Nutt SL, Kallies A. Whole transcriptome analysis for T cell receptor-affinity and IRF4-regulated clonal expansion of T cells. Genom Data 2014; 2:396-8. [PMID: 26484137 PMCID: PMC4536053 DOI: 10.1016/j.gdata.2014.10.019] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Accepted: 10/28/2014] [Indexed: 11/24/2022]
Abstract
Clonal population expansion of T cells during an immune response is dependent on the affinity of the T cell receptor (TCR) for its antigen [1]. However, there is little understanding of how this process is controlled transcriptionally. We found that the transcription factor IRF4 was induced in a manner dependent on TCR-affinity and was critical for the clonal expansion and maintenance of effector function of antigen-specific CD8+ T cells. We performed a genome-wide expression profiling experiment using RNA sequencing technology (RNA-seq) to interrogate global expression changes when IRF4 was deleted in CD8+ T cells activated with either a low or high affinity peptide ligand. This allowed us not only to determine IRF4-dependent transcriptional changes but also to identify transcripts dependent on TCR-affinity [2]. Here we describe in detail the analyses of the RNA-seq data, including quality control, read mapping, quantification, normalization and assessment of differential gene expression. The RNA-seq data can be accessed from Gene Expression Omnibus database (accession number GSE49929).
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Affiliation(s)
- Wei Shi
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia ; The Department of Computing and Information Systems, University of Melbourne, Parkville, Australia
| | - Kevin Man
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia ; The Department of Medical Biology, University of Melbourne, Parkville, Australia
| | - Gordon K Smyth
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia ; The Department of Mathematics and Statistics, University of Melbourne, Parkville, Australia
| | - Stephen L Nutt
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia ; The Department of Medical Biology, University of Melbourne, Parkville, Australia
| | - Axel Kallies
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia ; The Department of Medical Biology, University of Melbourne, Parkville, Australia
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