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Cho HT, Lee M, Choi HS, Maeng KH, Lee K, Lee HY, Ganguly A, Park H, Ho CH. A dose-dependent bimodal switch by homologous Aux/IAA transcriptional repressors. MOLECULAR PLANT 2024; 17:1407-1422. [PMID: 39095993 DOI: 10.1016/j.molp.2024.07.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Revised: 07/15/2024] [Accepted: 07/30/2024] [Indexed: 08/04/2024]
Abstract
Combinatorial interactions between different regulators diversify and enrich the chance of transcriptional regulation in eukaryotic cells. However, a dose-dependent functional switch of homologous transcriptional repressors has rarely been reported. Here, we show that SHY2, an auxin/indole-3-acetic acid (Aux/IAA) repressor, exhibits a dose-dependent bimodal role in auxin-sensitive root-hair growth and gene transcription in Arabidopsis, whereas other Aux/IAA homologs consistently repress the auxin responses. The co-repressor (TOPLESS [TPL])-binding affinity of a bimodal Aux/IAA was lower than that of a consistently repressing Aux/IAA. The switch of a single amino acid residue in the TPL-binding motif between the bimodal form and the consistently repressing form switched their TPL-binding affinity and transcriptional and biological roles in auxin responses. Based on these data, we propose a model whereby competition between homologous repressors with different co-repressor-binding affinities could generate a bimodal output at the transcriptional and developmental levels.
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Affiliation(s)
- Hyung-Taeg Cho
- Department of Biological Sciences, Seoul National University, Seoul, Korea.
| | - Minsu Lee
- Department of Biological Sciences, Seoul National University, Seoul, Korea
| | - Hee-Seung Choi
- Department of Biological Sciences, Seoul National University, Seoul, Korea
| | - Kwang-Ho Maeng
- Department of Biological Sciences, Seoul National University, Seoul, Korea
| | - Kyeonghoon Lee
- Department of Biological Sciences, Seoul National University, Seoul, Korea
| | - Ha-Yeon Lee
- Department of Biological Sciences, Seoul National University, Seoul, Korea
| | - Anindya Ganguly
- Department of Biological Sciences, Seoul National University, Seoul, Korea
| | - Hoonyoung Park
- School of Earth and Environmental Sciences, Seoul National University, Seoul, Korea
| | - Chang-Hoi Ho
- School of Earth and Environmental Sciences, Seoul National University, Seoul, Korea; Department of Climate and Energy Systems Engineering, Ewha Womans University, Seoul, Korea
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Ce F, Mei J, Zhao Y, Li Q, Ren X, Song H, Qian W, Si J. Comparative Analysis of Transcriptomes Reveals Pathways and Verifies Candidate Genes for Clubroot Resistance in Brassica oleracea. Int J Mol Sci 2024; 25:9189. [PMID: 39273138 PMCID: PMC11395044 DOI: 10.3390/ijms25179189] [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: 07/10/2024] [Revised: 08/02/2024] [Accepted: 08/16/2024] [Indexed: 09/15/2024] Open
Abstract
Clubroot, a soil-borne disease caused by Plasmodiophora brassicae, is one of the most destructive diseases of Brassica oleracea all over the world. However, the mechanism of clubroot resistance remains unclear. In this research, transcriptome sequencing was conducted on root samples from both resistant (R) and susceptible (S) B. oleracea plants infected by P. brassicae. Then the comparative analysis was carried out between the R and S samples at different time points during the infection stages to reveal clubroot resistance related pathways and candidate genes. Compared with 0 days after inoculation, a total of 4991 differential expressed genes were detected from the S pool, while only 2133 were found from the R pool. Gene function enrichment analysis found that the effector-triggered immunity played a major role in the R pool, while the pathogen-associated molecular pattern triggered immune response was stronger in the S pool. Simultaneously, candidate genes were identified through weighted gene co-expression network analysis, with Bol010786 (CNGC13) and Bol017921 (SD2-5) showing potential for conferring resistance to clubroot. The findings of this research provide valuable insights into the molecular mechanisms underlying clubroot resistance and present new avenues for further research aimed at enhancing the clubroot resistance of B. oleracea through breeding.
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Affiliation(s)
- Fuquan Ce
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing 400716, China
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River, Ministry of Education, Chongqing 400716, China
- Academy of Agricultural Sciences, Southwest University, Chongqing 400716, China
| | - Jiaqin Mei
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
- Academy of Agricultural Sciences, Southwest University, Chongqing 400716, China
- Academy of Agricultural Sciences, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Southwest University, Chongqing 400716, China
| | - Yu Zhao
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing 400716, China
| | - Qinfei Li
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing 400716, China
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River, Ministry of Education, Chongqing 400716, China
- Chongqing Key Laboratory of Olericulture, Chongqing 400716, China
| | - Xuesong Ren
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing 400716, China
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River, Ministry of Education, Chongqing 400716, China
- Chongqing Key Laboratory of Olericulture, Chongqing 400716, China
| | - Hongyuan Song
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing 400716, China
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River, Ministry of Education, Chongqing 400716, China
- Chongqing Key Laboratory of Olericulture, Chongqing 400716, China
| | - Wei Qian
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
- Academy of Agricultural Sciences, Southwest University, Chongqing 400716, China
- Academy of Agricultural Sciences, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Southwest University, Chongqing 400716, China
| | - Jun Si
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing 400716, China
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River, Ministry of Education, Chongqing 400716, China
- Chongqing Key Laboratory of Olericulture, Chongqing 400716, China
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Gang D, Qing O, Yang Y, Masood M, Wang YH, Linhui J, Haotao S, Li G, Liu C, Nasser MI, Zhu P. Cyanidin prevents cardiomyocyte apoptosis in mice after myocardial infarction. NAUNYN-SCHMIEDEBERG'S ARCHIVES OF PHARMACOLOGY 2024; 397:5883-5898. [PMID: 38349396 DOI: 10.1007/s00210-024-02975-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 01/22/2024] [Indexed: 08/18/2024]
Abstract
Myocardial infarction is a worldwide disease with high morbidity and mortality and a major cause of chronic heart failure, seriously affecting patients' quality of life. Natural medicine has been used to cure or prevent cardiovascular disease for decades. As a natural flavonoid, anthocyanidin has been used to treat many diseases due to its antioxidative, anti-inflammatory, and other properties. A mouse model (C57BL/6) weighing 30-40 g was utilized to induce myocardial infarction by ligating the left anterior descending coronary artery. Cyanidin (30 mg/kg) was administered orally to mice for four weeks. A variety of assessments were used to evaluate cardiac function. The gene expression was measured using RNAseq and Western blot. Histological changes in myocardial tissue were assessed using staining techniques, including Masson, Hematoxylin Eosin (HE), and transmission electron microscopy. Tunnel staining was implemented as a method to detect cellular apoptosis. For the quantification of B-type natriuretic peptide (BNP) and atrial natriuretic peptide (ANP) in the serum, an enzyme-linked immunosorbent assay (ELISA) was employed. Furthermore, autodock simulation was executed in order to assess the interaction between cyanidin and a subset of genes. Cyanidin treatment inhibited myocardial cell apoptosis, improved cardiac function, and reduced serum concentrations of BNP and atrial natriuretic peptide ANP, as well as mitigated histological cardiac tissue damage. Cyanidin also inhibited the activity of matrix metalloproteinases (MMP2/9) and Fibronectin 1 (Fn1). Cyanidin improves heart function and reduces myocardial damage in mice after MI. Furthermore, cyanidin can prevent cardiomyocyte apoptosis. These effects are most likely caused by suppression of MMP9/2 and control of the Akt signaling pathway, suggesting an appropriate therapeutic target.
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Affiliation(s)
- Deng Gang
- School of Medicine, South China University of Technology, Guangzhou, 510006, People's Republic of China
- Department of Cardiac Surgery, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangdong Cardiovascular Institute, Guangzhou, Guangdong, 510100, People's Republic of China
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou, 510515, People's Republic of China
| | - Ouyang Qing
- School of Medicine, South China University of Technology, Guangzhou, 510006, People's Republic of China
- Department of Cardiac Surgery, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangdong Cardiovascular Institute, Guangzhou, Guangdong, 510100, People's Republic of China
- Guangdong Provincial Key Laboratory of Pathogenesis, Targeted Prevention and Treatment of Heart Disease, 106 Zhongshan Er Road, Guangzhou, 510080, People's Republic of China
| | - Yongzheng Yang
- Department of Cardiac Surgery, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangdong Cardiovascular Institute, Guangzhou, Guangdong, 510100, People's Republic of China
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou, 510515, People's Republic of China
- Guangdong Provincial Key Laboratory of Pathogenesis, Targeted Prevention and Treatment of Heart Disease, 106 Zhongshan Er Road, Guangzhou, 510080, People's Republic of China
| | - Muqaddas Masood
- Department of Cardiac Surgery, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangdong Cardiovascular Institute, Guangzhou, Guangdong, 510100, People's Republic of China
- Center for Discovery and Innovation, Hackensack University Medicial Center, Nutley, NJ, USA
| | - Yu-Hong Wang
- Department of Cardiac Surgery, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangdong Cardiovascular Institute, Guangzhou, Guangdong, 510100, People's Republic of China
- Guangdong Provincial Key Laboratory of Pathogenesis, Targeted Prevention and Treatment of Heart Disease, 106 Zhongshan Er Road, Guangzhou, 510080, People's Republic of China
| | - Jiang Linhui
- Department of Cardiac Surgery, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangdong Cardiovascular Institute, Guangzhou, Guangdong, 510100, People's Republic of China
- Guangdong Provincial Key Laboratory of Pathogenesis, Targeted Prevention and Treatment of Heart Disease, 106 Zhongshan Er Road, Guangzhou, 510080, People's Republic of China
| | - Su Haotao
- Department of Cardiac Surgery, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangdong Cardiovascular Institute, Guangzhou, Guangdong, 510100, People's Republic of China
- Guangdong Provincial Key Laboratory of Pathogenesis, Targeted Prevention and Treatment of Heart Disease, 106 Zhongshan Er Road, Guangzhou, 510080, People's Republic of China
| | - Ge Li
- Department of Cardiac Surgery, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangdong Cardiovascular Institute, Guangzhou, Guangdong, 510100, People's Republic of China
- Guangdong Provincial Key Laboratory of Pathogenesis, Targeted Prevention and Treatment of Heart Disease, 106 Zhongshan Er Road, Guangzhou, 510080, People's Republic of China
| | - Chi Liu
- Department of Cardiac Surgery, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangdong Cardiovascular Institute, Guangzhou, Guangdong, 510100, People's Republic of China.
- Department of Nephrology, Sichuan Academy of Medical Science and Sichuan, Provincial People's Hospital, Sichuan Renal Disease Clinical Research Center, University of Electronic Science and Technology of China, Chengdu, People's Republic of China.
| | - Moussa Ide Nasser
- Department of Cardiac Surgery, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangdong Cardiovascular Institute, Guangzhou, Guangdong, 510100, People's Republic of China.
- Guangdong Provincial Key Laboratory of Pathogenesis, Targeted Prevention and Treatment of Heart Disease, 106 Zhongshan Er Road, Guangzhou, 510080, People's Republic of China.
| | - Ping Zhu
- School of Medicine, South China University of Technology, Guangzhou, 510006, People's Republic of China.
- Department of Cardiac Surgery, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangdong Cardiovascular Institute, Guangzhou, Guangdong, 510100, People's Republic of China.
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou, 510515, People's Republic of China.
- Guangdong Provincial Key Laboratory of Pathogenesis, Targeted Prevention and Treatment of Heart Disease, 106 Zhongshan Er Road, Guangzhou, 510080, People's Republic of China.
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Fu S, Zhang Y, Jiao Y, Wang Q, Deng Y, Du X. The role of Pm-miR-184-3p in regulating the immune response in the pearl oyster Pinctada fucata martensii. FISH & SHELLFISH IMMUNOLOGY 2024; 150:109658. [PMID: 38801841 DOI: 10.1016/j.fsi.2024.109658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 05/09/2024] [Accepted: 05/24/2024] [Indexed: 05/29/2024]
Abstract
microRNAs are a class of non-coding RNAs with post-transcriptional regulatory functions in eukaryotes. In our previous study, miR-184-3p was identified in the hemocyte transcriptome of Pinctada fucata martensii (Pm-miR-184-3p), and its expression was shown to be up-regulated following transplantation surgery; however, its role in regulating transplantation immunity has not yet been clarified. Here, the role of Pm-miR-184-3p in regulating the immune response of P. f. martensii was studied. The expression of Pm-miR-184-3p increased following the stimulation of pathogen-associated molecular patterns, and Pm-miR-184-3p overexpression increased the activity of antioxidant-related enzymes, such as superoxide dismutase and catalase. Transcriptome analysis obtained 1096 differentially expressed genes (DEGs) after overexpression of Pm-miR-184-3p, and these DEGs were significantly enriched in conserved pathways such as the Cell cycle pathway and NF-kappa B signaling pathway, as well as GO terms including base excision repair, cell cycle, and DNA replication, suggesting that Pm-miR-184-3p could enhance the inflammation process. Target prediction and dual luciferase analysis revealed that pro-inflammatory related genes Pm-TLR3 and Pm-FN were the potential target of Pm-miR-184-3p. We speculate that Pm-miR-184-3p may utilize negative regulation of target genes to delay the activation of corresponding immune pathways, potentially preventing excessive inflammatory responses and achieving a delicate balance within the organism. Overall, Pm-miR-184-3p play a key role in regulating cellular responses to transplantation. Our findings provide new insights into the immune response of P. f. martensii to transplantation.
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Affiliation(s)
- Shirong Fu
- Fishery College, Guangdong Ocean University, Zhanjiang, 524088, China
| | - Yuting Zhang
- Fishery College, Guangdong Ocean University, Zhanjiang, 524088, China
| | - Yu Jiao
- Fishery College, Guangdong Ocean University, Zhanjiang, 524088, China; Pearl Breeding and Processing Engineering Technology Research Centre of Guangdong Province, Zhanjiang, 524088, China; Guangdong Science and Innovation Center for Pearl Culture, Zhanjiang, 524088, China.
| | - Qingheng Wang
- Fishery College, Guangdong Ocean University, Zhanjiang, 524088, China; Pearl Breeding and Processing Engineering Technology Research Centre of Guangdong Province, Zhanjiang, 524088, China; Guangdong Science and Innovation Center for Pearl Culture, Zhanjiang, 524088, China; Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture, Zhanjiang, 524088, China; Guangdong Provincial Engineering Laboratory for Mariculture Organism Breeding, Zhanjiang, 524088, China.
| | - Yuewen Deng
- Fishery College, Guangdong Ocean University, Zhanjiang, 524088, China; Pearl Breeding and Processing Engineering Technology Research Centre of Guangdong Province, Zhanjiang, 524088, China; Guangdong Science and Innovation Center for Pearl Culture, Zhanjiang, 524088, China; Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture, Zhanjiang, 524088, China; Guangdong Marine Ecology Early Warning and Monitoring Laboratory, Zhanjiang, 524088, China
| | - Xiaodong Du
- Fishery College, Guangdong Ocean University, Zhanjiang, 524088, China; Pearl Breeding and Processing Engineering Technology Research Centre of Guangdong Province, Zhanjiang, 524088, China; Guangdong Science and Innovation Center for Pearl Culture, Zhanjiang, 524088, China
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Deng J, Huang S, Kan Y, Song Y, Zhao X, Li N, Yao X, Luo Z, Zhang Y. A transcription factor-mediated regulatory network controls fungal pathogen colonization of insect body cavities. mBio 2024; 15:e0350423. [PMID: 38747587 PMCID: PMC11237471 DOI: 10.1128/mbio.03504-23] [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: 01/08/2024] [Accepted: 04/15/2024] [Indexed: 06/04/2024] Open
Abstract
Successful host tissue colonization is crucial for fungal pathogens to cause mycosis and complete the infection cycle, in which fungal cells undergo a series of morphological transition-included cellular events to combat with hosts. However, many transcription factors (TFs) and their mediated networks regulating fungal pathogen colonization of host tissue are not well characterized. Here, a TF (BbHCR1)-mediated regulatory network was identified in an insect pathogenic fungus, Beauveria bassiana, that controlled insect hemocoel colonization. BbHCR1 was highly expressed in fungal cells after reaching insect hemocoel and controlled the yeast (in vivo blastospores)-to-hyphal morphological switch, evasion of immune defense response, and fungal virulence. Comparative analysis of RNA sequencing and chromatin immunoprecipitation sequencing identified a core set of BbHCR1 target genes during hemocoel colonization, in which abaA and brlA were targeted to limit the rapid switch from blastospores to hyphae and fungal virulence. Two targets encoding hypothetical proteins, HP1 and HP2, were activated and repressed by BbHCR1, respectively, which acted as a virulence factor and repressor, respectively, suggesting that BbHCR1 activated virulence factors but repressed virulence repressors during the colonization of insect hemocoel. BbHCR1 tuned the expression of two dominant hemocoel colonization-involved metabolite biosynthetic gene clusters, which linked its regulatory role in evasion of immune response. Those functions of BbHCR1 were found to be collaboratively regulated by Fus3- and Hog1-MAP kinases via phosphorylation. These findings have drawn a regulatory network in which Fus3- and Hog1-MAP kinases phosphorylate BbHCR1, which in turn controls the colonization of insect body cavities by regulating fungal morphological transition and virulence-implicated genes.IMPORTANCEFungal pathogens adopt a series of tactics for successful colonization in host tissues, which include morphological transition and the generation of toxic and immunosuppressive molecules. However, many transcription factors (TFs) and their linked pathways that regulate tissue colonization are not well characterized. Here, we identified a TF (BbHCR1)-mediated regulatory network that controls the insect fungal pathogen, Beauveria bassiana, colonization of insect hemocoel. During these processes, BbHCR1 targeted the fungal central development pathway for the control of yeast (blastospores)-to-hyphae morphological transition, activated virulence factors, repressed virulence repressors, and tuned the expression of two dominant hemocoel colonization-involved immunosuppressive and immunostimulatory metabolite biosynthetic gene clusters. The BbHCR1 regulatory function was governed by Fus3- and Hog1-MAP kinases. These findings led to a new regulatory network composed of Fus3- and Hog1-MAP kinases and BbHCR1 that control insect body cavity colonization by regulating fungal morphological transition and virulence-implicated genes.
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Affiliation(s)
- Juan Deng
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), College of Plant Protection, Southwest University, Chongqing, China
- Key Laboratory of Entomology and Pest Control Engineering, Academy of Agricultural Sciences, Southwest University, Chongqing, China
- Beibei Culture Collection of Chongqing Agricultural Microbiology, Southwest University, Chongqing, China
| | - Shuaishuai Huang
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), College of Plant Protection, Southwest University, Chongqing, China
- Key Laboratory of Entomology and Pest Control Engineering, Academy of Agricultural Sciences, Southwest University, Chongqing, China
- Beibei Culture Collection of Chongqing Agricultural Microbiology, Southwest University, Chongqing, China
- Ministry of Education Key Laboratory of Biodiversity and Eco-Environmental Protection of the Qinghai-Tibetan Plateau, School of Ecology and Environment, Tibet University, Tibet, China
| | - Yanze Kan
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), College of Plant Protection, Southwest University, Chongqing, China
- Key Laboratory of Entomology and Pest Control Engineering, Academy of Agricultural Sciences, Southwest University, Chongqing, China
- Beibei Culture Collection of Chongqing Agricultural Microbiology, Southwest University, Chongqing, China
| | - Yue Song
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), College of Plant Protection, Southwest University, Chongqing, China
- Key Laboratory of Entomology and Pest Control Engineering, Academy of Agricultural Sciences, Southwest University, Chongqing, China
- Beibei Culture Collection of Chongqing Agricultural Microbiology, Southwest University, Chongqing, China
| | - Xin Zhao
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), College of Plant Protection, Southwest University, Chongqing, China
- Key Laboratory of Entomology and Pest Control Engineering, Academy of Agricultural Sciences, Southwest University, Chongqing, China
- Beibei Culture Collection of Chongqing Agricultural Microbiology, Southwest University, Chongqing, China
| | - Ning Li
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), College of Plant Protection, Southwest University, Chongqing, China
- Key Laboratory of Entomology and Pest Control Engineering, Academy of Agricultural Sciences, Southwest University, Chongqing, China
- Beibei Culture Collection of Chongqing Agricultural Microbiology, Southwest University, Chongqing, China
| | - Xuewen Yao
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), College of Plant Protection, Southwest University, Chongqing, China
- Key Laboratory of Entomology and Pest Control Engineering, Academy of Agricultural Sciences, Southwest University, Chongqing, China
- Beibei Culture Collection of Chongqing Agricultural Microbiology, Southwest University, Chongqing, China
| | - Zhibing Luo
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), College of Plant Protection, Southwest University, Chongqing, China
- Key Laboratory of Entomology and Pest Control Engineering, Academy of Agricultural Sciences, Southwest University, Chongqing, China
- Beibei Culture Collection of Chongqing Agricultural Microbiology, Southwest University, Chongqing, China
| | - Yongjun Zhang
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), College of Plant Protection, Southwest University, Chongqing, China
- Key Laboratory of Entomology and Pest Control Engineering, Academy of Agricultural Sciences, Southwest University, Chongqing, China
- Beibei Culture Collection of Chongqing Agricultural Microbiology, Southwest University, Chongqing, China
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Sun H, Li S, Wang Q, Luo C, Zhong L, Wan G, Li Z, Zhao G, Bu X, Zeng M, Feng G. Formyl peptide enhances cancer immunotherapy by activating antitumoral neutrophils, and T cells. Biomed Pharmacother 2024; 175:116670. [PMID: 38692065 DOI: 10.1016/j.biopha.2024.116670] [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: 02/22/2024] [Revised: 04/17/2024] [Accepted: 04/24/2024] [Indexed: 05/03/2024] Open
Abstract
Neutrophils are heterogeneous and plastic, with the ability to polarize from antitumour to protumour phenotype and modulate tumour microenvironment components. While some advances have been made, the neutrophil-targeting therapy remains underexplored. Activation of formyl peptide receptors (FPRs) by formylated peptides is needed for local control of infection through the recruitment of activated neutrophils while the potential contribution of antitumour activity remains underexplored. Here, we demonstrate that neutrophils can be harnessed to suppress tumour growth through the action of the formyl peptide (FP) on the formyl peptide receptor (FPR). Mechanistically, FP efficiently recruits neutrophils to produce reactive oxygen species production (ROS), resulting in the direct killing of tumours. Antitumour functions disappeared when neutrophils were depleted by anti-Ly6G antibodies. Interestingly, extensive T-cell activation was observed in mouse tumours treated with FP, showing the potential to alter the immune suppressed tumour microenvironment (TME) and further sensitize mice to anti-PD1 therapy. Transcriptomic and flow cytometry analyses revealed the mechanisms of FP-sensitized anti-PD1 therapy, mainly including stimulated neutrophils and an altered immune-suppressed tumour microenvironment. Collectively, these data establish FP as an effective combination partner for sensitizing anti-PD1 therapy by stimulating tumour-infiltrated neutrophils.
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Affiliation(s)
- Haixia Sun
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Department of Experimental Research, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Sun Yat-sen University, Guangzhou,Guangdong 510060, China; Department of Pharmacy, Shenzhen Third People's Hospital, Shenzhen, Guangdong Province 518112, China
| | - Shuxin Li
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Department of Experimental Research, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Sun Yat-sen University, Guangzhou,Guangdong 510060, China
| | - Qiaoli Wang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Department of Experimental Research, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Sun Yat-sen University, Guangzhou,Guangdong 510060, China
| | - Chunxiang Luo
- Guangxi Hospital Division of The First Affiliated Hospital, Sun Yat-Sen University, Nanning 530022, China
| | - Lanyi Zhong
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Department of Experimental Research, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Sun Yat-sen University, Guangzhou,Guangdong 510060, China
| | - Guohui Wan
- School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, China
| | - Ziqian Li
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Department of Experimental Research, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Sun Yat-sen University, Guangzhou,Guangdong 510060, China
| | - Gexin Zhao
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Department of Experimental Research, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Sun Yat-sen University, Guangzhou,Guangdong 510060, China
| | - Xianzhang Bu
- School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, China
| | - Musheng Zeng
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Department of Experimental Research, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Sun Yat-sen University, Guangzhou,Guangdong 510060, China
| | - Guokai Feng
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Department of Experimental Research, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Sun Yat-sen University, Guangzhou,Guangdong 510060, China.
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7
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Geng Z, Liu M, Wang Y, Wang Y, Wang Y, Sun Y, Wang H, Zhou L, Jiang J, Chen S, Chen F. Transcriptomic and metabolomic analyses reveal CmMYB308 as a key regulator in the pink flower color variation of 'Dante Purple' chrysanthemum. PLANT CELL REPORTS 2024; 43:157. [PMID: 38819475 DOI: 10.1007/s00299-024-03244-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Accepted: 05/22/2024] [Indexed: 06/01/2024]
Abstract
KEY MESSAGE CmMYB308 was identified as a key regulator in chrysanthemum flower color variation from purple to pink by conducting transcriptome and metabolome analysis. CmMYB308 can inhibit anthocyanin biosynthesis by suppressing the expression of CmPAL, CmC4H, and Cm4CL. Flower color variation is a widespread natural occurrence that plays a significant role in floral breeding. We discovered a variation in the flower of the chrysanthemum cultivar 'Dante Purple' (abbreviated as 'DP'), where the flower color shifted from purple to pink. We successfully propagated these pink flowers through tissue culture and designated them as DPM. By conducting transcriptome and metabolome analysis, we identified a reduction in the expression of critical genes involved in anthocyanin biosynthesis-CmPAL, CmC4H, and Cm4CL-in the DPM. This downregulation led to an accumulation of phenylalanine and cinnamic acid within the general phenylpropanoid pathway (GPP), which prevented their conversion into cyanidin and cyanidin 3-glucoside. As a result, the flowers turned pink. Additional transformation and biochemical experiments confirmed that the upregulation of CmMYB308 gene expression in the DPM directly suppressed CmPAL-1 and CmC4H genes, which indirectly affected Cm4CL-3 expression and ultimately inhibited anthocyanin biosynthesis in the DPM. This study offers a preliminary insight into the molecular mechanism underlying chrysanthemum flower color mutation, paving the way for genetic improvements in chrysanthemum flower color breeding.
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Affiliation(s)
- Zhiqiang Geng
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Landscaping, Key Laboratory of Flower Biology and Germplasm Innovation, Ministry of Agriculture and Rural Affairs, Key Laboratory of State Forestry and Grassland Administration on Biology of Ornamental Plants in East China, College of Horticulture, Nanjing Agricultural University, No.1 Weigang, Nanjing, 210095, China
| | - Miao Liu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Landscaping, Key Laboratory of Flower Biology and Germplasm Innovation, Ministry of Agriculture and Rural Affairs, Key Laboratory of State Forestry and Grassland Administration on Biology of Ornamental Plants in East China, College of Horticulture, Nanjing Agricultural University, No.1 Weigang, Nanjing, 210095, China
| | - Yiguang Wang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Landscaping, Key Laboratory of Flower Biology and Germplasm Innovation, Ministry of Agriculture and Rural Affairs, Key Laboratory of State Forestry and Grassland Administration on Biology of Ornamental Plants in East China, College of Horticulture, Nanjing Agricultural University, No.1 Weigang, Nanjing, 210095, China
| | - Yuxi Wang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Landscaping, Key Laboratory of Flower Biology and Germplasm Innovation, Ministry of Agriculture and Rural Affairs, Key Laboratory of State Forestry and Grassland Administration on Biology of Ornamental Plants in East China, College of Horticulture, Nanjing Agricultural University, No.1 Weigang, Nanjing, 210095, China
| | - You Wang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Landscaping, Key Laboratory of Flower Biology and Germplasm Innovation, Ministry of Agriculture and Rural Affairs, Key Laboratory of State Forestry and Grassland Administration on Biology of Ornamental Plants in East China, College of Horticulture, Nanjing Agricultural University, No.1 Weigang, Nanjing, 210095, China
| | - YanYan Sun
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Landscaping, Key Laboratory of Flower Biology and Germplasm Innovation, Ministry of Agriculture and Rural Affairs, Key Laboratory of State Forestry and Grassland Administration on Biology of Ornamental Plants in East China, College of Horticulture, Nanjing Agricultural University, No.1 Weigang, Nanjing, 210095, China
| | - Haibin Wang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Landscaping, Key Laboratory of Flower Biology and Germplasm Innovation, Ministry of Agriculture and Rural Affairs, Key Laboratory of State Forestry and Grassland Administration on Biology of Ornamental Plants in East China, College of Horticulture, Nanjing Agricultural University, No.1 Weigang, Nanjing, 210095, China
| | - Lijie Zhou
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Landscaping, Key Laboratory of Flower Biology and Germplasm Innovation, Ministry of Agriculture and Rural Affairs, Key Laboratory of State Forestry and Grassland Administration on Biology of Ornamental Plants in East China, College of Horticulture, Nanjing Agricultural University, No.1 Weigang, Nanjing, 210095, China
| | - Jiafu Jiang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Landscaping, Key Laboratory of Flower Biology and Germplasm Innovation, Ministry of Agriculture and Rural Affairs, Key Laboratory of State Forestry and Grassland Administration on Biology of Ornamental Plants in East China, College of Horticulture, Nanjing Agricultural University, No.1 Weigang, Nanjing, 210095, China
| | - Sumei Chen
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Landscaping, Key Laboratory of Flower Biology and Germplasm Innovation, Ministry of Agriculture and Rural Affairs, Key Laboratory of State Forestry and Grassland Administration on Biology of Ornamental Plants in East China, College of Horticulture, Nanjing Agricultural University, No.1 Weigang, Nanjing, 210095, China
| | - Fadi Chen
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Landscaping, Key Laboratory of Flower Biology and Germplasm Innovation, Ministry of Agriculture and Rural Affairs, Key Laboratory of State Forestry and Grassland Administration on Biology of Ornamental Plants in East China, College of Horticulture, Nanjing Agricultural University, No.1 Weigang, Nanjing, 210095, China.
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8
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Sun Z, Sun J, Hu H, Han S, Ma P, Zuo B, Wang Z, Liu Z. A novel microRNA miR-4433a-3p as a potential diagnostic biomarker for lung adenocarcinoma. Heliyon 2024; 10:e30646. [PMID: 38765119 PMCID: PMC11101798 DOI: 10.1016/j.heliyon.2024.e30646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 05/01/2024] [Accepted: 05/01/2024] [Indexed: 05/21/2024] Open
Abstract
Background Lung adenocarcinoma is one of the leading causes of cancer-related deaths because of the lack of early specific clinical indicators. MicroRNAs (miRNAs) have become the focus in lung cancer diagnosis. Further studies are required to explore miRNA expression in the serum of lung adenocarcinoma patients and their correlation with therapy and analyse specific messenger RNA targets to improve the specificity and sensitivity of early diagnosis. Methods The Toray 3D-Gene miRNA array was used to compare the expression levels of various miRNAs in the sera of patients with lung adenocarcinoma and healthy volunteers. Highly expressed miRNAs were selected for further analysis. To verify the screening results, serum and pleural fluid samples were analysed using qRT-PCR. Serum levels of the miRNAs and their correlation with the clinical information of patients with lung adenocarcinoma were analysed. The functions of miRNAs were further analysed using the Kyoto Encyclopedia of Gene and Genomes and Gene Ontology databases. Results Microarray analysis identified 60 and 50 miRNAs with upregulated and downregulated expressions, respectively, in the serum of patients with lung adenocarcinoma compared to those in healthy individuals. Using qRT-qPCR to detection of miRNAs expression in the serum or pleural effusion of patients with early and advanced lung adenocarcinoma, we found that miR-4433a-3p could be used as a diagnostic marker and therapeutic evaluation indicator for lung adenocarcinoma. Serum of miR-4433a-3p levels significantly correlated with the clinical stage. miR-4433a-3p may be more suitable than other tumour markers for the early diagnosis and evaluation of therapeutic effects in lung adenocarcinoma. miR-4433a-3p may affect tumour growth and metastasis by acting on target genes (PIK3CD, UBE2J2, ICMT, PRDM16 and others) and regulating tumour-related signalling pathways (MAPK signal pathway, Ras signalling pathway and others). Conclusion miR-4433a-3p may serve as a biomarker for the early diagnosis of lung adenocarcinoma and monitoring of therapeutic effects.
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Affiliation(s)
- Zhixiao Sun
- Department of Pulmonary and Critical Care Medicine, The Yancheng Clinical College of Xuzhou Medical University, The First People's Hospital of Yancheng, China
- Department of Central Laboratory, The Yancheng Clinical College of Xuzhou Medical University, The First People's Hospital of Yancheng, China
| | - Jian Sun
- Department of Cardiothoracic Surgery, The Yancheng Clinical College of Xuzhou Medical University, The First People's Hospital of Yancheng, China
| | - Hang Hu
- Department of Pulmonary and Critical Care Medicine, The Yancheng Clinical College of Xuzhou Medical University, The First People's Hospital of Yancheng, China
| | - Shuhua Han
- Department of Pulmonary and Critical Care Medicine, Zhongda Hospital, School of Medicine, Southeast University, China
| | - Panpan Ma
- Department of Clinical Laboratory, The Yancheng Clinical College of Xuzhou Medical University, The First People's Hospital of Yancheng, China
| | - Bingqing Zuo
- Department of Pulmonary and Critical Care Medicine, The Yancheng Clinical College of Xuzhou Medical University, The First People's Hospital of Yancheng, China
| | - Zheng Wang
- Department of Chronic Disease Medical Center, The Yancheng Clinical College of Xuzhou Medical University, The First People's Hospital of Yancheng, China
| | - Zhongxiang Liu
- Department of Pulmonary and Critical Care Medicine, The Yancheng Clinical College of Xuzhou Medical University, The First People's Hospital of Yancheng, China
- Department of Central Laboratory, The Yancheng Clinical College of Xuzhou Medical University, The First People's Hospital of Yancheng, China
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9
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Kanlayaprasit S, Saeliw T, Thongkorn S, Panjabud P, Kasitipradit K, Lertpeerapan P, Songsritaya K, Yuwattana W, Jantheang T, Jindatip D, Hu VW, Kikkawa T, Osumi N, Sarachana T. Sex-specific impacts of prenatal bisphenol A exposure on genes associated with cortical development, social behaviors, and autism in the offspring's prefrontal cortex. Biol Sex Differ 2024; 15:40. [PMID: 38750585 PMCID: PMC11094985 DOI: 10.1186/s13293-024-00614-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 04/29/2024] [Indexed: 05/19/2024] Open
Abstract
BACKGROUND Recent studies have shown that prenatal BPA exposure altered the transcriptome profiles of autism-related genes in the offspring's hippocampus, disrupting hippocampal neuritogenesis and causing male-specific deficits in learning. However, the sex differences in the effects of prenatal BPA exposure on the developing prefrontal cortex, which is another brain region highly implicated in autism spectrum disorder (ASD), have not been investigated. METHODS We obtained transcriptome data from RNA sequencing analysis of the prefrontal cortex of male and female rat pups prenatally exposed to BPA or control and reanalyzed. BPA-responsive genes associated with cortical development and social behaviors were selected for confirmation by qRT-PCR analysis. Neuritogenesis of primary cells from the prefrontal cortex of pups prenatally exposed to BPA or control was examined. The social behaviors of the pups were assessed using the two-trial and three-chamber tests. The male-specific impact of the downregulation of a selected BPA-responsive gene (i.e., Sema5a) on cortical development in vivo was interrogated using siRNA-mediated knockdown by an in utero electroporation technique. RESULTS Genes disrupted by prenatal BPA exposure were associated with ASD and showed sex-specific dysregulation. Sema5a and Slc9a9, which were involved in neuritogenesis and social behaviors, were downregulated only in males, while Anxa2 and Junb, which were also linked to neuritogenesis and social behaviors, were suppressed only in females. Neuritogenesis was increased in males and showed a strong inverse correlation with Sema5a and Slc9a9 expression levels, whereas, in the females, neuritogenesis was decreased and correlated with Anxa2 and Junb levels. The siRNA-mediated knockdown of Sema5a in males also impaired cortical development in utero. Consistent with Anxa2 and Junb downregulations, deficits in social novelty were observed only in female offspring but not in males. CONCLUSION This is the first study to show that prenatal BPA exposure dysregulated the expression of ASD-related genes and functions, including cortical neuritogenesis and development and social behaviors, in a sex-dependent manner. Our findings suggest that, besides the hippocampus, BPA could also exert its adverse effects through sex-specific molecular mechanisms in the offspring's prefrontal cortex, which in turn would lead to sex differences in ASD-related neuropathology and clinical manifestations, which deserves further investigation.
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Grants
- NRU59-031-HR National Research University Project, Office of Higher Education Commission
- HEA663700091 Thailand Science Research and Innovation Fund Chulalongkorn University
- GRU 6300437001-1 Ratchadapisek Somphot Fund for Supporting Research Unit, Chulalongkorn University
- GRU_64_033_37_004 Ratchadapisek Somphot Fund for Supporting Research Unit, Chulalongkorn University
- GRU 6506537004-1 Ratchadapisek Somphot Fund for Supporting Research Unit, Chulalongkorn University
- the Second Century Fund (C2F), Chulalongkorn University, Bangkok, Thailand the Second Century Fund (C2F), Chulalongkorn University, Bangkok, Thailand
- the Second Century Fund (C2F), Chulalongkorn University, Bangkok, Thailand the Second Century Fund (C2F), Chulalongkorn University, Bangkok, Thailand
- the Second Century Fund (C2F), Chulalongkorn University, Bangkok, Thailand the Second Century Fund (C2F), Chulalongkorn University, Bangkok, Thailand
- the Second Century Fund (C2F), Chulalongkorn University, Bangkok, Thailand the Second Century Fund (C2F), Chulalongkorn University, Bangkok, Thailand
- PHD/0029/2561 a Royal Golden Jubilee Ph.D. Programme Scholarship, the Thailand Research Fund and National Research Council of Thailand
- N41A650065 a Royal Golden Jubilee Ph.D. Programme Scholarship, the Thailand Research Fund and National Research Council of Thailand
- NRCT5-RGJ63001-018 a Royal Golden Jubilee Ph.D. Programme Scholarship, the Thailand Research Fund and National Research Council of Thailand
- GCUGR1125632108D-108 The 90th Anniversary Chulalongkorn University Fund (Ratchadaphiseksomphot Endowment Fund), Graduate School, Chulalongkorn University
- GCUGR1125632109D-109 The 90th Anniversary Chulalongkorn University Fund (Ratchadaphiseksomphot Endowment Fund), Graduate School, Chulalongkorn University
- GCUGR1125651062D-062 The 90th Anniversary Chulalongkorn University Fund (Ratchadaphiseksomphot Endowment Fund), Graduate School, Chulalongkorn University
- GCUGR1125651060D-060 The 90th Anniversary Chulalongkorn University Fund (Ratchadaphiseksomphot Endowment Fund), Graduate School, Chulalongkorn University
- The 100th Anniversary Chulalongkorn University Fund for Doctoral Scholarship The 100th Anniversary Chulalongkorn University Fund for Doctoral Scholarship
- The 100th Anniversary Chulalongkorn University Fund for Doctoral Scholarship The 100th Anniversary Chulalongkorn University Fund for Doctoral Scholarship
- The 100th Anniversary Chulalongkorn University Fund for Doctoral Scholarship The 100th Anniversary Chulalongkorn University Fund for Doctoral Scholarship
- The National Research Council of Thailand (NRCT) fund for research and innovation activity The National Research Council of Thailand (NRCT) fund for research and innovation activity
- The National Research Council of Thailand (NRCT) fund for research and innovation activity The National Research Council of Thailand (NRCT) fund for research and innovation activity
- The National Research Council of Thailand (NRCT) fund for research and innovation activity The National Research Council of Thailand (NRCT) fund for research and innovation activity
- The National Research Council of Thailand (NRCT) fund for research and innovation activity The National Research Council of Thailand (NRCT) fund for research and innovation activity
- The National Research Council of Thailand (NRCT) fund for research and innovation activity The National Research Council of Thailand (NRCT) fund for research and innovation activity
- Scholarship from the Graduate School Chulalongkorn University to commemorate the 72nd anniversary of His Majesty King Bhumibala Aduladeja Scholarship from the Graduate School Chulalongkorn University to commemorate the 72nd anniversary of His Majesty King Bhumibala Aduladeja
- Chulalongkorn University Laboratory Animal Center (CULAC) Grant Chulalongkorn University Laboratory Animal Center (CULAC) Grant
- PMU-B; B36G660008 Program Management Unit for Human Resources and Institutional Development, Research and Innovation
- CE66_046_3700_003 Ratchadapisek Somphot Fund for Supporting Center of Excellence, Chulalongkorn University
- The National Research Council of Thailand (NRCT) fund for research and innovation activity
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Affiliation(s)
- Songphon Kanlayaprasit
- Chulalongkorn Autism Research and Innovation Center of Excellence (Chula ACE), Department of Clinical Chemistry, Faculty of Allied Health Sciences, Chulalongkorn University, 154 Soi Chula 12, Rama 1 Road, Bangkok, Wangmai, Pathumwan, 10330, Thailand
| | - Thanit Saeliw
- Chulalongkorn Autism Research and Innovation Center of Excellence (Chula ACE), Department of Clinical Chemistry, Faculty of Allied Health Sciences, Chulalongkorn University, 154 Soi Chula 12, Rama 1 Road, Bangkok, Wangmai, Pathumwan, 10330, Thailand
| | - Surangrat Thongkorn
- Chulalongkorn Autism Research and Innovation Center of Excellence (Chula ACE), Department of Clinical Chemistry, Faculty of Allied Health Sciences, Chulalongkorn University, 154 Soi Chula 12, Rama 1 Road, Bangkok, Wangmai, Pathumwan, 10330, Thailand
- Department of Biotechnology and Biomedicine (DTU Bioengineering), Technical University of Denmark, Kongens Lyngby, Denmark
| | - Pawinee Panjabud
- The Ph.D. Program in Clinical Biochemistry and Molecular Medicine, Department of Clinical Chemistry, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok, Thailand
| | - Kasidit Kasitipradit
- The Ph.D. Program in Clinical Biochemistry and Molecular Medicine, Department of Clinical Chemistry, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok, Thailand
| | - Pattanachat Lertpeerapan
- The Ph.D. Program in Clinical Biochemistry and Molecular Medicine, Department of Clinical Chemistry, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok, Thailand
| | - Kwanjira Songsritaya
- The M.Sc. Program in Clinical Biochemistry and Molecular Medicine, Department of Clinical Chemistry, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok, Thailand
| | - Wasana Yuwattana
- The Ph.D. Program in Clinical Biochemistry and Molecular Medicine, Department of Clinical Chemistry, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok, Thailand
| | - Thanawin Jantheang
- The Ph.D. Program in Clinical Biochemistry and Molecular Medicine, Department of Clinical Chemistry, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok, Thailand
| | - Depicha Jindatip
- Chulalongkorn Autism Research and Innovation Center of Excellence (Chula ACE), Department of Clinical Chemistry, Faculty of Allied Health Sciences, Chulalongkorn University, 154 Soi Chula 12, Rama 1 Road, Bangkok, Wangmai, Pathumwan, 10330, Thailand
- Department of Anatomy, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Valerie W Hu
- Department of Biochemistry and Molecular Medicine, School of Medicine and Health Sciences, The George Washington University, Washington, DC, USA
| | - Takako Kikkawa
- Department of Developmental Neuroscience, Centers for Advanced Research and Translational Medicine (ART), Graduate School of Medicine, Tohoku University, Sendai, Miyagi, Japan
| | - Noriko Osumi
- Department of Developmental Neuroscience, Centers for Advanced Research and Translational Medicine (ART), Graduate School of Medicine, Tohoku University, Sendai, Miyagi, Japan
| | - Tewarit Sarachana
- Chulalongkorn Autism Research and Innovation Center of Excellence (Chula ACE), Department of Clinical Chemistry, Faculty of Allied Health Sciences, Chulalongkorn University, 154 Soi Chula 12, Rama 1 Road, Bangkok, Wangmai, Pathumwan, 10330, Thailand.
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10
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Bezjak D, Orellana N, Valdivia G, Acevedo CA, Valdes JH. Global transcriptome profiles provide insights into muscle cell development and differentiation on microstructured marine biopolymer scaffolds for cultured meat production. Sci Rep 2024; 14:10931. [PMID: 38740842 PMCID: PMC11091069 DOI: 10.1038/s41598-024-61458-9] [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: 09/15/2023] [Accepted: 05/06/2024] [Indexed: 05/16/2024] Open
Abstract
Biomaterial scaffolds play a pivotal role in the advancement of cultured meat technology, facilitating essential processes like cell attachment, growth, specialization, and alignment. Currently, there exists limited knowledge concerning the creation of consumable scaffolds tailored for cultured meat applications. This investigation aimed to produce edible scaffolds featuring both smooth and patterned surfaces, utilizing biomaterials such as salmon gelatin, alginate, agarose and glycerol, pertinent to cultured meat and adhering to food safety protocols. The primary objective of this research was to uncover variations in transcriptomes profiles between flat and microstructured edible scaffolds fabricated from marine-derived biopolymers, leveraging high-throughput sequencing techniques. Expression analysis revealed noteworthy disparities in transcriptome profiles when comparing the flat and microstructured scaffold configurations against a control condition. Employing gene functional enrichment analysis for the microstructured versus flat scaffold conditions yielded substantial enrichment ratios, highlighting pertinent gene modules linked to the development of skeletal muscle. Notable functional aspects included filament sliding, muscle contraction, and the organization of sarcomeres. By shedding light on these intricate processes, this study offers insights into the fundamental mechanisms underpinning the generation of muscle-specific cultured meat.
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Affiliation(s)
- Dragica Bezjak
- Centro de Biotecnología, Universidad Técnica Federico Santa María, Avenida España 1680, Valparaíso, Chile
| | - Nicole Orellana
- Centro de Biotecnología, Universidad Técnica Federico Santa María, Avenida España 1680, Valparaíso, Chile
| | - Guillermo Valdivia
- Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Avenida República 239, Santiago, Chile
| | - Cristian A Acevedo
- Centro de Biotecnología, Universidad Técnica Federico Santa María, Avenida España 1680, Valparaíso, Chile.
- Departamento de Física, Universidad Técnica Federico Santa María, Avenida España 1680, Valparaiso, Chile.
- Centro Científico Tecnológico de Valparaíso (CCTVal), Universidad Técnica Federico Santa María, Avenida España 1680, Valparaiso, Chile.
| | - Jorge H Valdes
- Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Avenida República 239, Santiago, Chile.
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11
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Kim JH, Lee CJ, Yu YS, Aryal YP, Kim S, Suh JY, Kim JY, Min SH, Cha IT, Lee HY, Shin SY, Cho SJ. Transcriptomic profiling and the first spatial expression analysis of candidate genes in the salivary gland of the East Asian medicinal leech, Hirudo nipponia. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2024; 154:105125. [PMID: 38158145 DOI: 10.1016/j.dci.2023.105125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Revised: 12/20/2023] [Accepted: 12/21/2023] [Indexed: 01/03/2024]
Abstract
Hirudo nipponia, a blood-sucking leech native to East Asia, possesses a rich repertoire of active ingredients in its saliva, showcasing significant medical potential due to its anticoagulant, anti-inflammatory, and antibacterial effects against human diseases. Despite previous studies on the transcriptomic and proteomic characteristics of leech saliva, which have identified medicinal compounds, our knowledge of tissue-specific transcriptomes and their spatial expression patterns remains incomplete. In this study, we conducted an extensive transcriptomic profiling of the salivary gland tissue in H. nipponia based on de novo assemblies of tissue-specific transcriptomes from the salivary gland, teeth, and general head region. Through gene ontology (GO) analysis and hierarchical clustering, we discovered a novel set of anti-coagulant factors-i.e., Hni-Antistasin, Hni-Ghilanten, Hni-Bdellin, Hni-Hirudin-as well as a previously unrecognized immune-related gene, Hni-GLIPR1 and uncharacterized salivary gland specific transcripts. By employing in situ hybridization, we provided the first visualization of gene expression sites within the salivary gland of H. nipponia. Our findings expand on our understanding of transcripts specifically expressed in the salivary gland of blood-sucking leeches, offering valuable resources for the exploration of previously unidentified substances with medicinal applications.
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Affiliation(s)
- Jung-Hyeuk Kim
- Department of Biological Sciences and Biotechnology, College of Natural Sciences, Chungbuk National University, Cheongju, Chungbuk, 28644, Republic of Korea; Wildlife Disease Response Team, National Institute of Wildlife Disease Control and Prevention, Incheon, 22689, Republic of Korea
| | - Chan-Jun Lee
- Department of Biological Sciences and Biotechnology, College of Natural Sciences, Chungbuk National University, Cheongju, Chungbuk, 28644, Republic of Korea
| | - Yun-Sang Yu
- Department of Biological Sciences and Biotechnology, College of Natural Sciences, Chungbuk National University, Cheongju, Chungbuk, 28644, Republic of Korea
| | - Yam Prasad Aryal
- Department of Biological Sciences and Biotechnology, College of Natural Sciences, Chungbuk National University, Cheongju, Chungbuk, 28644, Republic of Korea
| | - Sangil Kim
- Museum of Comparative Zoology and Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Jo-Young Suh
- Department of Periodontology, School of Dentistry, IHBR Kyungpook National University, Daegu, 41940, Republic of Korea
| | - Jae-Young Kim
- Department of Biochemistry, School of Dentistry, IHBR, Kyungpook National University, Daegu 41940, Republic of Korea
| | - Sun Hong Min
- Department of Cosmetics Engineering, Konkuk University, Seoul, 05029, Republic of Korea
| | - In-Tae Cha
- Species Diversity Research Division, National Institute of Biological Resources(NIBR), Incheon, 22689, Republic of Korea
| | - Hae-Youn Lee
- Department of Biological Sciences and Biotechnology, College of Natural Sciences, Chungbuk National University, Cheongju, Chungbuk, 28644, Republic of Korea.
| | - Song Yub Shin
- Department of Cellular & Molecular Medicine, School of Medicine, Chosun University, Gwangju, 61452, Republic of Korea.
| | - Sung-Jin Cho
- Department of Biological Sciences and Biotechnology, College of Natural Sciences, Chungbuk National University, Cheongju, Chungbuk, 28644, Republic of Korea.
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12
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Zhang X, Yang Y, Wang L, Qin Y. Histone H2B lysine 122 and lysine 130, as the putative targets of Penicillium oxalicum LaeA, play important roles in asexual development, expression of secondary metabolite gene clusters, and extracellular glycoside hydrolase synthesis. World J Microbiol Biotechnol 2024; 40:179. [PMID: 38668807 DOI: 10.1007/s11274-024-03978-0] [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: 10/17/2023] [Accepted: 04/03/2024] [Indexed: 05/01/2024]
Abstract
Core histones in the nucleosome are subject to a wide variety of posttranslational modifications (PTMs), such as methylation, phosphorylation, ubiquitylation, and acetylation, all of which are crucial in shaping the structure of the chromatin and the expression of the target genes. A putative histone methyltransferase LaeA/Lae1, which is conserved in numerous filamentous fungi, functions as a global regulator of fungal growth, virulence, secondary metabolite formation, and the production of extracellular glycoside hydrolases (GHs). LaeA's direct histone targets, however, were not yet recognized. Previous research has shown that LaeA interacts with core histone H2B. Using S-adenosyl-L-methionine (SAM) as a methyl group donor and recombinant human histone H2B as the substrate, it was found that Penicillium oxalicum LaeA can transfer the methyl groups to the C-terminal lysine (K) 108 and K116 residues in vitro. The H2BK108 and H2BK116 sites on recombinant histone correspond to P. oxalicum H2BK122 and H2BK130, respectively. H2BK122A and H2BK130A, two mutants with histone H2B K122 or K130 mutation to alanine (A), were constructed in P. oxalicum. The mutants H2BK122A and H2BK130A demonstrated altered asexual development and decreased extracellular GH production, consistent with the findings of the laeA gene deletion strain (ΔlaeA). The transcriptome data showed that when compared to wild-type (WT) of P. oxalicum, 38 of the 47 differentially expressed (fold change ≥ 2, FDR ≤ 0.05) genes that encode extracellular GHs showed the same expression pattern in the three mutants ΔlaeA, H2BK122A, and H2BK130A. The four secondary metabolic gene clusters that considerably decreased expression in ΔlaeA also significantly decreased in H2BK122A or H2BK130A. The chromatin of promotor regions of the key cellulolytic genes cel7A/cbh1 and cel7B/eg1 compacted in the ΔlaeA, H2BK122A, and H2BK130A mutants, according to the results of chromatin accessibility real-time PCR (CHART-PCR). The chromatin accessibility index dropped. The histone binding pocket of the LaeA-methyltransf_23 domain is compatible with particular histone H2B peptides, providing appropriate electrostatic and steric compatibility to stabilize these peptides, according to molecular docking. The findings of the study demonstrate that H2BK122 and H2BK130, which are histone targets of P. oxalicum LaeA in vitro, are crucial for fungal conidiation, the expression of gene clusters encoding secondary metabolites, and the production of extracellular GHs.
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Affiliation(s)
- Xiujun Zhang
- National Glycoengineering Research Center, Shandong University, Qingdao, China
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
- School of Biological Science and Technology, University of Jinan, Jinan, China
| | - Yuhong Yang
- School of Biological Science and Technology, University of Jinan, Jinan, China
| | - Lushan Wang
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
| | - Yuqi Qin
- National Glycoengineering Research Center, Shandong University, Qingdao, China.
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China.
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13
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Liu Z, Ouyang T, Yang Y, Sheng Y, Shi H, Liu Q, Bai Y, Ge Q. The Impact of Blood Sample Processing on Ribonucleic Acid (RNA) Sequencing. Genes (Basel) 2024; 15:502. [PMID: 38674435 PMCID: PMC11050547 DOI: 10.3390/genes15040502] [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: 02/24/2024] [Revised: 04/12/2024] [Accepted: 04/13/2024] [Indexed: 04/28/2024] Open
Abstract
In gene quantification and expression analysis, issues with sample selection and processing can be serious, as they can easily introduce irrelevant variables and lead to ambiguous results. This study aims to investigate the extent and mechanism of the impact of sample selection and processing on ribonucleic acid (RNA) sequencing. RNA from PBMCs and blood samples was investigated in this study. The integrity of this RNA was measured under different storage times. All the samples underwent high-throughput sequencing for comprehensive evaluation. The differentially expressed genes and their potential functions were analyzed after the samples were placed at room temperature for 0h, 4h and 8h, and different feature changes in these samples were also revealed. The sequencing results showed that the differences in gene expression were higher with an increased storage time, while the total number of genes detected did not change significantly. There were five genes showing gradient patterns over different storage times, all of which were protein-coding genes that had not been mentioned in previous studies. The effect of different storage times on seemingly the same samples was analyzed in this present study. This research, therefore, provides a theoretical basis for the long-term consideration of whether sample processing should be adequately addressed.
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Affiliation(s)
| | | | | | | | | | | | | | - Qinyu Ge
- State Key Laboratory of Digital Medical Engineering, Southeast University, Nanjing 211189, China; (Z.L.); (T.O.); (Y.Y.); (Y.S.); (H.S.); (Q.L.); (Y.B.)
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14
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Cai Z, Zhao X, Qian Y, Zhang K, Guo S, Kan Y, Wang Y, Ayra-Pardo C, Li D. Transcriptomic and Metatranscriptomic Analyses Provide New Insights into the Response of the Pea Aphid Acyrthosiphon pisum (Hemiptera: Aphididae) to Acetamiprid. INSECTS 2024; 15:274. [PMID: 38667404 PMCID: PMC11050337 DOI: 10.3390/insects15040274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 04/07/2024] [Accepted: 04/09/2024] [Indexed: 04/28/2024]
Abstract
Acetamiprid is a broad-spectrum neonicotinoid insecticide used in agriculture to control aphids. While recent studies have documented resistance to acetamiprid in several aphid species, the underlying mechanisms are still not fully understood. In this study, we analyzed the transcriptome and metatranscriptome of a laboratory strain of the pea aphid, Acyrthosiphon pisum (Harris, 1776), with reduced susceptibility to acetamiprid after nine generations of exposure to identify candidate genes and the microbiome involved in the adaptation process. Sequencing of the transcriptome of both selected (RS) and non-selected (SS) strains allowed the identification of 14,858 genes and 4938 new transcripts. Most of the differentially expressed genes were associated with catalytic activities and metabolic pathways involving carbon and fatty acids. Specifically, alcohol-forming fatty acyl-CoA reductase (FAR) and acyl-CoA synthetase (ACSF2), both involved in the synthesis of epidermal wax layer components, were significantly upregulated in RS, suggesting that adaptation to acetamiprid involves the synthesis of a thicker protective layer. Metatranscriptomic analyses revealed subtle shifts in the microbiome of RS. These results contribute to a deeper understanding of acetamiprid adaptation by the pea aphid and provide new insights for aphid control strategies.
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Affiliation(s)
- Zhiyan Cai
- Henan Key Laboratory of Insect Biology in Funiu Mountain, Henan International Joint Laboratory of Insect Biology, College of Life Science and Agricultural Engineering, Nanyang Normal University, 1638 Wolong Road, Nanyang 473061, China; (Z.C.); (X.Z.); (Y.Q.); (K.Z.); (S.G.); (Y.K.)
| | - Xuhui Zhao
- Henan Key Laboratory of Insect Biology in Funiu Mountain, Henan International Joint Laboratory of Insect Biology, College of Life Science and Agricultural Engineering, Nanyang Normal University, 1638 Wolong Road, Nanyang 473061, China; (Z.C.); (X.Z.); (Y.Q.); (K.Z.); (S.G.); (Y.K.)
| | - Yuxin Qian
- Henan Key Laboratory of Insect Biology in Funiu Mountain, Henan International Joint Laboratory of Insect Biology, College of Life Science and Agricultural Engineering, Nanyang Normal University, 1638 Wolong Road, Nanyang 473061, China; (Z.C.); (X.Z.); (Y.Q.); (K.Z.); (S.G.); (Y.K.)
| | - Kun Zhang
- Henan Key Laboratory of Insect Biology in Funiu Mountain, Henan International Joint Laboratory of Insect Biology, College of Life Science and Agricultural Engineering, Nanyang Normal University, 1638 Wolong Road, Nanyang 473061, China; (Z.C.); (X.Z.); (Y.Q.); (K.Z.); (S.G.); (Y.K.)
| | - Shigang Guo
- Henan Key Laboratory of Insect Biology in Funiu Mountain, Henan International Joint Laboratory of Insect Biology, College of Life Science and Agricultural Engineering, Nanyang Normal University, 1638 Wolong Road, Nanyang 473061, China; (Z.C.); (X.Z.); (Y.Q.); (K.Z.); (S.G.); (Y.K.)
| | - Yunchao Kan
- Henan Key Laboratory of Insect Biology in Funiu Mountain, Henan International Joint Laboratory of Insect Biology, College of Life Science and Agricultural Engineering, Nanyang Normal University, 1638 Wolong Road, Nanyang 473061, China; (Z.C.); (X.Z.); (Y.Q.); (K.Z.); (S.G.); (Y.K.)
- School of Life Science and Technology, Henan Institute of Science and Technology, 90 East of Hualan Avenue, Xinxiang 453003, China
| | - Yuqing Wang
- Scientific Research Center, Nanyang Medical College, Nanyang 473061, China;
| | - Camilo Ayra-Pardo
- CIIMAR—Interdisciplinary Centre of Marine and Environmental Research, Terminal de Cruzeiros do Porto de Leixões, University of Porto, Avda. General Norton de Matos s/n, 4450-208 Matosinhos, Portugal
| | - Dandan Li
- Henan Key Laboratory of Insect Biology in Funiu Mountain, Henan International Joint Laboratory of Insect Biology, College of Life Science and Agricultural Engineering, Nanyang Normal University, 1638 Wolong Road, Nanyang 473061, China; (Z.C.); (X.Z.); (Y.Q.); (K.Z.); (S.G.); (Y.K.)
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15
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Kan Y, He Z, Keyhani NO, Li N, Huang S, Zhao X, Liu P, Zeng F, Li M, Luo Z, Zhang Y. A network of transcription factors in complex with a regulating cell cycle cyclin orchestrates fungal oxidative stress responses. BMC Biol 2024; 22:81. [PMID: 38609978 PMCID: PMC11015564 DOI: 10.1186/s12915-024-01884-3] [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: 07/03/2023] [Accepted: 04/05/2024] [Indexed: 04/14/2024] Open
Abstract
BACKGROUND Response to oxidative stress is universal in almost all organisms and the mitochondrial membrane protein, BbOhmm, negatively affects oxidative stress responses and virulence in the insect fungal pathogen, Beauveria bassiana. Nothing further, however, is known concerning how BbOhmm and this phenomenon is regulated. RESULTS Three oxidative stress response regulating Zn2Cys6 transcription factors (BbOsrR1, 2, and 3) were identified and verified via chromatin immunoprecipitation (ChIP)-qPCR analysis as binding to the BbOhmm promoter region, with BbOsrR2 showing the strongest binding. Targeted gene knockout of BbOsrR1 or BbOsrR3 led to decreased BbOhmm expression and consequently increased tolerances to free radical generating compounds (H2O2 and menadione), whereas the ΔBbOsrR2 strain showed increased BbOhmm expression with concomitant decreased tolerances to these compounds. RNA and ChIP sequencing analysis revealed that BbOsrR1 directly regulated a wide range of antioxidation and transcription-associated genes, negatively affecting the expression of the BbClp1 cyclin and BbOsrR2. BbClp1 was shown to localize to the cell nucleus and negatively mediate oxidative stress responses. BbOsrR2 and BbOsrR3 were shown to feed into the Fus3-MAPK pathway in addition to regulating antioxidation and detoxification genes. Binding motifs for the three transcription factors were found to partially overlap in the promoter region of BbOhmm and other target genes. Whereas BbOsrR1 appeared to function independently, co-immunoprecipitation revealed complex formation between BbClp1, BbOsrR2, and BbOsrR3, with BbClp1 partially regulating BbOsrR2 phosphorylation. CONCLUSIONS These findings reveal a regulatory network mediated by BbOsrR1 and the formation of a BbClp1-BbOsrR2-BbOsrR3 complex that orchestrates fungal oxidative stress responses.
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Affiliation(s)
- Yanze Kan
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), College of Plant Protection, Southwest University, Chongqing, 400715, People's Republic of China
- Key Laboratory of Entomology and Pest Control Engineering, Beibei Culture Collection of Chongqing Agricultural Microbiology, Chongqing, 400715, People's Republic of China
| | - Zhangjiang He
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), College of Plant Protection, Southwest University, Chongqing, 400715, People's Republic of China
- Key Laboratory of Entomology and Pest Control Engineering, Beibei Culture Collection of Chongqing Agricultural Microbiology, Chongqing, 400715, People's Republic of China
- Biochemical Engineering Center of Guizhou Province, Guizhou University, Guiyang, 50025, People's Republic of China
| | - Nemat O Keyhani
- Department of Biological Sciences, University of Illinois, Chicago, IL, 60607, USA
| | - Ning Li
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), College of Plant Protection, Southwest University, Chongqing, 400715, People's Republic of China
- Key Laboratory of Entomology and Pest Control Engineering, Beibei Culture Collection of Chongqing Agricultural Microbiology, Chongqing, 400715, People's Republic of China
| | - Shuaishuai Huang
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), College of Plant Protection, Southwest University, Chongqing, 400715, People's Republic of China
- Key Laboratory of Entomology and Pest Control Engineering, Beibei Culture Collection of Chongqing Agricultural Microbiology, Chongqing, 400715, People's Republic of China
| | - Xin Zhao
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), College of Plant Protection, Southwest University, Chongqing, 400715, People's Republic of China
- Key Laboratory of Entomology and Pest Control Engineering, Beibei Culture Collection of Chongqing Agricultural Microbiology, Chongqing, 400715, People's Republic of China
| | - Pengfei Liu
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), College of Plant Protection, Southwest University, Chongqing, 400715, People's Republic of China
- Key Laboratory of Entomology and Pest Control Engineering, Beibei Culture Collection of Chongqing Agricultural Microbiology, Chongqing, 400715, People's Republic of China
| | - Fanqin Zeng
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), College of Plant Protection, Southwest University, Chongqing, 400715, People's Republic of China
- Key Laboratory of Entomology and Pest Control Engineering, Beibei Culture Collection of Chongqing Agricultural Microbiology, Chongqing, 400715, People's Republic of China
| | - Min Li
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), College of Plant Protection, Southwest University, Chongqing, 400715, People's Republic of China
- Key Laboratory of Entomology and Pest Control Engineering, Beibei Culture Collection of Chongqing Agricultural Microbiology, Chongqing, 400715, People's Republic of China
| | - Zhibing Luo
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), College of Plant Protection, Southwest University, Chongqing, 400715, People's Republic of China
- Key Laboratory of Entomology and Pest Control Engineering, Beibei Culture Collection of Chongqing Agricultural Microbiology, Chongqing, 400715, People's Republic of China
| | - Yongjun Zhang
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), College of Plant Protection, Southwest University, Chongqing, 400715, People's Republic of China.
- Key Laboratory of Entomology and Pest Control Engineering, Beibei Culture Collection of Chongqing Agricultural Microbiology, Chongqing, 400715, People's Republic of China.
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16
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Yang S, Jiao D, Song T, Rui P, Fan R, Ma Z. Gene expression profiles of skin from cyclin dependent kinases 5-knockdown mice. Anim Biosci 2024; 37:567-575. [PMID: 37946423 PMCID: PMC10915219 DOI: 10.5713/ab.23.0244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 07/15/2023] [Accepted: 10/02/2023] [Indexed: 11/12/2023] Open
Abstract
OBJECTIVE This study aimed to identify genes regulated by cyclin dependent kinases 5 (CDK5) that participate in hair pigmentation in mice. METHODS The mRNA expression profiles of skin samples from CDK5-knockdown mice were constructed using high-throughput RNA sequencing and compared with those of wild-type mice. RESULTS In total, 8,002 known genes were differentially expressed between CDK5-knockdown and wild-type mice. Of these, 3,658 were upregulated and 4,344 were downregulated in the skin of CDK5-knockdown mice. An additional 318 previously unknown genes were also differentially expressed, with 171 downregulated and 147 upregulated genes in the skin of CDK5-knockdown mice. Of the known genes expressed in mouse skin, 80 were associated with hair color, with 61 showing lower expression and 19 exhibiting higher expression in skin of CDK5-knockdown mice. Importantly, the expression of the tyrosinase-related protein 1 (TYRP1) and the calcium signaling pathway were also found to be regulated by CDK5, suggesting that pigmentation is regulated by CDK5 via the calcium signaling pathway and TYRP1. CONCLUSION The transcriptome profiles obtained from the skin of CDK5-knockdown mice compared to wild-type mice provide a valuable resource to help understand the mechanism by which CDK5 regulates melanogenesis in mice and other animals.
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Affiliation(s)
- Shanshan Yang
- College of Animal Science and Technology, Hebei Normal University of Science & Technology, Qinhuangdao 066600,
China
- Hebei Key Laboratory of Veterinary Preventive Medicine, College of Animal Science and Technology, Hebei Normal University of Science & Technology, Qinhuangdao 066600,
China
| | - Dingxing Jiao
- College of Animal Science and Technology, Hebei Normal University of Science & Technology, Qinhuangdao 066600,
China
- Hebei Key Laboratory of Veterinary Preventive Medicine, College of Animal Science and Technology, Hebei Normal University of Science & Technology, Qinhuangdao 066600,
China
| | - Tao Song
- College of Animal Science and Technology, Hebei Normal University of Science & Technology, Qinhuangdao 066600,
China
- Hebei Key Laboratory of Veterinary Preventive Medicine, College of Animal Science and Technology, Hebei Normal University of Science & Technology, Qinhuangdao 066600,
China
| | - Ping Rui
- College of Animal Science and Technology, Hebei Normal University of Science & Technology, Qinhuangdao 066600,
China
- Hebei Key Laboratory of Veterinary Preventive Medicine, College of Animal Science and Technology, Hebei Normal University of Science & Technology, Qinhuangdao 066600,
China
| | - Ruiwen Fan
- College of Veterinary Medicine, Shanxi Agricultural University, Taigu, Shanxi 030801,
China
| | - Zengjun Ma
- College of Animal Science and Technology, Hebei Normal University of Science & Technology, Qinhuangdao 066600,
China
- Hebei Key Laboratory of Veterinary Preventive Medicine, College of Animal Science and Technology, Hebei Normal University of Science & Technology, Qinhuangdao 066600,
China
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17
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Hannes L, Atzori M, Goldenberg A, Argente J, Attie-Bitach T, Amiel J, Attanasio C, Braslavsky DG, Bruel AL, Castanet M, Dubourg C, Jacobs A, Lyonnet S, Martinez-Mayer J, Pérez Millán MI, Pezzella N, Pelgrims E, Aerden M, Bauters M, Rochtus A, Scaglia P, Swillen A, Sifrim A, Tammaro R, Mau-Them FT, Odent S, Thauvin-Robinet C, Franco B, Breckpot J. Differential alternative splicing analysis links variation in ZRSR2 to a novel type of oral-facial-digital syndrome. Genet Med 2024; 26:101059. [PMID: 38158857 DOI: 10.1016/j.gim.2023.101059] [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: 03/02/2023] [Revised: 12/22/2023] [Accepted: 12/22/2023] [Indexed: 01/03/2024] Open
Abstract
PURPOSE Oral-facial-digital (OFD) syndromes are genetically heterogeneous developmental disorders, caused by pathogenic variants in genes involved in primary cilia formation and function. We identified a previously undescribed type of OFD with brain anomalies, ranging from alobar holoprosencephaly to pituitary anomalies, in 6 unrelated families. METHODS Exome sequencing of affected probands was supplemented with alternative splicing analysis in patient and control lymphoblastoid and fibroblast cell lines, and primary cilia structure analysis in patient fibroblasts. RESULTS In 1 family with 2 affected males, we identified a germline variant in the last exon of ZRSR2, NM_005089.4:c.1211_1212del NP_005080.1:p.(Gly404GlufsTer23), whereas 7 affected males from 5 unrelated families were hemizygous for the ZRSR2 variant NM_005089.4:c.1207_1208del NP_005080.1:p.(Arg403GlyfsTer24), either occurring de novo or inherited in an X-linked recessive pattern. ZRSR2, located on chromosome Xp22.2, encodes a splicing factor of the minor spliceosome complex, which recognizes minor introns, representing 0.35% of human introns. Patient samples showed significant enrichment of minor intron retention. Among differentially spliced targets are ciliopathy-related genes, such as TMEM107 and CIBAR1. Primary fibroblasts containing the NM_005089.4:c.1207_1208del ZRSR2 variant had abnormally elongated cilia, confirming an association between defective U12-type intron splicing, OFD and abnormal primary cilia formation. CONCLUSION We introduce a novel type of OFD associated with elongated cilia and differential splicing of minor intron-containing genes due to germline variation in ZRSR2.
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Affiliation(s)
- Laurens Hannes
- Department of Human Genetics, KU Leuven, Leuven, Belgium; Center for Human Genetics, University Hospitals Leuven, Leuven, Belgium
| | - Marta Atzori
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Alice Goldenberg
- Centre de Référence Anomalies du Développement et Syndromes Malformatifs, CHU Rouen, Rouen, France
| | - Jesús Argente
- Department of Pediatrics & Pediatric Endocrinology, Hospital Infantil Universitario Niño Jesús, Madrid, Spain; Department of Pediatrics, Universidad Autónoma de Madrid, Madrid, Spain; CIBEROBN de fisiopatología de la obesidad y nutrición, Instituto de Salud Carlos III, Madrid, Spain; IMDEA Food Institute, Madrid, Spain
| | - Tania Attie-Bitach
- Université Paris Cité, INSERM, IHU Imagine - Institut des maladies génétiques, Paris, France; Service de médecine génomique des maladies rares, Hôpital Universitaire Necker-Enfants Malades, AP-HP, Institut Imagine, Paris, France
| | - Jeanne Amiel
- Université Paris Cité, INSERM, IHU Imagine - Institut des maladies génétiques, Paris, France; Service de médecine génomique des maladies rares, Hôpital Universitaire Necker-Enfants Malades, AP-HP, Institut Imagine, Paris, France
| | | | - Débora G Braslavsky
- Centro de Investigaciones Endocrinológicas "Dr. César Bergadá" (CEDIE) CONICET - FEI - División de Endocrinología, Hospital de Niños Ricardo Gutiérrez. Buenos Aires, Argentina
| | - Ange-Line Bruel
- INSERM, U1231, Génétique des Anomalies du Développement, Université de Bourgogne Franche-Comté, UMR Lipides, Nutrition, Dijon, France; UF Innovation diagnostique des maladies rares, FHU TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | - Mireille Castanet
- Normandie Univ, UNIROUEN, Inserm U1239, CHU Rouen, Department of Pediatrics, Rouen, France
| | - Christèle Dubourg
- Department of Molecular Genetics and Genomics, Rennes University Hospital, Rennes, France; Univ Rennes, CNRS, INSERM, IGDR, UMR 6290, ERL U1305, Rennes, France
| | - An Jacobs
- Department of Pediatrics, University Hospitals Leuven, Leuven, Belgium
| | - Stanislas Lyonnet
- Université Paris Cité, INSERM, IHU Imagine - Institut des maladies génétiques, Paris, France; Service de médecine génomique des maladies rares, Hôpital Universitaire Necker-Enfants Malades, AP-HP, Institut Imagine, Paris, France
| | - Julian Martinez-Mayer
- Instituto de Biociencias, Biotecnología y Biología Traslacional (IB3), Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad de Buenos Aires, Argentina
| | - María Inés Pérez Millán
- Instituto de Biociencias, Biotecnología y Biología Traslacional (IB3), Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad de Buenos Aires, Argentina
| | - Nunziana Pezzella
- Telethon Institute of Genetics and Medicine-TIGEM, Naples, Italy; Scuola Superiore Meridionale, School for Advanced Studies, Genomics and Experimental Medicine program, Naples, Italy
| | - Elise Pelgrims
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Mio Aerden
- Department of Human Genetics, KU Leuven, Leuven, Belgium; Center for Human Genetics, University Hospitals Leuven, Leuven, Belgium
| | - Marijke Bauters
- Center for Human Genetics, University Hospitals Leuven, Leuven, Belgium
| | - Anne Rochtus
- Department of Pediatrics, University Hospitals Leuven, Leuven, Belgium
| | - Paula Scaglia
- Centro de Investigaciones Endocrinológicas "Dr. César Bergadá" (CEDIE) CONICET - FEI - División de Endocrinología, Hospital de Niños Ricardo Gutiérrez. Buenos Aires, Argentina
| | - Ann Swillen
- Department of Human Genetics, KU Leuven, Leuven, Belgium; Center for Human Genetics, University Hospitals Leuven, Leuven, Belgium
| | | | - Roberta Tammaro
- Telethon Institute of Genetics and Medicine-TIGEM, Naples, Italy
| | - Frederic Tran Mau-Them
- INSERM, U1231, Génétique des Anomalies du Développement, Université de Bourgogne Franche-Comté, UMR Lipides, Nutrition, Dijon, France; UF Innovation diagnostique des maladies rares, FHU TRANSLAD, CHU Dijon Bourgogne, Dijon, France; Unité Fonctionnelle Innovation en Diagnostic Génomique des maladies rares, CHU Dijon Bourgogne, Dijon, France
| | - Sylvie Odent
- Department of Molecular Genetics and Genomics, Rennes University Hospital, Rennes, France; Univ Rennes, CNRS, INSERM, IGDR, UMR 6290, ERL U1305, Rennes, France; Centre de Référence Anomalies du Développement et Syndromes Malformatifs de l'interrégion Ouest, ERN ITHACA, FHU GenOmedS, Centre Hospitalier Universitaire Rennes, Rennes, France
| | - Christel Thauvin-Robinet
- INSERM, U1231, Génétique des Anomalies du Développement, Université de Bourgogne Franche-Comté, UMR Lipides, Nutrition, Dijon, France; UF Innovation diagnostique des maladies rares, FHU TRANSLAD, CHU Dijon Bourgogne, Dijon, France; Centre de Référence Anomalies du Développement de l'Est, Centre de Génétique, Centre Hospitalier Universitaire Dijon Bourgogne, Dijon, France
| | - Brunella Franco
- Telethon Institute of Genetics and Medicine-TIGEM, Naples, Italy; Scuola Superiore Meridionale, School for Advanced Studies, Genomics and Experimental Medicine program, Naples, Italy; Department of Translational Medicine, Medical Genetics Federico II University of Naples, Naples, Italy
| | - Jeroen Breckpot
- Department of Human Genetics, KU Leuven, Leuven, Belgium; Center for Human Genetics, University Hospitals Leuven, Leuven, Belgium.
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18
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Chen Q, Zhang C, Chen Y, Wang C, Lai Z. Transcriptomic Analysis for Diurnal Temperature Differences Reveals Gene-Regulation-Network Response to Accumulation of Bioactive Ingredients of Protocorm-like Bodies in Dendrobium officinale. PLANTS (BASEL, SWITZERLAND) 2024; 13:874. [PMID: 38592895 PMCID: PMC10975105 DOI: 10.3390/plants13060874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Revised: 03/11/2024] [Accepted: 03/13/2024] [Indexed: 04/11/2024]
Abstract
Dendrobium officinale Kimura et Migo (D. officinale) is one of the most important traditional Chinese medicinal herbs, celebrated for its abundant bioactive ingredients. This study demonstrated that the diurnal temperature difference (DIF) (T1: 13/13 °C, T2: 25/13 °C, and T3: 25/25 °C) was more favorable for high chlorophyll, increased polysaccharide, and total flavonoid contents compared to constant temperature treatments in D. officinale PLBs. The transcriptome analysis revealed 4251, 4404, and 4536 differentially expressed genes (DEGs) in three different comparisons (A: 25/13 °C vs. 13/13 °C, B: 13/13 °C vs. 25/25 °C, and C: 25/13 °C vs. 25/25 °C, respectively). The corresponding up-/down-regulated DEGs were 1562/2689, 2825/1579, and 2310/2226, respectively. GO and KEGG enrichment analyses of DEGs showed that the pathways of biosynthesis of secondary metabolites, carotenoid biosynthesis, and flavonoid biosynthesis were enriched in the top 20; further analysis of the sugar- and flavonol-metabolism pathways in D. officinale PLBs revealed that the DIF led to a differential gene expression in the enzymes linked to sugar metabolism, as well as to flavonol metabolism. Certain key metabolic genes related to ingredient accumulation were identified, including those involved in polysaccharide metabolism (SUS, SUT, HKL1, HGL, AMY1, and SS3) and flavonol (UGT73C and UGT73D) metabolism. Therefore, these findings indicated that these genes may play an important role in the regulatory network of the DIF in the functional metabolites of D. officinale PLBs. In a MapMan annotation of abiotic stress pathways, the DEGs with significant changes in their expression levels were mainly concentrated in the heat-stress pathways, including heat-shock proteins (HSPs) and heat-shock transcription factors (HSFs). In particular, the expression levels of HSP18.2, HSP70, and HSF1 were significantly increased under DIF treatment, which suggested that HSF1, HSP70 and HSP18.2 may respond to the DIF. In addition, they can be used as candidate genes to study the effect of the DIF on the PLBs of D. officinale. The results of our qPCR analysis are consistent with those of the transcriptome-expression analysis, indicating the reliability of the sequencing. The results of this study revealed the transcriptome mechanism of the DIF on the accumulation of the functional metabolic components of D. officinale. Furthermore, they also provide an important theoretical basis for improving the quality of D. officinale via the DIF in production.
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Affiliation(s)
| | | | | | | | - Zhongxiong Lai
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Q.C.); (C.Z.); (Y.C.); (C.W.)
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Zhang H, Cai C, Li Q, Nie Z, Wang M, Liu Y, Shen W, Song H. Copper oxide nanoparticles suppress retinal angiogenesis via inducing endothelial cell cuproptosis. Nanomedicine (Lond) 2024; 19:597-613. [PMID: 38299352 DOI: 10.2217/nnm-2023-0301] [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] [Indexed: 02/02/2024] Open
Abstract
Background: Copper oxide nanoparticles (CuO NPs) exhibit antitumor activity; however, their potential as an antiangiogenesis agent is unknown. Materials & methods: The antiangiogenesis properties of CuO NPs were evaluated in vitro and in vivo and the underlying mechanism was examined using RNA sequencing and metabolomic analyses. Results: CuO NPs inhibited endothelial cell function in vitro. They also mitigated retinal vasculature development and alleviated pathological retinal angiogenesis in vivo. RNA sequencing and metabolomic analyses revealed that CuO NPs disrupt the tricarboxylic acid cycle and induce cuproptosis, which was further supported by evaluating cuproptosis-related metabolites and proteins. Conclusion: CuO NPs may be an effective antiangiogenic agent for the treatment of retinal angiogenesis.
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Affiliation(s)
- Haorui Zhang
- Department of Ophthalmology, Shanghai Changhai Hospital, Shanghai, 200433, China
| | - Chang Cai
- Department of Ophthalmology, Shanghai Changhai Hospital, Shanghai, 200433, China
- Department of Spine Surgery, Changzheng Hospital, Shanghai, 200040, China
| | - Qing Li
- Department of Ophthalmology, Shanghai Changhai Hospital, Shanghai, 200433, China
| | - Zheng Nie
- Department of Ophthalmology, Shanghai Changhai Hospital, Shanghai, 200433, China
| | - Mengzhu Wang
- Department of Ophthalmology, Shanghai Changhai Hospital, Shanghai, 200433, China
| | - Yongxuan Liu
- Department of Ophthalmology, Shanghai Changhai Hospital, Shanghai, 200433, China
| | - Wei Shen
- Department of Ophthalmology, Shanghai Changhai Hospital, Shanghai, 200433, China
| | - Hongyuan Song
- Department of Ophthalmology, Shanghai Changhai Hospital, Shanghai, 200433, China
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20
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Gómez-Montalvo J, de Obeso Fernández Del Valle A, De la Cruz Gutiérrez LF, Gonzalez-Meljem JM, Scheckhuber CQ. Replicative aging in yeast involves dynamic intron retention patterns associated with mRNA processing/export and protein ubiquitination. MICROBIAL CELL (GRAZ, AUSTRIA) 2024; 11:69-78. [PMID: 38414808 PMCID: PMC10897858 DOI: 10.15698/mic2024.02.816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 01/25/2024] [Accepted: 02/01/2024] [Indexed: 02/29/2024]
Abstract
Saccharomyces cerevisiae (baker's yeast) has yielded relevant insights into some of the basic mechanisms of organismal aging. Among these are genomic instability, oxidative stress, caloric restriction and mitochondrial dysfunction. Several genes are known to have an impact on the aging process, with corresponding mutants exhibiting short- or long-lived phenotypes. Research dedicated to unraveling the underlying cellular mechanisms can support the identification of conserved mechanisms of aging in other species. One of the hitherto less studied fields in yeast aging is how the organism regulates its gene expression at the transcriptional level. To our knowledge, we present the first investigation into alternative splicing, particularly intron retention, during replicative aging of S. cerevisiae. This was achieved by utilizing the IRFinder algorithm on a previously published RNA-seq data set by Janssens et al. (2015). In the present work, 44 differentially retained introns in 43 genes were identified during replicative aging. We found that genes with altered intron retention do not display significant changes in overall transcript levels. It was possible to functionally assign distinct groups of these genes to the cellular processes of mRNA processing and export (e.g., YRA1) in early and middle-aged yeast, and protein ubiquitination (e.g., UBC5) in older cells. In summary, our work uncovers a previously unexplored layer of the transcriptional program of yeast aging and, more generally, expands the knowledge on the occurrence of alternative splicing in baker's yeast.
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Affiliation(s)
- Jesús Gómez-Montalvo
- Tecnologico de Monterrey, Escuela de Ingeniería y Ciencias, Ave. Eugenio Garza Sada 2501, Monterrey, N.L., México
| | | | | | - Jose Mario Gonzalez-Meljem
- Tecnologico de Monterrey, Escuela de Ingeniería y Ciencias, Ave. Eugenio Garza Sada 2501, Monterrey, N.L., México
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21
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Wang Q, Wang L, Huang Z, Xiao Y, Liu M, Liu H, Yu Y, Liang M, Luo N, Li K, Mishra A, Huang Z. Abalone peptide increases stress resilience and cost-free longevity via SKN-1-governed transcriptional metabolic reprogramming in C. elegans. Aging Cell 2024; 23:e14046. [PMID: 37990605 PMCID: PMC10861207 DOI: 10.1111/acel.14046] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 10/30/2023] [Indexed: 11/23/2023] Open
Abstract
A major goal of healthy aging is to prevent declining resilience and increasing frailty, which are associated with many chronic diseases and deterioration of stress response. Here, we propose a loss-or-gain survival model, represented by the ratio of cumulative stress span to life span, to quantify stress resilience at organismal level. As a proof of concept, this is demonstrated by reduced survival resilience in Caenorhabditis elegans exposed to exogenous oxidative stress induced by paraquat or with endogenous proteotoxic stress caused by polyglutamine or amyloid-β aggregation. Based on this, we reveal that a hidden peptide ("cryptide")-AbaPep#07 (SETYELRK)-derived from abalone hemocyanin not only enhances survival resilience against paraquat-induced oxidative stress but also rescues proteotoxicity-mediated behavioral deficits in C. elegans, indicating its capacity against stress and neurodegeneration. Interestingly, AbaPep#07 is also found to increase cost-free longevity and age-related physical fitness in nematodes. We then demonstrate that AbaPep#07 can promote nuclear localization of SKN-1/Nrf, but not DAF-16/FOXO, transcription factor. In contrast to its effects in wild-type nematodes, AbaPep#07 cannot increase oxidative stress survival and physical motility in loss-of-function skn-1 mutant, suggesting an SKN-1/Nrf-dependent fashion of these effects. Further investigation reveals that AbaPep#07 can induce transcriptional activation of immune defense, lipid metabolism, and metabolic detoxification pathways, including many SKN-1/Nrf target genes. Together, our findings demonstrate that AbaPep#07 is able to boost stress resilience and reduce behavioral frailty via SKN-1/Nrf-governed transcriptional reprogramming, and provide an insight into the health-promoting potential of antioxidant cryptides as geroprotectors in aging and associated conditions.
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Affiliation(s)
- Qiangqiang Wang
- Institute for Food Nutrition and Human Health, School of Food Science and Engineering, South China University of TechnologyGuangzhouChina
- Guangdong Province Key Laboratory for BiocosmeticsGuangzhouChina
| | - Liangyi Wang
- Institute for Food Nutrition and Human Health, School of Food Science and Engineering, South China University of TechnologyGuangzhouChina
- Center for Bioresources and Drug Discovery, School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical UniversityGuangzhouChina
| | - Ziliang Huang
- Institute for Food Nutrition and Human Health, School of Food Science and Engineering, South China University of TechnologyGuangzhouChina
- Center for Bioresources and Drug Discovery, School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical UniversityGuangzhouChina
| | - Yue Xiao
- Institute for Food Nutrition and Human Health, School of Food Science and Engineering, South China University of TechnologyGuangzhouChina
- Guangdong Province Key Laboratory for BiocosmeticsGuangzhouChina
| | - Mao Liu
- Institute for Food Nutrition and Human Health, School of Food Science and Engineering, South China University of TechnologyGuangzhouChina
- Guangdong Province Key Laboratory for BiocosmeticsGuangzhouChina
| | - Huihui Liu
- Institute for Food Nutrition and Human Health, School of Food Science and Engineering, South China University of TechnologyGuangzhouChina
- Center for Bioresources and Drug Discovery, School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical UniversityGuangzhouChina
| | - Yi Yu
- Research and Development Center, Infinitus (China) Company LtdGuangzhouChina
| | - Ming Liang
- Research and Development Center, Infinitus (China) Company LtdGuangzhouChina
| | - Ning Luo
- Institute of Chinese Medicinal Sciences, Guangdong Pharmaceutical UniversityGuangzhouChina
| | - Kunping Li
- Institute of Chinese Medicinal Sciences, Guangdong Pharmaceutical UniversityGuangzhouChina
| | - Ajay Mishra
- European Bioinformatics InstituteCambridgeUK
| | - Zebo Huang
- Institute for Food Nutrition and Human Health, School of Food Science and Engineering, South China University of TechnologyGuangzhouChina
- Guangdong Province Key Laboratory for BiocosmeticsGuangzhouChina
- Center for Bioresources and Drug Discovery, School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical UniversityGuangzhouChina
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22
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Wang Y, Liu Z, Yin X, Liu S, Wang K, Wan R, Chen H, Li X, Huang B. Variation in Bombyx mori immune response against fungal pathogen Beauveria bassiana with variability in cell wall β-1,3-glucan. INSECT SCIENCE 2024; 31:211-224. [PMID: 37350124 DOI: 10.1111/1744-7917.13209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 04/03/2023] [Accepted: 04/04/2023] [Indexed: 06/24/2023]
Abstract
Entomopathogenic fungi are protected by a cell wall with dynamic structure for adapting to various environmental conditions. β-1,3-Glucan recognition proteins activate the innate immune system of insects by recognizing surface molecules of fungi. However, the associations between pathogenicity and the different components of entomopathogenic fungal cell walls remain unclear. Three Beauveria bassiana strains were selected that have significantly differing virulence against Bombyx mori. The molecular mechanisms underlying the immune response in B. mori were investigated using RNA sequencing, which revealed differences in the immune response to different B. bassiana strains at 12 h post-infection. Immunofluorescence assays revealed that β-1,3-glucan content had an opposite trend to that of fungal virulence. β-1,3-Glucan injection upregulated BmβGRP4 expression and significantly reduced the virulence of the high-virulence strain but not that of the medium-virulence or low-virulence strains. BmβGRP4 silencing in B. mori with RNA interference resulted in the opposite virulence pattern, indicating that the virulence of B. bassiana was affected by the cell walls' content of β-1,3-glucan, which could be recognized by BmβGRP4. Furthermore, interference with the gene CnA (calcineurin catalytic A subunit) involved in β-1,3-glucan synthesis eliminated differences in virulence between B. bassiana strains. These results indicate that strains of a single species of pathogenic fungi that have differing cell wall components are recognized differently by the innate immune system of B. mori.
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Affiliation(s)
- Yulong Wang
- Anhui Provincial Key Laboratory of Microbial Pest Control, Anhui Agricultural University, Hefei, China
| | - Zhen Liu
- Anhui Provincial Key Laboratory of Microbial Pest Control, Anhui Agricultural University, Hefei, China
| | - Xuebing Yin
- Anhui Provincial Key Laboratory of Microbial Pest Control, Anhui Agricultural University, Hefei, China
| | - Shihong Liu
- Anhui Provincial Key Laboratory of Microbial Pest Control, Anhui Agricultural University, Hefei, China
| | - Kai Wang
- Anhui Provincial Key Laboratory of Microbial Pest Control, Anhui Agricultural University, Hefei, China
| | - Rongjie Wan
- Anhui Provincial Key Laboratory of Microbial Pest Control, Anhui Agricultural University, Hefei, China
| | - Haoran Chen
- Anhui Provincial Key Laboratory of Microbial Pest Control, Anhui Agricultural University, Hefei, China
| | - Xinyang Li
- Anhui Provincial Key Laboratory of Microbial Pest Control, Anhui Agricultural University, Hefei, China
| | - Bo Huang
- Anhui Provincial Key Laboratory of Microbial Pest Control, Anhui Agricultural University, Hefei, China
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23
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Jian J, Wu Z, Silva-Núñez A, Li X, Zheng X, Luo B, Liu Y, Fang X, Workman CT, Larsen TO, Hansen PJ, Sonnenschein EC. Long-read genome sequencing provides novel insights into the harmful algal bloom species Prymnesium parvum. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 908:168042. [PMID: 37898203 DOI: 10.1016/j.scitotenv.2023.168042] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 10/20/2023] [Accepted: 10/20/2023] [Indexed: 10/30/2023]
Abstract
Prymnesium parvum is a toxin-producing haptophyte that causes harmful algal blooms worldwide, which are often associated with massive fish-kills and subsequent economic losses. In here, we present nuclear and plastid genome assemblies using PacBio HiFi long reads and DNBseq short reads for the two P. parvum strains UTEX 2797 and CCMP 3037, representing producers of type A prymnesins. Our results show that the P. parvum strains have a moderate haptophyte genome size of 97.56 and 107.32 Mb. The genome assemblies present one of highest contiguous assembled contig sequences to date consisting of 463 and 362 contigs with a contig N50 of 596.99 kb and 968.39 kb for strain UTEX 2797 and CCMP 3037, respectively. The assembled contigs of UTEX 2797 and CCMP 3037 were anchored to 34 scaffolds, with a scaffold N50 of 5.35 Mb and 3.61 Mb, respectively, accounting for 93.2 % and 97.9 % of the total length. Each plastid genome comprises a circular contig. A total of 20,578 and 19,426 protein-coding genes were annotated for UTEX 2797 and CCMP 3037. The expanded gene family analysis showed that starch and sucrose metabolism, sulfur metabolism, energy metabolism and ABC transporters are involved in the evolution of P. parvum. Polyketide synthase (PKS) genes responsible for the production of secondary metabolites such as prymnesins displayed different expression patterns under nutrient limitation. Overlap with repeats and horizontal gene transfer may be two contributing factors to the high number of PKS genes found in this species. The two high quality P. parvum genomes will serve as valuable resources for ecological, genetic, and toxicological studies of haptophytes that can be used to monitor and potentially manage harmful blooms of ichthyotoxic P. parvum in the future.
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Affiliation(s)
- Jianbo Jian
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark; BGI-Genomics, BGI-Shenzhen, Shenzhen, China
| | | | - Arisbe Silva-Núñez
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark; Tecnologico de Monterrey, School of Engineering and Science, Monterrey, Nuevo León, Mexico
| | - Xiaohui Li
- BGI-Genomics, BGI-Shenzhen, Shenzhen, China
| | | | - Bei Luo
- BGI-Genomics, BGI-Shenzhen, Shenzhen, China
| | - Yun Liu
- BGI-Genomics, BGI-Shenzhen, Shenzhen, China
| | | | - Christopher T Workman
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Thomas Ostenfeld Larsen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Per Juel Hansen
- Marine Biological Section, University of Copenhagen, Helsingør, Denmark
| | - Eva C Sonnenschein
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark; Department of Biosciences, Swansea University, Swansea, United Kingdom.
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24
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Wang S, Zhang Y, Yang X, Wang K, Yang X, Zhang B, Zhang B, Bie Q. Betulinic acid arrests cell cycle at G2/M phase by up-regulating metallothionein 1G inhibiting proliferation of colon cancer cells. Heliyon 2024; 10:e23833. [PMID: 38261922 PMCID: PMC10797151 DOI: 10.1016/j.heliyon.2023.e23833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 12/11/2023] [Accepted: 12/13/2023] [Indexed: 01/25/2024] Open
Abstract
Betulinic acid (BA) is a pentacyclic triterpene found in many plant species and has a broad-spectrum anti-tumor effect in various cancers, including colon cancer (CRC). However, its anticancer mechanism in CRC is no clear. RNA sequencing and bioinformatics analysis showed BA up-regulated 378 genes and down-regulated 137 genes in HT29 cells, while 2303 up-regulated and 1041 down-regulated genes were found in SW480 cells. KEGG enrichment analysis showed BA significantly stimulated the expression of metallothionein 1 (MT1) family genes in both HT29 and SW480 cells. Metallothionein 1G (MT1G) was the gene with the highest upregulation of MT1 family genes induced by BA dose-dependently. High MT1G expression enhanced the sensitivity of CRC cells to BA, whereas, MT1G knockdown had the opposite effect in vitro and in vivo. GSEA and GSCA showed genes affected by BA treatment were involved in cell cycle and G2/M checkpoint in CRC. Flow cytometry further exhibited BA reduced the percentage of G0/G1 cells and increased the percentage of G2/M cells in a dose-dependent manner, which could be rescued by MT1G knockdown. Moreover, MT1G also counteracted the BA-induced changes in cell cycle-related proteins (CDK2 and CDK4) and p-Rb. In summary, we have revealed a new anti-tumor mechanism that BA altered the cell cycle progression of CRC cells by upregulating MT1G gene, thereby inhibiting the proliferation of CRC cells.
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Affiliation(s)
- Sen Wang
- Department of Laboratory Medicine, Affiliated Hospital of Jining Medical University, Jining Medical University, Jining, Shandong, China
- Postdoctoral Mobile Station of Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China
| | - Yuqin Zhang
- Blood Transfusion Department, Affiliated Hospital of Jining Medical University, Jining Medical University, Jining, Shandong, China
| | - Xiaxia Yang
- Department of Laboratory Medicine, Affiliated Hospital of Jining Medical University, Jining Medical University, Jining, Shandong, China
| | - Kexin Wang
- Department of Radiology, Affiliated Hospital of Jining Medical University, Jining Medical University, Jining, Shandong, China
| | - Xiao Yang
- Department of Laboratory Medicine, Affiliated Hospital of Jining Medical University, Jining Medical University, Jining, Shandong, China
| | - Baogui Zhang
- Gastrointestinal Surgery, Affiliated Hospital of Jining Medical University, Jining Medical University, Jining, Shandong, China
| | - Bin Zhang
- Department of Laboratory Medicine, Affiliated Hospital of Jining Medical University, Jining Medical University, Jining, Shandong, China
- Institute of Forensic Medicine and Laboratory Medicine, Jining Medical University, Jining, Shandong, China
| | - Qingli Bie
- Department of Laboratory Medicine, Affiliated Hospital of Jining Medical University, Jining Medical University, Jining, Shandong, China
- Postdoctoral Mobile Station of Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China
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25
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Zhang W, Xu Y, Jing L, Jiang B, Wang Q, Wang Y. Preliminary Study on the Formation Mechanism of Malformed Sweet Cherry ( Prunus avium L.) Fruits in Southern China Using Transcriptome and Metabolome Data. Int J Mol Sci 2023; 25:153. [PMID: 38203324 PMCID: PMC10779264 DOI: 10.3390/ijms25010153] [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: 11/04/2023] [Revised: 12/13/2023] [Accepted: 12/18/2023] [Indexed: 01/12/2024] Open
Abstract
Gibberellin (GA) is an important plant hormone that is involved in various physiological processes during plant development. Sweet cherries planted in southern China have always encountered difficulty in bearing fruit. In recent years, gibberellin has successfully solved this problem, but there has also been an increase in malformed fruits. This study mainly explores the mechanism of malformed fruit formation in sweet cherries. By analyzing the synthesis pathway of gibberellin using metabolomics and transcriptomics, the relationship between gibberellin and the formation mechanism of deformed fruit was preliminarily determined. The results showed that the content of GA3 in malformed fruits was significantly higher than in normal fruits. The differentially expressed genes in the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway were mainly enriched in pathways such as "plant hormone signal transduction", "diterpenoid biosynthesis", and "carotenoid biosynthesis". Using Quantitative Real-Time Reverse Transcription PCR (qRT-PCR) analysis, the gibberellin hydrolase gene GA2ox and gibberellin synthase genes GA20ox and GA3ox were found to be significantly up-regulated. Therefore, we speculate that the formation of malformed fruits in sweet cherries may be related to the accumulation of GA3. This lays the foundation for further research on the mechanism of malformed sweet cherry fruits.
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Affiliation(s)
- Wangshu Zhang
- Ningbo Innovation Center, Zhejiang University, Ningbo 315000, China; (Y.X.); (B.J.); (Q.W.); (Y.W.)
- National & Local Joint Engineering Laboratory of Intelligent Food Technology and Equipment, College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China
| | - Yue Xu
- Ningbo Innovation Center, Zhejiang University, Ningbo 315000, China; (Y.X.); (B.J.); (Q.W.); (Y.W.)
| | - Luyang Jing
- Ningbo Innovation Center, Zhejiang University, Ningbo 315000, China; (Y.X.); (B.J.); (Q.W.); (Y.W.)
| | - Baoxin Jiang
- Ningbo Innovation Center, Zhejiang University, Ningbo 315000, China; (Y.X.); (B.J.); (Q.W.); (Y.W.)
| | - Qinghao Wang
- Ningbo Innovation Center, Zhejiang University, Ningbo 315000, China; (Y.X.); (B.J.); (Q.W.); (Y.W.)
| | - Yuxi Wang
- Ningbo Innovation Center, Zhejiang University, Ningbo 315000, China; (Y.X.); (B.J.); (Q.W.); (Y.W.)
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26
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Cao J, Wang W, Xu X, Li SY, Zheng Y, Li DD. Identification and Analysis of MADS-Box Genes Expressed in the Mesocarp of Oil Palm Fruit (Elaeis guineensis Jacq.). Biochem Genet 2023; 61:2382-2400. [PMID: 37060482 DOI: 10.1007/s10528-023-10376-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: 02/27/2021] [Accepted: 03/14/2023] [Indexed: 04/16/2023]
Abstract
Oil palm (Elaeis guineensis) is the most important tropical oil-bearing crop species worldwide. MADS-box proteins, which play crucial roles in plant growth and development and are involved in various physiological and biochemical processes, compose one of the largest families of plant transcription factors. In this study, 42 MADS-box genes were screened from the mesocarp transcriptome database of oil palm fruit, and their phylogenetic relationships with Arabidopsis thaliana MADS-box genes were analyzed. Based on the results, MADS-box genes from oil palm mesocarp were classified into four groups: MIKCc-type, MIKC*-type, Mα-type, and Mγ-type MADS-box genes. Members of the subfamilies were classified according to the presence of three specific protein motifs. To explore the differential expression of the MADS-box genes, the dynamic expression of all selected MADS-box genes in oil palm was measured by RNA-seq. The high expression of specific MADS-box genes in the mesocarp of oil palm during different developmental stages indicates that those genes may play important roles in the cell division of and metabolite accumulation in the fruit and could become important targets for fruit development and oil accumulation research in oil palm.
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Affiliation(s)
- Jiaqi Cao
- Sanya Nanfan Research Institute, College of Tropical Crops, Hainan University, Hainan, 570228, China
| | - Wei Wang
- Sanya Nanfan Research Institute, College of Tropical Crops, Hainan University, Hainan, 570228, China
| | - Xin Xu
- Sanya Nanfan Research Institute, College of Tropical Crops, Hainan University, Hainan, 570228, China
| | - Si-Yu Li
- Sanya Nanfan Research Institute, College of Tropical Crops, Hainan University, Hainan, 570228, China
| | - Yusheng Zheng
- Sanya Nanfan Research Institute, College of Tropical Crops, Hainan University, Hainan, 570228, China
| | - Dong-Dong Li
- Sanya Nanfan Research Institute, College of Tropical Crops, Hainan University, Hainan, 570228, China.
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27
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Zafar UB, Shahzaib M, Atif RM, Khan SH, Niaz MZ, Shahzad K, Chughtai N, Awan FS, Azhar MT, Rana IA. De novo transcriptome assembly of Dalbergia sissoo Roxb. (Fabaceae) under Botryodiplodia theobromae-induced dieback disease. Sci Rep 2023; 13:20503. [PMID: 37993468 PMCID: PMC10665356 DOI: 10.1038/s41598-023-45982-8] [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: 05/27/2023] [Accepted: 10/26/2023] [Indexed: 11/24/2023] Open
Abstract
Dalbergia sissoo Roxb. (Shisham) is a timber-producing species of economic, cultural, and medicinal importance in the Indian subcontinent. In the past few decades, Shisham's dieback disease caused by the fungus Botryodiplodia theobromae has become an evolving issue in the subcontinent endangering its survival. To gain insights into this issue, a standard transcriptome assembly was deployed to assess the response of D. sissoo at the transcriptomic level under the stress of B. theobromae infection. For RNA isolation, the control and infected leaf tissue samples were taken from 1-year-old greenhouse-grown D. sissoo plants after 20 days of stem-base spore inoculation. cDNA synthesis was performed from these freshly isolated RNA samples that were then sent for sequencing. About 18.14 Gb (Giga base) of data was generated using the BGISEQ-500 sequencing platform. In terms of Unigenes, 513,821 were identified after a combined assembly of all samples and then filtering the abundance. The total length of Unigenes, their average length, N50, and GC-content were 310,523,693 bp, 604 bp, 1,101 bp, and 39.95% respectively. The Unigenes were annotated using 7 functional databases i.e., 200,355 (NR: 38.99%), 164,973 (NT: 32.11%), 123,733 (Swissprot: 24.08%), 142,580 (KOG: 27.75%), 139,588 (KEGG: 27.17%), 99,752 (GO: 19.41%), and 137,281 (InterPro: 26.72%). Furthermore, the Transdecoder detected 115,762 CDS. In terms of SSR (Simple Sequence Repeat) markers, 62,863 of them were distributed on 51,508 Unigenes and on the predicted 4673 TF (Transcription Factor) coding Unigenes. A total of 16,018 up- and 19,530 down-regulated Differentially Expressed Genes (DEGs) were also identified. Moreover, the Plant Resistance Genes (PRGs) had a count of 9230. We are hopeful that in the future, these identified Unigenes, SSR markers, DEGs and PRGs will provide the prerequisites for managing Shisham dieback disease, its breeding, and in tree improvement programs.
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Affiliation(s)
- Ummul Buneen Zafar
- Centre of Agricultural Biochemistry and Biotechnology, University of Agriculture, Faisalabad, Faisalabad, 38000, Punjab, Pakistan
- Centre for Advanced Studies in Agriculture and Food Security, University of Agriculture, Faisalabad, Faisalabad, 38000, Punjab, Pakistan
| | - Muhammad Shahzaib
- Centre of Agricultural Biochemistry and Biotechnology, University of Agriculture, Faisalabad, Faisalabad, 38000, Punjab, Pakistan
- Centre for Advanced Studies in Agriculture and Food Security, University of Agriculture, Faisalabad, Faisalabad, 38000, Punjab, Pakistan
| | - Rana Muhammad Atif
- Centre for Advanced Studies in Agriculture and Food Security, University of Agriculture, Faisalabad, Faisalabad, 38000, Punjab, Pakistan
- Department of Plant Breeding and Genetics, University of Agriculture, Faisalabad, Faisalabad, 38000, Punjab, Pakistan
| | - Sultan Habibullah Khan
- Centre of Agricultural Biochemistry and Biotechnology, University of Agriculture, Faisalabad, Faisalabad, 38000, Punjab, Pakistan
- Centre for Advanced Studies in Agriculture and Food Security, University of Agriculture, Faisalabad, Faisalabad, 38000, Punjab, Pakistan
- National Center for Genome Editing (Gene Editing of Biological Agents for Nutritional, Biochemicals and Therapeutic Purposes), University of Agriculture, Faisalabad, Punjab, Pakistan
| | - Muhammad Zeeshan Niaz
- Plant Pathology Research Institute, Ayub Agriculture Research Institute, Faisalabad, 38850, Punjab, Pakistan
| | - Khalid Shahzad
- Punjab Forestry Research Institute, Faisalabad, 37620, Punjab, Pakistan
| | - Nighat Chughtai
- Punjab Forestry Research Institute, Faisalabad, 37620, Punjab, Pakistan
| | - Faisal Saeed Awan
- Centre of Agricultural Biochemistry and Biotechnology, University of Agriculture, Faisalabad, Faisalabad, 38000, Punjab, Pakistan
| | - Muhammad Tehseen Azhar
- Department of Plant Breeding and Genetics, University of Agriculture, Faisalabad, Faisalabad, 38000, Punjab, Pakistan
| | - Iqrar Ahmad Rana
- Centre of Agricultural Biochemistry and Biotechnology, University of Agriculture, Faisalabad, Faisalabad, 38000, Punjab, Pakistan.
- Centre for Advanced Studies in Agriculture and Food Security, University of Agriculture, Faisalabad, Faisalabad, 38000, Punjab, Pakistan.
- National Center for Genome Editing (Gene Editing of Biological Agents for Nutritional, Biochemicals and Therapeutic Purposes), University of Agriculture, Faisalabad, Punjab, Pakistan.
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Han C, Chen G, Zheng D, Feng N. Transcriptomic and metabolomic analyses reveal that ABA increases the salt tolerance of rice significantly correlated with jasmonic acid biosynthesis and flavonoid biosynthesis. Sci Rep 2023; 13:20365. [PMID: 37990109 PMCID: PMC10663488 DOI: 10.1038/s41598-023-47657-w] [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: 06/09/2023] [Accepted: 11/16/2023] [Indexed: 11/23/2023] Open
Abstract
Abscisic acid (ABA) has been shown to mitigate the deleterious effects of abiotic stresses and to regulate plant growth and development. Salinity is one of the important abiotic stresses affecting plant cell metabolism and physiology, which causes serious damages to crops. In this study, we investigated the protective role of exogenous ABA on leaves in response to salinity stress using rice seedlings (two leaf-one heart) subjected to three treatments: ZCK (control), ZS (50 mM NaCl), and ZSA (5 mg L-1 ABA + 50 mM NaCl). We carried out transcriptomic and metabolomic analyses to identify the molecular mechanisms by which ABA protects plants against salt stress. Results showed that 1159 differentially expressed genes (DEGs) (916 up-regulated, 243 down-regulated) and 63 differentially accumulated metabolites (DAMs) (42 up-regulated, 21 down-regulated) were identified between the ZS and ZSA treatments, respectively. In addition, ABA pretreatment regulated the expression pattern of genes responsible for oxidation redox, starch and sucrose metabolism, and phenylpropanoid biosynthesis. The combined transcriptomic and metabolomic analysis revealed that 16 DEGs and 2 DAMs were involved in Flavonoid biosynthesis and 8 DEGs and 2 DAMs were involved alpha-Linolenic acid metabolism which are responsible for salinity stress tolerance through induced by exogenous ABA. Overall, ABA could enhance rice leaves growth and development mainly by regulating flavonoid biosynthesis and linoleic acid metabolism pathway.
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Affiliation(s)
- Chunning Han
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088, China
- Shenzhen Research Institute of Guangdong Ocean University, Shenzhen, 518108, China
- South China Center of National Salt-Alkali Tolerant Rice Technology Innovation Center, Zhanjiang, 524088, Guangdong, China
| | - Guanjie Chen
- School of Tropical Crops, Hainan University, Haikou, 570228, China
| | - Dianfeng Zheng
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088, China.
- Shenzhen Research Institute of Guangdong Ocean University, Shenzhen, 518108, China.
- South China Center of National Salt-Alkali Tolerant Rice Technology Innovation Center, Zhanjiang, 524088, Guangdong, China.
| | - Naijie Feng
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088, China.
- Shenzhen Research Institute of Guangdong Ocean University, Shenzhen, 518108, China.
- South China Center of National Salt-Alkali Tolerant Rice Technology Innovation Center, Zhanjiang, 524088, Guangdong, China.
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Zhang Y, Ritonga FN, Zhang S, Wang F, Li J, Gao J. Genome-Wide Identification of the NRT1 Family Members and Their Expression under Low-Nitrate Conditions in Chinese Cabbage ( Brassica rapa L. ssp. pekinensis). PLANTS (BASEL, SWITZERLAND) 2023; 12:3882. [PMID: 38005779 PMCID: PMC10675746 DOI: 10.3390/plants12223882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 11/06/2023] [Accepted: 11/09/2023] [Indexed: 11/26/2023]
Abstract
Nitrate transporters (NRTs) actively take up and transform nitrate (N) to form a large family with many members and distinct functions in plant growth and development. However, few studies have identified them in the context of low nitrate concentrations in Chinese cabbage (Brassica rapa L. ssp. Pekinensis), an important vegetable in China. This study focuses on the identification and analysis of the nitrate transporter 1 (NRT1) gene family as well as various aspects, including its phylogenic distribution, chromosomal position, gene structure, conserved motifs, and duplication pattern. Using bioinformatics methods, we identified and analyzed 84 BrNRT1 genes distributed on ten chromosomes. Furthermore, we conducted an analysis of the expression profile of the NRT1 gene in various tissues of Chinese cabbage exposed to varying nitrate concentrations. A phylogenetic analysis revealed that BrNRT1s members are distributed in six distinct groups. Based on an analysis of gene structure and conserved motifs, it can be inferred that BrNRT1 exhibits a generally conserved structural pattern. The promoters of BrNRT1 were discovered to contain moosefs (MFS) elements, suggesting their potential role in the regulation of NO3- transport across the cell membrane in Chinese cabbage. A transcriptome study and a subsequent RT-qPCR analysis revealed that the expression patterns of some BrNRT1 genes were distinct to specific tissues. This observation implies these genes may contribute to nitrate uptake and transport in various tissues or organs. The results offer fundamental insights into investigating the NRT1 gene family in Chinese cabbage. These results provide basic information for future research on the functional characterization of NRT1 genes in Chinese cabbage and the elucidation of the molecular mechanisms underlying low nitrogen tolerance in Chinese cabbage.
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Affiliation(s)
- Yihui Zhang
- Shandong Branch of National Vegetable Improvement Center, Institute of Vegetables, Shandong Academy of Agricultural Science, Jinan 250100, China; (Y.Z.); (F.N.R.); (S.Z.); (F.W.)
| | - Faujiah Nurhasanah Ritonga
- Shandong Branch of National Vegetable Improvement Center, Institute of Vegetables, Shandong Academy of Agricultural Science, Jinan 250100, China; (Y.Z.); (F.N.R.); (S.Z.); (F.W.)
- Graduate School, Padjadjaran University, Bandung 40132, West Java, Indonesia
| | - Shu Zhang
- Shandong Branch of National Vegetable Improvement Center, Institute of Vegetables, Shandong Academy of Agricultural Science, Jinan 250100, China; (Y.Z.); (F.N.R.); (S.Z.); (F.W.)
| | - Fengde Wang
- Shandong Branch of National Vegetable Improvement Center, Institute of Vegetables, Shandong Academy of Agricultural Science, Jinan 250100, China; (Y.Z.); (F.N.R.); (S.Z.); (F.W.)
| | - Jingjuan Li
- Shandong Branch of National Vegetable Improvement Center, Institute of Vegetables, Shandong Academy of Agricultural Science, Jinan 250100, China; (Y.Z.); (F.N.R.); (S.Z.); (F.W.)
| | - Jianwei Gao
- Shandong Branch of National Vegetable Improvement Center, Institute of Vegetables, Shandong Academy of Agricultural Science, Jinan 250100, China; (Y.Z.); (F.N.R.); (S.Z.); (F.W.)
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Leesombun A, Sungpradit S, Sariya L, Taowan J, Boonmasawai S. Transcriptional Profiling of the Effect of Coleus amboinicus L. Essential Oil against Salmonella Typhimurium Biofilm Formation. Antibiotics (Basel) 2023; 12:1598. [PMID: 37998800 PMCID: PMC10668763 DOI: 10.3390/antibiotics12111598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Revised: 10/30/2023] [Accepted: 11/01/2023] [Indexed: 11/25/2023] Open
Abstract
Salmonella enterica serovar Typhimurium cause infections primarily through foodborne transmission and remains a significant public health concern. The biofilm formation of this bacteria also contributes to their multidrug-resistant nature. Essential oils from medicinal plants are considered potential alternatives to conventional antibiotics. Therefore, this study assessed the antimicrobial and antibiofilm activities of Coleus amboinicus essential oil (EO-CA) against S. Typhimurium ATCC 14028. Seventeen chemical compounds of EO-CA were identified, and carvacrol (38.26%) was found to be the main constituent. The minimum inhibitory concentration (MIC) of EO-CA for S. Typhimurium planktonic growth was 1024 µg/mL while the minimum bactericidal concentration was 1024 µg/mL. EO-CA at sub-MIC (≥1/16× MIC) exhibited antibiofilm activity against the prebiofilm formation of S. Typhimurium at 24 h. Furthermore, EO-CA (≥1/4× MIC) inhibited postbiofilm formation at 24 and 48 h (p < 0.05). Transcriptional profiling revealed that the EO-CA-treated group at 1/2× MIC had 375 differentially expressed genes (DEGs), 106 of which were upregulated and 269 were downregulated. Five significantly downregulated virulent DEGs responsible for motility (flhD, fljB, and fimD), curli fimbriae (csgD), and invasion (hilA) were screened via quantitative reverse transcription PCR (qRT-PCR). This study suggests the potential of EO-CA as an effective antimicrobial agent for combating planktonic and biofilm formation of Salmonella.
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Affiliation(s)
- Arpron Leesombun
- Department of Pre-Clinic and Applied Animal Science, Faculty of Veterinary Science, Mahidol University, Nakhon Pathom 73170, Thailand; (A.L.); (S.S.)
| | - Sivapong Sungpradit
- Department of Pre-Clinic and Applied Animal Science, Faculty of Veterinary Science, Mahidol University, Nakhon Pathom 73170, Thailand; (A.L.); (S.S.)
| | - Ladawan Sariya
- The Monitoring and Surveillance Center for Zoonotic Diseases in Wildlife and Exotic Animals (MoZWE), Faculty of Veterinary Science, Mahidol University, Nakhon Pathom 73170, Thailand; (L.S.); (J.T.)
| | - Jarupha Taowan
- The Monitoring and Surveillance Center for Zoonotic Diseases in Wildlife and Exotic Animals (MoZWE), Faculty of Veterinary Science, Mahidol University, Nakhon Pathom 73170, Thailand; (L.S.); (J.T.)
| | - Sookruetai Boonmasawai
- Department of Pre-Clinic and Applied Animal Science, Faculty of Veterinary Science, Mahidol University, Nakhon Pathom 73170, Thailand; (A.L.); (S.S.)
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Wang Y, Zhou LJ, Song A, Wang Y, Geng Z, Zhao K, Jiang J, Chen S, Chen F. Comparative transcriptome analysis and flavonoid profiling of floral mutants reveals CmMYB11 regulating flavonoid biosynthesis in chrysanthemum. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 336:111837. [PMID: 37611834 DOI: 10.1016/j.plantsci.2023.111837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 08/17/2023] [Accepted: 08/19/2023] [Indexed: 08/25/2023]
Abstract
Flavonoids, of which the major groups are flavones, flavonols, and anthocyanins, confer a variety of colors on plants. Bud sports with variation of floral colors occur occasionally during chrysanthemum cultivation. Although it has been reported that methylation at the promoter of CmMYB6 was related to anthocyanin contents, the regulatory networks of flavonoid biosynthesis still remain largely unknown in mutation of chrysanthemum. We compared phenotypes, pigment composition and transcriptomes in two chrysanthemum cultivars, 'Anastasia Dark Green' and 'Anastasia Pink', and regenerated bud sports of these cultivars with altered floral colors. Increased anthocyanins turned the 'Anastasia Dark Green' mutant red, while decreased anthocyanins turned the 'Anastasia Pink' mutant white. Moreover, total flavonoids were reduced in both mutants. Multiple flavonoid biosynthetic genes and regulatory genes encoding MYBs and bHLHs transcription factors were differentially expressed in pairwise comparisons of transcriptomes in 'Anastasia Dark Green' or 'Anastasia Pink' and their mutants at different flowering stages. Among these regulatory genes, the expression patterns of CmMYB6 and CmbHLH2 correlated to changes of anthocyanin contents, and down-regulation of CmMYB11 correlated to decreased total flavonoid contents in two mutants. CmMYB11 was shown to directly activate the promoter activities of CmCHS2, CmCHI, CmDFR, CmANS, CmFNS, and CmFLS. Furthermore, overexpression of CmMYB11 increased both flavonols and anthocyanins in tobacco petals. Our work provides new insights into regulatory networks involved in flavonoid biosynthesis and coloration in chrysanthemum.
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Affiliation(s)
- Yiguang Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, 210095 Nanjing, China
| | - Li-Jie Zhou
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, 210095 Nanjing, China
| | - Aiping Song
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, 210095 Nanjing, China
| | - Yuxi Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, 210095 Nanjing, China
| | - Zhiqiang Geng
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, 210095 Nanjing, China
| | - Kunkun Zhao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, 210095 Nanjing, China
| | - Jiafu Jiang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, 210095 Nanjing, China
| | - Sumei Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, 210095 Nanjing, China
| | - Fadi Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, 210095 Nanjing, China.
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Hu H, Quan G, Yang F, Du S, Ding S, Lun Y, Chen Q. MicroRNA-96-5p is negatively regulating GPC3 in the metastasis of papillary thyroid cancer. SAGE Open Med 2023; 11:20503121231205710. [PMID: 37915840 PMCID: PMC10617255 DOI: 10.1177/20503121231205710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 09/19/2023] [Indexed: 11/03/2023] Open
Abstract
Backgrounds Papillary thyroid cancer is the most common pathological type of thyroid cancer. miR-96-5p, a member of the miR-183 family, constitute a polycistronic miRNA cluster. In breast cancer, miR-96-5p promotes cell invasion, migration, and proliferation in vitro by inhibiting PTPN9. Moreover, miR-96-5p was reported to function as an oncogene in many cancers. However, whether miR-96-5p is involved in the development of papillary thyroid cancers and its potential mechanism is still unknown. The present study aims to explore the relationship between miR-96-5p and GPC3 expression in the development of papillary thyroid cancers. Methods Transcriptomic sequencing was carried out using six pairs of papillary thyroid cancer and adjacent normal tissues. Quantitative real-time polymerase chain reaction (PCR) experiments were performed to examine the expression of genes. Results In total, there were 1588 up-regulated and 1803 down-regulated differentially expressed genes between papillary thyroid cancer and normal tissues. Gene ontology and Kyoto encyclopedia of genes and genomes analysis revealed that extracellular matrix structure and proteoglycans were mainly involved in papillary thyroid cancer. Among the cluster of proteoglycans, GPC3 was significantly down-regulated in papillary thyroid cancer and is a target of miR-96. Conclusion miR-96-5p participates in the development of papillary thyroid cancer by regulating the expression of GPC3. Thus, targeting miR-96-5p may be a potential therapeutic approach for preventing and treating papillary thyroid cancer.
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Affiliation(s)
- Haibei Hu
- Department of Thyroid and Breast Surgery, Shenzhen Hospital (Guangming), University of Chinese Academy of Sciences, Shenzhen, Guangdong, China
- Key Laboratory of Medical Microecology, Fujian Province University, School of Pharmacy and Medical Technology, Putian University, Putian, Fujian, China
| | - Guangqian Quan
- Department of Breast Surgery, Nanping First Hospital, Fujian Medical University, Nanping, Fujian, China
| | - Feng Yang
- Department of General Surgery, The Third People’s Hospital of Fujian Province, Fuzhou, Fujian, China
| | - Shan Du
- Department of Pathology, Shenzhen Hospital (Guangming), University of Chinese Academy of Sciences, Shenzhen, Guangdong, China
| | - Siqin Ding
- Department of Thyroid and Breast Surgery, Shenzhen Hospital (Guangming), University of Chinese Academy of Sciences, Shenzhen, Guangdong, China
| | - Yongzhi Lun
- Key Laboratory of Medical Microecology, Fujian Province University, School of Pharmacy and Medical Technology, Putian University, Putian, Fujian, China
| | - Qiang Chen
- Department of Thyroid and Breast Surgery, Shenzhen Hospital (Guangming), University of Chinese Academy of Sciences, Shenzhen, Guangdong, China
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Cullen AE, Centner AM, Deitado R, Ismaeel A, Koutakis P, Muller-Delp J, Salazar G. AKT Mediates Adiponectin-Dependent Regulation of VSMC Phenotype. Cells 2023; 12:2493. [PMID: 37887338 PMCID: PMC10605922 DOI: 10.3390/cells12202493] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Revised: 10/11/2023] [Accepted: 10/17/2023] [Indexed: 10/28/2023] Open
Abstract
Adiponectin (adipoq), the most abundant hormone in circulation, has many beneficial effects on the cardiovascular system, in part by preserving the contractile phenotype of vascular smooth muscle cells (VSMCs). However, the lack of adiponectin or its receptor and treatment with recombinant adiponectin have shown contradictory effects on plaque in mice. RNA sequence of Adipoq+/+ and adipoq-/- VSMCs from male aortas identified a critical role for adiponectin in AKT signaling, the extracellular matrix (ECM), and TGF-β signaling. Upregulation of AKT activity mediated proliferation and migration of adipoq-/- cells. Activation of AMPK with metformin or AdipoRon reduced AKT-dependent proliferation and migration of adipoq-/- cells but did not improve the expression of contractile genes. Adiponectin deficiency impaired oxidative phosphorylation (OXPHOS), increased expression of glycolytic enzymes, and elevated mitochondrial reactive oxygen species (ROS) (superoxide, and hydrogen peroxide). Anti-atherogenic mechanisms targeted the ECM in adipoq-/- cells, downregulating MMP2 and 9 and upregulating decorin (DCN) and elastin (ELN). In vivo, the main sex differences in protein expression in aortas involved a more robust upregulation of MMP3 in females than males. Females also showed a reduction in DCN, which was not affected in males. Our study uncovered the AKT/MAPK/TGF-β network as a central regulator of VSMC phenotype.
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Affiliation(s)
- Abigail E. Cullen
- Department of Nutrition and Integrative Physiology, Florida State University, Tallahassee, FL 32306, USA; (A.E.C.); (A.M.C.); (R.D.)
- Department of Human Physiology, University of Oregon, Eugene, OR 97403, USA
| | - Ann M. Centner
- Department of Nutrition and Integrative Physiology, Florida State University, Tallahassee, FL 32306, USA; (A.E.C.); (A.M.C.); (R.D.)
| | - Riley Deitado
- Department of Nutrition and Integrative Physiology, Florida State University, Tallahassee, FL 32306, USA; (A.E.C.); (A.M.C.); (R.D.)
| | - Ahmed Ismaeel
- Department of Physiology, University of Kentucky, Lexington, KY 40536, USA;
| | | | - Judy Muller-Delp
- Department of Biological Sciences, Florida State University, Tallahassee, FL 32306, USA;
| | - Gloria Salazar
- Department of Nutrition and Integrative Physiology, Florida State University, Tallahassee, FL 32306, USA; (A.E.C.); (A.M.C.); (R.D.)
- Center for Advancing Exercise and Nutrition Research on Aging (CAENRA), Florida State University, Tallahassee, FL 32306, USA
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Dai S, Zhang C, Wei X, Wang X, Wen Y, Gao F, Zhao L, Shan B. RNA sequencing reveals the implication of the circRNA-associated ceRNA network in oesophageal squamous cell carcinoma. Carcinogenesis 2023; 44:596-609. [PMID: 37402652 DOI: 10.1093/carcin/bgad050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 06/05/2023] [Accepted: 07/03/2023] [Indexed: 07/06/2023] Open
Abstract
Circular RNAs (circRNAs) have attracted increasing attention in cancer research. However, there are few studies about the high-throughput sequencing for clinical cohorts focussing on the expression characteristics and regulatory networks of circRNAs in oesophageal squamous cell carcinoma (ESCC) until now. Present study aim to comprehensively recognize the functional and mechanistic patterns of circRNA through constructing a circRNA-related competing endogenous RNA (ceRNA) network in ESCC. Summarily, RNA high-throughput sequencing was adopted to assess the circRNA, miRNA and mRNA expression profiles in ESCC. Through bioinformatics methods, a circRNA-miRNA-mRNA coexpression network was constructed and hub genes was identified. Finally, cellular function experiments combined with bioinformatics analysis were conducted to verify the identified circRNA was involved in the progression of ESCC through ceRNA mechanism. In this study, we established a ceRNA regulatory network, including 5 circRNAs, 7 miRNAs and 197 target mRNAs, and 20 hub genes were screened and identified to exert important roles in the progression of ESCC. As a verification, hsa_circ_0002470 (circIFI6) was revealed to be highly expressed in ESCC and regulate the expression of hub genes by absorbing miR-497-5p and miR-195-5p through ceRNA mechanism. Our results further indicated that silencing of circIFI6 repressed proliferation and migration of ESCC cells, highlighting the tumour promotion effects of circIFI6 in ESCC. Collectively, our study contributes a new insight into the progression of ESCC from the perspective of the circRNA-miRNA-mRNA network, shedding light on the circRNA research in ESCC.
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Affiliation(s)
- Suli Dai
- Research Center, The Fourth Hospital of Hebei Medical University, Jiankang Road 12, Shijiazhuang 050011, China
- Key Laboratory of Tumor Gene Diagnosis, Prevention and Therapy; Clinical Oncology Research Center, Hebei Province, The Fourth Hospital of Hebei Medical University, Shijiazhuang 050011, China
| | - Cong Zhang
- Research Center, The Fourth Hospital of Hebei Medical University, Jiankang Road 12, Shijiazhuang 050011, China
- Key Laboratory of Tumor Gene Diagnosis, Prevention and Therapy; Clinical Oncology Research Center, Hebei Province, The Fourth Hospital of Hebei Medical University, Shijiazhuang 050011, China
| | - Xiaojian Wei
- Research Center, The Fourth Hospital of Hebei Medical University, Jiankang Road 12, Shijiazhuang 050011, China
- Key Laboratory of Tumor Gene Diagnosis, Prevention and Therapy; Clinical Oncology Research Center, Hebei Province, The Fourth Hospital of Hebei Medical University, Shijiazhuang 050011, China
| | - Xiaohan Wang
- Research Center, The Fourth Hospital of Hebei Medical University, Jiankang Road 12, Shijiazhuang 050011, China
- Key Laboratory of Tumor Gene Diagnosis, Prevention and Therapy; Clinical Oncology Research Center, Hebei Province, The Fourth Hospital of Hebei Medical University, Shijiazhuang 050011, China
| | - Yang Wen
- Research Center, The Fourth Hospital of Hebei Medical University, Jiankang Road 12, Shijiazhuang 050011, China
- Key Laboratory of Tumor Gene Diagnosis, Prevention and Therapy; Clinical Oncology Research Center, Hebei Province, The Fourth Hospital of Hebei Medical University, Shijiazhuang 050011, China
| | - Feng Gao
- Thoracic Surgery Department, The Fourth Hospital of Hebei Medical University, Jiankang Road 12, Shijiazhuang 050011, China
| | - Lianmei Zhao
- Research Center, The Fourth Hospital of Hebei Medical University, Jiankang Road 12, Shijiazhuang 050011, China
- Key Laboratory of Tumor Gene Diagnosis, Prevention and Therapy; Clinical Oncology Research Center, Hebei Province, The Fourth Hospital of Hebei Medical University, Shijiazhuang 050011, China
| | - Baoen Shan
- Research Center, The Fourth Hospital of Hebei Medical University, Jiankang Road 12, Shijiazhuang 050011, China
- Key Laboratory of Tumor Gene Diagnosis, Prevention and Therapy; Clinical Oncology Research Center, Hebei Province, The Fourth Hospital of Hebei Medical University, Shijiazhuang 050011, China
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Provasek VE, Kodavati M, Guo W, Wang H, Boldogh I, Van Den Bosch L, Britz G, Hegde ML. lncRNA Sequencing Reveals Neurodegeneration-Associated FUS Mutations Alter Transcriptional Landscape of iPS Cells That Persists in Motor Neurons. Cells 2023; 12:2461. [PMID: 37887305 PMCID: PMC10604943 DOI: 10.3390/cells12202461] [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: 09/18/2023] [Revised: 10/13/2023] [Accepted: 10/13/2023] [Indexed: 10/28/2023] Open
Abstract
Fused-in sarcoma (FUS) gene mutations have been implicated in amyotrophic lateral sclerosis (ALS). This study aimed to investigate the impact of FUS mutations (R521H and P525L) on the transcriptome of induced pluripotent stem cells (iPSCs) and iPSC-derived motor neurons (iMNs). Using RNA sequencing (RNA Seq), we characterized differentially expressed genes (DEGs) and differentially expressed lncRNAs (DELs) and subsequently predicted lncRNA-mRNA target pairs (TAR pairs). Our results show that FUS mutations significantly altered the expression profiles of mRNAs and lncRNAs in iPSCs. Using this large dataset, we identified and verified six key differentially regulated TAR pairs in iPSCs that were also altered in iMNs. These target transcripts included: GPR149, NR4A, LMO3, SLC15A4, ZNF404, and CRACD. These findings indicated that selected mutant FUS-induced transcriptional alterations persist from iPSCs into differentiated iMNs. Functional enrichment analyses of DEGs indicated pathways associated with neuronal development and carcinogenesis as likely altered by these FUS mutations. Furthermore, ingenuity pathway analysis (IPA) and GO network analysis of lncRNA-targeted mRNAs indicated associations between RNA metabolism, lncRNA regulation, and DNA damage repair. Our findings provide insights into potential molecular mechanisms underlying the pathophysiology of ALS-associated FUS mutations and suggest potential therapeutic targets for the treatment of ALS.
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Affiliation(s)
- Vincent E. Provasek
- Division of DNA Repair Research within the Center for Neuroregeneration, Department of Neurosurgery, Houston Methodist Research Institute, Houston, TX 77030, USA; (V.E.P.); (M.K.); (H.W.)
- School of Medicine, Texas A&M University, College Station, TX 77843, USA
| | - Manohar Kodavati
- Division of DNA Repair Research within the Center for Neuroregeneration, Department of Neurosurgery, Houston Methodist Research Institute, Houston, TX 77030, USA; (V.E.P.); (M.K.); (H.W.)
| | - Wenting Guo
- INSERM, UMR-S1118, Mécanismes Centraux et Périphériques de la Neurodégénérescence, Université de Strasbourg, CRBS, 67000 Strasbourg, France;
- VIB, Center for Brain & Disease Research, 3000 Leuven, Belgium
- Leuven Brain Institute (LBI), 3000 Leuven, Belgium
- Stem Cell Institute, Department of Development and Regeneration, KU Leuven, 3000 Leuven, Belgium;
| | - Haibo Wang
- Division of DNA Repair Research within the Center for Neuroregeneration, Department of Neurosurgery, Houston Methodist Research Institute, Houston, TX 77030, USA; (V.E.P.); (M.K.); (H.W.)
| | - Istvan Boldogh
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA;
| | - Ludo Van Den Bosch
- Stem Cell Institute, Department of Development and Regeneration, KU Leuven, 3000 Leuven, Belgium;
| | - Gavin Britz
- Department of Neurosurgery, Houston Methodist Research Institute, Houston, TX 77030, USA;
| | - Muralidhar L. Hegde
- Division of DNA Repair Research within the Center for Neuroregeneration, Department of Neurosurgery, Houston Methodist Research Institute, Houston, TX 77030, USA; (V.E.P.); (M.K.); (H.W.)
- School of Medicine, Texas A&M University, College Station, TX 77843, USA
- Department of Neurosurgery, Weill Cornell Medical College, New York, NY 10065, USA
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Yao T, Huang Y, Huai Z, Liu X, Liu X, Liu Y, Sun H, Pang Y. Response mechanisms to acid stress promote LF82 replication in macrophages. Front Cell Infect Microbiol 2023; 13:1255083. [PMID: 37881369 PMCID: PMC10595154 DOI: 10.3389/fcimb.2023.1255083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Accepted: 09/25/2023] [Indexed: 10/27/2023] Open
Abstract
Background Adherent-invasive E. coli (AIEC) LF82 is capable of adhering to and invading intestinal epithelial cells, as well as replicating within macrophages without inducing host cell death. Methods We compared the transcriptomics of LF82 at pH=7.5 and pH=5.8 by RNA-sequencing, and qRT-PCR verified differentially expressed genes (DEGs). The deletion mutants of DEGs in the treatment group (pH=5.8) compared to the control group (pH=7.5) were constructed by λ recombinant. The replication differences between the mutants and WT infected Raw 264.7 at 24 h.p.i were analyzed by combining LB solid plate count and confocal observation. NH4Cl and chloroquine diphosphate (CQ) were used for acid neutralization to study the effect of pH on the replication of LF82 in macrophages. Na2NO3 was added to RPMI 1640 to study the effect of nitrate on the replication of LF82 in macrophages. 0.3% solid LB was used for flagellar motility assay and Hela was used to study flagellar gene deletion mutants and WT adhesion and invasion ability. Results In this study, we found that infection with LF82 results in acidification of macrophages. Subsequent experiments demonstrated that an intracellular acidic environment is necessary for LF82 replication. Transcriptome and phenotypic analysis showed that high expression of acid shock genes and acid fitness genes promotes LF82 replication in macrophages. Further, we found that the replication of LF82 in macrophages was increased under nitrate treatment, and nitrogen metabolism genes of LF82 were upregulated in acid treatment. The replication in macrophages of ΔnarK, ΔnarXL, ΔnarP, and Δhmp were decreased. In addition, we found that the expression of flagellar genes was downregulated in acidic pH and after LF82 invading macrophages. Motility assay shows that the movement of LF82 on an acidic semisolid agar plate was limited. Further results showed that ΔfliC and ΔfliD decreased in motility, adhesion ability, and invasion of host cells, but no significant effect on replication in macrophages was observed. Conclusion In this study, we simulated the acidic environment in macrophages, combined with transcriptome technology, and explained from the genetic level that LF82 promotes replication by activating its acid shock and fitness system, enhancing nitrate utilization, and inhibiting flagellar function.
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Affiliation(s)
- Ting Yao
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China
- The Key Laboratory of Molecular Microbiology and Technology, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Ministry of Education, Tianjin, China
| | - Yu Huang
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China
- The Key Laboratory of Molecular Microbiology and Technology, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Ministry of Education, Tianjin, China
| | - Zimeng Huai
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China
- The Key Laboratory of Molecular Microbiology and Technology, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Ministry of Education, Tianjin, China
| | - Xingmei Liu
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China
- The Key Laboratory of Molecular Microbiology and Technology, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Ministry of Education, Tianjin, China
| | - Xiaowen Liu
- Academy of Psychology and Behavior, Faculty of Psychology, Tianjin Normal University, Tianjin, China
| | - Yutao Liu
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China
- The Key Laboratory of Molecular Microbiology and Technology, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Ministry of Education, Tianjin, China
| | - Hao Sun
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China
- The Key Laboratory of Molecular Microbiology and Technology, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Ministry of Education, Tianjin, China
| | - Yu Pang
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjin, China
- The Key Laboratory of Molecular Microbiology and Technology, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Ministry of Education, Tianjin, China
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Lai Z, Afriyie G, Cui H, Chen L, Xu Z, Chen Z, Liang Q, Luo J, Dong Z, Shao C, Guo Y, Wang Z. The First High-Quality Chromosome-Level Genome of the Lutjanus erythropterus (Bloch, 1790) Using Single-Tube Long Fragment Reads and Hi-C Technologies. Genome Biol Evol 2023; 15:evad171. [PMID: 37768150 PMCID: PMC10558211 DOI: 10.1093/gbe/evad171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 09/10/2023] [Accepted: 09/17/2023] [Indexed: 09/29/2023] Open
Abstract
Lutjanus erythropterus (Bloch, 1790), a Perciformes from the Lutjanidae family, is a commercially important species because of its taste and abundance. Despite the increase in genome resources in recent years, few genome assemblies are available within this fish family for comparative and functional studies. In this study, we determined the chromosomal genome of Crimson snapper using high-throughput Single-Tube Long Fragment Reads sequencing technology and Hi-C data. The final assembly size was 973.04 Mb with contig and scaffold N50 values of 1.51 and 40.65 Mb, respectively. We successfully scaffolded 95.84% of the genome sequence onto 24 chromosomes ranging in length from 19.37 to 49.48 Mb. A total of 22,663 genes and 13,877 gene families were identified in the genome, with 29 gene families being L. erythropterus-specific. A phylogenetic analysis using single-copy gene families showed that L. erythropterus and Larimichthys crocea had the closest genetic relationship with a divergence time of ∼47.7 Ma. This new genomic resource will facilitate comparative genomic studies as well as genetic breeding programs for L. erythropterus.
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Affiliation(s)
- Zhuoxin Lai
- Key Laboratory of Aquaculture in South China Sea for Aquatic Economic Animal of Guangdong Higher Education Institutes, Fisheries College, Guangdong Ocean University, Zhanjiang, China
| | - Gyamfua Afriyie
- Key Laboratory of Aquaculture in South China Sea for Aquatic Economic Animal of Guangdong Higher Education Institutes, Fisheries College, Guangdong Ocean University, Zhanjiang, China
| | - Haitao Cui
- Key Laboratory of Aquaculture in South China Sea for Aquatic Economic Animal of Guangdong Higher Education Institutes, Fisheries College, Guangdong Ocean University, Zhanjiang, China
| | - Lujun Chen
- Key Laboratory of Aquaculture in South China Sea for Aquatic Economic Animal of Guangdong Higher Education Institutes, Fisheries College, Guangdong Ocean University, Zhanjiang, China
| | - Zhenmin Xu
- Key Laboratory of Aquaculture in South China Sea for Aquatic Economic Animal of Guangdong Higher Education Institutes, Fisheries College, Guangdong Ocean University, Zhanjiang, China
| | - Zizhao Chen
- Key Laboratory of Aquaculture in South China Sea for Aquatic Economic Animal of Guangdong Higher Education Institutes, Fisheries College, Guangdong Ocean University, Zhanjiang, China
| | - Quilu Liang
- Key Laboratory of Aquaculture in South China Sea for Aquatic Economic Animal of Guangdong Higher Education Institutes, Fisheries College, Guangdong Ocean University, Zhanjiang, China
| | - Jie Luo
- Key Laboratory of Aquaculture in South China Sea for Aquatic Economic Animal of Guangdong Higher Education Institutes, Fisheries College, Guangdong Ocean University, Zhanjiang, China
| | - Zhongdian Dong
- Key Laboratory of Aquaculture in South China Sea for Aquatic Economic Animal of Guangdong Higher Education Institutes, Fisheries College, Guangdong Ocean University, Zhanjiang, China
| | - Changwei Shao
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Yusong Guo
- Key Laboratory of Aquaculture in South China Sea for Aquatic Economic Animal of Guangdong Higher Education Institutes, Fisheries College, Guangdong Ocean University, Zhanjiang, China
| | - Zhongduo Wang
- Key Laboratory of Aquaculture in South China Sea for Aquatic Economic Animal of Guangdong Higher Education Institutes, Fisheries College, Guangdong Ocean University, Zhanjiang, China
- Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animals, Fisheries College, Guangdong, China
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Lyu YZ, Jiang H, Sun HN, Yang Y, Chao Y, Huang LB, Dong XY. Lipidomic and comparative transcriptomic analysis of fatty acid synthesis pathway in Carya illinoinensis embryo. TREE PHYSIOLOGY 2023; 43:1675-1690. [PMID: 37171624 DOI: 10.1093/treephys/tpad061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 04/03/2023] [Accepted: 05/08/2023] [Indexed: 05/13/2023]
Abstract
Pecan (Carya illinoinensis (Wagenh.) K. Koch) is an important oilseed nut and is rich in fatty acids (FAs) and flavonols. Pecan FA has significantly edible, industrial and clinical value. To investigate the dynamic patterns and compositions of FA, and the molecular mechanism that controls FA accumulation in pecan, lipidomic and transcriptomic analyses were performed to determine lipid profiles and gene expression in pecan's FA biosynthesis pathway. In the present study, compared with cultivars 'Caddo' and 'Y-01', 'Mahan' formed larger and heavier embryos and accumulated higher oil content. Lipidomic analysis showed that FA and (O-acyl)-1-hydroxy FA contents were higher in 'Mahan' at the mature stage. Based on full-length and comparative RNA-Seq, differential expression gene enrichment analysis revealed that many functional genes participated in the pathways of 'fatty acid biosynthesis', 'fatty acid metabolism' and 'linoleic acid metabolism'. High FA accumulation model from 'Mahan' demonstrated that key enzyme-encoding genes played an important role in regulating FA biosynthesis. Co-expression module analysis indicated that several transcription factors (TFs; MYB, TCP, bHLH, Dof, ERF, NAC) were involved in FA accumulation by regulating the expression of functional genes, and real-time quantitative PCR verification proved that these TFs had a high correlation with the pecan FA accumulation pattern. These findings provided an insight into the molecular mechanism of FA accumulation in C. illinoinensis embryo, which contributes to pecan oil yielding and pecan molecular breeding.
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Affiliation(s)
- Yun-Zhou Lyu
- Institute of Landscape Trees and Flowers, Jiangsu Academy of Forestry, Nanjing 211153, China
| | - Hao Jiang
- Institute of Landscape Trees and Flowers, Jiangsu Academy of Forestry, Nanjing 211153, China
| | - Hai-Nan Sun
- Institute of Landscape Trees and Flowers, Jiangsu Academy of Forestry, Nanjing 211153, China
| | - Yong Yang
- Institute of Landscape Trees and Flowers, Jiangsu Academy of Forestry, Nanjing 211153, China
| | - Yang Chao
- Changzhou Golden Land Agriculture and Animal Husbandry Technology Service Co., Ltd, Changzhou 213139, China
| | - Li-Bin Huang
- Institute of Landscape Trees and Flowers, Jiangsu Academy of Forestry, Nanjing 211153, China
| | - Xiao-Yun Dong
- Institute of Landscape Trees and Flowers, Jiangsu Academy of Forestry, Nanjing 211153, China
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Zhu X, Chen C, Wei D, Xu Y, Liang S, Jia W, Li J, Qu Y, Zhai J, Zhang Y, Wu P, Hao Q, Zhang L, Zhang W, Yang X, Pan L, Qi R, Li Y, Wang F, Yi R, Yang Z, Wang J, Zhao Y. FOXP2 confers oncogenic effects in prostate cancer. eLife 2023; 12:e81258. [PMID: 37668356 PMCID: PMC10513481 DOI: 10.7554/elife.81258] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 09/05/2023] [Indexed: 09/06/2023] Open
Abstract
Identification oncogenes is fundamental to revealing the molecular basis of cancer. Here, we found that FOXP2 is overexpressed in human prostate cancer cells and prostate tumors, but its expression is absent in normal prostate epithelial cells and low in benign prostatic hyperplasia. FOXP2 is a FOX transcription factor family member and tightly associated with vocal development. To date, little is known regarding the link of FOXP2 to prostate cancer. We observed that high FOXP2 expression and frequent amplification are significantly associated with high Gleason score. Ectopic expression of FOXP2 induces malignant transformation of mouse NIH3T3 fibroblasts and human prostate epithelial cell RWPE-1. Conversely, FOXP2 knockdown suppresses the proliferation of prostate cancer cells. Transgenic overexpression of FOXP2 in the mouse prostate causes prostatic intraepithelial neoplasia. Overexpression of FOXP2 aberrantly activates oncogenic MET signaling and inhibition of MET signaling effectively reverts the FOXP2-induced oncogenic phenotype. CUT&Tag assay identified FOXP2-binding sites located in MET and its associated gene HGF. Additionally, the novel recurrent FOXP2-CPED1 fusion identified in prostate tumors results in high expression of truncated FOXP2, which exhibit a similar capacity for malignant transformation. Together, our data indicate that FOXP2 is involved in tumorigenicity of prostate.
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Affiliation(s)
- Xiaoquan Zhu
- The Key Laboratory of Geriatrics, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical SciencesBeijingChina
| | - Chao Chen
- Department of Thoracic Surgery, Peking University Shenzhen Hospital, Shenzhen Peking UniversityShenzhenChina
- The Hong Kong University of Science and Technology Medical CenterHong KongChina
| | - Dong Wei
- Department of Urology, Beijing Hospital, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical SciencesBeijingChina
| | - Yong Xu
- Tianjin Institute of Urology, Second Hospital of Tianjin Medical UniversityTianjingChina
- Department of Urology, Second Hospital of Tianjing Medical UniversityTianjingChina
| | - Siying Liang
- Genetic Testing Center, Qingdao Women and Children's HospitalQingdaoChina
| | - Wenlong Jia
- Department of Computer Science, City University of Hong KongHong KongChina
| | - Jian Li
- The Key Laboratory of Geriatrics, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical SciencesBeijingChina
| | - Yanchun Qu
- Tianjin Institute of Urology, Second Hospital of Tianjin Medical UniversityTianjingChina
| | - Jianpo Zhai
- Department of Urology, Beijing Jishuitan HospitalBeijingChina
| | - Yaoguang Zhang
- Department of Urology, Beijing Hospital, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical SciencesBeijingChina
| | - Pengjie Wu
- Department of Urology, Beijing Hospital, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical SciencesBeijingChina
| | - Qiang Hao
- Department of Urology, Beijing Tian Tan Hospital, Capital Medical UniversityBeijingChina
| | - Linlin Zhang
- School of Nursing, Harbin Medical UniversityHarbinChina
| | - Wei Zhang
- Department of Pathology, Beijing Hospital, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical SciencesBeijingChina
| | - Xinyu Yang
- Department of Urology, Peking University First Hospital, Institute of UrologyBeijingChina
| | - Lin Pan
- Clinical Institute of China-Japan Friendship HospitalBeijingChina
| | - Ruomei Qi
- The Key Laboratory of Geriatrics, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical SciencesBeijingChina
| | - Yao Li
- Department of Surgery, Beijing Hospital, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical ScienceBeijingChina
| | - Feiliang Wang
- The Department of Ultrasonography, Beijing Hospital, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical SciencesBeijingChina
| | - Rui Yi
- The Key Laboratory of Geriatrics, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical SciencesBeijingChina
| | - Ze Yang
- The Key Laboratory of Geriatrics, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical SciencesBeijingChina
| | - Jianye Wang
- Department of Urology, Beijing Hospital, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical SciencesBeijingChina
| | - Yanyang Zhao
- The Key Laboratory of Geriatrics, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical SciencesBeijingChina
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Yang Y, He Y, Lv S, Zhu H, Wang T, Wang G, Hong N, Wang L. The PcMYB44-mediated miR397-PcLACs module regulates defence-induced lignification in pear resistance to fungal disease. MOLECULAR PLANT PATHOLOGY 2023; 24:1107-1125. [PMID: 37312259 PMCID: PMC10423334 DOI: 10.1111/mpp.13357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Revised: 05/11/2023] [Accepted: 05/14/2023] [Indexed: 06/15/2023]
Abstract
Diseases caused by Alternaria alternata and Botryosphaeria dothidea diminish pear yield and quality, and restrict the pear agricultural industry. Lignification is a conserved mechanism for plant resistance against pathogen invasion. The regulatory mechanisms underlying defence-induced lignification in pear in response to fungal pathogen infection remain unknown. In this study, analysis of lignification level and lignin content in pear revealed that A. alternata and B. dothidea induced lignification, and transcriptomics showed that lignin biosynthesis was affected. To explore whether laccases (LACs) mediated by miR397 regulate lignification in pear, we investigated the role of PcmiR397 in repressing the expression of PcLACs using 5'-RNA ligase-mediated-RACE and co-transformation in tobacco. Opposite expression patterns for PcmiR397 and PcLAC target genes were observed in pear in response to pathogens. Transient transformation in pear demonstrated that silencing PcmiR397 and overexpressing a single PcLAC enhanced resistance to pathogens via lignin synthesis. To further reveal the mechanism underpinning the PcMIR397 response of pear to pathogens, the PcMIR397 promoter was analysed, and pMIR397-1039 was found to be inhibited by pathogen infection. The transcription factor PcMYB44 was up-regulated, and it bound to the PcMIR397 promoter and inhibited transcription following pathogen infection. The results demonstrate the role of PcmiR397-PcLACs in broad-spectrum resistance to fungal disease, and the potential role of PcMYB44 involved in the miR397-PcLAC module in regulating defence-induced lignification. The findings provide valuable candidate gene resources and guidance for molecular breeding to improve resistance to fungal disease in pear.
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Affiliation(s)
- Yuekun Yang
- College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
- Key Laboratory of Plant Pathology of Hubei ProvinceHuazhong Agricultural UniversityWuhanChina
| | - Ying He
- College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
- Key Laboratory of Plant Pathology of Hubei ProvinceHuazhong Agricultural UniversityWuhanChina
| | - Shamei Lv
- College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
- Key Laboratory of Plant Pathology of Hubei ProvinceHuazhong Agricultural UniversityWuhanChina
| | - Haodong Zhu
- College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
- Key Laboratory of Plant Pathology of Hubei ProvinceHuazhong Agricultural UniversityWuhanChina
| | - Tingting Wang
- College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
- Key Laboratory of Plant Pathology of Hubei ProvinceHuazhong Agricultural UniversityWuhanChina
| | - Guoping Wang
- College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
- Key Laboratory of Plant Pathology of Hubei ProvinceHuazhong Agricultural UniversityWuhanChina
| | - Ni Hong
- College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
- Key Laboratory of Plant Pathology of Hubei ProvinceHuazhong Agricultural UniversityWuhanChina
| | - Liping Wang
- College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina
- Key Laboratory of Plant Pathology of Hubei ProvinceHuazhong Agricultural UniversityWuhanChina
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Dai M, Zhang Y, Jiao Y, Deng Y, Du X, Yang C. Immunomodulatory effects of one novel microRNA miR-63 in pearl oyster Pinctada fucata martensii. FISH & SHELLFISH IMMUNOLOGY 2023; 140:109002. [PMID: 37586600 DOI: 10.1016/j.fsi.2023.109002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Revised: 08/13/2023] [Accepted: 08/14/2023] [Indexed: 08/18/2023]
Abstract
Novel microRNA miR-63 (novel-miR-63) from pearl oyster Pinctada fucata martensii (Pm-novel-miR-63) is a species-specific miRNA. Our previous research has shown that the expression of Pm-novel-miR-63 was significantly downregulated at 24 h after nucleus transplantation. In this study, we analyzed the function and regulatory role of Pm-novel-miR-63 in the immune response of pearl oysters. The results showed that Pm-novel-miR-63 expression increased after the stimulation of pathogen associated molecular patterns at 6-12 h, and the activity of immune and antioxidant enzymes in the serum decreased after Pm-novel-miR-63 overexpression. Transcriptome analysis revealed that Pm-novel-miR-63 participated in regulating transplantation immunity through the Notch and mRNA surveillance signaling pathways. Target prediction and dual luciferase analysis revealed that Pm-GDP-FucTP, Pm-CysLTR2, and Pm-RLR were the target genes of Pm-novel-miR-63. These results suggested that Pm-novel-miR-63 participated in regulating the immune response in pearl oysters and can serve as a new interference target to reasonably control excessive immune rejection in pearl culture.
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Affiliation(s)
- Meiqi Dai
- Fishery College, Guangdong Ocean University, Zhanjiang, 524025, China
| | - Yuting Zhang
- Fishery College, Guangdong Ocean University, Zhanjiang, 524025, China
| | - Yu Jiao
- Fishery College, Guangdong Ocean University, Zhanjiang, 524025, China; Pearl Breeding and Processing Engineering Technology Research Centre of Guangdong Province, Zhanjiang, 524088, China; Guangdong Science and Innovation Center for Pearl Culture, Zhanjiang, 524088, China.
| | - Yuewen Deng
- Fishery College, Guangdong Ocean University, Zhanjiang, 524025, China; Pearl Breeding and Processing Engineering Technology Research Centre of Guangdong Province, Zhanjiang, 524088, China; Guangdong Science and Innovation Center for Pearl Culture, Zhanjiang, 524088, China; Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animals, Zhanjiang, 524088, China; Guangdong Marine Ecology Early Warning and Monitoring Laboratory, Zhanjiang, 524088, China
| | - Xiaodong Du
- Fishery College, Guangdong Ocean University, Zhanjiang, 524025, China; Pearl Breeding and Processing Engineering Technology Research Centre of Guangdong Province, Zhanjiang, 524088, China; Guangdong Science and Innovation Center for Pearl Culture, Zhanjiang, 524088, China
| | - Chuangye Yang
- Fishery College, Guangdong Ocean University, Zhanjiang, 524025, China; Pearl Breeding and Processing Engineering Technology Research Centre of Guangdong Province, Zhanjiang, 524088, China; Guangdong Marine Ecology Early Warning and Monitoring Laboratory, Zhanjiang, 524088, China
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Kim HJ, Kim KE, Kim YJ, Kang H, Shin JW, Kim S, Lee SH, Jung SW, Lee TK. Marine Bacterioplankton Community Dynamics and Potentially Pathogenic Bacteria in Seawater around Jeju Island, South Korea, via Metabarcoding. Int J Mol Sci 2023; 24:13561. [PMID: 37686367 PMCID: PMC10487856 DOI: 10.3390/ijms241713561] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 08/23/2023] [Accepted: 08/24/2023] [Indexed: 09/10/2023] Open
Abstract
Understanding marine bacterioplankton composition and distribution is necessary for improving predictions of ecosystem responses to environmental change. Here, we used 16S rRNA metabarcoding to investigate marine bacterioplankton diversity and identify potential pathogenic bacteria in seawater samples collected in March, May, September, and December 2013 from two sites near Jeju Island, South Korea. We identified 1343 operational taxonomic units (OTUs) and observed that community diversity varied between months. Alpha- and Gamma-proteobacteria were the most abundant classes, and in all months, the predominant genera were Candidatus Pelagibacter, Leisingera, and Citromicrobium. The highest number of OTUs was observed in September, and Vibrio (7.80%), Pseudoalteromonas (6.53%), and Citromicrobium (6.16%) showed higher relative abundances or were detected only in this month. Water temperature and salinity significantly affected bacterial distribution, and these conditions, characteristic of September, were adverse for Aestuariibacter but favored Citromicrobium. Potentially pathogenic bacteria, among which Vibrio (28 OTUs) and Pseudoalteromonas (six OTUs) were the most abundant in September, were detected in 49 OTUs, and their abundances were significantly correlated with water temperature, increasing rapidly in September, the warmest month. These findings suggest that monthly temperature and salinity variations affect marine bacterioplankton diversity and potential pathogen abundance.
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Affiliation(s)
- Hyun-Jung Kim
- Library of Marine Samples, Korea Institute of Ocean Science & Technology, Geoje 53201, Republic of Korea; (H.-J.K.); (K.E.K.); (Y.J.K.); (J.W.S.); (S.K.)
- Department of Oceanography and Marine Research Institute, Pusan National University, Busan 46241, Republic of Korea;
| | - Kang Eun Kim
- Library of Marine Samples, Korea Institute of Ocean Science & Technology, Geoje 53201, Republic of Korea; (H.-J.K.); (K.E.K.); (Y.J.K.); (J.W.S.); (S.K.)
- Department of Ocean Science, University of Science & Technology, Daejeon 34113, Republic of Korea
| | - Yu Jin Kim
- Library of Marine Samples, Korea Institute of Ocean Science & Technology, Geoje 53201, Republic of Korea; (H.-J.K.); (K.E.K.); (Y.J.K.); (J.W.S.); (S.K.)
- Department of Ocean Science, University of Science & Technology, Daejeon 34113, Republic of Korea
| | - Hangoo Kang
- Vessel Operation & Observation Team, Korea Institute of Ocean Science & Technology, Geoje 53201, Republic of Korea;
| | - Ji Woo Shin
- Library of Marine Samples, Korea Institute of Ocean Science & Technology, Geoje 53201, Republic of Korea; (H.-J.K.); (K.E.K.); (Y.J.K.); (J.W.S.); (S.K.)
| | - Soohyun Kim
- Library of Marine Samples, Korea Institute of Ocean Science & Technology, Geoje 53201, Republic of Korea; (H.-J.K.); (K.E.K.); (Y.J.K.); (J.W.S.); (S.K.)
| | - Sang Heon Lee
- Department of Oceanography and Marine Research Institute, Pusan National University, Busan 46241, Republic of Korea;
| | - Seung Won Jung
- Library of Marine Samples, Korea Institute of Ocean Science & Technology, Geoje 53201, Republic of Korea; (H.-J.K.); (K.E.K.); (Y.J.K.); (J.W.S.); (S.K.)
- Department of Ocean Science, University of Science & Technology, Daejeon 34113, Republic of Korea
| | - Taek-Kyun Lee
- Department of Ocean Science, University of Science & Technology, Daejeon 34113, Republic of Korea
- Ecological Risk Research Department, Korea Institute of Ocean Science & Technology, Geoje 53201, Republic of Korea
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Xia H, Hao Z, Shen Y, Tu Z, Yang L, Zong Y, Li H. Genome-wide association study of multiyear dynamic growth traits in hybrid Liriodendron identifies robust genetic loci associated with growth trajectories. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 115:1544-1563. [PMID: 37272730 DOI: 10.1111/tpj.16337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 04/30/2023] [Accepted: 05/29/2023] [Indexed: 06/06/2023]
Abstract
The genetic factors underlying growth traits differ over time points or stages. However, most current studies of phenotypes at single time points do not capture all loci or explain the genetic differences underlying growth trajectories. Hybrid Liriodendron exhibits obvious heterosis and is widely cultivated, although its complex genetic mechanism underlying growth traits remains unknown. A genome-wide association study (GWAS) is an effective method for elucidating the genetic architecture by identifying genetic loci underlying complex quantitative traits. In the present study, using a GWAS, we identified robust loci associated with growth trajectories in hybrid Liriodendron populations. We selected 233 hybrid progenies derived from 25 crosses for resequencing, and measured their tree height (H) and diameter at breast height (DBH) for 11 consecutive years; 192 972 high-quality single nucleotide polymorphisms (SNPs) were obtained. The dynamics of the multiyear single-trait GWAS showed that year-specific SNPs predominated, and only five robust SNPs for DBH were identified in at least three different years. Multitrait GWAS analysis with model parameters as latent variables also revealed 62 SNPs for H and 52 for DBH associated with the growth trajectory, displaying different biomass accumulation patterns, among which four SNPs exerted pleiotropic effects. All identified SNPs also exhibited temporal variations in effect sizes and inheritance patterns potentially related to different growth and developmental stages. The haplotypes resulting from these significant SNPs might pyramid favorable loci, benefitting the selection of superior genotypes. The present study provides insights into the genetic architecture of dynamic growth traits and lays a basis for future molecular-assisted breeding.
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Affiliation(s)
- Hui Xia
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
| | - Ziyuan Hao
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
| | - Yufang Shen
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
| | - Zhonghua Tu
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
| | - Lichun Yang
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
| | - Yaxian Zong
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
| | - Huogen Li
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
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Qiu CW, Ma Y, Wang QQ, Fu MM, Li C, Wang Y, Wu F. Barley HOMOCYSTEINE METHYLTRANSFERASE 2 confers drought tolerance by improving polyamine metabolism. PLANT PHYSIOLOGY 2023; 193:389-409. [PMID: 37300541 DOI: 10.1093/plphys/kiad333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 04/25/2023] [Accepted: 05/18/2023] [Indexed: 06/12/2023]
Abstract
Drought stress poses a serious threat to crop production worldwide. Genes encoding homocysteine methyltransferase (HMT) have been identified in some plant species in response to abiotic stress, but its molecular mechanism in plant drought tolerance remains unclear. Here, transcriptional profiling, evolutionary bioinformatics, and population genetics were conducted to obtain insight into the involvement of HvHMT2 from Tibetan wild barley (Hordeum vulgare ssp. agriocrithon) in drought tolerance. We then performed genetic transformation coupled with physio-biochemical dissection and comparative multiomics approaches to determine the function of this protein and the underlying mechanism of HvHMT2-mediated drought tolerance. HvHMT2 expression was strongly induced by drought stress in tolerant genotypes in a natural Tibetan wild barley population and contributed to drought tolerance through S-adenosylmethionine (SAM) metabolism. Overexpression of HvHMT2 promoted HMT synthesis and efficiency of the SAM cycle, leading to enhanced drought tolerance in barley through increased endogenous spermine and less oxidative damage and growth inhibition, thus improving water status and final yield. Disruption of HvHMT2 expression led to hypersensitivity under drought treatment. Application of exogenous spermine reduced accumulation of reactive oxygen species (ROS), which was increased by exogenous mitoguazone (inhibitor of spermine biosynthesis), consistent with the association of HvHMT2-mediated spermine metabolism and ROS scavenging in drought adaptation. Our findings reveal the positive role and key molecular mechanism of HvHMT2 in drought tolerance in plants, providing a valuable gene not only for breeding drought-tolerant barley cultivars but also for facilitating breeding schemes in other crops in a changing global climate.
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Affiliation(s)
- Cheng-Wei Qiu
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, P.R. China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, P.R. China
| | - Yue Ma
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, P.R. China
| | - Qing-Qing Wang
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, P.R. China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, P.R. China
| | - Man-Man Fu
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, P.R. China
| | - Chengdao Li
- Western Barley Genetics Alliance, State Agricultural Biotechnology Centre, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, WA 6150, Australia
| | - Yizhou Wang
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, P.R. China
| | - Feibo Wu
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, P.R. China
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Yu SF, Sun ZB, Li SD, Hu YF, Ren Q, Xu JL, Song HJ, Sun MH. The Adenylate Cyclase-Encoding Gene crac Is Involved in Clonostachys rosea Mycoparasitism. J Fungi (Basel) 2023; 9:861. [PMID: 37623632 PMCID: PMC10455997 DOI: 10.3390/jof9080861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 08/08/2023] [Accepted: 08/14/2023] [Indexed: 08/26/2023] Open
Abstract
Clonostachys rosea is an excellent biocontrol fungus against numerous fungal plant pathogens. The cAMP signaling pathway is a crucial signal transduction pathway in fungi. To date, the role of the cAMP signaling pathway in C. rosea mycoparasitism remains unknown. An adenylate cyclase-encoding gene, crac (an important component of the cAMP signaling pathway), was previously screened from C. rosea 67-1, and its expression level was dramatically upregulated during the C. rosea mycoparasitization of the sclerotia of Sclerotinia sclerotiorum. In this study, the function of crac in C. rosea mycoparasitism was explored through gene knockout and complementation. The obtained results show that the deletion of crac influenced the growth rate and colony morphology of C. rosea, as well as the tolerance to NaCl and H2O2 stress. The mycoparasitic effects on the sclerotia of S. sclerotiorum and the biocontrol capacity on soybean Sclerotinia stem rot in ∆crac-6 and ∆crac-13 were both attenuated compared with that of the wild-type strain and complementation transformants. To understand the regulatory mechanism of crac during C. rosea mycoparasitism, transcriptomic analysis was conducted between the wild-type strain and knockout mutant. A number of biocontrol-related genes, including genes encoding cell wall-degrading enzymes and transporters, were significantly differentially expressed during C. rosea mycoparasitism, suggesting that crac may be involved in C. rosea mycoparasitism by regulating the expression of these DEGs. These findings provide insight for further exploring the molecular mechanism of C. rosea mycoparasitism.
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Affiliation(s)
- Shu-Fan Yu
- School of Light Industry, Beijing Technology and Business University, Beijing 100048, China
| | - Zhan-Bin Sun
- School of Light Industry, Beijing Technology and Business University, Beijing 100048, China
| | - Shi-Dong Li
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Ya-Feng Hu
- School of Light Industry, Beijing Technology and Business University, Beijing 100048, China
| | - Qing Ren
- School of Light Industry, Beijing Technology and Business University, Beijing 100048, China
| | - Jia-Liang Xu
- School of Light Industry, Beijing Technology and Business University, Beijing 100048, China
| | - Han-Jian Song
- School of Light Industry, Beijing Technology and Business University, Beijing 100048, China
| | - Man-Hong Sun
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
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Gomes I, Gallego-Paez LM, Jiménez M, Santamaria PG, Mansinho A, Sousa R, Abreu C, Suárez EG, Costa L, Casimiro S. Co-targeting RANK pathway treats and prevents acquired resistance to CDK4/6 inhibitors in luminal breast cancer. Cell Rep Med 2023; 4:101120. [PMID: 37451269 PMCID: PMC10439176 DOI: 10.1016/j.xcrm.2023.101120] [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: 11/22/2022] [Revised: 05/11/2023] [Accepted: 06/21/2023] [Indexed: 07/18/2023]
Abstract
The combination of endocrine therapy (ET) and cyclin-dependent kinase 4/6 (CDK4/6) inhibitors (CDK4/6i) was a hallmark in metastatic luminal breast cancer (BC). However, intrinsic and acquired resistance affects long-term efficacy. Here, we study the role of the receptor activator of nuclear factor-κB (RANK) pathway in CDK4/6i resistance. We find that RANK overexpression in luminal BC is associated with intrinsic resistance to CDK4/6i, both in vitro and in mouse xenografts, and decreased proliferation rate and chronic interferon (IFN) γ response are highlighted as resistance drivers. Gene expression data from the NeoPalAna CDK4/6i clinical trial, and studies with palbociclib-resistant cell lines, show that RANK is upregulated after treatment with CDK4/6i, supporting a role in acquired resistance. Our study shows that RANK ligand (RANKL) inhibitors can restore sensitivity to CDK4/6i and prevent acquired resistance. On the basis of these findings, we conclude that pharmacological inhibition of the RANK pathway through RANKL blocking could represent an add-on to ET + CDK4/6i, warranting further clinical studies.
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Affiliation(s)
- Inês Gomes
- Luis Costa Laboratory, Institute of Molecular Medicine (iMM), Lisbon Medical School, 1649-028 Lisbon, Portugal
| | - Lina M Gallego-Paez
- Luis Costa Laboratory, Institute of Molecular Medicine (iMM), Lisbon Medical School, 1649-028 Lisbon, Portugal
| | - Maria Jiménez
- Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain
| | | | - André Mansinho
- Oncology Division, Hospital de Santa Maria-CHULN, 1649-028 Lisbon, Portugal
| | - Rita Sousa
- Oncology Division, Hospital de Santa Maria-CHULN, 1649-028 Lisbon, Portugal
| | - Catarina Abreu
- Oncology Division, Hospital de Santa Maria-CHULN, 1649-028 Lisbon, Portugal
| | - Eva González Suárez
- Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain; Oncobell, Bellvitge Biomedical Research Institute, IDIBELL, 08908 Barcelona, Spain
| | - Luis Costa
- Luis Costa Laboratory, Institute of Molecular Medicine (iMM), Lisbon Medical School, 1649-028 Lisbon, Portugal; Oncology Division, Hospital de Santa Maria-CHULN, 1649-028 Lisbon, Portugal.
| | - Sandra Casimiro
- Luis Costa Laboratory, Institute of Molecular Medicine (iMM), Lisbon Medical School, 1649-028 Lisbon, Portugal.
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Shin B, Lee JY, Im Y, Yoo H, Park J, Lee JS, Lee KY, Jeon K. Prognostic implication of downregulated exosomal miRNAs in patients with sepsis: a cross-sectional study with bioinformatics analysis. J Intensive Care 2023; 11:35. [PMID: 37537685 PMCID: PMC10399058 DOI: 10.1186/s40560-023-00683-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 07/30/2023] [Indexed: 08/05/2023] Open
Abstract
BACKGROUND Despite the understanding of sepsis-induced extracellular vesicles (EVs), such as exosomes, and their role in intercellular communication during sepsis, little is known about EV contents such as microRNA (miRNA), which modulate important cellular processes contributing to sepsis in body fluids. This study aimed to analyze the differential expression of exosomal miRNAs in plasma samples collected from sepsis patients and healthy controls, and to identify potential miRNA regulatory pathways contributing to sepsis pathogenesis. METHODS Quantitative real-time PCR-based microarrays were used to profile plasma exosomal miRNA expression levels in 135 patients with sepsis and 11 healthy controls from an ongoing prospective registry of critically ill adult patients admitted to the intensive care unit. The identified exosomal miRNAs were tested in an external validation cohort (35 sepsis patients and 10 healthy controls). And then, functional enrichment analyses of gene ontology, KEGG pathway analysis, and protein-protein interaction network and cluster analyses were performed based on the potential target genes of the grouped miRNAs. Finally, to evaluate the performance of the identified exosomal miRNAs in predicting in-hospital and 90-day mortalities of sepsis patients, receiver operating characteristic curve (ROC) and Kaplan-Meier analyses were performed. RESULTS Compared with healthy controls, plasma exosomes from sepsis patients showed significant changes in 25 miRNAs; eight miRNAs were upregulated and 17 downregulated. Additionally, the levels of hsa-let-7f-5p, miR-331-3p miR-301a-3p, and miR-335-5p were significantly lower in sepsis patients than in healthy controls (p < 0.0001). These four miRNAs were confirmed in an external validation cohort. In addition, the most common pathway for these four miRNAs were PI3K-Akt and mitogen-activated protein kinase (MAPK) signaling pathways based on the KEGG analysis. The area under the ROC of hsa-let-7f-5p, miR-331-3p, miR-301a-3p, and miR-335-5p level for in-hospital mortality was 0.913, 0.931, 0.929, and 0.957, respectively (p < 0.001), as confirmed in an external validation cohort. Also, the Kaplan-Meier analysis showed a significant difference in 90-day mortality between sepsis patients with high and low miR-335-5p, miR-301a-3p, hsa-let-7f-5p, and miR-331-3p levels (p < 0.001, log-rank test). CONCLUSION Among the differentially-expressed miRNAs detected in microarrays, the top four downregulated exosomal miRNAs (hsa-let-7f-5p, miR-331-3p miR-301a-3p, and miR-335-5p) were identified as independent prognostic factors for in-hospital and 90-day mortalities among sepsis patients. Bioinformatics analysis demonstrated that these four microRNAs might provide a significant contribution to sepsis pathogenesis through PI3K-Akt and MAPK signaling pathway.
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Affiliation(s)
- Beomsu Shin
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Samsung Changwon Hospital, Sungkyunkwan University School of Medicine, Changwon, Republic of Korea
| | - Jin Young Lee
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, 81 Irwon-Ro, Gangnam-Gu, Seoul, 06351, Republic of Korea
| | - Yunjoo Im
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, 81 Irwon-Ro, Gangnam-Gu, Seoul, 06351, Republic of Korea
| | - Hongseok Yoo
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, 81 Irwon-Ro, Gangnam-Gu, Seoul, 06351, Republic of Korea
| | - Junseon Park
- Department of Critical Care Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Joo Sang Lee
- Department of Artificial Intelligence and Department of Precision Medicine, Sungkyunkwan University School of Medicine, Suwon, Republic of Korea
| | - Ki-Young Lee
- Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon, Republic of Korea
| | - Kyeongman Jeon
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, 81 Irwon-Ro, Gangnam-Gu, Seoul, 06351, Republic of Korea.
- Department of Health Sciences and Technology, SAIHST, Sungkyunkawan University, Seoul, Republic of Korea.
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48
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Sun ZB, Yu SF, Sun MH, Li SD, Hu YF, Song HJ. Transcriptomic Response of Clonostachys rosea Mycoparasitizing Rhizoctonia solani. J Fungi (Basel) 2023; 9:818. [PMID: 37623589 PMCID: PMC10455738 DOI: 10.3390/jof9080818] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 07/28/2023] [Accepted: 08/01/2023] [Indexed: 08/26/2023] Open
Abstract
Clonostachys rosea is an important mycoparasitism biocontrol agent that exhibits excellent control efficacy against numerous fungal plant pathogens. Transcriptomic sequencing may be used to preliminarily screen mycoparasitism-related genes of C. rosea against fungal pathogens. The present study sequenced and analyzed the transcriptome of C. rosea mycoparasitizing a Basidiomycota (phylum) fungal pathogen, Rhizoctonia solani, under three touch stages: the pre-touch stage, touch stage and after-touch stage. The results showed that a number of genes were differentially expressed during C. rosea mycoparasitization of R. solani. At the pre-touch stage, 154 and 315 genes were up- and down-regulated, respectively. At the touch stage, the numbers of up- and down-regulated differentially expressed genes (DEGs) were 163 and 188, respectively. The after-touch stage obtained the highest number of DEGs, with 412 and 326 DEGs being up- and down-regulated, respectively. Among these DEGs, ABC transporter-, glucanase- and chitinase-encoding genes were selected as potential mycoparasitic genes according to a phylogenetic analysis. A comparative transcriptomic analysis between C. rosea mycoparasitizing R. solani and Sclerotinia sclerotiorum showed that several DEGs, including the tartrate transporter, SDR family oxidoreductase, metallophosphoesterase, gluconate 5-dehydrogenase and pyruvate carboxylase, were uniquely expressed in C. rosea mycoparasitizing R. solani. These results significantly expand our knowledge of mycoparasitism-related genes in C. rosea and elucidate the mycoparasitism mechanism of C. rosea.
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Affiliation(s)
- Zhan-Bin Sun
- School of Light Industry, Beijing Technology and Business University, Beijing 100048, China
| | - Shu-Fan Yu
- School of Light Industry, Beijing Technology and Business University, Beijing 100048, China
| | - Man-Hong Sun
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Shi-Dong Li
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Ya-Feng Hu
- School of Light Industry, Beijing Technology and Business University, Beijing 100048, China
| | - Han-Jian Song
- School of Light Industry, Beijing Technology and Business University, Beijing 100048, China
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Padilla-Benavides T, Olea-Flores M, Sharma T, Syed SA, Witwicka H, Zuñiga-Eulogio MD, Zhang K, Navarro-Tito N, Imbalzano AN. Differential Contributions of mSWI/SNF Chromatin Remodeler Sub-Families to Myoblast Differentiation. Int J Mol Sci 2023; 24:11256. [PMID: 37511016 PMCID: PMC10378909 DOI: 10.3390/ijms241411256] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 07/03/2023] [Accepted: 07/06/2023] [Indexed: 07/30/2023] Open
Abstract
Mammalian SWI/SNF (mSWI/SNF) complexes are ATP-dependent chromatin remodeling enzymes that are critical for normal cellular functions. mSWI/SNF enzymes are classified into three sub-families based on the presence of specific subunit proteins. The sub-families are Brm- or Brg1-associated factor (BAF), ncBAF (non-canonical BAF), and polybromo-associated BAF (PBAF). The biological roles for the different enzyme sub-families are poorly described. We knocked down the expression of genes encoding unique subunit proteins for each sub-family, Baf250A, Brd9, and Baf180, which mark the BAF, ncBAF, and PBAF sub-families, respectively, and examined the requirement for each in myoblast differentiation. We found that Baf250A and the BAF complex were required to drive lineage-specific gene expression. KD of Brd9 delayed differentiation. However, while the Baf250A-dependent gene expression profile included myogenic genes, the Brd9-dependent gene expression profile did not, suggesting Brd9 and the ncBAF complex indirectly contributed to differentiation. Baf180 was dispensable for myoblast differentiation. The results distinguish between the roles of the mSWI/SNF enzyme sub-families during myoblast differentiation.
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Affiliation(s)
- Teresita Padilla-Benavides
- Department of Molecular Biology and Biochemistry, Wesleyan University, Middletown, CT 06459, USA; (M.O.-F.); (M.D.Z.-E.); (K.Z.)
| | - Monserrat Olea-Flores
- Department of Molecular Biology and Biochemistry, Wesleyan University, Middletown, CT 06459, USA; (M.O.-F.); (M.D.Z.-E.); (K.Z.)
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA; (T.S.); (S.A.S.); (H.W.)
| | - Tapan Sharma
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA; (T.S.); (S.A.S.); (H.W.)
| | - Sabriya A. Syed
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA; (T.S.); (S.A.S.); (H.W.)
| | - Hanna Witwicka
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA; (T.S.); (S.A.S.); (H.W.)
| | - Miriam D. Zuñiga-Eulogio
- Department of Molecular Biology and Biochemistry, Wesleyan University, Middletown, CT 06459, USA; (M.O.-F.); (M.D.Z.-E.); (K.Z.)
- Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Chilpancingo de los Bravo 39086, GRO, Mexico;
| | - Kexin Zhang
- Department of Molecular Biology and Biochemistry, Wesleyan University, Middletown, CT 06459, USA; (M.O.-F.); (M.D.Z.-E.); (K.Z.)
| | - Napoleon Navarro-Tito
- Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Chilpancingo de los Bravo 39086, GRO, Mexico;
| | - Anthony N. Imbalzano
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA; (T.S.); (S.A.S.); (H.W.)
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50
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Lin S, Liu Z, Sun S, Xue F, Li H, Tursun A, Cao L, Zhang L, Wilson ZA, Zhang D, Liang W. Rice HEAT SHOCK PROTEIN60-3B maintains male fertility under high temperature by starch granule biogenesis. PLANT PHYSIOLOGY 2023; 192:2301-2317. [PMID: 36861636 PMCID: PMC10315285 DOI: 10.1093/plphys/kiad136] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 01/18/2023] [Accepted: 01/29/2023] [Indexed: 06/18/2023]
Abstract
Heat stress has a deleterious effect on male fertility in rice (Oryza sativa), but mechanisms to protect against heat stress in rice male gametophytes are poorly understood. Here, we have isolated and characterized a heat-sensitive male-sterile rice mutant, heat shock protein60-3b (oshsp60-3b), that shows normal fertility at optimal temperatures but decreasing fertility as temperatures increase. High temperatures interfered with pollen starch granule formation and reactive oxygen species (ROS) scavenging in oshsp60-3b anthers, leading to cell death and pollen abortion. In line with the mutant phenotypes, OsHSP60-3B was rapidly upregulated in response to heat shock and its protein products were localized to the plastid. Critically, overexpression of OsHSP60-3B enhanced the heat tolerance of pollen in transgenic plants. We demonstrated that OsHSP60-3B interacted with FLOURY ENDOSPERM6(FLO6) in plastids, a key component involved in the starch granule formation in the rice pollen. Western blot results showed that FLO6 level was substantially decreased in oshsp60-3b anthers at high temperature, indicating that OsHSP60-3B is required to stabilize FLO6 when temperatures exceed optimal conditions. We suggest that in response to high temperature, OsHSP60-3B interacts with FLO6 to regulate starch granule biogenesis in rice pollen and attenuates ROS levels in anthers to ensure normal male gametophyte development in rice.
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Affiliation(s)
- Sen Lin
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Ze Liu
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Shiyu Sun
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Feiyang Xue
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Huanjun Li
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Askar Tursun
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Lichun Cao
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Long Zhang
- Key Laboratory of Crop Genetics and Physiology of Jiangsu Province, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou 225009, China
| | - Zoe A Wilson
- Division of Plant & Crop Sciences, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire LE12 5RD, UK
| | - Dabing Zhang
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
- School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Glen Osmond, South Australia 5064, Australia
| | - Wanqi Liang
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
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