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Kaur J, Tiwari N, Asif MH, Dharmesh V, Naseem M, Srivastava PK, Srivastava S. Integrated genome-transcriptome analysis unveiled the mechanism of Debaryomyces hansenii-mediated arsenic stress amelioration in rice. J Hazard Mater 2024; 469:133954. [PMID: 38484657 DOI: 10.1016/j.jhazmat.2024.133954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 02/22/2024] [Accepted: 03/02/2024] [Indexed: 04/07/2024]
Abstract
Globally, rice is becoming more vulnerable to arsenic (As) pollution, posing a serious threat to public food safety. Previously Debaryomyces hansenii was found to reduce grain As content of rice. To better understand the underlying mechanism, we performed a genome analysis to identify the key genes in D. hansenii responsible for As tolerance and plant growth promotion. Notably, genes related to As resistance (ARR, Ycf1, and Yap) were observed in the genome of D. hansenii. The presence of auxin pathway and glutathione metabolism-related genes may explain the plant growth-promoting potential and As tolerance mechanism of this novel yeast strain. The genome annotation of D. hansenii indicated that it contains a repertoire of genes encoding antioxidants, well corroborated with the in vitro studies of GST, GR, and glutathione content. In addition, the effect of D. hansenii on gene expression profiling of rice plants under As stress was also examined. The Kyoto Encyclopedia of Genes and Genomes (KEGG) database revealed 307 genes, annotated in D. hansenii-treated rice, related to metabolic pathways (184), photosynthesis (12), glutathione (10), tryptophan (4), and biosynthesis of secondary metabolite (117). Higher expression of regulatory elements like AUX/IAA and WRKY transcription factors (TFs), and defense-responsive genes dismutases, catalases, peroxiredoxin, and glutaredoxins during D. hansenii+As exposure was also observed. Combined analysis revealed that D. hansenii genes are contributing to stress mitigation in rice by supporting plant growth and As-tolerance. The study lays the foundation to develop yeast as a beneficial biofertilizer for As-prone areas.
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Affiliation(s)
- Jasvinder Kaur
- CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow 226001, India
| | - Nikita Tiwari
- CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow 226001, India
| | - Mehar Hasan Asif
- CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow 226001, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Varsha Dharmesh
- CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow 226001, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Mariya Naseem
- CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow 226001, India
| | - Pankaj Kumar Srivastava
- CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow 226001, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Suchi Srivastava
- CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow 226001, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
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Yang JJ, Goff A, Wild DJ, Ding Y, Annis A, Kerber R, Foote B, Passi A, Duerksen JL, London S, Puhl AC, Lane TR, Braunstein M, Waddell SJ, Ekins S. Computational drug repositioning identifies niclosamide and tribromsalan as inhibitors of Mycobacterium tuberculosis and Mycobacterium abscessus. Tuberculosis (Edinb) 2024; 146:102500. [PMID: 38432118 PMCID: PMC10978224 DOI: 10.1016/j.tube.2024.102500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 02/20/2024] [Accepted: 02/24/2024] [Indexed: 03/05/2024]
Abstract
Tuberculosis (TB) is still a major global health challenge, killing over 1.5 million people each year, and hence, there is a need to identify and develop novel treatments for Mycobacterium tuberculosis (M. tuberculosis). The prevalence of infections caused by nontuberculous mycobacteria (NTM) is also increasing and has overtaken TB cases in the United States and much of the developed world. Mycobacterium abscessus (M. abscessus) is one of the most frequently encountered NTM and is difficult to treat. We describe the use of drug-disease association using a semantic knowledge graph approach combined with machine learning models that has enabled the identification of several molecules for testing anti-mycobacterial activity. We established that niclosamide (M. tuberculosis IC90 2.95 μM; M. abscessus IC90 59.1 μM) and tribromsalan (M. tuberculosis IC90 76.92 μM; M. abscessus IC90 147.4 μM) inhibit M. tuberculosis and M. abscessus in vitro. To investigate the mode of action, we determined the transcriptional response of M. tuberculosis and M. abscessus to both compounds in axenic log phase, demonstrating a broad effect on gene expression that differed from known M. tuberculosis inhibitors. Both compounds elicited transcriptional responses indicative of respiratory pathway stress and the dysregulation of fatty acid metabolism.
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Affiliation(s)
- Jeremy J Yang
- School of Informatics, Computing and Engineering, Indiana University, Bloomington, IN, USA; Data2Discovery, Inc., Bloomington, IN, USA; Department of Internal Medicine Translational Informatics Division, University of New Mexico, Albuquerque, NM, USA
| | - Aaron Goff
- Department of Global Health and Infection, Brighton & Sussex Medical School, University of Sussex, UK
| | - David J Wild
- School of Informatics, Computing and Engineering, Indiana University, Bloomington, IN, USA; Data2Discovery, Inc., Bloomington, IN, USA
| | - Ying Ding
- School of Informatics, Computing and Engineering, Indiana University, Bloomington, IN, USA; Data2Discovery, Inc., Bloomington, IN, USA; School of Information, Dell Medical School, University of Texas, Austin, TX, USA
| | - Ayano Annis
- Department of Microbiology and Immunology, School of Medicine, University of North Carolina at Chapel Hill, NC, 27599, USA
| | | | | | - Anurag Passi
- Department of Pediatrics, UC San Diego, San Diego, CA, USA
| | | | | | - Ana C Puhl
- Collaborations Pharmaceuticals Inc., 840 Main Campus Drive, Lab 3510, Raleigh, NC, 27606, USA
| | - Thomas R Lane
- Collaborations Pharmaceuticals Inc., 840 Main Campus Drive, Lab 3510, Raleigh, NC, 27606, USA
| | - Miriam Braunstein
- Department of Microbiology and Immunology, School of Medicine, University of North Carolina at Chapel Hill, NC, 27599, USA
| | - Simon J Waddell
- Department of Global Health and Infection, Brighton & Sussex Medical School, University of Sussex, UK
| | - Sean Ekins
- Collaborations Pharmaceuticals Inc., 840 Main Campus Drive, Lab 3510, Raleigh, NC, 27606, USA.
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Tuppurainen H, Laurila N, Nätynki M, Eshraghi L, Tervasmäki A, Erichsen L, Sørensen CS, Pylkäs K, Winqvist R, Peltoketo H. PALB2-mutated human mammary cells display a broad spectrum of morphological and functional abnormalities induced by increased TGFβ signaling. Cell Mol Life Sci 2024; 81:173. [PMID: 38597967 PMCID: PMC11006627 DOI: 10.1007/s00018-024-05183-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 02/16/2024] [Accepted: 02/19/2024] [Indexed: 04/11/2024]
Abstract
Heterozygous mutations in any of three major genes, BRCA1, BRCA2 and PALB2, are associated with high-risk hereditary breast cancer susceptibility frequently seen as familial disease clustering. PALB2 is a key interaction partner and regulator of several vital cellular activities of BRCA1 and BRCA2, and is thus required for DNA damage repair and alleviation of replicative and oxidative stress. Little is however known about how PALB2-deficiency affects cell function beyond that, especially in the three-dimensional setting, and also about its role during early steps of malignancy development. To answer these questions, we have generated biologically relevant MCF10A mammary epithelial cell lines with mutations that are comparable to certain clinically important PALB2 defects. We show in a non-cancerous background how both mono- and biallelically PALB2-mutated cells exhibit gross spontaneous DNA damage and mitotic aberrations. Furthermore, PALB2-deficiency disturbs three-dimensional spheroid morphology, increases the migrational capacity and invasiveness of the cells, and broadly alters their transcriptome profiles. TGFβ signaling and KRT14 expression are enhanced in PALB2-mutated cells and their inhibition and knock down, respectively, lead to partial restoration of cell functions. KRT14-positive cells are also more abundant with DNA damage than KRT14-negative cells. The obtained results indicate comprehensive cellular changes upon PALB2 mutations, even in the presence of half dosage of wild type PALB2 and demonstrate how PALB2 mutations may predispose their carriers to malignancy.
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Affiliation(s)
- Hanna Tuppurainen
- Laboratory of Cancer Genetics and Tumor Biology, Translational Medicine Research Unit, Biocenter Oulu and Faculty of Medicine, Medical Research Center Oulu, University of Oulu, Oulu, Finland
| | - Niina Laurila
- Laboratory of Cancer Genetics and Tumor Biology, Translational Medicine Research Unit, Biocenter Oulu and Faculty of Medicine, Medical Research Center Oulu, University of Oulu, Oulu, Finland
| | - Marjut Nätynki
- Laboratory of Cancer Genetics and Tumor Biology, Translational Medicine Research Unit, Biocenter Oulu and Faculty of Medicine, Medical Research Center Oulu, University of Oulu, Oulu, Finland
| | - Leila Eshraghi
- Laboratory of Cancer Genetics and Tumor Biology, Translational Medicine Research Unit, Biocenter Oulu and Faculty of Medicine, Medical Research Center Oulu, University of Oulu, Oulu, Finland
- Garvan Institute of Medical Research, Sydney, Australia
| | - Anna Tervasmäki
- Laboratory of Cancer Genetics and Tumor Biology, Translational Medicine Research Unit, Biocenter Oulu and Faculty of Medicine, Medical Research Center Oulu, University of Oulu, Oulu, Finland
| | - Louisa Erichsen
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark
| | | | - Katri Pylkäs
- Laboratory of Cancer Genetics and Tumor Biology, Translational Medicine Research Unit, Biocenter Oulu and Faculty of Medicine, Medical Research Center Oulu, University of Oulu, Oulu, Finland
- Northern Finland Laboratory Centre, Oulu, Finland
| | - Robert Winqvist
- Laboratory of Cancer Genetics and Tumor Biology, Translational Medicine Research Unit, Biocenter Oulu and Faculty of Medicine, Medical Research Center Oulu, University of Oulu, Oulu, Finland.
| | - Hellevi Peltoketo
- Laboratory of Cancer Genetics and Tumor Biology, Translational Medicine Research Unit, Biocenter Oulu and Faculty of Medicine, Medical Research Center Oulu, University of Oulu, Oulu, Finland.
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Jantaravinid J, Tirawanchai N, Ampawong S, Kengkoom K, Somkasetrin A, Nakhonsri V, Aramwit P. Transcriptomic screening of novel targets of sericin in human hepatocellular carcinoma cells. Sci Rep 2024; 14:5455. [PMID: 38443583 PMCID: PMC10914811 DOI: 10.1038/s41598-024-56179-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 03/03/2024] [Indexed: 03/07/2024] Open
Abstract
Sericin, a natural protein derived from Bombyx mori, is known to ameliorate liver tissue damage; however, its molecular mechanism remains unclear. Herein, we aimed to identify the possible novel targets of sericin in hepatocytes and related cellular pathways. RNA sequencing analysis indicated that a low dose of sericin resulted in 18 differentially expressed genes (DEGs) being upregulated and 68 DEGs being downregulated, while 61 DEGs were upregulated and 265 DEGs were downregulated in response to a high dose of sericin (FDR ≤ 0.05, fold change > 1.50). Functional analysis revealed that a low dose of sericin regulated pathways associated with the complement and coagulation cascade, metallothionine, and histone demethylate (HDMs), whereas a high dose of sericin was associated with pathways involved in lipid metabolism, mitogen-activated protein kinase (MAPK) signaling and autophagy. The gene network analysis highlighted twelve genes, A2M, SERPINA5, MT2A, MT1G, MT1E, ARID5B, POU2F1, APOB, TRAF6, HSPA8, FGFR1, and OGT, as novel targets of sericin. Network analysis of transcription factor activity revealed that sericin affects NFE2L2, TFAP2C, STAT1, GATA3, CREB1 and CEBPA. Additionally, the protective effects of sericin depended on the counterregulation of APOB, POU2F1, OGT, TRAF6, and HSPA5. These findings suggest that sericin exerts hepatoprotective effects through diverse pathways at different doses, providing novel potential targets for the treatment of liver diseases.
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Affiliation(s)
- Jiraporn Jantaravinid
- Center of Excellence in Bioactive Resources for Innovative Clinical Applications, Department of Pharmacy Practice, Faculty of Pharmaceutical Sciences, Chulalongkorn University, 254 Phayathai Road, Pathumwan, Bangkok, 10330, Thailand
| | - Napatara Tirawanchai
- Department of Biochemistry, Faculty of Medicine Siriraj Hospital, Mahidol University, 2, Wanglang Road, Bangkoknoi, Bangkok, 10700, Thailand
| | - Sumate Ampawong
- Department of Tropical Pathology, Faculty of Tropical Medicine, Mahidol University, 420/6, Ratchawithi Road, Ratchathewi, Bangkok, 10400, Thailand
| | - Kanchana Kengkoom
- Research and Academic Support Office, National Laboratory Animal Center, Mahidol University, 999, Salaya, Puttamonthon, Nakorn Pathom, 73170, Thailand
| | - Anchaleekorn Somkasetrin
- Department of Biochemistry, Faculty of Medicine Siriraj Hospital, Mahidol University, 2, Wanglang Road, Bangkoknoi, Bangkok, 10700, Thailand
| | - Vorthunju Nakhonsri
- National Biobank of Thailand (NBT), National Science and Technology Development Agency (NSTDA), 144 Innovation Cluster 2 Building (INC) Tower A, Thailand Science Park, Khlong Nueng, Khlong Luang District, Pathum Thani, 12120, Thailand
| | - Pornanong Aramwit
- Center of Excellence in Bioactive Resources for Innovative Clinical Applications, Department of Pharmacy Practice, Faculty of Pharmaceutical Sciences, Chulalongkorn University, 254 Phayathai Road, Pathumwan, Bangkok, 10330, Thailand.
- The Academy of Science, The Royal Society of Thailand, Dusit, Bangkok, 10330, Thailand.
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Luo Y, Liu L, Zhang C. Identification and analysis of diverse cell death patterns in diabetic kidney disease using microarray-based transcriptome profiling and single-nucleus RNA sequencing. Comput Biol Med 2024; 169:107780. [PMID: 38104515 DOI: 10.1016/j.compbiomed.2023.107780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Revised: 11/11/2023] [Accepted: 11/28/2023] [Indexed: 12/19/2023]
Abstract
BACKGROUND Diabetic kidney disease (DKD) is the most lethal complication of diabetes. Diverse programmed cell death (PCD) has emerged as a crucial disease phenotype that has the potential to serve as an indicator of renal function decline and can be used as a target for researching drugs for DKD. METHODS Microarray-based transcriptome profiling and single-nucleus transcriptome sequencing (snRNA-seq) related to DKD were retrieved from the Gene Expression Omnibus (GEO) database. 13 PCD-related genes (including alkaliptosis, apoptosis, autophagy-dependent cell death, cuproptosis, disulfidptosis, entotic cell death, ferroptosis, lysosome-dependent cell death, necroptosis, netotic cell death, oxeiptosis, parthanatos, and pyroptosis) were obtained from various public databases and reviews. The gene set variation analysis (GSVA) analysis was used to explore the pathway activity of these 13 PCDs in DKD, and the pathway activity of these PCDs in different renal cells was studied based on DKD-related snRNA-seq data. To identify the core PCDs that play a significant role in DKD, we analyzed the relationships between different types of PCD and immune infiltration, fibrosis-related gene expression levels, glomerular filtration rate (GFR), and diagnostic efficiency in DKD. Using the Weighted Gene Co-expression Network Analysis (WGCNA) algorithm, we screened for core death genes among the core PCDs and constructed a cell death-related signature (CDS) risk score based on the Least Absolute Shrinkage and Selection Operator (LASSO). Finally, we validated the predictive performance of the CDS risk score in an independent validation set. RESULTS We identified 4 core PCD pathways, namely entotic cell death, apoptosis, necroptosis, and pyroptosis in DKD, and further applied the WGCNA algorithm to screen 4 core death genes (CASP1, CYBB, PLA2G4A, and CTSS) and constructed a CDS risk score based on these genes. The CDS risk score demonstrated high diagnostic efficiency for DKD patients, and those with higher scores had higher levels of immune cell infiltration and poorer GFR. CONCLUSION Our study sheds light on the fact that multiple PCDs contribute to the progression of DKD, highlighting potential therapeutic targets for treating this disease.
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Affiliation(s)
- Yuanyuan Luo
- Department of Endocrinology, Chongqing University Three Gorges Hospital, Chongqing, 404000, China; Chongqing Municipality Clinical Research Center for Endocrinology and Metabolic Diseases, Chongqing University Three Gorges Hospital, Chongqing, 404000, China.
| | - Lerong Liu
- Department of Endocrinology, Southern Medical University Nanfang Hospital, Guangzhou, 510515, China.
| | - Cheng Zhang
- Department of Endocrinology, Chongqing University Three Gorges Hospital, Chongqing, 404000, China; Chongqing Municipality Clinical Research Center for Endocrinology and Metabolic Diseases, Chongqing University Three Gorges Hospital, Chongqing, 404000, China.
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Monfeuga T, Norlin J, Bugge A, Gaalsgaard ED, Prada-Medina CA, Latta M, Veidal SS, Petersen PS, Feigh M, Holst D. Evaluation of long acting GLP1R/GCGR agonist in a DIO and biopsy-confirmed mouse model of NASH suggest a beneficial role of GLP-1/glucagon agonism in NASH patients. Mol Metab 2024; 79:101850. [PMID: 38065435 PMCID: PMC10772820 DOI: 10.1016/j.molmet.2023.101850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 11/28/2023] [Accepted: 12/02/2023] [Indexed: 12/18/2023] Open
Abstract
OBJECTIVE The metabolic benefits of GLP-1 receptor (GLP-1R) agonists on glycemic and weight control are well established as therapy for type 2 diabetes and obesity. Glucagon's ability to increase energy expenditure is well described, and the combination of these mechanisms-of-actions has the potential to further lower hepatic steatosis in metabolic disorders and could therefore be attractive for the treatment for non-alcoholic steatohepatitis (NASH). Here, we have investigated the effects of a dual GLP-1/glucagon receptor agonist NN1177 on hepatic steatosis, fibrosis, and inflammation in a preclinical mouse model of NASH. Having observed strong effects on body weight loss in a pilot study with NN1177, we hypothesized that direct engagement of the hepatic glucagon receptor (GCGR) would result in a superior effect on steatosis and other liver related parameters as compared to the GLP-1R agonist semaglutide at equal body weight. METHODS Male C57Bl/6 mice were fed a diet high in trans-fat, fructose, and cholesterol (Diet-Induced Obese (DIO)-NASH) for 36 weeks. Following randomization based on the degree of fibrosis at baseline, mice were treated once daily with subcutaneous administration of a vehicle or three different doses of NN1177 or semaglutide for 8 weeks. Hepatic steatosis, inflammation and fibrosis were assessed by immunohistochemistry and morphometric analyses. Plasma levels of lipids and liver enzymes were determined, and hepatic gene expression was analyzed by RNA sequencing. RESULTS NN1177 dose-dependently reduced body weight up to 22% compared to vehicle treatment. Plasma levels of ALT, a measure of liver injury, were reduced in all treatment groups with body weight loss. The dual agonist reduced hepatic steatosis to a greater extent than semaglutide at equal body weight loss, as demonstrated by three independent methods. Both the co-agonist and semaglutide significantly decreased histological markers of inflammation such as CD11b and Galectin-3, in addition to markers of hepatic stellate activation (αSMA) and fibrosis (Collagen I). Interestingly, the maximal beneficial effects on above mentioned clinically relevant endpoints of NN1177 treatment on hepatic health appear to be achieved with the middle dose tested. Administering the highest dose resulted in a further reduction of liver fat and accompanied by a massive induction in genes involved in oxidative phosphorylation and resulted in exaggerated body weight loss and a downregulation of a module of co-expressed genes involved in steroid hormone biology, bile secretion, and retinol and linoleic acid metabolism that are also downregulated due to NASH itself. CONCLUSIONS These results indicate that, in a setting of overnutrition, the liver health benefits of activating the fasting-related metabolic pathways controlled by the glucagon receptor displays a bell-shaped curve. This observation is of interest to the scientific community, due to the high number of ongoing clinical trials attempting to leverage the positive effects of glucagon biology to improve metabolic health.
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Affiliation(s)
- Thomas Monfeuga
- AI & Digital Research, Research & Early Development, Novo Nordisk Research Centre Oxford, UK
| | - Jenny Norlin
- Novo Nordisk A/S, Novo Park, DK-2750 Maaloev, Denmark
| | - Anne Bugge
- Novo Nordisk A/S, Novo Park, DK-2750 Maaloev, Denmark
| | | | - Cesar A Prada-Medina
- AI & Digital Research, Research & Early Development, Novo Nordisk Research Centre Oxford, UK
| | - Markus Latta
- Novo Nordisk A/S, Novo Park, DK-2750 Maaloev, Denmark
| | - Sanne S Veidal
- Gubra A/S, Hørsholm Kongevej 11, B, DK-2970 Hørsholm, Denmark
| | - Pia S Petersen
- Gubra A/S, Hørsholm Kongevej 11, B, DK-2970 Hørsholm, Denmark
| | - Michael Feigh
- Gubra A/S, Hørsholm Kongevej 11, B, DK-2970 Hørsholm, Denmark
| | - Dorte Holst
- Novo Nordisk A/S, Novo Park, DK-2750 Maaloev, Denmark.
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Kim YY, Kim SW, Kim E, Kim YJ, Kang BC, Ku SY. Transcriptomic Profiling of Reproductive Age Marmoset Monkey Ovaries. Reprod Sci 2024; 31:81-95. [PMID: 37710086 DOI: 10.1007/s43032-023-01342-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Accepted: 08/28/2023] [Indexed: 09/16/2023]
Abstract
The decline in ovarian reserve and the aging of the ovaries is a significant concern for women, particularly in the context of delayed reproduction. However, there are ethical limitations and challenges associated with conducting long-term studies to understand and manipulate the mechanisms that regulate ovarian aging in human. The marmoset monkey offers several advantages as a reproductive model, including a shorter gestation period and similar reproductive physiology to that of human. Additionally, they have a relatively long lifespan compared to other mammals, making them suitable for long-term studies. In this study, we focused on analyzing the structural characteristics of the marmoset ovary and studying the mRNA expression of 244 genes associated with ovarian aging. We obtained ovaries from marmosets at three different reproductive stages: pre-pubertal (1.5 months), reproductive (82 months), and menopausal (106 months) ovaries. The structural analyses revealed the presence of numerous mitochondria and lipid droplets in the marmoset ovaries. Many of the genes expressed in the ovaries were involved in multicellular organism development and transcriptional regulation. Additionally, we identified the expression of protein-binding genes. Within the expressed genes, VEGFA and MMP9 were found to be critical for regulating ovarian reserve. An intriguing finding of the study was the strong correlation between genes associated with female infertility and genes related to fibrosis and wound healing. The authors suggest that this correlation might be a result of the repeated rupture and subsequent healing processes occurring in the ovary due to the menstrual cycle, potentially leading to the indirect onset of fibrosis. The expression profile of ovarian aging-related gene set in the marmoset monkey ovaries highlight the need for further studies to explore the relationship between fibrosis, wound healing, and ovarian aging.
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Affiliation(s)
- Yoon Young Kim
- Department of Obstetrics and Gynecology, Seoul National University Hospital, Daehak-ro 101, Jongno-gu, Seoul, 03080, South Korea
- Institute of Reproductive Medicine and Population, Medical Research Center, Seoul National University, Seoul, South Korea
| | - Sung Woo Kim
- Department of Obstetrics and Gynecology, Seoul National University Hospital, Daehak-ro 101, Jongno-gu, Seoul, 03080, South Korea
| | - Eunjin Kim
- Department of Obstetrics and Gynecology, Seoul National University Hospital, Daehak-ro 101, Jongno-gu, Seoul, 03080, South Korea
| | - Yong Jin Kim
- Department of Obstetrics and Gynecology, Korea University College of Medicine, Seoul, South Korea
| | - Byeong-Cheol Kang
- Department of Medicine, Seoul National University College of Medicine, Seoul, South Korea
| | - Seung-Yup Ku
- Department of Obstetrics and Gynecology, Seoul National University Hospital, Daehak-ro 101, Jongno-gu, Seoul, 03080, South Korea.
- Institute of Reproductive Medicine and Population, Medical Research Center, Seoul National University, Seoul, South Korea.
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Sportes A, Hériché M, Mounier A, Durney C, van Tuinen D, Trouvelot S, Wipf D, Courty PE. Comparative RNA sequencing-based transcriptome profiling of ten grapevine rootstocks: shared and specific sets of genes respond to mycorrhizal symbiosis. Mycorrhiza 2023; 33:369-385. [PMID: 37561219 DOI: 10.1007/s00572-023-01119-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 06/23/2023] [Indexed: 08/11/2023]
Abstract
Arbuscular mycorrhizal symbiosis improves water and nutrient uptake by plants and provides them other ecosystem services. Grapevine is one of the major crops in the world. Vitis vinifera scions generally are grafted onto a variety of rootstocks that confer different levels of resistance against different pests, tolerance to environmental stress, and influence the physiology of the scions. Arbuscular mycorrhizal fungi are involved in the root architecture and in the immune response to soil-borne pathogens. However, the fine-tuned regulation and the transcriptomic plasticity of rootstocks in response to mycorrhization are still unknown. We compared the responses of 10 different grapevine rootstocks to arbuscular mycorrhizal symbiosis (AMS) formed with Rhizophagus irregularis DAOM197198 using RNA sequencing-based transcriptome profiling. We have highlighted a few shared regulation mechanisms, but also specific rootstock responses to R. irregularis colonization. A set of 353 genes was regulated by AMS in all ten rootstocks. We also compared the expression level of this set of genes to more than 2000 transcriptome profiles from various grapevine varieties and tissues to identify a class of transcripts related to mycorrhizal associations in these 10 rootstocks. Then, we compared the response of the 351 genes upregulated by mycorrhiza in grapevine to their Medicago truncatula homologs in response to mycorrhizal colonization based on available transcriptomic studies. More than 97% of the 351 M. truncatula-homologous grapevine genes were expressed in at least one mycorrhizal transcriptomic study, and 64% in every single RNAseq dataset. At the intra-specific level, we described, for the first time, shared and specific grapevine rootstock genes in response to R. irregularis symbiosis. At the inter-specific level, we defined a shared subset of mycorrhiza-responsive genes.
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Affiliation(s)
- Antoine Sportes
- Agroécologie, INRAE, Institut Agro, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, Dijon, France
| | - Mathilde Hériché
- Agroécologie, INRAE, Institut Agro, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, Dijon, France
| | - Arnaud Mounier
- Agroécologie, INRAE, Institut Agro, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, Dijon, France
| | - Célien Durney
- Agroécologie, INRAE, Institut Agro, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, Dijon, France
| | - Diederik van Tuinen
- Agroécologie, INRAE, Institut Agro, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, Dijon, France
| | - Sophie Trouvelot
- Agroécologie, INRAE, Institut Agro, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, Dijon, France
| | - Daniel Wipf
- Agroécologie, INRAE, Institut Agro, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, Dijon, France
| | - Pierre Emmanuel Courty
- Agroécologie, INRAE, Institut Agro, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, Dijon, France.
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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 Sci 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] [What about the content of this article? (0)] [Affiliation(s)] [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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10
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Zhu C, Sun Z, Wang J, Meng X, Ma Z, Guo R, Niu J, Tran LJ, Zhang J, Jiang T, Liu Y, Ye F, Ma B. Exploring oncogenes for renal clear cell carcinoma based on G protein-coupled receptor-associated genes. Discov Oncol 2023; 14:182. [PMID: 37816979 PMCID: PMC10564696 DOI: 10.1007/s12672-023-00795-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 09/19/2023] [Indexed: 10/12/2023] Open
Abstract
G protein-coupled receptors (GPCRs) are a class of receptors on cell membranes that regulate various biological processes in cells, such as cell proliferation, differentiation, migration, apoptosis, and metabolism, by interacting with G proteins. However, the role of G protein-coupled receptors in predicting the prognosis of renal clear cell carcinoma is still unknown. The transcriptome data and clinical profiles of renal clear cell carcinoma patients, were downloaded from TCGA databases, and the validation group data were downloaded from number GSE167573, including 63 tumor samples and 14 normal samples. Single-cell RNA sequencing data were downloaded from the GEO database, No. GSE152938 and selected samples were used for GSEA enrichment analysis, WGCNA subgroup analysis, single-cell data analysis, and mutation analysis to explore the role of G protein-coupled receptor-related genes in the diagnosis and prognosis of renal clear cell carcinoma and to verify their reliability with cellular experiments. Finally, this study establishes a disease model based on G protein-coupled receptor-related genes, which may help to propose targeted therapeutic regimens in different strata of renal cell carcinoma patients.Author names: Please confirm if the author names are presented accurately and in the correct sequence (given name, middle name/initial, family name). Author: Given name [Lisa Jia] Last name [Tran].It's ok!
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Affiliation(s)
- Chengcun Zhu
- Department of Urology, The First People’s Hospital of Jiangxia District, Wuhan, 430200 Hubei China
| | - Zhou Sun
- Department of Urology, China-Japan Union Hospital of Jilin University, Changchun, 130000 Jilin China
| | - Jie Wang
- Department of Urology, China-Japan Union Hospital of Jilin University, Changchun, 130000 Jilin China
- Department of Urology, The Second People’s Hospital of Meishan City, Meishan, Sichuan China
| | - Xiangdi Meng
- Department of Urology, China-Japan Union Hospital of Jilin University, Changchun, 130000 Jilin China
| | - Zhaosen Ma
- Department of Urology, China-Japan Union Hospital of Jilin University, Changchun, 130000 Jilin China
| | - Rui Guo
- Department of Urology, China-Japan Union Hospital of Jilin University, Changchun, 130000 Jilin China
| | - Jiqiang Niu
- Department of Urology, China-Japan Union Hospital of Jilin University, Changchun, 130000 Jilin China
| | - Lisa Jia Tran
- Department of General, Visceral, and Transplant Surgery, Ludwig-Maximilians-University Munich, 81377 Munich, Germany
| | - Jing Zhang
- Division of Basic Biomedical Sciences, The University of South Dakota Sanford School of Medicine, Vermillion, SD 57069 USA
| | - Tianxiao Jiang
- Department of General, Visceral, and Transplant Surgery, Ludwig-Maximilians-University Munich, 81377 Munich, Germany
| | - Yunfei Liu
- Department of General, Visceral, and Transplant Surgery, Ludwig-Maximilians-University Munich, 81377 Munich, Germany
| | - Fangdie Ye
- Department of Urology, Huashan Hospital, Fudan University, Shanghai, China
| | - Baoluo Ma
- Department of Urology, Xiangyang Central Hospital, Affiliated Hospital of Hubei University of Arts and Science, Xiangyang, Hubei China
- Department of Urology, China-Japan Union Hospital of Jilin University, Changchun, 130000 Jilin China
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11
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Hecker M, Fitzner B, Boxberger N, Putscher E, Engelmann R, Bergmann W, Müller M, Ludwig-Portugall I, Schwartz M, Meister S, Dudesek A, Winkelmann A, Koczan D, Zettl UK. Transcriptome alterations in peripheral blood B cells of patients with multiple sclerosis receiving immune reconstitution therapy. J Neuroinflammation 2023; 20:181. [PMID: 37533036 PMCID: PMC10394872 DOI: 10.1186/s12974-023-02859-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 07/25/2023] [Indexed: 08/04/2023] Open
Abstract
BACKGROUND Multiple sclerosis (MS) is a chronic, inflammatory and neurodegenerative disease that leads to irreversible damage to the brain and spinal cord. The goal of so-called "immune reconstitution therapies" (IRTs) is to achieve long-term disease remission by eliminating a pathogenic immune repertoire through intense short-term immune cell depletion. B cells are major targets for effective immunotherapy in MS. OBJECTIVES The aim of this study was to analyze the gene expression pattern of B cells before and during IRT (i.e., before B-cell depletion and after B-cell repopulation) to better understand the therapeutic effects and to identify biomarker candidates of the clinical response to therapy. METHODS B cells were obtained from blood samples of patients with relapsing-remitting MS (n = 50), patients with primary progressive MS (n = 13) as well as healthy controls (n = 28). The patients with relapsing MS received either monthly infusions of natalizumab (n = 29) or a pulsed IRT with alemtuzumab (n = 15) or cladribine (n = 6). B-cell subpopulation frequencies were determined by flow cytometry, and transcriptome profiling was performed using Clariom D arrays. Differentially expressed genes (DEGs) between the patient groups and controls were examined with regard to their functions and interactions. We also tested for differences in gene expression between patients with and without relapse following alemtuzumab administration. RESULTS Patients treated with alemtuzumab or cladribine showed on average a > 20% lower proportion of memory B cells as compared to before IRT. This was paralleled by profound transcriptome shifts, with > 6000 significant DEGs after adjustment for multiple comparisons. The top DEGs were found to regulate apoptosis, cell adhesion and RNA processing, and the most highly connected nodes in the network of encoded proteins were ESR2, PHB and RC3H1. Higher mRNA levels of BCL2, IL13RA1 and SLC38A11 were seen in patients with relapse despite IRT, though these differences did not pass the false discovery rate correction. CONCLUSIONS We show that B cells circulating in the blood of patients with MS undergoing IRT present a distinct gene expression signature, and we delineated the associated biological processes and gene interactions. Moreover, we identified genes whose expression may be an indicator of relapse risk, but further studies are needed to verify their potential value as biomarkers.
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Affiliation(s)
- Michael Hecker
- Division of Neuroimmunology, Department of Neurology, Rostock University Medical Center, Gehlsheimer Str. 20, 18147, Rostock, Germany.
| | - Brit Fitzner
- Division of Neuroimmunology, Department of Neurology, Rostock University Medical Center, Gehlsheimer Str. 20, 18147, Rostock, Germany
| | - Nina Boxberger
- Division of Neuroimmunology, Department of Neurology, Rostock University Medical Center, Gehlsheimer Str. 20, 18147, Rostock, Germany
| | - Elena Putscher
- Division of Neuroimmunology, Department of Neurology, Rostock University Medical Center, Gehlsheimer Str. 20, 18147, Rostock, Germany
| | - Robby Engelmann
- Clinic III (Hematology, Oncology and Palliative Medicine), Special Hematology Laboratory, Rostock University Medical Center, Ernst-Heydemann-Str. 6, 18057, Rostock, Germany
| | - Wendy Bergmann
- Core Facility for Cell Sorting and Cell Analysis, Rostock University Medical Center, Schillingallee 70, 18057, Rostock, Germany
| | - Michael Müller
- Core Facility for Cell Sorting and Cell Analysis, Rostock University Medical Center, Schillingallee 70, 18057, Rostock, Germany
| | | | - Margit Schwartz
- Division of Neuroimmunology, Department of Neurology, Rostock University Medical Center, Gehlsheimer Str. 20, 18147, Rostock, Germany
| | - Stefanie Meister
- Division of Neuroimmunology, Department of Neurology, Rostock University Medical Center, Gehlsheimer Str. 20, 18147, Rostock, Germany
| | - Ales Dudesek
- Division of Neuroimmunology, Department of Neurology, Rostock University Medical Center, Gehlsheimer Str. 20, 18147, Rostock, Germany
| | - Alexander Winkelmann
- Division of Neuroimmunology, Department of Neurology, Rostock University Medical Center, Gehlsheimer Str. 20, 18147, Rostock, Germany
| | - Dirk Koczan
- Institute of Immunology, Rostock University Medical Center, Schillingallee 70, 18057, Rostock, Germany
| | - Uwe Klaus Zettl
- Division of Neuroimmunology, Department of Neurology, Rostock University Medical Center, Gehlsheimer Str. 20, 18147, Rostock, Germany
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12
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Sehar S, Adil MF, Askri SMH, Feng Q, Wei D, Sahito FS, Shamsi IH. Pan-transcriptomic Profiling Demarcates Serendipita Indica-Phosphorus Mediated Tolerance Mechanisms in Rice Exposed to Arsenic Toxicity. Rice (N Y) 2023; 16:28. [PMID: 37354226 DOI: 10.1186/s12284-023-00645-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 06/10/2023] [Indexed: 06/26/2023]
Abstract
Inadvertent accumulation of arsenic (As) in rice (Oryza sativa L.) is a concern for people depending on it for their subsistence, as it verily causes epigenetic alterations across the genome as well as in specific cells. To ensure food safety, certain attempts have been made to nullify this highest health hazard encompassing physiological, chemical and biological methods. Albeit, the use of mycorrhizal association along with nutrient reinforcement strategy has not been explored yet. Mechanisms of response and resistance of two rice genotypes to As with or without phosphorus (P) nutrition and Serendipita indica (S. indica; S.i) colonization were explored by root transcriptome profiling in the present study. Results revealed that the resistant genotype had higher auxin content and root plasticity, which helped in keeping the As accumulation and P starvation response to a minimum under alone As stress. However, sufficient P supply and symbiotic relationship switched the energy resources towards plant's developmental aspects rather than excessive root proliferation. Higher As accumulating genotype (GD-6) displayed upregulation of ethylene signaling/biosynthesis, root stunting and senescence related genes under As toxicity. Antioxidant defense system and cytokinin biosynthesis/signaling of both genotypes were strengthened under As + S.i + P, while the upregulation of potassium (K) and zinc (Zn) transporters depicted underlying cross-talk with iron (Fe) and P. Differential expression of phosphate transporters, peroxidases and GSTs, metal detoxification/transport proteins, as well as phytohormonal metabolism were responsible for As detoxification. Taken together, S. indica symbiosis fortified with adequate P-fertilizer can prove to be effective in minimizing As acquisition and accumulation in rice plants.
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Affiliation(s)
- Shafaque Sehar
- Zhejiang Key Laboratory of Crop Germplasm Resource, Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Muhammad Faheem Adil
- Zhejiang Key Laboratory of Crop Germplasm Resource, Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Syed Muhammad Hassan Askri
- Zhejiang Key Laboratory of Crop Germplasm Resource, Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Qidong Feng
- Zhejiang Key Laboratory of Crop Germplasm Resource, Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Dongming Wei
- Zhejiang Key Laboratory of Crop Germplasm Resource, Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Falak Sehar Sahito
- Dow International Medical College, Dow University of Health Sciences, Karachi, 74200, Pakistan
| | - Imran Haider Shamsi
- Zhejiang Key Laboratory of Crop Germplasm Resource, Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China.
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Tsers I, Marenina E, Meshcherov A, Petrova O, Gogoleva O, Tkachenko A, Gogoleva N, Gogolev Y, Potapenko E, Muraeva O, Ponomareva M, Korzun V, Gorshkov V. First genome-scale insights into the virulence of the snow mold causal fungus Microdochium nivale. IMA Fungus 2023; 14:2. [PMID: 36627722 PMCID: PMC9830731 DOI: 10.1186/s43008-022-00107-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Accepted: 12/16/2022] [Indexed: 01/12/2023] Open
Abstract
Pink snow mold, caused by a phytopathogenic and psychrotolerant fungus, Microdochium nivale, is a severe disease of winter cereals and grasses that predominantly occurs under snow cover or shortly after its melt. Snow mold has significantly progressed during the past decade, often reaching epiphytotic levels in northern countries and resulting in dramatic yield losses. In addition, M. nivale gradually adapts to a warmer climate, spreading to less snowy territories and causing different types of plant diseases throughout the growing period. Despite its great economic importance, M. nivale is poorly investigated; its genome has not been sequenced and its crucial virulence determinants have not been identified or even predicted. In our study, we applied a hybrid assembly based on Oxford Nanopore and Illumina reads to obtain the first genome sequence of M. nivale. 11,973 genes (including 11,789 protein-encoding genes) have been revealed in the genome assembly. To better understand the genetic potential of M. nivale and to obtain a convenient reference for transcriptomic studies on this species, the identified genes were annotated and split into hierarchical three-level functional categories. A file with functionally classified M. nivale genes is presented in our study for general use. M. nivale gene products that best meet the criteria for virulence factors have been identified. The genetic potential to synthesize human-dangerous mycotoxins (fumonisin, ochratoxin B, aflatoxin, and gliotoxin) has been revealed for M. nivale. The transcriptome analysis combined with the assays for extracellular enzymatic activities (conventional virulence factors of many phytopathogens) was carried out to assess the effect of host plant (rye) metabolites on the M. nivale phenotype. In addition to disclosing plant-metabolite-upregulated M. nivale functional gene groups (including those related to host plant protein destruction and amino acid metabolism, xenobiotic detoxication (including phytoalexins benzoxazinoids), cellulose destruction (cellulose monooxygenases), iron transport, etc.), the performed analysis pointed to a crucial role of host plant lipid destruction and fungal lipid metabolism modulation in plant-M. nivale interactions.
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Affiliation(s)
- Ivan Tsers
- grid.465285.80000 0004 0637 9007Federal Research Center, Kazan Scientific Center of the Russian Academy of Sciences, Kazan, Russia 420111
| | - Ekaterina Marenina
- grid.465285.80000 0004 0637 9007Federal Research Center, Kazan Scientific Center of the Russian Academy of Sciences, Kazan, Russia 420111
| | - Azat Meshcherov
- grid.465285.80000 0004 0637 9007Federal Research Center, Kazan Scientific Center of the Russian Academy of Sciences, Kazan, Russia 420111
| | - Olga Petrova
- grid.465285.80000 0004 0637 9007Federal Research Center, Kazan Scientific Center of the Russian Academy of Sciences, Kazan, Russia 420111
| | - Olga Gogoleva
- grid.465285.80000 0004 0637 9007Federal Research Center, Kazan Scientific Center of the Russian Academy of Sciences, Kazan, Russia 420111
| | - Alexander Tkachenko
- grid.35915.3b0000 0001 0413 4629Laboratory of Computer Technologies, ITMO University, Saint Petersburg, Russia 197101
| | - Natalia Gogoleva
- grid.465285.80000 0004 0637 9007Federal Research Center, Kazan Scientific Center of the Russian Academy of Sciences, Kazan, Russia 420111
| | - Yuri Gogolev
- grid.465285.80000 0004 0637 9007Federal Research Center, Kazan Scientific Center of the Russian Academy of Sciences, Kazan, Russia 420111
| | - Evgenii Potapenko
- grid.18098.380000 0004 1937 0562Institute of Evolution, University of Haifa, 3498838 Haifa, Israel ,grid.18098.380000 0004 1937 0562Department of Evolutionary and Environmental Biology, University of Haifa, 3498838 Haifa, Israel
| | - Olga Muraeva
- grid.512700.1Bioinformatics Institute, Saint Petersburg, Russia 197342
| | - Mira Ponomareva
- grid.465285.80000 0004 0637 9007Federal Research Center, Kazan Scientific Center of the Russian Academy of Sciences, Kazan, Russia 420111
| | - Viktor Korzun
- grid.465285.80000 0004 0637 9007Federal Research Center, Kazan Scientific Center of the Russian Academy of Sciences, Kazan, Russia 420111 ,grid.425691.dKWS SAAT SE & Co. KGaA, 37555 Einbeck, Germany
| | - Vladimir Gorshkov
- grid.465285.80000 0004 0637 9007Federal Research Center, Kazan Scientific Center of the Russian Academy of Sciences, Kazan, Russia 420111
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14
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Li Z, Qin H, Zhang Y, He X, Bao X, Sun G, Cui C, Xu X, Liu X, Yang J, Zhang G. Transcriptome analysis preliminary reveals the immune response mechanism of golden cuttlefish (Sepia esculenta) larvae exposed to Cd. Fish Shellfish Immunol 2023; 132:108494. [PMID: 36565999 DOI: 10.1016/j.fsi.2022.108494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 11/18/2022] [Accepted: 12/08/2022] [Indexed: 06/17/2023]
Abstract
As a well-known marine metal element, Cd can significantly affect bivalve mollusk life processes such as growth and development. However, the effects of Cd on the molecular mechanisms of the economically important cephalopod species Sepia esculenta remain unclear. In this study, S. esculenta larval immunity exposed to Cd is explored based on RNA-Seq. The analyses of GO, KEGG, and protein-protein interaction (PPI) network of 1,471 differentially expressed genes (DEGs) reveal that multiple immune processes are affected by exposure such as inflammatory reaction and cell adhesion. Comprehensive analyses of KEGG signaling pathways and the PPI network are first used to explore Cd-exposed S. esculenta larval immunity, revealing the presence of 16 immune-related key and hub genes involved in exposure response. Results of gene and pathway functional analyses increase our understanding of Cd-exposed S. esculenta larval immunity and improve our overall understanding of mollusk immune functions.
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Affiliation(s)
- Zan Li
- School of Agriculture, Ludong University, Yantai, 264025, China
| | - Huimin Qin
- School of Agriculture, Ludong University, Yantai, 264025, China
| | - Yining Zhang
- School of Agriculture, Ludong University, Yantai, 264025, China
| | - Xiaohua He
- School of Agriculture, Ludong University, Yantai, 264025, China
| | - Xiaokai Bao
- School of Agriculture, Ludong University, Yantai, 264025, China
| | - Guohua Sun
- School of Agriculture, Ludong University, Yantai, 264025, China
| | - Cuiju Cui
- School of Agriculture, Ludong University, Yantai, 264025, China
| | - Xiaohui Xu
- School of Agriculture, Ludong University, Yantai, 264025, China
| | - Xiumei Liu
- College of Life Sciences, Yantai University, Yantai, 264005, China
| | - Jianmin Yang
- School of Agriculture, Ludong University, Yantai, 264025, China.
| | - Guoguang Zhang
- School of Agriculture, Ludong University, Yantai, 264025, China; Laizhou Marine Development and Fishery Service Center, Yantai, 261499, China.
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15
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Ul-Rahman A, Rabani M, Shabbir MZ. A comparative evaluation of transcriptome changes in lung and spleen tissues of chickens infected with velogenic and mesogenic Avian Orthoavulavirus 1. Microb Pathog 2023; 174:105956. [PMID: 36572195 DOI: 10.1016/j.micpath.2022.105956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 12/15/2022] [Accepted: 12/16/2022] [Indexed: 12/24/2022]
Abstract
Newcastle disease is an acute, highly contagious disease responsible for severe economic losses to the poultry industry worldwide. Clinical assessment of different pathotypes of AOaV-1 strains is well-elucidated in chickens. However, a paucity of data exists for a comparative assessment of avian innate immune responses in birds after infection with two different pathotypes of AOaV-1. We compared early immune responses in chickens infected with a duck-originated velogenic strain (high virulent: genotype VII) and a pigeon-originated mesogenic stain (moderate virulent; genotype VI). Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) identified 4737 differentially expressed genes (DEGs) in the transcriptional profiles of lung and spleen tissues of chickens infected with both pathotypes. More DEGs were expressed in spleen tissue infected with velogenic strain compared to spleen or lung exposed to mesogenic strain. An enriched expression was observed for genes involved in metabolic processes and cellular components, including innate immune-associated signaling pathways. Most DEGs were involved in RIG-I, Toll-like, NF-Kappa B, and MAPK signaling pathways to activate interferon-stimulated genes (ISGs). This study provided a comparative insight into complicated molecular mechanisms and associated DEGs involved in early immune responses of birds to two different AOaV-1 strains.
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Affiliation(s)
- Aziz Ul-Rahman
- Department of Pathobiology, Faculty of Veterinary and Animal Sciences, MNS University of Agriculture, Multan, 66000, Pakistan
| | - Masood Rabani
- Institute of Microbiology, University of Veterinary and Animal Sciences Lahore, 54600, Pakistan
| | - Muhammad Zubair Shabbir
- Institute of Microbiology, University of Veterinary and Animal Sciences Lahore, 54600, Pakistan.
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16
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Kong C, Yang EJ, Shin J, Park J, Kim SH, Park SW, Chang WS, Lee CH, Kim H, Kim HS, Chang JW. Enhanced delivery of a low dose of aducanumab via FUS in 5×FAD mice, an AD model. Transl Neurodegener 2022; 11:57. [PMID: 36575534 PMCID: PMC9793531 DOI: 10.1186/s40035-022-00333-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 12/08/2022] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Aducanumab (Adu), which is a human IgG1 monoclonal antibody that targets oligomer and fibril forms of beta-amyloid, has been reported to reduce amyloid pathology and improve impaired cognition after administration of a high dose (10 mg/kg) of the drug in Alzheimer's disease (AD) clinical trials. The purpose of this study was to investigate the effects of a lower dose of Adu (3 mg/kg) with enhanced delivery via focused ultrasound (FUS) in an AD mouse model. METHODS The FUS with microbubbles opened the blood-brain barrier (BBB) of the hippocampus for the delivery of Adu. The combined therapy of FUS and Adu was performed three times in total and each treatment was performed biweekly. Y-maze test, Brdu labeling, and immunohistochemical experimental methods were employed in this study. In addition, RNA sequencing and ingenuity pathway analysis were employed to investigate gene expression profiles in the hippocampi of experimental animals. RESULTS The FUS-mediated BBB opening markedly increased the delivery of Adu into the brain by approximately 8.1 times in the brains. The combined treatment induced significantly less cognitive decline and decreased the level of amyloid plaques in the hippocampi of the 5×FAD mice compared with Adu or FUS alone. Combined treatment with FUS and Adu activated phagocytic microglia and increased the number of astrocytes associated with amyloid plaques in the hippocampi of 5×FAD mice. Furthermore, RNA sequencing identified that 4 enriched canonical pathways including phagosome formation, neuroinflammation signaling, CREB signaling and reelin signaling were altered in the hippocami of 5×FAD mice receiving the combined treatment. CONCLUSION In conclusion, the enhanced delivery of a low dose of Adu (3 mg/kg) via FUS decreases amyloid deposits and attenuates cognitive function deficits. FUS-mediated BBB opening increases adult hippocampal neurogenesis as well as drug delivery. We present an AD treatment strategy through the synergistic effect of the combined therapy of FUS and Adu.
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Affiliation(s)
- Chanho Kong
- Department of Neurosurgery, Yonsei University College of Medicine, 50 Yonsei-Ro, Seodaemun-Gu, Seoul, Republic of Korea
| | - Eun-Jeong Yang
- Department of Pharmacology, College of Medicine, Seoul National University, 103 Daehakro, Jongro-Gu, Seoul, Republic of Korea
- Neuroscience Research Center, College of Medicine, Seoul National University, 103 Daehakro, Jongro-Gu, Seoul, Republic of Korea
| | - Jaewoo Shin
- Department of Neurosurgery, Yonsei University College of Medicine, 50 Yonsei-Ro, Seodaemun-Gu, Seoul, Republic of Korea
| | - Junwon Park
- Department of Neurosurgery, Yonsei University College of Medicine, 50 Yonsei-Ro, Seodaemun-Gu, Seoul, Republic of Korea
| | - Si-Hyun Kim
- Department of Pharmacology, College of Medicine, Seoul National University, 103 Daehakro, Jongro-Gu, Seoul, Republic of Korea
- Neuroscience Research Center, College of Medicine, Seoul National University, 103 Daehakro, Jongro-Gu, Seoul, Republic of Korea
| | - Seong-Wook Park
- Department of Pharmacology, College of Medicine, Seoul National University, 103 Daehakro, Jongro-Gu, Seoul, Republic of Korea
| | - Won Seok Chang
- Department of Neurosurgery, Yonsei University College of Medicine, 50 Yonsei-Ro, Seodaemun-Gu, Seoul, Republic of Korea
| | - Chang-Han Lee
- Department of Pharmacology, College of Medicine, Seoul National University, 103 Daehakro, Jongro-Gu, Seoul, Republic of Korea
- Department of Biomedical Sciences, College of Medicine, Seoul National University, 103 Daehakro, Jongro-Gu, Seoul, Republic of Korea
| | - Hyunju Kim
- Department of Pharmacology, College of Medicine, Seoul National University, 103 Daehakro, Jongro-Gu, Seoul, Republic of Korea.
- Neuroscience Research Center, College of Medicine, Seoul National University, 103 Daehakro, Jongro-Gu, Seoul, Republic of Korea.
| | - Hye-Sun Kim
- Department of Biomedical Sciences, College of Medicine, Seoul National University, 103 Daehakro, Jongro-Gu, Seoul, Republic of Korea.
- Bundang Hospital, Seoul National University College of Medicine, Bundang-Gu, Sungnam, Republic of Korea.
| | - Jin Woo Chang
- Department of Neurosurgery, Yonsei University College of Medicine, 50 Yonsei-Ro, Seodaemun-Gu, Seoul, Republic of Korea.
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Wu X, Yun D, Sang M, Liu J, Zhou L, Shi J, Wang L, Bu T, Li L, Huang Y, Lin D, Sun F, Cheng CY. Defects of microtubule cytoskeletal organization in NOA human testes. Reprod Biol Endocrinol 2022; 20:154. [PMID: 36329464 PMCID: PMC9632130 DOI: 10.1186/s12958-022-01026-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Accepted: 10/16/2022] [Indexed: 11/06/2022] Open
Abstract
The importance of actin and microtubule (MT) cytoskeletons in testis function in rodents is known to some extent, but its role in the etiology of azoospermia in humans remains unexplored. Here, we examined if MT cytoskeleton was defective in NOA (non-obstructive azoospermia) testes versus normal human testes based on histopathological, immunofluorescence (IF), and scRNA-Seq transcriptome profiling. Testis biopsy samples from n = 6 normal men versus n = 3 Sertoli cell only (SCO) and n = 3 MA (meiotic arrest) of NOA patients were used for histopathological analysis. IF analysis was also used to examine MT organization across the seminiferous epithelium, investigating the likely involvement of microtubule-associated proteins (MAPs). scRNA-Seq transcriptome profiling datasets from testes of 3 SCO patients versus 3 normal men in public domain in Gene Expression Omnibus (GEO) Sample (GSM) with identifiers were analyzed to examine relevant genes that regulate MT dynamics. NOA testes of MA and SCO patients displayed notable defects in MT organization across the epithelium with extensive truncation, mis-alignments and appeared as collapsed structures near the base of the tubules. These changes are in contrast to MTs in testes of normal men. scRNA-Seq analyses revealed considerable loss of spermatogenesis capacity in SCO testes of NOA patients versus normal men. An array of genes that support MT dynamics displayed considerable changes in expression and in spatial distribution. In summary, defects in MT cytoskeleton were noted in testes of NOA (SCO) patients, possibly mediated by defective spatial expression and/or distribution of MAPs. These changes, in turn, may impede spermatogenesis in SCO testes of NOA patients.
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Affiliation(s)
- Xiaolong Wu
- Department of Urology and Andrology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, 310016, Zhejiang, China
- Institute of Reproductive Medicine, Nantong University School of Medicine, Nantong, 226001, Jiangsu, China
| | - Damin Yun
- Institute of Reproductive Medicine, Nantong University School of Medicine, Nantong, 226001, Jiangsu, China
| | - Mengmeng Sang
- Institute of Reproductive Medicine, Nantong University School of Medicine, Nantong, 226001, Jiangsu, China
| | - Jianpeng Liu
- Department of Pathology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325027, Zhejiang, China
| | - Liwei Zhou
- Institute of Reproductive Medicine, Nantong University School of Medicine, Nantong, 226001, Jiangsu, China
| | - Jie Shi
- Institute of Reproductive Medicine, Nantong University School of Medicine, Nantong, 226001, Jiangsu, China
| | - Lingling Wang
- Institute of Reproductive Medicine, Nantong University School of Medicine, Nantong, 226001, Jiangsu, China
| | - Tiao Bu
- Institute of Reproductive Medicine, Nantong University School of Medicine, Nantong, 226001, Jiangsu, China
| | - Linxi Li
- The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325027, Zhejiang, China
| | - YingYing Huang
- Institute of Reproductive Medicine, Nantong University School of Medicine, Nantong, 226001, Jiangsu, China
| | - Dengfeng Lin
- Institute of Reproductive Medicine, Nantong University School of Medicine, Nantong, 226001, Jiangsu, China
| | - Fei Sun
- Department of Urology and Andrology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, 310016, Zhejiang, China.
| | - C Yan Cheng
- Department of Urology and Andrology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, 310016, Zhejiang, China.
- Institute of Reproductive Medicine, Nantong University School of Medicine, Nantong, 226001, Jiangsu, China.
- Center for Biomedical Research, The Mary M. Wohlford Laboratory for Male Contraceptive Research, Population Council, 1230 York Ave, New York, NY, 10065, USA.
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18
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Taghizadeh E, Heydarheydari S, Saberi A, JafarpoorNesheli S, Rezaeijo SM. Breast cancer prediction with transcriptome profiling using feature selection and machine learning methods. BMC Bioinformatics 2022; 23:410. [PMID: 36183055 PMCID: PMC9526906 DOI: 10.1186/s12859-022-04965-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 09/27/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND We used a hybrid machine learning systems (HMLS) strategy that includes the extensive search for the discovery of the most optimal HMLSs, including feature selection algorithms, a feature extraction algorithm, and classifiers for diagnosing breast cancer. Hence, this study aims to obtain a high-importance transcriptome profile linked with classification procedures that can facilitate the early detection of breast cancer. METHODS In the present study, 762 breast cancer patients and 138 solid tissue normal subjects were included. Three groups of machine learning (ML) algorithms were employed: (i) four feature selection procedures are employed and compared to select the most valuable feature: (1) ANOVA; (2) Mutual Information; (3) Extra Trees Classifier; and (4) Logistic Regression (LGR), (ii) a feature extraction algorithm (Principal Component Analysis), iii) we utilized 13 classification algorithms accompanied with automated ML hyperparameter tuning, including (1) LGR; (2) Support Vector Machine; (3) Bagging; (4) Gaussian Naive Bayes; (5) Decision Tree; (6) Gradient Boosting Decision Tree; (7) K Nearest Neighborhood; (8) Bernoulli Naive Bayes; (9) Random Forest; (10) AdaBoost, (11) ExtraTrees; (12) Linear Discriminant Analysis; and (13) Multilayer Perceptron (MLP). For evaluating the proposed models' performance, balance accuracy and area under the curve (AUC) were used. RESULTS Feature selection procedure LGR + MLP classifier achieved the highest prediction accuracy and AUC (balanced accuracy: 0.86, AUC = 0.94), followed by an LGR + LGR classifier (balanced accuracy: 0.84, AUC = 0.94). The results showed that achieved AUC for the LGR + LGR classifier belonged to the 20 biomarkers as follows: TMEM212, SNORD115-13, ATP1A4, FRG2, CFHR4, ZCCHC13, FLJ46361, LY6G6E, ZNF323, KRT28, KRT25, LPPR5, C10orf99, PRKACG, SULT2A1, GRIN2C, EN2, GBA2, CUX2, and SNORA66. CONCLUSIONS The best performance was achieved using the LGR feature selection procedure and MLP classifier. Results show that the 20 biomarkers had the highest score or ranking in breast cancer detection.
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Affiliation(s)
- Eskandar Taghizadeh
- Department of Medical Genetic, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Sahel Heydarheydari
- Department of Radiology Technology, Shoushtar Faculty of Medical Sciences, Shoushtar, Iran
| | - Alihossein Saberi
- Department of Medical Genetic, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | | | - Seyed Masoud Rezaeijo
- Department of Medical Physics, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.
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Jiang X, Dai J, Zhang X, Wu H, Tong J, Shi J, Fang W. Enhanced Cd efflux capacity and physiological stress resistance: The beneficial modulations of Metarhizium robertsii on plants under cadmium stress. J Hazard Mater 2022; 437:129429. [PMID: 35753299 DOI: 10.1016/j.jhazmat.2022.129429] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 06/07/2022] [Accepted: 06/18/2022] [Indexed: 06/15/2023]
Abstract
Due to the high migration capacity in agricultural soil-crop systems, cadmium (Cd) is accumulated in various crops and severely inhibits plant growth. In this study, we showed that, under Cd stress, the plant-symbiotic fungus Metarhizium robertsii reduced Cd accumulation in Arabidopsis thaliana shoots and roots by 21.8 % and 23.8 %, respectively. This is achieved by M. robertsii colonization-induced elevation of Cd efflux capacity via upregulation of three PCR genes, which is confirmed by the fact that the extent to which M. robertsii reduced Cd accumulation in the WT plants was greater than the inactivating mutants of the PCR genes. M. robertsii also alleviated Cd-induced leaf etiolation in A. thaliana by increasing the chlorophyll amount and modified plant physiological status to increase Cd stress tolerance via increasing production of catalase, peroxidase and glutathione and upregulating multiple HIPP proteins involved in sequestration of Cd. Notably, consistent with that in A. thaliana, the colonization of M. robertsii also reduced the Cd accumulation in Oryza sativa seedlings by upregulating the PCR gene OsPCR1, and increased chlorophyll amount and alleviated oxidative stress. Therefore, M. robertsii colonization reduced Cd accumulation in plants, and promoted plant growth and health by elevating Cd efflux capacity and modifying physiological status.
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Affiliation(s)
- Xiaohan Jiang
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Jin Dai
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Institute of Microbiology, College of Life Science, Zhejiang University, Hangzhou 310058, China
| | - Xing Zhang
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Institute of Microbiology, College of Life Science, Zhejiang University, Hangzhou 310058, China
| | - Hanxin Wu
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - JianHao Tong
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Jiyan Shi
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China.
| | - Weiguo Fang
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Institute of Microbiology, College of Life Science, Zhejiang University, Hangzhou 310058, China.
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20
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Shen H, Li C, He M, Huang Y, Wang J, Luo J, Wang M, Yue B, Zhang X. Whole blood transcriptome profiling identifies candidate genes associated with alopecia in male giant pandas (Ailuropoda melanoleuca). BMC Genomics 2022; 23:297. [PMID: 35413801 PMCID: PMC9004003 DOI: 10.1186/s12864-022-08501-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 03/22/2022] [Indexed: 11/16/2022] Open
Abstract
Background The giant panda (Ailuropoda melanoleuca) is a threatened species endemic to China. Alopecia, characterized by thinning and broken hair, mostly occurs in breeding males. Alopecia significantly affects the health and public image of the giant panda and the cause of alopecia is unclear. Results Here, we researched gene expression profiles of four alopecia giant pandas and seven healthy giant pandas. All pandas were approximately ten years old and their blood samples collected during the breeding season. A total of 458 up-regulated DEGs and 211 down-regulated DEGs were identified. KEGG pathway enrichment identified that upregulated genes were enriched in the Notch signaling pathway and downregulated genes were enriched in ribosome, oxidative phosphorylation, and thermogenesis pathways. We obtained 28 hair growth-related DEGs, and identified three hub genes NOTCH1, SMAD3, and TGFB1 in PPI analysis. Five hair growth-related signaling pathways were identified with abnormal expression, these were Notch, Wnt, TGF-β, Mapk, and PI3K-Akt. The overexpression of NOTCH1 delays inner root sheath differentiation and results in hair shaft abnormalities. The delayed hair regression was associated with a significant decrease in the expression levels of TGFB1. Conclusions Our data confirmed the abnormal expression of several hair-related genes and pathways and identified alopecia candidate genes in the giant panda. Results of this study provide theoretical basis for the establishment of prevention and treatment strategies for giant pandas with alopecia. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08501-z.
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Affiliation(s)
- Haibo Shen
- Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, College of Life Science, Sichuan University, Chengdu, 610064, PR China
| | - Caiwu Li
- Key Laboratory of State Forestry and Grassland Administration On Conservation Biology of Rare Animals in The Giant Panda National Park, China Conservation and Research Center for the Giant Panda, Dujiangyan, 611830, Sichuan, PR China
| | - Ming He
- Key Laboratory of State Forestry and Grassland Administration On Conservation Biology of Rare Animals in The Giant Panda National Park, China Conservation and Research Center for the Giant Panda, Dujiangyan, 611830, Sichuan, PR China
| | - Yan Huang
- Key Laboratory of State Forestry and Grassland Administration On Conservation Biology of Rare Animals in The Giant Panda National Park, China Conservation and Research Center for the Giant Panda, Dujiangyan, 611830, Sichuan, PR China
| | - Jing Wang
- Key Laboratory of State Forestry and Grassland Administration On Conservation Biology of Rare Animals in The Giant Panda National Park, China Conservation and Research Center for the Giant Panda, Dujiangyan, 611830, Sichuan, PR China
| | - Jing Luo
- Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, College of Life Science, Sichuan University, Chengdu, 610064, PR China
| | - Minglei Wang
- Key Laboratory of State Forestry and Grassland Administration On Conservation Biology of Rare Animals in The Giant Panda National Park, China Conservation and Research Center for the Giant Panda, Dujiangyan, 611830, Sichuan, PR China
| | - Bisong Yue
- Sichuan Key Laboratory of Conservation Biology On Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, 610064, PR China
| | - Xiuyue Zhang
- Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, College of Life Science, Sichuan University, Chengdu, 610064, PR China. .,No. 24 South Section 1, Yihuan Road, Chengdu, 610065, Sichuan, China.
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21
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Jaree P, Boonchuen P, Thawonsuwan J, Kondo H, Hirono I, Somboonwiwat K. Transcriptome profiling reveals the novel immunometabolism-related genes against WSSV infection from Fenneropenaeus merguiensis. Fish Shellfish Immunol 2022; 120:31-44. [PMID: 34758397 DOI: 10.1016/j.fsi.2021.11.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 11/02/2021] [Accepted: 11/04/2021] [Indexed: 06/13/2023]
Abstract
The white spot syndrome virus (WSSV) has been considered a serious threat to shrimp aquaculture. Besides, the activation of cell metabolism as an immune reaction to the virus is now recognized as a piece of the pivotal puzzle of the antiviral responses. Hence, this study explores the relationship between metabolic gene expression and antiviral responses in shrimp using transcriptome analysis. The RNA-seq libraries of Fenneropenaeus merguensis hemocytes after WSSV challenge at early (6 hpi) and late (24 hpi) stages of infection were analyzed to identify differentially expressed genes (DEGs) that the WSSV subverted the expression. One-hundred-thirty-three DEGs that were expressed in response to WSSV infection at both stages were identified. Based on the GO annotation, they were related to innate immunity and metabolic pathway. The expression correlation between "full term" (NGS) and qRT-PCR of 16 representative DEGs is shown. Noticeably, the expression profiles of all the selected metabolic genes involved in glucose metabolism, lipid metabolism, amino acid metabolism, and nucleotide metabolism showed a specific correlation between NGS and qRT-PCR upon WSSV infection. Of these, we further characterized the function related to the WSSV response of glutamine: fructose-6-phosphate aminotransferase (FmGFAT), the rate-limiting enzyme of the hexosamine biosynthesis pathway, which was found to be up-regulated at the late stage of WSSV infection. Suppression of FmGFAT by RNA interference resulted in postponing the death of WSSV-infected shrimp and reduction of viral copy number. These results suggested that the FmGFAT is linked between metabolic change and WSSV responses in shrimp, where the virus-induced metabolic rewiring hijack biological compounds and/or energy sources to benefit the viral replication process.
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Affiliation(s)
- Phattarunda Jaree
- Center of Applied Shrimp Research and Innovation, Institute of Molecular Biosciences, Mahidol University, Salaya, Nakhon Pathom, Thailand
| | - Pakpoom Boonchuen
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima, Thailand
| | - Jumroensri Thawonsuwan
- Songkhla Aquatic Animal Health Research Center, Department of Fisheries, Songkhla, Thailand
| | - Hidehiro Kondo
- Graduate School of Marine Science and Technology, Tokyo University of Marine Science and Technology, Minato-ku, Tokyo, Japan
| | - Ikuo Hirono
- Graduate School of Marine Science and Technology, Tokyo University of Marine Science and Technology, Minato-ku, Tokyo, Japan
| | - Kunlaya Somboonwiwat
- Center of Excellence for Molecular Biology and Genomics of Shrimp, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand.
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Cregut M, Hua A, Jouanneau S, Assaf A, Cordella CBY, Thouand G, Durand MJ. Screening of metallic pollution in complex environmental samples through a transcriptomic fingerprint method. Environ Sci Pollut Res Int 2022; 29:1037-1050. [PMID: 34341931 DOI: 10.1007/s11356-021-15545-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 07/16/2021] [Indexed: 06/13/2023]
Abstract
Characterizing waste ecotoxicity is laborious because of both the undefined nature of environmental samples and the diversity of contaminants that can be present. With regard to these limitations, traditional approaches do not provide information about the nature of the pollution encountered. To improve such assessments, a fluorescent library of 1870 transcriptomic reporters from Escherichia coli K12 MG1655 was used to report the ecotoxic status of environmental samples. The reliability of the approach was evaluated with 6 metallic pollutants (As, Cu, Cd, Hg, Pb, Zn) used alone and in mixture in pure and complex matrices. A total of 18 synthetic samples were used to characterize the specificity of the resulting metallic contamination fingerprints. Metallic contamination impacted 4.5 to 10.2% of the whole transcriptomic fingerprint of E. coli. The analysis revealed that a subset of 175 transcriptomic reporters is sufficient to characterize metallic contamination, regardless of the nature of the sample. A statistical model distinguished patterns due to metallic contamination and provided information about the level of toxicity with 93 to 98% confidence. The use of the transcriptomic assessment was validated for 17 complex matrices with various toxicities and metal contaminants, such as activated sludge, wastewater effluent, soil, wood and river water. The presence of metals and their associated toxicity, which seems linked to their bioavailabilities, were thereby determined. This method constitutes a possible tool to screen unknown complex samples for their metallic status and identify those for which a deeper characterization must be achieved by the use of traditional biosensors and analytical methods.
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Affiliation(s)
- Mickael Cregut
- University of Nantes, Oniris, CNRS, GEPEA, UMR 6144, F-85000, La Roche sur Yon, France.
- University of Nantes, CAPACITES, 26 Bd Vincent Gâche, F-44200, Nantes, France.
| | - Anna Hua
- University of Nantes, Oniris, CNRS, GEPEA, UMR 6144, F-85000, La Roche sur Yon, France
| | - Sulivan Jouanneau
- University of Nantes, Oniris, CNRS, GEPEA, UMR 6144, F-85000, La Roche sur Yon, France
| | - Ali Assaf
- University of Nantes, Oniris, CNRS, GEPEA, UMR 6144, F-85000, La Roche sur Yon, France
| | - Christophe B Y Cordella
- University of Paris-Saclay, UMR AgroParisTech/INRA 914 Physiologie de la Nutrition et du Comportement Alimentaire, Rue Claude Bernard, 75, ,005, Paris, France
| | - Gérald Thouand
- University of Nantes, Oniris, CNRS, GEPEA, UMR 6144, F-85000, La Roche sur Yon, France
| | - Marie-José Durand
- University of Nantes, Oniris, CNRS, GEPEA, UMR 6144, F-85000, La Roche sur Yon, France
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Verma R, Sharma PC. Identification of stage-specific differentially expressed genes and SNPs in gastric cancer employing RNA-Seq based transcriptome profiling. Genomics 2021; 114:61-71. [PMID: 34839019 DOI: 10.1016/j.ygeno.2021.11.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 11/23/2021] [Indexed: 12/24/2022]
Abstract
We analysed over 400 million reads obtained from Illumina sequencing of six pairs of libraries representing two each of stage I, II, and III gastric tumors and corresponding normal tissues to identify differentially expressed genes (DEGs), single nucleotide polymorphisms (SNPs), and transcription factors (TFs). In total, 2207 DEGs including 972 upregulated genes and 1235 downregulated genes were detected. Of these, several stage-specific signature genes were identified. The protein-protein interaction networks involving DEGs and TFs were constructed. The KEGG pathway analysis of SNP harbouring genes revealed their involvement in different cancer related pathways like apoptosis, mTOR pathway, and MAPK signaling pathway. The SNP analysis showed implication of host genes in GO categories like immune system process, regulation of signaling, response to stress, and transport. A biased chromosomal distribution of DEGs and SNP harbouring genes was observed. Our study would provide further insights into the complex regulatory mechanisms operating during gastric tumorigenesis.
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Affiliation(s)
- Renu Verma
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, New Delhi, India
| | - Prakash Chand Sharma
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, New Delhi, India.
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Belluti S, Semeghini V, Rigillo G, Ronzio M, Benati D, Torricelli F, Reggiani Bonetti L, Carnevale G, Grisendi G, Ciarrocchi A, Dominici M, Recchia A, Dolfini D, Imbriano C. Alternative splicing of NF-YA promotes prostate cancer aggressiveness and represents a new molecular marker for clinical stratification of patients. J Exp Clin Cancer Res 2021; 40:362. [PMID: 34782004 PMCID: PMC8594157 DOI: 10.1186/s13046-021-02166-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 11/02/2021] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Approaches based on expression signatures of prostate cancer (PCa) have been proposed to predict patient outcomes and response to treatments. The transcription factor NF-Y participates to the progression from benign epithelium to both localized and metastatic PCa and is associated with aggressive transcriptional profile. The gene encoding for NF-YA, the DNA-binding subunit of NF-Y, produces two alternatively spliced transcripts, NF-YAs and NF-YAl. Bioinformatic analyses pointed at NF-YA splicing as a key transcriptional signature to discriminate between different tumor molecular subtypes. In this study, we aimed to determine the pathophysiological role of NF-YA splice variants in PCa and their association with aggressive subtypes. METHODS Data on the expression of NF-YA isoforms were extracted from the TCGA (The Cancer Genome Atlas) database of tumor prostate tissues and validated in prostate cell lines. Lentiviral transduction and CRISPR-Cas9 technology allowed the modulation of the expression of NF-YA splice variants in PCa cells. We characterized 3D cell cultures through in vitro assays and RNA-seq profilings. We used the rank-rank hypergeometric overlap approach to identify concordant/discordant gene expression signatures of NF-YAs/NF-YAl-overexpressing cells and human PCa patients. We performed in vivo studies in SHO-SCID mice to determine pathological and molecular phenotypes of NF-YAs/NF-YAl xenograft tumors. RESULTS NF-YA depletion affects the tumorigenic potential of PCa cells in vitro and in vivo. Elevated NF-YAs levels are associated to aggressive PCa specimens, defined by Gleason Score and TNM classification. NF-YAl overexpression increases cell motility, while NF-YAs enhances cell proliferation in PCa 3D spheroids and xenograft tumors. The transcriptome of NF-YAs-spheroids has an extensive overlap with localized and metastatic human PCa signatures. According to PCa PAM50 classification, NF-YAs transcript levels are higher in LumB, characterized by poor prognosis compared to LumA and basal subtypes. A significant decrease in NF-YAs/NF-YAl ratio distinguishes PCa circulating tumor cells from cancer cells in metastatic sites, consistently with pro-migratory function of NF-YAl. Stratification of patients based on NF-YAs expression is predictive of clinical outcome. CONCLUSIONS Altogether, our results indicate that the modulation of NF-YA isoforms affects prostate pathophysiological processes and contributes to cancer-relevant phenotype, in vitro and in vivo. Evaluation of NF-YA splicing may represent a new molecular strategy for risk assessment of PCa patients.
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Affiliation(s)
- Silvia Belluti
- Department of Life Sciences, University of Modena and Reggio Emilia, via Campi 213/D, Modena, Italy
| | - Valentina Semeghini
- Department of Life Sciences, University of Modena and Reggio Emilia, via Campi 213/D, Modena, Italy
| | - Giovanna Rigillo
- Department of Life Sciences, University of Modena and Reggio Emilia, via Campi 213/D, Modena, Italy
| | - Mirko Ronzio
- Department of Biosciences, University of Milan, Milan, Italy
| | - Daniela Benati
- Centre for Regenerative Medicine, Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Federica Torricelli
- Laboratory of Translational Research, Azienda Unità Sanitaria Locale-IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - Luca Reggiani Bonetti
- Department of Medical and Surgical Sciences for Children & Adults, Division of Pathology, University-Hospital of Modena and Reggio Emilia, Modena, Italy
| | - Gianluca Carnevale
- Surgical, Medical and Dental Department of Morphological Sciences Related to Transplant, Oncology and Regenerative Medicine, University of Modena and Reggio Emilia, Modena, Italy
| | - Giulia Grisendi
- Laboratory of Cellular Therapy, Program of Cell Therapy and Immuno-Oncology, Division of Oncology, Department of Medical and Surgical Sciences for Children & Adults, University-Hospital of Modena and Reggio Emilia, Modena, Italy
| | - Alessia Ciarrocchi
- Laboratory of Translational Research, Azienda Unità Sanitaria Locale-IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - Massimo Dominici
- Laboratory of Cellular Therapy, Program of Cell Therapy and Immuno-Oncology, Division of Oncology, Department of Medical and Surgical Sciences for Children & Adults, University-Hospital of Modena and Reggio Emilia, Modena, Italy
| | - Alessandra Recchia
- Centre for Regenerative Medicine, Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Diletta Dolfini
- Department of Biosciences, University of Milan, Milan, Italy
| | - Carol Imbriano
- Department of Life Sciences, University of Modena and Reggio Emilia, via Campi 213/D, Modena, Italy.
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Jatuponwiphat T, Namrak T, Nitisinprasert S, Nakphaichit M, Vongsangnak W. Integrative growth physiology and transcriptome profiling of probiotic Limosilactobacillus reuteri KUB-AC5. PeerJ 2021; 9:e12226. [PMID: 34707932 PMCID: PMC8500091 DOI: 10.7717/peerj.12226] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 09/08/2021] [Indexed: 12/26/2022] Open
Abstract
Limosilactobacillus reuteri KUB-AC5 has been widely used as probiotic in chicken for Salmonella reduction. However, a preferable carbon source and growth phase is poorly characterized underlying metabolic responses on growth and inhibition effects of L. reuteri KUB-AC5. This study therefore aimed to investigate transcriptome profiling of L. reuteri KUB-AC5 revealing global metabolic responses when alteration of carbon sources and growth phases. Interestingly, L. reuteri KUB-AC5 grown under sucrose culture showed to be the best for fast growth and inhibition effects against Salmonella Enteritidis S003 growth. Towards the transcriptome profiling and reporter proteins/metabolites analysis, the results showed that amino acid transport via ABC systems as well as sucrose metabolism and transport are key metabolic responses at Logarithmic (L)-phase of L. reuteri KUB-AC5 growth. Considering the Stationary (S)-phase, we found the potential reporter proteins/metabolites involved in carbohydrate metabolism e.g., levansucrase and levan. Promisingly, levansucrase and levan were revealed to be candidates in relation to inhibition effects of L. reuteri KUB-AC5. Throughout this study, L. reuteri KUB-AC5 had a metabolic control in acclimatization to sucrose and energy pools through transcriptional co-regulation, which supported the cell growth and inhibition potentials. This study offers a perspective in optimizing fermentation condition through either genetic or physiological approaches for enhancing probiotic L. reuteri KUB-AC5 properties.
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Affiliation(s)
- Theeraphol Jatuponwiphat
- Interdisciplinary Graduate Program in Bioscience, Faculty of Science, Kasetsart University, Bangkok, Thailand
| | - Thanawat Namrak
- Department of Biotechnology, Faculty of Agro-Industry, Kasetsart University, Bangkok, Thailand
| | - Sunee Nitisinprasert
- Department of Biotechnology, Faculty of Agro-Industry, Kasetsart University, Bangkok, Thailand
| | - Massalin Nakphaichit
- Department of Biotechnology, Faculty of Agro-Industry, Kasetsart University, Bangkok, Thailand
| | - Wanwipa Vongsangnak
- Department of Zoology, Faculty of Science, Kasetsart University, Bangkok, Thailand.,Omics Center for Agriculture, Bioresources, Food, and Health, Kasetsart University (OmiKU), Bangkok, Thailand
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Han S, Zhang Q, Wang H, Pei D. Comparison of the transcriptomic responses of two Chrysanthemum morifolium cultivars to low light. Mol Biol Rep 2021; 48:7293-301. [PMID: 34689280 DOI: 10.1007/s11033-021-06729-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Accepted: 09/28/2021] [Indexed: 10/20/2022]
Abstract
BACKGROUND Low light is a primary regulator of chrysanthemum growth. Our aim was to analyse the different transcriptomic responses of two Chrysanthemum morifolium cultivars to low light. METHODS AND RESULTS We conducted a transcriptomic analysis of leaf samples from the 'Nannonggongfen' and 'Nannongxuefeng' chrysanthemum cultivars following a 5-day exposure to optimal light (70%, control [CK]) or low-light (20%, LL) conditions. Gene Ontology (GO) classification of upregulated genes revealed these genes to be associated with 11 cellular components, 9 molecular functions, and 15 biological processes, with the majority being localized to the chloroplast, highlighting the role of chloroplast proteins as regulators of shading tolerance. Downregulated genes were associated with 11 cellular components, 8 molecular functions, and 16 biological processes. Heat map analyses suggested that basic helix-loop-helix domain genes and elongation factors were markedly downregulated in 'Nannongxuefeng' leaves, consistent with the maintenance of normal stem length, whereas no comparable changes were observed in 'Nanonggongfen' leaves. Subsequent qPCR analyses revealed that phytochrome-interacting factors and dormancy-associated genes were significantly upregulated under LL conditions relative to CK conditions, while succinate dehydrogenase 1, elongated hypocotyls 5, and auxin-responsive gene of were significantly downregulated under LL conditions. CONCLUSIONS These findings suggest that LL plants were significantly lower than those of the CK plants. Low-light tolerant chrysanthemum cultivars may maintain reduced indole-3-acetic acid (IAA) and elongation factor expression as a means of preventing the onset of shade-avoidance symptoms.
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Liu JB, Chen K, Liu TB, Wang ZY, Wang L. Global transcriptome profiling reveals antagonizing response of head kidney of juvenile common carp exposed to glyphosate. Chemosphere 2021; 280:130823. [PMID: 34162096 DOI: 10.1016/j.chemosphere.2021.130823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Revised: 04/23/2021] [Accepted: 05/05/2021] [Indexed: 06/13/2023]
Abstract
Glyphosate (GLY) frequently detected in various water bodies has imposed a serious risk on fish. Head kidney of fish is an important defense organ, playing a vital part in antagonizing exogenous hazardous matter. The objective of this study was to characterize toxic mechanisms of GLY in head kidney of common carp based on transcriptome profiling. After 45-days exposure of GLY at environmentally relevant concentrations, juvenile common carp were used as experimental subjects to analyze how the head kidney responded to GLY. The transcriptome profiling identified 1381 different expressed genes (DEGs) between the control and exposure groups (5 and 50 mg/L). Functional analysis of DEGs substantiated over-representative pathways mainly involving cellular stress responses, cell proliferation and turnover, apoptosis, lipid metabolism, and innate immune processes in both treated groups compared with the control group. Predicted network of gene regulation indicated that GLY-induced tp53 played a vital role in linking a battery of signals. Furthermore, the expression of 10 candidate genes by qRT-PCR aligned with transcriptional profiling. In addition, western blotting analysis confirmed that GLY-induced apoptosis and cellular proliferation were closely involved in activating MAKP signaling pathway and lipid metabolism pathway in both treated groups. Collectively, these data demonstrate that head kidney of juvenile common carp mainly leverages upregulation of genes related to cell proliferation and turnover, apoptosis, and lipid metabolism to combat sub-chronic exposure of GLY. This study casts new understanding into the risk of GLY in aquatic animals.
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Affiliation(s)
- Jing-Bo Liu
- College of Animal Science and Veterinary Medicine, Shandong Agricultural University, 61 Daizong Street, Tai'an City, Shandong Province, 271018, China; Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, 61 Daizong Street, Tai'an City, Shandong Province, 271018, China; Shandong Provincial Engineering Technology Research Center of Animal Disease Control and Prevention, Shandong Agricultural University, 61 Daizong Street, Tai'an City, Shandong Province, 271018, China
| | - Kai Chen
- New Drug Evaluation Center of Shandong Academy of Pharmaceutical Sciences, Shandong Academy of Pharmaceutical Sciences, 989 Xinluo Street, Ji'nan City, Shandong Province, 250101, China
| | - Tian-Bin Liu
- New Drug Evaluation Center of Shandong Academy of Pharmaceutical Sciences, Shandong Academy of Pharmaceutical Sciences, 989 Xinluo Street, Ji'nan City, Shandong Province, 250101, China
| | - Zhen-Yong Wang
- College of Animal Science and Veterinary Medicine, Shandong Agricultural University, 61 Daizong Street, Tai'an City, Shandong Province, 271018, China; Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, 61 Daizong Street, Tai'an City, Shandong Province, 271018, China; Shandong Provincial Engineering Technology Research Center of Animal Disease Control and Prevention, Shandong Agricultural University, 61 Daizong Street, Tai'an City, Shandong Province, 271018, China
| | - Lin Wang
- College of Animal Science and Veterinary Medicine, Shandong Agricultural University, 61 Daizong Street, Tai'an City, Shandong Province, 271018, China; Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, 61 Daizong Street, Tai'an City, Shandong Province, 271018, China; Shandong Provincial Engineering Technology Research Center of Animal Disease Control and Prevention, Shandong Agricultural University, 61 Daizong Street, Tai'an City, Shandong Province, 271018, China.
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Jana B, Kaczmarek MM, Romaniewicz M, Brzozowska M. Profile for mRNA transcript abundances in the pig endometrium where inflammation was induced by Escherichia coli. Anim Reprod Sci 2021; 232:106824. [PMID: 34403834 DOI: 10.1016/j.anireprosci.2021.106824] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 08/05/2021] [Accepted: 08/06/2021] [Indexed: 11/28/2022]
Abstract
Uterine inflammation is a common reproductive disorder in domestic animals, leading to disturbances in many reproductive processes and economic losses. More information on inflammatory pathways, however, is needed to understand mechanisms of uterine inflammation. The aim of the study was to investigate transcriptomic profiles of the pig endometrium affected by inflammation. On day 3 of the estrous cycle (day 0 = initial day of study), saline or Escherichia coli suspension were injected into uterine horns. In endometrial tissues collected 8 days later, microarray analysis results indicated there were 189 differentially abundant mRNA transcripts (DEGs, 95 in relatively greater and 94 in lesser abundance) after saline injections compared with samples where there was severe acute inflammation. Relative abundance of mRNA transcripts for proteins assigned to inflammatory response, movement of phagocytes, quantity of phagocytes, leukocyte migration and adhesion of immune cells and many other functions related to inflammation were different in the Escherichia coli-treated endometrium than in samples from gilts treated with saline. Among others, S100A9, SLC11A1, CCL15, CCL3L3, CCR1, CD48, CD163, THBS1, KIT, ITGB3, JAK3 and NFKB2 mRNA transcripts were in relatively greater abundance and there were those in relatively lesser abundance including IL24, FGG, SST, CXCL16 and CREB. In this study, for the first time, there was detection of alterations in the transcriptome of the inflamed pig endometrium which may be an important finding for maintaining uterine homeostasis and functions. Results form the basis for future studies focusing on regulation of uterine inflammation in animals and women.
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Affiliation(s)
- Barbara Jana
- Division of Reproductive Biology, Institute of Animal Reproduction and Food Research of the Polish Academy of Sciences, Tuwima 10, 10-748 Olsztyn, Poland.
| | - Monika M Kaczmarek
- Division of Reproductive Biology, Institute of Animal Reproduction and Food Research of the Polish Academy of Sciences, Tuwima 10, 10-748 Olsztyn, Poland
| | - Marta Romaniewicz
- Division of Reproductive Biology, Institute of Animal Reproduction and Food Research of the Polish Academy of Sciences, Tuwima 10, 10-748 Olsztyn, Poland
| | - Marta Brzozowska
- Department of Clinical Physiology, Faculty of Veterinary Medicine, University of Warmia and Mazury, Oczapowskiego 13, 10-718 Olsztyn, Poland
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Theine J, Holtgräwe D, Herzog K, Schwander F, Kicherer A, Hausmann L, Viehöver P, Töpfer R, Weisshaar B. Transcriptomic analysis of temporal shifts in berry development between two grapevine cultivars of the Pinot family reveals potential genes controlling ripening time. BMC Plant Biol 2021; 21:327. [PMID: 34233614 PMCID: PMC8265085 DOI: 10.1186/s12870-021-03110-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 06/22/2021] [Indexed: 05/16/2023]
Abstract
BACKGROUND Grapevine cultivars of the Pinot family represent clonally propagated mutants with major phenotypic and physiological differences, such as different colour or shifted ripening time, as well as changes in important viticultural traits. Specifically, the cultivars 'Pinot Noir' (PN) and 'Pinot Noir Precoce' (PNP, early ripening) flower at the same time, but vary in the beginning of berry ripening (veraison) and, consequently, harvest time. In addition to genotype, seasonal climatic conditions (i.e. high temperatures) also affect ripening times. To reveal possible regulatory genes that affect the timing of veraison onset, we investigated differences in gene expression profiles between PN and PNP throughout berry development with a closely meshed time series and over two separate years. RESULTS The difference in the duration of berry formation between PN and PNP was quantified to be approximately two weeks under the growth conditions applied, using plant material with a proven PN and PNP clonal relationship. Clusters of co-expressed genes and differentially expressed genes (DEGs) were detected which reflect the shift in the timing of veraison onset. Functional annotation of these DEGs fit to observed phenotypic and physiological changes during berry development. In total, we observed 3,342 DEGs in 2014 and 2,745 DEGs in 2017 between PN and PNP, with 1,923 DEGs across both years. Among these, 388 DEGs were identified as veraison-specific and 12 were considered as berry ripening time regulatory candidates. The expression profiles revealed two candidate genes for ripening time control which we designated VviRTIC1 and VviRTIC2 (VIT_210s0071g01145 and VIT_200s0366g00020, respectively). These genes likely contribute the phenotypic differences observed between PN and PNP. CONCLUSIONS Many of the 1,923 DEGs show highly similar expression profiles in both cultivars if the patterns are aligned according to developmental stage. In our work, putative genes differentially expressed between PNP and PN which could control ripening time as well as veraison-specific genes were identified. We point out connections of these genes to molecular events during berry development and discuss potential candidate genes which may control ripening time. Two of these candidates were observed to be differentially expressed in the early berry development phase. Several down-regulated genes during berry ripening are annotated as auxin response factors / ARFs. Conceivably, general changes in auxin signaling may cause the earlier ripening phenotype of PNP.
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Affiliation(s)
- Jens Theine
- Genetics and Genomics of Plants, Faculty of Biology & Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Daniela Holtgräwe
- Genetics and Genomics of Plants, Faculty of Biology & Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Katja Herzog
- Julius Kühn-Institute, Institute for Grapevine Breeding Geilweilerhof, Siebeldingen, Germany
| | - Florian Schwander
- Julius Kühn-Institute, Institute for Grapevine Breeding Geilweilerhof, Siebeldingen, Germany
| | - Anna Kicherer
- Julius Kühn-Institute, Institute for Grapevine Breeding Geilweilerhof, Siebeldingen, Germany
| | - Ludger Hausmann
- Julius Kühn-Institute, Institute for Grapevine Breeding Geilweilerhof, Siebeldingen, Germany
| | - Prisca Viehöver
- Genetics and Genomics of Plants, Faculty of Biology & Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Reinhard Töpfer
- Julius Kühn-Institute, Institute for Grapevine Breeding Geilweilerhof, Siebeldingen, Germany
| | - Bernd Weisshaar
- Genetics and Genomics of Plants, Faculty of Biology & Center for Biotechnology, Bielefeld University, Bielefeld, Germany
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Ooi SE, Feshah I, Nuraziyan A, Sarpan N, Ata N, Lim CC, Choo CN, Wong WC, Wong FH, Wong CK, Ong-Abdullah M. Leaf transcriptomic signatures for somatic embryogenesis potential of Elaeis guineensis. Plant Cell Rep 2021; 40:1141-1154. [PMID: 33929599 DOI: 10.1007/s00299-021-02698-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Accepted: 04/13/2021] [Indexed: 06/12/2023]
Abstract
Potentially embryogenic oil palms can be identified through leaf transcriptomic signatures. Differential expression of genes involved in flowering time, and stress and light responses may associate with somatic embryogenesis potential. Clonal propagation is an attractive approach for the mass propagation of high yielding oil palms. A major issue hampering the effectiveness of oil palm tissue culture is the low somatic embryogenesis rate. Previous studies have identified numerous genes involved in oil palm somatic embryogenesis, but their association with embryogenic potential has not been determined. In this study, differential expression analysis of leaf transcriptomes from embryogenic and non-embryogenic mother palms revealed that transcriptome profiles from non- and poor embryogenic mother palms were more similar than highly embryogenic palms. A total of 171 genes exhibiting differential expression in non- and low embryogenesis groups could also discriminate high from poor embryogenesis groups of another tissue culture agency. Genes related to flowering time or transition such as FTIP, FRIGIDA-LIKE, and NF-YA were up-regulated in embryogenic ortets, suggesting that reproduction timing of the plant may associate with somatic embryogenesis potential. Several light response or photosynthesis-related genes were down-regulated in embryogenic ortets, suggesting a link between photosynthesis activity and embryogenic potential. As expression profiles of the differentially expressed genes are very similar between non- and low embryogenic groups, machine learning approaches with several candidate genes may generate a more sensitive model to better discriminate non-embryogenic from embryogenic ortets.
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Affiliation(s)
- Siew-Eng Ooi
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, 6 Persiaran Institusi, 43000, Kajang, Selangor, Malaysia.
| | - Ishak Feshah
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, 6 Persiaran Institusi, 43000, Kajang, Selangor, Malaysia
| | - Azimi Nuraziyan
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, 6 Persiaran Institusi, 43000, Kajang, Selangor, Malaysia
| | - Norashikin Sarpan
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, 6 Persiaran Institusi, 43000, Kajang, Selangor, Malaysia
| | - Nabeel Ata
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, 6 Persiaran Institusi, 43000, Kajang, Selangor, Malaysia
| | - Chin-Ching Lim
- United Plantations Bhd., Jenderata Estate, 36009, Teluk Intan, Perak, Malaysia
| | - Chin-Nee Choo
- Advanced Agriecological Research Sdn. Bhd., 11 Jalan Teknologi 3/6, Taman Sains Selangor 1, Kota Damansara, 47810, Petaling Jaya, Selangor, Malaysia
| | - Wei-Chee Wong
- Advanced Agriecological Research Sdn. Bhd., 11 Jalan Teknologi 3/6, Taman Sains Selangor 1, Kota Damansara, 47810, Petaling Jaya, Selangor, Malaysia
| | - Foo-Hin Wong
- United Plantations Bhd., Jenderata Estate, 36009, Teluk Intan, Perak, Malaysia
| | - Choo-Kien Wong
- Advanced Agriecological Research Sdn. Bhd., 11 Jalan Teknologi 3/6, Taman Sains Selangor 1, Kota Damansara, 47810, Petaling Jaya, Selangor, Malaysia
| | - Meilina Ong-Abdullah
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, 6 Persiaran Institusi, 43000, Kajang, Selangor, Malaysia
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Li F, Hu Q, Chen F, Jiang JF. Transcriptome analysis reveals Vernalization is independent of cold acclimation in Arabidopsis. BMC Genomics 2021; 22:462. [PMID: 34154522 PMCID: PMC8218483 DOI: 10.1186/s12864-021-07763-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Accepted: 05/31/2021] [Indexed: 01/08/2023] Open
Abstract
Background Through vernalization, plants achieve flowering competence by sensing prolonged cold exposure (constant exposure approximately 2-5 °C). During this process, plants initiate defense responses to endure cold conditions. Here, we conducted transcriptome analysis of Arabidopsis plants subjected to prolonged cold exposure (6 weeks) to explore the physiological dynamics of vernalization and uncover the relationship between vernalization and cold stress. Results Time-lag initiation of the two pathways and weighted gene co-expression network analysis (WGCNA) revealed that vernalization is independent of cold acclimation. Moreover, WGCNA revealed three major networks involving ethylene and jasmonic acid response, cold acclimation, and chromatin modification in response to prolonged cold exposure. Finally, throughout vernalization, the cold stress response is regulated via an alternative splicing-mediated mechanism. Conclusion These findings illustrate a comprehensive picture of cold stress- and vernalization-mediated global changes in Arabidopsis. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07763-3.
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Affiliation(s)
- Fei Li
- 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, Nanjing, 210095, China
| | - Qian Hu
- 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, Nanjing, 210095, 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, Nanjing, 210095, China
| | - Jia Fu 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, Nanjing, 210095, China.
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Chen Y, Zhou X, Guo K, Chen SN, Su X. Transcriptomic insights into the effects of CytCo, a novel nematotoxic protein, on the pine wood nematode Bursaphelenchus xylophilus. BMC Genomics 2021; 22:394. [PMID: 34044778 PMCID: PMC8157652 DOI: 10.1186/s12864-021-07714-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Accepted: 05/04/2021] [Indexed: 11/24/2022] Open
Abstract
Background The pine wood nematode Bursaphelenchus xylophilus is a destructive pest of Pinus trees worldwide and lacks effective control measures. Screening for nematotoxic proteins has been undertaken to develop new strategies for nematode control. Results The results of the present study provided initial insights into the responses of B. xylophilus exposed to a nematotoxic cytolytic-like protein (CytCo) based on transcriptome profiling. A large set of differentially expressed genes (DEGs = 1265) was found to be related to nematode development, reproduction, metabolism, motion, and immune system. In response to the toxic protein, B. xylophilus upregulated DEGs encoding cuticle collagens, transporters, and cytochrome P450. In addition, many DEGs related to cell death, lipid metabolism, major sperm proteins, proteinases/peptidases, phosphatases, kinases, virulence factors, and transthyretin-like proteins were downregulated. Gene Ontology enrichment analysis showed that the CytCo treatment substantially affected DEGs involved in muscle contraction, lipid localization, and the mitogen-activated protein kinase cascade. The pathway richness of the Kyoto Encyclopedia of Genes and Genomes showed that the DEGs were concentrated in lysosomes and involved in fatty acid degradation. Weighted co-expression network analysis indicated that the hub genes affected by CytCo were associated with the nematode cuticular collagen. Conclusions These results showed that CytCo toxin interferes with gene expression to exert multiple nematotoxic effects, thereby providing insights into its potential use in pine wood nematode control. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07714-y.
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Affiliation(s)
- Ye Chen
- Collaborative Innovation Center of Zhejiang Green Pesticide, National Joint Local Engineering Laboratory for High-Efficient Preparation of Biopesticide, School of Forestry and Biotechnology, Zhejiang A&F University, 311300, Hangzhou, People's Republic of China
| | - Xiang Zhou
- Collaborative Innovation Center of Zhejiang Green Pesticide, National Joint Local Engineering Laboratory for High-Efficient Preparation of Biopesticide, School of Forestry and Biotechnology, Zhejiang A&F University, 311300, Hangzhou, People's Republic of China
| | - Kai Guo
- Collaborative Innovation Center of Zhejiang Green Pesticide, National Joint Local Engineering Laboratory for High-Efficient Preparation of Biopesticide, School of Forestry and Biotechnology, Zhejiang A&F University, 311300, Hangzhou, People's Republic of China.
| | - Sha-Ni Chen
- Collaborative Innovation Center of Zhejiang Green Pesticide, National Joint Local Engineering Laboratory for High-Efficient Preparation of Biopesticide, School of Forestry and Biotechnology, Zhejiang A&F University, 311300, Hangzhou, People's Republic of China
| | - Xiu Su
- Collaborative Innovation Center of Zhejiang Green Pesticide, National Joint Local Engineering Laboratory for High-Efficient Preparation of Biopesticide, School of Forestry and Biotechnology, Zhejiang A&F University, 311300, Hangzhou, People's Republic of China
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Konstantinov DK, Zubairova US, Ermakov AA, Doroshkov AV. Comparative transcriptome profiling of a resistant vs susceptible bread wheat ( Triticum aestivum L.) cultivar in response to water deficit and cold stress. PeerJ 2021; 9:e11428. [PMID: 34026365 PMCID: PMC8123233 DOI: 10.7717/peerj.11428] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 04/19/2021] [Indexed: 11/28/2022] Open
Abstract
Bread wheat (Triticum aestivum L.) is one of the most important agricultural plants wearing abiotic stresses, such as water deficit and cold, that cause its productivity reduction. Since resistance to abiotic factors is a multigenic trait, therefore modern genome-wide approaches can help to involve various genetic material in breeding. One technique is full transcriptome analysis that reveals groups of stress response genes serving marker-assisted selection markers. Comparing transcriptome profiles of the same genetic material under several stresses is essential and makes the whole picture. Here, we addressed this by studying the transcriptomic response to water deficit and cold stress for two evolutionarily distant bread wheat varieties: stress-resistant cv. Saratovskaya 29 (S29) and stress-sensitive cv. Yanetzkis Probat (YP). For the first time, transcriptomes for these cultivars grown under abiotic stress conditions were obtained using Illumina based MACE technology. We identified groups of genes involved in response to cold and water deficiency stresses, including responses to each stress factor and both factors simultaneously that may be candidates for resistance genes. We discovered a core group of genes that have a similar pattern of stress-induced expression changes. The particular expression pattern was revealed not only for the studied varieties but also for the published transcriptomic data on cv. Jing 411 and cv. Fielder. Comparative transcriptome profiling of cv. S29 and cv. YP in response to water deficit and cold stress confirmed the hypothesis that stress-induced expression change is unequal within a homeologous gene group. As a rule, at least one changed significantly while the others had a relatively lower expression. Also, we found several SNPs distributed throughout the genomes of cv. S29 and cv. YP and distinguished the studied varieties from each other and the reference cv. Chinese Spring. Our results provide new data for genomics-assisted breeding of stress-tolerant wheat cultivars.
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Affiliation(s)
- Dmitrii K Konstantinov
- The Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russian Federation.,Novosibirsk State University, Novosibirsk, Russian Federation
| | - Ulyana S Zubairova
- The Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russian Federation.,Novosibirsk State University, Novosibirsk, Russian Federation
| | - Anton A Ermakov
- The Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russian Federation
| | - Alexey V Doroshkov
- The Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russian Federation.,Novosibirsk State University, Novosibirsk, Russian Federation
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Kumawat S, Khatri P, Ahmed A, Vats S, Kumar V, Jaswal R, Wang Y, Xu P, Mandlik R, Shivaraj SM, Deokar A, Sonah H, Sharma TR, Deshmukh R. Understanding aquaporin transport system, silicon and other metalloids uptake and deposition in bottle gourd (Lagenaria siceraria). J Hazard Mater 2021; 409:124598. [PMID: 33234398 DOI: 10.1016/j.jhazmat.2020.124598] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 11/01/2020] [Accepted: 11/13/2020] [Indexed: 06/11/2023]
Abstract
Aquaporins (AQPs) facilitates the transport of small solutes like water, urea, carbon dioxide, boron, and silicon (Si) and plays a critical role in important physiological processes. In this study, genome-wide characterization of AQPs was performed in bottle gourd. A total of 36 AQPs were identified in the bottle gourd, which were subsequently analyzed to understand the pore-morphology, exon-intron structure, subcellular-localization. In addition, available transcriptome data was used to study the tissue-specific expression. Several AQPs showed tissue-specific expression, more notably the LsiTIP3-1 having a high level of expression in flowers and fruits. Based on the in-silico prediction of solute specificity, LsiNIP2-1 was predicted to be a Si transporter. Silicon was quantified in different tissues, including root, young leaves, mature leaves, tendrils, and fruits of bottle gourd plants. More than 1.3% Si (d.w.) was observed in bottle gourd leaves, testified the in-silico predictions. Silicon deposition evaluated with an energy-dispersive X-ray coupled with a scanning electron microscope showed a high Si accumulation in the shaft of leaf trichomes. Similarly, co-localization of Si with arsenic and antimony was observed. Expression profiling performed with real-time quantitative PCR showed differential expression of AQPs in response to Si supplementation. The information provided in the present study will be helpful to better understand the AQP transport mechanism, particularly Si and other metalloids transport and localization in plants.
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Affiliation(s)
- Surbhi Kumawat
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab, India; Department of Biotechnology, Panjab University, Chandigarh, India
| | - Praveen Khatri
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab, India
| | - Ashique Ahmed
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab, India; Darrang College, Tezpur, Sonitpur, Assam, India
| | - Sanskriti Vats
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab, India
| | - Virender Kumar
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab, India
| | - Rajdeep Jaswal
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab, India
| | - Ying Wang
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Pei Xu
- College of Life Sciences, China Jiliang University, Hangzhou, China
| | - Rushil Mandlik
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab, India; Department of Biotechnology, Panjab University, Chandigarh, India
| | - S M Shivaraj
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab, India
| | - Amit Deokar
- Department of Plant Sciences, Crop Development Centre, University of Saskatchewan, Saskatoon, Canada
| | - Humira Sonah
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab, India
| | - Tilak Raj Sharma
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab, India; Division of Crop Science, Indian Council of Agricultural Research, New Delhi, India
| | - Rupesh Deshmukh
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab, India.
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Wang H, Tian Q, Zhang J, Liu H, Zhang J, Cao W, Zhang X, Li X, Wu L, Song M, Kong Y, Wang W, Wang Y. Blood transcriptome profiling as potential biomarkers of suboptimal health status: potential utility of novel biomarkers for predictive, preventive, and personalized medicine strategy. EPMA J 2021; 12:103-115. [PMID: 34194583 DOI: 10.1007/s13167-021-00238-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 03/01/2021] [Indexed: 02/06/2023]
Abstract
The early identification of Suboptimal Health Status (SHS) creates a window opportunity for the predictive, preventive, and personalized medicine (PPPM) in chronic diseases. Previous studies have observed the alterations in several mRNA levels in SHS individuals. As a promising "omics" technology offering comprehension of genome structure and function at RNA level, transcriptome profiling can provide innovative molecular biomarkers for the predictive identification and targeted prevention of SHS. To explore the potential biomarkers, biological functions, and signalling pathways involved in SHS, an RNA sequencing (RNA-Seq)-based transcriptome analysis was firstly conducted on buffy coat samples collected from 30 participants with SHS and 30 age- and sex-matched healthy controls. Transcriptome analysis identified a total of 46 differentially expressed genes (DEGs), in which 22 transcripts were significantly increased and 24 transcripts were decreased in the SHS group. A total of 23 transcripts were selected as candidate predictive biomarkers for SHS. Gene Ontology (GO) annotations and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis revealed that several biological processes were related to SHS, such as ATP-binding cassette (ABC) transporter and neurodegeneration. Protein-protein interaction (PPI) network analysis identified 10 hub genes related to SHS, including GJA1, TWIST2, KRT1, TUBB3, AMHR2, BMP10, MT3, BMPER, NTM, and TMEM98. A transcriptome predictive model can distinguish SHS individuals from the healthy controls with a sensitivity of 83.3% (95% confidence interval (CI): 73.9-92.7%), a specificity of 90.0% (95% CI: 82.4-97.6%), and an area under the receiver operating characteristic curve of 0.938 (95% CI: 0.882-0.994). In the present study, we demonstrated that blood (buffy coat) samples appear to be a very promising and easily accessible biological material for the transcriptomic analyses focused on the objective identification of SHS by using our transcriptome predictive model. The pattern of particularly determined DEGs can be used as predictive transcriptomic biomarkers for the identification of SHS in an individual who may, subjectively, feel healthy, but at the level of subcellular mechanisms, the changes can provide early information about potential health problems in this person. Our findings also indicate the potential therapeutic targets in dealing with chronic diseases related to SHS, such as T2DM and CVD, and an early onset of neurodegenerative diseases, such as Alzheimer's and Parkinson's diseases, as well as the findings suggest the targets for personalized interventions as promoted in PPPM. Supplementary Information The online version contains supplementary material available at 10.1007/s13167-021-00238-1.
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Affiliation(s)
- Hao Wang
- Department of Clinical Epidemiology and Evidence-Based Medicine, National Clinical Research Center for Digestive Diseases, Beijing Friendship Hospital, Capital Medical University, Beijing, China.,Beijing Key Laboratory of Clinical Epidemiology, School of Public Health, Capital Medical University, Beijing, China.,Center for Precision Health, School of Medical and Health Sciences, Edith Cowan University, Perth, Australia
| | - Qiuyue Tian
- Beijing Key Laboratory of Clinical Epidemiology, School of Public Health, Capital Medical University, Beijing, China
| | - Jie Zhang
- Beijing Key Laboratory of Clinical Epidemiology, School of Public Health, Capital Medical University, Beijing, China
| | - Hongqi Liu
- Student Healthcare Center, Weifang University, Weifang, China
| | - Jinxia Zhang
- Beijing Key Laboratory of Clinical Epidemiology, School of Public Health, Capital Medical University, Beijing, China
| | - Weijie Cao
- Beijing Key Laboratory of Clinical Epidemiology, School of Public Health, Capital Medical University, Beijing, China.,Center for Precision Health, School of Medical and Health Sciences, Edith Cowan University, Perth, Australia
| | - Xiaoyu Zhang
- Beijing Key Laboratory of Clinical Epidemiology, School of Public Health, Capital Medical University, Beijing, China.,Department of Anesthesiology, Sanbo Brain Hospital, Capital Medical University, Beijing, China
| | - Xingang Li
- Center for Precision Health, School of Medical and Health Sciences, Edith Cowan University, Perth, Australia
| | - Lijuan Wu
- Beijing Key Laboratory of Clinical Epidemiology, School of Public Health, Capital Medical University, Beijing, China
| | - Manshu Song
- Center for Precision Health, School of Medical and Health Sciences, Edith Cowan University, Perth, Australia
| | - Yuanyuan Kong
- Department of Clinical Epidemiology and Evidence-Based Medicine, National Clinical Research Center for Digestive Diseases, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Wei Wang
- Center for Precision Health, School of Medical and Health Sciences, Edith Cowan University, Perth, Australia
| | - Youxin Wang
- Beijing Key Laboratory of Clinical Epidemiology, School of Public Health, Capital Medical University, Beijing, China
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Paczkowska-Abdulsalam M, Kretowski A. Obesity, metabolic health and omics: Current status and future directions. World J Diabetes 2021; 12:420-436. [PMID: 33889288 PMCID: PMC8040086 DOI: 10.4239/wjd.v12.i4.420] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 02/22/2021] [Accepted: 03/30/2021] [Indexed: 02/06/2023] Open
Abstract
The growing obesity epidemic is becoming a major public health concern, and the associated costs represent a considerable burden on societies. Among the most common complications of severe obesity are the development of hypertension, dyslipidemia, type 2 diabetes, cardiovascular disease, and various types of cancer. Interestingly, some obese individuals have a favorable metabolic profile and appear to be somehow protected from the detrimental effects of excessive adipose tissue accumulation. These individuals remain normoglycemic, insulin sensitive, and hypotensive with proper blood lipid levels, despite their high body mass index and/or waist circumference. Multiple independent observations have led to the concept of the metabolically healthy obese (MHO) phenotype, yet no consensus has been reached to date regarding a universal definition or the main mechanism behind this phenomenon. Recent technological advances and the use of high-throughput analysis techniques have revolutionized different areas of biomedical research. A multi-omics approach, which is used to investigate changes at different molecular levels in an organism or tissue, may provide valuable insights into the interplay between the molecules or pathways and the roles of different factors involved in the mechanisms underlying metabolic health deterioration. The aim of this review is to present the current status regarding the use of omics technologies to investigate the MHO phenotype, as well as the results of targeted analyses conducted in MHO individuals.
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Affiliation(s)
| | - Adam Kretowski
- Clinical Research Centre, Medical University of Bialystok, Bialystok 15-276, Poland
- Department of Endocrinology, Diabetology and Internal Medicine, Medical University of Bialystok, Bialystok 15-276, Poland
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Feng F, Cheng Q, Li B, Liu C, Wang H, Li B, Xu X, Yu Y, Chen Z, Wu X, Dong H, Chu K, Xie Z, Gao Q, Xiong L, Li F, Yi B, Zhang D, Jiang X. Establishment and characterization of 38 novel patient-derived primary cancer cell lines using multi-region sampling revealing intra-tumor heterogeneity of gallbladder carcinoma. Hum Cell 2021; 34:918-31. [PMID: 33813726 DOI: 10.1007/s13577-021-00492-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 01/15/2021] [Indexed: 02/06/2023]
Abstract
Gallbladder carcinoma (GBC) is a lethal biliary tract malignant neoplasm. Patient-derived primary cancer cell lines (PDPCs) are appropriate models to explore biological characteristics and potential therapeutics; however, there is a lack of PDPCs in GBC. In this study, we aimed to establish and characterize the GBC PDPCs, and further investigated the intra-tumor heterogeneity (ITH). Multi-region sampling (3–9 regions) of the operable tumor tissue samples was used to establish PDPCs. Short tandem repeat genotyping for cell authentication and karyotyping was performed, followed by whole-exome sequencing and RNA sequencing to assess the ITH at the genetic and transcriptional levels, respectively. Thirty-eight PDPCs were successfully established from seven GBC patients and characterized. ITH was observed with a median of 38.3% mutations being heterogeneous (range, 26.6–59.4%) across all patients. Similar with other tumor types, TP53 mutations were always truncal. In addition, there were three genes, KMT2C, CDKN2A, and ARID1A, with truncal mutations in at least two patients. A median of 370 differentially expressed genes (DEGs) was identified per patient. Distinct expression patterns were observed between major histocompatibility complex (MHC) class I and II genes. We found the expression of MHC class II genes in the PDPC samples was closely regulated by CIITA, while that of MHC class I genes were not correlated with CIITA expression. The PDPCs established from GBC patients can serve as novel in vitro models to identify the ITH, which may pave a crucial molecular foundation for enhanced understanding of tumorigenesis and progression.
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Català-Senent JF, Hidalgo MR, Berenguer M, Parthasarathy G, Malhi H, Malmierca-Merlo P, de la Iglesia-Vayá M, García-García F. Hepatic steatosis and steatohepatitis: a functional meta-analysis of sex-based differences in transcriptomic studies. Biol Sex Differ 2021; 12:29. [PMID: 33766130 PMCID: PMC7995602 DOI: 10.1186/s13293-021-00368-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 02/18/2021] [Indexed: 02/07/2023] Open
Abstract
Background Previous studies have described sex-based differences in the epidemiological and clinical patterns of non-alcoholic fatty liver disease (NAFLD); however, we understand relatively little regarding the underlying molecular mechanisms. Herein, we present the first systematic review and meta-analysis of NAFLD transcriptomic studies to identify sex-based differences in the molecular mechanisms involved during the steatosis (NAFL) and steatohepatitis (NASH) stages of the disease. Methods Transcriptomic studies in the Gene Expression Omnibus database were systematically reviewed following the PRISMA statement guidelines. For each study, NAFL and NASH in premenopausal women and men were compared using a dual strategy: gene-set analysis and pathway activity analysis. Finally, the functional results of all studies were integrated into a meta-analysis. Results We reviewed a total of 114 abstracts and analyzed seven studies that included 323 eligible patients. The meta-analyses identified significantly altered molecular mechanisms between premenopausal women and men, including the overrepresentation of genes associated with DNA regulation, vinculin binding, interleukin-2 responses, negative regulation of neuronal death, and the transport of ions and cations in premenopausal women. In men, we discovered the overrepresentation of genes associated with the negative regulation of interleukin-6 and the establishment of planar polarity involved in neural tube closure. Conclusions Our meta-analysis of transcriptomic data provides a powerful approach to identify sex-based differences in NAFLD. We detected differences in relevant biological functions and molecular terms between premenopausal women and men. Differences in immune responsiveness between men and premenopausal women with NAFLD suggest that women possess a more immune tolerant milieu, while men display an impaired liver regenerative response. Graphical abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1186/s13293-021-00368-1.
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Affiliation(s)
- José F Català-Senent
- Bioinformatics and Biostatistics Unit, Principe Felipe Research Center, Valencia, Spain.,Spanish National Bioinformatics Institute, ELIXIR-Spain (INB, ELIXIR-ES), Madrid, Spain
| | - Marta R Hidalgo
- Bioinformatics and Biostatistics Unit, Principe Felipe Research Center, Valencia, Spain.
| | - Marina Berenguer
- Liver Transplantation and Hepatology Unit, Hospital Universitario y Politécnico La Fe, Valencia, Spain.,Grupo de Hepatología, Cirugía HBP y Trasplantes, Instituto de Investigación Sanitaria La Fe, Valencia, Spain.,CIBERehd, Centro de Investigación Biomédica en Red en Enfermedades Hepáticas y Digestivas, Instituto de Salud Carlos III, Madrid, Spain.,Department of Medicine, Universitat de València, Valencia, Spain
| | | | - Harmeet Malhi
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA
| | - Pablo Malmierca-Merlo
- Bioinformatics and Biostatistics Unit, Principe Felipe Research Center, Valencia, Spain.,Atos Research & Innovation (ARI), Madrid, Spain
| | - María de la Iglesia-Vayá
- Biomedical Imaging Unit FISABIO-CIPF, Fundación para el Fomento de la Investigación Sanitario y Biomédica de la Comunidad Valenciana, Valencia, Spain
| | - Francisco García-García
- Bioinformatics and Biostatistics Unit, Principe Felipe Research Center, Valencia, Spain. .,Spanish National Bioinformatics Institute, ELIXIR-Spain (INB, ELIXIR-ES), Madrid, Spain.
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Zhang Z, Zhai T, Li M, Zhang K, Li J, Zheng X, Tian C, Chen R, Dong J, Zhou EM, Nan Y, Wu C. A broadly neutralizing monoclonal antibody induces broad protection against heterogeneous PRRSV strains in piglets. Vet Res 2021; 52:45. [PMID: 33726857 DOI: 10.1186/s13567-021-00914-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 01/21/2021] [Indexed: 11/10/2022] Open
Abstract
Neutralizing antibodies (NAbs) have attracted attention as tools for achieving PRRSV control and prevention, but viral antigenic variation undermines the abilities of NAbs elicited by attenuated PRRSV vaccines to confer full protection against heterogeneous PRRSV field isolates. As demonstrated in this study, the monoclonal antibody (mAb) mAb-PN9cx3 exhibited broad-spectrum recognition and neutralizing activities against PRRSV-1 and PRRSV-2 strains in vitro. Furthermore, in vivo experiments revealed that the administration of two 10-mg doses of mAb-PN9cx3 before and after the inoculation of piglets with heterologous PRRSV isolates (HP-PRRSV-JXA1 or PRRSV NADC30-like strain HNhx) resulted in significant reduction of the PRRSV-induced pulmonary pathological changes and virus loads in porcine alveolar macrophages (PAMs) compared with the results obtained with mAb-treated isotype controls. Moreover, minimal hilar lymph node PRRSV antigen levels were observed in mAb-PN9cx3-treated piglets. A transcriptome profile analysis of PAMs extracted from lung tissues of piglets belonging to different groups (except for antibody-isotype controls) indicated that mAb-PN9cx3 treatment reversed the PRRSV infection-induced alterations in expression profiles. A gene ontology (GO) enrichment analysis of these genes traced their functions to pathways that included the immune response, inflammatory response, and response to steroid hormone, and their functions in oogenesis and positive regulation of angiogenesis have been implicated in PRRSV pathogenesis. Overall, NADC30-like HNhx infection affected more gene pathways than HP-PRRSV infection. In conclusion, our research describes a novel immunologic approach involving the use of mAbs that confer cross-protection against serious illness resulting from infection with heterogeneous PRRSV-2 isolates, which is a feat that has not yet been achieved through vaccination. Ultimately, mAb-PN9cx3 will be a powerful addition to our current arsenal for achieving PRRSV prevention and eradication.
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Ong EZ, Kalimuddin S, Chia WC, Ooi SH, Koh CW, Tan HC, Zhang SL, Low JG, Ooi EE, Chan KR. Temporal dynamics of the host molecular responses underlying severe COVID-19 progression and disease resolution. EBioMedicine 2021; 65:103262. [PMID: 33691247 PMCID: PMC7937043 DOI: 10.1016/j.ebiom.2021.103262] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 01/28/2021] [Accepted: 02/11/2021] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND The coronavirus disease-19 (COVID-19) pandemic has cost lives and economic hardships globally. Various studies have found a number of different factors, such as hyperinflammation and exhausted/suppressed T cell responses to the etiological SARS coronavirus-2 (SARS-CoV-2), being associated with severe COVID-19. However, sieving the causative from associative factors of respiratory dysfunction has remained rudimentary. METHODS We postulated that the host responses causative of respiratory dysfunction would track most closely with disease progression and resolution and thus be differentiated from other factors that are statistically associated with but not causative of severe COVID-19. To track the temporal dynamics of the host responses involved, we examined the changes in gene expression in whole blood of 6 severe and 4 non-severe COVID-19 patients across 15 different timepoints spanning the nadir of respiratory function. FINDINGS We found that neutrophil activation but not type I interferon signaling transcripts tracked most closely with disease progression and resolution. Moreover, transcripts encoding for protein phosphorylation, particularly the serine-threonine kinases, many of which have known T cell proliferation and activation functions, were increased after and may thus contribute to the upswing of respiratory function. Notably, these associative genes were targeted by dexamethasone, but not methylprednisolone, which is consistent with efficacy outcomes in clinical trials. INTERPRETATION Our findings suggest neutrophil activation as a critical factor of respiratory dysfunction in COVID-19. Drugs that target this pathway could be potentially repurposed for the treatment of severe COVID-19. FUNDING This study was sponsored in part by a generous gift from The Hour Glass. EEO and JGL are funded by the National Medical Research Council of Singapore, through the Clinician Scientist Awards awarded by the National Research Foundation of Singapore.
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Affiliation(s)
- Eugenia Z Ong
- Viral Research and Experimental Medicine Center, SingHealth Duke-NUS Academic Medical Centre (ViREMiCS), 169856 Singapore; Program in Emerging Infectious Diseases, Duke-NUS Medical School, 169857 Singapore
| | - Shirin Kalimuddin
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, 169857 Singapore; Department of Infectious Diseases, Singapore General Hospital, 169608 Singapore
| | - Wen Chong Chia
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, 169857 Singapore
| | - Sarah H Ooi
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, 169857 Singapore
| | - Clara Wt Koh
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, 169857 Singapore
| | - Hwee Cheng Tan
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, 169857 Singapore
| | - Summer L Zhang
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, 169857 Singapore
| | - Jenny G Low
- Viral Research and Experimental Medicine Center, SingHealth Duke-NUS Academic Medical Centre (ViREMiCS), 169856 Singapore; Program in Emerging Infectious Diseases, Duke-NUS Medical School, 169857 Singapore; Department of Infectious Diseases, Singapore General Hospital, 169608 Singapore.
| | - Eng Eong Ooi
- Viral Research and Experimental Medicine Center, SingHealth Duke-NUS Academic Medical Centre (ViREMiCS), 169856 Singapore; Program in Emerging Infectious Diseases, Duke-NUS Medical School, 169857 Singapore; Department of Infectious Diseases, Singapore General Hospital, 169608 Singapore; Saw Swee Hock School of Public Health, National University of Singapore, Singapore.
| | - Kuan Rong Chan
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, 169857 Singapore.
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Saedi S, Jafarzadeh Shirazi MR, Niazi A, Tahmasebi A, Ebrahimie E. Prepubertal exposure to high dose of cadmium induces hypothalamic injury through transcriptome profiling alteration and neuronal degeneration in female rats. Chem Biol Interact 2021; 337:109379. [PMID: 33453195 DOI: 10.1016/j.cbi.2021.109379] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 12/23/2020] [Accepted: 01/10/2021] [Indexed: 11/20/2022]
Abstract
Cadmium (Cd) is a toxic metal, which seems to be crucial during the prepubertal period. Cd can destroy the structural integrity of the blood-brain barrier (BBB) and enters into the brain. Although the brain is susceptible to neurotoxicity induced by Cd, the effects of Cd on the brain, particularly hypothalamic transcriptome, are still relatively poorly understood. Therefore, we investigated the molecular effects of Cd exposure on the hypothalamus by profiling the transcriptomic response of the hypothalamus to high dose of Cd (25 mg/kg bw/day cadmium chloride (CdCl2)) during the prepubertal period in Sprague-Dawley female rats. After sequencing and annotation, differential expression analysis revealed 1656 genes that were differentially expressed that 108 of them were classified into 37 transcription factor (TF) families. According to gene ontology (GO) annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, these differentially expressed genes (DEGs) were involved in different biological processes and neurological disorders including Alzheimer's disease (AD), Huntington's disease (HD), and Parkinson's disease (PD), prolactin signaling pathway, PI3K/Akt signaling, and dopaminergic synapse. Five transcripts were selected for further analyses with Real-time quantitative PCR (RT-qPCR). The RT-qPCR results were mostly consistent with those from the high throughput RNA sequencing (RNA-seq). Cresyl violet staining clearly showed an increased neuronal degeneration in the dorsomedial hypothalamus (DMH) and arcuate (Arc) nuclei of the CdCl2 group. Overall, this study demonstrates that prepubertal exposure to high doses of Cd induces hypothalamic injury through transcriptome profiling alteration in female rats, which reveals the new mechanisms of pathogenesis of Cd in the hypothalamus.
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Shan W, Zhang H, Kan J, Yin M, Zhang J, Wan L, Chang R, Li M. Acquired mucoid phenotype of Acinetobacter baumannii: Impact for the molecular characteristics and virulence. Microbiol Res 2021; 246:126702. [PMID: 33465557 DOI: 10.1016/j.micres.2021.126702] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Revised: 10/23/2020] [Accepted: 01/06/2021] [Indexed: 10/22/2022]
Abstract
Mucoid phenotype is an important adaptive defense response for Acinetobacter baumannii (A. baumannii). The aim of this study was to analyze the impact of mucoid phenotype for the molecular characteristics and virulence of A. baumannii. We observed that the colonies of mucoid A. baumannii were moist, with an elevated surface, and the wire drawing result was positive. Transmission electron microscopy data showed that the outer wall of the mucoid colonies was not smooth, had protruding pseudopodia, and was surrounded by a layer of unknown material. Antibiotic susceptibility testing showed that the mucoid strains were multidrug resistant. Notably, the mucoid phenotype and antibiotic resistance were not correlated with the amount of biofilm produced by A. baumannii. MLST data demonstrated that the mucoid A. baumannii strains belonged to type ST2. Most (82.6 %, 38/46) of the multidrug-resistant nonmucoid strains also belonged to the molecular type ST2 and to other types, including ST129, ST158, ST195, ST80 and ST3. Moreover, mucoid A. baumannii strains were more virulent than nonmucoid isolates in a mouse model. The comparative transcriptomic data indicated that 15 genes, especially IX87_RS16955 (acnA), IX87_RS10800 (XanP), IX87_RS12875 (GlmM), IX87_RS00885 and IX87_RS12395 (bfr), were possibly associated with the phenotype and virulence of mucoid A. baumannii. In conclusions, the study comprehensively describes the molecular characteristics and virulence regulatory mechanism of mucoid A. baumannii, and provides novel insights for the prevention and treatment of infections associated with these strains.
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Affiliation(s)
- Wulin Shan
- Department of Laboratory Diagnostics, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230031, China.
| | - Huanhuan Zhang
- Department of Laboratory Diagnostics, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230031, China
| | - Jinsong Kan
- Department of Laboratory Diagnostics, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230031, China
| | - Meiling Yin
- Department of Laboratory Diagnostics, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230031, China
| | - Jiayun Zhang
- Department of Laboratory Diagnostics, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230031, China
| | - Lingling Wan
- Department of Laboratory Diagnostics, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230031, China
| | - Renliang Chang
- Department of Laboratory Diagnostics, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230031, China
| | - Ming Li
- Department of Laboratory Diagnostics, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230031, China
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Chen X, Wu H, Feng J, Li Y, Lv J, Shi W, Fan W, Xiao L, Sun D, Jiang M, Shi M. Transcriptome profiling unveils GAP43 regulates ABC transporters and EIF2 signaling in colorectal cancer cells. BMC Cancer 2021; 21:24. [PMID: 33402155 PMCID: PMC7786480 DOI: 10.1186/s12885-020-07728-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 12/11/2020] [Indexed: 02/08/2023] Open
Abstract
Background The growth- and plasticity-associated protein-43 (GAP43) is biasedly expressed in indigestive system and nervous system. Recent study has shown that GAP43 is responsible for the development of neuronal growth and axonal regeneration in normal nervous tissue, while serves as a specific biomarker of relapsed or refractory neuroblastoma. However, its expression pattern and function in digestive system cancer remains to be clarified. Methods In this study, we examined the GAP43 status with qRT-PCR and bisulfite genomic sequencing in colorectal cancer (CRC). We investigated the effect of overexpressed GAP43 in CRC cells with RNA-seq. The RNA-seq data was analyzed with DAVID and IPA. Results GAP43 was downregulated in CRC compared to the adjacent tissues. DNA methylase inhibitor 5-Aza-CdR treatment could significantly induce GAP43, indicated that the silencing of GAP43 gene in CRC is closely related to DNA methylation. Bisulfite genomic sequencing confirmed the promoter methylation of GAP43 in CRC. To explore the transcriptional alterations by overexpressed GAP43 in CRC, we performed RNA-seq and found that upregulated genes were significantly enriched in the signaling pathways of ABC transporters and ECM-receptor interaction, while downregulated genes were significantly enriched in Ribosome signaling pathway. Further Ingenuity Pathway Analysis (IPA) showed that EIF2 signaling pathway was significantly repressed by overexpression of GAP43. Conclusion Our findings provide a novel mechanistic insight of GAP43 in CRC. Transcriptome profiling of overexpressed GAP43 in CRC uncovered the functional roles of GAP43 in the development of human CRC. Supplementary Information The online version contains supplementary material available at 10.1186/s12885-020-07728-x.
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Affiliation(s)
- Xi Chen
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, 150001, China
| | - Hongjin Wu
- Department of Clinical Laboratory, Hangzhou Cancer Hospital, Hangzhou,, 320000, Zhejiang, China.,The NHC Key Laboratory of Drug Addition Medicine, The First Affiliated Hospital of Kunming Medical University, Kunming, 650000, China
| | - Jia Feng
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, 150001, China
| | - Ying Li
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, 150001, China
| | - Jiao Lv
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, 150001, China
| | - Weikai Shi
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, 150001, China
| | - Weiwei Fan
- Department of Infectious and Medicine, Heilongjiang Provincial Hospital, Harbin, 150036, China
| | - Li Xiao
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, 150001, China
| | - Danmeng Sun
- Department of Pediatrics, Data People's hospital, Shenmu, 719301, China
| | - Mingfeng Jiang
- Department of Clinical Laboratory, Hangzhou Cancer Hospital, Hangzhou,, 320000, Zhejiang, China.
| | - Ming Shi
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, 150001, China.
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Bednarek R, David M, Fuentes S, Kreuze J, Fei Z. Transcriptome analysis provides insights into the responses of sweet potato to sweet potato virus disease (SPVD). Virus Res 2021; 295:198293. [PMID: 33412165 PMCID: PMC7985617 DOI: 10.1016/j.virusres.2020.198293] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 12/19/2020] [Accepted: 12/28/2020] [Indexed: 12/27/2022]
Abstract
Transcriptome responses in sweet potato infected with SPCSV and/or SPFMV were studied. Numerous genes, miRNAs and phasiRNAs were responsive mainly to the dual infection. Salicylic acid-mediated pathways play important roles in antiviral defense responses.
Sweet potato (Ipomoea batatas) ranks among the most important crops in the world and provides nutritional and economic sustainability for subsistence farmers in sub-Saharan Africa. Its production is mainly constrained by sweet potato virus disease (SPVD) caused by the coinfection of two positive-sense single-stranded RNA viruses, sweet potato chlorotic stunt virus (SPCSV) and sweet potato feathery mottle virus (SPFMV). Current understanding of sweet potato responses to SPCSV and SPFMV at the molecular level remains very limited. In this study, we performed deep sequencing of both messenger RNA (mRNA) and small RNA (sRNA) populations in an SPVD-susceptible cultivar ‘Beauregard’ upon viral infection, to identify biological pathways that contribute to both general and specific host responses to these important viral pathogens. We found that pathways related to stress response and signaling were significantly affected by viral infection. sRNA components of these pathways were predominantly affected in late stages of the coinfection by SPCSV and SPFMV. We identified several novel microRNAs that were responsive to viral infection, some of which were predicted to target nucleotide-binding site leucine-rich repeat (NBS-LRR) disease resistance genes. The downregulation of the salicylic acid-mediated defense response pathway in particular seems to be a result of the viral infection process, and can in part explain the susceptible nature of the ‘Beauregard’ cultivar.
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Affiliation(s)
- Ryland Bednarek
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA; Boyce Thompson Institute for Plant Research, Ithaca, NY, 14853, USA
| | - Maria David
- Virology Laboratory, Crop and Systems Science Division, International Potato Center (CIP), Lima 12, Peru
| | - Segundo Fuentes
- Virology Laboratory, Crop and Systems Science Division, International Potato Center (CIP), Lima 12, Peru
| | - Jan Kreuze
- Virology Laboratory, Crop and Systems Science Division, International Potato Center (CIP), Lima 12, Peru.
| | - Zhangjun Fei
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA; Boyce Thompson Institute for Plant Research, Ithaca, NY, 14853, USA; USDA-ARS, Robert W. Holley Center for Agriculture and Health, Ithaca, NY, USA.
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45
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Dhaliwal NK, Mitchell JA. Nuclear RNA Isolation and Sequencing. Methods Mol Biol 2021; 2372:75-83. [PMID: 34417744 DOI: 10.1007/978-1-0716-1697-0_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Most transcriptome studies involve sequencing and quantification of steady-state mRNA by isolating and sequencing poly (A) RNA. Although this type of sequencing data is informative to determine steady-state mRNA levels, it does not provide information on transcriptional output and thus may not always reflect changes in transcriptional regulation of gene expression . Furthermore, sequencing poly (A) RNA may miss transcribed regions of the genome not usually modified by polyadenylation which includes many long non-coding RNAs including enhancer RNA (eRNA). Here, we describe nuclear RNA sequencing (nucRNA-seq) which investigates the transcriptional landscape through sequencing and quantification of nuclear RNAs which are both unspliced and spliced transcripts for protein-coding genes and nuclear-retained long non-coding RNAs.
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Affiliation(s)
- Navroop K Dhaliwal
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
| | - Jennifer A Mitchell
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada.
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46
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Ghiasvand S, Javidi MA, Mohammadian A, Mousavi SA, Shahriari F, Alavian F. Transcriptome analysis evinces anti-neoplastic mechanisms of hypericin: A study on U87 glioblastoma cell line. Life Sci 2020; 266:118874. [PMID: 33358904 DOI: 10.1016/j.lfs.2020.118874] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 11/25/2020] [Accepted: 11/30/2020] [Indexed: 12/13/2022]
Abstract
AIMS Hypericin (HYP) from Hypericum perforatum has cytotoxic effects on a variety of malignant cell types, but the pattern of gene expression mediating the effect is largely unknown. Here we sought to analyze the response of U87 glioblastoma (GBM) cell lines in response to HYP. MATERIALS AND METHODS U87 cell line was treated by HYP. Cytotoxicity was assessed using MTT and Annexin V/PI assays. Gene expression profile was obtained using high-throughput sequencing. Enrichment analysis was performed on differentially expressed genes (DEGs). Upstream transcription factors and microRNAs regulating DEGs were predicted. The effects of DEGs on survival of GBM patients were calculated. Protein-protein interaction analysis was conducted to obtain key altered genes. The possible effect of HYP treatment on immunity response was evaluated. KEY FINDINGS The IC50 of HYP on U87 cell line was determined to be 1.5 μg/ml. The main type of cell death was apoptosis. A total of 312 DEGs were found. Affected Gene Ontology terms and pathways were identified. Analysis of upstream modulators of DEGs pointed out to transcription factors that significantly overlap with GBM stem cell transcription factor. Survival analysis suggested that HYP works best for the mesenchymal subtype patients. Tumor infiltration analysis predicted that HYP may affect Treg and macrophage infiltration in vivo. Using expression pattern of GBM patients and HYP-induced DEGs we suggested Fedratinib as a complementary drug to HYP. SIGNIFICANCE Our study represents the response of U87 cell line to HYP, with analyses on survival, transcription factors and personalization according to GBM subtype.
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Affiliation(s)
- Saeedeh Ghiasvand
- Departments of Biology, Faculty of Science, Malayer University, Malayer, Iran.
| | - Mohammad Amin Javidi
- Integrative Oncology Department, Breast Cancer Research Center, Motamed Cancer Institute, ACECR, Tehran, Iran
| | - Ali Mohammadian
- Department of Medical Biotechnology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Seyed Ahmad Mousavi
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran; Department of Genetics, Reproductive Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACECR, Tehran, Iran
| | - Fatemeh Shahriari
- Department of Molecular Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Firoozeh Alavian
- Department of Biology, Faculty of Science, Farhangian University, Tehran, Iran
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Kaipa JM, Starkuviene V, Erfle H, Eils R, Gladilin E. Transcriptome profiling reveals Silibinin dose-dependent response network in non-small lung cancer cells. PeerJ 2020; 8:e10373. [PMID: 33362957 PMCID: PMC7749657 DOI: 10.7717/peerj.10373] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 10/26/2020] [Indexed: 12/20/2022] Open
Abstract
Silibinin (SIL), a natural flavonolignan from the milk thistle (Silybum marianum), is known to exhibit remarkable hepatoprotective, antineoplastic and EMT inhibiting effects in different cancer cells by targeting multiple molecular targets and pathways. However, the predominant majority of previous studies investigated effects of this phytocompound in a one particular cell line. Here, we carry out a systematic analysis of dose-dependent viability response to SIL in five non-small cell lung cancer (NSCLC) lines that gradually differ with respect to their intrinsic EMT stage. By correlating gene expression profiles of NSCLC cell lines with the pattern of their SIL IC50 response, a group of cell cycle, survival and stress responsive genes, including some prominent targets of STAT3 (BIRC5, FOXM1, BRCA1), was identified. The relevancy of these computationally selected genes to SIL viability response of NSCLC cells was confirmed by the transient knockdown test. In contrast to other EMT-inhibiting compounds, no correlation between the SIL IC50 and the intrinsic EMT stage of NSCLC cells was observed. Our experimental results show that SIL viability response of differently constituted NSCLC cells is linked to a subnetwork of tightly interconnected genes whose transcriptomic pattern can be used as a benchmark for assessment of individual SIL sensitivity instead of the conventional EMT signature. Insights gained in this study pave the way for optimization of customized adjuvant therapy of malignancies using Silibinin.
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Affiliation(s)
- Jagan Mohan Kaipa
- Helmholtz Center for Infection Research, Braunschweig, Germany.,BioQuant, University Heidelberg, Heidelberg, Germany.,Theoretical Bioinformatics, German Cancer Research Center, Heidelberg, Germany
| | - Vytaute Starkuviene
- BioQuant, University Heidelberg, Heidelberg, Germany.,Institute of Biosciences, Vilnius University Life Science Center, Vilnius, Lithuania
| | - Holger Erfle
- BioQuant, University Heidelberg, Heidelberg, Germany
| | - Roland Eils
- Center for Digital Health, Berlin Institute of Health and Charité Universitätsmedizin Berlin, Berlin, Germany.,Health Data Science Unit, Heidelberg University Hospital, Heidelberg, Germany
| | - Evgeny Gladilin
- BioQuant, University Heidelberg, Heidelberg, Germany.,Leibniz Institute of Plant Genetics and Crop Plant Research, Seeland, Germany.,Applied Bioinformatics, German Cancer Research Center, Heidelberg, Germany
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48
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Ge C, Zhao W, Nie L, Niu S, Fang S, Duan Y, Zhao J, Guo K, Zhang Q. Transcriptome profiling reveals the occurrence mechanism of bisexual flowers in melon (Cucumis melo L.). Plant Sci 2020; 301:110694. [PMID: 33218617 DOI: 10.1016/j.plantsci.2020.110694] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 09/24/2020] [Accepted: 09/25/2020] [Indexed: 06/11/2023]
Abstract
Most cultivated melons are andromonoecies in which male flowers arose both in main stem and lateral branches but bisexual flowers only emerged from the leaf axils of lateral branches. However, bisexual flowers emerged in leaf axils of main stem after ethephon treatment. Therefore, the mechanism regulating the occurrence of bisexual flowers were investigated by performing transcriptome analysis in two comparison sets: shoot apex of main stem (MA) versus that of lateral branches (LA), and shoot apex of main stem after ethephon treatment (Eth) versus control (Cont). KEGG results showed that genes involved in "plant hormone signal transduction", "MAPK signaling pathway" and "carbon metabolism" were significantly upregulated both in LA and Eth. Further, details of DEGs involved in ethylene signaling pathway were surveyed and six genes were co-upregulated in two comparison sets. Among these, CmERF1, downstream in ethylene signaling pathway, showed the most significantly difference and expressed higher in bisexual buds than that in male buds. Furthermore, fifteen DEGs were found to contain GCC box or CRT/DRE cis-element for CmERF1 in their putative promoter region, and these DEGs involved in several plant hormones signaling pathway, camalexin synthesis, carbon metabolism and plant pathogen interaction.
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Affiliation(s)
- Chang Ge
- College of Horticulture, Hebei Agricultural University, Baoding, Hebei, China
| | - Wensheng Zhao
- College of Horticulture, Hebei Agricultural University, Baoding, Hebei, China; Hebei Key Laboratory of Vegetable Germplasm Innovation and Utilization, Baoding, Hebei, China; Collaborative Innovation Center of Vegetable Industry of Hebei Province, Baoding, Hebei, China.
| | - Lanchun Nie
- College of Horticulture, Hebei Agricultural University, Baoding, Hebei, China; Hebei Key Laboratory of Vegetable Germplasm Innovation and Utilization, Baoding, Hebei, China; Collaborative Innovation Center of Vegetable Industry of Hebei Province, Baoding, Hebei, China.
| | - Shance Niu
- College of Horticulture, Hebei Agricultural University, Baoding, Hebei, China
| | - Siyu Fang
- College of Horticulture, Hebei Agricultural University, Baoding, Hebei, China
| | - Yaqian Duan
- College of Horticulture, Hebei Agricultural University, Baoding, Hebei, China
| | - Jiateng Zhao
- College of Horticulture, Hebei Agricultural University, Baoding, Hebei, China
| | - Kedong Guo
- College of Horticulture, Hebei Agricultural University, Baoding, Hebei, China
| | - Qian Zhang
- College of Horticulture, Hebei Agricultural University, Baoding, Hebei, China
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Christensen R, Gunnarsson AP, Jensen UB. The role of stem cell antigen-1/Lymphocyte antigen 6A-2/6E-1 knock out in murine epidermis. Stem Cell Res 2020; 49:102047. [PMID: 33157392 DOI: 10.1016/j.scr.2020.102047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 09/30/2020] [Accepted: 10/09/2020] [Indexed: 11/27/2022] Open
Abstract
Stem Cell Antigen-1 (SCA-1) is a central positive marker for isolating stem cells in several tissues in the mouse. However, for the epidermis, this appears to be the opposite since lack of SCA-1 has been shown to identify keratinocyte populations with progenitor characteristics. This study investigates the effect of SCA-1 knockout in murine keratinocytes. We compared Sca-1EGFP/EGFP knockout and wildtype mice with respect to the three-dimensional morphology of the epidermis, performed functional assays, and generated gene expression profiles on FACS sorted cells. There were no morphological abnormalities on skin, fur, or hair follicles in transgenic knockout mice compared to wild type mice. SCA-1 knockout keratinocytes showed significantly reduced colony-forming efficiency, colony size and proliferation rate in vitro, however, SCA-1 knockout did not alter wound healing efficiency or keratinocyte proliferation rate in vivo. Moreover, gene expression profiling shows that the effect from knockout of SCA-1 in keratinocytes is dissimilar from what has been observed in other tissues. Additionally, tumor assay indicated that SCA-1 knockout decreases the number of formed papillomas. The results indicate a more complex role for SCA-1, which might differ between epidermal keratinocytes during homeostasis and activated conditions.
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Affiliation(s)
- Rikke Christensen
- Department of Clinical Genetics, Aarhus University Hospital, Brendstrupgaardsvej 21C, 8200 Aarhus N, Denmark; Department of Biomedicine, Aarhus University, Høegh-Guldbergs Gade 10, 8000 Aarhus C, Denmark.
| | - Anders Patrik Gunnarsson
- Department of Clinical Genetics, Aarhus University Hospital, Brendstrupgaardsvej 21C, 8200 Aarhus N, Denmark; Department of Biomedicine, Aarhus University, Høegh-Guldbergs Gade 10, 8000 Aarhus C, Denmark.
| | - Uffe Birk Jensen
- Department of Clinical Genetics, Aarhus University Hospital, Brendstrupgaardsvej 21C, 8200 Aarhus N, Denmark.
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50
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Fan Z, Gao Y, Ren Y, Guan C, Liu R, Zhang Q. To bloom once or more times: the reblooming mechanisms of Iris germanica revealed by transcriptome profiling. BMC Genomics 2020; 21:553. [PMID: 32787785 PMCID: PMC7430825 DOI: 10.1186/s12864-020-06951-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Accepted: 07/27/2020] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND The reblooming bearded iris (Iris germanica) can bloom twice a year, in spring and autumn. The extended ornamental period makes it more popular and brings additional commercial values. However, little is known about the reblooming mechanisms, making the breeding programs time-consuming and labor-wasting. Therefore, a comparative transcriptome profiling was conducted on once-bloomers and rebloomers from the same F1 generation on six development stages, and the candidate genes associated with reblooming were identified. RESULTS A total of 100,391 unigenes were generated, the mean length being 785 bp. In the three comparisons (the floral initiation stage of spring flowering in once-bloomers (OB-T1) vs the floral initiation stage of spring flowering in rebloomers (RB-T1); RB-T1 vs the floral initiation stage of autumn flowering in rebloomers (RB-T5); OB-T1 vs RB-T5), a total of 690, 3515 and 2941 differentially expressed genes (DEGs) were annotated against the public databases, respectively. The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis focused on the photoperiod response, the temperature insensitivity and the growth speed, to remove the redundant DEGs and figure out the candidate key genes. As a result, the following four genes, PHYTOCHROME A (PHYA), GIGANTEA (GI), SHORT VEGETATIVE PERIOD (SVP) and AUXIN RESPONSE FACTOR (ARF), were considered to be involved in the second floral initiation of the rebloomers. CONCLUSION This research provides valuable information for the discovery of the reblooming-related genes. The insights into the molecular mechanisms of reblooming may accelerate the breeding of bearded iris and other perennials.
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Affiliation(s)
- Zhuping Fan
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, School of Landscape Architecture, Beijing Forestry University, No. 35 Qinghua East Road, Haidian District, Beijing, China
| | - Yike Gao
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, School of Landscape Architecture, Beijing Forestry University, No. 35 Qinghua East Road, Haidian District, Beijing, China.
| | - Yi Ren
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, School of Landscape Architecture, Beijing Forestry University, No. 35 Qinghua East Road, Haidian District, Beijing, China
| | - Chunjing Guan
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, School of Landscape Architecture, Beijing Forestry University, No. 35 Qinghua East Road, Haidian District, Beijing, China
| | - Rong Liu
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, School of Landscape Architecture, Beijing Forestry University, No. 35 Qinghua East Road, Haidian District, Beijing, China
| | - Qixiang Zhang
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, School of Landscape Architecture, Beijing Forestry University, No. 35 Qinghua East Road, Haidian District, Beijing, China
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