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Ismail NZ, Khairuddean M, Alidmat MM, Abubakar S, Arsad H. Investigating the potential of mono-chalcone compounds in targeting breast cancer receptors through network pharmacology, molecular docking, molecular dynamics simulation, antiproliferative effects, and gene expressions. 3 Biotech 2024; 14:151. [PMID: 38737798 PMCID: PMC11087420 DOI: 10.1007/s13205-024-03991-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Accepted: 04/17/2024] [Indexed: 05/14/2024] Open
Abstract
The study aims to investigate various aspects of synthesized mono-chalcone compounds 5 and 8 concerning breast cancer, including network pharmacology, molecular docking, molecular dynamics (MD) simulations, antiproliferative effects, and gene expressions. Initially, the compounds underwent a network pharmacology analysis targeting breast cancer-related targets, with MalaCards, SwissTargetPrediction, and PharmMapper identifying 70 breast cancer target receptors. Subsequently, protein-protein interaction (PPI) network analysis revealed two distinct target gene clusters. Survival analysis identified seven significant target genes following Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment and Gene Ontology (GO) evaluation. Molecular docking and MD simulations were conducted on these seven target genes (AKT2, BRAF, ESR1, FGFR1, IGF1, IGF1R, and KIT), revealing that compound 8 exhibited the highest binding affinities, as well as better stability and compactness when interacting with the targeted proteins. Next, the compounds underwent cell viability assay and gene expression analysis to validate the in silico findings. Both compounds demonstrated the ability to suppress breast cancer proliferation, with compound 8 showing increased selectivity in targeting breast cancer cells while causing minimal harm to normal breast cells. The suppression of breast cancer cell proliferation was attributed to decreased expression levels of AKT2, BRAF, FGFR1, IGF1, IGF1R, KIT, and ESR1. Hence, the results provide insights into the molecular interaction responsible for the anti-breast cancer capabilities of mono-chalcone compounds. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-024-03991-y.
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Affiliation(s)
- Noor Zafirah Ismail
- School of Chemical Sciences, Universiti Sains Malaysia, 11800 Penang, Malaysia
| | - Melati Khairuddean
- School of Chemical Sciences, Universiti Sains Malaysia, 11800 Penang, Malaysia
| | | | - Sadiq Abubakar
- School of Chemical Sciences, Universiti Sains Malaysia, 11800 Penang, Malaysia
- Department of Pure and Industrial Chemistry, Bayero University Kano, Kano, 3011 Nigeria
| | - Hasni Arsad
- Advanced Medical and Dental Institute, Universiti Sains Malaysia, Bertam, 13200 Kepala Batas, Penang Malaysia
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2
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Ivanova Z, Petrova V, Grigorova N, Vachkova E. Identification of the Reference Genes for Relative qRT-PCR Assay in Two Experimental Models of Rabbit and Horse Subcutaneous ASCs. Int J Mol Sci 2024; 25:2292. [PMID: 38396967 PMCID: PMC10889259 DOI: 10.3390/ijms25042292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 02/09/2024] [Accepted: 02/13/2024] [Indexed: 02/25/2024] Open
Abstract
Obtaining accurate and reliable gene expression results in real-time RT-PCR (qRT-PCR) data analysis requires appropriate normalization by carefully selected reference genes, either a single or a combination of multiple housekeeping genes (HKGs). The optimal reference gene/s for normalization should demonstrate stable expression across varying conditions to diminish potential influences on the results. Despite the extensive database available, research data are lacking regarding the most appropriate HKGs for qRT-PCR data analysis in rabbit and horse adipose-derived stem cells (ASCs). Therefore, in our study, we comprehensively assessed and compared the suitability of some widely used HKGs, employing RefFinder and NormFinder, two extensively acknowledged algorithms for robust data interpretation. The rabbit and horse ASCs were obtained from subcutaneous stromal vascular fraction. ASCs were induced into tri-lineage differentiation, followed by the eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) treatment of the adipose-differentiated rabbit ASCs, while horse experimental groups were formed based on adipogenic, osteogenic, and chondrogenic differentiation. At the end of the experiment, the total mRNA was obtained and used for the gene expression evaluation of the observed factors. According to our findings, glyceraldehyde 3-phosphate dehydrogenase was identified as the most appropriate endogenous control gene for rabbit ASCs, while hypoxanthine phosphoribosyltransferase was deemed most suitable for horse ASCs. The obtained results underscore that these housekeeping genes exhibit robust stability across diverse experimental conditions, remaining unaltered by the treatments. In conclusion, the current research can serve as a valuable baseline reference for experiments evaluating gene expression in rabbit and horse ASCs. It highlights the critical consideration of housekeeping gene abundance and stability in qPCR experiments, emphasizing the need for an individualized approach tailored to the specific requirements of the study.
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Affiliation(s)
- Zhenya Ivanova
- Department of Pharmacology, Animal Physiology, Biochemistry and Chemistry, Faculty of Veterinary Medicine, Trakia University, 6000 Stara Zagora, Bulgaria; (V.P.); (N.G.); (E.V.)
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3
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Guo W, Yang Y, Ma B, Wang W, Hu Z, Leng P. Selection and Validation of Reference Genes for Gene Expression Studies in Euonymus japonicus Based on RNA Sequencing. Genes (Basel) 2024; 15:131. [PMID: 38275612 PMCID: PMC10815735 DOI: 10.3390/genes15010131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 01/13/2024] [Accepted: 01/19/2024] [Indexed: 01/27/2024] Open
Abstract
Euonymus japonicus is one of the most low-temperature-tolerant evergreen broad-leaved tree species in the world and is widely used in urban greening. However, there are very few molecular biology studies on its low-temperature tolerance mechanism. So far, no researcher has selected and reported on its reference genes. In this study, 21 candidate reference genes (12 traditional housekeeping genes and 9 other genes) were initially selected based on gene expression and coefficient of variation (CV) through RNA-Seq (unpublished data), and qRT-PCR was used to detect the expression levels of candidate reference genes in three different groups of samples (leaves under different temperature stresses, leaves of plants at different growth stages, and different organs). After further evaluating the expression stability of these genes using geNorm, NormFinder, Bestkeeper, and RefFind, the results show that the traditional housekeeping gene eIF5A and the new reference gene RTNLB1 have good stability in the three different groups of samples, so they are reference genes with universality. In addition, we used eIF5A and RTNLB1 as reference genes to calibrate the expression pattern of the target gene EjMAH1, which confirmed this view. This article is the first to select and report on the reference gene of E. japonicus, laying the foundation for its low-temperature tolerance mechanism and other molecular biology research.
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Affiliation(s)
- Wei Guo
- College of Landscape Architecture, Beijing University of Agriculture, Beijing 102206, China; (W.G.); (B.M.); (W.W.)
| | - Yihui Yang
- College of Landscape Architecture, Beijing University of Agriculture, Beijing 102206, China; (W.G.); (B.M.); (W.W.)
| | - Bo Ma
- College of Landscape Architecture, Beijing University of Agriculture, Beijing 102206, China; (W.G.); (B.M.); (W.W.)
| | - Wenbo Wang
- College of Landscape Architecture, Beijing University of Agriculture, Beijing 102206, China; (W.G.); (B.M.); (W.W.)
| | - Zenghui Hu
- Engineering Research Center for Ancient Tree Health and Ancient Tree Culture of National Forestry and Grassland Administration, Beijing 102206, China
| | - Pingsheng Leng
- College of Landscape Architecture, Beijing University of Agriculture, Beijing 102206, China; (W.G.); (B.M.); (W.W.)
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4
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Zhou Y, Li X, Zhang X, Li M, Luo N, Zhao Y. Screening of Candidate Housekeeping Genes in Uterus Caruncle by RNA-Sequence and qPCR Analyses in Different Stages of Goat ( Capra hircus). Animals (Basel) 2023; 13:1897. [PMID: 37370406 DOI: 10.3390/ani13121897] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Revised: 05/25/2023] [Accepted: 05/29/2023] [Indexed: 06/29/2023] Open
Abstract
The uterus is a critical pregnancy organ for mammals. The normal growth and development of ruminant uterus caruncles are crucial to maintain gestation and fetal health in goats. Quantitative real-time polymerase chain reaction (qRT-PCR) is a reliable tool to study gene expression profiling for exploring the intrinsic mechanism underlying the conversion process of uterus caruncle tissue. However, the candidate housekeeping genes (HKGs) are required for normalizing the expression of function genes. In our study, 22 HKGs were selected from analyzing transcriptome data at non-pregnancy and pregnancy processes and previous reports about HKGs in goat tissues. We assessed them for expression suitability in 24 samples from uterus tissues at 15 non-pregnant days (Stage 1), early (Stage 2), and medium-later pregnant days (Stage 3). The expression stability of these genes was evaluated by using geNorm, Normfinder, Bestkeeper, and Delta Ct algorithms and, comprehensively, by ReFinder. In addition, the most and least stable HKGs were used to normalize the target genes expression of SPP1, VEGFA, and PAG8. It was found that traditional reference genes, such as ACTB and GAPDH, were not suitable for target gene normalization. In contrast, PPIB selected from RNA sequencing data and EIF3K selected from previous references showed the least variation and were recommended as the best HKGs during the nonpregnant stage and the whole stages of goat uterus caruncle tissue, respectively. It is the first time the HKGs genes in uterus during the non-pregnant day and throughout the total pregnancy have been explored. These findings found suitable HKGs in uterus caruncle tissues at various stages of non-pregnancy and pregnancy; these can be useful for gene expression studies to reveal the molecular mechanisms of uterus development in goats.
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Affiliation(s)
- Yumei Zhou
- College of Animal Science and Technology, Southwest University, Chongqing 400715, China
- Chongqing Key Laboratory of Herbivore Science, Chongqing Key Laboratory of Forage and Herbivore, Chongqing Engineering Research Center for Herbivores Resource Protection and Utilization, Chongqing Herbivore Engineering Research Center, Chongqing 400715, China
| | - Xingchun Li
- College of Animal Science and Technology, Southwest University, Chongqing 400715, China
- Chongqing Key Laboratory of Herbivore Science, Chongqing Key Laboratory of Forage and Herbivore, Chongqing Engineering Research Center for Herbivores Resource Protection and Utilization, Chongqing Herbivore Engineering Research Center, Chongqing 400715, China
| | - Xinyue Zhang
- College of Animal Science and Technology, Southwest University, Chongqing 400715, China
- Chongqing Key Laboratory of Herbivore Science, Chongqing Key Laboratory of Forage and Herbivore, Chongqing Engineering Research Center for Herbivores Resource Protection and Utilization, Chongqing Herbivore Engineering Research Center, Chongqing 400715, China
| | - Minghui Li
- College of Animal Science and Technology, Southwest University, Chongqing 400715, China
- Chongqing Key Laboratory of Herbivore Science, Chongqing Key Laboratory of Forage and Herbivore, Chongqing Engineering Research Center for Herbivores Resource Protection and Utilization, Chongqing Herbivore Engineering Research Center, Chongqing 400715, China
| | - Nanjian Luo
- College of Animal Science and Technology, Southwest University, Chongqing 400715, China
- Chongqing Key Laboratory of Herbivore Science, Chongqing Key Laboratory of Forage and Herbivore, Chongqing Engineering Research Center for Herbivores Resource Protection and Utilization, Chongqing Herbivore Engineering Research Center, Chongqing 400715, China
- School of Preclinical Medicine, Zunyi Medical University, Zunyi 563000, China
| | - Yongju Zhao
- College of Animal Science and Technology, Southwest University, Chongqing 400715, China
- Chongqing Key Laboratory of Herbivore Science, Chongqing Key Laboratory of Forage and Herbivore, Chongqing Engineering Research Center for Herbivores Resource Protection and Utilization, Chongqing Herbivore Engineering Research Center, Chongqing 400715, China
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Xue M, Wen H, Xu P, Chen J, Wang Q, Tang Y, Ma X, Lv G, Li H, Song C. Validation and Functional Analysis of Reference and Tissue-Specific Genes in Adipose Tissue of Freshwater Drum, Aplodinotus grunniens, under Starvation and Hypothermia Stress. Cells 2023; 12:cells12091328. [PMID: 37174728 PMCID: PMC10177597 DOI: 10.3390/cells12091328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 04/23/2023] [Accepted: 05/04/2023] [Indexed: 05/15/2023] Open
Abstract
Adipose tissue is critical to the growth, development, and physiological health of animals. Reference genes play an essential role in normalizing the expression of mRNAs. Tissue-specific genes are preferred for their function and expression in specific tissues or cell types. Identification of these genes contributes to understanding the tissue-gene relationship and the etiology and discovery of new tissue-specific targets. Therefore, reference genes and tissue-specific genes in the adipose tissue of Aplodinotus grunniens were identified to explore their function under exogenous starvation (1 d, 2 w, 6 w) and hypothermic stress (18 °C and 10 °C for 2 d and 8 d) in this study. Results suggest that 60SRP was the most stable reference gene in adipose tissue. Meanwhile, eight genes were validated as tissue-specific candidates from the high-throughput sequencing database, while seven of them (ADM2, β2GP1, CAMK1G, CIDE3, FAM213A, HSL, KRT222, and NCEH1) were confirmed in adipose tissue. Additionally, these seven tissue-specific genes were active in response to starvation and hypothermic stress in a time- or temperature-dependent manner. These results demonstrate that adipose-specific genes can be identified using stable internal reference genes, thereby identifying specific important functions under starvation and hypothermic stress, which provides tissue-specific targets for adipose regulation in A. grunniens.
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Affiliation(s)
- Miaomiao Xue
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China
| | - Haibo Wen
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China
| | - Pao Xu
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China
| | - Jianxiang Chen
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China
| | - Qingyong Wang
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China
| | - Yongkai Tang
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China
| | - Xueyan Ma
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China
| | - Guohua Lv
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China
| | - Hongxia Li
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China
| | - Changyou Song
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China
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6
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Nevone A, Lattarulo F, Russo M, Panno G, Milani P, Basset M, Avanzini MA, Merlini G, Palladini G, Nuvolone M. A Strategy for the Selection of RT-qPCR Reference Genes Based on Publicly Available Transcriptomic Datasets. Biomedicines 2023; 11:biomedicines11041079. [PMID: 37189697 DOI: 10.3390/biomedicines11041079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 03/23/2023] [Accepted: 03/27/2023] [Indexed: 04/05/2023] Open
Abstract
In the next-generation sequencing era, RT-qPCR is still widely employed to quantify levels of nucleic acids of interest due to its popularity, versatility, and limited costs. The measurement of transcriptional levels through RT-qPCR critically depends on reference genes used for normalization. Here, we devised a strategy to select appropriate reference genes for a specific clinical/experimental setting based on publicly available transcriptomic datasets and a pipeline for RT-qPCR assay design and validation. As a proof-of-principle, we applied this strategy to identify and validate reference genes for transcriptional studies of bone-marrow plasma cells from patients with AL amyloidosis. We performed a systematic review of published literature to compile a list of 163 candidate reference genes for RT-qPCR experiments employing human samples. Next, we interrogated the Gene Expression Omnibus to assess expression levels of these genes in published transcriptomic studies on bone-marrow plasma cells from patients with different plasma cell dyscrasias and identified the most stably expressed genes as candidate normalizing genes. Experimental validation on bone-marrow plasma cells showed the superiority of candidate reference genes identified through this strategy over commonly employed “housekeeping” genes. The strategy presented here may apply to other clinical and experimental settings for which publicly available transcriptomic datasets are available.
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Affiliation(s)
- Alice Nevone
- Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy
- Amyloidosis Research and Treatment Center, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy
| | - Francesca Lattarulo
- Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy
- Amyloidosis Research and Treatment Center, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy
| | - Monica Russo
- Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy
- Amyloidosis Research and Treatment Center, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy
| | - Giada Panno
- Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy
- Amyloidosis Research and Treatment Center, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy
| | - Paolo Milani
- Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy
- Amyloidosis Research and Treatment Center, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy
| | - Marco Basset
- Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy
- Amyloidosis Research and Treatment Center, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy
| | - Maria Antonietta Avanzini
- Pediatric Hematology Oncology, Cell Factory, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy
| | - Giampaolo Merlini
- Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy
- Amyloidosis Research and Treatment Center, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy
| | - Giovanni Palladini
- Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy
- Amyloidosis Research and Treatment Center, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy
| | - Mario Nuvolone
- Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy
- Amyloidosis Research and Treatment Center, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy
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Zhao L, Yang H, Li X, Zhou Y, Liu T, Zhao Y. Transcriptome-based selection and validation of optimal reference genes in perirenal adipose developing of goat ( Capra hircus). Front Vet Sci 2022; 9:1055866. [PMID: 36467654 PMCID: PMC9712442 DOI: 10.3389/fvets.2022.1055866] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 11/02/2022] [Indexed: 06/15/2024] Open
Abstract
Brown adipose tissue (BAT) is mainly present in young mammals and is important for maintaining body temperature in neonatal mammals because of its ability to produce non-shivering thermogenesis. There is usually a large amount of BAT around the kidneys of newborn kids, but the BAT gradually "whiting" after birth. Screening and validating appropriate reference genes is a prerequisite for further studying the mechanism of goat brown adipose tissue "whiting" during the early stages. In this study, the expression stability of 17 candidate reference genes: 12 COPS8, SAP18, IGF2R, PARL, SNRNP200, ACTG1, CLTA, GANAB, GABARAP, PCBP2, CTSB, and CD151) selected based on previous transcriptome data as new candidate reference genes, 3 (PFDN5, CTNNB1, and EIF3M) recommended in previous studies, and 2 traditional reference genes (ACTB and GAPDH) was evaluated. Real-time quantitative PCR (RT-qPCR) technology was used to detect the expression level of candidate reference genes during goat BAT "whiting". Four algorithms: Normfinder, geNorm, ΔCt method, and BestKeeper, and two comprehensive algorithms: ComprFinder and RefFinder, were used to analyze the stability of each candidate reference genes. GABARAP, CLTA, GAPDH, and ACTB were identified as the most stable reference genes, while CTNNB1, CTSB, and EIF3M were the least stable. Moreover, two randomly selected target genes IDH2 and RBP4, were effectively normalized using the selected most stable reference genes. These findings collectively suggest that GABARAP, CLTA, GAPDH, and ACTB are relatively stable reference genes that can potentially be used for the development of perirenal fat in goats.
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Hildyard JC, Wells DJ, Piercy RJ. Identification of qPCR reference genes suitable for normalising gene expression in the developing mouse embryo. Wellcome Open Res 2022; 6:197. [PMID: 35509373 PMCID: PMC9024131 DOI: 10.12688/wellcomeopenres.16972.1] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/14/2022] [Indexed: 07/30/2023] Open
Abstract
Background: Progression through mammalian embryogenesis involves many interacting cell types and multiple differentiating cell lineages. Quantitative polymerase chain reaction (qPCR) analysis of gene expression in the developing embryo is a valuable tool for deciphering these processes, but normalisation to stably-expressed reference genes is essential for such analyses. Gene expression patterns change globally and dramatically as embryonic development proceeds, rendering identification of consistently appropriate reference genes challenging. Methods: We have investigated expression stability in mouse embryos from mid to late gestation (E11.5-E18.5), both at the whole-embryo level, and within the head and forelimb specifically, using 15 candidate reference genes ( ACTB, 18S, SDHA, GAPDH, HTATSF1, CDC40, RPL13A, CSNK2A2, AP3D1, HPRT1, CYC1, EIF4A, UBC, B2M and PAK1IP1), and four complementary algorithms (geNorm, Normfinder, Bestkeeper and deltaCt). Results: Unexpectedly, all methods suggest that many genes within our candidate panel are acceptable references, though AP3D1, RPL13A and PAK1IP1 are the strongest performing genes overall (scoring highly in whole embryos, heads or forelimbs alone, and in all samples collectively). HPRT1 and B2M are conversely poor choices, and show strong developmental regulation. We further show that normalisation using our three highest-scoring references can reveal subtle patterns of developmental expression even in genes ostensibly ranked as acceptably stable ( CDC40, HTATSF1). Conclusion: AP3D1, RPL13A and PAK1IP1 represent universally suitable reference genes for expression studies in the E11.5-E18.5 mouse embryo.
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Affiliation(s)
- John C.W. Hildyard
- Comparative Neuromuscular Diseases Laboratory, Clinical Science and Services, Royal Veterinary College, London, NW1 0TU, UK
| | - Dominic J. Wells
- Comparative Biomedical Sciences, Royal Veterinary College, London, London, NW1 0TU, UK
| | - Richard J. Piercy
- Comparative Neuromuscular Diseases Laboratory, Clinical Science and Services, Royal Veterinary College, London, NW1 0TU, UK
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9
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Hildyard JC, Wells DJ, Piercy RJ. Identification of qPCR reference genes suitable for normalising gene expression in the developing mouse embryo. Wellcome Open Res 2022; 6:197. [PMID: 35509373 PMCID: PMC9024131 DOI: 10.12688/wellcomeopenres.16972.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/14/2022] [Indexed: 11/22/2022] Open
Abstract
Background: Progression through mammalian embryogenesis involves many interacting cell types and multiple differentiating cell lineages. Quantitative polymerase chain reaction (qPCR) analysis of gene expression in the developing embryo is a valuable tool for deciphering these processes, but normalisation to stably-expressed reference genes is essential for such analyses. Gene expression patterns change globally and dramatically as embryonic development proceeds, rendering identification of consistently appropriate reference genes challenging. Methods: We have investigated expression stability in mouse embryos from mid to late gestation (E11.5–E18.5), both at the whole-embryo level, and within the head and forelimb specifically, using 15 candidate reference genes (
ACTB, 18S, SDHA, GAPDH, HTATSF1, CDC40, RPL13A, CSNK2A2, AP3D1, HPRT1, CYC1, EIF4A, UBC, B2M and
PAK1IP1), and four complementary algorithms (geNorm, Normfinder, Bestkeeper and deltaCt). Results: Unexpectedly, all methods suggest that many genes within our candidate panel are acceptable references, though
AP3D1,
RPL13A and
PAK1IP1 are the strongest performing genes overall (scoring highly in whole embryos, heads or forelimbs alone, and in all samples collectively).
HPRT1 and
B2M are conversely poor choices, and show strong developmental regulation. We further show that normalisation using our three highest-scoring references can reveal subtle patterns of developmental expression even in genes ostensibly ranked as acceptably stable (
CDC40,
HTATSF1). Conclusion:
AP3D1,
RPL13A and
PAK1IP1 represent universally suitable reference genes for expression studies in the E11.5-E18.5 mouse embryo.
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Affiliation(s)
- John C.W. Hildyard
- Comparative Neuromuscular Diseases Laboratory, Clinical Science and Services, Royal Veterinary College, London, NW1 0TU, UK
| | - Dominic J. Wells
- Comparative Biomedical Sciences, Royal Veterinary College, London, London, NW1 0TU, UK
| | - Richard J. Piercy
- Comparative Neuromuscular Diseases Laboratory, Clinical Science and Services, Royal Veterinary College, London, NW1 0TU, UK
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Huang Q, Xu J, Ge Y, Shi Y, Wang F, Zhu M. NR4A1 inhibits the epithelial–mesenchymal transition of hepatic stellate cells: Involvement of TGF-β–Smad2/3/4–ZEB signaling. Open Life Sci 2022; 17:447-454. [PMID: 35600274 PMCID: PMC9070444 DOI: 10.1515/biol-2022-0047] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 01/06/2022] [Accepted: 01/07/2022] [Indexed: 12/24/2022] Open
Abstract
This study aimed to examine whether nuclear receptor 4a1 (NR4A1) is involved in inhibiting hepatic stellate cell (HSC) activation and liver fibrosis through the epithelial–mesenchymal transition (EMT). HSC-T6 cells were divided into the control group, the acetaldehyde (200 μM, an EMT activator) group, and the NR4A1 activation group (Cytosporone B; 1 μM). The expression levels of the epithelial marker E-cadherin, the mesenchymal markers fibronectin (FN), vimentin, smooth muscle alpha-actin (α-SMA), and fibroblast-specific protein 1 (FSP-1), and the components of the transforming growth factor (TGF)-β pathway were detected by real-time polymerase chain reaction and western blotting. Compared with the control group, E-cadherin in the acetaldehyde group was downregulated, whereas FN, FSP-1, vimentin, α-SMA, and COL1A1/COL1A2 were upregulated (P < 0.05). Compared with the acetaldehyde group, NR4A1 agonist upregulated E-cadherin and downregulated FN, FSP-1, vimentin, α-SMA, and COL1A1/COL1A2 (P < 0.05). After acetaldehyde stimulation, TGF-β, Smad2/3/4, and zinc finger E-box-binding homeobox (ZEB) were upregulated, while Smad7 mRNA levels were downregulated (all P < 0.05). Compared with acetaldehyde alone, NR4A1 agonist increased Smad7 mRNA levels and reduced TGF-β, Smad2/3/4, and ZEB mRNA levels (all P < 0.05). NR4A1 activation suppresses acetaldehyde-induced EMT, as shown by epithelial and mesenchymal marker expression. The inhibition of the TGF-β–Smad2/3/4–ZEB signaling during HSC activation might be involved.
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Affiliation(s)
- Qian Huang
- Department of Infectious Diseases, Hangzhou Xixi Hospital, Zhejiang University of Traditional Chinese Medicine , Hangzhou , 310023 , China
| | - Jingying Xu
- Department of Infectious Diseases, Hangzhou Xixi Hospital, Zhejiang University of Traditional Chinese Medicine , Hangzhou , 310023 , China
| | - Yanyan Ge
- Department of Internal Medicine, Hangzhou Third People’s Hospital, Zhejiang University of Traditional Chinese Medicine , Hangzhou , 310009 , China
| | - Yue Shi
- Department of Infectious Diseases, Hangzhou Xixi Hospital, Zhejiang University of Traditional Chinese Medicine , Hangzhou , 310023 , China
| | - Fei Wang
- Department of Infectious Diseases, Hangzhou Xixi Hospital, Zhejiang University of Traditional Chinese Medicine , Hangzhou , 310023 , China
| | - Mingli Zhu
- Department of Laboratory Medicine, Hangzhou Xixi Hospital, Zhejiang University of Traditional Chinese Medicine , Hangzhou , 310023 , China
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11
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da Conceição Braga L, Gonçalves BÔP, Coelho PL, da Silva Filho AL, Silva LM. Identification of best housekeeping genes for the normalization of RT-qPCR in human cell lines. Acta Histochem 2022; 124:151821. [PMID: 34861601 DOI: 10.1016/j.acthis.2021.151821] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Revised: 11/22/2021] [Accepted: 11/25/2021] [Indexed: 11/01/2022]
Abstract
The identification of the best reference gene is a critical step to evaluate the relative change in mRNA expression of a target gene by RT-qPCR. In this work, we evaluated nineteen genes of different functional classes using Real Time Human Reference Gene Panel (Roche Applied Sciences), to identify the internal housekeeping genes (HKGs) most suitable for gene expression normalization data in human cell lines. Normal cell lines CCD-19LU (lung fibroblast), HEK-293 (epithelial cell of embryonic kidney), WI-26 VA4 (lung fibroblast), and human cancer cells, BT-549 (breast cancer), Hs 578T (breast cancer), MACL-1 (breast cancer), HeLa (cervical carcinoma), U-87 MG (glioblastoma/astrocytoma), RKO-AS45-1 (colorectal carcinoma), and TOV-21G (ovarian adenocarcinoma) were cultivated according to manufacturer's protocol. Twelve candidate reference genes were commonly expressed in five cell lines (CCD-19Lu, HEK-293, RKO-AS45-1, TOV-21G, and U-87 MG). To verify the expression stability, we used the RefFinder web tool, which integrates data from the computational programs Normfinder, BestKeeper, geNorm, and the comparative Delta-Ct method. The ACTB was the most stable reference gene to the CCD-19Lu and HEK-293 cells. The best combination of HKGs for the RKO-AS45-1 and TOV-21G cell lines were B2M/GAPDH and PBGD/B2M, respectively. For the U-87 MG cells, GAPDH and IPO8 were the most suitable HKGs. Thus, our findings showed that it is crucial to use the right HKGs to precise normalize gene expression levels in cancer studies, once a suitable HKG for one cell type cannot be to the other.
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Rashid M, Shah SG, Natu A, Verma T, Rauniyar S, Gera PB, Gupta S. RPS13, a potential universal reference gene for normalisation of gene expression in multiple human normal and cancer tissue samples. Mol Biol Rep 2021; 48:7967-7974. [PMID: 34657252 DOI: 10.1007/s11033-021-06828-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 09/24/2021] [Indexed: 11/25/2022]
Abstract
BACKGROUND Reference genes are considered stable genes and are used for normalizing the gene expression profile across different cell types; as well as, in normal and diseased samples. However, these gene associates with different biological processes, and hence expression vary in different pathological conditions. Therefore, in the present study, eight different reference genes were used and compared to identify common reference gene usable for an array of different cell types and human cancers. METHODS AND RESULTS The expression stability of the eight reference genes across eleven normal and cancerous tissues was confirmed through real time-qPCR. Ribosomal protein S13 (RPS13) was found to be a common and stable reference gene across intra- and inter-comparison between various normal and tumor tissue types. Further, TCGA data analysis across and between normal and tumor tissue types also showed minimum deviation in expression of RPS13 gene out of eight routinely used reference genes. CONCLUSION RPS13 is the common stable reference gene in normalization for gene expression based analysis in cancer research.
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Affiliation(s)
- Mudasir Rashid
- Epigenetics and Chromatin Biology Group, Gupta Lab, Cancer Research Institute, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai, MH, 410210, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, MH, India
| | - Sanket Girish Shah
- Epigenetics and Chromatin Biology Group, Gupta Lab, Cancer Research Institute, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai, MH, 410210, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, MH, India
| | - Abhiram Natu
- Epigenetics and Chromatin Biology Group, Gupta Lab, Cancer Research Institute, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai, MH, 410210, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, MH, India
| | - Tripti Verma
- Epigenetics and Chromatin Biology Group, Gupta Lab, Cancer Research Institute, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai, MH, 410210, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, MH, India
| | - Sukanya Rauniyar
- Epigenetics and Chromatin Biology Group, Gupta Lab, Cancer Research Institute, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai, MH, 410210, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, MH, India
| | - Poonam B Gera
- Biorepository, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai, MH, 410210, India
| | - Sanjay Gupta
- Epigenetics and Chromatin Biology Group, Gupta Lab, Cancer Research Institute, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai, MH, 410210, India.
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, MH, India.
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13
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Ppia is the most stable housekeeping gene for qRT-PCR normalization in kidneys of three Pkd1-deficient mouse models. Sci Rep 2021; 11:19798. [PMID: 34611276 PMCID: PMC8492864 DOI: 10.1038/s41598-021-99366-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Accepted: 09/13/2021] [Indexed: 01/08/2023] Open
Abstract
Autosomal Dominant Polycystic Kidney Disease (ADPKD) is the most common inherited renal disorder, characterized by renal cyst development leading to end-stage renal disease. Although the appropriate choice of suitable reference is critical for quantitative RNA analysis, no comparison of frequently used “housekeeping” genes is available. Here, we determined the validity of 7 candidate housekeeping genes (Actb, Actg1, B2m, Gapdh, Hprt, Pgam1 and Ppia) in kidney tissues from mouse models orthologous to ADPKD, including a cystic mice (CY) 10–12 weeks old (Pkd1flox/flox:Nestincre/Pkd1flox/−:Nestincre, n = 10) and non-cystic (NC) controls (Pkd1flox/flox/Pkd1flox/-, n = 10), Pkd1-haploinsufficient (HT) mice (Pkd1+/−, n = 6) and wild-type (WT) controls (Pkd1+/+, n = 6) and a severely cystic (SC) mice 15 days old (Pkd1V/V, n = 7) and their controls (CO, n = 5). Gene expression data were analyzed using six distinct statistical softwares. The estimation of the ideal number of genes suggested the use of Ppia alone as sufficient, although not ideal, to analyze groups altogether. Actb, Hprt and Ppia expression profiles were correlated in all samples. Ppia was identified as the most stable housekeeping gene, while Gapdh was the least stable for all kidney samples. Stat3 expression level was consistent with upregulation in SC compared to CO when normalized by Ppia expression. In conclusion, present findings identified Ppia as the best housekeeping gene for CY + NC and SC + CO groups, while Hprt was the best for the HT + WT group.
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Johnson R, Rafuse M, Selvakumar PP, Tan W. Effects of recipient age, heparin release and allogeneic bone marrow-derived stromal cells on vascular graft remodeling. Acta Biomater 2021; 125:172-182. [PMID: 33639311 DOI: 10.1016/j.actbio.2021.02.028] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 02/17/2021] [Accepted: 02/18/2021] [Indexed: 02/07/2023]
Abstract
Small-caliber vascular grafts are used in a wide range of clinical conditions. However, there remains a substantial unfulfilled need for readily-available, synthetic vascular grafts with high long-term patency rate. To fulfill the translational goal for bioengineered vascular grafts, important considerations for the pre-clinical evaluation include the graft design, cell incorporation and selection of an animal model. To assess the three factors, we used vascular grafts consisting of core/shell-structured microfibers of polycaprolactone/gelatin with a thin polycaprolactone overlay. The respective influences of the heparin release mode, animal age, and allogeneic bone marrow-derived stromal cells (MSCs) seeded in the lumen on the graft remodeling were assessed after four-and-half-month implantation on an interposition graft of abdominal aorta model. Except two rats dying from graft-unrelated issues, all other rats (18 out of 20) showed good graft patency upon explantation. The cell phenotype, matrix content and structure in the neotissues around the graft, as well as the flow perfusion through the graft were examined. More grafts in the aged rats showed local narrowing and flow incongruence than the other grafts in young adult rats. Compared to acellular grafts, cellular grafts showed efficient recruitment of vascular cells to form more organized structures with elastin in the vascular wall. Endothelialization and α-smooth muscle actin-positive cells were shown in all four types of vascular grafts. This study revealed the significant effects of MSC and recipient age but not heparin release pattern on graft remodeling. STATEMENT OF SIGNIFICANCE: The vascular graft is a mainstream of surgical intervention to treat vascular diseases. Currently, vascular grafts, particularly small-diameter ones, still show high failure rates. This study has evaluated the respective impacts of heparin release pattern, allogeneic bone marrow-derived stromal cell seeding, and recipient age on the long-term remodeling of vascular grafts. There is a dearth of literature which considers the recipient age as an influencing factor for vascular grafting. However, adults particularly elderly constitute the majority of vascular graft recipients in the "real" clinical environment. While juvenile animals were widely used for graft evaluations, this study involved adult animals. The study outcomes provided important implications regarding graft designs and evaluation approaches.
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15
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Vermani L, Kumar R, Senthil Kumar N. GAPDH and PUM1: Optimal Housekeeping Genes for Quantitative Polymerase Chain Reaction-Based Analysis of Cancer Stem Cells and Epithelial-Mesenchymal Transition Gene Expression in Rectal Tumors. Cureus 2020; 12:e12020. [PMID: 33457124 PMCID: PMC7797410 DOI: 10.7759/cureus.12020] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Background The overwhelming majority of published articles have taken colon and rectal cancer as a single group, i.e., colorectal cancer, when normalizing gene expression data with housekeeping genes (HKG) in quantitative polymerase chain reaction (qPCR) experiments though there are published reports that suggest the differential expression pattern of genes between the colon and rectal cancer groups and hence the current experiment was attempted to find out the optimal set of housekeeping genes from the list of common HKG for rectal tumor gene expression analysis. Methods The expression of five potential housekeeping genes GAPDH, RPNI, PUM1, B2M, and PMM1 was analyzed through qPCR and Bestkeeper software (http://www.wzw.tum.de/gene-quantification/bestkeeper.html) in 20 stage II-IV rectal cancer samples to check for uniformity in their expression pattern. Cancer stem cell (CSC) marker ALDH1 and epithelial-mesenchymal transition marker (EMT) markers E cadherin, vimentin, Twist, and SNAI2 expression were evaluated in conjunction with the two optimal reference genes in 10 rectal cancers as part of validation. Results The standard deviation of the cycle threshold value of GAPDH was found the lowest at 0.65 followed by RPN1 at 0.88, PUM1 at 0.94, PMM1 at 0.94, and B2M at 1.21 when analyzed with BestKeeper software. Using GAPDH and PUM1 as the reference gene for the validation phase, rectal cancer patients with stage III/IV showed a 4.79-fold change (P=0.006) in ALDH1 expression, and an 11.76-fold change in Twist expression (P=0.003) with respect to stage II rectal tumor when normalized with GAPDH and PUM1. Conclusion GAPDH and PUM1 can be used as an optimal set of housekeeping genes for gene expression-related experiments in rectal tumors. ALDH1 and Twist were found significantly overexpressed in stage III/IV rectal tumors in comparison to stage II rectal cancer. Genes associated with cancer stem cells and EMT markers could be optimally analyzed by normalizing them with GAPDH and PUM1 as housekeeping genes.
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Affiliation(s)
| | - Rajeev Kumar
- Research, Cachar Cancer Hospital and Research Centre, Silchar, IND
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16
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Using RNA-Seq to Identify Reference Genes of the Transition from Brown to White Adipose Tissue in Goats. Animals (Basel) 2020; 10:ani10091626. [PMID: 32927876 PMCID: PMC7552189 DOI: 10.3390/ani10091626] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 09/02/2020] [Accepted: 09/09/2020] [Indexed: 12/25/2022] Open
Abstract
Simple Summary Brown adipose tissue (BAT) plays important roles in unique non-shivering thermogenesis. It is necessary to select reference genes during the transition process from brown (BAT) to white adipose tissue (WAT) for Quantitative PCR (qPCR) analysis. In this study, CTNNB, PFDN5 and EIF3M, selected from RNA sequencing data, were the most suitable reference genes. The present study provides a detailed analysis of the expression stability of reference genes for the study of gene expression profiling during the transition process from BAT to WAT. Abstract Brown adipose tissues have unique non-shivering thermogenesis functions, can be found in newborn ruminate animals, and then are gradually replaced by white adipose tissues in adulthood. For the purpose of exploring the intrinsic mechanism underlying the conversion process from brown (BAT) to white adipose tissue (WAT), it is necessary to utilize Quantitative PCR (qPCR) to study gene expression profiling. In this study, we identified reference genes that were consistently expressed during the transformation from goat BAT to WAT using RNA-seq data. Then, twelve genes were evaluated as candidate reference genes for qPCR in goat perirenal adipose tissue using three tools (geNorm, Normfinder, and BestKeeper). In addition, the selected reference genes were used to normalize the gene expression of PGC-1α and GPAT4. It was found that traditional reference genes, such as GAPDH, RPLP0, HPRT1, and PPIA were not suitable for target gene normalization. In contrast, CTNNB, PFDN5, and EIF3M, selected from RNA sequencing data, showed the least variation and were recommended as the best reference genes during the transformation from BAT to WAT.
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Lee GKC, Tessier L, Bienzle D. Salivary Scavenger and Agglutinin (SALSA) Is Expressed in Mucosal Epithelial Cells and Decreased in Bronchial Epithelium of Asthmatic Horses. Front Vet Sci 2019; 6:418. [PMID: 31850379 PMCID: PMC6896824 DOI: 10.3389/fvets.2019.00418] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2019] [Accepted: 11/07/2019] [Indexed: 12/13/2022] Open
Abstract
The Salivary Scavenger and Agglutinin (SALSA) protein is an innate immune protein with various alleged functions, including the regulation of inflammation and tissue remodeling. Transcriptomic studies of severe equine asthma (SEA) showed downregulation of the gene encoding SALSA in bronchial epithelium of asthmatic compared to non-asthmatic horses. This study aimed to characterize expression of SALSA in equine tissues by immunohistochemistry (IHC), corroborate potential differences in epithelial gene expression between asthmatic and non-asthmatic horses, and assess the structure of equine SALSA. An antibody against SALSA was validated through immunoprecipitation followed by mass spectrometry and Western blotting to recognize the equine protein. This antibody was applied to tissue microarrays (TMAs) containing 22 tissues each from four horses. A quantitative PCR assay was designed to compare gene expression for SALSA between six asthmatic and six non-asthmatic horses, before and after an asthmatic challenge, using cDNA from endoscopic bronchial biopsies as source material. The SALSA gene from bronchial cDNA samples of 10 horses, was amplified and sequenced, and translated to characterize the protein structure. Immunostaining for SALSA was detected in the mucosal surfaces of the trachea, bronchi, bronchioles, stomach, small intestine and bladder, in pancreatic and salivary gland ducts, and in uterine gland epithelium. Staining was strongest in the duodenum, and the intercalated ducts and Demilune cells of the salivary gland. SALSA was concentrated in the apical regions of the epithelial cell cytoplasm, suggestive of a secreted protein. Gene expression was significantly lower (p = 0.031) in asthmatic compared to non-asthmatic horses. Equine SALSA consisted of three to five scavenger receptor cysteine-rich (SRCR) domains, two CUB (C1r/C1s, uegf, bmp-1) domains and one Zona Pellucida domain. These domains mediate the binding of ligands involved in innate immunity. Varying numbers of SRCR domains were identified in different horses, indicating different isoforms. In summary, equine SALSA has a predilection for mucosal sites, has multiple isoforms, and has decreased expression in asthmatic horses, suggesting alterations in innate immunity in equine asthma.
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Affiliation(s)
| | - Laurence Tessier
- Department of Pathobiology, University of Guelph, Guelph, ON, Canada
| | - Dorothee Bienzle
- Department of Pathobiology, University of Guelph, Guelph, ON, Canada
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18
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Borkowska P, Zielińska A, Paul-Samojedny M, Stojko R, Kowalski J. Evaluation of reference genes for quantitative real-time PCR in Wharton's Jelly-derived mesenchymal stem cells after lentiviral transduction and differentiation. Mol Biol Rep 2019; 47:1107-1115. [PMID: 31781918 DOI: 10.1007/s11033-019-05207-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 11/22/2019] [Indexed: 02/07/2023]
Abstract
Quantitative real time reverse transcription PCR, qRT-PCR, is one of the most important techniques for assessing the level of gene expression. Selecting the correct reference gene to normalize the results is a key step in this method. Inaccurate data can be generated if the correct reference gene is not selected. The level of the expression of reference genes is tissue-variable, and in the case of mesenchymal stem cells (MSC), it can be different depending on the source of their origin. The aim of this study was to select the reference gene for Wharton's Jelly-derived MSC (WJ- MSC) that were undergoing transduction and differentiation. In this work, the expression of 32 genes was analyzed, of which two (RPS17 and 18S rRNA), which had the most stable expression level, were selected. A comparative analysis of the expression stability of the selected genes was then performed with the genes that are most commonly used in the literature, i.e. β-actin and GAPDH. Next, it was determined that a false picture of the expression level of the studied genes can be obtained when a reference gene with variable expression level is used for normalization. RPS17 and 18S rRNA proved to be the most stable reference genes for the WJ-MSC that had been subjected to the lentiviral transfection procedure followed by differentiation. The expression of β-actin and GAPDH was highly unstable and therefore these genes are not suitable for use as reference genes in studies involving WJ- MSC.
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Affiliation(s)
- P Borkowska
- Department of Medical Genetics, Medical University of Silesia, Jednosci 8 Street, 41-200, Sosnowiec, Poland.
| | - A Zielińska
- Department of Medical Genetics, Medical University of Silesia, Jednosci 8 Street, 41-200, Sosnowiec, Poland
| | - M Paul-Samojedny
- Department of Medical Genetics, Medical University of Silesia, Jednosci 8 Street, 41-200, Sosnowiec, Poland
| | - R Stojko
- School of Health Sciences in Katowice, Medical University of Silesia, Medyków 12 Street, Katowice, Poland
| | - J Kowalski
- Department of Medical Genetics, Medical University of Silesia, Jednosci 8 Street, 41-200, Sosnowiec, Poland
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19
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Jin Y, Liu F, Huang W, Sun Q, Huang X. Identification of reliable reference genes for qRT-PCR in the ephemeral plant Arabidopsis pumila based on full-length transcriptome data. Sci Rep 2019; 9:8408. [PMID: 31182737 PMCID: PMC6557819 DOI: 10.1038/s41598-019-44849-1] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Accepted: 05/23/2019] [Indexed: 01/23/2023] Open
Abstract
Arabidopsis pumila, an annual ephemeral plant, plays important roles in preventing wind and sand erosion, water and soil conservation, and microhabitat improvement in the North of Xinjiang, China. Studies of adaptive mechanisms in harsh desert environments at the genetic and genomic levels can be used to more effectively develop and protect this species. The quantitative real-time polymerase chain reaction (qRT-PCR) method is one of the essential means to achieve these goals, and the selection of an appropriate reference gene is the prerequisite for qRT-PCR. In this study, 10 candidate reference genes were identified from the full-length transcriptome data of A. pumila, and their expression stabilities under four abiotic stresses (drought, heat, cold and salt) and in seven different tissues (roots, hypocotyl, cotyledon, leaves, stems, flowers and siliques) were evaluated with four programmes geNorm, NormFinder, Bestkeeper and RefFinder. Although the most stable reference genes were variable under different treatments using different software, comprehensive ranking revealed that UEP and HAF1 under drought stress, UBQ9 and GAPDH under heat stress, UBC35 and GAPDH under cold stress, GAPDH and ACT1 under salt stress, and ACT1 and GAPDH in different tissues were the most stable reference genes. Moreover, GAPDH and UBQ9 were the most suitable reference gene combinations for all samples. The expression pattern of the K+ uptake permease gene KUP9 further validated that the selected reference genes were suitable for normalization of gene expression. The identification of reliable reference genes guarantees more accurate qRT-PCR quantification for A. pumila and facilitates functional genomics studies of ephemeral plants.
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Affiliation(s)
- Yuhuan Jin
- Special Plant Genomics Laboratory, College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832000, China
| | - Fang Liu
- Special Plant Genomics Laboratory, College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832000, China.,State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Wei Huang
- Special Plant Genomics Laboratory, College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832000, China
| | - Qi Sun
- Special Plant Genomics Laboratory, College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832000, China
| | - Xianzhong Huang
- Special Plant Genomics Laboratory, College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832000, China.
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Li M, Wang M, Liu Y, Huang S, Yi X, Yin C, Wang S, Zhang M, Yu Q, Li P, Xiao Y. TNF-α Upregulates IKKε Expression via the Lin28B/let-7a Pathway to Induce Catecholamine Resistance in Adipocytes. Obesity (Silver Spring) 2019; 27:767-776. [PMID: 30933434 DOI: 10.1002/oby.22434] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 01/14/2019] [Indexed: 11/07/2022]
Abstract
OBJECTIVE Overexpression of inhibitor of nuclear factor kappa-B kinase subunit epsilon (IKKε) contributes to blunted catecholamine-induced lipolysis. Tumor necrosis factor α (TNF-α) upregulates adipose IKKε expression to inhibit stimulated lipolysis, which can be reversed by IKKε inhibitors. This study investigated adipose IKKε expression in children with and without obesity and potential involvement of the Lin28B/let-7a axis in posttranscriptional regulation of TNF-α-stimulated IKKε in adipocytes. METHODS Adipose IKKε was detected in children both with and without obesity. The effects of TNF-α on IKKε expression of adipocytes were investigated. Inhibitor and mimics of microRNA let-7a or short interfering RNA of protein lin-28 homolog B (Lin28B) were used to determine the effect of the Lin28B/let-7a axis on TNF-α-mediated IKKε upregulation. Reporter assays were performed to confirm that let-7a targets the IKKε gene. RESULTS Adipose IKKε expression in children with obesity was upregulated to a greater extent than that in children without obesity and was positively correlated with BMI. TNF-α increased IKKε expression through activation of Lin28B/let-7a and then inhibited isoproterenol-stimulated lipolysis in adipocytes. Blocking the Lin28B /let-7a axis rescued inhibition of isoproterenol-stimulated lipolysis produced by TNF-α by inhibiting IKKε expression. Reporter assays confirmed that IKKε is a target of let-7a. CONCLUSIONS Adipose IKKε expression in children with obesity is substantially elevated and positively correlated with BMI. TNF-α induces catecholamine resistance via activation of the Lin28B/let-7a/IKKε pathway.
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Affiliation(s)
- Min Li
- Department of Pediatrics, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an Shaanxi, People's Republic of China
| | - Min Wang
- Department of Pediatrics, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an Shaanxi, People's Republic of China
| | - Yuesheng Liu
- Department of Pediatrics, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an Shaanxi, People's Republic of China
| | - Shanlong Huang
- Department of Urology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an Shaanxi, People's Republic of China
| | - Xiaoqing Yi
- Department of Pediatrics, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an Shaanxi, People's Republic of China
| | - Chunyan Yin
- Department of Pediatrics, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an Shaanxi, People's Republic of China
| | - Sisi Wang
- Department of Pediatrics, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an Shaanxi, People's Republic of China
| | - Meizhen Zhang
- Department of Pediatrics, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an Shaanxi, People's Republic of China
| | - Qiang Yu
- Department of Pediatric Surgery, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an Shaanxi, People's Republic of China
| | - Peng Li
- Department of Pediatric Surgery, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an Shaanxi, People's Republic of China
| | - Yanfeng Xiao
- Department of Pediatrics, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an Shaanxi, People's Republic of China
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Duan M, Wang J, Zhang X, Yang H, Wang H, Qiu Y, Song J, Guo Y, Li X. Identification of Optimal Reference Genes for Expression Analysis in Radish ( Raphanus sativus L.) and Its Relatives Based on Expression Stability. FRONTIERS IN PLANT SCIENCE 2017; 8:1605. [PMID: 28966627 PMCID: PMC5605625 DOI: 10.3389/fpls.2017.01605] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2017] [Accepted: 08/31/2017] [Indexed: 05/19/2023]
Abstract
Radish (Raphanus sativus) is an important cruciferous root crop with a close relationship to Chinese cabbage (Brassica rapa). RT-qPCR is used extensively to evaluate the expression levels of target genes, and accurate measurement of target gene expression with this method is determined by the valid reference genes used for data nomalization in different experimental conditions. Screening for appropriate reference genes with stable expression based on RT-qPCR data is important for gene expression and functional analysis research in radish and its relatives. However, many researches have thought that almost no single reference gene is widely suitable for all experimental conditions, and few researchers have paid attention to the validation of reference genes in radish gene expression analysis. In the present study, 12 candidate reference genes were selected for analysis. Their expression in 28 samples, including 20 radish samples from different organs and conditions, four Chinese cabbage organs and four organs of their distant hybrid, was assessed by RT-qPCR and then five software tools-ΔCt, geNorm, NormFinder, BestKeeper and RefFinder-were used to compare their expression stability. The results showed that the most suitable reference genes were different in different organs and conditions. GAPDH, DSS1, and UP2 were optimal reference genes for gene expression analysis in all organs and conditions in radish. UPR, GSNOR1, and ACTIN2/7 were the most stable reference genes in different radish organs. UP2 and GAPDH were suitable reference genes for radish pistil development studies. RPII, UBC9, and GAPDH had the most stable expression in radish under various stresses. DSS1, UP2, and TEF2 were the optimal reference genes for Chinese cabbage organs, whereas TUA was optimal for the distant hybrid. UP2, and TEF2 were appropriate reference genes for all of the samples together. The optimal reference genes we identified, UP2, GAPDH, UPR, and GSNOR1 were verified by normalizing the expression patterns of YAB3, RPL, and FUL. These results will provide important information for selecting target reference genes in different research contexts and improve the accuracy and precision of gene expression analysis for radish, Chinese cabbage and their distant hybrid.
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Affiliation(s)
- Mengmeng Duan
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural SciencesBeijing, China
- Department of Vegetable Sciences, College of Horticulture, China Agricultural UniversityBeijing, China
| | - Jinglei Wang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural SciencesBeijing, China
| | - Xiaohui Zhang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural SciencesBeijing, China
| | - Haohui Yang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural SciencesBeijing, China
| | - Haiping Wang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural SciencesBeijing, China
| | - Yang Qiu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural SciencesBeijing, China
| | - Jiangping Song
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural SciencesBeijing, China
| | - Yangdong Guo
- Department of Vegetable Sciences, College of Horticulture, China Agricultural UniversityBeijing, China
| | - Xixiang Li
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural SciencesBeijing, China
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22
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Kim BS, Tilstam PV, Springenberg-Jung K, Boecker AH, Schmitz C, Heinrichs D, Hwang SS, Stromps JP, Ganse B, Kopp R, Knobe M, Bernhagen J, Pallua N, Bucala R. Characterization of adipose tissue macrophages and adipose-derived stem cells in critical wounds. PeerJ 2017; 5:e2824. [PMID: 28070458 PMCID: PMC5217526 DOI: 10.7717/peerj.2824] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 11/22/2016] [Indexed: 01/14/2023] Open
Abstract
Background Subcutaneous adipose tissue is a rich source of adipose tissue macrophages and adipose-derived stem cells which both play a key role in wound repair. While macrophages can be divided into the classically-activated M1 and the alternatively-activated M2 phenotype, ASCs are characterized by the expression of specific stem cell markers. Methods In the present study, we have investigated the expression of common macrophage polarization and stem cell markers in acutely inflamed adipose tissue. Subcutaneous adipose tissue adjacent to acutely inflamed wounds of 20 patients and 20 healthy subjects were harvested and underwent qPCR and flow cytometry analysis. Results Expression levels of the M1-specific markers CD80, iNOS, and IL-1b were significantly elevated in inflammatory adipose tissue when compared to healthy adipose tissue, whereas the M2-specific markers CD163 and TGF-β were decreased. By flow cytometry, a significant shift of adipose tissue macrophage populations towards the M1 phenotype was confirmed. Furthermore, a decrease in the mesenchymal stem cell markers CD29, CD34, and CD105 was observed whereas CD73 and CD90 remained unchanged. Discussion This is the first report describing the predominance of M1 adipose tissue macrophages and the reduction of stem cell marker expression in acutely inflamed, non-healing wounds.
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Affiliation(s)
- Bong-Sung Kim
- Plastic and Reconstructive Surgery, Hand Surgery-Burn Center, Rheinisch-Westfälische Technische Hochschule Aachen, Aachen, Germany.,Department of Medicine, Yale University, New Haven, United States.,Institute of Biochemistry and Molecular Cell Biology, Rheinisch-Westfälische Technische Hochschule Aachen, Aachen, Germany
| | | | - Katrin Springenberg-Jung
- Plastic and Reconstructive Surgery, Hand Surgery-Burn Center, Rheinisch-Westfälische Technische Hochschule Aachen, Aachen, Germany
| | - Arne Hendrick Boecker
- Plastic and Reconstructive Surgery, Hand Surgery-Burn Center, Rheinisch-Westfälische Technische Hochschule Aachen, Aachen, Germany
| | - Corinna Schmitz
- Institute of Biochemistry and Molecular Cell Biology, Rheinisch-Westfälische Technische Hochschule Aachen, Aachen, Germany
| | - Daniel Heinrichs
- Institute of Biochemistry and Molecular Cell Biology, Rheinisch-Westfälische Technische Hochschule Aachen, Aachen, Germany
| | - Soo Seok Hwang
- Department of Immunology, Yale University, New Haven, United States
| | - Jan Philipp Stromps
- Plastic and Reconstructive Surgery, Hand Surgery-Burn Center, Rheinisch-Westfälische Technische Hochschule Aachen, Aachen, Germany
| | - Bergita Ganse
- Department of Orthopedic Trauma Surgery, Rheinisch-Westfälische Technische Hochschule Aachen, Aachen, Germany
| | - Ruedger Kopp
- Department of Intensive Care Medicine, Rheinisch-Westfälische Technische Hochschule Aachen, Aachen, Germany
| | - Matthias Knobe
- Department of Orthopedic Trauma Surgery, Rheinisch-Westfälische Technische Hochschule Aachen, Aachen, Germany
| | - Juergen Bernhagen
- Department of Vascular Biology, Institute for Stroke and Dementia Research, Ludwig-Maximilians-Universität München (LMU), Munich, Germany.,Munich Cluster for Systems Neurology (SyNergy), Ludwig-Maximilians-Universität München (LMU), Munich, Germany
| | - Norbert Pallua
- Plastic and Reconstructive Surgery, Hand Surgery-Burn Center, Rheinisch-Westfälische Technische Hochschule Aachen, Aachen, Germany
| | - Richard Bucala
- Department of Medicine, Yale University, New Haven, United States
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Zhang WX, Fan J, Ma J, Rao YS, Zhang L, Yan YE. Selection of Suitable Reference Genes for Quantitative Real-Time PCR Normalization in Three Types of Rat Adipose Tissue. Int J Mol Sci 2016; 17:ijms17060968. [PMID: 27338366 PMCID: PMC4926500 DOI: 10.3390/ijms17060968] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Revised: 05/30/2016] [Accepted: 06/13/2016] [Indexed: 01/26/2023] Open
Abstract
Quantitative real-time PCR (qRT-PCR) is the most classical technique in the field of gene expression study. This method requires an appropriate reference gene to normalize mRNA levels. In this study, the expression stability of four frequently-used reference genes in epididymal white adipose tissue (eWAT), inguinal beige adipose tissue (iBeAT) and brown adipose tissue (BAT) from obese and lean rats were evaluated by geNorm, NormFinder and BestKeeper. Based on the Minimum Information for Publication of Quantitative Real-Time PCR Experiments (MIQE) guidelines, the two most stable reference genes were recommended in each type of adipose tissue. Two target genes were applied to test the stability of the reference genes. The geNorm and NormFinder results revealed that GAPDH and 36B4 exhibited the highest expression stabilities in eWAT, while 36B4 and β-actin had the highest expression stabilities in iBeAT and BAT. According to the results of the BestKeeper analysis, 36B4 was the most stable gene in eWAT, iBeAT and BAT, in terms of the coefficient of variance. In terms of the coefficient of correlation, GAPDH, 36B4 and β-actin were the most stable genes in eWAT, iBeAT and BAT, respectively. Additionally, expected results and statistical significance were obtained using a combination of two suitable reference genes for data normalization. In conclusion, 36B4 and GAPDH, in combination, are the best reference genes for eWAT, while 36B4 and β-actin are two most suitable reference genes for both iBeAT and BAT. We recommend using these reference genes accordingly.
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Affiliation(s)
- Wan-Xia Zhang
- Department of Pharmacology, Basic Medical School of Wuhan University, 185, DongHu Road, Wuhan 430071, China.
| | - Jie Fan
- Department of Pharmacology, Basic Medical School of Wuhan University, 185, DongHu Road, Wuhan 430071, China.
| | - Jing Ma
- Department of Anesthesiology, Zhongnan Hospital of Wuhan University, Wuhan 430071, China.
| | - Yi-Song Rao
- Department of Pharmacology, Basic Medical School of Wuhan University, 185, DongHu Road, Wuhan 430071, China.
| | - Li Zhang
- Department of Pharmacology, Basic Medical School of Wuhan University, 185, DongHu Road, Wuhan 430071, China.
| | - You-E Yan
- Department of Pharmacology, Basic Medical School of Wuhan University, 185, DongHu Road, Wuhan 430071, China.
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24
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Liu Q, Lei K, Ma Q, Qiao F, Li ZC, An LH. Ribosomal protein L7 as a suitable reference gene for quantifying gene expression in gastropod Bellamya aeruginosa. ENVIRONMENTAL TOXICOLOGY AND PHARMACOLOGY 2016; 43:120-127. [PMID: 26991845 DOI: 10.1016/j.etap.2016.03.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Revised: 03/04/2016] [Accepted: 03/06/2016] [Indexed: 06/05/2023]
Abstract
Expression levels of eight candidate reference genes were quantified in tissues of gastropod Bellamya aeruginosa exposed for 10 d to various stressors, including fasting, 17β-estradiol, 17α-methyltestosterone, and Cd(2+). The results showed that 18s rRNA was the most highly expressed of the candidate reference genes, while H2A was the least expressed. There were no significant changes (p>0.05) in the expression of the eight genes in tissues among the different treatments. Using RefFinder to evaluate the expression stabilities of the eight candidate reference genes, ribosomal protein was shown to be the most stable reference gene, and no effects were observed among the different stressor treatments. These results indicate that RPL 7 is the most suitable reference gene for quantifying gene expression in B. aeruginosa under environmental stress, which was verified in B. aeruginosa exposed to high doses of E2 for 24 and 72h.
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Affiliation(s)
- Qing Liu
- College of Resources and Civil Engineering, Northeastern University, Shenyang 110819, China; State Environmental Protection Key Laboratory of Estuarine and Coastal Research, Chinese Research Academy of Environment Sciences, Beijing 100012, China
| | - Kun Lei
- State Environmental Protection Key Laboratory of Estuarine and Coastal Research, Chinese Research Academy of Environment Sciences, Beijing 100012, China
| | - Qingqing Ma
- State Environmental Protection Key Laboratory of Estuarine and Coastal Research, Chinese Research Academy of Environment Sciences, Beijing 100012, China
| | - Fei Qiao
- State Environmental Protection Key Laboratory of Estuarine and Coastal Research, Chinese Research Academy of Environment Sciences, Beijing 100012, China
| | - Zi-Cheng Li
- State Environmental Protection Key Laboratory of Estuarine and Coastal Research, Chinese Research Academy of Environment Sciences, Beijing 100012, China
| | - Li-Hui An
- State Environmental Protection Key Laboratory of Estuarine and Coastal Research, Chinese Research Academy of Environment Sciences, Beijing 100012, China.
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