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Bok EY, Kim SB, Thakur G, Choe YH, Oh SJ, Hwang SC, Ock SA, Rho GJ, Lee SI, Lee WJ, Lee SL. Insensitive Effects of Inflammatory Cytokines on the Reference Genes of Synovial Fluid Resident-Mesenchymal Stem Cells Derived from Rheumatoid Arthritis Patients. Int J Mol Sci 2023; 24:15159. [PMID: 37894839 PMCID: PMC10607131 DOI: 10.3390/ijms242015159] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 10/07/2023] [Accepted: 10/11/2023] [Indexed: 10/29/2023] Open
Abstract
Mesenchymal stem cells derived from rheumatoid arthritis patients (RA-MSCs) provide an understanding of a variety of cellular and immunological responses within the inflammatory milieu. Sustained exposure of MSCs to inflammatory cytokines is likely to exert an influence on genetic variations, including reference genes (RGs). The sensitive effect of cytokines on the reference genes of RA-SF-MSCs may be a variation factor affecting patient-derived MSCs as well as the accuracy and reliability of data. Here, we comparatively evaluated the stability levels of nine RG candidates, namely GAPDH, ACTB, B2M, EEF1A1, TBP, RPLP0, PPIA, YWHAZ, and HPRT1, to find the most stable ones. Alteration of the RG expression was evaluated in MSCs derived from the SF of healthy donors (H-SF-MSCs) and in RA-SF-MSCs using the geNorm and NormFinder software programs. The results showed that TBP, PPIA, and YWHAZ were the most stable RGs for the normalization of H-SF-MSCs and RA-SF-MSCs using RT-qPCR, whereas ACTB, the most commonly used RG, was less stable and performed poorly. Additionally, the sensitivity of RG expression upon exposure to proinflammatory cytokines (TNF-α and IL-1β) was evaluated. RG stability was sensitive in the H-SF-MSCs exposed to TNF-α and IL-1β but insensitive in the RA-SF-MSCs. Furthermore, the normalization of IDO expression using ACTB falsely diminished the magnitude of biological significance, which was further confirmed with a functional analysis and an IDO activity assay. In conclusion, the results suggest that TBP, PPIA, and YWHAZ can be used in SF-MSCs, regardless of their exposure to inflammatory cytokines.
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Affiliation(s)
- Eun-Yeong Bok
- College of Veterinary Medicine, Gyeongsang National University, Jinju 52828, Republic of Korea; (E.-Y.B.); (S.-B.K.); (G.T.); (Y.-H.C.); (S.-J.O.); (G.-J.R.)
| | - Saet-Byul Kim
- College of Veterinary Medicine, Gyeongsang National University, Jinju 52828, Republic of Korea; (E.-Y.B.); (S.-B.K.); (G.T.); (Y.-H.C.); (S.-J.O.); (G.-J.R.)
| | - Gitika Thakur
- College of Veterinary Medicine, Gyeongsang National University, Jinju 52828, Republic of Korea; (E.-Y.B.); (S.-B.K.); (G.T.); (Y.-H.C.); (S.-J.O.); (G.-J.R.)
| | - Yong-Ho Choe
- College of Veterinary Medicine, Gyeongsang National University, Jinju 52828, Republic of Korea; (E.-Y.B.); (S.-B.K.); (G.T.); (Y.-H.C.); (S.-J.O.); (G.-J.R.)
| | - Seong-Ju Oh
- College of Veterinary Medicine, Gyeongsang National University, Jinju 52828, Republic of Korea; (E.-Y.B.); (S.-B.K.); (G.T.); (Y.-H.C.); (S.-J.O.); (G.-J.R.)
| | - Sun-Chul Hwang
- Department of Orthopaedic Surgery, Gyeongsang National University, School of Medicine and Hospital, Jinju 52727, Republic of Korea;
| | - Sun-A. Ock
- Animal Biotechnology Division, National Institute of Animal Science (NIAS), Rural Development Administration (RDA), 1500, Kongjwipatjwi-ro, Isero-myeon, Wanju-gun 565851, Republic of Korea;
| | - Gyu-Jin Rho
- College of Veterinary Medicine, Gyeongsang National University, Jinju 52828, Republic of Korea; (E.-Y.B.); (S.-B.K.); (G.T.); (Y.-H.C.); (S.-J.O.); (G.-J.R.)
- Research Institute of Life Sciences, Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Sang-Il Lee
- Department of Internal Medicine and Institute of Health Sciences, Gyeongsang National University School of Medicine and Hospital, Jinju 52727, Republic of Korea;
| | - Won-Jae Lee
- College of Veterinary Medicine, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Sung-Lim Lee
- College of Veterinary Medicine, Gyeongsang National University, Jinju 52828, Republic of Korea; (E.-Y.B.); (S.-B.K.); (G.T.); (Y.-H.C.); (S.-J.O.); (G.-J.R.)
- Research Institute of Life Sciences, Gyeongsang National University, Jinju 52828, Republic of Korea
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Hou S, Zhao T, Yang D, Li Q, Liang L, Wang G, Ma Q. Selection and Validation of Reference Genes for Quantitative RT-PCR Analysis in Corylus heterophylla Fisch. × Corylus avellana L. PLANTS 2021; 10:plants10010159. [PMID: 33467497 PMCID: PMC7830083 DOI: 10.3390/plants10010159] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 01/07/2021] [Accepted: 01/08/2021] [Indexed: 11/16/2022]
Abstract
(1) Background: the species of Corylus have sporophytic type of self-incompatibility. Several genes related to recognition reaction between pollen and stigma have been identified in hazelnuts. To better understand the self-incompatibility (SI) response, we screened the suitable reference genes by using quantitative real-time reverse transcription PCR (qRT-PCR) analysis in hazelnut for the first time. (2) Methods: the major cultivar "Dawei" was used as material. A total of 12 candidate genes were identified and their expression profiles were compared among different tissues and in response to various treatments (different times after self- and cross-pollination) by RT-qPCR. The expression stability of these 12 candidate reference genes was evaluated using geNorm, NormFinder, BestKeeper, Delta Ct, and RefFinder programs. (3) Results: the comprehensive ranking of RefFinder indicated that ChaActin, VvActin,
ChaUBQ14, and ChaEF1-α were the most suitable reference genes. According to the stability analysis of 12 candidate reference genes for each sample group based on four software packages, ChaActin and ChaEF1-α were most stable in different times after self-pollination and 4 h after self- and cross-pollination, respectively. To further validate the suitability of the reference genes identified in this study, CavPrx, which the expression profiles in Corylus have been reported, was quantified by using ChaActin and ChaEF1-α as reference genes. (4) Conclusions: our study of reference genes selection in hazelnut shows that the two reference genes, ChaActin and ChaEF1-α, are suitable for the evaluation of gene expression, and can be used for the analysis of pollen-pistil interaction in Corylus. The results supply a reliable foundation for accurate gene quantifications in Corylus species, which will facilitate the studies related to the reproductive biology in Corylus.
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Affiliation(s)
- Sihao Hou
- Key Laboratory of Tree Breeding and Cultivation of the State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China; (S.H.); (T.Z.); (D.Y.); (Q.L.); (L.L.); (G.W.)
- Hazelnut Engineering and Technical Research Center of the State Forestry and Grassland Administration, Beijing 100091, China
- National Hazelnut Industry Innovation Alliance of the State Forestry and Grassland Administration, Beijing 100091, China
| | - Tiantian Zhao
- Key Laboratory of Tree Breeding and Cultivation of the State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China; (S.H.); (T.Z.); (D.Y.); (Q.L.); (L.L.); (G.W.)
- Hazelnut Engineering and Technical Research Center of the State Forestry and Grassland Administration, Beijing 100091, China
- National Hazelnut Industry Innovation Alliance of the State Forestry and Grassland Administration, Beijing 100091, China
| | - Dan Yang
- Key Laboratory of Tree Breeding and Cultivation of the State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China; (S.H.); (T.Z.); (D.Y.); (Q.L.); (L.L.); (G.W.)
- Hazelnut Engineering and Technical Research Center of the State Forestry and Grassland Administration, Beijing 100091, China
- National Hazelnut Industry Innovation Alliance of the State Forestry and Grassland Administration, Beijing 100091, China
| | - Qing Li
- Key Laboratory of Tree Breeding and Cultivation of the State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China; (S.H.); (T.Z.); (D.Y.); (Q.L.); (L.L.); (G.W.)
- Hazelnut Engineering and Technical Research Center of the State Forestry and Grassland Administration, Beijing 100091, China
- National Hazelnut Industry Innovation Alliance of the State Forestry and Grassland Administration, Beijing 100091, China
| | - Lisong Liang
- Key Laboratory of Tree Breeding and Cultivation of the State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China; (S.H.); (T.Z.); (D.Y.); (Q.L.); (L.L.); (G.W.)
- Hazelnut Engineering and Technical Research Center of the State Forestry and Grassland Administration, Beijing 100091, China
- National Hazelnut Industry Innovation Alliance of the State Forestry and Grassland Administration, Beijing 100091, China
| | - Guixi Wang
- Key Laboratory of Tree Breeding and Cultivation of the State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China; (S.H.); (T.Z.); (D.Y.); (Q.L.); (L.L.); (G.W.)
- Hazelnut Engineering and Technical Research Center of the State Forestry and Grassland Administration, Beijing 100091, China
- National Hazelnut Industry Innovation Alliance of the State Forestry and Grassland Administration, Beijing 100091, China
| | - Qinghua Ma
- Key Laboratory of Tree Breeding and Cultivation of the State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China; (S.H.); (T.Z.); (D.Y.); (Q.L.); (L.L.); (G.W.)
- Hazelnut Engineering and Technical Research Center of the State Forestry and Grassland Administration, Beijing 100091, China
- National Hazelnut Industry Innovation Alliance of the State Forestry and Grassland Administration, Beijing 100091, China
- Correspondence: ; Tel.: +86-1381-139-0689
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Evaluation of the stability of standard reference genes of adipose-derived mesenchymal stem cells during in vitro proliferation and differentiation. Mol Biol Rep 2020; 47:2109-2122. [DOI: 10.1007/s11033-020-05311-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 02/07/2020] [Indexed: 12/11/2022]
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Li HB, Dai CG, Zhang CR, He YF, Ran HY, Chen SH. Screening potential reference genes for quantitative real-time PCR analysis in the oriental armyworm, Mythimna separata. PLoS One 2018; 13:e0195096. [PMID: 29617430 PMCID: PMC5884543 DOI: 10.1371/journal.pone.0195096] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2017] [Accepted: 03/18/2018] [Indexed: 11/19/2022] Open
Abstract
The oriental armyworm, Mythimna separata, is a major insect pest in China and other Asian countries. Unfortunately, suitable reference genes for quantitative real-time PCR (qRT-PCR) have not been previously identified in M. separata for normalizing target gene expression. In this study, we evaluated the expression stability of eight candidate genes (18S, ACT, EF1-α, GAPDH, RPS7, RPS13, RPL32 and TUB) in M. separata using the comparative ΔCt method, BestKeeper, Normfinder geNorm and ReFinder, a comprehensive software platform. The results indicated that the appropriate reference gene varied depending on the experimental conditions. We found that ACTIN, EF1-α and TUB were optimal for different developmental stages; TUB, RPS13 and EF1-α showed the most stable expresssion in different tissues; RPS13 and 18S were the best reference genes for monitoring expression under high temperature conditions; TUB, RPS13 and RPS7 exhibited the most stable expression under larval-crowding conditions; RPS7, EF1-α, RPL32 and GAPDH were the best for pesticide exposure experiments. This study provides tools for reliable normalization of qRT-PCR data and forms a foundation for functional studies of target gene expression in M. separata.
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Affiliation(s)
- Hong-Bo Li
- Institute of Plant Protection, Guizhou Academy of Agricultural Science, Guiyang, China
- * E-mail: (HBL); (YFH)
| | - Chang-Geng Dai
- Institute of Plant Protection, Guizhou Academy of Agricultural Science, Guiyang, China
| | - Chang-Rong Zhang
- Institute of Plant Protection, Guizhou Academy of Agricultural Science, Guiyang, China
| | - Yong-Fu He
- Institute of Plant Protection, Guizhou Academy of Agricultural Science, Guiyang, China
- * E-mail: (HBL); (YFH)
| | - Hai-Yan Ran
- Institute of Plant Protection, Guizhou Academy of Agricultural Science, Guiyang, China
| | - Shi-Hong Chen
- Institute of Plant Protection, Guizhou Academy of Agricultural Science, Guiyang, China
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Selection of Suitable Reference Genes for Quantitative Real-Time PCR Normalization in Human Stem Cell Research. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1119:151-168. [PMID: 30267307 DOI: 10.1007/5584_2018_277] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Quantitative real-time polymerase chain reaction (qRT-PCR) is a widely utilized method for evaluating the gene expressions in stem cell research. This method enables researchers to obtain fast and precise results, but the accuracy of the data depends on certain factors, such as those associated with biological sample preparation and PCR efficiency. In order to achieve accurate and reliable results, it is of utmost importance to designate the reference genes, the expressions of which are suitable to all kinds of experimental conditions. Hence it is vital to normalize the qRT-PCR data by using the reference genes. In recent years, it has been found that the expression levels of reference genes widely used in stem cell research present a substantial amount of variation and are not necessarily suitable for normalization. This chapter at hand stresses the significance of selecting suitable reference genes from the point view of human stem cell research.
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Selection of internal references for qRT-PCR assays of human hepatocellular carcinoma cell lines. Biosci Rep 2017; 37:BSR20171281. [PMID: 29180379 PMCID: PMC5741833 DOI: 10.1042/bsr20171281] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Revised: 11/24/2017] [Accepted: 11/27/2017] [Indexed: 12/13/2022] Open
Abstract
Selecting internal references is important for normalizing the loading quantity of samples in quantitative reverse-transcription PCR (qRT-PCR). In the present study, a systematic evaluation of reference genes among nine hepatocellular carcinoma (HCC) cell lines was conducted. After screening the microarray assay data of ten HCC cell lines, 19 candidate reference genes were preselected and then evaluated by qRT-PCR, together with ACTB, GAPDH, HPRT1 and TUBB The expression evenness of these candidate genes was evaluated using RefFinder. The stabilities of the reference genes were further evaluated under different experimental perturbations in Huh-7 and MHCC-97L, and the applicability of the reference genes was assessed by measuring the mRNA expression of CCND1, CCND3, CDK4 and CDK6 under sorafenib treatment in Huh-7. Results showed that TFG and SFRS4 are among the most reliable reference genes, and ACTB ranks third and acts quite well as a classical choice, whereas GAPDH, HPRT1 and TUBB are not proper reference genes in qRT-PCR assays among the HCC cell lines. SFRS4, YWHAB, SFRS4 and CNPY3 are the most stable reference genes of the MHCC-97L under the perturbations of chemotherapy, oxidative stress, starvation and hypoxia respectively, whereas YWHAB is the most stable one of Huh-7 under all perturbations. GAPDH is recommended as a reference gene under chemotherapy perturbations. YWHAB and UBE2B, TMED2 and TSFM, and GAPDH and TSFM are the two best reference genes under oxidative stress, starvation and hypoxia perturbations respectively. TSFM is stable in both cell lines across all the perturbations.
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Rauh J, Jacobi A, Stiehler M. Identification of stable reference genes for gene expression analysis of three-dimensional cultivated human bone marrow-derived mesenchymal stromal cells for bone tissue engineering. Tissue Eng Part C Methods 2014; 21:192-206. [PMID: 25000821 DOI: 10.1089/ten.tec.2014.0230] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
The principles of tissue engineering (TE) are widely used for bone regeneration concepts. Three-dimensional (3D) cultivation of autologous human mesenchymal stromal cells (MSCs) on porous scaffolds is the basic prerequisite to generate newly formed bone tissue. Quantitative reverse transcription polymerase chain reaction (qRT-PCR) is a specific and sensitive analytical tool for the measurement of mRNA-levels in cells or tissues. For an accurate quantification of gene expression levels, stably expressed reference genes (RGs) are essential to obtain reliable results. Since the 3D environment can affect a cell's morphology, proliferation, and gene expression profile compared with two-dimensional (2D) cultivation, there is a need to identify robust RGs for the quantification of gene expression. So far, this issue has not been adequately investigated. The aim of this study was to identify the most stably expressed RGs for gene expression analysis of 3D-cultivated human bone marrow-derived MSCs (BM-MSCs). For this, we analyzed the gene expression levels of n=31 RGs in 3D-cultivated human BM-MSCs from six different donors compared with conventional 2D cultivation using qRT-PCR. MSCs isolated from bone marrow aspirates were cultivated on human cancellous bone cube scaffolds for 14 days. Osteogenic differentiation was assessed by cell-specific alkaline phosphatase (ALP) activity and expression of osteogenic marker genes. Expression levels of potential reference and target genes were quantified using commercially available TaqMan(®) assays. mRNA expression stability of RGs was determined by calculating the coefficient of variation (CV) and using the algorithms of geNorm and NormFinder. Using both algorithms, we identified TATA box binding protein (TBP), transferrin receptor (p90, CD71) (TFRC), and hypoxanthine phosphoribosyltransferase 1 (HPRT1) as the most stably expressed RGs in 3D-cultivated BM-MSCs. Notably, genes that are routinely used as RGs, for example, beta actin (ACTB) and ribosomal protein L37a (RPL37A), were among the least stable genes. We recommend the combined use of TBP, TFRC, and HPRT1 for the accurate and robust normalization of qRT-PCR data of 3D-cultivated human BM-MSCs.
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Affiliation(s)
- Juliane Rauh
- University Center for Orthopedics and Trauma Surgery, Centre for Translational Bone, Joint and Soft Tissue Research, University Hospital Carl Gustav Carus at Technische Universität Dresden , Dresden, Germany
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Tratwal J, Follin B, Ekblond A, Kastrup J, Haack-Sørensen M. Identification of a common reference gene pair for qPCR in human mesenchymal stromal cells from different tissue sources treated with VEGF. BMC Mol Biol 2014; 15:11. [PMID: 24885696 PMCID: PMC4045907 DOI: 10.1186/1471-2199-15-11] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Accepted: 05/13/2014] [Indexed: 12/18/2022] Open
Abstract
Background Human mesenchymal stromal cells from the bone marrow (BMSCs) are widely used as experimental regenerative treatment of ischemic heart disease, and the first clinical trials using adipose-derived stromal cells (ASCs) are currently being conducted. Regenerative mechanisms of BMSCs and ASCs are manifold and in vitro pretreatment of the cells with growth factors has been applied to potentially enhance these properties. When characterizing the transcriptional activity of these cellular mechanisms in vitro it is important to consider the effect of the growth factor treatment on reference genes (RGs) for the normalization of qPCR data. Results BMSCs and ASCs were stimulated with vascular endothelial growth factor A-165 (VEGF) for one week, and compared with un-stimulated cells from the same donor. The stability of nine RGs through VEGF treatment as well as the donor variation was assessed using the GenEx software with the subprograms geNorm and Normfinder. The procedure of stepwise elimination was validated by poor performance of eliminated RGs in a normalization experiment using vWF as target gene. Normfinder found the TATA box binding protein (TBP) to be the most stable single RG for both BMSCs and ASCs. The optimal number of RGs for ASCs was two, and the lowest variance for vWF normalization was found using TBP and YWHAZ. For BMSCs, the optimal number of RGs was four, while the two-RG combination producing the most similar results was TBP and YWHAZ. Conclusions A common reference gene, TBP, was found to be the most stable standalone gene, while TBP and YWHAZ were found to be the best two-RG combination for qPCR analyses for both BMSCs and ASCs through the VEGF stimulation. The presented stepwise elimination procedure was validated, while we found the final normalization experiment to be essential.
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Affiliation(s)
| | | | | | | | - Mandana Haack-Sørensen
- Cardiology Stem Cell Centre, The Heart Centre, Rigshospitalet, Copenhagen University Hospital, Juliane Maries Vej 20, dept, 9302, 2100 Copenhagen, Denmark.
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Vossaert L, O'Leary T, Van Neste C, Heindryckx B, Vandesompele J, De Sutter P, Deforce D. Reference loci for RT-qPCR analysis of differentiating human embryonic stem cells. BMC Mol Biol 2013; 14:21. [PMID: 24028740 PMCID: PMC3848990 DOI: 10.1186/1471-2199-14-21] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2012] [Accepted: 09/11/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Selecting stably expressed reference genes is essential for proper reverse transcription quantitative polymerase chain reaction gene expression analysis. However, this choice is not always straightforward. In the case of differentiating human embryonic stem (hES) cells, differentiation itself introduces changes whereby reference gene stability may be influenced. RESULTS In this study, we evaluated the stability of various references during retinoic acid-induced (2 microM) differentiation of hES cells. Out of 12 candidate references, beta-2-microglobulin, ribosomal protein L13A and Alu repeats are found to be the most stable for this experimental set-up. CONCLUSIONS Our results show that some of the commonly used reference genes are actually not amongst the most stable loci during hES cell differentiation promoted by retinoic acid. Moreover, a novel normalization strategy based on expressed Alu repeats is validated for use in hES cell experiments.
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Affiliation(s)
- Liesbeth Vossaert
- Laboratory for Pharmaceutical Biotechnology, Ghent University, Harelbekestraat 72, Ghent 9000, Belgium.
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Amable PR, Teixeira MVT, Carias RBV, Granjeiro JM, Borojevic R. Identification of appropriate reference genes for human mesenchymal cells during expansion and differentiation. PLoS One 2013; 8:e73792. [PMID: 24023904 PMCID: PMC3759474 DOI: 10.1371/journal.pone.0073792] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2013] [Accepted: 07/31/2013] [Indexed: 02/06/2023] Open
Abstract
Background Quantitative real time polymerase chain reaction (qPCR) is an extremely powerful technique for monitoring gene expression. The quantity of the messenger ribonucleic acids (mRNA) of interest should be normalized using a reference gene, in order to avoid unreliable results originated by the obtained RNA quality and quantity, manipulation errors and inhibitory contaminants. A reference gene is any gene that is stably and consistently expressed under the conditions being studied. Completely false data can be generated if a reference gene is not chosen adequately. Results In the present study, we compared expression levels of five putative reference genes (HPRT1, ACTB, GAPDH, RPL13A and B2M) in primary cultures of four different human cells: mesenchymal stromal cells obtained from bone marrow, adipose tissue or umbilical cord Whartońs Jelly, and dermal fibroblasts, under different expansion and differentiation conditions. We observed that reference genes are not the same for different cells under the same culture conditions. Conclusion Most stable reference genes under our experimental conditions were: RPL13A for adipose tissue- and Whartońs Jelly-derived mesenchymal stromal cells, and HPRT1 for bone marrow-derived mesenchymal stromal cells and dermal fibroblasts. ACTB was the most unstable gene when evaluating adipose tissue- and Whartońs Jelly-derived mesenchymal stromal cells, whilst GAPDH and B2M were the most unstable genes for bone marrow-derived mesenchymal stromal cells and dermal fibroblasts, respectively.
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Affiliation(s)
| | | | | | - José Mauro Granjeiro
- Bioengineering, National Institute of Metrology, Quality and Technology, Rio de Janeiro, Brazil
| | - Radovan Borojevic
- Excellion Biomedical Services, Petrópolis, Rio de Janeiro, Brazil
- Bioengineering, National Institute of Metrology, Quality and Technology, Rio de Janeiro, Brazil
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Chen Y, Yu B, Xue G, Zhao J, Li RK, Liu Z, Niu B. Effects of Storage Solutions on the Viability of Human Umbilical Cord Mesenchymal Stem Cells for Transplantation. Cell Transplant 2013; 22:1075-86. [DOI: 10.3727/096368912x657602] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Human umbilical cord-derived mesenchymal stem cell (UC-MSC) transplantation has shown promise for the treatment of various diseases. For clinical applications, UC-MSCs have been stored in 0.9% saline, 5% dextrose, dextrose and sodium chloride injection, Plasma-Lyte A, 1% human serum albumin (1% HSA), or 5% HSA before administration, but the effect of storage conditions on the viability and biological function of the cells remains unknown. Freshly harvested UC-MSCs were resuspended and incubated in these solutions for 2, 4, or 6 h at 4°C or room temperature (24°C). Cell viability, apoptotic/necrotic fraction, poststorage growth potential, immunophenotype, immunosuppressive capacity, and differentiation capacity were analyzed. When stored in parenteral solutions, UC-MSCs showed progressive deterioration in survival viability and adhesion ability. After 6-h storage, the best viability and attachment rate of UC-MSCs decreased to 83.0 ± 1.6% and 71.8 ± 3.2%, respectively. Our results suggested that UC-MSCs in these conditions lose their viability in a short time. However, it seems that the other biological functions of the surviving UC-MSCs were little affected. Since UC-MSCs suspended in these mediums lose their survival viability in a short time to levels significantly below the permissible limits (70%) by FDA, precautions need to be taken on using these solutions as suspension medium and further studies on the optimal methods for preservation are urgent.
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Affiliation(s)
- Yan Chen
- Department of Respiratory Medicine, The Second Clinical Medical College, Shanxi Medical University, Taiyuan, China
| | - Baofeng Yu
- Department of Biochemistry and Molecular Biology, Shanxi Medical University, Taiyuan, China
| | - Guofang Xue
- Department of Biochemistry and Molecular Biology, Shanxi Medical University, Taiyuan, China
| | - Jie Zhao
- Department of Biochemistry and Molecular Biology, Shanxi Medical University, Taiyuan, China
| | - Ren-Ke Li
- Department of Biochemistry and Molecular Biology, Shanxi Medical University, Taiyuan, China
- Division of Cardiovascular Surgery, Department of Surgery, University of Toronto, Toronto, Ontario, Canada
| | - Zhuola Liu
- Department of Respiratory Medicine, The Second Clinical Medical College, Shanxi Medical University, Taiyuan, China
| | - Bo Niu
- Department of Biochemistry and Molecular Biology, Shanxi Medical University, Taiyuan, China
- Biotechnology Research Laboratory, Capital Institute of Pediatrics, Beijing, China
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Ragni E, Viganò M, Rebulla P, Giordano R, Lazzari L. What is beyond a qRT-PCR study on mesenchymal stem cell differentiation properties: how to choose the most reliable housekeeping genes. J Cell Mol Med 2013; 17:168-80. [PMID: 23305553 PMCID: PMC3823147 DOI: 10.1111/j.1582-4934.2012.01660.x] [Citation(s) in RCA: 120] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2012] [Accepted: 10/10/2012] [Indexed: 12/18/2022] Open
Abstract
In the last years, mesenchymal stem cells (MSCs) have been identified as an attractive cell population in regenerative medicine. In view of future therapeutic applications, the study of specific differentiation-related gene expression is a pivotal prerequisite to define the most appropriate MSC source for clinical translation. In this context, it is crucial to use stable housekeeping genes (HGs) for normalization of qRT-PCR to obtain validated and comparable results. By our knowledge, an exhaustive validation study of HGs comparing MSCs from different sources under various differentiation conditions is still missing. In this pivotal study, we compared the expression levels of 12 genes (ACTB, Β2M, EF1alpha, GAPDH, GUSB, PPIA, RPL13A, RPLP0, TBP, UBC, YWHAZ and 18S rRNA) to assess their suitability as HGs in MSCs during adipogenic, osteogenic and chondrogenic differentiation. We demonstrated that many of the most popular HGs including 18S rRNA, B2M and ACTB were inadequate for normalization, whereas TBP/YWHAZ/GUSB were frequently identified among the best performers. Moreover, we showed the dramatic effects of suboptimal HGs choice on the quantification of cell differentiation markers, thus interfering with a reliable comparison of the lineage potential properties among various MSCs. Thus, in the emerging field of regenerative medicine, the identification of the most appropriate MSC source and cell line is so crucial for the treatment of patients that being inaccurate in the first step of the stem cell characterization can bring important consequences for the patients and for the promising potential of stem cell therapy.
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Affiliation(s)
- Enrico Ragni
- Cell Factory Franco Calori, Center for Transfusion Medicine, Cellular Therapy and Cryobiology, Department of Regenerative Medicine, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milano, Italy
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Teng X, Zhang Z, He G, Yang L, Li F. Validation of reference genes for quantitative expression analysis by real-time rt-PCR in four lepidopteran insects. JOURNAL OF INSECT SCIENCE (ONLINE) 2012; 12:60. [PMID: 22938136 PMCID: PMC3481461 DOI: 10.1673/031.012.6001] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Quantitative real-time polymerase chain reaction (qPCR) is an efficient and widely used technique to monitor gene expression. Housekeeping genes (HKGs) are often empirically selected as the reference genes for data normalization. However, the suitability of HKGs used as the reference genes has been seldom validated. Here, six HKGs were chosen (actin A3, actin A1, GAPDH, G3PDH, E2F, rp49) in four lepidopteran insects Bombyx mori L. (Lepidoptera: Bombycidae), Plutella xylostella L. (Plutellidae), Chilo suppressalis Walker (Crambidae), and Spodoptera exigua Hübner (Noctuidae) to study their expression stability. The algorithms of geNorm, NormFinder, stability index, and ΔCt analysis were used to evaluate these HKGs. Across different developmental stages, actin A1 was the most stable in P. xylostella and C. suppressalis, but it was the least stable in B. mori and S. exigua. Rp49 and GAPDH were the most stable in B. mori and S. exigua, respectively. In different tissues, GAPDH, E2F, and Rp49 were the most stable in B. mori, S. exigua, and C. suppressalis, respectively. The relative abundances of Siwi genes estimated by 2(-ΔΔCt) method were tested with different HKGs as the reference gene, proving the importance of internal controls in qPCR data analysis. The results not only presented a list of suitable reference genes in four lepidopteran insects, but also proved that the expression stabilities of HKGs were different among evolutionarily close species. There was no single universal reference gene that could be used in all situations. It is indispensable to validate the expression of HKGs before using them as the internal control in qPCR.
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Affiliation(s)
- Xiaolu Teng
- Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China
- Key Laboratory of Integrated Management of Crop Diseases and Pests, Nanjing Agricultural University, Ministry of Education, 210095, China
- 2009102089@.njau.edu.cn
| | - Zan Zhang
- Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China
- Key Laboratory of Integrated Management of Crop Diseases and Pests, Nanjing Agricultural University, Ministry of Education, 210095, China
| | - Guiling He
- Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China
- Key Laboratory of Integrated Management of Crop Diseases and Pests, Nanjing Agricultural University, Ministry of Education, 210095, China
- Department of Chemistry, Jiaying University, Meizhou, Guangzhou, 514015, China
| | - Liwen Yang
- Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China
- Key Laboratory of Integrated Management of Crop Diseases and Pests, Nanjing Agricultural University, Ministry of Education, 210095, China
| | - Fei Li
- Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China
- Key Laboratory of Integrated Management of Crop Diseases and Pests, Nanjing Agricultural University, Ministry of Education, 210095, China
- Corresponding author
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