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Ferreira DB, Gasparoni LM, Bronzeri CF, Paiva KBS. RPLP0/TBP are the most stable reference genes for human dental pulp stem cells under osteogenic differentiation. World J Stem Cells 2024; 16:656-669. [PMID: 38948092 PMCID: PMC11212553 DOI: 10.4252/wjsc.v16.i6.656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 01/23/2024] [Accepted: 04/12/2024] [Indexed: 06/25/2024] Open
Abstract
BACKGROUND Validation of the reference gene (RG) stability during experimental analyses is essential for correct quantitative real-time polymerase chain reaction (RT-qPCR) data normalisation. Commonly, in an unreliable way, several studies use genes involved in essential cellular functions [glyceraldehyde-3-phosphate dehydrogenase (GAPDH), 18S rRNA, and β-actin] without paying attention to whether they are suitable for such experimental conditions or the reason for choosing such genes. Furthermore, such studies use only one gene when Minimum Information for Publication of Quantitative Real-Time PCR Experiments guidelines recommend two or more genes. It impacts the credibility of these studies and causes distortions in the gene expression findings. For tissue engineering, the accuracy of gene expression drives the best experimental or therapeutical approaches. AIM To verify the most stable RG during osteogenic differentiation of human dental pulp stem cells (DPSCs) by RT-qPCR. METHODS We cultivated DPSCs under two conditions: Undifferentiated and osteogenic differentiation, both for 35 d. We evaluated the gene expression of 10 candidates for RGs [ribosomal protein, large, P0 (RPLP0), TATA-binding protein (TBP), GAPDH, actin beta (ACTB), tubulin (TUB), aminolevulinic acid synthase 1 (ALAS1), tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, zeta (YWHAZ), eukaryotic translational elongation factor 1 alpha (EF1a), succinate dehydrogenase complex, subunit A, flavoprotein (SDHA), and beta-2-microglobulin (B2M)] every 7 d (1, 7, 14, 21, 28, and 35 d) by RT-qPCR. The data were analysed by the four main algorithms, ΔCt method, geNorm, NormFinder, and BestKeeper and ranked by the RefFinder method. We subdivided the samples into eight subgroups. RESULTS All of the data sets from clonogenic and osteogenic samples were analysed using the RefFinder algorithm. The final ranking showed RPLP0/TBP as the two most stable RGs and TUB/B2M as the two least stable RGs. Either the ΔCt method or NormFinder analysis showed TBP/RPLP0 as the two most stable genes. However, geNorm analysis showed RPLP0/EF1α in the first place. These algorithms' two least stable RGs were B2M/GAPDH. For BestKeeper, ALAS1 was ranked as the most stable RG, and SDHA as the least stable RG. The pair RPLP0/TBP was detected in most subgroups as the most stable RGs, following the RefFinfer ranking. CONCLUSION For the first time, we show that RPLP0/TBP are the most stable RGs, whereas TUB/B2M are unstable RGs for long-term osteogenic differentiation of human DPSCs in traditional monolayers.
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Affiliation(s)
- Daniel B Ferreira
- Laboratory of Extracellular Matrix Biology and Cellular Interaction, Department of Anatomy, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, São Paulo, Brazil
| | - Leticia M Gasparoni
- Laboratory of Extracellular Matrix Biology and Cellular Interaction, Department of Anatomy, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, São Paulo, Brazil
| | - Cristiane F Bronzeri
- Laboratory of Extracellular Matrix Biology and Cellular Interaction, Department of Anatomy, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, São Paulo, Brazil
| | - Katiucia B S Paiva
- Laboratory of Extracellular Matrix Biology and Cellular Interaction, Department of Anatomy, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, São Paulo, Brazil.
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Ferreira DB, Gasparoni LM, Bronzeri CF, Paiva KBS. RPLP0/TBP are the most stable reference genes for human dental pulp stem cells under osteogenic differentiation. World J Stem Cells 2024; 16:655-668. [DOI: 10.4252/wjsc.v16.i6.655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 01/23/2024] [Accepted: 04/12/2024] [Indexed: 06/25/2024] Open
Abstract
BACKGROUND Validation of the reference gene (RG) stability during experimental analyses is essential for correct quantitative real-time polymerase chain reaction (RT-qPCR) data normalisation. Commonly, in an unreliable way, several studies use genes involved in essential cellular functions [glyceraldehyde-3-phosphate dehydrogenase (GAPDH), 18S rRNA, and β-actin] without paying attention to whether they are suitable for such experimental conditions or the reason for choosing such genes. Furthermore, such studies use only one gene when Minimum Information for Publication of Quantitative Real-Time PCR Experiments guidelines recommend two or more genes. It impacts the credibility of these studies and causes distortions in the gene expression findings. For tissue engineering, the accuracy of gene expression drives the best experimental or therapeutical approaches.
AIM To verify the most stable RG during osteogenic differentiation of human dental pulp stem cells (DPSCs) by RT-qPCR.
METHODS We cultivated DPSCs under two conditions: Undifferentiated and osteogenic differentiation, both for 35 d. We evaluated the gene expression of 10 candidates for RGs [ribosomal protein, large, P0 (RPLP0), TATA-binding protein (TBP), GAPDH, actin beta (ACTB), tubulin (TUB), aminolevulinic acid synthase 1 (ALAS1), tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, zeta (YWHAZ), eukaryotic translational elongation factor 1 alpha (EF1a), succinate dehydrogenase complex, subunit A, flavoprotein (SDHA), and beta-2-microglobulin (B2M)] every 7 d (1, 7, 14, 21, 28, and 35 d) by RT-qPCR. The data were analysed by the four main algorithms, ΔCt method, geNorm, NormFinder, and BestKeeper and ranked by the RefFinder method. We subdivided the samples into eight subgroups.
RESULTS All of the data sets from clonogenic and osteogenic samples were analysed using the RefFinder algorithm. The final ranking showed RPLP0/TBP as the two most stable RGs and TUB/B2M as the two least stable RGs. Either the ΔCt method or NormFinder analysis showed TBP/RPLP0 as the two most stable genes. However, geNorm analysis showed RPLP0/EF1α in the first place. These algorithms’ two least stable RGs were B2M/GAPDH. For BestKeeper, ALAS1 was ranked as the most stable RG, and SDHA as the least stable RG. The pair RPLP0/TBP was detected in most subgroups as the most stable RGs, following the RefFinfer ranking.
CONCLUSION For the first time, we show that RPLP0/TBP are the most stable RGs, whereas TUB/B2M are unstable RGs for long-term osteogenic differentiation of human DPSCs in traditional monolayers.
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Affiliation(s)
- Daniel B Ferreira
- Laboratory of Extracellular Matrix Biology and Cellular Interaction, Department of Anatomy, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, São Paulo, Brazil
| | - Leticia M Gasparoni
- Laboratory of Extracellular Matrix Biology and Cellular Interaction, Department of Anatomy, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, São Paulo, Brazil
| | - Cristiane F Bronzeri
- Laboratory of Extracellular Matrix Biology and Cellular Interaction, Department of Anatomy, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, São Paulo, Brazil
| | - Katiucia B S Paiva
- Laboratory of Extracellular Matrix Biology and Cellular Interaction, Department of Anatomy, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, São Paulo, Brazil
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Ai Y, Peng K, Li C, Zhang J, Wang G, Wang B, Huang E. Assessment of Reference Genes Stability in Cortical Bone of Obese and Diabetic Mice. Diabetes Metab Syndr Obes 2024; 17:1081-1091. [PMID: 38455760 PMCID: PMC10917645 DOI: 10.2147/dmso.s453458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 02/15/2024] [Indexed: 03/09/2024] Open
Abstract
Introduction Bone, a pivotal structural organ, is susceptible to disorders with profound health implications. The investigation of gene expression in bone tissue is imperative, particularly within the context of metabolic diseases such as obesity and diabetes that augment the susceptibility to bone fractures. The objective of this study is to identify a set of internal control genes for the analysis of gene expression. Methods This study employs reverse transcription-quantitative real-time polymerase chain reaction (RT-qPCR) to assess gene expression in bone tissue. We selected fourteen housekeeping genes and assessed their stability in the cortical bone of mouse models for obesity and diabetes using four well-established algorithms (GeNorm, BestKeeper, NormFinder, and the comparative Delta Ct method). Results and Conclusion We identified Rpl13a as the mostly stably expressed reference gene in cortical bone tissue from mouse models of obesity and diabetes (db/db), while Gapdh was found to be the most stable reference gene in another diabetes model, KKAy mice. Additionally, Ef1a, Ppia, Rplp0, and Rpl22 were identified as alternative genes suitable for normalizing gene expression in cortical bone from obesity and diabetes mouse models. These findings enhance RT-qPCR accuracy and reliability, offering a strategic guide to select reference gene for studying bone tissue gene expression in metabolic disorders.
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Affiliation(s)
- Yuanli Ai
- Institute of Life Sciences, College of Basic Medicine, Chongqing Medical University, Chongqing, People’s Republic of China
| | - Kun Peng
- Chongqing Medical and Pharmaceutical College, Chongqing, People’s Republic of China
| | - Chunli Li
- Institute of Life Sciences, College of Basic Medicine, Chongqing Medical University, Chongqing, People’s Republic of China
| | - Jun Zhang
- Institute of Life Sciences, College of Basic Medicine, Chongqing Medical University, Chongqing, People’s Republic of China
| | - Gang Wang
- Chongqing Key Laboratory of Oral Diseases and Biomedical Sciences, Stomatological Hospital of Chongqing Medical University, Chongqing, People’s Republic of China
- Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher Education College of Stomatology, College of Stomatology, Chongqing Medical University, Chongqing, People’s Republic of China
| | - Bin Wang
- Institute of Life Sciences, College of Basic Medicine, Chongqing Medical University, Chongqing, People’s Republic of China
| | - Enyi Huang
- Chongqing Key Laboratory of Oral Diseases and Biomedical Sciences, Stomatological Hospital of Chongqing Medical University, Chongqing, People’s Republic of China
- Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher Education College of Stomatology, College of Stomatology, Chongqing Medical University, Chongqing, People’s Republic of China
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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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Mineralizing Gelatin Microparticles as Cell Carrier and Drug Delivery System for siRNA for Bone Tissue Engineering. Pharmaceutics 2022; 14:pharmaceutics14030548. [PMID: 35335924 PMCID: PMC8949427 DOI: 10.3390/pharmaceutics14030548] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 02/24/2022] [Accepted: 02/25/2022] [Indexed: 11/19/2022] Open
Abstract
The local release of complexed siRNA from biomaterials opens precisely targeted therapeutic options. In this study, complexed siRNA was loaded to gelatin microparticles cross-linked (cGM) with an anhydride-containing oligomer (oPNMA). We aggregated these siRNA-loaded cGM with human mesenchymal stem cells (hMSC) to microtissues and stimulated them with osteogenic supplements. An efficient knockdown of chordin, a BMP-2 antagonist, caused a remarkably increased alkaline phosphatase (ALP) activity in the microtissues. cGM, as a component of microtissues, mineralized in a differentiation medium within 8–9 days, both in the presence and in the absence of cells. In order to investigate the effects of our pre-differentiated and chordin-silenced microtissues on bone homeostasis, we simulated in vivo conditions in an unstimulated co-culture system of hMSC and human peripheral blood mononuclear cells (hPBMC). We found enhanced ALP activity and osteoprotegerin (OPG) secretion in the model system compared to control microtissues. Our results suggest osteoanabolic effects of pre-differentiated and chordin-silenced microtissues.
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Hinkelmann S, Springwald AH, Starke A, Kalwa H, Wölk C, Hacker MC, Schulz-Siegmund M. Microtissues from mesenchymal stem cells and siRNA-loaded cross-linked gelatin microparticles for bone regeneration. Mater Today Bio 2022; 13:100190. [PMID: 34988418 PMCID: PMC8693629 DOI: 10.1016/j.mtbio.2021.100190] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 11/20/2021] [Accepted: 12/11/2021] [Indexed: 12/13/2022] Open
Abstract
The aim of this study was the evaluation of cross-linked gelatin microparticles (cGM) as substrates for osteogenic cell culture to assemble 3D microtissues and their use as delivery system for siRNA to cells in these assemblies. In a 2D transwell cultivation system, we found that cGM are capable to accumulate calcium ions from the surrounding medium. Such a separation of cGM and SaOS-2 cells consequently led to a suppressed matrix mineral formation in the SaOS-2 culture on the well bottom of the transwell system. Thus, we decided to use cGM as component in 3D microtissues and get a close contact between calcium ion accumulating microparticles and cells to improve matrix mineralization. Gelatin microparticles were cross-linked with a N,N-diethylethylenediamine-derivatized (DEED) maleic anhydride (MA) containing oligo (pentaerythritol diacrylate monostearate-co-N-isopropylacrylamide-co-MA) (oPNMA) and aggregated with SaOS-2 or human mesenchymal stem cells (hMSC) to microtissue spheroids. We systematically varied the content of cGM in microtissues and observed cell differentiation and tissue formation. Microtissues were characterized by gene expression, ALP activity and matrix mineralization. Mineralization was detectable in microtissues with SaOS-2 cells after 7 days and with hMSC after 24–28 days in osteogenic culture. When we transfected hMSC via cGM loaded with Lipofectamine complexed chordin siRNA, we found increased ALP activity and accelerated mineral formation in microtissues in presence of BMP-2. As a model for positive paracrine effects that indicate promising in vivo effects of these microtissues, we incubated pre-differentiated microtissues with freshly seeded hMSC monolayers and found improved mineral formation all over the well in the co-culture model. These findings may support the concept of microtissues from hMSC and siRNA-loaded cGM for bone regeneration.
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Affiliation(s)
- Sandra Hinkelmann
- Institute of Pharmacy, Pharmaceutical Technology, Faculty of Medicine, University of Leipzig, Germany
| | - Alexandra H Springwald
- Institute of Pharmacy, Pharmaceutical Technology, Faculty of Medicine, University of Leipzig, Germany
| | - Annett Starke
- Institute of Pharmacy, Pharmaceutical Technology, Faculty of Medicine, University of Leipzig, Germany
| | - Hermann Kalwa
- Rudolf-Boehm-Institute for Pharmacology and Toxicology, Faculty of Medicine, University of Leipzig, Leipzig, Germany
| | - Christian Wölk
- Institute of Pharmacy, Pharmaceutical Technology, Faculty of Medicine, University of Leipzig, Germany
| | - Michael C Hacker
- Institute of Pharmacy, Pharmaceutical Technology, Faculty of Medicine, University of Leipzig, Germany.,Institute of Pharmaceutics and Biopharmaceutics, Heinrich Heine University, Düsseldorf, Germany
| | - Michaela Schulz-Siegmund
- Institute of Pharmacy, Pharmaceutical Technology, Faculty of Medicine, University of Leipzig, Germany
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Zucherato VS, Penariol LBC, Silva LECM, Padovan CC, Poli-Neto OB, Rosa-E-Silva JC, Ferriani RA, Meola J. Identification of suitable reference genes for mesenchymal stem cells from menstrual blood of women with endometriosis. Sci Rep 2021; 11:5422. [PMID: 33686153 PMCID: PMC7970877 DOI: 10.1038/s41598-021-84884-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 02/22/2021] [Indexed: 02/06/2023] Open
Abstract
It has been suggested that menstrual blood-derived mesenchymal stem/stromal cells (MenMSCs) are associated with the etiopathogenesis of endometriosis and considerable effort has been invested in searching for target genes and deciphering associated molecular pathways. However, reference gene stability for proper reproducible normalization in the analyses of the expression data validation is still unexplored in this experimental context. Therefore, in this exploratory study, we used stringent case and control selection criteria and collected menstrual blood from women with a laparoscopic diagnosis of advanced endometriosis and from fertile women without endometriosis. We tested for the first time the stability of 32 candidate reference genes to achieve increased accuracy and reliable results in the quantification of gene expression and direct future experiments using reverse transcription-quantitative PCR (RT-qPCR) in MenMSCs for endometriosis studies. Using the RefFinder web tool, we recommend the EIF2B1 and POP4 reference genes for the normalization of RT-qPCR data in study designs similar to ours. Furthermore, we suggest avoiding the commonly used GAPDH and ACTB reference genes as they are unstable. This high-visibility study is capable of directing different experimental designs as MenMSCs are derived from a minimally invasive tissue source with multifunctional roles in regenerative medicine.
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Affiliation(s)
- Victoria S Zucherato
- Gynecology and Obstetrics Department, Ribeirao Preto Medical School, University of Sao Paulo, Bandeirantes Avenue, 3900, 8th Floor of the Clinic Hospital, Universitary Campus, Ribeirao Preto, SP, 14049-900, Brazil
| | - Leticia B C Penariol
- Gynecology and Obstetrics Department, Ribeirao Preto Medical School, University of Sao Paulo, Bandeirantes Avenue, 3900, 8th Floor of the Clinic Hospital, Universitary Campus, Ribeirao Preto, SP, 14049-900, Brazil
| | - Lilian E C M Silva
- Multiuser Laboratory, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirao Preto, SP, Brazil
| | - Cristiana C Padovan
- Gynecology and Obstetrics Department, Ribeirao Preto Medical School, University of Sao Paulo, Bandeirantes Avenue, 3900, 8th Floor of the Clinic Hospital, Universitary Campus, Ribeirao Preto, SP, 14049-900, Brazil
| | - Omero B Poli-Neto
- Gynecology and Obstetrics Department, Ribeirao Preto Medical School, University of Sao Paulo, Bandeirantes Avenue, 3900, 8th Floor of the Clinic Hospital, Universitary Campus, Ribeirao Preto, SP, 14049-900, Brazil
| | - Julio C Rosa-E-Silva
- Gynecology and Obstetrics Department, Ribeirao Preto Medical School, University of Sao Paulo, Bandeirantes Avenue, 3900, 8th Floor of the Clinic Hospital, Universitary Campus, Ribeirao Preto, SP, 14049-900, Brazil
| | - Rui A Ferriani
- Gynecology and Obstetrics Department, Ribeirao Preto Medical School, University of Sao Paulo, Bandeirantes Avenue, 3900, 8th Floor of the Clinic Hospital, Universitary Campus, Ribeirao Preto, SP, 14049-900, Brazil
- National Institute of Hormones and Woman's Health, CNPq, Porto Alegre, RS, Brazil
| | - Juliana Meola
- Gynecology and Obstetrics Department, Ribeirao Preto Medical School, University of Sao Paulo, Bandeirantes Avenue, 3900, 8th Floor of the Clinic Hospital, Universitary Campus, Ribeirao Preto, SP, 14049-900, Brazil.
- National Institute of Hormones and Woman's Health, CNPq, Porto Alegre, RS, Brazil.
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Gonzalez-Pujana A, de Lázaro I, Vining KH, Santos-Vizcaino E, Igartua M, Hernandez RM, Mooney DJ. 3D encapsulation and inflammatory licensing of mesenchymal stromal cells alter the expression of common reference genes used in real-time RT-qPCR. Biomater Sci 2020; 8:6741-6753. [PMID: 33136110 DOI: 10.1039/d0bm01562h] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Human mesenchymal stromal cells (hMSCs) hold great promise in the treatment of inflammatory and immune diseases, due to their immunomodulatory capacity. Their therapeutic activity is often assessed measuring levels of expression of immunomodulatory genes such as indoleamine 2,3-dioxygenase 1 (IDO1) and real-time RT-qPCR is most predominantly the method of choice due to its high sensitivity and relative simplicity. Currently, multiple strategies are explored to promote hMSC-mediated immunomodulation, overlooking the effects they pose in the expression of genes commonly used as internal calibrators in real-time RT-qPCR analyses. However, variations in their expression could introduce significant errors in the evaluation of the therapeutic potential of hMSCs. This work investigates, for the first time, how some of these strategies - 3D encapsulation, the mechanical properties of the 3D matrix and inflammatory licensing - influence the expression of common reference genes in hMSCs. Both 3D encapsulation and inflammatory licensing alter significantly the expression of β-actin (ACTB) and Ubiquitin C (UBC), respectively. Using them as normalization factors leads to an erroneous assessment of IDO1 mRNA levels, therefore resulting in over or underestimation of the therapeutic potential of hMSCs. In contrast, the range of mechanical properties of the matrix encapsulating the cells did not significantly affect the expression of any of the reference genes studied. Moreover, we identify RPS13 and RPL30 as reference genes of choice under these particular experimental conditions. These results demonstrate the vital importance of validating the expression of reference genes to correctly assess the therapeutic potential of hMSCs by real-time RT-qPCR.
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Affiliation(s)
- Ainhoa Gonzalez-Pujana
- NanoBioCel Research Group, Laboratory of Pharmaceutics, School of Pharmacy, University of the Basque Country (UPV/EHU), Vitoria-Gasteiz, Spain.
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Stable Reference Genes for qPCR Analysis in BM-MSCs Undergoing Osteogenic Differentiation within 3D Hyaluronan-Based Hydrogels. Int J Mol Sci 2020; 21:ijms21239195. [PMID: 33276559 PMCID: PMC7729573 DOI: 10.3390/ijms21239195] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 11/22/2020] [Accepted: 11/30/2020] [Indexed: 11/17/2022] Open
Abstract
Reverse transcription quantitative polymerase chain reaction (RT-qPCR) enables the monitoring of changes in cell phenotype via the high-throughput screening of numerous genes. RT-qPCR is a fundamental approach in numerous research fields, including biomaterials, yet little attention has been given to the potential impact of 3D versus monolayer (2D) cell culture and to the requirement for a constant validation of the multiple steps of gene expression analysis. The aim of this study is to use high-quality RNA to identify the most suitable reference genes for RT-qPCR analysis during the osteogenic differentiation of human bone marrow mesenchymal stem/stromal cells (BM-MSCs). BM-MSCs are cultured under osteogenic conditions for 28 days in 2D or within hyaluronic acid hydrogels (3D). RNA is subject to quality controls and is then used to identify the most stable reference genes using geNorm, NormFinder, and the ∆Cq method. The effect of the reverse transcriptase is investigated, as well as the expression of osteogenic-related markers. This study shows marked differences in the stability of reference genes between 2D (RPLP0/GAPDH) and 3D (OAZ1/PPIA) culture, suggesting that it is critical to choose appropriate reference genes for 3D osteogenic cell cultures. Thus, a thorough validation under specific experimental settings is essential to obtain meaningful gene expression results.
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10
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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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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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CAGNAN I, AERTS KAYA F, UÇKAN D, GÜNEL ÖZCAN A. Stably expressed reference genes during differentiation ofbone marrow-derived mesenchymal stromal cells. Turk J Biol 2017; 41:88-97. [DOI: 10.3906/biy-1511-93] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/29/2023] Open
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Santos BPD, da Costa Diesel LF, da Silva Meirelles L, Nardi NB, Camassola M. Identification of suitable reference genes for quantitative gene expression analysis in rat adipose stromal cells induced to trilineage differentiation. Gene 2016; 594:211-219. [PMID: 27601259 DOI: 10.1016/j.gene.2016.09.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Revised: 08/03/2016] [Accepted: 09/02/2016] [Indexed: 10/21/2022]
Abstract
This study was designed to (i) identify stable reference genes for the analysis of gene expression during in vitro differentiation of rat adipose stromal cells (rASCs), (ii) recommend stable genes for individual treatment conditions, and (iii) validate these genes by comparison with normalization results from stable and unstable reference genes. On the basis of a literature review, eight genes were selected: Actb, B2m, Hprt1, Ppia, Rplp0, Rpl13a, Rpl5, and Ywhaz. Genes were ranked according to their stability under different culture conditions as assessed using GenNorm, NormFinder, and RefFinder algorithms. Although the employed algorithms returned different rankings, the most frequently top-ranked genes were: B2m and/or Ppia for all 28day treatments (ALL28); Ppia and Hprt1 (adipogenic differentiation; A28), B2m (chondrogenic differentiation; C28), Rpl5 (controls maintained in complete culture medium; CCM), Rplp0 (osteogenic differentiation for 3days; O3), Rpl13a and Actb (osteogenic differentiation for 7days; O7), Rplp0 and Ppia (osteogenic differentiation for 14days; O14), Hprt1 and Ppia (osteogenic differentiation for 28days; O28), as well as Actb (all osteogenesis time points combined; ALLOSTEO). The obtained results indicate that the performance of reference genes depends on the differentiation protocol and on the analysis time, thus providing valuable information for the design of RT-PCR experiments.
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Affiliation(s)
- Bruno Paiva Dos Santos
- Laboratory of Stem Cells and Tissue Engineering, Lutheran University of Brazil, Canoas 92425-900, RS, Brazil.
| | | | - Lindolfo da Silva Meirelles
- Laboratory of Stem Cells and Tissue Engineering, Lutheran University of Brazil, Canoas 92425-900, RS, Brazil.
| | - Nance Beyer Nardi
- Laboratory of Stem Cells and Tissue Engineering, Lutheran University of Brazil, Canoas 92425-900, RS, Brazil.
| | - Melissa Camassola
- Laboratory of Stem Cells and Tissue Engineering, Lutheran University of Brazil, Canoas 92425-900, RS, Brazil.
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Sedaghati B, Jahroomishirazi R, Starke A, Hacker MC, Schulz-Siegmund M. Rat Osteosarcoma Cells as a Therapeutic Target Model for Osteoregeneration via Sclerostin Knockdown. Cells Tissues Organs 2016; 201:366-79. [DOI: 10.1159/000444634] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/11/2016] [Indexed: 11/19/2022] Open
Abstract
There are various conceptually different strategies to improve bone regeneration and to treat osteoporosis, each with distinct inherent advantages and disadvantages. The use of RNA interference strategies to suppress the biological action of catabolic factors or antagonists of osteogenic proteins is promising, and such strategies can be applied locally. They are comparably inexpensive and do not suffer from stability problems as protein-based approaches. In this study, we focus on sclerostin, encoded by the SOST gene, a key regulator of bone formation and remodeling. Sclerostin is expressed by mature osteocytes but also by late osteogenically differentiated cells. Thus, it is difficult and requires long-term cultures to investigate the effects of SOST silencing on the expression of osteogenic markers using primary cells. We, therefore, selected a rat osteosarcoma cell line, UMR-106, that has been shown to express SOST and secrete sclerostin in a comparable fashion as late osteoblasts and osteocytes. We investigated the effects of differentiating supplements on SOST expression and sclerostin secretion in UMR-106 cells and found that addition of 100 ng/ml of bone morphogenetic protein (BMP)-2 strongly induced sclerostin secretion, whereas dexamethasone inhibited secretion. Effects of silencing SOST in UMR-106 cells cultured in various differentiation media including BMP-2 and/or dexamethasone were determined next with the aim to find promising test conditions for a readout system for the evaluation of future small interfering RNA release formulations for local induction of bone formation. We found a direct correlation between attenuated SOST expression and an increase in the osteogenic potential of UMR-106 cells. The combination of SOST silencing and BMP-2 could synergistically improve osteogenic factors. A lowered proliferation rate in silenced groups may indicate a faster switch to differentiation.
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Pattabhi SR, Lehaf AM, Schlenoff JB, Keller TCS. Human mesenchymal stem cell osteoblast differentiation, ECM deposition, and biomineralization on PAH/PAA polyelectrolyte multilayers. J Biomed Mater Res A 2014; 103:1818-27. [PMID: 25203301 DOI: 10.1002/jbm.a.35322] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Revised: 07/31/2014] [Accepted: 08/26/2014] [Indexed: 01/14/2023]
Abstract
Polyelectrolyte multilayer (PEMU) coatings built layer by layer with alternating pairs of polyelectrolytes can be tuned to improve cell interactions with surfaces and may be useful as biocompatible coatings to improve fixation between implants and tissues. Here, we show that human mesenchymal stromal cells (hMSCs) induced with bone differentiation medium (BDM) to become osteoblasts biomineralize crosslinked PEMUs built with the polycation poly(allylamine hydrochloride) (PAH) and the polyanion poly(acrylic acid) (PAA). Degrees of hMSC osteoblast differentiation and surface biomineralization on the smooth PAH-terminated PEMUs (PAH-PEMUs) and microstructured PAA-terminated PEMUs (PAA-PEMUs) reflect differences in cell-deposited extracellular matrix (ECM). BDM-induced hMSCs expressed higher levels of the early osteoblast differentiation marker alkaline phosphatase and collagen 1 (COL1) sooner on PAA-PEMUs than on PAH-PEMUs. Cells on both types of PEMUs proceeded to express the later stage osteoblast differentiation marker bone sialoprotein (BSP), but the BDM-induced cells organized a more amorphous Collagen I and denser BSP localization on PAA-PEMUs than on PAH-PEMUs. These ECM properties correlated with greater biomineralization on the PAA-PEMUs than on PAH-PEMUs. Together, these results confirm the suitability of PAH/PAA PEMUs as a substrate for hMSC osteogenesis and highlight the importance of substrate effects on ECM organization and BSP presentation on biomineralization.
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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: 29] [Impact Index Per Article: 2.9] [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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Schildberg T, Rauh J, Bretschneider H, Stiehler M. Identification of suitable reference genes in bone marrow stromal cells from osteoarthritic donors. Stem Cell Res 2013; 11:1288-98. [PMID: 24080205 DOI: 10.1016/j.scr.2013.08.015] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/27/2013] [Revised: 08/20/2013] [Accepted: 08/31/2013] [Indexed: 12/28/2022] Open
Abstract
Bone marrow stromal cells (BMSCs) are key cellular components for musculoskeletal tissue engineering strategies. Furthermore, recent data suggest that BMSCs are involved in the development of Osteoarthritis (OA) being a frequently occurring degenerative joint disease. Reliable reference genes for the molecular evaluation of BMSCs derived from donors exhibiting OA as a primary co-morbidity have not been reported on yet. Hence, the aim of the study was to identify reference genes suitable for comparative gene expression analyses using OA-BMSCs. Passage 1 bone marrow derived BMSCs were isolated from n=13 patients with advanced stage idiopathic hip osteoarthritis and n=15 age-matched healthy donors. The expression of 31 putative reference genes was analyzed by quantitative reverse transcription polymerase chain reaction (qRT-PCR) using a commercially available TaqMan(®) assay. Calculating the coefficient of variation (CV), mRNA expression stability was determined and afterwards validated using geNorm and NormFinder algorithms. Importin 8 (IPO8), TATA box binding protein (TBP), and cancer susceptibility candidate 3 (CASC3) were identified as the most stable reference genes. Notably, commonly used reference genes, e.g. beta-actin (ACTB) and beta-2-microglobulin (B2M) were among the most unstable genes. For normalization of gene expression data of OA-BMSCs the combined use of IPO8, TBP, and CASC3 gene is recommended.
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Affiliation(s)
- Theresa Schildberg
- University Centre for Orthopaedics & Trauma Surgery and Centre for Translational Bone, Joint & Soft Tissue Research, University Hospital Carl Gustav Carus at the Technische Universität Dresden, Dresden, Germany.
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