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Xie F, Wang J, Zhang B. RefFinder: a web-based tool for comprehensively analyzing and identifying reference genes. Funct Integr Genomics 2023; 23:125. [PMID: 37060478 DOI: 10.1007/s10142-023-01055-7] [Citation(s) in RCA: 60] [Impact Index Per Article: 60.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 04/07/2023] [Accepted: 04/10/2023] [Indexed: 04/16/2023]
Abstract
Although many genes may serve as reference genes, they may cause different expression patterns by selecting different reference genes because no single gene is expressed consistently in all tested tissues of an organism under all environmental and developmental conditions. Thus, it is becoming increasingly important and necessary to identify suitable reference genes before performing gene expression analysis. Currently, there are several computational tools available for evaluating the stability of candidate reference genes. These tools are based on different statistical algorithms and may produce different rankings in stability within the same reference gene study. To date, the RefFinder is the only web-based tool available for comparing and evaluating housekeeping genes as candidates to be reference genes. In this tool, we integrated the four currently available computational programs (geNorm, NormFinder, BestKeeper, and the comparative ΔCt method) into a web-based tool for evaluating the stability and reliability of reference genes. According to the gene stability rankings derived from the four programs, we assigned an appropriate weight to each gene and calculated the geometric mean of weights for the final rankings. Aside from the overall ranking, a single program or combination of the four programs can be selected for evaluating the ranking of candidate reference genes. This tool has been widely used and validated by many research laboratories around the world. You may use this tool at http://www.heartcure.com.au/reffinder/ or https://blooge.cn/RefFinder/ . You can also download this algorithm program from https://github.com/fulxie/RefFinder and setup on your own computer. RefFinder is developed by PHP. Users can deploy it to a Php-based server (Apache + PHP) and run it.
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Affiliation(s)
- Fuliang Xie
- Department of Biology, East Carolina University, Greenville, NC, 27858, USA
| | - Jianyu Wang
- Guangxi University of Finance and Economics, Nanning, 530031, Guangxi, China
| | - Baohong Zhang
- Department of Biology, East Carolina University, Greenville, NC, 27858, USA.
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Hazarika A, Nongkhlaw B, Mukhopadhyay A. Identification of stable reference genes in peripheral blood mononuclear cells from type 2 diabetes mellitus patients. Sci Rep 2023; 13:486. [PMID: 36627346 PMCID: PMC9831022 DOI: 10.1038/s41598-023-27460-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 01/02/2023] [Indexed: 01/12/2023] Open
Abstract
Reference genes are obligatory for accurate normalization of mRNA transcript levels across samples and experimental conditions in Real Time-polymerase chain reaction (qRT-PCR) based quantitative gene expression assays. Selection of stably expressed reference genes is therefore crucial for ensuring reproducibility of such assays. However, there is a complete dearth of data on stability of commonly used reference genes in Peripheral Blood Mononuclear Cells (PBMCs) from Type 2 diabetes mellitus (T2DM) patients. We have evaluated the gene expression stability of 4 widely used reference genes (Beta-actin, ACTB; Peptidylprolyl Isomerase B, PPIB; Tyrosine 3 Monooxygenase/Tryptophan 5-Monooxygenase Activation Protein Zeta, YWHAZ; and Glyceraldehyde-3-Phosphate Dehydrogenase, GAPDH); in PBMCs from 39 T2DM patients and 47 normoglycemic (NGT) subjects. ACTB and YWHAZ were found to be the most stable genes in PBMCs from T2DM patients and therefore, can be recommended as suitable reference genes in similar contexts. GAPDH and PPIB expressions were not stable in PBMCs from T2DM patients. On using ACTB and YWHAZ as reference genes for measuring relative expression of GAPDH and PPIB in these subjects, relative GAPDH expression was found to be significantly lower in female T2DM patients, compared to female NGT subjects [GAPDH relative normalization unit (RNU): female T2DM (n = 19), median (Q1, Q3): 9.0 (8.1, 9.9); female NGT (n = 18): median (Q1, Q3): 10.1 (9.1, 11.0); P = 0.034]. Dysregulation of GAPDH in PBMCs from female T2DM patients could be associated with sex-specific differences in pathogenesis and outcomes of T2DM.
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Affiliation(s)
- Ankita Hazarika
- grid.418280.70000 0004 1794 3160Division of Nutrition, St. John’s Research Institute, St. John’s National Academy of Health Sciences, Sarjapur Road, Bangalore, India
| | - Bajanai Nongkhlaw
- grid.418280.70000 0004 1794 3160Division of Nutrition, St. John’s Research Institute, St. John’s National Academy of Health Sciences, Sarjapur Road, Bangalore, India ,grid.464649.d0000 0004 1792 1201Present Address: Department of Pathology, North Eastern Indira Gandhi Regional Institute of Health and Medical Sciences, Shillong, Meghalaya India
| | - Arpita Mukhopadhyay
- Division of Nutrition, St. John's Research Institute, St. John's National Academy of Health Sciences, Sarjapur Road, Bangalore, India.
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Sola IM, Karin-Kujundzic V, Paic F, Lijovic L, Glibo M, Serman N, Duic T, Skrtic A, Kuna K, Vranic S, Serman L. WNT5A, β‑catenin and SUFU expression patterns, and the significance of microRNA deregulation in placentas with intrauterine growth restriction. Mol Med Rep 2022; 27:28. [PMID: 36524356 PMCID: PMC9813565 DOI: 10.3892/mmr.2022.12914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 10/05/2022] [Indexed: 12/15/2022] Open
Abstract
Placental insufficiency is a common cause of intrauterine growth restriction (IUGR). It affects ~10% of pregnancies and increases fetal and neonatal morbidity and mortality. Although Wnt and Hh pathways are crucial for embryonic development and placentation, their role in the pathology of IUGR is still not sufficiently explored. The present study analyzed the expression of positive regulators of the Wnt pathway, WNT5A and β‑catenin, and the expression of the Hh pathway negative regulator suppressor of fused (SUFU). Immunohistochemical and reverse transcription‑quantitative PCR (RT‑qPCR) assays were performed on 34 IUGR and 18 placental tissue samples from physiologic singleton‑term pregnancies. Epigenetic mechanisms of SUFU gene regulation were also investigated by methylation‑specific PCR analysis of its promoter and RT‑qPCR analysis of miR‑214‑3p and miR‑378a‑5p expression. WNT5A protein expression was higher in endothelial cells of placental villi from IUGR compared with control tissues. That was also the case for β‑catenin protein expression in trophoblasts and endothelial cells and SUFU protein expression in trophoblasts from IUGR placentas. The SUFU gene promoter remained unmethylated in all tissue samples, while miR‑214‑3p and miR‑378a‑5p were downregulated in IUGR. The present results suggested altered Wnt and Hh signaling in IUGR. DNA methylation did not appear to be a mechanism of SUFU regulation in the pathogenesis of IUGR, but its expression could be regulated by miRNA targeting.
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Affiliation(s)
- Ida Marija Sola
- Department of Obstetrics and Gynecology, University Hospital Sestre Milosrdnice, 10000 Zagreb, Croatia
| | - Valentina Karin-Kujundzic
- Department of Biology, University of Zagreb, 10000 Zagreb, Croatia,Centre of Excellence in Reproductive and Regenerative Medicine, School of Medicine, University of Zagreb, 10000 Zagreb, Croatia,Correspondence to: Dr Valentina Karin-Kujundzic, Department of Biology, School of Medicine, University of Zagreb, Salata 3, 10000 Zagreb, Croatia, E-mail:
| | - Frane Paic
- Department of Biology, University of Zagreb, 10000 Zagreb, Croatia
| | - Lada Lijovic
- Department of Anesthesiology and Critical Care, General Hospital Fra Mihovil Sučić, 80101 Livno, Bosnia and Herzegovina
| | - Mislav Glibo
- Department of Biology, University of Zagreb, 10000 Zagreb, Croatia
| | - Nikola Serman
- Zagreb Emergency Medicine Service, School of Medicine, University of Zagreb, 10000 Zagreb, Croatia
| | - Tihana Duic
- Department of Biology, University of Zagreb, 10000 Zagreb, Croatia
| | - Anita Skrtic
- Centre of Excellence in Reproductive and Regenerative Medicine, School of Medicine, University of Zagreb, 10000 Zagreb, Croatia,Department of Pathology, School of Medicine, University of Zagreb, 10000 Zagreb, Croatia,Department of Pathology, University Hospital Merkur, 10000 Zagreb, Croatia
| | - Krunoslav Kuna
- Department of Obstetrics and Gynecology, University Hospital Sestre Milosrdnice, 10000 Zagreb, Croatia
| | - Semir Vranic
- College of Medicine, QU Health, Qatar University, 2713 Doha, Qatar
| | - Ljiljana Serman
- Department of Biology, University of Zagreb, 10000 Zagreb, Croatia,Centre of Excellence in Reproductive and Regenerative Medicine, School of Medicine, University of Zagreb, 10000 Zagreb, Croatia
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Gu W, Tu X, Lu W, Yin Y, Meng Q, Wang X, Zhang F, Fu Y. Identification of RNU44 as an Endogenous Reference Gene for Normalizing Cell-Free RNA in Tuberculosis. Open Forum Infect Dis 2022; 9:ofac540. [DOI: 10.1093/ofid/ofac540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 10/11/2022] [Indexed: 12/13/2022] Open
Abstract
Abstract
Background
Normalization of cell-free RNA (cf-RNA) concentration can be affected by variable experimental conditions and thus impact the performance of their diagnostic potential. Our study aimed to identify appropriate endogenous reference genes for cf-RNA biomarker evaluation in the diagnosis of tuberculosis (TB).
Methods
Subjects consisting of patients with TB with and without malignancy, patients with pneumonia, and healthy controls were recruited. Candidate reference genes were screened and identified by literature reviewing and RNA-Seq analysis. Expression levels of the candidate genes were determined by reverse-transcription real-time quantitative polymerase chain reaction in plasma from patients with TB and healthy controls. The stability of gene expression was assessed by geNorm, NormFinder, BestKeeper, the Comparative Delta Ct method, and RefFinder. Differential expression of 2 small RNAs (sRNAs) encoding by genome of Mycobacterium tuberculosis in plasma of patients with TB were determined by both absolute quantification and relative quantification with candidate reference genes.
Results
According to the stability ranking analyzed with the 5 computational programs, the top 4 candidates—miR-93, RNU44, miR-16, and glyceraldehyde 3-phosphate dehydrogenase—were used to normalize the transcript levels of 2 mycobacterial sRNAs, MTS2823 and MTS1338, which were observed to have higher copy numbers in the plasma of patients with TB. Normalization with RNU44 displayed significantly higher levels of the 2 M tuberculosis sRNAs in the patients’ plasma than those of healthy controls.
Conclusions
RNU44 was demonstrated as a proper endogenous gene for cf-RNA normalization in TB diagnosis.
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Affiliation(s)
- Wei Gu
- Department of Microbiology, Harbin Medical University , Harbin , China
| | - Xilin Tu
- Department of Respiratory Medicine, First Affiliated Hospital, Harbin Medical University , Harbin , China
| | - Weinan Lu
- Department of Microbiology, Harbin Medical University , Harbin , China
| | - Yian Yin
- Department of Microbiology, Harbin Medical University , Harbin , China
| | - Qingtai Meng
- Department of Microbiology, Harbin Medical University , Harbin , China
| | - Xinyang Wang
- Department of Microbiology, Harbin Medical University , Harbin , China
| | - Fengmin Zhang
- Department of Microbiology, Harbin Medical University , Harbin , China
| | - Yingmei Fu
- Department of Microbiology, Harbin Medical University , Harbin , China
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Kochhar P, Dwarkanath P, Ravikumar G, Thomas A, Crasta J, Thomas T, Kurpad AV, Mukhopadhyay A. Placental expression of miR-21-5p, miR-210-3p and miR-141-3p: relation to human fetoplacental growth. Eur J Clin Nutr 2021; 76:730-738. [PMID: 34611295 DOI: 10.1038/s41430-021-01017-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 09/06/2021] [Accepted: 09/21/2021] [Indexed: 12/29/2022]
Abstract
BACKGROUND/OBJECTIVES Dysregulation of microRNAs (miRNAs) and their target genes in placental tissue is associated with foetal growth restriction. We aimed to evaluate associations of placental miR-21-5p, miR-141-3p and miR-210-3p expression with maternal, placental and newborn parameters and with placental expression of their potential target genes PTEN, VEGF, FLT and ENG in a set of well-characterized small- (SGA) and appropriate- (AGA) for gestational age full-term singleton pregnancies. SUBJECTS/METHODS Placental samples (n = 80) from 26 SGA and 54 AGA were collected from full-term singleton pregnancies. Placental transcript abundances of miR-21-5p, miR-141-3p and miR-210-3p were assessed after normalization to a reference miRNA, mir-16-5p by real-time quantitative PCR. Placental transcript abundances of PTEN, VEGF, FLT and ENG were assessed after normalizing to a panel of reference genes. RESULTS Placental miR-21-5p transcript abundance was negatively associated with placental weight (n = 80, r = -0.222, P = 0.047) and this association was specific to the AGA births (n = 54, r = -0.292, P = 0.032). Placental transcript abundances of miR-210-3p and miR-141-3p were not associated with placental weight or birth weight in all 80 births. However, placental miR-210-3p transcript abundance was positively associated with birth weight specifically in the SGA births (n = 26, r = 0.449, P = 0.021). Placental transcript abundance of miR-21-5p was negatively associated with PTEN transcript abundance (Spearman's ρ = -0.245, P = 0.028) while that of miR-141-3p was positively associated with FLT (Spearman's ρ = 0.261, P = 0.019) and ENG (Spearman's ρ = 0.259, P = 0.020) transcript abundances in all 80 births. CONCLUSION We conclude that placental miR-21-5p and miR-210-3p may be involved in fetoplacental growth. However, this regulation is unlikely to be mediated through placental expression of PTEN, VEGF, FLT or ENG.
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Affiliation(s)
- P Kochhar
- Division of Nutrition, St. John's Research Institute, A recognized research centre of University of Mysore, Bangalore, India
| | - P Dwarkanath
- Division of Nutrition, St. John's Research Institute, A recognized research centre of University of Mysore, Bangalore, India
| | - G Ravikumar
- Department of Pathology, St John's Medical College Hospital, Bangalore, India
| | - A Thomas
- Department of Obstetrics and Gynaecology, St John's Medical College Hospital, Bangalore, India
| | - J Crasta
- Department of Pathology, St John's Medical College Hospital, Bangalore, India
| | - T Thomas
- Department of Biostatistics, St. John's Medical College Hospital, Bangalore, India
| | - A V Kurpad
- Division of Nutrition, St. John's Research Institute, A recognized research centre of University of Mysore, Bangalore, India
| | - A Mukhopadhyay
- Division of Nutrition, St. John's Research Institute, A recognized research centre of University of Mysore, Bangalore, India.
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