1
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Awrahman HA, Mohamad D. Advanced breast cancer diagnosis: Multiplex RT-qPCR for precise typing and angiogenesis profiling. Biochem Biophys Rep 2024; 37:101615. [PMID: 38205186 PMCID: PMC10776909 DOI: 10.1016/j.bbrep.2023.101615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 12/09/2023] [Accepted: 12/12/2023] [Indexed: 01/12/2024] Open
Abstract
Breast cancer (BC) remains the foremost cause of cancer-related mortality, with an estimated 2.3 million new cases anticipated globally. The timely diagnosis of BC is pivotal for effective treatment. Currently, BC diagnosis predominantly relies on Immunohistochemistry (IHC), a method known for its sluggishness, expense, and dependence on proficient pathologists for confident cancer typing. In this study, we introduce a novel approach to enhance the accuracy, speed, and cost-effectiveness of BC diagnosis. We employ multiplex Reverse Transcription quantitative Polymerase Chain Reaction (RT-qPCR) with touch-down methods, which consistently yield significantly lower Cycle Threshold (CT) values. The study evaluates gene expression profiles of HER2, PGR, ESR, and Ki67 genes across 61 samples representing four BC subtypes, using RPL13A as the endogenous control gene. The results demonstrate that our method offers remarkable precision, nearly equivalent to IHC, in detecting gene expressions vital for BC diagnosis and subtyping. Moreover, we explore the gene expression of Hif1A, ANG, and VEGFR genes involved in angiogenesis, shedding light on the metastatic potential of the tested BC tumours. Notably, numerous samples exhibit elevated levels of Hif1A and VEGFR, indicating their potential as valuable biomarkers for assessing metastatic status. Collectively, our RT-qPCR methodology emerges as a powerful diagnostic tool for swiftly identifying BC subtypes and can be complemented with other essential tumorigenic biomarker assessments, such as angiogenesis, to further refine cancer characterisation and inform personalised therapeutic strategies for BC patients. This innovation holds the promise of revolutionising BC diagnosis and treatment, offering expedited and reliable insights for improved patient care.
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Affiliation(s)
- Harem Abdalla Awrahman
- University of Sulaimani and Hiwa Hospital, Sulaymaniyah General Directory of Health, Ministry of Health, Sulaymaniyah, Iraq
| | - Dlnya Mohamad
- University of Sulaimani, Biology Department KRG, Iraq
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2
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Huang M, Claussnitzer M, Saadat A, Coral DE, Kalamajski S, Franks PW. Engineered allele substitution at PPARGC1A rs8192678 alters human white adipocyte differentiation, lipogenesis, and PGC-1α content and turnover. Diabetologia 2023; 66:1289-1305. [PMID: 37171500 PMCID: PMC10244287 DOI: 10.1007/s00125-023-05915-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 03/17/2023] [Indexed: 05/13/2023]
Abstract
AIMS/HYPOTHESIS PPARGC1A encodes peroxisome proliferator-activated receptor γ coactivator 1-α (PGC-1α), a central regulator of energy metabolism and mitochondrial function. A common polymorphism in PPARGC1A (rs8192678, C/T, Gly482Ser) has been associated with obesity and related metabolic disorders, but no published functional studies have investigated direct allele-specific effects in adipocyte biology. We examined whether rs8192678 is a causal variant and reveal its biological function in human white adipose cells. METHODS We used CRISPR-Cas9 genome editing to perform an allelic switch (C-to-T or T-to-C) at rs8192678 in an isogenic human pre-adipocyte white adipose tissue (hWAs) cell line. Allele-edited single-cell clones were expanded and screened to obtain homozygous T/T (Ser482Ser), C/C (Gly482Gly) and heterozygous C/T (Gly482Ser) isogenic cell populations, followed by functional studies of the allele-dependent effects on white adipocyte differentiation and mitochondrial function. RESULTS After differentiation, the C/C adipocytes were visibly less BODIPY-positive than T/T and C/T adipocytes, and had significantly lower triacylglycerol content. The C allele presented a dose-dependent lowering effect on lipogenesis, as well as lower expression of genes critical for adipogenesis, lipid catabolism, lipogenesis and lipolysis. Moreover, C/C adipocytes had decreased oxygen consumption rate (OCR) at basal and maximal respiration, and lower ATP-linked OCR. We determined that these effects were a consequence of a C-allele-driven dysregulation of PGC-1α protein content, turnover rate and transcriptional coactivator activity. CONCLUSIONS/INTERPRETATION Our data show allele-specific causal effects of the rs8192678 variant on adipogenic differentiation. The C allele confers lower levels of PPARGC1A mRNA and PGC-1α protein, as well as disrupted dynamics of PGC-1α turnover and activity, with downstream effects on cellular differentiation and mitochondrial function. Our study provides the first experimentally deduced insights on the effects of rs8192678 on adipocyte phenotype.
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Affiliation(s)
- Mi Huang
- Department of Clinical Sciences, Genetic and Molecular Epidemiology Unit, Clinical Research Centre, Lund University, Malmö, Sweden
| | - Melina Claussnitzer
- Metabolism Program, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Alham Saadat
- Metabolism Program, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Daniel E Coral
- Department of Clinical Sciences, Genetic and Molecular Epidemiology Unit, Clinical Research Centre, Lund University, Malmö, Sweden
| | - Sebastian Kalamajski
- Department of Clinical Sciences, Genetic and Molecular Epidemiology Unit, Clinical Research Centre, Lund University, Malmö, Sweden.
| | - Paul W Franks
- Department of Clinical Sciences, Genetic and Molecular Epidemiology Unit, Clinical Research Centre, Lund University, Malmö, Sweden.
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
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3
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Nevone A, Lattarulo F, Russo M, Panno G, Milani P, Basset M, Avanzini MA, Merlini G, Palladini G, Nuvolone M. A Strategy for the Selection of RT-qPCR Reference Genes Based on Publicly Available Transcriptomic Datasets. Biomedicines 2023; 11:biomedicines11041079. [PMID: 37189697 DOI: 10.3390/biomedicines11041079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 03/23/2023] [Accepted: 03/27/2023] [Indexed: 04/05/2023] Open
Abstract
In the next-generation sequencing era, RT-qPCR is still widely employed to quantify levels of nucleic acids of interest due to its popularity, versatility, and limited costs. The measurement of transcriptional levels through RT-qPCR critically depends on reference genes used for normalization. Here, we devised a strategy to select appropriate reference genes for a specific clinical/experimental setting based on publicly available transcriptomic datasets and a pipeline for RT-qPCR assay design and validation. As a proof-of-principle, we applied this strategy to identify and validate reference genes for transcriptional studies of bone-marrow plasma cells from patients with AL amyloidosis. We performed a systematic review of published literature to compile a list of 163 candidate reference genes for RT-qPCR experiments employing human samples. Next, we interrogated the Gene Expression Omnibus to assess expression levels of these genes in published transcriptomic studies on bone-marrow plasma cells from patients with different plasma cell dyscrasias and identified the most stably expressed genes as candidate normalizing genes. Experimental validation on bone-marrow plasma cells showed the superiority of candidate reference genes identified through this strategy over commonly employed “housekeeping” genes. The strategy presented here may apply to other clinical and experimental settings for which publicly available transcriptomic datasets are available.
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Affiliation(s)
- Alice Nevone
- Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy
- Amyloidosis Research and Treatment Center, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy
| | - Francesca Lattarulo
- Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy
- Amyloidosis Research and Treatment Center, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy
| | - Monica Russo
- Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy
- Amyloidosis Research and Treatment Center, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy
| | - Giada Panno
- Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy
- Amyloidosis Research and Treatment Center, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy
| | - Paolo Milani
- Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy
- Amyloidosis Research and Treatment Center, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy
| | - Marco Basset
- Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy
- Amyloidosis Research and Treatment Center, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy
| | - Maria Antonietta Avanzini
- Pediatric Hematology Oncology, Cell Factory, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy
| | - Giampaolo Merlini
- Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy
- Amyloidosis Research and Treatment Center, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy
| | - Giovanni Palladini
- Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy
- Amyloidosis Research and Treatment Center, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy
| | - Mario Nuvolone
- Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy
- Amyloidosis Research and Treatment Center, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy
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4
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Song R, He S, Wu Y, Chen W, Song J, Zhu Y, Chen H, Wang Q, Wang S, Tan S, Tan S. Validation of reference genes for the normalization of the RT-qPCR in peripheral blood mononuclear cells of septic patients. Heliyon 2023; 9:e15269. [PMID: 37089378 PMCID: PMC10119759 DOI: 10.1016/j.heliyon.2023.e15269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 03/29/2023] [Accepted: 03/31/2023] [Indexed: 04/25/2023] Open
Abstract
Objective To screen and validate reference genes suitable for gene mRNA expression study in peripheral blood mononuclear cells (PBMCs) between septic patients and healthy controls (HC). Methods Total RNA in PBMCs was extracted and RT-qPCR was used to determine the mRNA expression profiles of 9 candidate genes, including ACTB, B2M, GAPDH, GUSB, HPRT1, PGK1, RPL13A, SDHA and YWHAZ. The genes expression stabilities were assessed by both geNorm and NormFinder software. Results YWHAZ was the most stable gene among the 9 candidate genes evaluated by both geNorm and NormFinder in mixed and sepsis groups. The most stable gene combination in mixed group analyzed by geNorm was the combination of GAPDH, PKG1 and YWHAZ, while that in sepsis group was the combination of ACTB, PKG1 and YWHAZ. Conclusion Our first systematic analysis of the reference genes in PBMC of septic patients suggested YWHAZ was the best candidate. The combination of ACTB, PKG1 and YWHAZ could improve RT-qPCR accuracy in septic patients. Our results identified the most stable reference genes to standardize RT-qPCR of sepsis patients, which can serve as a useful tool for gene function exploration in the future.
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Affiliation(s)
- Ruoyu Song
- Department of Pathophysiology, School of Basic Medicine Science, Central South University, Changsha, Hunan 410078, PR China
- Sepsis Translational Medicine Key Laboratory of Hunan Province, Central South University, Changsha, Hunan 410078, PR China
- National Medicine Functional Experimental Teaching Center, Central South University, Changsha, Hunan 410078, PR China
| | - Shijun He
- Department of Pathophysiology, School of Basic Medicine Science, Central South University, Changsha, Hunan 410078, PR China
- Sepsis Translational Medicine Key Laboratory of Hunan Province, Central South University, Changsha, Hunan 410078, PR China
- National Medicine Functional Experimental Teaching Center, Central South University, Changsha, Hunan 410078, PR China
| | - Yongbin Wu
- Department of Pathophysiology, School of Basic Medicine Science, Central South University, Changsha, Hunan 410078, PR China
- Sepsis Translational Medicine Key Laboratory of Hunan Province, Central South University, Changsha, Hunan 410078, PR China
- National Medicine Functional Experimental Teaching Center, Central South University, Changsha, Hunan 410078, PR China
| | - Wanxin Chen
- Department of Laboratory Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan, 410011, PR China
| | - Jie Song
- Department of Pathophysiology, School of Basic Medicine Science, Central South University, Changsha, Hunan 410078, PR China
- Sepsis Translational Medicine Key Laboratory of Hunan Province, Central South University, Changsha, Hunan 410078, PR China
- National Medicine Functional Experimental Teaching Center, Central South University, Changsha, Hunan 410078, PR China
| | - Yaxi Zhu
- Department of Pathophysiology, School of Basic Medicine Science, Central South University, Changsha, Hunan 410078, PR China
- Sepsis Translational Medicine Key Laboratory of Hunan Province, Central South University, Changsha, Hunan 410078, PR China
- National Medicine Functional Experimental Teaching Center, Central South University, Changsha, Hunan 410078, PR China
| | - Huan Chen
- Department of Pathophysiology, School of Basic Medicine Science, Central South University, Changsha, Hunan 410078, PR China
- Sepsis Translational Medicine Key Laboratory of Hunan Province, Central South University, Changsha, Hunan 410078, PR China
- National Medicine Functional Experimental Teaching Center, Central South University, Changsha, Hunan 410078, PR China
| | - Qianlu Wang
- Department of Pathophysiology, School of Basic Medicine Science, Central South University, Changsha, Hunan 410078, PR China
- Sepsis Translational Medicine Key Laboratory of Hunan Province, Central South University, Changsha, Hunan 410078, PR China
- National Medicine Functional Experimental Teaching Center, Central South University, Changsha, Hunan 410078, PR China
| | - Shouman Wang
- Department of Traditional Chinese Medicine, The Third Xiangya Hospital, Central South University, Changsha, Hunan, 410008, PR China
| | - Sichuang Tan
- Department of Thoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan, 410011, PR China
- Corresponding author.
| | - Sipin Tan
- Department of Pathophysiology, School of Basic Medicine Science, Central South University, Changsha, Hunan 410078, PR China
- Corresponding author.
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Ji A, Chen W, Zhang T, Shi R, Wang X, Wang Y, Xu H, Li D. Whey protein and soy protein prevent obesity by upregulating uncoupling protein 1 to activate brown adipose tissue and promote white adipose tissue browning in high-fat diet-fed mice. Food Funct 2022; 13:12836-12851. [PMID: 36440964 DOI: 10.1039/d2fo01935c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
There are inconsistent conclusions regarding the effect of whey protein and soy protein supplementation on obesity, and the underlying mechanisms of a high-protein diet for reducing weight gain remain to be elucidated. The aim of the present study was to investigate the preventive effect of whey protein and soy protein on obesity and its possible mechanism. Eighty-four male C57BL/6J mice were randomly divided into seven dietary groups: control group (10% fat) and 6 groups fed with a high-fat diet (HFD): 10% whey protein isolate (WPI), 20% WPI, 30% WPI, 10% soy protein isolate (SPI), 20% SPI and 30% SPI for 12 weeks. Compared with the 20% SPI group, the 20% WPI group had a significantly lower body weight, serum levels of insulin, total cholesterol and leptin, weight of inguinal white adipose tissue (iWAT), and size of adipocytes in iWAT and epididymal white adipose tissue (eWAT). The body mass index (BMI) and the Lee index were significantly lower in the WPI groups than those in the SPI groups at the same protein level. The body weight, body weight gain and BMI were significantly lower with the decreasing ratio of protein to carbohydrate (P/C). Compared with the 20% SPI group, the expressions of browning-related genes such as UCP1 (uncoupling protein 1), PGC-1α, AMPKα and Cidea and the protein expression of UCP1 were significantly higher in brown adipose tissue (BAT) and iWAT in the 20% WPI group. Moreover, the expressions of lipogenesis-related genes such as SREBP1c, PPARγ, LPL and DGAT1 in BAT, iWAT and eWAT in the 10% WPI group were significantly lower compared with the 10% SPI group. In conclusion, whey protein was more effective than soy protein in preventing obesity in mice, probably by suppressing lipogenesis in adipose tissues, activating BAT and promoting the browning of iWAT. In addition, lowering the P/C ratio was beneficial for combating obesity in the context of a HFD.
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Affiliation(s)
- Andong Ji
- Institute of Nutrition and Health, School of Public Health, Qingdao University, Qingdao 266071, China.
| | - Wei Chen
- Department of Clinical Nutrition, Chinese Academy of Medical Sciences-Peking Union Medical College, Peking Union Medical College Hospital, Beijing 100730, China
| | - Tianyu Zhang
- Institute of Nutrition and Health, School of Public Health, Qingdao University, Qingdao 266071, China.
| | - Runjia Shi
- Institute of Nutrition and Health, School of Public Health, Qingdao University, Qingdao 266071, China.
| | - Xinqi Wang
- Institute of Nutrition and Health, School of Public Health, Qingdao University, Qingdao 266071, China.
| | - Yan Wang
- Institute of Nutrition and Health, School of Public Health, Qingdao University, Qingdao 266071, China.
| | - Huina Xu
- Institute of Nutrition and Health, School of Public Health, Qingdao University, Qingdao 266071, China.
| | - Duo Li
- Institute of Nutrition and Health, School of Public Health, Qingdao University, Qingdao 266071, China. .,Department of Food Science and Nutrition, Zhejiang University, Hangzhou 310058, China.,Department of Nutrition, Dietetics and Food, Monash University, Melbourne, VIC 3168, Australia
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6
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Hildyard JC, Wells DJ, Piercy RJ. Identification of qPCR reference genes suitable for normalising gene expression in the developing mouse embryo. Wellcome Open Res 2022; 6:197. [PMID: 35509373 PMCID: PMC9024131 DOI: 10.12688/wellcomeopenres.16972.1] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/14/2022] [Indexed: 07/30/2023] Open
Abstract
Background: Progression through mammalian embryogenesis involves many interacting cell types and multiple differentiating cell lineages. Quantitative polymerase chain reaction (qPCR) analysis of gene expression in the developing embryo is a valuable tool for deciphering these processes, but normalisation to stably-expressed reference genes is essential for such analyses. Gene expression patterns change globally and dramatically as embryonic development proceeds, rendering identification of consistently appropriate reference genes challenging. Methods: We have investigated expression stability in mouse embryos from mid to late gestation (E11.5-E18.5), both at the whole-embryo level, and within the head and forelimb specifically, using 15 candidate reference genes ( ACTB, 18S, SDHA, GAPDH, HTATSF1, CDC40, RPL13A, CSNK2A2, AP3D1, HPRT1, CYC1, EIF4A, UBC, B2M and PAK1IP1), and four complementary algorithms (geNorm, Normfinder, Bestkeeper and deltaCt). Results: Unexpectedly, all methods suggest that many genes within our candidate panel are acceptable references, though AP3D1, RPL13A and PAK1IP1 are the strongest performing genes overall (scoring highly in whole embryos, heads or forelimbs alone, and in all samples collectively). HPRT1 and B2M are conversely poor choices, and show strong developmental regulation. We further show that normalisation using our three highest-scoring references can reveal subtle patterns of developmental expression even in genes ostensibly ranked as acceptably stable ( CDC40, HTATSF1). Conclusion: AP3D1, RPL13A and PAK1IP1 represent universally suitable reference genes for expression studies in the E11.5-E18.5 mouse embryo.
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Affiliation(s)
- John C.W. Hildyard
- Comparative Neuromuscular Diseases Laboratory, Clinical Science and Services, Royal Veterinary College, London, NW1 0TU, UK
| | - Dominic J. Wells
- Comparative Biomedical Sciences, Royal Veterinary College, London, London, NW1 0TU, UK
| | - Richard J. Piercy
- Comparative Neuromuscular Diseases Laboratory, Clinical Science and Services, Royal Veterinary College, London, NW1 0TU, UK
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7
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Hildyard JC, Wells DJ, Piercy RJ. Identification of qPCR reference genes suitable for normalising gene expression in the developing mouse embryo. Wellcome Open Res 2022; 6:197. [PMID: 35509373 PMCID: PMC9024131 DOI: 10.12688/wellcomeopenres.16972.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/14/2022] [Indexed: 11/22/2022] Open
Abstract
Background: Progression through mammalian embryogenesis involves many interacting cell types and multiple differentiating cell lineages. Quantitative polymerase chain reaction (qPCR) analysis of gene expression in the developing embryo is a valuable tool for deciphering these processes, but normalisation to stably-expressed reference genes is essential for such analyses. Gene expression patterns change globally and dramatically as embryonic development proceeds, rendering identification of consistently appropriate reference genes challenging. Methods: We have investigated expression stability in mouse embryos from mid to late gestation (E11.5–E18.5), both at the whole-embryo level, and within the head and forelimb specifically, using 15 candidate reference genes (
ACTB, 18S, SDHA, GAPDH, HTATSF1, CDC40, RPL13A, CSNK2A2, AP3D1, HPRT1, CYC1, EIF4A, UBC, B2M and
PAK1IP1), and four complementary algorithms (geNorm, Normfinder, Bestkeeper and deltaCt). Results: Unexpectedly, all methods suggest that many genes within our candidate panel are acceptable references, though
AP3D1,
RPL13A and
PAK1IP1 are the strongest performing genes overall (scoring highly in whole embryos, heads or forelimbs alone, and in all samples collectively).
HPRT1 and
B2M are conversely poor choices, and show strong developmental regulation. We further show that normalisation using our three highest-scoring references can reveal subtle patterns of developmental expression even in genes ostensibly ranked as acceptably stable (
CDC40,
HTATSF1). Conclusion:
AP3D1,
RPL13A and
PAK1IP1 represent universally suitable reference genes for expression studies in the E11.5-E18.5 mouse embryo.
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Affiliation(s)
- John C.W. Hildyard
- Comparative Neuromuscular Diseases Laboratory, Clinical Science and Services, Royal Veterinary College, London, NW1 0TU, UK
| | - Dominic J. Wells
- Comparative Biomedical Sciences, Royal Veterinary College, London, London, NW1 0TU, UK
| | - Richard J. Piercy
- Comparative Neuromuscular Diseases Laboratory, Clinical Science and Services, Royal Veterinary College, London, NW1 0TU, UK
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8
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Lee J, Kim YH, Kim K, Kim D, Lee SH, Kim S. Selection of stable reference genes for quantitative real-time PCR in the Varroa mite, Varroa destructor. ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY 2022; 110:e21905. [PMID: 35393698 DOI: 10.1002/arch.21905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Revised: 03/23/2022] [Accepted: 03/28/2022] [Indexed: 06/14/2023]
Abstract
To investigate the acaricide toxicity and resistance mechanisms in the Varroa mite, it is essential to understand the genetic responses of Varroa mites to acaricides, which are usually evaluated by transcriptional profiling based on quantitative real-time polymerase chain reaction (qPCR). In this study, to select reference genes showing consistent expression patterns regardless of the acaricide treatment or the type of tissue, Varroa mites treated with each of the three representative acaricides (coumaphos, fluvalinate, and amitraz) were processed for transcriptomic analysis, from which eight genes (NADH dehydrogenase [NADHD], glyceraldehyde-3-phosphate dehydrogenase [GAPDH], eukaryotic translation elongation factor 1 α 1 [eEF1A1], eukaryotic translation elongation factor 2 [eEF2], ribosomal protein L5 [RpL5], Actin, tubulin α-1D chain [α-tubulin], and Rab1) were selected as candidates. The transcription profiles of these genes, depending on the treatment of the three acaricides or across different tissues (cuticle, legs, gut/fat bodies, and synganglion), were analyzed using qPCR with four validation programs, BestKeeper, geNorm, NormFinder, and RefFinder. Following acaricide treatment, eEF1A1 and NADHD showed the least variation in their expression levels, whereas the expression levels of α-tubulin and RpL5 were the most stable across different tissue groups. Rab1/GAPDH and Actin/eEF2 showed the least stable expression patterns following acaricide treatments and across different tissues, respectively, requiring precautions for use. When vitellogenin gene expression was analyzed by different reference genes, its expression profiles varied significantly depending on the reference genes, highlighting the importance of proper reference gene use. Thus, it is recommended using eEF1A1 and NADHD as reference genes for the comparison of the effects of acaricide on the whole body, whereas α-tubulin and RpL5 are recommended for investigating the tissue-specific expression profiles of target genes.
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Affiliation(s)
- Joonhee Lee
- Entomology Program, Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea
| | - Young Ho Kim
- Department of Applied Biology, Kyungpook National University, Sangju, Gyeongbuk, Republic of Korea
- Department of Ecological Science, Kyungpook National University, Sangju, Gyeongbuk, Republic of Korea
| | - Kyungmun Kim
- Division of Apiculture, Department of Agricultural Biology, National Institute of Agricultural Science, RDA, Wanju, Republic of Korea
| | - Dongwon Kim
- Division of Apiculture, Department of Agricultural Biology, National Institute of Agricultural Science, RDA, Wanju, Republic of Korea
| | - Si Hyeock Lee
- Entomology Program, Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Sanghyeon Kim
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
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9
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Yuan W, Velasquez SC, Wu CW, Fulgar CC, Zhang Q, Young DE, Bein KJ, Vogel CFA, Li W, Cui L, Wei H, Pinkerton KE. Pulmonary health effects of wintertime particulate matter from California and China following repeated exposure and cessation. Toxicol Lett 2022; 354:33-43. [PMID: 34757175 PMCID: PMC8671358 DOI: 10.1016/j.toxlet.2021.10.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 10/22/2021] [Accepted: 10/27/2021] [Indexed: 11/27/2022]
Abstract
Epidemiological studies show strong associations between fine particulate matter (PM2.5) air pollution and adverse pulmonary effects. In the present study, wintertime PM2.5 samples were collected from three geographically similar regions-Sacramento, California, USA; Jinan, Shandong, China; and Taiyuan, Shanxi, China-and extracted to form PMCA, PMSD, and PMSX, respectively, for comparison in a BALB/c mouse model. Each of four groups was oropharyngeally administered Milli-Q water vehicle control (50 μL) or one type of PM extract (20 μg/50 μL) five times over two weeks. Mice were necropsied on post-exposure days 1, 2, and 4 and examined using bronchoalveolar lavage (BAL), histopathology, and assessments of cytokine/chemokine mRNA and protein expression. Chemical analysis demonstrated all three extracts contained black carbon, but PMSX contained more sulfates and polycyclic aromatic hydrocarbons (PAHs) associated with significantly greater neutrophil numbers and greater alveolar/bronchiolar inflammation on post-exposure days 1 and 4. On day 4, PMSX-exposed mice also exhibited significant increases in interleukin-1 beta, tumor necrosis factor-alpha, and chemokine C-X-C motif ligands-3 and -5 mRNA, and monocyte chemoattractant protein-1 protein. These combined findings suggest greater sulfate and PAH content contributed to a more intense and progressive inflammatory response with repeated PMSX compared to PMCA or PMSD exposure.
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Affiliation(s)
- Wanjun Yuan
- University of California, Davis, Center for Health and the Environment, Davis, USA; Shanxi University, College of Environmental and Resource Sciences, Taiyuan, China.
| | - Sandra C Velasquez
- University of California, Davis, Center for Health and the Environment, Davis, USA
| | - Ching-Wen Wu
- University of California, Davis, Center for Health and the Environment, Davis, USA
| | - Ciara C Fulgar
- University of California, Davis, Center for Health and the Environment, Davis, USA
| | - Qi Zhang
- University of California, Davis, Department of Environmental Toxicology, Davis, USA
| | - Dominique E Young
- University of California, Davis, Department of Environmental Toxicology, Davis, USA
| | - Keith J Bein
- University of California, Davis, Center for Health and the Environment, Davis, USA; University of California, Davis, Air Quality Research Center, Davis, USA
| | - Christoph F A Vogel
- University of California, Davis, Center for Health and the Environment, Davis, USA; University of California, Davis, Department of Environmental Toxicology, Davis, USA
| | - Wei Li
- Shandong University, Biomedical Engineering Institute, School of Control Science and Engineering, Jinan, China
| | - Liangliang Cui
- Jinan Municipal Center for Disease Control and Prevention, Jinan, China
| | - Haiying Wei
- Shanxi University, College of Environmental and Resource Sciences, Taiyuan, China.
| | - Kent E Pinkerton
- University of California, Davis, Center for Health and the Environment, Davis, USA.
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10
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Na W, Wang Y, Gong P, Zhang X, Zhang K, Zhang H, Wang N, Li H. Screening of Reference Genes for RT-qPCR in Chicken Adipose Tissue and Adipocytes. Front Physiol 2021; 12:676864. [PMID: 34054585 PMCID: PMC8160385 DOI: 10.3389/fphys.2021.676864] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Accepted: 04/20/2021] [Indexed: 11/16/2022] Open
Abstract
Reverse transcription quantitative real-time PCR is the most commonly used method to detect gene expression levels. In experiments, it is often necessary to correct and standardize the expression level of target genes with reference genes. Therefore, it is very important to select stable reference genes to obtain accurate quantitative results. Although application examples of reference genes in mammals have been reported, no studies have investigated the use of reference genes in studying the growth and development of adipose tissue and the proliferation and differentiation of preadipocytes in chickens. In this study, GeNorm, a reference gene stability statistical algorithm, was used to analyze the expression stability of 14 candidate reference genes in the abdominal adipose tissue of broilers at 1, 4, and 7 weeks of age, the proliferation and differentiation of primary preadipocytes, as well as directly isolated preadipocytes and mature adipocytes. The results showed that the expression of the TATA box binding protein (TBP) and hydroxymethylbilane synthase (HMBS) genes was most stable during the growth and development of abdominal adipose tissue of broilers, the expression of the peptidylprolyl isomerase A (PPIA) and HMBS genes was most stable during the proliferation of primary preadipocytes, the expression of the TBP and RPL13 genes was most stable during the differentiation of primary preadipocytes, and the expression of the TBP and HMBS genes was most stable in directly isolated preadipocytes and mature adipocytes. These results provide reference bases for accurately detecting the mRNA expression of functional genes in adipose tissue and adipocytes of chickens.
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Affiliation(s)
- Wei Na
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Harbin, China.,Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin, China.,College of Animal Science and Technology, Northeast Agricultural University, Harbin, China.,College of Animal Science and Technology, Hainan University, Haikou, China
| | - Yuxiang Wang
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Harbin, China.,Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin, China.,College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
| | - Pengfei Gong
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Harbin, China.,Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin, China.,College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
| | - Xinyang Zhang
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Harbin, China.,Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin, China.,College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
| | - Ke Zhang
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Harbin, China.,Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin, China.,College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
| | - Hui Zhang
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Harbin, China.,Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin, China.,College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
| | - Ning Wang
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Harbin, China.,Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin, China.,College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
| | - Hui Li
- Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Harbin, China.,Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, Harbin, China.,College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
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11
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HDAC inhibitors improve CRISPR-mediated HDR editing efficiency in iPSCs. SCIENCE CHINA-LIFE SCIENCES 2021; 64:1449-1462. [PMID: 33420926 DOI: 10.1007/s11427-020-1855-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 11/17/2020] [Indexed: 12/20/2022]
Abstract
Genome-edited human induced pluripotent stem cells (iPSCs) hold great promise for therapeutic applications. However, low editing efficiency has hampered the applications of CRISPR-Cas9 technology in creating knockout and homology-directed repair (HDR)-edited iPSC lines, particularly for silent genes. This is partially due to chromatin compaction, inevitably limiting Cas9 access to the target DNA. Among the six HDAC inhibitors we examined, vorinostat, or suberoylanilide hydroxamic acid (SAHA), led to the highest HDR efficiency at both open and closed loci, with acceptable toxicity. HDAC inhibitors equally increased non-homologous end joining (NHEJ) editing efficiencies (∼50%) at both open and closed loci, due to the considerable HDAC inhibitor-mediated increase in Cas9 and sgRNA expression. However, we observed more substantial HDR efficiency improvement at closed loci relative to open chromatin (2.8 vs. 1.7-fold change). These studies provide a new strategy for HDR-editing of silent genes in iPSCs.
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12
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Kamikawa Y, Yokota K, Oikawa K, Sato F, Muragaki Y. Suppression of MKL1 promotes adipocytic differentiation and reduces the proliferation of myxoid liposarcoma cells. Oncol Lett 2020; 20:369. [PMID: 33154767 DOI: 10.3892/ol.2020.12232] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 09/23/2020] [Indexed: 11/05/2022] Open
Abstract
Myxoid liposarcoma (MLS) is thought to occur due to defective adipocytic differentiation in mesenchymal stem cells. A promising strategy for MLS treatment is the prevention of sarcomagenesis by promoting the terminal differentiation of MLS cells into adipocytes. Previous studies have reported that the suppression of megakaryoblastic leukemia 1 (MKL1) expression induces adipocytic differentiation in preadipocyte cell lines. The present study aimed to investigate the effects of MKL1 suppression on MLS cells. In the present study, MKL1 knockdown was demonstrated to promote the adipocytic differentiation of an MLS-derived cell line, designated 1955/91, under adipogenic conditions. This suggests that therapeutic targeting of the MKL1-associated molecular pathway has potential as a promising method of MLS treatment. However, the induction of adipogenesis by MKL knockdown was incomplete, and Oil Red O staining indicated that intracellular lipid droplets were only sporadically generated. Conversely, MKL1 knockdown reduced the growth of the MLS cells. As adipocytic differentiation in vitro requires cellular confluence, the decreased growth rate of the MLS cells following MKL1 knockdown could be attributed to the incomplete induction of adipogenesis. Translocated in liposarcoma-CCAAT/enhancer-binding protein homologous protein (TLS-CHOP) is an MLS-specific oncoprotein that is thought to play key roles in sarcomagenesis and the suppression of adipocytic differentiation. However, the results of western blotting analyses suggest that TLS-CHOP has limited effects on MKL1 expression in MLS cells and that MKL1 knockdown hardly affects TLS-CHOP expression. Thus, it is postulated that the inhibitory effect of TLS-CHOP on adipogenesis is not associated with MKL1 expression. However, MKL1 and the molecular pathway involving MKL1 appear to be attractive targets for the differentiation therapy of MLS.
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Affiliation(s)
- Yohei Kamikawa
- Department of Pathology, Wakayama Medical University, Wakayama 641-8509, Japan
| | - Kento Yokota
- Department of Pathology, Wakayama Medical University, Wakayama 641-8509, Japan
| | - Kosuke Oikawa
- Department of Pathology, Wakayama Medical University, Wakayama 641-8509, Japan
| | - Fuyuki Sato
- Department of Pathology, Wakayama Medical University, Wakayama 641-8509, Japan
| | - Yasuteru Muragaki
- Department of Pathology, Wakayama Medical University, Wakayama 641-8509, Japan
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13
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Implication of Pseudo Reference Genes in Normalization of Data from Reverse Transcription-Quantitative PCR. Gene 2020; 757:144948. [DOI: 10.1016/j.gene.2020.144948] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 07/01/2020] [Accepted: 07/06/2020] [Indexed: 01/17/2023]
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14
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Zhang W, Eckwahl MJ, Zhou KI, Pan T. Sensitive and quantitative probing of pseudouridine modification in mRNA and long noncoding RNA. RNA (NEW YORK, N.Y.) 2019; 25:1218-1225. [PMID: 31227565 PMCID: PMC6800517 DOI: 10.1261/rna.072124.119] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 06/20/2019] [Indexed: 05/25/2023]
Abstract
Pseudouridine (Ψ) is the most abundant RNA modification in cellular RNA present in tRNA/rRNA/snRNA and also in mRNA and long noncoding RNA (lncRNA). Elucidation of Ψ function in mRNA/lncRNA requires mapping and quantitative assessment of its modification fraction at single-base resolution. The most widely used Ψ mapping method for mRNA/lncRNA relies on its reaction with N-Cyclohexyl-N'-(2-morpholinoethyl)carbodiimide (CMC), forming an adduct with the Ψ base in RNA that is detectable by reverse transcription (RT) stops. However, this method has not produced consistent Ψ maps in mRNAs; furthermore, available protocols do not lend confidence to the estimation of Ψ fraction at specific sites, which is a crucial parameter for investigating the biological relevance of mRNA modifications. Here we develop a quantitative RT-PCR based method that can detect and quantify the modification fraction of target Ψ sites in mRNA/lncRNA, termed CMC-RT and ligation assisted PCR analysis of Ψ modification (CLAP). The method still relies on RT stop at a CMC-Ψ site, but uses site-specific ligation and PCR to generate two distinct PCR products in the same sample, corresponding to the modified and unmodified site, that are visualized by gel electrophoresis. CLAP not only requires a small amount of cellular RNA to validate Ψ sites but also determines the Ψ fraction semiquantitatively at target sites in mRNA/lncRNA. We determined the Ψ status of four mRNA sites and one lncRNA site whose modification fractions range from 30% to 84% in three human cell lines. Our method enables precise mapping and assessment of Ψ modification levels in low abundance cellular RNAs.
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Affiliation(s)
- Wen Zhang
- Department of Chemistry, University of Chicago, Chicago, Illinois 60637, USA
| | - Matthew J Eckwahl
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637, USA
| | - Katherine I Zhou
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637, USA
| | - Tao Pan
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637, USA
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15
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Verbrugghe E, Martel A, Pasmans F. Reference Gene Validation for Quantitative Real-time PCR Studies in Amphibian Kidney-derived A6 Epithelial Cells. Altern Lab Anim 2019; 47:63-70. [PMID: 31333044 DOI: 10.1177/0261192919862936] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Quantitative real-time polymerase chain reaction is a widely used technique that relies on reference genes for the normalisation of gene expression. These reference genes are constitutively expressed and must remain stable across all samples and treatments. Stability of housekeeping genes may vary and must be optimised for a specific tissue, sample or cell line. Here we present a study screening for possible reference gene candidates, eef1a1, rpl8, sub1.L, clta, H4 and odc1, in the Xenopus laevis (A6) kidney cell line. Quantification cycle results were analysed using geNorm to calculate the average expression stability and the coefficient of variation (CV) for each candidate reference gene. All of the tested genes met the guidelines for stable reference genes, namely an average expression stability of < 0.5 and a CV value of < 0.2, with eef1a1 > sub1.L > rpl8 > clta > odc1 > H4. By using pairwise variation analysis, the optimal number of reference targets was determined to be 2. As such, we report that the reference genes eef1a1 and sub1.L should be used to achieve optimal normalisation in A6 cells.
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Affiliation(s)
- Elin Verbrugghe
- Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - An Martel
- Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Frank Pasmans
- Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
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16
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Krautgasser C, Mandl M, Hatzmann FM, Waldegger P, Mattesich M, Zwerschke W. Reliable reference genes for expression analysis of proliferating and adipogenically differentiating human adipose stromal cells. Cell Mol Biol Lett 2019; 24:14. [PMID: 30815013 PMCID: PMC6377720 DOI: 10.1186/s11658-019-0140-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 02/11/2019] [Indexed: 12/28/2022] Open
Abstract
Background The proliferation and adipogenic differentiation of adipose stromal cells (ASCs) are complex processes comprising major phenotypical alterations driven by up- and downregulation of hundreds of genes. Quantitative RT-PCR can be employed to measure relative changes in the expression of a gene of interest. This approach requires constitutively expressed reference genes for normalization to counteract inter-sample variations due to differences in RNA quality and quantity. Thus, a careful validation of quantitative RT-PCR reference genes is needed to accurately measure fluctuations in the expression of genes. Here, we evaluated candidate reference genes applicable for quantitative RT-PCR analysis of gene expression during proliferation and adipogenesis of human ASCs with the immunophenotype DLK1+/CD34+/CD90+/CD105+/CD45−/CD31−. Methods We evaluated the applicability of 10 candidate reference genes (GAPDH, TBP, RPS18, EF1A, TFRC, GUSB, PSMD5, CCNA2, LMNA and MRPL19) using NormFinder, geNorm and BestKeeper software. Results The results indicate that EF1A and MRPL19 are the most reliable reference genes for quantitative RT-PCR analysis of proliferating ASCs. PSMD5 serves as the most reliable endogenous control in adipogenesis. CCNA2 and LMNA were among the least consistent genes. Conclusions Applying these findings for future gene expression analyses will help elucidate ASC biology. Electronic supplementary material The online version of this article (10.1186/s11658-019-0140-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Claudia Krautgasser
- 1Division of Cell Metabolism and Differentiation Research, Institute for Biomedical Aging Research, University of Innsbruck, Rennweg 10, A-6020 Innsbruck, Austria
| | - Markus Mandl
- 1Division of Cell Metabolism and Differentiation Research, Institute for Biomedical Aging Research, University of Innsbruck, Rennweg 10, A-6020 Innsbruck, Austria
| | - Florian M Hatzmann
- 1Division of Cell Metabolism and Differentiation Research, Institute for Biomedical Aging Research, University of Innsbruck, Rennweg 10, A-6020 Innsbruck, Austria
| | - Petra Waldegger
- 1Division of Cell Metabolism and Differentiation Research, Institute for Biomedical Aging Research, University of Innsbruck, Rennweg 10, A-6020 Innsbruck, Austria
| | - Monika Mattesich
- 2Department of Plastic and Reconstructive Surgery, Innsbruck Medical University, Anichstraße 35, A-6020 Innsbruck, Austria
| | - Werner Zwerschke
- 1Division of Cell Metabolism and Differentiation Research, Institute for Biomedical Aging Research, University of Innsbruck, Rennweg 10, A-6020 Innsbruck, Austria
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17
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Okino CH, Ibelli AMG, Brentano L, Zanella R, Groke Marques M. Evaluation of candidate reference genes for investigation of the uterine tissue and corpus luteum of pigs on day 6 after artificial insemination. Anim Reprod Sci 2018; 198:202-209. [DOI: 10.1016/j.anireprosci.2018.09.020] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 09/06/2018] [Accepted: 09/27/2018] [Indexed: 11/26/2022]
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18
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Toscano JHB, Lopes LG, Giraldelo LA, da Silva MH, Okino CH, de Souza Chagas AC. Identification of appropriate reference genes for local immune-related studies in Morada Nova sheep infected with Haemonchus contortus. Mol Biol Rep 2018; 45:1253-1262. [DOI: 10.1007/s11033-018-4281-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 07/24/2018] [Indexed: 01/23/2023]
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19
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Xiao J, Li X, Liu J, Fan X, Lei H, Li C. Identification of reference genes in blood before and after entering the plateau for SYBR green RT-qPCR studies. PeerJ 2017; 5:e3726. [PMID: 28970964 PMCID: PMC5622608 DOI: 10.7717/peerj.3726] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 08/01/2017] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND Tibetans have lived at high altitudes for thousands of years, and they have unique physiological traits that enable them to tolerate this hypoxic environment. However, the genetic basis of these traits is still unknown. As a sensitive and highly efficient technique, RT-qPCR is widely used in gene expression analyses to provide insight into the molecular mechanisms underlying environmental changes. However, the quantitative analysis of gene expression in blood is limited by a shortage of stable reference genes for the normalization of mRNA levels. Thus, systematic approaches were used to identify potential reference genes. RESULTS The expression levels of eight candidate human reference genes (GAPDH, ACTB, 18S RNA, β2-MG, PPIA, RPL13A, TBP and SDHA) were assessed in blood from hypoxic environments. The expression stability of these selected reference genes was evaluated using the geNorm, NormFinder and BestKeeper programs. Interestingly, RPL13A was identified as the ideal reference gene for normalizing target gene expression in human blood before and after exposure to high-altitude conditions. CONCLUSION These results indicate that different reference genes should be selected for the normalization of gene expression in blood from different environmental settings.
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Affiliation(s)
- Jun Xiao
- Department of Blood Transfusion, General Hospital of Air Force, PLA, Beijing, China
| | - Xiaowei Li
- Department of Blood Transfusion, General Hospital of Air Force, PLA, Beijing, China
| | - Juan Liu
- Department of Blood Transfusion, General Hospital of Air Force, PLA, Beijing, China
| | - Xiu Fan
- Department of Blood Transfusion, General Hospital of Air Force, PLA, Beijing, China
| | - Huifen Lei
- Department of Blood Transfusion, General Hospital of Air Force, PLA, Beijing, China
| | - Cuiying Li
- Department of Blood Transfusion, General Hospital of Air Force, PLA, Beijing, China
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20
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Gong H, Sun L, Chen B, Han Y, Pang J, Wu W, Qi R, Zhang TM. Evaluation of candidate reference genes for RT-qPCR studies in three metabolism related tissues of mice after caloric restriction. Sci Rep 2016; 6:38513. [PMID: 27922100 PMCID: PMC5138604 DOI: 10.1038/srep38513] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Accepted: 11/09/2016] [Indexed: 12/24/2022] Open
Abstract
Reverse transcription quantitative-polymerase chain reaction (RT-qPCR) is a routine method for gene expression analysis, and reliable results depend on proper normalization by stable reference genes. Caloric restriction (CR) is a robust lifestyle intervention to slow aging and delay onset of age-associated diseases via inducing global changes in gene expression. Reliable normalization of RT-qPCR data becomes crucial in CR studies. In this study, the expression stability of 12 candidate reference genes were evaluated in inguinal white adipose tissue (iWAT), skeletal muscle (Sk.M) and liver of CR mice by using three algorithms, geNorm, NormFinder, and Bestkeeper. Our results showed β2m, Ppia and Hmbs as the most stable genes in iWAT, Sk.M and liver, respectively. Moreover, two reference genes were sufficient to normalize RT-qPCR data in each tissue and the suitable pair of reference genes was β2m-Hprt in iWAT, Ppia-Gusb in Sk.M and Hmbs-β2m in liver. By contrast, the least stable gene in iWAT or Sk.M was Gapdh, and in liver was Pgk1. Furthermore, the expression of Leptin and Ppar-γ were profiled in these tissues to validate the selected reference genes. Our data provided a basis for gene expression analysis in future CR studies.
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Affiliation(s)
- Huan Gong
- The MOH key laboratory of Geriatrics, Beijing Hospital, National Center of Gerontology, Beijing, P.R. China
| | - Liang Sun
- The MOH key laboratory of Geriatrics, Beijing Hospital, National Center of Gerontology, Beijing, P.R. China
| | - Beidong Chen
- The MOH key laboratory of Geriatrics, Beijing Hospital, National Center of Gerontology, Beijing, P.R. China
| | - Yiwen Han
- The MOH key laboratory of Geriatrics, Beijing Hospital, National Center of Gerontology, Beijing, P.R. China
| | - Jing Pang
- The MOH key laboratory of Geriatrics, Beijing Hospital, National Center of Gerontology, Beijing, P.R. China
| | - Wei Wu
- The MOH key laboratory of Geriatrics, Beijing Hospital, National Center of Gerontology, Beijing, P.R. China
| | - Ruomei Qi
- The MOH key laboratory of Geriatrics, Beijing Hospital, National Center of Gerontology, Beijing, P.R. China
| | - Tie-Mei Zhang
- The MOH key laboratory of Geriatrics, Beijing Hospital, National Center of Gerontology, Beijing, P.R. China
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