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Zareinejad M, Faghih Z, Ramezani A, Safaei A, Ghaderi A. Exploring heterogeneous expression of beta-actin (ACTB) in bladder cancer by producing a monoclonal antibody 6D6. BMC Urol 2024; 24:124. [PMID: 38867273 PMCID: PMC11167769 DOI: 10.1186/s12894-024-01489-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Accepted: 04/22/2024] [Indexed: 06/14/2024] Open
Abstract
BACKGROUND To predict outcomes and identify potential therapeutic targets for cancers, it is critical to find novel specific biomarkers. The objective of this study was to search for and explore novel bladder cancer-associated protein biomarkers. METHODS A library of monoclonal antibodies (mAbs) against the JAM-ICR cell line was first generated, and clones with high affinity were selected. Hybridomas were screened using bladder cancer (BLCA) cell lines and normal cells. The target of the selected mAb was then characterized through immunoaffinity purification, western blotting, and mass spectrometry analysis. Expression of the target antigen was assessed by flow cytometry and IHC methods. Several databases were also used to evaluate the target antigen in BLCA and other types of cancers. RESULTS Based on screenings, a 6D6 clone was selected that recognized an isoform of beta-actin (ACTB). Our data showed that ACTB expression on different cell lines was heterogeneous and varied significantly from low to high intensity. 6D6 bound strongly to epithelial cells while showing weak to no reactivity to stromal, endothelial, and smooth muscle cells. There was no association between ACTB intensity and related prognostic factors in BLCA. In silico evaluations revealed a significant correlation between ACTB and overexpressed genes and biomarkers in BLCA. Additionally, the differential expression of ACTB in tumor and healthy tissue as well as its correlation with survival time in a number of cancers were shown. CONCLUSIONS The heterogeneous expression of ACTB may suggest the potential value of this marker in the diagnosis or prognosis of cancer.
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Affiliation(s)
- Mohammadrasul Zareinejad
- Shiraz Institute for Cancer Research, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
- Department of Immunology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Zahra Faghih
- Shiraz Institute for Cancer Research, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Amin Ramezani
- Shiraz Institute for Cancer Research, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Akbar Safaei
- Department of Pathology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Abbas Ghaderi
- Shiraz Institute for Cancer Research, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran.
- Department of Immunology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran.
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2
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Chen Y, He Q, Li X, Zhang Y, Li J, Zhang L, Yao X, Zhang X, Liu C, Wang H. Identification of Accurate Reference Genes for qRT-PCR Analysis of Gene Expression in Eremochloa ophiuroides under Multiple Stresses of Phosphorus Deficiency and/or Aluminum Toxicity. PLANTS (BASEL, SWITZERLAND) 2023; 12:3751. [PMID: 37960107 PMCID: PMC10649868 DOI: 10.3390/plants12213751] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 10/26/2023] [Accepted: 10/31/2023] [Indexed: 11/15/2023]
Abstract
Centipedegrass (Eremochloa ophiuroides (Munro.) Hack.) is a species originating in China and is an excellent warm-season turfgrass. As a native species in southern China, it is naturally distributed in the phosphorus-deficient and aluminum-toxic acid soil areas. It is important to research the molecular mechanism of centipedegrass responses to phosphorus-deficiency and/or aluminum-toxicity stress. Quantitative Real-Time PCR (qRT-PCR) is a common method for gene expression analysis, and the accuracy of qRT-PCR results depends heavily on the stability of internal reference genes. However, there are still no reported stable and effective reference genes for qRT-PCR analysis of target genes under the acid-soil-related stresses in different organs of centipedegrass. For scientific rigor, the gene used as a reference for any plant species and/or any stress conditions should be first systematically screened and evaluated. This study is the first to provide a group of reliable reference genes to quantify the expression levels of functional genes of Eremochloa ophiuroides under multiple stresses of P deficiency and/or aluminum toxicity. In this study, centipedegrass seedlings of the acid-soil-resistant strain 'E041' and acid-soil-sensitive strain 'E089' were used for qRT-PCR analysis. A total of 11 candidate reference genes (ACT, TUB, GAPDH, TIP41, CACS, HNR, EP, EF1α, EIF4α, PP2A and actin) were detected by qRT-PCR technology, and the stability of candidate genes was evaluated with the combination of four internal stability analysis software programs. The candidate reference genes exhibited differential stability of expression in roots, stems and leaves under phosphorus-deficiency and/or aluminum-toxicity stress. On the whole, the results showed that GAPDH, TIP41 and HNR were the most stable in the total of samples. In addition, for different tissues under various stresses, the selected reference genes were also different. CACS and PP2A were identified as two stable reference genes in roots through all three stress treatments (phosphate deficiency, aluminum toxicity, and the multiple stress treatment of aluminum toxicity and phosphate deficiency). Moreover, CACS was also stable as a reference gene in roots under each treatment (phosphate deficiency, aluminum toxicity, or multiple stresses of aluminum toxicity and phosphate deficiency). In stems under all three stress treatments, GAPDH and EIF4α were the most stable reference genes; for leaves, PP2A and TIP41 showed the two highest rankings in all three stress treatments. Finally, qRT-PCR analysis of the expression patterns of the target gene ALMT1 was performed to verify the selected reference genes. The application of the reference genes identified as internal controls for qRT-PCR analysis will enable accurate analysis of the target gene expression levels and expression patterns in centipedegrass under acid-soil-related stresses.
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Affiliation(s)
- Ying Chen
- State Key Laboratory of Tree Genetics and Breeding, Ministry of Education of China, Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China; (Y.C.)
| | - Qingqing He
- State Key Laboratory of Tree Genetics and Breeding, Ministry of Education of China, Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China; (Y.C.)
| | - Xiaohui Li
- The National Forestry and Grassland Administration Engineering Research Center for Germplasm Innovation and Utilization of Warm-Season Turfgrasses, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing 210014, China
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing 210014, China
| | - Yuan Zhang
- The National Forestry and Grassland Administration Engineering Research Center for Germplasm Innovation and Utilization of Warm-Season Turfgrasses, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing 210014, China
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing 210014, China
| | - Jianjian Li
- The National Forestry and Grassland Administration Engineering Research Center for Germplasm Innovation and Utilization of Warm-Season Turfgrasses, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing 210014, China
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing 210014, China
| | - Ling Zhang
- The National Forestry and Grassland Administration Engineering Research Center for Germplasm Innovation and Utilization of Warm-Season Turfgrasses, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing 210014, China
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing 210014, China
| | - Xiang Yao
- The National Forestry and Grassland Administration Engineering Research Center for Germplasm Innovation and Utilization of Warm-Season Turfgrasses, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing 210014, China
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing 210014, China
| | - Xueli Zhang
- State Key Laboratory of Tree Genetics and Breeding, Ministry of Education of China, Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China; (Y.C.)
| | - Chuanqiang Liu
- State Key Laboratory of Tree Genetics and Breeding, Ministry of Education of China, Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China; (Y.C.)
| | - Haoran Wang
- The National Forestry and Grassland Administration Engineering Research Center for Germplasm Innovation and Utilization of Warm-Season Turfgrasses, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing 210014, China
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing 210014, China
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Centrifugal microfluidic-based multiplex recombinase polymerase amplification assay for rapid detection of SARS-CoV-2. iScience 2023; 26:106245. [PMID: 36845031 PMCID: PMC9941069 DOI: 10.1016/j.isci.2023.106245] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 01/03/2023] [Accepted: 02/16/2023] [Indexed: 02/23/2023] Open
Abstract
The COVID-19 pandemic has spread worldwide, and rapid detection of the SARS-CoV-2 virus is crucial for infection surveillance and epidemic control. This study developed a centrifugal microfluidics-based multiplex reverse transcription recombinase polymerase amplification (RT-RPA) assay for endpoint fluorescence detection of the E, N, and ORF1ab genes of SARS-CoV-2. The microscope slide-shaped microfluidic chip could simultaneously accomplish three target genes and one reference human gene (i.e., ACTB) RT-RPA reactions in 30 min, and the sensitivity was 40 RNA copies/reaction for the E gene, 20 RNA copies/reaction for the N gene, and 10 RNA copies/reaction for the ORF1ab gene. The chip demonstrated high specificity, reproducibility, and repeatability. Chip performance was also evaluated using real clinical samples. Thus, this rapid, accurate, on-site, and multiplexed nucleic acid test microfluidic chip would significantly contribute to detecting patients with COVID-19 in low-resource settings and point-of-care testing (POCT) and, in the future, could be used to detect emerging new variants of SARS-CoV-2.
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Jin S, Wijerathne CUB, Au-Yeung KKW, Lei H, Yang C, O K. Effects of high- and low-fiber diets on intestinal oxidative stress in growing-finishing pigs. J Anim Sci 2022; 100:skac306. [PMID: 36104002 PMCID: PMC9667964 DOI: 10.1093/jas/skac306] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 09/13/2022] [Indexed: 09/16/2023] Open
Abstract
Feed is the most expensive facet of commercial pork production. In order to reduce feed costs, using high-fiber ingredients has become a common practice. Moderate levels of fiber can maintain intestinal physiological function and promote intestinal health. Oxidative stress is linked to impaired nutrient absorption and growth performance. This study investigated the effects of high-fiber (5.26% crude fiber) and low-fiber (2.46% crude fiber) diets on growth performance and intestinal oxidative stress parameters in growing-finishing pigs. Forty growing pigs with initial body weight (27.07 ± 1.26 kg) were randomly assigned to 2 treatment groups with 10 replicates of 2 pigs per pen. Pigs were weighed on day 35, 42, and 70. The feed intake was recorded daily to calculate growth performance parameters. On day 70, eight pigs in each treatment group were randomly selected and euthanized to obtain jejunum to measure oxidative stress status. Pigs fed a high-fiber diet were heavier than those fed a low-fiber diet on days 35, 42, and 70 (P < 0.05). During the whole feeding period, pigs fed a high-fiber diet had a higher average daily gain than those fed a low-fiber diet (P < 0.05). The low-fiber diet resulted in increased levels of malondialdehyde (P < 0.05) in the jejunum, suggesting that the low-fiber diet contributed to oxidative stress in the jejunum. The low-fiber diet also led to a significant increase in glutathione and oxidized glutathione levels (P < 0.05) in the jejunum, indicating that pigs fed a low-fiber diet needed to produce more antioxidant substances to cope with oxidative stress in the intestine. This was accompanied by a significant increase in the expression of glutathione synthesizing enzymes in the jejunum of the low-fiber group (P < 0.05). These results suggest that the high-fiber diet can improve growth performance and maintain intestinal health in growing-finishing pigs by reducing intestinal oxidative stress.
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Affiliation(s)
- Shunshun Jin
- Department of Animal Science, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
- CCARM, St. Boniface Hospital Research Centre, Winnipeg, MB R2H 2A6, Canada
| | - Charith U B Wijerathne
- Department of Animal Science, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
- CCARM, St. Boniface Hospital Research Centre, Winnipeg, MB R2H 2A6, Canada
| | - Kathy K W Au-Yeung
- CCARM, St. Boniface Hospital Research Centre, Winnipeg, MB R2H 2A6, Canada
| | - Huaigang Lei
- Topigs Norsvin Canada Inc., Oak Bluff, MB R4G 0C4, Canada
| | - Chengbo Yang
- Department of Animal Science, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Karmin O
- Department of Animal Science, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
- CCARM, St. Boniface Hospital Research Centre, Winnipeg, MB R2H 2A6, Canada
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Broggini C, Abril N, Carranza J, Membrillo A. Evaluation of candidate reference genes for quantitative real-time PCR normalization in blood from red deer developing antlers. Sci Rep 2022; 12:16264. [PMID: 36171416 PMCID: PMC9519901 DOI: 10.1038/s41598-022-20676-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 09/16/2022] [Indexed: 12/03/2022] Open
Abstract
Sexual selection favors male traits that increase their ability to monopolize the breeding access to several females. Deer antlers are cranial appendages that regenerate annually in males. Throughout life, the phenology of antler growth advances and antler mass increases until the stag reaches, between 8 and 10 years old, maximum body mass and highest reproductive success. The molecular mechanisms of antler development are of great interest in both evolutionary and regenerative medicine studies. To minimize errors in the assessment of gene expression levels by qRT-PCR, we analyzed the stability of a panel of eight candidate reference genes and concluded that qRT-PCR normalization to three stable genes is strongly convenient in experiments performed in red deer antler blood. To validate our proposal, we compared the expression level of three genes linked to red deer antler growth (ANXA2, APOD and TPM1) in fifteen male red deer classified as young (up to 4 years old) and adults (4–6 years old). Our data confirms that B2M, ACTB and RPLP0 are valuable reference genes for future gene expression studies in red deer antler blood, which would provide increased insight into the effects of intrinsic factors that determine antler development in red deer.
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Affiliation(s)
- Camilla Broggini
- Wildlife Research Unit (UIRCP-UCO), University of Cordoba, 14014, Cordoba, Spain.
| | - Nieves Abril
- Department of Biochemistry and Molecular Biology, University of Cordoba, Cordoba, Spain
| | - Juan Carranza
- Wildlife Research Unit (UIRCP-UCO), University of Cordoba, 14014, Cordoba, Spain
| | - Alberto Membrillo
- Wildlife Research Unit (UIRCP-UCO), University of Cordoba, 14014, Cordoba, Spain
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6
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Zhao ZQ, Zheng KY, Ou Q, Xu PZ, Qin S, Sun X, Li MW, Wu YC, Wang XY. Identification of optimal reference genes in Bombyx mori (Lepidoptera) for normalization of stress-responsive genes after challenge with pesticides. ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY 2022; 110:e21896. [PMID: 35355317 DOI: 10.1002/arch.21896] [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: 01/19/2022] [Revised: 03/16/2022] [Accepted: 03/17/2022] [Indexed: 06/14/2023]
Abstract
Pesticides are frequently used to control pests in agriculture due to their ease of use and effectiveness, but their use causes serious economic losses to sericulture when their production overlaps with agriculture. However, no suitable internal reference genes (RGs) have been reported in the study of silkworms in response to pesticides. In this study, a standard curve was established to detect the expression levels of seven RGs in different tissues of different silkworm strains after feeding with pesticides using reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR), including BmGAPDH, BmActin3, BmTBP, BmRPL3, Bm28sRNA, Bmα-tubulin, and BmUBC, and the stability of them was evaluated by using NormFinder, geNorm, Delta CT, BestKeeper, and RefFinder. The results showed that BmGAPDH and Bmα-tubulin were relatively stable in the midgut after feeding with fenvalerate, BmGAPDH and Bmactin3 were relatively stable in the fat body, and Bmα-tubulin and Bmactin3 were relatively stable in the hemolymph, indicating that Bmactin3 was the most suitable RG when evaluating fenvalerate, followed by BmGAPDH and Bmα-tubulin. Besides, BmGAPDH and Bmactin3 were relatively stable in the midgut after treatment with DDVP, BmGAPDH and Bmα-tubulin were relatively stable in the fat body, and BmGAPDH and Bmα-tubulin were relatively stable in the hemolymph, indicating that Bmα-tubulin was the most stable RG when evaluating DDVP, followed by BmGAPDH and Bmactin3. Of note, BmGAPDH was shared by the two pesticides. The results will be valuable for RG selection in studying the pesticide response mechanism of silkworms and other lepidopteran insects.
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Affiliation(s)
- Zi-Qin Zhao
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, China
| | - Kai-Yi Zheng
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, China
| | - Qi Ou
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, China
| | - Ping-Zhen Xu
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, China
- The Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture, Sericultural Research Institute, Chinese Academy of Agricultural Science, Zhenjiang, Jiangsu, China
| | - Sheng Qin
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, China
- The Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture, Sericultural Research Institute, Chinese Academy of Agricultural Science, Zhenjiang, Jiangsu, China
| | - Xia Sun
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, China
- The Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture, Sericultural Research Institute, Chinese Academy of Agricultural Science, Zhenjiang, Jiangsu, China
| | - Mu-Wang Li
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, China
- The Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture, Sericultural Research Institute, Chinese Academy of Agricultural Science, Zhenjiang, Jiangsu, China
| | - Yang-Chun Wu
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, China
- The Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture, Sericultural Research Institute, Chinese Academy of Agricultural Science, Zhenjiang, Jiangsu, China
| | - Xue-Yang Wang
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, China
- The Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture, Sericultural Research Institute, Chinese Academy of Agricultural Science, Zhenjiang, Jiangsu, China
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Kanji JN, Pabbaraju K, Wong A, Beitku C, Deo A, Kailey S, Ma R, Tipples G, Zelyas N. Effect of not vortexing nasopharyngeal and throat swabs on SARS-CoV-2 nucleic acid detection: a pilot study. J Virol Methods 2022; 301:114468. [PMID: 35051444 PMCID: PMC8762992 DOI: 10.1016/j.jviromet.2022.114468] [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: 12/07/2021] [Revised: 01/14/2022] [Accepted: 01/15/2022] [Indexed: 11/27/2022]
Abstract
The processing of swabs for respiratory virus detection involves vortexing while still in the viral transport medium (VTM). The effect of not vortexing swabs prior to analysis has not been studied extensively for SARS-CoV-2 detection, and presents an opportunity to improve pre-analytic laboratory workflow. We aimed to assess the impact of not vortexing nasopharyngeal/throat swabs submitted in VTM for SARS-CoV-2 testing. To assess the impact of not vortexing swabs, 277 swab samples were tested for SARS-CoV-2 RNA in paired vortexed and non-vortexed aliquots using eight routine nucleic acid amplification assays. We compared the qualitative (positive/negative) and semi-quantitative (cycle threshold, Ct) results. Following discordant analysis, all but one non-vortexed sample had the same qualitative result as the vortexed sample. 27.4 % of samples were SARS-CoV-2 positive. Comparison of Ct values revealed an apparent reduction in human cellular nucleic acid in the non-vortexed samples (mean Ct values of 24.0 and 26.5 for vortexed and non-vortexed samples, respectively, p < 0.0001) and increased Ct values for non-vortexed samples using a laboratory-developed SARS-CoV-2 assay (mean Ct values of 4.1 and 4.2 for vortexed and non-vortexed samples, respectively; p < 0.0001), but this was not observed for a more automated commercial SARS-CoV-2 assay (mean Ct values of 15.2 for both vortexed and non-vortexed samples, respectively; p = 0.68). While vortexing swabs appears to improve the recovery of cellular material, it does not have an appreciable impact on the qualitative sensitivity of SARS-CoV-2 nucleic acid tests, which may support omission of this step and simplification of front-end sample processing.
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Affiliation(s)
- Jamil N Kanji
- Public Health Laboratory, Alberta Precision Laboratories, Calgary, AB, Canada; Division of Infectious Diseases, Department of Medicine, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada; Department of Pathology & Laboratory Medicine, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada; Department of Laboratory Medicine & Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada.
| | - Kanti Pabbaraju
- Public Health Laboratory, Alberta Precision Laboratories, Calgary, AB, Canada
| | - Anita Wong
- Public Health Laboratory, Alberta Precision Laboratories, Calgary, AB, Canada
| | - Candace Beitku
- Public Health Laboratory, Alberta Precision Laboratories, Edmonton, AB, Canada
| | - Ashwin Deo
- Public Health Laboratory, Alberta Precision Laboratories, Edmonton, AB, Canada
| | - Seema Kailey
- Public Health Laboratory, Alberta Precision Laboratories, Edmonton, AB, Canada
| | - Raymond Ma
- Public Health Laboratory, Alberta Precision Laboratories, Edmonton, AB, Canada
| | - Graham Tipples
- Public Health Laboratory, Alberta Precision Laboratories, Edmonton, AB, Canada; Department of Medical Microbiology & Immunology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada; Li Ka Shing Institute for Virology, University of Alberta, Edmonton, AB, Canada
| | - Nathan Zelyas
- Department of Laboratory Medicine & Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada; Public Health Laboratory, Alberta Precision Laboratories, Edmonton, AB, Canada
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8
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Yu Q, Liu YL, Sun GZ, Liu YX, Chen J, Zhou YB, Chen M, Ma YZ, Xu ZS, Lan JH. Genome-Wide Analysis of the Soybean Calmodulin-Binding Protein 60 Family and Identification of GmCBP60A-1 Responses to Drought and Salt Stresses. Int J Mol Sci 2021; 22:13501. [PMID: 34948302 PMCID: PMC8708795 DOI: 10.3390/ijms222413501] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 12/05/2021] [Accepted: 12/09/2021] [Indexed: 12/17/2022] Open
Abstract
Calmodulin-binding protein 60 (CBP60) members constitute a plant-specific protein family that plays an important role in plant growth and development. In the soybean genome, nineteen CBP60 members were identified and analyzed for their corresponding sequences and structures to explore their functions. Among GmCBP60A-1, which primarily locates in the cytomembrane, was significantly induced by drought and salt stresses. The overexpression of GmCBP60A-1 enhanced drought and salt tolerance in Arabidopsis, which showed better state in the germination of seeds and the root growth of seedlings. In the soybean hairy roots experiment, the overexpression of GmCBP60A-1 increased proline content, lowered water loss rate and malondialdehyde (MDA) content, all of which likely enhanced the drought and salt tolerance of soybean seedlings. Under stress conditions, drought and salt response-related genes showed significant differences in expression in hairy root soybean plants of GmCBP60A-1-overexpressing and hairy root soybean plants of RNAi. The present study identified GmCBP60A-1 as an important gene in response to salt and drought stresses based on the functional analysis of this gene and its potential underlying mechanisms in soybean stress-tolerance.
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Affiliation(s)
- Qian Yu
- College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China; (Q.Y.); (Y.-L.L.); (Y.-X.L.)
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS)/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing 100081, China; (G.-Z.S.); (J.C.); (Y.-B.Z.); (M.C.); (Y.-Z.M.)
| | - Ya-Li Liu
- College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China; (Q.Y.); (Y.-L.L.); (Y.-X.L.)
| | - Guo-Zhong Sun
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS)/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing 100081, China; (G.-Z.S.); (J.C.); (Y.-B.Z.); (M.C.); (Y.-Z.M.)
| | - Yuan-Xia Liu
- College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China; (Q.Y.); (Y.-L.L.); (Y.-X.L.)
| | - Jun Chen
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS)/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing 100081, China; (G.-Z.S.); (J.C.); (Y.-B.Z.); (M.C.); (Y.-Z.M.)
| | - Yong-Bin Zhou
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS)/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing 100081, China; (G.-Z.S.); (J.C.); (Y.-B.Z.); (M.C.); (Y.-Z.M.)
| | - Ming Chen
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS)/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing 100081, China; (G.-Z.S.); (J.C.); (Y.-B.Z.); (M.C.); (Y.-Z.M.)
| | - You-Zhi Ma
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS)/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing 100081, China; (G.-Z.S.); (J.C.); (Y.-B.Z.); (M.C.); (Y.-Z.M.)
| | - Zhao-Shi Xu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS)/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing 100081, China; (G.-Z.S.); (J.C.); (Y.-B.Z.); (M.C.); (Y.-Z.M.)
| | - Jin-Hao Lan
- College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China; (Q.Y.); (Y.-L.L.); (Y.-X.L.)
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Identification of Reference Genes for Expression Studies in the Whole-Blood from Three Cattle Breeds under Two States of Livestock Weather Safety. Animals (Basel) 2021; 11:ani11113073. [PMID: 34827805 PMCID: PMC8614315 DOI: 10.3390/ani11113073] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 09/08/2021] [Accepted: 09/14/2021] [Indexed: 01/03/2023] Open
Abstract
Simple Summary Reductions in the fertility, body weight, and growth rate of cattle across the world are associated with the global warming phenomenon. Developing optimal management strategies is an important aspect of breeding programs for different breeds. Blood tissue undergoes dramatic physiological and metabolic changes during heat stress conditions, which involves the expression and regulation of a great number of genes across species. Real-time quantitative PCR (qPCR) is a method for the rapid and reliable quantification of mRNA transcription. Reference genes are used to normalize mRNA levels between different samples. Thus, the selection of high-quality reference genes is necessary for the interpretation of data generated by real-time PCR. Abstract Real-time PCR is widely used to study the relative abundance of mRNA due to its specificity, sensitivity, and repeatability quantification. However, relative quantification requires a reference gene, which should be stable in its expression, showing lower variation by experimental conditions or tissues. The aim of this study was to evaluate the stability of the expression of five commonly used reference genes (actb, ywhaz, b2m, sdha, and 18s rRNA) at different physiological stages (alert and emergency) in three different cattle breeds. In this study, five genes (actb, ywhaz, b2m, sdha, and 18s rRNA) were selected as candidate reference genes for expression studies in the whole blood from three cattle breeds (Romosinuano, Gyr, and Brahman) under heat stress conditions. The transcription stability of the candidate reference genes was evaluated using geNorm and NormFinder. The results showed that actb, 18SrRNA, and b2m expression were the most stable reference genes for whole blood of Gyr and Brahman breeds under two states of livestock weather safety (alert and emergency). Meanwhile, actb, b2m, and ywhaz were the most stable reference genes for the Romosinuano breed.
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10
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Ren J, Zhang N, Li X, Sun X, Song J. Identification of reference genes for gene expression studies among different developmental stages of murine hearts. BMC DEVELOPMENTAL BIOLOGY 2021; 21:13. [PMID: 34496746 PMCID: PMC8425138 DOI: 10.1186/s12861-021-00244-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 08/24/2021] [Indexed: 02/01/2023]
Abstract
Background Real-time quantitative polymerase chain reaction (RT-qPCR) is a widely-used standard assay for assessing gene expression. RT-qPCR data requires reference genes for normalization to make the results comparable. Therefore, the selected reference gene should be highly stable in its expression throughout the experimental datasets. So far, reports about the optimal set of reference genes in murine left ventricle (LV) across embryonic and postnatal stages are few. The objective of our research was to identify the appropriate reference genes in murine LV among different developmental stages. Methods We investigated the gene expression profiles of 21 widely used housekeeping genes in murine LV from 7 different developmental stages (almost throughout the whole period of the mouse lifespan). The stabilities of the potential reference genes were evaluated by five methods: GeNorm, NormFinder, BestKeeper, Delta-Ct and RefFinder. Results We proposed a set of reliable reference genes for normalization of RT-qPCR experimental data in different conditions. Furthermore, our results showed that 6 genes (18S, Hmbs, Ubc, Psmb4, Tfrc and Actb) are not recommended to be used as reference genes in murine LV development studies. The data also suggested that the Rplp0 gene might serve as an optimal reference gene in gene expression analysis. Conclusions Our study investigated the expression stability of the commonly used reference genes in process of LV development and maturation. We proposed a set of optimal reference genes that are suitable for accurate normalization of RT-qPCR data in specific conditions. Our findings may be helpful in future studies for investigating the gene expression patterns and mechanism of mammalian heart development. Supplementary Information The online version contains supplementary material available at 10.1186/s12861-021-00244-6.
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Affiliation(s)
- Jie Ren
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, 167A Beilishi Road, Xi Cheng District, Beijing, 100037, People's Republic of China.
| | - Ningning Zhang
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, 167A Beilishi Road, Xi Cheng District, Beijing, 100037, People's Republic of China
| | - Xiangjie Li
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, 167A Beilishi Road, Xi Cheng District, Beijing, 100037, People's Republic of China
| | - Xiaogang Sun
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, 167A Beilishi Road, Xi Cheng District, Beijing, 100037, People's Republic of China
| | - Jiangping Song
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, 167A Beilishi Road, Xi Cheng District, Beijing, 100037, People's Republic of China.
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11
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Kuribara T, Imagawa A, Hirano M, Ito Y, Totani K. Metabolic syndrome perturbs deglucosylation and reglucosylation in the glycoprotein folding cycle. FEBS Lett 2020; 594:1759-1769. [DOI: 10.1002/1873-3468.13780] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2019] [Revised: 03/05/2020] [Accepted: 03/05/2020] [Indexed: 12/26/2022]
Affiliation(s)
- Taiki Kuribara
- Department of Materials and Life Science Seikei University Musashino Japan
| | - Ayami Imagawa
- Department of Materials and Life Science Seikei University Musashino Japan
| | - Makoto Hirano
- Department of Pharmacy Yasuda Women’s University Hiroshima Japan
| | - Yukishige Ito
- Synthetic Cellular Chemistry Laboratory RIKEN Wako Japan
| | - Kiichiro Totani
- Department of Materials and Life Science Seikei University Musashino Japan
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12
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Molina CE, Jacquet E, Ponien P, Muñoz-Guijosa C, Baczkó I, Maier LS, Donzeau-Gouge P, Dobrev D, Fischmeister R, Garnier A. Identification of optimal reference genes for transcriptomic analyses in normal and diseased human heart. Cardiovasc Res 2019; 114:247-258. [PMID: 29036603 DOI: 10.1093/cvr/cvx182] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 09/20/2017] [Indexed: 11/13/2022] Open
Abstract
Aims Quantitative real-time RT-PCR (RT-qPCR) has become the method of choice for mRNA quantification, but requires an accurate normalization based on the use of reference genes showing invariant expression across various pathological conditions. Only few data exist on appropriate reference genes for the human heart. The objective of this study was to determine a set of suitable reference genes in human atrial and ventricular tissues, from right and left cavities in control and in cardiac diseases. Methods and results We assessed the expression of 16 reference genes (ACTB, B2M, GAPDH, GUSB, HMBS, HPRT1, IPO8, PGK1, POLR2A, PPIA, RPLP0, TBP, TFRC, UBC, YWHAZ, 18S) in tissues from: right and left ventricles from healthy controls and heart failure (HF) patients; right-atrial tissue from patients in sinus rhythm with (SRd) or without (SRnd) atrial dilatation, patients with paroxysmal (pAF) or chronic (cAF) atrial fibrillation or with HF; and left-atrial tissue from patients in SR or cAF. Consensual analysis (by geNorm and Normfinder algorithms, BestKeeper software tool and comparative delta-Ct method) of the variability scores obtained for each reference gene expression shows that the most stably expressed genes are: GAPDH, GUSB, IPO8, POLR2A, and YWHAZ when comparing either right and left ventricle or ventricle from healthy controls and HF patients; GAPDH, IPO8, POLR2A, PPIA, and RPLP0 when comparing either right and left atrium or right atria from all pathological groups. ACTB, TBP, TFRC, and 18S genes were identified as the least stable. Conclusions The overall most stable reference genes across different heart cavities and disease conditions were GAPDH, IPO8, POLR2A and PPIA. YWHAZ or GUSB could be added to this set for some specific experiments. This study should provide useful guidelines for reference gene selection in RT-qPCR studies in human heart.
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Affiliation(s)
- Cristina E Molina
- Inserm, UMR-S 1180, University of Paris-Sud, Université Paris-Saclay, Châtenay-Malabry, France.,Institute of Pharmacology and Toxicology, Heart Research Center Göttingen, University Medical Center, Georg-August University Göttingen, Germany.,German Center for Cardiovascular Research (DZHK), Partner Site Göttingen, Germany
| | - Eric Jacquet
- Institut de Chimie des Substances Naturelles, UPR 2301, CNRS, University of Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Prishila Ponien
- Institut de Chimie des Substances Naturelles, UPR 2301, CNRS, University of Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | | | - Istvan Baczkó
- Department Pharmacology and Pharmacotherapy, University of Szeged, Hungary
| | - Lars S Maier
- Department Internal Medicine II, University Heart Center, University Hospital Regensburg, Regensburg, Germany
| | | | - Dobromir Dobrev
- West German Heart and Vascular Center, Institute of Pharmacology, University Duisburg-Essen, Essen, Germany
| | - Rodolphe Fischmeister
- Inserm, UMR-S 1180, University of Paris-Sud, Université Paris-Saclay, Châtenay-Malabry, France
| | - Anne Garnier
- Inserm, UMR-S 1180, University of Paris-Sud, Université Paris-Saclay, Châtenay-Malabry, France
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Hao X, Han F, Ma B, Zhang N, Chen H, Jiang X, Yin L, Liu W, Ao L, Cao J, Liu J. SOX30 is a key regulator of desmosomal gene suppressing tumor growth and metastasis in lung adenocarcinoma. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2018; 37:111. [PMID: 29855376 PMCID: PMC5984358 DOI: 10.1186/s13046-018-0778-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 05/21/2018] [Indexed: 02/02/2023]
Abstract
Background The expression of desmosomal genes in lung adenocarcinoma and lung squamous carcinoma is different. However, the regulatory mechanism of desmosomal gene expression in lung adenocarcinoma and lung squamous carcinoma remains unknown. Methods The correlation between expression of desmosomal gene expression and SOX30 expression were analyzed by bioinformatics. The expression of SOX30, DSP, JUP and DSC3 were detected in lung cancer cell lines, lung tissues of mice and patients’ tissues by qPCR, WB, Immunofluorescence and Immunohistochemistry. A chromatin Immunoprecipitation assay was used to investigate the mechanisms of the SOX30 regulation on desmosomal gene expression. In vitro proliferation, migration and invasion assays, and an in vivo nude mice model were utilized to assess the important role of desmosomal genes on SOX30-induced tumor suppression. A WB assay and TOP/FOP flash reporter assay was used to investigate the downstream pathway regulated by the SOX30-desmosomal gene axis. A chemical carcinogenic model of SOX30-knockout mice was generated to confirm the role of the SOX30-desmosomal gene axis in tumorigenesis. Results The expression of desmosomal genes were upregulated by SOX30 in lung adenocarcinoma but not in lung squamous carcinoma. Further mechanism studies showed that SOX30 acts as a key transcriptional regulator of desmosomal genes by directly binding to the ACAAT motif of desmosomal genes promoter region and activating their transcription in lung adenocarcinoma. Knockdown of the expression of related desmosomal genes by miRNA significantly attenuated the inhibitory effect of SOX30 on cell proliferation, migration and invasion in vitro and on tumor growth and metastasis in vivo. In addition, knockout of SOX30 promotes lung tumor development and loss the inhibition of desmosomal genes on downstream Wnt and ERK signal in urethane-induced lung carcinogenesis in SOX30-knockout mice. Conclusions Overall, these findings demonstrate for the first time that SOX30 acts as a master switch of desmosomal genes, inhibits lung adenocarcinoma cell proliferation, migration and invasion by activating the transcription of desmosomal genes. This study provides novel insights on the regulatory mechanism of desmosomal genes in lung adenocarcinoma. Electronic supplementary material The online version of this article (10.1186/s13046-018-0778-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xianglin Hao
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University, 30 Gaotanyan Street, Shapingba District, Chongqing, 400038, People's Republic of China
| | - Fei Han
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University, 30 Gaotanyan Street, Shapingba District, Chongqing, 400038, People's Republic of China
| | - Bangjin Ma
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University, 30 Gaotanyan Street, Shapingba District, Chongqing, 400038, People's Republic of China
| | - Ning Zhang
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University, 30 Gaotanyan Street, Shapingba District, Chongqing, 400038, People's Republic of China
| | - Hongqiang Chen
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University, 30 Gaotanyan Street, Shapingba District, Chongqing, 400038, People's Republic of China
| | - Xiao Jiang
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University, 30 Gaotanyan Street, Shapingba District, Chongqing, 400038, People's Republic of China
| | - Li Yin
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University, 30 Gaotanyan Street, Shapingba District, Chongqing, 400038, People's Republic of China
| | - Wenbin Liu
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University, 30 Gaotanyan Street, Shapingba District, Chongqing, 400038, People's Republic of China
| | - Lin Ao
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University, 30 Gaotanyan Street, Shapingba District, Chongqing, 400038, People's Republic of China
| | - Jia Cao
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University, 30 Gaotanyan Street, Shapingba District, Chongqing, 400038, People's Republic of China
| | - Jinyi Liu
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University, 30 Gaotanyan Street, Shapingba District, Chongqing, 400038, People's Republic of China.
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ALX4, an epigenetically down regulated tumor suppressor, inhibits breast cancer progression by interfering Wnt/β-catenin pathway. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2017; 36:170. [PMID: 29183346 PMCID: PMC5706407 DOI: 10.1186/s13046-017-0643-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2017] [Accepted: 11/20/2017] [Indexed: 12/29/2022]
Abstract
Background ALX4 is a paired-like homedomain transcription factor mainly expressed in the mesenchymal compartment of variety of developing tissues, but its functions, regulation mechanisms and clinical values in breast cancer remains unclear. Methods The expression of ALX4 in breast cancer cell lines and patients’ tissues were detected by RT-PCR, qPCR and western blot. Furthermore TCGA database was applied to confirm these results. MSP and BSP methods were used to assess the methylation of ALX4 promoter region. In vitro proliferation, metastasis and in vivo nude mice model were used to evaluate the anti-tumor effect of ALX4 on breast cancer cell lines. Luciferase reporter assay, western blot and TCGA database were used to investigate the tumor suppression mechanisms of ALX4. TMA of 142 breast patients was generated to evaluate the clinical significance of ALX4. Results Expression analysis revealed that ALX4 expression is down regulated in breast cancer cell lines and tissues. MSP study showed that the promoter region of ALX4 was hyper-methylated 100% (3/3) in breast cancer cell lines and 69.44% (75/108) in primary breast tumors tissues while 0% (0/8) in normal breast tissues. 5-aza-dc de-methylation treatment restored ALX4 expression in breast cancer cell lines. Functional studies showed that ectopic expression of ALX4 in breast cancer cells inhibited cell proliferation, metastasis in vitro and in vivo. Mechanism study found that ALX4 exerted its anti-tumor function by suppressing the Wnt/β-catenin pathway through promoting the phosphorylation degradation of β-catenin in a GSK3β dependent manner. Clinically multivariate analysis showed that ALX4 expression was an independent favorable prognostic factor in breast cancer patients. Conclusions We reveal for the first time that ALX4 acts as a novel functional tumor suppressor inactivated by DNA methylation and is an independent prognostic factor in breast cancer. Electronic supplementary material The online version of this article (10.1186/s13046-017-0643-9) contains supplementary material, which is available to authorized users.
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Chromosome copy number variation in telomerized human bone marrow stromal cells; insights for monitoring safe ex-vivo expansion of adult stem cells. Stem Cell Res 2017; 25:6-17. [PMID: 28988007 DOI: 10.1016/j.scr.2017.09.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Revised: 07/14/2017] [Accepted: 09/20/2017] [Indexed: 12/24/2022] Open
Abstract
Adult human bone marrow stromal cells (hBMSC) cultured for cell therapy require evaluation of potency and stability for safe use. Chromosomal aberrations upsetting genomic integrity in such cells have been contrastingly described as "Limited" or "Significant". Previously reported stepwise acquisition of a spontaneous neoplastic phenotype during three-year continuous culture of telomerized cells (hBMSC-TERT20) didn't alter a diploid karyotype measured by spectral karyotype analysis (SKY). Such screening may not adequately monitor abnormal and potentially tumorigenic hBMSC in clinical scenarios. We here used array comparative genomic hybridization (aCGH) to more stringently compare non-tumorigenic parental hBMSC-TERT strains with their tumorigenic subcloned populations. Confirmation of a known chromosome 9p21 microdeletion at locus CDKN2A/B, showed it also impinged upon the adjacent MTAP gene. Compared to reference diploid human fibroblast genomic DNA, the non-tumorigenic hBMSC-TERT4 cells had a copy number variation (CNV) in at least 14 independent loci. The pre-tumorigenic hBMSC-TERT20 cell strain had further CNV including 1q44 gain enhancing SMYD3 expression and 11q13.1 loss downregulating MUS81 expression. Bioinformatic analysis of gene products reflecting 11p15.5 CNV gain in tumorigenic hBMSC-TERT20 cells highlighted networks implicated in tumorigenic progression involving cell cycle control and mis-match repair. We provide novel biomarkers for prospective risk assessment of expanded stem cell cultures.
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Mahanty A, Purohit GK, Mohanty S, Nayak NR, Mohanty BP. Suitable reference gene for quantitative real-time PCR analysis of gene expression in gonadal tissues of minnow Puntius sophore under high-temperature stress. BMC Genomics 2017; 18:617. [PMID: 28810828 PMCID: PMC5557063 DOI: 10.1186/s12864-017-3974-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Accepted: 07/31/2017] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND High ambient temperature is known to affect fish gonadal development and physiology in a variety of ways depending on the severity and duration of exposure; however, the underlying molecular mechanisms are poorly understood. Gonadal gene expression influence the gonadal development, physiology and the quality of egg/sperm produced in teleosts and the mechanistic understanding of spatio-temporal changes in the gonadal gene expression could be instrumental in controlling the fate of egg/sperm and the quality of seed produced. Real time-quantititative polymerase chain reaction (RT-qCR), is a high throughput, sensitive and reproducible methodology used for understanding gene expression patterns by measuring the relative abundance of mRNA transcripts. However, its accuracy relies upon a suitable reference gene whose expression levels remain stable across various experimental conditions. In the present study, we evaluated the suitability of ten potential reference genes to be used as internal controls in RT-qPCR analysis in gonadal tissues (ovary and testis) of minnow Puntius sophore exposed to high temperature stress for different time periods (7 days, 60 days). Expression analysis of ten different constitutively expressed genes viz. 18S ribosomal RNA (18S rRNA), beta actin (βactin), β-2 microglobulin (b2mg), eukaryotic elongation factor-1 (eef1), glyceraldehyde-3phosphate dehydrogenase (gapdh), glucose-6-phosphate dehydrogenase (g6pd), ribosomal binding protein L13 (rpl13), tubulin (tub), tata box binding protein (tbp), ubiquitin (ubi) was carried out by using RT-qPCR and the stability in their expressions were evaluated by using four different algorithms; namely, delta Ct, BestKeeper, geNorm and NormFinder. RESULTS In ovary, eef1 was found to be the most suitable reference gene in all the algorithms used. In testis, b2mg was found to be the most suitable reference gene in delta Ct, BestKeeper, NormFinder analysis while tbp and eef1 were found to be the most suitable reference genes in geNorm analysis. CONCLUSIONS In conclusion, eef1 and b2mg were found to be the most suitable reference genes in ovary and testis, respectively, of Puntius sophore exposed to high temperature stress, and could be used as internal controls for gene expression analysis in gonadal tissues of Puntius sophore.
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Affiliation(s)
- Arabinda Mahanty
- Fishery Resource and Environmental Management Division, ICAR- Central Inland Fisheries Research Institute, Barrackpore, Kolkata, 700120, India
- School of Biotechnology, KIIT University, Bhubaneswar, Odisha, 751024, India
| | | | - Sasmita Mohanty
- School of Biotechnology, KIIT University, Bhubaneswar, Odisha, 751024, India.
| | - Nihar Ranjan Nayak
- Wayne State University Perinatal Initiative, Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI, 48201, USA.
| | - Bimal Prasanna Mohanty
- Fishery Resource and Environmental Management Division, ICAR- Central Inland Fisheries Research Institute, Barrackpore, Kolkata, 700120, India.
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Yang J, Han F, Liu W, Zhang M, Huang Y, Hao X, Jiang X, Yin L, Chen H, Cao J, Zhang H, Liu J. LHX6, An Independent Prognostic Factor, Inhibits Lung Adenocarcinoma Progression through Transcriptional Silencing of β-catenin. J Cancer 2017; 8:2561-2574. [PMID: 28900494 PMCID: PMC5595086 DOI: 10.7150/jca.19972] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 06/10/2017] [Indexed: 12/27/2022] Open
Abstract
Introduction: Our previous study identified LIM homeobox domain 6 (LHX6) as a frequently epigenetically silenced tumor-suppressor gene in lung cancer. However, its clinical value has never been evaluated, and the in-depth anti-tumor mechanism remains unclear. Methods: Public database was used for lung cancer, lung adenocarcinoma and lung squamous carcinoma patients and tissue microarray data was used for lung adenocarcinoma patients to study prognostic outcome of LHX6 expression by Kaplan-Meier and Cox-regression analysis. In vitro proliferation, metastasis and in vivo nude mice model were used to evaluate the anti-tumor effect of LHX6 on lung adenocarcinoma cell lines. The mechanisms were explored using western blot, TOP/FOP flash assays and luciferase reporter assays. LHX6 expression and clinical stages data were collected from The Cancer Genome Atlas database (TCGA). Results: Expression of LHX6 was found to be a favorable independent prognostic factor for overall survival (OS) of total lung adenocarcinoma patients (P=0.014) and patients with negative lymph nodes status (P=0.014) but not related the prognostic outcome of lung squamous cell carcinoma patients. The expression status of LHX6 significantly correlated to histological grade (P<0.01), tumor size (P=0.026), lymph node status (P=0.039) and clinical stages (P<0.01) of lung adenocarcinoma patients. Functionally, LHX6 inhibited the proliferation and metastasis of lung adenocarcinoma cells in vitro and in vivo. Furthermore, LHX6 suppressed the Wnt/β-catenin pathway through transcriptionally silencing the expression of β-catenin, and the promoter region (-1161 bp to +27 bp) was crucial for its inhibitory activity. Conclusions: Our data indicate that the expression of LHX6 may serve as a favorable prognostic biomarker for lung adenocarcinoma patients and provide a novel mechanism of LHX6 involving in the tumorigenesis of lung adenocarcinoma.
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Affiliation(s)
- Juntang Yang
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University, Chongqing 400038, PR China
| | - Fei Han
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University, Chongqing 400038, PR China
| | - Wenbin Liu
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University, Chongqing 400038, PR China
| | - Mingqian Zhang
- Department of emergency, Yan'an Hospital, Kunming Medical University, Kunming 650500, PR China
| | - Yongsheng Huang
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University, Chongqing 400038, PR China
| | - Xianglin Hao
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University, Chongqing 400038, PR China
| | - Xiao Jiang
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University, Chongqing 400038, PR China
| | - Li Yin
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University, Chongqing 400038, PR China
| | - Hongqiang Chen
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University, Chongqing 400038, PR China
| | - Jia Cao
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University, Chongqing 400038, PR China
| | - Huidong Zhang
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University, Chongqing 400038, PR China
| | - Jinyi Liu
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University, Chongqing 400038, PR China
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Kawarai T, Montecchiani C, Miyamoto R, Gaudiello F, Caltagirone C, Izumi Y, Kaji R, Orlacchio A. Spastic paraplegia type 4: A novel SPAST splice site donor mutation and expansion of the phenotype variability. J Neurol Sci 2017; 380:92-97. [PMID: 28870597 DOI: 10.1016/j.jns.2017.07.011] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Revised: 06/29/2017] [Accepted: 07/06/2017] [Indexed: 01/30/2023]
Abstract
Mutations in SPG4/SPAST are the most frequent molecular aetiology in the autosomal dominant form of hereditary spastic paraplegia (HSP). Loss-of-function and haploinsufficiency in SPAST have been demonstrated and the pure form of spastic paraplegia is a main clinical manifestation. This study is to explore the novel SPAST splice site donor variant, c.1004+3A>C, in seven patients from two families, one from Italy and the other from Japan. Exon 6 is skipped out by the variant, leading to a premature termination of translation, p.Gly290Trpfs*5. Measurement of SPAST transcripts in lymphocytes demonstrated a reduction through nonsense-mediated mRNA decay (NMD). Intra- and inter-familial phenotypic variations were observed, including age-at-onset, severity of spasticity, and scoliosis. Our study demonstrated further evidence of allelic heterogeneity in SPG4, dosage effects through NMD, and broad clinical features of the SPAST mutation.
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Affiliation(s)
- Toshitaka Kawarai
- Department of Clinical Neuroscience, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, 770-0042, Japan.
| | - Celeste Montecchiani
- Laboratorio di Neurogenetica, Centro Europeo di Ricerca sul Cervello (CERC) - Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Santa Lucia, Rome, Italy; Dipartimento di Scienze Chirurgiche e Biomediche, Università di Perugia, Perugia, Italy
| | - Ryosuke Miyamoto
- Department of Clinical Neuroscience, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, 770-0042, Japan
| | - Fabrizio Gaudiello
- Laboratorio di Neurogenetica, Centro Europeo di Ricerca sul Cervello (CERC) - Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Santa Lucia, Rome, Italy
| | - Carlo Caltagirone
- Laboratorio di Neurologia Clinica e Comportamentale, IRCCS Santa Lucia, Rome, Italy; Dipartimento di Medicina dei Sistemi, Università di Roma "Tor Vergata", Rome, Italy
| | - Yuishin Izumi
- Department of Clinical Neuroscience, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, 770-0042, Japan
| | - Ryuji Kaji
- Department of Clinical Neuroscience, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, 770-0042, Japan
| | - Antonio Orlacchio
- Laboratorio di Neurogenetica, Centro Europeo di Ricerca sul Cervello (CERC) - Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Santa Lucia, Rome, Italy; Dipartimento di Scienze Chirurgiche e Biomediche, Università di Perugia, Perugia, Italy.
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19
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Wysokinski WE, Tafur A, Ammash N, Asirvatham SJ, Wu Y, Gosk-Bierska I, Grill DE, Slusser JP, Mruk J, McBane RD. Impact of atrial fibrillation on platelet gene expression. Eur J Haematol 2017; 98:615-621. [PMID: 28306170 DOI: 10.1111/ejh.12879] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/08/2017] [Indexed: 02/01/2023]
Abstract
AIMS Platelets retain cytoplasmic messenger RNA and are capable of protein biosynthesis. Several diseases are known to impact the platelet transcriptome but the effect of non-valvular atrial fibrillation (NVAF) on platelet RNA transcript is essentially unknown. The aim of this study was to evaluate the impact of NVAF on platelet RNA transcript by measuring platelet genes expression in consecutive NVAF patients before and 3-4 months after pulmonary vein isolation (PVI) and compared to normal sinus rhythm controls (NSR). METHODS AND RESULTS RNA from isolated platelets were reverse transcribed, assayed against 15 genes using real-time qPCR, and expressed as mean cycle threshold (ΔCt) using beta-2-microglobulin as endogenous control. Expression of all evaluated genes, except cathepsin A gene, was significantly lower (higher ΔCt) in 103 NVAF patients compared to 55 NSR controls. Insulin-like growth factor binding protein acid labile subunit gene (IGFALS) had expression more than 16 fold-lower (17.0±2.8 vs 12.5±3.8, P<.001), follow by genes encoding for prostacyclin receptor, and for von Willebrand factor which had fourfold lower expression compared to NSR controls. Gender, type of atrial fibrillation, heart failure, hypertension, prior stroke, diabetes mellitus, and atherosclerosis were associated with different gene expression. Following PVI, expression of four genes significantly increased, particularly IGFALS gene (increased 256-fold) and ADAMT gene increased 16-fold); expression of three genes significantly decreased, and expression of eight genes has not changed. CONCLUSIONS Platelets are capable to respond to the circulatory environment of NVAF by altering transcript and changing prothrombotic status. This shows platelet potential for molecular "reprogramming" possibly induced by flow disturbances of NVAF.
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Affiliation(s)
| | - Alfonso Tafur
- Department of Cardiovascular Medicine, Vascular Surgery and Medicine Section, NorthShore University HealthSystem, Skokie, USA
| | - Naser Ammash
- Mayo Clinic and Foundation for Education and Research, Rochester, MN, USA
| | | | - Yanhong Wu
- Mayo Clinic and Foundation for Education and Research, Rochester, MN, USA
| | | | - Diane E Grill
- Mayo Clinic and Foundation for Education and Research, Rochester, MN, USA
| | - Joshua P Slusser
- Mayo Clinic and Foundation for Education and Research, Rochester, MN, USA
| | - Jozef Mruk
- Department of Internal Medicine, University of Kansas, School of Medicine-Wichita, Wichita, KS, USA
| | - Robert D McBane
- Mayo Clinic and Foundation for Education and Research, Rochester, MN, USA
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20
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Simpson SD, Ramsdell JS, Watson III WH, Chabot CC. The Draft Genome and Transcriptome of the Atlantic Horseshoe Crab, Limulus polyphemus. Int J Genomics 2017; 2017:7636513. [PMID: 28265565 PMCID: PMC5317147 DOI: 10.1155/2017/7636513] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2016] [Accepted: 12/28/2016] [Indexed: 01/21/2023] Open
Abstract
The horseshoe crab, Limulus polyphemus, exhibits robust circadian and circatidal rhythms, but little is known about the molecular mechanisms underlying those rhythms. In this study, horseshoe crabs were collected during the day and night as well as high and low tides, and their muscle and central nervous system tissues were processed for genome and transcriptome sequencing, respectively. The genome assembly resulted in 7.4 × 105 contigs with N50 of 4,736, while the transcriptome assembly resulted in 9.3 × 104 contigs and N50 of 3,497. Analysis of functional completeness by the identification of putative universal orthologs suggests that the transcriptome has three times more total expected orthologs than the genome. Interestingly, RNA-Seq analysis indicated no statistically significant changes in expression level for any circadian core or accessory gene, but there was significant cycling of several noncircadian transcripts. Overall, these assemblies provide a resource to investigate the Limulus clock systems and provide a large dataset for further exploration into the taxonomy and biology of the Atlantic horseshoe crab.
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Affiliation(s)
- Stephen D. Simpson
- Hubbard Center for Genome Studies, University of New Hampshire, Durham, NH 03824, USA
| | - Jordan S. Ramsdell
- Hubbard Center for Genome Studies, University of New Hampshire, Durham, NH 03824, USA
| | - Winsor H. Watson III
- Department of Biological Sciences, University of New Hampshire, Durham, NH 03824, USA
| | - Christopher C. Chabot
- Department of Biological Sciences, MSC#64, Plymouth State University, Plymouth, NH 03264, USA
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21
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Ohashi Y, Kumagai K, Miyata Y, Matsubara R, Kitaura K, Suzuki S, Hamada Y, Suzuki R. Overexpression of ErbB4 is an independent marker for lymph node metastasis in Japanese patients with oral squamous cell carcinoma. Oral Surg Oral Med Oral Pathol Oral Radiol 2016; 122:313-21. [DOI: 10.1016/j.oooo.2016.04.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Revised: 04/23/2016] [Accepted: 04/28/2016] [Indexed: 11/30/2022]
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22
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Chen G, Zou Y, Zhang X, Xu L, Hu Q, Li T, Yao C, Yu S, Wang X, Wang C. β-Actin protein expression differs in the submandibular glands of male and female mice. Cell Biol Int 2016; 40:779-86. [PMID: 27079296 DOI: 10.1002/cbin.10613] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 04/10/2016] [Indexed: 12/15/2022]
Abstract
β-actin, a cytoskeletal protein, is the most widely used housekeeping gene. Although housekeeping genes are expressed in all tissues, the β-actin gene is expressed in certain cell types because of differential binding of transcriptional factors to the regulatory elements of the gene. The expression and localization of β-actin protein in the submandibular glands (SMG) of mice were investigated in this study, using Western blot analysis and immunohistochemistry. In ICR and C57BL/6J mice, the levels of β-actin protein in the SMG of females are significantly higher than those in the SMG of males. β-actin protein is majorly distributed in acinar cells of SMG. There is no significant difference in the expression level of β-actin protein between females and castrated males. After castrated male ICR mice are treated with 10 mg/kg/day testosterone propionate (TP) for 3 weeks, the levels of β-actin protein in SMG decrease. The numbers of duct per unit area increase, whereas the numbers of acinus per unit area decrease after TP administration. These data suggest that β-actin protein is mainly distributed in acinar cells of SMG and results in a marked sexual dimorphism in mice.
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Affiliation(s)
- Gang Chen
- Department of Environmental Health, School of Public Health, Nantong University, Nantong, 226007, Jiangsu, China
| | - Ye Zou
- Department of Environmental Health, School of Public Health, Nantong University, Nantong, 226007, Jiangsu, China
| | - Xuan Zhang
- Shanghai Public Health Clinical Center, Shanghai, 201508, Shanghai, China
| | - Lingfei Xu
- Department of Environmental Health, School of Public Health, Nantong University, Nantong, 226007, Jiangsu, China
| | - Qiaoyun Hu
- Department of Environmental Health, School of Public Health, Nantong University, Nantong, 226007, Jiangsu, China
| | - Ting Li
- Department of Environmental Health, School of Public Health, Nantong University, Nantong, 226007, Jiangsu, China
| | - Chenjuan Yao
- Department of Environmental Health, School of Public Health, Nantong University, Nantong, 226007, Jiangsu, China
| | - Shali Yu
- Department of Environmental Health, School of Public Health, Nantong University, Nantong, 226007, Jiangsu, China
| | - Xiaoke Wang
- Department of Environmental Health, School of Public Health, Nantong University, Nantong, 226007, Jiangsu, China
| | - Chun Wang
- Department of Environmental Health, School of Public Health, Nantong University, Nantong, 226007, Jiangsu, China
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Nagaoka T, Kitaura K, Miyata Y, Kumagai K, Kaneda G, Kanazawa H, Suzuki S, Hamada Y, Suzuki R. Downregulation of epidermal growth factor receptor family receptors and ligands in a mutant K-ras group of patients with colorectal cancer. Mol Med Rep 2016; 13:3514-20. [PMID: 26935861 DOI: 10.3892/mmr.2016.4951] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Accepted: 09/03/2015] [Indexed: 11/06/2022] Open
Abstract
The present study investigated the expression profiles of the epidermal growth factor receptor (EGFR) family, which consists of four transmembrane tyrosine kinase receptors and their eight ligands, in 122 patients with colorectal cancer (CRC) using reverse transcription-quantitative polymerase chain reaction analysis. On comparison of the CRC primary tumor and matched adjacent normal mucosa (ANM) tissue samples, the mRNA expression levels of ErbB3, but not ErbB1, were significantly increased in CRC tissue samples, compared with those in the ANM tissues. The expression levels of the ligands exhibited opposing trends to their corresponding receptors, including EGF, BTC, AREG, EREG and HB‑EGF, which were increased in the CRC tissues, whereas NRG1 and NGR2 were decreased in thee CRC tissues, compared with those in the AMN tissues. Subsequently, the present study investigated the frequency of K-ras mutations in the patients with CRC. The K‑ras mutations were found to be present in 36.8% (45/122) of the cases, however, no correlation was observed between K‑ras mutations and clinicopathological characteristics. In the CRC tissues, the expression levels of the EGFR family receptors and their ligands were determined in wild-type and mutant K-ras CRC cases. The expression levels of ErbB1, ErbB2, ErbB3, BTC, AREG, EREG, NRG1 and NRG2 were significantly decreased in the mutant K‑ras cases, compared with those in the wild‑type K‑ras cases. These results suggested that the tumorigenesis of CRC with wild‑type K‑ras was mediated through, not only ErbB1, but also through the ErbB2 and ErbB3 pathways. Notably, although ErbB2 does not bind any ErbB ligands, ErbB2 may activate tumorigenesis via a heterodimer, rather than a homodimer. Therefore, the results of the present study suggest that the most effective strategy to target not only ErbB1, but also ErbB2 and ErbB3, is the use of monoclonal antibody treatment.
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Affiliation(s)
- Tomoko Nagaoka
- Department of Oral and Maxillofacial Surgery, School of Dental Medicine, Tsurumi University, Tsurumi‑ku, Yokohama 230‑8501, Japan
| | - Kazutaka Kitaura
- Department of Rheumatology and Clinical Immunology, Clinical Research Center for Rheumatology and Allergy, Sagamihara National Hospital, National Hospital Organization, Sagamihara, Kanagawa 252‑0392, Japan
| | - Yukinaga Miyata
- Department of Oral and Maxillofacial Surgery, School of Dental Medicine, Tsurumi University, Tsurumi‑ku, Yokohama 230‑8501, Japan
| | - Kenichi Kumagai
- Department of Oral and Maxillofacial Surgery, School of Dental Medicine, Tsurumi University, Tsurumi‑ku, Yokohama 230‑8501, Japan
| | - Goro Kaneda
- Department of Surgery, Sagamihara National Hospital, National Hospital Organization, Sagamihara, Kanagawa 252‑0392, Japan
| | - Hideki Kanazawa
- Department of Surgery, Sagamihara National Hospital, National Hospital Organization, Sagamihara, Kanagawa 252‑0392, Japan
| | - Satsuki Suzuki
- Section of Biological Science, Research Center for Odontology, Nippon Dental University, School of Dentistry, Chiyoda‑ku, Tokyo 102‑0071, Japan
| | - Yoshiki Hamada
- Department of Oral and Maxillofacial Surgery, School of Dental Medicine, Tsurumi University, Tsurumi‑ku, Yokohama 230‑8501, Japan
| | - Ryuji Suzuki
- Department of Rheumatology and Clinical Immunology, Clinical Research Center for Rheumatology and Allergy, Sagamihara National Hospital, National Hospital Organization, Sagamihara, Kanagawa 252‑0392, Japan
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Borowska D, Rothwell L, Bailey RA, Watson K, Kaiser P. Identification of stable reference genes for quantitative PCR in cells derived from chicken lymphoid organs. Vet Immunol Immunopathol 2016; 170:20-4. [PMID: 26872627 DOI: 10.1016/j.vetimm.2016.01.001] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Revised: 12/21/2015] [Accepted: 01/05/2016] [Indexed: 12/20/2022]
Abstract
Quantitative polymerase chain reaction (qPCR) is a powerful technique for quantification of gene expression, especially genes involved in immune responses. Although qPCR is a very efficient and sensitive tool, variations in the enzymatic efficiency, quality of RNA and the presence of inhibitors can lead to errors. Therefore, qPCR needs to be normalised to obtain reliable results and allow comparison. The most common approach is to use reference genes as internal controls in qPCR analyses. In this study, expression of seven genes, including β-actin (ACTB), β-2-microglobulin (B2M), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), β-glucuronidase (GUSB), TATA box binding protein (TBP), α-tubulin (TUBAT) and 28S ribosomal RNA (r28S), was determined in cells isolated from chicken lymphoid tissues and stimulated with three different mitogens. The stability of the genes was measured using geNorm, NormFinder and BestKeeper software. The results from both geNorm and NormFinder were that the three most stably expressed genes in this panel were TBP, GAPDH and r28S. BestKeeper did not generate clear answers because of the highly heterogeneous sample set. Based on these data we will include TBP in future qPCR normalisation. The study shows the importance of appropriate reference gene normalisation in other tissues before qPCR analysis.
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Affiliation(s)
- D Borowska
- The Roslin Institute and R(D)SVS, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, United Kingdom.
| | - L Rothwell
- The Roslin Institute and R(D)SVS, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, United Kingdom
| | - R A Bailey
- Aviagen Ltd., Edinburgh EH28 8SZ, United Kingdom
| | - K Watson
- Aviagen Ltd., Edinburgh EH28 8SZ, United Kingdom
| | - P Kaiser
- The Roslin Institute and R(D)SVS, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, United Kingdom
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25
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Late-onset spastic paraplegia: Aberrant SPG11 transcripts generated by a novel splice site donor mutation. J Neurol Sci 2015; 359:250-5. [DOI: 10.1016/j.jns.2015.10.045] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2015] [Revised: 10/14/2015] [Accepted: 10/22/2015] [Indexed: 12/12/2022]
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26
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Nazari F, Parham A, Maleki AF. GAPDH, β-actin and β2-microglobulin, as three common reference genes, are not reliable for gene expression studies in equine adipose- and marrow-derived mesenchymal stem cells. JOURNAL OF ANIMAL SCIENCE AND TECHNOLOGY 2015; 57:18. [PMID: 26290738 PMCID: PMC4540241 DOI: 10.1186/s40781-015-0050-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Accepted: 04/15/2015] [Indexed: 01/16/2023]
Abstract
Background Quantitative real time reverse transcription PCR (qRT-PCR) is one of the most important techniques for gene-expression analysis in molecular based studies. Selecting a proper internal control gene for normalizing data is a crucial step in gene expression analysis via this method. The expression levels of reference genes should be remained constant among cells in different tissues. However, it seems that the location of cells in different tissues might influence their expression. The purpose of this study was to determine whether the source of mesenchymal stem cells (MSCs) has any effect on expression level of three common reference genes (GAPDH, β-actin and β2-microglobulin) in equine marrow- and adipose- derived undifferentiated MSCs and consequently their reliability for comparative qRT-PCR. Materials and methods Adipose tissue (AT) and bone marrow (BM) samples were harvested from 3 mares. MSCs were isolated and cultured until passage 3 (P3). Total RNA of P3 cells was extracted for cDNA synthesis. The generated cDNAs were analyzed by quantitative real-time PCR. The PCR reactions were ended with a melting curve analysis to verify the specificity of amplicon. Results The expression levels of GAPDH were significantly different between AT- and BM- derived MSCs (p < 0.05). Differences in expression level of β-actin (P < 0.001) and B2M (P < 0.006.) between MSCs derived from AT and BM were substantially higher than GAPDH. In addition, the fold change in expression levels of GAPDH, β-actin and B2M in AT-derived MSCs compared to BM-derived MSCs were 2.38, 6.76 and 7.76, respectively. Conclusion This study demonstrated that GAPDH and especially β-actin and B2M express in different levels in equine AT- and BM- derived MSCs. Thus they cannot be considered as reliable reference genes for comparative quantitative gene expression analysis in MSCs derived from equine bone marrow and adipose tissue.
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Affiliation(s)
- Fatemeh Nazari
- Division of Physiology, Department of Basic Sciences, Veterinary Faculty, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Abbas Parham
- Division of Physiology, Department of Basic Sciences, Veterinary Faculty, Ferdowsi University of Mashhad, Mashhad, Iran ; Embryonic and Stem Cell Biology and Biotechnology Research Group, Institute of Biotechnology, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Adham Fani Maleki
- Division of Physiology, Department of Basic Sciences, Veterinary Faculty, Ferdowsi University of Mashhad, Mashhad, Iran
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27
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Blok DC, Kager LM, Hoogendijk AJ, Lede IO, Rahman W, Afroz R, Bresser P, van der Zee JS, Ghose A, Visser CE, de Jong MD, Zahed ASM, Husain MA, Alam KM, Barua PC, Hassan M, Hossain A, Tayab MA, Lutter R, Day N, Dondorp AM, de Vos AF, van 't Veer C, van der Poll T. Expression of inhibitory regulators of innate immunity in patients with active tuberculosis. BMC Infect Dis 2015; 15:98. [PMID: 25887604 PMCID: PMC4365962 DOI: 10.1186/s12879-015-0833-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Accepted: 02/12/2015] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Tuberculosis (TB) is an important cause of morbidity and mortality worldwide. Toll-like-receptors (TLRs) are important for the recognition of the causative agent Mycobacterium tuberculosis. Negative regulation of TLRs is necessary to control deleterious inflammatory damage, but could provide a means of immune evasion by M. tuberculosis as well. METHODS To obtain insight in the extent of expression of inhibitory regulators of immunity in patients with active TB, peripheral-blood-mononuclear-cells (PBMCs) and plasma were obtained from 54 TB patients and 29 healthy blood donors from Chittagong, Bangladesh. Bilateral alveolar macrophages were obtained from an infected versus a contralateral normal lung segment of 9 patients. Statistical analyses were performed using Mann-Whitney U and Wilcoxon matched pairs testing. Correlations were calculated using the Spearman rho test. RESULTS PBMCs harvested from TB patients demonstrated increased mRNA expression of IL-1-receptor-associated-kinase-M, suppressor-of-cytokine-signalling-3 and Toll-interacting-protein. Flow cytometry revealed enhanced expression of IL-1-receptor-like-1 (ST2) on lymphocytes. Plasma soluble ST2 was elevated in patients with TB and correlated with established TB biomarkers, most strongly with soluble interleukin-2 receptor subunit α and interleukin-8. Alveolar macrophage mRNA expression of negative TLR regulators did not differ between the infected and contralateral lung side. CONCLUSION These results show enhanced expression of distinct negative regulators of innate immunity in PBMCs of patients with TB and identify plasma soluble ST2 as a potential novel biomarker for TB disease activity.
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Affiliation(s)
- Dana C Blok
- Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center/ University of Amsterdam, Amsterdam, The Netherlands. .,Center for Experimental and Molecular Medicine (CEMM), Academic Medical Center/ University of Amsterdam, Amsterdam, The Netherlands.
| | - Liesbeth M Kager
- Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center/ University of Amsterdam, Amsterdam, The Netherlands. .,Center for Experimental and Molecular Medicine (CEMM), Academic Medical Center/ University of Amsterdam, Amsterdam, The Netherlands.
| | - Arie J Hoogendijk
- Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center/ University of Amsterdam, Amsterdam, The Netherlands. .,Center for Experimental and Molecular Medicine (CEMM), Academic Medical Center/ University of Amsterdam, Amsterdam, The Netherlands.
| | - Ivar O Lede
- Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center/ University of Amsterdam, Amsterdam, The Netherlands. .,Department of Microbiology, Academic Medical Center/ University of Amsterdam, Amsterdam, The Netherlands.
| | - Wahid Rahman
- Department of Internal Medicine, Chittagong Medical College and Hospital (CMCH), Chittagong, Bangladesh.
| | - Rumana Afroz
- Department of Internal Medicine, Chittagong Medical College and Hospital (CMCH), Chittagong, Bangladesh.
| | - Paul Bresser
- Department of Pulmonology, Academic Medical Center/ University of Amsterdam, Amsterdam, The Netherlands. .,Department of Pulmonology, Chittagong Medical College and Hospital (CMCH), Chittagong, Bangladesh.
| | - Jaring S van der Zee
- Department of Pulmonology, Academic Medical Center/ University of Amsterdam, Amsterdam, The Netherlands. .,Department of Pulmonology, Chittagong Medical College and Hospital (CMCH), Chittagong, Bangladesh.
| | - Aniruddha Ghose
- Department of Internal Medicine, Chittagong Medical College and Hospital (CMCH), Chittagong, Bangladesh.
| | - Caroline E Visser
- Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center/ University of Amsterdam, Amsterdam, The Netherlands. .,Department of Microbiology, Academic Medical Center/ University of Amsterdam, Amsterdam, The Netherlands.
| | - Menno D de Jong
- Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center/ University of Amsterdam, Amsterdam, The Netherlands. .,Department of Microbiology, Academic Medical Center/ University of Amsterdam, Amsterdam, The Netherlands.
| | - Abu Shahed Md Zahed
- Department of Internal Medicine, Chittagong Medical College and Hospital (CMCH), Chittagong, Bangladesh.
| | - Md Anwar Husain
- Department of Microbiology, Chittagong Medical College and Hospital (CMCH), Chittagong, Bangladesh.
| | - Khan Mashrequl Alam
- Department of Microbiology, Chittagong Medical College and Hospital (CMCH), Chittagong, Bangladesh.
| | | | - Mahtabuddin Hassan
- Department of Internal Medicine, Chittagong Medical College and Hospital (CMCH), Chittagong, Bangladesh.
| | - Ahmed Hossain
- Chest Disease Clinic Chittagong (CDCC), Chittagong, Bangladesh
| | - Md Abu Tayab
- Chittagong General Hospital, Chittagong, Bangladesh.
| | - Rene Lutter
- Department of Pulmonology, Academic Medical Center/ University of Amsterdam, Amsterdam, The Netherlands. .,Department of Experimental Immunology, Onze Lieve Vrouwe Gasthuis, Amsterdam, The Netherlands.
| | - Nick Day
- Mahidol Oxford Tropical Research Unit, Mahidol University, Bangkok, Thailand.
| | - Arjen M Dondorp
- Mahidol Oxford Tropical Research Unit, Mahidol University, Bangkok, Thailand.
| | - Alex F de Vos
- Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center/ University of Amsterdam, Amsterdam, The Netherlands. .,Center for Experimental and Molecular Medicine (CEMM), Academic Medical Center/ University of Amsterdam, Amsterdam, The Netherlands.
| | - Cornelis van 't Veer
- Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center/ University of Amsterdam, Amsterdam, The Netherlands. .,Center for Experimental and Molecular Medicine (CEMM), Academic Medical Center/ University of Amsterdam, Amsterdam, The Netherlands.
| | - Tom van der Poll
- Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center/ University of Amsterdam, Amsterdam, The Netherlands. .,Center for Experimental and Molecular Medicine (CEMM), Academic Medical Center/ University of Amsterdam, Amsterdam, The Netherlands. .,Division of Infectious Diseases, Academic Medical Center/ University of Amsterdam, Amsterdam, The Netherlands.
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Khan SA, Tyagi M, Sharma AK, Barreto SG, Sirohi B, Ramadwar M, Shrikhande SV, Gupta S. Cell-type specificity of β-actin expression and its clinicopathological correlation in gastric adenocarcinoma. World J Gastroenterol 2014; 20:12202-12211. [PMID: 25232253 PMCID: PMC4161804 DOI: 10.3748/wjg.v20.i34.12202] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/14/2013] [Revised: 03/13/2014] [Accepted: 05/26/2014] [Indexed: 02/06/2023] Open
Abstract
AIM: To investigate cell type specific distribution of β-actin expression in gastric adenocarcinoma and its correlation with clinicopathological parameters.
METHODS: β-actin is a housekeeping gene, frequently used as loading control, but, differentially expresses in cancer. In gastric cancer, an overall increased expression of β-actin has been reported using tissue disruptive techniques. At present, no histological data is available to indicate its cell type-specific expression and distribution pattern. In the present study, we analyzed β-actin expression and distribution in paired normal and tumor tissue samples of gastric adenocarcinoma patients using immunohistochemistry (IHC), a tissue non-disruptive technique as well as tissue disruptive techniques like reverse transcriptase-polymerase chain reaction (RT-PCR) and western blotting. Correlation of β-actin level with clinicopathological parameters was done using univariate analysis.
RESULTS: The results of this study showed significant overexpression, at both mRNA and protein level in tumor tissues as confirmed by RT-PCR (1.47 ± 0.13 vs 2.36 ± 0.16; P < 0.001) and western blotting (1.92 ± 0.26 vs 2.88 ± 0.32; P < 0.01). IHC revealed that β-actin expression is majorly distributed between epithelial and inflammatory cells of the tissues. Inflammatory cells showed a significantly higher expression compared to epithelial cells in normal (2.46 ± 0.13 vs 5.92 ± 0.23, P < 0.001), as well as, in tumor tissues (2.79 ± 0.24 vs 6.71 ± 0.14, P < 0.001). Further, comparison of immunostaining between normal and tumor tissues revealed that both epithelial and inflammatory cells overexpress β-actin in tumor tissues, however, significant difference was observed only in inflammatory cells (5.92 ± 0.23 vs 6.71 ± 0.14, P < 0.01). Moreover, combined expression in epithelial and inflammatory cells also showed significant increase (4.19 ± 0.15 vs 4.75 ± 0.14, P < 0.05) in tumor tissues. In addition, univariate analysis showed a positive correlation of β-actin level of inflammatory cells with tumor grade (P < 0.05) while epithelial cells exhibited negative correlation (P > 0.05).
CONCLUSION: In gastric cancer, β-actin showed an overall higher expression predominantly contributed by inflammatory or tumor infiltrating immune cells of the tissue microenvironment and correlates with tumor grade.
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Vossaert L, O'Leary T, Van Neste C, Heindryckx B, Vandesompele J, De Sutter P, Deforce D. Reference loci for RT-qPCR analysis of differentiating human embryonic stem cells. BMC Mol Biol 2013; 14:21. [PMID: 24028740 PMCID: PMC3848990 DOI: 10.1186/1471-2199-14-21] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2012] [Accepted: 09/11/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Selecting stably expressed reference genes is essential for proper reverse transcription quantitative polymerase chain reaction gene expression analysis. However, this choice is not always straightforward. In the case of differentiating human embryonic stem (hES) cells, differentiation itself introduces changes whereby reference gene stability may be influenced. RESULTS In this study, we evaluated the stability of various references during retinoic acid-induced (2 microM) differentiation of hES cells. Out of 12 candidate references, beta-2-microglobulin, ribosomal protein L13A and Alu repeats are found to be the most stable for this experimental set-up. CONCLUSIONS Our results show that some of the commonly used reference genes are actually not amongst the most stable loci during hES cell differentiation promoted by retinoic acid. Moreover, a novel normalization strategy based on expressed Alu repeats is validated for use in hES cell experiments.
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Affiliation(s)
- Liesbeth Vossaert
- Laboratory for Pharmaceutical Biotechnology, Ghent University, Harelbekestraat 72, Ghent 9000, Belgium.
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Brown-Borg HM, Rakoczy S. Metabolic adaptations to short-term every-other-day feeding in long-living Ames dwarf mice. Exp Gerontol 2013; 48:905-19. [PMID: 23832075 DOI: 10.1016/j.exger.2013.06.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2013] [Revised: 06/24/2013] [Accepted: 06/27/2013] [Indexed: 10/26/2022]
Abstract
Restrictive dietary interventions exert significant beneficial physiological effects in terms of aging and age-related disease in many species. Every other day feeding (EOD) has been utilized in aging research and shown to mimic many of the positive outcomes consequent with dietary restriction. This study employed long living Ames dwarf mice subjected to EOD feeding to examine the adaptations of the oxidative phosphorylation and antioxidative defense systems to this feeding regimen. Every other day feeding lowered liver glutathione (GSH) concentrations in dwarf and wild type (WT) mice but altered GSH biosynthesis and degradation in WT mice only. The activities of liver OXPHOS enzymes and corresponding proteins declined in WT mice fed EOD while in dwarf animals, the levels were maintained or increased with this feeding regimen. Antioxidative enzymes were differentially affected depending on the tissue, whether proliferative or post-mitotic. Gene expression of components of liver methionine metabolism remained elevated in dwarf mice when compared to WT mice as previously reported however, enzymes responsible for recycling homocysteine to methionine were elevated in both genotypes in response to EOD feeding. The data suggest that the differences in anabolic hormone levels likely affect the sensitivity of long living and control mice to this dietary regimen, with dwarf mice exhibiting fewer responses in comparison to WT mice. These results provide further evidence that dwarf mice may be better protected against metabolic and environmental perturbations which may in turn, contribute to their extended longevity.
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Affiliation(s)
- Holly M Brown-Borg
- Department of Pharmacology, Physiology and Therapeutics, University of North Dakota School of Medicine and Health Sciences, Grand Forks, ND 58202, USA.
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Selection of stable reference genes in heat stressed peripheral blood mononuclear cells of tropically adapted Indian cattle and buffaloes. Mol Cell Probes 2013; 27:140-4. [DOI: 10.1016/j.mcp.2013.02.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2012] [Revised: 02/26/2013] [Accepted: 02/26/2013] [Indexed: 11/19/2022]
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Guo C, Liu S, Wang J, Sun MZ, Greenaway FT. ACTB in cancer. Clin Chim Acta 2012; 417:39-44. [PMID: 23266771 DOI: 10.1016/j.cca.2012.12.012] [Citation(s) in RCA: 106] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2012] [Revised: 11/27/2012] [Accepted: 12/01/2012] [Indexed: 01/27/2023]
Abstract
Beta-actin (ACTB) has traditionally been regarded as an endogenous housekeeping gene and has been widely used as a reference gene/protein in quantifying expression levels in tumors. However, ACTB is closely associated with a variety of cancers and accumulating evidence indicates that ACTB is de-regulated in liver, melanoma, renal, colorectal, gastric, pancreatic, esophageal, lung, breast, prostate, ovarian cancers, leukemia and lymphoma. ACTB is generally found to be up-regulated in the majority of tumor cells and tissues. The abnormal expression and polymerization of ACTB and the resulting changes to the cytoskeleton are revealed to be associated with the invasiveness and metastasis of cancers. The current review explores relevant mechanisms, integrates current understandings, and provides suggestions for future studies of the roles of ACTB in tumors.
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Affiliation(s)
- Chunmei Guo
- Department of Biotechnology, Dalian Medical University, Dalian 116044, China
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Apparent versus true gene expression changes of three hypoxia-related genes in autopsy derived tissue and the importance of normalisation. Int J Legal Med 2012; 127:335-44. [DOI: 10.1007/s00414-012-0787-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2012] [Accepted: 10/16/2012] [Indexed: 01/21/2023]
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Housekeeping gene selection advisory: glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and β-actin are targets of miR-644a. PLoS One 2012; 7:e47510. [PMID: 23091630 PMCID: PMC3472982 DOI: 10.1371/journal.pone.0047510] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2012] [Accepted: 09/12/2012] [Indexed: 12/17/2022] Open
Abstract
Results of overexpression or downregulation of a microRNA (miRNA) on its target mRNA expression are often validated by reverse-transcription and quantitative PCR analysis using an appropriate housekeeping gene as an internal control. The possible direct or indirect effects of a miRNA on the expression of housekeeping genes are often overlooked. Among many housekeeping genes, expressions of glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and β-actin have been used extensively for normalization of gene expression data. Here, we show that GAPDH and β-actin are direct targets of miR-644a. Our data demonstrate the unsuitability of GAPDH and β-actin as internal controls in miR-644a functional studies and emphasize the need to carefully consider the choice of a reference gene in miRNA experiments.
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Mendu SK, Bhandage A, Jin Z, Birnir B. Different subtypes of GABA-A receptors are expressed in human, mouse and rat T lymphocytes. PLoS One 2012; 7:e42959. [PMID: 22927941 PMCID: PMC3424250 DOI: 10.1371/journal.pone.0042959] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2012] [Accepted: 07/16/2012] [Indexed: 11/19/2022] Open
Abstract
γ-aminobutyric acid (GABA) is the most prominent neuroinhibitory transmitter in the brain, where it activates neuronal GABA-A receptors (GABA-A channels) located at synapses and outside of synapses. The GABA-A receptors are primary targets of many clinically useful drugs. In recent years, GABA has been shown to act as an immunomodulatory molecule. We have examined in human, mouse and rat CD4+ and CD8+ T cells which subunit isoforms of the GABA-A channels are expressed. The channel physiology and drug specificity is dictated by the GABA-A receptor subtype, which in turn is determined by the subunit isoforms that make the channel. There were 5, 8 and 13 different GABA-A subunit isoforms identified in human, mouse and rat CD4+ and CD8+ T cells, respectively. Importantly, the γ2 subunit that imposes benzodiazepine sensitivity on the GABA-A receptors, was only detected in the mouse T cells. Immunoblots and immunocytochemistry showed abundant GABA-A channel proteins in the T cells from all three species. GABA-activated whole-cell transient and tonic currents were recorded. The currents were inhibited by picrotoxin, SR95531 and bicuculline, antagonists of GABA-A channels. Clearly, in both humans and rodents T cells, functional GABA-A channels are expressed but the subtypes vary. It is important to bear in mind the interspecies difference when selecting the appropriate animal models to study the physiological role and pharmacological properties of GABA-A channels in CD4+ and CD8+ T cells and when selecting drugs aimed at modulating the human T cells function.
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Affiliation(s)
| | | | | | - Bryndis Birnir
- Molecular Physiology and Neuroscience, Department of Neuroscience, Uppsala University, Uppsala, Sweden
- * E-mail:
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Valdés A, Simó C, Ibáñez C, Rocamora-Reverte L, Ferragut JA, García-Cañas V, Cifuentes A. Effect of dietary polyphenols on K562 leukemia cells: A Foodomics approach. Electrophoresis 2012; 33:2314-27. [DOI: 10.1002/elps.201200133] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
| | | | - Clara Ibáñez
- Laboratory of Foodomics; CIAL (CSIC); Madrid; Spain
| | - Lourdes Rocamora-Reverte
- Institute of Molecular and Cellular Biology; Miguel Hernández University; Elche, Alicante; Spain
| | - José Antonio Ferragut
- Institute of Molecular and Cellular Biology; Miguel Hernández University; Elche, Alicante; Spain
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Sharma S, Darland D, Lei S, Rakoczy S, Brown-Borg HM. NMDA and kainate receptor expression, long-term potentiation, and neurogenesis in the hippocampus of long-lived Ames dwarf mice. AGE (DORDRECHT, NETHERLANDS) 2012; 34:609-20. [PMID: 21544578 PMCID: PMC3337943 DOI: 10.1007/s11357-011-9253-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2010] [Accepted: 04/15/2011] [Indexed: 05/08/2023]
Abstract
In the current study, we investigated changes in N-methyl D-aspartate (NMDA) and kainate receptor expression, long-term potentiation (LTP), and neurogenesis in response to neurotoxic stress in long-living Ames dwarf mice. We hypothesized that Ames dwarf mice have enhanced neurogenesis that enables retention of spatial learning and memory with age and promotes neurogenesis in response to injury. Levels of the NMDA receptors (NR)1, NR2A, NR2B, and the kainate receptor (KAR)2 were increased in Ames dwarf mice, relative to wild-type littermates. Quantitative assessment of the excitatory postsynaptic potential in Schaffer collaterals in hippocampal slices from Ames dwarf mice showed an increased response in high-frequency induced LTP over time compared with wild type. Kainic acid (KA) injection was used to promote neurotoxic stress-induced neurogenesis. KA mildly increased the number of doublecortin-positive neurons in wild-type mice, but the response was significantly enhanced in the Ames dwarf mice. Collectively, these data support our hypothesis that the enhanced learning and memory associated with the Ames dwarf mouse may be due to elevated levels of NMDA and KA receptors in hippocampus and their ability to continue producing new neurons in response to neuronal damage.
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Affiliation(s)
- Sunita Sharma
- Department of Physiology, Pharmacology and Therapeutics, University of North Dakota School of Medicine and Health Sciences, Grand Forks, ND 58203 USA
| | - Diane Darland
- Department of Biology, University of North Dakota, Grand Forks, ND 58202 USA
| | - Saobo Lei
- Department of Physiology, Pharmacology and Therapeutics, University of North Dakota School of Medicine and Health Sciences, Grand Forks, ND 58203 USA
| | - Sharlene Rakoczy
- Department of Physiology, Pharmacology and Therapeutics, University of North Dakota School of Medicine and Health Sciences, Grand Forks, ND 58203 USA
| | - Holly M. Brown-Borg
- Department of Physiology, Pharmacology and Therapeutics, University of North Dakota School of Medicine and Health Sciences, Grand Forks, ND 58203 USA
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Antidiabetic Effect of an Active Components Group from Ilex kudingcha and Its Chemical Composition. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2012; 2012:423690. [PMID: 22474502 PMCID: PMC3303728 DOI: 10.1155/2012/423690] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2011] [Revised: 11/21/2011] [Accepted: 11/22/2011] [Indexed: 01/23/2023]
Abstract
The leaves of Ilex kudingcha are used as an ethnomedicine in the treatment of symptoms related with diabetes mellitus and obesity throughout the centuries in China. The present study investigated the antidiabetic activities of an active components group (ACG) obtained from Ilex kudingcha in alloxan-induced type 2 diabetic mice. ACG significantly reduced the elevated levels of serum glycaemic and lipids in type 2 diabetic mice. 3-Hydroxy-3-methylglutaryl coenzyme A reductase and glucokinase were upregulated significantly, while fatty acid synthetase, glucose-6-phosphatase catalytic enzyme was downregulated in diabetic mice after treatment of ACG. These findings clearly provided evidences regarding the antidiabetic potentials of ACG from Ilex kudingcha. Using LC-DAD/HR-ESI-TOF-MS, six major components were identified in ACG. They are three dicaffeoylquinic acids that have been reported previously, and three new triterpenoid saponins, which were the first time to be identified in Ilex kudingcha. It is reasonable to assume that antidiabetic activity of Ilex kudingcha against hyperglycemia resulted from these six major components. Also, synergistic effects among their compounds may exist in the antidiabetic activity of Ilex kudingcha.
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Moreno LI, Tate CM, Knott EL, McDaniel JE, Rogers SS, Koons BW, Kavlick MF, Craig RL, Robertson JM. Determination of an Effective Housekeeping Gene for the Quantification of mRNA for Forensic Applications*. J Forensic Sci 2012; 57:1051-8. [DOI: 10.1111/j.1556-4029.2012.02086.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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40
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Goh WWB, Lee YH, Ramdzan ZM, Chung MC, Wong L, Sergot MJ. A network-based maximum link approach towards MS identifies potentially important roles for undetected ARRB1/2 and ACTB in liver cancer progression. INTERNATIONAL JOURNAL OF BIOINFORMATICS RESEARCH AND APPLICATIONS 2012; 8:155-70. [PMID: 22961449 PMCID: PMC3784647 DOI: 10.1504/ijbra.2012.048967] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Hepatocellular Carcinoma (HCC) ranks among the deadliest of cancers and has a complex etiology. Proteomics analysis using iTRAQ provides a direct way to analyse perturbations in protein expression during HCC progression from early- to late-stage but suffers from consistency and coverage issues. Appropriate use of network-based analytical methods can help to overcome these issues. We built an integrated and comprehensive Protein-Protein Interaction Network (PPIN) by merging several major databases. Additionally, the network was filtered for GO coherent edges. Significantly differential genes (seeds) were selected from iTRAQ data and mapped onto this network. Undetected proteins linked to seeds (linked proteins) were identified and functionally characterised. The process of network cleaning provides a list of higher quality linked proteins, which are highly enriched for similar biological process gene ontology terms. Linked proteins are also enriched for known cancer genes and are linked to many well-established cancer processes such as apoptosis and immune response. We found that there is an increased propensity for known cancer genes to be found in highly linked proteins. Three highly-linked proteins were identified that may play an important role in driving HCC progression - the G-protein coupled receptor signalling proteins, ARRB1/2 and the structural protein beta-actin, ACTB. Interestingly, both ARRB proteins evaded detection in the iTRAQ screen. ACTB was not detected in the original dataset derived from Mascot but was found to be strongly supported when we re-ran analysis using another protein detection database (Paragon). Identification of linked proteins helps to partially overcome the coverage issue in shotgun proteomics analysis. The set of linked proteins are found to be enriched for cancer-specific processes, and more likely so if they are more highly linked. Additionally, a higher quality linked set is derived if network-cleaning is performed prior. This form of network-based analysis complements the cluster-based approach, and can provide a larger list of proteins on which to perform functional analysis, as well as for biomarker identification.
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Affiliation(s)
| | - Yie Hou Lee
- Singapore-MIT Alliance for Research and Technology, Singapore
| | | | - Maxey C.M. Chung
- Department of Biological Sciences and Department of Biochemistry, National University of Singapore, Singapore
| | - Limsoon Wong
- Department of Computer Science and Department of Pathology, National University of Singapore, Singapore
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Wang EH, Truong LD, Mendoza L, Jung ES, Choi YJ. 28S-ribosomal RNA is superior to glyceraldehyde-3-phosphate dehydrogenase as a RNA reference gene in p53-deficient mice with unilateral ureteral obstruction. Exp Mol Pathol 2011; 91:368-72. [PMID: 21565186 DOI: 10.1016/j.yexmp.2011.04.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2011] [Accepted: 04/19/2011] [Indexed: 11/30/2022]
Abstract
Although there are many kinds of reference genes, glyceraldehyde-3-phosphate dehydrogenase (GAPDH) has been commonly used by many researchers to assess the amount and integrity of RNA transcripts in RNA studies including Northern blot and reverse transcription real time-PCR. Although some data suggest that GAPDH could be inconstant in their situations or experiments, there is limited evidence that GAPDH expression is influenced by conditions of experiment, especially in mouse kidney model with unilateral ureteral obstruction (UUO). Therefore, the establishment of excellent reference gene according to the tissue types or conditions of experiment is a bottom line for the RNA study. Here we compared the expression of GAPDH with 28S rRNA gene by Northern blot analysis in the p53-deficient mice with UUO. We observed that GAPDH mRNA levels in ligated kidneys were significantly lower than those in contralateral kidneys, especially after postoperative day 15. In contrast, 28S rRNA levels were constant among control, ligated and contralateral kidneys. We also demonstrated that 28S rRNA signal was proportional to the amount of RNA loaded. In conclusion, these data indicate that much caution should be taken when using GAPDH as a RNA reference gene and 28S rRNA is an excellent gene for the RNA study in p53-deficient mice with UUO.
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Affiliation(s)
- Eun-Hui Wang
- Department of Hospital Pathology, The Catholic University of Korea, Seocho-Gu, Seoul, Republic of Korea
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Zhao C, Zha Y, Wu X, Chen L, Shi J, Cui L. The quantification of ADAMTS4 and 8 expression and selection of reference genes for quantitative real-time PCR analysis in myocardial infarction. Biomed Pharmacother 2010; 65:555-9. [PMID: 21257285 DOI: 10.1016/j.biopha.2010.12.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2010] [Accepted: 12/06/2010] [Indexed: 12/11/2022] Open
Abstract
INTRODUCTION ADAMTS4 and ADAMTS8 are proteases involved in ECM proteolysis and antiangiogenesis, but little is known about their expression and function in myocardial infarction (MI). We examined ADAMTS4 and ADAMTS8 expression in a rat MI model by quantitative real-time polymerase chain reaction (qPCR) and enzyme linked immunosorbent assay (ELISA). The expressions of glyseraldehyde-3-phosphate dehydrogenase (GAPDH), beta-actin (ACTB), acidic ribosomal phosphoprotein P0 (ARBP), and ribosomal protein L13A (RPL13A) were examined in order to validate the appropriate housekeeping genes after MI. METHODS Male Wistar rats were subjected to MI, and infarcted myocardial tissue was collected at 3, 6, 12, 24h, 3, 7, 14 and 21days after MI. ADAMTS4, ADAMTS8, and the four housekeeping genes were quantified using qPCR and the expression stability of the four housekeeping genes was investigated using GeNorm software. The protein levels of ADAMTS4 were detected using ELISA kits. RESULTS The M values of GAPDH, ACTB, ARBP and RPL13A were 0.721, 1.2, 0.812 and 0.812 respectively. GAPDH and ARBP were ranked the most stable genes. ADAMTS4 mRNA increased at 3h after MI, peaked at 6h, then decreased rapidly. ADAMTS8 mRNA increased at 6h, peaked at 24h, remained high at 3d, then decreased gradually. The protein levels of ADAMTS4 were significantly increased at 6h, 12h, 24h and 3d after MI. CONCLUSION The results suggest that GAPDH and ARBP are two appropriate housekeeping genes for the rat MI model. Both ADAMTS4 and ADAMTS8 mRNA levels and ADAMTS4 protein level increased, but they exhibited different expression profiles.
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Affiliation(s)
- Chuanyan Zhao
- Department of Cardiology, Shandong Provincial Hospital, Shandong University, 324, Jingwu Road, Jinan 250021, PR China
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Sharma S, Rakoczy S, Dahlheimer K, Brown-Borg H. The hippocampus of Ames dwarf mice exhibits enhanced antioxidative defenses following kainic acid-induced oxidative stress. Exp Gerontol 2010; 45:936-49. [PMID: 20804841 PMCID: PMC6432800 DOI: 10.1016/j.exger.2010.08.013] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2010] [Revised: 08/09/2010] [Accepted: 08/19/2010] [Indexed: 12/19/2022]
Abstract
INTRODUCTION The vulnerability of the hippocampus to the effects of aging has been found to be associated with a decline in growth hormone/insulin like growth factor-1 (GH/IGF-1), and an increase in oxidative stress. We have evidence that long-living GH-deficient Ames dwarf mice have enhanced antioxidant protection in the periphery but the protection in the central nervous system is less clear. MATERIAL AND METHODS In the present study, we evaluated the antioxidative defense enzyme status in the hippocampus of Ames dwarf and wild type mice at 3, 12 and 24 months of age and examined the ability of each genotype to resist kainic acid-induced (KA) oxidative stress. An equiseizure concentration of KA was administered such that both genotypes responded with similar seizure scores and lipid peroxidation. RESULTS We found that GH-sufficient wild type mice showed an increase in oxidative stress as indicated by the reduced ratio of glutathione: glutathione disulfide following KA injection while this ratio was maintained in GH-deficient Ames dwarf mice. In addition, glutathione peroxidase activity (GPx) as well as GPx1 mRNA expression was enhanced in KA-injected Ames dwarf mice but decreased in wild type mice. There was no induction of Nrf-2 (an oxidative stress-induced transcription factor) gene expression in Ames dwarf mice following KA further suggesting maintenance of antioxidant defense in GH-deficiency under oxidative stress conditions. DISCUSSION Therefore, based on equiseizure administration of KA, Ames dwarf mice have an enhanced antioxidant defense capacity in the hippocampus similar to that observed in the periphery. This improved defense capability in the brain is likely due to increased GPx availability in Ames mice and may contribute to their enhanced longevity.
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Affiliation(s)
- Sunita Sharma
- Department of Pharmacology, Physiology and Therapeutics, University of North Dakota School of Medicine and Health Sciences, Grand Forks, ND 58203, USA
| | - Sharlene Rakoczy
- Department of Pharmacology, Physiology and Therapeutics, University of North Dakota School of Medicine and Health Sciences, Grand Forks, ND 58203, USA
| | - Kristine Dahlheimer
- Department of Pharmacology, Physiology and Therapeutics, University of North Dakota School of Medicine and Health Sciences, Grand Forks, ND 58203, USA
| | - Holly Brown-Borg
- Department of Pharmacology, Physiology and Therapeutics, University of North Dakota School of Medicine and Health Sciences, Grand Forks, ND 58203, USA
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van der Windt GJW, Florquin S, de Vos AF, van't Veer C, Queiroz KCS, Liang J, Jiang D, Noble PW, van der Poll T. CD44 deficiency is associated with increased bacterial clearance but enhanced lung inflammation during Gram-negative pneumonia. THE AMERICAN JOURNAL OF PATHOLOGY 2010; 177:2483-94. [PMID: 20864681 DOI: 10.2353/ajpath.2010.100562] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Klebsiella pneumoniae is a frequently isolated causative pathogen in respiratory tract infections. CD44 is a transmembrane adhesion molecule that has been implicated in several immunological processes. To determine the role of CD44 during Klebsiella pneumonia, we intranasally infected wild-type and CD44 knockout (KO) mice with 10(2) to 10(4) colony-forming units of K. pneumoniae or administered Klebsiella lipopolysaccharide. During lethal infection, CD44 deficiency was associated with reduced bacterial growth and dissemination accompanied by enhanced pulmonary inflammation. After infection with lower Klebsiella doses, CD44 KO mice but not wild-type mice demonstrated mortality. After infection with even lower bacterial doses, which were cleared by most mice of both strains, CD44 KO mice displayed enhanced lung inflammation 4 and 10 days postinfection, indicating that CD44 is important for the resolution of pulmonary inflammation after nonlethal pneumonia. In accordance, CD44 KO mice showed a diminished resolution of lung inflammation 4 days after intrapulmonary delivery of lipopolysaccharide. CD44 deficiency was associated with the accumulation of hyaluronan together with reduced gene expression levels of the negative regulators of Toll-like receptor signaling, interleukin-1R-associated kinase M, A20, and suppressor of cytokine signaling 3. In conclusion, the absence of CD44 affects various components and phases of the host response during Klebsiella pneumonia, reducing bacterial outgrowth and dissemination and enhancing pulmonary pathology during lethal infection, and diminishing the resolution of lung inflammation during sublethal infection.
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Affiliation(s)
- Gerritje J W van der Windt
- Center for Infection and Immunity Amsterdam, Department of Pathology, Academic Medical Center, Meibergdreef 9, Room G2-130, 1105 AZ Amsterdam, The Netherlands
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Sharma S, Haselton J, Rakoczy S, Branshaw S, Brown-Borg HM. Spatial memory is enhanced in long-living Ames dwarf mice and maintained following kainic acid induced neurodegeneration. Mech Ageing Dev 2010; 131:422-35. [PMID: 20561541 DOI: 10.1016/j.mad.2010.06.004] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2010] [Revised: 05/18/2010] [Accepted: 06/05/2010] [Indexed: 12/29/2022]
Abstract
INTRODUCTION Age associated cognitive impairment is associated with low levels of IGF-1, oxidative stress, and neuronal loss in the hippocampus. Ames dwarf mice are long-lived animals that exhibit peripheral IGF-1 deficiency. Hippocampal-based spatial memory (a homolog of cognitive function) has not been evaluated in these long-living mice. MATERIALS AND METHODS We evaluated the hippocampal-based spatial memory in 3-, 12- and 24-month-old Ames dwarf and wild type mice using the Barnes maze and the T-maze. We also examined the effect of a hippocampal-specific toxin, kainic acid (KA), on spatial memory to determine whether Ames mice were resistant to the cognitive impairment induced by this compound. RESULTS We found that Ames dwarf mice exhibit enhanced learning, making fewer errors and using less time to solve both the Barnes and T-mazes. Dwarf mice also have significantly better short-term memory as compared to wild type mice. Both genotypes exhibited neuronal loss in the CA1 and CA3 areas of the hippocampus following KA, but Ames dwarf mice retained their spatial memory. DISCUSSION Our results show that Ames dwarf mice retained their spatial memory despite neurodegeneration when compared to wild type mice at an "equiseizure" dose of KA.
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Affiliation(s)
- Sunita Sharma
- Department of Pharmacology, Physiology and Therapeutics, University of North Dakota School of Medicine and Health Sciences, Grand Forks, North Dakota 58203, USA
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Brizova H, Kalinova M, Krskova L, Mrhalova M, Kodet R. A novel quantitative PCR of proliferation markers (Ki-67, topoisomerase IIalpha, and TPX2): an immunohistochemical correlation, testing, and optimizing for mantle cell lymphoma. Virchows Arch 2010; 456:671-9. [PMID: 20419314 DOI: 10.1007/s00428-010-0922-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2010] [Revised: 03/18/2010] [Accepted: 04/06/2010] [Indexed: 11/30/2022]
Abstract
A clinical course of patients with mantle cell lymphoma (MCL) is aggressive, and the disease is rarely curable. Proliferation rate is the most important prognostic factor. We developed a novel, reliable, rapid, and routinely applicable approach allowing a precise quantitative assessment of three proliferation markers, Ki-67, topoisomerase IIalpha, and TPX2. A total of 95 lymphoma specimens were measured in the study by real-time reverse transcription PCR (RQ-RT-PCR). We tested the reproducibility and accuracy of the assay and correlated the results with the immunohistochemical staining of the corresponding proteins. The results obtained indicated individual variability of the mRNA expression levels, reflecting heterogeneity of the proliferation rate in individual patients. In general, we observed the highest mRNA expression in the group of Burkitt lymphomas and the lowest in patients with reactive lymphadenopathies. We found increased proliferation rate in MCLs with high cyclin D1 mRNA, indicating a quantitative control of the cell cycle. We observed a correlation between mRNA expression level and the immunohistochemical staining of corresponding proteins, which significantly argues for the prognostic significance of the mRNA expression measuring. We confirmed the accuracy of the current assay for a precise quantitative examination of the proliferation activity. Real-time RT-PCR provides a novel approach applicable for clinical trials, and it represents a potent approach allowing to stratify MCL patients for entry into clinical trials according to the expression of the proliferation signature genes in their tumors. This approach may contribute to improved and individualized therapeutic options respecting the individual progression risk of patients with MCL.
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Affiliation(s)
- Helena Brizova
- Department of Pathology and Molecular Medicine, 2nd Medical School, Charles University in Prague and Faculty Hospital in Motol, V Uvalu 84, 150 06, Prague 5, Czech Republic.
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Koppelkamm A, Vennemann B, Fracasso T, Lutz-Bonengel S, Schmidt U, Heinrich M. Validation of adequate endogenous reference genes for the normalisation of qPCR gene expression data in human post mortem tissue. Int J Legal Med 2010; 124:371-80. [PMID: 20300940 DOI: 10.1007/s00414-010-0433-9] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2009] [Accepted: 02/18/2010] [Indexed: 11/26/2022]
Abstract
Gene expression analyses based on messenger RNA (mRNA) profiling require accurate data normalisation. When using endogenous reference genes, these have to be validated carefully. Therefore, we examined the transcript stability of 10 potential reference genes using quantitative real-time polymerase chain reaction: beta actin, 18S rRNA, glyceraldehyde-3-phosphate dehydrogenase, TATA box-binding protein, hypoxanthine phosphoribosyl-transferase I, beta-2-microglobulin, hydroxymethylbilane synthase, succinate dehydrogenase complex, subunit A, cyclophilin A and ubiquitin C. The aim of the current study was to assess which reference genes show stable mRNA levels in human post mortem cardiac muscle, skeletal muscle and brain tissue. Considering cardiac muscle tissue, CYCA and TBP were identified as the most stable while in skeletal muscle tissue, SDHA and TBP, and in brain tissue, SDHA and HMBS turned out to be the most stable. Furthermore, we recommend a minimum of four carefully validated endogenous control genes for reliable data normalisation in human post mortem tissue. Parameters influencing the stability of transcript amounts were found to be mainly the post mortem interval in cardiac muscle and skeletal muscle tissue and the donor's cause of death in skeletal muscle and brain samples. Further parameters like gender, age at death and body mass index were found to influence mRNA quantities in skeletal muscle only. The set of stable control genes identified in this study may be used in further studies if the composition of the samples is similar to the one used here.
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Affiliation(s)
- Antje Koppelkamm
- Institute of Legal Medicine, University of Freiburg, Albertstr. 9, 79104, Freiburg, Germany
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Mortensen DM, Røge R, Øzbay A, Koefoed-Nielsen PB, Jørgensen KA. Gene expression analysis of calcineurin isoforms in T-lymphocytes--a method applied on kidney-transplant recipients. Transpl Immunol 2010; 23:24-7. [PMID: 20226242 DOI: 10.1016/j.trim.2010.02.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2009] [Revised: 01/15/2010] [Accepted: 02/26/2010] [Indexed: 11/16/2022]
Abstract
BACKGROUND Tacrolimus exerts its immunosuppressive effect through inhibition of the intracellular enzyme calcineurin phosphatase (CaN). In this study, we set-up a validated real-time PCR method to measure the gene expression of the two major isoforms of the catalytic subunit of CaN in T-lymphocytes. METHODS 20 stable kidney-transplant recipients, 10 early kidney-transplant recipients and 10 healthy non-medicated subjects had blood drawn and T-lymphocytes were isolated using E-rosette gradient centrifugation method. The cell counts were analyzed by DNA quantification using Hoeschst 33285. Gene expressions were analyzed using real-time PCR for CaN Aalpha, CaN Abeta and the reference genes CD3E and PPIB. RESULTS The real-time PCR method was found to be with high efficiencies and low intra- and inter-assay variabilities. No statistically significant differences were found in the gene expression levels of the two reference genes among the three groups. The two major isoforms of CaN A were expressed in equal amounts in the T-lymphocytes. CONCLUSION We found no significant difference in the reference genes between the three groups, but looking at the data there was a trend towards an up-regulation of CD3E. PPIB appears to be the more stable of the two reference genes tested in our study.
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Affiliation(s)
- D M Mortensen
- Research Laboratory C, Department of Renal Medicine C, Aarhus University Hospital, Skejby, Brendstrupgaardsvej 100, DK 8200 Aarhus N, Denmark.
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Caradec J, Sirab N, Keumeugni C, Moutereau S, Chimingqi M, Matar C, Revaud D, Bah M, Manivet P, Conti M, Loric S. 'Desperate house genes': the dramatic example of hypoxia. Br J Cancer 2010; 102:1037-43. [PMID: 20179706 PMCID: PMC2844028 DOI: 10.1038/sj.bjc.6605573] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
BACKGROUND Microenvironmental conditions in normal or tumour tissues and cell lines may interfere on further biological analysis. To evaluate transcript variations carefully, it is common to use stable housekeeping genes (HKG) to normalise quantitative microarrays or real-time polymerase chain reaction results. However, recent studies argue that HKG fluctuate according to tissues and treatments. So, as an example of HKG variation under an array of conditions that are common in the cancer field, we evaluate whether hypoxia could have an impact on HKG expression. METHODS Expression of 10 commonly used HKG was measured on four cell lines treated with four oxygen concentrations (from 1 to 20%). RESULTS Large variations of HKG transcripts were observed in hypoxic conditions and differ along with the cell line and the oxygen concentration. To elect the most stable HKG, we compared the three statistical means based either on PCR cycle threshold coefficient of variation calculation or two specifically dedicated software. Nevertheless, the best HKG dramatically differs according to the statistical method used. Moreover, using, as a reference, absolute quantification of a target gene (here the proteinase activating receptor gene 1 (PAR1) gene), we show that the conclusions raised about PAR1 variation in hypoxia can totally diverge according to the selected HKG used for normalisation. CONCLUSION The choice of a valid HKG will determine the relevance of the results that will be further interpreted, and so it should be seriously considered. The results of our study confirm unambiguously that HKG variations must be precisely and systematically determined before any experiment for each situation, to obtain reliable normalised results in the experimental setting that has been designed. Indeed, such assay design, functional for all in vitro systems, should be carefully evaluated before any extension to other experimental models including in vivo ones.
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Affiliation(s)
- J Caradec
- INSERM, U955 EQ07, Paris Est University, Créteil, France
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Wiersinga WJ, Kager LM, Hovius JWR, van der Windt GJW, de Vos AF, Meijers JCM, Roelofs JJ, Dondorp A, Levi M, Day NP, Peacock SJ, van der Poll T. Urokinase receptor is necessary for bacterial defense against pneumonia-derived septic melioidosis by facilitating phagocytosis. THE JOURNAL OF IMMUNOLOGY 2010; 184:3079-86. [PMID: 20142364 DOI: 10.4049/jimmunol.0901008] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Urokinase receptor (urokinase-type plasminogen activator receptor [uPAR], CD87), a GPI-anchored protein, is considered to play an important role in inflammation and fibrinolysis. The Gram-negative bacterium Burkholderia pseudomallei is able to survive and replicate within leukocytes and causes melioidosis, an important cause of pneumonia-derived community-acquired sepsis in Southeast Asia. In this study, we investigated the expression and function of uPAR both in patients with septic melioidosis and in a murine model of experimental melioidosis. uPAR mRNA and surface expression was increased in patients with septic melioidosis in/on both peripheral blood monocytes and granulocytes as well as in the pulmonary compartment during experimental pneumonia-derived melioidosis in mice. uPAR-deficient mice intranasally infected with B. pseudomallei showed an enhanced growth and dissemination of B. pseudomallei when compared with wild-type mice, corresponding with increased pulmonary and hepatic inflammation. uPAR knockout mice demonstrated significantly reduced neutrophil migration toward the pulmonary compartment after inoculation with B. pseudomallei. Further in vitro experiments showed that uPAR-deficient macrophages and granulocytes display a markedly impaired phagocytosis of B. pseudomallei. Additional studies showed that uPAR deficiency did not influence hemostatic and fibrinolytic responses during severe melioidosis. These data suggest that uPAR is crucially involved in the host defense against sepsis caused by B. pseudomallei by facilitating the migration of neutrophils toward the primary site of infection and subsequently facilitating the phagocytosis of B. pseudomallei.
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Affiliation(s)
- W Joost Wiersinga
- Center for Infection and Immunity Amsterdam, University of Amsterdam, Amsterdam, The Netherlands.
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