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Nevone A, Lattarulo F, Russo M, Panno G, Milani P, Basset M, Avanzini MA, Merlini G, Palladini G, Nuvolone M. A Strategy for the Selection of RT-qPCR Reference Genes Based on Publicly Available Transcriptomic Datasets. Biomedicines 2023; 11:1079. [PMID: 37189697 PMCID: PMC10135859 DOI: 10.3390/biomedicines11041079] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 03/23/2023] [Accepted: 03/27/2023] [Indexed: 04/05/2023] Open
Abstract
In the next-generation sequencing era, RT-qPCR is still widely employed to quantify levels of nucleic acids of interest due to its popularity, versatility, and limited costs. The measurement of transcriptional levels through RT-qPCR critically depends on reference genes used for normalization. Here, we devised a strategy to select appropriate reference genes for a specific clinical/experimental setting based on publicly available transcriptomic datasets and a pipeline for RT-qPCR assay design and validation. As a proof-of-principle, we applied this strategy to identify and validate reference genes for transcriptional studies of bone-marrow plasma cells from patients with AL amyloidosis. We performed a systematic review of published literature to compile a list of 163 candidate reference genes for RT-qPCR experiments employing human samples. Next, we interrogated the Gene Expression Omnibus to assess expression levels of these genes in published transcriptomic studies on bone-marrow plasma cells from patients with different plasma cell dyscrasias and identified the most stably expressed genes as candidate normalizing genes. Experimental validation on bone-marrow plasma cells showed the superiority of candidate reference genes identified through this strategy over commonly employed "housekeeping" genes. The strategy presented here may apply to other clinical and experimental settings for which publicly available transcriptomic datasets are available.
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Affiliation(s)
- Alice Nevone
- Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy
- Amyloidosis Research and Treatment Center, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy
| | - Francesca Lattarulo
- Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy
- Amyloidosis Research and Treatment Center, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy
| | - Monica Russo
- Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy
- Amyloidosis Research and Treatment Center, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy
| | - Giada Panno
- Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy
- Amyloidosis Research and Treatment Center, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy
| | - Paolo Milani
- Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy
- Amyloidosis Research and Treatment Center, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy
| | - Marco Basset
- Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy
- Amyloidosis Research and Treatment Center, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy
| | - Maria Antonietta Avanzini
- Pediatric Hematology Oncology, Cell Factory, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy
| | - Giampaolo Merlini
- Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy
- Amyloidosis Research and Treatment Center, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy
| | - Giovanni Palladini
- Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy
- Amyloidosis Research and Treatment Center, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy
| | - Mario Nuvolone
- Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy
- Amyloidosis Research and Treatment Center, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy
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Shibuya Y, Hokugo A, Okawa H, Kondo T, Khalil D, Wang L, Roca Y, Clements A, Sasaki H, Berry E, Nishimura I, Jarrahy R. Therapeutic downregulation of neuronal PAS domain 2 ( Npas2) promotes surgical skin wound healing. eLife 2022; 11:e71074. [PMID: 35040776 PMCID: PMC8789286 DOI: 10.7554/elife.71074] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 01/14/2022] [Indexed: 11/13/2022] Open
Abstract
Attempts to minimize scarring remain among the most difficult challenges facing surgeons, despite the use of optimal wound closure techniques. Previously, we reported improved healing of dermal excisional wounds in circadian clock neuronal PAS domain 2 (Npas2)-null mice. In this study, we performed high-throughput drug screening to identify a compound that downregulates Npas2 activity. The hit compound (Dwn1) suppressed circadian Npas2 expression, increased murine dermal fibroblast cell migration, and decreased collagen synthesis in vitro. Based on the in vitro results, Dwn1 was topically applied to iatrogenic full-thickness dorsal cutaneous wounds in a murine model. The Dwn1-treated dermal wounds healed faster with favorable mechanical strength and developed less granulation tissue than the controls. The expression of type I collagen, Tgfβ1, and α-smooth muscle actin was significantly decreased in Dwn1-treated wounds, suggesting that hypertrophic scarring and myofibroblast differentiation are attenuated by Dwn1 treatment. NPAS2 may represent an important target for therapeutic approaches to optimal surgical wound management.
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Affiliation(s)
- Yoichiro Shibuya
- Regenerative Bioengineering and Repair Laboratory, Division of Plastic and Reconstructive Surgery, Department of Surgery, David Geffen School of MedicineLos AngelesUnited States
- Weintraub Center for Reconstructive BiotechnologyLos AngelesUnited States
- Department of Plastic and Reconstructive Surgery, Faculty of Medicine, University of TsukubaTsukubaJapan
| | - Akishige Hokugo
- Regenerative Bioengineering and Repair Laboratory, Division of Plastic and Reconstructive Surgery, Department of Surgery, David Geffen School of MedicineLos AngelesUnited States
- Weintraub Center for Reconstructive BiotechnologyLos AngelesUnited States
| | - Hiroko Okawa
- Weintraub Center for Reconstructive BiotechnologyLos AngelesUnited States
- Division of Molecular and Regenerative Prosthodontics, Tohoku University Graduate School of DentistryMiyagiJapan
| | - Takeru Kondo
- Weintraub Center for Reconstructive BiotechnologyLos AngelesUnited States
- Division of Molecular and Regenerative Prosthodontics, Tohoku University Graduate School of DentistryMiyagiJapan
| | - Daniel Khalil
- Regenerative Bioengineering and Repair Laboratory, Division of Plastic and Reconstructive Surgery, Department of Surgery, David Geffen School of MedicineLos AngelesUnited States
| | - Lixin Wang
- Regenerative Bioengineering and Repair Laboratory, Division of Plastic and Reconstructive Surgery, Department of Surgery, David Geffen School of MedicineLos AngelesUnited States
| | - Yvonne Roca
- Regenerative Bioengineering and Repair Laboratory, Division of Plastic and Reconstructive Surgery, Department of Surgery, David Geffen School of MedicineLos AngelesUnited States
| | - Adam Clements
- Regenerative Bioengineering and Repair Laboratory, Division of Plastic and Reconstructive Surgery, Department of Surgery, David Geffen School of MedicineLos AngelesUnited States
| | - Hodaka Sasaki
- Weintraub Center for Reconstructive BiotechnologyLos AngelesUnited States
| | - Ella Berry
- Regenerative Bioengineering and Repair Laboratory, Division of Plastic and Reconstructive Surgery, Department of Surgery, David Geffen School of MedicineLos AngelesUnited States
| | - Ichiro Nishimura
- Weintraub Center for Reconstructive BiotechnologyLos AngelesUnited States
| | - Reza Jarrahy
- Regenerative Bioengineering and Repair Laboratory, Division of Plastic and Reconstructive Surgery, Department of Surgery, David Geffen School of MedicineLos AngelesUnited States
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Cadenas J, Pors SE, Nikiforov D, Zheng M, Subiran C, Bøtkjær JA, Mamsen LS, Kristensen SG, Andersen CY. Validating Reference Gene Expression Stability in Human Ovarian Follicles, Oocytes, Cumulus Cells, Ovarian Medulla, and Ovarian Cortex Tissue. Int J Mol Sci 2022; 23:ijms23020886. [PMID: 35055072 PMCID: PMC8778884 DOI: 10.3390/ijms23020886] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 01/08/2022] [Accepted: 01/11/2022] [Indexed: 11/30/2022] Open
Abstract
Human ovarian cells are phenotypically very different and are often only available in limited amounts. Despite the fact that reference gene (RG) expression stability has been validated in oocytes and other ovarian cells from several animal species, the suitability of a single universal RG in the different human ovarian cells and tissues has not been determined. The present study aimed to validate the expression stability of five of the most used RGs in human oocytes, cumulus cells, preantral follicles, ovarian medulla, and ovarian cortex tissue. The selected genes were glyceraldehyde 3-phosphate dehydrogenase (GAPDH), beta-2-microglobulin (B2M), large ribosomal protein P0 (RPLP0), beta-actin (ACTB), and peptidylprolyl isomerase A (PPIA). Overall, the stability of all RGs differed among ovarian cell types and tissues. NormFinder identified ACTB as the best RG for oocytes and cumulus cells, and B2M for medulla tissue and isolated follicles. The combination of two RGs only marginally increased the stability, indicating that using a single validated RG would be sufficient when the available testing material is limited. For the ovarian cortex, depending on culture conditions, GAPDH or ACTB were found to be the most stable genes. Our results highlight the importance of assessing RGs for each cell type or tissue when performing RT-qPCR analysis.
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Liu Y, Cao G, Xie Y, Chu M. Identification of differentially expressed genes associated with precocious puberty by suppression subtractive hybridization in goat pituitary tissues. Anim Biotechnol 2021:1-14. [PMID: 34747679 DOI: 10.1080/10495398.2021.1990940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
The aim of this study was to identify genes related to precocious puberty expressed in the pituitary of goats at different growth stages by suppression subtractive hybridization (SSH). The pituitary glands from Jining Gray (JG) goats (early puberty) and Liaoning Cashmere (LC) goats (late puberty) at 30, 90, and 180 days were used in this study. To identify differentially expressed genes (DEGs) in the pituitary glands, mRNA was extracted from these tissues, and SSH libraries were constructed and divided into the following groups: juvenile group (30-JG vs. 30-LC, API), puberty group (90-JG vs. 180-LC, BPI), and control group (90-JG vs. 90-LC, EPI). A total of 60, 49, and 58 DEGs were annotated by 222 Gene Ontology (GO) terms and 75 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Most of the DEGs were significantly enriched in GO terms related to 'structural constituent of ribosome', 'translation' and 'GTP binding', and numerous DEGs were also significantly enriched in KEGG terms related to the Jak-STAT signaling and oocyte meiosis pathways. Candidate genes associated with precocious puberty and sexual development were screened from the SSH libraries. These genes were analyzed to determine if they were expressed in the pituitary tissues of the goats at different growth stages and to identify genes that may influence the hypothalamic-pituitary-gonadal (HPG) axis. In this study, we found precocious puberty-related genes (such as PRLP0, EIF5A, and YWHAH) that may be interesting from an evolutionary perspective and that could be investigated for use in future goat breeding programs. Our results provide a valuable dataset that will facilitate further research into the reproductive biology of goats.
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Affiliation(s)
- Yufang Liu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China.,College of Life Sciences and Food Engineering, Hebei University of Engineering, Handan, China
| | - Guiling Cao
- College of Agriculture, Liaocheng University, Liaocheng, China
| | - Yujing Xie
- College of Agriculture, Liaocheng University, Liaocheng, China
| | - Mingxing Chu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
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Identification of robust reference genes for studies of gene expression in FFPE melanoma samples and melanoma cell lines. Melanoma Res 2020; 30:26-38. [PMID: 31567589 PMCID: PMC6940030 DOI: 10.1097/cmr.0000000000000644] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Supplemental Digital Content is available in the text. There is an urgent need for novel diagnostic melanoma biomarkers that can predict increased risk of metastasis at an early stage. Relative quantification of gene expression is the preferred method for quantitative validation of potential biomarkers. However, this approach relies on robust tissue-specific reference genes. In the melanoma field, this has been an obstacle due to lack of validated reference genes. Accordingly, we aimed to identify robust reference genes for normalization of gene expression in melanoma. The robustness of 24 candidate reference genes was evaluated across 80 formalin-fixed paraffin-embedded melanomas of different thickness, −/+ ulceration, −/+ reported cases of metastases and of different BRAF mutation status using quantitative real-time PCR. The expression of the same genes and their robustness as normalizers was furthermore evaluated across a number of melanoma cell lines. We show that housekeeping genes like GAPDH do not qualify as stand-alone normalizers of genes expression in melanoma. Instead, we have as the first identified a panel of robust reference genes for normalization of gene expression in melanoma tumors and cultured melanoma cells. We recommend using a geometric mean of the expression of CLTA, MRPL19 and ACTB for normalization of gene expression in melanomas and a geometric mean of the expression of CASC3 and RPS2 for normalization of gene expression in melanoma cell lines. Normalization, according to our recommendation will allow for quantitative validation of potential novel melanoma biomarkers by quantitative real-time PCR.
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Engqvist H, Parris TZ, Kovács A, Rönnerman EW, Sundfeldt K, Karlsson P, Helou K. Validation of Novel Prognostic Biomarkers for Early-Stage Clear-Cell, Endometrioid and Mucinous Ovarian Carcinomas Using Immunohistochemistry. Front Oncol 2020; 10:162. [PMID: 32133296 PMCID: PMC7040170 DOI: 10.3389/fonc.2020.00162] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 01/29/2020] [Indexed: 12/17/2022] Open
Abstract
Early-stage (I and II) ovarian carcinoma patients generally have good prognosis. Yet, some patients die earlier than expected. Thus, it is important to stratify early-stage patients into risk groups to identify those in need of more aggressive treatment regimens. The prognostic value of 29 histotype-specific biomarkers identified using RNA sequencing was evaluated for early-stage clear-cell (CCC), endometrioid (EC) and mucinous (MC) ovarian carcinomas (n = 112) using immunohistochemistry on tissue microarrays. Biomarkers with prognostic significance were further evaluated in an external ovarian carcinoma data set using the web-based Kaplan-Meier plotter tool. Here, we provide evidence of aberrant protein expression patterns and prognostic significance of 17 novel histotype-specific prognostic biomarkers [10 for CCC (ARPC2, CCT5, GNB1, KCTD10, NUP155, RPL13A, RPL37, SETD3, SMYD2, TRIO), three for EC (CECR1, KIF26B, PIK3CA), and four for MC (CHEK1, FOXM1, KIF23, PARPBP)], suggesting biological heterogeneity within the histotypes. Combined predictive models comprising the protein expression status of the validated CCC, EC and MC biomarkers together with established clinical markers (age, stage, CA125, ploidy) improved the predictive power in comparison with models containing established clinical markers alone, further strengthening the importance of the biomarkers in ovarian carcinoma. Further, even improved predictive powers were demonstrated when combining these models with our previously identified prognostic biomarkers PITHD1 (CCC) and GPR158 (MC). Moreover, the proteins demonstrated improved risk prediction of CCC-, EC-, and MC-associated ovarian carcinoma survival. The novel histotype-specific prognostic biomarkers may not only improve prognostication and patient stratification of early-stage ovarian carcinomas, but may also guide future clinical therapy decisions.
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Affiliation(s)
- Hanna Engqvist
- Department of Oncology, Sahlgrenska Cancer Center, Institute of Clinical Sciences, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | - Toshima Z. Parris
- Department of Oncology, Sahlgrenska Cancer Center, Institute of Clinical Sciences, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | - Anikó Kovács
- Department of Clinical Pathology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Elisabeth Werner Rönnerman
- Department of Oncology, Sahlgrenska Cancer Center, Institute of Clinical Sciences, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
- Department of Clinical Pathology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Karin Sundfeldt
- Department of Obstetrics and Gynecology, Sahlgrenska Cancer Center, Institute of Clinical Sciences, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | - Per Karlsson
- Department of Oncology, Sahlgrenska Cancer Center, Institute of Clinical Sciences, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | - Khalil Helou
- Department of Oncology, Sahlgrenska Cancer Center, Institute of Clinical Sciences, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
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Tikhonova MA, Amstislavskaya TG, Belichenko VM, Fedoseeva LA, Kovalenko SP, Pisareva EE, Avdeeva AS, Kolosova NG, Belyaev ND, Aftanas LI. Modulation of the expression of genes related to the system of amyloid-beta metabolism in the brain as a novel mechanism of ceftriaxone neuroprotective properties. BMC Neurosci 2018; 19:13. [PMID: 29745864 PMCID: PMC5998892 DOI: 10.1186/s12868-018-0412-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Background The dominant hypothesis about the pathogenesis of Alzheimer’s disease (AD) is the “amyloid cascade” concept and modulating the expression of proteins involved in the metabolism of amyloid-beta (Aβ) is proposed as an effective strategy for the prevention and therapy of AD. Recently, we found that an antibiotic ceftriaxone (CEF), which possesses neuroprotective activity, reduced cognitive deficits and neurodegenerative changes in OXYS rats, a model of sporadic AD. The molecular mechanisms of this effect are not completely clear, we suggested that the drug might serve as the regulator of the expression of the genes involved in the metabolism of Aβ and the pathogenesis of AD. The study was aimed to determine the effects of CEF on mRNA levels of Bace1 (encoding β-secretase BACE1 involved in Aβ production), Mme, Ide, Ece1, Ace2 (encoding enzymes involved in Aβ degradation), Epo (encoding erythropoietin related to endothelial function and clearance of Aβ across the blood brain barrier) in the frontal cortex, hippocampus, striatum, hypothalamus, and amygdala of OXYS and Wistar (control strain) male rats. Starting from the age of 14 weeks, animals received CEF (100 mg/kg/day, i.p., 36 days) or saline. mRNA levels were evaluated with RT-qPCR method. Biochemical parameters of plasma were measured for control of system effects of the treatment. Results To better understand strain variations studied here, we compared the gene expression between untreated OXYS and Wistar rats. This comparison showed a significant decrease in mRNA levels of Ace2 in the frontal cortex and hypothalamus, and of Actb in the amygdala of untreated OXYS rats. Analysis of potential effects of CEF revealed its novel targets. In the compound-treated OXYS cohort, CEF diminished mRNA levels of Bace1 and Ace2 in the hypothalamus, and Aktb in the frontal cortex. Furthermore, CEF augmented Mme, Ide, and Epo mRNA levels in the amygdala as well as the levels of Ece1 and Aktb in the striatum. Finally, CEF also attenuated the activity of ALT and AST in plasma of OXYS rats. Conclusion Those findings disclosed novel targets for CEF action that might be involved into neuroprotective mechanisms at early, pre-plaque stages of AD-like pathology development.
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Affiliation(s)
- Maria A Tikhonova
- Federal State Budgetary Scientific Institution "Scientific Research Institute of Physiology and Basic Medicine" (SRIPhBM), Timakov St., 4, Novosibirsk, 630117, Russia. .,Novosibirsk State University, Novosibirsk, 630090, Russia.
| | - Tamara G Amstislavskaya
- Federal State Budgetary Scientific Institution "Scientific Research Institute of Physiology and Basic Medicine" (SRIPhBM), Timakov St., 4, Novosibirsk, 630117, Russia.,Novosibirsk State University, Novosibirsk, 630090, Russia
| | - Victor M Belichenko
- Federal State Budgetary Scientific Institution "Scientific Research Institute of Physiology and Basic Medicine" (SRIPhBM), Timakov St., 4, Novosibirsk, 630117, Russia
| | - Larisa A Fedoseeva
- Federal State Budgetary Scientific Institution "Scientific Research Institute of Physiology and Basic Medicine" (SRIPhBM), Timakov St., 4, Novosibirsk, 630117, Russia.,Federal Research Center "Institute of Cytology and Genetics", Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia
| | - Sergey P Kovalenko
- Federal State Budgetary Scientific Institution "Scientific Research Institute of Physiology and Basic Medicine" (SRIPhBM), Timakov St., 4, Novosibirsk, 630117, Russia
| | - Ekaterina E Pisareva
- Federal State Budgetary Scientific Institution "Scientific Research Institute of Physiology and Basic Medicine" (SRIPhBM), Timakov St., 4, Novosibirsk, 630117, Russia
| | - Alla S Avdeeva
- Federal State Budgetary Scientific Institution "Scientific Research Institute of Physiology and Basic Medicine" (SRIPhBM), Timakov St., 4, Novosibirsk, 630117, Russia
| | - Nataliya G Kolosova
- Federal Research Center "Institute of Cytology and Genetics", Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia
| | | | - Lyubomir I Aftanas
- Federal State Budgetary Scientific Institution "Scientific Research Institute of Physiology and Basic Medicine" (SRIPhBM), Timakov St., 4, Novosibirsk, 630117, Russia.,Novosibirsk State University, Novosibirsk, 630090, Russia
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Yang P, Chen N, Yang D, Crane J, Huang B, Dong R, Yi X, Guo J, Cai J, Wang Z. Cervical cancer cell-derived angiopoietins promote tumor progression. Tumour Biol 2017; 39:1010428317711658. [PMID: 28720059 DOI: 10.1177/1010428317711658] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Metastatic or recurrent cervical cancer has limited treatment options and a high rate of mortality. Although anti-vascular endothelial growth factor drugs have shown great promise as a therapeutic target for treatment of advanced cervical cancer, drug resistance and class-specific side effects negate long-term benefits. The identification of alternative anti-angiogenic factors will be critical for future drug development for advanced or recurrent cervical cancer. In this study, we found that angiopoietins and Tie receptors were highly expressed in cervical cancer cells. Tie-2 expression in tumor cells predicted poorer prognosis. Wound closure assay and Transwell assay showed that upregulated or downregulated Ang-1 and Ang-2 expression promoted or reduced cervical cancer cell lines migration and invasion, respectively. In subcutaneous xenograft models of cervical cancer, downregulation of Ang-1 and Ang-2 attenuated tumor growth. The expression of vimentin and endomucin and microvessel density were all significantly decreased in the siAng-1 group and siAng-2 group relative to the infection control group. Our data support that dual inhibition of Ang-1 and Ang-2 may be an alternative target for anti-angiogenic adjuvant therapy in advanced or recurrent cervical squamous cell cancer.
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Affiliation(s)
- Ping Yang
- 1 Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P.R. China.,2 Department of Obstetrics and Gynecology, First Affiliated Hospital, School of Medicine, Shihezi University, Shihezi, P.R. China.,3 Department of Orthopaedic Surgery, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Na Chen
- 1 Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P.R. China
| | - Dongyun Yang
- 1 Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P.R. China
| | - Janet Crane
- 3 Department of Orthopaedic Surgery, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,4 Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Bangxing Huang
- 1 Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P.R. China
| | - Ruiqing Dong
- 5 Department of Obstetrics and Gynecology, Tianyou Hospital Attended to Wuhan University of Science and Technology, Wuhan, P.R. China
| | - Xiaoqing Yi
- 1 Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P.R. China
| | - Jing Guo
- 1 Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P.R. China
| | - Jing Cai
- 1 Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P.R. China
| | - Zehua Wang
- 1 Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P.R. China
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Watanabe M, Hashida S, Yamamoto H, Matsubara T, Ohtsuka T, Suzawa K, Maki Y, Soh J, Asano H, Tsukuda K, Toyooka S, Miyoshi S. Estimation of age-related DNA degradation from formalin-fixed and paraffin-embedded tissue according to the extraction methods. Exp Ther Med 2017; 14:2683-2688. [PMID: 28962212 DOI: 10.3892/etm.2017.4797] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 02/14/2017] [Indexed: 12/12/2022] Open
Abstract
Techniques for the extraction and use of nucleic acids from formalin-fixed and paraffin-embedded (FFPE) tissues, preserved over long time periods in libraries, have been developed. However, DNA extracted from FFPE tissues is generally damaged, and long-term storage may affect DNA quality. Therefore, it is important to elucidate the effect of long-term storage on FFPE tissues and evaluate the techniques used to extract DNA from them. In the present study, the yield, purity, and integrity of DNA in FFPE tissue samples was evaluated. Two DNA extraction techniques were used: A silica-binding DNA collection method using QIAamp DNA FFPE Tissue kit (QIA) and a total tissue DNA collection method using a WaxFree DNA extraction kit (WAX). A total of 25 FFPE tissues from lung adenocarcinomas were studied, which had been surgically resected and fixed at Okayama University Hospital prior to examination and subsequent storage at room temperature for 0.5, 3, 6, 9 and 12 years. Extracted DNA was quantified using ultraviolet absorbance, fluorescent dye, and quantitative polymerase chain reaction (qPCR). The quality of the DNA was defined by the absorbance ratio of 260 to 280 nm (A260/280) and Q-score, which is the quantitative value of qPCR product size ratio. The results demonstrated that the yield of total DNA extracted using WAX was significantly greater than when QIA was used (P<0.01); however, DNA extracted using WAX included more contaminants and was significantly more fragmented compared with DNA extracted using QIA (P<0.01). Aging had no significant effect on absolute DNA yield or DNA purity, although it did significantly contribute to increased DNA degradation for both QIA and WAX extraction (QIA P=0.02, WAX P=0.03; 0.5 years vs. 3 years, QIA P<0.01, WAX P=0.03; 9 years vs. 12 years). Both extraction methods are viable depending on whether high yield or high quality of extracted DNA is required. However, due to the increased degradation with age, storage time limits the available DNA in FFPE tissues regardless of the extraction method.
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Affiliation(s)
- Mototsugu Watanabe
- Department of Thoracic, Breast and Endocrine Surgery, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama 700-8558, Japan
| | - Shinsuke Hashida
- Department of Thoracic, Breast and Endocrine Surgery, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama 700-8558, Japan.,Department of Clinical Genomic Medicine, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama 700-8558, Japan
| | - Hiromasa Yamamoto
- Department of Thoracic, Breast and Endocrine Surgery, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama 700-8558, Japan
| | - Takehiro Matsubara
- Okayama University Hospital Biobank, Okayama University Hospital, Okayama 700-8558, Japan
| | - Tomoaki Ohtsuka
- Department of Thoracic, Breast and Endocrine Surgery, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama 700-8558, Japan
| | - Ken Suzawa
- Department of Thoracic, Breast and Endocrine Surgery, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama 700-8558, Japan
| | - Yuho Maki
- Department of Thoracic, Breast and Endocrine Surgery, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama 700-8558, Japan
| | - Junichi Soh
- Department of Thoracic, Breast and Endocrine Surgery, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama 700-8558, Japan
| | - Hiroaki Asano
- Department of Thoracic, Breast and Endocrine Surgery, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama 700-8558, Japan
| | - Kazunori Tsukuda
- Department of Thoracic, Breast and Endocrine Surgery, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama 700-8558, Japan
| | - Shinichi Toyooka
- Department of Thoracic, Breast and Endocrine Surgery, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama 700-8558, Japan.,Department of Clinical Genomic Medicine, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama 700-8558, Japan
| | - Shinichiro Miyoshi
- Department of Thoracic, Breast and Endocrine Surgery, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama 700-8558, Japan
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10
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Wu J, Li S, Ma R, Sharma A, Bai S, Dun B, Cao H, Jing C, She J, Feng J. Tumor profiling of co-regulated receptor tyrosine kinase and chemoresistant genes reveal different targeting options for lung and gastroesophageal cancers. Am J Transl Res 2016; 8:5729-5740. [PMID: 28078044 PMCID: PMC5209524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Accepted: 09/10/2016] [Indexed: 06/06/2023]
Abstract
The expression of a number of genes can influence the response rates to chemotherapy while genes encoding receptor tyrosine kinases (RTKs) determine the response to most targeted cancer therapies currently used in clinics. In this study, we evaluated seven genes known to influence chemotherapeutic response (ERCC1, BRCA1, RRM1, TUBB3, STMN1, TYMS, and TOP2A) and five RTKs (EGFR, ERBB2, PDGFRB, VEGFR1 and VEGFR2) in non-small cell lung cancer (NSCLC) and esophagus cancer (EC) and the data are compared to gastric cancer (GC) data reported previously. We demonstrate significant differences in the expression profiles between different cancer types as well as heterogeneity among patients within the same cancer type. In all three cancer types, five chemoresistant genes (TOP2A, STMN1, TYMS, BRCA1 and RRM1) are coordinately up-regulated in almost all EC, approximately 90% of NSCLC and one third of GC patients. Most EC and nearly half of GC patients have increased expression of the three RTKs critical to angiogenesis (PDGFR, VEGFR1 and VEGFR2), while almost none of the NSCLC patients have elevated expression of angiogenic RTKs. A variable percentage of patients in the three cancer types show upregulation of the EGFR family RTKs, EGFR and/or ERBB2. It is of interest to note that approximately 10% of the NSCLC and GC patients are triple-negative for the chemosensitivity genes, angiogenic and EGFR RTK genes. The results suggest significant gene expression differences between different cancer types as well as heterogeneity within each cancer type and therefore different molecules should be targeted for future drug development and clinical trials.
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Affiliation(s)
- Jianzhong Wu
- Clinical Oncology Research Center, Jiangsu Cancer HospitalNanjing, Jiangsu Province, People’s Republic of China
| | - Shuchun Li
- Center for Biotechnology and Genomic Medicine, Medical College of Georgia, Augusta UniversityAugusta, GA, USA
| | - Rong Ma
- Clinical Oncology Research Center, Jiangsu Cancer HospitalNanjing, Jiangsu Province, People’s Republic of China
| | - Ashok Sharma
- Center for Biotechnology and Genomic Medicine, Medical College of Georgia, Augusta UniversityAugusta, GA, USA
| | - Shan Bai
- Center for Biotechnology and Genomic Medicine, Medical College of Georgia, Augusta UniversityAugusta, GA, USA
| | - Boying Dun
- Center for Biotechnology and Genomic Medicine, Medical College of Georgia, Augusta UniversityAugusta, GA, USA
| | - Haixia Cao
- Clinical Oncology Research Center, Jiangsu Cancer HospitalNanjing, Jiangsu Province, People’s Republic of China
| | - Changwen Jing
- Clinical Oncology Research Center, Jiangsu Cancer HospitalNanjing, Jiangsu Province, People’s Republic of China
| | - Jinxiong She
- Center for Biotechnology and Genomic Medicine, Medical College of Georgia, Augusta UniversityAugusta, GA, USA
| | - Jifeng Feng
- Clinical Oncology Research Center, Jiangsu Cancer HospitalNanjing, Jiangsu Province, People’s Republic of China
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11
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Liu BR, Huang YW, Aronstam RS, Lee HJ. Identification of a Short Cell-Penetrating Peptide from Bovine Lactoferricin for Intracellular Delivery of DNA in Human A549 Cells. PLoS One 2016; 11:e0150439. [PMID: 26942714 PMCID: PMC4778846 DOI: 10.1371/journal.pone.0150439] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Accepted: 02/12/2016] [Indexed: 11/19/2022] Open
Abstract
Cell-penetrating peptides (CPPs) have been shown to deliver cargos, including protein, DNA, RNA, and nanomaterials, in fully active forms into live cells. Most of the CPP sequences in use today are based on non-native proteins that may be immunogenic. Here we demonstrate that the L5a CPP (RRWQW) from bovine lactoferricin (LFcin), stably and noncovalently complexed with plasmid DNA and prepared at an optimal nitrogen/phosphate ratio of 12, is able to efficiently enter into human lung cancer A549 cells. The L5a CPP delivered a plasmid containing the enhanced green fluorescent protein (EGFP) coding sequence that was subsequently expressed in cells, as revealed by real-time PCR and fluorescent microscopy at the mRNA and protein levels, respectively. Treatment with calcium chloride increased the level of gene expression, without affecting CPP-mediated transfection efficiency. Zeta-potential analysis revealed that positively electrostatic interactions of CPP/DNA complexes correlated with CPP-mediated transport. The L5a and L5a/DNA complexes were not cytotoxic. This biomimetic LFcin L5a represents one of the shortest effective CPPs and could be a promising lead peptide with less immunogenic for DNA delivery in gene therapy.
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Affiliation(s)
- Betty R. Liu
- Department of Natural Resources and Environmental Studies, National Dong Hwa University, Hualien, 974, Taiwan
| | - Yue-Wern Huang
- Department of Biological Sciences, Missouri University of Science and Technology, Rolla, Missouri, 65409–1120, United States of America
| | - Robert S. Aronstam
- College of Science and Technology, Bloomsburg University of Pennsylvania, Bloomsburg, Pennsylvania, 17815–1301, United States of America
| | - Han-Jung Lee
- Department of Natural Resources and Environmental Studies, National Dong Hwa University, Hualien, 974, Taiwan
- * E-mail:
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12
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The Orthology Clause in the Next Generation Sequencing Era: Novel Reference Genes Identified by RNA-seq in Humans Improve Normalization of Neonatal Equine Ovary RT-qPCR Data. PLoS One 2015; 10:e0142122. [PMID: 26536597 PMCID: PMC4633174 DOI: 10.1371/journal.pone.0142122] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 10/16/2015] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND Vertebrate evolution is accompanied by a substantial conservation of transcriptional programs with more than a third of unique orthologous genes showing constrained levels of expression. Moreover, there are genes and exons exhibiting excellent expression stability according to RNA-seq data across a panel of eighteen tissues including the ovary (Human Body Map 2.0). RESULTS We hypothesized that orthologs of these exons would also be highly uniformly expressed across neonatal ovaries of the horse, which would render them appropriate reference genes (RGs) for normalization of reverse transcription quantitative PCR (RT-qPCR) data in this context. The expression stability of eleven novel RGs (C1orf43, CHMP2A, EMC7, GPI, PSMB2, PSMB4, RAB7A, REEP5, SNRPD3, VCP and VPS29) was assessed by RT-qPCR in ovaries of seven neonatal fillies and compared to that of the expressed repetitive element ERE-B, two universal (OAZ1 and RPS29) and four traditional RGs (ACTB, GAPDH, UBB and B2M). Expression stability analyzed with the software tool RefFinder top ranked the normalization factor constituted of the genes SNRPD3 and VCP, a gene pair that is not co-expressed according to COEXPRESdb and GeneMANIA. The traditional RGs GAPDH, B2M, ACTB and UBB were only ranked 3rd and 12th to 14th, respectively. CONCLUSIONS The functional diversity of the novel RGs likely facilitates expression studies over a wide range of physiological and pathological contexts related to the neonatal equine ovary. In addition, this study augments the potential for RT-qPCR-based profiling of human samples by introducing seven new human RG assays (C1orf43, CHMP2A, EMC7, GPI, RAB7A, VPS29 and UBB).
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13
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Iser I, de Campos R, Bertoni A, Wink M. Identification of valid endogenous control genes for determining gene expression in C6 glioma cell line treated with conditioned medium from adipose-derived stem cell. Biomed Pharmacother 2015; 75:75-82. [DOI: 10.1016/j.biopha.2015.08.035] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2015] [Accepted: 08/23/2015] [Indexed: 12/12/2022] Open
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14
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Li SC, Ma R, Wu JZ, Xiao X, Wu W, Li G, Chen B, Sharma A, Bai S, Dun BY, She JX, Tang JH. Delineation of gastric cancer subtypes by co-regulated expression of receptor tyrosine kinases and chemosensitivity genes. Am J Transl Res 2015; 7:1429-1439. [PMID: 26396673 PMCID: PMC4568798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2015] [Accepted: 06/22/2015] [Indexed: 06/05/2023]
Abstract
Chemotherapy plays a key role in improving disease-free survival and overall survival of gastric cancer (GC); however, response rates are variable and a non-negligible proportion of patients undergo toxic and costly chemotherapeutic regimens without a survival benefit. Several studies have shown the existence of GC subtypes which may predict survival and respond differently to chemotherapy. It is also known that the expression level of chemotherapy-related and target therapy-related genes correlates with response to specific antitumor drugs. Nevertheless, these genes have not been considered jointly to define GC subtypes. In this study, we evaluated seven genes known to influence chemotherapeutic response (ERCC1, BRCA1, RRM1, TUBB3, STMN1, TYMS and TOP2A) and five receptor tyrosine kinases (RTKs) (EGFR, ERBB2, PDGFRB, VEGFR1 and VEGFR2). We demonstrate significant heterogeneity of gene expression among GC patients and identified four GC subtypes using the expression profiles of eight genes in two co-regulation groups: chemosensitivity (BRCA1, STMN1, TYMS and TOP2A) and RTKs (EGFR, PDGFRB, VEGFR1 and VEGFR2). The results are of immediate translational value regarding GC diagnostics and therapeutics, as many of these genes are curently widely used in relevant clinical testing.
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Affiliation(s)
- Shu-Chun Li
- Clinical Oncology Research Center, Jiangsu Cancer Hospital Nanjing, Jiangsu Province, People's Republic of China ; Center for Biotechnology and Genomic Medicine, Medical College of Georgia, Georgia Regents University Augusta, GA ; Sino-American Institute of Translational Medicine, Nanjing Tech University Nanjing, Jiangsu Province, People's Republic of China
| | - Rong Ma
- Clinical Oncology Research Center, Jiangsu Cancer Hospital Nanjing, Jiangsu Province, People's Republic of China
| | - Jian-Zhong Wu
- Clinical Oncology Research Center, Jiangsu Cancer Hospital Nanjing, Jiangsu Province, People's Republic of China
| | - Xia Xiao
- Sino-American Institute of Translational Medicine, Nanjing Tech University Nanjing, Jiangsu Province, People's Republic of China
| | - Wei Wu
- Zhenjiang Jintai Life Technologies Zhenjiang, Jiangsu Province, People's Republic of China
| | - Gang Li
- Clinical Oncology Research Center, Jiangsu Cancer Hospital Nanjing, Jiangsu Province, People's Republic of China
| | - Bo Chen
- Center for Biotechnology and Genomic Medicine, Medical College of Georgia, Georgia Regents University Augusta, GA ; Sino-American Institute of Translational Medicine, Nanjing Tech University Nanjing, Jiangsu Province, People's Republic of China
| | - Ashok Sharma
- Center for Biotechnology and Genomic Medicine, Medical College of Georgia, Georgia Regents University Augusta, GA
| | - Shan Bai
- Center for Biotechnology and Genomic Medicine, Medical College of Georgia, Georgia Regents University Augusta, GA
| | - Bo-Ying Dun
- Center for Biotechnology and Genomic Medicine, Medical College of Georgia, Georgia Regents University Augusta, GA
| | - Jin-Xiong She
- Center for Biotechnology and Genomic Medicine, Medical College of Georgia, Georgia Regents University Augusta, GA
| | - Jin-Hai Tang
- Clinical Oncology Research Center, Jiangsu Cancer Hospital Nanjing, Jiangsu Province, People's Republic of China
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15
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Wen HC, Chuu CP, Chen CY, Shiah SG, Kung HJ, King KL, Su LC, Chang SC, Chang CH. Elevation of soluble guanylate cyclase suppresses proliferation and survival of human breast cancer cells. PLoS One 2015; 10:e0125518. [PMID: 25928539 PMCID: PMC4416047 DOI: 10.1371/journal.pone.0125518] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2014] [Accepted: 03/24/2015] [Indexed: 01/22/2023] Open
Abstract
Nitric oxide (NO) is an essential signaling molecule in biological systems. Soluble guanylate cyclase (sGC), composing of α1 and β1 subunit, is the receptor for NO. Using radioimmunoassay, we discovered that activation of sGC by treatment with bradykinin or sodium nitroprusside (SNP) is impaired in MCF-7 and MDA-MB-231 breast cancer cells as compared to normal breast epithelial 184A1 cells. The 184A1 cells expressed both sGC α1 and sGCβ1 mRNAs. However, levels of sGCβ1 mRNAs were relatively lower in MCF-7 cells while both mRNA of sGC subunits were absent in MDA-MB-231 cells. Treatment with DNA methyltransferase inhibitor 5-aza-2’-deoxycytidine (5-aza-dC) increased mRNA levels of both sGCα1 and sGCβ1 in MDA-MB-231 cells but only sGCβ1 mRNAs in MCF-7 cells. The 5-aza-dC treatment increased the SNP-induced cGMP production in MCF-7 and MDA-MB-231, but not in 184A1 cells. Bisulfite sequencing revealed that the promoter of sGCα1 in MDA-MB-231 cells and promoter of sGCβ1 in MCF-7 cells were methylated. Promoter hypermethylation of sGCα1 and sGCβ1 was found in 1 out of 10 breast cancer patients. Over-expression of both sGC subunits in MDA-MB-231 cells induced apoptosis and growth inhibition in vitro as well as reduced tumor incidence and tumor growth rate of MDA-MB-231 xenografts in nude mice. Elevation of sGC reduced protein abundance of Bcl-2, Bcl-xL, Cdc2, Cdc25A, Cyclin B1, Cyclin D1, Cdk6, c-Myc, and Skp2 while increased protein expression of p53. Our study demonstrated that down-regulation of sGC, partially due to promoter methylation, provides growth and survival advantage in human breast cancer cells.
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Affiliation(s)
- Hui-Chin Wen
- Institute of Cellular and System Medicine, National Health Research Institutes, Miaoli County, Taiwan
| | - Chih-Pin Chuu
- Institute of Cellular and System Medicine, National Health Research Institutes, Miaoli County, Taiwan
| | - Chen-Yu Chen
- Institute of Cellular and System Medicine, National Health Research Institutes, Miaoli County, Taiwan
| | - Shine-Gwo Shiah
- National Institute of Cancer Research, National Health Research Institutes, Miaoli County, Taiwan
| | - Hsing-Jien Kung
- Institute of Molecular and Genomic Medicine, National Health Research Institutes, Miaoli County, Taiwan
| | - Kuang-Liang King
- Division of General Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei City, Taiwan
| | - Liang-Chen Su
- Institute of Cellular and System Medicine, National Health Research Institutes, Miaoli County, Taiwan
| | - Shi-Chuan Chang
- Chest Department, Taipei Veterans General Hospital, Taipei City, Taiwan
- Institute of Emergency and Critical Care Medicine, National Yang-Ming University, Taipei City, Taiwan
- * E-mail: (SCC); (CHC)
| | - Chung-Ho Chang
- Institute of Cellular and System Medicine, National Health Research Institutes, Miaoli County, Taiwan
- Graduate Institute of Basic Medical Science, Ph.D. Program of Aging, China Medical University, Taichung City, Taiwan
- * E-mail: (SCC); (CHC)
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16
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Aithal MGS, Rajeswari N. Validation of housekeeping genes for gene expression analysis in glioblastoma using quantitative real-time polymerase chain reaction. Brain Tumor Res Treat 2015; 3:24-9. [PMID: 25977903 PMCID: PMC4426273 DOI: 10.14791/btrt.2015.3.1.24] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Revised: 03/23/2015] [Accepted: 04/02/2015] [Indexed: 11/21/2022] Open
Abstract
Background Quantitative real-time polymerase chain reaction (qPCR) is the most reliable tool for gene expression studies. Selection of housekeeping genes (HKGs) that are having most stable expression is critical to carry out accurate gene expression profiling. There is no 'universal' HKG having stable expression in all kinds of tissues under all experimental conditions. Methods The present study aims to identify most appropriate HKGs for gene expression analysis in glioblastoma (GBM) samples. Based on literature survey, six most commonly used HKGs that are invariant in GBM were chosen. We performed qPCR using RNA from formalin fixed paraffin embedded GBM samples and normal brain samples to investigate the expression pattern of HPRT, GAPDH, TBP, B2M, B2M, RPL13A, and RN18S1 with different abundance. A simple Δcycle threshold approach was employed to calculate the fold change. Results Our study shows that the expression of RPL13A and TBP were found to be most stable across all the samples and are thus suitable for gene expression analysis in human GBM. Except for TBP, none of the other conventionally used HKGs in GBM studies e.g., HPRT and GAPDH were found to be suitable as they showed variation in RNA expression. Conclusion Validation of HKGs is therefore immensely specific for a particular experimental setup and is crucial in assessing any new setup.
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Affiliation(s)
- Madhuri G S Aithal
- Department of Biotechnology, Dayananda Sagar College of Engineering, Bangalore, India
| | - Narayanappa Rajeswari
- Department of Biotechnology, Dayananda Sagar College of Engineering, Bangalore, India
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17
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Aggerholm-Pedersen N, Safwat A, Bærentzen S, Nordsmark M, Nielsen OS, Alsner J, Sørensen BS. The importance of reference gene analysis of formalin-fixed, paraffin-embedded samples from sarcoma patients - an often underestimated problem. Transl Oncol 2014; 7:687-93. [PMID: 25500077 PMCID: PMC4311021 DOI: 10.1016/j.tranon.2014.09.012] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Revised: 09/24/2014] [Accepted: 09/26/2014] [Indexed: 02/07/2023] Open
Abstract
OBJECTIVE Reverse transcription quantitative real-time polymerase chain reaction is efficient for quantification of gene expression, but the choice of reference genes is of paramount importance as it is essential for correct interpretation of data. This is complicated by the fact that the materials often available are routinely collected formalin-fixed, paraffin-embedded (FFPE) samples in which the mRNA is known to be highly degraded. The purpose of this study was to investigate 22 potential reference genes in sarcoma FFPE samples and to study the variation in expression level within different samples taken from the same tumor and between different histologic types. METHODS Twenty-nine patients treated for sarcoma were enrolled. The samples encompassed 82 (FFPE) specimens. Extraction of total RNA from 7-μm FFPE sections was performed using a fully automated, bead-base RNA isolation procedure, and 22 potential reference genes were analyzed by reverse transcription quantitative real-time polymerase chain reaction. The stability of the genes was analyzed by RealTime Statminer. The intrasamples variation and the interclass correlation coefficients were calculated. The linear regression model was used to calculate the degradation of the mRNA over time. RESULTS The quality of RNA was sufficient for analysis in 84% of the samples. Recommended reference genes differed with histologic types. However, PPIA, SF3A1, and MRPL19 were stably expressed regardless of the histologic type included. The variation in ∆Cq value for samples from the same patients was similar to the variation between patients. It was possible to compensate for the time-dependent degradation of the mRNA when normalization was made using the selected reference genes. CONCLUSION PPIA, SF3A1, and MRPL19 are suitable reference genes for normalization in gene expression studies of FFPE samples from sarcoma regardless of the histology.
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Affiliation(s)
| | - Akmal Safwat
- Department of Oncology, Aarhus University Hospital, Aarhus, Denmark
| | - Steen Bærentzen
- Department of Pathology, Aarhus University Hospital, Aarhus, Denmark
| | | | | | - Jan Alsner
- Department of Experimental Clinical Oncology, Aarhus University Hospital, Aarhus, Denmark
| | - Brita S Sørensen
- Department of Experimental Clinical Oncology, Aarhus University Hospital, Aarhus, Denmark
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18
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Zhang H, Qiu J, Ye C, Yang D, Gao L, Su Y, Tang X, Xu N, Zhang D, Xiong L, Mao Y, Li F, Zhu J. ROR1 expression correlated with poor clinical outcome in human ovarian cancer. Sci Rep 2014; 4:5811. [PMID: 25056203 PMCID: PMC4108928 DOI: 10.1038/srep05811] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Accepted: 07/03/2014] [Indexed: 12/18/2022] Open
Abstract
The receptor-tyrosine-kinase-like orphan receptor 1 (ROR1) is a transmembrane protein belongs to receptor tyrosine kinase (RTK) family. This study aimed to examine the expression of ROR1 in human ovarian cancer and investigate the relationship between its expression and the prognosis of ovarian cancer patients. In this present study, one-step quantitative reverse transcription-polymerase chain reaction (15 ovarian cancer samples of high FIGO stage, 15 ovarian cancer samples of low FIGO stage and nine normal ovary tissue samples) and immunohistochemistry by tissue microarrays (100 ovarian cancer samples and 50 normal ovary samples) were performed to characterize expression of the ROR1 gene in ovarian cancer. Kaplan-Meier survival and Cox regression analyses were executed to evaluate the prognosis of ovarian cancer. The results of qPCR and IHC analysis showed that the expression of ROR1 in ovarian cancer was significantly higher than that in normal ovary tissues (all p < 0.05). Survival analysis showed that ROR1 protein expression was one of the independent prognostic factors for disease-free survival and overall survival (both p < 0.05). The data suggest that ROR1 expression is correlated with malignant attributes of ovarian cancer and it may serve as a novel prognostic marker in ovarian cancer.
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Affiliation(s)
- Huilin Zhang
- 1] Department of Gynecology and Obstetrics, Nanjing Maternal and Children Care Hospital Affiliated to Nanjing Medical University, Jiangsu, China [2]
| | - Jinrong Qiu
- 1] Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Jiangsu, China [2]
| | - Chunping Ye
- Department of Gynecology and Obstetrics, Nanjing Maternal and Children Care Hospital Affiliated to Nanjing Medical University, Jiangsu, China
| | - Dazhen Yang
- Department of Gynecology and Obstetrics, Nanjing Maternal and Children Care Hospital Affiliated to Nanjing Medical University, Jiangsu, China
| | - Lingjuan Gao
- Department of Gynecology and Obstetrics, Nanjing Maternal and Children Care Hospital Affiliated to Nanjing Medical University, Jiangsu, China
| | - Yiping Su
- Department of Gynecology and Obstetrics, Nanjing Maternal and Children Care Hospital Affiliated to Nanjing Medical University, Jiangsu, China
| | - Xiaojun Tang
- The Key Laboratory of Cancer Biomarkers, Prevention & Treatment Cancer Center and The Key Laboratory of Antibody Technique of Ministry of Health, Nanjing Medical University, Jiangsu, China
| | - Ning Xu
- The Key Laboratory of Cancer Biomarkers, Prevention & Treatment Cancer Center and The Key Laboratory of Antibody Technique of Ministry of Health, Nanjing Medical University, Jiangsu, China
| | - Dawei Zhang
- Department of Otolaryngology-Head and Neck Surgery, The Second Affiliated Hospital of Nanjing Medical University, Jiangsu, China
| | - Lin Xiong
- Department of Pathology, The Second Affiliated Hospital of Nanjing Medical University, Jiangsu, China
| | - Yuan Mao
- Department of Otolaryngology-Head and Neck Surgery, Jiangsu Provincial Hospital, Jiangsu, China
| | - Fengshan Li
- Department of Pathology, Nanjing Maternal and Children Care Hospital Affiliated to Nanjing Medical University, Jiangsu, China
| | - Jin Zhu
- 1] The Key Laboratory of Cancer Biomarkers, Prevention & Treatment Cancer Center and The Key Laboratory of Antibody Technique of Ministry of Health, Nanjing Medical University, Jiangsu, China [2] Huadong Medical Institute of Biotechniques, Jiangsu, China
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