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Mirsalami SM, Mirsalami M. Evolutionary adaptation in the laboratory and the process of retrograde engineering augment autotrophic proliferation in Saccharomyces cerevisiae. Biochem Eng J 2024; 205:109278. [DOI: 10.1016/j.bej.2024.109278] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/15/2024]
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2
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Cressoni ACL, Penariol LBC, Padovan CC, Orellana MD, Rosa-E-Silva JC, Poli-Neto OB, Ferriani RA, de Paz CCP, Meola J. Downregulation of DROSHA: Could It Affect miRNA Biogenesis in Endometriotic Menstrual Blood Mesenchymal Stem Cells? Int J Mol Sci 2023; 24:ijms24065963. [PMID: 36983035 PMCID: PMC10057010 DOI: 10.3390/ijms24065963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Revised: 03/18/2023] [Accepted: 03/19/2023] [Indexed: 03/30/2023] Open
Abstract
Menstrual blood mesenchymal stem cells (MenSCs) have gained prominence in the endometriosis scientific community, given their multifunctional roles in regenerative medicine as a noninvasive source for future clinical applications. In addition, changes in post-transcriptional regulation via miRNAs have been explored in endometriotic MenSCs with a role in modulating proliferation, angiogenesis, differentiation, stemness, self-renewal, and the mesenchymal-epithelial transition process. In this sense, homeostasis of the miRNA biosynthesis pathway is essential for several cellular processes and is related to the self-renewal and differentiation of progenitor cells. However, no studies have investigated the miRNA biogenesis pathway in endometriotic MenSCs. In this study, we profiled the expression of eight central genes for the miRNA biosynthesis pathway under experimental conditions involving a two-dimensional culture of MenSCs obtained from healthy women (n = 10) and women with endometriosis (n = 10) using RT-qPCR and reported a two-fold decrease in DROSHA expression in the disease. In addition, miR-128-3p, miR-27a-3p, miR-27b-3p, miR-181a-5p, miR-181b-5p, miR-452-3p, miR-216a-5p, miR-216b-5p, and miR-93-5p, which have been associated with endometriosis, were identified through in silico analyses as negative regulators of DROSHA. Because DROSHA is essential for miRNA maturation, our findings may justify the identification of different profiles of miRNAs with DROSHA-dependent biogenesis in endometriosis.
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Affiliation(s)
- Ana Clara Lagazzi Cressoni
- Department of Gynecology and Obstetrics, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirão Preto, São Paulo 14049-900, Brazil
| | - Letícia B C Penariol
- Department of Gynecology and Obstetrics, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirão Preto, São Paulo 14049-900, Brazil
| | - Cristiana Carolina Padovan
- Department of Gynecology and Obstetrics, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirão Preto, São Paulo 14049-900, Brazil
| | - Maristela D Orellana
- Regional Blood Center, Medical School of Hemocenter Foundation of Ribeirão Preto, University of Sao Paulo, Ribeirão Preto, São Paulo 14051-140, Brazil
| | - Júlio Cesar Rosa-E-Silva
- Department of Gynecology and Obstetrics, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirão Preto, São Paulo 14049-900, Brazil
| | - Omero Benedicto Poli-Neto
- Department of Gynecology and Obstetrics, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirão Preto, São Paulo 14049-900, Brazil
| | - Rui Alberto Ferriani
- Department of Gynecology and Obstetrics, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirão Preto, São Paulo 14049-900, Brazil
- National Institute of Hormones and Women's Health (Hormona)-CNPq, Porto Alegre 90035-003, Brazil
| | - Cláudia Cristina Paro de Paz
- Department of Genetics, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirão Preto, São Paulo 14049-900, Brazil
| | - Juliana Meola
- Department of Gynecology and Obstetrics, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirão Preto, São Paulo 14049-900, Brazil
- National Institute of Hormones and Women's Health (Hormona)-CNPq, Porto Alegre 90035-003, Brazil
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3
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Kemfack AM, Hernandez-Morato I, Moayedi Y, Pitman MJ. An optimized method for high-quality RNA extraction from distinctive intrinsic laryngeal muscles in the rat model. Sci Rep 2022; 12:21665. [PMID: 36522411 PMCID: PMC9755529 DOI: 10.1038/s41598-022-25643-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 12/02/2022] [Indexed: 12/23/2022] Open
Abstract
Challenges related to high-quality RNA extraction from post-mortem tissue have limited RNA-sequencing (RNA-seq) application in certain skeletal muscle groups, including the intrinsic laryngeal muscles (ILMs). The present study identified critical factors contributing to substandard RNA extraction from the ILMs and established a suitable method that permitted high-throughput analysis. Here, standard techniques for tissue processing were adapted, and an effective means to control confounding effects during specimen preparation was determined. The experimental procedure consistently provided sufficient intact total RNA (N = 68) and RIN ranging between 7.0 and 8.6, which was unprecedented using standard RNA purification protocols. This study confirmed the reproducibility of the workflow through repeated trials at different postnatal time points and across the distinctive ILMs. High-throughput diagnostics from 90 RNA samples indicated no sequencing alignment scores below 70%, validating the extraction strategy. Significant differences between the standard and experimental conditions suggest circumvented challenges and broad applicability to other skeletal muscles. This investigation remains ongoing given the prospect of therapeutic insights to voice, swallowing, and airway disorders. The present methodology supports pioneering global transcriptome investigations in the larynx previously unfounded in literature.
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Affiliation(s)
- Angela M Kemfack
- Department of Otolaryngology-Head & Neck Surgery, Columbia University College of Physicians and Surgeons, New York, NY, 10032, USA
| | - Ignacio Hernandez-Morato
- Department of Otolaryngology-Head & Neck Surgery, Columbia University College of Physicians and Surgeons, New York, NY, 10032, USA.
| | - Yalda Moayedi
- Department of Otolaryngology-Head & Neck Surgery, Columbia University College of Physicians and Surgeons, New York, NY, 10032, USA
- Department of Neurology, Irving Medical Center, Columbia University College of Physicians and Surgeons, New York, NY, USA
| | - Michael J Pitman
- Department of Otolaryngology-Head & Neck Surgery, Columbia University College of Physicians and Surgeons, New York, NY, 10032, USA
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4
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Analysis of therapeutic nucleic acids by capillary electrophoresis. J Pharm Biomed Anal 2022; 219:114928. [PMID: 35853263 DOI: 10.1016/j.jpba.2022.114928] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Revised: 05/04/2022] [Accepted: 07/02/2022] [Indexed: 12/19/2022]
Abstract
Nucleic acids are getting increased attention to fulfill unmet medical needs. The past five years have seen more than ten FDA approvals of nucleic acid based therapeutics. New analytical challenges have been posed in discovery, characterization, quality control and bioanalysis of therapeutic nucleic acids. Capillary electrophoresis (CE) has proven to be an efficient separation technique and has been widely used for analyzing oligonucleotides and nucleic acids. This review discusses the recent technical advances of CE in nucleic acid analysis such as polymeric matrices, separation conditions and detection methods, and the applications of CE to various therapeutic nucleic acids including antisense oligonucleotide (ASO), small interfering ribonucleic acid (siRNA), messenger RNA (mRNA), gene editing tools such as clustered regularly interspaced short palindromic repeats (CRISPR)-based gene and cell therapy, and other nucleic acid related therapeutics.
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5
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A bioinformatics framework for targeted gene expression assay design: Application to in vitro developmental neurotoxicity screening in a rat model. Regul Toxicol Pharmacol 2022; 133:105211. [PMID: 35724854 DOI: 10.1016/j.yrtph.2022.105211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 05/05/2022] [Accepted: 06/13/2022] [Indexed: 11/23/2022]
Abstract
Brain development involves a series of intricately choreographed neuronal differentiation and maturation steps that are acutely vulnerable to interferences from chemical exposures. Many genes involved in neurodevelopmental processes show evolutionarily conserved expression patterns in mammals and may constitute useful indicators/biomarkers for the evaluation of potential developmental neurotoxicity. Based on these premises, this study developed a bioinformatics framework to guide the design of a gene expression-based in vitro developmental neurotoxicity assay targeting evolutionary conserved genes associated with neuronal differentiation and maturation in rat cerebellar granule cells (CGCs). Rat, mouse and human genes involved in neurodevelopment and presenting one-to-one orthology were selected and orthologous exons within these genes were identified. PCR primer sets were designed within these orthologous exons and their specificity was evaluated in silico. The performance and specificity of rat, mouse and human PCR primer sets were then confirmed experimentally. Finally, RT-qPCR analyses in CGCs exposed in vitro to well-known neurotoxicants (Chlorpyrifos and Chlorpyrifos oxon) uncovered perturbations of expression levels for most of the selected genes. This bioinformatics framework for gene and target sequence selection may facilitate the identification of transcriptional biomarkers for developmental neurotoxicity assays and the comparison of gene expression data across experimental models from different mammalian species.
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6
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Vervaeke P, Borgos SE, Sanders NN, Combes F. Regulatory guidelines and preclinical tools to study the biodistribution of RNA therapeutics. Adv Drug Deliv Rev 2022; 184:114236. [PMID: 35351470 PMCID: PMC8957368 DOI: 10.1016/j.addr.2022.114236] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 02/09/2022] [Accepted: 03/23/2022] [Indexed: 12/27/2022]
Abstract
The success of the messenger RNA-based COVID-19 vaccines of Moderna and Pfizer/BioNTech marks the beginning of a new chapter in modern medicine. However, the rapid rise of mRNA therapeutics has resulted in a regulatory framework that is somewhat lagging. The current guidelines either do not apply, do not mention RNA therapeutics, or do not have widely accepted definitions. This review describes the guidelines for preclinical biodistribution studies of mRNA/siRNA therapeutics and highlights the relevant differences for mRNA vaccines. We also discuss the role of in vivo RNA imaging techniques and other assays to fulfill and/or complement the regulatory requirements. Specifically, quantitative whole-body autoradiography, microautoradiography, mass spectrometry-based assays, hybridization techniques (FISH, bDNA), PCR-based methods, in vivo fluorescence imaging, and in vivo bioluminescence imaging, are discussed. We conclude that this new and rapidly evolving class of medicines demands a multi-layered approach to fully understand its biodistribution and in vivo characteristics.
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Affiliation(s)
- P Vervaeke
- Laboratory of Gene Therapy, Department of Veterinary and Biosciences, Faculty of Veterinary Medicine, Ghent University, Heidestraat 19, B-9820 Merelbeke, Belgium
| | - S E Borgos
- SINTEF Industry, Dept. of Biotechnology and Nanomedicine, Research Group Mass Spectrometry, Sem Sælands v. 2A, N-7034 Trondheim, Norway
| | - N N Sanders
- Laboratory of Gene Therapy, Department of Veterinary and Biosciences, Faculty of Veterinary Medicine, Ghent University, Heidestraat 19, B-9820 Merelbeke, Belgium.
| | - F Combes
- SINTEF Industry, Dept. of Biotechnology and Nanomedicine, Research Group Mass Spectrometry, Sem Sælands v. 2A, N-7034 Trondheim, Norway.
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Razak MR, Aris AZ, Md Yusoff F, Yusof ZNB, Kim SD, Kim KW. Assessment of RNA extraction protocols from cladocerans. PLoS One 2022; 17:e0264989. [PMID: 35472091 PMCID: PMC9041806 DOI: 10.1371/journal.pone.0264989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 02/18/2022] [Indexed: 11/18/2022] Open
Abstract
The usage of cladocerans as non-model organisms in ecotoxicological and risk assessment studies has intensified in recent years due to their ecological importance in aquatic ecosystems. The molecular assessment such as gene expression analysis has been introduced in ecotoxicological and risk assessment to link the expression of specific genes to a biological process in the cladocerans. The validity and accuracy of gene expression analysis depends on the quantity, quality and integrity of extracted ribonucleic acid (RNA) of the sample. However, the standard methods of RNA extraction from the cladocerans are still lacking. This study evaluates the extraction of RNA from tropical freshwater cladocerans Moina micrura using two methods: the phenol-chloroform extraction method (QIAzol) and a column-based kit (Qiagen Micro Kit). Glycogen was introduced in both approaches to enhance the recovery of extracted RNA and the extracted RNA was characterised using spectrophotometric analysis (NanoDrop), capillary electrophoresis (Bioanalyzer). Then, the extracted RNA was analysed with reverse transcription polymerase chain reaction (RT-PCR) to validate the RNA extraction method towards downstream gene expression analysis. The results indicate that the column-based kit is most suitable for the extraction of RNA from M. micrura, with the quantity (RNA concentration = 26.90 ± 6.89 ng/μl), quality (A260:230 = 1.95 ± 0.15, A280:230 = 1.85 ± 0.09) and integrity (RNA integrity number, RIN = 7.20 ± 0.16). The RT-PCR analysis shows that the method successfully amplified both alpha tubulin and actin gene at 33-35 cycles (i.e. Ct = 32.64 to 33.48). The results demonstrate that the addition of glycogen is only suitable for the phenol-chloroform extraction method. RNA extraction with high and comprehensive quality control assessment will increase the accuracy and reliability of downstream gene expression, thus providing more ecotoxicological data at the molecular biological level on other freshwater zooplankton species.
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Affiliation(s)
- Muhammad Raznisyafiq Razak
- Faculty of Forestry and Environment, Department of Environment, Universiti Putra Malaysia, Selangor, Malaysia
| | - Ahmad Zaharin Aris
- Faculty of Forestry and Environment, Department of Environment, Universiti Putra Malaysia, Selangor, Malaysia
- International Institute of Aquaculture and Aquatic Sciences, Universiti Putra Malaysia, Negeri Sembilan, Malaysia
| | - Fatimah Md Yusoff
- International Institute of Aquaculture and Aquatic Sciences, Universiti Putra Malaysia, Negeri Sembilan, Malaysia
- Faculty of Agriculture, Department of Aquaculture, Universiti Putra Malaysia, Selangor, Malaysia
| | - Zetty Norhana Balia Yusof
- Faculty of Biotechnology and Biomolecular Science, Department of Biochemistry, Universiti Putra Malaysia, Selangor, Malaysia
- Institute of Bioscience, Universiti Putra Malaysia, Selangor, Malaysia
| | - Sang Don Kim
- School of Earth Sciences and Environmental Engineering, Gwangju Institute of Science and Technology, Buk-gu, Gwangju, Republic of Korea
| | - Kyoung Woong Kim
- School of Earth Sciences and Environmental Engineering, Gwangju Institute of Science and Technology, Buk-gu, Gwangju, Republic of Korea
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8
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Integrity and Stability of PTC Bearing CFTR mRNA and Relevance to Future Modulator Therapies in Cystic Fibrosis. Genes (Basel) 2021; 12:genes12111810. [PMID: 34828417 PMCID: PMC8621375 DOI: 10.3390/genes12111810] [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: 09/29/2021] [Revised: 11/16/2021] [Accepted: 11/18/2021] [Indexed: 12/26/2022] Open
Abstract
Major advances have recently been made in the development and application of CFTR (cystic fibrosis transmembrane conductance regulator) mutation class-specific modulator therapies, but to date, there are no approved modulators for Class I mutations, i.e., those introducing a premature termination codon (PTC) into the CFTR mRNA. Such mutations induce nonsense-mediated decay (NMD), a cellular quality control mechanism that reduces the quantity of PTC bearing mRNAs, presumably to avoid translation of potentially deleterious truncated CFTR proteins. The NMD-mediated reduction of PTC-CFTR mRNA molecules reduces the efficacy of one of the most promising approaches to treatment of such mutations, namely, PTC readthrough therapy, using molecules that induce the incorporation of near-cognate amino acids at the PTC codon, thereby enabling translation of a full-length protein. In this study, we measure the effect of three different PTC mutations on the abundance, integrity, and stability of respective CFTR mRNAs, using CFTR specific RT-qPCR-based assays. Altogether, our data suggest that optimized rescue of PTC mutations has to take into account (1) the different steady-state levels of the CFTR mRNA associated with each specific PTC mutation; (2) differences in abundance between the 3' and 5' regions of CFTR mRNA, even following PTC readthrough or NMD inhibition; and (3) variable effects on CFTR mRNA stability for each specific PTC mutation.
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9
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Evidence for increased thermogenesis in female C57BL/6J mice housed aboard the international space station. NPJ Microgravity 2021; 7:23. [PMID: 34145277 PMCID: PMC8213760 DOI: 10.1038/s41526-021-00150-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 05/12/2021] [Indexed: 11/09/2022] Open
Abstract
Sixteen-week-old female C57BL/6J mice were sacrificed aboard the International Space Station after 37 days of flight (RR-1 mission) and frozen carcasses returned to Earth. RNA was isolated from interscapular brown adipose tissue (BAT) and gonadal white adipose tissue (WAT). Spaceflight resulted in differential expression of genes in BAT consistent with increased non-shivering thermogenesis and differential expression of genes in WAT consistent with increased glucose uptake and metabolism, adipogenesis, and β-oxidation.
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10
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Development of a 3':5' digital PCR assay to determine horse mRNA integrity. Anal Biochem 2021; 626:114217. [PMID: 33939972 DOI: 10.1016/j.ab.2021.114217] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Revised: 04/16/2021] [Accepted: 04/18/2021] [Indexed: 10/21/2022]
Abstract
Accurate tools to measure RNA integrity are essential to obtain reliable gene expression data. The reverse transcription quantitative PCR (RT-qPCR) based 3':5' assay permits a direct determination of messenger RNA (mRNA) integrity. However, the use of standard curves and the possible effect of PCR inhibitors make this method cumbersome and prone to variation, especially in small samples. Here we developed a triplex digital PCR (dPCR) 3':5' assay for assessing RNA integrity in equine samples as rapid and simple alternative to RT-qPCR. This dPCR assay not only provides a straight forward analysis of the mRNA integrity, but also of its quantity.
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11
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Marimuthu C, Pushpa Rani V. Elucidating the role of cell-mediated inflammatory cytokines on allogeneic mouse-derived nucleus pulposus mesenchymal stem cells. J Food Biochem 2021; 45:e13681. [PMID: 33694170 DOI: 10.1111/jfbc.13681] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 02/11/2021] [Accepted: 02/16/2021] [Indexed: 12/28/2022]
Abstract
In this present study, our aim was to evaluate the cell-mediated specific anti-donor antibody and its associated inflammatory cytokine secretion along with its succeeding effects on Nucleus pulposus-derived mesenchymal stem cells (NPMSCs). Tissue from the NP compartment of 12 normal mice was isolated, expanded in cell culture, and the cell phenotypes were confirmed by flow cytometry. Multipotent differentiation and its specific gene expression analysis were confirmed by reverse transcriptase PCR. T and B cells were monitored for both donor and recipient mouse and further analysis of anti-donor antibody secretion was confirmed by lymphocyte crossmatch. In conjunction with anti-donor-specific antibody analysis, the associated inflammatory cytokine expression was analyzed by ELISA. In co-culture, cell-mediated antibody secretion was elevated in T and B cells positive mouse group, when compared to control mouse group. Allogeneic-derived donor NPMSCs were found to be stimulated the secretion of pro-inflammatory cytokines and the level of pro-inflammatory cytokines showed reduced expression in control mouse serum. In co-culture group the concentration of the cell-mediated pro- and anti-inflammatory cytokines found to be increased. PRACTICAL APPLICATIONS: Mesenchymal stem cell exhibit good regeneration capacity for many types of disease, and the mechanism belongs to regeneration is not clear. In intervertebral disc, the nucleus pulposus-derived mesenchymal stem cells showed a better regeneration capacity. On the contrary, the NP cells-based therapy, the Mesenchymal stem cells showed expanded anabolic and reduced catabolic activity together with induced anti-inflammatory effect. In this study, the T & B cells were used to evaluate the anti-donor antibody secretion and also to study how it stimulates the production of anti-donor antibodies against the donor cells. Finally, it was found that T & B cells lead the synthesis of inflammatory cytokines are IL-1, IL-6, and TNF-α. From this study, the results proved that the cell-mediated pro- and anti-inflammatory cytokines to be monitored in allogeneic stem cells-based therapy of intervertebral disc degeneration.
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Affiliation(s)
- Chinnarasu Marimuthu
- Department of Advanced Zoology and Biotechnology, Loyola College, Chennai, India
| | - Vedham Pushpa Rani
- Department of Advanced Zoology and Biotechnology, Loyola College, Chennai, India
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12
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A rapid RNA extraction method from oil palm tissues suitable for reverse transcription quantitative real-time PCR (RT-qPCR). 3 Biotech 2020; 10:530. [PMID: 33214977 DOI: 10.1007/s13205-020-02514-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 10/27/2020] [Indexed: 10/23/2022] Open
Abstract
Cetyltrimethylammonium bromide (CTAB) is the preferred detergent in RNA extraction of oil palm tissues. However, the CTAB-based protocol is time-consuming. In this study, a combination of the CTAB-based method and silica-based purification reduced the extraction time from two days to five hours. Quality of total RNA from 27 different tissues of oil palm was shown to have an RNA integrity number (RIN) value of more than seven. The extracted RNA was evaluated by RT-qPCR using three reference oil palm genes (GRAS, CYP2, and SLU7) and three putative mesocarp-specific transcripts annotated as WRKY DNA-binding protein 70 (WRKY-70), metallothionein (MT) and pentatricopeptide repeat (PPR) genes. Tissue-specific expression profiling across complete developmental stages of mesocarp and vegetative tissues was determined in this study. Overall, the RNA extraction protocol described here is rapid, simple and yields good quality RNAs from oil palm tissues.
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Characterization of the rat Acetylcholinesterase readthrough (AChE-R) splice variant: Implications for toxicological studies. Biochem Biophys Res Commun 2020; 532:528-534. [PMID: 32896378 DOI: 10.1016/j.bbrc.2020.08.065] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 08/21/2020] [Indexed: 11/23/2022]
Abstract
Exposure to chemicals and other environmental stressors can differentially impact the expression of Acetylcholinesterase (AChE) splice variants. Surprisingly, despite the widespread use of the rat model in toxicological studies and the wealth of literature on this important biomarker of neurotoxicity, AChE coding exons and splice variants are not yet fully annotated in this species. To address this knowledge gap, a short problematic region of the rat AChE genomic DNA present in GenBank was first re-sequenced. This revised genomic sequence was then aligned to rat AChE RefSeq mRNA and compared to orthologous mammalian sequences, in order to map the coding exon and intron boundaries of the rat AChE gene. Based on these bioinformatics analyses, a sequence was predicted for the yet-unannotated rat Acetylcholinesterase readthrough (AChE-R) splice variant. PCR primers designed to specifically amplify rat AChE-R were used to confirm its expression in rat PC12 cells. Compared to the canonical AChE-S splice variant, AChE-R was expressed at much lower levels but presented distinct regulation patterns in PC12 cells and rat primary cerebral granule cells (CGCs) following exposure to Chlorpyrifos (a well-known neurotoxic organophosphate pesticide). Taken together, these observations point to the evolutionary conservation of the AChE-R splicing event between rodents and human and to the distinct regulation of AChE splice variants in response to toxicological challenges.
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14
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Piprode V, Mohanty S, Bonavita R, Loh S, Anbazhagan R, Saini C, Pinelli R, Pricop P, Dahia CL. An optimized step-by-step protocol for isolation of nucleus pulposus, annulus fibrosus, and end plate cells from the mouse intervertebral discs and subsequent preparation of high-quality intact total RNA. JOR Spine 2020; 3:e1108. [PMID: 33015579 PMCID: PMC7524240 DOI: 10.1002/jsp2.1108] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 05/27/2020] [Accepted: 06/29/2020] [Indexed: 12/14/2022] Open
Abstract
Intervertebral disc degeneration is the most significant, and least understood, cause of chronic back pain, affecting almost one in seven individuals at some point of time. Each intervertebral disc has three components; central nucleus pulposus (NP), concentric layers of annulus fibrosus (AF), and a pair of end plate (EP) that connects the disc to the vertebral bodies. Understanding the molecular and cellular basis of intervertebral disc growth, health, and aging will generate significant information for developing therapeutic approaches. Rapid and efficient preparations of homogeneous and pure cells are crucial for meaningful and rigorous downstream analysis at the cellular, molecular, and biochemical level. Cross-sample contamination may influence the interpretation of the results. In addition to altering gene expression, slow or delayed isolation procedures will also cause the degradation of cells and biomolecules that create a bias in the outcomes of the study. The mouse model system is extensively used to understand the intervertebral disc biology. Here we describe two protocols: (a) for efficient isolation of pure NP, AF, and EP cells from mouse lumbar intervertebral disc. We validated the purity of the NP and AF cells using Shh Cre/+ ; R26 mT/mG/+ dual-fluorescent reporter mice where all NP cells are GPF+ve, and by the sensitive approach of qPCR analysis using TaqMan probes for Shh, and Brachyury as NP-specific markers, Tenomodulin as AF-specific marker, and Osteocalcin as bone-specific marker. (b) For isolation of high-quality intact RNA with RIN of 9.3 to 10 from disc cells. These methods will be useful for the rigorous analysis of NP and AF cells, and improve our understanding of intervertebral disc biology.
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Affiliation(s)
| | | | | | - Sarah Loh
- Hospital for Special Surgery New York New York USA
| | | | | | | | - Paul Pricop
- Hospital for Special Surgery New York New York USA
| | - Chitra L Dahia
- Hospital for Special Surgery New York New York USA
- Department of Cell and Developmental Biology, Weill Cornell Medicine Graduate School of Medical Sciences New York New York USA
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15
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A bioinformatics workflow for the evaluation of RT-qPCR primer specificity: Application for the assessment of gene expression data reliability in toxicological studies. Regul Toxicol Pharmacol 2020; 111:104575. [PMID: 31945455 DOI: 10.1016/j.yrtph.2020.104575] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2019] [Accepted: 01/02/2020] [Indexed: 12/11/2022]
Abstract
The reliability of Reverse Transcription quantitative real-time PCR (RT-qPCR) gene expression data depends on proper primer design and RNA quality controls. Despite freely available genomic databases and bioinformatics tools, primer design deficiencies can be found across life science publications. In order to assess the prevalence of such deficiencies in the toxicological literature, 504 primer sets extracted from a random selection of 70 recent rat toxicological studies were evaluated. The specificity of each primer set was systematically analysed using a bioinformatics workflow developed from publicly available resources (NCBI Primer BLAST, in silico PCR in UCSC genome browser, Ensembl DNA database). Potential mismatches (9%), cross-matches (13.5%), co-amplification of multiple gene splice variants (9%) and sub-optimal amplicon sizes (25%) were identified for a significant proportion of the primer sets assessed in silico. Quality controls for gDNA contamination of RNA samples were infrequently reported in the surveyed manuscripts. Hence, the impacts of gDNA contamination on RT-qPCR data were further investigated, revealing that lowly expressed genes presented higher susceptibility to contaminating gDNA. In addition to the retrospective identification of potential primer design issues presented in this study, the described bioinformatics workflow can also be used prospectively to select candidate primer sets for experimental validation.
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Reimann E, Abram K, Kõks S, Kingo K, Fazeli A. Identification of an optimal method for extracting RNA from human skin biopsy, using domestic pig as a model system. Sci Rep 2019; 9:20111. [PMID: 31882887 PMCID: PMC6934780 DOI: 10.1038/s41598-019-56579-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Accepted: 12/13/2019] [Indexed: 11/22/2022] Open
Abstract
To evaluate skin tissue gene expression patterns correctly, extracting sufficient quantities of good quality RNA is essential. However, RNA extraction from skin tissue is challenging, as the hyaluronic acid-collagen matrix is extremely difficult to homogenize. Although there are multiple ways to extract RNA from skin, there are no comparative studies that identify the most critical steps, e.g. sample collection, storage and homogenization. We analysed the various steps involved in RNA extraction (i.e. biopsy collection as dry biopsy or into nucleotide stabilizing reagents, different storage conditions, enzymatic digestion, stator-rotor and bead motion-based homogenizing combined with column-based RNA purification). We hypothesised that domestic pig skin is applicable as a model for human skin studies. Altogether twenty different workflows were tested on pig skin and the four most promising workflows were tested on human skin samples. The optimal strategy for extracting human skin RNA was to collect, store and homogenize the sample in RLT lysis buffer from the RNeasy Fibrous Tissue Kit combined with beta-mercaptoethanol. Both stator-rotor and bead motion-based homogenizing were found to result in high quality and quantity of extracted RNA. Our results confirmed that domestic pig skin can be successfully used as a model for human skin RNA studies.
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Affiliation(s)
- Ene Reimann
- Department of Pathophysiology, University of Tartu, Tartu, Estonia.
| | - Kristi Abram
- Department of Dermatology, University of Tartu, Tartu, Estonia.,Clinic of Dermatology, Tartu University Hospital, Tartu, Estonia
| | - Sulev Kõks
- Centre for Comparative Genomics, Murdoch University, Perth, 6150, Australia.,The Perron Institute for Neurological and Translational Science, Perth, 6009, Australia
| | - Külli Kingo
- Department of Dermatology, University of Tartu, Tartu, Estonia.,Clinic of Dermatology, Tartu University Hospital, Tartu, Estonia
| | - Alireza Fazeli
- Department of Pathophysiology, University of Tartu, Tartu, Estonia.,Academic Unit of Reproductive and Developmental Medicine, Department of Oncology and Metabolism, The Medical School, University of Sheffield, Sheffield, United Kingdom
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