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Nguyen LT, Pollock CA, Saad S. Extraction of high quality and high yield RNA from frozen EDTA blood. Sci Rep 2024; 14:8628. [PMID: 38622175 PMCID: PMC11018810 DOI: 10.1038/s41598-024-58576-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Accepted: 04/01/2024] [Indexed: 04/17/2024] Open
Abstract
Peripheral blood RNA profiling, which can reveal systemic changes in gene expression and immune responses to disease onset and progression, is a powerful tool for diagnosis and biomarker discovery. This technique usually requires high quality RNA, which is only obtainable from fresh blood, or frozen blood that has been collected in special RNA-stabilisation systems. The current study aimed to develop a novel protocol to extract high quality RNA from frozen blood that had been collected in the conventional EDTA tubes. We determined that thawing EDTA blood in the presence of cell lysis/RNA stabilisation buffers (Paxgene or Nucleospin) significantly improved RNA quality (RIN) from below 5 to above 7, which to date has not been shown possible. The EDTA-Nucleospin protocol resulted in 5 times higher yield than the EDTA-Paxgene-PreAnalytix method. The average RIN and mRNA expression levels of five different genes including 18 s, ACTB, MCP1, TNFa and TXNIP using this protocol were also indifferent to those from Paxgene blood, suggesting similar RNA quality and blood transcriptome. Moreover, the protocol allows DNA to be extracted simultaneously. In conclusion, we have developed a practical and efficient protocol to extract high quality, high yield RNA from frozen EDTA blood.
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Affiliation(s)
- Long T Nguyen
- Renal Medicine, Kolling Institute, University of Sydney, Camperdown, Australia.
| | - Carol A Pollock
- Renal Medicine, Kolling Institute, University of Sydney, Camperdown, Australia
| | - Sonia Saad
- Renal Medicine, Kolling Institute, University of Sydney, Camperdown, Australia
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2
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Wilfinger WW, Eghbalnia HR, Mackey K, Miller R, Chomczynski P. Whole blood RNA extraction efficiency contributes to variability in RNA sequencing data sets. PLoS One 2023; 18:e0291209. [PMID: 37972054 PMCID: PMC10653446 DOI: 10.1371/journal.pone.0291209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 08/23/2023] [Indexed: 11/19/2023] Open
Abstract
Numerous methodologies are used for blood RNA extraction, and large quantitative differences in recovered RNA content are reported. We evaluated three archived data sets to determine how extraction methodologies might influence mRNA and lncRNA sequencing results. The total quantity of RNA recovered /ml of blood affects RNA sequencing by impacting the recovery of weakly expressed mRNA, and lncRNA transcripts. Transcript expression (TPM counts) plotted in relation to transcript size (base pairs, bp) revealed a 30% loss of short to midsized transcripts in some data sets. Quantitative recovery of RNA is of considerable importance, and it should be viewed more judiciously. Transcripts common to the three data sets were subsequently normalized and transcript mean TPM counts and TPM count coefficient of variation (CV) were plotted in relation to increasing transcript size. Regression analysis of mean TPM counts versus transcript size revealed negative slopes in two of the three data sets suggesting a reduction of TPM transcript counts with increasing transcript size. In the third data set, the regression slope line of mRNA transcript TPM counts approximates zero and TPM counts increased in proportion to transcript size over a range of 200 to 30,000 bp. Similarly, transcript TPM count CV values also were uniformly distributed over the range of transcript sizes. In the other data sets, the regression CV slopes increased in relation to transcript size. The recovery of weakly expressed and /or short to midsized mRNA and lncRNA transcripts varies with different RNA extraction methodologies thereby altering the fundamental sequencing relationship between transcript size and TPM counts. Our analysis identifies differences in RNA sequencing results that are dependent upon the quantity of total RNA recovery from whole blood. We propose that incomplete RNA extraction directly impacts the recovery of mRNA and lncRNA transcripts from human blood and speculate these differences contribute to the "batch" effects commonly identified between sequencing results from different archived data sets.
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Affiliation(s)
| | - Hamid R. Eghbalnia
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, CT, United States of America
| | - Karol Mackey
- Molecular Research Center, Inc. Cincinnati, OH, United States of America
| | - Robert Miller
- Robert Miller Enterprises, LLC, Cincinnati, OH, United States of America
| | - Piotr Chomczynski
- Molecular Research Center, Inc. Cincinnati, OH, United States of America
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3
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Gonzalez DI, Ynalvez RA. Comparison of the effects of nitrogen-, sulfur- and combined nitrogen- and sulfur-deprivations on cell growth, lipid bodies and gene expressions in Chlamydomonas reinhardtii cc5373-sta6. BMC Biotechnol 2023; 23:35. [PMID: 37684579 PMCID: PMC10492388 DOI: 10.1186/s12896-023-00808-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Accepted: 08/29/2023] [Indexed: 09/10/2023] Open
Abstract
BACKGROUND Biofuel research that aims to optimize growth conditions in microalgae is critically important. Chlamydomonas reinhardtii is a green microalga that offers advantages for biofuel production research. This study compares the effects of nitrogen-, sulfur-, and nitrogen and sulfur- deprivations on the C. reinhardtii starchless mutant cc5373-sta6. Specifically, it compares growth, lipid body accumulation, and expression levels of acetyl-CoA carboxylase (ACC) and phosphoenolpyruvate carboxylase (PEPC). RESULTS Among nutrient-deprived cells, TAP-S cells showed significantly higher total chlorophyll, cell density, and protein content at day 6 (p < 0.05). Confocal analysis showed a significantly higher number of lipid bodies in cells subjected to nutrient deprivation than in the control over the course of six days; N deprivation for six days significantly increased the size of lipid bodies (p < 0.01). In comparison with the control, significantly higher ACC expression was observed after 8 and 24 h of NS deprivation and only after 24 h with N deprivation. On the other hand, ACC and PEPC expression at 8 and 24 h of S deprivation was not significantly different from that in the control. A significantly lower PEPC expression was observed after 8 h of N and NS deprivation (p < 0.01), but a significantly higher PEPC expression was observed after 24 h (p < 0.01). CONCLUSIONS Based on our findings, it would be optimum to cultivate cc5373-sta6 cells in nutrient deprived conditions (-N, -S or -NS) for four days; whereby there is cell growth, and both a high number of lipid bodies and a larger size of lipid bodies produced.
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Affiliation(s)
- David I Gonzalez
- Department of Biological Science, Vanderbilt University, 465 21st Ave S, Nashville, TN, 37240, USA
| | - Ruby A Ynalvez
- Department of Biology and Chemistry, Texas A&M International University, 5201 University Blvd, Laredo, TX, 78041, USA.
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4
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Abid F, Khan K, Badshah Y, Ashraf NM, Shabbir M, Hamid A, Afsar T, Almajwal A, Razak S. Non-synonymous SNPs variants of PRKCG and its association with oncogenes predispose to hepatocellular carcinoma. Cancer Cell Int 2023; 23:123. [PMID: 37344815 PMCID: PMC10286404 DOI: 10.1186/s12935-023-02965-z] [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: 03/23/2023] [Accepted: 06/07/2023] [Indexed: 06/23/2023] Open
Abstract
BACKGROUND PRKCG encodes PKC γ, which is categorized under the classical protein kinase C family. No studies have specifically established the relationship between PRKCG nsSNPs with structural and functional variations in PKC γ in the context of hepatocellular carcinoma (HCC). The present study aims to uncover this link through in-silico and experimental studies. METHODS The 3D structure of PKC γ was predicted. Molecular Dynamic (MD) Simulations were run and estimates were made for interactions, stability, conservation and post-translational alterations between wild and mutant structures. The association of PRKCG levels with HCC survival rate was determined. Genotyping analyses were conducted to investigate the deleterious PRKCG nsSNP association with HCC. mRNA expression of PKC γ, HIF-1 alpha, AKT, SOCS3 and VEGF in the blood of controls and HCC patients was analyzed and a genetic cascade was constructed depicting these interactions. RESULTS The expression level of studied oncogenes was compared to tumour suppressor genes. Through Alphafold, the 3D structure of PKC γ was explored. Fifteen SNPs were narrowed down for in-silico analyses that were identified in exons 5, 10 and 18 and the regulatory and kinase domain of PKC γ. Root mean square deviation and fluctuation along with the radius of gyration unveiled potential changes between the wild and mutated variant structures. Mutant genotype AA (homozygous) corresponding to nsSNP, rs386134171 had more frequency in patients with OR (2.446), RR (1.564) and P-values (< 0.0029) that highlights its significant association with HCC compared to controls in which the wild genotype GG was found more prevalent. CONCLUSION nsSNP rs386134171 can be a genetic marker for HCC diagnosis and therapeutic studies. This study has laid down a road map for future studies to be conducted on HCC.
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Affiliation(s)
- Fizzah Abid
- Department of Healthcare Biotechnology, Atta-Ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, 44010, Pakistan
| | - Khushbukhat Khan
- Department of Healthcare Biotechnology, Atta-Ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, 44010, Pakistan
| | - Yasmin Badshah
- Department of Healthcare Biotechnology, Atta-Ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, 44010, Pakistan
| | - Naeem Mahmood Ashraf
- School of Biochemistry and Biotechnology, University of the Punjab, Lahore, 54590, Pakistan
| | - Maria Shabbir
- Department of Healthcare Biotechnology, Atta-Ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, 44010, Pakistan.
| | - Arslan Hamid
- LIMES Institute (AG-Netea), University of Bonn, Carl-Troll-Str. 31, 53115, Bonn, Germany
| | - Tayyaba Afsar
- Department of Community Health Sciences, College of Applied Medical Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Ali Almajwal
- Department of Community Health Sciences, College of Applied Medical Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Suhail Razak
- Department of Community Health Sciences, College of Applied Medical Sciences, King Saud University, Riyadh, Saudi Arabia.
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Transcriptional Biomarkers for Treatment Monitoring of Pulmonary Drug-Resistant Tuberculosis: Protocol for a Prospective Observational Study in Indonesia. Trop Med Infect Dis 2022; 7:tropicalmed7110326. [DOI: 10.3390/tropicalmed7110326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 10/18/2022] [Accepted: 10/20/2022] [Indexed: 11/05/2022] Open
Abstract
Many blood-based gene expression biomarkers for monitoring tuberculosis (TB) treatment have been suggested so far, but promising biomarker results for drug-resistant TB treatment response have not been studied. This protocol presents a prospective observational study in Indonesia to profile the human blood transcriptome for predicting the response to drug-resistant TB treatment, focusing on pulmonary TB, and to adapt the specific RNA signature to the qRT-PCR platform. Longitudinal blood samples will be collected from 44 subjects with rifampicin resistant TB, confirmed by Xpert MTB/RIF, and 52 healthy controls. RNA-Seq will be performed to identify changes in the transcriptome following TB treatment. A discriminative RNA signature will be chosen and translated into a score for use in a quantitative PCR-based assay. This study will provide crucial information to guide the discovery and design of a clinically implementable tool to monitor the response of TB treatment.
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Zou C, Ji C, Zhu Y, Liu N, Zhang S, Peng H, Zhang X, Wang H, Deng Y, Qian K. Effects of Freezing and Rewarming Methods on RNA Quality of Blood Samples. Biopreserv Biobank 2022; 21:176-183. [PMID: 35759420 DOI: 10.1089/bio.2022.0007] [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: 11/12/2022] Open
Abstract
Background: RNA extracted from human blood has been widely applied to biological, medical, and clinical research of numerous diseases. Previous studies have demonstrated that high-quality RNA is indispensable to guarantee the reliability of downstream assays. In this study, we investigated the effects of freezing procedures, rewarming methods, and blood components on RNA quality of blood samples. Methods: Rabbit blood samples were divided into two groups: (1) whole blood (WB) and (2) blood cell components (BCC) with plasma removed. Samples were frozen using four representative freezing procedures (snap freezing in liquid nitrogen, snap freezing at -80°C, traditional slow freezing, and programmable controlled rate freezing) and rewarmed by placing at 4°C or by vortexing. RNA was extracted using the phenol-chloroform RNA extraction method and measured by an Agilent bioanalyzer. Then, human blood was used to verify the best protocol obtained from the rabbit blood experiment. Results: For the four freezing procedures, there were no differences in RNA integrity. For different rewarming methods, RNA integrity number (RIN) values of RNA extracted from frozen WB and BCC samples in the vortex group were above 9, while RNA obtained from WB showed worse quality compared with BCC in the 4°C group. For verification using human blood, RIN values of frozen human WB rewarmed by vortexing ranged from 8.0 to 9.1. Conclusions: Blood components and rewarming methods could affect the RNA quality of blood samples. For scenarios where WB samples have already been cryopreserved, the vortex rewarming method is optimal for high-quality RNA. Otherwise, we would recommend centrifuging fresh WB and cryopreserving it in the form of BCC, which showed a tendency to obtain high-quality RNA by either of the two rewarming methods.
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Affiliation(s)
- Cong Zou
- Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Chundong Ji
- Department of Urology, Affiliated Hospital of Panzhihua University, Panzhihua, China
| | - Yuan Zhu
- Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Nan Liu
- Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Shanshan Zhang
- Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Hongwei Peng
- Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Xin Zhang
- Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Hui Wang
- Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Yanhua Deng
- Department of Urology, Affiliated Hospital of Panzhihua University, Panzhihua, China
| | - Kaiyu Qian
- Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan, China.,Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, China.,Human Genetic Resources Preservation Center of Hubei Province, Wuhan, China
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7
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Lima G, Kolliari-Turner A, Malinsky FR, Guppy FM, Martin RP, Wang G, Voss SC, Georgakopoulos C, Borrione P, Pigozzi F, Pitsiladis Y. Integrating Whole Blood Transcriptomic Collection Procedures Into the Current Anti-Doping Testing System, Including Long-Term Storage and Re-Testing of Anti-Doping Samples. Front Mol Biosci 2021; 8:728273. [PMID: 34765642 PMCID: PMC8576497 DOI: 10.3389/fmolb.2021.728273] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 08/31/2021] [Indexed: 11/13/2022] Open
Abstract
Introduction: Recombinant human erythropoietin (rHuEPO) administration studies involving transcriptomic approaches have demonstrated a gene expression signature that could aid blood doping detection. However, current anti-doping testing does not involve collecting whole blood into tubes with RNA preservative. This study investigated if whole blood in long-term storage and whole blood left over from standard hematological testing in short-term storage could be used for transcriptomic analysis despite lacking RNA preservation. Methods: Whole blood samples were collected from twelve and fourteen healthy nonathletic males, for long-term and short-term storage experiments. Long-term storage involved whole blood collected into Tempus™ tubes and K2EDTA tubes and subjected to long-term (i.e., ‒80°C) storage and RNA extracted. Short-term storage involved whole blood collected into K2EDTA tubes and stored at 4°C for 6‒48 h and then incubated at room temperature for 1 and 2 h prior to addition of RNA preservative. RNA quantity, purity, and integrity were analyzed in addition to RNA-Seq using the MGI DNBSEQ-G400 on RNA from both the short- and long-term storage studies. Genes presenting a fold change (FC) of >1.1 or < ‒1.1 with p ≤ 0.05 for each comparison were considered differentially expressed. Microarray analysis using the Affymetrix GeneChip® Human Transcriptome 2.0 Array was additionally conducted on RNA from the short-term study with a false discovery ratio (FDR) of ≤0.05 and an FC of >1.1 or < ‒1.1 applied to identify differentially expressed genes. Results: RNA quantity, purity, and integrity from whole blood subjected to short- and long-term storage were sufficient for gene expression analysis. Long-term storage: when comparing blood tubes with and without RNA preservation 4,058 transcripts (6% of coding and non-coding transcripts) were differentially expressed using microarray and 658 genes (3.4% of mapped genes) were differentially expressed using RNA-Seq. Short-term storage: mean RNA integrity and yield were not significantly different at any of the time points. RNA-Seq analysis revealed a very small number of differentially expressed genes (70 or 1.37% of mapped genes) when comparing samples stored between 6 and 48 h without RNA preservative. None of the genes previously identified in rHuEPO administration studies were differently expressed in either long- or short-term storage experiments. Conclusion: RNA quantity, purity, and integrity were not significantly compromised from short- or long-term storage in blood storage tubes lacking RNA stabilization, indicating that transcriptomic analysis could be conducted using anti-doping samples collected or biobanked without RNA preservation.
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Affiliation(s)
- Giscard Lima
- Department of Movement, Human and Health Sciences, University of Rome "Foro Italico", Rome, Italy.,School of Sport and Health Sciences, University of Brighton, Eastbourne, United Kingdom.,Centre for Stress and Age Related Disease, University of Brighton, Brighton, United Kingdom
| | - Alexander Kolliari-Turner
- School of Sport and Health Sciences, University of Brighton, Eastbourne, United Kingdom.,Centre for Stress and Age Related Disease, University of Brighton, Brighton, United Kingdom
| | | | - Fergus M Guppy
- Centre for Stress and Age Related Disease, University of Brighton, Brighton, United Kingdom.,School of Applied Sciences, University of Brighton, Brighton, United Kingdom
| | - Renan Paulo Martin
- Department of Biophysics, Federal University of Sao Paulo, Sao Paulo, Brazil.,McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Guan Wang
- School of Sport and Health Sciences, University of Brighton, Eastbourne, United Kingdom.,Sport and Exercise Science and Sports Medicine Research and Enterprise Group, University of Brighton, Brighton, United Kingdom
| | | | | | - Paolo Borrione
- Department of Movement, Human and Health Sciences, University of Rome "Foro Italico", Rome, Italy.,NADO Italia, National Antidoping Organization, Rome, Italy
| | - Fabio Pigozzi
- Department of Movement, Human and Health Sciences, University of Rome "Foro Italico", Rome, Italy.,NADO Italia, National Antidoping Organization, Rome, Italy.,International Federation of Sports Medicine (FIMS), Lausanne, Switzerland
| | - Yannis Pitsiladis
- Department of Movement, Human and Health Sciences, University of Rome "Foro Italico", Rome, Italy.,Centre for Stress and Age Related Disease, University of Brighton, Brighton, United Kingdom.,International Federation of Sports Medicine (FIMS), Lausanne, Switzerland
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Yamagata H, Kobayashi A, Tsunedomi R, Seki T, Kobayashi M, Hagiwara K, Chen C, Uchida S, Okada G, Fuchikami M, Kamishikiryo T, Iga JI, Numata S, Kinoshita M, Kato TA, Hashimoto R, Nagano H, Okamoto Y, Ueno S, Ohmori T, Nakagawa S. Optimized protocol for the extraction of RNA and DNA from frozen whole blood sample stored in a single EDTA tube. Sci Rep 2021; 11:17075. [PMID: 34426633 PMCID: PMC8382694 DOI: 10.1038/s41598-021-96567-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 08/11/2021] [Indexed: 01/27/2023] Open
Abstract
Cryopreservation of whole blood is useful for DNA collection, and clinical and basic research. Blood samples in ethylenediaminetetraacetic acid disodium salt (EDTA) tubes stored at − 80 °C are suitable for DNA extraction, but not for high-quality RNA extraction. Herein, a new methodology for high-quality RNA extraction from human blood samples is described. Quickly thawing frozen whole blood on aluminum blocks at room temperature could minimize RNA degradation, and improve RNA yield and quality compared with thawing the samples in a 37 °C water bath. Furthermore, the use of the NucleoSpin RNA kit increased RNA yield by fivefold compared with the PAXgene Blood RNA Kit. Thawing blood samples on aluminum blocks significantly increased the DNA yield by ~ 20% compared with thawing in a 37 °C water bath or on ice. Moreover, by thawing on aluminum blocks and using the NucleoSpin RNA and QIAamp DNA Blood kits, the extraction of RNA and DNA of sufficient quality and quantity was achieved from frozen EDTA whole blood samples that were stored for up to 8.5 years. Thus, extracting RNA from frozen whole blood in EDTA tubes after long-term storage is feasible. These findings may help advance gene expression analysis, as well as biomarker research for various diseases.
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Affiliation(s)
- Hirotaka Yamagata
- Division of Neuropsychiatry, Department of Neuroscience, Yamaguchi University Graduate School of Medicine, 1-1-1 Minami-kogushi, Ube, Yamaguchi, 755-8505, Japan. .,Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama, 332-0012, Japan.
| | - Ayumi Kobayashi
- Division of Neuropsychiatry, Department of Neuroscience, Yamaguchi University Graduate School of Medicine, 1-1-1 Minami-kogushi, Ube, Yamaguchi, 755-8505, Japan
| | - Ryouichi Tsunedomi
- Department of Gastroenterological, Breast and Endocrine Surgery, Yamaguchi University Graduate School of Medicine, 1-1-1 Minami-kogushi, Ube, Yamaguchi, 755-8505, Japan
| | - Tomoe Seki
- Division of Neuropsychiatry, Department of Neuroscience, Yamaguchi University Graduate School of Medicine, 1-1-1 Minami-kogushi, Ube, Yamaguchi, 755-8505, Japan.,Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama, 332-0012, Japan
| | - Masaaki Kobayashi
- Division of Neuropsychiatry, Department of Neuroscience, Yamaguchi University Graduate School of Medicine, 1-1-1 Minami-kogushi, Ube, Yamaguchi, 755-8505, Japan
| | - Kosuke Hagiwara
- Division of Neuropsychiatry, Department of Neuroscience, Yamaguchi University Graduate School of Medicine, 1-1-1 Minami-kogushi, Ube, Yamaguchi, 755-8505, Japan
| | - Chong Chen
- Division of Neuropsychiatry, Department of Neuroscience, Yamaguchi University Graduate School of Medicine, 1-1-1 Minami-kogushi, Ube, Yamaguchi, 755-8505, Japan
| | - Shusaku Uchida
- Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama, 332-0012, Japan.,SK Project, Medical Innovation Center, Kyoto University Graduate School of Medicine, 53 Shogoin‑Kawahara‑cho, Sakyo‑ku, Kyoto, 606‑8507, Japan
| | - Go Okada
- Department of Psychiatry and Neurosciences, Graduate School of Biomedical Sciences, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima, 734-8551, Japan
| | - Manabu Fuchikami
- Department of Psychiatry and Neurosciences, Graduate School of Biomedical Sciences, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima, 734-8551, Japan
| | - Toshiharu Kamishikiryo
- Department of Psychiatry and Neurosciences, Graduate School of Biomedical Sciences, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima, 734-8551, Japan
| | - Jun-Ichi Iga
- Department of Neuropsychiatry, Molecules and Function, Ehime University Graduate School of Medicine, Shitsukawa, Toon, Ehime, 791-0295, Japan
| | - Shusuke Numata
- Department of Psychiatry, Graduate School of Biomedical Sciences, Tokushima University, 3-18-5 Kuramoto-cho, Tokushima, 770-8503, Japan
| | - Makoto Kinoshita
- Department of Psychiatry, Graduate School of Biomedical Sciences, Tokushima University, 3-18-5 Kuramoto-cho, Tokushima, 770-8503, Japan
| | - Takahiro A Kato
- Department of Neuropsychiatry, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi Higashi-Ku, Fukuoka, 812-8582, Japan
| | - Ryota Hashimoto
- Department of Pathology of Mental Diseases, National Institute of Mental Health, National Center of Neurology and Psychiatry, 4-1-1 Ogawa-Higashi, Kodaira, Tokyo, 187-8553, Japan
| | - Hiroaki Nagano
- Department of Gastroenterological, Breast and Endocrine Surgery, Yamaguchi University Graduate School of Medicine, 1-1-1 Minami-kogushi, Ube, Yamaguchi, 755-8505, Japan
| | - Yasumasa Okamoto
- Department of Psychiatry and Neurosciences, Graduate School of Biomedical Sciences, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima, 734-8551, Japan
| | - Shuichi Ueno
- Department of Neuropsychiatry, Molecules and Function, Ehime University Graduate School of Medicine, Shitsukawa, Toon, Ehime, 791-0295, Japan
| | - Tetsuro Ohmori
- Department of Psychiatry, Graduate School of Biomedical Sciences, Tokushima University, 3-18-5 Kuramoto-cho, Tokushima, 770-8503, Japan
| | - Shin Nakagawa
- Division of Neuropsychiatry, Department of Neuroscience, Yamaguchi University Graduate School of Medicine, 1-1-1 Minami-kogushi, Ube, Yamaguchi, 755-8505, Japan
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Tootee A, Nikbin B, Ghahary A, Esfahani EN, Arjmand B, Aghayan H, Qorbani M, Larijani B. Assessment of immune-alternations and their correlations with therapeutic outcomes of transplantation of autologous Mesenchymal and Allogenic fetal stem cells in patients with type 1 diabetes: a study protocol. J Diabetes Metab Disord 2021; 20:1067-1073. [PMID: 34222099 DOI: 10.1007/s40200-020-00716-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 12/22/2020] [Indexed: 11/26/2022]
Abstract
Introduction Stem-cell therapy, which has recently emerged as a potentially therapeutic option for diabetes, is demonstrated to significantly alter both cellular and non-cellular elements of the immune system. In addition, it is demonstrated that allogenic stem-cells, once considered immune-privileged, can be rejected by the host immune system almost similar to any other somatic cell. To date, nonetheless, details of these intricate interactions remain obscure. The current study is designed to illuminate both aforementioned favorable and unfavorable stem cell-mediated immune reactions. Findings of this study may shed some light on how stem cells may exert their therapeutic effect in type 1 diabetes through immune system-mediated mechanisms and illuminate the partially-obscure immune-caused rejection of these cells. Methods and analysis For the purpose of this study, frozen whole blood samples obtained from patients with type 1 diabetes who received stem cells at the Endocrinology and Metabolism Research Institute of Tehran University of Medical Sciences in two different clinical trials will be thawed and analyzed. These clinical trials were carried out using two different sources of stem cells, namely allogenic fetal and autologous mesenchymal cells. The samples we aim to analyze were obtained from the patients before the procedure and regularly after it, one, three, six, 12, and 24 months later. For the purpose of this study, the following parameters will be measured: C-peptide levels, IDAA1c (a surrogate marker of beta cell function which is calculated as HbA1c (%) + [4 × insulin dose (units per kilogram per day)]), frequencies of islet-specific autoreactive CD8+ T cells (CTL), different lymphocyte subsets, thymic function indicators, T cell repertoire diversity (including Treg/Tconv ratios), plasma levels of several pro- and anti-inflammatory cytokines, diabetes autoantibodies, and HLA typing. Ethics and dissemination The stem cell transplantation clinical trials which provided the primary source of our samples were carried out at the Endocrinology and Metabolism Research Institute of Tehran University of Medical Sciences between 2008 and 2012. These series of clinical trials have secured approval of the ethics committee of Tehran University of Medical Sciences (ethical code number: E-0089) and registered on the national clinical trial registry of Islamic Republic of Iran (IRCT) with the identifier codes: IRCT138810271414N8 (for autologous mesenchymal cells) and IRCT201103171414N23 (for allogenic fetal cells). Our findings are to be presented at international scientific events, published in peer-reviewed journals, and disseminated both electronically and in print. Besides, results of the current study will be used for design and implementation of future laboratory investigations and clinical trials at the Endocrinology and Metabolism Research Institute of Tehran University of Medical Sciences.
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Affiliation(s)
- Ali Tootee
- Diabetes Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Behrouz Nikbin
- Research Center of Molecular Immunology, Tehran University of Medical Sciences, Tehran, Iran
| | - Aziz Ghahary
- Burn and Wound Healing Research Laboratory, Department of Surgery, Plastic Surgery, University of British Columbia, Vancouver, Canada
| | - Ensieh Nasli Esfahani
- Diabetes Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Babak Arjmand
- Cell Therapy and Regenerative Medicine Research Center, Endocrinology and Metabolism Molecular Cellular Sciences Institute, Tehran university of Medical Sciences, Tehran, Iran
| | - Hamidreza Aghayan
- Cell Therapy and Regenerative Medicine Research Center, Endocrinology and Metabolism Molecular Cellular Sciences Institute, Tehran university of Medical Sciences, Tehran, Iran
| | - Mostafa Qorbani
- Non-communicable Diseases Research Center, Alborz University of Medical Sciences, Karaj, Iran
| | - Bagher Larijani
- Endocrinology and Metabolism Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
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10
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Halouani A, Jmii H, Michaux H, Renard C, Martens H, Pirottin D, Mastouri M, Aouni M, Geenen V, Jaïdane H. Housekeeping Gene Expression in the Fetal and Neonatal Murine Thymus Following Coxsackievirus B4 Infection. Genes (Basel) 2020; 11:genes11030279. [PMID: 32150956 PMCID: PMC7140870 DOI: 10.3390/genes11030279] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 01/18/2020] [Accepted: 02/05/2020] [Indexed: 12/23/2022] Open
Abstract
The thymus fulfills the role of T-cell production and differentiation. Studying transcription factors and genes involved in T-cell differentiation and maturation during the fetal and neonatal periods is very important. Nevertheless, no studies to date have been interested in evaluating the expressions of housekeeping genes as internal controls to assess the varying expressions of different genes inside this tissue during that period or in the context of viral infection. Thus, we evaluated by real-time quantitative polymerase chain reaction (qPCR) the expression of the most common internal control genes in the thymus of Swiss albino mice during the fetal and neonatal period, and following in utero infection with Coxsackievirus B4. The stability of expression of these reference genes in different samples was investigated using the geNorm application. Results demonstrated that the expression stability varied greatly between genes. Oaz1 was found to have the highest stability in different stages of development, as well as following Coxsackievirus B4 infection. The current study clearly demonstrated that Oaz1, with very stable expression levels that outperformed other tested housekeeping genes, could be used as a reference gene in the thymus and thymic epithelial cells during development and following Coxsackievirus B4 infection.
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Affiliation(s)
- Aymen Halouani
- Faculté de Pharmacie de Monastir, Université de Monastir, Laboratoire des Maladies Transmissibles et Substances Biologiquement Actives LR99ES27, Monastir 5000, Tunisia; (A.H.); (H.J.); (M.M.); (M.A.)
- Faculté des Sciences de Tunis, Université de Tunis El Manar, Tunis 1068, Tunisia
- Faculté de Médicine, Université de Liège, GIGA-I3 Immunoendocrinologie, CHU-B34, B-4000 Liege, Sart Tilman, Belgium; (H.M.); (C.R.); (H.M.); (V.G.)
| | - Habib Jmii
- Faculté de Pharmacie de Monastir, Université de Monastir, Laboratoire des Maladies Transmissibles et Substances Biologiquement Actives LR99ES27, Monastir 5000, Tunisia; (A.H.); (H.J.); (M.M.); (M.A.)
- Faculté des Sciences de Tunis, Université de Tunis El Manar, Tunis 1068, Tunisia
| | - Hélène Michaux
- Faculté de Médicine, Université de Liège, GIGA-I3 Immunoendocrinologie, CHU-B34, B-4000 Liege, Sart Tilman, Belgium; (H.M.); (C.R.); (H.M.); (V.G.)
| | - Chantal Renard
- Faculté de Médicine, Université de Liège, GIGA-I3 Immunoendocrinologie, CHU-B34, B-4000 Liege, Sart Tilman, Belgium; (H.M.); (C.R.); (H.M.); (V.G.)
| | - Henri Martens
- Faculté de Médicine, Université de Liège, GIGA-I3 Immunoendocrinologie, CHU-B34, B-4000 Liege, Sart Tilman, Belgium; (H.M.); (C.R.); (H.M.); (V.G.)
| | - Dimitri Pirottin
- University of Liège, GIGA-I3 and Department of Functional Sciences, Laboratory of Cellular and Molecular Immunology, CHU-B34, B-4000 Liège, Sart Tilman, Belgium;
| | - Maha Mastouri
- Faculté de Pharmacie de Monastir, Université de Monastir, Laboratoire des Maladies Transmissibles et Substances Biologiquement Actives LR99ES27, Monastir 5000, Tunisia; (A.H.); (H.J.); (M.M.); (M.A.)
| | - Mahjoub Aouni
- Faculté de Pharmacie de Monastir, Université de Monastir, Laboratoire des Maladies Transmissibles et Substances Biologiquement Actives LR99ES27, Monastir 5000, Tunisia; (A.H.); (H.J.); (M.M.); (M.A.)
| | - Vincent Geenen
- Faculté de Médicine, Université de Liège, GIGA-I3 Immunoendocrinologie, CHU-B34, B-4000 Liege, Sart Tilman, Belgium; (H.M.); (C.R.); (H.M.); (V.G.)
| | - Hela Jaïdane
- Faculté de Pharmacie de Monastir, Université de Monastir, Laboratoire des Maladies Transmissibles et Substances Biologiquement Actives LR99ES27, Monastir 5000, Tunisia; (A.H.); (H.J.); (M.M.); (M.A.)
- Correspondence:
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11
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Rodríguez A, Duyvejonck H, Van Belleghem JD, Gryp T, Van Simaey L, Vermeulen S, Van Mechelen E, Vaneechoutte M. Comparison of procedures for RNA-extraction from peripheral blood mononuclear cells. PLoS One 2020; 15:e0229423. [PMID: 32084228 PMCID: PMC7034890 DOI: 10.1371/journal.pone.0229423] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 02/05/2020] [Indexed: 02/06/2023] Open
Abstract
RNA quality and quantity are important factors for ensuring the accuracy of gene expression analysis and other RNA-based downstream applications. Thus far, only a limited number of methodological studies have compared sample storage and RNA extraction procedures for human cells. We compared three commercially available RNA extraction kits, i.e., (NucliSENS) easyMAG, RNeasy (Mini Kit) and RiboPure (RNA Purification Kit–blood). In addition, additional conditions, such as storage medium and storage temperature of human peripheral blood mononuclear cells were evaluated, i.e., 4 °C for RNAlater or -80 °C for QIAzol and for the respective cognate lysis buffers; easyMAG, RNeasy or RiboPure. RNA was extracted from aliquots that had been stored for one day (Run 1) or 83 days (Run 2). After DNase treatment, quantity and quality of RNA were assessed by means of a NanoDrop spectrophotometer, 2100 Bioanalyzer and RT-qPCR for the ACTB reference gene. We observed that high-quality RNA can be obtained using RNeasy and RiboPure, regardless of the storage medium, whereas samples stored in RNAlater resulted in the least amount of RNA extracted. In addition, RiboPure combined with storage of samples in its cognate lysis buffer yielded twice as much RNA as all other procedures. These results were supported by RT-qPCR and by the reproducibility observed for two independent extraction runs.
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Affiliation(s)
- Antonio Rodríguez
- Laboratory Bacteriology Research, Department of Diagnostic Sciences, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
- * E-mail:
| | - Hans Duyvejonck
- Laboratory Bacteriology Research, Department of Diagnostic Sciences, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
- Department of Biosciences, Faculty of Education, Health and Social Work, University College Ghent, Ghent, Belgium
| | - Jonas D. Van Belleghem
- Laboratory Bacteriology Research, Department of Diagnostic Sciences, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, California, United States of America
| | - Tessa Gryp
- Laboratory Bacteriology Research, Department of Diagnostic Sciences, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Leen Van Simaey
- Laboratory Bacteriology Research, Department of Diagnostic Sciences, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Stefan Vermeulen
- Department of Biosciences, Faculty of Education, Health and Social Work, University College Ghent, Ghent, Belgium
| | - Els Van Mechelen
- Department of Biosciences, Faculty of Education, Health and Social Work, University College Ghent, Ghent, Belgium
| | - Mario Vaneechoutte
- Laboratory Bacteriology Research, Department of Diagnostic Sciences, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
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12
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Evaluation of RNA purification methods by using different blood stabilization tubes: identification of key features for epidemiological studies. BMC Res Notes 2020; 13:77. [PMID: 32070402 PMCID: PMC7026973 DOI: 10.1186/s13104-020-04943-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 02/08/2020] [Indexed: 11/30/2022] Open
Abstract
Objective Peripheral blood is the most promising source of RNA biomarkers for diagnostic and epidemiological studies, because the presence of disease and prognostic information is reflected in the gene expression pattern. Quality RNA is used by a number of different downstream applications, so the selection of the most appropriate RNA stabilization and purification method is important. We have analyzed the RNA purified from 300 blood samples from 25 donors processed by two technicians using three methodologies with Tempus and PaxGene tubes. Results The best quality sample results were obtained with the Tempus Spin RNA Isolation Kit and the PaxGene Blood miRNA Kit, although larger amounts of RNA were obtained with the Tempus Spin RNA Isolation Kit. Lower Cq values were observed for RNA and miRNA genes in samples that were tested with PaxGene Blood miRNA Kit and Tempus Spin RNA Isolation Kit respectively. We identify the Tempus Spin RNA Isolation Kit as the most robust methodology, whilst the MagMax for Stabilized Blood Tubes RNA Isolation Kit showed the most instability. For biobanks, which process a large cohort and conduct epidemiological studies, the Tempus Spin RNA Isolation Kit is the most appropriate methodology. The study demonstrates the robustness of real-life procedures.
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13
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Shan J, Chouchane A, Mokrab Y, Saad M, Boujassoum S, Sayaman RW, Ziv E, Bouaouina N, Remadi Y, Gabbouj S, Roelands J, Ma X, Bedognetti D, Chouchane L. Genetic Variation in CCL5 Signaling Genes and Triple Negative Breast Cancer: Susceptibility and Prognosis Implications. Front Oncol 2019; 9:1328. [PMID: 31921621 PMCID: PMC6915105 DOI: 10.3389/fonc.2019.01328] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 11/13/2019] [Indexed: 12/17/2022] Open
Abstract
Triple-negative breast cancer (TNBC) accounts for ~15–20% of breast cancer (BC) and has a higher rate of early relapse and mortality compared to other subtypes. The Chemokine (C-C motif) ligand 5 (CCL5) and its signaling pathway have been linked to TNBC. We aimed to investigate the susceptibility and prognostic implications of genetic variation in CCL5 signaling genes in TNBC in the present study. We characterized variants in CCL5 and that of six other CCL5 signaling genes (CCND1, ZMIZ1, CASP8, NOTCH2, MAP3K21, and HS6ST3) among 1,082 unrelated Tunisian subjects (544 BC patients, including 196 TNBC, and 538 healthy controls), assessed the association of the variants with BC-specific overall survival (OVS) and progression-free survival (PFS), and correlated CCL5 mRNA and serum levels with CCL5 genotypes. We found a highly significant association between the CCND1 rs614367-TT genotype (OR = 5.14; P = 0.004) and TNBC risk, and identified a significant association between the rs614367-T allele and decreased PFS in TNBC. A decreased risk of lymph node metastasis was associated with the MAP3K21 rs1294255-C allele, particularly in rs1294255-GC (OR = 0.47; P = 0.001). CCL5 variants (rs2107538 and rs2280789) were linked to CCL5 serum and mRNA levels. In the TCGA TNBC/Basal-like cohort the MAP3K21 rs1294255-G allele was associated with a decreased OVS. High expression of CCL5 in breast tumors was significantly associated with an increased OVS in all BC patients, but particularly in TNBC/Basal-like patients. In conclusion, genetic variation in CCL5 signaling genes may predict not only TNBC risk but also disease aggressiveness.
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Affiliation(s)
- Jingxuan Shan
- Department of Genetic Medicine, Weill Cornell Medicine, New York, NY, United States.,Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY, United States.,Laboratory of Genetic Medicine and Immunology, Weill Cornell Medicine-Qatar, Doha, Qatar
| | - Aziz Chouchane
- Faculta di Medicina e Chirurgia, Universita Cattolica del Sacro Cuero, Rome, Italy
| | - Younes Mokrab
- Translational Genetics and Bioinformatics Section, Research Division, Sidra Medicine, Doha, Qatar
| | - Mohamad Saad
- Qatar Computing Research Institute, Hamad Bin Khalifa University, Doha, Qatar
| | - Salha Boujassoum
- Department of Medical Oncology, National Center for Cancer Care and Research, Hamad Medical Corporation, Doha, Qatar
| | - Rosalyn W Sayaman
- Department of Population Sciences, City of Hope, Duarte, CA, United States.,Department of Laboratory Medicine at UCSF, San Francisco, CA, United States.,Helen Diller Family Comprehensive Cancer Center at UCSF, San Francisco, CA, United States
| | - Elad Ziv
- Helen Diller Family Comprehensive Cancer Center at UCSF, San Francisco, CA, United States.,Division of General Internal Medicine, Department of Medicine, Institute for Human Genetics at UCSF, San Francisco, CA, United States
| | - Noureddine Bouaouina
- Service de Cancérologie Radiothérapie, CHU Farhat Hached, Sousse, Tunisia.,Laboratoire d'Immuno-Oncologie Moléculaire, Faculté de Médecine de Monastir, Université de Monastir, Monastir, Tunisia
| | - Yasmine Remadi
- Laboratoire d'Immuno-Oncologie Moléculaire, Faculté de Médecine de Monastir, Université de Monastir, Monastir, Tunisia
| | - Sallouha Gabbouj
- Laboratoire d'Immuno-Oncologie Moléculaire, Faculté de Médecine de Monastir, Université de Monastir, Monastir, Tunisia
| | - Jessica Roelands
- Tumor Biology Section, Research Division, Sidra Medicine, Doha, Qatar
| | - Xiaojing Ma
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY, United States
| | - Davide Bedognetti
- Tumor Biology Section, Research Division, Sidra Medicine, Doha, Qatar
| | - Lotfi Chouchane
- Department of Genetic Medicine, Weill Cornell Medicine, New York, NY, United States.,Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY, United States.,Laboratory of Genetic Medicine and Immunology, Weill Cornell Medicine-Qatar, Doha, Qatar
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14
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Comparison of three different pretreatment methods for blood RNA extraction. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2019. [DOI: 10.1016/j.fsigss.2019.09.126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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15
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Measurement of mRNA therapeutics: method development and validation challenges. Bioanalysis 2019; 11:2003-2010. [DOI: 10.4155/bio-2019-0120] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The progression of chemically modified mRNA therapeutics through development pipelines is accelerating for many disease indications and the need to assess these analytes is becoming more routine for the pharmaceutical industry and contract research organizations. This article describes some of the challenges and strategies for performing regulated bioanalysis of modified mRNA therapeutics by comparing the two main analytical approaches – quantitative reverse transcription PCR and branched DNA.
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16
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Oh AC, Lee JK, Kim JY, Jin HO, Jung JW, Chang YH, Hong YJ. Utilization of Archived Plasma to Detect Epidermal Growth Factor Receptor Mutation in Non-Small Cell Lung Cancer Patients. Biopreserv Biobank 2019; 17:319-325. [PMID: 30888199 PMCID: PMC6703236 DOI: 10.1089/bio.2018.0126] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Precision medicine has received increased attention as an effective approach for the treatment of cancer patients. Because of challenges associated with the availability of archived tissue, liquid biopsies are often performed to detect cancer-specific mutations. One of the major advantages of the liquid biopsy is that the treatment can be monitored longitudinally, even after the tumor tissue is no longer available. In a clinical setting, one component of precision medicine is the detection of cancer-specific mutations using archived samples. In this study, we evaluated the epidermal growth factor receptor (EGFR) mutation status of samples of lung cancer patients stored before introduction of the plasma EGFR test at our institution. The aim of this study was to validate the utility of archived plasma samples for detection of the EGFR mutation in nonsmall cell lung cancer (NSCLC) patients. The Cobas® EGFR Mutation Test v2 was the first liquid biopsy test approved as a companion diagnostic test for patients with NSCLC treated with tyrosine kinase inhibitors. We tested for the EGFR mutation in 116 plasma samples archived in the biobank, and the results were compared with those obtained in the tissue or cytology EGFR mutation test. The EGFR mutation-positive rate from archived plasma was lower than that determined from tissue or cytology at 19.0% and 53.4%, respectively, and the concordance rate between the two tests was 58.6%. Of interest, five (4.3%) samples showed the T790M mutation in the plasma test, whereas this mutation was only detected in two (1.7%) tissue/cytology samples. Five (4.3%) samples were additionally positive in the plasma test. Overall, these results indicate that archived plasma samples can serve as an alternative source for the plasma EGFR mutation test when tissue samples are not available, and can improve precision medicine and long-term follow-up in a noninvasive manner.
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Affiliation(s)
- Ae-Chin Oh
- 1Department of Laboratory Medicine, Korea Cancer Center Hospital, Seoul, Republic of Korea
| | - Jin Kyung Lee
- 1Department of Laboratory Medicine, Korea Cancer Center Hospital, Seoul, Republic of Korea.,2KIRAMS Radiation Biobank, Korea Institute of Radiological and Medical Sciences, Seoul, Republic of Korea
| | - Ji-Young Kim
- 2KIRAMS Radiation Biobank, Korea Institute of Radiological and Medical Sciences, Seoul, Republic of Korea
| | - Hyeon-Ok Jin
- 2KIRAMS Radiation Biobank, Korea Institute of Radiological and Medical Sciences, Seoul, Republic of Korea
| | - Jae Won Jung
- 1Department of Laboratory Medicine, Korea Cancer Center Hospital, Seoul, Republic of Korea
| | - Yoon Hwan Chang
- 1Department of Laboratory Medicine, Korea Cancer Center Hospital, Seoul, Republic of Korea
| | - Young Jun Hong
- 1Department of Laboratory Medicine, Korea Cancer Center Hospital, Seoul, Republic of Korea
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17
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Targeted expression profiling by RNA-Seq improves detection of cellular dynamics during pregnancy and identifies a role for T cells in term parturition. Sci Rep 2019; 9:848. [PMID: 30696862 PMCID: PMC6351599 DOI: 10.1038/s41598-018-36649-w] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 11/26/2018] [Indexed: 12/29/2022] Open
Abstract
Development of maternal blood transcriptomic markers to monitor placental function and risk of obstetrical complications throughout pregnancy requires accurate quantification of gene expression. Herein, we benchmark three state-of-the-art expression profiling techniques to assess in maternal circulation the expression of cell type-specific gene sets previously discovered by single-cell genomics studies of the placenta. We compared Affymetrix Human Transcriptome Arrays, Illumina RNA-Seq, and sequencing-based targeted expression profiling (DriverMapTM) to assess transcriptomic changes with gestational age and labor status at term, and tested 86 candidate genes by qRT-PCR. DriverMap identified twice as many significant genes (q < 0.1) than RNA-Seq and five times more than microarrays. The gap in the number of significant genes remained when testing only protein-coding genes detected by all platforms. qRT-PCR validation statistics (PPV and AUC) were high and similar among platforms, yet dynamic ranges were higher for sequencing based platforms than microarrays. DriverMap provided the strongest evidence for the association of B-cell and T-cell gene signatures with gestational age, while the T-cell expression was increased with spontaneous labor at term according to all three platforms. We concluded that sequencing-based techniques are more suitable to quantify whole-blood gene expression compared to microarrays, as they have an expanded dynamic range and identify more true positives. Targeted expression profiling achieved higher coverage of protein-coding genes with fewer total sequenced reads, and it is especially suited to track cell type-specific signatures discovered in the placenta. The T-cell gene expression signature was increased in women who underwent spontaneous labor at term, mimicking immunological processes at the maternal-fetal interface and placenta.
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18
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Missaglia S, Tavian D, Moro L, Angelini C. Characterization of two ETFDH mutations in a novel case of riboflavin-responsive multiple acyl-CoA dehydrogenase deficiency. Lipids Health Dis 2018; 17:254. [PMID: 30424791 PMCID: PMC6234560 DOI: 10.1186/s12944-018-0903-5] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 10/29/2018] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Deficiency of electron transfer flavoprotein dehydrogenase (ETFDH) is associated with multiple acyl-CoA dehydrogenase deficiency (MADD). This disorder is an autosomal recessive lipid storage myopathy (LSM) that exhibits a wide range of clinical features, including myopathy, weakness and multisystem dysfunctions. Many patients with late onset of MADD improve when treated with riboflavin and are also referred to as RR-MADD (riboflavin-responsive multiple Acyl-CoA dehydrogenase disorder). METHODS In this study, we report the clinical and genetic characterization of a novel RR-MADD patient. Biochemical data were obtained from analysis of muscle and plasma samples. DNA and RNA were extracted from peripheral blood, and sequence analysis and expression study of ETFDH gene were performed. Finally, the impact of mutations on ETFDH folding was evaluated using bioinformatic tools. RESULTS Patient initially presented with vomiting, muscle weakness, and acidosis. Muscle biopsy revealed typical myopathological patterns of lipid storage myopathy and blood acylcarnitine profiles showed a combined elevation of long and medium chain acylcarnitines, supporting the diagnosis of RR-MADD. Molecular analysis of ETFDH gene revealed two heterozygous mutations, a novel splice variation in intron 10, c.1285 + 1G > A, and the previously reported c.560C > T missense mutation. RT-PCR analysis showed an alteration of ETFDH RNA splicing which in turn should lead to the production of a truncated protein. The in silico prediction analysis of ETFDH tridimensional structure demonstrated that the missense mutation resulted in instability and loss of protein activation, while the splice site variation induced a dramatic conformational change of the truncated protein. After MCT diet supplemented with carnitine and riboflavin, the patient showed significant biochemical and clinical improvement, in spite of severe molecular defect. CONCLUSION This case report extends the spectrum of ETFDH mutations in MADD, providing further evidence that patients presenting at least one missense mutation in the FAD-binding domain may respond to either carnitine or riboflavin treatment, due to the recovery of some enzymatic activity.
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Affiliation(s)
- Sara Missaglia
- Laboratory of Cellular Biochemistry and Molecular Biology, CRIBENS, Catholic University of the Sacred Heart, pz Buonarroti 30, 20145, Milan, Italy.,Psychology Department, Catholic University of the Sacred Heart, Largo Gemelli 1, 20123, Milan, Italy
| | - Daniela Tavian
- Laboratory of Cellular Biochemistry and Molecular Biology, CRIBENS, Catholic University of the Sacred Heart, pz Buonarroti 30, 20145, Milan, Italy.,Psychology Department, Catholic University of the Sacred Heart, Largo Gemelli 1, 20123, Milan, Italy
| | - Laura Moro
- Department of Pharmaceutical Sciences, University of Piemonte Orientale, Lgo Donegani 2, 28100, Novara, Italy
| | - Corrado Angelini
- Fondazione Ospedale San Camillo IRCCS, via Alberoni 70, 30126, Venice, Italy.
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19
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Direct DNA and RNA detection from large volumes of whole human blood. Sci Rep 2018; 8:3410. [PMID: 29467420 PMCID: PMC5821888 DOI: 10.1038/s41598-018-21224-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 01/21/2018] [Indexed: 11/25/2022] Open
Abstract
PCR inhibitors in clinical specimens negatively affect the sensitivity of diagnostic PCR and RT-PCR or may even cause false-negative results. To overcome PCR inhibition, increase the sensitivity of the assays and simplify the detection protocols, simple methods based on quantitative nested real-time PCR and RT-PCR were developed to detect exogenous DNA and RNA directly from large volumes of whole human blood (WHB). Thermus thermophilus (Tth) polymerase is resistant to several common PCR inhibitors and exhibits reverse transcriptase activity in the presence of manganese ions. In combination with optimized concentrations of magnesium ions and manganese ions, Tth polymerase enabled efficient detection of DNA and RNA from large volumes of WHB treated with various anticoagulants. The applicability of these methods was further demonstrated by examining WHB specimens collected from different healthy individuals and those stored under a variety of conditions. The detection limit of these methods was determined by detecting exogenous DNA, RNA, and bacteria spiked in WHB. To the best of our knowledge, direct RNA detection from large volumes of WHB has not been reported. The results of the developed methods can be obtained within 4 hours, making them possible for rapid and accurate detection of disease-causing agents from WHB.
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20
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Kim DD, Yang CS, Chae HD, Kwak SG, Jeon CH. Melanoma antigen-encoding gene family member A1-6 and hTERT in the detection of circulating tumor cells following CD45 - depletion and RNA extraction. Oncol Lett 2017; 14:837-843. [PMID: 28693240 PMCID: PMC5494678 DOI: 10.3892/ol.2017.6226] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Accepted: 03/23/2017] [Indexed: 12/31/2022] Open
Abstract
A total of 76 blood samples from patients without malignant disease and 107 blood samples from patients with malignant disease were investigated for the presence of circulating tumor cells (CTCs). To detect CTCs, hematopoietic cells were removed from the blood samples and different RNA extraction methods were used to amplify the melanoma antigen-encoding gene family member A1-family member A6 (MAGE A1-6) and the human telomerase reverse transcriptase (hTERT) gene as potential CTC markers. Comparison between four methods for extracting RNA from the blood was performed. The samples were enriched by cluster of differentiation 45 (CD45) antibody capturing, and the reverse transcription-quantitative polymerase chain reaction was used to amplify the MAGE A1-6 and hTERT genes. MAGE A1-6 and hTERT gene expression levels were also evaluated in 14 cancer cell lines, and the MAGE A1-6 and hTERT expression levels were 85.7 and 100%, respectively. The RNeasy method demonstrated the most sensitivity in the SNU1 cells mixed with blood, although the differences between methods was non-significant. The positive expression levels of MAGE A1-6 and hTERT was 11.8% in the control group and 58.9% in those with malignant disease. In the 70 patients with colorectal cancer, positive expression levels of MAGE A1-6 or hTERT were significantly higher in stages T3 and T4 compared with in stages T1 and T2. The CTC detection method involving CD45 antibody capture, RNA extraction and MAGE A1-6 and hTERT reverse transcription resulted in good rates of sensitivity and specificity. Thus, the present study concluded that MAGE A1-6 and hTERT genes may be potential and practical markers for CTCs in a clinical setting.
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Affiliation(s)
- Dae-Dong Kim
- Department of Surgery, School of Medicine, Catholic University of Daegu, Daegu 42472, Republic of Korea
| | - Chun-Seok Yang
- Department of Surgery, School of Medicine, Catholic University of Daegu, Daegu 42472, Republic of Korea
| | - Hyun-Dong Chae
- Department of Surgery, School of Medicine, Catholic University of Daegu, Daegu 42472, Republic of Korea
| | - Sang-Gyu Kwak
- Department of Medical Statistics, School of Medicine, Catholic University of Daegu, Daegu 42472, Republic of Korea
| | - Chang-Ho Jeon
- Department of Laboratory Medicine, School of Medicine, Catholic University of Daegu, Daegu 42472, Republic of Korea
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Feddersen S, Bastholt L, Pedersen SM. Stabilization of circulating thyroglobulin mRNA transcripts in patients treated for differentiated thyroid carcinoma. Ann Clin Biochem 2016; 54:558-566. [PMID: 27629910 DOI: 10.1177/0004563216671538] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Background The clinical utility of serum thyroglobulin in the follow-up of patients with differentiated thyroid carcinoma may be compromised by the presence of endogenous antithyroglobulin antibodies. To prevent interference by antithyroglobulin antibodies several groups have developed real-time PCR-based assays for quantification of blood thyroglobulin mRNA levels. For accurate quantification of thyroglobulin mRNA in blood preanalytical factors must be recognized and controlled. In this study, we evaluate the effect of different blood RNA stabilizing systems - the Tempus Blood RNA system and the PAXgene Blood RNA system - and storage time on RNA yield and quality, and thyroglobulin mRNA stability. Methods Blood samples from 11 patients previously treated for differentiated thyroid carcinoma were collected in K2-EDTA, Tempus and PAXgene tubes and maintained at room temperature. RNA was isolated following storage for 0 and 72 h, and RNA yield, integrity and purity was determined. Thyroglobulin, GAPDH and ACTB mRNA levels were quantified by semi-quantitative real-time PCR. Results The RNA yield was significantly higher for blood collected in Tempus tubes compared with PAXgene tubes following storage for 72 h at room temperature ( P = 0.0011). High-quality RNA could be extracted from blood collected in PAXgene and Tempus tubes. Blood collected in K2-EDTA tubes, but not in PAXgene and Tempus tubes, showed significant changes in thyroglobulin mRNA levels following storage for 72 h at room temperature ( P = 0.0263). Conclusions Stabilization of blood in PAXgene and Tempus tubes enables storage at room temperature for up to 72 h, without compromising thyroglobulin mRNA levels.
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Affiliation(s)
- Søren Feddersen
- 1 Department of Clinical Biochemistry and Pharmacology, Odense University Hospital, Odense, Denmark.,2 Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Lars Bastholt
- 3 Department of Oncology, Odense University Hospital, Odense, Denmark
| | - Susanne M Pedersen
- 1 Department of Clinical Biochemistry and Pharmacology, Odense University Hospital, Odense, Denmark
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22
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Sun Y, Gong X, Tan JY, Kang L, Li D, Vikash, Yang J, Du G. In vitro Antiviral Activity of Rubia cordifolia Aerial Part Extract against Rotavirus. Front Pharmacol 2016; 7:308. [PMID: 27679574 PMCID: PMC5020101 DOI: 10.3389/fphar.2016.00308] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Accepted: 08/30/2016] [Indexed: 11/13/2022] Open
Abstract
The root of Rubia cordifolia has been used traditionally as a hemostatic agent, while the aerial part of the plant consisting of leaf and stem is known to exhibit anti-diarrheal properties and has been widely used as a remedy in many parts of China. As rotavirus is one of the most commonly associated diarrhea-causing pathogen, this study aims to investigate the anti-rotaviral effect of R. cordifolia aerial part (RCAP). The cytotoxicity of RCAP toward MA-104 cells was evaluated using the WST-8 assay. Colloidal gold method and real time polymerase chain reaction (qPCR) assay were used to confirm the findings of the antiviral assay. Then, 4',6-diamidino-2-phenylindole (DAPI) staining method was subsequently used to investigate the mode of death among the cells. And the representative components of aqueous extract were isolated and identified. It was shown that both the viability of MA-104 cells and the viral load were reduced with increasing concentration of the extract. DAPI staining showed that virus-induced apoptosis was the cause of the low cell viability and viral load, an effect which was accelerated with incubation in the aqueous herbal extract. The major compounds postulated to exhibit this activity were isolated from the aqueous herbal extract and identified to be compounds Xanthopurpurin and Vanillic Acid. This study showed that RCAP extract effectively inhibited rotavirus multiplication by promoting virus-induced apoptosis in MA-104 cells.
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Affiliation(s)
- Yuanyuan Sun
- Department of Pharmacy, Tongji Hospital, Tongji Medical College, Huazhong University of Science and TechnologyWuhan, China; Department of Pharmacy, National University of SingaporeSingapore, Singapore
| | - Xuepeng Gong
- Department of Pharmacy, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology Wuhan, China
| | - Jia Y Tan
- Department of Pharmacy, National University of Singapore Singapore, Singapore
| | - Lifeng Kang
- Department of Pharmacy, National University of Singapore Singapore, Singapore
| | - Dongyan Li
- Department of Pharmacy, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology Wuhan, China
| | - Vikash
- Department of Infectious Diseases, Wuhan Union Hospital, Tongji Medical College, Huazhong University of Science and Technology Wuhan, China
| | - Jihong Yang
- College of Life Sciences, Central China Normal University Wuhan, China
| | - Guang Du
- Department of Pharmacy, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology Wuhan, China
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23
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Leidinger P, Backes C, Rheinheimer S, Keller A, Meese E. Towards Clinical Applications of Blood-Borne miRNA Signatures: The Influence of the Anticoagulant EDTA on miRNA Abundance. PLoS One 2015; 10:e0143321. [PMID: 26599228 PMCID: PMC4658123 DOI: 10.1371/journal.pone.0143321] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Accepted: 11/03/2015] [Indexed: 12/23/2022] Open
Abstract
Background Circulating microRNAs (miRNAs) from blood are increasingly recognized as biomarker candidates for human diseases. Clinical routine settings frequently include blood sampling in tubes with EDTA as anticoagulant without considering the influence of phlebotomy on the overall miRNA expression pattern. We collected blood samples from six healthy individuals each in an EDTA blood collection tube. Subsequently, the blood was transferred into PAXgeneTM tubes at three different time points, i.e. directly (0 min), 10 min, and 2 h after phlebotomy. As control blood was also directly collected in PAXgeneTM blood RNA tubes that contain a reagent to directly lyse blood cells and stabilize their content. For all six blood donors at the four conditions (24 samples) we analyzed the abundance of 1,205 miRNAs by human Agilent miRNA V16 microarrays. Results While we found generally a homogenous pattern of the miRNA abundance in all 24 samples, the duration of the EDTA treatment appears to influence the miRNA abundance of specific miRNAs. The most significant changes are observed after longer EDTA exposition. Overall, the impact of the different blood sample conditions on the miRNA pattern was substantially lower than intra-individual variations. While samples belonging to one of the six individuals mostly cluster together, there was no comparable clustering for any of the four tested blood sampling conditions. The most affected miRNA was miR-769-3p that was not detected in any of the six PAXgene blood samples, but in all EDTA 2h samples. Accordingly, hsa-miR-769-3p was also the only miRNA that showed a significantly different abundance between the 4 blood sample conditions by an ANOVA analysis (Benjamini-Hochberg adjusted p-value of 0.003). Validation by qRT-PCR confirmed this finding. Conclusion The pattern of blood-borne miRNA abundance is rather homogenous between the four tested blood sample conditions of six blood donors. There was a clustering between the miRNA profiles that belong to a specific blood donor, but not between any of the four tested blood sampling conditions. The results show a limited overall impact of the blood sampling conditions on the miRNA pattern. Notwithstanding, the abundance of single miRNAs can be significantly altered by different blood sampling conditions.
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Affiliation(s)
- Petra Leidinger
- Department of Human Genetics, Medical School, Saarland University, Building 60, 66421, Homburg/Saar, Germany
| | - Christina Backes
- Department of Clinical Bioinformatics, Saarland University, Building E2.1, 66123, Saarbrücken, Germany
| | - Stefanie Rheinheimer
- Department of Human Genetics, Medical School, Saarland University, Building 60, 66421, Homburg/Saar, Germany
| | - Andreas Keller
- Department of Clinical Bioinformatics, Saarland University, Building E2.1, 66123, Saarbrücken, Germany
| | - Eckart Meese
- Department of Human Genetics, Medical School, Saarland University, Building 60, 66421, Homburg/Saar, Germany
- * E-mail:
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24
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Liu X, Li Q, Wang X, Zhou X, Liao Q, He X, Zhang J, Sun J, Wu J, Cheng L, Zhang Y. Comparison of six different pretreatment methods for blood RNA extraction. Biopreserv Biobank 2015; 13:56-60. [PMID: 25686049 DOI: 10.1089/bio.2014.0090] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Human blood specimens serve as important research materials in the field of translational medicine research. The RNA extracted from blood, for example, represents the gene expression profiles of individuals or groups, and can be indicative of the pathological basis for human diseases. Meanwhile, the RNA quality may have severe impacts on the results of RNA studies. RNA is susceptible to many factors, such as the time of sample collection, transportation conditions, protectants, pretreatments, and extraction methods. In this study, six different pretreatment methods are evaluated for their effects on blood RNA extraction including the RNA yields and quality. Results show that most of these methods meet the basic requirements for RNA studies. While considering the simplicity of the procedure, the cost factor, and how to make full use of the samples, the proper method should be employed by researchers who have specific requirements for their research.
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Affiliation(s)
- Xiaopan Liu
- 1 China National Genebank, BGI-Shenzhen , Shenzhen, China
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25
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Kelly H, Downing T, Tuite NL, Smith TJ, Kerin MJ, Dwyer RM, Clancy E, Barry T, Reddington K. Cross Platform Standardisation of an Experimental Pipeline for Use in the Identification of Dysregulated Human Circulating MiRNAs. PLoS One 2015; 10:e0137389. [PMID: 26355751 PMCID: PMC4565682 DOI: 10.1371/journal.pone.0137389] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Accepted: 08/17/2015] [Indexed: 12/21/2022] Open
Abstract
Introduction Micro RNAs (miRNAs) are a class of highly conserved small non-coding RNAs that play an important part in the post-transcriptional regulation of gene expression. A substantial number of miRNAs have been proposed as biomarkers for diseases. While reverse transcriptase Real-time PCR (RT-qPCR) is considered the gold standard for the evaluation and validation of miRNA biomarkers, small RNA sequencing is now routinely being adopted for the identification of dysregulated miRNAs. However, in many cases where putative miRNA biomarkers are identified using small RNA sequencing, they are not substantiated when RT-qPCR is used for validation. To date, there is a lack of consensus regarding optimal methodologies for miRNA detection, quantification and standardisation when different platform technologies are used. Materials and Methods In this study we present an experimental pipeline that takes into consideration sample collection, processing, enrichment, and the subsequent comparative analysis of circulating small ribonucleic acids using small RNA sequencing and RT-qPCR. Results, Discussion, Conclusions Initially, a panel of miRNAs dysregulated in circulating blood from breast cancer patients compared to healthy women were identified using small RNA sequencing. MiR-320a was identified as the most dysregulated miRNA between the two female cohorts. Total RNA and enriched small RNA populations (<30 bp) isolated from peripheral blood from the same female cohort samples were then tested for using a miR-320a RT-qPCR assay. When total RNA was analysed with this miR-320a RT-qPCR assay, a 2.3-fold decrease in expression levels was observed between blood samples from healthy controls and breast cancer patients. However, upon enrichment for the small RNA population and subsequent analysis of miR-320a using RT-qPCR, its dysregulation in breast cancer patients was more pronounced with an 8.89-fold decrease in miR-320a expression. We propose that the experimental pipeline outlined could serve as a robust approach for the identification and validation of small RNA biomarkers for disease.
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Affiliation(s)
- Helena Kelly
- Nucleic Acid Diagnostics Research Laboratory (NADRL), Microbiology, School of Natural Sciences, National University of Ireland, Galway, Ireland
| | - Tim Downing
- School of Biotechnology, Dublin City University, Dublin, Ireland
| | - Nina L. Tuite
- Nucleic Acid Diagnostics Research Laboratory (NADRL), Microbiology, School of Natural Sciences, National University of Ireland, Galway, Ireland
| | - Terry J. Smith
- Molecular Diagnostics Research Group (MDRG), School of Natural Sciences, National University of Ireland, Galway, Ireland
- Biomedical Diagnostics Institute (BDI) Programme, National University of Ireland, Galway, Ireland
| | - Michael J. Kerin
- Discipline of Surgery, School of Medicine, National University of Ireland Galway, Galway, Ireland
| | - Róisín M. Dwyer
- Discipline of Surgery, School of Medicine, National University of Ireland Galway, Galway, Ireland
| | - Eoin Clancy
- Molecular Diagnostics Research Group (MDRG), School of Natural Sciences, National University of Ireland, Galway, Ireland
- Biomedical Diagnostics Institute (BDI) Programme, National University of Ireland, Galway, Ireland
| | - Thomas Barry
- Nucleic Acid Diagnostics Research Laboratory (NADRL), Microbiology, School of Natural Sciences, National University of Ireland, Galway, Ireland
- * E-mail:
| | - Kate Reddington
- Nucleic Acid Diagnostics Research Laboratory (NADRL), Microbiology, School of Natural Sciences, National University of Ireland, Galway, Ireland
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26
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Locascio JJ, Eberly S, Liao Z, Liu G, Hoesing AN, Duong K, Trisini-Lipsanopoulos A, Dhima K, Hung AY, Flaherty AW, Schwarzschild MA, Hayes MT, Wills AM, Shivraj Sohur U, Mejia NI, Selkoe DJ, Oakes D, Shoulson I, Dong X, Marek K, Zheng B, Ivinson A, Hyman BT, Growdon JH, Sudarsky LR, Schlossmacher MG, Ravina B, Scherzer CR. Association between α-synuclein blood transcripts and early, neuroimaging-supported Parkinson's disease. Brain 2015. [PMID: 26220939 DOI: 10.1093/brain/awv202] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
There are no cures for neurodegenerative diseases and this is partially due to the difficulty of monitoring pathogenic molecules in patients during life. The Parkinson's disease gene α-synuclein (SNCA) is selectively expressed in blood cells and neurons. Here we show that SNCA transcripts in circulating blood cells are paradoxically reduced in early stage, untreated and dopamine transporter neuroimaging-supported Parkinson's disease in three independent regional, national, and international populations representing 500 cases and 363 controls and on three analogue and digital platforms with P < 0.0001 in meta-analysis. Individuals with SNCA transcripts in the lowest quartile of counts had an odds ratio for Parkinson's disease of 2.45 compared to individuals in the highest quartile. Disease-relevant transcript isoforms were low even near disease onset. Importantly, low SNCA transcript abundance predicted cognitive decline in patients with Parkinson's disease during up to 5 years of longitudinal follow-up. This study reveals a consistent association of reduced SNCA transcripts in accessible peripheral blood and early-stage Parkinson's disease in 863 participants and suggests a clinical role as potential predictor of cognitive decline. Moreover, the three independent biobank cohorts provide a generally useful platform for rapidly validating any biological marker of this common disease.
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Affiliation(s)
- Joseph J Locascio
- 1 Neurogenomics Lab and Parkinson Personalized Medicine Program, Harvard Medical School and Brigham and Women's Hospital, Cambridge, MA 02139, USA 2 Department of Neurology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Shirley Eberly
- 3 Department of Biostatistics and Computational Biology, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Zhixiang Liao
- 1 Neurogenomics Lab and Parkinson Personalized Medicine Program, Harvard Medical School and Brigham and Women's Hospital, Cambridge, MA 02139, USA 4 Ann Romney Centre for Neurologic Diseases, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Ganqiang Liu
- 1 Neurogenomics Lab and Parkinson Personalized Medicine Program, Harvard Medical School and Brigham and Women's Hospital, Cambridge, MA 02139, USA 4 Ann Romney Centre for Neurologic Diseases, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Ashley N Hoesing
- 1 Neurogenomics Lab and Parkinson Personalized Medicine Program, Harvard Medical School and Brigham and Women's Hospital, Cambridge, MA 02139, USA 4 Ann Romney Centre for Neurologic Diseases, Brigham and Women's Hospital, Boston, MA 02115, USA 5 Biomarkers Program, Harvard NeuroDiscovery Center, Boston, MA 02115, USA
| | - Karen Duong
- 1 Neurogenomics Lab and Parkinson Personalized Medicine Program, Harvard Medical School and Brigham and Women's Hospital, Cambridge, MA 02139, USA 4 Ann Romney Centre for Neurologic Diseases, Brigham and Women's Hospital, Boston, MA 02115, USA 5 Biomarkers Program, Harvard NeuroDiscovery Center, Boston, MA 02115, USA
| | - Ana Trisini-Lipsanopoulos
- 1 Neurogenomics Lab and Parkinson Personalized Medicine Program, Harvard Medical School and Brigham and Women's Hospital, Cambridge, MA 02139, USA 4 Ann Romney Centre for Neurologic Diseases, Brigham and Women's Hospital, Boston, MA 02115, USA 5 Biomarkers Program, Harvard NeuroDiscovery Center, Boston, MA 02115, USA
| | - Kaltra Dhima
- 1 Neurogenomics Lab and Parkinson Personalized Medicine Program, Harvard Medical School and Brigham and Women's Hospital, Cambridge, MA 02139, USA 4 Ann Romney Centre for Neurologic Diseases, Brigham and Women's Hospital, Boston, MA 02115, USA 5 Biomarkers Program, Harvard NeuroDiscovery Center, Boston, MA 02115, USA
| | - Albert Y Hung
- 2 Department of Neurology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Alice W Flaherty
- 2 Department of Neurology, Massachusetts General Hospital, Boston, MA 02114, USA 6 Department of Psychiatry, Massachusetts General Hospital, Boston, MA 02114, USA
| | | | - Michael T Hayes
- 7 Department of Neurology, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Anne-Marie Wills
- 2 Department of Neurology, Massachusetts General Hospital, Boston, MA 02114, USA 5 Biomarkers Program, Harvard NeuroDiscovery Center, Boston, MA 02115, USA
| | - U Shivraj Sohur
- 2 Department of Neurology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Nicte I Mejia
- 2 Department of Neurology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Dennis J Selkoe
- 4 Ann Romney Centre for Neurologic Diseases, Brigham and Women's Hospital, Boston, MA 02115, USA 7 Department of Neurology, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - David Oakes
- 3 Department of Biostatistics and Computational Biology, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Ira Shoulson
- 8 Program for Regulatory Science and Medicine, Department of Neurology, Georgetown University, Washington, DC 20007, USA
| | - Xianjun Dong
- 1 Neurogenomics Lab and Parkinson Personalized Medicine Program, Harvard Medical School and Brigham and Women's Hospital, Cambridge, MA 02139, USA 4 Ann Romney Centre for Neurologic Diseases, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Ken Marek
- 8 Program for Regulatory Science and Medicine, Department of Neurology, Georgetown University, Washington, DC 20007, USA
| | - Bin Zheng
- 1 Neurogenomics Lab and Parkinson Personalized Medicine Program, Harvard Medical School and Brigham and Women's Hospital, Cambridge, MA 02139, USA 4 Ann Romney Centre for Neurologic Diseases, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Adrian Ivinson
- 4 Ann Romney Centre for Neurologic Diseases, Brigham and Women's Hospital, Boston, MA 02115, USA 5 Biomarkers Program, Harvard NeuroDiscovery Center, Boston, MA 02115, USA
| | - Bradley T Hyman
- 2 Department of Neurology, Massachusetts General Hospital, Boston, MA 02114, USA 5 Biomarkers Program, Harvard NeuroDiscovery Center, Boston, MA 02115, USA
| | - John H Growdon
- 2 Department of Neurology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Lewis R Sudarsky
- 7 Department of Neurology, Brigham and Women's Hospital, Boston, MA 02115, USA
| | | | - Bernard Ravina
- 10 Program in Neuroscience, Ottawa Hospital Research Institute, University of Ottawa, Ottawa, Ontario K1H8M5, Canada
| | - Clemens R Scherzer
- 1 Neurogenomics Lab and Parkinson Personalized Medicine Program, Harvard Medical School and Brigham and Women's Hospital, Cambridge, MA 02139, USA 2 Department of Neurology, Massachusetts General Hospital, Boston, MA 02114, USA 4 Ann Romney Centre for Neurologic Diseases, Brigham and Women's Hospital, Boston, MA 02115, USA 5 Biomarkers Program, Harvard NeuroDiscovery Center, Boston, MA 02115, USA 7 Department of Neurology, Brigham and Women's Hospital, Boston, MA 02115, USA
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27
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Igaz I, Nyírő G, Nagy Z, Butz H, Nagy Z, Perge P, Sahin P, Tóth M, Rácz K, Igaz P, Patócs A. Analysis of Circulating MicroRNAs In Vivo following Administration of Dexamethasone and Adrenocorticotropin. Int J Endocrinol 2015; 2015:589230. [PMID: 26161091 PMCID: PMC4487905 DOI: 10.1155/2015/589230] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Revised: 06/02/2015] [Accepted: 06/10/2015] [Indexed: 12/21/2022] Open
Abstract
Purpose. The interaction of hormones of the pituitary-adrenal axis and adrenal cortex-associated circulating microRNAs is mostly unknown. We have studied the effects of dexamethasone and adrenocorticotropin on the expression of five circulating microRNAs (hsa-miR-27a, hsa-miR-200b, hsa-miR-214, hsa-miR-483-5p, and hsa-miR-503) reported to be related to the adrenal cortex in plasma samples. Methods. Expression of microRNAs was studied in plasma samples of 10 individuals examined by 1 mg dexamethasone suppression test and another 10 individuals stimulated by 250 μg tetracosactide (adrenocorticotropin). Total RNA was isolated and microRNA expression was analyzed by real-time reverse transcription quantitative polymerase chain reaction normalized to cel-miR-39 as reference. Results. Only circulating hsa-miR-27a proved to be significantly modulated in vivo by hormonal treatments: its expression was upregulated by dexamethasone whereas it was suppressed by adrenocorticotropin. Secreted hsa-miR-27a was significantly induced by dexamethasone in vitro in NCI-H295R cells, as well. The expression of hsa-miR-483-5p proposed as diagnostic marker for adrenocortical malignancy was not affected by dexamethasone or tetracosactide administration. Conclusions. hsa-miR-27a expression is modulated by hormones of the hypothalamic-pituitary-adrenal axis both in vitro and in vivo. The biological relevance of hsa-miR-27a modulation by hormones is unclear, but the responsiveness of circulating microRNAs to hormones of the pituitary-adrenal axis is noteworthy.
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Affiliation(s)
- Ivan Igaz
- Department of Gastroenterology, Szent Imre Teaching Hospital, Tétényi Street 12-16, Budapest 1115, Hungary
| | - Gábor Nyírő
- Molecular Medicine Research Group, Hungarian Academy of Sciences and Semmelweis University, Szentkirályi Street 46, Budapest 1088, Hungary
| | - Zoltán Nagy
- 2nd Department of Medicine, Faculty of Medicine, Semmelweis University, Szentkirályi Street 46, Budapest 1088, Hungary
| | - Henriett Butz
- Molecular Medicine Research Group, Hungarian Academy of Sciences and Semmelweis University, Szentkirályi Street 46, Budapest 1088, Hungary
| | - Zsolt Nagy
- 2nd Department of Medicine, Faculty of Medicine, Semmelweis University, Szentkirályi Street 46, Budapest 1088, Hungary
- “Lendület-2013” Hereditary Endocrine Tumors Research Group, Hungarian Academy of Sciences and Semmelweis University, Szentkirályi Street 46, Budapest 1088, Hungary
| | - Pál Perge
- 2nd Department of Medicine, Faculty of Medicine, Semmelweis University, Szentkirályi Street 46, Budapest 1088, Hungary
| | - Peter Sahin
- Department of Gastroenterology, Szent Imre Teaching Hospital, Tétényi Street 12-16, Budapest 1115, Hungary
| | - Miklós Tóth
- 2nd Department of Medicine, Faculty of Medicine, Semmelweis University, Szentkirályi Street 46, Budapest 1088, Hungary
| | - Károly Rácz
- Molecular Medicine Research Group, Hungarian Academy of Sciences and Semmelweis University, Szentkirályi Street 46, Budapest 1088, Hungary
- 2nd Department of Medicine, Faculty of Medicine, Semmelweis University, Szentkirályi Street 46, Budapest 1088, Hungary
| | - Peter Igaz
- 2nd Department of Medicine, Faculty of Medicine, Semmelweis University, Szentkirályi Street 46, Budapest 1088, Hungary
| | - Attila Patócs
- “Lendület-2013” Hereditary Endocrine Tumors Research Group, Hungarian Academy of Sciences and Semmelweis University, Szentkirályi Street 46, Budapest 1088, Hungary
- *Attila Patócs:
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