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Li S, Liu J, Zhao M, Su Y, Cong B, Wang Z. RNA quality score evaluation: A preliminary study of RNA integrity number (RIN) and RNA integrity and quality number (RNA IQ). Forensic Sci Int 2024; 357:111976. [PMID: 38447345 DOI: 10.1016/j.forsciint.2024.111976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 02/17/2024] [Accepted: 03/01/2024] [Indexed: 03/08/2024]
Abstract
In the past several years, with the in-depth development of RNA-related research, exploring the application of transcriptome and corresponding RNA biomarkers has become one of the research hotspots in the field of forensic science. High-quality RNA is essential for successful downstream workflows, especially in the steps of screening biomarkers by microarray or RNA sequencing (RNA-seq). Thus, accurately evaluating the quality of RNA samples is a critical step in obtaining meaningful expression data. The RNA integrity number (RIN) generated from the Agilent Bioanalyzer system has been widely used for RNA quality control in the past two decades. Recently, Thermo Fisher Scientific launched a ratiometric fluorescence-based method to quickly check whether an RNA sample has degraded, and the results are presented as RNA integrity and quality number (RNA IQ). Both quality score systems determine RNA quality using a numerical system based on a scale of 1-10, with 1 denoting significantly degraded specimens and 10 representing high-quality, intact RNA samples. In this preliminary study, we evaluated the consistency, reproducibility and linearity of two quality scores in RNA quality determination by analyzing heat- and RNase- artificially degraded samples. Meanwhile, the expression levels of three microRNAs (hsa-let-7 g-5p, hsa-miR-93-5p and hsa-miR-191-5p) in intact and severely degraded RNA samples were estimated by TaqMan-qPCR and droplet digital PCR. Overall, both quality scores showed good repeatability and reproducibility in their respective tests. In the samples subjected to thermal degradation, RIN showed a trend corresponding to heating time, while RNA IQ value showed almost no change on the time gradient. However, in RNase A mediated degradation, RNA IQ value observed better linearity. Furthermore, the expression levels of three microRNAs in the severely degraded samples did not show significant changes compared to the intact RNA samples. RNA degradation is a very complex and highly variable process, which is difficult to comprehensively evaluate through any one index and cannot directly compare these two parameters. Nevertheless, combined with previous research results and the expression levels of three microRNAs in this study, analyzing RNA biomarkers with stable regions or small sizes in challenged samples may be a conservative and reliable approach.
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Affiliation(s)
- Suyu Li
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Jing Liu
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China; College of Forensic Medicine, Hebei Medical University, Hebei Key Laboratory of Forensic Medicine, Shijiazhuang 050017, China
| | - Mengyao Zhao
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Yonglin Su
- Department of Rehabilitation Medicine, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Bin Cong
- College of Forensic Medicine, Hebei Medical University, Hebei Key Laboratory of Forensic Medicine, Shijiazhuang 050017, China.
| | - Zheng Wang
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China.
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Noda Y, Sakagami T, Suzuki K, Fujisawa T, Yagi M, Iwai H, Tsuta K. Direct specimen collection during routine operation improves nucleic acid quality in genetic analysis samples for head and neck tumors: A retrospective study. Pathol Res Pract 2023; 252:154943. [PMID: 37977036 DOI: 10.1016/j.prp.2023.154943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 11/07/2023] [Accepted: 11/10/2023] [Indexed: 11/19/2023]
Abstract
The nucleic acid integrity of head and neck squamous cell carcinoma (HNSCC) samples is poor, and the material available for genetic analysis is limited. Therefore, to expand the effectiveness of personalized medicine in patients with HNSCC, a new sampling method is needed. In total, 128 samples from 44 patients with HNSCC were studied: 32 genetic analysis samples (GASs) collected as 5 × 5 × 5 mm tissue fragments from resected large tumors and immediately embedded in a small formalin bottle within 10 min (i.e., the ischemic time), 43 primary tumor components (primary), 14 decalcified tumor (DC) samples, 32 metastatic tumors in lymph nodes (LNs), and 7 parakeratinized components (PKCs). The nucleic acid quality in the GAS, primary, DC, LN, and PKC groups was compared and next-generation sequencing (NGS) was performed. DNA integrity number and percentage of RNA fragments with > 200 nucleotides were significantly higher in the GAS group than those in the other groups. RNA integrity number decreased first in LN, followed by GAS, primary, and DC. No significant differences were observed in DIN, RIN and DV200 among the PKC, primary and LN. Following methyl green-pyronin staining, preserved DNA and RNA were not visualized in DC samples. Most NGS metrics did not differ significantly among primary, LN, and PKC samples. In conclusion, GASs should be collected during routine hospital activities. When the volume of viable materials is limited, PKCs should be considered for genetic analysis.
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Affiliation(s)
- Yuri Noda
- Department of Pathology and Laboratory Medicine, Kansai Medical University Hospital, 2-3-1 Shin-machi, Hirakata, Osaka 573-1191, Japan; Department of Pathology, Kansai Medical University, 2-5-1 Shin-machi, Hirakata, Osaka 573-1010, Japan.
| | - Tomofumi Sakagami
- Department of Otolaryngology, Head and Neck Surgery, Kansai Medical University Hospital, 2-3-1 Shin-machi, Hirakata, Osaka 573-1191, Japan
| | - Kensuke Suzuki
- Department of Otolaryngology, Head and Neck Surgery, Kansai Medical University Hospital, 2-3-1 Shin-machi, Hirakata, Osaka 573-1191, Japan
| | - Takuo Fujisawa
- Department of Otolaryngology, Head and Neck Surgery, Kansai Medical University Hospital, 2-3-1 Shin-machi, Hirakata, Osaka 573-1191, Japan
| | - Masao Yagi
- Department of Otolaryngology, Head and Neck Surgery, Kansai Medical University Hospital, 2-3-1 Shin-machi, Hirakata, Osaka 573-1191, Japan
| | - Hiroshi Iwai
- Department of Otolaryngology, Head and Neck Surgery, Kansai Medical University Hospital, 2-3-1 Shin-machi, Hirakata, Osaka 573-1191, Japan
| | - Koji Tsuta
- Department of Pathology and Laboratory Medicine, Kansai Medical University Hospital, 2-3-1 Shin-machi, Hirakata, Osaka 573-1191, Japan; Department of Pathology, Kansai Medical University, 2-5-1 Shin-machi, Hirakata, Osaka 573-1010, Japan
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Walker JE, Oliver JC, Stewart AM, Beh ST, Arce RA, Glass MJ, Vargas DE, Qiji SH, Intorcia AJ, Borja CI, Cline MP, Hemmingsen SJ, Krupp AN, McHattie RD, Mariner MR, Lorenzini I, Aslam S, Tremblay C, Beach TG, Serrano GE. Measuring Up: A Comparison of TapeStation 4200 and Bioanalyzer 2100 as Measurement Tools for RNA Quality in Postmortem Human Brain Samples. Int J Mol Sci 2023; 24:13795. [PMID: 37762097 PMCID: PMC10531353 DOI: 10.3390/ijms241813795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 08/26/2023] [Accepted: 09/01/2023] [Indexed: 09/29/2023] Open
Abstract
The determination of RNA integrity is a critical quality assessment tool for gene expression studies where the experiment's success is highly dependent on the sample quality. Since its introduction in 1999, the gold standard in the scientific community has been the Agilent 2100 Bioanalyzer's RNA integrity number (RIN), which uses a 1-10 value system, from 1 being the most degraded, to 10 being the most intact. In 2015, Agilent launched 4200 TapeStation's RIN equivalent, and reported a strong correlation of r2 of 0.936 and a median error < ±0.4 RIN units. To evaluate this claim, we compared the Agilent 4200 TapeStation's RIN equivalent (RINe) and DV200 to the Agilent 2100 Bioanalyzer's RIN for 183 parallel RNA samples. In our study, using RNA from a total of 183 human postmortem brain samples, we found that the RIN and RINe values only weakly correlate, with an r2 of 0.393 and an average difference of 3.2 RIN units. DV200 also only weakly correlated with RIN (r2 of 0.182) and RINe (r2 of 0.347). Finally, when applying a cut-off value of 6.5 for both metrics, we found that 95.6% of samples passed with RIN, while only 23.5% passed with RINe. Our results suggest that even though RIN (Bioanalyzer) and RINe (TapeStation) use the same 1-10 value system, they should not be used interchangeably, and cut-off values should be calculated independently.
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Miyahara K, Hino M, Yu Z, Ono C, Nagaoka A, Hatano M, Shishido R, Yabe H, Tomita H, Kunii Y. The influence of tissue pH and RNA integrity number on gene expression of human postmortem brain. Front Psychiatry 2023; 14:1156524. [PMID: 37520228 PMCID: PMC10379646 DOI: 10.3389/fpsyt.2023.1156524] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 06/26/2023] [Indexed: 08/01/2023] Open
Abstract
Background Evaluating and controlling confounders are necessary when investigating molecular pathogenesis using human postmortem brain tissue. Particularly, tissue pH and RNA integrity number (RIN) are valuable indicators for controlling confounders. However, the influences of these indicators on the expression of each gene in postmortem brain have not been fully investigated. Therefore, we aimed to assess these effects on gene expressions of human brain samples. Methods We isolated total RNA from occipital lobes of 13 patients with schizophrenia and measured the RIN and tissue pH. Gene expression was analyzed and gene sets affected by tissue pH and RIN were identified. Moreover, we examined the functions of these genes by enrichment analysis and upstream regulator analysis. Results We identified 2,043 genes (24.7%) whose expressions were highly correlated with pH; 3,004 genes (36.3%) whose expressions were highly correlated with RIN; and 1,293 genes (15.6%) whose expressions were highly correlated with both pH and RIN. Genes commonly affected by tissue pH and RIN were highly associated with energy production and the immune system. In addition, genes uniquely affected by tissue pH were highly associated with the cell cycle, whereas those uniquely affected by RIN were highly associated with RNA processing. Conclusion The current study elucidated the influence of pH and RIN on gene expression profiling and identified gene sets whose expressions were affected by tissue pH or RIN. These findings would be helpful in the control of confounders for future postmortem brain studies.
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Affiliation(s)
- Kazusa Miyahara
- Department of Disaster Psychiatry, International Research Institute of Disaster Science, Tohoku University, Sendai, Japan
| | - Mizuki Hino
- Department of Disaster Psychiatry, International Research Institute of Disaster Science, Tohoku University, Sendai, Japan
- Department of Neuropsychiatry, School of Medicine, Fukushima Medical University, Fukushima, Japan
| | - Zhiqian Yu
- Department of Psychiatry, Graduate School of Medicine, Tohoku University, Sendai, Miyagi, Japan
| | - Chiaki Ono
- Department of Psychiatry, Graduate School of Medicine, Tohoku University, Sendai, Miyagi, Japan
| | - Atsuko Nagaoka
- Department of Neuropsychiatry, School of Medicine, Fukushima Medical University, Fukushima, Japan
| | - Masataka Hatano
- Department of Neuropsychiatry, School of Medicine, Fukushima Medical University, Fukushima, Japan
| | - Risa Shishido
- Department of Neuropsychiatry, School of Medicine, Fukushima Medical University, Fukushima, Japan
| | - Hirooki Yabe
- Department of Neuropsychiatry, School of Medicine, Fukushima Medical University, Fukushima, Japan
| | - Hiroaki Tomita
- Department of Psychiatry, Graduate School of Medicine, Tohoku University, Sendai, Miyagi, Japan
- Department of Psychiatry, Tohoku University Hospital, Sendai, Miyagi, Japan
| | - Yasuto Kunii
- Department of Disaster Psychiatry, International Research Institute of Disaster Science, Tohoku University, Sendai, Japan
- Department of Neuropsychiatry, School of Medicine, Fukushima Medical University, Fukushima, Japan
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Acharayothin O, Thiengtrong B, Juengwiwattanakitti P, Anekwiang P, Riansuwan W, Chinswangwatanakul V, Tanjak P. Impact of Washing Processes on RNA Quantity and Quality in Patient-Derived Colorectal Cancer Tissues. Biopreserv Biobank 2023; 21:31-37. [PMID: 35230139 DOI: 10.1089/bio.2021.0134] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Background: Colorectal cancer (CRC) is a common and lethal cancer worldwide. Extraction of high-quality RNA from CRC samples plays a key role in scientific research and translational medicine. Specimen collection and washing methods that do not compromise RNA quality or quantity are needed to ensure high quality specimens for gene expression analysis and other RNA-based downstream applications. We investigated the effect of tissue specimen collection and different preparation processes on the quality and quantity of RNA extracted from surgical CRC tissues. Materials and Methods: After surgical resection, tissues were harvested and prepared with various washing processes in a room adjacent to the operating room. One hundred fourteen tissues from 36 CRC patients were separately washed in either cold phosphate-buffered saline reagent (n = 34) or Dulbecco's modified Eagle's medium (DMEM; n = 34) for 2-3 minutes until the stool was removed, and unwashed specimens served as controls (n = 34). Six tissue specimens were washed and immersed in DMEM for up to 1 hour at 4°C. Before RNA extraction, all specimens were kept in the stabilizing reagent for 3 months at -80°C. RNA was extracted, and the concentration per milligram of tissue was measured. RNA quality was assessed using the RNA integrity number (RIN) value. Results: Different washing processes did not result in significant differences in RNA quantity or RIN values. In the six tissues that were washed and immersed in DMEM for 1 hour, RIN values significantly decreased. The quality of the extracted RNA from most specimens was excellent with the average RIN greater than 7. Conclusions: RNA is stable in specimens washed in different processes for short periods, but RIN values may decrease with prolonged wash times.
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Affiliation(s)
- Onchira Acharayothin
- Department of Surgery, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Benjarat Thiengtrong
- Department of Surgery, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand.,Siriraj Cancer Center, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Panudeth Juengwiwattanakitti
- Department of Surgery, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand.,Siriraj Cancer Center, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Panatna Anekwiang
- Department of Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Woramin Riansuwan
- Department of Surgery, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Vitoon Chinswangwatanakul
- Department of Surgery, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand.,Siriraj Cancer Center, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Pariyada Tanjak
- Department of Surgery, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand.,Siriraj Cancer Center, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
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Lu W, Zhou Q, Chen Y. Impact of RNA degradation on next-generation sequencing transcriptome data. Genomics 2022; 114:110429. [PMID: 35810931 DOI: 10.1016/j.ygeno.2022.110429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 06/16/2022] [Accepted: 07/06/2022] [Indexed: 11/04/2022]
Abstract
RNA sequencing is an innovative technology to study transcriptomes in both biological and clinical research. However, clinical specimens from patients undergoing surgical operations have a major challenge due to sample degradation. This study replicated the process of RNA degradation by maintaining cells at room temperature to achieve none, slight, middle, and high levels of RNA degradation with decreasing RNA integrity numbers (RIN) of approximately 9.8, 6.7, 4.4, and 2.5, respectively. Next, the differential expression of mRNA and long non-coding RNA (lncRNA) was analyzed in the four degradation groups along with pathway enrichment analysis. The results showed that the similarity of lncRNAs exhibited significant differences even for a slight level of RNA degradation compared with the non-degraded RNA sample. Also, the RNA degradation process was found to be universal, global, and random; the differentially expressed genes increased with an increase in degradation but the pathway enrichment phenomenon was not significantly observed.
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Affiliation(s)
- Wenxiang Lu
- State Key Lab of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, Jiangsu 210096, China
| | - Qin Zhou
- Department of Obstetrics and Gynecology, Kunshan Hospital of Traditional Chinese Medicine, Kunshan 215300, China
| | - Yi Chen
- Department of Obstetrics and Gynecology, Kunshan Hospital of Traditional Chinese Medicine, Kunshan 215300, China.
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7
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Wani UM, Wani ZA, Koul AM, Amin A, Shah BA, Farooq F, Qadri RA. Isolation of high-quality RNA for high throughput applications from secondary metabolite-rich Crocus sativus L. BMC Res Notes 2022; 15:214. [PMID: 35725612 PMCID: PMC9208216 DOI: 10.1186/s13104-022-06095-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 06/07/2022] [Indexed: 11/30/2022] Open
Abstract
Objective Isolating high-quality RNA is a basic requirement while performing high throughput sequencing, microarray, and various other molecular investigations. However, it has been quite challenging to isolate RNA with absolute purity from plants like Crocus sativus that are rich in secondary metabolites, polysaccharides, and other interfering compounds which often irreversibly co-precipitate with the RNA. While many methods have been proposed for RNA extraction including CTAB, TriZol, and SDS-based methods, which invariably yield less and poor quality RNA and hence it necessitated the isolation of high-quality RNA suitable for high throughput applications. Results In the present study we made certain adjustments to the available protocols including modifications in the extraction buffer itself and the procedure employed. Our method led to the isolation of clear and non-dispersive total RNA with an RNA Integrity Number (RIN) value greater than 7.5. The quality of the RNA was further assessed by qPCR-based amplification of mRNA and mature miRNAs such as Cs-MIR166c and Cs-MIR396a. Supplementary Information The online version contains supplementary material available at 10.1186/s13104-022-06095-z.
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Affiliation(s)
- Umer Majeed Wani
- Immunobiology Lab, Department of Biotechnology, University of Kashmir, Srinagar, 190 006, Jammu and Kashmir, India
| | - Zubair Ahmad Wani
- Immunobiology Lab, Department of Biotechnology, University of Kashmir, Srinagar, 190 006, Jammu and Kashmir, India
| | - Aabid M Koul
- Immunobiology Lab, Department of Biotechnology, University of Kashmir, Srinagar, 190 006, Jammu and Kashmir, India
| | - Asif Amin
- Immunobiology Lab, Department of Biotechnology, University of Kashmir, Srinagar, 190 006, Jammu and Kashmir, India
| | - Basit Amin Shah
- Immunobiology Lab, Department of Biotechnology, University of Kashmir, Srinagar, 190 006, Jammu and Kashmir, India
| | - Faizah Farooq
- Immunobiology Lab, Department of Biotechnology, University of Kashmir, Srinagar, 190 006, Jammu and Kashmir, India
| | - Raies A Qadri
- Immunobiology Lab, Department of Biotechnology, University of Kashmir, Srinagar, 190 006, Jammu and Kashmir, India.
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Pedersen KB, Williams A, Watt J, Ronis MJ. Improved method for isolating high-quality RNA from mouse bone with RNA later at room temperature. Bone Rep 2019; 11:100211. [PMID: 31198821 PMCID: PMC6558217 DOI: 10.1016/j.bonr.2019.100211] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 04/24/2019] [Accepted: 05/25/2019] [Indexed: 11/20/2022] Open
Abstract
Accurate gene expression analysis of bone requires the ability to isolate RNA of good quality. Isolation of intact RNA from frozen bone tissue is problematic since RNA rapidly becomes degraded after thawing. Since we are interested in assessing gene expression from both bone marrow and mineralized bone, we aimed to develop improved simple, robust and statistically validated methods providing high-quality RNA from both mouse femur shaft and femur marrow. RNA integrity was quantified by the RNA Integrity Number (RIN) measured on a TapeStation. While the RNA stabilization reagent RNAlater is not commonly used or recommended for mineralized bone, we found that preservation methods with RNAlater significantly improved the RNA quality with a mean RIN for the femur shaft of 8.0 and a mean RIN for femur marrow of 9.6. With RNAlater, high quality RNA with a mean RIN of 9.3 could also be isolated from lumbar vertebral bone. A further advantage of using RNAlater is that the tissue can be allowed to thaw to room temperature before TRI Reagent lysis without any loss of RNA integrity. A comparison of the TRI Reagent method with a hybrid method combining TRI Reagent lysis with RNeasy column purification showed no difference in RNA integrity. However, the hybrid method seemed to give femur shaft RNA with fewer impurities inhibiting qRT-PCR.
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Affiliation(s)
- Kim B. Pedersen
- Department of Pharmacology & Experimental Therapeutics, Louisiana State University Health Sciences Center (LSUHSC), New Orleans, LA, United States of America
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Nakatsuji N, Adachi K, Morioka K. Long-term stability of RNA isolated from muscle of red seabream (Pagrus major) during ice storage. Fish Physiol Biochem 2019; 45:819-828. [PMID: 30456581 DOI: 10.1007/s10695-018-0588-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 11/08/2018] [Indexed: 06/09/2023]
Abstract
Recovering high-quality intact RNA from postmortem tissue is of major concern for gene expression studies. However, it is difficult to perform RNA extraction from aquacultured fish immediately after death, as rapid and accurate skills are needed for the procedure. The objective of this study was to quantitatively assess the integrity of total RNA extracted from muscle, liver, and digestive tract tissues of red seabream stored in ice as whole bodies, at a range of time points up to 10 days postmortem, using RNA integrity number (RIN) and quantitative PCR (qPCR). The RIN of total RNA in muscle remained over 8.0 for 5 days postmortem. The RINs in the liver and digestive tract were under 5.0 at 2 days postmortem. The mRNA levels of tissue inhibitor metalloproteinase 2 (TIMP-2) and β-actin, measured using qPCR in muscle, decreased to 87.8% at 1 day postmortem and to 45.5% at 2 days postmortem, from that at 0 days postmortem. In the liver and digestive tract, the mRNA levels were not significantly changed until 1 day postmortem. These results indicate that RNA, especially from fish muscle, can be maintained at high quality for several days postmortem solely by storing the fish body in ice.
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Affiliation(s)
- Nobuyoshi Nakatsuji
- Faculty of Agriculture and Marine Science, Kochi University, Nankoku, Kochi, 783-8502, Japan
- The United Graduate School of Agricultural Sciences, Ehime University, Matsuyama, Ehime, 790-8566, Japan
| | - Kohsuke Adachi
- Faculty of Agriculture and Marine Science, Kochi University, Nankoku, Kochi, 783-8502, Japan
| | - Katsuji Morioka
- Faculty of Agriculture and Marine Science, Kochi University, Nankoku, Kochi, 783-8502, Japan.
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Acosta-Maspons A, González-Lemes I, Covarrubias AA. Improved protocol for isolation of high-quality total RNA from different organs of Phaseolus vulgaris L. Biotechniques 2019; 66:96-98. [PMID: 30744411 DOI: 10.2144/btn-2018-0129] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
A modified protocol was developed to obtain high-quality total RNA from various mature organs, including leaves, seeds, pods and testae, from different cultivars of Phaseolus vulgaris L. grown under optimal conditions or subjected to severe drought; stress conditions leading to the accumulation of numerous secondary metabolites can affect RNA quality. This modified procedure is based on CTAB extraction protocols. Modifications in this protocol prevent oxidation of phenolic complexes, the precipitation of proteins, DNA and degradation of RNA; also, it is effective at removing secondary metabolites. The RNA obtained following this procedure showed high quality as revealed by a high RNA integrity number and high 260/280 nm (>2) ratio, the requirements needed to increase reliability of diverse molecular analyses.
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Affiliation(s)
- Alexis Acosta-Maspons
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México (UNAM), Av. Universidad 2001, Cuernavaca, 62210 México
| | - Ingrid González-Lemes
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México (UNAM), Av. Universidad 2001, Cuernavaca, 62210 México
| | - Alejandra A Covarrubias
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México (UNAM), Av. Universidad 2001, Cuernavaca, 62210 México
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Carlsson J, Davidsson S, Fridfeldt J, Giunchi F, Fiano V, Grasso C, Zelic R, Richiardi L, Andrén O, Pettersson A, Fiorentino M, Akre O. Quantity and quality of nucleic acids extracted from archival formalin fixed paraffin embedded prostate biopsies. BMC Med Res Methodol 2018; 18:161. [PMID: 30518332 PMCID: PMC6280346 DOI: 10.1186/s12874-018-0628-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 11/26/2018] [Indexed: 01/10/2023] Open
Abstract
Background In Sweden, human tissue samples obtained from diagnostic and surgical procedures have for decades been routinely stored in a formalin-fixed, paraffin-embedded, form. Through linkage with nationwide registers, these samples are available for molecular studies to identify biomarkers predicting mortality even in slow-progressing prostate cancer. However, tissue fixation causes modifications of nucleic acids, making it challenging to extract high-quality nucleic acids from formalin fixated tissues. Methods In this study, the efficiency of five commercial nucleic acid extraction kits was compared on 30 prostate biopsies with normal histology, and the quantity and quality of the products were compared using spectrophotometry and Agilent’s BioAnalyzer. Student’s t-test’s and Bland-Altman analyses were performed in order to investigate differences in nucleic acid quantity and quality between the five kits. The best performing extraction kits were subsequently tested on an additional 84 prostate tumor tissues. A Spearman’s correlation test and linear regression analyses were performed in order to investigate the impact of tissue age and amount of tissue on nucleic acid quantity and quality. Results Nucleic acids extracted with RNeasy® FFPE and QIAamp® DNA FFPE Tissue kit had the highest quantity and quality, and was used for extraction from 84 tumor tissues. Nucleic acids were successfully extracted from all biopsies, and the amount of tumor (in millimeter) was found to have the strongest association with quantity and quality of nucleic acids. Conclusions To conclude, this study shows that the choice of nucleic acid extraction kit affects the quantity and quality of extracted products. Furthermore, we show that extraction of nucleic acids from archival formalin-fixed prostate biopsies is possible, allowing molecular studies to be performed on this valuable sample collection.
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Affiliation(s)
- Jessica Carlsson
- Department of Urology, Faculty of Medicine and Health, University Hospital in Örebro, Örebro University, Södra Grevrosengatan, 70185, Örebro, Sweden.
| | - Sabina Davidsson
- Department of Urology, Faculty of Medicine and Health, University Hospital in Örebro, Örebro University, Södra Grevrosengatan, 70185, Örebro, Sweden
| | - Jonna Fridfeldt
- Department of Urology, Faculty of Medicine and Health, University Hospital in Örebro, Örebro University, Södra Grevrosengatan, 70185, Örebro, Sweden
| | - Francesca Giunchi
- Department of Pathology, F. Addari Institute of Oncology S. Orsola Hospital, Bologna, Italy
| | - Valentina Fiano
- Cancer Epidemiology Unit-CERMS, Department of Medical Sciences, University of Turin and CPO-Piemonte, Turin, Italy
| | - Chiara Grasso
- Cancer Epidemiology Unit-CERMS, Department of Medical Sciences, University of Turin and CPO-Piemonte, Turin, Italy
| | - Renata Zelic
- Clinical Epidemiology Unit, Department of Medicine Solna, Karolinska Institute, Stockholm, Sweden
| | - Lorenzo Richiardi
- Cancer Epidemiology Unit-CERMS, Department of Medical Sciences, University of Turin and CPO-Piemonte, Turin, Italy
| | - Ove Andrén
- Department of Urology, Faculty of Medicine and Health, University Hospital in Örebro, Örebro University, Södra Grevrosengatan, 70185, Örebro, Sweden
| | - Andreas Pettersson
- Clinical Epidemiology Unit, Department of Medicine Solna, Karolinska Institute, Stockholm, Sweden
| | | | - Olof Akre
- Department of Medicine Solna, Karolinska Institute, and Department of Urology, Karolinska University Hospital, Stockholm, Sweden
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Jikuzono T, Horikawa A, Ishikawa T, Hirokawa M, Sugitani I, Inui T, Ishibashi O. Proteinase K treatment improves RNA recovery from thyroid cells fixed with liquid-based cytology solution. BMC Res Notes 2018; 11:822. [PMID: 30454013 PMCID: PMC6245812 DOI: 10.1186/s13104-018-3914-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 11/09/2018] [Indexed: 01/06/2023] Open
Abstract
OBJECTIVE Fine-needle aspiration biopsy (FNAB), an important diagnostic tool given its simplicity, safety, and cost-effectiveness, is fast becoming a popular procedure in the diagnosis of thyroid diseases. Generally, cells isolated from biopsies are transferred directly to microscope slides to prepare smears for cytopathological examination; however, the technical difficulties of this procedure often cause poor reproducibility, which limits the accuracy of diagnostic results. Liquid-based cytology (LBC), in which isolated cells are collected in a fixative solution, is advantageous in that it facilitates the preparation of homogenous cytological specimens. However, LBC has not been applied to molecular diagnoses, such as RNA expression-based diagnosis, mainly because of difficulties in cell recovery and RNA isolation. This study was aimed to improve RNA extraction from papillary cancer-derived K1 cells and thyroid FNAB specimens suspended in LBC solutions. RESULTS K1 cells suspended in CytoRich-Red and CytoRich-Blue, fixatives for LBC, were efficiently recovered by trapping to glass-fiber filters. Importantly, subsequent Proteinase K treatment was essential for efficient RNA extraction from the fixed cells. This finding was also applicable to RNA extraction from CytoRich-Red-fixed thyroid FNAB specimens processed in the same way. Consistently, U6 small nuclear RNA was detected in these RNA samples by reverse transcription-polymerase chain reaction.
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Affiliation(s)
- Tomoo Jikuzono
- Laboratory of Biological Macromolecules, Department of Applied Life Sciences, Graduate School of Life & Environmental Sciences, Osaka Prefecture University, 1-1 Gakuen-cho, Sakai, 599-8531, Japan.,Department of Endocrine Surgery, Kanaji Thyroid Hospital, 1-5-6 Nakazato, Kita-ku, Tokyo, 114-0015, Japan.,Department of Endocrine Surgery, Nippon Medical School, 1-1-5 Sendagi, Bunkyo-ku, Tokyo, 113-8602, Japan
| | - Aya Horikawa
- Laboratory of Biological Macromolecules, Department of Applied Life Sciences, Graduate School of Life & Environmental Sciences, Osaka Prefecture University, 1-1 Gakuen-cho, Sakai, 599-8531, Japan
| | - Tomoko Ishikawa
- Institute for Human Life Innovation, Ochanomizu University, 2-1-1 Otsuka, Bunkyo-ku, Tokyo, 112-8610, Japan
| | - Mitsuyoshi Hirokawa
- Department of Diagnostic Pathology and Cytology, Kuma Hospital, 8-2-35 Shimoyamate-dori, Chuo-ku, Kobe, 650-0011, Japan
| | - Iwao Sugitani
- Department of Endocrine Surgery, Nippon Medical School, 1-1-5 Sendagi, Bunkyo-ku, Tokyo, 113-8602, Japan
| | - Takashi Inui
- Laboratory of Biological Macromolecules, Department of Applied Life Sciences, Graduate School of Life & Environmental Sciences, Osaka Prefecture University, 1-1 Gakuen-cho, Sakai, 599-8531, Japan
| | - Osamu Ishibashi
- Laboratory of Biological Macromolecules, Department of Applied Life Sciences, Graduate School of Life & Environmental Sciences, Osaka Prefecture University, 1-1 Gakuen-cho, Sakai, 599-8531, Japan. .,Department of Endocrine Surgery, Nippon Medical School, 1-1-5 Sendagi, Bunkyo-ku, Tokyo, 113-8602, Japan.
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Abstract
Leukocytes function as central effectors in innate immunity (such as phagocytosis) as well as adaptive immunity (e.g., antigen-dependent T cell activation), and serve as an important resource in the fields of translational medicine, precision medicine, and cell therapy. Isolation of leukocytes from whole blood is necessary for high-quality RNA and downstream research. This process is susceptible to the variability of many factors, such as blood collection, isolation reagents, and extraction methods. In this study, three methods were applied for leukocytes separation, followed by RNA extraction and quality testing to evaluate the methods. Results showed that leukocytes were purified using lymphocyte separation medium (LSM), optimized LSM method, or red blood cell lysis buffer (RBC lysis), and RNA quality met the basic requirements for downstream studies. Although considering the simplicity of the procedure and RNA quality from donated samples, the RBC lysis method should be recommended to biobanks for further research.
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Affiliation(s)
- Zhang Heng
- Shanghai Clinical Research Center, Shanghai, China.,Shanghai Engineering Research Center of Biobank, Shanghai, China
| | - Liangliang Ruan
- Shanghai Clinical Research Center, Shanghai, China.,Shanghai Engineering Research Center of Biobank, Shanghai, China
| | - Rongxing Gan
- Shanghai Clinical Research Center, Shanghai, China.,Shanghai Engineering Research Center of Biobank, Shanghai, China
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14
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Abstract
Objective With the goal of identifying fast, reliable, and broadly applicable RNA isolation methods in European pear fruit for downstream transcriptome analysis, we evaluated several commercially available kit-based RNA isolation methods, plus our modified version of a published cetyl trimethyl ammonium bromide (CTAB)-based method. Results We confirmed previous work indicating chaotropic agent-based kits produced sufficient, high-quality RNA in freshly harvested, mature ‘Bartlett’ fruit. However, RNA isolation from ‘d’Anjou’ pear peel and especially cortical tissues of fruit stored for 11 months proved challenging to all but our modified CTAB-based method. Generally, more RNA was recovered from peel tissues than cortical tissues. Less toxic dithiothreitol was confirmed to be an acceptable reducing agent as its substitution for 2-mercaptoethanol often yielded high quality RNA. Finally, we present evidence that erroneous signals in the 5S region of Bioanalyzer RNA size plot histograms, that interfered with RNA integrity number calculation, were small RNA fragments that are reduced by simple cleanup procedures, not artifacts as previously reported. Electronic supplementary material The online version of this article (doi:10.1186/s13104-017-2564-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Loren Honaas
- US Department of Agriculture, Agricultural Research Service, Physiology and Pathology of Tree Fruits Research Unit, Wenatchee, WA, 98801, USA.
| | - Elena Kahn
- US Department of Agriculture, Agricultural Research Service, Physiology and Pathology of Tree Fruits Research Unit, Wenatchee, WA, 98801, USA
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15
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Lalmahomed ZS, Coebergh van den Braak RRJ, Oomen MHA, Arshad SP, Riegman PHJ, IJzermans JNM; MATCH study working group. Multicenter fresh frozen tissue sampling in colorectal cancer: does the quality meet the standards for state of the art biomarker research? Cell Tissue Bank 2017; 18:425-31. [PMID: 28258397 DOI: 10.1007/s10561-017-9613-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Accepted: 02/23/2017] [Indexed: 02/07/2023]
Abstract
The growing interest in the molecular subclassification of colorectal cancers is increasingly facilitated by large multicenter biobanking initiatives. The quality of tissue sampling is pivotal for successful translational research. This study shows the quality of fresh frozen tissue sampling within a multicenter cohort study for colorectal cancer (CRC) patients. Each of the seven participating hospitals randomly contributed ten tissue samples, which were collected following Standard Operating Procedures (SOP) using established techniques. To indicate if the amount of intact RNA is sufficient for molecular discovery research and prove SOP compliance, the RNA integrity number (RIN) was determined. Samples with a RIN < 6 were measured a second time and when consistently low a third time. The highest RIN was used for further analysis. 91% of the tissue samples had a RIN ≥ 6 (91%). The remaining six samples had a RIN between 5 and 6 (4.5%) or lower than 5 (4.5%). The median overall RIN was 7.3 (range 2.9-9.0). The median RIN of samples in the university hospital homing the biobank was 7.7 and the median RIN for the teaching hospitals was 7.3, ranging from 6.5 to 7.8. No differences were found in the outcome of different hospitals (p = 0.39). This study shows that the collection of high quality fresh frozen samples of colorectal cancers is feasible in a multicenter design with complete SOP adherence. Thus, using basic sampling techniques large patient cohorts can be organized for predictive and prognostic (bio)marker research for CRC.
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16
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Appleby-Mallinder C, Wyles MD, Simpson JE, Wharton SB, Ince PG, Heath PR. Expression microdissection isolation of enriched cell populations from archival brain tissue. J Neurosci Methods 2016; 268:125-30. [PMID: 27178137 DOI: 10.1016/j.jneumeth.2016.05.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Revised: 04/26/2016] [Accepted: 05/04/2016] [Indexed: 12/14/2022]
Abstract
BACKGROUND Laser capture microdissection (LCM) is an established technique for the procurement of enriched cell populations that can undergo further downstream analysis, although it does have limitations. Expression microdissection (xMD) is a new technique that begins to address these pitfalls, such as operator dependence and contamination. NEW METHOD xMD utilises immunohistochemistry in conjunction with a chromogen to isolate specific cell types by extending the fundamental principles of LCM to create an operator-independent method for the procurement of specific CNS cell types. RESULTS We report how xMD enables the isolation of specific cell populations, namely neurones and astrocytes, from rat formalin fixed-paraffin embedded (FFPE) tissue. Subsequent reverse transcriptase-polymerase chain reaction (RT-PCR) analysis confirms the enrichment of these specific populations. RIN values after xMD indicate samples are sufficient to carry out further analysis. COMPARISON WITH EXISTING METHOD xMD offers a rapid method of isolating specific CNS cell types without the need for identification by an operator, reducing the amount of unintentional contamination caused by operator error, whilst also significantly reducing the time required by the current basic LCM technique. CONCLUSIONS xMD is a superior method for the procurement of enriched cell populations from post-mortem tissue, which can be utilised to create transcriptome profiles, aiding our understanding of the contribution of these cells to a range of neurological diseases. xMD also addresses the issues associated with LCM, such as reliance on an operator to identify target cells, which can cause contamination, as well as addressing the time consuming nature of LCM.
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Affiliation(s)
- C Appleby-Mallinder
- Sheffield Institute for Translational Neuroscience, University of Sheffield, UK
| | - M D Wyles
- Sheffield Institute for Translational Neuroscience, University of Sheffield, UK
| | - J E Simpson
- Sheffield Institute for Translational Neuroscience, University of Sheffield, UK
| | - S B Wharton
- Sheffield Institute for Translational Neuroscience, University of Sheffield, UK
| | - P G Ince
- Sheffield Institute for Translational Neuroscience, University of Sheffield, UK
| | - P R Heath
- Sheffield Institute for Translational Neuroscience, University of Sheffield, UK.
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17
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Augereau C, Lemaigre FP, Jacquemin P. Extraction of high-quality RNA from pancreatic tissues for gene expression studies. Anal Biochem 2016; 500:60-2. [PMID: 26896683 DOI: 10.1016/j.ab.2016.02.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Revised: 02/03/2016] [Accepted: 02/08/2016] [Indexed: 11/24/2022]
Abstract
Extracting RNA from pancreatic tissue is notoriously challenging because of the organ's high RNase content. Standard methods using TriPure or TRIzol classically yield RNA of sufficient quality for routine gene expression analysis but not for microarray or deep sequencing analysis. Here we developed a simple method to extract high-quality RNA from mouse pancreas. Our method uses an RNase inhibitor and combines different protocols using guanidium thiocyanate-phenol extraction. It enables reproducible isolation of RNA with an RNA integrity number around 9.
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18
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Peters MC, Mekonnen ZK, Yuan S, Bhakta NR, Woodruff PG, Fahy JV. Measures of gene expression in sputum cells can identify TH2-high and TH2-low subtypes of asthma. J Allergy Clin Immunol 2013; 133:388-94. [PMID: 24075231 DOI: 10.1016/j.jaci.2013.07.036] [Citation(s) in RCA: 210] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2013] [Revised: 07/15/2013] [Accepted: 07/30/2013] [Indexed: 01/22/2023]
Abstract
BACKGROUND The 3-gene signature of periostin, chloride channel accessory 1 (CLCA1), and Serpin β2 (SERPINB2) in airway epithelial brushings is used to classify asthma into TH2-high and TH2-low endotypes. Little is known about the utility of gene profiling in sputum as a molecular phenotyping method. OBJECTIVE We sought to determine whether gene profiling in sputum cells can identify T(H)2-high and T(H)2-low subtypes of asthma. METHODS In induced sputum cell pellets from 37 asthmatic patients and 15 healthy control subjects, PCR was used to profile gene expression of the epithelial cell signature of IL-13 activation (periostin, CLCA1, and SERPINB2), TH2 genes (IL4, IL5, and IL13), and other genes associated with airway TH2 inflammation. RESULTS Gene expression levels of CLCA1 and periostin, but not SerpinB2, were significantly higher than normal in sputum cells from asthmatic subjects. Expression levels of IL-4, IL-5, and IL-13 were also significantly increased in asthmatic patients and highly correlated within individual subjects. By combining the expression levels of IL-4, IL-5, and IL-13 in a single quantitative metric ("T(H)2 gene mean"), 26 (70%) of the 37 asthmatic patients had T(H)2-high asthma, which was characterized by more severe measures of asthma and increased blood and sputum eosinophilia. TH2 gene mean values tended to be stable when initial values were very high or very low but fluctuated above or below the T(H)2-high cutoff when initial values were intermediate. CONCLUSION IL-4, IL-5, and IL-13 transcripts are easily detected in sputum cells from asthmatic patients, and their expression levels can be used to classify asthma into T(H)2-high and T(H)2-low endotypes.
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Affiliation(s)
- Michael C Peters
- Division of Pulmonary and Critical Care Medicine, University of California, San Francisco, Calif; Cardiovascular Research Institute, University of California, San Francisco, Calif
| | - Zesemayat K Mekonnen
- Cardiovascular Research Institute, University of California, San Francisco, Calif
| | - Shaopeng Yuan
- Cardiovascular Research Institute, University of California, San Francisco, Calif
| | - Nirav R Bhakta
- Division of Pulmonary and Critical Care Medicine, University of California, San Francisco, Calif; Cardiovascular Research Institute, University of California, San Francisco, Calif
| | - Prescott G Woodruff
- Division of Pulmonary and Critical Care Medicine, University of California, San Francisco, Calif; Cardiovascular Research Institute, University of California, San Francisco, Calif
| | - John V Fahy
- Division of Pulmonary and Critical Care Medicine, University of California, San Francisco, Calif; Cardiovascular Research Institute, University of California, San Francisco, Calif.
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19
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Vegh P, Foroushani ABK, Magee DA, McCabe MS, Browne JA, Nalpas NC, Conlon KM, Gordon SV, Bradley DG, MacHugh DE, Lynn DJ. Profiling microRNA expression in bovine alveolar macrophages using RNA-seq. Vet Immunol Immunopathol 2013; 155:238-44. [PMID: 24021155 DOI: 10.1016/j.vetimm.2013.08.004] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2013] [Revised: 08/06/2013] [Accepted: 08/13/2013] [Indexed: 11/17/2022]
Abstract
MicroRNAs (miRNAs) are important regulators of gene expression and are known to play a key role in regulating both adaptive and innate immunity. Bovine alveolar macrophages (BAMs) help maintain lung homeostasis and constitute the front line of host defense against several infectious respiratory diseases, such as bovine tuberculosis. Little is known, however, about the role miRNAs play in these cells. In this study, we used a high-throughput sequencing approach, RNA-seq, to determine the expression levels of known and novel miRNAs in unchallenged BAMs isolated from lung lavages of eight different healthy Holstein-Friesian male calves. Approximately 80 million sequence reads were generated from eight BAM miRNA Illumina sequencing libraries, and 80 miRNAs were identified as being expressed in BAMs at a threshold of at least 100 reads per million (RPM). The expression levels of miRNAs varied over a large dynamic range, with a few miRNAs expressed at very high levels (up to 800,000RPM), and the majority lowly expressed. Notably, many of the most highly expressed miRNAs in BAMs have known roles in regulating immunity in other species (e.g. bta-let-7i, bta-miR-21, bta-miR-27, bta-miR-99b, bta-miR-146, bta-miR-147, bta-miR-155 and bta-miR-223). The most highly expressed miRNA in BAMs was miR-21, which has been shown to regulate the expression of antimicrobial peptides in Mycobacterium leprae-infected human monocytes. Furthermore, the predicted target genes of BAM-expressed miRNAs were found to be statistically enriched for roles in innate immunity. In addition to profiling the expression of known miRNAs, the RNA-seq data was also analysed to identify potentially novel bovine miRNAs. One putatively novel bovine miRNA was identified. To the best of our knowledge, this is the first RNA-seq study to profile miRNA expression in BAMs and provides an important reference dataset for investigating the regulatory roles miRNAs play in this important immune cell type.
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Affiliation(s)
- Peter Vegh
- Animal & Bioscience Research Department, Animal & Grassland Research and Innovation Centre, Teagasc, Grange, Dunsany, Co. Meath, Ireland; Smurfit Institute of Genetics, Trinity College, Dublin 2, Ireland
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20
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Karagianni AE, Kapetanovic R, McGorum BC, Hume DA, Pirie SR. The equine alveolar macrophage: functional and phenotypic comparisons with peritoneal macrophages. Vet Immunol Immunopathol 2013; 155:219-28. [PMID: 23978307 PMCID: PMC3795452 DOI: 10.1016/j.vetimm.2013.07.003] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2013] [Revised: 07/01/2013] [Accepted: 07/06/2013] [Indexed: 02/02/2023]
Abstract
Alveolar macrophages (AMs) constitute the first line of defence in the lung of all species, playing a crucial role in the regulation of immune responses to inhaled pathogens. A detailed understanding of the function and phenotype of AMs is a necessary pre-requisite to both elucidating their role in preventing opportunistic bacterial colonisation of the lower respiratory tract and developing appropriate preventative strategies. The purpose of the study was to characterise this important innate immune cell at the tissue level by making functional and phenotypic comparisons with peritoneal macrophages (PMs). We hypothesised that the tissue of origin determines a unique phenotype of AMs, which may constitute an appropriate therapeutic target for certain equine respiratory diseases. Macrophages isolated from the lung and the peritoneal cavity of 9 horses were stimulated with various toll like receptor (TLR) ligands and the production of nitrite, tumour necrosis factor alpha (TNFα), interleukin (IL) 10 and indoleamine 2,3-dioxygenase (IDO) were measured by the Griess reaction and enzyme linked immunosorbent assay (ELISA) and/or quantitative polymerase chain reaction, respectively. Cells were also compared on the basis of phagocytic-capacity and the expression of several cell surface markers. AMs, but not PMs, demonstrated increased TNFα release following stimulation with LPS, polyinosinic polycytidylic acid (Poly IC) and heat-killed Salmonella typhinurium and increased TNFα and IDO mRNA expression when stimulated with LPS. AMs showed high expression of the specific macrophage markers cluster of differentiation (CD) 14, CD163 and TLR4, whereas PMs showed high expression of TLR4 only. AMs, but not PMs, demonstrated efficient phagocytic activity. Our results demonstrate that AMs are more active than PMs when stimulated with various pro-inflammatory ligands, thus supporting the importance of the local microenvironment in the activation status of the macrophage. This information provides a valuable knowledge base on which to improve our understanding of the role of macrophages and their microenvironment in equine innate immunity.
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Affiliation(s)
- Anna E Karagianni
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian EH25 9PS, UK.
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Saito K, Negishi M, James Squires E. Sexual dimorphisms in zonal gene expression in mouse liver. Biochem Biophys Res Commun 2013; 436:730-5. [PMID: 23791742 DOI: 10.1016/j.bbrc.2013.06.025] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2013] [Accepted: 06/08/2013] [Indexed: 02/08/2023]
Abstract
Many of the metabolic functions of the liver are localized either in the pericentral region (zone 3) or in the periportal region (zone 1). However, a systematic analysis of the heterogeneity and sexual dimorphism of gene expression in the liver is lacking. Our objective was to obtain sections of intact tissue from zone 1 and zone 3 from both male and female mouse liver, and to measure the patterns of gene expression in these sections. Zone 1 and zone 3 areas were isolated by laser capture microdissection of liver sections, total RNA was isolated and microarray analysis was conducted using Agilent Whole Mouse Genome oligo arrays. To investigate functional characteristics as well as upstream regulators of specific gene lists, we used Ingenuity Pathway Analysis. We identified more than 925 genes in zone 1 and more than 450 genes in zone 3 of both male and female mice. Sexual dimorphism in metabolic functions was present in zone 1 but not zone 3. In zone 1, canonical pathways related to gluconeogenesis were male predominant, while canonical pathways related to hepatic progenitor cells were female predominant. In addition, we also analyzed the upstream regulators of zone-specific genes. SREBF1 was male-specific in zone 1, while TRIM24 was female-specific in zone 3. These results demonstrate the heterogeneity and sexually dimorphic differences in gene expression in the liver.
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Affiliation(s)
- Kosuke Saito
- Laboratory of Reproductive and Developmental Toxicology, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
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Jackson AF, Williams A, Moffat I, Phillips SL, Recio L, Waters MD, Lambert IB, Yauk CL. Preparation of archival formalin-fixed paraffin-embedded mouse liver samples for use with the Agilent gene expression microarray platform. J Pharmacol Toxicol Methods 2013; 68:260-268. [PMID: 23458726 DOI: 10.1016/j.vascn.2013.02.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2012] [Revised: 02/14/2013] [Accepted: 02/17/2013] [Indexed: 01/08/2023]
Abstract
INTRODUCTION Tissue samples are routinely formalin-fixed and paraffin-embedded (FFPE) for long term preservation. Gene expression analysis of archival FFPE tissues may advance knowledge of the molecular perturbations contributing to disease. However, formalin causes extensive degradation of RNA. METHODS We compared RNA quality/yield from FFPE samples using six commercial FFPE RNA extraction kits. In addition we compared four DNA microarray protocols for the Agilent 8×60K platform using 16year old FFPE mouse liver samples treated with phenobarbital or vehicle. RESULTS Despite low quality RNA, archival phenobarbital samples exhibited strong induction of the positive control genes Cyp2b9 and Cyp2b10 by quantitative real-time PCR (qPCR). We tested one- and two-color microarray designs and evaluated the effects of increasing the amount of hybridized cDNA. Canonical gene responders to phenobarbital were measurably induced under each experimental condition. Increasing the amount of labeled cDNA did not improve the overall signal intensity. One-color experiments yielded larger fold changes than two-color and the number of differentially expressed genes varied between protocols. Gene expression changes were validated by qPCR and literature searches. Individual protocols exhibited high rates of false positives; however, pathway analysis revealed that nine of the top ten canonical pathways were consistent across experiments. Genes that were differentially expressed in more than one experiment were more likely to be validated. Thus, we recommend that experiments on FFPE samples be done in duplicate to reduce false positives. DISCUSSION In this analysis of archival FFPE samples we were able to identify pathways that are consistent with phenobarbital's mechanism of action. Therefore, we conclude that FFPE samples can be used for meaningful microarray gene expression analyses.
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Affiliation(s)
- A Francina Jackson
- Mechanistic Studies Division, Environmental Health Science and Research Bureau, Health Canada, Ottawa K1A 0K9, Canada; Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, Ontario K1S 5B6, Canada
| | - Andrew Williams
- Mechanistic Studies Division, Environmental Health Science and Research Bureau, Health Canada, Ottawa K1A 0K9, Canada
| | - Ivy Moffat
- Mechanistic Studies Division, Environmental Health Science and Research Bureau, Health Canada, Ottawa K1A 0K9, Canada
| | | | - Leslie Recio
- ILS, Inc., P.O. Box 13501, Research Triangle Park, NC 27709, USA
| | - Michael D Waters
- ILS, Inc., P.O. Box 13501, Research Triangle Park, NC 27709, USA
| | - Iain B Lambert
- Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, Ontario K1S 5B6, Canada
| | - Carole L Yauk
- Mechanistic Studies Division, Environmental Health Science and Research Bureau, Health Canada, Ottawa K1A 0K9, Canada
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