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Zheng HY, Qin PH, Yang K, Liu TX, Zhang YJ, Chu D. Genome-Wide Identification and Analysis of the Heat-Shock Protein Gene Superfamily in Bemisia tabaci and Expression Pattern Analysis under Heat Shock. INSECTS 2022; 13:insects13070570. [PMID: 35886746 PMCID: PMC9319060 DOI: 10.3390/insects13070570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 06/20/2022] [Accepted: 06/21/2022] [Indexed: 02/04/2023]
Abstract
Simple Summary Bemisia tabaci MED is an invasive pest that had caused considerable economic damage in the past decades. Its successful colonization is closely related to heat-shock proteins (HSPs), which are related to heat resistance. In this study, 33 BtaHsps were identified based on the sequenced genome of B. tabaci MED belonging to six HSP families, among which 22 BtaHsps were newly identified. Analysis of the secondary structure and evolutionary relationship showed that they were all closely related. In addition, BtaHsp90A3 of the HSP90 family was screened by analyzing the expression level changes of these genes under 42 °C heat shock and RNAi was performed on the BtaHsp90A3. The results showed that the silencing of BtaHsp90A3 is closely related to the heat resistance of B. tabaci MED. Taken together, this study conducted an in-depth identification of BtaHsps that clarifies their evolutionary relationships and their response to thermal stress in B. tabaci MED. Abstract The thermal tolerance of Bemisia tabaci MED, an invasive whitefly species with worldwide distribution, plays an important role in its ecological adaptation during the invasion process. Heat-shock proteins (HSPs) are closely related to heat resistance. In this study, 33 Hsps (BtaHsps) were identified based on sequenced genome of B. tabaci MED belonging to six HSP families, among which 22 Hsps were newly identified. The secondary structures of a further 22 BtaHsps were also predicted. The results of RT-qPCR showed that heat shock could affect the expression of 14 of the 22 Hsps newly identified in this study. Among them, the expression level of six Hsps increased under 42 °C treatment. As the unstudied gene, BtaHsp90A3 had the highest increase rate. Therefore, BtaHsp90A3 was chosen for the RNAi test, and silencing BtaHsp90A3 by RNAi decreased the survival rate of adult B. tabaci at 42 °C. The results indicated that only a few Hsps were involved in the thermal tolerance of host whitefly although many Hsps would response under heat stress. This study conducted a more in-depth and comprehensive identification that demonstrates the evolutionary relationship of BtaHsps and illustrates the response of BtaHsps under the influence of thermal stress in B. tabaci MED.
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Affiliation(s)
- Hao-Yuan Zheng
- Shandong Engineering Research Center for Environment-Friendly Agricultural Pest Management, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao 266109, China; (H.-Y.Z.); (P.-H.Q.); (K.Y.); (T.-X.L.)
| | - Peng-Hao Qin
- Shandong Engineering Research Center for Environment-Friendly Agricultural Pest Management, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao 266109, China; (H.-Y.Z.); (P.-H.Q.); (K.Y.); (T.-X.L.)
| | - Kun Yang
- Shandong Engineering Research Center for Environment-Friendly Agricultural Pest Management, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao 266109, China; (H.-Y.Z.); (P.-H.Q.); (K.Y.); (T.-X.L.)
| | - Tong-Xian Liu
- Shandong Engineering Research Center for Environment-Friendly Agricultural Pest Management, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao 266109, China; (H.-Y.Z.); (P.-H.Q.); (K.Y.); (T.-X.L.)
| | - You-Jun Zhang
- Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China;
| | - Dong Chu
- Shandong Engineering Research Center for Environment-Friendly Agricultural Pest Management, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao 266109, China; (H.-Y.Z.); (P.-H.Q.); (K.Y.); (T.-X.L.)
- Correspondence: ; Tel.: +86-58957712
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Ishiguro T, Hayashi M, Fujiwara W, Okumura S, Yoshinaga M, Yamada R, Ueda S, Ito T, Niwa Y, Miyazaki A, Harada M, Naruse H, Ishii J, Ozaki Y, Izawa H. Circulating miR-489 as a potential new biomarker for idiopathic dilated cardiomyopathy. FUJITA MEDICAL JOURNAL 2022; 7:18-22. [PMID: 35111539 PMCID: PMC8749486 DOI: 10.20407/fmj.2020-001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 04/20/2020] [Indexed: 01/15/2023]
Abstract
Objectives:
MicroRNAs (miRNA) are functional RNAs that have emerged as pivotal gene expression
regulators in cardiac disease. Although several cardiomyocyte miRNAs have been reported to
play roles in heart failure progression among patients with idiopathic dilated cardiomyopathy
(DCM), the role of circulating miRNAs has not yet been well-examined. Methods:
After total RNA extraction from the peripheral blood samples of three control
participants and six patients with DCM, miRNA profiling was performed using miRNA arrays.
Based on the results of this initial screening, real-time polymerase chain reaction (RT-PCR)
was used to perform a quantitative analysis of blood samples from a larger number of matched
patients (DCM, n=20; controls, n=5). Finally, the
correlations between specific miRNA expression levels and hemodynamic parameters were
analyzed. Results:
A primary screening of 2,565 miRNAs resulted in the identification of nine miRNA
candidates. Quantitative RT-PCR results revealed significantly increased miR-489 expression
levels in the DCM group. Moreover, there was a significant positive correlation between
miR-489 expression level and left ventricular ejection fraction. Conclusions:
Our results suggest that circulating miR-489 could be a potential noninvasive
diagnostic biomarker for DCM. Additionally, the quantification of circulating miR-489 may have
value as a potential prognostic marker for patients with DCM.
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Affiliation(s)
- Tomoya Ishiguro
- Department of Cardiology, Fujita Health University Bantane Hospital, Nagoya, Aichi, Japan
| | - Mutsuharu Hayashi
- Department of Cardiology, Fujita Health University Bantane Hospital, Nagoya, Aichi, Japan
| | - Wakaya Fujiwara
- Department of Cardiology, Fujita Health University Bantane Hospital, Nagoya, Aichi, Japan
| | - Satoshi Okumura
- Department of Cardiology, Fujita Health University Bantane Hospital, Nagoya, Aichi, Japan
| | - Masataka Yoshinaga
- Department of Cardiology, Fujita Health University Bantane Hospital, Nagoya, Aichi, Japan
| | - Ryo Yamada
- Department of Cardiology, Fujita Health University Bantane Hospital, Nagoya, Aichi, Japan
| | - Sayano Ueda
- Department of Cardiology, Fujita Health University Bantane Hospital, Nagoya, Aichi, Japan
| | - Takehiro Ito
- Department of Cardiology, Fujita Health University Bantane Hospital, Nagoya, Aichi, Japan
| | - Yudai Niwa
- Department of Cardiology, Fujita Health University Bantane Hospital, Nagoya, Aichi, Japan
| | - Akane Miyazaki
- Department of Cardiology, Fujita Health University Bantane Hospital, Nagoya, Aichi, Japan
| | - Masahide Harada
- Department of Cardiology, Fujita Health University, School of Medicine, Toyoake, Aichi, Japan
| | - Hiroyuki Naruse
- Department of Cardiology, Fujita Health University, School of Medicine, Toyoake, Aichi, Japan
| | - Junnichi Ishii
- Department of Cardiology, Fujita Health University, School of Medicine, Toyoake, Aichi, Japan
| | - Yukio Ozaki
- Department of Cardiology, Fujita Health University, School of Medicine, Toyoake, Aichi, Japan
| | - Hideo Izawa
- Department of Cardiology, Fujita Health University Bantane Hospital, Nagoya, Aichi, Japan
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Kim J, Cho S, Park Y, Lee J, Park J. Evaluation of micro-RNA in extracellular vesicles from blood of patients with prostate cancer. PLoS One 2021; 16:e0262017. [PMID: 34972164 PMCID: PMC8719659 DOI: 10.1371/journal.pone.0262017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 12/15/2021] [Indexed: 12/14/2022] Open
Abstract
Extracellular vesicles (EVs) contain various types of molecules including micro-RNAs, so isolating EVs can be an effective way to analyze and diagnose diseases. A lot of micro-RNAs have been known in relation to prostate cancer (PCa), and we evaluate miR-21, miR-141, and miR-221 in EVs and compare them with prostate-specific antigen (PSA). EVs were isolated from plasma of 38 patients with prostate cancer and 8 patients with benign prostatic hyperplasia (BPH), using a method that showed the highest recovery of RNA. Isolation of EVs concentrated micro-RNAs, reducing the cycle threshold (Ct) value of RT-qPCR amplification of micro-RNA such as miR-16 by 5.12 and miR-191 by 4.65, compared to the values before EV isolation. Normalization of target micro-RNAs was done using miR-191. For miR-221, the mean expression level of patients with localized PCa was significantly higher than that of the control group, having 33.45 times higher expression than the control group (p < 0.01). Area under curve (AUC) between BPH and PCa for miR-221 was 0.98 (p < 0.0001), which was better than AUC for prostate-specific antigen (PSA) level in serum for the same patients. The levels of miR-21 and miR-141 in EVs did not show significant changes in patients with PCa compared to the control group in this study. This study suggests isolating EVs can be a helpful approach in analyzing micro-RNAs with regard to disease.
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Affiliation(s)
- Jiyoon Kim
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, Pohang, Gyeong-buk, Republic of Korea
| | - Siwoo Cho
- Department of Mechanical Engineering, Pohang University of Science and Technology, Pohang, Gyeong-buk, Republic of Korea
| | - Yonghyun Park
- Department of Urology, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Jiyoul Lee
- Department of Urology, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Jaesung Park
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, Pohang, Gyeong-buk, Republic of Korea
- Department of Mechanical Engineering, Pohang University of Science and Technology, Pohang, Gyeong-buk, Republic of Korea
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Ghanbari S, Salimi A, Rahmani S, Nafissi N, Sharifi-Zarchi A, Mowla SJ. miR-361-5p as a promising qRT-PCR internal control for tumor and normal breast tissues. PLoS One 2021; 16:e0253009. [PMID: 34101749 PMCID: PMC8186776 DOI: 10.1371/journal.pone.0253009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Accepted: 05/27/2021] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND One of the most widely used evaluation methods in miRNA experiments is qRT-PCR. However, selecting suitable internal controls (IC) is crucial for qRT-PCR experiments. Currently, there is no consensus on the ICs for miRNA qRT-PCR experiments in breast cancer. To this end, we tried to identify the most stable (the least expression alteration) and promising miRNAs in normal and tumor breast tissues by employing TCGA miRNA-Seq data and then experimentally validated them on fresh clinical samples. METHODS A multi-component scoring system was used which takes into account multiple expression stability criteria as well as correlation with clinical characteristics. Furthermore, we extended the scoring system for more than two biological sub-groups. TCGA BRCA samples were analyzed based on two grouping criteria: Tumor & Normal samples and Tumor subtypes. The top 10 most stable miRNAs were further investigated by differential expression and survival analysis. Then, we examined the expression level of the top scored miRNA (hsa-miR-361-5p) along with two commonly used ICs hsa-miR-16-5p and U48 on 34 pairs of Primary breast tumor and their adjacent normal tissues using qRT-PCR. RESULTS According to our multi-component scoring system, hsa-miR-361-5p had the highest stability score in both grouping criteria and hsa-miR-16-5p showed significantly lower scores. Based on our qRT-PCR assay, while U48 was the most abundant IC, hsa-miR-361-5p had lower standard deviation and also was the only IC capable of detecting a significant up-regulation of hsa-miR-21-5p in breast tumor tissue. CONCLUSIONS miRNA-Seq data is a great source to discover stable ICs. Our results demonstrated that hsa-miR-361-5p is a highly stable miRNA in tumor and non-tumor breast tissue and we recommend it as a suitable reference gene for miRNA expression studies in breast cancer. Additionally, although hsa-miR-16-5p is a commonly used IC, it's not a suitable one for breast cancer studies.
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Affiliation(s)
- Sogol Ghanbari
- Molecular Genetics Department, Biological Sciences Faculty, Tarbiat Modares University, Tehran, Iran
| | - Adel Salimi
- Computer Engineering Department, Sharif University of Technology, Tehran, Iran
| | - Saeid Rahmani
- Computer Engineering Department, Sharif University of Technology, Tehran, Iran
| | - Nahid Nafissi
- Surgical Department, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Ali Sharifi-Zarchi
- Computer Engineering Department, Sharif University of Technology, Tehran, Iran
| | - Seyed Javad Mowla
- Molecular Genetics Department, Biological Sciences Faculty, Tarbiat Modares University, Tehran, Iran
- * E-mail:
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Šatrauskienė A, Navickas R, Laucevičius A, Krilavičius T, Užupytė R, Zdanytė M, Ryliškytė L, Jucevičienė A, Holvoet P. Mir-1, miR-122, miR-132, and miR-133 Are Related to Subclinical Aortic Atherosclerosis Associated with Metabolic Syndrome. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:ijerph18041483. [PMID: 33557426 PMCID: PMC7915826 DOI: 10.3390/ijerph18041483] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 01/29/2021] [Accepted: 02/01/2021] [Indexed: 01/08/2023]
Abstract
Previously, miR-1, miR-122, miR-126, miR-132, miR-133, and miR-370 were found to be related to coronary artery disease (CAD) progression. However, their relationship with subclinical atherosclerosis, especially in subjects with metabolic syndrome, is unknown. Therefore, our aim was to determine their relationship with arterial markers of subclinical atherosclerosis. Metabolic syndrome subjects (n = 182) with high cardiovascular risk but without overt cardiovascular disease (CVD) were recruited from the Lithuanian High Cardiovascular Risk (LitHiR) primary prevention program. The ardio-ankle vascular index (CAVI), augmentation index normalized to a heart rate of 75 bpm (AIxHR75), aortic pulse wave velocity (AoPWV), and carotid artery stiffness were assessed. MicroRNAs (miRs) were analyzed in serum. Pearson correlation and a univariate linear regression t-test showed that miR-1, miR-133b, and miR-133a were negatively associated with CAVI mean, whereas miR-122 was positively associated. MiR-1, miR-133b and miR-133a, and miR-145 were negatively associated with AIxHR75. MiR-122 correlated negatively with AoPWV. In multivariate linear regression models, miR-133b and miR-122 predicted CAVImean, miR-133 predicted AIxHR75, and miR-122 predicted AoPWV. MiR-132 predicted right carotid artery stiffness, and miR-1 predicted left carotid artery stiffness. The addition of smoking to miR-133b and miR-122 enhanced the prediction of CAVI. Age and triglycerides enhanced the prediction of AoPWV by miR-122. A cluster of four miRs are related to subclinical atherosclerosis in subjects with metabolic syndrome. Combined, they may have a more substantial diagnostic or prognostic value than any single miR. Future follow-up studies are needed to establish their clinical relevance.
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Affiliation(s)
- Agnė Šatrauskienė
- Clinic of Cardiac and Vascular Diseases, Institute of Clinical Medicine, Faculty of Medicine, Vilnius University, 08661 Vilnius, Lithuania; (A.Š.); (A.L.); (L.R.); (A.J.)
- Centre of Cardiology and Angiology, Vilnius University Hospital, Santaros Klinikos, 08410 Vilnius, Lithuania
| | - Rokas Navickas
- Clinic of Cardiac and Vascular Diseases, Institute of Clinical Medicine, Faculty of Medicine, Vilnius University, 08661 Vilnius, Lithuania; (A.Š.); (A.L.); (L.R.); (A.J.)
- Centre of Cardiology and Angiology, Vilnius University Hospital, Santaros Klinikos, 08410 Vilnius, Lithuania
- Correspondence:
| | - Aleksandras Laucevičius
- Clinic of Cardiac and Vascular Diseases, Institute of Clinical Medicine, Faculty of Medicine, Vilnius University, 08661 Vilnius, Lithuania; (A.Š.); (A.L.); (L.R.); (A.J.)
- Centre of Cardiology and Angiology, Vilnius University Hospital, Santaros Klinikos, 08410 Vilnius, Lithuania
- Experimental, Preventive, and Clinic Medicine Department, Centre for Innovative Medicine, 08406 Vilnius, Lithuania
| | - Tomas Krilavičius
- Informatics Faculty, Vytautas Magnus University, 44248 Kaunas, Lithuania; (T.K.); (R.U.)
- Baltic Institute of Advanced Technology, 01124 Vilnius, Lithuania
| | - Rūta Užupytė
- Informatics Faculty, Vytautas Magnus University, 44248 Kaunas, Lithuania; (T.K.); (R.U.)
- Baltic Institute of Advanced Technology, 01124 Vilnius, Lithuania
- Faculty of Mathematics and Informatics, Vilnius University, 03225 Vilnius, Lithuania
| | - Monika Zdanytė
- Department of Cardiology and Cardiovascular Medicine, Universität Tübingen, 72074 Tübingen, Germany;
| | - Ligita Ryliškytė
- Clinic of Cardiac and Vascular Diseases, Institute of Clinical Medicine, Faculty of Medicine, Vilnius University, 08661 Vilnius, Lithuania; (A.Š.); (A.L.); (L.R.); (A.J.)
- Centre of Cardiology and Angiology, Vilnius University Hospital, Santaros Klinikos, 08410 Vilnius, Lithuania
| | - Agnė Jucevičienė
- Clinic of Cardiac and Vascular Diseases, Institute of Clinical Medicine, Faculty of Medicine, Vilnius University, 08661 Vilnius, Lithuania; (A.Š.); (A.L.); (L.R.); (A.J.)
- Centre of Cardiology and Angiology, Vilnius University Hospital, Santaros Klinikos, 08410 Vilnius, Lithuania
| | - Paul Holvoet
- Experimental Cardiology, Department of Cardiovascular Sciences, KU Leuven, 3000 Leuven, Belgium;
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Yang YX, Lin RH, Li Z, Wang AY, Xue C, Duan AL, Zhao M, Zhang JH. Function Analysis of P450 and GST Genes to Imidacloprid in Aphis craccivora (Koch). Front Physiol 2021; 11:624287. [PMID: 33551847 PMCID: PMC7854575 DOI: 10.3389/fphys.2020.624287] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Accepted: 12/21/2020] [Indexed: 01/25/2023] Open
Abstract
Aphis craccivora (Koch) is an economically important pest that affects legumes in worldwide. Chemical control is still the primary efficient method for A. craccivora management. However, the mechanism underlying insecticide resistance in A. craccivora has not been elucidated. A previous study observed that piperonyl butoxide (PBO) and diethyl maleate (DEM) significantly synergized imidacloprid in A. craccivora field populations, indicating that cytochrome P450 (P450) and glutathione S-transferase (GST) genes may play pivotal roles in imidacloprid resistance. In this study, 38 P450 genes and 10 GST genes were identified in A. craccivora through transcriptomic analysis. The expression levels of these P450 and GST genes were measured in susceptible (SUS) strains of A. craccivora under imidacloprid treatment with LC15, LC50, and LC85 doses. The expression levels of CYP18A1, CYP6CY21, CYP6DA1, CYP6DA2, CYP4CJ1, CYP4CJ2, and CYP380C6 were up-regulated in the three treatments. Most of these genes belong to CYP3 and CYP4 Clans. In addition, the expression levels of all P450 and GST genes in A. craccivora were also measured in the Juye (JY) and Linqing (LQ) field populations. The expression levels of CYP6DA2, CYP4CJ1, and CYP380C6 were up-regulated in the SUS strain after imidacloprid treatment at three doses, and these genes were overexpressed in the JY population. Furthermore, the sensitivity of A. craccivora to imidacloprid was significantly increased after knockdown of CYP380C6 and CYP6DA2 through RNA interference. These results may help to elucidate the mechanisms underlying of imidacloprid resistance in A. craccivora.
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Affiliation(s)
- Yuan-Xue Yang
- Cotton Research Center, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Rong-Hua Lin
- Institute for the Control of Agrochemicals, Ministry of Agriculture and Rural Affairs, Beijing, China
| | - Zhuo Li
- Cotton Research Center, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Ai-Yu Wang
- Cotton Research Center, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Chao Xue
- Cotton Research Center, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Ai-Ling Duan
- Cotton Research Center, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Ming Zhao
- Cotton Research Center, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Jian-Hua Zhang
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, China
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Mishra N, Raina K, Agarwal R. Deciphering the role of microRNAs in mustard gas-induced toxicity. Ann N Y Acad Sci 2020; 1491:25-41. [PMID: 33305460 DOI: 10.1111/nyas.14539] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 10/26/2020] [Accepted: 11/01/2020] [Indexed: 12/16/2022]
Abstract
Mustard gas (sulfur mustard, SM), a highly vesicating chemical warfare agent, was first deployed in warfare in 1917 and recently during the Iraq-Iran war (1980s) and Syrian conflicts (2000s); however, the threat of exposure from stockpiles and old artillery shells still looms large. Whereas research has been long ongoing on SM-induced toxicity, delineating the precise molecular pathways is still an ongoing area of investigation; thus, it is important to attempt novel approaches to decipher these mechanisms and develop a detailed network of pathways associated with SM-induced toxicity. One such avenue is exploring the role of microRNAs (miRNAs) in SM-induced toxicity. Recent research on the regulatory role of miRNAs provides important results to fill in the gaps in SM toxicity-associated mechanisms. In addition, differentially expressed miRNAs can also be used as diagnostic markers to determine the extent of toxicity in exposed individuals. Thus, in our review, we have summarized the studies conducted so far in cellular and animal models, including human subjects, on the expression profiles and roles of miRNAs in SM- and/or SM analog-induced toxicity. Further detailed research in this area will guide us in devising preventive strategies, diagnostic tools, and therapeutic interventions against SM-induced toxicity.
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Affiliation(s)
- Neha Mishra
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado-Anschutz Medical Campus, Aurora, Colorado
| | - Komal Raina
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado-Anschutz Medical Campus, Aurora, Colorado.,Department of Pharmaceutical Sciences, South Dakota State University, Brookings, South Dakota
| | - Rajesh Agarwal
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado-Anschutz Medical Campus, Aurora, Colorado
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Zhao J, Zhu XC, Wu XS, Wang L, Zhu CC, Yang K, Deng GQ, Wang A, Liu Y, Jia WD, Zhu L. Identification of miR-4644 as a suitable endogenous normalizer for circulating miRNA quantification in hepatocellular carcinoma. J Cancer 2020; 11:7032-7044. [PMID: 33123293 PMCID: PMC7592003 DOI: 10.7150/jca.48903] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Accepted: 10/04/2020] [Indexed: 12/12/2022] Open
Abstract
Background: Circulating microRNAs (miRNAs) have proved to be promising biomarkers for early diagnosis and therapeutic monitoring in cancers. Particularly for hepatocellular carcinoma (HCC), detection of circulating miRNA biomarkers as a new diagnostic approach has been written into the latest Guidelines for Diagnosis and Treatment of Primary Liver Cancer in China (2019 edition). However, no general consensus on an ideal endogenous normalizer for circulating miRNAs quantification has been reached, so it will affect the accuracy of quantitative results. In this study, we aim to identify a stable endogenous normalizer for analyzing circulating miRNAs. Methods: Candidate miRNAs were selected by screening dataset GSE104310, as well as data statistics and analysis. Five commonly reference genes were chosen for further comparison and verification. Then, the expression levels of these genes in serum were analyzed by quantitative reverse transcription PCR (RT-qPCR) among four groups, including patients diagnosed with HCC, chronic hepatitis B (CHB), liver cirrhosis, and healthy subjects. Furthermore, the stability of target genes was evaluated using geNorm, NormFinder, comparative ΔCq programs, and validated by database. We also explored the availability of the miRNA combination, and compared the performance difference between combination and individuals, as well as the selectivity of miRNA references in the combinations. Results: 11 candidate miRNAs were obtained, and miR-4644 stood out among these miRNAs, and proved to be much more stable than other endogenous miRNAs. Further study showed that miR-4644 exhibited higher stability and expression abundance than other commonly miRNA reference controls. Finally, we discovered the combination of miR-4644 and miR-16 revealed high performance in stability when compared to miRNA individuals. Furthermore, the combination consisted of references with closer nature could give rise to amplification effects in stability. Conclusions: Our findings demonstrated that miR-4644 is an ideal endogenous normalizer for circulating microRNA quantification in hepatocellular carcinoma. Besides, combining miR-4644 with miR-16 into a whole as a reference control would greatly improve the accuracy of quantification.
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Affiliation(s)
- Jun Zhao
- Center of Engineering Technology Research for Biomedical Optical Instrument, Anhui Institute of Optics and Fine Mechanics, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China.,Science Island Branch of Graduate School, University of Science and Technology of China, Hefei 230026, China
| | - Xin-Chao Zhu
- Center of Engineering Technology Research for Biomedical Optical Instrument, Anhui Institute of Optics and Fine Mechanics, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China.,Science Island Branch of Graduate School, University of Science and Technology of China, Hefei 230026, China
| | - Xiao-Song Wu
- Center of Engineering Technology Research for Biomedical Optical Instrument, Anhui Institute of Optics and Fine Mechanics, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China.,Science Island Branch of Graduate School, University of Science and Technology of China, Hefei 230026, China
| | - Lin Wang
- Center of Engineering Technology Research for Biomedical Optical Instrument, Anhui Institute of Optics and Fine Mechanics, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China.,Science Island Branch of Graduate School, University of Science and Technology of China, Hefei 230026, China
| | - Can-Can Zhu
- Center of Engineering Technology Research for Biomedical Optical Instrument, Anhui Institute of Optics and Fine Mechanics, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China
| | - Ke Yang
- Center of Engineering Technology Research for Biomedical Optical Instrument, Anhui Institute of Optics and Fine Mechanics, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China
| | - Guo-Qing Deng
- Center of Engineering Technology Research for Biomedical Optical Instrument, Anhui Institute of Optics and Fine Mechanics, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China
| | - An Wang
- Center of Engineering Technology Research for Biomedical Optical Instrument, Anhui Institute of Optics and Fine Mechanics, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China
| | - Yong Liu
- Center of Engineering Technology Research for Biomedical Optical Instrument, Anhui Institute of Optics and Fine Mechanics, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China
| | - Wei-Dong Jia
- Department of General Surgery, Anhui Provincial Hospital & the First Affiliated Hospital of USTC, Division of Life Science and Medicine, University of Science and Technology of China, Hefei 230001, China
| | - Ling Zhu
- Center of Engineering Technology Research for Biomedical Optical Instrument, Anhui Institute of Optics and Fine Mechanics, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China
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Cheema AK, Sarria L, Bekheit M, Collado F, Almenar‐Pérez E, Martín‐Martínez E, Alegre J, Castro‐Marrero J, Fletcher MA, Klimas NG, Oltra E, Nathanson L. Unravelling myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS): Gender-specific changes in the microRNA expression profiling in ME/CFS. J Cell Mol Med 2020; 24:5865-5877. [PMID: 32291908 PMCID: PMC7214164 DOI: 10.1111/jcmm.15260] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 03/16/2020] [Accepted: 03/18/2020] [Indexed: 12/15/2022] Open
Abstract
Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) is a multisystem illness characterized by medically unexplained debilitating fatigue with suggested altered immunological state. Our study aimed to explore peripheral blood mononuclear cells (PBMCs) for microRNAs (miRNAs) expression in ME/CFS subjects under an exercise challenge. The findings highlight the immune response and inflammation links to differential miRNA expression in ME/CFS. The present study is particularly important in being the first to uncover the differences that exist in miRNA expression patterns in males and females with ME/CFS in response to exercise. This provides new evidence for the understanding of differential miRNA expression patterns and post-exertional malaise in ME/CFS. We also report miRNA expression pattern differences associating with the nutritional status in individuals with ME/CFS, highlighting the effect of subjects' metabolic state on molecular changes to be considered in clinical research within the NINDS/CDC ME/CFS Common Data Elements. The identification of gender-based miRNAs importantly provides new insights into gender-specific ME/CFS susceptibility and demands exploration of sex-suited ME/CFS therapeutics.
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Affiliation(s)
- Amanpreet K. Cheema
- Institute for Neuro Immune MedicineDr. Kiran C. Patel College of Osteopathic MedicineNova Southeastern UniversityFort LauderdaleFLUSA
- Department of NutritionDr. Kiran C. Patel College of Osteopathic MedicineNova Southeastern UniversityFort LauderdaleFLUSA
| | - Leonor Sarria
- Institute for Neuro Immune MedicineDr. Kiran C. Patel College of Osteopathic MedicineNova Southeastern UniversityFort LauderdaleFLUSA
| | - Mina Bekheit
- Halmos College of Natural Sciences and OceanographyNova Southeastern UniversityFort LauderdaleFLUSA
| | - Fanny Collado
- Department of Veterans AffairsMiami VA Healthcare System, Research ServiceMiamiFLUSA
- South Florida Veterans Affairs Foundation for Research and Education IncFort LauderdaleFLUSA
| | - Eloy Almenar‐Pérez
- Escuela de DoctoradoUniversidad Católica de Valencia San Vicente MártirValenciaSpain
| | | | - Jose Alegre
- Vall d'Hebron University HospitalVall d'Hebron Research InstituteUniversitat Autónoma de BarcelonaBarcelonaSpain
| | - Jesus Castro‐Marrero
- Vall d'Hebron University HospitalVall d'Hebron Research InstituteUniversitat Autónoma de BarcelonaBarcelonaSpain
| | - Mary A. Fletcher
- Institute for Neuro Immune MedicineDr. Kiran C. Patel College of Osteopathic MedicineNova Southeastern UniversityFort LauderdaleFLUSA
- Department of Veterans AffairsMiami VA Healthcare System, Research ServiceMiamiFLUSA
- South Florida Veterans Affairs Foundation for Research and Education IncFort LauderdaleFLUSA
| | - Nancy G. Klimas
- Institute for Neuro Immune MedicineDr. Kiran C. Patel College of Osteopathic MedicineNova Southeastern UniversityFort LauderdaleFLUSA
- Department of Veterans AffairsMiami VA Healthcare System, Research ServiceMiamiFLUSA
- South Florida Veterans Affairs Foundation for Research and Education IncFort LauderdaleFLUSA
| | - Elisa Oltra
- School of MedicineUniversidad Católica de Valencia San Vicente MártirValenciaSpain
| | - Lubov Nathanson
- Institute for Neuro Immune MedicineDr. Kiran C. Patel College of Osteopathic MedicineNova Southeastern UniversityFort LauderdaleFLUSA
- Department of NutritionDr. Kiran C. Patel College of Osteopathic MedicineNova Southeastern UniversityFort LauderdaleFLUSA
- Halmos College of Natural Sciences and OceanographyNova Southeastern UniversityFort LauderdaleFLUSA
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10
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Mansouri S, Khansarinejad B, Mosayebi G, Eghbali A, Mondanizadeh M. Alteration in Expression of miR-32 and FBXW7 Tumor Suppressor in Plasma Samples of Patients with T-cell Acute Lymphoblastic Leukemia. Cancer Manag Res 2020; 12:1253-1259. [PMID: 32110099 PMCID: PMC7035948 DOI: 10.2147/cmar.s238470] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2019] [Accepted: 02/13/2020] [Indexed: 12/12/2022] Open
Abstract
Background T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive and malignant neoplasm that arises from the hematopoietic T-cell precursors. Inactivation of FBXW7 gene is frequently observed in T-cell acute lymphoblastic leukemia, suggesting a significant tumor-suppressive role for FBXW7 in the pathobiology of this leukemia. Considering the role of microRNAs in cell proliferation and regulation of apoptosis, the aim of this study was to identify novel oncogenic microRNAs that suppress FBXW7 in patients with T-ALL. Patients and Methods The expression levels of two bioinformatically predicted microRNAs – miR-32 and miR-107 were compared in patients with T-ALL and a control group. A total of 80 plasma samples were subjected to RNA extraction, and the microRNA expression profiles were assessed by the RT-qPCR. The expression level of miR-103 was used as the endogenous reference for normalization of quantitative data. Results The plasma levels of miR-32 and miR-107 in patients with T-ALL were significantly higher (5.65, P < 0.001) and lower (0.432, P = 0.002), respectively. On the other hand, the expression levels of FBXW7 gene were significantly downregulated by –76.9 fold in T-ALL patients (P < 0.001). The results of the ROC curve analysis indicated that overexpression of miR-32 might be used to distinguish T-ALL patients with reasonable sensitivity and specificity. Conclusion miR-32 is considered as a novel oncomir that targets FBXW7 and might have a role in the etiology or progression of T-ALL. Furthermore, miR-32 can potentially serve as a non-invasive biomarker for detection of T-ALL.
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Affiliation(s)
- Sanaz Mansouri
- Department of Biotechnology and Molecular Medicine, Arak University of Medical Sciences, Arak, Iran
| | - Behzad Khansarinejad
- Department of Microbiology and Immunology, Arak University of Medical Sciences, Arak, Iran
| | - Ghasem Mosayebi
- Department of Microbiology and Immunology, Arak University of Medical Sciences, Arak, Iran
| | - Aziz Eghbali
- Department of Pediatrics, School of Medicine, Arak University of Medical Sciences, Arak, Iran
| | - Mahdieh Mondanizadeh
- Department of Biotechnology and Molecular Medicine, Arak University of Medical Sciences, Arak, Iran.,Molecular and Medicine Research Center, Arak University of Medical Sciences, Arak, Iran
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11
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Lu Y, Che J, Xu X, Pang B, Zhao X, Liu Y, Shi J. Metabolomics Reveals the Response of the Phenylpropanoid Biosynthesis Pathway to Starvation Treatment in the Grape Endophyte Alternaria sp. MG1. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:1126-1135. [PMID: 31891261 DOI: 10.1021/acs.jafc.9b05302] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Phenylpropanoid (PPPN) compounds are widely used in agriculture, medical, food, and cosmetic industries because of their multiple bioactivities. Alternaria sp. MG1, an endophytic fungus isolated from grape, is a new natural source of PPPNs. However, the PPPN biosynthesis pathway in MG1 tends to be suppressed under normal growth conditions. Starvation has been reported to stimulate the PPPN pathway in plants, but this phenomenon has not been well studied in endophytic fungi. Here, metabolomics analysis was used to examine the profile of PPPN compounds, and quantitative reverse transcription-polymerase chain reaction was used to detect the expression of key genes in the PPPN biosynthesis pathway under starvation conditions. Starvation treatment significantly increased the accumulation of shikimate and PPPN compounds and upregulated the expression of key genes in their biosynthesis pathways. In addition to previously reported PPPNs, sinapate, 4-hydroxystyrene, piceatannol, and taxifolin were also detected under starvation treatment. These findings suggest that starvation treatment provides an effective way to optimize the production of PPPN compounds and may permit the investigation of compounds that are undetectable under normal conditions. Moreover, the diversity of its PPPNs makes strain MG1 a rich repository of valuable compounds and an extensive genetic resource for future studies.
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Affiliation(s)
- Yao Lu
- Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences , Northwestern Polytechnical University , 127 Youyi West Road , Xi'an , Shaanxi Province 710072 , China
| | - Jinxin Che
- Department of Biological and Food Engineering, College of Chemical Engineering , Xiangtan University , Xiangtan , Hunan 411105 , China
| | - Xiaoguang Xu
- Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences , Northwestern Polytechnical University , 127 Youyi West Road , Xi'an , Shaanxi Province 710072 , China
| | - Bing Pang
- Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences , Northwestern Polytechnical University , 127 Youyi West Road , Xi'an , Shaanxi Province 710072 , China
| | - Xixi Zhao
- Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences , Northwestern Polytechnical University , 127 Youyi West Road , Xi'an , Shaanxi Province 710072 , China
| | - Yanlin Liu
- College of Enology , Northwest A&F University , 22 Xinong Road , Yangling , Shaanxi Province 712100 , China
| | - Junling Shi
- Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences , Northwestern Polytechnical University , 127 Youyi West Road , Xi'an , Shaanxi Province 710072 , China
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12
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Di Pietro V, Yakoub KM, Scarpa U, Di Pietro C, Belli A. MicroRNA Signature of Traumatic Brain Injury: From the Biomarker Discovery to the Point-of-Care. Front Neurol 2018; 9:429. [PMID: 29963002 PMCID: PMC6010584 DOI: 10.3389/fneur.2018.00429] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 05/22/2018] [Indexed: 12/21/2022] Open
Abstract
Traumatic brain injury (TBI) is a serious problem that causes high morbidity and mortality around the world. Currently, no reliable biomarkers are used to assess the severity and predict the recovery. Many protein biomarkers were extensively studied for diagnosis and prognosis of different TBI severities such as S-100β, glial fibrillary acidic protein (GFAP), neuron-specific enolase (NSE), neurofilament light chain (NFL), cleaved tau protein (C-tau), and ubiquitin C-terminal hydrolase-L1 (UCH-L1). However, none of these candidates is currently used in the clinical practice, due to relatively low sensitivity, for the diagnosis of mild TBI (mTBI) or mild to moderate TBI (MMTBI) patients who are clinically well and do not have a detectable intracranial pathology on the scans. MicroRNAs (miRNAs or miRs) are a class of small endogenous molecular regulators, which showed to be altered in different pathologies, including TBI and for this reason, their potential role in diagnosis, prognosis and therapeutic applications, is explored. Promising miRNAs such as miR-21, miR-16 or let-7i were identified as suitable candidate biomarkers for TBI and can differentiate mild from severe TBI. Also, they might represent new potential therapeutic targets. Identification of miRNA signature in tissue or biofluids, for several pathological conditions, is now possible thanks to the introduction of new high-throughput technologies such as microarray platform, Nanostring technologies or Next Generation Sequencing. This review has the aim to describe the role of microRNA in TBI and to explore the most commonly used techniques to identify microRNA profile. Understanding the strengths and limitations of the different methods can aid in the practical use of miRNA profiling for diverse clinical applications, including the development of a point-of-care device.
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Affiliation(s)
- Valentina Di Pietro
- Neurotrauma and Ophthalmology Research Group, Institute of Inflammation and Ageing, University of Birmingham, Birmingham, United Kingdom.,Surgical Reconstruction and Microbiology Research Centre, National Institute for Health Research, Queen Elizabeth Hospital, Birmingham, United Kingdom.,Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Illinois, IL, United States
| | - Kamal M Yakoub
- Surgical Reconstruction and Microbiology Research Centre, National Institute for Health Research, Queen Elizabeth Hospital, Birmingham, United Kingdom
| | - Ugo Scarpa
- Surgical Reconstruction and Microbiology Research Centre, National Institute for Health Research, Queen Elizabeth Hospital, Birmingham, United Kingdom
| | - Cinzia Di Pietro
- BioMolecular, Genome and Complex Systems BioMedicine Unit, Section of Biology and Genetics G Sichel, Department of Biomedical Sciences and Biotechnology, University of Catania, Catania, Italy
| | - Antonio Belli
- Neurotrauma and Ophthalmology Research Group, Institute of Inflammation and Ageing, University of Birmingham, Birmingham, United Kingdom.,Surgical Reconstruction and Microbiology Research Centre, National Institute for Health Research, Queen Elizabeth Hospital, Birmingham, United Kingdom
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13
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Gharbi S, Khateri S, Soroush MR, Shamsara M, Naeli P, Najafi A, Korsching E, Mowla SJ. MicroRNA expression in serum samples of sulfur mustard veterans as a diagnostic gateway to improve care. PLoS One 2018; 13:e0194530. [PMID: 29566027 PMCID: PMC5864010 DOI: 10.1371/journal.pone.0194530] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Accepted: 03/05/2018] [Indexed: 01/01/2023] Open
Abstract
Sulfur mustard is a vesicant chemical warfare agent, which has been used during Iraq-Iran-war. Many veterans and civilians still suffer from long-term complications of sulfur mustard exposure, especially in their lung. Although the lung lesions of these patients are similar to Chronic Obstructive Pulmonary Disease (COPD), there are some differences due to different etiology and clinical care. Less is known on the molecular mechanism of sulfur mustard patients and specific treatment options. microRNAs are master regulators of many biological pathways and proofed to be stable surrogate markers in body fluids. Based on that microRNA expression for serum samples of sulfur mustard patients were examined, to establish specific microRNA patterns as a basis for diagnostic use and insight into affected molecular pathways. Patients were categorized based on their long-term complications into three groups and microRNA serum levels were measured. The differentially regulated microRNAs and their corresponding gene targets were identified. Cell cycle arrest, ageing and TGF-beta signaling pathways showed up to be the most deregulated pathways. The candidate microRNA miR-143-3p could be validated on all individual patients. In a ROC analysis miR-143-3p turned out to be a suitable diagnostic biomarker in the mild and severe categories of patients. Further microRNAs which might own a link to the biology of the sulfur mustard patients are miR-365a-3p, miR-200a-3p, miR-663a. miR-148a-3p, which showed up only in a validation study, might be linked to the airway complications of the sulfur mustard patients. All the other candidate microRNAs do not directly link to COPD phenotype or lung complications. In summary the microRNA screening study characterizes several molecular differences in-between the clinical categories of the sulfur mustard exposure groups and established some useful microRNA biomarkers. qPCR raw data is available via the Gene Expression Omnibus https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE110797.
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Affiliation(s)
- Sedigheh Gharbi
- Department of Biology, Faculty of Sciences, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Shahriar Khateri
- Janbazan Medical and Engineering Research Center (JMERC), Tehran, Iran
| | | | - Mehdi Shamsara
- National Institute of Genetic Engineering and Biotechnology, Tehran, Iran
| | - Parisa Naeli
- Department of Molecular Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Ali Najafi
- Molecular Biology Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Eberhard Korsching
- Institute of Bioinformatics, University Hospital of Münster, University of Münster, Münster, Germany
| | - Seyed Javad Mowla
- Department of Molecular Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
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14
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Netz U, Carter J, Eichenberger MR, Feagins K, Galbraith NJ, Dryden GW, Pan J, Rai SN, Galandiuk S. Plasma microRNA Profile Differentiates Crohn's Colitis From Ulcerative Colitis. Inflamm Bowel Dis 2018; 24:159-165. [PMID: 29272478 PMCID: PMC5858028 DOI: 10.1093/ibd/izx009] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
BACKGROUND Inflammatory bowel disease (IBD) is commonly divided into 2 entities: Crohn's disease (CD) and ulcerative colitis (UC). Differentiating between these entities when dealing with IBD confined to the colon is important, especially when planning surgical treatment. Due to ambiguous histological or endoscopic findings, accurate diagnosis is not possible in up to 15% of cases. The aim of this study was to determine whether plasma microRNAs (miRNAs) can help differentiate Crohn's colitis (CC) from ulcerative colitis. METHODS Patients with isolated CC and with UC were enrolled in our study from January 2010 to May 2016. Peripheral blood was collected, and total RNA was isolated from plasma. Screening was performed for 380 common miRNAs. miRNAs that were differentially expressed between these 2 groups were chosen, and their differential expression was confirmed using single miRNA assays in a larger sample size. A predictive model was generated using these data. Significantly differentially expressed miRNAs were then validated utilizing the predictive model to assess blinded data from the single assays. RESULTS Screening was performed on 8 patients from each group. Seven differentially expressed miRNAs were chosen for single assay confirmation. Two miRNAs (miR-598, miR-642) were consistently different between the patient groups (P = 0.013, P = 0.005). Using blinded data, these 2 miRNAs were validated using the predictive model, achieving an overall accuracy of 75% (95% confidence interval, 40.7-92.9). CONCLUSIONS We identified 2 plasma miRNAs that differentiated CC from UC. Our data indicate the promise and feasibility of a plasma miRNA-based assay to distinguish between these 2 conditions.
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Affiliation(s)
- Uri Netz
- Price Institute of Surgical Research, The Hiram C. Polk Jr., MD Department of
Surgery, University of Louisville, Louisville, Kentucky,Department of Surgery A, Soroka University Medical Center, Beer Sheva,
Israel,Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva,
Israel
| | - Jane Carter
- Price Institute of Surgical Research, The Hiram C. Polk Jr., MD Department of
Surgery, University of Louisville, Louisville, Kentucky
| | - M Robert Eichenberger
- Price Institute of Surgical Research, The Hiram C. Polk Jr., MD Department of
Surgery, University of Louisville, Louisville, Kentucky
| | - Kayla Feagins
- Price Institute of Surgical Research, The Hiram C. Polk Jr., MD Department of
Surgery, University of Louisville, Louisville, Kentucky
| | - Norman J Galbraith
- Price Institute of Surgical Research, The Hiram C. Polk Jr., MD Department of
Surgery, University of Louisville, Louisville, Kentucky
| | - Gerald W Dryden
- Department of Medicine, Division of Gastroenterology, Hepatology, and
Nutrition University of Louisville School of Medicine Louisville, Kentucky
| | - Jianmin Pan
- Department of Bioinformatics and Biostatistics, University of Louisville
School of Public Health and Information Sciences, Louisville, Kentucky
| | - Shesh N Rai
- Department of Bioinformatics and Biostatistics, University of Louisville
School of Public Health and Information Sciences, Louisville, Kentucky
| | - Susan Galandiuk
- Price Institute of Surgical Research, The Hiram C. Polk Jr., MD Department of
Surgery, University of Louisville, Louisville, Kentucky,Address correspondence to: Susan Galandiuk, MD, FACG, AGAF, The Hiram C.
Polk Jr, MD Department of Surgery, 550 South Jackson Street, Louisville, KY 40202 (e-mail:
)
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15
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Li T, Diao H, Zhao L, Xing Y, Zhang J, Liu N, Yan Y, Tian X, Sun W, Liu B. Identification of suitable reference genes for real-time quantitative PCR analysis of hydrogen peroxide-treated human umbilical vein endothelial cells. BMC Mol Biol 2017; 18:10. [PMID: 28381210 PMCID: PMC5381023 DOI: 10.1186/s12867-017-0086-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Accepted: 03/21/2017] [Indexed: 11/25/2022] Open
Abstract
Background Oxidative stress can induce cell injury in vascular endothelial cells, which is the initial event in the development of atherosclerosis. Although quantitative real-time polymerase chain reaction (qRT-PCR) has been widely used in gene expression studies in oxidative stress injuries, using carefully validated reference genes has not received sufficient attention in related studies. The objective of this study, therefore, was to select a set of stably expressed reference genes for use in qRT-PCR normalization in oxidative stress injuries in human umbilical vein endothelial cells (HUVECs) induced by hydrogen peroxide (H2O2). Results Using geNorm analysis, we found that five stably expressed reference genes were sufficient for normalization in qRT-PCR analysis in HUVECs treated with H2O2. Genes with the most stable expression according to geNorm were U6, TFRC, RPLP0, GAPDH, and ACTB, and according to NormFinder were ALAS1, TFRC, U6, GAPDH, and ACTB. Conclusion Taken together, our study demonstrated that the expression stability of reference genes may differ according to the statistical program used. U6, TFRC, RPLP0, GAPDH, and ACTB was the optimal set of reference genes for studies on gene expression performed by qRT-PCR assays in HUVECs under oxidative stress study.
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Affiliation(s)
- Tianyi Li
- Department of Cardiology, The Second Hospital of Jilin University, Changchun, 130041, Jilin, China
| | - Hongying Diao
- Department of Cardiology, The Second Hospital of Jilin University, Changchun, 130041, Jilin, China
| | - Lei Zhao
- Department of Cardiology, The Second Hospital of Jilin University, Changchun, 130041, Jilin, China
| | - Yue Xing
- Department of Cardiology, The Second Hospital of Jilin University, Changchun, 130041, Jilin, China
| | - Jichang Zhang
- Department of Cardiology, The Second Hospital of Jilin University, Changchun, 130041, Jilin, China
| | - Ning Liu
- Department of Cardiology, The Second Hospital of Jilin University, Changchun, 130041, Jilin, China
| | - Youyou Yan
- Department of Cardiology, The Second Hospital of Jilin University, Changchun, 130041, Jilin, China
| | - Xin Tian
- Department of Cardiology, The Second Hospital of Jilin University, Changchun, 130041, Jilin, China
| | - Wei Sun
- Department of Cardiology, The Second Hospital of Jilin University, Changchun, 130041, Jilin, China
| | - Bin Liu
- Department of Cardiology, The Second Hospital of Jilin University, Changchun, 130041, Jilin, China.
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16
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Wang X, Li Y, Zhang J, Zhang Q, Liu X, Li Z. De novo characterization of microRNAs in oriental fruit moth Grapholita molesta and selection of reference genes for normalization of microRNA expression. PLoS One 2017; 12:e0171120. [PMID: 28158242 PMCID: PMC5291412 DOI: 10.1371/journal.pone.0171120] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Accepted: 01/16/2017] [Indexed: 11/19/2022] Open
Abstract
MicroRNAs (miRNAs) are a group of endogenous non-coding small RNAs that have critical regulatory functions in almost all known biological processes at the post-transcriptional level in a variety of organisms. The oriental fruit moth Grapholita molesta is one of the most serious pests in orchards worldwide and threatens the production of Rosacea fruits. In this study, a de novo small RNA library constructed from mixed stages of G. molesta was sequenced through Illumina sequencing platform and a total of 536 mature miRNAs consisting of 291 conserved and 245 novel miRNAs were identified. Most of the conserved and novel miRNAs were detected with moderate abundance. The miRNAs in the same cluster normally showed correlated expressional profiles. A comparative analysis of the 79 conserved miRNA families within 31 arthropod species indicated that these miRNA families were more conserved among insects and within orders of closer phylogenetic relationships. The KEGG pathway analysis and network prediction of target genes indicated that the complex composed of miRNAs, clock genes and developmental regulation genes may play vital roles to regulate the developmental circadian rhythm of G. molesta. Furthermore, based on the sRNA library of G. molesta, suitable reference genes were selected and validated for study of miRNA transcriptional profile in G. molesta under two biotic and six abiotic experimental conditions. This study systematically documented the miRNA profile in G. molesta, which could lay a foundation for further understanding of the regulatory roles of miRNAs in the development and metabolism in this pest and might also suggest clues to the development of genetic-based techniques for agricultural pest control.
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Affiliation(s)
- Xiu Wang
- Department of Entomology, China Agricultural University, Beijing, China
| | - Yisong Li
- Department of Entomology, China Agricultural University, Beijing, China
- Department of Plant Protection, Shihezi University, Shihezi, China
| | - Jing Zhang
- Department of Entomology, China Agricultural University, Beijing, China
| | - Qingwen Zhang
- Department of Entomology, China Agricultural University, Beijing, China
| | - Xiaoxia Liu
- Department of Entomology, China Agricultural University, Beijing, China
- * E-mail: (ZL); (XXL)
| | - Zhen Li
- Department of Entomology, China Agricultural University, Beijing, China
- * E-mail: (ZL); (XXL)
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17
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Chen L, Jin Y, Wang L, Sun F, Yang X, Shi M, Zhan C, Shi Y, Wang Q. Identification of reference genes and miRNAs for qRT-PCR in human esophageal squamous cell carcinoma. Med Oncol 2016; 34:2. [PMID: 27889881 DOI: 10.1007/s12032-016-0860-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2016] [Accepted: 11/22/2016] [Indexed: 02/06/2023]
Abstract
It is important to select an appropriate reference gene and miRNA when using quantitative real-time polymerase chain reaction (qRT-PCR) to analyze gene and miRNA expression. However, many commonly used reference genes and miRNAs are not stably expressed and therefore not suitable for normalization or quantification of qRT-PCR data. This study aims to identify appropriate reference genes and miRNAs for use in human esophageal squamous carcinoma qRT-PCR analysis. Using data provided by The Cancer Genome Atlas, we identified DDX5, LAPTM4A, P4HB, RHOA, miR-28-5p, miR-34a-5p, and miR-186-5p as candidate reference genes and miRNAs. We used qRT-PCR to verify the expression levels of these candidates and another seven commonly used reference genes and miRNAs. A set of 50 paired human normal esophageal tissues and squamous cell carcinoma samples were used in the analysis. We then used geNorm and NormFinder to analyze the results. DDX5, LAPTM4A, RHOA, ACTB, RNU48, miR-28-5p, miR-34a-5p, and miR-186-5p were stably expressed, indicating they are suitable for used as references in qRT-PCR analysis of esophageal squamous cell carcinoma. However, expression levels of 18s rRNA, GAPDH, P4HB, 5s rRNA, U6, and RNU6B varied greatly between esophageal normal and squamous cell carcinoma samples, indicating that they are not suitable for use as references in the qRT-PCR analysis of esophageal squamous cell carcinoma.
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Affiliation(s)
- Li Chen
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, 20032, China
| | - Yulin Jin
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, 20032, China
| | - Lin Wang
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, 20032, China
| | - Fenghao Sun
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, 20032, China
| | - Xiaodong Yang
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, 20032, China
| | - Mengkun Shi
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, 20032, China
| | - Cheng Zhan
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, 20032, China.
| | - Yu Shi
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, 20032, China.
| | - Qun Wang
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, 20032, China
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18
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Wang J, Zhu Y, Jin F, Tang L, He Z, He Z. Differential expression of circulating microRNAs in blood and haematoma samples from patients with intracerebral haemorrhage. J Int Med Res 2016; 44:419-32. [PMID: 27020596 PMCID: PMC5536709 DOI: 10.1177/0300060516630852] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Accepted: 01/14/2016] [Indexed: 12/19/2022] Open
Abstract
Objective To measure the differential expression of microRNAs (miRNAs) in peripheral blood samples from patients with intracerebral haemorrhage (ICH) and to measure the levels of hsa-miR-21-5p in peripheral blood and haematoma samples from patients with ICH. Methods This case–control study enrolled individuals with ICH in the putamen treated by craniotomy and age- and sex-matched healthy control subjects. Serum miRNA expression profiles were determined in the patient and control groups using miRNA polymerase chain reaction (PCR) arrays. The ICH-related miRNA hsa-miR-21-5p was selected and its differential expression was assessed in peripheral blood and haematoma specimens from patients with ICH compared with peripheral blood samples controls using real-time PCR. Results Seven patients and five control subjects were included in the miRNA expression profile analysis; and 31 patients and 22 control subjects provided samples for the real-time PCR of hsa-miR-21-5p expression. A total of 59 miRNAs were significantly downregulated in patients with ICH. Relative hsa-miR-21-5p levels of 0.43 and 0.31 for peripheral blood and haematoma samples, respectively, were obtained in the patient group compared with the control subjects. Conclusion Hsa-miR-21-5p levels were significantly reduced in both peripheral blood and haematoma samples in patients with ICH.
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Affiliation(s)
- Jialu Wang
- Department of Neurology, First Affiliated Hospital of China Medical University, Shenyang, Liaoning Province, China
| | - Ying Zhu
- Department of Neurology, First Affiliated Hospital of China Medical University, Shenyang, Liaoning Province, China
| | - Feng Jin
- Department of Neurology, First Affiliated Hospital of China Medical University, Shenyang, Liaoning Province, China
| | - Ling Tang
- Department of Neurology, First Affiliated Hospital of China Medical University, Shenyang, Liaoning Province, China
| | - Zhenwei He
- Department of Neurology, First Affiliated Hospital of China Medical University, Shenyang, Liaoning Province, China
| | - Zhiyi He
- Department of Neurology, First Affiliated Hospital of China Medical University, Shenyang, Liaoning Province, China
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