MicroRNA expression profile of gastrointestinal stromal tumors is distinguished by 14q loss and anatomic site

Choi, Hee-Jung,Lee, Hanna,Kim, Hyunki,Kwon, Ji Eun,Kang, Hyun Ju,You, Kwon Tae,Rhee, Hwanseok,Noh, Sung Hoon,Paik, Young-Ki,Hyung, Woo Jin,Kim, Hoguen Wiley Subscription Services, Inc., A Wiley Company 2010 International journal of cancer: Journal internati Vol.126 No.7

<P>MicroRNAs are known to regulate gene expression. Although unique microRNA expression profiles have been reported in several tumors, little is known about microRNA expression profiles in GISTs. To evaluate the relationship between microRNA expression and clinicopathologic findings of GISTs, we analyzed the microRNA expression profiles of GISTs. We used fresh frozen tissues from 20 GISTs and analyzed KIT and PDGFRA mutations and chromosomal loss status. MicroRNA expression was analyzed using a microRNA chip containing 470 microRNAs. Using unsupervised hierarchical clustering analysis, we found four distinct microRNA expression patterns in our 20 GISTs. Six GISTs that did not have 14q loss formed a separate cluster. In the 14 GISTs with 14q loss, 5 small bowel GISTs formed a separate cluster and the remaining 9 GISTs could be divided into two groups according to frequent chromosomal losses and tumor risk. We found 73 microRNAs that were significantly down-regulated in the GISTs with 14q loss; 38 of these microRNAs are encoded on 14q. We also found many microRNAs that were down-regulated in small bowel and high-risk group GISTs. Most of the microRNAs down-regulated in the high-risk group and small bowel GISTs are known to be involved in tumor progression, specifically by stimulating mitogen-activated protein kinase (MAPK) and the cell cycle. The microRNA expression patterns of GISTs are closely related to the status of 14q loss, anatomic site, and tumor risk. These findings suggest that microRNA expression patterns can differentiate several subsets of GISTs.</P>

췌관내 유두상 점액종에서의 마이크로 RNA 발현 양상

박윤경 ( Yun Gyoung Park ),이광혁 ( Kwang Hyuck Lee ),이종균 ( Jong Kyun Lee ),이규택 ( Kyu Taek Lee ),최동욱 ( Dong Wook Choi ),최성호 ( Seong Ho Choi ),허진석 ( Jin Seok Heo ),장기택 ( Kee Taek Jang ),이은미 ( Eun Mi Lee ),김정 대한소화기학회 2011 대한소화기학회지 Vol.58 No.4

Background/Aims: Intraductal papillary mucinous neoplasms (IPMN) are precursor lesions of fatal pancreatic cancer. Physiological function of microRNA is to regulate the stability and translation of mRNA. The aberrant microRNA expression is commonly observed in many cancers. The aim of this study was to analyze the expression pattern of microRNA in IPMN and evaluate the role of the microRNA. Methods: Using two paraffin-embedded IPMN tissues, microRNA expression of normal tissue, IPMN adenoma and carcinoma were compared by cDNA-mediated annealing, selection, extension and ligation microarray assay. Using real time PCR, expression levels of aberrantly up-regulated microRNAs were assessed in another 20 IPMNs, four pancreatic cancer cell lines (Panc1, MiaPaCa-2, XPA-3, BxPC-3) and immortalized pancreatic ductal cell line (HPNE). Effect of suppressing highly over-expressed two microRNAs in pancreatic cancer cell lines with anti-microRNA inhibitors were evaluated using CCK-8 assay. Results: Among aberrantly expressed 122 microRNAs in IPMN, miR-552, miR-25*, miR-183, miR-1300, miR-196a, miR-182*, and miR-30c-1* were consistently increased more than 3-fold. On average, miR-196a and miR-183 increased 10,824 folds and 26,519 folds in four pancreatic cancer cell lines compared with HPNE. These two microRNAs were also over-expressed in 20 IPMNs compared with HPNE. After applying anti-miRNA inhibitors, cell survival of four pancreatic cancer cell lines decreased by 24.5% with anti-miR-196a and by 14.2% with anti-miR-183 on average. Conclusions: Aberrant expression of 122 microRNAs was observed in IPMN. Two microRNAs, miR-196a and miR-183-increased in IPMN and pancreatic cancer cell lines compared with immortalized dancreatic ductal cell line. The inhibitions of these microRNAs repressed cell proliferation of pancreatic cancer cell lines. (Korean J Gastroenterol 2011;58:190-200)

Identification of Loop Nucleotide Polymorphisms Affecting MicroRNA Processing and Function

Xiaoxing Xiong,Shengmei Zhu,Xianhui Kang,Yueying Zheng,Sibiao Yue 한국분자세포생물학회 2013 Molecules and cells Vol.36 No.6

MicroRNAs are short 21-22 nucleotide single strand RNAs that are involved in post-transcriptional regulation of gene expression. Most microRNAs are first transcribed as long primary microRNAs and then undergo a two step-wise sequential processing to yield single-stranded mature microRNAs. It has been suggested that the loop region of primary microRNAs plays an important role in regulating microRNA biogenesis and target recognition. However, despite the fact that several single nucleotide polymorphisms have been identified in mature microRNA sequences and are related to human diseases, it remains unclear whether and how the single nucleotide polymorphisms in the loop regions of primary microRNAs would affect the biogenesis and function of microRNAs. Herein, we provide evidence that primary microRNAs loop nucleo-tides control the accuracy and efficiency of microRNA processing. Accordingly, we identified 32 single nucleotide polymorphisms in the loop regions of human primary microRNAs using bioinformatics, and further validated three loss-of-function and one gain-of-function single nucleotide polymorphisms using dual-luciferase assays. Thus, these results reveal a critical regulatory role encoded in the loop nucleotides of primary microRNAs for microRNA processing and function.

Inhibition of microRNA-449a prevents IL-1β-induced cartilage destruction via SIRT1

Park, K.W.,Lee, K.M.,Yoon, D.S.,Park, K.H.,Choi, W.J.,Lee, J.W.,Kim, S.H. Published for the Society by Baillère Tinda 2016 Osteoarthritis and cartilage Vol.24 No.12

<P>Objective: SIRT1 has anti-inflammatory as well as protective effects in chondrocytes. The object of this study was to investigate whether microRNA-449a regulates expression of SIRT1, which inhibits expression of catabolic genes in IL-1 beta-induced cartilage destruction. Materials and methods: MicroRNA-449a expression was determined in OA chondrocytes and IL-1 beta induced chondrocytes by real-time PCR. MicroRNA-449a binding sites on the 3'-UTR of SIRT1 mRNA and binding site conservation were examined using microRNA target prediction tools. SIRT1-overexpressing or knockdown chondrocytes were transfected with microRNA-449a or anti-microRNA-449a mimic and stimulated by IL-1 beta. Expression of catabolic and anabolic genes was examined by real-time PCR and western blotting. Finally, positive effects of anti-microRNA-449a on expression of these genes were confirmed by western analysis of OA chondrocytes. Results: Expression of microRNA-449a was increased in OA chondrocytes and IL-1 beta-induced chondrocytes. MMP-13 expression was enhanced, whereas type II collagen and SIRT1 expression were decreased in IL-1 beta-induced chondrocytes. SIRT1 overexpression resulted in decreased expression of catabolic genes such as MMPs and ADAMTSs in response to IL-1 beta, but these effects were moderated by microRNA-449a. Suppression of microRNA-449a by anti-microRNA-449a inhibited expression of catabolic genes despite IL-1 beta stimulation, but these effects were abolished in SIRT1 knockdown chondrocytes. Furthermore, expression of catabolic genes was decreased and expression of type II collagen as well as SIRT1 was restored by anti-microRNA-449a in OA chondrocytes as well as in IL-1 beta-induced chondrocytes. Conclusion: Silencing of microRNA-449a had a protective effect, inhibiting catabolic gene expression and restoring anabolic gene expression, by targeting SIRT1 in IL-1 beta-induced cartilage destruction. (C) 2016 Osteoarthritis Research Society International. Published by Elsevier Ltd. All rights reserved.</P>

Diagnostic performance of microRNA- 34a, let-7f and microRNA-31 in epithelial ovarian cancer prediction

Vivek Kumar,Sameer Gupta,Kachnar Varma,Amrita Chaurasia,Manisha Sachan 대한부인종양학회 2022 Journal of Gynecologic Oncology Vol.33 No.4

Objective: To correlate the genome-wide methylation signature of microRNA genes with dysregulated expression of selected candidate microRNA in tissue and serum samples of epithelial ovarian cancer (EOC) and control using quantitative reverse transcription polymerase chain reaction (qRT-PCR), and evaluation of EOC predictive value of candidate microRNA at an early stage. Methods: We performed Methylated DNA Immunoprecipitation coupled with NGS (MeDIP- NGS) sequencing of 6 EOC and 2 normal tissue samples of the ovary. Expression of selected microRNA from tissue (EOC=85, normal=30) and serum (EOC=50, normal=15) samples was evaluated using qRT-PCR. We conducted bioinformatics analysis to identify the candidate miRNA’s potential target and functional role. Results: MeDIP-NGS sequencing revealed hypermethylation of several microRNAsgene promoters. Three candidate microRNAs were selected (microRNA-34a, let-7f, and microRNA-31) from MeDIP-NGS data analysis based on log2FC and P-value. The relative expression level of microRNA-34a, let-7f, and microRNA-31 was found to be significantly reduced in early-stage EOC tissues and serum samples (p<0.0001). The receiver operating characteristic analysis of microRNA-34a, let-7f and miR-31 showed improved diagnostic value with area under curve(AUC) of 92.0 (p<0.0001), 87.9 (p<0.0001), and 85.6 (p<0.0001) and AUC of 82.7 (p<0.0001), 82.0 (p<0.0001), and 81.0 (p<0.0001) in stage III-IV and stage I-II EOC serum samples respectively. The integrated diagnostic performance of microRNA panel (microRNA-34a+let-7f+microRNA-31) in late-stage and early-stage serum samples was 95.5 and 96.9 respectively. Conclusion: Our data correlated hypermethylation-associated downregulation of microRNA in EOC. In addition, a combined microRNA panel from serum could predict the risk of EOC with greater AUC, sensitivity, and specificity.

Down-Regulation of microRNA-100 and Up-Regulation of microRNA-582 Are Associated with Vascular Invasion and Poor Prognosis in Hepatocellular Carcinoma

( Yongkeun Park ) 대한간학회 2018 춘·추계 학술대회 (KASL) Vol.2018 No.1

Aims: Although gross vascular invasion (VI) has prognostic value for patients with hepatocellular carcinoma (HCC) who have undergone hepatic resection, few studies have investigated the relationship between gross VI and the aberrant expression of microRNAs. This study identified microRNAs selectively expressed in HCC with gross VI and investigated their prognostic roles. Methods: Clinical data and microRNA expression profiles for 372 HCC patients were extracted from The Cancer Genome Atlas database. MicroRNAs that were differentially expressed in the patients with gross VI and those without VI were identified and investigated as potential prognostic factors for HCC. Results: MicroRNA-338 and microRNA-582 were upregulated more (log2 FC of 1.34 with FDR = 0.014 and log₂ FC of 1.09 with FDR = 0.015, respectively), and microRNA-100 and microRNA-99a were downregulated to a greater extent in gross VI group (log₂ FC of -1.45 with FDR < 0.001 and log₂ FC of -1.12 with FDR = 0.009, respectively). Receiver operating characteristic curve analysis showed the discriminatory power of these microRNAs in predicting MVI(figure). Multivariate survival analysis revealed that the types of surgery (HR 1.676, 95% CI 1.205-2.332, P=0.002), advanced TNM stage (HR 1.795, 95% CI 1.266-2.547, P=0.001) and under-expression of microRNA-100 (HR 1.511, 95% CI 1.041-2.194, P=0.029) were independently associated with tumor recurrence, and that the types of surgery, advanced TNM stage, under-expression of microRNA-100 and over-expression of microRNA-582 were independent risk factors for overall survival after hepatic resection for HCC (HR 1.844, 95% CI 1.110-3.065, P=0.018; HR 2.401, 95% CI 1.433-4.024, P<0.001; HR 2.652, 95% CI 1.519-4.629, P<0.001; HR 2.016, 95% CI 1.109-3.663, P=0.021, respectively). PLK1 was considered a target gene of microRNA-100 with strong evidence. Conclusions: Under-expression of microRNA-100 and over-expression of microRNA-582 were associated with gross VI and poor survival of patients after hepatic resection for HCC.

Exosome-derived microRNA-29c Induces Apoptosis of BIU-87 Cells by Down Regulating BCL-2 and MCL-1

Xu, Xiang-Dong,Wu, Xiao-Hou,Fan, Yan-Ru,Tan, Bing,Quan, Zhen,Luo, Chun-Li Asian Pacific Journal of Cancer Prevention 2014 Asian Pacific journal of cancer prevention Vol.15 No.8

Background: Aberrant expression of the microRNA-29 family is associated with tumorigenesis and cancer progression. As transport carriers, tumor-derived exosomes are released into the extracellular space and regulate multiple functions of target cells. Thus, we assessed the possibility that exosomes could transport microRNA-29c as a carrier and correlations between microRNA-29c and apoptosis of bladder cancer cells. Materials and Methods: A total of 28 cancer and adjacent tissues were examined by immunohistochemistry to detect BCL-2 and MCL-1 expression. Disease was Ta-T1 in 12 patients, T2-T4 in 16, grade 1 in 8, 2 in 8 and 3 in 12. The expression of microRNA-29c in cancer tissues was detected by quantitative reverse transcriptase PCR (QRT-PCR). An adenovirus containing microRNA-29c was used to infect the BIU-87 human bladder cancer cell line. MicroRNA-29c in exosomes was measured by QRT-PCR. After BIU-87 cells were induced by exosomes-derived microRNA-29c, QRT-PCR was used to detect the level of microRNA-29c. Apoptosis was examined by flow cytometry and BCL-2 and MCL-1 mRNA expressions were assessed by reverse transcription-polymerase chain reaction. Western blotting was used to determine the protein expression of BCL-2 and MCL-1. Results: The expressions of BCL-2 and MCL-1 protein were remarkably increased in bladder carcinoma (p<0.05), but was found mainly in the basal and suprabasal layers in adjacent tissues. The expression of microRNA-29c in cancer tissues was negatively correlated with the BCL-2 and MCL-1. The expression level of microRNA-29c in exosomes and BIU-87 cells from the experiment group was higher than that in control groups (p<0.05). Exosome-derived microRNA-29c induced apoptosis (p<0.01). Although only BCL-2 was reduced at the mRNA level, both BCL-2 and MCL-1 were reduced at the protein level. Conclusions: Human bladder cancer cells infected by microRNA-29c adenovirus can transport microRNA-29c via exosomes. Moreover, exosome-derived microRNA29c induces apoptosis in bladder cancer cells by down-regulating BCL-2 and MCL-1.

MicroRNA-21 Regulates the Invasion and Metastasis in Cholangiocarcinoma and May Be a Potential Biomarker for Cancer Prognosis

Huang, Qiang,Liu, Lei,Liu, Chen-Hai,You, Hao,Shao, Feng,Xie, Fang,Lin, Xian-Sheng,Hu, San-Yuan,Zhang, Chuan-Hai Asian Pacific Journal of Cancer Prevention 2013 Asian Pacific journal of cancer prevention Vol.14 No.2

Background: MicroRNAs are noncoding RNA molecules that posttranscriptionally regulate gene expression. The aim of this study was to determine the role of microRNA-21 in cholangiocarcinomas and its relationship to cholangiocarcinoma RBE cell capacity for invasion and metastasis. Methods: MicroRNA-21 expression was investigated in 41 cases of cholangiocarcinoma samples by in situ hybridization and real-time PCR. Influence on cholangiocarcinoma cell line invasion and metastasis was analyzed with microRNA-21 transfected cells. In addition, regulation of reversion-inducing-cysteine-rich protein with kazal motifs (RECK) by microRNA-21 was elucidated to identify mechanisms. Results: In situ hybridization and real-time quantitative PCR results for patients with lymph node metastasis or perineural invasion showed significantly high expression of microRNA-21 (P<0.05). There was a dramatic decrease in cholangiocarcinoma cell line invasion and metastasis ability after microRNA-21 knockdown (P<0.05). However, overexpression significantly increased invasion and metastasis (P<0.05). Real-time PCR and Western-blot analysis showed that microRNA-21 could potentially inhibit RECK expression in RBE cells. Survival analysis showed that patients with higher expression levels of microRNA-21 more often had a poor prognosis (P<0.05). Conclusions: MicroRNA-21 may play an important role in cholangiocarcinoma invasion and metastasis, suggesting that MicroRNA-21 should be further evaluated as a biomarker for predicting cholangiocarcinoma prognosis.

MicroRNA profiling of tacrolimus-stimulated Jurkat human T lympocytes

Ho Kyun Lee,Sang Young Chung,Soo Jin Na Choi 대한외과학회 2013 Annals of Surgical Treatment and Research(ASRT) Vol.85 No.4

Purpose: This study investigated the Jurkat T cell line expresses cytotoxicity when treated with different concentrations of FK506, and analyzed the expression pattern of microRNA when stimulated by FK506 using the microRNAs microarray, as well as the expression pattern of a gene that is related to the differentiation, activation and proliferation of T cells after being affected by the change of microRNAs. Methods: To investigate the effects of FK506 on microRNA expression, we purified total RNA of Jurkat cells treated with 20 μM FK506 for 72 hours and used to analyze microRNA profiling by using Agilent’s chip. Results: These results demonstrated that treatment with FK506 markedly induced the down-regulation of 20 microRNAs as well as the up-regulation of 20 microRNAs in a time-dependent manner. The genes that down-regulated by FK506 include let-7a*, miR-20a*, and miR-487a. Otherwise miR-202, miR-485-5p, and miR-518c* are gradually up-regulated in expression. Sanger Institute and DAVIDs bioinformatics indicated that microRNAs regulated the several transcriptomes including nuclear factor of activated T cell-related, T cell receptor/interleukin-2 signaling, and Ca<SUP>2+</SUP>-calmodulin-dependent phosphatase calcineurin pathways. Conclusion: As a result of treating FK506 to a Jurkat cell line and running the microRNA microarray, it was found that FK506 not only took part in the suppression of T cell proliferation/activation by inhibiting calcineurin in Jurkat apoptosis, but also affected the microRNAs that are involved in the regulation of various signal transduction pathways.

MicroRNA-21 inhibition attenuates airway inflammation and remodelling by modulating the transforming growth factor β-Smad7 pathway

( Jung Hur ),( Chin Kook Rhee ),( Sook Young Lee ),( Young Kyoon Kim ),( Ji Young Kang ) 대한내과학회 2021 The Korean Journal of Internal Medicine Vol.36 No.3

Background/Aims: Current asthma therapies remain unsatisfactory for controlling airway remodelling in asthma. MicroRNA-21 is a key player in asthma pathogenesis, but the molecular mechanisms underlying its effects on airway remodelling are not completely understood. We investigated the effects of inhibition of microRNA-21 on allergic airway inflammation and remodelling. Methods: Female BALB/c mice were divided into four groups: control, ovalbumin-sensitized and -challenged for 3 months, microRNA-negative control-treated ovalbumin-treated, and microRNA-21 inhibitor-treated ovalbumin-treated groups. Parameters related to airway remodelling, cytokine production, airway inflammation, and airway hyperresponsiveness were compared between groups. Human bronchial smooth muscle cells were used in a mechanism study. Results: In this asthma model, ovalbumin-sensitized and -challenged mice exhibited allergic airway inf lammation and airway remodelling. MicroRNA-21 inhibitor-treated mice had fewer inflammatory cells, lower T_H2 cytokine production, and suppressed parameters related to remodelling such as goblet cell hyperplasia, collagen deposition, hydroxyproline content, and expression of smooth muscle actin. Inhibition of microRNA-21 decreased transforming growth factor β1 expression and induced Smad7 expression in lung tissue. In human bronchial smooth muscle cells stimulated with transforming growth factor β1, microRNA-21 inhibition upregulated Smad7 expression and decreased markers of airway remodelling. Conclusions: Inhibition of microRNA-21 had both anti-inflammatory and anti-remodelling effects in this model of ovalbumin-induced chronic asthma. Our data suggest that the microRNA-21-transforming growth factor β1-Smad7 axis modulates the pathogenesis of ovalbumin-induced chronic asthma and in human bronchial smooth muscle cells. MicroRNA-21 inhibitors may be a novel therapeutic target in patients with allergic asthma, especially those with airway remodelling.