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基于 RNA 测序的总 RNA 分析;致癌 miR-191 被鉴定为乳腺癌的新型生物标志物。

RNA Sequencing-Based Total RNA Profiling; The Oncogenic MiR-191 Identification as a Novel Biomarker for Breast Cancer.

机构信息

Biology Department, Education College, Salahaddin University-Erbil, Kurdistan Region-Iraq.

出版信息

Cell Mol Biol (Noisy-le-grand). 2022 May 22;68(1):177-191. doi: 10.14715/cmb/2022.68.1.22.

Abstract

This study aims to screen the differential expression of total RNA transcripts in formalin-fixed paraffin-embedded tissues (FFPETs) in breast cancer (BRCA) and normal adjacent tissues (NATs) and identify miR-191 as a new biomarker for early diagnosing BRCA. Differentially expressed genes (DEGs) by MACE-Seq and differentially expressed ncRNAs (DEncRNAs) by the TrueQuant technique were examined in this study. The miR-191 expression level was measured by Real Time-qPCR. An average of 4,739 coding genes from 25,713 significantly down-regulated genes was identified, whereas 3,954 coding genes were significantly up-regulated in the BRCA against NAT. An average of 1450 ncRNAs, including up-regulated= 679 and down-regulated= 780, were differentially expressed in 7 paired samples of BRCA and NAT. Among the ncRNAs, 227 microRNAs, including unchanged= 152, down=53, and up=22, were differentially expressed. MiR-191 was one of the 22 significant up-regulation, with p=0.0001. RT-qPCR results confirmed that miR-191, p=0.003, was significantly over-expressed in 120 paired samples of BRCA and NAT. Furthermore, NextSeq 500 revealed that a single nucleotide polymorphism (C>T) newly occurred in the mature sequence of miR-191-5p seed region in BRCA samples. However, the putative target genes regulated by the miR-191-5p were recognized by the above ten computational programs for the prediction. MACE-Seq outcomes showed that the genes of CDK6(P=0.0001), DAPK1(P=0.02), MTC7(P=0.04), SETD1B(P=0.005), CALN1(P=0.01), and TMOD2(P=0.001) were significantly over-expressed in the BRCA against the NATs. The expression level of the targets was adversely related to the miR-191-5p.

摘要

本研究旨在筛选福尔马林固定石蜡包埋组织(FFPET)中乳腺癌(BRCA)和正常相邻组织(NAT)中总 RNA 转录本的差异表达,并鉴定 miR-191 作为早期诊断 BRCA 的新生物标志物。本研究通过 MACE-Seq 检测差异表达基因(DEGs),通过 TrueQuant 技术检测差异表达 ncRNA(DEncRNAs)。通过 Real Time-qPCR 测量 miR-191 的表达水平。在 BRCA 与 NAT 中,分别鉴定出平均 4739 个显著下调基因和 3954 个显著上调基因。在 7 对 BRCA 和 NAT 的样本中,平均有 1450 个 ncRNA 表达差异,其中上调=679,下调=780。在 ncRNAs 中,有 227 个 microRNAs 表达差异,其中不变=152,下调=53,上调=22。miR-191 是 22 个显著上调 microRNAs 之一,p=0.0001。RT-qPCR 结果证实,miR-191 在 120 对 BRCA 和 NAT 的样本中表达显著上调,p=0.003。此外,NextSeq 500 显示,BRCA 样本中 miR-191-5p 成熟序列种子区新发生单核苷酸多态性(C>T)。然而,通过上述十种计算程序预测,miR-191-5p 调控的靶基因被识别。MACE-Seq 结果显示,BRCA 中 CDK6(P=0.0001)、DAPK1(P=0.02)、MTC7(P=0.04)、SETD1B(P=0.005)、CALN1(P=0.01)和 TMOD2(P=0.001)的基因表达显著上调。靶基因的表达水平与 miR-191-5p 呈负相关。

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