Investigating microRNA-Target Interaction-Supported Tissues in Human Cancer Tissues Based on miRNA and Target Gene Expression Profiling

Recent studies have revealed that a small non-coding RNA, microRNA (miRNA) down-regulates its mRNA targets. This effect is regarded as an important role in various biological processes. Many studies have been devoted to predicting miRNA-target interactions. These studies indicate that the interactions may only be functional in some specific tissues, which depend on the characteristics of an miRNA. No systematic methods have been established in the literature to investigate the correlation between miRNA-target interactions and tissue specificity through microarray data. In this study, we propose a method to investigate miRNA-target interaction-supported tissues, which is based on experimentally validated miRNA-target interactions. The tissue specificity results by our method are in accordance with the experimental results in the literature.

Availability and Implementation

Our analysis results are available at http://tsmti.mbc.nctu.edu.tw/ and http://www.stat.nctu.edu.tw/hwang/tsmti.html.     

Age-Correlated Gene Expression in Normal and Neurodegenerative Human Brain Tissues

Background

Human brain aging has received special attention in part because of the elevated risks of neurodegenerative disorders such as Alzheimer''s disease in seniors. Recent technological advances enable us to investigate whether similar mechanisms underlie aging and neurodegeneration, by quantifying the similarities and differences in their genome-wide gene expression profiles.

Principal Findings

We have developed a computational method for assessing an individual''s “physiological brain age” by comparing global mRNA expression datasets across a range of normal human brain samples. Application of this method to brains samples from select regions in two diseases – Alzheimer''s disease (AD, superior frontal gyrus), frontotemporal lobar degeneration (FTLD, in rostral aspect of frontal cortex ∼BA10) – showed that while control cohorts exhibited no significant difference between physiological and chronological ages, FTLD and AD exhibited prematurely aged expression profiles.

Conclusions

This study establishes a quantitative scale for measuring premature aging in neurodegenerative disease cohorts, and it identifies specific physiological mechanisms common to aging and some forms of neurodegeneration. In addition, accelerated expression profiles associated with AD and FTLD suggest some common mechanisms underlying the risk of developing these diseases.     

Staufen基因在结直肠癌组织中的表达

为研究甲基化差异相关基因Staufen在结直肠癌不同组织中的表达情况,采用RT-PCR和免疫组织化学等方法在结直肠癌病人中检测Staufen基因在腺癌、癌旁粘膜和相应远端切缘正常组织中的表达。研究发现,在mRNA水平上,远端切缘正常组织中Staufen基因的表达水平显著高于癌旁粘膜和腺癌（P<0.05）;从正常组织、癌旁粘膜到腺癌,Staufen基因的表达有降低的趋势;未发现性别、年龄、肿瘤部位（结肠/直肠）、分化程度、淋巴结转移等临床病理因素与Staufen基因的表达有关（P均>0.05）。正常组织与腺癌组织的Staufen蛋白的表达水平显著高于癌旁粘膜（P<0.05）,而正常组织与腺癌组织之间未发现有统计学差别（P>0.05）。结果表明,Staufen基因在癌旁粘膜和肿瘤中有低表达的趋势,该基因可能在结直肠癌的发生、发展中起作用。     

颊粘膜癌与舌癌差异基因表达的对比分析

目的:研究颊粘膜癌(Buccal Mucosa Cancer,BMC)与舌癌(Tongue Cancer,TC)的基因差异表达,探讨BMC与TC发生发展的基因学基础。方法:应用cDNA芯片技术对5例BMC和5例TC组织mRNA检测,通过芯片杂交、生物信息学处理,找出两者间差异表达基因。结果:BioStarH-40芯片发现差异表达基因503条,差异表达基因占12.9%,其中表达增强274条(显著增强69条),表达降低229条(显著降低54条)。结论:MBC与TC基因表达比较,差异有统计学意义,这些差异可能在两类肿瘤不同的生物学行为中起重要作用。     

应用组织芯片技术研究Survivin基因蛋白在前列腺肿瘤组织中的表达及其意义

目的:应用组织芯片技术分析Survivin基因蛋白在人类前列腺癌组织、前列腺正常组织及前列腺良性痛变组织中的表达情况.方法:采用兔抗人survivin单克隆抗体的免疫组织化学ABC法,研究Survivin在不同前列腺组织的表达,并分析Survivin在不同前列腺组织中的表达差异.结果:免疫组化结果显示,前列腺癌组织与前列腺良性病变组织及正常前列腺组织中Survivin的表达相比呈显著性差异(P<0.05).结论:Survivin在前列腺癌组织中呈高表达,提示其可能对前列腺癌的发生或发展有重要作用.     

Cell-Type-Specific Gene Expression Profiling in Adult Mouse Brain Reveals Normal and Disease-State Signatures

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基因表达谱微阵列网络数据库在肿瘤研究中的应用

基因表达谱微阵列数据库是一类可提供存储、查询、下载分析的在线网络数据库,在肿瘤相关领域的研究中提供了大量的数据来源。由于微阵列分析对于无生物/医学信息学专业背景的研究人员仍然有较多困难,致使该数据库的使用尚未普及。本文从数据查询、下载分析和使用方法等方面对常用基因表达谱微阵列数据库进行概述,并对现阶段基因表达微阵列数据库的应用策略进行总结,旨在帮助该领域研究的初学工作者了解数据库的基本知识并推动其在科研工作中的应用。     

Mammary Fat of Breast Cancer: Gene Expression Profiling and Functional Characterization

Mammary fat is the main composition of breast, and is the most probable candidate to affect tumor behavior because the fat produces hormones, growth factors and adipokines, a heterogeneous group of signaling molecules. Gene expression profiling and functional characterization of mammary fat in Chinese women has not been reported. Thus, we collected the mammary fat tissues adjacent to breast tumors from 60 subjects, among which 30 subjects had breast cancer and 30 had benign lesions. We isolated and cultured the stromal vascular cell fraction from mammary fat. The expression of genes related to adipose function (including adipogenesis and secretion) was detected at both the tissue and the cellular level. We also studied mammary fat browning. The results indicated that fat tissue close to malignant and benign lesions exhibited distinctive gene expression profiles and functional characteristics. Although the mammary fat of breast tumors atrophied, it secreted tumor growth stimulatory factors. Browning of mammary fat was observed and browning activity of fat close to malignant breast tumors was greater than that close to benign lesions. Understanding the diversity between these two fat depots may possibly help us improve our understanding of breast cancer pathogenesis and find the key to unlock new anticancer therapies.     

人鼻咽与鼻咽癌及肺癌基因表达谱差异的研究

研究鼻咽癌、肺癌与正常鼻咽组织基因表达谱差异及筛选鼻咽癌相关基因,采用α- ³²P逆转录标记组织总RNA,将cDNA探针与有5 184个基因或表达序列标签EST(expression sequence tag)的高密度cDNA微阵列GF200杂交,软件分析表达谱差异.结果发现三者均呈低表达为主的表达谱,密度值在200以上的基因及EST在鼻咽癌有110个,肺癌134个而鼻咽组织有158个;5个EST在鼻咽高表达但鼻咽癌低表达,3个EST在鼻咽癌高表达但正常鼻咽低表达.结果表明鼻咽癌与正常鼻咽及肺癌组织存在差异表达基因,可能还有新基因在鼻咽癌发生中起作用;采用高密度cDNA微阵列是一种筛选差异表达基因的快速有效方法.     

Spexin Expression in Normal Rat Tissues

Spexin is a highly conserved peptide which was recently identified through the bioinformatics approach. Immunohistochemical analysis of its expression has not yet been performed. Thus, in this study, we examined spexin location in a wide range of rat organs by both RT-PCR and IHC. RT-PCR identified spexin mRNA in all tissues examined. Spexin immunoreaction was mainly cytoplasmic. Spexin was immunohistochemically detected, although with different staining intensities, in epithelia and glands of skin and respiratory, digestive, urinary, and reproductive systems. Smooth muscle cells showed weak immunostaining, and connective tissue was negative. In the central nervous system, neuronal groups showed different intensities for reaction product. Immunoreaction was also found in ganglionic cells of both trigeminal and superior cervical ganglia and in photoreceptor, inner nuclear, and ganglionic layers of the retina. In the endocrine system, spexin immunoreaction was detected in the hypothalamic paraventricular and supraoptic nuclei; adenohypophysis, thyroid, and parathyroid glands; adrenal cortex and medulla (mainly ganglionic cells); Leydig cells; and thecal, luteal, and interstitial cells of the ovary. Because of its widespread expression, spexin is probably involved in many different physiological functions; in particular, location of spexin in neurons and endocrine cells suggests its roles as neurotransmitter/neuromodulator and endocrine factor. (J Histochem Cytochem 58:825–837, 2010)     

RhoGDI2 在结直肠癌组织中的表达及其与临床侵袭转移的关系

目的:研究鸟嘌呤核苷酸解离抑制因子2(Rho GDI2)在结直肠癌(CRC)组织中的表达及其与临床侵袭转移的关系。方法:收集本院于2015年1月至2015年12月收治的80例CRC患者手术切除的原发灶组织和正常癌旁组织。采用免疫组化法检测各组织标本中Rho GDI2的表达情况,并分析其表达量与临床病理特征的相关性。结果:(1)Rho GDI2主要表达于CRC癌细胞胞浆中,在肿瘤原发灶和正常癌旁组织中的阳性表达率分别为26.25%和0.00%,差异具有统计学意义(P0.05);(2)肿瘤原发灶中Rho GDI2的阳性表达率与患者的性别、年龄、肿瘤位置、大小、数量、组织学分级、原发灶分期、血管浸润、神经浸润间均不存在相关关系(P0.05),而与淋巴结转移及远端转移有关(P0.05)。结论:Rho GDI2在CRC肿瘤原发灶中呈阳性表达,且其高表达可促进CRC的侵袭转移,可作为CRC治疗的作用靶点。     

F10蛋白及mRNA在部分正常组织及癌组织中的表达

目的:了解F10基因在部分正常组织及肿瘤组织中的表达情况。方法:利用原位杂交和免疫组化方法对F10在部分正常组织和肿瘤组织中的mRNA和蛋白表达情况进行分析。结果:F10基因不仅在腺癌组织中表达呈阳性,在鳞癌组织中表现出较腺癌更强的强阳性,并且在正常组织中也有一定的表达。结论:F10是一个在多种组织普遍表达的细胞内蛋白,其功能可能与物质转运相关。     

抑制Hedgehog信号通路改变结肠癌细胞基因表达谱

Hedgehog（Hh）信号通路在机体发育和肿瘤发生中发挥着重要作用。在该研究中,Western blot检测三株结肠癌细胞Hedgehog信号通路组分的表达,结果表明三株结肠癌细胞中HT-29细胞Hedgehog信号通路组分较完整。采用MTT和BrdU法检测Hedgehog信号通路膜受体Smo特异性抑制剂环杷明和末端转录因子Gli1/2的特异性抑制剂GANT61对HT-29细胞的影响,提示这两种抑制剂均显著抑制HT-29细胞生存率和细胞增殖率,且GANT61比环杷明更敏感。表达谱芯片检测阻断Hedgehog信号通路后HT-29细胞基因谱的变化,结合生物信息学分析,揭示HT-29细胞经环杷明和GANT61处理后基因表达呈现抑制特征,其差异基因表达主要以下调为主,其中环杷明主要影响细胞内源刺激等,而GANT61主要影响代谢和类固醇合成,并与MAPK信号通路有关联,两者均能影响细胞免疫及凋亡相关通路。这些结果提示,Hh信号通路有可能作为结肠癌的治疗靶点。     

Evaluation of Radiotherapy on miR-374 Gene Expression in Colorectal Cancer Patient Blood Samples

Background:Current cancer treatments include surgery, radiotherapy, chemotherapy, and immunotherapy. Despite these treatments, a main issue in cancer treatment is early detection. microRNAs (miRNAs) can be used as markers to diagnose and treat cancers. This study investigated the effect of radiotherapy on miR-374 expression, and APC and GSK-3β, two of its target genes, in the WNT pathway, in peripheral blood samples from radiotherapy-treated colorectal cancer (CRC) patients. Methods:Peripheral blood was collected from 25 patients before and after radiotherapy. RNA was extracted from the blood and cDNA synthesized. miR-374, APC, and GSK-3β expression was determined by real-time polymerase chain reaction (RT-PCR) and the amplicons were sequenced. Finally, the data were statistically evaluated.Results:Quantitative RT-PCR revealed significant down-regulation of miR-374 (0.63-fold) and up-regulation of APC (1.12-fold) and GSK-3β (1.22-fold) in CRC patients after five weeks of radiotherapy. Sequencing of PCR-produced amplicons confirmed the conservation of mature and precursor sequences encoding miR-374. miR-374 expression changed with time after radiotherapy treatment and related tumor grading. Increased age and tumor grade positively correlated with decreased miR-374 expression.Conclusion:miR-374 expression, and that of its two target genes, APC and GSK-3β, changed after radiotherapy. These genes can likely be used as diagnostic radiotherapy markers in CRC.Key Words: Biomarker, Colorectal cancer, Mir-374, Radiotherapy