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Cancer Biology & Medicine 2018年第S1期15卷 16-16页

作者： Xiwen Liao Tao Peng Department of Hepatobiliary Surgery The First Affiliated Hospital of Guangxi Medical UniversityNanningChina

Objective:The aim of the current study was to identify the prognostic long non-coding RNA(lncRNA)biomarkers to predict the survival of patients with hepatocellular carcinoma(HCC)using The Cancer Genome Atlas(TCGA)data... 详细信息

关键词： Identification potential non-coding

Reconstructing the phytogeny of new world monkeys(platyrrhini):evidence from multiple non-coding loci

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Current Zoology 2019年第5期65卷 579-588页

作者： Xiaoping WANG Burton K.LIM Nelson TING Jingyang HU Yunpeng LIANG Christian ROOS Li YU State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan Yunnan UniversityKunmingChina School of Life Sciences Yunnan UniversityKunmingChina epartm ent of Natural History Royal Ontario MuseumTorontoONCanada Department of Anthropology and Institute of Ecology and Evolution University of OregonEugeneOregonUSA State Key Laboratory of Genetic Resources and Evolution Kunming Institute of ZoologyChinese Academy of SciencesKunmingChina Kunming College of Life Science University of Chinese Academy of SciencesKunmingChina Gene Bank of Primates and Primate Genetics Laboratory German Primate CenterLeibniz Institute for Primate ResearchKellnerwegGottingenGermany

Among mammalian phylogenies,those characterized by rapid radiations are particularly *** New World monkeys(NWMs,Platyrrhini)comprise 3 families and 7 subfamilies,which radiated within a relatively short time ***,their phylogenetic relationships are still largely *** the present study,56 nuclear non-coding loci,including 33 introns(INs)and 23 intergenic regions(IGs),from 20 NWM individuals representing 18 species were used to investigate phylogenetic relationships among families and *** the 56 loci,43 have not been used in previous NWM *** applied concatenation and coalescence tree-inference methods,and a recently proposed question-specific approach to address NWM *** results indicate incongruence between concatenation and coalescence methods for the IN and IG ***,a consensus was reached with a single tree topology from all analyses of combined INs and IGs as well as all analyses of question-specific loci using both concatenation and coalescence methods,albeit with varying degrees of statistical *** detail,our results indicated the sister-group relationships between the families Atelidae and Pitheciidae,and between the subfamilies Aotinae and Callithrichinae among *** study provides insights into the disputed phylogenetic relationships among NWM families and subfamilies from the perspective of multiple non-coding loci and various tree-inference ***,the present phylogenetic framework needs further evaluation by adding more independent sequence data and a deeper taxonomic ***,our work has important implications for phylogenetic studies dealing with rapid radiations.

关键词： coalescence concatenation non-coding nuclear genes primates phylogenetics

Long non-coding RNAs era in liver cancer

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World Journal of Hepatology 2015年第16期7卷 1971-1973页

作者： Francesca Guerrieri Istituto Italiano di Tecnologia (CLNS IIT Sapienza)

Hepatocellular carcinoma(HCC) is one of the most common malignancies leading to high mortality rates in the general population and the sixth most common cancer worldwide. HCC is characterized by deregulation of multiple genes and signalling pathways. These genetic effects can involve both protein coding genes as well as non-coding RNA genes. Long noncoding RNAs(lnc RNAs) are transcripts longer than 200 nt, constituting a subpopulation of nc RNAs. Their biological effects are not well understood comparedto small non-coding RNA(micro RNAs), but they have been recently recognized to exert a crucial role in the regulation of gene expression and modulation of signalling pathways. Notably, several studies indicated that lnc RNAs contribute to the pathogenesis and progression of HCC. Investigating the molecular mechanisms underlying lnc RNAs expression opens potential applications in diagnosis and treatment of liver disease. This editorial provides three examples(MALAT-1 metastasis associated lung adenocarcinoma transcript, HULC highly upregulated in liver cancer and HOTAIR HOX transcript antisense intergenic RNA) of well-known lnc RNAs upregulated in HCC, whose mechanisms of action are known, and for which therapeutic applications are delineated. Targeting of lnc RNAs using several approaches(siR NA-mediated silencing or changing their secondary structure) offers new possibility to treat HCC.

关键词： Hepatocellular carcinoma Epigenetics Sequencing Liver Long non-coding RNAs

Discovery and characterization of the first non-coding RNA that regulates gene expression,micF RNA:A historical perspective

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World Journal of Biological Chemistry 2015年第4期6卷 272-280页

作者： Nicholas Delihas Department of Molecular Genetics and Microbiology School of MedicineStony Brook University

The first evidence that RNA can function as a regulator of gene expression came from experiments with prokaryotes in the 1980 s. It was shown that Escherichia coli micF isan independent gene,has its own promoter,and encodes a small non-coding RNA that base pairs with and inhibits translation of a target messenger RNA in response to environmental stress conditions. The mic F RNA was isolated,sequenced and shown to be a primary transcript. In vitro experiments showed binding to the target ompF mR NA. Secondary structure probing revealed an imperfect micF RNA/ompF RNA duplex interaction and the presence of a non-canonical base pair. Several transcription factors,including OmpR,regulate micF transcription in response to environmental factors. micF has also been found in other bacterial species,however,recently Gerhart Wagner and J?rg Vogel showed pleiotropic effects and found micF inhibits expression of multiple target mR NAs; importantly,one is the global regulatory gene lrp. In addition,micF RNA was found to interact with its targets in different ways; it either inhibits ribosome binding or induces degradation of the message. Thus the concept and initial experimental evidence that RNA can regulate gene expression was born with prokaryotes.

关键词： non-coding RNAs RNA/RNA interaction Regulation of

Conserved sequences identify the closest living relatives of primates

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Zoological Research 2019年第6期40卷 532-540页

作者： Mei-Ling Zhang Ming-Li Li Adeola Oluwakemi Ayoola Robert W. Murphy Dong-Dong Wu Yong Shao Department of Acute Infectious Diseases Control and Prevention Yunnan Provincial Centre for Disease Control and PreventionKunming Yunnan 650022China State Key Laboratory of Genetic Resources and Evolution Kunming Institute of ZoologyChinese Academy of SciencesKunming Yunnan 650223China Centre for Biodiversity and Conservation Biology Royal Ontario MuseumToronto M5S 2C6Canada Kunming College of Life Science University of the Chinese Academy of SciencesKunming Yunnan 650223China

Elucidating the closest living relatives of extant primates is essential for fully understanding important biological processes related to the genomic and phenotypic evolution of primates, especially of humans. However, the phylogenetic placement of these primate relatives remains controversial, with three primary hypotheses currently espoused based on morphological and molecular evidence. In the present study, we used two algorithms to analyze differently partitioned genomic datasets consisting of 45.4 Mb of conserved non-coding elements and 393 kb of concatenated coding sequences to test these hypotheses. We assessed different genomic histories and compared with other molecular studies found solid support for colugos being the closest living relatives of primates. Our phylogeny showed Cercopithecinae to have low levels of nucleotide divergence, especially for Papionini, and gibbons to have a high rate of divergence. The MCMCtree comprehensively updated divergence dates of early evolution of Primatomorpha and Primates.

关键词： Phylogeny Colugos Primates Conserved non-coding elements Divergence time

Mitochondrion-processed TERC regulates senescence without affecting telomerase activities

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Protein & Cell 2019年第9期10卷 631-648页

作者： Qian Zheng Peipei Liu Ge Gao Jiapei Yuan Pengfeng Wang Jinliang Huang Leiming Xie Xinping Lu Fan Di Tanjun Tong Jun Chen Zhi Lu Jisong Guan Geng Wang MOE Key laboratory of Bioinformatics Cell Biology and Development CenterSchool of Life SciencesTsinghua University Beijing 100084China Peking University Research Center on Aging Beijing 100191China Department of Biochemistry and Molecular Biology Peking University Health Science CenterBeijing 100191China

Mitochondrial dysfunctions play major roles in *** mitochondrial stresses invoke downstream responses and how specificity of the signaling is achieved, however, remains unclear. We have previously discovered that the RNA component of Telomerase TERC is imported into mitochondria, processed to a shorter form TERC-53, and then exported back to the cytosol. Cytosolic TERC-53 levels respond to mitochondrial functions, but have no direct effect on these functions, suggesting that cytosolic TERC-53 functions downstream of mitochondria as a signal of mitochondrial functions. Here, we show that cytosolic TERC-53 plays a regulatory role on cellular senescence and is involved in cognition decline in 10 months old mice, independent of its telomerase function. Manipulation of cytosolic TERC-53 levels affects cellular senescence and cognition decline in 10 months old mouse hippocampi without affecting telomerase activity, and most importantly, affects cellular senescence in terc^-/- cells. These findings uncover a senescence-related regulatory pathway with a non-coding RNA as the signal in mammals.

关键词： mitochondria retrograde signal nucleus transcription regulation non-coding RNA telomerase

Circular RNAs in early brain development and their influence and clinical significance in neuropsychiatric disorders

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Neural Regeneration Research 2020年第5期15卷 817-823页

作者： Chuan-Jun Zhuo Wei-Hong Hou De-Guo Jiang Hong-Jun Tian Li-Na Wang Feng Jia Chun-Hua Zhou Jing-Jing Zhu Department of Psychiatry and Genetics School of Mental HealthJining Medical UniversityJiningShandong ProvinceChina Department of Psychiatry and Molecular Psychiatry Wenzhou Seventh People’s HospitalWenzhouZhejiang ProvinceChina Department of Psychiatry and Imaging-Genetics and Co-morbidity (PNGC-Lab) Tianjin Anding HospitalTianjin Mental Health CenterMental Health Teaching HospitalTianjin Medical UniversityDepartment of PsychiatrySchool of Basic Medical ResearchTianjin Medical UniversityTianjinChina Department of Biochemistry and Molecular Biology Medical College of Zhengzhou UniversityZhengzhouHenan ProvinceChina Department of Biology University of North Carolina at CharlotteCharlotteNCUSA Department of Pharmacy First Hospital of Hebei Medical UniversityShijiazhuangHebei ProvinceChina

Neuropsychiatric disorders represent a set of severe and complex mental illnesses,and the exact etiologies of which are *** has been well documented that impairments in the early development of the brain contribute to the pathogenesis of many neuropsychiatric ***,the diagnosis of neuropsychiatric disorders largely relies on subjective cognitive assessment,because there are no widely accepted biochemical or genetic biomarkers for diagnosing mental *** RNAs (circRNAs) are a novel class of endogenous non-coding RNA (ncRNA) with a closed-loop *** recent years,there have been tremendous advances in our understanding of the expression profiles and biological roles of *** the brain,circRNAs are particularly enriched and are expressed more abundantly in contrast to linear counterpart *** are highly active at neuronal *** features make circRNAs uniquely crucial for understanding brain health,disease,and neuropsychiatric *** review focuses on the role of circRNAs in early brain development and other brain-related processes that have been associated with the development of neuropsychiatric *** addition,we discuss the potential for blood or cerebrospinal fluid circRNAs to be used as novel biomarkers in the early diagnosis of neuropsychiatric *** findings reviewed here may provide new insight into the pathological mechanisms underlying the onset and progression of neuropsychiatric disorders.

关键词： autism spectrum disorders bipolar disorder brain exosomal circRNAs microRNAs nerve regeneration non-coding RNAs obsessive-compulsive disorders schizophrenia

Construction of an oesophageal cancer-specific ceRNA network based on miRNA, lncRNA, and mRNA expression data

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World Journal of Gastroenterology 2018年第1期24卷 23-34页

作者： Wen-Hua Xue Zhi-Rui Fan Li-Feng Li Jing-Li Lu Bing-Jun Ma Quan-Cheng Kan Jie Zhao Department of Pharmacy the First Affiliated Hospital of Zhengzhou University Cancer Centre the First Affiliated Hospital of Zhengzhou University

AIM To explore the expression profiles of microRNAs(miRNAs), long non-coding RNAs(lncRNAs), and mRNAs in oesophageal squamous cell carcinoma(ESCC) in order to construct an oesophageal cancer-specific competing endogenous RNA(ceRNA) *** In this work, the expression data of miRNAs, lncRNAs, and mRNAs in ESCC were obtained. An oesophageal cancer-specific ceRNA network was then constructed and *** CeRNAs have the ability to reduce the targeting activityof miRNAs, leading to the de-repression of specific mRNAs with common miRNA response elements. CeRNA interactions have a critical effect in gene regulation and cancer *** This study suggests a novel perspective on potential oesophageal cancer mechanisms as well as novel pathways for modulating ceRNA networks for treating cancers.

关键词： Competing endogenous RNA MicroRNA Long non-coding RNA mRNA Oesophageal squamous cell carcinoma

Identification of hepatitis B virus and liver cancer bridge molecules based on functional module network

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World Journal of Gastroenterology 2019年第33期25卷 4921-4932页

作者： Xiao-Bing Huang Yong-Gang He Lu Zheng Huan Feng Yu-Ming Li Hong-Yan Li Feng-Xia Yang Jing Li Department of Hepatobiliary Surgery Second Hospital Affiliated to Third Military Medical University of Xinqiao HospitalChongqing 400037China Division of Nursing Second Hospital Affiliated to Third Military Medical UniversityXinqiao HospitalChongqing 400037China

BACKGROUND The potential role of chronic inflammation in the development of cancer has been widely ***,there has been little research fully and thoroughly exploring the molecular link between hepatitis B virus(HBV)and hepatocellular carcinoma(HCC).AIM To elucidate the molecular links between HBV and HCC through analyzing the molecular processes of HBV-HCC using a multidimensional *** First,maladjusted genes shared between HBV and HCC were identified by disease-related differentially expressed ***,the protein-protein interaction network based on dysfunctional genes identified a series of dysfunctional modules and significant crosstalk between modules based on the hypergeometric *** addition,key regulators were detected by pivot ***,targeted drugs that have regulatory effects on diseases were predicted by modular methods and drug target *** The study found that 67 genes continued to increase in the HBV-HCC ***,366 overlapping genes in the module network participated in multiple functional *** could be presumed that these genes and their interactions play an important role in the relationship between inflammation and ***,significant crosstalk constructed a module level bridge for HBV-HCC molecular *** the other hand,a series of non-coding RNAs and transcription factors that have potential pivot regulatory effects on HBV and HCC were *** them,some of the regulators also had persistent disorders in the process of HBV-HCC including microRNA-192,microRNA-215,and microRNA-874,and early growth response 2,FOS,and Kruppel-like factor ***,the study concluded that these pivots are the key bridge molecules outside the *** but not least,a variety of drugs that may have some potential pharmacological or toxic side effects on HBV-induced HCC were predicted,but their mechanisms still need to be further *** The results sugges

关键词： Hepatitis B virus Hepatocellular carcinoma Molecular linkage Transcription factors non-coding RNA

Association of twelve polymorphisms in three onco-lncRNA genes with hepatocellular cancer risk and prognosis:A case-control study

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World Journal of Gastroenterology 2018年第23期24卷 2482-2490页

作者： Ben-Gang Wang Qian Xu Zhi Lv Xin-Xin Fang Han-Xi Ding Jing Wen Yuan Yuan Tumor Etiology and Screening Department of Cancer Institute and General Surgery the First Hospital of China Medical Universityand Key Laboratory of Cancer Etiology and Prevention (China Medical University)Liaoning Provincial Education Department Hepatobiliary Surgery Department of General Surgery Institute the First Hospital of China Medical University

AIM To evaluate the association of 12 tag single nucleotide polymorphisms(tag SNPs) in three onco-long non-coding RNA(lnc RNA) genes(HOTTIP,CCAT2,MALAT1) with the risk and prognosis of hepatocellular cancer(HCC). METHODS Twelve tag SNPs covering the three onco-lnc RNAs were genotyped by the KASP method in a total of 1338 samples,including 521 HCC patients and frequencymatched 817 controls. The samples were obtained from an unrelated Chinese population at the First Hospital ofChina Medical University from 2012-2015. The expression quantitative trait loci(e QTL) analyses were conducted to explore further the potential function of the promising SNPs. RESULTS Three SNPs in HOTTIP,one promoter SNP in MALAT1,and one haplotype of HOTTIP were associated with HCC risk. The HOTTIP rs17501292,rs2067087,and rs17427960 SNPs were increased to 1.55-,1.20-,and 1.18-fold HCC risk under allelic models(P = 0.012,0.017 and 0.049,respectively). MALAT1 rs4102217 SNP was increased to a 1.32-fold HCC risk under dominant models(P = 0.028). In addition,the two-way interaction of HOTTIP rs17501292-MALAT1 rs619586 polymorphisms showed a decreased effect on HCC risk(P interaction = 0.028,OR = 0.30) and epistasis with each other. HOTTIP rs3807598 variant genotype showed significantly longer survival time in HBV negative subgroup(P = 0.049,HR = 0.12),and MALAT1 rs591291 showed significantly better prognosis in female and HBV negative subgroups(P = 0.022,HR = 0.37; P = 0.042,HR = 0.25,respectively). In the study,no significant effect was observed in e QTL analysis. CONCLUSION Specific lnc RNA(HOTTIP and MALAT1) SNPs have potential to be biomarkers for HCC risk and prognosis.

关键词： Hepatocellular cancer Single nucleotide polymorphism Long non-coding RNA Risk Prognosis