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Comprehensive profiling and evaluation of the alteration of RNA modifications in thyroid carcinoma by liquid chromatography-tandem mass spectrometry

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Chinese Chemical Letters 2022年第8期33卷 3772-3776页

作者： Meng-Yuan Chen Chu-Bo Qi Xiao-Meng Tang Jiang-Hui Ding Bi-Feng Yuan Yu-Qi Feng School of Public Health Wuhan UniversityWuhan 430071China Department of Chemistry Sauvage Center for Molecular SciencesWuhan UniversityWuhan 430072China Jiangxi Provincial People's Hospital Affiliated to Nanchang University Nanchang 330006China

RNA molecules contain diverse modifications that display important functions in a variety of physiological and pathological processes.So far over 150 chemical modifications have been characterized to be present in various RNA species,such as in messenger RNA(mRNA),ribosomal RNA(rRNA),and transfer RNA(tRNA).Previous studies revealed that certain RNA modifications were correlated to specific human diseases,indicating RNA modifications could serve as the potential indicator of human diseases.However,systemic investigation of the alteration of RNA modifications in different RNA species of carcinoma tissues are still lacked.Herein,we carried out the comprehensive profiling and evaluation of the alteration of RNA modifications in thyroid carcinoma by liquid chromatography-tandem mass spectrometry(LC-ESIMS/MS)analysis.The developed method allowed us to simultaneously detect 48 different types of RNA modifications.Using this method,we detected 10,15,14,and 25 modifications in m RNA,18 S r RNA,28 S rRNA and small RNA(<200 nt),respectively.Compared to the normal tissues,we revealed a total of 14 RNA modification exhibited significant increase and 2 RNA modifications showed significant decrease in thyroid carcinoma tissues.Our study provided the first comprehensive profile as well as the alteration of modifications in different RNA species in thyroid carcinoma and matched tumor-adjacent normal tissues.The altered pattern RNA modifications may serve as the indicator of thyroid carcinoma.Moreover,this study may promote the in-depth understanding of the regulatory roles of RNA modifications in thyroid carcinoma.

关键词： RNA modification Liquid chromatography-mass spectrometry Thyroid carcinoma profiling

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Advances of supercritical fluid chromatography in lipid profiling

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Journal of Pharmaceutical Analysis 2019年第1期9卷 1-8页

作者： Yang Yang Yanshan Liang Jina Yang Fengying Ye Ting Zhou Gongke Li School of Biology and Biological Engineering South China University of Technology School of Chemistry Sun Yat-sen University

Supercritical fluid chromatography(SFC) meets with great favor due to its high efficiency, low organic solvent consumption, and the specialty for the identification of the isomeric species. This review describes the advances of SFC in targeted and untargeted lipid profiling. The advancement of the SFC instruments and the stationary phases are summarized. Typical applications of SFC to the targeted and untargeted lipid profiling are discussed in detail. Moreover, the perspectives of SFC in the lipid profiling are also proposed. As a useful and promising tool for investigating lipids in vitro and in vivo, SFC will predictably obtain further development.

关键词： Supercritical fluid chromatography Online SFC technique Untargeted lipid profiling Targeted lipid profiling Lipidomics

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Copy number alteration profiling facilitates differential diagnosis between ossifying fibroma and fibrous dysplasia of the jaws

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International Journal of Oral Science 2021年第2期13卷 200-209页

作者： Ming Ma Lu Liu Ruirui Shi Jianyun Zhang Xiaotian Li Xuefen Li Jiaying Bai Jianbin Wang Yanyi Huang Tiejun Li Department of Oral Pathology Peking University School and Hospital of Stomatology&National Center of Stomatology&National Clinical Research Center for Oral Diseases&National Engineering Laboratory for Digital and Material Technology of Stomatology&Beijing Key Laboratory of Digital Stomatology&Research Center of Engineering and Technology for Computerized Dentistry Ministry of Health&NMPA Key Laboratory for Dental MaterialsBeijingChina Research Unit of Precision Pathologic Diagnosis in Tumors of the Oral and Maxillofacial Regions Chinese Academy of Medical Sciences(2019RU034)BeijingChina Beijing Advanced Innovation Center for Genomics(ICG) Biomedical Pioneering Innovation Center(BIOPIC)School of Life SciencesPeking UniversityBeijingChina Central Laboratory Peking University School and Hospital of StomatologyBeijingChina School of Life Sciences and Beijing Advanced Innovation Center for Structural Biology Tsinghua UniversityBeijingChina College of Chemistry and Molecular Engineering and Beijing National Laboratory for Molecular Sciences Peking UniversityBeijingChina Institute for Cell Analysis Shenzhen Bay LaboratoryGuangdongChina

Ossifying fibroma(OF)and fibrous dysplasia(FD)are two fibro-osseous lesions with overlapping clinicopathological features,making diagnosis challenging.In this study,we applied a whole-genome shallow sequencing approach to facilitate differential diagnosis via precise profiling of copy number alterations(CNAs)using minute amounts of DNA extracted from morphologically correlated microdissected tissue samples.Freshly frozen tissue specimens from OF(n=29)and FD(n=28)patients were obtained for analysis.Lesion fibrous tissues and surrounding normal tissues were obtained by laser capture microdissection(LCM),with~30–50 cells(5000–10000µm2)per sample.We found that the rate of recurrent CNAs in OF cases was much higher(44.8%,13 of 29)than that in FD cases(3.6%,1 of 28).Sixty-nine percent(9 of 13)of the CNA-containing OF cases involved segmental amplifications and deletions on Chrs 7 and 12.We also identified eight CNA-associated genes(HILPDA,CALD1,C1GALT1,MICALL2,PHF14,AIMP2,MDM2,and CDK4)with amplified expression,which was consistent with the copy number changes.We further confirmed a jaw lesion with a previous uncertain diagnosis due to its ambiguous morphological features and the absence of GNAS mutation as OF based on the typical Chr 12 amplification pattern in its CNA profile.Moreover,analysis of a set of longitudinal samples collected from an individual with a cellular lesion in suspicion of OF at the first surgery,recurrence and the latest malignant transformation revealed identical CNA patterns at the three time points,suggesting that copy number profiling can be used as an important tool to identify borderline lesions or lesions with malignant potential.Overall,CNA profiling of fibro-osseous lesions can greatly improve differential diagnosis between OF and FD and help predict disease progression.

关键词： diagnosis precise profiling

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Ribosome profiling analysis identified a KRAS-interacting microprotein that represses oncogenic signaling in hepatocellular carcinoma cells

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Science China(Life Sciences) 2020年第4期63卷 529-542页

作者： Wenli Xu Bing Deng Penghui Lin Chang Liu Bin Li Qiaojuan Huang Hui Zhou Jianhua Yang Lianghu Qu MOE Key Laboratory of Gene Function and Regulation State Key Laboratory for BiocontrolSchool of Life SciencesSun Yat-Sen UniversityGuangzhou 510275China The Fifth Affiliated Hospital Sun Yat-Sen UniversityZhuhai 519000China

The roles of concealed microproteins encoded by long noncoding RNAs(lncRNAs)are gradually being exposed,but their functions in tumorigenesis are still largely unclear.Here,we identify and characterize a conserved 99-amino acid microprotein named KRASIM that is encoded by the putative lncRNA NCBP2-AS2.KRASIM is differentially expressed in normal hepatocytes and hepatocellular carcinoma(HCC)cells and can suppress HCC cell growth and proliferation.Mechanistically,KRASIM interacts and colocalizes with the KRAS protein in the cytoplasm of human HuH-7 hepatoma cells.More importantly,the overexpression of KRASIM decreases the KRAS protein level,leading to the inhibition of ERK signaling activity in HCC cells.These results demonstrate a novel microprotein repressor of the KRAS pathway for the first time and provide new insights into the regulatory mechanisms of oncogenic signaling and HCC therapy.

关键词： KRAS lncRNA microprotein ribosome profiling hepatocellular carcinoma

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Epigenomic profiling identifies the role of Nr5a2 and CYP1B1 in hepatocellular carcinoma stemness maintenance

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Science Bulletin 2019年第16期64卷 1132-1135页

作者： Jun Cao Hong Jiang Ran Zhang Amr.R.Ghanam Honghai Xia Yuting Zhu Zhen Yang Xiaoyuan Song Hefei National Laboratory for Physical Sciences at the Microscale CAS Key Laboratory of Brain Function and DiseaseNeurodegenerative Disorder Research CenterSchool of Life SciencesDivision of Life Sciences and MedicineUniversity of Science and Technology of ChinaHefei 230026China Department of Emergency Surgery The First Affiliated Hospital of USTCDivision of Life Sciences and MedicineUniversity of Science and Technology of ChinaHefei 230001China Core Facility Center for Life Sciences School of Life SciencesUniversity of Science and Technology of ChinaHefei 230026China

Cancer stem cells (CSCs) are largely responsible for the formation of tumor heterogeneity and tumor’s resistance to traditional treatments such as chemotherapy due to its self-renew capability and multi-lineage differentiation potential (1)However, it remains elusive how the CSCs maintain their stemness, thus restricting the development of therapeutic treatments specifically targeting the CSCs.

关键词： HCC Epigenomic profiling identifies the role of Nr5a2 and CYP1B1 in hepatocellular carcinoma stemness maintenance CYP

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Community structure, dispersal ability and functional profiling of microbiome existing in fat body and ovary of the brown planthopper, Nilaparvata lugens

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Insect Science 2019年第4期26卷 683-694页

作者： Jian-Hua Zhang Na Yu Xi-Xia Xu Ze-Wen Liu Key laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education) College of Plant Protection Nanjing Agricultural University Nanjing China

The endosymbionts play vital roles in growth, development and reproduction in insects. Yeast-like endosymbionts (YLSs) have been well studied in Nilaparvata lugens (N. lugens), but little is known about the tissue-specific bacterial microbiomes, especially on the microbial intersection among internal tissues. Here, the correlation of microbial composition, structure, dispersal ability and functional profiling were illuminated in two tissues, the fat body and ovary in N. lugens. A total of 11 phyla and 105 genera were captured from all samples;Firmicutes and Proteobacteria were the most predominant and accounted for more than 99% in all samples. However, the relative abundance ofFirmicutes and Proteobacteria was significantly different in ovary and fat body through Fisher's Least Significant Difference test. Microbial diversity but not the richness index in the two tissues exhibited significant difference. Furthermore, the microbial community structure of the ovary and fat body were primarily determined by tissue quality. Firmicutes showed strong dispersal ability between ovary and fat body based on the quantitative null model assessing, indicating the frequent interaction of these microbiomes in the two tissues. In addition, the Kyoto Encyclopedia of Genes and Genomes pathways of microbial participation were delineated. The ten most abundant pathways counted for over 46% of the annotation and were shared between the two tissues, mainly containing Energy Metabolism and Amino Acid Metabolism/Biosynthesis. The results will provide insights into the correlation of microbial community structure between ovary and fat body of N. lugens.

关键词： dispersal ability fat body functional profiling microbial structure Nilaparvata lugens ovary

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Transcriptomic profiling of sorghum leaves and roots responsive to drought stress at the seedling stage

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Journal of Integrative Agriculture 2019年第9期18卷 1980-1995页

作者： ZHANG Deng-feng ZENG Ting-ru LIU Xu-yang GAO Chen-xi LI Yong-xiang LI Chun-hui SONG Yan-chun SHI Yun-su WANG Tian-yu LI Yu Institute of Crop Sciences Chinese Academy of Agricultural Sciences

Drought stress affects the growth and productivity of crop plants including sorghum.To study the molecular basis of drought tolerance in sorghum,we conducted the transcriptomic profiling of sorghum leaves and roots under drought stress using RNA-Seq method.A total of 510,559,and 3 687 differentially expressed genes(DEGs)in leaves,3 368,5 093,and 4 635 DEGs in roots responding to mild drought,severe drought,and re-watering treatments were identified,respectively.Among them,190 common DEGs in leaves and 1 644 common DEGs in roots were responsive to mild drought,severe drought,and re-watering environment.Gene Ontology(GO)enrichment analysis revealed that the GO categories related to drought tolerance include terms related to response to stimulus especially response to water deprivation,abscisic acid stimulus,and reactive oxygen species.The major transcription factor genes responsive to drought stress include heat stress transcription factor(HSF),ethylene-responsive transcription factor(ERF),Petunia NAM,Arabidopsis ATAF1/2 and CUC2(NAC),WRKY transcription factor(WRKY),homeodomain leucine zipper transcription factor(HD-ZIP),basic helix-loop-helix transcription factor(bHLH),and V-myb myeloblastosis viral oncogene homolog transcription facotr(MYB).Functional protein genes for heat shock protein(HSPs),late-embryogenesis-abundant protein(LEAs),chaperones,aquaporins,and expansins might play important roles in sorghum drought tolerance.Moreover,the genomic regions enriched with HSP,expansin,and aquaporin genes responsive to drought stress could be used as powerful targets for improvement of drought tolerance in sorghum and other cereals.Overall,our results provide a genome-wide analysis of DEGs in sorghum leaves and roots under mild drought,severe drought,and re-watering environments.This study contributes to a better understanding of the molecular basis of drought tolerance of sorghum and can be useful for crop improvement.

关键词： sorghum(Sorghum bicolor L.) transcriptomic profiling drought leaves roots

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Evaluation of neuroactive effects of ethanol extract of Schisandra chinensis, Schisandrin, and Schisandrin B and determination of underlying mechanisms by zebrafish behavioral profiling

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Chinese Journal of Natural Medicines 2018年第12期16卷 916-925页

作者： WANG Jia-Wei LIANG Feng-Yin OUYANG Xiang-Shuo LI Pei-Bo PEI Zhong SU Wei-Wei Guangdong Engineering and Technology Research Centre for Quality and Efficacy Re-evaluation of Post-marketed TCM Guangdong Key Laboratory of Plant Resources School of Life Sciences Sun Yat-sen University Department of Neurology National Key Clinical Department and Key Discipline of Neurology Guangdong Provincial Key Laboratory for Diagnosis and Treatment of Major Neurological Diseases The First Affiliated Hospital Sun Yat-sen University

Schisandra chinensis, a traditional Chinese medicine(TCM), has been used to treat sleep disorders. Zebrafish sleep/wake behavioral profiling provides a high-throughput platform to screen chemicals, but has never been used to study extracts and components from TCM. In the present study, the ethanol extract of Schisandra chinensis and its two main lignin components, schisandrin and schisandrin B, were studied in zebrafish. We found that the ethanol extract had bidirectional improvement in rest and activity in zebrafish. Schisandrin and schisandrin B were both sedative and active components. We predicted that schisandrin was related to serotonin pathway and the enthanol extract of Schisandra chinensis was related to seoronin and domapine pathways using a database of zebrafish behaviors. These predictions were confirmed in experiments using Caenorhabditis elegans. In conclusion, zebrafish behavior profiling could be used as a high-throughput platform to screen neuroactive effects and predict molecular pathways of extracts and components from TCM.

关键词： Traditional Chinese medicine Schisandra chinensis Zebrafish Behavior profiling Neurotransmitter

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Molecular cloning, expression profiling and RNA interference of a vitellogenin gene from Harmonia axyridis(Coleoptera: Coccinellidae)

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Journal of Integrative Agriculture 2019年第10期18卷 2311-2320页

作者： LIANG Chao LIU Ting-hui HAN Shi-peng HE Yun-zhuan College of Plant Protection Hebei Agricultural University

In this study, the Harmonia axyridis vitellogenin gene 2 (HmVg2) sequence was identified from transcriptomic databases of female adult H. axyridis and cloned into pMD18-T vector. The HmVg2 gene was 5 460 bp in length, and formed with an open reading frame (ORF) of 5 361 nucleotides (GenBank accession no. KY794939). The putative molecular weight of the primary HmVg2 protein was 203.459 kDa and the predicted isoelectric point (pI) was 8.59. HmVg2 contained a signal peptide, vitellogenin N-terminal (vitellogenin-N) domain, domain of unknown function 1943 (DUF1934) domain and von Willebrand factor type D (VWD) domain. The developmental expression profiling showed that HmVg2 was extremely highly expressed in female insects, but was expressed at lower levels in male insects. In female insects, HmVg2 was mainly expressed in the wing and fat body. The double-stranded RNA-HmVg2/-GFP was injected into H. axyridis, and qRT-PCR results showed that the HmVg2 gene was specifically silenced. The eggs laid during the first five days and the hatching rate of eggs was lower than controls after dsHmVg2 injection. This investigation demonstrated that the HmVg2 gene plays an important role in H. axyridis reproduction and enriches the function of the insect vitellogenin gene.

关键词： vitellogenin Harmonia axyridis expression profiling RNAi

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Serum Metabolic profiling in a Mouse Model of Adriamycin-Induced Focal Segmental Glomerulosclerosis

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Chinese Medical Journal 2018年第22期131卷 2743-2746页

作者： Li Lyu Cai-Li Wang Zeng-Yan Li Ying-Jin Shi Yan-Hui Zhang Yan Mi Zhao Hu Department of Nephrology Qilu Hospital of Shandong UniversityJinanShandong 250012China Department of Nephrology The First Affiliated Hospital of Baotou Medical CollegeBaotouInner Mongolia 014010China

To the Editor:Focal segmental glomerulosclerosis (FSGS)is one of the leading causes of end-stage kidney disease.[1,2] However,no ideal intervention prevents FSGS progression due to the unclear physiopathological mechanisms.Adriamycin (ADR)-induced FSGS is a well-accepted model that mimics human FSGS.ADR,a common chemotherapeutic agent associated with nephrotoxicity,causes kidney damage by triggering imbalances between free oxygen radicals and antioxidant enzymes.

关键词： Serum Metabolic profiling Mouse Model

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