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transcriptome sequencing reveals novel biomarkers and immune cell infiltration in esophageal tumorigenesis

World Journal of Gastrointestinal Oncology 2024年第4期16卷 1500-1513页

作者： Jian-Rong Sun Dong-Mei Chen Rong Huang Rui-Tao Wang Li-Qun Jia School of Clinical Medicine Beijing University of Chinese MedicineBeijing 100029China Integrated Chinese and Western Medicine Oncology China-Japan Friendship HospitalBeijing 100029China

BACKGROUND Esophageal squamous cell carcinoma(ESCC)is one of the most common malignancies worldwide,and its development comprises a multistep process from intraepithelial neoplasia(IN)to carcinoma(CA).However,the critical regulators and underlying molecular mechanisms remain largely *** To explore the genes and infiltrating immune cells in the microenvironment that are associated with the multistage progression of ESCC to facilitate diagnosis and early *** A mouse model mimicking the multistage development of ESCC was established by providing warter containing 4-nitroquinoline 1-oxide(4NQO)to C57BL/6 ***,we established a control group without 4NQO treatment of ***,transcriptome sequencing was performed for esophageal tissues from patients with different pathological statuses,including low-grade IN(LGIN),high-grade IN(HGIN),and CA,and controlled normal tissue(NOR)*** expressed genes(DEGs)were identified in the LGIN,HGIN,and CA groups,and the biological functions of the DEGs were analyzed via Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment *** CIBERSORT algorithm was used to detect the pattern of immune cell ***(IHC)was also conducted to validate our ***,the Luminex multiplex cytokine analysis was utilized to measure the serum cytokine levels in the *** Compared with those in the NOR group,a total of 681541,and 840 DEGs were obtained in the LGIN,HGIN,and CA groups,*** the intersection of the three sets of DEGs,we identified 86 genes as key genes involved in the development of *** analysis revealed that these genes were enriched mainly in the keratinization,epidermal cell differentiation,and interleukin(IL)-17 signaling *** analysis revealed that,compared with those in the NOR group,M0 and M1 macrophages in the 4NQO group showed stronger infiltration,which was validated by *** cytok

关键词： Esophageal squamous cell carcinoma Intraepithelial neoplasia Tumorigenesis transcriptome sequencing Biomarkers Immune cell infiltration 4-nitroquinoline 1-oxid

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Analyses of Chicken Tenderness Traits Based on transcriptome sequencing

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Agricultural Biotechnology 2024年第2期13卷 17-19页

作者： Zengrong ZHANG Mohan QIU Chunlin YU Xia XIONG Xiaoyan SONG Bo XIA Shiliang ZHU Jialei CHEN Chaowu YANG Sichuan Animal Science Academy Chengdu 610066China Animal Breeding and Genetics key Laboratory of Sichuan Province Chengdu 610066China

The calpain system is ubiquitous in cells, mainly comprising calpains and calpain inhibitors, and is a widespread calcium-dependent cysteine protease in organisms that is involved in many cellular processes such as muscle degradation in vivo and affects the tenderness of meat after animal slaughter. The study found 128 DEGs that probably regulated tenderness traits were selected from 16 significantly enriched GO terms by transcriptome sequencing analysis, and found that the developmental changes in the expression levels of the CAPN1 gene in the pectoral and leg muscles were significantly positively correlated ( P <0.05) with the cumulative growth values of live weight and comb weight. The developmental changes in the expression levels of the CAST gene in the pectoral and leg muscles were not significantly correlated with the cumulative growth values of live weight and comb weight. Our results helped demonstrate the potential molecular mechanisms of tenderness in chickens and provide valuable information for chicken breeding.

关键词： Chicken Tenderness traits transcriptome sequencing

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transcriptome sequencing of essential marine brown and red algal species in China and its significance in algal biology and phylogeny

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Acta Oceanologica Sinica 2014年第2期33卷 1-12页

作者： WU Shuangxiu SUN Jing CHI Shan WANG Liang WANG Xumin LIU Cui LI Xingang YIN Jinlong LIU Tao YU Jun CAS Key Laboratory of Genome Sciences and Information Beijing Key Laboratory of Genome and Precision Medicine TechnologiesBeijing Institute of GenomicsChinese Academy of Sciences Beijing Key Laboratory of Functional Genomics for Dao-di Herbs Beijing Institute of GenomicsChinese Academy of Sciences University of Chinese Academy of Sciences College of Marine Life Science Ocean University of China

Most phaeophytes （brown algae） and rhodophytes （red algae） dwell exclusively in marine habitats and play important roles in marine ecology and biodiversity. Many of these brown and red algae are also important resources for industries such as food, medicine and materials due to their unique metabolisms and me-tabolites. However, many fundamental questions surrounding their origins, early diversification, taxonomy, and special metabolisms remain unsolved because of poor molecular bases in brown and red algal study. As part of the 1 000 Plant Project, the marine macroalgal transcriptomes of 19 Phaeophyceae species and 21 Rhodophyta species from China＇s coast were sequenced, covering a total of 2 phyla, 3 classes, 11 orders, and 19 families. An average of 2 Gb per sample and a total 87.3 Gb of RNA-seq raw data were generated. Approxi-mately 15 000 to 25 000 unigenes for each brown algal sample and 5 000 to 10 000 unigenes for each red algal sample were annotated and analyzed. The annotation results showed obvious differences in gene expres-sion and genome characteristics between red algae and brown algae;these differences could even be seen between multicellular and unicellular red algae. The results elucidate some fundamental questions about the phylogenetic taxonomy within phaeophytes and rhodophytes, and also reveal many novel metabolic pathways. These pathways include algal CO2 fixation and particular carbohydrate metabolisms, and related gene/gene family characteristics and evolution in brown and red algae. These findings build on known algal genetic information and significantly improve our understanding of algal biology, biodiversity, evolution, and potential utilization of these marine algae.

关键词： Phaeophyceae brown algae Rhodophyta red algae marine macroalgae transcriptome sequencing secondary generation sequencing

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transcriptome sequencing analysis of ursolic acid-mediated proliferation suppression on cutaneous T-cell lymphoma cells

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Traditional Medicine Research 2023年第2期8卷 36-44页

作者： Cheng Wang Peng-Cheng Ma Bao-Le Cai Hong-Yang Li Ling-Jun Li Pharmacal Research Laboratory Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIsInstitute of DermatologyChinese Academy of Medical SciencesPeking Union Medical CollegeNanjing 210042China Department of Dermatology Zhongda Hospital Southeast UniverstiyNanjing 210009China

Background:Ursolic acid is a triterpenoid compound found in natural plants that exhibits antiproliferative effects in various cancer *** study is the first to demonstrate the strong inhibitory effects of ursolic acid on the proliferation of cutaneous T-cell lymphoma(CTCL)*** aimed to further investigate the underlying mechanism of the proliferation inhibition induced by ursolic acid in CTCL cells using transcriptome ***:Cell counting kit-8 assays were used to observe the effects of six traditional medicine monomers on the proliferation of CTCL *** sequencing was used to identify differentially expressed genes after ursolic acid *** analysis was performed to determine the potential ***-time quantitative PCR and western blotting analyses were performed to confirm the sequencing results and verify the possible mechanisms of ursolic acid-mediated proliferation inhibition in CTCL ***:Ursolic acid exhibited the strongest inhibitory effect on the proliferation of CTCL cells among the six traditional medicine *** sequencing analysis showed that 2,466 genes were significantly *** with Kyoto Encyclopedia of Genes and Genomes functional enrichment analysis and protein-protein interaction network analysis,the interaction of various pathways and signaling molecules,such as tumor necrosis factor-α,NLR family pyrin domain containing 1,c-Jun N-terminal kinase,and melanoma differentiation-associated gene 5,accounted for the anti-tumor effects of ursolic acid in CTCL ***:Ursolic acid significantly inhibited the proliferation of CTCL cells,and our study laid a theoretical foundation for the future treatment of CTCL using ursolic acid.

关键词： ursolic acid cutaneous T-cell lymphoma transcriptome sequencing proliferation apoptosis

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Integrative Analyses of Lung Squamous Cell Carcinoma in Ten Chinese Patients with transcriptome sequencing

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Journal of Genetics and Genomics 2015年第10期42卷 579-587页

作者： Lu-Lu Yang Xu-Chao Zhang Shao-Kun Chuai Zhi-Hong Chen Zhi Xie Wei-Bang Guo Shi-Liang Chen Yuan-Yuan Lei Long-Hua Guo Lan Ying Gou Hui-Wen Sun Qi Zhang Jin-Ji Yang Hai-Yan Tu Jian Su Yi-Long Wu Guangdong Lung Cancer Institute Guangdong Provincial Key Laboratory of Translational Medicine in Lung Cancer Guangdong General Hospital &Guangdong Academy of Medical Sciences The First Clinic College of South China University of Technology Burning Rock Biotech First Department of Chemotherapy Meizhou People Hospital

Few effective therapies have been developed for the treatment of lung squamous cell carcinoma （SQCC）, in part due to a lack of un- derstanding regarding the mechanisms underlying the initiation and development of this disease. Whole transcriptome sequencing not only provides insight into the expression of all transcribed genes, but offers an efficient approach for identifying genetic variations, including gene fusions, mutations and alternative splicing. In this study, we performed whole transcriptome sequencing of 10 patients with stage IIIA lung SQCC, and discovered a large number of single nucleotide variants （SNVs： mean of 12.2 SNVs/Mb）, with C〉T/G〉A and A〉G/T〉C transitions being the most frequently observed. Additionally, a total of 132 gene fusions were identified based upon TopHat alignments, 70.5% （93/132） of which occurred as a result of intra-chromosomal rearrangements. Based on the number of supporting reads for each fusion, we further validated 20 of the 26 top gene fusions by RT-PCR and Sanger sequencing. Taken together, these data provide an in-depth view of transcriptional alterations in lung SQCC patients, and may be useful for identification of new therapeutic targets.

关键词： Lung squamous cell carcinoma transcriptome sequencing Gene fusion

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Characterization of Chiton Ischnochiton hakodadensis Foot Based on transcriptome sequencing

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Journal of Ocean University of China 2018年第3期17卷 632-640页

作者： DOU Huaiqian MIAO Yan LI Yuli LI Yangping DAI Xiaoting ZHANG Xiaokang LIANG Pengyu LIU Weizhi WANG Shi BAO Zhenmin Key Laboratory of Marine Genetics and Breeding of Ministry of Education Ocean University of China Laboratory for Marine Biology and Biotechnology Qingdao National Laboratory for Marine Science and Technology Laboratory for Marine Fisheries Science and Food Production Processes Qingdao National Laboratory for Marine Science and Technology

Chiton(Ischnochiton hakodadensis) is one of marine mollusks well known for its eight separate shell plates. I. hakodadensis is important, which plays a vital role in the ecosystems it inhabits. So far, the genetic studies on the chiton are scarce due in part to insufficient genomic resources available for this species. In this study, we investigated the transcriptome of the chiton foot using Illumina sequencing technology. The reads were assembled and clustered into 256461 unigenes, of which 42247 were divided into diverse functional categories by Gene Ontology(GO) annotation terms, and 17256 mapped onto 365 pathways by KEGG pathway mapping. Meanwhile, a set of differentially expressed genes(DEGs) between distal and proximal muscles were identified as the foot adhesive locomotion associated, thus were useful for our future studies. Moreover, up to 679384 high-quality single nucleotide polymorphisms(SNPs) and 19814 simple sequence repeats(SSRs) were identified in this study, which are valuable for subsequent studies on genetic diversity and variation. The transcriptomic resource obtained in this study should aid to future genetic and genomic studies of chiton.

关键词： chiton transcriptome sequencing DEG SNP SSR

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Use of transcriptome sequencing to explore the effect of CSRP3 on chicken myoblasts

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Journal of Integrative Agriculture 2023年第4期22卷 1159-1171页

作者： SHAN Yan-ju JI Gai-ge ZHANG Ming LIU Yi-fan TU Yun-jie JU Xiao-jun SHU Jing-ting ZOU Jian-min Key Laboratory for Poultry Genetics and Breeding of Jiangsu Province Poultry InstituteChinese Academy of Agricultural SciencesYangzhou 225125P.R.China Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education Yangzhou UniversityYangzhou 225009P.R.China

The mechanisms that regulate the specificity and maintenance of chicken muscle fiber types remain largely unknown. In mammals, CSRP3 has been shown to play a vital role in the maintenance of typical muscle structure and function. This study investigated the role that CSRP3 plays in chicken skeletal muscle. First, the antibody against chicken CSRP3 protein was prepared, and the expression levels of the mRNA and protein of the CSRP3 gene in four chicken skeletal muscles with different myofiber compositions were compared. Then the effects of CSRP3 silencing on the expression profile of chicken myoblast transcriptomes were analyzed. The results showed that the expression levels of the mRNA and protein of the CSRP3 gene were both associated with the composition of fiber types in chicken skeletal muscles. A total of 650 genes with at least 1.5-fold differences(Q<0.05) were identified, of which 255 genes were upregulated and 395 genes were downregulated by CSRP3 silencing. Functional enrichment showed that several pathways, including adrenergic signaling in cardiomyocytes, adipocytokine signaling pathway and apelin signaling pathway, were significantly(P<0.05) enriched both in differentially expressed genes and all expressed genes. The co-expressed gene network suggested that CSRP3 silencing caused a compensatory upregulation(Q<0.05) of genes related to the assembly of myofibrils, muscle differentiation, and contraction. Meanwhile, two fast myosin heavy chain genes(MyH1B and MyH1E)were upregulated(Q<0.05) upon CSRP3 silencing. These results suggested that CSRP3 plays a crucial role in chicken myofiber composition, and affects the distribution of chicken myofiber types, probably by regulating the expression of MyH1B and MyH1E.

关键词： CSRP3 chicken myofiber type transcriptome sequencing

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Integrated transcriptome sequencing and RNA interference reveals molecular changes in Diaphorina citri after exposure to validamycin

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Insect Science 2021年第6期28卷 1690-1707页

作者： Hai-Zhong Yu Yan-Xin Xie Jie Wang Ying Wang Yi-Min Du He-Gui Wang Ba-Lian Zhong Bo Zhu Xiu-Dao Yu Zhan-Jun Lu College of Life Sciences Gannan Normal UniversityGanzhouJiangxi ProvinceChina National Navel Orange Engineering Research Center GanzhouJiangxi ProvinceChina College of Life Science Anhui Agricultural UniversityHefeiChina

Validamycin has been widely used as a specific competitive inhibitor of *** our previous research,validamycin significantly inhibited trehalase activity and chitin synthesis in Diaphorina citri,resulting in abnormal ***,the mechanism of validamycin's action on *** remains ***,using a comparative transcriptome analysis,464 differentially expressed genes(DEGs)in *** were identified after validamycin treatment.A Gene Ontology enrichment analysis revealed that these DEGs were mainly involved in“small molecule process”,“structural molecule ac-tivity”and“transition metal ion binding”.DEGs involved in chitin metabolism,cuticle synthesis and insecticide detoxification were validated by reverse transcription quantitative polymerase chain *** RNA interference of *** chitinase-like protein EN03 and *** cuticle protein 7 genes significantly affected *** ***,the recombinant chitinase-like protein EN03 exhibited a chitin-binding property,and an antimicrobial activity against Bacillus *** study provides a first insight into the molecular changes in *** after exposure to validamycin and identifies two effective RNA interference targets for *** control.

关键词： chitin-binding Diaphorina citric RNA interference transcriptome sequencing validamycin

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transcriptome sequencing and Analysis of Agaricus blazei Mycelia Under Cadmium Stress

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Agricultural Science & Technology 2022年第4期23卷 54-64页

作者： ZHANG Yu-hui MA Xin-wang XIA Zhi-lan HUANG Min-feng SU Rong-rong Hunan Agricultural Industrialization Development Service Center Changsha 410006PRC Hunan Agricultural University Changsha 410125PRC Southwest Guizhou Institute of Karst Regional Development Xingyi 562400PRC

To explore the mechanism of Agaricus blazei Murrill enrichment of the heavy metal cadmium,we employed Illumina high-throughput sequencing to analyze the transcriptomes of *** mycelia treated with and without exogenous cadmium addition,and then the differentially expressed genes(DEGs)of the strains with high and low cadmium enrichment between the control and cadmium treatment were screened *** results showed that the DEGs were mainly involved in steroid biosynthesis,antibiotic biosynthesis,protein processing in endoplasmic reticulum,glutathione metabolism and other *** metabolism and glutathione metabolism may play an important role in the response of *** mycelium to cadmium stress.

关键词： Agaricus blazei Murrill Cadmium stress transcriptome sequencing GO analysis

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transcriptome sequencing analysis of lncRNA expression in peripheral blood mononuclear cells from patients with COPD

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Journal of Hainan Medical University 2020年第21期26卷 48-52页

作者： Quan-Ni Li Jie Zhao Yi-Xiu Yang Juan Sun Xiao-Man Zhou Jian-Fang Liu Qiong Feng Yi-Peng Ding Hainan Hospital Affiliated to Hainan Medical University Haikou 570311China Department of General Practice Hainan General HospitalHaikou 570311China Hainan Hospital Affiliated to Nanhua University

Objective:To screen abnormally expressed lncRNAs in peripheral blood mononuclear cells from patients with ***:The peripheral blood of 3 COPD patients and 3 normal controls were collected from our hospital,mononuclear cells were isolated,RNA was extracted and then transcriptome sequencing was *** expression difference between the two groups of samples was calculated based on p*** the difference lncRNA heat map and volcano *** Lncpro database may predict mRNAs regulated by differential lncRNA,and perform the GO function and KEGG signaling ***:There were 67 lncRNAs between the COPD group and the control group that met the difference of p1,of which 33 were up-regulated and 34 were *** the two *** target genes are mainly enriched in GO functions:regulatory functions of multicellular biological processes,regulatory functions of development processes,structured morphogenesis functions,system development functions,and development process *** genes are mainly enriched in KEGG signaling pathways:multi-species apoptotic pathway,TGF-βsignaling pathway,complement and coagulation cascade pathway,colorectal cancer pathway and apoptosis ***:Our results provide general information and possible regulatory functions and pathways of lncRNA expression changes in peripheral blood mononuclear cells of COPD,which may help clarify the underlying mechanism of COPD.

关键词： COPD transcriptome sequencing Mononuclear cells LncRNA

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