21 results on '"Jian Pan"'
Search Results
2. Inflammation-mediated fibroblast activation and immune dysregulation in collagen VII-deficient skin.
- Author
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Anderson-Crannage, Morgan, Ascensión, Alex M., Ibanez-Solé, Olga, Hongwen Zhu, Schaefer, Edo, Ottomanelli, Darcy, Hochberg, Bruno, Jian Pan, Wen Luo, Tian, Meijuan, Yaya Chu, Cairo, Mitchell S., Izeta, Ander, and Yanling Liao
- Subjects
FIBROBLASTS ,CELL populations ,EPIDERMOLYSIS bullosa ,LANGERHANS cells ,SQUAMOUS cell carcinoma ,GENE expression ,LANGERHANS-cell histiocytosis - Abstract
Inflammation is known to play a critical role in all stages of tumorigenesis; however, less is known about how it predisposes the tissue microenvironment preceding tumor formation. Recessive dystrophic epidermolysis bullosa (RDEB), a skin-blistering disease secondary to COL7A1 mutations and associated with chronic wounding, inflammation, fibrosis, and cutaneous squamous cell carcinoma (cSCC), models this dynamic. Here, we used single-cell RNA sequencing (scRNAseq) to analyze gene expression patterns in skin cells from a mouse model of RDEB. We uncovered a complex landscape within the RDEB dermal microenvironment that exhibited altered metabolism, enhanced angiogenesis, hyperproliferative keratinocytes, infiltration and activation of immune cell populations, and inflammatory fibroblast priming. We demonstrated the presence of activated neutrophil and Langerhans cell subpopulations and elevated expression of PD-1 and PD-L1 in T cells and antigen-presenting cells, respectively. Unsupervised clustering within the fibroblast population further revealed two differentiation pathways in RDEB fibroblasts, one toward myofibroblasts and the other toward a phenotype that shares the characteristics of inflammatory fibroblast subsets in other inflammatory diseases as well as the IL-1-induced inflammatory cancerassociated fibroblasts (iCAFs) reported in various cancer types. Quantitation of inflammatory cytokines indicated dynamic waves of IL-1α, TGF-β1, TNF, IL-6, and IFN-γ concentrations, along with dermal NF-κB activation preceding JAK/STAT signaling. We further demonstrated the divergent and overlapping roles of these cytokines in inducing inflammatory phenotypes in RDEB patients as well as RDEB mouse-derived fibroblasts together with their healthy controls. In summary, our data have suggested a potential role of inflammation, driven by the chronic release of inflammatory cytokines such as IL-1, in creating an immune-suppressed dermal microenvironment that underlies RDEB disease progression. [ABSTRACT FROM AUTHOR]
- Published
- 2023
- Full Text
- View/download PDF
3. Long noncoding RNA and messenger RNA abnormalities in pediatric sepsis: a preliminary study
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Yanhong Li, Jian Pan, Zhenjiang Bai, Yi-Ping Li, Fang Fang, and Jian Wang
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Male ,lcsh:Internal medicine ,lcsh:QH426-470 ,Microarray ,Biology ,Bioinformatics ,Sepsis ,Expression profile ,Gene expression ,Genetics ,medicine ,Humans ,Pediatric sepsis ,RNA, Messenger ,lcsh:RC31-1245 ,Child ,Genetics (clinical) ,Oligonucleotide Array Sequence Analysis ,Messenger RNA ,Microarray analysis techniques ,Gene Expression Profiling ,Infant ,medicine.disease ,Long non-coding RNA ,Human genetics ,lcsh:Genetics ,Gene Expression Regulation ,Child, Preschool ,Female ,RNA, Long Noncoding ,DNA microarray ,Research Article - Abstract
Background Sepsis represents a complex disease with dysregulated inflammatory response and high mortality rate. Long noncoding RNAs (lncRNAs) have been reported to play regulatory roles in a variety of biological processes. However, studies evaluating the function of lncRNAs in pediatric sepsis are scarce, and current knowledge of the role of lncRNAs in pediatric sepsis is still limited. The present study explored the expression patterns of both lncRNAs and mRNAs between pediatric sepsis patients and healthy controls based on a comprehensive microarray analysis. Methods LncRNA and mRNA microarray was used to detect the expression of lncRNAs and mRNAs in the septic and control groups. Aberrantly expressed mRNAs and lncRNAs identified were further interpreted by enrichment analysis, receiver operating characteristic (ROC) curve analysis, co-expression network analysis, and quantitative real-time PCR (qPCR). Results A total of 1488 differetially expressed lncRNAs and 1460 differentially expressed mRNAs were identified. A co-expression network of the identified lncRNAs and mRNAs was constructed. In this network, lncRNA lnc-RP11-1220 K2.2.1–7 is correlated with mRNA CXCR1 and CLEC4D; lncRNA lnc-ANXA3–2 is correlated with mRNA CLEC4D; lncRNA lnc-TRAPPC5–1 is correlated with mRNA DYSF and HLX; lncRNA lnc-ZNF638–1 is correlated with mRNA DYSF and HLX. Significantly different expressions between pediatric sepsis patients and controls were validated by qPCR for the 4 lncRNAs and 4 co-expressed mRNAs, validating the microarray results. Conclusions Our study contributes to a comprehensive understading of the involvment of lncRNAs and mRNAs in pediatric sepsis, which may guide subsequent experimental research. Furthermore, our study may also provide potential candidate lncRNAs and mRNAs for the diagnosis and treatment of pediatric sepsis.
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- 2020
4. Differential Gene Expression Caused by the F and M Loci Provides Insight Into Ethylene-Mediated Female Flower Differentiation in Cucumber
- Author
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Huanle He, Run Cai, Hongli Lian, Jian Pan, Junsong Pan, Hui Du, Haifan Wen, and Gang Wang
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0106 biological sciences ,0301 basic medicine ,unisexual flower ,Flower differentiation ,Plant Science ,Biology ,lcsh:Plant culture ,01 natural sciences ,Transcriptome ,03 medical and health sciences ,Gene expression ,Primordium ,lcsh:SB1-1110 ,Gene ,Original Research ,Sexual differentiation ,fungi ,food and beverages ,biology.organism_classification ,ethylene response ,Cell biology ,floral development ,030104 developmental biology ,sex differentiation ,Homeotic gene ,Cucumis ,cucumber ,010606 plant biology & botany - Abstract
In cucumber (Cucumis sativus L.), the differentiation and development of female flowers are important processes that directly affect the fruit yield and quality. Sex differentiation is mainly controlled by three ethylene synthase genes, F (CsACS1G), M (CsACS2), and A (CsACS11). Thus, ethylene plays a key role in the sex differentiation in cucumber. The "one-hormone hypothesis" posits that F and M regulate the ethylene levels and initiate female flower development in cucumber. Nonetheless, the precise molecular mechanism of this process remains elusive. To investigate the mechanism by which F and M regulate the sex phenotype, three cucumber near-isogenic lines, namely H34 (FFmmAA, hermaphroditic), G12 (FFMMAA, gynoecious), and M12 (ffMMAA, monoecious), with different F and M loci were generated. The transcriptomic analysis of the apical shoots revealed that the expression of the B-class floral homeotic genes, CsPI (Csa4G358770) and CsAP3 (Csa3G865440), was immensely suppressed in G12 (100% female flowers) but highly expressed in M12 (∼90% male flowers). In contrast, CAG2 (Csa1G467100), which is an AG-like C-class floral homeotic gene, was specifically highly expressed in G12. Thus, the initiation of female flowers is likely to be caused by the downregulation of B-class and upregulation of C-class genes by ethylene production in the floral primordium. Additionally, CsERF31, which was highly expressed in G12, showed temporal and spatial expression patterns similar to those of M and responded to the ethylene-related chemical treatments. The biochemical experiments further demonstrated that CsERF31 could directly bind the promoter of M and promote its expression. Thus, CsERF31 responded to the ethylene signal derived from F and mediated the positive feedback regulation of ethylene by activating M expression, which offers an extended "one-hormone hypothesis" of sex differentiation in cucumber.
- Published
- 2018
5. Expression analysis of dihydroflavonol 4-reductase genes in Petunia hybrida
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H R Chen, Y X Chu, Run Cai, A Z Wu, and Jian Pan
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Calibrachoa ,Color ,Flowers ,Rosa ,Petunia ,Pelargonidin ,Anthocyanins ,chemistry.chemical_compound ,Gene Expression Regulation, Plant ,Gene expression ,Botany ,Genetics ,Transgenes ,Promoter Regions, Genetic ,Molecular Biology ,Gene ,Solanaceae ,Plant Proteins ,Flavonoids ,biology ,fungi ,food and beverages ,General Medicine ,Plants, Genetically Modified ,biology.organism_classification ,Molecular biology ,Enzyme assay ,Alcohol Oxidoreductases ,chemistry ,Anthocyanin ,biology.protein ,Petal - Abstract
Dihydroflavonol 4-reductase (DFR) genes from Rosa chinensis (Asn type) and Calibrachoa hybrida (Asp type), driven by a CaMV 35S promoter, were integrated into the petunia (Petunia hybrida) cultivar 9702. Exogenous DFR gene expression characteristics were similar to flower-color changes, and effects on anthocyanin concentration were observed in both types of DFR gene transformants. Expression analysis showed that exogenous DFR genes were expressed in all of the tissues, but the expression levels were significantly different. However, both of them exhibited a high expression level in petals that were starting to open. The introgression of DFR genes may significantly change DFR enzyme activity. Anthocyanin ultra-performance liquid chromatography results showed that anthocyanin concentrations changed according to DFR enzyme activity. Therefore, the change in flower color was probably the result of a DFR enzyme change. Pelargonidin 3-O-glucoside was found in two different transgenic petunias, indicating that both CaDFR and RoDFR could catalyze dihydrokaempferol. Our results also suggest that transgenic petunias with DFR gene of Asp type could biosynthesize pelargonidin 3-O-glucoside.
- Published
- 2015
6. Identification of potential transcriptomic markers in developing asthma: An integrative analysis of gene expression profiles
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Yiping Li, Jian Pan, Yanhong Li, Jian Wang, Fang Fang, and Xing Feng
- Subjects
0301 basic medicine ,Genetics ,Male ,Microarray ,Microarray analysis techniques ,Gene Expression Profiling ,Immunology ,Retina homeostasis ,Biology ,Fold change ,Asthma ,Immunity, Humoral ,Bioconductor ,Transcriptome ,03 medical and health sciences ,030104 developmental biology ,0302 clinical medicine ,030228 respiratory system ,Gene expression ,Databases, Genetic ,Humans ,Female ,Molecular Biology ,Gene - Abstract
The goal of this study was to identify potential transcriptomic markers in developing asthma by an integrative analysis of multiple public microarray data sets. Using the R software and bioconductor packages, we performed a statistical analysis to identify differentially expressed (DE) genes in asthma, and further performed functional interpretation (enrichment analysis and co-expression network construction) and classification quality evaluation of the DE genes identified. 3 microarray datasets (192 cases and 91 controls in total) were collected for this analysis. 62 DE genes were identified in asthma, among which 43 genes were up-regulated and 19 genes were down-regulated. The up-regulated gene with the highest Log2 Fold Change (LFC) was CLCA1 (LFC=2.81). The down-regulated gene with the highest absolute LFC was BPIFA1 (LFC=-1.45). Enrichment analysis revealed that those DE genes strongly associated with proteolysis, retina homeostasis, humoral immune response, and salivary secretion. A support vector machine classifier (asthma versus healthy control) was also trained based on DE genes. In conclusion, the consistently DE genes identified in this study are suggested as candidate transcriptomic markers for asthma diagnosis, and provide novel insights into the pathogenesis of asthma.
- Published
- 2017
7. Differential mRNA Expression Levels of Human Histone-Modifying Enzymes in Normal Karyotype B Cell Pediatric Acute Lymphoblastic Leukemia
- Author
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Dong Wu, Lan Cao, Xing Feng, Xiao-Juan Du, Na Wang, Lichao Sun, Jun Lu, Jian Ni, Shaoyan Hu, Jian Pan, Li Pang, Wenli Zhao, Yan-Fang Tao, and Jian Wang
- Subjects
Histone-modifying enzymes ,histone-modifying enzymes ,real-time PCR array ,Article ,Catalysis ,pediatric acute lymphoblastic leukemia ,lcsh:Chemistry ,Inorganic Chemistry ,Gene expression ,medicine ,Physical and Theoretical Chemistry ,EP300 ,lcsh:QH301-705.5 ,Molecular Biology ,Gene ,Spectroscopy ,biology ,Histone deacetylase 2 ,Organic Chemistry ,Promoter ,General Medicine ,medicine.disease ,Computer Science Applications ,Leukemia ,Histone ,lcsh:Biology (General) ,lcsh:QD1-999 ,Immunology ,biology.protein ,Cancer research - Abstract
Histone modification enzymes regulate gene expression by altering the accessibility of promoters to transcription factors. We sought to determine whether the genes encoding histone modification enzymes are dysregulated in pediatric acute lymphoblastic leukemia (ALL). A real-time PCR array was designed, tested and used to profile the expression of 85 genes encoding histone modification enzymes in bone marrow mononuclear cells from 30 pediatric ALL patients and 20 normal controls. The expression profile of histone-modifying genes was significantly different between normal karyotype B cell pediatric ALL and normal controls. Eleven genes were upregulated in pediatric ALL, including the histone deacetylases HDAC2 and PAK1, and seven genes were downregulated, including PRMT2 and the putative tumor suppressor EP300. Future studies will seek to determine whether these genes serve as biomarkers of pediatric ALL. Ingenuity Pathway Analysis revealed that Gene Expression and Organ Morphology was the highest rated network, with 13 focus molecules (significance score = 35). Ingenuity Pathway Analysis also indicated that curcumin and miR-34 are upstream regulators of histone-modifying enzymes; future studies will seek to validate these results and examine the role of curcumin and miR-34 in leukemia. This study provides new clues into the molecular mechanisms of pediatric ALL.
- Published
- 2013
8. Shotgun and targeted proteomics reveal that pre-surgery serum levels of LRG1, SAA, and C4BP may refine prognosis of resected squamous cell lung cancer
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Rong Xia Li, Rui Wang, Xiao Yang Luo, Chen Li, Hong Ni, Hong Li, Rong Zeng, Yansheng Liu, Haichuan Hu, Qing Run Li, Haiquan Chen, and Yun Jian Pan
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Adult ,Male ,Proteomics ,Lung Neoplasms ,Shotgun ,Biology ,Bioinformatics ,Squamous cell lung cancer ,Pre-surgery ,Text mining ,Carcinoma, Non-Small-Cell Lung ,Gene expression ,Genetics ,Humans ,Molecular Biology ,Aged ,Glycoproteins ,Serum Amyloid A Protein ,business.industry ,Complement C4b-Binding Protein ,Cell Biology ,General Medicine ,Middle Aged ,Prognosis ,Targeted proteomics ,LRG1 ,Carcinoma, Squamous Cell ,Female ,business - Published
- 2012
9. Expression and molecular characterization of zebrafish rnf141 gene
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Ke-jian Pan, Ming-kong Huang, Lun-an Wang, Ya Li, Yu-ming Wang, and Ping Yang
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Gene expression ,General Medicine ,Biology ,biology.organism_classification ,Gene ,Zebrafish ,Cell biology - Published
- 2009
10. T cell epitopes of the La/SSB autoantigen in humanized transgenic mice expressing the hLa class II haplotype DRB1*0301/DQB1*0201
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Zhen Jun Chen, Weiguang Zeng, Shannon Maier, James McCluskey, Karen Davis-Schwarz, Nadine L. Dudek, Michael Bachmann, Stuart I. Mannering, Catherine L. Keech, Philip A. Mudd, Jennifer Workman-Azbill, A. Darise Farris, Kassie L. Hamlin, Zi Jian Pan, and David C. Jackson
- Subjects
musculoskeletal diseases ,T cell ,Immunology ,Epitopes, T-Lymphocyte ,Gene Expression ,Mice, Transgenic ,Peptide binding ,Immunodominance ,Human leukocyte antigen ,Biology ,Autoantigens ,Epitope ,Mice ,Immune system ,Rheumatology ,immune system diseases ,HLA-DQ Antigens ,medicine ,Animals ,HLA-DQ beta-Chains ,Immunology and Allergy ,Pharmacology (medical) ,skin and connective tissue diseases ,HLA-DQ Antigen ,Histocompatibility Antigens Class II ,HLA-DR Antigens ,Virology ,Mice, Inbred C57BL ,medicine.anatomical_structure ,Haplotypes ,Ribonucleoproteins ,Antibodies, Antinuclear ,biology.protein ,Antibody ,HLA-DRB1 Chains - Abstract
Objective T cells are implicated in the production of anti-La/SSB and anti-Ro/SSA autoantibodies commonly associated with the DR3/DQ2 haplotype in systemic lupus erythematosus and Sjogren's syndrome. This study was undertaken to investigate the DR3/DQ2-restricted T cell response to wild-type human La (hLa) and a truncated form of mutant La. Methods Humanized transgenic mice expressing HLA–DRB1*0301/DQB1*0201 (DR3/DQ2) were immunized with recombinant antigen and examined for development of autoantibodies and T cell proliferation against overlapping peptides spanning the La autoantigen. HLA restriction and peptide binding of identified T cell epitopes to DR3 or DQ2 were determined using blocking monoclonal antibodies and a direct binding assay. Results DR3/DQ2-transgenic mice generated an unusually rapid class-switched humoral response to hLa with characteristic spreading to Ro 52 and Ro 60 proteins following hLa protein immunization. Seven T cell determinants in hLa were restricted to the HLA–DR3/DQ2 haplotype. Six epitopes tested were restricted to HLA–DR and bound DR3 with semiconserved DR3 binding motifs. No DQ restriction of these epitopes was demonstrable despite efficient DQ binding activity in some cases. No neo–T cell epitopes were identified in mutant La; however, T cells primed with mutant La exhibited a striking increase in proliferation to the epitope hLa151–168 compared with T cells primed with hLa. Conclusion Multiple DR3-restricted epitopes of hLa have been identified. These findings suggest that truncation of La produced by somatic mutation or possibly granzyme B–mediated cleavage alters the immunodominance hierarchy of T cell responsiveness to hLa and may be a factor in the initiation or maintenance of anti-La autoimmunity.
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- 2007
11. Analyzing the gene expression profile of anaplastic histology Wilms’ tumor with real-time polymerase chain reaction arrays
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Fang Fang, Yanhong Li, Xiao-Juan Du, Lichao Sun, Jian Pan, Jian Ni, Li-Xiao Xu, Na-Na Wang, Shaoyan Hu, He Zhao, Peifang Xiao, Zhi-Heng Li, Jian Wang, Xing Feng, Gang Li, Lan Cao, Yan-Fang Tao, Wenli Zhao, and Jun Lu
- Subjects
Pathology ,medicine.medical_specialty ,Cancer Research ,Ingenuity pathway analysis ,law.invention ,Real-time PCR array ,law ,Gene expression ,Genetics ,Medicine ,TP53 ,Gene ,Polymerase chain reaction ,business.industry ,TGFβ1 ,Cancer ,Histology ,Wilms' tumor ,medicine.disease ,Phenotype ,Real-time polymerase chain reaction ,Oncology ,HDAC7 ,Cancer research ,business ,Primary Research ,Pediatric anaplastic histology Wilms’ tumor - Abstract
Background Wilms’ tumor (WT) is one of the most common malignant neoplasms of the urinary tract in children. Anaplastic histology (unfavorable histology) accounts for about 10% of whole WTs, and it is the single most important histologic predictor of treatment response and survival in patients with WT; however, until now the molecular basis of this phenotype is not very clearly. Methods A real-time polymerase chain reaction (PCR) array was designed and tested. Next, the gene expression profile of pediatric anaplastic histology WT and normal adjacent tissues were analyzed. These expression data were anlyzed with Multi Experiment View (MEV) cluster software further. Datasets representing genes with altered expression profiles derived from cluster analyses were imported into the Ingenuity Pathway Analysis Tool (IPA). Results 88 real-time PCR primer pairs for quantitative gene expression analysis of key genes involved in pediatric anaplastic histology WT were designed and tested. The gene expression profile of pediatric anaplastic histology WT is significantly different from adjacent normal controls; we identified 15 genes that are up-regulated and 16 genes that are down-regulated in the former. To investigate biological interactions of these differently regulated genes, datasets representing genes with altered expression profiles were imported into the IPA for further analysis, which revealed three significant networks: Cancer, Hematological Disease, and Gene Expression, which included 27 focus molecules and a significance score of 43. The IPA analysis also grouped the differentially expressed genes into biological mechanisms related to Cell Death and Survival 1.15E−12, Cellular Development 2.84E−11, Cellular Growth and Proliferation 2.84E-11, Gene Expression 4.43E−10, and DNA Replication, Recombination, and Repair 1.39E−07. The important upstream regulators of pediatric anaplastic histology WT were TP53 and TGFβ1 signaling (P = 1.15E−14 and 3.79E−13, respectively). Conclusions Our study demonstrates that the gene expression profile of pediatric anaplastic histology WT is significantly different from adjacent normal tissues with real-time PCR array. We identified some genes that are dysregulated in pediatric anaplastic histology WT for the first time, such as HDAC7, and IPA analysis showed the most important pathways for pediatric anaplastic histology WT are TP53 and TGFβ1 signaling. This work may provide new clues into the molecular mechanisms behind pediatric anaplastic histology WT. Electronic supplementary material The online version of this article (doi:10.1186/s12935-015-0197-x) contains supplementary material, which is available to authorized users.
- Published
- 2015
12. Histone deacetylase 5 promotes Wilms' tumor cell proliferation through the upregulation of c-Met
- Author
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Jian Pan, Li‑Qun Yuan, Yun Zhou, Xiang‑Ming Yan, Xu Cao, De‑Hong Liu, Ming‑Cui Fu, Ting Zhang, and Jian Wang
- Subjects
0301 basic medicine ,Male ,Cancer Research ,C-Met ,Gene Expression ,Biology ,Biochemistry ,Wilms Tumor ,Histone Deacetylases ,03 medical and health sciences ,chemistry.chemical_compound ,Downregulation and upregulation ,Cell Line, Tumor ,Genetics ,Transcriptional regulation ,medicine ,Humans ,Molecular Biology ,Cell Proliferation ,Histone deacetylase 5 ,Oncogene ,Infant ,Receptor Protein-Tyrosine Kinases ,Wilms' tumor ,Cell cycle ,medicine.disease ,Kidney Neoplasms ,Up-Regulation ,030104 developmental biology ,Oncology ,chemistry ,Child, Preschool ,Cancer research ,Molecular Medicine ,Female ,Histone deacetylase - Abstract
The histone deacetylase (HDAC) family is comprised of enzymes, which are involved in modulating the majority of critical cellular processes, including transcriptional regulation, apoptosis, proliferation and cell cycle progression. However, the biological function of HDAC5 in Wilms' tumor remains to be fully elucidated. The present study aimed to investigate the expression and function of HDAC5 in Wilm's tumor. It was demonstrated that the mRNA and protein levels of HDAC5 were upregulated in human Wilms' tumor tissues. Overexpression of HDAC5 in G401 cells was observed to significantly promote cellular proliferation, as demonstrated by the results of an MTT assay and bromodeoxyuridine incorporation assay. By contrast, HDAC5 knockdown using small interfering RNA suppressed the proliferation of the G401 cells. At the molecular level, the present study demonstrated that HDAC5 promoted the expression of c‑Met, which has been previously identified as an oncogene. In addition, downregulation of c‑Met inhibited the proliferative effects of HDAC5 in human Wilms' tumor cells. Taken together, these results suggested that HDAC5 promotes cellular proliferation through the upregulation of c‑Met, and may provide a novel therapeutic target for the treatment of patients with Wilms' tumor.
- Published
- 2014
13. [Effects of gamma knife on gene expression of animal model for temporal lobe epilepsy in rat]
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Chunlei, Han, Fangang, Meng, Jian, Pan, Ali, Liu, Kai, Zhang, and Jianguo, Zhang
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Male ,Disease Models, Animal ,Epilepsy, Temporal Lobe ,Animals ,Gene Expression ,Rats, Wistar ,Radiosurgery ,Transcriptome ,Oligonucleotide Array Sequence Analysis ,Rats - Abstract
To explore the core controlling genes and their functions and pathways of gamma knife in the treatment of epilepsy in rats.The temporal epilepsy rats induced by stereotactic technique were irradiated with gamma knife. Total RNA samples were isolated at 3 weeks post-irradiation. After hybridization, washing and staining, the probe arrays were scanned to acquire the gene chip data. The functional categories and affected pathways of differentially regulated genes were analyzed. And the gene co-expression network was constructed to determine the core controlling genes.The differentiated genes of normal, epileptic and epileptic rats treated with gamma knife were screened by 1.5-fold method. There were a total of 766 union genes. The differentiated up-regulated and down-regulated genes were obtained. These genes were involved in functional categories such as ion transport (P = 6.85 × 10(-24)), cell adhesion (P = 1.55 × 10(-8)) , response to mechanical stimulus (P = 7.86 × 10(-7)) , potassium ion transport (P = 2.63 × 10(-6)) and such pathways as MAPK signaling (P = 5.55 × 10(-6)), calcium signaling (P = 4.29 × 10(-5)) and TGF-beta signaling (P0.01), etc. And the core controlling genes from the gene co-expression network included Arf3, Akap5, Omd and Rtn4r, etc.Gamma knife achieves its antiepileptic effect through modulating target genes involved in different functions and pathways.
- Published
- 2014
14. Association between interleukin 1 receptor antagonist gene 86-bp VNTR polymorphism and sepsis: a meta-analysis
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Fang Fang, Jian Pan, Gang Li, Jian Wang, Yi-Ping Li, Guang-Hao Su, and Li-Xiao Xu
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Risk ,medicine.medical_specialty ,Immunology ,Gene Expression ,Minisatellite Repeats ,Gastroenterology ,Sepsis ,Gene Frequency ,Internal medicine ,Genetic model ,medicine ,Odds Ratio ,Immunology and Allergy ,Humans ,Genetic Predisposition to Disease ,Allele ,Alleles ,Polymorphism, Genetic ,Models, Genetic ,business.industry ,Receptors, Interleukin-1 ,General Medicine ,Odds ratio ,medicine.disease ,Survival Analysis ,Confidence interval ,Interleukin 1 Receptor Antagonist Protein ,Interleukin 1 receptor antagonist ,Meta-analysis ,business ,Vntr polymorphism - Abstract
Objective Many studies have focused on the relationship between interleukin 1 receptor antagonist ( IL1RN ) gene 86-bp VNTR polymorphism and sepsis, but the results remain inconsistent. Thus, a meta-analysis was carried out to derive a more precise estimation of the association between IL1RN 86-bp VNTR polymorphism and risk of sepsis and sepsis-related mortality. Methods Relevant publications were searched in several widely used databases and six eligible studies were included in the meta-analysis. Pooled odds ratios (ORs) and 95% confidence intervals (CIs) were calculated to evaluate the strength of the association between IL1RN 86-bp VNTR polymorphism and risk of sepsis and sepsis-related mortality. Results Significant associations between IL1RN 86-bp VNTR polymorphism and sepsis risk were observed in both overall meta-analysis for L2 versus 22 (OR = 0.75, 95% CI = 0.59–0.94) and severe sepsis subgroup for LL + L2 versus 22 (OR = 0.67, 95% CI = 0.47–0.93). L stands for long alleles containing three to six repeats; 2 stands for short allele containing two repeats. However, no significant sepsis mortality variation was detected for all genetic models. Conclusions According to the results of our meta-analysis, the IL1RN 86-bp VNTR polymorphism probably associates with sepsis risk but not with sepsis-related mortality.
- Published
- 2014
15. Molecular cloning and expression analysis of the ethylene insensitive3 (EIN3) gene in cucumber (Cucumis sativus)
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H.L. He, Jian Pan, J.L. Zhao, Beibei Bie, X.Q. Yang, and R. Cai
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Models, Molecular ,Sequence analysis ,Molecular Sequence Data ,Gene Expression ,Sequence alignment ,Flowers ,Molecular cloning ,Polymerase Chain Reaction ,Rapid amplification of cDNA ends ,Gene Expression Regulation, Plant ,Complementary DNA ,Genetics ,Amino Acid Sequence ,Cloning, Molecular ,Molecular Biology ,Gene ,Phylogeny ,Plant Proteins ,Binding Sites ,biology ,Base Sequence ,Sequence Homology, Amino Acid ,General Medicine ,Sequence Analysis, DNA ,biology.organism_classification ,Protein Structure, Tertiary ,Open reading frame ,Biochemistry ,Organ Specificity ,Cucumis sativus ,Cucumis ,Transcription Factors - Abstract
The plant gaseous hormone ethylene regulates many aspects of plant growth, development, and responses to the environment. Ethylene insensitive3 (EIN3) is a key transcription factor involved in the ethylene signal transduction pathway. To gain a better understanding of this particular pathway in cucumber, the full-length cDNA encoding EIN3 (designated as CsEIN3) was cloned from cucumber for the first time by rapid amplification of cDNA ends. The full length of CsEIN3 was 2560 bp, with an open reading frame of 1908 bp encoding 635 amino acids. Sequence alignment and phylogenetic analyses revealed that CsEIN3 has high homology with other plant EIN3/EIL proteins that were derived from a common ancestor during evolution, and CsEIN3 was grouped into a cluster along with melon. Homology modeling demonstrated that CsEIN3 has a highly similar structure to the specific DNA-binding domain contained in EIN3/EIL proteins. Based on quantitative reverse transcription-polymerase chain reaction analysis, we found that CsEIN3 was constitutively expressed in all organs examined, and was increased during flower development and maturation in both male and female flowers. Our results suggest that CsEIN3 is involved in processes of flower development. In conclusion, this study will provide the basis for further study on the role of EIN3 in relevant biological processes of cucumber and on the molecular mechanism of the cucumber ethylene signaling pathway.
- Published
- 2013
16. Differential Gene Expression Caused by the F and M Loci Provides Insight Into Ethylene-Mediated Female Flower Differentiation in Cucumber.
- Author
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Jian Pan, Gang Wang, Haifan Wen, Hui Du, Hongli Lian, Huanle He, Junsong Pan, and Run Cai
- Subjects
GENE expression ,FLOWERS ,CUCUMBER genetics ,PHYSIOLOGY - Abstract
In cucumber (Cucumis sativus L.), the differentiation and development of female flowers are important processes that directly affect the fruit yield and quality. Sex differentiation is mainly controlled by three ethylene synthase genes, F (CsACS1G), M (CsACS2), and A (CsACS11). Thus, ethylene plays a key role in the sex differentiation in cucumber. The "one-hormone hypothesis" posits that F and M regulate the ethylene levels and initiate female flower development in cucumber. Nonetheless, the precise molecular mechanism of this process remains elusive. To investigate the mechanism by which F and M regulate the sex phenotype, three cucumber near-isogenic lines, namely H34 (FFmmAA, hermaphroditic), G12 (FFMMAA, gynoecious), and M12 (ffMMAA, monoecious), with different F and M loci were generated. The transcriptomic analysis of the apical shoots revealed that the expression of the B-class floral homeotic genes, CsPI (Csa4G358770) and CsAP3 (Csa3G865440), was immensely suppressed in G12 (100% female flowers) but highly expressed in M12 (~90% male flowers). In contrast, CAG2 (Csa1G467100), which is an AG-like C-class floral homeotic gene, was specifically highly expressed in G12. Thus, the initiation of female flowers is likely to be caused by the downregulation of B-class and upregulation of C-class genes by ethylene production in the floral primordium. Additionally, CsERF31, which was highly expressed in G12, showed temporal and spatial expression patterns similar to those of M and responded to the ethylene-related chemical treatments. The biochemical experiments further demonstrated that CsERF31 could directly bind the promoter of M and promote its expression. Thus, CsERF31 responded to the ethylene signal derived from F and mediated the positive feedback regulation of ethylene by activating M expression, which offers an extended "one-hormone hypothesis" of sex differentiation in cucumber. [ABSTRACT FROM AUTHOR]
- Published
- 2018
- Full Text
- View/download PDF
17. Identification of potential transcriptomic markers in developing pediatric sepsis: a weighted gene co-expression network analysis and a case-control validation study.
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Yiping Li, Yanhong Li, Zhenjiang Bai, Jian Pan, Jian Wang, Fang Fang, Li, Yiping, Li, Yanhong, Bai, Zhenjiang, Pan, Jian, Wang, Jian, and Fang, Fang
- Subjects
SEPTICEMIA in children ,GENE expression ,CHILD mortality ,TRANSCRIPTION factors ,MICRORNA ,POLYMERASE chain reaction - Abstract
Background: Sepsis represents a complex disease with the dysregulated inflammatory response and high mortality rate. The goal of this study was to identify potential transcriptomic markers in developing pediatric sepsis by a co-expression module analysis of the transcriptomic dataset.Methods: Using the R software and Bioconductor packages, we performed a weighted gene co-expression network analysis to identify co-expression modules significantly associated with pediatric sepsis. Functional interpretation (gene ontology and pathway analysis) and enrichment analysis with known transcription factors and microRNAs of the identified candidate modules were then performed. In modules significantly associated with sepsis, the intramodular analysis was further performed and "hub genes" were identified and validated by quantitative real-time PCR (qPCR) in this study.Results: 15 co-expression modules in total were detected, and four modules ("midnight blue", "cyan", "brown", and "tan") were most significantly associated with pediatric sepsis and suggested as potential sepsis-associated modules. Gene ontology analysis and pathway analysis revealed that these four modules strongly associated with immune response. Three of the four sepsis-associated modules were also enriched with known transcription factors (false discovery rate-adjusted P < 0.05). Hub genes were identified in each of the four modules. Four of the identified hub genes (MYB proto-oncogene like 1, killer cell lectin like receptor G1, stomatin, and membrane spanning 4-domains A4A) were further validated to be differentially expressed between septic children and controls by qPCR.Conclusions: Four pediatric sepsis-associated co-expression modules were identified in this study. qPCR results suggest that hub genes in these modules are potential transcriptomic markers for pediatric sepsis diagnosis. These results provide novel insights into the pathogenesis of pediatric sepsis and promote the generation of diagnostic gene sets. [ABSTRACT FROM AUTHOR]- Published
- 2017
- Full Text
- View/download PDF
18. TM4SF3 promotes esophageal carcinoma metastasis via upregulating ADAM12m expression
- Author
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Liang Peng, Long Yu, Li Xin Sun, Zhi Hua Yang, Jian Pan, Xi Lu Zhao, Zhuan Zhou, Zhi Feng Li, Yu Liang Ran, Hai Hu, Li Zhao Chen, and Li Chao Sun
- Subjects
Male ,Cancer Research ,medicine.medical_specialty ,Pathology ,Esophageal Neoplasms ,Tetraspanins ,Blotting, Western ,ADAM12 Protein ,Gene Expression ,Mice, Nude ,Transfection ,Metastasis ,Mice ,Tetraspanin ,Downregulation and upregulation ,Surgical oncology ,Antigens, Neoplasm ,Cell Movement ,Internal medicine ,Cell Line, Tumor ,medicine ,Carcinoma ,Animals ,Humans ,Neoplasm Invasiveness ,Neoplasm Metastasis ,Aged ,Oligonucleotide Array Sequence Analysis ,Hematology ,Membrane Glycoproteins ,business.industry ,Membrane Proteins ,Cell migration ,General Medicine ,Esophageal cancer ,Middle Aged ,medicine.disease ,Up-Regulation ,Gene Expression Regulation, Neoplastic ,ADAM Proteins ,Oncology ,Carcinoma, Squamous Cell ,Female ,business - Abstract
Esophageal cancer is characterized by rapid clinical progression and poor prognosis due to adjacent tissue invasion and distant organs metastasis at a very early stage. TM4SF3 (transmembrane 4 superfamily 3), a member of tetraspanin family, has been reported as a metastasis associated gene in many types of tumors. Herein, we described new properties of TM4SF3 in tumor metastasis, which suggested that this gene might be involved in esophageal carcinoma metastasis. Western blotting revealed that TM4SF3 was overexpressed in 57.1% (8/14) of esophageal carcinomas and esophageal carcinoma cell lines with high-invasive potential. Exogenous expression of TM4SF3 in two low-invasive esophageal carcinoma cell lines, KYSE150 and EC9706, significantly promoted cell migration and invasion. Upregulating TM4SF3 expression in EC9706 cells promoted xenograft tumor invading into surrounding tissues, enhanced lung metastasis, and shortened the lifespan of mice (median survival EC9706-TM4SF3 106.5 days versus EC9706-Vector 169.0 days, P < 0.0001) in a spontaneous metastasis model. Further studies demonstrated that ADAM12m was upregulated by TM4SF3 overexpression in vitro and in vivo. Abrogating up-expression of ADAM12m by siRNA significantly suppressed TM4SF3-mediated invasion. Together, these data from our studies indicated that overexpression of TM4SF3 in esophageal cancer conferred advantage to the invasion and metastasis of this destructive disease. Upregulated expression of ADAM12m by TM4SF3 might play a key role in TM4SF3-mediated invasion and metastasis. TM4SF3 and ADAM12m might be potential targets of esophageal carcinoma for anti-metastasis therapy.
- Published
- 2007
19. Expression of angiopoietin-like 4 and tenascin C but not cathepsin C mRNA predicts prognosis of oral tongue squamous cell carcinoma
- Author
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Jian Pan, Bo Han, Zhuomin Wang, Hui Xia, and Zhuang Zhang
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Pathology ,medicine.medical_specialty ,Health, Toxicology and Mutagenesis ,Clinical Biochemistry ,Biochemistry ,Cathepsin C ,Tongue ,Predictive Value of Tests ,Gene expression ,Carcinoma ,medicine ,Angiopoietin-Like Protein 4 ,Humans ,RNA, Messenger ,Neoplasm Metastasis ,biology ,business.industry ,Reverse Transcriptase Polymerase Chain Reaction ,Gene Expression Profiling ,Tenascin C ,Cancer ,RNA ,Tenascin ,medicine.disease ,Prognosis ,Tongue Neoplasms ,Real-time polymerase chain reaction ,medicine.anatomical_structure ,embryonic structures ,biology.protein ,Carcinoma, Squamous Cell ,RNA extraction ,business ,Angiopoietins - Abstract
Analysis of gene expression using RNA from the paraffin-embedded tissues is becoming an important way to study cancer pathogenesis. In this article, total RNA was extracted from tissue of 158 cases of paraffin-embedded tongue cancer, and expression of angiopoietin-like 4, tenascin-C and cathepsin-C were detected by real-time reverse transcriptase-polymerase chain reaction (RT-PCR). Our results demonstrated that high expression level of angiopoietin-like 4 or tenascin-C was predictive of poor prognosis of tongue cancer patients (p = 0.024 and p = 0.011, respectively), especially when expression levels of both genes were concomitantly high (p = 0.001). Additionally, high expression of angiopoietin-like 4 and tenascin-C, or concomitant high expression of angiopoietin-like 4 and tenascin-C were independent prognostic factors of poor survival in patients with tongue cancer. These results suggest that the improved method of RNA extraction is suitable for analysing gene expression of paraffin-embedded solid tumours. Angiopoietin-like and tenascin-C, especially the combination of angiopoietin-like 4 and tenascin-C, are useful for predicting the prognosis of the patients with tongue cancer, independent of lymph node metastasis status.
- Published
- 2009
20. Analyzing the gene expression profile of anaplastic histology Wilms' tumor with real-time polymerase chain reaction arrays.
- Author
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Jun Lu, Yan-Fang Tao, Zhi-Heng Li, Lan Cao, Shao-Yan Hu, Na-Na Wang, Xiao-Juan Du, Li-Chao Sun, Wen-Li Zhao, Pei-Fang Xiao, Fang Fang, Li-xiao Xu, Yan-Hong Li, Gang Li, He Zhao, Jian Ni, Jian Wang, Xing Feng, and Jian Pan
- Subjects
POLYMERASE chain reaction ,NEPHROBLASTOMA ,GENE expression ,PHENOTYPES ,CLUSTER analysis (Statistics) - Abstract
Background: Wilms' tumor (WT) is one of the most common malignant neoplasms of the urinary tract in children. Anaplastic histology (unfavorable histology) accounts for about 10% of whole WTs, and it is the single most important histologic predictor of treatment response and survival in patients with WT; however, until now the molecular basis of this phenotype is not very clearly. Methods: A real-time polymerase chain reaction (PCR) array was designed and tested. Next, the gene expression profile of pediatric anaplastic histology WT and normal adjacent tissues were analyzed. These expression data were anlyzed with Multi Experiment View (MEV) cluster software further. Datasets representing genes with altered expression profiles derived from cluster analyses were imported into the Ingenuity Pathway Analysis Tool (IPA). Results: 88 real-time PCR primer pairs for quantitative gene expression analysis of key genes involved in pediatric anaplastic histology WT were designed and tested. The gene expression profile of pediatric anaplastic histology WT is significantly different from adjacent normal controls; we identified 15 genes that are up-regulated and 16 genes that are down-regulated in the former. To investigate biological interactions of these differently regulated genes, datasets representing genes with altered expression profiles were imported into the IPA for further analysis, which revealed three significant networks: Cancer, Hematological Disease, and Gene Expression, which included 27 focus molecules and a significance score of 43. The IPA analysis also grouped the differentially expressed genes into biological mechanisms related to Cell Death and Survival 1.15E
-12 , Cellular Development 2.84E-11 , Cellular Growth and Proliferation 2.84E-11 , Gene Expression 4.43E-10 , and DNA Replication, Recombination, and Repair 1.39E-07 . The important upstream regulators of pediatric anaplastic histology WT were TP53 and TGFβ1 signaling (P = 1.15E-14 and 3.79E-13 , respectively). Conclusions: Our study demonstrates that the gene expression profile of pediatric anaplastic histology WT is significantly different from adjacent normal tissues with real-time PCR array. We identified some genes that are dysregulated in pediatric anaplastic histology WT for the first time, such as HDAC7, and IPA analysis showed the most important pathways for pediatric anaplastic histology WT are TP53 and TGFβ1 signaling. This work may provide new clues into the molecular mechanisms behind pediatric anaplastic histology WT. [ABSTRACT FROM AUTHOR]- Published
- 2015
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21. Oral cancer cells with different potential of lymphatic metastasis displayed distinct biologic behaviors and gene expression profiles.
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Zhuang, Zhang, Jian, Pan, Longjiang, Li, Bo, Han, and Wenlin, Xiao
- Subjects
- *
ORAL cancer , *CANCER cells , *GENE expression , *METASTASIS , *SQUAMOUS cell carcinoma - Abstract
J Oral Pathol Med (2010) 39 168–175 Objective: Oral squamous cell carcinoma (OSCC) often spreads from the primary tumor to regional lymph nodes in the early stage. Better understanding of the biology of lymphatic spread of oral cancer cells is important for improving the survival rate of cancer patients. Methods: We established the cell line LNMTca8113 by repeated injections in foot pads of nude mice, which had a much higher lymphatic metastasis rate than its parental cell line Tca8113. Then, we compared the biologic behaviors of cancer cells between them. Moreover, microarray-based expression profiles between them were also compared, and a panel of differential genes was validated using real-time-PCR. Results: In contrast to Tca8113 cells, LNMTca8113 cells were more proliferative and resistant to apoptosis in the absence of serum, and had enhanced ability of inducing capillary-like structures. Moreover, microarray-based expression profiles between them identified 1341 genes involved in cell cycle, cell adhesion, lymphangiogenesis, regulation of apoptosis, and so on. Some genes dedicating to the metastatic potential, including JAM2, TNC, CTSC, LAMB1, VEGFC, HAPLN1, ACPP, GDF9 and FGF11, were upregulated in LNMTca8113 cells. Conclusion: These results suggested that LNMTca8113 and Tca8113 cells were proper models for lymphatic metastasis study because there were differences in biologic behaviors and metastasis-related genes between them. Additionally, the differentially expressed gene profiles in cancer progression may be helpful in exploring therapeutic targets and provide the foundation for further functional validation of these specific candidate genes for OSCC. [ABSTRACT FROM AUTHOR]
- Published
- 2010
- Full Text
- View/download PDF
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