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Lu Y, Zhao C, Wang C, Cai H, Hu Y, Chen L, Yu S, Zhu H, Liu P, Wan'e W, Zhang H. The effect and mechanism of Qingre Huashi formula in the treatment of chronic hepatitis B with Gan-dan-shi-Re syndrome: An integrated transcriptomic and targeted metabolomic analysis. JOURNAL OF ETHNOPHARMACOLOGY 2024; 319:117092. [PMID: 37634751 DOI: 10.1016/j.jep.2023.117092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 08/20/2023] [Accepted: 08/24/2023] [Indexed: 08/29/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Qingre Huashi (QRHS) formula is an empirical prescription for the treatment of Gan-Dan-Shi-Re syndrome (GDSR) syndrome in traditional Chinese medicine (TCM). GDSR is one of the typical TCM syndromes in chronic hepatitis B (CHB). However, little is known about the mechanism of the QRHS formula in treating CHB patients with GDSR. The biological basis of GDSR also remains largely unknown. AIM OF THE STUDY GDSR mostly occurs in the acute and early stages of chronic liver disease. Effectively alleviating GDSR stalls disease development and benefits patients. The purpose of this study was to explore the molecular basis of GDSR in CHB and then study the mechanism of the QRHS formula treating GDSR using transcriptomics and metabolomics. MATERIALS AND METHODS The transcriptome and metabolome of CHB patients with GDSR syndrome were detected using RNA microarray combined with ultra-high performance liquid chromatography/mass spectrometry and information mining. The potential biomarkers were identified from differentially expressed genes and metabolites, and the metabolic pathway was analyzed. We also investigated the callback of metabolic biomarkers after treatment with the QRHS formula, an empirical prescription for the treatment of GDSR syndrome. RT-PCR analysis was carried out in an independent patient cohort of CHB for validation. RESULTS Four candidate genes-GPT2, HK2, DDIT3, and HIF1A-and 14 candidate metabolic biomarkers, including L-alpha-aminobutyric acid, selenomethionine, and fructose 1,6-bisphosphate, were identified and validated. All four transcripts of GPT2, HK2, DDIT3, and HIF1A were significantly differentially expressed between the GDSR and non-GDSR groups through independent microarray data and RT-PCR. After treatment with the QRHS formula, the clinical indexes and TCM syndrome were significantly improved, and the 14 disturbed biomarkers were obviously corrected. Three metabolic pathways were confirmed to be perturbed in CHB GDSR patients: alanine, aspartate, and glutamate metabolism, arginine biosynthesis, and aminoacyl-tRNA biosynthesis. CONCLUSION Using integrated transcriptomic and targeted metabolomic methods, we identified the potential biomarkers and dysregulated metabolic pathways in CHB patients with GDSR syndrome, which was alleviated by the QRHS formula treatment. These results may provide the mechanism of metabolic dysregulation in GDSR syndrome as well as that underlying the curative effect of the QRHS formula.
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Affiliation(s)
- Yiyu Lu
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Chaoqun Zhao
- Institute of Liver Diseases, Key Laboratory of Liver and Kidney Diseases (Ministry of Education), Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Chengbao Wang
- Shandong Medical College, Jinan, Shandong, 250004, China
| | - Hong Cai
- Xiamen Hospital of Traditional Chinese Medicine, Xiamen, 361015, China
| | - Yuting Hu
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Long Chen
- Institute of Liver Diseases, Key Laboratory of Liver and Kidney Diseases (Ministry of Education), Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Shanghai Yu
- Institute of Liver Diseases, Key Laboratory of Liver and Kidney Diseases (Ministry of Education), Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Huiming Zhu
- Fifth People's Hospital of Suzhou, Jiangsu, 215007, China
| | - Ping Liu
- Institute of Liver Diseases, Key Laboratory of Liver and Kidney Diseases (Ministry of Education), Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Wang Wan'e
- Huai'an Fourth People's Hospital, Huai'an, Jiangsu, 223300, China.
| | - Hua Zhang
- Institute of Liver Diseases, Key Laboratory of Liver and Kidney Diseases (Ministry of Education), Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China.
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Ravichandran P, Parsana P, Keener R, Hansen KD, Battle A. Aggregation of recount3 RNA-seq data improves inference of consensus and tissue-specific gene co-expression networks. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.20.576447. [PMID: 38328080 PMCID: PMC10849507 DOI: 10.1101/2024.01.20.576447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Background Gene co-expression networks (GCNs) describe relationships among expressed genes key to maintaining cellular identity and homeostasis. However, the small sample size of typical RNA-seq experiments which is several orders of magnitude fewer than the number of genes is too low to infer GCNs reliably. recount3, a publicly available dataset comprised of 316,443 uniformly processed human RNA-seq samples, provides an opportunity to improve power for accurate network reconstruction and obtain biological insight from the resulting networks. Results We compared alternate aggregation strategies to identify an optimal workflow for GCN inference by data aggregation and inferred three consensus networks: a universal network, a non-cancer network, and a cancer network in addition to 27 tissue context-specific networks. Central network genes from our consensus networks were enriched for evolutionarily constrained genes and ubiquitous biological pathways, whereas central context-specific network genes included tissue-specific transcription factors and factorization based on the hubs led to clustering of related tissue contexts. We discovered that annotations corresponding to context-specific networks inferred from aggregated data were enriched for trait heritability beyond known functional genomic annotations and were significantly more enriched when we aggregated over a larger number of samples. Conclusion This study outlines best practices for network GCN inference and evaluation by data aggregation. We recommend estimating and regressing confounders in each data set before aggregation and prioritizing large sample size studies for GCN reconstruction. Increased statistical power in inferring context-specific networks enabled the derivation of variant annotations that were enriched for concordant trait heritability independent of functional genomic annotations that are context-agnostic. While we observed strictly increasing held-out log-likelihood with data aggregation, we noted diminishing marginal improvements. Future directions aimed at alternate methods for estimating confounders and integrating orthogonal information from modalities such as Hi-C and ChIP-seq can further improve GCN inference.
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Affiliation(s)
| | - Princy Parsana
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
| | - Rebecca Keener
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Kaspar D Hansen
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
- Department of Biostatistics, Johns Hopkins School of Public Health, Baltimore, MD, USA
- Department of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Alexis Battle
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
- Department of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
- Malone Center for Engineering in Healthcare, Johns Hopkins University, Baltimore, MD, USA
- Data Science and AI Institute, Johns Hopkins University, Baltimore, MD, USA
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Li M, Yu H, Zhou B, Gan L, Li S, Zhang C, Yu B. JANUS, a spliceosome-associated protein, promotes miRNA biogenesis in Arabidopsis. Nucleic Acids Res 2024; 52:420-430. [PMID: 37994727 PMCID: PMC10783502 DOI: 10.1093/nar/gkad1105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 10/27/2023] [Accepted: 11/06/2023] [Indexed: 11/24/2023] Open
Abstract
MicroRNAs (miRNAs) are important regulators of genes expression. Their levels are precisely controlled through modulating the activity of the microprocesser complex (MC). Here, we report that JANUS, a homology of the conserved U2 snRNP assembly factor in yeast and human, is required for miRNA accumulation. JANUS associates with MC components Dicer-like 1 (DCL1) and SERRATE (SE) and directly binds the stem-loop of pri-miRNAs. In a hypomorphic janus mutant, the activity of DCL1, the numbers of MC, and the interaction of primary miRNA transcript (pri-miRNAs) with MC are reduced. These data suggest that JANUS promotes the assembly and activity of MC through its interaction with MC and/or pri-miRNAs. In addition, JANUS modulates the transcription of some pri-miRNAs as it binds the promoter of pri-miRNAs and facilitates Pol II occupancy of at their promoters. Moreover, global splicing defects are detected in janus. Taken together, our study reveals a novel role of a conserved splicing factor in miRNA biogenesis.
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Affiliation(s)
- Mu Li
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE 68588–0666, USA
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE 68588–0118, USA
| | - Huihui Yu
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE 68588–0666, USA
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE 68588–0118, USA
| | - Bangjun Zhou
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE 68588–0666, USA
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE 68588–0118, USA
| | - Lu Gan
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE 68588–0666, USA
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE 68588–0118, USA
| | - Shengjun Li
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Shandong Energy Institute, Qingdao New Energy Shangdong Laboratory, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
| | - Chi Zhang
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE 68588–0666, USA
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE 68588–0118, USA
| | - Bin Yu
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE 68588–0666, USA
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE 68588–0118, USA
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Bukharina TA, Golubyatnikov VP, Furman DP. The central regulatory circuit in the gene network controlling the morphogenesis of Drosophila mechanoreceptors: an in silico analysis. Vavilovskii Zhurnal Genet Selektsii 2023; 27:746-754. [PMID: 38213705 PMCID: PMC10777295 DOI: 10.18699/vjgb-23-87] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 09/20/2023] [Accepted: 09/25/2023] [Indexed: 01/13/2024] Open
Abstract
Identification of the mechanisms underlying the genetic control of spatial structure formation is among the relevant tasks of developmental biology. Both experimental and theoretical approaches and methods are used for this purpose, including gene network methodology, as well as mathematical and computer modeling. Reconstruction and analysis of the gene networks that provide the formation of traits allow us to integrate the existing experimental data and to identify the key links and intra-network connections that ensure the function of networks. Mathematical and computer modeling is used to obtain the dynamic characteristics of the studied systems and to predict their state and behavior. An example of the spatial morphological structure is the Drosophila bristle pattern with a strictly defined arrangement of its components - mechanoreceptors (external sensory organs) - on the head and body. The mechanoreceptor develops from a single sensory organ parental cell (SOPC), which is isolated from the ectoderm cells of the imaginal disk. It is distinguished from its surroundings by the highest content of proneural proteins (ASC), the products of the achaete-scute proneural gene complex (AS-C). The SOPC status is determined by the gene network we previously reconstructed and the AS-C is the key component of this network. AS-C activity is controlled by its subnetwork - the central regulatory circuit (CRC) comprising seven genes: AS-C, hairy, senseless (sens), charlatan (chn), scratch (scrt), phyllopod (phyl), and extramacrochaete (emc), as well as their respective proteins. In addition, the CRC includes the accessory proteins Daughterless (DA), Groucho (GRO), Ubiquitin (UB), and Seven-in-absentia (SINA). The paper describes the results of computer modeling of different CRC operation modes. As is shown, a cell is determined as an SOPC when the ASC content increases approximately 2.5-fold relative to the level in the surrounding cells. The hierarchy of the effects of mutations in the CRC genes on the dynamics of ASC protein accumulation is clarified. AS-C as the main CRC component is the most significant. The mutations that decrease the ASC content by more than 40 % lead to the prohibition of SOPC segregation.
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Affiliation(s)
- T A Bukharina
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Novosibirsk State University, Novosibirsk, Russia
| | - V P Golubyatnikov
- Sobolev Institute of Mathematics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - D P Furman
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Novosibirsk State University, Novosibirsk, Russia
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A preliminary analysis of prognostic genes in advanced laryngeal squamous cell carcinoma patients with postoperative radiotherapy. Pathol Res Pract 2023; 241:154229. [PMID: 36509010 DOI: 10.1016/j.prp.2022.154229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Revised: 11/12/2022] [Accepted: 11/16/2022] [Indexed: 11/30/2022]
Abstract
Advanced laryngeal squamous cell carcinoma (LSCC) has a high mortality rate, and the prognosis is poor. However, the underlying molecular biological mechanisms bringing about the development and progression of advanced LSCC are not entirely clarified. This study aimed to find out the potential biomarkers to predict the prognosis in advanced LSCC patients who had undergone postoperative radiotherapy alone. The next-generation sequencing of RNA was performed to detect the mRNAs expression profiling in 10 advanced LSCC samples, comprised of 5 samples from LSCC patients with favorable outcome and 5 samples from paired patients with poor outcome. Then bioinformatics analysis including Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway were used to find out functional core genes that were significantly different between the two groups. 1630 differentially expressed genes (DEGs) were confirmed to have significant differences between the two groups. 53 GO terms and 19 pathways which were closely related to the DEGs were identified. Finally, 52 intersection DEGs which were both related to the top three GO terms and pathways were identified. The expression of several core genes was confirmed with RT-qPCR in tissues from another 75 patients. RT-qPCR confirmed that the genes of c-JUN, LYN, PIK3R2, and TNFAIP3 were significantly differentially expressed between the two groups, which was in accordance with the RNA sequencing data. The DEGs identified above may be potential prognostic markers for advanced LSCC patients with postoperative radiotherapy, and may provide essential guidance for following-up.
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Synthetic negative genome screen of the GPN-loop GTPase NPA3 in Saccharomyces cerevisiae. Curr Genet 2022; 68:343-360. [PMID: 35660944 DOI: 10.1007/s00294-022-01243-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 04/21/2022] [Accepted: 04/30/2022] [Indexed: 11/03/2022]
Abstract
The GPN-loop GTPase Npa3 is encoded by an essential gene in the yeast Saccharomyces cerevisiae. Npa3 plays a critical role in the assembly and nuclear accumulation of RNA polymerase II (RNAPII), a function that may explain its essentiality. Genetic interactions describe the extent to which a mutation in a particular gene affects a specific phenotype when co-occurring with an alteration in a second gene. Discovering synthetic negative genetic interactions has long been used as a tool to delineate the functional relatedness between pairs of genes participating in common or compensatory biological pathways. Previously, our group showed that nuclear targeting and transcriptional activity of RNAPII were unaffected in cells expressing exclusively a C-terminal truncated mutant version of Npa3 (npa3∆C) lacking the last 106 residues naturally absent from the single GPN protein in Archaea, but universally conserved in all Npa3 orthologs of eukaryotes. To gain insight into novel cellular functions for Npa3, we performed here a genome-wide Synthetic Genetic Array (SGA) study coupled to bulk fluorescence monitoring to identify negative genetic interactions of NPA3 by crossing an npa3∆C strain with a 4,389 nonessential gene-deletion collection. This genetic screen revealed previously unknown synthetic negative interactions between NPA3 and 15 genes. Our results revealed that the Npa3 C-terminal tail extension regulates the participation of this essential GTPase in previously unknown biological processes related to mitochondrial homeostasis and ribosome biogenesis.
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Li M, Yu H, Liu K, Yang W, Zhou B, Gan L, Li S, Zhang C, Yu B. Serrate-Associated Protein 1, a splicing-related protein, promotes miRNA biogenesis in Arabidopsis. THE NEW PHYTOLOGIST 2021; 232:1959-1973. [PMID: 34449907 PMCID: PMC8568667 DOI: 10.1111/nph.17691] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 08/20/2021] [Indexed: 06/02/2023]
Abstract
MicroRNAs (miRNAs) are essential regulators of gene expression in metazoans and plants. In plants, most miRNAs are generated from primary miRNA transcripts (pri-miRNAs), which are processed by the Dicer-like 1 (DCL1) complex along with accessory proteins. Serrate-Associated Protein 1 (SEAP1), a conserved splicing-related protein, has been studied in human and yeast. However, the functions of SEAP1 in plants remain elusive. Lack of SEAP1 results in embryo lethality and knockdown of SEAP1 by an artificial miRNA (amiRSEAP1 ) causes pleiotropic developmental defects and reduction in miRNA accumulation. SEAP1 associates with the DCL1 complex, and may promote the interaction of the DCL1 complexes with pri-miRNAs. SEAP1 also enhances pri-miRNA accumulation, but does not affect pri-miRNA transcription, suggesting it may indirectly or directly stabilize pri-miRNAs. In addition, SEAP1 affects the splicing of some pri-miRNAs and intron retention of messenger RNAs at global levels. Our findings uncover both conserved and novel functions of SEAP1 in plants. Besides the role as a splicing factor, SEPA1 may promote miRNA biogenesis by positively modulating pri-miRNA splicing, processing and/or stability.
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Affiliation(s)
- Mu Li
- School of Biological Sciences & Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, Nebraska 68588–0666, USA
| | - Huihui Yu
- School of Biological Sciences & Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, Nebraska 68588–0666, USA
| | - Kan Liu
- School of Biological Sciences & Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, Nebraska 68588–0666, USA
| | - Weilong Yang
- School of Biological Sciences & Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, Nebraska 68588–0666, USA
| | - Bangjun Zhou
- School of Biological Sciences & Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, Nebraska 68588–0666, USA
| | - Lu Gan
- School of Biological Sciences & Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, Nebraska 68588–0666, USA
| | - Shengjun Li
- School of Biological Sciences & Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, Nebraska 68588–0666, USA
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Shandong Institute of Energy Technology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
| | - Chi Zhang
- School of Biological Sciences & Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, Nebraska 68588–0666, USA
| | - Bin Yu
- School of Biological Sciences & Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, Nebraska 68588–0666, USA
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Huang J, Sheng J, Wang D. Manifold learning analysis suggests strategies to align single-cell multimodal data of neuronal electrophysiology and transcriptomics. Commun Biol 2021; 4:1308. [PMID: 34799674 PMCID: PMC8604989 DOI: 10.1038/s42003-021-02807-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 10/26/2021] [Indexed: 12/30/2022] Open
Abstract
Recent single-cell multimodal data reveal multi-scale characteristics of single cells, such as transcriptomics, morphology, and electrophysiology. However, integrating and analyzing such multimodal data to deeper understand functional genomics and gene regulation in various cellular characteristics remains elusive. To address this, we applied and benchmarked multiple machine learning methods to align gene expression and electrophysiological data of single neuronal cells in the mouse brain from the Brain Initiative. We found that nonlinear manifold learning outperforms other methods. After manifold alignment, the cells form clusters highly corresponding to transcriptomic and morphological cell types, suggesting a strong nonlinear relationship between gene expression and electrophysiology at the cell-type level. Also, the electrophysiological features are highly predictable by gene expression on the latent space from manifold alignment. The aligned cells further show continuous changes of electrophysiological features, implying cross-cluster gene expression transitions. Functional enrichment and gene regulatory network analyses for those cell clusters revealed potential genome functions and molecular mechanisms from gene expression to neuronal electrophysiology.
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Affiliation(s)
- Jiawei Huang
- Department of Statistics, University of Wisconsin - Madison, Madison, WI, 53706, USA
- Carl H. Lindner College of Business, University of Cincinnati, Cincinnati, OH, 45223, USA
| | - Jie Sheng
- Waisman Center, University of Wisconsin - Madison, Madison, WI, 53705, USA
| | - Daifeng Wang
- Waisman Center, University of Wisconsin - Madison, Madison, WI, 53705, USA.
- Department of Biostatistics and Medical Informatics, University of Wisconsin - Madison, Madison, WI, 53706, USA.
- Department of Computer Sciences, University of Wisconsin - Madison, Madison, WI, 53706, USA.
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Duru IC, Bucur FI, Andreevskaya M, Nikparvar B, Ylinen A, Grigore-Gurgu L, Rode TM, Crauwels P, Laine P, Paulin L, Løvdal T, Riedel CU, Bar N, Borda D, Nicolau AI, Auvinen P. High-pressure processing-induced transcriptome response during recovery of Listeria monocytogenes. BMC Genomics 2021; 22:117. [PMID: 33579201 PMCID: PMC7881616 DOI: 10.1186/s12864-021-07407-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 01/25/2021] [Indexed: 12/18/2022] Open
Abstract
Background High-pressure processing (HPP) is a commonly used technique in the food industry to inactivate pathogens, including L. monocytogenes. It has been shown that L. monocytogenes is able to recover from HPP injuries and can start to grow again during long-term cold storage. To date, the gene expression profiling of L. monocytogenes during HPP damage recovery at cooling temperature has not been studied. In order identify key genes that play a role in recovery of the damage caused by HPP treatment, we performed RNA-sequencing (RNA-seq) for two L. monocytogenes strains (barotolerant RO15 and barosensitive ScottA) at nine selected time points (up to 48 h) after treatment with two pressure levels (200 and 400 MPa). Results The results showed that a general stress response was activated by SigB after HPP treatment. In addition, the phosphotransferase system (PTS; mostly fructose-, mannose-, galactitol-, cellobiose-, and ascorbate-specific PTS systems), protein folding, and cobalamin biosynthesis were the most upregulated genes during HPP damage recovery. We observed that cell-division-related genes (divIC, dicIVA, ftsE, and ftsX) were downregulated. By contrast, peptidoglycan-synthesis genes (murG, murC, and pbp2A) were upregulated. This indicates that cell-wall repair occurs as a part of HPP damage recovery. We also observed that prophage genes, including anti-CRISPR genes, were induced by HPP. Interestingly, a large amount of RNA-seq data (up to 85%) was mapped to Rli47, which is a non-coding RNA that is upregulated after HPP. Thus, we predicted that Rli47 plays a role in HPP damage recovery in L. monocytogenes. Moreover, gene-deletion experiments showed that amongst peptidoglycan biosynthesis genes, pbp2A mutants are more sensitive to HPP. Conclusions We identified several genes and mechanisms that may play a role in recovery from HPP damage of L. monocytogenes. Our study contributes to new information on pathogen inactivation by HPP. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07407-6.
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Affiliation(s)
- Ilhan Cem Duru
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland.
| | - Florentina Ionela Bucur
- Faculty of Food Science and Engineering, Dunarea de Jos University of Galati, Galati, Romania
| | | | - Bahareh Nikparvar
- Department of Chemical Engineering, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Anne Ylinen
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Leontina Grigore-Gurgu
- Faculty of Food Science and Engineering, Dunarea de Jos University of Galati, Galati, Romania
| | - Tone Mari Rode
- Department of Process Technology, Nofima - Norwegian Institute of Food, Fisheries and Aquaculture Research, N-4068, Stavanger, Norway
| | - Peter Crauwels
- Institute of Microbiology and Biotechnology, Ulm, University, Albert-Einstein-Allee 11, D-89081, Ulm, Germany
| | - Pia Laine
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Lars Paulin
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Trond Løvdal
- Department of Process Technology, Nofima - Norwegian Institute of Food, Fisheries and Aquaculture Research, N-4068, Stavanger, Norway
| | - Christian U Riedel
- Institute of Microbiology and Biotechnology, Ulm, University, Albert-Einstein-Allee 11, D-89081, Ulm, Germany
| | - Nadav Bar
- Department of Chemical Engineering, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Daniela Borda
- Faculty of Food Science and Engineering, Dunarea de Jos University of Galati, Galati, Romania
| | - Anca Ioana Nicolau
- Faculty of Food Science and Engineering, Dunarea de Jos University of Galati, Galati, Romania
| | - Petri Auvinen
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
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Transcriptomic time-series analysis of cold- and heat-shock response in psychrotrophic lactic acid bacteria. BMC Genomics 2021; 22:28. [PMID: 33413101 PMCID: PMC7788899 DOI: 10.1186/s12864-020-07338-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 12/22/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Psychrotrophic lactic acid bacteria (LAB) species are the dominant species in the microbiota of cold-stored modified-atmosphere-packaged food products and are the main cause of food spoilage. Despite the importance of psychrotrophic LAB, their response to cold or heat has not been studied. Here, we studied the transcriptome-level cold- and heat-shock response of spoilage lactic acid bacteria with time-series RNA-seq for Le. gelidum, Lc. piscium, and P. oligofermentans at 0 °C, 4 °C, 14 °C, 25 °C, and 28 °C. RESULTS We observed that the cold-shock protein A (cspA) gene was the main cold-shock protein gene in all three species. Our results indicated that DEAD-box RNA helicase genes (cshA, cshB) also play a critical role in cold-shock response in psychrotrophic LAB. In addition, several RNase genes were involved in cold-shock response in Lc. piscium and P. oligofermentans. Moreover, gene network inference analysis provided candidate genes involved in cold-shock response. Ribosomal proteins, tRNA modification, rRNA modification, and ABC and efflux MFS transporter genes clustered with cold-shock response genes in all three species, indicating that these genes could be part of the cold-shock response machinery. Heat-shock treatment caused upregulation of Clp protease and chaperone genes in all three species. We identified transcription binding site motifs for heat-shock response genes in Le. gelidum and Lc. piscium. Finally, we showed that food spoilage-related genes were upregulated at cold temperatures. CONCLUSIONS The results of this study provide new insights on the cold- and heat-shock response of psychrotrophic LAB. In addition, candidate genes involved in cold- and heat-shock response predicted using gene network inference analysis could be used as targets for future studies.
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María Hernández-Domínguez E, Sofía Castillo-Ortega L, García-Esquivel Y, Mandujano-González V, Díaz-Godínez G, Álvarez-Cervantes J. Bioinformatics as a Tool for the Structural and Evolutionary Analysis of Proteins. Comput Biol Chem 2020. [DOI: 10.5772/intechopen.89594] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
This chapter deals with the topic of bioinformatics, computational, mathematics, and statistics tools applied to biology, essential for the analysis and characterization of biological molecules, in particular proteins, which play an important role in all cellular and evolutionary processes of the organisms. In recent decades, with the next generation sequencing technologies and bioinformatics, it has facilitated the collection and analysis of a large amount of genomic, transcriptomic, proteomic, and metabolomic data from different organisms that have allowed predictions on the regulation of expression, transcription, translation, structure, and mechanisms of action of proteins as well as homology, mutations, and evolutionary processes that generate structural and functional changes over time. Although the information in the databases is greater every day, all bioinformatics tools continue to be constantly modified to improve performance that leads to more accurate predictions regarding protein functionality, which is why bioinformatics research remains a great challenge.
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Wang H, Hu A, Liang Y, Wang K, Zhou X, Dong J. Genome-wide analysis of long non-coding RNA expression profile in lung adenocarcinoma compared to spinal metastasis. ANNALS OF TRANSLATIONAL MEDICINE 2020; 8:1516. [PMID: 33313261 PMCID: PMC7729335 DOI: 10.21037/atm-20-7046] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Background Long non-coding RNAs (lncRNAs) play important roles in tumor metastasis. The aim of the present study was to investigate their expression profile and potential functions in spinal metastasis (SM) of lung adenocarcinoma. Methods We conducted lncRNA and mRNA expression in lung adenocarcinoma and its SM tissue using microarray analysis. Quantitative reverse-transcriptase polymerase chain reaction (qRT-PCR) revealed 10 differentially expressed lncRNAs. Gene ontology and pathway analysis were performed to test the gene effect. Possible target genes of lncRNAs were predicted based on precise algorithms. Results Microarray analysis found many significantly differentially expressed lncRNAs and mRNAs in lung adenocarcinoma compared with SM. qRT-PCR results aligned with those of the microarray analysis. The expression level of 10 lncRNAs showed the same trend (P<0.05). Biologic pathways known to be involved in cancer were identified among the differentially expressed mRNAs; these include cell adhesion molecules (related to 42 genes), focal adhesion (related to 31 genes), cytokine-cytokine receptor interaction (related to 48 genes), and extracellular matrix-receptor interaction (related to 23 genes). About 9,458 lncRNAs were found to have cis- or trans-genes. A total of 2,317 cis target genes were discovered to be abnormally expressed and could be regulated by lncRNAs in SM of lung adenocarcinoma. Conclusions Our results offer a genome-wide differential expression of lncRNA in lung adenocarcinoma and SM, as well as laying the foundation for further investigations of lncRNAs correlated with lung adenocarcinoma metastasis.
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Affiliation(s)
- Houlei Wang
- Department of Orthopaedic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Annan Hu
- Department of Orthopaedic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yun Liang
- Department of Orthopaedic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Ketao Wang
- Department of Orthopaedic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Xiaogang Zhou
- Department of Orthopaedic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Jian Dong
- Department of Orthopaedic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
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Zhao J, Xu C, Cao H, Zhang L, Wang X, Chen S. Identification of target genes in neuroinflammation and neurodegeneration after traumatic brain injury in rats. PeerJ 2019; 7:e8324. [PMID: 31875163 PMCID: PMC6925952 DOI: 10.7717/peerj.8324] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Accepted: 12/01/2019] [Indexed: 01/01/2023] Open
Abstract
Background Traumatic brain injury (TBI) is a common neurological emergency observed in hospitals. A considerable number of patients suffer from long-term disabilities after TBI. This study aimed to identify altered gene expression signatures and mechanisms related to TBI-induced chronic neuroinflammation and neurodegeneration. Methods An integrated analysis was performed using published RNA-sequencing studies to determine TBI-induced differentially expressed genes (DEGs). Based on the DEG data, functional annotation, signal-net, and transcription factor analyses were conducted to understand the mechanism of chronic neuroinflammation and neurodegeneration induced after TBI. Results Two datasets were obtained using the Gene Expression Omnibus database, of which, 6,513 DEGs were identified (6,464 upregulated and 49 downregulated). Positive regulation of biological process, positive regulation of cellular process, nucleus, and heterocyclic compound binding were Gene Ontology terms significantly enriched in post-TBI rat models. Leukocyte transendothelial migration, chemokine signaling pathway, neurotrophin signaling pathway, and longevity-regulating pathway were significantly enriched after TBI. With regard to the signal-net analysis, FOXO3, DGKZ and ILK were considered the most critical genes derived using high–betweenness centrality calculation. A total of 44 TFs, including FOXO1, SRY and KLF4, were predicted to play an important role in the upregulation of gene expression. Using integrated bioinformatics analysis, TBI was found to be associated with a significant inflammatory response and neurodegeneration. FOXO3, apolipoprotein (APOE), microtubule-associated protein tau (MAPT), and TREM2 were probably associated with the TBI pathological process. The mitochondrial electron transport chain may be associated with neurodegeneration in patients with TBI, serving as a potential therapeutic target.
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Affiliation(s)
- Jianwei Zhao
- Department of Neurosurgery, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Chen Xu
- Department of Neurosurgery, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Heli Cao
- Department of Neurosurgery, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Lin Zhang
- Department of Neurosurgery, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Xuyang Wang
- Department of Neurosurgery, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Shiwen Chen
- Department of Neurosurgery, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
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Wang C, Cao H, Gu S, Shi C, Chen X, Han X. Expression analysis of microRNAs and mRNAs in myofibroblast differentiation of lung resident mesenchymal stem cells. Differentiation 2019; 112:10-16. [PMID: 31838455 DOI: 10.1016/j.diff.2019.11.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 09/17/2019] [Accepted: 11/17/2019] [Indexed: 12/11/2022]
Abstract
Idiopathic pulmonary fibrosis (IPF) is a serious lung disease that involved the myofibroblast differentiation of lung resident mesenchymal stem cells (LR-MSCs). However, the specific molecular mechanisms of myofibroblast differentiation of LR-MSCs still remain a mystery. In this study, a comprehensive analysis of miRNAs and mRNAs changes in LR-MSCs treated with TGF-β1 was performed. Through computational approaches, the pivotal roles of differentially expressed miRNAs that were associated with tight junction, pathways in cancer, focal adhesion, and cytokine-cytokine receptor interaction were shown. Kruppel-like factor 4 (Klf4) and inhibitor of growth family, member 5 (Ing5) may be the targets for the therapy of pulmonary fibrosis by inhibiting myofibroblast differentiation of LR-MSCs and EMT. Collectively, a molecular paradigm for understanding myofibroblast differentiation of LR-MSCs in IPF was provided by the integrated miRNA/mRNA analyses.
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Affiliation(s)
- Cong Wang
- Immunology and Reproduction Biology Laboratory & State Key Laboratory of Analytical Chemistry for Life Science, Medical School, Nanjing University, Nanjing, Jiangsu, 210093, China; State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Discovery for Metabolic Diseases, Center of New Drug Discovery, China Pharmaceutical University, 24 Tong Jia Xiang, Nanjing, 210009, China; Jiangsu Key Laboratory of Molecular Medicine, Nanjing University, Nanjing, Jiangsu, 210093, China
| | - Honghui Cao
- Immunology and Reproduction Biology Laboratory & State Key Laboratory of Analytical Chemistry for Life Science, Medical School, Nanjing University, Nanjing, Jiangsu, 210093, China; Jiangsu Key Laboratory of Molecular Medicine, Nanjing University, Nanjing, Jiangsu, 210093, China
| | - Shen Gu
- Immunology and Reproduction Biology Laboratory & State Key Laboratory of Analytical Chemistry for Life Science, Medical School, Nanjing University, Nanjing, Jiangsu, 210093, China; Jiangsu Key Laboratory of Molecular Medicine, Nanjing University, Nanjing, Jiangsu, 210093, China
| | - Chaowen Shi
- Immunology and Reproduction Biology Laboratory & State Key Laboratory of Analytical Chemistry for Life Science, Medical School, Nanjing University, Nanjing, Jiangsu, 210093, China; Jiangsu Key Laboratory of Molecular Medicine, Nanjing University, Nanjing, Jiangsu, 210093, China
| | - Xiang Chen
- Immunology and Reproduction Biology Laboratory & State Key Laboratory of Analytical Chemistry for Life Science, Medical School, Nanjing University, Nanjing, Jiangsu, 210093, China; Jiangsu Key Laboratory of Molecular Medicine, Nanjing University, Nanjing, Jiangsu, 210093, China
| | - Xiaodong Han
- Immunology and Reproduction Biology Laboratory & State Key Laboratory of Analytical Chemistry for Life Science, Medical School, Nanjing University, Nanjing, Jiangsu, 210093, China; Jiangsu Key Laboratory of Molecular Medicine, Nanjing University, Nanjing, Jiangsu, 210093, China.
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Large-scale analyses identify a cluster of novel long noncoding RNAs as potential competitive endogenous RNAs in progression of hepatocellular carcinoma. Aging (Albany NY) 2019; 11:10422-10453. [PMID: 31761783 PMCID: PMC6914412 DOI: 10.18632/aging.102468] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 11/08/2019] [Indexed: 12/12/2022]
Abstract
The abnormal expression of noncoding RNAs has attracted increasing interest in the field of hepatocellular carcinoma progression. However, the underlying molecular mechanisms mediated by noncoding RNAs in these processes are unclear. Here, we obtained the expression profiles of long noncoding RNAs, microRNAs, and mRNAs from the Gene Expression Omnibus database and identified hepatocarcinogenesis-specific differentially expressed transcripts. Next, we identified significant Gene Ontology and pathway terms that the differentially expressed transcripts involved in. Using functional analysis and target prediction, we constructed a hepatocellular carcinoma-associated deregulated competitive endogenous RNA network to reveal the potential mechanisms underlying tumor progression. By analyzing The Cancer Genome Atlas dataset, six key long noncoding RNAs showed significant association with overall survival as well as strong correlation with some microRNAs and mRNAs in the competitive endogenous RNA network. We further validated the above results and determined their diagnostic and prognostic value in clinical samples. Importantly, by large-scale analyses, we identified a cluster of long noncoding RNAs, GBAP1, MCM3AP-AS1, SLC16A1-AS1, C3P1, DIO3OS, and HNF4A-AS1 as candidate biomarkers for the diagnosis and prognosis of hepatocellular carcinoma, which will improve our understanding of competitive endogenous RNA-mediated regulatory mechanisms underlying hepatocellular carcinoma development and will provide novel therapeutic targets in the future.
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Diao S, Yang H, Cao Y, Yang D, Fan Z. IGF2 enhanced the osteo-/dentinogenic and neurogenic differentiation potentials of stem cells from apical papilla. J Oral Rehabil 2019; 47 Suppl 1:55-65. [PMID: 31291686 DOI: 10.1111/joor.12859] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2019] [Revised: 07/02/2019] [Accepted: 07/04/2019] [Indexed: 12/27/2022]
Abstract
OBJECTIVES In dental tissue engineering, niche is important for maintaining stem cell function and regenerating the dental tissues. However, there is limited knowledge for the growth factors in niche to maintain the function of stem cells. In this study, we investigated the effect of IGF2, a growth factor in stem cells from apical papilla (SCAPs) niche, on differentiation and proliferation potentials of SCAPs. MATERIALS AND METHODS Recombinant human IGF2 protein (rhIGF2) was used. Cell counting kit-8 assay, Carboxyfluorescein succinimidyl ester assay, alkaline phosphatase (ALP) activity, Alizarin Red staining, quantitative calcium analysis, immunofluorescence staining and real-time RT-PCR were performed to investigate the cell proliferation and differentiation potentials of SCAPs. And proteomic analysis was used to identify the differential secreted proteins. RESULTS By ALP activity assay, we found that 5 ng/mL rhIGF2 might be the optimal concentration for treatment. Then, Alizarin Red staining, quantitative calcium analysis and osteogenesis-related gene expression results showed that 5 ng/mL rhIGF2 could enhance the osteo-/dentinogenic differentiation potentials in SCAPs. Immunofluorescence staining and real-time RT-PCR results showed that neurogenic markers were significantly induced by 5 ng/mL rhIGF2 in SCAPs. Then, CCK-8 assay and CFSE assay results showed that 5 ng/mL rhIGF2 could enhance the cell proliferation in SCAPs. Furthermore, proteomic analysis showed that IGF2 could induce some secreted proteins which function related to the osteogenesis, neurogenesis and cell proliferation. CONCLUSIONS Our results identified that IGF2 might be the potential mediator in niche to promote SCAP function and dental tissue regeneration.
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Affiliation(s)
- Shu Diao
- Laboratory of Molecular Signaling and Stem Cells Therapy, Beijing Key Laboratory of Tooth Regeneration and Function Reconstruction, Capital Medical University School of Stomatology, Beijing, China.,Department of Pediatric dentistry, Capital Medical University School of Stomatology, Beijing, China
| | - Haoqing Yang
- Laboratory of Molecular Signaling and Stem Cells Therapy, Beijing Key Laboratory of Tooth Regeneration and Function Reconstruction, Capital Medical University School of Stomatology, Beijing, China
| | - Yangyang Cao
- Laboratory of Molecular Signaling and Stem Cells Therapy, Beijing Key Laboratory of Tooth Regeneration and Function Reconstruction, Capital Medical University School of Stomatology, Beijing, China
| | - Dongmei Yang
- Laboratory of Molecular Signaling and Stem Cells Therapy, Beijing Key Laboratory of Tooth Regeneration and Function Reconstruction, Capital Medical University School of Stomatology, Beijing, China.,Department of Pediatric dentistry, Capital Medical University School of Stomatology, Beijing, China
| | - Zhipeng Fan
- Laboratory of Molecular Signaling and Stem Cells Therapy, Beijing Key Laboratory of Tooth Regeneration and Function Reconstruction, Capital Medical University School of Stomatology, Beijing, China
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Huang Y, Xu Y, Lu Y, Zhu S, Guo Y, Sun C, Xu L, Chen X, Zhao Y, Yu B, Yang Y, Wang Z. lncRNA Gm10451 regulates PTIP to facilitate iPSCs-derived β-like cell differentiation by targeting miR-338-3p as a ceRNA. Biomaterials 2019; 216:119266. [PMID: 31220795 DOI: 10.1016/j.biomaterials.2019.119266] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 06/03/2019] [Accepted: 06/08/2019] [Indexed: 02/08/2023]
Abstract
iPSCs-derived insulin-producing cell transplantation is a promising strategy for diabetes therapy. Although there have been many protocols of mature, glucose-responsive β cells induced in vitro over the past few years, many underlying problems remain to be resolved. As a crucial regulator, long noncoding RNAs (lncRNAs) participate in numerous biological processes, including the maintenance of pluripotency, and stem cell differentiation. In this study, we identified a novel lncRNA Gm10451 as a functional regulator for β-like cell differentiation. Localized to the cytoplasm, Gm10451 regulates histone H3K4 methyltransferase complex PTIP to facilitate Insulin+/Nkx6.1+ β-like cell differentiation by targeting miR-338-3p as a competing endogenous RNA (ceRNA). miR-338-3p has also been shown to suppress Nkx6.1+ early-stage β-like cell differentiation by targeting PTIP. Following transplantation into streptozotocin (STZ)-mice, Gm10451 loss in β-like cells prevented the expression of mature β-cell makers, such as Insulin, Nkx6.1, and Mafa. Accordingly, hyperglycemia in the mice was not resolved. Taken together, this study provides an efficient epigenetic target for generating more mature and functional iPSCs-derived β-like cells. We anticipate that pancreatic organoids, which are generated from human stem cells, biological materials, and epigenetic modifications, can be used in the future as a novel diabetes treatment option.
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Affiliation(s)
- Yan Huang
- Department of Hepatobiliary and Pancreatic Surgery, Affiliated Hospital of Nantong University, Nantong, 226001, China; Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, 226001, China
| | - Yang Xu
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, 226001, China
| | - Yuhua Lu
- Department of Hepatobiliary and Pancreatic Surgery, Affiliated Hospital of Nantong University, Nantong, 226001, China; Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, 226001, China.
| | - Shajun Zhu
- Department of Hepatobiliary and Pancreatic Surgery, Affiliated Hospital of Nantong University, Nantong, 226001, China
| | - Yibing Guo
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, 226001, China
| | - Cheng Sun
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, Nantong University, Nantong, 226001, China
| | - Lianchen Xu
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, 226001, China
| | - Xiaolan Chen
- Department of Nephrology, Affiliated Hospital of Nantong University, Nantong, 226001, China
| | - Yahong Zhao
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, Nantong University, Nantong, 226001, China
| | - Bin Yu
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, Nantong University, Nantong, 226001, China; Jiangsu Clinical Medicine Center of Tissue Engineering and Nerve Injury Repair, Affiliated Hospital of Nantong University, Nantong 226001, China
| | - Yumin Yang
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, Nantong University, Nantong, 226001, China.
| | - Zhiwei Wang
- Department of Hepatobiliary and Pancreatic Surgery, Affiliated Hospital of Nantong University, Nantong, 226001, China.
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Guo G, Ren S, Kang Y, Liu Y, Duscher D, Machens HG, Chen Z. Microarray analyses of lncRNAs and mRNAs expression profiling associated with diabetic peripheral neuropathy in rats. J Cell Biochem 2019; 120:15347-15359. [PMID: 31025414 DOI: 10.1002/jcb.28802] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 02/01/2019] [Accepted: 02/04/2019] [Indexed: 12/12/2022]
Abstract
Diabetic peripheral neuropathy (DPN) is considered to be the most frequent neuropathic complication of diabetes, and severely affects the quality of life of patients. Long noncoding RNAs (lncRNAs) participate in various pathophysiological processes and associate with many diseases. However, the exact impact of lncRNAs on DPN remains obscure. To discover a potential connection, a microarray study was conducted to analyze the expression profiling of lncRNAs and messenger RNAs (mRNAs) in dorsal root ganglia (DRG) from streptozotocin-induced diabetic rats with DPN. As a result, 983 lncRNAs and 1357 mRNAs were aberrantly expressed compared with control samples. Using bioinformatics analyses, we identified 558 Gene Ontology terms and 94 Kyoto Encyclopedia of Genes and Genomes pathways to be significantly enriched. Additionally, the signal-net analysis indicated that integrin receptors, including Itgb3, Itgb1, Itgb8, and Itga6, might be important players in network regulation. Furthermore, the lncRNA-mRNA network analysis showed dynamic interactions between the dysregulated lncRNAs and mRNAs. This is the first study to present an overview of lncRNA and mRNA expressions in DRG tissues from DPN rats. Our results indicate that these differentially expressed lncRNAs may have crucial roles in pathological processes of DPN by regulating their coexpressed mRNAs. The data may provide novel targets for future studies, which should focus on validating their roles in the progression of DPN.
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Affiliation(s)
- Guojun Guo
- Department of Hand Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Sen Ren
- Department of Hand Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yu Kang
- Department of Hand Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yutian Liu
- Department of Hand Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Dominik Duscher
- Department of Plastic and Hand Surgery, Technical University of Munich, Munich, Germany
| | - Hans-Günther Machens
- Department of Plastic and Hand Surgery, Technical University of Munich, Munich, Germany
| | - Zhenbing Chen
- Department of Hand Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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Li L, Peng M, Xue W, Fan Z, Wang T, Lian J, Zhai Y, Lian W, Qin D, Zhao J. Integrated analysis of dysregulated long non-coding RNAs/microRNAs/mRNAs in metastasis of lung adenocarcinoma. J Transl Med 2018; 16:372. [PMID: 30587197 PMCID: PMC6307237 DOI: 10.1186/s12967-018-1732-z] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 12/06/2018] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Lung adenocarcinoma (LUAD), largely remains a primary cause of cancer-related death worldwide. The molecular mechanisms in LUAD metastasis have not been completely uncovered. METHODS In this study, we identified differentially expressed genes (DEGs), miRNAs (DEMs) and lncRNAs (DELs) underlying metastasis of LUAD from The Cancer Genome Atlas database. Intersection mRNAs were used to perform gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway and co-expression network analysis. In addition, survival analyses of intersection mRNAs were conducted. Finally, intersection mRNAs, miRNAs and lncRNAs were subjected to construct miRNA-mRNA-lncRNA network. RESULTS A total of 1015 DEGs, 54 DEMs and 22 DELs were identified in LUAD metastasis and non-metastasis samples. GO and KEGG pathway analysis had proven that the functions of intersection mRNAs were closely related with many important processes in cancer pathogenesis. Among the co-expression interactions network, 22 genes in the co-expression network were over the degree 20. These genes imply that they have connections with many other gene nodes. In addition, 14 target genes (ARHGAP11A, ASPM, HELLS, PRC1, TMPO, ARHGAP30, CD52, IL16, IRF8, P2RY13, PRKCB, PTPRC, SASH3 and TRAF3IP3) were found to be associated with survival in patients with LUAD significantly (log-rank P < 0.05). Two lncRNAs (LOC96610 and ADAM6) acting as ceRNAs were identified based on the miRNA-mRNA-lncRNA network. CONCLUSIONS Taken together, the results may provide a novel perspective to develop a multiple gene diagnostic tool for LUAD prognosis, which might also provide potential biomarkers or therapeutic targets for LUAD.
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Affiliation(s)
- Lifeng Li
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China.,Cancer Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China.,National Engineering Laboratory for Internet Medical Systems and Applications, Zhengzhou, 450052, Henan, China
| | - Mengle Peng
- Department of Clinical Laboratory, The Third People's Hospital of Henan Province, Zhengzhou, 450052, Henan, China
| | - Wenhua Xue
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Zhirui Fan
- Cancer Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Tian Wang
- Cancer Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Jingyao Lian
- Cancer Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Yunkai Zhai
- National Engineering Laboratory for Internet Medical Systems and Applications, Zhengzhou, 450052, Henan, China
| | - Wenping Lian
- Department of Clinical Laboratory, The Third People's Hospital of Henan Province, Zhengzhou, 450052, Henan, China
| | - Dongchun Qin
- Department of Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University, Key Laboratory of Laboratory Medicine of Henan Province, Zhengzhou, 450052, Henan, China.
| | - Jie Zhao
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China. .,Cancer Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China. .,National Engineering Laboratory for Internet Medical Systems and Applications, Zhengzhou, 450052, Henan, China.
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20
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Guo G, Liu Y, Ren S, Kang Y, Duscher D, Machens HG, Chen Z. Comprehensive analysis of differentially expressed microRNAs and mRNAs in dorsal root ganglia from streptozotocin-induced diabetic rats. PLoS One 2018; 13:e0202696. [PMID: 30118515 PMCID: PMC6097669 DOI: 10.1371/journal.pone.0202696] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2018] [Accepted: 08/06/2018] [Indexed: 01/22/2023] Open
Abstract
Diabetic peripheral neuropathy is a common complication associated with diabetes mellitus with a pathogenesis that is incompletely understood. By regulating RNA silencing and post-transcriptional gene expression, microRNAs participate in various biological processes and human diseases. However, the relationship between microRNAs and the progress of diabetic peripheral neuropathy still lacks a thorough exploration. Here we used microarray microRNA and mRNA expression profiling to analyze the microRNAs and mRNAs which are aberrantly expressed in dorsal root ganglia from streptozotocin-induced diabetic rats. We found that 37 microRNAs and 1357 mRNAs were differentially expressed in comparison to non-diabetic samples. Bioinformatics analysis indicated that 399 gene ontology terms and 29 Kyoto Encyclopedia of Genes and Genomes pathways were significantly enriched in diabetic rats. Additionally, a microRNA-gene network evaluation identified rno-miR-330-5p, rno-miR-17-1-3p and rno-miR-346 as important players for network regulation. Finally, quantitative real-time polymerase chain reaction analysis was used to confirm the microarray results. In conclusion, this study provides a systematic perspective of microRNA and mRNA expression in dorsal root ganglia from diabetic rats, and suggests that dysregulated microRNAs and mRNAs may be important promotors of peripheral neuropathy. Our results may be the underlying framework of future studies regarding the effect of the aberrantly expressed genes on the pathophysiology of diabetic peripheral neuropathy.
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Affiliation(s)
- Guojun Guo
- Department of Hand Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yutian Liu
- Department of Hand Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Sen Ren
- Department of Hand Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yu Kang
- Department of Hand Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Dominik Duscher
- Department of Plastic and Hand Surgery, Technical University of Munich, Munich, Germany
| | - Hans-Günther Machens
- Department of Plastic and Hand Surgery, Technical University of Munich, Munich, Germany
| | - Zhenbing Chen
- Department of Hand Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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Cheng YL, Zhang XH, Sun YW, Wang WJ, Huang J, Chu NL, Fang SP, Wu ZK. Genomewide DNA Methylation Responses in Patients with β-Thalassemia Treated with Yisui Shengxue Granules (). Chin J Integr Med 2018; 25:490-496. [PMID: 29761313 DOI: 10.1007/s11655-018-2777-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2016] [Accepted: 01/09/2016] [Indexed: 11/24/2022]
Abstract
OBJECTIVE To examine the clinical effects of Yisui Shengxue Granules () in the treatment of β-thalassemia and explore its mechanism on DNA methylation levels. METHODS A randomized placebo-controlled double-blinded trial was conducted. Forty patients with β-thalassemia were recruited and distributed randomly by envelope method into an experimental group and a control group, 20 patients in each group. The patients were given Yisui Shengxue Granules in the experimental group and placebo in the control group (12 g/bag three times a day) during a 3-month intervention. Before and after 1, 2, and 3 months of treatment, peripheral intravenous blood was sampled, and blood parameters such as hemoglobin (Hb), red blood cells (RBCs), reticulocytes (Ret), and fetal hemoglobin (HbF) were analyzed. Mononuclear cells from 5 patients, who showed an obvious treatment effect, were isolated by density gradient centrifugation. DNA methylation was analyzed using an Affymetrix USA GeneChip Human Promoter 1.0 Array and Input-promoter 1.0. RESULTS Compared with pre-treatment, there was an obvious increase in Hb and RBCs counts after 1, 2, and 3 months in the experiment group (P<0.01 or P<0.05). Meanwhile, HbF increased from the 2nd to the 3rd month (P<0.05). In the control group, Hb and RBCs showed no obvioas change. After 3-month treatment, DNA methylation results from 5 patients revealed that there were 24 hypomethylated genes and 3,685 hypermethylated genes compared with pre-treatment. Genes of insulin-like growth factor 1 receptor (IGF1R) and Janus kinase 3 (JAK3) revealed the most relations with other genes (degree: 21) and genes of 1-phosphatidylinositol-4, 5-bisphosphate phosphodiesterase gamma 2 (PLCG2) and mitogen-activated protein kinase 10 (MAPK10) showed a stronger intermediary role (betweenness centrality=0.04). CONCLUSIONS JAK3 and MAPK10 are two key genes in bone marrow and the lymphatic system, and JAK3 is likely to be related to hematopoietic cytokines in the process of early hematopoiesis. (Registration No. NCT01549080).
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Affiliation(s)
- Yan-Ling Cheng
- Molecular Biology Labaratory, South of Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, 102618, China
| | - Xin-Hua Zhang
- Department of Hematology, 303rd Hospital of People's Liberatory Army, Nanning, 530021, China
| | - Yu-Wen Sun
- Molecular Biology Laboratory of Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, 100053, China
| | - Wen-Juan Wang
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, 100069, China
| | - Jie Huang
- Department of Hematology, 303rd Hospital of People's Liberatory Army, Nanning, 530021, China
| | - Na-Li Chu
- Molecular Biology Laboratory of Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, 100053, China
| | - Su-Ping Fang
- Molecular Biology Laboratory of Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, 100053, China
| | - Zhi-Kui Wu
- Molecular Biology Laboratory of Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, 100053, China.
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Lin X, Meng G, Liu X, Yu T, Bai C, Fei X, Deng S, Zhao J, Ren S, Zhang J, Wu Z, Wang S, Zhang J, Zhang L. The Differentially Expressed Genes of Human Sporadic Cerebral Cavernous Malformations. World Neurosurg 2018; 113:e247-e270. [DOI: 10.1016/j.wneu.2018.02.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Revised: 01/31/2018] [Accepted: 02/02/2018] [Indexed: 10/18/2022]
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An T, Zhang T, Teng F, Zuo JC, Pan YY, Liu YF, Miao JN, Gu YJ, Yu N, Zhao DD, Mo FF, Gao SH, Jiang G. Long non-coding RNAs could act as vectors for paternal heredity of high fat diet-induced obesity. Oncotarget 2018; 8:47876-47889. [PMID: 28599310 PMCID: PMC5564612 DOI: 10.18632/oncotarget.18138] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Accepted: 04/24/2017] [Indexed: 12/12/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) play an important role in epigenetic regulation, and abnormalities may lead to male infertility. To investigate whether lncRNAs are involved in intergenerational inheritance of obesity and obesity-induced decline in fertility, we divided mice into obesity (F0 mice fed a high-fat diet, F0-HFD) and non-obese (F0 mice fed normal chow, F0-NC) model groups and their male offspring (F1-HFD and F1-NC, respectively). We examined the differences in the expression levels of lncRNAs and mRNAs in the F0-HFD/F0-NC and F1-HFD/F1-NC groups. The results revealed similar expression patterns in the F1-HFD/F0-HFD groups at both the lncRNA and mRNA levels. The maximum difference in the lncRNA expression was observed between the F0-HFD and F0-NC groups. The differentially expressed lncRNA targets and mRNAs identified in our study are mainly involved in GnRH signalling pathway, metabolic process, and Hippo signalling pathway; similarly expressed lncRNAs and mRNAs in F1-HFD/F0-HFD are closely linked with G-protein coupled receptor signalling pathway, pancreatic polypeptide receptor activity, and lysine biosynthesis, which may play an important role in the molecular mechanism of intergenerational inheritance of obesity. Furthermore, potential genes that might play important roles in the pathogenesis of obesity-related low fertility were revealed by lncRNA-and mRNA-interaction studies based on the microarray expression profiles. In conclusion, we found that lncRNA could be involved in obesity-induced infertility by expressing abnormalities, which could act as genetic vectors of paternal inheritance of obesity.
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Affiliation(s)
- Tian An
- Diabetes Research Center, Beijing University of Chinese Medicine, Beijing, China
| | - Teng Zhang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Fei Teng
- Diabetes Research Center, Beijing University of Chinese Medicine, Beijing, China
| | - Jia-Cheng Zuo
- Diabetes Research Center, Beijing University of Chinese Medicine, Beijing, China
| | - Yan-Yun Pan
- Diabetes Research Center, Beijing University of Chinese Medicine, Beijing, China
| | - Yu-Fei Liu
- The Third Affiliated Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Jia-Nan Miao
- Diabetes Research Center, Beijing University of Chinese Medicine, Beijing, China
| | - Yu-Jie Gu
- Diabetes Research Center, Beijing University of Chinese Medicine, Beijing, China
| | - Na Yu
- Diabetes Research Center, Beijing University of Chinese Medicine, Beijing, China
| | - Dan-Dan Zhao
- Diabetes Research Center, Beijing University of Chinese Medicine, Beijing, China
| | - Fang-Fang Mo
- Diabetes Research Center, Beijing University of Chinese Medicine, Beijing, China
| | - Si-Hua Gao
- Diabetes Research Center, Beijing University of Chinese Medicine, Beijing, China
| | - Guangjian Jiang
- Diabetes Research Center, Beijing University of Chinese Medicine, Beijing, China
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Jin L, Li Y, Zhou X, Yuan H. Co-expression network analysis of lncRNAs and mRNAs in OPTN-silenced cells. Int J Mol Med 2017; 41:1013-1020. [PMID: 29251316 DOI: 10.3892/ijmm.2017.3313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Accepted: 11/30/2017] [Indexed: 11/06/2022] Open
Abstract
The aim of the present study was to reveal the role of long noncoding RNAs (lncRNAs) in the regulation of the pathogenesis of optineurin (OPTN)-silenced cells. The microarray data set GSE12452 was re-annotated using the non-coding RNA function annotation server to identify differentially expressed lncRNAs. Weighted correlation network analysis was used to construct an lncRNA-lncRNA co-expression network and identify co-expression modules. Three OPTN small interfering RNAs (siRNAs) were transiently transfected into HeLa cells. Reverse transcription‑quantitative polymerase chain reaction (RT-qPCR) and western blot analysis were used to detect OPTN expression and select the most effective OPTN siRNA to construct stably transfected cells. RT-qPCR was used to quantify the identified lncRNAs in the OPTN-silenced cells. The potential functions of these modules were explored by the functional enrichment of the corresponding co-expressed genes. A total of 3,495 lncRNAs were re-annotated. Of these, matrix metalloprotease 12 and RP11-169D4.1 were upregulated, and RP1-212P9.2 was downregulated. The results of the RT-qPCR analysis of RP1-212P9.2 and RP11‑169D4.1 were consistent with the re-annotated data in the OPTN‑silenced cells. Gene Ontology analyses indicated that the biological functions of the mRNAs co-expressed with these lncRNAs were associated with gene product regulation, and neuronal migration, polarity and differentiation. In addition, Kyoto Encyclopedia of Genes and Genomes analysis indicated that the two validated lncRNAs were associated with the transforming growth factor-β signaling pathway and the apoptosis pathway, respectively. In conclusion, the abnormal lncRNAs identified in OPTN-silenced cells indicate that lncRNAs may contribute to the molecular pathogenesis of OPTN-associated diseases.
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Affiliation(s)
- Lin Jin
- Department of Ophthalmology, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150081, P.R. China
| | - Yuanyuan Li
- Department of Ophthalmology, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150081, P.R. China
| | - Xinrong Zhou
- Department of Ophthalmology, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150081, P.R. China
| | - Huiping Yuan
- Department of Ophthalmology, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150081, P.R. China
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Wang R, Su C, Wang X, Fu Q, Gao X, Zhang C, Yang J, Yang X, Wei M. Global gene expression analysis combined with a genomics approach for the identification of signal transduction networks involved in postnatal mouse myocardial proliferation and development. Int J Mol Med 2017; 41:311-321. [PMID: 29115400 PMCID: PMC5746306 DOI: 10.3892/ijmm.2017.3234] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 10/26/2017] [Indexed: 11/26/2022] Open
Abstract
Mammalian cardiomyocytes may permanently lose their ability to proliferate after birth. Therefore, studying the proliferation and growth arrest of cardiomyocytes during the postnatal period may enhance the current understanding regarding this molecular mechanism. The present study identified the differentially expressed genes in hearts obtained from 24 h-old mice, which contain proliferative cardiomyocytes; 7-day-old mice, in which the cardiomyocytes are undergoing a proliferative burst; and 10-week-old mice, which contain growth-arrested cardiomyocytes, using global gene expression analysis. Furthermore, myocardial proliferation and growth arrest were analyzed from numerous perspectives, including Gene Ontology annotation, cluster analysis, pathway enrichment and network construction. The results of a Gene Ontology analysis indicated that, with increasing age, enriched gene function was not only associated with cell cycle, cell division and mitosis, but was also associated with metabolic processes and protein synthesis. In the pathway analysis, 'cell cycle', proliferation pathways, such as the 'PI3K-AKT signaling pathway', and 'metabolic pathways' were well represented. Notably, the cluster analysis revealed that bone morphogenetic protein (BMP)1, BMP10, cyclin E2, E2F transcription factor 1 and insulin like growth factor 1 exhibited increased expression in hearts obtained from 7-day-old mice. In addition, the signal transduction pathway associated with the cell cycle was identified. The present study primarily focused on genes with altered expression, including downregulated anaphase promoting complex subunit 1, cell division cycle (CDC20), cyclin dependent kinase 1, MYC proto-oncogene, bHLH transcription factor and CDC25C, and upregulated growth arrest and DNA damage inducible α in 10-week group, which may serve important roles in postnatal myocardial cell cycle arrest. In conclusion, these data may provide important information regarding myocardial proliferation and development.
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Affiliation(s)
- Ruoxin Wang
- Department of Cardiovascular Surgery, Tianjin Medical University General Hospital, Tianjin 300070, P.R. China
| | - Chao Su
- Department of Biochemistry and Molecular Biology, Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, P.R. China
| | - Xinting Wang
- Department of Biochemistry and Molecular Biology, Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, P.R. China
| | - Qiang Fu
- Department of Cardiovascular Surgery, Tianjin Medical University General Hospital, Tianjin 300070, P.R. China
| | - Xingjie Gao
- Department of Biochemistry and Molecular Biology, Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, P.R. China
| | - Chunyan Zhang
- Department of Biochemistry and Molecular Biology, Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, P.R. China
| | - Jie Yang
- Department of Immunology, University of Manitoba, Winnipeg, MB R3E 0T5, Canada
| | - Xi Yang
- Department of Immunology, University of Manitoba, Winnipeg, MB R3E 0T5, Canada
| | - Minxin Wei
- Department of Cardiovascular Surgery, Tianjin Medical University General Hospital, Tianjin 300070, P.R. China
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Transcriptome analysis of mRNA and microRNAs in intramuscular fat tissues of castrated and intact male Chinese Qinchuan cattle. PLoS One 2017; 12:e0185961. [PMID: 29073274 PMCID: PMC5657623 DOI: 10.1371/journal.pone.0185961] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 09/24/2017] [Indexed: 11/19/2022] Open
Abstract
Intramuscular fat (IMF) is known to enhance beef palatability and can be markedly increased by castration. However, there is little understanding of the molecular mechanism underlying the IMF deposition after castration of beef cattle. We hypothesize that genetic regulators function differently in IMF from bulls and steers. Therefore, after detecting serum testosterone and lipid parameter, as well as the contents of IMF at 6, 12, 18 and 24 months, we have investigated differentially expressed (DE) microRNAs (miRNAs) and mRNAs in IMF of bulls and steers at 24 months of age in Qinchuan cattle using next-generation sequencing, and then explored the possible biopathways regulating IMF deposition. Serum testosterone levels were significantly decreased in steers, whereas IMF content, serum total cholesterol (TC), low-density lipoprotein cholesterol (LDL-C) and triglycerides (TGs) were markedly increased in steers. Comparing the results of steers and bulls, 580 upregulated genes and 1,120 downregulated genes in IMF tissues were identified as DE genes correlated with IMF deposition. The upregulated genes were mainly associated with lipid metabolism, lipogenesis and fatty acid transportation signalling pathways, and the downregulated genes were correlated with immune response and intracellular signal transduction. Concurrently, the DE miRNAs—important players in adipose tissue accumulation induced by castration—were also examined in IMF tissues; 52 DE miRNAs were identified. The expression profiles of selected genes and miRNAs were also confirmed by quantitative real-time PCR (qRT-PCR) assays. Using integrated analysis, we constructed the microRNA-target regulatory network which was supported by target validation using the dual luciferase reporter system. Moreover, Ingenuity Pathway Analysis (IPA) software was used to construct a molecular interaction network that could be involved in regulating IMF after castration. The detected molecular network is closely associated with lipid metabolism and adipocyte differentiation, which is supported by functional identification results of bta-let-7i on bovine preadipocytes. These results provided valuable insights into the molecular mechanisms of the IMF phenotype differences between steers and bulls.
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27
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Ji ZH, Chen J, Gao W, Zhang JY, Quan FS, Hu JP, Yuan B, Ren WZ. Cutaneous transcriptome analysis in NIH hairless mice. PLoS One 2017; 12:e0182463. [PMID: 28787439 PMCID: PMC5546695 DOI: 10.1371/journal.pone.0182463] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Accepted: 07/19/2017] [Indexed: 12/16/2022] Open
Abstract
Mice with spontaneous coat mutations are ideal animal models for studying skin development and tumorigenesis. In this study, skin hair growth cycle abnormalities were examined in NIH hairless mice 42 days after birth (P42) by using hematoxylin-eosin (H&E) staining. To examine the gene expression patterns in the skin of mutant mice, the dorsal skin of P42 female NIH mice and NIH hairless mice was sequenced by RNA-Seq, and 5,068 differentially expressed genes (DEGs) were identified (false discovery rate [FDR] ≥ 2, P < 0.05). A pathway analysis showed that basal cell carcinoma, the cell cycle and the Hippo, Hedgehog and Wnt signaling pathways were up-regulated in NIH hairless mice. Previous studies have shown that these pathways are closely associated with cell proliferation, cell cycle, organ size and cancer development. In contrast, signal transduction, bacterial and parasitic infection, and receptor-mediated pathways, including calcium signaling, were down-regulated in NIH hairless mice. A gene interaction network analysis was performed to identify genes related to hair follicle development. To verify the reliability of the RNA-Seq results, we used q-PCR to analyze 12 key genes identified from the gene interaction network analysis, including eight down-regulated and four up-regulated genes, and the results confirmed the reliability of the RNA-Seq results. Finally, we constructed the differential gene expression profiles of mutant mice by RNA-Seq. NIH hairless mice exhibited abnormalities in hair development and immune-related pathways. Pik3r1 and Pik3r3 were identified as key genes, laying the foundation for additional in-depth studies of hairless mice.
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Affiliation(s)
- Zhong-Hao Ji
- Department of Laboratory Animals, College of Animal Sciences, Jilin University, Changchun, Jilin, China
| | - Jian Chen
- Department of Laboratory Animals, College of Animal Sciences, Jilin University, Changchun, Jilin, China
| | - Wei Gao
- Department of Laboratory Animals, College of Animal Sciences, Jilin University, Changchun, Jilin, China
| | - Jin-Yu Zhang
- Department of Laboratory Animals, College of Animal Sciences, Jilin University, Changchun, Jilin, China
| | - Fu-Shi Quan
- Department of Laboratory Animals, College of Animal Sciences, Jilin University, Changchun, Jilin, China
| | - Jin-Ping Hu
- Department of Laboratory Animals, College of Animal Sciences, Jilin University, Changchun, Jilin, China
| | - Bao Yuan
- Department of Laboratory Animals, College of Animal Sciences, Jilin University, Changchun, Jilin, China
| | - Wen-Zhi Ren
- Department of Laboratory Animals, College of Animal Sciences, Jilin University, Changchun, Jilin, China
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The Profile of Serum microRNAs Predicts Prognosis for Resected Gastric Cancer Patients Receiving Platinum-Based Chemotherapy. Dig Dis Sci 2017; 62:1223-1234. [PMID: 28341869 DOI: 10.1007/s10620-017-4513-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Accepted: 02/25/2017] [Indexed: 12/19/2022]
Abstract
BACKGROUND AND AIM Adjuvant chemotherapy is an important component in the treatment of gastric cancer (GC) patients; however, some patients do not respond to the drugs. We aimed to develop a practical profile based on serum microRNAs (miRNAs) that can be used to predict patients likely to respond to treatment. METHODS Microarrays were used to screen cisplatin-resistant SGC7901/DDP GC cells and the parental SGC7901 cell lines for miRNAs related to chemotherapy sensitivity. The correlation between the expression patterns of identified serum miRNAs and overall survival was confirmed in 68 GC patients. Furthermore, we also validated the signature of the serum miRNAs in an independent cohort of 50 GC patients. RESULTS From the screening microarrays, we focused on miR-15a, miR-15b and miR-93 as downregulated miRNAs in the SGC7901/DDP cells and miR-27a, miR-106a and miR-664 as upregulated miRNAs. Only serum miR-106, miR-15a, miR-93 and miR-664 were useful in predicting the prognosis of patients who received adjuvant chemotherapy. We identified a signature of four serum miRNAs (miR-106, miR-15a, miR-93 and miR-664) that, when combined, can be used as a risk score for overall survival. Patients with a higher risk score had worse prognosis (p < 0.05). For the independent cohort of patients, the signature of the four miRNAs predicted prognosis well. CONCLUSION Our data showed that the risk score derived from the four serum miRNAs was closely associated with the overall survival in GC patients who received adjuvant chemotherapy.
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Fang M, Zhang P, Zhao Y, Liu X. Bioinformatics and co-expression network analysis of differentially expressed lncRNAs and mRNAs in hippocampus of APP/PS1 transgenic mice with Alzheimer disease. Am J Transl Res 2017; 9:1381-1391. [PMID: 28386363 PMCID: PMC5376028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 02/01/2017] [Indexed: 06/07/2023]
Abstract
APP/PS1 transgenic mice with Alzheimer disease (AD) are widely used as a reliable animal model in studies about behaviors, physiology, biochemistry and histomorphology of AD, but few studies have been conducted to investigate the role of lncRNAs in this model. In this study, lncRNA microarray was employed to detect the gene expression profile and lncRNA expression profile in the mouse brain. Then, bioinformatics was used to predict the differentially expressed genes related to AD (n=20). Among different lncRNAs (n=249), 99 were downregulated and 150 upregulated. Co-expression network was applied to analyze the co-expression of differential lncRNAs and different genes. In network, lncRNA Gm13498 and lncRNA 1700030L20Rik correlated with the most genes and their degrees were 6 and 5, respectively. Then, the function and signal transduction pathways related to the differentially co-expressed lncRNAs were analyzed with bioinformatics, and results showed that these lncRNAs were involved in the systemic development of neurons, intercellular communication, regulation of action potential of neurons, development and differentiation of oligodendrocytes, neurotransmitters transmission, and neuronal regeneration. Realtime PCR was employed to detect the expression of relevant lncRNAs and differentially expressed RNAs in 10 samples, and results were consistent with above findings from microarray.
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Affiliation(s)
- Min Fang
- Department of Neurology, Shanghai Tenth People's Hospital, Tongji University Shanghai, China
| | - Pei Zhang
- Department of Neurology, Shanghai Tenth People's Hospital, Tongji University Shanghai, China
| | - Yanxin Zhao
- Department of Neurology, Shanghai Tenth People's Hospital, Tongji University Shanghai, China
| | - Xueyuan Liu
- Department of Neurology, Shanghai Tenth People's Hospital, Tongji University Shanghai, China
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30
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Bao Y, Gao Y, Shi Y, Cui X. Dynamic gene expression analysis in a H1N1 influenza virus mouse pneumonia model. Virus Genes 2017; 53:357-366. [PMID: 28243843 DOI: 10.1007/s11262-017-1438-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Accepted: 02/16/2017] [Indexed: 11/29/2022]
Abstract
H1N1, a major pathogenic subtype of influenza A virus, causes a respiratory infection in humans and livestock that can range from a mild infection to more severe pneumonia associated with acute respiratory distress syndrome. Understanding the dynamic changes in the genome and the related functional changes induced by H1N1 influenza virus infection is essential to elucidating the pathogenesis of this virus and thereby determining strategies to prevent future outbreaks. In this study, we filtered the significantly expressed genes in mouse pneumonia using mRNA microarray analysis. Using STC analysis, seven significant gene clusters were revealed, and using STC-GO analysis, we explored the significant functions of these seven gene clusters. The results revealed GOs related to H1N1 virus-induced inflammatory and immune functions, including innate immune response, inflammatory response, specific immune response, and cellular response to interferon-beta. Furthermore, the dynamic regulation relationships of the key genes in mouse pneumonia were revealed by dynamic gene network analysis, and the most important genes were filtered, including Dhx58, Cxcl10, Cxcl11, Zbp1, Ifit1, Ifih1, Trim25, Mx2, Oas2, Cd274, Irgm1, and Irf7. These results suggested that during mouse pneumonia, changes in the expression of gene clusters and the complex interactions among genes lead to significant changes in function. Dynamic gene expression analysis revealed key genes that performed important functions. These results are a prelude to advancements in mouse H1N1 influenza virus infection biology, as well as the use of mice as a model organism for human H1N1 influenza virus infection studies.
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Affiliation(s)
- Yanyan Bao
- Biosafety Laboratory, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Yingjie Gao
- Biosafety Laboratory, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Yujing Shi
- Biosafety Laboratory, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Xiaolan Cui
- Biosafety Laboratory, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China.
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Knüppel R, Kuttenberger C, Ferreira-Cerca S. Toward Time-Resolved Analysis of RNA Metabolism in Archaea Using 4-Thiouracil. Front Microbiol 2017; 8:286. [PMID: 28286499 PMCID: PMC5323407 DOI: 10.3389/fmicb.2017.00286] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 02/13/2017] [Indexed: 11/13/2022] Open
Abstract
Archaea are widespread organisms colonizing almost every habitat on Earth. However, the molecular biology of archaea still remains relatively uncharacterized. RNA metabolism is a central cellular process, which has been extensively analyzed in both bacteria and eukarya. In contrast, analysis of RNA metabolism dynamic in archaea has been limited to date. To facilitate analysis of the RNA metabolism dynamic at a system-wide scale in archaea, we have established non-radioactive pulse labeling of RNA, using the nucleotide analog 4-thiouracil (4TU) in two commonly used model archaea: the halophile Euryarchaeota Haloferax volcanii, and the thermo-acidophile Crenarchaeota Sulfolobus acidocaldarius. In this work, we show that 4TU pulse labeling can be efficiently performed in these two organisms in a dose- and time-dependent manner. In addition, our results suggest that uracil prototrophy had no critical impact on the overall 4TU incorporation in RNA molecules. Accordingly, our work suggests that 4TU incorporation can be widely performed in archaea, thereby expanding the molecular toolkit to analyze archaeal gene expression network dynamic in unprecedented detail.
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Affiliation(s)
- Robert Knüppel
- Biochemistry III, Institute for Biochemistry, Genetics and Microbiology, University of Regensburg Regensburg, Germany
| | - Corinna Kuttenberger
- Biochemistry III, Institute for Biochemistry, Genetics and Microbiology, University of Regensburg Regensburg, Germany
| | - Sébastien Ferreira-Cerca
- Biochemistry III, Institute for Biochemistry, Genetics and Microbiology, University of Regensburg Regensburg, Germany
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Diao S, Lin X, Wang L, Dong R, Du J, Yang D, Fan Z. Analysis of gene expression profiles between apical papilla tissues, stem cells from apical papilla and cell sheet to identify the key modulators in MSCs niche. Cell Prolif 2017; 50. [PMID: 28145066 DOI: 10.1111/cpr.12337] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Accepted: 01/04/2017] [Indexed: 12/11/2022] Open
Abstract
OBJECTIVES The microenvironmental niche plays the key role for maintaining the cell functions. The stem cells from apical papilla (SCAPs) are important for tooth development and regeneration. However, there is limited knowledge about the key factors in niche for maintaining the function of SCAPs. In this study, we analyse the gene expression profiles between apical papilla tissues, SCAPs and SCAPs cell sheet to identify the key genes in SCAPs niche. MATERIALS AND METHODS Microarray assays and bioinformatic analysis were performed to screen the differential genes between apical papilla tissues and SCAPs, and SCAPs and SCAPs cell sheet. Recombinant human BMP6 protein was used in SCAPs. Then CCK-8 assay, CFSE assay, alkaline phosphatase activity, alizarin red staining, quantitative calcium analysis and real-time reverse transcriptase-polymerase chain reaction were performed to investigate the cell proliferation and differentiation potentials of SCAPs. RESULTS Microarray analysis found that 846 genes were up-regulated and 1203 genes were down-regulated in SCAPs compared with apical papilla tissues. While 240 genes were up-regulated and 50 genes were down-regulated in SCAPs compared to in SCAPs cell sheet. Moreover, only 31 gene expressions in apical papilla tissues were recovered in cell sheet compared with SCAPs. Bioinformatic analysis identified that TGF-β, WNT and MAPK signalling pathways may play an important role in SCAPs niche. Based on the analysis, we identified one key growth factor in niche, BMP6, which could enhance the cell proliferation, the osteo/dentinogenic, neurogenic and angiogenic differentiation potentials of SCAPs. CONCLUSIONS Our results provided insight into the mechanisms of the microenvironmental niche which regulate the function of SCAPs, and identified the key candidate genes in niche to promote mesenchymal stem cells-mediated dental tissue regeneration.
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Affiliation(s)
- Shu Diao
- Laboratory of Molecular Signaling and Stem Cells Therapy, Beijing Key Laboratory of Tooth Regeneration and Function Reconstruction, Capital Medical University School of Stomatology, Beijing, China.,Department of Pediatric dentistry, Capital Medical University School of Stomatology, Beijing, China
| | - Xiao Lin
- Laboratory of Molecular Signaling and Stem Cells Therapy, Beijing Key Laboratory of Tooth Regeneration and Function Reconstruction, Capital Medical University School of Stomatology, Beijing, China.,Department of Implant Dentistry, Capital Medical University School of Stomatology, Beijing, China
| | - Liping Wang
- Laboratory of Molecular Signaling and Stem Cells Therapy, Beijing Key Laboratory of Tooth Regeneration and Function Reconstruction, Capital Medical University School of Stomatology, Beijing, China
| | - Rui Dong
- Laboratory of Molecular Signaling and Stem Cells Therapy, Beijing Key Laboratory of Tooth Regeneration and Function Reconstruction, Capital Medical University School of Stomatology, Beijing, China
| | - Juan Du
- Laboratory of Molecular Signaling and Stem Cells Therapy, Beijing Key Laboratory of Tooth Regeneration and Function Reconstruction, Capital Medical University School of Stomatology, Beijing, China.,Molecular Laboratory for Gene Therapy and Tooth Regeneration, Beijing Key Laboratory of Tooth Regeneration and Function Reconstruction, Capital Medical University School of Stomatology, Beijing, China
| | - Dongmei Yang
- Laboratory of Molecular Signaling and Stem Cells Therapy, Beijing Key Laboratory of Tooth Regeneration and Function Reconstruction, Capital Medical University School of Stomatology, Beijing, China.,Department of Pediatric dentistry, Capital Medical University School of Stomatology, Beijing, China
| | - Zhipeng Fan
- Laboratory of Molecular Signaling and Stem Cells Therapy, Beijing Key Laboratory of Tooth Regeneration and Function Reconstruction, Capital Medical University School of Stomatology, Beijing, China
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Zhao J, Li G, Bo W, Zhou Y, Dang S, Wei J, Li X, Liu M. Multiple effects of ellagic acid on human colorectal carcinoma cells identified by gene expression profile analysis. Int J Oncol 2017; 50:613-621. [PMID: 28101576 DOI: 10.3892/ijo.2017.3843] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Accepted: 11/25/2016] [Indexed: 11/06/2022] Open
Abstract
Colorectal carcinoma (CRC) is the third most commonly diagnosed cancer in the world. Phytochemicals have become a research hotspot in recent years as cancer prevention and treatment agents due to their low toxicity and limited side-effects. Ellagic acid (EA), a natural phenolic constituent, displays various biological activities, including anticancer effects. However, the detailed anticancer mechanisms of EA remain unclear. In the present study, we found that EA inhibited the growth of HCT-116 colon cancer cells. Moreover, we identified differentially expressed genes (DEGs) by microarray profiling of HCT-116 cells treated with EA. A total of 857 DEGs (363 upregulated and 494 downregulated) were identified with a >1.5-fold change in expression after treatment with EA for 72 h. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis showed that a large number of cellular functions were modified by EA including proliferation, apoptosis, cell cycle and angiogenesis. Interaction network analysis using DEGs provided details of their interactions and predicted the key target pathways of EA. To verify the result of cDNA microarray, 10 selected DEGs related to proliferation, apoptosis or cell cycle were further confirmed by real-time RT-PCR. Based on microarray data, we identified several crucial functions of EA. These results provide important new data for EA in anti-CRC research.
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Affiliation(s)
- Jinlu Zhao
- Department of General Surgery, Τhe Fourth Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150001, P.R. China
| | - Guodong Li
- Department of General Surgery, Τhe Fourth Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150001, P.R. China
| | - Wanlan Bo
- Department of Gastroenterology, Τhe Fourth Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150001, P.R. China
| | - Yuhui Zhou
- Department of General Surgery, Τhe Fourth Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150001, P.R. China
| | - Shuwei Dang
- Department of General Surgery, Τhe Fourth Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150001, P.R. China
| | - Jiufeng Wei
- Department of General Surgery, Τhe Fourth Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150001, P.R. China
| | - Xinglong Li
- Department of General Surgery, Τhe Fourth Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150001, P.R. China
| | - Ming Liu
- Department of General Surgery, Τhe Fourth Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150001, P.R. China
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Zhan H, Huang F, Yan F, Zhao Z, Zhang J, Cui T, Yang F, Hai G, Jia X, Shi Y. Alterations in splenic function and gene expression in mice with depressive-like behavior induced by exposure to corticosterone. Int J Mol Med 2017; 39:327-336. [PMID: 28075471 PMCID: PMC5358716 DOI: 10.3892/ijmm.2017.2850] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2016] [Accepted: 12/13/2016] [Indexed: 11/07/2022] Open
Abstract
Depressed patients present with increased cortisol levels and attenuated immune responses. However, little is known about the association between depression and the spleen, as this is the largest peripheral immune organ. In this study, we examined alterations in splenic function and gene expression in mice with depressive-like behavior, well as the expression of certain proteins in related pathways. A mouse model of depression was established with the use of corticosterone. Splenic function and histopathology were assessed using Wright and H&E staining. The Agilent Whole Mouse Genome Oligo Microarray containing >41,174 transcript probes was used to measure the levels of gene-expression in the spleens from control and model mice, and the levels of certain proteins associated with depression were measured by western blot analysis in the brain and spleen separately. We found that splenic function and immunity in the mice with depressive-like behavior were markedly impaired. A total of 53 genes exhibited a differential response in the mice with depressive-like behavior, 11 of which were more notable, including collagen, type VI, α5 (Col6a5), immunoglobulin superfamily, member 11 (Igsf11), D site albumin promoter binding protein (Dbp), tachykinin 2 (Tac2) and γ-aminobutyric acid B receptor 2 (Gabbr2). Pathway analysis revealed that the amino acid biosynthesis and the clock gene pathways were more meaningful among these genes. The levels of GABBR2, DBP and substance P (SP; encoded by the Tac2 gene) related proteins in the brain were markedly downregulated, and similar results were observed in the spleen. The anti-depressant, fluoxetine, reversed the changes in the levels of these proteins. The findings of our study regarding changes occurring in the spleen during depression may indirectly elucidate and shed light into the pathogenesis of depression and depressive-like behavior.
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Affiliation(s)
- Heqin Zhan
- Department of Pharmacology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi 710061, P.R. China
| | - Feng Huang
- Department of Pharmacology, College of Pharmacy, Xinxiang Medical University, Xinxiang, Henan 453003, P.R. China
| | - Fulin Yan
- Department of Pharmacology, College of Pharmacy, Xinxiang Medical University, Xinxiang, Henan 453003, P.R. China
| | - Zhenghang Zhao
- Department of Pharmacology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi 710061, P.R. China
| | - Jixia Zhang
- Department of Pharmacology, College of Pharmacy, Xinxiang Medical University, Xinxiang, Henan 453003, P.R. China
| | - Taizhen Cui
- Department of Pharmacology, College of Pharmacy, Xinxiang Medical University, Xinxiang, Henan 453003, P.R. China
| | - Fan Yang
- Department of Pathogenic Microorganism, College of Basic Medical Sciences, Xinxiang Medical University, Xinxiang, Henan 453003, P.R. China
| | - Guangfan Hai
- Department of Pharmacology, College of Pharmacy, Xinxiang Medical University, Xinxiang, Henan 453003, P.R. China
| | - Xiaoman Jia
- Department of Basic Medical Sciences, College of Sanquan, Xinxiang Medical University, Xinxiang, Henan 453003, P.R. China
| | - Yongji Shi
- Department of Basic Medical Sciences, College of Sanquan, Xinxiang Medical University, Xinxiang, Henan 453003, P.R. China
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Du Y, Xia W, Zhang J, Wan D, Yang Z, Li X. Comprehensive analysis of long noncoding RNA–mRNA co-expression patterns in thyroid cancer. MOLECULAR BIOSYSTEMS 2017; 13:2107-2115. [PMID: 28817151 DOI: 10.1039/c7mb00375g] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Novel molecular-targeted treatments show great prospects for radioiodine-refractory and surgically inoperable thyroid carcinomas.
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Affiliation(s)
- Yaying Du
- Department of Thyroid and Breast Surgery
- Tongji Hospital
- Tongji Medical College of Huazhong University of Science and Technology
- Wuhan
- P. R. China
| | - Wenfei Xia
- Department of Thyroid and Breast Surgery
- Tongji Hospital
- Tongji Medical College of Huazhong University of Science and Technology
- Wuhan
- P. R. China
| | - Jinjun Zhang
- Department of Thyroid and Breast Surgery
- Tongji Hospital
- Tongji Medical College of Huazhong University of Science and Technology
- Wuhan
- P. R. China
| | - Dongyi Wan
- Department of Obstetrics and Gynecology
- Tongji Hospital
- Tongji Medical College
- Huazhong University of Science and Technology
- Wuhan
| | - Zhifang Yang
- Department of Thyroid and Breast Surgery
- Tongji Hospital
- Tongji Medical College of Huazhong University of Science and Technology
- Wuhan
- P. R. China
| | - Xingrui Li
- Department of Thyroid and Breast Surgery
- Tongji Hospital
- Tongji Medical College of Huazhong University of Science and Technology
- Wuhan
- P. R. China
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Zhou C, Zhang T, Liu F, Zhou J, Ni X, Huo R, Shi Z. The differential expression of mRNAs and long noncoding RNAs between ectopic and eutopic endometria provides new insights into adenomyosis. MOLECULAR BIOSYSTEMS 2016; 12:362-70. [PMID: 26662114 DOI: 10.1039/c5mb00733j] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Adenomyosis, defined as ectopic endometrial tissue within the myometrium, can often be misdiagnosed as multiple uterine leiomyomata or endometrial thickening. We therefore performed a combined mRNA and long noncoding (lnc)RNA microarray and bioinformatic analysis of eutopic and ectopic endometria in women with adenomyosis to better understand its pathogenesis and help in the development of a semi-invasive diagnostic test. A total of 586 mRNAs were increased and 305 mRNAs decreased in the ectopic endometrium of adenomyosis compared with the eutopic endometrium, while 388 lncRNA transcripts were up-regulated and 188 down-regulated in ectopic compared with paired eutopic endometrial tissue. Bioinformatic analysis suggested a series of metabolic and molecular abnormalities in adenomyosis, which have many similarities with endometriosis. Furthermore, our study constitutes the first known report of lncRNA expression patterns in human adenomyosis ectopic and eutopic endometrial tissue.
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Affiliation(s)
- Cheng Zhou
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing, China.
| | - Ting Zhang
- Wuxi Maternity and Child Health Hospital, Wuxi city, China
| | - Fei Liu
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing, China.
| | - Ji Zhou
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing, China.
| | - Xiaobei Ni
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing, China.
| | - Ran Huo
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing, China.
| | - Zhonghua Shi
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing, China. and State Key Laboratory of Reproductive Medicine, Nanjing Maternity and Child Health Hospital, Nanjing Medical University, Nanjing, China
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Sun Y, Sang Z, Jiang Q, Ding X, Yu Y. Transcriptomic characterization of differential gene expression in oral squamous cell carcinoma: a meta-analysis of publicly available microarray data sets. Tumour Biol 2016; 37:10.1007/s13277-016-5439-6. [PMID: 27704359 DOI: 10.1007/s13277-016-5439-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 09/23/2016] [Indexed: 01/04/2023] Open
Abstract
Oral squamous cell carcinoma (OSCC) is a highly prevalent cancer worldwide, and OSCC often goes undiagnosed until advanced disease is present, which contributes to a low survival rate for OSCC patients. The identification of biomarkers for the early detection OSCC and novel therapeutic targets for OSCC treatment is an important research objective. We performed bioinformatics analyses of the gene expression profile of OSCC using microarray data to identify genes that contribute to the development of OSCC. We also predicted the transcription factors involved in the regulation of differential gene expression in OSCC. Our results showed that PI3K, EGFR, STAT1, and CPBP are important contributors to the changes in cellular physiology that occur during the development of OSCC. Therefore, these genes represent potential diagnostic biomarkers and therapeutic targets for OSCC.
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Affiliation(s)
- Yang Sun
- Department of Stomatology, Zhongshan Hospital, Fudan University, 111 Yixueyuan Road, Shanghai, 200032, China
| | - Zhijian Sang
- Department of Stomatology, Zhongshan Hospital, Fudan University, 111 Yixueyuan Road, Shanghai, 200032, China
| | - Qian Jiang
- Department of Stomatology, Zhongshan Hospital, Fudan University, 111 Yixueyuan Road, Shanghai, 200032, China
| | - Xiaojun Ding
- Department of Stomatology, Zhongshan Hospital, Fudan University, 111 Yixueyuan Road, Shanghai, 200032, China.
| | - Youcheng Yu
- Department of Stomatology, Zhongshan Hospital, Fudan University, 111 Yixueyuan Road, Shanghai, 200032, China
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Xing Z, Yu L, Li X, Su X. Anticancer bioactive peptide-3 inhibits human gastric cancer growth by targeting miR-338-5p. Cell Biosci 2016; 6:53. [PMID: 27688872 PMCID: PMC5034486 DOI: 10.1186/s13578-016-0112-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Accepted: 06/30/2016] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Cancer incidence and mortality have been increasing in China, making cancer the leading cause of death since 2010 and a major public health concern in the country. Cancer stem cells have been studied in relation to the treatment of different malignancies, including gastric cancer. Anticancer bioactive peptide-3 (ACBP-3) can induce the apoptosis of gastric cancer stem cells (GCSCs) and reduce their tumorigenicity. In the present study, for the first time, we used a miRNA microarray and bioinformatics analysis to identify differentially expressed miRNAs in ACBP-3-treated GCSCs and GCSC-derived tumors in a xenograft model and functionally verified the identified miRNAs. miR-338-5p was selected based on its significant upregulation by ACBP-3 both in cultured GCSCs and in tumor tissues. RESULTS miR-338-5p was downregulated in GCSCs compared with normal gastric epithelial cells, and the ectopic restoration of miR-338-5p expression in GCSCs inhibited cell proliferation and induced apoptosis, which correlated with the upregulation of the pro-apoptotic Bcl-2 proteins BAK and BIM. We also found that ACBP-3-treated GCSCs could respond to lower effective doses of cisplatin (DDP) or 5-fluorouracil (5-FU), possibly because ACBP-3 induced the expression of miR-338-5p and the BAK and BIM proteins and promoted GCSC apoptosis. CONCLUSIONS Our data indicate that miR-338-5p is part of an important pathway for the inhibition of human gastric cancer stem cell proliferation by ACBP-3 combined with chemotherapeutics. ACBP-3 could suppress GCSC proliferation and lower the required effective dose of cisplatin or 5-fluorouracil. Therefore, this study provides not only further evidence for the remarkable anti-tumor effect of ACBP-3 but also a possible new approach for the development of GCSC-targeting therapies.
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Affiliation(s)
- Zhiwei Xing
- Department of Cell Biology, Capital Medical University, Beijing, China
| | - Lan Yu
- The Inner Mongolia Autonomous Region People’s Hospital, Hohhot, Inner Mongolia China
| | - Xian Li
- Clinical Medical Research Center of the Affiliated Hospital, Inner Mongolia Medical University, Hohhot, Inner Mongolia China
| | - Xiulan Su
- Department of Cell Biology, Capital Medical University, Beijing, China
- Clinical Medical Research Center of the Affiliated Hospital, Inner Mongolia Medical University, Hohhot, Inner Mongolia China
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Li G, Li QS, Li WB, Wei J, Chang WK, Chen Z, Qiao HY, Jia YW, Tian JH, Liang BS. miRNA targeted signaling pathway in the early stage of denervated fast and slow muscle atrophy. Neural Regen Res 2016; 11:1293-303. [PMID: 27651778 PMCID: PMC5020829 DOI: 10.4103/1673-5374.189195] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Denervation often results in skeletal muscle atrophy. Different mechanisms seem to be involved in the determination between denervated slow and fast skeletal muscle atrophy. At the epigenetic level, miRNAs are thought to be highly involved in the pathophysiological progress of denervated muscles. We used miRNA microarrays to determine miRNA expression profiles from a typical slow muscle (soleus muscle) and a typical fast muscle (tibialis anterior muscle) at an early denervation stage in a rat model. Results showed that miR-206, miR-195, miR-23a, and miR-30e might be key factors in the transformation process from slow to fast muscle in denervated slow muscles. Additionally, certain miRNA molecules (miR-214, miR-221, miR-222, miR-152, miR-320, and Let-7e) could be key regulatory factors in the denervated atrophy process involved in fast muscle. Analysis of signaling pathway networks revealed the miRNA molecules that were responsible for regulating certain signaling pathways, which were the final targets (e.g., p38 MAPK pathway; Pax3/Pax7 regulates Utrophin and follistatin by HDAC4; IGF1/PI3K/Akt/mTOR pathway regulates atrogin-1 and MuRF1 expression via FoxO phosphorylation). Our results provide a better understanding of the mechanisms of denervated skeletal muscle pathophysiology.
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Affiliation(s)
- Gang Li
- Department of Orthopedics, Second Affiliated Hospital of Shanxi Medical University, Taiyuan, Shanxi Province, China
| | - Qing-Shan Li
- Department of Orthopedics, Second Affiliated Hospital of Shanxi Medical University, Taiyuan, Shanxi Province, China
| | - Wen-Bin Li
- Department of Orthopedics, Second Affiliated Hospital of Shanxi Medical University, Taiyuan, Shanxi Province, China
| | - Jian Wei
- Department of Orthopedics, Second Affiliated Hospital of Shanxi Medical University, Taiyuan, Shanxi Province, China
| | - Wen-Kai Chang
- Department of Orthopedics, Second Affiliated Hospital of Shanxi Medical University, Taiyuan, Shanxi Province, China
| | - Zhi Chen
- Department of Orthopedics, Second Affiliated Hospital of Shanxi Medical University, Taiyuan, Shanxi Province, China
| | - Hu-Yun Qiao
- Department of Orthopedics, Second Affiliated Hospital of Shanxi Medical University, Taiyuan, Shanxi Province, China
| | - Ying-Wei Jia
- Department of Orthopedics, Second Affiliated Hospital of Shanxi Medical University, Taiyuan, Shanxi Province, China
| | - Jiang-Hua Tian
- Department of Orthopedics, Second Affiliated Hospital of Shanxi Medical University, Taiyuan, Shanxi Province, China
| | - Bing-Sheng Liang
- Department of Orthopedics, Second Affiliated Hospital of Shanxi Medical University, Taiyuan, Shanxi Province, China
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Aberrant LncRNA Expression Profile in a Contusion Spinal Cord Injury Mouse Model. BIOMED RESEARCH INTERNATIONAL 2016; 2016:9249401. [PMID: 27689092 PMCID: PMC5027055 DOI: 10.1155/2016/9249401] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Accepted: 06/26/2016] [Indexed: 12/23/2022]
Abstract
Long noncoding RNAs (LncRNAs) play a crucial role in cell growth, development, and various diseases related to the central nervous system. However, LncRNA differential expression profiles in spinal cord injury are yet to be reported. In this study, we profiled the expression pattern of LncRNAs using a microarray method in a contusion spinal cord injury (SCI) mouse model. Compared with a spinal cord without injury, few changes in LncRNA expression levels were noted 1 day after injury. The differential changes in LncRNA expression peaked 1 week after SCI and subsequently declined until 3 weeks after injury. Quantitative real-time polymerase chain reaction (qRT-PCR) was used to validate the reliability of the microarray, demonstrating that the results were reliable. Gene ontology (GO) analysis indicated that differentially expressed mRNAs were involved in transport, cell adhesion, ion transport, and metabolic processes, among others. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed that the neuroactive ligand-receptor interaction, the PI3K-Akt signaling pathway, and focal adhesions were potentially implicated in SCI pathology. We constructed a dynamic LncRNA-mRNA network containing 264 LncRNAs and 949 mRNAs to elucidate the interactions between the LncRNAs and mRNAs. Overall, the results from this study indicate for the first time that LncRNAs are differentially expressed in a contusion SCI mouse model.
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Microarray and Co-expression Network Analysis of Genes Associated with Acute Doxorubicin Cardiomyopathy in Mice. Cardiovasc Toxicol 2016; 15:377-93. [PMID: 25575753 DOI: 10.1007/s12012-014-9306-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Clinical use of doxorubicin (DOX) in cancer therapy is limited by its dose-dependent cardiotoxicity. But molecular mechanisms underlying this phenomenon have not been well defined. This study was to investigate the effect of DOX on the changes of global genomics in hearts. Acute cardiotoxicity was induced by giving C57BL/6J mice a single intraperitoneal injection of DOX (15 mg/kg). Cardiac function and apoptosis were monitored using echocardiography and TUNEL assay at days 1, 3 and 5. Myocardial glucose and ATP levels were measured. Microarray assays were used to screen gene expression profiles in the hearts at day 5, and the results were confirmed with qPCR analysis. DOX administration caused decreased cardiac function, increased cardiomyocyte apoptosis and decreased glucose and ATP levels. Microarrays showed 747 up-regulated genes and 438 down-regulated genes involved in seven main functional categories. Among them, metabolic pathway was the most affected by DOX. Several key genes, including 2,3-bisphosphoglycerate mutase (Bpgm), hexokinase 2, pyruvate dehydrogenase kinase, isoenzyme 4 and fructose-2,6-bisphosphate 2-phosphatase, are closely related to glucose metabolism. Gene co-expression networks suggested the core role of Bpgm in DOX cardiomyopathy. These results obtained in mice were further confirmed in cultured cardiomyocytes. In conclusion, genes involved in glucose metabolism, especially Bpgm, may play a central role in the pathogenesis of DOX-induced cardiotoxicity.
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Chen QY, Jiao DM, Yan L, Wu YQ, Hu HZ, Song J, Yan J, Wu LJ, Xu LQ, Shi JG. Comprehensive gene and microRNA expression profiling reveals miR-206 inhibits MET in lung cancer metastasis. MOLECULAR BIOSYSTEMS 2016; 11:2290-302. [PMID: 26075299 DOI: 10.1039/c4mb00734d] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
MiRNAs associated with the metastasis of lung cancer remain largely unexplored. In this study, gene and miRNA expression profiling were performed to analyze the global expression of mRNAs and miRNAs in human high- and low-metastatic lung cancer cell strains. By developing an integrated bioinformatics analysis, six miRNAs (miR-424-3p, miR-450b-5p, miR-335-5p, miR-34a-5p, miR-302b-3p and miR-206) showed higher target gene degrees in the miRNA-gene network and might be potential metastasis-related miRNAs. Using the qRT-PCR method, the six miRNAs were further confirmed to show a significant expression difference between human lung cancer and normal tissue samples. Since miR-206 showed lower expression both in lung cancer tissues and cell lines, it was used as an example for further functional verification. The wound healing assay and transwell invasion assay showed that miR-206 mimics significantly inhibited the cell migration and invasion of the high-metastatic lung cancer 95D cell strain. One of its predicted targets in our miRNA-gene network, MET, was also obviously decreased at the protein level when miR-206 was overexpressed. Instead, miR-206 inhibitors increased MET protein expression, cell migration and invasion of the low-metastatic lung cancer 95C cell strain. Meanwhile, the luciferase assay showed that MET was a direct target of miR-206. Furthermore, MET gene silence showed a similar anti-migration and anti-invasion effect with miR-206 mimics in 95D cells and could partially attenuate the migration- and invasion-promoting effect of miR-206 inhibitors in 95C cells, suggesting that miR-206 targets MET in lung cancer metastasis. Finally, we also demonstrated that miR-206 can significantly inhibit lung cancer proliferation and metastasis in mouse models. In conclusion, our study provided a miRNA-gene regulatory network in lung cancer metastasis and further demonstrated the roles of miR-206 and MET in this process, which enhances the understanding of the regulatory mechanism in lung cancer metastasis.
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Affiliation(s)
- Qing-yong Chen
- Department of Respiratory Disease, The 117th Hospital of PLA, Hangzhou, Zhejiang 310013, P. R. China.
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Liu X, Duan H, Zhang HH, Gan L, Xu Q. Integrated Data Set of microRNAs and mRNAs Involved in Severe Intrauterine Adhesion. Reprod Sci 2016; 23:1340-7. [PMID: 27052751 DOI: 10.1177/1933719116638177] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
BACKGROUND Adhesion tissue is formed following injury to the uterine basal layer. Currently, there is no effective treatment for severe intrauterine adhesion (IUA), which causes loss of reproductive function. Enhanced understanding of the molecular mechanisms driving severe IUA would be beneficial for the treatment. METHODS Differentially expressed microRNAs (miRNAs) and messenger RNAs (mRNAs) in severe IUA (n = 3) and normal (n = 3) endometrium were analyzed by high-throughput microarray analysis. Subsequently, the target genes of the differentially expressed miRNAs were predicted and found to overlap with the differentially expressed mRNAs. Gene Ontology and pathway analyses were performed for the intersecting genes. Three of the significantly dysregulated miRNAs and 4 of their target mRNAs were further assessed using quantitative real-time polymerase chain reaction (PCR) in 10 severe IUA and 10 normal endometrium samples. RESULTS Microarray analysis indicated that 26 miRNAs and 1180 mRNAs were significantly different between the 2 groups. Of these, 16 miRNAs and 54 mRNAs overlapped with putative miRNA target genes and prediction of target gene. Real-time PCR revealed upregulation of hsa-miR-513a-5p and has-miR-135a-3p and downregulation of hsa-miR-543 and their corresponding target genes, plus downregulation of ADAM9 (a disintegrin-containing and metalloproteinases) and lysyl oxidase and upregulation of CDH2 (N-cadherin) and COL16A1 (collagen 16A1). Both CDH2 and COL16A1 were bioinformatically predicted and confirmed in vitro as target genes of miR-543. CONCLUSION This study provides an integrated data set of the miRNA and mRNA profiles in severe IUA, showing involvement of many miRNAs and their target genes. Further analysis of these genes will help in understanding of the molecular mechanism of IUA formation.
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Affiliation(s)
- Xin Liu
- Department of Minimally Invasive Gynecology, Obstetrics and Gynecology Hospital Beijing, Capital Medical University, Beijing, PR China
| | - Hua Duan
- Department of Minimally Invasive Gynecology, Obstetrics and Gynecology Hospital Beijing, Capital Medical University, Beijing, PR China
| | - Heng-Hui Zhang
- Beijing Key Laboratory of Hepatitis C and Immunotherapy for Liver Diseases, Peking University Hepatology Institute, Peking University People's Hospital, Beijing, PR China
| | - Lu Gan
- Department of Minimally Invasive Gynecology, Obstetrics and Gynecology Hospital Beijing, Capital Medical University, Beijing, PR China
| | - Qian Xu
- Department of Minimally Invasive Gynecology, Obstetrics and Gynecology Hospital Beijing, Capital Medical University, Beijing, PR China
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Suzuki Y, Lu M, Ben-Jacob E, Onuchic JN. Periodic, Quasi-periodic and Chaotic Dynamics in Simple Gene Elements with Time Delays. Sci Rep 2016; 6:21037. [PMID: 26876008 PMCID: PMC4753448 DOI: 10.1038/srep21037] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 01/15/2016] [Indexed: 01/24/2023] Open
Abstract
Regulatory gene circuit motifs play crucial roles in performing and maintaining vital cellular functions. Frequently, theoretical studies of gene circuits focus on steady-state behaviors and do not include time delays. In this study, the inclusion of time delays is shown to entirely change the time-dependent dynamics for even the simplest possible circuits with one and two gene elements with self and cross regulations. These elements can give rise to rich behaviors including periodic, quasi-periodic, weak chaotic, strong chaotic and intermittent dynamics. We introduce a special power-spectrum-based method to characterize and discriminate these dynamical modes quantitatively. Our simulation results suggest that, while a single negative feedback loop of either one- or two-gene element can only have periodic dynamics, the elements with two positive/negative feedback loops are the minimalist elements to have chaotic dynamics. These elements typically have one negative feedback loop that generates oscillations, and another unit that allows frequent switches among multiple steady states or between oscillatory and non-oscillatory dynamics. Possible dynamical features of several simple one- and two-gene elements are presented in details. Discussion is presented for possible roles of the chaotic behavior in the robustness of cellular functions and diseases, for example, in the context of cancer.
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Affiliation(s)
- Yoko Suzuki
- Department of Physics, School of Science and Engineering, Meisei University, 2-1-1 Hodokubo, Hino-shi, Tokyo 191-8506, Japan.,Center for Theoretical Biological Physics, Rice University, Houston, TX 77005-1827, USA
| | - Mingyang Lu
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005-1827, USA
| | - Eshel Ben-Jacob
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005-1827, USA.,School of Physics and Astronomy and The Sagol School of Neuroscience, Tel-Aviv University, Tel-Aviv 69978, Israel
| | - José N Onuchic
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005-1827, USA.,Department of Physics and Astronomy, Rice University, Houston, TX 77005-1827, USA.,Department of Chemistry, Rice University, Houston, TX 77005-1827, USA.,Department of Biochemistry and Cell Biology, Rice University, Houston, TX 77005-1827, USA
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45
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Androgen Modulates Functions of Endothelial Progenitor Cells through Activated Egr1 Signaling. Stem Cells Int 2015; 2016:7057894. [PMID: 26697079 PMCID: PMC4677258 DOI: 10.1155/2016/7057894] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Revised: 08/31/2015] [Accepted: 09/13/2015] [Indexed: 01/09/2023] Open
Abstract
Researches show that androgens have important effects on migration of endothelial cells and endothelial protection in coronary heart disease. Endothelial progenitor cells (EPCs) as a progenitor cell type that can differentiate into endothelial cells, have a critical role in angiogenesis and endothelial protection. The relationship between androgen and the functions of EPCs has animated much interest and controversy. In this study, we investigated the angiogenic and migratory functions of EPCs after treatment by dihydrotestosterone (DHT) and the molecular mechanisms as well. We found that DHT treatment enhanced the incorporation of EPCs into tubular structures formed by HUVECs and the migratory activity of EPCs in the transwell assay dose dependently. Moreover, microarray analysis was performed to explore how DHT changes the gene expression profiles of EPCs. We found 346 differentially expressed genes in androgen-treated EPCs. Angiogenesis-related genes like Egr-1, Vcan, Efnb2, and Cdk2ap1 were identified to be regulated upon DHT treatment. Furthermore, the enhanced angiogenic and migratory abilities of EPCs after DHT treatment were inhibited by Egr1-siRNA transfection. In conclusion, our findings suggest that DHT markedly enhances the vessel forming ability and migration capacity of EPCs. Egr1 signaling may be a possible pathway in this process.
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Wang J, Zhang W, Zou H, Lin Y, Lin K, Zhou Z, Qiang J, Lin J, Chuka CM, Ge R, Zhao S, Yang X. 10-Hydroxy-2-decenoic acid inhibiting the proliferation of fibroblast-like synoviocytes by PI3K–AKT pathway. Int Immunopharmacol 2015; 28:97-104. [DOI: 10.1016/j.intimp.2015.05.036] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2014] [Revised: 05/19/2015] [Accepted: 05/21/2015] [Indexed: 01/05/2023]
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47
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Genome-wide analysis of long noncoding RNA expression profile in papillary thyroid carcinoma. Gene 2015; 569:109-17. [DOI: 10.1016/j.gene.2015.05.046] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Revised: 05/10/2015] [Accepted: 05/17/2015] [Indexed: 12/15/2022]
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48
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Yu S, Hong Q, Wang Y, Hou K, Wang L, Zhang Y, Fu B, Zhou Y, Zheng W, Chen X, Wu D. High concentrations of uric acid inhibit angiogenesis via regulation of the Krüppel-like factor 2-vascular endothelial growth factor-A axis by miR-92a. Circ J 2015; 79:2487-98. [PMID: 26299712 DOI: 10.1253/circj.cj-15-0283] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
BACKGROUND Angiogenesis is a critical component of many pathological conditions, and microRNAs (miRNAs) are indispensable in angiogenesis. It is unclear whether miRNAs regulate angiogenesis in the presence of high concentrations of uric acid (HUA), and the underlying mechanisms remain unknown. METHODS AND RESULTS It was found that HUA inhibited the angiogenic ability of endothelial cells. miRNA expression profiling was conducted using microarray assays in HUA-stimulated endothelial cells. Eighteen differentially expressed miRNAs were subjected to bioinformatic analyses. The results indicated that miR-92a was negatively regulated and was closely related to angiogenesis. Furthermore, the effects of miR-92a on HUA-stimulated endothelial cell angiogenesis and the underlying mechanisms were investigated in dual-luciferase reporter assays, electrophoretic mobility shift assays, immunoblot assays, and tube formation assays. It was determined that Krüppel-like factor 2 (KLF2) is a target gene of miR-92a, and KLF2 binds the vascular endothelial growth factor-A (VEGFA) promoter to inhibit its expression. miR-92a and VEGFA overexpression or KLF2 downregulation alleviates the HUA-mediated inhibition of angiogenesis in endothelial cells in vitro. CONCLUSIONS This study reported that there is a novel pathway regulating angiogenesis under HUA conditions. In the presence of HUA, miR-92a downregulation increased KLF2 expression, subsequently inhibiting VEGFA, which resulted in decreased angiogenesis. Thus, this study reports a possible mechanism for cardiovascular injury caused by hyperuricemia and suggests that the miR-92a-KLF2-VEGFA axis may be a target for hyperuricemia treatment.
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Affiliation(s)
- Shandong Yu
- State Key Laboratory of Kidney Diseases, Department of Nephrology, Chinese PLA Institute of Nephrology, National Clinical Research Center for Kidney Disease, Chinese PLA General Hospital
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Differentially expressed protein-coding genes and long noncoding RNA in early-stage lung cancer. Tumour Biol 2015; 36:9969-78. [DOI: 10.1007/s13277-015-3714-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2015] [Accepted: 06/23/2015] [Indexed: 01/01/2023] Open
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50
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MicroRNA expression profiles and networks in mouse lung infected with H1N1 influenza virus. Mol Genet Genomics 2015; 290:1885-97. [PMID: 25893419 DOI: 10.1007/s00438-015-1047-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Accepted: 03/31/2015] [Indexed: 11/27/2022]
Abstract
Influenza A viruses can cause localized outbreaks and worldwide pandemics, owing to their high transmissibility and wide host range. As such, they are among the major diseases that cause human death. However, the molecular changes induced by influenza A virus infection in lung tissue are not entirely clear. Changes in microRNA (miRNA) expression occur in many pathological and physiological processes, and influenza A virus infection has been shown to alter miRNA expression in cultured cells and animal models. In this study, we mined key miRNAs closely related to influenza A virus infection and explored cellular regulatory mechanisms against influenza A virus infection, by building networks among miRNAs and genes, gene ontologies (GOs), and pathways. In this study, miRNAs and mRNAs induced by H1N1 influenza virus infection were measured by gene chips, and we found that 82 miRNAs and 3371 mRNAs were differentially expressed. The 82 miRNAs were further analyzed with the series test of cluster (STC) analysis. Three of the 16 cluster profiles identified by STC, which include 46 miRNAs in the three profiles, changed significantly. Using potential target genes of the 46 miRNAs, we looked for intersections of these genes with 3371 differentially expressed mRNAs; 719 intersection genes were identified. Based on the GO or KEGG databases, we attained GOs or pathways for all of the above intersection genes. Fisher's and χ (2) test were used to calculate p value and false discovery rate (FDR), and according to the standard of p < 0.001, 241 GOs and 76 pathways were filtered. Based on these data, miRNA-gene, miRNA-GO, and miRNA-pathway networks were built. We then extracted three classes of GOs (related to inflammatory and immune response, cell cycle, proliferation and apoptosis, and signal transduction) to build three subgraphs, and pathways strictly related with H1N1 influenza virus infection were filtered to extract a subgraph of the miRNA-pathway network. Last, according to the pathway analysis and miRNA-pathway network analysis, 17 miRNAs were found to be associated with the "influenza A" pathway. This study provides the most complete miRNAome profiles, and the most detailed miRNA regulatory networks to date, and is the first to report the most important 17 miRNAs closely related with the pathway of influenza A. These results are a prelude to advancements in mouse H1N1 influenza virus infection biology and the use of mice as a model for human H1N1 influenza virus infection studies.
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