scholarly journals Integrative transcriptomic and proteomic analysis reveals mechanisms of silica-induced pulmonary fibrosis in rats

2022 ◽  
Vol 22 (1) ◽  
Author(s):  
Cunxiang Bo ◽  
Juan Zhang ◽  
Linlin Sai ◽  
Zhongjun Du ◽  
Gongchang Yu ◽  
...  
Keyword(s):  
Pulmonary Fibrosis ◽  
Proteomic Analysis ◽  
Systemic Disease ◽  
Cellular Adhesion ◽  
Differentially Expressed ◽  
Integrated Analysis ◽  
Control Group ◽  
Targeted Prevention ◽  
Great Effort ◽  
Cellular Adhesion Molecule

Abstract Background Silicosis is a systemic disease characterized by persistent inflammation and incurable pulmonary fibrosis. Although great effort has been made to understand the pathogenesis of the disease, molecular mechanism underlying silicosis is not fully elucidated. This study was aimed to explore proteomic and transcriptomic changes in rat model of silicosis. Methods Twenty male Wistar rats were randomly divided into two groups with 10 rats in each group. Rats in the model group were intratracheally instilled with 50 mg/mL silicon dioxide (1 mL per rat) and rats in the control group were treated with 1.0 mL saline (1 mL per rat). Twenty-eight days later, transcriptomic analysis by microarray and tandem mass tags (TMT)-based proteomic analysis were performed to reveal the expression of mRNAs and proteins in lung tissues. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) were applied to analyze the altered genes and proteins. The integrated analysis was performed between transcriptome and proteome. The data were further verified by RT-qPCR and parallel reaction monitoring (PRM). Results In total, 1769 differentially expressed genes (DEGs) and 650 differentially expressed proteins (DEPs) were identified between the silicosis model and control groups. The integrated analysis showed 250 DEPs were correlated to the corresponding DEGs (cor-DEPs-DEGs), which were mainly enriched in phagosome, leukocyte transendothelial migration, complement and coagulation cascades and cellular adhesion molecule (CAM). These pathways are interrelated and converged at common points to produce an effect. GM2a, CHI3L1, LCN2 and GNAI1 are involved in the extracellular matrix (ECM) and inflammation contributing to fibrosis. Conclusion Our comprehensive transcriptome and proteome data provide new insights into the mechanisms of silicosis and helpful information for more targeted prevention and treatment of silicosis.

scholarly journals Serum Proteomic Analysis of Cannabis Use Disorder in Male Patients

Molecules ◽  
2021 ◽  
Vol 26 (17) ◽  
pp. 5311
Author(s):  
Fawaz Alasmari ◽  
Sary Alsanea ◽  
Assim A. Alfadda ◽  
Ibrahim O. Alanazi ◽  
Mohthash Musambil ◽  
...  
Keyword(s):  
Signaling Pathways ◽  
Proteomic Analysis ◽  
Cannabis Use ◽  
Farnesoid X Receptor ◽  
Differentially Expressed ◽  
Interleukin 12 ◽  
Control Group ◽  
Cannabis Use Disorder ◽  
Differentially Expressed Proteins ◽  
Healthy Control

Cannabis use has been growing recently and it is legally consumed in many countries. Cannabis has a variety of phytochemicals including cannabinoids, which might impair the peripheral systems responses affecting inflammatory and immunological pathways. However, the exact signaling pathways that induce these effects need further understanding. The objective of this study is to investigate the serum proteomic profiling in patients diagnosed with cannabis use disorder (CUD) as compared with healthy control subjects. The novelty of our study is to highlight the differentially changes proteins in the serum of CUD patients. Certain proteins can be targeted in the future to attenuate the toxicological effects of cannabis. Blood samples were collected from 20 male individuals: 10 healthy controls and 10 CUD patients. An untargeted proteomic technique employing two-dimensional difference in gel electrophoresis coupled with mass spectrometry was employed in this study to assess the differentially expressed proteins. The proteomic analysis identified a total of 121 proteins that showed significant changes in protein expression between CUD patients (experimental group) and healthy individuals (control group). For instance, the serum expression of inactive tyrosine protein kinase PEAK1 and tumor necrosis factor alpha-induced protein 3 were increased in CUD group. In contrast, the serum expression of transthyretin and serotransferrin were reduced in CUD group. Among these proteins, 55 proteins were significantly upregulated and 66 proteins significantly downregulated in CUD patients as compared with healthy control group. Ingenuity pathway analysis (IPA) found that these differentially expressed proteins are linked to p38MAPK, interleukin 12 complex, nuclear factor-κB, and other signaling pathways. Our work indicates that the differentially expressed serum proteins between CUD and control groups are correlated to liver X receptor/retinoid X receptor (RXR), farnesoid X receptor/RXR activation, and acute phase response signaling.

scholarly journals Identification of Differentially Expressed Genes Triggered by Aberrant Methylation in Idiopathic Pulmonary Fibrosis Using Integrated Bioinformatic Analysis

2020 ◽  
Author(s):  
Shuaijun Chen ◽  
Jun Zhang ◽  
Wanli Ma ◽  
Hong Ye
Keyword(s):  
Idiopathic Pulmonary Fibrosis ◽  
Pulmonary Fibrosis ◽  
Differentially Expressed Genes ◽  
Expression Profiles ◽  
Gene Set Enrichment Analysis ◽  
Differentially Expressed ◽  
Epigenetic Mechanism ◽  
Integrated Analysis ◽  
Aberrant Methylation ◽  
Mrna Levels

Abstract BackgroundIdiopathic pulmonary fibrosis (IPF) is a relentlessly progressive and fatal fibrotic lung disease all over the world, and specific pathogenesis is still not well understood. DNA methylation is an essential epigenetic mechanism, which likely contributes to the progress of IPF. The purpose of this study is to identify aberrantly methylated differentially expressed genes (DEGs) in IPF and to explore the underlying mechanisms of IPF by using integrated bioinformatics analysis.MethodGene expression profiles and gene methylation profile were downloaded and analyzed to identify the aberrantly methylated‐differentially expressed genes. Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), Search Tool for the Retrieval of Interacting Genes Database (STRING) and Gene set enrichment analysis (GSEA) were used to evaluate function of DEGs. RT-PCR was used to verify the mRNA levels of DEGs in mice with pulmonary fibrosis.ResultsBy analyzing the differentially expressed genes of the three IPF expression profiles, and taking the intersection, we got 143 co-upregulated genes and 104 co-downregulated genes; GO and KEGG pathway analysis of the DEGs suggested these genes involved in the extracellular matrix organization, multicellular organismal homeostasis. Combining the sequencing data of two IPF methylation chips, we have identified genes that may be regulated by methylation in IPF. Finally, we obtained the mRNA expression of DEGs using a mouse model of pulmonary fibrosis.ConclusionThrough integrated analysis and experimental verification, we found a series of biomarkers which were regulated by methylation should be potential therapeutic targets for IPF.

scholarly journals A blood RNA transcriptome signature for COVID-19

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Philip Kam Weng Kwan ◽  
Gail B. Cross ◽  
Claire M. Naftalin ◽  
Bintou A. Ahidjo ◽  
Chee Keng Mok ◽  
...  
Keyword(s):  
Ethnic Groups ◽  
Disease Severity ◽  
Differentially Expressed Genes ◽  
Whole Blood ◽  
Systemic Disease ◽  
Differentially Expressed ◽  
Control Group ◽  
Disease Score ◽  
Asian Ethnicity ◽  
Syncytial Virus

Abstract Background COVID-19 is a respiratory viral infection with unique features including a more chronic course and systemic disease manifestations including multiple organ involvement; and there are differences in disease severity between ethnic groups. The immunological basis for disease has not been fully characterised. Analysis of whole-blood RNA expression may provide valuable information on disease pathogenesis. Methods We studied 45 patients with confirmed COVID-19 infection within 10 days from onset of illness and a control group of 19 asymptomatic healthy volunteers with no known exposure to COVID-19 in the previous 14 days. Relevant demographic and clinical information was collected and a blood sample was drawn from all participants for whole-blood RNA sequencing. We evaluated differentially-expressed genes in COVID-19 patients (log2 fold change ≥ 1 versus healthy controls; false-discovery rate < 0.05) and associated protein pathways and compared these to published whole-blood signatures for respiratory syncytial virus (RSV) and influenza. We developed a disease score reflecting the overall magnitude of expression of internally-validated genes and assessed the relationship between the disease score and clinical disease parameters. Results We found 135 differentially-expressed genes in the patients with COVID-19 (median age 35 years; 82% male; 36% Chinese, 53% South Asian ethnicity). Of the 117 induced genes, 14 were found in datasets from RSV and 40 from influenza; 95 genes were unique to COVID-19. Protein pathways were mostly generic responses to viral infections, including apoptosis by P53-associated pathway, but also included some unique pathways such as viral carcinogenesis. There were no major qualitative differences in pathways between ethnic groups. The composite gene-expression score was correlated with the time from onset of symptoms and nasal swab qPCR CT values (both p < 0.01) but was not related to participant age, gender, ethnicity or the presence or absence of chest X-ray abnormalities (all p > 0.05). Conclusions The whole-blood transcriptome of COVID-19 has overall similarity with other respiratory infections but there are some unique pathways that merit further exploration to determine clinical relevance. The approach to a disease score may be of value, but needs further validation in a population with a greater range of disease severity.

scholarly journals Integrated Analysis of a circRNA-miRNA-mRNA Axis in Intervertebral Disc Degeneration

2020 ◽  
Author(s):  
Laifu Wei ◽  
Bizhi Tu ◽  
Fei Gao ◽  
Jun Qian
Keyword(s):  
Intervertebral Disc ◽  
Disc Degeneration ◽  
Intervertebral Disc Degeneration ◽  
Underlying Mechanism ◽  
Differentially Expressed ◽  
Circular Rnas ◽  
Integrated Analysis ◽  
Control Group ◽  
Common Symptom ◽  
Sequencing Data

Abstract Background: Low back pain (LBP) is a common symptom in daily life and one of the primary causes is intervertebral disc degeneration (IDD). Growing studies have indicated that circular RNAs (circRNAs) are intimately associated with IDD; however, the underlying mechanism has not yet been elucidated. We aimed to explore how circRNAs regulate IDD in an effort to provide novel insight for clinical diagnosis and treatment. Methods: The sequencing data of circRNAs, microRNAs (miRNAs), and mRNA were acquired from Gene Expression Omnibus (GEO) datasets. By analyzing the dataset consisting of a control group and degenerated group, differentially expressed circRNAs, miRNAs, and mRNAs were collected, and then the intersection of circRNAs, miRNAs, and mRNAs was screened. According to these intersectional RNAs, we constructed an integrally circRNA-miRNA-mRNA network. Finally, using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses, we further clarified functions of the intersectional mRNA in IDD. Results: we obtained 620 differentially expressed circRNAs(DEcircRNAs), 13 miRNA (DEmiRNA), 273 mRNAs(DEmRNAs), 12 intersectional miRNAs, and 47 intersectional mRNAs. Finally, based on interactional 8 circRNA, 5 miRNAs and 15 mRNAs, an integrally circRNA-miRNA-mRNA network was constructed. Eight circRNAs, contained hsa_circ_0032254, hsa_circ_0003183, hsa_circ_0032253, hsa_circ_0001293, hsa_circ_0004565, hsa_circ_0091570, hsa_circ_0077526, and hsa_circ_0057552, may regulate IDD onset and progression by acting as competing endogenous RNAs. The results of GO and KEGG analyses implied that the targeted genes might significantly correlate to IDD.Conclusion: our findings improved a better understanding of the circRNA-related ceRNA regulatory mechanism in IDD and offered possible targets for IDD treatment.

scholarly journals Comparative Transcriptomic and Proteomic Analysis of Exopalaemon carinicauda in Response to Alkalinity Stress

2021 ◽  
Vol 8 ◽  
Author(s):  
Zhen Qin ◽  
Qianqian Ge ◽  
Jiajia Wang ◽  
Mingdong Li ◽  
Ping Liu ◽  
...  
Keyword(s):  
Ion Transport ◽  
Proteomic Analysis ◽  
Differentially Expressed ◽  
Ammonium Transporter ◽  
Integrated Analysis ◽  
Molecular Response ◽  
Exopalaemon Carinicauda ◽  
Kegg Pathways ◽  
Transmembrane Transporter ◽  
Alkaline Waters

Saline-alkaline waters are stressful environments where most aquatic animals can’t survive normally, and alkalinity is one of the key limited environmental factors. Due to strong adaptability to environment, the ridgetail white prawn Exopalaemon carinicauda is a potential good species suitable for large-scale culture in saline-alkaline waters. Exploring its alkaline adaptability mechanism will help to guide more marine crustaceans to saline-alkaline culture. In this study, an integrative analysis of the gill-specific transcriptome and proteome at 0, 12, and 36 h after alkalinity stress was performed to identify important regulators and pathways involved in alkalinity adaption of E. carinicauda. A total of 3,157 differentially expressed genes (DEGs) and 443 differentially expressed proteins (DEPs) were identified at 12 and 36 h compared with 0 h. Base on the transcriptome analysis, the Gene Ontology (GO) enriched terms were mainly related to ion transport, including “calcium-transporting ATPase activity,” “ATPase coupled ion transmembrane transporter activity,” “divalent inorganic cation transmembrane transporter activity,” etc., and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways mainly refer to the processes of endocrine system at both 12, and 36 h. Based on the proteomic analysis, KEGG pathways related to lipolysis and amino acids metabolism were significantly enriched at 12 h, and carbohydrate metabolism and immune response were significantly enriched at 36 h. There were significantly up-regulated expressions of ion transport related genes including aquaporin, carbonic anhydrase, ammonium transporter Rh type A-like, Na+/H+-exchanger, etc., as well as ion transport proteins including V-type proton ATPase 116 kDa subunit a-like isoform X1, sodium-potassium ATPase beta, vesicle associated membrane protein, etc. after alkalinity exposure, which indicating their important roles in response to alkalinity stress. The results of integrated analysis between proteome and transcriptome showed that up-regulated DEG/DEP (aldehyde dehydrogenase) was significantly enriched at 12 h and the up-regulated DEG/DEP (peptidylglycine alpha) was significantly enriched at 36 h, suggesting the two molecules may be critical in response to alkalinity change. This study reveals the first time-course, gill-specific, combined transcriptomic and proteomic profiling associated with alkalinity adaption of E. carinicauda and provides new insights into the mechanisms underlying the molecular response to alkalinity stress in shrimp.

scholarly journals Identification of differentially expressed genes triggered by aberrant methylation in idiopathic pulmonary fibrosis using integrated bioinformatic analysis

2021 ◽  
Author(s):  
Shuaijun Chen ◽  
Jun Zhang ◽  
Wanli Ma ◽  
Hong Ye
Keyword(s):  
Idiopathic Pulmonary Fibrosis ◽  
Pulmonary Fibrosis ◽  
Differentially Expressed Genes ◽  
Expression Profiles ◽  
Gene Set Enrichment Analysis ◽  
Differentially Expressed ◽  
Epigenetic Mechanism ◽  
Integrated Analysis ◽  
Aberrant Methylation ◽  
Mrna Levels

Abstract Background Idiopathic pulmonary fibrosis (IPF) is a relentlessly progressive and fatal fibrotic lung disease all over the world, and specific pathogenesis is still not well understood. DNA methylation is an essential epigenetic mechanism, which likely contributes to the progress of IPF. The purpose of this study is to identify aberrantly methylated differentially expressed genes (DEGs) in IPF and to explore the underlying mechanisms of IPF by using integrated bioinformatics analysis.Methods Gene expression profiles and gene methylation profiles were downloaded and analyzed to identify the aberrantly methylated‐differentially expressed genes. Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), Search Tool for the Retrieval of Interacting Genes Database (STRING), and Gene set enrichment analysis (GSEA) were used to evaluate the function of DEGs. RT-PCR was used to verify the mRNA levels of DEGs in mice with pulmonary fibrosis.Results By analyzing the differentially expressed genes of the three IPF expression profiles, and taking the intersection, we got 143 co-upregulated genes and 104 co-downregulated genes; GO and KEGG pathway analysis of the DEGs suggested these genes involved in the extracellular matrix organization, multicellular organismal homeostasis. Combining the sequencing data of two IPF methylation chips, we have identified genes that may be regulated by methylation in IPF. Finally, we obtained the mRNA expression of DEGs using a mouse model of pulmonary fibrosis.Conclusions Through integrated analysis and experimental verification, we found a series of biomarkers that were regulated by methylation should be potential therapeutic targets for IPF.

scholarly journals Integrated analysis of transcriptomic and proteomic data from tree peony (P. ostii) seeds reveals key developmental stages and candidate genes related to oil biosynthesis and fatty acid metabolism

2019 ◽  
Vol 6 (1) ◽  
Author(s):  
Xiaojing Wang ◽  
Haiying Liang ◽  
Dalong Guo ◽  
Lili Guo ◽  
Xiangguang Duan ◽  
...  
Keyword(s):  
Fatty Acid ◽  
Seed Development ◽  
Fatty Acid Metabolism ◽  
Proteomic Analysis ◽  
Acid Metabolism ◽  
Expression Patterns ◽  
Differentially Expressed ◽  
Integrated Analysis ◽  
Tree Peony ◽  
Oil Biosynthesis

Abstract Tree peony (Paeonia section Moutan DC.) seeds are an excellent source of beneficial natural compounds that promote health, and they contain high levels of alpha-linolenic acid (ALA). In recent years, tree peony has been emerging as an oil crop. Therefore, combined analysis of the transcriptome and proteome of tree peony (P. ostii) seeds at 25, 32, 39, 53, 67, 81, 88, 95, and 109 days after pollination (DAP) was conducted to better understand the transcriptional and translational regulation of seed development and oil biosynthesis. A total of 38,482 unigenes and 2841 proteins were identified. A total of 26,912 differentially expressed genes (DEGs) and 592 differentially expressed proteins (DEPs) were clustered into three groups corresponding to the rapid growth, seed inclusion enrichment and conversion, and late dehydration and mature stages of seed development. Fifteen lipid metabolism pathways were identified at both the transcriptome and proteome levels. Pathway enrichment analysis revealed that a period of rapid fatty acid biosynthesis occurred at 53–88 DAP. Furthermore, 211 genes and 35 proteins associated with the fatty acid metabolism pathway, 63 genes and 11 proteins associated with the biosynthesis of unsaturated fatty acids (UFAs), and 115 genes and 24 proteins associated with ALA metabolism were identified. Phylogenetic analysis revealed that 16 putative fatty acid desaturase (FAD)-encoding genes clustered into four FAD groups, eight of which exhibited the highest expression at 53 DAP, suggesting that they play an important role in ALA accumulation. RT-qPCR analysis indicated that the temporal expression patterns of oil biosynthesis genes were largely similar to the RNA-seq results. The expression patterns of fatty acid metabolism- and seed development-related proteins determined by MRM were also highly consistent with the results obtained in the proteomic analysis. Correlation analysis indicated significant differences in the number and abundance of DEGs and DEPs but a high level of consistency in expression patterns and metabolic pathways. The results of the present study represent the first combined transcriptomic and proteomic analysis of tree peony seeds and provide insight into tree peony seed development and oil accumulation.

scholarly journals Integrated Analysis of microRNA and mRNA Transcriptome Reveals the Molecular Mechanism of Solanum lycopersicum Response to Bemisia tabaci and Tomato chlorosis virus

2021 ◽  
Vol 12 ◽  
Author(s):  
Hao Yue ◽  
Li-Ping Huang ◽  
Ding-Yi-Hui Lu ◽  
Zhan-Hong Zhang ◽  
Zhuo Zhang ◽  
...  
Keyword(s):  
Molecular Mechanism ◽  
Bemisia Tabaci ◽  
Tomato Plant ◽  
Carbon Fixation ◽  
Mapk Signaling ◽  
Differentially Expressed ◽  
Integrated Analysis ◽  
Control Group ◽  
Tomato Plants ◽  
Tomato Chlorosis Virus

Tomato chlorosis virus (ToCV), is one of the most devastating cultivated tomato viruses, seriously threatened the growth of crops worldwide. As the vector of ToCV, the whitefly Bemisia tabaci Mediterranean (MED) is mainly responsible for the rapid spread of ToCV. The current understanding of tomato plant responses to this virus and B. tabaci is very limited. To understand the molecular mechanism of the interaction between tomato, ToCV and B. tabaci, we adopted a next-generation sequencing approach to decipher miRNAs and mRNAs that are differentially expressed under the infection of B. tabaci and ToCV in tomato plants. Our data revealed that 6199 mRNAs were significantly regulated, and the differentially expressed genes were most significantly associated with the plant-pathogen interaction, the MAPK signaling pathway, the glyoxylate, and the carbon fixation in photosynthetic organisms and photosynthesis related proteins. Concomitantly, 242 differentially expressed miRNAs were detected, including novel putative miRNAs. Sly-miR159, sly-miR9471b-3p, and sly-miR162 were the most expressed miRNAs in each sample compare to control group. Moreover, we compared the similarities and differences of gene expression in tomato plant caused by infection or co-infection of B. tabaci and ToCV. Taken together, the analysis reported in this article lays a solid foundation for further research on the interaction between tomato, ToCV and B. tabaci, and provide evidence for the identification of potential key genes that influences virus transmission in tomato plants.

scholarly journals Proteomic Analysis Reveals Key Proteins in Extracellular Vesicles Cargo Associated with Idiopathic Pulmonary Fibrosis In Vitro

Biomedicines ◽  
2021 ◽  
Vol 9 (8) ◽  
pp. 1058
Author(s):  
Juan Manuel Velázquez-Enríquez ◽  
Jovito Cesar Santos-Álvarez ◽  
Alma Aurora Ramírez-Hernández ◽  
Edilburga Reyes-Jiménez ◽  
Armando López-Martínez ◽  
...  
Keyword(s):  
Idiopathic Pulmonary Fibrosis ◽  
Pulmonary Fibrosis ◽  
Cell Lines ◽  
Extracellular Vesicles ◽  
Proteomic Analysis ◽  
Fibroblast Cell ◽  
Differentially Expressed ◽  
Differentially Expressed Proteins ◽  
Collagen Chain ◽  
Fibroblast Cell Lines

Idiopathic pulmonary fibrosis (IPF) is a chronic, progressive, irreversible, and highly fatal disease. It is characterized by the increased activation of both fibroblast and myofibroblast that results in excessive extracellular matrix (ECM) deposition. Extracellular vesicles (EVs) have been described as key mediators of intercellular communication in various pathologies. However, the role of EVs in the development of IPF remains poorly understood. This study aimed to characterize the differentially expressed proteins contained within EVs cargo derived from the fibroblast cell lines LL97A (IPF-1) and LL29 (IPF-2) isolated from lungs bearing IPF as compared to those derived from the fibroblast cell lines CCD8Lu (NL-1) and CCD19Lu (NL-2) isolated from healthy donors. Isolated EVs were subjected to label-free quantitative proteomic analysis by LC-MS/MS, and as a result, 331 proteins were identified. Differentially expressed proteins were obtained after the pairwise comparison, including all experimental groups. A total of 86 differentially expressed proteins were identified in either one or more comparison groups. Of note, proteins involved in fibrogenic processes, such as tenascin-c (TNC), insulin-like-growth-factor-binding protein 7 (IGFBP7), fibrillin-1 (FBN1), alpha-2 collagen chain (I) (COL1A2), alpha-1 collagen chain (I) (COL1A1), and lysyl oxidase homolog 1 (LOXL1), were identified in EVs cargo isolated from IPF cell lines. Additionally, KEGG pathway enrichment analysis revealed that differentially expressed proteins participate in focal adhesion, PI3K-Akt, and ECM–receptor interaction signaling pathways. In conclusion, our findings reveal that proteins contained within EVs cargo might play key roles during IPF pathogenesis.

scholarly journals Integrated Analysis of lncRNA and mRNA Transcriptomes Reveals New Regulators of Ubiquitination and the Immune Response in Silica-Induced Pulmonary Fibrosis

2019 ◽  
Vol 2019 ◽  
pp. 1-11
Author(s):  
Yao Zhou ◽  
Li He ◽  
Xiao-Dan Liu ◽  
Hua Guan ◽  
Ying Li ◽  
...  
Keyword(s):  
Immune Response ◽  
Pulmonary Fibrosis ◽  
Molecular Mechanisms ◽  
Kegg Pathway ◽  
Differentially Expressed ◽  
Coexpression Network ◽  
Receptor Interaction ◽  
Integrated Analysis ◽  
Biological Processes ◽  
Biological Functions

Objectives. As an epigenetic player, long noncoding RNAs (LncRNAs) have been reported to participate in multiple biological processes; however, their biological functions in silica-induced pulmonary fibrosis (SIPF) occurrence and development remain incompletely understood.Methods. Five case/control pairs were used to perform integrated transcriptomes analysis of lncRNA and mRNA. Prediction of lncRNA and mRNA functions was aided by the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. Additionally, we constructed a coexpression network of lncRNAs and mRNAs to identify targets of regulation.Results. In total, 1069 differentially expressed mRNAs and 366 lncRNAs were identified with the changes more than 2 times (p<0.05), of which 351 downregulated mRNA and 31 downregulated lncRNA were <0.5 (p<0.05) and those of 718 upregulated mRNAs and 335 upregulated lncRNA were >2 (p<0.05). The levels of 10 lncRNAs were measured via qRT-PCR; the results were consistent with the microarray data. Four genes named of FEM1B, TRIM39, TRIM32, and KLHL15 were enriched significantly with ubiquitination and immune response. Cytokine-cytokine receptor interaction was the most significantly enriched KEGG pathway in both mRNAs and lncRNAs. The coexpression network revealed that a single lncRNA can interact with multiple mRNAs, and vice versa.Conclusions. lncRNA and mRNA expression were aberrant in patients with SIPF compared to controls, indicating that differentially expressed lncRNAs and mRNAs may play critical roles in SIPF development. Our study affords new insights into the molecular mechanisms of SIPF and identifies potential biomarkers and targets for SIPF diagnosis and treatment.

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