Journal articles: 'MRNA profiling'

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Fortina, Paolo, and Saul Surrey. "Digital mRNA profiling." Nature Biotechnology 26, no. 3 (2008): 293–94. http://dx.doi.org/10.1038/nbt0308-293.

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Fisunov, G. Yu, D. V. Evsyutina, A. A. Arzamasov, I. O. Butenko, and V. M. Govorun. "Profiling of Mycoplasma gallisepticum Ribosomes." Acta Naturae 7, no. 4 (2015): 107–12. http://dx.doi.org/10.32607/20758251-2015-7-4-107-112.

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The development of high-throughput technologies is increasingly resulting in identification of numerous cases of low correlation between mRNA and the protein level in cells. These controversial observations were made on various bacteria, such as E. coli, Desulfovibrio vulgaris, and Lactococcus lactis. Thus, it is important to develop technologies, including high-throughput techniques, aimed at studying gene expression regulation at the level of translation. In the current study, we performed proteomic profiling of M. gallisepticum ribosomes and identified high abundant noncanonical proteins. We found that binding of mRNAs to ribosomes is mainly determined by two parameters: (1) abundance of mRNA itself and (2) complimentary interactions between the 3 end of 16S rRNA and the ribosome binding site in the 5-untranslated region of mRNA.

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Flintoft, Louisa. "mRNA profiling of activated neurons." Nature Reviews Genetics 14, no. 1 (2012): 4. http://dx.doi.org/10.1038/nrg3398.

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Vennemann, Marielle, and Antje Koppelkamm. "Postmortem mRNA profiling II: Practical considerations." Forensic Science International 203, no. 1-3 (2010): 76–82. http://dx.doi.org/10.1016/j.forsciint.2010.07.007.

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Haas, C., B. Klesser, A. Kratzer, and W. Bär. "mRNA profiling for body fluid identification." Forensic Science International: Genetics Supplement Series 1, no. 1 (2008): 37–38. http://dx.doi.org/10.1016/j.fsigss.2007.10.064.

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Fabbri, M., M. Venturi, A. Talarico, P. Frisoni, R. M. Gaudio, and M. Neri. "mRNA profiling in ancient blood stains." Forensic Science International: Genetics Supplement Series 6 (December 2017): e500-e503. http://dx.doi.org/10.1016/j.fsigss.2017.09.182.

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Li, Y., X. Zhou, M. A. R. St. John, and D. T. W. Wong. "RNA Profiling of Cell-free Saliva Using Microarray Technology." Journal of Dental Research 83, no. 3 (2004): 199–203. http://dx.doi.org/10.1177/154405910408300303.

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Saliva, like other bodily fluids, has been used to monitor human health and disease. This study tests the hypothesis that informative human mRNA exists in cell-free saliva. If present, salivary mRNA may provide potential biomarkers to identify populations and patients at high risk for oral and systemic diseases. Unstimulated saliva was collected from ten normal subjects. RNA was isolated from the cell-free saliva supernatant and linearly amplified. High-density oligonucleotide microarrays were used to profile salivary mRNA. The results demonstrated that there are thousands of human mRNAs in cell-free saliva. Quantitative PCR (Q-PCR) analysis confirmed the present of mRNA identified by our microarray study. A reference database was generated based on the mRNA profiles in normal saliva. Our finding proposes a novel clinical approach to salivary diagnostics, Salivary Transcriptome Diagnostics (STD), for potential applications in disease diagnostics as well as normal health surveillance.

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Wang, Ena, Lance D. Miller, Galen A. Ohnmacht, Edison T. Liu, and Francesco M. Marincola. "High-fidelity mRNA amplification for gene profiling." Nature Biotechnology 18, no. 4 (2000): 457–59. http://dx.doi.org/10.1038/74546.

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Fabbri, M., M. Venturi, A. Talarico, R. Inglese, R. M. Gaudio, and M. Neri. "mRNA profiling: Application to an old casework." Forensic Science International: Genetics Supplement Series 6 (December 2017): e380-e382. http://dx.doi.org/10.1016/j.fsigss.2017.09.170.

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Munchel, Sarah E., Ryan K. Shultzaberger, Naoki Takizawa, and Karsten Weis. "Dynamic profiling of mRNA turnover reveals gene-specific and system-wide regulation of mRNA decay." Molecular Biology of the Cell 22, no. 15 (2011): 2787–95. http://dx.doi.org/10.1091/mbc.e11-01-0028.

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RNA levels are determined by the rates of both transcription and decay, and a mechanistic understanding of the complex networks regulating gene expression requires methods that allow dynamic measurements of transcription and decay in living cells with minimal perturbation. Here, we describe a metabolic pulse-chase labeling protocol using 4-thiouracil combined with large-scale RNA sequencing to determine decay rates of all mRNAs in Saccharomyces cerevisiae. Profiling in various growth and stress conditions reveals that mRNA turnover is highly regulated both for specific groups of transcripts and at the system-wide level. For example, acute glucose starvation induces global mRNA stabilization but increases the degradation of all 132 detected ribosomal protein mRNAs. This effect is transient and can be mimicked by inhibiting the target-of-rapamycin kinase. Half-lives of mRNAs critical for galactose (GAL) metabolism are also highly sensitive to changes in carbon source. The fast reduction of GAL transcripts in glucose requires their dramatically enhanced turnover, highlighting the importance of mRNA decay in the control of gene expression. The approach described here provides a general platform for the global analysis of mRNA turnover and transcription and can be applied to dissect gene expression programs in a wide range of organisms and conditions.

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Kage, Udaykumar, Jonathan J. Powell, Donald M. Gardiner, and Kemal Kazan. "Ribosome profiling in plants: what is not lost in translation?" Journal of Experimental Botany 71, no. 18 (2020): 5323–32. http://dx.doi.org/10.1093/jxb/eraa227.

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Abstract Translation is a highly dynamic cellular process whereby genetic information residing in an mRNA molecule is converted into a protein that in turn executes specific functions. However, pre-synthesized mRNA levels do not always correlate with corresponding protein levels, suggesting that translational control plays an essential role in gene regulation. A better understanding of how gene expression is regulated during translation will enable the discovery of new genes and mechanisms that control important traits in plants. Therefore, in recent years, several methods have been developed to analyse the translatome; that is, all mRNAs being actively translated at a given time, tissue, and/or developmental stage. Ribosome profiling or ribo-seq is one such technology revolutionizing our ability to analyse the translatome and in turn understand translational control of gene expression. Ribo-seq involves isolating mRNA–ribosome complexes, treating them with a RNase, and then identifying ribosome-protected mRNA regions by deep sequencing. Here, we briefly review recent ribosome profiling studies that revealed new insights into plant biology. Manipulation of novel genes identified using ribosome profiling could prove useful for increasing yield through improved biotic and abiotic stress tolerance.

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Leclerc, N., CA Luppen, VV Ho, et al. "Gene expression profiling of glucocorticoid-inhibited osteoblasts." Journal of Molecular Endocrinology 33, no. 1 (2004): 175–93. http://dx.doi.org/10.1677/jme.0.0330175.

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Glucocorticoid (GC) treatment for the management of autoimmune and inflammatory diseases is associated with decreased bone formation and increased risk for fracture. In MC3T3-E1 cell cultures, 0.1-1 microM dexamethasone (DEX) arrests development of the osteoblast phenotype when administration commences at a commitment stage around the time of confluency. To gain new insights into GC-induced osteoporosis, we performed microarray-based gene expression analysis of GC-arrested MC3T3-E1 cultures, 2.5 days after the administration of DEX. Of the >12 000 transcripts interrogated, 74 were up-regulated and 17 were down-regulated by at least 2.5-fold (P < or = 0.05). Some of these genes, such as Mmp13, Serum/GC-regulated kinase and Tieg, have previously been reported as GC-responsive. Others are shown here for the first time to respond to GCs. DEX strongly repressed Krox20/Egr2 at both the mRNA and the protein level. This is especially significant because mice lacking this transcription factor develop osteoporosis. The data also suggest that the bone morphogenetic protein (BMP) pathway, which is involved in regulating bone mass, and other pathways that influence BMP signaling, are abrogated by GCs: (i) DEX increased the mRNA levels of the BMP antagonists Follistatin and Dan; (ii) DEX increased the levels of p21 Rasgap3 and Ptpn16/MKP-1 mRNAs, negative regulators of the MAP kinase pathway; and (iii) DEX decreased Cox mRNA levels. DEX also increased thrombospondin mRNA levels, which negatively regulate bone mass in vivo, as well as the adipocytic marker Fkbp51. These and other observations disclose novel gene targets, whose regulation by GCs in osteoblasts may shed light on and provide new therapeutic approaches to osteoporosis.

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Abu-Halima, Masood, Viktoria Wagner, Lea Simone Becker, et al. "Integrated microRNA and mRNA Expression Profiling Identifies Novel Targets and Networks Associated with Ebstein’s Anomaly." Cells 10, no. 5 (2021): 1066. http://dx.doi.org/10.3390/cells10051066.

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Little is known about abundance level changes of circulating microRNAs (miRNAs) and messenger RNAs (mRNA) in patients with Ebstein’s anomaly (EA). Here, we performed an integrated analysis to identify the differentially abundant miRNAs and mRNA targets and to identify the potential therapeutic targets that might be involved in the mechanisms underlying EA. A large panel of human miRNA and mRNA microarrays were conducted to determine the genome-wide expression profiles in the blood of 16 EA patients and 16 age and gender-matched healthy control volunteers (HVs). Differential abundance level of single miRNA and mRNA was validated by Real-Time quantitative PCR (RT-qPCR). Enrichment analyses of altered miRNA and mRNA abundance levels were identified using bioinformatics tools. Altered miRNA and mRNA abundance levels were observed between EA patients and HVs. Among the deregulated miRNAs and mRNAs, 76 miRNAs (49 lower abundance and 27 higher abundance, fold-change of ≥2) and 29 mRNAs (25 higher abundance and 4 lower abundance, fold-change of ≥1.5) were identified in EA patients compared to HVs. Bioinformatics analysis identified 37 pairs of putative miRNA-mRNA interactions. The majority of the correlations were detected between the lower abundance level of miRNA and higher abundance level of mRNA, except for let-7b-5p, which showed a higher abundance level and their target gene, SCRN3, showed a lower abundance level. Pathway enrichment analysis of the deregulated mRNAs identified 35 significant pathways that are mostly involved in signal transduction and cellular interaction pathways. Our findings provide new insights into a potential molecular biomarker(s) for the EA that may guide the development of novel targeting therapies.

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Yamamoto, T., F. Myokai, F. Nishimura, et al. "Gene Profiling in Human Periodontal Ligament Fibroblasts by Subtractive Hybridization." Journal of Dental Research 82, no. 8 (2003): 641–45. http://dx.doi.org/10.1177/154405910308200814.

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Genes expressed by human periodontal ligament fibroblasts (HPFs) are likely to be associated with specific functions of the ligament. The aim of this study is to profile genes expressed highly by HPFs. A library (6 × 103 pfu) was constructed, followed by subtraction of HPF cDNAs with human gingival fibroblast (HGF) cDNAs. Reverse-dot hybridization revealed that 33 clones expressed higher levels of specific mRNAs in HPFs than in HGFs. These were mRNAs for known genes, including several associated with maturation and differentiation of cells. None had been reported in PFs. One clone, PDL-29, identified as a COX assembly factor, showed much stronger mRNA expression in HPFs than in HGFs in culture. In rat periodontium, however, PDL-29 mRNA expression was similar in PFs and GFs. These results suggest that HPFs express many previously unreported genes associated with maturation and differentiation, but expression can differ in vitro and in vivo.

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Zhu, J. "Single Molecule Profiling of Alternative Pre-mRNA Splicing." Science 301, no. 5634 (2003): 836–38. http://dx.doi.org/10.1126/science.1085792.

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Schueler, Markus, Mathias Munschauer, Lea Haarup Gregersen, et al. "Differential protein occupancy profiling of the mRNA transcriptome." Genome Biology 15, no. 1 (2014): R15. http://dx.doi.org/10.1186/gb-2014-15-1-r15.

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Thiadens, Klaske A. M. H., and Marieke von Lindern. "Selective mRNA translation in erythropoiesis." Biochemical Society Transactions 43, no. 3 (2015): 343–47. http://dx.doi.org/10.1042/bst20150009.

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The daily production of up to 1011 erythrocytes is tightly controlled to maintain the number of erythrocytes in peripheral blood between narrow boundaries. Availability of growth factors and nutrients, particularly iron, control the proliferation and survival of precursor cells partly through control of mRNA translation. General translation initiation mechanisms can selectively control translation of transcripts that carry specific structures in the UTRs. This selective mRNA translation is an important layer of gene expression regulation in erythropoiesis. Ribosome profiling is a recently developed high throughput sequencing technique for global mapping of translation initiation sites across the transcriptome. Here we describe what is known about control of mRNA translation in erythropoiesis and how ribosome profiling will help to further our knowledge. Ribosome footprinting will give insight in transcript-specific translation at codon resolution, which is of great value to understand many cellular processes during erythropoiesis. It will be of particular interest to understand responses to iron availability and reactive oxygen species (ROS), which affects translation initiation of transcripts harbouring upstream ORFs (uORF) and potential alternative downstream ORFs (aORF).

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Gong, Yan, Yuebo Zhang, Biao Li, et al. "Insight into Liver lncRNA and mRNA Profiling at Four Developmental Stages in Ningxiang Pig." Biology 10, no. 4 (2021): 310. http://dx.doi.org/10.3390/biology10040310.

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Ningxiang pigs, a fat-type pig, are native to Ningxiang County in Hunan Province, with thousands of years of breeding history. This study aims to explore the expression profiles and functional networks on messenger RNAs (mRNAs) and long non-coding RNAs (lncRNAs) in the liver. Liver tissue of Ningxiang piglets was collected at 30, 90, 150, and 210 days after birth (four development stages), and the mRNA and lncRNA expression was profiled. Compared to mRNA and lncRNA expression profiles, most differentially expressed mRNAs (DEmRNAs) were upregulated at 30 days; however, most DElncRNAs were downregulated at 210 days. Via Short Time-series Expression Miner (STEM) analysis and weighted gene co-expression network analysis (WGCNA), a complex interaction between mRNAs and lncRNAs was identified, indicating that lncRNAs may be a critical regulatory element for mRNAs. One module of genes in particular (module profile 4) was related to fibril organization, vasculogenesis, GTPase activator activity, and regulation of kinase activity. The mRNAs and lncRNAs in module profile 4 had a similar pattern of expression, indicating that they have functional and regulatory relationships. Only CAV1, PACSIN2, and CDC42 in the particular mRNA profile 4 were the target genes of lncRNAs in that profile, which shows the possible regulatory relationship between lncRNAs and mRNAs. The expression of these genes and lncRNAs in profile 4 was the highest at 30 days, and it is believed that these RNAs may play a critical role during the suckling period in order to meet the dietary requirements of piglets. In the lncRNA–mRNA co-expression network, the identified gene hubs and associated lncRNAs were shown to be involved in saccharide, lipid, and glucose metabolism, which may play an important role in the development and health of the liver. This result will lead to further investigation of liver lncRNA functions at various stages of development in Ningxiang pigs.

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Lin, Selena Y., Shu-Ching Chang, Stella Lam, et al. "Prospective Molecular Profiling of Circulating Tumor Cells from Patients with Melanoma Receiving Combinatorial Immunotherapy." Clinical Chemistry 66, no. 1 (2019): 169–77. http://dx.doi.org/10.1373/clinchem.2019.307140.

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Abstract BACKGROUND Blood molecular profiling of circulating tumor cells (CTCs) can enable monitoring of patients with metastatic melanoma during checkpoint inhibitor immunotherapy (CII) and in combination with targeted therapies. We developed a microfluidics-based CTC platform to explore CTC profiling utility in CII-treated patients with melanoma using a melanoma messenger RNA (mRNA)/DNA biomarker panel. METHODS Blood samples (n = 213) were collected prospectively from 75 American Joint Committee on Cancer-staged III/IV melanoma patients during CII treatment and those enriched for CTCs. CTC profiling was performed using 5 known melanoma mRNA biomarkers and BRAF V600E DNA mutation. CTC biomarker status associations with clinical outcomes were assessed. RESULTS CTCs were detected in 88% of blood samples from patients with melanoma. CTC-derived biomarkers and clinical variables analyzed using classification and regression tree analysis revealed that a combination of lactate dehydrogenase, CTC-mRNA biomarkers, and tumor BRAF–mutation status was indicative of clinical outcomes for patients with stage IV melanoma (n = 52). The panel stratified low-risk and high-risk patients, whereby the latter had poor disease-free (P = 0.03) and overall survival (P = 0.02). Incorporation of a DNA biomarker with mRNA profiling increased overall CTC-detection capability by 57% compared to mRNA profiling only. RNA sequencing of isolated CTCs identified significant catenin beta 1 (CTNNB1) overexpression (P &lt;0.01) compared to nondisease donor blood. CTC-CTNNB1 was associated with progressive disease/stable disease compared to complete-responder patient status (P = 0.02). Serial CTC profiling identified subclinical disease in patients who developed progressive disease during treatment/follow-up. CONCLUSIONS CTC-derived mRNA/DNA biomarkers have utility for monitoring CII, targeted, and combinatorial therapies in metastatic melanoma patients.

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Mills, Eric W., Rachel Green, and Nicholas T. Ingolia. "Slowed decay of mRNAs enhances platelet specific translation." Blood 129, no. 17 (2017): e38-e48. http://dx.doi.org/10.1182/blood-2016-08-736108.

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Key Points Ribosome profiling of primary human platelets defines the platelet translatome, derived from a biased subset of MK mRNAs. Restoration of the ribosome rescue/mRNA surveillance factor Pelota, which is normally absent in wild-type platelets, promotes RNA decay.

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Azouz, Francine, Komal Arora, Keeton Krause, Vivek Nerurkar, and Mukesh Kumar. "Integrated MicroRNA and mRNA Profiling in Zika Virus-Infected Neurons." Viruses 11, no. 2 (2019): 162. http://dx.doi.org/10.3390/v11020162.

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Zika virus (ZIKV) infections have caused a wide spectrum of neurological diseases, such as Guillain-Barré syndrome, myelitis, meningoencephalitis, and congenital microcephaly. No effective therapies currently exist for treating patients infected with ZIKV. MicroRNAs (miRNAs) are a group of small RNAs involved in the regulation of a wide variety of cellular and physiological processes. In this study, we analyzed digital miRNA and mRNA profiles in ZIKV-infected primary mouse neurons using the nCounter technology. A total of 599 miRNAs and 770 mRNAs were examined. We demonstrate that ZIKV infection causes global downregulation of miRNAs with only few upregulated miRNAs. ZIKV-modulated miRNAs including miR-155, miR-203, miR-29a, and miR-124-3p are known to play critical role in flavivirus infection, anti-viral immunity and brain injury. ZIKV infection also results in downregulation of miRNA processing enzymes. In contrast, ZIKV infection induces dramatic upregulation of anti-viral, inflammatory and apoptotic genes. Furthermore, our data demonstrate an inverse correlation between ZIKV-modulated miRNAs and target host mRNAs induced by ZIKV. Biofunctional analysis revealed that ZIKV-modulated miRNAs and mRNAs regulate the pathways related to neurological development and neuroinflammatory responses. Functional studies targeting specific miRNA are warranted to develop therapeutics for the management of ZIKV neurological disease.

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Volkova, Oxana A., Yury V. Kondrakhin, Ivan S. Yevshin, Tagir F. Valeev, and Ruslan N. Sharipov. "Assessment of translational importance of mammalian mRNA sequence features based on Ribo-Seq and mRNA-Seq data." Journal of Bioinformatics and Computational Biology 14, no. 02 (2016): 1641006. http://dx.doi.org/10.1142/s0219720016410067.

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Ribosome profiling technology (Ribo-Seq) allowed to highlight more details of mRNA translation in cell and get additional information on importance of mRNA sequence features for this process. Application of translation inhibitors like harringtonine and cycloheximide along with mRNA-Seq technique helped to assess such important characteristic as translation efficiency. We assessed the translational importance of features of mRNA sequences with the help of statistical analysis of Ribo-Seq and mRNA-Seq data. Translationally important features known from literature as well as proposed by the authors were used in analysis. Such comparisons as protein coding versus non-coding RNAs and high- versus low-translated mRNAs were performed. We revealed a set of features that allowed to discriminate the compared categories of RNA. Significant relationships between mRNA features and efficiency of translation were also established.

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Li, Ting, Changjie Lin, Yifan Zhu, et al. "Transcriptome Profiling of m6A mRNA Modification in Bovine Mammary Epithelial Cells Treated with Escherichia coli." International Journal of Molecular Sciences 22, no. 12 (2021): 6254. http://dx.doi.org/10.3390/ijms22126254.

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Mastitis is a common disease in dairy cows that is mostly caused by E. coli, and it brings massive losses to the dairy industry. N6-Methyladenosine (m6A), a methylation at the N6 position of RNA adenine, is a type of modification strongly associated with many diseases. However, the role of m6A in mastitis has not been investigated. In this study, we used MeRIP-seq to sequence the RNA of bovine mammary epithelial cells treated with inactivated E. coli for 24 h. In this in vitro infection model, there were 16,691 m6A peaks within 7066 mRNA transcripts in the Con group and 10,029 peaks within 4891 transcripts in the E. coli group. Compared with the Con group, 474 mRNAs were hypermethylated and 2101 mRNAs were hypomethylated in the E. coli group. Biological function analyses revealed differential m6A-modified genes mainly enriched in the MAPK, NF-κB, and TGF-β signaling pathways. In order to explore the relationship between m6A and mRNA expression, combined MeRIP-seq and mRNA-seq analyses revealed 212 genes with concomitant changes in the mRNA expression and m6A modification. This study is the first to present a map of RNA m6A modification in mastitis treated with E. coli, providing a basis for future research.

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Chen, Yuanyuan, Bin Cai, Xiaofeng Lian, Jianguang Xu, and Tao Zhang. "Transcriptional Profiling Uncovers Biologically Significant RNAs and Regulatory Networks in Nucleus Pulposus from Intervertebral Disc Degeneration Patients." BioMed Research International 2021 (February 20, 2021): 1–33. http://dx.doi.org/10.1155/2021/6696335.

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Objective. This study aimed to uncover biologically significant RNAs in nucleus pulposus tissues of human intervertebral disc degeneration (IVDD) by integrated transcriptional profiling. Methods. From the Gene Expression Omnibus (GEO) database, three IVDD-related microarray profiling datasets were retrieved and assessed by intragroup data repeatability test. Then, differentially expressed circRNAs, lncRNAs, mRNAs, and miRNAs were screened in nucleus pulposus tissues between IVDD and control samples via the limma package. Coexpression networks were separately conducted via weighted gene correlation network analysis (WGCNA). Based on the feature RNAs in the IVDD-related modules, IVDD-related circRNA-miRNA-mRNA and lncRNA-miRNA-mRNA networks were conducted. The differentially expressed mRNAs in the two networks were analyzed by protein-protein interaction (PPI) and functional enrichment analyses. Results. By the intragroup data repeatability test, outlier samples were removed. Abnormally expressed RNAs were separately identified in nucleus pulposus between IVDD and controls. Via WGCNA, IVDD-related coexpression modules were constructed and the feature circRNAs, lncRNAs, mRNAs, and miRNAs were identified. Then, the circRNA- and lncRNA-miRNA-mRNA networks were built for IVDD. These mRNAs in the network exhibited complex interactions. Moreover, they were involved in distinct IVDD-related biological processes and pathways such as transcription, cell proliferation, TNF, TGF-β, and HIF signaling pathways. Conclusion. This study revealed biologically significant noncoding RNAs and their complex regulatory networks for IVDD.

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Jiang, Li-hua, Nian-yun Yang, Xiao-lin Yuan та ін. "Microarray Analysis of mRNA and MicroRNA Expression Profile Reveals the Role ofβ-Sitosterol-D-glucoside in the Proliferation of Neural Stem Cell". Evidence-Based Complementary and Alternative Medicine 2013 (2013): 1–12. http://dx.doi.org/10.1155/2013/360302.

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Neural stem cells (NSCs) are self-regenerating cells, but their regenerative capacity is limited. The present study was conducted to investigate the effect ofβ-sitosterol-D-glucoside (BSSG) on the proliferation of hippocampal NSCs and to determine the corresponding molecular mechanism. Results of CCK-8 assay showed that BSSG significantly increased NSC proliferation and the effectiveness of BSSG was similar to that of basic fibroblast growth factor and epidermal growth factor. mRNA expression profiling showed that 960 genes were differentially expressed after NSCs were treated with BSSG. Among the 960 genes, IGF1 is considered as a key regulatory gene that functionally promotes NSC proliferation. MicroRNA (miRNA) expression profiling indicated that 30 and 84 miRNAs were upregulated and downregulated, respectively. miRNA-mRNA relevance analysis revealed that numerous mRNAs including IGF1 mRNA were negatively regulated by miRNAs with decreased expression, thereby increasing the corresponding mRNA expression. The increased expression of IGF1 protein was validated by ELISA. Picropodophyllin (PPP, an inhibitor of IGF-1R) inhibition test confirmed that the proliferation-enhancing effect depended on IGF1. This study provided information about BSSG as an efficient and inexpensive growth factor alternative, of which the effect is closely involved in IGF1.

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Sayeed, Aejaz, Brielle E. Dalvano, David E. Kaplan, et al. "Profiling the circulating mRNA transcriptome in human liver disease." Oncotarget 11, no. 23 (2020): 2216–32. http://dx.doi.org/10.18632/oncotarget.27617.

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Ren, Chang-Wei, Jia-Ji Liu, Jin-Hua Li, Jing-Wei Li, Jiang Dai, and Yong-Qiang Lai. "RNA-seq profiling of mRNA associated with hypertrophic cardiomyopathy." Molecular Medicine Reports 14, no. 6 (2016): 5573–86. http://dx.doi.org/10.3892/mmr.2016.5931.

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Cloonan, Nicole, Alistair R. R. Forrest, Gabriel Kolle, et al. "Stem cell transcriptome profiling via massive-scale mRNA sequencing." Nature Methods 5, no. 7 (2008): 613–19. http://dx.doi.org/10.1038/nmeth.1223.

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Li, B., C. Hartono, R. Ding, et al. "Renal allograft surveillance by mRNA profiling of urinary cells." Transplantation Proceedings 33, no. 7-8 (2001): 3280–82. http://dx.doi.org/10.1016/s0041-1345(01)02393-4.

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Grimplet, Jerome, Laurent G. Deluc, Richard L. Tillett, et al. "Tissue-specific mRNA expression profiling in grape berry tissues." BMC Genomics 8, no. 1 (2007): 187. http://dx.doi.org/10.1186/1471-2164-8-187.

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Reid, David W., Shirish Shenolikar, and Christopher V. Nicchitta. "Simple and inexpensive ribosome profiling analysis of mRNA translation." Methods 91 (December 2015): 69–74. http://dx.doi.org/10.1016/j.ymeth.2015.07.003.

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Los, Gerrit, Fei Yang, Goli Samimi, et al. "Using mRNA expression profiling to determine anticancer drug efficacy." Cytometry 47, no. 1 (2001): 66–71. http://dx.doi.org/10.1002/cyto.10037.

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Chen, Edward Y., Huilei Xu, Simon Gordonov, Maribel P. Lim, Matthew H. Perkins, and Avi Ma'ayan. "Expression2Kinases: mRNA profiling linked to multiple upstream regulatory layers." Bioinformatics 28, no. 1 (2011): 105–11. http://dx.doi.org/10.1093/bioinformatics/btr625.

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Nair, T. Murlidharan. "On selecting mRNA isoform features for profiling prostate cancer." Computational Biology and Chemistry 33, no. 6 (2009): 421–28. http://dx.doi.org/10.1016/j.compbiolchem.2009.09.006.

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Juusola, Jane, and Jack Ballantyne. "Multiplex mRNA profiling for the identification of body fluids." Forensic Science International 152, no. 1 (2005): 1–12. http://dx.doi.org/10.1016/j.forsciint.2005.02.020.

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Vennemann, Marielle, and Antje Koppelkamm. "mRNA profiling in forensic genetics I: Possibilities and limitations." Forensic Science International 203, no. 1-3 (2010): 71–75. http://dx.doi.org/10.1016/j.forsciint.2010.07.006.

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Kohlmeier, Fanni, and Peter M. Schneider. "Successful mRNA profiling of 23 years old blood stains." Forensic Science International: Genetics 6, no. 2 (2012): 274–76. http://dx.doi.org/10.1016/j.fsigen.2011.04.007.

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Jakubowska, Joanna, Agnieszka Maciejewska, Ryszard Pawłowski, and Krzysztof Piotr Bielawski. "mRNA profiling for vaginal fluid and menstrual blood identification." Forensic Science International: Genetics 7, no. 2 (2013): 272–78. http://dx.doi.org/10.1016/j.fsigen.2012.11.005.

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Narayanan, Gunaseelan, Anuradha Poonepalli, Jinmiao Chen, et al. "Single-Cell mRNA Profiling Identifies Progenitor Subclasses in Neurospheres." Stem Cells and Development 21, no. 18 (2012): 3351–62. http://dx.doi.org/10.1089/scd.2012.0232.

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Willis, Dianna E., Erna A. van Niekerk, Yukio Sasaki, et al. "Extracellular stimuli specifically regulate localized levels of individual neuronal mRNAs." Journal of Cell Biology 178, no. 6 (2007): 965–80. http://dx.doi.org/10.1083/jcb.200703209.

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Subcellular regulation of protein synthesis requires the correct localization of messenger RNAs (mRNAs) within the cell. In this study, we investigate whether the axonal localization of neuronal mRNAs is regulated by extracellular stimuli. By profiling axonal levels of 50 mRNAs detected in regenerating adult sensory axons, we show that neurotrophins can increase and decrease levels of axonal mRNAs. Neurotrophins (nerve growth factor, brain-derived neurotrophic factor, and neurotrophin-3) regulate axonal mRNA levels and use distinct downstream signals to localize individual mRNAs. However, myelin-associated glycoprotein and semaphorin 3A regulate axonal levels of different mRNAs and elicit the opposite effect on axonal mRNA levels from those observed with neurotrophins. The axonal mRNAs accumulate at or are depleted from points of ligand stimulation along the axons. The translation product of a chimeric green fluorescent protein–β-actin mRNA showed similar accumulation or depletion adjacent to stimuli that increase or decrease axonal levels of endogenous β-actin mRNA. Thus, extracellular ligands can regulate protein generation within subcellular regions by specifically altering the localized levels of particular mRNAs.

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Zhang, Xiang, Ya Hu, Mengyi Wang, et al. "Profiling analysis of long non-coding RNA and mRNA in parathyroid carcinoma." Endocrine-Related Cancer 26, no. 2 (2019): 163–76. http://dx.doi.org/10.1530/erc-18-0480.

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Parathyroid carcinoma (PCa) is a rare endocrine neoplasia that typically has unfavourable outcomes. The contribution of long non-coding RNAs (lncRNAs) to the development of malignant and benign parathyroid tumours remains largely unknown. In this study, we explored transcriptomic profiling of lncRNA and mRNA expression in 6 PCa, 6 parathyroid adenoma (PAd) and 4 normal parathyroid (PaN) tissues. In total, 2641 lncRNA transcripts and 2165 mRNA transcripts were differentially expressed between PCa and PAd. Enrichment analysis demonstrated that dysregulated transcripts were involved mainly in the extracellular matrix (ECM)–receptor interaction and energy metabolism pathways. Bioinformatics analysis suggested that ATF3, ID1, FOXM1, EZH2 and MITF may be crucial to parathyroid carcinogenesis. Series test of cluster analysis segregated differentially expressed lncRNAs and mRNAs into several expression profile models, among which the ‘plateau’ profile representing components specific to parathyroid carcinogenesis was selected to build a co-expression network. Seven lncRNAs and three mRNAs were selected for quantitative RT-PCR validation in 16 PCa, 41 PAd and 4 PaN samples. Receiver-operator characteristic curves analysis showed that lncRNA PVT1 and GLIS2-AS1 yielded the area under the curve values of 0.871 and 0.860, respectively. Higher hybridization signals were observed in PCa for PVT1 and PAd for GLIS2-AS1. In conclusion, the current evidence indicates that PAd and PCa partially share common signalling molecules and pathways, but have independent transcriptional events. Differentially expressed lncRNAs and mRNAs have intricate interactions and are involved in parathyroid tumourigenesis. The lncRNA PVT1 and GLIS2-AS1 may be new potential markers for the diagnosis of PCa.

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CARMEL, JASON B., ANTHONY GALANTE, PATRICIA SOTEROPOULOS, et al. "Gene expression profiling of acute spinal cord injury reveals spreading inflammatory signals and neuron loss." Physiological Genomics 7, no. 2 (2001): 201–13. http://dx.doi.org/10.1152/physiolgenomics.00074.2001.

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We have completed the first large-scale gene expression study of acute spinal cord injury (SCI) in rat. Oligonucleotide microarrays containing 1,200 gene-specific probes were used to quantify mRNA levels, relative to uninjured controls, in spinal cords injured using a standard contusion model. Our results revealed a marked loss of neuron-specific mRNAs at the injury site. The surviving cells showed a characteristic inflammatory response that started at the injury site and spread to the distal cord. Changes in several mRNA levels were associated with putative regenerative responses in the spinal cord. Notably, phosphodiesterase 4, nestin, glia-derived neurite promoting factor, and GAP-43 mRNAs increased significantly. Other mRNAs clustered temporally and spatially with these regeneration-associated genes. Thus we have described global patterns of gene expression following acute SCI, and we have identified targets for future study and possible therapeutic intervention.

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Zhu, L. K., H. Ming, S. C. Liu, et al. "47 High-resolution ribosome profiling reveals translational selectivity in the mammalian blastocyst." Reproduction, Fertility and Development 33, no. 2 (2021): 130. http://dx.doi.org/10.1071/rdv33n2ab47.

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Transcriptomic analyses of early mammalian embryos from multiple species have been comprehensively conducted in the last decade. However, mRNAs detected from overall transcriptomic profile of an embryo or a single cell do not necessarily represent their functional status, as there is a gap between the overall transcriptome and mRNAs that are actively translated. Ribosome profiling has been developed to infer the translational status of a specific mRNA species and thus analyse the genome-wide translatome. However, the broad application of ribosome profiling has been slowed by its complexity and the difficulty of adapting it to low-input samples such as embryos. In this study, we developed an ultra-low-input ribosome profiling protocol optimized for mammalian embryos and systematically analysed both polysome- and non-polysome-bound mRNA profiles of invitro-produced bovine blastocysts. Ten equal fractions were collected by means of sucrose density gradient and ultracentrifugation of lysates from 100 pooled blastocysts (n=2 pools), and subjected to RNA isolation and RNA sequencing. Our bioinformatics analyses of the mRNA profiles from each fraction along with the whole-transcriptome data revealed that compared with the overall transcriptome, there is a strong selection of mRNAs in the ribosome- and polysome-associated fractions, including transcriptional factors (e.g. POU5F1, ESRRB, AQP3, and APOA1) and genes involved in ribosome biogenesis, oxidative phosphorylation, and metabolic pathways, many of which are essential for the function of embryo implantation. We also identified novel epigenetic regulators selectively translated, including regulatory enzymes on histone modifications and RNA modifications (e.g. JMJD7, ALKBH4, ALKBH7, and METTL26). In addition, we confirmed the translation of the highly expressed, yet developmentally essential pathways in the blastocysts (e.g. Wnt and Notch signalling pathways). The selectively translated mRNAs were further validated by immunofluorescent staining at the protein level and cross-validated in both bovine and mouse blastocysts. Some of these genes show only modest expression in the overall transcriptome data. Their selective translation at the blastocyst stage is only being revealed by the ribosome fractions analyses, and their functions warrant future detailed investigations. In conclusion, this study reveals bona fide active translating mRNAs in the mammalian blastocyst. The low-input ribosome profiling protocol and the data presented here set an example and open future avenues for detailed ribosome fraction–based translatome analyses to reveal novel cellular/embryonic functional regulators beyond transcriptomic data.

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Zhu, L. K., H. Ming, S. C. Liu, et al. "47 High-resolution ribosome profiling reveals translational selectivity in the mammalian blastocyst." Reproduction, Fertility and Development 33, no. 2 (2021): 130. http://dx.doi.org/10.1071/rdv33n2ab47.

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Transcriptomic analyses of early mammalian embryos from multiple species have been comprehensively conducted in the last decade. However, mRNAs detected from overall transcriptomic profile of an embryo or a single cell do not necessarily represent their functional status, as there is a gap between the overall transcriptome and mRNAs that are actively translated. Ribosome profiling has been developed to infer the translational status of a specific mRNA species and thus analyse the genome-wide translatome. However, the broad application of ribosome profiling has been slowed by its complexity and the difficulty of adapting it to low-input samples such as embryos. In this study, we developed an ultra-low-input ribosome profiling protocol optimized for mammalian embryos and systematically analysed both polysome- and non-polysome-bound mRNA profiles of invitro-produced bovine blastocysts. Ten equal fractions were collected by means of sucrose density gradient and ultracentrifugation of lysates from 100 pooled blastocysts (n=2 pools), and subjected to RNA isolation and RNA sequencing. Our bioinformatics analyses of the mRNA profiles from each fraction along with the whole-transcriptome data revealed that compared with the overall transcriptome, there is a strong selection of mRNAs in the ribosome- and polysome-associated fractions, including transcriptional factors (e.g. POU5F1, ESRRB, AQP3, and APOA1) and genes involved in ribosome biogenesis, oxidative phosphorylation, and metabolic pathways, many of which are essential for the function of embryo implantation. We also identified novel epigenetic regulators selectively translated, including regulatory enzymes on histone modifications and RNA modifications (e.g. JMJD7, ALKBH4, ALKBH7, and METTL26). In addition, we confirmed the translation of the highly expressed, yet developmentally essential pathways in the blastocysts (e.g. Wnt and Notch signalling pathways). The selectively translated mRNAs were further validated by immunofluorescent staining at the protein level and cross-validated in both bovine and mouse blastocysts. Some of these genes show only modest expression in the overall transcriptome data. Their selective translation at the blastocyst stage is only being revealed by the ribosome fractions analyses, and their functions warrant future detailed investigations. In conclusion, this study reveals bona fide active translating mRNAs in the mammalian blastocyst. The low-input ribosome profiling protocol and the data presented here set an example and open future avenues for detailed ribosome fraction–based translatome analyses to reveal novel cellular/embryonic functional regulators beyond transcriptomic data.

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Zhao, Dengke, William D. Baez, Kurt Fredrick, and Ralf Bundschuh. "RiboProP: a probabilistic ribosome positioning algorithm for ribosome profiling." Bioinformatics 35, no. 9 (2018): 1486–93. http://dx.doi.org/10.1093/bioinformatics/bty854.

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Abstract Motivation Ribosome profiling has been widely used to study translation in a genome-wide fashion. It requires deep sequencing of ribosome protected mRNA fragments followed by mapping of fragments to the reference genome. For applications such as identification of ribosome pausing sites, it is not enough to map a fragment to a given gene, but the exact position of the ribosome represented by the fragment must be identified for each mRNA fragment. The assignment of the correct ribosome position is complicated by the broad length distribution of the ribosome protected fragments caused by the known sequence bias of micrococcal nuclease (MNase), the most widely used nuclease for digesting mRNAs in bacteria. Available mapping algorithms suffer from either MNase bias or low accuracy in characterizing the ribosome pausing kinetics. Results In this paper, we introduce a new computational method for mapping the ribosome protected fragments to ribosome locations. We first develop a mathematical model of the interplay between MNase digestion and ribosome protection of the mRNAs. We then use the model to reconstruct the ribosome occupancy profile on a per gene level. We demonstrate that our method has the capability of mitigating the sequence bias introduced by MNase and accurately locating ribosome pausing sites at codon resolution. We believe that our method can be broadly applied to ribosome profiling studies on bacteria where codon resolution is necessary. Availability and implementation Source code implementing our approach can be downloaded under GPL3 license at http://bioserv.mps.ohio-state.edu/RiboProP. Supplementary information Supplementary data are available at Bioinformatics online.

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Lupinacci, Fernanda Cristina Sulla, Hellen Kuasne, Martin Roffé, et al. "Polysome Profiling of a Human Glioblastoma Reveals Intratumoral Heterogeneity." International Journal of Molecular Sciences 20, no. 9 (2019): 2177. http://dx.doi.org/10.3390/ijms20092177.

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Glioblastoma (GBM) is one of the most aggressive cancers, with median survival of less than 2 years. Despite of considerable advance in molecular classification of GBMs, no improvements in therapy have been described. The scenario is further complicated by tumor heterogeneity and the relationship among genetic, transcriptional and functional findings. Classically, gene expression has been evaluated by steady-state mRNA, however, this does not take translational control into consideration, which contributes considerably to the composition of the proteome. In this study, we evaluated the transcriptomic and translatomic signature of a GBM obtained from a single patient focusing in tumor heterogeneity. In a sampling of eight fragments, we investigated the translation rates, mTORC1 and ERK1/2 pathways and identified both total and polysome associated mRNAs. An increased translation rate was observed in fragments with high-grade histological features. High-grade histology was also associated with the expression of genes related to extracellular matrix (ECM) and angiogenesis, in both transcriptomes and translatomes. However, genes associated with epithelial to mesenchymal transition and stress response, were observed only in translatomes from high-grade fragments. Overall, our results demonstrate that isolation of translated mRNA can be used to identify biomarkers and reveal previously unrecognized determinants of heterogeneity in GBMs.

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Sun, Fangfang, Weiwei Liang, Kejun Tang, Mengying Hong, and Jing Qian. "Profiling the lncRNA-miRNA-mRNA ceRNA network to reveal potential crosstalk between inflammatory bowel disease and colorectal cancer." PeerJ 7 (August 26, 2019): e7451. http://dx.doi.org/10.7717/peerj.7451.

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Background Because of the increasing dysplasia rate in the lifelong course of inflammatory bowel disease (IBD) patients, it is imperative to characterize the crosstalk between IBD and colorectal cancer (CRC). However, there have been no reports revealing the occurrence of the ceRNA network in IBD-related CRC. Methods In this study, we conducted gene expression profile studies of databases and performed an integrated analysis to detect the potential of lncRNA-miRNA-mRNA ceRNA in regulating disease transformation. R packages were used to screen differentially expressed mRNA, lncRNA and miRNA among CRC, IBD and normal tissue. The lncRNA-miRNA-mRNA network was constructed based on predicted miRNA-targeted lncRNAs and miRNA-targeted mRNAs. Functional analyses were then conducted to identify genes involved in the ceRNA network, and key lncRNAs were evaluated based on several clinical outcomes. Results A total of three lncRNAs, 15 miRNAs, and 138 mRNAs were identified as potential mediators in the pathophysiological processes of IBD-related CRC. Gene Ontology annotation enrichment analysis confirmed that the dysplasia process was strongly associated with immune response, response to lipopolysaccharide, and inflammatory response. Survival analysis showed that LINC01106 (HR = 1.7; p < 0.05) were strongly associated with overall survival of colorectal cancer patients. The current study identified a series of IBD-related mRNAs, miRNA, and lncRNAs, and highlighted the important role of ceRNAs in the pathogenesis of IBD-related CRC. Among them, the LINC01106-miRNA-mRNA axis was identified as vital targets for further research.

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Shah, Manasvi S., Scott L. Schwartz, Chen Zhao, et al. "Integrated microRNA and mRNA expression profiling in a rat colon carcinogenesis model: effect of a chemo-protective diet." Physiological Genomics 43, no. 10 (2011): 640–54. http://dx.doi.org/10.1152/physiolgenomics.00213.2010.

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We have recently demonstrated that nutritional bioactives (fish oil and pectin) modulate microRNA molecular switches in the colon. Since integrated analysis of microRNA and mRNA expression at an early stage of colon cancer development is lacking, in this study, four computational approaches were utilized to test the hypothesis that microRNAs and their posttranscriptionally regulated mRNA targets, i.e., both total mRNAs and actively translated mRNA transcripts, are differentially modulated by carcinogen and diet treatment. Sprague-Dawley rats were fed diets containing corn oil ± fish oil with pectin ± cellulose and injected with azoxymethane or saline (control). Colonic mucosa was assayed at an early time of cancer progression, and global gene set enrichment analysis was used to obtain those microRNAs significantly enriched by the change in expression of their putative target genes. In addition, cumulative distribution function plots and functional network analyses were used to evaluate the impact of diet and carcinogen combination on mRNA levels induced via microRNA alterations. Finally, linear discriminant analysis was used to identify the best single-, two-, and three-microRNA combinations for classifying dietary effects and colon tumor development. We demonstrate that polysomal profiling is tightly related to microRNA changes when compared with total mRNA profiling. In addition, diet and carcinogen exposure modulated a number of microRNAs (miR-16, miR-19b, miR-21, miR26b, miR27b, miR-93, and miR-203) linked to canonical oncogenic signaling pathways. Complementary gene expression analyses showed that oncogenic PTK2B, PDE4B, and TCF4 were suppressed by the chemoprotective diet at both the mRNA and protein levels.

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Luo, Honglin, Yaoyao Zhang, Zhaoan Sheng, et al. "Long Noncoding RNA Profiling from Fasciola Gigantica Excretory/Secretory Product-Induced M2 to M1 Macrophage Polarization." Cellular Physiology and Biochemistry 47, no. 2 (2018): 505–22. http://dx.doi.org/10.1159/000489984.

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Background/Aims: Long noncoding RNAs (lncRNAs) are well known regulators of gene expression that play essential roles in macrophage activation and polarization. However, the role of lncRNA in Fasciola gigantica excretory/secretory products (ESP)-induced M2 polarization into M1 macrophages is unclear. Herein, we performed lncRNA profiling of lncRNAs and mRNAs during the ESP-induced macrophage polarization process. Methods: F. gigantica ESP was used to induce peritoneal cavity M2 macrophages in BALB/c mice (5-6 weeks old) in vivo, and these cells were subsequently isolated and stimulated with IFN-γ + LPS to induce M1 cells in vitro. LncRNA and mRNA profiling was performed via microarray at the end of both polarization stages. Results: In total, 2,844 lncRNAs (1,579 upregulated and 1,265 downregulated) and 1,782 mRNAs (789 upregulated and 993 downregulated) were differentially expressed in M2 macrophages compared to M1 macrophages, and six lncRNAs were identified during polarization. We selected 34 differentially expressed lncRNAs and mRNAs to validate the results of microarray analysis using quantitative real-time PCR (qPCR). Pathway and Gene Ontology (GO) analyses demonstrated that these altered transcripts were involved in multiple biological processes, particularly peptidase activity and carbohydrate metabolism. Furthermore, coding and non-coding gene (CNC) and mRNA-related ceRNA network analyses were conducted to predict lncRNA expression trends and the potential target genes of these lncRNAs and mRNAs. Moreover, we determined that four lncRNAs and four mRNAs might participate in F. gigantica ESP-induced M2 polarization into M1 macrophages. Conclusions: This study illustrates the basic profiling of lncRNAs and mRNAs during F. gigantica ESP-induced M2 polarization into M1 macrophages and deepens our understanding of the mechanism underlying this process.

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Bezzina Wettinger, Stephanie, Carine J. M. Doggen, C. Arnold Spek, Frits R. Rosendaal, and Pieter H. Reitsma. "High throughput mRNA profiling highlights associations between myocardial infarction and aberrant expression of inflammatory molecules in blood cells." Blood 105, no. 5 (2005): 2000–2006. http://dx.doi.org/10.1182/blood-2004-08-3283.

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AbstractStudies on the role of inflammation in cardiovascular disease focus on surrogate markers like plasma levels of C-reactive protein or interleukins that are affected by several factors. In this study we employ an approach in which the inflammatory mRNA profile of leucocytes is measured directly in a multigene system. We investigated the mRNA profile for 35 inflammatory markers in blood samples in a case-control study including 524 men with a history of myocardial infarction and 628 control subjects. Compared with controls, patients showed mRNA profiles with increased levels of most inflammatory mRNAs. The 2 most prominent mRNA risk indicators encoded the secreted protein macrophage migration inhibitory factor (crude odds ratio [OR], 3.4 for the highest quartile versus the lowest quartile (95% confidence interval [CI95], 2.3-4.9), and the intracellular regulator proteinase inhibitor 9 (OR, 2.5 for the highest versus the lowest quartile (CI95, 1.8-3.5), both showing an increase in odds ratio with increasing quartiles. Leucocytes in the blood of patients with myocardial infarction are more active in transcription of inflammatory genes, as evidenced by mRNA profiling. These data support the hypothesis that an inflammatory response involving leucocytes plays a role in the pathogenesis of myocardial infarction.

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Journal articles on the topic 'MRNA profiling'

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