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Journal articles on the topic 'MiRNA-screening'

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Published: 1 April 2023

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1

Ying, Huanchun, Jing Lyu, Tianshu Ying, Jun Li, Shanshan Jin, Jingru Shao, Lili Wang, and Hongying Xu. "Risk miRNA screening of ovarian cancer based on miRNA functional synergistic network." Journal of Ovarian Research 7, no. 1 (2014): 9. http://dx.doi.org/10.1186/1757-2215-7-9.

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2

Nielsen, Søren Jensby, Hanni Willenbrock, Jacob Fog, Jan Stenvang, Thorarinn Blondal, Torben Orntoft, Nils Brünner, Claus Lindbjerg Andersen, Hans J. Nielsen, and Adam Baker. "Validation of a plasma-based miRNA PCR test for early detection of colorectal cancer." Journal of Clinical Oncology 30, no. 4_suppl (February 1, 2012): 424. http://dx.doi.org/10.1200/jco.2012.30.4_suppl.424.

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424 Background: Colorectal cancer (CRC) is a major cause of mortality in the western world. Early detection of CRC improves survival and screening for CRC has been clinically proven to lower CRC-related mortality in the screening population. However, although population screening programs have been implemented in a number of countries, screening rates among the 50-75 year olds are unsatisfactory. There is therefore a clear unmet need for a quick, sensitive, specific, and minimally invasive screening assay to select at risk individuals for definitive diagnosis by colonoscopy. Methods: In order to detect microRNA (miRNA) biomarkers for CRC in blood plasma, we developed an LNA-enhanced miRNA RT-qPCR platform with high sensitivity and linearity for optimal quantitation of miRNAs from limited plasma samples. A clinical reference- lab compatible workflow that allows for the entire procedure from sample preparation through data acquisition and QC to test result to be completed within one working day was established. A reference melting curve database has been implemented to ensure the integrity of each data point, and appropriate controls monitor plate-to-plate and day-to-day variation. State-of-the-art normalization protocols have been evaluated to ensure optimal normalization of datasets prior to data analysis. Results: We previously determined a miRNA signature in a multi hospital discovery cohort that is differentially expressed between healthy individuals and stage II CRC patients. Here we report on the validation of this miRNA signature in an independent set of plasma samples from CRC patients and healthy volunteers. We have counter-screened the miRNA signature in a set of patients with other prevalent diseases, including hypertension, diabetes, diverticulitis, and others. Conclusions: A plasma miRNA signature for early detection of CRC from patient plasma was developed and validated in an independent clinical sample set. The signature was specific with respect to other diseases prevalent in the screening population. A second large-scale validation project is on-going. We conclude that plasma miRNA biomarkers can constitute an effective minimally invasive approach to population-wide CRC screening.
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3

Eulalio, Ana, and Miguel Mano. "MicroRNA Screening and the Quest for Biologically Relevant Targets." Journal of Biomolecular Screening 20, no. 8 (March 30, 2015): 1003–17. http://dx.doi.org/10.1177/1087057115578837.

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MicroRNAs (miRNAs) are a class of genome-encoded small RNAs that post-transcriptionally regulate gene expression by repressing target transcripts containing partially or fully complementary binding sites. Despite their relatively low number, miRNAs have been shown to directly regulate a large fraction of the transcriptome. In agreement with their pervasive role in the regulation of eukaryotic gene expression, miRNAs have been implicated in virtually all biological processes, including different pathologies. The use of screening technologies to systematically analyze miRNA function in cell-based assays offers a unique opportunity to gain new insights into complex biological and disease-relevant processes. Given the low complexity of the miRNome and the similarities to small interfering RNA (siRNA) screening experimental approaches, phenotypic screening using genome-wide libraries of miRNA mimics or inhibitors is not, per se, technically challenging. The identification of miRNA targets and, more importantly, the characterization of their mechanisms of action through the identification of the key targets underlying observed phenotypes remain the major challenges of this approach. This article provides an overview of cell-based screenings for miRNA function that were performed in different biological contexts. The advantages and limitations of computational and experimental approaches commonly used to identify miRNA targets are also discussed.
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Roa, W., L. J. Xing, J. Amanie, A. Fairchild, Z. Gabos, T. Nijjar, R. Scrimger, and D. Yee. "14 SCREENING LUNG CANCER WITH MIRNA EXPRESSION PROFILES." Radiotherapy and Oncology 92 (September 2009): S5. http://dx.doi.org/10.1016/s0167-8140(12)72401-5.

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Oka, Hiroyuki, Koichi Masuno, Takeki Uehara, Toru Okamoto, Yoshiharu Matsuura, Toru Nakano, and Shinpei Yamaguchi. "Novel miRNA biomarkers for genotoxicity screening in mouse." Toxicology 404-405 (July 2018): 68–75. http://dx.doi.org/10.1016/j.tox.2018.05.009.

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Siebert, Marina, Wendy Westbroek, Yu-Chi Chen, Nima Moaven, Yan Li, Maria Luiza Saraiva-Pereira, Scott Martin, and Ellen Sidransky. "MiRNAs and glucocerebrosidase: lessons from miRNA mimic screening." Molecular Genetics and Metabolism 111, no. 2 (February 2014): S98. http://dx.doi.org/10.1016/j.ymgme.2013.12.239.

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7

Zanutto, Susanna, Chiara Maura Ciniselli, Antonino Belfiore, Mara Lecchi, Enzo Masci, Gabriele Delconte, Massimo Primignani, et al. "Plasma miRNA‐based signatures in CRC screening programs." International Journal of Cancer 146, no. 4 (August 5, 2019): 1164–73. http://dx.doi.org/10.1002/ijc.32573.

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8

Lorenz, Daniel A., Steve Vander Roest, Martha J. Larsen, and Amanda L. Garner. "Development and Implementation of an HTS-Compatible Assay for the Discovery of Selective Small-Molecule Ligands for Pre-microRNAs." SLAS DISCOVERY: Advancing the Science of Drug Discovery 23, no. 1 (July 7, 2017): 47–54. http://dx.doi.org/10.1177/2472555217717944.

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microRNAs (miRNAs) are small gene regulatory RNAs, and their expression has been found to be dysregulated in a number of human diseases. To facilitate the discovery of small molecules capable of selectively modulating the activity of a specific miRNA, we have utilized new high-throughput screening technology targeting Dicer-mediated pre-miRNA maturation. Pilot screening of ~50,000 small molecules and ~33,000 natural product extract libraries against pre-miR-21 processing indicated the potential of our assay for this goal, yielding a campaign Z′ factor of 0.52 and an average plate signal-to-background (S/B) ratio of 13. Using two-dimensional screening against a second pre-miRNA, pre-let-7d, we evaluated the selectivity of confirmed hits. The results presented demonstrate how high-throughput screening can be used to identify selective small molecules for a target RNA.
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9

Mellis, David, and Andrea Caporali. "MicroRNA-based therapeutics in cardiovascular disease: screening and delivery to the target." Biochemical Society Transactions 46, no. 1 (December 1, 2017): 11–21. http://dx.doi.org/10.1042/bst20170037.

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MicroRNAs (miRNAs) are small non-coding RNAs of ∼22 nucleotides, which have increasingly been recognized as potent post-transcriptional regulators of gene expression. MiRNA targeting is defined by the complementarities between positions 2–8 of miRNA 5′-end with generally the 3′-untranslated region of target mRNAs (messenger RNAs). The capacity of miRNAs to simultaneously inhibit many different mRNAs allows for an amplification of biological responses. Hence, miRNAs are extremely attractive targets for therapeutic regulation in several diseases, including cardiovascular. Novel approaches are emerging to identify the miRNA functions in cardiovascular biology processes and to improve miRNA delivery in the heart and vasculature. In the present study, we provide an overview of current studies of miRNA functions in cardiovascular cells by the use of high-content screening. We also discuss the challenge to achieve a safe and targeted delivery of miRNA therapeutics in cardiovascular cells.
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Pfaff, Nils, Jan Fiedler, Angelika Holzmann, Axel Schambach, Thomas Moritz, Tobias Cantz, and Thomas Thum. "miRNA screening reveals a new miRNA family stimulating iPS cell generation via regulation of Meox2." EMBO reports 12, no. 11 (September 23, 2011): 1153–59. http://dx.doi.org/10.1038/embor.2011.176.

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Ren, Mingyao, Zhe Chen, Chuandong Ge, Wei Hu, Jing Xu, Limin Yang, Mingming Luan, and Nianxing Wang. "Visualizing MiRNA Regulation of Apoptosis for Investigating the Feasibility of MiRNA-Targeted Therapy Using a Fluorescent Nanoprobe." Pharmaceutics 14, no. 7 (June 25, 2022): 1349. http://dx.doi.org/10.3390/pharmaceutics14071349.

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MiRNA-targeted therapy is an active research field in precision cancer therapy. Studying the effect of miRNA expression changes on apoptosis is important for evaluating miRNA-targeted therapy and realizing personalized precision therapy for cancer patients. Here, a new fluorescent nanoprobe was designed for the simultaneous imaging of miRNA-21 and apoptotic protein caspase-3 in cancer cells by using gold nanoparticles as the core and polydopamine as the shell. Confocal imaging indicated that the nanoprobe could be successfully applied for in situ monitoring of miRNA regulation of apoptosis. This design strategy is critical for investigating the feasibility of miRNA-targeted therapy, screening new anti-cancer drugs targeting miRNA, and developing personalized treatment plans.
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Kura, Branislav, Barbora Kalocayova, Barbara Szeiffova Bacova, Marko Fulop, Andrea Sagatova, Matus Sykora, Katarina Andelova, Ziad Abuawad, and Jan Slezak. "The effect of selected drugs on the mitigation of myocardial injury caused by gamma radiation." Canadian Journal of Physiology and Pharmacology 99, no. 1 (January 2021): 80–88. http://dx.doi.org/10.1139/cjpp-2020-0323.

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Radiation damage of healthy tissues represents one of the complications of radiotherapy effectiveness. This study is focused on the screening of potentially effective drugs routinely used in medical practice and involved in the mechanism of radiation injury, namely for radiation-induced production of free radicals in the body. Experiments in rats revealed significant reduction of oxidative stress (malondialdehyde) and inflammatory marker (tumor necrosis factor α) in 10 Gy irradiated groups after administration of atorvastatin and a slight decrease after tadalafil administration, which indicates that one of the possible mechanisms for mitigation of radiation-induced cardiac damage could be the modulation of nitric oxide (NO) in endothelium and phosphodiesterase 5. In addition, miRNAs were analyzed as potential markers and therapeutically effective molecules. Expression of miRNA-21 and miRNA-15b showed the most significant changes after irradiation. Atorvastatin and tadalafil normalized changes of miRNA (miRNA-1, miRNA-15b, miRNA-21) expression levels in irradiated hearts. This screening study concludes that administration of specific drugs could mitigate the negative impact of radiation on the heart, but more detailed experiments oriented to other aspects of drug effectiveness and their exact mechanisms are still needed.
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13

Roa, Wilson, Bryan Brunet, Linghong Guo, John Amanie, Alysa Fairchild, Zsolt Gabos, Tirath Nijjar, Rufus Scrimger, Don Yee, and James Xing. "Identification of a new microRNA expression profile as a potential cancer screening tool." Clinical & Investigative Medicine 33, no. 2 (April 1, 2010): 124. http://dx.doi.org/10.25011/cim.v33i2.12351.

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Purpose: Small non-coding microRNAs (miRNAs) are key components of cancer development and are considered as potential biomarkers for cancer diagnosis and treatment monitoring. This study investigated miRNA expression profiles of human cancer cells in order to develop a screening method for lung cancer. Methods: A series of lung cancer related miRNAs (miR-21, miR-145, miR-155, miR-205, miR-210, miR-92, miR-17-5p, miR-143, miR-182, miR-372, let-7a) were selected as candidates for miRNA expression profiles of human lung cancer cell lines (A549, SK-mes-1). MicroRNA u6 was the endogenous control. Cancer cell lines for positive controls; breast MCF-7, prostate Du-145, and glioblastoma U118. The negative control was normal lung fibroblast cell line MRC-5. RT-PCR was performed on StepOnePlus (Applied Biosystem, USA). MiRNA expressions of malignant cells were compared with normal fibroblast cells as well as endogenous control (u6) using the thermal cycle at threshold. Assessment of miRNA expression profiles were then performed using agglomerative hierarchical cluster analysis software (SPSS13, USA). Results: We demonstrated that miR-21, miR-182 and let7-5a were over-expressed, and miR-145 and miR-155 were under-expressed in all cancer cell lines. Combined with the cluster analysis we were able to clearly distinguish cell lines for normal fibroblasts, breast cancer, prostate cancer, glioblastoma, and lung cancer. Conclusion: There is potential utility of screening for lung cancer with miRNA expression profiles. Future work will focus on the sensitivity of such miRNA expression profiles in screening sputum for lung cancer, which can be performed in real time.
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Mayr, Manuel. "Integration of miRNA and proteomic screening for cardiovascular disease." Vascular Pharmacology 56, no. 5-6 (May 2012): 343. http://dx.doi.org/10.1016/j.vph.2011.08.106.

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Ren, Mingyao, Zhe Chen, Chuandong Ge, Wei Hu, Nianxing Wang, Limin Yang, Mingming Luan, and Jing Xu. "Simultaneous Visualization of MiRNA-221 and Caspase-3 in Cancer Cells for Investigating the Feasibility of MiRNA-Targeted Therapy with a Dual-Color Fluorescent Nanosensor." Biosensors 12, no. 7 (June 23, 2022): 444. http://dx.doi.org/10.3390/bios12070444.

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MiRNA-targeted therapy holds great promise for precision cancer therapy. It is important to investigate the effect of changes in miRNA expression on apoptosis in order to evaluate miRNA-targeted therapy and achieve personalized therapy. In this study, we designed a dual-color fluorescent nanosensor consisting of grapheme oxide modified with a molecular beacon and peptide. The nanosensor can simultaneously detect and image miRNA-221 and apoptotic protein caspase-3 in living cells. Intracellular experiments showed that the nanosensor could be successfully applied for in situ monitoring of the effect of miRNA-221 expression changes on apoptosis by dual-color imaging. The current strategy could provide new avenues for investigating the feasibility of miRNA-targeted therapy, screening new anti-cancer drugs targeting miRNA and developing personalized treatment plans.
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Ito, Yoshiaki, Atsushi Inoue, Timothy Seers, Yukari Hato, Arisa Igarashi, Tatsuya Toyama, Konstantin D. Taganov, Mark P. Boldin, and Hiroshi Asahara. "Identification of targets of tumor suppressor microRNA-34a using a reporter library system." Proceedings of the National Academy of Sciences 114, no. 15 (March 29, 2017): 3927–32. http://dx.doi.org/10.1073/pnas.1620019114.

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miRNAs play critical roles in various biological processes by targeting specific mRNAs. Current approaches to identifying miRNA targets are insufficient for elucidation of a miRNA regulatory network. Here, we created a cell-based screening system using a luciferase reporter library composed of 4,891 full-length cDNAs, each of which was integrated into the 3′ UTR of a luciferase gene. Using this reporter library system, we conducted a screening for targets of miR-34a, a tumor-suppressor miRNA. We identified both previously characterized and previously uncharacterized targets. miR-34a overexpression in MDA-MB-231 breast cancer cells repressed the expression of these previously unrecognized targets. Among these targets, GFRA3 is crucial for MDA-MB-231 cell growth, and its expression correlated with the overall survival of patients with breast cancer. Furthermore, GFRA3 was found to be directly regulated by miR-34a via its coding region. These data show that this system is useful for elucidating miRNA functions and networks.
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Zhao, Shan, Desheng Yao, Junying Chen, and Nan Ding. "Circulating miRNA-20a and miRNA-203 for Screening Lymph Node Metastasis in Early Stage Cervical Cancer." Genetic Testing and Molecular Biomarkers 17, no. 8 (August 2013): 631–36. http://dx.doi.org/10.1089/gtmb.2013.0085.

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18

Huang, Guocheng, Benlin Wei, Zebo Chen, Jingyao Wang, Liwen Zhao, Xiqi Peng, Kaihao Liu, Yongqing Lai, and Liangchao Ni. "Identification of a four-microRNA panel in serum as promising biomarker for colorectal carcinoma detection." Biomarkers in Medicine 14, no. 9 (June 2020): 749–60. http://dx.doi.org/10.2217/bmm-2019-0605.

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Background: Screening for colorectal carcinoma (CRC) lacks an efficient, inexpensive and noninvasive approach. The stable presence of serum miRNA is expected to become a new diagnostic marker. Materials & methods: Based on 135 CRC patients and 135 normal controls, this study was conducted in three phases to identify suitable serum miRNA for CRC diagnosis by using quantitative reverse transcription PCR. Bioinformatic assays were used for target genes prediction and functional annotation. Results: Serum expression level of seven miRNAs were significantly different between CRC patients and the normal controls. The final diagnostic panel (area under the curve = 0.893; sensitivity = 81.25%, specificity = 73.33%) consists of miR-203a-3p, miR-145-5p, miR-375-3p and miR-200c-3p. Conclusion: The four-miRNA panel may serve as a novel, noninvasive biomarker for CRC diagnosis and screening.
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Ahmed, Farid E., Farid E. Ahmed, Farid E. Ahmed, Mostafa M. Gouda, Mostafa M. Gouda, Nancy C. Ahmed, Nancy C. Ahmed, and Laila Hussein. "Quantification of Micrornas by Absolute Dpcr for the Diagnostic Screening of Colon Cancer." Journal Of Colon And Rectal Cancer 1, no. 3 (February 8, 2019): 10–37. http://dx.doi.org/10.14302/issn.2471-7061.jcrc-18-2526.

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There is currently no validated micro(mi)RNA diagnostic stool test to screen for colon cancer (CC) on the market because of the complexity of fecal density, vulnerability of stool to daily changes, and the presence of three sources of miRNAs in stool (cell-free from fecal homogenates, exsosomal miRNAs from fecal exosomes, and fecal colonocytes). To address these complexities, we have first carried out a microarray miRNA experiment, using Affymetrix GeneChip miRNA 2.0 Arrays, on immunocaptured and enriched stool colonocytes of 15 subjects (three healthy controls and twelve colon cancer patients [three TNM stage 0-1 (e.g., polyps ³ 1 cm, villous or tubvillous, or with high grade dysplasia), three stage 2, three stage 3, and three stage 4 in triplicates to select a smaller panel of 14 preferentially expressed mature miRNAs associated with colon cancer (12 Up-Regulated, miR-19a, miR-20a, miR-21, miR-31, miR-34a, miR-96, miR-106a, miR-133a, miR-135b, miR-206, miR-224 and miR-302; and 2 Down-Regulated, miR-143 and miR-145). In a subsequent validation study carried out on total small RNA extracted by immunocapture, followed by RT that employed TaqMan® miRNA Reverse Transcription (RT) Kit and a Custom TaqMan RT Primer Pool, absolute quantification of miRNAs, in copies/µl, was measured using a chip-based Absolute QuantStudio 3D Digital PCR analysis. To ensure that we have chosen human and not bacterial small total RNA, we have carried out coextraction protocols with E. coli K1 strain RS18, compare Agilent electrophoretic patterns, and also sequenced random samples throughout this research using mRNA/miRNA sequencing. Our initial quantitative dPCR miRNA data presented herein showe that the quantitative changes in the expression of a few mature miRNA genes in stool, which are associated with right and left colon cancer, would provide for a more convenient, sensitive and specific diagnostic screening markers thatare more useful than those test markers currently available on the market, such as the low-sensitivity (<15%) fecal occult blood test (FOBT); result in better compliance; and is more economical than the invasive and expensive colonoscopy exam in colon cancer, which can be cured if that cancer is detected at the early TNM stages, and that becomes incurable and deadly if not diagnosed before metastasis. Initial test performance characteristics of the miRNA approach showed that the test has a high numerical predictive value in colon cancer. Moreover, underpinning of the miRNA markers as a function of total RNA showed that the test can numerically differentiate between control subjects and colon cancer patients, particularly at the early stages of that curable cancer. We propose to extend our initial research results to a larger prospective and randomized five-years nested case-control study, to validate the expression of the above 14 miRNAs, in stool of 180 individuals in an epidemiologically designed study, using (30 controls and 150 colon cancer patients (thirty precancerous polyps (stage 0-1), forty five stage 2, and seventy-five colon cancer stages 3 or 4). chosen randomly by an epidemiological method from 900 control and CC subjects to allow for an adequate time to collect the required 900 stool samples, as well as allowing for statistically valid analysis, standardized test conditions, and to provide a mean for determining the true sensitivity and specificity of a miRNA-screening approach in noninvasive human stool. Power-analysis has indicated that a total of 180 individuals, which will take us 5 years to enroll in testing, is an appropriate number of subjects to standardize and validate our proposed miRNA screening test. We may find out at the end of the proposed validation study in stool that fewer miRNAs, or even one miRNA, may suffice to serve as an efficient and a quantitative marker for the non-invasive diagnostic screening of colon cancer in human stool. The above approach when combined with bioinformatics analysis, to correlate miRNA seed data with our previously published messenger (m)RNA target data in stool, allows for a thorough mechanistic understanding of how miRNA genes regulate mRNA expression, and would offer a better comprehensive diagnostic screening test for the non-invasive early detection stage (0-1) of colon cancer. In order to show the clinical sensitivity and specificity of the proposed miRNA test, the absolute miRNA PCR values, in copies/µl, will be correlated with FOBT, colonoscopy, and pathology data. Standardization will establish test’s performance characteristics (sample selection, optimal sample running conditions, preservation and storage) to ensure that the assay will perform the same way in any laboratory, by any trained personnel, anywhere in the World. Ultimately, a smaller number of selected validated miRNAs (<10) showing increased and reduced expression could suffice to give quantitative miRNAs colon cancer expression values, useful for the early diagnostic screening of that curable cancer.
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Kalantzakos, Thomas J., Luke E. Sebel, James Trussler, Travis B. Sullivan, Eric J. Burks, Carmen D. Sarita-Reyes, David Canes, Alireza Moinzadeh, and Kimberly M. Rieger-Christ. "MicroRNA Associated with the Invasive Phenotype in Clear Cell Renal Cell Carcinoma: Let-7c-5p Inhibits Proliferation, Migration, and Invasion by Targeting Insulin-like Growth Factor 1 Receptor." Biomedicines 10, no. 10 (September 28, 2022): 2425. http://dx.doi.org/10.3390/biomedicines10102425.

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Differential microRNA (miRNA) expression can portend clear cell renal cell carcinoma (ccRCC) progression. In a previous study, we identified a subset of dysregulated miRNA in small renal masses, pT1 ccRCC (≤5 cm) that are associated with an aggressive phenotype. The present study investigated miRNA expression in clinical stage I (cT1) tumors (≤5 cm), comparing pathologic stage I (pT1) tumors to those upstaged to pathologic stage 3 (pT3) after surgery following identification of renal vein invasion or invasion into adjacent fat tissue within Gerota’s fascia. Twenty cT1 tumors were examined in an miRNA screening, 10 pT1 and 10 pT3 tumors. The ccRCC cell lines 786-O and Caki-1 were used to assess the impact of let-7c-5p and its protein target insulin-like growth factor 1 receptor (IGF1R). Cells were transfected with pre-let-7c-5p and assessed through cell proliferation, migration, and invasion assays. IGF1R expression was evaluated through Simple Western, and interaction between let-7c-5p and IGF1R was confirmed via luciferase reporter assay. Screening identified 20 miRNA, including let-7c-5p, that were dysregulated between pT1 and pT3 upstaged tumors. This miRNA was also downregulated in our previous study of pT1 tumors that progressed to metastatic disease. Transfection of ccRCC cells with pre-let-7c-5p significantly inhibited proliferation, migration, invasion, and IGF1R expression. These findings suggest that miRNA dysregulation is involved in ccRCC progression, specifically through invasion, and that let-7c-5p downregulation contributes to the aggressiveness of small ccRCC tumors, in part, through its regulation of IGF1R.
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Zhao, Zitong, Anna Zhu, Megha Bhardwaj, Petra Schrotz-King, and Hermann Brenner. "Fecal microRNAs, Fecal microRNA Panels, or Combinations of Fecal microRNAs with Fecal Hemoglobin for Early Detection of Colorectal Cancer and Its Precursors: A Systematic Review." Cancers 14, no. 1 (December 23, 2021): 65. http://dx.doi.org/10.3390/cancers14010065.

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Colorectal cancer (CRC) is the third most common cancer and the second leading cause of cancer mortality globally. Fecal miRNAs have been suggested to be promising biomarkers for CRC early detection. We aimed to conduct a systematic literature review on the diagnostic performance of fecal miRNA markers for CRC and its precursors. PubMed and Web of Science were searched to retrieve relevant articles published up to 7 December 2021. Information on study design, characteristics of study population, pre-analytics (sample collection, processing, and storage), fecal miRNA extraction and quantification technologies, and diagnostic performance (including sensitivity, specificity, and area under the curve (AUC)) were summarized. Twenty studies reporting on 31 individual miRNAs and 16 miRNA panels (with 2–9 markers) for CRC diagnosis were identified. Substantial heterogeneity existed regarding stool sample collection, processing, storage, and miRNA extraction and normalization. For two individual miRNAs and one miRNA panel, values ≥ 80% were reported for both sensitivity and specificity; however, none of these results were either internally or externally validated. In a study among fecal immunochemical test-positive cases recruited from a true screening setting, better diagnostic performance was identified and internally validated for a combination panel including two miRNAs, fecal hemoglobin level, and patient age and sex, compared with fecal hemoglobin concentration alone. Fecal miRNAs or miRNA panels, possibly in combination with fecal hemoglobin test, may be promising candidates for noninvasive CRC early detection. However, large prospective and well-designed studies in CRC screening cohorts are required to validate promising miRNAs or miRNA panels.
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Fisher, Leonid, Olga Fisher, Dmitry Chebanov, Sergey Vesnin, Alexey Goltsov, Arran Turnbull, Mike Dixon, et al. "Passive Microwave Radiometry and microRNA Detection for Breast Cancer Diagnostics." Diagnostics 13, no. 1 (December 30, 2022): 118. http://dx.doi.org/10.3390/diagnostics13010118.

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Breast cancer prevention is an important health issue for women worldwide. In this study, we compared the conventional breast cancer screening exams of mammography and ultrasound with the novel approaches of passive microwave radiometry (MWR) and microRNA (miRNA) analysis. While mammography screening dynamics could be completed in 3–6 months, MWR provided a prediction in a matter of weeks or even days. Moreover, MWR has the potential of being complemented with miRNA diagnostics to further improve its predictive quality. These novel techniques can be used alone or in conjunction with more established techniques to improve early breast cancer diagnosis.
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Smolarz, Mateusz, and Piotr Widlak. "Serum Exosomes and Their miRNA Load—A Potential Biomarker of Lung Cancer." Cancers 13, no. 6 (March 18, 2021): 1373. http://dx.doi.org/10.3390/cancers13061373.

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Early detection of lung cancer in screening programs is a rational way to reduce mortality associated with this malignancy. Low-dose computed tomography, a diagnostic tool used in lung cancer screening, generates a relatively large number of false-positive results, and its complementation with molecular biomarkers would greatly improve the effectiveness of such programs. Several biomarkers of lung cancer based on different components of blood, including miRNA signatures, were proposed. However, only a few of them have been positively validated in the context of early cancer detection yet, which imposes a constant need for new biomarker candidates. An emerging source of cancer biomarkers are exosomes and other types of extracellular vesicles circulating in body fluids. Hence, different molecular components of serum/plasma-derived exosomes were tested and showed different levels in lung cancer patients and healthy individuals. Several studies focused on the miRNA component of these vesicles. Proposed signatures of exosome miRNA had promising diagnostic value, though none of them have yet been clinically validated. These signatures involved a few dozen miRNA species overall, including a few species that recurred in different signatures. It is worth noting that all these miRNA species have cancer-related functions and have been associated with lung cancer progression. Moreover, a few of them, including known oncomirs miR-17, miR-19, miR-21, and miR-221, appeared in multiple miRNA signatures of lung cancer based on both the whole serum/plasma and serum/plasma-derived exosomes.
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Ahmed, Farid E. "miRNA as markers for the diagnostic screening of colon cancer." Expert Review of Anticancer Therapy 14, no. 4 (March 3, 2014): 463–85. http://dx.doi.org/10.1586/14737140.2014.869479.

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Jia, Youchao, Aimin Zang, Yanguang Feng, Xiao-Fang Li, Ke Zhang, Hefei Li, Ruiyao Wang, Yaning Wei, and Ran Huo. "miRNA-486 and miRNA-499 in human plasma evaluate the clinical stages of lung cancer and play a role as a tumor suppressor in lung tumorigeneisis not pathogenesis." Bangladesh Journal of Pharmacology 11, no. 1 (January 27, 2016): 264. http://dx.doi.org/10.3329/bjp.v11i1.25318.

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<p class="Abstract">It was aimed to explore the expression level of miRNA-486 and miRNA-499 in the plasma of lung cancer patients and analysis their differences in expre-ssion. The expression level of both miRNA-486 and miRNA-499 in the plasma of non-small cell lung cancer (NSCLC) and small cell lung cancer (SCLC) were lower than that of the control group (p&lt;0.05) and the decrease was more obvious in NSCLC. Compare with the miRNA-499，expression quantity in NSCLC patients plasma. There was statistical significance difference (p&lt;0.05) between III～Ⅳstage and I～II stage. The expression quantity of miRNA in plasma of patients with extensive-stage SCLC was lower than that of patients with limited-stage SCLC (p&lt;0.05). The sensitivity and specificity of plasms miRNA-486 respectively were 88.5% and 83.3%. The expression of miRNA-499 and miRNA-486 in lung cancer patients were up-regulated, and might be closely related to the occurrence and prognosis of lung cancer, and might be used as potential screening and prognosis index for lung cancer.</p><p> </p>
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Liu, Chun-Jie, Xin Fu, Mengxuan Xia, Qiong Zhang, Zhifeng Gu, and An-Yuan Guo. "miRNASNP-v3: a comprehensive database for SNPs and disease-related variations in miRNAs and miRNA targets." Nucleic Acids Research 49, no. D1 (September 29, 2020): D1276—D1281. http://dx.doi.org/10.1093/nar/gkaa783.

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Abstract MicroRNAs (miRNAs) related single-nucleotide variations (SNVs), including single-nucleotide polymorphisms (SNPs) and disease-related variations (DRVs) in miRNAs and miRNA-target binding sites, can affect miRNA functions and/or biogenesis, thus to impact on phenotypes. miRNASNP is a widely used database for miRNA-related SNPs and their effects. Here, we updated it to miRNASNP-v3 (http://bioinfo.life.hust.edu.cn/miRNASNP/) with tremendous number of SNVs and new features, especially the DRVs data. We analyzed the effects of 7 161 741 SNPs and 505 417 DRVs on 1897 pre-miRNAs (2630 mature miRNAs) and 3′UTRs of 18 152 genes. miRNASNP-v3 provides a one-stop resource for miRNA-related SNVs research with the following functions: (i) explore associations between miRNA-related SNPs/DRVs and diseases; (ii) browse the effects of SNPs/DRVs on miRNA-target binding; (iii) functional enrichment analysis of miRNA target gain/loss caused by SNPs/DRVs; (iv) investigate correlations between drug sensitivity and miRNA expression; (v) inquire expression profiles of miRNAs and their targets in cancers; (vi) browse the effects of SNPs/DRVs on pre-miRNA secondary structure changes; and (vii) predict the effects of user-defined variations on miRNA-target binding or pre-miRNA secondary structure. miRNASNP-v3 is a valuable and long-term supported resource in functional variation screening and miRNA function studies.
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Cox, Jennifer E., Lydia V. McClure, Andrei Goga, and Christopher S. Sullivan. "Pan-viral-microRNA screening identifies interferon inhibition as a common function of diverse viruses." Proceedings of the National Academy of Sciences 112, no. 6 (January 26, 2015): 1856–61. http://dx.doi.org/10.1073/pnas.1417891112.

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Diverse viruses encode regulatory RNAs called microRNAs (miRNAs). Despite much progress, the functions of the majority of viral miRNAs remain unknown. Most previous studies have used biochemical methods to uncover targets of viral miRNAs, but it is unclear what fraction of these targets is functionally important. Here, we apply an alternative strategy based on the premise that assorted viral miRNAs will share functionality. Screening a library of >70 human viral miRNAs showed that three unrelated miRNAs from distantly related herpesviruses significantly inhibited IFN signaling. Strikingly, each of these miRNAs directly reduced expression of the cyclic AMP-responsive element-binding protein (CBP), which as part of the p300-CBP complex, mediates IFN signaling. We show that both 5′ and 3′ derivatives from Epstein–Barr virus (EBV) encoded miR-BART-18 precursor miRNA (pre-miRNA) and the orthologous pre-miRNA from Rhesus lymphocryptovirus contribute to reducing IFN signaling. Thus, through both convergent and divergent evolutionary mechanisms, varied herpesviral miRNAs share the ability to decrease IFN signaling. Restoring miR-BART-18 to cells infected with an EBV miRNA mutant conveyed a cellular growth advantage upon IFN treatment, and relevant miRNAs from other herpesviruses were able to complement this activity. Blocking miR-BART-18 function in an EBV+tumor cell line renders cells more susceptible to IFN-mediated effects. These findings provide a mechanism that can at least partially explain the resistance of some EBV-associated tumors to IFN therapy. Our work suggests that similar pan-viral-miRNA functional-based screening strategies are warranted for determining relevant activities of other viral miRNAs.
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Dama, Elisa, Valentina Melocchi, Francesco Mazzarelli, Tommaso Colangelo, Roberto Cuttano, Leonarda Di Candia, Gian Maria Ferretti, Marco Taurchini, Paolo Graziano, and Fabrizio Bianchi. "Non-Coding RNAs as Prognostic Biomarkers: A miRNA Signature Specific for Aggressive Early-Stage Lung Adenocarcinomas." Non-Coding RNA 6, no. 4 (December 15, 2020): 48. http://dx.doi.org/10.3390/ncrna6040048.

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Lung cancer burden can be reduced by adopting primary and secondary prevention strategies such as anti-smoking campaigns and low-dose CT screening for high risk subjects (aged >50 and smokers >30 packs/year). Recent CT screening trials demonstrated a stage-shift towards earlier stage lung cancer and reduction of mortality (~20%). However, a sizable fraction of patients (30–50%) with early stage disease still experience relapse and an adverse prognosis. Thus, the identification of effective prognostic biomarkers in stage I lung cancer is nowadays paramount. Here, we applied a multi-tiered approach relying on coupled RNA-seq and miRNA-seq data analysis of a large cohort of lung cancer patients (TCGA-LUAD, n = 510), which enabled us to identify prognostic miRNA signatures in stage I lung adenocarcinoma. Such signatures showed high accuracy (AUC ranging between 0.79 and 0.85) in scoring aggressive disease. Importantly, using a network-based approach we rewired miRNA-mRNA regulatory networks, identifying a minimal signature of 7 miRNAs, which was validated in a cohort of FFPE lung adenocarcinoma samples (CSS, n = 44) and controls a variety of genes overlapping with cancer relevant pathways. Our results further demonstrate the reliability of miRNA-based biomarkers for lung cancer prognostication and make a step forward to the application of miRNA biomarkers in the clinical routine.
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Huang, Zhou, Yu Han, Leibo Liu, Qinghua Cui, and Yuan Zhou. "LE-MDCAP: A Computational Model to Prioritize Causal miRNA-Disease Associations." International Journal of Molecular Sciences 22, no. 24 (December 19, 2021): 13607. http://dx.doi.org/10.3390/ijms222413607.

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MicroRNAs (miRNAs) are associated with various complex human diseases and some miRNAs can be directly involved in the mechanisms of disease. Identifying disease-causative miRNAs can provide novel insight in disease pathogenesis from a miRNA perspective and facilitate disease treatment. To date, various computational models have been developed to predict general miRNA-disease associations, but few models are available to further prioritize causal miRNA-disease associations from non-causal associations. Therefore, in this study, we constructed a Levenshtein-Distance-Enhanced miRNA-disease Causal Association Predictor (LE-MDCAP), to predict potential causal miRNA-disease associations. Specifically, Levenshtein distance matrixes covering the sequence, expression and functional miRNA similarities were introduced to enhance the previous Gaussian interaction profile kernel-based similarity matrix. LE-MDCAP integrated miRNA similarity matrices, disease semantic similarity matrix and known causal miRNA-disease associations to make predictions. For regular causal vs. non-disease association discrimination task, LF-MDCAP achieved area under the receiver operating characteristic curve (AUROC) of 0.911 and 0.906 in 10-fold cross-validation and independent test, respectively. More importantly, LE-MDCAP prominently outperformed the previous MDCAP model in distinguishing causal versus non-causal miRNA-disease associations (AUROC 0.820 vs. 0.695). Case studies performed on diabetic retinopathy and hsa-mir-361 also validated the accuracy of our model. In summary, LE-MDCAP could be useful for screening causal miRNA-disease associations from general miRNA-disease associations.
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Matsuyama, Hironori, and Hiroshi I. Suzuki. "Systems and Synthetic microRNA Biology: From Biogenesis to Disease Pathogenesis." International Journal of Molecular Sciences 21, no. 1 (December 24, 2019): 132. http://dx.doi.org/10.3390/ijms21010132.

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MicroRNAs (miRNAs) are approximately 22-nucleotide-long, small non-coding RNAs that post-transcriptionally regulate gene expression. The biogenesis of miRNAs involves multiple steps, including the transcription of primary miRNAs (pri-miRNAs), nuclear Drosha-mediated processing, cytoplasmic Dicer-mediated processing, and loading onto Argonaute (Ago) proteins. Further, miRNAs control diverse biological and pathological processes via the silencing of target mRNAs. This review summarizes recent findings regarding the quantitative aspects of miRNA homeostasis, including Drosha-mediated pri-miRNA processing, Ago-mediated asymmetric miRNA strand selection, and modifications of miRNA pathway components, as well as the roles of RNA modifications (epitranscriptomics), epigenetics, transcription factor circuits, and super-enhancers in miRNA regulation. These recent advances have facilitated a system-level understanding of miRNA networks, as well as the improvement of RNAi performance for both gene-specific targeting and genome-wide screening. The comprehensive understanding and modeling of miRNA biogenesis and function have been applied to the design of synthetic gene circuits. In addition, the relationships between miRNA genes and super-enhancers provide the molecular basis for the highly biased cell type-specific expression patterns of miRNAs and the evolution of miRNA–target connections, while highlighting the importance of alterations of super-enhancer-associated miRNAs in a variety of human diseases.
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Zhang, Jin, Renqing Nie, Mengxi Liu, and Xiaoyi Zhang. "A Novel Strategy for Identifying NSCLC MicroRNA Biomarkers and Their Mechanism Analysis Based on a Brand-New CeRNA-Hub-FFL Network." International Journal of Molecular Sciences 23, no. 19 (September 25, 2022): 11303. http://dx.doi.org/10.3390/ijms231911303.

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Finding reliable miRNA markers and revealing their potential mechanisms will play an important role in the diagnosis and treatment of NSCLC. Most existing computational methods for identifying miRNA biomarkers only consider the expression variation of miRNAs or rely heavily on training sets. These deficiencies lead to high false-positive rates. The independent regulatory model is an important complement to traditional models of co-regulation and is more impervious to the dataset. In addition, previous studies of miRNA mechanisms in the development of non-small cell lung cancer (NSCLC) have mostly focused on the post-transcriptional level and did not distinguish between NSCLC subtypes. For the above problems, we improved mainly in two areas: miRNA identification based on both the NOG network and biological functions of miRNA target genes; and the construction of a 4-node directed competitive regulatory network to illustrate the mechanisms. NSCLC was classified as lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC) in this work. One miRNA biomarker of LUAD (miR-708-5p) and four of LUSC (miR-183-5p, miR-140-5p, miR-766-5p, and miR-766-3p) were obtained. They were validated using literature and external datasets. The ceRNA-hub-FFL involving transcription factors (TFs), microRNAs (miRNAs), mRNAs, and long non-coding RNAs (lncRNAs) was constructed. There were multiple interactions among these components within the net at the transcriptional, post-transcriptional, and protein levels. New regulations were revealed by the network. Meanwhile, the network revealed the reasons for the previous conflicting conclusions on the roles of CD44, ACTB, and ITGB1 in NSCLC, and demonstrated the necessity of typing studies on NSCLC. The novel miRNA markers screening method and the 4-node directed competitive ceRNA-hub-FFL network constructed in this work can provide new ideas for screening tumor markers and understanding tumor development mechanisms in depth.
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Zou, Ruiyang, Sau Yeen Loke, Yew Chung Tang, Heng-Phon Too, Lihan Zhou, Ann S. G. Lee, and Mikael Hartman. "Development and validation of a circulating microRNA panel for the early detection of breast cancer." British Journal of Cancer 126, no. 3 (January 10, 2022): 472–81. http://dx.doi.org/10.1038/s41416-021-01593-6.

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Abstract Background Mammography is widely used for breast cancer screening but suffers from a high false-positive rate. Here, we perform the largest comprehensive, multi-center study to date involving diverse ethnic groups, for the identification of circulating miRNAs for breast cancer screening. Methods This study had a discovery phase (n = 289) and two validation phases (n = 374 and n = 379). Quantitative PCR profiling of 324 miRNAs was performed on serum samples from breast cancer (all stages) and healthy subjects to identify miRNA biomarkers. Two-fold cross-validation was used for building and optimising breast cancer-associated miRNA panels. An optimal panel was validated in cohorts with Caucasian and Asian samples. Diagnostic ability was evaluated using area under the curve (AUC) analysis. Results The study identified and validated 30 miRNAs dysregulated in breast cancer. An optimised eight-miRNA panel showed consistent performance in all cohorts and was successfully validated with AUC, accuracy, sensitivity, and specificity of 0.915, 82.3%, 72.2% and 91.5%, respectively. The prediction model detected breast cancer in both Caucasian and Asian populations with AUCs ranging from 0.880 to 0.973, including pre-malignant lesions (stage 0; AUC of 0.831) and early-stage (stages I–II) cancers (AUC of 0.916). Conclusions Our panel can potentially be used for breast cancer screening, in conjunction with mammography.
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Hong, Hui, Shun Yao, Yuanyuan Zhang, Yi Ye, Cheng Li, Liang Hu, Yihua Sun, Hsin-Yi Huang, and Hongbin Ji. "In vivo miRNA knockout screening identifies miR-190b as a novel tumor suppressor." PLOS Genetics 16, no. 11 (November 2, 2020): e1009168. http://dx.doi.org/10.1371/journal.pgen.1009168.

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MicroRNAs (miRNAs) play important roles in the development of various cancers including lung cancer which is one of the devastating diseases worldwide. How miRNAs function in de novo lung tumorigenesis remains largely unknown. We here developed a CRISPR/Cas9-mediated dual guide RNA (dgRNA) system to knockout miRNAs in genetically engineered mouse model (GEMM). Through bioinformatic analyses of human lung cancer miRNA database, we identified 16 downregulated miRNAs associated with malignant progression and performed individual knockout with dgRNA system in KrasG12D/Trp53L/L (KP) mouse model. Using this in vivo knockout screening, we identified miR-30b and miR-146a, which has been previously reported as tumor suppressors and miR-190b, a new tumor-suppressive miRNA in lung cancer development. Over-expression of miR-190b in KP model as well as human lung cancer cell lines significantly suppressed malignant progression. We further found that miR-190b targeted the Hus1 gene and knockout of Hus1 in KP model dramatically suppressed lung tumorigenesis. Collectively, our study developed an in vivo miRNA knockout platform for functionally screening in GEMM and identified miR-190b as a new tumor suppressor in lung cancer.
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Rogucki, Mariusz, Angelika Buczyńska, Adam Jacek Krętowski, and Anna Popławska-Kita. "The Importance of miRNA in the Diagnosis and Prognosis of Papillary Thyroid Cancer." Journal of Clinical Medicine 10, no. 20 (October 15, 2021): 4738. http://dx.doi.org/10.3390/jcm10204738.

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In recent years, the global incidence of thyroid cancer has been increasing. Despite the significant progress in the diagnostic tools applied for papillary thyroid cancer (PTC) diagnosis, commonly used methods require undergoing invasive diagnostic procedures, such as liquid biopsy, which still, in some cases, remains imprecise. In this case, novel screening and diagnostic biomarkers are still being evaluated using highly specialized techniques, which could increase PTC detection. Currently, a number of genes and proteins associated with PTC development are currently under investigation to assess their clinical utility. Accordingly, a literature search was undertaken to collect novel information about the diagnosis of and prognosis for PTC with a particular emphasis on the role of microRNA (miRNA) evaluation. The early identification of novel biomarkers is essential for facilitating appropriate therapeutic decisions. Moreover, the evaluation of plasma- and serum-derived miRNA measurements could be considered as equivalent thyroid cancer screening tools in the future. On the other hand, the PTC pathogenesis could be evaluated further with the use of miRNA evaluation, which may bring novel insights for potential medical target determination.
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Wang, Beibei, and Yuejun Xu. "Research Progress of Mirna in Screening and Diagnosis of Cervical Cancer." International Journal of Clinical and Experimental Medicine Research 4, no. 3 (June 24, 2020): 58–62. http://dx.doi.org/10.26855/ijcemr.2020.07.005.

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Iivonen, Anna-Pauliina, Johanna Känsäkoski, Kirsi Vaaralahti, and Taneli Raivio. "Screening for mutations in selected miRNA genes in hypogonadotropic hypogonadism patients." Endocrine Connections 8, no. 5 (May 2019): 506–9. http://dx.doi.org/10.1530/ec-19-0080.

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In approximately half of congenital hypogonadotropic hypogonadism (cHH) patients, the genetic cause remains unidentified. Since the lack of certain miRNAs in animal models has led to cHH, we sequenced human miRNAs predicted to regulate cHH-related genes (MIR7-3, MIR141, MIR429 and MIR200A-C) in 24 cHH patients with Sanger sequencing. A heterozygous variant in MIR200A (rs202051309; general population frequency of 0.02) was found in one patient. Our results suggest that mutations in the studied miRNAs are unlikely causes of cHH. However, the complex interplay between miRNAs and their target genes in these diseases requires further investigations.
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Hou, Yawei, Yameng Li, Yichuan Wang, Wenpu Li, and Zhenwei Xiao. "Screening and Analysis of Key Genes in miRNA-mRNA Regulatory Network of Membranous Nephropathy." Journal of Healthcare Engineering 2021 (November 16, 2021): 1–13. http://dx.doi.org/10.1155/2021/5331948.

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Background. MicroRNAs (miRNAs) are confirmed to participate in occurrence, development, and prevention of membranous nephropathy (MN), but their mechanism of action is unclear. Objective. With the GEO database and the use of bioinformatics, miRNA-mRNA regulatory network genes relevant to MN were explored and their potential mechanism of action was explained. Methods. The MN-related miRNA chip data set (GSE51674) and mRNA chip data set (GSE108109) were downloaded from the GEO database. Differential analysis was performed using the GEO2R online tool. TargetScan, miRTarBase, and StarBase databases were used to predict potential downstream target genes regulated by differentially expressed miRNAs, and the intersection with differential genes were taken to obtain candidate target genes. According to the regulatory relationship between miRNA and mRNA, the miRNA-mRNA relationship pair was clarified and Cytoscape was used to construct a miRNA-mRNA regulatory network. WebGestalt was used to conduct enrichment analysis of the biological process of differential mRNAs in the regulatory network; FunRich analyzes the differential mRNA pathways in the miRNA-mRNA regulatory network. And the STRING database was used to construct a PPI network for candidate target genes, and Cytoscape visually analyzes the PPI network. Results. Experiments were conducted to screen differentially expressed miRNAs and mRNAs. There were 30 differentially expressed miRNAs, including 22 upregulated and 8 downregulated; and 1267 differentially expressed mRNAs, including 536 upregulated and 731 downregulated. Using TargetScan, miRTarBase, and StarBase databases to predict the downstream targets of differentially expressed miRNAs, 2957 downstream target genes coexisting in the 3 databases were predicted to intersect with differentially expressed mRNAs to obtain 175 candidate target genes. Finally, 36 miRNA-mRNA relationship pairs comprising 10 differentially expressed miRNAs and 27 differentially expressed mRNAs were screened out, and the regulatory network was constructed. Further analysis revealed that the miRNA regulatory network genes may be involved in the development of membranous nephropathy by mTOR, PDGFR-β, LKB1, and VEGF/VEGFR signaling pathways. Conclusion. The miRNA regulatory network genes may participate in the regulation of podocyte autophagy, lipid metabolism, and renal fibrosis through mTOR, PDGFR-β, LKB1, and VEGF/VEGFR signaling pathways, thereby affecting the occurrence and development of membranous nephropathy.
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Navratilova, Zdenka, Stanislav Losse, Pavla Petrova, Katerina Sikorova, Alzbeta Chabronova, and Martin Petrek. "The Effect of Tobacco Smoking and Smoking Cessation on Urinal miRNAs in a Pilot Study." Life 10, no. 9 (September 10, 2020): 191. http://dx.doi.org/10.3390/life10090191.

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The diseases associated with tobacco smoking affect miRNAs and small single-stranded non-coding RNAs. However, there are no data on urinal miRNAs in healthy smokers. We searched for the possible effect of smoking and smoking cessation on miRNA urine expression. For screening, Affymetrix miRNA 4.0 arrays were used in 33 urine samples obtained from six never smokers and from current smokers in three time-points before smoking cessation (n = 10), after short time abstinence (3–8 weeks), and after long-term abstinence (1 year). For validation, a quantitative (q) polymerase chain reaction (PCR) method was used in 93 urine samples obtained from 18 never smokers and 25 current smokers in three time-points before smoking cessation, after short time abstinence (3–8 weeks), and after long-term abstinence (1 year). In screening analysis, 5 miRNAs (hsa-miR-3620-5p, hsa-miR-3613-5p, hsa-miR-3921, hsa-miR-5094, and hsa-miR-337-3p) were dysregulated in current vs. never smokers after multiple testing corrections. Smoking cessation was accompanied by miRNA dysregulation that did not reach a significant level after a multiple testing correction. In validation analysis, three miRNAs correlated with cotinine, but they were affected neither after smoking cessation nor between current and never smokers. Our whole-genome screening of 2.578 miRNAs and validation suggest that tobacco smoking has no or only a small effect on urinal miRNAs.
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Zhang, Hao, Mengping Zhan, Haowu Chang, Shizeng Song, Chunhe Zhang, and Yuanning Liu. "Research Progress of Exogenous Plant MiRNAs in Cross-Kingdom Regulation." Current Bioinformatics 14, no. 3 (March 7, 2019): 241–45. http://dx.doi.org/10.2174/1574893613666181113142414.

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Background:Studies have shown that exogenous miRNAs have cross-kingdom regulatory effects on bacteria and viruses, but whether exogenous plant miRNAs are stable in human body or participate in cross-kingdom regulation is still controversial.Objective:This study aims to propose a new method for the presence and cross-kingdom regulation pathway of exogenous Plant miRNA, which combines biological calculations and biological experiments.Method:Based on the high-throughput sequencing data of human health tissue, the tissue specificity model of exogenous plant miRNA can be constructed and the absorption characteristics will be excavated and analyzed. Then screening the exogenous Plant miRNA based on the crosskingdom regulation model of plant-human miRNA, and isotope labeling can be used to verify the presence and regulation pathway of exogenous plant miRNA.Results:Only based on a comprehensive analysis to human high-throughput miRNA data, establishing cross-kingdom regulation model and designing effective biological experiments, can we reveal the existence, access pathways and regulation of exogenous plant miRNAs.Conclusion:Here, we reviewed the most recent advances in the presence and pathway of exogenous plant miRNAs into human and their cross-kingdom regulation.
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Alexandre, Daniela, Bernardo Teixeira, André Rico, Salete Valente, Ana Craveiro, Pedro V. Baptista, and Carla Cruz. "Molecular Beacon for Detection miRNA-21 as a Biomarker of Lung Cancer." International Journal of Molecular Sciences 23, no. 6 (March 19, 2022): 3330. http://dx.doi.org/10.3390/ijms23063330.

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Lung cancer (LC) is the leading cause of cancer-related death worldwide. Although the diagnosis and treatment of non-small cell lung cancer (NSCLC), which accounts for approximately 80% of LC cases, have greatly improved in the past decade, there is still an urgent need to find more sensitive and specific screening methods. Recently, new molecular biomarkers are emerging as potential non-invasive diagnostic agents to screen NSCLC, including multiple microRNAs (miRNAs) that show an unusual expression profile. Moreover, peripheral blood mononuclear cells’ (PBMCs) miRNA profile could be linked with NSCLC and used for diagnosis. We developed a molecular beacon (MB)-based miRNA detection strategy for NSCLC. Following PBMCs isolation and screening of the expression profile of a panel of miRNA by RT-qPCR, we designed a MB targeting of up-regulated miR-21-5p. This MB 21-5p was characterized by FRET-melting, CD, NMR and native PAGE, allowing the optimization of an in-situ approach involving miR-21-5p detection in PBMCs via MB. Data show the developed MB approach potential for miR-21-5p detection in PBMCs from clinical samples towards NSCLC.
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Nie, Renqing, Wenling Niu, Tang Tang, Jin Zhang, and Xiaoyi Zhang. "Integrating microRNA expression, miRNA-mRNA regulation network and signal pathway: a novel strategy for lung cancer biomarker discovery." PeerJ 9 (October 25, 2021): e12369. http://dx.doi.org/10.7717/peerj.12369.

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Background Since there are inextricably connections among molecules in the biological networks, it would be a more efficient and accurate research strategy to screen microRNA (miRNA) markers combining with miRNA-mRNA regulatory networks. The independent regulation mode is more “fragile” and “influential” than the co-regulation mode. miRNAs can be used as biomarkers if they can independently regulate hub genes with important roles in the PPI network, simultaneously the expression products of the regulated hub genes play important roles in the signaling pathways of related tissue diseases. Methods We collected miRNA expression of non-small cell lung cancer (NSCLC) from The Cancer Genome Atlas (TCGA) database and the Gene Expression Omnibus (GEO) database. Volcano plot and signal-to-noise ratio (SNR) methods were used to obtain significant differentially expressed (SDE) miRNAs from the TCGA database and GEO database, respectively. A human miRNA-mRNA regulatory network was constructed and the number of genes uniquely targeted (NOG) by a certain miRNA was calculated. The area under the curve (AUC) values were used to screen for clinical sensitivity and specificity. The candidate markers were obtained using the criteria of the top five maximum AUC values and NOG ≥ 3. The protein–protein interaction (PPI) network was constructed and independently regulated hub genes were obtained. Gene Ontology (GO) analysis and KEGG pathway analysis were used to identify genes involved in cancer-related pathways. Finally, the miRNA which can independently regulate a hub gene and the hub gene can participate in an important cancer-related pathway was considered as a biomarker. The AUC values and gene expression profile analysis from two external GEO datasets as well as literature validation were used to verify the screening capability and reliability of this marker. Results Fifteen SDE miRNAs in lung cancer were obtained from the intersection of volcano plot and SNR based on the GEO database and the TCGA database. Five miRNAs with the top five maximum AUC values and NOG ≥ 3 were screened out. A total of 61 hub genes were obtained from the PPI network. It was found that the hub gene GTF2F2 was independently regulated by miR-708-5p. Further pathway analysis indicated that GTF2F2 participates in protein expression by binding with polymerase II, and it can regulate transcription and accelerate tumor growth. Hence, miR-708-5p could be used as a biomarker. The good screening capability and reliability of miR-708-5p as a lung cancer marker were confirmed by AUC values and gene expression profiling of external datasets, and experimental literature. The potential mechanism of miR-708-5p was proposed. Conclusions This study proposes a new idea for lung cancer marker screening by integrating microRNA expression, regulation network and signal pathway. miR-708-5p was identified as a biomarker using this novel strategy. This study may provide some help for cancer marker screening.
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Meyer, Sara E., David E. Muench, Andrew M. Rogers, Tess J. Newkold, Emily Orr, Eric O’Brien, John P. Perentesis, et al. "miR-196b target screen reveals mechanisms maintaining leukemia stemness with therapeutic potential." Journal of Experimental Medicine 215, no. 8 (July 11, 2018): 2115–36. http://dx.doi.org/10.1084/jem.20171312.

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We have shown that antagomiR inhibition of miRNA miR-21 and miR-196b activity is sufficient to ablate MLL-AF9 leukemia stem cells (LSC) in vivo. Here, we used an shRNA screening approach to mimic miRNA activity on experimentally verified miR-196b targets to identify functionally important and therapeutically relevant pathways downstream of oncogenic miRNA in MLL-r AML. We found Cdkn1b (p27Kip1) is a direct miR-196b target whose repression enhanced an embryonic stem cell–like signature associated with decreased leukemia latency and increased numbers of leukemia stem cells in vivo. Conversely, elevation of p27Kip1 significantly reduced MLL-r leukemia self-renewal, promoted monocytic differentiation of leukemic blasts, and induced cell death. Antagonism of miR-196b activity or pharmacologic inhibition of the Cks1-Skp2–containing SCF E3-ubiquitin ligase complex increased p27Kip1 and inhibited human AML growth. This work illustrates that understanding oncogenic miRNA target pathways can identify actionable targets in leukemia.
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Giroux, Pierre, Ricky Bhajun, Stéphane Segard, Claire Picquenot, Céline Charavay, Lise Desquilles, Guillaume Pinna, et al. "miRViz: a novel webserver application to visualize and interpret microRNA datasets." Nucleic Acids Research 48, W1 (April 22, 2020): W252—W261. http://dx.doi.org/10.1093/nar/gkaa259.

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Abstract MicroRNAs (miRNAs) are small non-coding RNAs that are involved in the regulation of major pathways in eukaryotic cells through their binding to and repression of multiple mRNAs. With high-throughput methodologies, various outcomes can be measured that produce long lists of miRNAs that are often difficult to interpret. A common question is: after differential expression or phenotypic screening of miRNA mimics, which miRNA should be chosen for further investigation? Here, we present miRViz (http://mirviz.prabi.fr/), a webserver application designed to visualize and interpret large miRNA datasets, with no need for programming skills. MiRViz has two main goals: (i) to help biologists to raise data-driven hypotheses and (ii) to share miRNA datasets in a straightforward way through publishable quality data representation, with emphasis on relevant groups of miRNAs. MiRViz can currently handle datasets from 11 eukaryotic species. We present real-case applications of miRViz, and provide both datasets and procedures to reproduce the corresponding figures. MiRViz offers rapid identification of miRNA families, as demonstrated here for the miRNA-320 family, which is significantly exported in exosomes of colon cancer cells. We also visually highlight a group of miRNAs associated with pluripotency that is particularly active in control of a breast cancer stem-cell population in culture.
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Wang, Xian-min, Kui Zhang, Yan Li, Kun Shi, Yi-ling Liu, Yan-feng Yang, Yu Fang, and Meng Mao. "Screening miRNA and their target genes related to tetralogy of Fallot with microarray." Cardiology in the Young 24, no. 3 (May 17, 2013): 442–46. http://dx.doi.org/10.1017/s104795111300053x.

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AbstractOur aim is to screen miRNAs and genes related to tetralogy of Fallot and construct a co-expression network based on integrating miRNA and gene microarrays. We downloaded the gene expression profile GSE35490 (miRNA) and GSE35776 (mRNA) of tetralogy of Fallot from the Gene Expression Omnibus database, which includes eight normal and 15 disease samples from infants, and screened differentially expressed miRNAs and genes between normal and disease samples (cut-off: p < 0.05; FDR < 0.05; and log FC > 2 or log FC < −2); in addition, we downloaded human miRNA and their targets, which were collected in the miRNA targets prediction database TargetScan, and selected ones that also appeared in our differentially expressed miRNAs and their predicted targets (score >0.9) and then made a relationship of diff_miRNAs and diff_genes of our results. Finally, we uploaded all the diff_target genes into String, constructed a co-expression network regulated by diff_miRNAs, and performed functional analysis with the software DAVID. Comparing normal and disease lesion tissue, we got 32 and 875 differentially expressed miRNAs and genes, respectively, and found hsa-miR-124 with 34 diff_target genes and hsa-miR-138 with two diff_target genes. Then we constructed a co-expression network that contains 231 pairs of genes. Genes in the network were enriched into 14 function clusters, and the most significant one is protein localisation. We screened the tetralogy of Fallot-related hsa-miR-124 and hsa-miR-138 with their direct and indirect differentially expressed target genes, and found that protein localisation is the significant cause affecting tetralogy of Fallot. Our approach may provide the groundwork for a new therapy approach to treating tetralogy of Fallot.
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Whittaker, Ross, Patricia A. Loy, Eugene Sisman, Eigo Suyama, Pedro Aza-Blanc, Randall S. Ingermanson, Jeffrey H. Price, and Patrick M. MCdonough. "Identification of MicroRNAs That Control Lipid Droplet Formation and Growth in Hepatocytes via High-Content Screening." Journal of Biomolecular Screening 15, no. 7 (July 16, 2010): 798–805. http://dx.doi.org/10.1177/1087057110374991.

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Hepatic lipid droplets (LDs) are associated with metabolic syndrome, type 2 diabetes, hepatitis C, and both alcoholic and nonalcoholic fatty liver disease. MicroRNAs (miRNAs) are small noncoding RNAs that regulate gene expression at the level of translation. Approximately 1000 different miRNA species are encoded within the human genome, and many are differentially expressed by healthy and diseased liver. However, few studies have investigated the role of miRNAs in regulating LD expression. Accordingly, a high-content assay (HCA) was performed in which human hepatocytes (Huh-7 cells) were transiently transfected with 327 unique human miRNAs; the cells were then fixed, labeled for nuclei and lipid droplets, and imaged with an automated digital microscopy workstation. LD expression was analyzed on a cell-by-cell basis, using automated image analysis. Eleven miRNAs were identified that altered LDs. MiR-181d was the most efficacious inhibitor, decreasing LDs by about 60%. miRNA-181d was also confirmed to reduce cellular triglycerides and cholesterol ester via biochemical assays. Furthermore, a series of proteins was identified via miRNA target analysis, and siRNAs directed against many of these proteins also modified LDs. Thus, HCA-based screening identified novel miRNA and protein regulators of LDs and cholesterol metabolism that may be relevant to hepatic diseases arising from obesity and alcohol abuse.
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Marcuello, María, Saray Duran-Sanchon, Lorena Moreno, Juan José Lozano, Luis Bujanda, Antoni Castells, and Meritxell Gironella. "Analysis of A 6-Mirna Signature in Serum from Colorectal Cancer Screening Participants as Non-Invasive Biomarkers for Advanced Adenoma and Colorectal Cancer Detection." Cancers 11, no. 10 (October 12, 2019): 1542. http://dx.doi.org/10.3390/cancers11101542.

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Early detection of colorectal cancer (CRC) and its precancerous lesion, advanced adenomas (AA), is critical to improve CRC incidence and prognosis. Circulating microRNAs (miRNAs or miR) are promising non-invasive biomarkers for cancer detection. Our previous results showed that a plasma 6-miRNA signature (miR-15b-5p, miR-18a-5p, miR-29a-3p, miR-335-5p, miR-19a-3p and miR-19b-3p) could distinguish between CRC or AA and healthy individuals (controls). However, its diagnostic performance in serum is unknown. In this exploratory study we aim to evaluate the diagnostic performance of the 6-miRNA signature in serum samples in a cohort of individuals participating in Barcelona’s CRC Screening Programme. We prospectively collected serums from 264 faecal immunochemical test (FIT)-positive participants and total RNA was extracted. Finally, 213 individuals (CRC, 59, AA, 74, controls, 80) were included. MiRNA expression was quantified by real-time RT-qPCR and data analysis was performed by logistic regression. Faecal hemoglobin concentration (f(Hb)) from FIT of the same individuals was also considered. As previously described in plasma, serum from patients with AA or CRC presented significant differences in the 6-miRNA signature compared to controls. Moreover, when combined with f(Hb), the final signature showed high discriminative capacity to distinguish CRC from controls (area under the curve (AUC) = 0.88), and even AA (AUC = 0.81) that otherwise are poorly detected if we only consider f(Hb) (AUC = 0.64). Addition of the serum 6-miRNA signature to quantitative f(Hb) show high accuracy to detect patients with advanced colorectal neoplasia in average-risk individuals. A combination of these two non-invasive methods could be a good strategy to improve diagnostic performances of current CRC screening programmes.
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Babayan, Anna, Martin H. D. Neumann, Andrei Herdean, Jonathan M. Shaffer, Melanie Janning, Franca Kobus, Sonja Loges, et al. "Multicenter Evaluation of Independent High-Throughput and RT-qPCR Technologies for the Development of Analytical Workflows for Circulating miRNA Analysis." Cancers 12, no. 5 (May 5, 2020): 1166. http://dx.doi.org/10.3390/cancers12051166.

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Background: Among emerging circulating biomarkers, miRNA has the potential to detect lung cancer and follow the course of the disease. However, miRNA analysis deserves further standardization before implementation into clinical trials or practice. Here, we performed international ring experiments to explore (pre)-analytical factors relevant to the outcome of miRNA blood tests in the context of the EU network CANCER-ID. Methods: Cell-free (cfmiRNA) and extracellular vesicle-derived miRNA (EVmiRNA) were extracted using the miRNeasy Serum/Plasma Advanced, and the ExoRNeasy Maxi kit, respectively, in a plasma cohort of 27 NSCLC patients and 20 healthy individuals. Extracted miRNA was investigated using small RNA sequencing and hybridization platforms. Validation of the identified miRNA candidates was performed using quantitative PCR. Results: We demonstrate the highest read counts in healthy individuals and NSCLC patients using QIAseq. Moreover, QIAseq showed 15.9% and 162.9% more cfmiRNA and EVmiRNA miRNA counts, respectively, in NSCLC patients compared to healthy control samples. However, a systematic comparison of selected miRNAs revealed little agreement between high-throughput platforms, thus some miRNAs are detected with one technology, but not with the other. Adding to this, 35% (9 of 26) of selected miRNAs in the cfmiRNA and 42% (11 of 26) in the EVmiRNA fraction were differentially expressed by at least one qPCR platform; about half of the miRNAs (54%) were concordant for both platforms. Conclusions: Changing of (pre)-analytical methods of miRNA analysis has a significant impact on blood test results and is therefore a major confounding factor. In addition, to confirm miRNA biomarker candidates screening studies should be followed by targeted validation using an independent platform or technology.
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Qin, Qiu, Xuan Wang, Ni Yan, Rong-Hua Song, Tian-Tian Cai, Wen Zhang, Li-Juan Guan, Fatuma-Said Muhali, and Jin-An Zhang. "Aberrant Expression of miRNA and mRNAs in Lesioned Tissues of Graves' Disease." Cellular Physiology and Biochemistry 35, no. 5 (2015): 1934–42. http://dx.doi.org/10.1159/000374002.

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Background and Aims: Abnormal microRNA (miRNA) expression is found in many diseases including autoimmune diseases. However, little is known about the role of miRNA regulation in Graves' disease (GD). Here, we simultaneously detected different expressions of miRNA and mRNAs in thyroid tissues via a high-throughput transcriptomics approach, known as microarray, in order to reveal the relationship between aberrant expression of miRNAs and mRNAs spectrum and GD. Methods: Totally 7 specimens of thyroid tissue from 4 GD patients and 3 controls were obtained by surgery for microarray analysis. Then, 30 thyroid specimens (18 GD and 12 controls) were also collected for further validation by quantitative real-time PCR ( qRT-PCR ). Results: Statistical analysis showed that the expressions of 5 specific miRNA were increased significantly while those of other 18 miRNA were decreased in thyroid tissue of GD patients (FC≥1.3 or≤0.77 and p<0.05). In addition, the transcription of 1271 mRNAs was up-regulated, while the expression of 777 mRNAs transcripts was down-regulated (FC≥2.0 or≤0.5 and p<0.05). Furthermore, integrated analysis of differentially expressed miRNA and their target mRNAs demonstrated that 2 miRNA (miR-22 and miR-183) were increased while their potential target mRNAs were decreased. 3 miRNA (miR-101, miR-197 and miR-660) were decreased while their potential target mRNAs were increased. The above findings from microarray screening were confirmed by qRT-PCR in more samples. The results were consistent with those observed in the microarray assays. Conclusion: Our study highlights the possibility that miRNA-target gene network may be involved in the pathogenesis of GD and could provide new insights into understanding the pathophysiological mechanisms of GD.
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Zhu, Tao, Wen Gao, Xi Chen, Ying Zhang, Meijuan Wu, Ping Zhang, and Shihua Wang. "A Pilot Study of Circulating MicroRNA-125b as a Diagnostic and Prognostic Biomarker for Epithelial Ovarian Cancer." International Journal of Gynecologic Cancer 27, no. 1 (January 1, 2016): 3–10. http://dx.doi.org/10.1097/igc.0000000000000846.

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ObjectiveEarly diagnosis of epithelial ovarian cancer is critical for patient survival. The objective of this pilot study is to identify a circulating micro (mi)RNA as a potential biomarker for epithelial ovarian cancer.MethodsA total of 135 epithelial ovarian cancer patients and 54 benign ovarian tumor patients were recruited for this study. Using customized TaqMan low density miRNA arrays, we first screened expression levels of 48 miRNAs in sera from 18 epithelial ovarian cancer patients and 16 benign ovarian tumor patients. The most significantly and differentially expressed miRNA was then further examined in all serum samples using real-time polymerase chain reaction. Its expression was further analyzed in relationship with clinicopathological factors and patient survival.ResultsArray screening data showed that expression levels of serum miRNA-20a, miRNA-125b, miRNA-126, miRNA-355, and let-7c were significantly different between malignant and benign ovarian tumor patients. Subsequent real-time polymerase chain reaction results showed that serum miRNA-125b levels were significantly higher in epithelial ovarian cancer patients compared to benign controls. Moreover, serum miRNA-125b levels were significantly higher in ovarian cancer patients in early stages I and II, and in patients having no residual tumor following surgery, but were not associated with differentiation and histological types of ovarian cancer. Notably, the higher level of miR-125b was significantly positively correlated with progression-free survival (P= 0.035) and marginally, with overall survival (P =0.069).ConclusionsmiRNA-125b plays an important role in the pathogenesis and progression of epithelial ovarian cancer. Circulating miRNA-125b has the potential to become a novel biomarker for early diagnosis and prognosis prediction of epithelial ovarian cancer.
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JIN, NING, XUEFEI JIN, XINQUAN GU, WANLI NA, MUCHUN ZHANG, and RUI ZHAO. "Screening biomarkers of bladder cancer using combined miRNA and mRNA microarray analysis." Molecular Medicine Reports 12, no. 2 (May 7, 2015): 3170–76. http://dx.doi.org/10.3892/mmr.2015.3739.

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