Contribution of Bioinformatics Prediction in MicroRNA-based Cancer Therapeutics

Overview

Journal Adv Drug Deliv Rev

Specialty Pharmacology

Date 2014 Dec 3

PMID 25450261

Citations 21

Authors

Jasjit K Banwait

Dhundy R Bastola

Affiliations

Soon will be listed here.

Abstract

Despite enormous efforts, cancer remains one of the most lethal diseases in the world. With the advancement of high throughput technologies massive amounts of cancer data can be accessed and analyzed. Bioinformatics provides a platform to assist biologists in developing minimally invasive biomarkers to detect cancer, and in designing effective personalized therapies to treat cancer patients. Still, the early diagnosis, prognosis, and treatment of cancer are an open challenge for the research community. MicroRNAs (miRNAs) are small non-coding RNAs that serve to regulate gene expression. The discovery of deregulated miRNAs in cancer cells and tissues has led many to investigate the use of miRNAs as potential biomarkers for early detection, and as a therapeutic agent to treat cancer. Here we describe advancements in computational approaches to predict miRNAs and their targets, and discuss the role of bioinformatics in studying miRNAs in the context of human cancer.

Citing Articles

MGAT4EP promotes tumor progression and serves as a prognostic marker for breast cancer.

Zhong L, Zhu J, Chen J, Jin X, Liu L, Ji S Cancer Biol Ther. 2025; 26(1):2475604.

PMID: 40069131 PMC: 11901376. DOI: 10.1080/15384047.2025.2475604.

The Impact of COVID-19 on RNA Therapeutics: A Surge in Lipid Nanoparticles and Alternative Delivery Systems.

Parvin N, Mandal T, Joo S Pharmaceutics. 2024; 16(11).

PMID: 39598489 PMC: 11597542. DOI: 10.3390/pharmaceutics16111366.

A Bioinformatics-Based Approach to Discover Novel Biomarkers in Hepatocellular Carcinoma.

Shourideh A, Maddah R, Amiri B, Basharat Z, Shadpirouz M Iran J Public Health. 2024; 53(6):1332-1342.

PMID: 39430152 PMC: 11488550.

Lymph node metastasis determined miRNAs in esophageal squamous cell carcinoma.

Wei F, Bi S, Li M, Yu J Aging (Albany NY). 2024; 16(20):13104-13116.

PMID: 39401765 PMC: 11552642. DOI: 10.18632/aging.206122.

Significance of as a biomarker for clinical prognosis, immune infiltration, and drug therapy in lung squamous cell carcinoma.

Lin H, Wang J, Shi Q, Wu M PeerJ. 2024; 12:e17338.

PMID: 38708353 PMC: 11069361. DOI: 10.7717/peerj.17338.

References

Li W, LeBrun D, Li M . The expression and functions of microRNAs in pancreatic adenocarcinoma and hepatocellular carcinoma. Chin J Cancer. 2011; 30(8):540-50. PMC: 4013404. DOI: 10.5732/cjc.011.10197. View

Voorhoeve P, le Sage C, Schrier M, Gillis A, Stoop H, Nagel R . A genetic screen implicates miRNA-372 and miRNA-373 as oncogenes in testicular germ cell tumors. Cell. 2006; 124(6):1169-81. DOI: 10.1016/j.cell.2006.02.037. View

Bittner M, Meltzer P, Chen Y, Jiang Y, Seftor E, Hendrix M . Molecular classification of cutaneous malignant melanoma by gene expression profiling. Nature. 2000; 406(6795):536-40. DOI: 10.1038/35020115. View

Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A . A mammalian microRNA expression atlas based on small RNA library sequencing. Cell. 2007; 129(7):1401-14. PMC: 2681231. DOI: 10.1016/j.cell.2007.04.040. View

Gomes C, Cho J, Hood L, Franco O, Pereira R, Wang K . A Review of Computational Tools in microRNA Discovery. Front Genet. 2013; 4:81. PMC: 3654206. DOI: 10.3389/fgene.2013.00081. View

Lee Y, Kim M, Han J, Yeom K, Lee S, Baek S . MicroRNA genes are transcribed by RNA polymerase II. EMBO J. 2004; 23(20):4051-60. PMC: 524334. DOI: 10.1038/sj.emboj.7600385. View

Calin G, Sevignani C, Dumitru C, Hyslop T, Noch E, Yendamuri S . Human microRNA genes are frequently located at fragile sites and genomic regions involved in cancers. Proc Natl Acad Sci U S A. 2004; 101(9):2999-3004. PMC: 365734. DOI: 10.1073/pnas.0307323101. View

Johnson S, Grosshans H, Shingara J, Byrom M, Jarvis R, Cheng A . RAS is regulated by the let-7 microRNA family. Cell. 2005; 120(5):635-47. DOI: 10.1016/j.cell.2005.01.014. View

Hageman Blair R, Trichler D, Gaille D . Mathematical and statistical modeling in cancer systems biology. Front Physiol. 2012; 3:227. PMC: 3385354. DOI: 10.3389/fphys.2012.00227. View

10.

Takamizawa J, Konishi H, Yanagisawa K, Tomida S, Osada H, Endoh H . Reduced expression of the let-7 microRNAs in human lung cancers in association with shortened postoperative survival. Cancer Res. 2004; 64(11):3753-6. DOI: 10.1158/0008-5472.CAN-04-0637. View

11.

Mu P, Han Y, Betel D, Yao E, Squatrito M, Ogrodowski P . Genetic dissection of the miR-17~92 cluster of microRNAs in Myc-induced B-cell lymphomas. Genes Dev. 2009; 23(24):2806-11. PMC: 2800095. DOI: 10.1101/gad.1872909. View

12.

Park J, Henry J, Jiang J, Esau C, Gusev Y, Lerner M . miR-132 and miR-212 are increased in pancreatic cancer and target the retinoblastoma tumor suppressor. Biochem Biophys Res Commun. 2011; 406(4):518-23. PMC: 3069485. DOI: 10.1016/j.bbrc.2011.02.065. View

13.

Zhao G, Wang B, Liu Y, Zhang J, Deng S, Qin Q . miRNA-141, downregulated in pancreatic cancer, inhibits cell proliferation and invasion by directly targeting MAP4K4. Mol Cancer Ther. 2013; 12(11):2569-80. DOI: 10.1158/1535-7163.MCT-13-0296. View

14.

Croft D, Mundo A, Haw R, Milacic M, Weiser J, Wu G . The Reactome pathway knowledgebase. Nucleic Acids Res. 2013; 42(Database issue):D472-7. PMC: 3965010. DOI: 10.1093/nar/gkt1102. View

15.

Fire A, Xu S, Montgomery M, Kostas S, Driver S, Mello C . Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature. 1998; 391(6669):806-11. DOI: 10.1038/35888. View

16.

Bloomston M, Frankel W, Petrocca F, Volinia S, Alder H, Hagan J . MicroRNA expression patterns to differentiate pancreatic adenocarcinoma from normal pancreas and chronic pancreatitis. JAMA. 2007; 297(17):1901-8. DOI: 10.1001/jama.297.17.1901. View

17.

Chandra B, Gupta M . An efficient statistical feature selection approach for classification of gene expression data. J Biomed Inform. 2011; 44(4):529-35. DOI: 10.1016/j.jbi.2011.01.001. View

18.

Penrod N, Moore J . Key genes for modulating information flow play a temporal role as breast tumor coexpression networks are dynamically rewired by letrozole. BMC Med Genomics. 2013; 6 Suppl 2:S2. PMC: 3654875. DOI: 10.1186/1755-8794-6-S2-S2. View

19.

Lee Y, Ahn C, Han J, Choi H, Kim J, Yim J . The nuclear RNase III Drosha initiates microRNA processing. Nature. 2003; 425(6956):415-9. DOI: 10.1038/nature01957. View

20.

Mi H, Thomas P . PANTHER pathway: an ontology-based pathway database coupled with data analysis tools. Methods Mol Biol. 2009; 563:123-40. PMC: 6608593. DOI: 10.1007/978-1-60761-175-2_7. View