Abstract
MicroRNAs (miRNAs) are short non-coding RNAs that are recognized to epigenetically modulate gene expression by weakly binding to the 3′UTR and/or other sites of target mRNAs. A number of miRNAs have been recognized to be aberrantly expressed in cancer. These findings have led researchers to aggressively pursue miRNAs for cancer diagnostic and therapeutics. However, both identification and targeting of miRNAs is not very straight forward because each miRNA can modulate scores of different genes which in-turn can influence exponential number of different targets. In recent years, there has been a consensus that the complexity of miRNAs requires holistic systems biology approaches to tease out the specific targets of each miRNA, which appears to be context dependent. In this chapter we present the recent advancements in systems and network biology and how these and related technologies are aiding in the design of effective miRNA-based therapeutics against cancer.
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References
Ambros V (2001) microRNAs: tiny regulators with great potential. Cell 107:823–826
Lund E, Guttinger S, Calado A, Dahlberg JE, Kutay U (2004) Nuclear export of microRNA precursors. Science 303:95–98
Lai EC (2002) Micro RNAs are complementary to 3’ UTR sequence motifs that mediate negative post-transcriptional regulation. Nat Genet 30:363–364
Bartel DP (2004) MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116:281–297
Judson RL, Babiarz JE, Venere M, Blelloch R (2009) Embryonic stem cell-specific microRNAs promote induced pluripotency. Nat Biotechnol 27:459–461
Esteller M (2011) Non-coding RNAs in human disease. Nat Rev Genet 12:861–874
Jackson AL, Levin AA (2012) Developing microRNA therapeutics: approaching the unique complexities. Nucleic Acid Ther 22:213–225
Das N (2012) MicroRNA Targets - How to predict? Bioinformation 8:841–845
Fang Z, Rajewsky N (2011) The impact of miRNA target sites in coding sequences and in 3’UTRs. PLoS One 6:e18067
Kitano H (2002) Computational systems biology. Nature 420:206–210
Azmi AS (2013) Systems and Network Biology in Pharmaceutical Drug Discovery. Curr Pharm Des 31:1592–1605
Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N et al (2007) A mammalian microRNA expression atlas based on small RNA library sequencing. Cell 129:1401–1414
Yoon S, De MG (2006) Computational identification of microRNAs and their targets. Birth Defect Res C Embryo Today 78:118–128
Guruceaga E, Segura V (2014) Functional interpretation of microRNA-mRNA association in biological systems using R. Comput Biol Med 44:124–131
Gusev Y (2008) Computational methods for analysis of cellular functions and pathways collectively targeted by differentially expressed microRNA. Methods 44:61–72
Hong L, Yang Z, Ma J, Fan D (2013) Function of miRNA in controlling drug resistance of human cancers. Curr Drug Targets 14:1118–1127
Ragusa M, Statello L, Maugeri M, Majorana A, Barbagallo D et al (2012) Specific alterations of the microRNA transcriptome and global network structure in colorectal cancer after treatment with MAPK/ERK inhibitors. J Mol Med (Berl) 90:1421–1438
Vera J, Schmitz U, Lai X, Engelmann D, Khan FM et al (2013) Kinetic modeling-based detection of genetic signatures that provide chemoresistance via the E2F1-p73/DNp73-miR-205 network. Cancer Res 73:3511–3524
Uboldi S, Calura E, Beltrame L, Fuso Nerini I, Marchini S et al (2012) A systems biology approach to characterize the regulatory networks leading to trabectedin resistance in an in vitro model of myxoid liposarcoma. PLoS One 7:e35423
Ali S, Almhanna K, Chen W, Philip PA, Sarkar FH (2010) Differentially expressed miRNAs in the plasma may provide a molecular signature for aggressive pancreatic cancer. Am J Transl Res 3:28–47
Ali S, Banerjee S, Logna F, Bao B, Philip PA et al (2012) Inactivation of Ink4a/Arf leads to deregulated expression of miRNAs in K-Ras transgenic mouse model of pancreatic cancer. J Cell Physiol 227:3373–3380
Ali S, Saleh H, Sethi S, Sarkar FH, Philip PA (2012) MicroRNA profiling of diagnostic needle aspirates from patients with pancreatic cancer. Br J Cancer 107:1354–1360
Meacham CE, Morrison SJ (2013) Tumour heterogeneity and cancer cell plasticity. Nature 501:328–337
Holohan C, Van SS, Longley DB, Johnston PG (2013) Cancer drug resistance: an evolving paradigm. Nat Rev Cancer 13:714–726
Azmi AS, Sarkar FH (2012) Prostate cancer stem cells: molecular characterization for targeted therapy. Asian J Androl 14:659–660
Bao B, Ahmad A, Azmi AS, Ali S, Sarkar FH (2013) Overview of cancer stem cells (CSCs) and mechanisms of their regulation: implications for cancer therapy. Curr Protoc Pharmacol. Chapter 14: Unit. doi:10.1002/0471141755.ph1425s61
Hermann PC, Huber SL, Herrler T, Aicher A, Ellwart JW et al (2007) Distinct populations of cancer stem cells determine tumor growth and metastatic activity in human pancreatic cancer. Cell Stem Cell 1:313–323
Bao B, Azmi AS, Li Y, Ahmad A, Ali S et al (2014) Targeting CSCs in tumor microenvironment: the potential role of ROS-associated miRNAs in tumor aggressiveness. Curr Stem Cell Res Ther 9:22–35
Bao B, Li Y, Ahmad A, Azmi AS, Bao G et al (2012) Targeting CSC-related miRNAs for cancer therapy by natural agents. Curr Drug Targets 13:1858–1868
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Mohammad, R.M., Bao, B., Sarkar, F.H., Philip, P.A., Azmi, A.S. (2014). Systems Biology Approaches in the Design of Effective miRNA-Targeted Therapeutics. In: Sarkar, F. (eds) MicroRNA Targeted Cancer Therapy. Springer, Cham. https://doi.org/10.1007/978-3-319-05134-5_18
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DOI: https://doi.org/10.1007/978-3-319-05134-5_18
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