TEAM Programme

In search of new pathways of tumorigenesis - genome-wide functional analysis of microRNAs deregulated in human cancers.

MicroRNAs (miRs) are small (19-25 nucleotides) non-coding RNA molecules that typically function as negative regulators of the expression of protein-encoding genes [1]. It is speculated that miRs altogether regulate around 30% of the human genome, which highlights their potential importance as global regulators of gene expression [2]. MiRs regulate such major processes as development, apoptosis, cell proliferation, immune response, and hematopoiesis [3]; they also may act as tumor suppressor genes and oncogenes [4, 5]. Mature miRs target and inhibit translation or promote mRNA degradation by annealing to complementary sequences in mRNA 3’untranslated regions (UTRs). Watson-Crick complementarity between the target and the “seed” region comprising 2-8 nucleotides of the mature miR is both necessary and sufficient for targeting and regulation of mRNAs by miRs. The sequence of this “seed” region is the basis of most genome-wide predictions of miR binding sites within miR- regulated genes [6]. A single nucleotide polymorphism (SNP) located in the crucial “seed” sequence affects its complementarity to potential target genes determining the functionality of a miR [7]. Individual miRNAs typically target dozens of mRNAs, often encoding proteins with related functions [2]. Therefore, although their inhibitory effects on individual mRNAs are generally modest, their combined effects on multiple mRNAs can induce strong biological responses [8-10]. As they were discovered only relatively recently, the study of miRs is a young and rapidly changing field in which many genes remain to be discovered and the sequence modifications are not well understood.

To further clarify the roles of miRs in tumorigenesis it is crucial to generate complete datasets of variations in miR sequences and to profile the expression of miR isoforms and their target genes in cancer tissues. Towards this goal we propose:

Specific Aim 1: To discover and annotate on the genome-wide level previously unidentified RNA genes, including miRs, by the next-generation deep sequencing technology in colon and liver cancers.

Specific Aim 2: To detect and characterize on the genome-wide level the germline and somatic sequence variations of all known and newly discovered miRs in cancer/unaffected tissue pairs of liver or colon origin.

Specific Aim 3: To detect the genome-wide expression changes of all known and newly discovered miRs and their isoforms in cancer/unaffected tissue pairs and in normal tissue from cancer-free individuals.

Specific Aim 4: To characterize the effects of miR isoforms on the transcriptome of protein- encoding genes.

The long term goal of our proposal is to use this information to develop new approaches to the diagnosis and treatment of liver and colon cancer. We believe that our findings will serve as a model for other cancers and diseases.

 

LITERATURE CITED

1.  Bartel, D.P., MicroRNAs: Target Recognition and Regulatory Functions. Cell, 2009. 136(2): p. 215-233. 

2.  Santarpia, L., M. Nicoloso, and G.A. Calin, MicroRNAs: a complex regulatory network drives the acquisition of malignant cell phenotype. Endocr Relat Cancer, 2010. 17(1): p. F51-75.

3.   Croce, C.M. and G.A. Calin, miRNAs, cancer, and stem cell division. Cell, 2005. 122(1): p. 6-7.

4.   Zhang, B., et al., microRNAs as oncogenes and tumor suppressors. Developmental Biology, 2007. 302(1): p. 1-12.

5.   Esquela-Kerscher, A. and F.J. Slack, Oncomirs - microRNAs with a role in cancer. Nat Rev Cancer, 2006. 6(4): p. 259-269.

6.   Nielsen, C.B., et al., Determinants of targeting by endogenous and exogenous microRNAs and siRNAs. RNA, 2007. 13(11): p. 1894-1910.

7.   Jazdzewski, K., et al., Polymorphic mature microRNAs from passenger strand of pre-miR-146a contribute to thyroid cancer. Proc Natl Acad Sci U S A, 2009. 106(5): p. 1502-1505.

8.   Lim, L.P., et al., Microarray analysis shows that some microRNAs downregulate large numbers oftarget mRNAs. Nature, 2005. 433(7027): p. 769-773.

9.   Volinia, S., et al., Reprogramming of miRNA networks in cancer and leukemia. Genome Res, 2010. 20(5): p. 589-99.

10. Negrini, M., M.S. Nicoloso, and G.A. Calin, MicroRNAs and cancer--new paradigms in molecular oncology. Curr Opin Cell Biol, 2009. 21(3): p. 470-479.