MicroRNAs as Predictive and Prognostic Biomarkers inHuman Neoplasia : With Specific Focus on Colorectal Cancer, Giant Cell Tumor of Bone, and Leukemias (2013)

Recently, discovery of microRNA has provided new insights into cancer research, revealing the role of miRNAs in various biological processes, and evidence shows that their deregulation in many cancers has prognostic and predictive significance. Although specific miRNAs have been discovered in the malignancies studied in this thesis: colorectal cancer (CRC), giant cell tumor of bone (GCTB), acute lymphoblastic leukemia (ALL), and acute myeloid leukemia (AML), very little still is known about the association of miRNAs with progression and their response to treatment. By applying novel microarray techniques, we profiled miRNA expression in CRC, GCTB, ALL and, AML. In the study focusing on primary tumors of 60 metastatic CRC (mCRC) patients, we detected BRAF mutations in 5 and KRAS mutations in 15 cases. In addition to 46 altered miRNAs in mCRC patients with and without KRAS mutation vs. normal colon tissue, we observed an miRNA signature associated with KRAS status when we compared 15 patients with mutant KRAS with 40 patients without this mutation. Four differentially expressed miRNAs, over-expressed miR-92a, miR-127-3p, miR-486-5p, and under-expressed miR-378, were evident in the mutated KRAS group vs. wild-type KRAS group. In another study on CRC, miRNA profiling in primary tumors of 33 mCRC patients with wild-type BRAF and KRAS allowed identification of miRNAs related to their response to anti-EGFR monoclonal antibody treatment. We found up-regulated miR-31* and down-regulated miR-592 in progressive disease (PD) compared to that in disease control (DC). Evaluation of mRNA levels of SLC26A3 and ATN1, drug-related genes and of miR-31* target genes showed their lower level of expression in PD vs. DC. Moreover, correlation between overall survival and miRNA expression assessed by two approaches, cluster analysis and the Cox proportional hazard regression model, revealed two common miRNAs, miR-140-3p and miR-1224-5p, to be related to survival in both analyses. As for the study of the metastatic and non-metastatic GCTBs, we found 12 miRNAs as being differentially expressed (miR-136, miR-513a-5p, miR-494, miR-224, miR-542-5p). Expression levels of eight genes such as NFIB, TNC, and FLRT2 correlated inversely with miRNA results. The expression levels of miR-136 and its target gene, NFIB, were verified by use of qRT-PCR. The level of NFIB protein also was higher in metastatic than in non-metastatic GCTBs. Further, we tested the protein expression level of NFIB in an independent validation cohort of 74 primary archival GCTB specimens to assess the power of NFIB as a prognostic marker. Immunodetection showed a higher frequency of NFIB over-expression in primary tumors that developed metastases than in the disease-free group. Moreover, we studied the miRNA expression profiles of primary tumors of 90 bone marrow core biopsies of ALL patients, including 11 patients with paired samples at diagnosis and at relapse. We found a set of miRNAs (miR-1281, miR-1225-3p, miR-877*, miR-423-5p, miR-29c) significantly related to survival (q less than 0.05). Further validation of miR-423-5p expression by qRT-PCR confirmed microarray analysis results and showed a direct correlation with survival. In comparisons between the diagnosis-relapse pairs, expression of miR-654-5p and miR-431 between the two groups significantly differed, and these miRNAs were down-regulated in relapse samples. Comparison of miRNA profiling of 15 chemorefractory and 18 chemosensitive AML patients showed that the differentially expressed miRNAs were miR-363, miR-532-5p, and 342-3p, all of which were over-expressed in chemorefractory vs. chemosensitive patients. Verification by use of qRT-PCR of both miR-363 and miR-532-5p revealed similar results as with microarray. The miR-363 target genes RGS17 and HIPK3 both have been associated with drug response. These studies provide new information about genomic changes involved in progression and resistance to treatment in various types of cancer, and also highlight the power of applying genomic-wide array screening techniques in malignancies. The novel findings in these studies may serve as a useful resource for future studies and aid in development of novel therapeutic targets to increase the survival rates of cancer patients.