Supplementary Methods, Figure Legend from Optical Detection of Buccal Epithelial Nanoarchitectural Alterations in Patients Harboring Lung Cancer: Implications for Screening

Supplementary Figures 1-12 - PDF file 897K, Relative expression of miR-520d-3p (miR-520d) and miR-520d-5p (miR-520d*) in ovarian cancer cell lines (Figure S1), Kaplan-Meier curves representing the percent progression-free survival in patients with ovarian cancer based on miR-520d-3p median expression levels (Figure S2), miR-520d-5p does not target EphA2 (Figure S3), miR-520d-3p and EphA2 expression levels in miR-520d-3p overexpressing stable clones (Figure S4), Effect of miR-520d-3p expression on cell proliferation (Figure S5), miR-520d-3p and EphA2 levels in xenograft models of miR-520d-3p overexpressing HeyA8 and SKOV3ip1 models (Figure S6), Efficiency of EphA2 targeting siRNAs in HeyA8 cells (Figure S7), Combination of miR-520d-3p and siRNA-EphA2 treatment shows enhanced EphA2 inhibition in vitro (Figure S8), Dose-response curve of miR-520d-3p, si-EphA2-1 and combined miR-520d-3p + si-EphA2-1 in SKOV3ip1 and HeyA8 cells (Figure S9), Treatment with anti-miR-520d-3p can restore EphA2 protein levels in a dose-dependent manner in SKOV3ip1 cells (Figure S10), Effect of combined miR-520d-3p+siEphA2-1 treatment on angiogenesis, proliferation and apoptosis in HeyA8 cells (Figure S11), and Differentially expressed coding genes in miR-520d-3p overexpressing stable clones (Figure S12)

Supplementary Tables 1-2 - PDF file 85K, MicroRNAs significantly associated with overall survival and response to therapy in ovarian cancer patients using TCGA 2009 database (Table S1) and Clinical and bio-pathological features of the 91 MDACC ovarian cancer samples used in the study (Table S2)

BACKGROUND & AIMS: Chromosomal instability (CIN) is a carcinogenesis event that promotes metastasis and resistance to therapy by unclear mechanisms. Expression of the colon cancer-associated transcript 2 gene (CCAT2), which encodes a long noncoding RNA (lncRNA), associates with CIN, but little is known about how CCAT2 lncRNA regulates this cancer enabling characteristic. METHODS: We performed cytogenetic analysis of colorectal cancer (CRC) cell lines (HCT116, KM12C/SM, and HT29) overexpressing CCAT2 and colon organoids from C57BL/6N mice with the CCAT2 transgene and without (controls). CRC cells were also analyzed by immunofluorescence microscopy, g-H2AX, and senescence assays. CCAT2 transgene and control mice were given azoxymethane and dextran sulfate sodium to induce colon tumors. We performed gene expression array and mass spectrometry to detect downstream targets of CCAT2 lncRNA. We characterized interactions between CCAT2 with downstream proteins using MS2 pull-down, RNA immunoprecipitation, and selective 20-hydroxyl acylation analyzed by primer extension analyses. Downstream proteins were overexpressed in CRC cells and analyzed for CIN. Gene expression levels were measured in CRC and non-tumor tissues from 5 cohorts, comprising more than 900 patients. RESULTS: High expression of CCAT2 induced CIN in CRC cell lines and increased resistance to 5-fluorouracil and oxaliplatin. Mice that expressed the CCAT2 transgene developed chromosome abnormalities, and colon organoids derived from crypt cells of these mice had a higher percentage of chromosome abnormalities compared with organoids from control mice. The transgenic mice given azoxymethane and dextran sulfate sodium developed more and larger colon polyps than control mice given these agents. Microarray analysis and mass spectrometry indicated that expression of CCAT2 increased expression of genes involved in ribosome biogenesis and protein synthesis. CCAT2 lncRNA interacted directly with and stabilized BOP1 ribosomal biogenesis factor (BOP1). CCAT2 also increased expression of MYC, which activated expression of BOP1. Overexpression of BOP1 in CRC cell lines resulted in chromosomal missegregation errors, and increased colony formation, and invasiveness, whereas BOP1 knockdown reduced viability. BOP1 promoted CIN by increasing the active form of aurora kinase B, which regulates chromosomal segregation. BOP1 was overexpressed in polyp tissues from CCAT2 transgenic mice compared with healthy tissue. CCAT2 lncRNA and BOP1 mRNA or protein were all increased in micro satellite stable tumors (characterized by CIN), but not in tumors with microsatellite instability compared with nontumor tissues. Increased levels of CCAT2 lncRNA and BOP1 mRNA correlated with each other and with shorter survival times of patients. CONCLUSIONS: We found that overexpression of CCAT2 in colon cells promotes CIN and carcinogenesis by stabilizing and inducing expression of BOP1 an activator of aurora kinase B. Strategies to target this pathway might be developed for treatment of patients with microsatellite stable colorectal tumors.

The cancer-risk-associated rs6983267 single nucleotide polymorphism (SNP) and the accompanying long noncoding RNA CCAT2 in the highly amplified 8q24.21 region have been implicated in cancer predisposition, although causality has not been established. Here, using allele-specific CCAT2 transgenic mice, we demonstrate that CCAT2 overexpression leads to spontaneous myeloid malignancies. We further identified that CCAT2 is overexpressed in bone marrow and peripheral blood of myelodysplastic/myeloproliferative neoplasms (MDS/MPN) patients. CCAT2 induces global deregulation of gene expression by down-regulating EZH2 in vitro and in vivo in an allele-specific manner. We also identified a novel non-APOBEC, non-ADAR, RNA editing at the SNP locus in MDS/MPN patients and CCAT2-transgenic mice. The RNA transcribed from the SNP locus in malignant hematopoietic cells have different allelic composition from the corresponding genomic DNA, a phenomenon rarely observed in normal cells. Our findings provide fundamental insights into the functional role of rs6983267 SNP and CCAT2 in myeloid malignancies.

The pervasive role of microRNAs (miRNAs) in cancer pathobiology drives the introduction of new drug development approaches such as miRNA inhibition. In order to advance miRNA-therapeutics, meticulous screening strategies addressing specific tumor targets are needed. Small molecule inhibitors represent an attractive goal for these strategies. In this study, we devised a strategy to screen for small molecule inhibitors that specifically inhibit, directly or indirectly, miR-10b (SMIRs) which is overexpressed in metastatic tumors. We found that the multi-tyrosine kinase inhibitor linifanib could significantly inhibit miR-10b and reverse its oncogenic function in breast cancer and liver cancer both in vitro and in vivo. In addition, we showed that the efficacy of linifanib to inhibit tyrosine kinases was reduced by high miR-10b levels. When the level of miR-10b is high, it can "hijack" the linifanib and reduce its kinase inhibitory effects in cancer resulting in reduced anti-tumor efficacy. In conclusion, our study describes an effective strategy to screen for small molecule inhibitors of miRNAs. We further propose that miR-10b expression levels, due to the newly described "hijacking" effect, may be used as a biomarker to select patients for linifanib treatment.

Clinico-pathological characteristics of the metastatic colorectal carcinoma from the third CRC patient cohort. (XLSX 9 kb)

BACKGROUND:Non-coding RNAs have been drawing increasing attention in recent years as functional data suggest that they play important roles in key cellular processes. N-BLR is a primate-specific long non-coding RNA that modulates the epithelial-to-mesenchymal transition, facilitates cell migration, and increases colorectal cancer invasion.RESULTS:We performed multivariate analyses of data from two independent cohorts of colorectal cancer patients and show that the abundance of N-BLR is associated with tumor stage, invasion potential, and overall patient survival. Through in vitro and in vivo experiments we found that N-BLR facilitates migration primarily via crosstalk with E-cadherin and ZEB1. We showed that this crosstalk is mediated by a pyknon, a short ~20 nucleotide-long DNA motif contained in the N-BLR transcript and is targeted by members of the miR-200 family. In light of these findings, we used a microarray to investigate the expression patterns of other pyknon-containing genomic loci. We found multiple such loci that are differentially transcribed between healthy and diseased tissues in colorectal cancer and chronic lymphocytic leukemia. Moreover, we identified several new loci whose expression correlates with the colorectal cancer patients' overall survival.CONCLUSIONS:The primate-specific N-BLR is a novel molecular contributor to the complex mechanisms that underlie metastasis in colorectal cancer and a potential novel biomarker for this disease. The presence of a functional pyknon within N-BLR and the related finding that many more pyknon-containing genomic loci in the human genome exhibit tissue-specific and disease-specific expression suggests the possibility of an alternative class of biomarkers and therapeutic targets that are primate-specific.

Altered energy metabolism is a cancer hallmark as malignant cells tailor their metabolic pathways to meet their energy requirements. Glucose and glutamine are the major nutrients that fuel cellular metabolism, and the pathways utilizing these nutrients are often altered in cancer. Here, we show that the long ncRNA CCAT2, located at the 8q24 amplicon on cancer risk-associated rs6983267 SNP, regulates cancer metabolism in vitro and in vivo in an allele-specific manner by binding the Cleavage Factor I (CFIm) complex with distinct affinities for the two subunits (CFIm25 and CFIm68). The CCAT2 interaction with the CFIm complex fine-tunes the alternative splicing of Glutaminase (GLS) by selecting the poly(A) site in intron 14 of the precursor mRNA. These findings uncover a complex, allele-specific regulatory mechanism of cancer metabolism orchestrated by the two alleles of a long ncRNA.

MicroRNAs (miRNAs) are an evolutionarily conserved class of small, regulatory non-coding RNAs that negatively regulate protein coding gene and other non-coding transcripts expression. miRNAs have been established as master regulators of cellular processes, and they play a vital role in tumor initiation, progression and metastasis. Further, widespread deregulation of microRNAs have been reported in several cancers, with several microRNAs playing oncogenic and tumor suppressive roles. Based on these, miRNAs have emerged as promising therapeutic tools for cancer management. In this review, we have focused on the roles of miRNAs in tumorigenesis, the miRNA-based therapeutic strategies currently being evaluated for use in cancer, and the advantages and current challenges to their use in the clinic.

Long non-coding RNAs (lncRNAs) form the largest part of the mammalian non-coding transcriptome and control gene expression at various levels including chromatin modification, transcriptional and post-transcriptional processing. LncRNAs are implicated in initiation and progression of several cancers.Cancer-associated genomic regions are regions showing high frequency of cancer related abnormalities, such as loss of heterozygosity or amplifications. One such widely studied CAGR is the 8q24.21 genomic region. One SNP of particular importance present at this locus is rs6983267, with the G allele of the SNP conferring increased risk of colorectal, prostate, breast and bladder cancers. CCAT2 is a lncRNA that spans this highly conserved region. CCAT2 has been shown to play an important role in inducing chromosomal instability and supporting cell proliferation and cell cycle arrest. Despite advances in diagnosis of MDS patients, the underlying mechanisms that lead to spontaneous induction of MDS remains poorly understood. Here we attempted to elucidate the role of CCAT2 and its specific alleles (G/T) in regulation of cellular processes that drive spontaneous tumorigenesis using a genetically engineered mouse model. We generated transgenic mice for each CCAT2 allele using random integration approach in C57Bl6/N background, expressing CCAT2 in all tissues of mice.

Non-coding RNAs have been commanding increasingly greater attention in recent years as the few that have been functionalized to date play important roles in key cellular processes. Here we show that N-BLR, a ∼900 bp non-coding RNA, modulates the epithelial-to-mesenchymal transition, increases colorectal cancer invasion, and functions as a migration enabler by affecting the expression of ZEB1 and E-cadherin. In patients with colorectal cancer, N-BLR expression associates with tumor stage and invasion potential. As N-BLR contains several instances of a category of DNA motifs known as pyknons, we also designed a custom-made array to investigate the possibility that other pyknon loci may be transcribed. For several of the loci probed by the array we found that the corresponding pyknons are differentially expressed between cancer and normal tissue samples. Taken together the data suggest that a systematic study of other pyknon-containing non-coding RNAs like N-BLR may be warranted in the context of colorectal cancer.

Abstract EphA2 has emerged as an important target for ovarian cancer therapy in recent years. In the present study, we identified miR-520d-3p as an independent favorable prognostic marker for epithelial ovarian cancer patients. We demonstrate that dual targeting of EphA2 in vitro using EphA2-siRNA and miR-520d-3p exhibits synergistic downregulation of EphA2 and inhibits cell proliferation, migration and invasion. In vivo treatment using DOPC (1,2-dioleoyl-sn-glycero-3-phosphatidylcholine) nano-liposomes conjugated with miR-520d-3p and EphA2-siRNA showed synergistic therapeutic efficacy and superior inhibition of tumor proliferation and angiogenesis than either monotherapy alone. We also identified that EphA2(low)/EphB2(low)/miR-520d-3p(high) gene signature predicts favorable clinical prognosis for ovarian cancer patients. This study addresses a new concept of RNA inhibition therapy by combining miRNA and siRNA to target oncogenic pathways altered in ovarian cancer. Citation Format: Maitri Shah, Gabriel Berestein Lopez, Anil Sood, George Calin. Therapeutic synergy between novel tumor suppressor miR-520d-3p and EphA2-targeting siRNA in ovarian cancer. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 1455. doi:10.1158/1538-7445.AM2014-1455

Background. Posttranscriptional regulation is a critical control point for the expression of genes that promote or retard tumor growth. The mRNA-binding protein hnRNP A1 is required for the processing of miR-18a, an inhibitor of k-ras expression. In this study we hypothesized that downmodulation of hnRNP A1 by miR-25 and miR-15a controls the expression of miR-18a and k-ras by modulating nuclear and cytoplasmic miRNA processing at the posttranscriptional level. Methods. In this study, we determined the expression of hnRNP A1 at mRNA and protein levels in three parental ovarian cancer cells lines (Skov3ip1, HeyA8, and A2780) and their chemotherapy-resistant derivatives (Skov3-TR, HeyA8 MDR, and A2780 cp20). We also predicted in silico which miRNAS can target hnRNP A1 and confirmed the miRNA expression by real-time PCR. Moreover, we inhibited miR-25 and mir-15a to determine their tumorigenic potential in vitro. We also correlated the expression of miR-25 and miR-15a and/or miR-18a and k-ras expression in the TCGA data. Results. Downregulation of hnRNP A1 at the RNA and protein levels was observed in the taxane-resistant cell lines but not in the cisplatin-resistant cell line. Furthermore, we predicted in silico that miR-25and miR-15a can target hnRNP A1 and confirmed the overexpression of these microRNAs in SKOV3-TR (5- and 3-fold, respectively) and HeyA8 MDR (3-fold) by real-time PCR. We also analyzed overall survival, trying to find a correlation between k-ras and miR-15a (high 23.77, low 33.97 months), k-ras and miR-25 (high 16.95, low 35.21 months), and the combination of k-ras, miR-25, and miR18a (k-ras high, miR25 high, mir18a low, 20.73 months; k-ras low, miR25 low, mir18a high, 31.49 months). Comparison of these data with a validation set yielded similar results. Conclusion. These results underscore the importance of a previously uncharacterized circuit of posttranscriptional regulation between miR-25 or -15a and RNA-binding protein hnRNP A1 that regulates miR-18a and k-ras expression. This circuit represents a unique opportunity for novel therapeutics approaches. Citation Format: Cristian Rodriguez-Aguayo, Paloma Monroig, Maria I. Almeida, Cristina Ivan, Vianey Gonzalez-Villasana, Maitri Y. Shah, Anil K. Sood, George Calin, Gabriel Lopez-Berestein. Downregulation of hnRNP A1 by miRNAs as a new mechanism of survival in ovarian cancer. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 539. doi:10.1158/1538-7445.AM2014-539

MicroRNAs ( miRNAs ) are evolutionarily conserved, small, regulatory RNAs that negatively regulate gene expression. Extensive research in the last decade has implicated miRNAs as master regulators of cellular processes with essential role in cancer initiation, progression, and metastasis, making them promising therapeutic tools for cancer management. In this article, we will briefly review the structure, biogenesis, functions, and mechanism of action of these miRNAs , followed by a detailed analysis of the therapeutic potential of these miRNAs . We will focus on the strategies presently used for miRNA therapy; discuss their use and drawbacks; and the challenges and future directions for the development of miRNA ‐based therapy for human cancers. WIREs RNA 2014, 5:537–548. doi: 10.1002/wrna.1229 This article is categorized under: RNA in Disease and Development > RNA in Disease RNA in Disease and Development > RNA in Development