TWIST1-Induced miR-424 Reversibly Drives Mesenchymal Programming while Inhibiting Tumor Initiation

Epithelial-to-mesenchymal transition (EMT) is a dynamic process that relies on cellular plasticity. Recently, the process of an oncogenic EMT, followed by a reverse mesenchymal-to-epithelial transition (MET), has been implicated as critical in the metastatic colonization of carcinomas. Unlike governance of epithelial programming, regulation of mesenchymal programming is not well understood in EMT. Here, we describe and characterize the first microRNA that enhances exclusively mesenchymal programming. We demonstrate that miR-424 is upregulated early during a TWIST1 or SNAI1-induced EMT, and that it causes cells to express mesenchymal genes without affecting epithelial genes, resulting in a mixed/intermediate EMT. Furthermore, miR-424 increases motility, decreases adhesion, and induces a growth arrest, changes associated with a complete EMT that can be reversed when miR-424 expression is lowered, concomitant with an MET-like process. Breast cancer patient miR-424 levels positively associate with TWIST1/2 and EMT-like gene signatures, and miR-424 is increased in primary tumors versus matched normal breast. However, miR-424 is downregulated in patient metastases versus matched primary tumors. Correspondingly, miR-424 decreases tumor initiation and is posttranscriptionally downregulated in macrometastases in mice, suggesting the need for biphasic expression of miR-424 to transit the EMT-MET axis. Next-generation RNA sequencing revealed miR-424 regulates numerous EMT and cancer stemness-associated genes, including TGFBR3, whose downregulation promotes mesenchymal phenotypes, but not tumor-initiating phenotypes. Instead, we demonstrate that increased MAPK-ERK signaling is critical for miR-424-mediated decreases in tumor-initiating phenotypes. These findings suggest miR-424 plays distinct roles in tumor progression, potentially facilitating earlier, but repressing later, stages of metastasis by regulating an EMT-MET axis.

microRNA expression profiling identifies a four microRNA signature as a novel diagnostic and prognostic biomarker in triple negative breast cancers

Triple Negative Breast Cancers (TNBC) is a heterogeneous disease at the molecular and clinical level with poor outcome. Molecular subclassification of TNBCs is essential for optimal use of current therapies and for development of new drugs. microRNAs (miRNA) are widely recognized as key players in cancer progression and drug resistance; investigation of their involvement in a TNBC cohort may reveal biomarkers for diagnosis and prognosis of TNBC. Here we stratified a large TNBC cohort into Core Basal (CB, EGFR and/or CK5, 6 positive) and five negative (5NP) if all markers are negative. We determined the complete miRNA expression profile and found a subset of miRNAs specifically deregulated in the two subclasses.

We identified a 4-miRNA signature given by miR-155, miR-493, miR-30e and miR-27a expression levels, that allowed subdivision of TNBCs not only into CB and 5NP subgroups (sensitivity 0.75 and specificity 0.56; AUC=0.74) but also into high risk and low risk groups. We tested the diagnostic and prognostic performances of both the 5 IHC marker panel and the 4-miRNA expression signatures, which clearly identify worse outcome patients in the treated and untreated subcohorts. Both signatures have diagnostic and prognostic value, predicting outcomes of patient treatment with the two most commonly used chemotherapy regimens in TNBC: anthracycline or anthracycline plus taxanes. Further investigation of the patients' overall survival treated with these regimens show that regardless of IHC group subdivision, taxanes addition did not benefit patients, possibly due to miRNA driven taxanes resistance. TNBC subclassification based on the 5 IHC markers and on the miR-155, miR-493, miR-30e, miR-27a expression levels are powerful diagnostic tools. Treatment choice and new drug development should consider this new subtyping and miRNA expression signature in planning low toxicity, maximum efficacy therapies.

Abstract 2766: Inhibition of Chk1 and Wee1 as a new therapeutic approach in Mantle Cell Lymphoma

Mantle Cell Lymphoma (MCL) is an aggressive lymphoma, for which there is not yet a standard therapy. Deregulation of cell cycle is its main pathogenic feature due to the presence of the t(11;14)(q13;q32) translocation, which leads to cyclin D1 over-expression and to frequent alterations in cell cycle and DNA damage response. Chk1 and Wee1 proteins regulate replication initiation, replication fork stability, and mitotic entry. Combined treatment of Chk1 and Wee1 inhibitors has a strong synergistic cytotoxic effect in solid tumors, but little is known on their effect in hematologic cancer such as lymphomas. The effects of a Chk1 inhibitor (PF-00477736) and a Wee1 inhibitor (MK-1775) alone or in combination was investigated in a panel of 10 MCL cell lines. The PF-00477736 median IC50 value was 30 nM, significantly lower than in 9 solid tumor models (337 nM, p=0.0041) and in 8 hematologic tumors (184 nM, p= 0.0057). The MK-1775 median IC50 value was 106 nM, significantly lower than in solid tumors (615 nM, p<0.0001), but not than in other hematologic cells (287 nM). A strong synergism of the combination was observed in all MCL cell lines. Detailed molecular analysis showed that the combination caused a general deregulation of cell cycle with an increased activity of CDK2 and CDK1 and an activation of apoptosis. Inhibition of the CDK4/6-CyclinD1 complex with the selective inhibitor PD0332991 either strongly or slightly neutralize the cytotoxic effect of PF-00477736 and MK-1775 respectively in Jeko-1 MCL cells. In addition, the sensitivity to PF-00477736 and MK-1775 was higher in 2 multiple myeloma (MM) cell lines bearing the t(11;14) deregulating cyclinD1 than in 3 MM cell lines without the translocation (with median IC50 values 40 times lower for PF-00477736 and two times lower for MK-1775). The combination of Chk1 and Wee1 inhibitors was then tested in vivo in nude mice bearing Jeko-1 MCL and important tumor regressions were observed at drug doses lower than the ones used in solid tumors xenografts (best T/C%=0.54%). Tumor samples obtained from xenografts untreated, treated with single drug or the combination were profiled for gene expression and the analysis corroborated that genes involved in apoptosis were up-regulated after combined treatment in vivo. In conclusion, our data provide a strong preclinical evidence for the role of Chk1 and Wee1 inhibitors as new therapeutic approach in MCL and warrant investigation in clinical setting.

Citation Format: Laura Carrassa, Rosaria Chilà, Alessandra Basana, Francesca Ricci, Federica Guffanti, Monica Lupi, Andrea Rinaldi, Luciano Cascione, Francesco Bertoni, Massimo Broggini, Giovanna Damia. Inhibition of Chk1 and Wee1 as a new therapeutic approach in Mantle Cell Lymphoma. [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 2766. doi:10.1158/1538-7445.AM2014-2766

Abstract 2604: Characterization of the activity and the mechanism of action of the new retinoid derivative ST5589 in pre-clinical models of lymphomas: involvement of MYC and cell cycle genes

Innovative and effective treatments are necessary for lymphomas that are common and still deadly cancers for many patients. Atypical retinoids show cytotoxic activity in different pre-clinical tumor models even though their mechanism of action is still largely unclear. Here, we report activity and mechanistic data with ST5589 (adarotene derivative), an active representative of this new class of agents (1), in pre-clinical lymphoma models.

Methods. Cell lines from diffuse large B-cell lymphoma (DLBCL, n=17), mantle cell lymphoma (MCL, n=4), splenic marginal zone lymphoma (SMZL, n=3) underwent 72 hr exposure to increasing doses of ST5589 (Sigma Tau, Pomezia, IT) to assess anti-proliferative activity by MTT assay. Apoptosis was assessed by Annexin-V/7-AAD staining. Gene expression profiling (GEP) was done with Illumina HumanHT-12 Expression BeadChips at baseline on all cell lines and, in triplicate, on 1 ABC- (TMD8) and 1 GCB-DLBCL (DOHH2) cell line treated with 300 nM ST5589 or DMSO for 8 hrs. Cell lines with IC50 < than the median were defined as sensitive. GEP/IC50 correlation was assessed by Pearson correlation. Differential expression analysis was performed with LIMMA, GSEA, Metacore.

Results. Median IC50 was 235 nM (91-2652) for all the cell lines without significant differences among histological subtypes or between GCB- and ABC-DLBCL: DLBCL, 269 (97-2652); GCB-DLBCL 250, (97-1684); ABC-DLBCL, 531 (181-2625); MCL, 237 (91-401); SMZL, 144 (135-203). ST5589 induced apoptosis in 4/5 DLBCL cell lines (DOHH2, TMD8, SU-DHL-2, VAL). GEP in two DLBCL treated with ST5589 or DMSO was performed, and ST5589 significantly affected transcripts involved in multiple cell cycle-related gene-sets. Aurora kinase A coding gene was one of the most down-regulated.

MYC translocation was associated with lower IC50 (P 0.045) and higher number of responders (P 0.021). Transcripts associated with resistance to ST5589 were significantly enriched of genes involved in MYD88/TLR/STAT3 signaling and MAPK pathway, while transcripts associated with sensitivity were enriched of MYC target genes, genes high in Burkitt lymphoma, and involved in cellular respiration, and proteoglycan biosynthesis.

Conclusions. ST5589 showed anti-proliferative and cytotoxic preclinical activity in lymphoma, affecting cell-cycle regulation. While MYD88, TLR, STAT3 and MAPK pathways activation correlated with reduced drug activity, MYC deregulation was associated with sensitivity to ST5589. Our data, together with direct cytotoxicity and immune-system mediated activity reported for the parent compound adarotene ST1926 (2), make ST5589 worth of further studies in MYC-driven lymphomas as a representative of the innovative therapeutic class of atypical retinoids.

References

1 Giannini et al. Bioorganic and Med Chemistry 2012, 20: 2405-15

2 Pisano et al. Proceedings AACR 2004 Abstract #2075

Citation Format: Elena Bernasconi, Ivo Kwee, Andrea Rinaldi, Luciano Cascione, Maurilio Ponzoni, Loredana Vesci, Giuseppe Giannini, Anastasios Stathis, Emanuele Zucca, Eugenio Gaudio, Francesco Bertoni. Characterization of the activity and the mechanism of action of the new retinoid derivative ST5589 in pre-clinical models of lymphomas: involvement of MYC and cell cycle genes. [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 2604. doi:10.1158/1538-7445.AM2014-2604

MicroRNA-135b promotes cancer progression by acting as a downstream effector of oncogenic pathways in colon cancer

MicroRNA deregulation is frequent in human colorectal cancers (CRCs), but little is known as to whether it represents a bystander event or actually drives tumor progression in vivo. We show that miR-135b overexpression is triggered in mice and humans by APC loss, PTEN/PI3K pathway deregulation, and SRC overexpression and promotes tumor transformation and progression. We show that miR-135b upregulation is common in sporadic and inflammatory bowel disease-associated human CRCs and correlates with tumor stage and poor clinical outcome. Inhibition of miR-135b in CRC mouse models reduces tumor growth by controlling genes involved in proliferation, invasion, and apoptosis. We identify miR-135b as a key downsteam effector of oncogenic pathways and a potential target for CRC treatment.

miR-Synth: a computational resource for the design of multi-site multi-target synthetic miRNAs

RNAi is a powerful tool for the regulation of gene expression. It is widely and successfully employed in functional studies and is now emerging as a promising therapeutic approach. Several RNAi-based clinical trials suggest encouraging results in the treatment of a variety of diseases, including cancer. Here we present miR-Synth, a computational resource for the design of synthetic microRNAs able to target multiple genes in multiple sites. The proposed strategy constitutes a valid alternative to the use of siRNA, allowing the employment of a fewer number of molecules for the inhibition of multiple targets. This may represent a great advantage in designing therapies for diseases caused by crucial cellular pathways altered by multiple dysregulated genes. The system has been successfully validated on two of the most prominent genes associated to lung cancer, c-MET and Epidermal Growth Factor Receptor (EGFR). (See http://microrna.osumc.edu/mir-synth).

Androgen receptor status is a prognostic marker in non-basal triple negative breast cancers and determines novel therapeutic options

Triple negative breast cancers are a heterogeneous group of tumors characterized by poor patient survival and lack of targeted therapeutics. Androgen receptor has been associated with triple negative breast cancer pathogenesis, but its role in the different subtypes has not been clearly defined. We examined androgen receptor protein expression by immunohistochemical analysis in 678 breast cancers, including 396 triple negative cancers. Fifty matched lymph node metastases were also examined. Association of expression status with clinical (race, survival) and pathological (basal, non-basal subtype, stage, grade) features was also evaluated. In 160 triple negative breast cancers, mRNA microarray expression profiling was performed, and differences according to androgen receptor status were analyzed. In triple negative cancers the percentage of androgen receptor positive cases was lower (24.8% vs 81.6% of non-triple negative cases), especially in African American women (16.7% vs 25.5% of cancers of white women). No significant difference in androgen receptor expression was observed in primary tumors vs matched metastatic lesions. Positive androgen receptor immunoreactivity was inversely correlated with tumor grade (p<0.01) and associated with better overall patient survival (p = 0.032) in the non-basal triple negative cancer group. In the microarray study, expression of three genes (HER4, TNFSF10, CDK6) showed significant deregulation in association with androgen receptor status; eg CDK6, a novel therapeutic target in triple negative cancers, showed significantly higher expression level in androgen receptor negative cases (p<0.01). These findings confirm the prognostic impact of androgen receptor expression in non-basal triple negative breast cancers, and suggest targeting of new androgen receptor-related molecular pathways in patients with these cancers.

MIDClass: microarray data classification by association rules and gene expression intervals

We present a new classification method for expression profiling data, called MIDClass (Microarray Interval Discriminant CLASSifier), based on association rules. It classifies expressions profiles exploiting the idea that the transcript expression intervals better discriminate subtypes in the same class. A wide experimental analysis shows the effectiveness of MIDClass compared to the most prominent classification approaches.

A Sleeping Beauty screen reveals NF-kB activation in CLL mouse model

TCL1 oncogene is overexpressed in aggressive form of human chronic lymphocytic leukemia (CLL) and its dysregulation in mouse B cells causes a CD5-positive leukemia similar to the aggressive form of human CLLs. To identify oncogenes that cooperate with Tcl1, we performed genetic screen in Eμ-TCL1 mice using Sleeping Beauty transposon-mediated mutagenesis. Analysis of transposon common insertion sites identified 7 genes activated by transposon insertions. Overexpression of these genes in mouse CLL was confirmed by real time reverse transcription-polymerase chain reaction. Interestingly, the main known function of 4 of 7 genes (Nfkb1, Tab2, Map3K14, and Nfkbid) is participation in or activation of the nuclear factor-kB (NF-kB) pathway. In addition, activation of the NF-kB is 1 of main functions of Akt2, also identified in the screen. These findings demonstrate cooperation of Tcl1 and the NF-kB pathway in the pathogenesis of aggressive CLL. Identification cooperating cancer genes will result in the development of combinatorial therapies to treat CLL.

Micro-RNA signature differences in lung adenocarcinoma with specific driver alterations

11066

Background: Oncogenic driving alterations define types of lung adenocarcinoma with different prognosis and sensitivity to targeted agents. MicroRNAs (miRNAs) are a new class of non-coding RNAs involved in gene expression regulation. How miRNAs are dysregulated in lung cancer with ALK translocation, EGFR or KRAS mutation is unknown. In this study we aimed to identify miRNA signatures according to the presence of specific driver and to correlate miRNAs deregulation with patient outcome. Methods: The study was conducted in a cohort of 70 lung cancer patients (pts) including 18 ALK+ tumors, 11 ALK-/EGFR mutation+, 15 ALK-/KRAS mutation+, 26 ALK-/EGFR and KRAS wild-type and defined as triple negative. Matched normal lung tissue from 18 cases representative of the entire cohort were also included onto the analysis. RNA was isolated from formalin-fixed paraffin-embedded tissue (FFPE), using the Recover ALL kit (Ambion). NanoString nCounter system platform was used to generate the miRNA profile. We used Limma to test for differential expression analysis of data. The miR-515 family expression between tissues was validated by RT-qPCRs, analyzed using the parametric t-test (unpaired, 2-tailed for validation). Results: miRNA expression profile clusters distinctly ALK+ pts from ALK- and normal lung tissue. Within the ALK- group we found specific miRNAs subsets able to sub-stratify KRAS versus EGFR careers clustering sharply triple negative versus EGFR mutation+ and triple negative versus KRAS mutation+. miRNAs belonging to the miR-515 family seems to be the most deregulated in the ALK+ versus ALK-. Although their expression is stably high in normal tissues and ALK+ class, they are highly downregulated in KRAS mutated versus EGFR mutated and versus triple negative (p-value <0.001 for all comparisons). Conclusions: miRNAs profile significantly differs in pts with ALK translocation, EGFR mutations and KRAS mutations. Analysis of miR-515 family members is ongoing in order to correlate their expression levels with pts’ outcome. In vitro modulation of miR-515 family expression levels, together with drugs treatment are ongoing in order to find possible chemo-resistance/chemo-sensitivity miRNA dependent, in ALK+ and ALK- model.

In vivo NCL targeting affects breast cancer aggressiveness through miRNA regulation

Numerous studies have described the altered expression and the causal role of microRNAs (miRNAs) in human cancer. However, to date, efforts to modulate miRNA levels for therapeutic purposes have been challenging to implement. Here we find that nucleolin (NCL), a major nucleolar protein, posttranscriptionally regulates the expression of a specific subset of miRNAs, including miR-21, miR-221, miR-222, and miR-103, that are causally involved in breast cancer initiation, progression, and drug resistance. We also show that NCL is commonly overexpressed in human breast tumors and that its expression correlates with that of NCL-dependent miRNAs. Finally, inhibition of NCL using guanosine-rich aptamers reduces the levels of NCL-dependent miRNAs and their target genes, thus reducing breast cancer cell aggressiveness both in vitro and in vivo. These findings illuminate a path to novel therapeutic approaches based on NCL-targeting aptamers for the modulation of miRNA expression in the treatment of breast cancer.

Abstract 3061: Micro-RNA signature differences in lung cancer patients with ALK translocation, EGFR mutations and KRAS mutations

Background: Oncogenic driving mutations identify lung adenocarcinoma with different prognosis and sensitivity to targeted therapies. miRNAs are a new class of non-coding RNA involved in gene expression regulation and recent studies have suggested that miRNAs could be useful for stratifying lung cancer subtypes. How miRNAs are dysregulated in lung cancer patients with ALK translocation, EGFR or KRAS mutation is unknown. Aim of the present study is to identify miRNA signature differences according to the presence of specific oncogenic driver and correlation between miRNAs deregulation and drug response.

Materials and methods: The study was conducted in a cohort of 70 lung cancer patients including 68 primary cancer tissue (17 ALK positive tumors, 11 ALK negative EGFR positive tumors, 15 ALK negative KRAS positive tumors, 24 ALK negative EGFR and KRAS negative tumors defined as wild-type) with matched normal lung tissue (N=18) and 2 metastatic tissue. RNA was isolated from formalin-fixed paraffin-embedded tissue (FFPE), using the Recover ALL kit (Ambion). Data were processed according to manufacture guidelines. We used Limma to test for differential expression analysis of data. The miRNAs expression between tissues for all RT-qPCR was analyzed using the parametric t-test (unpaired, 2-tailed for validation).

Results: miRNA expression profile, cluster distinctly ALK+ patients from ALK- and normal lung tissue. Furthermore we found specific miRNAs subsets, within the ALK- group, able to sub-stratify KRAS versus EGFR careers and cluster sharply wild-type versus EGFR and wild-type versus KRAS as well. miRNAs belonging to the miR-515 family seems to be the most deregulated in the ALK+ vs ALK- comparison. Although their expression is stably high in normal tissues and ALK+ class they are highly downregulated in KRAS mutated versus EGFR mutated and versus ALK-/KRAS wild type/EGFR wild type (p-value &lt;0.001 for all comparisons).

Conclusions: miRNAs profile significantly differs in lung cancer patients with ALK translocation, EGFR mutations and KRAS mutations. Molecular analysis of the pathways involving the miR-515 family is ongoing in order to correlate their expression levels with patients’ outcome. Since miRNAs can induce resistance or sensitize to chemotherapies, in vitro modulation of miR-515 family expression level together with drugs test are ongoing in order to find better targeted therapies for ALK+ and ALK- patients.

Citation Format: Pierluigi Gasparini, Lorenza Landi, Stefania Carasi, Carmelo Tibaldi, Luciano Cascione, Greta Alì, Armida D'Incecco, Gabriele Minuti, Antonio Chella, Gabriella Fontanini, Federico Cappuzzo, Carlo M. Croce. Micro-RNA signature differences in lung cancer patients with ALK translocation, EGFR mutations and KRAS mutations. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 3061. doi:10.1158/1538-7445.AM2013-3061

Note: This abstract was not presented at the AACR Annual Meeting 2013 because the presenter was unable to attend.

Abstract 1951: miRNA expression profile of Blastic plasmacytoid dendritic cell neoplasm

Background:

Blastic plasmacytoid dendritic cell neoplasm (BPDCN) is a rare neoplasm currently included among acute myeloid leukemias in the WHO classification. BPDCN is an orphan tumor characterized by an unknown biology with clinical aggressive course and dismal prognosis.

Only few studies explored its genetics, documenting a complex karyotype and sporadic genetic alterations. Unfortunately, data were based on a limited number of patients and lacked functional elucidation. Conversely, studies on the transcriptome only compared BPDCN with other leukemias, failing to identify pathogenetic events.

In this study we aimed to assess whether miRNA deregulation contribute to BPDCN pathogenesis and clinical behaviour.

Methods:

We studied by miRNA profiling (NanoString Technologies) 30 BPDCN samples, 9 normal plasmacytoid dendritic cell (pDCs) samples and the CAL-1 tumor cell line. In addition, 25 independent BPDCN cases were studied by qRT-PCR and IHC as validation. To investigate the functional consequences of miRNA deregulation, we also performed a global gene expression profile (GEP) analysis on the same cases by using the Illumina Whole Genome DASL Assay. We applied ANOVA and Student t-test to find genes and miRNAs differentially expressed between BPDCNs and normal pDCs. The selected miRNAs were further filtered based on their predicted impact on the GEP using Linear Discriminant Analysis, Spearman correlation and Gene Set Enrichment Analysis. Finally, the functional effects of selected miRNAs were assessed ex vivo on CAL-1 cell line.

Results:

We found that, according to the unsupervised analysis of miRNAs, BPDCN patients have a molecular signature well distinct from their normal counterpart.

The following supervised analysis identified a set of 114 miRNAs significantly deregulated whose aberrant expression might have a relevant impact on cancer-related cellular pathways.

Therefore, after validating their expression in an independent set of cases, we integrated the miRNA and mRNA expression profiles on the same patients, in order to assess the functional impact of deregulated miRNAs on gene expression profile.

Pathway analysis of the predicted miRNA target genes, revealed that most of them were involved in the same gene ontology category: miRNAs synergic action appeared to strongly affect the biological process of programmed cell death.

We thus focused on miRNA-mRNA anti-correlations affecting the apoptotic pathway: we transfected specific mimics and inhibitors into CAL-1 cell line; we evaluated their functional impact by gene expression profile and, finally, we confirmed their relation with specific targets by Luciferase assay.

In conclusion, for the first time we investigated the miRNA profile of BPDCN, defining previously uncovered molecular mechanisms underlying the pathogenesis of the disease. Specifically, we found a subset of miRNAs significantly deregulated and highly affecting the apoptotic pathway.

Citation Format: Maria Rosaria Sapienza, Fabio Fuligni, Maria Antonella Laginestra, Maura Rossi, Luciano Cascione, Alessandro Laganà, Claudio Agostinelli, Maryam Etebari, Anna Gazzola, Claudia Mannu, Elena Sabattini, Francesco Bacci, Carlo Maria Croce, Stefano Aldo Pileri, Pier Paolo Piccaluga. miRNA expression profile of Blastic plasmacytoid dendritic cell neoplasm. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 1951. doi:10.1158/1538-7445.AM2013-1951

Abstract 1122: In vivo NCL-targeting affects breast cancer aggressiveness through miRNA regulation

MicroRNAs (miRNAs) are noncoding single-stranded RNA molecules of ∼22 nucleotides in length. They have a critical role in regulating gene expression by targeting messenger RNAs (mRNAs) in a sequence-specific manner. Active mature miRNAs are produced from primary miRNA transcripts (pri-miRNAs) through sequential cleavages by the microprocessor complex, which includes DROSHA, DGCR8, and DICER proteins. Several miRNAs are specifically up-regulated in various types of tumors, and a wide range of studies have demonstrated how their down-regulation could potentially affect tumorigenesis, metastasis formation and drug resistance. However, most of these studies have indicated the possibility of modulating miRNA expression at the transcriptional level, while only a few focused on post-transcriptional control. Nucleolin (NCL) is a highly conserved multifunctional protein involved in ribosomal RNA (rRNA) biogenesis and in the stabilization of different mRNAs, in the nucleus and in the cytoplasm of normal and cancer cells. NCL was also found on the surface of different types of cancer cells, but not on their normal counterparts, shuttling between the inner and the outer part of the cell membrane. These observations suggested that NCL might be considered a cancer cell specific receptor, able to mediate tumor-selective uptake of specific ligands such as RNA and DNA G-rich aptamers. Here we show that NCL binds the terminal loop and promotes the maturation of a specific set of miRNAs, including miR-21, miR-103, miR-221 and miR-222, whose over-expression is causally associated with greater aggressiveness and resistance to anti-neoplastic therapies of several kind of tumors, such as breast cancer. Accordingly, a direct correlation between the expression levels of NCL and NCL-dependent miRNAs in human breast cancer samples was also observed. Conversely, NCL impairment down-regulated NCL-dependent miRNAs and up-regulates their target in vitro, affecting cancer cell proliferation, migration and anti-neoplastic drug resistance. Finally, we used AS1411, the first NCL-targeting G-rich aptamer that has reached phase II clinical trials for cancer therapy, to inhibit NCL activity in orthotopc xenograft models of breast cancer. Our in vivo data demonstrate that AS1411 down-regulates NCL-dependent miRNAs, hindering breast cancer metastasis. These findings provide insights into the molecular function of NCL in miRNA biology, as well as one of the first realistic strategies for miRNA regulation in cancer therapy.

Citation Format: Dario Palmieri, Luciana De Luca, Jessica Consiglio, Alberto Rocci, Tiffany Talabere, Claudia Piovan, Alessandro Lagana, Luciano Cascione, Jingwen Guan, Pierluigi Gasparini, Veronica Balatti, Vincenzo Coppola, Craig Hofmeister, Guido Marcucci, John Byrd, Stefano Volinia, Charles Shapiro, Michael Freitas, Carlo Croce, Flavia Pichiorri. In vivo NCL-targeting affects breast cancer aggressiveness through miRNA regulation. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 1122. doi:10.1158/1538-7445.AM2013-1122

Integrated microRNA and mRNA signatures associated with survival in triple negative breast cancer

Triple negative breast cancer (TNBC) is a heterogeneous disease at the molecular, pathologic and clinical levels. To stratify TNBCs, we determined microRNA (miRNA) expression profiles, as well as expression profiles of a cancer-focused mRNA panel, in tumor, adjacent non-tumor (normal) and lymph node metastatic lesion (mets) tissues, from 173 women with TNBCs; we linked specific miRNA signatures to patient survival and used miRNA/mRNA anti-correlations to identify clinically and genetically different TNBC subclasses. We also assessed miRNA signatures as potential regulators of TNBC subclass-specific gene expression networks defined by expression of canonical signal pathways.

Tissue specific miRNAs and mRNAs were identified for normal vs tumor vs mets comparisons. miRNA signatures correlated with prognosis were identified and predicted anti-correlated targets within the mRNA profile were defined. Two miRNA signatures (miR-16, 155, 125b, 374a and miR-16, 125b, 374a, 374b, 421, 655, 497) predictive of overall survival (P = 0.05) and distant-disease free survival (P = 0.009), respectively, were identified for patients 50 yrs of age or younger. By multivariate analysis the risk signatures were independent predictors for overall survival and distant-disease free survival. mRNA expression profiling, using the cancer-focused mRNA panel, resulted in clustering of TNBCs into 4 molecular subclasses with different expression signatures anti-correlated with the prognostic miRNAs.

Our findings suggest that miRNAs play a key role in triple negative breast cancer through their ability to regulate fundamental pathways such as: cellular growth and proliferation, cellular movement and migration, Extra Cellular Matrix degradation. The results define miRNA expression signatures that characterize and contribute to the phenotypic diversity of TNBC and its metastasis.

miR-EdiTar: a database of predicted A-to-I edited miRNA target sites

MOTIVATION

A-to-I RNA editing is an important mechanism that consists of the conversion of specific adenosines into inosines in RNA molecules. Its dysregulation has been associated to several human diseases including cancer. Recent work has demonstrated a role for A-to-I editing in microRNA (miRNA)-mediated gene expression regulation. In fact, edited forms of mature miRNAs can target sets of genes that differ from the targets of their unedited forms. The specific deamination of mRNAs can generate novel binding sites in addition to potentially altering existing ones.

RESULTS

This work presents miR-EdiTar, a database of predicted A-to-I edited miRNA binding sites. The database contains predicted miRNA binding sites that could be affected by A-to-I editing and sites that could become miRNA binding sites as a result of A-to-I editing.

AVAILABILITY

miR-EdiTar is freely available online at http://microrna.osumc.edu/mireditar.

CONTACT

alessandro.lagana@osumc.edu or carlo.croce@osumc.edu

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Use of microRNA (miR) expression profiling to identify distinct subclasses of triple-negative breast cancers (TNBC)

1007

Background: TNBC is divided into basal and non-basal subclasses. To further subclassify TNBC we performed microRNA (miR) expression profiles and linked them to patient overall survival. Methods: During 1996-2005, 365 consecutive TNBC (phenotypically estrogen, progesterone and HER2 negative by immunohistochemistry [IHC]) were identified from the NCCN Breast Cancer Data Base/Tumor Registry at OSU Medical Center. One hundred fifty-eight (43%) formalin-fixed paraffin embedded (FFPE) breast cancer and 40 normal breast tissue blocks were available and tissue cores were obtained for RNA. RNA was isolated using the Ambion recoverall total nucleic acid isolation kit and the expression of ~700 miRs was assessed for each sample using the nanoString nCounter method. A consensus-clustering algorithm (ConsensusClusterPlus, Bioconductor www.bioconductor.org) was used to identify subclasses of TNBC and Kaplan-Meier overall survival curves were compared using the log-rank test. Censoring occurred at the date of death from causes other than breast cancer or at time of the last known follow-up, whichever occurred first. The median follow-up was 67 mo. (range 4-171 mo.). Results: The median age was 52 yrs. (range 20-84 yrs.); 81% white and 9% African-American; stages I, II, and III were 31%, 54% and 15%, respectively; and most patients received adjuvant anthracycline-based regimens with (25%) or without taxanes (75%). The algorithm identified 5 distinct subclasses; 1 clustering with normal breast miR expression whereas the other 4 each had a unique pattern of deregulated miRs. The median overall survivals were significantly different across the 5 cancer subclasses (log-rank p=0.028) (Table). Conclusions: miR expression profiling identifies and discriminates 5 TNBC subclasses, which do not coincide with those identified as basal and non-basal by IHC. Molecular analyses are ongoing to associate the miR-based subclasses with specific clinical features or the expression of specific pathways. [Table: see text]

EGFR and MET receptor tyrosine kinase-altered microRNA expression induces tumorigenesis and gefitinib resistance in lung cancers

The involvement of the MET oncogene in de novo and acquired resistance of non-small cell lung cancers (NSCLCs) to tyrosine kinase inhibitors (TKIs) has previously been reported, but the precise mechanism by which MET overexpression contributes to TKI-resistant NSCLC remains unclear. MicroRNAs (miRNAs) negatively regulate gene expression, and their dysregulation has been implicated in tumorigenesis. To understand their role in TKI-resistant NSCLCs, we examined changes in miRNA that are mediated by tyrosine kinase receptors. Here we report that miR-30b, miR-30c, miR-221 and miR-222 are modulated by both epidermal growth factor (EGF) and MET receptors, whereas miR-103 and miR-203 are controlled only by MET. We showed that these miRNAs have important roles in gefitinib-induced apoptosis and epithelial-mesenchymal transition of NSCLC cells in vitro and in vivo by inhibiting the expression of the genes encoding BCL2-like 11 (BIM), apoptotic peptidase activating factor 1 (APAF-1), protein kinase C ɛ (PKC-ɛ) and sarcoma viral oncogene homolog (SRC). These findings suggest that modulation of specific miRNAs may provide a therapeutic approach for the treatment of NSCLCs.

Recombinant alpha-interferon 2b in the treatment of HIV-related thrombocytopenia

OBJECTIVE

To assess the efficacy and the mechanism of action of alpha-interferon (alpha-IFN) in the treatment of HIV-related thrombocytopenia.

METHODS

Thirteen HIV-positive subjects [nine men and four women with severe thrombocytopenia (platelets, < or = 30 x 10(9)/l)] were treated with alpha-IFN 2b alone at a dose of 3 x 10(6) U three times a week for 5 weeks. Haematological parameters, platelet kinetic and bone-marrow myeloid progenitor cultures [megakaryocyte colony-forming units (CFU-MK); granulocyte macrophage CFU (CFU-GM) and erythroid burst-forming units (BFU-E)] were evaluated before and after treatment in responsive subjects.

RESULTS

Seven out of 13 subjects showed a partial response (platelets, 50-149 x 10(9)/l) after alpha-IFN 2b therapy. Platelet survival as evaluated by 111In-oxine significantly increased, while platelet turnover showed a slight but not statistically significant increase after treatment. The growth of bone-marrow myeloid progenitor cells decreased after alpha-IFN 2b therapy, again without statistical significance.

CONCLUSION

alpha-IFN 2b may increase the platelet count in HIV-positive subjects with severe symptomatic thrombocytopenia by prolonging platelet survival. The immunomodulatory and antiviral action of this drug may be responsible for prolonged platelet survival.