Maria Inês Almeida

Long non-coding RNAs and cancer: a new frontier of translational research?

Tiling array and novel sequencing technologies have made available the transcription profile of the entire human genome. However, the extent of transcription and the function of genetic elements that occur outside of protein-coding genes, particularly those involved in disease, are still a matter of debate. In this review, we focus on long non-coding RNAs (lncRNAs) that are involved in cancer. We define lncRNAs and present a cancer-oriented list of lncRNAs, list some tools (for example, public databases) that classify lncRNAs or that scan genome spans of interest to find whether known lncRNAs reside there, and describe some of the functions of lncRNAs and the possible genetic mechanisms that underlie lncRNA expression changes in cancer, as well as current and potential future applications of lncRNA research in the treatment of cancer.

MicroRNA history: discovery, recent applications, and next frontiers.

Since 1993, when the first small non-coding RNA was identified, our knowledge about microRNAs has grown exponentially. In this review, we focus on the main progress in this field and discuss the most important findings under a historical perspective. In addition, we examine microRNAs as markers of disease diagnosis and prognosis, and as new therapeutic targets.

Strand-Specific miR-28-5p and miR-28-3p Have Distinct Effects in Colorectal Cancer Cells

BACKGROUND & AIMS MicroRNAs (miRNAs) can promote or inhibit tumor growth and are therefore being developed as targets for cancer therapies. They are diverse not only in the messenger RNAs (mRNA) they target, but in their production; the same hairpin RNA structure can generate mature products from each strand, termed 5p and 3p, that can bind different mRNAs. We analyzed the expression, functions, and mechanisms of miR-28-5p and miR-28-3p in colorectal cancer (CRC) cells. METHODS We measured levels of miR-28-5p and miR-28-3p expression in 108 CRC and 49 normal colorectal samples (47 paired) by reverse transcription, quantitative real-time polymerase chain reaction. The roles of miR-28 in CRC development were studied using cultured HCT116, RKO, and SW480 cells and tumor xenograft analyses in immunodeficient mice; their mRNA targets were also investigated. RESULTS miR-28-5p and miR-28-3p were down-regulated in CRC samples compared with normal colon samples. Overexpression of miRNAs in CRC cells had different effects and the miRNAs interacted with different mRNAs: miR-28-5p altered expression of CCND1 and HOXB3, whereas miR-28-3p bound NM23-H1. Overexpression of miR-28-5p reduced CRC cell proliferation, migration, and invasion in vitro, whereas miR-28-3p increased CRC cell migration and invasion in vitro. CRC cells overexpressing miR-28 developed tumors more slowly in mice compared with control cells, but miR-28 promoted tumor metastasis in mice. CONCLUSION miR-28-5p and miR-28-3p are transcribed from the same RNA hairpin and are down-regulated in CRC cells. Overexpression of each has different effects on CRC cell proliferation and migration. Such information has a direct application for the design of miRNA gene therapy trials.

MicroRNA down-regulated in human cholangiocarcinoma control cell cycle through multiple targets involved in the G1/S checkpoint

MicroRNAs (miRs) recently emerged as prominent regulators of cancer processes. In the current study we aimed at elucidating regulatory pathways and mechanisms through which miR‐494, one of the miR species found to be down‐regulated in cholangiocarcinoma (CCA), participates in cancer homeostasis. miR‐494 was identified as down‐regulated in CCA based on miR arrays. Its expression was verified with quantitative real‐time reverse‐transcription polymerase chain reaction (qRT‐PCR). To enforce miR expression, we employed both transfection methods, as well as a retroviral construct to stably overexpress miR‐494. Up‐regulation of miR‐494 in cancer cells decreased growth, consistent with a functional role. mRNA arrays of cells treated with miR‐494, followed by pathway analysis, suggested that miR‐494 impacts cell cycle regulation. Cell cycle analyses demonstrated that miR‐494 induces a significant G1/S checkpoint reinforcement. Further analyses demonstrated that miR‐494 down‐regulates multiple molecules involved in this transition checkpoint. Luciferase reporter assays demonstrated a direct interaction between miR‐494 and the 3′‐untranslated region of cyclin‐dependent kinase 6 (CDK6). Last, xenograft experiments demonstrated that miR‐494 induces a significant cancer growth retardation in vivo. Conclusion: Our findings demonstrate that miR‐494 is down‐regulated in CCA and that its up‐regulation induces cancer cell growth retardation through multiple targets involved in the G1‐S transition. These findings support the paradigm that miRs are salient cellular signaling pathway modulators, and thus represent attractive therapeutic targets. miR‐494 emerges as an important regulator of CCA growth and its further study may lead to the development of novel therapeutics. (HEPATOLOGY 2011)

The clinical and biological significance of MIR-224 expression in colorectal cancer metastasis

Objective MicroRNA (miRNA) expression profile can be used as prognostic marker for human cancers. We aim to explore the significance of miRNAs in colorectal cancer (CRC) metastasis. Design We performed miRNA microarrays using primary CRC tissues from patients with and without metastasis, and validated selected candidates in 85 CRC samples by quantitative real-time PCR (qRT-PCR). We tested metastatic activity of selected miRNAs and identified miRNA targets by prediction algorithms, qRT-PCR, western blot and luciferase assays. Clinical outcomes were analysed in six sets of CRC cases (n=449), including The Cancer Genome Atlas (TCGA) consortium and correlated with miR-224 status. We used the Kaplan–Meier method and log-rank test to assess the difference in survival between patients with low or high levels of miR-224 expression. Results MiR-224 expression increases consistently with tumour burden and microsatellite stable status, and miR-224 enhances CRC metastasis in vitro and in vivo. We identified SMAD4 as a miR-224 target and observed negative correlation (Spearman Rs=−0.44, p<0.0001) between SMAD4 and miR-224 expression in clinical samples. Patients with high miR-224 levels display shorter overall survival in multiple CRC cohorts (p=0.0259, 0.0137, 0.0207, 0.0181, 0.0331 and 0.0037, respectively), and shorter metastasis-free survival (HR 6.51, 95% CI 1.97 to 21.51, p=0.0008). In the TCGA set, combined analysis of miR-224 with SMAD4 expression enhanced correlation with survival (HR 4.12, 95% CI 1.1 to 15.41, p=0.0175). Conclusions MiR-224 promotes CRC metastasis, at least in part, through the regulation of SMAD4. MiR-224 expression in primary CRC, alone or combined with its targets, may have prognostic value for survival of patients with CRC.

Modulation of MicroRNA-194 and cell migration by HER2-targeting trastuzumab in breast cancer

Trastuzumab, a humanized monoclonal antibody directed against the extracellular domain of the HER2 oncoprotein, can effectively target HER2-positive breast cancer through several mechanisms. Although the effects of trastuzumab on cancer cell proliferation, angiogenesis and apoptosis have been investigated in depth, the effect of trastuzumab on microRNA (miRNA) has not been extensively studied. We have performed miRNA microarray profiling before and after trastuzumab treatment in SKBr3 and BT474 human breast cancer cells that overexpress HER2. We found that trastuzumab treatment of SKBr3 cells significantly decreased five miRNAs and increased three others, whereas treatment of BT474 cells significantly decreased two miRNAs and increased nine. The only change in miRNA expression observed in both cell lines following trastuzumab treatment was upregulation of miRNA-194 (miR-194) that was further validated in vitro and in vivo. Forced expression of miR-194 in breast cancer cells that overexpress HER2 produced no effect on apoptosis, modest inhibition of proliferation, significant inhibition of cell migration/invasion in vitro and significant inhibition of xenograft growth in vivo. Conversely, knockdown of miR-194 promoted cell migration. Increased miR-194 expression markedly reduced levels of the cytoskeletal protein talin2 and specifically inhibited luciferase reporter activity of a talin2 wild-type 3′-untranslated region, but not that of a mutant reporter, indicating that talin2 is a direct downstream target of miR-194. Trastuzumab treatment inhibited breast cancer cell migration and reduced talin2 expression in vitro and in vivo. Knockdown of talin2 inhibited cell migration/invasion. Knockdown of trastuzumab-induced miR-194 expression with a miR-194 inhibitor compromised trastuzumab-inhibited cell migration in HER2-overexpressing breast cancer cells. Consequently, trastuzumab treatment upregulates miR-194 expression and may exert its cell migration-inhibitory effect through miR-194-mediated downregulation of cytoskeleton protein talin2 in HER2-overexpressing human breast cancer cells.

Extracellular Vesicles: Immunomodulatory messengers in the context of tissue repair/regeneration.

&NA; Inflammation is a complex and highly regulated biological process, crucial for a variety of functions in the human body, from host response against infectious agents to initiation of repair/regeneration of injured tissues. In the context of tissue repair, the action of different immune cell populations and their interplay with tissue specific cells, including stem cells, is still being uncovered. Extracellular Vesicles (EV) are small membrane vesicles secreted by cells in a controlled manner, which can act locally and systemically. The ability of EV to influence tissue repair and regeneration has been proposed as a physiologically intelligent and targeted strategy of cell communication. Herein, the role of EV in tissue repair is reviewed, summarising first their contribution to the regulation of immune cell function, and discussing the implications for the resolution of inflammation during repair. Next, the impact of EV on cell proliferation and differentiation, and on extracellular matrix remodelling, key aspects of the subsequent phases of tissue repair, is addressed. Finally, EV‐based therapies are discussed, focusing on the application of naturally produced EV, and the use of EV as delivery vehicles. Graphical Abstract Figure. No caption available.

miR-195 in human primary mesenchymal stromal/stem cells regulates proliferation, osteogenesis and paracrine effect on angiogenesis

Mesenchymal Stromal/Stem Cells (MSC) are currently being explored in diverse clinical applications, including regenerative therapies. Their contribution to regeneration of bone fractures is dependent on their capacity to proliferate, undergo osteogenesis and induce angiogenesis. This study aimed to uncover microRNAs capable of concomitantly regulate these mechanisms. Following microRNA array results, we identified miR-195 and miR-497 as downregulated in human primary MSC under osteogenic differentiation. Overexpression of miR-195 or miR-497 in human primary MSC leads to a decrease in osteogenic differentiation and proliferation rate. Conversely, inhibition of miR-195 increased alkaline phosphatase expression and activity and cells proliferation. Then, miR-195 was used to study MSC capacity to recruit blood vessels in vivo. We provide evidence that the paracrine effect of MSC on angiogenesis is diminishedwhen cells over-express miR-195. VEGF may partially mediate this effect, as its expression and secreted protein levels are reduced by miR-195, while increased by anti-miR-195, in human MSC. Luciferase reporter assays revealed a direct interaction between miR-195 and VEGF 3′-UTR in bone cancer cells. In conclusion, our results suggest that miR-195 regulates important mechanisms for bone regeneration, specifically MSC osteogenic differentiation, proliferation and control of angiogenesis; therefore, it is a potential target for clinical bone regenerative therapies.

Decoy activity through microRNAs: the therapeutic implications

Introduction: microRNAs (miRNAs), small noncoding RNAs, are deregulated in several diseases including cancer. miRNAs regulate gene expression at a posttranscriptional level by binding to 5′UTR, coding regions or 3′UTR of messenger RNAs (mRNA), inhibiting mRNA translation or causing mRNA degradation. The same miRNA can have multiple mRNA targets, and the same mRNA can be regulated by various miRNAs. Areas covered: Recently, seminal contributions by several groups have implicated miRNAs as components of an RNA–RNA language that involves cross-talk between competing endogenous RNAs through a decoy mechanism. We review the studies that described miRNAs as players in a biological decoy activity. miRNAs can either be trapped by competing endogenous RNAs or interact with proteins that have binding sites for mRNAs. Expert opinion: The miRNA decoy functions have implications for the design of therapeutic approaches in human diseases, including specific ways to overcome resistance to drug therapy and future miRNA-based clinical trials design.

Circulating extracellular vesicles: Their role in tissue repair and regeneration

Extracellular vesicles (EVs) have been a growing interest of the scientific community in recent years due to the wide possibilities of their evaluation as biomarkers of disease, and their potential to be used as therapeutic agents or vehicles. EVs that circulate in plasma carry proteins and nucleic acids, potentially to distant locations in the body where they can interfere with several cellular processes. To aid understanding of this rapidly evolving field, circulating EVs, including immune cell-derived ones, are reviewed here. Their cellular origins and described functions are discussed in a perspective of their contribution to regenerative processes. Different techniques for EV engineering and examples of their application are reviewed as a strong future direction of EV research. A summary of important aspects yet to be addressed ties up this review.