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4. A bile-based microRNA signature for differentiating malignant from benign pancreaticobiliary disease

Author

Mato Prado, Mireia, Puik, Jisce R., Castellano, Leandro, López-Jiménez, Elena, Liu, Daniel S. K., Meijer, Laura L., Le Large, Tessa Y. S., Rees, Eleanor, Funel, Niccola, Sivakumar, Shivan, Pereira, Stephen P., Kazemier, Geert, Zonderhuis, Babs M., Erdmann, Joris I., Swijnenburg, Rutger-Jan, Frilling, Andrea, Jiao, Long R., Stebbing, Justin, Giovannetti, Elisa, Krell, Jonathan, and Frampton, Adam E.

Published
2023
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6. The Non-Coding RNA Journal Club: Highlights on Recent Papers—13

Author

Shiu, Patrick K. T., primary, DiStefano, Johanna K., additional, Alahari, Suresh K., additional, Enguita, Francisco J., additional, Feinberg, Mark W., additional, Sideris, Nikolaos, additional, Bayraktar, Salih, additional, Castellano, Leandro, additional, Buitrago, Diana Luna, additional, Caporali, Andrea, additional, Mannucci, Alessandro, additional, and Goel, Ajay, additional

Published
2023
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10. Expression of targets of the RNA-binding protein AUF-1 in human airway epithelium indicates its role in cellular senescence and inflammation

Author

Salvato, Ilaria, primary, Ricciardi, Luca, additional, Dal Col, Jessica, additional, Nigro, Annunziata, additional, Giurato, Giorgio, additional, Memoli, Domenico, additional, Sellitto, Assunta, additional, Lamparelli, Erwin Pavel, additional, Crescenzi, Maria Assunta, additional, Vitale, Monica, additional, Vatrella, Alessandro, additional, Nucera, Francesco, additional, Brun, Paola, additional, Caicci, Federico, additional, Dama, Paola, additional, Stiff, Thomas, additional, Castellano, Leandro, additional, Idrees, Sobia, additional, Johansen, Matt D., additional, Faiz, Alen, additional, Wark, Peter A., additional, Hansbro, Philip M., additional, Adcock, Ian M., additional, Caramori, Gaetano, additional, and Stellato, Cristiana, additional

Published
2023
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13. Author Correction: Differential epigenetic reprogramming in response to specific endocrine therapies promotes cholesterol biosynthesis and cellular invasion

Author

Nguyen, Van T. M., Barozzi, Iros, Faronato, Monica, Lombardo, Ylenia, Steel, Jennifer H., Patel, Naina, Darbre, Philippa, Castellano, Leandro, Győrffy, Balázs, Woodley, Laura, Rodriguez-Meira, Alba, Patten, Darren K., Vircillo, Valentina, Periyasamy, Manikandan, Ali, Simak, Frige, Gianmaria, Minucci, Saverio, Coombes, R. Charles, and Magnani, Luca

Published
2019
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14. Table S5 from SCIRT lncRNA Restrains Tumorigenesis by Opposing Transcriptional Programs of Tumor-Initiating Cells

Author

Zagorac, Sladjana, primary, de Giorgio, Alex, primary, Dabrowska, Aleksandra, primary, Kalisz, Mark, primary, Casas-Vila, Nuria, primary, Cathcart, Paul, primary, Yiu, Angela, primary, Ottaviani, Silvia, primary, Degani, Neta, primary, Lombardo, Ylenia, primary, Tweedie, Alistair, primary, Nissan, Tracy, primary, Vance, Keith W., primary, Ulitsky, Igor, primary, Stebbing, Justin, primary, and Castellano, Leandro, primary

Published
2023
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15. Supplementary Data from SCIRT lncRNA Restrains Tumorigenesis by Opposing Transcriptional Programs of Tumor-Initiating Cells

Author

Zagorac, Sladjana, primary, de Giorgio, Alex, primary, Dabrowska, Aleksandra, primary, Kalisz, Mark, primary, Casas-Vila, Nuria, primary, Cathcart, Paul, primary, Yiu, Angela, primary, Ottaviani, Silvia, primary, Degani, Neta, primary, Lombardo, Ylenia, primary, Tweedie, Alistair, primary, Nissan, Tracy, primary, Vance, Keith W., primary, Ulitsky, Igor, primary, Stebbing, Justin, primary, and Castellano, Leandro, primary

Published
2023
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16. Data from SCIRT lncRNA Restrains Tumorigenesis by Opposing Transcriptional Programs of Tumor-Initiating Cells

Author

Zagorac, Sladjana, primary, de Giorgio, Alex, primary, Dabrowska, Aleksandra, primary, Kalisz, Mark, primary, Casas-Vila, Nuria, primary, Cathcart, Paul, primary, Yiu, Angela, primary, Ottaviani, Silvia, primary, Degani, Neta, primary, Lombardo, Ylenia, primary, Tweedie, Alistair, primary, Nissan, Tracy, primary, Vance, Keith W., primary, Ulitsky, Igor, primary, Stebbing, Justin, primary, and Castellano, Leandro, primary

Published
2023
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17. Supplementary Figure 2 from Downregulation of microRNA-515-5p by the Estrogen Receptor Modulates Sphingosine Kinase 1 and Breast Cancer Cell Proliferation

Author

Pinho, Filipa G., primary, Frampton, Adam E., primary, Nunes, Joao, primary, Krell, Jonathan, primary, Alshaker, Heba, primary, Jacob, Jimmy, primary, Pellegrino, Loredana, primary, Roca-Alonso, Laura, primary, de Giorgio, Alexander, primary, Harding, Victoria, primary, Waxman, Jonathan, primary, Stebbing, Justin, primary, Pchejetski, Dmitry, primary, and Castellano, Leandro, primary

Published
2023
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18. Supplementary Figure 1 from Downregulation of microRNA-515-5p by the Estrogen Receptor Modulates Sphingosine Kinase 1 and Breast Cancer Cell Proliferation

Author

Pinho, Filipa G., primary, Frampton, Adam E., primary, Nunes, Joao, primary, Krell, Jonathan, primary, Alshaker, Heba, primary, Jacob, Jimmy, primary, Pellegrino, Loredana, primary, Roca-Alonso, Laura, primary, de Giorgio, Alexander, primary, Harding, Victoria, primary, Waxman, Jonathan, primary, Stebbing, Justin, primary, Pchejetski, Dmitry, primary, and Castellano, Leandro, primary

Published
2023
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19. Supplementary Figure 3 from Downregulation of microRNA-515-5p by the Estrogen Receptor Modulates Sphingosine Kinase 1 and Breast Cancer Cell Proliferation

Author

Pinho, Filipa G., primary, Frampton, Adam E., primary, Nunes, Joao, primary, Krell, Jonathan, primary, Alshaker, Heba, primary, Jacob, Jimmy, primary, Pellegrino, Loredana, primary, Roca-Alonso, Laura, primary, de Giorgio, Alexander, primary, Harding, Victoria, primary, Waxman, Jonathan, primary, Stebbing, Justin, primary, Pchejetski, Dmitry, primary, and Castellano, Leandro, primary

Published
2023
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20. Supplementary Tables 1 through 6 from Downregulation of microRNA-515-5p by the Estrogen Receptor Modulates Sphingosine Kinase 1 and Breast Cancer Cell Proliferation

Author

Pinho, Filipa G., primary, Frampton, Adam E., primary, Nunes, Joao, primary, Krell, Jonathan, primary, Alshaker, Heba, primary, Jacob, Jimmy, primary, Pellegrino, Loredana, primary, Roca-Alonso, Laura, primary, de Giorgio, Alexander, primary, Harding, Victoria, primary, Waxman, Jonathan, primary, Stebbing, Justin, primary, Pchejetski, Dmitry, primary, and Castellano, Leandro, primary

Published
2023
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21. Supplementary Figure 5 from Downregulation of microRNA-515-5p by the Estrogen Receptor Modulates Sphingosine Kinase 1 and Breast Cancer Cell Proliferation

Author

Pinho, Filipa G., primary, Frampton, Adam E., primary, Nunes, Joao, primary, Krell, Jonathan, primary, Alshaker, Heba, primary, Jacob, Jimmy, primary, Pellegrino, Loredana, primary, Roca-Alonso, Laura, primary, de Giorgio, Alexander, primary, Harding, Victoria, primary, Waxman, Jonathan, primary, Stebbing, Justin, primary, Pchejetski, Dmitry, primary, and Castellano, Leandro, primary

Published
2023
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22. Data from Downregulation of microRNA-515-5p by the Estrogen Receptor Modulates Sphingosine Kinase 1 and Breast Cancer Cell Proliferation

Author

Pinho, Filipa G., primary, Frampton, Adam E., primary, Nunes, Joao, primary, Krell, Jonathan, primary, Alshaker, Heba, primary, Jacob, Jimmy, primary, Pellegrino, Loredana, primary, Roca-Alonso, Laura, primary, de Giorgio, Alexander, primary, Harding, Victoria, primary, Waxman, Jonathan, primary, Stebbing, Justin, primary, Pchejetski, Dmitry, primary, and Castellano, Leandro, primary

Published
2023
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23. Supplementary Figure Legends from Downregulation of microRNA-515-5p by the Estrogen Receptor Modulates Sphingosine Kinase 1 and Breast Cancer Cell Proliferation

Author

Pinho, Filipa G., primary, Frampton, Adam E., primary, Nunes, Joao, primary, Krell, Jonathan, primary, Alshaker, Heba, primary, Jacob, Jimmy, primary, Pellegrino, Loredana, primary, Roca-Alonso, Laura, primary, de Giorgio, Alexander, primary, Harding, Victoria, primary, Waxman, Jonathan, primary, Stebbing, Justin, primary, Pchejetski, Dmitry, primary, and Castellano, Leandro, primary

Published
2023
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24. Supplementary Figure 4 from Downregulation of microRNA-515-5p by the Estrogen Receptor Modulates Sphingosine Kinase 1 and Breast Cancer Cell Proliferation

Author

Pinho, Filipa G., primary, Frampton, Adam E., primary, Nunes, Joao, primary, Krell, Jonathan, primary, Alshaker, Heba, primary, Jacob, Jimmy, primary, Pellegrino, Loredana, primary, Roca-Alonso, Laura, primary, de Giorgio, Alexander, primary, Harding, Victoria, primary, Waxman, Jonathan, primary, Stebbing, Justin, primary, Pchejetski, Dmitry, primary, and Castellano, Leandro, primary

Published
2023
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25. Supplementary Table 7 from Downregulation of microRNA-515-5p by the Estrogen Receptor Modulates Sphingosine Kinase 1 and Breast Cancer Cell Proliferation

Author

Pinho, Filipa G., primary, Frampton, Adam E., primary, Nunes, Joao, primary, Krell, Jonathan, primary, Alshaker, Heba, primary, Jacob, Jimmy, primary, Pellegrino, Loredana, primary, Roca-Alonso, Laura, primary, de Giorgio, Alexander, primary, Harding, Victoria, primary, Waxman, Jonathan, primary, Stebbing, Justin, primary, Pchejetski, Dmitry, primary, and Castellano, Leandro, primary

Published
2023
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29. MicroRNAs Cooperatively Inhibit a Network of Tumor Suppressor Genes to Promote Pancreatic Tumor Growth and Progression

Author

Frampton, Adam E., Castellano, Leandro, Colombo, Teresa, Giovannetti, Elisa, Krell, Jonathan, Jacob, Jimmy, Pellegrino, Loredana, Roca-Alonso, Laura, Funel, Niccola, Gall, Tamara M.H., De Giorgio, Alexander, Pinho, Filipa G., Fulci, Valerio, Britton, David J., Ahmad, Raida, Habib, Nagy A., Coombes, R. Charles, Harding, Victoria, Knösel, Thomas, Stebbing, Justin, and Jiao, Long R.

Published
2014
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33. Polymeric Carriers for Delivery of RNA Cancer Therapeutics

Author

Mirón-Barroso, Sofía, primary, Correia, Joana S., additional, Frampton, Adam E., additional, Lythgoe, Mark P., additional, Clark, James, additional, Tookman, Laura, additional, Ottaviani, Silvia, additional, Castellano, Leandro, additional, Porter, Alexandra E., additional, Georgiou, Theoni K., additional, and Krell, Jonathan, additional

Published
2022
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35. A pyroptosis‐related lncRNA signature in bladder cancer.

Author

Wang, Peng, Wang, Zhiqiang, Zhu, Liping, Sun, Yilan, Castellano, Leandro, Stebbing, Justin, Yu, Zhentao, and Peng, Ling

Subjects
RECEIVER operating characteristic curves, LINCRNA, APOPTOSIS, DISEASE risk factors, BLADDER cancer, CANCER prognosis
Abstract

Purpose: Pyroptosis, a type of programmed cell death, is implicated in the tumorigenesis, development and migration of cancer, which can be regulated by long non‐coding RNAs (lncRNAs). Our research aimed to investigate the prognostic role of pyroptosis‐related lncRNAs and the relationship to the tumor immune microenvironment through bioinformatics analysis. Methods: The clinical and RNA‐sequencing data of bladder cancer patients were downloaded from The Cancer Genome Atlas (TCGA). And 412 bladder cancer subjects with clinical information were divided into training and testing cohort. And 52 reported pyroptosis‐related genes were used to screen pyroptosis‐related lncRNAs. A pyroptosis‐related lncRNA signature was constructed based on Cox regression analyses. Results: A 9‐pyroptosis‐related‐lncRNA signature was identified to separate patients with bladder cancer into two groups. The prognosis of bladder cancer patients in the high‐risk group was significantly inferior compared with those in the low‐risk group. Risk scores were validated to develop an independent prognostic indicator based on multivariate Cox regression analysis. Receiver operating characteristic curve (ROC) analysis examined the signature on overall survival. The area under time‐dependent ROC curve (AUC) at 1‐, 3, and 5‐years measured 0.747, 0.783, and 0.768, respectively. Analysis of the immune landscape and PD‐L1 expression showed that PD‐L1 is upregulated in the high‐risk group. The immunocyte subtypes of the two groups were different. Conclusion: A novel pyroptosis‐related lncRNA signature was identified with prognostic value for bladder cancer patients. Pyroptosis‐related lncRNAs have a potential role in cancer immunology and may serve as prognostic or therapeutic targets. [ABSTRACT FROM AUTHOR]

Published
2023
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36. The Non-Coding RNA Journal Club: Highlights on Recent Papers—10

Author

Pinzon Cortes, Jairo A., primary, El-Osta, Assam, additional, Fontemaggi, Giulia, additional, Delihas, Nicholas, additional, Miyazaki, Katsuki, additional, Goel, Ajay, additional, Brazane, Mira, additional, Carré, Clément, additional, Dama, Paola, additional, Bayraktar, Salih, additional, Castellano, Leandro, additional, Enguita, Francisco J., additional, Mitic, Tijana, additional, Caporali, Andrea, additional, Gerber, André P., additional, and Amodio, Nicola, additional

Published
2022
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38. Kinome screening for regulators of the estrogen receptor identifies LMTK3 as a new therapeutic target in breast cancer

Author

Giamas, Georgios, Filipovic, Aleksandra, Jacob, Jimmy, Messier, Walter, Zhang, Hua, Yang, Dongyun, Zhang, Wu, Shifa, Belul Assefa, Photiou, Andrew, Tralau-Stewart, Cathy, Castellano, Leandro, Green, Andrew R., Coombes, R. Charles, Ellis, Ian O., Ali, Simak, Lenz, Heinz-Josef, and Stebbing, Justin

Subjects
Estrogen -- Receptors, Genes -- Physiological aspects -- Research -- Genetic aspects, Protein kinases -- Research -- Physiological aspects -- Genetic aspects, Breast cancer -- Care and treatment -- Genetic aspects -- Research, Biological sciences, Health
Abstract

Therapies targeting estrogen receptor α (ERα, encoded by ESR1) have transformed the treatment of breast cancer. However, large numbers of women relapse, highlighting the need for the discovery of new regulatory targets modulating ERα pathways (1-5). An siRNA screen identified kinases whose silencing alters the estrogen response including those previously implicated in regulating ERα activity (such as mitogen-activated protein kinase and AKT). Among the most potent regulators was lemur tyrosine kinase-3 (LMTK3), for which a role has not previously been assigned. In contrast to other modulators of ERα activity, LMTK3 seems to have been subject to Darwinian positive selection, a noteworthy result given the unique susceptibility of humans to [ERα.sup.+] breast cancer. LMTK3 acts by decreasing the activity of protein kinase C (PKC) and the phosphorylation of AKT (Ser473), thereby increasing binding of forkhead box O3 (FOXO3) to the ESR1 promoter. LMTK3 phosphorylated ERα, protecting it from proteasomal degradation in vitro. Silencing of LMTK3 reduced tumor volume in an orthotopic mouse model and abrogated proliferation of [ERα.sup.+] but not [ERα.sup.-] cells, indicative of its role in ERα activity. In human cancers, LMTK3 abundance and intronic polymorphisms were significantly associated with disease-free and overall survival and predicted response to endocrine therapies. These findings yield insights into the natural history of breast cancer in humans and reveal LMTK3 as a new therapeutic target., More than two-thirds of breast tumors express ERα (ref. 2), and patients with [ERα.sup.+] disease respond to antiestrogens (tamoxifen), estrogen withdrawal (aromatase inhibitors) and direct targeting of the receptor (fulvestrant) [...]

Published
2011
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39. 5′ isomiR variation is of functional and evolutionary importance

Author

Tan, Geok Chin, Chan, Elcie, Molnar, Attila, Sarkar, Rupa, Alexieva, Diana, Isa, Ihsan Mad, Robinson, Sophie, Zhang, Shuchen, Ellis, Peter, Langford, Cordelia F., Guillot, Pascale V., Chandrashekran, Anil, Fisk, Nick M., Castellano, Leandro, Meister, Gunter, Winston, Robert M., Cui, Wei, Baulcombe, David, and Dibb, Nick J.

Published
2014
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42. The estrogen receptor-[alpha]-induced microRNA signature regulates itself and its transcriptional response

Author

Castellano, Leandro, Giamas, Georgios, Jacob, Jimmy, Coombes, R. Charles, Lucchesi, Walter, Thiruchelvam, Paul, Barton, Geraint, Jiao, Long R., Wait, Robin, Waxman, Jonathan, Hannon, Gregory J., and Stebbing, Justin

Subjects
Genetic regulation -- Research, RNA -- Physiological aspects, RNA -- Research, Estrogen -- Receptors, Estrogen -- Physiological aspects, Estrogen -- Genetic aspects, Estrogen -- Research, Science and technology
Abstract

Following estrogenic activation, the estrogen receptor-[alpha] (ER[alpha]) directly regulates the transcription of target genes via DNA binding. MicroRNAs (miRNAs) modulated by ERa have the potential to fine tune these regulatory systems and also provide an alternate mechanism that could impact on estrogen-dependent developmental and pathological systems. Through a microarray approach, we identify the subset of microRNAs (miRNAs) modulated by ERa, which include upregulation of miRNAs derived from the processing of the paralogous primary transcripts (pri-) mir-17-92 and mir-106a-363. Characterization of the mir-17-92 locus confirms that the ERa target protein c-MYC binds its promoter in an estrogen-dependent manner. We observe that levels of pri-mir-17-92 increase earlier than the mature miRNAs derived from it, implicating precursor cleavage modulation after transcription. Pri-mir-17-92 is immediately cleaved by DROSHA to pre-miR-18a, indicating that its regulation occurs during the formation of the mature molecule from the precursor. The clinical implications of this novel regulatory system were confirmed by demonstrating that pre-miR-18a was significantly upregulated in ER[alpha]-positive compared to ER[alpha]-negative breast cancers. Mechanistically, miRNAs derived from these paralogous pri-miRNAs (miR-18a, miR-19b, and miR-20b) target and downregulate ER[alpha], while a subset of pri-miRNA-derived miRNAs inhibit protein translation of the ERa transcriptional p160 coactivator, AIB1. Therefore, different subsets of miRNAs identified act as part of a negative autoregulatory feedback loop. We propose that ER[alpha], c-MYC, and miRNA transcriptional programs invoke a sophisticated network of interactions able to provide the wide range of coordinated cellular responses to estrogen. AIB1 | autoregulatory feedback loop | primary transcript | processing

Published
2009

43. Repurposed floxacins targeting RSK4 prevent chemoresistance and metastasis in lung and bladder cancer

Author

Chrysostomou, Stelios, primary, Roy, Rajat, additional, Prischi, Filippo, additional, Thamlikitkul, Lucksamon, additional, Chapman, Kathryn L., additional, Mufti, Uwais, additional, Peach, Robert, additional, Ding, Laifeng, additional, Hancock, David, additional, Moore, Christopher, additional, Molina-Arcas, Miriam, additional, Mauri, Francesco, additional, Pinato, David J., additional, Abrahams, Joel M., additional, Ottaviani, Silvia, additional, Castellano, Leandro, additional, Giamas, Georgios, additional, Pascoe, Jennifer, additional, Moonamale, Devmini, additional, Pirrie, Sarah, additional, Gaunt, Claire, additional, Billingham, Lucinda, additional, Steven, Neil M., additional, Cullen, Michael, additional, Hrouda, David, additional, Winkler, Mathias, additional, Post, John, additional, Cohen, Philip, additional, Salpeter, Seth J., additional, Bar, Vered, additional, Zundelevich, Adi, additional, Golan, Shay, additional, Leibovici, Dan, additional, Lara, Romain, additional, Klug, David R., additional, Yaliraki, Sophia N., additional, Barahona, Mauricio, additional, Wang, Yulan, additional, Downward, Julian, additional, Skehel, J. Mark, additional, Ali, Maruf M.U., additional, Seckl, Michael J., additional, and Pardo, Olivier E., additional

Published
2021
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44. Quantitative technologies establish a novel microRNA profile of chronic lymphocytic leukemia

Author

Fulci, Valerio, Chiaretti, Sabina, Goldoni, Marina, Azzalin, Gianluca, Carucci, Nicoletta, Tavolaro, Simona, Castellano, Leandro, Magrelli, Armando, Citarella, Franca, Messina, Monica, Maggio, Roberta, Peragine, Nadia, Santangelo, Simona, Mauro, Francesca Romana, Landgraf, Pablo, Tuschl, Thomas, Weir, David B., Chien, Minchen, Russo, James J., Ju, Jingyue, Sheridan, Robert, Sander, Chris, Zavolan, Mihaela, Guarini, Anna, Foà, Robin, and Macino, Giuseppe

Published
2007
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45. SCIRT lncRNA Restrains Tumorigenesis by Opposing Transcriptional Programs of Tumor-Initiating Cells

Author

Zagorac, Sladjana, primary, de Giorgio, Alex, additional, Dabrowska, Aleksandra, additional, Kalisz, Mark, additional, Casas-Vila, Nuria, additional, Cathcart, Paul, additional, Yiu, Angela, additional, Ottaviani, Silvia, additional, Degani, Neta, additional, Lombardo, Ylenia, additional, Tweedie, Alistair, additional, Nissan, Tracy, additional, Vance, Keith W., additional, Ulitsky, Igor, additional, Stebbing, Justin, additional, and Castellano, Leandro, additional

Published
2021
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49. Background splicing as a predictor of aberrant splicing in genetic disease

Author

Alexieva, Diana, Long, Yi, Sarkar, Rupa, Dhayan, Hansraj, Bruet, Emmanuel, Winston, Robert Maurice, Vorechovsky, Igor, Castellano, Leandro, and Dibb, Nicholas John

Abstract

ABSTRACTMutations of splice sites, auxiliary splicing elements and the splicing machinery cause a wide range of genetic disease. Here we report that many of the complex effects of splicing mutations can be predicted from background splicing information, with emphasis on BRCA1, BRCA2 and DMD. Background splicing arises from very low level splicing between rarely used background splice sites and from low-level exon skipping between intron splice sites. We show how this information can be downloaded from the Snaptron database of spliced RNA, which we then compared with databases of human splice site mutations. We report that inactivating mutations of intron splice sites typically caused the non-mutated partner splice site to splice to a known background splice site in over 90% of cases and to the strongest background splice site in the large majority of cases. Consequently, background splicing information can usefully predict the effects of splice site mutations, which include cryptic splice activation and single or multiple exon skipping. In addition, de novo splice sites and splice sites involved in pseudoexon formation, recursive splicing and aberrant splicing in cancer show a 90% match to background splice sites, so establishing that the enhancement of background splicing causes a wide range of splicing aberrations. We also discuss how background splicing information can identify cryptic splice sites that might be usefully targeted by antisense oligonucleotides (ASOs) and how it might indicate possible multiple exon skipping side effects of ASOs designed to induce single exon skipping.

Published
2022
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