Review
Plant Sciences
Yi Ren, Yue Song, Lipeng Zhang, Dinghan Guo, Juan He, Lei Wang, Shiren Song, Wenping Xu, Caixi Zhang, Amnon Lers, Chao Ma, Shiping Wang
Summary: Peptides composed of a short chain of amino acids play important roles in plant growth, development, and stress responses, derived from precursor proteins or small open reading frames. They act as local signal molecules for intercellular communication and ligands for cellular signaling transduction. Recent studies have shown that non-coding RNAs can also encode peptides, such as miRNA-encoded peptides (miPEPs), which can increase the expression of corresponding miRNAs by enhancing MIRNA gene transcription.
FRONTIERS IN PLANT SCIENCE
(2021)
Review
Medicine, Research & Experimental
Negin Soghli, Tooba Yousefi, Maryam Abolghasemi, Durdi Qujeq
Summary: The incidence of cancer is increasing globally, with long non-coding RNAs (lncRNAs) playing a key role in regulating biological functions by controlling gene expressions. The highly conserved lncRNA NORAD is crucial for genome stability and dysregulated in various types of cancers, affecting processes such as cell proliferation, apoptosis, invasion, and metastasis. This review provides insights into the role of lncRNA NORAD in different human cancers, offering directions for future research.
Review
Cell Biology
Soudeh Ghafouri-Fard, Sajad Najafi, Bashdar Mahmud Hussen, Aryan R. Ganjo, Mohammad Taheri, Mohammad Samadian
Summary: Long non-coding RNAs (lncRNAs) are a heterogeneous group of ncRNAs with a characteristic size of more than 200 nucleotides. DLX6-AS1 is an lncRNA that has been found to be up-regulated in various cancers, and it promotes the oncogenic phenotype of cancer cells by affecting signaling pathways. It is associated with clinicopathological features and shorter survival in cancer patients.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Review
Biochemistry & Molecular Biology
Qingshui Wang, Youyu Lin, Wenting Zhong, Yu Jiang, Yao Lin
Summary: DAPKs family plays a crucial role in the development of malignant tumors, while non-coding RNAs are involved in the regulation of DAPKs.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Article
Medicine, General & Internal
Sofiane Bendifallah, Stephane Suisse, Anne Puchar, Lea Delbos, Mathieu Poilblanc, Philippe Descamps, Francois Golfier, Ludmila Jornea, Delphine Bouteiller, Cyril Touboul, Yohann Dabi, Emile Darai
Summary: The ENDO-miRNA study is the first prospective study to report a saliva-based diagnostic miRNA signature for endometriosis. By applying small RNA sequencing and the Random Forest algorithm, a saliva signature consisting of 109 miRNAs with high sensitivity and specificity was obtained, providing a non-invasive tool for early diagnosis of endometriosis.
JOURNAL OF CLINICAL MEDICINE
(2022)
Article
Medicine, Research & Experimental
Soudeh Ghafouri-Fard, Atefe Abak, Hamed Shoorei, Seyedeh Fahimeh Talebi, Mahdi Mohaqiq, Parisa Sarabi, Mohammad Taheri, Majid Mokhtari
Summary: This review explores the interaction between Toll-like receptors (TLRs) and non-coding RNAs (miRNAs and lncRNAs), emphasizing their crucial roles in the pathogenesis of various diseases.
BIOMEDICINE & PHARMACOTHERAPY
(2021)
Review
Biochemistry & Molecular Biology
Soudeh Ghafouri-Fard, Bashdar Mahmud Hussen, Hazha Hadayat Jamal, Mohammad Taheri, Guive Sharifi
Summary: Non-coding RNAs, especially lncRNAs and miRNAs, play important roles in regulating viral infections and immune responses. The expression of various host and viral lncRNAs is altered during viral infection, which can either inhibit viral infection, promote viral replication, or suppress antiviral responses.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Yafei Wang, Zhonghua Wang, Qingguo Du, Kai Wang, Chunqin Zou, Wen-Xue Li
Summary: The open reading regions of ZmPHT1s in maize contain target sites of miR399. It has been discovered that the long non-coding RNA PILNCR2 interferes with miR399-guided cleavage of ZmPHT1 mRNAs, resulting in increased low-Pi tolerance in maize.
Review
Cell Biology
Xixia Zhang, Jing Yang
Summary: Head and neck cancers (HNCs) are a common and deadly form of cancer worldwide, with radiotherapy being a common treatment method. However, the overall survival rates for patients are still low. Studies have shown that non-coding RNAs (ncRNAs) play a role in regulating the sensitivity of HNC cancer cells to radiotherapy, potentially affecting the response of cancer cells to treatment.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Review
Biochemistry & Molecular Biology
Radu Pirlog, Rares Drula, Andreea Nutu, George Adrian Calin, Ioana Berindan-Neagoe
Summary: CCAT2 is a highly studied lncRNA with diverse functions in cancer regulation, including interactions with various RNA binding proteins and transcription factors. It has been shown to play a role in promoting chromosome instability and altering glutamine metabolism, potentially affecting cancer therapy resistance and metastasis.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Review
Immunology
Lina Tingo, Emelie Ahlberg, Lovisa Johansson, Sindre Andre Pedersen, Konika Chawla, Pal Saetrom, Erika Cione, Melanie Rae Simpson
Summary: Breast milk contains a variety of RNA types, including miRNAs, with some miRNAs being widely reported across different fractions. It is currently challenging to determine which factors influence the characteristics of the miRNA profile, but studies suggest that certain miRNAs are highly expressed and stable in breast milk. Future research needs to further explore the biological effects of miRNAs in breast milk and characterize other ncRNAs.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Immunology
Steven D. Hicks, Alexandra Confair, Kaitlyn Warren, Desirae Chandran
Summary: Emerging evidence suggests that non-coding RNAs in maternal breast milk have unique effects on the metabolism and immune system of infants. This study provides the largest dataset of non-coding RNAs in breast milk and demonstrates a relationship between microRNAs in breast milk and maternal diet.
FRONTIERS IN IMMUNOLOGY
(2022)
Review
Oncology
Muhammad Irfan, Zeeshan Javed, Khushbukhat Khan, Naila Khan, Anca Oana Docea, Daniela Calina, Javad Sharifi-Rad, William C. Cho
Summary: Long non-coding RNA (LncRNA) is a class of regulatory transcripts that are frequently dysregulated in various tumor types, including colorectal cancer (CRC). They play a role in regulating gene expression and modulating cellular activities in CRC, such as cell proliferation, invasion, metastasis, chemoresistance, and apoptosis.
CANCER CELL INTERNATIONAL
(2022)
Review
Oncology
Ghafouri-Fard Soudeh, Jamal Majidpoor, Hamed Shoorei, Bashdar Mahmud Hussen, Hazha MahmudHussen Jamal, Aria Baniahmad, Mohammad Taheri, Majid Mokhtari
Summary: Calcium binding proteins mediate the effects of calcium on cellular functions, and recent studies have shown their interactions with non-coding RNAs, which play a role in various diseases.
FRONTIERS IN ONCOLOGY
(2022)
Review
Medicine, Research & Experimental
Jie Liu, Gang Zhao, Xin-Li Liu, Ge Zhang, Shi-Qi Zhao, Shi-Long Zhang, Li-Heng Luo, Da-Chuan Yin, Chen-Yan Zhang
Summary: Non-coding RNAs (ncRNAs) play important roles in the occurrence and development of triple negative breast cancer (TNBC), and may serve as potential therapeutic targets.
Article
Immunology
E. G. De Smet, H. P. Van Eeckhoutte, F. Avila Cobos, E. Blomme, F. M. Verhamme, S. Provoost, S. E. Verleden, K. Venken, T. Maes, G. F. Joos, P. Mestdagh, G. G. Brusselle, K. R. Bracke
MUCOSAL IMMUNOLOGY
(2020)
Article
Biochemistry & Molecular Biology
Ruben Van Paemel, Andries De Koker, Christa Caggiano, Annelien Morlion, Pieter Mestdagh, Bram De Wilde, Jo Vandesompele, Katleen De Preter
Summary: The study evaluated the impact of blood collection tube type and time delay on cfDNA methylation analysis, finding that all preservation tubes performed similarly on quality metrics. A significant increase in cfDNA concentration and the fraction derived from NK cells was observed after a 72-hour time delay in EDTA tubes.
Article
Oncology
Jingwei Chen, Christopher Nelson, Matthew Wong, Andrew E. Tee, Pei Y. Liu, Ting La, Jamie I. Fletcher, Alvin Kamili, Chelsea Mayoh, Christoph Bartenhagen, Toby N. Trahair, Ning Xu, Nisitha Jayatilleke, Marie Wong, Hui Peng, Bernard Atmadibrata, Belamy B. Cheung, Qing Lan, Tracy M. Bryan, Pieter Mestdagh, Jo Vandesompele, Valerie Combaret, Valentina Boeva, Jenny Y. Wang, Isabelle Janoueix-Lerosey, Mark J. Cowley, Karen L. MacKenzie, Alla Dolnikov, Jinyan Li, Patsie Polly, Glenn M. Marshall, Roger R. Reddel, Murray D. Norris, Michelle Haber, Matthias Fischer, Xu D. Zhang, Hilda A. Pickett, Tao Liu
Summary: The combination therapy of OTX015 and carfilzomib shows synergistic anticancer effects on TERT-rearranged neuroblastoma by reducing TERT expression, inducing cell apoptosis, and suppressing tumor progression. This treatment approach is likely to be translated into the first clinical trial of targeted therapy in patients with TERT-rearranged neuroblastoma.
CLINICAL CANCER RESEARCH
(2021)
Article
Oncology
Liselot M. Mus, Stephane Van Haver, Mina Popovic, Wim Trypsteen, Steve Lefever, Nadja Zeltner, Yudelca Ogando, Eva Z. Jacobs, Geertrui Denecker, Ellen Sanders, Christophe Van Neste, Suzanne Vanhauwaert, Bieke Decaesteker, Dieter Deforce, Filip Van Nieuwerburgh, Pieter Mestdagh, Jo Vandesompele, Bjorn Menten, Katleen De Preter, Lorenz Studer, Bjorn Heindryckx, Kaat Durinck, Stephen Roberts, Frank Speleman
Summary: Human embryonic stem cells and embryonal tumors both exhibit compromised G1/S checkpoint, leading to replicative stress and genomic instability. Long-term in vitro cultured hESCs show a high incidence of DNA copy number gains, which may provide a proliferative advantage.
GENES CHROMOSOMES & CANCER
(2021)
Review
Oncology
Eva Hulstaert, Annelien Morlion, Keren Levanon, Jo Vandesompele, Pieter Mestdagh
Summary: This systematic review presents 75 RNA biomarkers detectable in human biofluids for early diagnosis of ovarian cancer, with the majority identified using RT-qPCR or microarrays in blood-based fluids. Some studies utilized RNA-sequencing and looked into alternative fluids like urine and ascites. Promising biomarkers include miR-21, the miR-200 family, miR-205, miR-10a, and miR-346, while validation and further research are needed before clinical implementation. Challenges in biomarker validation and future perspectives are discussed to accelerate progress in this field.
GYNECOLOGIC ONCOLOGY
(2021)
Article
Oncology
Mathieu Spaas, Nora Sundahl, Eva Hulstaert, Vibeke Kruse, Sylvie Rottey, Daan De Maeseneer, Veerle Surmont, Annabel Meireson, Lieve Brochez, Dries Reynders, Els Goetghebeur, Robbe Van den Begin, Dirk Van Gestel, Vincent Renard, Piet Dirix, Pieter Mestdagh, Piet Ost
Summary: The CHEERS trial aims to evaluate whether concurrent administration of SBRT and CPIs can prolong progression-free survival in advanced solid tumor patients. This multicenter randomized phase II trial will assess the impact of SBRT on disease control time and explore outcomes such as survival, objective response, local control, quality of life, and toxicity in 98 patients.
Article
Pathology
Pieter Mestdagh, Michel Gillard, Sharonjit K. Dhillon, Jean-Paul Pirnay, Jeroen Poels, Jan Hellemans, Veronik Hutse, Celine Vermeiren, Maxime Boutier, Veerle De Wever, Patrick Soentjens, Sarah Djebara, Hugues Malonne, Emmanuel Andre, Marc Arbyn, John Smeraglia, Jo Vandesompele
Summary: Saliva specimens have lower sensitivity in detecting SARS-CoV-2 compared to nasopharyngeal swabs, but show higher sensitivity for cases with medium to high viral loads, potentially aiding in the identification of the most contagious cases.
JOURNAL OF MOLECULAR DIAGNOSTICS
(2021)
Correction
Biotechnology & Applied Microbiology
Lucia Lorenzi, Hua-Sheng Chiu, Francisco Avila Cobos, Stephen Gross, Pieter-Jan Volders, Robrecht Cannoodt, Justine Nuytens, Katrien Vanderheyden, Jasper Anckaert, Steve Lefever, Aidan P. Tay, Eric J. de Bony, Wim Trypsteen, Fien Gysens, Marieke Vromman, Tine Goovaerts, Thomas Birkballe Hansen, Scott Kuersten, Nele Nijs, Tom Taghon, Karim Vermaelen, Ken R. Bracke, Yvan Saeys, Tim De Meyer, Nandan P. Deshpande, Govardhan Anande, Ting-Wen Chen, Marc R. Wilkins, Ashwin Unnikrishnan, Katleen De Preter, Jorgen Kjems, Jan Koster, Gary P. Schroth, Jo Vandesompele, Pavel Sumazin, Pieter Mestdagh
NATURE BIOTECHNOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Lucia Lorenzi, Hua-Sheng Chiu, Francisco Avila Cobos, Stephen Gross, Pieter-Jan Volders, Robrecht Cannoodt, Justine Nuytens, Katrien Vanderheyden, Jasper Anckaert, Steve Lefever, Aidan P. Tay, Eric J. de Bony, Wim Trypsteen, Fien Gysens, Marieke Vromman, Tine Goovaerts, Thomas Birkballe Hansen, Scott Kuersten, Nele Nijs, Tom Taghon, Karim Vermaelen, Ken R. Bracke, Yvan Saeys, Tim De Meyer, Nandan P. Deshpande, Govardhan Anande, Ting-Wen Chen, Marc R. Wilkins, Ashwin Unnikrishnan, Katleen De Preter, Jorgen Kjems, Jan Koster, Gary P. Schroth, Jo Vandesompele, Pavel Sumazin, Pieter Mestdagh
Summary: The study identified numerous novel non-coding RNAs from 300 human tissues and cell lines, expanding the existing catalog of ncRNAs. By analyzing pre-mRNA abundance estimates from total RNA sequencing, the research revealed several microRNAs and long non-coding RNAs with potential roles in regulating protein-coding genes and pathways.
NATURE BIOTECHNOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Shanna Dewaele, Louis Delhaye, Boel De Paepe, Eric James de Bony, Jilke De Wilde, Katrien Vanderheyden, Jasper Anckaert, Nurten Yigit, Justine Nuytens, Eveline Vanden Eynde, Joel Smet, Maxime Verschoore, Fariba Nemati, Didier Decaudin, Manuel Rodrigues, Peihua Zhao, Aart Jochemsen, Eleonora Leucci, Jo Vandesompele, Jo Van Dorpe, Jean-Christophe Marine, Rudy Van Coster, Sven Eyckerman, Pieter Mestdagh
Summary: The inhibition of SAMMSON in uveal melanoma cells has shown to impair cell growth and viability, induce apoptosis, and affect protein translation levels, highlighting its potential as a therapeutic target. This study demonstrates the essential role of SAMMSON expression in uveal melanoma cell survival, suggesting ASO-mediated silencing of SAMMSON as a promising treatment strategy for both primary and metastatic uveal melanoma patients.
Article
Biochemistry & Molecular Biology
Annelien Morlion, Celine Everaert, Justine Nuytens, Eva Hulstaert, Jo Vandesompele, Pieter Mestdagh
Summary: Long non-coding RNAs (lncRNAs) are transcripts without protein coding potential that play regulatory roles in cellular processes. They have emerged as potential diagnostic and therapeutic targets, and a custom lncRNA capture sequencing approach allows for more accurate detection and higher coverage compared to traditional methods.
Article
Cell Biology
Geert A. Martens, Geert Stange, Lorenzo Piemonti, Jasper Anckaert, Zhidong Ling, Daniel G. Pipeleers, Frans K. Gorus, Pieter Mestdagh, Dieter De Smet, Jo Vandesompele, Bart Keymeulen, Sarah Roels
Summary: This study identified multiple beta cell-enriched microRNAs that are co-released with miR-375 and can be used as complementary biomarkers of beta cell death, with miR-375 and miR-132 showing potential for graft outcome.
Article
Cell Biology
Glenn Vergauwen, Joeri Tulkens, Claudio Pinheiro, Francisco Avila Cobos, Sandor Dedeyne, Marie-Angelique De Scheerder, Linos Vandekerckhove, Francis Impens, Ilkka Miinalainen, Geert Braems, Kris Gevaert, Pieter Mestdagh, Jo Vandesompele, Hannelore Denys, Olivier De Wever, An Hendrix
Summary: This study fractionated blood plasma using SEC and OptiPrep density gradient centrifugation to investigate clinical and time-dependent variations in the biomolecular landscape of systemically circulating EV. Results showed that EV carry context-dependent and/or time-dependent protein and small RNA compositions, with differential analysis providing a catalogue of proteins not associated with EV. Overall, blood plasma fractionation can advance the biological understanding and biomarker development of systemically circulating EV.
JOURNAL OF EXTRACELLULAR VESICLES
(2021)
Article
Biochemical Research Methods
Eva Hulstaert, Anneleen Decock, Annelien Morlion, Celine Everaert, Kimberly Verniers, Justine Nuytens, Nele Nijs, Gary P. Schroth, Scott Kuersten, Stephen M. Gross, Pieter Mestdagh, Jo Vandesompele
Summary: The optimized workflow described in this study addresses the challenges of analyzing extracellular RNA (exRNA) from human biofluids with low RNA concentration and compromised integrity. It includes synthetic spike-in RNA molecules as processing controls and an alternative data normalization strategy.
Article
Biochemistry & Molecular Biology
Blake A. Sweeney, Anton Petrov, Carlos E. Ribas, Robert D. Finn, Alex Bateman, Maciej Szymanski, Wojciech M. Karlowski, Stefan E. Seemann, Jan Gorodkin, Jamie J. Cannone, Robin R. Gutell, Simon Kay, Steven Marygold, Gil dos Santos, Adam Frankish, Jonathan M. Mudge, Ruth Barshir, Simon Fishilevich, Patricia P. Chan, Todd M. Lowe, Ruth Seal, Elspeth Bruford, Simona Panni, Pablo Porras, Dimitra Karagkouni, Artemis G. Hatzigeorgiou, Lina Ma, Zhang Zhang, Pieter-Jan Volders, Pieter Mestdagh, Sam Griffiths-Jones, Bastian Fromm, Kevin J. Peterson, Ioanna Kalvari, Eric P. Nawrocki, Anton S. Petrov, Shuai Weng, Philia Bouchard-Bourelle, Michelle Scott, Lauren M. Lui, David Hoksza, Ruth C. Lovering, Barbara Kramarz, Prita Mani, Sridhar Ramachandran, Zasha Weinberg
Summary: RNAcentral is a comprehensive database of non-coding RNA sequences, providing a single access point to over 18 million ncRNA sequences from diverse organisms and RNA types, as well as information on the secondary structure for over 13 million sequences. The database also includes a fast sequence similarity search tool with filtering options, making it a central data resource for the RNA community.
NUCLEIC ACIDS RESEARCH
(2021)