Article
Biochemical Research Methods
Mingmin Xu, Yuanyuan Chen, Zhihui Xu, Liangyun Zhang, Hangjin Jiang, Cong Pian
Summary: In this paper, a computational framework called MiRLoc is described for predicting the subcellular localization of miRNAs. Unlike existing methods, MiRLoc utilizes the functional similarity between miRNAs and incorporates information about the subcellular localization of target mRNAs, resulting in improved prediction performance.
BRIEFINGS IN BIOINFORMATICS
(2022)
Review
Cell Biology
Yi-Li Zheng, Ge Song, Jia-Bao Guo, Xuan Su, Yu-Meng Chen, Zheng Yang, Pei-Jie Chen, Xue-Qiang Wang
Summary: Musculoskeletal degenerative diseases (MSDDs) encompass a range of pathological conditions affecting muscle, bone, cartilage, joints, and connective tissues. Long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs) play key roles in biological regulation and are potential targets for therapeutic interventions in MSDD. Further research is needed to uncover the mutual regulatory mechanisms between lncRNA/circRNA regulation and effective therapeutic interventions in MSDD pathology.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Review
Mathematical & Computational Biology
Dorian Kariuki, Kesava Asam, Bradley E. Aouizerat, Kimberly A. Lewis, Jose C. Florez, Elena Flowers
Summary: This article reviews databases for cataloging validated miR targets, identifies 10 databases, and summarizes their features and functionality. The study suggests that these databases can be enhanced by adding features such as flexible queries, downloadable data, ongoing updates, and integrated tools.
DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION
(2023)
Article
Biology
Priyash Dhakal, Hilal Tayara, Kil To Chong
Summary: We developed a stacking classifier algorithm that surpasses previous algorithms in predicting functional miRNA targets by effectively selecting conservative candidate target sites using feature encoding techniques.
COMPUTERS IN BIOLOGY AND MEDICINE
(2023)
Article
Biochemistry & Molecular Biology
Dheeraj Chitara, Richa Anand, B. S. Sanjeev
Summary: RNA interference (RNAi) plays a role in genetic interference and is identified as an antiviral response mechanism in humans. The study on the interfaces between Ago, miRNA and Target RNA in the presence of molecular crowders through molecular dynamics simulations reveals that crowding changes dynamics, stabilizes the complex and aids in binding free energy. Conserved features and amino acid residues with crowding resilient interactions with RNA are identified in all three systems.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2021)
Review
Cell Biology
Hui Kong, Ming-Li Sun, Xin-An Zhang, Xue-Qiang Wang
Summary: By investigating the roles and interactions of miRNA, lncRNA, and circRNA in osteoarthritis, their significance in the prevention, diagnosis, and treatment of OA can be identified as potential future therapeutic targets.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Fisheries
Chenyang Yue, Qi Li, Hong Yu
Summary: This study focused on the miRNA and mRNA expression profiles in the gonads of Pacific oyster during different stages of gametogenesis, revealing sex-specific patterns and potential regulatory mechanisms in sexual development. The findings suggest that certain sex-biased miRNAs might participate in the regulation of gametogenesis, providing insights into the molecular mechanisms of bivalve sex differentiation.
Article
Oncology
Xingchen Fan, Xuan Zou, Cheng Liu, Shuang Peng, Shiyu Zhang, Xin Zhou, Tongshan Wang, Wei Zhu
Summary: This study identifies miRNA-mRNA regulation pairs related to bladder cancer pathogenesis through analyzing miRNA and mRNA datasets. One of the miRNA-mRNA regulation pairs was experimentally validated, and the diagnostic performance of these pairs in distinguishing bladder cancer was confirmed through ROC and DCA analysis. Additionally, the study found a correlation between these regulation pairs and tumor immunity.
WORLD JOURNAL OF SURGICAL ONCOLOGY
(2022)
Article
Cell Biology
Xingchen Fan, Xuan Zou, Cheng Liu, Shuang Peng, Shiyu Zhang, Xin Zhou, Jun Zhu, Wei Zhu
Summary: This study aimed to identify critical miRNA-mRNA regulation pairs contributing to lung adenocarcinoma (LUAD) pathogenesis. Through analysis of miRNA and mRNA expression data, potential regulation pairs were identified and their diagnostic value and biological functions were confirmed. The study also analyzed the expression and clinical characteristics of these regulation pairs under different conditions.
Article
Genetics & Heredity
Sushil Shakyawar, Siddesh Southekal, Chittibabu Guda
Summary: Identification of miRNA-mRNA interactions is critical and challenging in gene regulation. This study proposed mintRULS, a method that combines miRNA and mRNA features to predict miRNA-target site interactions. The results demonstrated its superior performance compared to existing tools, as well as high accuracy when validated against experimental data.
Article
Oncology
Bai Xue, Shupeng Li, Xianyu Jin, Lifeng Liu
Summary: The study identified key signaling pathways and cellular activities related to cisplatin-resistant ovarian cancer through analyzing differentially expressed genes and miRNAs, and established a miRNA-mRNA regulatory pair (mir-454-UBB) as a potential therapeutic target for drug resistance in ovarian cancer.
Article
Horticulture
Li Zhou, Qiu-Wei Lu, Bei-Fen Yang, Lyuben Zagorchev, Jun-Min Li
Summary: The study analyzed the miRNA-mRNA interaction network in host Trifolium repens in response to parasitism by Cuscuta australis, revealing a plethora of miRNAs and DEGs that shed light on the interactions between plants during parasitism. The most significantly affected pathways by parasitism were plant hormone signal transduction, ribosome, and plant-pathogen interaction pathways. The identified miRNA-mRNA pairs likely play crucial roles in the interactions between host T. repens and parasitic C. australis.
SCIENTIA HORTICULTURAE
(2021)
Article
Genetics & Heredity
Chuan Xing Li, Jing Gao, C. Magnus Skold, Asa M. Wheelock
Summary: A dysregulated network of miRNA-mRNA-protein related to female COPD was constructed in this study, identifying novel biomarkers and disease pathways, and providing new hypotheses about COPD pathology.
FRONTIERS IN GENETICS
(2022)
Review
Medical Laboratory Technology
Meilan Zhang, Xue Bai, Xuemei Zeng, Jiangrong Liu, Feng Liu, Zhiwei Zhang
Summary: Breast cancer has the highest incidence rate among women and the circRNA-miRNA-mRNA axis plays a crucial role in its progression, serving as a potential marker for early diagnosis and treatment.
CLINICA CHIMICA ACTA
(2021)
Article
Plant Sciences
Zhenyi Li, Zongyong Tong, Feng He, Xianglin Li, Juan Sun
Summary: This study investigated the response of alfalfa to phosphate deficiency stress by integrating transcriptional and post-transcriptional data. Differentially expressed genes and miRNAs were identified, and their target genes and regulatory relationships were predicted. The study revealed the post-transcriptional regulation mechanism of phosphate deficiency responses in alfalfa.
FRONTIERS IN PLANT SCIENCE
(2022)
Letter
Oncology
Roser Vilarrasa-Blasi, Nuria Verdaguer-Dot, Laura Belver, Paula Soler-Vila, Renee Beekman, Vicente Chapaprieta, Marta Kulis, Ana C. Queiros, Maribel Parra, Maria Jose Calasanz, Xabier Agirre, Felipe Prosper, Silvia Bea, Dolors Colomer, Marc A. Marti-Renom, Adolfo Ferrando, Elias Campo, Jose Ignacio Martin-Subero
Letter
Hematology
Ane Amundarain, Luis V. Valcarcel, Raquel Ordonez, Leire Garate, Estibaliz Miranda, Xabier Cendoya, Arantxa Carrasco-Leon, Maria Jose Calasanz, Bruno Paiva, Cem Meydan, Christopher E. Mason, Ari Melnick, Paula Rodriguez-Otero, Jose I. Martin-Subero, Jesus San Miguel, Francisco J. Planes, Felipe Prosper, Xabier Agirre
AMERICAN JOURNAL OF HEMATOLOGY
(2022)
Article
Biochemical Research Methods
Juan A. Ferrer-Bonsoms, Xabier Morales, Pegah T. Afshar, Wing H. Wong, Angel Rubio
Summary: It is still unclear whether gene structure and isoform concentration can be uniquely inferred given paired-end reads, and no objective method to select the fragment length has been found. We propose a method to determine the identifiability of the deconvolution problem and find that the optimal average fragment length and read length for the human transcriptome are 400-600 nt and 150-200 nt, respectively.
Article
Pharmacology & Pharmacy
Laura Saludas, Elisa Garbayo, Adrian Ruiz-Villalba, Silvia Hernandez, Pieter Vader, Felipe Prosper, Maria J. Blanco-Prieto
Summary: Extracellular vesicles (EVs), as the next-generation therapies, have attracted great interest. This study investigated the effects of different cell culture conditions and purification methods on EV isolation using cardiac progenitor cells (CPCs). The findings contribute to the establishment of the basis for the use of EVs as therapeutic platforms.
EUROPEAN JOURNAL OF PHARMACEUTICS AND BIOPHARMACEUTICS
(2022)
Article
Oncology
Silvia Saumell, Miranda Fernandez-Serrano, Alba Mesa, Felix Lopez-Cadenas, Leonor Arenillas, Ana Alfonso, Maria Julia Montoro, Antonieta Molero, Pilar Leoz, Victoria Riego, Laura Gallur, Olga Salamero, Mayda Navarrete, Barbara Tazon-Vega, Margarita Ortega, Oscar Reig, Gael Roue, Xavier Calvo, Felipe Prosper, Maria Diez-Campelo, David Valcarcel
Summary: The presence of Micromegakaryocytes (microMKs) in MDS patients indicates poorer outcomes, including lower overall survival rate and higher risk of progression to AML. Additionally, incorporating microMKs into the IPSS-R score can improve accuracy, leading to reclassification of some patients into higher-risk groups.
LEUKEMIA & LYMPHOMA
(2022)
Article
Biochemistry & Molecular Biology
Tom Van Loy, Steven De Jonghe, Karolien Castermans, Wouter Dheedene, Reinout Stoop, Lars Verschuren, Matthias Versele, Patrick Chaltin, Aernout Luttun, Dominique Schols
Summary: The ACKR3 agonist shows pharmacological activity in vitro and in vivo, with a modest anti-fibrotic effect in the liver fibrosis model. However, its inhibitory effect on lung fibrosis is lacking. More interventions in signaling pathways may be needed to achieve satisfactory clinical outcomes.
CELLULAR AND MOLECULAR LIFE SCIENCES
(2022)
Article
Biochemical Research Methods
Luis J. Valcarcel, Edurne L. San Jose-Eneriz, Xabier Cendoya, Angel L. Rubio, Xabier Agirre, Felipe L. Prosper, Francisco Planes
Summary: The study introduces a novel method called BOSO for feature selection in linear regression models. BOSO demonstrates a better combination of accuracy and simplicity in dealing with high-dimensional datasets, making it important for predictive modeling in biomedical research.
PLOS COMPUTATIONAL BIOLOGY
(2022)
Article
Agriculture, Dairy & Animal Science
Marta Moya-Jodar, Giulia Coppiello, Juan Roberto Rodriguez-Madoz, Gloria Abizanda, Paula Barlabe, Amaia Vilas-Zornoza, Asier Ullate-Agote, Chiara Luongo, Ernesto Rodriguez-Tobon, Sergio Navarro-Serna, Evelyne Paris-Oller, Maria Oficialdegui, Xonia Carvajal-Vergara, Laura Ordovas, Felipe Prosper, Francisco Alberto Garcia-Vazquez, Xabier L. Aranguren
Summary: The generation of organs using pluripotent stem cells combined with genetically engineered pig embryos through blastocyst complementation could provide a solution to the worldwide shortage of transplantable organs. In this study, a protocol to create vascular-disabled pig embryos using the CRISPR/Cas9 system was optimized, which could contribute to the generation of rejection-free humanized organs in pigs.
Article
Cardiac & Cardiovascular Systems
Jef Van den Eynde, Xander Jacquemyn, Nicolas Cloet, Dries Noe, Hilde Gillijns, Marleen Lox, Willy Gsell, Uwe Himmelreich, Aernout Luttun, Keir McCutcheon, Stefan Janssens, Wouter Oosterlinck
Summary: In this study, a rat model was established to investigate the effects of AVFs on the cardiovascular system and kidneys. The findings showed that AVF creation exacerbated inflammation and organ dysfunction in chronic kidney disease. Additionally, gene expression changes were identified, which could provide important information for the management of cardiorenal syndrome.
JOURNAL OF THE AMERICAN HEART ASSOCIATION
(2022)
Article
Oncology
Maria Victoria Mateos, Felipe Prosper, Jesus Martin Sanchez, Enrique M. Ocio, Albert Oriol, Cristina Motllo, Jean-Marie Michot, Isidro Jarque, Rebeca Iglesias, Maria Sole, Sara Martinez, Carmen Kahatt, Salvador Fudio, Gema Corral, Ali Zeaiter, Lola Montilla, Vincent Ribrag
Summary: The triple combination of plitidepsin, BTZ, and DXM showed moderate activity and acceptable safety in adult patients with relapsed/refractory multiple myeloma.
Review
Oncology
Ane Amundarain, Fernando Pastor, Felipe Prosper, Xabier Agirre
Summary: Multiple Myeloma (MM) remains an incurable disease due to high relapse rates and fast development of drug resistances. The introduction of monoclonal antibodies (mAb) has caused a paradigm shift in MM treatment, paving the way for targeted approaches with increased efficacy and reduced toxicities. Nevertheless, antibody-based therapies face several difficulties such as high immunogenicity, high production costs and limited conjugation capacity, which we believe could be overcome by the introduction of nucleic acid aptamers. Similar to antibodies, aptamers can bind to their targets with great affinity and specificity. However, their chemical nature reduces their immunogenicity and production costs, while it enables their conjugation to a wide variety of cargoes for their use as delivery agents. In this review, we summarize several aptamers that have been tested against MM specific targets with promising results, establishing the rationale for the further development of aptamer-based strategies against MM. In this direction, we believe that the study of novel plasma cell surface markers, the development of intracellular aptamers and further research on aptamers as building blocks for complex nanomedicines will lead to the generation of next-generation targeted approaches that will undoubtedly contribute to improve the management and life quality of MM patients.
Review
Biochemical Research Methods
Marian Gimeno, Katyna Sada del Real, Angel Rubio
Summary: This study compared six different machine learning methods and found that tree-based methods are the most interpretable.
BRIEFINGS IN BIOINFORMATICS
(2023)
Article
Biochemistry & Molecular Biology
Federica Grilli, Ennio Albanesi, Beatriz Pelacho, Felipe Prosper, Paolo Decuzzi, Daniele Di Mascolo
Summary: Depositing stem cells at the injury site is a clinically relevant strategy for tissue repair and angiogenesis, but insufficient cell engraftment and survival requires the development of new scaffolds. In this study, a microstructured poly(lactic-co-glycolic acid) (PLGA) fabric was investigated as a promising biodegradable scaffold for adipose-derived stem cell (ADSC) tissue integration. The results showed that ADSCs reassembled into spheroidal-like structures on the PLGA fabric, preserving cell viability and promoting a nonlinear actin organization. Moreover, the secretion of specific factors involved in angiogenesis, extracellular matrix remodeling, and stem cell homing was enhanced on the PLGA fabric compared to conventional substrates.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Helen Willcockson, Huseyin Ozkan, Jose Valdes-Fernandez, Liubov Arbeeva, Esra Mucahit, Layla Musawwir, Lola B. B. Hooper, Froilan Granero-Molto, Felipe Prosper, Lara Longobardi
Summary: This study investigated the role of Ccr2 in osteoblasts in the progression of post-traumatic osteoarthritis (PTOA) and pain. Early inactivation of Ccr2 in osteoblasts delayed cartilage damage and matrix degeneration, as well as DMM-induced bone thickness. Late deletion had less evident improvements. Our findings suggest that Ccr2 in osteoblasts contributes to PTOA progression and pain.
Article
Biochemistry & Molecular Biology
Sophia Mueller-Dott, Eirini Tsirvouli, Miguel Vazquez, Ricardo O. Ramirez Flores, Pau Badia-i-Mompel, Robin Fallegger, Denes Tuerei, Astrid Laegreid, Julio Saez-Rodriguez
Summary: Gene regulation plays a crucial role in cellular processes related to human health and disease. This study presents and evaluates a collection of reliable and comprehensive TF regulons created using the CollecTRI meta-resource. These regulons accurately estimate TF activities and help interpret transcriptomics data.
NUCLEIC ACIDS RESEARCH
(2023)