ibs.GRANADA scientists develop software for the analysis of RNA, key molecules in multiple diseases and potential biomarkers

The study, published in the prestigious journal Nucleic Acids Research, presents the latest update of sRNAbench, a software for analysis of microRNA sequencing data, which is very useful in the biomedical field.

The multidisciplinary group TEC-16 of Advanced Therapies: differentiation, regeneration and cancer of the Biosanitary Research Institute of Granada (ibs.GRANADA), which includes researchers from the Faculty of Sciences and Medicine of the University of Granada, in collaboration with Several international groups from the Netherlands and Norway have published the latest version of the sRNAbench software. Used in more than 200 scientific publications, it is one of the leading programs in the analysis of microRNA massive sequencing data.

MicroRNAs or miRNAs are small RNAs that are very important for the regulation of gene expression and cell behavior. These molecules are present both inside cells and in different biofluids such as blood, urine, cerebrospinal fluid, etc. They are usually released by cells freely or inside extracellular vesicles. Its deregulation has been associated with different types of cancer and autoimmune diseases. For this reason, they have great potential as biomarkers of these pathologies, and in recent years the number of sequencing of these molecules has increased considerably.

In this latest version of the sRNAbench software developed by ibs.GRANADA and the University of Granada, and recently published in Nucleic Acids Research, it has been optimized for ease of use by inexperienced users, as well as to allow the analysis of large amounts of samples simultaneously. This is expected to reach a greater number of researchers.

In this study carried out from the ibs.GRANADA, an example of application with patients with bronchiectasis is shown. This disease, where there is an abnormal and irreversible dilation of the bronchial tree, can be aggravated when an infection by the bacteria occurs. Pseudomonas aureginosa. Thanks to the new functionalities incorporated in this new version of sRNAbench, it is possible to detect the presence of this bacterium in samples from infected patients who presented symptoms, even with a negative culture.

In addition, as miRNAs can also be released inside vesicles into body fluids, in another study by researchers from the Advanced Therapies and Biomedical Technologies area of ibs.GRANADA, for which this software called sRNAbench was used, they related the presence of certain miRNAs associated with vesicles with Hodgkin's lymphoma, detected in patients using diagnostic imaging techniques such as PDF-PET.

The development of this new version of the software by these scientists from Granada facilitates the work of all researchers in the field of miRNAs, a field with application to many biomedical aspects and with great potential for clinical translation.

The work has been funded by the European project ELBA: Towards widespread clinical application of blood-based diagnostic tolos, the research project of excellence "Implementation of a novel platform to monitor tumor heterogeneity as a crucial determinant for individualized diagnostic and therapeutic outcome" (PIE16/00045), financed by the Carlos III Health Institute and by the Doctors Galera and Requena Chair of Cancer Stem Cell Research at the University of Granada.

About the research group

The research group "Advanced Therapies: differentiation, regeneration and cancer" of ibs.GRANADA, led by Juan Antonio Marchal Corrales, focuses its research on two main axes: regenerative medicine and experimental oncology, from a translational and interdisciplinary perspective, with application in diagnosis and therapeutic use to benefit the health of patients with highly prevalent diseases, such as degenerative diseases and cancer. This multidisciplinary and interdisciplinary orientation is based on the use of knowledge in nanotechnology and nanomedicine to meet these objectives. Some of its lines of research are the therapeutic application of adult and progenitor stem cells in pathologies, 3D bioprinting and development of bioinks and generation of natural and synthetic biomaterials with application to prevalent pathologies, the development of preclinical models for new useful treatments in regenerative medicine and cancer, cancer gene therapy: suicide genes and CAR-T systems for solid tumors and the use of chimeric cytokines in cell differentiation.

More information about the group at https://www.ibsgranada.es/grupos-de-investigacion/tec16-terapias-avanzadas-diferenciacion-regeneracion-y-cancer/

Referencias bibliográficas:

Ernesto Aparicio-Puerta, Cristina Gómez-Martín, Stavros Giannoukakos, José María Medina, Chantal Scheepbouwer, Adrián García-Moreno, Pedro Carmona-Saez, Bastian Fromm, Michiel Pegtel, Andreas Keller, Juan Antonio Marchal, Michael Hackenberg, sRNAbench and sRNAtoolbox 2022 update: accurate miRNA and sncRNA profiling for model and non-model organisms, Nucleic Acids Research, 2022; gkac363, https://doi.org/10.1093/nar/gkac363

Esther EE Drees,Margaretha GM Roemer,Nils J. Groenewegen,Jennifer Perez-Boza,Monique AJ van Eijndhoven,Leah I. Prins,Sandra AWM Verkuijlen,Xuan-Mai Tran,Julia Driessen,GJC Zwezerijnen,Phylicia Stathi,Kevin Mol,Joey JJP Karregat,Aikaterini Kalantidou,Andrea Vallés-Martí,TJ Molenaar,Ernesto Aparicio-Puerta,Erik van Dijk,Bauke Ylstra,Catharina GM Groothuis-Oudshoorn,Michael Hackenberg,Daphne de Jong,Josée M. Zijlstra,D. Michiel Pegtel, Extracellular vesicle miRNA predict FDG-PET status in patients with classical Hodgkin Lymphoma, Journal of Extracellular Vesicles, 2021; jev2.12121, https://doi.org/10.1002/jev2.12121