DES-ROD: Exploring Literature to Develop New Links between RNA Oxidation and Human Diseases

Essack, Magbubah; Salhi, Adil; Van Neste, Christophe Marc; Raies, Arwa B.; Tifratene, Faroug; Uludag, Mahmut; Hungler, Arnaud; Zaric, Bozidarka; Zafirovic, Sonja; Gojobori, Takashi; Isenovic, Esma; Bajic, Vladan P.

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KAUST Department

Biological and Environmental Sciences and Engineering (BESE) Division
Bioscience Program
Computational Bioscience Research Center (CBRC)
Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division
Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), Computational Bioscience Research Center, Computer (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia

KAUST Grant Number

BAS/1/1606-01-01
FCC/1/1976-17-01
OSR#4129

Date

2020-03-28

Submitted Date

2020-01-09

Permanent link to this record

http://hdl.handle.net/10754/662427

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Abstract

Normal cellular physiology and biochemical processes require undamaged RNA molecules. However, RNAs are frequently subjected to oxidative damage. Overproduction of reactive oxygen species (ROS) leads to RNA oxidation and disturbs redox (oxidation-reduction reaction) homeostasis. When oxidation damage affects RNA carrying protein-coding information, this may result in the synthesis of aberrant proteins as well as a lower efficiency of translation. Both of these, as well as imbalanced redox homeostasis, may lead to numerous human diseases. The number of studies on the effects of RNA oxidative damage in mammals is increasing by year due to the understanding that this oxidation fundamentally leads to numerous human diseases. To enable researchers in this field to explore information relevant to RNA oxidation and effects on human diseases, we developed DES-ROD, an online knowledgebase that contains processed information from 298,603 relevant documents that consist of PubMed abstracts and PubMed Central full-text articles. The system utilizes concepts/terms from 38 curated thematic dictionaries mapped to the analyzed documents. Researchers can explore enriched concepts, as well as enriched pairs of putatively associated concepts. In this way, one can explore mutual relationships between any combinations of two concepts from used dictionaries. Dictionaries cover a wide range of biomedical topics, such as human genes and proteins, pathways, Gene Ontology categories, mutations, noncoding RNAs, enzymes, toxins, metabolites, and diseases. This makes insights into different facets of the effects of RNA oxidation and the control of this process possible. The usefulness of the DES-ROD system is demonstrated by case studies on some known information, as well as potentially novel information involving RNA oxidation and diseases. DES-ROD is the first knowledgebase based on text and data mining that focused on the exploration of RNA oxidation and human diseases.

Citation

Essack, M., Salhi, A., Van Neste, C., Raies, A. B., Tifratene, F., Uludag, M., … Bajic, V. P. (2020). DES-ROD: Exploring Literature to Develop New Links between RNA Oxidation and Human Diseases. Oxidative Medicine and Cellular Longevity, 2020, 1–13. doi:10.1155/2020/5904315

Sponsors

This work is part of the collaboration between the Laboratory of Radiobiology and Molecular Genetics, Institute of Nuclear Sciences Vinca, University of Belgrade, Belgrade, Serbia, and King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal, Saudi Arabia. This work has been supported by grants 173033 (EI) and 173034 (VPB) from the Ministry of Education, Science and Technological Development, Republic of Serbia, and by the KAUST Office of Sponsored Research (OSR) grant OSR#4129 (to EI and VPB). VPB has been supported by the KAUST Base Research Fund (BAS/1/1606-01-01), while ME has been supported by KAUST OSR grant no. FCC/1/1976-17-01. TG has been supported by the King Abdullah University of Science and Technology (KAUST) Base Research Fund (BAS/1/1059-01-01). This article is dedicated to the memory of our coauthor, colleague, and world-class leader and researcher in his field, Professor Vladimir Bajic, who passed away after a valiant battle against lymphatic cancer on 31 October 2019.