Long non-coding RNAs annotation and identification of potential therapeutic targets in Schistosoma mansoni

• Grant number: 18/19591-2
• Support Opportunities: Scholarships in Brazil - Master
• Start date: March 01, 2019
• End date: January 31, 2020
• Field of knowledge: Biological Sciences - Parasitology - Helminthology of Parasites
• Principal Investigator: Sergio Verjovski Almeida
• Grantee: Lucas Ferreira Maciel
• Host Institution: Instituto Butantan. Secretaria da Saúde (São Paulo - Estado). São Paulo , SP, Brazil

Abstract

Schistosomiasis is a tropical neglected disease, caused by worms from the genus Schistosoma, with estimates of more than 250 million infected people worldwide. Praziquantel is the only effective drug in schistosomiasis treatment, and therefore new therapeutic targets and drugs that could negatively affect its reproductive biology have been studied. However, research done until now has not explored the potential of long non-coding RNAs (lncRNAs). LcnRNAs in S. mansoni were recently identified by three studies, but because each work used different tools and definitions, part of the lncRNAs is redundant and they were annotated against an obsolete protein-coding transcriptome version. Besides, these works used whole parasites; on the other hand, it has already been shown that lncRNAs have tissue- and cell-specific expression. Thus, our objective is to identify a robust and complete lncRNAs set, that agrees with the present transcriptome, and to re-analyze RNA-seq datasets still non-annotated for the presence of lncRNAs in order to understand the role of lncRNAs in this organism's biology and to identify potential new therapeutic targets. For this, all lncRNAs annotated until now will be compared to the gene sequences of the new proteins to remove pre-mRNAs, and their propensity to be an lncRNA will be re-evaluated by means of the FEELnc tool that uses a random forest algorithm. New lncRNAs in RNA-Seq datasets of single stem cells and of gonads will be identified with a pipeline involving reads mapping and transcripts reconstruction, classification with FEELnc and filtering of potential mRNAs. Based on this new lncRNAs final set, we will perform a quantitative re-analysis of public RNA-Seq datasets to identify differentially expressed genes in different conditions, either physiological or involving drug treatments, with a focus on lncRNAs. (AU)

Scientific publications

(References retrieved automatically from Web of Science and SciELO through information on FAPESP grants and their corresponding numbers as mentioned in the publications by the authors)

MACIEL, LUCAS F.; MORALES-VICENTE, DAVID A.; VERJOVSKI-ALMEIDA, SERGIO. Dynamic Expression of Long Non-Coding RNAs Throughout Parasite Sexual and Neural Maturation in Schistosoma Japonicum. NON-CODING RNA, v. 6, n. 2, JUN 2020. (14/03620-2, 18/19591-2, 18/23693-5)

SILVEIRA, GILBERT O.; AMARAL, MURILO S.; COELHO, HELENA S.; MACIEL, LUCAS F.; PEREIRA, ADRIANA S. A.; OLBERG, GIOVANNA G. O.; MIYASATO, PATRICIA A.; NAKANO, ELIANA; VERJOVSKI-ALMEIDA, SERGIO. Assessment of reference genes at six different developmental stages of Schistosoma mansoni for quantitative RT-PCR. SCIENTIFIC REPORTS, v. 11, n. 1, p. 18-pg., 2021-08-19. (18/19591-2, 16/10046-6, 18/24015-0, 18/23693-5)

AMARAL, MURILO S.; MACIEL, LUCAS F.; SILVEIRA, GILBERT O.; OLBERG, GIOVANNA G. O.; LEITE, JOAO V. P.; IMAMURA, LUCAS K.; PEREIRA, ADRIANA S. A.; MIYASATO, PATRICIA A.; NAKANO, ELIANA; VERJOVSKI-ALMEIDA, SERGIO. Long non-coding RNA levels can be modulated by 5-azacytidine in Schistosoma mansoni. SCIENTIFIC REPORTS, v. 10, n. 1, DEC 9 2020. (18/19591-2, 18/23693-5, 16/10046-6, 18/24015-0)

Academic Publications

(References retrieved automatically from State of São Paulo Research Institutions)

MACIEL, Lucas Ferreira. Long non-coding RNAs identification and annotation in Schistosoma mansoni and Schistosoma japonicum. 2020. Master's Dissertation - Universidade de São Paulo (USP). Instituto de Matemática e Estatística (IME/SBI) São Paulo.