Retroelements in primary and metastatic colorectal tumors.

• Grant number: 15/25020-0
• Support Opportunities: Scholarships in Brazil - Doctorate
• Start date: April 01, 2016
• End date: October 31, 2020
• Field of knowledge: Biological Sciences - Biochemistry - Molecular Biology
• Principal Investigator: Pedro Alexandre Favoretto Galante
• Grantee: Fernanda Orpinelli Ramos do Rego
• Host Institution: Hospital Sírio-Libanês. São Paulo , SP, Brazil
• Associated scholarship(s): 17/23575-0 - A comprehensive study of novel Alu insertions in cancer., BE.EP.DR

Abstract

Colorectal cancer (CRC) is the third most common cancer in the world, with nearly 1 million new cases annually diagnosed. Of these, about 50% of the patients evolve to death mainly due to the development of secondary tumors, metastatic, originated from primary colorectal tumors. Thus, studying genetic variations in secondary tumors is central to understand better tumor progression and to provide treatments that are more effective to CRC-affected patients. In this Ph.D. project, we will develop and use bioinformatics methodologies, add next-generation DNA sequencing data, information about gene expression and epigenetics to study genomic variation present in primary and secondary tumors of CRC. Among genomic variations, we will develop methods to identify and evaluate the functional role from those caused by retrocopies of protein-coding genes and Alus, two types of unexplored genomic variations with great potential to be functional. As results, we expect, in a new way, to be the first group to catalog somatic events of protein-coding gene retrocopies and Alus in CRC secondary tumors (metastatic). We also intend to be pioneers in systematic investigation of possible causal relation between the occurrences of variations, generated by retroelements, and tumorigenesis for CRC. Thereby, our work aims to investigate two types of variations poorly studied, mostly in secondary tumors, and contribute to an understanding of the frequency and importance of these variations in tumorigenesis and metastasis of a very relevant type of cancer, the colorectal cancer.

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)

MILLER, THIAGO L. A.; REGO, FERNANDA ORPINELLI; BUZZO, JOSE LEONEL L.; GALANTE, PEDRO A. F.. sideRETRO: a pipeline for identifying somatic and polymorphic insertions of processed pseudogenes or retrocopies. Bioinformatics, v. 37, n. 3, p. 419-421, FEB 1 2021. (15/25020-0, 12/24731-1, 18/15579-8)

DOUILLARD, VENCESLAS; SILVA, NAYANE DOS SANTOS BRITO; BOURGUIBA-HACHEMI, SONIA; NASLAVSKY, MICHEL S.; SCLIAR, MARILIA O.; DUARTE, YEDA A. O.; ZATZ, MAYANA; PASSOS-BUENO, MARIA RITA; LIMOU, SOPHIE; GOURRAUD, PIERRE-ANTOINE; et al. Optimal population-specific HLA imputation with dimension reduction. HLA, v. 103, n. 1, p. 14-pg., 2023-11-11. (12/24731-1, 15/25020-0, 14/50931-3, 13/08028-1, 17/19223-0, 18/15579-8, 13/17084-2, 20/02413-4, 14/50649-6)

NASLAVSKY, MICHEL S.; SCLIAR, MARILIA O.; YAMAMOTO, GUILHERME L.; WANG, JAQUELINE YU TING; ZVERINOVA, STEPANKA; KARP, TATIANA; NUNES, KELLY; MAGLIOCCO CERONI, JOSE RICARDO; DE CARVALHO, DIEGO LIMA; DA SILVA SIMOES, CARLOS EDUARDO; et al. Whole-genome sequencing of 1,171 elderly admixed individuals from Sao Paulo, Brazil. NATURE COMMUNICATIONS, v. 13, n. 1, p. 11-pg., 2022-03-04. (12/24731-1, 20/02413-4, 14/50649-6, 13/08028-1, 18/15579-8, 15/25020-0, 17/19223-0, 13/17084-2)