Integration of multi-omics data for the detection of molecular markers of clinical interest.
Objective: Given the high inter- and intra-tumoral heterogeneity present in different cancer types and the unknown drug resistance mechanisms, it is increasingly importante to establish prevention and treatment strategies considering each individual and tumor variability using high throughput analysis. The development of next generation sequencing (NGS) technologies has led to the generation of a massive volume of genomic, transcriptomic, and epigenomic data. The integration of these high throughput data types, while presenting a challenge, allows us to have a systemic view of tumor biology and metabolic pathways affected by these alterations. Then, these data can be associated with clinical data in order to allow us to better understand the impact these alterations have on the patients' clinical outcomes.
Related publications:
Poubel, C. P. ; Mansur M. B. ; Boroni M. ; Emerenciano, M. . FLT3 overexpression in acute leukaemias: New insights into the search for molecular mechanisms. Biochimica et Biophysica Acta-Reviews on Cancer v. 1872, p. 80-88, 2019. http://dx.doi.org/10.1016/j.bbcan.2019.06.001
Guerra JV da S, Pereira BM de S, Cruz JGV da, Scherer N de M, Furtado C, Montalvão de Azevedo R, Oliveira PSL de, Faria P, Boroni M, de Camargo B, et al. Genes controlled by DNA methylation are involved in Wilms tumor progression. Cells v. 8. 2019. http://dx.doi.org/10.3390/cells8080921
Costa RL, Boroni M, Soares MA. Distinct co-expression networks using multi-omic data reveal novel interventional targets in HPV-positive and negative head-and-neck squamous cell cancer. Sci Rep. 2018 Oct 15;8(1):15254. https://doi.org/10.1038/s41598-018-33498-5
Studying tumor microenvironment populetions and their interactions with malignant cells
Objective: Communication between tumor cells and the tumor microenvironment is an essential mechanism for the support or prevention of tumor development or progression. Using Single-Cell sequencing, our group has studied how cell populations in the tumor microenvironment influence tumor progression as well as the predominant immune response type, through antigen prediction, evaluation of TCR and BCR receptor repertoires, immunomodulatory molecule panels, among others. We also investigated the role of molecules such as miRNAs that are released through extracellular vesicles as a mechanism for mediating paracrine signaling between cells. They play an important role in regulating cell pathways in target cells, modulating various processes related to tumor progression and metastasis, such as angiogenesis, immune escape, epithelial-mesenchymal transition, invasion and resistance to multiple drugs.
Related publications:
Jorge, N.A.N., Cruz, J.G.V., Pretti, M.A.M., Bonamino, H.M., Possik, A.P., Boroni, M. Poor clinical outcome in metastatic melanoma is associated with a microRNA-modulated immunosuppressive tumor microenvironment. J Transl Med 18, 56, 2020. https://doi.org/10.1186/s12967-020-02235-w
Pretti, M. A. M. ; Bernardes S. ; Cruz, J. G. V. ; Boroni, M. ; Possik, P. A. . Extracellular vesicle-mediated crosstalk between melanoma and the immune system: impact on tumor progression and therapy response. Journal of Leukocyte Biology, v. 108, p. 1, 2020. http://dx.doi.org/10.1002/JLB.3MR0320-644R
Pereira, M B ; Barros, L R C ; Bracco, P A ; Vigo, A ; Boroni, M ; Bonamino, M H ; Lenz, G. Transcriptional characterization of immunological infiltrates and their relation with glioblastoma patients overall survival. OncoImmunology, v. 01, p. e1431083, 2018. https://doi.org/10.1080/2162402X.2018.1431083
Barros, L. R. C. ; Souza-Santos, P. T. ; Pretti, M. A. M. ; Vieira, G. F. ; Bragatte, M. A. S. ; Mendes, M. F. A. ; De Freitas, M. V. ; Scherer, N. M. ; De Oliveira, I. M. ; Rapozo, D. C. M. ; Fernandes, P. V. ; Simão, T. A. ; Soares-Lima, S. C. ; Boroni, M. ; Ribeiro Pinto, L. F. ; Bonamino, M. H. High infiltration of B cells in tertiary lymphoid structures, TCR oligoclonality, and neoantigens are part of esophageal squamous cell carcinoma microenvironment. Journal of Leukocyte Biology, v. 12, p. 1e, 2020. http://dx.doi.org/10.1002/jlb.5ma0720-710rrr