INPhINIT PhD fellowships 2020 – open
Apply to a PhD studentship from the INPhINIT “La Caixa” Fellowship Programme to work with us.
Deadline February 4 2020!
-Title: Identification of neo-epitopes in cancer using massive RNA sequencing data (Dr. M.Mar Albà Soler)
The generation of novel transcripts is a continuous process in evolution. Many of these transcripts are species or lineage-specific. We have recently discovered that many novel transcripts contain small ORFs that can be translated into new proteins, providing abundant raw material for the formation of new protein-coding genes (Ruiz-Orera et al., 2018). These de novo originated proteins have unique sequences that do not resemble any previously existing protein.
In cancer, genomic structural rearrangements and gene expression dysregulation also result in the expression of many novel transcripts, called tumor specific transcripts. Recent experiments indicate that de novo proteins arising from these transcripts are often presented by MHC molecules and are thus an important source of targetable neo-epitopes (Laumon et al., 2018). Current immunotherapy strategies are based on boosting the immune response against neo-epitopes derived from mutated variants of already existing proteins. However, de novo proteins are also probably very relevant in the generation of an immune response against cancer cells. This project will exploit the large amount of available RNA sequencing data from cancer tissues to investigate de novo protein formation in tumors and its potential use in immunotherapy.
Ruiz-Orera, J., Grau-Verdaguer, P., Villanueva-Cañas, J-L., Messeguer, X., Albà, M.M. (2018). Translation of neutrally evolving peptides provides a basis for de novo gene evolution. Nature Ecology and Evolution, 2:890–896.
Laumont, C.M., Vincent, K., Hesnard, L., Audemard, E., Bonneil, E., et al. (2018). Noncoding regions are the main source of targetable tumor-specific antigens. Science Translational Medicine, 10 (470). pii: eaau5516
-Job position description:
The pre-doctoral researcher will use computational tools to quantify the abundance of novel transcripts in RNA sequencing data from cancer and non-cancer samples. Translated proteins will be identified using proteomics and ribosome profiling data from a subset of the samples. The data will be used to build predictive models and to identity putatively translated ORFs in a large cohort of patient samples. The potential of the peptides to bind MHC molecules will be investigated using a combination of experimental data and computational tools.
We are accepting informal applications from outstanding predoctoral and postdoctoral candidates to pursue research on comparative genomics and evolution. Postdoctoral candidates should have a proven research record, with at least one published paper as first author. To be eligible for open PhD fellowship calls (see below) it is often a pre-requisite to have an excellent academic record (average grade 2.5 or higher, corresponding to second first or first class). We offer a highly stimulating research environment in a well-established international research centre (PRBB).
There are a number of regular calls to apply for grants/fellowships:
- Postdoctoral contracts “Beatriu Pinos Programme” from the Catalan Government:
- Postdoctoral contracts “Juan de la Cierva Programme” from the Spanish Ministry of Science:
Juan de la Cierva
- Postdoctoral contracts “Marie Curie” from the European Commission:
- PhD fellowships Spanish Government (FPU):
- PhD fellowships Catalan Government:
- PD fellowships Eurecat:
Vicente López PhD fellowships