Lunch Talk May 26 2023
Campus Groenenborger, room S.207
Groenenborgerlaan 171, 2020 Antwerp
Gabriel Negreira - Institute of Tropical Medicine Antwerp: Unraveling the dynamics and molecular drivers of mosaic aneuploidy in Leishmania using single-cell genomics
Charlotte Adams - UAntwerp: Fragment ion intensity prediction improves the identification rate of non-tryptic peptides in TimsTOF
About the Lunch Talks
The Biomina Lunch Talks are an initiative of a number of young researchers in the biomina network and is sponsored by the Flemish Government. We aim to stimulate the interaction between researchers from different disciplines who encounter bioinformatics and computational biology, and consequently we focus on a broad and multidisciplinary public. With this informal medium we would like to provide a platform where knowledge and experience can be presented and exchanged, across partners from both academia and industry. In this manner we have had the pleasure to welcome speakers from various institutes such as the University of Antwerp, the Institute of Tropical Medicine, Janssen Pharmaceutica, the Antwerp University Hospital and Open Analytics. Last, but not least, these sessions can provide a great opportunity for young researchers to acquaint themselves with new ideas and methods in the field of bioinformatics and medical informatics.
Leishmania is a protozoan parasite with a unique biology compared to other eukaryotes. One of its many idiosyncrasies is its highly plastic genome, which is characterized, among others, by constant changes in the copy number of individual chromosomes along proliferation. This quickly leads to the co-existence of parasite subpopulation displaying a wide range of distinct karyotypes – and consequently phenotypes – in few generations, a phenomenon named mosaic aneuploidy. This unique mechanism of phenotypic diversification plays an important role in the adaptive skills of these parasites. However, the dynamics of how new karyotypes are generated as well as the molecular factors contributing to this process are still poorly understood.
In this talk, I will discuss how we have been addressing these questions using single-cell DNA and single-cell RNA sequencing technologies, as well as the challenges associated with applying these technologies to non-model organisms such as Leishmania.
The adaptive immune system can recognize and eliminate infected or malignant cells by identifying peptides present on cell surfaces. These peptides, commonly termed immunopeptides, are potential targets for immunotherapy and vaccine development. In recent years, mass spectrometry (MS)-based immunopeptidomics has been used to discover T cell targets against cancer, autoimmune diseases, and pathogens. However, the identification of immunopeptides is challenging because large search spaces are needed that lead to a high false positive rate and a low peptide identification sensitivity. To address this, we propose a rescoring approach that utilizes peptide fragment intensity predictions to leverage the intensity dimension of tandem MS spectra, thereby enhancing the sensitivity and reliability of peptide identifications. I will show how rescoring immunopeptidomics data obtained using a timsTOF instrument could result in new biological insights.