Università degli Studi di Milano, Milan, Italy
Universita’ degli Studi di Milano, Milan, Italy
Liceo Scientifico “G. Marconi”, Pesaro (PU), Italy
11/2019-present Bioinformatician in Dr. Nicassio’s laboratory , IIT, Milan, Italy
04/2018-04/2019 Master student in Dr. Tiana’s laboratory of Theoretical Biophysics, Università degli Studi, Milan, Italy
Internship in Dr. Giorgetti's laboratory, Friedrich Miescher Institute, Basel, Switzerland
Nanopore sequencing is a novel technology that permits to sequence single DNA or RNA molecules. In particular, for the first time, it allows to directly sequence full-length RNA molecules without intermediate steps (retrotranscription or amplification), therefore making it possible to profile transcriptomes at an unprecedented level of detail.
As such, Nanopore sequencing is a very promising tool. In our lab we are using Nanopore and breast cancer models to gain insight into the transcriptional landscape of cancer cells and to see how it changes and adapts in response to chemoterapy.
Single molecule sequencing through Nanopore constitutes a new frontier in genomic studies, in particular in the field of cancer. Our knowledge of genome organization and regulation will be profoundly affected by this unprecedented ability to investigate genomic sequences directly.
TNBC is an aggressive subtype of breast cancer that does not express the genes for estrogen receptor (ER), progesterone receptor (PR) and the growth factor receptor HER2/neu. Most hormone therapies target those receptors and this is why TNBC cannot be treated with standard methods. Furthermore, TNBC exhibits a certain grade of plasticity when subjected to chemotherapy, but little is known of the regulatory mechanisms responsible for this behavior. Recently, non-coding RNAs (ncRNAs) have been shown to provide an additional layer of gene expression control through various mechanisms. An important class of ncRNAs are microRNA primary transcripts (pri-miRNAs), which act as precursors in miRNA biogenesis but could also exert other functions as cis- or trans-acting regulatory ncRNAs.
The aims of my project are:
- leveraging full-length, direct RNA Nanopore sequencing to profile the transcriptional landscape of cancer cells;
- gaining new insights into the mechanisms linked to the processing of transcripts and to potential functions of pri-miRNAs.
We are using Nanopore direct RNA sequencing to profile chromatin-associated and cytoplasmic RNAs in breast cancer cells prior to and after chemotherapy treatment. Nanopore generates long genomic reads that need to be analysed and quantified in order to identify lncRNA and pri-miRNA transcripts. Consequently we are developing specific bioinformatic pipelines to filter and cluster the genomic data, dealing with the experimental and systematic bias that could eventually occur.
We expect to unambiguosly identify and quantify the expression of pri-miRNAs, lncRNAs and their processing intermediates.
These data will allow us to compare naive tumour cells with cells subjected to chemo-treatment and detect the influence of any possible sequence rearrangement on the development of drug resistance.