Development of specific antibodies to study R-loops dynamics in response to anticancer treatment

R-loops are unusual nucleic acid structures consisting of an RNA/DNA hybrid and a single stranded DNA (ssDNA). They form during transcription and regulate key physiological processes, including gene expression. However, R-loop imbalance, caused by their unscheduled formation or failure to be timely resolved, can lead to genome instability and deregulated gene expression and has been involved in oncogenesis and cancer progression. To assess R-loop contribution to these processes, accurate R-loop detection and quantification in cancer contexts is necessary.

Our project aims to develop and apply structure-specific antibodies to quantitatively detect R-loops and use them to monitor R-loop dynamics in cancer cell lines. To achieve this, we will use a validated library to select specific antibodies by phage display. Selected candidates will be validated in vitro and in cells, in comparison with reagents currently used in the field. They will then be applied to imaging, sequencing, and proteomics approaches to monitor R-loops in response to anticancer therapies in human cancer cell lines. This project will not only develop new tools that are versatile across different biological applications and experimental settings, but also advance our mechanistic understanding of the cellular response to anticancer treatments, paving the way for the development of therapeutic strategies aimed at improving the efficacy of anticancer therapies.

3 Selected Publications (PhD and Master students are underlined)

1) Geraud M*, Cristini A*, Salimbeni S*, Bery N, Jouffret V, Russo M, Ajello AC, Fernandez Martinez L, (…) Capranico G^#, Sordet O^#. TDP1 mutation causing SCAN1 neurodegenerative syndrome hampers the repair of transcriptional DNA double-strand breaks. Cell Rep. 2024 May 16;43(5):114214. *Co-first authors.

2) McCann JL*, Cristini A*, (…) Miller KM^#, Gromak N^# and Harris RS^#. APOBEC3B regulates R-loops and promotes transcription-associated mutagenesis in cancer. Nat Genet. 2023 Oct;55(10):1721-1734. *Co-first authors.

3) Cornebois A, Sorbara M, Cristol M, Vigne E, Cordelier P, Desrumeaux K, Bery N. Discovery of SOCS7 as a versatile E3 ligase for protein-based degraders. iScience 2024 Apr 23;27(5):109802.

Main Techniques: We will employ a wide range of techniques, including cell culture, pahge display, ELISA, cloning, high-content and confocal imaging, live imaging, NGS (such as DRIP-seq, RNA-seq, ChIP-seq), mass spectrometry.

The student will work in two teams of the CRCT. He will work under the supervision of Dr Nicolas Béry (webpage: https://www.crct-inserm.fr/en/oncoproteins-and-protein-protein-interactions-involved-in-therapeutic-resistance/) for antibody selection and in vitro validation; and with Dr Agnese Cristini (webpage: https://www.crct-inserm.fr/en/exploring-transcription-in-oncogenesis-and-response-to-anticancer-treatment/) for imaging and sequencing in cancer cell lines. The PhD student will also benefit from the scientific environment of the SIGNATHER (Favre/Sordet) and the ImPact (Cordelier) teams, which includes several PhD students. We are located at the CRCT, a new center built in 2014 and representing the research unit of the Oncopole campus, which is a great example in France of symbiosis between research, care and pharmaceutical companies. The CRCT comprises 20 research groups and a cutting edge technological cluster (flow cytometry, imaging, genomics…). The student will benefit from the facilities, equipment and expertise available within the team and at the CRCT, ensuring optimal conditions to carry out the PhD.

We are looking for a highly self-motivated candidate who is curious and enthusiastic about working in a collaborative team, with a strong interest in antibody, RNA, and cancer progression. The candidate should hold a M.Sc. degree in Biology, Oncology, Biochemistry, or a related field, and possess wet-lab experience, demonstrated through at least a 6-month internship. Supervision will be provided for all aspects of the work; however, expertise in standard molecular biology techniques, along with a strong interest or expertise in bioinformatics, is particularly welcome. Strong communication skills and the ability to work both autonomously and as part of a team are essential. French is not required if the candidate is fluent in English (writing, speaking, and comprehension).