Maintenance of genome integrity during DNA replication

  • The human body is made of 3.7x1013 cells, which contain about two meters of DNA each. As our cells undergo a total of 1016 divisions in a life time, they synthesize therefore more than 2x1016 meters of DNA, which represents 130,000 times the distance from Earth to the sun! This daunting task is executed by micro-machines called replisomes, containing hundreds of proteins. Replisomes assemble at replication origins and generate DNA structures called replication forks. As they progress along the chromosomes, replisomes often encounter obstacles such as DNA lesions or transcription complexes, leading to replication fork arrest. Stalled forks are fragile structures that can give rise to chromosome breaks and trigger genomic instability if they are not rapidly restarted. Fork stalling occurs even more frequently in cancer cells due to the deregulation of oncogenic pathways. Oncogene-induced replication stress (RS) promotes genomic instability and is therefore the driving force of tumorigenesis. However, RS represents also the Achilles’ heel of cancer cells as it interferes with cell proliferation and sensitizes them to chemotherapeutic agents. Understanding how normal and cancer cells respond to replication stress represents therefore a major challenge in cancer biology.

    Our group investigates the cellular responses to replication stress in budding yeast and in human cell lines. Owing to the small size of its genome and the power of molecular genetics, budding yeast is an invaluable model organism to study the RS response and to characterize novel mechanisms that are conserved in human cells and are relevant to cancer biology. This is achieved through the use of powerful technologies to monitor the progression, arrest and recovery of replication forks. These methods include single-molecule approaches such as DNA combing and DNA fiber spreading, chromosome-based assays such as pulsed-field gel electrophoresis and NGS-based assays such as ChIP-seq, BrdU-IP-seq, DRIP-seq and BLESS. Together, these methods provide a comprehensive view of the replication stress response in yeast and human cells, from individual DNA molecules to whole genomes.

    To further investigate the links between replication stress and cancer, we have recently teamed up with the group of Jérôme Moreaux (Hematology Department of the University Hospital of Montpellier) who is an expert of the pathophysiology of malignant plasma cells and in particular of Multiple Myeloma (MM).

    To date, our research is funded by:

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    Caroline Bret
    Bret Caroline
    Armelle Lengronne
    Lengronne Armelle
    Yea-Lih Lin
    Lin Yea-Lih
    Jérôme Moreaux
    Moreaux Jérôme
    Benjamin Pardo
    Pardo Benjamin
    Philippe Pasero
    Pasero Philippe
    Jérôme Poli
    Poli Jérôme
    Hélène Tourriere
    Tourriere Hélène
    Antoine Barthe
    Barthe Antoine
    Angelique Bruyer
    Bruyer Angelique
    Guilhem Requirand
    Requirand Guilhem
    Nicolas Robert
    Robert Nicolas
    Matthieu Abouladze
    Abouladze Matthieu
    Elvira Garcia de paco
    Garcia de paco Elvira
    Ouissem Karmous gadacha
    Karmous gadacha Ouissem
    Sylvain Kumanski
    Kumanski Sylvain
    Audrey Vernet
    Vernet Audrey
    Flavie Coquel
    Coquel Flavie
    Hugues De Boussac
    De Boussac Hugues
    Diyavarshini Gopaul
    Gopaul Diyavarshini
    Mélanie Larcher
    Larcher Mélanie
    Herve Techer
    Techer Herve
    Julie Devin
    Devin Julie
    Romain Forey
    Forey Romain
    Samira Kemiha
    Kemiha Samira
    Veronika Vikova
    Vikova Veronika
    Lavinia Grasso
    Grasso Lavinia
    Emmanuel Varlet
    Varlet Emmanuel
    Thibaud Vicat
    Vicat Thibaud


    SAMHD1 acts at stalled replication forks to prevent interferon induction.

    Coquel F, Silva MJ, Técher H, Zadorozhny K, Sharma S, Nieminuszczy J, Mettling C, Dardillac E, Barthe A, Schmitz AL, Promonet A, Cribier A, Sarrazin A, Niedzwiedz W, Lopez B, Costanzo V, Krejci L, Chabes A, Benkirane M, Lin YL, Pasero P

    2018 - Nature, 557(7703):57-61

    Request for full article29670289

    Transcription-Replication Conflicts: Orientation Matters

    Lin, YL., Pasero, P.

    2017 - CELL, 170(4):603-604

    Request for full article28802036

    Senataxin resolves RNA:DNA hybrids forming at DNA double-strand breaks to prevent translocations.

    Cohen S, Puget N, Lin YL, Clouaire T, Aguirrebengoa M, Rocher V, Pasero P, Canitrot Y, Legube G

    2018 - Nat Commun, 9(1):533

    Request for full article29416069

    DDR Inc., one business, two associates.

    Moriel-Carretero M, Pasero P, Pardo B

    2018 - Curr Genet

    Request for full article30467717
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    Publications of the team

  • Current research projects address different aspects of the RS response. One of our aims is to identify the source of intrinsic RS in yeast and in human cancer cell lines, with a focus on the regulation of dNTP pools and the conflicts between replication and transcription. Another objective is to characterize the mechanism by which cells process stalled replication forks to activate checkpoint pathways and promote fork restart. This poorly characterized process requires the coordinated action of nucleases, recombinases, SMC proteins and a chromatin remodellers. Understanding these mechanisms is highly relevant to cancer biology as they impact both the stability of the genome and the ability of cancer cells to resist chemotherapy. Interestingly, we have recently found that the processing of stalled replication forks also generate small ssDNA fragments that accumulate in the cytosol and trigger the production of type I interferons and pro-inflammatory cytokines. Since inflammation contributes to the rejection of cancer cells by the immune system, the existence of a direct link between the replication stress response and inflammation has major implications for cancer therapy.

    Figure 1
    Figure 3

    MM is a neoplasia of clonal malignant plasma cells that accumulate in the bone marrow. MM is a genetically and clinically heterogeneous disease and genome sequencing studies have recently revealed considerable heterogeneity and genomic instability, a complex mutational landscape and a branching pattern of clonal evolution. Given these observations, our vision is that treatment improvements will come from a better comprehension of MM tumorigenesis and detailed molecular analyses to develop individualized therapies taking into account the molecular heterogeneity and subclonality evolution. We use genome data, computing, mathematical modeling and unique cellular models to study plasma cell neoplasms and their normal counterparts with a focus on epigenome modifications and genomic instability. These approaches work in tandem with rapid technological advances to understand the mechanisms of tumor progression and drug resistance in order to develop new strategies to diagnose and treat myeloma patients.

    Figure 1