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Presentation

Stem cells are essential for tissue and organ development, as well as their maintenance throughout life. They are characterized by their ability to self-renew and as well as to produce differentiated progeny. Understanding the balance between these dual properties is an important aim of regenerative medicine and has crucial implications for cancer biology. Our group aims to uncover the mechanisms that govern these processes and their collective role in promoting tissue homeostasis.

 

Our Key Research Questions

 

The Bardin lab work addresses three fundamental questions:

  1. How is self-renewal and differentiation orchestrated?
  2. What are the causes and consequences of loss of stem cell genome integrity?
  3. Which mechanisms integrate homeostasis at the tissue level?

 

Drosophila melanogaster Midgut: Our Model System

 

To address these questions, we use the Drosophila melanogaster midgut as a simplified yet powerful model, characterized by the availability of an extensive range of genetics tools facilitating its study. The midgut contains around 2,000 multipotent intestinal stem cells (ISCs) that give rise to two differentiated cell types required for intestinal function: enterocytes (ECs) and enteroendocrine cells (EEs). While these differentiated cells are replaced approximately once a week in healthy animals, they can be rapidly regenerated upon bacterial infection or chemical treatment. Thus, the Drosophila midgut is an efficient and simple system for modelling mammalian tissues such as the intestine, lung or skin that need to regenerate in response to environmental stimuli.

 

1. Regulation of Self-Renewal and Differentiation

 

To gain insight into self-renewal and differentiation controls of ISCs, we have used both unbiased genetic screen and candidate gene approaches that identified several regulators or lineage decisions (Bardin et al 2010, Development ; Perdigoto et al 2011, Development ; Sallé et al 2017, EMBO J).

Our subsequent work highlighted the role of chromatin remodeling in stem cell proliferation, revealing critical remodelers conserved in mammals (Andriatsilavo et al 2018, PLoS Genet ; Gervais et al 2019, Dev Cell).

To further explore gene and cell-specific transitions, we performed mapping of chromatin associated factors using a statistical modeling approach, which enabled us to characterize genome-wide chromatin state transitions associated with differentiation and lineage priming (Josserand et al 2023, Dev Cell).

 

Figure 2. Chromatin state transitions between ISCs and ECs, ISCs and EEs. Boxes represent the proportion of genes marked by each chromatin state. The flows represent the proportion of genes undergoing chromatin state transitions from one state to another between cell types.

 

We are now investigating both cell-intrinsic and extrinsic factors, such as the diet and microbiome, that may impact the function of chromatin remodelers and gene expression.

 

2. Causes and Consequences of Genome Integrity Loss

 

Past work from the lab demonstrated that ISCs acquire frequent spontaneous mutations during aging,  with easily identifiable phenotypic alteration including frequent mutations in the tumor suppressor gene Notch which drive tumor formation (Siudeja et al 2015, Cell Stem Cell)

 

Figure 3. During aging, spontaneous mutations arise in adult stem cells. This leads to the frequent inactivation of the tumor suppressor gene, Notch, promoting neoplasia formation (in red) in 10% of aged male flies.

 

Using this model, we have made several key discoveries:

  • Clonal analysis of stem cell mutations highlighted the existence of drivers and passengers of Notch inactivation and showed that these fly tumors have a similar mutation burden to some human cancers (Riddiford et al 2021, Genome Res).

  • Whole genome sequencing (WGS) analysis of clonally expanded tissue revealed that somatic transposable element mobility alters stem cell genomes (Siudeja, van den Beek et al 2021, EMBO J).

  • Loss of heterozygosity, a process integral to human familial cancers, was shown to be driver by mitotic recombination, depending on double Holiday Junction resolution (Al Zouabi et al 2023, Cell Rep)

Currently, our focus lies on studying the early effects of spontaneous disruptions of genome integrity, and identifying the buffering mechanisms that may mitigate these changes.

 

3. What mechanisms integrate homeostasis at the tissue level?

 

Tissue homeostasis depends on a delicate balance between stem cell self-renewal and differentiation. To investigate factors that may impact this balance, we investigated replication stress as a potential vulnerability of ISCs upon challenge. Our recent findings revealed that replication stress due to altered nucleotide pools can be buffered through gap junction-mediated nucleotide exchange between cells in larval wing disc progenitors. However, ISCs lack gap junction, preventing similar mechanisms which may predispose the midgut to replication stress (Boumard, Le Meur et al, accepted in principle, Dev Cell)

 

Figure 4. Model of nucleotide sharing through gap junctions in different tissues, buffering replication stress in the wing disc progenitor cells but not in midgut ISCs.

 

Building on these findings, we are now exploring the role of a broader range of metabolic sharing in maintaining tissue homeostasis.

 

Bardin Lab, October 2024.

Members

Former team members

  • MARINE STEFANUTTI (2015-2024), Engineer assistant
  • BENJAMIN BOUMARD (2022-2023), Post-Doctoral Researcher
  • HOJUN JEON (2019-2023), Post-Doctoral Researcher
  • NATALIA RUBANOVA (2019-2023), Post-Doctoral Researcher
  • ANNABELLE SUISSE (2019-2023), Post-Doctoral Researcher
  • MANON JOSSERAND (2018-2022), PhD Student
  • KATARZYNA SIUDEJA (2016-2022), Permanent researcher
  • LARA AL ZOUABI (2020-2021), Post-Doctoral Researcher
  • BENJAMIN BOUMARD (2017-2021), PhD Student
  • NICK RIDDIFORD (2016-2021), Post-Doctoral Researcher
  • LARA AL ZOUABI (2016-2020), PhD Student
  • MARIUS VAN DEN BEEK (2016-2019), Post-Doctoral Researcher
  • KATARZYNA SIUDEJA (2011-2016), Post-Doctoral Researcher
  • PATRICIA SKORSKI (2011-2015), Engineer
  • JEREMY SALLE (2011-2015), Post-Doctoral Researcher
  • MAHEVA ANDRIATSILAVO (2010-2015), PhD Student

Publications

Life of the team

More news on the lab's BlueSky account: https://bsky.app/profile/bardinlab.bsky.social.

2025.04-05 - International meetings

 

Clara (left) and Laila (right) after their respective poster session.

Conferences are an opportunity to present one's work, obtain constructive feedback and get immersed in the scientific community.

In late April, Clara (2nd year PhD candidate) travelled to Italy to attend the EMBO Workshop on Chromosome Segregation and Aneuploidy. This was a great opportunity as the work was selected for both a flash talk and a poster.

Laila (1st year PhD candidate) attended the Cell Symposium Metabolites: Organellar communication in health and disease in Spain with Allison. She presented a poster and received very positive feedback on her project.

2025.03.21 - American Drosophila Research Conference

 

Bénédicte (left) before her talk and Allison (right) at the EQDB stand.

Bénédicte (4th year post-doctoral fellow) and Allison attended the 66th Annual American Drosophila Research Conference held in San Diego, USA.

Bénédicte had the opportunity to give a short oral presentation on her research project that focuses on understanding the effects of mechanical forces on tissue homeostasis. She also introduced the En Quête de Bio workshop (EQDB, https://www.eqd-bio.org/) that she has been co-organising with Allison, for several years with the support of the Société Française de Biologie du Développement (SFBD).

2025.03.05 - Lab dinner

 

Allison was elected EMBO Member in 2024.

Earlier this year, the Bardin Lab celebrated 2025 by meeting at Allison's place for "apéro" after work, before having dinner together. 

This first lab event of the year also allowed the lab to reflect on 2024 accomplishments. 

Allison was elected an EMBO member, which "recognises a scientist’s research excellence and outstanding achievements". 

Moreover, several new minds joined the lab and secured selective grants (post-doctoral grant from Fondation ARC for Shiva, PhD grant from ED515 Complexité du Vivant for Laila), leading to the initiation of some new research projects we are quite excited about. 

We are looking forward to see what 2025 will bring!

2025.01.06 - Welcome, Maia and Caterina!

 

Maia Collin (left) and Caterina Vitali (right)

From this week until the end of June, the lab will be hosting Maia and Caterina for their respective Master 2 internships.

Maia is enrolled in the MD-PhD program between the Université Lyon 1 and the École Normale Supérieure of Lyon. She will be working with Bénédicte, who is interested in the physical forces exerted on the Drosophila midgut, and the consequences these may have on tissue homeostasis.

Caterina is an Italian student from the Università degli Studi di Milano-Bicocca, enrolled in a double degree program with the Magistère Européen de Génétique at Université Paris Cité. Under Louis' supervision, she will be investigating the links between nutrition and epigenetic changes.

2024.10.10 - Scientific lab retreat

 

The Bardin lab held its bi-annual 3-day scientific retreat in Nibelle (near Orleans). On the menu? Project presentations, brainstorming sessions, but also convivial moments preparing meals and exploring the small town.

This event was also the opportunity to properly welcome Dr. Shivakshi (Shiva) Sulekh, a post-doctoral fellow who joined the team in early October.

Join us

We are always open to hiring highly motivated and curious scientists with a strong background in cell biology and genetics. 

 

If you want to join us as an undergraduate student, a PhD candidate or a post-doctoral fellow, please get in touch directly with Allison (allison.bardin[at]curie.fr) with a CV and brief statement of interest.

There is currently no job offer.

See more job offers from the Research Center

Scientific events

Cours international - séminaireDevelopmental Biology: from stem cells to morphogenesis - 15th edition
Du 21/10/2024 00:00 au 30/10/2024 23:59
Centre de recherche - Paris - Amphithéâtre Hélène Martel-Massignac (BDD)
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