CECAD Winter Retreat 2023

Friday December 15th, 2023

Come and join us for a full day of science and celebration at CECAD!


Puck Knipscheer is a group leader at the Hubrecht Institute and the Oncode institute. She is also professor of Biochemistry of Genome Maintenance at the Human Genetics Department of the Leiden University Medical Center (LUMC).

Puck Knipscheer studied Molecular Sciences at the Wageningen University and specialized in Molecular Biology and Biochemistry. In 2007 she obtained her PhD cum laude from the Erasmus University in Rotterdam based on work performed at the Netherlands Cancer Institute. Under supervision of Dr. Titia Sixma she used X-ray crystallography and biochemistry to identify several mechanisms by which posttranslational modification by SUMO is regulated. With a postdoctoral fellowship by the Dutch cancer society (KWF) she moved to the laboratory of Johannes Walter at Harvard Medical School in Boston. Here she decided to study biochemical pathways in more physiological conditions. She co-developed a Xenopus laevis egg extract-based system that recapitulates the repair of toxic DNA interstrand crosslink (ICL) lesions and used this system to show how the Fanconi anemia pathway acts in a specific step of this process. In 2011 she returned to The Netherlands where she was appointed junior group leader, and later senior group leader (2016), at the Hubrecht Institute in Utrecht. In 2017 her group joined the Oncode Institute, a virtual institute that brings together outstanding fundamental cancer research and valorisation teams in the Netherlands. In 2023 Knipscheer was appointed professor of Biochemistry of Genome Maintenance at the Human Genetics Department of the Leiden University Medical Center (LUMC). During her career she received several prizes and grants including the Heineken Young Scientist Award for Biochemistry and Biophysics (2010), an VIDI grant from the Dutch scientific organization (2011), a project grant from the Dutch Cancer Society (2015), and an ERC Consolidator grant (2020).

Current interests
In her laboratory she uses the Xenopus laevis egg extract-based system to recapitulate complex biochemical pathways and combines this with mass spectrometry, high-throughput sequencing, and biochemical, biophysical and cell biological techniques to gain insights into the molecular details of processes that occur at the replication fork to maintain genome integrity. The repair mechanism(s) of ICLs is still an important subject in the Knipscheer lab, some of our main findings in the past years are: 1) We defined how and when ICL unhooking incisions take place during the Fanconi anemia pathway of ICL repair, 2) we found that ICLs induced by endogenous aldehydes are repaired by the Fanconi anemia pathway but also by a second novel pathway, 3) in collaboration with the Kanaar laboratory (Erasmus Medical Center) we identified and functionally characterized a novel negative regulator of ICL repair. We are currently further investigating the FA pathway and the new pathway of ICL repair, with particular interest in the role of chromatin in these processes. In addition, we are very much interested in the mechanisms that regulate the unwinding of mutagenic secondary DNA structures, specifically G-quadruplex (or G4) structures.­ We have recently identified a multistep mechanism, involving two accessory helicases, that resolves G4s coupled to DNA replication. We are currently defining how this mechanism is regulated and what other mechanisms resolve G4 structures.

The Keynote Lecture
"Functions and mechanisms of DNA G-quadruplex structure regulation"

My group focuses on deciphering the molecular details of processes that maintain genome integrity. Specifically, we are interested in replication fork blocking lesions such as DNA interstrand crosslinks (ICLs) and G-quadruplex structures. We use a powerful biochemical system to recapitulate DNA replication and repair under physiological conditions in vitro, based on Xenopus laevis egg extracts.  For this talk I will focus on mechanisms that regulated G-quadruplex structures.
Our genome contains thousands of guanine-rich DNA sequences that can fold into stable alternative DNA structures called G-quadruplexes or G4 structures. These structures form preferentially at promoters of highly transcribed genes and at telomeres, and are thought to play regulatory roles at these loci. However, they can also cause genome instability when not properly resolved. Therefore, proper regulation of these G4 structures is crucial, and yet, very little is known about the mechanisms that resolve these structures.
Using Xenopus laevis egg extracts we defined an intricate DNA replication-coupled mechanism that resolves G4 structures involving the FANCJ and DHX36 helicases (Sato et al. 2021). Recently, we identified another G4 resolution mechanism that is independent of DNA replication and regulates G4 structures throughout the cell cycle. This mechanism involves the formation of a G-loop, a structure in which an RNA-DNA hybrid (R-loop) is formed across from the G4 structure. Colocalization of G4s and R-loops has been observed genome wide and is thought to regulate gene expression. However, if not properly resolved, both structures can cause genomic instability. Formation of G4 and R-loop structures therefore needs to be carefully controlled, yet how these colocalized G4s and R-loops are formed or resolved remains unknown. Using Xenopus egg extracts, we show G4 structures induce RNA transcript invasion on the opposite strand through a homology-directed process, forming G-loops. Formation of this G-loop is required for DHX36-FANCJ-mediated G4 structure unwinding and subsequent incision of the hybrid strand by the XPF-ERCC1 endonuclease. This allows renewal of the hybrid strand, leading to G-loop dismantling. Consistent with this observation, we showed that deletion of DHX36 and FANCJ in mouse embryonic stem cells causes a concomitant increase in G4 and R-loop formation, leading to DNA double-strand break accumulation and growth defects. Moreover, loss of DHX36 and FANCJ activates a large number of genes that are normally silenced in in these cells, suggesting a direct role for this mechanism in transcriptional silencing. These findings strongly indicate that G-loops represent structural hubs that regulate transcriptional and genomic stability.

Frank Bradke is a group leader at the German Center for Neurodegenerative Diseases (DZNE). He is a Professor at the  the Rhenish Friedrich Wilhelm University of Bonn and member of the Editorial Board for Current Biology.

After studying at the Freie Universität Berlin and University College London, Bradke carried out research at the European Molecular Biology Laboratory (EMBL) in Heidelberg as part of his doctoral thesis. As a postdoctoral researcher, he moved to the University of California in San Francisco and Stanford University in 2000. In 2003, he was appointed a group leader at the Max Planck Institute of Neurobiology in Martinsried. In 2011, he was awarded the IRP Schellenberg Prize, one of the most prestigious awards in the field of regeneration research. In the same year he became full professor at the University of Bonn, and was appointed head of the Axon Growth and Regeneration research group at the DZNE. Bradke is an elected a member of the Leopoldina (the German National Academy of Sciences), the Academia Europaea, and the European Molecular Biology Organization (EMBO). In 2016, he was awarded the Leibniz Prize, which is the most important research award in Germany. In 2018, he received the Roger de Spoelberch Prize and in 2021 he was selected for the Carl Zeiss Lecture. In 2023, he was awarded the Remedios Caro Almela Prize for Research in Developmental Neurobiology.

The Keynote Lecture
"Mechanisms of axon growth and regeneration"

Almost everybody who has seen neurons under a microscope for the first time is fascinated by their beauty and their complex shape.  Early on during development, however, neurons look round and simple without signs of their future complexity.  How do neurons develop their sophisticated structure?  How do they initially generate domains that later have distinct functions within neuronal circuits, such as the axon?  And, can a better understanding of the underlying developmental mechanisms help us in pathological conditions, such as a spinal cord injury, to induce axons to regenerate? 

Here, I will talk about the cytoskeleton as a driving force for initial neuronal polarization and axon growth.  I will then explore how cytoskeletal changes help to reactivate the growth program of injured CNS axons to elicit axon regeneration after a spinal cord injury.  Finally, I will discuss whether axon growth and synapse formation could represent mutually excluding processes.  Following this developmental hypothesis helps us to generate a novel perspective on regeneration failure in the adult CNS and to envisage new paths to overcome it.   Thus, this talk will describe how we can exploit developmental mechanisms to induce axon regeneration in the adult after a spinal cord injury.


  • 9:55-10:00   Welcome
Session I
Chair: Ina Huppertz
  • 10:00-10:25   Adam Antebi
                          "Refeeding-associated AMPKγ1 complex activity is a hallmark of health and longevity"
  • 10:25-10:50   Achim Tresch
                          "Spatial transcriptome analysis of the ageing liver"
  • 10:50-11:15   Orsolya Leidecker
                          "ADP-ribosylation at the nuclear pore complex"
  • 11:15-11:40   Leo Kurian (Goethe University, Frankfurt)
                          "RNA biology of (re)building the heart"
  • 11:40-12:05   Kasia Bozek
                          "Predicting disease recurrence in cutaneous squamous cell carcinoma"
  • 12:05-13:15   Lunch break
Session II
Chair: Aleksandra Trifunovic
  • 13:15-14:00   **KEYNOTE SPEAKER**
                           Puck Knipscheer (Hubrecht Laboratory, Utrecht)
                          "Functions and mechanisms of DNA G-quadruplex structure regulation"
  • 14:00-14:25   Stephanie Panier
                          "The Good, the Bad and the Ugly: Balancing DNA Recombination in the Alternative
                           Lengthening of Telomeres Pathway"

  • 14:25-14:50   Thomas Wunderlich
                          "Improving gut barrier integrity in metabolic diseases"
  • 14:50-15:15   CECAD Member Meeting
  • 15:15-15:45   Coffee/Tea break
Session III
Chair: Thorsten Hoppe
  • 15:45-16:10   Jan Riemer
                         "Redox Regulation of Mitochondrial Biogenesis"
  • 16:10-16:35   Gilles Storelli
                         "Bacterial control of gastrointestinal transit"
  • 16:35-17:20   **KEYNOTE SPEAKER**
                           Frank Bradke (DZNE, Bonn)
                          "Mechanisms of Axon Growth and Regeneration"


  • 17:20-20:00   Get-Together

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After the talks, at about 17:20, we will meet to celebrate with international music, food, and drinks.
The traditional Glühwein & Bratwurst will be served, including alcohol-free drinks, hot chocolate as well as poultry and vegan meal options.

Let’s avoid FOOD WASTE!
* Whether team #Piggy #Chicky or #Vegan...
Register on the provided doodle by December 8th and tell us your choice!

Register using the QR-Code or following this LINK.