Dr. Stephanie Panier

1. Research Background

The accurate replication and transmission of genetic material is of fundamental importance for cellular homeostasis and organism viability. Yet, cells are continually exposed to environmental and endogenous genotoxic agents that threaten DNA integrity. To protect their genomic stability, cells mount a complex network of DNA damage response pathways that activate cell cycle checkpoints, coordinate DNA repair, regulate gene expression and, if necessary, induce cell death. DNA damage signalling and repair is a powerful barrier to tumourigenesis, and defects in these pathways promote cell proliferation and genomic instability in premalignant lesions. Critically, genomic instability is also a hallmark of ageing. As such, the accumulation of DNA damage promotes not only the normal ageing process but is also linked to pre-mature aging syndromes and to the onset of age-associated neurodegenerative diseases.

2. Research questions addressed by the group:

Our lab seeks to understand how cells detect, signal and repair DNA damage to protect genomic stability. We are particularly interested in identifying and characterizing new regulators of the DNA damage response. We generally pursue the following questions:

• a) How do DNA damage response factors ensure genome stability at various types of DNA lesions?
• b) How does their dysfunction contribute to genome instability-triggered and ageing-associated diseases such as cancer and neurodegeneration?
• c) Can these factors be exploited to develop personalized disease treatment approaches?

3. Possible project:

Somatic cells have finite replicative lifespans because telomeres undergo progressive shortening after DNA replication, which can lead to genome instability and induce cellular senescence. To counteract telomere erosion and to achieve replicative immortality, cells activate one of two distinct telomere maintenance mechanisms (TMMs). The first mechanism relies on the re-expression of the reverse transcriptase telomerase. The second mechanism, known as alternative lengthening of telomeres (ALT), extends telomeres by upregulating homology-directed DNA recombination pathways. ALT is employed by 10-15% of tumours and is often associated with aggressive clinicopathologic behavior, which is likely due to the fact that these tumours are genomically highly unstable and are resistant to therapies based on telomerase inhibition. The molecular mechanisms underpinning ALT are very poorly understood. We have recently identified the protein SLX4IP as a novel regulator of telomere recombination specifically in ALT-positive cancer cells. While SLX4IP is dispensable for telomere maintenance in telomerase-positive cells, its loss in ALT cancer cells leads to telomere hyper-recombination and genome instability. The clinical importance of SLX4IP is highlighted by its frequent inactivation in ALT-positive osteosarcomas.

We offer a PhD project that will investigate how ALT pathways interact with homeostatic pathways and microenvironmental cues to ensure telomere length maintenance. Specifically, we aim to:

1. Identify novel factors that drive the ALT process
   Although SLX4IP is crucial for the processing of telomeric recombination intermediates in ALT-positive cells, its loss is not sufficient to induce ALT phenotypes in ALT-negative cells. Indeed, to date no single factor has been identified whose loss alone can drive full ALT establishment and maintenance. This observation suggests that SLX4IP (and other known ALT proteins) act in combination with additional factors or homeostatic cues to induce ALT. We will perform unbiased genome-wide loss-of-function screens as well as transcriptomic and metabolomic analyses to identify such factors and cues.

2. Investigate how the cell microenvironment influences telomere maintenance and vice versa.
   The tumour microenvironment (TME) plays a significant role in cancer progression and metastasis. Indeed, TME changes such as hypoxic stress lead to the dysregulation of DNA repair pathways, which then contributes to the genomic instability that is a hallmark of cancer. Whether changes in the cellular microenvironment influence telomere length homeostasis has so far not been addressed. We will employ 3D spheroid tumour models to uncover and dissect interactions between the TME and ALT- and telomere-mediated telomere length homeostasis.

4. Applied Methods and model organisms:

We are an interdisciplinary lab that employs a wide range of molecular, genetic, cell biological and systems biology approaches. Applied methods include:

• State-of-the-art methods of molecular and cell biology (including molecular cloning as well as protein, DNA and RNA biochemistry)
• Advanced microscopy (including microlaser irradiation, live cell- and super-resolution microscopy)
• DNA combing
• FACS
• Proteomics
• Cutting-edge CRISPR-Cas9-based genetics and screening

We work primarily with mammalian 2D and 3D tissue cultures.

5. Desirable skills and qualifications:

We seek an ambitious and pro-active student to join our new research team. Experience in mammalian tissue culture and omics approaches are desirable but not required. The student will receive extensive training in all relevant techniques.

6. References and key publications:

1. Panier, S., Maric,M., Hewitt,G., Mason-Osann,E., Gali,H., Dai,A., Labadorf, A., Guervilly,J.H., Ruis,P., Segura-Bayona, S., Belan, O., Marzec,P., Gaillard,P.H.L., Flynn,R.L., Boulton,S.J. (2019) SLX4IP antagonizes promiscuous BLM activity during ALT maintenance.Mol Cell 76, 1-17.
2. Leon-Ortiz, A.M., Panier, S., Sarek, G., Vannier, J.B., Patel, H., Campbell, P.J., and Boulton, S.J. (2018). A Distinct Class of Genome Rearrangements Driven by Heterologous Recombination. Mol Cell 69, 292-305 e296.
3. Margalef, P., Kotsantis, P., Borel, V., Bellelli, R., Panier, S., and Boulton, S.J. (2018). Stabilization of Reversed Replication Forks by Telomerase Drives Telomere Catastrophe. Cell 172, 439-453 e414.
4. Panier, S., Ichijima, Y., Fradet-Turcotte, A., Leung, C.C., Kaustov, L., Arrowsmith, C.H., and Durocher, D. (2012). Tandem protein interaction modules organize the ubiquitin-dependent response to DNA double-strand breaks. Mol Cell 47, 383-395.
5. O'Donnell, L.*, Panier, S.*, Wildenhain, J.*, Tkach, J.M., Al-Hakim, A., Landry, M.C., Escribano-Diaz, C., Szilard, R.K., Young, J.T., Munro, M., et al. (2010). The MMS22L-TONSL complex mediates recovery from replication stress and homologous recombination. Mol Cell 40, 619-631. *co-first authors
6. Stewart, G.S.*, Panier, S.*, Townsend, K., Al-Hakim, A.K., Kolas, N.K., Miller, E.S., Nakada, S., Ylanko, J., Olivarius, S., Mendez, M., et al. (2009). The RIDDLE syndrome protein mediates a ubiquitin-dependent signaling cascade at sites of DNA damage. Cell 136, 420-434 *co-first authors
7. Panier, S., and Boulton, S.J. (2014). Double-strand break repair: 53BP1 comes into focus. Nat Rev Mol Cell Biol 15, 7-18. Review.
8. Panier, S.*, and Durocher, D.* (2013). Push back to respond better: regulatory inhibition of the DNA double-strand break response. Nat Rev Mol Cell Biol 14, 661-672. Review. *co-corresponding authors
9. Al-Hakim, A., Escribano-Diaz, C., Landry, M.C., O'Donnell, L., Panier, S., Szilard, R.K., and Durocher, D. (2010). The ubiquitous role of ubiquitin in the DNA damage response. DNA Repair (Amst) 9, 1229-1240. Review.
10. Panier, S., and Durocher, D. (2009). Regulatory ubiquitylation in response to DNA double-strand breaks. DNA Repair (Amst) 8, 436-443. Review.