1. Research Background

Our group is interested in ADP-ribosylation (ADPr) signaling through two biomedically important PARP enzymes: PARP1, which is a crucial player in genome stability maintenance and a target of 4 FDA-approved anticancer drugs, and PARP11, a regulator of innate immunity and a potential novel immuno-oncology target. Both enzymes target components of the nuclear pore complex (NPC), a multiprotein assembly that is hijacked during certain viral infections and is often dysregulated in cancer. We study the modulation of DNA repair and immune response through PARP1 and PARP11 by identifying the molecular mechanism of ADPr on their diverse substrates at the NPC at such depth that other labs often fail to achieve. For this, we first unambiguously identify the modification sites on the substrates by modern proteomics technology. Next, we further study the modification using recently established tools, such as site-specific or modification-specific modular antibodies in live cell imaging and proteomics approaches. Moreover, we are establishing collaborations and mouse models to validate our findings in vivo. With this, we aim to create the necessary knowledge base to modulate genome stability and NPC biology by targetable ADPr enzymes in diseases, such as cancer, which exploit dysregulation of these vital processes.

2. Research questions addressed by the group:

Building on recent advances, such as the identification of physiologically relevant PARP1 modifications on several substrates and the emerging role of PARP enzymes in innate immunity, our group aims to:

• Identify new regulators of DNA repair among ADPr substrates and enzymes at the nuclear periphery.
• Unravel the crosstalk between NPC biology, PARP1 signaling, and immune responses, employing cutting-edge proteomics and microscopy.
• Investigate the functional roles of PARP11 at the nuclear periphery, focusing on its impact on NPC functions and immune cell activity, and how PARP11-mediated ADPr influences immune regulation alongside genome maintenance.

By integrating insights from DNA repair and immune modulation, we seek to develop a comprehensive understanding of how PARPs coordinate nuclear integrity, cellular stress responses, and immunity, opening new therapeutic perspectives across multiple aging- and disease-related contexts.

3. Possible project(s):

This PhD project will investigate the role of PARP11 in bone marrow-derived macrophages (BMDMs) and their function within the tumor microenvironment. While PARP1’s effects have been studied, PARP11 remains unexplored, particularly regarding how it influences macrophage polarization and anti-tumor activity. Additionally, we will examine whether ADP-ribosylation (ADPr) catalyzed by PARP11 or other PARPs changes at the nuclear periphery during aging. Specifically, we aim to determine if ADPr regulates age-related alterations in the nuclear pore complex (NPC) and to identify the consequences of these changes in macrophage function from aging mice. This research could reveal novel mechanisms of immune regulation, with implications for cancer therapy and aging-related immune decline.

A second potential project will focus on how aging affects nuclear integrity, particularly examining the nuclear lamina and its regulation by ADP-ribosylation (ADPr), using a model of premature aging—Hutchinson-Gilford Progeria Syndrome (HGPS). This project aims to determine whether the ADPr profile is altered in HGPS and how the interaction between PARP11 activity and the nuclear lamina impacts nuclear and genome stability. Since ADPr modifies nuclear envelope proteins, including lamin A and nucleoporins, we will utilize HGPS patient-derived iPSC models to investigate how ADPr signaling responds to lamina pathology. Employing immunofluorescence, immunoblotting, and ADPr proteomics, the study seeks to uncover whether changes in ADPr contribute to nuclear dysfunction and genome instability in this premature aging context. Insights gained could translate into a better understanding of the mechanisms underlying natural aging and age-related diseases, complementing the exploration of ADPr’s role within the immune system in the other project.

4. Applied Methods and model organisms:

Methods: advanced proteomics, biochemical enrichment (immunoprecipitation/pull downs), cell culture, iPSC models, western blotting, live-cell imaging, immunofluorescence, STED microscopy, Crisp-Paint and Crisp-Pitch for knockout and knock-in cell lines and endogenous tagging. Model organisms: mammalian cell culture and primary (ex vivo)macrophages from mice.

5. Desirable skills and qualifications:

We are welcoming applications from highly motivated and ambitious individuals eager to contribute to our dynamic and collaborative research environment. We value flexibility, curiosity, and a strong drive to excel in cutting-edge research.

6. References and key publications:

1. Ribeiro VC, Wirtz J, Leidecker O. The beauty of ADP-ribosylation: versatility in every link and organelle. BIOspektrum. 2025;31(3):258-61.
2. Strachan J, Leidecker O, Spanos C, Le Coz C, Chapman E, Arsenijevic A, et al. SUMOylation regulates Lem2 function in centromere clustering and silencing. J Cell Sci. 2023;136(23).
3. Bonfiglio JJ*, Leidecker O*, Dauben H*, Longarini EJ*, Colby T, San Segundo-Acosta P, et al. An HPF1/PARP1-Based Chemical Biology Strategy for Exploring ADP-Ribosylation. Cell. 2020;183(4):1086-102 e23.
4. Fatima A, Irmak D, Noormohammadi A, Rinschen MM, Das A, Leidecker O, et al. The ubiquitin-conjugating enzyme UBE2K determines neurogenic potential through histone H3 in human embryonic stem cells. Commun Biol. 2020;3(1):262.
5. Palazzo L*, Leidecker O*, Prokhorova E*, Dauben H, Matic I, Ahel I. Serine is the major residue for ADP-ribosylation upon DNA damage. Elife. 2018;7.
6. Leidecker O*, Bonfiglio JJ*, Colby T, Zhang Q, Atanassov I, Zaja R, et al. Serine is a new target residue for endogenous ADP-ribosylation on histones. Nat Chem Biol. 2016;12(12):998-1000.
7. Palazzo L, Thomas B, Jemth AS, Colby T, Leidecker O, Feijs KL, et al. Processing of protein ADP-ribosylation by Nudix hydrolases. Biochem J. 2015;468(2):293-301.
8. Rack JG, Morra R, Barkauskaite E, Kraehenbuehl R, Ariza A, Qu Y, et al. Identification of a Class of Protein ADP-Ribosylating Sirtuins in Microbial Pathogens. Mol Cell. 2015;59(2):309-20.