Ongoing Projects

Targeting the essentialome of radiotherapy-resistant cancer

(TETHER, ERC-AdG 883877)

More than 50% of the cancer patients undergo irradiation as part of their cancer treatment. Although radiotherapy (RT) significantly contributes to cancer cure, local therapy resistance and the subsequent emergence of distant metastasis remain major obstacles for its success. The molecular mechanisms underlying tumor cell-intrinsic RT resistance are ill-defined. It is therefore crucial to better define these mechanisms and identify new vulnerabilities of RT-resistant tumors in order to decrease the current annual cancer mortality of >1.3 million persons in EU member states alone.

In the TETHER project, we are addressing the problem of RT resistance by synergizing the power of genetic essentiality analyses with unique mouse models and organoids that we have established. We recently found that members of the shieldin and CST complexes are essential for tumor cells to survive irradiation, while causing PARP inhibitor resistance when lost in BRCA1-deficient tumors. Based on this unexpected finding, we have started to dissect the RT "essentialome". As we show with the discovery and functional characterization of ERCC6l2 as a novel DNA repair factor in this network, the technology we have in place is perfectly suited to tackle this question. In addition, we are applying distinct CRISPR/Cas9-based tests to map the functional interactome of genes that are essential for RT resistance.

To follow the plasticity and RT escape of tumor cells in vivo, we have also developed innovative model systems. Similar to the situation in cancer patients, we observe that residual cancer cells in our mouse models escape the deadly effects of RT by local resistance or metastasis formation. Thus, these models provide a unique opportunity to explore and target RT escape mechanisms.

Mechanisms of HR-independent chemoresistance in BRCA1/2-mutated tumors

(SNSF co-investigator grant with J. Jonkers (NKI)(320030M_219453))

In recent years various poly(ADP-ribose) (PAR) polymerase inhibitors (PARPi) have entered the clinic for the treatment of patients with breast or ovarian cancers defective in DNA repair by homologous recombination (HR), e.g. due to the loss of BRCA1/2 function. In particular for high-grade serous ovarian cancer patients, the use of PARPi as frontline maintenance therapy following platinum-based chemotherapy has resulted in an unprecedented increase in the median progression-free survival. The specific targeting of these HR-deficient tumors by platinum drugs and PARPi is explained by the increased DNA damage that BRCA1/2-deficient tumors cannot cope with. Despite the success of this therapeutic approach, chemoresistance often emerges, and we do not fully understand how resistance occurs. One underlying resistance mechanism was found to be the restoration of BRCA1/2 function due to secondary mutations (genetic reversion). However, genetic reversion only explains some cases of PARPi resistance and in many patients the cause of resistance is unknown. It is therefore crucial to understand the resistance mechanisms that are independent of HR restoration.

In this project, we are addressing the problem of HR restoration-independent chemoresistance mechanisms of BRCA1/2-mutated tumors by synergizing the power of genetic essentiality analyses with unique mouse models and patient-derived organoids that we have established. For our genome-wide screens we have unique BRCA1/2-deficient mouse mammary tumor cell lines which cannot restore BRCA1 or BRCA2 function due to large deletions of the Brca1 and Brca2 genes. Thus far unexplored resistance mechanisms can be identified with this approach. In particular, we found the loss of poly(ADP-ribose) glycohydrolase (PARG) as frequently occurring PARPi resistance and the loss of the histone H2AX as frequent PARPi and platinum drug resistance mechanisms; both of which are independent of HR restoration. PARG and H2AX both play key roles in regulating the signaling of single-stranded (SSBs) or double-stranded DNA breaks (DSBs), and we hypothesize that there is a novel role for H2AX in replication fork biology that is different from its classical role in DNA damage signaling and DSB repair. Regarding BRCA1/2-deficient cells that acquired resistance due to loss of PARG, we found an increased dependence on EXO1- and FEN1-dependent DNA repair. We believe that this provides a new vulnerability to target PARPi-resistant tumors.

Targeting platinum drug resistance 

(KFS-5519-02-2022)

Platinum (Pt) compounds have been used as anti-cancer drugs to treat various types of solid tumors since the advent of cisplatin in 1978. Today, cis-, carbo- and oxaliplatin are among the most frequently used anti-cancer therapies. Hence, even in the era of precision medicine and immunotherapy, Pt drugs remain a cornerstone of current cancer treatment. As Pt drugs mainly target DNA, it is not surprising that recent insights into alterations of DNA repair mechanisms provide a useful explanation for their success. Many cancers have defective DNA repair. Striking examples are breast and ovarian cancer patients with tumors that are defective in DNA repair by homologous recombination (HR) due to loss of BRCA1 or BRCA2 function. This feature also sheds new light on the mechanisms of secondary drug resistance, i.e. the restoration of DNA repair pathways. However, restoration of DNA repair does not explain resistance in all cases, and we have a poor understanding why many cancers do not respond to Pt compounds upfront. Thus, overcoming resistance to Pt drugs is crucial for prolonging the survival of many of the approximately 44,000 patients diagnosed with cancer in Switzerland each year.

In this project, we study another basic resistance mechanism using state-of-the-art techniques: reduced uptake of Pt drugs into tumor cells. The precise mechanisms underlying this resistance mechanism have long been enigmatic. Using genome-wide functional screening approaches, we have provided interesting insights into Pt drug uptake. About half of cisplatin and carboplatin appear to enter cells through the widely expressed volume-regulated anion channel (VRAC), composed of LRRC8A and LRR8D subunits. We have also provided further retrospective evidence for the clinical relevance of this mechanism.

Moreover, we found that NAA60 is crucial for the regulation of LRRC8A/D function, as it neutralizes the N termini of LRRC8A/D by acetylation. Since there is no targeted therapy available at present that could be offered to patients with low LRRC8A/D-mediated Pt drug uptake in their tumors, we are also searching for specific vulnerabilities of LRRC8A/D-deficient cells.

In the future, Pt-based approaches will be improved by the optimization of combinations with immunotherapy, management of side effects and use of nanodelivery devices. Hence, Pt drugs will still be part of the standard of care for different cancers in the coming years. Therefore, we are convinced that the understanding of Pt drug resistance mechanisms will yield useful additional information for designing effective approaches to circumvent or reverse therapy escape in cancer patients.