Claudio Sette

Dual inhibition of CDK12 and CDK13 uncovers actionable vulnerabilities in patient-derived ovarian cancer organoids

Abstract Background High grade serous ovarian cancer (HGSOC) is highly lethal, partly due to chemotherapy resistance and limited availability of targeted approaches. Cyclin dependent kinases 12 and 13 (CDK12/13) are promising therapeutic targets in human cancers, including HGSOC. Nevertheless, the effects of their inhibition in HGSOC and the potential synergy with other drugs are poorly known. Methods We analyzed the effects of the CDK12/13 inhibitor THZ531 in HGSOC cells and patient-derived organoids (PDOs). RNA sequencing and quantitative PCR analyses were performed to identify the genome-wide effects of short-term CDK12/13 inhibition on the transcriptome of HGSOC cells. Viability assays with HGSOC cells and PDOs were performed to assess the efficacy of THZ531 as single agent or in combination with clinically relevant drugs. Results The CDK12 and CDK13 genes are deregulated in HGSOC and their concomitant up-regulation with the oncogene MYC predicts poor prognosis. HGSOC cells and PDOs display high sensitivity to CDK12/13 inhibition, which synergizes with drugs in clinical use for HGSOC. Transcriptome analyses revealed cancer-relevant genes whose expression is repressed by dual CDK12/13 inhibition through impaired splicing. Combined treatment with THZ531 and inhibitors of pathways regulated by these cancer relevant genes (EGFR, RPTOR, ATRIP) exerted synergic effects on HGSOC PDO viability. Conclusions CDK12 and CDK13 represent valuable therapeutic targets for HGSOC. We uncovered a wide spectrum of CDK12/13 targets as potential therapeutic vulnerabilities for HGSOC. Moreover, our study indicates that CDK12/13 inhibition enhances the efficacy of approved drugs that are already in use for HGSOC or other human cancers.

Patient-derived organoids and high grade serous ovarian cancer: from disease modeling to personalized medicine

Abstract Background High grade serous ovarian cancer (HGSOC) is among the deadliest human cancers and its prognosis remains extremely poor. Tumor heterogeneity and rapid acquisition of resistance to conventional chemotherapeutic approaches strongly contribute to poor outcome of patients. The clinical landscape of HGSOC has been radically transformed since the advent of targeted therapies in the last decade. Nevertheless, the lack of predictive biomarkers informing on the differential clinical benefit in select subgroups, and allowing patient-centric approaches, currently limits the efficacy of these novel therapies. Thus, rational selection of the best possible treatment for each patient represents a clinical priority in order to improve outcome, while limiting undesirable effects. Main body In this review, we describe the state of the art and the unmet needs in HGSOC management, illustrate the treatment options that are available and the biomarkers that are currently employed to orient clinical decisions. We also describe the ongoing clinical trials that are testing new therapeutic approaches for HGSOC. Next, we introduce the organoid technology as a promising, expanding strategy to study cancer and to develop personalized therapeutic approaches. In particular, we discuss recent studies that have characterized the translational potential of Patient’s Derived Organoids (PDOs) to inform on drug sensitivity of HGSOC patients. Conclusions PDOs can predict the response of patients to treatments and may therefore guide therapeutic decisions. Although preliminary results appear encouraging, organoids still need to be generated and expanded efficiently to enable drug screening in a clinically meaningful time window. A new generation of clinical trials based on the organoid technology should guarantee tailored approaches to ovarian cancer management, as it is now clear that the one-size-fits-all approach cannot lead to efficient and meaningful therapeutic advancements.

Single-cell transcriptome analysis of patient-derived organoids captures inter- and intratumor heterogeneity and uncovers targetable pathways in high grade serous ovarian cancer

High grade serous ovarian cancer (HGSOC) is the most aggressive subtype of ovarian cancer. HGSOC is characterized by high inter- and intra-tumoral heterogeneity, which contributes to chemotherapy resistance. Patient-derived organoids (PDOs) are valuable preclinical models to elucidate the biology of human cancers and to test their response to treatments. This study aims at characterizing the cellular heterogeneity of PDOs and to uncover vulnerabilities of chemotherapy resistant HGSOC. Single-cell transcriptomics of PDOs developed from biopsies of platinum-resistant and platinum-sensitive HGSOC. Chemotherapeutic treatments of HGSOC PDOs and of ascitic-derived ovarian cancer cells and immunohistochemistry analyses of tissues from independent HGSOC patients. HGSOC PDOs comprise subclusters of cells exhibiting different transcriptional states and patient-specific signatures. Proliferative and non-proliferative subclusters co-exist in PDOs and their relative proportion is altered by chemotherapy. Proliferative cell sub-populations exhibit expression of cell cycle and DNA damage response related genes, whereas non-proliferative sub-populations display inflammatory signatures. Furthermore, sensitivity to platinum-based treatments was inversely correlated with oxidative phosphorylation (OXHPOS) in PDOs, indicating a metabolic switch associated with chemoresistance. Accordingly, platinum-resistant PDOs and ascitic HGSOC cells show higher sensitivity to OXHPOS inhibition. We found that neoadjuvant chemotherapy (NACT) directly up-regulates oncogenic and metabolic pathways that are involved in development of recurrence, such as the MYC and OXPHOS genes. NACT also induces the expression of major histocompatibility complex type II (MHC-II) molecules. Immunohistochemistry confirmed MHC-II up-regulation in post-NACT biopsies, indicating that tumour cells mount a general antigen-presenting response upon chemotherapy, associated with recruitment of infiltrating immune cells. PDOs maintain the inter- and intra-tumoral cellular heterogeneity of HGSOC. Chemotherapy targets proliferative cell subclusters, sparing non-proliferative ones. Dependency on OXPHOS represents an actionable vulnerability in PDOs, which can be exploited to hijack chemoresistance. Sequential chemotherapy and immunotherapy may also improve clinical response of HGSOC patients.