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Bladder Cancer (BLCa) inter-patient heterogeneity is considered the primary cause of tumor reoccurrence and treatment failure, suggesting that BLCa patients could benefit from a more personalized treatment approach. Patient-derived organoids (PDOs) have been successfully used as a functional model for predicting drug response in different cancer types. In our study, we established BLCa PDO cultures from different BLCa stages. BLCa PDOs preserve the histological and molecular heterogeneity of the parental tumors, including their multiclonal genetic landscapes. BLCa PDOs consistently share key genetic alterations detected in parental tumors, mirroring tumor evolution in longitudinal sampling. Our drug screening pipeline was implemented using BLCa PDOs, testing both standard-of-care and additional FDA-approved compounds for other solid tumors. Integrative analysis of drug response profiles with matched PDO genomic analysis was used to determine enrichment thresholds for candidate markers of therapy resistance and sensitivity. By assessing the clinical history of longitudinally sampled cases, the clonal evolution of the disease could be determined and matched with drug response profiles. In conclusion, we have developed a clinically relevant pipeline for drug response profile assessment and discovery of candidate markers of therapy resistance.

Introduction: Interpatient heterogeneity is one of the causes of treatment failure in bladder cancer (BLCa) patients, who would therefore profit from tailor-made therapies. Toward the direction of precision medicine, patient-derived organoids (PDOs), which retain parental tumor (PT) features, have been successfully tested in different cancer types and shown to predict patients’ responses. Therefore, our study aimed to explore the ability of BLCa PDOs to retain PT features and to determine patient drug sensitivity. We correlated PDO drug response profiles to their genomic profiles and the patient's clinical history. Methods: PDOs were derived from the suspension culture of single cells. Whole exome sequencing was performed on genomic DNA and scRNA sequencing on 3 PT/PDO pairs. Histological evaluation of PDO and PT marker expression and morphology was performed. PDOs were treated for 48h and drug response was evaluated by viability assay. Results: We derived PDOs from non-muscle-invasive and muscle-invasive BLCa. Genomic analysis of 15 representative PT/PDOs pairs showed high similarity in terms of copy number variations and single nucleotide variants (SNVs) with preservation of peculiar BLCa alterations. PT genomic heterogeneity was preserved in PDOs as demonstrated by the correlation between SNVs clonality profiles of PT/PDOs pairs. Moreover, marker analyses at the scRNA and protein levels supported that PDOs retained the main tumor phenotype. Interestingly, PDO grew accordingly to three morphologies linked to marker expression and PT stage.PDOs were used in drug screen assays for testing standard-of-care (SOC) and FDA-approved drugs. PDO responses were highly heterogeneous highlighting interpatient heterogeneity. In 2 case, PDO sensitivity mimicked the patient’s response to SOC and in a few cases correlated with the sample-specific genomic background. Due to the high relapse rate of BLCa, we performed 2 longitudinal studies. In the first one, PDOs from a relapse collected after epirubicin treatment showed less sensitivity to the drug compared to the baseline sample. Moreover, the SNVs' mean clonality of relapse PDOs was significantly higher than the baseline PDOs which were characterized by mutations in DNA damage repair genes (e.g., ATM, FANC1, ERCC2, and BRCA2). We hypothesize a drug-induced selection of a pre-existing epirubicin-resistant population. In the second study, PDOs from the cystectomy and the following relapse showed similar genomic and drug sensitivity profiles suggesting that the first sample could be informative for adjuvant therapy. Conclusion: We established PDOs from different BLCa stages and grades which preserve PT features and can be implemented in drug screening assays for personalized approaches. The power of PDOs in precision medicine was highlighted by the longitudinal studies that showed that PDOs mirrored patient response and tumor evolution in vitro. Citation Format: Martina Minoli, Thomas Cantore, Daniel Hanhart, Mirjam Kiener, Tarcisio Fedrizzi, Federico La Manna, Sofia Karkampouna, Panagiotis Chouvardas, Vera Genitsch, José Antonio Rodriguez-Calero, Eva Compérat, Irena Klima, Paola Gasperini, Bernhard Kiss, Roland Seiler-Blarer, Francesca Demichelis, George N. Thalmann, Marianna Kruithof-de Julio. Bladder cancer organoids as a functional system to model different disease stages and therapy response [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 182.

INTRODUCTION AND OBJECTIVE:Bladder cancer (BLCa) is the 10th most frequent cancer worldwide [1]. Non-muscle invasive (NMBC) and muscle invasive BLCa (MIBC) are the two major categories used to defi...

Idiopathic Pulmonary fibrosis (IPF) is an incurable chronic disease characterized by progressive loss of lung function. IPF is thought to occur due to repetitive micro injuries in the distal lung and/or genetic predisposition leading to aberrant tissue repair. Increased ECM deposition by myofibroblasts results in tissue stiffening and thickening of alveolar walls, causing progressive decline of pulmonary function and ultimately, fatal respiratory failure. Due to the inherent complexity of the human disease, advanced in vitro human models including physiological mechanical cues appear as a promising tool to investigate IPF and potential therapeutic interventions. We aimed to develop an advanced in vitro alveolar model mimicking some features of IPF. Primary alveolar epithelial cells and lung fibroblasts were co-cultured on the AlveoliX lung-chip-device and exposed to Transforming Growth Factor β (TGF-β), a central mediator of fibrogenesis. The effects on barrier disruption and gene expression of profibrotic markers were investigated. According to our results, fibroblasts supported alveolar barrier formation as detected by a faster development of barrier function and higher integrity. On the other hand, stimulation with TGF-s for 48h led to a decrease in barrier integrity over time, together with an increased expression of pro-fibrotic markers such as Col1a and Vimentin at the epithelial and fibroblast side. No significant effects on cytotoxicity or metabolic activity between treated and untreated wells were observed after 48h stimulation. In conclusion, our human in vitro model recapitulates some relevant features of IPF, hence, it may be a valuable tool for investigating new biomarkers and for efficacy studies of new antifibrotic drugs.

The coronavirus disease 2019 (COVID-19) pandemic has caused considerable socio-economic burden, which fueled the development of treatment strategies and vaccines at an unprecedented speed. However, our knowledge on disease recovery is sparse and concerns about long-term pulmonary impairments are increasing. Causing a broad spectrum of symptoms, COVID-19 can manifest as acute respiratory distress syndrome (ARDS) in the most severely affected patients. Notably, pulmonary infection with Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2), the causing agent of COVID-19, induces diffuse alveolar damage (DAD) followed by fibrotic remodeling and persistent reduced oxygenation in some patients. It is currently not known whether tissue scaring fully resolves or progresses to interstitial pulmonary fibrosis. The most aggressive form of pulmonary fibrosis is idiopathic pulmonary fibrosis (IPF). IPF is a fatal disease that progressively destroys alveolar architecture by uncontrolled fibroblast proliferation and the deposition of collagen and extracellular matrix (ECM) proteins. It is assumed that micro-injuries to the alveolar epithelium may be induced by inhalation of micro-particles, pathophysiological mechanical stress or viral infections, which can result in abnormal wound healing response. However, the exact underlying causes and molecular mechanisms of lung fibrosis are poorly understood due to the limited availability of clinically relevant models. Recently, the emergence of SARS-CoV-2 with the urgent need to investigate its pathogenesis and address drug options, has led to the broad application of in vivo and in vitro models to study lung diseases. In particular, advanced in vitro models including precision-cut lung slices (PCLS), lung organoids, 3D in vitro tissues and lung-on-chip (LOC) models have been successfully employed for drug screens. In order to gain a deeper understanding of SARS-CoV-2 infection and ultimately alveolar tissue regeneration, it will be crucial to optimize the available models for SARS-CoV-2 infection in multicellular systems that recapitulate tissue regeneration and fibrotic remodeling. Current evidence for SARS-CoV-2 mediated pulmonary fibrosis and a selection of classical and novel lung models will be discussed in this review.

COVID-19 is an infectious disease caused by the newly discovered coronavirus named SARS-CoV-2. The virus enters the body through the airways by exploiting the angiotensin-converting enzyme 2 (ACE2) and serine proteinase TMPRSS2. Thus, especially lung epithelial cells are attacked by the virus. In the distal lung, the virus infection leads to life-threatening alveolar damage and cytokine storm. Many excellent clinical studies described the pathology of COVID-19 progression in patients. However, impactful in vitro studies are still missing due to the exceptional difficulty to model the alveolar setting in vitro. Here, we introduce two advanced models based on organoids and lung-on-chip (LOC) technology. The models derived from primary alveolar epithelial cells were characterized by fluorescence imaging and gene expression. Barrier function and cell polarity were assessed by confocal microscopy of tight junction and transporter proteins. We showed that the LOC model and the newly developed organoids preserve alveolar type II specific markers (SP-C and HTII-280). In both models we could detect relevant amounts of ACE2 and TMPRSS2 mRNA as compared to whole lung extracts. As a next step we will optimize the infection titer for both systems to further analyze transcriptomic changes upon SARS-CoV-2 infection. The here presented advanced in vitro models, recapitulating the distal lung, serve as complementary SARS-CoV-2 lung infection models. The LOC model will allow to simulate alveolar breakdown and cytokine storm whereas the organoid models will facilitate high-content drug screening.

Therapy resistance and metastatic processes in prostate cancer (PCa) remain undefined, due to lack of experimental models that mimic different disease stages. We describe a novel androgen-dependent PCa patient-derived xenograft (PDX) model from treatment-naïve, soft tissue metastasis (PNPCa). RNA and whole-exome sequencing of the PDX tissue and organoids confirmed transcriptomic and genomic similarity to primary tumor. PNPCa harboursBRCA2 and CHD1somatic mutations, shows anSPOP/FOXA1-like transcriptomic signature and microsatellite instability, which occurs in 3% of advanced PCa and has never been modelledin vivo. Comparison of the treatment-naïve PNPCa with additional metastatic PDXs (BM18, LAPC9), in a medium-throughput organoid screen of FDA-approved compounds, revealed differential drug sensitivities. Multikinase inhibitors (ponatinib, sunitinib, sorafenib) were broadly effective on all PDX- and patient-derived organoids from advanced cases with acquired resistance to standard-of-care compounds. This proof-of-principle study may provide a preclinical tool to screen drug responses to standard-of-care and newly identified, repurposed compounds.

Therapy resistance and metastatic processes in prostate cancer (PCa) remain undefined, due to lack of experimental models that mimic different disease stages. We describe an androgen-dependent PCa patient-derived xenograft (PDX) model from treatment-naïve, soft tissue metastasis (PNPCa). RNA and whole-exome sequencing of the PDX tissue and organoids confirmed transcriptomic and genomic similarity to primary tumor. PNPCa harbors BRCA2 and CHD1 somatic mutations, shows an SPOP/FOXA1-like transcriptomic signature and microsatellite instability, which occurs in 3% of advanced PCa and has never been modeled in vivo. Comparison of the treatment-naïve PNPCa with additional metastatic PDXs (BM18, LAPC9), in a medium-throughput organoid screen of FDA-approved compounds, revealed differential drug sensitivities. Multikinase inhibitors (ponatinib, sunitinib, sorafenib) were broadly effective on all PDX- and patient-derived organoids from advanced cases with acquired resistance to standard-of-care compounds. This proof-of-principle study may provide a preclinical tool to screen drug responses to standard-of-care and newly identified, repurposed compounds., To date, patients still succumb to cancer, due to tumors not responding to therapy or ultimately acquiring resistance. Here the authors show that by exploiting patient derived organoids and a treatment-naïve patient derived xenograft, patient therapy can be personalized.

Transient receptor potential melastatin 4 (TRPM4) is a broadly expressed Ca2+ activated monovalent cation channel that contributes to the pathophysiology of several diseases. For this study, we generated stable CRISPR/Cas9 TRPM4 knockout (K.O.) cells from the human prostate cancer cell line DU145 and analyzed the cells for changes in cancer hallmark functions. Both TRPM4-K.O. clones demonstrated lower proliferation and viability compared to the parental cells. Migration was also impaired in the TRPM4-K.O. cells. Additionally, analysis of 210 prostate cancer patient tissues demonstrates a positive association between TRPM4 protein expression and local/metastatic progression. Moreover, a decreased adhesion rate was detected in the two K.O. clones compared to DU145 cells. Next, we tested three novel TRPM4 inhibitors with whole-cell patch clamp technique for their potential to block TRPM4 currents. CBA, NBA and LBA partially inhibited TRPM4 currents in DU145 cells. However, none of these inhibitors demonstrated any TRPM4-specific effect in the cellular assays. To evaluate if the observed effect of TRPM4 K.O. on migration, viability, and cell cycle is linked to TRPM4 ion conductivity, we transfected TRPM4-K.O. cells with either TRPM4 wild-type or a dominant-negative mutant, non-permeable to Na+. Our data showed a partial rescue of the viability of cells expressing functional TRPM4, while the pore mutant was not able to rescue this phenotype. For cell cycle distribution, TRPM4 ion conductivity was not essential since TRPM4 wild-type and the pore mutant rescued the phenotype. In conclusion, TRPM4 contributes to viability, migration, cell cycle shift, and adhesion; however, blocking TRPM4 ion conductivity is insufficient to prevent its role in cancer hallmark functions in prostate cancer cells.

Bladder cancer is a heterogeneous disease that is not depicted by current classification systems. It was originally classified into non-muscle invasive and muscle invasive. However, clinically and genetically variable tumors are summarized within both classes. A definition of three groups may better account for the divergence in prognosis and probably also choice of treatment. The first group represents mostly non-invasive tumors that reoccur but do not progress. Contrarily, the second group represent non-muscle invasive tumors that likely progress to the third group, the muscle invasive tumors. High throughput tumor profiling improved our understanding of the biology of bladder cancer. It allows the identification of molecular subtypes, at least three for non-muscle invasive bladder cancer (Class I, Class II and Class III) and six for muscle-invasive bladder cancer (luminal papillary, luminal non-specified, luminal unstable, stroma-rich, basal/squamous and neuroendocrine-like) with distinct clinical and molecular phenotypes. Molecular subtypes can be potentially used to predict the response to treatment (e.g., neoadjuvant chemotherapy and immune checkpoint inhibitors). Moreover, they may allow to characterize the evolution of bladder cancer through different pathways. However, to move towards precision medicine, the understanding of the biological meaning of these molecular subtypes and differences in the composition of cell subpopulations will be mandatory.

Therapy resistance and metastatic processes in prostate cancer (PCa) remain undefined, mainly due to the lack of experimental models representing different disease stages. We aim to provide functional experimental and preclinical drug tools applicable for direct use with patient-derived material. Biopsies from metastatic PCa were used for the establishment of patient-derived xenografts (PDXs) by subcutaneous implantation. In vivo tumor growth kinetic in response to androgens was assessed by surgical castration and testosterone supplementation. RNA and whole-exome sequencing (WES) and organoid drug screens were used to characterize the genomic, transcriptomic, and functional properties. Organoid culture methodology was adapted in order to set up an automated medium-throughput organoid drug screen (Nexus Theragnostics automated platform) for screening standard-of-care compounds and candidates for drug repurposing. A novel case of PCa xenograft model derived from soft tissue metastasis (PNPCa) was established. RNAseq and WES confirmed transcriptomic and genomic similarity to the primary tumor. PNPCa harbors BRAC2 and CHD1 mutations and shows SPOP-like and FOXA1-like transcriptomic signature with microsatellite instability. PNPCa tumor growth is inhibited after androgen deprivation by castration, while androgen replacement leads to tumor reformation. No spontaneous tumor growth occurred after prolonged period of castration; however, scarce micrometastases were found in the bone marrow and lymph nodes. The treatment-naive and androgen-dependent properties of the PNPCa made it a candidate model for identification of potent drug compounds. PNPCa-derived organoid screens on standard-of-care and 74 FDA-approved compounds showed that mTOR pathway and multi-tyrosine kinase inhibitors, used for clinical treatment of other cancer types, have high impact on PCa organoid viability. Application of the organoid drug screen panel on two additional metastatic PDXs of advanced disease has allowed shortlisting of compounds for repurposing use in patient-derived organoid screens that can be routinely performed in a timeframe of few weeks, and thus, provide information on treatment decision. Treatment response of a treatment-naive, early metastatic PCa case (PNPCa PDX) highlights the potential of organoid screens to assess therapy response with extended applications for personalized screens. Citation Format: Sofia Karkampouna, Federico la Manna, Maria R. De Filippo, Mirjam Kiener, Marta De Menna, Eugenio Zoni, Joel Grosjean, Irena Klima, Andrea Garofoli, Marco Bolis, Jean-Philippe Theurillat, Vera Genitsch, David Keller, Booij Tijmen, Christian U. Stirnimann, Andrea Sboner, Charlotte K.Y. Ng, Salvatore Piscuoglio, Martin Spahn, Mark A. Rubin, George N. Thalmann, Marianna Kruithof-de Julio. Patient-derived xenograft and organoids models of prostate cancer [abstract]. In: Proceedings of the AACR Special Conference on the Evolving Landscape of Cancer Modeling; 2020 Mar 2-5; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2020;80(11 Suppl):Abstract nr B18.