Photon and Proton irradiation in Patient-derived, Three-Dimensional Soft Tissue Sarcoma Models

BACKGROUND

Despite their heterogeneity, the current standard preoperative radiotherapy regimen for localized high-grade soft tissue sarcoma (STS) follows a one fits all approach for all STS subtypes. Sarcoma patient-derived three-dimensional cell culture models represent an innovative tool to overcome challenges in clinical research enabling reproducible subtype-specific research on STS. In this pilot study, we present our methodology and preliminary results using STS patient-derived 3D cell cultures that were exposed to different doses of photon and proton radiation. Our aim was: (i) to establish a reproducible method for irradiation of STS patient-derived 3D cell cultures and (ii) to explore the differences in tumor cell viability of two different STS subtypes exposed to increasing doses of photon and proton radiation at different time points.

METHODS

Two patient-derived cell cultures of untreated localized high-grade STS (an undifferentiated pleomorphic sarcoma (UPS) and a pleomorphic liposarcoma (PLS)) were exposed to a single fraction of photon or proton irradiation using doses of 0 Gy (sham irradiation), 2 Gy, 4 Gy, 8 Gy and 16 Gy. Cell viability was measured and compared to sham irradiation at two different time points (four and eight days after irradiation).

RESULTS

The proportion of viable tumor cells four days after photon irradiation for UPS vs. PLS were significantly different with 85% vs. 65% (4 Gy), 80% vs. 50% (8 Gy) and 70% vs. 35% (16 Gy). Proton irradiation led to similar diverging viability curves between UPS vs. PLS four days after irradiation with 90% vs. 75% (4 Gy), 85% vs. 45% (8 Gy) and 80% vs. 35% (16 Gy). Photon and proton radiation displayed only minor differences in cell-killing properties within each cell culture (UPS and PLS). The cell-killing effect of radiation sustained at eight days after irradiation in both cell cultures.

CONCLUSIONS

Pronounced differences in radiosensitivity are evident among UPS and PLS 3D patient-derived sarcoma cell cultures which may reflect the clinical heterogeneity. Photon and proton radiation showed similar dose-dependent cell-killing effectiveness in both 3D cell cultures. Patient-derived 3D STS cell cultures may represent a valuable tool to enable translational studies towards individualized subtype-specific radiotherapy in patients with STS.

Abstract 6223: PD3D®models: New age in cancer research and clinical diagnostics

Patient-derived 3D cell culture models (PD3D®) developed as a powerful tool for disease modelling, biomarker and drug discovery. Currently, they are gaining increasing significance in the field of personalized oncology, as they recapitulate the histopathology of the original tumor tissue and preserve its genetic markup. PD3D® can be used to model intratumoral heterogeneity and for medium and high throughput drug screens. Using a reverse clinical engineering approach, PD3D® models allow identification of chemoresistance/sensitivity signatures (i.e., biomarkers) and can be applied in personalized oncology to identify treatment for an individual patient. We successfully established PD3D® models from more than 300 tumor tissue samples, ranging from more prevalent cancers like colorectal, breast and pancreas carcinoma, to rare tumor entities including various sarcoma types and thymoma. PD3D® models from different tumor entities differ in morphology and culture media requirements. When treating PD3D® from the same tumor entity with standard of care drugs, we found that their response differed, as does clinical response of patients. Furthermore, we successfully used PD3D® models to identify a biomarker for predicting chemosensitivity towards a targeted drug. For application of PD3D® in truly personalized oncology, we developed a protocol that allows us to generate a PD3D® culture and perform a drug sensitivity assay for an individual patient within a therapy-relevant timeframe. Using this protocol, we identified a combination therapy for a pretreated, metastasized appendix carcinoma within 29 days, that resulted in stable disease of the patient. In conclusion, PD3D® models can be derived from various cancer entities and used to analyze drug response in cohorts of models for drug development or identification of signatures related to drug resistance or sensitivity. Furthermore, PD3D® models can be used to predict a patient tumor’s drug response in a personalized manner, supporting the oncologist to identify the best treatment option for the patient.

Citation Format: Alina Pflaume, Samantha Exner, Katja Herrera-Glomm, Jürgen Loskutov, Ulrike Pfohl, Manuela Regenbrecht, Sushmitha Sankarasubramanian, Lena Wedeken, Sabine Finkler, Larissa Ruhe, Quirin Graf Adelmann, Christoph Reinhard, Philipp Stroebel, Christian R. Regenbrecht. PD3D®models: New age in cancer research and clinical diagnostics [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 6223.

Establishment of PD3D models of sarcomas: A promising preclinical tool for improvement of sarcoma treatment

e23538

Background: Compared to the progress in understanding and treating carcinomas in the past decade, the options and related clinical benefit in terms of response rates and overall survival for sarcoma patients lacks behind. Increasing incidence, low 5-year-survival rates and nearly endless heterogeneity of sarcomas are challenging oncologists every day. The necessity of so far missing representative preclinical models is obvious. PD3D cell culture models have already proven to be a useful tool to reverse clinical engineer patient outcome in carcinomas. Here we report the establishing and refining of PD3D models for the plethora of sarcoma entities. Methods: We obtained viable sarcoma tissue samples from incisional biopsies or tumor resections. We continuously optimized media conditions. For quality control and pathological evaluation, we embedded the cells in FFPE, stained patient-specific models according to original tumor samples and evaluated them pathologically. Upon histopathological evaluation, we performed semi-automated drug response assays on patient-specific models with up to 12 drugs and drug combinations, including standard of care drugs plus a selection of additional drugs. In the fashion of a prospective observatory study, we compared the results from the in vitro screen with the actual clinical outcome. Results: More than 25 patient derived 3D-cell culture models have been established from various subtypes of sarcomas. Optimized media conditions and sampling operation improved the take rates from ca. 10 to 80% irrespective of the tumor subtype. Pathological examination of the models confirmed original diagnoses and revealed that the patient-specific models recapitulate the key properties of the original tumor. Negative predictive value of drug sensitivity testing was close to 100 %, while the positive predictive value was > 80 %. These results in a limited number of cases puts the predictive value en par with recently published data about the predictive value of patient-derived organoids in carcinomas. Conclusions: Patient derived 3D-cell culture models of sarcomas can be routinely established, irrespective of subtype Models can be used for multi-omics analyses including drug sensitivity screenings

Pretherapeutic drug sensitivity screenings could support clinical decision making

Findings need to be confirmed in a prospective observatory trial.

A RAS-independent biomarker panel pedicts response to MEK-inhibitors in colorectal cancer

e15524

Background: Biomarker discovery and development are essential for stratifying cancer patients in order to improve treatment outcomes. In colorectal cancer (CRC), mutations in the TGF-β/BMP pathway, especially in the SMAD4 gene have been correlated with decreased overall survival and are suspected to modulate drug sensitivity on the cellular level, hence SMAD4 mutations are worthwile targets for novel targeted therapy aproaches. Methods: In the present study, we uncover the mechanistic role of a loss-of-function mutation in SMAD4 in syngeneic patient-derived organoids (PDOs). CRISPR-engineered SMAD4R361H PDOs were subjected to a comparative drug screening, RNA-Sequencing and multiplex protein profiling analysis (DigiWest®). We have confirmed the response towards MEK inhibition of the initial model in an additional set of 62 PDOs with known mutational status. Results: We show that acquisition of SMAD4 loss-of-function mutations renders PDOs sensitive to MEK-inhibitors. Further, an activation of the TGF-β/BMP signaling pathway, specifically of the BMP branch was observed in SMAD4wt PDOs; indicating that BMP signaling is likely responsible for the resistance towards MEK inhibition. It is plausible that functional loss of SMAD4 and thus loss of BMP signaling renders SMAD4 mutated tumors more sensitive to MEK-inhibitors. By looking at additional genes involved in TGF-β/BMP signaling that are frequently mutated in CRC, we identified the novel gene mutational SFAB-signature ( SMAD4, FBXW7, ARID1A, or BMPR2), when at least one pathogenic mutation is present in these genes. The frequency of SFAB in CRC patient cohort (TCGA, n = 594) was comparable to the frequency of SFAB in our PDOs. For PDOs with SFAB-signature, we found up to 95% and 70% significant positive prediction for cobimetinib and selumetinib, respectively and also up to 70% positive prediction for trametinib. Thus, the SFAB-signature predicts response to MEK inhibition in PDOs with a very high confidence. We further investigated whether the RAS status of CRC PDOs does predict sensitivity to MEK inhibition. The RAS status alone and in combination with SFAB-signature failed to yield better prediction sensitivity to MEK-inhibitors. Conclusions: The present study is a significant step forward to more personalized treatment regimens for CRC patients by early inclusion of MEK-inhibitors. The SFAB-signature should be put to clinical testing as a RAS-independent biomarker for stratification of patients providing a valuable alternative treatment option against CRC, thus ensuring that all patients receive effective and specific therapies as early as possible.