Stratifying esophago-gastric cancer treatment using a patient-derived organoid-based threshold

BACKGROUND AND AIMS

This study sought to determine the value of patient-derived organoids (PDOs) from esophago-gastric adenocarcinoma (EGC) for response prediction to neoadjuvant chemotherapy (neoCTx).

METHODS

Endoscopic biopsies of patients with locally advanced EGC (n = 120) were taken into culture and PDOs expanded. PDOs' response towards the single substances of the FLOT regimen and the combination treatment were correlated to patients' pathological response using tumor regression grading. A classifier based on FLOT response of PDOs was established in an exploratory cohort (n = 13) and subsequently confirmed in an independent validation cohort (n = 13).

RESULTS

EGC PDOs reflected patients' diverse responses to single chemotherapeutics and the combination regimen FLOT. In the exploratory cohort, PDOs response to single 5-FU and FLOT combination treatment correlated with the patients' pathological response (5-FU: Kendall's τ = 0.411, P = 0.001; FLOT: Kendall's τ = 0.694, P = 2.541e-08). For FLOT testing, a high diagnostic precision in receiver operating characteristic (ROC) analysis was reached with an AUCROC of 0.994 (CI 0.980 to 1.000). The discriminative ability of PDO-based FLOT testing allowed the definition of a threshold, which classified in an independent validation cohort FLOT responders from non-responders with high sensitivity (90%), specificity (100%) and accuracy (92%).

CONCLUSION

In vitro drug testing of EGC PDOs has a high predictive accuracy in classifying patients' histological response to neoadjuvant FLOT treatment. Taking into account the high rate of successful PDO expansion from biopsies, the definition of a threshold that allows treatment stratification paves the way for an interventional trial exploring PDO-guided treatment of EGC patients.

Abstract 2852: A gene activating in vivo screen identifies EBAG9 as novel metastasis regulator in human colorectal cancer

As colorectal cancer (CRC) mortality remains high due to metastatic spread in patients with advanced disease stages, we here aimed at identifying novel metastasis regulators in CRC and at understanding their mechanism of action. In CRC, tumor progression and metastasis formation are driven by cells that possess tumor-initiating cell (TIC) activity. We therefore employed a collection of primary patient-derived CRC tumor spheroid cultures (TSC) that are enriched for cells with TIC activity to perform a gene activating in vivo screen, intending to identify genes that enhance metastasis formation. To this end, TSC (n=4) were transduced with a lentiviral trapping vector that integrates into the genome and thereby drives the overexpression of genes located in the vicinity of the integration site (IS). Transduced TSC were then serially transplanted under the kidney capsule of immunodeficient mice (NSG) and monitored for the induction of metastasis formation. Analysis of lentiviral IS by linear amplification-mediated (LAM)-PCR revealed an enrichment of an IS within the gene locus of Estrogen Receptor Binding Site Associated Antigen 9 (EBAG9) in metastases. RNA sequencing confirmed the trapping vector mediated upregulation of a truncated version of the EBAG9 gene (exon 5-7), which strongly suggested a contribution of EBAG9 to metastatic spread. To validate these findings, both the truncated (TR) as well as the physiologically occurring full length (FL) EBAG9 gene were overexpressed in TSC (n=4) and serially transplanted into NSG mice. In addition to an augmentation in metastasis upon EBAG9 overexpression compared to controls (FL: 1.4-fold, TR: 2.4-fold), we also detected the occurrence of lymphogenous metastases when EBAG9 levels were increased, indicating that EBAG9 not only contributes to metastatic spread but also modulates tropism. To further characterize the underlying processes, global gene and protein expression analyses were performed in primary TSC as well as in the CRC cell line DLD1. Compared to control transduced cells, EBAG9 overexpression induced expression changes in cell adhesion and microtubule molecules, which led us to investigate cell migration and adhesion as potential contributing mechanisms to metastasis formation. We here observed an increase both in cell migration as well as in adhesion to the extracellular matrix protein collagen I upon EBAG9 overexpression in DLD1. Interestingly, DLD1 adhesion to lymphatic endothelial cells was significantly higher in EBAG9 FL (p=0.008) and EBAG9 TR (p=0.016) overexpressing cells, underscoring the role of EBAG9 in tropism modulation. In summary, we here identified EBAG9 as novel metastasis regulator in CRC which will not only contribute to a better mechanistic understanding of metastatic spread but also to the development of novel future strategies for preventing and targeting advanced disease stages.

Citation Format: Karin Laaber, Taronish D. Dubash, Anna Maria Melzer, Tania Christiansen, Nati Ha, Benedikt Brors, Martin Schneider, Friederike Herbst, Hanno Glimm, Claudia R. Ball. A gene activating in vivo screen identifies EBAG9 as novel metastasis regulator in human colorectal cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2852.

Degradation of CCNK/CDK12 is a druggable vulnerability of colorectal cancer

Novel treatment options for metastatic colorectal cancer (CRC) are urgently needed to improve patient outcome. Here, we screen a library of non-characterized small molecules against a heterogeneous collection of patient-derived CRC spheroids. By prioritizing compounds with inhibitory activity in a subset of-but not all-spheroid cultures, NCT02 is identified as a candidate with minimal risk of non-specific toxicity. Mechanistically, we show that NCT02 acts as molecular glue that induces ubiquitination of cyclin K (CCNK) and proteasomal degradation of CCNK and its complex partner CDK12. Knockout of CCNK or CDK12 decreases proliferation of CRC cells in vitro and tumor growth in vivo. Interestingly, sensitivity to pharmacological CCNK/CDK12 degradation is associated with TP53 deficiency and consensus molecular subtype 4 in vitro and in patient-derived xenografts. We thus demonstrate the efficacy of targeted CCNK/CDK12 degradation for a CRC subset, highlighting the potential of drug-induced proteolysis for difficult-to-treat types of cancer.

The balance between the intronic miR-342 and its host gene Evl determines hematopoietic cell fate decision

Protein-coding and non-coding genes like miRNAs tightly control hematopoietic differentiation programs. Although miRNAs are frequently located within introns of protein-coding genes, the molecular interplay between intronic miRNAs and their host genes is unclear. By genomic integration site mapping of gamma-retroviral vectors in genetically corrected peripheral blood from gene therapy patients, we identified the EVL/MIR342 gene locus as a hotspot for therapeutic vector insertions indicating its accessibility and expression in human hematopoietic stem and progenitor cells. We therefore asked if and how EVL and its intronic miRNA-342 regulate hematopoiesis. Here we demonstrate that overexpression (OE) of Evl in murine primary Lin^- Sca1⁺ cKit⁺ cells drives lymphopoiesis whereas miR-342 OE increases myeloid colony formation in vitro and in vivo, going along with a profound upregulation of canonical pathways essential for B-cell development or myelopoietic functions upon Evl or miR-342 OE, respectively. Strikingly, miR-342 counteracts its host gene by targeting lymphoid signaling pathways, resulting in reduced pre-B-cell output. Moreover, EVL overexpression is associated with lymphoid leukemia in patients. In summary, our data show that one common gene locus regulates distinct hematopoietic differentiation programs depending on the gene product expressed, and that the balance between both may determine hematopoietic cell fate decision.

Abstract 1491: Transcriptional heterogeneity identifies functional states of tumor-initiating cell differentiation in human colorectal cancer

Tumor progression in colorectal cancer (CRC) is driven by a subpopulation of cells with tumor-initiating cell (TIC) activity. In the past, bulk experiments provided strong evidence for functional heterogeneity of the CRC TIC compartment with distinct types of TICs driving CRC progression. However, in these retrospective experiments direct assignment of functional states to individual functionally relevant cell types in CRC has not been possible.

We here asked whether functional states of individual cells can be assigned to specific CRC cell subpopulations. Therefore, 4,663 single-cell profiles were generated by single-cell RNA-sequencing (scRNA-seq) of patient-derived CRC spheroid cultures (n=12). Non-negative matrix factorization identified 13 gene expression modules linked to cell states or cell types that resemble differentiation states of normal intestinal epithelial cells.

To evaluate their presence in CRC patient tumors, the identified transcriptional programs were applied to publicly available expression data (TCGA cohort; n=459). Clustering of samples based on the contribution of individual expression signatures revealed six patient clusters with significantly different progression-free survival (p=0.043) and a trend towards different overall survival (p=0.12), indicating a relevance for patient outcome.

Comparing cell state meta-signature expression in cell type-associated subpopulations revealed differences in functional states, i.e. proliferative and metabolic activity. Interestingly, stem-like cells showed significantly increased oxidative phosphorylation (OXPHOS) and decreased glycolysis scores, suggesting a link between metabolic states and cell differentiation. scRNA-seq of patient-derived organoid and xenograft models as well as primary tumors revealed similar trends.

To assess whether metabolic states are linked to TIC activity, CRC spheroid cells were sorted according to mitochondrial membrane potential (MMP), and sphere forming cell (SFC) as well as TIC frequency were assessed by limiting dilutions. Strikingly, MMPhigh cells exhibited a pronounced increase of SFC frequencies in vitro compared to MMPlow cells in 80% of patients (n=5). In addition, TIC frequencies were strongly increased in the MMPhigh compared to the MMPlow subpopulation in vivo (n=2; 1/46,535 vs. 1/211,305 and 1/249 vs. 1/2,089), demonstrating that TIC activity relies on OXPHOS. In line with this, pretreatment with the OXPHOS inhibitor CCCP decreased SFC frequencies (n=3), indicating targetable metabolic vulnerability of CRC spheroid cells.

In summary, we here show that transcriptional heterogeneity identifies functional states during CRC TIC differentiation. Targeting context-dependent regulation of tumor cell differentiation might unravel novel vulnerabilities for therapeutic intervention in human CRC.

Citation Format: Martina K. Zowada, Stephan M. Tirier, Sebastian M. Dieter, Teresa Krieger, Ava Oberlack, Robert L. Chua, Mario Huerta, Foo Wei Ten, Karin Laaber, Jeongbin Park, Katharina Jechow, Torsten Müller, Mathias Kalxdorf, Mark Kriegsmann, Katharina Kriegsmann, Friederike Herbst, Jeroen Krijgsveld, Martin Schneider, Roland Eils, Hanno Glimm, Christian Conrad, Claudia R. Ball. Transcriptional heterogeneity identifies functional states of tumor-initiating cell differentiation in human colorectal cancer [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 1491.