Overcoming MET-mediated resistance in oncogene-driven NSCLC

This study evaluates the efficacy of combining targeted therapies with MET or SHP2 inhibitors to overcome MET-mediated resistance in different NSCLC subtypes. A prevalence study was conducted for MET amplification and overexpression in samples from patients with NSCLC who relapsed on ALK, ROS1, or RET tyrosine kinase inhibitors. MET-mediated resistance was detected in 37.5% of tissue biopsies, which allow the detection of MET overexpression, compared to 7.4% of liquid biopsies. The development of drug resistance by MET overexpression was confirmed in EGFRex19del-, KRASG12C-, HER2ex20ins-, and TPM3-NTRK1-mutant cell lines. The combination of targeted therapy with MET or SHP2 inhibitors was found to overcome MET-mediated resistance in both in vitro and in vivo assays. This study highlights the importance of considering MET overexpression as a resistance driver to NSCLC targeted therapies to better identify patients who could potentially benefit from combination approaches with MET or SHP2 inhibitors.

Abstract 1105: MET or SHP2 inhibition enhances targeted therapies and delays the emergence of resistance in oncogene-driven NSCLC

Background: Although advancements have been made in available targeted therapies for non-small cell lung cancer (NSCLC), most patients have an incomplete response and eventually acquire resistance. It is well known that MET signaling is a key pathway that mediates osimertinib resistance. Concurrently targeting multiple proteins in critical signaling pathways, including the MET receptor or SHP2, a key node downstream of receptor tyrosine kinases, may prevent or delay resistance. Here, we explore the promising concept of combining upfront targeted therapies with a selective MET inhibitor or SHP2 inhibitor as promising therapeutic strategies for oncogene-driven NSCLC.

Methods: All cell lines were obtained from commercial vendors. Drugs were synthesized at Merck KGaA or purchased from commercial vendors. Cell viability upon inhibitor treatment was investigated by Resazurin Cell Viability Assay (R&D Systems), and the effect of the inhibitors on colony forming ability was assessed using colony formation assays. Western blot was conducted to analyze pathway activity. The emergence of resistance was investigated by measuring the cell surface confluence using the IncuCyte S3 system (Essen Bioscience).

Results: The lung cancer cell lines used were NCI-H358 (KRAS G12C), HCC-827 (EGFR L858R), NCI-H2228 (ALK fusion), HCC-78 (ROS1 fusion), and NCI-H1781 (HER2 exon 20 insertion), with their respective targeted therapies sotorasib, osimertinib, alectinib, entrectinib, and poziotinib. The antiproliferative effects of targeted therapies combined with a MET or SHP2 inhibitor were assessed using combination dose matrices in 6-day viability assays. While MET inhibition did not further sensitize the already sensitive cells to the targeted therapies, synergism occurred when the drugs were combined with the SHP2 inhibitor. Similar results were obtained by colony formation assays lasting 2 weeks. Furthermore, the combination of the targeted therapies with the SHP2 inhibitor led to stronger ERK signaling abrogation than with single therapies. In a long-term proliferation assay, the combined inhibition of EGFR and MET receptor delayed the emergence of osimertinib resistance in the EGFR mutant HCC827 cells, which have MET protein overexpression and phosphorylation.

Conclusions: Our data show that combining targeted therapies with a SHP2 inhibitor synergistically decreases the viability of oncogene-driven NSCLC cell lines, indicating that initial combination therapy may be an appealing approach to improve patient outcomes. The observed delay in the emergence of osimertinib resistance, from combining a MET inhibitor with osimertinib, provides preclinical evidence to support further investigating MET inhibition upfront to improve the long-term therapeutic efficacy of EGFR inhibitors.

Citation Format: Nadine Reischmann, Lorenz Pudelko, Christopher Stroh, Nina Linde, Doreen Musch, Marina Keil, Linda Pudelko, Christina Esdar, Andree Blaukat, Karl M. Schumacher, Niki Karachaliou. MET or SHP2 inhibition enhances targeted therapies and delays the emergence of resistance in oncogene-driven NSCLC [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 1105.

Abstract 1106: Detection of MET alterations at the DNA, RNA and protein levels in NSCLC patients progressing on ALK and ROS1 targeted therapies

Background: ALK and ROS1 fusion-positive NSCLC patients derive clinical benefit from tyrosine kinase inhibitors (TKIs) but ultimately relapse. Acquired resistance mechanisms include on-target secondary mutations or copy number gains and activation of bypass signaling. Although MET amplification has been described as a bypass resistance mechanism to ALK and ROS1 inhibitors, there are limited data on MET gene and protein overexpression. Aims: (i) detection of MET alterations at the DNA, mRNA and protein levels in ALK and ROS1 fusion-positive NSCLC patients progressing on TKIs, and (ii) establishment of primary cultures using samples from those patients.

Methods: MET alterations were studied in 12 patients after progression on TKIs, 10 ALK and 2 ROS1 fusion-positive. Informed consent was obtained from all patients. NGS and FISH were used to detect resistance mutations and amplifications. MET mRNA expression levels were determined by nCounter. Total and phospho-MET levels were assessed by IHC and Western blotting.

Results: A total of 21 samples were available from the 12 patients, including tumor biopsies (n=5), plasma (n=10), pleural effusions (n=3) and cerebrospinal fluids (n=3). MET alterations were detected in 4 patients, 3 ALK fusion-positive progressing on lorlatinib and one ROS1 fusion-positive patient progressing on crizotinib. The 3 ALK fusion-positive patients had MET amplification detected in liquid biopsy (n=2) or tumor tissue (n=1), collected after progression on lorlatinib. In the patient with tissue biopsy available, the increased MET copy number was in line with the presence of MET protein and RNA overexpression. MET amplification was not present on the pre-treatment biopsy available for one of the 3 patients. In primary cultures established from pleural effusion samples of 2 ALK fusion-positive patients, MET amplification was maintained, particularly if the cells were cultured in presence of an ALK TKI. Although the ROS1 fusion-positive patient had no MET amplification after progression on crizotinib, MET and phospho-MET upregulation were detected by IHC. These alterations were also present in primary culture that could be established from a pleural effusion sample of the patient.

Conclusions: We found MET alterations in 4 out of 12 (33%) fusion-positive patients after progression on TKIs. Three of them had MET amplification and one MET protein overexpression in the absence of MET copy number gain. Despite the small size of the cohort, our results suggest that testing not only at the DNA but also at the RNA and protein levels, discovers amplification-negative patients with MET alterations who may derive benefit from a MET targeted therapy. Finally, our findings highlight the potential of pleural effusion as a source of material for the establishment of primary cultures.

Citation Format: Núria Jordana-Ariza, Nadine Reischmann, Carlos Esparré, Ruth Román, Cristina Aguado-Esteban, Silvia García-Román, Christopher Stroh, Andrés Aguilar Aguilar, Rafael Rosell, Niki Karachaliou, Miguel A. Molina-Vila. Detection of MET alterations at the DNA, RNA and protein levels in NSCLC patients progressing on ALK and ROS1 targeted therapies [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 1106.

BRAFV600E drives dedifferentiation in small intestinal and colonic organoids and cooperates with mutant p53 and Apc loss in transformation

BRAF^V600E confers poor prognosis and is associated with a distinct subtype of colorectal cancer (CRC). Little is known, however, about the genetic events driving the initiation and progression of BRAF^V600E mutant CRCs. Recent genetic analyses of CRCs indicate that BRAF^V600E often coexists with alterations in the WNT- and p53 pathways, but their cooperation remains ill-defined. Therefore, we systematically compared small and large intestinal organoids from mice harboring conditional Braf^floxV600E, Trp53^LSL-R172H, and/or Apc^flox/flox alleles. Using these isogenic models, we observe tissue-specific differences toward sudden BRAF^V600E expression, which can be attributed to different ERK-pathway ground states in small and large intestinal crypts. BRAF^V600E alone causes transient proliferation and suppresses epithelial organization, followed by organoid disintegration. Moreover, BRAF^V600E induces a fetal-like dedifferentiation transcriptional program in colonic organoids, which resembles human BRAF^V600E-driven CRC. Co-expression of p53^R172H delays organoid disintegration, confers anchorage-independent growth, and induces invasive properties. Interestingly, p53^R172H cooperates with BRAF^V600E to modulate the abundance of transcripts linked to carcinogenesis, in particular within colonic organoids. Remarkably, WNT-pathway activation by Apc deletion fully protects organoids against BRAF^V600E-induced disintegration and confers growth/niche factor independence. Still, Apc-deficient BRAF^V600E-mutant organoids remain sensitive toward the MEK inhibitor trametinib, albeit p53^R172H confers partial resistance against this clinically relevant compound. In summary, our systematic comparison of the response of small and large intestinal organoids to oncogenic alterations suggests colonic organoids to be better suited to model the human situation. In addition, our work on BRAF-, p53-, and WNT-pathway mutations provides new insights into their cooperation and for the design of targeted therapies.

Abstract 2854: Reconstruction of BRAFV600E driven colorectal carcinogenesis and identification of novel drug combinations involving BRAF and RTK inhibitors

BRAF mutations are found in approximately 10% of colorectal cancers (CRC) and are associated with an aggressive, less-differentiated and therapy-resistant phenotype. Inhibitors targeting BRAFV600E elicit only limited survival benefits when used as single agents. This unresponsiveness was mechanistically attributed to the relief of negative feedbacks on the epidermal growth factor receptor (EGFR) and initiated dual and triple combinatorial trials. These trials often involve the combination of BRAF inhibitors (BRAFi) and/or MEK inhibitors with anti-EGFR antibodies such as cetuximab or panitumumab. Although first results of these dual or triple therapies demonstrated improved efficacy, the response rates still were heterogeneous. Here, we show that BRAFi upregulate a variety of receptor tyrosine kinases (RTK) in CRC cell lines, including not only the EGFR, but also human epidermal growth factor receptor (HER) 2 and HER3. Importantly, combination of BRAFi (vemurafenib, dabrafenib or encorafenib) with inhibitors dually targeting the EGFR and HER2 (lapatinib, canertinib or afatinib) significantly reduced the metabolic activity and proliferation of CRC cells. Similarly, genetic depletion of HER2 and HER3 re-sensitized CRC cells to BRAF inhibition. Interestingly, BRAF inhibition also led to increased levels of the GRB2-associated binders (Gab) 1 and Gab2, two important mediators of RTK signaling. The Gab2 upregulation was directly dependent on the loss of BRAFV600E signaling and not caused by “off-target” effects, as demonstrated by allele-specific shRNA mediated BRAFV600E knockdown. These findings suggest new escape mechanisms for current treatment regimens and indicate that targeted therapy in BRAF mutant CRC could benefit from broad RTK pathway blockade.

Importantly, the BRAF/HER family inhibitor combination was also more effective in murine intestinal MouseT1 cells (originating from a Vil-Cre;BrafLSL-V637E/+;Tp53LSL-R172H/+ mouse model), which indicates a species-independent phenomenon. These novel and our previous findings that BRAFV600E suppresses features of epithelial differentiation and effector function prompted us to establish crypt organoid cultures from mice carrying conditional BraffloxV600E/+ and/or Tp53LSL-R172H/+ knock-in alleles, either singly or in combination. Using a Vil-CreERT2 transgene, we were able to induce expression of oncogenic BRAF and dominant-negative p53R172H in organoids by 4-hydroxy-tamoxifen mediated Cre activation. We demonstrate that the sudden expression of BRAFV600E and TP53R172H induce marked morphological and molecular changes in small and large intestinal crypts. This organoid model system represents an excellent tool to better understand key characteristics of BRAF mutant CRC such as intrinsic aggressiveness, poor differentiation and resistance to BRAFi.

Citation Format: Nadine Reischmann, Ricarda Herr, Sebastian Halbach, Miriam Heizmann, Hauke Busch, Melanie Boerries, Tilman Brummer. Reconstruction of BRAFV600E driven colorectal carcinogenesis and identification of novel drug combinations involving BRAF and RTK inhibitors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2854.

A RhoA-FRET Biosensor Mouse for Intravital Imaging in Normal Tissue Homeostasis and Disease Contexts

The small GTPase RhoA is involved in a variety of fundamental processes in normal tissue. Spatiotemporal control of RhoA is thought to govern mechanosensing, growth, and motility of cells, while its deregulation is associated with disease development. Here, we describe the generation of a RhoA-fluorescence resonance energy transfer (FRET) biosensor mouse and its utility for monitoring real-time activity of RhoA in a variety of native tissues in vivo. We assess changes in RhoA activity during mechanosensing of osteocytes within the bone and during neutrophil migration. We also demonstrate spatiotemporal order of RhoA activity within crypt cells of the small intestine and during different stages of mammary gestation. Subsequently, we reveal co-option of RhoA activity in both invasive breast and pancreatic cancers, and we assess drug targeting in these disease settings, illustrating the potential for utilizing this mouse to study RhoA activity in vivo in real time.

The Atypical Kinase RIOK1 Promotes Tumor Growth and Invasive Behavior

Despite being overexpressed in different tumor entities, RIO kinases are hardly characterized in mammalian cells. We investigated the role of these atypical kinases in different cancer cells. Using isogenic colon-, breast- and lung cancer cell lines, we demonstrate that knockdown of RIOK1, but not of RIOK2 or RIOK3, strongly impairs proliferation and invasiveness in conventional and 3D culture systems. Interestingly, these effects were mainly observed in RAS mutant cancer cells. In contrast, growth of RAS wildtype Caco-2 and Bcr-Abl-driven K562 cells is not affected by RIOK1 knockdown, suggesting a specific requirement for RIOK1 in the context of oncogenic RAS signaling. Furthermore, we show that RIOK1 activates NF-κB signaling and promotes cell cycle progression. Using proteomics, we identified the pro-invasive proteins Metadherin and Stathmin1 to be regulated by RIOK1. Additionally, we demonstrate that RIOK1 promotes lung colonization in vivo and that RIOK1 is overexpressed in different subtypes of human lung- and breast cancer. Altogether, our data suggest RIOK1 as a potential therapeutic target, especially in RAS-driven cancers.

Intravital FRAP Imaging using an E-cadherin-GFP Mouse Reveals Disease- and Drug-Dependent Dynamic Regulation of Cell-Cell Junctions in Live Tissue

E-cadherin-mediated cell-cell junctions play a prominent role in maintaining the epithelial architecture. The disruption or deregulation of these adhesions in cancer can lead to the collapse of tumor epithelia that precedes invasion and subsequent metastasis. Here we generated an E-cadherin-GFP mouse that enables intravital photobleaching and quantification of E-cadherin mobility in live tissue without affecting normal biology. We demonstrate the broad applications of this mouse by examining E-cadherin regulation in multiple tissues, including mammary, brain, liver, and kidney tissue, while specifically monitoring E-cadherin mobility during disease progression in the pancreas. We assess E-cadherin stability in native pancreatic tissue upon genetic manipulation involving Kras and p53 or in response to anti-invasive drug treatment and gain insights into the dynamic remodeling of E-cadherin during in situ cancer progression. FRAP in the E-cadherin-GFP mouse, therefore, promises to be a valuable tool to fundamentally expand our understanding of E-cadherin-mediated events in native microenvironments.

Measurement and modeling of transcriptional noise in the cell cycle regulatory network

Fifty years of genetic and molecular experiments have revealed a wealth of molecular interactions involved in the control of cell division. In light of the complexity of this control system, mathematical modeling has proved useful in analyzing biochemical hypotheses that can be tested experimentally. Stochastic modeling has been especially useful in understanding the intrinsic variability of cell cycle events, but stochastic modeling has been hampered by a lack of reliable data on the absolute numbers of mRNA molecules per cell for cell cycle control genes. To fill this void, we used fluorescence in situ hybridization (FISH) to collect single molecule mRNA data for 16 cell cycle regulators in budding yeast, Saccharomyces cerevisiae. From statistical distributions of single-cell mRNA counts, we are able to extract the periodicity, timing, and magnitude of transcript abundance during the cell cycle. We used these parameters to improve a stochastic model of the cell cycle to better reflect the variability of molecular and phenotypic data on cell cycle progression in budding yeast.

Synthetic biology: programming cells for biomedical applications

The emerging field of synthetic biology is a novel biological discipline at the interface between traditional biology, chemistry, and engineering sciences. Synthetic biology aims at the rational design of complex synthetic biological devices and systems with desired properties by combining compatible, modular biological parts in a systematic manner. While the first engineered systems were mainly proof-of-principle studies to demonstrate the power of the modular engineering approach of synthetic biology, subsequent systems focus on applications in the health, environmental, and energy sectors. This review describes recent approaches for biomedical applications that were developed along the synthetic biology design hierarchy, at the level of individual parts, of devices, and of complex multicellular systems. It describes how synthetic biological parts can be used for the synthesis of drug-delivery tools, how synthetic biological devices can facilitate the discovery of novel drugs, and how multicellular synthetic ecosystems can give insight into population dynamics of parasites and hosts. These examples demonstrate how this new discipline could contribute to novel solutions in the biopharmaceutical industry.