Recurrent RhoGAP gene fusion CLDN18-ARHGAP26 promotes RHOA activation and focal adhesion kinase and YAP-TEAD signalling in diffuse gastric cancer

OBJECTIVE

Genomic studies of gastric cancer have identified highly recurrent genomic alterations impacting RHO signalling, especially in the diffuse gastric cancer (DGC) histological subtype. Among these alterations are interchromosomal translations leading to the fusion of the adhesion protein CLDN18 and RHO regulator ARHGAP26. It remains unclear how these fusion constructs impact the activity of the RHO pathway and what is their broader impact on gastric cancer development. Herein, we developed a model to allow us to study the function of this fusion protein in the pathogenesis of DGC and to identify potential therapeutic targets for DGC tumours with these alterations.

DESIGN

We built a transgenic mouse model with LSL-CLDN18-ARHGAP26 fusion engineered into the Col1A1 locus where its expression can be induced by Cre recombinase. Using organoids generated from this model, we evaluated its oncogenic activity and the biochemical effects of the fusion protein on the RHOA pathway and its downstream cell biological effects in the pathogenesis of DGC.

RESULTS

We demonstrated that induction of CLDN18-ARHGAP26 expression in gastric organoids induced the formation of signet ring cells, characteristic features of DGC and was able to cooperatively transform gastric cells when combined with the loss of the tumour suppressor geneTrp53. CLDN18-ARHGAP26 promotes the activation of RHOA and downstream effector signalling. Molecularly, the fusion promotes activation of the focal adhesion kinase (FAK) and induction of the YAP pathway. A combination of FAK and YAP/TEAD inhibition can significantly block tumour growth.

CONCLUSION

These results indicate that the CLDN18-ARHGAP26 fusion is a gain-of-function DGC oncogene that leads to activation of RHOA and activation of FAK and YAP signalling. These results argue for further evaluation of emerging FAK and YAP-TEAD inhibitors for these deadly cancers.

Aberrant cell state plasticity mediated by developmental reprogramming precedes colorectal cancer initiation

Cell state plasticity is carefully regulated in adult epithelia to prevent cancer. The aberrant expansion of the normally restricted capability for cell state plasticity in neoplasia is poorly defined. Using genetically engineered and carcinogen-induced mouse models of intestinal neoplasia, we observed that impaired differentiation is a conserved event preceding cancer development. Single-cell RNA sequencing (scRNA-seq) of premalignant lesions from mouse models and a patient with hereditary polyposis revealed that cancer initiates by adopting an aberrant transcriptional state characterized by regenerative activity, marked by Ly6a (Sca-1), and reactivation of fetal intestinal genes, including Tacstd2 (Trop2). Genetic inactivation of Sox9 prevented adenoma formation, obstructed the emergence of regenerative and fetal programs, and restored multilineage differentiation by scRNA-seq. Expanded chromatin accessibility at regeneration and fetal genes upon Apc inactivation was reduced by concomitant Sox9 suppression. These studies indicate that aberrant cell state plasticity mediated by unabated regenerative activity and developmental reprogramming precedes cancer development.

Abstract B023: Sox9 drives an aberrant transcriptional program impeding intestinal differentiation in colorectal cancer initiation

Despite the implementation of screening and preventative strategies, colorectal cancer (CRC) remains the second most deadly cancer worldwide and is responsible for an alarming trend of increasing prevalence among younger patients. Inappropriate WNT activation is the initiating step in sporadic CRC development, typically through deleterious mutations in the pathway negative regulator Adenomatous polyposis coli (APC). WNT pathway hinders whereas transforming growth factor (TGF-β)/bone morphogenetic protein (BMP) signaling supports differentiation of progenitors into mature enterocytes, establishing a crypt-villus gradient. Genomic alterations that dysregulate intestinal stem cell differentiation are central to CRC development. Impairment of differentiation and inappropriate Sox9 overexpression are conserved events in CRC initiation based on the evaluation of two genetically engineered mouse models, two carcinogen-induced mouse models, and a patient with familial adenomatous polyposis (FAP), a hereditary polyposis syndrome in which a mutant copy of APC is inherited. Single cell RNA-sequencing (scRNA-seq) of adenomas from an ApcKO mouse model and FAP sample implicates an aberrant stem cell-like program (herein referred to as AbSC) as a key aspect of CRC initiation. The AbSc program is characterized by selective intestinal stem cell activity, indiscriminate attenuation of differentiated lineages, and aberrant activation of genes associated with fetal intestinal development. Histopathology and scRNA-seq of adenomas and derivative organoids from a patient with FAP demonstrated a partial block in differentiation and confirmed reactivation of genes reserved for intestinal development. Assay for Transposase-Accessible Chromatin with high-throughput sequencing (ATAC-seq) of APCKO epithelial cells revealed increased chromatin accessibility at fetal intestinal genes. Genetic inactivation of Sox9 prevented adenoma formation in ApcKO mice and induced differentiation of ApcKO organoids, obstructing the emergence of the ApcKO transcriptional state, including reactivation of a fetal-like intestinal program, restored multi-lineage differentiation, and markedly reduced the gained chromatin accessibility at developmental genes in neoplasia. These studies indicate that an aberrant transcriptional state hindering intestinal differentiation mediated by Sox9 is an early conserved event in CRC and carry important implications for developing therapeutics directed at inducing intestinal differentiation.

Citation Format: Pratyusha Bala, Jonathan P. Rennhack, Clare Morris, Daulet Aitymbayev, Sydney M. Moyer, Gina Nicole Duronio, Paul Doan, William C. Hahn, Nilay S. Sethi. Sox9 drives an aberrant transcriptional program impeding intestinal differentiation in colorectal cancer initiation [abstract]. In: Proceedings of the AACR Special Conference on Colorectal Cancer; 2022 Oct 1-4; Portland, OR. Philadelphia (PA): AACR; Cancer Res 2022;82(23 Suppl_1):Abstract nr B023.

Abstract PR012: Aberrant cell state plasticity mediates colorectal cancer initiation

Cell state plasticity – the ability of cells to acquire new states via differentiation programs - is an important feature of embryogenesis, allowing for tissue specification during development, and adult homeostasis, enabling adaptive responses to physiological cues and pathological states. Epigenetic governance and gene regulation endow epithelia with restricted cell state plasticity that enable tissue homeostasis while avoiding properties that may facilitate neoplasia. There is emerging evidence that aberrant expansion of the normally restricted capability for cell state plasticity to escape terminal differentiation is a key aspect of cancer initiation. The nongenetic factors and specific programs that mediate aberrant cell state plasticity require deeper characterization to understand this elusive aspect of cancer pathogenesis. Previously challenging to study, cell state plasticity can now be investigated using single cell technology, offering unprecedented molecular resolution. We applied state-of-the-art methods on primary human tissue and derivative organoids as well as different mouse models to (a) characterize aberrant transcriptional cell states enabling cancer initiation and (b) define a functional mediator of expanded cell state plasticity. Using genetically engineered and carcinogen-induced murine models of intestinal neoplasia, we demonstrate that inappropriate Sox9 expression and loss of post-mitotic villus differentiation are early events preceding cancer development. By applying single cell RNA-sequencing (scRNA-seq) to flow-sorted epithelial cells from the Lgr5Cre; Apcf/f; R26tdT genetic model, we observed that preneoplastic cells express specific intestinal stem cell genes but are otherwise transcriptionally rewired, evading resemblance to normal intestinal cell types; we therefore refer to these cells as aberrant stem cell-like (AbSC). We further analyzed the AbSC transcriptional state, searching for features that explain its distinguished gene expression profile, and found that it is characterized by impaired differentiation, enhanced regenerative capacity, and reactivation of fetal genes. The evaluation of preneoplastic colonic lesions from the carcinogen-induced mouse model and a patient with familial adenomatous polyposis (FAP) by scRNA-seq confirmed these findings. Notably, while chromatin accessibility increased at regenerative genes, new accessibility was observed at fetal intestinal genes by ATAC-seq. Genetic inactivation of Sox9 prevented adenoma formation in ApcKO mice, obstructed emergence of the aberrant transcriptional state, including genes reserved for fetal intestinal development, and restored multi-lineage differentiation by scRNA-seq. SOX9 knockdown in human adenoma organoids compromised expression of fetal genes and induced differentiation. These studies indicate that cancer initiation requires aberrant phenotypic plasticity mediated by unabated regenerative activity and developmental reprogramming.

Citation Format: Pratyusha Bala, Jonathan Rennhack, Clare Morris, Daulet Aitymbayev, Sydney M. Moyer, Gina N. Duronio, William Hahn, Nilay S. Sethi. Aberrant cell state plasticity mediates colorectal cancer initiation [abstract]. In: Proceedings of the AACR Special Conference on Colorectal Cancer; 2022 Oct 1-4; Portland, OR. Philadelphia (PA): AACR; Cancer Res 2022;82(23 Suppl_1):Abstract nr PR012.

A novel β-catenin/BCL9 complex inhibitor blocks oncogenic Wnt signaling and disrupts cholesterol homeostasis in colorectal cancer

Dysregulated Wnt/β-catenin signaling is implicated in the pathogenesis of many human cancers, including colorectal cancer (CRC), making it an attractive clinical target. With the aim of inhibiting oncogenic Wnt activity, we developed a high-throughput screening AlphaScreen assay to identify selective small-molecule inhibitors of the interaction between β-catenin and its coactivator BCL9. We identified a compound that consistently bound to β-catenin and specifically inhibited in vivo native β-catenin/BCL9 complex formation in CRC cell lines. This compound inhibited Wnt activity, down-regulated expression of the Wnt/β-catenin signature in gene expression studies, disrupted cholesterol homeostasis, and significantly reduced the proliferation of CRC cell lines and tumor growth in a xenograft mouse model of CRC. This study has therefore identified a specific small-molecule inhibitor of oncogenic Wnt signaling, which may have value as a probe for functional studies and has important implications for the development of novel therapies in patients with CRC.