The Bcl9-beta-catenin interface as a potential therapeutic target for colorectal cancer

Aberrantly active Wnt signaling is the hallmark driver of colorectal cancer (CRC). Bcl9/9l proteins are components of the main transcriptional activation complex of canonical Wnt signaling and interact with beta-catenin via a highly conserved homology domain (HD2). Intestinal loss of Bcl9 affects wound healing and Lgr5+-cancer stem cell (CSC) maintenance, but does not perturb normal tissue homeostasis. The aim of the present thesis was to validate the Bcl9-Î²-catenin interaction as a potential target for modulating Wnt signaling and abolishing intestinal stemness traits in colorectal cancer. We investigated the role of the Bcl9-beta-catenin interaction in the mouse AOM-DSS chemical carcinogenesis CRC model. Subsequently, we validated our observations in an independent transgenic APC-Kras CRC model (truncated APC tumor suppressor and mutated Kras expressed in the intestine). The expression of Bcl9 proteins was abolished exclusively in the gastrointestinal epithelium using constitutive or inducible Cre-recombinase expressed under the control of the Villin promoter. To corroborate that the loss of Bcl9 phenotype was due to the abrogation of the Bcl9-beta-catenin interaction and not to a Î²-catenin-independent function of Bcl9, we made use of an additional Bcl9 mutant mouse strain in which only the HD2 of both Bcl9 proteins was deleted, selectively preventing the Bcl9-beta-catenin interaction. The inducible deletion of Bcl9 in established AOM-DSS tumors led to a loss in stem cell, Wnt and EMT gene expression signatures, recapitulating the phenotype that we previously described when Bcl9 was deleted constitutively. A 14d partial decrease of Bcl9 proved sufficient to suppress the expression of mesenchymal marker Vimentin in a cell autonomous fashion. Importantly, AOM-DSS tumors with Bcl9 proteins selectively lacking the HD2 beta-catenin interaction domain displayed the same phenotype as observed in tumors that entirely lacked Bcl9 proteins. Bcl9-knockout tumors induced in the Wnt active APC-Kras tumor model were compared with their wild-type counterparts. Wild-type APC-Kras mutant tumors displayed fewer mesenchymal traits when compared to AOM-DSS induced tumors. Global gene expression analysis by RNA sequencing confirmed a strong positive correlation between Bcl9/9l-dependent transcriptional changes in both independent tumor models. Genes differentially expressed between wild-type and Bcl9/9l ablated tumors were used to probe CRC databases for correlation with patient outcome and revealed a strong association with vastly improved disease-free and overall survival, independent of clinical and molecular parameters. We have shown that preventing the interaction of Bcl9 with beta-catenin in established tumors in Wnt-activated CRC models rapidly resulted in the loss of stemness and mesenchymal traits and concomitant induction of a more differentiated phenotype. Importantly, these loss-of-Bcl9 traits are prognostic for favorable outcome in CRC patients and we have not observed any overt anomalies upon intestinal ablation of Bcl9 in adult mice. Overall, our observations indicate that targeting the Bcl9-beta-catenin interaction in Wnt-activated tumors might be well tolerated and a generally applicable pharmacological strategy to target CSCs to potentially prevent tumor recurrence and improve progression free survival.

Role of Bcl9 and Bcl9l in Homeostasis, Regeneration and Tumorigenesis of the Gastrointestinal Epithelium

Norbert Wiedemann

Wnt signaling is essential for embryogenesis and adult tissue homeostasis and contributes to cancer development, especially in the colon. A new essential pathway component, legless, was identified in Drosophila melanogaster. Mice with Cre/loxP-mediated conditional ablation of the legless homologues Bcl9 and Bcl9l in the intestinal epithelium were generated to assess the contribution of the genes to Wnt signaling and their potential suitability as therapeutic drug targets. Initial analysis had revealed that both genes were not required for self-renewal of the intestinal epithelium during homeostasis, but for regeneration of experimentally induced colon wounds. Furthermore, formation of chemically induced colon tumors was not impaired and Bcl9/Bcl9-mutant tumors were morphologically indistinguishable from wild-type tumors and displayed hallmarks of active Wnt signaling. This study aimed at further investigating the molecular processes involving Bcl9 and Bcl9l in wound regeneration and tumorigenesis in the colon, and in particular relatedness of the genes to Wnt signaling. To this end, transcriptomes of laser microdissected wound regions were analyzed by microarray-based gene expression profiling and realtime quantitative PCR, but did not reveal significant changes in gene expression at the time point chosen for analysis. However, expression profiling of homeostatic colon epithelium revealed a reduced expression of several intestinal stem cell marker genes in Bcl9/Bcl9l-mutant colon epithelium, suggesting that the regeneration deficit has been caused by functional impairment of intestinal stem cells. This stem cell deficiency did not differ between young and old mice and was also weakly detectable in small intestinal epithelium. To verify that tumors originated from cells in which complete deletion of all four Bcl9 and Bcl9l alleles had occurred and to assess Wnt signaling activity more comprehensively, laser microdissected tumor regions were profiled using microarrays and realtime quantitative PCR. This analysis confirmed that Bcl9 and Bcl9l were not required for colon tumorigenesis and revealed that despite the morphological similarity, transcriptional profiles of Bcl9/Bcl9l-mutant tumors were very different from wild-type tumors. Notably, loss of Bcl9 and Bcl9l caused reduced expression of a subset of direct Wnt target genes, genes related to epithelial-mesenchymal transition (EMT) and intestinal stem cell traits. While wild-type tumor epithelium appeared to be in a metastable state, characterized by co-expression of epithelial and mesenchymal traits, Bcl9/Bcl9l-mutant tumor epithelium predominantly expressed epithelial traits. In addition, a marked reduction in expression of several genes associated with malignant tumor properties was observed in Bcl9/Bcl9l-mutant tumors. This was highlighted by the preservation of an intact basement membrane around Bcl9/Bcl9l-mutant tumor epithelium, which was absent in wild-type tumors, and indicated that loss of Bcl9/Bcl9l decreased tumor aggressiveness. Of note, EMT and stemness traits are correlated to tumor resistance to therapy and thus interfering with Bcl9/Bcl9l function might restore drug responsiveness. As a proof of concept, it was shown that the malignant traits mediated by Bcl9/Bcl9l could be abrogated in wild-type tumors by inducing deletion of the genes. These findings suggest that targeting Bcl9 and Bcl9l with therapeutic drugs has the potential to attenuate the malignancy of colon tumors.

EPFL2011

Roles of Epigenetic Dysregulation in Cancer Progression and Metastasis

Mohammad Sadegh Saghafinia

Nearly all the cells of an organism share the same DNA sequence or genome, and yet they show different phenotypes and carry out different functions. This diversity is made possible by a verity of molecular modifications acting on the DNA sequence that collectively define the cell's epigenome. Failure in the proper regulation of epigenome can lead to abnormal activation or inhibition of vital signaling pathways, which contributes to the initiation and progression of multiple diseases, including cancer. In this thesis, I used a combination of in silico, in vitro, and in vivo techniques to explore the roles of epigenetic dysregulation in tumor progression and metastasis. In the first part, I performed a systematic and unbiased investigation of cancer-associated DNA methylation and gene expression changes across human cancers. I designed a novel algorithmic approach (RESET) to identify aberrant DNA methylation and associated gene expression changes across >6,000 human tumors. We identified a DNA Methylation Instability (DMI) phenotype in tumors acquiring numerous hyper and hypomethylated transcription start sites, which is associated with mutations of chromatin remodeling factors and Wnt-signaling. We showed that silenced genes coalesced in specific pathways including apoptosis, transcriptional regulation, and cell metabolism. The majority of the enhanced genes belonged to cancer-germline antigens (CG), whose expression correlated with response to anti-PD-1 in melanoma patients. Finally, we demonstrated the potential of RESET to explore aberrant DNA methylation in pediatric tumors; pediatric Wilms tumors with diffuse anaplasia exhibit DMI, and specific silencing events predict a worse outcome in cases with favorable histology. These results established a new approach to explore pan-cancer epigenetic modifications and provided a resource of candidate oncogenic events for future functional and therapeutic studies. In the second part, I studied the dynamics of cancer progression and metastasis in Pancreatic Neuroendocrine Tumors (PanNET). This rare tumor is the second most common form of pancreatic cancer. Two principal subtypes of PanNET has been identified: insulinomas (IT) and metastasis-like primaries (MLP), corresponding to the low and high grade of human PanNETs, respectively. From the mouse model of PanNET (RT2), we profiled the single-cell, bulk mRNA and miRNA transcriptomes, and the proteomes of primary and metastasis specimens. We demonstrated that the tumor progression from IT to MLP follows the reverse embryonic and postnatal developmental path. Transcriptomic data from human patients showed that aggressive human PanNETs also follow the same reverse developmental trajectory of dedifferentiation. We established one possible mechanism underlying IT-to-MLP transition. Over-expression of the miR-181cd cluster in IT-like cancer cell-lines resulted in acquisition of the MLP phenotypes. miR-181cd mediated its effect through suppressing the expression of Meis2 and, indirectly, inducing the expression of Hmgb3 and Mycn transcription factors. Inhibiting the expression of Hmgb3 in MLP-like cancer cell-lines resulted in a significant growth decrease both in vitro and in vivo, demonstrating the importance of Hmgb3 in the maintenance of MLP-like cell state. These data presented dedifferentiation as a mechanism by which malignant neuroendocrine cancer cells acquire progenitor-like features, enabling them to become more aggressive and metastatic.

EPFL2020

Intestinal stem cells differentiation and its application in cancer therapy

Maxim Norkin

Colorectal cancer (CRC) is one of the deadliest cancers worldwide. Despite extensive research in the field, new therapies targeting CRC are in urgent need. CRC is a highly heterogeneous disease with high levels of intra- and inter-patient heterogeneity. Cancer stem cells are the driving force of tumor development and metastasis. One of the approaches to treat CRC is differentiation therapy thereby induction of cancer stem cell differentiation may lead to tumor regression. Intestinal normal and cancer organoids represent an ideal model for studying the differentiation process ex vivo. Gene expression profiling of drug-treated organoids can be used for quantification of the differentiation process with high precision. RNA-seq based drug-screening platforms in organoids are not yet established. Here we developed a high-throughput high-content targeted RNA-seq-based platform (TORNADO-seq) for monitoring gene expression of large gene signatures in intestinal organoids which allowed us to quantify and evaluate complex cellular phenotypes and cellular alterations upon drug treatment. We applied TORNADO-seq in drug screening in wt and cancer intestinal organoids. We found many differentiation-inducing drugs in wt organoids, including some drugs specifically enriching for certain cell phenotypes, e.g. enteroendocrine cells. Further, we applied identified differentiation-inducing drugs to cancer organoids (APClof;KRASG12D;TP53lof) and discovered that the majority of those differentiation-inducing drugs also targeted cancer organoids. Differentiation induction seems to be a common mode of action of cancer-targeting drugs. Based on gene expression profiles of treated cancer organoids, we were able to propose and confirm the mechanism of action of several drugs indicating that cancer cells may to be sensitive to alterations in the cholesterol biosynthesis pathway. In general, utilization of TORNADO-seq allows predicting connections between cellular phenotypes and signaling pathways in organoids which can be used for hypothesis generation in a variety of biological systems. The second part of the thesis is devoted to the investigation of mechanisms underlying the accumulation of genetic alterations in CRC tumors. It is not known whether cancer driver genes affect the rate of mutation acquisition. Here we performed exome sequencing of single cell-derived organoids obtained from tumors with either APClof, APClof;KRASG12D or APClof;KRASG12D;TP53lof mutation phenotypes that reflect early stages of CRC development. We discovered that presence of KRAS and P53 mutations didn't affect the number of single nucleotide substitutions (SNSs) in tumors, while the latter was increased in APC mutated tumors compared to wt cells and was highly correlated with the tumor age. P53 inactivation was highly correlated with the presence of large-scale (>10 Mb) copy number alterations (CNAs).

EPFL2021