Esophageal adenocarcinoma (EAC) is a genetically heterogeneous malignancy with few recurrent drivers, limiting effective targeted therapies. Although EAC arises from Barrett's esophagus (BE), mechanisms driving progression from this premalignant state to invasive cancer remain unclear. We combined pooled CRISPR-Cas9 loss-of-function screening, in vivo tumorigenicity assays, and Perturb-seq profiling to define functional drivers of BE transformation. We identified 37 tumor suppressors whose loss promotes progression to EAC, defining a functional landscape of tumor initiation. Despite genetic diversity, these losses converged on four transcriptional programs involving metabolic reprogramming, cell cycle progression, RNA processing, and cellular motility. Furthermore, we identify loss of NIPBL , TGFBR2 , and RPL22 as key mediators of resistance to platinum- and taxane-based chemotherapy. Collectively, these findings provide a unifying framework for genomic heterogeneity in EAC, uncover underappreciated tumor suppressor pathways, and establish a resource to guide mechanistic and translational studies aimed at improving treatment strategies in this aggressive cancer.

Esophageal adenocarcinoma (EAC) is an aggressive malignancy with a rising incidence and limited treatment options. It develops from Barrett’s esophagus, a pre-cancerous metaplastic condition, yet the molecular mechanisms driving its progression remain poorly understood. Genomic studies have identified ∼76 candidate genes as potential drivers of EAC. In our previous work, we demonstrated that in the context of mutant TP53, the inactivation of one such candidate tumour suppressor, SMAD4, was sufficient to drive tumorigenesis in non-tumorigenic CP-B Barrett’s esophagus xenografts. Building on this, we combined our EAC tumorigenesis model with Perturb-Seq (CRISPR-mediated gene editing coupled with single-cell RNA sequencing (scRNA-Seq)) to enable high-throughput functional characterization of EAC driver genes. The study specifically aimed to: (i) identify the molecular perturbations driving tumorigenesis in EAC, (ii) understand the transcriptional changes underlying the oncogenic effects of these perturbations, and (iii) tackle the genetic heterogeneity of EAC by categorizing driver genes according to shared transcriptional phenotypes. In vivo loss-of-function CRISPR screen was conducted using a boutique pooled CRISPR/Cas9 sgRNA library (6 sgRNAs per gene) targeting 57 known and putative tumour suppressor genes. To analyze the gene knockout-specific effects on the transcriptome at single-cell resolution, capture sequences compatible with 10X Feature Barcoding were incorporated into the sgRNAs. The library was transduced into two independent esophageal pre-malignant cell models, CP-B and CP-D, followed by xenotransplantation in NSG immunodeficient mice. We established that the knockout of 40 out of the 57 candidate tumour suppressors were independently sufficient to induce tumour formation in vivo. By integrating the scRNA-Seq data corresponding to each tumour suppressor knockout, we found that depletion of these tumour suppressor genes inhibited the proteasomal degradation of oncogenes and anti-apoptotic proteins, such as cyclin E, c-Myc, and Mcl-1. Additionally, this depletion led to the upregulation of genes involved in cell cycle progression, DNA repair, and lipid and carbohydrate metabolism. Perturb-seq also showed that driver-dependent transcriptional changes can be categorized into a smaller number of functional pathways allowing us to potentially consider groups of drivers as functional units. Collectively, the findings of this study enhance our understanding of the molecular events driving EAC tumorigenesis and offer a comprehensive view of the transcriptional phenotypes that can be targeted in future research. These insights lay the foundation for the development of novel therapeutic strategies for this highly heterogeneous disease. Ebtihal H. Mustafa, Julia Milne, Ka Meng Wu, Katherine Papastratos, Niko Thio, Wayne Phillips, Nicholas Clemons. Unveiling drivers of esophageal adenocarcinoma with CRISPR pooled screen and single-cell RNA-sequencing [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 4065.

Mutations in PIK3CA, the gene encoding the p110α catalytic subunit of PI3K, are among the most common mutations in human cancers and overgrowth syndromes. The ubiquitous expression of the activating Pik3caH1047R mutation results in reduced survival, organomegaly, hypoglycaemia and hypoinsulinemia in mice. Here we demonstrate that in vivo expression of Pik3caH1047R attenuates the rise in blood glucose in response to oral glucose administration, stimulates glucose uptake in peripheral tissues, inhibits hepatic gluconeogenesis and pancreatic insulin secretion, and increases adipose lipolysis and white adipose tissue browning. Together, our data reveal that the systemic activation of the PI3K pathway in mice disrupts glucose homeostasis through the regulation of hepatic gluconeogenesis, and leads to increased lipolysis of adipose tissue.

Background Androgen deprivation therapy (ADT) is a front-line treatment for prostate cancer. In some men, their tumors can become refractory leading to the development of castration-resistant prostate cancer (CRPC). This causes tumors to regrow and metastasize, despite ongoing treatment, and impacts negatively on patient survival. ADT is known to stimulate the accumulation of immunosuppressive cells like protumoral tumor-associated macrophages (TAMs), myeloid-derived suppressor cells and regulatory T cells in prostate tumors, as well as hypofunctional T cells. Protumoral TAMs have been shown to accumulate around tumor blood vessels during chemotherapy and radiotherapy in other forms of cancer, where they drive tumor relapse. Our aim was to see whether such perivascular (PV) TAMs also accumulate in ADT-treated prostate tumors prior to CRPC, and, if so, whether selectively inducing them to express a potent immunostimulant, interferon beta (IFNβ), would stimulate antitumor immunity and delay CRPC.Methods We used multiplex immunofluorescence to assess the effects of ADT on the distribution and activation status of TAMs, CD8+T cells, CD4+T cells and NK cells in mouse and/or human prostate tumors. We then used antibody-coated, lipid nanoparticles (LNPs) to selectively target a STING agonist, 2′3′-cGAMP (cGAMP), to PV TAMs in mouse prostate tumors during ADT.Results TAMs accumulated at high density around blood vessels in response to ADT and expressed markers of a protumoral phenotype including folate receptor-beta (FR-β), MRC1 (CD206), CD169 and VISTA. Additionally, higher numbers of inactive (PD-1-) CD8+T cells and reduced numbers of active (CD69+) NK cells were present in these PV tumor areas. LNPs coated with an antibody to FR-β selectively delivered cGAMP to PV TAMs in ADT-treated tumors, where they activated STING and upregulated the expression of IFNβ. This resulted in a marked increase in the density of active CD8+T cells (along with CD4+T cells and NK cells) in PV tumor areas, and significantly delayed the onset of CRPC. Antibody depletion of CD8+T cells during LNP administration demonstrated the essential role of these cells in delay in CRPC induced by LNPs.Conclusion Together, our data indicate that targeting a STING agonist to PV TAMs could be used to extend the treatment window for ADT in prostate cancer.

Abstract Application of molecular targeted therapies for esophageal adenocarcinoma (EAC) has been limited by a lack of druggable oncogenic drivers. We propose that synthetic lethal interactions may provide new opportunities for targeted therapies in EAC. We have taken an integrated multi-omics approach incorporating Perturb-Seq (CRISPR editing combined with single cell RNA sequencing) and in vivo tumorigenesis assays to perform high-throughput characterisation of >70 high-confidence EAC driver genes, and genome-wide CRISPR-Cas9 knockout screens in isogenic models of EAC tumorigenesis to identify disease relevant synthetic lethal genetic interactions. MS-based proteomics, reverse phase protein arrays, polysome profiling and bulk RNA-sequencing of isogenic models were utilised to interrogate the biology of bona fide EAC drivers and associated driver specific gene dependencies. The overall goals were to (i) enhance our understanding of EAC tumorigenesis, (ii) identify potential opportunities for therapeutic interventions targeting EAC drivers via synthetic lethal-like approaches, and (iii) reduce the complexity of genetic heterogeneity by categorising EAC drivers with similar phenotypic outcomes. Through our approach we have identified complex crosstalk between the tumor suppressor SMAD4 and regulation of mTOR signaling, with specific downstream effects on translational reprogramming in EAC. Mutation or loss of SMAD4 occurs in up to 20% of EAC, but not pre-malignant tissue (Barrett’s esophagus), and is sufficient to promote transformation of pre-malignant cells in our in vivo tumorigenesis model. In this model, xenotransplanted SMAD4-deficient (via CRISPR-Cas9 knockout or shRNA knockdown) Barrett’s metaplasia cells formed invasive, metastatic tumors after a period of latency. SMAD4 deficient cells had downregulated expression of 4E-BP1, which inhibits EIF4E, the cap-dependent translation initiation factor. This was accompanied by increased mTOR activity, including phosphorylation and inactivation of 4EBP1. Moreover, we found that SMAD4-deficient cells preferentially upregulate cap-dependent translation at the expense of IRES mediated translation. Furthermore, perturbation of additional negative regulators of mTOR signaling in combination with SMAD4 knockout exacerbated these effects and accelerated tumorigenesis in vivo. We have extended these findings to a model of Barrett’s esophagus patient-derived organoids (PDOs) and observed increased proliferative potential of our genetically modified PDOs. Finally, analysing gene ontologies for differentially expressed genes from Perturb-seq revealed that driver-dependent transcriptional changes can be categorized into a smaller number of functional pathways allowing us to potentially consider groups of drivers as functional units. This work advances our understanding of EAC tumorigenesis, provides new mechanistic insights into SMAD4-driven transformation as well as novel potential therapeutic avenues for SMAD4-deficient EAC. Citation Format: Julia V. Milne, Ebtihal Mustafa, Kenji Fujihara, Eric Kusnadi, Anna Trigos, Niko Thio, Maree Pechlivanis, Carlos Cabalag, Twishi Gulati, Kaylene Simpson, Cuong Duong, Luc Furic, Wayne Phillips, Nicholas Clemons. Delineating functional drivers of esophageal adenocarcinoma to identify synthetic lethal interactions [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Expanding and Translating Cancer Synthetic Vulnerabilities; 2024 Jun 10-13; Montreal, Quebec, Canada. Philadelphia (PA): AACR; Mol Cancer Ther 2024;23(6 Suppl):Abstract nr PR007.

Abstract Esophageal adenocarcinoma (EAC) is a cancer of high mutation burden with negligible recurrent and druggable driver genes and, therefore, a paucity of options for targeted therapy. Mutation or loss of the tumor suppressor gene SMAD4 occurs in up to 20% of EAC cases, and we have previously shown that loss of SMAD4 is sufficient to promote EAC tumorigenesis in an in vivo xenograft model. The present study aimed to delineate the role of SMAD4 in EAC tumorigenesis and identify synthetic lethal interactions in SMAD4-deficient cancers as a novel approach for treating EAC. Our multi-omics methodology integrated RNA-sequencing, proteomics, polysome-sequencing, reverse-phase protein arrays, and genome-wide CRISPR-Cas9 screening to unveil a SMAD4-deficiency signature and new therapeutic avenues for EAC. These data reveal a complex interplay between SMAD4 loss and regulation of mTOR signaling, with specific downstream effects to reprogram translation. SMAD4-deficient cells express decreased levels of 4E-BP1, the inhibitory binding partner of EIF4E, which is the rate-limiting component of the cap-dependent translation initiation complex. This was accompanied by increased mTOR activity, including phosphorylation and inactivation of 4E-BP1. We found that SMAD4-deficient cells exhibit vastly different polysome traces compared to their wildtype counterparts and preferentially upregulate cap-dependent translation, acquiring an addiction to translation of oncogenic mRNAs. Furthermore, perturbation of additional negative regulators of mTOR signaling in combination with SMAD4 knockout exacerbated these effects and accelerated tumorigenesis in vivo and growth of patient-derived organoids in vitro. This work advances our knowledge of EAC tumorigenesis, provides new mechanistic insights into SMAD4-driven transformation as well as novel potential therapeutic avenues for SMAD4-deficient EAC. Citation Format: Julia V. Milne, Kenji Fujihara, Eric Kusnadi, Maree Pechlivanis, Niko Thio, Carlos Cabalag, Twishi Gulati, Jovana Gotovac, Kaylene Simpson, Cuong Duong, Luc Furic, Wayne Phillips, Nicholas Clemons. Multi-omics approach reveals a SMAD4-deficiency signature, translational reprogramming and synthetic lethality in esophageal adenocarcinom [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 5578.

Preclinical models that replicate patient tumours as closely as possible are crucial for translational cancer research. While in vitro cancer models have many advantages in assessing tumour response therapy, in vivo systems are essential to enable evaluation of the role of the tumour cell extrinsic factors, such as the tumour microenvironment and host immune system. The requirement for a functional immune system is particularly important given the current focus on immunotherapies. Therefore, we set out to generate an immunocompetent, transplantable model of colorectal cancer suitable for in vivo assessment of immune-based therapeutic approaches. Intestinal tumours from a genetically engineered mouse model, driven by expression of a Pik3ca mutation and loss of Apc, were transplanted into wild type C57BL/6 host mice and subsequently passaged to form a novel syngeneic transplant model of colorectal cancer. Our work confirms the potential to develop a panel of mouse syngeneic grafts, akin to human PDX panels, from different genetically engineered, or carcinogen-induced, mouse models. Such panels would allow the in vivo testing of new pharmaceutical and immunotherapeutic treatment approaches across a range of tumours with a variety of genetic driver mutations.

Abstract Background Intra-operative molecular imaging (IMI) is an emerging field that utilises tumour-targeting fluorescent probes to improve oncological outcomes. A novel class of probe known as quenched activity-based probes (qABP), developed to measure enzyme activity in-vitro, has been repurposed to target tumour-expressed proteases known as cathepsins. Unlike other tumour-targeting probes, fluorescence is inhibited up until the qABP covalently bonds to cathepsins, releasing an inhibitory quencher which results in fluorescence. This may improve the contrast between normal tissue and tumour. Our laboratory group sought to obtain pre-clinical evidence to eventually translate qABP’s into the operating room for oesophageal, junctional and gastric cancer. Methods Cathepsin activity was screened in cell lines from the normal oesophagus, Barrett’s metaplasia, oesophageal adenocarcinoma (OAC), squamous cell carcinoma (SCC) and gastric adenocarcinoma (GAC) with two qABP’s known as BMV109 and VGT309. We additionally screened patient biopsies from oesophageal, junctional and gastric cancers. Cell line and tissue samples were analysed using in-gel fluorescence (Amersham Typhoon®) and Western blot. In-vivo, cell line xenografts were established in NSG mice using subcutaneous and orthotopic models. Tumour-bearing mice were then injected with VGT-309 and then imaged at specific timepoints using the IVIS® spectrum imager. Results Cathepsin activity was found in all oesophago-gastric cell lines and selectivity proven with a cathepsin inhibitor. Matched biopsies were collected from patients prior before and after neoadjuvant chemo-radiotherapy. Baseline tumour biopsies exhibited significantly higher cathepsin activity than normal biopsies, with these differences preserved in biopsies collected after chemo-radiotherapy (p <0.001). In-vivo, OAC and GAC xenografts were identified in NSG mice as early as 12 hours post injection of VGT-309, exhibiting a 2.5-fold increase in fluorescence compared to normal background stomach. Bio-distribution analysis demonstrated that VGT-309 accumulated in liver and kidney, but less so in the murine oesophagus and stomach. Conclusion Translating qABP’s into the operating room has the potential to detect early cancers in Barrett’s metaplasia, reduce positive margin rates and identify lymph node metastasis. Our research group continues to investigate qABP’s, including determining their sensitivity to detect lymph node metastasis with the aim of translating this technology into a phase 1 clinical trial.

Abstract This abstract is being presented as a short talk in the scientific program. A full abstract is printed in the Proffered Abstracts section (PR007) of the Conference Program/Proceedings. Citation Format: Julia V Milne, Ebtihal Mustafa, Kenji Fujihara, Eric Kusnadi, Anna Trigos, Niko Thio, Maree Pechlivanis, Carlos Cabalag, Twishi Gulati, Kaylene Simpson, Cuong Duong, Luc Furic, Wayne Phillips, Nicholas Clemons. Delineating functional drivers of esophageal adenocarcinoma to identify synthetic lethal interactions [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Expanding and Translating Cancer Synthetic Vulnerabilities; 2024 Jun 10-13; Montreal, Quebec, Canada. Philadelphia (PA): AACR; Mol Cancer Ther 2024;23(6 Suppl):Abstract nr A006.

Intracellular phosphoinositide 3-kinase (PI3K) signaling is activated by multiple bone-active receptors. Genetic mutations activating PI3K signaling are associated with clinical syndromes of tissue overgrowth in multiple organs, often including the skeleton. While one formation is increased by removing the PI3K inhibitor (phosphatase and TENsin homolog deleted on chromosome 10 (PTEN)), the effect of direct PI3K activation in the osteoblast lineage has not been reported. We introduced a known gain-of-function mutation in Pik3ca, the gene encoding the p110α catalytic subunit of PI3K, in osteocytes and late osteoblasts using the dentin matrix protein-1 Cre (Dmp1Cre) mouse and assessed the skeletal phenotype. Femur shape was grossly normal, but cortical thickness was significantly greater in both male and female Dmp1Cre.Pik3caH1047R mice, leading to almost doubled bone strength at 12 wk of age. Both sexes had smaller marrow areas from 6 wk of age. Female mice also exhibited greater cross-sectional area, which continued to increase until 24 wk of age, resulting in a further increase in bone strength. Although both male and female mice had increased endocortical mineralizing surface, only female mice had increased periosteal mineralizing surface. The bone formed in the Dmp1Cre.Pik3caH1047R mice showed no increase in intracortical remodeling nor any defect in cortical bone consolidation. In contrast, on both endocortical and periosteal surfaces, there was more lamellar bone formation, including highly organized osteocyte networks extending along the entire surface at a greater thickness than in control mice. In conclusion, direct activation of PI3Kα in cells targeted by Dmp1Cre leads to high cortical bone mass and strength with abundant lamellar cortical bone in female and male mice with no increase in intracortical remodeling. This differs from the effect of PTEN deletion in the same cells, suggesting that activating PI3Kα in osteoblasts and osteocytes may be a more suitable target to promote formation of lamellar bone.

Caspase-2, one of the most evolutionarily conserved members of the caspase family, is an important regulator of the cellular response to oxidative stress. Given that ferroptosis is suppressed by antioxidant defense pathways, such as that involving selenoenzyme glutathione peroxidase 4 (GPX4), we hypothesized that caspase-2 may play a role in regulating ferroptosis. This study provides the first demonstration of an important and unprecedented function of caspase-2 in protecting cancer cells from undergoing ferroptotic cell death. Specifically, we show that depletion of caspase-2 leads to the downregulation of stress response genes including SESN2, HMOX1, SLC7A11, and sensitizes mutant-p53 cancer cells to cell death induced by various ferroptosis-inducing compounds. Importantly, the canonical catalytic activity of caspase-2 is not required for its role and suggests that caspase-2 regulates ferroptosis via non-proteolytic interaction with other proteins. Using an unbiased BioID proteomics screen, we identified novel caspase-2 interacting proteins (including heat shock proteins and co-chaperones) that regulate cellular responses to stress. Finally, we demonstrate that caspase-2 limits chaperone-mediated autophagic degradation of GPX4 to promote the survival of mutant-p53 cancer cells. In conclusion, we document a novel role for caspase-2 as a negative regulator of ferroptosis in cells with mutant p53. Our results provide evidence for a novel function of caspase-2 in cell death regulation and open potential new avenues to exploit ferroptosis in cancer therapy.

<p>PDF file, 1038K, Ad-SPC-Cre initiation of BRafCA; Pik3calat mice leads to malignant lung cancer.</p>

PDF file, 638K, Pathology grading system used to determine progression of lung tumors.

PDF file, 161K, BRAFV600E/PIK3CAH1047R expressing lung tumors are clonally derived.

<p>PDF file, 161K, BRAFV600E/PIK3CAH1047R expressing lung tumors are clonally derived.</p>

Supplementary Fig. 1 from The Ras/Mitogen-Activated Protein Kinase Pathway Inhibitor and Likely Tumor Suppressor Proteins, Sprouty 1 and Sprouty 2 Are Deregulated in Breast Cancer

In heterogeneous head and neck cancer (HNC), subtype-specific treatment regimens are currently missing. An integrated analysis of patient HNC subtypes using single-cell sequencing and proteome profiles reveals an epithelial-mesenchymal transition (EMT) signature within the epithelial cancer-cell population. The EMT signature coincides with PI3K/mTOR inactivation in the mesenchymal subtype. Conversely, the signature is suppressed in epithelial cells of the basal subtype which exhibits hyperactive PI3K/mTOR signalling. We further identify YBX1 phosphorylation, downstream of the PI3K/mTOR pathway, restraining basal-like cancer cell proliferation. In contrast, YBX1 acts as a safeguard against the proliferation-to-invasion switch in mesenchymal-like epithelial cancer cells, and its loss accentuates partial-EMT and in vivo invasion. Interestingly, phospho-YBX1 that is mutually exclusive to partial-EMT, emerges as a prognostic marker for overall patient outcomes. These findings create a unique opportunity to sensitise mesenchymal cancer cells to PI3K/mTOR inhibitors by shifting them towards a basal-like subtype as a promising therapeutic approach against HNC.

Figure S5 shows MYC directly regulates SLC7A11 levels and APR-246 sensitivity.

Supplementary Figure 6: Pik3ca+/HR and Ptenfl/fl prostate cancers acquire CRPC, while Pik3ca+/HR;Ptenfl/fl mutants are resistant to castration. (A) Representative H&E images of Pik3ca+/HR, Ptenfl/fl and Pik3ca+/HR;Ptenfl/fl anterior (AP) and ventral (VP) prostate lobes post-castration (scale bar: 50 um, n = 3). (B) Representative IHC images of Pik3ca+/HR, Ptenfl/fl and Pik3ca+/HR;Ptenfl/fl prostate tissue stained to detect Androgen receptor (AR) 2 weeks post-castration compared to uncastrated, age-matched controls (scale bar: 50 um, n = 3). Mice were castrated when prostate carcinoma was prevalent; Pik3ca+/HR = 400 d old, Ptenfl/fl = 200 d old and Pik3ca+/HR;Ptenfl/fl = 100 d old. Insert displays positive AR nuclei (arrows) in Pik3ca+/HR;Ptenfl/fl compound mutants (scale bar: 5 um). (C) Bar chart displaying total prostate weight normalised to body weight for Pik3ca+/HR mice 0, 2 and 42 weeks post-castration (n = 8, 7 and 7, respectively). Error bars: SEM, *P <0.05 compared to 0 weeks post-castration, or as indicated, one-way ANOVA with Tukey's multiple comparison test. (D) Representative H&E images of Pik3ca+/HR mice 0, 2 and 42 weeks post-castration (scale bar: 100 um). Mice were castrated at 100 d of age.

PDF file - 578K, Characterization of a new, syngeneic, orthotopic mouse model of PDA