Chromosomal instability (CIN) and epigenetic reprogramming are central drivers of breast cancer progression, yet the mechanisms connecting them remain elusive. Here, we uncover a direct role for EZH2 histone methyltransferase in promoting CIN in triple-negative breast cancer. Across breast cancers, EZH2 expression correlates with copy-number alterations, and its catalytic activity is associated with increased CIN in metastasis-initiating cells. Pharmacologic EZH2 inhibition suppresses CIN, revealing an unexpected vulnerability. Integrated chromatin and transcriptome profiling identified tankyrase (TNKS), a PARP, as a direct transcriptional target of EZH2. Mechanistically, EZH2-mediated TNKS suppression disrupts centrosomal P4.1-associated protein (CPAP), driving centrosome overduplication, multipolar mitosis, and exacerbated CIN. In vivo, CIN suppression is a critical mechanism underlying the antimetastatic effects of EZH2 inhibition. These findings delineate a previously unrecognized epigenetic mechanism governing CIN and establish EZH2 inhibitors as the first therapeutic agents capable of directly suppressing CIN, underscoring the need for trials with metastasis-focused endpoints. SIGNIFICANCE:We elucidate epigenetic regulation of CIN through EZH2-TNKS-CPAP-axis and show that CIN suppression is important for the efficacy of EZH2 inhibition on metastasis. These mechanistic insights are informative for developing CIN-suppressing therapies.

Abstract Perturbation of cell polarity is a hallmark of pancreatic ductal adenocarcinoma (PDAC) progression. Scribble (SCRIB) is a well-characterized polarity regulator that has diverse roles in the pathogenesis of human neoplasms. To investigate the impact of SCRIB deficiency in PDAC development and progression, Scrib expression was genetically ablated in well-established mouse models of PDAC. Scrib loss in combination with KrasG12D did not influence development of pancreatic intraepithelial neoplasms in mice. However, Scrib deletion cooperated with KrasG12D and concomitant Trp53 heterozygous deletion to promote invasive PDAC and metastatic dissemination, leading to reduced overall survival. Immunohistochemical and transcriptome analyses revealed that Scrib-null tumors display a pronounced reduction of collagen content and an abundance of cancer-associated fibroblasts (CAF). Mechanistically, IL1α levels were reduced in Scrib-deficient tumors, and Scrib knockdown downregulated IL1α in mouse PDAC organoids (mPDO), which impaired CAF activation. Furthermore, Scrib loss increased YAP activation in mPDOs and established PDAC cell lines, enhancing cell survival. Clinically, SCRIB expression was decreased in human PDAC, and SCRIB mislocalization was associated with poorer patient outcome. These results indicate that SCRIB deficiency enhances cancer cell survival and remodels the tumor microenvironment to accelerate PDAC development and progression, establishing the tumor suppressor function of SCRIB in advanced pancreatic cancer. Significance: SCRIB loss promotes invasive pancreatic cancer development via both cell-autonomous and non–cell-autonomous processes and is associated with poorer outcomes, denoting SCRIB as a tumor suppressor and potential biomarker for the prediction of recurrence.

KRAS is mutationally activated in 45-50% of colorectal cancer (CRC) cases, and while KRAS-targeted therapies have shown some clinical promise, upfront and acquired resistance limit their efficacy. To explore the acute response and mechanisms underlying KRAS inhibitor resistance, we used targeted exome sequencing and single-cell spatial transcriptomics to analyze patient-matched pre-treatment, on-treatment, and progression biopsies from patients treated with combined KRASG12C and EGFR inhibition. Acquired genetic events were identified in most patients at progression but were often subclonal and coexisted with transcriptional adaptive states. Mesenchymal, YAP, and fetal-like transcriptional signatures predominated in resistant tumors, while tumor cell-intrinsic inflammatory programs were induced in the early treatment phase. Single-cell spatial analysis revealed significant intratumoral heterogeneity, with diverse adaptive states predominating in different zones of individual tumors. Using human and murine organoid models, we show that these drug-induced inflammatory programs are cancer-cell autonomous and precede the emergence of regenerative fetal-like programs associated with drug resistance. We uncover TBK1 as a promising target to abrogate the early inflammatory adaptive phase and enhance responses to KRAS inhibition.

Inflammation in the pancreas drives acinar-to-ductal metaplasia (ADM), a progenitor-like state that can be hijacked by mutant Kras in the formation of pancreatic ductal adenocarcinoma. How these cell fate decisions vary according to KRAS mutation remains poorly understood. To define mutation-specific lineage reversion and tumor initiation, we implement Ptf1a-tdTomato mice and multiple KRAS mutants across several genetic, pharmacologic, and inflammatory perturbations in vivo. Whereas KRASG12D co-opts injury to enable lineage reversion, enhancer reprogramming, and tumor initiation, KRASG12R/V cannot sustain dedifferentiated and neoplastic transcriptional and epigenetic programs. Specifically, KRASG12R/V mutants fail to invoke robust EGFR, AKT, and RAC1/VAV1 signaling and to license Pou2f3 and Vav1 in chromatin, such that only constitutive AKT activation is sufficient to rescue the tumorigenic potential of KRASG12Rin vivo. As the marked heterogeneity among KRAS variants begins early in tumorigenesis, these data are crucial to deciphering mutation-specific oncogenic trajectories and directing the implementation of KRAS-directed therapeutics.

KRAS mutations are among the most prevalent oncogenic drivers in non-small cell lung cancer (NSCLC), yet the mechanisms of therapeutic resistance to KRAS inhibitors in these cancers remains poorly understood. Here, we deploy high-throughput CRISPR base editing screens to systematically map resistance mutations to three mechanistically distinct KRAS-targeted therapies, including KRAS-G12C(OFF) inhibitor (adagrasib), RAS(ON) G12C-selective tri-complex inhibitor (RMC-4998), and RAS(ON) multi-selective tri-complex inhibitor (RMC-7977). Using both a saturation Kras tiling approach and cancer-associated mutation library, we identify common and compound-selective second-site resistance mutations in Kras, as well as gain-of-function and loss-of-function variants across cancer-associated genes that rewire signaling networks in a context-dependent manner. Notably, we identify a recurrent missense mutation in capicua (Cic), that promotes resistance to RMC-7977 in vitro and in vivo. Moreover, we show that targeting NFκB signaling in CIC-mutant cells can resensitize them to RAS pathway inhibition and overcome resistance.

Pancreatic ductal adenocarcinoma (PDAC) is a highly aggressive malignancy with abysmal survival rates. The highly immunosuppressive microenvironment of PDAC poses a major barrier to effective therapy. KRAS mutations are near-ubiquitous in PDAC, and studies indicate clinical outcomes vary depending on the specific KRAS genotype. Given that tumor genotype can shape the immune cell composition of tumors, we examined the immune cell composition of pancreatic tumors with specific KRAS mutations, focusing on KRASG12D mutations (representing 40% of PDAC cases which have the worst prognosis) and KRASG12R mutations (which make up 20% of PDAC cases and have a better prognosis). Orthotopically implanted KrasG12R/+;Trp53KO mouse pancreatic tumors have a distinct immune profile in comparison to KrasG12D/+;Trp53KO tumors, characterized by an influx of intratumoral CD3+ T cells and mature dendritic cells. Selective depletion of CD4+ T cells induces a rapid progression in KRASG12R, but not KRASG12D mouse tumors. RNA sequencing of KRASG12R tumor cells revealed enrichment of Type I interferon (IFN) pathways accompanied by related chemokines, CXCL9 and CXCL10 in comparison to KRASG12D tumors. Analysis of publicly available and real-world human PDAC datasets an enrichment of dendritic cells and other immune related cell pathways in KRASG12R tumors. Collectively, these data link the KRASG12R mutation to an unique immunogenic role. Andrew Wenger, Katherine Bacchi, Huanhuan Sun, Adrian Vega, Whitney Sisso, Erika Hissong, Lukas Dow, Despina Siolas. Divergent immune responses in pancreatic cancer driven by KRAS mutations [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 3966.

RNA interference (RNAi) is emerging as a powerful strategy for therapeutic targeting of "undruggable" targets. However, efficacy of currently used siRNA-based therapies is often hindered by transient effects and limited modeling possibilities. Artificial microRNAs (amiRNAs or miRNA scaffolds) present a durable and precise approach to gene silencing, opening new avenues for developing long lasting targeted therapies. In this study, we engineered highly expressed primary miRNAs (pri-miRNAs) with sequence determinants known to enhance processing efficacy and precision. The resulting amiRNAs were extensively tested both in vitro and in vivo and proved to efficiently silence a target gene when virally delivered via adeno-associated virus (AAV) into mice brains. This study provides a set of novel amiRNAs with potential therapeutic application as well as a pipeline to generate and validate novel amiRNAs from endogenous pri-miRNAs.

Pancreatic ductal adenocarcinoma (PDAC) is one of the most lethal malignancies, with limited effective treatment options. While activating mutations in KRAS occur in over 90% of PDAC cases, emerging evidence suggests that distinct KRAS alleles confer distinct biological and clinical phenotypes. Notably, patients with the KRASG12R mutation, present in 18% of PDAC cases, have exhibit significantly improved survival compared to those with the more common KRASG12D mutation, found in 40% of cases. To futher explore this clinical observation, we analyzed human RNA sequencing data from the “Know Your Tumor” program and identified an enrichment of immune-related pathways in KRASG12R tumors compared to KRASG12D tumors. We then developed an orthotopic transplantation mouse model using genetically engineered pancreatic organoids expressing either KRASG12R or KRASG12D mutations to investigate underlying immune related mechanisms. Orthotopically implanted Kras G12R/+ ;Trp53 KO mouse pancreatic tumors in syngeneic C57/Bl6 mice have a distinct immune profile in comparison to Kras G12D/+ ;Trp53 KO tumors, characterized by an influx of intratumoral CD3+ T cells and mature dendritic cells. These findings were also seen in human PDAC samples from the Clinical Proteomic Tumor Analysis Consortium (CPTAC) and in patient resection specimens, which demonstrated enrichment of dendritic cell subtypes in KRASG12R tumors compared to KRASG12D mutant tumors. Functional studies using preclinical models revealed KRASG12R tumor growth was T cell-dependent, whereas KRASG12D tumors were unaffected by loss of T cells. Collectively, these data link the KRASG12R mutation to an unique immunogenic role, that may be susceptible to immune-based therapies. Huanhuan Sun, Katherine Bacchi, Andrew Wenger, Adrian Vega, Whitney Sisso, Kawther Abdilleh, Maria Paz. Zafra, Rohit Chandwani, Lukas Dow, Despina Siolas. KRAS Mutation-Specific Immune Microenvironments in Pancreatic Cancer [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Advances in Pancreatic Cancer Research—Emerging Science Driving Transformative Solutions; Boston, MA; 2025 Sep 28-Oct 1; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2025;85(18_Suppl_3):Abstract nr A091.

Precision medicine approaches to cancer treatment aim to exploit genomic alterations that are specific to individual patients to tailor therapeutic strategies. Yet, some targetable genes and pathways are essential for tumor cell viability even in the absence of direct genomic alterations. In underrepresented populations, the mutational landscape and determinants of response to existing therapies are poorly characterized because of limited inclusion in clinical trials and studies. One way to reveal tumor essential genes is with genetic screens. Most screens are conducted on cell lines that bear little resemblance to patient tumors, after years of culture under nonphysiologic conditions. To address this problem, we aimed to develop a CRISPR screening pipeline in three-dimensionally grown patient-derived tumor organoid (PDTO) models. A breast cancer PDTO biobank that focused on underrepresented populations, including West African patients, was established and used to conduct a negative-selection kinome-focused CRISPR screen to identify kinases essential for organoid growth and potential targets for combination therapy with EGFR or MEK inhibitors. The screen identified several previously unidentified kinase targets, and the combination of FGFR1 and EGFR inhibitors synergized to block organoid proliferation. Together, these data demonstrate the feasibility of CRISPR-based genetic screens in patient-derived tumor models, including PDTOs from underrepresented patients with cancer, and identify targets for cancer therapy.Significance: Generation of a breast cancer patient-derived tumor organoid biobank focused on underrepresented populations enabled kinome-focused CRISPR screening that identified essential kinases and potential targets for combination therapy with EGFR or MEK inhibitors.See related commentary by Trembath and Spanheimer, p. 407

Statement of Significance:We showed that loss of the orphan G protein-coupled receptor GPR52 in human breast cell lines leads to increased cell clustering, hybrid/partial EMT, and increased tumor burden in zebrafish. Background:G protein-coupled receptors (GPCRs) are the largest class of membrane-bound receptors that transmit critical signals from extracellular to intracellular spaces. Transcriptomic data of resected breast tumors show that low mRNA expression of orphan GPCR GPR52 correlates with reduced overall survival in patients with breast cancer, leading to the hypothesis that loss of GPR52 supports breast cancer progression. Methods:CRISPR-Cas9 was used to knockout GPR52 in the human triple-negative breast cancer (TNBC) cell lines MDA-MB-468 and MDA-MB-231, and in the non-cancerous breast epithelial cell line MCF10A. 2D and 3D in vitro studies, electron microscopy, Matrigel culture, and a zebrafish xenograft model were used to assess the morphology and behavior of GPR52 KO cells. RNA-sequencing and proteomic analyses were also conducted on these cell lines, and transcriptomic data from The Cancer Genome Atlas (TCGA) database were used to compare GPR52-null and wild-type (WT) signatures in breast cancer. Results:Loss of GPR52 was found to be associated with increased cell-cell interaction in 2D cultures, altered 3D spheroid morphology, and increased propensity to organize and invade collectively in Matrigel. Furthermore, GPR52 loss was associated with features of EMT in MDA-MB-468 cells, and zebrafish injected with GPR52 KO cells developed a greater total cancer area than those injected with control cells. RNA sequencing and proteomic analyses of GPR52-null breast cancer cells revealed an increased cAMP signaling signature. Consistently, we found that treatment of wild-type (WT) cells with forskolin, which stimulates the production of cAMP, induces phenotypic changes associated with GPR52 loss, and inhibition of cAMP production rescued some GPR52 KO phenotypes. Conclusion:GPR52 is an orphan GPCR and its role in cancer progression has not been previously characterized. We found that GPR52 loss in breast cancer cells can lead to increased cell clustering, collective invasion, and EMT in vitro . These are features of increased cancer aggression. Our results reveal that GPR52 loss is a potential mechanism by which breast cancer progression may occur and support the investigation of GPR52 agonism as a therapeutic option for breast cancer. Abstract Figure:

Understanding patient-specific responses to anticancer therapies and how individual tumors interact with their tumor microenvironment (TME) is a challenging task. To measure the impact of the TME on diverse and clinically relevant treatments, Ramos Zapatero and colleagues coupled patient-derived organoid (PDO) and cancer-associated fibroblast (CAF) cocultures with high-throughput mass cytometry-based assessment of cell state. Using a newly developed "Trellis" algorithm enabled integration and analysis of highly complex, multidimensional treatment response data. This work showed that tumor cell response to chemotherapy was associated with both intrinsic and nonintrinsic signaling states, whereby proliferative rate, growth factor signaling, and CAFs interaction influenced chemoprotection. Furthermore, the work suggests a potential role for the TME in promoting lineage plasticity associated with drug resistance. In all, the pipeline described provides a blueprint for exploring the intricate interplay of factors influencing cancer treatment response.

Perturbation of cell polarity is a hallmark of pancreatic ductal adenocarcinoma (PDAC) progression. Scribble (SCRIB) is a well-characterized polarity regulator that has diverse roles in the pathogenesis of human neoplasms. To investigate the impact of SCRIB deficiency in PDAC development and progression, Scrib expression was genetically ablated in well-established mouse models of PDAC. Scrib loss in combination with KrasG12D did not influence development of pancreatic intraepithelial neoplasms in mice. However, Scrib deletion cooperated with KrasG12D and concomitant Trp53 heterozygous deletion to promote invasive PDAC and metastatic dissemination, leading to reduced overall survival. Immunohistochemical and transcriptome analyses revealed that Scrib-null tumors display a pronounced reduction of collagen content and an abundance of cancer-associated fibroblasts (CAF). Mechanistically, IL1α levels were reduced in Scrib-deficient tumors, and Scrib knockdown downregulated IL1α in mouse PDAC organoids (mPDO), which impaired CAF activation. Furthermore, Scrib loss increased YAP activation in mPDOs and established PDAC cell lines, enhancing cell survival. Clinically, SCRIB expression was decreased in human PDAC, and SCRIB mislocalization was associated with poorer patient outcome. These results indicate that SCRIB deficiency enhances cancer cell survival and remodels the tumor microenvironment to accelerate PDAC development and progression, establishing the tumor suppressor function of SCRIB in advanced pancreatic cancer.  Significance: SCRIB loss promotes invasive pancreatic cancer development via both cell-autonomous and non-cell-autonomous processes and is associated with poorer outcomes, denoting SCRIB as a tumor suppressor and potential biomarker for the prediction of recurrence.

Selenocysteine-containing proteins play a central role in redox homeostasis. Their translation is a highly regulated process dependent on two tRNA Sec isodecoders differing by a single 2’-O-ribose methylation, called Um34. We characterized FTSJ1 as the Um34 methyltransferase and show that its activity is required for efficient selenocysteine insertion at the UGA stop codon during translation. Specifically, Loss of Um34 leads to ribosomal stalling and decreased UGA recoding. FTSJ1-deficient cells are more sensitive to oxidative stress and have decreased metastatic colonization in xenograft models of melanoma metastasis. Our findings uncover a role for tRNA Sec Um34 modification in oxidative stress resistance and highlight FTSJ1 as a potential therapeutic target specific for metastatic disease.

Abstract The immune microenvironment plays a critical role in cancer development, progression and resistance to therapy. KRAS mutations are near-ubiquitous in pancreatic ductal adenocarcinoma (PDAC) and several studies have demonstrated that KRASG12D can create an immunosuppressive tumor microenvironment. However, the immune effects of other oncogenic KRAS variants, such as KRASG12R (representing 20% of PDAC cases) are unknown. Given that specific KRAS mutants display distinct molecular phenotypes, we examined the immune cell composition of KRASG12R pancreatic tumors. Orthotopically implanted mouse tumors derived from KrasG12R/+;Trp53KO pancreatic organoids have a distinct immune profile in comparison to KrasG12D/+;Trp53KO tumors, characterized by an influx of intratumoral CD4+ T cells and mature dendritic cells. RNA sequencing of KRASG12R tumor cells revealed enrichment of Type I interferon (IFN) pathways accompanied by related chemokines, CXCL9 and CXCL10 in comparison to KRASG12D tumors. Analysis of publicly available human PDAC cohorts revealed enrichment of genes in inflammatory pathways in KRASG12R tumors. Collectively, these data link KRASG12R to a unique immune landscape that is distinct from KRASG12D tumors. Citation Format: Andrew wenger, Tal Baron, Erika Hissong, Adrian Vega-Perez, Whitney Sisso, Maria Paz Zafra, Rohit Chandwani, Lukas Dow, Despina Siolas. KRAS Mutation-Specific effects on the Tumor Immune Microenvironment Drive Tumor Progression [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Advances in Pancreatic Cancer Research; 2024 Sep 15-18; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2024;84(17 Suppl_2):Abstract nr A034.

Cancers arise through acquisition of mutations in genes that regulate core biological processes like cell proliferation and cell death. Decades of cancer research have led to the identification of genes and mutations causally involved in disease development and evolution, yet defining their precise function across different cancer types and how they influence therapy responses has been challenging. Mouse models have helped define the in vivo function of cancer-associated alterations, and genome-editing approaches using CRISPR have dramatically accelerated the pace at which these models are developed and studied. Here, we highlight how CRISPR technologies have impacted the development and use of mouse models for cancer research and discuss the many ways in which these rapidly evolving platforms will continue to transform our understanding of this disease.

Abstract Background: Breast cancer is the most diagnosed cancer worldwide and is the second leading cause of cancer death among women in the United States. Despite breakthroughs in targeted therapies for breast cancer, the 5-year survival rate for women with metastatic breast cancer is 30%. There is a strong rationale to explore the therapeutic potential of G-protein coupled receptors (GPCRs), which comprise the largest class of proteins successfully targeted by FDA-approved drugs. Importantly, at least one-third of GPCRs are “orphans” and remain largely uncharacterized. One of these orphan GPCRs is GPR52. To date, there is no literature on the role of GPR52 in any cancer type, but we find from publicly available clinical data that low mRNA expression of GPR52 in breast tumors correlates with reduced overall survival (hazard ratio=0.67 [0.53-0.83], logrank P= 0.00035) and that GPR52 mRNA levels tend to be lower in tumor metastases compared to primary tumor (n>80, p=4.45e-17). Therefore, we hypothesize that loss of GPR52 may support breast cancer metastasis. Results: We used CRISPR-Cas9 to knockout (KO) GPR52 in triple-negative breast cancer cell lines MDA-MB-468 and MDA-MB-231, and in the non-cancerous breast epithelial cell line MCF10A, and confirmed the generation of frameshift mutations by Sanger sequencing. Interestingly, we observed that GPR52 KO cells clustered together in vitro in 2D and hypothesized that this characteristic may allow GPR52 KO breast cancer cells to increase their metastatic potential. We conducted invasion assays though Matrigel and found that GPR52 KO cells were more likely to invade as sheets or clusters. To determine the in vivo impact of GPR52 loss, we injected MDA-MB-468 GPR52 KO cells in zebrafish (Danio rerio) two days post-fertilization and observed that GPR52 loss led to increased metastatic foci and total cancer surface area thirty hours post-injection (n≥12, p<0.05). We determined from RNA-sequencing (n=3, p<.0001) and confirmed with western blotting that the melanoma cell adhesion molecule (MCAM) is upregulated in the MCF10A and MDA-MB-468 GPR52 KO cells. Increased mRNA expression of MCAM has been associated with reduced overall survival in breast cancer patients (hazard ratio=1.33 [1.05-1.62], logrank P= 0.02) Conclusion: Knockout of GPR52 from breast cancer cells promotes increased cell clustering in vitro and metastasis in zebrafish. These data support the investigation of GPR52 as a biomarker of cancer aggression and a potential therapeutic target for breast cancer patients whose tumors express GPR52. Citation Format: Sarah Z. Hanif, CheukMan C. Au, Ingrid Torregroza, Bhavneet Bhinder, Lukas Dow, Olivier Elemento, Todd Evans, Kristy A. Brown. The GPR52-MCAM axis as a novel regulatory mechanism of breast cancer cell clustering and metastatic potential [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 197.