Early Tumorigenesis Research Articles

Genome Engineering of Primary and Pluripotent Stem Cell-Derived Hepatocytes for Modeling Liver Tumor Formation.

Genome editing has demonstrated its utility in generating isogenic cell-based disease models, enabling the precise introduction of genetic alterations into wild-type cells to mimic disease phenotypes and explore underlying mechanisms. However, its application in liver-related diseases has been limited by challenges in genetic modification of mature hepatocytes in a dish. Here, we conducted a systematic comparison of various methods for primary hepatocyte culture and gene delivery to achieve robust genome editing of hepatocytes ex vivo. Our efforts yielded editing efficiencies of up to 80% in primary murine hepatocytes cultured in monolayer and 20% in organoids. To model human hepatic tumorigenesis, we utilized hepatocytes differentiated from human pluripotent stem cells (hPSCs) as an alternative human hepatocyte source. We developed a series of cellular models by introducing various single or combined oncogenic alterations into hPSC-derived hepatocytes. Our findings demonstrated that distinct mutational patterns led to phenotypic variances, affecting both overgrowth and transcriptional profiles. Notably, we discovered that the PI3KCA E542K mutant, whether alone or in combination with exogenous c-MYC, significantly impaired hepatocyte functions and facilitated cancer metabolic reprogramming, highlighting the critical roles of these frequently mutated genes in driving liver neoplasia. In conclusion, our study demonstrates genome-engineered hepatocytes as valuable cellular models of hepatocarcinoma, providing insights into early tumorigenesis mechanisms.

Tumor editing suppresses innate and adaptive antitumor immunity and is reversed by inhibiting DNA methylation.

Cancer cells edit gene expression to evade immunosurveillance. However, genome-wide studies of gene editing during early tumorigenesis are lacking. Here we used single-cell RNA sequencing in a breast cancer genetically engineered mouse model (GEMM) to identify edited genes without bias. Late tumors repressed antitumor immunity genes, reducing infiltrating immune cells and tumor-immune cell communications. Innate immune genes, especially interferon-stimulated genes, dominated the list of downregulated tumor genes, while genes that regulate cell-intrinsic malignancy were mostly unedited. Naive and activated CD8+ T cells in early tumors were replaced with exhausted or precursor-exhausted cells in late tumors. Repression of immune genes was reversed by inhibiting DNA methylation using low-dose decitabine, which suppressed tumor growth and restored immune control, increasing the number, functionality and memory of tumor-infiltrating lymphocytes and reducing the number of myeloid suppressor cells. Decitabine induced important interferon, pyroptosis and necroptosis genes, inflammatory cell death and immune control in GEMM and implanted breast and melanoma tumors.

Titration of RAS alters senescent state and influences tumour initiation

Oncogenic RAS-induced senescence (OIS) is an autonomous tumour suppressor mechanism associated with premalignancy1,2. Achieving this phenotype typically requires a high level of oncogenic stress, yet the phenotype provoked by lower oncogenic dosage remains unclear. Here we develop oncogenic RAS dose-escalation models in vitro and in vivo, revealing a RAS dose-driven non-linear continuum of downstream phenotypes. In a hepatocyte OIS model in vivo, ectopic expression of NRAS(G12V) does not induce tumours, in part owing to OIS-driven immune clearance3. Single-cell RNA sequencing analyses reveal distinct hepatocyte clusters with typical OIS or progenitor-like features, corresponding to high and intermediate levels of NRAS(G12V), respectively. When titred down, NRAS(G12V)-expressing hepatocytes become immune resistant and develop tumours. Time-series monitoring at single-cell resolution identifies two distinct tumour types: early-onset aggressive undifferentiated and late-onset differentiated hepatocellular carcinoma. The molecular signature of each mouse tumour type is associated with different progenitor features and enriched in distinct human hepatocellular carcinoma subclasses. Our results define the oncogenic dosage-driven OIS spectrum, reconciling the senescence and tumour initiation phenotypes in early tumorigenesis.

Single-nucleus and spatial transcriptome reveal adrenal homeostasis in normal and tumoural adrenal glands.

The human adrenal gland is a complex endocrine tissue. Studies on adrenal renewal have been limited to animal models or human foetuses. Enhancing our understanding of adult human adrenal homeostasis is crucial for gaining insights into the pathogenesis of adrenal diseases, such as adrenocortical tumours. Here, we present a comprehensive cellular genomics analysis of the adult human normal adrenal gland, combining single-nuclei RNA sequencing and spatial transcriptome data to reconstruct adrenal gland homeostasis. As expected, we identified primary cells of the various zones of the adrenal cortex and medulla, but we also uncovered additional cell types. They constitute the adrenal microenvironment, including immune cells, mostly composed of a large population of M2 macrophages, and new cell populations, including different subpopulations of vascular-endothelial cells and cortical-neuroendocrine cells. Utilizing spatial transcriptome and pseudotime trajectory analysis, we support evidence of the centripetal dynamics of adrenocortical cell maintenance and the essential role played by Wnt/β-catenin, sonic hedgehog, and fibroblast growth factor pathways in the adult adrenocortical homeostasis. Furthermore, we compared single-nuclei transcriptional profiles obtained from six healthy adrenal glands and twelve adrenocortical adenomas. This analysis unveiled a notable heterogeneity in cell populations within the adenoma samples. In addition, we identified six distinct adenoma-specific clusters, each with varying distributions based on steroid profiles and tumour mutational status. Overall, our results provide novel insights into adrenal homeostasis and molecular mechanisms potentially underlying early adrenocortical tumorigenesis and/or autonomous steroid secretion. Our cell atlas represents a powerful resource to investigate other adrenal-related pathologies.

Endothelial RUNX3 controls LSEC dysfunction and angiocrine LRG1 signaling to prevent liver fibrosis.

Liver fibrosis represents a global health burden, given the paucity of approved antifibrotic therapies. Liver sinusoidal endothelial cells (LSECs) play a major gatekeeping role in hepatic homeostasis and liver disease pathophysiology. In early tumorigenesis, runt-related transcription factor 3 (RUNX3) functions as a sentinel; however, its function in liver fibrosis in LSECs remains unclear. This study aimed to investigate the role of RUNX3 as an important regulator of the gatekeeping functions of LSECs and explore novel angiocrine regulators of liver fibrosis. Mice with endothelial Runx3 deficiency develop gradual and spontaneous liver fibrosis secondary to LSEC dysfunction, thereby more prone to liver injury. Mechanistic studies in human immortalized LSECs and mouse primary LSECs revealed that IL-6/JAK/STAT-3 pathway activation was associated with LSEC dysfunction in the absence of RUNX3. Single-cell RNA sequencing and quantitative RT-PCR revealed that leucine-rich alpha-2-glycoprotein 1 (LRG1) was highly expressed in RUNX3-deficient and dysfunctional LSECs. In in vitro and coculture experiments, RUNX3-depleted LSECs secreted LRG1, which activated hepatic stellate cells via TGFBR1-SMAD2/3 signaling in a paracrine manner. Furthermore, circulating LRG1 levels were elevated in mouse models of liver fibrosis and in patients with fatty liver and cirrhosis. RUNX3 deficiency in the endothelium induces LSEC dysfunction, LRG1 secretion, and liver fibrosis progression. Therefore, endothelial RUNX3 is a crucial gatekeeping factor in LSECs, and profibrotic angiocrine LRG1 may be a novel target for combating liver fibrosis.

Tumor Promoters and Opportunities for Molecular Cancer Prevention.

Environmental carcinogens increase cancer incidence via both mutagenic and non-mutagenic mechanisms. There are over 500 known or suspected carcinogens classified by the International Agency for Research on Cancer. Sequencing of both cancerous and histologically non-cancerous tissue has been instrumental in improving our understanding of how environmental carcinogens cause cancer. Understanding how and defining which environmental or lifestyle exposures drive cancer will support cancer prevention. Recent research is revisiting the mechanisms of early tumorigenesis, paving the way for an era of molecular cancer prevention. Significance: Recent data have improved our understanding of how carcinogens cause cancer, which may reveal novel opportunities for molecular cancer prevention.

Cholesterol Dietary Intake and Tumor Cell Homeostasis Drive Early Epithelial Tumorigenesis: A Potential Modelization of Early Prostate Tumorigenesis.

Epidemiological studies point to cholesterol as a possible key factor for both prostate cancer incidence and progression. It could represent a targetable metabolite as the most aggressive tumors also appear to be sensitive to therapies designed to decrease hypercholesterolemia, such as statins. However, it remains unknown whether and how cholesterol, through its dietary uptake and its metabolism, could be important for early tumorigenesis. Oncogene clonal induction in the Drosophila melanogaster accessory gland allows us to reproduce tumorigenesis from initiation to early progression, where tumor cells undergo basal extrusion to form extra-epithelial tumors. Here we show that these tumors accumulate lipids, and especially esterified cholesterol, as in human late carcinogenesis. Interestingly, a high-cholesterol diet has a limited effect on accessory gland tumorigenesis. On the contrary, cell-specific downregulation of cholesterol uptake, intracellular transport, or metabolic response impairs the formation of such tumors. Furthermore, in this context, a high-cholesterol diet suppresses this impairment. Interestingly, expression data from primary prostate cancer tissues indicate an early signature of redirection from cholesterol de novo synthesis to uptake. Taken together, these results reveal that during early tumorigenesis, tumor cells strongly increase their uptake and use of dietary cholesterol to specifically promote the step of basal extrusion. Hence, these results suggest the mechanism by which a reduction in dietary cholesterol could lower the risk and slow down the progression of prostate cancer.

Role of NEDD9 expression in non-metastatic HER2-positive breast cancer.

e12645 Background: Neural Precursor Cell Expressed Developmentally Downregulated Protein 9 (NEDD9) is a member of the associated substrate family. Our previous studies demonstrated the role of NEDD9 overexpression in early tumorigenesis in HER2-positive (HER2+) breast cancer in vivo. Tissue microarray-based analysis showed a strong correlation between NEDD9 mRNA and relapse-free survival (RFS) and pathologic complete response (pCR) rate in HER2+ breast cancers. In this study, NEDD9 expression in non-metastatic HER2+ breast cancer was evaluated by tissue microarray. Methods: A total of 64 patients with non-metastatic HER2+ cancer of the breast who had received neoadjuvant chemotherapy and had sufficient pathology specimens were included in the study. NEDD9 was stained by tissue microarray, and the expression was subclassified as low, intermediate, and high based on the NEDD9 expression score. The correlations of NEDD9 expression with the clinical/biological characteristics, treatment, and treatment response were analyzed by Fisher Exact test. Results: A total of 64 patients were included in the study, with a medium follow-up duration of 4.6 years. The median age was 54, 1 patient was male, 79.3% of patients had stage 2 disease, 1 patient had inflammatory breast cancer, and 37.5% of patients had ER/PR negative disease. The most common neoadjuvant chemotherapy regimen was TCHP (82.5%), 44.4% of patients underwent lumpectomy, and 67.7% of patients underwent axillary lymph node dissection (ALND). 54% of patients achieved complete pathologic response (pCR), all patients received adjuvant anti-HER2 treatment, 85.7% received adjuvant radiotherapy, and 74.6% received adjuvant endocrine therapy. The NEDD9 expression distribution for low, intermediate, and high were 37.5%, 50.0%, and 12.5%, respectively. NEDD9-high patients had higher tumor stage and grade than NEDD9-low/ intermediate patients (p = 0.004, p= 0.041). More NEDD9-high patients underwent ALND compared to NEDD9- low/intermediate patients (p = 0.09). There is no statistically significant difference in pCR rate between NEDD9 expression groups, although numerically more NEDD9-high patients achieved pCR (75%, 56.2%, and 43.5% in NEDD9-high, intermediate, and low patients). Conclusions: In non-metastatic HER2+ breast cancer, NEDD9 expression is associated with more advanced tumor grade and stage. There is no statistically significant difference in pCR rate between groups, although more patients achieved pCR with a higher level of NEDD9 expression. The sample size limits our study. Additional study is needed to evaluate the correlation between NEDD9 expression and pCR rate following neoadjuvant chemotherapy in HER2+ breast cancer.

Genomic landscape and tumor mutational features of resected preinvasive to invasive lung adenocarcinoma.

Adenocarcinoma in situ (AIS) and minimally invasive adenocarcinoma (MIA) are considered pre-invasive forms of lung adenocarcinoma (LUAD) with a 5-year recurrence-free survival of 100%. We investigated genomic profiles in early tumorigenesis and distinguished mutational features of preinvasive to invasive adenocarcinoma (IAC) for early diagnosis. Molecular information was obtained from a 689-gene panel in the 90 early-stage LUAD Chinese patients using next-generation sequencing. Gene signatures were identified between pathology subtypes, including AIS/MIA (n=31) and IAC (n=59) in this cohort. Mutational and clinicopathological information was also obtained from the Cancer Genome Atlas (TCGA) as a comparison cohort. A higher mutation frequency of TP53, RBM10, MUC1, CSMD, MED1, LRP1B, GLI1, MAP3K, and RYR2 was observed in the IAC than in the AIS/MIA group. The AIS/MIA group showed higher mutation frequencies of ERBB2, BRAF, GRIN2A, and RB1. Comparable mutation rates for mutually exclusive genes (EGFR and KRAS) across cohorts highlight the critical transition to invasive LUAD. Compared with the TCGA cohort, EGFR, KRAS, TP53, and RBM10 were frequently mutated in both cohorts. Despite limited gene mutation overlap between cohorts, we observed variant mutation types in invasive LUAD. Additionally, the tumor mutation burden (TMB) values were significantly lower in the AIS/MIA group than in the IAC group in both the Chinese cohort (P=0.0053) and TCGA cohort (P<0.01). These findings highlight the importance of distinguishing preinvasive from invasive LUAD in the early stages of LUAD and both pathology and molecular features in clinical practice, revealing genomic tumor heterogeneity and population differences.

Examination of the role of mutualism in immune evasion.

Though the earliest stages of oncogenesis, post initiation, are not well understood, it is generally appreciated that a successful transition from a collection of dysregulated cells to an aggressive tumour requires complex ecological interactions between cancer cells and their environment. One key component of tumorigenesis is immune evasion. To investigate the interplay amongst the ecological behaviour of mutualism and immune evasion, we used a computational simulation framework. Sensitivity analyses of the growth of a virtual tumour implemented as a 2D-hexagonal lattice model suggests tumour survival depends on the interplay between growth rates, mutualism and immune evasion. In 60% of simulations, cancer clones with low growth rates, but exhibiting mutualism were able to evade the immune system and continue progressing suggesting that tumours with equivalent growth rates and no mutualism are more likely to be eliminated than tumours with mutualism. Tumours with faster growth rates showed a lower dependence upon mutualism for progression. Geostatistical analysis showed decreased spatial heterogeneity over time for polyclonal tumours with a high division rate. Overall, these results suggest that in slow growing tumours, mutualism is critical for early tumorigenesis.

SRRM2 splicing factor modulates cell fate in early development.

Embryo development is an orchestrated process that relies on tight regulation of gene expression to guide cell differentiation and fate decisions. The Srrm2 splicing factor has recently been implicated in developmental disorders and diseases, but its role in early mammalian development remains unexplored. Here, we show that Srrm2 dosage is critical for maintaining embryonic stem cell pluripotency and cell identity. Srrm2 heterozygosity promotes loss of stemness, characterised by the coexistence of cells expressing naive and formative pluripotency markers, together with extensive changes in gene expression, including genes regulated by serum-response transcription factor (SRF) and differentiation-related genes. Depletion of Srrm2 by RNA interference in embryonic stem cells shows that the earliest effects of Srrm2 heterozygosity are specific alternative splicing events on a small number of genes, followed by expression changes in metabolism and differentiation-related genes. Our findings unveil molecular and cellular roles of Srrm2 in stemness and lineage commitment, shedding light on the roles of splicing regulators in early embryogenesis, developmental diseases and tumorigenesis.

Abstract LB223: The molecular landscape of injury-induced mammary epithelial cell fate switching

Abstract The most aggressive cancers, such as triple negative basal-like breast cancer (TNBC), have high intratumoral heterogeneity that is often attributed to cell state reprogramming and contributes to cancer progression, treatment resistance, and ultimately cancer death. Tissue injury and microenvironmental changes can cause adult differentiated cells to acquire a plastic “developmentally unstable hybrid cell state” (DUHCS) enabling transdifferentiation into other cell types to effect repair. Yet, the relevant mechanisms that enable cell state reprogramming to arise remain under-explored. Here, we used CRISPR mediated homologous recombination to generate mice in which the mammary basal and luminal cells could be distinguished by their expression of Krt14-mClover-NLS or Krt18-tdTomato-NLS, respectively. We used this novel system to identify mammary epithelial cells undergoing cell state transitions in real time. Using a transplantation paradigm, we found that transplanted basal cells rapidly exhibited a DUHCS resembling mammary embryonic progenitors expressing Sox11, a tightly regulated differentiation factor shut off before birth. We discovered that Sox11 is also expressed in many murine models of TNBC and in single cell transcriptomes from untreated human BRCA1 mutant TNBCs. This suggests that Sox11-expressing cells might be developmentally plastic intermediates in TNBC malignant progression. In a preliminary cohort of patient-derived xenografts from TNBC patients diagnosed at different stages, we detected SOX11-expressing cells in earlier but not in advanced stages. Re-expression of Sox11 in TNBC is consistent with TNBCs being transcriptomically related to fetal mammary stem cells and p53 dysfunction resulting in enhanced cellular plasticity. Taken together, these studies highlight a role for mammary epithelial cell state reprogramming in early breast tumorigenesis, and reveals actionable steps to mitigate tumor heterogeneity by halting tumor progression. Citation Format: Queralt Vallmajó Martín, Nikki K. Lytle, Divya Murali, Sumana Srinivasan, Zhibo Ma, Kavitha Mukund, Christopher Dravis, Liliana Zamora, Ana Peterson, Galina Khramtsova, Funmi Olopade, Shankar Subramaniam, Geoffrey M. Wahl. The molecular landscape of injury-induced mammary epithelial cell fate switching [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 2 (Late-Breaking, Clinical Trial, and Invited Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(7_Suppl):Abstract nr LB223.

Cancer-associated fibroblasts drive colorectal cancer cell progression through exosomal miR-20a-5p-mediated targeting of PTEN and stimulating interleukin-6 production.

This study evaluated the clinical relevance of a set of five serum-derived circulating microRNAs (miRNAs) in colorectal cancer (CRC). Additionally, we investigated the role of miR-20a-5p released by exosomes derived from cancer-associated fibroblasts (CAFs) in the context of CRC. The expression levels of five circulating serum-derived miRNAs (miR-20a-5p, miR-122-5p, miR-139-3p, miR-143-5p, and miR-193a-5p) were quantified by real-time quantitative PCR (RT-qPCR), and their associations with clinicopathological characteristics in CRC patients were assessed. The diagnostic accuracy of these miRNAs was determined through Receiver Operating Characteristic (ROC) curve analysis. CAFs and normal fibroblasts (NFs) were isolated from tissue samples, and subsequently, exosomes derived from these cells were isolated and meticulously characterized using electron microscopy and Western blotting. The cellular internalization of fluorescent-labeled exosomes was visualized by confocal microscopy. Gain- and loss-of-function experiments were conducted to elucidate the oncogenic role of miR-20a-5p transferred by exosomes derived from CAFs in CRC progression. The underlying mechanisms were uncovered through luciferase reporter assay, Western blotting, enzyme-linked immunosorbent assays, as well as proliferation and migration assays. The expression levels of serum-derived circulating miR-20a-5p and miR-122-5p were significantly higher in CRC and were positively correlated with advanced stages of tumorigenesis and lymph node metastasis (LNM). In contrast, circulating miR-139-3p, miR-143-5p, and miR-193a-5p were down-regulated in CRC and associated with early tumorigenesis. Except for miR-139-3p, they showed a negative correlation with LNM status. Among the candidate miRNAs, significantly elevated levels of miR-20a-5p were observed in both cellular and exosomal fractions of CAFs. Our findings indicated that miR-20a-5p induces the expression of EMT markers, partly by targeting PTEN. Exosomal miR-20a secreted by CAFs emerged as a key factor enhancing the proliferation and migration of CRC cells. The inhibition of miR-20a impaired the proliferative and migratory potential of CAF-derived exosomes in SW480 CRC cells, suggesting that the oncogenic effects of CAF-derived exosomes are mediated through the exosomal transfer of miR-20a. Furthermore, exosomes originating from CAFs induced increased nuclear translocation of the NF-kB p65 transcription factor in SW480 CRC cells, leading to increased interleukin-6 (IL-6) production. We established a set of five circulating miRNAs as a non-invasive biomarker for CRC diagnosis. Additionally, our findings shed light on the intricate mechanisms underpinning the oncogenic impacts of CAF-derived exosomes and underscore the pivotal role of miR-20a-5p in CRC progression.

Abstract 4294: The emerging role of deubiquitinase enzymes in lung cancer plasticity

Abstract Lung cancer is characterized by a high degree of genetic and molecular heterogeneity. Lineage plasticity has emerged as a source of intratumoral heterogeneity and drug resistance, resulting in poor prognosis and treatment failure. The molecular mechanisms driving lung cancer plasticity remain unclear. Ubiquitin-Specific Peptidase 13 (USP13), a deubiquitinating enzyme, is one of the most amplified genes in lung squamous cell carcinoma (LUSC). We developed a USP13 knock-in overexpressing mouse model in KrasLSL-G12D/+; Trp53fl/fl (KP) background (KPU mice). USP13 overexpression resulted in aggressive tumorigenesis and a shortened survival in Kras/Trp53-driven lung cancer. Notably, while KP mice developed lung adenocarcinoma (LUAD), KPU mice developed LUSC and LUAD. LUSC in KPU mice faithfully recapitulated the key pathohistological, molecular features, and cellular pathways of human LUSC. Bulk RNA-sequencing analysis showed that KPU tumors were heterogeneous and enriched in lineage reprogramming pathways including basal cell signaling, stem cell pluripotency, and epithelial-mesenchymal transition (EMT). Using cell-type-restricted adenoviral Cre to target cells expressing surfactant protein C (SPC) or club cell antigen 10 (CC10), we identified bronchiolar secretory club cells as the predominant cell origin of LUSC. USP13 altered the levels of lineage transcription factors such as TTF-1 and SOX2 in club cells during early tumorigenesis. Altered expression of these factors reinforced the fate of CC10+ club cells to squamous carcinoma development rather than adenocarcinoma. In addition, USP13 directly acted on the K48-linked ubiquitination of c-Myc and increased its protein stability, contributing to the elevation of squamous gene expression (SOX2, CK5, P40) in the primary mouse and advanced human lung cancer cells. These results suggest that USP13 promotes lineage plasticity in club cells during the early stage of cancer development and drives reprogramming into LUSC. We also found a potential functional association between USP13 and EMT pathway. Notably, irrespective of cell origin, USP13 overexpression enhanced EMT marker expression including N-cadherin, SNAI1, and ZEB1 in lung cancer cells, promoting cell migration and invasion. USP13 increased tumorigenic and metastatic abilities of lung cancer cells in 3D organoid culture and syngeneic mouse models. Collectively, our research highlights the pivotal significance of USP13 in unleashing lineage plasticity during lung cancer progression, suggesting the potential role of deubiquitinase enzymes in regulating lineage plasticity, which may lead to novel therapeutics for treating lung cancer. Citation Format: Juntae Kwon, Jinmin Zhang, Boram Mok, Samuel Allsup, Cecil Han. The emerging role of deubiquitinase enzymes in lung cancer plasticity [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 4294.

Abstract 1262: Comparative analysis of TP53 alleles in pancreatic ductal adenocarcinoma

Abstract The transcription factor p53 is a tumor suppressor capable of inducing cell cycle arrest, senescence, and apoptosis. Both truncating loss-of-function mutations and point mutations of the TP53 gene (mouse gene Trp53), which encodes for the p53 protein, are frequently observed across human cancers. While point mutations in p53 result in loss of canonical tumor suppressor function, recent studies suggest that these mutated proteins acquire pro-tumorigenic gain-of-function properties. For example, Trp53R172H mutations (the murine homolog of TP53R175H, the most common human TP53 variant) enhance metastatic spread relative to deletion mutations in mouse models of advanced pancreatic ductal adenocarcinoma (PDAC). To further explore the differential functions of p53 point and deletion mutants in cancer progression, we performed a rigorous comparative analysis of Trp53 alleles in vivo using Mosaic Analysis with Double Markers (MADM) in mice. MADM uses stochastic mitotic recombination to induce two genotypically distinct daughter cells - created at 1-to-1 ratios - expressing different Trp53 variants dependent on the genotype of the mouse (+/+ vs. -/-, R172H/R172H vs. +/+, R172H/R172H vs. -/-) and simultaneously label them with unique genetically encoded fluorescent markers (TdTomato vs. GFP). We integrated MADM into a faithful Kras-driven model of pancreatic tumorigenesis and used fluorescence microscopy to trace subclonal populations with various p53 alleles within the same mouse. By analyzing the ratio of TdTomato+ to GFP+ cells, we studied the functional differences between alleles in driving pancreatic cancer at various stages of progression. We found that Trp53−/− cells exhibited greater tumor initiation of preinvasive pancreatic intraepithelial neoplasia (PanINs) and early PanIN cell expansion compared to Trp53+/+ cells. Surprisingly, Trp53R172H/R172H cells were comparable in number to Trp53+/+ cells in early PanINs but were outcompeted by Trp53−/− cells.In contrast, both Trp53R172H/R172H and Trp53−/− cells were capable of facilitating the transition to advanced PDAC with comparable survival times. These phenotypic differences imply that p53R172H retains tumor suppressive properties in early pancreatic tumorigenesis, but similar to the loss of p53, it is incapable of constraining progression to advanced disease, arguing that p53R172H is a separation of function mutation in vivo. Ongoing studies examining the molecular differences between Trp53 alleles by fluorescence-activated cell sorting and RNA-sequencing will shed further light onto the underlying mechanisms that explain these phenotypic differences. Citation Format: Andy Tang, Sherry Agabiti, Hannah Chung, Mandar Deepak Muzumdar. Comparative analysis of TP53 alleles in pancreatic ductal adenocarcinoma [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 1262.

Abstract 6356: Novel antibody targeting tumor NKG2D ligand MIC: Preclinical studies and clinical development plan for mCRPC

Abstract In response to genomic insults and DNA double-strand breaks, the stressed epithelial cells express the MHC I-chain related molecule (MIC) on the surface as a byproduct of activating the ATM pathway. The MIC molecule itself has no known impact on tumor survival or growth. In the context of immune microenvironment, tumor cell surface MIC can activate NK cells and co-stimulate CD8 T cells by engaging in the activating receptor NKG2D to hinder the early tumorigenesis. However, in established malignancies, in particular metastatic diseases, tumor cells shed surface MIC to release the soluble form MIC (sMIC). It has been well demonstrated that, in contrary to cell surface MIC, sMIC is highly immune suppressive by disturbing NK cell homeostasis and repolarizing NK cells function, impairing antigen-specific CD8 T cell function by downmodulating NKG2D expression and CD3z expression, and facilitating immune suppression of MDSCs and TAMs in tumor microenvironment. We have demonstrated that MIC is prevalently expressed by prostate tumor cells and significantly upregulated in mCRPC tumors. We have shown significantly elevated levels of serum sMIC in prostate cancer patients with metastatic diseases. We have developed a novel class of clinical candidate monoclonal antibody huB10G5 that can target both sMIC and surface MIC to re-invigorate both NK and CD8 T cell function and inhibit MDSCs and TAMs in preclinical models. The huB10G5 has an acceptable safety profile and is currently completing CMC for IND enabling. We hypothesize that huB10G5 is a novel immune therapeutic reagent for mCRPC patients. To test our hypothesis, we first conducted serial studies of the clinical candidate huB10G5 in pre-clinical models of prostate cancers. We found that huB10G5 can effectively induce 100% long-term tumor complete regression (CR) as low as 1.0 mg/KG. These animals are fully protected from tumor re-challenge. The anti-tumor effect is mediated by the combined action of NK and CD8 T cells. With the support of our pre-clinical efficacy and safety data, we have planned to initiate Phase I clinical trial with huB10G5 for mCRPC patients in 2024. Citation Format: Jennifer Donglan Wu, Jeff Sosman, Masha Kocherginsky, Anthony Serritella, Maha Hussian, David J. Vanderweele. Novel antibody targeting tumor NKG2D ligand MIC: Preclinical studies and clinical development plan for mCRPC [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 6356.

Combined PIK3CA and SOX2 Gene Amplification Predicts Laryngeal Cancer Risk beyond Histopathological Grading.

The PIK3CA and SOX2 genes map at 3q26, a chromosomal region frequently amplified in head and neck cancers, which is associated with poor prognosis. This study explores the clinical significance of PIK3CA and SOX2 gene amplification in early tumorigenesis. Gene copy number was analyzed by real-time PCR in 62 laryngeal precancerous lesions and correlated with histopathological grading and laryngeal cancer risk. Amplification of the SOX2 and PIK3CA genes was frequently detected in 19 (31%) and 32 (52%) laryngeal dysplasias, respectively, and co-amplification in 18 (29%) cases. The PIK3CA and SOX2 amplifications were predominant in high-grade dysplasias and significantly associated with laryngeal cancer risk beyond histological criteria. Multivariable Cox analysis further revealed PIK3CA gene amplification as an independent predictor of laryngeal cancer development. Interestingly, combined PIK3CA and SOX2 amplification allowed us to distinguish three cancer risk subgroups, and PIK3CA and SOX2 co-amplification was found the strongest predictor by ROC analysis. Our data demonstrate the clinical relevance of PIK3CA and SOX2 amplification in early laryngeal tumorigenesis. Remarkably, PIK3CA amplification was found to be an independent cancer predictor. Furthermore, combined PIK3CA and SOX2 amplification is emerging as a valuable and easy-to-implement tool for cancer risk assessment in patients with laryngeal precancerous lesions beyond current WHO histological grading.

Cold-Inducible RNA Binding Protein Impedes Breast Tumor Growth in the PyMT Murine Model for Breast Cancer.

RNA binding proteins (RBPs) post-transcriptionally regulate gene expression by associating with regulatory sequences in the untranslated regions of mRNAs. Cold-inducible RBP (CIRP) is a stress-induced RBP that was recently shown to modulate inflammation in response to cellular stress, where it increases or decreases pro-tumorigenic (proinflammatory) cytokines in different contexts. CIRP expression is altered in several cancers, including breast cancer, but the effects of CIRP on inflammation in breast cancer is not known. Here, we investigate if CIRP alters growth and the inflammatory profile of breast tumors. Transgenic mice overexpressing CIRP in the mammary epithelium were crossed with the PyMT mouse model of breast cancer, and the effects on both early and late tumorigenesis and inflammation were assessed. The effects of CIRP knockdown were also assessed in Py2T cell grafts. Overexpression of CIRP led to decreased tumorigenesis in the PyMT mouse model. Conversely, the knockdown of CIRP in Py2T cell grafts led to increased tumor growth. Luminex cytokine assays assessed the effects on the inflammatory environment. CIRP/PyMT mammary glands/mammary tumors and serum had decreased cytokines that promote inflammation, angiogenesis, and metastasis compared to PyMT mammary glands and serum, documenting a shift towards an environment less supportive of tumorigenesis. CIRP overexpression also decreased CD4+ helper T cells and increased CD8+ cytotoxic T cells in mammary tumors. Overall, these data support a role for CIRP as a potent antitumor molecule that suppresses both local and systemic pro-tumorigenic inflammation.

PTCH1-mutant human cerebellar organoids exhibit altered neural development and recapitulate early medulloblastoma tumorigenesis.

Patched 1 (PTCH1) is the primary receptor for the sonic hedgehog (SHH) ligand and negatively regulates SHH signalling, an essential pathway in human embryogenesis. Loss-of-function mutations in PTCH1 are associated with altered neuronal development and the malignant brain tumour medulloblastoma. As a result of differences between murine and human development, molecular and cellular perturbations that arise from human PTCH1 mutations remain poorly understood. Here, we used cerebellar organoids differentiated from human induced pluripotent stem cells combined with CRISPR/Cas9 gene editing to investigate the earliest molecular and cellular consequences of PTCH1 mutations on human cerebellar development. Our findings demonstrate that developmental mechanisms in cerebellar organoids reflect in vivo processes of regionalisation and SHH signalling, and offer new insights into early pathophysiological events of medulloblastoma tumorigenesis without the use of animal models.

Abstract A069: The molecular landscape of injury-induced mammary epithelial cell fate switching

Abstract The most aggressive cancers, such as triple negative basal-like breast cancer (TNBC), have high intratumoral heterogeneity that is often attributed to cell state reprogramming and contributes to cancer progression, treatment resistance, and ultimately cancer death. Tissue injury and microenvironmental changes can cause adult differentiated cells to acquire a plastic “developmentally unstable hybrid cell state” (DUHCS) enabling transdifferentiation into other cell types to effect repair. Yet, the relevant mechanisms that enable cell state reprogramming to arise remain under-explored. Here, we used CRISPR mediated homologous recombination to generate mice in which the mammary basal and luminal cells could be distinguished by their expression of Krt14-mClover-NLS or Krt18-tdTomato-NLS, respectively. We used this novel system to identify mammary epithelial cells undergoing cell state transitions in real time. Using a transplantation paradigm, we found that transplanted basal cells rapidly exhibited a DUHCS resembling mammary embryonic progenitors expressing Sox11, a tightly regulated differentiation factor shut off before birth. We discovered that Sox11 is also expressed in many murine models of TNBC and in single cell transcriptomes from untreated human BRCA1 mutant TNBCs. This suggests that Sox11-expressing cells might be developmentally plastic intermediates in TNBC malignant progression. In a preliminary cohort of patient-derived xenografts from TNBC patients diagnosed at different stages, we detected SOX11-expressing cells in earlier but not in advanced stages. Re-expression of Sox11 in TNBC is consistent with TNBCs being transcriptomically related to fetal mammary stem cells and p53 dysfunction resulting in enhanced cellular plasticity. Taken together, these studies highlight a role for mammary epithelial cell state reprogramming in early breast tumorigenesis, and reveals actionable steps to mitigate tumor heterogeneity by halting tumor progression. Citation Format: Queralt Vallmajo-Martin, Nikki K. Lytle, Divya Murali, Sumana Srinivasan, Zhibo Ma, Kavitha Mukund, Christopher Dravis, Liliana Zamora, Ana Peterson, Galina Khramtsova, Funmi Olopade, Shankar Subramaniam, Geoffrey M. Wahl. The molecular landscape of injury-induced mammary epithelial cell fate switching [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Advances in Breast Cancer Research; 2023 Oct 19-22; San Diego, California. Philadelphia (PA): AACR; Cancer Res 2024;84(3 Suppl_1):Abstract nr A069.