Loss Of P53 Research Articles

Sustained ERK signaling promotes G2 cell cycle exit and primes cells for whole-genome duplication

Whole-genome duplication (WGD) is a frequent event in cancer evolution that fuels chromosomal instability. WGD can result from mitotic errors or endoreduplication, yet the molecular mechanisms that drive WGD remain unclear. Here, we use live single-cell analysis to characterize cell-cycle dynamics upon aberrant Ras-ERK signaling. We find that sustained ERK signaling in human cells leads to reactivation of the APC/C in G2, resulting in tetraploid G0-like cells that are primed for WGD. This process is independent of DNA damage or p53 but dependent on p21. Transcriptomics analysis and live-cell imaging showed that constitutive ERK activity promotes p21 expression, which is necessary and sufficient to inhibit CDK activity and which prematurely activates the anaphase-promoting complex (APC/C). Finally, either loss of p53 or reduced ERK signaling allowed for endoreduplication, completing a WGD event. Thus, sustained ERK signaling-induced G2 cell cycle exit represents an alternative path to WGD.

GATA3 functions downstream of BRCA1 to promote DNA damage repair and suppress dedifferentiation in breast cancer

BackgroundInadequate DNA damage repair promotes aberrant differentiation of mammary epithelial cells. Mammary luminal cell fate is mainly determined by a few transcription factors including GATA3. We previously reported that GATA3 functions downstream of BRCA1 to suppress aberrant differentiation in breast cancer. How GATA3 impacts DNA damage repair preventing aberrant cell differentiation in breast cancer remains elusive. We previously demonstrated that loss of p18, a cell cycle inhibitor, in mice induces luminal-type mammary tumors, whereas depletion of either Brca1 or Gata3 in p18 null mice leads to basal-like breast cancers (BLBCs) with activation of epithelial-mesenchymal transition (EMT). We took advantage of these mutant mice to examine the role of Gata3 as well as the interaction of Gata3 and Brca1 in DNA damage repair in mammary tumorigenesis.ResultsDepletion of Gata3, like that of Brca1, promoted DNA damage accumulation in breast cancer cells in vitro and in basal-like breast cancers in vivo. Reconstitution of Gata3 improved DNA damage repair in Brca1-deficient mammary tumorigenesis. Overexpression of GATA3 promoted homologous recombination (HR)-mediated DNA damage repair and restored HR efficiency of BRCA1-deficient cells. Depletion of Gata3 sensitized tumor cells to PARP inhibitor (PARPi), and reconstitution of Gata3 enhanced resistance of Brca1-deficient tumor cells to PARP inhibitor.ConclusionsThese results demonstrate that Gata3 functions downstream of BRCA1 to promote DNA damage repair and suppress dedifferentiation in mammary tumorigenesis and progression. Our findings suggest that PARP inhibitors are effective for the treatment of GATA3-deficient BLBCs.

Endothelial Cell Flow-Mediated Quiescence Is Temporally Regulated and Utilizes the Cell Cycle Inhibitor p27.

Endothelial cells regulate their cell cycle as blood vessels remodel and transition to quiescence downstream of blood flow-induced mechanotransduction. Laminar blood flow leads to quiescence, but how flow-mediated quiescence is established and maintained is poorly understood. Primary human endothelial cells were exposed to laminar flow regimens and gene expression manipulations, and quiescence depth was analyzed via time-to-cell cycle reentry after flow cessation. Mouse and zebrafish endothelial expression patterns were examined via scRNA-seq (single-cell RNA sequencing) analysis, and mutant or morphant fish lacking p27 were analyzed for endothelial cell cycle regulation and in vivo cellular behaviors. Arterial flow-exposed endothelial cells had a distinct transcriptome, and they first entered a deep quiescence, then transitioned to shallow quiescence under homeostatic maintenance conditions. In contrast, venous flow-exposed endothelial cells entered deep quiescence early that did not change with homeostasis. The cell cycle inhibitor p27 (CDKN1B) was required to establish endothelial flow-mediated quiescence, and expression levels positively correlated with quiescence depth. p27 loss in vivo led to endothelial cell cycle upregulation and ectopic sprouting, consistent with loss of quiescence. HES1 and ID3, transcriptional repressors of p27 upregulated by arterial flow, were required for quiescence depth changes and the reduced p27 levels associated with shallow quiescence. Endothelial cell flow-mediated quiescence has unique properties and temporal regulation of quiescence depth that depends on the flow stimulus. These findings are consistent with a model whereby flow-mediated endothelial cell quiescence depth is temporally regulated downstream of p27 transcriptional regulation by HES1 and ID3. The findings are important in understanding endothelial cell quiescence misregulation that leads to vascular dysfunction and disease.

Evaluation of prognostic biomarkers in meningiomas and their clinical implications in settings with limited resources.

The 5th edition of the World Health Organization (WHO) Central Nervous System (CNS) tumor classification for meningiomas acknowledges the clinical relevance of genomic profiling studies and emphasizes the importance of incorporating molecular information alongside histopathological features, leading to more accurate diagnoses and improved patient care. We analyzed 206 meningioma samples (108 histological grade 1, 89 grade 2, and 9 grade 3) to study pTERT mutations, CDKN2A/B homozygous deletion, loss of H3K27me3, and p16 expression. The association of these molecular markers with survival outcomes was also assessed. pTERT mutation was found in 4.85% of cases, predominantly occurring in histological grade 2 (11.24%), while none of the histological grade 1 or 3 meningiomas exhibited this mutation. CDKN2A/B gene deletion was absent in grade 1 and detected in 2.24% of grade2, and 33.3% of histological grade 3 cases. There was a significant increase in loss of H3K27me3 with higher tumor grades, while p16 loss was observed in over 50% of cases across all histological grades. The presence of pTERT mutation and CDKN2A/B homozygous deletion resulted in the reclassification of 5.33% (11/206) of meningiomas as integrated grade 3. pTERT mutation and CDKN2A/B deletion, emerged as prognostically relevant markers, showing significant differences in progression-free survival (PFS) between integrated grade 3 and histological grade 2 meningiomas (P = .0002). pTERT mutations are the most clinically relevant genetic alterations in meningiomas. Routine testing for pTERT mutations can identify high-risk cases of histologically grade 2 meningiomas, providing crucial prognostic information for treatment planning. CDKN2A/B alteration is rare and not cost-effective in assessing meningiomas. Immunohistochemical assessment of p16 and H3K27me3 expression lacks significant prognostic value. Assessment of pTERT mutations offers a cost-effective and valuable diagnostic tool for meningiomas.

Abstract LB303: Suppression of stress granule formation is a novel vulnerability imposed by mutant p53

Abstract Mutation of the tumor suppressor p53 is the most common cancer specific event. Most of these mutations are missense mutations in the DNA-binding domain of p53, causing loss of wild-type p53 (wtp53) transcriptional activity. Missense mutant p53 (mutp53) also enhances cancer malignancy in a manner independent of wtp53. Hence, mutp53 is an ideal therapeutic target due to its uniqueness and high expression levels in cancers; however, directly targeting mutp53 protein itself has been challenging. To better understand the mechanism of oncogenic function of mutp53, we performed in silico TCGA database analysis and found that patients with missense mutp53-carrying hepatocellular carcinoma (HCC), but not other types of cancer, had unexpectedly better overall survival than patients with p53-null HCC. Since sorafenib (SOR) has historically been used as a single agent chemotherapy for HCC, unlike other cancer types, we hypothesized that SOR treatment may have yet unappreciated advantages for treating mutp53-expressing tumors. Indeed, knockdown of mutp53 rendered HCC cells and xenografts more resistant to SOR. Consistent with a report showing that SOR induces ER stress-mediated pro-survival stress granule (SG) formation, mutp53-expressing HCC cells, treated with SOR or other ER stress inducers, formed significantly fewer SGs with increased apoptosis, as compared with mutp53-knockdown cells. This result was partly due to mutp53’s ability to interact with an eIF2α kinase PERK and a key SG core protein, G3BP1. Moreover, the oligomerization domain of mutp53 was required for the interaction of mutp53 with G3BP1 and subsequent suppression of ER-stress-mediated SG formation and survival. These results suggest that inhibition of SG formation is a novel vulnerability imposed by mutp53, leading to sensitization of cancer cells to ER stress. Our results also emphasize the use of ER stress inducers to treat mutp53-expressing tumors and mutp53 as a biomarker of SOR sensitivity. Citation Format: Elizabeth Thoenen, Atul Ranjan, Alejandro Parrales, Shigeto Nishikawa, Dan Dixon, Sugako Oka, Tomoo Iwakuma. Suppression of stress granule formation is a novel vulnerability imposed by mutant p53 [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 LB303.

Loss of mutant p53 in HaCaT keratinocytes promotes cadmium-induced keratin 17 expression and cell death

BackgroundCadmium exposure induces dermatotoxicity and epidermal barrier disruption and leads to the development of various pathologies. HaCaT cells are immortalized human keratinocytes that are widely used as alternatives to primary human keratinocytes, particularly for evaluating cadmium toxicity. HaCaT cells bear two gain-of-function (GOF) mutations in the TP53 gene, which strongly affect p53 function. Mutant forms of p53 are known to correlate with increased resistance to various stimuli, including exposure to cytotoxic substances. In addition, keratin 17 (KRT17) was recently shown to be highly expressed in HaCaT cells in response to genotoxic stress. Moreover, p53 is a direct transcriptional repressor of KRT17. However, the impact of TP53 mutations in HaCaT cells on the regulation of cell death and keratin 17 expression is unclear. In this study, we aimed to evaluate the impact of p53 on the response to Cd-induced cytotoxicity. Methods and resultsEmploying the MTT assay and Annexin V/propidium iodide staining, we demonstrated that knockout of TP53 leads to a decrease in the sensitivity of HaCaT cells to the cytotoxic effects of cadmium. Specifically, HaCaT cells with TP53 knockout (TP53 KO HaCaT) exhibited cell death at a cadmium concentration of 10 μM or higher, whereas wild-type cells displayed cell death at a concentration of 30 μM. Furthermore, apoptotic cells were consistently detected in TP53 KO HaCaT cells upon exposure to low concentrations of cadmium (10 and 20 μM) but not in wild-type cells. Our findings also indicate that cadmium cytotoxicity is mediated by reactive oxygen species (ROS), which were significantly increased only in TP53 knockout cells treated with 30 μM cadmium. An examination of proteomic data revealed that TP53 knockout in HaCaT cells resulted in the upregulation of proteins involved in the regulation of apoptosis, redox systems, and DNA repair. Moreover, RT‒qPCR and immunoblotting showed that cadmium toxicity leads to dose-dependent induction of keratin 17 in p53-deficient cells but not in wild-type cells. ConclusionsThe connection between mutant p53 in HaCaT keratinocytes and increased resistance to cadmium toxicity was demonstrated for the first time. Proteomic profiling revealed that TP53 knockout in HaCaT cells led to the activation of apoptosis regulatory circuits, redox systems, and DNA repair. In addition, our data support the involvement of keratin 17 in the regulation of DNA repair and cell death. Apparently, the induction of keratin 17 is p53-independent but may be inhibited by mutant p53.

Abstract 270: Dissecting the effects of p53 mutation and p53 loss on pancreatic tumor microenvironment

Abstract Pancreatic ductal adenocarcinoma (PDAC) is a devastating malignant disease with a dismal prognosis. In the past decades, a plethora of genetically engineered mouse models (GEMMs) with autochthonous pancreatic tumor development have greatly facilitated the studies of pancreatic cancer. Commonly used GEMMs of PDAC often harbor the oncogenic KRAS driver mutation (KrasG12D), in combination with either p53 mutation by knock-in strategy (Trp53R172H) or p53 loss by conditional knockout (Trp53cKO) strategy, in pancreatic cell lineages. However, the systematic comparison of the tumor microenvironment between KrasG12D; Trp53R172H (KPmut) mouse models and KrasG12D; Trp53cKO (KPloss) mouse models is still lacking. In this study, we conducted cross-dataset single-cell RNA-sequencing (scRNA-seq) analyses to compare the pancreatic tumor microenvironment from KPmut mouse models and KPloss mouse models, especially focusing on the cell compositions and transcriptomic phenotypes of major cell types including cancer cells, B cells, T cells, granulocytes, myeloid cells, cancer-associated fibroblasts, and endothelial cells. We identified the similarities and differences between KPmut and KPloss mouse models, revealing the effects of p53 mutation and p53 loss on oncogenic KRAS-driven pancreatic tumor progression. Citation Format: Yang Chen. Dissecting the effects of p53 mutation and p53 loss on pancreatic tumor microenvironment [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 270.

Abstract 1565: USP13 influences metastatic features in fallopian tube-originated high-grade serous carcinoma

Abstract High-grade serous ovarian carcinoma (HGSOC), originating from the fallopian tube, stands as a formidable challenging gynecologic malignancy with the highest mortality rate worldwide. Ubiquitin-specific peptidase 13 (USP13) has garnered attention due to the highly frequent USP13 gene copy amplification in human ovarian cancer. However, its precise pathological role in ovarian cancer remained elusive. To uncover the underlying role of USP13 in HGSOC, we developed a novel genetically engineered mouse model (GEMM) of HGSOC. Ovgp1-iCreERT2;Trp53flox/flox;Ptenflox/flox mouse (OPT) was crossed with Rosa26−LSL-Usp13 knockin mouse model (U), generating Ovgp1-iCreERT2;Trp53flox/flox;Ptenflox/flox ; Rosa26−LSL-Usp13 mouse model (OPTU). Usp13 overexpression with loss of p53 and Pten was induced specifically in fallopian tube secretory epithelial cells in OPTU mice. OPTU mice demonstrated the development of STIC and early HGSOC in the fallopian tube as well as invasive metastatic HGSOC. While OPT tumors largely retained mucinous and HGSOC subtypes, displaying limited metastatic behavior, OPTU tumors exhibited more complex ovarian tumor subtypes, including mucinous, HGSOC, and Mixed Mesodermal Mullerian Tumor (MMMT) histology. Furthermore, OPTU tumors showed invasive and metastatic phenotypes, characterized by an increased incidence of ovary invasion, metastasis to distant organs, and ascites development. Importantly, OPTU-driven HGSOC tumors closely resemble human HGSOC histology features, making the OPTU model a valuable tool for exploring fallopian tube-originated ovarian cancer. Primary ovarian cancer cells established from ascites of the OPTU mouse reproduced metastatic HGSOC tumorigenesis in the syngeneic mouse study. Stable USP13 knockdown in OPTU cells exhibited reduced cell proliferation and metastatic abilities in 2D and 3D cultures. In summary, this study underscores the pivotal role of USP13 in facilitating metastasis in fallopian tube-originated HGOSC. Our findings may provide a promising avenue for future therapeutic strategies aimed at mitigating the aggressive nature of USP13-amplified fallopian tube-originated HGOSC. Citation Format: Boram Mok, Juntae Kwon, Jinmin Zhang, Samuel Allsup, Hyeongjwa Choi, Cecil Han. USP13 influences metastatic features in fallopian tube-originated high-grade serous carcinoma [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 1565.

Abstract 3009: ATRX loss blocks the differentiation of mesenchymal stem cells and promotes undifferentiated sarcoma development

Abstract Soft tissue sarcomas (STSs) are a collection of rare tumor types originated from the mesenchymal tissues. Among the over 70 histological subtypes of STS, undifferentiated sarcoma (US), which lacks any discernible morphological features of differentiated tissues, accounts for over 20% of all STSs and is correlated with high tumor grade and poor prognosis. Recent genomic profiling in US has identified p53 and ATRX among the most frequently mutated or deleted genes. ATRX is a SWI/SNF2 type of chromatin remodeling factor which functions in a histone variant H3.3-specific chaperone complex to orchestrates replication-independent nucleosome assembly at repetitive heterochromatic DNA regions including telomeres. Loss-of-function mutations occur frequently in many tumor types and is associated with the development of alternative lengthening of telomere (ALT). However, how loss of ATRX function may contribute to tumorigenesis is largely unknown. Here, we demonstrated that ATRX is required for the terminal differentiation of mouse mesenchymal stem cells (MSCs) into multiple lineages, such as adipocytes and osteocytes. Targeted deletion of Atrx in mouse MSCs, but not terminally differentiated mesenchymal lineage cells, accelerated sarcoma initiation induced by loss of p53 and significantly shortened the overall survival. Atrx-deficient tumors express high level of MSC markers such as CD44 and CD29 and exhibit pathological features highly reminiscent of human high-grade US. Transcriptomic analysis indicates that Atrx deficiency is associated with enhanced proliferation. Together, our data indicates that ATRX deficiency contributes to undifferentiated sarcoma development by inhibiting mesenchymal stem cell differentiation. Citation Format: Yiming Cai, Jun Yao, Dean N. Pan, Yanqiang Jin, James M. You, Wantong Yao, Haoqiang Ying. ATRX loss blocks the differentiation of mesenchymal stem cells and promotes undifferentiated sarcoma development [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 3009.

Abstract 1138: A single-cell spatially resolved atlas of immune-mediated control of lung adenocarcinoma using 1,000-plex single-cell spatial molecular imaging in a transgenic mouse model

Abstract Background: Lung adenocarcinoma is one of the leading causes of cancer-related mortality. One of the most frequently occurring mutations in lung cancer is KRAS mutations. Recent development of chemical inhibitors that specifically target oncogenic variants of Ras, particularly the commonly mutated KRAS-G12D isoform, represents a significant breakthrough in targeted therapeutics. The tissue-level mechanisms underlying the cell-autonomous and non-cell-autonomous effects of KRas-G12D inhibitors are poorly understood. Additionally, the effectiveness of KRas-G12D inhibitors in lung cancer models remains unknown. To address these gaps in knowledge, we analyzed the spatial interactions between cancer cells and the surrounding tissue microenvironment during the process of tumor eradication mediated through KRas-G12D inhibitors. Methods: We utilized a genetic mouse model of non-small cell lung cancer (NSCLC), driven by the activation of KRas-G12D in combination with the loss of p53. We investigated the immune-mediated tumor recognition following the targeting of KRas-G12D in an immunocompetent setting. Lung samples were collected from control mice and treated. Spatial transcriptomic analysis (CosMxTM SMI 1,000-plex Mouse Universal Cell Characterization Panel) were employed to obtain a high-plex, single-cell, temporal and spatially resolved molecular atlas of lung tumor regression. Results: Prior to Kras inhibitor treatment, mice displayed both LuAD and lung adenomas. Lesion size and histological grade progressively decrease during pharmacological treatment with Kras inhibitor. 906 unique genes were detected above background on intact FFPE tissue slides, along with 4 protein markers for optimal single-cell segmentation results. Concordance between CosMx SMI and scRNAseq was assessed and demonstrated high assay sensitivity and specificity of the CosMx assay. LUAD cell subtypes were identified and showed distinct spatial features. Molecular states, and receptor-ligand interactions, within niche-specific signaling networks were investigated to underline molecular mechanism of immune attack and eventual eradication of tumors. Conclusion: This study provides novel insights into the temporal and spatial dynamics of KRas-G12D inhibitor-mediated tumor regression in lung cancer, shedding light on the previously unknown cell-cell interactions occurring during this process. By investigating these spatiotemporal aspects, we aim to enhance our understanding of lung cancer biology and potentially identify new immunotherapeutic biomarkers. Moreover, the research tools used in this study have implications for the design of future preclinical studies exploring the potential of immuno-oncology combination therapies. FOR RESEARCH USE ONLY. Not for use in diagnostic procedures. Citation Format: Tito Panciera, Francesca Zanconato, Michelangelo Cordenonsi, Mattia Forcato, Giada Vanni, Silvio Bicciato, Julian Preciado, Saskia Ilcisin, Katrina V. Raay, Margaret Hoang, Michael Patrick, Shanshan He, Joseph Beechem, Stefano Piccolo. A single-cell spatially resolved atlas of immune-mediated control of lung adenocarcinoma using 1,000-plex single-cell spatial molecular imaging in a transgenic mouse model [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 1138.

Abstract 1437: Generating primary mouse models of diffuse midline glioma through a combination of the RCAS/tv-a retrovirus system and CRISPR/Cas9 gene editing

Abstract Diffuse midline gliomas (DMGs) are deadly brain tumors that arise in the brainstem of children and young adults, resulting in a median survival of less than two years. Genetically engineered mouse models (GEMMs) are critical to studying tumorigenesis and tumor-immune interactions in DMG, which may inform the design of new urgently-needed treatment approaches. One approach to generate DMG GEMMs uses RCAS/tv-a, an avian retrovirus gene delivery system to express transgenes in specific brain cell lineages in the mouse brain. However, this approach often requires resource-intensive breeding to generate mice with the desired genetic alterations in their germline. As a result, we aimed to establish a new approach that combines this system with CRISPR/Cas9 gene editing technology. This methodology has been described for model adult supratentorial gliomas in mice but has not been described for pediatric or brainstem gliomas. To express Cas9 and the avian retrovirus receptor TVA in mouse neural stem cells, we bred mice of genotype Nestin-TVA; Nestin-Cre; LoxP-STOP-LoxP-Cas9-EGFP. RCAS retrovirus plasmids were generated containing various guide RNAs (gRNAs) targeting DMG-relevant genes for disruption by Cas9, including Trp53, Cdkn2a, Atm, Ppm1d, Pten, and a non-targeting control (Cntl). For each gRNA, two plasmids were generated, one with a platelet-derived growth factor beta ligand (PDGFB) oncogene driver and one with a blue fluorescent protein (BFP) marker. In a pilot experiment, avian fibroblast cells transduced with RCAS-Trp53_gRNA_BFP and RCAS-Cntl_gRNA-PDGFB were injected into postnatal day 4 mouse brainstems of the aforementioned genotype and observed for tumor formation. High grade tumor formation was observed. We also observed high grade tumors in mice of genotype Nestin-TVA; LoxP-STOP-LoxP-Cas9-EGFP when injected with an additional RCAS-Cre construct, indicating that Cre can be expressed from the mouse germline or delivered via a retrovirus payload to drive tumorigenesis. Immunohistochemistry confirmed tumor features that model human DMG, expression of Cas9 and PDGFB, and loss of p53. Thus, RCAS/tv-a and CRISPR/Cas9 can be combined to model pediatric glioma tumorigenesis in the mouse brainstem. This approach to mouse modeling will streamline future GEMM DMG research by allowing new genes of interest to be rapidly perturbed by simply generating RCAS retrovirus constructs. The workflow may also enable sophisticated experiments such as pooled in vivo genetic experiments that screen gRNAs targeting various tumor suppressor genes or therapeutic targets. Citation Format: Sophie R. Wu, Harrison Q. Liu, Joshua Tolliver, Spencer M. Maingi, Vennesa Valentine, Nerissa T. Williams, Zachary J. Reitman. Generating primary mouse models of diffuse midline glioma through a combination of the RCAS/tv-a retrovirus system and CRISPR/Cas9 gene editing [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 1437.

Abstract 1111: Poor radiation sensitivity and potential radiosensitizers for betel-nuts related head and neck squamous cell carcinoma in Taiwan

Abstract Background: Betel nut chewing might contribute to strong invasion & treatment refractoriness in HNSCC from Taiwan. Betel-nuts exposed HNSCC cell line, TW2.6, had high PDL1, defective p53 mutation, p16 loss, & BCL2 overexpression. In our studies, PI3K/AKT/mTOR inhibitors, anti-angiogenesis therapies, CDK4/6 inhibitors, DDR interventions, epigenetic modifications, and immunotherapy-containing regimens will be future combination options. The genomic signature of TW2.6 has been figured out in our study(AACR2020 & 2023), too, mainly with PIK3CA H1047R mutation, high TMB(8.42 muts/Mb)/MSS, VEGF-A amplification, p53/MYC/HRAS/DDR2/PDGFRbeta/EPHB1/ATM mutations, FAT1 loss, amplification of TERT/FGF10/CCND3/SOX9/IL-7R/SDHA/RICTOR/FLCN, CDK12/PTPRD loss of function, CDK8 mutation, & deletions of STK11/ARID1B/MITF/TNFAIP3 and molecularly-guided novel interventions will be designed. Purpose & Methods: Polo-like kinase 1 inhibitor(volasertib), gluconate(blocking citrate transport & glucose metabolism), IAP inhibitor(Debio1143), glutaminase 1 inhibitor(CB839) were tested on TW2.6 to evaluate synergistic effects with radiation. Results: TW2.6 was resistant to volasertib, gluconate, or radiation alone; but sensitive to Debio1143 and CB839. Volasertib significantly enhanced radiation. The flow cytometry revealed volasertib and radiation resulted in a significant G2/M arrest. Western blotting showed volasertib and radiation increased p-histone3, p-CDK1, & cyclin B levels and induced apoptosis. Gluconate, CB839, or Debio1143 each had significant synergistic effects with radiation. The radiosensitization efficacy would be volasertib>gluconate>CB839>Debio1143. Conclusions: In Taiwan, patients with R/M HNSCC progressing within 3 months after CCRT could be rescued by early ICIs. Recently, sequential CCRT followed by ICI or Debio-1143 with CCRT showed potential survival benefits. In our studies, novel agents such as PLK inhibitor, gluconate, and CB839 had even better radiosensitization compared with Debio1143. Sequential CCRT with novel agents followed by ICI will be the future trend, esp. in biology-aggressive betel-nuts related locally advanced HNSCC in Taiwan. Citation Format: Jo-Pai Chen, Jui-Ying Chang, Ruey-Long Hong. Poor radiation sensitivity and potential radiosensitizers for betel-nuts related head and neck squamous cell carcinoma in Taiwan [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 1111.

Abstract 6516: Single-cell protein activity inference reveals lymphocytic immune infiltration in diffuse intrinsic pontine glioma induced by focused ultrasound

Abstract Diffuse intrinsic pontine glioma (DIPG) is a highly aggressive pediatric brain tumor, located in the brainstem, and traditionally thought to be immune-excluded with no significant infiltration by cytotoxic T-cells, and therefore not amenable to immunotherapies. Focused ultrasound technology (FUS) for drug delivery is being investigated for DIPG in both preclinical and clinical trial settings. In this study, we sought to study the effects of FUS and radiation therapy (RT) on immune cell infiltration in DIPG tumors to assess their ability to alter the immune microenvironment and potentially enhance combination immunotherapies. Specifically, we generated single-cell RNAseq profiles for 27,780 cells from syngeneic orthotopic DIPG tumors (KPAP cell line containing H3K27M mutation, ATRX and P53 loss, and PDGFRA overexpression) after 14 days of tumor growth across the following treatment arms: vehicle control, FUS, and RT (n=2 each group). FUS was applied by 4-point sonication around the tumor with a pressure of 0.6 Mpa at days 8 and 11 post tumor implantation (PTI). RT was administered in fractions of 3 Gy daily from days 8 to 11 PTI (12Gy total). We leveraged a set of algorithms for network-based inference of regulatory protein activity to infer a set of context-matched gene regulatory networks from which protein activity can be inferred by expression of downstream targets. By this approach, we identified distinct clusters of immune cells segregating by cell type as inferred by singleR and activity of known lineage markers. Strikingly, we found that both RT and FUS significantly depleted a TGFb-expressing population of immune-suppressive macrophages as compared to vehicle controls. Importantly, FUS only additionally increased T-cell infiltration into the tumor micro-environment over three-fold as compared to vehicle controls, which was not observed in response to RT. Further protein validation is underway. This has significant implications for therapeutic combinations of FUS-mediated drug delivery with immune checkpoint inhibitors in DIPG, such that in addition to drug delivery, FUS-mediated immune modulatory effects may provide more proinflammatory response to enhance immunotherapy. Citation Format: Erin White, Hong-Jian Wei, Ester Calvo Fernández, Hanna Minns, Jovana Pavisic, Robyn Gartrell, Cheng-Chia Wu, Andrea Califano, Aleksandar Obradovic. Single-cell protein activity inference reveals lymphocytic immune infiltration in diffuse intrinsic pontine glioma induced by focused ultrasound [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 6516.

Abstract 3959: Unraveling the anti-tumor partnership of CD169+ macrophages and CD8+ T cells in a preclinical breast cancer model

Abstract In this study, we describe both the individual and the cooperative mechanisms by which CD169+ macrophages (MP) and CD8+ T cells support an anti-tumor immune response against breast cancer tumors. Breast cancer is the second leading cause of death in women of all ages each year, thus a deeper understanding of the molecular determinants that promote tumor development and suppress the anti-tumor immune response is still greatly needed. Here we use high dimensional flow cytometry, functional assays, and new mouse models to investigate the MP - T cell anti-tumor partnership. With our collaborators, we developed a preclinical mouse model of breast cancer by genetically engineering mammary stem cells to harbor three cancer driver mutations that are frequently associated in human patients: functional loss of the tumor suppressor genes p53 and mixed-lineage leukemia protein 3, and constitutive activation of the PI3 kinase. To characterize the immune cells in this tumor model, we developed a powerful 30-color high dimensional spectral flow cytometry panel to track and phenotype most known immune cell subsets. We found that CD169+ MP rapidly infiltrated and outnumbered all other populations during tumor growth, suggesting that they play an important role in shaping the tumor microenvironment. Surprisingly, although current literature describes breast cancer MP to be highly immunosuppressive, our phenotypic analysis showed only low expression of the pro-tumor MP markers TREM2 and CD206, but extremely high expression of the anti-tumor markers FOLR2 and CD64. To further investigate if these MP promoted or prevented tumor growth, we selectively depleted CD169+ MP in tumor-bearing mice and observed significantly accelerated tumor growth compared to the non-depleted control group, suggesting that these MP promoted anti-tumor responses. MP depletion also affected tumor-infiltrating CD8+ T cells, which produced lower effector functions (e.g., secretion of IFNγ, CCL3, TNF), indicating that MP may also boost anti-tumor CD8+ T cell responses. To further test if CD8+ T cells control tumor growth, we depleted either CD8+ or CD4+ T cells in tumor-bearing mice and observed that only CD8+ but not CD4+ T cell depletion accelerated tumor growth compared to the control group. MP have been documented to provide type I IFN signals to CD8+ T cells via the triggering of the STING pathway. To explore this mechanism in our model, we created a CD169creSTINGflox/KO mouse in which MP lack functional STING. Tumors in these mice grew much faster compared to those in the control group, consistent with the hypothesis that STING sensing occurs in tumor MP and promotes anti-tumor effector CD8+ T cell responses. Overall, our data provide evidence for an unexpected anti-tumor role for CD169+ MP in breast tumors, presumably through enhancing anti-tumor effector CD8+ T cell responses. Citation Format: Nicole Couturier, Marie Boutet, Kenta Nishitani, Wenjun Guo, Gregoire Lauvau. Unraveling the anti-tumor partnership of CD169+ macrophages and CD8+ T cells in a preclinical breast cancer model [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 3959.

Abstract 1595: Persistence of fetal gene signatures along the mesenchymal lineage trajectory defines heterogeneity and function of pancreatic cancer associated fibroblasts

Abstract In pancreatic ductal adenocarcinoma (PDAC), cancer associated fibroblasts (CAFs) play critical and complex roles in the tumor microenvironment. CAFs are also a major cell type in the desmoplastic stroma in PDAC and may account for half of the entire tumor tissue. Here we aimed to investigate the origin, diversification, and function of CAFs. We constructed a dual-DNA-recombinase mouse genetic model carrying KrasG12D/+; Trp53frt/+; Pdx1Flpo/+; Isl1creER/+; R26Tomato/+ alleles, referred to as KPFIT. The DNA recombinase FlpO directs expression of an oncogene Kras (G12D mutation) and loss of a tumor suppressor p53 in pancreatic epithelial cells, while creER recombines the Tomato reporter in the splanchnic mesenchyme and its descendants. The splanchnic mesenchyme is a layer of fetal tissue surrounding the endoderm where the pancreatic epithelium arises. This approach capitalized on the independent functions of FlpO/Frt and CreER/LoxP systems, allowing us to lineage trace Tomato labeled splanchnic progenies (via IT) in a spontaneous pancreatic cancer model (via KPF) within the same mouse. Our study identified the splanchnic mesenchyme as the fetal origin of pancreatic fibroblasts during homeostasis and tumorigenesis. Notably, the other two postulated origins, bone marrow and epithelial cells, have minimal contributions to fibroblasts. Importantly, single cell transcriptomic analysis indicated persistent and dynamic gene expressions along the pancreatic mesenchymal trajectory during development, homeostasis, precancer lesion and cancer. Intriguingly, certain splanchnic factors are expressed in only subtypes of adult pancreatic fibroblasts in temporally and spatially distinct patterns. Furthermore, we constructed mouse genetic models to delete one of the splanchnic factors, Gata6, specifically in CAFs, which resulted in increased tumor burden in the pancreas. This suggests a non-cell autonomous function of GATA6 in CAFs to restrain pancreatic cancer progression. In summary, this study delineated a continuous cell trajectory of the mesenchymal lineage in the pancreas across different life stages. Moreover, persistent gene expressions along the mesenchymal trajectory contributes to pancreatic CAF heterogeneity. Importantly, such persistence may constitute an inherent mechanism to suppress pancreatic cancer. The enhancement of this mechanism could be explored further for therapeutic benefits. Citation Format: Lu Han, Tom Walter, Joseph Beaudet, Caroline Everett, Kun Fang, Michael Zimmermann, Angela Mathison, Raul Urrutia, Victor Jin, Gustavo Leone, Michael Ostrowski. Persistence of fetal gene signatures along the mesenchymal lineage trajectory defines heterogeneity and function of pancreatic cancer associated fibroblasts [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 1595.

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 5610: Investigating the role of BRCA2 in the development of pediatric rhabdomyosarcoma

Abstract Introduction: In a large-scale exome sequencing study of pediatric rhabdomyosarcoma (RMS) patients, we identified a statistical enrichment of patients with germline variants in BRCA2 (Li, et al. JNCI, 2020), which prompted this study to assess the role of heterozygous BRCA2 variants in the development of pediatric RMS in both precursor cell and mouse models. Methods: We engineered BRCA2 loss of function (LoF) variants in lines of immortalized mesenchymal stem cells, a potential precursor cell to RMS, using CRISPR and Prime Editing (PE). CRISPR was used to induce frameshift alleles in Exons 10 and 11 and with PE, we created two RMS patient specific LOF variants in Exons 5 and 17. We generated a genetically engineered mouse model (GEMM) with heterozygous excision of Exon 11 of Brca2. This allele is now being crossed into two different previously established GEMMs of RMS: a myoblast-specific (MyoD1-Cre) conditional loss of p53, and a gain-of-function mutant p53, LSL-p53R172H (Nakahata, et al. Dis. Model. Mech., 2022), to assess changes in the pace of tumorigenesis and metastatic potential. Through an X01 agreement with the Gabriella Miller Kids First Program, we have submitted paired tumor-normal samples for additional whole-genome sequencing and RNA sequencing (tumor only) on >500 patients with RMS, including those with germline variants in BRCA2. Results: Using CRISPR, we generated cell lines heterozygous for the frameshift variants c.1345dup, c.5680del, and c.5680dup. With Prime Editing, we created heterozygous lines mimicking two specific variants detected in the RMS cohort, c.462_463del and c.7857G>A. Generation of a C57BL6 GEMM with a heterozygous removal of Exon 11 in Brca2 has been successful. No homozygous mice were obtained following 7 heterozygous crosses (50 pups), a departure from Mendelian ratios (p=0.0001) consistent with embryonic lethality. Heterozygous Brca2 mice derived from crosses into two RMS models are being monitored for tumor development. We have completed tumor-normal whole-genome and tumor RNA sequencing for 609 RMS patients, including 228 subjects not previously analyzed. We will directly assess whether there is evidence for mutation or loss of expression of the remaining BRCA2 allele in tumors and whether these tumor genomes exhibit signatures of DNA repair deficiency. Conclusions: The goal of this project is to determine the molecular basis for the enrichment in germline BRCA2 LOF variants in pediatric malignancies, including RMS. Ongoing experiments using the engineered heterozygous BRCA2 in vitro cell line models will assess genomic stability, homologous recombination proficiency, and DNA replication fork stability. Assessment of the effect of heterozygous Brca2 variants in GEMMs of RMS, and subsequent analysis of additional sequencing data, will further elucidate what role this gene may play in increasing risk or progression of pediatric cancers. Citation Format: P. Adam Weinstein, Ryan Zabriskie, Cem Ozdemir, Kyle M. Miller, Olga Medina-Martinez, Jason D. Heaney, Aniko Sabo, Philip J. Lupo, Sharon E. Plon. Investigating the role of BRCA2 in the development of pediatric rhabdomyosarcoma [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 5610.

Abstract 6621: Development of a melanocyte lineage-specific knockout system in zebrafish

Abstract Zebrafish have emerged as an ideal model organism for investigating melanocyte and melanoma biology. While CRISPR-Cas9 technology has significantly advanced our understanding of gene functions in zebrafish, two challenges remain: 1) how do we knock out embryonic lethal genes in adult melanocytes? and 2) how do we knock out tumor promoting genes (rather than tumor suppressors)? To address this, we have developed a new transgenic line in which Cas9 is knocked into the melanocyte-specific endogenous mitfa locus. To test this system in normal melanocytes, Tg(mitfa:Cas9) embryos were injected with a plasmid containing albino sgRNA. Cells with integration of this plasmid exhibited almost complete loss of pigmentation, demonstrating the high efficiency of our approach. This system can now be rapidly used to knock out embryonic essential genes specifically in melanocytes and evaluate the phenotype of adult fish. In melanoma, the commonly available zebrafish lines overexpress the oncogene BRAFV600E in melanocytes with germline knockout of tp53. This is not comparable to the situation in humans, where global p53 loss is rare. By utilizing our mitfa:Cas9 system, we have generated tumors with melanoma-specific loss of tp53 or ptena/b, thereby eliminating non-specific tumors that originate from knockout of tumor suppressors in other cell types. Using this system, we are now testing whether knockout of tumor promoting genes delays melanoma onset and progression, something that has previously been difficult to efficiently achieve in zebrafish. In addition to specificity, an additional advantage of our system is that we can create nearly complete knockout of genes in the melanocytes by the F1, rather than the F2 generation. This saves several months of time and reduces the number of uninformative animals without the relevant genotype. Collectively, our system provides a highly efficient mechanism to study essential genes in melanocytes and melanoma in the zebrafish system. Citation Format: Sarah Perlee, Yilun Ma, Jacob Swanson, Zhitao Ming, Julia Xia, Timothée Lionnet, Maura McGrail, Richard White. Development of a melanocyte lineage-specific knockout system in zebrafish [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 6621.

Uterine Leiomyosarcoma Associated With Perivascular Epithelioid Cell Tumor: A Phenomenon of Differentiation/Dedifferentiation and Evidence Suggesting Cell-of-Origin.

Perivascular epithelioid cell tumor (PEComa) is a mesenchymal tumor thought to originate from perivascular epithelioid cells (PECs). The normal counterpart to PEC, however, has not been identified in any human organ, and the debate as to whether PEComa is related to smooth muscle tumors has persisted for many years. The current series characterizes 4 cases of uterine leiomyosarcoma (LMS) coexisting with PEComas. All cases exhibited an abrupt transition from the LMS to PEComa components. The LMS component displayed typical spindled morphology and fascicular growth pattern and was diffusely positive for desmin and smooth muscle myosin heavy chain, completely negative for HMB-45 and Melan A, and either negative or had focal/weak expression of cathepsin K and GPNMB. In contrast, the PEComa tumor cells in case 1 contained glycogen or lipid-distended cytoplasm with a foamy appearance (low grade), and in cases 2, 3, and 4, they displayed a similar morphology characterized by epithelioid cells with eosinophilic and granular cytoplasm and high-grade nuclear atypia. Different from the LMS component, the epithelioid PEComa cells in all cases were focally positive for HMB-45, and diffusely immunoreactive for cathepsin K and GPNMB. Melan A was focally positive in cases 1 and 3. Loss of fumarate hydratase expression (case 1) and RB1 expression (cases 2, 3, 4) was identified in both LMS and PEComa components, indicating that they are clonally related. In addition, both components showed an identical TP53 p.R196* somatic mutation and complete loss of p53 and ATRX expression in case 2 and complete loss of p53 expression in case 3. We hypothesize that LMSs containing smooth muscle progenitor cells may give rise to divergent, lineage-specific PEComatous lesions through differentiation or dedifferentiation. While we do not dispute the recognition of PEComas as a distinct entity, we advocate the hypothesis that modified smooth muscle cells represent the origin of a subset of PEComas, and our case series provides evidence to suggest this theory.

Functional genomic screens with death rate analyses reveal mechanisms of drug action.

A common approach for understanding how drugs induce their therapeutic effects is to identify the genetic determinants of drug sensitivity. Because 'chemo-genetic profiles' are performed in a pooled format, inference of gene function is subject to several confounding influences related to variation in growth rates between clones. In this study, we developed Method for Evaluating Death Using a Simulation-assisted Approach (MEDUSA), which uses time-resolved measurements, along with model-driven constraints, to reveal the combination of growth and death rates that generated the observed drug response. MEDUSA is uniquely effective at identifying death regulatory genes. We apply MEDUSA to characterize DNA damage-induced lethality in the presence and absence of p53. Loss of p53 switches the mechanism of DNA damage-induced death from apoptosis to a non-apoptotic death that requires high respiration. These findings demonstrate the utility of MEDUSA both for determining the genetic dependencies of lethality and for revealing opportunities to potentiate chemo-efficacy in a cancer-specific manner.