Aggressive Subtype Research Articles

Study of NALT1 and CTBP1-AS1 lncRNAs expression levels in triple-negative breast cancer patients in the Iranian population

BackgroundTriple-negative breast cancer (TNBC), an aggressive subtype with a poor prognosis, is notably difficult to treat. Emerging research highlights the significant roles of long non-coding RNAs (lncRNAs) in cancer biology. LncRNAs, such as NALT1 and CTBP1-AS1 are implicated in oncogenic processes; this study hypothesizes that NALT1 and CTBP1-AS1 are overexpressed in TNBC tissues compared to adjacent non-tumor tissues and may serve as biomarkers. Methods: One hundred pairs of tumor and adjacent non-tumor tissues were obtained from female patients with triple-negative breast cancer. After extracting RNA, cDNA synthesis was carried out for all samples. Quantitative real-time PCR (qRT-PCR) was employed to assess differential gene expression. Results: The expression of NALT1 (p-value <0.0001) and CTBP1-AS1 (p-value <0.0002) lncRNAs increased in TNBC tumor tissues in comparison to adjacent non-tumor tissues. A statistically positive correlation (ρ = 0.5844, p < 0.0001) was observed between the expression levels of NALT1 and CTBP1-AS1 in breast cancer patients. The ROC analysis indicated that NALT1 (AUC = 0.718, specificity = 61 %, sensitivity = 70 %) shows moderate potential and CTBP1-AS1 (AUC = 0.648, specificity = 65 %, sensitivity = 55 %) exhibits poor potential as a diagnostic biomarker for breast cancer. Conclusion: This study shows that NALT1 and CTBP1-AS1 lncRNAs are upregulated in TNBC tissues. Additionally, a positive correlation exists between their expression levels in breast cancer. Further research is needed to understand their mechanisms as molecular biomarkers.

Simultaneous targeting and suppression of heat shock protein 60 to overcome heat resistance and induce mitochondrial death of tumor cells in photothermal immunotherapy

As the most aggressive and metastatic subtype of breast cancer, clinical demands of triple negative breast cancer (TNBC) have far not been met. Heat shock protein 60 (HSP60) is over expressed in tumor cells and impair the efficacy of photothermal therapy. In this work, a conjugate composed of self-designed peptide targeting HSP60 and gold nanorods was constructed, referred to as AuNR-P17. Results showed that AuNR-P17 was able to simultaneously down regulate the level of HSP60 and locate in the mitochondria where HSP60 is enriched in the tumor cells of TNBC, which also impeded the interaction between HSP60 and integrin α3, thereby reducing the tumor cells' heat tolerance and metastatic capabilities. At the same time, AuNR-P17 induced remarkable mitochondrial apoptosis when exposed to the laser irradiation of 808 nm. The dual functions of AuNR-P17 led to the decrement of BCL-2 and the activation of p53 and cleaved caspase-3. The danger associated molecular patterns (DAMPs) generated from the mitochondrial apoptosis elicited strong and long-term specific immune responses against TNBC in vivo and ultimately inhibited the tumor metastasis and recurrence with significantly prolonged survival (>100 days) on TNBC mice. In conclusion, this study demonstrated HSP60 a promising potential therapeutic target for triple negative breast cancer and exhibited powerful capacity of AuNR-P17 in photothermal immune therapy.

Plant-derived extracellular vesicles release combined with systemic DOX exhibits synergistic effects in 3D bioprinted triple-negative breast cancer

Triple-negative breast cancer (TNBC) is a highly aggressive subtype of breast cancer, lacking targeted therapeutic options. Hydrogels, particularly gelatin methacrylate (GelMA), have emerged as promising materials for localized drug delivery due to their biocompatibility and tunable properties. This study investigates a dual-delivery system for enhancing the treatment efficacy of triple-negative breast cancer (TNBC) using a combination of extracellular vesicles (EVs) derived from Citrus limon L. and the chemotherapeutic drug doxorubicin (DOX). We fabricated 3D bioprinted GelMA scaffolds to achieve localized and controlled release of EVs and evaluated their synergistic effects with systemic DOX delivery on both primary and metastatic 3D TNBC models.The GelMA scaffolds, especially those with 95 % methacrylation, exhibited higher stiffness, which enhanced their sustained release. Following 48-h incubation, the combination of EVs and DOX significantly increased cytotoxicity in the primary 3D TNBC model, reducing cell viability to approximately 30 % compared to controls. This was notably more effective than treatments with DOX or EVs alone. During the extended 7-day incubation period, the combination treatment continued to show superior efficacy, with persistently high levels of ROS generation and further reduction in cell viability. In a metastatic 3D TNBC model, a significant sensitivity to the combined treatment was observed, which notably inhibited aggregate formation and migration. Importantly, EVs-embedded scaffolds promoted the proliferation of human fibroblasts, highlighting their non-toxic nature, while concurrently inhibiting TNBC cell growth. This approach provides a promising strategy to improve the treatment outcomes of TNBC by exploiting the synergistic effects of local EVs release and systemic chemotherapy.

Abstract C045: The extracellular matrix glycoprotein periostin supports chemotherapy resistance by modulating macrophage recruitment and phagocytosis in triple negative breast cancer

Abstract Triple-negative breast cancer (TNBC) accounts for approximately 15–20% of all breast cancer cases and is notoriously aggressive, often developing resistance to standard chemotherapy thus leading to a high rate of metastatic relapse. Evidence suggests that this resistance is linked to changes in the extracellular matrix (ECM) composition, particularly an increase in periostin (POSTN) expression, which is also associated with poor prognosis in breast cancer. Our recent publication showed that the ECM alone can influence macrophage phenotypes. Furthermore, another study from our lab has demonstrated that POSTN mediates resistance to anti-angiogenic therapy by recruiting macrophages in pancreatic neuroendocrine tumors. Notably, POSTN deletion reduced monocyte/macrophage recruitment and enhanced cytotoxic CD8+ T-cell infiltration. Based on these findings, we hypothesized that paclitaxel (PTX), a widely used chemotherapeutic drug for the management of TNBC, may stimulate POSTN production by fibroblasts leading to the recruitment of pro-tumoral macrophages that facilitate tumor growth resulting into therapy resistance. In this study, we showed that PTX induces increased POSTN expression in mouse models of TNBC through immunohistochemistry, and in both 2D and 3D in vitro models via interactions between TNBC cell lines and mammary fibroblasts, as demonstrated by immunofluorescence. An in vitro migration assay confirmed that PTX-induced POSTN enhances the recruitment of human monocytes and macrophages, which display a mixed immunosuppressive and inflammatory phenotype, as revealed by flow cytometry. Not only did these recruited macrophages exhibit a reduced phagocytic capacity against labelled TNBC cells in an in vitro phagocytosis assay, but we also found that POSTN plays a crucial role in inducing SIRPα expression, that may diminish macrophage phagocytic potential. Increased sialylation and Siglec-1 expression are known to be linked to poor prognosis and polarization towards a more immunosuppressive macrophage phenotype in TNBC. Interestingly in our model, we observed that higher concentrations of recombinant human POSTN induce increased Siglec-1 expression on macrophages, a receptor that interacts with sialic acids in the tumor ECM. Further work using a decellularized tissue model that preserves only the ECM from patient-derived tumor biopsies pre- and post-chemo, aims to further explore the correlation between PTX-induced POSTN, ECM sialylation, and Siglec-1 expression on macrophages. Additionally, we have developed POSTN-knockout murine cancer cells and fibroblasts using CRISPR/Cas9, allowing us to investigate how POSTN influences macrophage phenotypes and chemotherapy responses in vivo. Understanding the mechanisms behind chemotherapy resistance in TNBC is crucial for developing effective treatments for this aggressive cancer subtype. By elucidating the intricate interplay between POSTN, macrophages, and chemotherapy response, we aim to identify new therapeutic strategies to improve outcomes for TNBC patients. Citation Format: Ludovica Tarantola, Ioanna Keklikoglou, Oliver M. Pearce. The extracellular matrix glycoprotein periostin supports chemotherapy resistance by modulating macrophage recruitment and phagocytosis in triple negative breast cancer [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Tumor-body Interactions: The Roles of Micro- and Macroenvironment in Cancer; 2024 Nov 17-20; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2024;84(22_Suppl):Abstract nr C045.

Chaga Mushroom Triterpenoids Inhibit Dihydrofolate Reductase and Act Synergistically with Conventional Therapies in Breast Cancer

Inonotus obliquus (Chaga) is a medicinal mushroom with several pharmacological properties that is used as a tea in traditional Chinese medicine. In this study, Chaga water extract was digested in vitro to mimic the natural processing and absorption of its biocomponents when it is consumed as functional beverage, and its anticancer activities were evaluated in breast cancer (BC) cell lines, representing HER2-positive and triple-negative subtypes. After chemical characterization by liquid chromatography/mass spectrometry (HR-QTOF) analysis, the effect of Chaga biocomponents on cell viability and cell cycle progression was assessed by MTT assay, FACS analysis, and Western blot. Dihydrofolate reductase (DHFR) activity was measured by an enzymatic assay. Four highly bioactive triterpenoids (inotodiol, trametenolic acid, 3-hydroxy-lanosta-8,24-dien-21-al, and betulin) were identified as the main components, able to decrease BC cell viability and block the cell cycle in G0/G1 by inducing the downregulation of cyclin D1, CDK4, cyclin E, and phosphorylated retinoblastoma protein. DHFR was identified as their crucial target. Moreover, bioactive Chaga components exerted a synergistic action with cisplatin and with trastuzumab in SK-BR-3 cells by inhibiting both HER2 and HER1 activation and displayed an immunomodulatory effect. Thus, Inonotus obliquus represents a source of triterpenoids that are effective against aggressive BC subtypes and display properties of targeted drugs.

Abstract C041: MYC and p53 alterations cooperate through VEGF signaling to repress cytotoxic T cell and immunotherapy responses in prostate cancer

Abstract Patients with castration-resistant prostate cancer (CRPC) are generally unresponsive to tumor targeted and immunotherapies. Whether genetic alterations acquired during the evolution of CRPC impact immune and immunotherapy responses is largely unknown. Using our innovative electroporation-based mouse models, we generated distinct genetic subtypes of CRPC found in patients and uncovered unique immune microenvironments. Specifically, mouse and human prostate tumors with MYC amplification and p53 disruption had weak cytotoxic lymphocyte infiltration and an overall dismal prognosis. MYC and p53 cooperated to induce tumor intrinsic secretion of VEGF, which by signaling through VEGFR2 expressed on CD8+ T cells, could directly inhibit T cell activity. Targeting VEGF-VEGFR2 signaling in vivo led to CD8+ T cell-mediated tumor and metastasis growth suppression and significantly increased overall survival in MYC and p53 altered CPRC. VEGFR2 blockade also led to induction of PD-L1, and in combination with PD-L1 immune checkpoint blockade produced anti-tumor efficacy in multiple preclinical CRPC mouse models. Thus, our results identify a genetic mechanism of immune suppression through VEGF signaling in prostate cancer that can be targeted to reactivate immune and immunotherapy responses in an aggressive subtype of CRPC. Citation Format: Katherine Murphy. MYC and p53 alterations cooperate through VEGF signaling to repress cytotoxic T cell and immunotherapy responses in prostate cancer [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Tumor-body Interactions: The Roles of Micro- and Macroenvironment in Cancer; 2024 Nov 17-20; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2024;84(22_Suppl):Abstract nr C041.

Abstract C016: Age dictates immune response within the tumor microenvironment of triple negative breast cancer

Abstract Age is the biggest risk factor for developing most forms of cancer. In breast cancer, over 50% of patients are over 60 years old; however, less than 25% of patients enrolled in clinical trials are in this age bracket. Furthermore, most mouse modeling is performed in young mice, meaning that from preclinical through clinical stages patients ages are not accurately reflected in trials designs. Triple negative breast cancer (TNBC) is an aggressive subtype of breast cancer with no targeted therapies, so many treatment strategies utilize chemotherapy in combination with immunotherapy – which relies on a functional immune response. It is well known that immune function declines as we age, and thus therapeutic responses may differ with age. It is yet unclear how the tumor immune microenvironment changes with age, and how this may impact therapeutic response. Here, we utilize a mouse model which mimics hallmarks of human immune aging to understand how age impacts TNBC immune responses to dictate disease progression and therapeutic response. Immunologically young (8 weeks old) and aged (∼12 months old) FVB mice were orthotopically injected with syngeneic Met1 TNBC cells. Once tumors became palpable, mice were treated with paclitaxel chemotherapy or vehicle control and/or anti-PDL1 immunotherapy to mimic first-line therapeutic strategies. Tumors grew significantly faster in young control mice compared to aged, but young mice had a more robust response to therapy. Notable, only young mice had a significant benefit of combo therapy over monotherapy alone. Despite aged mice having more circulating CD8+ and CD4+ T cells, tumors in aged mice had significantly more infiltration of CD8+ cytotoxic T cells and FOXP3+ inhibitory T-regulatory cells compared to young control mice, yet only tumors in young mice exhibited an increase in T cell infiltration with therapy. Additionally, the ratio of CD8+ T cells and FOXP3+ Tregs was unchanged with age or treatment. Depletion of either CD8+ or CD4+ T cells led to a complete loss of age-associated differences in tumor growth. RNA sequencing analysis suggests that infiltrating T cells in aged mice may be exhausted due to a chronic interferon (IFN) phenotype, indicated by enrichment of IFN-alpha, IFN-gamma, and IL2 pathways, as well as increased expression of immune exhaustion markers PD1, CTLA4, TIM3 and LAG3. Neutralization of IFN-gamma blocks therapeutic response to anti-PDL1 in young mice but has no impact on aged mice. Analysis of published single cell RNAseq data indicated the same IFN response pathways enriched with age in human TNBC. These results demonstrate that the aging tumor immune microenvironment significantly impacts tumor progression and therapeutic response and suggest that targeting IFN signaling may lead to improved therapeutic responses. Together these findings establish a significant impact of immune aging on TNBC disease progression and response to therapy, highlighting the importance of developing age- stratified treatment strategies to improve responses in patients of all ages. Citation Format: Milos Spasic, Adrienne Parsons, Abigail Recko, Elizabeth Mittendorf, Peter van Galen, Sandra McAllister. Age dictates immune response within the tumor microenvironment of triple negative breast cancer [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Tumor-body Interactions: The Roles of Micro- and Macroenvironment in Cancer; 2024 Nov 17-20; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2024;84(22_Suppl):Abstract nr C016.

Pitfalls of frozen section diagnosis in ureter margin evaluation of plasmacytoid urothelial carcinoma of urinary bladder.

Plasmacytoid urothelial carcinoma (PUC) is a rare and aggressive subtype that often presents at advanced stages with poor prognosis. This study investigated tumor invasion to better understand tumor behavior and potentially to improve management strategies by comparing the clinicopathologic characteristics of PUC with positive ureter resection margin (+ URM) with PUC with negative URMs (-URM). This retrospective analysis used pathology reports from 2017 to 2023 for cases diagnosed with PUC during radical cystectomy (RC). All applicable H&E slides of RC specimens were reviewed. Cases with a plasmacytoid component greater than 25% in the RC specimens were analyzed. Frozen section analyses (FSAs) and permanent section analyses (PSAs) of ureter resection margins were performed. Fifteen patients with a plasmacytoid component greater than 25% in their RC specimens were identified. Compared with -URM PUC cases, +URM PUC cases were located more frequently at the trigone or bladder neck, and all + URM cases exhibited ureter orifice involvement. Among 6 PSA-positive cases, three (50%) cases showed discrepancies with FSA. Three + URM cases exhibited PUC tumor cells along the submucosa and muscularis propria layer, and the 3 remaining cases showed PUC tumor cells along the adventitia. We observed a consistent adventitia invasion in all the discordant cases, with sectioning errors and misinterpretation identified as the primary causal factors. To the best of our knowledge, this is the first study to demonstrate two separate patterns of tumor infiltration along the ureter and to discuss the significance of comparing FSA with PSA in PUC. The significance of comprehensive management strategies for PUC patients, including a thorough evaluation of ureteral margins and accurate interpretation of periureteral fat tissue, is highlighted. Large, well-designed studies are needed to strengthen the evidence and to establish optimal management strategies for patients with PUC.

Cytologic hallmarks and differential diagnosis of papillary thyroid carcinoma subtypes

Papillary thyroid carcinoma (PTC) is the most common thyroid malignancy, characterized by a range of subtypes that differ in their cytologic features, clinical behavior, and prognosis. Accurate cytologic evaluation of PTC using fine-needle aspiration is essential but can be challenging due to the morphologic diversity among subtypes. This review focuses on the distinct cytologic characteristics of various PTC subtypes, including the classic type, follicular variant, tall cell, columnar cell, hobnail, diffuse sclerosing, Warthin-like, solid/trabecular, and oncocytic PTCs. Each subtype demonstrates unique nuclear features, architectural patterns, and background elements essential for diagnosis and differentiation from other thyroid lesions. Recognizing these distinct cytologic patterns is essential for identifying aggressive subtypes like tall cell, hobnail, and columnar cell PTCs, which have a higher risk of recurrence, metastasis, and poorer clinical outcomes. Additionally, rare subtypes such as diffuse sclerosing and Warthin-like PTCs present unique cytologic profiles that must be carefully interpreted to avoid diagnostic errors. The review also highlights the cytologic indicators of lymph node metastasis and high-grade features, such as differentiated high-grade thyroid carcinoma. The integration of molecular testing can further refine subtype diagnosis by identifying specific genetic mutations. A thorough understanding of these subtype-specific cytologic features and molecular profiles is vital for accurate diagnosis, risk stratification, and personalized management of PTC patients. Future improvements in diagnostic techniques and standardization are needed to enhance cytologic evaluation and clinical decision-making in thyroid cancer.

Abstract B013: Investigation of a novel lncRNA, TROLL-9, in breast cancer formation and progression

Abstract Breast cancer (BC) is the most diagnosed cancer and the second leading cancer-related cause of mortality among women in the US. Despite advances in treatment, BC remains a challenge due to its metastatic potential. The most aggressive BC subtype, triple negative (TN), often harbors mutations in the tumor suppressor gene, p53. One of the effects of mutant p53 involves the inhibition of the tumor and metastatic suppressive functions of TAp63, a p53 family member. Loss of TAp63 leads to the formation of metastatic mammary adenocarcinomas in mice, in part through the regulation of a group of nine long non-coding RNAs (lncRNAs), that we identified and named TAp63 regulated oncogenic lncRNAs (TROLLs). We previously characterized two TROLLs, TROLL-2 and TROLL-3, as markers of tumor progression in multiple cancer types via the activation of the AKT pathway. Currently we are investigating the role of another member, TROLL-9. To investigate the biological role of TROLL-9, we performed in vivo experiments using preclinical mouse models. Specifically, MCF-DCIS, MCF-CA1D, and MDA-MB-231 triple negative breast cancer (TNBC) cells constitutively expressing TROLL-9 were generated and utilized for two mouse models: orthotopic xenografts for primary tumor growth and spontaneous metastasis. The former was designed to identify the potential role of TROLL-9 in tumor formation, whereas the latter involved the resection of a primary tumor and monitoring for metastases via bioluminescence imaging. Notably, TROLL-9 overexpression led to increased formation of lung and livers metastases in all these models, suggesting a role for TROLL-9 in the metastatic cascade. In order to elucidate the mechanism of function of TROLL-9, two complementary approaches were used. Firstly, pulldown using MS2-TRAP followed by mass spectrometry (MS) was performed and led to the identification of putative protein interactors. In parallel, Laser Capture Microscopy (LCM) of the lung metastases followed by RNA-sequencing was used to assess for any gene expression changes due to TROLL-9 overexpression. Integration of the two datasets is currently being performed to unveil the network of genes and proteins perturbed by TROLL-9. Furthermore, to understand the relevance in BC patients, TROLL-9 expression levels were analyzed in the TCGA BC dataset. Interestingly, differences in TROLL-9 levels across BC subtypes were observed, thus supporting its putative role in TNBC. Overall, our data suggest a role for TROLL-9 in BC progression. Our findings provide evidence for further characterizing its mechanism of function as a potential therapeutic target for the treatment of invasive BC, particularly TNBC harboring TP53 mutations. Citation Format: Avani A Deshpande, Marco Napoli, John H Lockhart, Christina L Carr, Jaden R Baldwin, Elsa R Flores. Investigation of a novel lncRNA, TROLL-9, in breast cancer formation and progression [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: RNAs as Drivers, Targets, and Therapeutics in Cancer; 2024 Nov 14-17; Bellevue, Washington. Philadelphia (PA): AACR; Mol Cancer Ther 2024;23(11_Suppl):Abstract nr B013.

Decoding Acute Myeloid Leukemia: A Clinician’s Guide to Functional Profiling

Acute myeloid leukemia (AML) is a complex clonal disorder characterized by clinical, genetic, metabolomic, and epigenetic heterogeneity resulting in the uncontrolled proliferation of aberrant blood-forming precursor cells. Despite advancements in the understanding of the genetic, metabolic, and epigenetic landscape of AML, it remains a significant therapeutic challenge. Functional profiling techniques, such as BH3 profiling (BP), gene expression profiling (GEP), proteomics, metabolomics, drug sensitivity/resistance testing (DSRT), CRISPR/Cas9, and RNAi screens offer valuable insights into the functional behavior of leukemia cells. BP evaluates the mitochondrial response to pro-apoptotic BH3 peptides, determining a cell’s apoptotic threshold and its reliance on specific anti-apoptotic proteins. This knowledge can pinpoint vulnerabilities in the mitochondria-mediated apoptotic pathway in leukemia cells, potentially informing treatment strategies and predicting therapeutic responses. GEP, particularly RNA sequencing, evaluates the transcriptomic landscape and identifies gene expression alterations specific to AML subtypes. Proteomics and metabolomics, utilizing mass spectrometry and nuclear magnetic resonance (NMR), provide a detailed view of the active proteins and metabolic pathways in leukemia cells. DSRT involves exposing leukemia cells to a panel of chemotherapeutic and targeted agents to assess their sensitivity or resistance profiles and potentially guide personalized treatment strategies. CRISPR/Cas9 and RNAi screens enable systematic disruption of genes to ascertain their roles in leukemia cell survival and proliferation. These techniques facilitate precise disease subtyping, uncover novel biomarkers and therapeutic targets, and provide a deeper understanding of drug-resistance mechanisms. Recent studies utilizing functional profiling have identified specific mutations and gene signatures associated with aggressive AML subtypes, aberrant signaling pathways, and potential opportunities for drug repurposing. The integration of multi-omics approaches, advances in single-cell sequencing, and artificial intelligence is expected to refine the precision of functional profiling and ultimately improve patient outcomes in AML. This review highlights the diverse landscape of functional profiling methods and emphasizes their respective advantages and limitations. It highlights select successes in how these methods have further advanced our understanding of AML biology, identifies druggable targets that have improved outcomes, delineates challenges associated with these techniques, and provides a prospective view of the future where these techniques are likely to be increasingly incorporated into the routine care of patients with AML.

DNA tetrahedral nanoparticles: Co-delivery of siOTUD6B/DOX against triple-negative breast cancer.

Triple-negative breast cancer (TNBC) is an aggressive subtype of breast cancer with limited targeted therapeutic options. Recently, the deubiquitinizing enzyme ovarian tumor domain-containing 6B (OTUD6B) has been reported to play a potential role in TNBC progression. Therefore, this study investigates the role and underlying molecular mechanisms of OTUD6B in vitro and xenograft models of TNBC. Specifically, we examined the therapeutic effects of siOTUD6B and doxorubicin (DOX) co-delivery using synthesized tetrahedral DNA nanoparticles (Tds) on tumor growth and progression. Additionally, the uptake and efficacy of the siOTUD6B/DOX@Td in TNBC cells were evaluated. Notably, the siOTUD6B/DOX@Td nanoparticle demonstrated efficient cellular uptake by TNBC cells, resulting in OTUD6B knockdown and controlled release of DOX. Additionally, siOTUD6B/DOX@Td treatment enhanced apoptosis rates increased DOX sensitivity, and inhibited TNBC cell growth, migration, and metastasis. Moreover, in vivo experiments confirmed that siOTUD6B/DOX@Td treatment inhibited tumor growth and metastasis without damaging the primary organs. Mechanistically, OTUD6B regulates TNBC progression by stabilizing murine double minute 2 (MDM2) and degrading forkhead box O3a (FOXO3a). Conclusively, this study demonstrates the potential applicability of DNA nanoparticles loaded with DOX and siOTUD6B for TNBC treatment.

Abstract A052: Circulating tumor DNA (ctDNA) in plasma and urine of renal cell carcinoma patients with localized disease

Abstract Introduction: Circulating tumor DNA (ctDNA) is increasingly valuable in cancer care. Early diagnosis of renal cell carcinoma (RCC) significantly improves prognosis. Clear cell RCC (ccRCC), the most prevalent and aggressive subtype, often leads to recurrence in over 20% of localized cases post-nephrectomy. Thus, risk-stratifying tools are crucial for tailored treatment strategies. In this study, we tracked tumor mutations in DNA from plasma (ctDNA) and urine (utDNA) in patients with localized ccRCC to explore their potential as risk-stratifying biomarkers for recurrence. We evaluated ctDNA/utDNA pre-surgery in all RCC patients and conducted longitudinal assessments post-surgery in ccRCC patients. Additionally, for one ccRCC patient with aggressive disease, we analyzed tumor mutations in the plasma of patient- derived xenograft (PDX) replicates. Methodology: RCC patients were recruited from A.C.Camargo Cancer Center. Urine and plasma samples were taken pre-surgery (BL-baseline), and for ccRCC patients, samples were collected at 6-8 weeks and 6, 18 and 30 months post- surgery (M1, M2, M3 and M4, respectively). Patients were monitored for recurrence for up to 6,3 years. We used a customized 28-gene RCC panel and a commercial 409-gene solid tumor panel to identify tumor somatic mutations using Illumina NextSeq 500 and Ion S5 platforms, respectively. Tumor specific mutations were tracked in DNA from patient plasma and urine, and PDX plasma, using the PATS (Personalized amplicon target sequencing) method on Ion S5 Plus platform. Results: Out of 79 RCC patients (58% ccRCC), 57 (72%) had tumor somatic mutations, including 39 (68%) in ccRCC. VHL and PBRM1 were the most frequently mutated genes. Baseline ctDNA/utDNA were analyzed in 51 RCC patients, with 18% (13% plasma, 12% urine) positivity in RCC and 19% (12% plasma, 12% urine) in ccRCC. During ccRCC monitoring, ctDNA/utDNA was positive only in M1 and M3, with 9% (9% plasma, 0% urine) and 18% (12% plasma, 6% urine), respectively. ctDNA-positive baseline plasma was associated to disease progression (p=0.0155) and tumor staging ≥pT3 (p=0.002); these patients also experienced reduced progression-free (p=0.004) and overall (p98%, resembling the patient’s tumor aggressiveness. Conclusions: ccRCC tumors release low levels of tumor DNA in urine and plasma. Pre-surgery plasma positivity for ctDNA appears to indicate a higher risk of recurrence in ccRCC patients. The ctDNA release of PDX tumors replicated that observed in one ccRCC patient with aggressive disease. Citation Format: Ana Carolina Kerekes Miguez, Isabella Tanus Job e Meira, Stephania Martins Bezerra, Adriano de Oliveira Beserra, Walter Henriques da Costa, Tiago Goss dos Santos, Stenio de Cassio Zequi, Giovana Tardin Torrezan, Dirce Maria Carraro. Circulating tumor DNA (ctDNA) in plasma and urine of renal cell carcinoma patients with localized disease [abstract]. In: Proceedings of the AACR Special Conference: Liquid Biopsy: From Discovery to Clinical Implementation; 2024 Nov 13-16; San Diego, CA. Philadelphia (PA): AACR; Clin Cancer Res 2024;30(21_Suppl):Abstract nr A052.

Radiologic imaging biomarkers in triple-negative breast cancer: a literature review about the role of artificial intelligence and the way forward

Abstract Breast cancer is one of the most common and deadly cancers in women. Triple-negative breast cancer (TNBC) accounts for approximately 10-15% of breast cancer diagnoses and is an aggressive molecular breast cancer subtype associated with important challenges in its diagnosis, treatment, and prognostication. This poses an urgent need for developing more effective and personalized imaging biomarkers for TNBC. Toward this direction, artificial intelligence (AI) for radiologic imaging holds a prominent role, leveraging unique advantages of radiologic breast images, being used routinely for TNBC diagnosis, staging, and treatment planning, and offering high-resolution whole-tumor visualization, combined with the immense potential of AI to elucidate anatomical and functional properties of tumors that may not be easily perceived by the human eye. In this review, we synthesize the current state-of-the-art radiologic imaging applications of AI in assisting TNBC diagnosis, treatment, and prognostication. Our goal is to provide a comprehensive overview of radiomic and deep-learning-based AI developments and their impact on advancing TNBC management over the last decade (2013-2024). For completeness of the review, we start with a brief introduction of AI, radiomics and deep learning. Next, we focus on clinically relevant AI-based diagnostic, predictive and prognostic models for radiologic breast images evaluated in TNBC. We conclude with opportunities and future directions for AI towards advancing diagnosis, treatment response predictions and prognostic evaluations for TNBC.

Extra-Axial Poorly Differentiated Chordoma Initially Misdiagnosed as Epithelioid Sarcoma.

Poorly differentiated chordoma is an exceedingly rare, aggressive subtype of chordoma. These tumors typically arise in the axial skeleton of young patients, most commonly the skull base, followed by the cervical spine. Herein, we present a 60-year-old patient with longstanding knee pain and nondiagnostic imaging, initially thought to be due to osteoarthritis. No discrete mass-forming lesion was identified by radiology. Synovial histology at the time of arthroplasty revealed a multinodular proliferation of epithelioid-to-histiocytoid cells with a moderate amount of eosinophilic-to-clear, vacuolated cytoplasm. Scattered cells with high-grade nuclear atypia were present. A diagnosis of metastatic carcinoma was considered due to immunohistochemical positivity for keratin and GATA3. However, a diagnosis of epithelioid sarcoma was rendered based on clinical context, morphology, and loss of immunohistochemical expression for SMARCB1 (INI1). However, upon re-review of the tumor, brachyury was retrospectively added to the immunohistochemistry panel and showed strong positivity, thus prompting amendment of the initial diagnosis of epithelioid sarcoma to extra-axial poorly differentiated chordoma. Given the rarity of this diagnosis, molecular testing was performed which revealed a unique SMARCB1 molecular profile with a single-nucleotide variant in addition to the commonly reported loss of chromosome 22q. This report of an ultra-rare sarcoma in an uncommon anatomic site highlights multiple potential pitfalls in the diagnosis of poorly differentiated chordoma, emphasizes the importance of brachyury immunohistochemistry in rendering a correct interpretation, and underscores an opportunity for further molecular analysis to better define the molecular profile of this entity.

Abstract B035: Detection and monitoring of translocation renal cell carcinoma via epigenomic profiling of cell-free DNA

Abstract We evaluated the ability of plasma chromatin immunoprecipitation and sequencing (ChIP-seq) and methylated DNA immunoprecipitation sequencing (MeDIP-seq) to detect translocation renal cell carcinoma (tRCC), to distinguish tRCC from clear cell renal cell carcinoma (ccRCC), and to monitor the disease evolution. tRCC is an aggressive subtype of kidney cancer usually driven by a fusion involving the TFE3 gene. Due to histologic overlap with other subtypes of RCC, tRCC is frequently misclassified. Methods for accurate diagnosis and detection of this molecularly distinct entity are therefore a pressing need. Most cell-free DNA (cfDNA) technologies are genomic-based and not optimized for tRCC as molecular fusions are not easily detected in circulating tumor DNA (ctDNA), and 50% of tRCC cases do not have other alteration. Epigenomic profiling of ctDNA via ChIP-seq has recently emerged as a powerful tool to detect and molecularly subtype cancers and may offer a more sensitive and specific detection of fusion- driven tumors. We first identified differentially methylated regions (DMRs) and regulatory elements (REs) specific to tRCC vs. ccRCC via MeDIP-seq and H3K4me3/H3K27Ac ChIP-Seq, of 4 tRCC and 5 ccRCC cell lines. We also identified TFE3 transcription factor binding sites (TFBS) via TFE3 ChIP-seq in 3 tRCC cell lines. We collected 30 plasma samples from metastatic patients with tRCC, 12 with ccRCC and 9 healthy individuals. Ultra low pass whole genome sequencing (ulpWGS) was performed to infer ctDNA fraction (TF), and cfMeDIP-seq, H3K4me3/H3K27ac cfChIP-seq for epigenomic profiling. Signal at tRCC-specific regions derived from cell lines profiling was aggregated for each mark and normalized to common active REs/methylated regions and used to discriminate tRCC vs. ccRCC vs. healthy plasma. Classification performance was evaluated using the area under the receiver operating characteristic (AUROC) curve. Overall 10/30 tRCC and 5/12 ccRCC samples had &amp;gt;3% TF by ulpWGS. H3K4me3 cfChIP-seq signal was significantly higher in all tRCC samples compared to healthy plasma (AUROC=1) at tRCC-specific REs and TFE3 TFBS. Furthermore, H3K27ac and H3K4me3 cfChIP-seq signal in plasma were also significantly higher at tRCC-specific REs and TFE3 TFBS in tRCC samples compared to ccRCC (AUROC=0.86-0.89). A cfDNA-based classifier combining the four scores distinguished tRCC from ccRCC with an AUROC=0.94. MeDIP-seq could not discriminate between tRCC and ccRCC. Moreover, three patients had multiple time points, and the integrated cfChIP H3K4me3/H3K27Ac score was able to accurately monitor the evolution of the disease. In conclusion, although a majority of tRCC plasma samples profiled had TF &amp;lt;3%, all could be distinguished from healthy samples on the basis of cfChIP. The combined score of H3K27ac and H3K4me3 cfChIP-Seq was also discriminatory for tRCC vs. ccRCC. Epigenomic profiling of cfDNA appears as a powerful tool for both detection of tRCC and discrimination from ccRCC/healthy plasma, with potential implications for diagnosis, disease monitoring and guiding therapy. Citation Format: Simon Garinet, Karl Semaan, John Caniff, Noa Phillips, Jacob Berchuck, Jiao Li, Kevin Lyons, Ananthan Sadagopan, Brad Fortunato, Mary Lee, Jack Horst, Rachel Trowbridge, Ji-Heui Seo, Matthew Freedman, Toni Choueiri, Sylvan Baca, Srinivas Viswanathan. Detection and monitoring of translocation renal cell carcinoma via epigenomic profiling of cell-free DNA [abstract]. In: Proceedings of the AACR Special Conference: Liquid Biopsy: From Discovery to Clinical Implementation; 2024 Nov 13-16; San Diego, CA. Philadelphia (PA): AACR; Clin Cancer Res 2024;30(21_Suppl):Abstract nr B035.

DNAR-15. GROUP 3 MEDULLOBLASTOMAS EXPLOIT A TRANSIENT MECHANISM OF TELOMERE REPAIR MEDIATED BY ZSCAN4 WHICH IS TARGETABLE FOR THERAPEUTIC BENEFIT WITH BRAIN-PENETRANT DRUGS

Abstract All cancers need some mechanism of telomere repair. However, it is unknown how Group 3 (G3) medulloblastomas (MB) repair their telomeres, even though MB is the most common malignant brain tumor in kids and G3 is its most aggressive subtype. With rare exceptions, G3 MBs lack telomerase gain-of-function alterations or evidence of constitutive alternative-lengthening-of-telomeres pathway activation. We profiled tumors from N=38 MB patients from UCSF via single-nucleus RNA sequencing; 13 cases were also subjected to single-cell assay for transposase-accessible chromatin by sequencing, and 4 were subjected to single-cell cleavage under targets and tagmentation for H3K27ac. These data identified a network of gene enhancers that were specifically active in rhombic-lip progenitor-like MB cells, the putative G3 MB cell of origin. This program was driven by zinc finger and SCAN domain containing 4 (ZSCAN4), a gene reported to drive transient telomere repair during zygotic genome activation in early embryos. CRISPR inhibition of ZSCAN4 led to significant telomere shortening, telomeric DNA damage, telomere fusions, decreased proliferation, and increased survival of orthotopic xenografts. Conversely, ZSCAN4 over-expression induced significant telomere elongation, increased proliferation, and decreased survival in vivo. Analysis of endogenous-reporter cells indicated that ZSCAN4 is transiently expressed in response to telomere shortening and increases global histone acetylation by inducing chromatin-remodeling factors. Rebastinib targeted ZSCAN4, histone acetylation, and telomere repair, was brain penetrant, and significantly enhanced orthotopic-xenograft survival with no toxicity. Acetyltransferase inhibitor CPI-1612 was brain penetrant and extended xenograft survival with no toxicity. Our data support the hypothesis that G3 MBs exploit a transient mechanism of telomere repair mediated by ZSCAN4. Targeting ZSCAN4 or downstream histone acetylation is therapeutically viable. Pan-cancer whole-genome sequencing data showed that MBs have lower telomeric content than most other cancers. Thus, MBs may be particularly vulnerable to therapeutic strategies that inhibit telomere repair.

EXTH-06. DEVELOPMENT OF ANTISENSE OLIGONUCLEOTIDE THERAPY AGAINST ZFTA-RELA EPENDYMOMA

Abstract Treatment for ependymoma (EPN), the third most common pediatric brain tumor, has not changed in the last 30 years, consisting of surgery and radiotherapy. When EPNs relapse, there are very limited therapeutic options, thus highlighting a dire need for more effective treatment for these tumors. Over 95% of supratentorial EPN are driven by ZFTA fusion oncoproteins, the most common variant being ZFTA-RELA. ZFTA fusion oncoproteins (FO) alone are sufficient to drive tumors in murine models. We hypothesize that: these tumors continue to depend on ZFTA-RELA expression, and that the FO represents a lead target for therapeutic development. RESULTS To assess this dependency, we utilized CRISPR-Cas9 mediated knockout (KO) of ZFTA-RELA oncoproteins from a series of patient derived cell lines as compared to control cells. We found that ZFTA FO driven patient models were dependent upon ZFTA FO expression, and KO led to impaired cellular proliferation. To determine whether a reduction in FO protein levels would also be sufficient to reduce tumor growth, we screened a series of antisense oligonucleotides (ASOs) for ZFTA FO knockdown efficiency in patient-derived cell lines. We quantified knockdown efficiency by western blot and selected the top-performing ASOs targeting a functionally important zinc finger domain of ZFTA. Top-performing ASOs reduced tumor cell proliferation in single dose experiments by 50%, while a non-targeting ASO treated population was unaffected. Repeated ASO doses over 96 hours saw a 75% reduction compared to a 10% reduction in the non-targeting group. CONCLUSION Our findings suggest that ZFTA-RELA drives tumor initiation and continued maintenance and proliferation of EPN. Tumor proliferation can be slowed by reducing FO levels below a required threshold. ASO therapy, potentially in combination with translation inhibitors, is one promising route for targeted treatments in this aggressive EPN subtype and could be expanded against other EPN driver proteins such as EZHIP.

PATH-65. MONITORING MENINGIOMA CELL CYCLE ACTIVITY THROUGH DREAM-MMB ACTIVITY SWITCHING

Abstract Meningiomas account for over 40% of all primary intracranial brain tumors, with approximately one-fifth of these tumors recurring. Our lab has previously used molecular techniques to identify three subgroups: MenG A, B, and C, which have been independently validated. Interestingly, only MenG C tumors harbor recurring patients, making it an aggressive subtype of meningioma. One hallmark of MenG C tumors is the overexpression of a distinct set of genes that harbor in their promoter the CDE-CHR DNA-binding element, used by a transcriptional complex that in dormant cells functions as a repressor (DREAM). Before phosphorylation, this complex functions as an activator (MBB) in cycling cells. Upon a phosphorylation-dependent switch, the dual-specificity tyrosine kinase DYRK1A phosphorylates S28 on LIN52, which itself is dimerized with LIN9 of the core complex. Phosphorylation shifts the complex to DREAM, while lack thereof allows the core complex to interact with MYBL2 (now MBB) and activate the same genes repressed in quiescent cells. We seek to quantify this switch activity using an in vivo luciferase sensor using NanoBiT technology. Our biosensor is based on a split nanoluciferase, where one half is fused to the LIN52/LIN9 dimer and the other is fused to MYBL2. When MYBL2 binds to the LIN52/LIN9 dimer, a functional nanoluciferase is formed, and its activity can be measured using a luciferase-specific substrate. As proof of principle, we have increased cell proliferation by increasing FBS concentration in cultured cells as well as by blocking S28 phosphorylation using the DYRK1A-specific inhibitor Harmine. We screened all possible combinations (alternating NanoBiT fragments) for the highest luciferase activity after stimulation. In the future, this biosensor can be used to monitor cell cycle activity in vitro as well as in vivo using low-cost Luciferase reporter assays to better understand the regulation of specific genes in MenG C tumors.

MGAT4A/Galectin9-Driven N-Glycosylation Aberration as a Promoting Mechanism for Poor Prognosis of Endometrial Cancer with TP53 Mutation.

Emerging evidence recognizes aberrant glycosylation as the malignant characteristics of cancer cells, but little is known about glycogenes' roles in endometrial carcinoma (EC), especially the most aggressive subtype carrying TP53 mutations. Using unsupervised hierarchical clustering, an 11-glycogene cluster is identified to distinguish an EC subtype associated with frequent TP53 mutation and worse prognosis. Among them, MGAT4A (alpha-1,3-mannosyl-glycoprotein 4-β-N-acetylglucosaminyltransferase A) emerges as the most consistently overexpressed glycogene, contributing to EC aggressiveness. In the presence of galectin-9, MGAT4A increases EC cell proliferation and invasion via promoting glucose metabolism. N-glycoproteomics further revealed GLUT1, a glucose transporter, as a glycoprotein modified by MGAT4A. Binding of galectin-9 to the MGAT4A-branched N-glycan on GLUT1 enhances its cell membrane distribution, leading to glucose uptake increase. In addition, oncogenic mutations of TP53 gene in EC cells upregulate MGAT4A expression by disrupting the regulatory oversight exerted by wild-type p53 on tumor-suppressive miRNAs, including miR-34a and miR-449a/b. The findings highlight a new molecular mechanism involving MGAT4A-regulated N-glycosylation on the key regulator of glucose metabolism in p53 mutants-driven EC aggressiveness, which may provide a strategic avenue to combat advanced EC.