Cancer research最新文献

{"title":"Abstract B036: NRF2 promotes hepatoblastoma cell migration via mTORC1/2 signaling","authors":"Nicholas A O'Brien, Priyanka Rao, Roma Patel, Brian T Hickner, Andrew Badachhape, Shuai Zhao, Sai Govindu, Sanjeev Vasudevan, Sarah E Woodfield","doi":"10.1158/1538-7445.pediatric25-b036","DOIUrl":"https://doi.org/10.1158/1538-7445.pediatric25-b036","url":null,"abstract":"The purpose of this study was to investigate the mechanism of transcription factor NRF2 in promoting cell migration/metastasis in hepatoblastoma. The role of NRF2 in cell migration was assessed with shRNA knock down of NFE2L2 (NRF2) as well as modulation of NRF2 transcriptional activity with small molecule NRF2 inducer DMF and inhibitor ML385. Proliferation and migration assays found that shNFE2L2 and ML385 decreased both cell proliferation and wound healing ability of HepT1 hepatoblastoma cells. Conversely, DMF increased wound healing ability of HepT1 cells but did not affect cell proliferation. Preliminary data also shows that NRF2 inhibitor ML385 is able to decrease primary tumor growth in an orthotopic PDX model of hepatoblastoma. To determine possible downstream targets of NRF2, bulk RNA sequencing was performed with shNFE2L2 compared to shNS control. Over-representation analysis showed downregulation of known NRF2 functions (xenobiotic metabolism, epithelial-mesenchymal transition) as well as targets less known to be linked to NRF2 function (mTORC1 signaling). To investigate the role of mTOR downstream of NRF2, mTORC1-specific inhibitor ridaforolimus and mTORC1/2-dual inhibitor sapanisertib were assessed in cell migration assays. While both ridaforolimus and sapanisertib decreased wound healing ability, sapanisertib did so to a greater magnitude than ridaforolimus, suggesting an additional role of mTORC2 signaling downstream of NRF2 in cell migration. Co-treatment of NRF2 agonist DMF did not rescue the loss of wound healing seen with ridaforolimus or sapanisertib, suggesting that mTOR signaling acts downstream of NRF2. Overall, our results highlight the importance of NRF2 signaling in promoting cell migration and show that mTOR inhibition may be a viable strategy to treat hepatoblastoma patients that harbor tumors/metastases with increased NRF2 activity. Citation Format: Nicholas A O'Brien, Priyanka Rao, Roma Patel, Brian T Hickner, Andrew Badachhape, Shuai Zhao, Sai Govindu, Sanjeev Vasudevan, Sarah E Woodfield. NRF2 promotes hepatoblastoma cell migration via mTORC1/2 signaling [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Discovery and Innovation in Pediatric Cancer— From Biology to Breakthrough Therapies; 2025 Sep 25-28; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2025;85(18_Suppl_2): nr B036.","PeriodicalId":9441,"journal":{"name":"Cancer research","volume":"63 1","pages":""},"PeriodicalIF":11.2,"publicationDate":"2025-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145140996","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Abstract A023-PR006: CBL mutations in pediatric solid and CNS tumours are a marker of receptor tyrosine kinase activation and a potential therapeutic target","authors":"Lauren M Brown, Chelsea Mayoh, Katherine A Camper, Pablo Acera Mateos, Wenyan Li, James Bradley, Teresa Sadras, Robert Salomon, Marie Wong, Mark J Cowley, Antoine de Weck, Loretta Lau, Neevika Manoharan, Paul G Ekert","doi":"10.1158/1538-7445.pediatric25-a023-pr006","DOIUrl":"https://doi.org/10.1158/1538-7445.pediatric25-a023-pr006","url":null,"abstract":"Molecularly targeted therapies, selected using precision medicine approaches like the Zero Childhood Cancer Program (ZERO), improve outcomes for childhood cancer patients. Mutations in the E3 ubiquitin ligase, CBL, represent one such molecular target in acute myeloid leukaemia, where mutation mediates activation of the Receptor Tyrosine Kinase (RTK), FLT3, and sensitivity to FLT3-targeted Tyrosine Kinase Inhibitors (TKIs). We have identified novel CBL mutations in pediatric CNS and solid tumours, raising the possibility of targeting RTKs activated by CBL mutations in other tumour types. We analyzed whole genome and RNA sequencing data from the ZERO cohort and identified 34 somatic and 2 germline CBL variants in 31 individual patients. The majority of CBL variants (72% [26/36], including 24 somatic and 2 germline), clustered around key functional domains, the linker region and RING finger domain, and were predicted to be pathogenic based on their location. Somatic CBL variants were identified in 6 leukemia samples (27% [6/22]), including 5 AML cases. The remaining CBL mutated samples were from non-hematological malignancies (73% [16/22]), including 1 neuroblastoma, 1 germ cell tumour and 14 CNS tumour samples. The neuroblastoma and germ cell tumour cases both harbored the established pathogenic CBL exon8/9 genomic deletion (CBL ex8/9Δ), while CNS tumours expressed either CBL missense (8 samples) or splice (6 samples) mutations that were either novel, variants of uncertain significance and/or not previously identified in this tumour type. CBL mutated CNS tumours were molecularly diverse and commonly did not classify into pre-defined DNA methylation-based subtypes (5/13 cases, where methylation analysis was performed). We show that overexpression of the CBL ex8/9Δ in neuroblastoma cell lines enhanced cell proliferation and blocked CBL mediated degradation of RTKs, resulting in maintained RTK signaling. Interestingly, high-throughput screening of the patient sample in which this variant was identified, revealed sensitivity to the multi-TKI pazopanib. We also demonstrate that novel CBL variants, identified in pediatric CNS tumours, can cooperate with RTK overexpression to drive transformation. Thus, we show that CBL mutations are a marker of RTK activation in non-hematological tumors. This finding will extend the potential benefit of TKIs, which have proven efficacy in paediatric cancer, to more patients. Citation Format: Lauren M Brown, Chelsea Mayoh, Katherine A Camper, Pablo Acera Mateos, Wenyan Li, James Bradley, Teresa Sadras, Robert Salomon, Marie Wong, Mark J Cowley, Antoine de Weck, Loretta MS Lau, Neevika Manoharan, Paul G Ekert. CBL mutations in pediatric solid and CNS tumours are a marker of receptor tyrosine kinase activation and a potential therapeutic target [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Discovery and Innovation in Pediatric Cancer— From Biology to Breakthrough Therapies; 2025 Sep 25-28; B","PeriodicalId":9441,"journal":{"name":"Cancer research","volume":"154 1","pages":""},"PeriodicalIF":11.2,"publicationDate":"2025-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145140875","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Abstract B043: Dysregulated AKT signaling reprograms osteosarcoma to drive selective reliance on EP300","authors":"Ian Delahunty, Stephanie Nance, Yang Zhang, Francois Lamoureux, Qi Liu, Charlie Wright, Noha Shendy, Sandra Kietlinska, Barbara De Kegel, Matthew Rees, Anoop Kavirayani, Paris Prinsen, Yousef Khashana, Melissa Ronan, Jennifer Roth, Alejandro Sweet-Cordero, Lilly Guenther, Paul Geeleher, Ben Ory, Jun Qi, Brian Abraham, Adam Durbin","doi":"10.1158/1538-7445.pediatric25-b043","DOIUrl":"https://doi.org/10.1158/1538-7445.pediatric25-b043","url":null,"abstract":"Cancer cells are highly dependent on the control of transcription for maintenance of the malignant cell state. EP300 and CBP are paralogous, commonly expressed, master epigenetic enzymes, whose activity controls normal and malignant transcription. Here, we perform an integrative chemical-genetic cancer-wide analysis, identifying that most cancer lineages, including osteosarcoma (OS), a highly lethal malignancy of bone, have enhanced dependency on EP300, compared with CBP. To take advantage of selective pharmacology targeting EP300 alone, which spares CBP in untransformed cells and thereby reduces toxicity, we used the EP300-targeted degrader JQAD1. A specific genetic subgroup of OS marked by dysregulation of the PIK3CA-AKT-mTOR pathway is genetically dependent on EP300 and uniquely sensitive to EP300 degradation. Expression of constituitively active AKT in insensitive OS cells induces sensitivity to JQAD1, driven by physical relocalization of EP300, CBP and H3K27ac to genetic subtype-enriched dependency loci. Mechanistically, combinations of AKT inhibitors and JQAD1 suppress the growth of AKT-dysregulated OS in vitro and in orthotopic xenografts. These observations extend across >850 cancer cell lines, where these agents positively combine in a manner mechanistically dependent on control of protein synthesis. These findings reveal genetic and transcriptional determinants of EP300 degrader function in high-risk OS and provide a foundation for biomarker-directed investigation of co-targeting of EP300 and AKT for therapeutic gain across cancers marked by enhanced protein translation. Citation Format: Ian Delahunty, Stephanie Nance, Yang Zhang, Francois Lamoureux, Qi Liu, Charlie Wright, Noha Shendy, Sandra Kietlinska, Barbara De Kegel, Matthew Rees, Anoop Kavirayani, Paris Prinsen, Yousef Khashana, Melissa Ronan, Jennifer Roth, Alejandro Sweet-Cordero, Lilly Guenther, Paul Geeleher, Ben Ory, Jun Qi, Brian Abraham, Adam Durbin. Dysregulated AKT signaling reprograms osteosarcoma to drive selective reliance on EP300 [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Discovery and Innovation in Pediatric Cancer— From Biology to Breakthrough Therapies; 2025 Sep 25-28; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2025;85(18_Suppl_2): nr B043.","PeriodicalId":9441,"journal":{"name":"Cancer research","volume":"14 1","pages":""},"PeriodicalIF":11.2,"publicationDate":"2025-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145140871","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Abstract A029: Histotripsy induces an anti-tumor immune response with an abscopal effect in a syngeneic neuroblastoma mouse model","authors":"Yuqing Xue, Natalia Antonides-Jensen, Fernando Flores-Guzman, Lydia L. Wu, Jacky Gomez-Villa, Muskan Singh, Kenneth B. Bader, Sonia L. Hernandez, Mark A. Applebaum","doi":"10.1158/1538-7445.pediatric25-a029","DOIUrl":"https://doi.org/10.1158/1538-7445.pediatric25-a029","url":null,"abstract":"Background: Despite recent therapeutic advances, patients with high-risk neuroblastoma (NB) remain in need of improved treatment options. Histotripsy is a focused ultrasound therapy for nonthermal-tissue ablation via bubble activation. Recent pre-clinical and clinical reports suggest histotripsy stimulates an anti-tumor immune response in the adult population. We previously demonstrated that histotripsy ablation of NB xenograft tumors enhances tumor necrosis factor-alpha secretion, inducing apoptosis. We hypothesized that histotripsy induces both local and distal abscopal anti-tumor immune response in neuroblastoma, resulting in increased killing of tumor cells. Methods: Myc-expressing neuro-2a cells were subcutaneously and synchronously injected into each flank of immunocompetent A/J mice. Histotripsy was applied with a custom system to approximately 80% of one flank tumor when it reached 200 – 300 mm3. Six days later, single cell RNA sequencing (scRNAseq) libraries were prepared for histotripsy treated tumors, synchronous contralateral tumors, and tumors from untreated control mice. Sequencing files were processed with Cell Ranger and downstream analyses were done with Seurat, followed by Kruskal-Wallis test for cell proportions comparison. Flow cytometry was used to corroborate these findings using anti-CD8 (T cells) and CD11b (macrophages). Results: Tumors from untreated control mice were over two-fold larger than both histotripsy-treated tumors six days after treatment (p=0.03) as well as tumors contralateral to the histotripsy treated tumors (p<0.05), suggesting an abscopal effect. High-quality scRNAseq data were obtained from 3 untreated tumors and 2 each from histotripsy and contralateral tumors. The proportion of cytotoxic CD8+ T cells were significantly higher in histotripsy as well as contralateral tumors compared to untreated controls (p=0.029). Similarly, anti-tumor M1 macrophages had a non-significant trend higher (p=0.27) while pro-tumor M2 macrophages were significantly decreased (p=0.029) in controls compared to treated and contralateral tumors. These findings were validated with flow cytometry of both CD8 and CD11b markers (p<0.05, respectively). NB cells from treated and contralateral tumors had decreased Myc expression (p<0.001) in addition to suppression of cell cycle and growth-related pathways relative to control tumors, including Myc targets, G2M checkpoint, and E2F targets pathways (p<0.001, respectively). Treated and contralateral tumor cells also had activated expression pathways of inflammatory response, regulation of chemokines and cytokines, response to interferon, and antigen processing and presentation when compared to controls (p<0.001, respectively). Conclusions: Our findings show that histotripsy can generate an immune cell activation response in treated and distal tumors in NB models, reducing proliferation of the targeted tumor as well as having an abscopal effect. These find","PeriodicalId":9441,"journal":{"name":"Cancer research","volume":"23 1","pages":""},"PeriodicalIF":11.2,"publicationDate":"2025-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145140874","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Abstract A017-PR013: Alectinib in children and adolescents with solid or CNS tumors harboring ALK-fusions: An update from the iMATRIX alectinib phase I/II open-label, multi-center study","authors":"Francois Doz, Michela Casanova, Kyung-Nam Koh, Karsten Nysom, Adela Canete, Hyoung Jin Kang, Matthias Karajannis, Darren Hargrave, Nadege Corradini, Yeming Wu, Huanmin Wang, David Ziegler, Nicolas Prud'homme, Carla Manzitti, Quentin Campbell-Hewson, Carolina Sturm-Pellanda, Tao Xu, Dhruvitkumar S. Sutaria, Livingstone Fultang, Clare Devlin, Francis Mussai, Amar J Gajjar","doi":"10.1158/1538-7445.pediatric25-a017-pr013","DOIUrl":"https://doi.org/10.1158/1538-7445.pediatric25-a017-pr013","url":null,"abstract":"Background: Alectinib is a next generation, oral, ALK inhibitor being investigated in children and adolescents with ALK-fusion bearing tumors. Here we present updated safety and efficacy data from iMATRIX Alectinib phase I-II study (NCT04774718). Methods: Patients, less than 18 years of age, with ALK fusion-positive CNS and non-CNS tumors for whom prior treatment had proven to be ineffective or for whom there was no satisfactory treatment available were eligible. Patients were recruited to Part 1 to confirm the recommended phase 2 dose (RP2D) and to study drug pharmacokinetics. Alectinib was administered as an oral tablet or suspension twice a day according to initial weight. Investigators reported Best Overall Response according to RANO (CNS tumors) or RECIST v1.1 (solid tumors) criteria (data cut off February 2025). Results: In total 25 patients with a median age of 7.5 years (range 0-17 years) were enrolled. Fifteen patients were diagnosed with solid tumors: inflammatory myofibroblastic tumor (n = 10), renal cell carcinoma (n = 2), mesothelioma (n = 1), nephroblastoma (n = 1), and atypical melanocytic tumor (n = 1). Eight patients were diagnosed with CNS tumors: high grade glioma (n = 7) and pleomorphic xanthoastrocytoma (n = 1). Two patients had ineligible conditions: histiocytosis (n = 1) and anaplastic large cell lymphoma (n = 1). Ten of 25 patients had received prior systemic therapy. ALK fusion partners were EML4 and CLTC in 3 patients, TPM3, KIF5C, PPP1CB and FN1 in 2 patients, and DCTN1, KIF5B, NPM, STRN, CLIP1, RANBP2, ZEB2, PLEKHA7, CDC42BPB, HNRNPA3, and ZNF397 in 1 patient each. In the 24 safety evaluable patients, only 1 Dose Limiting Toxicity (DLT) of Grade 3 increased alanine aminotransferase, during multiple viral infections, was reported. The DLT resolved after treatment interruption and Alectinib was successfully tolerated at a reduced dose level. Twenty patients (83%) experienced at least one Adverse Event (AE) reported as related to Alectinib, mostly Grade 1 or 2. Grade ≥ 3 AEs assessed as related to alectinib by the investigator were reported for 6 patients (25%) and consisted of increases in CPK,AST, ALT, bilirubin; neutropenia, optic neuropathy, encephalopathy and weight gain. Of these the increased ALT (DLT) and optic neuropathy/ encephalopathy in 2 patients were serious AEs. No new safety signals were detected. Investigator reported Best Overall Response rate in 19 patients was 89.5%; (3 CRs, 14 PRs) and 2 patients were reported to have confirmed stable disease. One complete response and 5 partial responses were observed in 6/6 evaluable patients with CNS tumors. Two complete responses and 9 partial responses were seen in 11 evaluable patients with solid tumours. Four patients were excluded from the efficacy analysis due to ineligible tumor type (n = 2), not dosed (n = 1), no measurable disease according to RANO criteria (n = 1). Conclusions: Alectinib continues to have a favourable safety profile in pediatric patients.","PeriodicalId":9441,"journal":{"name":"Cancer research","volume":"69 1","pages":""},"PeriodicalIF":11.2,"publicationDate":"2025-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145140931","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Abstract B025: Multi-omic characterisation of the immune microenvironment in Rhabdoid Tumours","authors":"Erin Coll, Chelsea Mayoh, Lauren Brown, Anne-Lise Gerard, Helen McGuire, Paul Ekert","doi":"10.1158/1538-7445.pediatric25-b025","DOIUrl":"https://doi.org/10.1158/1538-7445.pediatric25-b025","url":null,"abstract":"The University of Sydney, Sydney, NSWRhabdoid Tumours (RTs) are highly aggressive rare pediatric malignancies that primarily affect infants and young children, arising as malignant Rhabdoid Tumours (MRTs) in the kidney or Atypical Teratoid/Rhabdoid Tumours (AT/RTs) in the brain. These tumours are driven by SMARCB1 mutations or deletions and exhibit a low tumour mutation burden (TMB), traditionally suggesting poor immunogenicity. However, immune profiling has revealed substantial immune infiltration into the tumour immune microenvironment (TIME), including robust T-cell and myeloid cell presence, PD-L1 expression, and SMARCB1-dependent re-expression of endogenous retroviruses (ERVs), which can activate anti-tumour immune responses. Despite these features, RTs remain incurable, underscoring the need to elucidate their immune landscape to inform novel therapeutic strategies. Using data from the ZERO Childhood Cancer program, we applied bulk RNA sequencing and whole-genome sequencing to deconvolute the immune cell composition beyond T cells, preform IPASS, and assess associations between genomic alterations and immune features. Notably, we identified a strong correlation between high inflammation/IPASS scores and pathogenic SWI/SNF complex mutations, including SMARCB1 loss. Among immune modulators, leukemia inhibitory factor (LIF) emerged as a key player, displaying high expression in RTs and an inverse relationship with SWI/SNF gene expression. To spatially resolve the TIME of RTs, we performed spatial transcriptomics and proteomics, focusing on immune cell infiltration and exclusion mechanisms mediated by LIF-LIFR signalling. We found that LIF is predominantly expressed by tumour cells, while LIFR is enriched on myeloid cells, suggesting a tumour-driven immunosuppressive axis. Moreover, MRTs and AT/RTs exhibit distinct immune architectures: MRTs are highly inflamed, with dispersed T cells and myeloid cells across tumour and stromal regions, whereas AT/RTs are dominated by myeloid infiltration localized to stromal regions and perivascular niches. Xenium-based differential gene expression analysis of macrophages from AT/RT and MRT patients reveals that AT/RT-associated macrophages exhibit reduced interferon signalling and proliferation, but enhanced tissue remodelling and immunosuppressive M2-like polarization. This study underscores the power of multiomic approaches in dissecting the immune landscape of rare and incurable paediatric solid tumours. By leveraging the IPASS gene signature and LIF-LIFR axis, we identified immune exclusion mechanisms that could serve as therapeutic targets. Future investigations will focus on validating these findings and assessing their potential for combinatorial immunotherapies in rhabdoid tumours. Lastly, the dataset generated by this study is a rare and invaluable resource in the advancement of rhabdoid tumour research. Citation Format: Erin Coll, Chelsea Mayoh, Lauren Brown, Anne-Lise Gerard, Helen McGuire, Paul Ek","PeriodicalId":9441,"journal":{"name":"Cancer research","volume":"3 1","pages":""},"PeriodicalIF":11.2,"publicationDate":"2025-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145140935","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Abstract B002: Rapid and accurate diagnosis of childhood cancers using long-read nanopore RNA sequencing","authors":"Matt Hudson, Sandy Fong, Pedro Lemos Ballester, Resel Pereira, Srdjana Filipovic, Reem Khan, Johann Hitzler, Sarah Cohen-Gogo, Anita Villani, David Malkin, Adam Shlien","doi":"10.1158/1538-7445.pediatric25-b002","DOIUrl":"https://doi.org/10.1158/1538-7445.pediatric25-b002","url":null,"abstract":"The SickKids Cancer Sequencing (KiCS) program at the Hospital for Sick Children performs DNA and RNA sequencing of the tumors of all pediatric patients diagnosed with hard-to-cure cancers (metastatic, refractory, relapsed, or others with predicted survival <50%) to determine clinically actionable mutations that would be of immediate benefit to the patient while also building a large dataset of childhood cancer genomes and transcriptomes to guide future study. RNA-seq at SickKids is performed using short-read sequencing; while very powerful, this technique can miss important mutations and typically has a long turnaround time. In a pilot study, we examined the feasibility of long-read nanopore RNA-seq to improve turnaround time (from biopsy to diagnosis) and detection of rare mutations and fusions compared to traditional short-read RNA-seq. Long-read RNA-seq of KiCS tumors with matched short-read RNA-seq and a pathologist-confirmed diagnosis showed high diagnostic concordance between sequencing methods using OTTER, our in-house machine-learning diagnostic classifier. Strikingly, downsampling analyses showed that only 500,000 long reads were necessary for accurate OTTER classification, corresponding to 1-2 hours of sequencing on a nanopore device compared to 24-26 hours on a short-read sequencer. Furthermore, cDNA-PCR long-read libraries require only 3 hours of preparation when starting with extracted total RNA, compared to at least 7 hours when using SickKids’ clinically validated short-read protocol, showing that same-day diagnosis is feasible when using long-read RNA-seq. Analyses are currently underway using prospectively collected samples through the KiCS program. Ultimately, long-read nanopore RNA-seq holds great promise in improving the speed and accuracy of pediatric diagnostics. Citation Format: Matt Hudson, Sandy Fong, Pedro Lemos Ballester, Resel Pereira, Srdjana Filipovic, Reem Khan, Johann Hitzler, Sarah Cohen-Gogo, Anita Villani, David Malkin, Adam Shlien. Rapid and accurate diagnosis of childhood cancers using long-read nanopore RNA sequencing [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Discovery and Innovation in Pediatric Cancer— From Biology to Breakthrough Therapies; 2025 Sep 25-28; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2025;85(18_Suppl_2): nr B002.","PeriodicalId":9441,"journal":{"name":"Cancer research","volume":"53 1","pages":""},"PeriodicalIF":11.2,"publicationDate":"2025-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145140989","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Abstract A012: THROUGH THE LENS OF TUMOR HETEROGENEITY: UNRAVELING DEVELOPMENTAL DYNAMICS AND CHEMOTHERAPY RESISTANCE IN RETINOBLASTOMA","authors":"Shannon R Sweeney, Madison Parks, Jackie Norrie, Asha Jacob Jannu, Cody Ramirez, Michael A Dyer","doi":"10.1158/1538-7445.pediatric25-a012","DOIUrl":"https://doi.org/10.1158/1538-7445.pediatric25-a012","url":null,"abstract":"Retinoblastoma is a rare and aggressive pediatric tumor of the developing retina that originates in utero following biallelic inactivation of the tumor suppressor gene RB1. The early onset and biological complexity of this disease present unique challenges for researchers and clinicians, including difficulties in diagnosis and variability in treatment outcomes. Tumor heterogeneity in retinoblastoma arises from cellular, genetic, and developmental differences. Patients with germline RB1 mutations, and to a lesser extent those without, often develop multifocal tumors, though the origins and relationships between these lesions have remained unclear. Histopathological studies suggest that retinoblastoma tumors consist of two major cellular populations resembling either photoreceptors or retinal progenitor cells. However, molecular characterization of retinoblastoma tumors has historically been limited to cases of advanced disease requiring enucleation of the eye, restricting opportunities for comprehensive research on earlier stages of tumor development. To address this challenge, retinal organoids differentiated from stem cells were used to model early developmental stages of the retina and to study tumor initiation in a controlled environment. Patient-derived xenograft models were employed to investigate tumor progression, heterogeneity, and response to treatment in advanced disease. Additionally, single-cell RNA sequencing and cellular barcoding enabled detailed analysis of the developmental trajectory and differentiation status of tumor cell populations, revealing their roles in disease initiation, progression, and therapeutic outcomes. Our study definitively demonstrates the relationship between two the major cellular populations in retinoblastoma tumors: photoreceptor-like and progenitor-like cells. We further reveal that chemotherapy preferentially targets one of these populations, challenging traditional assumptions about treatment mechanisms and highlighting the influence of development and differentiation status on therapeutic outcomes. These findings underscore the critical importance of developmental heterogeneity in retinoblastoma biology and its influence on treatment response. By redefining the interplay between tumor composition and therapeutic outcomes, our work provides a foundation for developing more precise and effective treatment strategies for this devastating childhood cancer. Citation Format: Shannon R Sweeney, Madison Parks, Jackie Norrie, Asha Jacob Jannu, Cody Ramirez, Michael A Dyer. THROUGH THE LENS OF TUMOR HETEROGENEITY: UNRAVELING DEVELOPMENTAL DYNAMICS AND CHEMOTHERAPY RESISTANCE IN RETINOBLASTOMA [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Discovery and Innovation in Pediatric Cancer— From Biology to Breakthrough Therapies; 2025 Sep 25-28; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2025;85(18_Suppl_2): nr A012.","PeriodicalId":9441,"journal":{"name":"Cancer research","volume":"17 1","pages":""},"PeriodicalIF":11.2,"publicationDate":"2025-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145140997","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Abstract B003: Characterization of CD20 transcriptional diversity using short- and long-read sequencing in pediatric acute lymphoblastic leukemia: potential implications for rituximab plus chemotherapy treatment","authors":"Maria Sol Ruiz, Lucila Viappiani, Daniel Avendaño, Ignacio Gomez Mercado, Marina L Ingravidi, Geraldine Gueron, Javier Cotignola","doi":"10.1158/1538-7445.pediatric25-b003","DOIUrl":"https://doi.org/10.1158/1538-7445.pediatric25-b003","url":null,"abstract":"Randomized trials in adult patients have shown that rituximab, a monoclonal antibody targeting CD20 (MS4A1 gene), can improve treatment response in de novo Acute Lymphoblastic Leukemia (ALL). These findings have led to clinical trials incorporating rituximab into first-line chemotherapy for pediatric patients with high- or intermediate-risk CD20+ ALL. While immunotherapy in this context might improve survival, resistance to antibody-based therapies remains a major challenge, and its interaction with chemotherapy has not been studied in large cohorts of childhood ALL (cALL). Given the potential toxicities of immunotherapies, identifying predictive markers is critical for precision medicine. We hypothesized that the expression and relative abundance of MS4A1 isoforms influence the response of leukemic cells to rituximab in combination with standard chemotherapy. To test this, we studied MS4A1 transcriptional variability at cALL diagnosis using short-read (Illumina, n=31) and long-read (Oxford Nanopore Technologies ONT, n=2) RNA-seq. We obtained bone marrow aspirates of patients enrolled in the ALLIC-GATLA 2010 clinical protocol. ONT RNA-seq was performed at the Genomics Center of Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, while Illumina RNA-seq was conducted at Macrogen, Korea. We used Salmon, FLAIR and IsoQuant to annotate and quantify known and novel MS4A1 transcripts. Our results showed high heterogeneity among patients, both in transcriptional diversity and total transcript abundance. Notably, the MS4A1-204 isoform, which lacks the rituximab-binding domain, was expressed at diagnosis in >50% of patients. Isoform quantification differed significantly between ONT and Illumina, despite similar relative sequencing coverage of exons. Illumina predicted similar proportions of isoforms 201, 212, and 206, whereas ONT predicted dominance of the 201 isoform. Nevertheless, despite ONT sequencing depth was 6 to 11-fold lower than Illumina, molecular subtype predictions were concordant between both platforms. The discovery of novel MS4A1 transcripts using FLAIR and IsoQuant in ONT-sequenced samples showed differences in transcript identities. Structural analysis of two novel isoforms suggested the coding of putative proteins lacking extracellular or transmembrane domains, which are important for rituximab binding or may interfere with protein function. In conclusion, we successfully implemented ONT transcriptome sequencing in Argentina for ALL molecular subtyping, isoform annotation, quantification and novel transcript discovery. However, we detected high variability between sequencing platforms and bioinformatic tools, highlighting the need for further studies to improve reproducibility. These results are crucial for designing prospective studies evaluating patients treated with rituximab plus chemotherapy, currently underway in a multicentric clinical trial in Argentina. Additionally, this analysis could be extended to w","PeriodicalId":9441,"journal":{"name":"Cancer research","volume":"18 1","pages":""},"PeriodicalIF":11.2,"publicationDate":"2025-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145140994","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Abstract B049: Bispecific Aptamers for Enhanced Binding, Internalization, and Therapeutic Delivery in Burkitt Lymphoma","authors":"Joshua Shelton, Xue Bai, Brian J. Thomas, Agustin T. Barcellona, Donald H. Burke, Bret D. Ulery","doi":"10.1158/1538-7445.pediatric25-b049","DOIUrl":"https://doi.org/10.1158/1538-7445.pediatric25-b049","url":null,"abstract":"Burkitt lymphoma is an aggressive cancer that accounts for 30% of all pediatric lymphomas. Due to its aggressive clinical course, patients are immediately started on a high-intensity chemo-immunotherapy protocol with central nervous system (CNS) prophylaxis to prevent relapse or CNS involvement. The Magrath regimen (CODOX-M/IVAC – cyclophosphamide, vincristine, doxorubicin, high-dose methotrexate, ifosfamide, cytarabine, etoposide, and intrathecal methotrexate) is most commonly used for medical management, yielding two-year event-free survival rates as high as 90%. However, this drug regimen consists of nonspecific, broadly toxic medications and has frequently led to off-target toxicity. To prevent these unwanted effects, it is necessary to design a more targeted therapeutic that utilizes tumor-specific markers. Burkitt lymphoma cells (Ramos) have been shown to inappropriately display a component of the spliceosomal complex (hnRNP U) on their cell surface and many human tumors have been shown to overexpress the transferrin receptor (TfR) relative to native tissues, making these exciting targets. We aimed to produce dual-targeting aptamers and to characterize their binding to, internalization by, and therapeutic deliver to Ramos cells. Anti-hnRNP U DNA aptamer (c10.36) and an anti-TfR RNA aptamer (E3) each containing a 3’-terminal 21-nucleotide antitail or tail, respectively, were synthesized and annealed together using sense:antisense complexation. For fluorescent experiments, monospecific aptamers were annealed to a cyanine 3 (Cy3)-labelled antitail and bispecific aptamers were constructed using DNA aptamers with 3’ cy3 modification. Ramos cells were treated with bispecific, monospecific, or control aptamers for 1 hour prior to flow cytometric analysis or fixation, staining, and imaging by a confocal microscope. Ramos cells treated with c10.36-E3 bispecific aptamers demonstrated 9-fold higher fluorescence by flow cytometry relative to monospecific controls. Confocal microscopy showed greater fluorescent intensity and diffuse punctate staining pattern in Ramos cells treated with c10.36-E3 bispecific aptamers relative to their monospecific controls. In Ramos cells stained with LysoTracker dye, co-localization of c10.36-E3 bispecific aptamers with lysosomes was observed whereas this was not observed with control aptamers. When Ramos cells were pre-treated with endocytic inhibitors or transferrin, internalization of c10.36-E3 was found to be reduced by treatment with sucrose, low temperature, or human transferrin. Finally, Ramos cells were treated with on- or off-target bispecific aptamers containing 3’-Val-Cit-PABA-MMAF and viability was assessed using live-dead stain HelixNP via flow cytometry. Over 48 hours, c10.36-E3 led to dramatic reductions in viability relative to appropriate control products. In conclusion, the c10.36-E3 bispecific aptamer is internalized through TfR-mediated endocytosis with superior binding and trafficking relative to con","PeriodicalId":9441,"journal":{"name":"Cancer research","volume":"19 1","pages":""},"PeriodicalIF":11.2,"publicationDate":"2025-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145140932","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}