bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 4955: An analytic pipeline of neoantigen selection for both MHC-I and MHC-II pathways
Authors: Lee Ko-Han , Sears Timothy , Castro Andrea , Zanetti Maurizio , Carter Hannah 
Published: March 2024

Abstract
Background: Accurate neoantigen selection is pivotal for assessing mutation burden and optimizing cancer vaccine formulation thereby playing a crucial role in cancer immunotherapy. The concurrent activation of CD4+ and CD8+ T cells engenders a robust immune response, which is key to effective treatment. However, currently analytic tools predominantly focus on the MHC-I pathway, typically relying on metrics such as gene expression level and MHC-binding affinity of mutated peptides. To address this gap, our study presents a comprehensive pipeline that encompasses both MHC-I and MHC-II pathways and integrates three critical dimensions of immune response: neoantigen abundance, presentation, and immunogenicity.
Methods: We estimated mutated peptide abundance by analyzing genomic allelic frequency, transcriptomic allelic frequency, and RNA expression level. Antigen presentation was assessed using the patient harmonic binding rank (PHBR, a composite binding score for all potential MHC-peptide pairs) and MHC diversity (the variety of MHC alleles involved in peptide binding), with additional consideration for the loss of heterozygosity of MHC-I alleles, potentially indicative of immune escape. For immunogenicity, we factored in agretopicity (comparison of MHC-binding affinity between mutated and wild-type peptides), foreignness (similarity to immunogenic foreign antigens), and dissimilarity (sequence disparity with self-peptides, reflecting T cell negative selection process).
Results: Implementing our pipeline on a dataset from Parkhurst et al. (2019), we analyzed immune reactivity in relation to 11,537 somatic mutations from 75 gastrointestinal cancer patients. Key metrics—RNA expression, transcriptomic allelic frequencies, PHBR, and MHC diversity—demonstrated significant correlations with both CD4+ and CD8+ activity (p&lt;0.05). Notably, genomic allelic frequency was a significant factor in CD8+ reactivity, whereas agretopicity was crucial for CD4+ reactivity.
Conclusion: Our pipeline elucidates the necessity for implementing both MHC-I and MHC-II pathway analyses to effectively select neoantigen candidates for CD8+ and CD4+ T cells respectively. The study confirms that abundance and antigen presentation metrics are robust indicators of neoantigen immunogenicity, supporting their use as potential markers in crafting more effective cancer vaccines. The findings highlight the critical role of this dual-pathway selection approach in generating a comprehensive immune response through neoantigen vaccination.
Citation Format: Ko-Han Lee, Timothy Sears, Andrea Castro, Maurizio Zanetti, Hannah Carter. An analytic pipeline of neoantigen selection for both MHC-I and MHC-II pathways [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 4955.
Abstract 4991: Radiotherapy-induced immunological and therapeutic response depends on stem-like TCF-1+PD-1+CD8+ T-cells
Authors: Köksal Hakan , Herbst Michael , Marti Nicola , Broek Maries van den 
Published: March 2024

Abstract
Radiotherapy is a frequently used treatment for cancer. Recent data, including ours, showed that radiotherapy promotes an inflammatory response in the tumor that supports tumor-specific immunity, and in fact, the efficacy of radiotherapy in pre-clinical models depends on CD8+ T-cells. According to our preliminary data, the response to radiotherapy is independent of de novo recruited CD8+ T-cells, suggesting that radiation drives differentiation and proliferation of preexisting intratumoral CD8+ T-cells. Intratumoral CD8+ T-cells are heterogeneous concerning phenotype and function. Under conditions of chronic stimulation by antigen, a subset of CD8+ T-cells expressing PD-1 and the transcription factor TCF-1 was described. These so-called stem-like CD8+ T-cells, which give rise to effector cells, were shown to be essential for the clinical response to PD-1 blockade. How radiotherapy influences the different CD8+ T-cell subsets in the tumor microenvironment has not been comprehensively investigated. We propose that the efficacy of radiotherapy depends on the presence of stem-like CD8+ T-cells, presumably by giving rise to effector cells. To address this, we selectively depleted TCF-1+ cells from tumor-bearing mice immediately before radiotherapy. Subsequently, we correlated tumor regression with the immunological response using single-cell analyses of intratumoral CD8+ T-cells. In the absence of TCF-1+ cells, we found a reduced efficacy and reduced number of intratumoral effector cells after radiotherapy. We currently analyze our single-cell RNA-sequencing data and expect to discover novel radiotherapy-induced pathways in CD8+ T-cells that contribute to therapeutic efficacy.
Citation Format: Hakan Köksal, Michael Herbst, Nicola Marti, Maries van den Broek. Radiotherapy-induced immunological and therapeutic response depends on stem-like TCF-1+PD-1+CD8+ T-cells [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 4991.
Abstract 4998: Pralsetinib induces opportunistic infection in RET fusion-positive NSCLC patients via inhibition of IL-2 production by blocking Jak3-Stat5 activation
Authors: Yoon Shinkyo , Ryu Hyun-Min , Kim Sang-We , Park Kang-Seo , Lee Dae Ho 
Published: March 2024

Abstract
Background: Oncogenic alteration in RET, representing 1-2% of non-small cell lung cancer (NSCLC), is one of the important targets. Pralsetinib is a selective RET inhibitor that targets RET fusions. We present a case series on opportunistic infections and the mechanism of immunosuppression.
Methods: From October 2021 to March 2022, we administered pralsetinib to a total of 15 patients with NSCLC harboring RET fusion. We retrospectively analyzed the clinical efficacy and adverse event related to pralsetinib. To investigate the potential impact of pralsetinib on T-cells, we examined cytokine release from Jurkat T (JT) cells after pralsetinib treatment. To test if Stat5 bind to IL-2 promotor, we conducted Chromatin Immunoprecipitation (ChIP).
Results: Out of a total of 18 patients with measurable disease, 14 patients (93%) achieved a partial response. With the median follow-up duration of 8.7 months, four cases of opportunistic infections were occurred. Notably, three patients (16.6%) experienced invasive pulmonary aspergillosis, and one patient (5.5%) experienced cytomegalovirus pneumonia. To mimic conditions akin to activated T cells, we treated JT cells with PMA and ionomycin, inducing IL-2 release through the binding of NFAT, AP-1, and NF-κB to the IL-2 promoter. Following approximately two weeks of pralsetinib treatment, a decrease of IL-2 releases, the inhibition of Jak3 and the reduced-expression of JunB and c-Jun was observed. Additionally, to investigate the direct correlation between Jak3 and IL-2 release, JT cells were treated with ritlecitinib, the Jak3-selective inhibitor, for approximately two weeks. Like pralsetinib, a reduction in IL-2 release was observed. Furthermore, based on the evidence that Stat5 inhibition leads to reduced IL-2 release, we also showed that the transcription factor Stat5, a direct downstream signaling component of Jak3, binds to the IL-2 promoter during the activation of Jurkat T cells.
Conclusion: Pralsetinib inhibits additional IL-2 production by blocking Jak3/Stat5 activation triggered by IL-2 released during early T cell activation. As a result, the Jak3 inhibition induced by pralsetinib leads to a decrease in JunB/c-Jun expression and blocking Stat5 activation by reducing IL-2 release. Consequently, Pralsetinib-related opportunistic infections may be caused by inhibition of the JAK3 pathway and IL-2 release.
Citation Format: Shinkyo Yoon, Hyun-Min Ryu, Sang-We Kim, Kang-Seo Park, Dae Ho Lee. Pralsetinib induces opportunistic infection in RET fusion-positive NSCLC patients via inhibition of IL-2 production by blocking Jak3-Stat5 activation [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 4998.
Abstract 5039: Preanalytical workflow enabling cfDNA analysis from urine samples
Authors: Mancarella Daniela , Rutsch Julia , Erkelenz Lisa , Meyer Moritz , Witthaus Laura Sofie , Rath Moritz , Voss Thorsten 
Published: March 2024

Abstract
Introduction: Urine has become an important source of information in the liquid biopsy field. In contrast to blood, specifications for the collection, storage, transport and processing of urine intended for molecular examination are not widely established. Preanalytical specifications were published for urine cell-free DNA (cfDNA) only recently (CEN/TS 17811:2022). In this study, we investigated post-collection changes to cfDNA profiles in urine samples and present the performance of an optimized preanalytical workflow for cfDNA analysis.
Methods: Urine from apparently healthy, consented female individuals was spiked with processed cell-free male urine or with a cfDNA standard containing PIK3CA mutations (SensID). The urine was stabilized with a urine collection/stabilization solution under development at PreAnalytiX or was left unstabilized. Urine samples were stored for varying durations at different temperatures in a time course experiment to simulate different urine storage conditions. After storage, urine samples were centrifuged to remove cells and cfDNA was isolated from the supernatant via the QIAsymphony® platform (QIAGEN). Autosomal and male-specific targets were quantified using the Rotor-Gene® Q instrument and the therascreen® PIK3CA qPCR Kit (both QIAGEN) or the QIAcuity® Digital PCR System and a dPCR LNA PIK3CA Mutation Assay (both QIAGEN). Fragment size distribution was determined by TapeStation® Cell-free DNA ScreenTape® (Agilent Technologies).
Results: Analysis of cfDNA profiles in unstabilized urine stored for varying durations and temperatures highlighted changes which create artificial cfDNA profiles. The yield of cfDNA drastically decreased over time. Furthermore, the size distribution of cfDNA isolated from unstabilized urine was impacted by release of gDNA as well as DNA degradation. Urine stabilization minimized cfDNA degradation and gDNA release and allowed isolation of cfDNA that was analyzed with qPCR and dPCR even after urine storage. Analysis of isolated cfDNA revealed positive detection of PIK3CA mutations in spiked urine samples.
Conclusions: Changes in post-collection cfDNA profile can hinder downstream analysis, resulting in artificial or failed outcomes. Urine stabilization with a collection/stabilization solution under development at PreAnalytiX minimized DNA degradation and gDNA release. It enabled urine storage, allowed analysis of urine cfDNA and target detection by qPCR and dPCR.
Citation Format: Daniela Mancarella, Julia Rutsch, Lisa Erkelenz, Moritz Meyer, Laura Sofie Witthaus, Moritz Rath, Thorsten Voss. Preanalytical workflow enabling cfDNA analysis from urine samples [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 5039.
Abstract 5048: NF2 mutations are enriched in FH deficient renal cell cancer
Authors: Satter Khaled Bin , Xi Liqian , Rickets Christopher , Linehan William M. , Merino Maria J. 
Published: March 2024

Abstract
Introduction: NF2 is a tumor suppressor gene in charge of producing a protein called Merlin that controls cell growth and division. Mutations in the NF2 gene affect predominantly the nervous system causing the development of benign tumors. NF2 mutations have been reported in Renal cancers with morphologically specific tumor types and in aggressive tumors. We studied a cohort of 16 cases of RCC in which the NF2 mutation was identified and describe other molecular changes as well as morphology and clinic-pathological correlation.
Materials and Methods: Sixteen patients had been consented and treated for renal masses in protocols of the UOB division of the NCI. Next generation sequencing was performed with tumor DNA from FFPE tissue using the Illumina TruSight Oncology 500 Kit (TSO500) NextSeq 550DX. TSO500 assay was designed to detect single nucleotide variations, small insertions/deletions, copy number variations from 92 genes, TMB and MSI. Morphology and IHC stains were performed.
Results: Nine patients were female and 7 males, ranging in age from 21 to 87 years. Fourteen patients underwent partial or total nephrectomies, one case had a biopsy and in 1 case a metastatic tumor to a lymph node was studied. Morphologically, nine cases were diagnosed as HLRCC, three clear cells, two cases with clear and papillary cell, one medullary and one oncocytoma. Genetic findings revealed mutations in NF2, FH,VHL, SMARCB1, HOBB13, ARID1B, B2M, EP300, BCORL1 and MGA. Concurrent coexistence of NF2 and FH mutations was present in 9 cases. Three patients with concurrent FH and NF2 mutations died of the disease.
Conclusions: NF2 mutations have been identified in a variety of morphologic types of Renal cell cancer. However, we were surprised by the number of cases with NF2 mutation in tumors that also harbor the FH (HLRCC) mutation. NF2 tumors have been reported to have an aggressive behavior, and FH cancers are also known to have poor survival. Genomic studies of renal cancers is recommended since some genetic alterations are targetable and may provide adequate therapies that will lead to longer survivals.
Citation Format: Khaled Bin Satter, Liqian Xi, Christopher Rickets, William M. Linehan, Maria J. Merino. NF2 mutations are enriched in FH deficient renal cell cancer [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 5048.
Abstract 5108: Immunomodulatory and anti-tumor effect of radiation and induced telomere damage to treat pediatric high-grade gliomas
Authors: Banlanjo Umaru , Kumar Shiva Senthil , Gryaznov Sergei , Drissi Rachid 
Published: March 2024

Abstract
Pediatric high-grade gliomas (pHGGs), including diffuse intrinsic pontine glioma (DIPG) are among the most treatment refractory cancers in children. Despite multimodal therapy, prognosis is dismal with survival of &lt;1 year for DIPG and a 5-year overall survival &lt;10% for other pHGGs. Radiotherapy remains the only standard of care for DIPG that extends the survival by few months. In recent years, immunotherapy is emerging as a potential alternative treatment option. However, several factors have hindered the use of immunotherapy for pHGGs including “cold” immune environment with lack of immune cells infiltration, low tumor mutational burden, and lack of neo-antigen expression that prevents tumor recognition by the immune system. Therefore, novel therapies that activate the immune system while evading the tumor immunosuppression are highly needed. Here, we aim to demonstrate the immunomodulatory anti-tumor effects of THIO (6-thio-2’deoxyguanosine), a nucleoside analog and a telomerase-dependent telomere targeting agent, in DIPG mouse models. Our preclinical in vitro and in vivo data have demonstrated the efficacy of THIO in inducing telomeric damage, G2/M cell cycle arrest, and apoptosis in high-risk medulloblastoma and DIPG. Importantly, we have demonstrated that THIO crosses the blood-brain barrier and specifically targets tumor cells in an orthotopic mouse model of DIPG. THIO was shown to induce anti-tumor immunity through micronuclei formation leading to cGAS-STING pathway mediated activation of the innate and adaptive immune response in colon, lung, and hepatocellular carcinoma tumor models. Our preliminary data demonstrate the THIO-dependent induction of micronuclei formation co-localizing with cGAS and leading to STAT1 activation in DIPG cell lines. We have also shown that THIO synergistically sensitizes DIPG cells to ionizing radiation (IR), significantly decreasing cell proliferation. We are currently testing the combination of THIO+IR in an orthotopic mouse model for DIPG. We will present results on the potential of THIO and IR treatments to stimulate anti-tumor immunity through the activation of STING pathway in a syngeneic mouse model of DIPG. These preclinical studies will support the potential use of THIO and IR to treat children with high-risk pediatric brain tumors.
Citation Format: Umaru Banlanjo, Shiva Senthil Kumar, Sergei Gryaznov, Rachid Drissi. Immunomodulatory and anti-tumor effect of radiation and induced telomere damage to treat pediatric high-grade gliomas [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 5108.
Abstract 512: Cell-cycle inhibition may influence differences in 2D vs 3D tumor sensitivity profiles
Authors: Kumar Jahanvi , Maestri Chiara , Nitiyanandan Rajeshwar , Trus Ivan , Parker Ricardo J. , Apfel Brigitte , Apfel Christian 
Published: March 2024

Abstract
Background: Traditional cell culture methods involve growing cells on flat surfaces, which do not fully replicate the human physiological conditions. In contrast, 3D cell cultures accurately reproduce aspects of the in-vitro malignant and non-malignant cell behavior. However, differences in tumor sensitivity platforms between 2D vs. 3D models might be relevant for some, but not for other drugs.
Methods: The colorectal cancer cell line HCT-116 was cultured and plated in flat bottom well plates for the 2D condition and in Ultra Low Attachment round-bottom plates for the 3D condition. After plating, cells were treated with chemotherapies and targeted therapies for four days; cellular sensitivity was assessed through a viability assay. Four-parameter logistic (4PL) dose response curves were generated and IC50s were quantified to understand the differences in responses between 2D and 3D cellular environments.
Results: HCT-116 exhibited similar responses to platinum drugs, taxanes, and several other tested drugs in both platforms, with the exception of gemcitabine (2D IC50 0.04 mcM; 3D IC50 12.8 mcM), lapatinib (2D IC50 23; 3D IC50 418), tucatinib (2D IC50 23.3; 3D IC50 79.3), and palbociclib (2D IC50 7.0; 3D IC50 24.0). Interestingly, these drugs share a common mechanism of action, which is the inhibition of cell cycle progression from G1 to S phase. Hence, we hypothesize that this shared mechanism may account for the observed differences in drug efficacy between the two environments.
Conclusions: Similar dose responses have been observed with various drugs on both platforms, yet drugs that inhibit cell cycle progression from G1 to S phase, revealed higher sensitivity in 2D and more resistance in the 3D platform. Confirmatory cell-cycle results analyses are in progress. Further research is needed to understand if this applies to patient samples.
Citation Format: Jahanvi Kumar, Chiara Maestri, Rajeshwar Nitiyanandan, Ivan Trus, Ricardo J. Parker, Brigitte Apfel, Christian Apfel. Cell-cycle inhibition may influence differences in 2D vs 3D tumor sensitivity profiles [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 512.
Abstract 515: Endocycling cancer cells undergo multiple S phases while repressing myc activity
Authors: Loycano Michael A. , Pienta Kenneth J. , Amend Sarah R. 
Published: March 2024

Abstract
Chemotherapy resistance remains a major challenge when treating patients with metastatic cancer. While intrinsic resistance to therapy has been well studied, phenotypic plasticity that drives entry and exit of resistant cell states is poorly understood. One of these plastic cell states used by cancer cells under chemotherapy treatment is characterized by the reprogramming of the mitotic cell cycle to enter a non-proliferative endocycle. Cells in this endocycling state decouple DNA synthesis from cell division by actively progressing through G1, S, and G2 phases of the cell cycle while repeatedly skipping mitosis. After a dormant period, cells can switch back to a mitotic cell cycle to repopulate a tumor. The underlying mechanisms that drive this cell cycle reprogramming remain unknown. C-myc is an oncogenic transcription factor that is dysregulated in ~70% of human cancers. C-myc is responsible for the activation of several cell cycle drivers, including cyclins and CDKs, and represses cell cycle inhibitors, such as CDK inhibitors. High levels of myc activity allow cells to move through the cell cycle quickly with a rapid doubling time. Documented endocycles in polyploid cells rely on high c-myc activity; however, our data shows that endocycling cancer cells have repressed levels of c-myc protein and transcriptional activity. Transcriptomic data shows that myc target genes are expressed at very low levels compared to the mitotic parental cells, and complementary data shows low protein levels. While myc downregulation is expected in non-proliferative cells, the compensatory mechanisms mediating the G1/S transition in the cancer endocycle remain unknown. Recent data has shown that myc suppression alone is not sufficient to induce a sustained endocycle at a population level, despite premature APCCdh1 activation during G2 in a subset of cells. We hypothesize that restoring myc activity to the levels of mitotic parental cells will drive endocycling cells to resume a proliferative mitotic cell cycle and produce mitotic progeny cells. Understanding the mechanisms that govern this transition is crucial to generate next-generation cancer therapeutics to disrupt endocycling cells, blocking acquired resistance and disease recurrence.
Citation Format: Michael A. Loycano, Kenneth J. Pienta, Sarah R. Amend. Endocycling cancer cells undergo multiple S phases while repressing myc activity [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 515.