tbuckley/cabot-search huggingface dataset:
Abstract 5890: ZNF451 and doxorubicin resistance
Authors: Amy Rees, Alexandra Blackman, Della Evans, Joe Delaney
Journal: Cancer Research (2024)

Abstract Precision medicine most often utilizes mutations in patient selection, however targetable mutations are exceedingly rare in high-grade serous ovarian cancer (OV). Aneuploidy and chromosome instability are major contributors to such genomic changes in OV. Genes are pervasively disrupted by copy-number alterations: 39% of all genes in the median solid tumor of all cancer types, and 67% in OV. A common second-line OV chemotherapeutic is peggylated-liposomal doxorubicin, a topoisomerase-II poison. To address which genes in OV contribute to doxorubicin sensitivity and resistance, we performed a CRISPR-Cas9 screen on 19,114 human genes in the presence or absence of doxorubicin. Positive control genes involved in drug-efflux and DNA repair were significant hits. The gene with both the highest significance and greatest magnitude of doxorubicin sensitization upon knockout was the E3 SUMO2/3 ligase ZNF451. ZNF451 exhibits a copy-number loss in 14% of patients and corresponds to ZNF451 protein reduction. ZNF451 is an attractive target for future combination therapies with doxorubicin to induce conditional lethality. ZNF451 may be valuable to study as a prognostic biomarker for topoisomerase-II inhibitor chemotherapy. Citation Format: Amy Rees, Alexandra Blackman, Della Evans, Joe Delaney. ZNF451 and doxorubicin resistance [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 5890.
Abstract 5894: Novel splicing-derived neoantigen in triple negative breast cancer uncovered by SpliceIO™ a robust platform for the discovery and validation of disease-specific immunotherapies
Authors: Nicole Williams, Miguel A. Manzanares, Kendall Anderson, Hasan Zunrut, Sakshi Gera, Nayab Habib, Shaleigh Stanton, Taylor Floyd, Sanjana Shah, Devon Trahan, Martin Akerman, Gayatri Arun
Journal: Cancer Research (2024)

Abstract Splicing dysregulation is a major hallmark of cancer, affecting tumor progression, metastasis, and therapy resistance. Aberrant alternative splicing (AS) plays a critical role in generating tumor-specific neoantigens targetable through an arsenal of immunotherapeutic modalities. Such neoantigens cannot be discovered using conventional DNA-based tools; they require specialized software for AS analysis using RNA-seq data. SpliceIO is Envisagenics’ AI platform for AS-derived neoantigen discovery. SpliceIO uses a “predictive ensemble” approach to uncover neoantigens that are both stably expressed and located on the extracellular membrane of cancer cells. Using SpliceIO, we have analyzed more than 10,000 RNA-seq samples from 5 patient cohorts covering 5 breast cancer subtypes as well as 2,647 normal RNA-seq samples from GTEx. Our analysis has identified tumor-specific neoantigens present in AS transmembrane proteins specific for Triple Negative Breast Cancer. SpliceIO target candidates were validated experimentally using our well-established pipeline in which isoform specific transcripts are tested in cancer cell lines by PCR and primary tumor tissues by qPCR to confirm RNA expression. Tumor heterogeneity and prevalence is confirmed by RNA in-situ hybridization in Tissue Microarrays. Extracellular localization of the novel epitope is confirmed by clone generation with GFP and c-Myc tagging followed by microscopy, Western blotting, and proteomic analysis. Our top validated target presents high TNBC tumor specificity and heterogeneous distribution, and contains a novel extracellular N-terminal domain. These results strongly support the role of aberrant AS as a major source of tumor-specific neoantigens. Our combined computational and experimental approach promotes novel target discovery, enabling the development of novel immunotherapeutic for TNBC patients who are in critical need of better treatment options. Citation Format: Nicole Williams, Miguel A. Manzanares, Kendall Anderson, Hasan Zunrut, Sakshi Gera, Nayab Habib, Shaleigh Stanton, Taylor Floyd, Sanjana Shah, Devon Trahan, Martin Akerman, Gayatri Arun. Novel splicing-derived neoantigen in triple negative breast cancer uncovered by SpliceIO™ a robust platform for the discovery and validation of disease-specific immunotherapies [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 5894.
Abstract 184: M1-like macrophage infiltration, CD8+ T cell activation, and increased cancer cell apoptosis in immunologically cold Lewis lung carcinoma treated with tumor-trophic Salmonella Typhimurium expressing anticancer proteins in immunocompetent C57BL/6 mice
Authors: Qiuhong He, Lindsay R. Brncick, Boxi Gong, Julia L. Flowers
Journal: Cancer Research (2024)

Abstract Immunotherapy has revolutionized cancer treatment with Immune checkpoint inhibitors (ICIs) and genetically engineered T-Cells expressing chimeric antigen receptors (CARs). CAR-T treatment of hematologic malignancies has achieved outstanding patient response rate. CAR T therapy, however, is thwarted in solid tumor treatment due to two major factors: the immune-suppressive tumor microenvironment that Inhibits T-cell infiltration and T-cell function. In addition, cancer resistance to ICIs treatment also limits the solid tumor response rate. This research aims to activate proinflammatory anticancer immune responses in immunologically cold solid tumors using the genetically engineered Salmonella typhimurium VNP20009 strains that express anticancer proteins. Previously, we have shown that the Salmonella Typhimurium VNP20009 strain expressing methioninase (METase) and/or Tumor Necrosis Factor (TNFα) caused rapid tumor destruction of cold Lewis Lung Carcinoma (LLC) grown on immunocompetent C57BL/6 mice. In this investigation, several mechanisms of this tumor tropic anti-cancer bacteria were studied including the innate and adaptive immune system responses and cancer cell apoptosis. In a pilot study, we selected eight tumor tissues treated with several different bacteria strains and performed histological analysis to observe the effectiveness of each. We found that in the tumor tissues treated with VNP20009_rMETase_TNFα, there was infiltration and activation of CD8+ T cells coupled with reduced amounts of T regulatory cells, as well as an increased ratio of M1-like to M2-like macrophages. We also observed increased tumor apoptosis associated with an elevated detection of an apoptosis biomarker and a suppressed amount of the Ki67 tumor growth signal. These findings indicate that VNP20009_rMETase_TNFα anticancer bacteria can disrupt the tumor microenvironment in the cold LLC tumors and active innate and adaptive anti-cancer immune response in immunocompetent mice. Further, we are investigating additional cold solid mouse tumor models to validate our findings and how this can apply to bacteria-based immunotherapy. Citation Format: Qiuhong He, Lindsay R. Brncick, Boxi Gong, Julia L. Flowers. M1-like macrophage infiltration, CD8+ T cell activation, and increased cancer cell apoptosis in immunologically cold Lewis lung carcinoma treated with tumor-trophic Salmonella Typhimurium expressing anticancer proteins in immunocompetent C57BL/6 mice [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 184.
Abstract 6458: Clinical significance of cancer genome profiling tests for gastrointestinal cancer patients with liver metastasis
Authors: Takashi Sakuma, Masakazu Yashiro, Yasuhiro Fukui, Koji Maruo, Gen Tsujio, Yurie Yamamoto, Hiroaki Kasashima, Kiyoshi Maeda
Journal: Cancer Research (2024)

Abstract Introduction: Distant metastasis is one of critical prognostic factors for patients with gastrointestinal cancer. Especially, liver metastasis shows high effects on prognosis of patients with gastrointestinal cancer. In Japan, cancer genome profiling (CGP) testing have been available for patients who have no selective standard treatment options since 2019. Based on the genetic mutations by CGP test, therapeutic drugs with evidence have been discussed at expert panels. CGP data has been accumulated in around 60,000 cases. It is necessary to evaluate the clinical significance of CGP tests for gastrointestinal cancer patients with liver metastasis to receive high benefits of CGP testing through C-CAT. Aims: We aimed to analyze the clinical significance CGP tests for gastrointestinal cancer patients with liver metastasis. Materials and methods: A total of 3,738 patients of gastrointestinal cancer with liver metastases including 215 cases of esophageal cancer, 347 cases of gastric cancer, and 3,176 cases of colorectal cancer, was enrolled in this study. Three types of CGP tests, including NCC Oncopanel, FoundationOne CDx, and FoundationOne Liquid, were performed, and the CGP data was collected to Center for Cancer Genomics and Advanced Therapeutics in Japan (C-CAT) database. Adequate treatment for each patient was discussed at the expert panel meeting according to the results from the CGP tests. Results: A total of 2,882 cases (77.1%) in 3,176 cases have been revealed druggable. However, only 216 cases (13.3%) were medicated by anti-cancer treatments. In the 216 treated cases, disease control case, complete response (CR), partial response (PR), or stable disease (SD) was only 52 cases. In 52 cases, six cases (4 of SD cases and 2 of PR cases) was administered encorafenib-based chemotherapies based on BRAF gene mutation. Five genes, ZNF217, SRC, ARFRP1, BARD1, FGF10, were significantly more frequently expressed on liver metastasis cases, in compared to other metastasis cases in gastrointestinal cancer. Conclusion: Around 13% of gastrointestinal cancer patients with liver metastasis might have a druggable benefit by CGP testing. BRAF mutation might be promising target for patients with liver metastasis. ZNF217, SRC, ARFRP1, BARD1, FGF10 might be associated with metastatic process to liver in gastrointestinal cancer. Citation Format: Takashi Sakuma, Masakazu Yashiro, Yasuhiro Fukui, Koji Maruo, Gen Tsujio, Yurie Yamamoto, Hiroaki Kasashima, Kiyoshi Maeda. Clinical significance of cancer genome profiling tests for gastrointestinal cancer patients with liver metastasis [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 6458.
Abstract 649: SOX11 regulates BCR signaling via the PAX5/CD19 axis in MCL
Authors: Rudra Prasad Dutta, Heng-Huan Lee, Violetta V Leshchenko, Ravi Prakash Shukla, Yang Liu, Jian Jin, Michael Wang, Samir Parekh
Journal: Cancer Research (2024)

Abstract Background: Mantle cell lymphoma (MCL) is an incurable lymphoid neoplasm, comprising about 6% of all non-Hodgkin lymphoma (NHL). The transcription factor SOX11 is overexpressed in the majority of MCL patients and linked to a more aggressive disease course and poorer clinical outcomes. In MCL, naïve B cells experience continuous proliferation because of the dysregulation of the B-cell receptor (BCR) pathway. Our previously published data (Kuo et. al., Blood 2018) identified that SOX11 aberrantly upregulated BCR signaling in transgenic mouse models. The current study describes the exact mechanism by which SOX11 regulates the BCR pathway using a combination of functional and pharmacological approaches. Methods: To investigate the alterations in signaling pathways regulated by SOX11, we utilized a small molecule SOX11 inhibitor (Jatiani et. al., CCR 2021), performed CRISPR/CAS9 knockout of SOX11, 3X FLAG TAG overexpression, as well as conducted western blot and flow-cytometry experiments. Results: Our prior published results (Kuo et. al., Oncogene 2015), as well as others (Vegliante et. al., Blood 2013), have shown that PAX5 is a direct target of SOX11. We confirmed PAX5 downregulation after SOX11 depletion in three human MCL cell lines (JEKO, MINO, Z138) using CRISPR-CAS9. Decrease of PAX5 expression was associated with reduction in CD19 expression and a concurrent reduction in phospho-BTK (Bruton tyrosine kinase). Conversely, overexpression of SOX11 could rescue PAX5/CD19 expression and restore p-BTK levels. Furthermore, the treatment of SOX11 expressing cells with small molecule SOX11-specific inhibitors resulted in a reduction in PAX5, CD19 and BCR activation (p-BTK). Conclusion: Taken together, these findings delineate PAX5 as the direct target and PAX5/CD19 axis as the downstream pathway by which SOX11 regulates B-cell receptor (BCR) signaling in MCL. Notably, our treatment using a SOX11 inhibitor successfully replicated the effects observed with genetic knockdown. In conclusion, our findings provide valuable insights into the molecular mechanisms by which SOX11 contributes to MCL pathogenesis. The further development of pharmacological inhibitors targeting SOX11 holds promise as a beneficial therapeutic strategy for MCL patients, as these will block signaling upstream of current resistance mechanisms. Citation Format: Rudra Prasad Dutta, Heng-Huan Lee, Violetta V Leshchenko, Ravi Prakash Shukla, Yang Liu, Jian Jin, Michael Wang, Samir Parekh. SOX11 regulates BCR signaling via the PAX5/CD19 axis in MCL [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 649.
Abstract 3660: Plasma cell free DNA hydroxymethylation profiling reveals anti-PD1 treatment response and resistance biology in non-small cell lung cancer
Authors: Gulfem D. Guler, Yuhong Ning, Ceyda Coruh, Tierney Phillips, Maryam Nabiyouni, Kyle Hazen, Aaron Scott, Wayne Volkmuth, Samuel Levy
Journal: Cancer Research (2024)

Abstract Background: Treatment with immune checkpoint inhibitors (ICIs) targeting programmed death-1 (PD-1) can yield durable anti-tumor responses, yet not all patients respond to ICIs. Current approaches to select patients who may benefit from anti-PD-1 treatment are insufficient. 5-hydroxymethylation (5hmC) analysis of plasma-derived cell free DNA (cfDNA) presents a novel non-invasive approach for identification of therapy response biomarkers which can tackle challenges associated with tumor biopsies such as tumor heterogeneity and serial sample collection. Methods: 151 blood samples were collected from 31 non-small cell lung cancer (NSCLC) patients before therapy start and at multiple timepoints whilst on therapy. Blood samples were processed to obtain plasma-derived cfDNA, followed by enrichment of 5hmC-containing cfDNA fragments through biotinylation via a two-step chemistry and binding to streptavidin coated beads. 5hmC-enriched cfDNA and whole genome libraries were prepared in parallel and sequenced to obtain whole hydroxymethylome and whole genome plasma profiles, respectively. Results: Comparison of on-treatment timepoint to matched pre-treatment samples from same patients revealed that anti-PD-1 treatment induced distinct changes in plasma cfDNA 5hmC profiles of responders, as judged by RECIST, relative to non-responders. In responders, 5hmC accumulated over genes involved in immune activation such as IFNγ and IFNα response, inflammatory response, and TNFα signaling, whereas in non-responders 5hmC increased over epithelial to mesenchymal transition genes. The Molecular Response to anti-PD-1 treatment, as measured by 5hmC changes in plasma cfDNA profiles were observed early, starting with the first cycle of treatment. Comparison of pre-treatment plasma samples revealed that anti-PD-1 treatment response- and resistance-associated genes can be captured by 5hmC profiling of plasma-derived cfDNA. Conclusions: These results demonstrate that 5hmC profiling can identify response and resistance associated biological pathways in plasma samples, offering a novel method for non-invasive prediction and monitoring of immunotherapy response in NSCLC. Citation Format: Gulfem D. Guler, Yuhong Ning, Ceyda Coruh, Tierney Phillips, Maryam Nabiyouni, Kyle Hazen, Aaron Scott, Wayne Volkmuth, Samuel Levy. Plasma cell free DNA hydroxymethylation profiling reveals anti-PD1 treatment response and resistance biology in non-small cell lung 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 3660.
Abstract 50: ALK inhibitors increase ALK expression and sensitize neuroblastoma cells to ALK.CAR-T cells
Authors: Elisa Bergaggio, Wei-Tien Tai, Andrea Aroldi, Carmen Mecca, Elisa Landoni, Manuel Nüesch, Ines Mota, Jasna Metovic, Luca Molinaro, Leyuan Ma, Diego Alvarado, Chiara Ambrogio, Claudia Voena, Rafael B. Blasco, Tongqing Li, Daryl Klein, Darrell J. Irvine, Mauro Papotti, Barbara Savolodo, Gianpietro Dotti, Roberto Chiarle
Journal: Cancer Research (2024)

Abstract Neuroblastoma is the most common extracranial solid tumor of childhood, with limited success in treating refractory or relapsed cases using current therapies. Chimeric antigen receptor (CAR) T cell therapy targeting GD2 has shown promise in neuroblastoma treatment, but relapses are associated with loss of antigen expression. The selection of the best tumor antigen is critical for the therapeutic success of CAR-T cells in hematologic malignancies and solid tumors. The Anaplastic Lymphoma Kinase (ALK) receptor is expressed by most neuroblastomas while virtually absent in most normal tissues. ALK is an oncogenic driver in neuroblastoma and ALK inhibitors show promising clinical activity. All these features make ALK an attractive target for CAR-T cell therapy. We developed ALK.CAR-T cells that show potent efficacy in monotherapy against neuroblastoma with high ALK expression without toxicity. For neuroblastoma with low ALK expression, combination with ALK inhibitors specifically potentiates ALK.CAR-T cells but not GD2.CAR-T cells. In neuroblastoma cell lines and in a patient-derived xenograft (PDX), the combination of ALK inhibitors and ALK.CAR-T cells significantly reduced tumor growth and extended mice survival. Mechanistically, ALK inhibitors impair tumor growth and upregulate the expression of ALK, thereby facilitating the activity of ALK.CAR-T cells against neuroblastoma. Thus, while neither ALK inhibitors nor ALK.CAR-T cells will likely be sufficient as monotherapy in neuroblastoma with low ALK density, their combination specifically enhances therapeutic efficacy. These findings provide insights into the potential of ALK.CAR-T cells as a novel therapeutic strategy for neuroblastoma. A Phase I clinical trial to test ALK.CAR-T cells in combination with ALK TKIs in children with refractory/relapsed neuroblastoma is being implemented based on these results. Citation Format: Elisa Bergaggio, Wei-Tien Tai, Andrea Aroldi, Carmen Mecca, Elisa Landoni, Manuel Nüesch, Ines Mota, Jasna Metovic, Luca Molinaro, Leyuan Ma, Diego Alvarado, Chiara Ambrogio, Claudia Voena, Rafael B. Blasco, Tongqing Li, Daryl Klein, Darrell J. Irvine, Mauro Papotti, Barbara Savolodo, Gianpietro Dotti, Roberto Chiarle. ALK inhibitors increase ALK expression and sensitize neuroblastoma cells to ALK.CAR-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 50.
Abstract 4611: The co-targeting of PLK1 and FoxM1 contributes to synergistic antitumor effects in PTC
Authors: Pratheeshkumar Poyil, Abdul K. Siraj, Divya Padmaja, Sandeep Kumar Parvathareddy, Saravanan Thangavel, Saif S. Al-Sobhi, Fouad Al-Dayel, Khawla S. Al-Kuraya
Journal: Cancer Research (2024)

Abstract Polo-like Kinase 1 (PLK1) plays a key role in cell proliferation with vital regulatory functions in mitosis and cell survival. We investigated the expression of PLK1 protein in a large cohort of PTC patient’s samples and explored its functional role in PTC cell lines in vitro and in vivo. PLK1 overexpression was observed in 54% of all PTC and was significantly associated with aggressive clinico-pathological parameter and it was found to be independent prognostic marker for recurrence-free survival. PLK1 inhibition indeed inhibited cell proliferation and induced cell cycle arrest and apoptosis in PTC cell lines. Importantly, silencing of PLK1 decreases the self-renewal ability of spheroids generated from PTC cells. Immunoprecipitation analysis shows that PLK1 binds to FoxM1 and vice versa in vitro. Mechanistically, PLK1 knockdown suppresses FoxM1 expression, whereas inhibition of FoxM1 does not affect PLK1 expression, which suggests that PLK1 acts through the FoxM1 pathway. The combined inhibition of PLK1 with volasertib and FoxM1 with thiostrepton synergistically attenuated PTC cell growth in vitro and in vivo. Our findings suggest that co-targeting of PLK1 and FoxM1 could be a viable therapeutic strategy for treating patients with an aggressive subtype of PTC. Citation Format: Pratheeshkumar Poyil, Abdul K. Siraj, Divya Padmaja, Sandeep Kumar Parvathareddy, Saravanan Thangavel, Saif S. Al-Sobhi, Fouad Al-Dayel, Khawla S. Al-Kuraya. The co-targeting of PLK1 and FoxM1 contributes to synergistic antitumor effects in PTC [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 4611.