tbuckley/cabot-search huggingface dataset:
Abstract 395: An alternating magnetic field suppresses tumor growth
Authors: Masanari Umemura, Taisuke Akimoto, Rafikul Islam, Kazuhito Kishi, Akane Nagasako, Rina Nakakaji, Takashi Yamaguchi, Yuto Mizuno, Soichiro Ishikawa, Tetsuya Yamamoto, Yoshihiro Ishikawa
Journal: Cancer Research (2024)

Abstract Application of physical forces, ranging from ultrasound to electric field, is recommended in various clinical practice guidelines, including those for bone fracture or cancer treatment. However, mechanistic information for such treatments has been poorly provided, due to the lack of comprehensive study model. Here, we show an alternating magnetic field (AMF) per se exhibits direct anti-cancer effect through enhancing oxidative phosphorylation (OXPOHS) and thus metabolic reprograming. Proliferation of human glioblastoma cells (U87 and LN229), but not normal human astrocytes (NHA), was inhibited upon exposure to AMF within the narrow frequency range. Extracellular acidification rate was decreased while oxygen consumption was increased. These data indicated that AMF induced metabolic reprograming. This was accompanied by increased reactive oxygen species (ROS) production. Mouse models grafted with human glioblastoma cells showed that AMF exposure, 30 minutes per day for two weeks, suppressed the tumor growth and prolonged the overall survival. Our results suggest that the AMF exposure may be a simple strategy to inhibit cancer cell growth by utilizing oxidative stress via metabolic reprograming. Citation Format: Masanari Umemura, Taisuke Akimoto, Rafikul Islam, Kazuhito Kishi, Akane Nagasako, Rina Nakakaji, Takashi Yamaguchi, Yuto Mizuno, Soichiro Ishikawa, Tetsuya Yamamoto, Yoshihiro Ishikawa. An alternating magnetic field suppresses tumor growth [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 395.
Abstract 3037: Sex-specific differences in <i>Yap1</i> and <i>Cd276</i> function and expression regulate medulloblastoma progression and immune evasion
Authors: Nourhan Abdelfattah, Sivaraman Natarajan, Han Nhat Tran, Jose Maldonado, Rachael McMinimy, Hannah Borland, Shu-hsia Chen, Fernando Camargo, James Olson, Joshy George, Kyuson Yun
Journal: Cancer Research (2024)

Abstract Unveiling the molecular mechanisms underlying sex-specific differences in cancer initiation, progression and treatment outcomes will provide novel insights that will advance cancer research and clinical care. This study highlights an unexpected, sex-biased role of the oncogene Yap1 in SHH medulloblastoma (MB). We discovered that Yap1 deletion in SmoM2-driven SHH MB significantly prolongs survival in male but not female mice. Using an integrated multi-omics approach, we show that YAP1 promotes cancer stem cell maintenance through concurrent transcriptional activation of stemness genes, such as Sox2, and repression of differentiation genes such as NeuroD1 and Zic1/2. Interestingly, while Yap1 is essential for maintaining cancer stem cells in both sexes, it plays a more critical role in immune evasion in males. Specifically, YAP1 regulates the expression of an immune checkpoint molecule Cd276 to suppress T cell function. Blocking CD276 or deleting Yap1 is sufficient to significantly reverse T cell suppression in males but not females. Furthermore, YAP1 direct targets of transcriptional regulation, including CD276, predicts survival in male but not female patients across multiple human cancers, suggesting that our findings have broader implications beyond medulloblastomas and is conserved across species. This study provides compelling evidence for male-biased susceptibility to Yap1 inhibition and uncovers the YAP1-CD276 axis as a sexually diverse pathway in T cell suppression in tumors. Citation Format: Nourhan Abdelfattah, Sivaraman Natarajan, Han Nhat Tran, Jose Maldonado, Rachael McMinimy, Hannah Borland, Shu-hsia Chen, Fernando Camargo, James Olson, Joshy George, Kyuson Yun. Sex-specific differences in Yap1 and Cd276 function and expression regulate medulloblastoma progression and immune evasion [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 3037.
Abstract 123: Establishment of humanized CD3EDG/4-1BB mice for testing novel T cell engagers
Authors: Chengzhang Shang, Chong Li, Lei Zhao, Qingqing Xu, James Jin, Menglian Ren
Journal: Cancer Research (2024)

Abstract Agonism of the 4-1BB receptor is an attractive therapeutic strategy for tumor cell therapy, due to the ability of this receptor to stimulate activity of T and NK cells for tumor cell killing. Many classes of biologics targeting 4-1BB have been generated to date, including bispecific or multispecific engagers designed to stimulate 4-1BB and CD3 activity on the T cell surface. To provide a preclinical platform to test such therapies, Biocytogen generated a humanized B-hCD3EDG/h4-1BB mouse model. This was achieved by crossing humanized mice expressing chimeric CD3E, CD3D and CD3G with mice expressing the human extracellular region of 4-1BB. Previously, we showed that these humanized CD3EDG mice and humanized 4-1BB mice can be used for validating efficacy of anti-human CD3 and 4-1BB antibody-based therapies, respectively. Here, we confirmed expression of human CD3 and 4-1BB on splenocytes in homozygous humanized B-hCD3EDG/h4-1BB mice by flow cytometry, which also demonstrated lack of murine CD3 and 4-1BB expression. Assessment of leukocyte subpopulations in the spleen and peripheral blood confirmed that humanization of the mice did not significantly alter the development or frequency of blood cell populations. Further evaluation of lymphocyte frequency was also performed, which demonstrates no significant alterations in the CD4/CD8 T cell ratio in spleen, lymph node, or peripheral blood of the animals. Presence of Treg and NK cells was also confirmed. Taken together, these data indicate that the humanized B-hCD3EDG/h4-1BB model is a novel, robust tool for testing novel T cell engagers. Citation Format: Chengzhang Shang, Chong Li, Lei Zhao, Qingqing Xu, James Jin, Menglian Ren. Establishment of humanized CD3EDG/4-1BB mice for testing novel T cell engagers [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 123.
Abstract 5622: Uncovering the transcriptional regulation of TPPP3
Authors: James W. Lord, Dmitry Leshchiner, Sachi Horibata
Journal: Cancer Research (2024)

Abstract Tubulin Polymerization Promoting Protein 3 (TPPP3) is a protein coding gene primarily associated with microtubule bundling. However more recent research is beginning to reveal more diverse roles it may play in the cell, including B-catenin signaling and endothelial injury. TPPP3 has also been associated with increased cancer growth and proliferation as well epithelial to mesenchymal transition. However, it is unknown how TPPP3 is regulated. We used high grade serous ovarian cancer (HGSOC) as a model to uncover the regulation of TPPP3 as it is highly expressed in many HGSOC cases. To start, we downloaded ~500 HGSOC RNA-seq datasets from The Cancer Genome Atlas (TCGA) and, using python, created a co-expression network to identify a subset of genes exhibiting expression patterns correlated with TPPP3 across all datasets, resulting in the identification of 222 genes. Dynein arm assembly, cilia movement and assembly, and microtubule movement and structure were among the top GO-terms after gene ontology analysis. The genes associated with these processes are typically upregulated in the fallopian tube tissue which aligns with the fact that a majority of HGSOCs originate in the fallopian tube. Fork-head box J1 (FOXJ1) is a transcription factor associated with ciliogenesis and was among the top 222 genes from the co-expression network. It has not been confirmed to transcriptionally regulate TPPP3, but their expression patterns line up across many tissue types. In addition, the TPPP3 promoter contains an RFX2 binding site. RFX2 is DNA binding protein that FOXJ1 uses as a scaffold to bind to proximal promoters due to it binding at to DNA at a distal location. As a result of this evidence, we hypothesize that FOXJ1 transcriptionally regulates TPPP3 via RFX2. To test this hypothesis, we inhibited FOXJ1 and identified TPPP3 downregulation. We are further investigating the regulatory function of how TPPP3 is regulated. Citation Format: James W. Lord, Dmitry Leshchiner, Sachi Horibata. Uncovering the transcriptional regulation of TPPP3 [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 5622.
Abstract 6302: Home-based supportive care programs for quality-of-life outcomes among patients with advanced cancer: A systematic review
Authors: Inyoung Hwang, Go-Un Wo, Sun-Young Lee, Shin Hye Yoo, Kyae Hyung Kim, Min-Sun Kim, Jeongmi Shin, Hyejin Jeong, Min Seol Jang, Sun Kyung Baek, Eun Hee Jung, Dong-Wook Lee, Belong Cho, Jin Ho Park, Hyuktae Kwon
Journal: Cancer Research (2024)

Abstract Objectives This study systematically reviews the literature on the effect of home-based supportive care (HbSC) programs on the quality of life (QoL) of patients with advanced cancer. Methods: The research question ‘Do home-based supportive care programs for patients with advanced cancer improve their QoL?’ was addressed. After registering the plan with PROSPERO (CRD42021235007), literature published from 1 January 1990 to 11 July 2022 was searched on Ovid Medline, Embase, Cochrane library, Web of Science, and Google Scholar and reviewed for inclusion based on predefined criteria. This review only included trial studies published in English. Results: Of 5288 articles identified, 17 studies were judged suitable for inclusion in this review. The components of HbSC programs included home visits, patient and caregiver education, home nursing, psychotherapy, exercise, and telephone consultation. Eight programs included conducting multidisciplinary team meetings. Improvements in QoL were reported in six studies. Specific areas of QoL improved when interventions included home nursing, psychotherapy, patient and caregiver education, and exercise. Conclusion: HbSC programs appear to enable the improvement of the QoL of patients with advanced cancer. The area of QoL that shows improvement could vary depending on the HbSC components. More studies that address HbSC programs are needed to select patients at the proper time and provide suitable programs for patients to benefit most. Citation Format: Inyoung Hwang, Go-Un Wo, Sun-Young Lee, Shin Hye Yoo, Kyae Hyung Kim, Min-Sun Kim, Jeongmi Shin, Hyejin Jeong, Min Seol Jang, Sun Kyung Baek, Eun Hee Jung, Dong-Wook Lee, Belong Cho, Jin Ho Park, Hyuktae Kwon. Home-based supportive care programs for quality-of-life outcomes among patients with advanced cancer: A systematic review [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 6302.
Abstract 5157: Development and evaluation of a high-throughput method for rapid detection of surface antigen expression in fixed cells
Authors: Kaja Holtorf, Anne-Lise Peille, Daniel Feger, Vincent Vuaroqueaux, Jan Erik Ehlert, Nadine Obier
Journal: Cancer Research (2024)

Abstract Cell surface proteins are increasingly considered in the development of novel anticancer agents, as demonstrated by recent clinical successes in the field of immuno-oncology and antibody-drug conjugates (ADCs). These conjugates specifically target antigens present on the surface of tumor cells, enabling the delivery of cytotoxic agents to specific tumor sites. During the preclinical development of such compounds, for example, when they are tested on a wide panel of cell lines, it is essential to have a rapid and reliable method for monitoring target expression and distribution. Complementing our 160 Cell line panel ProLiFiler™, we report here the development of a novel method named oncoFLOW-Profiler™ which includes steps of cell fixation, micronic storage, staining, and measurement by flow cytometry. This method is applied in a 96-well format, enabling screening of all cell lines in parallel and analysis of the expression of different targets in just one day. In this proof-of-concept study, we investigated the level of ERBB2 expression across the ProLiFiler panel of 160-cell lines in order to validate this methodology. We first compared the impact of fixation methods and sample storage on knowingly positive and negative control cell lines over a period of several months. ERBB2 measurements from the oncoFLOW-Profiler™ will be analyzed and validated by comparison with various OMICs datasets from the Cancer DataMiner platform (4HF Biotec), including RNA expression, mutational status, and protein expression levels. To determine the expression cutoff of ERBB2 amplified models, results will be analyzed according to gene copy number variation. Finally, the flow cytometry data generated will be investigated for use as a predictor of response to clinically approved ADCs targeting ERBB2: Kadcyla and Enhertu. Here we present a method that we have demonstrated is feasible for investigating cell surface receptor/antigens during preclinical phase of drug development. Our method has enabled us to successfully assess ERBB2 in biological samples and to identify models sensitive to ADCs targeting ERBB2. We will also discuss the results of ongoing experiments analyzing the applicability of this screen to intracellular targets and carbohydrate-based surface antigens, which cannot be analyzed either by transcriptomics or proteomics. Citation Format: Kaja Holtorf, Anne-Lise Peille, Daniel Feger, Vincent Vuaroqueaux, Jan Erik Ehlert, Nadine Obier. Development and evaluation of a high-throughput method for rapid detection of surface antigen expression in fixed 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 5157.
Abstract 563: Targeting PDE4D reinstates toxic PARP trapping via cAMP-ROS-DNA damage axis and restores the efficacy of standard of care in treatment-refractory ER+ breast cancer
Authors: Ozge Saatci, Metin Cetin, Meral Uner, Unal M. Tokat, Ioulia Chatzistamou, Elodie Montaudon, Aytekin Akyol, Sercan Aksoy, Aysegul Uner, Elisabetta Marangoni, Mathew Sajish, Ozgur Sahin
Journal: Cancer Research (2024)

Abstract Endocrine therapies, modulating ER level and/or activity, and the CDK4/6 inhibitors are among the standard-of-care (SOC) therapies used in estrogen receptor-positive (ER+) breast cancer. However, most ER+ breast cancer patients eventually develop resistance to SOC, representing a major clinical challenge that reduces clinical outcome. Therefore, elucidating the common mechanisms of sensitivity and resistance to SOC therapies, and identifying novel actionable targets are urgently needed. Here, we demonstrated that cell death induced by endocrine therapies and CDK4/6 inhibitors involves toxic PARP1 trapping and generation of a functional BRCAness (i.e., BRCA1/2 deficiency) phenotype, leading to transcriptional blockage. We showed that this is achieved by activation of the cAMP/reactive oxygen species (ROS)/DNA damage axis upon downregulation of phosphodiesterase 4D (PDE4D). Importantly, we identified PDE4D as a novel ER target gene that in turn stimulates ER activity in a feedforward loop in endocrine-responsive models. However, during SOC resistance, an ER-to-EGFR switch induces PDE4D overexpression via c-Jun. Inhibition of PDE4D using BPN14770, the first-in-class PDE4D allosteric inhibitor that has successfully completed Phase II trials in Fragile X syndrome, reinstates PARP1 trapping and BRCAness, leading to drug sensitization in vitro and in vivo. Furthermore, inhibition of EGFR or PARP1 recapitulates the effects of PDE4D targeting and overcomes SOC resistance irrespective of the BRCA1/2 status in cell line models, primary cultures and organoids of endocrine resistant ER+ PDXs. Notably, we demonstrated that high PDE4D mRNA and protein expression is associated with dramatically worse disease-free survival and overall survival in endocrine therapy-treated ER+ breast cancer. Given the availability of potent and non-toxic PDE4D inhibitors, and clinically approved EGFR and PARP1 inhibitors, our findings have great translational potential to improve the clinical outcome of refractory ER+ breast cancers. Citation Format: Ozge Saatci, Metin Cetin, Meral Uner, Unal M. Tokat, Ioulia Chatzistamou, Elodie Montaudon, Aytekin Akyol, Sercan Aksoy, Aysegul Uner, Elisabetta Marangoni, Mathew Sajish, Ozgur Sahin. Targeting PDE4D reinstates toxic PARP trapping via cAMP-ROS-DNA damage axis and restores the efficacy of standard of care in treatment-refractory ER+ breast 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 563.
Abstract 5182: Exploiting tumor RNA-sequencing data for prediction of immune checkpoint inhibition response
Authors: Pieter Mestdagh, Pieter-Jan Van Dam, Frederick De Baene, Carolina Fierro, Elise Van Hoof, Emmanuel Rivière, Hanne Dangreau, Reindert Van Cauwenberge, Jo Vandesompele
Journal: Cancer Research (2024)

Abstract Immune checkpoint inhibitors (ICI) have become the standard of care as a first- or second-line systemic treatment for patients with various cancer types. Unfortunately, many patients do not respond to this treatment and the occurrence of immune-related adverse events varies widely. There is an urgent need for robust predictive biomarkers for ICI response to identify patients with likely clinical benefit from this costly treatment. Several biomarkers, aimed at predicting response to ICI, have been proposed, including PD-L1 expression, tumor mutation burden (TMB), infiltration of cytotoxic T-cells in the tumor, Microsatellite Instability (MSI) and expression of various immune gene signatures. However, these individual biomarkers have suboptimal performance and multiple complementary omics technologies are required to properly quantify them. Integration of these multi-omic biomarkers has proven valuable in increasing the accuracy and robustness of ICI response prediction.We have developed a computational pipeline that determines the expressed mutation burden (eTMB), MSI status, fraction of infiltrating immune cells and various immune gene expression signatures directly from the RNA-sequencing profile of the tumor. Each biomarker is quantified using a dedicated algorithm that applies machine learning (eTMB and MSI) or computational deconvolution (infiltrating immune cells) and integrates external data sources to maximize performance. Algorithm performance has been validated on large cohorts of tumor RNA-sequencing data with matching gold standard quantification of said biomarkers. As a proof of concept, we applied our pipeline to tumor RNA-sequencing data of 45 gastric cancer patients treated with pembrolizumab. Responders showed significantly higher eTMB scores and were enriched among the MSI-H patients. Fractions of CD8 T-cells and M1 Macrophages, together with interferon gamma and cytotoxic T-cell gene expression signatures, were significantly increased in responders. Notably, integrating these biomarkers into a single prediction model improved prediction of response to checkpoint inhibition therapy compared to predictions based on eTMB or MSI alone. Taken together, our approach enables the quantification of various ICI response biomarkers from a single omics layer (RNA-sequencing) and can contribute to ICI response prediction. Citation Format: Pieter Mestdagh, Pieter-Jan Van Dam, Frederick De Baene, Carolina Fierro, Elise Van Hoof, Emmanuel Rivière, Hanne Dangreau, Reindert Van Cauwenberge, Jo Vandesompele. Exploiting tumor RNA-sequencing data for prediction of immune checkpoint inhibition response [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 5182.
Abstract 5147: Identification of pharmacodynamic biomarkers in PBMCs and cancer cells for SIK2 kinase inhibitor therapy
Authors: Hailing Yang, Weiqun Mao, Philip Rask, Markus Peter, Gayathri Swaminath, Stephan W. Morris, Zhen Lu, Robert C. Bast
Journal: Cancer Research (2024)

Abstract Salt-inducible kinase 2 (SIK2) is an AMPK family kinase involved in multiple signaling pathways including the LBK1-SIK-HDAC, LKB1-SIK-CRTC/CREB, PI3K-PKA-mTOR and Hippo pathways. The expression of SIK2 is significantly upregulated in fraction of ovarian and breast cancers, and associated with poor prognosis. Inhibition of SIK2 kinase activity suppresses growth of ovarian and breast cancers as well as progression of acute myeloid leukemia. SIK2 inhibitors synergistically enhance sensitivity of ovarian and breast cancer cells to paclitaxel, carboplatin and PARP inhibitors. Utilization of SIK2 inhibitors to treat cancers has been investigated in preclinical studies and in a Phase I clinical trial (NCT04711161). To enable pharmacodynamic (PD) analysis in clinical studies, we have developed biomarkers that measure the effect of GRN-300, a SIK2/3 inhibitor, on SIK2 signaling in ovarian cancer cells. Class IIa histone deacetylases (HDAC4/5/7) are SIK2 substrates in cancer cells; and are also expressed in peripheral blood mononuclear cells (PBMCs). We found that GRN-300 decreased phosphorylated HDAC4/5/7 levels in ovarian and breast cancer cells (Lu et al. J Clin Invest, 2022) and now report that this SIK2 inhibitor also decreases pHDAC4/5/7 in PBMCs ex vivo in a dose-dependent manner using Western blot analysis. We also identified three mRNA markers in PBMCs by RNAseq analysis - SEPP1, RNASE1 and MS4A6A - which are up-regulated by GRN-300 in PBMCs isolated from healthy donors. However, these mRNA markers were either expressed at very low levels or not dramatically changed in cancer cells. We identified an additional mRNA marker panel using RNAseq technology by screening seven ovarian and six breast cancer cell lines: A2780, Caov3, IGROV1, OC316, OVCAR3, OVCAR8, SKOv3ip, BT549, Cal51, HCC1937, MDA-MB-231, MDA-MB-436 and MDA-MB-468. mRNA expression of three genes - DDIT4, NUPR1 and IL6 - is upregulated by GRN-300 in more than 9 of 13 cell lines tested. Five genes - ID1, ID2, ID3, ID4 and TGFBI - are down-regulated in response to GRN-300 treatment in more than 10 of 13 cell lines. The decrease in HDAC4/5/7 phosphorylation, and alterations in mRNA markers we discovered could serve as PD biomarkers for clinical trials to evaluate the effects of SIK2 inhibitors and provide insights in the mechanisms of drug action. Citation Format: Hailing Yang, Weiqun Mao, Philip Rask, Markus Peter, Gayathri Swaminath, Stephan W. Morris, Zhen Lu, Robert C. Bast. Identification of pharmacodynamic biomarkers in PBMCs and cancer cells for SIK2 kinase inhibitor therapy [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 5147.