tbuckley/cabot-search huggingface dataset:
Abstract 6424: A patient centric full spectrum flow cytometry assay for comprehensive phenotyping of CAR T cells in clinical trials
Authors: Keegan Vaughan, Selvam Muthusamy, Coral Zhao, Austin Carbajal, Charlie Fu, Naveen Dakappagari, Zeni Alfonso
Journal: Cancer Research (2024)

Abstract Purpose While there is a strong desire to fully understand next generation CAR-T product characteristics in clinical trials, limited amounts of blood specimens are available as the enrolled patients are very sick and lymphodepleted. To address this high unmet need, we developed a single tube 20-color full spectrum flow cytometry assay for an in-depth characterization of CAR-T cells that support fulfilment of five key clinical trial endpoints, namely, manufacturing success (fitness and memory state), pharmacokinetics, response or resistance (ICIs), efficacy (gross tumor burden) and safety (B cell regeneration) for use across a broad range of CAR-T therapies and clinical indications. Study Design: The single tube 20-parameter full spectrum flow cytometry (FC) assay was designed to include CD45, HLA-DR, CD3, CD4, CD8, CD56 as backbone markers, CD45RA, CCR7, CD95, CD25 and CD127 antibodies allowed for the identification of all major subsets of CD4 and CD8 T cells. CXCR3, CD38, PD1, LAG3, and TIM3 were used for identification of activation/exhaustion phenotypes, while CD20 and HLA-DR were useful for identification of B cells and monocytes respectively. Additionally, we left two parameters (PE and AF647) open for customized CAR-T detection reagents or other customized markers. This assay was developed using Cytek® Northern Lights™ and frozen PBMCs. Results This robust 20-color full spectrum FC assay allowed a thorough analysis of the major T cell populations cells. FMO (Fluorescence-Minus-One) control studies confirmed the specificity of the antibodies and of the panel in identifying Naïve, EMRA, CM, EM, Th17, T stem cell memory and regulatory T cells with minimum background on all parameters. This method showed to be highly reproducible and can be adapted for use with many CAR-T detection reagents. Conclusion In summary, we developed a robust 20-parameter multiparameter full spectrum flow cytometry assay focused on different populations of T cells in a single tube. The inclusion of drop ins for prospective CAR-T cell detection reagents allows for easy integration of future advances in CAR-T cell research. This universal panel shows great potential for usage across CAR-T clinical trials, as it serves as a valuable tool understand product fitness, PK, biomarker monitoring and disease burden simultaneously. Citation Format: Keegan Vaughan, Selvam Muthusamy, Coral Zhao, Austin Carbajal, Charlie Fu, Naveen Dakappagari, Zeni Alfonso. A patient centric full spectrum flow cytometry assay for comprehensive phenotyping of CAR T cells in clinical trials [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 6424.
Abstract 5098: Second-line treatment outcomes in Extensive Stage Small Cell Lung Cancer (ES-SCLC) patients after first-line immuno-chemotherapy
Authors: Rui Wan, Linjie Fan, Jia Zhong, Jianchun Duan, Zhijie Wang, Xuezhi Hao, Jie Wang
Journal: Cancer Research (2024)

Abstract Background: First-line immune checkpoint inhibitors (ICIs) has significantly improved overall survival (OS) of ES-SCLC. However, second-line treatment options are still controversial with limited overall survival. This study aims to evaluate the efficacy of different second-line regimens for relapsed ES-SCLC after first-line immuno-chemotherapy. Patients and Methods: We retrospectively reviewed 96 ES-SCLC patients receiving first-line immuno-chemotherapy in Cancer Hospital Chinese Academy of Medical Sciences, from Jan 2019 to Dec 2022. Clinical data were collected from electronic medical records. The clinical outcomes, including objective response rate (ORR), progression-free survival (PFS) and overall survival (OS) were assessed by Kaplan-Meier method and standard log-rank test. Results: From January 4, 2019 to December 18, 2022, a total of 96 ES-SCLC patients received first-line immuno-chemotherapy and 49 of them went through second-line treatment in our center. Patient characteristics were listed as follows : median age 63 (31-79), male 76 (79.2%) , heavy smoker 59 (61.5%), liver metastasis 40 (41.7%), brain metastasis 33 (34.4%) and refractory recurrence 58 (60.4%). Second-line treatments included immunotherapy crossover and combination with chemotherapy (n=40), anlotinib with or without chemotherapy (n=5), chemotherapy alone (n=4). ORR of the whole group in the second-line setting was 22.4%. Median PFS was 3.23 months (95% CI 1.96-4.50). Cross-line immunotherapy failed to improved survival for relapsed ES-SCLC compared with those without ICIs ( mPFS 3.23 vs 3.13m, p=0.829). Anlotinib based treatment showed numerically superior PFS for relapsed SCLC compared with those without anlotinib therapy (mPFS 6.00 vs 3.13m, p=0.089). Conclusion: This retrospective study indicated cross-line ICIs failure to improve clinical outcome for relapsed ES-SCLC, and implied the potential benefits of anlotinib in second-line setting. Citation Format: Rui Wan, Linjie Fan, Jia Zhong, Jianchun Duan, Zhijie Wang, Xuezhi Hao, Jie Wang. Second-line treatment outcomes in Extensive Stage Small Cell Lung Cancer (ES-SCLC) patients after first-line immuno-chemotherapy [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 5098.
Abstract 4319: HSF1 inhibition induces pancreatic ductal adenocarcinoma autophagy through JNK
Authors: Shruti Ghai, Alex Young, Kuo-Hui Su
Journal: Cancer Research (2024)

Abstract Background: Pancreatic ductal adenocarcinoma (PDAC) is the third leading cause of cancer-related mortality, with a 5-year survival rate of 12%. Chemoresistance due to autophagy, a natural process of proteotoxic stress response, is the most common chemotherapy challenge for pancreatic cancer. Autophagy, which maintains cellular homeostasis by removing damaged or unnecessary proteins and organelles, is a self-degradation process regulated by the mammalian target of rapamycin complex (mTORC1). Excessive levels of autophagy can be detrimental and lead to cell death. Nevertheless, this dual function of autophagy in regulating pancreatic cancer remains poorly understood. It has been reported that heat shock factor 1 (HSF1), a critical pro-oncogenic transcription factor in the proteotoxic stress response, inhibits c-Jun N-terminal kinase 1/2 (JNK1/2) signaling pathway to maintain mTORC1 activity and control cell size. HSF1 is highly expressed in pancreatic tumors, and inhibition of HSF1 via small molecules enhances the chemotherapy drug effect on PDAC programmed cell death. However, the PDAC autophagy response in HSF1 inhibition is currently not fully understood. Objective: The objective of this study is to investigate the molecular mechanism of HSF1 inhibition in PDAC autophagy. Methods and Results: In human PDAC cells, Western blotting analysis revealed that HSF1 inhibition via small molecular including CCT361814/NXP800, an HSF1 inhibitor in phase I clinical trials, increased autophagy marker microtubule-associated protein 1A/1B-light chain 3 (LC3) lipidation and decreased expression of phosphorylation of HSF1 at Ser326 and total HSF1 protein, conversely using HSF1 overexpression model reversed this effect. Inhibition of autophagy via 3-methyladenine reversed HSF1 inhibition-induced autophagy. Results from transmission electron microscopy and GFP-LC3 reporter revealed that HSF1 inhibition induced autophagosome formation and accumulation. Furthermore, HSF1 inhibition induced phosphorylation of JNK1/2 at Thr183/Tyr185 and decreased mTORC1 activity, while knockdown JNK1/2 diminished HSF1 inhibition-induced LC3 lipidation. The combination of chemotherapy drugs with HSF1 inhibitors decreased PDAC cell viability. Additionally, blocking autophagy increased HSF1 inhibition-induced apoptosis. Conclusions: In conclusion, JNK1/2 is involved in HSF1 inhibition-induced PDAC autophagy, targeting autophagy could unveil a novel treatment strategy for pancreatic cancer through targeted HSF1 inhibition. Citation Format: Shruti Ghai, Alex Young, Kuo-Hui Su. HSF1 inhibition induces pancreatic ductal adenocarcinoma autophagy through JNK [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 4319.
Abstract 2998: Regulation of epidermal growth factor receptor signaling by BRCA1-microRNA 146a network
Authors: Easwari Kumaraswamy, Raeann M. Koren Shimak, Sumedha Gunewardena, Karen L. Wendt, Dani Alexander, Stacey L. Hembruff, Roy A. Jensen
Journal: Cancer Research (2024)

Abstract Inherited defects in the breast cancer susceptibility gene, BRCA1 are associated with an increased risk for hereditary breast, ovarian, and other cancers. BRCA1-associated basal like breast cancers (BLBCs) are high-grade ductal carcinomas that do not express ER, PR or HER2, but frequently overexpress epidermal growth factor receptor (EGFR/ErbB1/HER1). The EGFR-driven signaling network plays a pivotal role in BLBC pathogenesis. EGFR overexpression is associated with tumor progression and metastasis, resistance to radiation and chemotherapy, and poor prognosis. Growth factor receptors are regulated by multiple miRNAs, each having many targets, coordinately controlling the complex pathways of downstream signaling. We have previously reported a post-transcriptional mechanism by which BRCA1 regulates EGFR expression through the induction of miR-146a and provided a rationale for the development of miR-146a based therapeutic strategies. In addition, we have shown that BRCA1 also exerts regulatory control over dozens of important miRNAs that appear to play a critical role in breast neoplasia. From TCGA analysis, we show that low expression of these miRNAs is associated with distinctively poor overall survival of TNBC patients. Using miR-146a loss or gain of function experiments in vitro, we show that BRCA1 and miR-146a regulate EGFR signaling, stemness, epithelial-to-mesenchymal transition (EMT), extracellular matrix (ECM) remodeling and chemoresistance. Using in vivo mouse models, we demonstrate that miR-146a overexpression delays tumor formation leading to better overall survival. BLBC unlike the other subtypes, lacks targeted therapy approaches making cytotoxic chemotherapy essentially the only option for treatment. Though EGFR inhibitors have been used to treat other cancers, clinical trials for breast cancer have so far been unsuccessful due to poor response rates. Since one miRNA can target multiple genes and regulate multiple signaling pathways, our study provides evidence to suggest that restoring miR-146a could suppress EGFR-RAS-MEK signaling and the other compensatory pathways, providing a targeted therapeutic option for BRCA1 associated BLBC. Citation Format: Easwari Kumaraswamy, Raeann M. Koren Shimak, Sumedha Gunewardena, Karen L. Wendt, Dani Alexander, Stacey L. Hembruff, Roy A. Jensen. Regulation of epidermal growth factor receptor signaling by BRCA1-microRNA 146a network [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 2998.
Abstract 2103: Small extracellular vesicles derived from macrophages show anti-tumor effects in MDA-MB-231 cells
Authors: Parth Desai, Anjali Kumari, Saqer Al Abdullah, Kristen Dellinger
Journal: Cancer Research (2024)

Abstract Triple-negative breast cancer is the primary cause of death in women globally due to the absence of targeted receptors on the tumor, making it hard to treat. In addition, the rapid spread of triple-negative breast cancer makes it difficult to manage using current treatment options such as lumpectomies, mastectomies, radiation, and chemotherapy. The survival rate for patients with triple-negative breast cancer is only 8-16%. Therefore, there is a critical need to develop new and effective treatment options. The objective of this study was to investigate the potential of M1 macrophage-derived exosomes to induce cancer cell apoptosis. To test this, we isolated M1 macrophage-derived exosomes to see their effects on triple-negative breast cancer MDA-MB-231 cells. We induce polarization in RAW 264.7 macrophage cells via lipopolysaccharide (LPS). Macrophage polarization was characterized using an enzyme-linked immunosorbent assay (ELISA), real-time PCR, nitric oxide production, and bright field microscopy. We characterized exosomes using nanoparticle tracking analysis (NTA) and scanning electron microscopy (SEM). The apoptosis marker, caspase 3/7 activation, was assessed using confocal microscopy in MDA-MB-231 cells. M1 macrophage-derived exosomes were isolated, characterized, and incubated with breast cancer cells to see their anticancer effects. Data showed the induction of apoptosis in 48 hours in triple-negative breast cancer cells. We conclude that exosomes derived from M1 macrophages may have the capability to induce apoptosis in triple-negative breast cancer. Citation Format: Parth Desai, Anjali Kumari, Saqer Al Abdullah, Kristen Dellinger. Small extracellular vesicles derived from macrophages show anti-tumor effects in MDA-MB-231 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 2103.
Abstract 2642: <i>KEAP1</i> mutation in lung cancer cells leads to increased immunosuppressive capability
Authors: Christopher John Occhiuto, Karen T. Liby
Journal: Cancer Research (2024)

Abstract Considerable advances have been made in lung cancer therapies, but there is still an unmet clinical need to improve survival for lung cancer patients. Immunotherapies have improved survival, although only 20-30% of patients respond to these treatments. Interestingly, cancers with mutations in KEAP1, the negative regulator of the NRF2 cytoprotective pathway, are resistant to immune checkpoint inhibition and correlate with decreased immune cell infiltration. NRF2 is known for promoting an anti-inflammatory phenotype when activated in immune cells, but the study of NRF2 activation in cancer cells has not been adequately assessed. The overall objective of this study is to determine how lung cancer cells with constitutive NRF2 activity interact with the immune microenvironment to promote cancer progression and metastasis. To assess this, we generated CRISPR-edited mouse lung cancer cell lines (Lewis Lung Carcinoma/LL2) with knockouts (KO) of the KEAP1 and NFE2L2 genes. The transcriptomic profiles of 3 KEAP1 KO and 1 NRF2 KO cell lines were compared to the parental wildtype (WT) line using RNA-sequencing. On unsupervised hierarchical clustering of differentially expressed genes, the 3 KEAP1 KO cell lines clustered together and the NRF2 KO clustered with WT cells. Importantly, canonical NRF2 pathway-related genes were significantly increased in KEAP1 KO clones, but the same genes were either decreased or similar to WT in the NRF2 KO clone. We then used flow cytometry to evaluate immunosuppressive surface markers known to suppress T cell function when expressed on cancer cells. Importantly, PD-L1, CD155, CD80, and CD86 were increased in the KEAP1 KO lines compared to WT, but not in the NRF2 KO clone. In addition, the cytokine release profile was differentially regulated in the KEAP1 KO clones in a manner that could alter T cell recruitment and function. These results were also consistent with gene expression in the sequencing dataset. Finally, using an orthotopic allograft model, we completed a preliminary immunophenotyping study of lung tumors for WT, KEAP1 KO, and NRF2 KO cell lines. The activation status of CD8+ T cells and the ratio of CD8+/CD4+CD25+ T cells (a prognostic marker) were decreased in KEAP1 KO tumors. Taken together, these data suggest cancers with KEAP1 mutations may increase tumor growth through suppression of T cells. Citation Format: Christopher John Occhiuto, Karen T. Liby. KEAP1 mutation in lung cancer cells leads to increased immunosuppressive capability [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 2642.
Abstract 242: Development of organoids-bacteria co-cultures for medium-to-high throughput screening
Authors: Eider Valle-Encinas, Mayke Doorn, Farzin Pourfarzad, Lani San Mateo, Prashanth Gokare, David Pocalyko, Sylvia F. Boj, Carla S. Verissimo
Journal: Cancer Research (2024)

Abstract HUB patient derived organoids, (HUB-OrganoidsTM or PDOs) are self-organized epithelial cell structures with near-physiological features, extensively used to model aspects of cancer initiation and progression. Microinjection of colibactin-producing pks+ E. coli into the lumen of PDOs resulted in the appearance of two co-occurring mutational signatures identified in a subset of colorectal cancer (CRC) patients, demonstrating that pks+ E. coli plays a causative role in CRC development. The scalability of PDO bacteria microinjection is, however, limited and represent a bottleneck in the screening of preventive therapies for these patients. Here we develop a bacteria-PDO co-culture system (PDO-fragment exposure model), alternative to PDO microinjection, that is compatible with medium-to-high throughput screening methods. We validated the genotoxicity of colibactin-producing bacteria and showed the potential of the PDO fragment exposure model for the screening of drugs targeting colibactin-dependent genotoxicity. Citation Format: Eider Valle-Encinas, Mayke Doorn, Farzin Pourfarzad, Lani San Mateo, Prashanth Gokare, David Pocalyko, Sylvia F. Boj, Carla S. Verissimo. Development of organoids-bacteria co-cultures for medium-to-high throughput screening [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 242.
Abstract 1729: SUV420H1 depletion reveals therapeutic potential in HPV-negative head and neck squamous cell carcinoma
Authors: Arfa Moshiri, Sohyoung Kim, Marie Luff, Vassiliki Saloura
Journal: Cancer Research (2024)

Abstract Human Papilloma Virus (HPV)-negative head and neck squamous cell carcinoma (HNSCC) poses a significant clinical challenge with limited treatment options. SUV420H1, which encodes for a protein lysine methyltransferase (PMT) that methylates H4K20 (H4K20me3), is recurrently amplified in ~5% of HPV-negative HNSCC tumors and is the second most frequently amplified PMT in this disease, suggesting an oncogenic function in this subset of HPV-negative HNSCC patients. Gene set enrichment analysis using the TCGA database of HPV-negative HNSCC tumors revealed that SUV420H1 overexpressing tumors showed enrichment in the mitotic spindle related pathways, and repression of immune-related pathways. To assess whether SUV420H1 depletion affects the proliferation of HPV-negative HSNCC cells, CCK8 and colony formation assays were pursued after siRNA-mediated knockdown of SUV420H1 in five SUV420H1-overexpressing HPV-negative HNSCC cell lines and revealed a significant reduction in cell proliferation and colony forming capacity. SUV420H1 CRISPR knockout (KO) HPV-negative HNSCC human and mouse cell lines were generated. Proliferation and colony formation assays with the SUV420H1 KO cell lines are ongoing to validate the aforementioned phenotypes. To identify oncogenic mechanism of SUV420H1, genome-wide mapping of H4K20me3 after siRNA-mediated depletion or enzymatic inhibition of SUV420H1 (A-196) was pursued using CUT&amp;RUN assays combined with RNA-seq in a SUV420H1 amplified cell line (SCC-151), and analysis is ongoing. Preliminary RNA-seq analysis revealed upregulation of a number of type I IFN response genes after siRNA-mediated knockdown of SUV420H1. In vivo mouse experiments using SUV420H1 KO mouse cell lines are planned in a syngeneic HPV-negative HNSCC flank mouse model (MOC1) with or without anti-PD-1 treatment with the goal to assess whether SUV420H1 depletion affects tumor growth and/or sensitizes cancer cells to anti-PD-1 therapy. These data provide preliminary support for the function of SUV420H1 as an oncogene in HPV-negative HNSCC. Citation Format: Arfa Moshiri, Sohyoung Kim, Marie Luff, Vassiliki Saloura. SUV420H1 depletion reveals therapeutic potential in HPV-negative head and neck squamous cell carcinoma [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 1729.
Abstract 4630: Clinical and epidemiological profile of neuroendocrine differentiation- A hospital-based retrospective study
Authors: Yaru Wen, Susheng Shi
Journal: Cancer Research (2024)

Abstract Background: Neuroendocrine differentiation (NED) in carcinomas is poorly studied globally, despite its distinct clinical features, disease progression, pathology, treatment outcomes, and poor prognosis. Therefore, it is imperative to conduct further analysis utilizing extensive clinical samples to unveil the clinical and epidemiological profile of NED. Methods: A retrospective study was conducted to analyze the histopathological samples of patients diagnosed with malignant tumor using immunohistochemical techniques for NED markers, such as ChrA, Syno and CD56. The morbidity and prognosis of NED patient would be analyzed subsequently. Eligible patients must have pathologically confirmed gastric cancer, colorectal cancer, lung cancer, esophageal cancer and prostate cancer with no prior neoadjuvant chemotherapy or radiotherapy received before surgery. Patients aged 18-75 years with normal organ functions were enrolled. Results: Between January 2017 and June 2018, over 450 cases were enrolled. Preliminary analysis focused on 36 esophageal cancer (EC) and 44 prostatic cancer (PC) samples. NED markers were expressed in 4 (11.1%) of 36 EC patients, including 4 cases positive for Syno, 1 case positive for ChrA, and 2 cases positive for CD56. Meanwhile, NED markers were expressed in 15 (34.1%) of 44 PC patients, including 10 cases positive for Syno, 15 cases positive for ChrA, and 2 cases positive for CD56. Conclusion: Neuroendocrine differentiation is obviously observed in EC and PC. The encouraging prevalence rate of NED may have clinical implications for individualized treatment. Further research is needed to explore this area in more detail. Citation Format: Yaru Wen, Susheng Shi. Clinical and epidemiological profile of neuroendocrine differentiation- A hospital-based retrospective study [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 4630.