tbuckley/cabot-search huggingface dataset:
Melanoma TIL therapy commences era of cell-based immunotherapies
Authors: Ronan Talty, Rhys Richmond, Goran Micevic
Journal: British Journal of Dermatology (2024)

Two decades ago, the median survival for metastatic melanoma was only 5-9 months (1).Breakthroughs in research and clinical trials have spearheaded the approval of targeted therapies (BRAF-and MEK-inhibitors) and immune checkpoint inhibitors (PD-1, PD-L1, and CTLA-4) that have revolutionized the treatment landscape and led to improved survival for many patients with melanoma(2).The latest survival data for combined PD-1 and CTLA-4 blockade (Checkmate-067 trial) show a median survival of approximately 6 years (3).Despite this remarkable progress, only half of the patients with advanced melanoma respond to checkpoint therapy.Patients who do not respond have few treatment options, but that may be changing soon.In February 2024, the United States Food and Drug Administration approved lifileucel, a cell therapy using patient's own tumor-infiltrating T lymphocytes (TILs) to treat melanoma.This also represents the first cell therapy to be approved for a solid tumor of any type and marks a monumental step forward in cancer treatment.Cell therapies use live immune cells, rather than chemical compounds or molecules, to combat cancer.A form of cell therapy, CAR (chimeric antigen receptor) T cell therapy is well established in the treatment of hematologic malignancies, such as non-Hodgkin lymphoma, multiple myeloma, and acute lymphoblastic leukemia(4).However, the application of cell therapies to solid tumors has been limited thus far, despite proof-of-concept studies pioneered by Dr. Steven Rosenberg's group over three decades ago(5).With TIL therapy, T cells are isolated directly from the patients' tumors during surgery, expanded ex vivo with different cytokines, and reinfused back into the patient following a lymphocyte depleting protocol (Figure 1).Using
Abstract 2528: Genomic and immune microenvironment features influencing chemoimmunotherapy response in gastric cancer with peritoneal metastasis: A retrospective cohort study
Authors: Pengfei Yu, Guangyu Ding, Xingmao Huang, Chenxuan Wang, Jingquan Fang, Ling Huang, Zeyao Ye, Qi Xu, Xiaoying Wu, Junrong Yan, Qiuxiang Ou, Haimeng Tang, Yian Du, Xiangdong Cheng
Journal: Cancer Research (2024)

Abstract Background: Patients with peritoneal metastasis (PM) from gastric cancer (GC) exhibit poor prognosis. Chemoimmunotherapy offers promising clinical benefits; however, its efficacy and predictive biomarkers in a conversion therapy setting remain unclear. We aimed to retrospectively evaluate chemoimmunotherapy efficacy in a conversion therapy setting for GC patients with PM and establish a prediction model for assessing clinical benefits. Methods: A retrospective evaluation of clinical outcomes encompassed 55 GC patients with PM who underwent chemoimmunotherapy in a conversion therapy setting. Baseline PM specimens were collected for genomic and transcriptomic profiling. Clinicopathological factors, gene signatures, and tumor immune microenvironment were evaluated to identify predictive markers and develop a prediction model. Results: Chemoimmunotherapy achieved a 41.8% objective response rate and 72.4% R0 resection rate in GC patients with PM. Patients with conversion surgery showed better overall survival (OS) than those without the surgery (median OS: not reached vs 7.82m, P&amp;lt;0.0001). Responders to chemoimmunotherapy showed higher ERBB2 and ERBB3 mutation frequencies, CTLA4 and HLA-DQB1 expression, and CD8+ T cell infiltration, but lower CDH1 mutation and naïve CD4+ T cell infiltration, compared to non-responders. A prediction model was established integrating CDH1 and ERBB3 mutations, HLA-DQB1 expression, and naïve CD4+ T cell infiltration (AUC=0.918, 95%CI: 0.846-0.991), which were validated using an independent external cohort (AUC=0.785, 95%CI: 0.637-0.933). Conclusion: Our study comprehensively evaluated clinicopathological, genomic, and immune features and developed a novel prediction model, providing a rational basis for the selection of GC patients with PM for chemoimmunotherapy-involved conversion therapy. Citation Format: Pengfei Yu, Guangyu Ding, Xingmao Huang, Chenxuan Wang, Jingquan Fang, Ling Huang, Zeyao Ye, Qi Xu, Xiaoying Wu, Junrong Yan, Qiuxiang Ou, Haimeng Tang, Yian Du, Xiangdong Cheng. Genomic and immune microenvironment features influencing chemoimmunotherapy response in gastric cancer with peritoneal metastasis: A retrospective cohort 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 2528.
Abstract 6926: Tracing clonal evolution and immune evasion in glioblastoma progression
Authors: Davide Ceresa, Sebastian A. Garcia Mena, Francesca Piaggio, Appolloni Irene, Daniela Marubbi, Paolo Malatesta
Journal: Cancer Research (2024)

Abstract Glioblastoma continues to be a daunting obstacle in oncology research, with its early-stage progression being particularly enigmatic. In a recent published work, we traced the clonal dynamics of glioblastoma evolution by the simultaneous transfer of PDGFB and genetic barcodes into mouse brains. We observed a continuous clonal loss during the acquisition of a malignant phenotype, underlined by the modulation of the levels of c-Myc expression and their functional targets. In this study, we delve deeper into the evolution of glioblastoma by transplanting multiclonal, early-stage glioma cells into multiple immunodeficient NOD-SCID mice. This experimental design allowed us to track the clonal dynamics over serial transplants, revealing how early-stage glioma clones acquire immune-evasive features capable of initiating tertiary tumors in immune-competent hosts. Through barcode sequencing and single-cell RNA sequencing of early-stage gliomas, coupled with bulk RNA sequencing of secondary and tertiary gliomas, we dissected the clonal and transcriptomic landscape of these tumors. We observed that, of the various clones composing primary tumors, just a few of them are predominating in subsequent passages. Furthermore, the clonal composition of secondary tumors derived from the same primary glioma showed partial overlap, indicating a partial predetermination in the development of immune-evasive behavior. Our intra- and inter-clonal transcriptomic analysis across various stages of tumor progression is shedding light on how new functional traits can emerge in gliomas. Further analysis of our data will determine whether it is the result of the expansion of clones already possessing these traits, or if they stem from functional adaptations within the clones themselves. Our insights further reinforce the concept of clonal competition, highlighting the significant influence of immune-system interactions in driving these competitive dynamics. Citation Format: Davide Ceresa, Sebastian A. Garcia Mena, Francesca Piaggio, Appolloni Irene, Daniela Marubbi, Paolo Malatesta. Tracing clonal evolution and immune evasion in glioblastoma progression [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 6926.
Abstract 4793: Effects of treatment delays on lung cancer survival
Authors: Percy Guzman Montero, Sharon Segura Cordero
Journal: Cancer Research (2024)

Abstract Background: Previous studies have established a link between treatment initiation delays and reduced overall survival in individuals diagnosed with lung cancer. These delays are often influenced by diagnostic complexities, logistical hurdles, and patient-related factors. However, the association between treatment delays and survival outcomes has yet to be extensively investigated using data from a large national cohort. This study aims to fill this research gap and provide unique insights into the relationship between treatment delays and lung cancer survival by utilizing data from a substantial national cohort. Methods: The study population consisted of 3,723 lung cancer patients participating in the NCI PLCO Cancer Screening Trial. Cox Proportional Hazards (PH) Regression analyses examined the time between cancer diagnosis and treatment initiation using several measures including intervals from tumor doubling/stage progression time models by Spratt et al. (1964) and Detterbeck et al. (2008). Analyses controlled for patient and clinical characteristics including age, sex, race/ethnicity, smoking status, histopathologic type, cancer stage, and treatment modality. Data analysis was conducted using Microsoft Excel, STATA, and IBM SPSS software. Results: PH Regression analyses demonstrated a clear association between longer time intervals from diagnosis to treatment initiation and increased risk of mortality. Patients with time intervals exceeding 20 days exhibited a hazard ratio (HR) for mortality of 1.21 (p &amp;lt; 0.001, 95% confidence interval [CI] 1.1158-1.3176). The Spratt tumor progression model, considering intervals exceeding 88 days, revealed a HR of 1.22 (p = 0.03, 95% CI 1.0146-1.4885). On the other hand, the Detterbeck model, which considered intervals exceeding 118 days, did not show a statistically significant association with increased mortality risk. Furthermore, PH analysis identified cigarette smoking status, marital status, and tumor grade as significant predictors of mortality risk. Conclusions: Data from a large national cohort study indicate that delays in lung cancer treatment initiation have detrimental impacts on survival. Treatment initiation shortly after diagnosis had the most significant differential impact on mortality risk. Timely initiation of treatment is of utmost importance and should be prioritized in lung cancer care. By addressing factors contributing to treatment delays, it is likely possible to improve the survival rates of patients with lung cancer. Citation Format: Percy Guzman Montero, Sharon Segura Cordero. Effects of treatment delays on lung cancer survival [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 4793.
Abstract 2517: The amplification of TPX2 is a potential biomarker of oxaliplatin-sensitivity of colorectal cancers (CRCs) with CIN phenotype
Authors: Shohei Ueno, Taichi Isobe, Ryosuke Taguchi, Kenji Tsuchihashi, Koichi Akashi, Eishi Baba
Journal: Cancer Research (2024)

Abstract The amplification of Chr20q11.21 harboring TPX2 gene is the most frequent copy number alteration among the cases of colorectal cancers (CRCs), especially left-sided ones. We retrospectively examined 2828 cases of CRC patients who took cancer-genome panel tests in Japan between June 2019 and November 2022. The time to first-line treatment failure was longer with regimen with oxaliplatin than with those with irinotecan in CRC patients with Chr20q11,21 amplification (12.2 versus 9.2 months, p=0.0481). Oxaliplatin induces double-strand breaks (DSBs) and then cellular apoptosis. A key event of the DNA damage response to DSBs for cellular survival is the extensive phosphorylation of Ser139 of Histone H2AX adjacent to the chromosomal break. TPX2 whose gene resides in Chr20q11,21 has been reported to repress the phosphorylation of H2AX upon ionizing radiation. The purpose of this study is to identify the relationship between the amplification of TPX2 and oxaliplatin sensitivity in human CRCs. The knockdown of TPX2 decreased the oxaliplatin-susceptibility of COLO320 and Caco-2, CIN phenotype CRC cell lines which highly expressed TPX2. However, TPX2 knockdown did not reduce the oxaliplatin sensitivity of HCT-116, an MSI phenotype CRC cell line with low-level of TPX2 expression. The knockdown of TPX2 in CIN phenotype CRC cells, not in the MSI phenotype CRC cells, enhanced the phosphorylation of H2AX upon the DNA-damage induced by oxaliplatin. These findings suggest that amplification of TPX2 contributes to the oxaliplatin-susceptibility of CRCs with CIN phenotype through DNA repair machinery. Citation Format: Shohei Ueno, Taichi Isobe, Ryosuke Taguchi, Kenji Tsuchihashi, Koichi Akashi, Eishi Baba. The amplification of TPX2 is a potential biomarker of oxaliplatin-sensitivity of colorectal cancers (CRCs) with CIN phenotype [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 2517.
Abstract 2514: Adjuvant chemotherapy drug response-related gene detection using JASPAC01 pancreatic cancer resection cohort
Authors: Yukiyasu Okamura, Tomohisa Otsu, Masamichi Hayashi, Ryo Ashida, Katsuhiko Uesaka
Journal: Cancer Research (2024)

Abstract Background of Purpose: Although various multidisciplinary treatments have been attempted for pancreatic cancer, sufficient improvement in prognosis has not been achieved. It is necessary to establish biomarkers that can predict the malignant potential for each patient and the therapeutic effect of chemotherapy in order to select the optimal treatment for each individual case.This study was designed as a companion study to the phase III comparative study (JASPAC 01 of gemcitabine (GEM) and S-1 therapy as adjuvant chemotherapy after pancreatectomy. Among the 22 candidate biomarker genes that have been reported to be involved in pancreatic cancer treatment prognosis, we focused on E2F transcription factor 7 (E2F7), which is associated with a significantly poor overall survival rate when highly expressed. E2F7 is one of the target proteins of p53 and has been reported to be involved in cell cycle regulation. We examined the possibility of E2F7 expression in pancreatic cancer surgery and the effect of adjuvant chemotherapy. Patients and Methods: After optimizing the E2F7 imunostaining protocol, we scored E2F7 protein expression using the slides from excised tissues from JASPAC 01 registered cases. We investigated the relationship between malignancy and treatment efficacy using the case cohort treatment allocation information, clinicopathological information, and prognosis data. Results: Immunostaining was performed on approximately 330 resected pancreatic cancer specimens from 24 facilities nationwide. Of the 311 patients for whom E2F7 protein expression could be scored, 202 patients who completed the assigned treatment were included in the analysis. In 88 cases with high E2F7 expression, no significant difference in clinicopathological factors was observed between the S-1 treatment group and the GEM treatment group, but the S-1 treatment group showed better recurrence-free survival (RFS, P=0.066) and overall survival (OS, P=0.015) were observed. On the other hand, in the 114 patients with low E2F7 expression, there was no significant difference in clinicopathological factors between the two groups (RFS, P=0.168, OS: P=0.276). High E2F7 expression in pancreatic cancer tissues may affect S-1 sensitivity, GEM resistance, or both. Conclusions: It is considered that high expression E2F7 in pancreatic cancer may affect the therapeutic efficacy of GEM and S-1, which are frequently used in adjuvant chemotherapy for pancreatic cancer. Citation Format: Yukiyasu Okamura, Tomohisa Otsu, Masamichi Hayashi, Ryo Ashida, Katsuhiko Uesaka. Adjuvant chemotherapy drug response-related gene detection using JASPAC01 pancreatic cancer resection cohort [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 2514.
Abstract 4737: The combination of the BET inhibitor JQ1 and gemcitabine induces regressions in gemcitabine resistant patient-derived xenograft models of pancreatic cancer
Authors: Aubrey L. Miller, Samuel C. Fehling, Eric Josh Brown, Eric O. Heard, Tracy L. Gamblin, Rebecca B. Vance, Karina J. Yoon
Journal: Cancer Research (2024)

Abstract Efforts to develop targeted therapies for drug resistant tumors have been relatively unsuccessful. The 5-year survival for patients with advanced pancreatic cancer is ~3%. Gemcitabine is usually combined with nab-paclitaxel as a standard of care for treatment of locally advanced or metastatic pancreatic ductal adenocarcinoma (PDAC). However, no chemotherapeutic regimens thus far evaluated have been curative. We developed the first PDAC patient-derived xenograft (PDX) models in which resistance against gemcitabine was acquired in vivo. We used RNA-seq and ingenuity pathway analysis to compare expression profiles of paired parent vs gemcitabine resistant PDX models. This comparison suggested a previously unreported mechanism for gemcitabine resistance, involving aberrations of cholesterol biosynthesis and lipid metabolism pathways. We also made the unexpected observation that gemcitabine-resistant PDAC models derived from primary tumors have high levels of 3-hydroxy-3-methylglutaryl-CoA synthase 2 (HMGCS2), an enzyme essential to cholesterol biosynthesis and rate limiting in ketogenesis. Notably, the BET bromodomain inhibitor JQ1 decreases HMGCS2 levels; and BET inhibitors + gemcitabine exert synergistic cytotoxicity in gemcitabine-resistant PDAC cells. We determined that the BET bromodomain inhibitor JQ1 + gemcitabine induces regressions of two in vivo gemcitabine-resistant tumor models which we developed directly from primary human tumor tissue. These mechanism-based studies suggest that inhibiting HMGCS2 represents a novel approach to therapy for PDAC. We propose that combining gemcitabine with agents that decrease levels of HMGCS2 comprises effective treatment for patients with drug resistant PDAC. Citation Format: Aubrey L. Miller, Samuel C. Fehling, Eric Josh Brown, Eric O. Heard, Tracy L. Gamblin, Rebecca B. Vance, Karina J. Yoon. The combination of the BET inhibitor JQ1 and gemcitabine induces regressions in gemcitabine resistant patient-derived xenograft models of pancreatic 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 4737.
Abstract 360: Dissecting the role of oncogenic KRAS and ferroptosis within colorectal cancer
Authors: Alexandra Rosa-Vázquez, Vincent Bernard-Pagan, Jasper Chen, Cullen Taniguchi
Journal: Cancer Research (2024)

Abstract Introduction: Ferroptosis is a novel iron-dependent regulated cell death mechanism triggered by a toxic accumulation of membrane lipid peroxidation. This mechanism is counteracted by ferroptosis defense systems, such as the GPX4/GSH system, which function as antioxidants that limit lipid peroxidation. Oncogenic KRAS (KRASmut) is a key driver for many aggressive cancers, including colorectal cancer (CRC). Previous studies have suggested that oncogenic KRAS plays a pleiotropic role in the ferroptosis pathway. Yet, the interplay between oncogenic KRAS and ferroptosis has not been fully elucidated in CRC. Here, we aimed to dissect the role of oncogenic KRAS in ferroptosis using CRC as a cancer model. Methods: Cells from a KRAS-inducible model (iKAP) were seeded and treated with ferroptosis-inducing drugs (e.g., Erastin and RSL3) and/or a KRAS inhibitor (MRTX1133). Lipid peroxidation was then measured by BODIPY assay followed by flow cytometry to detect the quantity of BODIPY-stained cells. Protein expression of known ferroptosis defense mechanisms was also profiled (e.g., SLC7A11 [xCT] and GPX4). Results: Results from this study demonstrate that KRASmut activation leads to a reduction in mean fluorescence intensity when compared to KRASWT of BODIPY-stained cells. This decreased mean fluorescence intensity is indicative of lower levels of lipid peroxidation and, consequently, ferroptosis. KRASmut cells were also found to be resistant to ferroptosis following treatment with ferroptosis inducers. To replicate a pharmacologically induced KRASWT phenotype, iKAP cells were treated with MRTX1133, which led to a significant decrease in viability when combined with RSL3. We observed a decreased protein expression of the membrane antiporter xCT following treatment with MRTX1133, which we believe works synergistically with the GPX4 inhibition of RSL3. Conclusion: We observed that KRASmut may induce resistance to ferroptosis in vitro in CRC cells. Genetic and pharmacological inhibition of KRAS resulted in sensitization to ferroptosis inducers. Future work will uncover mechanisms through which oncogenic KRAS leads to ferroptosis resistance in CRC. More importantly, understanding the interaction between ferroptosis, oncogenic KRAS, and its antagonist systems has significant therapeutic potential in oncology. Citation Format: Alexandra Rosa-Vázquez, Vincent Bernard-Pagan, Jasper Chen, Cullen Taniguchi. Dissecting the role of oncogenic KRAS and ferroptosis within colorectal 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 360.