tbuckley/cabot-search huggingface dataset:
Abstract 6937: High throughput single cell simultaneous DNA and RNA sequencing identified cell-of-origin of breast cancer
Authors: Kaile Wang, Rui Ye, Shanshan Bai, Zhenna Xiao, Lei Yano, Jianzhuo Li, Yiyun Lin, Emi Sei, Steven Lin, Alastair Thompson, Savitri Krishnamurthy, Nicholas Navin
Journal: Cancer Research (2024)

Abstract Understanding the relationship between genotype and phenotype in breast cancer cells has been challenging at single cell resolution, mainly because existing high-throughput methods are limited to measuring a single modality and data must be integrated indirectly via computational methods. To address this challenge, we developed wellDR-seq, a high-throughput single cell method that can simultaneously measure the single cell whole genome and transcriptome directly from thousands of single cells in parallel. Using this method, we profiled 17,427 single cells in 6 different ER+ breast cancer patients with either premalignant disease (Ductal-carcinoma-in-situ) or invasive ductal carcinoma (IDC). From these data we identified the epithelial cell-of-origin in 3 cases, showing that ER+ breast cancer cells originated from Luminal Hormone Responsive (LumHR) in the normal breast tissues. We also found that autosomal somatic copy number aberrations were exclusively present in LumSec (&amp;lt; 2%) and LumHR epithelial cells, while chrX gain or loss also occurred in stromal cells (eg fibroblast and endothelial) but a low frequency (&amp;lt;2%) in our datasets. Additionally, our data show the impact of subclonal copy number profiles on gene expression programs, which reflects both gene dosage effects in CNA regions and more complex deregulation in copy-neutral regions. wellDR-seq offers a powerful tool for large-scale single cell genome and transcriptome simultaneous sequencing across different clinical samples, opens new avenue to investigate genotype and phenotypes interactions, identify tumor cells origins, reveal somatic copy number and mutation events, quantify the gene dosage effect and discerning differential genes expression between tumor subclones. Citation Format: Kaile Wang, Rui Ye, Shanshan Bai, Zhenna Xiao, Lei Yano, Jianzhuo Li, Yiyun Lin, Emi Sei, Steven Lin, Alastair Thompson, Savitri Krishnamurthy, Nicholas Navin. High throughput single cell simultaneous DNA and RNA sequencing identified cell-of-origin of 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 6937.
Abstract 668: Enhancing chemosensitivity of lung adenocarcinoma via Y-box binding protein 1 (YB-1) inhibition
Authors: Jee Min Lee, Dhanir Tailor, Fernando J. Garcia-Marques, Abel Bermudez, Sharon Pitteri, Sanjay V. Malhotra
Journal: Cancer Research (2024)

Abstract Background: Y-box binding protein 1 (YB-1, YBX1) is a multifunctional nucleic acid binding protein that regulates the expression of various genes by binding to their mRNA and stabilizing them. In over 20 cancer types, including lung adenocarcinoma (LUAD), YBX1 expression is significantly elevated in tumor samples compared to normal tissue. Within cancer cells, YB-1 promotes the expression of genes involved in tumorigenesis and chemoresistance. Consequently, elevated YBX1 expression in tumor is associated with poor clinical outcomes and significantly reduced overall survival in LUAD patients. Therefore, YB-1 emerges as a promising therapeutic target for LUAD treatment. Utilizing a small molecule YB-1 inhibitor, CET056, we performed a series of in vitro and in vivo analyses to assess the therapeutic efficacy of YB-1 inhibition and unravel YB-1’s role in tumorigenesis and disease progression in LUAD. Methods: Four human and one mouse LUAD cell lines were treated with CET056 and/or chemotherapeutic drugs and analyzed for the in vitro therapeutic activity of CET056. Using xenograft and syngeneic LUAD mouse models, the preclinical therapeutic efficacy of CET056 on disease progression of LUAD was also tested. Results: CET056 was shown to effectively decrease YB-1 expression in both human and mouse LUAD cell lines and exert inhibitory effects on LUAD in vitro and in vivo. This treatment delayed tumor progression and metastasis in CMT-64 syngeneic mouse model. Proteomics analysis revealed that translational machinery-associated pathways were down-regulated in LUAD cells after CET056 treatment whereas apoptosis and cell death-associated pathways were up-regulated. In alignment with this finding, CET056 treatment in combination with cisplatin showed chemo-sensitizing effect on LUAD in vitro and in vivo. Conclusion: Our studies suggest that YB-1 could be a promising target for combating chemoresistance in LUAD. Inhibition of YB-1 with a small molecule drug as a monotherapy or combination therapy could an effective strategy to treat LUAD. Citation Format: Jee Min Lee, Dhanir Tailor, Fernando J. Garcia-Marques, Abel Bermudez, Sharon Pitteri, Sanjay V. Malhotra. Enhancing chemosensitivity of lung adenocarcinoma via Y-box binding protein 1 (YB-1) inhibition [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 668.
Abstract 4822: Disparities in receiving non-surgical therapy impact outcomes in non-metastatic gastric cancer in Louisiana
Authors: Conner D. Hartupee, Kyla Maupin, Denise M. Danos, Omeed Moaven
Journal: Cancer Research (2024)

Abstract Background: Given the history of evolving medical therapies and advancements in cancer treatments over the last decades, resectable gastric cancer has presented multiple strategies for care. Previous literature indicates historically decreased use of multimodal therapies in minority populations. This study aims to evaluate Louisiana patient populations for rates of definitive treatment, inequities in access to care, and evaluating its impact on the outcomes of minorities and underserved population. Methods: Patients with non-metastatic primary invasive gastric cancer, with T2-4 or any T status with positive lymph nodes, were identified in the Louisiana Tumor Registry using ICD-O codes and AJCC staging system. Receipt of non-surgical therapy was modeled using logistic regression. Overall survival (OS) was modeled using a Cox proportional hazards model. Results: The study included 561 patients, of which 37.6% (n=211) did not receive surgical treatment and 16.2% (n=91) did not receive non-surgical therapy. A subset of the cohort received no definitive treatment, (6.8%, n=38). In a demographic only multivariable model, adjusting for age, sex, and race, age 70 and over [OR (95%CI) =0.18 (0.08-0.42), p&amp;lt;0.001] and female sex [OR (95%CI) =0.48 (0.28-0.85), p=0.011] was associated with decreased rates of non-surgical therapy. Black [OR (95%CI) = 0.54 (0.31-0.93), p=0.027] and Hispanic [OR (95%CI) = 0.38 (0.13-1.08), p=0.070] race was associated with decreased receipt of non-surgical therapies. However, after adjusting for domestic partner, insurance status, rurality, area poverty, and surgery status, racial disparities were no longer significant compared to whites: Black [OR (95% CI) = 0.59 (0.33-1.06), p=0.075]; Hispanic [OR (95% CI) = 0.52 (0.17-1.66), p=0.272]. In multivariable analyses, receipt of surgery [HR (95% CI) = 0.3 (0.23 - 0.38), p&amp;lt;0.001) and any non-surgical therapy [HR (95% CI) = 0.43 (0.31 - 0.60), p&amp;lt;0.001) were associated with increased overall survival. Conclusion: A significant number of patients did not receive all modalities of the multidisciplinary treatment that is recommended for patients with non-metastatic gastric adenocarcinoma. Black patients and females are less likely to receive non-surgical modalities for gastric cancer in Louisiana, which is, at least, partially driven by socioeconomic determinants. Identifying patients with these risk factors is a crucial step in allocating resources to increase access the care and improve outcomes. Citation Format: Conner D. Hartupee, Kyla Maupin, Denise M. Danos, Omeed Moaven. Disparities in receiving non-surgical therapy impact outcomes in non-metastatic gastric cancer in Louisiana [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 4822.
Abstract 5523: granulocyte-colony stimulating factor secreted from cancer associated fibroblasts initiates tumorigenesis and metastasis in triple negative breast cancer
Authors: Noriko Gotoh, Yasuto Tacheuchi, Takahiko Murayama, Risa Kashimura, Kazuhiro Ikeda, Kuniko Horie, Satoshi Inoue, Koji Okamoto
Journal: Cancer Research (2024)

Abstract Although cancer stem-like cells (CSCs) interact with cancer-associated fibroblasts (CAFs), it remains obscure how it occurs and what are the functional roles of this interaction. When patient-derived breast cancer cells (BCCs) were co-cultured with CAFs, significantly more spheroids were formed compared to those cells cultured alone. This suggests that CAFs produce soluble factors that increase the tumor-initiating ability of CSCs. Transcriptome analysis revealed that the expression of granulocyte colony stimulating factor (G-CSF) was highly upregulated in the conditioned medium of CAFs co-cultured with BCCs. Tumor-initiating ability was increased in the presence of G-CSF. Furthermore, G-CSF neutralizing antibody treatment suppressed tumorigenesis and bone metastasis in the patient-derived xenograft (PDX) model. These findings indicate that G-CSF secreted by CAFs induces CSCs to initiate tumors and metastasis. Inhibition of G-CSF would be a novel therapeutic target for breast cancer. Citation Format: Noriko Gotoh, Yasuto Tacheuchi, Takahiko Murayama, Risa Kashimura, Kazuhiro Ikeda, Kuniko Horie, Satoshi Inoue, Koji Okamoto. granulocyte-colony stimulating factor secreted from cancer associated fibroblasts initiates tumorigenesis and metastasis in triple negative 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 5523.
Abstract 5899: Evaluation of Up284 as a selective proteasome inhibitor for prostate cancer therapy
Authors: Balasubramanyam Karanam, Ravi Anchoori, Yung Chang
Journal: Cancer Research (2024)

Abstract Recent research into prostate cancer treatment has unveiled a promising contender known as Up284. In laboratory experiments, this compound has exhibited a remarkable preference for targeting prostate cancer cells as opposed to normal cells. Specifically, in vitro cell viability assays using MTT have shown that prostate cancer cells display high sensitivity to Up284 at low nanomolar IC50 values, while primary human prostate epithelial cells and mouse keratinocytes exhibit minimal sensitivity. This establishes a notable therapeutic window between cancerous and non-cancerous cells, with Up284 significantly inhibiting colony formation in PC3 cells. Additional functional assays have confirmed Up284's potential, including the 4UbFL Reporter Gene assay, which has revealed robust, dose-dependent proteasome inhibition. This effect is supported by the accumulation of polyubiquitinated proteins in various prostate cancer cell lines following Up284 treatment, suggesting a distinct mechanism of toxicity compared to bortezomib. Furthermore, Up284 has been found to induce apoptosis in PC3 cells, surpassing the efficacy of bortezomib. Competitive binding assays have shown that Up284 exhibits a stronger binding affinity to the proteasomal receptor RPN13 than the prototype inhibitor RA190B. This is further supported by a Cellular Thermo Stabilization Assay (CETSA), which indicates that Up284 stabilizes RPN13 in cells. A preliminary in vivo study utilizing the bone metastatic prostate cancer genetically engineered mouse model(BMPC GEMM) model for metastatic prostate adenocarcinoma has demonstrated that Up284 leads to significant tumor regression and increased levels of poly-ubiquitinated proteins in residual tumor tissues. Moreover, when Up284 is conjugated with an E3 ligase ligand, it successfully degrades RPN13, resulting in the death of PC3 cells. Up284 has also shown favorable pharmacokinetics/pharmacodynamics (PK/PD) profiles and safety in animal models. It is well-tolerated in mice and holds promise for oral administration, demonstrating a proteasome-dependent reporter protein stabilization effect superior to ixazomib. Importantly, Up284 has induced tumor regression and improved survival rates in various cancer models, including ovarian and breast cancers. In conclusion, Up284 emerges as a lead candidate for targeted prostate cancer therapy due to its high specificity, substantial therapeutic index, and potent anti-cancer activity both in vitro and in vivo. Further development and clinical investigation of Up284 are warranted to fully explore its therapeutic potential. Citation Format: Balasubramanyam Karanam, Ravi Anchoori, Yung Chang. Evaluation of Up284 as a selective proteasome inhibitor for prostate cancer 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 5899.
Abstract 3970: Impairment of tumor reactive CD8 T cells in liver cancer
Authors: Rajiv S. Trehan, Marlaine Soliman, Xin Wang, Patrick Huang, Noemi Kedei, Xiao Bin Zhu, Matthias Seifert, Mohamed-Reda Benmebarek, Amran Nur, Firouzeh Korangy, Chi Ma, Tim F. Greten
Journal: Cancer Research (2024)

Abstract Tumor reactive (TR) CD8 T cells in the liver have been studied in the setting of both immunotherapy and cellular therapy with the predominant dogma that these cells have equivalent functionality in the liver as compared to other organ sites. Herein, we detail that TR+ CD8 T cells are functionally impaired in the liver immune microenvironment in mice with liver tumors.TR+ CD8 T cells were studied in BALB/c and C57BL/6 mice injected intrahepatic, intravenous, and subcutaneously with either a colon (CT26) or a melanoma (B16F10) cancer cell line to create intrahepatic, pulmonary and subcutaneous tumors, respectively. Additionally, an ⍺CD8 antibody with IgG control was used to conduct functional studies. Samples were analyzed using flow cytometry and liver weights were measured. A high frequency of TR+ CD8 T cells were found in the liver in mice with intrahepatic tumors. Despite ~70% of CD8 T cells being tumor reactive in intrahepatic tumors, liver tumor growth kinetics were faster than subcutaneous tumors. Higher proportion of the TR+ CD8 T cells were found to be exhausted in the liver tumor by flow cytometry. Functional depletion of the CD8 T cells caused a fivefold higher tumor growth in the subcutaneous model but in contrast had no effect on intrahepatic tumors. In conclusion, despite the high frequency of “killer” tumor reactive T cells in the liver, the growth kinetics of the liver tumors, flow cytometry as well as functional studies demonstrate the impairment of TR+ CD8 T cells in the liver. We aim to dissect the mechanisms mediating intrahepatic TR CD8+ T cell exhaustion in primary liver tumors as well as metastatic models. Additionally, we aim to determine significant costimulatory molecules specific to intrahepatic exhaustion which could lead to better therapeutic models. Citation Format: Rajiv S. Trehan, Marlaine Soliman, Xin Wang, Patrick Huang, Noemi Kedei, Xiao Bin Zhu, Matthias Seifert, Mohamed-Reda Benmebarek, Amran Nur, Firouzeh Korangy, Chi Ma, Tim F. Greten. Impairment of tumor reactive CD8 T cells in liver 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 3970.
Abstract 1717: RAS and PP2A co-regulated phosphosite on KDM1A dictates its substrate specificity &amp; transcriptional outcome
Authors: Mukund Sharma, Anna Aakula, Jesse Kamila, Reetta Nätkin, Tiziana Bonaldi, Saverio Minucci, Matti Nykter, Jukka Westermarck
Journal: Cancer Research (2024)

Abstract RAS-mediated human cell transformation requires simultaneous inhibition of tumor suppressor phosphatase PP2A; however, the target phosphosites co-regulated by RAS and PP2A are poorly characterized. In this study, we describe the phosphoregulation of an epigenetic regulator, KDM1A, by RAS and PP2A. KDM1A is a lysine-specific demethylase that can act as a transcriptional activator or inhibitor, depending on its specific activity toward various histone marks. However, the post-translational modifications regulating the substrate specificity of KDM1A are poorly addressed. We found that KDM1A physically interacts with PP2A through a conserved binding motif, and that mutating the motif residues decreased its interaction with PP2A. Additionally, PP2A activation or RAS inhibition led to increased chromatin recruitment of KDM1A. This enhanced chromatin recruitment of KDM1A was recapitulated upon CRISPR/CAS9-mediated substitution of the PP2A/RAS-targeted serine to alanine. Using histone proteomics, we further identified that the RAS/PP2A-regulated phosphosite determines the substrate specificity of KDM1A. This is evidenced by an increased demethylation of histone H3K9me2/3, a marker of gene activation. The differential gene expression profile of the phosphorylation mutants of KDM1A predominantly showed increased gene expression, further validating our findings. The gene expression profiles of KDM1A phosphomutant RAS mutant cells demonstrate gene level specificity indicating that this newly discovered KDM1A phosphoswitch has an important role in specifying KDM1A function in cancer. Collectively, our results demonstrate that RAS and PP2A activities converge on phosphoregulation of epigenetic machinery in cancer cells. This RAS and PP2A co-regulated phosphosite on KDM1A dictates both its histone mark specificity and transcriptional outcome. Citation Format: Mukund Sharma, Anna Aakula, Jesse Kamila, Reetta Nätkin, Tiziana Bonaldi, Saverio Minucci, Matti Nykter, Jukka Westermarck. RAS and PP2A co-regulated phosphosite on KDM1A dictates its substrate specificity &amp; transcriptional outcome [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 1717.
Abstract 5926: YB-1 inhibition as an effective approach for the treatment of osteosarcoma
Authors: Kirsten Stefan, Arpit Dheeraj, Dhanir Tailor, Lara E. Davis, Sanjay V. Malhotra
Journal: Cancer Research (2024)

Abstract Background: Osteosarcoma (OS) is a bone cancer primarily affecting adolescents and young adults, with about 20% of patients having detectable metastatic disease at the time of diagnosis. Despite a large number of clinical trial efforts, metastatic sarcoma remains a lethal disease, and there have been no meaningful advances in therapy or improvements in patient outcomes for decades. Y-box binding protein 1 (YB-1) is a multifunctional cold-shock protein that translationally activates diverse stress response factors with pro-metastatic activities in many cancer types. Importantly, YB-1 is strongly associated with poor outcomes in sarcoma patients and is a major metastatic driver in high-risk sarcomas. Methods: We recently described a novel compound, CET056, that inhibits cancer progression via YB-1 inhibition. We hypothesized that CET056 had the potential to suppress the progression of OS and could provide a new treatment for this disease. We screened osteosarcoma human and mouse cell lines for YB-1 protein expression. OS cells were functionally characterized for responses to CET056 in vitro and in vivo. Results: YB-1 expression was seen in nearly all cell lines tested. CET056 treatment of OS cells resulted in reduced cell viability and YB-1 protein expression in a dose- and time- dependent manner, as well as reduced formation of colonies and spheroids. In vivo efficacy studies, which employed a syngeneic subcutaneous tumor model, revealed that CET056 effectively inhibited tumor progression and enhanced overall survival in contrast to vehicle treated control mice. Conclusion: These results support our hypothesis and illustrate that YB-1 inhibition by CET056 is a promising candidate for further development as a therapy for OS. Citation Format: Kirsten Stefan, Arpit Dheeraj, Dhanir Tailor, Lara E. Davis, Sanjay V. Malhotra. YB-1 inhibition as an effective approach for the treatment of osteosarcoma [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 5926.
Abstract 2536: Multimodal stratification of predictive biomarkers in head and neck cancers: A focus on cytokine-based immunotherapy
Authors: Corinne Ramos, Richard Ruez, Sandra Delebecq, Victor Senechal
Journal: Cancer Research (2024)

Abstract Background Immunotherapy, particularly cytokine-based therapy, has been gaining traction in the treatment of head and neck cancers. Cytokines are small proteins that play a crucial role in the immune response to cancer. However, not all patients respond to cytokine-based immunotherapies, and some may experience severe side effects. The ability to predict which patients are most likely to benefit from these therapies could greatly improve the efficacy and tolerability of treatment. In this context, the study of predictive biomarkers, such as the expression of immune checkpoint molecules like PD-L1 and TIGIT, and the profiling of cytokines within the tumor microenvironment, has become crucial. These biomarkers could provide valuable information about the patient's immune response to the tumor and their likelihood of responding to cytokine-based immunotherapies. Method A multimodal approach to stratify predictive biomarkers in head and neck cancers was used. The methodology was founded on combining metabolic, transcriptomic, and proteomic data to offer a comprehensive understanding of potential biomarkers. The data from different modalities were integrated using bioinformatics and machine learning algorithms. This comprehensive dataset was analyzed to identify multimodal biomarker signatures that could predict patient responses to cytokine-based therapies. Result Preliminary finding showed significant heterogeneity in the expression of PD-L1, TIGIT, and various cytokines across the tumor microenvironment. This underscored the complexity of head and neck cancers. Certain multimodal biomarker signatures, which included specific patterns of immune checkpoint molecule expression, cytokine profiles, and immune cell infiltration, correlated robustly with patient responses to cytokine-based therapies. Conclusion Our study demonstrates the considerable potential of a multimodal stratification approach in deciphering the complexity of head and neck cancers and predicting responses to cytokine-based immunotherapies. By integrating metabolomic, transcriptomic, and proteomic data, we identified unique biomarker signatures that strongly correlated with therapy responses. This work underscores the invaluable role of integrated predictive biomarker profiles in enhancing the precision of immunotherapy. Citation Format: Corinne Ramos, Richard Ruez, Sandra Delebecq, Victor Senechal. Multimodal stratification of predictive biomarkers in head and neck cancers: A focus on cytokine-based immunotherapy [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 2536.