tbuckley/cabot-search huggingface dataset:
Abstract 4633: Differentiation driver gene HOXD4 as a potential prognostic indicator and therapeutic target in anaplastic thyroid cancer
Authors: Kaci Kopec, Tara Jarboe, Nicole R. DeSouza, Humayun K. Islam, Jan Geliebter, Raj K. Tiwari
Journal: Cancer Research (2024)

Abstract Anaplastic thyroid cancer (ATC) is always diagnosed as stage IV with a 5 year survival rate of less than 3% due to its aggressive metastatic phenotype. ATC lacks differentiation and loses its thyroid-like functions making it a difficult cancer to treat due to its lack of targetable genetic lesions and unresponsiveness to conventional treatments. Therefore, we investigated genes that had aberrant expression in ATC in relation to differentiation. Using NCBI Gene expression omnibus (GSE33630, GSE85457), which provides publicly available transcriptomic datasets, and bioinformatics software, GEO2R, we found that Homeobox D4 (HOXD4) has 12.5FC higher expression in ATC vs. normal tissue (p=0.000552) and 4.36FC higher in ATC vs. papillary thyroid cancer (PTC) in human patients (p=6.69e-08). HOXD4 is a transcription factor that plays a crucial role in cell differentiation and has been associated with a worse prognosis in cancers such as ovarian serous carcinoma. As loss of differentiation is essential to ATC’s refractory nature and therapeutic resistance, we are exploring modulation of differentiation by all-trans retinoic acid (ATRA). ATRA was used to induce differentiation in ATC cell line T238 therefore abrogating the aggressive phenotype of this cancer. T238 treated with ATRA had a 26% decrease in proliferation at 24 hours, 46% at 48 hours, and 87% at 72 hours measured using a trypan blue exclusion assay. T238 treated with ATRA also had a 44% decrease in migratory capacity at 24 hours and 24% at 48 hours measured by a cell scratch wound assay. Immortalized normal thyroid cell line NTHY-ori-3-1 did not have a significant decrease in either proliferation or migratory capacity when treated with ATRA. T238 cells treated with ATRA for 24 hours had a 30% decrease in HOXD4 protein levels. Lastly, immunohistochemistry staining of HOXD4 in human patient tissue samples confirmed the over-expression of HOXD4 in ATC (19.5% staining) vs. normal tissue (2.5%) and PTC (7.5%). Overall, we hypothesize that the aberrant expression of HOXD4 in ATC plays a crucial role in the aggressive metastatic phenotype and therefore differentiation agents such as ATRA can target this biomarker to modulate the ATC phenotype. Therefore, HOXD4 can be used as a potential prognostic indicator for early detection of ATC. Future studies will involve CRISPRi based knockdown of HOXD4 in vitro and validation of these results in animal in vivo models. Citation Format: Kaci Kopec, Tara Jarboe, Nicole R. DeSouza, Humayun K. Islam, Jan Geliebter, Raj K. Tiwari. Differentiation driver gene HOXD4 as a potential prognostic indicator and therapeutic target in anaplastic thyroid 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 4633.
Abstract 583: Spatiotemporal analyses of longitudinal specimens reveal mechanisms of response and resistance to immune checkpoint blockade in metastatic melanoma
Authors: Gao Zhang, Lisa Coussens, Meenhard Herlyn, Keith T. Flaherty, Genevieve Boland, Gordon Mills
Journal: Cancer Research (2024)

Abstract Although durable responses to immune checkpoint blockade (ICB) therapies exhibit by a subgroup of patients with metastatic melanoma, most of patients have no response or develop to acquired resistance to ICB therapies within few years. Molecular mechanisms of primary and acquired resistance to ICB therapies are still elusive, which warrants further elucidation. Here, we used a holistic approach to profile 35 longitudinal tumor specimens at pre-, on-, and post-treatment time points which were derived from 7 patients (3 responders and 4 non-responders) with metastatic melanoma who progressed on sequential ICB therapies, including anti-PD-1 and anti-CTLA-4 therapies. We integrated analyses of RNA sequencing, Whole-exome Sequencing (WES), NanoString nCounter vantage 3D, Cyclic Immunofluorescence (Cyc-IF), NanoString Digital Spatial Profiling (DSP) and Multiplex Immunohistochemistry (mIHC) data of these longitudinal tumor specimens to elucidate evolutionary trajectories that occurred in both the tumor and the tumor immune microenvironment (TiME) that may have orchestrated response and resistance to ICB therapies. Simultaneous analyses of genomic, transcriptomic and proteomic data identified the re-activation of MAPK-RAS as well as PI3K pathway upon or after ICB therapies, which may elucidate the mechanism of resistance to ICB therapies. Spatially-resolved, image-based immune monitoring analysis at single cell resolution revealed that the activation status of T cell markers and T-cell checkpoint is conversely associated with potential mechanism of resistance to ICB therapies. In summary, integrated analyses of muti-oics and spatially image-based data from longitudinal tumor specimens allow us not only to reveal the dynamic co-revolution of both tumor and immune cells in TiME following sequential ICB therapies but also to provide a comprehensive perspective to molecular mechanisms of response and resistance to ICB therapies in patients with metastatic melanoma. Citation Format: Gao Zhang, Lisa Coussens, Meenhard Herlyn, Keith T. Flaherty, Genevieve Boland, Gordon Mills. Spatiotemporal analyses of longitudinal specimens reveal mechanisms of response and resistance to immune checkpoint blockade in metastatic melanoma [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 583.
Abstract 1665: Investigating Daple-FLT3 gene fusion in leukemia cells and its response to kinase inhibitors
Authors: Elena Nguyen, Jason Ear
Journal: Cancer Research (2024)

Abstract Gene fusions are frequently found in leukemia and other cancers. The signaling scaffold protein, Daple (CCDC88C), has been found to undergo gene fusion to the receptor tyrosine kinase, FLT3. Specifically, a fragment of the coiled-coil domain from Daple and tyrosine kinase domain (TKD) of FLT3 are found fused together. How the gene product from this gene fusion functions in rewiring the signaling network in cells and whether this gene product can be targeted though pharmacological inhibitions remain unclear. Cell surface receptors, such as receptor tyrosine kinases (RTKs), activate cell signaling and genetic mutations that lead to constitutive receptor activation can promote unregulated cell proliferation, survival, and migration. Leukemia patients with hyperactive RTKs are treated with tyrosine kinase inhibitors (TKIs), such as Imatinib and Sorafenib. Here we demonstrate how TKIs can directly block the activation of Daple-FLT3 and prevent hyperactivation of its downstream pathways. Our studies unveil a strategy to identify other compounds which may serve as an additive, or alternative, approach to treating patients with Daple gene fusion. Citation Format: Elena Nguyen, Jason Ear. Investigating Daple-FLT3 gene fusion in leukemia cells and its response to kinase inhibitors [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 1665.
Abstract 5860: Understanding the biological role of MMP16 in cisplatin resistance in ovarian cancer
Authors: Jesennia Bonilla-Liriano, Mariela Rivera-Serrano, Victor Reyes-Burgos, Jose Rolon-Perez, Fatima Valiyeva, Pablo Vivas-Mejia
Journal: Cancer Research (2024)

Abstract High-Grade Serous Ovarian Cancer (HGSOC) is the most common and lethal of Ovarian Cancer (OC) types, which accounts for eighty percent of deaths. Treatment for OC includes surgery and platinum-based therapy. However, around 70% of women with HGSOC become resistant to chemotherapy. Therefore, new therapeutic agents with higher specificity and efficacy are needed for women with advanced and drug-resistant OC. Matrix metalloproteases (MMPs) are a group of enzymes involved in the degradation of the extracellular matrix (ECM). Deregulation of MMPs contributes to tumor growth and metastasis in several cancer types. Preliminary studies of our research team found that MMP16 is higher in cisplatin-resistant as compared with cisplatin-sensitive OC cells. The aim of this project is to understand the role of MMP16 in the cisplatin resistance of OC cells. We hypothesize that MMP16 increased expression may contribute to cancer progression and drug-resistance. We performed experiments in A2780/A2780CP20 and OVCAR3/OVCAR3CIS human OC cells. To assess the MMP16 protein levels we used western blot analysis. To measure the mRNA levels, we used qRT-PCR. Kaplan-Meier survival curves were generated by interrogation of the KM Plotter patient database. The MMP16 protein and qRT-PCR experiments confirmed that protein and mRNA levels are more abundant in cisplatin-resistant as compared with cisplatin-sensitive cells. Interrogation of the KM plotter database showed that OC patients with higher MMP16 mRNA levels live less as compared with OC patients with lower MMP16 levels. Ongoing experiments are testing the biological effect of small interference RNA (siRNA) targeting MMP16 in cisplatin-resistant OC cells. Citation Format: Jesennia Bonilla-Liriano, Mariela Rivera-Serrano, Victor Reyes-Burgos, Jose Rolon-Perez, Fatima Valiyeva, Pablo Vivas-Mejia. Understanding the biological role of MMP16 in cisplatin resistance in ovarian 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 5860.
Abstract 4650: RalBP1, a novel approach for ovarian cancer therapy
Authors: Sharad S. Singhal, Sravani Ramisetty, Atish Mohanty, Prakash Kulkarni, David Horne, Sanjay Awasthi, Ravi Salgia
Journal: Cancer Research (2024)

Abstract Ovarian cancer (OC) is the most devastating gynecologic cancer. The ever-climbing incidence rate of OC makes it the most lethal female reproductive disorder. Triggering apoptosis is one of the potential strategies to overcome chemoresistance. Recent evidence suggests that the failure of drug-induced apoptosis may be an underlying cause of drug-resistance. Molecular mechanisms of failed apoptosis in chemoresistant OC cells include p53 mutations, abnormal expression of the Bcl2 family proteins, and upregulation of other inhibitors of apoptosis that block caspases and stabilize the mitochondrial permeability pore. RalBP1 (Ral-binding protein) is a required stress-defense protein for OC, and its specific depletion or inhibition will cause apoptosis in cancer cells expressing RalBP1. RalBP1 is a multifunctional 76 kDa protein encoded as a splice variant in the human RALBP1 gene (18p11.22). RalBP1 is an ATP dependent efflux transporter for glutathione (GSH) conjugates (GS-E) of products of oxidative stress, like 4HNE and GSH-conjugates of chemotherapy drugs. Our recent studies indicate that upon depletion/inhibition of RalBP1, malignant cells are significantly more sensitive to apoptosis than non-malignant cells, suggesting that the stress-protective, anti-apoptotic activity of RalBP1 is necessary for malignant cells. This differential sensitivity to RalBP1 translates into tumor regression, a lack of toxicity, and the prolonged survival of mice bearing subcutaneous OC cells in which RalBP1 is inhibited by anti-RalBP1 IgG or depleted using RalBP1 antisense oligonucleotides. These studies demonstrate that inhibition or depletion of RalBP1 exerts anti-neoplastic effects in OC and indicate that this GS-E and xenobiotic transporter occupies an important position in the hierarchy of stress defense mechanisms necessary for cancer cell survival. Overall, the present research focuses on hypothesis-driven studies to define novel relationships between RalBP1 and signaling pathways, and to determine the suitability of RalBP1 as an anticancer target for OC. Citation Format: Sharad S. Singhal, Sravani Ramisetty, Atish Mohanty, Prakash Kulkarni, David Horne, Sanjay Awasthi, Ravi Salgia. RalBP1, a novel approach for ovarian 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 4650.
Abstract 2782: Characterization of quiescence-associated secretory profile (QuASP) in cancer: A novel defining feature and therapeutic target
Authors: Qi Jiang, Santiago Panesso-Gómez, Divya Natesan, Matthew L. MacDonald, Ronald J. Buckanovich
Journal: Cancer Research (2024)

Abstract Senescent cells have a unique senescence-associated secretory profile (SASP) and understanding SASP has contributed to numerous advances in knowledge on aging and cancer biology. Quiescence, which is an important yet poorly understood mechanism for chemoresistance, is related but distinct from senescence. Quiescence shares a non-proliferative feature with senescence but is a reversible state in which quiescent cells can reenter the cell cycle. We hypothesized that, analogous to senescent cells, quiescent cells have a distinct quiescence-associated secretory profile (QuASP) and that defining the QuASP will uncover new genes and pathways associated with cancer cell viability and therapeutic resistance. Indeed, suggesting quiescent cells have a unique and biologically important secretome, we found that tumor conditioned medium (TCM) from quiescent ovarian cancer cells (qOvCa) vs. TCM from proliferating cancer cells increased chemoresistance. Similarly, TCM from quiescent cancer cells vs. TCM from proliferating cancer cells suppressed T cell proliferation and INF-gamma/Granzyme B secretion, suggesting a QuASP immunosuppressive effect. RNASeq analysis of qOvCa cells revealed the secreted factor Follistatin (FST) is upregulated in qOvCa and acted as a paracrine pattern to induce chemoresistance. Furthermore, FST was found to be upregulated in peritumoral fluid following chemotherapy and FST levels in patients with OvCa predicted poor prognosis. To identify additional QuASP factors, we used an ER-BIOID labeled system and LC-MS/MS to characterize the secreted proteins from qOvCa induced by serum starvation compared with normal cells in three OvCa cell lines (PT412, PT340, HEY1). Quiescent OvCa cells indeed have a secretome that is highly unique from proliferating cells, with 137/577 upregulated proteins (LFC&amp;gt;1) and 65/577 downregulated proteins (LFC←1 or no detection in quiescence). Several proteins identified as upregulated have been linked to immunosuppression and/or chemoresistance, oncogenesis and cell cycle were selected for validation and further analysis (CLU, VGF, SERPINE1). In conclusion, we find quiescent cells have a unique quiescence associated secretory profile and that the QuASP induces chemoresistance and immunosuppression. As such, this study has important implications for cancer therapy. Citation Format: Qi Jiang, Santiago Panesso-Gómez, Divya Natesan, Matthew L. MacDonald, Ronald J. Buckanovich. Characterization of quiescence-associated secretory profile (QuASP) in cancer: A novel defining feature and therapeutic target [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 2782.
Abstract 2228: Long-term trajectories of functional disability in older adults with cancer
Authors: Gina E. Nam, Elizabeth Rose Mayeda, Zuo-Feng Zhang
Journal: Cancer Research (2024)

Abstract Background: Older individuals with cancer history have lower risk of developing Alzheimer’s disease (AD). Cognitive impairment is associated with lower functioning in Instrumental Activities of Daily Living (IADL) and Activities of Daily Living (ADL). However, little is known about long-term IADL and ADL trajectories among individuals with cancer, hindering understanding of the underlying biological mechanisms between cancer and AD. We investigated the long-term functional disability trajectories of adults with cancer, comparing them with similarly aged individuals without a cancer diagnosis. Methods: Our study included 16,006 individuals aged 50 and older without a cancer history at baseline from the Health and Retirement Study. Biennial assessments were conducted from 1998 to 2020, including self-reported cancer status, IADL, and ADL. Linear probability models with repeated measures were used to assess IADL and ADL independence probabilities, adjusting for demographic and socioeconomic covariates. Results: Among 16,006 participants (mean [SD] baseline age, 66.1 [9.9] years; 9,169 [57.3%] female), 3,723 (23.3%) reported a cancer diagnosis during follow-up. Before cancer diagnosis, individuals who later developed cancer had a higher probability of IADL independence and experienced a slower decline in independence compared to their similarly aged counterparts who remained cancer-free. Probability of IADL independence was 0.05 lower immediately after cancer diagnosis compared to the pre-cancer phase, followed by accelerated independence losses relative to the pre-cancer period. After diagnosis, the rate of decline in probability of IADL independence remained slower for individuals with cancer than their cancer-free counterparts, but differences in the rate of decline were smaller than prior to cancer diagnosis. Similar trends were observed for ADL independence. Conclusions: We observed a decline in both IADL and ADL independence around the time of cancer diagnosis, possibly attributed to treatments. Overall, individuals with cancer experienced a more gradual loss in functional independence compared to individuals who remained cancer-free, consistent with the documented inverse association between cancer and AD. Funding information: The current research was supported by the National Cancer Institute of the National Institutes of Health (T32CA009142), T32 Training Grants from the NCI/NIH, and the National Institute on Aging (RF1AG059872). Citation Format: Gina E. Nam, Elizabeth Rose Mayeda, Zuo-Feng Zhang. Long-term trajectories of functional disability in older adults with 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 2228.
Abstract 7416: GeneSetR: A web server for gene set analysis based on genome-wide Perturb-Seq data
Authors: Omer Faruk Kuzu, Fahri Saatcioglu
Journal: Cancer Research (2024)

Abstract Identification of genotype-phenotype relationships is of utmost importance and a core effort in biology. Recent developments in efficient and precise gene targeting approaches coupled to omics methods have significantly improved deciphering of molecular interactions and relationships. However, many single gene perturbations can affect the expression of hundreds of other genes and analysis of the resulting omics-derived gene lists currently remains a significant challenge. Here we present Perturb-Seq based Gene Set Analyzer (GeneSetR), a user-friendly web-server that can analyze user-defined gene lists based on the data from a recently published genome-wide Perturb-Seq study, which targeted 9,866 genes with 11,258 sgRNAs in the K562 cell line. Through this tool, users can cluster gene lists following dimensionality reduction by various algorithms, undertake network analysis from RNA sequencing data, identify key nodes among the submitted genes, perform gene signature analyses, and generate heatmaps based on perturbation or gene expression data. GeneSetR enables researchers to readily identify gene clusters associated with specific phenotypes or biological processes, providing insights into the potential functional roles of these clusters and the role of single genes in them. With robust analysis capabilities, GeneSetR is a powerful resource to facilitate the exploration of genotype-phenotype relationships. Citation Format: Omer Faruk Kuzu, Fahri Saatcioglu. GeneSetR: A web server for gene set analysis based on genome-wide Perturb-Seq data [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 7416.
Abstract 7479: Targeting the lipid kinase PIKfyve upregulates surface expression of MHC class I to augment cancer immunotherapy
Authors: Parth Borker, Yi Bao, Yuanyuan Qiao, Arul Chinnaiyan, Jae Eun Choi, Yuping Zhang, Rahul Mannan, Caleb Cheng, Tongchen He, Yang Zheng, Jiali Yu, Mahnoor Gondal, Gabriel Cruz, Sara Sara Grove, Xuhong Cao, Fengyun Su, Rui Wang, Yu Chang, Ilona Kryczek, Marcin Cieslik, Michael D. Green, Weiping Zou
Journal: Cancer Research (2024)

Abstract The widespread success of cancer immunotherapies suggests a promising future - but has been subverted by unresponsiveness and resistance. Current research has furthered the understanding of immunotherapy resistance through the findings of “hot” (responsive) and “cold” (unresponsive) tumors. Here, we focus on the genetic and pharmacological inhibition of PIKfyve, a lipid kinase regulator of autophagic flux and lysosomal biogenesis. We find that inhibition of PIKfyve results in the upregulation of major histocompatibility complex class I (MHC-I) surface expression in cancer cells (through inhibition of autophagic flux), resulting in increased CD8+ T cell-mediated cancer cell death. These findings were corroborated in multiple syngeneic mouse models, which also displayed increased intratumoral functional CD8+ T cells. In addition, the Pikfyve-depletion antitumor responses are CD8+ T cell and MHC-I dependent - as CD8+ T cell and B2m knockout rescued tumor growth - resulting in improved response to immune checkpoint blockable (ICB), adoptive cell therapy, and a therapeutic vaccine. Further, high PIKfyve expression predicts poor ICB response and is prognostic of poor survival in ICB-treated cohorts. Ultimately, these findings collectively suggest PIKfyve as an effective target to enhance immunotherapies through elevation of MHC-I surface expression in cancer cells, and accordingly, PIKfyve inhibitors have novel potential to increase immunotherapy response in cancer patients. Citation Format: Parth Borker, Yi Bao, Yuanyuan Qiao, Arul Chinnaiyan, Jae Eun Choi, Yuping Zhang, Rahul Mannan, Caleb Cheng, Tongchen He, Yang Zheng, Jiali Yu, Mahnoor Gondal, Gabriel Cruz, Sara Sara Grove, Xuhong Cao, Fengyun Su, Rui Wang, Yu Chang, Ilona Kryczek, Marcin Cieslik, Michael D. Green, Weiping Zou. Targeting the lipid kinase PIKfyve upregulates surface expression of MHC class I to augment cancer 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 7479.