tbuckley/cabot-search huggingface dataset:
Abstract 1014: Disparities of triple negative breast cancer in Mississippi
Authors: Navdeep Kaur, Javaria A. Khan, Jinghe Mao, Diva Melvin, Muhammad M. Hassan, Xinchun Zho
Journal: Cancer Research (2024)

Abstract Background: Triple-negative breast cancer (TNBC) accounts for about 10-15% of all breast cancers nationwide with disparities of incidence and outcomes among races, geographic locations, and other factors. This study is aimed to analyze the differences in the rate of TNBC, patient conditions at time of diagnosis, and death from TNBC among women in Mississippi. Methods: A retrospective study was conducted to serially review breast cancer cases diagnosed in the University of Mississippi Medical Center during May 2016 to May 2023. The entire breast cancer population was then stratified by race. The rate of TNBC, age and BMI at time of diagnosis, the rate of expiration were compared between African American (AA) and Caucasian American (CA) women with breast cancer. Two-tailed Student’s T-test was used to calculate the difference in mean values, and Chi-Square Test was used to compare the difference in rates or percentages. The significant p value was set at p&amp;lt;0.05. Results: In total 291 women with breast cancer, AA patients were 195 (67.01%), CA patients were 88 (30.24%), and other were 8 (2.75%). The mean age of all patients was 58.3 years-old (ranged 24-97). The mean BMI was 31.19. The patients with TNBC were 109 (37.46%) in entire studied population. A total of 32 (1.6%) patients, including 14 TNBC and 18 non-TNBC were expired with an average age of 61.84 and an average survival time of 20 months from diagnosis to expiration. As compared to CA patient population, AA breast cancer patients had onset at younger age (58.08±0.88 vs. 59.18±1.36), had a higher BMI (31.79±0.62 vs. 28.25±1.05, p=0.017), higher percentage of TNBC (41.54% vs. 30.68%, p=0.082 and OR=1.605), and higher rate of expiration (11.28% vs, 9.1%). Also, as compared to CA expired patients with breast cancer, AA expired patients had higher BMI (29.57 vs. 28.61), shorter survival time (17.5 months vs. 19.4 months), and died at younger age (61.84-year old vs. 66.38-year old) with a higher proportion of TNBC subtype (54.6% vs 12.5%, p=0.045, OR=9.6). Conclusions: Breast cancer is greatly disparate racially between AA and CA and geographically between Mississippi and US national average. The disparities are manifested in the proportion of TNBC subtype, age at onset of breast cancer, BMI at time of diagnosis, and death rate. Citation Format: Navdeep Kaur, Javaria A. Khan, Jinghe Mao, Diva Melvin, Muhammad M. Hassan, Xinchun Zho. Disparities of triple negative breast cancer in Mississippi [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 1014.
Abstract 1990: TIP60-mediated acetylation of ΔNp63α is associated with cisplatin resistance
Authors: Akshay Hira, Jin Zhang, Mike Kemp, Madhavi P. Kadakia
Journal: Cancer Research (2024)

Abstract The chemotherapeutic drug Cisplatin is often used to treat squamous cell carcinoma (SCC) patients, but low response rates and disease recurrence are common. About 5.4 million basal and squamous cell skin cancers are diagnosed each year in the US. ΔNp63α, a member of the p53 family of transcription factors, is overexpressed and considered oncogenic in non-melanoma skin cancer where it regulates cell survival, promotes proliferation, and inhibits cell apoptosis. ΔNp63α has also been shown to promote resistance to cisplatin by orchestrating the transcriptional regulation of several DNA damage response (DDR) genes. Our previous study showed that the histone acetyltransferase (HAT) TIP60 promotes SCC proliferation by positively regulating ΔNp63α protein levels in a manner reliant on the catalytic activity of TIP60. This observation suggested that TIP60 may contribute to the failure of platinum-based drugs in SCC and led us to hypothesize that TIP60-mediated acetylation of ΔNp63α regulates its stability and transcriptional activity to promote chemoresistance. We found that TIP60 levels positively correlated with ΔNp63α stability, protein levels, and cisplatin resistance. Further, silencing endogenous TIP60 led to a decrease in ΔNp63α transcript and protein levels in multiple cisplatin resistant SCC cell lines. Further, stable expression of TIP60 or ΔNp63α individually promoted resistance to cisplatin and reduced cell death, whereas loss of ΔNp63α or TIP60 induced G2/M arrest, increased cell death, and sensitized cells to cisplatin. Additionally, pharmacological inhibition of TIP60 reduced acetylation of ΔNp63α, decreased colony formation, and sensitized resistant cells to cisplatin. Finally, we demonstrated that ΔNp63α and TIP60 levels positively correlated with DNA repair capacity and negatively correlated with cisplatin-DNA adduct formation. Silencing of either TIP60 or ΔNp63α intensified cisplatin-DNA adduct formation and significantly reduced the expression of drug efflux transporters. Taken together, our data indicate that TIP60-mediated stabilization of ΔNp63α increases cisplatin resistance and provides critical insights into the mechanisms by which ΔNp63α confers cisplatin resistance in SCC. Our findings suggest that the inhibition of TIP60 may be therapeutically advantageous in overcoming cisplatin resistance in SCC and other epithelial cancers. Citation Format: Akshay Hira, Jin Zhang, Mike Kemp, Madhavi P. Kadakia. TIP60-mediated acetylation of ΔNp63α is associated with cisplatin resistance [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 1990.
Abstract 6841: Mutation specific mechanisms of resistance to oncogenic KRAS inhibition
Authors: Ivana Barravecchia, Emily Lasse-Opsahl, Sophia Cavanaugh, Lily Rober, Rachael Baliira, Marzia Robotti, Rachael Hinshaw, Jennifer M. Lee, Yaqing Zhang, Marina Pasca di Magliano, Stefanie Galbán
Journal: Cancer Research (2024)

Abstract Mechanisms of resistance to inhibitors against mutant KRAS are linked to the remodeling of the tumor microenvironment (TME). Understanding this remodeling process during intervention and tumor recurrence will likely guide the development of future therapeutic treatment paradigms with long-term responses. 56% of never-smokers with non-small cell lung cancer have KRASG12D mutant cancer and respond little to immune checkpoint therapy (ICI) compared to smokers, who often have mutations in KRASG12C. Our analysis of the TME in a unique KrasG12D inducible and reversible mouse model of NSCLC using single cell RNA sequencing data shows KrasG12D-dependent control of the TME, particularly of the expression of PDL1 in a subset of myeloid cells. PDL1 expression was found to be KrasG12D dependent as it was reduced significantly when KrasG12D was turned ON in mouse lungs. Interestingly, when KrasG12D was turned OFF, the expression of PDL1 increased, indicating mechanisms of resistance. Furthermore, the cytokine expression and secretion of IL6, a known regulator of PDL1 expression, increased in lung tissue and lung cancer cells derived from this model upon genetic and chemical (MRTX1133) Kras inhibition. Moreover, the mechanisms of resistance to oncogenic Kras inhibition appear to be mutant specific. Transcriptome and secretome analyses in human and murine KrasG12D or KrasG12C mutant lung cancer cells show distinct cytokine regulation upon KRAS inhibition. Identification of mechanisms of resistance like the induction of PDL1 expression upon KrasG12D inhibition may provide a strong rationale for co-treatment of KRAS inhibitors with ICI for KrasG12D never-smokers with NSCLC. Citation Format: Ivana Barravecchia, Emily Lasse-Opsahl, Sophia Cavanaugh, Lily Rober, Rachael Baliira, Marzia Robotti, Rachael Hinshaw, Jennifer M. Lee, Yaqing Zhang, Marina Pasca di Magliano, Stefanie Galbán. Mutation specific mechanisms of resistance to oncogenic KRAS 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 6841.
Abstract 4245: Selection of AAV capsids by evaluating transgene delivery using human organoid models
Authors: Yingying Fu, Zhen Qi, Zhanguan Zuo, Spencer Chiang, An Ouyang, Glory Gao, Shuge Guan, Jin-Qiu (Jessie) Chen, Rosanna Zhang, Cheng Wang
Journal: Cancer Research (2024)

Abstract Recombinant adeno-associated viruses (AAVs) play a pivotal role in gene therapy, a promising approach aimed at treating various genetic disorders by introducing modified genetic material into cells or tissues. These AAV capsids are utilized as a vector in transferring genetic material into host cells. In discovery research, many AAV serotypes are developed in parallel to identify the optimal subtype for subsequent preclinical and clinical use. However, gene therapies have found limited success in clinical translation, in part, due to variable transgene delivery efficacy between traditional in vitro and in vivo models and human models. This study presents an organoid-based approach that mimics human physiology, as well as organ-specific features and cell diversity within an organ. Organoids are 3D structures derived from stem cells that resemble the cellular architecture and functionality of a specific organ. Compared to conventional 2D cell cultures, organoids provide a more comprehensive modeling of complex cell signaling, cell-cell and cell-extracellular matrix interactions, simulating the complex interplay between various cell types and functions. Within this study, several human-based organoid models were built, cerebral and cardiac, and verified by identifying the expression level of known marker genes through RNA sequencing. Five different AAV serotypes were utilized to evaluate transgene efficacy using each type of organoid model. Expression of delivered GFP transgene within each organoid was then compared to evaluate transduction and select the optimal AAV serotype in comparison to commercial wild-type AAVs. We outline the use of human organoid as an improved preclinical model for selecting AAV serotypes and evaluating transgene delivery efficacy to help provide better guidance for gene therapy development when moving into clinical research. Citation Format: Yingying Fu, Zhen Qi, Zhanguan Zuo, Spencer Chiang, An Ouyang, Glory Gao, Shuge Guan, Jin-Qiu (Jessie) Chen, Rosanna Zhang, Cheng Wang. Selection of AAV capsids by evaluating transgene delivery using human organoid models [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 4245.
Abstract 7018: Application of HiTIMED and cell type adjusted epigenome-wide models identifies driver tumor DNA methylation alterations in multiple cancers
Authors: Irma M. Vlasac, Ze Zhang, Lucas A. Salas, Brock C. Christensen
Journal: Cancer Research (2024)

Abstract DNA methylation (DNAm) is an epigenetic mark crucial in lineage specification and cellular differentiation, resulting in distinct patterns by cell type. These patterns can serve as biomarkers in deconvolution approaches inferring cell proportions from composite DNAm signals in biospecimens like blood and tumor tissue. Adjusting for cellular heterogeneity is critical to avoid confounding by cell type. The HiTIMED (hierarchical tumor immune microenvironment epigenetic deconvolution) algorithm provides high-resolution tumor microenvironment profiling, up to 17 cell types, including tumor, myeloid, and angiogenic compartments. We analyzed bladder, prostate, and uterine cancers, applying HiTIMED on the tumor (n=1,341) and normal adjacent tissue (n=105), adjusting for age, sex, and cell types. DNAm data from The Cancer Genome Atlas (TCGA) was used, and HiTIMED was applied to deconvolute various cell proportions. Linear model comparisons to identify significantly differentiated loci with/without cell type adjustment are summarized in Table 1. We demonstrate greater than 99% reduction in both hypermethylated and hypomethylated loci in all cancer types after adjustment for cell type. Our study demonstrates HiTIMED's applicability to deconvolve the tumor microenvironment in multiple cancer types and demonstrates the importance of adjusting for cell type in epigenome-wide association studies to identify differentially methylated loci, offering greater biological insight into the etiology of specific cancer types. Significant differentially methylated loci in tumor versus normal adjacent tissue, FDR &amp;lt;0.05 Cancer type Linear model Hypermethylated in tumor (logFC &amp;gt;2.0) Hypomethylated in tumor (logFC &amp;lt; -2.0) Bladder cancer n = 21, normal adjacent tissue n = 413 tumor Model 1 (Cancer Status, Age, Sex) 4495 19,936 Model 2: (Cancer Status, Sex, age, six cell types) 27 39 Prostate adenocarcinoman = 50, normal adjacent tissuen = 499 tumor Model 1 (Cancer Status, Age) 8988 2207 Model 2: (Cancer Status, age, six cell types) 2 4 Uterine carcinoman = 34 normal adjacent tissuen = 429 tumor Model 1 (Cancer Status, Age) 11,698 16,249 Model 2: (Cancer Status, age, six cell types) 250 8245 Citation Format: Irma M. Vlasac, Ze Zhang, Lucas A. Salas, Brock C. Christensen. Application of HiTIMED and cell type adjusted epigenome-wide models identifies driver tumor DNA methylation alterations in multiple cancers [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 7018.
Abstract 4589: Synergistic effects of EZH1/2 dual inhibition and cisplatin on lung cancer cell lines with loss of <i>SMARCA4</i> and <i>SMARCA2</i>
Authors: Jeongjae Lee, Bhumsuk Keam, Soyeon Kim, Jeonghwan Youk, Miso Kim, Tae Min Kim, Dong-Wan Kim, Heo Dae Seog
Journal: Cancer Research (2024)

Abstract Purpose: SMARCA4 mutations are observed in approximately 10% of non-small cell lung cancer (NSCLC) cases and are implicated in various biological functions. Lung cancers harboring these mutations are associated with poor prognosis and often exhibit resistance to conventional chemotherapies, highlighting the urgent need for innovative therapeutic strategies. We evaluated the efficacy of a novel EZH1/2 dual inhibitor, HM97662, and its synergistic potential with cisplatin in SMARCA4-deficient lung cancer cell lines. Experimental Design: CCLE datasets were employed to identify cell lines harboring truncated mutations in the SMARCA4 gene. Immunoblotting was conducted to verify the inactivation of SMARCA4 and to check for the expression of SMARCA2. We assessed cellular viability and colony-forming capabilities of lung cancer cell lines (NCI-H1975, PC9, A549, HCC15, NCI-H522, NCI-H1581, NCI-H1048, NCI-H841) to determine the cytotoxic effects of an EZH1/2 dual inhibitor as well as cisplatin, both as single agents and in combination. Results: Immunoblotting showed distinct lung cancer cell lines characterized by three profiles: proficient SMARCA4 expression, absent SMARCA4 but present SMARCA2 expression, and concurrent loss of both SMARCA4 and SMARCA2. After 14 days of treatment with the EZH1/2 dual inhibitor HM97662, there was a significant reduction in cell proliferation, particularly in the both SMARCA4- and SMARCA2-loss cell lines. Furthermore, colony-forming assays demonstrated a significant decrease in colony-forming ability upon HM97662 treatment, an effect exclusive to the both SMARCA4 and SMARCA2 loss cell lines. Pre-treatment with 1 µM of HM97662 for 7 days potentiated the cytotoxicity of cisplatin compared to untreated controls in the SMARCA4/2 loss cell lines, as indicated by a lower IC50 value. Conclusion: The novel EZH1/2 dual inhibitor, HM97662, exhibits antitumor activity and a synergistic effect with cisplatin in lung cancer cell lines with concomitant loss of SMARCA4 and SMARCA2. These findings suggest the potential utility of EZH1/2 dual inhibition as a targeted therapeutic approach in lung cancers characterized by the dual loss of SMARCA4/2. Citation Format: Jeongjae Lee, Bhumsuk Keam, Soyeon Kim, Jeonghwan Youk, Miso Kim, Tae Min Kim, Dong-Wan Kim, Heo Dae Seog. Synergistic effects of EZH1/2 dual inhibition and cisplatin on lung cancer cell lines with loss of SMARCA4 and SMARCA2 [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 4589.
Abstract 7043: Genomic profiling of DLL3-positive and negative CTCs in small cell lung cancer
Authors: Zoltan Simandi, Thai Bui, Alberto Ferrarini, Steven Hepburn, Richard G. Del Mastro
Journal: Cancer Research (2024)

Abstract BACKGROUND: Delta-like ligand 3 (DLL3), an atypical Notch family protein implicated in neuroendocrine tumorigenesis, has emerged as a promising therapeutic target in small cell lung cancer (SCLC), prompting numerous clinical trials investigating DLL3-targeted treatments. Exploring DLL3 in circulating tumor cells (CTCs) through liquid biopsy, coupled with comprehensive genomic analysis, presents an invaluable and minimally-invasive avenue for monitoring disease progression. This approach holds the potential to tailor personalized treatment strategies, emphasizing the critical need for in-depth investigations into both DLL3-positive and negative cell genomic compositions. METHODS: This study examined blood collected in CellSave preservative tubes from stage I (n=17) and stage IV (n=12) SCLC patients, as well as healthy donors (n=10). The CELLSEARCH® platform was employed to count EpCAM-enriched CTCs and evaluate DLL3 protein expression. Subsequently, individual CTCs were isolated based on the presence and absence of DLL3 expression using the DEPArray™ PLUS. The isolated DLL3-negative and positive CTCs were subjected to low-pass sequencing using the Ampli1™ LowPass Kit to uncover genomic aberrations. RESULTS: CTCs were absent in the healthy control group. In stage I patients, CTCs were identified in 5.8% of blood samples, while in stage IV patients, they were present in 50% of samples, with an average CTC count of 148 in stage IV. Among a total of 2074 detected CTCs, 460 were DLL3-positive, accounting for 6-28% of EpCAM-enriched CTCs in individual patients. Analysis of &amp;gt;300 copy number alteration (CNA) profiles of sorted single cells revealed considerable inter-patient and intra-patient heterogeneity, delineating recurrent clonality and specific genomic alterations in DLL3-negative CTCs. In contrast, DLL3-positive cells showed more stochastic CNA profiles, suggestive of apoptosis-related DNA fragmentation. CONCLUSIONS: Integrating CellSearch, DEPArray, and low-pass sequencing provides a minimally-invasive approach to compare genomic characteristics in DLL3-positive and negative CTCs from SCLC patients. Extension of this approach to a larger patient cohort and employing machine learning algorithms will facilitate identification of patterns within diverse CNA profiles, improving patient stratification and predicting treatment responses for personalized therapeutic strategies in SCLC. Citation Format: Zoltan Simandi, Thai Bui, Alberto Ferrarini, Steven Hepburn, Richard G. Del Mastro. Genomic profiling of DLL3-positive and negative CTCs in small cell lung 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 7043.
Abstract 706: Advancing radiotherapy strategies for high-risk rhabdomyosarcoma: Unveiling BCL-xL inhibition as a potent sensitizer to radiotherapy
Authors: Sammy Se Whee Park, Nona Struyf, Tom Erkers, Sören Lehmann, Michael T. Meister, Jarno Drost, Frank C. Holstege, Nikolas Herold, Päivi Östling, Jakob Stenman, Olli Kallioniemi, Jan-Inge Henter, Brinton Seashore-Ludlow, Kasper Karlsson
Journal: Cancer Research (2024)

Abstract Pediatric soft-tissue sarcomas are a group of solid tumors that account for about 7% of childhood cancer cases. Rhabdomyosarcoma (RMS), the most common subtype, further stratifies into PAX3 or PAX7 and FOXO1 fusion-negative (FN) or fusion-positive (FP) RMS. FP RMS is the higher risk subtype and is more aggressive, metastatic, and less responsive to treatment. Front-line treatments for RMS FP patients have had limited progress in the recent years and existing treatments such as radiotherapy lacks tumor cell selectivity, resulting in toxic side effects. To address this, we conducted a high-throughput drug screen to identify radiosensitizers to enhance efficacy of RMS radiotherapy. Using three patient-derived FP RMS tumoroids, we screened a comprehensive drug library with and without radiation, comprising 528 drugs at varying stages of pre-clinical and clinical trials. A validation screen of the top 29 drugs was conducted on a larger cohort of samples including eight patient-derived FP RMS tumoroids and three non-cancer models. The screening revealed that drugs targeting the anti-apoptotic protein B-cell lymphoma-extra-large (BCL-xL) exhibited both potent radiosensitization and cytotoxicity selectively for FP RMS. Notably, the sensitivity to BCL-xL inhibitors correlated with elevated BCL2L1 expression and PAX3 fusion status. Additionally, drugs targeting polo-like kinase 1 (PLK1) and other cell cycle-related genes exhibited robust radioprotective effects across both RMS and non-cancer models. Our findings propose the therapeutic potential of BCL-xL inhibition, either as a standalone treatment or in combination with radiotherapy. In parallel, we show the protective potential of PLK1 inhibition to mitigate radiation toxicity. In the long term, we aspire to integrate the identified radiosensitizing and radioprotecting compounds with existing treatment regiments for RMS, maximizing precision and efficacy in RMS radiotherapy. Citation Format: Sammy Se Whee Park, Nona Struyf, Tom Erkers, Sören Lehmann, Michael T. Meister, Jarno Drost, Frank C. Holstege, Nikolas Herold, Päivi Östling, Jakob Stenman, Olli Kallioniemi, Jan-Inge Henter, Brinton Seashore-Ludlow, Kasper Karlsson. Advancing radiotherapy strategies for high-risk rhabdomyosarcoma: Unveiling BCL-xL inhibition as a potent sensitizer to radiotherapy [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 706.