bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 6213: Determination of permissive and restraining cancer-associated fibroblast (DeCAF) subtypes
Authors: Peng Xianlu Laura , Kharitonova Elena , Kearney Joseph , Xu Yi , Chan Priscilla , Luan Changfei , Belt Brian , Panni Roheena , Hariharan Arthi , McCabe Ian , Morrison Ashley , Cliff Ashley , Linehan David C. , Iuga Alina , Rashid Naim U. , Yeh Jen Jen 
Published: March 2024

Abstract
Cancer-associated fibroblasts (CAFs) in pancreatic adenocarcinoma (PDAC) are known to play a significant role in regulating tumor progression, invasion, and metastasis. Multiple studies using experimental strategies, as well as single-cell RNA-sequencing (scRNAseq) technology, have shown the existence of subpopulations of PDAC CAFs, with divergent physical and biological characteristics. However, how these CAF subpopulations translate to clinical practice remains unclear. Using a combination of sc- and bulk RNAseq data, we present two CAF subtypes with permissive (permCAF) and restraining (restCAF) characteristics in patients, and developed a clinically usable single-sample classifier (DeCAF) using using 11 independent datasets with high reproducibility (AUC = 0.961). We found that the permCAF patients tend to be associated with a “myxoid” histological features, while restCAF samples were more “collagenized” (p = 0.018). Patients with permCAF tumors had a median overall survival (OS) of 18.5 m compared to 30.2 m for restCAF tumors, with a stratified HR = 1.66 (p &lt; 0.001) for patients with permCAF tumors. Basal-like tumors were found to be associated permCAF subtype (p &lt; 0.001). DeCAF and PurIST (basal-like/classical) subtypes were independently associated with OS (p &lt; 0.001). Analysis of a phase Ib trial FOLFIRINOX in combination with a CCR2 inhibitor (PF-04136309; NCT01413022) , we found that in patients with classical tumors, increasing permCAF probability was associated with response (r = -0.688, p&lt;0.001). Tumors with permCAF subtype are enriched in neutrophils using CIBERSORT and may explain the positive response to CCR2 inhibition. More intriguingly, we found similar associations with OS in kidney renal clear cell carcinoma (KIRC, p = 0.001) and mesothelioma (MESO, p = 0.019). DeCAF subtypes are associated with histological subtype in MESO (p = 0.021) and grade in KIRC (p = 0.056). Taken together, DeCAF subtypes explain the role of CAF subtypes in patients, provide a foundation for the translation of preclinical studies, and facilitate the design of future therapeutic approaches and clinical trials.
Citation Format: Xianlu Laura Peng, Elena Kharitonova, Joseph Kearney, Yi Xu, Priscilla Chan, Changfei Luan, Brian Belt, Roheena Panni, Arthi Hariharan, Ian McCabe, Ashley Morrison, Ashley Cliff, David C. Linehan, Alina Iuga, Naim U. Rashid, Jen Jen Yeh. Determination of permissive and restraining cancer-associated fibroblast (DeCAF) subtypes [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 6213.
Abstract 6233: Characterizing variants of uncertain significance in the tumor suppressor gene known as phosphatase and tensin homolog (PTEN)
Authors: Singh Ajay P. , Wen Jasmine , Nguyen David , Khan Vedanta , Dhami Kiran , Meier-Ross Kaitlynn , Martin Benjamin , Chao Jesse T. 
Published: March 2024

Abstract
PTEN is an important tumor suppressor that plays an essential role in regulating cell proliferation. Loss of PTEN function is implicated in approximately 50% of metastatic cancers. Individuals with pathogenic PTEN variants are at significantly elevated risk of developing hereditary cancer syndromes such as PTEN hamartoma tumor syndrome. While genetic testing for PTEN is valuable for identifying individuals at risk, 47% of 3065 publicly reported PTEN variants are not conclusively classified; they either have conflicting interpretations of pathogenicity or are labeled as “Variants of Uncertain Significance (VUS)” and are not clinically actionable. The lack of a clear interpretation for these PTEN variants hinders the targeted care and surveillance of patients and places a strain on the healthcare system. To overcome this issue, our aim is to develop a clinically relevant tool for assessing the pathogenic effects of PTEN variants.We hypothesize that loss of function (LoF) PTEN variants will lead to changes in cellular phenotypic profiles that can be measured through single-cell phenotypic profiling. Thus, our goal is to investigate the functional status of exogenously expressed PTEN variants in PTEN-/- HEK 293 cells. We developed a multiplexed high content imaging assay to characterize PTEN and its key signaling partners such as phospho-Akt. Additionally, we developed a deep learning based single-cell phenotypic profiling pipeline named Paracell that uses subcellular segmentation to extract 540 phenotypic features. Cells that exhibit abnormal phenotypic profiles are indicative of loss of PTEN function. Preliminary results from testing 73 missense variants of PTEN showed that functional and LoF PTEN variants form distinctive clusters in a two-dimensional UMAP plot based on Paracell outputs, suggesting that our approach can identify potentially pathogenic variants of PTEN.Through characterizing novel VUS, we can elucidate structural domains involved in PTEN’s tumor suppressing activity. The result of these classifications will enable more optimized detection, diagnosis, and surveillance strategies for PTEN-related cancers. Ultimately, we aim to contribute to improving the genetic testing of PTEN and the development of targeted therapies.
Citation Format: Ajay P. Singh, Jasmine Wen, David Nguyen, Vedanta Khan, Kiran Dhami, Kaitlynn Meier-Ross, Benjamin Martin, Jesse T. Chao. Characterizing variants of uncertain significance in the tumor suppressor gene known as phosphatase and tensin homolog (PTEN) [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 6233.
Abstract 6258: Inference of gene expression using fragmentation patterns from targeted high-depth sequencing of cell-free DNA
Authors: Leff Emily , Tseng Alexander , Cheung Victoria , Tabari Ehsan , Walter Kimberly , Lovejoy Alex , Lin Cheng-Ho J. 
Published: March 2024

Abstract
Cell-free DNA (cfDNA) circulating in blood plasma arises primarily from cellular chromatin fragmentation and release due to cell death. Studies have demonstrated that the assessment of fragmentomic features of cfDNA enables gene expression inference and tissue-of-origin classification with potential applications for noninvasive cancer detection. However, due to low depth of coverage of sites of interest, current whole genome sequencing (WGS) methods have not been able to infer expression of individual genes or limited gene sets. Therefore, we developed a targeted sequencing approach that enables individual gene expression inference from cfDNA fragmentation patterns based on transcriptional start-site gene activation probability (TSS-GAP).
To assess the sensitivity of this method for cfDNA-inferred gene expression profiling, we applied TSS-GAP to blends of micrococcal nuclease (MNase)-digested DNA from a cancer cell line (LS180) and sorted peripheral blood mononuclear cells (PBMC), with LS180 DNA at varying concentrations (0.1-10%). This enabled the determination of the limit of detection (LoD), relative to healthy donor background levels, on the basis of the genes’ activation probabilities (TSS-GAP scores).
We found 936 genes with high inferred expression in the LS180 cancer cell line and low inferred expression in non-cancer samples (i.e. CD4, CD14, and plasma cfDNA from 4 healthy donors) and used those for healthy donor background and LoD assessment. Using these gene-level background values as cutoffs, blends were assessed to determine the lowest blend level at which expression of the gene was able to be differentiated from background. Out of the 936 genes, 326 (34.8%) were detectable at a blend level of 0.1%, 59 (6.3%) at 0.3%, 31 (3.3%) at 1%, 19 (2.0%) at 3%, and 39 (4.2%) at 10%. In total, 416 genes could be detected by TSS-GAP at levels 1% of or lower above background, highlighting the potential of our method for detecting expression of certain genes even from a small fraction of cells contributing cfDNA to liquid biopsy samples. Further expansion of this work could consider the utility of such a method for circulating tumor DNA (ctDNA) detection, cfDNA tissue-of-origin classification, and deconvolution of cell types contributing to cfDNA found in blood.
Citation Format: Emily Leff, Alexander Tseng, Victoria Cheung, Ehsan Tabari, Kimberly Walter, Alex Lovejoy, Cheng-Ho J. Lin. Inference of gene expression using fragmentation patterns from targeted high-depth sequencing of cell-free DNA [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 6258.
Abstract 6276: In vitro neuroendocrine differentiation of BPH-1 cells under beta-adrenergic stimulation
Authors: Pigat Natascha , Garrido Laura N. , Lefevre Coline , Baures Manon , Goffin Vincent , Armand Anne-Sophie , Capiod Thierry 
Published: March 2024

Abstract
Recent studies have shown that adrenergic fibers from the sympathetic nervous system (SNS), acting through stromal β2-adrenergic receptors, play an important role in the initial phases of cancer development by promoting tumor cell survival. Recent epidemiological data suggest that β-blocker intake is associated with improved survival of prostate cancer patients. Hypertension and high blood pressure have been suggested to increase prostate cancer development suggesting that the use of β-blockers in these patients could also reduce prostate cancer risk. β-adrenoceptors signal through the cAMP/PKA pathway that is known to promote neuroendocrine differentiation (NED) in LNCaP prostate cancer cell line. While neuroendocrine (NE) cells expressing synaptophysin (SYN) represent a minor cell population in the epithelial compartment of normal prostate glands, the population of NE-like cells, exhibiting NE phenotypes and expressing NE markers, is increased in, and correlates with, cancer progression, androgen-independent state and poor prognosis. Expression of the routine tissue biomarker of prostate cancer AMACR in NE-like cells discriminates them from NE cells. Our aim was to investigate whether NED could also be associated with benign prostatic hyperplasia (BPH) as recent studies showed that an increase in neuroendocrine cell density occurred before development of BPH in hypertensive rats. Our results showed that a 10-day treatment with 100µM IBMX (blocking cAMP degradation) and 10µM forskolin (FSK, adenylate cyclase activator) to trigger sustained activation of the cAMP/PKA pathway led to an increase in SYN and AMACR expression in BPH-1 cells (qPCR and WB). Similar results were observed by combining the effect of the β-adrenoceptor agonist isoproterenol (1µM) and FSK. The same treatments reduced BPH-1 cell proliferation rates by 40% and 60%, respectively, as expected for NED. Effects on AMACR and SYN expression and cell proliferation were fully reversed by the β-blocker carvedilol (5µM). This data suggests that β-adrenoceptors could be linked to the development of NE-like cells in BPH, a non-lethal disease affecting the transition zone (TZ). As 20% of the prostate cancer occur in this TZ, this observation may need further investigation.
Citation Format: Natascha Pigat, Laura N. Garrido, Coline Lefevre, Manon Baures, Vincent Goffin, Anne-Sophie Armand, Thierry Capiod. In vitro neuroendocrine differentiation of BPH-1 cells under beta-adrenergic stimulation [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 6276.
Abstract 6281: Context dependent role of glucocorticoids in breast cancer
Authors: Effah Wendy , Ponnusamy Suriyan , Asemota Sarah , Khosrosereski Yekta , Narayanan Ramesh 
Published: March 2024

Abstract
Glucocorticoids bind to the transcription factor glucocorticoid receptor (GR) and regulate genes in response to cellular metabolism, inflammation, and stress. Although GR has been extensively evaluated in inflammation and metabolic diseases, its role as a therapeutic target in cancer has not been thoroughly studied. Results from studies with another member of the steroid receptor family, androgen receptor (AR), demonstrated that the AR is an oncogene in estrogen receptor (ER)-negative breast cancer, but a tumor suppressor in ER-positive breast cancer. We expected a comparable mechanism with GR in different breast cancer subtypes. In this study, we evaluated the role of GR in various breast cancer subtypes and discerned the mechanism of action. Six breast cancer cell lines and seven patient-derived xenografts (PDXs) were characterized by Western blot for their expression of GR, ER and AR. Proliferation assays were performed in cell lines with a dose-response of a synthetic glucocorticoid, dexamethasone. Subsequently, we performed xenograft studies in cell line xenografts (CDXs) and PDXs. GR was ubiquitously expressed in various cell lines and PDX models. Dexamethasone reduced cell proliferation in ER-positive models, while it increased the proliferation in ER-negative cell lines, suggesting that the GR might have a mechanism of action that is similar to AR. GR antagonist, mifepristone, reversed the effects of dexamethasone. CDX studies in an ER-positive cell line, MCF7 suggested that dexamethasone (10 mpk) inhibited the tumor growth significantly that was better than the standard of care fulvestrant. This result was confirmed in an ER positive PDX model HCI013. Study by Obradović et al, indicates that glucocorticoids have an oncogenic role and furthermore promote breast cancer metastasis in TNBC model thereby validating the subtype and context dependent role of the glucocorticoid receptor. We are currently exploring the mechanism of GR’s context-dependent tumor suppressor and oncogenic role in distinct breast cancer subtypes.
Citation Format: Wendy Effah, Suriyan Ponnusamy, Sarah Asemota, Yekta Khosrosereski, Ramesh Narayanan. Context dependent role of glucocorticoids in 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 6281.
Abstract 6285: Defining androgen receptor function and the effects of PARP inhibition in BRCA1/2-deficient vs. proficient prostate cancer
Authors: Traphagen Nicole A. , Wheeler Esme , Li Rong , Qiu Xintao , Brown Myles 
Published: March 2024

Abstract
Mutation or loss of the tumor suppressor genes BRCA1 and BRCA2 promotes the development of aggressive prostate cancer with poor outcomes and a high risk of metastatic relapse. Approximately 15% of metastatic prostate tumors are BRCA1/2-deficient. These tumors are frequently resistant to standard-of-care treatments that block androgen receptor (AR) function, although the mechanisms underlying this effect remain unclear. PARP inhibitors are synthetically lethal with BRCA1/2-deficiency and are commonly used as a late-line treatment in metastatic prostate cancer; however, both preclinical and clinical data have provided conflicting results on whether PARP inhibitors can be effective in BRCA1/2-proficient prostate tumors. BRCA1, BRCA2, PARP-1, and PARP-2 all have proposed roles in regulating transcription and the chromatin landscape. We therefore hypothesized that loss of BRCA1, BRCA2, and/or inhibition of PARP modulates AR function through changes in global chromatin structure and transcriptional pathways. We used patient-derived xenograft models and next-generation sequencing techniques to profile AR function in BRCA1/2-deficient vs. proficient prostate tumors. We found that loss of BRCA1 and BRCA2 is associated with chromatin accessibility changes, and differentially accessible regions correlate with DNA binding motifs for AR and AR cofactors. ChIP-seq for AR in these tumors demonstrated that BRCA1/2-deficiency is associated with an altered AR cistrome and a global decrease in AR genomic binding. Corresponding RNA-seq data confirmed a downregulated androgen response in BRCA1/2-deficient tumors. In cell line models, inhibition of PARP1 and PARP1/2 inhibited AR-driven transcription. Combining PARP inhibition with either androgen deprivation or the AR antagonist enzalutamide dampened the growth-inhibitory effects of PARP inhibitor treatment. Together, these results indicate that BRCA1/2-deficiency and PARP inhibition modulate AR function in prostate cancer.
Citation Format: Nicole A. Traphagen, Esme Wheeler, Rong Li, Xintao Qiu, Myles Brown. Defining androgen receptor function and the effects of PARP inhibition in BRCA1/2-deficient vs. proficient prostate 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 6285.
Abstract 630: The role of AKT pathway in β-catenin mutated hepatocellular carcinoma
Authors: Wang Xue , Chen Xin 
Published: March 2024

Abstract
The Wnt/β-catenin and PI3K/AKT pathways are pivotal contributors to the development of the malignant phenotype in cancer. The activated Wnt/β-catenin pathway synergizes with various signaling cascades to propel HCC formation, operating through its downstream effectors. It has been well-established that the mammalian target of rapamycin complex 2 (mTORC2) serves as an upstream regulator of AKT, orchestrating the phosphorylation and activation of AKT. Once activated, AKT phosphorylates and inhibits canonical downstream targets like forkhead box O protein (FOXO) and tuberous sclerosis complex 2 (TSC2). Studies indicated that AKT-mediated phosphorylation of TSC2 activates mTORC1, subsequently suppressing autophagy. However, there are limited data exist on the interplay between Wnt/β-catenin and AKT pathways in HCC. In this study, we sought to explore the role of the AKT pathway in β-catenin activated HCC tumors. Sleeping beauty-mediated hydrodynamic transfection was used to overexpress constitutively active forms of β-catenin (N90-β-catenin) and c-MET in the livers of mice to establish the HCC model (c-Met/β-catenin model). Notably, the knockout of Rictor, a component of the mTORC2 complex, significantly impeded tumor growth, underscoring the pivotal role of AKT in c-Met/β-catenin tumor development. AKT1 and AKT2 are the two main isoforms expressed in the liver. We determined that both AKT1 and AKT2 isoforms are critical for c-Met/β-catenin tumor growth. Intriguingly, simultaneous knockout of Rictor and activation of mTORC1 in the c-Met/β-catenin model resulted in delayed tumor growth, indicating that mTORC1 is not the sole downstream determinant of AKT signaling during c-Met/β-Catenin tumor development. Furthermore, overexpression of the activated FOXO1 (FOXO1AAA) significantly delayed the tumor growth, which highlighted the importance of FOXO1. Given the limited understanding of FOXO1 in HCC, we extended our investigation on FOXO1 to human HCC cell lines. Overexpression of FOXO1AAA notably delayed tumor growth in vitro. RNAseq analysis of FOXO1AAA-overexpressed human HCC cell lines revealed a significant upregulation of "metabolic pathways", suggesting metabolic reprogramming post FOXO1 activation. This study, for the first time, unveils the role of the AKT pathway in β-catenin-mutated HCC growth and highlights the potential therapeutic value of targeting the AKT pathway in patients with β-catenin-mutated HCC.
Citation Format: Xue Wang, Xin Chen. The role of AKT pathway in β-catenin mutated hepatocellular carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 630.
Abstract 6316: Exploring the resistant mechanism of CAR T cell therapy targeting CLDN18.2 by single-cell sequencing
Authors: Ma Mingyang , Qi Changsong , Liu Chang , Jiang Lei , Tao Min , Liu Dan , Zhang Panpan , Peng Zhi , Zhang Xiaotian , Gong Jifang , Chen Yang , Zheng Chunhong , Deng Mi , Shen Lin 
Published: March 2024

Abstract
Chimeric antigen receptor T cell (CAR T) therapy has achieved remarkable success in treating hematological malignancies but still faces overwhelming challenges for solid tumors. Our previous clinical trial (NCT03874897) has demonstrated promising results in patients with advanced CLDN18.2-positive gastric after receiving CT041 CAR T cell product. Though the disease control rate (DCR) reached 73% in 37 patients, it was unclear who would benefit from this therapy. Here in this study, we dynamically collected peripheral blood and ascites samples from 5 patients in this clinical trial before and at 3 and 7 days after the infusion of CT041, respectively. Utilizing single-cell sequencing analysis, we found that patients with a high proportion of naive-like T cells were more likely to benefit from CT041. Furthermore, we discovered that the high expression of CLDN18 in the ascites epithelial cells was correlated with a favorable prognosis, while ascites epithelial cells showing high MYC expression and the strong interaction between tumor cells and T cells were identified as adverse prognostic factors for CT041 treatment. These findings may provide theoretical evidence for subsequent screening of CAR T cell therapy benefitable population and improving the efficacy of CAR T cell therapy.
Citation Format: Mingyang Ma, Changsong Qi, Chang Liu, Lei Jiang, Min Tao, Dan Liu, Panpan Zhang, Zhi Peng, Xiaotian Zhang, Jifang Gong, Yang Chen, Chunhong Zheng, Mi Deng, Lin Shen. Exploring the resistant mechanism of CAR T cell therapy targeting CLDN18.2 by single-cell sequencing [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 6316.