bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 213: NEK1-mediated phosphorylation of YAP1 is key to prostate cancer progression
Authors: Olatunde Damilola M. , Ghosh Ishita , De Benedetti Arrigo 
Published: March 2024

Abstract
The key to preventing metastatic castration-resistant prostate cancer (mCRPC) progression is understanding how androgen-sensitive (AS) PCa cells progress to independence and modify accordingly their transcriptional repertoire. We recently identified a novel axis of the Hippo pathway characterized by the sequential kinase cascade induced by androgen deprivation, AR−&gt;mTOR&gt;TLK1B&gt;NEK1&gt;pYAP1-Y407, leading to CRPC adaptation. Phosphorylation of YAP1-Y407 increases upon androgen deprivation therapy (ADT), correlated with increased NEK1 activity, and this is suppressed in a YAP-Y407F mutant. Overexpression of wt-GFP-YAP but not the Y407F SDM resulted in dramatic morphologic changes. In fact, LNCaP expressing wt-YAP were AI whereas the Y407F mutant were AS, and LNCaP expressing wt-GFP-YAP underwent EMT transformation. This, largely reflecting transcriptional differences in both AR-dependent genes (FKBP5, PSA) and some involved in EMT (ZEB1, TWIST, E-CAD); all of which could be effectively reversed with J54-mediated inhibition of TLK1&gt;NEK!&gt;YAP signaling. We found that J54, a pharmacological inhibitor of the TLK1&gt;NEK1&gt;YAP1 nexus led to degradation of YAP1, suggesting that the Y407 phosphorylation is critical for transcriptional activation and stabilization of YAP. Specifically, Nek1-mediated phosphorylation of YAP-Y407 increases its productive interaction with transcriptional activators like TEAD or AR, resulting in its nuclear retention and stabilization. This was later demonstrated by coIP of TEAD4 or the AR with GFP-YAP antiserum, as well as via LUC expression transfections using ARE and Hippo reporter plasmids in LNCaP expressing wt-GFP-YAP or Y407F proteins, as well as by ChIP for key AR-responsive gene promoters. Further, in NEK1 haploinsufficient TRAMP mice we determined reduced YAP1 expression, a key transcriptional activator of CRPC progression, and, if castrated at 12 weeks, the mice failed to show to overt prostate carcinomas, even while displaying reduced E-Cadherin (E-Cad) expression in hyperplastic ductules. Finally, IHC examination of prostate cancer biopsies revealed that pYAP1-Y407 nuclear signal is low in samples of low-grade cancer but elevated in high GS specimens.
Citation Format: Damilola M. Olatunde, Ishita Ghosh, Arrigo De Benedetti. NEK1-mediated phosphorylation of YAP1 is key to prostate cancer progression [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 213.
Abstract 2178: Metagenomic analysis unveils the microbial landscape of pancreatic tumors
Authors: Khan Sheema , Banerjee Goutam , Setua Saini , Dhasmana Anupam , Banerjee Pratik , Yallapu Murali Mohan , Behrman Stephen W. , Chauhan Subhash , Jones Daleniece Higgins , Chauhan Bhavin 
Published: March 2024

Abstract
The composition of resident microbes in the human body is linked to various diseases and their treatment outcomes. Although studies have identified pancreatic ductal adenocarcinoma (PDAC) associated bacterial communities in the oral and gut samples, herein we hypothesize the prevalence of microbiota in pancreatic tumor tissues is different as compared to their matched adjacent, histologically normal appearing tissues and these microbial molecular signatures can be highly useful for PDAC diagnosis/prognosis. In this study, we performed comparative profiling of bacterial populations in pancreatic tumors and their respective adjacent normal tissues using 16S rRNA-based metagenomics analysis. This study revealed a higher abundance of Proteobacteria and Actinomycetota in tumor tissues compared to adjacent normal tissues. Interestingly, the Linear Discriminant Analysis (LDA) scores unambiguously revealed an enrichment of Delftia in tumor tissues, whereas Sphingomonas, Streptococcus, and Citrobacter exhibited depletion in tumor tissues. Furthermore, we analyzed the microbial composition between different groups of patients with different tumor differentiation stages. The bacterial genera, Delftia and Staphylococcus were very high in G1 stages (well differentiated) compared to G2 (well to moderate/moderately differentiated) and G3/G4 (poorly differentiated). However, the abundance of Actinobacter and Cloacibacterium was found to be very high in G2 and G3, respectively. Additionally, we evaluated the correlation of PD-L1 expression with the abundance of bacterial genera in tumor lesions. Our results indicated that three genus such as Streptomyces, Cutibacterium, and Delftia have a positive correlation with PD-L1 expression. Collectively, these findings demonstrate that PDAC lesions harbor relatively different microbiota compared to their normal tumor-adjacent tissues, and this information might be helpful for the diagnosis and prognosis of PADC patients.
Citation Format: Sheema Khan, Goutam Banerjee, Saini Setua, Anupam Dhasmana, Pratik Banerjee, Murali Mohan Yallapu, Stephen W. Behrman, Subhash Chauhan, Daleniece Higgins Jones, Bhavin Chauhan. Metagenomic analysis unveils the microbial landscape of pancreatic tumors [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 2178.
Abstract 218: Deciphering tumoroid-CAF interactions through a spatially segregated coculture model
Authors: Kim Sung Min , Ko Yoo Ri , Park Hye Seon , Jang Se Jin 
Published: March 2024

Abstract
In the context of lung cancers, cancer-associated fibroblast (CAF) plays a pivotal role as a key component of the tumor microenvironment (TME), affecting tumor growth, invasion, metastasis, immune modulation, and drug resistance. Despite the recognized impact of CAFs, the precise interaction between the CAF and tumor cell remains elusive. Previous studies have reported that CAFs stimulate tumor cell growth both in vitro and in vivo. However, our tumoroid models reveal an intriguing phenomenon where CAFs inhibit tumoroids growth within Matrigel. This led us to hypothesize that paracrine signaling might be the primary mode of interaction between CAFs and tumor cells. To unravel the intricacies of this interaction, we developed an innovative coculture method. Using hydrophobic barrier, we segregated the coculture of nine sets of CAFs and tumoroids within a single well, preventing CAFs from infiltrating the tumoroid culture area. This setup enabled interaction solely through paracrine signaling. Surprisingly, cocultured tumoroids exhibited no significant differences compared to individually cultured tumoroids. Conversely, cocultured CAFs displayed a remarkable increase in growth compared to their individually cultured counterparts. This suggests that tumoroids influence CAF growth, while CAFs do not significantly impact tumoroid growth. Furthermore, in three coculture sets, tumor cells within the Matrigel migrated towards the CAF culture area, indicating that CAFs induce tumor cell metastasis. Immunofluorescence staining confirmed this metastatic phenomenon. To identify the paracrine factors influencing CAFs and tumoroids, we employed RNA-sequencing, single-cell RNA-sequencing, and proteomic analysis of culture soup. Proteomic analysis revealed a substantial increase in proteins and signaling pathways related to the extracellular matrix in cocultures compared to single cultures. Our findings suggest that tumor cells recruit CAFs, promoting CAF growth to establish and fortify their TME, ultimately leading to drug resistance, metastasis, and immune modulation
Citation Format: Sung Min Kim, Yoo Ri Ko, Hye Seon Park, Se Jin Jang. Deciphering tumoroid-CAF interactions through a spatially segregated coculture model [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 218.
Abstract 2185: Mechanism of antitumor effects of saffron in human prostate cancer cells
Authors: Khan Mohammad , Hearn Kaitlyn , Parry Christian , Rashid Mudasir , Brim Hassan , Ashktorab Hassan , Kwabi-Addo Bernard 
Published: March 2024

Abstract
Prostate cancer is the most common malignancy in men in the USA and the second leading cause of cancer deaths. Several studies have suggested the antitumor properties of saffron in many types of cancers including prostate. The objective of this study was to carry out in vitro studies of saffron-treated prostate cancer cells to ascertain the effects of saffron on key intermediates in prostate carcinogenesis. Our studies demonstrate significant inhibition of cell proliferation of androgen-sensitive prostate cancer cell lines via apoptotic pathways. We also demonstrate statistically significant down-regulation of DNA methyltransferase; COMT, MGMT, EHMT2, and SIRT1 in saffron-treated prostate cancer cells. In addition, saffron-treated prostate cancer cells displayed statistically significant dysregulation of DNA repair intermediates; WRN, p53, RECQ5, MST1R, and WDR70 in a time-dependent manner. Furthermore, Western blot analysis demonstrated that saffron treatment induced changes in the expression of other key genes; DNMT1, DNMT3b, MBD2, CD44, HDAC3, c-Myc, NF-kB, TNFα, AR, N-RAS and PTEN in prostate cancer cells. Collectively, our findings demonstrate important mechanistic targets of saffron mediating anti-tumor properties in prostate cancer. These findings suggest that the use of saffron supplements alongside standard treatment protocols may yield beneficial effects for individuals with prostate cancer.
Citation Format: Mohammad Khan, Kaitlyn Hearn, Christian Parry, Mudasir Rashid, Hassan Brim, Hassan Ashktorab, Bernard Kwabi-Addo. Mechanism of antitumor effects of saffron in human prostate cancer cells [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 2185.
Abstract 2265: Distinct alternative splicing patterns in genetic subtypes of diffuse large B-cell lymphoma
Authors: An Sanyeowool , Koh Youngil , Yoon Sung-Soo 
Published: March 2024

Abstract
Advances in sequencing techniques have made molecular subgrouping of Diffuse Large B-cell Lymphoma (DLBCL) based on DNA cahnges, which has led to the development of Lymphgen classification. By the way, although alternative splicing (AS) in cancer cells contributes to proliferation, invasion and metastasis, and immune escape, their role and association with DLBCL molecular subtypes are unknown. Therefore, we analyzed whole-exome sequencing (WES) and bulk RNA-Seq data paired in the public EGA dataset (EGAD00001003600) to explore the patterns of AS events that differ between Lymphgene subtypes. The WES data of 620 DLBCL samples that passed quality control were aligned to the reference using BWA-MEM, and variants were called with Mutect2. We used the information of copy number variants provided by cBioPortal. The RNA-Seq analysis was performed using the STAR-RSEM pipeline and differential splicing events were detected using rMATS to compare subtypes. Among 620 DLBCL samples, there were 19 MCDs, 95 EZBs, 22 BN2s, and 137 ST2s (50 samples with multiple genetic classes, and 291 samples unclassified). Mutations in spliceosome complex genes (ZRSR2 and SF1) were found in 14 and 27 samples, respectively. In BN2 and MCD subtypes, splicing events with significantly different exon inclusion levels were observed at a high frequency of 29 and 16 occurrences, respectively, compared to other subtypes. (P-value &lt; 0.05). In contrast, retained intron is the only event observed in the EZB subtype (Table 1). Samples with mutations in ZRSR2 and SF1 showed four and two aberrant events, respectively, compared to samples without these mutations. Of note, rMATS detected an alternative 3’ splice site event in exon 6 of CD37 in the MCD. CD37 is involved in tumorigenesis in leukocytes and has been suggested as a potential biomarker in blood cancer, and its dysregulation may have influenced the poor prognosis of MCD. In summary, molecular subtypes of DLBCL had unique features in terms of alternative splicing. Functional consequences of these selective exon usages for each DLBCL subtype are being warranted.
Citation Format: Sanyeowool An, Youngil Koh, Sung-Soo Yoon. Distinct alternative splicing patterns in genetic subtypes of diffuse large B-cell lymphoma [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 2265.
Abstract 2296: Liquid biopsy of cerebrospinal fluid in breast to brain metastases
Authors: Shishido Stephanie N. , Marvit Amelia , Priceman Saul , Portnow Jana , Kuhn Peter 
Published: March 2024

Abstract
Up to 30% of patients with breast cancers will develop brain metastases, and this risk is especially high with HER2-positive cancers. For patients with central nervous system metastases, cerebrospinal fluid (CSF) liquid biopsies are a promising opportunity to monitor disease, inform treatment, and predict prognosis. This study explores the CSF liquid biopsy analytes from 3 patients with central nervous system metastases analyzed with the third generation non-enrichment high-definition single cell assay (HDSCA3.0) workflow. The detection of cellular analytes was compared between the CSF and matched peripheral blood (PB) samples. Circulating tumor cells (CTCs) were detected in the CSF but not the PB and were subsequently molecularly characterized by single cell genomics and targeted multiplexed proteomics to reveal a clonal population of phenotypically heterogeneous cells. There was a lack of concordance between CTCs and cfDNA of the CSF in the copy number alteration profiles. In an extracellular vesicle surface marker analysis of the CSF, there was a high signal among tetraspanin CD9/CD63/CD81, with CD81 signal the highest across all 3 patients. The data indicates that the CSF may be used as a diagnostic or potentially prognostic tool to measure and characterize disease burden.
Citation Format: Stephanie N. Shishido, Amelia Marvit, Saul Priceman, Jana Portnow, Peter Kuhn. Liquid biopsy of cerebrospinal fluid in breast to brain metastases [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 2296.
Abstract 2297: Longitudinal monitoring of HPV circulating tumor DNA in cervical cancer
Authors: Parida Preetiparna , Sharan Krishna , Lewis Shirley , Damerla Rama Rao 
Published: March 2024

Abstract
Introduction
Detecting circulating tumor DNA (ctDNA) in the blood using minimally invasive techniques known as a "liquid biopsy", is gaining tremendous popularity in oncology research. Integration of human papillomavirus (HPV) DNA and the overexpression of the E6 and E7 oncogenes are crucial steps in the development of cervical cancer. We investigated the potential utility of HPV ctDNA as a biomarker for monitoring treatment outcomes in patients with cervical cancer.
Material and Methods
We use droplet digital PCR (ddPCR) to measure the amount of HPV16/18 ctDNA in plasma of cervical cancer patients. The HPV standard GP5+/6+ primers were used to determine HPV positivity in our patients. Specific primers were designed to amplify specifically the E6 oncogene of HPV16 and HPV18. Plasmid constructs were made using the PCR-purified products of HeLa and SiHa cell lines which would act as a positive control for the assay. HPV16 and 18 plasmids were serially diluted and then tested in qPCR as a template using different primer sets. Standard curves were made from the recombinant plasmids. This will serve as a positive control and will also provide a correlation between the sensitivity and specificity of qPCR vs ddPCR.
Results and Discussions
We hypothesize that our dPCR test will be able to detect minute quantities of HPV ctDNA in plasma of cervical cancer patients as ctDNA levels are expected to be decrease as treatment progresses. The assay sensitivity and specificity will be obtained by comparing results to QPCR. The study samples involve a tumor biopsy and a blood sample at the baseline prior to the therapy and serial blood sampling in different stages of treatment and follow-ups. These samples will also serve for treatment monitoring of these patients through ddPCR. Tumor samples are used to confirm the HPV status of patients using HPV-specific GP5+/GP6+ qPCR. We have recruited 75 cervical cancer patients with majority of them being squamous cell carcinoma and stage IIB disease. The qPCR results from tumor biopsy revealed HPV 16 was most prevalent (32/43), followed by HPV18 (6/43) and HPV 33(2/43).
Conclusion
we will now use Qiagen digital PCR system to understand HPV ctDNA levels in our patient cohort. we believe that our comprehensive sample collection after every treatment milestone and thorough follow-up for upto 2 years after diagnosis will allow us to study the utility of this sensitive test in monitoring disease and relapse.
Citation Format: Preetiparna Parida, Krishna Sharan, Shirley Lewis, Rama Rao Damerla. Longitudinal monitoring of HPV circulating tumor DNA in cervical 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 2297.
Abstract 2328: Next-generation sequencing-based regression algorithm to determine homologous recombination deficiency scores in a pan-cancer cohort
Authors: Choi Boram , Choi Youn Jin 
Published: March 2024

Abstract
Background: Homologous recombination deficiency (HRD) inhibits double strand breaks from being repaired in DNA, leading to cancer cells failing to recover themselves and cell death. Previous studies found that HRD-positive ovarian cancer patients had more significant clinical benefits from poly ADP-ribose polymerase inhibitors (PARPi) treatment. For accurate detection of HRD, next-generation sequencing (whole exome, whole genome) was used to identify large-scale genomic aberrations including telomeric allelic imbalance (HRD-TAI score), loss of heterozygosity profiles (HRD-LOH score), and large-scale state transitions (HRD-LST score). So far, many studies (HRDetect, SigMA, CHORD and shallowHRD) have been conducted to accurately determine HRD in a pan-cancer cohort. As the study progressed, it has been revealed that PARPi is effective when applied to patients with HRD in not only ovarian cancer but also breast cancer, prostate cancer, and pancreatic cancer.
Purpose: To develop an algorithm that accurately predict HRD score in patients with ovarian cancer, breast cancer, prostate cancer, and pancreatic cancer utilizing a machine learning algorithm.
Methods: We used whole-genome sequencing (WGS) data of 710 samples from 309 patients, whole-exome sequencing (WES) data of 4,650 samples from 2,193 patients from the pan-cancer cohort of the TCGA (TCGA-OV, TCGA-BRCA, TCGA-PRAD, and TCGA-PAAD). The HRD-TAI/HRD-LST/HRD-LOH scores were calculated through structural variation analyses. After data cleaning processes, machine-learning models were trained and tested on 228 out of 2,502 samples, and validation was performed on 1,248 out of 2,502 samples from the TCGA dataset.
Results: To assess the performance of the machine-learning regressor, the concordance between predictions and annotations was quantified by calculating the R squared (𝑅;;;^2). As a result of training using machine learning algorithm, we achieved a high 𝑅;;;^2 (0.904) with a RMSE (root mean squared error) score (7.649) for a pan-cancer cohort.
Conclusions: Our regressor was robust and accurate when applied to 4 cancer types. Using our systematic pan-cancer analysis, we found novel insights into the mechanisms of HRD across cancer types with potential contribution to clinical practice.
Citation Format: Boram Choi, Youn Jin Choi. Next-generation sequencing-based regression algorithm to determine homologous recombination deficiency scores in a pan-cancer cohort [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 2328.
Abstract 2342: BARTsc: A transcription factor analysis suite for single-cell omics data
Authors: Zhang Hongpan , Wang Jingyi , Wang Zhenjia , Zang Chongzhi 
Published: March 2024

Abstract
In Eukaryotic cells, the expression of a small set of transcription factors (TFs) is usually sufficient to set up a cell-type-specific gene expression program. The underlying complicated epigenetic mechanisms that explain how cells change their states in response to intra- and extra-cellular signals in different scenarios remain to be fully understood. Importantly, epigenetic regulation of gene expression has been considered a central regulatory mechanism of cell fate determination and cellular plasticity. Insights into it will also profoundly impact our understanding of misregulation of gene expression in diseases such as cancer. However, the functional TFs of many cell types remain unclear, which greatly hinders the study of epigenetic regulatory mechanisms.
The rapid development of single-cell technology is a promising opportunity that enables us to infer functional TFs for different cell types. Some computational methods have been published in this area. However, existing methods have various pitfalls. For instance, some methods use transcription factor binding motifs (TFBMs) as the reference of TF binding, overlooking widespread non-specific binding. Some other methods hold strict criteria for training data and thus can only predict a small number of TFs. To overcome these issues, we propose to leverage publicly available high-quality ChIP-seq data to predict TFs functional in single-cell omics data. Here, we present BARTsc, a comprehensive suite for a series of TF analysis functionalities, including inference of signature TFs of given cell types/clusters, cross-cell-type/cluster TF activity comparative analysis, and TF clustering based on their cross cell-type distributions. The input of BARTsc can be either scRNA-seq, scATAC-seq, or scMultiome data. We demonstrate that BARTsc outperforms several existing tools in both sensitivity and specificity in identifying key cell type regulators in single-cell datasets of well-studied systems. Applying BARTsc to a scRNA-seq dataset for cancer-associated fibroblasts (CAFs), we identified distinct regulatory activities of some TFs in different subtypes of CAFs, but the TF genes are universally expressed in these subtypes. In addition, by time course BARTsc analysis, we identified a list of TFs that may either promote or suppress CAF differentiation, offering a new approach to find potential candidate therapeutic targets.
Citation Format: Hongpan Zhang, Jingyi Wang, Zhenjia Wang, Chongzhi Zang. BARTsc: A transcription factor analysis suite for single-cell omics 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 2342.