bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract 2126: Efficacy and underlying mechanisms of surufatinib in non-small cell lung cancer treatment
Authors: Zheng Yanfang , Shan Binjie , Wang Meng , Wu Xiaoran , Cai Rui , Niu Feiyu , Yuan Yan , Liu Lu , Zhu Xiongjie
Published: March 2024

Background: The prevalence and fatality of lung cancer, especially non-small cell lung cancer (NSCLC), highlight the urgency for efficacious therapies. Surufatinib, an inhibitor of tyrosine kinases like VEGF receptors (VEGFR) 1, 2, and 3, Fibroblast growth factor receptor 1 (FGFR1), and CSF-1R, shows potential in augmenting chemotherapy efficacy and reducing adverse effects. Preliminary clinical studies (NCT04922658) have indicated survival benefits for NSCLC patients treated with surufatinib. This investigation seeks to delineate the therapeutic efficacy of surufatinib, correlating clinical benefits with mechanistic insights.

Methods: To elucidate mechanisms, proliferation assays (CCK8), migration (scratch assay), and apoptosis (flow cytometry) were conducted in A549 and H1299 cell lines. Angiogenesis and macrophage polarization were examined via vascular junction points and mRNA expression profiling. In nude mice, subcutaneous tumors were induced and treated with the study drugs, with tumor growth and angiogenic markers assessed.

Results: In vitro, surufatinib potently inhibited angiogenesis and exerted a dose-dependent suppression of proliferation and colony formation in lung cancer A549 and PC9 cell lines. It also enhanced apoptosis and cell migration. Additionally, surufatinib shifted macrophage polarization towards an M1 phenotype while diminishing M2 macrophages, thereby, contributing to a more robust anti-tumor immune milieu. In vivo studies corroborated these findings, with surufatinib and vinorelbine combination therapy significantly curtailing tumor growth and reducing CD31 expression in tumor tissues, highlighting its potential for substantial therapeutic gains in NSCLC management.

Conclusion: Surufatinib achieved notable antitumor effect consistent with clinical findings in NSCLC, effectively inhibiting cellular proliferation and migration, attenuating angiogenesis, and enhancing apoptosis. Significantly, it also modulated macrophage polarization to favor an M1/M2 balance, thus activating the immune response. Therapeutic strategies with surufatinib have underscored augmented antineoplastic efficacy, meriting additional clinical investigations.

Citation Format: Yanfang Zheng, Binjie Shan, Meng Wang, Xiaoran Wu, Rui Cai, Feiyu Niu, Yan Yuan, Lu Liu, Xiongjie Zhu. Efficacy and underlying mechanisms of surufatinib in non-small cell lung cancer treatment [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 2126.
Abstract 2127: Enhancing radiosensitivity in biliary tract cancer: The dual role of surufatinib in tumor suppression and macrophage reprogramming
Authors: Wang Ningyu , Ma Hong , Mei Xiangping , Huang Ai , Xiao Yong , Yao Jing
Published: March 2024

Background: Biliary tract cancer (BTC) is notorious for its unfavorable clinical outcomes. Radiotherapy (RT) is a crucial component in BTC treatment. This study explores the radiosensitizing potential and mechanisms of Surufatinib (SF), an oral tyrosine kinase inhibitor, distinguished by its anti-angiogenic and immunomodulatory effects.

Methods: In a NOZ mouse xenograft model, tumor growth and expressions of Ki-67, CD31 were analyzed. NOZ and TFK1 BTC cells treated with SF and/or RT underwent assessments for viability, cycle, and apoptosis using CCK8, colony formation, and flow cytometry. Macrophage polarization in SF/RT-treated tumor cell-macrophage co-cultures was studied using Elisa, qRT-PCR, and flow cytometry.

Results: In vivo, SF impeded angiogenesis and bolsters the anti-tumor effect of radiotherapy. SF combined with RT significantly reduced subcutaneous tumor growth in nude mice, and diminished Ki-67 and CD31 expressions. In vitro, SF heightened cholangiocarcinoma cells' radio-sensitivity, causing DNA double-strand breaks and apoptosis. SF and radiotherapy combined notably increased γ-H2A expression and apoptosis levels (P<0.05). SF induced inflammatory response changes, favoring M2 to M1 macrophage polarization. In a tumor cell-macrophage co-culture, the SF-radiotherapy group showed increased IL-6 and decreased TGF-β (P<0.05), with upregulated M1 markers (IL-6, CXCL10) and downregulated M2 markers (TGF-β, CCL22, Arg-1) in macrophages (P<0.05). Both in vivo and in vitro, SF significantly reduced CD206+ M2-type macrophages (P<0.05).

Conclusion: Surufatinib alters the immune microenvironment in cholangiocarcinoma, reversing the immunosuppressive macrophage polarization induced by radiotherapy and reprogramming M2-type macrophages into M1-type, thereby enhancing the radiosensitivity of cholangiocarcinoma.

Citation Format: Ningyu Wang, Hong Ma, Xiangping Mei, Ai Huang, Yong Xiao, Jing Yao. Enhancing radiosensitivity in biliary tract cancer: The dual role of surufatinib in tumor suppression and macrophage reprogramming [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 2127.
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

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−>mTOR>TLK1B>NEK1>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>NEK!>YAP signaling. We found that J54, a pharmacological inhibitor of the TLK1>NEK1>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

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

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

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

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 < 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

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

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

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

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.
Abstract 2347: Zuclopenthixol as an inhibitor of glioblastoma-induced neuronal hyperexcitability
Authors: Negussie Mikias B. , Krishna Saritha , Wei Ying , Gonzales Cesar Nava , Mehari Mulki , Hervey-Jumper Shawn L.
Published: March 2024

Introduction

Drug repurposing serves as a promising avenue for glioblastoma treatment, especially as new evidence emerges about the role of neuronal activity dependent tumor proliferation. Structure based drug discovery with virtual screening requires highly accurate 3D information about the target of choice. Recent developments in machine learning based protein structure prediction have allowed for the exploration of chemical space with virtual screening tools not previously accessible via traditional methods. Netrin-G1 (NTNG1) is an axonal guidance molecule implicated in glioblastoma with high functional connectivity to the cortex. In this study, we explore pharmacologic inhibition of NTNG1 with a clinically approved compound.

Methods

We perform protein structure predictions with AlphaFold2, followed by structure relaxation in an explicit solvent environment with NAMD 2.14. A final confirmation of NTNG1 was used as input to an AutoDock Vina based virtual screening platform. Zuclopenthixol (ZP) was chosen from a list of hits for microelectrode array (MEA) experiments in a mouse neuron/patient-derived tumor cell co-culture environment.

Results

A list of clinically approved compounds were returned from our virtual screen. ZP was chosen for validation studies, as it readily crosses the blood-brain barrier and occupies the entire TSP1 binding site in NTNG1. Preliminary results from MEA studies suggest ZP reduces tumor-mediated hyperexcitability and adequately modulates a protein-protein interaction between NTNG1 and TSP1.

Conclusion

By demonstrating that ZP decreases tumor-mediated hyperexcitability, this study offers evidence for the novel application of ZP to reduce glioblastoma proliferation. Further work will focus on survival analyses in mice treated with ZP and validation of experimental compounds that are structurally similar to ZP.

Citation Format: Mikias B. Negussie, Saritha Krishna, Ying Wei, Cesar Nava Gonzales, Mulki Mehari, Shawn L. Hervey-Jumper. Zuclopenthixol as an inhibitor of glioblastoma-induced neuronal hyperexcitability [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 2347.
Abstract 2381: The bispecific antibody KA-3001, targeting PSMA and CD28, specifically enhances T cell activation within prostate tumors
Authors: Liang Jiabei , Su Chen , Peng Hao , Hao Feng , Liu Tongtong , Ning Jinying , Wu Guojin
Published: March 2024

Immunotherapy, which involves blocking PD-1 signaling, has revolutionized the treatment paradigm for advanced solid tumors. However, prostate cancer exhibits a low response ratio to anti-PD-1 therapy. In this study, we have developed a bispecific antibody (BsAb), KA-3001, targeting PSMA and human CD28, aiming to enhance T cell activation in the tumor microenvironment. KA-3001, in a regular IgG1 format, features an identical light chain and was designed using our common light chain bispecific antibody discovery platform with knob-into-hole technology. Mutations in the Fc domain were introduced to eliminate ADCC, ADCP, and CDC activity. KA-3001's two Fabs demonstrate high affinity for PSMA and relatively low affinity for CD28. In comparison to REGN5678, KA-3001 exhibits significantly stronger binding to PSMA-expressing prostate tumor cells, along with relatively lower CD28 activation, minimizing toxicity while maintaining anti-tumor efficacy. In PBMC humanized immunodeficient mouse tumor models, KA-3001 effectively suppresses the growth of 22Rv1 tumors with or without PD-1 antagonist antibody. Furthermore, KA-3001 has a half-life of more than five days in the blood of Balb/c mice. Finally, we assessed the developability of this antibody through various treatments such as high concentration, low pH, repeated freezing and thawing, and high temperature. The BsAb demonstrates neither aggregation nor degradation. In conclusion, the BsAb KA-3001, developed using our common light chain antibody discovery platform, stands out as a promising pre-clinical candidate drug for the treatment of prostate cancer.

Citation Format: Jiabei Liang, Chen Su, Hao Peng, Feng Hao, Tongtong Liu, Jinying Ning, Guojin Wu. The bispecific antibody KA-3001, targeting PSMA and CD28, specifically enhances T cell activation within prostate 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 2381.
Abstract 241: Patient-derived organoids as a reliable screening platform for assessing ADC efficacy and specificity
Authors: Mori Daniele , Adegbenro Vineeta , Morales Francisco , Overmeer René , Lukovac Sabina , Boj Sylvia , Derksen Merel
Published: March 2024

Antibody-drug conjugates (ADCs) are a new class of pharmaceutical drugs designed to deliver cytotoxic agents to cells expressing specific antigens selectively. Based on Paul Ehrlich’s “magic bullet” concept, ADCs are designed to target cancer cells, minimizing systemic toxicity typical of conventional chemotherapy. ADCs structurally consist of a particular monoclonal antibody linked to a cytotoxic agent.

Patient-derived Organoids (PDOs) provide a new tool for studying cancer biology and patient stratification. PDOs are adult stem cell-based culture systems maintaining the patient-specific genetic and phenotypic characteristics, including surface marker expression. HUB Organoids has generated a large biobank of PDOs characterized on the genomic and transcriptomic level.

The work presented here shows the suitability of the organoid platform for performing ADC screening. Organoids were selected based on their target-antigen (TA) expression, assessed by flow cytometry and RPKM. Organoid killing was assessed with a viability readout (CellTiter Glo) after six days of treatment. Results of viability screening show a correlation between TA-targeting ADC-induced organoid killing and TA expression in the organoids.

These results reveal that PDOs hold value for the preclinical development of ADCs and for evaluating their tumor specificity. Moreover, PDOs have the potential to predict patient specific response to ADCs.

Citation Format: Daniele Mori, Vineeta Adegbenro, Francisco Morales, René Overmeer, Sabina Lukovac, Sylvia Boj, Merel Derksen. Patient-derived organoids as a reliable screening platform for assessing ADC efficacy and specificity [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 241.
Abstract 2436: In-depth analysis of microRNA signature in breast cancer derived extracellular vesicles: A potential biomarker repository for breast cancer diagnosis
Authors: Kim Jee Ye , Kim Min Woo , Kim Young , Moon Sol , Lee Suji , Lee Hyojung , Kim Joon Ye , Kim Seung Il
Published: March 2024

Breast cancer remains one of the leading causes of cancer-related mortality among women worldwide. With the rising incidence of breast cancer, early and accurate diagnosis is pivotal in improving survival rates and patient outcomes. Our study addresses to identify vesicles associated with breast cancer in scope of miRNA signature. We focused on isolating breast cancer-derived extracellular vesicles (BEVs) from the bloodstream with immune affinity capture techniques. Then, we analyzed the miRNA profiles of BEVs in plasma samples from 120 breast cancer patients, 46 individuals with benign tumors, and 45 healthy controls. In this study, we analyzed to discover miRNA candidates for diagnosis of breast cancer with The Gene Expression Omnibus (GEO) database and found 379 down-regulated and 584 up-regulated differentially expressed miRNAs (DEMs) in tissue samples across 5 GEO datasets, and 28 down-regulated and 80 up-regulated DEMS in blood samples. Subsequently, we measured the expression levels of these 10 candidate miRNAs in BEVs from breast cancer cells and compared them with EVs from human mammary cells (MCF10a), using our BEV isolation method. The expression profiles of these miRNAs in BEVs were significantly elevated, supporting their potential as surrogate markers for breast cancer diagnosis. When comparing the AUC values of 10 candidate miRNAs through ROC analysis, 5 EV miRNAs (miR-21, miR-106b, miR-181a, miR-484, and miR-1260b) showed a high AUC values above 0.8. Subsequently, we verified a distinct signature of 5 EV miRNAs that effectively differentiate breast cancer patients from normal controls with 57.14% of sensitivity and 95% of specificity. Overall, our study not only complements existing diagnostic methods with high accuracy but also provides a deeper understanding of the molecular aspects of breast cancer, heralding a significant advancement in precision medicine and personalized cancer care.

Citation Format: Jee Ye Kim, Min Woo Kim, Young Kim, Sol Moon, Suji Lee, Hyojung Lee, Joon Ye Kim, Seung Il Kim. In-depth analysis of microRNA signature in breast cancer derived extracellular vesicles: A potential biomarker repository for breast cancer diagnosis [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 2436.
Abstract 2440: Cancer driver mutations as quantitative biomarkers of cancer risk interspecies analyses using CarcSeq
Authors: Harris Kelly L. , Gong Binsheng , Parsons Barbara , Faske Jennifer , Xu Joshua
Published: March 2024

Unmet needs in cancer risk assessment include the ability to predict rodent life-time tumor responses from short-term exposures and a scientific basis for rodent to human extrapolation. As an approach to address these needs, the use of hotspot cancer driver mutations (CDMs) as biomarkers of cancer risk was integrated with an error-corrected, next generation sequencing (NGS) approach. We have developed and investigated the sensitivity of a high-throughput NGS method capable of detecting a panel of the most prevalent point mutations observed in human oncogenes and tumor suppressor genes. This method, CarcSeq, involves performing multiple, high-fidelity PCR reactions to amplify the most prevalent mutations reported to occur in human tumors, tagging the amplicons with 9 bp unique identifier sequences at each end, constructing libraries using Illumina ChIP Seq kits, sequencing the libraries on an Illumina NextSeq500 platform and generating single-strand consensus sequences (SSCS), bioinformatically, as a means of error-correction. We validated CarcSeq mutant fraction measurements through observations related to known cancer driver tissue-specificities and mutation spectra for normal human breast and lung, ductal carcinoma, and lung adenocarcinoma samples. Performance of a reconstruction experiment established CarcSeq has a sensitivity of 104. The approach has now been adapted to analyze analogous conserved codons in rat and mouse. For each of the three species, the developed panel includes 13-15 amplicons encompassing known cancer driver genes (e.g., KRAS, PIK3CA, and TP53) encompasses the equivalent of 30 known human hotspot codons and has a combined target sequence length of ~1 kb. Amplicons were generated from DNA isolated from 16-week-old, untreated rodent tissue samples with known differences in spontaneous tumor incidence: female Wistar, Sprague Dawley, and F344 rat mammary samples and male and female B6C3F1 and CD-1 mouse lung samples. The rodent panel was optimized to generate ~100,000 SSCS/amplicon. CDMs were observed at conserved codons in young, untreated rodents, and results are consistent with what was expected based on strain differences in spontaneous tumorigenesis.

Citation Format: Kelly L. Harris, Binsheng Gong, Barbara Parsons, Jennifer Faske, Joshua Xu. Cancer driver mutations as quantitative biomarkers of cancer risk interspecies analyses using CarcSeq [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 2440.
Abstract 2441: Higher levels of LPS in blood plasma as potential novel biomarker for cancer risk in Puerto Rican people living with HIV
Authors: Reyes Jurelis Torres , Shull Tanner L. , Borges-Velez Gabriel , Gonzalez Veronica S. Sanchez , Montilla Jeannette L. Salgado , Santiago Josue Perez
Published: March 2024

Background: People living with HIV (PWH) have a significantly higher risk of developing cancers than people without HIV (PWOH), even with suppressive antiretroviral therapy. Puerto Rico (PR) is considered a high-risk group disproportionately affected by HIV and a priority group for cancer prevention strategies. Dysbiosis of the human microbiota can contribute to persistent inflammation by upregulating TGF-β (microbial-induced oncogenesis biomarker), which can promote the translocation of microbial products into the bloodstream, increasing cancer risk at local and distant sites. However, the relationship between TGF-β, and microbial products such as lipopolysaccharide (LPS) and short-chain fatty acids (SCFA) in relation to HIV infection is poorly understood, therefore we aimed to quantify the levels of LPS and SCFA in the blood plasma of PWH vs. PWOH and investigated their relationship with cancer risk measured by TGF-β.

Methods: Blood samples, sociodemographic, and clinical data from 80 adults (50 PWH and 30 PWOH) were collected. PWH were virally suppressed (<50 copies/mL) with a median CD4 count of 699.8 cells/µL. We measured TGF-β, LPS, and soluble CD14 (sCD14. marker of innate immune activation and microbial translocation) using immunoassays. SCFA (acetate, butyrate, and propionate) were measured using gas chromatography followed by mass spectrometry. Differences in the median levels of TGF-β, LPS, and SCFAs were evaluated using a Mann-Whitney test. We assessed the effects of LPS, SCFAs, and HIV infections in relationship with levels of TGF-β using multivariate fixed-effects regression analysis in R-statistical software.

Results: PWH had significantly higher levels of TGF-β (4397 pg/mL vs. 1121 pg/mL, p=0.017), higher levels of LPS (38.97 pg/mL vs. 19.26 pg/mL, p<0.001), higher levels of sCD14 (1326 pg/mL vs. 1137 pg/mL, p=0.007), and significantly lower levels of butyrate (84.5 ng/mL vs. 62.0 ng/mL, p<0.001). Higher levels of TGF-b were associated with higher levels of LPS (rho=0.38, p=0.017) and higher levels of sCD14 (rho=0.27, p=0.016) these relationships remain significant after adjusting for HIV status (p<0.001).

Conclusion: Our findings suggest that microbial products in blood plasma can contribute to higher cancer risk in Puerto Rican PWH and may represent potential novel biomarkers for cancer prevention.

Citation Format: Jurelis Torres Reyes, Tanner L. Shull, Gabriel Borges-Velez, Veronica S. Sanchez Gonzalez, Jeannette L. Salgado Montilla, Josue Perez Santiago. Higher levels of LPS in blood plasma as potential novel biomarker for cancer risk in Puerto Rican people living with HIV [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 2441.
Abstract 2469: PROTAC mediated NR4A1 degradation as a novel strategy for cancer immunotherapy
Authors: Wang Lei , Xiao Yufeng , Luo Yuewan , Master Rohan , Mo Jiao , Kim Myung-Chul , Liu Yi , Maharjan Chandra , Patel Urvi , Li Xiangming , Shaffer Donald , Kevin Guertin , Zhuang Haoyang , Moser Emily , Smalley Keiran , Zhou Daohong , Zheng Guangrong , Zhang Weizhou
Published: March 2024

An effective cancer therapy requires both killing cancer cells and targeting tumor-promoting pathways or cell populations within the tumor microenvironment (TME). We purposely search for molecules that are critical for multiple cell types in the TME and identified nuclear receptor subfamily 4 group A member 1 (NR4A1) as one such molecule. NR4A1 has been shown to promote the aggressiveness of cancer cells and maintain the immune suppressive TME. Using genetic and pharmacological approaches, we establish NR4A1 as a valid therapeutic target for cancer therapy. Importantly, we have developed the first-of-its kind proteolysis-targeting chimera (PROTAC, named NR-V04) against NR4A1. NR-V04 effectively degrades NR4A1 within hours of treatment in vitro and sustains for at least 4 days in vivo, exhibiting long-lasting NR4A1-degradation in tumors and an excellent safety profile. NR-V04 leads to robust tumor inhibition and sometimes eradication of established melanoma tumors. At the mechanistic level, we have identified an unexpected novel mechanism via significant induction of tumor-infiltrating (TI) B cells as well as an inhibition of monocytic myeloid derived suppressor cells (m-MDSC), two clinically relevant immune cell populations in human melanomas. Overall, NR-V04-mediated NR4A1 degradation holds promise for enhancing anti-cancer immune responses and offers a new avenue for treating various types of cancer such as melanoma.

Citation Format: Lei Wang, Yufeng Xiao, Yuewan Luo, Rohan Master, Jiao Mo, Myung-Chul Kim, Yi Liu, Chandra Maharjan, Urvi Patel, Xiangming Li, Donald Shaffer, Guertin Kevin, Haoyang Zhuang, Emily Moser, Keiran Smalley, Daohong Zhou, Guangrong Zheng, Weizhou Zhang. PROTAC mediated NR4A1 degradation as a novel strategy for 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 2469.