bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract 5243: Functional characterization of genetic loci in basal cell carcinoma
Authors: Li Mingyue , Turman Constance , Kraft Peter , Han Jiali
Published: April 2023

Background: Genome-wide association studies (GWAS) have identified over 30 loci associated with basal cell carcinoma (BCC) susceptibility. However, the causal variants and mechanisms at these loci remain unknown. We performed statistical fine mapping and functional enrichment to identify credible causal variants at 31 established BCC risk loci.

Methods: We performed statistical fine mapping by applying the sum of single effects (SuSiE) method to a previously published GWAS from 12,945 BCC cases and 274,252 controls. To identify genomic annotations enriched for BCC-associated variants, we compared high Posterior Inclusion Probability (PIP) variants from SuSIE to low PIP variants: we performed multivariable logistic regression of high-PIP status on 17 variant annotations from the Functional Annotation of Variants Online Resources (FAVOR) database, including sequence-contextual and functional annotations.

Results: We identified 6 variants with PIP>0.99: rs1126809 (TYR), rs1805007 (MC1R), rs78378222 (TP53), rs12203592 (IRF4), rs35407(SLC45A2 a.k.a. MATP), rs12916300 (HERC2). Five of these six variants are in pigmentation genes; the sixth is in the tumor suppressor TP53. At a seventh region, the 95% credible set contained two variants in or upstream of RALY, which has previously been shown to be associated with pigmentation traits and multiple non-skin cancers. Another four regions had fewer than 10 variants in the credible set; the median size of the credible set was 11 (range: 1-76). After adjusting for sequence context (including location relative to exons, introns, UTRs; GC content; local mutation density, and nucleotide diversity) variants in active chromatin regions (as determined from multi-tissue methylation marks), variants in transcription factor binding sites, and skin eQTLs were significantly more likely to be high-PIP variants.

Conclusions: Our results identify candidate variants, genes, and mechanisms for further study in BCC carcinogenesis.

Citation Format: Mingyue Li, Constance Turman, Peter Kraft, Jiali Han. Functional characterization of genetic loci in basal cell carcinoma. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5243.
Abstract 5251: Skeletonema marinoi algae extract and carotenoid fucoxanthin are endowed with potential chemopreventive and angiopreventive properties for prostate cancer
Authors: Albini Adriana , Calabrone Luana , Noonan Douglas M. , Festa Marco , Ferrario Cinzia , Carlini Valentina , Macis Debora , Pistelli Luigi , Brunet Christophe , Sansone Clementina
Published: April 2023

Background: Research and production of natural anti-oxidants is growing and is developed both in experimental laboratories and in nutraceuticals and pharmaceutical industries. Marine microorganisms represent underestimated sources of bioactive compounds endowed with anti-oxidant, anti-inflammatory, cardiovascular protective and anti-angiogenic properties, all beneficial effects on human health.

Methods: Chemopreventive and anti-angiogenic activities of extracts from the marine coastal diatom Skeletonema marinoi (Sm) and carotenoid fucoxanthin, that is present in Sm, were evaluated in prostate cancer (PCa) and endothelial cell lines in in vitro. Morphogenesis assay was carried out to evaluate effects on HUVEC ability to form capillary-like structure on Matrigel. Gene expression analysis was performed by qPCR, measuring different inflammation and angiogenesis gene expression in cells treated with Sm extract and fucoxanthin. Membrane antibodies arrays were used to see alterations at protein level of pro- or anti-angiogenic factors.

Results: Sm extract and fucoxanthin were able to decrease cell viability, in MTT and Crystal violet assays. Furthermore, we observed that fucoxanthin enhanced the effects of chemotherapeutic drugs, 5-Fluorouracil (5-FU) and cisplatin (Cis-Pt), two of the most commonly used anti-cancer drugs. Sm extract and fucoxanthin hindered vascular mimicry of PCa cells and also inhibited capillary structure formation in endothelial cells. Finally, Sm extract and fucoxanthin shown a down-regulation of inflammation and angiogenesis associated genes.

Conclusions: Our study suggests promising potential chemopreventive and angiopreventive activities of Skeletonema marinoi extract and fucoxanthin for prostate cancer. Microalgae derived drugs can be a potential and relevant source of novel nutraceutical and preventive compounds, which can be considered as dietary supplements or in combination treatments in cancer prevention approaches.

Citation Format: Adriana Albini, Luana Calabrone, Douglas M. Noonan, Marco Festa, Cinzia Ferrario, Valentina Carlini, Debora Macis, Luigi Pistelli, Christophe Brunet, Clementina Sansone. Skeletonema marinoi algae extract and carotenoid fucoxanthin are endowed with potential chemopreventive and angiopreventive properties for prostate cancer. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5251.
Abstract 5269: RF-1302, a novel dual inhibitor of PIM1 and FLT3 in preclinical treatment of acute myeloid leukemia
Authors: Qi Weiwei , Zhang Yanjun , Zhao Lei , Zhang Ailian , Zhang Chunze , Zhang Xiaoming , Li Lijuan , Wang Huaquan , Shao Zonghong , Fu Rong
Published: April 2023

It was reported that PIM (Proviral Insertion site in Moloney murine leukemia virus) proteins are family kinases (PIM1, PIM2, and PIM3), which are upregulated in several cancer types, especially PIM1 is highly expressed in hematopoietic malignancies. PIM kinase family are responsible for enhancement of cell cycle, inhibition of apoptosis, activation of transcription, and cell homing/migration. Fms-like tyrosine kinase 3 (FLT3) is part of a family of receptor tyrosine kinases (RTKs), and a molecular therapeutic target of acute myeloid leukemia (AML). There are three FTL3 inhibitors, midostaurin, gilteritinib, and quizartinib have been approved for clinical treatment of AML. We have developed a novel dual inhibitor of PIM1 and FLT3, RF-1302 and evaluated its inhibition of cell proliferation in vitro and antitumor activity in vivo. RF1302 was found to have a strong inhibitory activity against target enzymes (PIM1 IC50 at 1.0-2.3 nM and FLT3 IC50 at 0.8-2.2 nM), which were more potent than the tested positive control drugs gilteritinib, quizartinib, and midostaurin. RF-1302 showed to be highly cytotoxic to cultured human acute myeloid leukemia (AML) cells (MV4-11 and Molm-13) with IC50 at 5.7nM and 9.5 nM, respectively. The in vivo antitumor activity of RF-1302 was evaluated and compared with midostaurin and gilteritinib in the treatment of the two AML xenograft models. RF-1302 at 20 mg/kg/daily x 14, oral) significantly delayed tumor growth and resulted in a tumor growth inhibition (TGI) of 95% (p<0.001 compared with the control group) in the Molm-13 AML model, and cured all of the tumor-bearing mice in the MV4-11 AML model. The antitumor activity of RF-1302 was superior to gilteritinib (TGI=46-55%) and midostaurin (TGI=63-75%). The treatment with RF-1302 showed very little toxicity (only 2% body weight loss) which were well below the maximum tolerated dose. These preclinical results suggest that RF-1302 represents a novel dual inhibitor of PIM1 and FLT3, which may constitute a highly efficacious modality for the treatment of FLT3 mutant AML, and is worthy of further clinical evaluation.

Citation Format: Weiwei Qi, Yanjun Zhang, Lei Zhao, Ailian Zhang, Chunze Zhang, Xiaoming Zhang, Lijuan Li, Huaquan Wang, Zonghong Shao, Rong Fu. RF-1302, a novel dual inhibitor of PIM1 and FLT3 in preclinical treatment of acute myeloid leukemia. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5269.
Abstract 5310: An expanded quantitative protein expression atlas of human cancers
Authors: Liang Han
Published: April 2023

The Cancer Genome Atlas (TCGA) and Cancer Cell Line Encyclopedia (CCLE) are the most widely used and deeply characterized resources for cancer research. Despite rich molecular and phenotypic data available for these cohorts, large-scale proteomic data across cancer lineages remain limited. Here we expanded our previous effort to generate high-quality protein expression data of 447 clinically relevant proteins for ~8,000 TCGA patient samples and ~900 CCLE cell line samples using reverse phase protein arrays. We show that the protein expression profiles provide deeper mechanistic insights into cancer dependency and serve as a sensitive functional readout for the fitness effect of somatic mutations, e.g., BRAF mutations. We develop a protein-centered strategy to identify synthetic lethality pairs with high confidence. We identify pro- and anti-metastasis protein markers and demonstrate their prognostic relevance in patient cohorts. Collectively, this dataset provides a valuable resource for elucidating cancer mechanisms, identifying protein biomarkers, and developing therapeutic strategies.

Citation Format: Han Liang. An expanded quantitative protein expression atlas of human cancers. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5310.
Abstract 5342: Assessment of polyphenolic secondary metabolites and small molecules against the xenobiotic metabolic and cell cycle regulatory proteins in prostate cancer
Authors: Sheoran Sumit , Arora Swati , Basu Tanmay , Subbarao Naidu , Upadhyay Atul Kumar , Vuree Sugunakar
Published: April 2023

Background: Prostate cancer (PCa) is the second most frequent kind of cancer in males globally after Lung Cancer. In clinical practice, medicines that act as antagonists/partial agonists of hormone receptors against prostate tissue are employed in PCa treatment. Cyproterone acetate, Flutamide, and Bicalutamide are prominent medications that induce acute and long-term toxicity and create drug resistance in patients and remission. We concentrated on flavonoids since they are non-cytotoxic and have substantial showing inhibitory action.

Methodology: We selected 560 flavonoids and small compounds along with 3 targets from the extensive literature review. Three-dimensional (3D) structures of selected proteins were obtained from Protein Data Bank, docked with 560 flavonoids and small molecules 3D structures, obtained from PubChem and CHEMBL database using Gold Docking Software. ADME characteristics were used to determine their bioactivities in the human body and drug-like investigations by using SwissADME and Zinc database, while Lipinski's rule of five was used to evaluate the flavonoids' anti-prostate cancer efficacy. Additionally, we have performed molecular simulation at 100ns and furthermore, we will perform cytotoxicity analysis.

Results: Diosmetin (58.72), Lapatinib Ditosylate (121.61), and Estramustine Phosphate Sodium (143.38) has the highest binding affinity for CDKN2 (4EK3), CYP17A1(3RUK), and CYP19A1(3S79), respectively, and are stable throughout 100ns simulation studies. At present, we are working on cytotoxicity studies on PC3 cell lines. As per the literature review by Ansar et al. 2022 quercetin and thymoquinone induce cytotoxicity in breast, lung, and prostate cancer cells effectively; MCF-7 cells were the most sensitive cells to quercetin with an IC50 value of 50 μM and PC3 cells were more sensitive to thymoquinone with an IC50 value of 20 μM.

Conclusion: As a result of our findings, these four Flavonoids may be viable candidates for additional research into PCa prevention or management.Keywords: Diosmetin, Lapatinib Ditosylatye, Prostate cancer, In-silico, Simulation

Citation Format: Sumit Sheoran, Swati Arora, Tanmay Basu, Naidu Subbarao, Atul Kumar Upadhyay, Sugunakar Vuree. Assessment of polyphenolic secondary metabolites and small molecules against the xenobiotic metabolic and cell cycle regulatory proteins in prostate cancer. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5342.
Abstract 5427: Improving non-small cell lung cancer segmentation on a challenging dataset
Authors: Wei Yi , Selvaraj Balaji , Patwari Mayank , Li Qin , Xu Meng , Sidiropoulos Konstantinos , Zhang Zhenning , Fedden Leon , Madabhushi Anant , Khorrami Mohammadhadi , Viswanathan Vidya Sankar , Gupta Amit
Published: April 2023

When applied to different datasets, performance of the same deep learning tumor segmentation model can greatly vary. In a non-small cell lung cancer CT scan segmentation study that consists of two datasets, we found that the SwinUNETR model achieves state-of-the-art DICE score on a public dataset NSCLC but performs badly on a private dataset of curated data collected clinically. This performance variation reduces the applicability of such models. To mitigate this gap, through experimentation, we identified a set of techniques and applied them in the following order: (1) normalize a dataset to reduce differences between images. (2) stratify a dataset according to tumor sizes to form a more diverse training set. (3) isolate the lung area before training to help the model focus on the right area. (4) before training, initialize models with self-supervised pre-training weights (5) use a new loss function to give more weights on the cancerous area (6) after a model is trained, perform 3-axis test time flipping augmentation and ensemble the final predictions. In our experiments, our set of techniques improved the test DICE score for both datasets we tested on, where the best improvement was a 53% improvement from 0.32 to 0.49 DICE score.

Citation Format: Yi Wei, Balaji Selvaraj, Mayank Patwari, Qin Li, Meng Xu, Konstantinos Sidiropoulos, Zhenning Zhang, Leon Fedden, Anant Madabhushi, Mohammadhadi Khorrami, Vidya Sankar Viswanathan, Amit Gupta. Improving non-small cell lung cancer segmentation on a challenging dataset. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5427.
Abstract 5582: Liquid biopsy-based comprehensive genomic profiling reveal mutational landscape in real-world patients with unresectable NSCLC
Authors: Tang Haoran , Xie Feng , Zhang Yue , Jia Shidong
Published: April 2023

Introduction: NSCLC accounts for more than 80% of all lung cancer, and has been shown for clinical benefits from targeted therapies, according to tests of multiple genes, such as EGFR, KRAS, ALK, ERBB2. Previous studies revealed molecular characteristics and responses of targeted therapies in NSCLC. However, most studies used tissue biopsies. There is increasing interest to characterize the molecular profile of NSCLC through liquid biopsy. Hence, here we report a comprehensive genomic profiling study in unresectable NSCLC patients using liquid biopsy.

Methods: The prospective study is part of the Predicine’s Phoenix Program, a global molecular biomarkers screening program in multiple solid tumors. Currently, the study enrolled 352 unresectable advanced NSCLC patients from 24 centers in China, who were naïve to the 1st line treatment or recurrent after 1st line targeted therapies. 10ml of blood was collected from each patient and delivered to a central lab for ctDNA analysis. The study applied PredicineCARE, an NGS-based liquid biopsy assay, to profile somatic mutations, copy number variations, and gene fusions among these patients.

Results: The study identified 1614 somatic mutations and 202 copy number variants among blood samples from 352 patients. The most common altered genes were TP53(176/352, 50%), EGFR(144/352, 41%), PIK3CA(35/352, 10%), CDNK2A(35/352, 10%), KRAS(28/352, 8%), and RB1(28/352, 8%). Gene copy number gain incidents were identified on MYC(n=22), PIK3CA(n=16), EGFR(n=15), and MET(n=7), etc. Notably, the study also reported gene copy number loss incidents through liquid biopsy, such as CDKN2A(n=16), PTEN(n=11), and RB1(n=10). The study identified 12 gene fusion incidents, including 7 EML4-ALK fusions, 2 RET fusions(KIF5B-RET and NCOA4-RET), 2 NTRK fusions(ETV6-NTRK3 and NOS1AP-NTRK1), and 1 rare CD74-NRG1 fusion.

Conclusions: This study revealed the comprehensive mutational landscape of advanced NSCLC through liquid biopsy, providing novel biomarkers for clinical diagnosis and targeted therapy mechanism studies.

Citation Format: Haoran Tang, Feng Xie, Yue Zhang, Shidong Jia. Liquid biopsy-based comprehensive genomic profiling reveal mutational landscape in real-world patients with unresectable NSCLC. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5582.
Abstract 5613: Tumor glucose metabolism profiles detected via [18F]-FDG PET/CT correlate with the immune landascape in soft-tissue sarcomas
Authors: Crombe Amandine , Bertolo Frédéric , Guegan Jean-Philippe , Bessede Alban , Perret Raul , Spalato-Ceruso Mariella , Toulmonde Maud , Laroche Audrey , Loarer Francois Le , Chaire Vanessa , Kind Michèle , Lucchesi Carlo , Italiano Antoine
Published: April 2023

Background: Improving the assessment of the immune landscape of soft-tissue sarcoma (STS) through imaging biomarkers could help better selecting and monitoring patients that could benefit from immunotherapy. Our aim was identify whether metabolic patterns of soft-tissue sarcoma (STS) on pre-treatment 18F-Fluorodeoxyglucose (18F-FDG) positron emission tomography (PET/CT) were associated with different immune profiles on molecular and cellular levels.

Methods: This single-center prospective study included consecutive adult patients with newly-diagnosed, non-metastatic, high-grade STS treated in a curative intent with available pre-treatement 18F-FDG-PET/CT. Maximal standardized uptake value (SUVmax), SUVpeak, SUVmean, metabolic tumor volume (MTV) and total lesion glycolysis (TLG) were extracted. A cross-validated principal component analysis (PCA) was developed on the PET/CT metrics. The first two principal components (PC1 and PC2) and an unsupervised metabolic classifications were computed.

Differential gene expression (DGE), oncogenesis pathways analyses, complexity index in sarcoma (CINSARC) molecular signature and immunohistochemistry panels (CD8, CD14, CD20, CD45, CD68, c-MAF) were performed. Correlations between nuclear imaging, immunohistochemistry and transcriptomics data were achieved.

Results: 85 patients were included (median age: 62 years, 37 women) between 2016 and 2021. The robust PCA defined 3 metabolic groups (high [n=21], intermediate [n=15] and low [n=49]). PC1 reflected the tumor metabolism and PC2 the size and amount of necrosis. Transcriptomics and immunohistochemistry data were available in 32 and 31 patients, respectively. PC1 was significantly positively correlated with CINSARC (P=0.0029) and the cellular densities in CD8+, CD14+, CD45+, CD68+ and c-MAF (range of P-values: 0.0175-0.0499). The metabolic-high group was characterized by the upregulation of 13 immune pathways, including ICOS, CD27, IFNG, CXCL9-10/CXCL3 genes.

Conclusion: Metabolic profiles on 18F-FDG-PET/CT of high-grade STS highlights distinct immune profiles, which could pave the way for potential biomarkers of STS immunophenotyping.

Citation Format: Amandine Crombe, Frédéric Bertolo, Jean-Philippe Guegan, Alban Bessede, Raul Perret, Mariella Spalato-Ceruso, Maud Toulmonde, Audrey Laroche, Francois Le Loarer, Vanessa Chaire, Michèle Kind, Carlo Lucchesi, Antoine Italiano. Tumor glucose metabolism profiles detected via [18F]-FDG PET/CT correlate with the immune landascape in soft-tissue sarcomas. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5613.
Abstract 5631: Expanding tools for multiplex mRNA imaging in spatialomics through the ViewRNA tissue assay kits
Authors: Mooney Nancie
Published: April 2023

Spatialomics is a rapidly growing field as it allows researchers to gain a deeper understanding of transcriptomes and corresponding protein expression profiles in cells within complex tissue microenvironments. One critical technology for spatialomics is in-situ hybridization (ISH) technology, which enables direct visualization and quantitation of nucleic acid in cells with single molecule resolution. The Invitrogen ViewRNA ISH assays incorporate branched DNA (bDNA) technology provides tools for interrogating multiple RNA transcripts at the same time, paving the way for improved spatialomics research. This technology is a powerful tool for spatialomics, giving insight into important mechanisms within cells and tissue. With researchers increasingly using spatialomic data in fields like neuroscience, immuno-oncology & single-cell analysis, these scientists will need the rapid and efficient detection of mRNA co-expression profiles that ViewRNA portfolio provides. In our newest offering, ViewRNA fluorescence tissue kits we extended our branched DNA technology, proprietary probe set design and signal amplification technology with Alexa Fluor probes offering a unique, robust, and sensitive in situ hybridization assay for RNA localization in fixed tissues. With fluorescence detection using Alexa Fluor 488, Alexa Fluor 546, Alexa Fluor 594, Alexa Fluor 647, and Alexa Fluor 750, these kits allow multiplexed detection and imaging paving the way for improved spatialomics. This technology lays the foundation for expanded fluorescent profiles to provide scientists additional tools to probe multiple transcripts per sample, allow broader spatialomics research. For Research Use Only. Not for use in diagnostic procedures.

Citation Format: Nancie Mooney. Expanding tools for multiplex mRNA imaging in spatialomics through the ViewRNA tissue assay kits. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5631.
Abstract 5652: IL-19 blockade reprograms glioblastoma immunosuppressive microenvironment and overcomes chemo-resistance as revealed by single-cell transcriptome analyses
Authors: Lee Gilbert A. , Chen Cheng-Yu
Published: April 2023

Glioblastoma multiforme (GBM) is the most aggressive brain tumor with chemo-resistant, immunosuppressive, and invasive property. Despite the application of standard therapies which include a combination of surgery, radiotherapy, and temozolomide (TMZ) chemotherapy, tumor inevitably recurred (in patients) at peritumoral region. Targeting multiple arms of the GBM-mediated immunosuppressive ability and their invasiveness can improve therapeutic efficacy. Genomic screening identified that IL-19 is a predicted immune suppressive cytokine in peritumoral region and was associated with poor survival in patients with GBM. IL-19 blockade inhibited both TMZ-sensitive and resistant tumor progression. Molecular studies revealed that silencing IL-19 markedly abrogated IL-19-WISP1-AKT signaling to inhibit TMZ-resistant GBM cell invasion, as well as weaken its suppressive ability on CD8+T cell activation. Single cell transcriptome analysis revealed that IL-19 blockade promoted T cell activation, upregulated effector function of T cell subsets, and reprogrammed tumor-associated macrophage subsets toward a weakened pro-tumoral phenotypes. Thus, Targeting IL-19 can be a novel therapeutic strategy to reverse immunosuppressive microenvironment and restrict invasiveness of chemo-resistant GBM.

Citation Format: Gilbert A. Lee, Cheng-Yu Chen. IL-19 blockade reprograms glioblastoma immunosuppressive microenvironment and overcomes chemo-resistance as revealed by single-cell transcriptome analyses. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5652.
Abstract 570: Dual acting bone defender agents inhibit prostate cancer-mediated bone destruction
Authors: Qiao Fangfang , Gordon Ryan , Pattanayak Abhinandan , O’Neill Katelyn , Chaika Nina , Chen Weining , Rhatigan Rachel , Bergan Raymond
Published: April 2023

Introduction: Bone metastasis is clinically observed in approximately 90% of patients with advanced prostate cancer (PCa). Metastatic bone destruction is driven by a self-reinforcing process coupling osteoclast (OC)-mediated bone degradation to PCa growth, and where cell movement acts to keep these two cooperating cell types in close proximity and to move them across the bone surface. We sought to create a new class of therapeutics that would be highly effective at inhibiting PCa-mediated bone destruction by targeting both OC function and cell motility.

Methods: We synthesized new chemical entities, termed Dual Acting Bone Defender agents (DABDs), that couple the small molecule anti-motility agent, KBU2046, with bisphosphonate (bis), through a chemical linker. Assays for in vitro efficacy included: cell migration and invasion, binding to bone mineral, inhibiting osteoclast (OC)-mediated bone destruction, inhibition of Raf1 phosphorylation and inhibition of protein prenylation. In vivo assays included intra-cardiac (IC) injection of human PCa cells into mice, followed by real time monitoring of tumor growth and bone destruction by IVIS and CT imaging, respectively.

Findings: We successfully created a novel route of chemical synthesis allowing us to access and probe unique chemical space, providing for single small molecules with bis functional groups linked to a KBU2046 core through a linker moiety. DABDs retain the cellular and molecular characteristics of KBU2046 and bis. Like KBU2046, they inhibit PCa cell motility and phosphorylation of Raf1 on its activation motif. They also inhibit the motility of breast and lung cancer cells. Like bis, they inhibit OC-mediated bone mineral destruction, prenylation of Ras small GTPase proteins, and chemically bind hydroxyapatite. Administered prior to IC injection, DABDs are so effective that they prolong animal survival and inhibit bone destruction in a dose-dependent manner. In mice with established bone metastasis to the femur, after IC injection, DABDs inhibit the growth of tumors. Doses 3,000 fold higher than that required for efficacy had no clinical or critical organ toxicity.

Conclusions: DABDs represent a new multifunctional class of therapeutic agents that inhibit PCa-mediated bone destruction and have a high potential for advancing clinical efficacy in PCa patients with bone metastasis.

Citation Format: Fangfang Qiao, Ryan Gordon, Abhinandan Pattanayak, Katelyn O’Neill, Nina Chaika, Weining Chen, Rachel Rhatigan, Raymond Bergan. Dual acting bone defender agents inhibit prostate cancer-mediated bone destruction [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 570.
Abstract 5710: Detection and monitoring of t(11;14) in liquid biopsies from patients with relapsed/refractory multiple myeloma treated with venetoclax-based regimens
Authors: Li Xiaotong , Saal Lao H. , Brueffer Christian , Chen Yilun , Asklin Johanna , Alvi Saman , Venkatram Srinivas , Ross Jeremy A.
Published: April 2023

Venetoclax (Ven) is a selective B-cell lymphoma 2 inhibitor being studied in t(11;14)+ relapsed/refractory multiple myeloma (MM) Detection of t(11;14) in MM requires bone marrow (BM) aspiration and evaluation of CD138+ plasma cells by fluorescence in situ hybridization (FISH) Innovative techniques may provide less invasive detection of t(11;14) in liquid biopsies Here we present results of the SAGAsign® integrated approach combining low-coverage whole-genome sequencing (WGS) to characterize t(11;14) breakpoints together with personalized digital polymerase chain reaction (dPCR) assays to efficiently detect and monitor the genomic rearrangements in circulating tumor DNA (ctDNA) Baseline BM aspirates were collected from 270 patients (pts) from Ven clinical trials (NCT02755597, NCT01794520, NCT03314181, NCT02899052) Previously generated WGS to an average coverage ~22 × was used Paired samples of peripheral blood mononuclear cell (PBMC) DNA and plasma circulating cell-free DNA (cfDNA) were analyzed by dPCR at timepoints after Ven-based treatment Of the 90 t(11;14)+ pts by FISH, 160 t(11;14) breakpoints were identified by WGS in 74 pts (concordance in Table) At the time of data cutoff, dPCR assays were designed and evaluated in 8 t(11;14)+ pts; 7/8 (88%) and 6/8 (75%) pts had detectable t(11;14) in cfDNA or PBMCs, respectively Higher levels of t(11;14) mutant allele frequency (MAF) were observed in cfDNA compared with PBMCs After Ven-based treatment, t(11;14) MAF in cfDNA became undetectable in pts with a complete response In conclusion, this approach has the capability to reconstruct t(11;14) breakpoints from WGS data that is highly concordant with FISH; translocations appear more readily detectable in cfDNA than PBMC samples from pts with MM SAGAsign assays detected and monitored t(11;14) in liquid biopsies thus highlighting its potential utility for identifying pts with t(11;14) for targeted therapies

Concordance between WGS and FISH testing for t(11;14) Samples, n FISH+ FISH− Total WGS+ 74 11 83 WGS− 16 169 187 Total 90 180 270 Concordance, % n/N 95% CI t(11;14) positive 82.2 74/90 72.7-89.5 t(11;14) negative 93.9 169/180 89.3-96.9 Overall testing 90.0 243/270 85.8-93.3

Citation Format: Xiaotong Li, Lao H. Saal, Christian Brueffer, Yilun Chen, Johanna Asklin, Saman Alvi, Srinivas Venkatram, Jeremy A. Ross. Detection and monitoring of t(11;14) in liquid biopsies from patients with relapsed/refractory multiple myeloma treated with venetoclax-based regimens. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5710.
Abstract 5753: RUNX3 disrupts MYC/MAX complex and promotes MYC degradation
Authors: Ito Yoshiaki , Oei Vincent , Chuang Linda , Matsuo Junichi , Srivastava Supriya , Teh Ming
Published: April 2023

We reported earlier that heterozygous deletion of RUNX3 in the mouse induces adenoma in small intestine, mammary gland (1) and lung (2) and a precancerous stomach epithelium that is highly sensitive to a chemical carcinogen (3). We therefore propose that RUNX3 is a gatekeeper of cancer development (1).

In our recent study on how RUNX3 inhibits early-stage cancer development in multiple tissues, we uncovered a previously unknown mode of MYC destabilization by RUNX3. From RNA sequencing, knockdown experiments, tumorigenic assays, protein interaction and ubiquitination studies, we show that the strong inhibitory effects of RUNX3 on proliferation and tumor growth may, in part, be attributed to its ability to promote MYC degradation. The evolutionarily conserved Runt domain of RUNX3 interacts directly with the basic helix-loop-helix leucine zipper of MYC, resulting in the disruption of MYC/MAX interaction, enhanced GSK3β-mediated phosphorylation of MYC protein at threonine-58 and its subsequent degradation via the ubiquitin-proteasomal pathway (4). MYC inhibitor Omomyc, a short peptide comprising the b HLH LZ domain of MYC with 4 amino acid substitutions, is extremely effective in disrupting MYC/MAX interaction (5). RUNX3 appears to function similarly to Omomyc: is RUNX3 a Nature-designed Omomyc?

References:(1) Ito K et al, Cancer Cell 14;226-237, 2008; (2) Lee YS et al, Cancer Cell 24: 603-616, 2013; (3) Ito K et al, Gastroenterol 140:1536-1546, 2011; (4) Oei V, Chuang LSH, et al, Submitted; (5) Soucek et al, Nature 455:679-683, 2008

Citation Format: Yoshiaki Ito, Vincent Oei, Linda Chuang, Junichi Matsuo, Supriya Srivastava, Ming Teh. RUNX3 disrupts MYC/MAX complex and promotes MYC degradation. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5753.
Abstract 5767: Pan-viral response in African Americans and European Americans with hepatocellular carcinoma
Authors: Ewa Theressa , Do Whitney L. , Wang Limin , Forgues Marshonna , Wang Xin W.
Published: April 2023

Hepatocellular carcinoma (HCC) is often diagnosed at late-stages, with African Americans (AA) being diagnosed at a later stage with worse prognosis and high mortality rates. The poor screening and diagnosis of HCC and differences between racial/ethnic groups show a disproportion in mortality rates. Examining an individual’s viral exposure history might serve as a useful biomarker of early disease that could address and, potentially, alleviate this disparity. We aim to investigate whether viral features can be used to identify HCC and individuals at high risk (HR) of HCC. Additionally, we examine the racial/ethnic differences in viral exposures and whether viral exposure history accounts for epidemiological disparity described previously. Herein we use a technique called VirScan, which conjugates Phage Immunoprecipitation sequencing (PhIP-seq) and DNA sequencing, to profile an individual’s epitope antibody repertoire upon viral exposure. We performed VirScan on serum and plasma samples from 199 AA (130 HR and 79 HCC) and 260 European Americans (EA) (210 HR and 50 HCC) participants from the NCI-UMD cohort (NCT00913757; clinicaltrials.gov). We used a machine-learning XGBoost model to classify viral features that can discriminate HCC or HR. A composite viral score was generated using the SHAP value of the most significant viral features from the model with a higher score more predictive of HCC. Secondary analyses using Wilcoxon-Rank sums tests and Cox proportional hazard analysis revealed that while race/ethnicity did not differentially predict HCC in this cohort, the viral score was significantly higher in AA compared to EA in the HR group (p = 0.027). XGBoost search identified 235 important viral features which distinguish HCC from HR. Out of the 235 viral features, 20 viruses were different between AA and EA (FDR < 0.05). We also found the viral score was positively associated with incident mortality in HCC group over the study period of 8 years (p=0.03). Thus, we demonstrate that the viral history of an individual might be useful in early detection of HCC. This approach could be used to account for the disparities we see in both incidence and mortality of HCC between AA and EA.

Citation Format: Theressa Ewa, Whitney L. Do, Limin Wang, Marshonna Forgues, Xin W. Wang. Pan-viral response in African Americans and European Americans with hepatocellular carcinoma. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5767.
Abstract 5838: Cancer-associated fibroblasts drive spheroid formation and pleural dissemination in non-small cell lung cancer
Authors: Ohki Masayoshi , Matsuda Naoki , Suzawa Ken , Habu Tomohiro , Yoshikawa Mao , Iwata Kazuma , Thu Yin Min , Shien Kazuhiko , Yamamoto Hiromasa , Toyooka Shinichi
Published: April 2023

Introduction: Cancer-associated fibroblasts (CAFs) play an important role in cancer progression and malignant transformation by interacting with cancer cells in the tumor microenvironment. Pleural dissemination of non-small cell lung cancer (NSCLC) is a condition in which cancer cells directly spread from the primary tumor site into the extrapulmonary thoracic cavity and colonize the pleura. However, not all free detached cancer cells can survive under anchorage-independent conditions in thoracic cavity, and some important factors are assumed to be involved in the formation of pleural dissemination. In this study, we investigated the role of CAFs in the formation of pleural dissemination in NSCLC.

Methods: Using in vitro co-culture models, conditioned medium, and in vivo xenograft models, we investigated CAF-induced phenotypic changes in lung cancer cell: proliferative ability, invasive ability, anchorage-independent growth ability, cell adhesion to extracellular matrix, and tumorigenicity in thoracic cavity. Next, we performed RNA sequencing analysis using 3D co-culture models of cancer cells and CAFs to explore a molecule that contributes to the formation of pleural dissemination, and then verified it using in vitro and in vivo mice models of pleural dissemination.

Results: Cancer cells showed enhanced migration, anchorage-independent growth, adhesion, and invasion ability by co-culture with CAFs. In 3D co-culture model of cancer cells and CAFs, even cancer cells which did not form spheroid by themselves acquired the ability of spheroid formation surrounding the CAF core, suggesting that the interactions with CAFs promote spheroid formation. Inoculation of cancer cells together with CAFs into mouse thoracic cavity developed pleural dissemination more efficiently than inoculation of cancer cells alone. RNA sequencing analysis revealed that co-culture with CAFs upregulated the expression of Cellular Communication Network Factor 1 (CCN1), a matricellular protein, in cancer cells. We then verified that ectopically CCN1-overexpressing lung cancer cell lines increased migration and adhesion ability in vitro, and tumorigenicity in thoracic cavity in mouse pleural dissemination model.

Conclusions: CAFs promote development of pleural dissemination via driving spheroid formation and upregulating CCN1 expression in NSCLC.

Citation Format: Masayoshi Ohki, Naoki Matsuda, Ken Suzawa, Tomohiro Habu, Mao Yoshikawa, Kazuma Iwata, Yin Min Thu, Kazuhiko Shien, Hiromasa Yamamoto, Shinichi Toyooka. Cancer-associated fibroblasts drive spheroid formation and pleural dissemination in non-small cell lung cancer. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5838.
Abstract 5841: Exploring the role of versican in immune exclusion within triple negative breast cancer
Authors: Hirani Priyanka , Alonge Kimberly M. , Pennington Daniel J. , Cutillas Pedro R. , Wight Thomas N. , Pearce Oliver M.
Published: April 2023

Immunotherapy has found limited success in solid tumors such as triple negative breast cancer (TNBC). The poor response can be attributed to the presence of the extracellular matrix (ECM) that can act biochemically or physically to interfere with cytotoxic T cell migration, leading to a limitation in tumor cell killing. Through previous work on deconstructing this matrix and outlining the spatial arrangement of proteins, we were able to identify versican as a key protein in T cell location. Versican is a chondroitin sulfate proteoglycan and has multiple functions in the ECM due to its ability to bind many ECM components. Using immunohistochemistry in this study, we analyzed the localization of CD8+ T cells within human TNBC tissues to classify them as inflamed (tumorhi, stromahi), desert (tumorlo, stromalo) or immune excluded (tumorlo, stromahi). From the analysis of 26 tissues, nearly half were classified as immune excluded with most of the CD8+ T cells restricted to the stroma, whilst only a quarter were inflamed. When comparing this to versican accumulation we noticed that immune excluded tissues have significantly higher levels of versican in the tumor epithelium compared to inflamed tissues where versican is mostly found within the stroma. To investigate the function of versican’s structure, we carried out transwell migration assays using versican enriched protein treated with or without chondroitinase ABC and showed that the chondroitin sulfates attached to versican’s peptide backbone are an important factor towards T cell trafficking with a reduction in migration following chondroitinase ABC treatment. Comparison of versican levels to chondroitin sulfate via immunohistochemistry showed a positive correlation within inflamed tissues, however no correlation was observed in immune excluded tissues. Versican isoforms expression in TNBC tissues and cell lines was examined with qRT-PCR which showed that within all tissues and cell lines the V0 and V1 isoform are the highest expressed out of the 5 isoforms. Overall, in this work, we have found that versican is differentially expressed in excluded tissues in comparison to inflamed tissues. With chondroitin sulfate shown to play a major role in immune cell trafficking, understanding how it differs between inflamed and excluded tumors can help identify potential targets to improve immunotherapy response.

Citation Format: Priyanka Hirani, Kimberly M. Alonge, Daniel J. Pennington, Pedro R. Cutillas, Thomas N. Wight, Oliver M. Pearce. Exploring the role of versican in immune exclusion within triple negative breast cancer. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5841.
Abstract 5845: Periostin secreted by cancer-associated fibroblasts promotes cancer progression and drug resistance in non-small cell lung cancer
Authors: Yoshikawa Mao , Takatsu Fumiaki , Suzawa Ken , Habu Tomohiro , Masayoshi Ohki , Iwata Kazuma , Matsuda Naoki , Thu Yin Min , Shien Kazuhiko , Yamamoto Hiromasa , Toyooka Shinichi
Published: April 2023

Background: Cancer-associated fibroblasts (CAFs) are key players in the tumor microenvironment (TME) due to their abundance in most solid tumors and active crosstalk with cancer cells, and promote the initiation of tumor formation, tumor growth, angiogenesis, metastasis, and therapeutic resistance. In this study, we sought to identify effective therapeutic targets in CAFs for non-small cell lung cancer (NSCLC).

Experimental Design: We established fibroblast cell lines from the cancerous and non-cancerous parts of surgical lung specimens from patients with NSCLC and evaluated the differences in behaviors towards NSCLC cells using in vitro co-culture models, conditioned medium, and in vivo xenograft mouse models. Next, RNA sequencing analysis was performed to investigate the differentially expressed genes between normal fibroblasts (NFs) and CAFs, and we then verified the biological activity of the identified molecule on NSCLC cells in vitro and in vivo mouse model.

Results: Cancer cells showed enhanced cell proliferation, migration, and drug resistance by co-culture with CAFs or CAF-derived conditioned medium. RNA sequencing analysis revealed that CAFs showed higher expressions of POSTN, a matricellular protein, than NFs. Single-cell RNA sequencing data of NSCLC from public database confirmed that POSTN-positive fibroblasts were highly enriched in lung tumor tissues but rarely observed in normal lung tissues, suggesting CAF-specific POSTN expression in lung cancer. Recombinant POSTN increased cell proliferation via NSCLC cells’ ERK pathway activation and induced epithelial-mesenchymal transition (EMT), which improved migration in vitro. In addition, POSTN knockdown in CAFs suppressed these effects, and in vivo experiments demonstrated that the POSTN knockdown improved the sensitivity of EGFR-mutant NSCLC cells for Osimertinib treatment.

Conclusion: Our results showed that CAF-derived POSTN is involved in tumor growth, migration, EMT induction, and drug resistance in NSCLC. Targeting CAF-secreted POSTN in TME could be a potential therapeutic strategy for NSCLC.

Citation Format: Mao Yoshikawa, Fumiaki Takatsu, Ken Suzawa, Tomohiro Habu, Ohki Masayoshi, Kazuma Iwata, Naoki Matsuda, Yin Min Thu, Kazuhiko Shien, Hiromasa Yamamoto, Shinichi Toyooka. Periostin secreted by cancer-associated fibroblasts promotes cancer progression and drug resistance in non-small cell lung cancer. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5845.
Abstract 5848: Identification of mechanosensitive cancer associated fibroblasts in pancreatic cancer
Authors: Xiao Weikun , Eun Chae-Young , Zhao Weian , Hill Reginald
Published: April 2023

The purpose of this study is to investigate whether a subpopulation of cancer associated fibroblasts (CAFs) are responsible for mechanosensation-mediated chemoresistance in pancreatic adenocarcinoma (PDAC). PDAC is one of the most lethal types of cancer with few effective treatments. The abundant stromal cells and the stiff desmoplastic microenvironment constitute more than 90% of the primary tumor bulk. However, there are few easily tunable models to recapitulate this stiff microenvironment. To address this issue, we have developed a Matrigel-based, orthogonally tunable 3-dimensional (3D) culture system to co-culture mouse derived PDAC organoids and host-matching cancer-associated fibroblasts (CAFs). Using this biomimetic model and a mechano-sensation-dependent reporter, we have identified a unique subpopulation of CAFs responsible for mechano-sensing the fibrotic matrix and facilitating CAF-mediated chemoresistance. Moreover, these mechanosensitive CAFs (mecCAFs) respond to increased stiffness through YAP-mediated pathways. Our results also demonstrate how ECM stiffness affects chemoresistance via the hypersecretion CAF-derived exosomes. Moving forward, therapies designed to interrupt the function of mecCAFs could be utilized to overcome matrix-mediated chemoresistance in PDAC.

Citation Format: Weikun Xiao, Chae-Young Eun, Weian Zhao, Reginald Hill. Identification of mechanosensitive cancer associated fibroblasts in pancreatic cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5848.