bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 3265: Secretome core fucosylation drives clonal drug resistance expansion and hypoxic control of metastasis
Authors: Aldonza Mark Borris D. , Son Keun Hong , Cho Je-Yoel 
Published: March 2024

Abstract
Cancer secretome is a reservoir for aberrant glycosylation. How therapies alter this post- translational cancer hallmark and the consequences thereof remain elusive. Here, we show that an elevated secretome fucosylation is a pan-cancer signature of both response and resistance to multiple targeted therapies. Large-scale pharmacogenomics revealed that fucosylation genes display widespread association with resistance to these therapies. In cancer cell cultures, xenograft mouse models, and patients, targeted kinase inhibitors distinctively induced core fucosylation of secreted proteins less than 60 kDa. Label-free proteomics of N-glycoproteomes identified fucosylation of the antioxidant PON1 as a critical component of the therapy-induced secretome (TIS). N-glycosylation of TIS and target core fucosylation of PON1 are mediated by the fucose salvage-FUT8-SLC35C1 axis with PON3 directly modulating GDP-Fuc transfer on PON1 scaffolds. Core fucosylation in the Golgi impacts PON1 stability and folding prior to secretion, promoting a more degradation-resistant PON1. Global secretome and PON1-specific de-N-glycosylation both limited the expansion of resistant clones in a tumor regression model. We defined the resistance-associated transcription factors (TFs) and genes modulated by the N-glycosylated TIS via a focused and transcriptome-wide analyses. In a spontaneous lung metastasis mouse model, global secretome and PON1-specific core fucosylation functionally drive hypoxia and hypoxic selection of drug-resistant clones. Our findings demonstrate that core fucosylation is a common modification indirectly induced by targeted therapies that paradoxically promotes resistance and metastasis.
Citation Format: Mark Borris D. Aldonza, Keun Hong Son, Je-Yoel Cho. Secretome core fucosylation drives clonal drug resistance expansion and hypoxic control of metastasis [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 3265.
Abstract 3285: Elevated expression of breast cancer stem cell marker alpha6-integrin is associated with reduced anti-estrogen efficacy in breast cancer
Authors: Viteri Gabriel , Angeloni Shawnee , Soto Ubaldo , Brantley Eileen J. 
Published: March 2024

Abstract
Most women diagnosed with breast cancer have tumors expressing the estrogen receptor and are prescribed agents such as aromatase inhibitors or the anti-estrogens tamoxifen or fulvestrant. However, up to 40% of these patients will experience relapse due to endocrine therapy resistance even when these agents are used in combination with cyclin dependent kinase inhibitors. A small population of cells within tumors known as breast cancer stem cells are generally resistant to endocrine therapy and are believed to promote patient relapse. We previously found that breast cancer stem cell marker α6-integrin is expressed at elevated levels in cells that are resistant to the anti-estrogen tamoxifen. We thus hypothesized that elevated levels of α6-integrin confer resistance to anti-estrogens. Quantitative PCR analyses revealed that tamoxifen-resistant and fulvestrant-resistant mammospheres (breast cancer spheroids) exhibit increased α6-integrin expression as compared to antiestrogen-sensitive mammospheres. Cells with enforced α6-integrin expression were less responsive to tamoxifen and fulvestrant than control cells. Further, pharmacological or genetic inhibition of α6-integrin enhanced anti-estrogen efficacy. Our data suggest that targeting α6-integrin represents a viable strategy to overcome endocrine therapy resistance.
Citation Format: Gabriel Viteri, Shawnee Angeloni, Ubaldo Soto, Eileen J. Brantley. Elevated expression of breast cancer stem cell marker alpha6-integrin is associated with reduced anti-estrogen efficacy in breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 3285.
Abstract 3288: Identification of Annexin A1 as a novel driver of lenvatinib resistance in hepatocellular carcinoma
Authors: GU Catherine Yujia , LEUNG Carmen Oi Ning , LEE Terence Kin Wah 
Published: March 2024

Abstract
Hepatocellular carcinoma (HCC) is the third leading cause of cancer-related deaths worldwide. Lenvatinib has recently been approved by the FDA for front-line treatment of HCC patients at advanced stages. However, the survival benefit of lenvatinib is modest due to the development of acquired drug resistance. In this study, we aimed to investigate the mechanisms underlying lenvatinib resistance in HCC and to identify potential therapeutic targets to combat lenvatinib resistance. For this purpose, we established a lenvatinib-resistant (LenR) HCC patient-derived tumor xenograft (PDTX) by administering four rounds of lenvatinib treatment, and their genetic profiles were analyzed using single-cell RNA sequencing (scRNA-seq). Based on single-cell regulatory network inference and clustering (SCENIC) analysis, Annexin A1 (ANXA1), the top gene that was enriched in the HCC cell-like cluster of LenR tumors, was identified and was consistently observed in LenR HCC cell lines and LenR tumors derived from Tp53KO/C-MycOE and RIL175 HCC mouse models. Using an in vitro differentiation model, limiting dilution assay, apoptosis assay and correlation analysis, we demonstrated the role of ANXA1 in the regulation of cancer stemness-driven lenvatinib resistance. Mechanistically, ANXA1 regulates cancer stemness and drug resistance by driving the STAT3/S100A6 signaling cascade, and ANXA1 expression is regulated by SOX2 via promoter activation, as demonstrated by a chromatin immunoprecipitation (ChIP) assay. Using the same set of scRNA-seq data, we showed that LenR HCC tumors reshaped the tumor microenvironment (TME) by inducing M2 macrophage polarization, as evidenced by a higher M2/M1 ratio of tumor-associated macrophages (TAM) in LenR HCC tumors than in their mock counterparts. Based on this observation, we further demonstrated the in vitro role of secretory ANXA1 in LenR HCC cells in inducing macrophage polarization towards the M2 phenotype. In conclusion, ANXA1 may regulate lenvatinib resistance intrinsically via the promotion of cancer stemness and extrinsically via the induction of an immunosuppressive TME.
Citation Format: Catherine Yujia GU, Carmen Oi Ning LEUNG, Terence Kin Wah LEE. Identification of Annexin A1 as a novel driver of lenvatinib resistance in hepatocellular carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 3288.
Abstract 330: FusionPlex™-HT and VariantPlex™-HT: Automation ready solutions for anchored multiplex PCR
Authors: Knupp David , Troutman Christine , Hadjis Allison , Legare Dhruti , Kalavakur Paula , Washburn Michael 
Published: March 2024

Abstract
Introduction: Anchored Multiplex PCR (AMP™) assays, VariantPlex and FusionPlex are amplicon-based, next generation sequencing (NGS) workflows that identify genomic variations present in DNA or RNA input, respectively. AMP reagents are available in a lyophilized format which are user-friendly and convenient to store. However, lyophilized reagents are not suitable for liquid handlers or high-throughput environments. Thus, we developed AMP reagents in liquid format to satisfy the need for a platform-agnostic method of high-throughput (-HT) AMP library preparation.
Methods: The performance of our liquid reagent-based VariantPlex-HT and FusionPlex-HT workflows were evaluated relative to legacy lyophilized reagents using several input of varying quantity, quality and type. In addition, we examined liquid reagent performance across multiple AMP panels, which target solid tumor and blood cancers variants. Prepared libraries were then sequenced and analyzed using Archer™ Analysis v7.0 software.
Results: When using 50ng SeraSeq® Myeloid DNA input (LGC Clinical Diagnostics, Inc.) and the VariantPlex Core Myeloid panel (37 gene targets), both the lyophilized VariantPlex and VariantPlex-HT detected 100% (22/22) known variants ranging from 3.8% to 20.4% allele frequency (AF). When using low-quality FFPE and the VariantPlex Complete Solid Tumor panel (430 gene targets), both workflows captured 28/28 (AF: 1.4%-20.2%) and 11/11 (AF:1.2%-18.9%) single nucleotide variants (SNVs) and Insertion and Deletions (InDels) when 50ng of SeraSeq compromised FFPE or 200ng Horizon Severe FFPE was used as input, respectively. The FusionPlex-HT workflow consistently showed increased library complexity using the FusionPlex Lung V2 panel with 20ng or 50ng of Seraseq RNA Fusion Mix v4 input. This, coupled with greater on-target percentage resulted in an average increase in fusion supporting reads of 1.95x ± 0.53 and 2.2x ± 0.41 for 20ng and 50ng input, respectively. Next, we prepared a dilution series of SeraSeq RNA Fusion Mix v4 FFPE material at 100%, 25%, 10% and 5% dilutions. We utilized our FusionPlex Pan Solid Tumor panel (137 gene targets) which covers all expected fusions in this input material. At 100% and 25% dilutions, all expected fusions were detected by lyophilized FusionPlex and FusionPlex-HT workflows. However, at 10% and 5% dilutions FusionPlex-HT detected 100% and 91% of expected fusions, respectively, while legacy lyophilized reagents detected 80% and 60% of expected fusions.
Citation Format: David Knupp, Christine Troutman, Allison Hadjis, Dhruti Legare, Paula Kalavakur, Michael Washburn. FusionPlex™-HT and VariantPlex™-HT: Automation ready solutions for anchored multiplex PCR [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 330.
Abstract 3316: LY3962673, an oral, highly potent, mutant-selective, and non-covalent KRAS G12D inhibitor demonstrates robust anti-tumor activity in KRAS G12D models
Authors: Gong Xueqian , Gao Hong , Bender Mark H. , Ming Wenyu , Zhang Youyan , Stewart Trent R. , Yu Chun Ping , Xu Wei Guo , You Aurthur Xintian , Bian Wen Ting , Li Binghui , Wang Tao , Bian Huimin , Tandon Manuj , Capen Andrew , Cavitt Rachel N. , Anderson Bryan D. , Bocchinfuso Wayne , Klippel Anke , Iyer Chandrasekar 
Published: March 2024

Abstract
KRAS G12D mutations are activating oncogenic events that occur in approximately 35%, 13%, and 4% of pancreatic, colorectal, and non-small cell lung cancers, respectively, and less commonly in other cancers. We previously demonstrated that LY3962673 is a highly potent inhibitor of KRAS G12D and is selective against wild-type (WT) KRAS in mutant -cell lines and -in vivo models. Here, we describe the mechanism by which LY3962673 inhibits KRAS G12D and report a more comprehensive evaluation of LY3962673 activity across a panel of genetically and histologically diverse cancer cell lines, as well as in multiple patient-derived xenograft (PDX) models.
LY3962673 is a non-covalent KRAS G12D inhibitor with high affinity binding to KRAS G12D-GDP (Kd 0.071 nM) compared to KRAS G12D-GTPγS (Kd 26.7 nM). In a panel of cancer cell lines with KRAS G12D mutations, non-G12D mutations or KRAS WT, LY3962673 selectively suppressed MAPK signaling and inhibited the growth of KRAS G12D mutant cancer cells while sparing KRAS WT and non-G12D mutant cells. Sensitivity to LY3962673 varied among the KRAS G12D-mutant cells tested, suggesting that not all cell lines share the same dependence on KRAS G12D for their growth and survival. Furthermore, in multiple KRAS G12D-mutant PDX models representing diverse tumor types, LY3962673 demonstrated anti-tumor activities, ranging from tumor growth inhibition to robust tumor regression. LY3962673 also showed enhanced efficacy when combined with other anti-cancer agents.
Taken together, the findings underscore the potential of LY3962673 as a monotherapy or in combination with other anti-cancer agents, as a promising oral therapeutic option for a range of cancer types with KRAS G12D mutations.
Citation Format: Xueqian Gong, Hong Gao, Mark H. Bender, Wenyu Ming, Youyan Zhang, Trent R. Stewart, Chun Ping Yu, Wei Guo Xu, Aurthur Xintian You, Wen Ting Bian, Binghui Li, Tao Wang, Huimin Bian, Manuj Tandon, Andrew Capen, Rachel N. Cavitt, Bryan D. Anderson, Wayne Bocchinfuso, Anke Klippel, Chandrasekar Iyer. LY3962673, an oral, highly potent, mutant-selective, and non-covalent KRAS G12D inhibitor demonstrates robust anti-tumor activity in KRAS G12D models [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 3316.
Abstract 3332: Kalkitoxin thiol amide suppresses the breast cancer metastasis to bone and brain
Authors: Soh Yunjo , Shrestha Saroj Kumar , Kim Se woong 
Published: March 2024

Abstract
Introduction: Breast cancer is the primary frequently diagnosed cancer worldwide, with a high fatality rate. Metastasis resulting from advanced breast cancer increases mortality in patients. MDA-MB-231 is triple-negative breast cancer that does not have any of the receptors that are commonly found in breast cancer. The lipopeptide toxin kalkitoxin thiol amide (KTA), generated from the marine cyanobacterium Moorena producens (formerly Lyngbya majuscule), has a wide range of biological and pharmacological effects. Its promise as a therapeutic agent for treating bone metastases from breast cancer is still uncertain. This study aimed to determine whether KTA could prevent breast cancer from metastasis to mice's bones and to elucidate any potential mechanisms causing this inhibition.
Experimental Procedures: MDA-MB-231 cells were transfected with pGL4.50 (Luc2/CMV/Hygro) vector using LipofectamineTM 2000. Positive clones of MDA-MB-231 cells were selected after treatment with 300 µg/ml hygromycin for one week. After cancer implantation to the heart, bioluminescent imaging of femurs was measured upto 5 weeks and signal intensity of KTA-treated groups was compared with the vehicle group.
Summary: KTA decreased breast cancer cell proliferation, migration, and invasion. KTA prevented MDA-MB-231 cells from breast cancer metastasizing to the bone and brain via inhibiting MAPK and STAT signaling. The epithelial-mesenchymal transition markers, which are responsible for distant metastasis, are highly opposed by KTA. Compared to mice in the control group, mice receiving KTA displayed considerably less bone and brain metastasis, a lower tumor burden, and less bone destruction in the murine breast cancer bone metastasis model.
Conclusion: KTA has new inhibitory effects on cancer cell invasion and migration both in vitro and in vivo. From these findings, KTA may have therapeutic promise for treating breast cancer patients with distant metastases.
Citation Format: Yunjo Soh, Saroj Kumar Shrestha, Se woong Kim. Kalkitoxin thiol amide suppresses the breast cancer metastasis to bone and brain [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 3332.
Abstract 3336: Regulation of liver X receptor protein stability by novel ligands in pancreatic cancer cells
Authors: Bagchi Abhinav , Gamage Kasuni T. , Gilbertson Scott R. , Lin Chin-Yo 
Published: March 2024

Abstract
Liver X Receptors (LXRs) are nuclear receptors that act as ligand-modulated transcription factors. LXRs are overexpressed in various cancers, including pancreatic cancer, and targeting LXR with small molecule ligands has emerged as a promising therapeutic strategy in cancer. Current small molecule LXR ligands were originally developed for the treatment of atherosclerosis and other metabolic diseases. To identify ligands specifically targeting cancer cells, we screened a focused library of drug-like molecules predicted to bind to LXR using molecular docking. In the screen, novel LXR ligand GAC0001E5 (1E5) exhibited significant anti-proliferative effects in human pancreatic ductal adenocarcinoma (PDAC) cell lines. Functionally, 1E5 is an LXR inverse agonist which decreases LXR target gene expression and a “degrader” of LXR proteins following prolonged treatment. We posit that this novel ligand inhibits PDAC cells by downregulating the expression of LXR target genes. To test this hypothesis, we treated cancer cells with the previously described LXR inverse agonist SR9238 and examined its effect on cancer cell proliferation. Interestingly, treatments with SR9238 had no effect on pancreatic cancer cell proliferation as compared to the novel ligand 1E5 and the 1E5 derivative KD-95, suggesting that LXR inverse agonism was insufficient to inhibit cell proliferation. To determine whether SR9238 has similar effects on LXR protein levels as novel ligands, we performed western analysis of protein expression following ligand treatment. In contrast to the novel ligands 1E5 and KD-95, treatments with SR9238 increased LXR protein levels. Furthermore, time-course studies in cycloheximide treated cells indicated that novel ligands decreased protein stability whereas SR9238 had the opposite effect. Inhibition of proteasomal degradation and autophagy abolished the effects of 1E5 and KD-95 in a cell line-dependent manner. Related to these observations, previously published data revealed that knockdown of LXR expression greatly diminished PDAC cell proliferation. Taken together, these findings indicate that LXR expression is essential in pancreatic cancer cells and suggest that the novel ligands may disrupt its involvement in protein-protein interactions and non-genomic mechanisms.
Citation Format: Abhinav Bagchi, Kasuni T. Gamage, Scott R. Gilbertson, Chin-Yo Lin. Regulation of liver X receptor protein stability by novel ligands in pancreatic 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 3336.
Abstract 3364: PELO is a synthetic lethal target in chromosome 9p21-deleted or MSI cancers
Authors: Chan Edmond M. , Borck Patricia , Bick Nolan , Jankovic Kristina , Boyle Isabella , Parker-Burns Lucy , Foster Kyla , Lau Anthony , Borah Ashir , Dempster Joshua , Vazquez Francisca 
Published: March 2024

Abstract
Homozygous deletion of chromosomal region 9p21.3 is one of the most frequently observed somatic copy number alterations in cancers, occurring in approximately 15% of all cancers. Many of the 9p21.3-deleted cancers are further characterized by poor clinical outcomes including subsets of glioblastoma, pancreatic, esophageal, and urothelial cancers. Large deletions of chromosomal regions may also provide unique therapeutic opportunities. Specifically, cancer-specific therapeutic opportunities can arise from co-deletions of passenger genes neighboring tumor suppressors. As such, we sought to identify novel therapeutic targets associated with Ch9p21.3 loss in cancers and identified the pelota mRNA surveillance and ribosome rescue factor (PELO) as the top preferential dependency in 9p21.3-deleted cancers. Intriguingly in another analysis, we identified PELO to be amongst the top preferential dependencies in cancers with microsatellite instability (MSI), which accounts for subsets of colorectal, endometrial, gastric, and ovarian cancers. Given the strength of PELO as a candidate synthetic lethal target in two distinct cancer subsets, we performed focused validation with CRISPR interference across multiple cell lines. Knockdown of PELO preferentially impaired the viability of MSI or 9p21-deleted as compared to control (9p21-proficient and microsatellite stable) cells. Further validation with patient-derived organoid and in vivo xenograft models confirmed these findings. We next sought to refine the predictive biomarkers for PELO dependency and identified loss of FOCAD (a 9p21.3 gene and an interactor of the SKI mRNA surveillance pathway) as necessary and sufficient for PELO dependency in the 9p21.3-deleted context. Our findings implicate splicing alterations involving TTC37, a key protein in the SKI mRNA surveillance complex, as the underlying cause of PELO dependency in MSI cancers. Together, we found that loss of large deletions of 9p21.3 and MSI independently impair the SKI complex, uncovering a dependency upon PELO and highlighting a novel functional interaction between PELO and the SKI complex. Furthermore, the strength of this synthetic lethal interaction in a broad range of cancers with poor outcomes underscores the potential of PELO as a promising drug target for patients with 9p21.3-deleted or MSI cancers.
Citation Format: Edmond M. Chan, Patricia Borck, Nolan Bick, Kristina Jankovic, Isabella Boyle, Lucy Parker-Burns, Kyla Foster, Anthony Lau, Ashir Borah, Joshua Dempster, Francisca Vazquez. PELO is a synthetic lethal target in chromosome 9p21-deleted or MSI cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 3364.
Abstract 338: Unraveling layers of proteogenomic complexity in cancer through multiomic exploration of archived FFPE tissue
Authors: O'Hara Andrea J. , Han Yang , DeVito Ilaria , Turner Laure , Latif Haythem 
Published: March 2024

Abstract
Formalin Fixed Paraffin Embedded (FFPE) tissues are a staple in clinical diagnostics associated with solid tumor. The preserved tumor tissue can be interrogated using classical histopathology and complemented with molecular approaches to elucidate cancerous SNPs, indels, structural variants, repeat expansion, copy number expansions, and mutational burden. Increasingly, approaches are being deployed to interrogate tissue not only through individual datasets but through integrated approaches that provide spatial information that defines the tumor microenvironment. Here, we illustrate using FFPE blocks from various tissues a multiomic workflow that allows for deep exploration of the molecular underpinnings of cancerous tissue. FFPE blocks were serially sliced into various FFPE slides with a single slide H&E stained. Individual slides were then utilized to explore the genome, epigenome, single cell RNA-seq, and digital spatial profiling. Genome information was captured using hybrid capture based approaches (whole exome sequencing and targeted cancer panel) followed by deep NGS on an Illumina platform and analyzed for a variety of variants and tumor mutational burden. DNA methylation was detailed using target capture probes targeting DNA methylation sites. Single cell approaches were applied to explore the transcriptome using 10X Genomics scRNAseq Flex kit. Digital spatial profiling was done using the NanoString for both transcriptomics and proteomics, with the GeoMx Whole Transcriptome Atlas and Human Core and Pan-Tumor protein panels. Aggregating these data illustrates the expanding landscape of information that can be extracted from FFPE derived tissue and the potential for novel discovery and diagnostic power integrating these complex data types holds.
Citation Format: Andrea J. O'Hara, Yang Han, Ilaria DeVito, Laure Turner, Haythem Latif. Unraveling layers of proteogenomic complexity in cancer through multiomic exploration of archived FFPE tissue [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 338.