bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 2782: Characterization of quiescence-associated secretory profile (QuASP) in cancer: A novel defining feature and therapeutic target
Authors: Jiang Qi , Panesso-Gómez Santiago , Natesan Divya , MacDonald Matthew L. , Buckanovich Ronald J. 
Published: March 2024

Abstract
Senescent cells have a unique senescence-associated secretory profile (SASP) and understanding SASP has contributed to numerous advances in knowledge on aging and cancer biology. Quiescence, which is an important yet poorly understood mechanism for chemoresistance, is related but distinct from senescence. Quiescence shares a non-proliferative feature with senescence but is a reversible state in which quiescent cells can reenter the cell cycle. We hypothesized that, analogous to senescent cells, quiescent cells have a distinct quiescence-associated secretory profile (QuASP) and that defining the QuASP will uncover new genes and pathways associated with cancer cell viability and therapeutic resistance. Indeed, suggesting quiescent cells have a unique and biologically important secretome, we found that tumor conditioned medium (TCM) from quiescent ovarian cancer cells (qOvCa) vs. TCM from proliferating cancer cells increased chemoresistance. Similarly, TCM from quiescent cancer cells vs. TCM from proliferating cancer cells suppressed T cell proliferation and INF-gamma/Granzyme B secretion, suggesting a QuASP immunosuppressive effect. RNASeq analysis of qOvCa cells revealed the secreted factor Follistatin (FST) is upregulated in qOvCa and acted as a paracrine pattern to induce chemoresistance. Furthermore, FST was found to be upregulated in peritumoral fluid following chemotherapy and FST levels in patients with OvCa predicted poor prognosis. To identify additional QuASP factors, we used an ER-BIOID labeled system and LC-MS/MS to characterize the secreted proteins from qOvCa induced by serum starvation compared with normal cells in three OvCa cell lines (PT412, PT340, HEY1). Quiescent OvCa cells indeed have a secretome that is highly unique from proliferating cells, with 137/577 upregulated proteins (LFC&gt;1) and 65/577 downregulated proteins (LFC←1 or no detection in quiescence). Several proteins identified as upregulated have been linked to immunosuppression and/or chemoresistance, oncogenesis and cell cycle were selected for validation and further analysis (CLU, VGF, SERPINE1). In conclusion, we find quiescent cells have a unique quiescence associated secretory profile and that the QuASP induces chemoresistance and immunosuppression. As such, this study has important implications for cancer therapy.
Citation Format: Qi Jiang, Santiago Panesso-Gómez, Divya Natesan, Matthew L. MacDonald, Ronald J. Buckanovich. Characterization of quiescence-associated secretory profile (QuASP) in cancer: A novel defining feature and therapeutic target [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 2782.
Abstract 2801: Identifying gut microbial determinants of clonal hematopoiesis of indeterminate potential (CHIP) in immunotherapy treated melanoma patients
Authors: Fallon Eleanor A. , Urrutia Samuel , Ayabe Reed , Chelvanambi Manoj , Damania Ashish , Johnson Sarah , Tanaka Tomoyuki , Li Zongrui , Seo Yongwoo David , Cass Samuel , Wong Matthew C. , Ajami Nadim , Wargo Jennifer , Takahashi Koichi 
Published: March 2024

Abstract
INTRO: Clonal hematopoiesis (CH) of indeterminate potential (CHIP) is associated with poor outcomes in those with non-hematologic cancers. CH mutated macrophages and neutrophils have increased capacity to home to peripheral tissues, driving local inflammation; they are also implicated in immunotherapy related toxicity. The relationship between CH and the microbiome in those treated with immunotherapy is not well understood.
RESULTS: 35 patients with stage IV melanoma treated with upfront immunotherapy; treatment and cohort characteristics are below (Table 1). We performed error corrected duplex sequencing on peripheral blood mononuclear cells using a panel previously validated for CH mutations. With a cutoff of 0.5% variant allele frequency (VAF), among 10 CHIP positive patients, we found mutations in TET2 (8/10), DNMT3A (7/10), PPM1D (2/10), and JAK2 (1/10). There was no difference in either survival or response based on CHIP status (Log-Rank Chi-Square p=0.44); however, CHIP positivity was associated with greater microbiome richness as measured by alpha diversity (p=0.0012 Shannon diversity) and distinct structural/compositional diversity vs CHIP negative patients as measured by beta diversity (p=0.032, R Squared= 0.045). We inferred KEGG pathway activity from whole genome sequencing and identified that CHIP positive patients were enriched for exopolysaccharide biosynthesis while CHIP negative patients had higher expression of nucleotide sugars biosynthesis and amino acid metabolism pathways.
DISCUSSION: In patients treated with immunotherapy for melanoma, microbiome diversity signatures correlate with presence of CHIP. The analysis suggests that there are distinct taxonomic and functional features defining CHIP positivity. The effect of these cells in the tumor microenvironment and their role in immunotherapy response requires further exploration.
Citation Format: Eleanor A. Fallon, Samuel Urrutia, Reed Ayabe, Manoj Chelvanambi, Ashish Damania, Sarah Johnson, Tomoyuki Tanaka, Zongrui Li, Yongwoo David Seo, Samuel Cass, Matthew C. Wong, Nadim Ajami, Jennifer Wargo, Koichi Takahashi. Identifying gut microbial determinants of clonal hematopoiesis of indeterminate potential (CHIP) in immunotherapy treated melanoma patients [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 2801.
Abstract 2817: Establishment of KRAS G12C mutant brain metastasis models for pre-clinical evaluation of KRAS G12C targeted anticancer therapy
Authors: Chen Qikuan , Wang Guilan , Yin Yingfei 
Published: March 2024

Abstract
KRAS is one of the most frequently mutated oncogenes in cancers, especially in lung cancer. Clinical research has shown that about 14% of non-small-cell lung cancers (NSCLCs) carry the KRASG12C mutation, and brain metastases are a relatively common occurrence in KRASG12C-mutated NSCLC. Approximately 30% of patients with KRASG12C mutations develop brain metastases, and those with KRAS-mutated NSCLC and untreated brain metastases have limited treatment options and poor clinical outcomes. AMG510 (Sotorasib) is a small molecule inhibitor of KRASG12C that specifically binds to inactive GDP-bound KRASG12C, preventing its oncogenic signaling. It has been approved for NSCLC by the FDA. Recent clinical studies have shown that Sotorasib exhibits some activity against KRASG12C NSCLC brain metastasis. To evaluate the in vivo activity of AMG510 for NSCLC brain metastasis treatment and provide insights for the preclinical development of new KRAS targeted inhibitors, we established advanced orthotopic models, including intracranial, intracarotid, and intracardiac metastatic models, using the NCI-H358-luc cell line, which harbors the KRASG12C mutation. We validated these models with AMG510 as a single agent or in combination with radiation, which is commonly used in brain tumor therapeutic strategies, to reveal the efficacy and brain concentration of AMG510 in KRASG12C brain metastasis models. Tumor growth and metastasis incidences were assessed using bioluminescence imaging (BLI). All animal studies were performed in an AAALAC accredited facility and aligned with animal welfare regulations. Our preliminary results reveal that AMG510 could penetrate the blood-brain barrier (BBB) and show therapeutic activity for KRASG12C brain metastatic tumors. These models represent powerful tools for clinically relevant assessment of the efficacy of novel KRAS G12C inhibitors and can be expanded for other KRAS mutations-associated brain metastasis or inhibitors.
Citation Format: Qikuan Chen, Guilan Wang, Yingfei Yin. Establishment of KRAS G12C mutant brain metastasis models for pre-clinical evaluation of KRAS G12C targeted anticancer therapy [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 2817.
Abstract 2828: Combining neratinib with trastuzumab deruxtecan to treat HER2;TP53 co-mutated breast cancers
Authors: Cheng Xiaoqing (Cathy) , Highkin Maureen , Hsia Jacob , Prior Julie L. , Hagemann Ian S. , Bose Ron 
Published: March 2024

Abstract
In metastatic breast cancer, HER2 activating mutations frequently co-occur with mutations in the TP53 gene and patients with these two co-occuring mutations have a lower response rate to neratinib. In order to address this clinical problem, we bred HER2 activating mutant transgenic mice with two different alleles of TP53. We used mice with the TP53 R172H mutation, which is the murine homolog of the human hotspot TP53 R175H mutation, and mice with TP53flox/flox allele, which mimics TP53 truncating mutations seen in human breast cancers.
All three H53 genotypes (H53null, H53172/WT, and H53172/null) developed breast cancers faster than H mice, with H53172/null mice developing breast tumors the fastest, at just 6 weeks after adenoviral-Cre injection into the mammary fat pad. We developed organoids from these murine breast cancers and found that all H53 genotype organoids were less sensitive to neratinib compared to H, however, neratinib was able to synergize with trastuzumab deruxtecan (T-DXd), likely through neratinib mediated increased internalization of T-DXd. Prior literature studies suggest TP53 mutant cancer cells may have therapeutic vulnerabilities to the topoisomerase 1 (Top1) inhibitors. Organoids from all three H53 genotypes were sensitive to the Top1 inhibitor, exatecan. H53172/WT behaved like H organoids with G1 phase cell cycle arrest and induction of p21 expression after exatecan treatment. In contrast, H53null and H53172/null failed to induce p21 and arrested at late-S/G2 phase. Additional animal experiments with these H53 genotypes are in progress and results will be presented at the AACR Annual Meeting.
Abbreviation Genotype Median tumor formation (weeks) Neratinib IC50 (nM) Neratinib +T-DXd H HER2V777L 28 10 Not determined H53null HER2V777L;TP53flox/flox 10 240 Synergy H53172/WT HER2V777L;TP53R172H/WT 11 100 Synergy H53172/null HER2V777L;TP53R172H/flox 6 150 Synergy
Citation Format: Xiaoqing (Cathy) Cheng, Maureen Highkin, Jacob Hsia, Julie L. Prior, Ian S. Hagemann, Ron Bose. Combining neratinib with trastuzumab deruxtecan to treat HER2;TP53 co-mutated breast 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 2828.
Abstract 2898: Development of the lipid kinase PIKfyve PROTAC degrader against neuroendocrine prostate cancer
Authors: Qiao Yuanyuan , Li Chungen , Zheng Yang , Jiang Xia , Yee Sarah Nicole , Cheng Caleb , Bao Yi , Zhang Yuping , Wang Yuzhuo , Wang Zhen , Ding Ke , Chinnaiyan Arul 
Published: March 2024

Abstract
Therapies targeting the androgen receptor (AR) as the main driver of prostate cancer (PCa) can lead to various mechanisms of resistance and promote progression to castration-resistant PCa (CRPC), which has a median survival of only 13-23 months. Amongst recurrent CRPC, 17%-30% of patients develop neuroendocrine prostate cancer (NEPC), which is a PCa subtype characterized by a unique histology. NEPC exhibits a loss of AR signaling during neuroendocrine transdifferentiation which results in resistance to AR-targeted therapies and gain of cell characteristics resembling poorly differentiated neuroendocrine tumors. Despite advances in the understanding of NEPC development, treatment options remain limited, with platinum-based chemotherapy as the first-line treatment for both de novo and treatment-induced NEPC. However, response to first-line chemotherapy in NEPC is short, with a median survival of only seven months. The poor prognosis of NEPC is attributed in part to late diagnosis and a lack of effective therapeutic agents. Our previous work demonstrated that NEPC and AR-negative PCa exhibit higher dependency on the lipid kinase PIKfyve than AR-positive CRPC. Thus, development of PIKfyve inhibitory therapies targeting the emergent vulnerabilities of NEPC or AR-negative forms of PCa is a promising approach.
Using a proteolysis targeting chimera (PROTAC) technology, we designed a class of PIKfyve specific degrader. The in vitro degradation efficiency were determined by immunoblotting, and DC50s (degradation concentration at 50%) were calculated for top candidates. Pharmacokinetic and pharmacodynamic were evaluated for in vivo study. In summary, we have developed a class of PIKfyve specific degrader using the E3 ligase von Hippel-Lindau (VHL) as a ligand via a diverse set of linkers. Mechanistic studies revealed that it induced PIKfyve degradation in a VHL- and proteasome-dependent manner.
Citation Format: Yuanyuan Qiao, Chungen Li, Yang Zheng, Xia Jiang, Sarah Nicole Yee, Caleb Cheng, Yi Bao, Yuping Zhang, Yuzhuo Wang, Zhen Wang, Ke Ding, Arul Chinnaiyan. Development of the lipid kinase PIKfyve PROTAC degrader against neuroendocrine prostate cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 2898.
Abstract 2910: Targeting thioredoxin reductase 1 (TrxR1) suppresses TAZ-driven glioblastoma progression
Authors: Tang Miaolu , Dirks Kaitlyn , Kim Soo Yeon , Thorpe Jessica , Li Wei 
Published: March 2024

Abstract
Glioblastoma (GBM) is the most common and aggressive primary brain malignancy in adults. Poor outcomes for traditional treatments demand targeted therapies based on identified mechanisms that drive tumor development and sustain its malignancy. Molecular pathology studies have classified GBM into subtypes differing in treatment responses and survival rates. Among these subtypes, the mesenchymal (MES) group is associated with the worst prognosis. The Hippo pathway transcriptional co-activator with PDZ-binding motif (TAZ) is one of the three transcriptional regulators that drive the GBM MES gene expression program. Studies from our lab and others have previously shown that TAZ activation is able to promote GBM MES differentiation and progression. Therefore, finding vulnerabilities of TAZ-driven tumors may help to develop targeted therapeutic methods for MES GBM. In an orthotopic GBM mouse model, we found that TAZ-driven tumors show increased expression of thioredoxin reductase 1 (TrxR1), which is responsible for catalyzing the reduction of thioredoxin and maintaining the cellular redox balance. In searching for the cause of increased expression of TrxR1, we found that glucose deprivation can induce TrxR1 expression, suggesting TrxR1 may be an adaptive mechanism for tumor cells to survive in glucose deprivation conditions. Indeed, either depleting TrxR1 genetically or inhibiting TrxR1 pharmacologically can promote tumor cell death under glucose deprivation. Furthermore, knockout TrxR1 in a TAZ-driven mouse GBM model significantly decelerated tumor progression. Collectively, our studies revealed that inhibition of the Trx redox system under glucose deprivation conditions leads to a synergistic cell death induction in GBM cells, therefore making targeting TrxR1 a potential therapeutic strategy for TAZ-driven MES GBM.
Citation Format: Miaolu Tang, Kaitlyn Dirks, Soo Yeon Kim, Jessica Thorpe, Wei Li. Targeting thioredoxin reductase 1 (TrxR1) suppresses TAZ-driven glioblastoma 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 2910.
Abstract 2918: Potential for a novel therapeutic target: Effects of lactate & lactylation in expression of key regulatory cancer proteins
Authors: Costeas Christos P. , Purcell Connor , El-Deiry Wafik S. 
Published: March 2024

Abstract
The purpose of our study is to investigate the immunologic, metastatic, and gene regulation effects of lactate in the context of cancer in normoxic and hypoxic conditions to identify novel biomarkers and potential therapeutic targets. We aim to modify the in-vitro cancer microenvironment to show how lactate and lactylation can be exploited using existing cancer treatments. While hyperlactatemia is defined as lactate levels between 2 mmol/L and 4 mmol/L (Foucher et al 2023), tumor biopsies have demonstrated extracellular concentrations as high as 40 mM (Pérez-Tomás et al 2020). Through CTG viability assays we identified lactate concentrations that PANC1 cells can survive, which are in agreement with the in-vivo findings of Brizel et al (2001). We observed pancreatic cancer cells achieving over 50% viability for 5 days at 50 mM lactate concentrations while at 30 mM on day 5 they proliferated past their initial plating numbers. Furthermore, Brizel et al (2001) found that patients with high tumor lactate concentrations had a significantly higher incidence of metastatic relapse. Through our scratch assay, we show qualitative evidence of increased mobility and inferred migration potential of PANC1 at 7.5mM [lactate] compared to the absence of lactate. We have also observed increased migration at higher lactate concentrations for which we are pursuing quantitative measurements to evaluate significance. Migration experiments will be followed by the investigation of gene regulation (eg. mRNA seq, lactylation profile) involved in the observed increased mobility. Lactate has been shown to affect immune regulation, namely suppression of iNKT (Fu et al, 2020), macrophages (Yang et al, 2020), dendritic cell differentiation and antigen recognition/presentation (Wang et al, 2022), however not much is known about its effect on NK cells and their cytokine expression. Through NK92MI/PANC1 cocultures we show the effects of lactate concentration on the killing ability of NK cells (in the works). And plan on investigating the cytokine profile leading to the phenotypic killing differences. Lastly, via lactate-titrated incubation of PANC1 cells in normoxia we have demonstrated a positive correlation of HIF1a expression, pan-lactyllysine lactylation, and microenvironment lactate concentration. We speculate HIF1a inhibition post-lactate-sensitization may induce cancer killing and we will investigate this theory in normoxia and hypoxia using existing treatment options.
Citation Format: Christos P. Costeas, Connor Purcell, Wafik S. El-Deiry. Potential for a novel therapeutic target: Effects of lactate & lactylation in expression of key regulatory cancer proteins [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 2918.
Abstract 2940: A comparative analysis of library preparation technologies for RNA sequencing from FFPE samples
Authors: Pavlica Jennifer , Sanders Travis , Gelagay David , Reed Kailee , Harrison Thomas , Corbet Giulia , Haimes Josh , Hanek Ariele , Giorda Kristina , Kudlow Brian 
Published: March 2024

Abstract
Formalin-fixed, paraffin-embedded (FFPE) samples are an invaluable resource in the oncology space, providing access to a vast library of archived diseased tissue samples paired with relevant donor information. Despite the broad utility of these samples, RNA extracted from FFPE tissue is typically difficult to process due to the presence of residual crosslinks and its degraded nature. Further, these samples often vary widely in performance, as the fixation process, block age, block storage, and extraction method can impart large impacts on resulting template quality. As a result, robust and reproducible RNA sequencing from FFPE-derived RNA remains a challenge with unpredictable and high failure rates. We evaluated four commercially available WTA solutions to determine which performed best with this challenging sample type with respect to library complexity, inter-input and intra-sample concordance, and overall reproducibility.
Matched fresh frozen and FFPE liver samples were used such that the fresh frozen data set serves as a comparative truth set for the FFPE data. RNA-Seq libraries were prepared from each sample at both 10 ng and 100 ng inputs. The higher input serves as a control while the lower input reflects achievable inputs from very challenging FFPE samples. For 10 ng FFPE-derived RNA, the Watchmaker RNA Library Prep Kit with Polaris Depletion detects more unique genes than other chemistries and has a much higher percentage of genes that overlap with the fresh frozen control libraries. Additionally, differential expression analysis between 10 ng and 100 ng FFPE libraries demonstrates that the Watchmaker solution better preserves the gene expression profile at low inputs, as fewer differentially expressed genes are identified.
The Watchmaker chemistry includes a number of features aimed at improving library complexity, including a novel FFPE decrosslinking step, a reverse transcriptase specifically engineered to improve conversion of RNA to cDNA, and fewer bead purification steps to prevent sample loss. The concordance between FF and FFPE samples at variable input masses observed when using the Watchmaker solution promotes a higher degree of confidence when making decisions based on lower quantity and quality samples and enables researchers to access more meaningful biological information.
Citation Format: Jennifer Pavlica, Travis Sanders, David Gelagay, Kailee Reed, Thomas Harrison, Giulia Corbet, Josh Haimes, Ariele Hanek, Kristina Giorda, Brian Kudlow. A comparative analysis of library preparation technologies for RNA sequencing from FFPE samples [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 2940.