bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 336: Genome integrity assessment by optical genome mapping for cell manufacturing/bioprocessing applications
Authors: Hastie Alex , Pang Andy W. , Chaubey Alka 
Published: March 2024

Abstract
Cells and cell lines are used for multiple applications such as bioprocessing, therapy, and research. To ensure quality of cells and downstream applications, appropriate quality control (QC) methods are critical. Historically, karyotyping has been employed, but it is limited by its very low resolution and tedious laboratory workflow. Other methods such as PCR and targeted sequencing can characterize only small genomic variants at specific loci. Whole genome sequencing can detect small variants genome-wide but has limited sensitivity in detecting structural variants (SVs). Optical genome mapping (OGM) is a novel genome analysis technique that can fill many of the gaps in current capabilities for assessing genome integrity. To find clonal variants, 400 Gbp of data is collected from the parental/control and test samples. For both samples, a de novo assembly is constructed, and homozygous or heterozygous SVs are assessed. Subsequently, the dual variant annotation pipeline identifies unique SVs in the test sample compared to the parental sample. To discover subclonal SVs down to 5% variant allele fraction (VAF), the workflow leverages the generation of 1.5 Tbp of data, requiring a simple adjustment to longer data collection time. Comparison of test sample to parental sample enables easy determination of acquired variants. Finally, generation of ~5 Tbp of data, requiring 2-3 flowcells to be run, enables the detection of SVs at ultra-low VAF down to ~1%. In this study, several dilutions and simulations were performed to examine OGM’s limit of detection. Targeting a coverage of 5 Tbp and analysis using the somatic SV-analysis workflow revealed that OGM has the sensitivity to detect deletions &gt;50kbp, insertions &gt;20kbp, duplications &gt;100 kbp, and translocations at ~1% VAF. We have applied the clonal and somatic workflows to verify genomes’ integrity after cell immortalization, induced pluripotency, transgene-integration, and gene-editing. The data using the robust and sensitive workflows demonstrate that the OGM platform is a cost-effective solution for cell manufacturing/bioprocessing QC applications.
Citation Format: Alex Hastie, Andy W. Pang, Alka Chaubey. Genome integrity assessment by optical genome mapping for cell manufacturing/bioprocessing applications [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 336.
Abstract 3366: FoRx-06-428 is a novel PARG inhibitor with potent anti-tumor efficacy in preclinical cancer models
Authors: Querolle Olivier , Lücking Ulrich , Iacovino Luca , Freudenmann Alena , Rossetti Giacomo , Gysin Marina , Bologna Serena , Dionellis Vasilis , Malattia Marta , Potenza Alessandro , Bocquet Nicolas , Konstantinova Irena , Goutopoulos Andreas , Sotiriou Sotirios , Halazonetis Thanos , Bashir Tarig , Zenke Frank 
Published: March 2024

Abstract
The formation of poly(ADP-ribose) (PAR) chains from NAD+ precursors by PARP enzymes is a characteristic posttranslational modification during DNA damage repair. PAR chains function as docking platforms for DNA repair proteins that are required to resolve DNA lesions. Equally important is the subsequent removal of PAR chains from protein substrates to conclude the repair process and restore genomic integrity. Poly(ADP-ribose) glycohydrolase (PARG) is the key enzyme in this process and has recently garnered significant attention as a novel cancer target. FoRx-06-428 is a novel, orally bioavailable and highly potent, low molecular weight PARG inhibitor. It binds to the catalytic domain of human PARG with high affinity, as evidenced by surface plasmon resonance (SPR), and displays potent inhibition of enzymatic activity. FoRx-06-428 shows selective reduction of viability in a panel of cancer cell lines highlighting therapeutic potential in multiple cancer indications. Pharmacological inhibition of PARG leads to accumulation of PAR chains and is indicative of target engagement, accompanied by modulation of DNA damage response markers, such as phosphorylation of replication protein A (pRPA) and phosphorylation of H2AX (γH2AX). Compelling anti-tumor efficacy as single agent was observed in several xenograft models (breast and gastric cancer) with excellent tolerability. Dose-dependent accumulation of PAR chains was demonstrated in vivo and constitutes a tractable target engagement biomarker for clinical exploration. Sensitivity to PARG inhibition is partly driven by distinct genomic instabilities, such as defects in homologous recombination (HR) repair, however the activity of PARG inhibitors is also influenced by aberrations in other cancer-relevant pathways. This report represents the first disclosure of the pharmacological characterization of FoRx-06-428 and highlights the value of PARG inhibition as a novel targeted approach to treat DNA repair-deficient cancers.
Citation Format: Olivier Querolle, Ulrich Lücking, Luca Iacovino, Alena Freudenmann, Giacomo Rossetti, Marina Gysin, Serena Bologna, Vasilis Dionellis, Marta Malattia, Alessandro Potenza, Nicolas Bocquet, Irena Konstantinova, Andreas Goutopoulos, Sotirios Sotiriou, Thanos Halazonetis, Tarig Bashir, Frank Zenke. FoRx-06-428 is a novel PARG inhibitor with potent anti-tumor efficacy in preclinical cancer 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 3366.
Abstract 3378: Acinar cell susceptibility for tumor development in the pancreas: Targeting the critical regulators for therapy
Authors: Pan Zhaolong , Bossche Jan-Lars Van den , Rodriguez-Aznar Eva , Janssen Pauline , Lara Olaya , Ates Gamze , Massie Ann , De Paep Diedert Luc , Houbracken Isabelle , Mambretti Marco , Rooman Ilse 
Published: March 2024

Abstract
Acinar to ductal metaplasia (ADM) or acinar cell dedifferentiation is one of the most notable features of chronic pancreatitis. It is also considered the initial step of pancreatic cancer development when oncogenic mutations accumulate. However, its precise mechanism and regulatory pathways remain unclear. This study profiled the transcriptome of dedifferentiated acinar cells from both humans and mice. Differential expression analysis integrated with a systematic literature search revealed several potential regulators (e.g., GDF15, GFRA1, MXRA5, CXCL17), of which the expression pattern over time was validated by qRT-PCR. We also focused on multiple conserved pathways of cell survival, among which SLC7A11 (xCT) is transiently upregulated in both species. The xCT subunit, integral to the cystine/glutamate antiporter system xc-, plays a critical role in cell survival across various cell types. To elucidate its role in acinar dedifferentiation, we employed gene silencing, pharmacological inhibition, and a knock-out mouse model. Acinar cells with diminished xCT function exhibit increased ferroptosis linked to lipid peroxidation. Antioxidants such as N-acetylcysteine and ferroptosis inhibitors like Ferrostatin-1 can mitigate lower glutathione levels and lipid ROS accumulation. Similarly, in mouse acute pancreatitis, xCT prevents lipid peroxidation. Our findings indicate that xCT fuels the glutathione pool and maintains ROS balance during ADM, thereby preventing pancreatic acinar cells from ferroptosis, a form of cell death rarely reported in relation to ADM. Next to xCT, a future and similar comprehensive study of the aforementioned genes could provide valuable insights into the dynamic changes that occur during acinar cell dedifferentiation and pave the way to the discovery of new intervention targets to suppress tumorigenesis in chronic pancreatitis.
Citation Format: Zhaolong Pan, Jan-Lars Van den Bossche, Eva Rodriguez-Aznar, Pauline Janssen, Olaya Lara, Gamze Ates, Ann Massie, Diedert Luc De Paep, Isabelle Houbracken, Marco Mambretti, Ilse Rooman. Acinar cell susceptibility for tumor development in the pancreas: Targeting the critical regulators for 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 3378.
Abstract 339: Universal synthetic TCR/BCR spike-in controls to evaluate immune receptor profiling assay and next-generation sequencing performance
Authors: Chenchik Alex , Liu Tianbing , Makhanov Mikhail , Hu Dongfang , Ghias Khadija , Diehl Paul 
Published: March 2024

Abstract
Adaptive immune receptor (AIR) repertoire diversity assays are susceptible to biases arising from variations in conditions in the RT-PCR and next-generation sequencing (NGS) steps. We designed synthetic TCR and BCR spike-in controls to mitigate these biases and to serve as universal standards for any PCR-based immune receptor profiling assay. We synthesized 48 BCR constructs representing different IGH, IGK, and IGL genes and 39 TCR constructs for TRB, TRA, TRG, and TRD genes. The spike-in controls were tested as (16 × 3) BCR constructs and (13 × 3) TCR Triplex isoform pools added to multiple samples in the same batch to detect cross-contamination across samples. We successfully discriminated between controls and background sequences by combining a unique molecular identifier (UMI)-based correction strategy with spike-in controls at the data analysis step. We also tested 48 BCR and 39 TCR Premixed Controls by spiking into peripheral blood mononuclear cells (PBMC) RNA samples before reverse transcription using Cellecta’s DriverMap™ Adaptive Immune Receptor Profiling Assay that uses a multiplex RT-PCR approach with gene-specific primers and UMIs. We successfully used it to evaluate assay performance by adding premixed controls at different concentrations. Results showed a linear trend as the number of spike-in molecules increased. Our analysis revealed an average sequencing error rate of 0.4%-0.8% per base, aligning with the reported error rate range of Illumina sequencing. This suggests the reliability of our spike-in controls, which can be used to rectify biases in the AIR protocol and accurately estimate error and mutation rates for the DriverMap AIR assay or any other sequencing-based immune receptor profiling assay. This innovative approach enhances the robustness of immune receptor profiling technology, facilitating more accurate assessments of repertoire diversity.
Citation Format: Alex Chenchik, Tianbing Liu, Mikhail Makhanov, Dongfang Hu, Khadija Ghias, Paul Diehl. Universal synthetic TCR/BCR spike-in controls to evaluate immune receptor profiling assay and next-generation sequencing performance [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 339.
Abstract 3393: Deciphering colorectal cancer: A model to study sex-based differences and role of estrogen amidst obesity
Authors: Wele Prachi , Shi Haifei , Wu Xian 
Published: March 2024

Abstract
Worldwide statistics indicate that obesity is increasing globally, mostly due to the consumption of Western diet. The literature points out that obesity is a potent risk factor for the development of colorectal cancer (CRC). Interestingly, CRC incidence is higher in men compared to women, and the sex hormone estrogen protects reproductive-age females from CRC despite obesity. In this project, we aim to understand the sex-based differences and protective role of estrogen in obesity-influenced CRC. An improved mouse model was devised where the effects of obesity and estrogen in CRC could be meticulously studied. We deployed 4-5-week-old male and female FVB/NJ mice and performed either sham surgery (males and females) or bilateral ovariectomy (OVX) (females). Post one week of recovery, all mice were randomly sub-grouped into either low-fat diet (LFD, 10% fat) or high-fat diet (HFD, 60% fat) groups, weekly injected with a colon-specific carcinogen azoxymethane (AOM; 5 mg/kg for week 1, 10 mg/kg for weeks 2-6), and cyclically every 4-5 days injected 17-beta-estradiol (E2; 4 μg/mouse) to a group of OVX mice for the study period of 22 weeks. The body weight of all mice was tracked every week. A whole-body composition analysis after 22 weeks showed that males and OVX females are more obese compared to females with sham surgery and OVX females with E2 injection (OVX+E2), respectively. Additionally, mice on HFD had a higher body weight compared to those on LFD; however, the absence of estrogen in OVX females led them to have higher body weight compared to sham and OVX+E2 females. Moreover, a significant difference was observed in the tumor size between males and females, females and OVX females, and OVX and OVX+E2 females. Study models have rarely incorporated both sex-dependent differences and diet-induced obesity in understanding CRC. With the current study model, it is anticipated to learn more about these differences at molecular, cellular, and metabolic levels. Acknowledgments: 1) NIH/NCI R15 [To HS, XW]; 2) Miami University CFR Faculty Research Grants [To HS, XW, JZ]; 3) Miami University's College of Education, Health, and Society Interdisciplinary Research Seed Grant [To HS, XW, JZ]; 4) Sigma Xi Grants in Aid Research [To PW]; and 5) We thank Jazzminn Hembree (Director of Laboratory Animal Resources, Miami University) and Laboratory Animal Resources, Dr. Jiangjiang Zhu (Department of Human Sciences, Ohio State University), Dr. Jing Zhang (Department of Statistics), and Dr. Ramiro Malgor (Director of Histology Core Facility, Ohio University)
Citation Format: Prachi Wele, Haifei Shi, Xian Wu. Deciphering colorectal cancer: A model to study sex-based differences and role of estrogen amidst obesity [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 3393.
Abstract 3395: Polyisoprenylated cysteinyl amide inhibitors: Effects on RAS signaling pathway intermediates and viability of mutant KRAS African American lung cancer cell line
Authors: Mensah-Mamfo Justin K. , Ofosu-Asante Kweku , Lazarte Jassy Mary , Burra Amarender Goud , Lugo Sofia A. , Huang Yong , Offringa Ite A. , Lamango Nazarius S. 
Published: March 2024

Abstract
Mutated KRAS is the most common cancer driver gene in lung adenocarcinomas in all racial and ethnic groups, including Blacks/African Americans (B/AAs). Drugs developed to combat KRAS-driven cancers become less effective due to intrinsic changes in the cells resulting in resistance and relapse. Due to the enormous challenges encountered in developing direct KRAS inhibitors, agents targeting alternative downstream RAS mediator kinase enzymes of the MAPK and PI3K/AKT signaling pathways have been developed. However, other avenues that directly target KRAS and similar cancer drivers must be explored to obtain alternative effective therapies. PCAIs constitute a group of potential anticancer agents that we developed to specifically disrupt and suppress signaling by hyperactive G-proteins such as mutated KRAS. In previous studies, PCAIs stimulated MEK1/2, ERK1/2, p90RSK and AKT phosphorylation resulting in cell death. The present study aims to determine whether specific inhibitors of the kinases can reverse PCAIs-stimulated phosphorylation and cell death. PCAIs were thus tested against the KRAS mutant NCI- cell line H23 (from a B/AA patient) and compared to KRASG12C inhibitor Sotorasib and other kinase inhibitors drugs. The EC50 values for the PCAIs NSL-YHJ-2-27 and NSL-AB-45 were 4.1 ± 0.3 and 5.5 ± 0.1 μM, respectively, compared to Gefitinib (EGFR), Sotorasib (KRASG12C), Dabrafenib (BRAF), Selumetinib (MEK1/2), Ulixertinib (ERK1/2) and Ipatasertib (AKT) whose EC50 values were 83 ± 12.9 μM, 38 ± 5.5 μM, 33 ± 1.2 μM, 71 ± 5.3 μM, 11 ± 0.2 μM, 12 ± 1.0 μM, respectively. The results indicate that the PCAIs are more effective against NCI-H23 than the other kinase inhibitor drugs. Future work will determine the effects of co-treating cells with the PCAIs and the respective kinase inhibitors on cell viability and PCAIs-induced phosphorylation of the kinases. Supported by grants U54CA233396, U54CA233444, and U54CA233465 from the National Institutes of Health (NIH)/National Cancer Institute (NCI) and the Norris Comprehensive Cancer Center core grant, award number P30CA014089 from the NIH/NCI
Citation Format: Justin K. Mensah-Mamfo, Kweku Ofosu-Asante, Jassy Mary Lazarte, Amarender Goud Burra, Sofia A. Lugo, Yong Huang, Ite A. Offringa, Nazarius S. Lamango. Polyisoprenylated cysteinyl amide inhibitors: Effects on RAS signaling pathway intermediates and viability of mutant KRAS African American lung cancer cell line [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 3395.
Abstract 3457: Distinct signatures of tumor-associated macrophage subpopulations predict survival in renal cell carcinoma
Authors: Han Youngsoo , Shen Aidan , Wang Zhaohui , Garrett Aliesha , Jiang Chongming 
Published: March 2024

Abstract
Background: Comprising 90% of renal cancer cases in adults, renal cell carcinoma (RCC) is marked by significant heterogeneity in its tumor microenvironment. This study aims to test the hypothesis that tumor-associated macrophages (TAMs) play a role in modulating RCC progression and patient response to treatment. We explored the prognostic implications of TAM signatures on RCC survival, leveraging immunomics to decipher TAM-related alterations in the tumor microenvironment.
Methods: Utilizing independent single-cell RNA-seq data from human RCC samples, we crafted 8 distinct RCC TAM signatures reflective of TAM presence. A LASSO Cox regression model was developed to prognosticate survival, tested against the TCGA dataset and independently validated across multiple RCC cohorts. Model performance was corroborated through Kaplan-Meier survival plots, receiver operating characteristic (ROC) curves, principal component analysis, and t-SNE analyses.
Results: We identified two TAM signatures that correlate positively with patient survival, indicative of the abundance of specific subsets of TAMs in RCC. These signatures showed a strong association of specific TAM markers and macrophage infiltration. Survival analysis demonstrated that specific TAM signature gene expressions are significant prognostic markers. Forest plots underscored their prognostic relevance. A 32-gene risk score model was established, successfully stratifying patients into distinct risk categories, with low-risk patients exhibiting markedly improved overall survival.
Conclusions: The study underscores the positive association between abundance of specific TAM subsets of and RCC patient survival. The precision of our LASSO Cox regression model, informed by novel abundance markers of specific TAM subsets, advances our understanding of TAM roles in TIME and RCC progression. These TAM signatures could potentially provide additional insights and targets to enhance the efficacy of RCC treatments.
Keywords: Tumor associated macrophage, renal cell carcinoma, prognosis, tumor microenvironment, immunomics.
Citation Format: Youngsoo Han, Aidan Shen, Zhaohui Wang, Aliesha Garrett, Chongming Jiang. Distinct signatures of tumor-associated macrophage subpopulations predict survival in renal cell 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 3457.
Abstract 3501: Concurrent amplification of TBXT and highly activated enhancers in extrachromosomal DNA (ecDNA) drives chordoma tumorigenesis
Authors: Zhao Bo , Ines Martin Barrio , Ye Lingqun , Wu Xizi , Soragni Alice , Futreal Andrew , Akdemir Kadir 
Published: March 2024

Abstract
Chordoma, a rare bone cancer characterized by limited actionable clinical targets, exhibits a pivotal hallmark in the activation of the developmental transcription factor gene TBXT (Brachyury) through its association with highly active enhancers. TBXT amplification emerges as a major causative factor in familial chordomas, yet the amplification mechanism and its consequential impact on genomic instability remain inadequately elucidated. In this study, we conducted a comprehensive analysis of multiple genomic and epigenomic sequencing datasets, including WGS-seq, H3K27ac ChIP-seq, and ATAC-seq in six chordoma cell lines, and HiC data in two of them, to unravel the mechanisms of structural variations and their biological implications. Notably, our focus extends to JHC7 cells, which exhibit extrachromosomal amplification of a 2.4M region encompassing TBXT and the associated enhancers. The existence of such extrachromosomal DNA (ecDNA) in JHC7 was further validated through DNA FISH and Sanger sequencing. Comparing JHC7 with CH22, a chordoma cell line lacking TBXT amplification, revealed heightened chromatin relaxation and increased DNA rearrangements in JHC7. Interestingly, FISH results showed significant genomic ploidy heterogeneity within JHC7 cells, a finding demonstrated by nucleus FACS sorting. Single-cell multiomic analysis, combining snRNA-seq and snATAC-seq, demonstrated heterogeneous gene expression and distinct copy number variations among JHC7 cells. However, the amplification of the TBXT locus was observed in nearly all cells examined, indicating the rapid genomic evolution in the cultured JHC7 cells. These results collectively show that TBXT is extensively amplified through the formation of ecDNA, providing a fitness advantage to chordoma cells and concurrently exacerbating genomic instability. The findings in this study provide an insight for understanding the pathogenesis of chordoma and may inform the development of targeted therapeutic strategies.
Citation Format: Bo Zhao, Martin Barrio Ines, Lingqun Ye, Xizi Wu, Alice Soragni, Andrew Futreal, Kadir Akdemir. Concurrent amplification of TBXT and highly activated enhancers in extrachromosomal DNA (ecDNA) drives chordoma tumorigenesis [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 3501.