bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 2093: Co-treatment with KRAS G12D inhibitor MRTX1133 plus TTFields against human pancreatic and Colorectal cancer cell lines results in synergistic up-regulation of cleaved PARP in KRAS G12D & unexpectedly in KRAS G12V as well
Authors: Tajiknia Vida , Srinivasan Praveen , PInho-Schwermann Maximilian , MacDonald William , Purcell Connor , El-Deiry Wafik 
Published: March 2024

Abstract
Background: Both colorectal and pancreatic cancers are major global health issues and among deadliest cancers with great disease burden. The most commonly mutated oncogenic alteration in human cancers is KRAS, which is prevalent in pancreatic malignancies. The KRAS G12D mutation subtype is present in more than 40% of pancreatic ductal adenocarcinoma (PDAC). To this date there is no available targeted therapy options for patients with KRAS subtype mutations. MRTX1133 has been identified as a non-covalent, potent, and selective inhibitor of KRASG12D. This small molecule inhibitor has been shown to suppress KRASG12D signaling in cells and in vivo. Tumor Treating Fields (TTFields) therapy is a novel approach to treating cancer, the electric fields alter the behavior of cancer cells and prevent them from growing and dividing. We hypothesize that the co-application of MRTX1133 with TTFields will enhance the effects of MRTX1133 in PDAC and colorectal cancer (CRC).
Martials and Methods: PDAC cell line CFPAC1 with KRAS G12 V mutation and LS513 CRC cell line with KRAS G12D Mutation were treated with same dose of MRTX1133 (500 nM) and were co-treated with 150kHz TTFields. After 48 hours western blot was used to probe for cleaved PARP, cleaved C3, phosphor-ERK and DUSP6.
Results: In both KRAS G12D & KRAS G12V cell lines, synergistic upregulation of cPARP was observed following 48-hour co-treatment. Synergistic inhibition of pERK happened in KRAS G12D cell line but no change in pERK level following TTFields or MRTX1133 treatment was seen. Upregulation of cC3 in KRAS G12D happened in only co-treatment conditions. DUSP6 levels increased following MRTX1133 treatment in KRAS G12V cell line.
Conclusions: The surprising synergistic upregulation of cPARP in both KRAS G12V and G12D cells following co-treatment of KRAS G12D inhibitor MRTX1133 and TTFields can bring hope for other KRAS mutation subtypes as well as G12D. the increase in cPARP in KRAS G12V with no effect on pERK is particularly interesting and demonstrates the need of more studies to investigate the mechanisms of this synergy.
Citation Format: Vida Tajiknia, Praveen Srinivasan, Maximilian PInho-Schwermann, William MacDonald, Connor Purcell, Wafik El-Deiry. Co-treatment with KRAS G12D inhibitor MRTX1133 plus TTFields against human pancreatic and Colorectal cancer cell lines results in synergistic up-regulation of cleaved PARP in KRAS G12D & unexpectedly in KRAS G12V as well [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 2093.
Abstract 211: Applying cellular thermal shift assays to uncover novel regulators of epithelial to mesenchymal transition in triple negative breast cancer
Authors: Lidster Jessica A. , Loo Ser Yue , Wu Zhengwei , Dai Lingyun , Ng Seow Qi , Prabhu Nayana , Kappei Dennis , Tam Wai Leong 
Published: March 2024

Abstract
Metastatic Breast Cancer is accountable for over half a million deaths worldwide each year, the majority of which are from the triple negative breast cancer (TNBC) subtype, known to be highly aggressive, metastatic and resistant to targeted therapy. Metastasis is driven by the ability of cancer cells to undergo epithelial to mesenchymal transition (EMT), a cell state transition involving a gain of stemness, cell motility and chemoresistance. EMT has been well characterized using a range of techniques based upon quantitative proteomics and transcription profiling, yet targeting EMT to prevent tumor metastasis and chemoresistance is an obstacle that remains to be fully overcome. Using a cellular thermal shift assay coupled with mass spectrometry (CETSA-MS), we have measured changes in protein stability upon induction of EMT and have uncovered key enzymes in the citric acid (TCA) cycle that are stabilized during EMT of human mammary epithelial cells. Such enzymes are responsible for the conversion of TCA cycle intermediates required for a recently discovered post-translational modification. In TNBC cells, we find that loss of these enzymes causes not only global changes to crucial post-translational modification of mitochondrial proteins, but very specific alterations in several cytoskeletal proteins, leading to altered EMT status as well as reduced tumor growth and initiation both in vitro and in vivo. This demonstrates the importance of TCA cycle-controlled post-translational modification of cytoskeletal proteins in tumorigenesis and establishes basis for further investigation into their role in EMT and metastasis of breast cancer. Through pharmacological inhibition and immunofluorescence imaging, we discovered regulators of post-translational modifications that may be viable drug targets to overcome chemoresistance and relapse in TNBC patients with limited and inefficacious options.
Citation Format: Jessica A. Lidster, Ser Yue Loo, Zhengwei Wu, Lingyun Dai, Seow Qi Ng, Nayana Prabhu, Dennis Kappei, Wai Leong Tam. Applying cellular thermal shift assays to uncover novel regulators of epithelial to mesenchymal transition in triple negative 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 211.
Abstract 2129: Efficacy and underlying mechanisms of surufatinib combined with PD-1 monoclonal antibody and chemotherapy in pancreatic cancer
Authors: Zhang Nan , Jia Ru , Dai Guanghai 
Published: March 2024

Abstract
Background: A phase 1b/2 study (NCT05218889) of surufatinib combined with camrelizumab, nab-paclitaxel, and S-1 (NASCA) as first-line therapy for metastatic pancreatic adenocarcinoma has shown promising results, potentially overcoming the limitations of current pancreatic immunotherapies. Animal studies are underway to further explore the synergistic effects and mechanisms of this combined therapeutic approach.
Methods: Genetically engineered KPC mouse cells were used to establish a subcutaneous transplantation tumor model in female mice, which were then divided into control group, AG group (nab-paclitaxel + gemcitabine), and NASCA group. Tumor metrics were recorded until euthanasia after 21 days. Blood and tumor samples were analyzed using Flow Cytometry.
Results: Compared with the control group, the NASCA and AG groups demonstrated tumor volume reductions of 14.7% (p=0.172) and -0.4% (p=0.972) on day 7, respectively. At day 14, the reductions were 48.8% and 29.9% (p&lt;0.001*, p=0.002*). At day 21, the reductions were 37.4% and 21.5% (p=0.001*, p=0.144). The tumor growth inhibitions (TGIs) for NASCA and AG group were 56.7% (p&lt;0.001*) and 21.2% (p=0.36), respectively. Compare to AG group, the tumor volume reduction in NASCA group were 15.1% (p=0.050*), 26.9% (p=0.001*) and 20.3% (p=0.116), respectively. And the TGIs for NASCA group compare AG group was 45.0% (p=0.020*). Distinguishingly, the NASCA group, when compared to the AG group, had a heightened proportion of M1 macrophages (28.5% vs. 15.5%, p=0.019*), mCD68+ Macrophages (99.7% vs. 99.1%, p=0,014*) and mPD-1+/mCD8+ T cells (24.8% vs. 9.8%, p=0.03*). Furthermore, T-regulatory cells (T-regs) in peripheral blood demonstrated uniformity across the groups, were no statistically. RNA-seq analysis revealed that the NASCA significantly suppressed multiple anti-angiogenic pathways while enhancing the cytokine pathway (p=0.005*), indicating potential immune system activation.
Conclusion: The NASCA group outperformed the AG group in controlling tumor growth and early tumor shrinkage, potentially due to macrophage polarization regulation. Further research is vital to understand the benefits of integrating targeted therapy, immunotherapy, and chemotherapy for pancreatic cancer.
Citation Format: Nan Zhang, Ru Jia, Guanghai Dai. Efficacy and underlying mechanisms of surufatinib combined with PD-1 monoclonal antibody and chemotherapy in pancreatic 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 2129.
Abstract 2130: Glioblastoma-derived extracellular vesicle cargo as a reporter of drug delivery and effect
Authors: DeLuca Valerie , Tang Nanyun , Hansen Nathaniel , Raju Anjali , Shaffer Charles , Hao Yue , Burns Terry C. , Sarkaria Jann N. , Parney Ian , Pirrotte Patrick , Van Keuren-Jensen Kendall , Berens Michael E. 
Published: March 2024

Abstract
The selectivity of the blood-brain-barrier (BBB) can prevent therapeutics from reaching the brain, and this may contribute to the high failure rate of new drugs for tumors like glioblastoma (GBM) and brain metastasis. The capacity to detect BBB penetrance in real-time in a noninvasive manner would arguably aid the rate of therapeutic development. Extracellular vesicles, which are membrane bound particles secreted by all cell types in the body, have potential as a neuro pharmacodynamic reporter given that their protein and RNA cargo reflect the originating cell population. We hypothesized that the exposure of GBM cells to therapy results in altered EV cargo, and that the detection of this shift can be leveraged as a liquid biopsy from patients during early clinical trials to determine BBB penetrance and tumor engagement. To identify cargo shifts indicative of treatment, we exposed four short-term patient derived glioma cell lines to arsenic trioxide (an idiopathic toxin), MLN4924 (a neddylation inhibitor), and the alkylating agent temozolomide, then harvested EVs for unbiased mass spectrometry and RNA sequencing. Interestingly, we identified conserved upregulated and downregulated protein and RNA species across cell lines and across drug treatments, despite the diverse mechanisms of action. Candidate proteins were further validated by mesoscale immunoassays and exoview evaluation of tetraspanin-captured EVs. RNA species were validated by qRT-PCR. Overall, we demonstrate that GBM-derived EV cargo changes in response to therapy, supporting the development of EVs as a reporter of drug delivery in GBM. Ongoing and future work is focused on identifying enrichment handles in order to selectively evaluate GBM-derived EV cargo from patient biofluids. Thus far, B7H3, PTPRZ1, EGFRvII and IL13Ra2 have been screened as putative handles. Success in this pursuit could substantially enhance findings and accelerate drug testing in early-stage clinical trials in brain tumor patients by reporting drug accessibility to the tumor and engagement with drug targets.
Citation Format: Valerie DeLuca, Nanyun Tang, Nathaniel Hansen, Anjali Raju, Charles Shaffer, Yue Hao, Terry C. Burns, Jann N. Sarkaria, Ian Parney, Patrick Pirrotte, Kendall Van Keuren-Jensen, Michael E. Berens. Glioblastoma-derived extracellular vesicle cargo as a reporter of drug delivery and effect [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 2130.
Abstract 2264: Identifying and analyzing independent clonal populations in single Barrett’s esophagus biopsies
Authors: Kazachkova Mariya , He Phoebe , Alexandrov Ludmil B. 
Published: March 2024

Abstract
Barrett’s esophagus (BE) is a non-obligate precursor of esophageal adenocarcinoma (EAC), often measuring multiple centimeters in length and characterized by columnar epithelium replacing normal squamous epithelium in the distal esophagus. Early studies in BE suggested that all cells within a patient’s Barrett’s segment are progenies of a single founder cell. However, in recent years this previously accepted model of BE as a monoclonal disease has been retired in favor of a multiclonal model with new evidence suggesting that a patient’s Barrett’s segment can be composed of multiple independent clones with independent founder cells. Nonetheless, single BE samples are still routinely assumed to be monoclonal, leading to independent sets of genomic aberrations erroneously being analyzed as a single set in the case of multiclonal samples. Here, we utilize a previously generated whole-genome sequenced BE dataset and repurpose an established pipeline for detecting subclonal populations to identify BE samples that are comprised of multiple independent clones. Additionally, we present a novel approach for validating multiclonality from sequencing data by phasing pair-end sequencing reads using germline variants. We demonstrate that 20/80 patients have at least one multiclonal sample and that the independent clones contained in these single biopsies can have drastically different genomic profiles. Further, we speculate that these multiclonal samples capture a snapshot of clonal competition and evolution within BE. These findings highlight the importance of accounting for multiclonality when studying BE and provide the first systematic analysis of multiclonal BE samples.
Citation Format: Mariya Kazachkova, Phoebe He, Ludmil B. Alexandrov. Identifying and analyzing independent clonal populations in single Barrett’s esophagus biopsies [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 2264.
Abstract 2278: Unraveling immune dynamics of CD4+ in non-small cell lung cancer through single-cell analysis and gene expression profiling
Authors: Woo Hyunmin , Yang JiHye , Yang Siyoung , Eyun Seong-il 
Published: March 2024

Abstract
Non-small cell lung cancer (NSCLC) is a type of epithelial lung cancer other than small cell lung cancer and represents the majority of cases in lung cancer. The immune response against NSCLC relies significantly on the vital role by CD4+ T cells, contributing to the regulation of immune system and the suppression of tumor growth. Various CD4+ T cell subtypes, such as T conventional cells (Tconv cells) and T regulatory cells (Treg cells), perform distinct functions within the immune system. Tconv cells boost immune responses against specific pathogens, while Treg cells play a role in suppressing immune reactions. Investigating the correlation between Tconv cells and Treg cells in NSCLC could serve a valuable biomarker for evaluating the immune status of lung cancer patients. We examine the connection between particular CD4+ T cells in the lung and specific gene expressions associated with NSCLC. Through single-cell analysis, we classified the proportions of Treg cells and Tconv cells within CD4+ T cells in both the lungs and spleen of mice. Our discovery revealed that the proportion of Tconv cells in the lungs exceeded that in the spleen. From the differential gene expression (DEG) analysis using RNA-Seq data for Treg cells and Tconv cells in NSCLC, compared to the control group of Peripheral Blood Mononuclear Cells (PMBC), we identified 1823 genes uniquely expressed in NSCLC Treg cells and 711 genes in Tconv cells. Within these genes, we verified the expression of IL2RA and CTLA4, known to be expressed in NSCLC. Additionally, we identified high expression of genes TM4SF1 and KRT6A. By comparing the genes specific to Tconv and Treg cells in the lungs with those significantly expressed in NSCLC, we were able to identify 114 co-expressed genes in Treg cells and 71 in Tconv cells. We conducted GO and KEGG pathway analyses on these genes and examined the interaction networks among the associated genes. Furthermore, we found receptor interactions between Tconv cell subtypes (Th1, Th2, Th17, and Tfh) and Treg cells through cell-cell interaction analysis. We explored the mouse phenotypes associated with these genes. These discoveries unveiled connections within lung-specific gene networks of Treg and Tconv cells associated with NSCLC, highlighting candidate genes for targeted therapy in cancer.
Citation Format: Hyunmin Woo, JiHye Yang, Siyoung Yang, Seong-il Eyun. Unraveling immune dynamics of CD4+ in non-small cell lung cancer through single-cell analysis and gene expression profiling [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 2278.
Abstract 2302: Innovative blood-based cell-free RNA whole transcriptome sequencing for comprehensive RNA profiling in patient plasma samples and its clinical applications
Authors: Liu Fang , Huang Yong , Wang Min , Sun Xiangying , Xiang Binggang , Jia Shidong , Du Pan , Luo Shujun 
Published: March 2024

Abstract
Background: Plasma cell-free RNA (cfRNA) holds promise for non-invasive cancer biomarker discovery, particularly in diseases like prostate cancer where specific biomarkers (AR splicing variants and TMPRSS2:ERG fusion) are detectable at the RNA level. Despite its potential, the technical challenges posed by blood cell-originated cfRNA abundance necessitates the development of robust and reliable assays for non-invasive cancer diagnostics. This study establishes and demonstrates the clinical utility of an innovative protocol for isolating and identifying tumor-originated cfRNA in plasma samples.
Methods: A novel methodology was developed for the simultaneous extraction of cfDNA and cfRNA from a single blood sample tube, enabling whole transcriptome sequencing (WTS) analysis with minimal input as low as 1ng. A proprietary method was developed to selectively deplete blood cell-originated transcripts in the library. An enrichment-based WTS assay was conducted, and a customized RNASeq analysis pipeline was employed to enable expression profiling and cancer biomarker testing from the cfRNA samples.
Results: The developed extraction method yielded substantial amounts of cfDNA and cfRNA from a 4 mL blood sample. Efficient depletion of blood cell-originated transcripts, achieving over 99% removal, enhanced the detection of a broader range of gene expressions in plasma. Implementation of the cfRNA WTS assay across healthy donor and cancer samples demonstrated consistency with documented biomarker status. The assay revealed significant differential clustering between cancer samples and healthy donors, with characteristic cancer genes contributing to the distinction. Reproducibility and analytical sensitivity of the developed cfRNA WTS assay were successfully validated.
Conclusions: This study introduces Predicine's proprietary cfRNA WTS assay, enabling concurrent expression profiling and RNA biomarker detection in plasma samples. Overcoming technical challenges associated with blood cell-originated cfRNA, this assay represents a significant advancement in liquid biopsy-based cancer diagnostics.
Citation Format: Fang Liu, Yong Huang, Min Wang, Xiangying Sun, Binggang Xiang, Shidong Jia, Pan Du, Shujun Luo. Innovative blood-based cell-free RNA whole transcriptome sequencing for comprehensive RNA profiling in patient plasma samples and its clinical 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 2302.
Abstract 2304: Detection of early-disseminated cancer cells with deep learning-enabled holographic imaging
Authors: Heller Nicholas , Mallery Kevin , Bristow Nathaniel , Travadi Yash , Lee Eng Hock , Hong Jiarong 
Published: March 2024

Abstract
Recent research increasingly validates the early dissemination of tumor cells in peripheral blood during the nascent stages of cancer, often preceding clinical identification of the primary tumor. This emerging evidence emphasizes the potential of Circulating Tumor Cells (CTCs) as early indicators for cancer. Despite their significance, CTCs are exceptionally rare compared to normal blood cells, which presents a considerable challenge in detection, particularly during early stages of cancer. Traditional detection methods, such as those based on nucleated cell enrichment, antibody labeling and fluorescence imaging, encounter notable limitations when applied in the context of early detection. These limitations arise from the inherent heterogeneity of CTCs, and the multistep process involved in labeling and manual enumeration, compromising cell viability and resulting in cell loss. This loss becomes particularly problematic in the context of early cancer detection scenarios where the tumor burden is extremely low, and any cell loss can significantly impact assay sensitivity. To overcome these challenges, we propose an innovative CTC detection approach employing a deep learning framework combined with holographic imaging. This technique utilizes coherent light to generate holograms from cell samples, capturing detailed 3D morphological and optical properties of individual cells. We developed a custom convolutional neural network designed to facilitate high-throughput cell sorting in real-time. Trained on healthy blood samples and diverse cancer cell lines, the dataset consists of more than 50 million cellular holograms enhanced by proprietary Gaussian annotation and image augmentation strategies. Moreover, by combining the morphological signatures from holography with antigen signatures (e.g. HER2/ER/PR) in real-time, our model demonstrates the ability to detect less than 1 false positive per 1 million nucleated cells, highlighting its potential as a robust tool for targeted early-stage breast cancer detection. Our technology represents highly sensitive alternative to traditional screening methods, with the promise of enhancing patient outcomes.
Citation Format: Nicholas Heller, Kevin Mallery, Nathaniel Bristow, Yash Travadi, Eng Hock Lee, Jiarong Hong. Detection of early-disseminated cancer cells with deep learning-enabled holographic imaging [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 2304.