bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 3169: The role and mechanism of m6A methylation modification of LncRNA-ATB in regulating the invasion and metastasis of colorectal cancer
Authors: Lang# Yu , Lin# Jia-Lin , Kang Jia-Peng , Yang Lu , Zhou Dan , Fang* Can-Bin , Ye* Feng , Tang* Wei-wei 
Published: March 2024

Abstract
Background: The epigenetic modification of LncRNA N6-methyladenosine (m6A) methylation plays a wide role in the invasion and metastasis of various malignant tumors. However, the role of LncRNA-ATB m6A methylation modification in colorectal cancer (CRC) has not been systematically elucidated.
Methods: Detect the regulatory effect of ALKBH5 on LncRNA-ATB by Luciferin reporter gene. LncRNA-ATB expression was detected by IHC and qPCR in CRC tissues and cells. Transwell and scratch tests were used to detect the effect of ALKBH5 overexpression after LncRNA-ATB knockdown and replacement on the invasion and migration ability of CRC cells. Western blotting was used to detect the expression changes of MMPs proteins.
Results: ALKBH5 could regulate the methylation level of the LncRNA-ATB 3’ UTR region (p&lt;0.05). ALKBH5 overexpression in CRC cells led to a significant decrease in the expression level of LncRNA-ATB (p&lt;0.05). LncRNA-ATB exhibited elevated expression in CRC cells and demonstrated significantly higher levels in CRC tissues compared to paracancerous tissues (p&lt;0.05), indicating the potential tumor-promoting effect of LncRNA-ATB in CRC, with the mechanism possibly regulated by ALKBH5-mediated m6A demethylation. ALKBH5 overexpression inhibited the proliferation and migration of CRC cells after LncRNA-ATB knockdown. However, this inhibitory effect was attenuated upon LncRNA-ATB rescue, accompanied by an increase in MMP9 and a decrease in TIMP1.
Conclusion: LncRNA-ATB plays a crucial role in ALKBH5-mediated m6A demethylation, regulating the invasion and metastasis of CRC. The ALKBH5-LncRNA-ATB m6A demethylation-MMPs signaling axis has been identified as a key regulatory pathway promoting CRC migration. m6A modification of lncRNA-ATB modulated by ALKBH5 provides a theoretical basis for novel therapeutic strategies for patients with metastatic CRC.
FUNDING: This study was supported by the National Natural Science Foundation of China (Grant No. 81702414), Natural Science Foundation of Fujian Province of China (Grant No. 2020J05306) and Xiamen Science and Technology Planning Project (Grant No. 3502Z20194003).
Citation Format: Yu Lang#, Jia-Lin Lin#, Jia-Peng Kang, Lu Yang, Dan Zhou, Can-Bin Fang*, Feng Ye*, Wei-wei Tang*. The role and mechanism of m6A methylation modification of LncRNA-ATB in regulating the invasion and metastasis of colorectal 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 3169.
Abstract 3181: Immune modulatory activity of radio-sensitizing gold nanoparticle
Authors: Kulkarni Tanmay , Dutta Shamit , Parent Hazel , Perry Karington , Mackeyev Yuri , Bhattacharya Santanu 
Published: March 2024

Abstract
Radiation therapy (RT) is frequently used in the neoadjuvant setting in borderline resectable and some resectable pancreatic ductal adenocarcinoma (PDAC) and in the definitive setting in locally advanced PDACs which is third leading cause of cancer associated death. Higher doses of RT improve overall treatment outcomes but increasing the dose significantly above 50Gy in standard 2Gy fractions risks profound gastrointestinal (GI) toxicity. Additionally, genotoxic stress such as RT, can induce CXCL12 secretion by cancer associated fibroblast (CAFs) and overexpression of CXC motif chemokine receptor 4 (CXCR4) in cancer cells. CXCL12-CXCR4 downstream signaling results in immune suppression and consequent enhanced tumor growth and metastasis and poor prognosis in PDAC. To overcome these clinical challenges, we have developed multimodal gold nanoparticle constructs (GNPs) by functionalizing the CXCR4 antagonists to (i) bind to CXCR4 and mediate GNP internalization, (ii) abolish the feedback immune inhibitory signals mediated by CXCR4 overexpression, and (iii) enhance therapeutic benefit of radiation. To achieve these multimodal activities, we have covalently attached the CXCR4 antagonist, AMD070, to thiol-terminated polyethylene glycol (PEG) to synthesize AMD-PEG which was then conjugated with GNPs to produce AMD-PEG-GNP. In our experiment AMD-PEG-GNP has successfully inhibited CXCL12-CXCR4 downstream signalling such as reduction of ERK phosphorylation in PDAC cells. To analyze the radiosensitization role of GNP nanoconjugates, PDAC cells were incubated with AMD-PEG, PEG-GNP and AMD-PEG-GNPs for 4 hours and then treated with increasing doses of radiated, from 1-4Gy. AMD-PEG-GNP demonstrated a systematic enhancement on reactive oxygen species (ROS) production and downregulation of a colony formation. Collectively, the results from in vitro study with PDAC cells confirm that the nanoconjugate with AMD070 enhances radio-cytotoxicity and impair CXCL12-CXCR4 downstream signaling. Hence AMD-PEG-GNP has strong merit to enhance radiation dose locally and simultaneously restrict RT induced immunosuppression in PDAC.
Citation Format: Tanmay Kulkarni, Shamit Dutta, Hazel Parent, Karington Perry, Yuri Mackeyev, Santanu Bhattacharya. Immune modulatory activity of radio-sensitizing gold nanoparticle [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 3181.
Abstract 3182: Role of Frizzled 7 in melanoma development and metastasis
Authors: Nihal Minakshi , Umar Sheikh A. , Chang An-Bo A. , Ahmad Nihal , Chang Hao 
Published: March 2024

Abstract
The frizzled (Fzd) family of proteins are 7-transmembrane G-protein coupled receptors (GPCRs) that transduce signals mainly for Wnt ligands. There are 10 Fzds identified in mammals, and they are involved in multiple cellular and biological functions via signaling through the canonical Wnt/beta-catenin, planar cell polarity, and calcium signaling pathways. Our previous work revealed a pro-metastasis role of Fzd6 in melanoma. This project focuses on Fzd7, a homolog of Fzd6, in melanoma. We found that FZD7 is highly expressed in multiple melanoma cell lines. siRNA knockdown of FZD7 does not affect cell proliferation but significantly reduces cell invasion in A375, Hs294T, and SK-MEL28 cells in vitro. To determine the in vivo role of Fzd7 in melanoma, we generated Fzd7 knockout YUMM1.7 cell lines for xenograft experiments using CRISPR. All three Fzd7 knockout clones showed a significant reduction in primary tumor growth when xenografted in C57BL/6 mice. To determine the potential mechanism of Fzd7 in melanoma growth and invasion, we performed bulk RNA-Seq on the YUMM1.7 knockout cell lines and identified 215 downregulated and 31 upregulated genes (with a fold change of 2, p&lt;0.05). We are in the process of confirming these transcriptional profile changes. Further functional analysis will be performed using gain- and loss-of-function approaches to determine the downstream mechanisms of Fzd7 in melanoma growth and invasion.
Citation Format: Minakshi Nihal, Sheikh A. Umar, An-Bo A. Chang, Nihal Ahmad, Hao Chang. Role of Frizzled 7 in melanoma development and 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 3182.
Abstract 3199: Nano gelasomes: Novel lamellar metal-protein suprastructures for nucleic acid delivery
Authors: Babu Agasthya Suresh , Suresh Dhananjay , Li Zhaohui , Upendran Anandhi , Kannan Raghuraman 
Published: March 2024

Abstract
There is considerable interest in the development of self-assembled charged nanocarriers that form organized, predictable structures to enhance stable packaging and delivery of nucleic acid materials in vivo. However, the synthesis of stably-charged, organized nanostructures is highly challenging, requiring a controlled balance of nanomaterial components, stabilizers, and hydrophobic forces. Herein, we report a significant step forward in the controlled lamellar assembly of a charged complex between ultra-small 2 nm gold nanoparticles and a lipidoid within an organic matrix to form Gelasomes. These spherical suprastructures feature an intricate 3D concentric arrangement with a constant interlayer distance (4nm). The cationic lipidoid within this arrangement aids in the highly efficient packaging of nucleic acid materials in the nanoparticle. To demonstrate the potential biomedical applications of Gelasomes, we have loaded siRNA (AXL or YAP), mRNA (EGFP), or CRISPR components (Cas9 mRNA and guide RNA) and validated their functionality by in vitro or in vivo studies. Gelasomes with AXL siRNA (~20 bp) demonstrated rapid uptake (&lt;2 hrs), successful endosomal escape, remarkable transfection efficiency (99.87 ± 0.04 %), gene downregulation (97 ± 2.8 %), and disassembly within the cell (&lt;24 hrs). In vivo downregulation studies in Lung Cancer PDX (Gelasomes with AXL siRNA) and CDX (Gelasomes with YAP siRNA) models confirm the gene-silencing capability (91% or 38 % respectively) of Gelasomes underscoring their potential in advancing nanomedicine. Similarly, Gelasome loaded with EGFP mRNA (1 kb) showed 47 ± 8.54 % expression efficiency within 48 h of treatment in vitro. We also show the packaging of larger nucleic acids such as CRISPR Cas9 mRNA (5 kb) along with the guide RNA (100 bp) in vitro for generating knockouts, that achieved an editing efficiency of ~6%. Together, the results from this study pave the way for the development of adaptable, biodegradable, and functionally versatile supraparticles for medical applications.
Citation Format: Agasthya Suresh Babu, Dhananjay Suresh, Zhaohui Li, Anandhi Upendran, Raghuraman Kannan. Nano gelasomes: Novel lamellar metal-protein suprastructures for nucleic acid delivery [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 3199.
Abstract 3208: A nano sized system for the treatment of gastrointestinal cancers
Authors: Vaskovich Daniella , Acúrcio Rita , Kleiner Ron , Carreira Barbara , Matos Ana , Florindo Helena , Satchi-Fainaro Ronit 
Published: March 2024

Abstract
Despite the recent progress in cancer immunotherapies, most patients do not benefit from the currently available immune checkpoint blockers, and many develop severe immune-related adverse events. Therefore, it is urgent to develop alternative, effective immunotherapeutic approaches. An example of non-responsive cancers are gastrointestinal (GI) cancers, which account for 26% of the global cancer incidence and 35% of all cancer-related deaths. In many GI cancers, the failure of immunotherapies to yield clinical response is partially attributed to the inefficient antigen presentation by DC, which results in insufficient T cell stimulation despite their expression of tumor-associated antigens (TAA). To overcome these hurdles, we designed novel polymeric-based nanoparticles (NP) to deliver a combination of GI cancers antigens of CEACAM5 protein and toll-like receptor ligands to DC. We chose to encapsulate CEACAM5 antigens because it is overexpressed in GI cancers, such as gastric cancer, colorectal cancer, and pancreatic cancer. With this approach, we aim to modulate the tumor milieu-immune cell interactions to an anti-cancer phenotype in order to control tumor growth and improve overall survival. Our NP present an average diameter below 200 nm, narrow polydispersity index, slightly negative surface charge, spherical morphology, and high antigens and immune potentiators loading. Cy5-labeled NPs were found to be extensively internalized by DC, which triggered their activation in vivo, shown by the increasing expression of DC-related co-stimulatory molecules such as CD80, CD86, and CD40. Furthermore, we assessed the immunotherapeutic effect of our NP on mouse models and on a human 3D multi-cellular spheroid ex-vivo model, composing the patient’s tumor cells and peripheral blood mononuclear cells (PBMC). We found that the NP successfully induced a potent immune-mediated anti-tumor response against CEACAM5-positive GI tumors, sensitizing the tumor microenvironment to other therapies and decreasing tumor volume, ultimately leading to prolonged survival. Taken together, the developed NP induced a strong antigen-specific immune response and overall sensitized CEACAM5-expressing GI cancers to the clinically relevant treatments in vivo, that so far have shown limited clinical outcomes in addition to a specific T cell anti-tumor activity that was shown on our patient-derived ex vivo model.
Citation Format: Daniella Vaskovich, Rita Acúrcio, Ron Kleiner, Barbara Carreira, Ana Matos, Helena Florindo, Ronit Satchi-Fainaro. A nano sized system for the treatment of gastrointestinal 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 3208.
Abstract 321: Optimized RNA Seq library preparation for fusion calling from FFPE samples
Authors: Corbet Giulia , Haimes Josh , Sanders Travis , Ranik Martin , Harrison Thomas , Casas Eduard , Reed Kailee , Wendel Doug , Giorda Kristina , Hanek Ariele , Pavlica Jen , Kudlow Brian 
Published: March 2024

Abstract
Gene fusions due to chromosomal rearrangement, duplication, or deletion can be important drivers of cancer. Detection of gene fusions plays a valuable role in selecting targeted therapies. A widely used method for detecting fusion transcripts is targeted RNA sequencing, which focuses sequencing reads on known fusions but does not allow for the detection of novel fusions. Whole transcriptome analysis (WTA), where the entire transcriptome is interrogated, offers an opportunity to detect both known and novel fusions.
Herein we examine the effect of sample quality, input mass, increased reverse transcriptase (RT) and insert size on fusion calling. Libraries are prepared using the Watchmaker RNA Library Preparation Kit with or without Polaris Depletion and, for target enrichment, the Twist Exome 2.0 panel prior to paired end 2 × 150 Illumina sequencing. First, control samples, specifically Seraseq Fusion RNA v4 high quality and FFPE samples, are used to determine if any of the parameters interrogated increase the number of breakpoint spanning reads both in a WTA and targeted sequencing context. Once established, the optimized workflow is applied to real FFPE samples.
Targeted sequencing results in a higher number of breakpoint spanning reads, compared to WTA, when controlling for sequencing depth, resulting in a higher number of reads supporting each fusion call. Longer insert sizes, achieved by modified SPRI ratios, maintain library complexity and may enhance fusion calling. Taken together, these data demonstrate an optimized protocol for fusion calling from FFPE and demonstrate the utility of both WTA and targeted sequencing for fusion detection.
Citation Format: Giulia Corbet, Josh Haimes, Travis Sanders, Martin Ranik, Thomas Harrison, Eduard Casas, Kailee Reed, Doug Wendel, Kristina Giorda, Ariele Hanek, Jen Pavlica, Brian Kudlow. Optimized RNA Seq library preparation for fusion calling 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 321.
Abstract 323: Optimization of a liquid biopsy assay to accommodate low cfDNA samples and increase throughput
Authors: Salmans Michael , Kim Dasom , Carson Andrew , Wang Mengchi , Lee Byung In , Leatham Bryan 
Published: March 2024

Abstract
Molecular testing that interrogates cell free DNA (cfDNA) from plasma has significant potential value across the cancer care continuum, including early cancer detection, driver mutation identification, and disease recurrence monitoring. To achieve this potential, liquid biopsy assays must be optimized to address multiple challenges. For one, cfDNA quantity in the blood is highly variable, with different amounts present depending on malignancy and stage of progression. This requires optimization to detect low concentrations of circulating tumor DNA (ctDNA) and to accommodate variable tumor fractions. In addition, minimizing assay costs will improve test accessibility and adoption. To address these issues, Genece Health is optimizing their lung cancer liquid biopsy assay to accommodate minimal cfDNA input into library preparation. Furthermore, Genece is testing algorithms that tolerate reduced read depths from low-pass whole genome sequencing (LP-WGS) while maintaining high performance. The Genece lung cancer liquid biopsy assay profiles fragment end-motif and size (FEMS) and fragment coverage signals using LP-WGS (Illumina) and proprietary machine learning algorithms. This study first tested the frequency of end motifs in pooled ctDNA after modifying library preparation (IDT) to reduce reagent volumes from 1X down to 0.5X, 0.25X, and 0.1X of manufacturer specification. A range of cfDNA input from 0.25 ng to 6 ng was tested with each library preparation volume. In addition, LP-WGS read coverage from 5X to 1X was evaluated to assess impact on end motif frequency and assay sensitivity. Performance characterization was further evaluated with a cohort of 50 clinical lung cancer and 100 healthy donor plasma samples tested at 1X and 0.25X library reagent volume. We observed an expected increase in library complexity at higher cfDNA input and library reagent volume. Assay performance was minimally impacted by variable cfDNA input and library reagent volume. However, reducing sequencing read depth is tolerated down to 1.25X depth before increasing the variability of end motif frequencies. These observations are corroborated in the 150 clinical sample cohort. This data shows that by altering standard library preparation conditions and reducing unique read depth, liquid biopsy assays can accommodate a wider range of cfDNA, while concurrently decreasing overall costs.
Citation Format: Michael Salmans, Dasom Kim, Andrew Carson, Mengchi Wang, Byung In Lee, Bryan Leatham. Optimization of a liquid biopsy assay to accommodate low cfDNA samples and increase throughput [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 323.
Abstract 3270: SH3GLB1 is involved with hydrogen peroxide/akt signaling in glioblastoma multiforme cells
Authors: Chien Chia-Hung , Chang Kwang-Yu 
Published: March 2024

Abstract
Glioblastoma (GBM), a malignant brain tumor, has poor survival outcomes due to recurrence or drug resistance. In our previous studies, it was found that superoxide dismutase 2 (SOD2) was associated with temozolomide (TMZ) resistance. Moreover, SOD2 can convert O2 •− to H2O2, and H2O2 redox signaling is vital for physiological reactions and promotes tumor progression. We used cell lines, patient primary cells and pharmacological inhibitors/activators to confirm the significance of H2O2 signaling. We used the cultured cells to verify roles of H2O2 signaling in the plasticity of cell fate and did animal experiments to identify the optimal treatment strategy. In the present study, SOD2 was found to be the upstream mediator, and combining SOD inhibitor and TMZ, the cells showed reduced SH3GLB1 and autophagy levels. We then found that SH3GLB1 was regulated by H2O2 through AKT signaling using experiments of regulating redox homeostasis. The change of intracellular H2O2 levels in mitochondria following the treatments is similar to that in cytosol, however, the cell fate of parental or resistant cells was quite diverse. Notably, CCCP, a mitochondrial membrane potential disrupter, increased endogenous H2O2 production, and TMZ-increased SH3GLB1 levels can be reversed by HgCl2, reflecting the aquaporin function. In animal models, a combination of TMZ and 4-hydroxynonenal reduced growth of the SH3GLB1-knockdown resistant cells, along with suppressed autophagy levels. Our results characterizing the mechanism of H2O2-SH3GLB1 axis signaling in acquired TMZ resistance of GBM cells will provide new therapeutic strategies against the disease in the future.
Citation Format: Chia-Hung Chien, Kwang-Yu Chang. SH3GLB1 is involved with hydrogen peroxide/akt signaling in glioblastoma multiforme 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 3270.
Abstract 3281: Silencing of necroptosis related genes in endocrine-resistant breast cancer cells causes PFKFB3 induced arrest of necroptosis and contributes to resistance
Authors: Jones Brandon C. , Onal Tuna , Sengupta Surojeet , Sevigny Catherine M. , Jin Lu , Pohlmann Paula R. , Shajahan-Haq Ayesha , Clarke Robert 
Published: March 2024

Abstract
Approximately 70% of newly diagnosed breast cancer patients are estrogen receptor positive. Patients treated with approved treatment strategies may develop resistance to these therapies. Because of this problem in treatment, new treatment regimens need to emerge. Altered reprogramming of metabolism and an intense dependence on glycolysis are hallmarks of cancer, which is necessary to support the high energy demand of rapidly proliferating cancer cells. Rapidly dividing cancer cells are known to have increased energy requirements and altered reprogramming of glucose metabolism, leading to an increased reliance on glycolysis. The conversion of fructose-6-phosphate to fructose-1,6-bisphosphate, a critical rate-limiting step in the glycolysis pathway, is greatly influenced by an allosteric activator produced by the enzyme PFKFB3 (6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3), thus making PFKFB3 an important regulator of glycolytic flux. Furthermore, PFKFB3 has been shown to be overexpressed in many human cancers, including breast cancer, and upregulated by estrogen. In our previous studies, we have shown that endocrine-resistant BC cells growth is strongly reduced by PFKFB3 targeting using PFKFB3 inhibitors, glucose uptake is reduced, triggered to necroptosis by RIPK1 and MLKL phosphorylation, and PFKFB3 inhibition reduces tumor size in mouse xenografts. In this study, we showed that silencing of RIPK1 and MLKL, genes involved in necroptosis, by siRNAs followed by inhibition of PFKFB3 by PFK158 did not induce necroptosis in endocrine-resistant BC cells. Furthermore, we further confirmed that phosphorylation of MLKL and RIPK occurs with PFKFB3 inhibition. In summary, this study reveals that necroptosis induced by PFKFB3 inhibition contributes to resistance by arresting necroptosis in endocrine-resistant BC cells after silencing of necroptosis-related genes.
Citation Format: Brandon C. Jones, Tuna Onal, Surojeet Sengupta, Catherine M. Sevigny, Lu Jin, Paula R. Pohlmann, Ayesha Shajahan-Haq, Robert Clarke. Silencing of necroptosis related genes in endocrine-resistant breast cancer cells causes PFKFB3 induced arrest of necroptosis and contributes to resistance [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 3281.