bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 1690: LSD1 and CoREST2 demethylate STAT3 to promote enteroendocrine cell differentiation in mucinous colorectal cancer
Authors: Ladaika Christopher A. , Ghobashi Ahmed H. , Boulton William C. , O'Hagan Heather M. 
Published: March 2024

Abstract
Across different cancer types, tumor heterogeneity has been shown to drive tumor progression, metastasis, and therapeutic resistance. Adenocarcinoma to neuroendocrine lineage transition is an emergent mechanism of targeted therapy resistance in several cancer types, including lung and prostate cancer. Therefore, understanding the dynamics and mechanisms driving neuroendocrine cell fates in cancer is critical. Mucinous colorectal cancer accounts for upwards of 20% of colorectal cancer cases and is characterized by tumors with mucous accounting for at least 50% of the tumor volume. The normal colon epithelium consists of several specialized cell types, including hormone secreting enteroendocrine cells (EECs), which are the neuroendocrine cell of the intestine. We have previously shown that EEC progenitors are enriched in mucinous colorectal cancer and promote cancer cell survival via secreted factors. Additionally, we have shown that lysine specific demethylase 1 (LSD1) promotes EEC differentiation in these tumors; however, the mechanism by which LSD1 promotes EEC differentiation has remained unknown. Typically to carry out its enzymatic function, LSD1 must be a part of a transcriptional regulatory complex. One such complex is the CoREST complex, which contains LSD1, HDAC1, and one of three CoREST protein family members. Here we report that LSD1 and CoREST2 promote EEC differentiation by demethylating the transcription factor signal transducer and activator of transcription 3 (STAT3) to promote STAT3 chromatin binding. Additionally, we demonstrate that knocking down CoREST2 decreases tumor growth and lung metastases of mucinous colorectal cancer cells injected orthotopically into the colons of immunocompromised mice. Furthermore, we utilized single cell multi-omics that combines single cell RNA sequencing with single cell ATAC sequencing to show that during EEC differentiation there is an increase in chromatin accessibility at regulatory regions of known EEC-promoting transcription factors. Finally, through our single cell multi-omics analysis we identify a new rare cell type with neuron-like but not secretory characteristics. Mucinous colorectal cancer is an aggressive and chemotherapeutically intractable form of CRC that is enriched for EEC progenitors. Our data demonstrates that LSD1 and STAT3 promote EEC differentiation, suggesting that inhibiting LSD1 and or STAT3 may have benefits for patients with mucinous colorectal cancer.
Citation Format: Christopher A. Ladaika, Ahmed H. Ghobashi, William C. Boulton, Heather M. O'Hagan. LSD1 and CoREST2 demethylate STAT3 to promote enteroendocrine cell differentiation in mucinous 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 1690.
Abstract 1719: Targeting H3.3 serine 28 phosphorylation as a novel therapeutic strategy for diffuse midline glioma
Authors: Yan Yuqian 
Published: March 2024

Abstract
Background: Diffuse midline glioma (DMG) is a highly aggressive pediatric brain cancer with a poor prognosis [1]. Mechanistically, DMG harbors a lysine-to-methionine substitution at position 27 of histone H3.3 (H3.3K27M), which leads to global hypomethylation and a dramatically altered epigenetic landscape [2, 3].
Aim: This study aims to explore the H3.3K27M mutation from a novel perspective by investigating its effects on H3.3 ubiquitination, with the goal of identifying effective, novel therapeutic targets.
Methods: Mass spectrometry was used to identify potential E3 ligases for H3.3, while immunoprecipitation to verify this interaction. Cell viability and survival were determined by MTS and clonogenic survival assays, respectively. Nucleosome fractionation was performed to detect the distribution of wild-type (WT) or K27M mutant H3.3 histones.
Results: Mass spectrometry identified UBR7, an E3 ligase, as exhibiting a stronger binding affinity with WT H3.3 than its K27M mutant counterpart. Further nucleosome fractionation assay revealed that K27M histones are more likely deposited in nucleosomes than WT H3.3. Further analysis demonstrated that a non-phosphorylation mimic mutation (serine to alanine) at amino acid 28 (S28A) restored the binding affinity of K27M mutant H3.3 with UBR7. Importantly, this mutation disrupted H3.3 phosphorylation and significantly diminished cell survival, whereas the constitutively activated phosphorylation mutation (S to glutamine (E)) on S28 (S28E) mimics K27M mutation in promoting cell proliferation and survival.
Conclusion: These findings suggest that S28ph impairs UBR7-mediated K27M ubiquitination and promotes DMG cell growth, suggesting that targeting S28ph is an effective therapeutic strategy. However, the underlying mechanisms by which K27M interplays with S28ph in promoting tumorigenesis require further investigation.
Citation Format: Yuqian Yan. Targeting H3.3 serine 28 phosphorylation as a novel therapeutic strategy for diffuse midline glioma [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 1719.
Abstract 1773: Deciphering the roles of germline predisposition variants and somatic mutations on breast cancer cells and the tumor microenvironment
Authors: Rodrigues Fernanda Martins , Gallant Kelsey , Jayasinghe Reyka , Iglesia Michael , Houston Andrew , Chen Siqi , Lal Preet , Fields Ryan , Gillanders William , Chen Feng , Ding Li 
Published: March 2024

Abstract
While great progress has been made in the understanding and treatment of cancer, tumor heterogeneity remains a diagnostic and prognostic challenge. Single-cell sequencing techniques and high-resolution cellular imaging now afford researchers the ability to investigate the effects of germline variants (especially when compared to somatic mutations) on molecular characteristics of cancer cells and non-cancer cells in the tumor microenvironment (TME). Here, we investigated a breast cancer (BRCA) cohort of over 100 individuals, for which we have generated sc/sn RNA-seq, snATAC-seq, and CODEX imaging data as well as bulk whole exome sequencing and RNA-seq data. We identified 21 BRCA cases carrying pathogenic and likely pathogenic rare germline variants in known cancer predisposition genes, such as BRCA2, BRIP1, ATM, and TP53. These predisposition genes showed diverse expression patterns across stromal and immune cell types, indicating roles in cell types beyond breast epithelia. For cases carrying pathogenic germline variants in such genes, we use snRNA-seq/snATAC-seq to assess gene expression changes and pathway alterations (e.g.,HRD and apoptosis) across all cell types and investigate phenotypic changes associated with pathogenic germline variants in cancer cells compared to stroma and immune cells in the TME. By evaluating chromatin accessibility changes and allele-specific expression, we reveal the connection between epigenetic regulators and differential roles of germline variants across cell types. Finally, the integrated analysis of germline variants and somatic mutations from predisposition genes at single cell resolution broadened our understanding of the role of germline variants in TME during tumorigenesis.
Citation Format: Fernanda Martins Rodrigues, Kelsey Gallant, Reyka Jayasinghe, Michael Iglesia, Andrew Houston, Siqi Chen, Preet Lal, Ryan Fields, William Gillanders, Feng Chen, Li Ding. Deciphering the roles of germline predisposition variants and somatic mutations on breast cancer cells and the tumor microenvironment [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 1773.
Abstract 1780: Utilizing bisbiguanide compounds to disrupt metabolic heterogeneity in non-small cell lung cancer
Authors: Matsuk Veronika Y. , Knippler Christina M. , Arnst Jamie L. , Robinson Isaac E. , Khatib Tala O. , Shanmugam Mala , Ganesh Thota , Mouw Janna K. , Marcus Adam I. 
Published: March 2024

Abstract
Metastasis accounts for 90% of cancer-related deaths; however, the molecularmechanisms by which cancer cells invade and metastasize remain poorly understood.Around 80% of lung cancer patients present with metastatic disease and have only a 5%5-year relative survival. Metastases are often seeded by heterogeneous cells that invadecollectively in cellular packs. However, most studies and treatments focus on bulk cellularpopulations leaving subpopulations that drive metastasis masked. We previouslypublished on metabolic heterogeneity within collectively invading lung cancer cells andidentified the bisbiguanide compound alexidine as a disrupter of lung cancermitochondrial metabolism and invasion. To expand on these findings, we developed newbiguanides and identified promising candidates, AX-4 and AX-7. These analogs inducemitochondrial structural defects and cause metabolic rewiring. Treated lung cancer cellsexhibited reduced oxygen consumption and increased lactate production. Importantly,AX-4 and AX-7 reduced collective cell invasion, highlighting the potential of these newbiguanides to limit cancer metastasis. Taken together, we have developed new chemicaltools to disrupt mitochondrial metabolism. These tools will be useful to further parse theroles of metabolically heterogenous cancer cells on tumor growth and metastasis.
Citation Format: Veronika Y. Matsuk, Christina M. Knippler, Jamie L. Arnst, Isaac E. Robinson, Tala O. Khatib, Mala Shanmugam, Thota Ganesh, Janna K. Mouw, Adam I. Marcus. Utilizing bisbiguanide compounds to disrupt metabolic heterogeneity in non-small cell lung 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 1780.
Abstract 179: Identification of a novel crosstalk between MDSC and NKregs in immunotherapy resistant triple negative breast cancer
Authors: Das Megha , Henry Samantha , Singh Shailesh , Santos Camila Dos , Chakrabarti Rumela 
Published: March 2024

Abstract
Triple-negative breast cancer (TNBC) is one of the most aggressive forms of breast cancer and lacks standard treatment options. Although immunotherapy shows some response in these patients along with chemotherapy, heterogeneity of tumor cells and immune cells results in significant low response to immunotherapy treatment. Based on single cell sequencing which enables identity of heterogenous population at single cell level and functional studies involving preclinical mouse models, our laboratory recently identified distinct CD56brightSOCS3highCD11b−CD27− immature NK cells subpopulations, with diminished cytotoxic granzyme signatures that promote TNBC tumor progression. However, the precise characterization and functionality of these rogue tumor promoting NK cells remains unclear in clinical samples. Here, we aimed to illustrate mechanistic insight of these novel immature NK subpopulation in context of immunotherapy resistant TNBC patient samples. The scRNA seq analysis of TNBC patient samples identified four specific subclusters of NK cells in TNBC. We further found that NK2 and NK3 subclusters are CD56dim Granzymehigh cytotoxic NK cells and the other two subclusters (NK0 and NK1) are CD56bright immature NKs. Interestingly, the NK0 and NK1 subcluster specifically exhibit distinctive characteristics and functions. Notably, CD56bright immature NK1 cells, identified as tissue-resident NK cells, were engaged in direct communication with myeloid-derived suppressor cells (MDSCs). The CD56bright NK0 possesses moderate to low SOCS3 expression and moderate to high granzyme expression with elevated early NK activation markers and inhibitory receptor expressions, suggesting its regulatory property (NKregs). scRNA seq and flow cytometry analysis showed higher NKregs and immunosuppressive MDSC population, specifically with high monocytic-MDSCs (mMDSCs) in non-responder TNBC (to adjuvant combinational treatment of chemo and immunotherapy) patient samples rather than responder patients’ tissue. Based on in silico analysis, we further found a potential crosstalk between these mMDSC & NKreg within the tumors of non-responsiveness of TNBC patients. Overall, our studies show a connection of MDSCs and NKregs in TNBC patients, who do not respond to immunotherapy, highlighting a possible mechanism for immunotherapy resistance, which could be targeted in near future for better treatment options in TNBC.
Citation Format: Megha Das, Samantha Henry, Shailesh Singh, Camila Dos Santos, Rumela Chakrabarti. Identification of a novel crosstalk between MDSC and NKregs in immunotherapy resistant 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 179.
Abstract 1843: Integrating machine learning with microfluidic technologies for proteomic profiling of extracellular vesicles in triple-negative breast cancer
Authors: Kim Min Woo , Kim Jee Ye , Kim Young , Lee Suji , Moon Sol , Hyon Ju-yong , Hyun Kyung-A , Yang Yeji , Ha Seongmin , Park Sunyoung , Gawk Hogyeong , Lee Haeji , Han Eun Hee , Kim Jin Young , Jung Hyo-Il , Chung Young-Ho , Kim Seung Il 
Published: March 2024

Abstract
Accurate diagnosis of breast cancer using circulating biomarkers present in plasma remains an important challenge. In particular, protein changes in tumor-derived extracellular vesicles (tdEVs) have emerged as potential biomarkers for breast cancer diagnosis because they accurately reflect dynamic changes in tumors. In this study, we compared the proteomes of extracellular vesicle (EV) isolated from the plasma of 100 breast cancer patients and 30 healthy individuals who visited Severance Hospital between Mar 2010 and Dec 2015. Microfluidic chip-based protocol that facilitates the removal of contaminants such as albumin and immunoglobulins was used for the extraction of enriched tdEVs with small amounts of plasma. Comparative analysis of the proteomes identified 26 significant biomarkers that could indicate differences between breast cancer patients and healthy individuals. Using the LsBoost-CNN-SVM hybrid machine learning algorithm, we especially identified key EV protein biomarkers for detecting triple-negative breast cancer (TNBC), a breast cancer subtype with a poor prognosis and a high recurrence rate, as well as lacking therapeutic and diagnostic targets. Remarkably, a signature consisting of three EV proteins, specifically extracellular matrix protein 1 (ECM1), mannose-binding lectin 2 (MBL2), and biotinidase (BTD), effectively distinguished TNBC patients from healthy individuals. In our proteomic analysis set (n=73), this signature exhibited impressive performance, achieving a sensitivity of 93.3% and specificity of 93% in the accurate discrimination of TNBC from the control group. The validation set (n=40) confirmed these findings, with 100% sensitivity and 80% specificity. This signature not only served as a diagnostic tool but also provided valuable insights into the risk of recurrence and patient prognosis. We found a novel diagnostic approach that holds the potential to revolutionize breast cancer diagnostics by enhancing the reliability of tumor-related information obtained from blood samples.
Citation Format: Min Woo Kim, Jee Ye Kim, Young Kim, Suji Lee, Sol Moon, Ju-yong Hyon, Kyung-A Hyun, Yeji Yang, Seongmin Ha, Sunyoung Park, Hogyeong Gawk, Haeji Lee, Eun Hee Han, Jin Young Kim, Hyo-Il Jung, Young-Ho Chung, Seung Il Kim. Integrating machine learning with microfluidic technologies for proteomic profiling of extracellular vesicles 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 1843.
Abstract 1845: 11,000-plex aptamer based proteomics of colorectal cancer stools for the discovery of novel disease biomarkers
Authors: Mohan Chandra , Vanarsa Kamala , Castillo Jessica , Bresalier Robert , Chia Nicholas 
Published: March 2024

Abstract
Given the morbidity and mortality associated with colorectal cancer, novel biomarkers are clearly warranted, especially for early detection, particularly for advanced adenomas. An earlier 1317-plex aptamer-based proteomic screen of stool proteins revealed 92 proteins to be significantly elevated in CRC stool, with the most discriminatory proteins being MMP9, haptoglobin, myeloperoxidase, fibrinogen, and adiponectin (PMID: 34117903). Results from a recent 2000-plex proteomic screen of CRC stools are detailed below, while a 11,000-plex aptamer based proteomic screen is in progress. Comprehensive proteomic screening revealed 116 proteins to be differentially expressed in CRC stool compared to control stool, with 45 being elevated 2-fold or higher. 37 of these proteins were ELISA validated in 3 independent cohorts. Stool MMP-8, MMP-9, Hemoglobin, PGRP-S, Haptoglobin, Myeloperoxidase and Fibrinogen emerged as being most discriminatory for distinguishing CRC from healthy controls (AUC: 0.91-0.95), while Stool Fibrinogen, MMP-9, Hemoglobin, MMP-8, and PGRP-S best distinguished advanced adenoma from healthy control (HC) stool, with stool Fibrinogen topping the list with an ROC AUC value of 0.86, as detailed in Table 1. Functional pathway analysis revealed a significant over-representation of pathways related to anti-oxidant activity, integrin/receptor binding, cytokines, blood coagulation, and lipoprotein biosynthesis in patients with CRC compared to HC. Nuclear Factor IC (NFIC) and IKZF2 were identified as key regulators of the molecular cascades over-represented in CRC. Stool Fibrinogen, MMP-8, MMP-9, PGRP-S, Haptoglobin, and Myeloperoxidase emerge as promising biomarkers for distinguishing CRC/advanced adenomas/healthy stools, outperforming Hemoglobin. Thus, comprehensive proteomics and independent ELISA validation have uncovered novel stool biomarkers for identifying CRC and advanced adenomas, that warrant further head to head comparison against current diagnostic tests.
Citation Format: Chandra Mohan, Kamala Vanarsa, Jessica Castillo, Robert Bresalier, Nicholas Chia. 11,000-plex aptamer based proteomics of colorectal cancer stools for the discovery of novel disease biomarkers [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 1845.
Abstract 1860: The smallest antibody class: Cow ultralong CDR3 knobs as a new class of biomolecule for therapeutics and diagnostics
Authors: Smider Vaughn 
Published: March 2024

Abstract
Engineered antibodies, including bispecifics and ADCs, are now a major drug class for oncology and other therapeutic areas. There are two fundamental antibody fragments: the Fv (heavy and light chain variable region fragments, derived from most species), and VHH (heavy chain ‘only’ V regions, derived from camelids and sharks). Cows produce antibodies with an unusually long VH CDR3 region, which can be up to seventy amino acids in length and is comprised of a β-ribbon “stalk” and disulfide-bonded “knob” minidomain which sits atop the stalk. The knob region is highly diverse and can bind cryptic epitopes with high affinity. We recently developed the technology to produce knob domains independently of the antibody, and at ~5 kDa are the smallest functional antibody fragment (https://doi.org/10.1073/pnas.2303455120). The high stability and small size could enable improved tissue penetration and development of novel therapeutics, including knob-drug conjugates or extremely small bispecific molecules.
Citation Format: Vaughn Smider. The smallest antibody class: Cow ultralong CDR3 knobs as a new class of biomolecule for therapeutics and diagnostics [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 1860.
Abstract 1873: AST-05X: A novel GCN2 inhibitor as a promising anti-cancer approach for sarcoma
Authors: Choi Youngki , Lim Jinback , Park Hyo-Hyun , Kang Jinho , Kim Hyosong , Yun Kumhee , Jung Hun 
Published: March 2024

Abstract
Background Integrated stress response (ISR) is an adaptive signaling pathway that responds to stress and plays an important role in cell fate determination. This pathway enables cellular adaptation and survival under stress conditions by activating specific genes that reduce protein synthesis. Tumors exist in a state characterized by heightened intrinsic and extrinsic stress, heavily relying on a balanced ISR to manage the metabolic demands for rapid growth. ISR (Integrated Stress Response) consists of four major kinases: GCN2, PERK, HRI, and PKR. GCN2 is activated by stress due to amino acid deprivation. Amino acids are crucial for cell survival, and cancer cells, require higher amounts than normal cells, particularly depending on conditionally essential amino acids like glutamine, asparagine, and arginine. GCN2 activation acts as a key mechanism for cancer cells to overcome amino acid deficiencies, making GCN2 a potential target, especially in conjunction with anticancer drugs like asparaginase. In this study, we aimed to identify a potential GCN2 inhibitor to explore a promising anti-cancer approach in sarcoma, a rare cancer with no new therapeutic alternatives.
Method The activity verification of ISR kinases was characterized using in-vitro enzyme assays. In-vitro panel assays were employed to determine the selectivity profiling for oncology kinases. The modulation of the ISR pathway was validated using a sarcoma cell line (HT-1080) and a cell line derived from sarcoma patients. Western blot or ELISA assays were employed to measure phospho-GCN2, ATF4, phospho-eIF2a, and CHOP under both basal conditions and amino acid starvation conditions. Gene expression profiling (GEP) of sarcoma patient tissue samples(n=17) was conducted through RNA sequencing (RNAseq) analysis.
Results AST-05X is a selective and potent GCN2 inhibitor. AST-05X inhibits the expression of GCN2 and ISR downstream factors (p-eIF2a, ATF, CHOP) in vitro cell-based experiments under amino acid deprivation. In addition, based on the results of ISR-related gene expression profiling GEP analysis, we identified potential CDx biomarkers for evaluating the diagnosis and treatment response of sarcoma.
Conclusion This study is currently investigating the efficacy of the drug in sarcoma patient-derived xenograft models. AST-05X is a GCN2 inhibitor that has the potential to validate the inhibition of GCN2 as a promising anti-cancer approach for sarcoma, a rare cancer with limited therapeutic alternatives.
Citation Format: Youngki Choi, Jinback Lim, Hyo-Hyun Park, Jinho Kang, Hyosong Kim, Kumhee Yun, Hun Jung. AST-05X: A novel GCN2 inhibitor as a promising anti-cancer approach for sarcoma [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 1873.