tbuckley/cabot-search huggingface dataset:
Abstract 5717: CDK4 inhibition suppresses Rab11 mediated collective cell migration in colon cancer cells
Authors: Chun Pu Cheng, Chia-En Ku, Shin-Ru Lee, Yu-Chun Wang, Yu-Chien Ching, Hui-Chun Chen, Wei-Ting Chao
Journal: Cancer Research (2024)

Abstract In tumor progression, cell proliferation and cell adhesion are critical for tumor growth and metastasis. It has been demonstrated cell division which associated with microtubule organization also has impact on tubulin mediated focal adhesion turnover, however, the mechanism is not clear in the cell cohort migration which is accompanied with both cell proliferation and cell migration. This study is to investigate the effect of cell cycle inhibition in the collective cell migration. HT-29 colon cancer cells were treated with CDK4 inhibitor CINK4, paclitaxel and focal adhesion inhibitor PF573228. The cell proliferation rate was determined by MTT assay, cell migration ability was analyzed by wound healing assay. Rab11, E-cadherin and focal adhesion kinase were revealed by immuno-confocal microscopy. When HT-29 cells were treated with lower dose of CDK4 inhibitor CINK4, cell migration was suppressed. Meanwhile, in the result of immunostaining, the recycling endosomal protein Rab11which is involved in E-cadherin turnover in collective cell migration was not distributed in the cell membrane after CINK4 treatment. Furthermore, when cellular FAK activity were inhibited by PF573228 and tubulin disassembly was inhibited by paclitaxel, the cell area was increased with stable attachment, however, the membrane translocation of Rab11 was not affected. This study demonstrated cell cycle inhibition in G1 phase affected Rab11 mediated collective cell migration through tubulin regulated focal adhesion turnover for cell attachment. Keywords: CDK4, cell cycle, focal adhesion kinase, paclitaxel, colon cancer Citation Format: Chun Pu Cheng, Chia-En Ku, Shin-Ru Lee, Yu-Chun Wang, Yu-Chien Ching, Hui-Chun Chen, Wei-Ting Chao. CDK4 inhibition suppresses Rab11 mediated collective cell migration in colon cancer 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 5717.
Abstract 6689: Modulation of MAITs by the tumor microbiome in anti-PD1 treated cancers
Authors: Pakhi Birla, Lansaol Yang, Cynthia Sears, Fyza Shaikh, Drew Pardoll, Franck Housseau
Journal: Cancer Research (2024)

Abstract Mucosal associated invariant T (MAIT) cells are innate like T-cells that recognize non-peptide metabolite antigens presented on monomorphic MHC related-1 (MR1) making them an attractive off the shelf tool for cancer immunotherapy. In this study, we investigate the function of MAITs in the tumor microenvironment of neoadjuvant anti-PD1 treated lung cancer patients (NCT02259621)). Paired single cell RNA/TCR sequencing analysis revealed an oligoclonal expansion of MAITs comprising of canonical TRAV1-2+ and non-canonical MAITs TRAV1-2-. TCR capture from canonical MAIT clonotypes confirmed their in vitro recognition of 5-OP-RU, bacteria derived riboflavin derivative as well as MR1 dependent recognition of live bacteria present in the tumor. However, the nature of antigens recognized by non-canonical MAITs remains poorly understood. On mining transcriptional profiles of MAITs, we observed that canonical MAITs were characterized by high clonal amplification whereas the non-canonical clonotypes expressed a strong activation/exhaustion gene signature. This suggests that both these MAIT populations recognize different types of antigens, differentially activate, and respond to immune checkpoint blockade (ICB), the non-canonical MAITs being highly dysfunctional. Using bacterial 16S RNA amplicon and metagenomics sequencing, we seek to identify microbial and metabolomics signatures associated with MAIT activation and response to ICB. We identified MAITs to express a cytotoxic signature making them a potential target for cancer immunotherapy. Our findings will provide further insights into the nature of ligands recognized by MAITs and the mechanisms associated with MR1 dependent recognition and tumor killing. Investigating the role of unconventional T-cells in response to ICB has the potential to reveal new tumor-associated antigens which could open avenues into innovative combination immunotherapies. Citation Format: Pakhi Birla, Lansaol Yang, Cynthia Sears, Fyza Shaikh, Drew Pardoll, Franck Housseau. Modulation of MAITs by the tumor microbiome in anti-PD1 treated 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 6689.
Abstract 3367: R-loop type determines the orientation of transcription-replication conflicts attenuated by transcription factor IIS
Authors: Renée C. Duardo, Jessica Marinello, Marco Russo, Sara Morelli, Simona Pepe, Federico Guerra, Belen Gomez-González, Andrés Aguilera, Giovanni Capranico
Journal: Cancer Research (2024)

Abstract During human Topoisomerase I (Top1) catalytic activity, a transient Top1-DNA cleavage complex (Top1cc) forms to allow DNA relaxation. Top1ccs can be stabilized by antitumor Top1 poisons, such as clinically-effective camptothecin analogs. Camptothecin-stabilized Top1ccs can lead to R-loop-dependent transcription-replication conflicts (TRCs), single-end DNA double-strand breaks (seDSBs) and genome instability in cancer cells. To define the genomic location of TRCs and the underlying mechanisms, we integrated genomic maps of Top1cc-induced DNA cleavage by END-seq and DNA:RNA hybrids by DRIP, determined the cell-cycle specificity of micronuclei formation and the effects of elongation transcription factor IIS (TFIIS). We have defined the genomic sites of both seDSBs and increased R-loop levels (gains) induced by Top1ccs. seDSBs are highly enriched at regions with R-loop gains at highly-transcribed genes in early replicating zones. Kinetics analyses of R-loops and genomic ChIP data of RNA polymerase II (RNAPII) revealed that R-loop gains can either be upstream or downstream of RNAPII. TFIIS effects showed that downstream R-loop gains can follow RNAPII backtracking and arrest. seDSB strandness showed that co-directional TRCs occur mainly at downstream hybrid-associated RNAPII, whereas head-on TRCs occur mainly at upstream hybrid-associated RNAPII. Therefore, Top1ccs can increase two structurally-different R-loops and R-loop-associated backtracked RNAPII causes co-directional TRCs at higher rate than head-on collisions. Moreover, Top1ccs trigger micronuclei formation at G1/early S, but not late S/G2, which are attenuated by TFIIS. Thus, our findings establish a role of RNAPII backtracking at highly-transcribed genes in Top1cc-induced co-directional TRCs and micronuclei formation. The findings can accelerate the development of new effective strategies to treat cancer patients. (Supported by Associazione Italiana per la Ricerca sul Cancro, Milan, Italy - IG 2019 - ID. 23032 to C.G. and by the European Union - NextGenerationEU through the Italian Ministry of University and Research under PNRR - M4C2-I1.3 Project PE_00000019 "HEAL ITALIA" to G.C., CUP J33C22002920006). Citation Format: Renée C. Duardo, Jessica Marinello, Marco Russo, Sara Morelli, Simona Pepe, Federico Guerra, Belen Gomez-González, Andrés Aguilera, Giovanni Capranico. R-loop type determines the orientation of transcription-replication conflicts attenuated by transcription factor IIS [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 3367.
Abstract 2917: Purifying cancer-associated fibroblasts (CAFs) from glioblastoma and defining their role in therapeutic resistance
Authors: Ankita Sati, Aakriti Mathur, Meeki Lad, Atul Saha, Manish K. Aghi
Journal: Cancer Research (2024)

Abstract Glioblastoma (GBM), a challenging brain tumor, necessitates the development of new therapies due to poor patient prognoses, with a median survival of 14-16 months. Standard of care, as established almost 20 years ago, remains to be surgical resection followed by chemotherapy and radiation and till date there is no defined standard of care for recurrent GBM, highlighting the urgent need for the development of novel therapies. Recent studies have implicated the tumor microenvironment in these poor prognoses. While cancer associated fibroblasts (CAFs) are a key cellular component of the microenvironment of many systemic tumors, their presence in GBM had been doubted until we recently developed intriguing data identifying cells in GBM that express fibroblast markers, have fibroblast-like morphology, and, most importantly, transcriptomically resemble CAFs from systemic cancers rather than other stromal cells that express similar surface markers such as pericytes (Jain et al. 2023). Similar to other solid cancers, GBM CAFs increase tumor growth and drive immunosuppression. The role of CAFs in regulating these processes could have significant implications in response to standard of care therapy as well as novel immunotherapies. While our initial CAF isolation had just 50% purity, we have developed a novel flow-sorting algorithm for CAF enrichment driven by our bioinformatic data. Through this protocol, we have successfully established, the first of its kind, a biobank of patient derived GBM CAFs with greater than 90% purity. These CAFs are now being utilized to investigate their contribution in conferring resistance to chemotherapy (Temozolomide) and radiotherapy. The CAFs are also being assessed for their role in suppressing T cell function and resistance to immunotherapies. In parallel, the origin of GBM CAFs and their development trajectory is being analyzed to find molecular markers to specifically target CAFs in the GBM microenvironment. The work put together will provide insight on mechanisms employed by CAFs in altering the GBM microenvironment and a basis for developing novel combination approaches, alleviating therapeutic resistance caused due to the presence of CAFs in the GBM microenvironment. The results of this study have the potential to significantly attenuate therapeutic resistance in GBM and provide much needed treatment options and improvement in survival, for what remains one of the most dismal diagnoses in the clinic. Citation Format: Ankita Sati, Aakriti Mathur, Meeki Lad, Atul Saha, Manish K. Aghi. Purifying cancer-associated fibroblasts (CAFs) from glioblastoma and defining their role in therapeutic 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 2917.
Abstract 370: BACH1 metastatic activity is regulated by oxygen-dependent proline hydroxylation in triple-negative breast cancer
Authors: Thomas Li, Long Chi Nguyen, Christopher Dann, Madeline Henn, Dongbo Yang, Emily Shi, Lydia Robinson-Mailman, Kazuhiko Igarashi, Marsha R. Rosner
Journal: Cancer Research (2024)

Abstract Hypoxia, low oxygen availability at the tissue level, is a key driver of metastasis in solid tumors. Oxygen-sensitive activation of hypoxia-induced transcription factors is in part regulated by prolyl hydroxylase domain proteins (PHDs). We and others previously showed that the BTB and CNC homolog 1 (BACH1) transcription factor promotes metastasis in various cancer types. In accompanying work, we show that BACH1 is prolyl-hydroxylated and degraded in an oxygen-dependent manner in triple-negative breast cancer (TNBC). Here we show that BACH1 lacking its hydroxylated proline sites (i.e., mutant BACH1) expressed in TNBC cells exhibits increased DNA binding to a canonical BACH1 binding site as well as greater transcriptional output of metastasis and hypoxia-response-related genes relative to wild-type BACH1. Furthermore, in vivo assays showed that mutant BACH1 promotes greater tumor metastasis of TNBC cells than wild-type BACH1. Our findings suggest that the proline hydroxylation of BACH1 directly regulates BACH1’s transcriptional activity by modulating its DNA-binding activity. Together, these results reveal a mechanism underlying oxygen-sensitive regulation of BACH1 that could potentially contribute to BACH1-mediated pro-metastatic signaling and therapeutic resistance under hypoxia in TNBC. Citation Format: Thomas Li, Long Chi Nguyen, Christopher Dann, Madeline Henn, Dongbo Yang, Emily Shi, Lydia Robinson-Mailman, Kazuhiko Igarashi, Marsha R. Rosner. BACH1 metastatic activity is regulated by oxygen-dependent proline hydroxylation 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 370.
Abstract 3704: Whole genome and targeted proteome analysis of single cancer cells
Authors: Atieh Alyasin, Kathrin Weidele, Catherine Botteron, Christoph A. Klein, Zbigniew T. Czyż
Journal: Cancer Research (2024)

Abstract The simultaneous genome and proteome analysis of very rare single cells would enable addressing important biological and diagnostic questions particularly in cancer. Here, we introduce a novel genome and proteome (G&amp;P) analytic workflow, a method allowing comprehensive analysis of single-cell DNA and targeted profiling of protein expression in single cells. As a proof of concept, we demonstrate the capability of the method by quantifying copy number of the ERBB2 gene alongside with protein expression levels of HER2 and phospho-HER2 in single cells. The G&amp;P workflow utilizes antibodies conjugated with DNA oligonucleotides designed to enable their amplification alongside the single-cell genome facilitating parallel genome and proteome profiling by either quantitative PCR (qPCR) or sequencing. We utilized antibodies targeting cytokeratin 8/18/19, HER2 and phospho-HER (Tyr1248). Performance of each DNA-conjugated antibody was assessed by immunofluorescence staining in a variety of breast cancer cell lines (MDA-MB231, MDA-MB453, BT474 and MCF7) and sample types. Stained cells were isolated by manual micromanipulation and subjected to whole genome amplification (WGA). Protein expression levels, derived from quantification of the amplified DNA tags, were measured by qPCR. Shallow whole genome sequencing was employed to facilitate genome-wide profiling of copy number variations (CNVs), including the ERBB2 locus. We successfully developed and tested a G&amp;P workflow allowing parallel genome-wide CNV profiling and quantification of three target proteins. G&amp;P measurement yielded concordant results to immunofluorescence quantification for all tested markers. Furthermore, the workflow allowed direct correlation of copy numbers of the ERBB2 gene with HER2 expression in single cancer cells. Notably, the method enabled measurements of cellular and molecular responses at the single-cell level to lapatinib treatment, i.e. monitoring of the HER2 pathway activation level. Our novel multiplex G&amp;P technique is capable of generating multiparametric measurements linking DNA copy numbers and expression levels of selected genes of interest. The method is optimized for analysis of single cells from rare cell populations and is readily translatable to study circulating tumor cells (CTCs) and disseminated cancer cells (DCCs), enabling for the first time pathway analysis via phosphoprotein analyses of these cells. Citation Format: Atieh Alyasin, Kathrin Weidele, Catherine Botteron, Christoph A. Klein, Zbigniew T. Czyż. Whole genome and targeted proteome analysis of single cancer 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 3704.
Abstract 3725: Exosomal Galactin-3 promotes pre-metastatic niche formation that accelerates peritoneal metastases of gastric adenocarcinoma
Authors: Yibo Fan, Shumei Song, Melissa Pool Pizzi, Katsuhiro Yoshimura, Jody V. Vykoukal, Samir Hanash, Jaffer Ajani
Journal: Cancer Research (2024)

Abstract Peritoneal carcinomatosis (PC) in gastric adenocarcinoma (GAC) lead to a short median survival (≤6 months). Pre-metastatic niche (PMN) formation, in a distant organ to prepare for tumor seeding and colonization, has long been recognized. However, the precise molecular and mechanistic contributions of exosomes in PMN formation of PC remain unclear. We identify that exosomes promote PMN formation in the peritoneal cavity by patient-derived orthotopic mouse model. Using an in-depth proteomic profiling of paired ascites cells and ascites-derived exosomes from PC patients, we discover that Galectin-3 as the exosomal payload is responsible for PC by promoting PMN formation in both patient-derived orthotopic model and syngeneic mouse model. Inhibition of exosomal Galectin-3 reverses PC. Furthermore, exosomal Galectin-3 activates cancer-associated fibroblasts (CAFs), which further activate the CXCL12/CXCR4 axis to orchestrate the immunosuppressive PMN. Simultaneous inhibition of exosomal Galectin-3, CXCR4, and PD-1 leads to tumor regression and durable anti-tumor responses. Thus, this study provides a rationale for the novel clinical strategy for GAC patients with PC. Citation Format: Yibo Fan, Shumei Song, Melissa Pool Pizzi, Katsuhiro Yoshimura, Jody V. Vykoukal, Samir Hanash, Jaffer Ajani. Exosomal Galactin-3 promotes pre-metastatic niche formation that accelerates peritoneal metastases of gastric adenocarcinoma [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 3725.
Abstract 2689: Mass cytometry analysis of CXCR3 expression in tumor-infiltrated myeloid cells as a predictive biomarker For immunotherapy response
Authors: Gabriel A. Valentin-Guillama, Nandini Chatterjee, Ahmad Alimadadi, Catherine C. Hedrick
Journal: Cancer Research (2024)

Abstract Monocytes have emerged as important regulators of cancer progression. We have recently found that CXCR3+ circulating monocytes in humans are associated with better response to immunotherapy. Here, we aimed to study the functions and heterogeneity of CXCR3+ monocytes in two different triple negative breast cancer (TNBC) tumors in mice, using either AT3 or EO771 tumor cell lines. AT-3 tumors exhibit higher resistance to anti-PD-1 and anti-CTLA-4 therapy in C57BL/6 breast cancer mouse models compared to EO771 tumors. We evaluated 36 surface protein markers on tumor-infiltrated myeloid cells in tumors isolated from each model using CyTOF mass cytometry. Analysis of monocytes, macrophages and dendritic cells in the tumors using unsupervised clustering identified 13 cell subsets. Significant differences were discovered between the two tumor types in frequencies of nine of 13 identified subsets. However, 3 of these subsets displayed relatively high expression of CXCR3 in EO771 tumors when compared to AT-3 tumors. The significant CXCR3 positive subsets were identified as CXCR3+ early macrophages, CXCR3+ Ly6C+CD11blo classical monocytes and Trem2+ CXCR3+ dendritic cells. We observed higher expression of CXCR4, Trem2, and CCR1 in CXCR3+ myeloid cells when compared to their CXCR3− counterparts in both tumor models. To elucidate the role of these CXCR3+ cells, we performed low-input bulk RNA sequencing of CD115+/CD11b+ cells from blood and spleen of EO771 tumor bearing mice with a wild type or CXCR3KO genotype. Ingenuity Pathway Analysis (IPA) of the differentially expressed genes suggests a significant inhibition of the IL-10 signaling pathway of CXCR3KO cells. These differentially expressed markers and genes suggest a functional importance in this subset in migration to the tumor and antigen presentation, both of which are anti-tumoral functions. Ongoing studies are aimed towards understanding the role of CXCR3+ myeloid cells in regulating response to immunotherapies. Citation Format: Gabriel A. Valentin-Guillama, Nandini Chatterjee, Ahmad Alimadadi, Catherine C. Hedrick. Mass cytometry analysis of CXCR3 expression in tumor-infiltrated myeloid cells as a predictive biomarker For immunotherapy response [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 2689.
Abstract 2265: Distinct alternative splicing patterns in genetic subtypes of diffuse large B-cell lymphoma
Authors: Sanyeowool An, Youngil Koh, Sung-Soo Yoon
Journal: Cancer Research (2024)

Abstract Advances in sequencing techniques have made molecular subgrouping of Diffuse Large B-cell Lymphoma (DLBCL) based on DNA cahnges, which has led to the development of Lymphgen classification. By the way, although alternative splicing (AS) in cancer cells contributes to proliferation, invasion and metastasis, and immune escape, their role and association with DLBCL molecular subtypes are unknown. Therefore, we analyzed whole-exome sequencing (WES) and bulk RNA-Seq data paired in the public EGA dataset (EGAD00001003600) to explore the patterns of AS events that differ between Lymphgene subtypes. The WES data of 620 DLBCL samples that passed quality control were aligned to the reference using BWA-MEM, and variants were called with Mutect2. We used the information of copy number variants provided by cBioPortal. The RNA-Seq analysis was performed using the STAR-RSEM pipeline and differential splicing events were detected using rMATS to compare subtypes. Among 620 DLBCL samples, there were 19 MCDs, 95 EZBs, 22 BN2s, and 137 ST2s (50 samples with multiple genetic classes, and 291 samples unclassified). Mutations in spliceosome complex genes (ZRSR2 and SF1) were found in 14 and 27 samples, respectively. In BN2 and MCD subtypes, splicing events with significantly different exon inclusion levels were observed at a high frequency of 29 and 16 occurrences, respectively, compared to other subtypes. (P-value &amp;lt; 0.05). In contrast, retained intron is the only event observed in the EZB subtype (Table 1). Samples with mutations in ZRSR2 and SF1 showed four and two aberrant events, respectively, compared to samples without these mutations. Of note, rMATS detected an alternative 3’ splice site event in exon 6 of CD37 in the MCD. CD37 is involved in tumorigenesis in leukocytes and has been suggested as a potential biomarker in blood cancer, and its dysregulation may have influenced the poor prognosis of MCD. In summary, molecular subtypes of DLBCL had unique features in terms of alternative splicing. Functional consequences of these selective exon usages for each DLBCL subtype are being warranted. Citation Format: Sanyeowool An, Youngil Koh, Sung-Soo Yoon. Distinct alternative splicing patterns in genetic subtypes of diffuse large B-cell lymphoma [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 2265.