tbuckley/cabot-search huggingface dataset:
Abstract 1498: TGFβ signaling in cancer-associated fibroblasts drives a hepatic gp130-dependent pro-metastatic inflammatory program in CMS4 colorectal cancer
Authors: Subinuer Abudukelimu, Tom J. Harryvan, Stef G. Janson, Imke Stouten, Els M. Verdegaal, Lukas JAC Hawinkels
Journal: Cancer Research (2024)

Abstract Background: Colorectal cancer (CRC) is characterized by a metastatic pattern that shows tropism towards the liver which is the major cause of CRC-related deaths. The current CRC classification, Consensus Molecular Subtypes (CMS), suggests an association between transforming growth factor (TGF)-β signaling, cancer-associated fibroblasts (CAFs), and the risk of liver metastasis. However, the key downstream effectors of TGFβ signaling in CAFs and their role in hepatic metastases remain poorly understood. Methods: The aim of this study was to investigate the TGF-β/CAF dependent cross talk with the hepatocytes in pre-metastatic niche formation. CAFs from 18 primary CRC tissues and 7 liver-metastasized CRC were stimulated with TGFβ1 and qPCR arrays/ELISAs were performed to identify differentially expressed genes. Results were cross-referenced with RNAseq expression data of CMS-classified CRC and in fresh samples from CRC patients. To investigate CAF-liver crosstalk hepatocytes were stimulated with the TGFβ primed CAF-derived cytokines and the effect on pro-inflammatory gene expression and neutrophil migration was determined. Subsequently, blockade of these pathways via chemical inhibition and CRISPR/Cas9 genetic ablation was performed to study the molecular mechanism involved in the induction of this hepatic pro-inflammatory program. Results: TGFβ signaling in primary CRC-derived CAFs leads to increased expression of different IL-6 cytokine family members, which was also reflected in human CRC samples. CAF-derived IL6 family members induce upregulation of myeloid chemoattractants, including SAA1, in hepatocytes and increased neutrophil-to-hepatocyte migration in vitro. Chemical blockade and genetic ablation of the IL-6 family cytokine signaling pathway showed the critical role of the gp130 co-receptor in the regulation of this inflammatory response in hepatocytes and the potential formation of a premetastatic niche. Conclusion: TGFβ signaling in CAFs actively contributes to the formation of a neutrophil-dependent, pre-metastatic hepatic niche, and this mechanism might play a role in CMS4 subtype CRC. Citation Format: Subinuer Abudukelimu, Tom J. Harryvan, Stef G. Janson, Imke Stouten, Els M. Verdegaal, Lukas JAC Hawinkels. TGFβ signaling in cancer-associated fibroblasts drives a hepatic gp130-dependent pro-metastatic inflammatory program in CMS4 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 1498.
Abstract 2940: A comparative analysis of library preparation technologies for RNA sequencing from FFPE samples
Authors: Jennifer Pavlica, Travis Sanders, David Gelagay, Kailee Reed, Thomas Harrison, Giulia Corbet, Josh Haimes, Ariele Hanek, Kristina Giorda, Brian Kudlow
Journal: Cancer Research (2024)

Abstract Formalin-fixed, paraffin-embedded (FFPE) samples are an invaluable resource in the oncology space, providing access to a vast library of archived diseased tissue samples paired with relevant donor information. Despite the broad utility of these samples, RNA extracted from FFPE tissue is typically difficult to process due to the presence of residual crosslinks and its degraded nature. Further, these samples often vary widely in performance, as the fixation process, block age, block storage, and extraction method can impart large impacts on resulting template quality. As a result, robust and reproducible RNA sequencing from FFPE-derived RNA remains a challenge with unpredictable and high failure rates. We evaluated four commercially available WTA solutions to determine which performed best with this challenging sample type with respect to library complexity, inter-input and intra-sample concordance, and overall reproducibility. Matched fresh frozen and FFPE liver samples were used such that the fresh frozen data set serves as a comparative truth set for the FFPE data. RNA-Seq libraries were prepared from each sample at both 10 ng and 100 ng inputs. The higher input serves as a control while the lower input reflects achievable inputs from very challenging FFPE samples. For 10 ng FFPE-derived RNA, the Watchmaker RNA Library Prep Kit with Polaris Depletion detects more unique genes than other chemistries and has a much higher percentage of genes that overlap with the fresh frozen control libraries. Additionally, differential expression analysis between 10 ng and 100 ng FFPE libraries demonstrates that the Watchmaker solution better preserves the gene expression profile at low inputs, as fewer differentially expressed genes are identified. The Watchmaker chemistry includes a number of features aimed at improving library complexity, including a novel FFPE decrosslinking step, a reverse transcriptase specifically engineered to improve conversion of RNA to cDNA, and fewer bead purification steps to prevent sample loss. The concordance between FF and FFPE samples at variable input masses observed when using the Watchmaker solution promotes a higher degree of confidence when making decisions based on lower quantity and quality samples and enables researchers to access more meaningful biological information. Citation Format: Jennifer Pavlica, Travis Sanders, David Gelagay, Kailee Reed, Thomas Harrison, Giulia Corbet, Josh Haimes, Ariele Hanek, Kristina Giorda, Brian Kudlow. A comparative analysis of library preparation technologies for RNA sequencing 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 2940.
Abstract 293: Distinctive roles of mammary adipomes in breast cancer progression: Insights from functional analysis and differential gene expression
Authors: Hariprasad Thangavel, Kezia Lizardo, Robert I. Glazer, Jyothi F. Nagajyothi
Journal: Cancer Research (2024)

Abstract Breast Cancer (BC) is a heterogeneous disease that impacts treatment response. This is due in part to the tumor microenvironment (TME), which contributes significantly to BC pathogenesis, including metastasis. Women with higher breast density and reduced breast fat face an increased BC risk across multiple tumor subtypes. This is exemplified by the correlation between increased tumor progression, the appearance of fibrosis and the loss of mature adipocytes. While the role of adipokines in this process has been studied extensively, the contribution of adipocyte-derived extracellular vesicles (EV) or "adipomes" in tumorigenesis and metastasis remains poorly understood. To address this question, we developed a novel technique for isolating intact adipomes from normal mammary fat (MF) obtained from wild-type C57BL/6 mice as well as from tumor-associated MF (TAMF) obtained from mice inoculated orthotopically with EO771 mammary tumor cells. Adipome isolation involved high-speed centrifugation to separate macro- and micro-vesicles, purification using the ExoQuick EV isolation system, and immunomagnetic capture of adipomes. Characterization of adipomes by transmission electron microscopy revealed two adipome populations, large L-adipomes of ~350 nm, and small S-adipomes of ~40 nm. Notably, the quantity of L-adipomes in tumor-associated mammary fat (TAMF) was 10-fold greater than the amount of L-adipomes in the MF of non-tumor-bearing mice. To identify possible functional roles of L-adipomes in the pathogenesis of BC, lipidomic profiling was undertaken. L-Adipomes from TAMF showed significantly altered lipid species in comparison to MF-derived L-adipomes. Adipomes were further characterized by treating EO771 cells for 72 hr with TAMF- or MF-derived adipomes at a cell to adipome ratio of 1:10, followed by RNAseq analysis. Differentially upregulated genes in TAMF-derived L-adipomes included Esr1, Erbb2, Tgfb1, Bcl2, MMP2, and Notch associated with fibrosis, EMT, angiogenesis and invasion and downregulation of genes linked to tumor suppression, apoptosis, and mitochondrial metabolism. Overall, our study illustrates the importance of tumor-associated adipomes in regulating gene expression in tumor cells, which emphasizes the specificity of adipome content relating to the cell-of-origin and the host's pathologic and metabolic state and in modulating signaling pathways involved in BC progression. Citation Format: Hariprasad Thangavel, Kezia Lizardo, Robert I. Glazer, Jyothi F. Nagajyothi. Distinctive roles of mammary adipomes in breast cancer progression: Insights from functional analysis and differential gene expression [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 293.
Abstract 17: Metabolic screening of T cells guides the enrichment of stem cell memory phenotype
Authors: Anthony Lauer, Natasha Karassina, Kayla Sylvester, Jolanta Vidugiriene
Journal: Cancer Research (2024)

Abstract The efficacy of T cell-mediated immunotherapy is improved by the proliferation of T cells with a stem cell memory phenotype (Tscm). These cells are capable of long-term persistence, self-renewal, multipotency, and robust engagement with cancer cells. This study focuses on refining T cell activation protocols to bolster the presence of Tscm within the therapeutic arsenal against cancer. Through a series of cell health and metabolic assays, we traced the activation-induced metabolic reprogramming that results from Tscm enrichment. Ex vivo activation was characterized by a rapid 2.5-3 fold increase in ATP production and a 2 fold shift in intracellular reducing potential, paralleling the metabolic demands of Tscm in the cancer microenvironment. Progression of activation intensified the metabolic flux through catabolic and anabolic pathways, with significant fluctuations in metabolites such as glucose, lactate, glutamine, glutamate, branched chain amino acids, and pyruvate. These metabolic alterations were accompanied by a 2 fold increase in the prevalence of Tscm cells, and demonstrated a dependency on media composition. Our findings reveal that metabolic profiling during T cell activation provides early and actionable insights into the enrichment of Tscm, and may serve as a strategic guideline for the enhancement of cancer immunotherapies. Citation Format: Anthony Lauer, Natasha Karassina, Kayla Sylvester, Jolanta Vidugiriene. Metabolic screening of T cells guides the enrichment of stem cell memory phenotype [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 17.
Abstract 7607: Single-cell genomics study before and after neoadjuvant therapy for triple-negative breast cancer
Authors: Yingkuan Shao, Kailun Xu
Journal: Cancer Research (2024)

Abstract Breast cancer has become the most common malignant tumor globally. Neoadjuvant chemotherapy (NAC) has become an important treatment option for locally advanced breast cancer, capable of eliminating circulating tumor cells (micrometastases) and achieving downstaging objectives. However, even after completing neoadjuvant chemotherapy or receiving local treatment, some patients may still have residual lesions, which are a key factor in distant recurrence and metastasis. The existing clinical biomarker tests such as CEA, CA-153, and imaging methods are unable to accurately assess the condition early on. Although tissue pathology biopsy of tumor specimens is the gold standard for clinical pathological diagnosis, it also has certain limitations. Traditional high-throughput sequencing technology for breast cancer primarily identifies "driver genes" associated with the occurrence and development of breast cancer. However, it has limitations in identifying genomic structural changes and subclones of breast cancer, and it overlooks the heterogeneity among tumor cells. The emergence of single-cell RNA sequencing (scRNA-seq) technology can detect these heterogeneous individuals, decode the heterogeneity of breast cancer cells, refine molecular subtypes, and open up new pathways to overcome drug resistance. We collected samples from 6 patients with locally advanced triple-negative breast cancer (ER-, PR-, HER2-negative, defined as HER2 immunohistochemistry 0, 1+ or 2+ but FISH-negative). We compared the cell subgroups and their gene expression in biopsy specimens before neoadjuvant chemotherapy with those in post-treatment specimens obtained during surgery, analyzing changes in cell composition in the tumor microenvironment before and after immunotherapy to identify specific cell types potentially contributing to the outcome of immunotherapy, particularly cell subtypes associated with T-cell clonal proliferation. We found that in the group with good neoadjuvant treatment response (Miller-Payne grade 4-5), B cells, CD4+ T cells, CD8+ T cells, and Tregs cells were all significantly downregulated, while endothelial cells and aSMA-positive fibroblast cells were significantly upregulated. By comparing changes in the immune microenvironment between patients with and without T-cell clonal proliferation before and after treatment, we revealed the differentiation patterns of various immune cells in immunotherapy and potential mechanisms of action. Citation Format: Yingkuan Shao, Kailun Xu. Single-cell genomics study before and after neoadjuvant therapy for 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 7607.
Abstract 1499: Senescent stromal cells drive lung metastases of breast cancer
Authors: Anupama Melam, Jiayu Ye, Sheila A. Stewart
Journal: Cancer Research (2024)

Abstract In 2022 in the United States, there were nearly 300,000 women diagnosed with breast cancer (BC) with the risk increasing significantly after age 50. The overall 5-year survival rate dramatically decreases, from 99% for patients with stage I, to a devastating 25% for those with stage IV (metastatic) BC, making distal metastasis the leading cause of BC mortality. This mortality rate has not changed in decades with lungs being one of the most common sites for distal metastasis of BC. The BC microenvironment is a complex mix, consisting of tumor cells and numerous nontumor cells including distinct subpopulations of cancer-associated fibroblasts (CAFs): vascular (vCAFs), inflammatory (iCAFs), and myofibroblastic CAFs (myCAFs), which can play pro- or anti-tumor roles. Senescent fibroblasts, which accumulate with age typically express p16INK4A and can modulate the cells around them via the secretion of a cadre of pro-tumorigenic factors including cytokines, chemokines, and extracellular matrix (ECM) modulating enzymes, collectively called the senescence-associated secretory phenotype (SASP). To investigate how p16+ senescent cells impact tumorigenesis, we mated the well-characterized MMTV-PyMT mouse, to the INK-ATTAC (INK) mouse, wherein treatment with AP20187 (AP) selectively eliminates p16+ senescent cells. Preliminary data showed that elimination of p16+ aSMA+ senescent fibroblasts (senCAF) resulted in a significant decrease in primary tumors, lung tumor foci and lung metastatic burden. Further, we found that senescent CAFs (senCAFs) were the only stromal cells eliminated in the PyMT-INK mouse treated with AP, suggesting that this CAF subtype is a key contributor to tumor progression. To determine if senCAFs directly impacted lung metastasis, EO771-LG Luc mammary tumor cells were injected in the tail vein of INKATTAC mice that were treated with AP to eliminate p16+ senCAFs. We found that metastatic tumor burdens were significantly reduced in INK+ versus control mice and immunohistochemical analysis revealed that tumor burden and foci was significantly reduced, suggesting that senCAFs in the lung promoted tumor cell seeding and outgrowth. Citation Format: Anupama Melam, Jiayu Ye, Sheila A. Stewart. Senescent stromal cells drive lung metastases of 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 1499.
Abstract 2939: Harnessing <i>in vivo</i> CRISPR screen to uncover metabolic dependencies during cancer progression
Authors: Seow Qi Ng, Zhengwei Wu, Jessica A. Lidster, Wai Leong Tam
Journal: Cancer Research (2024)

Abstract Triple-negative breast cancer (TNBC) is the most aggressive subtype of breast cancer, with the worst prognosis and limited treatment options. TNBC cells undergo metabolic reprogramming in response to nutrient limitations and changes in the tumor microenvironment throughout cancer progression. In the early stages, tumor cells are found to prioritize nutrient uptake and biosynthesis, but as they grow, intensified competition for nutrients fosters the emergence of subpopulations of cancer cells that excel in utilizing specific nutrients. The substantial metabolic pathways and genes that regulate each phase of cancer progression remain poorly understood. To address this, we have developed a stable integration, site-specific, and inducible CRISPR-Cas9 system that allows for temporal control of genetic perturbation. We conducted an unbiased in vivo loss-of-function CRISPR screen aimed at identifying metabolic vulnerabilities at different phases of cancer progression of TNBC. The inducible CRISPR system was activated only at the desired study period of each phase, thus capable of uncovering metabolic dependencies for TNBC proliferation at each distinct phase of cancer progression. As many large-scale CRISPR screens have previously been performed to identify gene dependencies for cancer progression in vitro, our CRISPR screen could address the shortcomings of in vitro screens by identifying novel essential metabolic genes that are significantly important for cancer growth in vivo. Preliminary data from our CRISPR screen revealed different pathways to be significantly important for tumor growth and proliferation at different phases of TNBC progression. For example, we find that ferroptosis is altered during the early lag phase of TNBC cancer progression, whereas, at the later stage of cancer progression, metastatic tumors upregulate serine metabolism, suggesting that secondary tumors could have distinct metabolism from the primary sites. Altogether, the findings from this study could provide valuable insights into stepwise metabolic dependencies arising from microenvironmental limitations and identify potential therapeutic targets at each phase of cancer progression. Moreover, our CRISPR-Cas9 model holds promise for dissecting the complex mechanisms of other cancer progressions. Citation Format: Seow Qi Ng, Zhengwei Wu, Jessica A. Lidster, Wai Leong Tam. Harnessing in vivo CRISPR screen to uncover metabolic dependencies during cancer progression [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 2939.
Abstract 1885: Developing a biparatopic anti-ROR1 antibody drug conjugate BR111 for hematological and solid tumor treatment
Authors: Xiaobei Zhao, Jie Zhu, zhenhua Wu, Yiqun Li, Jing Li, Yaqiong Zhou, Lei Nie, Haibin Wang, Gang Chen
Journal: Cancer Research (2024)

Abstract ROR1 is a type I transmembrane protein that belongs to the ROR family. It is a receptor for Wnt family signaling molecules Wnt5a, and plays a critical role in various cellular processes, such as cell proliferation, survival, and migration. Being an oncofetal protein, ROR1 exhibits limited expression in most normal tissues. However, it is abnormally expressed in various hematological and solid cancers, contributing to the development and progression of many types of cancer. Due to its overexpression in cancer, ROR1 presents as a highly attractive target for antibody-drug conjugate (ADC) therapy. The current clinical results of ROR1 ADCs have been promising in treating patients with relapsed and/or refractory (R/R) hematologic malignancies. BR111 is anti-ROR1 ADC that consists of a biparatopic antibody, stably conjugated to an antimitotic agent. The biparatopic antibodies demonstrate superior binding affinity to ROR1-expressing cancer cells compared to single epitope antibodies. Notably, our unique and innovative conjugation platform CysX™, not only prevents payload detachment during circulation and reducing the off-target toxicity, but also enables a uniformed drug-to-antibody ratio (DAR) of 4. Both in vitro and In vivo studies have highlighted the remarkable antitumor activity of BR111. Preclinical data have shown great safety profile in cynomolgus monkeys. BR111 demonstrated a wider therapeutic window for cancer treatment, outperforming the lead anti-ROR1 ADC currently in phase II/IIl trial. The promising outcome holds great potential as a therapeutic treatment for hematological and solid cancers, offering a better safety profile. BR111 has great potential in further clinical evaluations. Citation Format: Xiaobei Zhao, Jie Zhu, zhenhua Wu, Yiqun Li, Jing Li, Yaqiong Zhou, Lei Nie, Haibin Wang, Gang Chen. Developing a biparatopic anti-ROR1 antibody drug conjugate BR111 for hematological and solid tumor treatment [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 1885.