bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract IA019: Regulation of EMT tumor states by stromal cells
Authors: Blanpain Cédric 
Published: November 2024

Abstract
Epithelial-to-mesenchymal transition (EMT) is a reversible process during which epithelial cells lose their epithelial characteristics and acquire mesenchymal features, that are important for tumor initiation, progression, stemness, metastasis, and therapy resistance. Different EMT states, each with distinct functional properties, have been identified across various tumor models. These EMT states reside within specific physical niches, characterized by unique stromal cell populations. Understanding the cellular interactions within the tumor microenvironment (TME) and their influence on EMT could lead to novel therapeutic strategies. To understand how the TME regulates the distinct tumor states, we performed single-cell RNA sequencing of the tumor cells and their TME in mouse cancer models presenting EMT. We identified distinct subsets of cancer-associated fibroblasts (CAFs), macrophages, neutrophils, endothelial cells, pericytes, adipocytes, dendritic cells, mast cells, Schwann cells, and T cells in different tumor types. To unravel how TME-tumor cell interactions regulates EMT, we used different bioinformatic approaches to identify ligand-receptor pairs that are likely to organize the tumor niche and to regulate tumor transition states. In vitro treatment of tumor cells with some of these ligands demonstrated their EMT-promoting effects. These findings provide novel mechanistic insights on the crosstalk between tumor cells and the surrounding TME, that may have important implications for anti-cancer therapy.
Citation Format: Cédric Blanpain. Regulation of EMT tumor states by stromal cells [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Tumor-body Interactions: The Roles of Micro- and Macroenvironment in Cancer; 2024 Nov 17-20; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2024;84(22_Suppl):Abstract nr IA019.
Abstract IA027: Age-related stromal changes drive breast cancer tumor progression
Authors: Stewart Sheila A. 
Published: November 2024

Abstract
Age is the single largest risk factor for the development of cancer, but how age impacts the molecular mechanisms that drive cancer remain poorly understood. While it is clear that age-related accumulation of cell autonomous mutations contributes to tumorigenesis, the central role age-related changes in the tumor microenvironment play in the transformation process is becoming more fully appreciated. Underscoring the importance of an aged microenvironment in cancer development are findings that senescent fibroblasts, which accumulate with age, directly stimulate preneoplastic and neoplastic cell growth and tumor progression. Investigations into how senescent fibroblasts promote tumorigenesis revealed that they express a plethora of growth factors, extracellular matrix remodeling enzymes, chemokines, and cytokines collectively referred to as the senescence associated secretory phenotype (SASP). Chemotherapy induces similar changes that can negatively impact a patient’s quality of life. We will discuss how these changes impact tumor progression and therapy-induced bone loss.
Citation Format: Sheila A. Stewart. Age-related stromal changes drive breast cancer tumor progression [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Tumor-body Interactions: The Roles of Micro- and Macroenvironment in Cancer; 2024 Nov 17-20; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2024;84(22_Suppl):Abstract nr IA027.
Abstract PR004: Age-induced chronic accumulation of glucocorticoids drives therapy resistance in lung cancer
Authors: Raizada Devesh , Lazure Felicia , Drapela Stanislav , Sarigul Nadir , Tejero Joanne , Ilter Didem , Da Silva Gomes Ana 
Published: November 2024

Abstract
Non-small cell lung cancer (NSCLC), a highly aggressive cancer, is the leading cause of cancer- related deaths in the U.S. While chemotherapy and targeted therapy are the main treatment modalities in the clinic, many patients do not respond to these treatments. Strikingly, the median age for lung cancer diagnosis is 71. Yet, preclinical and clinical research have largely been skewed towards young mice and patients. Here, we address this gap in knowledge and evaluate if old age affects the response to standard of care NSCLC therapies in KRAS-driven NSCLC. Using human sera from young and old healthy subjects to treat NSCLC cell lines, we show that age-driven circulatory changes are sufficient to drive a state of profound resistance to both chemotherapies as well as KRASG12C targeted therapies. We confirmed the relevance of our findings in vivo, by transplanting cancer cells derived from the K-rasLSL-G12D/+; p53fl/fl genetically engineered mouse model of lung cancer into young and old C57BL/6 mice. Using this model we showed that unlike young lung tumor-bearing mice on chemotherapy, old tumor-bearing mice do not respond to treatment and have a poor prognosis. Mechanistically, we found that old age drives a transcriptional reprogramming that favors drug resistance and identified the glucocorticoid receptor as a major driver of these transcriptional changes. We traced this to an age-induced chronic accumulation of glucocorticoids in circulation and within the tumor interstitial fluid. Chronic treatment with age-relevant concentrations of cortisol alone was sufficient to drive glucocorticoid receptor activation and induce resistance to therapies mirroring the effects of old age. Further supporting a driving role for glucocorticoids in driving age- induced drug resistance, blocking the glucocorticoid receptor genetically or pharmacologically rescues the drug resistance state imposed by old age in NSCLC cells. Lastly, using TCGA patient data we show an inverse correlation between glucocorticoid receptor activation (GR score) and progression-free survival of lung cancer patients. Together, our work demonstrates a role for age-induced glucocorticoids in circulation in promoting therapy-resistance in NSCLC patients and supports the use of therapeutic agents that block the glucocorticoid receptor as a strategy to increase therapy efficacy in NSCLC patients.
Citation Format: Devesh Raizada, Felicia Lazure, Stanislav Drapela, Nadir Sarigul, Joanne Tejero, Didem Ilter, Ana Da Silva Gomes. Age-induced chronic accumulation of glucocorticoids drives therapy resistance in lung cancer [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Tumor-body Interactions: The Roles of Micro- and Macroenvironment in Cancer; 2024 Nov 17-20; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2024;84(22_Suppl):Abstract nr PR004.
Abstract PR005: Adiponectin inhibits high-fat diet feeding-induced tumor growth through restoration of anti-tumor activity of exhausted-CD8+ T cells
Authors: Nguyen Kem Thi , Park Hoon Pil 
Published: November 2024

Abstract
There is a growing appreciation that obesity is one of the significant risk factors for the development of various types of cancers. Obesity has been shown to dysregulate the immune system, including alteration of immune population in tumor microenvironments (TME) and dysfunction of immune cells. Recent studies have also indicated that obesity induces dysregulation of hormones and cytokines production by adipose tissue, collectively called adipokines. Among them, downregulation of adiponectin is implicated in various types of diseases related to obesity. In this study, we examined the effect of adiporon, an adiponectin receptor agonist, on high-fat diet (HFD) feeding-induced breast tumor growth, and population and function of immune cells in the tumor microenvironment (TME) of obese mice. Adiporon significantly inhibits HFD-acceleration of breast tumor growth and restores the dysregulation of immune population in TME. In following experiments to elucidate the underlying mechanisms, we also found that treatment with adiporon protects CD8+ T lymphocyte from apoptosis induced by treatment with cancer cell culture media (CM) and palmitic acid (PA), while reducing various features of exhausted T cell, such as downregulation of PD-1 and Tim-3 expression and restoration of cytokine-production in CD8+ T cell. Treatment with globular adiponectin generates essentially similar effects, collectively indicating the positive effects of adiponectin on survival and function of exhausted CD8+ T cells. In addition, we found that stimulation with adiporon increased mitochondrial biogenesis and modulates mitophagy in CD8 + T cell exposed to CM and PA. In summary, adiponectin signaling restores the survival and anti-tumor activity of exhausted CD8+ T cells through modulation of mitochondrial homeostasis.
Citation Format: Kem Thi Nguyen, Hoon Pil Park. Adiponectin inhibits high-fat diet feeding-induced tumor growth through restoration of anti-tumor activity of exhausted-CD8+ T cells [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Tumor-body Interactions: The Roles of Micro- and Macroenvironment in Cancer; 2024 Nov 17-20; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2024;84(22_Suppl):Abstract nr PR005.
Abstract PR009: FMRP upregulation in cancer: Implicating FMRP-expressing cancer-associated fibroblasts in immune evasion
Authors: Yucel Simge , Fournier Nadine , Gomez Mireia Blanco , Hanahan Douglas 
Published: November 2024

Abstract
Our research has uncovered a novel and significant role for Fragile-X-mental-retardation-protein (FMRP) in cancer biology, extending its well-established functions beyond neuronal development. In a recent Science publication (Zeng et al., 2022), we demonstrated that elevated FMRP levels drive immune evasion in various murine and human tumors by modulating immune cell subsets, particularly through the suppression of effector T-cells. To further elucidate the mechanisms of FMRP-mediated immune evasion, we investigated its influence on the stromal component of the tumor microenvironment. Single-cell RNA sequencing of pancreatic ductal adenocarcinoma (PDAC) tumors revealed cancer-associated fibroblasts (CAFs) as the primary stromal cell subtype expressing FMRP. Given the crucial roles that CAFs play in tumor progression and therapeutic resistance, we explored whether FMRP expression contributes to the immunosuppressive characteristics of CAFs in PDAC and breast tumors. Our findings reveal that FMRP expression is markedly upregulated in CAFs from both breast and PDAC tumors, in contrast to its absence in naïve fibroblasts from healthy tissues. Knockdown of FMRP in CAFs resulted in substantial changes in their myofibroblastic and inflammatory properties, while overexpression of FMRP in naïve fibroblasts was sufficient to induce a CAF-like phenotype. Notably, FMRP overexpression led to significantly elevated inflammatory CAF (iCAF) and myofibroblastic CAF (myCAF) signatures, highlighting its role as a key pan-CAF regulator that influences both extracellular matrix (ECM) modulation and the secretory phenotype of CAFs. We utilized the full-body knockout (KO) mice model of the Fmr1 gene, which encodes FMRP, to further delineate the functional importance of FMRP expression in CAFs in stimulating an immunosuppressive program in vivo. Through bulk RNA sequencing, we developed an FMRP- associated gene signature for CAFs and applied it to human datasets, where we observed a pronounced increase in FMRP signatures in CAFs from human PDAC and breast tumors, highlighting its translational relevance. In conclusion, our research underscores the pivotal role of FMRP in cancer biology, impacting both the immune and stromal components of the tumor microenvironment. Targeting FMRP, particularly within CAFs, emerges as a promising therapeutic strategy to improve cancer treatment outcomes.
Citation Format: Simge Yucel, Nadine Fournier, Mireia Blanco Gomez, Douglas Hanahan. FMRP upregulation in cancer: Implicating FMRP-expressing cancer-associated fibroblasts in immune evasion [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Tumor-body Interactions: The Roles of Micro- and Macroenvironment in Cancer; 2024 Nov 17-20; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2024;84(22_Suppl):Abstract nr PR009.
Abstract PR011: Efferocytic macrophage promotes pancreatic cancer liver metastasis
Authors: Astuti Yuliana , Raymant Meirion , Quaranta Valeria , Clarke Kim , Abudula Maidinaimu , Smith Olivia , Bellomo Gaia , Chandran-Gorner Vatshala , Nourse Craig , Halloran Christopher , Ghaneh Paula , Palmer Daniel , Jones Robert , Campbell Fiona , Pollard Jeffrey , Morton Jennifer , Mielgo Ainhoa , Schmid Michael 
Published: November 2024

Abstract
Pancreatic ductal adenocarcinoma (PDAC) presents a major therapeutic challenge due to its aggressive metastatic behavior. In the liver metastasis microenvironment of PDAC, macrophages are key drivers of tumor progression. Targeting these pro-tumorigenic macrophages requires a deep understanding of the various macrophage populations and the factors influencing their phenotypes. Our study has revealed a distinct subset of macrophages with a pro-tumorigenic phenotype that emerges early in PDAC liver metastasis. We found that the establishment of hepatic metastases triggers local tissue damage, which, through efferocytosis, reprograms macrophages into an immunosuppressive state, thereby facilitating metastasis. Inhibiting efferocytosis pharmacologically prevented the conversion of macrophages, enhanced CD8+ T cell responses, and reduced liver metastasis. These results highlight the role of macrophages in tissue repair processes that promote liver metastasis in PDAC and suggest potential therapeutic targets to hinder its progression.
Citation Format: Yuliana Astuti, Meirion Raymant, Valeria Quaranta, Kim Clarke, Maidinaimu Abudula, Olivia Smith, Gaia Bellomo, Vatshala Chandran-Gorner, Craig Nourse, Christopher Halloran, Paula Ghaneh, Daniel Palmer, Robert Jones, Fiona Campbell, Jeffrey Pollard, Jennifer Morton, Ainhoa Mielgo, Michael Schmid. Efferocytic macrophage promotes pancreatic cancer liver metastasis [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Tumor-body Interactions: The Roles of Micro- and Macroenvironment in Cancer; 2024 Nov 17-20; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2024;84(22_Suppl):Abstract nr PR011.
Abstract PR012: KRAS mutation-specific effects on the tumor immune microenvironment drive tumor progression in pancreatic cancer
Authors: Wenger Andrew , Baron Tal , Hissong Erika , Chandiwani Rohit , Dow Lukas , Siolas Despina , Bacchi Katherine , Sun Huanhuan , Hissong Erika , Vega Adrian , Sisso Whitney , Abdilleh Kawther 
Published: November 2024

Abstract
Pancreatic ductal adenocarcinoma (PDAC) is a highly aggressive malignancy with abysmal survival rates. The highly immunosuppressive microenvironment of PDAC poses a major barrier to effective therapy. KRAS mutations are near-ubiquitous in PDAC, and studies indicate clinical outcomes vary depending on the specific KRAS genotype. Given that tumor genotype can shape the immune cell composition of tumors, we examined the immune cell composition of pancreatic tumors with specific KRAS mutations, focusing on KRASG12D mutations (representing 40% of PDAC cases which have the worst prognosis) and KRASG12R mutations (which make up 20% of PDAC cases and have a better prognosis). Orthotopically implanted Kras G12R/+ ;Trp53 KO mouse pancreatic tumors have a distinct immune profile in comparison to Kras G12D/+ ;Trp53 KO tumors, characterized by an influx of intratumoral CD3+ T cells and mature dendritic cells. Selective depletion of CD4+ T cells induces a rapid progression in KRASG12R, but not KRASG12D mouse tumors. RNA sequencing of KRASG12R tumor cells revealed enrichment of Type I interferon (IFN) pathways accompanied by related chemokines, CXCL9 and CXCL10 in comparison to KRASG12D tumors. Analysis of publicly available and real-world human PDAC datasets and enrichment of dendritic cells and other immune related cell types in KRASG12R tumors. Collectively, these data link the KRASG12R mutation to a unique immunogenic role.
Citation Format: Andrew Wenger, Tal Baron, Erika Hissong, Rohit Chandiwani, Lukas Dow, Despina Siolas, Katherine Bacchi, Huanhuan Sun, Erika Hissong, Adrian Vega, Whitney Sisso, and Kawther Abdilleh. KRAS mutation-specific effects on the tumor immune microenvironment drive tumor progression in pancreatic cancer [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Tumor-body Interactions: The Roles of Micro- and Macroenvironment in Cancer; 2024 Nov 17-20; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2024;84(22_Suppl):Abstract nr PR012.
Abstract PR014: DNA associated with EVs is uniquely chromatinized and prevents metastasis by enhancing anti-tumor immunity
Authors: Wortzel Inbal , Kim Han-Sang , Lyden David C. 
Published: November 2024

Abstract
Cells release extracellular vesicles (EVs) loaded with functional biomolecules that facilitate intercellular communication in health and disease. These EVs contain DNA (EV-DNA), mirroring the mutational profile of parental cells, yet the mechanism of DNA packaging onto EVs and its role in diseases like cancer remain unclear. Using advanced imaging and biochemical techniques, we discovered that EV-DNA predominantly resides on the vesicle surface, bound to modified histones. Through genome-wide CRISPR knockout screens in cancer cell lines, we identified immune-related pathways and genes crucial for EV-DNA loading, such as APAF1 and NCF1. In several cancer models, loss of APAF1 reduced EV-DNA packaging, and enhancing metastasis, thus implicating EV-DNA in immune surveillance against cancer spread. We demonstrated that EV-DNA uptake by liver macrophages triggers DNA damage response, altering cytokine production and promoting immune activation in pre-metastatic sites. Moreover, quantifying EV-DNA in colorectal cancer biopsies revealed its potential as a predictive metastatic risk biomarker. Our findings shed light on EV-DNA packaging mechanisms and its significance, suggesting that elevated levels of tumor-derived EV-DNA bolster anti-tumor immunity and inhibit metastasis.
Citation Format: Inbal Wortzel, Han-Sang Kim, David C. Lyden. DNA associated with EVs is uniquely chromatinized and prevents metastasis by enhancing anti-tumor immunity [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Tumor-body Interactions: The Roles of Micro- and Macroenvironment in Cancer; 2024 Nov 17-20; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2024;84(22_Suppl):Abstract nr PR014.
Mutated LRRK2 induces a reactive phenotype and alters migration in human iPSC-derived pericyte-like cells
Authors: Peltonen Sanni , Sonninen Tuuli-Maria , Niskanen Jonna , Koistinaho Jari , Ruponen Marika , Lehtonen Šárka 
Published: November 2024

Abstract
Background
Pericytes play a crucial role in controlling inflammation and vascular functions in the central nervous system, which are disrupted in Parkinson’s disease (PD). Still, there is a lack of studies on the impact of pericytes on neurodegenerative diseases, and their involvement in the pathology of PD is unclear. Our objective was to investigate the molecular and functional differences between healthy pericytes and pericytes with the LRRK2 G2019S mutation, which is one of the most common mutations associated with PD.

Methods
Our study employed pericyte-like cells obtained from induced pluripotent stem cells produced from PD patients with the LRRK2 G2019S mutation as well as from healthy individuals. We examined the gene expression profiles of the cells and analyzed how the alterations reflect on their functionality.

Results
We have shown differences in the expression of genes related to inflammation and angiogenesis. Furthermore, we observe modified migration speed in PD pericyte-like cells as well as enhanced secretion of inflammatory mediators, such as soluble VCAM-1 and MCP-1, in these pericyte-like cells following exposure to proinflammatory stimuli.

Conclusions
In summary, our findings support the notion that pericytes play a role in the inflammatory and vascular changes observed in PD. Further investigation of pericytes could provide valuable insight into understanding the pathogenesis of PD.
Automated image registration of RGB, hyperspectral and chlorophyll fluorescence imaging data
Authors: Bethge Hans Lukas , Weisheit Inga , Dortmund Mauritz Sandro , Landes Timm , Zabic Miroslav , Linde Marcus , Debener Thomas , Heinemann Dag 
Published: November 2024

AbstractBackgroundThe early and specific detection of abiotic and biotic stresses, particularly their combinations, is a major challenge for maintaining and increasing plant productivity in sustainable agriculture under changing environmental conditions. Optical imaging techniques enable cost-efficient and non-destructive quantification of plant stress states. Monomodal detection of certain stressors is usually based on non-specific/indirect features and therefore is commonly limited in their cross-specificity to other stressors. The fusion of multi-domain sensor systems can provide more potentially discriminative features for machine learning models and potentially provide synergistic information to increase cross-specificity in plant disease detection when image data are fused at the pixel level.ResultsIn this study, we demonstrate successful multi-modal image registration of RGB, hyperspectral (HSI) and chlorophyll fluorescence (ChlF) kinetics data at the pixel level for high-throughput phenotyping ofA. thalianagrown in Multi-well plates and an assay with detached leaf discs ofRosa × hybridainoculated with the black spot disease-inducing fungusDiplocarpon rosae. Here, we showcase the effects of (i) selection of reference image selection, (ii) different registrations methods and (iii) frame selection on the performance of image registration via affine transform. In addition, we developed a combined approach for registration methods through NCC-based selection for each file, resulting in a robust and accurate approach that sacrifices computational time. Since image data encompass multiple objects, the initial coarse image registration using a global transformation matrix exhibited heterogeneity across different image regions. By employing an additional fine registration on the object-separated image data, we achieved a high overlap ratio. Specifically, for theA. thalianatest set, the overlap ratios (ORConvex) were 98.0 ± 2.3% for RGB-to-ChlF and 96.6 ± 4.2% for HSI-to-ChlF. For theRosa × hybridatest set, the values were 98.9 ± 0.5% for RGB-to-ChlF and 98.3 ± 1.3% for HSI-to-ChlF.ConclusionThe presented multi-modal imaging pipeline enables high-throughput, high-dimensional phenotyping of different plant species with respect to various biotic or abiotic stressors. This paves the way for in-depth studies investigating the correlative relationships of the multi-domain data or the performance enhancement of machine learning models via multi modal image fusion.