bluuebunny/crossref_metadata_2025_split huggingface dataset:
Increasing thermostability of the key photorespiratory enzyme glycerate 3‐kinase by structure‐based recombination
Authors: Roze Ludmila V. , Antoniak Anna , Sarkar Daipayan , Liepman Aaron H. , Tejera‐Nieves Mauricio , Vermaas Josh V. , Walker Berkley J. 
Published: November 2024

SummaryAs global temperatures rise, improving crop yields will require enhancing the thermotolerance of crops. One approach for improving thermotolerance is using bioengineering to increase the thermostability of enzymes catalysing essential biological processes. Photorespiration is an essential recycling process in plants that is integral to photosynthesis and crop growth. The enzymes of photorespiration are targets for enhancing plant thermotolerance as this pathway limits carbon fixation at elevated temperatures. We explored the effects of temperature on the activity of the photorespiratory enzyme glycerate kinase (GLYK) from various organisms and the homologue from the thermophilic alga Cyanidioschyzon merolae was more thermotolerant than those from mesophilic plants, including Arabidopsis thaliana. To understand enzyme features underlying the thermotolerance of C. merolae GLYK (CmGLYK), we performed molecular dynamics simulations using AlphaFold‐predicted structures, which revealed greater movement of loop regions of mesophilic plant GLYKs at higher temperatures compared to CmGLYK. Based on these simulations, hybrid proteins were produced and analysed. These hybrid enzymes contained loop regions from CmGLYK replacing the most mobile corresponding loops of AtGLYK. Two of these hybrid enzymes had enhanced thermostability, with melting temperatures increased by 6 °C. One hybrid with three grafted loops maintained higher activity at elevated temperatures. Whilst this hybrid enzyme exhibited enhanced thermostability and a similar Km for ATP compared to AtGLYK, its Km for glycerate increased threefold. This study demonstrates that molecular dynamics simulation‐guided structure‐based recombination offers a promising strategy for enhancing the thermostability of other plant enzymes with possible application to increasing the thermotolerance of plants under warming climates.
Antiproton annihilation at rest in thin solid targets and comparison with Monte Carlo simulations
Authors: Amsler C. , Breuker H. , Bumbar M. , Cerwenka M. , Costantini G. , Ferragut R. , Fleck M. , Giammarchi M. , Gligorova A. , Gosta G. , Hunter E. D. , Killian C. , Kolbinger B. , Kraxberger V. , Kuroda N. , Lackner M. , Leali M. , Maero G. , Mascagna V. , Matsuda Y. , Migliorati S. , Murtagh D. J. , Nanda A. , Nowak L. , Rheinfrank S. , Romé M. , Simon M. C. , Tajima M. , Toso V. , Ulmer S. , van Beuzekom M. , Venturelli L. , Weiser A. , Widmann E. , Yamazaki Y. , Zmeskal J. 
Published: November 2024

AbstractThe mechanism of antiproton–nucleus annihilation at rest is not fully understood, despite substantial previous experimental and theoretical work. In this study we used slow extracted antiprotons from the ASACUSA apparatus at CERN to measure the charged particle multiplicities and their energy deposits from antiproton annihilations at rest on three different nuclei: carbon, molybdenum and gold. The results are compared with predictions from different models in the simulation tools Geant4 and FLUKA. A model that accounts for all the observed features is still missing, as well as measurements at low energies, to validate such models.
Abstract A005: Patient-derived cancer associated fibroblasts induce varying rates of colorectal cancer cell invasion using an organ-on-chip model
Authors: Haliday Bethany 
Published: November 2024

Abstract
Colorectal cancer (CRC) is one of the most common cancers in the United States, with metastatic CRC having an especially poor prognosis. Because of this, significant effort has been put into understanding the metastatic cascade. However, very little is still understood about how the tumor microenvironment (TME) influences this process. Recent studies have implicated cancer associated fibroblasts (CAFs), a major component of the TME, to be involved in tumor cell invasion. CAFs have been reported to be highly heterogeneous, with classification into several subtypes, including inflammatory CAFs (iCAFs) and myofibroblastic CAFs (myCAFs), based on “-omics” based studies. However, there has been limited exploration into the specific functionality of these subtypes in contributing to cancer progression. Therefore, we have worked to develop an organ-on-chip model to study CAF influence on tumor invasion in CRC (CRC-on-chip). This microfluidic device simulates the fluid flow and peristalsis-like motions that occur in the gut and is composed of two extracellular matrix-coated overlapping channels separated by a porous membrane. CAFs and GFP-labelled tumor cells are seeded into the top “epithelial” channel and endothelial cells are seeded in the bottom “vascular” channel. Confocal microscopy is used to track and quantify GFP+ tumor cells intravasating into the vascular channel and determine rates of invasion. The CAFs are derived from our biobank of diverse CRC patient tumor samples. From previous work, we observed patient-specific differences in CAF-induced CRC invasion when exposing human CRC cells on-chip to CAF-conditioned media. Through physical co-cultures, we similarly observed that some CAF lines increased invasion while others did not change invasion. Bulk RNA-sequencing and flow cytometry analysis of the CAF lines revealed varied expression of invasion-related genes and trends toward specific CAF subtype signatures, such as the iCAF and myCAF subtypes. These results suggest that there may be specific CAF phenotypes that induce tumor invasion which could give insight into determining the invasive potential of a primary CRC tumor at diagnosis.
Citation Format: Bethany Haliday. Patient-derived cancer associated fibroblasts induce varying rates of colorectal cancer cell invasion using an organ-on-chip model [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 A005.
Abstract A009: PIEZO1 driven tumor aggressiveness in an organ-on-chip model of colorectal cancer
Authors: Shah Curran A. , Strelez Carly R. , Schatz Aaron , Jiang Hannah , Perez Rachel , Mumenthaler Shannon M. 
Published: November 2024

Abstract
Mechanical forces have long been known to affect the progression of cancer, however exact study of the specific consequences of these forces has been hampered by currently available model systems. Traditional cell culture models often lack the ability to incorporate physiologically relevant mechanical forces, and animal models offer too much complexity to be able to effectively isolate and study the mechanical forces. Organ-on-chip (OOC) technology allows for the integration of human relevant physiological forces in a setting conducive to their study. Here, we explore how the early metastatic spread of colorectal cancer (CRC) can be influenced by physiological mechanical forces. Specifically, we investigated the ability of peristaltic motions, responsible for natural bowel motility, to enhance the invasive capability of colon tumor cells. Our microfluidic OOC model comprises of an epithelial channel and endothelial channel separated by a porous membrane allowing for biological and chemical crosstalk between them. Vacuum channels spanning the length of the structure allow force to applied in a cyclic manner mimicking peristaltic contraction and relaxation. Our OOC model supports the addition of tumor microenvironment (TME) components in a piece-wise manner to better understand how specific factors influence the behavior of tumor cells. Analyzing gene and protein expression levels, we have found that peristaltic-like motions induce changes in the Hippo signaling and epithelial-to-mesenchymal (EMT) pathways resulting in greater invasion of tumor cells into the endothelial compartment as observed by on-chip confocal imaging. Moreover, knock down studies have demonstrated that the response to peristaltic-like stretch is driven through a PIEZO1-mediated mechanism. Furthermore, to increase the physiological relevance of our model, we administered peripheral blood mononuclear cells (PBMCs) to the endothelial channel to simulate aspects of the immune TME. Preliminary studies revealed that the recruitment of PBMCs can be altered by the presence of peristaltic-like stretch. Our findings demonstrate that mechanical forces in the CRC TME can dramatically alter tumor behavior as shown in our CRC-OOC model.
Citation Format: Curran A. Shah, Carly R. Strelez, Aaron Schatz, Hannah Jiang, Rachel Perez, Shannon M. Mumenthaler. PIEZO1 driven tumor aggressiveness in an organ-on-chip model of colorectal 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 A009.
Abstract A014: Effects of senescence on the lung tumor microenvironment
Authors: Prieto Luis 
Published: November 2024

Abstract
Despite progress in screening and treatment, lung cancer remains the leading cause of cancer- related deaths worldwide. An overarching issue is the complexity and heterogeneous nature of the tumor microenvironment and eventual tumor spread. While aging is a key determinant, the relationship between aging and cancer is multi-faceted and extends beyond the accumulation of mutations. Therefore, a much-needed framework integrating the mechanistic principles that change with aging to drive neoplastic transformation beyond genetics will help us uncover predictive biomarkers that inform treatment decision-making and how we may use them to prevent, postpone, suppress tumor growth, and limit spread. Here, we investigate the role of age-related senescent cell accumulation in lung tumorigenesis and propose a potential strategy to delay tumor progression and spread by selectively targeting tumor-promoting senescent cells that arise with increasing age to sustain protective antitumor immunity.
Citation Format: Luis Prieto. Effects of senescence on the lung tumor microenvironment [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 A014.
Abstract A018: Endothelial pyrimidine synthesis deficiency promotes tumor growth
Authors: Hyrossova Petra , Milisav Isidora , Novais Silvia , Milosevic Mirko , Rohlena Jakub , Rohlenova Katerina 
Published: November 2024

Abstract
The tumor microenvironment plays a crucial role in cancer progression and treatment response. Systemically administered metabolic cancer therapies target not only malignant but also stromal cells, including immune cells - the only stromal population previously addressed in this context. However, how such treatments impact other non-malignant cell types in tumors remains poorly understood. Here we show that inhibition of de novo pyrimidine synthesis in endothelial cells accelerates tumor growth and alters tumor immune repertoire. We found that whole-body de novo pyrimidine synthesis deficiency in mice, caused by the inducible whole-body ablation of DHODH, accelerates the growth rate of orthotopic lung tumors. Single-cell transcriptomic analysis of tumor-bearing lungs revealed that DHODH deficiency in the stroma impacts multiple cell populations, including immune and, surprisingly, endothelial cells. To explore the endothelial-specific effects, we generated a mouse model with inducible DHODH deficiency restricted to endothelial cells. The endothelium-specific model recapitulates the accelerated lung tumor growth observed in the whole-body DHODH deficiency model. Single-cell transcriptomics analysis of tumor-bearing lungs in the endothelium-specific model pointed to changes in the immune repertoire, particularly an enrichment of monocytes. We confirmed these results on the protein level using spectral flow cytometry, and we are currently in the process of uncovering the mechanism by which endothelial deficiency of pyrimidine synthesis affects the immune landscape of tumors. Inhibitors of pyrimidine de novo synthesis have been tested in clinical trials but failed due to their low efficiency. Our findings indicate that systemic treatment targeting pyrimidine synthesis may be hampered by its pro-tumorigenic effects in the endothelium, highlighting the unexpected role of endothelial metabolism in this context.
Citation Format: Petra Hyrossova, Isidora Milisav, Silvia Novais, Mirko Milosevic, Jakub Rohlena, Katerina Rohlenova. Endothelial pyrimidine synthesis deficiency promotes tumor growth [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 A018.
Abstract A019: Increased vulnerability of colorectal cancer with high alkylation damage to NTHL1 inactivation
Authors: Kim Hyeoncheol , Cazaubiel Jules , Chiang Tung-Lin , Gurjao Carino , Fitzgerald Samantha , Giannakis Marios 
Published: November 2024

Abstract
Background: NTHL1 is a DNA glycosylase, and mutations in this gene are linked to colorectal polyps and colorectal cancer (CRC). SBS30, a mutational signature associated with NTHL1 inactivation, correlates with c-alkylation (c-alkyl), a CRC mutational signature of alkylating damage. We aimed to investigate the potential for synthetic lethality between c-alkyl and NTHL1 inactivation as a novel therapeutic strategy for CRC. Methods: Using DepMap data, we categorized CRC cell lines into low and high c-alkyl groups. We performed CRISPR-mediated NTHL1 knockouts (KOs) in high vs low c-alkyl groups of cell lines and patient-derived CRC organoids and tested for synthetic lethality and its mechanisms. Results: High c-alkyl cells with NTHL1 KO showed decreased proliferation compared to low c-alkyl cells, with cell cycle arrest predominantly in the G2/S phase. Treatment with N-Nitroso-N-methylurea (MNU, alkylating reagent) converted low c-alkyl cells to a high c-alkyl state and conferred increased susceptibility to NTHL1 KO. High c-alkyl patient-derived organoids similarly showed lower proliferation with NTHL1 KO compared to low c-alkyl ones. High c-alkyl cells exhibited increased DNA damage, indicated by γH2AX and CHK1 phosphorylation. Low c-alkyl cells exhibited significant HDAC1 and HDAC2 upregulation, which was not seen in high c-alkyl cells. This could explain their protection against NTHL1 KO, whereas the lack of change in HDAC protein level may explain the failure of high c-alkyl cells to repair NTHL1-induced DNA damage. High c-alkyl cells with NTHL1 KO additionally showed increased DNA damage and cell death when treated with checkpoint inhibitors AZD-7762, LY2606368, and Rabusertib. Conclusions: NTHL1 KO presents a promising therapeutic target, especially for high c-alkyl CRCs that are more susceptible to DNA damage. Our findings also suggest that combining NTHL1 inhibition with CHK1 inhibition may offer new therapeutic opportunities in CRC.
Citation Format: Hyeoncheol Kim, Jules Cazaubiel,, Tung-Lin Chiang, Carino Gurjao, Samantha Fitzgerald, Marios Giannakis. Increased vulnerability of colorectal cancer with high alkylation damage to NTHL1 inactivation [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 A019.
Abstract A028: Direct interaction between cancer cells and fibroblasts drives epithelial- to- mesenchymal plasticity (EMP) and chemotherapy resistance
Authors: Dhungel Nilu , Dragoi Ana-Maria 
Published: November 2024

Abstract
The tumor microenvironment (TME), composed of immune cells and fibroblasts, blood vessels, signaling molecules and extracellular matrix, provides important cues that govern epithelial-to- mesenchymal transition (EMT) and facilitate the acquisition of aggressive traits such as chemotherapy resistance by cancer cells. Cancer cells exist in multiple hybrid epithelial/mesenchymal (E/M) states, ensuring survival in the ever-changing environment during tumor development and metastasis. How are these hybrid states generated and maintained is not fully understood. Using small cell lung carcinoma (SCLC) and lung fibroblasts model, we show that direct interaction between SCLC and lung fibroblasts induces a hybrid E/M phenotype in cancer cells in which several mesenchymal genes involved in receptor interaction with the extracellular matrix (ECM) and ECM remodeling are upregulated while epithelial genes such as E-cadherin remain unchanged. We also demonstrate that several core EMT-regulating transcription factors (EMT-TFs) are upregulated in cancer cells during direct contact with fibroblasts, including Yes-associated protein (YAP1), a major regulator of the Hippo pathway. Furthermore, we demonstrate that the upregulation of YAP1 in cancer cells, which occurs only during the direct interaction with fibroblasts, renders the cancer cells more resistant to chemotherapeutic agents resulting in more aggressive phenotypes. The cells become sensitive to chemotherapeutic agents when YAP1 is inhibited. Altogether, our results provide evidence that tumor cells’ direct contact with the fibroblasts in the TME initiates a signaling cascade responsible for hybrid E/M states of cancer cells. These hybrid states are maintained during the interaction and contribute to therapy resistance via YAP1 pathway, while interference with direct contact will result in slow recovery and a switch to the initial states.
Citation Format: Nilu Dhungel, Ana-Maria Dragoi. Direct interaction between cancer cells and fibroblasts drives epithelial- to- mesenchymal plasticity (EMP) and chemotherapy resistance [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 A028.
Abstract A032: Uncovering the impact of current therapies on LUAD dormant metastasis
Authors: Godet Inês , Wang Zhenghan , Massagué Joan 
Published: November 2024

Abstract
Despite recent therapeutic advances, Lung Adenocarcinoma (LUAD) remains a leading cause of mortality worldwide, with most deaths attributed to metastasis. Metastasis is mediated by disseminated metastasis initiating cells (MICs) that can persist in a dormant state in distant sites for months to years and ultimately drive metastatic relapse, which is clinically incurable. Adjuvant therapy seeks to prevent cancer relapse, however, efforts to improve adjuvant treatments are hindered by an insufficient understanding of the molecular mechanisms supporting the long-term viability of dormant MICs. We have established that primitive LUAD cells characterized by the spontaneous expression of the pluripotency transcription factor SOX2 can enter an immune-evasive dormant state with downregulation of immune response mediators (STING, NK ligands, MHC-I) to evade immune surveillance during dormancy. Now, we hypothesize that dormant and immune evasive progenitor MICs may also escape therapies targeting growth pathways. We have generated latency competent cells (LCCs) that can remain in a latent state for months by isolating progenitor cells from the Kras LSL-G12D/+ ;Trp53 flox/flox mouse model and screening their metastatic potential and progenitor state in the B6 background. LCCs entering a slow-cycling state in response to dormancy signals remain sensitive to targeted KRAS inhibitors but contain a resistant subpopulation that survives. To specifically characterize the progenitor state in these LCC populations, we have developed and validated two strategies to fluorescently mark SOX2 expression and activity, respectively. As speculated, the resistant population is mostly composed of SOX2+ progenitor LCCs after treatment with KRAS inhibitor under dormancy signaling. Furthermore, induced-dormancy also drives an accumulation of cells in the SOX2+ progenitor state in these LCC-rich populations. Ongoing studies are focused on delineating the emergence of the SOX2+ progenitor state in LCCs during dormancy and the biological mechanisms driving their persistence and resistance to targeted therapies. We aim to define (1) the dependence of dormant LCCs on oncogenic signaling, the (2) effect of targeted therapy on MICs, and (3) strategies to overcome potential resistance mechanisms in dormant MICs. Our ultimate goal is to delineate strategies to clear latent MICs and prevent LUAD recurrence.
Citation Format: Inês Godet, Zhenghan Wang, Joan Massagué. Uncovering the impact of current therapies on LUAD dormant 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 A032.
Abstract A036: DDR2 in ovarian tumor CAFs controls ferroptosis and response to Olaparib
Authors: Lesage Julien , DiMauro Alessandra , Fuh Katherine C. , Longmore Gregory D. 
Published: November 2024

Abstract
In ovarian cancer, resistance to conventional cancer treatments has stimulated finding alternative targets that induce tumor cell death. Ferroptosis, a lipid peroxide-triggered form of iron-dependent cell death, is one such pathway. Current research has focused primarily on tumor cell-intrinsic mechanisms or how tumor associated immune cells might impact tumor cell ferroptosis. Cancer-associated fibroblasts (CAFs) are other key stromal cells in the tumor microenvironment and play critical roles in cancer progression, metastasis, and chemotherapeutic response. In ovarian cancer, the collagen receptor tyrosine kinase DDR2 is predominantly expressed by tumor stromal CAFs, not immune cell, and high tumor stromal cell expression of DDR2 in ovarian tumors is associated with poor survival and resistance to therapy. Thus, we asked whether DDR2 could impact ferroptosis regulation in CAFs, and if so, how this effect of DDR2 could impact ovarian tumor cell responses to cytocidal therapies. Through various genetic means, we generated multiple DDR2-expressing and DDR2-deficient human ovarian tumor and mouse breast tumor CAFs. We evaluated the response of the various CAFs to ferroptosis inducers (Erastin and RSL3) and inhibitors (Ferrostatin-1 and Deferoxamine). We find that the presence of DDR2 in CAFs protects these cells from induced ferroptosis through regulation of the xCT- GSH-GPX4 antioxidant pathway and cellular iron metabolism. DDR2-dependent regulation of xCT-GSH-GPX4 occurs through non-canonical activation of NRF2 via the Sequestosome-1 (SQSTM1/p62) protein. In iron metabolism, DDR2 affects the labile iron pool (LIP) by regulating ferritinophagy. The actions of DDR2 in CAFs protects these cells against Olaparib therapy, by inhibiting Olaparib-induced ferroptosis. Ovarian tumor CAF culture supernatant was found to protect ovarian tumor cell response to Erastin-induced ferroptosis, in a DDR2- dependent manner. Overall, this study uncovered a novel function of the action of DDR2 in tumor stromal CAFs in controlling iron and the xCT-GSH-GPX4 ferroptosis regulatory axis through non-canonical p62-KEAP1-NRF2 activation. These findings suggest that CAFs, through DDR2-mediated regulation of ferroptosis, could play a role in therapeutic sensitivity/resistance in ovarian cancer.
Citation Format: Julien Lesage, Alessandra DiMauro, Katherine C. Fuh, Gregory D. Longmore. DDR2 in ovarian tumor CAFs controls ferroptosis and response to Olaparib [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 A036.