bluuebunny/crossref_metadata_2025 huggingface dataset:
What constitutes a stigma? A review of isolated pores in raphid diatoms (Bacillariophyceae) and the value of precise terminology
Authors: Cox Eileen J. , Van de Vijver Bart
Published: November 2024

Scanning electron microscopy has revealed variation in the ultrastructure of distinctive isolated pores in or near the central area of raphid diatoms, with different types of pores being restricted to phylogenetic groups. Thus, the widespread use of the term stigma for all such pores not only hides the structural diversity but also obscures the phylogenetic distribution of the different types. This paper provides images of the different types of isolated pores, particularly refining the discrimination of variants within the Cymbellales, and reveals some interesting ecological patterns. Revised definitions of stigmata and stigmoids are proposed, together with the recognition and definition of another type of stigmoid. The restricted distribution of more precisely defined pore types shows the importance of consistent use of terminology and its relevance to phylogenetic studies.
Inference on nonstationary heavy‐tailed AR processes via model selection
Authors: Guo Feifei , She Rui , Yang Yaxing
Published: November 2024

This article develops a series of Lasso‐based procedures for statistical inference in the autoregressive (AR) process with heavy‐tailed heteroscedastic noise. We first study the classical adaptive Lasso estimator for the nonstationary coefficient and show that it can distinguish between stationary and nonstationary autoregressions by detecting whether the coefficient is zero with high probability. After conducting unit‐root tests, we proceed to consider the self‐weighted least absolute deviation (SWLAD) estimator with an adaptive Lasso penalty applied to the stationary coefficients. As anticipated, the penalized SWLAD estimator exhibits the oracle properties. This implies that the penalized SWLAD estimator is consistent, accurately selects the correct sparsity pattern, and estimates the coefficients of the relevant variables with the same asymptotic efficiency as if only these variables had been included in the model. In particular, by assigning data‐dependent weights to different coefficients in the penalty term, our method can effectively circumvent the issue of non‐pivotal distributional ignorance in heavy‐tailed time series analysis, thereby enabling effective unit‐root tests and order selection without any prior information on the nuisance parameters, making it appealing in practice with wide applications in finance and econometrics. A simulation study is conducted to evaluate the performance of the test and estimator, and two real examples are presented to demonstrate their applicability.
Warm temperature perceived at the vegetative stage affects progeny seed germination in natural accessions of Arabidopsis thaliana
Authors: Wang Yu , Zhang Tania L. , Barnett Emma M. , Sureshkumar Sridevi , Balasubramanian Sureshkumar , Fournier‐Level Alexandre
Published: November 2024

Temperatures perceived early in the life cycle of mother plants can affect the germination of the offspring seeds. In Arabidopsis thaliana, vernalisation‐insensitive mutants showed altered germination response to elevated maternal temperature, hence revealing a strong genetic determinism. However, the genetic control of this maternal effect and its prevalence across natural populations remain unclear.

Here, we exposed a collection of European accessions of A. thaliana to increased temperature during the vegetative phase and assessed germination in their progeny to identify the genetic basis of transgenerational germination response. We found that genotypes with rapidly germinating progeny after early maternal exposure to elevated temperature originated from regions with low‐light radiation.

Combining genome‐wide association, expression analysis and functional assays across multiple genetic backgrounds, we show a central role for PHYB in mediating the response to maternally perceived temperature at the vegetative stage. Differential gene expression analysis in leaves identified a similar genetic network as previously found in seed endosperm under elevated temperature, supporting the pleiotropic involvement of PHYB signalling across different tissues and stages.

This provides evidence that complex environmental responses modulated by the maternal genotype can rely on a consistent set of genes yet produce different effects at the different stages of exposure.
Origins of xyloglucan‐degrading enzymes in fungi
Authors: Trudeau Emily D. , Brumer Harry , Berbee Mary L.
Published: November 2024

The origin story of land plants – the pivotal evolutionary event that paved the way for terrestrial ecosystems of today to flourish – lies within their closest living relatives: the streptophyte algae. Streptophyte cell wall composition has evolved such that profiles of cell wall polysaccharides can be used as taxonomic markers. Since xyloglucan is restricted to the streptophyte lineage, we hypothesized that fungal enzymes evolved in response to xyloglucan availability in streptophyte algal or land plant cell walls. The record of the origins of these enzymes is embedded in fungal genomes, and comparing genomes of fungi that share an ancient common ancestor can provide insights into fungal interactions with early plants. This Viewpoint contributes a review of evidence underlying current assumptions about the distribution of xyloglucan in plant and algal cell walls. We evaluate evolutionary scenarios that may have given rise to the observed distribution of putative xyloglucanases in fungi and discuss possible biological contexts in which these enzymes could have evolved. Our findings suggest that fungal xyloglucanase evolution was more likely driven by land plant diversification and biomass accumulation than by the first origins of xyloglucan in streptophyte algal cell walls.
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

As 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.
The first step towards FAIR-ness in Bulgarian archaeology: The Archaeological Map of Bulgaria in ARIADNE and ARIADNEplus
Authors:   National Archaeological Institute with Museum at the Bulgarian Academy of Sciences, Kecheva Nadezhda
Published: November 2024

Summary This article provides an overview of the participation of the National Archaeological Institute with Museum at the Bulgarian Academy of Sciences (NAIM-BAS) as a partner in both the ARIADNE and ARIADNEplus projects and the SEADDA COST Action. The article examines both the workflow and the results obtained when modifying and mapping part of the national site and monuments information system, also known as the 'Archaeological Map of Bulgaria' (AIS AKB). The article's focus is mainly on the technical preparation of data shared through the ARIADNE portal. The main workflow followed throughout the projects included mapping terms to the Getty AAT thesaurus, adding Bulgarian archaeological chronologies to PeriodO, and mapping metadata to the ARIADNE catalogue data model (ACDM) in ARIADNE and to the AO-cat ontology in ARIADNEplus. In 2016, a mapping of AIS AKB to the CIDOC CRM was also undertaken, and the first steps towards creating the geographic information system, 'Archaeological Map of Bulgaria' (GIS AKB), were taken. The experience gathered by the NAIM-BAS team members throughout the whole project was important for moving towards FAIR-ness in Bulgarian archaeology.
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

The 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.
Joint Power Control and Resource Allocation With Task Offloading for Collaborative Device‐Edge‐Cloud Computing Systems
Authors: Xie Shumin , Li Kangshun , Wang Wenxiang , Wang Hui , Jalil Hassan
Published: November 2024

Collaborative edge and cloud computing is a promising computing paradigm for reducing the task response delay and energy consumption of devices. In this paper, we aim to jointly optimize task offloading strategy, power control for devices, and resource allocation for edge servers within a collaborative device‐edge‐cloud computing system. We formulate this problem as a constrained multiobjective optimization problem and propose a joint optimization algorithm (JO‐DEC) based on a multiobjective evolutionary algorithm to solve it. To address the tight coupling of the variables and the high‐dimensional decision space, we propose a decoupling encoding strategy (DES) and a boundary point sampling strategy (BPS) to improve the performance of the algorithm. The DES is utilized to decouple the correlations among decision variables, and BPS is employed to enhance the convergence speed and population diversity of the algorithm. Simulation results demonstrate that JO‐DEC outperforms three state‐of‐the‐art algorithms in terms of convergence and diversity, enabling it to achieve a smaller task response delay and lower energy consumption.
Inverse Network DEA Incorporating Cost and Revenue Efficiencies Under Fuzzy Uncertainty
Authors: Gholami Golsefid Fatemeh , Jahani Sayyad Noveiri Monireh , Kordrostami Sohrab
Published: November 2024

The study of network cost and revenue efficiency and changes related to performance measures in uncertain environments is an important area of research in decision‐making analysis. A generalized inverse data envelopment analysis (DEA) approach is advanced in this examination for addressing the complexities associated with imprecise inputs and outputs within two‐stage networks. Additionally, the second stage of the network is evaluated for the existence of unwanted outputs. The proposed methodology focuses on estimating fuzzy performance measures in two‐stage processes while maintaining consistent fuzzy technical efficiency and cost efficiency (revenue efficiency). To demonstrate the practical application of this approach, data from various branches of a bank in Iran, which are characterized by inaccurate data and undesirable outputs, is analyzed, yielding logical and insightful results.
Saprochaete capitata Infection in Teen With Acute Myeloid Leukemia Receiving Echinocandin Prophylaxis
Authors: Killingsworth Jordan , Boren Rachel , Sheth Rachna , Chang Michael L.
Published: November 2024

We report a case of a 15‐year‐old with refractory and relapsed AML and profound prolonged neutropenia who developed a Saprochaete capitata disseminated invasive infection while on echinocandin prophylaxis for invasive fungal disease. Azole antifungal therapies, which are often used as prophylaxis, were initially avoided due to concerns for CYP drug interactions. Treatment with a combination of liposomal amphotericin B, voriconazole, and adjuvant granulocyte transfusions was successful as he awaited neutrophil recovery.
Identifying Baicalin Concentration in Scutellaria Spray Drying Powder With Disturbed Terahertz Spectra Based on Gaussian Mixture Model
Authors: Li Yizhang , Dong Xiaodi , Cao Guiyun , Guo Yongbin , Wang Zhongmin , Yang Xiuwei , Han Dongyue , Meng Zhaoqing
Published: November 2024

Baicalin concentration is concerned in manufacture of scutellaria spray drying powder as a traditional Chinese medicine, and the quality control based on high‐performance liquid chromatography is inconvenience. In this study, terahertz time domain spectroscopy was employed to achieve quality control of scutellaria spray drying powder; however, an acute difficulty was found that terahertz spectra overlapped due to the disturbance in both content matrix and measurement error. In this study, similar terahertz spectra of scutellaria spray drying powder were classified with the help of Gaussian mixture model and built a classifier based on probability feature instead of spectral features conventionally employed in previous investigations. To explore the feasibility of GMM, principal component analysis was given, indicating that it is possible to train GMM with original features and proper principal components. Probable advantage of training GMM based on PCA feature was discussed and so it was with the capacity of the model to identify the linear combined spectra by comparing the performance of GMM and a decision tree model. Above all, the reason why GMM shows potential in the analysis of TCM terahertz spectra was illustrated by comparing the thought of discriminative model and generative model. This study implied that generative model may have natural advantage of overcoming the inherent disturbance of terahertz spectroscopy, which would be promising in future studies.
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

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

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

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

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

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

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

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

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.
Abstract A042: Desmosome mutations in the microenvironment regulate melanoma proliferation
Authors: Tagore Mohita
Published: November 2024

Desmosomes are transmembrane protein complexes critical for cell-cell adhesion in epithelial tissues and other cell types. In skin cancers like melanoma, epithelial cells called keratinocytes are the predominant cells in the primary melanoma microenvironment, yet it remains largely unknown whether this cell type is subject to genetic alterations during melanoma development and its role in early melanoma progression. In this study, using an integrative analysis of tumor mutations and protein biophysical interactions, we identify a high frequency of genetic alterations in desmosome-related genes in human cancers, with the highest occurrences in cutaneous melanoma. Notably, over 70% of cutaneous melanoma cases exhibit mutations in desmosome genes and desmosome gene mutations are associated with lowered expression of the desmosome complex in melanoma. Using spatial transcriptomics and immunohistochemistry analyses, we find that the decrease in desmosome gene expression predominantly occurs in keratinocytes within the tumor microenvironment rather than in the melanoma cells themselves. To study the functional significance of this alteration in melanoma development, we used a human melanoma/keratinocyte co-culture system using primary melanoma cell lines. Our studies show that knockdown of desmosome genes in keratinocytes markedly increased proliferation of adjacent melanoma cells in melanoma/keratinocyte co-cultures. Additionally, melanoma cell proliferation is enhanced when exposed to media preconditioned by desmosome-deficient keratinocytes. These observations suggest that the gradual accumulation of mutations in desmosome genes within neighboring keratinocytes may create a conducive environment that primes melanoma cells for neoplastic transformation. This study underscores the critical role of genetic alterations in the tumor microenvironment in melanoma progression and highlights the potential for targeting desmosome-related pathways in therapeutic strategies against melanoma.

Citation Format: Mohita Tagore. Desmosome mutations in the microenvironment regulate melanoma proliferation [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 A042.
Abstract B004: Identification of distinct subpopulations of cancer associated fibroblasts in oral squamous cell carcinoma by imaging mass cytometry
Authors: Tornaas Stian , Fromreide Siren , Kleftogiannis Dimitrios , Aarstad Hans Jørgen , Vintermyr Olav K. , Akslen Lars , Dongre Harsh , Costea Daniela Elena
Published: November 2024

Background: Although cancer associated fibroblast (CAF) heterogeneity is recognized in oral squamous cell carcinoma (OSCC), the phenotype and role of CAF subpopulations in OSCC is still unknown. Objectives: This study aimed to dissect CAF heterogeneity and spatial location by using imaging mass cytometry on formalin fixed paraffin embedded (FFPE) tissues from primary OSCC. Methods: Imaging mass cytometry (Hyperion technology) was used to identify 24 markers (E-cadherin, EGFR, Ki-67, α-SMA, CD140β, FAP, FSP-1/S100A4, CD90/Thy-1, integrin α-11, collagen-1, tenascin-C, caveolin-1, CD4, CD8a, CD16, CD20, CD68, CD163, FoxP3, granzyme B, CD31, podoplanin, CD146, and YAP-1) in HPV-negative OSCC lesions (n=10). Tissue images were segmented employing the Steinbock framework. Unsupervised clustering of single-cell data was carried out using a bioinformatics pipeline developed in R language. Results: Unsupervised clustering identified several major cell types, with E-cadherin+ cells being the most abundant (30%) and CD146+ being the least abundant cell type (0.62%). Within the immune compartment CD4+ cells were most abundant (11.72%) followed by CD8+ cells (10.6%) and CD68+ cells (10.25%). Cells negative for other major lineage markers and positive for stromal markers were considered as CAFs and they clustered in 6 clusters defined as CAF1 to CAF6. CAF1-3 were high in FAP and CD140β while CAF 4-6 were low expressing FAP and CD140β. CAF1 and 6 expressed high αSMA, while CAF 3 and 5 expressed high collagen-1. CAF6 had high expression of integrin α-11. CAF1 and 3 subtypes were found closer to immune cells whereas CAF2 and 6 were closely located to cancer cells. Conclusions: We identified six distinct subpopulations of CAFs in OSCC by using imaging mass cytometry. Their clinical implications can be further revealed by using this method on larger patient cohorts with FFPE tissues available in diagnostic biobanks.

Citation Format: Stian Tornaas, Siren Fromreide, Dimitrios Kleftogiannis, Hans Jørgen Aarstad, Olav K. Vintermyr, Lars Akslen, Harsh Dongre, Daniela Elena Costea. Identification of distinct subpopulations of cancer associated fibroblasts in oral squamous cell carcinoma by imaging mass cytometry [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 B004.
Abstract B024: Deciphering the neurogenic tumor microenvironment: A novel gene network driving innervation in metastatic melanoma offers prognostic and therapeutic insights
Authors: Goli Anjana , Dutta Subhajit
Published: November 2024

Melanoma, a highly aggressive and life-threatening cancer, poses a significant therapeutic challenge, particularly for patients with distant metastasis, who face a 5-year survival rate of only approximately 22.5%. This underscores the urgent need for innovative therapeutic approaches. Emerging evidence suggests that sensory and parasympathetic innervation within the tumor microenvironment (TME) plays a crucial role in driving metastasis and immune evasion, partly through the promotion of M2 macrophages and cancer stem cells. To uncover the mechanisms behind tumor-specific innervation in metastatic melanoma, we employed a systems biology approach integrating bulk RNAseq from diverse melanoma cell lines, TCGA-SKCM data analysis, single-cell RNAseq, and spatial transcriptomics. This comprehensive analysis led us to identify a previously uncharacterized gene regulatory network (GRN) orchestrating tumor innervation. This GRN is driven by axon guidance cues (Netrin, Slit, Semaphorin), their receptors (DCC, Robo, Neuropilin, ITGB1), and transcription factors (RAS, RND1, TFAP2, CAMKII). We further discovered that the pioneer factor FOXC2, known for its association with metastasis, plays a critical role in opening the promoters of innervation-specific genes. Additionally, we identified Ephrin and CXCR4-mediated crosstalk between neurons and tumor cells. Machine learning models validated the accuracy of this GRN in predicting melanoma metastasis, and a neural network-based model confirmed the enrichment of nerve cells near metastatic tumor cells within the TME in TCGA immunohistochemistry data. The functional relevance of this network was further supported by CRISPR-mediated knockout studies, which disrupted tumor-specific signaling pathways. Notably, we also observed the enrichment of genes linked to mRNA processing bodies and neuron-specific membrane-less condensates in metastatic melanoma. These findings highlight the critical role of neuronal infiltration in melanoma metastasis. Currently, therapeutic strategies targeting this aspect of the TME remain limited. Our identified gene set offers potential as a metastatic predictor, and targeting the neural component of the TME represents a promising new therapeutic avenue for melanoma.

Citation Format: Anjana Goli, Subhajit Dutta. Deciphering the neurogenic tumor microenvironment: A novel gene network driving innervation in metastatic melanoma offers prognostic and therapeutic insights [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 B024.
Abstract B031: Lean adipocyte-derived lipid decreases metastatic potential of breast cancer cells
Authors: Jackson Abigail E. , Hilgendorf Keren I
Published: November 2024

Obesity rates are increasing globally, making it of critical importance to study obesity-linked diseases. Breast cancer is the most common cancer in women, and obesity is associated with both increased incidence and metastatic progression of breast cancer. Metastasis formation depends on a cancer cell leaving the primary site, migrating through the bloodstream, and establishing new growth in a distant site. Both metastasizing cell-intrinsic and metastatic site-dependent factors can help to regulate the effectiveness of this process; however, it is unknown whether obesity-linked metastasis depends on changes to the metastasizing cell and/or changes to the distant metastatic site. This study aims to characterize how the lean versus obese tumor microenvironment impacts breast cancer metastasis and identify adipocyte-derived molecules that modulate the metastatic potential of breast cancer cells. We and others have shown that obesity leads to increased metastasis formation in mouse models of orthotopic breast cancer. However, my preliminary data show that an obese metastatic site is not sufficient to increase metastasis formation in an intravenous injection model of metastasis, emphasizing the importance of the primary tumor microenvironment in programming breast cancer cells for metastasis. Cancer cell stemness helps to mediate metastasis formation and can be assessed in vitro with the mammosphere assay. Importantly, my data demonstrate that a secreted lipid from lean, but not obese, adipocytes potently inhibits the ability of breast cancer cells to form mammospheres. Furthermore, this inhibition induces a G1/S cell cycle arrest. Together, these data suggest that lean adipocytes in the breast cancer tumor microenvironment act in a paracrine manner to decrease the metastatic potential of breast cancer cells. My work demonstrates the role of adipocytes in the regulation of metastasis in breast cancer and provides important insight into the role of the tumor microenvironment in mediating metastasis in lean versus obese conditions.

Citation Format: Abigail E. Jackson, Keren I Hilgendorf. Lean adipocyte-derived lipid decreases metastatic potential of breast cancer 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 B031.