bluuebunny/crossref_metadata_2025 huggingface dataset:
The “insider” ethnographic diagnostic radiographer thinking like “an outsider”
Authors: Strudwick Ruth Mary
Published: November 2024

Purpose

The purpose of this paper is to explore how the ethnographic researcher navigates their insider–outsider status and provides a methodological contribution to this important aspect of ethnographic research; this will be framed from the researcher’s perspective using a semi-autoethnographic approach. The ethnographic study being reflected upon explored the culture in a Diagnostic Imaging Department (DID), looking at how radiographers work and what the issues were within their working environment. The original study was carried out within one DID in a District General Hospital in the East of England (Strudwick, 2011).

Design/methodology/approach

In the original study, the researcher used ethnography to study the culture in a DID. Observation was carried out for a four-month period. Field notes were recorded and used to formulate topics for the interviews that were to follow. After the observation, the researcher conducted semi-structured interviews with key informants from the DID. Ten key informants were purposefully sampled from the DID to provide a cross-section of opinion from the staff. The data collected were analysed to identify key themes. This paper reflects on the data from the original study to explore the tensions between the insider and outsider researcher role and how this contributes to the way the ethnographic researcher views the environment, reports on their findings and how they feel about the data from their own perspective.

Findings

Ethnographers carrying out research in their own area of practice need to try to think like an outsider in order to see the environment with a sense of strangeness but also try to make sense of what the participants are thinking and doing. There is a tension between becoming part of the group in order to understand it and looking at the environment as an outsider in order to make a note of what is happening. Findings from the original ethnographic study will be used to illustrate this point and will be used to reflect on the feelings of the researcher, considering her insider and outsider status.

Research limitations/implications

This study was carried out in one diagnostic imaging department in the east of England.

Originality/value

The author, who is a diagnostic radiographer and radiography educator reflects on how she managed the insider–outsider tension during her ethnographic observation and after the event when reflecting on the data from the original study.
FinTech Adoption and Corporate Greenwashing: A Technology Affordance Perspective
Authors: Sun Zhe , Liu Lei , Johan Sofia , Zhao Liang
Published: November 2024

Affordance theory suggests that technology offers certain opportunities or ‘affordances’ that can be exploited by users. In this context, we are exploring how FinTech adoption provides opportunities to address corporate greenwashing. Drawing on an affordance perspective, we assert that FinTech adoption effectively inhibits corporate greenwashing behaviour, primarily through facilitating green innovation and improving managerial efficiency. We also contend that the impact of FinTech adoption on reducing greenwashing behaviour is not uniform across all industries. It is more pronounced in heavy‐polluting industries, indicating that FinTech has a greater effect in encouraging accurate disclosure of environmental information in environmentally sensitive sectors. Conversely, its impact is weaker in high‐tech industries, which might already have strong environmental commitments. The findings contribute to the literature on sustainability, FinTech and governance.
Anthracological analysis of wooden shaft remains from the Roman‐period sacrificial lake of Nidajno, Czaszkowo 1 site, north‐eastern Poland
Authors: Rzeszotarska‐Nowakiewicz Aleksandra , Kontny Bartosz , Nowakiewicz Tomasz , Cywa Katarzyna
Published: November 2024

Here, we report on an archaeobotanical study of charred wood remains from eight iron spearhead sockets from a sacrificial aquatic site at Nidajno/Czaszkowo 1, Mazurian Lakeland, NE Poland (c. second–fifth c. CE), in search of botanical evidence for the selection of wood for manufacture of wooden shafts used with iron spearheads. The samples were analysed using a Nicon Eclipse ME600 metallographic microscope. The results show significant botanical data for Fraxinus excelsior L. and Tillia sp.

The results of this research illustrate the material standard of the finds from a unique sacrificial site of the Scandinavian ‘sacrificial bog’ type, such as the sacrificial site at Nidajno/Czaszkowo 1—one of the most scientifically prospective in the entire zone of the North European Barbaricum. They also reveal a clear preference in the way spears and javelins were made, linked to the use of ash wood for this purpose. This choice is rational, justified by the technological and operational properties of this type of wood, but it also has connotations from the world of symbolic religious imagery.
A Global Synthesis of Environmental Enrichment Effect on Fish Stress
Authors: Zhang Zonghang , He Yijie , Wang Jiujiang , Zheng Yating , Mo Jiezhang , Zhang Xiumei , Liu Wenhua
Published: November 2024

The stress‐coping ability (SCA) is one of the core aspects of fish welfare and is of vital importance for fish production in the aquaculture industry and for fish fitness in hatchery release. Environmental enrichment (EE), a method of introducing external stimuli into the husbandry environment, has been recently proposed to improve fish SCA, but the present experimental evidence is mixed, and the reasons for these discrepancies are unclear. Here, we conducted a global meta‐analysis using a data set that consists of 1786 cases from 107 studies across 42 fish species to solve this problem. Overall, we found that enriched fish had significantly higher SCA than control fish, reflected in either basal stress levels or stress responses. Meta‐regression analyses showed that specific subgroups of enrichment type, fish developmental stage, stress category, stress duration, stress place, sample tissue and indicator system showed significant positive EE effects on SCA. Multi‐model inference indicated that the indicator system, fish developmental stage, stress characteristic and enrichment mode are important drivers for the high heterogeneity among effect sizes. These results highlight the importance of introducing EE into the rearing systems, which will not only increase the welfare of aquaculture fish but also improve the ecological adaptability of released fish. The comprehensive knowledge obtained in this analysis will provide insights into fish ontogenetic plasticity and its responses to EE and have important implications for improving the production cycle in fish aquaculture and fisheries conservation.
Solving the minimum labeling global cut problem by mathematical programming
Authors: Koehler Victor J. de Sousa , Gouveia Thiago , Sousa Filho Gilberto Farias de , Ochi Luiz Satoru , Michelon Philippe , Gueye Serigne , Cabral Lucidio A. F.
Published: November 2024

An edge‐labeled graph (ELG) is a graph such that is the set of vertices, is the set of edges, is the set of labels (colors), and each edge has a label associated. Given an ELG , the goal of the minimum labeling global cut problem (MLGCP) is to find a subset such that the removal of all edges with labels in disconnects and is minimum. This work proposes three new mathematical formulations for the MLGCP, namely PART, VC, and TE as well as branch‐and‐cut algorithms to solve them. Additionally, a theoretical study was carried out on the MLGCP input graph, leading to the concept of chromatic closure, used in preprocessing algorithms for this model PART. Finally, a comprehensive polyhedral investigation of the model is performed. The computational experiments showed that the model, adopting the chromatic closure concept and its branch‐and‐cut algorithm, can solve small to average‐sized instances in reasonable times.
Immunosuppressive SOX9‐AS1 Resists Triple‐Negative Breast Cancer Senescence Via Regulating Wnt Signalling Pathway
Authors: Ye Xuan , Cen Yi , Li Quan , Zhang Yuan‐Ping , Li Qian , Li Jie
Published: November 2024

Long noncoding RNAs (lncRNAs) are involved in the regulation of triple‐negative breast cancer (TNBC) senescence, while pro‐carcinogenic lncRNAs resist senescence onset leading to the failure of therapy‐induced senescence (TIS) strategy, urgently identifying the key senescence‐related lncRNAs (SRlncRNAs). We mined seven SRlncRNAs (SOX9‐AS1, LINC01152, AC005152.3, RP11‐161 M6.2, RP5‐968 J1.1, RP11‐351 J23.1 and RP11‐666A20.3) by bioinformatics, of which SOX9‐AS1 was reported to be pro‐carcinogenic. In vitro experiments revealed the highest expression of SOX9‐AS1 in MDA‐MD‐231 cells. SOX9‐AS1 knockdown inhibited cell growth (proliferation, cycle and apoptosis) and malignant phenotypes (migration and invasion), while SOX9‐AS1 overexpression rescued these effects. Additionally, SOX9‐AS1 knockdown facilitated tamoxifen‐induced cellular senescence and the transcription of senescence‐associated secretory phenotype (SASP) factors (IL‐1α, IL‐1β, IL‐6 and IL‐8) mechanistically by resisting senescence‐induced Wnt signal (GSK‐3β/β‐catenin) activation. Immune infiltration analysis revealed that low SOX9‐AS1 expression was accompanied by a high infiltration of naïve B cells, CD8+ T cells and γδ T cells. In conclusion, SOX9‐AS1 resists TNBC senescence via regulating the Wnt signalling pathway and inhibits immune infiltration. Targeted inhibition of SOX9‐AS1 enhances SASP and thus mobilises immune infiltration to adjunct TIS strategy.
Genome sequences of toxigenic cyanobacteria from a bloom in Lake Mattamuskeet, North Carolina (United States)
Authors: Moretto Jéssica A. , Berthold David E. , Lefler Forrest W. , Mazzei Viviana , Loftin Keith A. , Laughinghouse H. Dail
Published: November 2024

Lake Mattamuskeet, the largest lake in North Carolina, USA, has undergone decades‐long eutrophication causing reduced water quality and promoting cyanobacterial blooms that may produce toxins. It is therefore necessary to evaluate the cyanobacterial diversity of the lake and their toxigenic potential. We present draft genomes of Microcystis, Pelatocladus, Raphidiopsis, and Umezakia strains isolated from Lake Mattamuskeet. The whole‐genome shotgun projects for Umezakia ovalisporum BLCC‐F208, Microcystis sp. BLCC‐F209, Microcystis sp. BLCC‐F210, Pelatocladus sp. BLCC‐F211, U. ovalisporum BLCC‐F215, and Raphidiopsis BLCC‐F218 have been deposited in GenBank under accession numbers JBHFLK000000000, JBHFLL000000000, CP169647, JBHFLM000000000, JBHFLN000000000, and JBHFLO000000000, respectively. Based on the genomic analysis, several biosynthetic gene clusters (BCGs) with varying degrees of similarity to known toxic and bioactive compound gene clusters were identified across the different cyanobacterial strains.
Estimating the minimal cost of delivering nutrition‐specific and nutrition‐sensitive interventions in Ethiopia
Authors: Maru Yetayesh , Mesfin Firehiwot , Laillou Arnaud , Noor Ramadhani , Adhikari Shiva Raj , Zelalem Meseret , Darsene Hiwot , Memire Solomon , Abie Andarge , Chitekwe Stanley
Published: November 2024

The Ethiopia Food and Nutrition Strategy (FNS 2021–2030) aims to provide evidence‐based, nutrition‐specific, and sensitive interventions to address malnutrition. A costing exercise was done to estimate the minimum financing needed to implement nutrition interventions for the ten‐year FNS, and further analysis was made to estimate the investment required to implement the prioritised recommended Lancet series interventions for 10 years. Activity‐based costing methodology was used to carry out the FNS costing for nutrition interventions prioritised by the different line ministries, and then estimated costs to implement the 2021 recommended Lancets interventions were examined from the FNS. The minimum cost of implementing the National FNS was estimated to be US$ 2.55bn with an average annual cost of US$ 250 million over 10 years (2021–2030). The cost of nutrition‐sensitive approaches represents US$ 1.8 billion (72%) and nutrition‐specific US$ 704 million (28%) of the total cost of the FNS. The Lancet series intervention costs accounted for US$ 1.7 billion (66%) of the total cost of the strategy. In this costing, half of the strong/moderate evidence (7 out of 13) Lancet interventions are costed. Therefore, the strategy's costing should be revised every 3 years to integrate new evidence and consider lessons from real expenditure. Furthermore, the need to establish a nutrition expenditure tracking system is urgent.
Identification of cell‐type specificity, trans‐ and cis‐acting functions of plant lincRNAs from single‐cell transcriptomes
Authors: Xu Jiwei , Shen Enhui , Guo Fu , Wang Kaiqiang , Hu Yurong , Shen Leti , Chen Hongyu , Li Xiaohan , Zhu Qian‐Hao , Fan Longjiang , Chu Qinjie
Published: November 2024

Long noncoding RNAs, including intergenic lncRNAs (lincRNAs), play a key role in various biological processes throughout the plant life cycle, and the advent of single‐cell RNA sequencing (scRNA‐seq) technology has opened up a valuable avenue for scrutinizing the intricate roles of lincRNAs in cellular processes.

Here, we identified a new batch of lincRNAs using scRNA‐seq data from diverse tissues of plants (rice, Arabidopsis, tomato, and maize). Based on well‐annotated single‐cell transcriptome atlases, plant lincRNAs were found to possess the same level of cell‐type specificity as mRNAs and to be involved in the differentiation of certain cell types based on pseudo‐time analysis.

Many lincRNAs were predicted to play a hub role in the cell‐type‐specific co‐expression networks of lincRNAs and mRNAs, suggesting their trans‐acting abilities. Besides, plant lincRNAs were revealed to have potential cis‐acting properties based on their genomic distances and expression correlations with the neighboring mRNAs.

Furthermore, an online platform, PscLncRNA (http://ibi.zju.edu.cn/psclncrna/), was constructed for searching and visualizing all identified plant lincRNAs with annotated potential functions. Our work provides new insights into plant lincRNAs at single‐cell resolution and an important resource for understanding and further investigation of plant lincRNAs.
Morphologic transformation of ferrofluid during micropump driving under field control
Authors: Li Wangxu , Li Zhenggui , Han Wei , Wang Ye , Zhao Jiali , Zhou Juping
Published: November 2024

The superiority of ferrofluid pumps in the fields of biomedical, life science, energy, and power research has been experimentally demonstrated. However, the mechanisms underlying the morphological transformations of ferrofluid fusion and separation during pump driving are not completely understood. To bridge the gap between the theory and practical applications of ferrofluid pumps, we employed optical methods to record the dynamic morphological transformation of rotating and fixed ferrofluids under different magnetic field polarities, magnetic field distributions, and ferrofluid mass fractions. The magnetic field polarity causes dynamic differences in the fusion‐separation process of the ferrofluid but does not affect the volume segmentation of the ferrofluid, which depends on the ratio of the magnetic field intensities. When this ratio deviates from one, the morphology of ferrofluid changes, reducing the pumping efficiency. Compared to external environmental factors, the mass fraction does not change the morphology of the ferrofluid. However, high mass fractions lead to wall‐clinging of the ferrofluid, and low mass fractions induce bubbles, both of which detrimentally affect the pumping performance. This study reveals the properties of ferrofluid and the effects of external environmental conditions on the morphological transformation of ferrofluid, providing references for optimizing ferrofluid pumps.
Comparison of the performance of classical and quantum machine‐learning methods on the detection of sugar beet Cercospora leaf disease
Authors: Katirci Ramazan , Adem Kemal , Tatar Muhammed , Ölmez Fatih
Published: November 2024

Image processing and machine‐learning (ML) techniques are essential for the detection of diseases and pests in plants. This study explored the application of quantum ML (QML) algorithms for the early detection of Cercospora beticola leaf disease in sugar beet, which causes significant impact on global sugar production. Using a dataset of 1065 images (739 diseased and 326 healthy), we extracted 70 ML statistical features, including 10 from the grey‐level co‐occurrence matrix (GLCM) and 60 colour‐related features. Performance evaluations of classical ML algorithms, such as random forest (RF; 91.95% accuracy) and extreme gradient boosting (91.95% accuracy), demonstrated strong results compared to quantum approaches. Notably, the quantum support vector classifier (QSVC) achieved an accuracy of 85% with perfect recall of 1.00, while the variational quantum classifier (VQC) recorded an accuracy of 88.73%. Dimensionality reduction via principal component analysis reduced features from 70 to 5, enabling effective classification with competitive results: ML (RF) 91.41%, VQC with limited‐memory Broyden–Fletcher–Goldfarb–Shanno with box constraints (L_BFGS_B) 88.73% and QSVC 85%. These findings highlight the potential of QML algorithms in improving agricultural disease identification and aiding in the advancement of more efficient, sustainable farming techniques.
Numerical model of N-level cascade systems for atomic Radio Frequency sensing applications
Authors: Bussey Liam W. , Kale Yogeshwar B. , Winter Samuel , Burton Fraser A. , Lien Yu-Hung , Bongs Kai , Constantinou Costas
Published: November 2024

A ready-to-use numerical model has been developed for the atomic ladder (cascade) systems which are widely exploited in Rydberg Radio Frequency (RF) sensors. The model has been explicitly designed for user convenience and to be extensible to arbitrary N-level non-thermal systems. The versatility and adaptability of the model is validated up to 4-level atomic systems by direct comparison with experimental results from the prior art. The numerical model provides a good approximation to the experimental results and provides experimentalists with a convenient ready-to-use model to optimise the operation of an N-level Rydberg RF sensor. Current sensors exploit the 4-level atomic systems based on alkali metal atoms which require visible frequency lasers and these can be expensive and also suffer from high attenuation within optical fiber. The ability to quickly and simply explore more complex N-level systems offers the potential to use cheaper and lower-loss near-infrared lasers.
Abstract A003: The role of aging in promoting immune mediated reactivation from metastatic melanoma dormancy
Authors: Coutant Kelly , Passamonte Jhon , Price Christopher , Datt Pulkit , Fane Mitchell
Published: November 2024

Metastasis is the primary cause of melanoma death. A major problem with the vast majority of previous studies is that young mice (8-weeks old, equivalent to 20 human years) are used to investigate the mechanisms of metastatic outgrowth, whereas the median age of melanoma diagnosis in humans is ∼65 years. Advanced age also correlates with metastasis, mortality, and immune dysfunction. Moreover, most studies often only focus on lung metastases, despite melanoma commonly metastasizing to sites such as the liver in patients, which are significantly more resistant to checkpoint inhibitors (ICIs) compared to patients with lung metastases. We have begun addressing these core limitations by developing novel syngeneic mouse models of melanoma metastasis and colonization in young (8-week), middle-aged (12-month), and geriatric (18-22 month) mice, in which metastatic colonization/dissemination can be targeted to either the lung or liver alone, or to both simultaneously. Our data now show that aging promotes reactivation of dormant tumor cells and subsequent outgrowth of lung and liver metastases. We have found that frontline innate lymphocytes such as NK-cells and γδ T-cells are decreased in the pre-metastatic lung and livers of aged mice relative to young mice and remain decreased during early and late-stage metastasis. Using inducible KO mouse models and antibody depletion methods in young growth restrictive mice, we find that depletion of either NK-cells or γδ T-cells is sufficient to promote reactivation from dormancy and resistance to anti-PD1 therapy. Secondly, we further delineated changes in the post-metastatic lung and liver niche. We find that PROS1 secretion by reactivated melanoma cells expressing high levels of the MER tyrosine kinase receptor (MER) in the aged metastatic lung and liver increases CD11b myeloid cells expressing the immunosuppressive factor ARG1. Within this CD11b subset, we see an increase in polymorphonuclear myeloid derived suppressor cells (PMN MDSCs). Treatment with recombinant ARG1 promotes reactivation from dormancy in young mice whilst depletion of PMN MDSCs inhibits age induced outgrowth in the lung and liver. Overall, our study highlights common immune-mediated age-related changes in the pre and post metastatic lung and liver which contribute to aggressive metastatic initiation, reactivation from dormancy, progression, and resistance to anti-PD1

Citation Format: Kelly Coutant, Jhon Passamonte, Christopher Price, Pulkit Datt, Mitchell Fane. The role of aging in promoting immune mediated reactivation from metastatic melanoma dormancy [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 A003.
Abstract A007: Emergence of metastasis-initiating cells during lung adenocarcinoma progression
Authors: Park Jin Suk , Kaygusuz Yasemin , Kenum Carson , Gatie Mohamed I. , He Lan , Sharma Roshan , Chaligné Ronan , Khan Abdul G. , Lorenz Ivo C. , Balderes Paul J. , Tammela Tuomas , Hadjantonakis Anna-Katerina , Ganesh Karuna , Rudin Charles M. , Massagué Joan
Published: November 2024

Metastatic lung adenocarcinoma (LUAD) is responsible for the most cancer-related deaths worldwide, and only a subset of cells is capable of metastasizing. Our lab has previously shown that these metastasis-initiating cells express the transmembrane glycoprotein called L1CAM and exhibit characteristics of a fetal lung developmental continuum, ranging from early progenitor states to more differentiated states. The exact signal by which progenitor cells with high metastatic potentials are generated remains unknown. Here, we demonstrate that L1CAM facilitates the signaling cascades necessary to initiate and maintain metastasis-initiating cells in LUAD. Mechanistically, L1CAM interacts with the planar cell polarity (PCP) complex and activates the transcription factor c-Jun. Activated c-Jun, as part of the AP-1 complex, binds to enhancer sites of progenitor genes and promotes the emergence of a metastasis-capable progenitor state. Pharmacological ablation of these metastatic progenitor cells by a cytotoxic L1CAM antibody effectively eliminated LUAD metastasis in vivo. Our findings identify a novel L1CAM-mediated mechanism that maintains a progenitor state essential for metastasis and can be targeted therapeutically.

Citation Format: Jin Suk Park, Yasemin Kaygusuz, Carson Kenum, Mohamed I. Gatie, Lan He, Roshan Sharma, Ronan Chaligné, Abdul G. Khan, Ivo C. Lorenz, Paul J. Balderes, Tuomas Tammela, Anna-Katerina Hadjantonakis, Karuna Ganesh, Charles M. Rudin, Joan Massagué. Emergence of metastasis-initiating cells during lung adenocarcinoma 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 A007.
Abstract A008: Microenvironmentally released cytokines mediate organ specific transcriptional profiles for metastatic colorectal cancer
Authors: Niesen Charlie , Wu Nathan , Rennhack Jonathan
Published: November 2024

Metastatic disease represents a complex series of interaction between tumors and their surrounding microenvironment. Here we utilize model systems to define organ specific transcriptional signatures present in metastatic seeding. We have identified unique epigenetic programing necessary for the colonization of the liver or the lung by colorectal cancer. We have shown that manipulation of master regulators of these signatures in vitro and in vivo changes the metastatic potential of the tumor. In specific, we have found that native cytokines within the liver and lung are engaged by the metastatic tumor cells to promote this reprograming. In the case of the liver, we have identified hepatocyte released CCL2 acts on metastasizing tumors to promote colonization. Through in vitro and in vivo models, we showed that CCL2 engagement drives upregulation of the transcription factor TCF7 and subsequent enhancer reprograming to promote survival of the metastatic cells in the liver. In the lung, we have identified additional, unique secreted cytokines which lead to the upregulation of other TCF family members. Together this data identifies an important signaling nodes in colorectal cancer. Here we propose a model in which secreted factors by the host organ, such as CCL2, reprogram genes within the tumor cell to promote growth and survival of the metastatic cell in foreign microenvironments such as the lung or liver. Targeting these proteins may kill existing metastatic lesions as well as block new metastases from forming which will be essential in improving the outcomes of patients with oligometastatic and premetastatic disease.

Citation Format: Charlie Niesen, Nathan Wu, Jonathan Rennhack. Microenvironmentally released cytokines mediate organ specific transcriptional profiles for metastatic 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 A008.
Abstract A021: HRI inhibition by hemin as a novel targeted therapy for glioblastoma via the integrated stress response
Authors: Ma Xingchuan
Published: November 2024

The treatment of glioblastoma (GBM), a highly malignant brain tumor, is critically hindered by the ineffectiveness of current modalities such as surgery, radiation, and chemotherapy. These traditional methods fail to completely remove the tumor mass and lack the ability to discriminate between cancerous and normal brain cells, often resulting in damage to healthy tissue and recurrence of the disease. This underscores an urgent necessity to develop novel therapeutic strategies that can target tumor cells with precision, offering hope for improved survival rates and quality of life for GBM patients. This study investigates targeted therapy, focusing on the Integrated Stress Response (ISR) that cancer cells harness to survive hypoxic stress. Specifically, it demonstrates that EIF2AK1, which encodes Heme-regulated eIF2α kinase (HRI), is activated under hypoxia and co-expressed with the glioma stem cell marker SOX2, which specifically happens in glioma cells, increasing the targeted accuracy of the repurposing drug. This correlation, indicating hypoxia-driven stemness, is confirmed at both the genetic level and through Gene Set Enrichment Analysis (GSEA). Furthermore, GSEA in Spatial Transcriptomics shows hypoxia-induced glycolysis, disrupting the tumor microenvironment and causing necrotic cell death. Stemness phenotype is induced in the peripheral cells due to the unfavorable hypoxic environment. Hemin, an HRI inhibitor, has been repurposed to inhibit ISR and mitigate hypoxia. Treatment with Hemin on the U87 cell line resulted in IC50 values of 23.50 µM and 52.46 µM at 24 and 48 hours, respectively, surpassing Temozolomide's efficacy. A decrease in HRI expression after the Hemin treatment suggests the and ISR activity and, potentially, hypoxia. This would reverse the unfavorable microenvironment so that the stemness phenotype doesn’t spread. Potentially, invasiveness and recurrences of GBM in clinic situation would decrease, thus potentially improving patient prognosis. The therapeutic potential of Hemin is enhanced by its ability to kill glioma cells directly and accurately in the glioma cell in original TME when cells are proliferating with adequate oxygen. Therefore, this study demonstrates the therapeutic potential of repurposing Hemin, an HRI inhibitor, to precisely target hypoxia-induced glioma stem cells in glioblastomas, disrupting the aggressive tumor microenvironment to potentially improve patient prognosis.

Citation Format: Xingchuan Ma. HRI inhibition by hemin as a novel targeted therapy for glioblastoma via the integrated stress response [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 A021.
Abstract A030: Polycomb repressive complex 2 (PRC2) mediates the epigenetic regulation of cancer-associated fibroblasts in esophageal cancer
Authors: Dunbar Karen J. , Fernandez de Bobadil Raul Navaridas , Cunningham Katherine M. , Esquea Emily , Efe Gizem , Rustgi Anil K.
Published: November 2024

Cancer-associated fibroblasts (CAFs) are a heterogenous cell population that can promote esophageal cancer progression through multiple molecular mechanisms including increased cancer cell proliferation and migration, immunosuppression, and therapeutic resistance. Despite the divergence of CAFs from normal fibroblasts with regards to phenotype and functions, CAFs rarely exhibit widespread genetic alterations. Instead, it is proposed that CAFs are regulated at the epigenetic level. Our objective is to delineate this epigenetic regulation of CAFs in esophageal cancer. Ultimately, we aim to identify the epigenetic regulatory complexes that mediate CAF heterogeneity and pro-tumorigenic functions. To this end, we completed RNA-seq and ATAC-seq on fibroblasts isolated from esophageal squamous cell carcinoma (ESCC), esophageal adenocarcinoma (EAC) and non-cancerous esophageal tissue. Enrichment analysis identified the polycomb repressive complex 2 (PRC2) as a potential regulator of ESCC and EAC CAFs. PRC2 catalyzes the methylation (mono-, di- or tri-) of lysine 27 on histone 3 (H3K27me1/2/3) resulting in transcriptional repression. Inhibition of two key proteins of PRC2 (EZH2 and SUZ12) through either pharmacological or genetic modulation, altered expression of multiple CAF phenotype related proteins and inhibited CAF functions including CAF proliferation. Ongoing studies, using co-cultures of fibroblasts and tumor cells, seek to identify if inhibition of PRC2 can prevent the initial transition of normal esophageal fibroblasts into CAFs. Importantly, we are conducting in vivo studies to determine if selective PRC2 inhibition in CAFs can inhibit esophageal tumor progression with specific focus on primary tumor growth and metastatic spread. In summary, initial studies have identify that PRC2 complex mediates CAF phenotype and functions, and we aim to establish the larger impact of these CAF specific effects on esophageal cancer.

Citation Format: Karen J. Dunbar, Raul Navaridas Fernandez de Bobadil, Katherine M. Cunningham, Emily Esquea, Gizem Efe, Anil K. Rustgi. Polycomb repressive complex 2 (PRC2) mediates the epigenetic regulation of cancer-associated fibroblasts in esophageal 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 A030.
Abstract A033: Integrating spatial transcriptomics and second harmonic generation imaging to identify targets of supermere-associated Discoidin Domain Receptor 1 involved in collagen alignment
Authors: Hamilton Maxwell S. , Tutanov Oleg , Kaur Harsimran , Simmons Alan J. , Massick Clark , Vickers Kasey , Lau Ken S. , Pozzi Ambra , Coffey Robert J.
Published: November 2024

Immune checkpoint blockade has been shown to be an effective treatment for colorectal cancers (CRCs) highly infiltrated by CD8+ T cells. However, there is a paucity of CD8+ T-cell infiltration in the majority of CRCs. We previously identified the collagen-activated receptor Discoidin Domain Receptor 1 (DDR1) as a member of a four-gene signature associated with T-cell exclusion in CRC. The cleaved ectodomain (cECD) of DDR1 induces collagen alignment, leading to T-cell exclusion in a breast cancer model. We found that almost all DDR1 cECD is found in supermeres, a novel secreted nanoparticle identified by our lab, and that DDR1 cECD is required for supermere signaling in recipient cells. We hypothesized that supermere-associated DDR1 cECD signals to CRC stromal cells, leading to collagen alignment. To test this hypothesis, we developed a method to determine which genes are associated with collagen alignment and DDR1 expression. To do this, 30 μm thick CRC sections are imaged using a Nikon AX multiphoton microscope by second harmonic generation imaging, which permits label-free imaging of collagen fibers. Spatial heatmaps of the collagen alignment are generated from the resulting images. Spatial transcriptomics is performed on a serial tumor section using the Visium v2 platform and the gene expression matrix is integrated with the collagen alignment heatmap data. As proof-of-principle, two CRC tumors have been analyzed using this method. Highly aligned regions were found to be associated with expression of genes involved in extracellular matrix organization, keloidal collagen and specific fibroblast subtypes. Genes which may be regulated by DDR1 cECD and be involved in collagen alignment will be confirmed at the protein level by multiplexed immunofluorescence on serial sections and in vitro experiments. This method will provide a rich dataset to elucidate the roles of supermeres and DDR1 cECD in T-cell exclusion and collagen fiber alignment and may support the discovery of new strategies to overcome immune exclusion in CRC.

Citation Format: Maxwell S. Hamilton, Oleg Tutanov, Harsimran Kaur, Alan J. Simmons, Clark Massick, Kasey Vickers, Ken S. Lau, Ambra Pozzi, Robert J. Coffey. Integrating spatial transcriptomics and second harmonic generation imaging to identify targets of supermere-associated Discoidin Domain Receptor 1 involved in collagen alignment [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 A033.
Abstract A041: Deciphering the crosstalk between cancer cells and stroma that drives EMT- coupled fibrosis
Authors: Spina Elena , Li Liangji , Lee Junho , Massaguè Joan
Published: November 2024

In the tumor microenvironment (TME) cancer cells engage dynamically with the stromal component in promoting tumor progression and metastasis formation that are accompanied by intratumor fibrosis. Extensive extracellular matrix (ECM) remodeling and stiffness boost fibrosis which co-occurs with poor immune infiltration. Very little is known about the cross-interactions between tumor cells and stroma. A better understanding of this dynamic relationship may advance the development of new therapies. Transforming growth factor (TGF)-β signaling in both cancer epithelial cells and stroma is crucial for the establishment of intratumor fibrosis that enhances tumor progression. We previously discovered that in cancer cells, TGF-β signaling synergizes with RAS signal to regulate classical EMT transcription factors (Snail, Zeb1) and fibrogenic factors (Il11, Pdgf, Ctgfb, Wisp and others). This synergistic program is required for metastasis formation in pancreatic and lung adenocarcinoma (LUAD) models. However, how this dual program is affecting the stromal population in vivo remains unknown. Additionally, the role of each TGF-β dependent fibrogenic factor in regulating the stroma is still unclear. Using metastasis in vivo assays, we tested the metastatic ability of LUAD cells wild-type in comparison to Knock-Out cells targeting each one of the TGF-β dependent fibrogenic factors. We found that these factors are drivers of metastasis. More interestingly, these fibrogenic factors have a preferential effect depending on the metastatic site, suggesting that survival of the cancer cells in a certain tissue is dependent on the stromal niche within the site, which will act in favor or not of their growth. We also deeply characterize the stroma of micro-metastatic lesions by using high-throughput multiplex immunofluorescence to analyze the whole tissue TME at single cell resolution and found that lack of any of these fibrogenic factors compromise the establishment of a robust ECM at the very beginning of the metastatic colonization, to favor immune infiltration and consequently lead to cancer cell clearance. Together, these findings shed light on the potential role of these specific fibrogenic factors in metastasis, how their absence impacts the TME and how targeting these factors could be beneficial in metastatic disease.

Citation Format: Elena Spina, Liangji Li, Junho Lee, Joan Massaguè. Deciphering the crosstalk between cancer cells and stroma that drives EMT- coupled fibrosis [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 A041.
Abstract A043: Senescent CAFs modulate tumor immunity and promote breast cancer progression
Authors: Ye Jiayu , Baer John M. , Faget Douglas V. , Morikis Vasilios A. , Ren Qihao , Melam Anupama , Delgado Ana Paula , Knudsen Erik , Witkiewicz Agnieszka , Powers Robert S. , Longmore Gregory D. , DeNardo David G. , Stewart Sheila A.
Published: November 2024

Cellular senescence is characterized by a series of markers such as p16INKA4(p16) positivity and a distinctive profile of secretory factors including mitogens, cytokines, and extracellular matrix (ECM) proteins that are collectively recognized as senescence-associated secretory phenotype (SASP). Interestingly, high p16 positivity in stroma strongly correlates with ductal carcinoma in situ (DCIS) recurrence, raising the possibility that p16+ senescent stromal cells contribute to breast cancer progression. To explore the hypothesis, we carried out single-cell RNA sequencing (scRNA-seq) analyses of murine and human HER2+/ER+/TNBC tumor samples and found that senescence was restricted to a specific cancer-associated fibroblasts (CAF) subpopulation that expresses numerous SASP factors that could impact tumor immunosurveillance, including cytokine SASP factors and ECM SASP factors such as collagens. We refer to these cells as senescent CAFs (senCAFs). To investigate how senCAFs impact tumorigenesis, we crossed MMTV-PyMT (PyMT) mice that spontaneously develop mammary tumors to INK-ATTAC (INK) mice, which allows selective elimination of p16+ senescent cells. Depletion of senCAFs in PyMT/INK mice led to significantly delayed tumor onset and changes in various tumor-infiltrating immune cells including natural killer (NK) cells, both of which could be recapitulated by treating PyMT mice with a senolytic drug. Monoclonal antibody- mediated NK cell depletion in the PyMT model further indicated that NK cells are indispensable for senCAF’s tumor-promoting effect. Finally, our bulk RNA-sequencing and cytotoxicity assays revealed that ECM derived from senescent but not cycling myofibroblastic mammary fibroblasts potently inhibited NK cell killing of tumor cells. Importantly, PyMT mice treated with Losartan (DuP-753), an inhibitor for collagen I synthesis, showed lower tumor burden and improved tumor-infiltrating NK cell status. Together our data highlight that senCAFs contribute to mammary gland tumorigenesis by modulating tumor ECM and immunity and suggest that senolytic treatment may limit breast cancer progression.

Citation Format: Jiayu Ye, John M. Baer, Douglas V. Faget, Vasilios A. Morikis, Qihao Ren, Anupama Melam, Ana Paula Delgado, Erik Knudsen, Agnieszka Witkiewicz, Robert S. Powers, Gregory D. Longmore, David G. DeNardo, Sheila A. Stewart. Senescent CAFs modulate tumor immunity and promote breast cancer 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 A043.
Abstract B005: Exploring breast cancer heterogeneity in the context of metastatic tumour microenvironments and therapy resistance
Authors: Gadipally Sreeja Reddy , Berthelet Jean , Lee Samuel C. , Bhuva Dharmesh D. , Roach Michael , El-Saafin Farrah , Bell Caroline , Wu Yunjian , Baloyan David , Ginestier Christphe , Emmanuelle Charafe Jauffret , Davis Melissa , Anderson Robin L. , Martelotto Luciano , Yeo Belinda , Merino Delphine
Published: November 2024

Breast tumors comprise several sub-populations of cells, so-called “clones”, with specific cellular and molecular characteristics. Some cancer clones can be more ‘aggressive’ than others in particular tumor microenvironments (TMEs), contributing to metastatic progression and drug resistance. Understanding the specific genes/pathways deregulated in these aggressive cancer cells is essential for developing new tailored treatment strategies. To accomplish this, we optimized the use of a lentiviral-based barcoding technique (Berthelet, J., et.al., Sci Adv 2021, Serrano, A., et.al., Nat Rev Cancer 2022) where cancer cells from cell lines and patient-derived xenografts are tagged with optical barcodes and transplanted into the mammary fat pads of immunodeficient mice. Upon resection of tumors and collection of metastatic organs at the experimental endpoint, we analyzed clonal fate and fitness using flow cytometry and imaging. The subsequent molecular characterization of individual clones was determined by bulk and single-cell RNA sequencing. We also leverage the use of these barcoded models to investigate the mechanisms of innate and acquired resistance to Sacituzumab Govitecan (SG), a drug recently approved for the treatment of patients with advanced breast cancer. Our studies revealed unique gene signatures and pathways associated with preferential organ tropism (in the lungs, liver and brain TMEs) and SG resistance. This comprehensive analysis, currently validated using autopsy samples and patient databases, will support the design of new predictive markers and targeted therapies for metastatic breast cancer.

Citation Format: Sreeja Reddy Gadipally, Jean Berthelet, Samuel C. Lee, Dharmesh D. Bhuva, Michael Roach, Farrah El-Saafin, Caroline Bell, Yunjian Wu, David Baloyan, Christphe Ginestier, Charafe Jauffret Emmanuelle, Melissa Davis, Robin L. Anderson, Luciano Martelotto, Belinda Yeo, Delphine Merino. Exploring breast cancer heterogeneity in the context of metastatic tumour microenvironments and therapy 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 B005.
Abstract B006: Role of the BAF complex in pancreatic cancer-associated fibroblast function
Authors: Gardiner Jaye C. , Tran Khoa A. , Franco-Barraza Janusz , Cukierman Edna
Published: November 2024

Fibroblasts comprise the majority cell type within connective tissue and play an important role in the support and repair of every organ. This homeostatic support occurs via the activation of fibroblasts (e.g. myofibroblasts) that then secrete growth factors, cytokines, and components of the extracellular matrix (ECM) that can further modulate residential cells. It has been demonstrated that cell-derived ECMs (CDMs) alone, generated in vitro, are sufficient to activate or maintain naive fibroblasts depending on the activation status of the fibroblasts that generated the CDM. Using this CDM system, we published that Netrin G1 is a regulator of pancreatic cancer-associated fibroblast (CAF) function that is pathologically expressed, and that its expression is dependent on the ECM. The mechanistic details behind how the ECM regulates fibroblasts’ gene expression to alter its function and activation status, however, is currently unknown. We previously showed that loss of the β5 integrin subunit negatively impacts the ability of pancreatic CAFs to maintain a constitutively activated state and dampens their pro- tumorigenic functions. RNA sequencing of these β5-deficient CAFs showed altered expression of Netrin G1, as well as members of the BAF (BRG/BRM-associated factor) family of chromatin remodelers. The goal of this project is to elucidate the role of the BAF complex in mediating the outside-in signaling from the ECM. To determine the role of the BAF complex on fibroblast activation and function, knockdown (KD) cell lines for the ATP-subunits Brg1 and Brm1 were generated in patient-derived pancreatic CAFs. Akin to β5 KD CAFs, loss of both Brg1 and Brm1 decreased the expression of published TGFβ-dependent markers of pancreatic CAF activation. However, unlike β5 KD CAFs that are unable to generate substantial, aligned CDMs, Brg1 and Brm1 KD CAFs had no effect on matrix deposition or alignment; like Netrin G1 KD CAFs that have decreased pro-tumor functions. Indeed, loss of Brm1 appears to decrease Netrin G1 akin to β5 KD CAFs. Expression levels of Netrin G1 were not restored in β5 nor Brm1 KD CAFs treated with recombinant TGFβ-1 during CDM production, whereas the TGFβ-dependent activation markers were. Collectively, these data begin to suggest that pro-tumorigenic ECM- mediated signaling may alter fibroblast gene expression via the BAF complex in a TGFβ dependent manner, opening the door to epigenetic drug targets as a new therapeutic access point to normalize the tumor-enabling microenvironment in pancreatic cancer patients.

Citation Format: Jaye C. Gardiner, Khoa A. Tran, Janusz Franco-Barraza, Edna Cukierman. Role of the BAF complex in pancreatic cancer-associated fibroblast function [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 B006.