bluuebunny/crossref_metadata_2025 huggingface dataset:
A combination of genomics and transcriptomics provides insights into the distribution and differential mRNA expression of type VI secretion system in clinical
Klebsiella pneumoniae
Authors: Li Wanzhen , Huang Xiaolan , Li Dan , Liu Xiaofen , Jiang Xiaoying , Bian Xingchen , Li Xin , Zhang Jing
Published: March 2024

The type VI secretion system (T6SS) serves as a crucial molecular weapon in interbacterial competition and significantly influences the adaptability of bacteria in their ecological niche. However, the distribution and function of T6SS in clinical
Klebsiella pneumoniae
, a common opportunistic nosocomial pathogen, have not been fully elucidated. Here, we conducted a genomic analysis of 65 clinical
K. pneumoniae
isolates obtained from patients with varying infections. Genes encoding a T6SS cluster present in all analyzed strains of
K. pneumoniae,
and strains with identical sequence type carried structurally and numerically identical T6SS. Our study also highlights the importance of selecting conserved regions within essential T6SS genes for PCR-based identification of T6SS in bacteria. Afterward, we utilized the predominant sequence type 11 (ST11)
K. pneumoniae
HS11286 to investigate the effect of knocking out T6SS marker genes
hcp
or
vgrG
. Transcriptome analysis identified a total of 1,298 co-upregulated and 1,752 co-downregulated differentially expressed genes in both mutants. Pathway analysis showed that only Δ
hcp
mutant exhibited alterations in transport, establishment of localization, localization, and cell processes. The absence of
hcp
or
vgrG
gene suppressed the expression of other T6SS-related genes within the locus I cluster. Additionally, interbacterial competition experiments showed that
hcp
and
vgrG
are essential for competitive ability of ST11
K. pneumoniae
HS11286. This study furthers our understanding of the genomic characteristics of T6SS in clinical
K. pneumoniae
and suggests the involvement of multiple genes in T6SS of strain HS11286.

IMPORTANCE

Gram-negative bacteria use type VI secretion system (T6SS) to deliver effectors that interact with neighboring cells for niche advantage.
Klebsiella pneumoniae
is an opportunistic nosocomial pathogen that often carries multiple T6SS loci, the function of which has not yet been elucidated. We performed a genomic analysis of 65 clinical
K. pneumoniae
strains isolated from various sources, confirming that all strains contained T6SS. We then used transcriptomics to further study changes in gene expression and its effect on interbacterial competition following the knockout of key T6SS genes in sequence type 11 (ST11)
K. pneumoniae
HS11286. Our findings revealed the distribution and genomic characteristics of T6SS in clinical
K. pneumoniae
. This study also described the overall transcriptional changes in the predominant Chinese ST11 strain HS11286 upon deletion of crucial T6SS genes. Additionally, this work provides a reference for future research on the identification of T6SS in bacteria.
Promoting Urban Studies and Practice with Emerging Technologies: City Laboratory, New City, and Future City Exploration
Authors: Long Ying , Zhang Enjia
Published: March 2024

The Fourth Industrial Revolution, marked by emerging/disruptive technologies like mobile internet, big data, robotics, artificial intelligence (AI), immersive media (VR/AR/MR), and the Internet of Things (IoT), is transforming cities and promoting urban development. This paper argues that these technologies foster urban studies and implementation in three pathways: methodology, epistemology, and practice. First, the new data environment offers a foundation for quantitative and objective urban studies, enabling researchers to treat cities as laboratories and conduct city experiments worldwide. Second, emerging technologies are reshaping contemporary urban life and space, promoting the update of urban theories. Third, these technologies are expected to be applied as new elements in the urban planning and design processes to create smart urban spatial forms that cater to contemporary needs. Overall, this paper highlights the potential significance of emerging technologies for urban research and development in terms of research methods and data support, theoretical updates and iterations, and practical urban planning and design.
East Barents Basin and Admiralty High Composite Tectono-Sedimentary Elements, Barents Sea
Authors: Drachev Sergey S. , Henriksen Erik , Shkarubo Sergey I. , Sobolev Peter
Published: March 2024

The East Barents Sea includes two major tectonic elements, the East Barents Basin (EBB) and the Admiralty High, which are, in the context of the volume, characterized as composite tectono-sedimentary elements. Whereas they share some stratigraphy, their early history may differ. The EBB is a dominant structural feature of the Barents Shelf, and one of the largest and deepest sedimentary basins in the Arctic. The Admiralty High rims the EBB in the east.

The advance in understanding the East Barents Sea geology was achieved during the 1980s and 1990s mainly due to a significant amount of multichannel reflection seismic data and a number of drilled deep exploration wells. These wells tested many large anticlinal structures and made several large gas discoveries, including the giant Shtokman gas and gas condensate accumulation. In the following decades, many important geological results were published in the international and Russian literature. In this chapter we provide a summary of the geology and petroleum geology of the East Barents Sea based on published results and public-domain geological reports.
A Survey on Content Retrieval on the Decentralised Web
Authors: Keizer Navin , Ascigil Onur , Król Michal , Kutscher Dirk , Pavlou George
Published: March 2024

The control, governance, and management of the web have become increasingly centralised, resulting in security, privacy, and censorship concerns. Decentralised initiatives have emerged to address these issues, beginning with decentralised file systems. These systems have gained popularity, with major platforms serving millions of content requests daily. Complementing the file systems are decentralised search engines and name-registry infrastructures, together forming the basis of a
decentralised web
. This survey article analyses research trends and emerging technologies for content retrieval on the decentralised web, encompassing both academic literature and industrial projects.

Several challenges hinder the realisation of a fully decentralised web. Achieving comparable performance to centralised systems without compromising decentralisation is a key challenge. Hybrid infrastructures, blending centralised components with verifiability mechanisms, show promise to improve decentralised initiatives. While decentralised file systems have seen more mature deployments, they still face challenges such as usability, performance, privacy, and content moderation. Integrating these systems with decentralised name-registries offers a potential for improved usability with human-readable and persistent names for content. Further research is needed to address security concerns in decentralised name-registries and enhance governance and crypto-economic incentive mechanisms.
Learning Nighttime Semantic Segmentation the Hard Way
Authors: Liu Wenxi , Cai Jiaxin , Li Qi , Liao Chenyang , Cao Jingjing , He Shengfeng , Yu Yuanlong
Published: March 2024

Nighttime semantic segmentation is an important but challenging research problem for autonomous driving. The major challenges lie in the small objects or regions from the under-/over-exposed areas or suffer from motion blur caused by the camera deployed on moving vehicles. To resolve this, we propose a novel hard-class-aware module that bridges the main network for full-class segmentation and the hard-class network for segmenting aforementioned hard-class objects. In specific, it exploits the shared focus of hard-class objects from the dual-stream network, enabling the contextual information flow to guide the model to concentrate on the pixels that are hard to classify. In the end, the estimated hard-class segmentation results will be utilized to infer the final results via an adaptive probabilistic fusion refinement scheme. Moreover, to overcome over-smoothing and noise caused by extreme exposures, our model is modulated by a carefully crafted pretext task of constructing an exposure-aware semantic gradient map, which guides the model to faithfully perceive the structural and semantic information of hard-class objects while mitigating the negative impact of noises and uneven exposures. In experiments, we demonstrate that our unique network design leads to superior segmentation performance over existing methods, featuring the strong ability of perceiving hard-class objects under adverse conditions.
Database Repairing with Soft Functional Dependencies
Authors: Carmeli Nofar , Grohe Martin , Kimelfeld Benny , Livshits Ester , Tibi Muhammad
Published: March 2024

A common interpretation of soft constraints penalizes the database for every violation of every constraint, where the penalty is the cost (weight) of the constraint. A computational challenge is that of finding an optimal subset: a collection of database tuples that minimizes the total penalty when each tuple has a cost of being excluded. When the constraints are strict (i.e., have an infinite cost), this subset is a “cardinality repair” of an inconsistent database; in soft interpretations, this subset corresponds to a “most probable world” of a probabilistic database, a “most likely intention” of a probabilistic unclean database, and so on. Within the class of functional dependencies, the complexity of finding a cardinality repair is thoroughly understood. Yet, very little is known about the complexity of finding an optimal subset for the more general soft semantics. The work described in this manuscript makes significant progress in that direction. In addition to general insights about the hardness and approximability of the problem, we present algorithms for two special cases (and some generalizations thereof): a single functional dependency, and a bipartite matching. The latter is the problem of finding an optimal “almost matching” of a bipartite graph where a penalty is paid for every lost edge and every violation of monogamy. For these special cases, we also investigate the complexity of additional computational tasks that arise when the soft constraints are used as a means to represent a probabilistic database in the case of a probabilistic unclean database.
Personalised Multi-modal Interactive Recommendation with Hierarchical State Representations
Authors: Wu Yaxiong , Macdonald Craig , Ounis Iadh
Published: March 2024

Multi-modal interactive recommender systems (MMIRS) can effectively guide users towards their desired items through multi-turn interactions by leveraging the users’ real-time feedback (in the form of natural-language critiques) on previously recommended items (such as images of fashion products). In this scenario, the users’ preferences can be expressed by both the users’ past interests from their historical interactions and their current needs from the real-time interactions. However, it is typically challenging to make satisfactory personalised recommendations across multi-turn interactions due to the difficulty in balancing the users’ past interests and the current needs for generating the users’ state (i.e., current preferences) representations over time. However, hierarchical reinforcement learning has been successfully applied in various fields by decomposing a complex task into a hierarchy of more easily addressed subtasks. In this journal article, we propose a novel personalised multi-modal interactive recommendation model (PMMIR) using hierarchical reinforcement learning to more effectively incorporate the users’ preferences from both their past and real-time interactions. In particular, PMMIR decomposes the personalised interactive recommendation process into a sequence of two subtasks with hierarchical state representations: a first subtask where a history encoder learns the users’ past interests with the hidden states of history for providing personalised initial recommendations and a second subtask where a state tracker estimates the current needs with the real-time estimated states for updating the subsequent recommendations. The history encoder and the state tracker are jointly optimised with a single objective by maximising the users’ future satisfaction with the recommendations. Following previous work, we train and evaluate our PMMIR model using a user simulator that can generate natural-language critiques about the recommendations as a surrogate for real human users. Experiments conducted on two derived fashion datasets from two well-known public datasets demonstrate that our proposed PMMIR model yields significant improvements in comparison to the existing state-of-the-art baseline models. The datasets and code are publicly available at:
https://github.com/yashonwu/pmmir
Dispase/collagenase cocktail allows for coisolation of satellite cells and fibroadipogenic progenitors from human skeletal muscle
Authors: Balayan Alis , DeBoutray Marie , Molley Thomas G. , Ruoss Severin , Maceda Matthew , Sevier Ashley , Robertson Catherine M. , Ward Samuel R. , Engler Adam J.
Published: March 2024

We demonstrated that a dispase/collagenase cocktail allows for simultaneous isolation of SCs and FAPs with 2× higher SC yield compared with other studies. We provide a thorough characterization of SC and FAP in vitro expansion that other studies have not reported. Following our dissociation, SCs and FAPs were able to expand by up to 1012 cells before reaching senescence and maintained differentiation capacity in vitro demonstrating their efficacy for clinical translation for muscle injury.
Distinct subpopulations of human subcutaneous adipose tissue precursor cells revealed by single-cell RNA sequencing
Authors: Divoux Adeline , Whytock Katie L. , Halasz Laszlo , Hopf Meghan E. , Sparks Lauren M. , Osborne Timothy F. , Smith Steven R.
Published: March 2024

Identification of distinct subpopulations of adipose-derived stem cells (ADSCs) in upper body abdominal subcutaneous (ABD) and lower body gluteofemoral subcutaneous (GF) adipose tissue depots. In ABD-ADSCs, subpopulations are more committed to adipocyte lineage. GF-ADSC subpopulations are enriched for genes involved in lipids and cholesterol metabolism. Similar depot differences were found in stem cell population identified in freshly isolated stoma vascular fraction. The repertoire of ADSCs subpopulations was different in apple-shaped versus pear-shaped women.
False Alarm Causes and Wind Field Sensitivity Analysis of a Severe Rainfall Event in the Guangdong-Hong Kong-Macao Greater Bay Area Urban Cluster
Authors: Zhang Lan , Zheng Jiawen , Li Huaiyu , Yu Rui , Wei Lei , Zhang Yufei
Published: March 2024

On May 11, 2022, despite the favorable upper and lower-level circulation patterns of the high-altitude trough, shear line, and southwest jet stream, the urban cluster of the Guangdong-Hong Kong-Macao Greater Bay Area experienced light to moderate rainfall, deviating significantly from the forecasted heavy rain and local heavy rainstorm. This study explores the reasons for false alarms and predictability using ground observation data, radar data, ECMWF-ERA5 reanalysis field data, and ECMWF and CMA-TRAMS forecast data. The results indicate that the warm and moist airflow transported by the low-level jet stream was intercepted by the upstream MCS (mesoscale convective system) along the coastal area of western Guangdong, and inadequate conditions of negative vorticity dynamics led to insufficient moisture, thermodynamic, and dynamic conditions over the urban cluster, preventing the triggering of heavy precipitation. In addition, the 700 hPa westerly flow guiding the airflow and the stable low-level shear line, coupled with surface convergence lines, influenced the northward or southward movement of MCSs along the coastal and inland regions of western Guangdong. The weak and discontinuous intensity of echoes in the upstream Zhaoqing region further hindered the influence of surrounding echoes on the urban cluster. Numerical forecast models ECMWF and CMA-TRAMS overestimated the 850 hPa windspeed and 925 hPa meridional windspeed, resulting in the forecasted urban cluster experiencing heavy rain. Sensitivity tests of wind fields indicate that the 850 hPa wind field information is more sensitive to precipitation in the urban cluster. In this process, weak signal correction can be achieved in strong precipitation forecasts using the distinct signal of lower 850 hPa water vapor flux divergence compared to 925 hPa. Therefore, in the future, when the Guangdong-Hong Kong-Macao Greater Bay Area encounters similar warm-sector heavy rainfall events, adjustments to model forecasts can be made using specific 850 hPa elements such as wind speed, water vapor flux divergence, or specific humidity to enhance predictive accuracy.
Effects of Different Carbon Sources on the Growth and Production of Rotifer (Brachionus plicatilis) in a Zero‐Water Exchange Biofloc Culture System
Authors: Hosain Md. Eilious , Amin S. M. Nurul , Kamarudin Mohd Salleh , Arshad Aziz , Karim Murni , Naser Md. Niamul , Fotedar Ravi
Published: March 2024

Brachionus plicatilis is considered an indispensable first live feed for many fish and crustacean larvae; the demand for the species has increased globally. The mass production of the rotifer involves quality microalga and a standard diet; this culture is expensive and needs a skilled workforce. The hatchery’s incubators are likely to have limited resources leading to sudden rotifer culture crashes that ultimately disrupt the larvae production. More recently, improved sustainable rotifer production has been achieved through biofloc technology (BFT) that uses fish wastes and wheat flour. However, various carbon sources, which are typically used in BFT‐based systems need to be explored and tested for their efficacies. A 4‐day rotifer, B. plicatilis batch culture, was conducted in BFT systems by adding four carbon sources: molasses, rice bran, maize starch, and palm kernel expeller versus a control (without any carbon source). Fifteen 125 L containing polyethylene tanks with a water volume of 100 L were used for this experiment, and each tank was stocked with 5 × 106 rotifer (50 rotifers mL−1). Different carbon sources in triplicates including a control were tested as treatments. The carbon : nitrogen ratio in the study was maintained at 10 : 1. The rotifers were fed with Baker’s yeast at 1.0, 0.50, and 0.25 g million-−1 rotifers for the first, second, and third day and continued after that. Total ammonia–nitrogen (TAN) and pH values were found to be significantly (p < 0.05) lower in all four treatments of the BFT system than in the control. Significantly higher (p < 0.05) settleable solids were obtained in the molasses and rice bran treatments than those in the maize starch or palm kernel expeller. Likewise, the significantly (p < 0.05) higher density of B. plicatilis and their specific growth rate were obtained in the molasses and rice bran‐adding treatments, followed by those in palm kernel expeller, maize starch, and the control. This study indicates that molasses and rice bran as carbon sources when added to BFT‐based systems enhance B. plicatilis production.
Supplementary Figure 1 from AXL/WRNIP1 Mediates Replication Stress Response and Promotes Therapy Resistance and Metachronous Metastasis in HER2+ Breast Cancer
Authors: Marquez-Palencia Mauricio , Reza Herrera Luis , Parida Pravat Kumar , Ghosh Suvranil , Kim Kangsan , Das Nikitha M. , Gonzalez-Ericsson Paula I. , Sanders Melinda E. , Mobley Bret C. , Diegeler Sebastian , Aguilera Todd A. , Peng Yan , Lewis Cheryl M. , Arteaga Carlos L. , Hanker Ariella B. , Whitehurst Angelique W. , Lorens James B. , Brekken Rolf A. , Davis Anthony J. , Malladi Srinivas
Published: March 2024

Supplementary Figure 1
Supplementary Data from Chronic Stress Dampens Lactobacillus Johnsonii–Mediated Tumor Suppression to Enhance Colorectal Cancer Progression
Authors: Cao Qiuhua , Zhao Mingrui , Su Yali , Liu Siliang , Lin Yanting , Da Huijuan , Yue Chongxiu , Liu Yiming , Jing Dongquan , Zhao Qixiang , Liu Ning , Du Juan , Zuo Zhanjie , Fu Yao , Chen Anqi , Birnbaumer Lutz , Yang Yong , Dai Beiying , Gao Xinghua
Published: March 2024

Figure S2
Supplementary File 2 from Adipose Triglyceride Lipase Is a Therapeutic Target in Advanced Prostate Cancer That Promotes Metabolic Plasticity
Authors: Awad Dominik , Cao Pham Hong Anh , Pulliam Thomas L. , Spradlin Meredith , Subramani Elavarasan , Tellman Tristen V. , Ribeiro Caroline F. , Muzzioli Riccardo , Jewell Brittany E. , Pakula Hubert , Ackroyd Jeffrey J. , Murray Mollianne M. , Han Jenny J. , Leng Mei , Jain Antrix , Piyarathna Badrajee , Liu Jingjing , Song Xingzhi , Zhang Jianhua , Klekers Albert R. , Drake Justin M. , Ittmann Michael M. , Coarfa Cristian , Piwnica-Worms David , Farach-Carson Mary C. , Loda Massimo , Eberlin Livia S. , Frigo Daniel E.
Published: March 2024

IP/MS summary table describing the ATGL interactome in C4-2 cells.
Supplementary Figure6 from Adipocyte Precursor-Derived NRG1 Promotes Resistance to FGFR Inhibition in Urothelial Carcinoma
Authors: Hosni Sana , Kilian Viola , Klümper Niklas , Gabbia Daniela , Sieckmann Katharina , Corvino Dillon , Winkler Anja , Saponaro Miriam , Wörsdörfer Karin , Schmidt Doris , Hahn Oliver , Zanotto Ilaria , Bertlich Marina , Toma Marieta , Bald Tobias , Eckstein Markus , Hölzel Michael , Geyer Matthias , Ritter Manuel , Wachten Dagmar , De Martin Sara , Alajati Abdullah
Published: March 2024

Supplementary Figure6
Table S6 from Pooled CRISPR Screening Identifies P-Bodies as Repressors of Cancer Epithelial–Mesenchymal Transition
Authors: Fang Liang , Zhang Li , Wang Mengran , He Yuhao , Yang Jiao , Huang Zengjin , Tan Ying , Fang Ke , Li Jun , Sun Zhiyuan , Li Yanping , Tang Yisen , Liang Weizheng , Cui Huanhuan , Zhu Qionghua , Wu Zhe , Li Yiming , Hu Yuhui , Chen Wei
Published: March 2024

Table S6. The list of differentially expressed proteins upon DDX6 or EDC4 knockout
Data from Adipocyte Precursor-Derived NRG1 Promotes Resistance to FGFR Inhibition in Urothelial Carcinoma
Authors: Hosni Sana , Kilian Viola , Klümper Niklas , Gabbia Daniela , Sieckmann Katharina , Corvino Dillon , Winkler Anja , Saponaro Miriam , Wörsdörfer Karin , Schmidt Doris , Hahn Oliver , Zanotto Ilaria , Bertlich Marina , Toma Marieta , Bald Tobias , Eckstein Markus , Hölzel Michael , Geyer Matthias , Ritter Manuel , Wachten Dagmar , De Martin Sara , Alajati Abdullah
Published: March 2024

Abstract
Aberrations of the fibroblast growth factor receptor (FGFR) family members are frequently observed in metastatic urothelial cancer (mUC), and blocking the FGF/FGFR signaling axis is used as a targeted therapeutic strategy for treating patients. Erdafitinib is a pan-FGFR inhibitor, which has recently been approved by the FDA for mUC with FGFR2/3 alterations. Although mUC patients show initial response to erdafitinib, acquired resistance rapidly develops. Here, we found that adipocyte precursors promoted resistance to erdafitinib in FGFR-dependent bladder and lung cancer in a paracrine manner. Moreover, neuregulin 1 (NRG1) secreted from adipocyte precursors was a mediator of erdafitinib resistance by activating human epidermal growth factor receptor 3 (ERBB3; also known as HER3) signaling, and knockdown of NRG1 in adipocyte precursors abrogated the conferred paracrine resistance. NRG1 expression was significantly downregulated in terminally differentiated adipocytes compared with their progenitors. Pharmacologic inhibition of the NRG1/HER3 axis using pertuzumab reversed erdafitinib resistance in tumor cells in vitro and prolonged survival of mice bearing bladder cancer xenografts in vivo. Remarkably, data from single-cell RNA sequencing revealed that NRG1 was enriched in platelet-derived growth factor receptor-A (PDGFRA) expressing inflammatory cancer-associated fibroblasts, which is also expressed on adipocyte precursors. Together, this work reveals a paracrine mechanism of anti-FGFR resistance in bladder cancer, and potentially other cancers, that is amenable to inhibition using available targeted therapies.
Significance:
Acquired resistance to FGFR inhibition can be rapidly promoted by paracrine activation of the NRG1/HER3 axis mediated by adipocyte precursors and can be overcome by the combination of pertuzumab and erdafitinib treatment.

See related commentary by Kolonin and Anastassiou, p. 648
Joint Associations of Diet and Device-Measured Physical Activity with Mortality and Incident CVD and Cancer: A Prospective Analysis of the UK Biobank Study
Authors: Inan-Eroglu Elif , Ahmadi Matthew , Biswas Raaj Kishore , Ding Ding , Rezende Leandro F.M. , Lee I-Min , Giovannucci Edward L. , Stamatakis Emmanuel
Published: March 2024

Background:

We examined the joint associations of diet and device-measured intensity-specific physical activity (PA) with all-cause mortality (ACM), cardiovascular disease (CVD), and cancer incidence.

Methods:

We used data from 79,988 participants from the UK Biobank, a population-based prospective cohort study. Light PA (LPA), moderate-to-vigorous PA (MVPA), vigorous PA (VPA), and total PA (TPA) were measured using a wrist-worn accelerometer. Diet quality score (DQS) was based on 10 foods and ranged from 0 (unhealthiest) to 100 (healthiest) points. We derived joint PA and diet variables. Outcomes were ACM, CVD, and cancer incidence including PA, diet and adiposity-related (PDAR) cancer.

Results:

During a median follow-up of 8 years, 2,863 deaths occurred, 11,053 participants developed CVD, 7,005 developed cancer, and 3,400 developed PDAR cancer. Compared with the least favorable referent group (bottom PA tertile/low DQS), participants with middle and high (total and intensity specific) PA, except for LPA, had lower ACM risk and incident CVD risk, regardless of DQS. For example, among middle and high VPA and high DQS groups, CVD HR were 0.79 (95% CI, 0.74–0.86) and 0.75 (95% CI, 0.69–0.82), respectively. The pattern of cancer results was less pronounced but in agreement with the ACM and CVD incidence findings (e.g., HR, 0.90, 95% CI, 0.81–0.99; 0.88, 0.79–0.98; and 0.82, 0.74–0.92 among high VPA for low, moderate, and high DQS groups, respectively).

Conclusions:

Device-measured PA reveals novel joint associations with diet on health outcomes.

Impact:

Our results emphasize the crucial role of PA in addition to a healthy diet for reducing chronic diseases and mortality risk.
Figure S4 from PUMA/RIP3 Mediates Chemotherapy Response via Necroptosis and Local Immune Activation in Colorectal Cancer
Authors: Chen Dongshi , Ermine Kaylee , Wang Yi-Jun , Chen Xiaojun , Lu Xinyan , Wang Peng , Beer-Stolz Donna , Yu Jian , Zhang Lin
Published: March 2024

Figure S4. Knockout or knockdown of RIP3, but not RIP1, suppressed necroptosis induced by 5-FU and other antimetabolites.
Supplementary Table S2 from Palazestrant (OP-1250), A Complete Estrogen Receptor Antagonist, Inhibits Wild-type and Mutant ER-positive Breast Cancer Models as Monotherapy and in Combination
Authors: Parisian Alison D. , Barratt Susanna A. , Hodges-Gallagher Leslie , Ortega Fabian E. , Peña Guadalupe , Sapugay Judevin , Robello Brandon , Sun Richard , Kulp David , Palanisamy Gopinath S. , Myles David C. , Kushner Peter J. , Harmon Cyrus L.
Published: March 2024

PROSeq gene ontology dataset following treatment of MCF7 and CAMA-1 cells with ER-alpha ligands.
Fig. S9 from Radiation Synergizes with IL2/IL15 Stimulation to Enhance Innate Immune Activation and Antitumor Immunity
Authors: Li Xuefeng , Huntoon Kristin , Wang Yifan , Lee DaeYong , Dong Shiyan , Antony Abin , Walkey Carl , Kim Betty Y.S. , Jiang Wen
Published: March 2024

Fig. S9
Abstract A045: Engineered systems for tumor modeling facilitate the assessment of theraputic interventions
Authors: Mueller Joseph , Yao Ryan , Selting Kim , Best-Popescu Catherine , Harley Brendan , Pedron-Haba Sara
Published: March 2024

Brain cancers remain some of the most challenging tumors to treat. The goal of our research is to use a 3D in vitro model to acquire in-depth understanding of the unique environment of brain tumors in order to find new biomarkers of disease and develop more efficient therapeutic approaches. Glioblastomas (GBM) present a very poor prognosis, they exhibit high infiltration into brain parenchyma, impairing surgical resection and leading to recurrence. The recurrent tumor is predominantly more aggressive and resistant to available therapeutic strategies. Brain extracellular matrix (ECM) plays a key role in glioblastoma invasion and therapeutic resistance. In particular, the aberrant biosynthesis of the main component of brain ECM, hyaluronic acid (HA), has been associated to pathological conditions. We investigate the influence of tumor extracellular microenvironment in glioblastoma progression. We focus on the tumor-associated HA biosynthesis in response to biophysical alterations, such as hypoxia and stiffness, and after radio and chemotherapeutic interventions. The ability to manipulate tumor ECM can improve therapeutic outcomes and restrict glioblastoma growth and infiltration.

Citation Format: Joseph Mueller, Ryan Yao, Kim Selting, Catherine Best-Popescu, Brendan Harley, Sara Pedron-Haba. Engineered systems for tumor modeling facilitate the assessment of theraputic interventions [abstract]. In: Proceedings of the AACR Special Conference on Brain Cancer; 2023 Oct 19-22; Minneapolis, Minnesota. Philadelphia (PA): AACR; Cancer Res 2024;84(5 Suppl_1):Abstract nr A045.
Abstract B014: CHD5 suppresses glioblastoma by inhibiting MYC
Authors: Sun Xueqin Sherine , Mills Alea
Published: March 2024

Fundamentally, cancer is a disease caused by genetic and epigenetic alterations that converge to reprogram gene expression networks, leading to unrestrained proliferation. Glioblastoma (GBM) is the most prevalent and aggressive primary brain cancer, median survival being approximately one year and the 5-year survival rate being only 5%. Despite decades of effort, this devastating picture has not appreciably improved and effective therapies have been elusive for GBM patients. A better understanding of GBM biology is essential for developing more effective therapies. Although several genetic alterations have been implicated in gliomagenesis, driving genetic factors responsible for GBM are still obscure, and the interplay between genetic alterations and epigenetic dysregulation is largely undocumented during the gliomagenic process. Here, we show that CHD5 — a gene mapping to the 1p36 chromosomal region that is notoriously deleted in many cancers, is recurrently deleted in over 20% of GBM cases and is further downregulated through epigenetic means. To delineate how CHD5 loss promotes gliomagenesis, we established a glioma-prone mouse model harboring conditional alleles of Pten, Trp53, and Chd5. We developed an engineered mouse neural stem cell (NSCs)-based strategy to elicit glioma formation, as NSCs are the major cell-of-origin for GBM. We show that Chd5 loss significantly impairs NSCs differentiation while promoting proliferation, transformation, and gliomagenesis in vivo. Mechanistically, Chd5 forms a Chd3-containing but Chd4-independent NuRD complex that directly binds the Myc promoter and super enhancers to govern Myc expression in normal NSCs, with the Snf2 domain of Chd5 playing the most critical chromatin regulating role in the context of GBM. Chd5 loss triggers the remodeling of chromatin, enhances accessibility, and augments Myc expression, leading to the formation of highly aggressive glioma. Furthermore, reactivating CHD5 in human GBM xenograft models significantly extends survival. This work demonstrates the tumor suppressive role of CHD5 in gliomagenesis, providing therapeutic insights for cancers with 1p36 deletions. In parallel, this work presents a powerful strategy for rapidly interrogating gene function during gliomagenesis using engineering NSCs and highlights the generation of novel mouse models with classic clinical features of GBM, offering new approaches for elucidating GBM biology that can inform on therapeutic opportunities for treating patients with GBM.

Citation Format: Xueqin Sherine Sun, Alea Mills. CHD5 suppresses glioblastoma by inhibiting MYC [abstract]. In: Proceedings of the AACR Special Conference on Brain Cancer; 2023 Oct 19-22; Minneapolis, Minnesota. Philadelphia (PA): AACR; Cancer Res 2024;84(5 Suppl_1):Abstract nr B014.
Abstract B033: Histone H3.3 K27M and G34R/V glioma driver mutations inhibit mitotic phosphorylation of H3.3 S31, driving tumor formation by inducing chromosomal instability
Authors: Day Charles A. , Grigore Florina , Langfald Alyssa , Hakkim Faruck , Daniels David , Vaughan Kevin , Robinson James , Hinchcliffe Edward
Published: March 2024

Diffuse gliomas are pediatric high-grade gliomas that frequently harbor heterozygous histone H3.3 K27M, G34R, or G34V mutations. These mutations alter histone methylations, although the precise mechanism(s) of gliomagenesis remains uncertain. H3.3 contains a unique Serine at position 31 that is phosphorylated in prophase and dephosphorylated in anaphase during normal cell division. Previously we have reported that chromosome missegregation triggers H3.3 S31 phosphorylation along chromosome arms in ana/telophase leading to p53-induced cell cycle arrest. Here we show, in vitro and in vivo, that H3.3 K27M, G34R, and G34V suppress S31 phosphorylation by its mitotic kinase, Chk1. In diploid cells, overexpression of H3.3 K27M, G34R, G34V, or non-phosphorylatable S31A significantly increases the frequency of chromosome missegregation, while H3.3 K36M did not. This missegregation phenotype could be rescued by overexpression of K27M/S31E or G34R/S31E double mutants. Next, we used CRISPR/Cas9 gene editing to revert K27M or G34V patient-derived DMG cells to WT or replace the mutant allele with S31A. Reversion to WT increased metaphase S31 phosphorylation and reduced chromosome missegregations, but inserting an S31A mutation caused more mitotic defects. Following a mitotic error, newly formed aneuploid cells overexpressing K27M, G34R, or G34V suppress p53 levels and continue to divide, while WT overexpressing cells always arrest. To test the effects of diminished S31 phosphorylation on gliomagenesis, we utilized a novel mouse model of glioma. Expression of PDGFß linked to H3.3K27M, H3.3G34R, and H3.3S31A in neural stem cells in vivo promoted the development of high-grade gliomas in under 100 days, whereas PDFß-H3.3WT did not. Notably, the S31A tumors had histologically normal levels of K27me3 and K36me3. This work shows that a single glioma-associated point mutation in H3.3 can generate chromosomal instability, and which is a major contributing factor to H3.3 K27M and G34-altered glioma formation.

Citation Format: Charles A. Day, Florina Grigore, Alyssa Langfald, Faruck Hakkim, David Daniels, Kevin Vaughan, James Robinson, Edward Hinchcliffe. Histone H3.3 K27M and G34R/V glioma driver mutations inhibit mitotic phosphorylation of H3.3 S31, driving tumor formation by inducing chromosomal instability [abstract]. In: Proceedings of the AACR Special Conference on Brain Cancer; 2023 Oct 19-22; Minneapolis, Minnesota. Philadelphia (PA): AACR; Cancer Res 2024;84(5 Suppl_1):Abstract nr B033.
Abstract B052: Hyaluronic acid influences amino acid metabolism in glioblastoma's U87-MG cell line in a 2D culture via LAT1 transporter expression
Authors: Bale Ashwin A. , Bhargava Rohit , Harley Brendan
Published: March 2024

Glioblastoma (GBM) is one of the deadliest forms of brain cancer with high inter and intra tumor heterogeneity and altered metabolism pathways. GBM’s microenvironment is highly complex and plays a key role in determining overall tumor growth and patient survival. Hyaluronic acid (HA) is one of the key components of this tumor microenvironment and is often associated with poor prognosis. HA is present in the form of polymeric chain units, and it is highly likely that the resulting molecular weight (MW) distribution influences how a tumor cell behaves. Through this study, we highlight this differential influence of HA MWs on GBM’s energy metabolism. GBM’s U87-MG cell lines were grown in an adherent culture with media supplemented with different MWs of HA (10, 60 and 500 kDa) and glucose concentrations (0 mM: glucose starved, 5.5 mM: normoglycemic and 25 mM: hyperglycemic). LC-MS analysis on supernatant media coupled with numerical analysis highlighted an interesting influence of HA on GBM’s amino acid metabolism via reduction in LAT1 transporter protein expression. The results also indicated a differential influence on mitochondrial respiration levels with changing ATP demands and a difference in the accumulation of some key products of cell fermentation (lactic acid, glutamic acid, and succinic acid). Overall, these results highlight the differential influence of HA MWs on the metabolic state of GBM.

Citation Format: Ashwin A. Bale, Rohit Bhargava, Brendan Harley. Hyaluronic acid influences amino acid metabolism in glioblastoma's U87-MG cell line in a 2D culture via LAT1 transporter expression [abstract]. In: Proceedings of the AACR Special Conference on Brain Cancer; 2023 Oct 19-22; Minneapolis, Minnesota. Philadelphia (PA): AACR; Cancer Res 2024;84(5 Suppl_1):Abstract nr B052.
Abstract A006: Loss of XIST induces tumor metabolism reprogramming in ovarian cancer
Authors: Naciri Ikrame , Liang Minzhi , Yang Ying , Andrade Ludena Maria De Lourdes , Karner Heather , Lin Benjamin , Lebron Alfredo , Kong Mei , Sun Sha
Published: March 2024

Long noncoding RNAs (lncRNAs) have emerged as key players in various physiological processes, with dysregulation linked to diseases such as cancer. As diagnostic markers and therapeutic targets, lncRNAs have attracted considerable interest in cancer biology. XIST is one of the most studied lncRNAs, known as the master regulator of X chromosome inactivation (XCI) in mammals. The molecular mechanisms and regulatory elements of XCI have been extensively studied. However, their role in cancer susceptibility, particularly in female cancers, and their alterations in cancer cells remain elusive. To gain insight into the role of XIST in ovarian cancer, we analyzed TCGA ovarian cancer data and observed a downregulation of XIST expression in patients with high-grade ovarian cancer. In subsequent experiments, we performed CRISPR Cas9 inhibition (CRISPRi) to efficiently downregulate XIST expression in two ovarian cancer cell lines, OVCAR3 and SKOV3. Our functional and transcriptional analyses revealed a surprising finding: XIST downregulation did not result in widespread reactivation of X chromosome genes; however, we found an enrichment of gene related to oxidative phosphorylation pathway (OXPHO) in our cells with XIST knockdown. This finding was validated through measurement of the oxygen consumption rate, an indicator of OXPHO, which was higher in cells with downregulated XIST. In addition, we examined sequencing data from ovarian cancer patient samples and found that patients with low XIST expression showed an enrichment of genes related to oxidative phosphorylation, in accordance with our in vitro data. Under hypoxic stress, this metabolic shift resulted in increased colony formation and enhanced proliferation of ovarian cancer cells. Preliminary results from our xenograft experiments indicate enhanced tumor development with XIST-low cancer cells. Overall, our findings provide insight into the potential tumor suppressor role of XIST in ovarian cancer. Our study presents novel evidence implicating the XIST lncRNA in the metabolic oxidative phosphorylation pathway, thereby opening up the possibility of targeting this pathway for ovarian cancer patients with low XIST expression.

Citation Format: Ikrame Naciri, Minzhi Liang, Ying Yang, Maria De Lourdes Andrade Ludena, Heather Karner, Benjamin Lin, Alfredo Lebron, Mei Kong, Sha Sun. Loss of XIST induces tumor metabolism reprogramming in ovarian cancer [abstract]. In: Proceedings of the AACR Special Conference on Ovarian Cancer; 2023 Oct 5-7; Boston, Massachusetts. Philadelphia (PA): AACR; Cancer Res 2024;84(5 Suppl_2):Abstract nr A006.
Abstract A026: Identifying mechanisms to target in combination with trametinib to improve therapeutic efficacy in low-grade serous ovarian cancer
Authors: Peplinski Rebekah M. , Nobre Silvana Pedra , Schillo Jacob L. , Ulmer Keely K. , Lyons Yasmin A. , Riordan Jesse D. , Goodheart Michael J. , Dupuy Adam J.
Published: March 2024

Low-grade serous ovarian cancer (LGSOC) has recently been characterized as a unique subtype of ovarian cancer with distinct molecular characteristics, clinical treatments, and therapeutic responses. Although LGSOC accounts for ~5% of ovarian cancers, the age of onset is younger (~45 years) than other subtypes and has a low response rate (~4%) to the standard of care chemotherapy. One defining characteristic of LGSOC is frequent genetic alterations in the MAPK pathway, which has led to recent MAPK-targeted therapeutic clinical trials. MEK inhibition, particularly with trametinib, has been shown to be effective in patients with recurrent LGSOC (Phase II/III Trial: GOG 281/LOGS). However, these patients eventually develop therapeutic resistance and progressive disease, with no remaining treatment options. Here we sought to characterize the biology of LGSOC and its response to trametinib in an effort to identify candidate mechanisms that may be targeted in combination with trametinib to improve therapeutic efficacy and outcomes for LGSOC patients. After characterizing trametinib responses and identifying cytotoxic doses for a panel of LGSOC cell lines (ES2, OVCAR8, VOA7681, OV7, and OV56), we performed RNA sequencing on each cell line under basal conditions, as well as after 24-hour or 7-day exposure to an IC95 dose of trametinib. These experiments identified both acute and longer-term transcriptional changes that occur in response to trametinib. CRISPR screens targeting the kinome were also performed to identify synthetic lethal interactions between trametinib treatment and loss of function of specific protein kinases. Integrated analysis of these approaches identified several potential candidates (AKT, mTOR, CDKs, among others) that may be targeted in combination with trametinib to improve LGSOC patient outcomes. Experiments testing synergistic relationships between trametinib and other FDA approved inhibitors were performed. Using these combination therapeutic approaches could re-sensitize cells to trametinib treatment or prevent the emergence of resistance, thereby improving therapeutic efficacy. If successful, a similar approach could be used in a clinical trial to treat patients with LGSOC.

Citation Format: Rebekah M. Peplinski, Silvana Pedra Nobre, Jacob L. Schillo, Keely K. Ulmer, Yasmin A. Lyons, Jesse D. Riordan, Michael J. Goodheart, Adam J. Dupuy. Identifying mechanisms to target in combination with trametinib to improve therapeutic efficacy in low-grade serous ovarian cancer [abstract]. In: Proceedings of the AACR Special Conference on Ovarian Cancer; 2023 Oct 5-7; Boston, Massachusetts. Philadelphia (PA): AACR; Cancer Res 2024;84(5 Suppl_2):Abstract nr A026.
Abstract A058: Mesenchymal stem cells act as a selective pressure for High Grade Serous Ovarian Cancer initiation
Authors: Garcia Geyon L. , Atiya Huda I. , Coffman Lan G.
Published: March 2024

High grade serous ovarian cancer (HGSOC) is the most common and lethal subtype of ovarian cancer accounting for 80-90% of diagnoses. Despite its high incidence and mortality, the mechanisms of cancer initiation are unclear. The majority of HGSOC originates in the fallopian tube epithelium (FTE) with support of underlying mesenchymal stromal/stem cells (MSCs). MSCs are stromal progenitor cells that play important roles in wound healing and, in the context of cancer, tumor progression. We showed that MSCs within the tumor microenvironment, termed cancer associated MSCs (CA-MSCs) harbor a unique, age-associated epigenetic signature that is essential for tumor growth and metastasis. Surprisingly, we identified rare subsets of MSCs from benign tubes that exhibit similar epigenetic changes to cancer educated CA-MSCs suggesting that the pro-oncogenic MSC phenotype exists prior to cancer initiation. These “high risk” MSCs (hrMSCs) increase with age, are enriched in BRCA mutation carrier patients, promote cancer cell proliferation, and most notably, elicit tumor formation in primary, non-cancerous FTE. To elucidate the mechanism of hrMSC-induced malignant transformation of FTE, we characterized the effect that hrMSCs have on primary FTE. HrMSCs promoted increased growth of FTE relative to normal/low risk MSCs (lrMSCs) derived from the same patient. These MSCs lack the epigenetic signature/transcriptome of hrMSCs/CA-MSCs. Intriguingly, we co-cultured FTE with hrMSCs at a 1:1 ratio and discovered robust DNA damage in the form of DNA double strand breaks (53BP1 foci) in FTE at 24 hours. Furthermore, conditioned media from hrMSCs supported the recovery of FTE following damage with other DNA damaging agents. We hypothesize that the DNA damage function of hrMSCs serves as a selective pressure for mutation in FTE (1st hit). Additionally, we hypothesize that hrMSCs simultaneously provide growth signals to FTE allowing for evasion of DNA damage-induced cell death (2nd hit). Lastly, we hypothesize that both hrMSC functions are required for genesis of HGSOC.

Citation Format: Geyon L. Garcia, Huda I. Atiya, Lan G. Coffman. Mesenchymal stem cells act as a selective pressure for High Grade Serous Ovarian Cancer initiation [abstract]. In: Proceedings of the AACR Special Conference on Ovarian Cancer; 2023 Oct 5-7; Boston, Massachusetts. Philadelphia (PA): AACR; Cancer Res 2024;84(5 Suppl_2):Abstract nr A058.
Abstract IA008: Rare ovarian cancers: the sequelae of specific interactions between cell contexts mutations and microenvironments
Authors: Huntsman David
Published: March 2024

There are many pathologically and clinically distinct types of ovarian cancer and uterine cancers. These are not flavors of the same disease nor can they be solely explained by different mutations or other genomic findings; rather each may be thought to represent distinct interactions between cells of origin, mutations, and the microenvironment in which these cancers occur. Although many know gaps remain this may explain many curious features of these cancers. Fors instance, how endometrioid and clear cell carcinomas have similar mutations yet are distinct biologic and clinical entities. Also, why they occur at similar rates from ovarian endometriomas, yet clear cell cancers are much rarer in the endometrium. As an example of the importance microenvironment, findings will be presented suggesting that expression of Cystathionine gamma-lyase (CTH or CSE), a key enzyme within the transsulfuration pathway, enables CCC precursor cells to survive in endometriotic cysts becoming a defining feature of this cancer, one that may explain its biologic properties, aggressive course and relative chemoresistance. Other cancers will be considered using this model including rare stromal cancers.

Citation Format: David Huntsman. Rare ovarian cancers: the sequelae of specific interactions between cell contexts mutations and microenvironments [abstract]. In: Proceedings of the AACR Special Conference on Ovarian Cancer; 2023 Oct 5-7; Boston, Massachusetts. Philadelphia (PA): AACR; Cancer Res 2024;84(5 Suppl_2):Abstract nr IA008.