tbuckley/cabot-search huggingface dataset:
Science × art: spotlighting unconventional collaborations
Authors: Charles C. Davis, Jackson Kehoe, Anna C. Knaap, Christopher D.M. Atkins
Journal: Trends in Ecology & Evolution (2025)

Science × art collaborations can effectively convey scientific insights to a wide audience. Throughout history, art has interpreted the natural world, offering vast, underexplored sources of biodiversity data. These artistic efforts also hold potential as valuable tools for understanding biodiversity.
Host hepatocyte senescence determines the success of hepatocyte transplantation in a mouse model of liver injury
Authors: Victoria L Gadd, Sofia Ferreira-Gonzalez, Tak Yung Man, Alastair M Kilpatrick, Rhona E Aird, Ian P Smith, Daniel Rodrigo-Torres, Dominic Kurian, John M Hallett, Candice Ashmore-Harris, Hannah Esser, Marisa F Ferreira, Mark T Macmillan, Wei-Yu Lu, Stuart J Forbes
Journal: Journal of Hepatology (2025)

Hepatocyte transplantation has shown promise for genetic diseases of the hepatocytes but to date has shown limited efficacy for non-genetic forms of severe liver injury. Limited cell engraftment and poor function of donor hepatocytes in recipient livers impacts the clinical utility of hepatocyte cell therapy. The mechanisms underpinning this are poorly understood. We explored this in a liver injury model, where predictable levels of injury and hepatocyte senescence was induced in AhCreMdm2
Adoptive T cell therapy targeting an inducible and broadly shared product of aberrant mRNA translation
Authors: Julien Champagne, Morten M. Nielsen, Xiaodong Feng, Jasmine Montenegro Navarro, Abhijeet Pataskar, Rhianne Voogd, Lisanne Giebel, Remco Nagel, Nadine Berenst, Amos Fumagalli, Adva Kochavi, Domenica Lovecchio, Lorenzo Valcanover, Yuval Malka, Weiwen Yang, Maarja Laos, Yingqian Li, Natalie Proost, Marieke van de Ven, Olaf van Tellingen, Onno B. Bleijerveld, John B.A.G. Haanen, Johanna Olweus, Reuven Agami
Journal: Immunity (2025)

Highlights•IFNγ-induced tryptophan depletion induces W>F substitutants neoepitopes•W>F neoepitopes are widespread and shared between cancer types•W>F neoepitopes are targets of adoptive T cell therapy•Conventional T cell therapy can benefit from targeting W>F neoepitopesSummaryProlonged exposure to interferon-gamma (IFNγ) and the associated increased expression of the enzyme indoleamine 2,3-dioxygenase 1 (IDO1) create an intracellular shortage of tryptophan in the cancer cells, which stimulates ribosomal frameshifting and tryptophan to phenylalanine (W>F) codon reassignments during protein synthesis. Here, we investigated whether such neoepitopes can be useful targets of adoptive T cell therapy. Immunopeptidomic analyses uncovered hundreds of W>F neoepitopes mainly presented by the HLA-A∗24:02 allele. We identified a T cell receptor (TCRTMBIM6W>F.1) possessing high affinity and specificity toward TMBIM6W>F/HLA-A∗24:02, the inducible W>F neoepitope with the broadest expression across cancer cell lines. TCRTMBIM6W>F.1 T cells are activated by tryptophan-depleted cancer cells but not by non-cancer cells. Finally, we provide in vivo proof of concept for clinical application, whereby TCRMART1 T cells promote cancer cell killing by TCRTMBIM6W>F.1 T cells through the generation of W>F neoepitopes. Thus, neoepitopes arising from W>F substitution present shared and highly expressed immunogenic targets with the potential to overcome current limitations in adoptive T cell therapy.Graphical abstract
Targeting Siglec-E facilitates tumor vaccine-induced antitumor immunity in renal carcinoma
Authors: Yanyan Zheng, Jiawei Wang, Guangya Zhao, Zichun Zhang, Yingxiang Shao, Bowen Lu, Yuchen Zhang, Renjin Chen, Li Sun, Xiaohui Xie, Jiage Ding, Junnian Zheng, Dafei Chai
Journal: Journal for ImmunoTherapy of Cancer (2025)

Siglec-E is an immune checkpoint inhibitory molecule. Expression of Siglec-E on the immune cells has been shown to promote tumor regression. This study aimed to develop an adenovirus (Ad) vaccine targeting Siglec-E and carbonic anhydrase IX (CAIX) (Ad-Siglec-E/CAIX) and to evaluate its potential antitumor effects in several preclinical renal cancer models. Ad vaccines encoding Siglec-E or CAIX were developed and evaluated for their therapeutic potential in mouse subcutaneous, lung metastatic, and orthotopic tumor models. The expression of Ad-Siglec-E/CAIX was confirmed via PCR and flow cytometry. Immune responses induced by Ad-Siglec-E/CAIX were assessed in vitro and in vivo using flow cytometry, immunohistochemistry, ELISA, histological analysis, cell proliferation, enzyme-linked immunosorbent spot, cytotoxic T lymphocytes (CTL) killing, and cell depletion assays. Ad-Siglec-E/CAIX vaccine induced the increase of tumor-infiltrated immune cells, and significantly suppressed the subcutaneous tumor growth of renal carcinoma. Immunization with Ad-Siglec-E/CAIX promoted the induction and maturation of CD11c+ dendritic cells and their subsets, which in turn enhanced tumor-specific CD8+ T cell immune responses, as evidenced by increased CD8+ T cell proliferation and CTL activity. Importantly, the deletion of CD8+ T cells in vivo abolished the antitumor effect of the Ad-Siglec-E/CAIX vaccine, highlighting the essential role of functional CD8+ T cell responses. The potent therapeutic efficacy of the Ad-Siglec-E/CAIX vaccine was also observed in lung metastasis and orthotopic tumor models through tumor-specific CD8+ T cell immune responses. Our results indicate that targeting Siglec-E enhances the therapeutic efficacy of Ad-CAIX against renal carcinoma, providing a promising therapeutic option for solid tumors.
SIGLEC11 promotes M2 macrophage polarization through AKT–mTOR signaling and facilitates the progression of gastric cancer
Authors: Jingxin Yin, Yang Lu, Yihao Liu, Qimeng Shi, Minmin Shi, Zhenggang Zhu, Da Fu, Zhenqiang Wang, Chen Li
Journal: Journal for ImmunoTherapy of Cancer (2025)

Sialic acid-binding immunoglobulin-like lectins (SIGLECs) are widely expressed on immune cell surfaces, play an important role in maintaining immune homeostasis and regulating inflammatory responses, and are increasingly emerging as potential targets for tumor immunotherapy. However, the expression profile and crucial role of SIGLEC11 in gastric cancer (GC) remain unclear. This study aimed to elucidate the prognostic relevance of SIGLEC11 expression and its role in the immune microenvironment in patients with GC. SIGLEC11 expression profile was analyzed using bioinformatics, immunohistochemistry, and immunofluorescence staining. Flow cytometry, mouse tumor models, patient-derived tumor organoid models, and RNA sequencing were used to explore the potential functions with the underlying mechanisms of SIGLEC11 in a coculture system of macrophages and GC cells. We demonstrated that SIGLEC11 was predominantly expressed in normal tissues. However, tumor-infiltrating SIGLEC11+ cells in the high SIGLEC11 expression subgroups showed poor overall survival, which was associated with the expression of an immunosuppressive regulator. Our results showed that SIGLEC11 was predominantly expressed in monocytes and macrophages and selectively upregulated in tumor-associated macrophages. Furthermore, SIGLEC11 promoted macrophage M2 polarization via AKT-mTOR signaling. In addition, SIGLEC11+ macrophages accelerate GC progression. The abundance of SIGLEC11+ M2-like macrophage-infiltrating tumors may serve as a biomarker for identifying immunosuppressive subtypes of GC. Thus, the potential role of SIGLEC11+ M2 macrophages as therapeutic targets warrants further investigation.
Salvage treatment of multi-refractory primary immune thrombocytopenia with CD19 CAR T cells
Authors: Karolin Trautmann-Grill, Malte von Bonin, Annabell Georgi, Jan Moritz Middeke, Martin Böttcher, Oliver Meyer, Dominic Borie, Martin Bornhäuser, Martin Mikusko, Denise Wolleschak, Dimitrios Mougiakakos
Journal: The Lancet (2025)
Risk of Interstitial Lung Disease in Adult Dermatomyositis Patients Treated with Methotrexate: A Retrospective Analysis of a Prospective Cohort
Authors: Catherine Z Shen, Hallie Carol, Rui Feng, Alannah Hill, Lais Lopes Almeida Gomes, Emily Z Hejazi, Victoria P Werth, Katharina S Shaw
Journal: Journal of the American Academy of Dermatology (2025)
Ara h 2–expressing cucumber mosaic virus–like particle (VLP Peanut) induces in vitro tolerogenic cellular responses in peanut-allergic individuals
Authors: Janice A Layhadi, Sviatlana Starchenka, Pieter-Jan De Kam, Elizabeth Palmer, Nandinee Patel, Sean T Keane, Prista Hikmawati, Gabija Drazdauskaite, Lily Y D Wu, Paulina Filipaviciute, Rebecca V Parkin, Kemi Oluwayi, Olesya Rusyn, Murray A Skinner, Matthew D Heath, Simon J Hewings, Matthias F Kramer, Paul Turner, Mohamed H Shamji
Journal: Journal of Allergy and Clinical Immunology (2025)
N2GNet tracks gait performance from subthalamic neural signals in Parkinson’s disease
Authors: Jin Woo Choi, Chuyi Cui, Kevin B. Wilkins, Helen M. Bronte-Stewart
Journal: npj Digital Medicine (2025)

Abstract Adaptive deep brain stimulation (DBS) provides individualized therapy for people with Parkinson’s disease (PWP) by adjusting the stimulation in real-time using neural signals that reflect their motor state. Current algorithms, however, utilize condensed and manually selected neural features which may result in a less robust and biased therapy. In this study, we propose Neural-to-Gait Neural network (N2GNet), a novel deep learning-based regression model capable of tracking real-time gait performance from subthalamic nucleus local field potentials (STN LFPs). The LFP data were acquired when eighteen PWP performed stepping in place, and the ground reaction forces were measured to track their weight shifts representing gait performance. By exhibiting a stronger correlation with weight shifts compared to the higher-correlation beta power from the two leads and outperforming other evaluated model designs, N2GNet effectively leverages a comprehensive frequency band, not limited to the beta range, to track gait performance solely from STN LFPs.
Data from the All of Us research program reinforces existence of activity inequality
Authors: Hayoung Jeong, Ali R. Roghanizad, Hiral Master, Juseong Kim, Aymone Kouame, Paul A. Harris, Melissa Basford, Kayla Marginean, Jessilyn Dunn
Journal: npj Digital Medicine (2025)

Large-scale and detailed analyses of activity in the United States (US) remain limited. In this work, we leveraged the comprehensive wearable, demographic, and survey data from the All of Us Research Program, the largest and most diverse population health study in the US to date, to apply and extend the previous global findings on activity inequality within the context of the US. We found that daily steps differed by sex at birth, age, body characteristics, geography, and built environment. Quantifying activity inequality using the modified Gini index, we found a strong correlation with obesity prevalence (R2 = 0.804) and a moderate correlation with perceived walkability (R2 = 0.426) and the activity gender gap (R2 = 0.385). This study demonstrates the value of digital health technologies in exploring and understanding public health practices while highlighting the need to examine complexities, including biopsychosocial factors that may contribute to activity inequality.
Department of Error
Journal: The Lancet (2025)

suggested by Engrand and Miry to collect information on nonrandomised people unfortunately are not standardised, often not reliable, and discouraged by many trialists. 4 However, we agree that more information on people treated outside the SWITCH trial would be of interest.We appreciate the comment by Marschner on the confidence distribution for the treatment effect (appendix p 35 of the SWITCH article). 1 The confidence distribution is an intuitive way to present uncertainty and might be more accessible than confidence intervals and p values. 5 Showing the complete distribution has the additional benefit that the confidence for a specific treatment effect of interest can be assessed.SWITCH informs caregivers, patients, and relatives on the probability of a beneficial treatment effect and this is how the results of the SWITCH trial should be interpreted.We declare no competing interests.
Artificially Tagging Tumors with Nano-Aluminum Adjuvant-Tethered Antigen mRNA Recruits and Activates Antigen-Specific Cytotoxic T Cells for Enhanced Cancer Immunotherapy
Authors: Lingxiao Zhang, Jie Bai, Aining Shen, Jing Zhao, Zhenwei Su, Maoze Wang, Mingdong Dong, Zhi Ping Xu
Journal: Biomaterials (2025)

T cell therapy for solid tumors faces significant challenges due to the immune off-target attack caused by the loss of tumor surface antigens and inactivation in acidic tumor microenvironment (TME). Herein, we developed a bifunctional immunomodulator (MO@NAL) by loading ovalbumin (OVA; model antigen) mRNA (mOVA) onto lysozyme-coated layered double hydroxide nano-aluminum adjuvant (NA). The NA's inherent alkalinity effectively neutralizes the excess acid within the TME and suppresses regulatory T cells, creating a favorable microenvironment to enhance cytotoxic T cell infiltration and activation in tumors. Particularly, once internalization by tumor cells, MO@NAL efficiently tags the tumor cell surface with OVA through the carried mOVA, providing targets for recruiting and directing the antigen-specific cytotoxic T cells to destroy tumor cells. In mice pre-vaccinated with the OVA vaccine, intratumoral administration of MO@NAL rapidly awakens OVA-specific immune memory, rapidly and effectively inhibiting the progression of colon tumors and melanoma at both early and advanced stages. In non-pre-vaccinated mice, combining MO@NAL with the OVA therapeutic vaccine or OVA-specific adoptive T cell transfusion similarly achieves robust solid tumor suppression. These findings thus underscore the potential of MO@NAL as an effective and safe immunomodulator for enhancing cytotoxic T cell responses and providing timely intervention in solid tumor progression.
Bioorthogonal Strategy-Triggered In situ Co-Activation of Aggregation-Induced Emission Photosensitizers and Chemotherapeutic Prodrugs for Boosting Synergistic Chemo-Photodynamic-Immunotherapy
Authors: Yu Teng, Dianyu Wang, Ziyu Yang, Ruxuan Wang, Shuyi Ning, Rongrong Zhang, Hong Yang, Xinchi Feng, Jianfeng Liu, Lijun Yang, Yulin Tian
Journal: Biomaterials (2025)
Immune-modulating nanomedicines for enhanced drug delivery to non-small-cell lung cancer
Authors: Feifei Liu, Christopher B Howard, Pie Huda, Nicholas L Fletcher, Craig A Bell, Idriss Blakey, Michael Agrez, Kristofer J Thurecht
Journal: Biomaterials (2025)

Immune-modulating peptides have shown potential as novel immune-stimulating agents which enhance the secretion of anticancer cytokines in vitro. However, fast clearance from blood hampers the ability of such peptides to accumulate in the tumour and results in limited therapeutic efficacy in animal studies. To address the fast blood clearance, this work reports the development and validation of a novel polymeric nanoparticle delivery system for the efficient localization of an immunomodulating peptide in the tumour microenvironment (TME). To identify the optimal polymeric nanoparticle for this study, two types of nanoparticles were developed as either branched polymers or micelles that have similar chemical functionality but different sizes. The effect of targeting the nanomedicine to the tumour-specific antigen, glycoprotein GPC-1, was explored using a bispecific antibody (BsAb) that shows an affinity for the cell protein (GPC-1) and the nanoparticle. These systems were evaluated for targeting efficiency and tumour penetration using tumour spheroids of Lewis Lung Cancer (LLC) cells and it was shown that the targeted system significantly enhanced cell association compared to the untargeted control with minor differences in penetration. The lead micelle-peptide conjugates were identified and using in vivo allograft models they were demonstrated to have high delivery efficiency of the peptide to tumours, prolonged blood circulation, enhanced tumour accumulation and tumour suppression that was associated with immune cell recruitment to the tumour.
Nano-polymeric platinum activates PAR2 gene editing to suppress tumor metastasis
Authors: Yuhong Jiang, Yuke Li, Dongmei Zheng, Xin Du, Huan Yang, Chuan Wang, Mengnan Zhao, Haihua Xiao, Lingpu Zhang, Xiaofang Li, Sanjun Shi
Journal: Biomaterials (2025)
International Union of Pharmacology. XVIII. Nomenclature of Receptors for Vasoactive Intestinal Peptide and Pituitary Adenylate Cyclase-Activating Polypeptide
Authors: Anthony J. Harmar, Akira Arimura, Illana Gozes, Laurent Journot, Marc Laburthe, Joseph R. Pisegna, Stephen R. Rawlings, Patrick Robberecht, Sami I. Said, Sunil P. Sreedharan, Stephen A. Wank, James A. Waschek
Journal: Pharmacological Reviews (1998)
Prolyl 4‐hydroxylase α‐subunit family regulation of type I collagen deposition and IL17RB/c‐Jun activation synergistically mediate choline dehydrogenase promotion of colorectal cancer metastasis
Authors: Xiaowen Yang, Yifei Li, Xinzhuang Shen, Shuying Wang, Zhuqing Zhang, Wenfei Du, Chenglong Yang, Xinyu Jiang, Xiaoyuan Zhang, Yongming Huang, Wenzhi Shen
Journal: MedComm (2025)

Abstract Metastasis continues to pose a significant challenge in tumor treatment. Evidence indicates that choline dehydrogenase (CHDH) is crucial in tumorigenesis. However, the functional role of CHDH in colorectal cancer (CRC) metastasis remains unreported. The study explored the functional role and mechanism of CHDH in CRC metastasis using human CRC tissues and a xenograft mouse model. CHDH expression was significantly higher in CRC compared to normal tissues and showed a positively correlation with CRC tumor‐nodes‐metastasis stage. CRC cell lines showed increased CHDH expression compared to normal controls. CHDH knockdown suppressed cell migration in vitro and tumor metastasis in vivo. Similarly, ectopic CHDH expression enhanced cell migration in vitro and tumor metastasis in vivo. Results suggested that CHDH affected the histone H3 trimethylation levels, which upregulated prolyl 4‐hydroxylase α‐subunit (P4HA) family gene (P4HA1/2/3) expression, further stabilizing collagen I expression and increasing IL17RB expression, which promoted downstream c‐Jun activation. Together, P4HA and IL17RB promote CRC cell metastasis. P4HA and c‐Jun inhibitors abolished CHDH‐mediated CRC cell metastasis in vitro and in vivo. Collectively, the above findings provide novel evidence that that CHDH mediates CRC cell metastasis and may be a promising target for metastatic CRC therapy.
Multiorgan proteomic analysis of infected animal models predict potential host factors for chikungunya virus
Authors: Dongdong Lin, Cong Tang, Junbin Wang, Yun Yang, Hao Yang, Yanan Zhou, Wenhai Yu, Bai Li, Qing Huang, Haixuan Wang, Ran An, Xiaoming Liang, Yuhuan Yan, Longhai Yuan, Xuena Du, Yuxia Yuan, Yanwen Li, Shuaiyao Lu
Journal: MedComm (2025)

Abstract Chikungunya virus (CHIKV) is a mosquito‐borne alphavirus that is primarily known for causing severe joint and muscle symptoms, but its pathological effects have extended beyond these tissues. In this study, we conducted a comprehensive proteomic analysis across various organs in rodent and nonhuman primate models to investigate CHIKV's impact on organs beyond joints and muscles and to identify key host factors involved in its pathogenesis. Our findings reveal significant species‐specific similarities and differences in immune responses and metabolic regulation, with proteins like Interferon‐Stimulated Gene 15 (ISG15) and Retinoic Acid‐Inducible Gene I (RIG‐I) playing crucial roles in the anti‐CHIKV defense. We observed upregulated and downregulated metabolic status in CHIKV‐infected rhesus monkeys and mice, respectively. Additionally, we identified host factors such as S100 Calcium‐Binding Protein A8/A9 (S100A8/A9), Voltage‐Dependent Anion Channel 1/2 (VDAC1/2), Complement Component 3 (C3), Apoptosis‐Inducing Factor Mitochondria‐Associated 1 (AIFM1), Endothelial Cell‐Specific Chemotaxis Regulator (ECSCR), and Kininogen 1 (KNG1) that may contribute to CHIKV‐induced inflammation and hemorrhage. These insights put emphases on the importance of understanding CHIKV's impact on organs beyond joints and muscles, providing potential therapeutic targets and enhancing our understanding of CHIKV pathogenesis. This research underscores the need for appropriate animal models in CHIKV studies and informs the development of targeted therapies to address its systemic effects.
RNA N4‐acetylcytidine modification and its role in health and diseases
Authors: Qiang Wang, Yixiao Yuan, Qiang Zhou, YingDong Jia, Jing Liu, GuangJun Xiao, Chunhong Li, Xiulin Jiang
Journal: MedComm (2025)

Abstract N4‐acetylcytidine (ac4C) modification is a crucial RNA modification widely present in eukaryotic RNA. Previous studies have demonstrated that ac4C plays a pivotal role in viral infections. Despite numerous studies highlighting the strong correlation between ac4C modification and cancer progression, its detailed roles and molecular mechanisms in normal physiological processes and cancer progression remain incompletely understood. This review first outlines the key regulatory enzyme mediating ac4C modification, N‐acetyltransferase 10 (NAT10), including its critical roles in regulating RNA stability, transcriptional efficiency, and translational fidelity. Additionally, it systematically summarizes the essential functions and mechanisms of ac4C modification in normal biological processes, including stem cell fate determination, spermatogenesis and oogenesis, embryonic development, cellular senescence, and bone remodeling. Furthermore, this review delves into the central roles and molecular mechanisms of ac4C modification in regulating malignant proliferation, cell cycle arrest, EMT, drug resistance, cell death, cancer metabolism, and tumor immunotherapy. It also emphasizes the potential of NAT10 as a prognostic biomarker and its therapeutic potential as a target for disease treatment. In summary, this review clarifies the multifaceted roles of ac4C modification in both health and disease and explores NAT10‐targeted therapies with the aim of advancing cancer research and improving patient outcomes.
Self-interactive learning: Fusion and evolution of multi-scale histomorphology features for molecular traits prediction in computational pathology
Authors: Yang Hu, Korsuk Sirinukunwattana, Bin Li, Kezia Gaitskell, Enric Domingo, Willem Bonnaffé, Marta Wojciechowska, Ruby Wood, Nasullah Khalid Alham, Stefano Malacrino, Dan J Woodcock, Clare Verrill, Ahmed Ahmed, Jens Rittscher
Journal: Medical Image Analysis (2025)