tbuckley/cabot-search huggingface dataset:
Gene therapy ameliorates bowel dysmotility and enteric neuron degeneration and extends survival in lysosomal storage disorder mouse models
Authors: Ewa A. Ziółkowska, Matthew J. Jansen, Letitia L. Williams, Sophie H. Wang, Elizabeth M. Eultgen, Keigo Takahashi, Steven Q. Le, Hemanth R. Nelvagal, Jaiprakash Sharma, Marco Sardiello, Brian J. DeBosch, Patricia I. Dickson, Jessica B. Anderson, Sophie E. Sax, Christina M. Wright, Rebecca P. Bradley, Ineka T. Whiteman, Takako Makita, John R. Grider, Mark S. Sands, Robert O. Heuckeroth, Jonathan D. Cooper
Journal: Science Translational Medicine (2025)

Children with neurodegenerative disease often have debilitating gastrointestinal symptoms. We hypothesized that this may be due at least in part to underappreciated degeneration of neurons in the enteric nervous system (ENS), the master regulator of bowel function. To test this hypothesis, we evaluated mouse models of neuronal ceroid lipofuscinosis type 1 and 2 (CLN1 and CLN2 disease, respectively), neurodegenerative lysosomal storage disorders caused by deficiencies in palmitoyl protein thioesterase-1 and tripeptidyl peptidase-1, respectively. Both mouse lines displayed slow bowel transit in vivo that worsened with age. Although the ENS appeared to develop normally in these mice, there was a progressive and profound loss of myenteric plexus neurons accompanied by changes in enteric glia in adult mice. Similar pathology was evident in colon autopsy material from a child with CLN1 disease. Neonatal administration of adeno-associated virus–mediated gene therapy prevented bowel transit defects, ameliorated loss of enteric neurons, and extended survival in mice. Treatment after weaning was less effective than treating neonatally but still extended the lifespan of CLN1 disease mice. These data provide proof-of-principle evidence of ENS degeneration in two lysosomal storage diseases and suggest that gene therapy can ameliorate ENS disease, also improving survival.
Epithelial OPA1 links mitochondrial fusion to inflammatory bowel disease
Authors: Li-Li Bao, Yu-Qiang Yu, Miguel González-Acera, Jay V. Patankar, Andreas Giessl, Gregor Sturm, Anja A. Kühl, Raja Atreya, Lena Erkert, Reyes Gámez-Belmonte, Susanne M. Krug, Benjamin Schmid, Philipp Tripal, Mircea T. Chiriac, Kai Hildner, Britta Siegmund, Stefan Wirtz, Michael Stürzl, Mariam Mohamed Abdou, Zlatko Trajanoski, Markus F. Neurath, Antonio Zorzano, Christoph Becker, Imke Atreya, Petra Bacher, Christian Bojarski, Nathalie Britzen-Laurent, Caroline Bosch-Voskens, Hyun-Dong Chang, Andreas Diefenbach, Claudia Günther, Ahmed N. Hegazy, Christoph S. N. Klose, Kristina Koop, Moritz Leppkes, Rocío López-Posadas, Leif S.-H. Ludwig, Clemens Neufert, Christina Plattner, Magdalena Prüß, Andreas Radbruch, Chiara Romagnani, Francesca Ronchi, Ashley Sanders, Alexander Scheffold, Jörg-Dieter Schulzke, Michael Schumann, Sebastian Schürmann, Antigoni Triantafyllopoulou, Maximilian Waldner, Carl Weidinger, Sebastian Zundler
Journal: Science Translational Medicine (2025)

Dysregulation at the intestinal epithelial barrier is a driver of inflammatory bowel disease (IBD). However, the molecular mechanisms of barrier failure are not well understood. Here, we demonstrate dysregulated mitochondrial fusion in intestinal epithelial cells (IECs) of patients with IBD and show that impaired fusion is sufficient to drive chronic intestinal inflammation. We found reduced expression of mitochondrial fusion–related genes, such as the dynamin-related guanosine triphosphatase (GTPase) optic atrophy 1 ( OPA1 ), and fragmented mitochondrial networks in crypt IECs of patients with IBD. Mice with Opa1 deficiency in the gut epithelium ( Opa1 i∆IEC ) spontaneously developed chronic intestinal inflammation with mucosal ulcerations and immune cell infiltration. Intestinal inflammation in Opa1 i∆IEC mice was driven by microbial translocation and associated with epithelial progenitor cell death and gut barrier dysfunction. Opa1 -deficient epithelial cells and human organoids exposed to a pharmacological OPA1 inhibitor showed disruption of the mitochondrial network with mitochondrial fragmentation and changes in mitochondrial size, ultrastructure, and function, resembling changes observed in patient samples. Pharmacological inhibition of the GTPase dynamin-1–like protein in organoids derived from Opa1 i∆IEC mice partially reverted this phenotype. Together, our data demonstrate a role for epithelial OPA1 in regulating intestinal immune homeostasis and epithelial barrier function. Our data provide a mechanistic explanation for the observed mitochondrial dysfunction in IBD and identify mitochondrial fusion as a potential therapeutic target in this disease.
Inhaled xenon modulates microglia and ameliorates disease in mouse models of amyloidosis and tauopathy
Authors: Wesley Brandao, Nimansha Jain, Zhuoran Yin, Kilian L. Kleemann, Madison Carpenter, Xin Bao, Javier R. Serrano, Eric Tycksen, Ana Durao, Jen-Li Barry, Caroline Baufeld, Dilansu Guneykaya, Xiaoming Zhang, Alexandra Litvinchuk, Hong Jiang, Neta Rosenzweig, Kristen M. Pitts, Michael Aronchik, Taha Yahya, Tian Cao, Marcelo Kenzo Takahashi, Rajesh Krishnan, Hayk Davtyan, Jason D. Ulrich, Mathew Blurton-Jones, Ilya Ilin, Howard L. Weiner, David M. Holtzman, Oleg Butovsky
Journal: Science Translational Medicine (2025)

Alzheimer’s disease (AD) is the most prevalent neurodegenerative disorder. Antiamyloid antibody treatments modestly slow disease progression in mild dementia due to AD. Emerging evidence shows that homeostatic dysregulation of the brain immune system, especially that orchestrated by microglia, plays an important role in disease onset and progression. Thus, a major question is how to modulate the phenotype and function of microglia to treat AD. Xenon (Xe) gas is a noble gas used in human patients as an anesthetic and a neuroprotectant used for treating brain injuries. Xe penetrates the blood-brain barrier, which could make it an effective therapeutic. To assess the effect of Xe on microglia and AD pathology, we designed a custom Xe inhalation chamber and treated several mouse models of AD with Xe gas. Xe treatment induced mouse microglia to adopt an intermediate activation state that we have termed pre–neurodegenerative microglia (pre-MGnD). This microglial phenotypic transition was observed in mouse models of acute neurodegeneration and amyloidosis (APP/PS1 and 5xFAD mice) and tauopathy (P301S mice). This microglial state enhanced amyloid plaque compaction and reduced dystrophic neurites in the APP/PS1 and 5xFAD mouse models. Moreover, Xe inhalation reduced brain atrophy and neuroinflammation and improved nest-building behavior in P301S mice. Mechanistically, Xe inhalation induced homeostatic brain microglia toward a pre-MGnD state through IFN-γ signaling that maintained the microglial phagocytic response in APP/PS1 and 5xFAD mice while suppressing the microglial proinflammatory phenotype in P301S mice. These results support the translation of Xe inhalation as an approach for treating AD.
Macrophage-specific in vivo RNA editing promotes phagocytosis and antitumor immunity in mice
Authors: Yuxuan Chen, Xiaohong Chen, Yao Zhang, Meng Wang, Minqi Yang, Ruiji Wang, Xiaojie Yan, Shiyi Shao, Huhu Xin, Qida Hu, Wei Wei, Yuan Ping
Journal: Science Translational Medicine (2025)

Macrophages play a central role in antitumor immunity, making them an attractive target for gene therapy strategies. However, macrophages are difficult to transfect because of nucleic acid sensors that can trigger the degradation of foreign plasmid DNA. Here, we developed a macrophage-specific editing (MAGE) system by which compact plasmid DNA encoding a CasRx editor can be delivered to macrophages by a poly(β-amino ester) (PBAE) carrier to bypass the DNA sensor and enable RNA editing in vitro and in vivo. We identified a four-arm branched PBAE with 1-(2-aminoethyl)-4-methylpiperazine end-capping (PBAE29) that enables highly efficient macrophage transfection. PBAE29-mediated transfection of cultured macrophages stimulated less inflammatory cytokine production and inflammasome activation compared with traditional lipofectamine or electroporation-mediated plasmid delivery. Transfection efficiency was further improved by delivering CasRx by minicircle plasmid. The MAGE system incorporated a layer of carboxylated-mannan coating to target macrophage mannose receptors and a macrophage-specific promoter for enhanced selectivity. The delivery of CasRx with guide RNA targeting the transcripts for sialic acid–binding immunoglobulin similar to lectin 10 and signal regulatory protein alpha expression resulted in effective protein knockdown, improving macrophage phagocytosis. The MAGE system also showed efficacy in targeting macrophages in vivo, stimulating antitumor immune responses and reducing tumor volume in murine tumor models, including patient-derived pancreatic adenocarcinoma xenografts in humanized mice. In sum, the MAGE system presents a promising platform for in vivo macrophage-specific delivery of RNA editing tools that can be applied as a cancer therapy.
A new twist on superantigen-activated autoimmune disease
Authors: Andrew L Mason, Doaa Waly, Mohammed S Osman
Journal: Journal of Clinical Investigation (2025)

Superantigen-induced (Sag-induced) autoimmunity has been proposed as a mechanism for many human disorders, without a clear understanding of the potential triggers. In this issue of the JCI, McCarthy and colleagues used the SKG mouse model of rheumatoid arthritis to characterize the role of Sag activity in inflammatory arthritis by profiling arthritogenic naive CD4+ T cells. Within the diseased joints, they found a marked enrichment of T cell receptor-variable β (TCR-Vβ) subsets that were reactive to the endogenously encoded mouse mammary tumor virus (MMTV) Sag. Arthritis was improved using reverse transcriptase inhibitors. Moreover, depletion of MMTV Sag-activated TCR-Vβ subsets affected the ability of transferred activated CD4+ T cells to induce disease in mice with severe combined immunodeficiency (SCID). Further virological studies should determine whether endogenous or exogenous MMTV is necessary or sufficient to trigger inflammatory arthritis in the SKG model.
Elucidating the role of autoreactive T cells and B cells in autoimmune hepatitis
Authors: Yoshiaki Yasumizu, David A. Hafler
Journal: Journal of Clinical Investigation (2025)

How are autoreactive T cells induced and regulated in patients with autoimmune disease? This question lies at the core of understanding autoimmune disease pathologies, yet it has remained elusive due to host variability and the complexity of the immune system. In this issue of the JCI, Kramer and colleagues used autoimmune hepatitis (AIH) as a model to explore the maintenance of autoreactive CD4+ T cells specific to O-phosphoseryl-tRNA:selenocysteine tRNA synthase (SepSecS). The findings provide insight into the interaction between T cells and B cells in AIH pathogenesis that may reflect a shared mechanism among other autoimmune diseases.
Fgfr3 enhancer deletion markedly improves all skeletal features in a mouse model of achondroplasia
Authors: Marco Angelozzi, Arnaud Molin, Anirudha Karvande, Ángela Fernández-Iglesias, Samantha Whipple, Andrew M. Bloh, Véronique Lefebvre
Journal: Journal of Clinical Investigation (2025)

Achondroplasia, the most prevalent short-stature disorder, is caused by missense variants overactivating the fibroblast growth factor receptor 3 (FGFR3). As current surgical and pharmaceutical treatments only partially improve some disease features, we sought to explore a genetic approach. We show that an enhancer located 29 kb upstream of mouse Fgfr3 (-29E) is sufficient to confer a transgenic mouse reporter with a domain of expression in cartilage matching that of Fgfr3. Its CRISPR/Cas9-mediated deletion in otherwise WT mice reduced Fgfr3 expression in this domain by half without causing adverse phenotypes. Importantly, its deletion in mice harboring the ortholog of the most common human achondroplasia variant largely normalized long bone and vertebral body growth, markedly reduced spinal canal and foramen magnum stenosis, and improved craniofacial defects. Consequently, mouse achondroplasia is no longer lethal, and adults are overall healthy. These findings, together with high conservation of -29E in humans, open a path to develop genetic therapies for people with achondroplasia.
An epigenetic pathway regulates MHC-II expression and function in B cell lymphoma models
Authors: Te Zhang, Oguzhan Beytullahoglu, Rima Tulaiha, Amanda Luvisotto, Aileen Szczepanski, Natsumi Tsuboyama, Zibo Zhao, Lu Wang
Journal: Journal of Clinical Investigation (2025)

Mutations or homozygous deletions of MHC class II (MHC-II) genes are commonly found in B cell lymphomas that develop in immune-privileged sites and have been associated with patient survival. However, the mechanisms regulating MHC-II expression, particularly through genetic and epigenetic factors, are not yet fully understood. In this study, we identified a key signaling pathway involving the histone H2AK119 deubiquitinase BRCA1 associated protein 1 (BAP1), the interferon regulatory factor interferon regulatory factor 1 (IRF1), and the MHC-II transactivator class II transactivator (CIITA), which directly activates MHC-II gene expression. Disruption of the BAP1/IRF1/CIITA axis leads to a functional attenuation of MHC-II expression and MHC-II-dependent immune cell infiltration, leading to accelerated tumor growth in immunocompetent mice. Additionally, we demonstrated that pharmacological inhibition of polycomb repressive complex 1 (PRC1) - which deposits histone H2K119Ub and opposes BAP1 activity - can restore MHC-II gene expression in BAP1-deficient B cell lymphoma cells. These findings suggest that BAP1 may function as a tumor suppressor by regulating the tumor microenvironment and immune response. Our study also establishes the rationale for therapeutic strategies to restore tumor-specific MHC-II expression and enhance immunotherapy outcomes at epigenetic levels in B cell lymphoma treatment.
Endothelial STING-JAK1 interaction promotes tumor vasculature normalization and antitumor immunity
Authors: Huanling Zhang, Zining Wang, Jiaxin Wu, Yong-Qiang Zheng, Qi Zhao, Shuai He, Hang Jiang, Chang Jiang, Tiantian Wang, Yongxiang Liu, Lei Cui, Hui Guo, Jiahong Yi, Huan Jin, Chunyuan Xie, Mengyun Li, Jiahui Li, Xiaojuan Wang, Liangping Xia, Xiao-Shi Zhang, Xiaojun Xia
Journal: Journal of Clinical Investigation (2025)

Stimulator of interferon genes (STING) agonists have been developed and tested in clinical trials for their antitumor activity. However, the specific cell population(s) responsible for such STING activation-induced antitumor immunity have not been completely understood. In this study, we demonstrated that endothelial STING expression was critical for STING agonist-induced antitumor activity. STING activation in endothelium promoted vessel normalization and CD8+ T cell infiltration - which required type I IFN (IFN-I) signaling- but not IFN-γ or CD4+ T cells. Rather than an upstream adaptor for inducing IFN-I signaling, STING acted downstream of interferon-α/β receptor (IFNAR) in endothelium for the JAK1-STAT signaling activation. Mechanistically, IFN-I stimulation induced JAK1-STING interaction and promoted JAK1 phosphorylation, which involved STING palmitoylation at the Cysteine 91 site but not its C-terminal tail (CTT) domain. Endothelial STING and JAK1 expression was significantly associated with immune cell infiltration in patients with cancer, and STING palmitoylation level correlated positively with CD8+ T cell infiltration around STING-positive blood vessels in tumor tissues from patients with melanoma. In summary, our findings uncover a previously unrecognized function of STING in regulating JAK1/STAT activation downstream of IFN-I stimulation and provide a new insight for future design and clinical application of STING agonists for cancer therapy.
Clonal analysis of SepSecS-specific B and T cells in autoimmune hepatitis
Authors: Michael Kramer, Federico Mele, Sandra Jovic, Blanca Maria Fernandez, David Jarrossay, Jun Siong Low, Christiane Sokollik, Magdalena Filipowicz Sinnreich, Sylvie Ferrari-Lacraz, Giorgina Mieli-Vergani, Diego Vergani, Antonio Lanzavecchia, Antonino Cassotta, Benedetta Terziroli Beretta-Piccoli, Federica Sallusto
Journal: Journal of Clinical Investigation (2025)

Autoimmune hepatitis (AIH) is a rare chronic inflammatory liver disease characterized by the presence of autoantibodies, including those targeting O-phosphoseryl-tRNA:selenocysteine-tRNA synthase (SepSecS), also known as soluble liver antigen (SLA). Anti-SepSecS antibodies have been associated with a more severe phenotype, suggesting a key role for the SepSecS autoantigen in AIH. To analyze the immune response to SepSecS in patients with AIH at the clonal level, we combined sensitive high-throughput screening assays with the isolation of monoclonal antibodies (mAbs) and T cell clones. The anti-SepSecS mAbs isolated were primarily IgG1, affinity-matured compared with their germline versions, and recognized at least 3 nonoverlapping epitopes. SepSecS-specific CD4+ T cell clones were found in patients with AIH who were anti-SLA-positive and anti-SLA-negative,and, to a lesser extent, in patients with non-AIH liver diseases and in healthy individuals. SepSecS-specific T cell clones from patients with AIH produced IFN-γ, IL-4, and IL-10, targeted multiple SepSecS epitopes, and, in one patient, were clonally expanded in both blood and liver biopsy. Finally, SepSecS-specific B cell clones, but not those of unrelated specificities, were able to present soluble SepSecS to specific T cells. Collectively, our study provides the first detailed analysis of B and T cell repertoires targeting SepSecS in patients with AIH, offering a rationale for improved targeted therapies.
T cells in cardiac health and disease
Authors: Pilar Martín, Francisco Sánchez-Madrid
Journal: Journal of Clinical Investigation (2025)

Cardiovascular disease (CVD) remains the leading cause of morbidity and mortality worldwide, with inflammation playing a pivotal role in its pathogenesis. T lymphocytes are crucial components of the adaptive immune system that have emerged as key mediators in both cardiac health and the development and progression of CVD. This Review explores the diverse roles of T cell subsets, including Th1, Th17, γδ T cells, and Tregs, in myocardial inflammatory processes such as autoimmune myocarditis and myocardial infarction. We discuss the contribution of T cells to myocardial injury and remodeling, with emphasis on specific immune receptors, e.g., CD69, that have a critical role in regulating immune tolerance and maintaining the balance between T cell subsets in the heart. Additionally, we offer a perspective on recent advances in T cell-targeted therapies and their potential to modulate immune responses and improve clinical outcomes in patients with CVD and in heart transplant recipients. Understanding the intricate interplay between T cells and cardiovascular pathology is essential for developing novel immunotherapeutic strategies against CVD.
No bones about it: regulatory T cells promote fracture healing
Authors: Jason W Griffith, Andrew D Luster
Journal: Journal of Clinical Investigation (2025)

Regulatory T cells (Tregs) are increasingly being recognized for their role in promoting tissue repair. In this issue of the JCI, Chen et al. found that Tregs at the site of bone injury contribute to bone repair. The CCL1/CCR8 chemokine system promoted the accumulation of Tregs at the site of bone injury, where Tregs supported skeletal stem cell (SSC) accumulation and osteogenic differentiation. CCL1 increased the transcription factor basic leucine zipper ATF-like transcription factor (BATF) in CCR8+ Tregs, which induced the secretion of progranulin that promoted SSC osteogenic function and new bone formation. This study highlights the ever-expanding role of Tregs in tissue repair by demonstrating their ability to expand stem cells at a site of injury.
Review of Artificial Intelligence in Lung Nodule Risk Assessment
Authors: Ying Wei, Qing Zhou, Jiaojiao Wu, Xiaoxian Xu, Yaozong Gao, Lei Chen, Yiqiang Zhan, Xiang Sean Zhou, Feng Shi, Dinggang Shen
Journal: IEEE Reviews in Biomedical Engineering (2025)

Lung cancer is the leading cause of cancerrelated mortality worldwide. In addition to localizing and segmenting lung nodules, a non-invasive risk assessment system can also help clinicians tailor treatment decisions in a timely manner, ultimately improving patient outcomes. Artificial intelligence (AI) technologies are increasingly being used in medical imaging to assess the risk of lung nodules, especially for malignancy classification. However, little research has been conducted on the assessment of other related risks. This work comprehensively reviews AI applications in lung nodule risk assessment, including malignancy diagnosis, pathological subtype assessment, metastasis risk evaluation, specific receptor expression identification, and disease progression tracking. It details common public databases used and state-of-the-art AI techniques, along with their benefits and challenges like data scarcity, generalizability, and interpretability. We anticipate that future research will tackle these issues, thereby increasing the improved interpretability and generalizability of AI methods in clinical workflows.
24-Month Outcomes of Endovascular Baroreflex Amplification With the MobiusHD Device in Heart Failure With Reduced Ejection Fraction
Authors: Kerstin Piayda, Stefan Bertog, Kolja Sievert, Horst Sievert, Tamaz Shaburishvili, Irakli Gogorishvili, Martin Rothman, James L Januzzi, JoAnn Lindenfeld, Gregg W Stone
Journal: JACC Heart Failure (2025)
Blood Eosinophil Count Stability in COPD and the Eosinophilic Exacerbator Phenotype
Authors: Federico Baraldi, Samuel Bartlett-Pestle, James P. Allinson, Mairi Macleod, Jordina Mah, Chloe Bloom, Aaron Brady-Green, Apolline Marion, Alberto Papi, Jadwiga A. Wedzicha, Lydia J. Finney
Journal: American Journal of Respiratory and Critical Care Medicine (2025)
Persistent, Private and Mobile genes: a model for gene dynamics in evolving pangenomes
Authors: Jasmine Gamblin, Amaury Lambert, François Blanquart
Journal: Molecular Biology and Evolution (2025)

The pangenome of a species is the set of all genes carried by at least one member of the species. In bacteria, pangenomes can be much larger than the set of genes carried by a single organism. Many questions remain unanswered regarding the evolutionary forces shaping the patterns of presence/absence of genes in pangenomes of a given species. We introduce a new model for bacterial pangenome evolution along a species phylogeny that explicitly describes the timing of appearance of each gene in the species and accounts for three generic types of gene evolutionary dynamics: persistent genes that are present in the ancestral genome, private genes that are specific to a given clade, and mobile genes that are imported once into the gene pool and then undergo frequent horizontal gene transfers. We call this model the Persistent-Private-Mobile (PPM) model. We develop an algorithm fitting the PPM model and apply it to a dataset of 902 Salmonella enterica genomes. We show that the best fitting model is able to reproduce the global pattern of some multivariate statistics like the gene frequency spectrum and the parsimony vs. frequency plot. Moreover, the gene classification induced by the PPM model allows us to study the position of accessory genes on the chromosome depending on their category, as well as the gene functions that are most present in each category. This work paves the way for a mechanistic understanding of pangenome evolution, and the PPM model developed here could be used for dynamics-aware gene classification.