Combining 3D imaging and single-cell genomics, Jafree et al. uncover how kidney lymphatics are uniquely organized and how they are rewired in chronic transplant rejection. The cover image shows 3D reconstruction of a confocal image stack from immunolabeled and optically cleared human kidney tissue with chronic transplant rejection. Image credit: Daniyal Jafree and David Long.
BACKGROUND. A key objective in managing HPV-positive oropharyngeal squamous cell carcinoma (OPSCC) is reducing radiation therapy (RT) doses without compromising cure rates. A recent Phase 2/3 HN005 trial revealed that clinical factors alone are insufficient to guide safe RT dose de-escalation. Our prior research demonstrated that the Genomic Adjusted Radiation Dose (GARD) predicts RT benefit and may inform dose selection. We hypothesize that GARD can guide personalized RT de-escalation in HPV-positive OPSCC patients. METHODS. Gene expression profiles were analyzed in 191 HPV-positive OPSCC patients enrolled in an international, multi-institutional observational study (AJCC 8th edition stages I–III). Most patients received 70 Gy in 35 fractions or 69.96 Gy in 33 fractions (median dose: 70 Gy, range: 51.0–74.0 Gy). Overall survival (OS) was 94.1% at 36 months and 87.3% at 60 months. Cox proportional hazards models assessed association between GARD and OS, and time-dependent ROC analyses compared GARD with traditional clinical predictors. RESULTS. Despite uniform RT dosing, GARD showed wide heterogeneity ([15.4–71.7]). Higher GARD values were significantly associated with improved OS in univariate (HR = 0.941, P = 0.041) and multivariable analyses (HR = 0.943, P = 0.046), while T and N stage were not. GARD demonstrated superior predictive performance at 36 months (AUC = 78.26) versus clinical variables (AUC = 71.20). Two GARD-based RT de-escalation strategies were identified, offering potential survival benefits while reducing radiation exposure. CONCLUSIONS. GARD predicts overall survival and outperforms clinical variables, supporting its integration into the diagnostic workflow for personalized RT in HPV-positive OPSCC.
Emily Ho, Loris De Cecco, Steven A. Eschrich, Stefano Cavalieri, Geoffrey Sedor, Frank J. Hoebers, Ruud H. Brakenhoff, Kathrin Scheckenbach, Tito Poli, Kailin Yang, Jessica A. Scarborough, Shivani Nellore, Shauna R. Campbell, Neil M. Woody, Timothy A. Chan, Jacob Miller, Natalie L. Silver, Shlomo Koyfman, James E. Bates, Jimmy J. Caudell, Michael W. Kattan, Lisa Licitra, Javier F. Torres-Roca, Jacob G. Scott
Activating mutations in PIK3CA, the gene encoding the catalytic p110-alpha subunit of PI3K, are some of the most frequent genomic alterations in breast cancer. Alpelisib, a small-molecule inhibitor that targets p110-alpha, is a recommended drug for patients with PIK3CA-mutant advanced breast cancer. However, clinical success for PI3K inhibitors has been limited by their narrow therapeutic window. The lipid phosphatase PTEN is a potent tumour suppressor and a major negative regulator of the PI3K pathway. Unsurprisingly, inactivating mutations in PTEN correlate with tumour progression and resistance to PI3K inhibition due to persistent PI3K signalling. Here we demonstrate that PI3K inhibition leads rapidly to the inactivation of PTEN. Using a functional genetic screen we show that this effect is mediated by a USP10-GSK3-B signalling axis, in which USP10 stabilizes GSK3-B resulting in GSK3-B-mediated phosphorylation of the C-terminal tail of PTEN. This phosphorylation inhibits PTEN dimerization and thus prevents its activation. Downregulation of GSK3-B or USP10 re-sensitizes PI3K inhibitor resistant breast cancer models and patient derived organoids to PI3K inhibition and induces tumour regression. Our study establishes that enhancing PTEN activity is a new strategy to treat PIK3CA mutant tumours and provides a strong rationale for pursuing USP10 inhibitors in the clinic.
Nishi Kumari, Sarah CE. Wright, Christopher M. Witham, Laia Monserrat, Marta Palafox, John Lalith Charles Richard, Carlotta Costa, Moshe Elkabets, Mark Agostino, Theresa Klemm, Melissa K. Eccles, Alexandra Garnham, Ting Wu, Jonas A. Nilsson, Nikita Walz, Veena Venugopal, Anthony Cerra, Natali Vasilevski, Stephanie C. Bridgeman, Sona Bassi, Azad Saei, Moutaz Helal, Philipp Neundorf, Angela Riedel, Mathias Rosenfeldt, Jespal Gill, Nikolett Pahor, Oliver Hartmann, Jacky Chung, Sachdev S. Sidhu, Nina Moderau, Sudhakar Jha, Jordi Rodon, Markus E. Diefenbacher, David Komander, Violeta Serra, Pieter Eichhorn
Allergic diseases have reached epidemic proportions globally, calling attention to the need for better treatment and preventive approaches. Herein, we developed allergen-encoding messenger RNA (mRNA) lipid nanoparticle (LNP) strategies for both therapy and prevention of allergic responses. Immunization with allergen-encoded mRNA-LNPs modulated T cell differentiation, inhibiting the generation of T helper type 2 (Th2) and type 17 (Th17) cells upon allergen exposure in experimental asthma models induced by ovalbumin (OVA), and naturally occurring house dust mite (HDM) and the major HDM allergen Der p1. Allergen-specific mRNA-LNP treatment attenuated clinicopathology in both preventive and established allergy models, including reduction in eosinophilia, mucus production, and airway hypersensitivity, while enhancing production of allergen-specific IgG antibodies and maintaining low IgE levels. Additionally, allergen-specific mRNA-LNP vaccines in mice elicited a CD8+CD38+KLRG- T cell response as seen following SARS-CoV-2 mRNA vaccination in human, underscoring a conserved immune mechanism across species, regardless of the mRNA-encoded protein. Notably, mRNA-LNP vaccination in combination with an mTOR inhibitor reduced the CD8+ T cell response without affecting the vaccine-induced anti-allergic effect in the preventive model of asthma. This technology renders allergen-specific mRNA-LNP therapy as a promising approach for prevention and treatment of allergic diseases.
Yrina Rochman, Michael Kotliar, Andrea M. Klingler, Mark Rochman, Mohamad-Gabriel Alameh, Jilian R. Melamed, Garrett A. Osswald, Julie M. Caldwell, Jennifer M. Felton, Lydia E. Mack, Julie Hargis, Ian P. Lewkowich, Artem Barski, Drew Weissman, Marc E. Rothenberg
The Integrator complex plays essential roles in RNA polymerase II transcription termination and RNA processing. Here, we identify INTS6, a subunit of the Integrator complex, as a novel gene associated with neurodevelopmental disorders (NDDs). Through analysis of large NDD cohorts and international collaborations, we identified 23 families harboring monoallelic likely gene-disruptive or de novo missense variants in INTS6. Phenotypic characterization revealed shared features, including language and motor delays, autism, intellectual disability, and sleep disturbances. Using a nervous-system conditional knockout (cKO) mouse model, we show that Ints6 deficiency disrupts early neurogenesis, cortical lamination, and synaptic development. Ints6 cKO mice displayed a thickened ventricular zone/subventricular zone, thinning of the cortical plate, reduced neuronal differentiation, and increased apoptosis in cortical layer 6. Behavioral assessments of heterozygous mice revealed deficits in social novelty preference, spatial memory, and hyperactivity, mirroring phenotypes observed in individuals with INTS6 variants. Molecular analyses further revealed that INTS6 deficiency alters RNA polymerase II dynamics, disrupts transcriptional regulation, and impairs synaptic gene expression. Treatment with a CDK9 inhibitor (CDK9i) reduced RNAPII phosphorylation, thereby limiting its binding to target genes. Notably, CDK9i reversed neurosphere over-proliferation and rescued the abnormal dendritic spine phenotype caused by Ints6 deficiency. This work advances understanding of INTS-related NDD pathogenesis and highlights potential therapeutic targets for intervention.
Xiaoxia Peng, Xiangbin Jia, Hanying Wang, Jingjing Chen, Xiaolei Zhang, Senwei Tan, Xinyu Duan, Can Qiu, Mengyuan Hu, Haiyan Hou, Ilaria Parenti, Alma Kuechler, Frank J. Kaiser, Alicia Renck, Raymond Caylor, Cindy Skinner, Joseph Peeden, Benjamin Cogne, Bertrand Isidor, Sandra Mercier, Gael Nicolas, Anne-Marie Guerrot, Flavio Faletra, Luciana Musante, Lior Cohen, Gaber Bergant, Goran Čuturilo, Borut Peterlin, Andrea Seeley, Kristine Bachman, Julian A. Martinez-Agosto, Conny van Ravenswaaij-Arts, Dennis Bos, Katherine H. Kim, Tobias Bartolomaeus, Zelia Schmederer, Rami Abou Jamra, Erfan Aref-Eshghi, Wenjing Zhao, Yongyi Zou, Zhengmao Hu, Qian Pan, Faxiang Li, Guodong Chen, Jiada Li, Zhangxue Hu, Kun Xia, Jieqiong Tan, Hui Guo
Polypyrimidine tract-binding protein PTBP1 is a heterogeneous nuclear ribonucleoprotein primarily known for its alternative splicing activity. It shuttles between the nucleus and cytoplasm via partially overlapping N-terminal nuclear localization (NLS) and export (NES) signals. Despite its fundamental role in cell growth and differentiation, its involvement in human disease remains poorly understood. We identified 27 individuals from 25 families harboring de novo or inherited pathogenic variants — predominantly start-loss (89%) and, to a lesser extent, missense (11%) — affecting NES/NLS motifs. Affected individual presented with a syndromic neurodevelopmental disorder and variable skeletal dysplasia with disproportionate short-limbed short stature. Intellectual functioning ranged from normal to moderately delayed. Start-loss variants led to translation initiation from an alternative downstream in-frame methionine, resulting in loss of the NES and the first half of the bipartite NLS, and increased cytoplasmic stability. Start-loss and missense variants shared a DNA methylation episignature in peripheral blood and altered nucleocytoplasmic distribution in vitro and in vivo with preferential accumulation in processing bodies, causing aberrant gene expression but normal RNA splicing. Transcriptomic analysis of patient-derived fibroblasts revealed dysregulated pathways involved in osteochondrogenesis and neurodevelopment. Overall, our findings highlight a cytoplasmic role for PTBP1 in RNA stability and disease pathogenesis.
Aymeric Masson, Julien Paccaud, Martina Orefice, Estelle Colin, Outi Mäkitie, Valérie Cormier-Daire, Raissa Relator, Sourav Ghosh, Jean-Marc Strub, Christine Schaeffer-Reiss, Carlo Marcelis, David A. Koolen, Rolph Pfundt, Elke de Boer, Lisenka E.L.M. Vissers, Thatjana Gardeitchik, Lonneke A.M. Aarts, Tuula Rinne, Paulien A. Terhal, Nienke E. Verbeek, Linda C. Zuurbier, Astrid S. Plomp, Marja W. Wessels, Stella A. de Man, Arjan Bouman, Lynne M. Bird, Reem Saadeh-Haddad, Maria J. Guillen Sacoto, Richard Person, Catherine Gooch, Anna C.E. Hurst, Michelle L. Thompson, Susan M. Hiatt, Rebecca O. Littlejohn, Elizabeth R. Roeder, Mari Mori, Scott Hickey, Jesse M. Hunter, Kristy Lee, Khaled Osman, Rana Halloun, Ruxandra Bachmann-Gagescu, Anita Rauch, Dagmar Wieczorek, Konrad Platzer, Johannes Luppe, Laurence Duplomb-Jego, Fatima El It, Yannis Duffourd, Frédéric Tran Mau-Them, Celine Huber, Christopher T. Gordon, Fulya Taylan, Riikka E. Mäkitie, Alice Costantini, Helena Valta, Stephen Robertson, Gemma Poke, Michel Francoise, Andrea Ciolfi, Marco Tartaglia, Nina Ekhilevitch, Rinat Zaid, Michael A. Levy, Jennifer Kerkhof, Haley McConkey, Julian Delanne, Martin Chevarin, Valentin Vautrot, Valentin Bourgeois, Sylvie Nguyen, Nathalie Marle, Patrick Callier, Hana Safraou, Angela Morgan, David J. Amor, Michael Hildebrand, David Coman, Marion Aubert Mucca, Julien Thevenon, Fanny Laffargue, Frédéric Bilan, Céline Pebrel-Richard, Grace Yoon, Michelle M. Axford, Luis A. Pérez-Jurado, Marta Sevilla-Porras, Douglas Black, Christophe Philippe, Bekim Sadikovic, Christel Thauvin-Robinet, Laurence Olivier-Faivre, Michela Ori, Quentin Thomas, Antonio Vitobello
Pancreatic ductal adenocarcinoma (PDAC) has among the poorest prognosis and highest refractory rates of all tumor types. The reviews in this series, by Dr. Ben Z. Stanger, bring together experts across multiple disciplines to explore what makes PDAC and other pancreatic cancers so distinctively challenging and provide an update on recent multipronged approaches aimed at improving early diagnosis and treatment.
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