Issue published November 17, 2025 Previous issue
- Volume 135, Issue 22
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On the cover: Xeroderma pigmentosum complementation group XP-J
Fassihi et al. and Nakazawa et al. report that a C-terminal deletion of the transcription factor TFIIH-p52 subunit (blue; C-terminus in white) causes xeroderma pigmentosum. The cover art was created using PyMOL. Image credit: Keiko Itano.
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Obituary
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Abstract
Authors
Alireza Haghighi, Salil A. Lachke, Natasha Y. Frank, Wolfram Goessling, Philip A. Cole
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Commentaries
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Abstract
Glycogen synthase kinase-3β (GSK3β) is an established regulator in the DNA double-strand break (DSB) repair pathway. Recent work by Allam et al. revealed a mechanism of DSB repair pathway choice through GSK3β-mediated, site-specific phosphorylation of the tumor suppressor p53 binding protein 1 (53BP1) at threonine 334 (T334). 53BP1 T334 phosphorylation prevented interaction between 53BP1 and its downstream functional partners, PTIP and RIF1, thereby inhibiting 53BP1-directed nonhomologous end joining (NHEJ). Additionally, 53BP1 T334 phosphorylation promoted recruitment of CtIP and RPA32 to DNA damage sites to facilitate homologous recombination (HR). In contrast with loss of 53BP1 function, a 53BP1 T334A phospho-deficient mutant accumulated aberrantly at DSBs, where it impaired end resection and suppressed HR activity. These surprising results suggest that GSK3β may select between NHEJ and HR DNA repair pathways. Additionally, these data support targeting the GSK3β/53BP1 axis to enhance PARP inhibitor efficacy in solid tumors, regardless of BRCA1 status.
Authors
Justin W. Leung, David Gius
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Pulmonary fibrosis, an unrelenting disease of lung scarring, has been associated with the expansion of a profibrotic fibroblast population and extensive extracellular matrix deposition. In this issue, Molina and colleagues provide foundational mechanistic evidence that fibroblast proliferation itself is a critical driver of fibrosis. Using lineage tracing in preclinical fibrosis models, the authors showed that naive Scube2+ alveolar fibroblasts underwent a profibrotic phenotypic switch prior to proliferating within areas of fibrotic remodeling. Induction of apoptosis via Esco2 deletion or directly preventing proliferation via Ect2 deletion in these fibroblasts attenuated fibrosis. Complementary analyses on explanted human lung tissue confirmed translational relevance, collectively providing compelling evidence for the importance of fibroblast proliferation in fibrotic disease.
Authors
Cody A. Schott, Elizabeth F. Redente
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Invasive fungal infections carry high morbidity and mortality, but there are no fungal vaccines. In this issue of the JCI, Okaa et al. report that endonuclease 2 (Eng2), an antigen shared by the Blastomyces, Histoplasma, and Coccidioides species of fungi, elicits protective immunity in mice against blastomycosis, histoplasmosis, and coccidioidomycosis. These results establish a common antigen that can elicit protection against multiple mycoses, encouraging the development of a pan-fungal vaccine. The road to fungal vaccines is made difficult by the need for effectiveness in immunocompromised individuals, the sporadic nature of fungal disease, and the economics of vaccine development. Despite these hurdles, there is optimism that such vaccines can be developed and perhaps find usefulness as adjuncts to antifungal therapy.
Authors
Arturo Casadevall
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DNA damage and repair are central to the onset of cancer, aging, and aging-related diseases. Rare genetic defects in the nucleotide excision repair pathway, such as those causing the cancer-prone disorder xeroderma pigmentosum (XP) or the progeroid condition Cockayne syndrome, highlight the dramatic consequences of unrepaired DNA lesions. In this issue of the JCI, two related papers from Ogi and coworkers — Fassihi et al. and Nakazawa et al. — describe a new XP clinical entity, XP-J, linked to a pathogenic variant in the p52 subunit of the transcription-repair complex TFIIH. The studies’ characterization of XP-J and the p52ΔC variant opened unexpected possibilities to ameliorate the molecular defect in another subunit of TFIIH that causes a different, more severe repair syndrome: trichothiodystrophy. This commentary provides a broader historical, medical, and molecular context for the intricate genotype-phenotype relationship between compromised repair and its clinical consequences and discusses next steps for the advances reported.
Authors
Arjan F. Theil, Jan H.J. Hoeijmakers
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Research Letters
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Abstract
Authors
Steven Q. Le, Alexander Sorensen, Soila Sukupolvi, Gianna Jewhurst, Grant Austin, Balraj Doray, Jonathan D. Cooper, Patricia I. Dickson
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Authors
Hiva Fassihi, Shehla Mohammed, Yuka Nakazawa, Heather Fawcett, Sally Turner, Joanne Palfrey, Isabel Garrood, Adesoji Abiona, Ana M.S. Morley, Mayuko Shimada, Kana Kato, Alan R. Lehmann, Tomoo Ogi
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Research Articles
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Abstract
Activating mutations in PIK3CA, the gene encoding the catalytic p110α subunit of PI3K, are some of the most frequent genomic alterations in breast cancer. Alpelisib, a small-molecule inhibitor that targets p110α, is a recommended drug for patients with PIK3CA-mutant advanced breast cancer. However, clinical success for PI3K inhibitors (PI3Kis) has been limited by their narrow therapeutic window. The lipid phosphatase PTEN is a potent tumor suppressor and a major negative regulator of the PI3K pathway. Unsurprisingly, inactivating mutations in PTEN correlate with tumor progression and resistance to PI3K inhibition due to persistent PI3K signaling. 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-GSK3β signaling axis, in which USP10 stabilizes GSK3β, resulting in GSK3β-mediated phosphorylation of the C-terminal tail of PTEN. This phosphorylation inhibits PTEN dimerization and thus prevents its activation. Downregulation of GSK3β or USP10 resensitizes PI3Ki-resistant breast cancer models and patient-derived organoids to PI3K inhibition and induces tumor regression. Our study establishes that enhancing PTEN activity is a new strategy to treat PIK3CA mutant tumors and provides a strong rationale for pursuing USP10 inhibitors in the clinic.
Authors
Nishi Kumari, Sarah C.E. Wright, Christopher M. Witham, Laia Monserrat, Marta Palafox, John L.C. Richard, Carlotta Costa, Moshe Elkabets, Mark Agostino, Theresa Klemm, Melissa Eccles, Alex Garnham, Ting Wu, Jonas A. Nilsson, Nikita Walz, Veena Venugopal, Anthony Cerra, Natali Vasilevski, Stephanie 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 Johan Adam Eichhorn
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Polypyrimidine tract-binding protein 1 (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 individuals presented with a syndromic neurodevelopmental disorder and variable skeletal dysplasia with disproportionate short stature with short limbs. 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.
Authors
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 E. 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 S. 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 L. Black, Christophe Philippe, Bekim Sadikovic, Christel Thauvin-Robinet, Laurence Olivier-Faivre, Michela Ori, Quentin Thomas, Antonio Vitobello
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3-O-sulfation of heparan sulfate (HS) is the key determinant for binding and activation of antithrombin III (AT). This interaction is the basis of heparin treatment to prevent thrombotic events and excess coagulation. Antithrombin-binding HS (HSAT) is expressed in human tissues but is thought to be expressed in the subendothelial space, mast cells, and follicular fluid. Here, we show that HSAT is ubiquitously expressed in the basement membranes of epithelial cells in multiple tissues. In the pancreas, HSAT is expressed by healthy ductal cells, and its expression is increased in premalignant pancreatic intraepithelial neoplasia lesions but not in pancreatic ductal adenocarcinoma (PDAC). Inactivation of HS3ST1, a key enzyme in HSAT synthesis, in PDAC cells eliminated HSAT expression, induced an inflammatory phenotype, suppressed markers of apoptosis, and increased metastasis in an experimental mouse PDAC model. HSAT-positive PDAC cells bind AT, which inhibits the generation of active thrombin by tissue factor and factor VIIa. Furthermore, plasma from patients with PDAC showed accumulation of HSAT, suggesting its potential as a marker of tumor formation. These findings suggest that HSAT exerts a tumor-suppressing function through recruitment of AT and that the decrease in HSAT during progression of pancreatic tumorigenesis increases inflammation and metastatic potential.
Authors
Thomas Mandel Clausen, Ryan J. Weiss, Jacob R. Tremblay, Benjamin P. Kellman, Joanna Coker, Leo A. Dworkin, Jessica P. Rodriguez, Ivy M. Chang, Timothy Chen, Vikram Padala, Richard Karlsson, Hyemin Song, Kristina L. Peck, Satoshi Ogawa, Daniel R. Sandoval, Hiren J. Joshi, Gaowei Wang, L. Paige Ferguson, Nikita Bhalerao, Allison Moores, Tannishtha Reya, Maike Sander, Thomas C. Caffrey, Jean L. Grem, Alexandra Aicher, Christopher Heeschen, Dzung Le, Nathan E. Lewis, Michael A. Hollingsworth, Paul M. Grandgenett, Susan L. Bellis, Rebecca L. Miller, Mark M. Fuster, David W. Dawson, Dannielle D. Engle, Jeffrey D. Esko
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The physiology of SARS-CoV-2 virus/host interactions is not well understood. To better understand host/virus interactions, we performed a CRISPR activation screen to identify host genes that confer resistance to authentic SARS-CoV-2. This highlighted 34 new candidate genes that may alter the course of infection. We validated that 7 of these genes can suppress authentic SARS-CoV-2 infection, including the innate immune receptor P selectin, which increases SARS-CoV-2 spike-dependent binding to cells, while protecting from infection. P selectin also promotes binding to SARS-CoV-2 variants, SARS-CoV-1, and Middle East respiratory syndrome spike proteins, suggesting a general role for P selectin in highly pathogenic coronavirus infections. Importantly, P selectin protein expression driven by synthetic mRNA can block SARS-CoV-2 infection. Naturally, P selectin is expressed on platelets, and we show that it promotes spike-mediated platelet aggregation. P selectin is also expressed on the endothelium, where SARS-CoV-2 spike interactions are also P selectin dependent. In vivo, SARS-CoV-2 uses P selectin to home to capillary beds where the virus interacts with platelets and endothelium, and blocking this interaction can clear vascular-associated pulmonary SARS-CoV-2.
Authors
Cesar L. Moreno, Fernanda V.S. Castanheira, Alberto Ospina Stella, Felicity Chung, Anupriya Aggarwal, Alexander J. Cole, Lipin Loo, Alexander Dupuy, Yvonne X. Kong, Lejla Hagimola, Jemma Fenwick, Paul R. Coleman, Rebecca Carr, Tian Y. Du, Tim Ison, Michelle Newton, Maxwell P. Bui-Marinos, Scott B. Cohen, Jennifer A. Corcoran, Daniel Hesselson, Jennifer R. Gamble, Freda H. Passam, Stuart G. Turville, Paul Kubes, G. Gregory Neely
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B lymphocytes play major adaptive immune roles, producing antibodies and driving T cell responses. However, how immunometabolism networks support B cell activation and differentiation in response to distinct receptor stimuli remains incompletely understood. To gain insights, we systematically investigated acute primary human B cell transcriptional, translational, and metabolomic responses to B cell receptor (BCR), TLR9, CD40-ligand (CD40L), IL-4, or combinations thereof. T cell–independent BCR/TLR9 costimulation, which drives malignant and autoimmune B cell states, highly induced transaminase branched chain amino acid transaminase 1 (BCAT1), which localized to lysosomal membranes to support branched chain amino acid synthesis and mTORC1 activation. BCAT1 inhibition blunted BCR/TLR9, but not CD40L/IL-4–triggered B cell proliferation, IL-10 expression, and BCR/TLR pathway–driven lymphoma xenograft outgrowth. These results provide a valuable resource, reveal receptor-mediated immunometabolism remodeling to support key B cell phenotypes, and identify BCAT1 as an activated B cell therapeutic target.
Authors
Rui Guo, Yizhe Sun, Matthew Y. Lim, Hardik Shah, Joao A. Paulo, Rahaman A. Ahmed, Weixing Li, Yuchen Zhang, Haopeng Yang, Liang Wei Wang, Daniel Strebinger, Nicholas A. Smith, Meng Li, Merrin Man Long Leong, Michael Lutchenkov, Jin Hua Liang, Zhixuan Li, Yin Wang, Rishi Puri, Ari Melnick, Michael R. Green, John M. Asara, Adonia E. Papathanassiu, Duane R. Wesemann, Steven P. Gygi, Vamsi K. Mootha, Benjamin E. Gewurz
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Intestinal function and white adipose tissue (WAT) function deteriorate with age, but whether and how their deterioration is intertwined remains unknown. Increased gut permeability, microbiota dysbiosis, and aberrant immune microenvironment are the hallmarks of intestinal dysfunctions in aging. Here, we show that subcutaneous WAT dysfunction triggered aging-like intestinal dysfunctions in mouse models. Removal of inguinal subcutaneous WAT (iWAT) increased intestinal permeability and inflammation and altered gut microbiota composition as well as susceptibility to pathogen infection in mouse models. These intestinal dysfunctions were accompanied by a reduction of immunoglobulin A–producing (IgA-producing) cells and IgA biosynthesis in the lamina propria of the small intestine. Retinoic acid (RA) is a key cargo within iWAT-derived extracellular vesicles (iWAT-EVs), which, at least in part, elicits IgA class-switching and production in the small intestine and maintains microbiota homeostasis. RA content in iWAT-EVs and intestinal IgA biosynthesis are reduced during aging in mice. Replenishment of “young” iWAT-EVs rejuvenates intestinal IgA production machinery and shifts microbiota composition of aged mice to a “youth” status, which alleviates leaky gut via RA. In conclusion, our findings suggest that iWAT-EVs with RA orchestrate IgA-mediated gut microbiota homeostasis by acting on intestinal B cells, thereby maintaining intestinal health during aging.
Authors
KeKao Long, Pujie Liu, Yi Wang, Jordy Evan Sulaiman, Moinul Hoque, Gloria Hoi Yee Li, Daisy Danyue Zhao, Pui-Kei Lee, Gilman Kit-hang Siu, Annie Wing-tung Lee, Zhuohao Liu, Pui-kin So, Yin Cai, Connie Wai-hong Woo, Chi-bun Chan, Aimin Xu, Kenneth King-yip Cheng
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Checkpoint inhibitors targeting CTLA-4 and PD-1 revolutionized the treatment of cancer patients, but their use is limited by the emergence of immune-related adverse events (irAEs). We assessed autoreactive B cell frequencies in the blood of cancer patients before and after treatment with checkpoint inhibitors by testing the reactivity of recombinant antibodies cloned from single B cells. We found that anti–PD-1 and anti–CTLA-4 combination therapy induced the emergence of autoreactive mature naive B cells, whereas central B cell tolerance remained functional. In contrast, anti–PD-1 alone did not alter autoreactive B cell counterselection. Anti–CTLA-4 injections in humanized mice also resulted in the production of autoreactive B cells, whereas anti–PD-1 did not. We conclude that CTLA-4 but not PD-1 is required for the removal of developing autoreactive mature naive B cells and that CTLA-4 blockade broadens the peripheral B cell repertoire, which likely contains clones that promote not only irAEs but also antitumor responses.
Authors
Elif Çakan, Meng Wang, Yile Dai, Adrien Mirouse, Clarence Rachel Villanueva-Pachas, Delphine Bouis, Joshua M. Boeckers, Ruchi Gera, Sally Yraita, Leslie Clapp, Ana Luisa Perdigoto, Fabien R. Delmotte, Christopher Massad, Antonietta Bacchiocchi, Aaron M. Ring, Yuval Kluger, Harriet M. Kluger, Kevan C. Herold, Eric Meffre
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BACKGROUND Localized high-risk prostate cancer (PCa) often recurs despite neoadjuvant androgen deprivation therapy (ADT). We sought to identify baseline molecular programs that predict pathologic response and reveal targetable vulnerabilities.METHODS We profiled 147 biopsy foci from 48 MRI-visible lesions in 37 patients before 6 months of ADT plus enzalutamide and radical prostatectomy. Residual cancer burden (RCB) at prostatectomy was the primary outcome. Analyses incorporated PTEN loss, TMPRSS2:ERG status, and HER2/androgen receptor (AR) immunohistochemistry on baseline and posttreatment tissues. Findings were evaluated in an external transcriptional cohort (n = 121) and by multiplex immunostaining in an independent cohort (n = 61). Functional assays tested enzalutamide-responsive enhancers near ERBB2 and sensitivity to HER2 inhibition.RESULTS A baseline, HER2-associated transcriptional program correlated with higher RCB and inversely with AR activity, independent of PTEN and ERG. Exceptional responders had lower HER2 protein levels in pretreatment biopsy specimens. The inverse AR-HER2 relationship recurred across data sets and multiplex immunostaining, which revealed coexisting AR-high/HER2-low and HER2-high/AR-low subpopulations. Enzalutamide inhibited AR-mediated repression of ERBB2. HER2-high/AR-low cells present before therapy resisted ADT yet were sensitive to HER2 inhibitors; combining HER2 inhibitors with enzalutamide increased tumor cell killing. These findings were reproduced in the external cohort and orthogonal assays.CONCLUSION Baseline HER2 activity marks intrinsic resistance to neoadjuvant ADT in localized high-risk PCa and identifies a preexisting, targetable AR-low subpopulation. HER2-directed therapy, alone or with AR blockade, warrants clinical evaluation.TRIAL REGISTRATION ClinicalTrials.gov registration: NCT02430480.FUNDING Prostate Cancer Foundation; Department of Defense Prostate Cancer Research Program; National Institutes of Health.
Authors
Scott Wilkinson, Anson T. Ku, Rosina T. Lis, Isaiah M. King, Daniel Low, Shana Y. Trostel, John R. Bright, Nicholas T. Terrigino, Anna Baj, Emily R. Summerbell, Kayla E. Heyward, Sumeyra Kartal, John M. Fenimore, Chennan Li, Cassandra Singler, BaoHan Vo, Caroline S. Jansen, Huihui Ye, Nichelle C. Whitlock, Stephanie A. Harmon, Nicole V. Carrabba, Rayann Atway, Ross Lake, David Y. Takeda, Haydn T. Kissick, Peter A. Pinto, Peter L. Choyke, Baris Turkbey, William L. Dahut, Fatima Karzai, Adam G. Sowalsky
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Resistance to genotoxic therapies remains a major contributor to tumor recurrence and treatment failure, yet the mechanisms by which cancer cells escape these therapies through DNA damage response (DDR) activation are not fully understood. Here, we identify a DDR regulatory pathway in which glycogen synthase kinase 3 β (GSK3B), a multifunctional serine/threonine kinase, governs DNA double-strand break (DSB) repair pathway choice by phosphorylating 53BP1 at threonine 334 (T334) — a site distinct from canonical ATM targets. This phosphorylation event disrupts 53BP1’s interaction with nonhomologous end joining (NHEJ) effectors PTIP and RIF1, promoting their dissociation from DSBs and inhibiting 53BP1-driven NHEJ. Simultaneously, T334 phosphorylation facilitates the recruitment of CtIP and RPA32 for DNA end resection and promotes homologous recombination (HR) by enabling BRCA1 and RAD51 loading. Notably, the phospho-deficient T334A mutant of 53BP1, unlike 53BP1 loss, accumulates aberrantly at DSBs along with PTIP/RIF1, impairs end resection, and suppresses HR activity. Importantly, both genetic and pharmacologic disruption of the GSK3B–53BP1 axis sensitizes tumors to PARP inhibitors (PARPi) independently of BRCA1 status. Together, these findings reveal a GSK3B-dependent mechanism that regulates DSB repair pathway choice and provide a rationale for targeting this axis to enhance PARPi efficacy in solid tumors regardless of BRCA1 status.
Authors
Heba S. Allam, Scarlett Acklin-Wehnert, Ratan Sadhukhan, Mousumi Patra, Fen Xia
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We describe here a shared surface and cell wall protein, endoglucanase 2 (Eng2), expressed on the etiological agents that cause the endemic systemic mycoses of North America — Blastomyces, Coccidioides, and Histoplasma. We demonstrate that, despite sequence variation of the protein across these related fungi, exposure to Eng2 vaccinated and protected inbred and humanized HLA-DR4 strains of mice against lethal experimental infections with these fungi by eliciting adaptive immunity mediated by CD4+ T cells. We also show that CD4+ T cell precursors against Eng2 were detectable in naive individuals and that patients who had recovered from these infections evinced a memory and recall CD4+ T cell response to Eng2 and its immunodominant epitopes that we have mapped. We created and cataloged new tools and information, such as immunodominant peptide epitopes of Eng2 from each fungus recognized by inbred mice and humans, and we engineered peptide–MHC II tetramers to track T cells in inbred and HLA-DR4–humanized mice. These tools and tetramers will be useful for those who study these infections in mice and humans. Last, because most patients demonstrated immune memory and recall responses against Eng2, our work offers tools for the diagnosis of this collection of infectious diseases across North America.
Authors
Uju J. Okaa, Cleison Ledesma Taira, Lucas dos Santos Dias, Hannah Dobson, Gregory C. Kujoth, Althea Campuzano, E. Jane Homan, George R. Thompson, Chiung-Yu Hung, George S. Deepe Jr, Marcel Wüthrich, Bruce S. Klein
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The Integrator complex plays essential roles in RNA polymerase II (RNAPII) 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 KO (cKO) mouse model, we show that Ints6 deficiency disrupts early neurogenesis, cortical lamination, and synaptic development. Ints6 cKO mice had 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 RNAPII 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 overproliferation 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.
Authors
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
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Pulmonary fibrosis (PF) has been called a fibroproliferative disease, yet the functional importance of proliferating fibroblasts to PF has not been systematically examined. In response to alveolar injury, quiescent alveolar fibroblasts differentiate into fibrotic fibroblasts that express high amounts of collagens. However, what role, if any, proliferation plays in the accumulation of fibrotic fibroblasts has remained unclear. Using 5-ethynyl-2′-deoxyuridine (EdU) incorporation, genetic lineage tracing, and single-cell RNA-Seq, we delineated the proliferation dynamics of lung fibroblasts during post-injury fibrogenesis. We found substantial DNA replication in progeny of alveolar fibroblasts in 2 independent models of PF. Lineage labeling revealed clonal expansion of these fibroblast descendants principally in regions of fibrotic remodeling. The transcriptome of proliferating fibroblasts closely resembled that of fibrotic fibroblasts, suggesting that fibroblasts can first differentiate into fibrotic fibroblasts and then proliferate. Genetic ablation of proliferating fibroblasts and selective inhibition of cytokinesis in alveolar fibroblast descendants significantly mitigated PF and rescued lung function. Furthermore, fibroblasts in precision-cut lung slices from human fibrotic lungs exhibited higher proliferation rates than did those in nondiseased lungs. Together, this work establishes fibroblast proliferation as a critical driver of PF and suggests that specifically targeting fibroblast proliferation could be a new therapeutic strategy for fibrotic diseases.
Authors
Christopher Molina, Tatsuya Tsukui, Imran S. Khan, Xin Ren, Wenli Qiu, Michael Matthay, Paul Wolters, Dean Sheppard
×Abstract
FOXP3+ natural regulatory T cells (nTregs) promote resolution of inflammation and repair of epithelial damage following viral pneumonia–induced lung injury, thus representing a cellular therapy for patients with severe viral pneumonia and the acute respiratory distress syndrome. Whether in vitro–induced Tregs (iTregs), which can be rapidly generated in substantial numbers from conventional T cells, also promote lung recovery is unknown. nTregs require specific DNA methylation patterns maintained by the epigenetic regulator ubiquitin-like with PHD and RING finger domains 1 (UHRF1). Here, we tested whether iTregs promote recovery following viral pneumonia and whether iTregs require UHRF1 for their pro-recovery function. We found that adoptive transfer of iTregs to mice with influenza virus pneumonia promotes lung recovery and that loss of UHRF1-mediated maintenance DNA methylation in iTregs leads to reduced engraftment and a delayed repair response. Transcriptional and DNA methylation profiling of adoptively transferred UHRF1-deficient iTregs that had trafficked to influenza-injured lungs demonstrated transcriptional instability with gain of transcription factors that define effector T cell lineage. Strategies to promote the stability of iTregs could be leveraged to further augment their pro-recovery function during viral pneumonia and other causes of severe lung injury.
Authors
Anthony M. Joudi, Jonathan K. Gurkan, Qianli Liu, Elizabeth M. Steinert, Manuel A. Torres Acosta, Kathryn A. Helmin, Luisa Morales-Nebreda, Nurbek Mambetsariev, Carla Patricia Reyes Flores, Hiam Abdala-Valencia, Samuel E. Weinberg, Benjamin D. Singer
×Abstract
Influenza and other respiratory viral pathogens remain leading causes of mortality and morbidity. Circadian rhythms play a critical role in regulating immune responses and can confer temporal protection from influenza infection. Here, we investigated whether this protection requires rhythmic function after the initial infection by manipulating environmental cycles. We found that disrupting environmental lighting cues within a critical window of vulnerability abrogated the time-of-day-specific protection. This poor outcome was mediated by a dysregulated immune response, as evidenced by the accumulation of inflammatory monocytes and CD8+ T cells in the lungs and a transcriptomic profile indicative of an exaggerated inflammation. Disruption of the light cycle did not affect outcomes in a clock mutant, indicating that it acts through the host’s circadian clock. Importantly, rhythmic meal timing mitigated the adverse effects of disrupted light cycles, supporting the idea that external cues acting through different body clocks can compensate for one another. Together, these findings underscore the critical interplay between environmental timing cues and endogenous circadian rhythms in determining influenza outcomes and offer translational insight into optimizing care for critically ill patients with respiratory viral infections.
Authors
Oindrila Paul, Thomas G. Brooks, Alisha Shetty, Y. Jane Choi, Martina Towers, Lora J. Assi, James P. Garifallou, Kaitlyn Forrest, Alecia Cameron, Amita Sehgal, Gregory Grant, Shaon Sengupta
×Abstract
Macrophage-mediated phagocytosis plays a critical role in the elimination of cancer cells and shaping antitumor immunity. However, the tumor-intrinsic pathways that regulate cancer cell sensitivity to macrophage-mediated phagocytosis remain poorly defined. In this study, we performed a genome-wide CRISPR screen in murine pancreatic cancer cells cocultured with primary macrophages and identified that disruption of the tumor-intrinsic pyrimidine synthesis pathway enhances phagocytosis. Mechanistically, we discovered that macrophages inhibit the pyrimidine salvage pathway in tumor cells by upregulating Upp1-mediated uridine degradation through cytokines TNF-α and IL-1. This shift increased tumor cells’ reliance on de novo pyrimidine synthesis. As a result, tumor cells with impaired de novo pyrimidine synthesis showed depleted UMP and displayed enhanced exposure of phosphatidylserine (PtdSer), a major “eat-me” signal, thereby promoting macrophage-mediated phagocytosis. In multiple pancreatic cancer models, Cad-deficient tumors exhibited markedly reduced tumor burden with increased levels of phagocytosis by macrophages. Importantly, the Cad-mediated suppression of pancreatic cancer was dependent on TAMs and cytokines IL-1 and TNF-α. Pharmacological inhibition of DHODH, which blocks de novo pyrimidine synthesis, similarly decreased tumor burden with enhanced phagocytosis in pancreatic cancer models. These findings highlight the critical role of the tumor-intrinsic pyrimidine synthesis pathway in modulating macrophage-mediated antitumor immunity, with potential therapeutic implications.
Authors
Jie Zhao, Xinghao Li, Xinyu Li, Pengfei Ren, Yilan Wu, Hao Gong, Lijian Wu, Junran Huang, Saisai Wang, Ziwei Guo, Mo Chen, Zexian Zeng, Deng Pan
×Abstract
BACKGROUND Spinal muscular atrophy (SMA) is a rare genetic neuromuscular disease caused by deletions or mutations of the survival motor neuron 1 (SMN1) gene. Despite the availability of genetically based treatments for SMA, functional impairments and weakness persist in treated symptomatic individuals. This study addresses whether additional treatment after gene transfer therapy could provide further clinical benefits.METHODS Interim day 302 findings are described from the phase IV open-label RESPOND trial evaluating nusinersen in participants aged ≤36 months who had suboptimal clinical status following onasemnogene abeparvovec (OA) treatment, as determined by the investigator.RESULTS Thirty-seven participants included in the interim analysis were symptomatic at the time of OA administration. Most (92%) had 2 SMN2 gene copies. Age at first nusinersen dose (median) was 9.1 (range, 3–33) months for participants with 2 SMN2 copies and 34.2 (range, 31–36) months for those with 3 SMN2 copies, while time from OA dose to first nusinersen dose (median) was 6.3 (range, 3–31) and 13.3 (range, 10–22) months, respectively. Participants had elevated neurofilament light chain (NfL) levels and low compound muscle action potential (CMAP) amplitudes at baseline, suggesting active neurodegeneration and severe denervation at study entry. Improvements from baseline were observed across a range of outcomes on day 302, including motor function (HINE-2 and CHOP-INTEND total score), achievement of independent sitting, NfL levels, CMAP, and investigator- and caregiver-reported outcomes. Mean NfL levels decreased rapidly from baseline to day 183 and remained low on day 302. Mean ulnar and peroneal CMAP amplitudes increased. No safety concerns were identified.CONCLUSION Improvements in clinical and biomarker outcomes support the benefit of nusinersen treatment in infants and children with suboptimal clinical status following OA.TRIAL REGISTRATION ClinicalTrials.gov NCT04488133; EudraCT 2020-003492-18.FUNDING This study was sponsored by Biogen.
Authors
Crystal M. Proud, Richard S. Finkel, Julie A. Parsons, Riccardo Masson, John F. Brandsema, Nancy L. Kuntz, Richard Foster, Wenjing Li, Ross Littauer, Jihee Sohn, Stephanie Fradette, Bora Youn, Angela D. Paradis, on behalf of the RESPOND Study Group
×Abstract
Venous thromboembolism (VTE) is a leading cause of morbidity and mortality, with risk heightened in premenopausal women with obesity or use estrogen-based oral contraceptives. When both risk factors are present, the thrombosis risk increases substantially. Protein S (PS), an essential anticoagulant cofactor, is downregulated by both estrogen and obesity, but the molecular basis for this suppression remains poorly defined. We investigated the effect of estrogen and obesity on PS expression using plasma samples from 157 women stratified by BMI and contraceptive use, alongside 40 mice categorized as lean or obese with or without estrogen pellet treatment. The levels of PS were reduced by either estrogen or obesity alone, and the combined effect increased thrombin generation. In HepG2 hepatocytes, hypoxic conditions (1%–10% O2) mimicking obesity, with or without 17 β-estradiol, suppressed PROS1 transcription and promoter activity. ChIP confirmed direct binding of hypoxia-inducible factor 1α (HIF1α) to the PROS1 promoter, repressing gene expression. These findings define a mechanistic pathway through which estrogen and obesity converge to suppress PS synthesis, providing insight into the elevated thrombosis risk observed in women with obesity using estrogen-based contraceptives.
Authors
Mohammad A. Mohammad, Narender Kumar, Sonali Ghosh, Ashley Paysse, Claudia Leonardi, Vijaya Pilli, Ma Lorena Duhaylungsod, Eric Lazartigues, Diana C. Polania-Villanueva, Sadaf Nouman, Logan A. Barrios, Rima Chattopadhyay, Rafika Yasmin, Alaina Guilbeau, Manoj Kumar, Tina Nguyen, Jovanny Zabaleta, Li Li, Luis Del Valle, Mallory T. Barbier, Samarpan Majumder, Laurent O. Mosnier, Rinku Majumder
×Abstract
A cornerstone of research to improve cancer outcomes involves studies of model systems to identify causal drivers of oncogenesis, understand mechanisms leading to metastases, and develop new therapeutics. Although most cancer types are represented by large cell line panels that reflect diverse neoplastic genotypes and phenotypes found in patients, prostate cancer is notable for a very limited repertoire of models that recapitulate the pathobiology of human disease. Of these, the lymph node carcinoma of the prostate (LNCaP) cell line has served as the major resource for basic and translational studies. Here, we delineated the molecular composition of LNCaP and multiple substrains through analyses of whole-genome sequences, transcriptomes, chromatin structure, androgen receptor (AR) cistromes, and functional studies. Our results determined that LNCaP exhibits substantial subclonal diversity, ongoing genomic instability, and phenotype plasticity. Several oncogenic features were consistently present across strains, but others were unexpectedly variable, such as ETV1 expression, Y chromosome loss, a reliance on WNT and glucocorticoid receptor activity, and distinct AR alterations maintaining AR pathway activation. These results document the inherent molecular heterogeneity and ongoing genomic instability that drive diverse prostate cancer phenotypes and provide a foundation for the accurate interpretation and reproduction of research findings.
Authors
Arnab Bose, Armand Bankhead III, Ilsa Coleman, Thomas Persse, Wanting Han, Patricia Galipeau, Brian Hanratty, Tony Chu, Jared Lucas, Dapei Li, Rabeya Bilkis, Pushpa Itagi, Sajida Hassan, Mallory Beightol, Minjeong Ko, Ruth Dumpit, Michael Haffner, Colin Pritchard, Gavin Ha, Peter S. Nelson
×Abstract
Few drugs are available for rare diseases due to economic disincentives. However, tailored medications for extremely rare disorders (N-of-1) offer a ray of hope. Artificial antisense oligonucleotides (ASOs) are now best known for their use in spinal muscular atrophy (SMA). The success of nusinersen/Spinraza for SMA indicates the potential of ASO therapies for other rare conditions. We propose a strategy to develop N-of-1 ASOs for treating one form of trichothiodystrophy (TTD), a rare condition with multisystem abnormalities and reduced life expectancy, associated with instability and greatly reduced amounts of the DNA-repair/transcription factor TFIIH. The therapeutic targets carry mutations in GTF2H5, encoding the TFIIH-p8 subunit. This approach was inspired by the diagnosis and molecular dissection of a xeroderma pigmentosum (XP) case with mutations in GTF2H4, encoding the TFIIH-p52 subunit. This is newly classified as a ninth XP complementation–group, XP-J, identified 5 decades after the discovery of the other XP complementation–groups. The p8-p52 interaction is required to support the TFIIH-complex formation, and the patient’s p52 C-terminal truncation results in the complete absence of p8 in TFIIH. However, intriguingly, TFIIH remained stable in vivo, and the patient with XP-J did not exhibit any TTD-features. The aim of our ASO-design is to induce a C-terminal truncation of p52 and we have successfully stabilized TFIIH in p8-deficient cells from patients with TTD-A.
Authors
Yuka Nakazawa, Lin Ye, Yasuyoshi Oka, Hironobu Morinaga, Kana Kato, Mayuko Shimada, Kotaro Tsukada, Koyo Tsujikawa, Yosuke Nishio, Hiva Fassihi, Shehla Mohammed, Alan R. Lehmann, Tomoo Ogi
×Abstract
Understanding the genetic causes of diseases that affect pancreatic β cells and neurons can give insights into pathways essential for both cell types. Microcephaly, epilepsy, and diabetes syndrome (MEDS) is a congenital disorder with two known etiological genes, IER3IP1 and YIPF5. Both genes encode proteins involved in endoplasmic reticulum (ER) to Golgi trafficking. We used genome sequencing to identify 6 individuals with MEDS caused by biallelic variants in the potentially novel disease gene TMEM167A. All had neonatal diabetes (diagnosed at <6 months) and severe microcephaly, and 5 also had epilepsy. TMEM167A is highly expressed in developing and adult human pancreas and brain. To gain insights into the mechanisms leading to diabetes, we silenced TMEM167A in EndoC-βH1 cells and knocked-in one patient’s variant, p.Val59Glu, in induced pluripotent stem cells (iPSCs). Both TMEM167A depletion in EndoC-βH1 cells and the p.Val59Glu variant in iPSC-derived β cells sensitized β cells to ER stress. The p.Val59Glu variant impaired proinsulin trafficking to the Golgi and induced iPSC-β cell dysfunction. The discovery of TMEM167A variants as a genetic cause of MEDS highlights a critical role of TMEM167A in the ER to Golgi pathway in β cells and neurons.
Authors
Enrico Virgilio, Sylvia Tielens, Georgia Bonfield, Fang-Shin Nian, Toshiaki Sawatani, Chiara Vinci, Molly Govier, Hossam Montaser, Romane Lartigue, Anoop Arunagiri, Alexandrine Liboz, Flavia Natividade Da Silva, Maria Lytrivi, Theodora Papadopoulou, Matthew N. Wakeling, James Russ-Silsby, Pamela Bowman, Matthew B. Johnson, Thomas W. Laver, Anthony Piron, Xiaoyan Yi, Federica Fantuzzi, Sirine Hendrickx, Mariana Igoillo-Esteve, Bruno J. Santacreu, Jananie Suntharesan, Radha Ghildiyal, Darshan Hegde, Nikhil Shah, Sezer Acar, Beyhan Özkaya Dönmez, Behzat Özkan, Fauzia Mohsin, Iman M. Talaat, Mohamed Tarek Abbas, Omar Tarek Abbas, Hamed Ali Alghamdi, Nurgun Kandemir, Sarah E. Flanagan, Raphael Scharfmann, Peter Arvan, Matthieu Raoux, Laurent Nguyen, Andrew T. Hattersley, Miriam Cnop, Elisa De Franco
×Abstract
Pancreatic cancer (PC) is notoriously resistant to both chemotherapy and immunotherapy, presenting a major therapeutic challenge. Epigenetic modifications play a critical role in PC progression, yet their contribution to chemoimmunotherapy resistance remains poorly understood. Here, we identified the transcription factor ZEB1 as a critical driver of chemoimmunotherapy resistance in PC. ZEB1 knockdown synergized with gemcitabine and anti–PD-1 therapy, markedly suppressed PC growth, and prolonged survival in vivo. Single-cell and spatial transcriptomics revealed that ZEB1 ablation promoted tumor pyroptosis by recruiting and activating GZMA+CD8+ T cells in the tumor core through epigenetic upregulation of CXCL16. Meanwhile, ZEB1 blockade attenuates CD44+ neutrophil–induced CD8+ T cell exhaustion by reducing tumor-derived SPP1 secretion, which otherwise promotes exhaustion through activation of the PD-L1/PD-1 pathway. Clinically, high ZEB1 expression correlated with chemoresistance, immunosuppression, and diminished CXCL16 levels in patients with PC. Importantly, the epigenetic inhibitor mocetinostat (targeting ZEB1) potentiated the efficacy of chemoimmunotherapy, including anti–PD-1 and CAR T therapies, in patient-derived organoids, xenografts, and orthotopic models. Our study unveils ZEB1 as a master epigenetic regulator of chemoimmunotherapy resistance and proposes its targeting as a transformative strategy for PC treatment.
Authors
Shaobo Zhang, Yumeng Hu, Zhijun Zhou, Gaoyuan Lv, Chenze Zhang, Yuanyuan Guo, Fangxia Wang, Yuxin Ye, Haoran Qi, Hui Zhang, Wenming Wu, Min Li, Mingyang Liu
×Abstract
BACKGROUND Statin therapy lowers the risk of major adverse cardiovascular events (MACE) among people with HIV (PWH). Residual risk pathways contributing to excess MACE beyond LDL-cholesterol (LDL-C) are not well understood. Our objective was to evaluate the association of statin-responsive and other inflammatory and metabolic pathways with MACE in the Randomized Trial to Prevent Vascular Events in HIV (REPRIEVE).METHODS Cox proportional hazards models were used to assess the relationship between MACE and proteomics measurements at study entry and year 2, adjusting for time-updated statin use and the baseline 10-year atherosclerotic cardiovascular disease risk score. We built a machine-learning (ML) model to predict MACE using baseline protein values with significant associations.RESULTS For 765 individuals (age: 50.8 ± 5.9 years, 82% men, 18% women), among 7 proteins changing with statin versus placebo, angiopoietin-related protein 3 (ANGPTL3) related most strongly to MACE (adjusted HR [aHR]: 2.31 per 2-fold-higher levels; 95% CI: 1.11–4.80; P = 0.03), such that lower levels of ANGPTL3 achieved with statin therapy were associated with lower MACE risk. Among 248 proteins that did not change in response to statin therapy, 26 were associated with MACE at a FDR below 0.05. These proteins represented a predominantly humoral immune response, leukocyte chemotaxis, and cytokine pathways. Our proteomics ML model achieved a 10-fold cross-validated concordance index (C-index) of 0.74 ± 0.11 to predict MACE, improving on models using traditional risk prediction scores only (C-index: 0.61 ± 0.18).CONCLUSIONS ANGPTL3, as well as key inflammatory pathways, may contribute to a residual risk of MACE among PWH, beyond LDL-C.TRIAL REGISTRATION ClinicalTrials.gov: NCT02344290.FUNDING NIH, Kowa Pharmaceuticals America, Gilead Sciences, ViiV Healthcare.
Authors
Márton Kolossváry, Irini Sereti, Markella V. Zanni, Carl J. Fichtenbaum, Judith A. Aberg, Gerald S. Bloomfield, Carlos D. Malvestutto, Judith S. Currier, Sarah M. Chu, Marissa R. Diggs, Alex B. Lu, Christopher deFilippi, Borek Foldyna, Sara McCallum, Craig A. Sponseller, Michael T. Lu, Pamela S. Douglas, Heather J. Ribaudo, Steven K. Grinspoon
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ISSN: 0021-9738 (print), 1558-8238 (online)