Genetics
Abstract
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.
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
Abstract
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.
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 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
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 ASO-therapies' potential 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 target 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 five 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 XP-J patient 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 stabilised TFIIH in p8-deficient TTD-A patient cells.
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
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
Abstract
Understanding the genetic causes of diseases affecting 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 aetiological 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 novel disease gene, TMEM167A. All had neonatal diabetes (diagnosed <6 months) and severe microcephaly, five 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 new 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 G. Hegde, Nikhil Avnish Shah, Sezer Acar, Beyhan Özkaya Dönmez, Behzat Özkan, Fauzia Mohsin, Iman M. Talaat, Mohamed Tarek Abbas, Omar Saied 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
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 in pretreatment biopsies. The inverse AR-HER2 relationship recurred across datasets 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
Abstract
Congenital hydrocephalus is a life-threatening condition that might affect brain development by increasing the pressure on the brain parenchyma. Here, we describe 6 male patients from 1 family, all presenting with an isolated X-linked congenital hydrocephalus. Exome sequencing identified a likely pathogenic variant of angiomotin (AMOT) that segregated with the phenotype in the extended family. We show that the variant, affecting the first methionine, translated into a shorter AMOT protein lacking 91 amino acids from the N-terminus. Mechanistically, we unraveled that the absence of the N-terminus leads to abnormally increased AMOT protein levels due to the loss of both the N-degron degradation signal and the tankyrase-binding domain. Altered degradation of AMOT disrupted the barrier integrity of the cells. Thus, the identified AMOT variant likely underlies the clinical presentation of isolated X-linked hydrocephalus in this family, and our data underscore the importance of tight regulation of AMOT protein level in the brain. AMOT now joins the list of genes involved in congenital hydrocephalus in humans. These findings are instrumental for the genetic counseling of affected families.
Authors
Nurcan Hastar, Hagit Daum, Nikoletta Kardos-Török, Gael Ganz, Leon Obendorf, Peter Vajkoczy, Orly Elpeleg, Petra Knaus
Abstract
Authors
Steven Q. Le, Alexander Sorensen, Soila Sukupolvi, Gianna Jewhurst, Grant L. Austin, Balraj Doray, Jonathan D. Cooper, Patricia I. Dickson
Abstract
Tumor gene alterations can serve as predictive biomarkers for therapy response. The nucleotide excision repair (NER) helicase ERCC2 carries heterozygous missense mutations in approximately 10% of bladder tumors, and these may predict sensitivity to cisplatin treatment. To explore the clinical actionability of ERCC2 mutations, we assembled a multinational cohort of 2,012 individuals with bladder cancer and applied the highly quantitative CRISPR-Select assay to functionally profile recurrent ERCC2 mutations. We also developed a single-allele editing version of CRISPR-Select to assess heterozygous missense variants in their native context. From the cohort, 506 ERCC2 mutations were identified, with 93% being heterozygous missense variants. CRISPR-Select pinpointed deleterious, cisplatin-sensitizing mutations, particularly within the conserved helicase domains. Importantly, single-allele editing revealed that heterozygous helicase-domain mutations markedly increased cisplatin sensitivity. Integration with clinical data confirmed that these mutations were associated with improved response to platinum-based neoadjuvant chemotherapy. Comparison with computational algorithms showed substantial discrepancies, highlighting the importance of precision functional assays for interpreting mutation effects in clinically relevant contexts. Our results demonstrate that CRISPR-Select provides a robust platform to advance biomarker-driven therapy in bladder cancer and supports its potential integration into precision oncology workflows.
Authors
Judit Börcsök, Diyavarshini Gopaul, Daphne Devesa-Serrano, Clémence Mooser, Nicolas Jonsson, Matteo Cagiada, Dag R. Stormoen, Maya N. Ataya, Brendan J. Guercio, Hristos Z. Kaimakliotis, Gopa Iyer, Kresten Lindorff-Larsen, Lars Dyrskjøt, Kent W. Mouw, Zoltan Szallasi, Claus S. Sørensen
Abstract
SLFN14-related thrombocytopenia is a rare bleeding disorder caused by SLFN14 mutations altering hemostasis in patients with platelet dysfunction. Schlafen (SLFN) proteins are highly conserved in mammals where SLFN14 is specifically expressed in megakaryocyte (MK) and erythroblast lineages. The role of SLFN14 in megakaryopoiesis and platelet function has not been elucidated. We generated a new murine model with a platelet- and MK-specific SLFN14 deletion using platelet factor-4 (PF4) cre-mediated deletion of exons 2 and 3 in Slfn14 (Slfn14;PF4-Cre) to decipher the molecular mechanisms driving the bleeding phenotype. SLFN14;PF4-Cre+ platelets displayed reduced platelet signaling to thrombin, reduced thrombin formation, increased bleeding tendency, and delayed thrombus formation as assessed by intravital imaging. Moreover, fewer in situ bone marrow MKs compared to controls. RNA sequencing and gene ontology analysis of MKs and platelets from Slfn14;PF4-Cre homozygous mice revealed altered pathways of ubiquitination, ATP activity, cytoskeleton and molecular function. In summary, we investigated how SLFN14 deletion in MKs and platelets leads to platelet dysfunction and alters their transcriptome, explaining the platelet dysfunction and bleeding in humans and mice with SLFN14 mutations.
Authors
Rachel J. Stapley, Xenia Sawkulycz, Gabriel H.M. Da Mota Araujo, Maximilian Englert, Lourdes Garcia-Quintanilla, Sophie R.M. Smith, Amna Ahmed, Elizabeth J. Haining, Nayandeep Kaur, Andrea Bacon, Andrey V. Pisarev, Natalie S. Poulter, Dean P.J. Kavanagh, Steven G. Thomas, Samantha J. Montague, Julie Rayes, Zoltan Nagy, Neil V. Morgan
Copyright © 2025 American Society for Clinical Investigation
ISSN: 0021-9738 (print), 1558-8238 (online)