PTBP1 variants displaying altered nucleocytoplasmic distribution are responsible for a neurodevelopmental disorder with skeletal dysplasia

• Text
• PDF

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

Ppp2r1a Haploinsufficiency Increases Excitatory Synaptic Transmission and Decreases Spatial Learning by Impairing Endocannabinoid Signaling

• Text
• PDF

Abstract

Protein phosphatase 2A (PP2A) is a serine/threonine phosphatase in the brain. Mutations in PPP2R1A, encoding the scaffolding subunit, are linked to intellectual disability, although the underlying mechanisms remain unclear. This study examined mice with heterozygous deletion of Ppp2r1a in forebrain excitatory neurons (NEX-het-conditional knockout, NEX-het-cKO). These mice exhibited impaired spatial learning and memory, resembling Ppp2r1a-associated intellectual disability. Ppp2r1a haploinsufficiency also led to increased excitatory synaptic strength and reduced inhibitory synapse numbers on pyramidal neurons. The increased excitatory synaptic transmission was attributed to increased presynaptic release probability (Pr), likely due to reduced levels of 2-arachidonoyl glycerol (2-AG). This reduction in 2-AG was associated with increased transcription of monoacylglycerol lipase (MAGL), driven by destabilization of enhancer of zeste homolog 2 (EZH2) in NEX-het-cKO mice. Importantly, the MAGL inhibitor JZL184 effectively restored both synaptic and learning deficits. Our findings uncover an unexpected role of PPP2R1A in regulating endocannabinoid signaling, providing fresh molecular and synaptic insights into the mechanisms underlying intellectual disability.

Authors

Yirong Wang, Weicheng Duan, Hua Li, Zhiwei Tang, Ruyi Cai, Shangxuan Cai, Guanghao Deng, Liangpei Chen, Hongyan Luo, Liping Chen, Yulong Li, Jian-Zhi Wang, Bo Xiong, Man Jiang

Chromatin factor YY1 controls fetal hematopoietic stem cell migration and engraftment in mice

• Text
• PDF

Abstract

The fetal liver is the primary site of hematopoietic stem cell (HSC) generation during embryonic development. However, the molecular mechanisms governing the transition of hematopoiesis from the fetal liver to the bone marrow (BM) remain incompletely understood. Here, we identify the mammalian Polycomb group (PcG) protein Yin Yang 1 (YY1) as a key regulator of this developmental transition. Conditional deletion of Yy1 in the hematopoietic system during fetal development results in neonatal lethality and depletion of the fetal HSC pool. YY1-deficient fetal HSCs exhibit impaired migration and fail to engraft in the adult BM, thereby losing their ability to reconstitute hematopoiesis. Transcriptomic analysis reveals that Yy1 knockout disrupts genetic networks controlling cell motility and adhesion in fetal hematopoietic stem and progenitor cells (HSPCs). Notably, YY1 does not directly bind the promoters of most dysregulated genes. Instead, it modulates chromatin accessibility at regulatory loci, orchestrating broader epigenetic programs essential for HSPC migration and adhesion. Together, these findings establish YY1 as a critical epigenetic regulator of fetal HSC function and provide a mechanistic framework to further decipher how temporal epigenomic configurations determine HSC fetal-to-adult transition during development.

Authors

Sahitya Saka, Zhanping Lu, Yinghua Wang, Peng Liu, Deependra K. Singh, Junki P. Lee, Carmen G. Palii, Tyler R. Alvarez, Anna L. F. V. Assumpção, Xiaona You, Jing Zhang, Marjorie Brand, Michael L. Atchison, Xuan Pan

Gene-environment interactions modulate the phenotypic severity in mouse models of congenital craniofacial syndromes

• Text
• PDF

Abstract

Birth defects are the leading cause of infant mortality, and most inborn errors of development are multifactorial in origin, resulting from complex gene-environment interactions. Defining specific gene-environment interactions in the etiology and pathogenesis of congenital disorders is critically needed in the absence of genotype-phenotype correlation but is challenging. This is particularly true for congenital craniofacial anomalies, which account for approximately one-third of all birth defects, as they typically exhibit considerable inter-familial and intra-familial variability. A classic example of this is Treacher Collins Syndrome (TCS), which, although primarily caused by mutations in TCOF1, is characterized by considerable variability in the severity of mandibulofacial dysostosis. Here, we describe the genetic and environmental factors with converging effects that mechanistically contribute to the etiology and pathogenesis of craniofacial variation in this rare congenital disorder. We discovered in Tcof1+/- mouse models of TCS, that the combination of different endogenous levels of Tcof1/Treacle protein and reactive oxygen species (ROS) within distinct genetic backgrounds correlates with TCS phenotype severity. Furthermore, geometric morphometric analyses revealed that genotype largely determines the craniofacial shape, but redox status determines the size of individual bones. Taken together, our results highlight the roles of ROS and genomic instability in modulating the variability and phenotypic severity of craniofacial anomalies.

Authors

Sharien Fitriasari, Roberta Fiorino, Thoa H.K. Truong, Mary C. McKinney, Jill Dixon, Michael J. Dixon, Paul A. Trainor

SOX2 regulates foregut squamous epithelial homeostasis and is lost during Barrett’s esophagus development

• Text
• PDF

Abstract

Esophageal adenocarcinoma (EA) is increasingly prevalent and is thought to arise from Barrett’s esophagus (BE), a metaplastic condition in which chronic acid and bile reflux transforms the esophageal squamous epithelium into a gastric-intestinal glandular mucosa. The molecular determinants driving this metaplasia are poorly understood. We developed a human BE organoid biobank that recapitulates BE’s molecular heterogeneity. Bulk and single-cell transcriptomics, supported by patient tissue analysis, revealed that BE differentiation reflects a balance between SOX2 (foregut/esophageal) and CDX2 (hindgut/intestinal) transcription factors. Using squamous-specific inducible Sox2 knockout (Krt5CreER/+; Sox2∆/∆; ROSA26tdTomato/+) mice, we observed increased basal proliferation, reduced squamous differentiation, and expanded metaplastic glands at the squamocolumnar junction, some tracing back to Krt5-expressing cells. CUT&RUN analysis showed SOX2 bound and promoted differentiation-associated (e.g., Krt13) and repressed proliferation-associated (e.g., Mki67) targets. Thus, SOX2 is critical for foregut squamous epithelial differentiation and its decreased expression is likely an initiating step in progression to BE and thence to EA.

Authors

Ramon U. Jin, Yuanwei Xu, Tung-Shing Lih, Yang-Zhe Huang, Toni M. Nittolo, Blake E. Sells, Olivia M. Dres, Jean S. Wang, Qing Kay Li, Hui Zhang, Jason C. Mills

Deficiency of the Fanconi anemia core complex protein FAAP100 results in severe Fanconi anemia

• Text
• PDF

Abstract

Fanconi anemia (FA) is a rare genetic disease characterized by loss-of-function variants in any of the 22 previously identified genes (FANCA-FANCW) that encode proteins participating in the repair of DNA interstrand crosslinks (ICLs). Patient phenotypes are variable, but may include developmental abnormalities, early onset pancytopenia, and predisposition to hematologic and solid tumors. Here, we describe two unrelated families with multiple pregnancy losses and offspring presenting with severe developmental and hematologic abnormalities leading to death in utero or in early life. Homozygous loss-of-function variants in FAAP100 were identified in affected children of both families. The FAAP100 protein associates with FANCB and FANCL, the E3 ubiquitin ligase responsible for the monoubiquitination of FANCD2 and FANCI, which is necessary for FA pathway function. Patient-derived cells exhibited phenotypes consistent with FA. Expression of the wild-type FAAP100 cDNA, but not the patient-derived variants, rescued the observed cellular phenotypes. This establishes FAAP100 deficiency as a cause of Fanconi anemia, with FAAP100 gaining an alias as FANCX. The extensive developmental malformations of individuals with FAAP100 loss-of-function variants are among the most severe across previously described FA phenotypes, indicating that the FA pathway is essential for human development.

Authors

Benjamin A. Harrison, Emma Mizrahi-Powell, John Pappas, Kristen Thomas, Subrahmanya Vasishta, Shripad Hebbar, Anju Shukla, Shalini S. Nayak, Tina K. Truong, Amy Woroch, Yara Kharbutli, Bruce D. Gelb, Cassie S. Mintz, Gilad D. Evrony, Agata Smogorzewska

Aberrant ERK signaling in astrocytes impairs learning and memory in RASopathy-associated BRAF mutant mouse models

• Text
• PDF

Abstract

RAS/MAPK pathway mutations often induce RASopathies with overlapping features, such as craniofacial dysmorphology, cardiovascular defects, dermatologic abnormalities, and intellectual disabilities. Although BRAF gene mutations are associated with cardio-facio-cutaneous (CFC) syndrome and Noonan syndrome, it remains unclear how these mutations impair cognition. Here, we investigated the underlying neural mechanisms using several mouse models harboring a gain-of-function BRAF mutation (K499E) discovered in RASopathy patients. We found expressing BRAF K499E (KE) in neural stem cells under the control of a Nestin-Cre promoter (Nestin;BRAFKE/+) induced hippocampal memory deficits, but expressing it in excitatory or inhibitory neurons did not. BRAF KE expression in neural stem cells led to aberrant reactive astrogliosis, increased astrocytic Ca2+ fluctuations, and reduced hippocampal long-term depression (LTD) in mice. Consistently, 3D human cortical spheroids expressing BRAF KE also showed reactive astrogliosis. Astrocyte-specific AAV-BRAF KE delivery induced memory deficits, reactive astrogliosis, and increased astrocytic Ca2+ fluctuations. Notably, reducing ERK activity in astrocytes rescued the memory deficits and altered astrocytic Ca2+ activity of Nestin;BRAFKE/+ mice. Furthermore, reducing astrocyte Ca2+ activity rescued the spatial memory impairments of BRAF KE-expressing mice. Our results demonstrate that ERK hyperactivity contributes to astrocyte dysfunction associated with Ca2+ dysregulation, leading to the memory deficits of BRAF-associated RASopathies.

Authors

Minkyung Kang, Jihye Choi, Jeongho Han, Toshiyuki Araki, Soo-Whee Kim, Hyun-Hee Ryu, Min-Gyun Kim, Seoyeon Kim, Hanbyul Jang, Sun Yong Kim, Kyoung-Doo Hwang, Soobin Kim, Myeongjong Yoo, Jaegeon Lee, Kitae Kim, Pojeong Park, Ja Eun Choi, Dae Hee Han, Yujin Kim, Jeongyeon Kim, Sunghoe Chang, Bong-Kiun Kaang, Jung Min Ko, Keun-Ah Cheon, Joon-Yong An, Sang Jeong Kim, Hyungju Park, Benjamin G. Neel, Chul Hoon Kim, Yong-Seok Lee

A whole-body imaging technique for tumor-specific diagnostics and screening of B7-H3-targeted therapies

• Text
• PDF

Abstract

BACKGROUND. B7-H3 or CD276 is notably overexpressed in various malignant tumor cells in humans, with extremely high expression rates. The development of a radiotracer that targets B7-H3 may provide a universal tumor-specific imaging agent and allow the noninvasive assessment of the whole-body distribution of B7-H3-expressing lesions. METHODS. We enhanced and optimized the structure of an affibody (ABY) that targets B7-H3 to create the radiolabeled radiotracer [68Ga]Ga-B7H3-BCH, and then, we conducted both foundational experiments and clinical translational studies. RESULTS. [68Ga]Ga-B7H3-BCH exhibited high affinity (Kd = 4.5 nM), and it was taken up in large amounts by B7-H3-transfected cells (A549CD276 and H1975CD276 cells); these phenomena were inhibited by unlabeled precursors. Moreover, PET imaging of multiple xenograft models revealed extensive [68Ga]Ga-B7H3-BCH uptake by tumors. In a clinical study including 20 patients with malignant tumors, the [68Ga]Ga-B7H3-BCH signal aggregated in both primary and metastatic lesions, surpassing 18F-FDG in overall diagnostic efficacy for tumors (85.0% vs 81.7%), including differentiated hepatocellular and metastatic gastric cancers. A strong correlation between B7-H3 expression and [68Ga]Ga-B7H3-BCH uptake in tumors was observed, and B7-H3 expression was detected with 84.38% sensitivity and 100% specificity when an SUVmax of 3.85 was set as the cutoff value. Additionally, B7-H3-specific PET imaging is expected to predict B7H3 expression levels in tumor cells, intratumoral stroma and peritumoral tissues. CONCLUSION. In summary, [68Ga]Ga-B7H3-BCH has potential for the noninvasive identification of B7H3 expression in systemic lesions in patients with malignant tumors. This agent has prospects for improving pretreatment evaluation, predicting therapeutic responses, and monitoring resistance to therapy in patients with malignancies. TRIAL REGISTRATION. ClinicalTrials.gov NCT06454955. FUNDING. This research was financially supported by the Natural Science Foundation of Beijing Municipality (No. 7242266), the National Natural Science Foundation of China (No. 82202201), and the Young Elite Scientists Sponsorship Program by CAST (No. YESS20220230).

Authors

Lei Xia, Yan Wu, Yanan Ren, Zhen Wang, Nina Zhou, Wenyuan Zhou, Lixin Zhou, Ling Jia, Chengxue He, Xiangxi Meng, Hua Zhu, Zhi Yang

Elevated microRNA-187 causes cardiac endothelial dysplasia to promote congenital heart disease through inhibition of NIPBL

• Text
• PDF

Abstract

Cardiac endothelial cells are essential for heart development, and disruption of this process can lead to congenital heart disease (CHD). However, how miRNAs influence cardiac endothelial cells in CHD remains unclear. This study identified elevated miR-187 expression in embryonic heart endothelial cells from CHD fetuses. Using a conditional knock-in model, we showed that increased miR-187 levels in embryonic endothelial cells induce CHD in homozygous fetal mice, closely mirroring human CHD. Mechanistically, miR-187 targets NIPBL, which is responsible for recruiting the cohesin complex and facilitating chromatin accessibility. Consequently, the endothelial cell-specific upregulation of miR-187 inhibited NIPBL, leading to reduced chromatin accessibility and impaired gene expression, which hindered endothelial cell development and ultimately caused heart septal defects and reduced heart size both in vitro and in vivo. Importantly, exogenous miR-187 expression in human cardiac organoids mimicked developmental defects in the cardiac endothelial cells, reversible by NIPBL replenishment. Our findings establish the miR-187/NIPBL axis as a potent regulator that inhibits cardiac endothelial cell development by attenuating the transcription of numerous endothelial genes, with our mouse and human cardiac organoid models effectively replicating severe defects from minor perturbations. This discovery suggests that targeting the miR-187/NIPBL pathway could offer a promising therapeutic approach for CHD.

Authors

Chao Li, Zizheng Tan, Hongdou Li, Xiaoying Yao, Chuyue Peng, Yue Qi, Bo Wu, Tong-Jin Zhao, Chengtao Li, Jianfeng Shen, Hongyan Wang

Transcription factor KROX20 marks epithelial stem cells for hair follicle formation

• Text
• PDF

Abstract

Epidermal stem cells control homeostasis and regeneration of skin and hair. In the hair follicle (HF) bulge of mammals, populations of slow-cycling stem cells regenerate the HF during cyclical rounds of anagen (growth), telogen (quiescence), and catagen (regression). Multipotent epidermal cells are also present in the HF above the bulge area, contributing to the formation and maintenance of sebaceous gland and upper and middle portions of the HF. Here, we report that the transcription factor Krox20 is enriched in an epidermal stem cell population located in the upper/ middle HF. Expression analyses and lineage tracing using inducible Krox20-CreERT showed that Krox20-lineage cells migrate out of this HF region and contribute to the formation of bulge in the HF, serving as ancestors of bulge stem cells. In vivo depletion of these cells arrests HF morphogenesis. This study identifies a novel marker for an epidermal stem cell population that is indispensable for hair homeostasis.

Authors

Elnaz Ghotbi, Edem Tchegnon, Zhiguo Chen, Stephen Li, Tracey Shipman, Yong Wang, Jenny Raman, Yumeng Zhang, Renee M. McKay, Chung-Ping Liao, Lu Q. Le