Genetics
Abstract
Despite substantial progress in understanding the molecular pathology of Parkinson’s disease (PD), the underlying drivers of PD in many cases remain unknown. Here we investigate the role of RNA modification in PD, following observations of selective m6A hypomethylation in the substantia nigra (SN) of mouse PD models and dysregulated METTL3 and ALKBH5 expression in dopaminergic (DA) neurons from PD patients. We find preferential m6A deposition on transcripts of PD risk genes and a previously unreported heterozygous METTL3 p.K480R mutation in PD patients. Mettl3K480R/+ mice exhibit progressive METTL3 reduction and m6A hypomethylation in the SN, leading to progressive DA neuron loss, phospho-α-synuclein increase, and levodopa-responsive motor and non-motor deficits, mimicking PD progression. Dopamine transporter-specific METTL3 knockout mice recapitulate m6A hypomethylation, neurodegeneration and levodopa-responsive parkinsonism. Mechanistically, m6A deficiency disrupts mitochondrial biogenesis and function through regulating Tfam expression, while mitochondrial dysfunction reciprocally impairs m6A deposition, creating a pathogenic loop. Importantly, supplementation with S-adenosylmethionine (SAMe) enhances m6A modification, disrupts the pathogenic loop and alleviates parkinsonism in mouse models. Our findings reveal m6A dysregulation as an important contributor to PD pathogenesis, provide a valuable preclinical mouse model for PD progression, and highlight RNA methylation-targeted therapies as a promising strategy for PD intervention.
Authors
Sun Liu, Qihuan Ren, Guiling Mo, Zengguang Li, Huili Huang, Yuhao Zhou, Ziteng Miao, Xin Cao, Bilian Wu, Zhuoyu Xiao, Shihui Yu, Guangjin Wu, Linjian Xia, Jinru Cui, Junyuan Mo, Yuan Li, Laixin Xia, Juan Shen, Shan Xiao
Abstract
PRC2/EZH2 inhibitors (PRC2i/EZH2i) are promising for treatment of advanced cancers including metastatic prostate cancer. Here we show that PRC2i/EZH2i alone or in combination with AR inhibitors induce diverse cell state programs (CSP) (e.g., response to stress or interferon, MYC targets, stem cell, EMT and multiple developmental programs) which led to increased tumor cell invasion, metastasis and resistance to other drugs, in addition to modest suppression of tumor growth. In contrast to the current perception, our comprehensive, integrated genomics and epigenomics profiling of PDX and clinical tumors revealed that PRC2/EZH2 suppresses CSP genes through maintaining chromatin bivalency. Hyperactive Wnt/β-catenin signaling and inhibitors of PRC2/EZH2 and AR alter chromatin bivalency through antagonizing PRC2 and stimulating MLL2/KMT2B in a feedforward manner. Circadian rhythm regulator REV-ERBα unexpectedly reprograms β-catenin in promoting bivalency resolution and CSP gene expression. Dual targeting of Wnt/β-catenin and EZH2 diminishes diverse cell states through restoring bivalency and effectively block tumor growth. Our findings provide unexpected insights of chromatin bivalency and dysregulated circadian rhythm in control of cell state diversity and offer alternative therapeutic strategies targeting PRC2/EZH2 for advanced malignancies.
Authors
Yatian Yang, Xiong Zhang, Varadha Balaji Venkadakrishnan, Hongye Zou, Xingling Zheng, Shiyao Guo, Christopher Z. Chen, Alexander D. Borowsky, Eva Corey, Ronald M. Evans, Allen C. Gao, Marc A. Dall'Era, Amina Zoubeidi, Primo N. Lara, Hsing-Jien Kung, Xinbin Chen, Himisha Beltran, Hong-Wu Chen
Abstract
The mammalian brain relies primarily on glucose for its energy needs. Delivery of this nutrient to the brain is mediated by the glucose transporter-1 (GLUT1) protein. Low GLUT1 thwarts glucose entry into the brain, causing an energy crisis and, triggering, in one instance, the debilitating neurodevelopmental condition – GLUT1 deficiency syndrome (GLUT1DS). Current treatments for GLUT1DS are sub-optimal, as none address the root cause – low GLUT1 – of the condition. Levels of this transporter must respond rapidly to the brain’s changing energy requirements. This necessitates fine-tuning its expression. Here we describe a long-noncoding RNA (lncRNA) antisense to GLUT1 (SLC2A1) and show that it is involved in such regulation. Raising levels of the lncRNA had a concordant effect on GLUT1 in cultured human cells and transgenic mice; reducing levels elicited the opposite effect. Delivering the lncRNA to GLUT1DS model mice via viral vectors induced GLUT1 expression, enhancing brain glucose levels to mitigate disease. Direct delivery of such a lncRNA to combat disease has not been reported previously and constitutes, to our knowledge, a unique therapeutic paradigm. Moreover, considering the importance of maintaining homeostatic GLUT1 levels, calibrating transporter expression via the lncRNA could become broadly relevant to myriad conditions, including Alzheimer’s disease, wherein GLUT1 is perturbed.
Authors
Maoxue Tang, Sasa Teng, Yueqing Peng, Ashley Y. Kim, Yoon-Ra Her, Peter Canoll, Jeffrey N. Bruce, Phyllis L. Faust, Kailash Adhikari, Darryl C. De Vivo, Umrao R. Monani
Abstract
Patients with malignant peripheral nerve sheath tumors (MPNSTs) have poor outcomes despite multimodal treatment with surgery, radiation, and systemic therapy. The responses to radiotherapy (RT) are mixed, and the biologic mechanisms underlying this heterogeneity in the radiation response of MPNSTs are not understood. Here, we combined bulk and single-cell transcriptomics, genome-wide CRISPR interference screens, and multiplatform molecular analysis across MPNST cells, mouse allograft models, and patients’ samples to understand the mediators of the radiation response. Our data revealed that MPNSTs, but not benign plexiform neurofibromas, induced a type I IFN signature that functionally mediated the radiation response. Moreover, irradiation of immunocompetent mouse MPNST allografts led to IFN-mediated T cell recruitment and activation. Both host mouse T cells and intact tumor IFN receptor signaling were required for RT’s efficacy in mouse MPNST allografts. Analysis of human MPNST resection specimens demonstrated that increased microenvironmental and CD8+ T cell infiltration were associated with improved local control following RT. These results provide a preclinical rationale for combining immunomodulatory agents targeting IFN signaling to improve radiation responses in MPNSTs and potentially other soft tissue sarcomas.
Authors
Iowis Zhu, Julian Chien, Gabriel E. Rech, Kanish Mirchia, Sixuan Pan, Kaeli Miller, Joanna Pak, Rosanna Wustrack, Varun Monga, Steve E. Braunstein, Mark D. Adams, Line Jacques, Melike Pekmezci, S. John Liu, Harish N. Vasudevan
Abstract
BACKGROUND Kidney stone disease (KSD) affects approximately 10% of the population. While genetic factors are known to play a role in KSD, determining the clinical relevance of rare variants in KSD genes identified in adults remains challenging.METHODS The Swiss Kidney Stone Cohort is a multicenter longitudinal, observational study consisting of kidney stone formers (KSFs) (n = 701) and non-kidney stone formers (NKSFs) (n = 200). Blood and urine samples were collected at enrollment and over 3 years for deep biochemical phenotyping. Results were correlated with rare genetic variants in established KSD genes identified through whole-exome sequencing and classified according to American College of Medical Genetics and Genomics and the Association of Molecular Pathology (ACMG/AMP) criteria.RESULTS Collectively, we found rare (likely) pathogenic (LP/P) variants representing strong KSD risk factors in 6.8% of KSFs, predominantly in genes involved in renal phosphate handling and cystinuria. Detailed biochemical analyses confirmed that KSFs carrying heterozygous LP/P SLC34A3 variants exhibited significant hyperphosphaturia. In contrast, monoallelic LP/P variants in SLC34A1, SLC9A3R1, or CYP24A1, which were also frequent in NKSFs, did not result in the expected biochemical alterations, calling into question their causative role as strong KSD risk factors. In cystinuria, monoallelic SLC7A9 variants represented intermediate risk factors, since they caused biochemical alterations but required additional factors for KSD occurrence, based on frequent LP/P variants in NKSFs. The presence of strong risk factors was associated with higher kidney stone (KS) recurrence over the 3-year observation period, supporting a predictive value for genetic testing.CONCLUSIONS Correlation of genetic findings with thorough biochemical phenotyping and comparison with NKSFs redefines the clinical relevance of variants in KSD genes and has prognostic value.
Authors
Johannes Münch, Jana Petrovska, Joana Figueiro-Silva, Isabel Rubio-Aliaga, Elena M. Cabello, Ivan Ivanovski, Michael Papik, Beatrice Oneda, Daniel G. Fuster, Harald Seeger, Thomas Ernandez, Florian Buchkremer, Gregoire Wuerzner, Nasser A. Dhayat, Alexander Ritter, Stephan Segerer, Beat Roth, Anita Rauch, Pietro Manuel Ferraro, Olivier Bonny, Carsten A. Wagner, Ruxandra Bachmann-Gagescu
Abstract
The multi-omics data represented by genomic data from patients with metastatic triple-negative breast cancer (TNBC) is crucial for precision treatment, yet data on genomic alterations in metastatic cohorts and Chinese populations remains limited. We performed targeted sequencing of 296 metastatic TNBC samples from 296 patients treated at Fudan University Shanghai Cancer Center (October 2018 to November 2020) using a 484-gene panel, identifying 796 metastatic events across 18 organ sites. We characterized the genomic landscape of TNBC metastases and identified marked enrichment of polycystin-1 (PKD1) mutations in metastatic lesions — a finding validated in an independent paired primary metastasis cohort (n = 105). Notably, PKD1 mutations were associated with resistance to anti–PD-1 therapy, as validated across 3 clinical trials (NCT03805399, NCT04129996, and NCT04395989). Multi-omics analyses, combined with functional in vitro and in vivo mechanistic studies, revealed that PKD1 modulated the “desert” tumor immune microenvironment via C-C motif chemokine ligand 2 (CCL2), and targeting CCL2 could reverse immunotherapy resistance. This comprehensive genomic characterization of metastases enhances our understanding of tumor evolution, identifies PKD1 as a previously uncharacterized regulator of immune evasion to our knowledge, and suggests a potential therapeutic strategy to overcome immunotherapy resistance.
Authors
Xiu-Zhi Zhu, Yi-Fan Zhou, Xiao-Han Ying, Yun-Yi Wang, Xiao-Hong Ding, Kun-Yu Zhang, Zhi-Ming Shao, Xi Jin, Yi-Zhou Jiang, Zhong-Hua Wang
Abstract
Osteofibrous dysplasia (OFD) is a skeletal RASopathy presenting with periosteal bone lesions that may progress to fracture and delayed healing (pseudarthrosis). MET gene mutations reducing ubiquitin-mediated protein degradation via loss of the juxtamembrane domain (METΔJMD) were previously identified in OFD patients, resulting in ligand-dependent gain-of-function. The impact of METΔJMD expression on skeletal progenitor cell differentiation and the potential efficacy of targeted therapies remain unclear. We engineered MetΔJMD mice and showed that MetΔJMD expression inhibited osteogenic differentiation of skeletal progenitor cells in vitro and impaired cortical bone development and reduced bone stiffness in vivo. In contrast, conditional deletion of Met enhanced osteogenic differentiation of periosteal progenitor cells. Inhibition of MAPK signaling with MEK inhibitors restored osteogenic differentiation of mouse MetΔJMD skeletal progenitor cells and promoted activation of transcriptional signatures associated with skeletal development and osteoblast differentiation in OFD patient pseudarthrosis-derived primary cells. With this preclinical support, we treated with the MEK inhibitor mirdametinib a pediatric OFD patient suffering from a 3-year history of persistent pseudarthrosis, resulting in fracture union. Our findings demonstrate a bi-directional role for MET in regulating osteogenic differentiation of skeletal progenitor cells and a therapeutic avenue to improve clinical outcomes for this, and potential other, skeletal RASopathies.
Authors
Aysha Khalid, Kristin Denton, Nandina Paria, Ila Oxendine, Meghan Wassell, Reuel Cornelia, Sasidhar Uppuganti, Jeffry S. Nyman, G. Jayashree Jagadeesh, Carlos R. Ferreira, Simon J. Conway, Robert E. Hammer, John O. Ritter, Mylinh Nguyen, David A. Podeszwa, Laura J. Klesse, Carol A. Wise, Jonathan J. Rios
Abstract
SLC13A5 citrate transporter disorder is a rare epileptic encephalopathy caused by loss of function pathogenic variants in the SLC13A5 gene. Loss of sodium/citrate cotransporter (NaCT) function causes a severe early life epilepsy resulting in life-long developmental disabilities and increased extracellular citrate. Current antiseizure medications may reduce seizure frequency, yet more targeted treatments are needed to address the epileptic and neurodevelopmental SLC13A5 phenotype. We performed preclinical studies in SLC13A5 deficient mice evaluating phenotype rescue with adeno-associated virus (AAV) vector carrying a functional copy of the human SLC13A5 gene (AAV9/SLC13A5). Cerebrospinal fluid-delivery of AAV9/SLC13A5 decreased extracellular citrate levels, normalized electrophysiologic and sleep architecture abnormalities, and restored resistance to chemically induced seizures and death. Treatment benefits were achieved with administration during early brain development and in young adult mice, indicating therapeutic efficacy across developmental and post-developmental stages. Comparison of delivery routes in young adult KO mice showed that higher brain targeting achieved with intra-cisterna magna delivery resulted in greater treatment benefit as compared to intrathecal lumbar puncture delivery. Together, these results support further development of AAV9/SLC13A5 for treating SLC13A5 citrate transporter disorder.
Authors
Lauren E. Bailey, Raegan M. Adams, Morgan K. Schackmuth, Irvin T. Garza, Krishanna Knight, Sydni K. Holmes, Meghan M. Eller, MinJae Lee, Rachel M. Bailey
Abstract
Mutations in SLC26A4 are the second most common cause of hereditary hearing loss in many Asian countries, leading to DFNB4, a condition characterized by progressive hearing loss and inner ear malformations. While gene therapy holds great potential, its postnatal application has remained unexplored due to the lack of suitable animal models and the challenges of prenatal intervention. This study represents the first preclinical investigation of postnatal gene therapy for DFNB4 using a clinically relevant Slc26a4 mutant mouse model that closely replicates human auditory phenotypes. Utilizing the synthetic AAV.Anc80L65 vector, we achieved robust SLC26A4 delivery to critical cochlear regions, including the endolymphatic sac and cochlear lateral wall. Comprehensive phenotypic analyses revealed a critical therapeutic window spanning the neonatal and juvenile stages, within which AAV.Anc80L65-mediated SLC26A4 delivery significantly improved hearing, as evidenced by lower auditory brainstem response thresholds. Moreover, the therapy preserved hair cells, reduced endolymphatic sac enlargement, partially restored the endocochlear potential, and mitigated inner ear structural degeneration. These therapeutic effects persisted into adulthood, highlighting the long-term efficacy of postnatal gene therapy. Together, these findings establish a critical therapeutic window for DFNB4 and demonstrate the feasibility of targeting the endolymphatic sac and cochlear lateral wall for effective intervention.
Authors
Yi-Hsiu Tsai, Peng-Yu Wu, Yu-Chi Chuang, Chun-Ying Huang, Hiroki Takeda, Hiroshi Hibino, Chen-Chi Wu, Yen-Fu Cheng
Abstract
SEL1L is a well-known protein in the ER-associated degradation (ERAD) pathway. While it is known to be expressed in platelets, SEL1L has never been shown to play an active role. Here, we present evidence that SEL1L regulates platelet function. We first identified SEL1L through the study of Atypical Equine Thrombasthenia (AET), an autosomal recessive platelet disorder found in thoroughbred horses. A missense variant in SEL1L (c.1810A>G p.Ile604Val) was found in AET-affected horses, which we show is associated with decreased protein expression. SEL1L is intracellular in equine platelets and localizes to the surface upon activation with thrombin. Platelets from homozygous horses exhibited substantially decreased spreading on immobilized collagen. Human megakaryocytes were found to have 2 SEL1L protein isoforms that increase in expression during megakaryopoiesis, although only 1 isoform was delivered to mature platelets. Studies using inducible mouse and constitutive zebrafish KOs demonstrated that SEL1L is necessary for efficient platelet or thrombocyte (fish equivalent) adhesion to sites of endothelial injury. These data reveal a previously undescribed and conserved role for the ERAD pathway in the etiology of AET and platelet function, and GWAS data suggest that it may play a role in human platelet disorders as well.
Authors
Anna R. Dahlgren, Francesca Careddu, Jeffrey W. Norris, Christian A. Di Buduo, Livia Stanger, Reheman Adili, Erin M. Kropp, Qing Li, Michael Holinstat, Ida Biunno, Alessandra Balduini, Fern Tablin, Jordan A. Shavit, Carrie J. Finno
Copyright © 2026 American Society for Clinical Investigation
ISSN: 0021-9738 (print), 1558-8238 (online)