Genetics
Abstract
The notion of clonal cell populations in human atherosclerosis has been suggested but not demonstrated. Somatic mutations are used to define cellular clones in tumors. Here, we characterized the mutational landscape of human carotid plaques through whole-exome sequencing to explore the presence of clonal cell populations. Somatic mutations were identified in 12 of 13 investigated plaques, while no mutations were detected in 11 non-atherosclerotic arteries. Mutated clones often constituted over 10% of the sample cell population, with genes related to the contractile apparatus enriched for mutations. In CHIP (clonal hematopoiesis of indeterminate potential) carriers, hematopoietic clones had infiltrated the plaque tissue and constituted substantial fractions of the plaque cell population alongside locally expanded clones. Our findings establish somatic mutations as a common feature of human atherosclerosis and demonstrate the existence of mutated clones expanding locally, as well as CHIP clones invading from the circulation. While our data do not support plaque monoclonality, we observe a pattern suggesting the coexistence of multiple mutated clones of considerable size spanning different regions of plaques. Mutated clones are likely to be relevant to disease development, and somatic mutations will serve as a convenient tool to uncover novel pathological processes of atherosclerosis in future studies.
Authors
Lasse Bach Steffensen, Stephanie Kavan, Pia Søndergaard Jensen, Matilde Kvist Pedersen, Steffen Møller Bøttger, Martin J. Larsen, Maja Dembic, Otto Bergman, Ljubica Matic, Ulf Hedin, Lars vB Andersen, Jes Sanddal Lindholt, Kim Christian Houlind, Lars P. Riber, Mads Thomassen, Lars Melholt Rasmussen
Abstract
An estimated 5-10% of cancer results from an underlying genetic predisposition, yet for the majority of these cases the genes in question remain unknown, suggesting a critical need to identify new cancer predisposition genes. The protein phosphatase 2A (PP2A) family exists as a trimeric holoenzyme and is a vital negative regulator of multiple oncogenic pathways. PP2A inhibition by somatic mutation, loss of expression, and upregulation of its exogenous inhibitors in tumors has been well described. However, it remains unknown whether germline loss of any PP2A subunits results in a predisposition to cancer in humans. In this study, we identified nine cancer patients with germline loss-of-function (LOF) variants in PPP2R1B (Aβ), the beta isoform of the PP2A scaffold subunit. All four patients for whom documentation was available also had a family history of cancer, including multiple indicators of hereditary cancer. The most highly represented cancer among the Aβ germline patients was breast cancer. Overexpression of these mutant forms of Aβ resulted in truncated proteins that were rapidly turned over. Characterization of an additional missense germline Aβ variant, R233C, that is also recurrently mutated at the somatic level found that it disrupts PP2A catalytic subunit binding resulting in loss of phosphatase activity. An analysis of Aβ expression among multiple breast cancer cohorts revealed that somatic, heterozygous loss of Aβ was a frequent event in this disease and decreased Aβ expression correlated with shorter disease-free and overall survival. Furthermore, Aβ levels were significantly lower in multiple histological subtypes of both in situ and malignant breast cancer compared to adjacent normal breast tissue, suggesting that Aβ loss is an early event in breast cancer development. Together, this highlights a role for Aβ as a predisposition gene in breast cancer and potentially additional cancers.
Authors
Sahar Mazhar, Caitlin M. O’Connor, Alexis Harold, Amanda C. Dowdican, Peter J. Ulintz, Erika N. Hanson, Yuping Zhang, Michelle F. Jacobs, Sofia D. Merajver, Mark W. Jackson, Anthony Scott, Anieta M. Sieuwerts, Arul M. Chinnaiyan, Goutham Narla
Abstract
As a major component of intracellular trafficking, the coat protein complex II (COPII) is indispensable for cellular function during embryonic development and throughout life. The four SEC24 proteins (A-D) are essential COPII components involved in cargo selection and packaging. A human disorder corresponding to alterations of SEC24 function is currently only known for SEC24D. Here, we report that biallelic loss of SEC24C leads to a syndrome characterized by primary microcephaly, brain anomalies, epilepsy, hearing loss, liver dysfunction, anemia, and cataracts in an extended consanguineous family with four affected individuals. We show that knockout of sec24C in zebrafish recapitulates important aspects of the human phenotype. SEC24C-deficient fibroblasts display alterations in the expression of several COPII components as well as impaired anterograde trafficking to the Golgi, indicating a severe impact on COPII function. Transcriptome analysis revealed that SEC24C deficiency also impacts the proteasome and autophagy pathways. Moreover, a shift in the N-glycosylation pattern and deregulation of the N-glycosylation pathway suggest a possible secondary alteration of protein glycosylation, linking the described disorder with the congenital disorders of glycosylation.
Authors
Nina Bögershausen, Büsranur Cavdarli, Taylor Nagai, Miroslav P. Milev, Alexander Wolff, Mahsa Mehranfar, Julia Schmidt, Dharmendra Choudhary, Óscar Gutiérrez-Gutiérrez, Lukas Cyganek, Djenann Saint-Dic, Arne Zibat, Karl Köhrer, Tassilo E. Wollenweber, Dagmar Wieczorek, Janine Altmüller, Tatiana Borodina, Dilek Kaçar, Göknur Haliloğlu, Yun Li, Christian Thiel, Michael Sacher, Ela W. Knapik, Gökhan Yigit, Bernd Wollnik
Abstract
The osteo-oto-hepato-enteric (O2HE) syndrome is a severe autosomal recessive disease ascribed to loss-of-function mutations in the Unc-45 myosin chaperone A (UNC45A) gene. The clinical spectrum includes bone fragility, hearing loss, cholestasis, and life-threatening diarrhea associated with microvillus inclusion disease–like enteropathy. Here, we present molecular and functional analysis of the UNC45A c.710T>C (p.Leu237Pro) missense variant, which revealed a unique pathogenicity compared with other genetic variants causing UNC45A deficiency. The UNC45A p.Leu237Pro mutant retained chaperone activity, prevented myosin aggregation, and supported proper nonmuscle myosin II (NMII) filament formation in patient fibroblasts and human osteosarcoma (U2OS) cells. However, the mutant formed atypically stable oligomers and prevented chaperone-myosin complex dissociation, thereby inhibiting NMII functions. Similar to biallelic UNC45A deficiency, this resulted in impaired intracellular trafficking, defective recycling, and abnormal retention of transferrin at various endocytic sites. In particular, coexpression of wild-type protein attenuated the pathogenic effects of the variant by inhibiting excessive oligomer formation. Our results elucidate the pathogenic mechanisms and recessive characteristics of this variant and may aid in the development of targeted therapies.
Authors
Stephanie Waich, Karin Kreidl, Julia Vodopiutz, Arzu Meltem Demir, Adam R. Pollio, Vojtěch Dostál, Kristian Pfaller, Marianna Parlato, Nadine Cerf-Bensussan, Rüdiger Adam, Georg F. Vogel, Holm H. Uhlig, Frank M. Ruemmele, Thomas Müller, Michael W. Hess, Andreas R. Janecke, Lukas A. Huber, Taras Valovka
Abstract
Mitogen-activated protein kinase 8 interacting protein 3 (MAPK8IP3/JIP3) is a member of the kinesin family known to play a role in axonal transport of cargo. Mutations in the gene have been linked to severe neurodevelopmental disorders, resulting in developmental delay, intellectual disability, ataxia, tremor, autism, seizures, and visual impairment. A patient who has a missense mutation in the MAPK8IP3 gene (c. 1714 C>T, Arg578Cys) (R578C) manifests dystonia, gross motor delay and developmental delay. Here we show that the mutation is a toxic gain of function mutation which alters the interactome of JIP3, disrupts axonal transport of late endosomes, increases signaling via c-Jun N-terminal kinase (JNK), resulting in apoptosis, and disrupts the dopamine receptor 1 (D1) signaling while not affecting the dopamine receptor 2 (D2) signaling. Further, in the presence of the mutant protein, we show that 80% reduction of mutant JIP3>80% and 60% reduction of wild-type JIP3 by non-allele selective phosphorothioate (PS)-modified antisense oligonucleotides (ASOs) is well tolerated by several types of cells in vitro. Our study identifies several important new roles for JIP3 and provides important insights for therapeutic approaches, including antisense oligonucleotide reduction of JIP3.
Authors
Wei Zhang, Swapnil Mittal, Ria Thomas, Anahid Foroughishafiei, Ricardo Nunes Bastos, Wendy K. Chung, Konstantina Skourti-Stathaki, Stanley T. Crooke
Abstract
Authors
Máté Sándor, Balázs Csaba Németh, Alexandra Demcsák, Miklós Sahin-Tóth
Abstract
Mutations in the anoctamin5 (ANO5) gene can lead to musculoskeletal disorders, with monoallelic (autosomal dominant) mutations typically presenting as skeletal abnormalities known as Gnathodiaphyseal dysplasia (GDD). Clinically, GDD is characterized by thickened cortices of long bones and mandibles, narrowed medullary cavities, and increased bone fragility. While autophagy is necessary in regulating bone formation, the specific relationship between ANO5 and autophagy remains poorly understood. In this study, we demonstrated that Ano5 deficiency activates autophagy in mouse cranial osteoblasts (mCOBs), leading to enhanced osteogenic capacity in Ano5-/- mCOBs. The application of 3-Methyladenine (3-MA) and chloroquine (CQ) reversed the excessive osteogenesis observed in Ano5-/- mCOBs. Further analysis revealed that Ano5 deficiency upregulates the expression of ATG9A, and silencing ATG9A significantly reduces both autophagy and osteogenic activity in Ano5-/- mCOBs. Additionally, the AMP-activated protein kinase (AMPK) was found to regulate ATG9A positively, and inhibiting AMPK reduced ATG9A expression, which in turn mitigated excessive osteogenesis of Ano5-/- mCOBs. Moreover, in vivo experiments confirmed that treatment with 3-MA alleviates the bone phenotype abnormalities in Ano5-/- mice. These findings suggest that Ano5 negatively regulates autophagy, contributing to illuminate pathogenesis of GDD. Meanwhile, this research highlights potential therapeutic strategies targeting autophagy to pave the way for the clinical manifestations of GDD.
Authors
Shuai Zhang, Shengnan Wang, Sirui Liu, Xiu Liu, Mingyue Zhang, Huichong Xu, Xiaoyu Wang, Hongyu Li, Ying Hu
Abstract
Mutations in the gap junction β2 (GJB2) gene, which encodes connexin 26, are the leading cause of genetic deafness. These mutations are characterized by the degeneration and fragmentation of gap junctions and gap junction plaques (GJPs) composed of connexin 26. Dominant-negative mutations of GJB2, such as R75W, cause syndromic hearing loss and palmoplantar keratoderma. We previously reported that the R75W mutation, a single-base substitution where C is replaced by T, causes fragmentation of GJPs. Therefore, an adenine base editor (ABE), which enables A-to-G base conversions, can potentially be useful for the treatment of this genetic disease. Here, we report that an all-in-one adeno-associated virus (AAV) vector, which includes a compact ABE (SaCas9-NNG-ABE8e) with broad targeting range, and a sgRNA targeting the R75W mutation in GJB2 corrected this pathogenic mutation and facilitated the recovery of the gap junction intercellular communication network of GJPs. In a transgenic mouse model with the GJB2 R75W mutation, AAV-mediated base editing also restored the fragmented GJPs to orderly outlines in cochlear supporting cells. Our findings suggest that an ABE-based base-editing strategy could be an optimal treatment for the dominant form of GJB2-related hearing loss, GJB2-related skin diseases, and other deafness-related mutations, especially single-base substitutions.
Authors
Takao Ukaji, Daisuke Arai, Harumi Tsutsumi, Ryoya Nakagawa, Fumihiko Matsumoto, Katsuhisa Ikeda, Osamu Nureki, Kazusaku Kamiya
Abstract
Prader-Willi syndrome (PWS) is a multigenic disorder caused by the loss of seven contiguous paternally expressed genes. Mouse models with inactivation of all PWS genes are lethal. Knockout (KO) mouse models for each candidate gene have been generated, but they lack the functional interactions between PWS genes. Here, we revealed an interplay between Necdin and Magel2 “PWS” genes and generated a mouse model (named “Del Ndn-Magel2” mice) with a deletion including both genes. A subset of Del Ndn-Magel2 mice showed neonatal lethality. Behaviorally, surviving mutant mice exhibited sensory delays during infancy and alterations in social exploration at adulthood. Del Ndn-Magel2 mice had a lower body weight before weaning, persisting after weaning in males only, with reduced fat mass and improved glucose tolerance, and altered puberty. Adult mutant mice displayed increased ventilation and a persistent increase in apneas following a hypercapnic challenge. Transcriptomics analyses revealed a dysregulation of key circadian genes and alterations of genes associated with axonal function similar to PWS patients. At neuroanatomical levels, Del Ndn-Magel2 mice had an impaired maturation of oxytocin neurons and a disrupted development of melanocortin circuits. Together, these data indicate that the Del Ndn-Magel2 mouse is a pertinent and genetically relevant model of PWS
Authors
Pierre-Yves Barelle, Alicia Sicardi, Fabienne Schaller, Julie Buron, Denis Becquet, Felix Omnes, Françoise Watrin, Marie-Sophie Alifrangis, Catarina Santos, Clément Menuet, Anne-Marie François-Bellan, Emilie Caron, Jessica Klucznik, Vincent Prevot, Sebastien G. Bouret, Françoise Muscatelli
Abstract
Leber hereditary optic neuropathy (LHON) is a paradigm for mitochondrial retinopathy due to mitochondrial DNA (mtDNA) mutations. However, the mechanism underlying retinal cell-specific effects of LHON-linked mtDNA mutations remains poorly understood and there has been no effective treatment or cure for this disorder. Using a mice model bearing a LHON-linked ND6P25L mutation, we demonstrated that the mutation caused retinal cell-specific deficiencies, especially in retinal ganglion cells (RGC), rods and Müller cells. Single-cell RNA sequencing revealed cell-specific dysregulation of oxidative phosphorylation and visual signaling pathways in the mutant retina. Strikingly, ND6 mutation-induced dysfunctions caused abnormal vitamin A (VA) metabolism essential for visual function. VA supplementation remarkably alleviated retinal deficiencies, including reduced fundus lesion and retinal thickness, and increasing numbers of RGCs, photoreceptors and Müller cell neurites. The restoration of visual functions with VA treatment were further evidenced by correcting dysregulations of phototransduction cascade and neurotransmitter transmission and restoring electrophysiological properties. Interestingly, VA supplementation markedly rescued the abnormal mitochondrial morphologies and functions in the mutant retina. These findings provide new insight into retina-specific pathophysiology of mitochondrial retinopathy arising from vitamin A deficiency and mitochondrial dysfunction induced by mtDNA mutation and step toward for therapeutic intervention for LHON and other mitochondrial retinopathy.
Authors
Cheng Ai, Huiying Li, Chunyan Wang, Yanchun Ji, Douglas C. Wallace, Junbin Qian, Yimin Zhu, Min-Xin Guan
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