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Tolosa-Tort P, DeWan AT. Leveraging Alzheimer's Disease Omics to Identify Pleiotropic Genes Contributing to Neurodegeneration in Primary Open-Angle Glaucoma. Mol Neurobiol 2025:10.1007/s12035-025-05074-2. [PMID: 40411683 DOI: 10.1007/s12035-025-05074-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2024] [Accepted: 05/13/2025] [Indexed: 05/26/2025]
Abstract
Primary open-angle glaucoma is the most common form of glaucoma worldwide and one of the leading causes of irreversible blindness. Current therapies focus on intraocular pressure control despite substantial evidence on the importance of additional pathogenic mechanisms involved in neuronal repair and regeneration. Some of these mechanisms may be shared with and across other neurodegenerative disorders, such as Alzheimer's disease. Joint analyses that address this pathogenic overlap can be leveraged to identify suspected neurodegenerative and neuroprotective pathways. In this study, we derived gene-level summary statistics from available genome-wide association studies for primary open-angle glaucoma and Alzheimer's Disease and employed a multivariate analysis to identify genes with an effect on both neurodegenerative diseases. We assessed the influence of the prioritized genes using Mendelian randomization to obtain the effect of retina- and brain cortex-specific gene expression on primary open-angle glaucoma risk. We identified ten genes with evidence of a pleiotropic effect on primary open-angle glaucoma and Alzheimer's disease: TMCO1, ANXA11, ARHGAP27, PLEKHM1, CRHR1, KANSL1, LRRC37A, ARL17A, LRRC37A2, and CBY1. Additionally, gene expression in either the retina or brain cortex of TMCO1, ANXA11, ARHGAP27, PLEKHM1, KANSL1, LRRC37A, ARL17A, LRRC37A2, and CBY1 influenced POAG risk. These genes have known roles in neurodegeneration-associated pathways. Our analysis uncovered evidence of pleiotropy and gene expression as a mechanism impacting disease risk. Further investigation into these genes may yield valuable insights into their involvement in neurodegenerative pathways potentially informing new approaches for early detection, classification, and treatment strategies.
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Affiliation(s)
- Paulina Tolosa-Tort
- Department of Chronic Disease Epidemiology, Yale School of Public Health, New Haven, CT, USA.
| | - Andrew T DeWan
- Department of Chronic Disease Epidemiology, Yale School of Public Health, New Haven, CT, USA
- Center for Perinatal, Pediatric and Environmental Epidemiology, Yale School of Public Health, New Haven, CT, USA
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Meng Y, Li W, Zhang Y, Li Y, He Y, Zhang N. ANXA11 Mutations in the FTD Spectrum: A Novel Finding in a Patient With Semantic Variant Primary Progressive Aphasia. Eur J Neurol 2025; 32:e70187. [PMID: 40345169 PMCID: PMC12062875 DOI: 10.1111/ene.70187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2025] [Revised: 04/24/2025] [Accepted: 04/28/2025] [Indexed: 05/11/2025]
Abstract
BACKGROUND Semantic variant primary progressive aphasia (svPPA) is typically a sporadic disorder, and few cases have been linked to ANXA11 mutations. Comprehensive analyses of genetic mutations in svPPA are limited. Furthermore, the clinical and genetic distinctions between typical svPPA and right temporal variant frontotemporal dementia (rtvFTD) are poorly understood. METHODS A 68-year-old patient with svPPA carrying a heterozygous ANXA11 c.119A>G (p.D40G) mutation underwent comprehensive neuropsychological, neuroimaging, and genetic assessments at baseline and at the one-year follow-up timepoint. Additionally, systematic reviews were conducted to identify reported cases of ANXA11 mutations in the FTD spectrum and the genetic mutations associated with svPPA. Clinical-genetic profiles of typical svPPA and rtvFTD were compared based on data from the literature. RESULTS Thirty-two patients with ANXA11 mutations were identified, including 11 with pure FTD phenotypes and the majority exhibiting FTD-amyotrophic lateral sclerosis (ALS). Among 167 svPPA-related cases, MAPT, GRN, and C9ORF72 mutations were most frequently implicated; ANXA11 mutations were primarily identified in East Asian patients. Comparative analysis revealed overlapping age at onset, disease duration, sex distribution, and APOE ε4 allele frequencies between typical svPPA and rtvFTD but differing clinical presentations. CONCLUSIONS This study reports a case of typical svPPA in China associated with the ANXA11 p.D40G mutation without ALS-related features. Our findings highlight the importance of ANXA11 mutations in FTD pathogenesis.
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Affiliation(s)
- Yaping Meng
- Department of NeurologyTianjin Neurological Institute, Tianjin Medical University General HospitalTianjinChina
- Clinical College of Neurology, Neurosurgery and NeurorehabilitationTianjin Medical UniversityTianjinChina
| | - Wenping Li
- Department of NeurologyTianjin Neurological Institute, Tianjin Medical University General HospitalTianjinChina
| | - Yanxin Zhang
- Department of NeurologyTianjin Neurological Institute, Tianjin Medical University General HospitalTianjinChina
| | - Yaoru Li
- Department of NeurologyTianjin Neurological Institute, Tianjin Medical University General HospitalTianjinChina
| | - Yong He
- Department of NeurologyTianjin Neurological Institute, Tianjin Medical University General HospitalTianjinChina
| | - Nan Zhang
- Department of NeurologyTianjin Neurological Institute, Tianjin Medical University General HospitalTianjinChina
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Mews MA, Naj AC, Griswold AJ, Below JE, Bush WS. Brain and blood transcriptome-wide association studies identify five novel genes associated with Alzheimer's disease. J Alzheimers Dis 2025; 105:228-244. [PMID: 40111921 DOI: 10.1177/13872877251326288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/22/2025]
Abstract
BackgroundGenome-wide association studies (GWAS) have identified numerous genetic variants associated with Alzheimer's disease (AD), but their functional implications remain unclear. Transcriptome-wide association studies (TWAS) offer enhanced statistical power by analyzing genetic associations at the gene level rather than at the variant level, enabling assessment of how genetically-regulated gene expression influences AD risk. However, previous AD-TWAS have been limited by small expression quantitative trait loci (eQTL) reference datasets or reliance on AD-by-proxy phenotypes.ObjectiveTo perform the most powerful AD-TWAS to date using summary statistics from the largest available brain and blood cis-eQTL meta-analyses applied to the largest clinically-adjudicated AD GWAS.MethodsWe implemented the OTTERS TWAS pipeline to predict gene expression using the largest available cis-eQTL data from cortical brain tissue (MetaBrain; N = 2683) and blood (eQTLGen; N = 31,684), and then applied these models to AD-GWAS data (Cases = 21,982; Controls = 44,944).ResultsWe identified and validated five novel gene associations in cortical brain tissue (PRKAG1, C3orf62, LYSMD4, ZNF439, SLC11A2) and six genes proximal to known AD-related GWAS loci (Blood: MYBPC3; Brain: MTCH2, CYB561, MADD, PSMA5, ANXA11). Further, using causal eQTL fine-mapping, we generated sparse models that retained the strength of the AD-TWAS association for MTCH2, MADD, ZNF439, CYB561, and MYBPC3.ConclusionsOur comprehensive AD-TWAS discovered new gene associations and provided insights into the functional relevance of previously associated variants, which enables us to further understand the genetic architecture underlying AD risk.
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Affiliation(s)
- Makaela A Mews
- System Biology and Bioinformatics, Department of Nutrition, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Adam C Naj
- Department of Biostatistics, Epidemiology, and Informatics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Anthony J Griswold
- John P. Hussman Institute for Human Genomics, University of Miami, Miami, FL, USA
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami, Miami, FL, USA
| | - Jennifer E Below
- Vanderbilt Genetics Institute and Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - William S Bush
- Department of Population and Quantitative Health Sciences, Cleveland Institute for Computational Biology, Case Western Reserve University School of Medicine, Cleveland, OH, USA
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Lee SM, Yoon SJ, Park KW, Kim A, Kim HJ, Jung N, Jang H, Seeley WW, Kim Y, Moon SY, Kim E, the Longitudinal study of Early onset dementia And Family members (LEAF) investigators. Semantic variant primary progressive aphasia with ANXA11 p.D40G. Alzheimers Dement 2025; 21:e14566. [PMID: 40042459 PMCID: PMC11881632 DOI: 10.1002/alz.14566] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2024] [Revised: 12/27/2024] [Accepted: 12/28/2024] [Indexed: 05/13/2025]
Abstract
INTRODUCTION Pathogenic variants of annexin A11 (ANXA11) have been identified in patients with amyotrophic lateral sclerosis (ALS) with or without frontotemporal dementia (FTD). We explored ANXA11 pathogenic variants in a Korean FTD cohort to investigate the prevalence and the role of ANXA11 variation in FTD. METHODS We used next-generation sequencing (NGS) to search for pathogenic variants in ANXA11 in two nationwide FTD cohorts in Korea. RESULTS We identified a pathogenic variant in ANXA11, c.119A > G (p.D40G), in six patients with semantic variant primary progressive aphasia (svPPA), representing 5.5% of the svPPA cohort (6/109), and representing 2.3% of the FTD cohort overall (6/259). Only one patient later developed features suggestive of ALS. DISCUSSION This study links a rare variant in ANXA11 to a sporadic clinical syndrome in which specific TAR DNA-binding protein-43 (TDP-43) forms an obligate co-fibril with annexin A11. The variant, p.D40G, lies within the N-terminal portion of annexin A11's TDP-43 type C interacting domain, suggesting that genetic variation in that region may promote co-fibrillization. HIGHLIGHTS The pathogenic variant of annexin A11 (ANXA11I) is linked to frontotemporal dementia (FTD) syndrome. ANXA11 (p.D40G) may be one of the possible genetic causes of semantic variant primary progressive aphasia (svPPA). ANXA11 (p.D40G) may enhance heteromeric amyloid filaments of annexin A11 and TDP-43, promoting frontotemporal lobar degeneration with TAR DNA-binding protein-43 (TDP-43) inclusions (FTLD-TDP) type C.
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Affiliation(s)
- Sun Min Lee
- Department of NeurologyAjou University School of MedicineSuwonSouth Korea
| | - Soo Jin Yoon
- Department of NeurologyDaejeon Eulji Medical CenterEulji UniversityDaejeonSouth Korea
| | - Kyung Won Park
- Department of NeurologyDong‐A Medical CenterDong‐A University College of MedicineBusanSouth Korea
| | - Ahro Kim
- Department of NeurologyUlsan University HospitalUniversity of Ulsan College of MedicineUlsanSouth Korea
| | - Hee Jin Kim
- Department of NeurologySamsung Medical CenterSungkyunkwan University School of MedicineSeoulSouth Korea
| | - Na‐Yeon Jung
- Department of NeurologyPusan National University Yangsan HospitalResearch Institute for Convergence of Biomedical Science and TechnologyYangsanSouth Korea
| | - Hyemin Jang
- Department of NeurologySeoul National University HospitalSeoulSouth Korea
| | - William W. Seeley
- Memory and Aging CenterDepartment of NeurologyUniversity of California, San FranciscoSan FranciscoCaliforniaUSA
- Department of PathologyUniversity of California, San FranciscoSan FranciscoCaliforniaUSA
| | - Young‐Eun Kim
- Department of Laboratory MedicineHanyang University College of MedicineSeoulSouth Korea
| | - So Young Moon
- Department of NeurologyAjou University School of MedicineSuwonSouth Korea
| | - Eun‐Joo Kim
- Department of NeurologyPusan National University HospitalPusan National University School of Medicine and Medical Research InstituteBusanSouth Korea
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Marchica V, Biasetti L, Barnard J, Li S, Nikolaou N, Frosch MP, Lucente DE, Eldaief M, King A, Fanto M, Troakes C, Houart C, Smith BN. Annexin A11 mutations are associated with nuclear envelope dysfunction in vivo and in human tissues. Brain 2025; 148:276-290. [PMID: 38989900 PMCID: PMC11706284 DOI: 10.1093/brain/awae226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 05/04/2024] [Accepted: 05/20/2024] [Indexed: 07/12/2024] Open
Abstract
Annexin A11 mutations are a rare cause of amyotrophic lateral sclerosis (ALS), wherein replicated protein variants P36R, G38R, D40G and D40Y are located in a small helix within the long, disordered N-terminus. To elucidate disease mechanisms, we characterized the phenotypes induced by a genetic loss-of-function and by misexpression of G38R and D40G in vivo. Loss of Annexin A11 results in a low-penetrant behavioural phenotype and aberrant axonal morphology in zebrafish homozygous knockout larvae, which is rescued by human wild-type Annexin A11. Both Annexin A11 knockout/down and ALS variants trigger nuclear dysfunction characterized by Lamin B2 mislocalization. The Lamin B2 signature also presented in anterior horn, spinal cord neurons from post-mortem ALS ± frontotemporal dementia patient tissue possessing G38R and D40G protein variants. These findings suggest mutant Annexin A11 acts as a dominant negative, revealing a potential early nucleopathy highlighting nuclear envelope abnormalities preceding behavioural abnormality in animal models.
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Affiliation(s)
- Valentina Marchica
- Department of Basic and Clinical Neuroscience, Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London SE5 9RX, UK
- Centre for Developmental Neurobiology, Institute of Psychiatry, Psychology and Neuroscience, Guy’s Campus, King’s College London, London SE1 1UL, UK
| | - Luca Biasetti
- Department of Basic and Clinical Neuroscience, Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London SE5 9RX, UK
| | - Jodi Barnard
- Department of Basic and Clinical Neuroscience, Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London SE5 9RX, UK
| | - Shujing Li
- Department of Basic and Clinical Neuroscience, Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London SE5 9RX, UK
| | - Nikolas Nikolaou
- Living Systems Institute, University of Exeter, Stocker Road, Exeter EX4 4QD, UK
| | - Matthew P Frosch
- Mass General Institute for Neurodegenerative Diseases, B114-2700, Charlestown, MA 02129, USA
- C.S. Kubik Laboratory for Neuropathology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Diane E Lucente
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Mark Eldaief
- Mass General Institute for Neurodegenerative Diseases, B114-2700, Charlestown, MA 02129, USA
| | - Andrew King
- Department of Basic and Clinical Neuroscience, Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London SE5 9RX, UK
- London Neurodegenerative Diseases Brain Bank, SGDP Centre, PO65, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London SE5 8AF, UK
| | - Manolis Fanto
- Department of Basic and Clinical Neuroscience, Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London SE5 9RX, UK
| | - Claire Troakes
- Department of Basic and Clinical Neuroscience, Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London SE5 9RX, UK
- London Neurodegenerative Diseases Brain Bank, SGDP Centre, PO65, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London SE5 8AF, UK
| | - Corinne Houart
- Centre for Developmental Neurobiology, Institute of Psychiatry, Psychology and Neuroscience, Guy’s Campus, King’s College London, London SE1 1UL, UK
| | - Bradley N Smith
- Department of Basic and Clinical Neuroscience, Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London SE5 9RX, UK
- Centre for Developmental Neurobiology, Institute of Psychiatry, Psychology and Neuroscience, Guy’s Campus, King’s College London, London SE1 1UL, UK
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Liu Q, Sun Y, He B, Chen H, Wang L, Wang G, Zhang K, Zhao X, Zhang X, Shen D, Zhang X, Cui L. Gain-of-function ANXA11 mutation cause late-onset ALS with aberrant protein aggregation, neuroinflammation and autophagy impairment. Acta Neuropathol Commun 2025; 13:2. [PMID: 39755715 DOI: 10.1186/s40478-024-01919-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2024] [Accepted: 12/20/2024] [Indexed: 01/06/2025] Open
Abstract
Mutations in the ANXA11 gene, encoding an RNA-binding protein, have been implicated in the pathogenesis of amyotrophic lateral sclerosis (ALS), but the underlying in vivo mechanisms remain unclear. This study examines the clinical features of ALS patients harboring the ANXA11 hotspot mutation p.P36R, characterized by late-onset motor neuron disease and occasional multi-system involvement. To elucidate the pathogenesis, we developed a knock-in mouse model carrying the p.P36R mutation. In both heterozygous and homozygous mutant mice, ANXA11 protein levels were comparable to those in wild-type. Both groups exhibited late-onset motor dysfunction at approximately 10 months of age, with similar survival rates to wild-type (> 24 months) and no signs of dementia. Pathological analysis revealed early abnormal aggregates in spinal cord motor neurons, cortical neurons, and muscle cells of homozygous mice. From 2 months of age, we observed mislocalized ANXA11 aggregates, SQSTM1/p62-positive inclusions, and cytoplasmic TDP-43 mislocalization, which intensified with disease progression. Importantly, mutant ANXA11 co-aggregated with TDP-43 and SQSTM1/p62-positive inclusions. Electron microscopy of the gastrocnemius muscle uncovered myofibrillar abnormalities, including sarcomeric disorganization, Z-disc dissolution, and subsarcolemmal electron-dense structures within autophagic vacuoles. Autophagic flux, initially intact at 2 months, was impaired by 9 months, as evidenced by decreased Beclin-1 and LC3BII/I levels and increased SQSTM1/p62 expression, coinciding with mTORC1 hyperactivation. Significant motor neuron loss and neuroinflammation were detected by 9 months, with marked muscle dystrophy apparent by 12 months compared to wild-type controls. These findings implicate the gain-of-function ANXA11 mutation drives late-onset motor neuron disease by early presymptomatic proteinopathy, progressive neuronal degeneration, neuroinflammation, and autophagic dysfunction.
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Affiliation(s)
- Qing Liu
- Department of Neurology, Peking Union Medical College Hospital, Peking Union Medical College (PUMC) and Chinese Academy of Medical Science (CAMS), Beijing, China.
| | - Ye Sun
- Department of Neurology, Peking Union Medical College Hospital, Peking Union Medical College (PUMC) and Chinese Academy of Medical Science (CAMS), Beijing, China
| | - Baodong He
- Department of Neurology, Peking Union Medical College Hospital, Peking Union Medical College (PUMC) and Chinese Academy of Medical Science (CAMS), Beijing, China
| | - Haodong Chen
- Department of Neurology, Peking Union Medical College Hospital, Peking Union Medical College (PUMC) and Chinese Academy of Medical Science (CAMS), Beijing, China
| | - Lijing Wang
- Department of Neurology, Peking Union Medical College Hospital, Peking Union Medical College (PUMC) and Chinese Academy of Medical Science (CAMS), Beijing, China
| | - Gaojie Wang
- Department of Neurology, Peking Union Medical College Hospital, Peking Union Medical College (PUMC) and Chinese Academy of Medical Science (CAMS), Beijing, China
| | - Kang Zhang
- Department of Neurology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- China National Clinical Research Center for Neurological Diseases, Beijing, China
| | - Ximeng Zhao
- State Key Laboratory of Medical Molecular Biology, Mckusick-Zhang Center for Genetic Medicine, Institute of Basic Medical Sciences, PUMC and CAMS, Beijing, China
| | - Xinzhe Zhang
- State Key Laboratory of Medical Molecular Biology, Mckusick-Zhang Center for Genetic Medicine, Institute of Basic Medical Sciences, PUMC and CAMS, Beijing, China
| | - Dongchao Shen
- Department of Neurology, Peking Union Medical College Hospital, Peking Union Medical College (PUMC) and Chinese Academy of Medical Science (CAMS), Beijing, China
| | - Xue Zhang
- State Key Laboratory of Medical Molecular Biology, Mckusick-Zhang Center for Genetic Medicine, Institute of Basic Medical Sciences, PUMC and CAMS, Beijing, China.
- State Key Laboratory of Complex, Severe, and Rare Diseases, PUMCH, Beijing, China.
| | - Liying Cui
- Department of Neurology, Peking Union Medical College Hospital, Peking Union Medical College (PUMC) and Chinese Academy of Medical Science (CAMS), Beijing, China.
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Khullar S, Huang X, Ramesh R, Svaren J, Wang D. NetREm: Network Regression Embeddings reveal cell-type transcription factor coordination for gene regulation. BIOINFORMATICS ADVANCES 2024; 5:vbae206. [PMID: 40260118 PMCID: PMC12011367 DOI: 10.1093/bioadv/vbae206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/05/2024] [Revised: 10/22/2024] [Accepted: 12/18/2024] [Indexed: 04/23/2025]
Abstract
Motivation Transcription factor (TF) coordination plays a key role in gene regulation via direct and/or indirect protein-protein interactions (PPIs) and co-binding to regulatory elements on DNA. Single-cell technologies facilitate gene expression measurement for individual cells and cell-type identification, yet the connection between TF-TF coordination and target gene (TG) regulation of various cell types remains unclear. Results To address this, we introduce our innovative computational approach, Network Regression Embeddings (NetREm), to reveal cell-type TF-TF coordination activities for TG regulation. NetREm leverages network-constrained regularization, using prior knowledge of PPIs among TFs, to analyze single-cell gene expression data, uncovering cell-type coordinating TFs and identifying revolutionary TF-TG candidate regulatory network links. NetREm's performance is validated using simulation studies and benchmarked across several datasets in humans, mice, yeast. Further, we showcase NetREm's ability to prioritize valid novel human TF-TF coordination links in 9 peripheral blood mononuclear and 42 immune cell sub-types. We apply NetREm to examine cell-type networks in central and peripheral nerve systems (e.g. neuronal, glial, Schwann cells) and in Alzheimer's disease versus Controls. Top predictions are validated with experimental data from rat, mouse, and human models. Additional functional genomics data helps link genetic variants to our TF-TG regulatory and TF-TF coordination networks. Availability and implementation https://github.com/SaniyaKhullar/NetREm.
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Affiliation(s)
- Saniya Khullar
- Waisman Center, University of Wisconsin-Madison, Madison, WI 53705, United States
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI 53076, United States
| | - Xiang Huang
- Waisman Center, University of Wisconsin-Madison, Madison, WI 53705, United States
| | - Raghu Ramesh
- Waisman Center, University of Wisconsin-Madison, Madison, WI 53705, United States
- Comparative Biomedical Sciences Training Program, University of Wisconsin-Madison, Madison, WI 53706, United States
| | - John Svaren
- Waisman Center, University of Wisconsin-Madison, Madison, WI 53705, United States
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI 53706, United States
| | - Daifeng Wang
- Waisman Center, University of Wisconsin-Madison, Madison, WI 53705, United States
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI 53076, United States
- Department of Computer Sciences, University of Wisconsin-Madison, Madison, WI 53706, United States
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Barnard J, Hunt R, Yucel M, Mazaud D, Smith BN, Fanto M. Human TDP43 is required for ALS‑related annexin A11 toxicity in Drosophila. Biomed Rep 2024; 21:165. [PMID: 39301564 PMCID: PMC11411402 DOI: 10.3892/br.2024.1853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 06/13/2024] [Indexed: 09/22/2024] Open
Abstract
Genomics allows identification of genes and mutations associated with amyotrophic lateral sclerosis (ALS). Mutations in annexin A11 (ANXA11) are responsible for ~1% of all familial ALS and fronto-temporal dementia cases. The present study used the fruit fly, Drosophila melanogaster, to assess the mechanism of toxicity of ANXA11 mutants in residues that are conserved in the fly ANXB11 protein, the closest homolog to human ANXA11. In immune fluorescence, lifespan and negative geotaxis assays ANXA11 mutants, while displaying some degree of alteration in localization and function, did not exert any relevant organism toxicity in Drosophila. However, they showed a specific interaction with human TAR DNA-binding protein (TDP43). The present study illustrated that the ANXA11 mutants interact with human TDP43, but not the fly TAR DNA-binding protein-43 homolog (TBPH) or other ALS-associated genes such as super oxide dismutase 1, to shorten lifespan and increase negative geotaxis defects. This sheds light both on the mechanisms underlying ALS, further elucidating the intricate molecular network implicated in ALS and placing ANXA11 as a key player in its pathology, and on the complexity of using Drosophila as a model organism for researching genes in ALS.
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Affiliation(s)
- Jodi Barnard
- Department of Basic and Clinical Neuroscience, Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London SE5 9NU, UK
| | - Rachel Hunt
- Department of Basic and Clinical Neuroscience, Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London SE5 9NU, UK
| | - Mert Yucel
- Department of Basic and Clinical Neuroscience, Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London SE5 9NU, UK
| | - David Mazaud
- Department of Basic and Clinical Neuroscience, Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London SE5 9NU, UK
| | - Bradley N Smith
- Department of Basic and Clinical Neuroscience, Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London SE5 9NU, UK
- Centre for Developmental Neurobiology and Medical Research Council Centre for Neurodevelopmental Disorders, Institute of Psychiatry, Psychology and Neuroscience, Guy's Campus, King's College London, London SE1 1UL, UK
| | - Manolis Fanto
- Department of Basic and Clinical Neuroscience, Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London SE5 9NU, UK
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Roychowdhury S, Joshi D, Singh VK, Faruq M, Das P. Genetic and in silico analysis of Indian sporadic young onset patient with amyotrophic lateral sclerosis. Amyotroph Lateral Scler Frontotemporal Degener 2024; 25:589-599. [PMID: 38450645 DOI: 10.1080/21678421.2024.2324896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Revised: 02/12/2024] [Accepted: 02/19/2024] [Indexed: 03/08/2024]
Abstract
BACKGROUND Amyotrophic lateral sclerosis (ALS) is an old onset devastating neurodegenerative disorder. Young-onset ALS cases especially sporadic ones who are between 25 and 45 years are rarely affected by the disease. Despite the identification of numerous candidate genes associated with ALS, the etiology of the disease remains elusive due to extreme genetic and phenotypic variability. The advent of affordable whole exome sequencing (WES) has opened new avenues for unraveling the disease's pathophysiology better. METHODS AND RESULTS We aimed to determine the genetic basis of an Indian-origin, young onset sporadic ALS patient with very rapid deterioration of the disease course without any cognitive decline who was screened for mutations in major ALS candidate genes by WES. Variants detected were reconfirmed by Sanger sequencing. The clinicopathological features were investigated and two heterozygous missense variants were identified: R452W, not previously associated with ALS, present in one of the four conserved C terminal domains in ANXA11 and R208W in SIGMAR1, respectively. Both of these variants were predicted to be damaging by pathogenicity prediction tools and various in silico methods. CONCLUSION Our study revealed two potentially pathogenic variants in two ALS candidate genes. The genetic makeup of ALS patients from India has been the subject of a few prior studies, but none of them examined ANXA11 and SIGMAR1 genes so far. These results establish the framework for additional research into the pathogenic processes behind these variations that result in sporadic ALS disease and further our understanding of the genetic makeup of Indian ALS patients.
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Affiliation(s)
- Saileyee Roychowdhury
- Centre for Genetic Disorders, Institute of Science, Banaras Hindu University, Varanasi, India
| | - Deepika Joshi
- Department of Neurology, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
| | - Vinay Kumar Singh
- School of Biotechnology, Centre for Bioinformatics, Institute of Science, Banaras Hindu University, Varanasi, India, and
| | - Mohammed Faruq
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Parimal Das
- Centre for Genetic Disorders, Institute of Science, Banaras Hindu University, Varanasi, India
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Clayton EL, Huggon L, Cousin MA, Mizielinska S. Synaptopathy: presynaptic convergence in frontotemporal dementia and amyotrophic lateral sclerosis. Brain 2024; 147:2289-2307. [PMID: 38451707 PMCID: PMC11224618 DOI: 10.1093/brain/awae074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 02/02/2024] [Accepted: 02/12/2024] [Indexed: 03/09/2024] Open
Abstract
Frontotemporal dementia and amyotrophic lateral sclerosis are common forms of neurodegenerative disease that share overlapping genetics and pathologies. Crucially, no significantly disease-modifying treatments are available for either disease. Identifying the earliest changes that initiate neuronal dysfunction is important for designing effective intervention therapeutics. The genes mutated in genetic forms of frontotemporal dementia and amyotrophic lateral sclerosis have diverse cellular functions, and multiple disease mechanisms have been proposed for both. Identification of a convergent disease mechanism in frontotemporal dementia and amyotrophic lateral sclerosis would focus research for a targetable pathway, which could potentially effectively treat all forms of frontotemporal dementia and amyotrophic lateral sclerosis (both familial and sporadic). Synaptopathies are diseases resulting from physiological dysfunction of synapses, and define the earliest stages in multiple neuronal diseases, with synapse loss a key feature in dementia. At the presynapse, the process of synaptic vesicle recruitment, fusion and recycling is necessary for activity-dependent neurotransmitter release. The unique distal location of the presynaptic terminal means the tight spatio-temporal control of presynaptic homeostasis is dependent on efficient local protein translation and degradation. Recently, numerous publications have shown that mutations associated with frontotemporal dementia and amyotrophic lateral sclerosis present with synaptopathy characterized by presynaptic dysfunction. This review will describe the complex local signalling and membrane trafficking events that occur at the presynapse to facilitate neurotransmission and will summarize recent publications linking frontotemporal dementia/amyotrophic lateral sclerosis genetic mutations to presynaptic function. This evidence indicates that presynaptic synaptopathy is an early and convergent event in frontotemporal dementia and amyotrophic lateral sclerosis and illustrates the need for further research in this area, to identify potential therapeutic targets with the ability to impact this convergent pathomechanism.
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Affiliation(s)
- Emma L Clayton
- UK Dementia Research Institute at King’s College London, London SE5 9RT, UK
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, Maurice Wohl Clinical Neuroscience Institute, London SE5 9RT, UK
| | - Laura Huggon
- UK Dementia Research Institute at King’s College London, London SE5 9RT, UK
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, Maurice Wohl Clinical Neuroscience Institute, London SE5 9RT, UK
| | - Michael A Cousin
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh EH8 9XD, UK
- Muir Maxwell Epilepsy Centre, University of Edinburgh, Edinburgh EH8 9XD, UK
- Simons Initiative for the Developing Brain, University of Edinburgh, Edinburgh EH8 9XD, UK
| | - Sarah Mizielinska
- UK Dementia Research Institute at King’s College London, London SE5 9RT, UK
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, Maurice Wohl Clinical Neuroscience Institute, London SE5 9RT, UK
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Nan H, Kim YJ, Chu M, Li D, Li J, Jiang D, Wu Y, Ohtsuka T, Wu L. Genetic and clinical landscape of Chinese frontotemporal dementia: dominance of TBK1 and OPTN mutations. Alzheimers Res Ther 2024; 16:127. [PMID: 38872230 PMCID: PMC11170894 DOI: 10.1186/s13195-024-01493-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2024] [Accepted: 06/07/2024] [Indexed: 06/15/2024]
Abstract
BACKGROUND Our study aims to evaluate the genetic and phenotypic spectrum of Frontotemporal dementia (FTD) gene variant carriers in Chinese populations, investigate mutation frequencies, and assess the functional properties of TBK1 and OPTN variants. METHODS Clinically diagnosed FTD patients underwent genetic analysis through exome sequencing, repeat-primed polymerase chain reaction, and Sanger sequencing. TBK1 and OPTN variants were biologically characterized in vitro using immunofluorescence, immunoprecipitation, and immunoblotting analysis. The frequencies of genes implicated in FTD in China were analyzed through a literature review and meta-analysis. RESULTS Of the 261 Chinese FTD patients, 61 (23.4%) carried potential causative variants in FTD-related genes, including MAPT (n = 17), TBK1 (n = 7), OPTN (n = 6), GRN (n = 6), ANXA11 (n = 4), CHMP2B (n = 3), C9orf72 GGGGCC repeats (n = 2), CYLD (n = 2), PRNP (n = 2), SQSTM1 (n = 2), TARDBP (n = 2), VCP (n = 1), CCNF (n = 1), CHCHD10 (n = 1), SIGMAR1 (n = 1), CHCHD2 (n = 1), FUS (n = 1), TMEM106B (n = 1), and UBQLN2 (n = 1). 29 variants can be considered novel, including the MAPT p.D54N, p.E342K, p.R221P, p.T263I, TBK1 p.E696G, p.I37T, p.E232Q, p.S398F, p.T78A, p.Q150P, p.W259fs, OPTN p.R144G, p.F475V, GRN p.V473fs, p.C307fs, p.R101fs, CHMP2B p.K6N, p.R186Q, ANXA11 p.Q155*, CYLD p.T157I, SQSTM1 p.S403A, UBQLN2 p.P509H, CCNF p.S160N, CHCHD10 p.A8T, SIGMAR1 p.S117L, CHCHD2 p.P53fs, FUS p.S235G & p.S236G, and TMEM106B p.L144V variants. Patients with TBK1 and OPTN variants presented with heterogeneous clinical phenotypes. Functional analysis demonstrated that TBK1 I37T and E232Q mutants showed decreased autophosphorylation, and the OPTN phosphorylation was reduced by the TBK1 I37T mutant. The OPTN-TBK1 complex formation was enhanced by the TBK1 E696G mutant, while OPTN R144G and F475V mutants exhibited reduced recruitment to autophagosomes compared to the wild-type. The overall frequency of TBK1 and OPTN in Chinese FTD patients was 2.0% and 0.3%, respectively. CONCLUSIONS Our study demonstrates the extensive genetic and phenotypic heterogeneity of Chinese FTD patients. TBK1 mutations are the second most frequent cause of clinical FTD after MAPT in the Chinese.
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Affiliation(s)
- Haitian Nan
- Department of Neurology, Xuanwu Hospital, Capital Medical University, 45 Changchun Street, Beijing, 100053, China
| | - Yeon-Jeong Kim
- Department of Biochemistry, Graduate School of Medical Sciences, University of Yamanashi, Yamanashi, 409-3898, Japan
| | - Min Chu
- Department of Neurology, Xuanwu Hospital, Capital Medical University, 45 Changchun Street, Beijing, 100053, China
| | - Dan Li
- Department of Neurology, Xuanwu Hospital, Capital Medical University, 45 Changchun Street, Beijing, 100053, China
| | - Jieying Li
- Sichuan Provincial Center for Mental Health, Sichuan Academy of Medical Science & Sichuan Provincial People's Hospital, Chengdu, 610072, China
| | - Deming Jiang
- Department of Neurology, Xuanwu Hospital, Capital Medical University, 45 Changchun Street, Beijing, 100053, China
| | - Yiming Wu
- The Experimental High School Attached to Beijing Normal University, Beijing, 100032, China
| | - Toshihisa Ohtsuka
- Department of Biochemistry, Graduate School of Medical Sciences, University of Yamanashi, Yamanashi, 409-3898, Japan.
| | - Liyong Wu
- Department of Neurology, Xuanwu Hospital, Capital Medical University, 45 Changchun Street, Beijing, 100053, China.
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Khullar S, Huang X, Ramesh R, Svaren J, Wang D. NetREm: Network Regression Embeddings reveal cell-type transcription factor coordination for gene regulation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.10.25.563769. [PMID: 37961577 PMCID: PMC10634989 DOI: 10.1101/2023.10.25.563769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Transcription factor (TF) coordination plays a key role in target gene (TG) regulation via protein-protein interactions (PPIs) and DNA co-binding to regulatory elements. Single-cell technologies facilitate gene expression measurement for individual cells and cell-type identification, yet the connection between TF coordination and TG regulation of various cell types remains unclear. To address this, we have developed a novel computational approach, Network Regression Embeddings (NetREm), to reveal cell-type TF-TF coordination activities for TG regulation. NetREm leverages network-constrained regularization using prior knowledge of direct and/or indirect PPIs among TFs to analyze single-cell gene expression data. We test NetREm by simulation data and benchmark its performance in 4 real-world applications that have gold standard TF-TG networks available: mouse (mESCs) and simulated human (hESCs) embryonic stem (ESCs), human hematopoietic stem (HSCs), and mouse dendritic (mDCs) cells. Further, we use NetREm to prioritize valid novel TF-TF coordination links in human Peripheral Blood Mononuclear cell (PBMC) sub-types. We apply NetREm to analyze various cell types in both central (CNS) and peripheral (PNS) nerve system (NS) (e.g. neuronal, glial, Schwann cells (SCs)) as well as in Alzheimers disease (AD). Our findings uncover cell-type coordinating TFs and identify new TF-TG candidate links. We validate our top predictions using Cut&Run and knockout loss-of-function expression data in rat/mouse models and compare results with additional functional genomic data, including expression quantitative trait loci (eQTL) and Genome-Wide Association Studies (GWAS) to link genetic variants (single nucleotide polymorphisms (SNPs)) to TF coordination.
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Mews MA, Naj AC, Griswold AJ, Below JE, Bush WS. Brain and Blood Transcriptome-Wide Association Studies Identify Five Novel Genes Associated with Alzheimer's Disease. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.04.17.24305737. [PMID: 38699333 PMCID: PMC11065015 DOI: 10.1101/2024.04.17.24305737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2024]
Abstract
INTRODUCTION Transcriptome-wide Association Studies (TWAS) extend genome-wide association studies (GWAS) by integrating genetically-regulated gene expression models. We performed the most powerful AD-TWAS to date, using summary statistics from cis -eQTL meta-analyses and the largest clinically-adjudicated Alzheimer's Disease (AD) GWAS. METHODS We implemented the OTTERS TWAS pipeline, leveraging cis -eQTL data from cortical brain tissue (MetaBrain; N=2,683) and blood (eQTLGen; N=31,684) to predict gene expression, then applied these models to AD-GWAS data (Cases=21,982; Controls=44,944). RESULTS We identified and validated five novel gene associations in cortical brain tissue ( PRKAG1 , C3orf62 , LYSMD4 , ZNF439 , SLC11A2 ) and six genes proximal to known AD-related GWAS loci (Blood: MYBPC3 ; Brain: MTCH2 , CYB561 , MADD , PSMA5 , ANXA11 ). Further, using causal eQTL fine-mapping, we generated sparse models that retained the strength of the AD-TWAS association for MTCH2 , MADD , ZNF439 , CYB561 , and MYBPC3 . DISCUSSION Our comprehensive AD-TWAS discovered new gene associations and provided insights into the functional relevance of previously associated variants.
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Bagyinszky E, Hulme J, An SSA. Studies of Genetic and Proteomic Risk Factors of Amyotrophic Lateral Sclerosis Inspire Biomarker Development and Gene Therapy. Cells 2023; 12:1948. [PMID: 37566027 PMCID: PMC10417729 DOI: 10.3390/cells12151948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 07/21/2023] [Accepted: 07/25/2023] [Indexed: 08/12/2023] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is an incurable neurodegenerative disease affecting the upper and lower motor neurons, leading to muscle weakness, motor impairments, disabilities and death. Approximately 5-10% of ALS cases are associated with positive family history (familial ALS or fALS), whilst the remainder are sporadic (sporadic ALS, sALS). At least 50 genes have been identified as causative or risk factors for ALS. Established pathogenic variants include superoxide dismutase type 1 (SOD1), chromosome 9 open reading frame 72 (c9orf72), TAR DNA Binding Protein (TARDBP), and Fused In Sarcoma (FUS); additional ALS-related genes including Charged Multivesicular Body Protein 2B (CHMP2B), Senataxin (SETX), Sequestosome 1 (SQSTM1), TANK Binding Kinase 1 (TBK1) and NIMA Related Kinase 1 (NEK1), have been identified. Mutations in these genes could impair different mechanisms, including vesicle transport, autophagy, and cytoskeletal or mitochondrial functions. So far, there is no effective therapy against ALS. Thus, early diagnosis and disease risk predictions remain one of the best options against ALS symptomologies. Proteomic biomarkers, microRNAs, and extracellular vehicles (EVs) serve as promising tools for disease diagnosis or progression assessment. These markers are relatively easy to obtain from blood or cerebrospinal fluids and can be used to identify potential genetic causative and risk factors even in the preclinical stage before symptoms appear. In addition, antisense oligonucleotides and RNA gene therapies have successfully been employed against other diseases, such as childhood-onset spinal muscular atrophy (SMA), which could also give hope to ALS patients. Therefore, an effective gene and biomarker panel should be generated for potentially "at risk" individuals to provide timely interventions and better treatment outcomes for ALS patients as soon as possible.
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Affiliation(s)
- Eva Bagyinszky
- Graduate School of Environment Department of Industrial and Environmental Engineering, Gachon University, Seongnam-si 13120, Republic of Korea;
| | - John Hulme
- Graduate School of Environment Department of Industrial and Environmental Engineering, Gachon University, Seongnam-si 13120, Republic of Korea;
| | - Seong Soo A. An
- Department of Bionano Technology, Gachon University, Seongnam-si 13120, Republic of Korea
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