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Baltar F, Simoes C, Garagorry F, Graña M, Rodríguez S, Haydée Aunchayna M, Tapié A, Cerisola A, González G, Naya H, Spangenberg L, Raggio V. Two compound heterozygous variants in the CLN8 gene are responsible for neuronal cereidolipofuscinoses disorder in a child: a case report. Front Pediatr 2024; 12:1379254. [PMID: 38751748 PMCID: PMC11094295 DOI: 10.3389/fped.2024.1379254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 04/16/2024] [Indexed: 05/18/2024] Open
Abstract
Background Neuronal Ceroid Lipofuscinosis (NCL) disorders, recognized as the primary cause of childhood dementia globally, constitute a spectrum of genetic abnormalities. CLN8, a subtype within NCL, is characterized by cognitive decline, motor impairment, and visual deterioration. This study focuses on an atypical case with congenital onset and a remarkably slow disease progression. Methods Whole-genome sequencing at 30× coverage was employed as part of a national genomics program to investigate the genetic underpinnings of rare diseases. This genomic approach aimed to challenge established classifications (vLINCL and EPMR) and explore the presence of a continuous phenotypic spectrum associated with CLN8. Results The whole-genome sequencing revealed two novel likely pathogenic mutations in the CLN8 gene on chromosome 8p23.3. These mutations were not previously associated with CLN8-related NCL. Contrary to established classifications (vLINCL and EPMR), our findings suggest a continuous phenotypic spectrum associated with CLN8. Pathological subcellular markers further validated the genomic insights. Discussion The identification of two previously undescribed likely pathogenic CLN8 gene mutations challenges traditional classifications and highlights a more nuanced phenotypic spectrum associated with CLN8. Our findings underscore the significance of genetic modifiers and interactions with unrelated genes in shaping variable phenotypic outcomes. The inclusion of pathological subcellular markers further strengthens the validity of our genomic insights. This research enhances our understanding of CLN8 disorders, emphasizing the need for comprehensive genomic analyses to elucidate the complexity of phenotypic presentations and guide tailored therapeutic strategies. The identification of new likely pathogenic mutations underscores the dynamic nature of CLN8-related NCL and the importance of individualized approaches to patient management.
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Affiliation(s)
- Federico Baltar
- Unidad Académica de Neuropediatría, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
- Departamento de Genética, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Camila Simoes
- Unidad de Bioinformática, Institut Pasteur de Montevideo, Montevideo, Uruguay
- Departamento Básico de Medicina, Hospital de Clínicas, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Francisco Garagorry
- Unidad Académica de Anatomía Patológica, Hospital de Clínicas, Facultad de Medicina Universidad de la República, Montevideo, Uruguay
| | - Martín Graña
- Unidad de Bioinformática, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Soledad Rodríguez
- Departamento de Genética, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - María Haydée Aunchayna
- Unidad Académica de Anatomía Patológica, Hospital de Clínicas, Facultad de Medicina Universidad de la República, Montevideo, Uruguay
| | - Alejandra Tapié
- Departamento de Genética, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Alfredo Cerisola
- Unidad Académica de Neuropediatría, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Gabriel González
- Unidad Académica de Neuropediatría, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Hugo Naya
- Unidad de Bioinformática, Institut Pasteur de Montevideo, Montevideo, Uruguay
- Departamento de Producción Animal y Pasturas, Facultad de Agronomía, Universidad de la República, Montevideo, Uruguay
| | - Lucía Spangenberg
- Unidad de Bioinformática, Institut Pasteur de Montevideo, Montevideo, Uruguay
- Departamento Básico de Medicina, Hospital de Clínicas, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Víctor Raggio
- Departamento de Genética, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
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Demir Karaman E, Işık Z. Multi-Omics Data Analysis Identifies Prognostic Biomarkers across Cancers. Med Sci (Basel) 2023; 11:44. [PMID: 37489460 PMCID: PMC10366886 DOI: 10.3390/medsci11030044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 06/18/2023] [Accepted: 06/20/2023] [Indexed: 07/26/2023] Open
Abstract
Combining omics data from different layers using integrative methods provides a better understanding of the biology of a complex disease such as cancer. The discovery of biomarkers related to cancer development or prognosis helps to find more effective treatment options. This study integrates multi-omics data of different cancer types with a network-based approach to explore common gene modules among different tumors by running community detection methods on the integrated network. The common modules were evaluated by several biological metrics adapted to cancer. Then, a new prognostic scoring method was developed by weighting mRNA expression, methylation, and mutation status of genes. The survival analysis pointed out statistically significant results for GNG11, CBX2, CDKN3, ARHGEF10, CLN8, SEC61G and PTDSS1 genes. The literature search reveals that the identified biomarkers are associated with the same or different types of cancers. Our method does not only identify known cancer-specific biomarker genes, but also proposes new potential biomarkers. Thus, this study provides a rationale for identifying new gene targets and expanding treatment options across cancer types.
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Affiliation(s)
- Ezgi Demir Karaman
- Department of Computer Engineering, Institute of Natural and Applied Sciences, Dokuz Eylul University, Izmir 35390, Turkey
| | - Zerrin Işık
- Department of Computer Engineering, Faculty of Engineering, Dokuz Eylul University, Izmir 35390, Turkey
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Holmes AD, White KA, Pratt MA, Johnson TB, Likhite S, Meyer K, Weimer JM. Sex-split analysis of pathology and motor-behavioral outcomes in a mouse model of CLN8-Batten disease reveals an increased disease burden and trajectory in female Cln8 mnd mice. Orphanet J Rare Dis 2022; 17:411. [PMID: 36369162 PMCID: PMC9652919 DOI: 10.1186/s13023-022-02564-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Accepted: 10/23/2022] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND CLN8-Batten disease (CLN8 disease) is a rare neurodegenerative disorder characterized phenotypically by progressive deterioration of motor and cognitive abilities, visual symptoms, epileptic seizures, and premature death. Mutations in CLN8 results in characteristic Batten disease symptoms and brain-wide pathology including accumulation of lysosomal storage material, gliosis, and neurodegeneration. Recent investigations of other subforms of Batten disease (CLN1, CLN3, CLN6) have emphasized the influence of biological sex on disease and treatment outcomes; however, little is known about sex differences in the CLN8 subtype. To determine the impact of sex on CLN8 disease burden and progression, we utilized a Cln8mnd mouse model to measure the impact and progression of histopathological and behavioral outcomes between sexes. RESULTS Several notable sex differences were observed in the presentation of brain pathology, including Cln8mnd female mice consistently presenting with greater GFAP+ astrocytosis and CD68+ microgliosis in the somatosensory cortex, ventral posteromedial/ventral posterolateral nuclei of the thalamus, striatum, and hippocampus when compared to Cln8mnd male mice. Furthermore, sex differences in motor-behavioral assessments revealed Cln8mnd female mice experience poorer motor performance and earlier death than their male counterparts. Cln8mnd mice treated with an AAV9-mediated gene therapy were also examined to assess sex differences on therapeutics outcomes, which revealed no appreciable differences between the sexes when responding to the therapy. CONCLUSIONS Taken together, our results provide further evidence of biologic sex as a modifier of Batten disease progression and outcome, thus warranting consideration when conducting investigations and monitoring therapeutic impact.
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Affiliation(s)
- Andrew D. Holmes
- grid.430154.70000 0004 5914 2142Pediatrics and Rare Diseases Group, Sanford Research, 2301 E 60Th St N, Sioux Falls, SD USA ,grid.267169.d0000 0001 2293 1795Department of Pediatrics, Sanford School of Medicine, University of South Dakota, Sioux Falls, SD USA
| | - Katherine A. White
- grid.430154.70000 0004 5914 2142Pediatrics and Rare Diseases Group, Sanford Research, 2301 E 60Th St N, Sioux Falls, SD USA
| | - Melissa A. Pratt
- grid.430154.70000 0004 5914 2142Pediatrics and Rare Diseases Group, Sanford Research, 2301 E 60Th St N, Sioux Falls, SD USA
| | - Tyler B. Johnson
- grid.430154.70000 0004 5914 2142Pediatrics and Rare Diseases Group, Sanford Research, 2301 E 60Th St N, Sioux Falls, SD USA
| | - Shibi Likhite
- grid.240344.50000 0004 0392 3476The Research Institute at Nationwide Children’s Hospital, Columbus, OH USA
| | - Kathrin Meyer
- grid.240344.50000 0004 0392 3476The Research Institute at Nationwide Children’s Hospital, Columbus, OH USA ,grid.261331.40000 0001 2285 7943Department of Pediatrics, The Ohio State University, Columbus, OH USA
| | - Jill M. Weimer
- grid.430154.70000 0004 5914 2142Pediatrics and Rare Diseases Group, Sanford Research, 2301 E 60Th St N, Sioux Falls, SD USA ,grid.267169.d0000 0001 2293 1795Department of Pediatrics, Sanford School of Medicine, University of South Dakota, Sioux Falls, SD USA
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Badura-Stronka M, Winczewska-Wiktor A, Pietrzak A, Hirschfeld AS, Zemojtel T, Wołyńska K, Bednarek-Rajewska K, Seget-Dubaniewicz M, Matheisel A, Latos-Bielenska A, Steinborn B. CLN8 Mutations Presenting with a Phenotypic Continuum of Neuronal Ceroid Lipofuscinosis-Literature Review and Case Report. Genes (Basel) 2021; 12:genes12070956. [PMID: 34201538 PMCID: PMC8307369 DOI: 10.3390/genes12070956] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 06/18/2021] [Accepted: 06/21/2021] [Indexed: 11/16/2022] Open
Abstract
CLN8 is a ubiquitously expressed membrane-spanning protein that localizes primarily in the ER, with partial localization in the ER-Golgi intermediate compartment. Mutations in CLN8 cause late-infantile neuronal ceroid lipofuscinosis (LINCL). We describe a female pediatric patient with LINCL. She exhibited a typical phenotype associated with LINCL, except she did not present spontaneous myoclonus, her symptoms occurrence was slower and developed focal sensory visual seizures. In addition, whole-exome sequencing identified a novel homozygous variant in CLN8, c.531G>T, resulting in p.Trp177Cys. Ultrastructural examination featured abundant lipofuscin deposits within mucosal cells, macrophages, and monocytes. We report a novel CLN8 mutation as a cause for NCL8 in a girl with developmental delay and epilepsy, cerebellar syndrome, visual loss, and progressive cognitive and motor regression. This case, together with an analysis of the available literature, emphasizes the existence of a continuous spectrum of CLN8-associated phenotypes rather than a sharp distinction between them.
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Affiliation(s)
- Magdalena Badura-Stronka
- Chair and Department of Medical Genetics, Poznan University of Medical Sciences, 60-352 Poznan, Poland; (A.S.H.); (K.W.); (A.L.-B.)
- Correspondence:
| | - Anna Winczewska-Wiktor
- Chair and Department of Developmental Neurology, Poznan University of Medical Sciences, 60-355 Poznan, Poland; (A.W.-W.); (B.S.)
| | - Anna Pietrzak
- Department of Neurology, 10th Military Research Hospital and Polyclinic, 85-681 Bydgoszcz, Poland;
| | - Adam Sebastian Hirschfeld
- Chair and Department of Medical Genetics, Poznan University of Medical Sciences, 60-352 Poznan, Poland; (A.S.H.); (K.W.); (A.L.-B.)
| | - Tomasz Zemojtel
- BIH Genomics Core Unit, Campus Mitte, Charite University Medicine, 13353 Berlin, Germany;
| | - Katarzyna Wołyńska
- Chair and Department of Medical Genetics, Poznan University of Medical Sciences, 60-352 Poznan, Poland; (A.S.H.); (K.W.); (A.L.-B.)
| | - Katarzyna Bednarek-Rajewska
- Department of Clinical Pathology, Poznan University of Medical Sciences, 60-355 Poznan, Poland; (K.B.-R.); (M.S.-D.)
| | - Monika Seget-Dubaniewicz
- Department of Clinical Pathology, Poznan University of Medical Sciences, 60-355 Poznan, Poland; (K.B.-R.); (M.S.-D.)
| | - Agnieszka Matheisel
- Department of Developmental Neurology, Gdansk Medical University, 80-307 Gdansk, Poland;
| | - Anna Latos-Bielenska
- Chair and Department of Medical Genetics, Poznan University of Medical Sciences, 60-352 Poznan, Poland; (A.S.H.); (K.W.); (A.L.-B.)
| | - Barbara Steinborn
- Chair and Department of Developmental Neurology, Poznan University of Medical Sciences, 60-355 Poznan, Poland; (A.W.-W.); (B.S.)
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Singh RB, Gupta P, Kartik A, Farooqui N, Singhal S, Shergill S, Singh KP, Agarwal A. Ocular Manifestations of Neuronal Ceroid Lipofuscinoses. Semin Ophthalmol 2021; 36:582-595. [PMID: 34106804 DOI: 10.1080/08820538.2021.1936571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Neuronal ceroid lipofuscinoses (NCLs) are a group of rare neurodegenerative storage disorders associated with devastating visual prognosis, with an incidence of 1/1,000,000 in the United States and comparatively higher incidence in European countries. The pathophysiological mechanisms causing NCLs occur due to enzymatic or transmembrane defects in various sub-cellular organelles including lysosomes, endoplasmic reticulum, and cytoplasmic vesicles. NCLs are categorized into different types depending upon the underlying cause i.e., soluble lysosomal enzyme deficiencies or non-enzymatic deficiencies (functions of identified proteins), which are sub-divided based on an axial classification system. In this review, we have evaluated the current evidence in the literature and reported the incidence rates, underlying mechanisms and currently available management protocols for these rare set of neuroophthalmological disorders. Additionally, we also highlighted the potential therapies under development that can expand the treatment of these rare disorders beyond symptomatic relief.
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Affiliation(s)
- Rohan Bir Singh
- Massachusetts Eye and Ear, Department of Ophthalmology, Harvard Medical School, Boston, MA, USA.,Department of Ophthalmology, Leiden University Medical Center, Leiden, The Netherlands
| | - Prakash Gupta
- Department of Internal Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - Akash Kartik
- Department of Hepatobiliary and Pancreatic Surgery, Mayo Clinic, Rochester, MN, USA
| | - Naba Farooqui
- Department of Internal Medicine, Mayo Clinic, Rochester, MN, USA
| | - Sachi Singhal
- Department of Internal Medicine, Mayo Clinic, Rochester, MN, USA
| | - Sukhman Shergill
- Department of Anesthesiology, Yale-New Haven Hospital, New Haven, CT, USA
| | - Kanwar Partap Singh
- Department of Ophthalmology, Dayanand Medical College & Hospital, Ludhiana, India
| | - Aniruddha Agarwal
- Eye Institute, Cleveland Clinic Abu Dhabi, Abu Dhabi, United Arab Emirates
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Pesaola F, Quassollo G, Venier AC, De Paul AL, Noher I, Bisbal M. The neuronal ceroid lipofuscinosis-related protein CLN8 regulates endo-lysosomal dynamics and dendritic morphology. Biol Cell 2021; 113:419-437. [PMID: 34021618 DOI: 10.1111/boc.202000016] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 05/18/2021] [Accepted: 05/22/2021] [Indexed: 11/29/2022]
Abstract
BACKGROUND INFORMATION The endo-lysosomal system (ELS) comprises a set of membranous organelles responsible for transporting intracellular and extracellular components within cells. Defects in lysosomal proteins usually affect a large variety of processes and underlie many diseases, most of them with a strong neuronal impact. Mutations in the endoplasmic reticulum-resident CLN8 protein cause CLN8 disease. This condition is one of the 14 known neuronal ceroid lipofuscinoses (NCLs), a group of inherited diseases characterised by accumulation of lipofuscin-like pigments within lysosomes. Besides mediating the transport of soluble lysosomal proteins, recent research suggested a role for CLN8 in the transport of vesicles and lipids, and autophagy. However, the consequences of CLN8 deficiency on ELS structure and activity, as well as the potential impact on neuronal development, remain poorly characterised. Therefore, we performed CLN8 knockdown in neuronal and non-neuronal cell models to analyse structural, dynamic and functional changes in the ELS and to assess the impact of CLN8 deficiency on axodendritic development. RESULTS CLN8 knockdown increased the size of the Golgi apparatus, the number of mobile vesicles and the speed of endo-lysosomes. Using the fluorescent fusion protein mApple-LAMP1-pHluorin, we detected significant lysosomal alkalisation in CLN8-deficient cells. In turn, experiments in primary rat hippocampal neurons showed that CLN8 deficiency decreased the complexity and size of the somatodendritic compartment. CONCLUSIONS Our results suggest the participation of CLN8 in vesicular distribution, lysosomal pH and normal development of the dendritic tree. We speculate that the defects triggered by CLN8 deficiency on ELS structure and dynamics underlie morphological alterations in neurons, which ultimately lead to the characteristic neurodegeneration observed in this NCL. SIGNIFICANCE This is, to our knowledge, the first characterisation of the effects of CLN8 dysfunction on the structure and dynamics of the ELS. Moreover, our findings suggest a novel role for CLN8 in somatodendritic development, which may account at least in part for the neuropathological manifestations associated with CLN8 disease.
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Affiliation(s)
- Favio Pesaola
- Programa de Investigación Translacional de Lipofuscinosis Ceroidea Neuronal, Hospital de Niños de Córdoba, Córdoba, 5014, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto de Investigaciones Médicas "Mercedes y Martin Ferreyra"- IMMF-UNC-CONICET, Laboratorio de Neurobiología, Av. Friuli 2434, 5016 Córdoba, Argentina, Universidad Nacional de Córdoba, Córdoba, 5000, Argentina
| | - Gonzalo Quassollo
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto de Investigaciones Médicas "Mercedes y Martin Ferreyra"- IMMF-UNC-CONICET, Laboratorio de Neurobiología, Av. Friuli 2434, 5016 Córdoba, Argentina, Universidad Nacional de Córdoba, Córdoba, 5000, Argentina
| | - Ana Clara Venier
- Programa de Investigación Translacional de Lipofuscinosis Ceroidea Neuronal, Hospital de Niños de Córdoba, Córdoba, 5014, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto de Investigación en Ciencias de la Salud (INICSA), Bv. de la Reforma y Enfermera Gordillo, Ciudad Universitaria, Córdoba, 5016, Argentina
| | - Ana Lucía De Paul
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto de Investigación en Ciencias de la Salud (INICSA), Bv. de la Reforma y Enfermera Gordillo, Ciudad Universitaria, Córdoba, 5016, Argentina.,Universidad Nacional de Córdoba, Facultad de Ciencias Médicas, Centro de Microscopía Electrónica, Bv. de la Reforma y Enfermera Gordillo, Ciudad Universitaria, Córdoba, 5016, Argentina
| | - Ines Noher
- Programa de Investigación Translacional de Lipofuscinosis Ceroidea Neuronal, Hospital de Niños de Córdoba, Córdoba, 5014, Argentina
| | - Mariano Bisbal
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto de Investigaciones Médicas "Mercedes y Martin Ferreyra"- IMMF-UNC-CONICET, Laboratorio de Neurobiología, Av. Friuli 2434, 5016 Córdoba, Argentina, Universidad Nacional de Córdoba, Córdoba, 5000, Argentina.,Instituto Universitario de Ciencias Biomédicas Córdoba, Córdoba, 5016, Argentina
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