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Zhou W, Wang C, Fu L, Shi W, Zhang A, Jia Z, Zhao X, Fu D, Zheng B. Copy number variants at 4q31.3 affecting the regulatory region of FBXW7 associated with neurodevelopmental delay. Clin Genet 2024; 106:354-359. [PMID: 38780184 DOI: 10.1111/cge.14548] [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: 01/11/2024] [Revised: 05/07/2024] [Accepted: 05/08/2024] [Indexed: 05/25/2024]
Abstract
Emerging research has demonstrated that genomic alterations disrupting topologically associated domains (TADs) and chromatin interactions underlie the pathogenic mechanisms of specific copy number variants (CNVs) in neurodevelopmental disorders. We report two patients with a de novo deletion and a duplication in chromosome 4q31, potentially causing FBX-related neurodevelopmental syndrome by affecting the regulatory region of FBXW7. High-throughput chromosome conformation capture (Hi-C) analysis using available capture data in neural progenitor cells revealed the rewiring of the TAD boundary close to FBXW7. Both patients exhibited facial dysmorphisms, cardiac and limb abnormalities, and neurodevelopmental delays, showing significant clinical overlap with previously reported FBXW7-related features. We also included an additional 10 patients with CNVs in the 4q31 region from the literature and the DECIPHER database for Hi-C analysis, which confirmed that disruption of the regulatory region of FBXW7 likely contributes to the developmental defects observed in these patients.
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Affiliation(s)
- Wei Zhou
- Nanjing Key Laboratory of Pediatrics, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Chunli Wang
- Nanjing Key Laboratory of Pediatrics, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Luhan Fu
- Nanjing Key Laboratory of Pediatrics, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Wei Shi
- Nanjing Key Laboratory of Pediatrics, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Aihua Zhang
- Nanjing Key Laboratory of Pediatrics, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Zhanjun Jia
- Nanjing Key Laboratory of Pediatrics, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Xiaoke Zhao
- Department of Rehabilitation Medicine, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Dalin Fu
- Department of Rehabilitation Medicine, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Bixia Zheng
- Nanjing Key Laboratory of Pediatrics, Children's Hospital of Nanjing Medical University, Nanjing, China
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2
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Tamura T, Shimojima Yamamoto K, Tohyama J, Morioka I, Kanno H, Yamamoto T. Reciprocal chromosome translocation t(3;4)(q27;q31.2) with deletion of 3q27 and reduced FBXW7 expression in a patient with developmental delay, hypotonia, and seizures. J Hum Genet 2024:10.1038/s10038-024-01286-x. [PMID: 39123068 DOI: 10.1038/s10038-024-01286-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Revised: 07/26/2024] [Accepted: 08/01/2024] [Indexed: 08/12/2024]
Abstract
Reciprocal chromosomal translocation is one of genomic variations. When cytogenetically de novo reciprocal translocations are identified in patients with some clinical manifestations, the genes in the breakpoints are considered to be related to the clinical features. In this study, we encountered a patient with severe developmental delay, intractable epilepsy, growth failure, distinctive features, and skeletal manifestations. Conventional karyotyping revealed a de novo translocation described as 46,XY,t(3;4)(q27;q31.2). Chromosomal microarray testing detected a 1.25-Mb microdeletion at 3q27.3q28. Although the skeletal manifestations may have been affected by this deletion, the neurological features of this patient were severe and could not be fully explained by this deletion. Since no genomic copy number aberration was detected on chromosome 4, long-read whole-genome sequencing analysis was performed and a precise breakpoint was confirmed. A 460-bp deletion was detected between the two breakpoints; however, no gene was disrupted. FBXW7, the gene responsible for developmental delay, hypotonia, and impaired language, is in the 0.5-Mb telomeric region. Most of the patient's clinical features were considered consistent with symptoms of FBXW7-related disorders, but were more severe. FBXW7 expression in the immortalized lymphoblasts of the patient was reduced compared to that in controls. Based on these findings, we suspect that FBXW7 is affected by downstream position effects of chromosomal translocations. The severe neurological features of the patient may have been affected not only by the 3q27-q28 deletion but also by impaired expression of FBXW7 derived from the breakage of chromosome 4.
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Affiliation(s)
- Takeaki Tamura
- Department of Pediatrics and Child Health, Nihon University School of Medicine, Tokyo, Japan
- Division of Gene Medicine, Graduate School of Medical Science, Tokyo Women's Medical University, Tokyo, Japan
- Department of Transfusion Medicine and Cell Processing, Tokyo Women's Medical University, Tokyo, Japan
| | - Keiko Shimojima Yamamoto
- Department of Transfusion Medicine and Cell Processing, Tokyo Women's Medical University, Tokyo, Japan
- Institute of Medical Genetics, Tokyo Women's Medical University, Tokyo, Japan
| | - Jun Tohyama
- Department of Child Neurology, National Hospital Organization Nishiniigata Chuo Hospital, Niigata, Japan
| | - Ichiro Morioka
- Department of Pediatrics and Child Health, Nihon University School of Medicine, Tokyo, Japan
| | - Hitoshi Kanno
- Department of Transfusion Medicine and Cell Processing, Tokyo Women's Medical University, Tokyo, Japan
| | - Toshiyuki Yamamoto
- Division of Gene Medicine, Graduate School of Medical Science, Tokyo Women's Medical University, Tokyo, Japan.
- Institute of Medical Genetics, Tokyo Women's Medical University, Tokyo, Japan.
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Meier-Abt F, Kraemer D, Braun N, Reinehr M, Stutz-Grunder E, Steindl K, Rauch A. Further evidence that the neurodevelopmental gene FBXW7 predisposes to Wilms tumor. Am J Med Genet A 2024; 194:e63528. [PMID: 38169111 DOI: 10.1002/ajmg.a.63528] [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: 11/20/2023] [Revised: 12/19/2023] [Accepted: 12/20/2023] [Indexed: 01/05/2024]
Abstract
Somatic variants in the NOTCH pathway regulator FBXW7 are frequently seen in a variety of malignancies. Heterozygous loss-of-function germline variants in FBXW7 have recently been described as causative for a neurodevelopmental syndrome. Independently, FBXW7 was also considered as a susceptibility gene for Wilms tumor due to a few observations of heterozygous germline variants in patients with Wilms tumor. Whether the same FBXW7 variants are implicated in both, neurodevelopmental delay and Wilms tumor formation, remained unclear. By clinical testing, we now observed a patient with neurodevelopmental delay due to a de novo constitutional mosaic FBXW7 splice site pathogenic variant who developed Wilms tumor. In the tumor, we identified a second hit frameshift variant in FBXW7. Immunohistochemical staining was consistent with mosaic loss of FBXW7 protein expression in the tumor. Our data support the role of constitutional FBXW7 pathogenic variants in both, neurodevelopmental disorder and the etiology of Wilms tumor. Therefore, Wilms tumor screening should be considered in individuals with constitutional or germline pathogenic variants in FBXW7 and associated neurodevelopmental syndrome.
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Affiliation(s)
- Fabienne Meier-Abt
- Institute of Medical Genetics, University of Zurich, Schlieren, Switzerland
- Department of Medical Oncology and Hematology, University Hospital Zurich, Zurich, Switzerland
| | - Dennis Kraemer
- Institute of Medical Genetics, University of Zurich, Schlieren, Switzerland
| | - Nils Braun
- Institute of Medical Genetics, University of Zurich, Schlieren, Switzerland
| | - Michael Reinehr
- Department of Pathology, University Hospital Zurich, Zurich, Switzerland
| | | | - Katharina Steindl
- Institute of Medical Genetics, University of Zurich, Schlieren, Switzerland
| | - Anita Rauch
- Institute of Medical Genetics, University of Zurich, Schlieren, Switzerland
- University Children's Hospital Zurich, Zurich, Switzerland
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Nishio Y, Kato K, Oishi H, Takahashi Y, Saitoh S. MYCN in human development and diseases. Front Oncol 2024; 14:1417607. [PMID: 38884091 PMCID: PMC11176553 DOI: 10.3389/fonc.2024.1417607] [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: 04/15/2024] [Accepted: 05/15/2024] [Indexed: 06/18/2024] Open
Abstract
Somatic mutations in MYCN have been identified across various tumors, playing pivotal roles in tumorigenesis, tumor progression, and unfavorable prognoses. Despite its established notoriety as an oncogenic driver, there is a growing interest in exploring the involvement of MYCN in human development. While MYCN variants have traditionally been associated with Feingold syndrome type 1, recent discoveries highlight gain-of-function variants, specifically p.(Thr58Met) and p.(Pro60Leu), as the cause for megalencephaly-polydactyly syndrome. The elucidation of cellular and murine analytical data from both loss-of-function (Feingold syndrome model) and gain-of-function models (megalencephaly-polydactyly syndrome model) is significantly contributing to a comprehensive understanding of the physiological role of MYCN in human development and pathogenesis. This review discusses the MYCN's functional implications for human development by reviewing the clinical characteristics of these distinct syndromes, Feingold syndrome, and megalencephaly-polydactyly syndrome, providing valuable insights into the understanding of pathophysiological backgrounds of other syndromes associated with the MYCN pathway and the overall comprehension of MYCN's role in human development.
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Affiliation(s)
- Yosuke Nishio
- Department of Pediatrics and Neonatology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
- Department of Genetics, Research Institute of Environmental Medicine, Nagoya University, Nagoya, Japan
| | - Kohji Kato
- Department of Pediatrics and Neonatology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
- Department of Genetics, Research Institute of Environmental Medicine, Nagoya University, Nagoya, Japan
| | - Hisashi Oishi
- Department of Comparative and Experimental Medicine, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Yoshiyuki Takahashi
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Shinji Saitoh
- Department of Pediatrics and Neonatology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
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Ash AS, Klifto KM, Willson TD. Craniosynostosis Associated With Novel TUBG1 Mutation (NM_001070.4:c.821C>T) (p.Thr274Ile). Cureus 2024; 16:e61132. [PMID: 38919239 PMCID: PMC11199001 DOI: 10.7759/cureus.61132] [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] [Accepted: 05/26/2024] [Indexed: 06/27/2024] Open
Abstract
TUBG1, a tubulin gene, plays an important role in neurodevelopment. Here we describe a case of a novel TUGB1 mutation (NM_001070.4:c.821C>T) (p.Thr274Ile). This patient presented similarly to previous cases with features including microcephaly, epilepsy, and speech and motor delay. Unique characteristics were also present such as trigonocephaly, tethered frenulum, scoliosis, nystagmus, and a concurrent FBXW7 mutation. This case expands our breadth of knowledge on TUBG1 genotypic and phenotypic variation. However, further work is needed to fully understand this rare mutation and the associations between TUBG1 and FBXW7 mutations.
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Affiliation(s)
- Angela S Ash
- Division of Plastic and Reconstructive Surgery, Department of Surgery, University of Missouri School of Medicine, Columbia, USA
| | - Kevin M Klifto
- Division of Plastic and Reconstructive Surgery, Department of Surgery, University of Missouri School of Medicine, Columbia, USA
| | - Thomas D Willson
- Division of Plastic and Reconstructive Surgery, Department of Surgery, University of Missouri School of Medicine, Columbia, USA
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Tesi B, Robinson KL, Abel F, Díaz de Ståhl T, Orrsjö S, Poluha A, Hellberg M, Wessman S, Samuelsson S, Frisk T, Vogt H, Henning K, Sabel M, Ek T, Pal N, Nyman P, Giraud G, Wille J, Pronk CJ, Norén-Nyström U, Borssén M, Fili M, Stålhammar G, Herold N, Tettamanti G, Maya-Gonzalez C, Arvidsson L, Rosén A, Ekholm K, Kuchinskaya E, Hallbeck AL, Nordling M, Palmebäck P, Kogner P, Smoler GK, Lähteenmäki P, Fransson S, Martinsson T, Shamik A, Mertens F, Rosenquist R, Wirta V, Tham E, Grillner P, Sandgren J, Ljungman G, Gisselsson D, Taylan F, Nordgren A. Diagnostic yield and clinical impact of germline sequencing in children with CNS and extracranial solid tumors-a nationwide, prospective Swedish study. THE LANCET REGIONAL HEALTH. EUROPE 2024; 39:100881. [PMID: 38803632 PMCID: PMC11129334 DOI: 10.1016/j.lanepe.2024.100881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 02/04/2024] [Accepted: 02/23/2024] [Indexed: 05/29/2024]
Abstract
Background Childhood cancer predisposition (ChiCaP) syndromes are increasingly recognized as contributing factors to childhood cancer development. Yet, due to variable availability of germline testing, many children with ChiCaP might go undetected today. We report results from the nationwide and prospective ChiCaP study that investigated diagnostic yield and clinical impact of integrating germline whole-genome sequencing (gWGS) with tumor sequencing and systematic phenotyping in children with solid tumors. Methods gWGS was performed in 309 children at diagnosis of CNS (n = 123, 40%) or extracranial (n = 186, 60%) solid tumors and analyzed for disease-causing variants in 189 known cancer predisposing genes. Tumor sequencing data were available for 74% (227/309) of patients. In addition, a standardized clinical assessment for underlying predisposition was performed in 95% (293/309) of patients. Findings The prevalence of ChiCaP diagnoses was 11% (35/309), of which 69% (24/35) were unknown at inclusion (diagnostic yield 8%, 24/298). A second-hit and/or relevant mutational signature was observed in 19/21 (90%) tumors with informative data. ChiCaP diagnoses were more prevalent among patients with retinoblastomas (50%, 6/12) and high-grade astrocytomas (37%, 6/16), and in those with non-cancer related features (23%, 20/88), and ≥2 positive ChiCaP criteria (28%, 22/79). ChiCaP diagnoses were autosomal dominant in 80% (28/35) of patients, yet confirmed de novo in 64% (18/28). The 35 ChiCaP findings resulted in tailored surveillance (86%, 30/35) and treatment recommendations (31%, 11/35). Interpretation Overall, our results demonstrate that systematic phenotyping, combined with genomics-based diagnostics of ChiCaP in children with solid tumors is feasible in large-scale clinical practice and critically guides personalized care in a sizable proportion of patients. Funding The study was supported by the Swedish Childhood Cancer Fund and the Ministry of Health and Social Affairs.
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Affiliation(s)
- Bianca Tesi
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Clinical Genetics and Genomics, Karolinska University Hospital, Solna, Sweden
- Department of Medicine, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Kristina Lagerstedt Robinson
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Clinical Genetics and Genomics, Karolinska University Hospital, Solna, Sweden
| | - Frida Abel
- Department of Clinical Genetics and Genomics, Sahlgrenska University Hospital, Gothenburg, Sweden
- Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Teresita Díaz de Ståhl
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
- Clinical Pathology and Cancer Diagnostics, Karolinska University Hospital, Stockholm, Sweden
| | - Sara Orrsjö
- Department of Clinical Genetics and Genomics, Sahlgrenska University Hospital, Gothenburg, Sweden
- Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Anna Poluha
- Clinical Genetics, Uppsala University Hospital, Uppsala, Sweden
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Maria Hellberg
- Department of Clinical Genetics, Pathology and Molecular Diagnostics, Office of Medical Services, Region Skåne, Lund, Sweden
| | - Sandra Wessman
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
- Clinical Pathology and Cancer Diagnostics, Karolinska University Hospital, Stockholm, Sweden
| | - Sofie Samuelsson
- Department of Clinical Genetics, Pathology and Molecular Diagnostics, Office of Medical Services, Region Skåne, Lund, Sweden
| | - Tony Frisk
- Department of Pediatric Hematology and Oncology, Karolinska University Hospital, Stockholm, Sweden
- Childhood Cancer Research Unit, Department of Women’s and Children’s Health, Karolinska Institutet, Stockholm, Sweden
| | - Hartmut Vogt
- Crown Princess Victoria Children’s Hospital, and Division of Children’s and Women’s Health, Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Karin Henning
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Pediatric Hematology and Oncology, Karolinska University Hospital, Stockholm, Sweden
| | - Magnus Sabel
- Department of Pediatrics, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Sweden
- Queen Silvia Children’s Hospital, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Torben Ek
- Department of Pediatrics, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Sweden
- Queen Silvia Children’s Hospital, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Niklas Pal
- Department of Pediatric Hematology and Oncology, Karolinska University Hospital, Stockholm, Sweden
| | - Per Nyman
- Department of Health, Medicine and Caring Sciences, Linköping University, Linköping, Sweden
- Centre for Medical Image Science and Visualization (CMIV), Linköping University, Linköping, Sweden
| | - Geraldine Giraud
- Department of Immunology, Genetics, and Pathology, Science for Life Laboratory, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
- Pediatric Oncology, Uppsala University Children’s Hospital, Uppsala, Sweden
- Department of Women’s and Children’s Health, Uppsala University, Sweden
| | - Joakim Wille
- Childhood Cancer Center, Skåne University Hospital, Lund, Sweden
| | - Cornelis Jan Pronk
- Childhood Cancer Center, Skåne University Hospital, Lund, Sweden
- Division of Molecular Hematology/Wallenberg Center for Molecular Medicine, Lund University, Sweden
| | | | - Magnus Borssén
- Department of Clinical Sciences, Pediatrics, Umeå University, Umeå, Sweden
| | - Maria Fili
- Division of Eye and Vision, Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
- St. Erik Eye Hospital, Stockholm, Sweden
| | - Gustav Stålhammar
- Division of Eye and Vision, Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
- St. Erik Eye Hospital, Stockholm, Sweden
| | - Nikolas Herold
- Department of Pediatric Hematology and Oncology, Karolinska University Hospital, Stockholm, Sweden
- Childhood Cancer Research Unit, Department of Women’s and Children’s Health, Karolinska Institutet, Stockholm, Sweden
| | - Giorgio Tettamanti
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Unit of Epidemiology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | | | - Linda Arvidsson
- Department of Clinical Genetics, Pathology and Molecular Diagnostics, Office of Medical Services, Region Skåne, Lund, Sweden
| | - Anna Rosén
- Department of Radiation Sciences, Oncology, Umeå University, Umeå, Sweden
| | - Katja Ekholm
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Clinical Genetics and Genomics, Karolinska University Hospital, Solna, Sweden
| | | | - Anna-Lotta Hallbeck
- Department of Clinical Genetics, Linköping University Hospital, Linköping, Sweden
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Margareta Nordling
- Department of Clinical Genetics, Linköping University Hospital, Linköping, Sweden
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Pia Palmebäck
- Department of Clinical Genetics, Linköping University Hospital, Linköping, Sweden
| | - Per Kogner
- Department of Pediatric Hematology and Oncology, Karolinska University Hospital, Stockholm, Sweden
- Childhood Cancer Research Unit, Department of Women’s and Children’s Health, Karolinska Institutet, Stockholm, Sweden
| | - Gunilla Kanter Smoler
- Department of Clinical Genetics and Genomics, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Päivi Lähteenmäki
- Childhood Cancer Research Unit, Department of Women’s and Children’s Health, Karolinska Institutet, Stockholm, Sweden
| | - Susanne Fransson
- Department of Clinical Genetics and Genomics, Sahlgrenska University Hospital, Gothenburg, Sweden
- Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Tommy Martinsson
- Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Alia Shamik
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
- Clinical Pathology and Cancer Diagnostics, Karolinska University Hospital, Stockholm, Sweden
| | - Fredrik Mertens
- Department of Clinical Genetics, Pathology and Molecular Diagnostics, Office of Medical Services, Region Skåne, Lund, Sweden
| | - Richard Rosenquist
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Clinical Genetics and Genomics, Karolinska University Hospital, Solna, Sweden
- Genomic Medicine Center Karolinska, Karolinska University Hospital, Stockholm, Sweden
| | - Valtteri Wirta
- Genomic Medicine Center Karolinska, Karolinska University Hospital, Stockholm, Sweden
- Science for Life Laboratory, Department of Microbiology, Tumour and Cell Biology, Karolinska Institutet, Stockholm, Sweden
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institutet of Technology, Stockholm, Sweden
| | - Emma Tham
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Clinical Genetics and Genomics, Karolinska University Hospital, Solna, Sweden
| | - Pernilla Grillner
- Department of Pediatric Hematology and Oncology, Karolinska University Hospital, Stockholm, Sweden
- Childhood Cancer Research Unit, Department of Women’s and Children’s Health, Karolinska Institutet, Stockholm, Sweden
| | - Johanna Sandgren
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
- Clinical Pathology and Cancer Diagnostics, Karolinska University Hospital, Stockholm, Sweden
| | - Gustaf Ljungman
- Pediatric Oncology, Uppsala University Children’s Hospital, Uppsala, Sweden
- Department of Women’s and Children’s Health, Uppsala University, Sweden
| | - David Gisselsson
- Department of Clinical Genetics, Pathology and Molecular Diagnostics, Office of Medical Services, Region Skåne, Lund, Sweden
| | - Fulya Taylan
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Clinical Genetics and Genomics, Karolinska University Hospital, Solna, Sweden
| | - Ann Nordgren
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Clinical Genetics and Genomics, Karolinska University Hospital, Solna, Sweden
- Department of Clinical Genetics and Genomics, Sahlgrenska University Hospital, Gothenburg, Sweden
- Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Genomic Medicine Center Karolinska, Karolinska University Hospital, Stockholm, Sweden
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7
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Serghini A, Portelli S, Troadec G, Song C, Pan Q, Pires DEV, Ascher DB. Characterizing and predicting ccRCC-causing missense mutations in Von Hippel-Lindau disease. Hum Mol Genet 2024; 33:224-232. [PMID: 37883464 PMCID: PMC10800015 DOI: 10.1093/hmg/ddad181] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Revised: 10/19/2023] [Accepted: 10/20/2023] [Indexed: 10/28/2023] Open
Abstract
BACKGROUND Mutations within the Von Hippel-Lindau (VHL) tumor suppressor gene are known to cause VHL disease, which is characterized by the formation of cysts and tumors in multiple organs of the body, particularly clear cell renal cell carcinoma (ccRCC). A major challenge in clinical practice is determining tumor risk from a given mutation in the VHL gene. Previous efforts have been hindered by limited available clinical data and technological constraints. METHODS To overcome this, we initially manually curated the largest set of clinically validated VHL mutations to date, enabling a robust assessment of existing predictive tools on an independent test set. Additionally, we comprehensively characterized the effects of mutations within VHL using in silico biophysical tools describing changes in protein stability, dynamics and affinity to binding partners to provide insights into the structure-phenotype relationship. These descriptive properties were used as molecular features for the construction of a machine learning model, designed to predict the risk of ccRCC development as a result of a VHL missense mutation. RESULTS Analysis of our model showed an accuracy of 0.81 in the identification of ccRCC-causing missense mutations, and a Matthew's Correlation Coefficient of 0.44 on a non-redundant blind test, a significant improvement in comparison to the previous available approaches. CONCLUSION This work highlights the power of using protein 3D structure to fully explore the range of molecular and functional consequences of genomic variants. We believe this optimized model will better enable its clinical implementation and assist guiding patient risk stratification and management.
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Affiliation(s)
- Adam Serghini
- School of Chemistry and Molecular Biosciences, Chemistry Building 68, Cooper Road, The University of Queensland, St Lucia, QLD 4072, Queensland, Australia
| | - Stephanie Portelli
- School of Chemistry and Molecular Biosciences, Chemistry Building 68, Cooper Road, The University of Queensland, St Lucia, QLD 4072, Queensland, Australia
| | - Guillaume Troadec
- School of Computing and Information Systems, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Catherine Song
- School of Computing and Information Systems, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Qisheng Pan
- School of Chemistry and Molecular Biosciences, Chemistry Building 68, Cooper Road, The University of Queensland, St Lucia, QLD 4072, Queensland, Australia
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, 75 Commercial Road, Melbourne, VIC 3004, Australia
| | - Douglas E V Pires
- School of Computing and Information Systems, University of Melbourne, Melbourne, VIC 3010, Australia
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, 75 Commercial Road, Melbourne, VIC 3004, Australia
| | - David B Ascher
- School of Chemistry and Molecular Biosciences, Chemistry Building 68, Cooper Road, The University of Queensland, St Lucia, QLD 4072, Queensland, Australia
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, 75 Commercial Road, Melbourne, VIC 3004, Australia
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8
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Rodrigues CHM, Portelli S, Ascher DB. Exploring the effects of missense mutations on protein thermodynamics through structure-based approaches: findings from the CAGI6 challenges. Hum Genet 2024:10.1007/s00439-023-02623-4. [PMID: 38227011 DOI: 10.1007/s00439-023-02623-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 11/18/2023] [Indexed: 01/17/2024]
Abstract
Missense mutations are known contributors to diverse genetic disorders, due to their subtle, single amino acid changes imparted on the resultant protein. Because of this, understanding the impact of these mutations on protein stability and function is crucial for unravelling disease mechanisms and developing targeted therapies. The Critical Assessment of Genome Interpretation (CAGI) provides a valuable platform for benchmarking state-of-the-art computational methods in predicting the impact of disease-related mutations on protein thermodynamics. Here we report the performance of our comprehensive platform of structure-based computational approaches to evaluate mutations impacting protein structure and function on 3 challenges from CAGI6: Calmodulin, MAPK1 and MAPK3. Our stability predictors have achieved correlations of up to 0.74 and AUCs of 1 when predicting changes in ΔΔG for MAPK1 and MAPK3, respectively, and AUC of up to 0.75 in the Calmodulin challenge. Overall, our study highlights the importance of structure-based approaches in understanding the effects of missense mutations on protein thermodynamics. The results obtained from the CAGI6 challenges contribute to the ongoing efforts to enhance our understanding of disease mechanisms and facilitate the development of personalised medicine approaches.
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Affiliation(s)
- Carlos H M Rodrigues
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, VIC, 3004, Australia
- School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, QLD, 4072, Australia
| | - Stephanie Portelli
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, VIC, 3004, Australia
- School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, QLD, 4072, Australia
| | - David B Ascher
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, VIC, 3004, Australia.
- School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, QLD, 4072, Australia.
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9
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Abstract
The greatest challenge in drug discovery remains the high rate of attrition across the different phases of the process, which cost the industry billions of dollars every year. While all phases remain crucial to ensure pharmaceutical-level safety, quality, and efficacy of the end product, streamlining these efforts toward compounds with success potential is pivotal for a more efficient and cost-effective process. The use of artificial intelligence (AI) within the pharmaceutical industry aims at just this, and has applications in preclinical screening for biological activity, optimization of pharmacokinetic properties for improved drug formulation, early toxicity prediction which reduces attrition, and pre-emptively screening for genetic changes in the biological target to improve therapeutic longevity. Here, we present a series of in silico tools that address these applications in small molecule development and describe how they can be embedded within the current pharmaceutical development pipeline.
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Affiliation(s)
- Adam Serghini
- School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, QLD, Australia
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, VIC, Australia
| | - Stephanie Portelli
- School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, QLD, Australia.
| | - David B Ascher
- School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, QLD, Australia.
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, VIC, Australia.
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10
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Binan L, Danquah S, Valakh V, Simonton B, Bezney J, Nehme R, Cleary B, Farhi SL. Simultaneous CRISPR screening and spatial transcriptomics reveals intracellular, intercellular, and functional transcriptional circuits. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.30.569494. [PMID: 38076932 PMCID: PMC10705493 DOI: 10.1101/2023.11.30.569494] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/17/2023]
Abstract
Pooled optical screens have enabled the study of cellular interactions, morphology, or dynamics at massive scale, but have not yet leveraged the power of highly-plexed single-cell resolved transcriptomic readouts to inform molecular pathways. Here, we present Perturb-FISH, which bridges these approaches by combining imaging spatial transcriptomics with parallel optical detection of in situ amplified guide RNAs. We show that Perturb-FISH recovers intracellular effects that are consistent with Perturb-seq results in a screen of lipopolysaccharide response in cultured monocytes, and uncover new intercellular and density-dependent regulation of the innate immune response. We further pair Perturb-FISH with a functional readout in a screen of autism spectrum disorder risk genes, showing common calcium activity phenotypes in induced pluripotent stem cell derived astrocytes and their associated genetic interactions and dysregulated molecular pathways. Perturb-FISH is thus a generally applicable method for studying the genetic and molecular associations of spatial and functional biology at single-cell resolution.
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Affiliation(s)
- Loϊc Binan
- Spatial Technology Platform, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Serwah Danquah
- Spatial Technology Platform, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Vera Valakh
- Spatial Technology Platform, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Brooke Simonton
- Present address: The Ken & Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA. (Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA)
| | - Jon Bezney
- Present address: Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA. (Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA)
| | - Ralda Nehme
- Spatial Technology Platform, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Brian Cleary
- Faculty of Computing and Data Sciences, Boston University, Boston, MA, USA; Department of Biology, Boston University, Boston, MA, USA; Department of Biomedical Engineering, Boston University, Boston, MA, USA; Program in Bioinformatics, Boston University, Boston, MA, USA; Biological Design Center, Boston University, Boston, MA, USA
| | - Samouil L Farhi
- Spatial Technology Platform, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
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11
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Nair VM, Sabu AS, Hussain A, Kombarakkaran DP, Lakshmi RB, Manna TK. E3-ubiquitin ligase, FBXW7 regulates mitotic progression by targeting BubR1 for ubiquitin-mediated degradation. Cell Mol Life Sci 2023; 80:374. [PMID: 38008853 PMCID: PMC11072012 DOI: 10.1007/s00018-023-05019-9] [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: 07/09/2023] [Revised: 10/17/2023] [Accepted: 10/26/2023] [Indexed: 11/28/2023]
Abstract
Faithful chromosome segregation requires correct attachment of kinetochores with the spindle microtubules. Erroneously-attached kinetochores recruit proteins to activate Spindle assembly checkpoint (SAC), which senses the errors and signals cells to delay anaphase progression for error correction. Temporal control of the levels of SAC activating-proteins is critical for checkpoint activation and silencing, but its mechanism is not fully understood. Here, we show that E3 ubiquitin ligase, SCF-FBXW7 targets BubR1 for ubiquitin-mediated degradation and thereby controls SAC in human cells. Depletion of FBXW7 results in prolonged metaphase arrest with increased stabilization of BubR1 at kinetochores. Similar kinetochore stabilization is also observed for BubR1-interacting protein, CENP-E. FBXW7 induced ubiquitination of both BubR1 and the BubR1-interacting kinetochore-targeting domain of CENP-E, but CENP-E domain degradation is dependent on BubR1. Interestingly, Cdk1 inhibition disrupts FBXW7-mediated BubR1 targeting and further, phospho-resistant mutation of Cdk1-targeted phosphorylation site, Thr 620 impairs BubR1-FBXW7 interaction and FBXW7-mediated BubR1 ubiquitination, supporting its role as a phosphodegron for FBXW7. The results demonstrate SCF-FBXW7 as a key regulator of spindle assembly checkpoint that controls stability of BubR1 and its associated CENP-E at kinetochores. They also support that upstream Cdk1 specific BubR1 phosphorylation signals the ligase to activate the process.
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Affiliation(s)
- Vishnu M Nair
- School of Biology, Indian Institute of Science Education and Research, Thiruvananthapuram, Vithura, Thiruvananthapuram, Kerala, 695551, India
| | - Amit Santhu Sabu
- School of Biology, Indian Institute of Science Education and Research, Thiruvananthapuram, Vithura, Thiruvananthapuram, Kerala, 695551, India
| | - Ahmed Hussain
- School of Biology, Indian Institute of Science Education and Research, Thiruvananthapuram, Vithura, Thiruvananthapuram, Kerala, 695551, India
| | - Delvin P Kombarakkaran
- School of Biology, Indian Institute of Science Education and Research, Thiruvananthapuram, Vithura, Thiruvananthapuram, Kerala, 695551, India
| | - R Bhagya Lakshmi
- School of Biology, Indian Institute of Science Education and Research, Thiruvananthapuram, Vithura, Thiruvananthapuram, Kerala, 695551, India
| | - Tapas K Manna
- School of Biology, Indian Institute of Science Education and Research, Thiruvananthapuram, Vithura, Thiruvananthapuram, Kerala, 695551, India.
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12
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Massri AJ, Fitzpatrick M, Cunny H, Li JL, Harry GJ. Differential gene expression profiling implicates altered network development in rat postnatal day 4 cortex following 4-Methylimidazole (4-MeI) induced maternal seizures. Neurotoxicol Teratol 2023; 100:107301. [PMID: 37783441 PMCID: PMC10843020 DOI: 10.1016/j.ntt.2023.107301] [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: 06/23/2023] [Revised: 08/31/2023] [Accepted: 09/19/2023] [Indexed: 10/04/2023]
Abstract
Compromised maternal health leading to maternal seizures can have adverse effects on the healthy development of offspring. This may be the result of inflammation, hypoxia-ischemia, and altered GABA signaling. The current study examined cortical tissue from F2b (2nd litter of the 2nd generation) postnatal day 4 (PND4) offspring of female Harlan SD rats chronically exposed to the seizuregenic compound, 4-Methylimidazole (0, 750, or 2500 ppm 4-MeI). Maternal seizures were evident only at 2500 ppm 4-MeI. GABA related gene expression as examined by qRT-PCR and whole genome microarray showed no indication of disrupted GABA or glutamatergic signaling. Canonical pathway hierarchical clustering and multi-omics combinatory genomic (CNet) plots of differentially expressed genes (DEG) showed alterations in genes associated with regulatory processes of cell development including neuronal differentiation and synaptogenesis. Functional enrichment analysis showed a similarity of cellular processes across the two exposure groups however, the genes comprising each cluster were primarily unique rather than shared and often showed different directionality. A dose-related induction of cytokine signaling was indicated however, pathways associated with individual cytokine signaling were not elevated, suggesting an alternative involvement of cytokine signaling. Pathways related to growth process and cell signaling showed a negative activation supporting an interpretation of disruption or delay in developmental processes at the 2500 ppm 4-MeI exposure level with maternal seizures. Thus, while GABA signaling was not altered as has been observed with maternal seizures, the pattern of DEG suggested a potential for alteration in neuronal network formation.
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Affiliation(s)
- Abdull J Massri
- Integrative Bioinformatics, Division of Intramural Research, National Institute of Environmental Health Sciences, National Institutes of Health, 111 T. W. Alexander Drive, Research Triangle Park, NC 27709, USA
| | - Mackenzie Fitzpatrick
- Mechanistic Toxicology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, 111 T. W. Alexander Drive, Research Triangle Park, NC 27709, USA
| | - Helen Cunny
- Office of the Scientific Director, Division of Translational Toxicology, National Institute of Environmental Health Sciences, National Institutes of Health, 111 T. W. Alexander Drive, Research Triangle Park, NC 27709, USA
| | - Jian-Liang Li
- Integrative Bioinformatics, Division of Intramural Research, National Institute of Environmental Health Sciences, National Institutes of Health, 111 T. W. Alexander Drive, Research Triangle Park, NC 27709, USA
| | - G Jean Harry
- Mechanistic Toxicology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, 111 T. W. Alexander Drive, Research Triangle Park, NC 27709, USA.
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13
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Tang M, Suraweera A, Nie X, Li Z, Lai P, Wells JW, O'Byrne KJ, Woods RJ, Bolderson E, Richard DJ. Mono-phosphorylation at Ser4 of barrier-to-autointegration factor (Banf1) significantly reduces its DNA binding capability by inducing critical changes in its local conformation and DNA binding surface. Phys Chem Chem Phys 2023; 25:24657-24677. [PMID: 37665626 DOI: 10.1039/d3cp02302h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Barrier-to-autointegration factor (Banf1) is a small DNA-bridging protein. The binding status of Banf1 to DNA is regulated by its N-terminal phosphorylation and dephosphorylation, which plays a critical role in cell proliferation. Banf1 can be phosphorylated at Ser4 into mono-phosphorylated Banf1, which is further phosphorylated at Thr3 to form di-phosphorylated Banf1. It was observed decades ago that mono-phosphorylated Banf1 cannot bind to DNA. However, the underlying molecular- and atomic-level mechanisms remain unclear. A clear understanding of these mechanisms will aid in interfering with the cell proliferation process for better global health. Herein, we explored the detailed atomic bases of unphosphorylated Banf1-DNA binding and how mono- and di-phosphorylation of Banf1 impair these atomic bases to eliminate its DNA-binding capability, followed by exploring the DNA-binding capability of mono- and di-phosphorylation Banf1, using comprehensive and systematic molecular modelling and molecular dynamics simulations. This work presented in detail the residue-level binding energies, hydrogen bonds and water bridges between Banf1 and DNA, some of which have not been reported. Moreover, we revealed that mono-phosphorylation of Banf1 causes its N-terminal secondary structure changes, which in turn induce significant changes in Banf1's DNA binding surface, thus eliminating its DNA-binding capability. At the atomic level, we also uncovered the alterations in interactions due to the induction of mono-phosphorylation that result in the N-terminal secondary structure changes of Banf1. Additionally, our modelling showed that phosphorylated Banf1 with their dominant N-terminal secondary structures bind to DNA with a significantly lower affinity and the docked binding pose are not stable in MD simulations. These findings help future studies in predicting effect of mutations in Banf1 on its DNA-binding capability and open a novel avenue for the development of therapeutics such as cancer drugs, targeting cell proliferation by inducing conformational changes in Banf1's N-terminal domain.
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Affiliation(s)
- Ming Tang
- Cancer and Ageing Research Program, Centre for Genomics and Personalised Health, Queensland University of Technology at the Translational Research Institute Australia, Brisbane, Australia.
- Faculty of Medicine, Frazer Institute, The University of Queensland at the Translational Research Institute Australia, Brisbane, Australia
| | - Amila Suraweera
- Cancer and Ageing Research Program, Centre for Genomics and Personalised Health, Queensland University of Technology at the Translational Research Institute Australia, Brisbane, Australia.
| | - Xuqiang Nie
- Cancer and Ageing Research Program, Centre for Genomics and Personalised Health, Queensland University of Technology at the Translational Research Institute Australia, Brisbane, Australia.
- College of Pharmacy, Key Lab of the Basic Pharmacology of the Ministry of Education, Zunyi Medical University, Zunyi, China
| | - Zilin Li
- School of Mechanics and Safety Engineering, Zhengzhou University, Zhengzhou 450001, China
- School of Mechanical, Medical and Process Engineering, Queensland University of Technology, Brisbane, Australia
| | - Pinglin Lai
- Academy of Orthopedics Guangdong Province, Guangdong Provincial Key Laboratory of Bone and Joint Degeneration Diseases, The Third Affiliated Hospital, Southern Medical University, Guangzhou, China
| | - James W Wells
- Faculty of Medicine, Frazer Institute, The University of Queensland at the Translational Research Institute Australia, Brisbane, Australia
| | - Kenneth J O'Byrne
- Cancer and Ageing Research Program, Centre for Genomics and Personalised Health, Queensland University of Technology at the Translational Research Institute Australia, Brisbane, Australia.
- Princess Alexandra Hospital, Brisbane, Australia
| | - Robert J Woods
- Complex Carbohydrate Research Centre, University of Georgia, 315 Riverbend Rd, Athens, GA, 30602, USA
| | - Emma Bolderson
- Cancer and Ageing Research Program, Centre for Genomics and Personalised Health, Queensland University of Technology at the Translational Research Institute Australia, Brisbane, Australia.
| | - Derek J Richard
- Cancer and Ageing Research Program, Centre for Genomics and Personalised Health, Queensland University of Technology at the Translational Research Institute Australia, Brisbane, Australia.
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14
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van Eyk CL, Fahey MC, Gecz J. Redefining cerebral palsies as a diverse group of neurodevelopmental disorders with genetic aetiology. Nat Rev Neurol 2023; 19:542-555. [PMID: 37537278 DOI: 10.1038/s41582-023-00847-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/28/2023] [Indexed: 08/05/2023]
Abstract
Cerebral palsy is a clinical descriptor covering a diverse group of permanent, non-degenerative disorders of motor function. Around one-third of cases have now been shown to have an underlying genetic aetiology, with the genetic landscape overlapping with those of neurodevelopmental disorders including intellectual disability, epilepsy, speech and language disorders and autism. Here we review the current state of genomic testing in cerebral palsy, highlighting the benefits for personalized medicine and the imperative to consider aetiology during clinical diagnosis. With earlier clinical diagnosis now possible, we emphasize the opportunity for comprehensive and early genomic testing as a crucial component of the routine diagnostic work-up in people with cerebral palsy.
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Affiliation(s)
- Clare L van Eyk
- Adelaide Medical School, The University of Adelaide, Adelaide, South Australia, Australia
- Robinson Research Institute, The University of Adelaide, Adelaide, South Australia, Australia
| | - Michael C Fahey
- Department of Paediatrics, Monash University, Melbourne, Victoria, Australia
| | - Jozef Gecz
- Adelaide Medical School, The University of Adelaide, Adelaide, South Australia, Australia.
- Robinson Research Institute, The University of Adelaide, Adelaide, South Australia, Australia.
- South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia.
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15
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Ennis H, McDonald DM. A widely used pan-isoform-FBXW7 antibody used in cell cycle studies does not detect FBXW7. Cell Cycle 2023; 22:1380-1390. [PMID: 37183425 DOI: 10.1080/15384101.2023.2210044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2023] Open
Abstract
FBXW7 is the substrate recognition component of the E3 ubiquitin ligase SCFFBW7 complex which controls the levels of CYCLINE, c-MYC and HIF1α proteins crucial for cell growth and differentiation. Mutations in FBXW7 are frequently associated with tumourigenesis. While examining FBXW7 regulation we were compelled to reevaluate a commonly used anti-FBXW7 antibody. Retinal microvascular endothelial cells (RMEC) were exposed to normoxia (21% oxygen) or hypoxia (1% oxygen) for 24 h or treated with MG132 and protein extracted for western blotting. Flag-tagged FBXW7-α, β or γ isoforms were transfected into HEK293A cells and processed using denaturing and native extraction protocols for western blotting or immunoprecipitation analysis. Two anti-FBXW7 antibodies were used, one raised to the unique FBXW7α N-terminus and the other to the C-terminus region common to all isoforms. Initial studies showed that the pan-isoform C-terminus antibody detected a single 64kDa band in RMEC rather than any of the predicted sizes for FBXW7. In contrast, expression of the isoform-specific constructs, detected with an anti-Flag antibody, confirmed the expected migratory distance of 110kDa, 68kDa and 65kDa for α, β and γ respectfully. Similarly, the N-terminus FBXW7α antibody also detected the 110kDa product. Notably, the C-terminus antibody did not recognize any of the isoforms but continued to detect a 64kDa band in all samples, including the non-transfected controls. Immunoprecipitation confirmed this lack of specificity and the inability to detect overexpressed or endogenous FBXW7α in HEK293A cells and RMEC. A commonly used C-terminus FBXW7 antibody does not detect FBXW7 under standard western blotting conditions.
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Affiliation(s)
- Hannah Ennis
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, Belfast, UK
| | - Denise M McDonald
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, Belfast, UK
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16
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Nussinov R, Yavuz BR, Arici MK, Demirel HC, Zhang M, Liu Y, Tsai CJ, Jang H, Tuncbag N. Neurodevelopmental disorders, like cancer, are connected to impaired chromatin remodelers, PI3K/mTOR, and PAK1-regulated MAPK. Biophys Rev 2023; 15:163-181. [PMID: 37124926 PMCID: PMC10133437 DOI: 10.1007/s12551-023-01054-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 03/21/2023] [Indexed: 04/05/2023] Open
Abstract
AbstractNeurodevelopmental disorders (NDDs) and cancer share proteins, pathways, and mutations. Their clinical symptoms are different. However, individuals with NDDs have higher probabilities of eventually developing cancer. Here, we review the literature and ask how the shared features can lead to different medical conditions and why having an NDD first can increase the chances of malignancy. To explore these vital questions, we focus on dysregulated PI3K/mTOR, a major brain cell growth pathway in differentiation, and MAPK, a critical pathway in proliferation, a hallmark of cancer. Differentiation is governed by chromatin organization, making aberrant chromatin remodelers highly likely agents in NDDs. Dysregulated chromatin organization and accessibility influence the lineage of specific cell brain types at specific embryonic development stages. PAK1, with pivotal roles in brain development and in cancer, also regulates MAPK. We review, clarify, and connect dysregulated pathways with dysregulated proliferation and differentiation in cancer and NDDs and highlight PAK1 role in brain development and MAPK regulation. Exactly how PAK1 activation controls brain development, and why specific chromatin remodeler components, e.g., BAF170 encoded by SMARCC2 in autism, await clarification.
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17
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Lu AKM, Hsieh S, Yang CT, Wang XY, Lin SH. DNA methylation signature of psychological resilience in young adults: Constructing a methylation risk score using a machine learning method. Front Genet 2023; 13:1046700. [PMID: 36712885 PMCID: PMC9877348 DOI: 10.3389/fgene.2022.1046700] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 12/29/2022] [Indexed: 01/15/2023] Open
Abstract
Resilience is a process associated with the ability to recover from stress and adversity. We aimed to explore the resilience-associated DNA methylation signatures and evaluate the abilities of methylation risk scores to discriminate low resilience (LR) individuals. The study recruited 78 young adults and used Connor-Davidson Resilience Scale (CD-RISC) to divide them into low and high resilience groups. We randomly allocated all participants of two groups to the discovery and validation sets. We used the blood DNA of the subjects to conduct a genome-wide methylation scan and identify the significant methylation differences of CpG Sites in the discovery set. Moreover, the classification accuracy of the DNA methylation probes was confirmed in the validation set by real-time quantitative methylation-specific polymerase chain reaction. In the genome-wide methylation profiling between LR and HR individuals, seventeen significantly differentially methylated probes were detected. In the validation set, nine DNA methylation signatures within gene coding regions were selected for verification. Finally, three methylation probes [cg18565204 (AARS), cg17682313 (FBXW7), and cg07167608 (LINC01107)] were included in the final model of the methylation risk score for LR versus HR. These methylation risk score models of low resilience demonstrated satisfactory discrimination by logistic regression and support vector machine, with an AUC of 0.81 and 0.93, accuracy of 72.3% and 87.1%, sensitivity of 75%, and 87.5%, and specificity of 70% and 80%. Our findings suggest that methylation signatures can be utilized to identify individuals with LR and establish risk score models that may contribute to the field of psychology.
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Affiliation(s)
- Andrew Ke-Ming Lu
- Institute of Clinical Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Shulan Hsieh
- Department of Psychology, College of Social Sciences, National Cheng Kung University, Tainan, Taiwan
| | - Cheng-Ta Yang
- Department of Psychology, College of Social Sciences, National Cheng Kung University, Tainan, Taiwan,Graduate Institute of Mind, Brain, and Consciousness, Taipei Medical University, Taipei, Taiwan
| | - Xin-Yu Wang
- Institute of Clinical Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Sheng-Hsiang Lin
- Institute of Clinical Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan,Department of Public Health, College of Medicine, National Cheng Kung University, Tainan, Taiwan,Biostatistics Consulting Center, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan,*Correspondence: Sheng-Hsiang Lin,
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18
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Wang G, Wang Y, Gao C, Xie W. Novel compound heterozygous variants in EMC1 associated with global developmental delay: a lesson from a non-silent synonymous exonic mutation. Front Mol Neurosci 2023; 16:1153156. [PMID: 37187958 PMCID: PMC10175691 DOI: 10.3389/fnmol.2023.1153156] [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: 01/29/2023] [Accepted: 04/10/2023] [Indexed: 05/17/2023] Open
Abstract
Background The endoplasmic reticulum-membrane protein complex (EMC) as a molecular chaperone is required for the proper synthesis, folding and traffic of several transmembrane proteins. Variants in the subunit 1 of EMC (EMC1) have been implicated in neurodevelopmental disorders. Methods Whole exome sequencing (WES) with Sanger sequencing validation was performed for a Chinese family, including the proband (a 4-year-old girl who displayed global developmental delay, severe hypotonia and visual impairment), her affected younger sister and her non-consanguineous parents. RT-PCR assay and Sanger sequencing were used to detect abnormal RNA splicing. Results Novel compound heterozygous variants in EMC1, including the maternally inherited chr1: 19566812_1956800delinsATTCTACTT[hg19];NM_015047.3:c.765_777delins ATTCTACTT;p.(Leu256fsTer10) and the paternally inherited chr1:19549890G> A[hg19];NM_015047.3:c.2376G>A;p.(Val792=) are identified in the proband and her affected sister. RT-PCR assay followed by Sanger sequencing reveals that the c.2376G>A variant leads to aberrant splicing, with retention of intron 19 (561bp) in the mature mRNA, which is presumed to introduce a premature translational termination codon (p.(Val792fsTer31)). Conclusion Novel compound heterozygous variants in EMC1 have been identified in individuals with global developmental delay. Non-silent synonymous mutations should be kept in mind in genetic analysis.
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Affiliation(s)
- Ge Wang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Yanli Wang
- Department of Rehabilitation Medicine, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou, China
| | - Chao Gao
- Department of Rehabilitation Medicine, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou, China
- *Correspondence: Chao Gao
| | - Wanqin Xie
- National Health Committee Key Laboratory of Birth Defects for Research and Prevention, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, China
- Wanqin Xie
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