1
|
Gregor A, Distel L, Ekici AB, Kirchner P, Uebe S, Krumbiegel M, Turan S, Winner B, Zweier C. Proteasomal activation ameliorates neuronal phenotypes linked to FBXO11-deficiency. HGG ADVANCES 2025; 6:100425. [PMID: 40114442 PMCID: PMC11999343 DOI: 10.1016/j.xhgg.2025.100425] [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: 11/15/2024] [Revised: 03/13/2025] [Accepted: 03/13/2025] [Indexed: 03/22/2025] Open
Abstract
Haploinsufficiency of FBXO11, encoding a ubiquitin ligase complex subunit, is associated with a variable neurodevelopmental disorder. So far, the underlying nervous system-related pathomechanisms are poorly understood, and specific therapies are lacking. Using a combined approach, we established an FBXO11-deficient human stem cell-based neuronal model using CRISPR-Cas9 and a Drosophila model using tissue-specific knockdown techniques. We performed transcriptomic analyses on iPSC-derived neurons and molecular phenotyping in both models. RNA sequencing revealed disrupted transcriptional networks related to processes important for neuronal development, such as differentiation, migration, and cell signaling. Consistently, we found that loss of FBXO11 leads to neuronal phenotypes such as impaired neuronal migration and abnormal proliferation/differentiation balance in human cultured neurons and impaired dendritic development and behavior in Drosophila. Interestingly, application of three different proteasome-activating substances could alleviate FBXO11-deficiency-associated phenotypes in both human neurons and flies. One of these substances is the long-approved drug Verapamil, opening the possibility of drug repurposing in the future. Our study shows the importance of FBXO11 for neurodevelopment and highlights the reversibility of related phenotypes, opening an avenue for potential development of therapeutic approaches through drug repurposing.
Collapse
Affiliation(s)
- Anne Gregor
- Department of Human Genetics, Inselspital University Hospital Bern, University of Bern, 3010 Bern, Switzerland; Department for Biomedical Research (DBMR), University of Bern, 3010 Bern, Switzerland.
| | - Laila Distel
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Arif B Ekici
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Philipp Kirchner
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany; Institute of Tissue Medicine and Pathology, University of Bern, 3010 Bern, Switzerland
| | - Steffen Uebe
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Mandy Krumbiegel
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Soeren Turan
- Department of Stem Cell Biology, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Beate Winner
- Department of Stem Cell Biology, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany; Centre for Rare Diseases Erlangen (ZSEER), University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Christiane Zweier
- Department of Human Genetics, Inselspital University Hospital Bern, University of Bern, 3010 Bern, Switzerland; Department for Biomedical Research (DBMR), University of Bern, 3010 Bern, Switzerland
| |
Collapse
|
2
|
Ashitomi H, Nakagawa T, Nakagawa M, Hosoi T. Cullin-RING Ubiquitin Ligases in Neurodevelopment and Neurodevelopmental Disorders. Biomedicines 2025; 13:810. [PMID: 40299365 PMCID: PMC12024872 DOI: 10.3390/biomedicines13040810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2025] [Revised: 03/26/2025] [Accepted: 03/27/2025] [Indexed: 04/30/2025] Open
Abstract
Ubiquitination is a dynamic and tightly regulated post-translational modification essential for modulating protein stability, trafficking, and function to preserve cellular homeostasis. This process is orchestrated through a hierarchical enzymatic cascade involving three key enzymes: the E1 ubiquitin-activating enzyme, the E2 ubiquitin-conjugating enzyme, and the E3 ubiquitin ligase. The final step of ubiquitination is catalyzed by the E3 ubiquitin ligase, which facilitates the transfer of ubiquitin from the E2 enzyme to the substrate, thereby dictating which proteins undergo ubiquitination. Emerging evidence underscores the critical roles of ubiquitin ligases in neurodevelopment, regulating fundamental processes such as neuronal polarization, axonal outgrowth, synaptogenesis, and synaptic function. Mutations in genes encoding ubiquitin ligases and the consequent dysregulation of these pathways have been increasingly implicated in a spectrum of neurodevelopmental disorders, including autism spectrum disorder, intellectual disability, and attention-deficit/hyperactivity disorder. This review synthesizes current knowledge on the molecular mechanisms underlying neurodevelopment regulated by Cullin-RING ubiquitin ligases-the largest subclass of ubiquitin ligases-and their involvement in the pathophysiology of neurodevelopmental disorders. A deeper understanding of these mechanisms holds significant promise for informing novel therapeutic strategies, ultimately advancing clinical outcomes for individuals affected by neurodevelopmental disorders.
Collapse
Affiliation(s)
- Honoka Ashitomi
- Department of Clinical Pharmacology, Faculty of Pharmaceutical Sciences, Sanyo-Onoda City University, Sanyo-Onoda 756-0084, Japan; (H.A.)
| | - Tadashi Nakagawa
- Department of Clinical Pharmacology, Faculty of Pharmaceutical Sciences, Sanyo-Onoda City University, Sanyo-Onoda 756-0084, Japan; (H.A.)
- Division of Cell Proliferation, United Centers for Advanced Research and Translational Medicine, Graduate School of Medicine, Tohoku University, Sendai 980-8575, Japan
| | - Makiko Nakagawa
- Institute of Gene Research, Yamaguchi University Science Research Center, Ube 755-8505, Japan
- Advanced Technology Institute, Life Science Division, Yamaguchi University, Ube 755-8611, Japan
| | - Toru Hosoi
- Department of Clinical Pharmacology, Faculty of Pharmaceutical Sciences, Sanyo-Onoda City University, Sanyo-Onoda 756-0084, Japan; (H.A.)
| |
Collapse
|
3
|
Yuan T, Liu H, Li F, Meng Q, Wang Y, Yuan M. The miR-155-5p/ FBXO11 axis inhibits the progression of gastric cancer via the mTOR pathway. Transl Cancer Res 2025; 14:1375-1387. [PMID: 40104748 PMCID: PMC11912068 DOI: 10.21037/tcr-2025-8] [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: 01/01/2025] [Accepted: 02/20/2025] [Indexed: 03/20/2025]
Abstract
Background Gastric cancer (GC) is a leading cause of cancer-related death. MicroRNAs (miRNAs or miRs) play a crucial role in the pathology of GC, including cell proliferation, invasion, and metastasis. In this study, genes targeted by miR-155-5p were predicted using bioinformatic tools. We found that the expression of miR-155-5p in GC cell lines differed relative to the expression of F-box protein 11 (FBXO11), which is involved in the regulation of cellular processes. This study sought to examine the function of miR-155-5p and the precise mechanism underlying its regulatory function in modulating proliferation and apoptosis in GC. Methods The luciferase reporter assay results showed that miR-155-5p bound directly to the three prime untranslated region (3'-UTR) of FBXO11, which further downregulated FBXO11 expression. Quantitative reverse transcription-polymerase chain reaction (qRT-PCR) and Western-blot analyses confirmed that miR-155-5p negatively regulated the messenger RNA (mRNA) and protein expression of FBXO11. The effects of FBXO11 on cell proliferation and apoptosis in GC cell lines was further examined using Cell Counting Kit-8 (CCK-8) and flow cytometry. Results We found that FBXO11 promoted proliferation and decreased apoptosis in GC cells. Conversely, rescue experiments showed that the knockdown of FBXO11 limited the effects of miR-155-5p on the proliferation and apoptosis of GC cells, providing further evidence that FBXO11 is a functional target of miR-155-5p. Further, the overexpression of miR-155-5p inhibited cell growth via the targeted inhibition of FBXO11 that regulated mammalian target of rapamycin (mTOR) signaling pathway in the GC cells. Conclusions Overall, these results showed that miR-155-5p may serve as a tumor suppressor in GC and that the miR-155-5p/FBXO11 axis regulates tumor progression via the mTOR signaling pathway. Consequently, our findings may lead to the development a novel treatment strategy for GC.
Collapse
Affiliation(s)
- Tao Yuan
- Hospital Office, The No. 3 People’s Hospital of Qingdao, Qingdao, China
| | - Haiyan Liu
- Department of Dermatology, The No. 8 People’s Hospital of Qingdao, Qingdao, China
| | - Fangfang Li
- Department of Respiratory Medicine, The No. 8 People’s Hospital of Qingdao, Qingdao, China
| | - Qingyue Meng
- Department of Health Management Center, The No. 8 People’s Hospital of Qingdao, Qingdao, China
| | - Yajuan Wang
- Department of Gerontology, The No. 8 People’s Hospital of Qingdao, Qingdao, China
| | - Mei Yuan
- Health Management Center, the Affiliated Hospital of Qingdao University, Qingdao, China
| |
Collapse
|
4
|
Zhang H, Yuan L, Fan M, Liu Z, Yan Y, Liu Q, Zhang K, Li C, Liu D. Clinical and genetic characteristics of a case of Koolen-De Vries syndrome caused by KANSL1 gene mutation and literature review: A case report. Medicine (Baltimore) 2024; 103:e40923. [PMID: 39654190 PMCID: PMC11631005 DOI: 10.1097/md.0000000000040923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/07/2024] [Accepted: 10/28/2024] [Indexed: 12/12/2024] Open
Abstract
RATIONALE Koolen-De Vries syndrome (KdVS, OMIM: 612452), also known as 17q21.31 microdeletion syndrome, is an autosomal dominant genetic disease. In the study, we analyze of clinical phenotype and gene variation of a child with Koolen-De Vries syndrome, review the literature to improve the understanding of the disease. PATIENT CONCERNS The patient is a male, aged 1 month and 3 days. The patient has poor airway development, difficulty weaning from respiratory support, seizures, and recurrent low granulocyte counts. DIAGNOSES High-throughput sequencing showed a heterozygous mutation NM_001193466.1: c.1574_1578del (P.525HFS *24) in the KANSL1 gene of the proband, which was considered a new mutation since neither of his parents carried this mutation based on Sanger sequencing results. Combining clinical features and genetic results, the proband was diagnosed as KdVS. INTERVENTIONS AND OUTCOMES The patient was in good condition after receiving bronchoscopy and laser interventional therapy, meeting the criteria for discharge. Follow-up for 1 year and 6 months indicated that the patient's physical signs were normal and there was no recurrence. LESSONS According to literature review, KdVS is a multi-organ disease characterized by feeding difficulties, seizures, characteristic facial features, dysplasia of the respiratory system and cardiac abnormalities. In this study, laryngeal malacia accounted for 23.2% of the clinical manifestations of KdVS patients, limb convulsions/seizures accounted for 62.5%, and cardiac development defects accounted for 23.5%. The disease was rare in China and had a variety of clinical manifestations. The summary of reported cases can enable doctors to have more understanding of the disease. The new mutations enrich the KANSL1 gene mutation spectrum.
Collapse
Affiliation(s)
- Haozheng Zhang
- Institute of Pediatric Research, Children’s Hospital Affiliated to Shandong University, Jinan, China
| | - Limei Yuan
- Obstetrical Department, Jinan Fifth People’s Hospital, Jinan, China
| | - Meili Fan
- Enuresis Clinic of Tuina Department, Children’s Hospital Affiliated to Shandong University, Jinan, China
| | - Zhaotian Liu
- Medical Imaging Department, Children’s Hospital Affiliated to Shandong University, Jinan, China
| | - Yuxi Yan
- Ultrasound Department, Children’s Hospital Affiliated to Shandong University, Jinan, China
| | - Qinghua Liu
- Ultrasound Department, Children’s Hospital Affiliated to Shandong University, Jinan, China
| | - Kaihui Zhang
- Institute of Pediatric Research, Children’s Hospital Affiliated to Shandong University, Jinan, China
| | - Chunmiao Li
- Blood Transfusion Department, Children’s Hospital Affiliated to Shandong University, Jinan, China
| | - Deyao Liu
- Shandong Vocational College of Special Education, Jinan, China
| |
Collapse
|
5
|
Pan X, Liu L, Zhang X, Tang X, Qian G, Qiu H, Lin S, Yao H, Dong X, Tan B. FBXO11 variants are associated with intellectual disability and variable clinical manifestation in Chinese affected individuals. J Hum Genet 2024; 69:391-400. [PMID: 38740982 DOI: 10.1038/s10038-024-01255-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 04/01/2024] [Accepted: 04/24/2024] [Indexed: 05/16/2024]
Abstract
F-box protein 11 (FBXO11) is a member of F-Box protein family, which has recently been proved to be associated with intellectual developmental disorder with dysmorphic facies and behavioral abnormalities (IDDFBA, OMIM: 618089). In this study, 12 intellectual disability individuals from 5 Chinese ID families were collected, and whole exome sequencing (WES), sanger sequencing, and RNA sequencing (RNA-seq) were conducted. Almost all the affected individuals presented with mild to severe intellectual disability (12/12), global developmental delay (10/12), speech and language development delay (8/12) associated with a range of alternate features including increased body weight (7/12), short stature (6/12), seizures (3/12), reduced visual acuity (4/12), hypotonia (1/12), and auditory hallucinations and hallucinations (1/12). Distinguishingly, malformation was not observed in all the affected individuals. WES analysis showed 5 novel FBXO11 variants, which include an inframe deletion variant, a missense variant, two frameshift variants, and a partial deletion of FBXO11 (exon 22-23). RNA-seq indicated that exon 22-23 deletion of FBXO11 results in a new mRNA structure. Conservation and protein structure prediction demonstrated deleterious effect of these variants. The DEGs analysis revealed 148 differentially expressed genes shared among 6 affected individuals, which were mainly associated with genes of muscle and immune system. Our research is the first report of FBXO11-associated IDDFBA in Chinese individuals, which expands the genetic and clinical spectrum of this newly identified NDD/ID syndrome.
Collapse
Affiliation(s)
- Xin Pan
- Department of Gynecology and Obstetrics, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, 400000, China
| | - Li Liu
- Department of Gynecology and Obstetrics, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, 400000, China
| | - Xu Zhang
- Department of Gynecology and Obstetrics, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, 400000, China
| | - Xianglan Tang
- Department of Gynecology and Obstetrics, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, 400000, China
| | - Guanhua Qian
- Department of Gynecology and Obstetrics, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, 400000, China
| | - Hao Qiu
- Center for Clinical Genetics and Genomics, DIAN Diagnostics, Hangzhou, 310058, Zhejiang, China
| | - Shuhong Lin
- Center for Clinical Genetics and Genomics, DIAN Diagnostics, Hangzhou, 310058, Zhejiang, China
| | - Hong Yao
- Department of Gynecology and Obstetrics, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, 400000, China
| | - Xiaojing Dong
- Department of Gynecology and Obstetrics, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, 400000, China
| | - Bo Tan
- Department of Gynecology and Obstetrics, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, 400000, China.
| |
Collapse
|
6
|
Shankar SS, Banarjee R, Jathar SM, Rajesh S, Ramasamy S, Kulkarni MJ. De novo structure prediction of meteorin and meteorin-like protein for identification of domains, functional receptor binding regions, and their high-risk missense variants. J Biomol Struct Dyn 2024; 42:4522-4536. [PMID: 37288801 DOI: 10.1080/07391102.2023.2220804] [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: 03/07/2023] [Accepted: 05/29/2023] [Indexed: 06/09/2023]
Abstract
Meteorin (Metrn) and Meteorin-like (Metrnl) are homologous secreted proteins involved in neural development and metabolic regulation. In this study, we have performed de novo structure prediction and analysis of both Metrn and Metrnl using Alphafold2 (AF2) and RoseTTAfold (RF). Based on the domain and structural homology analysis of the predicted structures, we have identified that these proteins are composed of two functional domains, a CUB domain and an NTR domain, connected by a hinge/loop region. We have identified the receptor binding regions of Metrn and Metrnl using the machine-learning tools ScanNet and Masif. These were further validated by docking Metrnl with its reported KIT receptor, thus establishing the role of each domain in the receptor interaction. Also, we have studied the effect of non-synonymous SNPs on the structure and function of these proteins using an array of bioinformatics tools and selected 16 missense variants in Metrn and 10 in Metrnl that can affect the protein stability. This is the first study to comprehensively characterize the functional domains of Metrn and Metrnl at their structural level and identify the functional domains, and protein binding regions. This study also highlights the interaction mechanism of the KIT receptor and Metrnl. The predicted deleterious SNPs will allow further understanding of the role of these variants in modulating the plasma levels of these proteins in disease conditions such as diabetes.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- S Shiva Shankar
- Proteomics Facility, Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Pune, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Reema Banarjee
- Proteomics Facility, Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Pune, India
| | - Swaraj M Jathar
- Proteomics Facility, Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Pune, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - S Rajesh
- Proteomics Facility, Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Pune, India
| | - Sureshkumar Ramasamy
- Proteomics Facility, Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Pune, India
| | - Mahesh J Kulkarni
- Proteomics Facility, Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Pune, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| |
Collapse
|
7
|
Mégarbané A, Mehawej C, Mahfoud D, Chouery E, Devriendt K, Hijazi M, Ryu SW, Kim J, McNeill A. How many phenotypes for the FBXO11 related disease? Report on a new patient with a tricho-rhino-phalangeal like phenotype. Eur J Med Genet 2024; 69:104944. [PMID: 38679370 DOI: 10.1016/j.ejmg.2024.104944] [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: 08/05/2023] [Revised: 03/11/2024] [Accepted: 04/25/2024] [Indexed: 05/01/2024]
Abstract
Here we report the case of a young boy with developmental delay, thin sparse hair, early closure of the anterior fontanel, bilateral choanal atresia, brachyturicephaly; and dysmorphic features closely resembling those seen in trichorhinophalangeal syndrome (TRPS). These features include sparse hair, sparse lateral eyebrows, a bulbous pear shaped nose, a long philtrum, thin lips, small/hypoplastic nails, pes planovalgus; bilateral cone-shaped epiphyses at the proximal 5th phalanx, slender long bones, coxa valga, mild scoliosis, and delayed bone age. Given that TRPS had been excluded by a thorough genetic analysis, whole exome sequencing was performed and a heterozygous likely pathogenic variant was identified in the FBXO11 gene (NM_001190274.2: c.1781A > G; p. His594Arg), confirming the diagnosis of the newly individualized IDDFBA syndrome: Intellectual Developmental Disorder, dysmorphic Facies, and Behavioral Abnormalities (OMIM# 618,089). Our findings further delineate the clinical spectrum linked to FBXO11 and highlight the importance of investigating further cases with mutations in this gene to establish a potential genotype-phenotype correlation.
Collapse
Affiliation(s)
- Andre Mégarbané
- Department of Human Genetics, Gilbert and Rose-Marie Chagoury School of Medicine, Lebanese American University, Beirut, Lebanon; Institut Jerome Lejeune, Paris, France.
| | - Cybel Mehawej
- Department of Human Genetics, Gilbert and Rose-Marie Chagoury School of Medicine, Lebanese American University, Beirut, Lebanon.
| | - Daniel Mahfoud
- Department of Radiology, Medical Center - Rizk Hospital, Gilbert and Rose-Marie Chagoury School of Medicine, Lebanese American University, Lebanon.
| | - Eliane Chouery
- Department of Human Genetics, Gilbert and Rose-Marie Chagoury School of Medicine, Lebanese American University, Beirut, Lebanon.
| | - Koenraad Devriendt
- Center for Human Genetics, University of Leuven (KU) and University Hospitals Leuven (UZ), Louvain, Belgium.
| | - Mariam Hijazi
- Department of Human Genetics, Gilbert and Rose-Marie Chagoury School of Medicine, Lebanese American University, Beirut, Lebanon.
| | | | - JiHye Kim
- 3 Billion Inc., Seoul, Republic of Korea.
| | - Alisdair McNeill
- Sheffield Institute for Translational Neuroscience, The University of Sheffield, Sheffield, UK.
| |
Collapse
|
8
|
Bosch E, Popp B, Güse E, Skinner C, van der Sluijs PJ, Maystadt I, Pinto AM, Renieri A, Bruno LP, Granata S, Marcelis C, Baysal Ö, Hartwich D, Holthöfer L, Isidor B, Cogne B, Wieczorek D, Capra V, Scala M, De Marco P, Ognibene M, Jamra RA, Platzer K, Carter LB, Kuismin O, van Haeringen A, Maroofian R, Valenzuela I, Cuscó I, Martinez-Agosto JA, Rabani AM, Mefford HC, Pereira EM, Close C, Anyane-Yeboa K, Wagner M, Hannibal MC, Zacher P, Thiffault I, Beunders G, Umair M, Bhola PT, McGinnis E, Millichap J, van de Kamp JM, Prijoles EJ, Dobson A, Shillington A, Graham BH, Garcia EJ, Galindo MK, Ropers FG, Nibbeling EAR, Hubbard G, Karimov C, Goj G, Bend R, Rath J, Morrow MM, Millan F, Salpietro V, Torella A, Nigro V, Kurki M, Stevenson RE, Santen GWE, Zweier M, Campeau PM, Severino M, Reis A, Accogli A, Vasileiou G. Elucidating the clinical and molecular spectrum of SMARCC2-associated NDD in a cohort of 65 affected individuals. Genet Med 2023; 25:100950. [PMID: 37551667 DOI: 10.1016/j.gim.2023.100950] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 08/01/2023] [Accepted: 08/01/2023] [Indexed: 08/09/2023] Open
Abstract
PURPOSE Coffin-Siris and Nicolaides-Baraitser syndromes are recognizable neurodevelopmental disorders caused by germline variants in BAF complex subunits. The SMARCC2 BAFopathy was recently reported. Herein, we present clinical and molecular data on a large cohort. METHODS Clinical symptoms for 41 novel and 24 previously published affected individuals were analyzed using the Human Phenotype Ontology. For genotype-phenotype correlations, molecular data were standardized and grouped into non-truncating and likely gene-disrupting (LGD) variants. Missense variant protein expression and BAF-subunit interactions were examined using 3D protein modeling, co-immunoprecipitation, and proximity-ligation assays. RESULTS Neurodevelopmental delay with intellectual disability, muscular hypotonia, and behavioral disorders were the major manifestations. Clinical hallmarks of BAFopathies were rare. Clinical presentation differed significantly, with LGD variants being predominantly inherited and associated with mildly reduced or normal cognitive development, whereas non-truncating variants were mostly de novo and presented with severe developmental delay. These distinct manifestations and non-truncating variant clustering in functional domains suggest different pathomechanisms. In vitro testing showed decreased protein expression for N-terminal missense variants similar to LGD. CONCLUSION This study improved SMARCC2 variant classification and identified discernible SMARCC2-associated phenotypes for LGD and non-truncating variants, which were distinct from other BAFopathies. The pathomechanism of most non-truncating variants has yet to be investigated.
Collapse
Affiliation(s)
- Elisabeth Bosch
- Institute of Human Genetics, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Bernt Popp
- Berlin Institute of Health at Charitè, Universitätsklinikum Berlin, Centre of Functional Genomics, Berlin, Germany; Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Esther Güse
- Institute of Human Genetics, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | | | | | - Isabelle Maystadt
- Center for Human Genetics, Institute of Pathology and Genetics, Gosselies, Belgium
| | - Anna Maria Pinto
- Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena, Italy
| | - Alessandra Renieri
- Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena, Italy; Medical Genetics Unit, University of Siena, Siena, Italy
| | - Lucia Pia Bruno
- Telethon Institute of Genetics and Medicine (TIGEM), Naples, Italy
| | - Stefania Granata
- Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena, Italy; Medical Genetics Unit, University of Siena, Siena, Italy
| | - Carlo Marcelis
- Human Genetics department, Radboud university medical center, Nijmegen, The Netherlands
| | - Özlem Baysal
- Human Genetics department, Radboud university medical center, Nijmegen, The Netherlands
| | - Dewi Hartwich
- Institute of Human Genetics - University Medical Center of the Johannes Gutenberg University Mainz, Germany
| | - Laura Holthöfer
- Institute of Human Genetics - University Medical Center of the Johannes Gutenberg University Mainz, Germany
| | - Bertrand Isidor
- Nantes Université, CHU de Nantes, Service de Génétique médicale, Nantes, France; Nantes Université, CHU de Nantes, CNRS, INSERM, l'institut du thorax, Nantes, France
| | - Benjamin Cogne
- Nantes Université, CHU de Nantes, Service de Génétique médicale, Nantes, France; Nantes Université, CHU de Nantes, CNRS, INSERM, l'institut du thorax, Nantes, France
| | - Dagmar Wieczorek
- Institute of Human Genetics, Medical Faculty and University Hospital Düsseldorf, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Valeria Capra
- Genomics and Clinical Genetics Unit, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Marcello Scala
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, Genoa, Italy; Medical Genetics Unit, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Patrizia De Marco
- Medical Genetics Unit, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Marzia Ognibene
- Medical Genetics Unit, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Rami Abou Jamra
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Konrad Platzer
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Lauren B Carter
- Department of Pediatrics, Division of Medical Genetics, Levine Children's Hospital, Atrium Health, Charlotte, NC
| | - Outi Kuismin
- Department of Clinical Genetics, Research Unit of Clinical Medicine, Medical Research Center Oulu, Oulu University Hospital and University of Oulu, Oulu, Finland
| | - Arie van Haeringen
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Reza Maroofian
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, University College London, London, United Kingdom
| | - Irene Valenzuela
- Department of Clinical and Molecular Genetics, University Hospital Vall d'Hebron, Barcelona, Spain; Medicine Genetics Group, Valle Hebron Research Institute, Barcelona, Spain
| | - Ivon Cuscó
- Department of Clinical and Molecular Genetics, University Hospital Vall d'Hebron, Barcelona, Spain; Medicine Genetics Group, Valle Hebron Research Institute, Barcelona, Spain
| | - Julian A Martinez-Agosto
- Departments of Human Genetics, Pediatrics, and Psychiatry, UCLA David Geffen School of Medicine, Los Angeles, CA
| | - Ahna M Rabani
- Department of Pediatrics & Institute for Precision Health, UCLA David Geffen School of Medicine, Los Angeles, CA
| | - Heather C Mefford
- Center for Pediatric Neurological Disease Research, St. Jude Children's Research Hospital, Memphis, TN
| | - Elaine M Pereira
- Division of Clinical Genetics, Department of Pediatrics, Columbia University Irving Medical Center, New York, NY
| | - Charlotte Close
- Division of Clinical Genetics, Department of Pediatrics, Columbia University Irving Medical Center, New York, NY
| | - Kwame Anyane-Yeboa
- Division of Clinical Genetics, Department of Pediatrics, Columbia University Irving Medical Center, New York, NY
| | - Mallory Wagner
- Division of Pediatric Genetics, Metabolism, and Genomic Medicine, Department of Pediatrics, University of Michigan Health System, University of Michigan, Ann Arbor, MI
| | - Mark C Hannibal
- Division of Pediatric Genetics, Metabolism, and Genomic Medicine, Department of Pediatrics, University of Michigan Health System, University of Michigan, Ann Arbor, MI
| | - Pia Zacher
- Epilepsy Center Kleinwachau, Radeberg, Germany
| | - Isabelle Thiffault
- Department of Pediatrics and Pathology, Genomic Medicine Center, Children's Mercy Kansas City and Children's Mercy Research Institute, Kansas City, MO
| | - Gea Beunders
- Department of Genetics, University Medical Center Groningen, Groningen, The Netherlands
| | - Muhammad Umair
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, MNGHA, Riyadh, Saudi Arabia; Department of Life Sciences, School of Science, University of Management and Technology (UMT), Lahore, Pakistan
| | - Priya T Bhola
- Department of Genetics, Children's Hospital of Eastern Ontario (CHEO), Ottawa, Canada
| | - Erin McGinnis
- Division of Neurology, Department of Pediatrics, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL
| | - John Millichap
- Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL
| | - Jiddeke M van de Kamp
- Department of Human Genetics, Amsterdam UMC, location VU Medical Center, Amsterdam, The Netherlands
| | | | | | - Amelle Shillington
- Department of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - Brett H Graham
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN
| | - Evan-Jacob Garcia
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN
| | | | - Fabienne G Ropers
- Willem-Alexander Children's Hospital, Department of Pediatrics, Leiden University Medical Center, The Netherlands
| | - Esther A R Nibbeling
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Gail Hubbard
- Department of Medical Genetics, Children's Hospital Los Angeles, Keck School of Medicine of University of Southern California, Los Angeles, CA
| | - Catherine Karimov
- Department of Medical Genetics, Children's Hospital Los Angeles, Keck School of Medicine of University of Southern California, Los Angeles, CA
| | - Guido Goj
- Vestische Kinder- und Jugendklinik, Datteln, Germany
| | - Renee Bend
- PreventionGenetics, Part of Exact Sciences, Marshfield, WI
| | - Julie Rath
- PreventionGenetics, Part of Exact Sciences, Marshfield, WI
| | | | | | - Vincenzo Salpietro
- Department of Neuromuscular Disorders, Queen Square Institute of Neurology, University College London, London, United Kingdom; Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, L'Aquila, Italy
| | - Annalaura Torella
- Telethon Institute of Genetics and Medicine (TIGEM), Naples, Italy; Department of Precision Medicine, University of Campania "Luigi Vanvitelli," Naples, Italy
| | - Vincenzo Nigro
- Telethon Institute of Genetics and Medicine (TIGEM), Naples, Italy; Department of Precision Medicine, University of Campania "Luigi Vanvitelli," Naples, Italy
| | - Mitja Kurki
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland; Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA
| | | | - Gijs W E Santen
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Markus Zweier
- Institute of Medical Genetics, University of Zürich, Schlieren-Zurich, Switzerland
| | - Philippe M Campeau
- Department of Pediatrics, CHU Sainte-Justine and University of Montreal, Montreal, QC, Canada
| | | | - André Reis
- Institute of Human Genetics, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany; Centre for Rare Diseases Erlangen (ZSEER), Erlangen, Germany
| | - Andrea Accogli
- Department of Specialized Medicine, Division of Medical Genetics, McGill University Health Centre; Department of Human Genetics, Faculty of Medicine, McGill University, Montreal, QC, Canada
| | - Georgia Vasileiou
- Institute of Human Genetics, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany; Centre for Rare Diseases Erlangen (ZSEER), Erlangen, Germany.
| |
Collapse
|
9
|
Gupta V, Ben-Mahmoud A, Ku B, Velayutham D, Jan Z, Yousef Aden A, Kubbar A, Alshaban F, Stanton LW, Jithesh PV, Layman LC, Kim HG. Identification of two novel autism genes, TRPC4 and SCFD2, in Qatar simplex families through exome sequencing. Front Psychiatry 2023; 14:1251884. [PMID: 38025430 PMCID: PMC10644705 DOI: 10.3389/fpsyt.2023.1251884] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 10/09/2023] [Indexed: 12/01/2023] Open
Abstract
This study investigated the genetic underpinnings of autism spectrum disorder (ASD) in a Middle Eastern cohort in Qatar using exome sequencing. The study identified six candidate autism genes in independent simplex families, including both four known and two novel autosomal dominant and autosomal recessive genes associated with ASD. The variants consisted primarily of de novo and homozygous missense and splice variants. Multiple individuals displayed more than one candidate variant, suggesting the potential involvement of digenic or oligogenic models. These variants were absent in the Genome Aggregation Database (gnomAD) and exhibited extremely low frequencies in the local control population dataset. Two novel autism genes, TRPC4 and SCFD2, were discovered in two Qatari autism individuals. Furthermore, the D651A substitution in CLCN3 and the splice acceptor variant in DHX30 were identified as likely deleterious mutations. Protein modeling was utilized to evaluate the potential impact of three missense variants in DEAF1, CLCN3, and SCFD2 on their respective structures and functions, which strongly supported the pathogenic natures of these variants. The presence of multiple de novo mutations across trios underscored the significant contribution of de novo mutations to the genetic etiology of ASD. Functional assays and further investigations are necessary to confirm the pathogenicity of the identified genes and determine their significance in ASD. Overall, this study sheds light on the genetic factors underlying ASD in Qatar and highlights the importance of considering diverse populations in ASD research.
Collapse
Affiliation(s)
- Vijay Gupta
- Neurological Disorder Research Center, Qatar Biomedical Research Institute (QBRI), Qatar Foundation, Hamad Bin Khalifa University (HBKU), Doha, Qatar
| | - Afif Ben-Mahmoud
- Neurological Disorder Research Center, Qatar Biomedical Research Institute (QBRI), Qatar Foundation, Hamad Bin Khalifa University (HBKU), Doha, Qatar
| | - Bonsu Ku
- Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - Dinesh Velayutham
- College of Health & Life Sciences, Qatar Foundation, Hamad Bin Khalifa University (HBKU), Doha, Qatar
| | - Zainab Jan
- College of Health & Life Sciences, Qatar Foundation, Hamad Bin Khalifa University (HBKU), Doha, Qatar
| | - Abdi Yousef Aden
- Neurological Disorder Research Center, Qatar Biomedical Research Institute (QBRI), Qatar Foundation, Hamad Bin Khalifa University (HBKU), Doha, Qatar
| | - Ahmad Kubbar
- Neurological Disorder Research Center, Qatar Biomedical Research Institute (QBRI), Qatar Foundation, Hamad Bin Khalifa University (HBKU), Doha, Qatar
| | - Fouad Alshaban
- Neurological Disorder Research Center, Qatar Biomedical Research Institute (QBRI), Qatar Foundation, Hamad Bin Khalifa University (HBKU), Doha, Qatar
- College of Health & Life Sciences, Qatar Foundation, Hamad Bin Khalifa University (HBKU), Doha, Qatar
| | - Lawrence W. Stanton
- Neurological Disorder Research Center, Qatar Biomedical Research Institute (QBRI), Qatar Foundation, Hamad Bin Khalifa University (HBKU), Doha, Qatar
- College of Health & Life Sciences, Qatar Foundation, Hamad Bin Khalifa University (HBKU), Doha, Qatar
| | - Puthen Veettil Jithesh
- College of Health & Life Sciences, Qatar Foundation, Hamad Bin Khalifa University (HBKU), Doha, Qatar
| | - Lawrence C. Layman
- Section of Reproductive Endocrinology, Infertility and Genetics, Department of Obstetrics and Gynecology, Augusta University, Augusta, GA, United States
- Department of Neuroscience and Regenerative Medicine, Augusta University, Augusta, GA, United States
| | - Hyung-Goo Kim
- Neurological Disorder Research Center, Qatar Biomedical Research Institute (QBRI), Qatar Foundation, Hamad Bin Khalifa University (HBKU), Doha, Qatar
- College of Health & Life Sciences, Qatar Foundation, Hamad Bin Khalifa University (HBKU), Doha, Qatar
| |
Collapse
|
10
|
Silva RG, Dupont J, Silva E, Sousa AB. New ocular findings in a patient with a novel pathogenic variant in the FBXO11 gene. J AAPOS 2022; 26:268-270. [PMID: 35940561 DOI: 10.1016/j.jaapos.2022.05.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 04/27/2022] [Accepted: 05/15/2022] [Indexed: 11/26/2022]
Abstract
Intellectual developmental disorder with dysmorphic facies and behavioral abnormalities (IDDFBA) is a recently described autosomal dominant entity caused by pathogenic variants, mostly de novo, in the FBXO11 gene. It presents in the first years of life with highly variable clinical manifestations. The main features of IDDFBA include borderline-to-severe intellectual disability, behavioral problems, hypotonia, facial dysmorphisms, minor skeletal abnormalities, and recurrent infections. Although eye problems, such as refractive errors, eye misalignment and minor visual changes, have been described in about 48% of patients, a major ocular defect, namely, bilateral optic nerve hypoplasia, has been reported in the literature only once. We report an 8-year-old boy with a novel de novo pathogenic variant in FBXO11 gene (NM_001190274.1: c.1166dup, p.Cys390Metfs∗3) and a complex ophthalmological phenotype, consisting of right microphthalmia, very shallow anterior chamber, and persistent pupillary membrane, right dense nuclear cataract, bilateral optic nerve hypoplasia, and bilateral horizontal manifest nystagmus.
Collapse
Affiliation(s)
- Raquel Gouveia Silva
- Serviço de Genética Médica, Departamento de Pediatria, Hospital de Santa Maria, Centro Hospitalar Universitário Lisboa Norte, Lisbon, Portugal.
| | - Juliette Dupont
- Serviço de Genética Médica, Departamento de Pediatria, Hospital de Santa Maria, Centro Hospitalar Universitário Lisboa Norte, Lisbon, Portugal
| | - Eduardo Silva
- CRI-OftaPED, Hospital Dona Estefânia, Centro Hospitalar Universitário de Lisboa Central, Lisbon, Portugal
| | - Ana Berta Sousa
- Serviço de Genética Médica, Departamento de Pediatria, Hospital de Santa Maria, Centro Hospitalar Universitário Lisboa Norte, Lisbon, Portugal; Laboratório de Imunologia Básica, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| |
Collapse
|
11
|
Krgovic D, Gorenjak M, Rihar N, Opalic I, Stangler Herodez S, Gregoric Kumperscak H, Dovc P, Kokalj Vokac N. Impaired Neurodevelopmental Genes in Slovenian Autistic Children Elucidate the Comorbidity of Autism With Other Developmental Disorders. Front Mol Neurosci 2022; 15:912671. [PMID: 35813072 PMCID: PMC9259896 DOI: 10.3389/fnmol.2022.912671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 05/11/2022] [Indexed: 11/13/2022] Open
Abstract
Autism spectrum disorders (ASD) represent a phenotypically heterogeneous group of patients that strongly intertwine with other neurodevelopmental disorders (NDDs), with genetics playing a significant role in their etiology. Whole exome sequencing (WES) has become predominant in molecular diagnostics for ASD by considerably increasing the diagnostic yield. However, the proportion of undiagnosed patients still remains high due to complex clinical presentation, reduced penetrance, and lack of segregation analysis or clinical information. Thus, reverse phenotyping, where we first identified a possible genetic cause and then determine its clinical relevance, has been shown to be a more efficient approach. WES was performed on 147 Slovenian pediatric patients with suspected ASD. Data analysis was focused on identifying ultrarare or “single event” variants in ASD-associated genes and further expanded to NDD-associated genes. Protein function and gene prioritization were performed on detected clinically relevant variants to determine their role in ASD etiology and phenotype. Reverse phenotyping revealed a pathogenic or likely pathogenic variant in ASD-associated genes in 20.4% of patients, with subsequent segregation analysis indicating that 14 were de novo variants and 1 was presumed compound heterozygous. The diagnostic yield was further increased by 2.7% by the analysis of ultrarare or “single event” variants in all NDD-associated genes. Protein function analysis established that genes in which variants of unknown significance (VUS) were detected were predominantly the cause of intellectual disability (ID), and in most cases, features of ASD as well. Using such an approach, variants in rarely described ASD-associated genes, such as SIN3B, NR4A2, and GRIA1, were detected. By expanding the analysis to include functionally similar NDD genes, variants in KCNK9, GNE, and other genes were identified. These would probably have been missed by classic genotype–phenotype analysis. Our study thus demonstrates that in patients with ASD, analysis of ultrarare or “single event” variants obtained using WES with the inclusion of functionally similar genes and reverse phenotyping obtained a higher diagnostic yield despite limited clinical data. The present study also demonstrates that most of the causative genes in our cohort were involved in the syndromic form of ASD and confirms their comorbidity with other developmental disorders.
Collapse
Affiliation(s)
- Danijela Krgovic
- Laboratory of Medical Genetics, University Medical Centre Maribor, Maribor, Slovenia
- Department of Molecular Biology, Faculty of Medicine, University of Maribor, Maribor, Slovenia
- *Correspondence: Danijela Krgovic,
| | - Mario Gorenjak
- Centre for Human Molecular Genetics, and Pharmacogenomics, Faculty of Medicine, University of Maribor, Maribor, Slovenia
| | - Nika Rihar
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Iva Opalic
- Laboratory of Medical Genetics, University Medical Centre Maribor, Maribor, Slovenia
| | - Spela Stangler Herodez
- Laboratory of Medical Genetics, University Medical Centre Maribor, Maribor, Slovenia
- Department of Molecular Biology, Faculty of Medicine, University of Maribor, Maribor, Slovenia
| | | | - Peter Dovc
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Nadja Kokalj Vokac
- Laboratory of Medical Genetics, University Medical Centre Maribor, Maribor, Slovenia
- Department of Molecular Biology, Faculty of Medicine, University of Maribor, Maribor, Slovenia
| |
Collapse
|