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Huang C, Huang Y, Pan L, Li L, Ling X, Wang C, Xiao Q, Zhai N, Long Y, Mo W, Lin F, Huang Y. A novel duplication mutation of SLC2A1 gene causing glucose transporter 1 deficiency syndrome. Gene 2024; 928:148762. [PMID: 39009233 DOI: 10.1016/j.gene.2024.148762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 07/05/2024] [Accepted: 07/10/2024] [Indexed: 07/17/2024]
Affiliation(s)
- Chaoyu Huang
- Department of Clinical Laboratory, The First Affiliated Hospital of Guangxi Medical University, Key Laboratory of Clinical Laboratory Medicine of Guangxi Department of Education, Nanning 530021, Guangxi, China
| | - Yunhua Huang
- Department of Clinical Laboratory, The First Affiliated Hospital of Guangxi Medical University, Key Laboratory of Clinical Laboratory Medicine of Guangxi Department of Education, Nanning 530021, Guangxi, China
| | - Liqiu Pan
- Department of Clinical Laboratory, The First Affiliated Hospital of Guangxi Medical University, Key Laboratory of Clinical Laboratory Medicine of Guangxi Department of Education, Nanning 530021, Guangxi, China
| | - Linlin Li
- Department of Clinical Laboratory, The First Affiliated Hospital of Guangxi Medical University, Key Laboratory of Clinical Laboratory Medicine of Guangxi Department of Education, Nanning 530021, Guangxi, China
| | - Xiaoting Ling
- Department of Clinical Laboratory, The First Affiliated Hospital of Guangxi Medical University, Key Laboratory of Clinical Laboratory Medicine of Guangxi Department of Education, Nanning 530021, Guangxi, China
| | - Chenghan Wang
- Department of Clinical Laboratory, The First Affiliated Hospital of Guangxi Medical University, Key Laboratory of Clinical Laboratory Medicine of Guangxi Department of Education, Nanning 530021, Guangxi, China
| | - Qingxing Xiao
- Department of Clinical Laboratory, The First Affiliated Hospital of Guangxi Medical University, Key Laboratory of Clinical Laboratory Medicine of Guangxi Department of Education, Nanning 530021, Guangxi, China
| | - Ningneng Zhai
- Department of Clinical Laboratory, The First Affiliated Hospital of Guangxi Medical University, Key Laboratory of Clinical Laboratory Medicine of Guangxi Department of Education, Nanning 530021, Guangxi, China
| | - Yan Long
- Department of Clinical Laboratory, The First Affiliated Hospital of Guangxi Medical University, Key Laboratory of Clinical Laboratory Medicine of Guangxi Department of Education, Nanning 530021, Guangxi, China
| | - Wuning Mo
- Department of Clinical Laboratory, The First Affiliated Hospital of Guangxi Medical University, Key Laboratory of Clinical Laboratory Medicine of Guangxi Department of Education, Nanning 530021, Guangxi, China.
| | - Faquan Lin
- Department of Clinical Laboratory, The First Affiliated Hospital of Guangxi Medical University, Key Laboratory of Clinical Laboratory Medicine of Guangxi Department of Education, Nanning 530021, Guangxi, China.
| | - Yifang Huang
- Department of Clinical Laboratory, The First Affiliated Hospital of Guangxi Medical University, Key Laboratory of Clinical Laboratory Medicine of Guangxi Department of Education, Nanning 530021, Guangxi, China.
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Barbarin-Bocahu I, Ulryck N, Rigobert A, Ruiz Gutierrez N, Decourty L, Raji M, Garkhal B, Le Hir H, Saveanu C, Graille M. Structure of the Nmd4-Upf1 complex supports conservation of the nonsense-mediated mRNA decay pathway between yeast and humans. PLoS Biol 2024; 22:e3002821. [PMID: 39331656 DOI: 10.1371/journal.pbio.3002821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Accepted: 08/29/2024] [Indexed: 09/29/2024] Open
Abstract
The nonsense-mediated mRNA decay (NMD) pathway clears eukaryotic cells of mRNAs containing premature termination codons (PTCs) or normal stop codons located in specific contexts. It therefore plays an important role in gene expression regulation. The precise molecular mechanism of the NMD pathway has long been considered to differ substantially from yeast to metazoa, despite the involvement of universally conserved factors such as the central ATP-dependent RNA-helicase Upf1. Here, we describe the crystal structure of the yeast Upf1 bound to its recently identified but yet uncharacterized partner Nmd4, show that Nmd4 stimulates Upf1 ATPase activity and that this interaction contributes to the elimination of NMD substrates. We also demonstrate that a region of Nmd4 critical for the interaction with Upf1 in yeast is conserved in the metazoan SMG6 protein, another major NMD factor. We show that this conserved region is involved in the interaction of SMG6 with UPF1 and that mutations in this region affect the levels of endogenous human NMD substrates. Our results support the universal conservation of the NMD mechanism in eukaryotes.
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Affiliation(s)
- Irène Barbarin-Bocahu
- Laboratoire de Biologie Structurale de la Cellule (BIOC), CNRS, Ecole polytechnique, Institut Polytechnique de Paris, Palaiseau, France
| | - Nathalie Ulryck
- Laboratoire de Biologie Structurale de la Cellule (BIOC), CNRS, Ecole polytechnique, Institut Polytechnique de Paris, Palaiseau, France
| | - Amandine Rigobert
- Laboratoire de Biologie Structurale de la Cellule (BIOC), CNRS, Ecole polytechnique, Institut Polytechnique de Paris, Palaiseau, France
| | - Nadia Ruiz Gutierrez
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL Research University, Paris, France
| | - Laurence Decourty
- Institut Pasteur, Université Paris Cité, Unité Biologie des ARN des Pathogènes Fongiques, Paris, France
| | - Mouna Raji
- Laboratoire de Biologie Structurale de la Cellule (BIOC), CNRS, Ecole polytechnique, Institut Polytechnique de Paris, Palaiseau, France
| | - Bhumika Garkhal
- Laboratoire de Biologie Structurale de la Cellule (BIOC), CNRS, Ecole polytechnique, Institut Polytechnique de Paris, Palaiseau, France
| | - Hervé Le Hir
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL Research University, Paris, France
| | - Cosmin Saveanu
- Institut Pasteur, Université Paris Cité, Unité Biologie des ARN des Pathogènes Fongiques, Paris, France
| | - Marc Graille
- Laboratoire de Biologie Structurale de la Cellule (BIOC), CNRS, Ecole polytechnique, Institut Polytechnique de Paris, Palaiseau, France
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3
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Azeem A, Ahmed AN, Khan N, Voutsina N, Ullah I, Ubeyratna N, Yasin M, Baple EL, Crosby AH, Rawlins LE, Saleha S. Investigating the genetic basis of hereditary spastic paraplegia and cerebellar Ataxia in Pakistani families. BMC Neurol 2024; 24:354. [PMID: 39304850 DOI: 10.1186/s12883-024-03855-1] [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: 04/02/2024] [Accepted: 09/06/2024] [Indexed: 09/22/2024] Open
Abstract
BACKGROUND Hereditary Spastic Paraplegias (HSPs) and Hereditary Cerebellar Ataxias (HCAs) are progressive neurodegenerative disorders encompassing a spectrum of neurogenetic conditions with significant overlaps of clinical features. Spastic ataxias are a group of conditions that have features of both cerebellar ataxia and spasticity, and these conditions are frequently clinically challenging to distinguish. Accurate genetic diagnosis is crucial but challenging, particularly in resource-limited settings. This study aims to investigate the genetic basis of HSPs and HCAs in Pakistani families. METHODS Families from Khyber Pakhtunkhwa with at least two members showing HSP or HCA phenotypes, and who had not previously been analyzed genetically, were included. Families were referred for genetic analysis by local neurologists based on the proband's clinical features and signs of a potential genetic neurodegenerative disorder. Whole Exome Sequencing (WES) and Sanger sequencing were then used to identify and validate genetic variants, and to analyze variant segregation within families to determine inheritance patterns. The mean age of onset and standard deviation were calculated to assess variability among affected individuals, and the success rate was compared with literature reports using differences in proportions and Cohen's h. RESULTS Pathogenic variants associated with these conditions were identified in five of eight families, segregating according to autosomal recessive inheritance. These variants included previously reported SACS c.2182 C > T, p.(Arg728*), FA2H c.159_176del, p.(Arg53_Ile58del) and SPG11 c.2146 C > T, p.(Gln716*) variants, and two previously unreported variants in SACS c.2229del, p.(Phe743Leufs*8) and ZFYVE26 c.1926_1941del, p.(Tyr643Metfs*2). Additionally, FA2H and SPG11 variants were found to have recurrent occurrences, suggesting a potential founder effect within the Pakistani population. Onset age among affected individuals ranged from 1 to 14 years (M = 6.23, SD = 3.96). The diagnostic success rate was 62.5%, with moderate effect sizes compared to previous studies. CONCLUSIONS The findings of this study expand the genotypic and phenotypic spectrum of HSPs and HCAs in Pakistan and emphasize the importance of utilizing exome/genome sequencing for accurate diagnosis or support accurate differential diagnosis. This approach can improve genetic counseling and clinical management, addressing the challenges of diagnosing neurodegenerative disorders in resource-limited settings.
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Affiliation(s)
- Arfa Azeem
- Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology, Kohat, 26000, Khyber Pakhtunkhwa, Pakistan
| | - Asif Naveed Ahmed
- Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology, Kohat, 26000, Khyber Pakhtunkhwa, Pakistan
| | - Niamat Khan
- Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology, Kohat, 26000, Khyber Pakhtunkhwa, Pakistan
| | - Nikol Voutsina
- 2Medical Research, RILD Wellcome Wolfson Centre (Level 4), Royal Devon and Exeter NHS Foundation Trust, Exeter, Devon, EX2 5DW, UK
| | - Irfan Ullah
- Department of Neurology, Khyber Teaching Hospital, Peshawar, 25000, Khyber Pakhtunkhwa, Pakistan
| | - Nishanka Ubeyratna
- 2Medical Research, RILD Wellcome Wolfson Centre (Level 4), Royal Devon and Exeter NHS Foundation Trust, Exeter, Devon, EX2 5DW, UK
| | - Muhammad Yasin
- Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology, Kohat, 26000, Khyber Pakhtunkhwa, Pakistan
| | - Emma L Baple
- 2Medical Research, RILD Wellcome Wolfson Centre (Level 4), Royal Devon and Exeter NHS Foundation Trust, Exeter, Devon, EX2 5DW, UK
| | - Andrew H Crosby
- 2Medical Research, RILD Wellcome Wolfson Centre (Level 4), Royal Devon and Exeter NHS Foundation Trust, Exeter, Devon, EX2 5DW, UK
| | - Lettie E Rawlins
- 2Medical Research, RILD Wellcome Wolfson Centre (Level 4), Royal Devon and Exeter NHS Foundation Trust, Exeter, Devon, EX2 5DW, UK.
- Peninsula Clinical Genetics Service, Royal Devon & Exeter Hospital (Heavitree), Exeter, UK.
| | - Shamim Saleha
- Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology, Kohat, 26000, Khyber Pakhtunkhwa, Pakistan.
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Ma K, Huang S, Ng KK, Lake NJ, Joseph S, Xu J, Lek A, Ge L, Woodman KG, Koczwara KE, Cohen J, Ho V, O'Connor CL, Brindley MA, Campbell KP, Lek M. Saturation mutagenesis-reinforced functional assays for disease-related genes. Cell 2024:S0092-8674(24)00976-0. [PMID: 39326416 DOI: 10.1016/j.cell.2024.08.047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 07/29/2024] [Accepted: 08/23/2024] [Indexed: 09/28/2024]
Abstract
Interpretation of disease-causing genetic variants remains a challenge in human genetics. Current costs and complexity of deep mutational scanning methods are obstacles for achieving genome-wide resolution of variants in disease-related genes. Our framework, saturation mutagenesis-reinforced functional assays (SMuRF), offers simple and cost-effective saturation mutagenesis paired with streamlined functional assays to enhance the interpretation of unresolved variants. Applying SMuRF to neuromuscular disease genes FKRP and LARGE1, we generated functional scores for all possible coding single-nucleotide variants, which aid in resolving clinically reported variants of uncertain significance. SMuRF also demonstrates utility in predicting disease severity, resolving critical structural regions, and providing training datasets for the development of computational predictors. Overall, our approach enables variant-to-function insights for disease genes in a cost-effective manner that can be broadly implemented by standard research laboratories.
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Affiliation(s)
- Kaiyue Ma
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA; Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China.
| | - Shushu Huang
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
| | - Kenneth K Ng
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
| | - Nicole J Lake
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
| | - Soumya Joseph
- Howard Hughes Medical Institute, Senator Paul D. Wellstone Muscular Dystrophy Specialized Research Center, Department of Molecular Physiology and Biophysics and Department of Neurology, Roy J. and Lucille A. Carver College of Medicine, The University of Iowa, Iowa City, IA, USA
| | - Jenny Xu
- Yale University, New Haven, CT, USA
| | - Angela Lek
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA; Muscular Dystrophy Association, Chicago, IL, USA
| | - Lin Ge
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA; Department of Neurology, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Keryn G Woodman
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
| | | | - Justin Cohen
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
| | - Vincent Ho
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
| | | | - Melinda A Brindley
- Department of Infectious Diseases, Department of Population Health, University of Georgia, Athens, GA, USA
| | - Kevin P Campbell
- Howard Hughes Medical Institute, Senator Paul D. Wellstone Muscular Dystrophy Specialized Research Center, Department of Molecular Physiology and Biophysics and Department of Neurology, Roy J. and Lucille A. Carver College of Medicine, The University of Iowa, Iowa City, IA, USA
| | - Monkol Lek
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA.
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Britto-Borges T, Gehring NH, Boehm V, Dieterich C. NMDtxDB: data-driven identification and annotation of human NMD target transcripts. RNA (NEW YORK, N.Y.) 2024; 30:1277-1291. [PMID: 39095083 PMCID: PMC11404449 DOI: 10.1261/rna.080066.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Accepted: 07/11/2024] [Indexed: 08/04/2024]
Abstract
The nonsense-mediated RNA decay (NMD) pathway is a crucial mechanism of mRNA quality control. Current annotations of NMD substrate RNAs are rarely data-driven, but use generally established rules. We present a data set with four cell lines and combinations for SMG5, SMG6, and SMG7 knockdowns or SMG7 knockout. Based on this data set, we implemented a workflow that combines Nanopore and Illumina sequencing to assemble a transcriptome, which is enriched for NMD target transcripts. Moreover, we use coding sequence information (CDS) from Ensembl, Gencode consensus Ribo-seq ORFs, and OpenProt to enhance the CDS annotation of novel transcript isoforms. In summary, 302,889 transcripts were obtained from the transcriptome assembly process, out of which 24% are absent from Ensembl database annotations, 48,213 contain a premature stop codon, and 6433 are significantly upregulated in three or more comparisons of NMD active versus deficient cell lines. We present an in-depth view of these results through the NMDtxDB database, which is available at https://shiny.dieterichlab.org/app/NMDtxDB, and supports the study of NMD-sensitive transcripts. We open sourced our implementation of the respective web-application and analysis workflow at https://github.com/dieterich-lab/NMDtxDB and https://github.com/dieterich-lab/nmd-wf.
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Affiliation(s)
- Thiago Britto-Borges
- Section of Bioinformatics and Systems Cardiology, Department of Internal Medicine III and Klaus Tschira Institute for Integrative Computational Cardiology, Heidelberg University Hospital, 69120 Heidelberg, Germany
- DZHK (German Centre for Cardiovascular Research), Partner site Heidelberg/Mannheim, 69120 Heidelberg, Germany
| | - Niels H Gehring
- Institute for Genetics, University of Cologne, 50674 Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50674 Cologne, Germany
| | - Volker Boehm
- Institute for Genetics, University of Cologne, 50674 Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50674 Cologne, Germany
| | - Christoph Dieterich
- Section of Bioinformatics and Systems Cardiology, Department of Internal Medicine III and Klaus Tschira Institute for Integrative Computational Cardiology, Heidelberg University Hospital, 69120 Heidelberg, Germany
- DZHK (German Centre for Cardiovascular Research), Partner site Heidelberg/Mannheim, 69120 Heidelberg, Germany
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6
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Yang W, Wang S, Huo X, Yang K, Guo Z, Li Y, Ji X, Hao B, Liao S. Novel autosomal recessive SINO syndrome-associated KIDINS220 variants provide insight into the genotype-phenotype correlation. Heliyon 2024; 10:e37355. [PMID: 39296002 PMCID: PMC11408833 DOI: 10.1016/j.heliyon.2024.e37355] [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: 03/21/2024] [Revised: 08/30/2024] [Accepted: 09/02/2024] [Indexed: 09/21/2024] Open
Abstract
Background KIDINS220 encodes a transmembrane scaffold protein, kinase D-interacting substrate of 220 kDa, that regulates neurotrophin signaling. Variants in KIDINS220 have been linked to spastic paraplegia, intellectual disability, nystagmus, and obesity (SINO) syndrome or prenatal fatal cerebral ventriculomegaly and arthrogryposis (VENARG). This study aimed to investigate the genotype-phenotype correlation of pathogenic KIDINS220 variants. Methods We performed whole-exome sequencing on a patient with SINO syndrome and epilepsy. Identified pathogenic variants were confirmed using Sanger sequencing and evaluated with in silico tools. A comprehensive literature review was conducted to analyze the genetic and phenotypic data of both the newly diagnosed patient and previously reported cases with KIDINS220 variants. Results We identified novel compound heterozygous variants in KIDINS220, c.1556C > T (p.Thr519Met) and c.2374C > T (p.Arg792*), in the patient. Our analysis revealed that biallelic loss-of-function variants in KIDINS220 are associated with VENARG or autosomal recessive SINO (AR-SINO), whereas carboxy-terminal truncated variants that escape nonsense-mediated mRNA decay and lack amino acid residues 1507-1529 are linked to autosomal dominant SINO (AD-SINO). Patients with AR-SINO exhibit more severe clinical features compared to those with AD-SINO. Conclusions Our study expands the spectrum of KIDINS220 variants associated with AR-SINO and provides a valuable genotype-phenotype correlation for pathogenic KIDINS220 variants.
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Affiliation(s)
- Wenke Yang
- Henan Provincial People's Hospital, People's Hospital of Henan University, People's Hospital of Zhengzhou University, Zhengzhou, China
- National Health Commission Key Laboratory of Birth Defects Prevention, Henan Provincial Key Laboratory of Genetic Diseases and Functional Genomics, Zhengzhou, China
- School of Basic Medical Sciences, Henan University, Kaifeng, China
| | - Shuyue Wang
- Henan Provincial People's Hospital, People's Hospital of Henan University, People's Hospital of Zhengzhou University, Zhengzhou, China
- Central Hospital of Wuhan, Wuhan, China
| | - Xiaodong Huo
- Henan Provincial People's Hospital, People's Hospital of Henan University, People's Hospital of Zhengzhou University, Zhengzhou, China
| | - Ke Yang
- Henan Provincial People's Hospital, People's Hospital of Henan University, People's Hospital of Zhengzhou University, Zhengzhou, China
| | - Zhenglong Guo
- Henan Provincial People's Hospital, People's Hospital of Henan University, People's Hospital of Zhengzhou University, Zhengzhou, China
- National Health Commission Key Laboratory of Birth Defects Prevention, Henan Provincial Key Laboratory of Genetic Diseases and Functional Genomics, Zhengzhou, China
| | - Yanjun Li
- Henan Provincial People's Hospital, People's Hospital of Henan University, People's Hospital of Zhengzhou University, Zhengzhou, China
| | - Xinying Ji
- School of Basic Medical Sciences, Henan University, Kaifeng, China
| | - Bingtao Hao
- Henan Provincial People's Hospital, People's Hospital of Henan University, People's Hospital of Zhengzhou University, Zhengzhou, China
- National Health Commission Key Laboratory of Birth Defects Prevention, Henan Provincial Key Laboratory of Genetic Diseases and Functional Genomics, Zhengzhou, China
| | - Shixiu Liao
- Henan Provincial People's Hospital, People's Hospital of Henan University, People's Hospital of Zhengzhou University, Zhengzhou, China
- National Health Commission Key Laboratory of Birth Defects Prevention, Henan Provincial Key Laboratory of Genetic Diseases and Functional Genomics, Zhengzhou, China
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Behera A, Panigrahi GK, Sahoo A. Nonsense-Mediated mRNA Decay in Human Health and Diseases: Current Understanding, Regulatory Mechanisms and Future Perspectives. Mol Biotechnol 2024:10.1007/s12033-024-01267-7. [PMID: 39264527 DOI: 10.1007/s12033-024-01267-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Accepted: 08/24/2024] [Indexed: 09/13/2024]
Abstract
Nonsense-mediated mRNA decay (NMD) is a surveillance mechanism that is conserved across all eukaryotes ensuring the quality of transcripts by targeting messenger RNA (mRNA) harbouring premature stop codons. It regulates the gene expression by targeting aberrant mRNA carrying pre-termination codons (PTCs) and eliminates C-terminal truncated proteins. NMD distinguishes aberrant and non-aberrant transcript by looking after long 3' UTRs and exon-junction complex (EJC) downstream of stop codon that indicate the presence of PTC. Therefore, NMD modulates cellular surveillance and eliminates the truncated proteins but if the PTC escapes the surveillance pathway it can lead to potential negative phenotype resulting in genetic diseases. The alternative splicing also contributes in formation of NMD-sensitive isoforms by introducing PTC. NMD plays a complex role in cancer, it can either aggravate or downregulates the tumour. Some tumours agitate NMD to deteriorate mRNAs encoding tumour suppressor proteins, stress response proteins and neoantigens. In other case, tumours suppress the NMD to encourage the expression of oncoproteins for tumour growth and survival. This mechanism augmented in the development of new therapeutics by PTC read-through mechanism and personalized medicine. Detailed studies on NMD surveillance will possibly lead towards development of strategies for improving human health aligning with United Nations sustainable development goals (SDG 3: Good health and well-being). The potential therapeutic applications of NMD pose a challenge in terms of safe and effective modulation. Understanding the complexities of NMD regulation and its interaction with other cellular processes can lead to the development of new interventions for various diseases.
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Affiliation(s)
- Amrita Behera
- Department of Zoology, School of Applied Sciences, Centurion University of Technology and Management, Jatni, Khordha, Odisha, India
| | - Gagan Kumar Panigrahi
- Department of Zoology, School of Applied Sciences, Centurion University of Technology and Management, Jatni, Khordha, Odisha, India.
| | - Annapurna Sahoo
- Department of Zoology, School of Applied Sciences, Centurion University of Technology and Management, Jatni, Khordha, Odisha, India.
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8
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Pelleter M, Desaintjean C, Gyapay R, Massenavette B, Baudin F, Couque N, Tamisier R, Dudoignon B, Franco P, Mougenel-Chantereau A, Coutier L. A new nonsense pathogenic variant in exon 1 of PHOX2B leads to the diagnosis of congenital central hypoventilation syndrome with intra-familial variability. Arch Pediatr 2024:S0929-693X(24)00130-1. [PMID: 39261201 DOI: 10.1016/j.arcped.2024.06.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 06/20/2024] [Accepted: 06/30/2024] [Indexed: 09/13/2024]
Abstract
Congenital central hypoventilation syndrome (CCHS) is a rare genetic disorder of the autonomic nervous system resulting in decreased brain sensitivity to hypercapnia and hypoxia characterized by a genetic abnormality in the pair-like homeobox 2B (PHOX2B) gene. Most patients have a heterozygous expansion of the polyalanine repeat in exon 3 (PARM), while 10 % of patients have non-PARM (NPARM) mutations that can span the entire gene. The majority of pathogenic variants are de novo, but variants with incomplete penetrance can be identified in the heterozygous state. In the present report, CCHS was diagnosed in a symptomatic 3-month-old infant with neonatal respiratory distress. Genetic analysis revealed a new mutation in exon 1 of the PHOX2B gene - p.Ser28* (c.83C>G) - which was further identified in two family members, one minimally symptomatic and one asymptomatic. The identification of this new mutation supports the importance of sequencing the entire gene even when the classic PARM mutation is not found and highlights the phenotypic variability of CCHS.
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Affiliation(s)
- Morgane Pelleter
- Service de pneumologie, allergologie, mucoviscidose, Hôpital Femme Mère Enfant, Hospices Civils de Lyon, 69500 Bron, France
| | - Charlène Desaintjean
- Service de pneumologie, allergologie, mucoviscidose, Hôpital Femme Mère Enfant, Hospices Civils de Lyon, 69500 Bron, France
| | - Romane Gyapay
- Service de pneumologie, allergologie, mucoviscidose, Hôpital Femme Mère Enfant, Hospices Civils de Lyon, 69500 Bron, France
| | - Bruno Massenavette
- Service de pneumologie, allergologie, mucoviscidose, Hôpital Femme Mère Enfant, Hospices Civils de Lyon, 69500 Bron, France; Service d'Épileptologie Clinique, des Troubles du Sommeil et de Neurologie Fonctionnelle de l'Enfant, Hôpital Femme Mère Enfant, Hospices Civils de Lyon, 69500 Bron, France
| | - Florent Baudin
- Service de réanimation pédiatrique, Hôpital Femme Mère Enfant, Hospices Civils de Lyon, 69500 Bron, France; Agressions Pulmonaires et Circulatoires dans le Sepsis (APCSe), VetAgro Sup, Universités de Lyon, Marcy, l'Etoile, France
| | - Nathalie Couque
- Département de Génétique, Hôpital Robert Debré, Assistance Publique - Hôpitaux de Paris, 75000 Paris, France
| | - Renaud Tamisier
- Grenoble Alpes University, HP2 Laboratory, INSERM, 38043 Grenoble, France; Pôle Thorax et Vaisseaux, Grenoble Alpes University Hospital, 38043 Grenoble, France
| | - Benjamin Dudoignon
- Université de Paris, AP-HP, Hôpital Robert Debré, Service de Physiologie Pédiatrique Centre du Sommeil-CRMR Hypoventilations alvéolaires rares, INSERM NeuroDiderot, F-75019 Paris, France
| | - Patricia Franco
- Service d'Épileptologie Clinique, des Troubles du Sommeil et de Neurologie Fonctionnelle de l'Enfant, Hôpital Femme Mère Enfant, Hospices Civils de Lyon, 69500 Bron, France; Unité INSERM U1028 CNRS UMR 5292, Université Lyon 1, Lyon, France
| | - Antoine Mougenel-Chantereau
- Service de pneumologie, allergologie, mucoviscidose, Hôpital Femme Mère Enfant, Hospices Civils de Lyon, 69500 Bron, France
| | - Laurianne Coutier
- Service de pneumologie, allergologie, mucoviscidose, Hôpital Femme Mère Enfant, Hospices Civils de Lyon, 69500 Bron, France; Service d'Épileptologie Clinique, des Troubles du Sommeil et de Neurologie Fonctionnelle de l'Enfant, Hôpital Femme Mère Enfant, Hospices Civils de Lyon, 69500 Bron, France; Unité INSERM U1028 CNRS UMR 5292, Université Lyon 1, Lyon, France.
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9
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Li F, Wang X, Zhang J, Zhang J, Jing X, Jiang Q, Zhou J, Cao L, Peng H, Tong D, Huang C. RBM8A, a new target of TEAD4, promotes breast cancer progression by regulating IGF1R and IRS-2. J Transl Med 2024; 22:823. [PMID: 39232805 PMCID: PMC11373126 DOI: 10.1186/s12967-024-05639-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Accepted: 08/27/2024] [Indexed: 09/06/2024] Open
Abstract
BACKGROUND Breast cancer (BC) is the most common malignant tumor in women worldwide, and further elucidation of the molecular mechanisms involved in BC pathogenesis is essential to improve the prognosis of BC patients. RNA Binding Motif Protein 8 A (RBM8A), with high affinity to a myriad of RNA transcripts, has been shown to play a crucial role in genesis and progression of multiple cancers. We attempted to explore its functional significance and molecular mechanisms in BC. METHODS Bioinformatics analysis was performed on publicly available BC datasets. qRT-PCR was used to determine the expression of RBM8A in BC tissues. MTT assay, clone formation assay and flow cytometry were employed to examine BC cell proliferation and apoptosis in vitro. RNA immunoprecipitation (RIP) and RIP-seq were used to investigate the binding of RBM8A/EIF4A3 to the mRNA of IGF1R/IRS-2. RBM8A and EIF4A3 interactions were determined by co-immunoprecipitation (Co-IP) and immunofluorescence. Chromatin immunoprecipitation (Ch-IP) and dual-luciferase reporter assay were carried out to investigate the transcriptional regulation of RBM8A by TEAD4. Xenograft model was used to explore the effects of RBM8A and TEAD4 on BC cell growth in vivo. RESULTS In this study, we showed that RBM8A is abnormally highly expressed in BC and knockdown of RBM8A inhibits BC cell proliferation and induces apoptosis in vitro. EIF4A3, which phenocopy RBM8A in BC, forms a complex with RBM8A in BC. Moreover, EIF4A3 and RBM8A complex regulate the expression of IGF1R and IRS-2 to activate the PI3K/AKT signaling pathway, thereby promoting BC progression. In addition, we identified TEAD4 as a transcriptional activator of RBM8A by Ch-IP, dual luciferase reporter gene and a series of functional rescue assays. Furthermore, we demonstrated the in vivo pro-carcinogenic effects of TEAD4 and RBM8A by xenograft tumor experiments in nude mice. CONCLUSION Collectively, these findings suggest that TEAD4 novel transcriptional target RBM8A interacts with EIF4A3 to increase IGF1R and IRS-2 expression and activate PI3K/AKT signaling pathway, thereby further promoting the malignant phenotype of BC cells.
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Affiliation(s)
- Fang Li
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Xi'an Jiaotong, University School of Health Science Center, Xi'an, 710301, Shaanxi, China
| | - Xiaofei Wang
- Biomedical Experimental Center, Xi'an Jiaotong University, Xi'an, 710061, Shaanxi, China
| | - Jing Zhang
- Institute of Basic Medical Sciences, Xi'an Medical University, No. 1 XinWang Road, Weiyang District, Xi'an, 710021, Shaanxi, China
- Medical Research and Experimental Center, The Second Affiliated Hospital of Xi 'an Medical University, Xi'an, 710077, Shaanxi Province, China
| | - Jinyuan Zhang
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Xi'an Jiaotong, University School of Health Science Center, Xi'an, 710301, Shaanxi, China
| | - Xintao Jing
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Xi'an Jiaotong, University School of Health Science Center, Xi'an, 710301, Shaanxi, China
| | - Qiuyu Jiang
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Xi'an Jiaotong, University School of Health Science Center, Xi'an, 710301, Shaanxi, China
| | - Jing Zhou
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Xi'an Jiaotong, University School of Health Science Center, Xi'an, 710301, Shaanxi, China
| | - Li Cao
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Xi'an Jiaotong, University School of Health Science Center, Xi'an, 710301, Shaanxi, China
| | - Hang Peng
- Second Department of General Surgery, Shaanxi Provincial People's Hospital, Xi'an, 710068, Shaanxi, China
| | - Dongdong Tong
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Xi'an Jiaotong, University School of Health Science Center, Xi'an, 710301, Shaanxi, China.
| | - Chen Huang
- The Comprehensive Breast Care Center, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710000, Shaanxi, China.
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Xi'an Jiaotong, University School of Health Science Center, Xi'an, 710301, Shaanxi, China.
- Biomedical Experimental Center, Xi'an Jiaotong University, Xi'an, 710061, Shaanxi, China.
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10
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Greene D, De Wispelaere K, Lees J, Katrinecz A, Pascoal S, Hales E, Codina-Solà M, Valenzuela I, Tizzano EF, Atton G, Donnelly D, Foulds N, Jarvis J, McKee S, O'Donoghue M, Suri M, Vasudevan P, Stirrups K, Morgan NP, Freson K, Mumford AD, Turro E. Mutations in the U2 snRNA gene RNU2-2P cause a severe neurodevelopmental disorder with prominent epilepsy. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.09.03.24312863. [PMID: 39281759 PMCID: PMC11398430 DOI: 10.1101/2024.09.03.24312863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/18/2024]
Abstract
The major spliceosome comprises the five snRNAs U1, U2, U4, U5 and U6. We recently showed that mutations in RNU4- 2, which encodes U4 snRNA, cause one of the most prevalent monogenic neurodevelopmental disorders. Here, we report that recurrent germline mutations in RNU2-2P , a 191bp gene encoding U2 snRNA, are responsible for a related disorder. By genetic association, we implicated recurrent de novo single nucleotide mutations at nucleotide positions 4 and 35 of RNU2-2P among nine cases. We replicated this finding in six additional cases, bringing the total to 15. The disorder is characterized by intellectual disability, neurodevelopmental delay, autistic behavior, microcephaly, hypotonia, epilepsy and hyperventilation. All cases display a severe and complex seizure phenotype. Our findings cement the role of major spliceosomal snRNAs in the etiologies of neurodevelopmental disorders.
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11
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Arana ÁJ, Sánchez L. Knockout, Knockdown, and the Schrödinger Paradox: Genetic Immunity to Phenotypic Recapitulation in Zebrafish. Genes (Basel) 2024; 15:1164. [PMID: 39336755 PMCID: PMC11431394 DOI: 10.3390/genes15091164] [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: 07/29/2024] [Revised: 08/27/2024] [Accepted: 08/30/2024] [Indexed: 09/30/2024] Open
Abstract
Previous research has highlighted significant phenotypic discrepancies between knockout and knockdown approaches in zebrafish, raising concerns about the reliability of these methods. However, our study suggests that these differences are not as pronounced as was once believed. By carefully examining the roles of maternal and zygotic gene contributions, we demonstrate that these factors significantly influence phenotypic outcomes, often accounting for the observed discrepancies. Our findings emphasize that morpholinos, despite their potential off-target effects, can be effective tools when used with rigorous controls. We introduce the concept of graded maternal contribution, which explains how the uneven distribution of maternal mRNA and proteins during gametogenesis impacts phenotypic variability. Our research categorizes genes into three types-susceptible, immune, and "Schrödinger" (conditional)-based on their phenotypic expression and interaction with genetic compensation mechanisms. This distinction provides new insights into the paradoxical outcomes observed in genetic studies. Ultimately, our work underscores the importance of considering both maternal and zygotic contributions, alongside rigorous experimental controls, to accurately interpret gene function and the mechanisms underlying disease. This study advocates for the continued use of morpholinos in conjunction with advanced genetic tools like CRISPR/Cas9, stressing the need for a meticulous experimental design to optimize the utility of zebrafish in genetic research and therapeutic development.
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12
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Aggarwal S, Vineeth VS, Padwal SS, Bhat SA, Singh A, Kulkarni A, Patil M, Tallapaka K, Pasumarthi D, Venkatapuram V, Thotakura PL, Dalal A, Bhandari R. SERPINA11 related novel serpinopathy - A perinatal lethal disorder. Clin Genet 2024; 106:367-373. [PMID: 38831697 DOI: 10.1111/cge.14564] [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: 03/02/2024] [Revised: 05/13/2024] [Accepted: 05/15/2024] [Indexed: 06/05/2024]
Abstract
SERPINA11 is a hitherto poorly characterised gene belonging to Clade A of the SERPIN superfamily, with unknown expression pattern and functional significance. We report a perinatal lethal phenotype in two foetuses from the same family associated with a biallelic loss of function variant in SERPINA11, and provide functional evidence to support its candidature as a Mendelian disorder. The SERPINA11 variant-associated foetal phenotype is characterised by gross and histopathological features of extracellular matrix disruption. Western blot and immunofluorescence analyses revealed SERPINA11 expression in multiple mouse tissues, with pronounced expression in the bronchiolar epithelium. We observed a significant decrease in SERPINA11 immunofluorescence in the affected foetal lung compared with a healthy gestation-matched foetus. Protein expression data from HEK293T cell lines following site-directed mutagenesis support the loss of function nature of the variant. Transcriptome analysis from the affected foetal liver indicated the possibility of reduced SERPINA11 transcript abundance. This novel serpinopathy appears to be a consequence of the loss of inhibition of serine proteases involved in extracellular matrix remodelling, revealing SERPINA11 as a protease inhibitor critical for embryonic development.
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Affiliation(s)
- Shagun Aggarwal
- Department of Medical Genetics, Nizam's Institute of Medical Sciences, Hyderabad, India
- Laboratory of Human and Medical Genetics, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | - Venugopal Satidevi Vineeth
- Laboratory of Human and Medical Genetics, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | - Shrutika S Padwal
- Laboratory of Human and Medical Genetics, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
- Laboratory of Cell Signalling, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
- Manipal Academy of Higher Education, Manipal, India
| | - Sameer Ahmed Bhat
- Laboratory of Cell Signalling, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | - Arpita Singh
- Laboratory of Cell Signalling, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
- Regional Centre for Biotechnology, Faridabad, India
| | - Aditya Kulkarni
- Department of Histopathology, Apollo Hospitals, Hyderabad, India
| | - Mallikarjun Patil
- Department of Medical Genetics, Nizam's Institute of Medical Sciences, Hyderabad, India
| | | | - Divya Pasumarthi
- Laboratory of Human and Medical Genetics, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | - Vijayasree Venkatapuram
- Department of Medical Genetics, Nizam's Institute of Medical Sciences, Hyderabad, India
- Laboratory of Human and Medical Genetics, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | - Pragna Lakshmi Thotakura
- Laboratory of Human and Medical Genetics, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | - Ashwin Dalal
- Laboratory of Human and Medical Genetics, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | - Rashna Bhandari
- Laboratory of Cell Signalling, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
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13
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Nunes L, Li F, Wu M, Luo T, Hammarström K, Torell E, Ljuslinder I, Mezheyeuski A, Edqvist PH, Löfgren-Burström A, Zingmark C, Edin S, Larsson C, Mathot L, Osterman E, Osterlund E, Ljungström V, Neves I, Yacoub N, Guðnadóttir U, Birgisson H, Enblad M, Ponten F, Palmqvist R, Xu X, Uhlén M, Wu K, Glimelius B, Lin C, Sjöblom T. Prognostic genome and transcriptome signatures in colorectal cancers. Nature 2024; 633:137-146. [PMID: 39112715 PMCID: PMC11374687 DOI: 10.1038/s41586-024-07769-3] [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: 04/24/2023] [Accepted: 07/01/2024] [Indexed: 08/17/2024]
Abstract
Colorectal cancer is caused by a sequence of somatic genomic alterations affecting driver genes in core cancer pathways1. Here, to understand the functional and prognostic impact of cancer-causing somatic mutations, we analysed the whole genomes and transcriptomes of 1,063 primary colorectal cancers in a population-based cohort with long-term follow-up. From the 96 mutated driver genes, 9 were not previously implicated in colorectal cancer and 24 had not been linked to any cancer. Two distinct patterns of pathway co-mutations were observed, timing analyses identified nine early and three late driver gene mutations, and several signatures of colorectal-cancer-specific mutational processes were identified. Mutations in WNT, EGFR and TGFβ pathway genes, the mitochondrial CYB gene and 3 regulatory elements along with 21 copy-number variations and the COSMIC SBS44 signature correlated with survival. Gene expression classification yielded five prognostic subtypes with distinct molecular features, in part explained by underlying genomic alterations. Microsatellite-instable tumours divided into two classes with different levels of hypoxia and infiltration of immune and stromal cells. To our knowledge, this study constitutes the largest integrated genome and transcriptome analysis of colorectal cancer, and interlinks mutations, gene expression and patient outcomes. The identification of prognostic mutations and expression subtypes can guide future efforts to individualize colorectal cancer therapy.
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Affiliation(s)
- Luís Nunes
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Fuqiang Li
- HIM-BGI Omics Center, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences (CAS), BGI Research, Hangzhou, China
- Guangdong Provincial Key Laboratory of Human Disease Genomics, Shenzhen Key Laboratory of Genomics, BGI Research, Shenzhen, China
- Institute of Intelligent Medical Research (IIMR), BGI Genomics, Shenzhen, China
| | - Meizhen Wu
- HIM-BGI Omics Center, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences (CAS), BGI Research, Hangzhou, China
- Guangdong Provincial Key Laboratory of Human Disease Genomics, Shenzhen Key Laboratory of Genomics, BGI Research, Shenzhen, China
- Institute of Intelligent Medical Research (IIMR), BGI Genomics, Shenzhen, China
| | - Tian Luo
- HIM-BGI Omics Center, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences (CAS), BGI Research, Hangzhou, China
- Guangdong Provincial Key Laboratory of Human Disease Genomics, Shenzhen Key Laboratory of Genomics, BGI Research, Shenzhen, China
- Institute of Intelligent Medical Research (IIMR), BGI Genomics, Shenzhen, China
| | - Klara Hammarström
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Emma Torell
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Ingrid Ljuslinder
- Department of Radiation Sciences, Oncology, Umeå University, Umeå, Sweden
| | - Artur Mezheyeuski
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Per-Henrik Edqvist
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | | | - Carl Zingmark
- Department of Medical Biosciences, Pathology, Umeå University, Umeå, Sweden
| | - Sofia Edin
- Department of Medical Biosciences, Pathology, Umeå University, Umeå, Sweden
| | - Chatarina Larsson
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Lucy Mathot
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Erik Osterman
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Emerik Osterlund
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Viktor Ljungström
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Inês Neves
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Nicole Yacoub
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Unnur Guðnadóttir
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Helgi Birgisson
- Department of Surgical Sciences, Uppsala University, Akademiska sjukhuset, Uppsala, Sweden
| | - Malin Enblad
- Department of Surgical Sciences, Uppsala University, Akademiska sjukhuset, Uppsala, Sweden
| | - Fredrik Ponten
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Richard Palmqvist
- Department of Medical Biosciences, Pathology, Umeå University, Umeå, Sweden
| | - Xun Xu
- HIM-BGI Omics Center, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences (CAS), BGI Research, Hangzhou, China
| | - Mathias Uhlén
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
- Science for Life Laboratory, Department of Protein Science, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Kui Wu
- HIM-BGI Omics Center, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences (CAS), BGI Research, Hangzhou, China.
- Guangdong Provincial Key Laboratory of Human Disease Genomics, Shenzhen Key Laboratory of Genomics, BGI Research, Shenzhen, China.
- Institute of Intelligent Medical Research (IIMR), BGI Genomics, Shenzhen, China.
| | - Bengt Glimelius
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
| | - Cong Lin
- HIM-BGI Omics Center, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences (CAS), BGI Research, Hangzhou, China.
- Guangdong Provincial Key Laboratory of Human Disease Genomics, Shenzhen Key Laboratory of Genomics, BGI Research, Shenzhen, China.
- Institute of Intelligent Medical Research (IIMR), BGI Genomics, Shenzhen, China.
| | - Tobias Sjöblom
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
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14
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Nadimpalli Kobren S, Moldovan MA, Reimers R, Traviglia D, Li X, Barnum D, Veit A, Willett J, Berselli M, Ronchetti W, Sherwood R, Krier J, Kohane IS, Sunyaev SR. Joint, multifaceted genomic analysis enables diagnosis of diverse, ultra-rare monogenic presentations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.13.580158. [PMID: 38405764 PMCID: PMC10888768 DOI: 10.1101/2024.02.13.580158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Genomics for rare disease diagnosis has advanced at a rapid pace due to our ability to perform "N-of-1" analyses on individual patients with ultra-rare diseases. The increasing sizes of ultra-rare disease cohorts internationally newly enables cohort-wide analyses for new discoveries, but well-calibrated statistical genetics approaches for jointly analyzing these patients are still under development.1,2 The Undiagnosed Diseases Network (UDN) brings multiple clinical, research and experimental centers under the same umbrella across the United States to facilitate and scale N-of-1 analyses. Here, we present the first joint analysis of whole genome sequencing data of UDN patients across the network. We introduce new, well-calibrated statistical methods for prioritizing disease genes with de novo recurrence and compound heterozygosity. We also detect pathways enriched with candidate and known diagnostic genes. Our computational analysis, coupled with a systematic clinical review, recapitulated known diagnoses and revealed new disease associations. We further release a software package, RaMeDiES, enabling automated cross-analysis of deidentified sequenced cohorts for new diagnostic and research discoveries. Gene-level findings and variant-level information across the cohort are available in a public-facing browser (https://dbmi-bgm.github.io/udn-browser/). These results show that N-of-1 efforts should be supplemented by a joint genomic analysis across cohorts.
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Affiliation(s)
| | | | | | - Daniel Traviglia
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA
| | - Xinyun Li
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT
| | | | - Alexander Veit
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA
| | - Julian Willett
- Department of Neurology, Massachusetts General Hospital, Boston, MA
| | - Michele Berselli
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA
| | - William Ronchetti
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA
| | - Richard Sherwood
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA
| | - Joel Krier
- Department of Genetics, Atrius Health, Boston, MA
| | - Isaac S. Kohane
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA
| | | | - Shamil R Sunyaev
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA
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15
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Nicolas-Martinez EC, Robinson O, Pflueger C, Gardner A, Corbett MA, Ritchie T, Kroes T, van Eyk CL, Scheffer IE, Hildebrand MS, Barnier JV, Rousseau V, Genevieve D, Haushalter V, Piton A, Denommé-Pichon AS, Bruel AL, Nambot S, Isidor B, Grigg J, Gonzalez T, Ghedia S, Marchant RG, Bournazos A, Wong WK, Webster RI, Evesson FJ, Jones KJ, Cooper ST, Lister R, Gecz J, Jolly LA. RNA variant assessment using transactivation and transdifferentiation. Am J Hum Genet 2024; 111:1673-1699. [PMID: 39084224 PMCID: PMC11339655 DOI: 10.1016/j.ajhg.2024.06.018] [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: 03/08/2024] [Revised: 06/27/2024] [Accepted: 06/28/2024] [Indexed: 08/02/2024] Open
Abstract
Understanding the impact of splicing and nonsense variants on RNA is crucial for the resolution of variant classification as well as their suitability for precision medicine interventions. This is primarily enabled through RNA studies involving transcriptomics followed by targeted assays using RNA isolated from clinically accessible tissues (CATs) such as blood or skin of affected individuals. Insufficient disease gene expression in CATs does however pose a major barrier to RNA based investigations, which we show is relevant to 1,436 Mendelian disease genes. We term these "silent" Mendelian genes (SMGs), the largest portion (36%) of which are associated with neurological disorders. We developed two approaches to induce SMG expression in human dermal fibroblasts (HDFs) to overcome this limitation, including CRISPR-activation-based gene transactivation and fibroblast-to-neuron transdifferentiation. Initial transactivation screens involving 40 SMGs stimulated our development of a highly multiplexed transactivation system culminating in the 6- to 90,000-fold induction of expression of 20/20 (100%) SMGs tested in HDFs. Transdifferentiation of HDFs directly to neurons led to expression of 193/516 (37.4%) of SMGs implicated in neurological disease. The magnitude and isoform diversity of SMG expression following either transactivation or transdifferentiation was comparable to clinically relevant tissues. We apply transdifferentiation and/or gene transactivation combined with short- and long-read RNA sequencing to investigate the impact that variants in USH2A, SCN1A, DMD, and PAK3 have on RNA using HDFs derived from affected individuals. Transactivation and transdifferentiation represent rapid, scalable functional genomic solutions to investigate variants impacting SMGs in the patient cell and genomic context.
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Affiliation(s)
- Emmylou C Nicolas-Martinez
- The Robinson Research Institute, University of Adelaide, Adelaide, SA 5005, Australia; School of Biomedicine, University of Adelaide, Adelaide, SA 5005, Australia
| | - Olivia Robinson
- The Robinson Research Institute, University of Adelaide, Adelaide, SA 5005, Australia; School of Biomedicine, University of Adelaide, Adelaide, SA 5005, Australia
| | - Christian Pflueger
- Harry Perkins Institute of Medical Research, Nedlands, WA 6009, Australia; Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Crawley, WA 6009, Australia; The Robinson Research Institute, University of Adelaide, Adelaide, SA 5005, Australia
| | - Alison Gardner
- The Robinson Research Institute, University of Adelaide, Adelaide, SA 5005, Australia; Adelaide Medical School, University of Adelaide, Adelaide, SA 5005, Australia
| | - Mark A Corbett
- The Robinson Research Institute, University of Adelaide, Adelaide, SA 5005, Australia; Adelaide Medical School, University of Adelaide, Adelaide, SA 5005, Australia; The Robinson Research Institute, University of Adelaide, Adelaide, SA 5005, Australia
| | - Tarin Ritchie
- The Robinson Research Institute, University of Adelaide, Adelaide, SA 5005, Australia; Adelaide Medical School, University of Adelaide, Adelaide, SA 5005, Australia
| | - Thessa Kroes
- The Robinson Research Institute, University of Adelaide, Adelaide, SA 5005, Australia; Adelaide Medical School, University of Adelaide, Adelaide, SA 5005, Australia
| | - Clare L van Eyk
- The Robinson Research Institute, University of Adelaide, Adelaide, SA 5005, Australia; Adelaide Medical School, University of Adelaide, Adelaide, SA 5005, Australia; The Robinson Research Institute, University of Adelaide, Adelaide, SA 5005, Australia
| | - Ingrid E Scheffer
- Epilepsy Research Centre, Department of Medicine, The University of Melbourne, Austin Health, Heidelberg, VIC 3084, Australia; Murdoch Children's Research Institute, Parkville, VIC 3052, Australia; Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville, VIC 3052, Australia; Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Parkville, VIC 3052, Australia
| | - Michael S Hildebrand
- Epilepsy Research Centre, Department of Medicine, The University of Melbourne, Austin Health, Heidelberg, VIC 3084, Australia; Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Parkville, VIC 3052, Australia; The Robinson Research Institute, University of Adelaide, Adelaide, SA 5005, Australia
| | - Jean-Vianney Barnier
- Institut des Neurosciences Paris-Saclay, UMR 9197, CNRS, Université Paris-Saclay, Saclay, France
| | - Véronique Rousseau
- Institut des Neurosciences Paris-Saclay, UMR 9197, CNRS, Université Paris-Saclay, Saclay, France
| | - David Genevieve
- Montpellier University, Inserm U1183, Reference Center for Rare Diseases Developmental Anomaly and Malformative Syndromes, Genetics Department, Montpellier Hospital, Montpellier, France
| | - Virginie Haushalter
- Genetic Diagnosis Laboratory, Strasbourg University Hospital, Strasbourg, France
| | - Amélie Piton
- Genetic Diagnosis Laboratory, Strasbourg University Hospital, Strasbourg, France
| | - Anne-Sophie Denommé-Pichon
- CRMRs "Anomalies du Développement et syndromes malformatifs" et "Déficiences Intellectuelles de causes rares", Centre de Génétique, CHU Dijon, Dijon, France; INSERM UMR1231, GAD "Génétique des Anomalies du Développement," FHU-TRANSLAD, University of Burgundy, Dijon, France
| | - Ange-Line Bruel
- CRMRs "Anomalies du Développement et syndromes malformatifs" et "Déficiences Intellectuelles de causes rares", Centre de Génétique, CHU Dijon, Dijon, France; INSERM UMR1231, GAD "Génétique des Anomalies du Développement," FHU-TRANSLAD, University of Burgundy, Dijon, France
| | - Sophie Nambot
- CRMRs "Anomalies du Développement et syndromes malformatifs" et "Déficiences Intellectuelles de causes rares", Centre de Génétique, CHU Dijon, Dijon, France; INSERM UMR1231, GAD "Génétique des Anomalies du Développement," FHU-TRANSLAD, University of Burgundy, Dijon, France
| | - Bertrand Isidor
- CRMRs "Anomalies du Développement et syndromes malformatifs" et "Déficiences Intellectuelles de causes rares", Centre de Génétique, CHU Dijon, Dijon, France; INSERM UMR1231, GAD "Génétique des Anomalies du Développement," FHU-TRANSLAD, University of Burgundy, Dijon, France
| | - John Grigg
- Speciality of Ophthalmology, Save Sight Institute, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2000, Australia
| | - Tina Gonzalez
- Department of Clinical Genetics, Royal North Shore Hospital, St Leonards, NSW 2065, Australia
| | - Sondhya Ghedia
- Department of Clinical Genetics, Royal North Shore Hospital, St Leonards, NSW 2065, Australia
| | - Rhett G Marchant
- Kids Neuroscience Centre, Kids Research, Children's Hospital at Westmead, Westmead, NSW 2145, Australia; Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2000, Australia
| | - Adam Bournazos
- Kids Neuroscience Centre, Kids Research, Children's Hospital at Westmead, Westmead, NSW 2145, Australia; Children's Medical Research Institute, Westmead, NSW 2145, Australia
| | - Wui-Kwan Wong
- Kids Neuroscience Centre, Kids Research, Children's Hospital at Westmead, Westmead, NSW 2145, Australia; Children's Medical Research Institute, Westmead, NSW 2145, Australia; Department of Paediatric Neurology, Children's Hospital at Westmead, Sydney, NSW 2000, Australia
| | - Richard I Webster
- Department of Paediatric Neurology, Children's Hospital at Westmead, Sydney, NSW 2000, Australia
| | - Frances J Evesson
- Kids Neuroscience Centre, Kids Research, Children's Hospital at Westmead, Westmead, NSW 2145, Australia; Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2000, Australia; Children's Medical Research Institute, Westmead, NSW 2145, Australia
| | - Kristi J Jones
- Kids Neuroscience Centre, Kids Research, Children's Hospital at Westmead, Westmead, NSW 2145, Australia; Children's Medical Research Institute, Westmead, NSW 2145, Australia; Department of Clinical Genetics, Children's Hospital at Westmead, Sydney, NSW 2000, Australia
| | - Sandra T Cooper
- Kids Neuroscience Centre, Kids Research, Children's Hospital at Westmead, Westmead, NSW 2145, Australia; Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2000, Australia; Children's Medical Research Institute, Westmead, NSW 2145, Australia
| | - Ryan Lister
- Harry Perkins Institute of Medical Research, Nedlands, WA 6009, Australia; Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Crawley, WA 6009, Australia
| | - Jozef Gecz
- The Robinson Research Institute, University of Adelaide, Adelaide, SA 5005, Australia; Adelaide Medical School, University of Adelaide, Adelaide, SA 5005, Australia; South Australian Health and Medical Research Institute, Adelaide, SA 5000, Australia.
| | - Lachlan A Jolly
- The Robinson Research Institute, University of Adelaide, Adelaide, SA 5005, Australia; School of Biomedicine, University of Adelaide, Adelaide, SA 5005, Australia.
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16
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Adduri A, Kim S. Ornaments for efficient allele-specific expression estimation with bias correction. Am J Hum Genet 2024; 111:1770-1781. [PMID: 39047729 PMCID: PMC11339617 DOI: 10.1016/j.ajhg.2024.06.014] [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: 09/27/2023] [Revised: 06/22/2024] [Accepted: 06/24/2024] [Indexed: 07/27/2024] Open
Abstract
Allele-specific expression plays a crucial role in unraveling various biological mechanisms, including genomic imprinting and gene expression controlled by cis-regulatory variants. However, existing methods for quantification from RNA-sequencing (RNA-seq) reads do not adequately and efficiently remove various allele-specific read mapping biases, such as reference bias arising from reads containing the alternative allele that do not map to the reference transcriptome or ambiguous mapping bias caused by reads containing the reference allele that map differently from reads containing the alternative allele. We present Ornaments, a computational tool for rapid and accurate estimation of allele-specific transcript expression at unphased heterozygous loci from RNA-seq reads while correcting for allele-specific read mapping biases. Ornaments removes reference bias by mapping reads to a personalized transcriptome and ambiguous mapping bias by probabilistically assigning reads to multiple transcripts and variant loci they map to. Ornaments is a lightweight extension of kallisto, a popular tool for fast RNA-seq quantification, that improves the efficiency and accuracy of WASP, a popular tool for bias correction in allele-specific read mapping. In experiments with simulated and human lymphoblastoid cell-line RNA-seq reads with the genomes of the 1000 Genomes Project, we demonstrate that Ornaments improves the accuracy of WASP and kallisto, is nearly as efficient as kallisto, and is an order of magnitude faster than WASP per sample, with the additional cost of constructing a personalized index for multiple samples. Additionally, we show that Ornaments finds imprinted transcripts with higher sensitivity than WASP, which detects imprinted signals only at gene level.
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Affiliation(s)
- Abhinav Adduri
- Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Seyoung Kim
- Department of Epidemiology, University of Pittsburgh, Pittsburgh, PA 15261, USA.
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17
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Fang N, Liu B, Pan Q, Gong T, Zhan M, Zhao J, Wang Q, Tang Y, Li Y, He J, Xiang T, Sun F, Lu L, Xia J. SMG5 Inhibition Restrains Hepatocellular Carcinoma Growth and Enhances Sorafenib Sensitivity. Mol Cancer Ther 2024; 23:1188-1200. [PMID: 38647536 DOI: 10.1158/1535-7163.mct-23-0729] [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: 10/23/2023] [Revised: 02/25/2024] [Accepted: 04/16/2024] [Indexed: 04/25/2024]
Abstract
Hepatocellular carcinoma (HCC) has a pathogenesis that remains elusive with restricted therapeutic strategies and efficacy. This study aimed to investigate the role of SMG5, a crucial component in nonsense-mediated mRNA decay (NMD) that degrades mRNA containing a premature termination codon, in HCC pathogenesis and therapeutic resistance. We demonstrated an elevated expression of SMG5 in HCC and scrutinized its potential as a therapeutic target. Our findings revealed that SMG5 knockdown not only inhibited the migration, invasion, and proliferation of HCC cells but also influenced sorafenib resistance. Differential gene expression analysis between the control and SMG5 knockdown groups showed an upregulation of methionine adenosyltransferase 1A in the latter. High expression of methionine adenosyltransferase 1A, a catalyst for S-adenosylmethionine (SAM) production, as suggested by The Cancer Genome Atlas data, was indicative of a better prognosis for HCC. Further, an ELISA showed a higher concentration of SAM in SMG5 knockdown cell supernatants. Furthermore, we found that exogenous SAM supplementation enhanced the sensitivity of HCC cells to sorafenib alongside changes in the expression of Bax and Bcl-2, apoptosis-related proteins. Our findings underscore the important role of SMG5 in HCC development and its involvement in sorafenib resistance, highlighting it as a potential target for HCC treatment.
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Affiliation(s)
- Nan Fang
- Guangdong Provincial Key Laboratory of Tumor Interventional Diagnosis and Treatment, Zhuhai Clinical Medical College of Jinan University (Zhuhai People's Hospital), Zhuhai, P. R. China
| | - Bing Liu
- Guangdong Provincial Key Laboratory of Tumor Interventional Diagnosis and Treatment, Zhuhai Clinical Medical College of Jinan University (Zhuhai People's Hospital), Zhuhai, P. R. China
| | - Qiuzhong Pan
- Department of Biotherapy, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China
| | - Tingting Gong
- Department of Ultrasound, The Fifth Affiliated Hospital of Sun Yat-Sen University, Zhuhai, P. R. China
| | - Meixiao Zhan
- Guangdong Provincial Key Laboratory of Tumor Interventional Diagnosis and Treatment, Zhuhai Clinical Medical College of Jinan University (Zhuhai People's Hospital), Zhuhai, P. R. China
| | - Jingjing Zhao
- Department of Biotherapy, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China
| | - Qijing Wang
- Department of Biotherapy, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China
| | - Yan Tang
- Department of Biotherapy, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China
| | - Yongqiang Li
- Department of Biotherapy, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China
| | - Jia He
- Department of Biotherapy, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China
| | - Tong Xiang
- Department of Experimental Research, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China
| | - Fengze Sun
- Guangdong Provincial Key Laboratory of Tumor Interventional Diagnosis and Treatment, Zhuhai Clinical Medical College of Jinan University (Zhuhai People's Hospital), Zhuhai, P. R. China
- Department of Biotherapy, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China
| | - Ligong Lu
- Guangdong Provincial Key Laboratory of Tumor Interventional Diagnosis and Treatment, Zhuhai Clinical Medical College of Jinan University (Zhuhai People's Hospital), Zhuhai, P. R. China
| | - Jianchuan Xia
- Department of Biotherapy, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China
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18
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Stawiński P, Płoski R. Genebe.net: Implementation and validation of an automatic ACMG variant pathogenicity criteria assignment. Clin Genet 2024; 106:119-126. [PMID: 38440907 DOI: 10.1111/cge.14516] [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: 11/17/2023] [Revised: 02/21/2024] [Accepted: 02/23/2024] [Indexed: 03/06/2024]
Abstract
We present GeneBe, an online platform streamlining the automated application of American College of Medical Genetics and Genomics (ACMG), Association for Molecular Pathology (AMP), and the College of American Pathologists (CAP) criteria for assessment of pathogenicity of genetic variants. GeneBe utilizes automated algorithms that evaluate 17 criteria from 28, closely aligning with current guidelines and leveraging data from diverse sources, including ClinVar. The user-friendly web interface enables manual refinement of assignments for specific criteria based on site-collected data. Our algorithm demonstrates a high correlation (r = 0.90) of assigned pathogenicity scores compared to expert assessments from the ClinGen Evidence Repository and substantial concordance with ClinVar verdict assignments (κ = 0.69). Comparative analysis with other published tools reveals that GeneBe performs similarly to VarSome while being superior over TAPES and InterVar. In contrast to some other tools, GeneBe's web implementation is tracker-free and third-party request-free, safeguarding user privacy. Additionally, GeneBe offers an Application Programming Interface (API) for enhanced flexibility and integration into existing workflows and is provided free of charge for research purposes. GeneBe is available at https://genebe.net.
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Affiliation(s)
- Piotr Stawiński
- Department of Medical Genetics, Medical University of Warsaw, Warsaw, Poland
| | - Rafał Płoski
- Department of Medical Genetics, Medical University of Warsaw, Warsaw, Poland
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19
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Moresco G, Bedeschi MF, Venturin M, Villa R, Costanza J, Mauri A, Santaniello C, Picciolini O, Messina L, Triulzi F, Miozzo MR, Rondinone O, Fontana L. Exploring the Impact of Genetics in a Large Cohort of Moebius Patients by Trio Whole Exome Sequencing. Genes (Basel) 2024; 15:971. [PMID: 39202332 PMCID: PMC11353404 DOI: 10.3390/genes15080971] [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: 07/03/2024] [Revised: 07/15/2024] [Accepted: 07/17/2024] [Indexed: 09/03/2024] Open
Abstract
Moebius syndrome (MBS) is a rare congenital disorder characterized by non-progressive facial palsy and ocular abduction paralysis. Most cases are sporadic, but also rare familial cases with autosomal dominant transmission and incomplete penetrance/variable expressivity have been described. The genetic etiology of MBS is still unclear: de novo pathogenic variants in REV3L and PLXND1 are reported in only a minority of cases, suggesting the involvement of additional causative genes. With the aim to uncover the molecular causative defect and identify a potential genetic basis of this condition, we performed trio-WES on a cohort of 37 MBS and MBS-like patients. No de novo variants emerged in REV3L and PLXND1. We then proceeded with a cohort analysis to identify possible common causative genes among all patients and a trio-based analysis using an in silico panel of candidate genes. However, identified variants emerging from both approaches were considered unlikely to be causative of MBS, mainly due to the lack of clinical overlap. In conclusion, despite this large cohort, WES failed to identify mutations possibly associated with MBS, further supporting the heterogeneity of this syndrome, and suggesting the need for integrated omics approaches to identify the molecular causes underlying MBS development.
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Affiliation(s)
- Giada Moresco
- Medical Genetics, Department of Health Sciences, Università degli Studi di Milano, 20142 Milan, Italy; (G.M.); (M.R.M.); (L.F.)
| | - Maria Francesca Bedeschi
- Medical Genetics Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy;
| | - Marco Venturin
- Department of Medical Biotechnology and Translational Medicine, Università degli Studi di Milano, 20054 Milan, Italy;
| | - Roberta Villa
- Medical Genetics Unit, ASST Santi Paolo e Carlo, 20142 Milan, Italy;
| | - Jole Costanza
- Research Laboratories Coordination Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy; (J.C.); (A.M.); (C.S.)
| | - Alessia Mauri
- Research Laboratories Coordination Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy; (J.C.); (A.M.); (C.S.)
| | - Carlo Santaniello
- Research Laboratories Coordination Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy; (J.C.); (A.M.); (C.S.)
| | - Odoardo Picciolini
- Pediatric Physical Medicine & Rehabilitation Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy; (O.P.); (L.M.)
| | - Laura Messina
- Pediatric Physical Medicine & Rehabilitation Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy; (O.P.); (L.M.)
| | - Fabio Triulzi
- Neuroradiology Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy;
| | - Monica Rosa Miozzo
- Medical Genetics, Department of Health Sciences, Università degli Studi di Milano, 20142 Milan, Italy; (G.M.); (M.R.M.); (L.F.)
- Medical Genetics Unit, ASST Santi Paolo e Carlo, 20142 Milan, Italy;
| | - Ornella Rondinone
- Medical Genetics, Department of Health Sciences, Università degli Studi di Milano, 20142 Milan, Italy; (G.M.); (M.R.M.); (L.F.)
| | - Laura Fontana
- Medical Genetics, Department of Health Sciences, Università degli Studi di Milano, 20142 Milan, Italy; (G.M.); (M.R.M.); (L.F.)
- Medical Genetics Unit, ASST Santi Paolo e Carlo, 20142 Milan, Italy;
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20
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Besedina E, Supek F. Copy number losses of oncogenes and gains of tumor suppressor genes generate common driver mutations. Nat Commun 2024; 15:6139. [PMID: 39033140 PMCID: PMC11271286 DOI: 10.1038/s41467-024-50552-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 07/11/2024] [Indexed: 07/23/2024] Open
Abstract
Cancer driver genes can undergo positive selection for various types of genetic alterations, including gain-of-function or loss-of-function mutations and copy number alterations (CNA). We investigated the landscape of different types of alterations affecting driver genes in 17,644 cancer exomes and genomes. We find that oncogenes may simultaneously exhibit signatures of positive selection and also negative selection in different gene segments, suggesting a method to identify additional tumor types where an oncogene is a driver or a vulnerability. Next, we characterize the landscape of CNA-dependent selection effects, revealing a general trend of increased positive selection on oncogene mutations not only upon CNA gains but also upon CNA deletions. Similarly, we observe a positive interaction between mutations and CNA gains in tumor suppressor genes. Thus, two-hit events involving point mutations and CNA are universally observed regardless of the type of CNA and may signal new therapeutic opportunities. An analysis with focus on the somatic CNA two-hit events can help identify additional driver genes relevant to a tumor type. By a global inference of point mutation and CNA selection signatures and interactions thereof across genes and tissues, we identify 9 evolutionary archetypes of driver genes, representing different mechanisms of (in)activation by genetic alterations.
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Affiliation(s)
- Elizaveta Besedina
- Institute for Research in Biomedicine (IRB Barcelona), 08028, Barcelona, Spain
| | - Fran Supek
- Institute for Research in Biomedicine (IRB Barcelona), 08028, Barcelona, Spain.
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, 2200, Copenhagen, Denmark.
- Catalan Institution for Research and Advanced Studies (ICREA), 08010, Barcelona, Spain.
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21
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Laugwitz L, Cheng F, Collins SC, Hustinx A, Navarro N, Welsch S, Cox H, Hsieh TC, Vijayananth A, Buchert R, Bender B, Efthymiou S, Murphy D, Zafar F, Rana N, Grasshoff U, Falb RJ, Grimmel M, Seibt A, Zheng W, Ghaedi H, Thirion M, Couette S, Azizimalamiri R, Sadeghian S, Galehdari H, Zamani M, Zeighami J, Sedaghat A, Ramshe SM, Zare A, Alipoor B, Klee D, Sturm M, Ossowski S, Houlden H, Riess O, Wieczorek D, Gavin R, Maroofian R, Krawitz P, Yalcin B, Distelmaier F, Haack TB. ZSCAN10 deficiency causes a neurodevelopmental disorder with characteristic oto-facial malformations. Brain 2024; 147:2471-2482. [PMID: 38386308 PMCID: PMC11224597 DOI: 10.1093/brain/awae058] [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: 03/08/2023] [Revised: 12/21/2023] [Accepted: 01/21/2024] [Indexed: 02/23/2024] Open
Abstract
Neurodevelopmental disorders are major indications for genetic referral and have been linked to more than 1500 loci including genes encoding transcriptional regulators. The dysfunction of transcription factors often results in characteristic syndromic presentations; however, at least half of these patients lack a genetic diagnosis. The implementation of machine learning approaches has the potential to aid in the identification of new disease genes and delineate associated phenotypes. Next generation sequencing was performed in seven affected individuals with neurodevelopmental delay and dysmorphic features. Clinical characterization included reanalysis of available neuroimaging datasets and 2D portrait image analysis with GestaltMatcher. The functional consequences of ZSCAN10 loss were modelled in mouse embryonic stem cells (mESCs), including a knockout and a representative ZSCAN10 protein truncating variant. These models were characterized by gene expression and western blot analyses, chromatin immunoprecipitation and quantitative PCR (ChIP-qPCR) and immunofluorescence staining. Zscan10 knockout mouse embryos were generated and phenotyped. We prioritized bi-allelic ZSCAN10 loss-of-function variants in seven affected individuals from five unrelated families as the underlying molecular cause. RNA-sequencing analyses in Zscan10-/- mESCs indicated dysregulation of genes related to stem cell pluripotency. In addition, we established in mESCs the loss-of-function mechanism for a representative human ZSCAN10 protein truncating variant by showing alteration of its expression levels and subcellular localization, interfering with its binding to DNA enhancer targets. Deep phenotyping revealed global developmental delay, facial asymmetry and malformations of the outer ear as consistent clinical features. Cerebral MRI showed dysplasia of the semicircular canals as an anatomical correlate of sensorineural hearing loss. Facial asymmetry was confirmed as a clinical feature by GestaltMatcher and was recapitulated in the Zscan10 mouse model along with inner and outer ear malformations. Our findings provide evidence of a novel syndromic neurodevelopmental disorder caused by bi-allelic loss-of-function variants in ZSCAN10.
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Affiliation(s)
- Lucia Laugwitz
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tübingen, 72076, Germany
- Department of Neuropediatrics, Developmental Neurology and Social Pediatrics, University of Tübingen, Tübingen 72076, Germany
| | - Fubo Cheng
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tübingen, 72076, Germany
| | | | - Alexander Hustinx
- Institute for Genomic Statistics and Bioinformatics, University Hospital Bonn, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn 53127, Germany
| | - Nicolas Navarro
- Biogeosciences, UMR 6282 CNRS, EPHE, Université de Bourgogne, Dijon 2100, France
- EPHE, PSL University, Paris 75014, France
| | - Simon Welsch
- Department of General Pediatrics, Neonatology and Pediatric Cardiology, Medical Faculty, Heinrich-Heine-University, Düsseldorf 40225, Germany
| | - Helen Cox
- West Midlands Regional Clinical Genetics Service and Birmingham Health Partners, Birmingham Women’s and Children’s Hospitals NHS Foundation Trust, Birmingham B15 2TG, UK
| | - Tzung-Chien Hsieh
- Institute for Genomic Statistics and Bioinformatics, University Hospital Bonn, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn 53127, Germany
| | - Aswinkumar Vijayananth
- Institute for Genomic Statistics and Bioinformatics, University Hospital Bonn, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn 53127, Germany
| | - Rebecca Buchert
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tübingen, 72076, Germany
| | - Benjamin Bender
- Diagnostic and Interventional Neuroradiology, Radiologic Clinics, University of Tübingen, Tübingen 72076, Germany
| | - Stephanie Efthymiou
- Department of Neuromuscular Disorders, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
| | - David Murphy
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, University College London, London WC1N 3BG, UK
| | - Faisal Zafar
- Pediatric Neurology, Children’s Hospital, Multan 60000, Pakistan
| | - Nuzhat Rana
- Pediatric Neurology, Children’s Hospital, Multan 60000, Pakistan
| | - Ute Grasshoff
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tübingen, 72076, Germany
- Center for Rare Disease, University of Tübingen, Tübingen 72072, Germany
| | - Ruth J Falb
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tübingen, 72076, Germany
| | - Mona Grimmel
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tübingen, 72076, Germany
| | - Annette Seibt
- Department of General Pediatrics, Neonatology and Pediatric Cardiology, Medical Faculty, Heinrich-Heine-University, Düsseldorf 40225, Germany
| | - Wenxu Zheng
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tübingen, 72076, Germany
| | - Hamid Ghaedi
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran 1985717443, Iran
| | - Marie Thirion
- Inserm UMR1231, Université de Bourgogne, Dijon Cedex 21070, France
| | - Sébastien Couette
- Biogeosciences, UMR 6282 CNRS, EPHE, Université de Bourgogne, Dijon 2100, France
- EPHE, PSL University, Paris 75014, France
| | - Reza Azizimalamiri
- Department of Pediatric Neurology, Golestan Medical, Educational, and Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz 6135715794, Iran
| | - Saeid Sadeghian
- Department of Pediatric Neurology, Golestan Medical, Educational, and Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz 6135715794, Iran
| | - Hamid Galehdari
- Department of Biology, Faculty of Science, Shahid Chamran University of Ahvaz, Ahvaz 6135783151, Iran
| | - Mina Zamani
- Department of Biology, Faculty of Science, Shahid Chamran University of Ahvaz, Ahvaz 6135783151, Iran
- Narges Medical Genetics and Prenatal Diagnosis Laboratory, Kianpars, Ahvaz 6155689467, Iran
| | - Jawaher Zeighami
- Narges Medical Genetics and Prenatal Diagnosis Laboratory, Kianpars, Ahvaz 6155689467, Iran
| | - Alireza Sedaghat
- Narges Medical Genetics and Prenatal Diagnosis Laboratory, Kianpars, Ahvaz 6155689467, Iran
- Diabetes Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz 6135715794, Iran
| | - Samira Molaei Ramshe
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran 1985717443, Iran
| | - Ali Zare
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran 1985717443, Iran
| | - Behnam Alipoor
- Department of Laboratory Sciences, Faculty of Paramedicine, Yasuj University of Medical Sciences, Yasuj 7591741417, Iran
| | - Dirk Klee
- Department of Pediatric Radiology, Medical Faculty, Institute of Radiology, Heinrich-Heine-University, Düsseldorf 40225, Germany
| | - Marc Sturm
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tübingen, 72076, Germany
- Genomics England, Queen Mary University of London, London EC1M 6BQ, UK
| | - Stephan Ossowski
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tübingen, 72076, Germany
- NGS Competence Center Tübingen (NCCT), University of Tübingen, Tübingen 72076, Germany
| | - Henry Houlden
- Department of Neuromuscular Disorders, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
| | - Olaf Riess
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tübingen, 72076, Germany
- Center for Rare Disease, University of Tübingen, Tübingen 72072, Germany
| | - Dagmar Wieczorek
- Medical Faculty and University Hospital Düsseldorf, Institute of Human Genetics, Heinrich-Heine-University Düsseldorf, Düsseldorf 40225, Germany
| | - Ryan Gavin
- West Midlands Regional Genetics Laboratory, Central and South Genomic Laboratory Hub, Birmingham B15 2TG, UK
| | - Reza Maroofian
- Department of Neuromuscular Disorders, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
| | - Peter Krawitz
- Institute for Genomic Statistics and Bioinformatics, University Hospital Bonn, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn 53127, Germany
| | - Binnaz Yalcin
- Inserm UMR1231, Université de Bourgogne, Dijon Cedex 21070, France
| | - Felix Distelmaier
- Department of General Pediatrics, Neonatology and Pediatric Cardiology, Medical Faculty, Heinrich-Heine-University, Düsseldorf 40225, Germany
| | - Tobias B Haack
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tübingen, 72076, Germany
- Center for Rare Disease, University of Tübingen, Tübingen 72072, Germany
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22
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Moffa JC, Bland IN, Tooley JR, Kalyanaraman V, Heitmeier M, Creed MC, Copits BA. Cell-Specific Single Viral Vector CRISPR/Cas9 Editing and Genetically Encoded Tool Delivery in the Central and Peripheral Nervous Systems. eNeuro 2024; 11:ENEURO.0438-23.2024. [PMID: 38871457 PMCID: PMC11228695 DOI: 10.1523/eneuro.0438-23.2024] [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: 10/24/2023] [Revised: 03/20/2024] [Accepted: 04/18/2024] [Indexed: 06/15/2024] Open
Abstract
CRISPR/Cas9 gene editing represents an exciting avenue to study genes of unknown function and can be combined with genetically encoded tools such as fluorescent proteins, channelrhodopsins, DREADDs, and various biosensors to more deeply probe the function of these genes in different cell types. However, current strategies to also manipulate or visualize edited cells are challenging due to the large size of Cas9 proteins and the limited packaging capacity of adeno-associated viruses (AAVs). To overcome these constraints, we developed an alternative gene editing strategy using a single AAV vector and mouse lines that express Cre-dependent Cas9 to achieve efficient cell-type specific editing across the nervous system. Expressing Cre-dependent Cas9 from a genomic locus affords space to package guide RNAs for gene editing together with Cre-dependent, genetically encoded tools to manipulate, map, or monitor neurons using a single virus. We validated this strategy with three common tools in neuroscience: ChRonos, a channelrhodopsin, for studying synaptic transmission using optogenetics, GCaMP8f for recording Ca2+ transients using photometry, and mCherry for tracing axonal projections. We tested these tools in multiple brain regions and cell types, including GABAergic neurons in the nucleus accumbens, glutamatergic neurons projecting from the ventral pallidum to the lateral habenula, dopaminergic neurons in the ventral tegmental area, and proprioceptive neurons in the periphery. This flexible approach could help identify and test the function of novel genes affecting synaptic transmission, circuit activity, or morphology with a single viral injection.
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Affiliation(s)
- Jamie C Moffa
- Washington University Pain Center, Department of Anesthesiology, Washington University School of Medicine, St. Louis, Missouri 63110
- Washington University Medical Scientist Training Program, Washington University School of Medicine, St. Louis, Missouri 63110
| | - India N Bland
- Washington University Pain Center, Department of Anesthesiology, Washington University School of Medicine, St. Louis, Missouri 63110
| | - Jessica R Tooley
- Washington University Pain Center, Department of Anesthesiology, Washington University School of Medicine, St. Louis, Missouri 63110
- Washington University Division of Biological and Behavioral Sciences, Washington University School of Medicine, St. Louis, Missouri 63110
| | - Vani Kalyanaraman
- Washington University Pain Center, Department of Anesthesiology, Washington University School of Medicine, St. Louis, Missouri 63110
| | - Monique Heitmeier
- Washington University Pain Center, Department of Anesthesiology, Washington University School of Medicine, St. Louis, Missouri 63110
| | - Meaghan C Creed
- Washington University Pain Center, Department of Anesthesiology, Washington University School of Medicine, St. Louis, Missouri 63110
- Departments of Neuroscience, Psychiatry, and Biomedical Engineering, Washington University School of Medicine, St. Louis, Missouri 63110
| | - Bryan A Copits
- Washington University Pain Center, Department of Anesthesiology, Washington University School of Medicine, St. Louis, Missouri 63110
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23
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Ward C, Beharry A, Tennakoon R, Rozik P, Wilhelm SDP, Heinemann IU, O’Donoghue P. Mechanisms and Delivery of tRNA Therapeutics. Chem Rev 2024; 124:7976-8008. [PMID: 38801719 PMCID: PMC11212642 DOI: 10.1021/acs.chemrev.4c00142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 04/11/2024] [Accepted: 04/26/2024] [Indexed: 05/29/2024]
Abstract
Transfer ribonucleic acid (tRNA) therapeutics will provide personalized and mutation specific medicines to treat human genetic diseases for which no cures currently exist. The tRNAs are a family of adaptor molecules that interpret the nucleic acid sequences in our genes into the amino acid sequences of proteins that dictate cell function. Humans encode more than 600 tRNA genes. Interestingly, even healthy individuals contain some mutant tRNAs that make mistakes. Missense suppressor tRNAs insert the wrong amino acid in proteins, and nonsense suppressor tRNAs read through premature stop signals to generate full length proteins. Mutations that underlie many human diseases, including neurodegenerative diseases, cancers, and diverse rare genetic disorders, result from missense or nonsense mutations. Thus, specific tRNA variants can be strategically deployed as therapeutic agents to correct genetic defects. We review the mechanisms of tRNA therapeutic activity, the nature of the therapeutic window for nonsense and missense suppression as well as wild-type tRNA supplementation. We discuss the challenges and promises of delivering tRNAs as synthetic RNAs or as gene therapies. Together, tRNA medicines will provide novel treatments for common and rare genetic diseases in humans.
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Affiliation(s)
- Cian Ward
- Department of Biochemistry, Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5C1, Canada
| | - Aruun Beharry
- Department of Biochemistry, Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5C1, Canada
| | - Rasangi Tennakoon
- Department of Biochemistry, Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5C1, Canada
| | - Peter Rozik
- Department of Biochemistry, Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5C1, Canada
| | - Sarah D. P. Wilhelm
- Department of Biochemistry, Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5C1, Canada
| | - Ilka U. Heinemann
- Department of Biochemistry, Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5C1, Canada
| | - Patrick O’Donoghue
- Department of Biochemistry, Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5C1, Canada
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24
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Ma K, Huang S, Ng KK, Lake NJ, Joseph S, Xu J, Lek A, Ge L, Woodman KG, Koczwara KE, Cohen J, Ho V, O'Connor CL, Brindley MA, Campbell KP, Lek M. Deep Mutational Scanning in Disease-related Genes with Saturation Mutagenesis-Reinforced Functional Assays (SMuRF). BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.07.12.548370. [PMID: 37873263 PMCID: PMC10592615 DOI: 10.1101/2023.07.12.548370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Interpretation of disease-causing genetic variants remains a challenge in human genetics. Current costs and complexity of deep mutational scanning methods hamper crowd-sourcing approaches toward genome-wide resolution of variants in disease-related genes. Our framework, Saturation Mutagenesis-Reinforced Functional assays (SMuRF), addresses these issues by offering simple and cost-effective saturation mutagenesis, as well as streamlining functional assays to enhance the interpretation of unresolved variants. Applying SMuRF to neuromuscular disease genes FKRP and LARGE1, we generated functional scores for all possible coding single nucleotide variants, which aid in resolving clinically reported variants of uncertain significance. SMuRF also demonstrates utility in predicting disease severity, resolving critical structural regions, and providing training datasets for the development of computational predictors. Our approach opens new directions for enabling variant-to-function insights for disease genes in a manner that is broadly useful for crowd-sourcing implementation across standard research laboratories.
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Affiliation(s)
- Kaiyue Ma
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
| | - Shushu Huang
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
- Equal second authors
| | - Kenneth K Ng
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
- Equal second authors
| | - Nicole J Lake
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
| | - Soumya Joseph
- Howard Hughes Medical Institute, Senator Paul D. Wellstone Muscular Dystrophy Specialized Research Center, Department of Molecular Physiology and Biophysics and Department of Neurology, Roy J. and Lucille A. Carver College of Medicine, The University of Iowa, Iowa City, IA, USA
| | - Jenny Xu
- Yale University, New Haven, CT, USA
| | - Angela Lek
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
- Muscular Dystrophy Association, Chicago, IL, USA
| | - Lin Ge
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
- Department of Neurology, National Center for Children's Health, Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - Keryn G Woodman
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
| | | | - Justin Cohen
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
| | - Vincent Ho
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
| | | | - Melinda A Brindley
- Department of Infectious Diseases, Department of Population Health, University of Georgia, Athens, GA, USA
- Senior Authors
| | - Kevin P Campbell
- Howard Hughes Medical Institute, Senator Paul D. Wellstone Muscular Dystrophy Specialized Research Center, Department of Molecular Physiology and Biophysics and Department of Neurology, Roy J. and Lucille A. Carver College of Medicine, The University of Iowa, Iowa City, IA, USA
- Senior Authors
| | - Monkol Lek
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
- Senior Authors
- Lead Contact
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25
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Cook AL, Sur S, Dobbyn L, Watson E, Cohen JD, Ptak B, Lee BS, Paul S, Hsiue E, Popoli M, Vogelstein B, Papadopoulos N, Bettegowda C, Gabrielson K, Zhou S, Kinzler KW, Wyhs N. Identification of nonsense-mediated decay inhibitors that alter the tumor immune landscape. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.28.573594. [PMID: 38234817 PMCID: PMC10793421 DOI: 10.1101/2023.12.28.573594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
Despite exciting developments in cancer immunotherapy, its broad application is limited by the paucity of targetable antigens on the tumor cell surface. As an intrinsic cellular pathway, nonsense-mediated decay (NMD) conceals neoantigens through the destruction of the RNA products from genes harboring truncating mutations. We developed and conducted a high throughput screen, based on the ratiometric analysis of transcripts, to identify critical mediators of NMD. This screen implicated disruption of kinase SMG1's phosphorylation of UPF1 as a potential disruptor of NMD. This led us to design a novel SMG1 inhibitor, KVS0001, that elevates the expression of transcripts and proteins resulting from truncating mutations in vivo and in vitro . Most importantly, KVS0001 concomitantly increased the presentation of immune-targetable HLA class I-associated peptides from NMD-downregulated proteins on the surface of cancer cells. KVS0001 provides new opportunities for studying NMD and the diseases in which NMD plays a role, including cancer and inherited diseases. One Sentence Summary Disruption of the nonsense-mediated decay pathway with a newly developed SMG1 inhibitor with in-vivo activity increases the expression of T-cell targetable cancer neoantigens resulting from truncating mutations.
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26
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Zhao Z, Cui R, Chi H, Wan T, Ma D, Zhang J, Cai M. A novel IRF6 gene mutation impacting the regulation of TGFβ2-AS1 in the TGFβ pathway: A mechanism in the development of Van der Woude syndrome. Front Genet 2024; 15:1397410. [PMID: 38903762 PMCID: PMC11188484 DOI: 10.3389/fgene.2024.1397410] [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: 03/07/2024] [Accepted: 05/13/2024] [Indexed: 06/22/2024] Open
Abstract
Several mutations in the IRF6 gene have been identified as a causative link to VWS. In this investigation, whole-exome sequencing (WES) and Sanger sequencing of a three-generation pedigree with an autosomal-dominant inheritance pattern affected by VWS identified a unique stop-gain mutation-c.748C>T:p.R250X-in the IRF6 gene that co-segregated exclusively with the disease phenotype. Immunofluorescence analysis revealed that the IRF6-p.R250X mutation predominantly shifted its localization from the nucleus to the cytoplasm. WES and protein interaction analyses were conducted to understand this mutation's role in the pathogenesis of VWS. Using LC-MS/MS, we found that this mutation led to a reduction in the binding of IRF6 to histone modification-associated proteins (NAA10, SNRPN, NAP1L1). Furthermore, RNA-seq results show that the mutation resulted in a downregulation of TGFβ2-AS1 expression. The findings highlight the mutation's influence on TGFβ2-AS1 and its subsequent effects on the phosphorylation of SMAD2/3, which are critical in maxillofacial development, particularly the palate. These insights contribute to a deeper understanding of VWS's molecular underpinnings and might inform future therapeutic strategies.
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Affiliation(s)
- Zhiyang Zhao
- Department of Oral and Craniomaxillofacial Surgery, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, College of Stomatology, Shanghai Jiao Tong University, National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of Stomatology, Shanghai, China
| | - Renjie Cui
- Department of Molecular Diagnostics & Endocrinology, The Core Laboratory in Medical Center of Clinical Research, State Key Laboratory of Medical Genomics, Shanghai Ninth People’s Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Haoshu Chi
- Shanghai Xuhui District Dental Disease Center, Shanghai, China
| | - Teng Wan
- Department of Oral and Craniomaxillofacial Surgery, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, College of Stomatology, Shanghai Jiao Tong University, National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of Stomatology, Shanghai, China
| | - Duan Ma
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, Collaborative Innovation Center of Genetics and Development, Institutes of Biomedical Sciences, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Jin Zhang
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, Collaborative Innovation Center of Genetics and Development, Institutes of Biomedical Sciences, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Ming Cai
- Department of Oral and Craniomaxillofacial Surgery, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, College of Stomatology, Shanghai Jiao Tong University, National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of Stomatology, Shanghai, China
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27
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Bernabéu-Herrero ME, Patel D, Bielowka A, Zhu J, Jain K, Mackay IS, Chaves Guerrero P, Emanuelli G, Jovine L, Noseda M, Marciniak SJ, Aldred MA, Shovlin CL. Mutations causing premature termination codons discriminate and generate cellular and clinical variability in HHT. Blood 2024; 143:2314-2331. [PMID: 38457357 PMCID: PMC11181359 DOI: 10.1182/blood.2023021777] [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: 07/06/2023] [Revised: 02/22/2024] [Accepted: 02/22/2024] [Indexed: 03/10/2024] Open
Abstract
ABSTRACT For monogenic diseases caused by pathogenic loss-of-function DNA variants, attention focuses on dysregulated gene-specific pathways, usually considering molecular subtypes together within causal genes. To better understand phenotypic variability in hereditary hemorrhagic telangiectasia (HHT), we subcategorized pathogenic DNA variants in ENG/endoglin, ACVRL1/ALK1, and SMAD4 if they generated premature termination codons (PTCs) subject to nonsense-mediated decay. In 3 patient cohorts, a PTC-based classification system explained some previously puzzling hemorrhage variability. In blood outgrowth endothelial cells (BOECs) derived from patients with ACVRL1+/PTC, ENG+/PTC, and SMAD4+/PTC genotypes, PTC-containing RNA transcripts persisted at low levels (8%-23% expected, varying between replicate cultures); genes differentially expressed to Bonferroni P < .05 in HHT+/PTC BOECs clustered significantly only to generic protein terms (isopeptide-bond/ubiquitin-like conjugation) and pulse-chase experiments detected subtle protein maturation differences but no evidence for PTC-truncated protein. BOECs displaying highest PTC persistence were discriminated in unsupervised hierarchical clustering of near-invariant housekeeper genes, with patterns compatible with higher cellular stress in BOECs with >11% PTC persistence. To test directionality, we used a HeLa reporter system to detect induction of activating transcription factor 4 (ATF4), which controls expression of stress-adaptive genes, and showed that ENG Q436X but not ENG R93X directly induced ATF4. AlphaFold accurately modeled relevant ENG domains, with AlphaMissense suggesting that readthrough substitutions would be benign for ENG R93X and other less rare ENG nonsense variants but more damaging for Q436X. We conclude that PTCs should be distinguished from other loss-of-function variants, PTC transcript levels increase in stressed cells, and readthrough proteins and mechanisms provide promising research avenues.
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Affiliation(s)
- Maria E. Bernabéu-Herrero
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
- NIHR Imperial Biomedical Research Centre, London, United Kingdom
| | - Dilipkumar Patel
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
- NIHR Imperial Biomedical Research Centre, London, United Kingdom
| | - Adrianna Bielowka
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
- NIHR Imperial Biomedical Research Centre, London, United Kingdom
| | - JiaYi Zhu
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
| | - Kinshuk Jain
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
- NIHR Imperial Biomedical Research Centre, London, United Kingdom
| | - Ian S. Mackay
- Ear, Nose and Throat Surgery, Charing Cross and Royal Brompton Hospitals, London, United Kingdom
| | | | - Giulia Emanuelli
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
| | - Luca Jovine
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Michela Noseda
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Stefan J. Marciniak
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
- Royal Papworth Hospital NHS Foundation Trust, Cambridge, United Kingdom
| | - Micheala A. Aldred
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN
| | - Claire L. Shovlin
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
- NIHR Imperial Biomedical Research Centre, London, United Kingdom
- Specialist Medicine, Imperial College Healthcare NHS Trust, London, United Kingdom
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28
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Ocieczek P, Oluonye N, Méjécase C, Schiff E, Tailor V, Moosajee M. Identification of a Novel Frameshift Variant in MYF5 Leading to External Ophthalmoplegia with Rib and Vertebral Anomalies. Genes (Basel) 2024; 15:699. [PMID: 38927634 PMCID: PMC11202668 DOI: 10.3390/genes15060699] [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: 04/28/2024] [Revised: 05/16/2024] [Accepted: 05/25/2024] [Indexed: 06/28/2024] Open
Abstract
Myogenic transcription factors with a basic helix-loop-helix (bHLH) such as MYOD, myogenin, MRF4, and MYF5 contribute to muscle differentiation and regulation. The MYF5 gene located on chromosome 12 encodes for myogenic factor 5 (MYF5), which has a role in skeletal and extraocular muscle development and rib formation. Variants in MYF5 were found to cause external ophthalmoplegia with rib and vertebral anomalies (EORVA), a rare recessive condition. To date, three homozygous variants in MYF5 have been reported to cause EORVA in six members of four unrelated families. Here, we present a novel homozygous MYF5 frameshift variant, c.596dupA p. (Asn199Lysfs*49), causing premature protein termination and presenting with external ophthalmoplegia, ptosis, and scoliosis in three siblings from a consanguineous family of Pakistani origin. With four MYF5 variants now discovered, genetic testing and paediatric assessment for extra-ocular features should be considered in all cases of congenital ophthalmoplegia.
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Affiliation(s)
- Paulina Ocieczek
- Moorfields Eye Hospital NHS Foundation Trust, London EC1V 9EL, UK; (P.O.)
- UCL Institute of Ophthalmology, London EC1V 9EL, UK
| | - Ngozi Oluonye
- Moorfields Eye Hospital NHS Foundation Trust, London EC1V 9EL, UK; (P.O.)
- Great Ormond Street Hospital for Children NHS Foundation Trust, London WC1N 9JH, UK
| | - Cécile Méjécase
- UCL Institute of Ophthalmology, London EC1V 9EL, UK
- Francis Crick Institute, London NW1 1AT, UK
| | - Elena Schiff
- Moorfields Eye Hospital NHS Foundation Trust, London EC1V 9EL, UK; (P.O.)
| | - Vijay Tailor
- Moorfields Eye Hospital NHS Foundation Trust, London EC1V 9EL, UK; (P.O.)
- UCL Institute of Ophthalmology, London EC1V 9EL, UK
| | - Mariya Moosajee
- Moorfields Eye Hospital NHS Foundation Trust, London EC1V 9EL, UK; (P.O.)
- UCL Institute of Ophthalmology, London EC1V 9EL, UK
- Great Ormond Street Hospital for Children NHS Foundation Trust, London WC1N 9JH, UK
- Francis Crick Institute, London NW1 1AT, UK
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29
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Edet OU, Ubi BE, Ishii T. Genomic analysis of a spontaneous unifoliate mutant reveals gene candidates associated with compound leaf development in Vigna unguiculata [L] Walp. Sci Rep 2024; 14:10654. [PMID: 38724579 PMCID: PMC11082238 DOI: 10.1038/s41598-024-61062-x] [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: 01/29/2024] [Accepted: 04/30/2024] [Indexed: 05/12/2024] Open
Abstract
Molecular mechanisms which underpin compound leaf development in some legumes have been reported, but there is no previous study on the molecular genetic control of compound leaf formation in Vigna unguiculata (cowpea), an important dryland legume of African origin. In most studied species with compound leaves, class 1 KNOTTED-LIKE HOMEOBOX genes expressed in developing leaf primordia sustain morphogenetic activity, allowing leaf dissection and the development of leaflets. Other genes, such as, SINGLE LEAFLET1 in Medicago truncatula and Trifoliate in Solanum lycopersicum, are also implicated in regulating compound leaf patterning. To set the pace for an in-depth understanding of the genetics of compound leaf development in cowpea, we applied RNA-seq and whole genome shotgun sequence datasets of a spontaneous cowpea unifoliate mutant and its trifoliate wild-type cultivar to conduct comparative reference-based gene expression, de novo genome-wide isoform switch, and genome variant analyses between the two genotypes. Our results suggest that genomic variants upstream of LATE ELONGATED HYPOCOTYL and down-stream of REVEILLE4, BRASSINOSTERIOD INSENSITIVE1 and LATERAL ORGAN BOUNDARIES result in down-regulation of key components of cowpea circadian rhythm central oscillator and brassinosteroid signaling, resulting in unifoliate leaves and brassinosteroid-deficient-like phenotypes. We have stated hypotheses that will guide follow-up studies expected to provide more insights.
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Affiliation(s)
- Offiong Ukpong Edet
- Arid Land Research Center, Tottori University, Tottori, 680-0001, Japan.
- Department of Crop Science, University of Calabar, PMB 1115, Calabar, Cross River State, Nigeria.
| | - Benjamin Ewa Ubi
- Department of Biotechnology, Ebonyi State University, Abakaliki, Ebonyi State, Nigeria
| | - Takayoshi Ishii
- Arid Land Research Center, Tottori University, Tottori, 680-0001, Japan.
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30
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Zhao J, Wang C, Zhao L, Zhou H, Wu R, Zhang T, Ding J, Zhou J, Zheng H, Zhang L, Kong T, Zhou J, Hu Z. A Novel Four-Gene Signature Based on Nonsense-Mediated RNA Decay for Predicting Prognosis in Hepatocellular Carcinoma: Bioinformatics Analysis and Functional Validation. J Hepatocell Carcinoma 2024; 11:747-766. [PMID: 38680213 PMCID: PMC11055534 DOI: 10.2147/jhc.s450711] [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: 12/05/2023] [Accepted: 04/18/2024] [Indexed: 05/01/2024] Open
Abstract
Purpose Nonsense-mediated RNA decay (NMD), a surveillance pathway for selective degradation of aberrant mRNAs, is associated with cancer progression. Its potential as a predictor for aggressive hepatocellular carcinoma (HCC) is unclear. Here, we present an innovative NMD risk model for predicting HCC prognosis. Methods The Cancer Genome Atlas (TCGA) data of 374 liver HCC (LIHC) and 50 normal liver samples were extracted. A risk model based on NMD-related genes was developed through least absolute shrinkage and selection operator Cox (LASSO-Cox) regression of the LIHC-TCGA data. Prognostic validation was done using GSE54236, GSE116174, and GSE76427 data. Univariate and multivariate Cox regression analyses were conducted to assess the prognostic value of the model. We also constructed nomograms for survival prediction. Tumor immune infiltration was evaluated using the CIBERSORT algorithm, and the tumor cell phenotype was assessed. Finally, mouse experiments verified UPF3B knockdown effects on HCC tumor characteristics. Results We developed a risk model based on four NMD-related genes (PABPC1, RPL8, SMG5, and UPF3B) and validated it using GSE54236, GSE116174, and GSE76427 data. The model effectively distinguished high- and low-risk groups corresponding to unfavorable and favorable HCC outcomes. Its prognostic prediction accuracy was confirmed through time-dependent ROC analysis, and clinical-use nomograms with calibration curves were developed. Single-cell RNA sequencing results indicated significantly higher expression of SMG5 and UPF3B in tumor cells. Knockdown of SMG5 and UPF3B inhibited HCC cell proliferation, invasion, and migration, while affecting cell-cycle progression and apoptosis. In vivo, UPF3B knockdown delayed tumor growth and increased immune cell infiltration. Conclusion Our NMD-related gene-based risk model can help identify therapeutic targets and biomarkers for HCC. Additionally, it assists clinicians in predicting the prognosis of HCC patients.
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Affiliation(s)
- Jiaxin Zhao
- Department of Hepatobiliary and Pancreatic Surgery, Department of Surgery, Fourth Affiliated Hospital, School of Medicine, Zhejiang University, Yiwu, Zhejiang Province, People’s Republic of China
| | - Cheng Wang
- Department of Hepatobiliary and Pancreatic Surgery, Department of Surgery, Fourth Affiliated Hospital, School of Medicine, Zhejiang University, Yiwu, Zhejiang Province, People’s Republic of China
| | - Liang Zhao
- Department of Hepatobiliary and Pancreatic Surgery, Department of Surgery, Fourth Affiliated Hospital, School of Medicine, Zhejiang University, Yiwu, Zhejiang Province, People’s Republic of China
| | - Huiying Zhou
- Department of Hepatobiliary and Pancreatic Surgery, Department of Surgery, Fourth Affiliated Hospital, School of Medicine, Zhejiang University, Yiwu, Zhejiang Province, People’s Republic of China
| | - Rui Wu
- Department of Hepatobiliary and Pancreatic Surgery, Department of Surgery, Fourth Affiliated Hospital, School of Medicine, Zhejiang University, Yiwu, Zhejiang Province, People’s Republic of China
| | - Tao Zhang
- Department of Hepatobiliary and Pancreatic Surgery, Department of Surgery, Fourth Affiliated Hospital, School of Medicine, Zhejiang University, Yiwu, Zhejiang Province, People’s Republic of China
| | - Jiawei Ding
- Department of Hepatobiliary and Pancreatic Surgery, Department of Surgery, Fourth Affiliated Hospital, School of Medicine, Zhejiang University, Yiwu, Zhejiang Province, People’s Republic of China
| | - Junjie Zhou
- Department of Radiology, Fourth Affiliated Hospital, School of Medicine, Zhejiang University, Yiwu, Zhejiang Province, People’s Republic of China
| | - Huilin Zheng
- Zhejiang Provincial Collaborative Innovation Center of Agricultural Biological Resource Biochemical Manufacturing, School of Biological and Chemical Engineering, Zhejiang University of Science and Technology, Hangzhou, Zhejiang Province, People’s Republic of China
| | - Lei Zhang
- Zhejiang Provincial Collaborative Innovation Center of Agricultural Biological Resource Biochemical Manufacturing, School of Biological and Chemical Engineering, Zhejiang University of Science and Technology, Hangzhou, Zhejiang Province, People’s Republic of China
| | - Tianci Kong
- Zhejiang Provincial Collaborative Innovation Center of Agricultural Biological Resource Biochemical Manufacturing, School of Biological and Chemical Engineering, Zhejiang University of Science and Technology, Hangzhou, Zhejiang Province, People’s Republic of China
| | - Jie Zhou
- Department of Hepatobiliary and Pancreatic Surgery, Department of Surgery, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, People’s Republic of China
| | - Zhenhua Hu
- Department of Hepatobiliary and Pancreatic Surgery, Department of Surgery, Fourth Affiliated Hospital, School of Medicine, Zhejiang University, Yiwu, Zhejiang Province, People’s Republic of China
- Department of Hepatobiliary and Pancreatic Surgery, Department of Surgery, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, People’s Republic of China
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Karimi E, Gohlke J, van der Borgh M, Lindqvist J, Hourani Z, Kolb J, Cossette S, Lawlor MW, Ottenheijm C, Granzier H. Characterization of NEB pathogenic variants in patients reveals novel nemaline myopathy disease mechanisms and omecamtiv mecarbil force effects. Acta Neuropathol 2024; 147:72. [PMID: 38634969 PMCID: PMC11026289 DOI: 10.1007/s00401-024-02726-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 03/19/2024] [Accepted: 03/26/2024] [Indexed: 04/19/2024]
Abstract
Nebulin, a critical protein of the skeletal muscle thin filament, plays important roles in physiological processes such as regulating thin filament length (TFL), cross-bridge cycling, and myofibril alignment. Pathogenic variants in the nebulin gene (NEB) cause NEB-based nemaline myopathy (NEM2), a genetically heterogeneous disorder characterized by hypotonia and muscle weakness, currently lacking curative therapies. In this study, we examined a cohort of ten NEM2 patients, each with unique pathogenic variants, aiming to understand their impact on mRNA, protein, and functional levels. Results show that pathogenic truncation variants affect NEB mRNA stability and lead to nonsense-mediated decay of the mutated transcript. Moreover, a high incidence of cryptic splice site activation was found in patients with pathogenic splicing variants that are expected to disrupt the actin-binding sites of nebulin. Determination of protein levels revealed patients with either relatively normal or markedly reduced nebulin. We observed a positive relation between the reduction in nebulin and a reduction in TFL, or reduction in tension (both maximal and submaximal tension). Interestingly, our study revealed a pathogenic duplication variant in nebulin that resulted in a four-copy gain in the triplicate region of NEB and a much larger nebulin protein and longer TFL. Additionally, we investigated the effect of Omecamtiv mecarbil (OM), a small-molecule activator of cardiac myosin, on force production of type 1 muscle fibers of NEM2 patients. OM treatment substantially increased submaximal tension across all NEM2 patients ranging from 87 to 318%, with the largest effects in patients with the lowest level of nebulin. In summary, this study indicates that post-transcriptional or post-translational mechanisms regulate nebulin expression. Moreover, we propose that the pathomechanism of NEM2 involves not only shortened but also elongated thin filaments, along with the disruption of actin-binding sites resulting from pathogenic splicing variants. Significantly, our findings highlight the potential of OM treatment to improve skeletal muscle function in NEM2 patients, especially those with large reductions in nebulin levels.
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Affiliation(s)
- Esmat Karimi
- Department of Cellular and Molecular Medicine, University of Arizona, Tucson, AZ, USA
| | - Jochen Gohlke
- Department of Cellular and Molecular Medicine, University of Arizona, Tucson, AZ, USA
| | - Mila van der Borgh
- Department of Cellular and Molecular Medicine, University of Arizona, Tucson, AZ, USA
| | - Johan Lindqvist
- Department of Cellular and Molecular Medicine, University of Arizona, Tucson, AZ, USA
| | - Zaynab Hourani
- Department of Cellular and Molecular Medicine, University of Arizona, Tucson, AZ, USA
| | - Justin Kolb
- Department of Cellular and Molecular Medicine, University of Arizona, Tucson, AZ, USA
| | - Stacy Cossette
- Department of Pathology, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Michael W Lawlor
- Department of Pathology, Medical College of Wisconsin, Milwaukee, WI, USA
- Diverge Translational Science Laboratory, Milwaukee, WI, USA
| | - Coen Ottenheijm
- Department of Cellular and Molecular Medicine, University of Arizona, Tucson, AZ, USA
- Department of Physiology, Amsterdam UMC (Location VUMC), Amsterdam, Netherlands
| | - Henk Granzier
- Department of Cellular and Molecular Medicine, University of Arizona, Tucson, AZ, USA.
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Gallagher D, Pérez-Palma E, Bruenger T, Ghanty I, Brilstra E, Ceulemans B, Chemaly N, de Lange I, Depienne C, Guerrini R, Mei D, Møller RS, Nabbout R, Regan BM, Schneider AL, Scheffer IE, Schoonjans AS, Symonds JD, Weckhuysen S, Zuberi SM, Lal D, Brunklaus A. Genotype-phenotype associations in 1018 individuals with SCN1A-related epilepsies. Epilepsia 2024; 65:1046-1059. [PMID: 38410936 DOI: 10.1111/epi.17882] [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: 09/17/2023] [Revised: 12/30/2023] [Accepted: 01/03/2024] [Indexed: 02/28/2024]
Abstract
OBJECTIVE SCN1A variants are associated with epilepsy syndromes ranging from mild genetic epilepsy with febrile seizures plus (GEFS+) to severe Dravet syndrome (DS). Many variants are de novo, making early phenotype prediction difficult, and genotype-phenotype associations remain poorly understood. METHODS We assessed data from a retrospective cohort of 1018 individuals with SCN1A-related epilepsies. We explored relationships between variant characteristics (position, in silico prediction scores: Combined Annotation Dependent Depletion (CADD), Rare Exome Variant Ensemble Learner (REVEL), SCN1A genetic score), seizure characteristics, and epilepsy phenotype. RESULTS DS had earlier seizure onset than other GEFS+ phenotypes (5.3 vs. 12.0 months, p < .001). In silico variant scores were higher in DS versus GEFS+ (p < .001). Patients with missense variants in functionally important regions (conserved N-terminus, S4-S6) exhibited earlier seizure onset (6.0 vs. 7.0 months, p = .003) and were more likely to have DS (280/340); those with missense variants in nonconserved regions had later onset (10.0 vs. 7.0 months, p = .036) and were more likely to have GEFS+ (15/29, χ2 = 19.16, p < .001). A minority of protein-truncating variants were associated with GEFS+ (10/393) and more likely to be located in the proximal first and last exon coding regions than elsewhere in the gene (9.7% vs. 1.0%, p < .001). Carriers of the same missense variant exhibited less variability in age at seizure onset compared with carriers of different missense variants for both DS (1.9 vs. 2.9 months, p = .001) and GEFS+ (8.0 vs. 11.0 months, p = .043). Status epilepticus as presenting seizure type is a highly specific (95.2%) but nonsensitive (32.7%) feature of DS. SIGNIFICANCE Understanding genotype-phenotype associations in SCN1A-related epilepsies is critical for early diagnosis and management. We demonstrate an earlier disease onset in patients with missense variants in important functional regions, the occurrence of GEFS+ truncating variants, and the value of in silico prediction scores. Status epilepticus as initial seizure type is a highly specific, but not sensitive, early feature of DS.
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Affiliation(s)
- Declan Gallagher
- School of Health and Wellbeing, University of Glasgow, Glasgow, UK
- Paediatric Neurosciences Research Group, Royal Hospital for Children, Glasgow, UK
| | - Eduardo Pérez-Palma
- Universidad del Desarrollo, Centro de Genética y Genómica, Facultad de Medicina Clínica Alemana, Santiago, Chile
- Cologne Center for Genomics, University of Cologne, Cologne, Germany
| | - Tobias Bruenger
- Cologne Center for Genomics, University of Cologne, Cologne, Germany
| | - Ismael Ghanty
- School of Health and Wellbeing, University of Glasgow, Glasgow, UK
- Paediatric Neurosciences Research Group, Royal Hospital for Children, Glasgow, UK
| | - Eva Brilstra
- Department of Genetics, University Medical Center, Utrecht, the Netherlands
| | - Berten Ceulemans
- Department of Child Neurology, University Hospital Antwerp, Antwerp, Belgium
| | - Nicole Chemaly
- Reference Center for Rare Epilepsies, Department of Pediatric Neurology, Hôpital Necker-Enfants Malades, Université de Paris, Paris, France
| | - Iris de Lange
- Department of Genetics, University Medical Center, Utrecht, the Netherlands
| | - Christel Depienne
- Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Renzo Guerrini
- Neuroscience Department, Children's Hospital A. Meyer Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) and University of Florence, Florence, Italy
| | - Davide Mei
- Neuroscience Department, Children's Hospital A. Meyer Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) and University of Florence, Florence, Italy
| | - Rikke S Møller
- Danish Epilepsy Center, Filadelfia, Dianalund, Denmark
- Department of Regional Health Research, Faculty of Health Sciences, University of Southern Denmark, Odense, Denmark
| | - Rima Nabbout
- Reference Center for Rare Epilepsies, Department of Pediatric Neurology, Hôpital Necker-Enfants Malades, Université de Paris, Paris, France
| | - Brigid M Regan
- Department of Medicine, Epilepsy Research Centre, University of Melbourne, Austin Health, Melbourne, Victoria, Australia
| | - Amy L Schneider
- Department of Medicine, Epilepsy Research Centre, University of Melbourne, Austin Health, Melbourne, Victoria, Australia
| | - Ingrid E Scheffer
- Department of Medicine, Epilepsy Research Centre, University of Melbourne, Austin Health, Melbourne, Victoria, Australia
- University of Melbourne, Royal Children's Hospital, Florey and Murdoch Children's Research Institutes, Melbourne, Victoria, Australia
| | - An-Sofie Schoonjans
- Department of Child Neurology, University Hospital Antwerp, Antwerp, Belgium
| | - Joseph D Symonds
- School of Health and Wellbeing, University of Glasgow, Glasgow, UK
- Paediatric Neurosciences Research Group, Royal Hospital for Children, Glasgow, UK
| | - Sarah Weckhuysen
- Applied & Translational Neurogenomics Group, VIB Center for Molecular Neurology, Antwerp, Belgium
- Neurology Department, University Hospital Antwerp, Antwerp, Belgium
- Translational Neurosciences, University of Antwerp, Antwerp, Belgium
| | - Sameer M Zuberi
- School of Health and Wellbeing, University of Glasgow, Glasgow, UK
- Paediatric Neurosciences Research Group, Royal Hospital for Children, Glasgow, UK
| | - Dennis Lal
- Cologne Center for Genomics, University of Cologne, Cologne, Germany
- Epilepsy Center, Neurological Institute, Cleveland Clinic, Cleveland, Ohio, USA
- Stanley Center for Psychiatric Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Neurology, McGovern Medical School, UTHealth Houston, Houston, Texas, USA
| | - Andreas Brunklaus
- School of Health and Wellbeing, University of Glasgow, Glasgow, UK
- Paediatric Neurosciences Research Group, Royal Hospital for Children, Glasgow, UK
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Xiao L, Sun H, Cheng R, Yang R, Jin X, Xu Z, Cai Y, Yang Y, Pang F, Xue G, Wang P, Jiang Q, Nie H. Functional requirement of alternative splicing in epithelial-mesenchymal transition of pancreatic circulating tumor. MOLECULAR THERAPY. NUCLEIC ACIDS 2024; 35:102129. [PMID: 38370981 PMCID: PMC10869908 DOI: 10.1016/j.omtn.2024.102129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 01/19/2024] [Indexed: 02/20/2024]
Abstract
Circulating tumor cells (CTCs) that undergo epithelial-to-mesenchymal transition (EMT) can provide valuable information regarding metastasis and potential therapies. However, current studies on the EMT overlook alternative splicing. Here, we used single-cell full-length transcriptome data and mRNA sequencing of CTCs to identify stage-specific alternative splicing of partial EMT and mesenchymal states during pancreatic cancer metastasis. We classified definitive tumor and normal epithelial cells via genetic aberrations and demonstrated dynamic changes in the epithelial-mesenchymal continuum in both epithelial cancer cells and CTCs. We provide the landscape of alternative splicing in CTCs at different stages of EMT, uncovering cell-type-specific splicing patterns and splicing events in cell surface proteins suitable for therapies. We show that MBNL1 governs cell fate through alternative splicing independently of changes in gene expression and affects the splicing pattern during EMT. We found a high frequency of events that contained multiple premature termination codons and were enriched with C and G nucleotides in close proximity, which influence the likelihood of stop codon readthrough and expand the range of potential therapeutic targets. Our study provides insights into the EMT transcriptome's dynamic changes and identifies potential diagnostic and therapeutic targets in pancreatic cancer.
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Affiliation(s)
- Lixing Xiao
- School of Life Science and Technology, Harbin Institute of Technology, Harbin 150000, China
| | - Haoxiu Sun
- School for Interdisciplinary Medicine and Engineering, Harbin Medical University, Harbin 150076, China
| | - Rui Cheng
- School of Life Science and Technology, Harbin Institute of Technology, Harbin 150000, China
| | - Rongrong Yang
- School of Life Science and Technology, Harbin Institute of Technology, Harbin 150000, China
| | - Xiyun Jin
- School of Life Science and Technology, Harbin Institute of Technology, Harbin 150000, China
| | - Zhaochun Xu
- School of Life Science and Technology, Harbin Institute of Technology, Harbin 150000, China
| | - Yideng Cai
- School of Life Science and Technology, Harbin Institute of Technology, Harbin 150000, China
| | - Yuexin Yang
- School of Life Science and Technology, Harbin Institute of Technology, Harbin 150000, China
| | - Fenglan Pang
- School of Life Science and Technology, Harbin Institute of Technology, Harbin 150000, China
| | - Guangfu Xue
- School of Life Science and Technology, Harbin Institute of Technology, Harbin 150000, China
| | - Pingping Wang
- School for Interdisciplinary Medicine and Engineering, Harbin Medical University, Harbin 150076, China
| | - Qinghua Jiang
- School of Life Science and Technology, Harbin Institute of Technology, Harbin 150000, China
- School for Interdisciplinary Medicine and Engineering, Harbin Medical University, Harbin 150076, China
| | - Huan Nie
- School of Life Science and Technology, Harbin Institute of Technology, Harbin 150000, China
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Herbst C, Bothe V, Wegler M, Axer-Schaefer S, Audebert-Bellanger S, Gecz J, Cogne B, Feldman HB, Horn AHC, Hurst ACE, Kelly MA, Kruer MC, Kurolap A, Laquerriere A, Li M, Mark PR, Morawski M, Nizon M, Pastinen T, Polster T, Saugier-Veber P, SeSong J, Sticht H, Stieler JT, Thifffault I, van Eyk CL, Marcorelles P, Vezain-Mouchard M, Abou Jamra R, Oppermann H. Heterozygous loss-of-function variants in DOCK4 cause neurodevelopmental delay and microcephaly. Hum Genet 2024; 143:455-469. [PMID: 38526744 PMCID: PMC11043173 DOI: 10.1007/s00439-024-02655-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 02/09/2024] [Indexed: 03/27/2024]
Abstract
Neurons form the basic anatomical and functional structure of the nervous system, and defects in neuronal differentiation or formation of neurites are associated with various psychiatric and neurodevelopmental disorders. Dynamic changes in the cytoskeleton are essential for this process, which is, inter alia, controlled by the dedicator of cytokinesis 4 (DOCK4) through the activation of RAC1. Here, we clinically describe 7 individuals (6 males and one female) with variants in DOCK4 and overlapping phenotype of mild to severe global developmental delay. Additional symptoms include coordination or gait abnormalities, microcephaly, nonspecific brain malformations, hypotonia and seizures. Four individuals carry missense variants (three of them detected de novo) and three individuals carry null variants (two of them maternally inherited). Molecular modeling of the heterozygous missense variants suggests that the majority of them affect the globular structure of DOCK4. In vitro functional expression studies in transfected Neuro-2A cells showed that all missense variants impaired neurite outgrowth. Furthermore, Dock4 knockout Neuro-2A cells also exhibited defects in promoting neurite outgrowth. Our results, including clinical, molecular and functional data, suggest that loss-of-function variants in DOCK4 probable cause a variable spectrum of a novel neurodevelopmental disorder with microcephaly.
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Affiliation(s)
- Charlotte Herbst
- Institute of Human Genetics, University of Leipzig Medical Center, 04103, Leipzig, Germany
| | - Viktoria Bothe
- Institute of Human Genetics, University of Leipzig Medical Center, 04103, Leipzig, Germany
| | - Meret Wegler
- Institute of Human Genetics, University of Leipzig Medical Center, 04103, Leipzig, Germany
| | - Susanne Axer-Schaefer
- Department of Epileptology, Krankenhaus Mara Bethel Epilepsy Center Medical School OWL, Bielefeld University, Campus Bethel, Bielefeld, Germany
| | | | - Jozef Gecz
- Adelaide Medical School and Robinson Research Institute, The University of Adelaide, Adelaide, SA, Australia
| | - Benjamin Cogne
- Service de Génétique Médicale, CHU Nantes, 44000, Nantes, France
- l'institut du Thorax, Nantes Université, CHU Nantes, CNRS, INSERM, 44000, Nantes, France
| | - Hagit Baris Feldman
- The Genetics Institute and Genomics Center, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Anselm H C Horn
- Institute of Biochemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
- Erlangen National High Performance Computing Center, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Anna C E Hurst
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Melissa A Kelly
- HudsonAlpha Clinical Services Lab, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Michael C Kruer
- Barrow Neurological Institute, Phoenix Children's Hospital University of Arizona College of Medicine, Phoenix, USA
| | - Alina Kurolap
- The Genetics Institute and Genomics Center, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - Annie Laquerriere
- Department of Anatomy, Inserm U1245 and CHU Rouen, Univ Rouen Normandie, 76000, Rouen, France
| | - Megan Li
- Invitae Corp, San Francisco, CA, USA
| | - Paul R Mark
- Division of Medical Genetics, Helen DeVos Children's Hospital, Corewell Health, Grand Rapids, MI, USA
| | - Markus Morawski
- Center of Neuropathology and Brain Research, Medical Faculty, Paul Flechsig Institute, University of Leipzig, Leipzig, Germany
| | - Mathilde Nizon
- Service de Génétique Médicale, CHU Nantes, 44000, Nantes, France
- l'institut du Thorax, Nantes Université, CHU Nantes, CNRS, INSERM, 44000, Nantes, France
| | - Tomi Pastinen
- Genomic Medicine Center, Children's Mercy Hospital, Kansas City, USA
- University of Missouri Kansas City School of Medicine, Kansas City, USA
| | - Tilman Polster
- Department of Epileptology, Krankenhaus Mara Bethel Epilepsy Center Medical School OWL, Bielefeld University, Campus Bethel, Bielefeld, Germany
| | - Pascale Saugier-Veber
- Department of Genetics and Reference Center for Developmental Disorders, Inserm U1245 and CHU Rouen, Univ Rouen Normandie, 76000, Rouen, France
| | - Jang SeSong
- Genomic Medicine Institute, Seoul National University, Seoul, Republic of Korea
| | - Heinrich Sticht
- Institute of Biochemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Jens T Stieler
- Center of Neuropathology and Brain Research, Medical Faculty, Paul Flechsig Institute, University of Leipzig, Leipzig, Germany
| | - Isabelle Thifffault
- Genomic Medicine Center, Children's Mercy Hospital, Kansas City, USA
- University of Missouri Kansas City School of Medicine, Kansas City, USA
| | - Clare L van Eyk
- Adelaide Medical School and Robinson Research Institute, The University of Adelaide, Adelaide, SA, Australia
| | | | - Myriam Vezain-Mouchard
- Department of Genetics and Reference Center for Developmental Disorders, Inserm U1245 and CHU Rouen, Univ Rouen Normandie, 76000, Rouen, France
| | - Rami Abou Jamra
- Institute of Human Genetics, University of Leipzig Medical Center, 04103, Leipzig, Germany
| | - Henry Oppermann
- Institute of Human Genetics, University of Leipzig Medical Center, 04103, Leipzig, Germany.
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Das R, Panigrahi GK. Messenger RNA Surveillance: Current Understanding, Regulatory Mechanisms, and Future Implications. Mol Biotechnol 2024:10.1007/s12033-024-01062-4. [PMID: 38411790 DOI: 10.1007/s12033-024-01062-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 01/02/2024] [Indexed: 02/28/2024]
Abstract
Nonsense-mediated mRNA decay (NMD) is an evolutionarily conserved surveillance mechanism in eukaryotes primarily deployed to ensure RNA quality control by eliminating aberrant transcripts and also involved in modulating the expression of several physiological transcripts. NMD, the mRNA surveillance pathway, is a major form of gene regulation in eukaryotes. NMD serves as one of the most significant quality control mechanisms as it primarily scans the newly synthesized transcripts and differentiates the aberrant and non-aberrant transcripts. The synthesis of truncated proteins is restricted, which would otherwise lead to cellular dysfunctions. The up-frameshift factors (UPFs) play a central role in executing the NMD event, largely by recognizing and recruiting multiple protein factors that result in the decay of non-physiological mRNAs. NMD exhibits astounding variability in its ability across eukaryotes in an array of pathological and physiological contexts. The detailed understanding of NMD and the underlying molecular mechanisms remains blurred. This review outlines our current understanding of NMD, in regulating multifaceted cellular events during development and disease. It also attempts to identify unanswered questions that deserve further investigation.
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Affiliation(s)
- Rutupurna Das
- Department of Zoology, School of Applied Sciences, Centurion University of Technology and Management, Jatni, Khordha, Odisha, India
| | - Gagan Kumar Panigrahi
- Department of Zoology, School of Applied Sciences, Centurion University of Technology and Management, Jatni, Khordha, Odisha, India.
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Wayhelova M, Vallova V, Broz P, Mikulasova A, Smetana J, Dynkova Filkova H, Machackova D, Handzusova K, Gaillyova R, Kuglik P. Exome sequencing improves the molecular diagnostics of paediatric unexplained neurodevelopmental disorders. Orphanet J Rare Dis 2024; 19:41. [PMID: 38321498 PMCID: PMC10845791 DOI: 10.1186/s13023-024-03056-6] [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: 06/25/2023] [Accepted: 01/29/2024] [Indexed: 02/08/2024] Open
Abstract
BACKGROUND Neurodevelopmental disorders (NDDs) and/or associated multiple congenital abnormalities (MCAs) represent a genetically heterogeneous group of conditions with an adverse prognosis for the quality of intellectual and social abilities and common daily functioning. The rapid development of exome sequencing (ES) techniques, together with trio-based analysis, nowadays leads to up to 50% diagnostic yield. Therefore, it is considered as the state-of-the-art approach in these diagnoses. RESULTS In our study, we present the results of ES in a cohort of 85 families with 90 children with severe NDDs and MCAs. The interconnection of the in-house bioinformatic pipeline and a unique algorithm for variant prioritization resulted in a diagnostic yield of up to 48.9% (44/90), including rare and novel causative variants (41/90) and intragenic copy-number variations (CNVs) (3/90). Of the total number of 47 causative variants, 53.2% (25/47) were novel, highlighting the clinical benefit of ES for unexplained NDDs. Moreover, trio-based ES was verified as a reliable tool for the detection of rare CNVs, ranging from intragenic exon deletions (GRIN2A, ZC4H2 genes) to a 6-Mb duplication. The functional analysis using PANTHER Gene Ontology confirmed the involvement of genes with causative variants in a wide spectrum of developmental processes and molecular pathways, which form essential structural and functional components of the central nervous system. CONCLUSION Taken together, we present one of the first ES studies of this scale from the central European region. Based on the high diagnostic yield for paediatric NDDs in this study, 48.9%, we confirm trio-based ES as an effective and reliable first-tier diagnostic test in the genetic evaluation of children with NDDs.
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Affiliation(s)
- Marketa Wayhelova
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic.
- Centre of Molecular Biology and Genetics, University Hospital Brno, Brno, Czech Republic.
| | - Vladimira Vallova
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
- Centre of Molecular Biology and Genetics, University Hospital Brno, Brno, Czech Republic
| | - Petr Broz
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
- Department of Biology and Medical Genetics, 2nd Faculty of Medicine, Charles University Prague and University Hospital Motol, Prague, Czech Republic
| | - Aneta Mikulasova
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle Upon Tyne, UK
| | - Jan Smetana
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Hana Dynkova Filkova
- Centre of Molecular Biology and Genetics, University Hospital Brno, Brno, Czech Republic
| | - Dominika Machackova
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Kristina Handzusova
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Renata Gaillyova
- Department of Medical Genetics and Genomics, University Hospital Brno, Brno, Czech Republic
| | - Petr Kuglik
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
- Centre of Molecular Biology and Genetics, University Hospital Brno, Brno, Czech Republic
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37
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Yang L, Lyu J, Li X, Guo G, Zhou X, Chen T, Lin Y, Li T. Phase separation as a possible mechanism for dosage sensitivity. Genome Biol 2024; 25:17. [PMID: 38225666 PMCID: PMC10789095 DOI: 10.1186/s13059-023-03128-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 11/27/2023] [Indexed: 01/17/2024] Open
Abstract
BACKGROUND Deletion of haploinsufficient genes or duplication of triplosensitive ones results in phenotypic effects in a concentration-dependent manner, and the mechanisms underlying these dosage-sensitive effects remain elusive. Phase separation drives functional compartmentalization of biomolecules in a concentration-dependent manner as well, which suggests a potential link between these two processes, and warrants further systematic investigation. RESULTS Here we provide bioinformatic and experimental evidence to show a close link between phase separation and dosage sensitivity. We first demonstrate that haploinsufficient or triplosensitive gene products exhibit a higher tendency to undergo phase separation. Assessing the well-established dosage-sensitive genes HNRNPK, PAX6, and PQBP1 with experiments, we show that these proteins undergo phase separation. Critically, pathogenic variations in dosage-sensitive genes disturb the phase separation process either through reduced protein levels, or loss of phase-separation-prone regions. Analysis of multi-omics data further demonstrates that loss-of-function genetic perturbations on phase-separating genes cause similar dysfunction phenotypes as dosage-sensitive gene perturbations. In addition, dosage-sensitive scores derived from population genetics data predict phase-separating proteins with much better performance than available sequence-based predictors, further illustrating close ties between these two parameters. CONCLUSIONS Together, our study shows that phase separation is functionally linked to dosage sensitivity and provides novel insights for phase-separating protein prediction from the perspective of population genetics data.
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Affiliation(s)
- Liang Yang
- Department of Medical Bioinformatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Jiali Lyu
- IDG/McGovern Institute for Brain Research, Tsinghua-Peking Joint Centre for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Xi Li
- IDG/McGovern Institute for Brain Research, Tsinghua-Peking Joint Centre for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Gaigai Guo
- Department of Medical Bioinformatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Xueya Zhou
- Department of Systems Biology, Columbia University, New York, NY, 10032, USA
| | - Taoyu Chen
- Department of Medical Bioinformatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Yi Lin
- IDG/McGovern Institute for Brain Research, Tsinghua-Peking Joint Centre for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
| | - Tingting Li
- Department of Medical Bioinformatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China.
- Key Laboratory for Neuroscience, Ministry of Education/National Health Commission of China, Peking University, Beijing, 100191, China.
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Torene RI, Guillen Sacoto MJ, Millan F, Zhang Z, McGee S, Oetjens M, Heise E, Chong K, Sidlow R, O'Grady L, Sahai I, Martin CL, Ledbetter DH, Myers SM, Mitchell KJ, Retterer K. Systematic analysis of variants escaping nonsense-mediated decay uncovers candidate Mendelian diseases. Am J Hum Genet 2024; 111:70-81. [PMID: 38091987 PMCID: PMC10806863 DOI: 10.1016/j.ajhg.2023.11.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 11/17/2023] [Accepted: 11/19/2023] [Indexed: 01/07/2024] Open
Abstract
Protein-truncating variants (PTVs) near the 3' end of genes may escape nonsense-mediated decay (NMD). PTVs in the NMD-escape region (PTVescs) can cause Mendelian disease but are difficult to interpret given their varying impact on protein function. Previously, PTVesc burden was assessed in an epilepsy cohort, but no large-scale analysis has systematically evaluated these variants in rare disease. We performed a retrospective analysis of 29,031 neurodevelopmental disorder (NDD) parent-offspring trios referred for clinical exome sequencing to identify PTVesc de novo mutations (DNMs). We identified 1,376 PTVesc DNMs and 133 genes that were significantly enriched (binomial p < 0.001). The PTVesc-enriched genes included those with PTVescs previously described to cause dominant Mendelian disease (e.g., SEMA6B, PPM1D, and DAGLA). We annotated ClinVar variants for PTVescs and identified 948 genes with at least one high-confidence pathogenic variant. Twenty-two known Mendelian PTVesc-enriched genes had no prior evidence of PTVesc-associated disease. We found 22 additional PTVesc-enriched genes that are not well established to be associated with Mendelian disease, several of which showed phenotypic similarity between individuals harboring PTVesc variants in the same gene. Four individuals with PTVesc mutations in RAB1A had similar phenotypes including NDD and spasticity. PTVesc mutations in IRF2BP1 were found in two individuals who each had severe immunodeficiency manifesting in NDD. Three individuals with PTVesc mutations in LDB1 all had NDD and multiple congenital anomalies. Using a large-scale, systematic analysis of DNMs, we extend the mutation spectrum for known Mendelian disease-associated genes and identify potentially novel disease-associated genes.
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Affiliation(s)
| | | | | | | | | | - Matthew Oetjens
- Geisinger, Danville, PA, USA; Geisinger Autism & Developmental Medicine Institute, Lewisburg, PA, USA
| | | | | | | | | | | | - Christa L Martin
- Geisinger, Danville, PA, USA; Geisinger Autism & Developmental Medicine Institute, Lewisburg, PA, USA
| | - David H Ledbetter
- University of Florida, College of Medicine-Jacksonville, Jacksonville, FL, USA
| | - Scott M Myers
- Geisinger, Danville, PA, USA; Geisinger Autism & Developmental Medicine Institute, Lewisburg, PA, USA
| | - Kevin J Mitchell
- Smurfit Institute of Genetics and Institute of Neuroscience, Trinity College Dublin, Dublin, Ireland
| | - Kyle Retterer
- GeneDx, Gaithersburg, MD, USA; Geisinger, Danville, PA, USA.
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Zavileyskiy LG, Pervouchine DD. Post-transcriptional Regulation of Gene Expression via Unproductive Splicing. Acta Naturae 2024; 16:4-13. [PMID: 38698955 PMCID: PMC11062102 DOI: 10.32607/actanaturae.27337] [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: 12/03/2023] [Accepted: 03/01/2024] [Indexed: 05/05/2024] Open
Abstract
Unproductive splicing is a mechanism of post-transcriptional gene expression control in which premature stop codons are inserted into protein-coding transcripts as a result of regulated alternative splicing, leading to their degradation via the nonsense-mediated decay pathway. This mechanism is especially characteristic of RNA-binding proteins, which regulate each other's expression levels and those of other genes in multiple auto- and cross-regulatory loops. Deregulation of unproductive splicing is a cause of serious human diseases, including cancers, and is increasingly being considered as a prominent therapeutic target. This review discusses the types of unproductive splicing events, the mechanisms of auto- and cross-regulation, nonsense-mediated decay escape, and problems in identifying unproductive splice isoforms. It also provides examples of deregulation of unproductive splicing in human diseases and discusses therapeutic strategies for its correction using antisense oligonucleotides and small molecules.
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Affiliation(s)
- L. G. Zavileyskiy
- Lomonosov Moscow State University, Moscow, 119192 Russian Federation
- Skolkovo Institute of Science and Technology, Moscow, 121205 Russian Federation
| | - D. D. Pervouchine
- Skolkovo Institute of Science and Technology, Moscow, 121205 Russian Federation
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Wimmer B, Friedrich A, Poeltner K, Edobor G, Mosshammer C, Temaj G, Rathner A, Karl T, Krauss J, von Hagen J, Gerner C, Breitenbach M, Hintner H, Bauer JW, Breitenbach-Koller H. En Route to Targeted Ribosome Editing to Replenish Skin Anchor Protein LAMB3 in Junctional Epidermolysis Bullosa. JID INNOVATIONS 2024; 4:100240. [PMID: 38282649 PMCID: PMC10810840 DOI: 10.1016/j.xjidi.2023.100240] [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: 06/04/2023] [Revised: 09/24/2023] [Accepted: 09/25/2023] [Indexed: 01/30/2024] Open
Abstract
Severe junctional epidermolysis bullosa is a rare genetic, postpartum lethal skin disease, predominantly caused by nonsense/premature termination codon (PTC) sequence variants in LAMB3 gene. LAMB3 encodes LAMB3, the β subunit of epidermal-dermal skin anchor laminin 332. Most translational reads of a PTC mRNA deliver truncated, nonfunctional proteins, whereas an endogenous PTC readthrough mechanism produces full-length protein at minimal and insufficient levels. Conventional translational readthrough-inducing drugs amplify endogenous PTC readthrough; however, translational readthrough-inducing drugs are either proteotoxic or nonselective. Ribosome editing is a more selective and less toxic strategy. This technique identified ribosomal protein L35/uL29 (ie, RpL35) and RpL35-ligands repurposable drugs artesunate and atazanavir as molecular tools to increase production levels of full-length LAMB3. To evaluate ligand activity in living cells, we monitored artesunate and atazanavir treatment by dual luciferase reporter assays. Production levels of full-length LAMB3 increased up to 200% upon artesunate treatment, up to 150% upon atazanavir treatment, and up to 170% upon combinatorial treatment of RpL35 ligands at reduced drug dosage, with an unrelated PTC reporter being nonresponsive. Proof of bioactivity of RpL35 ligands in selective increase of full-length LAMB3 provides the basis for an alternative, targeted therapeutic route to replenish LAMB3 in severe junctional epidermolysis bullosa.
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Affiliation(s)
- Bjoern Wimmer
- Department of Biosciences and Medical Biology, University of Salzburg, Salzburg, Austria
| | - Andreas Friedrich
- Department of Biosciences and Medical Biology, University of Salzburg, Salzburg, Austria
| | - Katharina Poeltner
- Department of Biosciences and Medical Biology, University of Salzburg, Salzburg, Austria
| | - Genevieve Edobor
- Department of Biosciences and Medical Biology, University of Salzburg, Salzburg, Austria
| | - Claudia Mosshammer
- Department of Biosciences and Medical Biology, University of Salzburg, Salzburg, Austria
| | | | - Adriana Rathner
- Institute of Biochemistry, Johannes Kepler University of Linz, Linz, Austria
| | - Thomas Karl
- Department of Biosciences and Medical Biology, University of Salzburg, Salzburg, Austria
| | - Jan Krauss
- Department of Biosciences and Medical Biology, University of Salzburg, Salzburg, Austria
- SKM-IP PartGmbB, Munich, Germany
| | - Joerg von Hagen
- Merck KGaA, Gernsheim, Germany
- ryon-Greentech Accelerator, Gernsheim, Germany
| | - Christopher Gerner
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
- Joint Metabolome Facility, University of Vienna, Vienna, Austria
| | - Michael Breitenbach
- Department of Biosciences and Medical Biology, University of Salzburg, Salzburg, Austria
| | - Helmut Hintner
- Department of Dermatology and Allergology, University Hospital Salzburg, Salzburg, Austria
| | - Johann W. Bauer
- Department of Dermatology and Allergology, University Hospital Salzburg, Salzburg, Austria
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Karimi E, van der Borgh M, Lindqvist J, Gohlke J, Hourani Z, Kolb J, Cossette S, Lawlor MW, Ottenheijm C, Granzier H. Characterization of NEB mutations in patients reveals novel nemaline myopathy disease mechanisms and omecamtiv mecarbil force effects. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.20.572678. [PMID: 38187705 PMCID: PMC10769406 DOI: 10.1101/2023.12.20.572678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Nebulin, a critical protein of the skeletal muscle thin filament, plays important roles in physiological processes such as regulating thin filament length (TFL), cross-bridge cycling, and myofibril alignment. Mutations in the nebulin gene ( NEB ) cause NEB-based nemaline myopathy (NEM2), a genetically heterogeneous disorder characterized by hypotonia and muscle weakness, currently lacking therapies targeting the underlying pathological mechanisms. In this study, we examined a cohort of ten NEM2 patients, each with unique mutations, aiming to understand their impact on mRNA, protein, and functional levels. Results show that truncation mutations affect NEB mRNA stability and lead to nonsense-mediated decay of the mutated transcript. Moreover, a high incidence of cryptic splice site activation was found in patients with splicing mutations which is expected to disrupt the actin-binding sites of nebulin. Determination of protein levels revealed patients with relatively normal nebulin levels and others with markedly reduced nebulin. We observed a positive relation between the reduction in nebulin and a reduction in TFL, and a positive relation between the reduction in nebulin level and the reduction in tension (both maximal and submaximal tension). Interestingly, our study revealed a duplication mutation in nebulin that resulted in a larger nebulin protein and longer TFL. Additionally, we investigated the effect of Omecamtiv mecarbil (OM), a small-molecule activator of cardiac myosin, on force production of type I muscle fibers of NEM2 patients. OM treatment substantially increased submaximal tension across all NEM2 patients ranging from 87-318%, with the largest effects in patients with the lowest level of nebulin. In summary, this study indicates that post-transcriptional or post-translational mechanisms regulate nebulin expression. Moreover, we propose that the pathomechanism of NEM2 involves not only shortened but also elongated thin filaments, along with the disruption of actin-binding sites resulting from splicing mutations. Significantly, our findings highlight the potential of OM treatment to improve skeletal muscle function in NEM2 patients, especially those with large reductions in nebulin levels.
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Bea-Mascato B, Valverde D. Genotype-phenotype associations in Alström syndrome: a systematic review and meta-analysis. J Med Genet 2023; 61:18-26. [PMID: 37321834 PMCID: PMC10803979 DOI: 10.1136/jmg-2023-109175] [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: 01/20/2023] [Accepted: 05/29/2023] [Indexed: 06/17/2023]
Abstract
BACKGROUND Alström syndrome (ALMS; #203800) is an ultrarare monogenic recessive disease. This syndrome is associated with variants in the ALMS1 gene, which encodes a centrosome-associated protein involved in the regulation of several ciliary and extraciliary processes, such as centrosome cohesion, apoptosis, cell cycle control and receptor trafficking. The type of variant associated with ALMS is mostly complete loss-of-function variants (97%) and they are mainly located in exons 8, 10 and 16 of the gene. Other studies in the literature have tried to establish a genotype-phenotype correlation in this syndrome with limited success. The difficulty in recruiting a large cohort in rare diseases is the main barrier to conducting this type of study. METHODS In this study we collected all cases of ALMS published to date. We created a database of patients who had a genetic diagnosis and an individualised clinical history. Lastly, we attempted to establish a genotype-phenotype correlation using the truncation site of the patient's longest allele as a grouping criteria. RESULTS We collected a total of 357 patients, of whom 227 had complete clinical information, complete genetic diagnosis and meta-information on sex and age. We have seen that there are five variants with high frequency, with p.(Arg2722Ter) being the most common variant, with 28 alleles. No gender differences in disease progression were detected. Finally, truncating variants in exon 10 seem to be correlated with a higher prevalence of liver disorders in patients with ALMS. CONCLUSION Pathogenic variants in exon 10 of the ALMS1 gene were associated with a higher prevalence of liver disease. However, the location of the variant in the ALMS1 gene does not have a major impact on the phenotype developed by the patient.
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Affiliation(s)
- Brais Bea-Mascato
- CINBIO, Universidad de Vigo, 36310 Vigo, Spain
- Grupo de Investigación en Enfermedades Raras y Medicina Pediátrica, Instituto de Investigación Sanitaria Galicia Sur (IIS Galicia Sur), SERGAS-UVIGO, Vigo, Spain
| | - Diana Valverde
- CINBIO, Universidad de Vigo, 36310 Vigo, Spain
- Grupo de Investigación en Enfermedades Raras y Medicina Pediátrica, Instituto de Investigación Sanitaria Galicia Sur (IIS Galicia Sur), SERGAS-UVIGO, Vigo, Spain
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Tian Y, Xing J, Shi Y, Yuan E. Exploring the relationship between IGHMBP2 gene mutations and spinal muscular atrophy with respiratory distress type 1 and Charcot-Marie-Tooth disease type 2S: a systematic review. Front Neurosci 2023; 17:1252075. [PMID: 38046662 PMCID: PMC10690808 DOI: 10.3389/fnins.2023.1252075] [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: 07/03/2023] [Accepted: 11/03/2023] [Indexed: 12/05/2023] Open
Abstract
Background IGHMBP2 is a crucial gene for the development and maintenance of the nervous system, especially in the survival of motor neurons. Mutations in this gene have been associated with spinal muscular atrophy with respiratory distress type 1 (SMARD1) and Charcot-Marie-Tooth disease type 2S (CMT2S). Methods We conducted a systematic literature search using the PubMed database to identify studies published up to April 1st, 2023, that investigated the association between IGHMBP2 mutations and SMARD1 or CMT2S. We compared the non-truncating mutations and truncating mutations of the IGHMBP2 gene and selected high-frequency mutations of the IGHMBP2 gene. Results We identified 52 articles that investigated the association between IGHMBP2 mutations and SMARD1/CMT2S. We found 6 hotspot mutations of the IGHMBP2 gene. The truncating mutations in trans were all associated with SMARD1. Conclusion This study provides evidence that the complete LOF mechanism of the IGHMBP2 gene defect may be an important cause of SMARD1.
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Affiliation(s)
- Yuan Tian
- Department of Clinical Laboratory, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Jinfang Xing
- Department of Clinical Laboratory, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Ying Shi
- Screening Center, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Enwu Yuan
- Department of Clinical Laboratory, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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Liu Y, Elmas A, Huang KL. Mutation Impact on mRNA Versus Protein Expression across Human Cancers. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.13.566942. [PMID: 38014015 PMCID: PMC10680725 DOI: 10.1101/2023.11.13.566942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Cancer mutations are often assumed to alter proteins, thus promoting tumorigenesis. However, how mutations affect protein expression has rarely been systematically investigated. We conduct a comprehensive analysis of mutation impacts on mRNA- and protein-level expressions of 953 cancer cases with paired genomics and global proteomic profiling across six cancer types. Protein-level impacts are validated for 47.2% of the somatic expression quantitative trait loci (seQTLs), including mutations from likely "long-tail" driver genes. Devising a statistical pipeline for identifying somatic protein-specific QTLs (spsQTLs), we reveal several gene mutations, including NF1 and MAP2K4 truncations and TP53 missenses showing disproportional influence on protein abundance not readily explained by transcriptomics. Cross-validating with data from massively parallel assays of variant effects (MAVE), TP53 missenses associated with high tumor TP53 proteins were experimentally confirmed as functional. Our study demonstrates the importance of considering protein-level expression to validate mutation impacts and identify functional genes and mutations.
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Patro I, Sahoo A, Nayak BR, Das R, Majumder S, Panigrahi GK. Nonsense-Mediated mRNA Decay: Mechanistic Insights and Physiological Significance. Mol Biotechnol 2023:10.1007/s12033-023-00927-4. [PMID: 37930508 DOI: 10.1007/s12033-023-00927-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 09/28/2023] [Indexed: 11/07/2023]
Abstract
Nonsense-mediated mRNA decay (NMD) is an evolutionarily conserved surveillance mechanism across eukaryotes and also regulates the expression of physiological transcripts, thus involved in gene regulation. It essentially ensures recognition and removal of aberrant transcripts. Therefore, the NMD protects the cellular system by restricting the synthesis of truncated proteins, potentially by eliminating the faulty mRNAs. NMD is an evolutionarily conserved surveillance mechanism across eukaryotes and also regulates the expression of physiological transcripts, thus involved in gene regulation as well. Primarily, the NMD machinery scans and differentiates the aberrant and non-aberrant transcripts. A myriad of cellular dysfunctions arise due to production of truncated proteins, so the NMD core proteins, the up-frameshift factors (UPFs) recognizes the faulty mRNAs and further recruits factors resulting in the mRNA degradation. NMD exhibits astounding variability in its ability in regulating cellular mechanisms including both pathological and physiological events. But, the detailed underlying molecular mechanisms in NMD remains blurred and require extensive investigation to gain insights on cellular homeostasis. The complexity in understanding of NMD pathway arises due to the involvement of numerous proteins, molecular interactions and their functioning in different steps of this process. Moreover methods such as alternative splicing generates numerous isoforms of mRNA, so it makes difficulties in understanding the impact of alternative splicing on the efficiency of NMD functioning. Role of NMD in cancer development is very complex. Studies have shown that in some cases cancer cells use NMD pathway as a tool to exploit the NMD mechanism to maintain tumor microenvironment. A greater level of understanding about the intricate mechanism of how tumor used NMD pathway for their benefits, a strategy can be developed for targeting and inhibiting NMD factors involved in pro-tumor activity. There are very little amount of information available about the NMD pathway, how it discriminate mRNAs that are targeted by NMD from those that are not. This review highlights our current understanding of NMD, specifically the regulatory mechanisms and attempts to outline less explored questions that warrant further investigations. Taken as a whole, a detailed molecular understanding of the NMD mechanism could lead to wide-ranging applications for improving cellular homeostasis and paving out strategies in combating pathological disorders leaping forward toward achieving United Nations sustainable development goals (SDG 3: Good health and well-being).
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Affiliation(s)
- Ipsita Patro
- School of Applied Sciences, Centurion University of Technology and Management, Bhubaneswar, Odisha, India
| | - Annapurna Sahoo
- School of Applied Sciences, Centurion University of Technology and Management, Bhubaneswar, Odisha, India.
| | - Bilash Ranjan Nayak
- School of Applied Sciences, Centurion University of Technology and Management, Bhubaneswar, Odisha, India
| | - Rutupurna Das
- School of Applied Sciences, Centurion University of Technology and Management, Bhubaneswar, Odisha, India
| | - Sanjoy Majumder
- School of Applied Sciences, Centurion University of Technology and Management, Bhubaneswar, Odisha, India
| | - Gagan Kumar Panigrahi
- School of Applied Sciences, Centurion University of Technology and Management, Bhubaneswar, Odisha, India.
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Oppermann H, Marcos-Grañeda E, Weiss LA, Gurnett CA, Jelsig AM, Vineke SH, Isidor B, Mercier S, Magnussen K, Zacher P, Hashim M, Pagnamenta AT, Race S, Srivastava S, Frazier Z, Maiwald R, Pergande M, Milani D, Rinelli M, Levy J, Krey I, Fontana P, Lonardo F, Riley S, Kretzer J, Rankin J, Reis LM, Semina EV, Reuter MS, Scherer SW, Iascone M, Weis D, Fagerberg CR, Brasch-Andersen C, Hansen LK, Kuechler A, Noble N, Gardham A, Tenney J, Rathore G, Beck-Woedl S, Haack TB, Pavlidou DC, Atallah I, Vodopiutz J, Janecke AR, Hsieh TC, Lesmann H, Klinkhammer H, Krawitz PM, Lemke JR, Jamra RA, Nieto M, Tümer Z, Platzer K. CUX1-related neurodevelopmental disorder: deep insights into phenotype-genotype spectrum and underlying pathology. Eur J Hum Genet 2023; 31:1251-1260. [PMID: 37644171 PMCID: PMC10620399 DOI: 10.1038/s41431-023-01445-2] [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: 12/21/2022] [Revised: 06/26/2023] [Accepted: 07/27/2023] [Indexed: 08/31/2023] Open
Abstract
Heterozygous, pathogenic CUX1 variants are associated with global developmental delay or intellectual disability. This study delineates the clinical presentation in an extended cohort and investigates the molecular mechanism underlying the disorder in a Cux1+/- mouse model. Through international collaboration, we assembled the phenotypic and molecular information for 34 individuals (23 unpublished individuals). We analyze brain CUX1 expression and susceptibility to epilepsy in Cux1+/- mice. We describe 34 individuals, from which 30 were unrelated, with 26 different null and four missense variants. The leading symptoms were mild to moderate delayed speech and motor development and borderline to moderate intellectual disability. Additional symptoms were muscular hypotonia, seizures, joint laxity, and abnormalities of the forehead. In Cux1+/- mice, we found delayed growth, histologically normal brains, and increased susceptibility to seizures. In Cux1+/- brains, the expression of Cux1 transcripts was half of WT animals. Expression of CUX1 proteins was reduced, although in early postnatal animals significantly more than in adults. In summary, disease-causing CUX1 variants result in a non-syndromic phenotype of developmental delay and intellectual disability. In some individuals, this phenotype ameliorates with age, resulting in a clinical catch-up and normal IQ in adulthood. The post-transcriptional balance of CUX1 expression in the heterozygous brain at late developmental stages appears important for this favorable clinical course.
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Affiliation(s)
- Henry Oppermann
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany.
| | - Elia Marcos-Grañeda
- Department of Cellular and Molecular Biology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC), Campus de Cantoblanco, Madrid, Spain
| | - Linnea A Weiss
- Department of Cellular and Molecular Biology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC), Campus de Cantoblanco, Madrid, Spain
| | - Christina A Gurnett
- Department of Neurology, Washington University in St Louis, St Louis, MO, USA
| | - Anne Marie Jelsig
- Dpt. of Clinical Genetics, Copenhagen University Hospital-Rigshospitalet, Copenhagen, Denmark
| | - Susanne H Vineke
- Dpt. of Clinical Genetics, Copenhagen University Hospital-Rigshospitalet, Copenhagen, Denmark
| | - Bertrand Isidor
- Service de Génétique Médicale, CHU de Nantes, Nantes, France
| | - Sandra Mercier
- Service de Génétique Médicale, CHU de Nantes, Nantes, France
- L'institut du thorax, Inserm, Cnrs, Univ Nantes, Nantes, France
| | - Kari Magnussen
- Randall Children's Hospital at Legacy Emanuel, Portland, OR, USA
| | - Pia Zacher
- Epilepsy Center Kleinwachau, Radeberg, Germany
| | - Mona Hashim
- NIHR Oxford Biomedical Research Centre, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Alistair T Pagnamenta
- NIHR Oxford Biomedical Research Centre, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Simone Race
- BC Children's Hospital, University of British Columbia, Vancouver, BC, Canada
| | | | - Zoë Frazier
- Department of Neurology, Boston Children's Hospital, Boston, MA, USA
| | - Robert Maiwald
- MVZ for Coagulation Diagnostics and Medical Genetics Cologne, ÜBAG Zotz/Klimas, Cologne, Germany
| | | | - Donatella Milani
- Fondazione IRCCS Ca'Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Martina Rinelli
- Laboratory of Medical Genetics, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
- Departmental Unit of Molecular and Genomic Diagnostics, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Jonathan Levy
- Genetics Department, CHU Robert-Debré, AP-HP, Paris, France
| | - Ilona Krey
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Paolo Fontana
- Medical Genetics Unit, A.O.R.N. San Pio, Benevento, Italy
| | | | - Stephanie Riley
- Department of Pediatrics, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Jasmine Kretzer
- Department of Pediatrics, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Julia Rankin
- Department of Clinical Genetics, Royal Devon University Healthcare NHS Trust, Exeter, UK
| | - Linda M Reis
- Department of Pediatrics and Children's Research Institute, Medical College of Wisconsin and Children's Hospital of Wisconsin, Milwaukee, WI, USA
| | - Elena V Semina
- Department of Pediatrics and Children's Research Institute, Medical College of Wisconsin and Children's Hospital of Wisconsin, Milwaukee, WI, USA
| | - Miriam S Reuter
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Stephen W Scherer
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Maria Iascone
- Laboratory of Medical Genetics, ASST Papa Giovanni XXIII, Bergamo, Italy
| | - Denisa Weis
- Department of Medical Genetics, Kepler University Hospital Med Campus IV, Johannes Kepler University, Linz, Austria
| | | | | | | | - Alma Kuechler
- Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen, Essen, Germany
| | - Nathan Noble
- Blank Children's Developmental Center, Unity Point Health, Des Moines, IA, USA
| | - Alice Gardham
- North West Thames Regional Genetic Service, North West London Hospitals, London, UK
| | - Jessica Tenney
- Division of Medical Genetics, University of California, San Francisco, CA, USA
| | - Geetanjali Rathore
- Dvision of Pediatric Neurology, University of Nebraska Medical Center, Omaha, NE, USA
| | - Stefanie Beck-Woedl
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Tobias B Haack
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Despoina C Pavlidou
- Division of Genetic Medicine, Lausanne Universitary Hospital and University of Lausanne, Lausanne, Switzerland
| | - Isis Atallah
- Division of Genetic Medicine, Lausanne Universitary Hospital and University of Lausanne, Lausanne, Switzerland
| | - Julia Vodopiutz
- Department of Pediatrics and Adolescent Medicine, Division of Pediatric Pulmonology, Allergology and Endocrinology, Comprehensive Center for Pediatrics, Medical University of Vienna, Vienna, Austria
- Vienna Bone and Growth Center, Vienna, Austria
| | - Andreas R Janecke
- Department of Pediatrics, Medical University of Innsbruck, Innsbruck, Austria
- Institute of Human Genetics, Medical University of Innsbruck, Innsbruck, Austria
| | - Tzung-Chien Hsieh
- Institute for Genomic Statistics and Bioinformatics, University Hospital Bonn, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Hellen Lesmann
- Institute for Genomic Statistics and Bioinformatics, University Hospital Bonn, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
- Institut für Humangenetik, Universitätsklinikum Bonn, Universität Bonn, Bonn, Germany
| | - Hannah Klinkhammer
- Institute for Genomic Statistics and Bioinformatics, University Hospital Bonn, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
- Institute for Medical Biometry, Informatics and Epidemiology, University Hospital Bonn, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Peter M Krawitz
- Institute for Genomic Statistics and Bioinformatics, University Hospital Bonn, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Johannes R Lemke
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
- Center for Rare Diseases, University of Leipzig Medical Center, Leipzig, Germany
| | - Rami Abou Jamra
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Marta Nieto
- Department of Cellular and Molecular Biology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC), Campus de Cantoblanco, Madrid, Spain.
| | - Zeynep Tümer
- Kennedy Center, Department of Clinical Genetics, Copenhagen University Hospital-Rigshospitalet, Copenhagen, Denmark.
- Department of Clinical Medicin, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
| | - Konrad Platzer
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
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Ha C, Jang JH, Kim YG, Kim JW. Reclassification of variants of tumor suppressor genes based on Sanger RNA sequencing without NMD inhibition. Front Genet 2023; 14:1283611. [PMID: 37900184 PMCID: PMC10602670 DOI: 10.3389/fgene.2023.1283611] [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: 08/26/2023] [Accepted: 10/02/2023] [Indexed: 10/31/2023] Open
Abstract
Introduction: RNA sequence analysis can be effectively used to identify aberrant splicing, and tumor suppressor genes are adequate targets considering their loss-of-function mechanisms. Sanger sequencing is the simplest method for RNA sequence analysis; however, because of its insufficient sensitivity in cases with nonsense-mediated mRNA decay (NMD), the use of cultured specimens with NMD inhibition has been recommended, hindering its wide adoption. Method: The results of Sanger sequencing of peripheral blood RNA without NMD inhibition performed on potential splicing variants of tumor suppressor genes were retrospectively reviewed. For negative cases, in which no change was identified in the transcript, the possibility of false negativity caused by NMD was assessed through a review of the up-to-date literature. Results: Eleven potential splice variants of various tumor suppressor genes were reviewed. Six variants were classified as pathogenic or likely pathogenic based on the nullifying effect identified by Sanger RNA sequencing. Four variants remained as variants of uncertain significance because of identified in-frame changes or normal expression of both alleles. The result of one variant was suspected to be a false negative caused by NMD after reviewing a recent study that reported the same variant as causing a nullifying effect on the affected transcript. Conclusion: Although RNA changes found in the majority of cases were expected to undergo NMD by canonical rules, most cases (10/11) were interpretable by Sanger RNA sequencing without NMD inhibition due to incomplete NMD efficiency or allele-specific expression despite highly efficient NMD.
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Monaghan L, Longman D, Cáceres JF. Translation-coupled mRNA quality control mechanisms. EMBO J 2023; 42:e114378. [PMID: 37605642 PMCID: PMC10548175 DOI: 10.15252/embj.2023114378] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 07/24/2023] [Accepted: 08/01/2023] [Indexed: 08/23/2023] Open
Abstract
mRNA surveillance pathways are essential for accurate gene expression and to maintain translation homeostasis, ensuring the production of fully functional proteins. Future insights into mRNA quality control pathways will enable us to understand how cellular mRNA levels are controlled, how defective or unwanted mRNAs can be eliminated, and how dysregulation of these can contribute to human disease. Here we review translation-coupled mRNA quality control mechanisms, including the non-stop and no-go mRNA decay pathways, describing their mechanisms, shared trans-acting factors, and differences. We also describe advances in our understanding of the nonsense-mediated mRNA decay (NMD) pathway, highlighting recent mechanistic findings, the discovery of novel factors, as well as the role of NMD in cellular physiology and its impact on human disease.
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Affiliation(s)
- Laura Monaghan
- MRC Human Genetics Unit, Institute of Genetics and CancerUniversity of EdinburghEdinburghUK
| | - Dasa Longman
- MRC Human Genetics Unit, Institute of Genetics and CancerUniversity of EdinburghEdinburghUK
| | - Javier F Cáceres
- MRC Human Genetics Unit, Institute of Genetics and CancerUniversity of EdinburghEdinburghUK
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49
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McGurk KA, Zhang X, Theotokis P, Thomson K, Harper A, Buchan RJ, Mazaika E, Ormondroyd E, Wright WT, Macaya D, Pua CJ, Funke B, MacArthur DG, Prasad SK, Cook SA, Allouba M, Aguib Y, Yacoub MH, O'Regan DP, Barton PJR, Watkins H, Bottolo L, Ware JS. The penetrance of rare variants in cardiomyopathy-associated genes: A cross-sectional approach to estimating penetrance for secondary findings. Am J Hum Genet 2023; 110:1482-1495. [PMID: 37652022 PMCID: PMC10502871 DOI: 10.1016/j.ajhg.2023.08.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 07/21/2023] [Accepted: 08/04/2023] [Indexed: 09/02/2023] Open
Abstract
Understanding the penetrance of pathogenic variants identified as secondary findings (SFs) is of paramount importance with the growing availability of genetic testing. We estimated penetrance through large-scale analyses of individuals referred for diagnostic sequencing for hypertrophic cardiomyopathy (HCM; 10,400 affected individuals, 1,332 variants) and dilated cardiomyopathy (DCM; 2,564 affected individuals, 663 variants), using a cross-sectional approach comparing allele frequencies against reference populations (293,226 participants from UK Biobank and gnomAD). We generated updated prevalence estimates for HCM (1:543) and DCM (1:220). In aggregate, the penetrance by late adulthood of rare, pathogenic variants (23% for HCM, 35% for DCM) and likely pathogenic variants (7% for HCM, 10% for DCM) was substantial for dominant cardiomyopathy (CM). Penetrance was significantly higher for variant subgroups annotated as loss of function or ultra-rare and for males compared to females for variants in HCM-associated genes. We estimated variant-specific penetrance for 316 recurrent variants most likely to be identified as SFs (found in 51% of HCM- and 17% of DCM-affected individuals). 49 variants were observed at least ten times (14% of affected individuals) in HCM-associated genes. Median penetrance was 14.6% (±14.4% SD). We explore estimates of penetrance by age, sex, and ancestry and simulate the impact of including future cohorts. This dataset reports penetrance of individual variants at scale and will inform the management of individuals undergoing genetic screening for SFs. While most variants had low penetrance and the costs and harms of screening are unclear, some individuals with highly penetrant variants may benefit from SFs.
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Affiliation(s)
- Kathryn A McGurk
- National Heart and Lung Institute, Imperial College London, London, UK; MRC London Institute of Medical Sciences, Imperial College London, London, UK
| | - Xiaolei Zhang
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Pantazis Theotokis
- National Heart and Lung Institute, Imperial College London, London, UK; MRC London Institute of Medical Sciences, Imperial College London, London, UK
| | - Kate Thomson
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine and the Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Andrew Harper
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine and the Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Rachel J Buchan
- National Heart and Lung Institute, Imperial College London, London, UK; MRC London Institute of Medical Sciences, Imperial College London, London, UK; Royal Brompton & Harefield Hospitals, Guy's and St. Thomas' NHS Foundation Trust, London, UK
| | - Erica Mazaika
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Elizabeth Ormondroyd
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine and the Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - William T Wright
- Northern Ireland Regional Genetics Centre, Belfast Health and Social Care Trust, Belfast City Hospital, Belfast, Northern Ireland, UK
| | | | - Chee Jian Pua
- National Heart Research Institute Singapore and Duke-National University of Singapore, Singapore, Singapore
| | - Birgit Funke
- Laboratory for Molecular Medicine, Partners Healthcare Center for Personalized Genetic Medicine, Boston, MA, USA
| | - Daniel G MacArthur
- Centre for Population Genomics, Garvan Institute of Medical Research and UNSW, Sydney, NSW, Australia; Centre for Population Genomics, Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Sanjay K Prasad
- National Heart and Lung Institute, Imperial College London, London, UK; Royal Brompton & Harefield Hospitals, Guy's and St. Thomas' NHS Foundation Trust, London, UK
| | - Stuart A Cook
- MRC London Institute of Medical Sciences, Imperial College London, London, UK; National Heart Research Institute Singapore and Duke-National University of Singapore, Singapore, Singapore
| | - Mona Allouba
- National Heart and Lung Institute, Imperial College London, London, UK; Aswan Heart Centre, Aswan, Egypt
| | - Yasmine Aguib
- National Heart and Lung Institute, Imperial College London, London, UK; Aswan Heart Centre, Aswan, Egypt
| | - Magdi H Yacoub
- National Heart and Lung Institute, Imperial College London, London, UK; Royal Brompton & Harefield Hospitals, Guy's and St. Thomas' NHS Foundation Trust, London, UK; Aswan Heart Centre, Aswan, Egypt
| | - Declan P O'Regan
- MRC London Institute of Medical Sciences, Imperial College London, London, UK
| | - Paul J R Barton
- National Heart and Lung Institute, Imperial College London, London, UK; MRC London Institute of Medical Sciences, Imperial College London, London, UK; Royal Brompton & Harefield Hospitals, Guy's and St. Thomas' NHS Foundation Trust, London, UK
| | - Hugh Watkins
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine and the Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Leonardo Bottolo
- Department of Medical Genetics, University of Cambridge, Cambridge, UK; The Alan Turing Institute, London, UK; MRC Biostatistics Unit, University of Cambridge, Cambridge, UK
| | - James S Ware
- National Heart and Lung Institute, Imperial College London, London, UK; MRC London Institute of Medical Sciences, Imperial College London, London, UK; Royal Brompton & Harefield Hospitals, Guy's and St. Thomas' NHS Foundation Trust, London, UK.
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50
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Klonowski J, Liang Q, Coban-Akdemir Z, Lo C, Kostka D. aenmd: annotating escape from nonsense-mediated decay for transcripts with protein-truncating variants. Bioinformatics 2023; 39:btad556. [PMID: 37688563 PMCID: PMC10534055 DOI: 10.1093/bioinformatics/btad556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 07/13/2023] [Accepted: 09/07/2023] [Indexed: 09/11/2023] Open
Abstract
SUMMARY DNA changes that cause premature termination codons (PTCs) represent a large fraction of clinically relevant pathogenic genomic variation. Typically, PTCs induce transcript degradation by nonsense-mediated mRNA decay (NMD) and render such changes loss-of-function alleles. However, certain PTC-containing transcripts escape NMD and can exert dominant-negative or gain-of-function (DN/GOF) effects. Therefore, systematic identification of human PTC-causing variants and their susceptibility to NMD contributes to the investigation of the role of DN/GOF alleles in human disease. Here we present aenmd, a software for annotating PTC-containing transcript-variant pairs for predicted escape from NMD. aenmd is user-friendly and self-contained. It offers functionality not currently available in other methods and is based on established and experimentally validated rules for NMD escape; the software is designed to work at scale, and to integrate seamlessly with existing analysis workflows. We applied aenmd to variants in the gnomAD, Clinvar, and GWAS catalog databases and report the prevalence of human PTC-causing variants in these databases, and the subset of these variants that could exert DN/GOF effects via NMD escape. AVAILABILITY AND IMPLEMENTATION aenmd is implemented in the R programming language. Code is available on GitHub as an R-package (github.com/kostkalab/aenmd.git), and as a containerized command-line interface (github.com/kostkalab/aenmd_cli.git).
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Affiliation(s)
- Jonathan Klonowski
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15201, United States
| | - Qianqian Liang
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15201, United States
| | - Zeynep Coban-Akdemir
- Department of Epidemiology, Human Genetics and Environmental Sciences, University of Texas School of Public Health, Houston, TX 77030, United States
| | - Cecilia Lo
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15201, United States
| | - Dennis Kostka
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15201, United States
- Department of Computational & Systems Biology and Center for Evolutionary Biology and Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260,United States
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