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Hejla D, Huynh S, Samra S, Richmond PA, Dalmann J, Del Bel KL, Byres L, Lehman A, Turvey SE, Boerkoel CF. Naturally occurring splice variants dissect the functional domains of BHC80 and emphasize the need for RNA analysis. Am J Med Genet A 2024; 194:e63548. [PMID: 38264805 DOI: 10.1002/ajmg.a.63548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 01/04/2024] [Accepted: 01/12/2024] [Indexed: 01/25/2024]
Abstract
Pathogenic PHF21A variation causes PHF21A-related neurodevelopmental disorders (NDDs). Although amorphic alleles, including haploinsufficiency, have been established as a disease mechanism, increasing evidence suggests that missense variants as well as frameshift variants extending the BHC80 carboxyl terminus also cause disease. Expanding on these, we report a proposita with intellectual disability and overgrowth and a novel de novo heterozygous PHF21A splice variant (NM_001352027.3:c.[153+1G>C];[=]) causing skipping of exon 6, which encodes an in-frame BHC80 deletion (p.(Asn30_Gln51del)). This deletion disrupts a predicted leucine zipper domain and implicates this domain in BHC80 function and as a target of variation causing PHF21A-related NDDs. This extension of understanding emphasizes the application of RNA analysis in precision genomic medicine practice.
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Affiliation(s)
- Duha Hejla
- Department of Pediatrics, University of British Columbia and Children's Hospital of British Columbia, Vancouver, British Columbia, Canada
| | - Stephanie Huynh
- Provincial Medical Genetics Program, B.C. Women's Hospital, Vancouver, British Columbia, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Simran Samra
- The Rare Disease Discovery Hub, BC Children's Hospital Research Institute, University of British Columbia and Children's Hospital of British Columbia, Vancouver, British Columbia, Canada
- Experimental Medicine Program, Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Phillip A Richmond
- The Rare Disease Discovery Hub, BC Children's Hospital Research Institute, University of British Columbia and Children's Hospital of British Columbia, Vancouver, British Columbia, Canada
| | - Joshua Dalmann
- The Rare Disease Discovery Hub, BC Children's Hospital Research Institute, University of British Columbia and Children's Hospital of British Columbia, Vancouver, British Columbia, Canada
| | - Kate L Del Bel
- The Rare Disease Discovery Hub, BC Children's Hospital Research Institute, University of British Columbia and Children's Hospital of British Columbia, Vancouver, British Columbia, Canada
| | - Loryn Byres
- The Rare Disease Discovery Hub, BC Children's Hospital Research Institute, University of British Columbia and Children's Hospital of British Columbia, Vancouver, British Columbia, Canada
| | - Anna Lehman
- The Rare Disease Discovery Hub, BC Children's Hospital Research Institute, University of British Columbia and Children's Hospital of British Columbia, Vancouver, British Columbia, Canada
| | - Stuart E Turvey
- The Rare Disease Discovery Hub, BC Children's Hospital Research Institute, University of British Columbia and Children's Hospital of British Columbia, Vancouver, British Columbia, Canada
| | - Cornelius F Boerkoel
- Provincial Medical Genetics Program, B.C. Women's Hospital, Vancouver, British Columbia, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
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Sun L, Han Y, Li B, Yang Y, Fang Y, Ren X, An L, Hou X, Fan H, Wu Y. A Novel Frameshift Variant of the ELF4 Gene in a Patient with Autoinflammatory Disease: Clinical Features, Transcriptomic Profiling and Functional Studies. J Clin Immunol 2024; 44:127. [PMID: 38773005 DOI: 10.1007/s10875-024-01732-7] [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: 12/07/2023] [Accepted: 05/07/2024] [Indexed: 05/23/2024]
Abstract
We described the diagnosis and treatment of a patient with autoinflammatory disease, named "Deficiency in ELF4, X-linked (DEX)". A novel ELF4 variant was discovered and its pathogenic mechanism was elucidated. The data about clinical, laboratory and endoscopic features, treatment, and follow-up of a patient with DEX were analyzed. Whole exome sequencing and Sanger sequencing were performed to identify potential pathogenic variants. The mRNA and protein levels of ELF4 were analyzed by qPCR and Western blotting, respectively. The association of ELF4 frameshift variant with nonsense-mediated mRNA decay (NMD) in the pathogenesis DEX was examined. Moreover, RNA-seq was performed to identify the key molecular events triggered by ELF4 variant. The relationship between ELF4 and IFN-β activity was validated using a dual-luciferase reporter assay and a ChIP-qPCR assay. An 11-year-old boy presented with a Behçet's-like phenotype. The laboratory abnormality was the most obvious in elevated inflammatory indicators. Endoscopy revealed multiple ileocecal ulcers. Intestinal histopathology showed inflammatory cell infiltrations. The patient was treated with long-term immunosuppressant and TNF-α blocker (adalimumab), which reaped an excellent response over 16 months of follow-up. Genetic analysis identified a maternal hemizygote frameshift variant (c.1022del, p.Q341Rfs*30) in ELF4 gene in the proband. The novel variant decreased the mRNA level of ELF4 via the NMD pathway. Mechanistically, insufficient expression of ELF4 disturbed the immune system, leading to immunological disorders and pathogen susceptibility, and disrupted ELF4-activating IFN-β responses. This analysis detailed the clinical characteristics of a Chinese patient with DEX who harbored a novel ELF4 frameshift variant. For the first time, we used patient-derived cells and carried out transcriptomic analysis to delve into the mechanism of ELF4 variant in DEX.
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Affiliation(s)
- Lina Sun
- MOE Key Laboratory of Environment and Genes Related to Diseases, School of Basic Medical Sciences, Xi'an Jiaotong University, No.28 Xianning West Road, Xi'an, Shaanxi, 710049, China
- Department of Gastroenterology, Xi'an Children's Hospital, Xi'an, China
| | - Ya'nan Han
- Department of Gastroenterology, Xi'an Children's Hospital, Xi'an, China
| | - Benchang Li
- Shaanxi Institute of Pediatric Diseases, Xi'an Children's Hospital, Xi'an, China
| | - Ying Yang
- Shaanxi Institute of Pediatric Diseases, Xi'an Children's Hospital, Xi'an, China
| | - Ying Fang
- Department of Gastroenterology, Xi'an Children's Hospital, Xi'an, China
| | - Xiaoxia Ren
- Department of Gastroenterology, Xi'an Children's Hospital, Xi'an, China
| | - Lu An
- Department of Pathology, Xi'an Children's Hospital, Xi'an, China
| | - Xin Hou
- Department of Imaging, Xi'an Children's Hospital, Xi'an, China
| | - Huafeng Fan
- Department of Education Science, Xi'an Children's Hospital, Xi'an, China
| | - Yi Wu
- MOE Key Laboratory of Environment and Genes Related to Diseases, School of Basic Medical Sciences, Xi'an Jiaotong University, No.28 Xianning West Road, Xi'an, Shaanxi, 710049, China.
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Sage AP, Lee HK, Dalmann J, Lin S, Samra S, Salman A, Del Bel KL, Li WL, Lehman A, Turvey SE, Boerkoel CF, Richmond PA. Generation of tandem alternative splice acceptor sites and CLTC haploinsufficiency: A cause of CLTC-related disorder. Am J Med Genet A 2023. [PMID: 37196051 DOI: 10.1002/ajmg.a.63249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Revised: 03/21/2023] [Accepted: 05/06/2023] [Indexed: 05/19/2023]
Abstract
Tandem splice acceptors (NAGNn AG) are a common mechanism of alternative splicing, but variants that are likely to generate or to disrupt tandem splice sites have rarely been reported as disease causing. We identify a pathogenic intron 23 CLTC variant (NM_004859.4:c.[3766-13_3766-5del];[=]) in a propositus with intellectual disability and behavioral problems. By RNAseq analysis of peripheral blood mRNA, this variant generates transcripts using cryptic proximal splice acceptors (NM_004859.4: r.3765_3766insTTCACAGAAAGGAACTAG, and NM_004859.4:r.3765_3766insAAAGGAACTAG). Given that the propositus expresses 38% the level of CLTC transcripts as unaffected controls, these variant transcripts, which encode premature termination codons, likely undergo nonsense mediated mRNA decay (NMD). This is the first functional evidence for CLTC haploinsufficiency as a cause of CLTC-related disorder and the first evidence that the generation of tandem alternative splice sites causes CLTC-related disorder. We suggest that variants creating tandem alternative splice sites are an underreported disease mechanism and that transcriptome-level analysis should be routinely pursued to define the pathogenicity of such variants.
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Affiliation(s)
- Adam P Sage
- MD Undergraduate Program, University of British Columbia, Vancouver, British Columbia, Canada
| | - Hyun Kyung Lee
- Department of Medical Genetics and Provincial Medical Genetics Program, University of British Columbia and Women's Hospital of British Columbia, Vancouver, British Columbia, Canada
| | - Joshua Dalmann
- The Rare Disease Discovery Hub, BC Children's Hospital Research Institute, University of British Columbia and Children's Hospital of British Columbia, Vancouver, British Columbia, Canada
| | - Susan Lin
- The Rare Disease Discovery Hub, BC Children's Hospital Research Institute, University of British Columbia and Children's Hospital of British Columbia, Vancouver, British Columbia, Canada
| | - Simran Samra
- The Rare Disease Discovery Hub, BC Children's Hospital Research Institute, University of British Columbia and Children's Hospital of British Columbia, Vancouver, British Columbia, Canada
| | - Areesha Salman
- The Rare Disease Discovery Hub, BC Children's Hospital Research Institute, University of British Columbia and Children's Hospital of British Columbia, Vancouver, British Columbia, Canada
| | - Kate L Del Bel
- The Rare Disease Discovery Hub, BC Children's Hospital Research Institute, University of British Columbia and Children's Hospital of British Columbia, Vancouver, British Columbia, Canada
| | | | - Anna Lehman
- The Rare Disease Discovery Hub, BC Children's Hospital Research Institute, University of British Columbia and Children's Hospital of British Columbia, Vancouver, British Columbia, Canada
| | - Stuart E Turvey
- The Rare Disease Discovery Hub, BC Children's Hospital Research Institute, University of British Columbia and Children's Hospital of British Columbia, Vancouver, British Columbia, Canada
| | - Cornelius F Boerkoel
- Department of Medical Genetics and Provincial Medical Genetics Program, University of British Columbia and Women's Hospital of British Columbia, Vancouver, British Columbia, Canada
| | - Phillip A Richmond
- The Rare Disease Discovery Hub, BC Children's Hospital Research Institute, University of British Columbia and Children's Hospital of British Columbia, Vancouver, British Columbia, Canada
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