1
|
Bernabéu-Herrero ME, Patel D, Bielowka A, Zhu J, Jain K, Mackay IS, Chaves Guererro 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:blood.2023021777. [PMID: 38457357 DOI: 10.1182/blood.2023021777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [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
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 sub-categorized pathogenic DNA variants in ENG/endoglin, ACVRL1/ALK1, and SMAD4 if they generated premature termination codons (PTCs) subject to nonsense mediated decay. In three pre-phenotyped patient cohorts, a PTC-based classification system explained some previously puzzling hemorrhage variability. In blood outgrowth endothelial cells (BOECs) derived from ACVRL1+/PTC, ENG+/PTC, and SMAD4+/PTC patients, PTC-containing RNA transcripts persisted at low levels (8-23% expected, varying between replicate cultures); genes differentially expressed to Bonferroni p<0.05 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 '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 (ATF)4 which controls expression of stress-adaptive genes, and showed that ENG Q436X but not ENG R93X directly induced ATF4. AlphaFold accurately modelled 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.
Collapse
Affiliation(s)
| | | | | | - JiaYi Zhu
- University of Cambridge, Cambridge, United Kingdom
| | | | | | | | | | | | | | | | - Micheala A Aldred
- Indiana University School of Medicine, Indianapolis, Indiana, United States
| | | |
Collapse
|
2
|
Shovlin CL, Patel D, Bielowka A, Ledermann JA, Modarresi A, Bernabeu-Herrero ME, Aldred MA, Alsafi A. MEK 1 inhibition and bleeding in hereditary haemorrhagic telangiectasia. Br J Haematol 2024; 204:361-365. [PMID: 37872650 DOI: 10.1111/bjh.19167] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 10/06/2023] [Accepted: 10/10/2023] [Indexed: 10/25/2023]
Affiliation(s)
- Claire L Shovlin
- National Heart and Lung Institute, Imperial College London, London, UK
- NIHR Imperial Biomedical Research Centre, London, UK
- Imperial College Healthcare NHS Trust, London, UK
| | - Dilip Patel
- National Heart and Lung Institute, Imperial College London, London, UK
- NIHR Imperial Biomedical Research Centre, London, UK
| | - Adrianna Bielowka
- National Heart and Lung Institute, Imperial College London, London, UK
- NIHR Imperial Biomedical Research Centre, London, UK
| | | | - Atieh Modarresi
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Maria E Bernabeu-Herrero
- National Heart and Lung Institute, Imperial College London, London, UK
- NIHR Imperial Biomedical Research Centre, London, UK
| | | | - Ali Alsafi
- Imperial College Healthcare NHS Trust, London, UK
| |
Collapse
|
3
|
Chen L, Wang YF, Liu L, Bielowka A, Ahmed R, Zhang H, Tombleson P, Roberts AL, Odhams CA, Cunninghame Graham DS, Zhang X, Yang W, Vyse TJ, Morris DL. Genome-wide assessment of genetic risk for systemic lupus erythematosus and disease severity. Hum Mol Genet 2021; 29:1745-1756. [PMID: 32077931 PMCID: PMC7322569 DOI: 10.1093/hmg/ddaa030] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 01/30/2020] [Accepted: 02/17/2020] [Indexed: 12/12/2022] Open
Abstract
Using three European and two Chinese genome-wide association studies (GWAS), we investigated the performance of genetic risk scores (GRSs) for predicting the susceptibility and severity of systemic lupus erythematosus (SLE), using renal disease as a proxy for severity. We used four GWASs to test the performance of GRS both cross validating within the European population and between European and Chinese populations. The performance of GRS in SLE risk prediction was evaluated by receiver operating characteristic (ROC) curves. We then analyzed the polygenic nature of SLE statistically. We also partitioned patients according to their age-of-onset and evaluated the predictability of GRS in disease severity in each age group. We found consistently that the best GRS in the prediction of SLE used SNPs associated at the level of P < 1e−05 in all GWAS data sets and that SNPs with P-values above 0.2 were inflated for SLE true positive signals. The GRS results in an area under the ROC curve ranging between 0.64 and 0.72, within European and between the European and Chinese populations. We further showed a significant positive correlation between a GRS and renal disease in two independent European GWAS (Pcohort1 = 2.44e−08; Pcohort2 = 0.00205) and a significant negative correlation with age of SLE onset (Pcohort1 = 1.76e−12; Pcohort2 = 0.00384). We found that the GRS performed better in the prediction of renal disease in the ‘later onset’ compared with the ‘earlier onset’ group. The GRS predicts SLE in both European and Chinese populations and correlates with poorer prognostic factors: young age-of-onset and lupus nephritis.
Collapse
Affiliation(s)
- Lingyan Chen
- Department of Medical and Molecular Genetics, King's College London, London, UK.,MRC/BHF Cardiovascular Epidemiology Unit, University of Cambridge, Cambridge, UK
| | - Yong-Fei Wang
- Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong
| | - Lu Liu
- Department of Dermatology, NO. 1 Hospital, Anhui Medical University, Hefei, Anhui, China.,Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, Anhui, China.,Department of Dermatology, Huashan Hospital of Fudan University, Shanghai, China
| | - Adrianna Bielowka
- Department of Medical and Molecular Genetics, King's College London, London, UK
| | - Rahell Ahmed
- Department of Medical and Molecular Genetics, King's College London, London, UK
| | - Huoru Zhang
- Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong
| | - Phil Tombleson
- Department of Medical and Molecular Genetics, King's College London, London, UK
| | - Amy L Roberts
- Department of Medical and Molecular Genetics, King's College London, London, UK.,Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | | | | | - Xuejun Zhang
- Department of Dermatology, NO. 1 Hospital, Anhui Medical University, Hefei, Anhui, China.,Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, Anhui, China.,Department of Dermatology, Huashan Hospital of Fudan University, Shanghai, China
| | - Wanling Yang
- Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong
| | - Timothy J Vyse
- Department of Medical and Molecular Genetics, King's College London, London, UK
| | - David L Morris
- Department of Medical and Molecular Genetics, King's College London, London, UK
| |
Collapse
|