Investigating genotype-phenotype relationship of extreme neuropathic pain disorders in a UK national cohort

Andreas C Themistocleous; Georgios Baskozos; Iulia Blesneac; Maddalena Comini; Karyn Megy; Sam Chong; Sri V V Deevi; Lionel Ginsberg; David Gosal; Robert D M Hadden; Rita Horvath; Mohamed Mahdi-Rogers; Adnan Manzur; Rutendo Mapeta; Andrew Marshall; Emma Matthews; Mark I McCarthy; Mary M Reilly; Tara Renton; Andrew S C Rice; Tom A Vale; Natalie van Zuydam; Suellen M Walker; Christopher Geoffrey Woods; David L H Bennett

doi:10.1093/braincomms/fcad037

Investigating genotype-phenotype relationship of extreme neuropathic pain disorders in a UK national cohort

Brain Commun. 2023 Feb 20;5(2):fcad037. doi: 10.1093/braincomms/fcad037. eCollection 2023.

Authors

Andreas C Themistocleous¹, Georgios Baskozos¹, Iulia Blesneac¹, Maddalena Comini¹, Karyn Megy^{2

3}, Sam Chong⁴, Sri V V Deevi^{2

3}, Lionel Ginsberg^{5

6}, David Gosal⁷, Robert D M Hadden⁸, Rita Horvath^{9

10}, Mohamed Mahdi-Rogers⁸, Adnan Manzur^{11

12}, Rutendo Mapeta^{2

3}, Andrew Marshall^{13

14

15}, Emma Matthews¹⁶, Mark I McCarthy^{17

18

19}, Mary M Reilly¹⁶, Tara Renton⁸, Andrew S C Rice^{20

21}, Tom A Vale¹, Natalie van Zuydam^{17

18

19}, Suellen M Walker^{11

12}, Christopher Geoffrey Woods^{22

23}, David L H Bennett¹

Affiliations

¹ Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK.
² NIHR BioResource, Cambridge University Hospitals NHS Foundation, Cambridge, UK.
³ Department of Haematology, University of Cambridge, Cambridge, UK.
⁴ National Hospital for Neurology and Neurosurgery, University College London Hospitals, London, UK.
⁵ Department of Neurology, Royal Free Hospital, London, UK.
⁶ Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK.
⁷ Salford Royal NHS Foundation Trust, Salford, UK.
⁸ King's College Hospital NHS Foundation Trust, London, UK.
⁹ Wellcome Centre for Mitochondrial Research, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, UK.
¹⁰ Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK.
¹¹ Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK.
¹² UCL Great Ormond Street Institute of Child Health, London, UK.
¹³ Faculty of Biology, Medicine and Health, School of Biological Sciences, Division of Neuroscience and Experimental Psychology, University of Manchester, Manchester, UK.
¹⁴ Department of Clinical Neurophysiology, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, UK.
¹⁵ Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool, UK.
¹⁶ Department of Neuromuscular Disease, UCL Queen Square Institute of Neurology and the National Hospital of Neurology and Neurosurgery, London, UK.
¹⁷ NIHR Oxford Biomedical Research Centre, Oxford University Hospitals Trust, Oxford, UK.
¹⁸ Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK.
¹⁹ Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, UK.
²⁰ Pain Research, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London, UK.
²¹ Pain Medicine, Chelsea and Westminster Hospital NHS Foundation Trust, London, UK.
²² Department of Medical Genetics, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK.
²³ Addenbrookes Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK.

Abstract

The aims of our study were to use whole genome sequencing in a cross-sectional cohort of patients to identify new variants in genes implicated in neuropathic pain, to determine the prevalence of known pathogenic variants and to understand the relationship between pathogenic variants and clinical presentation. Patients with extreme neuropathic pain phenotypes (both sensory loss and gain) were recruited from secondary care clinics in the UK and underwent whole genome sequencing as part of the National Institute for Health and Care Research Bioresource Rare Diseases project. A multidisciplinary team assessed the pathogenicity of rare variants in genes previously known to cause neuropathic pain disorders and exploratory analysis of research candidate genes was completed. Association testing for genes carrying rare variants was completed using the gene-wise approach of the combined burden and variance-component test SKAT-O. Patch clamp analysis was performed on transfected HEK293T cells for research candidate variants of genes encoding ion channels. The results include the following: (i) Medically actionable variants were found in 12% of study participants (205 recruited), including known pathogenic variants: SCN9A(ENST00000409672.1): c.2544T>C, p.Ile848Thr that causes inherited erythromelalgia, and SPTLC1(ENST00000262554.2):c.340T>G, p.Cys133Tr variant that causes hereditary sensory neuropathy type-1. (ii) Clinically relevant variants were most common in voltage-gated sodium channels (Na_v). (iii) SCN9A(ENST00000409672.1):c.554G>A, pArg185His variant was more common in non-freezing cold injury participants than controls and causes a gain of function of Na_V1.7 after cooling (the environmental trigger for non-freezing cold injury). (iv) Rare variant association testing showed a significant difference in distribution for genes NGF, KIF1A, SCN8A, TRPM8, KIF1A, TRPA1 and the regulatory regions of genes SCN11A, FLVCR1, KIF1A and SCN9A between European participants with neuropathic pain and controls. (v) The TRPA1(ENST00000262209.4):c.515C>T, p.Ala172Val variant identified in participants with episodic somatic pain disorder demonstrated gain-of-channel function to agonist stimulation. Whole genome sequencing identified clinically relevant variants in over 10% of participants with extreme neuropathic pain phenotypes. The majority of these variants were found in ion channels. Combining genetic analysis with functional validation can lead to a better understanding as to how rare variants in ion channels lead to sensory neuron hyper-excitability, and how cold, as an environmental trigger, interacts with the gain-of-function Na_V1.7 p.Arg185His variant. Our findings highlight the role of ion channel variants in the pathogenesis of extreme neuropathic pain disorders, likely mediated through changes in sensory neuron excitability and interaction with environmental triggers.

Keywords: neuropathic pain; peripheral neuropathy; sodium channels; whole genome sequencing.

Abstract

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