Patients and phenotypes
In ENISNIP, we aim to include patients with all forms of congenital insensitivity to pain (CIP) and/or hereditary sensory and autonomic neuropathy (HSAN). We will continuously enrol more patients through recruitment . ENISNIP aims to deliver high-quality cross-sectional data of a CIP/HSAN patient cohort. This will allow definition of subgroups with special health care needs and ensure early recognition, treatment or prevention of complications.
The ENISNIP biobank will support key scientific activities by facilitating access to and supporting sharing of samples within the consortium. ENISNIP will provide biomaterials required for DNA sequencing activities, validation of genetic variants, confirmation of disease gene candidacy, and exploration of disease mechanisms and phenotypic readouts in patient-specific cell models. We envision the ENISNIP biobank to develop into a source for patient-specific cellular disease models. Such models are expected to have translational potential in the preclinical drug development pipeline, e.g., for verification of candidate substances. We also envisage that ENISNIP collections of biomaterials will provide a useful source for the identification of biomarkers that can be potentially used as outcome measures for clinical research into CIP/HSAN.
Novel genetic causes
ENISNIP will make massive efforts to promote genetic classification of CIP/HSAN patients. Comprehensive clinical genetic testing will ensure build-up of sufficiently large cohorts of genetically unresolved cases for gene discovery studies.
For patients who will remain genetically undiagnosed after testing for known CIP/HSAN genes, the entire exome (all coding regions and flanking intron sequences) will be assessed to search for new candidate genes. To prioritize genes and variants, we will employ data and expert-driven approaches. We will then cross-reference all datasets to recognize genomic regions (specific genes or genes grouped in pathways), in which variants cluster among cases, especially in individuals with matching phenotypes.
Cases where analysis of WES data fails to pinpoint a likely gene defect will be considered for a ‘beyond the exome’ approach. We will focus on ‘unsolvable’ patients, based on highly recognizable phenotypes and availability of relevant biomaterials in the ENISNIP sample collection. Long-read ‘third generation’ whole-genome sequencing (WGS) on an Oxford Nanopore PromethION sequencer will uncover variants usually not detected by short-read sequencing technologies, i.e., structural variants and repeat expansions. We envisage to identify several genes harbouring unorthodox variants, usually missed by WES. This will provide proof-of-principle of the involvement of such underappreciated mechanisms in CIP/HSAN. Finally, transcriptome and metabolome profiles may serve to build ‘genome informed metabolic models’ (GIM) to predict perturbations of metabolic pathways. GIM models can also embrace the interaction of several genetic variants, allowing consideration of modifier genes or oligogenic inheritance.
Mechanisms and model systems
Based on complementary expertise of consortium members, ENISNIP will provide an environment for extensive functional validation of variants. Specifically, model systems are available to study membrane shaping and remodelling (ATL1, ATL3, FAM134B), axonal transport (KIF1A, RAB7A), ion channel excitability (SCN9A, SCN11A), epigenetic regulation (DNMT1, PRDM12), neurotrophin signalling (NGF, NTRK1), and sphingolipid metabolism (SPTLC1, SPTLC2).
In particular, potential disease-associated genes with no previously assigned function require innovative validation approaches. Since disease-relevant cells from CIP/HSAN patients are usually not directly accessible, we will resort to patient-specific, iPSC-derived sensory neurons which undergo comprehensive phenotyping (morphology, electrophysiology, expression of selected neuronal markers, calcium imaging).
Network management
Principal investigators (PIs) and patient advocacy organization (PAO) representatives (CMT-Austria, Spolecnost C-M-T) will promote our aims to ensure appropriate recognition of CIP/HSAN and improve patients’ access to accurate diagnosis, care and clinical research.
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