Driving therapeutic impact by comprehensively mapping variant function
Lead Research Organisation:
UNIVERSITY OF CAMBRIDGE
Abstract
Overview: Genomic sequencing has become a routine diagnostic investigation in both rare and common diseases. However, interpreting the pathogenicity of genetic variants remains challenging, particularly in individuals of non-European genetic ancestry resulting in inequities in diagnosis and access to precision treatments. Once pathogenicity is clearly defined, precision therapies using gene-editing and antisense oligonucleotides become feasible, but are prohibitively expensive to develop for each pathogenic variant. Precision treatments applicable to patients with diverse genetic variants are urgently needed.
Aims:
Accelerate the diagnosis of clinically actionable genetic conditions.
Develop novel precision treatments for genetic conditions, accessible to patients with diverse genetic variants.
Objectives:
1. Improve the interpretation of genetic variants by empirically testing variant function at scale (Aim 1).
2. Develop novel read-outs of non-coding variant function and apply these read-outs to:
a) Increase diagnostic yield (Aim 1).
b) Identify gene-editing regulatory targets with therapeutic potential for genetic conditions (Aim2).
3. Prospectively identify developmental disorders amenable to exon-skipping treatments (Aim 2).
The challenge - aim 1: Genetic sequencing is used to diagnose, quantify family members’ risk, enable preventative screening, prenatal testing and guide precise therapies. Newborn screening for clinically actionable genetic conditions by whole-genome sequencing is being trialled internationally. However, we cannot predict the functional impact of most rare genetic variants in disease-associated genes. The number of such variants of uncertain significance (VUS) is rising rapidly. VUS are now a major barrier to diagnosis and treatment.
Potential benefits – Aim 1/Objective 1: I will accelerate the diagnosis of clinically actionable conditions by generating large-scale, empirical, nucleotide-resolution maps of variant function, and work with the international community to integrate these data into clinical variant classification workflows. This approach is agnostic to genetic ancestry, enabling more equitable diagnosis and treatment. This is important, because receiving a definitive diagnosis and improving access to treatment are priorities for individuals affected by genetic conditions (UK Rare Disease Framework).
The challenge - Aim 2: Gene-editing, gene-therapy and RNA-based therapies hold enormous potential to treat genetic conditions. However, the cost of developing a novel therapy for individual patients is prohibitive.
Potential benefits – Aim 2: In haploinsufficient conditions a mutation in one allele is sufficient to cause disease and patients carry one intact allele. Upregulation of this intact allele by targeting the 5’UTR and promoter region of the gene is a novel therapeutic approach. Such therapies are already in limited clinical use: gene-editing therapies recently licensed for sickle-cell disease and thalassaemia introduce regulatory variants to upregulate fetal haemoglobin. Many haploinsufficient genes also cause disease if an extra copy is present – triplosensitivity. This makes conventional gene-therapy challenging, and manipulating endogenous regulatory sequence to engineer more physiological gene dosage attractive.
Another approach is to use antisense-oligonucleotides to induce exon-skipping around the pathogenic variant to partially restore protein expression and function, e.g. Eteplirsen, in the treatment of Duchenne’s Muscular Dystrophy. Large-scale screens are required to delineate which regulatory variants and redundant exons are tractable targets.
Aim2/Objective 2: I will use saturation mutagenesis techniques to identify gene-proximal regulatory variants which up-regulate expression of haploinsufficient genes.
Aim2/Objective3: I will conduct cellular screens to prospectively inform the development of exon-skipping treatments as novel therapies for genetic conditions.
As a paediatric neurologist with a background in developmental epigenetics and experimental saturation mutagenesis skills, I am uniquely placed to deliver this research programme.
Aims:
Accelerate the diagnosis of clinically actionable genetic conditions.
Develop novel precision treatments for genetic conditions, accessible to patients with diverse genetic variants.
Objectives:
1. Improve the interpretation of genetic variants by empirically testing variant function at scale (Aim 1).
2. Develop novel read-outs of non-coding variant function and apply these read-outs to:
a) Increase diagnostic yield (Aim 1).
b) Identify gene-editing regulatory targets with therapeutic potential for genetic conditions (Aim2).
3. Prospectively identify developmental disorders amenable to exon-skipping treatments (Aim 2).
The challenge - aim 1: Genetic sequencing is used to diagnose, quantify family members’ risk, enable preventative screening, prenatal testing and guide precise therapies. Newborn screening for clinically actionable genetic conditions by whole-genome sequencing is being trialled internationally. However, we cannot predict the functional impact of most rare genetic variants in disease-associated genes. The number of such variants of uncertain significance (VUS) is rising rapidly. VUS are now a major barrier to diagnosis and treatment.
Potential benefits – Aim 1/Objective 1: I will accelerate the diagnosis of clinically actionable conditions by generating large-scale, empirical, nucleotide-resolution maps of variant function, and work with the international community to integrate these data into clinical variant classification workflows. This approach is agnostic to genetic ancestry, enabling more equitable diagnosis and treatment. This is important, because receiving a definitive diagnosis and improving access to treatment are priorities for individuals affected by genetic conditions (UK Rare Disease Framework).
The challenge - Aim 2: Gene-editing, gene-therapy and RNA-based therapies hold enormous potential to treat genetic conditions. However, the cost of developing a novel therapy for individual patients is prohibitive.
Potential benefits – Aim 2: In haploinsufficient conditions a mutation in one allele is sufficient to cause disease and patients carry one intact allele. Upregulation of this intact allele by targeting the 5’UTR and promoter region of the gene is a novel therapeutic approach. Such therapies are already in limited clinical use: gene-editing therapies recently licensed for sickle-cell disease and thalassaemia introduce regulatory variants to upregulate fetal haemoglobin. Many haploinsufficient genes also cause disease if an extra copy is present – triplosensitivity. This makes conventional gene-therapy challenging, and manipulating endogenous regulatory sequence to engineer more physiological gene dosage attractive.
Another approach is to use antisense-oligonucleotides to induce exon-skipping around the pathogenic variant to partially restore protein expression and function, e.g. Eteplirsen, in the treatment of Duchenne’s Muscular Dystrophy. Large-scale screens are required to delineate which regulatory variants and redundant exons are tractable targets.
Aim2/Objective 2: I will use saturation mutagenesis techniques to identify gene-proximal regulatory variants which up-regulate expression of haploinsufficient genes.
Aim2/Objective3: I will conduct cellular screens to prospectively inform the development of exon-skipping treatments as novel therapies for genetic conditions.
As a paediatric neurologist with a background in developmental epigenetics and experimental saturation mutagenesis skills, I am uniquely placed to deliver this research programme.
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| Elizabeth Radford (Principal Investigator / Fellow) |