A study of four-generation Indian family with asthma and validation in a paediatric cohort led to the discovery of an associated olfactory gene variant. The expression of the gene is reduced in asthmatic people with the variant or suppression of gene expression by inflammation in those without the variant.
Based on a study of a four-generation family in Mysuru with high prevalence of asthma, a multi-institutional study by Indian researchers has shown that a variant of an olfactory gene (OR2AG2) is a novel candidate for asthma. This is the first time in India a four-generation large family with high asthma prevalence has been studied for the said purpose.
The gene was validated in a north Indian cohort of 141 children with asthma and 130 controls. About 80% of children with asthma carried a copy of the gene variant.
Searching for the needle in a hay stack
Twenty individuals representing the four generations were selected. Of the 20 studied, 14 had asthma and the rest served as a control group. Whole genome genotyping was undertaken on all the 20 participants and exome sequencing was carried out on five people with asthma and three controls. While whole genome genotyping helps in detecting variations across the genome, the exome sequencing allows variations in the protein-coding region of any gene to be identified.
Several variants were seen after genotyping and exome sequencing. The team led by Dr. Anurag Agrawal, Director of the Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, turned to computer modelling to narrow down the possible variants that might be responsible for asthma and finally confirmed the genetic variant through conventional sequencing.
Defect in the ability to smell
“Mutation in the sensory pathway such as olfaction is a plausible mechanism for increased asthma risk because of inability to mount an appropriate counter response. The inability to mount a counter response could lead to lung damage,” says Dr. Agrawal. The inability to smell could be a potential mechanism for lung damage.
To test this, the researchers evaluated the ability of the 20 participants to smell a sweet odour and the concentration at which they could identify the odour. All the 14 family members with asthma had one copy of the gene variant.
“Healthy individuals and those with asthma were able to identify and differentiate different smells, but those with asthma could detect smells only at higher concentrations,” he says. “This suggested a defect in their ability to smell. Also, family members with asthma said they could not smell burning odour.”
Association of olfactory gene and asthma
“Whether olfactory gene was associated with asthma or not was not known till now. Ours is the first study to find such an association,” says Dr. Samarpana Chakraborty from CSIR-IGIB and the first author of a paper published in the journal Scientific Reports. “The gene variant may cause olfactory dysfunction in the family members who have asthma.”
“By studying the four-generation family alone or the children cohort individually, we couldn’t have identified the gene. We needed both groups,” Dr. Chakraborty says. “In population-based studies that have been undertaken, it becomes difficult to identify such variants.”
“There are three main reasons why we could identify the gene variant — asthmatics in the family had difficulty in smelling, we saw the same variant in the cohort and we were looking for a novel genetic variant,” Dr. Agrawal says.
Suppression of gene expression
But during the validation studies, asthmatic children with or without the variant did not show significant difference in the ability to smell, which was unexpected. “Asthmatic children without the variant too had impaired smell threshold, which made us wonder if asthma-related pathway itself can cause suppression of the gene independent of the genetic variation,” he says.
To validate the hypothesis, the researchers directly measured the gene expression in lung samples of those with asthma and normal subjects. In people with asthma, there was significant reduction in the expression of the gene.
They also carried out cell culture studies. When the cultured human cells were treated with IL13 cytokine, which is associated with allergy, there was suppression of OR2AG2 gene expression.
“So there is either a genetic defect in the OR2AG2 gene at birth leading to suppressed expression or there is acquired suppression of gene expression later in life due to inflammation or environmental factors,” he says. “This supports our hypothesis that the gene may be a convergence point for asthma pathways at the lung level.”