What started as Ninad Oak’s side project turned out into something much larger, his doctorate thesis.
“The project started as my qualifying exam that I proposed at the end of my first year of graduate school,” said Oak, a graduate student in molecular and human genetics in Dr. Sharon E. Plon’s lab. “This was an off topic qualifying exam at the time, meaning the lab had not worked on this topic before.”
One of the main interests of the Plon lab is cancer predisposition, in particular looking at protein coding regions of gene variants that may be responsible for susceptibility to childhood cancers.
“I started the project thinking that we had focused on protein coding regions for a long time. But they only represent 1 percent of the genome, so I thought that by looking at the remaining 99 percent we might find some variations we have been missing that might explain some undiagnosed patient cases,” Oak said. In his qualifying exam, Oak proposed to look at variations on microRNA. “Although the amount of microRNA that is found in the cell is often studied in human disease, microRNA variations that are associated with disease are understudied,” Oak said.
MicroRNAs are small non-coding RNAs that are only about 18 to 25 nucleotides long; in comparison, genes that code for proteins are thousands of nucleotides long. MicroRNAs upregulate or downregulate the expression of more than 60 percent of genes by binding to matching sequences in other’s genes’ RNA. One microRNA might change the level of expression of up to 200 genes at a time, therefore affecting a number of different pathways.
Disturbing the normal function of microRNAs can lead to altered expression of their target genes, and this has been associated with a wide variety of human diseases, such as cancer, cardiovascular and developmental diseases.
“When he presented this proposal, I thought it was a good idea,” said Plon, who is professor of pediatrics – oncology and molecular and human genetics at Baylor and director of the Cancer Genetics Clinical and Research Programs at Texas Children’s Hospital.
ADmiRE helps prioritize microRNA variation linked to disease
Oak developed a novel computational tool called ADmiRE, which stands for Annotative Database for miRNA Elements. ADmiRE extensively annotates human microRNA variants to determine which ones are likely to contribute to or cause disease.
“There were multiple challenges when I started working on this project,” Oak said. “Most datasets of genomic sequencing are of whole exome sequencing (WES), which captures only protein coding regions. So first, I looked at how well WES datasets captured microRNAs and found that they captured about 50 percent.”
The second challenge was to determine how well were microRNA mutations annotated by different annotation tools that already were available. These annotation tools allow researchers to add notes of explanation or comments that provide more information about each microRNA.