Title:

Genotyping Canine MHC class II genes using RNA-seq data

 

Abstract:

At least 50% of canines older than ten years will develop cancer. The incidence of cancer in dogs is comparable to humans. Canine cancer models are analogous to humans for advanced immunotherapy. However, only 20% of cancer patients respond to immunotherapy. The genetic sequence of MHC plays a role in T cells recognizing the epitopes required for response, known as MHC-restricted antigen recognition.

MHC-II genes present antigens to CD-4 T cells for recognition and are known as classical MHC-II. In classical HLA-II, alpha, and beta subunits, encoded by individual genes, exist for the three classical HLA-II molecules, DR[A/B], DQ[A/B], and DP[A/B]. However, the DP[A/B] genes are not annotated in the canine genome. As current MHC genotyping softwares like Seq2HLA is based on comprehensive HLA-II allele data and does not suffice for the canine model, our lab has previously developed an assembler and genotyper for canine MHC-I, KPR. This study aims to modify KPR for canine DLA-II molecules.

From the IPD-MHC database, we have collected 178 DLA-DRB1, 30 DLA-DQA1, and 86 DLA-DQB1 reference alleles. DLA-DRA is monomorphic, so we did not include it in our software. Upon input of paired-end RNA-seq data, setting kmer value K value and the number of iterations, N, we output assembled and genotyped DLA-DRB1, DLA-DQA1, and DLA-DQB1 alleles within the sample with the relative expression of alleles for each gene. We estimate if the assembled contig is chimeric based on the depth of the paired reads. This is our first version of the software that still requires simulation to test parameters.

We can assemble and genotype all three genes in PRJNA489087. We chose this dataset because there are more than 200 samples that pass quality control. We identified novel alleles and breed-specific alleles using this dataset.

 

Biography:

Nikitha Sundaresha, a fourth-year graduate student at the University of Georgia, is pursuing her doctoral research in the laboratory of Dr. Shaying Zhao. Nikitha received her bachelor’s in biotechnology engineering from the PES Institute of Technology in India. Her undergraduate thesis focused on the evolutionary analysis of simple sequence repeats in vertebrates to identify their potential epigenetic functions.

 

Nikitha earned her master’s degree in bioinformatics from Northeastern University, Boston. During this time, she interned at EMD Serono, Billerica, performing RNA-seq, scRNA-seq metabolic cancer data analysis.

 

In her current role in Dr. Shaying Zhao’s lab, Nikitha tackles the challenges of working with canine cancers by building essential resources that are critically missing. This includes software development to genotype canine major biocomplexity complex (MHC) class II alleles using next-generation sequencing data. She is also investigating the mechanism of action of PIK3CA hotspot mutations in both human and canine cancers.

 

Beyond her academic pursuits, Nikitha enjoys hiking and discovering new trails.