Pabitra Khadka
Pabitra Khadka is a second-year graduate research assistant in Dr. Matthew Young’s lab in the Division of Biochemistry & Molecular Biology in the Department of Biomedical Science at Southern Illinois University (SIU) School of Medicine, Carbondale. Pabitra received her undergraduate Bachelor of Technology degree, with a focus on biotechnology, from Kathmandu University, Nepal. She joined the SIU School of Medicine as a Ph.D. student in the Fall of 2021. Pabitra is interested in understanding the molecular and biochemical alterations associated with cancer and finding cancer-specific diagnostic tools. Pabitra has been working on a project to understand if mitochondrial DNA (mtDNA) mutations can be used as a blood-based biomarker for endometrial cancer, the most common gynecological cancer. Pabitra is a co-author of a publication from the Young lab entitled Identification of somatic mitochondrial DNA mutations, heteroplasmy and increased level of catenanes in tumor specimens obtained from three endometrial cancer patients, which was published last year in the journal ‘Life’. Also, she has co-authored two publications from her undergraduate research project at Kathmandu University. Recently, Pabitra secured a competitive Doctoral Research Fellowship award from the SIU graduate school. Finally, for her Ph.D. work, Pabitra is working on a project entitled Effects of MEHP on C2C12 cell mitochondrial DNA replication, protein expression, and bioenergetics.†Pabitra has mastered laboratory techniques like whole-cell and tumor DNA extraction, PCR, Southern Blotting, and tissue culture for her various research projects.
Abstract
Pabitra Khadkaa, Carolyn Younga, Taryn Sauerbrunna, Kathleen Groeschb, Kathy Robinsonc, Andrea Braundmeier-Flemingd, Ravi Sachidanandame, Dale Buck Halesa, Laurent Brardb, Matthew Younga
aBiochemistry & Molecular Biology SIU SOM, Carbondale, IL, United States; bOb/Gyn, Center for Clinical Research SIU SOM, Springfield, IL, United States; cSCI, Hematology/Oncology SIU SOM, Springfield, IL, United States; dMMICB, Ob/Gyn, SCI SIU SOM, Springfield, IL, United States; eGirihlet Inc., Oakland, CA, United States
Endometrial cancer (EC) is one of the most common forms of gynecological cancer, with death rates from this disease doubling over the past 20 years. Most solid tumors harbor at least one mtDNA mutation, and cancer cells can have mixtures of polyploid wild-type and mutant mtDNA genomes, so-called heteroplasmy. We compared mtDNA genomes from three matched sets of peri-normal and EC tumor specimens and determined that each tumor harbors tumor-specific mtDNA mutations. Furthermore, somatic EC mtDNA mutations were investigated in aggregate from several published studies. Using a total of 361 single nucleotide variants from 153 EC patients, we determined that ~77% of the patients harbor at least one mtDNA mutation allele at 10% (WT 90%) to 90% (WT 10%) heteroplasmy. Of the total mutations, 278 are unique, and transitions are 24-fold higher than transversions. G>A and T>C are the most common transitions, comprising 85.3% of the unique mutations. Mutations occur across the mtDNA genome, but ~39% of the mutations localize to complex I genes, and nine tRNA genes lack mutations. NGS amplicon sequencing and Southern blotting were used to analyze cell-free serum mtDNA heteroplasmy and tissue-derived topoisomers in the three EC patients. Our preliminary amplicon sequencing data reveals that at least one tumor-specific heteroplasmic substitution can be detected in serum DNA extracts from all patients. Also, relative to matched peri-normal tissues, all tumors had increased levels of catenanes indicative of enhanced mtDNA replication. Our study suggests tumor mtDNA mutations in the bloodstream could be used as an EC biomarker.