RNA Vaccine Design Against Novel Onco-Antigens in Renal Cancers Involving VHL

Abstract:

Overall, renal cancers are the 8th most common type of cancer.  In 2021, there were approximately 76,000 new cases of renal cancer in the United States, with approximately 13,000 deaths.  Renal cancers exhibit a moderate 5-year relative survival rate of about 75%.  The most positive prognoses occur in patients in which the renal cancer cells are localized to the primary site or have regionally spread to nearby lymph nodes, but survival rates dramatically decline to about 14% in patients experiencing a renal tumor that has metastasized to disparate parts of the body.  Most new cases of renal cancer are seen in middle aged persons, from 55 to 74 years of age, accounting for nearly 60% of all renal cases.  The median age of death in renal cancer patients is 72 years of age, and persons aged 55-84 years old collectively account for about 75% of all deaths due to renal cancer.  Although the rate of new cases has steadily increased from 6 to 16 diagnosed persons per 100,000 persons in the population, the overall death rate has remained constant at 4 deaths per 100,000 persons per year since 1975 to present.  Thus with respect to death rate by renal cancer, little has changed in the last fifty years or so.  The two most common genetic loci that underly half of all renal cancer diagnoses are the VHL and PBRM1 genes.  The VHL gene encodes pVHL, a protein that binds to elongin C, elongin B, cullin-2 and Rbx1.  This pentameric complex catalyzes the polyubiquitination of specific proteins to shunt them for destruction by cellular proteasomes.  One target of pVHL is the HIF1a transcription factor.  HIF1a drives cellular proliferation and angiogenesis via VEGF signaling.  A functional pVHL diverts HIF1a to the proteasome, thus blocking excessive mitoses.  Somatic mutations in the human VHL gene uncouple the regulation of HIF1a, resulting in elevated cellular proliferation due to the inability to clear HIF1a.  Of the 214 documented nucleotide mutations in VHL that result in renal cancers, 96 alleles result in a frameshift mutation due to the insertion or deletion of 1 bp or 2 bp of sequence information within the open-reading-frame (ORF) of the VHL gene locus on the forward strand of chromosome 3.  We closely examined the precise nucleotide mutations, and identified a frameshift allele that resulted in the generation of a novel stretch of polypeptide sequence found nowhere else in the known human proteome.  Using EMBOSS Backtranseq and a human-optimized codon usage table, we reverse translated this onco-antigen and generated an RNA vaccine.  Our RNA vaccine design is thus personalized to this specific allelic basis for a renal cancer involving the VHL genetic locus.