A novel RNA variant of human concentrative nucleoside transporter 1 (hCNT1) that is a potential cancer biomarker

Chunmei Wang,John K Buolamwini

doi:10.1186/s40164-019-0144-y

Abstract

BackgroundThe human concentrative nucleoside transporter 1 (hCNT1) a product of the SLC28A1 gene is one of the three concentrative nucleoside transporters, with a substrate specificity for physiological pyrimidine nucleosides. It has recently been implicated in tumor suppression. We have unraveled a splice variant RNA transcript that is overexpressed in some tumor tissues and some cancer cells. This study established that observation.MethodsWe examined several clones of hCNT1 generated from RT-PCR of total RNA from human kidney tissue purchased from Ambion. The resulting cDNA clones were then sequenced, and a variant that retained intron 4, and skipped some exons fully or partly, specifically exons 5 and 13 were completely missed and only part of exon 6 was spliced. Tissue expression analysis by PCR indicated a similar distribution of expression of RNA of the splice variant hCNT1-IR as that of the dominant variant hCNT1, particularly in the small intestine, kidney and liver. Further, analysis of various tumor samples with PCR primers designed from this novel hCNT1 splice variant (hCNT1-IR) revealed interestingly that it is overexpressed in some cancer tissues relative to normal tissues, particularly kidney, liver and pancreatic cancers.ConclusionWe have identified a novel intron retaining and exon skipping splice variant of the hCNT1 nucleoside transporter, and designated it hCNT1-IR, which has a similar tissue expression distribution as the normal hCNT1 variant, but unlike the normal transcript, hCNT1-IR is overexpressed in some cancers and may serve as a potential cancer biomarker.

Highlights

Physiological nucleosides and most therapeutic nucleoside analogues are hydrophilic molecules that require specialized nucleoside transporter (NT) proteins to pass across cellular membranes
A novel splice variant of human concentrative nucleoside transporter 1 (hCNT1) was identified in normal human kidney RT-PCR product of hCNT1 from normal human kidney total RNA obtained from a pool of 14 male/female Caucasians at ages between 18 and 58 years old was subcloned into a mammalian expression vector
HCNT1‐IR is not translated To determine whether the hCNT1-IR mRNA encodes protein, we transfected PK15 nucleoside deficient cells [17] with the hCNT1-IR construct, similar to what we have described previously [18]

Summary

Introduction

Physiological nucleosides and most therapeutic nucleoside analogues are hydrophilic molecules that require specialized nucleoside transporter (NT) proteins to pass across cellular membranes. CNT1 mediates the cellular uptake of naturally occurring pyrimidine nucleosides and adenosine to a much lesser extent, as well as diverse anticancer and antiviral nucleoside analogues including gemcitabine, cytarabine, and zidovudine [4,5,6,7]. A number of coding region single nucleotide polymorphisms (SNPs) have been reported for human CNT1 The human concentrative nucleoside transporter 1 (hCNT1) a product of the SLC28A1 gene is one of the three concentrative nucleoside transporters, with a substrate specificity for physiological pyrimidine nucleosides. It has recently been implicated in tumor suppression.

Methods

Results

Discussion

Conclusion