Expression of the ZIP/SLC39A transporters in β-cells: a systematic review and integration of multiple datasets

Abstract

Background: Pancreatic β-cells require a constant supply of zinc to maintain normal insulin secretory function. Following co-exocytosis with insulin, zinc is replenished via the Zrt- and Irt-like (ZIP; SLC39A) family of transporters. However the ZIP paralogues of particular importance for zinc uptake, and associations with β-cell function and Type 2 Diabetes remain largely unexplored. We retrieved and statistically analysed publically available microarray and RNA-seq datasets to perform a systematic review on the expression of β-cell SLC39A paralogues. We complemented results with experimental data on expression profiling of human islets and mouse β-cell derived MIN6 cells, and compared transcriptomic and proteomic sequence conservation between human, mouse and rat.

Results: The 14 ZIP paralogues have 73-98% amino sequence conservation between human and rodents. We identified 18 datasets for β-cell SLC39A analysis, which compared relative expression to non-β-cells, and expression in response to PDX-1 activity, cytokines, glucose and type 2 diabetic status. Published expression data demonstrate enrichment of transcripts for ZIP7 and ZIP9 transporters within rodent β-cells and of ZIP6, ZIP7 and ZIP14 within human β-cells, with ZIP1 most differentially expressed in response to cytokines and PDX-1 within rodent, and ZIP6 in response to diabetic status in human and glucose in rat. Our qPCR expression profiling data indicate that SLC39A6, -9, -13, and - 14 are the highest expressed paralogues in human β-cells and Slc39a6 and -7 in MIN6 cells.

Conclusions: Our systematic review, expression profiling and sequence alignment reveal similarities and potentially important differences in ZIP complements between human and rodent β-cells. We identify ZIP6, ZIP7, ZIP9, ZIP13 and ZIP14 in human and rodent and ZIP1 in rodent as potentially biologically important for β-cell zinc trafficking. We propose ZIP6 and ZIP7 are key functional orthologues in human and rodent β-cells and highlight these zinc importers as important targets for exploring associations between zinc status and normal physiology of β-cells and their decline in Type 2 Diabetes.

Keywords: Expression data; Microarray; RNA-seq; SLC39A; Systematic review; Type 2 diabetes; ZIP; Zinc.

Fig. 1

The pipeline followed for identification of suitable microarray and RNA-seq datasets

Fig. 2

Enrichment of SLC39A paralogues within human and murine β-cells. a Expression within human β-cell-enriched pancreatic samples compared to 11 other tissues (pancreatic duct cells, cerebrum, kidney, lung, myocardial, skeletal muscle, small intestine, spleen, stomach, testis and thymus). b Expression within sorted mouse β-cells compared to mouse islets. c Expression within sorted mouse β-cells compared to six other cell types (brain, liver, lung fibroblasts, NPC, skeletal muscle, islets), after exclusion of β-cell depleted paralogues. Data for (a) analysed from dataset GSE30803 and (b-c) analysed from supplementary tables within [44]. ^# P < 0.15, *P < 0.05, ***P < 0.001. NPC = neural progenitor cells

Fig. 3

Slc39a transcripts differentially expressed in rat INS-1ab cells following PDX-1 overexpression and IL-1β stimulation. Black bars: PDX-1 overexpression; dark grey bars: IL-1β stimulation; light grey bars: PDX-1 overexpression and IL-1β stimulation. Data analysed from dataset GSE40642. *P < 0.05, ***P < 0.001

Fig. 4

SLC39A transcripts differentially expressed in human type 2 diabetic islets compared to non-diabetic islets. Probes targeting the same transcript(s) are averaged for each assay. Black bars: data analysed from dataset GSE25724; grey bars: data analysed from dataset GSE20966. *P < 0.05

Fig. 5

Expression profiles of SLC39A mRNA transcripts in human islets and murine MIN6 cells. a The human SLC39A transcriptome. N = 2 and error bars show ± range. b The MIN6 β-cell Slc39a transcriptome. N = 3 and error bars show ±SEM

Fig. 6

Predicted subcellular localisation of the identified ZIP transporters within human and rodent β-cells. Based on the data analysed in the present study ZIP6, ZIP7, ZIP9, ZIP13 and ZIP14 in human, and the same transporters in addition to ZIP1 in rodent appear to be of particular importance for β-cell biology and pathology. Zinc Transporter 8 (ZnT8) which transports zinc into the insulin granules is also shown. ER = endoplasmic reticulum; TGN = trans-Golgi network