Development of a live cell assay for the zinc transporter ZnT8.

Zinc is an essential trace element that is involved in many biological processes and in cellular homeostasis. In pancreatic ß-cells, zinc is crucial for the synthesis, processing, and secretion of insulin, which plays a key role in glucose homeostasis and which deficiency is the cause of diabetes. The accumulation of zinc in pancreatic cells is regulated by the solute carrier transporter SLC30A8 (or Zinc Transporter 8, ZnT8), which transports zinc from cytoplasm in intracellular vesicles. Allelic variants of SLC30A8 gene have been linked to diabetes. Given the physiological intracellular localization of SLC30A8 in pancreatic ß-cells and the ubiquitous endogenous expression of other Zinc transporters in different cell lines that could be used as cellular model for SLC30A8 recombinant over-expression, it is challenging to develop a functional assay to measure SLC30A8 activity. To achieve this goal, we have firstly generated a HEK293 cell line stably overexpressing SLC30A8, where the over-expression favors the partial localization of SLC30A8 on the plasma membrane. Then, we used the combination of this cell model, commercial FluoZin-3 cell permeant zinc dye and live cell imaging approach to follow zinc flux across SLC30A8 over-expressed on plasma membrane, thus developing a novel functional imaging- based assay specific for SLC30A8. Our novel approach can be further explored and optimized, paving the way for future small molecule medium-throughput screening.

Experimental and Computational Analysis of Newly Identified Pathogenic Mutations in the Creatine Transporter SLC6A8.

Creatine is an essential metabolite for the storage and rapid supply of energy in muscle and nerve cells. In humans, impaired metabolism, transport, and distribution of creatine throughout tissues can cause varying forms of mental disability, also known as creatine deficiency syndrome (CDS). So far, 80 mutations in the creatine transporter (SLC6A8) have been associated to CDS. To better understand the effect of human genetic variants on the physiology of SLC6A8 and their possible impact on CDS, we studied 30 missense variants including 15 variants of unknown significance, two of which are reported here for the first time. We expressed these variants in HEK293 cells and explored their subcellular localization and transport activity. We also applied computational methods to predict variant effect and estimate site-specific changes in thermodynamic stability. To explore variants that might have a differential effect on the transporter's conformers along the transport cycle, we constructed homology models of the inward facing, and outward facing conformations. In addition, we used mass-spectrometry to study proteins that interact with wild type SLC6A8 and five selected variants in HEK293 cells. In silico models of the protein complexes revealed how two variants impact the interaction interface of SLC6A8 with other proteins and how pathogenic variants lead to an enrichment of ER protein partners. Overall, our integrated analysis disambiguates the pathogenicity of 15 variants of unknown significance revealing diverse mechanisms of pathogenicity, including two previously unreported variants obtained from patients suffering from the creatine deficiency syndrome.

Automation of high-throughput mRNA-seq library preparation: a robust, hands-free and time efficient methodology.

Over the last decade, whole transcriptome profiling, also known as RNA-sequencing (RNA-seq), has quickly gained traction as a reliable method for unbiased assessment of gene expression. Integration of RNA-seq expression data into other omics datasets (e.g., proteomics, metabolomics, or epigenetics) solidifies our understanding of cell-specific regulatory patterns, yielding pathways to investigate the key rules of gene regulation. A limitation to efficient, at-scale utilization of RNA-seq is the time-demanding library preparation workflows, which is a 2-day or longer endeavor per cohort/sample size. To tackle this bottleneck, we designed an automated workflow that increases throughput capacity, while minimizing human error to enhance reproducibility. To this end, we converted the manual protocol of the NEBNext Directional Ultra II RNA Library Prep Kit for Illumina on the Beckman Coulter liquid handler, Biomek i7 Hybrid workstation. A total of 84 RNA samples were isolated from two human cell lines and subjected to comparative manual and automated library preparation methods. Qualitative and quantitative results indicated a high degree of similarity between libraries generated manually or through automation. Yet, there was a significant reduction in both hands-on and assay time from a 2-day manual to a 9-hour automated workflow. Using linear regression analysis, we found the Pearson correlation coefficient between libraries generated manually or by automation to be almost identical to a sample being sequenced twice (R²= 0.985 vs 0.983). This demonstrates that high-throughput automated workflows can be of great benefit to genomic laboratories by enhancing efficiency of library preparation, reducing hands-on time and increasing throughput potential.

Covalent dimerization of interleukin-like epithelial-to-mesenchymal transition (EMT) inducer (ILEI) facilitates EMT, invasion, and late aspects of metastasis.

The interleukin-like epithelial-to-mesenchymal transition (EMT) inducer (ILEI)/FAM3C is a member of the highly homologous FAM3 family and is essential for EMT and metastasis formation. It is upregulated in several cancers, and its altered subcellular localization strongly correlates with poor survival. However, the mechanism of ILEI action, including the structural requirements for ILEI activity, remains elusive. Here, we show that ILEI formed both monomers and covalent dimers in cancer cell lines and in tumors. Using mutational analysis and pulse-chase experiments, we found that the four ILEI cysteines, conserved throughout the FAM3 family and involved in disulfide bond formation were essential for extracellular ILEI accumulation in cultured cells. Modification of a fifth cysteine (C185), unique for ILEI, did not alter protein secretion, but completely inhibited ILEI dimerization. Wild-type ILEI monomers, but not C185A mutants, could be converted into covalent dimers extracellularly upon overexpression by intramolecular-to-intermolecular disulfide bond isomerization. Incubation of purified ILEI with cell culture medium showed that dimerization was triggered by bovine serum in a dose- and time-dependent manner. Purified ILEI dimers induced EMT and trans-well invasion of cancer cells in vitro. In contrast, ILEI monomers and the dimerization-defective C185A mutant affected only cell motility as detected by scratch assays and cell tracking via time-lapse microscopy. Importantly, tumor cells overexpressing wild-type ILEI caused large tumors and lung metastases in nude mice, while cells overexpressing the dimerization-defective C185A mutant behaved similar to control cells. These data show that covalent ILEI self-assembly is essential for EMT induction, elevated tumor growth, and metastasis.