Transcriptomic responses in human intestinal cells (Caco-2, HIEC-6) exposed to dietary nanoparticles

Use of nanoparticles (NPs) in the food industry raises health concerns particularly in the gastrointestinal system. Assessing dietary NPs remains challenged due the vast number of products and the resource-intensive nature of traditional toxicity testing. Recent advancements in high-throughput transcriptomics, coupled with benchmark dose (BMD) analysis are poised to modernize chemical safety assessments. The objective of this study was to derive transcriptomic point of departure (tPOD) values for common dietary NPs through dose-response analysis of 3’ RNA-sequencing data. Two intestinal cell lines (Caco-2, HIEC-6) were exposed to 9 forms of Ag, SiO2, and TiO2 (including Food Grade and Non-Food Grade particles, as well as Nanoparticles and Microparticles), and expression of L1000 landmark genes was characterized using the QIAseq UPX 3’ targeted RNA panel kit catalog number 333041 / CSHS-10608Z-990. Each transcript in each well of the RT plate was labeled with a unique molecular index (UMI) for each cDNA molecule, and samples in a given microplate well were labeled with a cell ID. Library quality control assays were performed with the seven prepared libraries and subsequently sequenced on an Illumina NextSeq500. This dataset provides the gene expression values for this study after they were demultiplexed according to the various indexes used (i.e., cell ID and UMI) by the GeneGlobe analysis hub (https://geneglobe.qiagen.com/) to yield UMI count matrices. These RNAseq data are in one spreadsheet. The data were next analyzed for transcriptomics points of departure using www.FastBMD.ca, and these data are provided in a separate zip file (1 file per chemical tested)