Dysregulated miRNAs modulate tumor microenvironment associated signaling networks in pancreatic ductal adenocarcinoma
Purpose: The goals of this study are to investigate the role of miRNAs in regulating pancreatic ductal adenocarcinoma (PDAC) tumor microenvironment (TME) and PDAC progress. Methods: Total RNA-seq and miRNA-seq were performed on PDAC tumor and adjacent benigh tissues, and the miRNA profile was also investigated from the patient and healthy subject plasma. Single-cell RNA-seq was performed on one PDAC tissue, using 10x Genomics 5 prime gene expression technology. Results: The RNA-seq and miRNA-seq libraries were sequenced on Illumina NextSeq 550 or HiSeq 4000 (Illumina, San Diego, CA). All sequencing data were demultiplexed and converted into fastq files by Illumina bcl2fastq2 v2.17.14. Filtered sequence reads were mapped to reference genome GRCh38 using STAR (RNA-seq) or Botwie (miRNA-seq) with default settings. Single cell data was mapped and counted uisng Cellranger (v5.0). Conclusions: We identifed 322 and 49 differentially expressed miRNAs in PDAC tissue and patient plasma, respectively. We also identify 1,445 differentially expressed genes from PDAC tissue and paired the DEGs with their regualtory miRNAs through miRNA functional prediction. Overall design: Tumor and adjacent benign tissues were obtained during surgical resections from PDAC patients. Plasma was obtained from peripheral blood of PDAC patients and healthy control subjects. Total RNA was extracted with Qiagen Allprep DNA/RNA/miRNA kit. RNA-seq libraries were constructed using Tecan Universal NuQuant kit and miRNA-seq libraries were constructed using QIAseq miRNA library kit.