Identification of signaling networks associated with lactate modulation of macrophages and dendritic cells

The advancement in the understanding of cancer immune evasion has manifested the development of cancer immunotherapeutic approaches such as checkpoint inhibitors and interleukin agonists. Although cancer immunotherapy breakthroughs have demonstrated improved potency for cancer treatment, only a fraction of patients effectively respond to these treatments. Moreover, there is compelling evidence indicating that cancer cells develop a unique microenvironment through adaptive metabolic reprogramming, which aberrantly modulates host immunity to evade immunosurveillance. As part of the tumor cell adaptive metabolic switch, lactate is produced and released into the tumor environment. Recent studies have shown that lactate significantly modulates immune functions, especially in innate immune cells. Dendritic cells (DCs) and macrophages (MΦs) are specialized antigen-presenting cells serving as key players in innate immunity and anticancer-associated immune responses. Although, most studies have ..., 1.1       RNA Isolation Procedures and Sequencing
RNA was harvested from DCs and MΦs (1 million cells/well) treated with either media (control) or 50 mM sLA for 48 h at 37°C using 1 mL of TRIzol Reagent (Thermo Fisher Scientific). Chloroform was added to each TRIzol sample for phase separation and RNA was precipitated from the aqueous phase using a 1:1 ratio of ethanol. The isolated nucleic acid material was purified, DNAse-treated, and concentrated using an RNA Clean & Concentrator kit (Zymo Research). The samples were sent to the UC Davis DNA Core for quality assessment using LabChip GX Nucleic Acid Analyzer. The top-scoring technical replicates were selected and sent to the DNA Core via 3’-Tag-Seq (QuantSeq) Library Preparation and Illumina HiSeq 4000. The gene expression levels were quantified and compared between sLA and control groups on R using limma-voom, and adjusted p-values were calculated via Bejamini-Hochberg Procedure. For each comparison, the log fold change (Log2FC) ..., , RNAseq Dataset

The attached folder contains all RNAseq datasets related to transcriptomic experiments measuring the differential gene expression of Macrophage and Dendritic Cell in response to lactate treatment.

\[Folder] archive_2020_03_02__22_59_13-macrophage: Contains macrophage RNAseq datasets

> analysis.html:
> \>Contains a summary of the RNAseq experiment performed with macrophages, provided by the UC Davis Bioinformatics Core
> \>Multidimensional scaling (MDS) plots shown by treatment group and metadata parameters
> \>Analysis method & R settings outlined
> \>Output of resulting differential gene expression data columns:
> \>logFC: log2 fold change, with the group listed first in the comparison or file name being the numerator of the fold change
> \>AveExpr: Average expression across all samples, in log2 counts per million reads
> \>P.Value: Raw p-value from the test that the log fold change differs from 0
> \>adj.P.Val: B...