Retinoic acid receptor responder 1 (RARRES1) is silenced in many cancers and is differentially expressed in metabolism associated diseases, such as hepatic steatosis, hyperinsulinemia and obesity. Here we report a novel function of RARRES1 in metabolic reprogramming of epithelial cells. Using non-targeted LC-MS, we discovered that RARRES1 depletion in epithelial cells caused a global increase in lipid synthesis. RARRES1-depleted cells rewire glucose metabolism by switching from aerobic glycolysis to glucose-dependent de novo lipogenesis (DNL). Treatment with fatty acid synthase (FASN) inhibitor, C75, reversed the effects of RARRES1 depletion. The increased DNL in RARRES1-depleted normal breast and prostate epithelial cells proved advantageous to the cells during starvation, as the increase in fatty acid availability lead to more oxidized fatty acids (FAO), which were used for mitochondrial respiration. Expression of RARRES1 in several common solid tumors is also contextually correlated with expression of fatty acid metabolism genes and fatty acid-regulated transcription factors. Pathway enrichment analysis led us to determine that RARRES1 is regulated by peroxisome proliferating activated receptor (PPAR) signaling. These findings open up a new avenue for metabolic reprogramming and identify RARRES1 as a potential target for cancers and other diseases with impaired fatty acid metabolism.
RARRES1 Co-expression Data
OncomineTM (Compendia Bioscience, Ann Arbor, MI, USA) was used to identify cancers where RARRES1 gene expression was significantly upregulated or downregulated. These cancers included breast, cervical, colorectal, esophageal, gastric, head and neck, kidney, liver, lung, lymphoma, pancreatic and prostate (S1 Table from OncomineTM). Of the identified cancers, three (breast, colorectal and prostate) were selected for further analysis given the number of datasets found to have significant RARRES1 gene expression changes as well as the literature known about RARRES1 and its molecular biology within these cancers. Within the cancers selected, individual datasets were chosen given their large sample sizes and subtype analyses. Thus, The Cancer Genome Atlas (TCGA) Breast Cancer, TCGA Colorectal Cancer, and Grasso Prostate datasets were selected. The Grasso Prostate dataset was also uniquely selected for its metastatic vs. primary analysis (21). For the TCGA Breast Cancer dataset, subtype analysis was stratified into ER+ vs. ER- status; PR+ vs. PR- status and Triple Negative (PR-, HER2- & ER-) vs. non-Triple Negative (22). Metastatic vs. primary site analysis was performed in the Grasso Prostate dataset. All colorectal cancer types (rectal mucinous adenocarcinoma, colon adenocarcinoma, rectal adenocarcinoma, colon mucinous adenocarcinoma and cecum adenocarcinoma) identified in the TCGA dataset were also analyzed in comparison to their respective normal samples (S1 File) (23).
Genes positively or negatively co-expressed with RARRES1 were further identified using OncomineTM with respect to each dataset of tumor vs. normal.
Supplementary Information_Supp. File 1 (1).xlsx
GC-MS Raw Data (RARRES1 siRNA)
CSV files and raw data files are included in the zip file. RARRES1 siRNA and scrambled siRNA samples were run.
GC-MS.zip
Sample Annotations for GC-MS and LC-MS Runs
Description of runs and sample annotations for GC-MS and LC-MS are included.
Sample Annotations for LCMS and GCMS.zip
LC-MS Raw Data RARRES1 KD (1) (xaa)
We split the LC-MS raw data using the "Split" Linux function into 4 files (combine using "cat xaa xab ... > lcms.zip")
xaa
LC-MS Raw Data RARRES1 KD (2) (xab)
We split the LC-MS raw data using the "Split" Linux function into 17 files (combine using "cat xaa xab ... > lcms.zip")
xab
LC-MS Raw Data RARRES1 KD (3) (xac)
We split the LC-MS raw data using the "Split" Linux function into 17 files (combine using "cat xaa xab ... > lcms.zip")
xac
LC-MS Raw Data RARRES1 KD (4) (xad)
We split the LC-MS raw data using the "Split" Linux function into 17 files (combine using "cat xaa xab ... > lcms.zip")
xad
LC-MS Raw Data RARRES1 KD (5) (xae)
We split the LC-MS raw data using the "Split" Linux function into 17 files (combine using "cat xaa xab ... > lcms.zip")
xae
LC-MS Raw Data RARRES1 KD (7) (xaf)
We split the LC-MS raw data using the "Split" Linux function into 17 files (combine using "cat xaa xab ... > lcms.zip")
xaf
LC-MS Raw Data RARRES1 KD (7) (xag)
We split the LC-MS raw data using the "Split" Linux function into 17 files (combine using "cat xaa xab ... > lcms.zip")
xag
LC-MS Raw Data RARRES1 KD (8) (xah)
We split the LC-MS raw data using the "Split" Linux function into 17 files (combine using "cat xaa xab ... > lcms.zip")
xah
LC-MS Raw Data RARRES1 KD (9) (xai)
We split the LC-MS raw data using the "Split" Linux function into 17 files (combine using "cat xaa xab ... > lcms.zip")
xai
LC-MS Raw Data RARRES1 KD (10) (xaj)
We split the LC-MS raw data using the "Split" Linux function into 17 files (combine using "cat xaa xab ... > lcms.zip")
xaj
LC-MS Raw Data RARRES1 KD (11) (xaK)
We split the LC-MS raw data using the "Split" Linux function into 17 files (combine using "cat xaa xab ... > lcms.zip")
xak
LC-MS Raw Data RARRES1 KD (12) (xaL)
We split the LC-MS raw data using the "Split" Linux function into 17 files (combine using "cat xaa xab ... > lcms.zip"
xal
LC-MS Raw Data RARRES1 KD (13) (xaM)
We split the LC-MS raw data using the "Split" Linux function into 17 files (combine using "cat xaa xab ... > lcms.zip")
xam
LC-MS Raw Data RARRES1 KD (14) (xaN)
We split the LC-MS raw data using the "Split" Linux function into 17 files (combine using "cat xaa xab ... > lcms.zip")
xan
LC-MS Raw Data RARRES1 KD (14) (xao)
We split the LC-MS raw data using the "Split" Linux function into 17 files (combine using "cat xaa xab ... > lcms.zip")
xao
LC-MS Raw Data RARRES1 KD (16) (xap)
We split the LC-MS raw data using the "Split" Linux function into 17 files (combine using "cat xaa xab ... > lcms.zip")
xap
LC-MS Raw Data RARRES1 KD (17) (xaq)
We split the LC-MS raw data using the "Split" Linux function into 17 files (combine using "cat xaa xab ... > lcms.zip")
xaq