Integration of Transcriptome and Metabolome Provides Unique Insights to Pathways Associated With Obese Breast Cancer Patients

Abstract

Information regarding transcriptome and metabolome has significantly contributed to identifying potential therapeutic targets for the management of a variety of cancers. Obesity has profound effects on both cancer cell transcriptome and metabolome that can affect the outcome of cancer therapy. The information regarding the potential effects of obesity on breast cancer (BC) transcriptome, metabolome, and its integration to identify novel pathways related to disease progression are still elusive. We assessed the whole blood transcriptome and serum metabolome, as circulating metabolites, of obese BC patients compared them with non-obese BC patients. In these patients' samples, 186 significant differentially expressed genes (DEGs) were identified, comprising 156 upregulated and 30 downregulated. The expressions of these gene were confirmed by qRT-PCR. Furthermore, 96 deregulated metabolites were identified as untargeted metabolomics in the same group of patients. These detected DEGs and deregulated metabolites enriched in many cellular pathways. Further investigation, by integration analysis between transcriptomics and metabolomics data at the pathway levels, revealed seven unique enriched pathways in obese BC patients when compared with non-obese BC patients, which may provide resistance for BC cells to dodge the circulating immune cells in the blood. In conclusion, this study provides information on the unique pathways altered at transcriptome and metabolome levels in obese BC patients that could provide an important Hassan et al. Breast Cancer Transcriptomics and Metabolomics tool for researchers and contribute further to knowledge on the molecular interaction between obesity and BC. Further studies are needed to confirm this and to elucidate the exact underlying mechanism for the effects of obesity on the BC initiation or/and progression.

Untargeted Metabolomics Identifies Key Metabolic Pathways Altered by Thymoquinone in Leukemic Cancer Cells

“…Further, dry extracts were reconstituted in 100 μL of acetonitrile: water (1:1, v/v ), vortexed for 10 min and spin for 15 min at 13,000 rpm at 4 °C to remove insoluble debris. Finally, the resultant supernatants were taken for LC-MS/MS run [ 9 , 10 ].…”

“…The mobile phase consisted of 0.1% Formic acid and 99.9% ACN formic acid (0.1%, v/v ), using a linear gradient programme where the component of solution was changed from 5% B to 100% B over 90 min, at a constant flow rate of 0.2 mL/min (95% A from 5% to 30% over 72 min, 30% to 100% over 10 min, and kept at 100% for 5 min at a flow rate of 0.25 mL/min). The column temperature was maintained at 30 °C [ 9 , 10 ].…”

“…Nitrogen was used as a sheath gas and the flow rate was set at 40 arbitrary units. Further, helium was used as the buffer gas for the run [ 9 , 10 ].…”

Urolithin A and B Alter Cellular Metabolism and Induce Metabolites Associated with Apoptosis in Leukemic Cells

“…Treated cells were lysed immediately using tissue homogenizer using a combination of ice-cold methanol:acetonitrile:water at a ratio of (2:1:1 v / v ) and vortexed for the 30 s and incubated for 60 min at −20 °C and spin for 15 min at 13,000 rpm at 4 °C. The supernatant was collected, and the samples were taken for LC–MS/MS analysis [ 35 , 36 , 37 , 38 , 39 ].…”

Suppression of circulating AP001429.1 long non‑coding RNA in obese patients with breast cancer

“…Quantitative polymerase chain reaction (qPCR). The gene expression levels of 29 lncRNAs, selected according to a suggested role in cancer or obesity as reported by the literature, including by our previous study (43) (Table I), were evaluated in the blood of obese and non-obese patients with BC by qPCR. Each experiment was run in duplicate in 96-well plates using a Bio-Rad IQ SYBR Green mix and the CFX Connect™ Real-Time PCR Detection system (both Bio-Rad Laboratories, Inc.), according to the manufacturers' protocols and guidelines.…”