RNA-Seq transcriptome analysis shows anti-tumor actions of melatonin in a breast cancer xenograft model

Abstract

Melatonin is a pleiotropic anti-cancer molecule that controls cancer growth by multiple mechanisms. RNA-Seq can potentially evaluate therapeutic response and its use in xenograft tumor models can differentiate the changes that occur specifically in tumor cells or in the tumor microenvironment (TME). Melatonin actions were evaluated in a xenograft model of triple-negative breast cancer. Balb/c nude mice bearing MDA-MB-231 tumors were treated with melatonin or vehicle. RNA-Seq was performed on the Illumina HiSeq. 2500 and data were mapped against human and mouse genomes separately to differentiate species-specific expression. Differentially expressed (DE) genes were identified and Weighted Gene Co-expression Network Analysis (WGCNA) was used to detect clusters of highly co-expressed genes. Melatonin treatment reduced tumor growth (p < 0.01). 57 DE genes were identified in murine cells, which represented the TME, and were mainly involved in immune response. The WGCNA detected co-expressed genes in tumor cells and TME, which were related to the immune system among other biological processes. The upregulation of two genes (Tnfaip8l2 and Il1f6) by melatonin was validated in the TME, these genes play important roles in the immune system. Taken together, the transcriptomic data suggests that melatonin anti-tumor actions occur through modulation of TME in this xenograft tumor model.

Crucial transcripts predict response to initial immunoglobulin treatment in acute Kawasaki disease

“…Modules that are highly relevant to clinical trait are further analyzed and crucial transcripts are identified. WGCNA has been proven to be useful in various types of diseases, such as cancer 11 , immune disease 12 , chronic disease 13 .…”

A meta‐analysis of microRNA networks regulated by melatonin in cancer: Portrait of potential candidates for breast cancer treatment

“…Given the number of miRNA‐associated predicted targets found in breast cancer, we extrapolated the study by re‐analyzing the transcriptome of breast tumor samples obtained from an in vivo mouse model treated with melatonin 37 ; these tumors displayed a significant growth inhibition after treatment. From 1105 upregulated and 979 downregulated genes by melatonin, we detected a broad involvement of the immunological component activation in addition to the control of cell proliferation and metastasis.…”

“…These biological samples were obtained from athymic BALB/c nude mice previously inoculated with human breast cancer cells (MDA‐MB‐231) and treated with melatonin (Sigma) at a dose of 40 mg/kg of body weight diluted in 100 μL of vehicle solution by intraperitoneal (IP) injection for 5 days a week for 21 days 36 . The protocol for sample preparation and processing to produce sequencing libraries is available elsewhere 37 . We first used the BioJupies platform (https://amp.pharm.mssm.edu/biojupies/) 38 to identify the differentially expressed genes (DEGs) in breast cancer samples after melatonin treatment.…”

“…36 The protocol for sample preparation and processing to produce sequencing libraries is available elsewhere. 37 We first used the BioJupies platform (https://amp. pharm.mssm.edu/bioju pies/) 38 to identify the differentially expressed genes (DEGs) in breast cancer samples after melatonin treatment.…”

CD36 identified by weighted gene co-expression network analysis as a hub candidate gene in lupus nephritis

“…At last, after relating modules to clinical traits, modules with high correlation to disease are further analyzed and hub genes of pivotal importance to disease are identified. WGCNA has been broadly used for studying of diseases such as cancer (Jardim-Perassi et al, 2019), neuropsychiatric disorder (Huggett & Stallings, 2019), chronic disease (Morrow et al, 2015) and proved to be quite useful.…”