Overexpression of Forkhead Box L1 (FOXL1) Inhibits the Proliferation and Invasion of Breast Cancer Cells

Transcriptomic analysis revealed potential regulatory biomarkers and repurposable drugs for breast cancer treatment

Breast cancer (BC) is the most widespread cancer worldwide. Over 2 million new cases of BC were identified in 2020 alone. Despite previous studies, the lack of specific biomarkers and signaling pathways implicated in BC impedes the development of potential therapeutic strategies. We employed several RNAseq datasets to extract differentially expressed genes (DEGs) based on the intersection of all datasets, followed by protein-protein interaction network construction. Using the shared DEGs, we also identified significant gene ontology (GO) and KEGG pathways to understand the signaling pathways involved in BC development. A molecular docking simulation was performed to explore potential interactions between proteins and drugs. The intersection of the four datasets resulted in 146 DEGs common, including AURKB, PLK1, TTK, UBE2C, CDCA8, KIF15, and CDC45 that are significant hub-proteins associated with breastcancer development. These genes are crucial in complement activation, mitotic cytokinesis, aging, and cancer development. We identified key microRNAs (i.e., hsa-miR-16-5p, hsa-miR-1-3p, hsa-miR-147a, hsa-miR-195-5p, and hsa-miR-155-5p) that are associated with aggressive tumor behavior and poor clinical outcomes in BC. Notable transcription factors (TFs) were FOXC1, GATA2, FOXL1, ZNF24 and NR2F6. These biomarkers are involved in regulating cancer cell proliferation, invasion, and migration. Finally, molecular docking suggested Hesperidin, 2-amino-isoxazolopyridines, and NMS-P715 as potential lead compounds against BC progression. We believe that these findings will provide important insight into the BC progression as well as potential biomarkers and drug candidates for therapeutic development.

Molecular mechanisms of microRNA-301a during tumor progression and metastasis

Cancer is known as one of the leading causes of human deaths globally. Late diagnosis is considered as one of the main reasons for the high mortality rate among cancer patients. Therefore, the introduction of early diagnostic tumor markers can improve the efficiency of therapeutic modalities. MicroRNAs (miRNAs) have a key role in regulation of cell proliferation and apoptosis. MiRNAs deregulation has been frequently reported during tumor progressions. Since, miRNAs have a high stability in body fluids; they can be used as the reliable non-invasive tumor markers. Here, we discussed the role of miR-301a during tumor progressions. MiR-301a mainly functions as an oncogene via the modulation of transcription factors, autophagy, epithelial-mesenchymal transition (EMT), and signaling pathways. This review paves the way to suggest miR-301a as a non-invasive marker for the early tumor diagnosis. MiR-301a can also be suggested as an effective target in cancer therapy.

Chromatin accessibility landscape and active transcription factors in primary human invasive lobular and ductal breast carcinomas

BACKGROUND

Invasive lobular breast carcinoma (ILC), the second most prevalent histological subtype of breast cancer, exhibits unique molecular features compared with the more common invasive ductal carcinoma (IDC). While genomic and transcriptomic features of ILC and IDC have been characterized, genome-wide chromatin accessibility pattern differences between ILC and IDC remain largely unexplored.

METHODS

Here, we characterized tumor-intrinsic chromatin accessibility differences between ILC and IDC using primary tumors from The Cancer Genome Atlas (TCGA) breast cancer assay for transposase-accessible chromatin with sequencing (ATAC-seq) dataset.

RESULTS

We identified distinct patterns of genome-wide chromatin accessibility in ILC and IDC. Inferred patient-specific transcription factor (TF) motif activities revealed regulatory differences between and within ILC and IDC tumors. EGR1, RUNX3, TP63, STAT6, SOX family, and TEAD family TFs were higher in ILC, while ATF4, PBX3, SPDEF, PITX family, and FOX family TFs were higher in IDC.

CONCLUSIONS

This study reveals the distinct epigenomic features of ILC and IDC and the active TFs driving cancer progression that may provide valuable information on patient prognosis.

Chromatin interactome mapping at 139 independent breast cancer risk signals

BACKGROUND

Genome-wide association studies have identified 196 high confidence independent signals associated with breast cancer susceptibility. Variants within these signals frequently fall in distal regulatory DNA elements that control gene expression.

RESULTS

We designed a Capture Hi-C array to enrich for chromatin interactions between the credible causal variants and target genes in six human mammary epithelial and breast cancer cell lines. We show that interacting regions are enriched for open chromatin, histone marks for active enhancers, and transcription factors relevant to breast biology. We exploit this comprehensive resource to identify candidate target genes at 139 independent breast cancer risk signals and explore the functional mechanism underlying altered risk at the 12q24 risk region.

CONCLUSIONS

Our results demonstrate the power of combining genetics, computational genomics, and molecular studies to rationalize the identification of key variants and candidate target genes at breast cancer GWAS signals.

RNA-seq reveal role of bovine TORC2 in the regulation of adipogenesis

Low intramuscular adipose tissue (marbling) continues to be challenge for improving beef quality in Chinese cattle. Highly marbled meat is very desirable; hence, methods to increase IMF content have become a key aspect of improving meat quality. Therefore, research on the mechanism of adipogenesis provides invaluable information for the improvement of meat quality. This study investigated the effect of TORC2 and its underlying mechanism on lipid metabolism in bovine adipocytes. The TORC2 gene was downregulated in bovine adipocytes by siRNA, and RNA sequencing was performed. Downregulation of TORC2 negatively affected bovine adipocyte differentiation. In addition, a total of 577 DEGs were found, containing 146 up-regulated and 376 down-regulated genes. KEGG pathway analysis revealed that the DEGs were linked with neuroactive ligand-receptor interaction pathway, calcium signaling pathway, cAMP pathway, chemokine signaling pathway and Wnt signaling pathway. Gene Ontology (GO) term analysis of the DEGs showed that down-regulation of TORC2 gene significantly suppressed the genes regulating important GO terms of adipogenesis-related processes in bovine adipocytes, especially regulation of biological activity, regulation of primary metabolic process, regulation of multicellular organismal process, cell adhesion, lipid metabolic process, secretion, chemical homeostasis, regulation of transport, cell-cell signaling, cAMP metabolic process, cellular calcium ion homeostasis, fat cell differentiation, and cell maturation. In conclusion, our results suggest that TORC2 at least in part regulates lipid metabolism in bovine adipocytes. The results of this study provide a basis for studying the function and molecular mechanism of the TORC2 gene in regulating adipogenesis.

Forkhead box (FOX) G1 promotes hepatocellular carcinoma epithelial-Mesenchymal transition by activating Wnt signal through forming T-cell factor-4/Beta-catenin/FOXG1 complex

Background

Forkhead box G1 (FOXG1) is a member of the Fox transcription factor family involved in regulation of many cancers. However, the role of FOXG1 in hepatocellular carcinogenesisis largely unclear. The present study aimed at examining the biological function and underlying mechanism of FOXG1 on hepatocellular carcinoma (HCC) tumor metastasis as well as its clinical significance.

Methods

Levels of FOXG1 were determined by immunohistochemical and real-time PCR analysis in HCC cell lines and human HCC samples. The effect of FOXG1 on cancer cell invasion and metastasis was investigated in vitro and in vivo in either FOXG1-silenced or overexpressing human HCC cell lines. Immunoprecipitation and chromatin immunoprecipitation assays were performed to investigate the interaction of FOXG1, β-catenin, TCF4 and the effect on Wnt target-gene promoters.

Results

In human HCC, the level of FOXG1 progressively increased from surrounding non tumorous livers to HCC, reaching the highest levels in metastatic HCC. Furthermore, expression levels of FOXG1 directly correlated with cancer cell epithelial-mesenchymal transition (EMT) phenotype. In FOXG1-overexpressing cells, FOXG1 promotes the stabilization and nuclear accumulation of β-catenin by directly binding to β-catenin and it associates with the lymphoid enhancer factor/T cell factor proteins (LEF/TCFs) on Wnt responsive enhancers (WREs) in chromatin.

Conclusions

The results show that FOXG1 plays a key role in mediating cancer cell metastasis through the Wnt/β-catenin pathway in HCC cells and predicts HCC prognosis after surgery. Targeting FOXG1 may provide a new approach for therapeutic treatment in the future.

Hsa_circ_0008945 promoted breast cancer progression by targeting miR-338-3p

PURPOSE

To detect the expression and function of circ_0008945 in breast cancer (BC) and to explore its potential molecular mechanisms in BC tumorigenesis.

MATERIALS AND METHODS

We measured expression levels of circ_0008945, miR-338-3p and homeobox A3 (HOXA3) in BC tissue specimens and cells using quantitative reverse transcriptase polymerase chain reaction (qRT-PCR). We examined the effects of all three genes on BC cell proliferation using Cell Counting Kit-8 (CCK-8) and colony formation assays. We also performed a Transwell assay to assess the migratory and invasive ability of treated BC cells. BC cell apoptosis was assessed using flow cytometric (FCM) analysis; interaction between miR-338-3p and circ_0008945 or HOXA3 was verified by dual-luciferase reporter assay as well as by ribonucleic-acid (RNA) pulldown. Finally, we used an in vivo tumor growth assay to assess the role of circ_0008945 overexpression in BC tumor growth.

RESULTS

We found that circ_0008945 expression was significantly increased in both BC tissue specimens and cells. This increase was correlated with poor prognosis in BC patients. Knockdown of circ_0008945 inhibited BC cell proliferation, migration and invasion while promoting BC cell apoptosis in vitro. Overexpression of circ_0008945 remarkably promoted BC tumor growth in vivo. Mechanistically, circ_0008945 acted as a miRNA sponge for miR-338-3p and inhibited its expression in BC cells. Moreover, miR-338-3p targeted and inhibited HOXA3.

CONCLUSION

We found that circ_0008945 acted as a BC oncogene by physically binding miR-338-3p, which further targeted and regulated HOXA3.

Long noncoding RNA EPB41L4A-AS2 inhibits hepatocellular carcinoma development by sponging miR-301a-5p and targeting FOXL1

BACKGROUND

Hepatocellular carcinoma (HCC) is the major histological type of liver cancer with high morbidity and mortality worldwide. Long noncoding RNAs (lncRNA) has been proved to be associated with various cancer types, while its regulation in HCC is largely unknown.

METHODS

To figure out the specific role of lncRNA EPB41L4A-AS2 in HCC. Fluorescence in situ hybridization (FISH) was first used to determine the cellular sublocalization of EPB41L4A-AS2 to determine its primary mode of action. QRT-PCR, Western blot and hematoxylin-eosin staining were then used to measure the expression of genes in cells and tissues. Cell proliferation and invasion assays were performed to determine the effects of EPB41L4A-AS2, miR-301a-5p and FOXL1 on the malignant phenotype of tumor cells. With luciferase reporter assay, the direct interaction between target genes were further confirmed for research on molecular mechanism. Finally, the mice hepatocarcinoma model was also established to disclose the tumor suppressor effects of EPB41L4A-AS2 in vivo.

RESULTS

Here, we have identified a novel lncRNA EPB41L4A-AS2, which is significantly downregulated both in HCC cells and tissues, and plays a negative regulatory role in HCC proliferation and invasion. Mechanistically, cytoplasmic lncRNA EPB41L4A-AS2 functions as an efficient miR-301a-5p sponge, thereby release the expression inhibition of forkhead box L1 (FOXL1). Indeed, lncRNA EPB41L4A-AS2 inhibits proliferation and migration by upregulating FOXL1 expression and FOXL1 was confirmed as a direct target of miR-301a-5p. MiR-301a-5p shows an inverse correlation with EPB41L4A-AS2 expression and was verified as a direct target of EPB41L4A-AS2 as well. Correspondingly, FOXL1 and miR-301a-5p show opposite biological effects in cell proliferation and migration. Moreover, miR-301a-5p overexpression rescued the EPB41L4A-AS2 upregulation induced depression in proliferation, migration and invasion of HCC cells, as well as promotion effect on FOXL1 expression. Also, in vivo experiments proved that EPB41L4A-AS2 suppress tumor growth and extrahepatic metastasis (lung) via the miR-301a-5p-FOXL1 axis.

CONCLUSIONS

Taken together, this research revealed a concrete mechanism of lncRNA EPB41L4A-AS2 in HCC, which may serve as a potential biomarkers and novel therapeutic targets for further clinical application.