The transcriptional STAT3 is a potential target, whereas transcriptional STAT5A/5B/6 are new biomarkers for prognosis in human breast carcinoma

Notch3 restricts metastasis of breast cancers through regulation of the JAK/STAT5A signaling pathway

PURPOSE

To explore the potential role of signal transducer and activator of transcription 5A (STAT5A) in the metastasis of breast cancer, and its mechanism of regulation underlying.

METHODS AND RESULTS

TCGA datasets were used to evaluate the expression of STAT5A in normal and different cancerous tissues through TIMER2.0, indicating that STAT5A level was decreased in breast cancer tissues compared with normal ones. Gene Set Enrichment Analysis predicted that STAT5A was associated with the activation of immune cells and cell cycle process. We further demonstrated that the infiltration of immune cells was positively associated with STAT5A level. Influorescence staining revealed the expression and distribution of F-actin was regulated by STAT5A, while colony formation assay, wound healing and transwell assays predicted the inhibitory role of STAT5A in the colony formation, migratory and invasive abilities in breast cancer cells. In addition, overexpression of the Notch3 intracellular domain (N3ICD), the active form of Notch3, resulted in the increased expression of STAT5A. Conversely, silencing of Notch3 expression by siNotch3 decreased STAT5A expression, supporting that STAT5A expression is positively associated with Notch3 in human breast cancer cell lines and breast cancer tissues. Mechanistically, chromatin immunoprecipitation showed that Notch3 was directly bound to the STAT5A promoter and induced the expression of STAT5A. Moreover, overexpressing STAT5A partially reversed the enhanced mobility of breast cancer cells following Notch3 silencing. Low expression of Notch3 and STAT5A predicted poorer prognosis of patients with breast cancer.

CONCLUSION

The present study demonstrates that Notch3 inhibits metastasis in breast cancer through inducing transcriptionally STAT5A, which was associated with tumor-infiltrating immune cells, providing a novel strategy to treat breast cancer.

moBRCA-net: a breast cancer subtype classification framework based on multi-omics attention neural networks

BACKGROUND

Breast cancer is a highly heterogeneous disease that comprises multiple biological components. Owing its diversity, patients have different prognostic outcomes; hence, early diagnosis and accurate subtype prediction are critical for treatment. Standardized breast cancer subtyping systems, mainly based on single-omics datasets, have been developed to ensure proper treatment in a systematic manner. Recently, multi-omics data integration has attracted attention to provide a comprehensive view of patients but poses a challenge due to the high dimensionality. In recent years, deep learning-based approaches have been proposed, but they still present several limitations.

RESULTS

In this study, we describe moBRCA-net, an interpretable deep learning-based breast cancer subtype classification framework that uses multi-omics datasets. Three omics datasets comprising gene expression, DNA methylation and microRNA expression data were integrated while considering the biological relationships among them, and a self-attention module was applied to each omics dataset to capture the relative importance of each feature. The features were then transformed to new representations considering the respective learned importance, allowing moBRCA-net to predict the subtype.

CONCLUSIONS

Experimental results confirmed that moBRCA-net has a significantly enhanced performance compared with other methods, and the effectiveness of multi-omics integration and omics-level attention were identified. moBRCA-net is publicly available at https://github.com/cbi-bioinfo/moBRCA-net .

STAT2 act a prognostic biomarker and associated with immune infiltration in kidney renal clear cell carcinoma

Renal clear cell carcinoma (KIRC) is a malignancy of the renal epithelial cells with poor prognosis. Notably, the JAK-STAT pathway mediates cell proliferation and immune response. Accumulating evidence suggests that STATs act as immune checkpoint inhibitors in various cancers. Nonetheless, the role of STAT2 in KIRC remains elusive. Herein, analyses were performed using a series of interactive web databases including Oncomine, GEPIA and TIMER. In sub-group analyses, STAT2 was upregulated at both the mRNA and protein levels in KIRC patients. Besides, KIRC patients with high STAT2 expression exhibited a poor overall survival. Moreover, Cox regression analysis revealed that STAT2 expression, nodal metastasis and clinical stage were independent factors affecting the prognosis of KIRC patients. There was a significant positive correlation between STAT2 expression, and the abundance of immune cells as well as the expression of immune biomarker sets. In addition, STAT2 was found to be implicated in immune response, cytokine-cytokine receptor interaction, and Toll-like receptor signaling pathways. Also, several cancer-related kinases, miRNAs, and transcription factors associated with STAT2 were identified. Conclusively, we revealed that STAT2 is a potential prognosis biomarker and associated with immune infiltration in kidney renal clear cell carcinoma. This study offers additional data that will help in further research on the roles of STAT2 protein in carcinogenesis.

STAT family of transcription factors in breast cancer: Pathogenesis and therapeutic opportunities and challenges

Breast cancer is the most commonly diagnosed cancer and second-leading cause of cancer deaths in women. Breast cancer stem cells (BCSCs) promote metastasis and therapeutic resistance contributing to tumor relapse. Through activating genes important for BCSCs, transcription factors contribute to breast cancer metastasis and therapeutic resistance, including the signal transducer and activator of transcription (STAT) family of transcription factors. The STAT family consists of six major isoforms, STAT1, STAT2, STAT3, STAT4, STAT5, and STAT6. Canonical STAT signaling is activated by the binding of an extracellular ligand to a cell-surface receptor followed by STAT phosphorylation, leading to STAT nuclear translocation and transactivation of target genes. It is important to note that STAT transcription factors exhibit diverse effects in breast cancer; some are either pro- or anti-tumorigenic while others maintain dual, context-dependent roles. Among the STAT transcription factors, STAT3 is the most widely studied STAT protein in breast cancer for its critical roles in promoting BCSCs, breast cancer cell proliferation, invasion, angiogenesis, metastasis, and immune evasion. Consequently, there have been substantial efforts in developing cancer therapeutics to target breast cancer with dysregulated STAT3 signaling. In this comprehensive review, we will summarize the diverse roles that each STAT family member plays in breast cancer pathobiology, as well as, the opportunities and challenges in pharmacologically targeting STAT proteins and their upstream activators in the context of breast cancer treatment.

Downregulated miR-129-5p expression inhibits rat pulmonary fibrosis by upregulating STAT1 gene expression in macrophages

OBJECTIVE

This study investigated the mechanism by which microRNA-129-5p (miR-129-5p) in macrophages affects pulmonary fibrosis in rats by regulating the expression of the signal transducer and activator of transcription 1 (STAT1) gene.

METHODS

After the establishment of a pulmonary fibrosis rat model, quantitative real-time polymerase chain reaction (qRT-PCR) was employed to detect the expression of miR-129-5p in the sham group and model group. The binding sites between miR-129-5p and STAT1 were predicted online and verified by using a dual luciferase reporter system. qRT-PCR and Western blot analyses were used to test the effect of miR-129-5p on STAT1 gene expression. M2 macrophages were isolated and induced, and exosomes were extracted. Cell proliferation was detected by EdU. Furthermore, qRT-PCR was performed to detect the expression of STAT1, collagen type I A2 (COL1A2), collagen type III A1 (COL3A1), fibronectin, and α-SMA in cells and tissues followed by the detection of CD9, CD63, CD81, CD31 and STAT1 protein expression using a Western blot analysis. The pulmonary fibrosis area was detected by Masson staining followed by the immunohistochemical detection of α-smooth muscle actin (α-SMA) and type I collagen (COL-I) expression in pulmonary fibroblasts.

RESULTS

Compared with the sham group, the expression level of miR-129-5p in the model group was significantly increased (P < 0.05). miR-129-5p was observed to negatively regulate the expression of STAT1 (P < 0.05). The in vitro cell transfection experiments showed that after inhibiting the expression of miR-129-5p, the expression of STAT1 was increased, and the proliferation of fibroblasts and pulmonary fibrosis were inhibited (all P < 0.05). Furthermore, compared with the fibroblasts without coculture, the proliferation of the fibroblasts cocultured with M2 macrophage-secreted exosomes was clearly increased, and the expression levels of COL1A2, COL3A1, fibronectin and α-SMA were significantly increased (all P < 0.05). Compared with the mimic NC-exo group, the miR-129-5p-exo group had significantly increased proliferation of fibroblasts, decreased expression of STAT1, and significantly increased expression of COL1A2, COL3A1, fibronectin and α-SMA, and M2 macrophage-secreted exosomes could carry miR-129-5p to fibroblasts. Furthermore, the in vivo experiment confirmed that the exosomes of M2 macrophages could carry miR-129-5p, which could regulate M2 macrophages with pulmonary fibrosis in vivo.

CONCLUSION

M2 macrophages can carry miR-129-5p to pulmonary interstitial fibroblasts and inhibit STAT1 gene expression, which may lead to the proliferation of fibroblasts and promote pulmonary fibrosis. The downregulation of miR-129-5p can significantly promote STAT1 gene expression in macrophages to inhibit pulmonary fibrosis in rats.

Randomized, Double-Blind, Placebo-Controlled Phase III Study of Paclitaxel ± Napabucasin in Pretreated Advanced Gastric or Gastroesophageal Junction Adenocarcinoma

PURPOSE

To compare napabucasin (generator of reactive oxygen species) plus paclitaxel with paclitaxel only in patients with second-line advanced gastric or gastroesophageal junction (GEJ) adenocarcinoma.

EXPERIMENTAL DESIGN

In the double-blind, phase III BRIGHTER study (NCT02178956), patients were randomized (1:1) to napabucasin (480 mg orally twice daily) plus paclitaxel (80 mg/m2 i.v. weekly for 3 of 4 weeks) or placebo plus paclitaxel. The primary endpoint was overall survival (OS). Secondary endpoints included progression-free survival (PFS), objective response rate (ORR), disease control rate (DCR), and safety.

RESULTS

Overall, 714 patients were randomized (napabucasin plus paclitaxel, n = 357; placebo plus paclitaxel, n = 357). 72.1% were male, 74.6% had gastric adenocarcinoma, and 46.2% had peritoneal metastases. The study was unblinded following an interim analysis at 380 deaths. The final efficacy analysis was performed on 565 deaths (median follow-up, 6.8 months). No significant differences were observed between napabucasin plus paclitaxel and placebo plus paclitaxel for OS (6.93 vs. 7.36 months), PFS (3.55 vs. 3.68 months), ORR (16% vs. 18%), or DCR (55% vs. 58%). Grade ≥3 adverse events occurred in 69.5% and 59.7% of patients administered napabucasin plus paclitaxel and placebo plus paclitaxel, respectively, with grade ≥3 diarrhea reported in 16.2% and 1.4%, respectively.

CONCLUSIONS

Adding napabucasin to paclitaxel did not improve survival in patients with pretreated advanced gastric or GEJ adenocarcinoma. Consistent with previous reports, the safety profile of napabucasin was driven by manageable gastrointestinal events; grade ≥3 diarrhea occurred at a higher frequency with napabucasin plus paclitaxel versus placebo plus paclitaxel.

Lestaurtinib Has the Potential to Inhibit the Proliferation of Hepatocellular Carcinoma Uncovered by Bioinformatics Analysis and Pharmacological Experiments

Patients diagnosed with hepatocellular carcinoma (HCC) seek a satisfactory prognosis. However, most HCC patients present a risk of recurrence, thus highlighting the lack of effectiveness of current treatments and the urgent need for improved treatment options. The purpose of this study was to identify new candidate factors in the STAT family, which is involved in hepatocellular carcinogenesis, and new targets for the treatment of HCC. Bioinformatics web resources, including Oncomine, Gene Expression Profiling Interactive Analysis (GEPIA), The Human Protein Atlas (HPA), Tumor Immune Estimation Resource (TIMER), and GSCALite, were used to identify candidate genes among the STAT family in HCC. STAT1 was significantly overexpressed in hepatocellular carcinoma. More meaningfully, the high STAT1 expression was significantly associated with poor prognosis. Therefore, STAT1 is expected to be a therapeutic target. The JAK2 inhibitor lestaurtinib was screened by the Genomics of Cancer Drug Sensitivity Project (GDSC) analysis. Pharmacological experiments showed that lestaurtinib has the ability to prevent cell migration and colony formation from single cells. We also found that STAT1 is involved in inflammatory responses and immune cell infiltration. Immune infiltration analysis revealed a strong association between STAT1 levels and immune cell abundance, immune biomarker levels, and immune checkpoints. This study suggests that STAT1 may be a key oncogene in hepatocellular carcinoma and provides evidence that the JAK2 inhibitor lestaurtinib is a potent antiproliferative agent that warrants further investigation as a targeted therapy for HCC.

High Expression of Interferon Pathway Genes CXCL10 and STAT2 Is Associated with Activated T-Cell Signature and Better Outcome of Oral Cancer Patients

To improve the survival rate of cancer patients, biomarkers for both early diagnosis and patient stratification for appropriate therapeutics play crucial roles in precision oncology. Investigation of altered gene expression and the relevant molecular pathways in cancer cells are helpful for discovering such biomarkers. In this study, we explore the potential prognostic biomarkers for oral cancer patients through systematically analyzing five oral cancer transcriptomic data sets (TCGA, GSE23558, GSE30784, GSE37991, and GSE138206). Gene Set Enrichment Analysis (GSEA) was individually applied to each data set and the upregulated Hallmark molecular pathways of each data set were intersected to generate 13 common pathways including interferon-α/γ pathways. Among the 5 oral cancer data sets, 43 interferon pathway genes were commonly upregulated and 17 genes exhibited prognostic values in TCGA cohort. After validating in another oral cancer cohort (GSE65858), high expressions of C-X-C motif chemokine ligand 10 (CXCL10) and Signal transducer and activator of transcription 2 (STAT2) were confirmed to be good prognostic biomarkers. GSEA of oral cancers stratified by CXCL10/STAT2 expression showed that activation of T-cell pathways and increased tumor infiltration scores of Type 1 T helper (Th1) and CD8+ T cells were associated with high CXCL10/STAT2 expression. These results suggest that high CXCL10/STAT2 expression can predict a favorable outcome in oral cancer patients.

Identification of key tumor stroma-associated transcriptional signatures correlated with survival prognosis and tumor progression in breast cancer

BACKGROUND

The aberrant expression of stromal gene signatures in breast cancer has been widely studied. However, the association of stromal gene signatures with tumor immunity, progression, and clinical outcomes remains lacking.

METHODS

Based on eight breast tumor stroma (BTS) transcriptomics datasets, we identified differentially expressed genes (DEGs) between BTS and normal breast stroma. Based on the DEGs, we identified dysregulated pathways and prognostic hub genes, hub oncogenes, hub protein kinases, and other key marker genes associated with breast cancer. Moreover, we compared the enrichment levels of stromal and immune signatures between breast cancer patients with bad and good clinical outcomes. We also investigated the association between tumor stroma-related genes and breast cancer progression.

RESULTS

The DEGs included 782 upregulated and 276 downregulated genes in BTS versus normal breast stroma. The pathways significantly associated with the DEGs included cytokine-cytokine receptor interaction, chemokine signaling, T cell receptor signaling, cell adhesion molecules, focal adhesion, and extracellular matrix-receptor interaction. Protein-protein interaction network analysis identified the stromal hub genes with prognostic value in breast cancer, including two oncogenes (COL1A1 and IL21R), two protein kinases encoding genes (PRKACA and CSK), and a growth factor encoding gene (PLAU). Moreover, we observed that the patients with bad clinical outcomes were less enriched in stromal and antitumor immune signatures (CD8 + T cells and tumor-infiltrating lymphocytes) but more enriched in tumor cells and immunosuppressive signatures (MDSCs and CD4 + regulatory T cells) compared with the patients with good clinical outcomes. The ratios of CD8 + /CD4 + regulatory T cells were lower in the patients with bad clinical outcomes. Furthermore, we identified the tumor stroma-related genes, including MCM4, SPECC1, IMPA2, and AGO2, which were gradually upregulated through grade I, II, and III breast cancers. In contrast, COL14A1, ESR1, SLIT2, IGF1, CH25H, PRR5L, ABCA6, CEP126, IGDCC4, LHFP, MFAP3, PCSK5, RAB37, RBMS3, SETBP1, and TSPAN11 were gradually downregulated through grade I, II, and III breast cancers. It suggests that the expression of these stromal genes has an association with the progression of breast cancers. These progression-associated genes also displayed an expression association with recurrence-free survival in breast cancer patients.

CONCLUSIONS

This study identified tumor stroma-associated biomarkers correlated with deregulated pathways, tumor immunity, tumor progression, and clinical outcomes in breast cancer. Our findings provide new insights into the pathogenesis of breast cancer.

Molecular Biology Networks and Key Gene Regulators for Inflammatory Biomarkers Shared by Breast Cancer Development: Multi-Omics Systems Analysis

As key inflammatory biomarkers C-reactive protein (CRP) and interleukin-6 (IL6) play an important role in the pathogenesis of non-inflammatory diseases, including specific cancers, such as breast cancer (BC). Previous genome-wide association studies (GWASs) have neither explained the large proportion of genetic heritability nor provided comprehensive understanding of the underlying regulatory mechanisms. We adopted an integrative genomic network approach by incorporating our previous GWAS data for CRP and IL6 with multi-omics datasets, such as whole-blood expression quantitative loci, molecular biologic pathways, and gene regulatory networks to capture the full range of genetic functionalities associated with CRP/IL6 and tissue-specific key drivers (KDs) in gene subnetworks. We applied another systematic genomics approach for BC development to detect shared gene sets in enriched subnetworks across BC and CRP/IL6. We detected the topmost significant common pathways across CRP/IL6 (e.g., immune regulatory; chemokines and their receptors; interferon γ, JAK-STAT, and ERBB4 signaling), several of which overlapped with BC pathways. Further, in gene–gene interaction networks enriched by those topmost pathways, we identified KDs—both well-established (e.g., JAK1/2/3, STAT3) and novel (e.g., CXCR3, CD3D, CD3G, STAT6)—in a tissue-specific manner, for mechanisms shared in regulating CRP/IL6 and BC risk. Our study may provide robust, comprehensive insights into the mechanisms of CRP/IL6 regulation and highlight potential novel genetic targets as preventive and therapeutic strategies for associated disorders, such as BC.

EGCG Inhibits Adipose-Derived Mesenchymal Stem Cells Differentiation into Adipocytes and Prevents a STAT3-Mediated Paracrine Oncogenic Control of Triple-Negative Breast Cancer Cell Invasive Phenotype

Obese subjects have an increased risk of developing triple-negative breast cancer (TNBC), in part associated with the chronic low-grade inflammation state. On the other hand, epidemiological data indicates that increased consumption of polyphenol-rich fruits and vegetables plays a key role in reducing incidence of some cancer types. Here, we tested whether green tea-derived epigallocatechin-3-gallate (EGCG) could alter adipose-derived mesenchymal stem cell differentiation into adipocytes, and how this impacts the secretome profile and paracrine regulation of the TNBC invasive phenotype. Here, cell differentiation was performed and conditioned media (CM) from preadipocytes and mature adipocytes harvested. Human TNBC-derived MDA-MB-231 real-time cell migration was performed using the exCELLigence system. Differential gene arrays and RT-qPCR were used to assess gene expression levels. Western blotting was used to assess protein expression and phosphorylation status levels. In vitro vasculogenic mimicry (VM) was assessed with Matrigel. EGCG was found to inhibit the induction of key adipogenic biomarkers, including lipoprotein lipase, adiponectin, leptin, fatty acid synthase, and fatty acid binding protein 4. Increased TNBC-derived MDA-MB-231 cell chemotaxis and vasculogenic mimicry were observed in response to mature adipocytes secretome, and this was correlated with increased STAT3 phosphorylation status. This invasive phenotype was prevented by EGCG, the JAK/STAT inhibitors Tofacitinib and AG490, as well as upon STAT3 gene silencing. In conclusion, dietary catechin-mediated interventions could, in part through the inhibition of adipogenesis and modulation of adipocytes secretome profile, prevent the onset of an obesogenic environment that favors TNBC development.

Mining therapeutic and prognostic significance of STATs in renal cell carcinoma with bioinformatics analysis

Renal cell carcinoma is one of the most common malignancies with high morbidity and mortality. STAT proteins play a significant role in cell biological behavior and immune response associated with cancer progression. In our study, the datasets analyzed for the expression and potential functions can be found in several bioinformatics analysis tools. We found that STAT1/2/4/6 were upregulated in RCC while STAT3/5B were downregulated. The expression of STAT2/4/5B were significantly associated with the pathological stage of RCC patients. RCC patients with high expression of STAT2/4 and low/medium expression of STAT5B had a poor overall survival. The function of STATs and the neighboring genes mainly enriched in JAK-STAT signaling pathway and NOD-like receptor signaling pathway. Several transcription factor, kinase, and miRNA targets were identified. Close correlations were obtained between immune cell infiltration and STATs in RCC. Our results have provided novel insights for the selection of immunotherapeutic targets and prognostic biomarkers.

Identification of immune checkpoint inhibitors and biomarkers among STAT family in stomach adenocarcinoma

Background: Gastric cancer is the fifth most prevalent malignancy worldwide, and the third leading cause of cancer-related death. Activating mutations of the JAK/STAT pathway on cellular biological process, inflammation, and immunity of cancer cells have made them promising biomarkers for drug exploitation and malignancy treatment. Specific functions of the STAT family in stomach adenocarcinoma (STAD) have not yet been systematically described. Methods: Bioinformatics web resources, including UALCAN, The Kaplan Meier plotter, and GSCALite, were used to identify immune checkpoint inhibitors and biomarkers among the STAT family in STAD. Results: STAT1, STAT4, STAT5A, and STAT6 were upregulated in STAD at both the mRNA and protein level. STAT1 and STAT5A may act as potential prognostic and prognostic biomarkers in STAD. Among all members of the STAT family, STAT5B (33%), STAT1 (27%), and STAT5A (18%) were the top three frequently mutated genes, and missense mutations were the most common types of genetic alteration. The STAT family has mainly been associated with the activity of several well-known cancer-associated pathways. Low expression of STAT5A and STAT5B were resistant to most of drugs or small molecules in the Genomics of drug Sensitivity in Cancer (GDSC). The functions and pathways of STAT5A in STAD were mainly associated with immune responses, chemokine signaling pathways, and cell adhesion molecules. In addition, we identified several STAT5A associated-targets (transcription factor, kinase, and miRNA targets). Immuno-infiltration analysis suggested a strong association between the STAT5A level, the abundance of immune cells, and the level of immune biomarkers. Conclusions: We identified the immune checkpoint inhibitor and biomarkers among the STAT family in STAD, thereby providing additional information about the significant role of the STAT family in STAD.

Loss of STAT6 leads to anchorage-independent growth and trastuzumab resistance in HER2+ breast cancer cells

Approximately 20% of breast cancers are HER2-positive. Trastuzumab has improved patient outcomes significantly for these cancers. However, acquired resistance remains a major hurdle in the clinical management of these patients. Therefore, identifying molecular changes that cause trastuzumab resistance is worthwhile. STAT6 is a transcription factor that regulates a variety of genes involved in cell cycle regulation, growth inhibition, and apoptosis. STAT6 expression is lost in approximately 3% of breast cancers, but little work has been done in the context of trastuzumab resistance in breast cancer. In isogenic cell line pairs, we observed that trastuzumab-resistant cells expressed significantly lower levels of STAT6 compared to trastuzumab-sensitive cells. Therefore, in order to study the consequences of STAT6 loss in HER2+ breast cancer, we knocked out both alleles of the STAT6 gene using somatic cell gene targeting. Interestingly, loss of STAT6 resulted in anchorage-independent growth and changes in several genes involved in epithelial to mesenchymal transition. This study suggests that STAT6 may play a role in the pathophysiology of HER2+ human breast cancer.

SIRT7 Is a Prognostic Biomarker Associated With Immune Infiltration in Luminal Breast Cancer

Background: Sirtuin 7 (SIRT7), a protein-coding gene whose abnormal expression and function are associated with carcinogenesis. However, the prognosis of SIRT7 in different breast cancer subtypes and its correlation with tumor-infiltrating lymphocytes remain unclear.

Methods: The expression and survival data of SIRT7 in patients with breast cancer were analyzed using Tumor Immune Estimation Resource (TIMER), Gene Expression Profiling Interaction Analysis (GEPIA), The Human Protein Atlas (HPA), UALCAN, Breast Cancer Gene-Expression Miner (BC-GenExMiner), and Kaplan-Meier plotter databases. Also, the expression correlations between SIRT7 and immune infiltration gene markers were analyzed using TIMER and further verified the results using immunohistochemistry.

Results: SIRT7 exhibited higher expression levels in breast cancer tissues than the adjacent normal tissues. SIRT7 expression was significantly correlated with sample type, subclass, cancer stage, menopause status, age, nodal status, estrogen receptor (ER), progesterone receptor (PR), and triple-negative status. High SIRT7 expression was associated with poor prognosis in breast cancer-luminal A [overall survival (OS): hazard ratio (HR) = 1.54, p = 1.70e-02; distant metastasis-free survival (DMFS): HR = 1.56, p = 2.60e-03]. Moreover, the expression of SIRT7 was positively correlated with the expression of IRF5 (M1 macrophages marker, r = 0.165, p = 1.13e-04) and PD1 (T cell exhaustion marker, r = 0.134, p = 1.74e-03). These results suggested that the expression of SIRT7 was related to M1 macrophages and T cell exhaustion infiltration in breast cancer-luminal.

Conclusions: These findings demonstrate that the high expression of SIRT7 indicates poor prognosis in breast cancer as well as increased immune infiltration levels of M1 macrophages and T cell exhaustion in breast cancer-luminal. Thus, SIRT7 may serve as a candidate prognostic biomarker for determining prognosis associated with immune infiltration in breast cancer-luminal.

Transcriptomics-based screening of molecular signatures associated with patients overall survival and their key regulators in subtypes of breast cancer

Molecular subtypes of breast cancer are associated with differences in prognosis and strategies of molecular targeted therapies. Gene regulatory mechanisms as one of the reasons might modulate these differences. In the present study, we proposed a comprehensive data analysis and systems biology approach to explore molecular signatures which reduce the chance of patients overall survival and the possible mechanisms of their regulation by transcription factors (TFs) and microRNAs (miRNAs) in the main subtypes of breast tumor consist of Basal like, Her2 enriched, Luminal A and Luminal B breast cancer. In this regards, we used available microarray datasets to assess common differentially expressed genes (DEGs) in breast cancer subtypes. Using Kaplan-Meier curve analysis we identified common DEGs which are associated with decreasing in the overall survival of breast cancer patients. Furthermore, gene regulatory networks (GRNs) were depicted based on TFs and miRNAs with interest target genes. Then GRNs were analyzed and using five algorithms (Control centrality, Betweenness, Degree, Classification, and MCDS) the key regulators were identified for each subtype. In this study, we highlighted mechanisms underlying the regulation of breast cancer molecular signatures by TFs and miRNAs which their alteration reduce the chance of survival rate in each subtype of breast cancer. Our current study in a holistic insight revealed the importance of some genes and their regulators as potential prognostic markers and/or therapeutic targets in breast cancer patients.

MiR-124 reversed the doxorubicin resistance of breast cancer stem cells through STAT3/HIF-1 signaling pathways

Various drug treatments including doxorubicin (DOX) have been proved efficient in the suppression of breast cancer. Nonetheless, drug resistance became an obstacle in the therapeutic process. According to recent literatures, breast cancer stem cells (BCSCs) were considered contributing to drug resistance, besides, microRNAs (miRNAs) could regulate proteins associated with drug resistance in human breast cancer. To further understand the inner mechanism of drug resistance in breast cancer and look for remedy methods, we referred to bioinformatic analysis and predicted that signal transducer and activator of transcription 3 (STAT3) and miR-124 was overexpressed in MCF7-R cells (MCF7 cells resistant to DOX) compared with MCF cells. Expression levels of RNA and protein were separately determined by qRT-PCR and western blot. Dual luciferase assay was performed to verify the targeting relationship between STAT3 and miR-124. Optical density (OD) values and apoptotic rates of cells were respectively determined via MTT assays and flow cytometric analysis. Cell invasion was detected to verify drug resistance. Results of above assays indicated that STAT3 was highly expressed in MCF7-R cells than in MCF7 cell lines and affected doxorubicin resistance of BCSCs, and miR-124 reversed the doxorubicin resistance of breast cancer stem cells through targeting STAT3 to control the HIF-1 signaling pathway. To conclude, this research may be valuable for the treatment of breast cancer as the restoration of miR-124 and inhibition of STAT3 could be applied to therapeutic strategy and help overcome drug resistance.

Prognostic roles of signal transducers and activators of transcription family in human breast cancer

Signal transducers and activators of transcription (STAT) family are critical transcription factors, which have been proved as prognostic predictors for a number of cancers. However, the prognostic roles of STAT family in breast cancer patients remain in dispute. In the present study, we mined the ‘Kaplan–Meier plotter’ (KM plotter) online database to explore the prognostic roles of STAT family mRNA expression in breast cancer including overall survival (OS), progression-free survival (PFS), as well as post-progression survival (PPS). The results suggest high mRNA expression of all the individual STATs, except STAT1 and STAT2, are significantly associated with favorable OS in breast cancer patients; high STAT1 mRNA expression is significantly associated with worse RFS and all the other individual STATs, except STAT3, are significantly associated with better RFS in breast cancer patients; only high STAT5b mRNA expression is significantly related to better PPS in breast cancer patients. Additionally, we explored the prognostic values of individual STATs in other clinicopathological features, such as pathological grades, estrogen receptor (ER) status and so on. The results suggest, except STAT2 and STAT6, high mRNA expression of STATs is related to a favorable prognosis especially for high pathological grade; high STAT5 mRNA expression indicates a favorable prognosis no matter under ER positive or negative status; high STAT4 mRNA expression suggests a favorable prognosis under human epidermal growth factor receptor 2 (HER2) negative status. Our results indicate that individual STATs, except STAT1 and STAT2, may act as a favorable prognostic biomarker in breast cancer. Nevertheless, further investigations on a larger population are warranted.

Regulatory network of circRNA-miRNA-mRNA contributes to the histological classification and disease progression in gastric cancer

Background

Little has been known about the role of non-coding RNA regulatory network in the patterns of growth and invasiveness of gastric cancer (GC) development.

Methods

MicroRNAs (miRNAs) microarray was used to screen differential miRNA expression profiles in Ming’s classification. The significant differential expressions of representative miRNAs and their interacting circular RNA (circRNA) were confirmed in GC cell line and 63 pairs of GC samples. Then, a circRNA/miRNA network was constructed by bioinformatics approaches to identify molecular pathways. Finally, we explored the clinical value of the common targets in the pathway by using receiver operating characteristic curve and survival analysis.

Results

Significantly differential expressed miRNAs were found in two pathological types of GC. Both of miR-124 and miR-29b were consistently down-regulated in GC. CircHIPK3 could play a negative regulatory role on miR-124/miR-29b expression and associated with T stage and Ming’s classification in GC. The bioinformatics analyses showed that targets expression of circHIPK3-miR-124/miR-29b axes in cancer-related pathways was able to predict the status of GC and associated with individual survival time.

Conclusions

The targets of circHIPK3-miR-124/miR-29b axes involved in the progression of GC. CircHIPK3 could take part in the proliferation process of GC cell and may be potential biomarker in histological classification of GC.

Electronic supplementary material

The online version of this article (10.1186/s12967-018-1582-8) contains supplementary material, which is available to authorized users.