Exosomal circular RNAs derived from serum: Promising biomarkers for therapeutic targets and prognosis of triple-negative breast cancer (TNBC).

2020 ◽  
Vol 38 (15_suppl) ◽  
pp. 3528-3528
Author(s):  
Sujin Yang ◽  
Jinhai Tang
Keyword(s):  
Breast Cancer ◽  
Rna Sequencing ◽  
Therapeutic Targets ◽  
Bioinformatic Analysis ◽  
Circular Rnas ◽  
Invasion And Metastasis ◽  
Tnbc Cell ◽  
Tumor Tissues ◽  
Serum Exosomes ◽  
Proliferation And Invasion

3528 Background: Exosomes are well known by the "exosomal shuttle" that delivers oncogenic microRNAs (miRNAs), mRNAs, circular RNAs (circRNAs) and proteins to the recipient cells and tumor microenvironment, and may be used as promising biomarkers for disease diagnosis. This study aims to provide a theoretical basis to use stable exosomal circRNAs as new biomarkers for predicting the development, metastasis and therapeutic targets of TNBC. Methods: A strategy combining RNA-sequencing technique, bioinformatic analysis and RT-qPCR was used to determine the level of differential expressed circRNAs in serum exosomes samples (n = 43) from TNBC patients compared with non-TNBC patients. The expression of circHSDL2 were also detected in tumor tissues (n = 20) from TNBC patients and breast cancer cell lines by qRT-PCR. Cell cycle analysis, the wound healing assays and transwell assays were used to investigate the function of circHSDL2 in proliferation, invasion and metastasis of TNBC cells. FISH, dual-luciferase reporter and functional assays were performed to confirm the interaction between circHSDL2 and let-7a-2-3p in TNBC cells. Results: We profiled the circRNAs in the serum exosomes samples from TNBC patients and non-TNBC patients by RNA sequencing and detected 803 significantly differentially-expressed circRNAs. After bioinformatic analysis, circHSDL2 was chose to further study. RT-qPCR results showed that higher expression of circHSDL2 in TNBC cell lines and tumor tissues from TNBC patients. Moreover, overexpression of circHSDL2 promoted TNBC cells proliferation and invasion, while knockdown of circHSDL2 inhibited TNBC cells proliferation and invasion. Mechanistically, circHSDL2 acted as a "miRNAs sponge" to absorb let-7a-2-3p; let-7a-2-3p inhibited TNBC cell invasion and metastasis. Kaplan-Meier plots showed lower expression of let-7a-2-3p was connected to poor prognosis in TNBC metastasis patients from TCGA database. Conclusions: The expression of circHSDL2 was found significantly upregulated in serum exosomes and tumor tissues from TNBC patients. Moreover, circHSDL2 could promote cell proliferation, invasion and metastasis in TNBC cells. CircHSDL2 might be function as competing endogenous RNAs (ceRNAs) by targeting let-7a-2-3p in the progression of TNBC. Therefore, this study provides a fresh perspective on novel therapeutic targets and potential biomarkers for TNBC from exosomal circRNAs.

Identification of circRNA–miRNA networks for exploring an underlying prognosis strategy for breast cancer

Epigenomics ◽  
2020 ◽  
Vol 12 (2) ◽  
pp. 101-125 ◽  
Author(s):  
Su-jin Yang ◽  
Dan-dan Wang ◽  
Si-ying Zhou ◽  
Qian Zhang ◽  
Jin-yan Wang ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Tumor Development ◽  
Bioinformatic Analysis ◽  
Circular Rnas ◽  
Rna Seq ◽  
Quantitative Real Time Pcr ◽  
Combination Strategy ◽  
Competing Endogenous Rnas ◽  
Serum Exosomes ◽  
Insight Into

Aim: Circular RNAs (circRNAs) still have many potential functions in the process of tumor development that are not completely understood. The study aims to explore novel circRNAs and their mechanisms of action in breast cancer (BCa). Materials & methods: A combination strategy of RNA-sequencing (RNA-seq) technique, quantitative real-time PCR and bioinformatic analysis was employed to identify the potential mechanisms involving differentially expressed circRNAs in the serum exosomes and tissues of BCa patients. Results: The expression levels of hsa-circRNA-0005795 and hsa-circRNA-0088088 were significantly different both in serum exosomes and tissues and might function as competing endogenous RNAs and play vital roles in BCa development. Conclusion: We constructed two circRNA–miRNA networks and provided new insight into the prognosis and therapy of BCa using circRNAs from serum exosomes.

scholarly journals CircNR3C2 promotes HRD1-mediated tumor-suppressive effect via sponging miR-513a-3p in triple-negative breast cancer

2021 ◽  
Vol 20 (1) ◽  
Author(s):  
Ya Fan ◽  
Jia Wang ◽  
Wen Jin ◽  
Yifei Sun ◽  
Yuemei Xu ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Rna Sequencing ◽  
Cancer Progression ◽  
Triple Negative Breast Cancer ◽  
Triple Negative ◽  
Proteasomal Degradation ◽  
Circular Rnas ◽  
Mesenchymal Transition

Abstract Background E3 ubiquitin ligase HRD1 (HMG-CoA reductase degradation protein 1, alias synoviolin with SYVN1 as the official gene symbol) was found downregulated and acting as a tumor suppressor in breast cancer, while the exact expression profile of HRD1 in different breast cancer subtypes remains unknown. Recent studies characterized circular RNAs (circRNAs) playing an regulatory role as miRNA sponge in tumor progression, presenting a new viewpoint for the post-transcriptional regulation of cancer-related genes. Methods Examination of the expression of HRD1 protein and mRNA was implemented using public microarray/RNA-sequencing datasets and breast cancer tissues/cell lines. Based on public RNA-sequencing results, online databases and enrichment/clustering analyses were used to predict the specific combinations of circRNA/miRNA that potentially govern HRD1 expression. Gain-of-function and rescue experiments in vitro and in vivo were executed to evaluate the suppressive effects of circNR3C2 on breast cancer progression through HRD1-mediated proteasomal degradation of Vimentin, which was identified using immunoblotting, immunoprecipitation, and in vitro ubiquitination assays. Results HRD1 is significantly underexpressed in triple-negative breast cancer (TNBC) against other subtypes and has an inverse correlation with Vimentin, inhibiting the proliferation, migration, invasion and EMT (epithelial-mesenchymal transition) process of breast cancer cells via inducing polyubiquitination-mediated proteasomal degradation of Vimentin. CircNR3C2 (hsa_circ_0071127) is also remarkably downregulated in TNBC, negatively correlated with the distant metastasis and lethality of invasive breast carcinoma. Overexpressing circNR3C2 in vitro and in vivo leads to a crucial enhancement of the tumor-suppressive effects of HRD1 through sponging miR-513a-3p. Conclusions Collectively, we elucidated a bona fide circNR3C2/miR-513a-3p/HRD1/Vimentin axis that negatively regulates the metastasis of TNBC, suggesting that circNR3C2 and HRD1 can act as potential prognostic biomarkers. Our study may facilitate the development of therapeutic agents targeting circNR3C2 and HRD1 for patients with aggressive breast cancer.

MicroRNA profiling in serum: Potential signatures for breast cancer diagnosis

2020 ◽  
pp. 1-13
Author(s):  
Xuan Zou ◽  
Tiansong Xia ◽  
Minghui Li ◽  
Tongshan Wang ◽  
Ping Liu ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Mirna Expression ◽  
Expression Patterns ◽  
External Validation ◽  
Breast Cancer Diagnosis ◽  
Serum Samples ◽  
Circulating Micrornas ◽  
Non Invasive ◽  
Tumor Tissues ◽  
Serum Exosomes

BACKGROUND: Circulating microRNAs (miRNAs) prove to be potential non-invasive indicators of cancers. The purpose of this study is to profile serum miRNA expression in breast cancer (BC) patients to find potential biomarkers for BC diagnosis. METHODS: The miRNA expression patterns of serum samples from 216 BC patients and 214 normal control subjects were compared. A four-phase validation was conducted for biomarker identification. In the screening phase, the Exiqon miRNA qPCR panel was employed to select candidates, which were further analyzed by quantitative reverse transcriptase PCR in the following training, testing, and external validation phases. RESULTS: A 12-miRNA (let-7b-5p, miR-106a-5p, miR-19a-3p, miR-19b-3p, miR-20a-5p, miR-223-3p, miR-25-3p, miR-425-5p, miR-451a, miR-92a-3p, miR-93-5p, and miR-16-5p) panel in serum was constructed. The diagnostic performance of the panel was assessed using ROC curve analyses. The area under the curves (AUCs) were 0.952, 0.956, 0.941 and 0.950 for the four separate phases, respectively. Additionally, the expression features of the 12 miRNAs were further explored in 32 pairs of BC tumor and para-tumor tissues, and 32 pairs of serum exosomes samples from patients and healthy subjects. miR-16-5p, miR-106a-5p, miR-25-3p, miR-425-5p, and miR-93-5p were highly overexpressed and let-7b-5p was conversely downregulated in tumor tissues. Excluding miR-20a-5p and miR-223-3p, the 10 other miRNAs were all significantly upregulated in BC serum-derived exosomes. CONCLUSION: A signature consisting of 12 serum miRNAs was identified and showed potential for use in non-invasive diagnosis of BC.

scholarly journals RNA-Sequencing Reveals Heat Shock 70-kDa Protein 6 (HSPA6) as a Novel Thymoquinone-Upregulated Gene That Inhibits Growth, Migration, and Invasion of Triple-Negative Breast Cancer Cells

2021 ◽  
Vol 11 ◽  
Author(s):  
Shiyi Shen ◽  
Chunli Wei ◽  
Junjiang Fu
Keyword(s):  
Breast Cancer ◽  
Rna Sequencing ◽  
Triple Negative Breast Cancer ◽  
Triple Negative ◽  
Regulatory Mechanism ◽  
Kegg Pathway ◽  
Migration And Invasion ◽  
Tnbc Cell ◽  
Anti Cancer ◽  
Cancer Tissues

ObjectiveBreast cancer has become the first highest incidence which surpasses lung cancer as the most commonly diagnosed cancer, and the second highest mortality among women worldwide. Thymoquinone (TQ) is a key component from black seed oil and has anti-cancer properties in a variety of tumors, including triple-negative breast cancer (TNBC).MethodsRNA-sequencing (RNA-seq) was conducted with and without TQ treatment in TNBC cell line BT-549. Gene Ontology (GO) function classification annotation, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses for these genes were conducted. Western blot and semi-quantitative RT-PCR were used to verify the regulated gene. Functional assays by overexpression or knocking down were performed for HSPA6 and its mediator TQ for inhibiting growth, migration and invasion of TNBC cells. The regulatory mechanisms and prognosis for HSPA6 for breast cancer survival were conducted through bioinformatics and online databases.ResultsAs a result, a total of 141 downregulated and 28 upregulated genes were identified and 18 differentially expressed genes, which might be related to carcinomas, were obtained. Interestingly, GO and KEGG pathway showed their roles on anti-cancer and anti-virus. Further analysis found that the HSPA6 gene was the high significantly upregulated gene, and showed to inhibit TNBC cell growth, migration and invasion. High expression of HSPA6 was positively correlated with long overall survival (OS) in patients with breast cancer, indicating the tumor-suppressive roles for HSPA6. But DNA methylation of HSPA6 may not be the regulatory mechanism for HSPA6 mRNA upregulation in breast cancer tissues, although the mRNA levels of HSPA6 were increased in these cancer tissues compared with normal tissues. Moreover, TQ enhanced the inhibitory effect of migration and invasion when HSPA6 was overexpressed; while HSPA6 was knocked down, TQ attenuated the effects of HSPA6-promoted migration and invasion, demonstrating a partially dependent manner through HSPA6 by TQ treatment.ConclusionWe have successfully identified a novel TQ-targeted gene HSPA6, which shows the inhibitory effects on growth, migration and invasion in TNBC cells. Therefore, identification of HSPA6 not only reveals a new TQ regulatory mechanism, but also provides a novel candidate gene for clinical management and treatment of breast cancer, particularly for TNBC.

scholarly journals Transcriptome Analysis Reveals MFGE8-HAPLN3 Fusion as a Novel Biomarker in Triple-Negative Breast Cancer

2021 ◽  
Vol 11 ◽  
Author(s):  
Meng-Yuan Wang ◽  
Man Huang ◽  
Chao-Yi Wang ◽  
Xiao-Ying Tang ◽  
Jian-Gen Wang ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Rna Sequencing ◽  
Triple Negative Breast Cancer ◽  
Triple Negative ◽  
Fusion Transcript ◽  
Sequencing Data ◽  
Chromosome 11 ◽  
Fusion Transcripts ◽  
Tumor Tissues ◽  
Fusion Type

BackgroundTriple-negative breast cancer (TNBC) is a highly aggressive cancer with poor prognosis. The lack of effective targeted therapies for TNBC remains a profound clinical challenge. Fusion transcripts play critical roles in carcinogenesis and serve as valuable diagnostic and therapeutic targets in cancer. The present study aimed to identify novel fusion transcripts in TNBC.MethodsWe analyzed the RNA sequencing data of 360 TNBC samples to identify and filter fusion candidates through SOAPfuse and ChimeraScan analysis. The characteristics, including recurrence, fusion type, chromosomal localization, TNBC subgroup distribution, and clinicopathological correlations, were analyzed in all candidates. Furthermore, we selected the promising fusion transcript and predicted its fusion type and protein coding capacity.ResultsUsing the RNA sequencing data, we identified 189 fusion transcripts in TNBC, among which 22 were recurrent fusions. Compared to para-tumor tissues, TNBC tumor tissues accumulated more fusion events, especially in high-grade tumors. Interestingly, these events were enriched at specific chromosomal loci, and the distribution pattern varied in different TNBC subtypes. The vast majority of fusion partners were discovered on chromosomes 1p, 11q, 19p, and 19q. Besides, fusion events mainly clustered on chromosome 11 in the immunomodulatory subtype and chromosome 19 in the luminal androgen receptor subtype of TNBC. Considering the tumor specificity and frameshift mutation, we selected MFGE8-HAPLN3 as a novel biomarker and further validated it in TNBC samples using PCR and Sanger sequencing. Further, we successfully identified three types of MFGE8-HAPLN3 (E6-E2, E5-E3, and E6-E3) and predicted the ORF of E6-E2, which could encode a protein of 712 amino acids, suggesting its critical role in TNBC.ConclusionsImproved bioinformatic stratification and comprehensive analysis identified the fusion transcript MFGE8-HAPLN3 as a novel biomarker with promising clinical application in the future.

Extracellular circular RNAs to promote the growth and metastasis of triple-negative breast cancer through remodeling the tumor immune microenvironment.

2021 ◽  
Vol 39 (15_suppl) ◽  
pp. e13047-e13047
Author(s):  
Sujin Yang ◽  
Jinhai Tang
Keyword(s):  
Breast Cancer ◽  
Cancer Patients ◽  
Cell Lines ◽  
Target Genes ◽  
Triple Negative ◽  
Circular Rnas ◽  
Breast Cancer Patients ◽  
Immune Microenvironment ◽  
Tnbc Cell ◽  
High Degree

e13047 Background: Triple-negative breast cancer (TNBC) has been confirmed to have a high degree of heterogeneity of breast cancer, which is more common in young women, with a high degree of malignancy, lack of effective clinical treatment and poor prognosis. Recently, many studies have also found that immune microenvironment (IME) can remarkablely affect the occurrence and metastasis of TNBC through exosome-mediated molecular transmission. Therefore, there is an urgent need to find new immune-related molecules as therapeutic targets and to predict the progress of TNBC and prognosis of treatment. Methods: Using RNA-sequencing and bioinformatics analysis, we found the differential-expressed circular RNAs (circRNAs) in exosomes from TNBC cell lines (BT549 and MDA-MB-231), non-TNBC cell lines (MCF-7 and MCF-10A) and tissues from breast cancer patients. Then, we used CIBERSORT and ESTIMATE algorithm to explore the tumor-infiltrating immune cells (TICs) or stromal components in IME, and identified the significant differential-expressed mRNAs in the immune cells between TNBC and non-TNBC samples. RT-qPCR was used to confirm the expression level of selected circRNAs and mRNAs in TNBC cell lines. Results: We profiled the circRNAs in the exosomes from TNBC cell lines and breast cancer patients by RNA sequencing and detected 27 significantly differentially-expressed circRNAs. After bioinformatic analysis and RT-qPCR, circRELB and circANXA1 were chose to further study. TICs and IME scores were found to associated with the survival and clinicopathological characteristics of TNBC patients and IME remodeling. Interestingly, 92 differentially-expressed genes were found to be enriched in the NF-kB signaling pathway and mTOR signaling pathway. Moreover, we identified 33 target genes of circRELB and circANXA1 by cross-analysis. Based on the predicted miRNAs and the corresponding mRNAs and circRNAs, we have established an IME-related circRNA-miRNA-mRNA network. Then, Kaplan-Meier plots showed the expression levels of certain targeted genes (PTEN, CCND1, IL6, CDKN1A, AKT1, TNF and WNT1) were connected to prognosis in TNBC metastasis patients. Conclusions: The expression levels of circRELB and circANXA1 was found significantly upregulated in exosomes from TNBC cell lines and tumor tissues from breast cancer patients. In addition, circRELB and circANXA1could affect the expression of downstream target genes by competing for endogenous RNA (ceRNAs), and ultimately promote the metastasis of TNBC and remodeling of IME. In summary, this study analyzes the mechanisms of exosome-contained circRNAs in TNBC and these targets from the IME-related circRNA-miRNA-mRNA network may be new potential prognostic biomarkers and immune treatment strategies to prevent the development and metastasis of TNBC.

scholarly journals Identification of differentially expressed lncRNAs and mRNAs in luminal-B breast cancer by RNA-sequencing

BMC Cancer ◽  
2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Cheng-Liang Yuan ◽  
Xiang-Mei Jiang ◽  
Ying Yi ◽  
Jian-Fei E ◽  
Nai-Dan Zhang ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Rna Sequencing ◽  
Differentially Expressed ◽  
Receptor Interaction ◽  
Cancer Tissue ◽  
Tissue Samples ◽  
Luminal B ◽  
Ppi Networks ◽  
Tumor Tissues ◽  
Cancer Tumor

Abstract Background Luminal B cancers show much worse outcomes compared to luminal A. This present study aims to screen key lncRNAs and mRNAs correlated with luminal-B breast cancer. Methods Luminal-B breast cancer tissue samples and adjacent tissue samples were obtained from 4 patients with luminal-B breast cancer. To obtain differentially expressed mRNAs (DEmRNAs) and lncRNAs (DElncRNAs) between luminal-B breast cancer tumor tissues and adjacent tissues, RNA-sequencing and bioinformatics analysis were performed. Functional annotation of DEmRNAs and protein-protein interaction networks (PPI) construction were performed. DEmRNAs transcribed within a 100 kb window up- or down-stream of DElncRNAs were searched, which were defined as cis nearby-targeted DEmRNAs of DElncRNAs. DElncRNA-DEmRNA co-expression networks were performed. The mRNA and lncRNA expression profiles were downloaded from The Cancer Genome Atlas (TCGA) database to validate the expression patterns of selected DEmRNAs and DElncRNAs. Results A total of 1178 DEmRNAs and 273 DElncRNAs between luminal-B breast cancer tumor tissues and adjacent tissues were obtained. Hematopoietic cell lineage, Cytokine-cytokine receptor interaction, Cell adhesion molecules (CAMs) and Primary immunodeficiency were significantly enriched KEGG pathways in luminal-B breast cancer. FN1, EGFR, JAK3, TUBB3 and PTPRC were five hub proteins of the PPI networks. A total of 99 DElncRNAs-nearby-targeted DEmRNA pairs and 1878 DElncRNA-DEmRNA co-expression pairs were obtained. Gene expression results validated in TCGA database were consistent with our RNA-sequencing results, generally. Conclusion This study determined key genes and lncRNAs involved in luminal-B breast cancer, which expected to present a new avenue for the diagnosis and treatment of luminal-B breast cancer.

scholarly journals Network pharmacology and RNA sequencing studies on triterpenoid saponins from Bupleurum chinense for the treatment of breast cancer

RSC Advances ◽  
2019 ◽  
Vol 9 (70) ◽  
pp. 41088-41098
Author(s):  
Danqi Li ◽  
Da Liu ◽  
Dandan Yue ◽  
Pinyi Gao ◽  
Cheng Du ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Rna Sequencing ◽  
Therapeutic Targets ◽  
Network Pharmacology ◽  
Biological Mechanisms ◽  
Triterpenoid Saponins ◽  
Sequencing Studies

The network pharmacology and RNA sequencing studies were used to explore potential therapeutic targets and biological mechanisms of B. chinense for the treatment of breast cancer.

scholarly journals miR-425 suppresses EMT and inhibits the development of TNBC (triple-negative breast cancer) by targeting TGF-β 1/SMAD 3 signaling pathway

2018 ◽  
Author(s):  
Yingping Liu ◽  
Hongfei Qiao ◽  
Jinglong Chen
Keyword(s):  
Breast Cancer ◽  
Signaling Pathway ◽  
Cell Lines ◽  
Mesenchymal Cell ◽  
Cell Proliferation And Migration ◽  
Tnbc Cell ◽  
Tumor Tissues ◽  
And Migration ◽  
Tgf Β1 ◽  
Proliferation And Migration

AbstractBackgroundEMT has the crucial effect on the progression and metastasis of tumor. This work will elucidate the role of miR-425 in EMT and development of TNBC.MethodsThe differential miRNA expression among non-tumor, para-tumor (adjacent tissue of tumor) and tumor tissues was analyzed. The luciferase activities of TGF-β1 3’ UTR treated with miR-425 were determined. Then human breast cancer cell lines were dealt with mimics or inhibitors of miR-425, and then the cell proliferation and migration, invasion ability were assessed. The expression of TGF-β1 and markers of epithelial cell and mesenchymal cell were analyzed. The influences of miR-425 on development of TNBC through inducing EMT by targeting TGF-β 1 and TGF-β1/SMAD3 signaling pathway in TNBC cell lines were investigated. Furthermore, Xenograft mice were used to explore the potential roles of miR-425 on EMT and development of TNBC in vivo.ResultsCompared with non-tumor tissues, 9 miRNAs were upregulated and 3 miRNAs were down-regulated in tumor tissues. The relative expression of miR-425 in tumor tissues was obviously much lower than that in para-tumor and non-tumor tissues. MiR-425 suppressed TGF-β1 expression, additionally inhibited expression of mesenchymal cell markers, while exerted effects on cell proliferation and migration of TNBC cell lines. Moreover, the agomir of miR-425 could protect against development process in murine TNBC xenogarft model.ConclusionsOur results demonstrated that miR-425 targets to TGF-β1, and was a crucial suppressor on EMT and development of TNBC through inhibiting TGF-β1/SMAD3 signaling pathway. It suggested that aim at TGF-β1/SMAD3 signaling pathway by enhancing relative miR-425 expression, was a feasible therapy strategy for TNBC.

Quantitative proteomics reveals stage-specific protein regulation of triple negative breast cancer

2020 ◽  
Author(s):  
Yuxiang Lin ◽  
Ling Lin ◽  
Fangmeng Fu ◽  
Chuan Wang ◽  
Anqi Hu ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Signaling Pathways ◽  
Quantitative Proteomics ◽  
Protein Identification ◽  
High Resolution Mass Spectrometry ◽  
Therapeutic Targets ◽  
Differentially Expressed ◽  
Amino Acid Synthesis ◽  
Tumor Tissues ◽  
Grade Iii

Abstract BackgroundTriple negative breast cancer (TNBC) is a heterogeneous disease with more aggressive clinical courses than other subtypes of breast cancer. In this study, we performed high-resolution mass spectrometry-based quantitative proteomics with TNBC clinical tissue specimens to explore the early and sensitive diagnostic signatures and potential therapeutic targets for TNBC patients. Methods We performed an iTRAQ-labeling coupled LC-MS/MS approach to explore the global proteome in tumor tissues and corresponding para-tumor tissues from 24 patients with grade I-II and grade III primary TNBC. Relative peptide quantification and protein identification were performed by Proteome Discoverer TM software with Mascot search engine. Differentially expressed proteins were analyzed by bioinformatic analyses, including GO function classification annotation and KEGG enrichment analysis. Pathway analyses for protein-protein interactions and upstream regulations of differentially expressed candidates were performed by Ingenuity Pathway Analysis (IPA) software. Results Totally, 5,401 unique proteins were identified and quantified in different stage of TNBCs. 865 proteins were changed in patients with grade I or II TNBC, among which 309 were up-regulated and 556 were down-regulated. Meanwhile, for patients with grade III TNBC, 359 proteins were increased and 672 proteins were decreased. Comparing to para-cancerous tissues, various signaling pathways and metabolic processes, including PPAR pathways, PI3K-Akt pathway, one-carbon metabolism, amino acid synthesis, and lipid metabolism were activated in TNBC cancer tissues. Death receptor signaling was significantly activated in grade I-II TNBCs, however, remarkably inhibited in grade III TNBCs. Conclusions Overall, our proteomic data presented precise quantification of potential signatures, signaling pathways, regulatory networks, and characteristic differences in each clinicopathological subgroup. The proteome provides complementary information for TNBC accurate subtype classification and therapeutic targets research.

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