Identification of the anti-breast cancer targets of triterpenoids in Liquidambaris Fructus and the hints for its traditional applications

Abstract Background Liquidambaris Fructus is the infructescences of Liquidambar formosana Hance and it has been used to treat some breast disease in Traditional Chinese Medicine. In the previous study we found the anti-breast cancer effect of triterpenoid in Liquidambaris Fructus. This study is a further investigation of the triterpenoids in Liquidambaris Fructus and aims to identify their anti-breast cancer targets, meanwhile, to estimate the rationality of the traditional applications of Liquidambaris Fructus. Methods Triterpenoids in Liquidambaris Fructus were isolated and their structures were identified by NMR spectrums. Potential targets of these triterpenoids were predicted using a reverse pharmacophore mapping strategy. Associations between these targets and the therapeutic targets of breast cancer were analyzed by constructing protein-protein interaction network, and targets played important roles in the network were identified using Molecular Complex Detection method. Binding affinity between the targets and triterpenoids was studied using molecular docking method. Gene ontology enrichment analysis was conducted to reveal the biological process and signaling pathways that the identified targets were involved in. Results Thirteen triterpenoids were identified and 6 of them were the first time isolated from Liquidambaris Fructus. Predicted ADME properties revealed a good druggability of these triterpenoids. We identified 18 protein targets which were closely related to breast cancer progression, especially triple-negative, basal-like or advanced stage breast cancers. The triterpenoids could bind with these targets as their inhibitors: hydrophobic skeleton is a favorable factor for them to stabilize at binding site and polar C17- or C3- substituent was necessary for binding. GO enrichment analysis indicated that inhibition of protein tyrosine kinases autophosphorylation might be the primary mechanism for the anti-breast cancer effect of the triterpenoids, and ErbB4 and EGFR were the most relevant targets. Conclusions The study revealed that triterpenoids from Liquidambaris Fructus might exert anti-breast cancer effect by directly inhibit multiple protein targets and signaling pathways, especially ErbB4 and EGFR and related pathways. This study also brings up another hint that the traditional applications of Liquidambaris Fructus on hypogalactia should be reassessed systematically because it might suppress rather than promote lactation by inhibiting the activity of ErbB4.

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Role of the NUDT Enzymes in Breast Cancer

International Journal of Molecular Sciences ◽

10.3390/ijms22052267 ◽

2021 ◽

Vol 22 (5) ◽

pp. 2267

Author(s):

Roni H. G. Wright ◽

Miguel Beato

Keyword(s):

Breast Cancer ◽

Signaling Pathways ◽

Cancer Progression ◽

Breast Cancers ◽

Metastatic Colonization ◽

Hormone Receptor Positive ◽

Aggressive Cancer ◽

Cancer Types ◽

Metastatic Process

Despite global research efforts, breast cancer remains the leading cause of cancer death in women worldwide. The majority of these deaths are due to metastasis occurring years after the initial treatment of the primary tumor and occurs at a higher frequency in hormone receptor-positive (Estrogen and Progesterone; HR+) breast cancers. We have previously described the role of NUDT5 (Nudix-linked to moiety X-5) in HR+ breast cancer progression, specifically with regards to the growth of breast cancer stem cells (BCSCs). BCSCs are known to be the initiators of epithelial-to-mesenchyme transition (EMT), metastatic colonization, and growth. Therefore, a greater understanding of the proteins and signaling pathways involved in the metastatic process may open the door for therapeutic opportunities. In this review, we discuss the role of NUDT5 and other members of the NUDT family of enzymes in breast and other cancer types. We highlight the use of global omics data based on our recent phosphoproteomic analysis of progestin signaling pathways in breast cancer cells and how this experimental approach provides insight into novel crosstalk mechanisms for stratification and drug discovery projects aiming to treat patients with aggressive cancer.

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Deciphering of Key Pharmacological Pathways of Poria Cocos Intervention in Breast Cancer Based on Integrated Pharmacological Method

Evidence-based Complementary and Alternative Medicine ◽

10.1155/2020/4931531 ◽

2020 ◽

Vol 2020 ◽

pp. 1-11

Author(s):

Xiaoran Ma ◽

Jibiao Wu ◽

Cun Liu ◽

Jie Li ◽

Shixia Dong ◽

...

Keyword(s):

Breast Cancer ◽

Molecular Mechanisms ◽

Interaction Network ◽

Enrichment Analysis ◽

Gene Set Enrichment Analysis ◽

Network Pharmacology ◽

Breast Cancers ◽

Active Ingredients ◽

Poria Cocos ◽

Pharmacological Method

Objective. Poria cocos (Fuling), a natural plant, has recently emerged as a promising strategy for cancer treatment. However, the molecular mechanisms of Poria cocos action in breast cancer remain poorly understood. Methods. TCMSP database was used to screen the potential active ingredients in Poria cocos. GEO database was used to identify differentially expressed genes. Network pharmacology was used to identify the specific pathways and key target proteins related to breast cancer. Finally, molecular docking was used to validate the results. Results. In our study, 237 targets were predicted for 15 potential active ingredients found in Poria cocos. An interaction network of predicted targets and genes differentially regulated in breast cancers was constructed. Based on the constructed network and further analysis including network topology, KEGG, survival analysis, and gene set enrichment analysis, 3 primary nodes were identified as key potential targets that were significantly enriched in the PPAR signaling pathway. Conclusion. The results showed that potential active ingredients of Poria cocos might interfere with breast cancer through synergistic regulation of PTGS2, ESR1, and FOS.

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E3 ligase-inactivation rewires CBL interactome to elicit oncogenesis by hijacking RTK–CBL–CIN85 axis

Oncogene ◽

10.1038/s41388-021-01684-x ◽

2021 ◽

Vol 40 (12) ◽

pp. 2149-2164

Author(s):

Syed Feroj Ahmed ◽

Lori Buetow ◽

Mads Gabrielsen ◽

Sergio Lilla ◽

Gary J. Sibbet ◽

...

Keyword(s):

Breast Cancer ◽

Cancer Progression ◽

Tyrosine Kinases ◽

Myeloproliferative Neoplasms ◽

Inverse Correlation ◽

Receptor Protein ◽

Cancer Tissue ◽

Endosomal Trafficking ◽

Breast Cancers ◽

Human Breast Cancer Tissue

AbstractCasitas B-lineage lymphoma (CBL) is a ubiquitin ligase (E3) that becomes activated upon Tyr371-phosphorylation and targets receptor protein tyrosine kinases for ubiquitin-mediated degradation. Deregulation of CBL and its E3 activity is observed in myeloproliferative neoplasms and other cancers, including breast, colon, and prostate cancer. Here, we explore the oncogenic mechanism of E3-inactive CBL mutants identified in myeloproliferative neoplasms. We show that these mutants bind strongly to CIN85 under normal growth conditions and alter the CBL interactome. Lack of E3 activity deregulates CIN85 endosomal trafficking, leading to an altered transcriptome that amplifies signaling events to promote oncogenesis. Disruption of CBL mutant interactions with EGFR or CIN85 reduces oncogenic transformation. Given the importance of the CBL–CIN85 interaction in breast cancers, we examined the expression levels of CIN85, CBL, and the status of Tyr371-phosphorylated CBL (pCBL) in human breast cancer tissue microarrays. Interestingly, pCBL shows an inverse correlation with both CIN85 and CBL, suggesting that high expression of inactivated CBL could coordinate with CIN85 for breast cancer progression. Inhibition of the CBL–CIN85 interaction with a proline-rich peptide of CBL that binds CIN85 reduced the proliferation of MDA-MB-231 cells. Together, these results provide a rationale for exploring the potential of targeting the EGFR–CBL–CIN85 axis in CBL-inactivated mutant cancers.

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A systems pharmacology approach to determine the mechanisms of action of pleiotropic natural products in breast cancer from transcriptome data

10.1101/2020.04.18.048454 ◽

2020 ◽

Author(s):

Regan Odongo ◽

Asuman Demiroğlu Zergeroğlu ◽

Tunahan Çakir

Keyword(s):

Breast Cancer ◽

Natural Products ◽

Signaling Pathways ◽

Interaction Network ◽

Mechanisms Of Action ◽

Oncogenic Signaling ◽

Protein Protein Interaction ◽

Systemic Mechanism ◽

Pathway Interaction ◽

Oncogenic Signaling Pathways

AbstractPlant-derived compounds as natural products have attracted a lot of attention in the treatment of complex diseases, especially cancers, primarily due to their poly-pharmacologic mechanisms of action. However, methodological limitations have impeded gaining complete knowledge of their molecular targets. While most of the current understanding of these compounds is based on reductive methods, it is increasingly becoming clear that holistic techniques, leveraging current improvements in omic data collection and bioinformatics methods, are better suited for elucidating their systemic effects. Here, to provide an explanation to the mechanisms of action of plant-derived natural products in breast cancer, we applied a data integration approach to comprehensively study oncogenic signaling pathways targeted by withaferin A, actein, compound kushen injection and indole-3-carbinol. Specifically, we mapped the transcriptome-level response of cancer cell lines to these molecules on a human protein-protein interaction network and constructed the underlying active subnetworks. We used these subnetworks to define the perturbed signaling pathways and validated their relevance in carcinogenesis. The similarity of each identified oncogenic signaling pathway in terms of overlapping genes was subsequently used to construct pathway-pathway interaction networks, which were used to reduce pathway redundancy and to identify pathway crosstalk. Filtered pathways were then mapped on three major carcinogenesis processes. The results showed that the pleiotropic effects of plant-derived drugs at the gene expression level can be used to predict targeted pathways. Thus, from such pathways, it is possible to infer a systemic mechanism of action of such natural products.

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Evaluation of the TRIP13 level in breast cancer and insights into potential molecular pathways

10.21203/rs.3.rs-19358/v1 ◽

2020 ◽

Author(s):

Jin Lan ◽

Jingzhan Huang ◽

Yuan Gao ◽

Jingbo Sun ◽

Longshan Zhang ◽

...

Keyword(s):

Breast Cancer ◽

Therapeutic Target ◽

Cancer Metastasis ◽

Interaction Network ◽

Enrichment Analysis ◽

Bioinformatic Analysis ◽

Breast Cancer Metastasis ◽

Gene Set Enrichment Analysis ◽

Protein Protein Interaction ◽

Kaplan Meier

Abstract Background: TRIP13 is a member belonging to a large AAA+ ATPases protein super family. Emerging evidences had shown that TRIP13 may serve as an oncogene However, the function of TRIP13 in BC has not yet been elucidated. Methods: By utilizing the multiple database across BC, we presented the expression of TRIP13 in BC tissue and normal control. We then verified the expression of TRIP13 in patients with BC by immunohistochemical (IHC) staining. Kaplan-Meier plots were used to perform the survival analysis. Further, gene ontology (GO) analysis, gene set enrichment analysis (GSEA), and PPI (protein-protein interaction) network were performed to explore the biological function and potential regular pathway of TRIP13 in BC. Results: The multiple database and immunohistochemical (IHC) showed that higher TRIP13 expression in BC tissue compared to normal tissue. TRIP13 was highly exprssed in lung metastasis lesion compared with primary tumor in our BALB/C mice 4T1 BC models. Kaplan-Meier plots also revealed that high TRIP13 expression correlated to poor survival in patients with BC. Moreover, GSEA analysis revealed that TRIP13 was primarily enriched in the processes of cell division and proliferation. Finally 10 hub genes with a high score of connectivity were filtered from the PPI network, including MAD2L1, CDC20, CDC5L, CDK1, CCNA2, BUB1B, RAD51, SPO11, KIF11 and AURKB. Conclusion: High TRIP13 expression predicted poor prognosis and contributed tumor growth and metastasis in the BC. Thus, ARL3 may be a prognostic marker and therapeutic target for glioma. TRIP13 may be a favorable biomarker and effective therapeutic target for BC. Keywords: TRIP13; breast cancer; metastasis; bioinformatic analysis, prognosis

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Bioinformatics Analysis Reveals Functions of MicroRNAs in Rice Under the Drought Stress

Current Bioinformatics ◽

10.2174/1574893615666200207092410 ◽

2021 ◽

Vol 15 (8) ◽

pp. 927-936 ◽

Cited By ~ 3

Author(s):

Yan Peng ◽

Yuewu Liu ◽

Xinbo Chen

Keyword(s):

Drought Stress ◽

Target Genes ◽

Hot Spot ◽

Interaction Network ◽

Enrichment Analysis ◽

Differentially Expressed ◽

Protein Protein Interaction ◽

Promising Tool ◽

Differentially Expressed Mirnas ◽

Aba Biosynthesis

Background: Drought is one of the most damaging and widespread abiotic stresses that can severely limit the rice production. MicroRNAs (miRNAs) act as a promising tool for improving the drought tolerance of rice and have become a hot spot in recent years. Objective: In order to further extend the understanding of miRNAs, the functions of miRNAs in rice under drought stress are analyzed by bioinformatics. Method: In this study, we integrated miRNAs and genes transcriptome data of rice under the drought stress. Some bioinformatics methods were used to reveal the functions of miRNAs in rice under drought stress. These methods included target genes identification, differentially expressed miRNAs screening, enrichment analysis of DEGs, network constructions for miRNA-target and target-target proteins interaction. Results: (1) A total of 229 miRNAs with differential expression in rice under the drought stress, corresponding to 73 rice miRNAs families, were identiﬁed. (2) 1035 differentially expressed genes (DEGs) were identified, which included 357 up-regulated genes, 542 down-regulated genes and 136 up/down-regulated genes. (3) The network of regulatory relationships between 73 rice miRNAs families and 1035 DEGs was constructed. (4) 25 UP_KEYWORDS terms of DEGs, 125 GO terms and 7 pathways were obtained. (5) The protein-protein interaction network of 1035 DEGs was constructed. Conclusion: (1) MiRNA-regulated targets in rice might mainly involve in a series of basic biological processes and pathways under drought conditions. (2) MiRNAs in rice might play critical roles in Lignin degradation and ABA biosynthesis. (3) MiRNAs in rice might play an important role in drought signal perceiving and transduction.

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CBP/p300: Critical Co-Activators for Nuclear Steroid Hormone Receptors and Emerging Therapeutic Targets in Prostate and Breast Cancers

Cancers ◽

10.3390/cancers13122872 ◽

2021 ◽

Vol 13 (12) ◽

pp. 2872

Author(s):

Aaron R. Waddell ◽

Haojie Huang ◽

Daiqing Liao

Keyword(s):

Breast Cancer ◽

Prostate Cancer ◽

Tumor Growth ◽

Signaling Pathways ◽

Cell Cycle Progression ◽

Hormone Receptors ◽

Steroid Hormone Receptors ◽

Breast Cancers ◽

Creb Binding Protein ◽

Breast And Prostate Cancer

The CREB-binding protein (CBP) and p300 are two paralogous lysine acetyltransferases (KATs) that were discovered in the 1980s–1990s. Since their discovery, CBP/p300 have emerged as important regulatory proteins due to their ability to acetylate histone and non-histone proteins to modulate transcription. Work in the last 20 years has firmly established CBP/p300 as critical regulators for nuclear hormone signaling pathways, which drive tumor growth in several cancer types. Indeed, CBP/p300 are critical co-activators for the androgen receptor (AR) and estrogen receptor (ER) signaling in prostate and breast cancer, respectively. The AR and ER are stimulated by sex hormones and function as transcription factors to regulate genes involved in cell cycle progression, metabolism, and other cellular functions that contribute to oncogenesis. Recent structural studies of the AR/p300 and ER/p300 complexes have provided critical insights into the mechanism by which p300 interacts with and activates AR- and ER-mediated transcription. Breast and prostate cancer rank the first and forth respectively in cancer diagnoses worldwide and effective treatments are urgently needed. Recent efforts have identified specific and potent CBP/p300 inhibitors that target the acetyltransferase activity and the acetytllysine-binding bromodomain (BD) of CBP/p300. These compounds inhibit AR signaling and tumor growth in prostate cancer. CBP/p300 inhibitors may also be applicable for treating breast and other hormone-dependent cancers. Here we provide an in-depth account of the critical roles of CBP/p300 in regulating the AR and ER signaling pathways and discuss the potential of CBP/p300 inhibitors for treating prostate and breast cancer.

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Decoding the molecular mechanism of parthenocarpy in Musa spp. through protein–protein interaction network

Scientific Reports ◽

10.1038/s41598-021-93661-3 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Suthanthiram Backiyarani ◽

Rajendran Sasikala ◽

Simeon Sharmiladevi ◽

Subbaraya Uma

Keyword(s):

Candidate Genes ◽

Protein Interaction ◽

Target Genes ◽

Interaction Network ◽

Enrichment Analysis ◽

Auxin Signaling ◽

Pathway Enrichment Analysis ◽

Ppi Network ◽

Protein Protein Interaction ◽

The Difference

AbstractBanana, one of the most important staple fruit among global consumers is highly sterile owing to natural parthenocarpy. Identification of genetic factors responsible for parthenocarpy would facilitate the conventional breeders to improve the seeded accessions. We have constructed Protein–protein interaction (PPI) network through mining differentially expressed genes and the genes used for transgenic studies with respect to parthenocarpy. Based on the topological and pathway enrichment analysis of proteins in PPI network, 12 candidate genes were shortlisted. By further validating these candidate genes in seeded and seedless accession of Musa spp. we put forward MaAGL8, MaMADS16, MaGH3.8, MaMADS29, MaRGA1, MaEXPA1, MaGID1C, MaHK2 and MaBAM1 as possible target genes in the study of natural parthenocarpy. In contrary, expression profile of MaACLB-2 and MaZEP is anticipated to highlight the difference in artificially induced and natural parthenocarpy. By exploring the PPI of validated genes from the network, we postulated a putative pathway that bring insights into the significance of cytokinin mediated CLAVATA(CLV)–WUSHEL(WUS) signaling pathway in addition to gibberellin mediated auxin signaling in parthenocarpy. Our analysis is the first attempt to identify candidate genes and to hypothesize a putative mechanism that bridges the gaps in understanding natural parthenocarpy through PPI network.

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Assessment of the Accuracy of the Gail Model in Women With Atypical Hyperplasia

Journal of Clinical Oncology ◽

10.1200/jco.2007.14.8833 ◽

2008 ◽

Vol 26 (33) ◽

pp. 5374-5379 ◽

Cited By ~ 66

Author(s):

V. Shane Pankratz ◽

Lynn C. Hartmann ◽

Amy C. Degnim ◽

Robert A. Vierkant ◽

Karthik Ghosh ◽

...

Keyword(s):

Breast Cancer ◽

Health Care Professionals ◽

Breast Disease ◽

Develop Breast Cancer ◽

Atypical Hyperplasia ◽

Individual Risk ◽

Breast Cancers ◽

Gail Model ◽

Patient Counseling

Purpose An accurate estimate of a woman's breast cancer risk is essential for optimal patient counseling and management. Women with biopsy-confirmed atypical hyperplasia of the breast (atypia) are at high risk for breast cancer. The Gail model is widely used in these women, but has not been validated in them. Patients and Methods Women with atypia were identified from the Mayo Benign Breast Disease (BBD) cohort (1967 to 1991). Their risk factors for breast cancer were obtained, and the Gail model was used to predict 5-year–and follow-up–specific risks for each woman. The predicted and observed numbers of breast cancers were compared, and the concordance between individual risk levels and outcomes was computed. Results Of the 9,376 women in the BBD cohort, 331 women had atypia (3.5%). At a mean follow-up of 13.7 years, 58 of 331 (17.5%) patients had developed invasive breast cancer, 1.66 times more than the 34.9 predicted by the Gail model (95% CI, 1.29 to 2.15; P < .001). For individual women, the concordance between predicted and observed outcomes was low, with a concordance statistic of 0.50 (95% CI, 0.44 to 0.55). Conclusion The Gail model significantly underestimates the risk of breast cancer in women with atypia. Its ability to discriminate women with atypia into those who did and did not develop breast cancer is limited. Health care professionals should be cautious when using the Gail model to counsel individual patients with atypia.

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