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Md Zaki FA, Mohamad Hanif EA. Identifying miRNA as biomarker for breast cancer subtyping using association rule. Comput Biol Med 2024; 178:108696. [PMID: 38850957 DOI: 10.1016/j.compbiomed.2024.108696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 05/03/2024] [Accepted: 06/01/2024] [Indexed: 06/10/2024]
Abstract
- This paper presents a comprehensive study focused on breast cancer subtyping, utilizing a multifaceted approach that integrates feature selection, machine learning classifiers, and miRNA regulatory networks. The feature selection process begins with the CFS algorithm, followed by the Apriori algorithm for association rule generation, resulting in the identification of significant features tailored to Luminal A, Luminal B, HER-2 enriched, and Basal-like subtypes. The subsequent application of Random Forest (RF) and Support Vector Machine (SVM) classifiers yielded promising results, with the SVM model achieving an overall accuracy of 76.60 % and the RF model demonstrating robust performance at 80.85 %. Detailed accuracy metrics revealed strengths and areas for refinement, emphasizing the potential for optimizing subtype-specific recall. To explore the regulatory landscape in depth, an analysis of selected miRNAs was conducted using MIENTURNET, a tool for visualizing miRNA-target interactions. While FDR analysis raised concerns for HER-2 and Basal-like subtypes, Luminal A and Luminal B subtypes showcased significant miRNA-gene interactions. Functional enrichment analysis for Luminal A highlighted the role of Ovarian steroidogenesis, implicating specific miRNAs such as hsa-let-7c-5p and hsa-miR-125b-5p as potential diagnostic biomarkers and regulators of Luminal A breast cancer. Luminal B analysis uncovered associations with the MAPK signaling pathway, with miRNAs like hsa-miR-203a-3p and hsa-miR-19a-3p exhibiting potential diagnostic and therapeutic significance. In conclusion, this integrative approach combines machine learning techniques with miRNA analysis to provide a holistic understanding of breast cancer subtypes. The identified miRNAs and associated pathways offer insights into potential diagnostic biomarkers and therapeutic targets, contributing to the ongoing efforts to improve breast cancer diagnostics and personalized treatment strategies.
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Affiliation(s)
- Fatimah Audah Md Zaki
- Department of Internet Engineering & Computer Science, Universiti Tunku Abdul Rahman (UTAR), Selangor, Malaysia.
| | - Ezanee Azlina Mohamad Hanif
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia Medical Centre, Kuala Lumpur, Malaysia.
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2
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Jiang T, Ma X, Liu H, Jia Q, Chen J, Ding Y, Sun M, Zhu H. SNAT2-mediated regulation of estrogen and progesterone in the proliferation of goat mammary epithelial cells. Amino Acids 2024; 56:17. [PMID: 38393495 PMCID: PMC10891196 DOI: 10.1007/s00726-024-03382-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 01/17/2024] [Indexed: 02/25/2024]
Abstract
The development of the goat mammary gland is mainly under the control of ovarian hormones particularly estrogen and progesterone (P4). Amino acids play an essential role in mammary gland development and milk production, and sodium-coupled neutral amino acid transporter 2 (SNAT2) was reported to be expressed in the mammary gland of rats and bovine mammary epithelial cells, which may affect the synthesis of milk proteins or mammary cell proliferation by mediating prolactin, 17β-estradiol (E2) or methionine function. However, whether SNAT2 mediates the regulatory effects of E2 and P4 on the development of the ruminant mammary gland is still unclear. In this study, we show that E2 and P4 could increase the proliferation of goat mammary epithelial cells (GMECs) and regulate SNAT2 mRNA and protein expression in a dose-dependent manner. Further investigation revealed that SNAT2 is abundantly expressed in the mammary gland during late pregnancy and early lactation, while knockdown and overexpression of SNAT2 in GMECs could inhibit or enhance E2- and P4-induced cell proliferation as well as mammalian target of rapamycin (mTOR) signaling. We also found that the accelerated proliferation induced by SNAT2 overexpression in GMECs was suppressed by the mTOR signaling pathway inhibitor rapamycin. This indicates that the regulation of GMECs proliferation mediated by SNAT2 in response to E2 and P4 is dependent on the mTOR signaling pathway. Finally, we found that the total content of the amino acids in GMECs changed after knocking-down and overexpressing SNAT2. In summary, the results demonstrate that the regulatory effects of E2 and P4 on GMECs proliferation may be mediated by the SNAT2-transported amino acid pathway. These results may offer a novel nutritional target for improving the development of the ruminant mammary gland and milk production.
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Affiliation(s)
- Tingting Jiang
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xiaoyue Ma
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
| | - Hanling Liu
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
| | - Qianqian Jia
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jianguo Chen
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yi Ding
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
| | - Ming Sun
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
| | - Hongmei Zhu
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China.
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Chen S, Li X, Ao W. Prognostic and immune infiltration features of disulfidptosis-related subtypes in breast cancer. BMC Womens Health 2024; 24:6. [PMID: 38166898 PMCID: PMC10763228 DOI: 10.1186/s12905-023-02823-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 12/01/2023] [Indexed: 01/05/2024] Open
Abstract
Breast cancer (BC) is a prominent cause of cancer incidence and mortality around the world. Disulfidptosis, a type of cell death, can induce tumor cell death. The purpose of this study was to analyze the potential impact of disulfidptosis-related genes (DRGs) on the prognosis and immune infiltration features of BC. Based on DRGs, we conducted an unsupervised clustering analysis on gene expression data of BC in TCGA-BRCA dataset and identified two BC subtypes, cluster1 and cluster2, with cluster1 showing a higher likelihood of favorable survival. Through immune analysis, we found that cluster1 had lower proportions of infiltration in immune-related cells, including aDCs, DCs, NK_cells, Th2_cells, and Treg. Based on the immunophenoscore (IPS) results, we inferred that cluster1 might benefit more from immune checkpoint inhibitors targeting CTLA-4 and PD1. Targeted small molecule prediction results showed that patients with cluster2 BC might respond better to antagonistic small molecule compounds, including clofazimine, lenalidomide, and epigallocatechin. Differentially expressed genes between the two subtypes were found to be enriched in signaling pathways related to steroid hormone biosynthesis, ovarian steroidogenesis, and neutrophil extracellular trap formation, according to enrichment analyses. In conclusion, this study identified BC subtypes based on DRGs so as to help predict patient prognosis and provide valuable tools for guiding clinical management and precise treatment of BC patients.
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Affiliation(s)
- Sheng Chen
- Oncology Department III, The Central Hospital of Xiaogan, No.6, Guangchang Road, Xiaogan City, 432000, Hubei Province, China
| | - Xiangrong Li
- Oncology Department III, The Central Hospital of Xiaogan, No.6, Guangchang Road, Xiaogan City, 432000, Hubei Province, China
| | - Wen Ao
- Oncology Department III, The Central Hospital of Xiaogan, No.6, Guangchang Road, Xiaogan City, 432000, Hubei Province, China.
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Abdelmaksoud NM, Abulsoud AI, Doghish AS, Abdelghany TM. From resistance to resilience: Uncovering chemotherapeutic resistance mechanisms; insights from established models. Biochim Biophys Acta Rev Cancer 2023; 1878:188993. [PMID: 37813202 DOI: 10.1016/j.bbcan.2023.188993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 09/13/2023] [Accepted: 09/26/2023] [Indexed: 10/11/2023]
Abstract
Despite the tremendous advances in cancer treatment, resistance to chemotherapeutic agents impedes higher success rates and accounts for major relapses in cancer therapy. Moreover, the resistance of cancer cells to chemotherapy is linked to low efficacy and high recurrence of cancer. To stand up against chemotherapy resistance, different models of chemotherapy resistance have been established to study various molecular mechanisms of chemotherapy resistance. Consequently, this review is going to discuss different models of induction of chemotherapy resistance, highlighting the most common mechanisms of cancer resistance against different chemotherapeutic agents, including overexpression of efflux pumps, drug inactivation, epigenetic modulation, and epithelial-mesenchymal transition. This review aims to open a new avenue for researchers to lower the resistance to the existing chemotherapeutic agents, develop new therapeutic agents with low resistance potential, and establish possible prognostic markers for chemotherapy resistance.
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Affiliation(s)
- Nourhan M Abdelmaksoud
- Department of Biochemistry, Faculty of Pharmacy, Heliopolis University, 3 Cairo-Belbeis Desert Road, P.O. Box 3020 El Salam, 11785 Cairo, Egypt.
| | - Ahmed I Abulsoud
- Department of Biochemistry, Faculty of Pharmacy, Heliopolis University, 3 Cairo-Belbeis Desert Road, P.O. Box 3020 El Salam, 11785 Cairo, Egypt; Department of Biochemistry and Molecular Biology, Faculty of Pharmacy (Boys), Al-Azhar University, Nasr City, Cairo 11823, Egypt
| | - Ahmed S Doghish
- Department of Biochemistry, Faculty of Pharmacy, Badr University in Cairo (BUC), Badr City, Cairo 11829, Egypt; Faculty of Pharmacy (Boys), Al-Azhar University, Nasr City, Cairo 11823, Egypt
| | - Tamer M Abdelghany
- Department of Pharmacology and Toxicology, Faculty of Pharmacy (Boys), Al-Azhar University, Nasr City, Cairo 11884, Egypt; Department of Pharmacology and Toxicology, Faculty of Pharmacy, Heliopolis University, 3 Cairo-Belbeis Desert Road, P.O. Box 3020 El Salam, 11785 Cairo, Egypt.
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Liu M, Wang Z, Li S, Deng Y, He N. Identification of PHB2 as a Potential Biomarker of Luminal A Breast Cancer Cells Using a Cell-Specific Aptamer. ACS APPLIED MATERIALS & INTERFACES 2022; 14:51593-51601. [PMID: 36346944 DOI: 10.1021/acsami.2c12291] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Precise diagnosis of breast cancer molecular subtypes remains a great challenge in clinics. The present molecular biomarkers are not specific enough to classify breast cancer subtypes precisely, which requests for more accurate and specific molecular biomarkers to be discovered. Aptamers evolved by the cell-systematic evolution of ligands by exponential enrichment (SELEX) method show great potential in the discovery and identification of cell membrane targets via aptamer-based cell membrane protein pull-down, which has been regarded as a novel and powerful weapon for the discovery and identification of new molecular biomarkers. Herein, a cell membrane protein PHB2 was identified as a potential molecular biomarker specifically expressed in the cell membranes of MCF-7 breast cancer cells using a DNA aptamer MF3Ec. Further experiments demonstrated that the PHB2 protein is differentially expressed in the cell membranes of MCF-7, SK-BR-3, and MDA-MB-231 breast cancer cells and MCF-10A cells, and the binding molecular domains of aptamer MF3Ec and anti-PHB2 antibodies to the PHB2 protein are different due to there being no obvious competitions between aptamer MF3Ec and anti-PHB2 antibodies in the binding to the cell membranes of target MCF-7 cells. Due to those four cells belonging to luminal A, HER2-positive, and triple-negative breast cancer cell subtypes and human normal mammary epithelial cells, respectively, the PHB2 protein in the cell membrane may be a potential biomarker for precise diagnosis of the luminal A breast cancer cell subtype, which is endowed with the ability to differentiate the luminal A breast cancer cell subtype from HER2-positive and triple-negative breast cancer cell subtypes and human normal mammary epithelial cells, providing a new molecular biomarker and therapeutic target for the accurate and precise classification and diagnostics and personalized therapy of breast cancer.
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Affiliation(s)
- Mei Liu
- State Key Laboratory of Bioelectronics, National Demonstration Center for Experimental Biomedical Engineering Education (Southeast University), School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, P. R. China
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, P. R. China
- Key Laboratory of Basic and Translational Research on Immune-Mediated Skin Diseases, Chinese Academy of Medical Sciences, Nanjing 210042, P. R. China
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing 210042, P. R. China
| | - Zhifei Wang
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, P. R. China
| | - Song Li
- Economical Forest Cultivation and Utilization of 2011 Collaborative Innovation Center in Hunan Province, Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, P. R. China
| | - Yan Deng
- Economical Forest Cultivation and Utilization of 2011 Collaborative Innovation Center in Hunan Province, Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, P. R. China
| | - Nongyue He
- State Key Laboratory of Bioelectronics, National Demonstration Center for Experimental Biomedical Engineering Education (Southeast University), School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, P. R. China
- Economical Forest Cultivation and Utilization of 2011 Collaborative Innovation Center in Hunan Province, Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, P. R. China
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Telang NT. Stem Cell Models for Breast and Colon Cancer: Experimental Approach for Drug Discovery. Int J Mol Sci 2022; 23:ijms23169223. [PMID: 36012489 PMCID: PMC9409032 DOI: 10.3390/ijms23169223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 08/09/2022] [Accepted: 08/09/2022] [Indexed: 11/16/2022] Open
Abstract
The progression of the early stages of female breast and colon cancer to metastatic disease represents a major cause of mortality in women. Multi-drug chemotherapy and/or pathway selective targeted therapy are notable for their off-target effects and are associated with spontaneous and/or acquired chemotherapy resistance and the emergence of premalignant chemo-resistant cancer-initiating stem cells. The stem cell populations are responsible for the evolution of therapy-resistant metastatic disease. These limitations emphasize an unmet need to develop reliable drug-resistant cancer stem cell models as novel experimental approaches for therapeutic alternatives in drug discovery platforms. Drug-resistant stem cell models for breast and colon cancer subtypes exhibit progressive growth in the presence of cytotoxic chemo-endocrine therapeutics. The resistant cells exhibit upregulated expressions of stem cell-selective cellular and molecular markers. Dietary phytochemicals, nutritional herbs and their constituent bioactive compounds have documented growth inhibitory efficacy for cancer stem cells. The mechanistic leads for the stem cell-targeted efficacy of naturally occurring agents validates the present experimental approaches for new drug discovery as therapeutic alternatives for therapy-resistant breast and colon cancer. The present review provides a systematic discussion of published evidence on (i) conventional/targeted therapy for breast and colon cancer, (ii) cellular and molecular characterization of stem cell models and (iii) validation of the stem cell models as an experimental approach for novel drug discovery of therapeutic alternatives for therapy-resistant cancers.
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Affiliation(s)
- Nitin T Telang
- Cancer Prevention Research Program, Palindrome Liaisons Consultants, Montvale, NJ 07645-1559, USA
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Drug-Resistant Stem Cells: Novel Approach for Colon Cancer Therapy. Int J Mol Sci 2022; 23:ijms23137055. [PMID: 35806056 PMCID: PMC9266363 DOI: 10.3390/ijms23137055] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Revised: 06/10/2022] [Accepted: 06/16/2022] [Indexed: 12/16/2022] Open
Abstract
Metastatic progression of female breast and colon cancer represents a major cause of mortality in women. Spontaneous/acquired resistance to conventional and targeted chemo-endocrine therapy is associated with the emergence of drug-resistant tumor-initiating cancer stem cell populations. The cancer-initiating premalignant stem cells exhibit activation of select cancer cell signaling pathways and undergo epithelial–mesenchymal transition, leading to the evolution of a metastatic phenotype. The development of reliable cancer stem cell models provides valuable experimental approaches to identify novel testable therapeutic alternatives for therapy-resistant cancer. Drug-resistant stem cell models for molecular subtypes of clinical breast cancer and for genetically predisposed colon cancer are developed by selecting epithelial cells that survive in the presence of cytostatic concentrations of relevant therapeutic agents. These putative stem cells are characterized by the expression status of select cellular and molecular stem cell markers. The stem cell models are utilized as experimental approaches to examine the stem-cell-targeted growth inhibitory efficacy of naturally occurring dietary phytochemicals. The present review provides a systematic discussion on (i) conceptual and experimental aspects relevant to the chemo-endocrine therapy of breast and colon cancer, (ii) molecular/cellular aspects of cancer stem cells and (iii) potential stem-cell-targeting lead compounds as testable alternatives against the progression of therapy-resistant breast and colon cancer.
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