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Xu L, Wang S, Zhang D, Wu Y, Shan J, Zhu H, Wang C, Wang Q. Machine learning- and WGCNA-mediated double analysis based on genes associated with disulfidptosis, cuproptosis and ferroptosis for the construction and validation of the prognostic model for breast cancer. J Cancer Res Clin Oncol 2023; 149:16511-16523. [PMID: 37712959 DOI: 10.1007/s00432-023-05378-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 08/30/2023] [Indexed: 09/16/2023]
Abstract
BACKGROUND Disulfidptosis, a recently discovered cellular death mechanism, has not been extensively studied in relation to breast cancer (BC). Specifically, no previous research has integrated disulfidptosis-related genes (DRGs), cuproptosis-related genes (CRGs), and ferroptosis-related genes (FRGs) to construct a prognostic signature for BC. METHODS DRGs, CRGs and FRGs with prognostic potential were identified through Cox regression analysis. A predictive model was constructed by intersecting the core genes obtained from unsupervised cluster analysis and weighted correlation network analysis (WGCNA). Differences in chemotherapy drug sensitivity, immune checkpoint levels were analyzed according to different risk score groups. The expression of the core disulfidptosis gene, SLC7A11, was analyzed using immunofluorescence. RESULTS Single-cell RNA sequencing analysis revealed differential expression of DRGs in the BC tumor microenvironment. We developed a prognostic model, consisting of six genes, based on machine learning which included unsupervised cluster analysis and Lasso-Cox analysis. An internal training set and a validation set, both derived from the Cancer Genome Atlas-Breast Cancer (TCGA-BRCA) database, GSE20685 and GSE42568 as external validation sets all verified the model's validity. The low-risk group exhibited increased sensitivity to paclitaxel. Additionally, the high-risk group demonstrated significantly higher expression of tumor mutation burden and microsatellite instability compared to the low-risk group. A nomogram confirmed that the risk score can be an independent risk factor for BC. Notably, our findings highlighted the impact of SLC7A11 on the BC tumor microenvironment. Immunofluorescence analysis revealed significantly higher expression of SLC7A11 in BC tissues compared to paracancerous tissues. CONCLUSION Multiplex analysis based on DRGs, CRGs and FRGs correlated strongly with BC, providing new insights for developing clinical prognostic tools and designing immunotherapy regimens for BC patients.
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Affiliation(s)
- Lijun Xu
- Department of General Surgery, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, 226001, China
| | - Shanshan Wang
- Department of General Surgery, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, 226001, China
| | - Dan Zhang
- Department of General Surgery, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, 226001, China
| | - Yunxi Wu
- Department of General Surgery, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, 226001, China
| | - Jiali Shan
- Department of General Surgery, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, 226001, China
| | - Huixia Zhu
- Department of Biochemistry, Medical College, Nantong University, Nantong, 226001, China
| | - Chongyu Wang
- Department of Medicine, Xinglin College, Nantong University, Nantong, 226007, China
| | - Qingqing Wang
- Department of General Surgery, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, 226001, China.
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Behera RN, Bisht VS, Giri K, Ambatipudi K. Realm of proteomics in breast cancer management and drug repurposing to alleviate intricacies of treatment. Proteomics Clin Appl 2023; 17:e2300016. [PMID: 37259687 DOI: 10.1002/prca.202300016] [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: 02/16/2023] [Revised: 05/10/2023] [Accepted: 05/15/2023] [Indexed: 06/02/2023]
Abstract
Breast cancer, a multi-networking heterogeneous disease, has emerged as a serious impediment to progress in clinical oncology. Although technological advancements and emerging cancer research studies have mitigated breast cancer lethality, a precision cancer-oriented solution has not been achieved. Thus, this review will persuade the acquiescence of proteomics-based diagnostic and therapeutic options in breast cancer management. Recently, the evidence of breast cancer health surveillance through imaging proteomics, single-cell proteomics, interactomics, and post-translational modification (PTM) tracking, to construct proteome maps and proteotyping for stage-specific and sample-specific cancer subtyping have outperformed conventional ways of dealing with breast cancer by increasing diagnostic efficiency, prognostic value, and predictive response. Additionally, the paradigm shift in applied proteomics for designing a chemotherapy regimen to identify novel drug targets with minor adverse effects has been elaborated. Finally, the potential of proteomics in alleviating the occurrence of chemoresistance and enhancing reprofiled drugs' effectiveness to combat therapeutic obstacles has been discussed. Owing to the enormous potential of proteomics techniques, the clinical recognition of proteomics in breast cancer management can be achievable and therapeutic intricacies can be surmountable.
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Affiliation(s)
- Rama N Behera
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India
| | - Vinod S Bisht
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India
| | - Kuldeep Giri
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India
| | - Kiran Ambatipudi
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India
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Jung HD, Sung YJ, Kim HU. Omics and Computational Modeling Approaches for the Effective Treatment of Drug-Resistant Cancer Cells. Front Genet 2021; 12:742902. [PMID: 34691155 PMCID: PMC8527086 DOI: 10.3389/fgene.2021.742902] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 09/20/2021] [Indexed: 02/05/2023] Open
Abstract
Chemotherapy is a mainstream cancer treatment, but has a constant challenge of drug resistance, which consequently leads to poor prognosis in cancer treatment. For better understanding and effective treatment of drug-resistant cancer cells, omics approaches have been widely conducted in various forms. A notable use of omics data beyond routine data mining is to use them for computational modeling that allows generating useful predictions, such as drug responses and prognostic biomarkers. In particular, an increasing volume of omics data has facilitated the development of machine learning models. In this mini review, we highlight recent studies on the use of multi-omics data for studying drug-resistant cancer cells. We put a particular focus on studies that use computational models to characterize drug-resistant cancer cells, and to predict biomarkers and/or drug responses. Computational models covered in this mini review include network-based models, machine learning models and genome-scale metabolic models. We also provide perspectives on future research opportunities for combating drug-resistant cancer cells.
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Affiliation(s)
- Hae Deok Jung
- Department of Chemical and Biomolecular Engineering (BK21 four), Korea Advanced Institute of Science and Technology (KAIST), Daejeon, South Korea
| | - Yoo Jin Sung
- Department of Chemical and Biomolecular Engineering (BK21 four), Korea Advanced Institute of Science and Technology (KAIST), Daejeon, South Korea
| | - Hyun Uk Kim
- Department of Chemical and Biomolecular Engineering (BK21 four), Korea Advanced Institute of Science and Technology (KAIST), Daejeon, South Korea.,KAIST Institute for Artificial Intelligence, KAIST, Daejeon, South Korea.,BioProcess Engineering Research Center and BioInformatics Research Center KAIST, Daejeon, South Korea
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Garcia-Mayea Y, Mir C, Carballo L, Castellvi J, Temprana-Salvador J, Lorente J, Benavente S, García-Pedrero JM, Allonca E, Rodrigo JP, LLeonart ME. TSPAN1: A Novel Protein Involved in Head and Neck Squamous Cell Carcinoma Chemoresistance. Cancers (Basel) 2020; 12:cancers12113269. [PMID: 33167355 PMCID: PMC7694336 DOI: 10.3390/cancers12113269] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 10/24/2020] [Accepted: 10/30/2020] [Indexed: 02/07/2023] Open
Abstract
Simple Summary Therapy resistance in head and neck squamous cell carcinoma (HNSCC) patients is the main obstacle to achieve more effective treatments that improve survival and quality of life of these patients. Therefore, it is of vital importance to unravel the molecular and cellular mechanisms by which tumor cells acquire resistance to chemotherapy. We conducted a comparative proteomic study involving cisplatin-resistant cells and cancer stem cells with the aim of identifying proteins potentially implicated in the acquisition of cisplatin resistance. Through this study, we identified for the first time tetraspanin-1 (TSPAN1) as an important protein involved in the development, progression and chemoresistance of HNSCC tumors. Abstract Sensitization of resistant cells and cancer stem cells (CSCs) represents a major challenge in cancer therapy. A proteomic study revealed tetraspanin-1 (TSPAN1) as a protein involved in acquisition of cisplatin (CDDP) resistance (Data are available via ProteomeXchange with identifier PXD020159). TSPAN1 was found to increase in CDDP-resistant cells, CSCs and biopsies from head and neck squamous cell carcinoma (HNSCC) patients. TSPAN1 depletion in parental and CDDP-resistant HNSCC cells reduced cell proliferation, induced apoptosis, decreased autophagy, sensitized to chemotherapeutic agents and inhibited several signaling cascades, with phospho-SRC inhibition being a major common target. Moreover, TSPAN1 depletion in vivo decreased the size and proliferation of parental and CDDP-resistant tumors and reduced metastatic spreading. Notably, CDDP-resistant tumors showed epithelial–mesenchymal transition (EMT) features that disappeared upon TSPAN1 inhibition, suggesting a link of TSPAN1 with EMT and metastasis. Immunohistochemical analysis of HNSCC specimens further revealed that TSPAN1 expression was correlated with phospho-SRC (pSRC), and inversely with E-cadherin, thus reinforcing TSPAN1 association with EMT. Overall, TSPAN1 emerges as a novel oncogenic protein and a promising target for HNSCC therapy.
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Affiliation(s)
- Yoelsis Garcia-Mayea
- Biomedical Research in Cancer Stem Cells, Vall d’Hebron Research Institute (VHIR), Autonomous University of Barcelona, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain; (Y.G.-M.); (C.M.); (L.C.); (J.C.); (J.T.-S.)
- Genetic, Microbiology and Statistics Department, Faculty of Biology, University of Barcelona, Avenida Diagonal 643, 08014 Barcelona, Spain
| | - Cristina Mir
- Biomedical Research in Cancer Stem Cells, Vall d’Hebron Research Institute (VHIR), Autonomous University of Barcelona, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain; (Y.G.-M.); (C.M.); (L.C.); (J.C.); (J.T.-S.)
| | - Laia Carballo
- Biomedical Research in Cancer Stem Cells, Vall d’Hebron Research Institute (VHIR), Autonomous University of Barcelona, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain; (Y.G.-M.); (C.M.); (L.C.); (J.C.); (J.T.-S.)
| | - Josep Castellvi
- Biomedical Research in Cancer Stem Cells, Vall d’Hebron Research Institute (VHIR), Autonomous University of Barcelona, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain; (Y.G.-M.); (C.M.); (L.C.); (J.C.); (J.T.-S.)
| | - Jordi Temprana-Salvador
- Biomedical Research in Cancer Stem Cells, Vall d’Hebron Research Institute (VHIR), Autonomous University of Barcelona, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain; (Y.G.-M.); (C.M.); (L.C.); (J.C.); (J.T.-S.)
| | - Juan Lorente
- Otorhinolaryngology Department, Hospital Vall d’Hebron (HUVH), Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain;
| | - Sergi Benavente
- Radiotherapy Unit, Vall d’Hebron Research Institute (VHIR), Autonomous University of Barcelona, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain;
| | - Juana M. García-Pedrero
- Department of Otolaryngology-Head and Neck Surgery, Central University Hospital of Asturias, University of Oviedo, ISPA, IUOPA, 33011 Oviedo, Spain; (J.M.G.-P.); (E.A.); (J.P.R.)
- Spanish Biomedical Research Network Centre in Oncology (CIBERONC), Av. Roma SN, 33011 Oviedo, Spain
| | - Eva Allonca
- Department of Otolaryngology-Head and Neck Surgery, Central University Hospital of Asturias, University of Oviedo, ISPA, IUOPA, 33011 Oviedo, Spain; (J.M.G.-P.); (E.A.); (J.P.R.)
| | - Juan P. Rodrigo
- Department of Otolaryngology-Head and Neck Surgery, Central University Hospital of Asturias, University of Oviedo, ISPA, IUOPA, 33011 Oviedo, Spain; (J.M.G.-P.); (E.A.); (J.P.R.)
- Spanish Biomedical Research Network Centre in Oncology (CIBERONC), Av. Roma SN, 33011 Oviedo, Spain
| | - Matilde E. LLeonart
- Biomedical Research in Cancer Stem Cells, Vall d’Hebron Research Institute (VHIR), Autonomous University of Barcelona, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain; (Y.G.-M.); (C.M.); (L.C.); (J.C.); (J.T.-S.)
- Spanish Biomedical Research Network Centre in Oncology (CIBERONC), Vall d’Hebron Research Institute (VHIR), Passeig Vall d´Hebron 119–129, 08035 Barcelona, Spain
- Correspondence: ; Tel.: +34-934894169; Fax: +34-932746708
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