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Zhou Y, Chapagain P, Desmarini D, Uredi D, Rameh LE, Djordjevic JT, Blind RD, Wang X. Design, synthesis and cellular characterization of a new class of IPMK kinase inhibitors. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.09.593371. [PMID: 38798512 PMCID: PMC11118372 DOI: 10.1101/2024.05.09.593371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Many genetic studies have established the kinase activity of inositol phosphate multikinase (IPMK) is required for the synthesis of higher-order inositol phosphate signaling molecules, the regulation of gene expression and control of the cell cycle. These genetic studies await orthogonal validation by specific IPMK inhibitors, but no such inhibitors have been synthesized. Here, we report complete chemical synthesis, cellular characterization, structure-activity relationships and rodent pharmacokinetics of a novel series of highly potent IPMK inhibitors. The first-generation compound 1 (UNC7437) decreased cellular proliferation and tritiated inositol phosphate levels in metabolically labeled human U251-MG glioblastoma cells. Compound 1 also regulated the transcriptome of these cells, selectively regulating genes that are enriched in cancer, inflammatory and viral infection pathways. Further optimization of compound 1 eventually led to compound 15 (UNC9750), which showed improved potency and pharmacokinetics in rodents. Compound 15 specifically inhibited cellular accumulation of InsP 5 , a direct product of IPMK kinase activity, while having no effect on InsP 6 levels, revealing a novel metabolic signature detected for the first time by rapid chemical attenuation of cellular IPMK activity. These studies designed, optimized and synthesized a new series of IPMK inhibitors, which reduces glioblastoma cell growth, induces a novel InsP 5 metabolic signature, and reveals novel aspects inositol phosphate cellular metabolism and signaling.
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Wang H, Blind RD, Shears SB. X-ray crystallographic analyses of 14 IPMK inhibitor complexes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.09.593385. [PMID: 38766172 PMCID: PMC11100778 DOI: 10.1101/2024.05.09.593385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Inositol polyphosphate multikinase (IPMK) is a ubiquitously expressed kinase that has been linked to several cancers. Here, we report 14 new co-crystal structures (1.7Å - 2.0Å resolution) of human IPMK complexed with various IPMK inhibitors developed by another group. The new structures reveal two ordered water molecules that participate in hydrogen-bonding networks, and an unoccupied pocket in the ATP-binding site of human IPMK. New Protein Data Bank (PDB) codes of these IPMK crystal structures are: 8V6W (1.95Å), 8V6X (1.75Å), 8V6Y (1.70Å), 8V6Z (1.85Å), 8V70 (1.85Å), 8V71 (1.70Å), 8V72 (2.0Å), 8V73 (1.90Å), 8V74 (1.85Å), 8V75 (1.85Å), 8V76 (1.95Å), 8V77 (1.95Å), 8V78 (1.95Å), 8V79 (1.95Å).
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Xia J, Zhou X. Necroptosis-related KLRB1 was a potent tumor suppressor and immunotherapy determinant in breast cancer. Heliyon 2024; 10:e27294. [PMID: 38509875 PMCID: PMC10951529 DOI: 10.1016/j.heliyon.2024.e27294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 02/27/2024] [Accepted: 02/27/2024] [Indexed: 03/22/2024] Open
Abstract
Breast cancer is a multifaceted and diverse illness that impacts millions of people globally. Identifying the underlying causes of BRCA and creating efficient treatment plans are urgent. Necroptosis is widely involved in cancer development. However, the specific roles of necroptosis in cancer immunotherapy of breast cancer have not been explored. In this study, we aim to establish the connection between necroptosis and immunotherapy in BRCA. TCGA, METABRIC, GSE103091, GSE159956, and GSE96058 were included for bioinformatics analysis. NMF and CoxBoost algorithms were used to develop the necroptosis-related patterns and model, respectively. A necroptosis-related model was developed and determined KLRB1 as a critical tumor suppressor by in vitro validation. The mutation characteristics, immune characteristics, and molecular functions of KLRB1 were explored. We further examined how necroptosis-related KLRB1 functions in BRCA as a powerful tumor suppressor and regulates the activity of macrophages by in vitro validation, including CCK8, EdU, and Transwell assays. KLRB1 was also revealed to be an immunotherapy determinant.
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Affiliation(s)
- Jie Xia
- Department of Respiratory and Critical Care Medicine, National Clinical Research Center of Respiratory Disease, Key Laboratory of Pulmonary Diseases of Health Ministry, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xudong Zhou
- Department of Thyroid and Breast Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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Liu X, Zhang HY, Deng HA. Transcriptome and single-cell transcriptomics reveal prognostic value and potential mechanism of anoikis in skin cutaneous melanoma. Discov Oncol 2024; 15:70. [PMID: 38460046 PMCID: PMC10924820 DOI: 10.1007/s12672-024-00926-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 03/05/2024] [Indexed: 03/11/2024] Open
Abstract
BACKGROUND Skin cutaneous melanoma (SKCM) is a highly lethal cancer, ranking among the top four deadliest cancers. This underscores the urgent need for novel biomarkers for SKCM diagnosis and prognosis. Anoikis plays a vital role in cancer growth and metastasis, and this study aims to investigate its prognostic value and mechanism of action in SKCM. METHODS Utilizing consensus clustering, the SKCM samples were categorized into two distinct clusters A and B based on anoikis-related genes (ANRGs), with the B group exhibiting lower disease-specific survival (DSS). Gene set enrichment between distinct clusters was examined using Gene Set Variation Analysis (GSVA) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis. RESULTS We created a predictive model based on three anoikis-related differently expressed genes (DEGs), specifically, FASLG, IGF1, and PIK3R2. Moreover, the mechanism of these prognostic genes within the model was investigated at the cellular level using the single-cell sequencing dataset GSE115978. This analysis revealed that the FASLG gene was highly expressed on cluster 1 of Exhausted CD8( +) T (Tex) cells. CONCLUSIONS In conclusion, we have established a novel classification system for SKCM based on anoikis, which carries substantial clinical implications for SKCM patients. Notably, the elevated expression of the FASLG gene on cluster 1 of Tex cells could significantly impact SKCM prognosis through anoikis, thus offering a promising target for the development of immunotherapy for SKCM.
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Affiliation(s)
- Xing Liu
- Medical Center of Burn Plastic and Wound Repair, The First Affiliated Hospital of Nanchang University, Nanchang, 330006, Jiangxi, China
| | - Hong-Yan Zhang
- Medical Center of Burn Plastic and Wound Repair, The First Affiliated Hospital of Nanchang University, Nanchang, 330006, Jiangxi, China.
| | - Hong-Ao Deng
- Medical Center of Burn Plastic and Wound Repair, The First Affiliated Hospital of Nanchang University, Nanchang, 330006, Jiangxi, China.
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Liang J, Wang X, Yang J, Sun P, Sun J, Cheng S, Liu J, Ren Z, Ren M. Identification of disulfidptosis-related subtypes, characterization of tumor microenvironment infiltration, and development of a prognosis model in breast cancer. Front Immunol 2023; 14:1198826. [PMID: 38035071 PMCID: PMC10684933 DOI: 10.3389/fimmu.2023.1198826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Accepted: 10/31/2023] [Indexed: 12/02/2023] Open
Abstract
Introduction Breast cancer (BC) is now the most common type of cancer in women. Disulfidptosis is a new regulation of cell death (RCD). RCD dysregulation is causally linked to cancer. However, the comprehensive relationship between disulfidptosis and BC remains unknown. This study aimed to explore the predictive value of disulfidptosis-related genes (DRGs) in BC and their relationship with the TME. Methods This study obtained 11 disulfidptosis genes (DGs) from previous research by Gan et al. RNA sequencing data of BC were downloaded from the Cancer Genome Atlas (TCGA) and Gene Expression Omnibus database (GEO) databases. First, we examined the effect of DG gene mutations and copy number changes on the overall survival of breast cancer samples. We then used the expression profile data of 11 DGs and survival data for consensus clustering, and BC patients were divided into two clusters. Survival analysis, gene set variation analysis (GSVA) and ss GSEA were used to compare the differences between them. Subsequently, DRGs were identified between the clusters used to perform Cox regression and least absolute shrinkage and selection operator regression (LASSO) analyses to construct a prognosis model. Finally, the immune cell infiltration pattern, immunotherapy response, and drug sensitivity of the two subtypes were analyzed. CCK-8 and a colony assay obtained by knocking down genes and gene sequencing were used to validate the model. Result Two DG clusters were identified based on the expression of 11DGs. Then, 225 DRGs were identified between them. RS, composed of six genes, showed a significant relationship with survival, immune cell infiltration, clinical characteristics, immune checkpoints, immunotherapy response, and drug sensitivity. Low-RS shows a better prognosis and higher immunotherapy response than high-RS. A nomogram with perfect stability constructed using signature and clinical characteristics can predict the survival of each patient. CCK-8 and colony assay obtained by knocking down genes have demonstrated that the knockdown of high-risk genes in the RS model significantly inhibited cell proliferation. Discussion This study elucidates the potential relationship between disulfidptosis-related genes and breast cancer and provides new guidance for treating breast cancer.
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Affiliation(s)
- Jiahui Liang
- Department of Breast Surgery, Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Xin Wang
- Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Jing Yang
- Department of Breast Surgery, Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Peng Sun
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Jingjing Sun
- Department of Breast Surgery, Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Shengrong Cheng
- Department of Plastic Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Jincheng Liu
- Department of Breast Surgery, Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Zhiyao Ren
- Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Min Ren
- Department of Breast Surgery, Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
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Hu K, He R, Xu M, Zhang D, Han G, Han S, Xiao L, Xia P, Ling J, Wu T, Li F, Sheng Y, Zhang J, Yu P. Identification of necroptosis-related features in diabetic nephropathy and analysis of their immune microenvironent and inflammatory response. Front Cell Dev Biol 2023; 11:1271145. [PMID: 38020922 PMCID: PMC10661379 DOI: 10.3389/fcell.2023.1271145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 10/23/2023] [Indexed: 12/01/2023] Open
Abstract
Background: Diabetic nephropathy (DN) was considered a severe microvascular complication of diabetes, which was recognized as the second leading cause of end-stage renal diseases. Therefore, identifying several effective biomarkers and models to diagnosis and subtype DN is imminent. Necroptosis, a distinct form of programmed cell death, has been established to play a critical role in various inflammatory diseases. Herein, we described the novel landscape of necroptosis in DN and exploit a powerful necroptosis-mediated model for the diagnosis of DN. Methods: We obtained three datasets (GSE96804, GSE30122, and GSE30528) from the Gene Expression Omnibus (GEO) database and necroptosis-related genes (NRGs) from the GeneCards website. Via differential expression analysis and machine learning, significant NRGs were identified. And different necroptosis-related DN subtypes were divided using consensus cluster analysis. The principal component analysis (PCA) algorithm was utilized to calculate the necroptosis score. Finally, the logistic multivariate analysis were performed to construct the necroptosis-mediated diagnostic model for DN. Results: According to several public transcriptomic datasets in GEO, we obtained eight significant necroptosis-related regulators in the occurrence and progress of DN, including CFLAR, FMR1, GSDMD, IKBKB, MAP3K7, NFKBIA, PTGES3, and SFTPA1 via diversified machine learning methods. Subsequently, employing consensus cluster analysis and PCA algorithm, the DN samples in our training set were stratified into two diverse necroptosis-related subtypes based on our eight regulators' expression levels. These subtypes exhibited varying necroptosis scores. Then, we used various functional enrichment analysis and immune infiltration analysis to explore the biological background, immune landscape and inflammatory status of the above subtypes. Finally, a necroptosis-mediated diagnostic model was exploited based on the two subtypes and validated in several external verification datasets. Moreover, the expression level of our eight regulators were verified in the singe-cell level and glomerulus samples. And we further explored the relationship between the expression of eight regulators and the kidney function of DN. Conclusion: In summary, our necroptosis scoring model and necroptosis-mediated diagnostic model fill in the blank of the relationship between necroptosis and DN in the field of bioinformatics, which may provide novel diagnostic insights and therapy strategies for DN.
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Affiliation(s)
- Kaibo Hu
- Department of Endocrinology and Metabolism, The Second Affiliated Hospital of Nanchang University, Nanchang, China
- The Second Clinical Medical College, Nanchang University, Nanchang, China
| | - Ruifeng He
- Department of Endocrinology and Metabolism, The Second Affiliated Hospital of Nanchang University, Nanchang, China
- The Second Clinical Medical College, Nanchang University, Nanchang, China
| | - Minxuan Xu
- Department of Endocrinology and Metabolism, The Second Affiliated Hospital of Nanchang University, Nanchang, China
- Branch of National Clinical Research Center for Metabolic Diseases, Nanchang, China
- Institute for the Study of Endocrinology and Metabolism in Jiangxi Province, Nanchang, China
| | - Deju Zhang
- Food and Nutritional Sciences, School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Guangyu Han
- Department of Endocrinology and Metabolism, The Second Affiliated Hospital of Nanchang University, Nanchang, China
- The Second Clinical Medical College, Nanchang University, Nanchang, China
| | - Shengye Han
- Department of Endocrinology and Metabolism, The Second Affiliated Hospital of Nanchang University, Nanchang, China
- The Second Clinical Medical College, Nanchang University, Nanchang, China
| | - Leyang Xiao
- Department of Endocrinology and Metabolism, The Second Affiliated Hospital of Nanchang University, Nanchang, China
- The Second Clinical Medical College, Nanchang University, Nanchang, China
| | - Panpan Xia
- Department of Endocrinology and Metabolism, The Second Affiliated Hospital of Nanchang University, Nanchang, China
- Branch of National Clinical Research Center for Metabolic Diseases, Nanchang, China
- Institute for the Study of Endocrinology and Metabolism in Jiangxi Province, Nanchang, China
| | - Jitao Ling
- Department of Endocrinology and Metabolism, The Second Affiliated Hospital of Nanchang University, Nanchang, China
- Branch of National Clinical Research Center for Metabolic Diseases, Nanchang, China
- Institute for the Study of Endocrinology and Metabolism in Jiangxi Province, Nanchang, China
| | - Tingyu Wu
- Department of Endocrinology and Metabolism, The Second Affiliated Hospital of Nanchang University, Nanchang, China
- Branch of National Clinical Research Center for Metabolic Diseases, Nanchang, China
- Institute for the Study of Endocrinology and Metabolism in Jiangxi Province, Nanchang, China
| | - Fei Li
- Department of Endocrinology and Metabolism, The Second Affiliated Hospital of Nanchang University, Nanchang, China
- Branch of National Clinical Research Center for Metabolic Diseases, Nanchang, China
- Institute for the Study of Endocrinology and Metabolism in Jiangxi Province, Nanchang, China
| | - Yunfeng Sheng
- Department of Endocrinology and Metabolism, The Second Affiliated Hospital of Nanchang University, Nanchang, China
- Branch of National Clinical Research Center for Metabolic Diseases, Nanchang, China
- Institute for the Study of Endocrinology and Metabolism in Jiangxi Province, Nanchang, China
| | - Jing Zhang
- Department of Anesthesiology, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Peng Yu
- Department of Endocrinology and Metabolism, The Second Affiliated Hospital of Nanchang University, Nanchang, China
- Branch of National Clinical Research Center for Metabolic Diseases, Nanchang, China
- Institute for the Study of Endocrinology and Metabolism in Jiangxi Province, Nanchang, China
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Gao Y, Huang Q, Qin Y, Bao X, Pan Y, Mo J, Ning S. A prognostic model related to necrotizing apoptosis of breast cancer based on biorthogonal constrained depth semi-supervised nonnegative matrix decomposition and single-cell sequencing analysis. Am J Cancer Res 2023; 13:3875-3897. [PMID: 37818066 PMCID: PMC10560928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 07/31/2023] [Indexed: 10/12/2023] Open
Abstract
Breast cancer (BC) is one of the most common malignant tumours in women, and its prognosis is poor. The prognosis of BC patients can be improved by immunotherapy. However, due to the heterogeneity of BC, the identification of new biomarkers is urgently needed to improve the prognosis of BC patients. Necrotic apoptosis has been shown to play an essential role in many cancers. First, this study proposed a novel clustering algorithm called biorthogonal constrained depth semisupervised nonnegative matrix factorization (DO-DSNMF). The DO-DSNMF algorithm added multilayer nonlinear transformation to the coefficient matrix obtained after decomposition, which was used to mine the nonlinear relationship between samples. In addition, we also added orthogonal constraints on the basis matrix and coefficient matrix to reduce the influence of redundant features and samples on the results. We applied the DO-DSNMF algorithm and analysed the differences in survival and immunity between the subtypes. Then, we used prognosis analysis to construct the prognosis model. Finally, we analysed single cells using single-cell sequencing (scRNA-seq) data from the GSE75688 dataset in the GEO database. We identified two BC subtypes based on the BC transcriptome data in the TCGA database. Immune infiltration analysis showed that the necrotizing apoptosis-related genes of BC were related to various immune cells and immune functions. Necrotizing apoptosis was found to play a role in BC progression and immunity. The role of prognosis-related NRGs in BC was also verified by cell experiments. This study proposed a novel clustering algorithm to analyse BC subtypes and constructed an NRG prognostic model for BC. The prognosis and immune landscape of BC patients were evaluated by this model. The cell experiment supported its role in BC, which provides a potential therapeutic target for the treatment of BC.
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Affiliation(s)
- Yuan Gao
- Department of Head and Neck Radiotherapy, Harbin Medical University Cancer Hospital Harbin 150000, Heilongjiang, China
| | - Qinghua Huang
- Department of Breast Surgery, Wuzhou Red Cross Hospital Wuzhou 543000, Guangxi, China
| | - Yuling Qin
- Department of Clinical Laboratory, Guangxi Medical University Cancer Hospital Nanning 530000, Guangxi, China
| | - Xianhui Bao
- Department of Neurology, Harbin The First Hospital Harbin 150000, Heilongjiang, China
| | - You Pan
- Department of Breast Surgery, Guangxi Medical University Cancer Hospital Nanning 530000, Guangxi, China
| | - Jianlan Mo
- Department of Anesthesiology, The Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region Nanning 530000, Guangxi, China
| | - Shipeng Ning
- Department of Breast Surgery, Guangxi Medical University Cancer Hospital Nanning 530000, Guangxi, China
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Qing X, Yuan C, Wang K. Characterization of protein-based risk signature to predict prognosis and evaluate the tumor immune environment in breast cancer. Breast Cancer 2023; 30:424-435. [PMID: 36732487 DOI: 10.1007/s12282-023-01435-8] [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: 08/08/2022] [Accepted: 01/14/2023] [Indexed: 02/04/2023]
Abstract
BACKGROUND Proteomics profiles have enabled a systematic insight into the prognosis of cancer. This study aimed to establish a valuable protein-based risk signature to assess the prognosis and immune status in patients with breast cancer (BC). METHODS Protein expression profile, RNA expression data, and clinical information were acquired from The Cancer Genome Atlas (TCGA). The whole cohort was randomly split into two cohorts, one for establishing the risk signature and the other for testing. Univariate Cox analysis and Least absolute shrinkage and selection operator (LASSO) Cox regression were utilized to construct the protein-based risk signature. All cohorts were divided into high- and low-risk groups, which were applied to investigate the clinical relevance, tumor microenvironment, and therapeutic response. RESULTS The prognostic proteomics signature was established based on prognostic proteins, thus categorizing patients into low-risk and high-risk groups with different prognoses. A predictive nomogram was also developed to predict 1, 3, and 5-year survival possibility for BC patients, and the calibration curves confirmed the predictive significance of this signature. Afterward, the low-risk group displayed higher immune activities, immune checkpoint expression, and immunotherapeutic response. Moreover, GSEA analysis indicated that immune-associated pathways were rich in the low-risk group. Additionally, this prognostic signature demonstrated potential predict significance for chemotherapeutic agents. CONCLUSION This study established an effective prognostic proteomics signature with reliable predictive performance for survival, immune activity, and drug sensitivity. It might provide a novel perspective into the protein function in BC, and guide the individual treatment strategies for BC patients.
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Affiliation(s)
- Xin Qing
- Clinical Laboratory, Boai Hospital of Zhongshan Affiliated to Southern Medical University, Zhongshan, China
- Department of General Surgery, West China Hospital, Sichuan University, Chengdu, China
| | - Chunlei Yuan
- Clinical Laboratory, Boai Hospital of Zhongshan Affiliated to Southern Medical University, Zhongshan, China.
| | - Ke Wang
- Clinical Laboratory, Boai Hospital of Zhongshan Affiliated to Southern Medical University, Zhongshan, China.
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Li W, Wang R, Wang W. Exploring the causality and pathogenesis of systemic lupus erythematosus in breast cancer based on Mendelian randomization and transcriptome data analyses. Front Immunol 2023; 13:1029884. [PMID: 36726984 PMCID: PMC9885086 DOI: 10.3389/fimmu.2022.1029884] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Accepted: 12/28/2022] [Indexed: 01/18/2023] Open
Abstract
Introduction There has been a cumulative interest in relationships between systemic lupus erythematosus (SLE) and cancer risk. Breast cancer is the most common cancer among women worldwide. However, the casual association and pathogenesis between SLE and breast cancer remains incompletely unknown. Methods Mendelian randomization (MR) analysis was first conducted to investigate the potential causality between SLE and breast cancer. Sensitivity analyses were applied to validate the reliability of MR results. Transcriptomic data analyses based on the Cancer Genome Atlas and Gene Expression Omnibus databases were then performed to identify and construct a SLE-related gene signature (SLEscore). Results The MR analysis demonstrated that genetic predisposition to SLE was casually associated with the decreased risk of breast cancer in the East Asian cohort (odds ratios: 0.95, 95% confidence interval: 0.92-0.98, p=0.006). However, no casual associations were observed in the European population. Furthermore, sensitivity analyses proved the robustness of the present MR results. A prognostic SLEscore consisting of five SLE-related genes (RACGAP1, HMMR, TTK, TOP2A, and KIF15) could distribute patients with breast cancer into the high- and low-risk groups according to survival rates with good predictive ability (p < 0.05). Conclusion Our MR study provided evidence that genetic changes in SLE were significantly associated with the decreased risk of breast cancer in the East Asian population, while no causality was found in the European cohorts. Transcriptome data analyses indicated that the SLEscore could serve as a novel biomarker for predicting prognosis when breast cancer and SLE coexisted in patients.
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Li J, Wu F, Li C, Sun S, Feng C, Wu H, Chen X, Wang W, Zhang Y, Liu M, Liu X, Cai Y, Jia Y, Qiao H, Zhang Y, Zhang S. The cuproptosis-related signature predicts prognosis and indicates immune microenvironment in breast cancer. Front Genet 2022; 13:977322. [PMID: 36226193 PMCID: PMC9548612 DOI: 10.3389/fgene.2022.977322] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 09/06/2022] [Indexed: 11/20/2022] Open
Abstract
Breast cancer (BC) is the most diagnosed cancer in women. Cuproptosis is new regulated cell death, distinct from known death mechanisms and dependent on copper and mitochondrial respiration. However, the comprehensive relationship between cuproptosis and BC is still blank until now. In the present study, we acquired 13 cuproptosis-related regulators (CRRs) from the previous research and downloaded the RNA sequencing data of TCGA-BRCA from the UCSC XENA database. The 13 CRRs were all differently expressed between BC and normal samples. Using consensus clustering based on the five prognostic CRRs, BC patients were classified into two cuproptosis-clusters (C1 and C2). C2 had a significant survival advantage and higher immune infiltration levels than C1. According to the Cox and LASSO regression analyses, a novel cuproptosis-related prognostic signature was developed to predict the prognosis of BC effectively. The high- and low-risk groups were divided based on the risk scores. Kaplan-Meier survival analysis indicated that the high-risk group had shorter overall survival (OS) than the low-risk group in the training, test and entire cohorts. GSEA indicated that the immune-related pathways were significantly enriched in the low-risk group. According to the CIBERSORT and ESTIMATE analyses, patients in the high-risk group had higher infiltrating levels of antitumor lymphocyte cell subpopulations and higher immune score than the low-risk group. The typical immune checkpoints were all elevated in the high-risk group. Furthermore, the high-risk group showed a better immunotherapy response than the low-risk group based on the Tumor Immune Dysfunction and Exclusion (TIDE) and Immunophenoscore (IPS). In conclusion, we identified two cuproptosis-clusters with different prognoses using consensus clustering in BC. We also developed a cuproptosis-related prognostic signature and nomogram, which could indicate the outcome, the tumor immune microenvironment, as well as the response to immunotherapy.
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Affiliation(s)
- Jia Li
- Department of Oncology, The Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Fei Wu
- Department of Oncology, The Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Chaofan Li
- Department of Oncology, The Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Shiyu Sun
- Department of Oncology, The Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Cong Feng
- Department of Oncology, The Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Huizi Wu
- Department of Oncology, The Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Xi Chen
- Department of Oncology, The Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Weiwei Wang
- Department of Oncology, The Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Yu Zhang
- Department of Oncology, The Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Mengji Liu
- Department of Oncology, The Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Xuan Liu
- Department of Oncology, The Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Yifan Cai
- Department of Oncology, The Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Yiwei Jia
- Department of Oncology, The Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Hao Qiao
- Department of Orthopedics, The Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Yinbin Zhang
- Department of Oncology, The Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
- *Correspondence: Yinbin Zhang, ; Shuqun Zhang,
| | - Shuqun Zhang
- Department of Oncology, The Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
- *Correspondence: Yinbin Zhang, ; Shuqun Zhang,
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