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Hu Y, Du Y, Qiu Z, Bai P, Bai Z, Zhu C, Wang J, Liang T, Da M. Construction of a Cuproptosis-Related Gene Signature for Predicting Prognosis in Gastric Cancer. Biochem Genet 2024; 62:40-58. [PMID: 37243753 DOI: 10.1007/s10528-023-10406-9] [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: 12/23/2022] [Accepted: 05/18/2023] [Indexed: 05/29/2023]
Abstract
This study aimed to develop and validate a cuproptosis-related gene signature for the prognosis of gastric cancer. The data in TCGA GC TPM format from UCSC were extracted for analysis, and GC samples were randomly divided into training and validation groups. Pearson correlation analysis was used to obtain cuproptosis-related genes co-expressed with 19 Cuproptosis genes. Univariate Cox and Lasso regression analyses were used to obtain cuproptosis-related prognostic genes. Multivariate Cox regression analysis was used to construct the final prognostic risk model. The risk score curve, Kaplan-Meier survival curves, and ROC curve were used to evaluate the predictive ability of Cox risk model. Finally, the functional annotation of the risk model was obtained through enrichment analysis. Then, a six-gene signature was identified in the training cohort and verified among all cohorts using Cox regression analyses and Kaplan-Meier plots, demonstrating its independent prognostic significance for gastric cancer. In addition, ROC analysis confirmed the significant predictive potential of this signature for the prognosis of gastric cancer. Functional enrichment analysis was mainly related to cell-matrix function. Therefore, a new cuproptosis-related six-gene signature (ACLY, FGD6, SERPINE1, SPATA13, RANGAP1, and ADGRE5) was constructed for the prognosis of gastric cancer, allowing for tailored prediction of outcome and the formulation of novel therapeutics for gastric cancer patients.
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Affiliation(s)
- Yongli Hu
- The First Clinical Medical College of Lanzhou University, Lanzhou University, Lanzhou, China
| | - Yan Du
- The First Clinical Medical College of Lanzhou University, Lanzhou University, Lanzhou, China
| | - Zhisheng Qiu
- Department of Oncology Surgery, Gansu Provincial Hospital, Lanzhou, China
| | - Pengwei Bai
- Clinical Medicine College, Ningxia Medical University, Yinchuan, China
| | - Zhaozhao Bai
- Clinical Medicine College, Ningxia Medical University, Yinchuan, China
| | - Chenglou Zhu
- The First Clinical Medical College of Lanzhou University, Lanzhou University, Lanzhou, China
| | - Junhong Wang
- The First Clinical Medical College of Lanzhou University, Lanzhou University, Lanzhou, China
| | - Tong Liang
- The First Clinical Medical College of Lanzhou University, Lanzhou University, Lanzhou, China
| | - Mingxu Da
- The First Clinical Medical College of Lanzhou University, Lanzhou University, Lanzhou, China.
- Department of Oncology Surgery, Gansu Provincial Hospital, Lanzhou, China.
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Joshi A, Gohil VM. Cardiolipin deficiency leads to the destabilization of mitochondrial magnesium channel MRS2 in Barth syndrome. Hum Mol Genet 2023; 32:3353-3360. [PMID: 37721533 DOI: 10.1093/hmg/ddad153] [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: 07/17/2023] [Revised: 09/10/2023] [Accepted: 09/11/2023] [Indexed: 09/19/2023] Open
Abstract
Barth syndrome (BTHS) is a debilitating X-linked cardio-skeletal myopathy caused by loss-of-function mutations in TAFAZZIN, a cardiolipin (CL)-remodeling enzyme required for the maintenance of normal levels of CL species in mitochondrial membranes. At present, how perturbations in CL abundance and composition lead to many debilitating clinical presentations in BTHS patients have not been fully elucidated. Inspired by our recent findings that CL is essential for optimal mitochondrial calcium uptake, we measured the levels of other biologically important metal ions in BTHS mitochondria and found that in addition to calcium, magnesium levels are significantly reduced. Consistent with this observation, we report a decreased abundance of the mitochondrial magnesium influx channel MRS2 in multiple models of BTHS including yeast, murine myoblast, and BTHS patient cells and cardiac tissue. Mechanistically, we attribute reduced steady-state levels of MRS2 to its increased turnover in CL-deficient BTHS models. By expressing Mrs2 in well-characterized yeast mutants of the phospholipid biosynthetic pathways, we demonstrate a specific requirement of CL for Mrs2 abundance and assembly. Finally, we provide in vitro evidence for the direct binding of CL with human MRS2. Together, our study has identified a critical requirement of CL for MRS2 stability and suggests perturbation of mitochondrial magnesium homeostasis as a novel contributing factor to BTHS pathology.
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Affiliation(s)
- Alaumy Joshi
- Department of Biochemistry and Biophysics, Texas A&M University, 301 Old Main Drive, TAMU 3474, College Station, TX 77843, United States
| | - Vishal M Gohil
- Department of Biochemistry and Biophysics, Texas A&M University, 301 Old Main Drive, TAMU 3474, College Station, TX 77843, United States
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Zhang Y, Wen MH, Qin G, Cai C, Chen TY. Subcellular redox responses reveal different Cu-dependent antioxidant defenses between mitochondria and cytosol. Metallomics 2022; 14:mfac087. [PMID: 36367501 PMCID: PMC9686363 DOI: 10.1093/mtomcs/mfac087] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 11/01/2022] [Indexed: 11/13/2023]
Abstract
Excess intracellular Cu perturbs cellular redox balance and thus causes diseases. However, the relationship between cellular redox status and Cu homeostasis and how such an interplay is coordinated within cellular compartments has not yet been well established. Using combined approaches of organelle-specific redox sensor Grx1-roGFP2 and non-targeted proteomics, we investigate the real-time Cu-dependent antioxidant defenses of mitochondria and cytosol in live HEK293 cells. The Cu-dependent real-time imaging experiments show that CuCl2 treatment results in increased oxidative stress in both cytosol and mitochondria. In contrast, subsequent excess Cu removal by bathocuproine sulfonate, a Cu chelating reagent, lowers oxidative stress in mitochondria but causes even higher oxidative stress in the cytosol. The proteomic data reveal that several mitochondrial proteins, but not cytosolic ones, undergo significant abundance change under Cu treatments. The proteomic analysis also shows that proteins with significant changes are related to mitochondrial oxidative phosphorylation and glutathione synthesis. The differences in redox behaviors and protein profiles in different cellular compartments reveal distinct mitochondrial and cytosolic response mechanisms upon Cu-induced oxidative stress. These findings provide insights into how redox and Cu homeostasis interplay by modulating specific protein expressions at the subcellular levels, shedding light on understanding the effects of Cu-induced redox misregulation on the diseases.
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Affiliation(s)
- Yuteng Zhang
- Department of Chemistry, University of Houston, Houston, TX 77204, USA
| | - Meng-Hsuan Wen
- Department of Chemistry, University of Houston, Houston, TX 77204, USA
| | - Guoting Qin
- Department of Chemistry, University of Houston, Houston, TX 77204, USA
- College of Optometry, University of Houston, Houston, TX 77204, USA
| | - Chengzhi Cai
- Department of Chemistry, University of Houston, Houston, TX 77204, USA
| | - Tai-Yen Chen
- Department of Chemistry, University of Houston, Houston, TX 77204, USA
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Zhao X, Chen J, Yin S, Shi J, Zheng M, He C, Meng H, Han Y, Han J, Guo J, Yuan Z, Wang Y. The expression of cuproptosis-related genes in hepatocellular carcinoma and their relationships with prognosis. Front Oncol 2022; 12:992468. [PMID: 36313717 PMCID: PMC9614267 DOI: 10.3389/fonc.2022.992468] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 09/22/2022] [Indexed: 11/22/2022] Open
Abstract
Background The mechanism of cuproptosis has recently been reported in lipoylated proteins of the tricarboxylic acid (TCA) cycle. Besides, the role of copper was previously recognized in cancer progression. We evaluated the prognostic value of cuproptosis-related gene expression in hepatocellular carcinoma (HCC). Methods Remarkable genes were selected both in differential expression analysis and Kaplan-Meier survival analysis from ninety-six cuproptosis-related genes using The Cancer Genome Atlas (TCGA) database. The relationships between clinical characteristics and gene expression were performed with Wilcoxon signed-rank test, Kruskal-Wallis test, and logistic regression. Clinicopathologic factors correlated with overall survival in HCCs conducting univariate and multivariate Cox regression analysis. Gene Expression Profiling Interactive Analysis 2 (GEPIA2) and Human Protein Atlas (HPA) databases were utilized to verify the results. Furthermore, Gene Set Enrichment Analysis (GSEA) identified the potential key pathways that dominate cuproptosis in HCC. Results Elevated ATP7A, SLC25A3, SCO2, COA6, TMEM199, ATP6AP1, LIPT1, DLAT, PDHA1, MTF1, ACP1, FDX2, NUBP2, CIAPIN1, ISCA2 and NDOR1 expression, as well as declined AOC1, FDX1, MT-CO1, and ACO1 expression were significantly emerged in HCC tumor tissues and were significantly associated with HCCs poor survival. The expressions of screened cuproptosis-related genes were prominently related to clinical features. GSEA analysis reported many key signaling pathways (such as natural killer cell mediated cytotoxicity, TCA cycle, glutathione metabolism, ATP-binding cassette (ABC) transporters, Notch signaling pathway, ErbB signaling pathway, and metabolism of xenobiotics by cytochrome p450) were differentially enriched in HCCs with varying degrees of cuproptosis-related genes expression. Conclusions The twenty cuproptosis-related genes might be utilized as new candidate prognostic biomarkers for HCC.
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Affiliation(s)
- Xueying Zhao
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Jin Chen
- Department of Clinical Laboratory, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Shangqi Yin
- Department of Clinical Laboratory, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Jingren Shi
- Department of Clinical Laboratory, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Mei Zheng
- Department of Clinical Laboratory, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Chaonan He
- Department of Clinical Laboratory, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Huan Meng
- Department of Clinical Laboratory, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Ying Han
- Department of Clinical Laboratory, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Jinyu Han
- Department of Clinical Laboratory, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Jingjing Guo
- Department of Clinical Laboratory, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Zhengrong Yuan
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- *Correspondence: Zhengrong Yuan, ; Yajie Wang,
| | - Yajie Wang
- Department of Clinical Laboratory, Beijing Ditan Hospital, Capital Medical University, Beijing, China
- *Correspondence: Zhengrong Yuan, ; Yajie Wang,
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Swaminathan AB, Soma S, Vicary AC, Zulkifli M, Kaur H, Gohil VM. A yeast suppressor screen links Coa4 to the mitochondrial copper delivery pathway for cytochrome c oxidase. Genetics 2022; 221:6603117. [PMID: 35666203 DOI: 10.1093/genetics/iyac090] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 05/25/2022] [Indexed: 11/13/2022] Open
Abstract
Cytochrome c oxidase (CcO) is a multimeric copper-containing enzyme of the mitochondrial respiratory chain that powers cellular energy production. The two core subunits of CcO, Cox1 and Cox2, harbor the catalytic CuB and CuA sites, respectively. Biogenesis of each copper site occurs separately and requires multiple proteins that constitute the mitochondrial copper delivery pathway. Currently, the identity of all the members of the pathway is not known, though several evolutionarily conserved twin CX9C motif-containing proteins have been implicated in this process. Here, we performed a targeted yeast suppressor screen that placed Coa4, a twin CX9C motif-containing protein, in the copper delivery pathway to the Cox1 subunit. Specifically, we show that overexpression of Cox11, a copper metallochaperone required for the formation of CuB site, can restore Cox1 abundance, CcO assembly, and mitochondrial respiration in coa4Δ cells. This rescue is dependent on the copper-coordinating cysteines of Cox11. The abundance of Coa4 and Cox11 in mitochondria is reciprocally regulated, further linking Coa4 to the CuB site biogenesis. Additionally, we find that coa4Δ cells have reduced levels of copper and exogenous copper supplementation can partially ameliorate its respiratory-deficient phenotype, a finding that connects Coa4 to cellular copper homeostasis. Finally, we demonstrate that human COA4 can replace the function of yeast Coa4 indicating its evolutionarily conserved role. Our work provides genetic evidences for the role of Coa4 in the copper delivery pathway to the CuB site of CcO.
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Affiliation(s)
- Abhinav B Swaminathan
- Department of Biochemistry and Biophysics, MS 3474, Texas A&M University, College Station, TX 77843, USA
| | - Shivatheja Soma
- Department of Biochemistry and Biophysics, MS 3474, Texas A&M University, College Station, TX 77843, USA
| | - Alison C Vicary
- Department of Biochemistry and Biophysics, MS 3474, Texas A&M University, College Station, TX 77843, USA
| | - Mohammad Zulkifli
- Department of Biochemistry and Biophysics, MS 3474, Texas A&M University, College Station, TX 77843, USA
| | - Harman Kaur
- Department of Biochemistry and Biophysics, MS 3474, Texas A&M University, College Station, TX 77843, USA
| | - Vishal M Gohil
- Department of Biochemistry and Biophysics, MS 3474, Texas A&M University, College Station, TX 77843, USA
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Shurygina IA, Prozorova GF, Trukhan IS, Korzhova SA, Dremina NN, Emel’yanov AI, Say OV, Kuznetsova NP, Pozdnyakov AS, Shurygin MG. Evaluation of the Safety and Toxicity of the Original Copper Nanocomposite Based on Poly-N-vinylimidazole. NANOMATERIALS (BASEL, SWITZERLAND) 2021; 12:16. [PMID: 35009966 PMCID: PMC8746882 DOI: 10.3390/nano12010016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 12/17/2021] [Accepted: 12/18/2021] [Indexed: 06/14/2023]
Abstract
A new original copper nanocomposite based on poly-N-vinylimidazole was synthesized and characterized by a complex of modern physicochemical and biological methods. The low cytotoxicity of the copper nanocomposite in relation to the cultured hepatocyte cells was found. The possibility to involve the copper from the nanocomposite in the functioning of the copper-dependent enzyme systems was evaluated during the incubation of the hepatocyte culture with this nanocomposite introduced to the nutrient medium. The synthesized new water-soluble copper-containing nanocomposite is promising for biotechnological and biomedical research as a new non-toxic hydrophilic preparation that is allowed to regulate the work of key enzymes involved in energy metabolism and antioxidant protection as well as potentially serving as an additional source of copper.
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Affiliation(s)
- Irina A. Shurygina
- Irkutsk Scientific Center of Surgery and Traumatology, 1 Bortsov Revolutsii Street, 664003 Irkutsk, Russia; (I.S.T.); (N.N.D.); (O.V.S.); (M.G.S.)
| | - Galina F. Prozorova
- A.E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch, Russian Academy of Sciences, 1 Favorsky Street, 664033 Irkutsk, Russia; (G.F.P.); (S.A.K.); (A.I.E.); (N.P.K.); (A.S.P.)
| | - Irina S. Trukhan
- Irkutsk Scientific Center of Surgery and Traumatology, 1 Bortsov Revolutsii Street, 664003 Irkutsk, Russia; (I.S.T.); (N.N.D.); (O.V.S.); (M.G.S.)
| | - Svetlana A. Korzhova
- A.E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch, Russian Academy of Sciences, 1 Favorsky Street, 664033 Irkutsk, Russia; (G.F.P.); (S.A.K.); (A.I.E.); (N.P.K.); (A.S.P.)
| | - Nataliya N. Dremina
- Irkutsk Scientific Center of Surgery and Traumatology, 1 Bortsov Revolutsii Street, 664003 Irkutsk, Russia; (I.S.T.); (N.N.D.); (O.V.S.); (M.G.S.)
| | - Artem I. Emel’yanov
- A.E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch, Russian Academy of Sciences, 1 Favorsky Street, 664033 Irkutsk, Russia; (G.F.P.); (S.A.K.); (A.I.E.); (N.P.K.); (A.S.P.)
| | - Olesya V. Say
- Irkutsk Scientific Center of Surgery and Traumatology, 1 Bortsov Revolutsii Street, 664003 Irkutsk, Russia; (I.S.T.); (N.N.D.); (O.V.S.); (M.G.S.)
| | - Nadezhda P. Kuznetsova
- A.E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch, Russian Academy of Sciences, 1 Favorsky Street, 664033 Irkutsk, Russia; (G.F.P.); (S.A.K.); (A.I.E.); (N.P.K.); (A.S.P.)
| | - Alexander S. Pozdnyakov
- A.E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch, Russian Academy of Sciences, 1 Favorsky Street, 664033 Irkutsk, Russia; (G.F.P.); (S.A.K.); (A.I.E.); (N.P.K.); (A.S.P.)
| | - Michael G. Shurygin
- Irkutsk Scientific Center of Surgery and Traumatology, 1 Bortsov Revolutsii Street, 664003 Irkutsk, Russia; (I.S.T.); (N.N.D.); (O.V.S.); (M.G.S.)
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