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Ni M, Wan D, Wu J, Gong W, Wang J, Zheng Z. Candidate prognostic biomarkers and prediction models for high-grade serous ovarian cancer from urinary proteomics. J Proteomics 2024; 304:105234. [PMID: 38925351 DOI: 10.1016/j.jprot.2024.105234] [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: 04/09/2024] [Revised: 06/22/2024] [Accepted: 06/22/2024] [Indexed: 06/28/2024]
Abstract
High-grade serous ovarian cancer (HGSOC) is one of the most common histologic types of ovarian cancer. The purpose of this study was to identify potential prognostic biomarkers in urine specimens from patients with HGSOC. First, 56 urine samples with information on relapse-free survival (RFS) months were collected and classified into good prognosis (RFS ≥ 12 months) and poor prognosis (RFS < 12 months) groups. Next, data-independent acquisition (DIA)-based mass spectrometry (MS) analysis was combined with MSFragger-DIA workflow to identify potential prognostic biomarkers in a discovery set (n = 31). With the aid of parallel reaction monitoring (PRM) analysis, four candidate biomarkers (ANXA1, G6PI, SPB3, and SPRR3) were finally validated in both the discovery set and an independent validation set (n = 25). Subsequent RFS and Cox regression analyses confirmed the utility of these candidate biomarkers as independent prognostic factors affecting RFS in patients with HGSOC. Regression models were constructed to predict the 12-month RFS rate, with area under the receiver operating characteristic curve (AUC) values ranging from 0.847 to 0.905. Overall, candidate prognostic biomarkers were identified in urine specimens from patients with HGSOC and prediction models for the 12-month RFS rate constructed. SIGNIFICANCE: OC is one of the leading causes of death due to gynecological malignancies. HGSOC constitutes one of the most common histologic types of OC with aggressive characteristics, accounting for the majority of advanced cases. In cases where patients with advanced HGSOC potentially face high risk of unfavorable prognosis or disease advancement within a 12-month period, intensive medical monitoring is necessary. In the era of precision cancer medicine, accurate prediction of prognosis or 12-month RFS rate is critical for distinguishing patient groups requiring heightened surveillance. Patients could significantly benefit from timely modifications to treatment regimens based on the outcomes of clinical monitoring. Urine is an ideal resource for disease surveillance purposes due to its easy accessibility. Furthermore, molecules excreted in urine are less complex and more stable than those in other liquid samples. In the current study, we identified candidate prognostic biomarkers in urine specimens from patients with HGSOC and constructed prediction models for the 12-month RFS rate.
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Affiliation(s)
- Maowei Ni
- Zhejiang Cancer Hospital, Hangzhou, Zhejiang 310022, China; Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Danying Wan
- Zhejiang Cancer Hospital, Hangzhou, Zhejiang 310022, China; Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Junzhou Wu
- Zhejiang Cancer Hospital, Hangzhou, Zhejiang 310022, China; Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Wangang Gong
- Zhejiang Cancer Hospital, Hangzhou, Zhejiang 310022, China; Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Junjian Wang
- Zhejiang Cancer Hospital, Hangzhou, Zhejiang 310022, China; Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Zhiguo Zheng
- Zhejiang Cancer Hospital, Hangzhou, Zhejiang 310022, China; Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China.
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Wu L, Dong J, Fei D, Le T, Xiao L, Liu J, Yu Z. Fructose-1, 6-Bisphosphate Aldolase B Suppresses Glycolysis and Tumor Progression of Gastric Cancer. Dig Dis Sci 2024:10.1007/s10620-024-08568-6. [PMID: 39068380 DOI: 10.1007/s10620-024-08568-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Accepted: 07/15/2024] [Indexed: 07/30/2024]
Abstract
OBJECTIVE Gastric cancer (GC) is believed to be one of the most common digestive tract malignant tumors. However, mounting evidence indicates a link between the glycolysis and tumorigenesis, including gastric cancer. METHODS Our research identified 5508 differently expressed mRNAs in gastric cancer. Then, the genes highly associated with tumorigenesis were identified through weighted correlation network analysis (WGCNA). Bioinformatics analysis observed that these hub genes were significantly linked to the regulation of cell cycle, drug metabolism, and glycolysis. Among these hub genes, there is a critical gene involved in glycolysis regulation, namely fructose-bisphosphate B (ALDOB). RESULTS Analysis based on The Cancer Genome Atlas (TCGA) and three Gene Expression Omnibus (GEO) datasets revealed that ALDOB was significantly downregulated in GC compared with normal tissues. In addition, cell viability assay confirmed that ALDOB acted as a tumor suppressor. Finally, drug sensitivity analysis revealed that ALDOB increased the sensitivity of gastric cancer cells to most antitumor drugs, especially talazoparib, XAV939, and FTI-277. Our results showed that the expression of ALDOB was significantly lower in GC tissues than in normal tissues. And ALDOB significantly inhibited proliferation and migration, delayed glycolysis in GC cells. Consequently, our study suggests that ALDOB may be a potential target for the clinical treatment of gastric cancer.
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Affiliation(s)
- Liping Wu
- The Department of Science and Education, Zhoushan Hospital, Wenzhou Medical University, Zhoushan, Zhejiang, China
| | - Jinliang Dong
- Department of General Surgery, Zhoushan Hospital, Wenzhou Medical University, No. 739 Dingshen Road, Lincheng New District, Zhoushan, Zhejiang, China
| | - Dailiang Fei
- Department of General Surgery, Zhoushan Hospital, Wenzhou Medical University, No. 739 Dingshen Road, Lincheng New District, Zhoushan, Zhejiang, China
| | - Ting Le
- The Laboratory of Cytobiology and Molecular Biology, Zhoushan Hospital, Wenzhou Medical University, No. 739 Dingshen Road, Lincheng New District, Zhoushan, Zhejiang, China
| | - Liang Xiao
- The Department of Surgery and Oncology, Shenzhen Second People's Hospital, Shenzhen, Guangdong, China
| | - Jia Liu
- School of Agriculture, Sun Yat-Sen University, No. 66 Gongchang Road, Guangming District, Shenzhen, Guangdong, China
- Shenzhen Zhongjia Bio-Medical Technology Co., Ltd, No. 66 Gongchang Road, Guangming District, Shenzhen, Guangdong, China
| | - Ze Yu
- Department of General Surgery, Zhoushan Hospital, Wenzhou Medical University, No. 739 Dingshen Road, Lincheng New District, Zhoushan, Zhejiang, China.
- The Laboratory of Cytobiology and Molecular Biology, Zhoushan Hospital, Wenzhou Medical University, No. 739 Dingshen Road, Lincheng New District, Zhoushan, Zhejiang, China.
- The Second Affiliated Hospital of Zhejiang University, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.
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Mi Y, Shan H, Wang B, Tang H, Jia J, Liu X, Yang Q. Genipin inhibits proliferation of gastric cancer cells by inducing ferroptosis: an integrated study of network pharmacology and bioinformatics study. Med Oncol 2024; 41:46. [PMID: 38175425 DOI: 10.1007/s12032-023-02283-4] [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: 11/01/2023] [Accepted: 12/07/2023] [Indexed: 01/05/2024]
Abstract
Ferroptosis has been demonstrated to suppress cancer development and is targeted for cancer therapy. Genipin, an iridoid constituent in Gardeniae Fructus, has been reported to exert anti-cancer abilities. However, whether genipin could induce ferroptosis remains unclear. The purpose of this study is to explore the anti-gastric cancer (GC) effects of genipin by inducing ferroptosis and to identify the potential targets. CCK-8 and colony formation assays were performed to evaluate the anti-GC effects of genipin. Flowcytometry and western blot were used to indicate ferroptosis-inducing ability of genipin. The potential targets of genipin were analyzed by network pharmacology, screened using UALCAN and KM-plotter database and evaluated by molecular docking. The results showed that genipin inhibited cell viability and proliferation of GC cells. Genipin treatment decreased levels of GPX4 and SLC7A11, induced accumulation of lipid peroxidation intracellularly and led to ferroptosis in GC cells. Network pharmacology analysis identified that lipid- and ROS-related pathways involved in ferroptosis ranked high among genipin-GC common targets. Data from UALCAN and KM-plotter database demonstrated that expression levels of ferroptosis-related targets, including AURKA, BCAT2, DHODH, and GPI, increased in GC tissues and the higher levels of the above four targets were related to tumor stage, tumor grade, and poor prognosis. Among these four targets, AURKA, BCAT2, and DHODH were confirmed by molecular docking with binding energies less than - 5. Taken together, our study demonstrates that genipin could exert anti-GC ability by inducing ferroptosis and provides evidence for the potential application of genipin in GC treatment.
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Affiliation(s)
- Yalu Mi
- College of Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan, 250355, Shandong, China
- Institute of Pathogen Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, 250012, Shandong, China
| | - Hui Shan
- Institute of Pathogen Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, 250012, Shandong, China
| | - Bo Wang
- Department of Traditional Medicine, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250012, Shandong, China
| | - Huidi Tang
- Institute of Pathogen Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, 250012, Shandong, China
| | - Jihui Jia
- Institute of Pathogen Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, 250012, Shandong, China
- Key Laboratory for Experimental Teratology of the Chinese Ministry of Education, School of Basic Medical Science, Cheeloo College of Medicine, Shandong University, Jinan, 250012, Shandong, China
- Shandong Key Laboratory of Infection and Immunity, Shandong University, Jinan, 250012, Shandong, China
| | - Xijian Liu
- College of Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan, 250355, Shandong, China.
| | - Qing Yang
- Institute of Pathogen Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, 250012, Shandong, China.
- Key Laboratory for Experimental Teratology of the Chinese Ministry of Education, School of Basic Medical Science, Cheeloo College of Medicine, Shandong University, Jinan, 250012, Shandong, China.
- Shandong Key Laboratory of Infection and Immunity, Shandong University, Jinan, 250012, Shandong, China.
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Xu H, Liu W, He C, Mirza M, Li B. Aberrant expression of multiple glycolytic enzyme genes is significantly associated with disease progression and survival outcomes in prostate cancers. AMERICAN JOURNAL OF CLINICAL AND EXPERIMENTAL UROLOGY 2023; 11:530-541. [PMID: 38148940 PMCID: PMC10749383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 09/26/2023] [Indexed: 12/28/2023]
Abstract
Prostate cancer is the leading cause of cancer death after lung cancer in men. Recent studies showed that aberrant metabolic pathways are involved in prostate cancer development and progression. In this study, we performed a systemic analysis of glycolytic enzyme gene expression using the TCGA-PRAD RNAseq dataset. Our analysis revealed that among 25 genes, only four genes (HK2/GPI/PFKL/PGAM5) were significantly upregulated while nine genes (HK1/GCK/PFKM/PFKP/ALDOC/PGK1/PGAM1/ENO2/PKM) were downregulated in primary prostate cancer tissues compared to benign compartments. Among these 13 altered genes, four genes (ENO2/ALDOC/GPI/GCK) exhibited strong diagnostic potential in distinguishing malignant and benign tissues. Meanwhile, GPI expression exerted as a prognostic factor of progression-free and disease-specific survival. PFKL and PGAM5 gene expressions were associated with AR signaling scores in castration-resistant patients, and AR-targeted therapy suppressed their expression. In LuCap35 xenograft tumors, PFKL and PGAM5 expression was significantly reduced after animal castration, confirming the AR dependency. Conversely, GCK/PKLR genes were significantly associated with neuroendocrinal progression, representing two novel neuroendocrinal biomarkers for prostate cancer. In conclusion, our results suggest that GPI expression is a strong prognostic factor for prostate cancer progression and survival while GCK/PKLR are two novel biomarkers of prostate cancer progression to neuroendocrinal status.
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Affiliation(s)
- Haixia Xu
- Department of Medical Oncology, The First Affiliated Hospital of Shenzhen University and Shenzhen Second People’s HospitalShenzhen 518035, Guangdong, China
| | - Wang Liu
- Department of Urology, The University of Kansas Medical CenterKansas, KS 66160, USA
| | - Chenchen He
- Department of Radiation Oncology, The First Affiliated Hospital of Xi’an Jiaotong University School of MedicineXi’an 710061, Shaanxi, China
| | - Moben Mirza
- Department of Urology, The University of Kansas Medical CenterKansas, KS 66160, USA
| | - Benyi Li
- Department of Urology, The University of Kansas Medical CenterKansas, KS 66160, USA
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Jayathirtha M, Jayaweera T, Whitham D, Sullivan I, Petre BA, Darie CC, Neagu AN. Two-Dimensional-PAGE Coupled with nLC-MS/MS-Based Identification of Differentially Expressed Proteins and Tumorigenic Pathways in MCF7 Breast Cancer Cells Transfected for JTB Protein Silencing. Molecules 2023; 28:7501. [PMID: 38005222 PMCID: PMC10673289 DOI: 10.3390/molecules28227501] [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: 09/27/2023] [Revised: 10/29/2023] [Accepted: 10/31/2023] [Indexed: 11/26/2023] Open
Abstract
The identification of new cancer-associated genes/proteins, the characterization of their expression variation, the interactomics-based assessment of differentially expressed genes/proteins (DEGs/DEPs), and understanding the tumorigenic pathways and biological processes involved in BC genesis and progression are necessary and possible by the rapid and recent advances in bioinformatics and molecular profiling strategies. Taking into account the opinion of other authors, as well as based on our own team's in vitro studies, we suggest that the human jumping translocation breakpoint (hJTB) protein might be considered as a tumor biomarker for BC and should be studied as a target for BC therapy. In this study, we identify DEPs, carcinogenic pathways, and biological processes associated with JTB silencing, using 2D-PAGE coupled with nano-liquid chromatography tandem mass spectrometry (nLC-MS/MS) proteomics applied to a MCF7 breast cancer cell line, for complementing and completing our previous results based on SDS-PAGE, as well as in-solution proteomics of MCF7 cells transfected for JTB downregulation. The functions of significant DEPs are analyzed using GSEA and KEGG analyses. Almost all DEPs exert pro-tumorigenic effects in the JTBlow condition, sustaining the tumor suppressive function of JTB. Thus, the identified DEPs are involved in several signaling and metabolic pathways that play pro-tumorigenic roles: EMT, ERK/MAPK, PI3K/AKT, Wnt/β-catenin, mTOR, C-MYC, NF-κB, IFN-γ and IFN-α responses, UPR, and glycolysis/gluconeogenesis. These pathways sustain cancer cell growth, adhesion, survival, proliferation, invasion, metastasis, resistance to apoptosis, tight junctions and cytoskeleton reorganization, the maintenance of stemness, metabolic reprogramming, survival in a hostile environment, and sustain a poor clinical outcome. In conclusion, JTB silencing might increase the neoplastic phenotype and behavior of the MCF7 BC cell line. The data is available via ProteomeXchange with the identifier PXD046265.
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Affiliation(s)
- Madhuri Jayathirtha
- Biochemistry & Proteomics Laboratories, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699, USA; (M.J.); (T.J.); (D.W.); (I.S.); (C.C.D.)
| | - Taniya Jayaweera
- Biochemistry & Proteomics Laboratories, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699, USA; (M.J.); (T.J.); (D.W.); (I.S.); (C.C.D.)
| | - Danielle Whitham
- Biochemistry & Proteomics Laboratories, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699, USA; (M.J.); (T.J.); (D.W.); (I.S.); (C.C.D.)
| | - Isabelle Sullivan
- Biochemistry & Proteomics Laboratories, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699, USA; (M.J.); (T.J.); (D.W.); (I.S.); (C.C.D.)
| | - Brîndușa Alina Petre
- Biochemistry & Proteomics Laboratories, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699, USA; (M.J.); (T.J.); (D.W.); (I.S.); (C.C.D.)
- Laboratory of Biochemistry, Department of Chemistry, “Alexandru Ioan Cuza” University of Iasi, Carol I bvd, No. 11, 700506 Iasi, Romania
- Center for Fundamental Research and Experimental Development in Translation Medicine–TRANSCEND, Regional Institute of Oncology, 700483 Iasi, Romania
| | - Costel C. Darie
- Biochemistry & Proteomics Laboratories, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699, USA; (M.J.); (T.J.); (D.W.); (I.S.); (C.C.D.)
| | - Anca-Narcisa Neagu
- Laboratory of Animal Histology, Faculty of Biology, “Alexandru Ioan Cuza” University of Iasi, Carol I Bvd. No. 22, 700505 Iasi, Romania
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Yang H, Tian Z. Sialic acid linkage-specific quantitative N-glycoproteomics using selective alkylamidation and multiplex TMT-labeling. Anal Chim Acta 2022; 1230:340391. [DOI: 10.1016/j.aca.2022.340391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 09/07/2022] [Accepted: 09/10/2022] [Indexed: 11/25/2022]
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Xiao C, Tian H, Zheng Y, Yang Z, Li S, Fan T, Xu J, Bai G, Liu J, Deng Z, Li C, He J. Glycolysis in tumor microenvironment as a target to improve cancer immunotherapy. Front Cell Dev Biol 2022; 10:1013885. [PMID: 36200045 PMCID: PMC9527271 DOI: 10.3389/fcell.2022.1013885] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 09/07/2022] [Indexed: 12/03/2022] Open
Abstract
Cancer cells and immune cells all undergo remarkably metabolic reprogramming during the oncogenesis and tumor immunogenic killing processes. The increased dependency on glycolysis is the most typical trait, profoundly involved in the tumor immune microenvironment and cancer immunity regulation. However, how to best utilize glycolytic targets to boost anti-tumor immunity and improve immunotherapies are not fully illustrated. In this review, we describe the glycolytic remodeling of various immune cells within the tumor microenvironment (TME) and the deleterious effects of limited nutrients and acidification derived from enhanced tumor glycolysis on immunological anti-tumor capacity. Moreover, we elucidate the underlying regulatory mechanisms of glycolytic reprogramming, including the crosstalk between metabolic pathways and immune checkpoint signaling. Importantly, we summarize the potential glycolysis-related targets that are expected to improve immunotherapy benefits. Our understanding of metabolic effects on anti-tumor immunity will be instrumental for future therapeutic regimen development.
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Affiliation(s)
- Chu Xiao
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - He Tian
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Yujia Zheng
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Zhenlin Yang
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Shuofeng Li
- Department of Colorectal Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Tao Fan
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Jiachen Xu
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Guangyu Bai
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Jingjing Liu
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Ziqin Deng
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Chunxiang Li
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
- *Correspondence: Chunxiang Li, ; Jie He,
| | - Jie He
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
- *Correspondence: Chunxiang Li, ; Jie He,
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Li L, Lu S, Ma C. Anti-proliferative and pro-apoptotic effects of curcumin on skin cutaneous melanoma: Bioinformatics analysis and in vitro experimental studies. Front Genet 2022; 13:983943. [PMID: 36171883 PMCID: PMC9510772 DOI: 10.3389/fgene.2022.983943] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 08/23/2022] [Indexed: 11/26/2022] Open
Abstract
Objective: To reveal the potential mechanisms of curcumin for the treatment of skin cutaneous melanoma (SKCM) and its identify novel prognostic biomarkers. Methods: We searched the Cancer Genome Atlas and Traditional Chinese Medicine Systems Pharmacology database for the data on SKCM and curcumin. We conducted data analysis using R and online tools. The propagation and migration of SKCM cells were assessed with CCK-8 and scratch wound assays, respectively. We assessed apoptosis by TUNEL assay and western blot. Results: The survival analysis revealed that the mRNA expressions of DPYD, DPYS, LYN, PRKCQ, and TLR1 were significantly related to a favorable overall survival in SKCM patients. Additionally, the mRNA expression level of DPYD was associated with GPI, LYN, PCSK9, PRKCQ, and TLR1 mRNAs. GSEA results showed that the prognostic hub genes were augmented with ultraviolet, apoptosis, and metastasis. Curcumin expressed proliferation and migration of SK-MEL-1 cells (p < 0.05), and induced apoptosis (p < 0.05) significantly. Conclusion: Curcumin may have potential therapeutic effects in SKCM by inhibiting cell proliferation and migration and inducing apoptosis by regulating oxygen-related signaling pathways. The hub genes might be identified as novel biomarkers for SKCM.
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Affiliation(s)
- Long Li
- Department of Ophthalmology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Shuwen Lu
- Department of Ophthalmology, the First Affiliated Hospital of Henan University of Chinese Medicine, Zhengzhou, China
| | - Chao Ma
- Department of Ophthalmology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- *Correspondence: Chao Ma,
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'Warburg effect' controls tumor growth, bacterial, viral infections and immunity - Genetic deconstruction and therapeutic perspectives. Semin Cancer Biol 2022; 86:334-346. [PMID: 35820598 DOI: 10.1016/j.semcancer.2022.07.004] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 07/06/2022] [Accepted: 07/07/2022] [Indexed: 12/16/2022]
Abstract
The evolutionary pressure for life transitioning from extended periods of hypoxia to an increasingly oxygenated atmosphere initiated drastic selections for a variety of biochemical pathways supporting the robust life currently present on the planet. First, we discuss how fermentative glycolysis, a primitive metabolic pathway present at the emergence of life, is instrumental for the rapid growth of cancer, regenerating tissues, immune cells but also bacteria and viruses during infections. The 'Warburg effect', activated via Myc and HIF-1 in response to growth factors and hypoxia, is an essential metabolic and energetic pathway which satisfies nutritional and energetic demands required for rapid genome replication. Second, we present the key role of lactic acid, the end-product of fermentative glycolysis able to move across cell membranes in both directions via monocarboxylate transporting proteins (i.e. MCT1/4) contributing to cell-pH homeostasis but also to the complex immune response via acidosis of the tumour microenvironment. Importantly lactate is recycled in multiple organs as a major metabolic precursor of gluconeogenesis and energy source protecting cells and animals from harsh nutritional or oxygen restrictions. Third, we revisit the Warburg effect via CRISPR-Cas9 disruption of glucose-6-phosphate isomerase (GPI-KO) or lactate dehydrogenases (LDHA/B-DKO) in two aggressive tumours (melanoma B16-F10, human adenocarcinoma LS174T). Full suppression of lactic acid production reduces but does not suppress tumour growth due to reactivation of OXPHOS. In contrast, disruption of the lactic acid transporters MCT1/4 suppressed glycolysis, mTORC1, and tumour growth as a result of intracellular acidosis. Finally, we briefly discuss the current clinical developments of an MCT1 specific drug AZ3965, and the recent progress for a specific in vivo MCT4 inhibitor, two drugs of very high potential for future cancer clinical applications.
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He J, Zhang W, Li F, Yu Y. Development of metastasis-associated seven gene signature for predicting lung adenocarcinoma prognosis using single-cell RNA sequencing data. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2021; 18:5959-5977. [PMID: 34517518 DOI: 10.3934/mbe.2021298] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Metastasis is the primary cause of lung adenocarcinoma (LUAD)-related death. This study evaluated the metastasis-associated genes (MAGs) in single-cell RNA sequencing (scRNA-seq) data from LUAD tissues and developed a MAG signature to predict overall survival (OS) of LUAD patients. The LUAD scRNA-seq data was downloaded from the Gene Expression Omnibus (GEO) Database and MAGs were identified from LUAD scRNA-seq data. The LUAD transcriptomic and clinical data were obtained from The Cancer Genome Atlas (TCGA). Cox and LASSO regression analyses were performed to identify differentially expressed MAGs (DEMAGs) with prognostic value that were then used to construct a MAG signature and MAG-nomogram model. Finally, a functional enrichment analysis was performed via Gene Set Enrichment Analysis (GSEA). 414 MAGs and 22 prognostic DEMAGs were revealed in the study. Multivariate Cox proportional hazards regression analysis was utilized to construct a 7-MAG signature for predicting the OS of LUAD patients. Patients with high risk scores had a significantly worse OS than those with low risk scores in the training group (n = 236), and the 7-MAG signature was successfully confirmed in the testing group (n = 232) and the entire TCGA-LUAD cohort (n = 468). Furthermore, univariate and multivariate Cox regression suggested that the 7-MAG signature was an independent prognostic indicator. Additionally, based on the 7-MAG signature, a nomogram was established that could more intuitively help to predict the OS of LUAD patients. The GSEA revealed the underlying molecular mechanisms of the 7-MAG signature in LUAD metastasis. In conclusion, a 7-MAG signature was developed based on LUAD scRNA-seq data that could effectively predict LUAD patient prognosis and provide novel insights for therapeutic targets and the potential molecular mechanism of metastatic LUAD.
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Affiliation(s)
- Jinqi He
- Department of Medical Oncology, Harbin Medical University Cancer Hospital, Harbin 150081, China
| | - Wenjing Zhang
- Department of Hematology Oncology, The Central Hospital of Shaoyang, Shaoyang 422000, China
| | - Faxiang Li
- Department of Hematology Oncology, The Central Hospital of Shaoyang, Shaoyang 422000, China
| | - Yan Yu
- Department of Medical Oncology, Harbin Medical University Cancer Hospital, Harbin 150081, China
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Jeoung NH, Jo AL, Park HS. The effect of autocrine motility factor alone and in combination with methyl jasmonate on liver cancer cell growth. Biosci Biotechnol Biochem 2021; 85:1711-1715. [PMID: 33988672 DOI: 10.1093/bbb/zbab087] [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: 03/21/2021] [Accepted: 05/10/2021] [Indexed: 11/14/2022]
Abstract
Neoplastic cells secrete autocrine motility factor (AMF) to stimulate the motility of cancer cells. In this study, AMF secreted from HT-29 colorectal cancer cells selectively suppressed liver cancer cells by downregulating pAKT and β-catenin. In addition, HT-29 AMF significantly augmented the activity of methyl jasmonate against liver cancer cells and is a promising alternative for liver cancer therapy.
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Affiliation(s)
- Nam Ho Jeoung
- Department of Pharmaceutical Engineering, Catholic University of Daegu, Gyeongsan, Korea
| | - Ae Lim Jo
- Department of Pharmaceutical Engineering, Catholic University of Daegu, Gyeongsan, Korea
| | - Hee Sung Park
- Department of Biomedical Science, Catholic University of Daegu, Gyeongsan, Korea
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12
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Yu S, Hu C, Cai L, Du X, Lin F, Yu Q, Liu L, Zhang C, Liu X, Li W, Zhan Y. Seven-Gene Signature Based on Glycolysis Is Closely Related to the Prognosis and Tumor Immune Infiltration of Patients With Gastric Cancer. Front Oncol 2020; 10:1778. [PMID: 33072557 PMCID: PMC7531434 DOI: 10.3389/fonc.2020.01778] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 08/11/2020] [Indexed: 12/24/2022] Open
Abstract
Background: Gastric cancer (GC) is one of the most common malignancies worldwide, exhibiting a high morbidity, and mortality. As the various treatment methods for gastric cancer are limited by disadvantages, many efforts to improve the efficacy of these treatments are being taken. Metabolic recombination is an important characteristic of cancer and has gradually caused a recent upsurge in research. However, systematic analysis of the interaction between glycolysis and GC patient prognosis and its potential associations with immune infiltration is lacking but urgently needed. Methods: We obtained the gene expression data and clinical materials of GC derived from The Cancer Genome Atlas (TCGA) dataset. Univariate and multivariate Cox proportional regression analyses were performed to select the optimal prognosis-related genes for subsequent modeling. We then validated our data in the GEO database and further verified the gene expression using the Oncomine database and PCR experiments. Besides, Gene set variation analysis (GSVA) analysis was employed to further explore the differences in activation status of biological pathways between the high and low risk groups. Furthermore, a nomogram was adopted to predict the individualized survival rate of GC patients. Finally, a violin plot and a TIMMER analysis were performed to analyse the characteristics of immune infiltration in the microenvironment. Results: A seven-gene signature, including STC1, CLDN9, EFNA3, ZBTB7A, NT5E, NUP50, and CXCR4, was established. Based on this seven-gene signature, the patients in the training set and testing sets could be divided into high-risk and low-risk groups. In addition, a nomogram based on risk and age showed good calibration and moderate discrimination. The results proved that the seven-gene signature had a strong capacity to predict the GC patient prognosis. Collectively, the violin plot and TIMMER analysis demonstrated that an immunosuppressive tumor microenvironment caused by hyperglycolysis led to poor prognosis. Conclusion: Taken together, these results established a genetic signature for gastric cancer based on glycolysis, which has reference significance for the in-depth study of the metabolic mechanism of gastric cancer and the exploration of new clinical treatment strategies.
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Affiliation(s)
- Shanshan Yu
- Department of Chemoradiation Oncology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Chuan Hu
- Department of Orthopaedic Surgery, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Luya Cai
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Xuedan Du
- Department of Chemoradiation Oncology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Fan Lin
- Department of Dermatology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Qiongjie Yu
- Department of Chemoradiation Oncology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Lixiao Liu
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Cheng Zhang
- Department of Dermatology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Xuan Liu
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Wenfeng Li
- Department of Chemoradiation Oncology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Yu Zhan
- Department of Ultrasound, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
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13
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Chen J, Cheuk IWY, Siu MT, Yang W, Cheng ASL, Shin VY, Kwong A. Human haptoglobin contributes to breast cancer oncogenesis through glycolytic activity modulation. Am J Cancer Res 2020; 10:2865-2877. [PMID: 33042622 PMCID: PMC7539774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 03/09/2020] [Indexed: 06/11/2023] Open
Abstract
Cellular metabolism reprogramming is a hallmark in cancers including breast cancer. Switching off the glycolytic energy in cancer has been indicated as one of the anti-cancer strategies. Aberrant haptoglobin (HP) expression has been shown to cause metabolic dysfunction and implicated in different malignancies. However, its roles in breast cancer and glycolysis remain elusive. Here, we reported HP was upregulated in breast cancer tissues and the circulation. HP conferred oncogenic roles by regulating cell cycle progression and apoptosis in breast cancer cells. Further analysis identified the correlation between HP and glycolytic enzymes such as glucose-6-phosphate isomerase (GPI) and hexokinase (HK). Glycolytic activities were altered upon HP knockdown which were confirmed by glucose uptake and LDH activity assays. GPI was found to be downstream effector of HP while knockdown of GPI led to decreased glycolytic activity and restored oxygen consumption. GPI silencing decreased cell migration/invasion ability and sensitized breast cancer cells to chemo-drug. Moreover, animal study suggested inhibition of both HP and GPI significantly impeded tumor growth in mice. Collectively, we report for the first time the oncogenic roles of HP, at least partially, through regulating glycolysis and its downstream effector, GPI, contributes in maintaining EMT and chemoresistance in breast cancer.
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Affiliation(s)
- Jiawei Chen
- Department of Surgery, The University of Hong Kong and The University of Hong Kong-Shenzhen HospitalChina
| | - Isabella Wai-Yin Cheuk
- Department of Surgery, The University of Hong Kong and The University of Hong Kong-Shenzhen HospitalChina
| | - Man-Ting Siu
- Department of Surgery, The University of Hong Kong and The University of Hong Kong-Shenzhen HospitalChina
| | - Weiqin Yang
- School of Biomedical Sciences, The Chinese University of Hong KongHong Kong SAR, China
| | - Alfred SL Cheng
- School of Biomedical Sciences, The Chinese University of Hong KongHong Kong SAR, China
| | - Vivian Yvonne Shin
- Department of Surgery, The University of Hong Kong and The University of Hong Kong-Shenzhen HospitalChina
| | - Ava Kwong
- Department of Surgery, The University of Hong Kong and The University of Hong Kong-Shenzhen HospitalChina
- Department of Surgery, The Hong Kong Sanatorium and HospitalHong Kong SAR, China
- The Hong Kong Hereditary Breast Cancer Family RegistryHong Kong SAR, China
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14
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Liu J, Yang Q, Sun H, Wang X, Saiyin H, Zhang H. The circ-AMOTL1/ENO1 Axis Implicated in the Tumorigenesis of OLP-Associated Oral Squamous Cell Carcinoma. Cancer Manag Res 2020; 12:7219-7230. [PMID: 32884340 PMCID: PMC7440838 DOI: 10.2147/cmar.s251348] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 07/10/2020] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Oral squamous cell carcinoma (OSCC) may develop from a variety of oral potentially malignant disorders, but the mechanism of malignant transformation is still unknown. Among them, oral lichen planus (OLP) has a high prevalence. Previous studies have shown that α-enolase (ENO1) can promote cell proliferation and play an important role in tumorigenesis. In this study, we aim to explore the mechanism of ENO1 regulation in the process of OSCC tumorigenesis from OLP. METHODS ENO1 expression in tissues was determined by real-time quantitative PCR and immunohistochemistry. ENO1 was knocked down in cal-27 to observe the change in cell proliferation. Then, RNA-seq and bioinformatics analyses were conducted between OLP and OSCC samples. The expression of circ-AMOTL1, miRNA-22-3p, and miRNA-1294 was assessed using the real-time quantitative PCR. With knockdown and overexpression of circ-AMOTL1 in vitro, the change of ENO1 in the mRNA level was also assessed. RESULTS ENO1 was enhanced in the OSCC samples in comparison with OLP. Immunohistochemistry and real-time quantitative PCR results showed that ENO1 was significantly higher in OSCC tissue than in the OLP group, with a statistically significant difference (p<0.05). When ENO1 was knocked down in cal-27, cell proliferation was inhibited (p<0.05). The expression of miR-22-3p and miR-1294 was decreased in OSCC tissues, whereas ENO1 and circ-AMOTL1 increased. In an in vitro study, knockdown of circ-AMOTL1 resulted in a decrease of ENO1, while overexpression of circ-AMOTL1 led to an increase of ENO1 in the mRNA level. CONCLUSION We confirmed that ENO1 expression was elevated in OSCC and increased cell proliferation. In an in vitro study, ENO1 expression was promoted by circ-AMOTL1. ENO1 may play a role as a tumor-promoting gene in OSCC through the circ-AMOTL1/miR-22-3p/miR-1294 network. These novel findings may shed further light on the pathogenesis from OLP to OSCC and the potential precursor markers.
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Affiliation(s)
- Jin Liu
- Department of Stomatology, Huashan Hospital, Fudan University, Shanghai, People’s Republic of China
| | - Qiaozhen Yang
- Department of Stomatology, Huashan Hospital, Fudan University, Shanghai, People’s Republic of China
| | - Hongying Sun
- Department of Stomatology, Huashan Hospital, Fudan University, Shanghai, People’s Republic of China
| | - Xiaxia Wang
- Department of Stomatology, Huashan Hospital, Fudan University, Shanghai, People’s Republic of China
| | - Hexige Saiyin
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, People’s Republic of China
| | - Hui Zhang
- Department of Stomatology, Huashan Hospital, Fudan University, Shanghai, People’s Republic of China
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15
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Luan F, Li X, Cheng X, Huangfu L, Han J, Guo T, Du H, Wen X, Ji J. TNFRSF11B activates Wnt/β-catenin signaling and promotes gastric cancer progression. Int J Biol Sci 2020; 16:1956-1971. [PMID: 32398963 PMCID: PMC7211174 DOI: 10.7150/ijbs.43630] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2020] [Accepted: 03/23/2020] [Indexed: 12/24/2022] Open
Abstract
Tumor necrosis factor receptor superfamily member 11B (TNFRSF11B) has been studied to be involved in the development and progression of several human malignancies. However, little is unveiled regarding the complex mechanisms of TNFRSF11B in human gastric cancer (GC). The clinical significance of TNFRSF11B was assessed in 70 and 160 GC tissues using immunohistochemistry method and gene microarray analysis, respectively. The biological function of TNFRSF11B was studied in vitro and in vivo assays. Immunofluorescence assay was used to evaluate the expression of β-catenin in the nucleus. The expression of β-catenin and related protein was determined by Western blot. The interaction between TNFRSF11B and GSK3β was detected by co-immunoprecipitation. We demonstrated that TNFRSF11B was highly expressed in the cytoplasm of GC and associated with the patient poor outcome. Our studies showed that TNFRSF11B in GC cells significantly promoted cell proliferation, migration, invasion in vitro and tumorigenic ability in vitro and in vivo. Meanwhile, TNFRSF11B inhibited GC cell apoptosis. The proportion of nuclear active β-catenin showed positively correlation with TNFRSF11B expression. TNFRSF11B directly combined with GSK-3β upregulating its phosphorylation, and increased expression of β-catenin and its downstream effectors. Collectively, these findings demonstrate that TNFRSF11B promote the aggressive phenotypes of GC cells and activated Wnt/β-catenin signaling. Accordingly, TNFRSF11B had potential as a biomarker and inhibition of TNFRSF11B expression might offer a new therapeutic target for GC patients.
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Affiliation(s)
- Fengming Luan
- Key laboratory of Carcinogenesis and Translational Research (Ministry of education), Division of gastrointestinal Cancer Translational Research laboratory, Peking University Cancer Hospital & Institute, Beijing, China
- Department of gastrointestinal surgery, Peking University Cancer Hospital & Institute, Beijing, China
| | - Xiaomei Li
- Key laboratory of Carcinogenesis and Translational Research (Ministry of education), Division of gastrointestinal Cancer Translational Research laboratory, Peking University Cancer Hospital & Institute, Beijing, China
| | - Xiaojing Cheng
- Key laboratory of Carcinogenesis and Translational Research (Ministry of education), Division of gastrointestinal Cancer Translational Research laboratory, Peking University Cancer Hospital & Institute, Beijing, China
| | - Longtao Huangfu
- Key laboratory of Carcinogenesis and Translational Research (Ministry of education), Division of gastrointestinal Cancer Translational Research laboratory, Peking University Cancer Hospital & Institute, Beijing, China
| | - Jing Han
- Key laboratory of Carcinogenesis and Translational Research (Ministry of education), Division of gastrointestinal Cancer Translational Research laboratory, Peking University Cancer Hospital & Institute, Beijing, China
| | - Ting Guo
- Key laboratory of Carcinogenesis and Translational Research (Ministry of education), Division of gastrointestinal Cancer Translational Research laboratory, Peking University Cancer Hospital & Institute, Beijing, China
| | - Hong Du
- Key laboratory of Carcinogenesis and Translational Research (Ministry of education), Division of gastrointestinal Cancer Translational Research laboratory, Peking University Cancer Hospital & Institute, Beijing, China
| | - Xianzi Wen
- Key laboratory of Carcinogenesis and Translational Research (Ministry of education), Division of gastrointestinal Cancer Translational Research laboratory, Peking University Cancer Hospital & Institute, Beijing, China
| | - Jiafu Ji
- Key laboratory of Carcinogenesis and Translational Research (Ministry of education), Division of gastrointestinal Cancer Translational Research laboratory, Peking University Cancer Hospital & Institute, Beijing, China
- Department of gastrointestinal surgery, Peking University Cancer Hospital & Institute, Beijing, China
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16
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Trilla-Fuertes L, Ghanem I, Gámez-Pozo A, Maurel J, G-Pastrián L, Mendiola M, Peña C, López-Vacas R, Prado-Vázquez G, López-Camacho E, Zapater-Moros A, Heredia V, Cuatrecasas M, García-Alfonso P, Capdevila J, Conill C, García-Carbonero R, Ramos-Ruiz R, Fortes C, Llorens C, Nanni P, Fresno Vara JÁ, Feliu J. Genetic Profile and Functional Proteomics of Anal Squamous Cell Carcinoma: Proposal for a Molecular Classification. Mol Cell Proteomics 2020; 19:690-700. [PMID: 32107283 PMCID: PMC7124473 DOI: 10.1074/mcp.ra120.001954] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Indexed: 12/21/2022] Open
Abstract
Anal squamous cell carcinoma is a rare tumor. Chemo-radiotherapy yields a 50% 3-year relapse-free survival rate in advanced anal cancer, so improved predictive markers and therapeutic options are needed. High-throughput proteomics and whole-exome sequencing were performed in 46 paraffin samples from anal squamous cell carcinoma patients. Hierarchical clustering was used to establish groups de novo Then, probabilistic graphical models were used to study the differences between groups of patients at the biological process level. A molecular classification into two groups of patients was established, one group with increased expression of proteins related to adhesion, T lymphocytes and glycolysis; and the other group with increased expression of proteins related to translation and ribosomes. The functional analysis by the probabilistic graphical model showed that these two groups presented differences in metabolism, mitochondria, translation, splicing and adhesion processes. Additionally, these groups showed different frequencies of genetic variants in some genes, such as ATM, SLFN11 and DST Finally, genetic and proteomic characteristics of these groups suggested the use of some possible targeted therapies, such as PARP inhibitors or immunotherapy.
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Affiliation(s)
| | - Ismael Ghanem
- Medical Oncology Department, Hospital Universitario La Paz, Paseo de la Castellana 261, 28046, Madrid, Spain
| | - Angelo Gámez-Pozo
- Molecular Oncology & Pathology Lab, Institute of Medical and Molecular Genetics-INGEMM, Hospital Universitario La Paz -IdiPAZ, Paseo de la Castellana 261, 28046, Madrid, Spain
| | - Joan Maurel
- Medical Oncology Department, Hospital Clinic of Barcelona, Translational Genomics and Targeted Therapeutics in Solid Tumors Group, IDIBAPS, University of Barcelona, Carrer de Villarroel 170, 08036, Barcelona, Spain
| | - Laura G-Pastrián
- Pathology Department, Hospital Universitario La Paz, Paseo de la Castellana 261, 28046, Madrid, Spain; Molecular Pathology and Therapeutic Targets Group, Hospital Universitario La Paz-IdiPAZ, Paseo de la Castellana 261, 28046, Madrid, Spain
| | - Marta Mendiola
- Molecular Pathology and Therapeutic Targets Group, Hospital Universitario La Paz-IdiPAZ, Paseo de la Castellana 261, 28046, Madrid, Spain; Biomedical Research Networking Center on Oncology-CIBERONC, ISCIII, Av. Monforte de Lemos 5, 28029, Madrid, Spain
| | - Cristina Peña
- Pathology Department, Hospital Universitario La Paz, Paseo de la Castellana 261, 28046, Madrid, Spain
| | - Rocío López-Vacas
- Molecular Oncology & Pathology Lab, Institute of Medical and Molecular Genetics-INGEMM, Hospital Universitario La Paz -IdiPAZ, Paseo de la Castellana 261, 28046, Madrid, Spain
| | | | - Elena López-Camacho
- Molecular Oncology & Pathology Lab, Institute of Medical and Molecular Genetics-INGEMM, Hospital Universitario La Paz -IdiPAZ, Paseo de la Castellana 261, 28046, Madrid, Spain
| | - Andrea Zapater-Moros
- Molecular Oncology & Pathology Lab, Institute of Medical and Molecular Genetics-INGEMM, Hospital Universitario La Paz -IdiPAZ, Paseo de la Castellana 261, 28046, Madrid, Spain
| | - Victoria Heredia
- Biomedical Research Networking Center on Oncology-CIBERONC, ISCIII, Av. Monforte de Lemos 5, 28029, Madrid, Spain; Translational Oncology Lab, Hospital Universitario La Paz -IdiPAZ, Paseo de la Castellana 261, 28046, Madrid, Spain
| | - Miriam Cuatrecasas
- Pathology Department, Hospital Clínic Universitari de Barcelona, Carrer de Villarroel 170, 08036, Barcelona, Spain
| | - Pilar García-Alfonso
- Medical Oncology Department, Hospital General Universitario Gregorio Marañón, /Dr. Esquerdo 46, 28007, Madrid, Spain
| | - Jaume Capdevila
- Medical Oncology Service, Vall Hebron University Hospital. Vall Hebron Institute of Oncology (VHIO), Paseigg de la Vall d'Hebron 119, 08035, Barcelona, Spain
| | - Carles Conill
- Radiotherapy Oncology Department, Hospital Clínic Universitari de Barcelona, Carrer de Villarroel 170, 08036, Barcelona, Spain
| | - Rocío García-Carbonero
- Medical Oncology Service, Hospital Universitario 12 de Ocubre, Av. de Córdoba s/n, 28041, Madrid, Spain
| | - Ricardo Ramos-Ruiz
- Genomics Unit Cantoblanco, Parque Científico de Madrid, C/ Faraday 7, 28049, Madrid, Spain
| | - Claudia Fortes
- Functional Genomics Center Zurich, University of Zurich/ETH Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
| | - Carlos Llorens
- Biotechvana SL, Parque Científico de Madrid, C/ Faraday 7, 28049, Madrid, Spain
| | - Paolo Nanni
- Functional Genomics Center Zurich, University of Zurich/ETH Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
| | - Juan Ángel Fresno Vara
- Molecular Oncology & Pathology Lab, Institute of Medical and Molecular Genetics-INGEMM, Hospital Universitario La Paz -IdiPAZ, Paseo de la Castellana 261, 28046, Madrid, Spain; Biomedical Research Networking Center on Oncology-CIBERONC, ISCIII, Av. Monforte de Lemos 5, 28029, Madrid, Spain
| | - Jaime Feliu
- Medical Oncology Department, Hospital Universitario La Paz, Paseo de la Castellana 261, 28046, Madrid, Spain; Biomedical Research Networking Center on Oncology-CIBERONC, ISCIII, Av. Monforte de Lemos 5, 28029, Madrid, Spain; Cátedra UAM-Amgen, Universidad Autónoma de Madrid, Ciudad Universitaria de Cantoblanco, 28049, Madrid, Spain.
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17
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Wang FS, Wu WH, Hsiu WS, Liu YJ, Chuang KW. Genome-Scale Metabolic Modeling with Protein Expressions of Normal and Cancerous Colorectal Tissues for Oncogene Inference. Metabolites 2019; 10:metabo10010016. [PMID: 31881674 PMCID: PMC7022839 DOI: 10.3390/metabo10010016] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 12/10/2019] [Accepted: 12/21/2019] [Indexed: 12/23/2022] Open
Abstract
Although cancer has historically been regarded as a cell proliferation disorder, it has recently been considered a metabolic disease. The first discovery of metabolic alterations in cancer cells refers to Otto Warburg’s observations. Cancer metabolism results in alterations in metabolic fluxes that are evident in cancer cells compared with most normal tissue cells. This study applied protein expressions of normal and cancer cells to reconstruct two tissue-specific genome-scale metabolic models. Both models were employed in a tri-level optimization framework to infer oncogenes. Moreover, this study also introduced enzyme pseudo-coding numbers in the gene association expression to avoid performing posterior decision-making that is necessary for the reaction-based method. Colorectal cancer (CRC) was the topic of this case study, and 20 top-ranked oncogenes were determined. Notably, these dysregulated genes were involved in various metabolic subsystems and compartments. We found that the average similarity ratio for each dysregulation is higher than 98%, and the extent of similarity for flux changes is higher than 93%. On the basis of surveys of PubMed and GeneCards, these oncogenes were also investigated in various carcinomas and diseases. Most dysregulated genes connect to catalase that acts as a hub and connects protein signaling pathways, such as those involving TP53, mTOR, AKT1, MAPK1, EGFR, MYC, CDK8, and RAS family.
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18
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Li Y, Bian Y, Wang K, Wan XP. POLE mutations improve the prognosis of endometrial cancer via regulating cellular metabolism through AMF/AMFR signal transduction. BMC MEDICAL GENETICS 2019; 20:202. [PMID: 31864301 PMCID: PMC6925869 DOI: 10.1186/s12881-019-0936-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 12/08/2019] [Indexed: 02/07/2023]
Abstract
Background The morbidity and mortality of endometrial tumors, a common type of malignant cancer in women, have increased in recent years. POLE encodes the DNA polymerase ε, which is responsible for the leading strand DNA replication. Somatic mutations of POLE have been acknowledged in numerous cancers, resulting in the accumulation of DNA errors, leading to ultra-mutated tumors. Mutations in the exonuclease domain of POLE have been reported to improve progression-free survival in endometrial cancer. However, the potential relationship and underlying mechanism between POLE mutations and the prognosis of endometrial cancer patients remains unclear. Methods The whole exome sequencing data, RNA sequencing data, and clinical information were obtained from the TCGA database and employed for the analyses in this study. The detailed mutational information was analyzed using whole exome sequencing data and the mutated genes were shown with OncoPlot. The survival curves and cox proportional hazards regression analysis were used to accessed patient prognosis, the association of clinical characteristics and prognosis. Differentially expressed genes were analyzed by the edgeR R/Bioconductor package, then the GSEA Pre-ranked tool was used for Gene Set Enrichment Analysis (GSEA) to estimate the function of genes. Expression values were clustered using hierarchical clustering with Euclidean distance and ward linkage by the dendextend R package. Results POLE mutational status was proven to be an independent prognostic factor for endometrial cancer patients. Patients with somatic POLE mutations presented a favorable prognosis. POLE mutations regulated glycolysis and cytokine secretion, affecting cell metabolism and immune response. Autocrine motility factor (AMF)/PGI and AMFR/gp78 exhibited higher expression levels in POLE mutant patients. The comprehensive high expressions of AMFR/gp78 and low expression of POLE were associated with the favorable prognosis of endometrial cancer patients. Conclusions This study showed the POLE mutations a vital factor in endometrial cancer patients, leading to a higher expression of AMF/PGI and AMFR/gp78. These results suggested comprehensive consideration of the POLE mutations, expression of AMF/PGI and AMFR/gp78 may provide a more feasible and effective approach for the treatment of endometrial cancer, which might improve the prognosis.
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Affiliation(s)
- Yiran Li
- Department of Gynecology, Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, 2699 Gaoke West Road, Shanghai, China
| | - Yiding Bian
- Department of Gynecology, Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, 2699 Gaoke West Road, Shanghai, China
| | - Kai Wang
- Clinical and Translational Research Center, Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai, China
| | - Xiao-Ping Wan
- Department of Gynecology, Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, 2699 Gaoke West Road, Shanghai, China.
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