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Bischoff ME, Shamsaei B, Yang J, Secic D, Vemuri B, Reisz JA, D'Alessandro A, Bartolacci C, Adamczak R, Schmidt L, Wang J, Martines A, Biesiada J, Vest KE, Scaglioni PP, Plas DR, Patra KC, Gulati S, Figueroa JAL, Meller J, Cunningham JT, Czyzyk-Krzeska MF. Copper drives remodeling of metabolic state and progression of clear cell renal cell carcinoma. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.16.575895. [PMID: 38293110 PMCID: PMC10827129 DOI: 10.1101/2024.01.16.575895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Copper (Cu) is an essential trace element required for mitochondrial respiration. Late-stage clear cell renal cell carcinoma (ccRCC) accumulates Cu and allocates it to mitochondrial cytochrome c oxidase. We show that Cu drives coordinated metabolic remodeling of bioenergy, biosynthesis and redox homeostasis, promoting tumor growth and progression of ccRCC. Specifically, Cu induces TCA cycle-dependent oxidation of glucose and its utilization for glutathione biosynthesis to protect against H 2 O 2 generated during mitochondrial respiration, therefore coordinating bioenergy production with redox protection. scRNA-seq determined that ccRCC progression involves increased expression of subunits of respiratory complexes, genes in glutathione and Cu metabolism, and NRF2 targets, alongside a decrease in HIF activity, a hallmark of ccRCC. Spatial transcriptomics identified that proliferating cancer cells are embedded in clusters of cells with oxidative metabolism supporting effects of metabolic states on ccRCC progression. Our work establishes novel vulnerabilities with potential for therapeutic interventions in ccRCC. Accumulation of copper is associated with progression and relapse of ccRCC and drives tumor growth.Cu accumulation and allocation to cytochrome c oxidase (CuCOX) remodels metabolism coupling energy production and nucleotide biosynthesis with maintenance of redox homeostasis.Cu induces oxidative phosphorylation via alterations in the mitochondrial proteome and lipidome necessary for the formation of the respiratory supercomplexes. Cu stimulates glutathione biosynthesis and glutathione derived specifically from glucose is necessary for survival of Cu Hi cells. Biosynthesis of glucose-derived glutathione requires activity of glutamyl pyruvate transaminase 2, entry of glucose-derived pyruvate to mitochondria via alanine, and the glutamate exporter, SLC25A22. Glutathione derived from glucose maintains redox homeostasis in Cu-treated cells, reducing Cu-H 2 O 2 Fenton-like reaction mediated cell death. Progression of human ccRCC is associated with gene expression signature characterized by induction of ETC/OxPhos/GSH/Cu-related genes and decrease in HIF/glycolytic genes in subpopulations of cancer cells. Enhanced, concordant expression of genes related to ETC/OxPhos, GSH, and Cu characterizes metabolically active subpopulations of ccRCC cells in regions adjacent to proliferative subpopulations of ccRCC cells, implicating oxidative metabolism in supporting tumor growth.
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Tang C, Xie AX, Liu EM, Kuo F, Kim M, DiNatale RG, Golkaram M, Chen YB, Gupta S, Motzer RJ, Russo P, Coleman J, Carlo MI, Voss MH, Kotecha RR, Lee CH, Tansey W, Schultz N, Hakimi AA, Reznik E. Immunometabolic coevolution defines unique microenvironmental niches in ccRCC. Cell Metab 2023; 35:1424-1440.e5. [PMID: 37413991 PMCID: PMC10603615 DOI: 10.1016/j.cmet.2023.06.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 03/10/2023] [Accepted: 06/06/2023] [Indexed: 07/08/2023]
Abstract
Tumor cell phenotypes and anti-tumor immune responses are shaped by local metabolite availability, but intratumoral metabolite heterogeneity (IMH) and its phenotypic consequences remain poorly understood. To study IMH, we profiled tumor/normal regions from clear cell renal cell carcinoma (ccRCC) patients. A common pattern of IMH transcended all patients, characterized by correlated fluctuations in the abundance of metabolites and processes associated with ferroptosis. Analysis of intratumoral metabolite-RNA covariation revealed that the immune composition of the microenvironment, especially the abundance of myeloid cells, drove intratumoral metabolite variation. Motivated by the strength of RNA-metabolite covariation and the clinical significance of RNA biomarkers in ccRCC, we inferred metabolomic profiles from the RNA sequencing data of ccRCC patients enrolled in 7 clinical trials, and we ultimately identifyied metabolite biomarkers associated with response to anti-angiogenic agents. Local metabolic phenotypes, therefore, emerge in tandem with the immune microenvironment, influence ongoing tumor evolution, and are associated with therapeutic sensitivity.
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Affiliation(s)
- Cerise Tang
- Computational Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Physiology, Biophysics and Systems Biology Graduate Program, Weill Cornell Medicine, New York, NY, USA
| | - Amy X Xie
- Computational Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Biochemistry, Structural Biology, Cell Biology, Developmental Biology and Molecular Biology Graduate Program, Weill Cornell Medicine, New York, NY, USA
| | - Eric Minwei Liu
- Computational Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Fengshen Kuo
- Urology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Minsoo Kim
- Computational Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Renzo G DiNatale
- Computational Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mahdi Golkaram
- Illumina, Inc., 5200 Illumina Way, San Diego, CA 92122, USA
| | - Ying-Bei Chen
- Department of Pathology, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sounak Gupta
- Department of Pathology, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Robert J Motzer
- Genitourinary Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Paul Russo
- Urology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Jonathan Coleman
- Urology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Maria I Carlo
- Genitourinary Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Martin H Voss
- Genitourinary Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ritesh R Kotecha
- Genitourinary Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Chung-Han Lee
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Wesley Tansey
- Computational Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nikolaus Schultz
- Computational Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - A Ari Hakimi
- Urology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
| | - Ed Reznik
- Computational Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
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3
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Verma R, Aggarwal P, Bischoff ME, Reigle J, Secic D, Wetzel C, VandenHeuvel K, Biesiada J, Ehmer B, Landero Figueroa JA, Plas DR, Medvedovic M, Meller J, Czyzyk-Krzeska MF. Microtubule-associated protein MAP1LC3C regulates lysosomal exocytosis and induces zinc reprogramming in renal cancer cells. J Biol Chem 2023; 299:104663. [PMID: 37003503 PMCID: PMC10173779 DOI: 10.1016/j.jbc.2023.104663] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Revised: 03/14/2023] [Accepted: 03/22/2023] [Indexed: 04/03/2023] Open
Abstract
Microtubule-associated protein 1 light chain 3 gamma (MAP1LC3C or LC3C) is a member of the microtubule-associated family of proteins that are essential in the formation of autophagosomes and lysosomal degradation of cargo. LC3C has tumor-suppressing activity, and its expression is dependent on kidney cancer tumor suppressors, such as von Hippel-Lindau protein and folliculin. Recently, we demonstrated that LC3C autophagy is regulated by noncanonical upstream regulatory complexes and targets for degradation postdivision midbody rings associated with cancer cell stemness. Here, we show that loss of LC3C leads to peripheral positioning of the lysosomes and lysosomal exocytosis (LE). This process is independent of the autophagic activity of LC3C. Analysis of isogenic cells with low and high LE shows substantial transcriptomic reprogramming with altered expression of zinc (Zn)-related genes and activity of polycomb repressor complex 2, accompanied by a robust decrease in intracellular Zn. In addition, metabolomic analysis revealed alterations in amino acid steady-state levels. Cells with augmented LE show increased tumor initiation properties and form aggressive tumors in xenograft models. Immunocytochemistry identified high levels of lysosomal-associated membrane protein 1 on the plasma membrane of cancer cells in human clear cell renal cell carcinoma and reduced levels of Zn, suggesting that LE occurs in clear cell renal cell carcinoma, potentially contributing to the loss of Zn. These data indicate that the reprogramming of lysosomal localization and Zn metabolism with implication for epigenetic remodeling in a subpopulation of tumor-propagating cancer cells is an important aspect of tumor-suppressing activity of LC3C.
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Affiliation(s)
- Rita Verma
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Parul Aggarwal
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Megan E Bischoff
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - James Reigle
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA; Department of Biomedical Informatics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA; Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Dina Secic
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Collin Wetzel
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Katherine VandenHeuvel
- Division of Pathology and Laboratory Medicine, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Jacek Biesiada
- Division of Biostatistics and Bioinformatics, Department of Environmental and Public Health Sciences, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Birgit Ehmer
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Julio A Landero Figueroa
- Department of Chemistry, Agilent Metallomics Center of the Americas, University of Cincinnati College of Arts and Science, Cincinnati, Ohio, USA; Department of Pharmacology and System Biology, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - David R Plas
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Mario Medvedovic
- Department of Biomedical Informatics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA; Division of Biostatistics and Bioinformatics, Department of Environmental and Public Health Sciences, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Jarek Meller
- Department of Biomedical Informatics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA; Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA; Division of Biostatistics and Bioinformatics, Department of Environmental and Public Health Sciences, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA; Department of Pharmacology and System Biology, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA; Department of Electrical Engineering and Computer Science, University of Cincinnati College of Engineering and Applied Sciences, Cincinnati, Ohio, USA
| | - Maria F Czyzyk-Krzeska
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA; Department of Pharmacology and System Biology, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA; Department of Veterans Affairss, Veteran Affairs Medical Center, Cincinnati, Ohio, USA.
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Wang Y, Smith M, Ruiz J, Liu Y, Kucera GL, Topaloglu U, Chan MD, Li W, Su J, Xing F. Modulation of oxidative phosphorylation and mitochondrial biogenesis by cigarette smoke influence the response to immune therapy in NSCLC patients. Lung Cancer 2023; 178:37-46. [PMID: 36773459 PMCID: PMC10065953 DOI: 10.1016/j.lungcan.2023.01.016] [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: 10/03/2022] [Revised: 01/20/2023] [Accepted: 01/30/2023] [Indexed: 02/06/2023]
Abstract
The treatment regimen of non-small cell lung cancer (NSCLC) has drastically changed owing to the superior anti-cancer effects generated by the immune-checkpoint blockade (ICB). However, only a subset of patients experience benefit after receiving ICBs. Therefore, it is of paramount importance to increase the response rate by elucidating the underlying molecular mechanisms and identifying novel therapeutic targets to enhance the efficacy of IBCs in non-responders. We analyzed the progression-free survival (PFS) and overall survival (OS) of 295 NSCLC patients who received anti-PD-1 therapy by segregating them with multiple clinical factors including sex, age, race, smoking history, BMI, tumor grade and subtype. We also identified key signaling pathways and mutations that are enriched in patients with distinct responses to ICB by gene set enrichment analysis (GSEA) and mutational analyses. We found that former and current smokers have a higher response rate to anti-PD-1 treatment than non-smokers. GSEA results revealed that oxidative phosphorylation (OXPHOS) and mitochondrial related pathways are significantly enriched in both responders and smokers, suggesting a potential role of cellular metabolism in regulating immune response to ICB. We also demonstrated that all-trans retinoic acid (ATRA) which enhances mitochondrial function significantly enhanced the efficacy of anti-PD-1 treatment in vivo. Our clinical and bioinformatics based analyses revealed a connection between smoking induced metabolic switch and the response to immunotherapy, which can be the basis for developing novel combination therapies that are beneficial to never smoked NSCLC patients.
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Affiliation(s)
- Yuezhu Wang
- Department of Cancer Biology, Wake Forest University School of Medicine, Winston-Salem, NC 27157, USA
| | - Margaret Smith
- Department of Cancer Biology, Wake Forest University School of Medicine, Winston-Salem, NC 27157, USA
| | - Jimmy Ruiz
- Department of Hematology and Oncology, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Yin Liu
- Department of Cancer Biology, Wake Forest University School of Medicine, Winston-Salem, NC 27157, USA
| | - Gregory L Kucera
- Department of Hematology and Oncology, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Umit Topaloglu
- Department of Cancer Biology, Wake Forest University School of Medicine, Winston-Salem, NC 27157, USA
| | - Michael D Chan
- Department of Radiation Oncology, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Wencheng Li
- Department of Pathology, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Jing Su
- Department of Biostatistics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Fei Xing
- Department of Cancer Biology, Wake Forest University School of Medicine, Winston-Salem, NC 27157, USA.
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Li S, Xu S, Chen Y, Zhou J, Ben S, Guo M, Chu H, Gu D, Zhang Z, Wang M. Metal Exposure Promotes Colorectal Tumorigenesis via the Aberrant N6-Methyladenosine Modification of ATP13A3. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:2864-2876. [PMID: 36745568 DOI: 10.1021/acs.est.2c07389] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Element contamination, including that from heavy metals, is associated with gastrointestinal tumorigenesis, but the effects and mechanisms of crucial element exposure associated with colorectal cancer remain unclear. We profiled 56 elements by ICP-MS and used logistic regression, LASSO, BKMR, and GAM to identify colorectal cancer-relevant elements. A series of biochemical experiments were performed to demonstrate the cytotoxicity and the mechanisms of malignant transformation after metal exposure. Using an elementomics approach, we first found that the metal thallium (Tl) was positively correlated with many toxic metals and was associated with a significantly increased risk of colorectal cancer. Acute exposure to Tl induced cytotoxicity and cell death by accelerating the generation of reactive oxygen species and DNA damage. Chronic exposure to Tl led to the inhibition of cell death and thereby induced the malignant transformation of normal colon cells and xenograft tumor formation in nude mice. Furthermore, we describe the first identification of a significant metal quantitative trait locus for the novel colorectal cancer susceptibility locus rs1511625 near ATP13A3. Mechanistically, Tl increased the level of aberrant N6-methyladenosine (m6A) modification of ATP13A3 via the METLL3/METTL14/ALKBH5-ATP13A3 axis to promote colorectal tumorigenesis. This study provides a basis for the development of public health strategies for reducing metal exposure among populations at high risk for colorectal cancer.
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Affiliation(s)
- Shuwei Li
- Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, Jiangsu, China
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, Jiangsu, China
| | - Shenya Xu
- Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, Jiangsu, China
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, Jiangsu, China
| | - Yehua Chen
- Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, Jiangsu, China
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, Jiangsu, China
| | - Jieyu Zhou
- Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, Jiangsu, China
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, Jiangsu, China
| | - Shuai Ben
- Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, Jiangsu, China
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, Jiangsu, China
| | - Mengfan Guo
- Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, Jiangsu, China
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, Jiangsu, China
| | - Haiyan Chu
- Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, Jiangsu, China
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, Jiangsu, China
| | - Dongying Gu
- Department of Oncology, Nanjing First Hospital, Nanjing Medical University, Nanjing 210006, Jiangsu, China
| | - Zhengdong Zhang
- Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, Jiangsu, China
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, Jiangsu, China
| | - Meilin Wang
- Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing 211166, Jiangsu, China
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, Jiangsu, China
- The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou 215000, Jiangsu, China
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Shen Y, Huang Q, Zhang Y, Hsueh CY, Zhou L. A novel signature derived from metabolism-related genes GPT and SMS to predict prognosis of laryngeal squamous cell carcinoma. Cancer Cell Int 2022; 22:226. [PMID: 35804447 PMCID: PMC9270735 DOI: 10.1186/s12935-022-02647-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 06/28/2022] [Indexed: 12/30/2022] Open
Abstract
Background A growing body of evidence has suggested the involvement of metabolism in the occurrence and development of tumors. But the link between metabolism and laryngeal squamous cell carcinoma (LSCC) has rarely been reported. This study seeks to understand and explain the role of metabolic biomarkers in predicting the prognosis of LSCC. Methods We identified the differentially expressed metabolism-related genes (MRGs) through RNA-seq data of The Cancer Genome Atlas (TCGA) and Gene set enrichment analysis (GSEA). After the screening of protein–protein interaction (PPI), hub MRGs were analyzed by least absolute shrinkage and selection operator (LASSO) and Cox regression analyses to construct a prognostic signature. Kaplan–Meier survival analysis and the receiver operating characteristic (ROC) was applied to verify the effectiveness of the prognostic signature in four cohorts (TCGA cohort, GSE27020 cohort, TCGA-sub1 cohort and TCGA-sub2 cohort). The expressions of the hub MRGs in LSCC cell lines and clinical samples were verified by quantitative reverse transcriptase PCR (qRT-PCR). The immunofluorescence staining of the tissue microarray (TMA) was carried out to further verify the reliability and validity of the prognostic signature. Cox regression analysis was then used to screen for independent prognostic factors of LSCC and a nomogram was constructed based on the results. Results Among the 180 differentially expressed MRGs, 14 prognostic MRGs were identified. A prognostic signature based on two MRGs (GPT and SMS) was then constructed and verified via internal and external validation cohorts. Compared to the adjacent normal tissues, SMS expression was higher while GPT expression was lower in LSCC tissues, indicating poorer outcomes. The prognostic signature was proven as an independent risk factor for LSCC in both internal and external validation cohorts. A nomogram based on these results was developed for clinical application. Conclusions Differentially expressed MRGs were found and proven to be related to the prognosis of LSCC. We constructed a novel prognostic signature based on MRGs in LSCC for the first time and verified it via different cohorts from both databases and clinical samples. A nomogram based on this prognostic signature was developed. Supplementary Information The online version contains supplementary material available at 10.1186/s12935-022-02647-2.
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Affiliation(s)
- Yujie Shen
- Department of Otorhinolaryngology, Eye & ENT Hospital, Fudan University, Shanghai, 200031, China
| | - Qiang Huang
- Department of Otorhinolaryngology, Eye & ENT Hospital, Fudan University, Shanghai, 200031, China
| | - Yifan Zhang
- Department of Otorhinolaryngology, Eye & ENT Hospital, Fudan University, Shanghai, 200031, China
| | - Chi-Yao Hsueh
- Department of Otorhinolaryngology, Eye & ENT Hospital, Fudan University, Shanghai, 200031, China.
| | - Liang Zhou
- Department of Otorhinolaryngology, Eye & ENT Hospital, Fudan University, Shanghai, 200031, China.
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Zhang Y, He J, Jin J, Ren C. Recent advances in the application of metallomics in diagnosis and prognosis of human cancer. Metallomics 2022; 14:6596881. [PMID: 35648480 DOI: 10.1093/mtomcs/mfac037] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 05/12/2022] [Indexed: 11/13/2022]
Abstract
Metals play a critical role in human health and diseases. In recent years, metallomics has been introduced and extensively applied to investigate the distribution, regulation, function, and crosstalk of metal(loid) ions in various physiological and pathological processes. Based on high-throughput multielemental analytical techniques and bioinformatics methods, it is possible to elucidate the correlation between the metabolism and homeostasis of diverse metals and complex diseases, in particular for cancer. This review aims to provide an overview of recent progress made in the application of metallomics in cancer research. We mainly focuses on the studies about metallomic profiling of different human biological samples for several major types of cancer, which reveal distinct and dynamic patterns of metal ion contents and the potential benefits of using such information in the detection and prognosis of these malignancies. Elevated levels of copper appear to be a significant risk factor for various cancers, and each type of cancer has a unique distribution of metals in biofluids, hair/nails, and tumor-affected tissues. Furthermore, associations between genetic variations in representative metalloprotein genes and cancer susceptibility have also been demonstrated. Overall, metallomics not only offers a better understanding of the relationship between metal dyshomeostasis and the development of cancer but also facilitates the discovery of new diagnostic and prognostic markers for cancer translational medicine.
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Affiliation(s)
- Yan Zhang
- Shenzhen Key Laboratory of Marine Bioresources and Ecology, Brain Disease and Big Data Research Institute, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518055, Guangdong Province, P. R. China.,Shenzhen-Hong Kong Institute of Brain Science-Shenzhen Fundamental Research Institutions, Shenzhen, 518055, Guangdong Province, P. R. China
| | - Jie He
- Shenzhen Key Laboratory of Marine Bioresources and Ecology, Brain Disease and Big Data Research Institute, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518055, Guangdong Province, P. R. China
| | - Jiao Jin
- Shenzhen Key Laboratory of Marine Bioresources and Ecology, Brain Disease and Big Data Research Institute, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518055, Guangdong Province, P. R. China
| | - Cihan Ren
- Experimental High School Attached to Beijing Normal University, Beijing 100052, P. R. China
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8
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Sohrabi SS, Rashidipour M, Sohrabi SM, Hadizadeh M, Shams MH, Mohammadi M. Genome-wide evaluation of transcriptomic responses of human tissues to smoke: A systems biology study. Gene X 2022; 820:146114. [PMID: 35077830 DOI: 10.1016/j.gene.2021.146114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 11/29/2021] [Accepted: 12/06/2021] [Indexed: 11/18/2022] Open
Abstract
The harmful compounds in various sources of smoke threaten human health. So far, many studies have investigated the effects of compounds of smoke on transcriptome changes in different human tissues. However, no study has been conducted on the effects of these compounds on transcriptome changes in different human tissues simultaneously. Hence, the present study was conducted to identify smoke-related genes (SRGs) and their response mechanisms to smoke in various human cells and tissues using systems biology based methods. A total of 6,484 SRGs were identified in the studied tissues, among which 4,095 SRGs were up-regulated and 2,389 SRGs were down-regulated. Totally, 459 SRGs were smoke-related transcription factors (SRTFs). Gene regulatory network analysis showed that the studied cells and tissues have different gene regulation and responses to compounds of smoke. The comparison of different tissues revealed no common SRG among the all studied tissues. However, the CYP1B1 gene was common among seven cells and tissues, and had the same expression trend. Network analysis showed that the CYP1B1 is a hub gene among SRGs in various cells and tissues. To the best of our knowledge, for the first time, our results showed that compounds of smoke induce and increase the expression of CYP1B1 key gene in all target and non-target tissues of human. Moreover, despite the specific characteristics of CYP1B1 gene and its identical expression trend in target and non-target tissues, it can be used as a biomarker for diagnosis and prognosis.
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Affiliation(s)
- Seyed Sajad Sohrabi
- Department of Production Engineering and Plant Genetics, Faculty of Agriculture, Lorestan University, Khorramabad, Iran; Environmental Health Research Center, Lorestan University of Medical Sciences, Khorramabad, Iran
| | - Marzieh Rashidipour
- Environmental Health Research Center, Lorestan University of Medical Sciences, Khorramabad, Iran; Nutritional Health Research Center, Lorestan University of Medical Sciences, Khorramabad, Iran.
| | - Seyyed Mohsen Sohrabi
- Department of Production Engineering and Plant Genetics, Faculty of Agriculture, Shahid Chamran University of Ahvaz, Ahvaz, Iran
| | - Morteza Hadizadeh
- Physiology Research Center, Institute of Basic and Clinical Physiology Sciences, Kerman University of Medical Sciences, Kerman, Iran
| | - Mohammad-Hossein Shams
- Department of Immunology, Faculty of Medicine, Lorestan University of Medical Sciences, Khorramabad, Iran
| | - Mohsen Mohammadi
- Razi Herbal Medicines Research Center and Department of Pharmacognosy and Pharmaceutical Biotechnology, Faculty of Pharmacy, Lorestan University of Medical Sciences, Khorramabad, Iran
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Gulati S, Vogelzang NJ. Biomarkers in renal cell carcinoma: Are we there yet? Asian J Urol 2021; 8:362-375. [PMID: 34765444 PMCID: PMC8566366 DOI: 10.1016/j.ajur.2021.05.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 02/02/2021] [Accepted: 03/03/2021] [Indexed: 12/30/2022] Open
Abstract
Management of kidney cancer has undergone a paradigm shift with the approval of new therapies over the last two decades. Although these drugs have improved clinical outcomes in patients with kidney cancer, there are still a large number of patients who do not show objective responses. A multitude of investigators, including those for The Cancer Genome Atlas have biologically characterized and sub-classified kidney cancer. However, we have not been able to identify molecular targets to effectively treat patients with kidney cancer. As we familiarize ourselves with newer drugs for patients with kidney cancer, it is important to understand that these drugs may not work in every patient and instead may expose patients to unnecessary toxic effects along with burdening society with the financial impact. As we head toward the era of "precision medicine", validated biomarkers are being utilized to guide treatment choices and help identify pathways of resistance in other tumor types. The current review aims at evaluating the progress made so far in this realm for patients with kidney cancer.
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Affiliation(s)
- Shuchi Gulati
- Division of Hematology and Oncology, University of Cincinnati, Cincinnati, Oh, USA
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Botero-Fonnegra C, Funes DR, Valera RJ, Gómez CO, Lo Menzo E, Szomstein S, Rosenthal RJ. Potential beneficial effects of bariatric surgery on the prevalence of kidney cancer: a national database study. Surg Obes Relat Dis 2021; 18:102-106. [PMID: 34565684 DOI: 10.1016/j.soard.2021.08.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 08/02/2021] [Accepted: 08/12/2021] [Indexed: 01/19/2023]
Abstract
BACKGROUND The incidence of obesity has been steadily increasing, especially in developed countries. Also, obesity is considered one of the modifiable risk factors of kidney cancer. OBJECTIVES This study aims to determine the impact of bariatric surgery-induced weight loss on the prevention of kidney cancer. SETTING Academic Hospital, United States. METHODS The National (Nationwide) Inpatient Sample (NIS) was queried for the period 2010 to 2015 for first-time kidney cancer-related hospitalization, used as a proxy for cancer incidence, in patients with a history of bariatric surgery (cases) and patients with obesity but no history of bariatric surgery (controls). Patients with a previous diagnosis of cancer were excluded from the analysis. In order to identify comparable patients, all controls had to have a body mass index ≥35 kg/m2, as per the existing qualification criteria for bariatric surgery. The International Classification of Diseases-9 codes (ICD-9) was used to identify admissions for kidney cancer. A univariate analysis was conducted to compare demographics and co-morbidities between groups. A multivariate logistic regression model was performed to assess differences between surgical and control groups and adjust for independent variables such as smoking history and family history of malignancy. All percentages and means (with confidence intervals [CIs]) were weighted. RESULTS A total of 2,300,845 were included in the analysis, of which 2,004,804 controls-subjects, with a mean age of 54.4 ± .05 years, and 296,041 treatment-subjects, with a mean age of 51.9 ± .05 years. Demographics and co-morbidities, such as tobacco use, diabetes, and hypertension, were also measured. Patients with a history of bariatric surgery were significantly less likely to experience renal cancer than patients without a history of bariatric surgery, with 5935 cases in the control group and 684 in the case group (P < .0001). After a multivariate logistic regression was performed, the OR was 1.10 (95% CI: 1.02-1.22, P < .0224). CONCLUSION Our finding suggests that bariatric surgery-induced weight loss could significantly prevent first-time kidney cancer-related hospitalizations in patients with obesity. Prospective studies are needed to confirm our findings.
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Affiliation(s)
- Cristina Botero-Fonnegra
- Department of General Surgery and The Bariatric and Metabolic Institute, Cleveland Clinic Florida, Weston, Florida
| | - David Romero Funes
- Department of General Surgery and The Bariatric and Metabolic Institute, Cleveland Clinic Florida, Weston, Florida
| | - Roberto J Valera
- Department of General Surgery and The Bariatric and Metabolic Institute, Cleveland Clinic Florida, Weston, Florida
| | - Camila Ortiz Gómez
- Department of General Surgery and The Bariatric and Metabolic Institute, Cleveland Clinic Florida, Weston, Florida
| | - Emanuele Lo Menzo
- Department of General Surgery and The Bariatric and Metabolic Institute, Cleveland Clinic Florida, Weston, Florida
| | - Samuel Szomstein
- Department of General Surgery and The Bariatric and Metabolic Institute, Cleveland Clinic Florida, Weston, Florida
| | - Raul J Rosenthal
- Department of General Surgery and The Bariatric and Metabolic Institute, Cleveland Clinic Florida, Weston, Florida.
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Czyzyk-Krzeska MF, Landero Figueroa JA, Gulati S, Cunningham JT, Meller J, ShamsaeI B, Vemuri B, Plas DR. Molecular and Metabolic Subtypes in Sporadic and Inherited Clear Cell Renal Cell Carcinoma. Genes (Basel) 2021; 12:genes12030388. [PMID: 33803184 PMCID: PMC7999481 DOI: 10.3390/genes12030388] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 03/02/2021] [Accepted: 03/04/2021] [Indexed: 01/18/2023] Open
Abstract
The promise of personalized medicine is a therapeutic advance where tumor signatures obtained from different omics platforms, such as genomics, transcriptomics, proteomics, and metabolomics, in addition to environmental factors including metals and metalloids, are used to guide the treatments. Clear cell renal carcinoma (ccRCC), the most common type of kidney cancer, can be sporadic (frequently) or genetic (rare), both characterized by loss of the von Hippel-Lindau (VHL) gene that controls hypoxia inducible factors. Recently, several genomic subtypes were identified with different prognoses. Transcriptomics, proteomics, metabolomics and metallomic data converge on altered metabolism as the principal feature of the disease. However, in view of multiple biochemical alterations and high level of tumor heterogeneity, identification of clearly defined subtypes is necessary for further improvement of treatments. In the future, single-cell combined multi-omics approaches will be the next generation of analyses gaining deeper insights into ccRCC progression and allowing for design of specific signatures, with better prognostic/predictive clinical applications.
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Affiliation(s)
- Maria F. Czyzyk-Krzeska
- Department of Cancer Biology, University of Cincinnati, Cincinnati, OH 45267, USA; (J.T.C.); (B.V.); (D.R.P.)
- Department of Veterans Affairs, Cincinnati Veteran Affairs Medical Center, Cincinnati, OH 45220, USA
- Department of Pharmacology and System Biology, College of Medicine, University of Cincinnati, Cincinnati, OH 45267, USA; (J.A.L.F.); (J.M.)
- Correspondence:
| | - Julio A. Landero Figueroa
- Department of Pharmacology and System Biology, College of Medicine, University of Cincinnati, Cincinnati, OH 45267, USA; (J.A.L.F.); (J.M.)
- Agilent Metallomics Center of the Americas, Department of Chemistry, University of Cincinnati, Cincinnati, OH 45221, USA
| | - Shuchi Gulati
- Division of Hematology and Oncology, Department of Medicine, University of Cincinnati, Cincinnati, OH 45267, USA;
| | - John T. Cunningham
- Department of Cancer Biology, University of Cincinnati, Cincinnati, OH 45267, USA; (J.T.C.); (B.V.); (D.R.P.)
| | - Jarek Meller
- Department of Pharmacology and System Biology, College of Medicine, University of Cincinnati, Cincinnati, OH 45267, USA; (J.A.L.F.); (J.M.)
- Department of Biomedical Informatics, University of Cincinnati, Cincinnati, OH 45267, USA
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
- Division of Biostatistics and Bioinformatics, Department of Environmental and Public Health Sciences, University of Cincinnati, Cincinnati, OH 45267, USA;
- Department of Electrical Engineering and Computer Science, College of Engineering and Applied Sciences, University of Cincinnati, Cincinnati, OH 45221, USA
| | - Behrouz ShamsaeI
- Division of Biostatistics and Bioinformatics, Department of Environmental and Public Health Sciences, University of Cincinnati, Cincinnati, OH 45267, USA;
| | - Bhargav Vemuri
- Department of Cancer Biology, University of Cincinnati, Cincinnati, OH 45267, USA; (J.T.C.); (B.V.); (D.R.P.)
| | - David R. Plas
- Department of Cancer Biology, University of Cincinnati, Cincinnati, OH 45267, USA; (J.T.C.); (B.V.); (D.R.P.)
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Czyzyk-Krzeska MF, Meller J, Landero Figueroa JA, Plas DR, Cunningham JT. Metabolic subtypes of clear cell renal cell carcinoma defined by tobacco smoking. Mol Cell Oncol 2021; 8:1859917. [PMID: 33860076 PMCID: PMC8018476 DOI: 10.1080/23723556.2020.1859917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 11/24/2020] [Accepted: 11/30/2020] [Indexed: 06/12/2023]
Abstract
Tobacco smoking (TS) results in reprogramming of major metabolic pathways, including glycolysis, the citric acid (TCA) cycle, oxidative phosphorylation, and metabolism of aspartate, glutamate and glutamine in clear cell renal cell carcinoma (ccRCC). TS alters the distribution and activities of cadmium, arsenic and copper in a manner mechanistically supporting metabolic remodeling. Alterations in metabolism and metal distribution identify new actionable targets for treatment of ccRCC.
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Affiliation(s)
- Maria F. Czyzyk-Krzeska
- Department of Cancer Biology, University of Cincinnati, Cincinnati, OH, USA
- Department of Veterans Affairs, Cincinnati Veteran Affairs Medical Center, Cincinnati, OH, USA
| | - Jarek Meller
- Department of Biomedical Informatics, University of Cincinnati, Cincinnati, OH, USA
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
- Division of Biostatistics and Bioinformatics, Department of Environmental and Public Health Sciences, University of Cincinnati, Cincinnati, OH, USA
| | - Julio A. Landero Figueroa
- Agilent Metallomics Center of the Americas, Department of Chemistry, University of Cincinnati, Cincinnati, OH, USA
| | - David R. Plas
- Department of Cancer Biology, University of Cincinnati, Cincinnati, OH, USA
| | - John T. Cunningham
- Department of Cancer Biology, University of Cincinnati, Cincinnati, OH, USA
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