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Panwoon C, Seubwai W, Thanee M, Sangkhamanon S. Identification of novel biomarkers to distinguish clear cell and non-clear cell renal cell carcinoma using bioinformatics and machine learning. PLoS One 2024; 19:e0305252. [PMID: 38857246 PMCID: PMC11164351 DOI: 10.1371/journal.pone.0305252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Accepted: 05/27/2024] [Indexed: 06/12/2024] Open
Abstract
Renal cell carcinoma (RCC), accounting for 90% of all kidney cancer, is categorized into clear cell RCC (ccRCC) and non-clear cell RCC (non-ccRCC) for treatment based on the current NCCN Guidelines. Thus, the classification will be associated with therapeutic implications. This study aims to identify novel biomarkers to differentiate ccRCC from non-ccRCC using bioinformatics and machine learning. The gene expression profiles of ccRCC and non-ccRCC subtypes (including papillary RCC (pRCC) and chromophobe RCC (chRCC)), were obtained from TCGA. Differential expression genes (DEGs) were identified, and specific DEGs for ccRCC and non-ccRCC were explored using a Venn diagram. Gene Ontology and pathway enrichment analysis were performed using DAVID. The top ten expressed genes in ccRCC were then selected for machine learning analysis. Feature selection was operated to identify a minimum highly effective gene set for constructing a predictive model. The expression of best-performing gene set was validated on tissue samples from RCC patients using immunohistochemistry techniques. Subsequently, machine learning models for diagnosing RCC were developed using H-scores. There were 910, 415, and 835 genes significantly specific for DEGs in ccRCC, pRCC, and chRCC, respectively. Specific DEGs in ccRCC enriched in PD-1 signaling, immune system, and cytokine signaling in the immune system, whereas TCA cycle and respiratory, signaling by insulin receptor, and metabolism were enriched in chRCC. Feature selection based on Decision Tree Classifier revealed that the model with two genes, including NDUFA4L2 and DAT, had an accuracy of 98.89%. Supervised classification models based on H-score of NDUFA4L2, and DAT revealed that Decision Tree models showed the best performance with 82% accuracy and 0.9 AUC. NDUFA4L2 expression was associated with lymphovascular invasion, pathologic stage and pT stage in ccRCC. Using integrated bioinformatics and machine learning analysis, NDUFA4L2 and DAT were identified as novel biomarkers to differential diagnosis ccRCC from non-ccRCC.
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Affiliation(s)
- Chanita Panwoon
- Faculty of Medicine, Department of Pathology, Khon Kaen University, Khon Kaen, Thailand
| | - Wunchana Seubwai
- Faculty of Medicine, Department of Forensic Medicine, Khon Kaen University, Khon Kaen, Thailand
- Faculty of Medicine, Center for Translational Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Malinee Thanee
- Faculty of Medicine, Department of Pathology, Khon Kaen University, Khon Kaen, Thailand
| | - Sakkarn Sangkhamanon
- Faculty of Medicine, Department of Pathology, Khon Kaen University, Khon Kaen, Thailand
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Baquero J, Tang XH, Ferrotta A, Zhang T, DiKun KM, Gudas LJ. The transcription factor BMI1 increases hypoxic signaling in oral cavity epithelia. Biochim Biophys Acta Mol Basis Dis 2024; 1870:167161. [PMID: 38599260 DOI: 10.1016/j.bbadis.2024.167161] [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: 11/29/2023] [Revised: 03/07/2024] [Accepted: 04/04/2024] [Indexed: 04/12/2024]
Abstract
The tongue epithelium is maintained by a proliferative basal layer. This layer contains long-lived stem cells (SCs), which produce progeny cells that move up to the surface as they differentiate. B-lymphoma Mo-MLV insertion region 1 (BMI1), a protein in mammalian Polycomb Repressive Complex 1 (PRC1) and a biomarker of oral squamous cell carcinoma, is expressed in almost all basal epithelial SCs of the tongue, and single, Bmi1-labelled SCs give rise to cells in all epithelial layers. We previously developed a transgenic mouse model (KrTB) containing a doxycycline- (dox) controlled, Tet-responsive element system to selectively overexpress Bmi1 in the tongue basal epithelial SCs. Here, we used this model to assess BMI1 actions in tongue epithelia. Genome-wide transcriptomics revealed increased levels of transcripts involved in the cellular response to hypoxia in Bmi1-overexpressing (KrTB+DOX) oral epithelia even though these mice were not subjected to hypoxia conditions. Ectopic Bmi1 expression in tongue epithelia increased the levels of hypoxia inducible factor-1 alpha (HIF1α) and HIF1α targets linked to metabolic reprogramming during hypoxia. We used chromatin immunoprecipitation (ChIP) to demonstrate that Bmi1 associates with the promoters of HIF1A and HIF1A-activator RELA (p65) in tongue epithelia. We also detected increased SC proliferation and oxidative stress in Bmi1-overexpressing tongue epithelia. Finally, using a human oral keratinocyte line (OKF6-TERT1R), we showed that ectopic BMI1 overexpression decreases the oxygen consumption rate while increasing the extracellular acidification rate, indicative of elevated glycolysis. Thus, our data demonstrate that high BMI1 expression drives hypoxic signaling, including metabolic reprogramming, in normal oral cavity epithelia.
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Affiliation(s)
- Jorge Baquero
- Department of Pharmacology, Weill Cornell Medical College, New York, NY, USA; Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Xiao-Han Tang
- Department of Pharmacology, Weill Cornell Medical College, New York, NY, USA; Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Annalisa Ferrotta
- Department of Pharmacology, Weill Cornell Medical College, New York, NY, USA; Department of Pharmacology, Weill Cornell Graduate School of Biomedical Sciences, New York, NY, USA
| | - Tuo Zhang
- Weill Cornell Genomics Core Facility, Weill Cornell Medical College, New York, NY, USA
| | - Krysta M DiKun
- Department of Pharmacology, Weill Cornell Medical College, New York, NY, USA; Department of Pharmacology, Weill Cornell Graduate School of Biomedical Sciences, New York, NY, USA
| | - Lorraine J Gudas
- Department of Pharmacology, Weill Cornell Medical College, New York, NY, USA; Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA; Department of Pharmacology, Weill Cornell Graduate School of Biomedical Sciences, New York, NY, USA.
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3
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Coffey NJ, Simon MC. Metabolic alterations in hereditary and sporadic renal cell carcinoma. Nat Rev Nephrol 2024; 20:233-250. [PMID: 38253811 PMCID: PMC11165401 DOI: 10.1038/s41581-023-00800-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/30/2023] [Indexed: 01/24/2024]
Abstract
Kidney cancer is the seventh leading cause of cancer in the world, and its incidence is on the rise. Renal cell carcinoma (RCC) is the most common form and is a heterogeneous disease comprising three major subtypes that vary in their histology, clinical course and driver mutations. These subtypes include clear cell RCC, papillary RCC and chromophobe RCC. Molecular analyses of hereditary and sporadic forms of RCC have revealed that this complex and deadly disease is characterized by metabolic pathway alterations in cancer cells that lead to deregulated oxygen and nutrient sensing, as well as impaired tricarboxylic acid cycle activity. These metabolic changes facilitate tumour growth and survival. Specifically, studies of the metabolic features of RCC have led to the discovery of oncometabolites - fumarate and succinate - that can promote tumorigenesis, moonlighting functions of enzymes, and substrate auxotrophy owing to the disruption of pathways that enable the production of arginine and cholesterol. These metabolic alterations within RCC can be exploited to identify new therapeutic targets and interventions, in combination with novel approaches that minimize the systemic toxicity of metabolic inhibitors and reduce the risk of drug resistance owing to metabolic plasticity.
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Affiliation(s)
- Nathan J Coffey
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - M Celeste Simon
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA, USA.
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Zheng Q, Lu C, Yu L, Zhan Y, Chen Z. Exploring the metastasis-related biomarker and carcinogenic mechanism in liver cancer based on single cell technology. Heliyon 2024; 10:e27473. [PMID: 38509894 PMCID: PMC10950590 DOI: 10.1016/j.heliyon.2024.e27473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Revised: 01/16/2024] [Accepted: 02/29/2024] [Indexed: 03/22/2024] Open
Abstract
Background Hepatocellular carcinoma (HCC) is a fatal primary malignancy characterized by high invasion and migration. We aimed to explore the underlying metastasis-related mechanism supporting the development of HCC. Methods The dataset of single cell RNA-seq (GSE149614) were collected for cell clustering by using the Seurat R package, the FindAllMarkers function was used to find the highly expression and defined the cell cluster. The WebGestaltR package was used for the GO and KEGG function analysis of shared genes, the Gene Set Enrichment Analysis (GSVA) was performed by clusterProfiler R package, the hTFtarget database was used to identify the crucial transcription factors (TFs), the Genomics of Drug Sensitivity in Cancer (GDSC) database was used for the drug sensitivity analysis. Finally, the overexpression and trans-well assay was used for gene function analysis. Results We obtained 9 cell clusters from the scRNA-seq data, including the nature killer (NK)/T cells, Myeloid cells, Hepatocytes, Epithelial cells, Endothelial cells, Plasma B cells, Smooth muscle cells, B cells, Liver bud hepatic cells. Further cell ecological analysis indicated that the Hepatocytes and Endothelial cell cluster were closely related to the cancer metastasis. Subsequently, the NDUFA4L2-Hepatocyte, GTSE1-Hepatocyte, ENTPD1-Endothelial and NDUFA4L2-Endothelial were defined as metastasis-supporting cell clusters, in which the NDUFA4L2-Hepatocyte cells was closely related to angiogenesis, while the NDUFA4L2-Endothelial was related with the inflammatory response and complement response. The overexpression and trans-well assay displayed that NDUFA4L2 exhibited clearly metastasis-promoting role in HCC progression. Conclusion We identified and defined 4 metastasis-supporting cell clusters by using the single cell technology, the specify shared gene was observed and played crucial role in promoting cancer progression, our findings were expected to provide new insight in control cancer metastasis.
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Affiliation(s)
- Qiuxiang Zheng
- Department of Oncology, Longyan First Hospital, Affiliated to Fujian Medical University, Longyan, 364000, China
| | - Cuiping Lu
- Department of Oncology, Longyan First Hospital, Affiliated to Fujian Medical University, Longyan, 364000, China
| | - Lian Yu
- Department of Hematology, Longyan First Hospital, Affiliated to Fujian Medical University, Longyan, 364000, China
| | - Ying Zhan
- Department of Oncology, Longyan First Hospital, Affiliated to Fujian Medical University, Longyan, 364000, China
| | - Zhiyong Chen
- Department of Oncology, Longyan First Hospital, Affiliated to Fujian Medical University, Longyan, 364000, China
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Mei Q, Chen P, Lv Y, Zheng L, Liu D, Zhang M, Liu W, Li P. Elevated of NDUFA4L2 expression in colon adenocarcinoma is correlated with an unfavorable prognosis and increased immune cell infiltration. Heliyon 2024; 10:e25462. [PMID: 38352787 PMCID: PMC10861987 DOI: 10.1016/j.heliyon.2024.e25462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 12/25/2023] [Accepted: 01/27/2024] [Indexed: 02/16/2024] Open
Abstract
Background Colon adenocarcinoma (COAD) is a prevalent malignancy worldwide, yet, its underlying pathogenesis and genetic characteristics are still unclear. Previous studies have suggested that NADH dehydrogenase 1 alpha subcomplex subunit 4-like 2 (NDUFA4L2) may affect tumor progression across various cancers. However, this effect on COAD has rarely been reported. Thus, this study investigated NDUFA4L2's prognostic and diagnostic relevance and explored its potential connection with immune cell infiltration in COAD. Methods To achieve this, RNA sequencing data from Cancer Genome Atlas (TCGA) was analyzed to assess NDUFA4L2's prognostic value in COAD, and factors relevant to the prognosis of COAD, including NDUFA4L2, were scrutinized using Kaplan-Meier analyses as well as univariate and multivariate Cox regression. A nomogram model was created to project prognosis based on the results of multivariate Cox analysis. Furthermore, gene set enrichment analysis (GSEA) was employed to pinpoint key NDUFA4L2-related pathways, and single-sample GSEA (ssGSEA) on TCGA data was employed to investigate the connections of NDUFA4L2 with cancer immune infiltrations. Results Our findings revealed significant associations of high NDUFA4L2 expression with poor overall survival, progression-free interval, and disease-specific survival of COAD patients. GSEA indicated close links of NDUFA4L2 with several signaling pathways implicated in tumorigenesis, including extracellular matrix receptor interaction, the intestinal immune network for immunoglobulin A production, natural killer (NK) cell-mediated cytotoxicity, pathways in cancer, cell adhesion molecules, mitogen-activated protein kinase signaling pathway, Hedgehog signaling pathway, transforming growth factor beta signaling pathway, and chemokine signaling pathway. Additionally, ssGSEA identified a positive link between increased NDUFA4L2 expression and higher infiltration degree of various immune cells, such as immature dendritic cells, macrophages, NK cells and dendritic cells. Conclusions Collectively, our findings demonstrate the association of increased NDUFA4L2 expression with adverse prognosis and heightened immune cell infiltration in COAD patients.
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Affiliation(s)
- Qingbu Mei
- Department of Medical Genetics, Qiqihar Medical University, Qiqihar 161006, China
| | - Ping Chen
- Department of Cell Biology, Qiqihar Medical University, Qiqihar 161006, China
| | - Ying Lv
- Department of Basic Medical Research Center, Qiqihar Medical University, Qiqihar 161006, China
| | - Lihong Zheng
- Department of Medical Genetics, Qiqihar Medical University, Qiqihar 161006, China
| | - Dan Liu
- Department of Medical Genetics, Qiqihar Medical University, Qiqihar 161006, China
| | - Minglong Zhang
- Department of Medical Genetics, Qiqihar Medical University, Qiqihar 161006, China
| | - Wanquan Liu
- Department of Medical Genetics, Qiqihar Medical University, Qiqihar 161006, China
| | - Penghui Li
- Department of Medical Genetics, Qiqihar Medical University, Qiqihar 161006, China
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Wang Y, Yang J, Zhang Y, Zhou J. Focus on Mitochondrial Respiratory Chain: Potential Therapeutic Target for Chronic Renal Failure. Int J Mol Sci 2024; 25:949. [PMID: 38256023 PMCID: PMC10815764 DOI: 10.3390/ijms25020949] [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: 11/30/2023] [Revised: 12/26/2023] [Accepted: 01/09/2024] [Indexed: 01/24/2024] Open
Abstract
The function of the respiratory chain is closely associated with kidney function, and the dysfunction of the respiratory chain is a primary pathophysiological change in chronic kidney failure. The incidence of chronic kidney failure caused by defects in respiratory-chain-related genes has frequently been overlooked. Correcting abnormal metabolic reprogramming, rescuing the "toxic respiratory chain", and targeting the clearance of mitochondrial reactive oxygen species are potential therapies for treating chronic kidney failure. These treatments have shown promising results in slowing fibrosis and inflammation progression and improving kidney function in various animal models of chronic kidney failure and patients with chronic kidney disease (CKD). The mitochondrial respiratory chain is a key target worthy of attention in the treatment of chronic kidney failure. This review integrated research related to the mitochondrial respiratory chain and chronic kidney failure, primarily elucidating the pathological status of the mitochondrial respiratory chain in chronic kidney failure and potential therapeutic drugs. It provided new ideas for the treatment of kidney failure and promoted the development of drugs targeting the mitochondrial respiratory chain.
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Affiliation(s)
| | | | | | - Jianhua Zhou
- Department of Pediatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science & Technology, Wuhan 430030, China; (Y.W.); (J.Y.); (Y.Z.)
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Long T, Li J, Yin T, Liu K, Wang Y, Long J, Wang J, Cheng L. A genetic variant in gene NDUFAF4 confers the risk of non-small cell lung cancer by perturbing hsa-miR-215 binding. Mol Carcinog 2024; 63:145-159. [PMID: 37787384 DOI: 10.1002/mc.23642] [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: 03/20/2023] [Revised: 09/11/2023] [Accepted: 09/18/2023] [Indexed: 10/04/2023]
Abstract
Hsa-microRNA-215 (hsa-miR-215) plays multiple roles in carcinogenesis through regulating its target genes. Genetic variants in hsa-miR-215 target sites thus may affect hsa-miR-215-mRNA interactions, result in altered expression of target genes and even influence cancer susceptibility. This study aimed to investigate the associations of genetic variants which located in the binding sites of hsa-miR-215 with non-small cell lung cancer (NSCLC) susceptibility in the Chinese population and reveal the potential regulatory mechanism of functional variants in NSCLC development. The candidate genetic variants were predicted and screened through bioinformatics analysis based on the degree of complementarity of hsa-miR-215 sequences. The potential effects of genetic variants on the binding ability of hsa-miR-215 and target genes were also predicted. A case-control study with 932 NSCLC patients and 1036 healthy controls was conducted to evaluate the association of candidate genetic variants with NSCLC susceptibility, and an independent case-control study with 552 NSCLC cases and 571 controls were used to further validate the promising associations. Dual luciferase reporter gene assay was applied to explore the regulation of the genetic variants on transcription activity of target gene. Cell phenotyping experiments in vitro and RNA sequencing (RNA-seq) were then carried out to preliminarily explore the potential regulatory mechanisms of the target genes in NSCLC. A total of five candidate genetic variants located in the binding sites of hsa-miR-215 were screened. The two-stage case-control study showed that a variant rs1854268 A > T, which located in the 3' untranslated (3'UTR) region of NDUFAF4 gene, was associated with decreased risk of NSCLC (additive model, odds ratio [OR] = 0.83, 95% confidence interval [CI]: 0.75-0.92, p < 0.001). Functional annotation displayed that rs1854268 A > T might downregulate the expression of NDUFAF4 by enhancing the binding affinity of hsa-miR-215-5p to NDUFAF4 mRNA. Additionally, transient knockdown of the NDUFAF4 could inhibit lung cancer cell migration and promote lung cancer cell apoptosis. Further RNA-seq analysis revealed that the knockdown of NDUFAF4 may affect NSCLC development by downregulating the nuclear factor kappa B (NF-κB) and phosphoinositide 3 kinase-AKT (PI3K-AKT) signaling pathways. Moreover, the overexpression of CCND1 could partially attenuate the effects of NDUFAF4 knock down on lung cancer cell migration and apoptosis, indicating that CCND1 may be involved in the tumor-promoting effects of NDUFAF4 as a downstream molecule of NDUFAF4 gene. In conclusion, the genetic variant rs1854268 (A > T) on NDUFAF4 confers NSCLC susceptibility by altering the binding affinity of hsa-miR-215-5p, thus regulating the expression of NDUFAF4 and subsequently influencing downstream tumor molecules and pathways such as CCND1, NF kappa B, and PI3K-AKT signaling pathways.
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Affiliation(s)
- Tingting Long
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jiaoyuan Li
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Tongxin Yin
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ke Liu
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yi Wang
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jieyi Long
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jianing Wang
- Department of Thoracic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Liming Cheng
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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Kubala JM, Laursen KB, Schreiner R, Williams RM, van der Mijn JC, Crowley MJ, Mongan NP, Nanus DM, Heller DA, Gudas LJ. NDUFA4L2 reduces mitochondrial respiration resulting in defective lysosomal trafficking in clear cell renal cell carcinoma. Cancer Biol Ther 2023; 24:2170669. [PMID: 36722045 PMCID: PMC9897797 DOI: 10.1080/15384047.2023.2170669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 12/23/2022] [Indexed: 02/02/2023] Open
Abstract
In clear cell renal cell carcinoma (ccRCC), activation of hypoxic signaling induces NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 4-like 2 (NDUFA4L2) expression. Over 90% of ccRCCs exhibit overexpression of NDUFA4L2, which we previously showed contributes to ccRCC proliferation and survival. The function of NDUFA4L2 in ccRCC has not been fully elucidated. NDUFA4L2 was reported to reduce mitochondrial respiration via mitochondrial complex I inhibition. We found that NDUFA4L2 expression in human ccRCC cells increases the extracellular acidification rate, indicative of elevated glycolysis. Conversely, NDUFA4L2 expression in non-cancerous kidney epithelial cells decreases oxygen consumption rate while increasing extracellular acidification rate, suggesting that a Warburg-like effect is induced by NDUFA4L2 alone. We performed mass-spectrometry (MS)-based proteomics of NDUFA4L2 associated complexes. Comparing RCC4-P (parental) ccRCC cells with RCC4 in which NDUFA4L2 is knocked out by CRISPR-Cas9 (RCC4-KO-643), we identified 3,215 proteins enriched in the NDUFA4L2 immunoprecipitates. Among the top-ranking pathways were "Metabolic Reprogramming in Cancer" and "Glycolysis Activation in Cancer (Warburg Effect)." We also show that NDUFA4L2 enhances mitochondrial fragmentation, interacts with lysosomes, and increases mitochondrial-lysosomal associations, as assessed by high-resolution fluorescence microscopy and live cell imaging. We identified 161 lysosomal proteins, including Niemann-Pick Disease Type C Intracellular Cholesterol Transporters 1 and 2 (NPC1, NPC2), that are associated with NDUFA4L2 in RCC4-P cells. RCC4-P cells have larger and decreased numbers of lysosomes relative to RCC4 NDUFA4L2 knockout cells. These findings suggest that NDUFA4L2 regulates mitochondrial-lysosomal associations and potentially lysosomal size and abundance. Consequently, NDUFA4L2 may regulate not only mitochondrial, but also lysosomal functions in ccRCC.
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Affiliation(s)
- Jaclyn M. Kubala
- Department of Pharmacology, Weill Cornell Medicine, New York, NY, USA
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | | | - Ryan Schreiner
- Division of Regenerative Medicine Research, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Ryan M. Williams
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Biomedical Engineering, the City College of New York, New York, NY, USA
| | | | - Michael J. Crowley
- Department of Physiology, Biophysics, and Systems Biology, Weill Cornell Medicine, New York, NY, USA
| | - Nigel P. Mongan
- Department of Pharmacology, Weill Cornell Medicine, New York, NY, USA
- Faculty of Medicine and Health Sciences, Center for Cancer Sciences, University of Nottingham, Sutton Bonington Campus, Loughborough, UK
| | - David M. Nanus
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
- Department of Urology; New York Presbyterian Hospital, Weill Cornell Medicine, New York, NY, USA
| | - Daniel A. Heller
- Department of Pharmacology, Weill Cornell Medicine, New York, NY, USA
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Physiology, Biophysics, and Systems Biology, Weill Cornell Medicine, New York, NY, USA
| | - Lorraine J. Gudas
- Department of Pharmacology, Weill Cornell Medicine, New York, NY, USA
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Department of Urology; New York Presbyterian Hospital, Weill Cornell Medicine, New York, NY, USA
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Lin Y, Xie H, Zhao W, Li Y, Zhang Z. NDUFA4L2 is a novel biomarker for colorectal cancer through bioinformatics analysis. Medicine (Baltimore) 2023; 102:e35893. [PMID: 37933010 PMCID: PMC10627684 DOI: 10.1097/md.0000000000035893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 10/11/2023] [Indexed: 11/08/2023] Open
Abstract
Colorectal cancer (CRC) is a major cause of cancer-related deaths worldwide. NDUFAL42 is an important mitochondrial respiratory chain subunit that plays a critical role in cellular energy metabolism. However, the role of NDUFA4L2 in CRC remains unclear. Therefore, we used the data obtained from The Cancer Genome Atlas (TCGA) database to prove the relationship between NDUFA4L2 and CRC. The expression levels of NDUFA4L2 in CRC tissues were analyzed by immunohistochemical staining of NDUFA4L2 from the HPA database. Wilcoxon rank sum test, Chi-square test, Fisher exact test and logistic regression were used to evaluate relationships between clinical-pathologic features and NDUFA4L2 expression. Receiver operating characteristic (ROC) curves were used to describe binary classifier value of NDUFA4L2 using area under curve (AUC) score. Kaplan-Meier method and Cox regression analysis were used to evaluate factors contributing to prognosis. Gene oncology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis were used to predict the function of differentially expressed genes associated with NDUFA4L2. Gene set enrichment analysis (GSEA) was used to predict canonical pathways associated with NDUFA4L2.Immune infiltration analysis was performed to identify the significantly involved functions of NDUFA4L2. Protein-protein interaction (PPI) networks were established and 20 hub genes identified with Cytoscape software. Increased NDUFA4L2 expression in CRC was associated with T stage (P = .019), N stage (P < .001), Pathologic stage (P = .020), Residual tumor (P = .023), Perineural invasion (P = .039), Lymphatic invasion (P = .007), Histological type(P < .001), PFI event (P = .007) and DSS event (P = .004).ROC curve suggested the significant diagnostic and prognostic ability of NDUFA4L2 (AUC = 0.878). High NDUFA4L2 expression predicted a poorer Overall-survival (P = .021), poorer progression-free interval (P = .001), and poorer Disease Specific Survival (P = .002). GO, KEGG, GSEA and immune infiltration analysis showed that NDUFA4L2 expression was correlated with regulating the function of DNA and some types of immune infiltrating cells. NDUFA4L2 expression was significantly correlated with poor survival and immune infiltrations in CRC, and it may be a promising prognostic biomarker in CRC.
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Affiliation(s)
- Yuning Lin
- Xiamen Key Laboratory of Biomarker Translational Medicine, Medical Laboratory of Xiamen Humanity Hospital Fujian Medical University, Xiamen, China
| | - Hongyan Xie
- Xiamen Key Laboratory of Biomarker Translational Medicine, Medical Laboratory of Xiamen Humanity Hospital Fujian Medical University, Xiamen, China
| | - Wenzhen Zhao
- Xiamen Key Laboratory of Biomarker Translational Medicine, Medical Laboratory of Xiamen Humanity Hospital Fujian Medical University, Xiamen, China
| | - Ying Li
- Ultrasonography Department, Women and Children’s Hospital, School of Medicine, Xiamen university, Xiamen, China
| | - Zhongying Zhang
- Xiamen Key Laboratory of Biomarker Translational Medicine, Medical Laboratory of Xiamen Humanity Hospital Fujian Medical University, Xiamen, China
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Pavithran M S, Lukose J, Barik BK, Periasami A, Kartha VB, Chawla A, Chidangil S. Laser induced fluorescence spectroscopy analysis of kidney tissues: A pilot study for the identification of renal cell carcinoma. JOURNAL OF BIOPHOTONICS 2023; 16:e202300021. [PMID: 37589180 DOI: 10.1002/jbio.202300021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 07/31/2023] [Accepted: 08/15/2023] [Indexed: 08/18/2023]
Abstract
The 325 nm-excited autofluorescence spectra from cancerous and normal renal tissues were collected ex vivo biopsy tissue samples, through an optical fiber probe-based system. Noticeable changes in intensity/wavelength were observed in the fluorescence emissions from endogenous fluorophores such as collagen, Nicotinamide adenine dinucleotide (NADH), Vitamin A (retinol), and flavin adenine dinucleotide, in pathological conditions with respect to the normal state. The energy metabolism involved in clear cell renal cell carcinoma (ccRCC) and chromophobe renal cell carcinoma (chRCC) are reflected in the fluorescence emission band at 445 nm due to bound NADH attributed to enhanced oxidative phosphorylation in chRCC and emission at 465 nm contributed by free NADH showing higher glycolytic action in ccRCC. The principal component analysis and one-way ANOVA effectively discriminate ccRCC from chRCC. It is shown that laser induced fluorescence technique with 325 nm excitation can be a suitable technique for optical pathology and in vivo surgical boundary demarcation in renal cell carcinoma.
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Affiliation(s)
- Sanoop Pavithran M
- Centre of Excellence for Biophotonics, Department of Atomic and Molecular Physics, Manipal Academy of Higher Education, Manipal, India
| | - Jijo Lukose
- Centre of Excellence for Biophotonics, Department of Atomic and Molecular Physics, Manipal Academy of Higher Education, Manipal, India
| | - Bijay Kumar Barik
- Department of Biochemistry, Cell Biology and Genetics, College Medicine, American University of Antigua, Cell Biology and Genetics, American University of Antigua, College of Medicine, St. John's, Antigua and Barbuda
| | - Ammasi Periasami
- W.M. Keck Center for Cellular Imaging (KCCI), Biology, University of Virginia, Charlottesville, Virginia, USA
| | - V B Kartha
- Centre of Excellence for Biophotonics, Department of Atomic and Molecular Physics, Manipal Academy of Higher Education, Manipal, India
| | - Arun Chawla
- Department of Urology, Kasturba Medical College Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Santhosh Chidangil
- Centre of Excellence for Biophotonics, Department of Atomic and Molecular Physics, Manipal Academy of Higher Education, Manipal, India
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11
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Apanovich N, Matveev A, Ivanova N, Burdennyy A, Apanovich P, Pronina I, Filippova E, Kazubskaya T, Loginov V, Braga E, Alimov A. Prediction of Distant Metastases in Patients with Kidney Cancer Based on Gene Expression and Methylation Analysis. Diagnostics (Basel) 2023; 13:2289. [PMID: 37443682 DOI: 10.3390/diagnostics13132289] [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: 06/09/2023] [Revised: 06/28/2023] [Accepted: 07/04/2023] [Indexed: 07/15/2023] Open
Abstract
Clear cell renal cell carcinoma (ccRCC) is the most common and aggressive histological type of cancer in this location. Distant metastases are present in approximately 30% of patients at the time of first examination. Therefore, the ability to predict the occurrence of metastases in patients at early stages of the disease is an urgent task aimed at personalized treatment. Samples of tumor and paired histologically normal kidney tissue from patients with metastatic and non-metastatic ccRCC were studied. Gene expression was analyzed using real-time PCR. The level of gene methylation was evaluated using bisulfite conversion followed by quantitative methylation-specific PCR. Two groups of genes were analyzed in this study. The first group includes genes whose expression is significantly reduced during metastasis: CA9, NDUFA4L2, EGLN3, and BHLHE41 (p < 0.001, ROC analysis). The second group includes microRNA genes: MIR125B-1, MIR137, MIR375, MIR193A, and MIR34B/C, whose increased methylation levels are associated with the development of distant metastases (p = 0.002 to <0.001, ROC analysis). Based on the data obtained, a combined panel of genes was formed to identify patients whose tumors have a high metastatic potential. The panel can estimate the probability of metastasis with an accuracy of up to 92%.
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Affiliation(s)
- Natalya Apanovich
- Research Centre for Medical Genetics, 1 Moskvorechye St., Moscow 115522, Russia
| | - Alexey Matveev
- Federal State Budgetary Institution (N.N. Blokhin National Medical Research Center of Oncology) of the Ministry of Health of the Russian Federation, 24 Kashirskoe Shosse, Moscow 115478, Russia
| | - Natalia Ivanova
- Institute of General Pathology and Pathophysiology, Baltijskaya St. 8, Moscow 125315, Russia
| | - Alexey Burdennyy
- Institute of General Pathology and Pathophysiology, Baltijskaya St. 8, Moscow 125315, Russia
| | - Pavel Apanovich
- Research Centre for Medical Genetics, 1 Moskvorechye St., Moscow 115522, Russia
| | - Irina Pronina
- Institute of General Pathology and Pathophysiology, Baltijskaya St. 8, Moscow 125315, Russia
| | - Elena Filippova
- Institute of General Pathology and Pathophysiology, Baltijskaya St. 8, Moscow 125315, Russia
| | - Tatiana Kazubskaya
- Federal State Budgetary Institution (N.N. Blokhin National Medical Research Center of Oncology) of the Ministry of Health of the Russian Federation, 24 Kashirskoe Shosse, Moscow 115478, Russia
| | - Vitaly Loginov
- Institute of General Pathology and Pathophysiology, Baltijskaya St. 8, Moscow 125315, Russia
| | - Eleonora Braga
- Research Centre for Medical Genetics, 1 Moskvorechye St., Moscow 115522, Russia
- Institute of General Pathology and Pathophysiology, Baltijskaya St. 8, Moscow 125315, Russia
| | - Andrei Alimov
- Research Centre for Medical Genetics, 1 Moskvorechye St., Moscow 115522, Russia
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12
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Zhou L, Mao LH, Li X, Wang QL, Chen SY, Chen ZJ, Lei J, Liu HT, Liao SQ, Ran T, Li XQ, Zhou ZH, He S. Transcriptional regulation of NDUFA4L2 by NFIB induces sorafenib resistance by decreasing reactive oxygen species in hepatocellular carcinoma. Cancer Sci 2023; 114:793-805. [PMID: 36369883 PMCID: PMC9986074 DOI: 10.1111/cas.15648] [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: 07/29/2022] [Revised: 10/28/2022] [Accepted: 11/02/2022] [Indexed: 11/15/2022] Open
Abstract
Sorafenib is one a first-line therapeutic drugs for advanced hepatocellular carcinoma (HCC). However, only 30% of patients benefit from sorafenib due to drug resistance. We and other groups have revealed that nuclear factor I B (NFIB) regulates liver regeneration and carcinogenesis, but its role in drug resistance is poorly known. We found that NFIB was more upregulated in sorafenib-resistant SMMC-7721 cells compared to parental cells. NFIB knockdown not only sensitized drug-resistant cells to sorafenib but also inhibited the proliferation and invasion of these cells. Meanwhile, NFIB promoted the proliferation and invasion of HCC cells in vitro and facilitated tumor growth and metastasis in vivo. Knocking down NFIB synergetically inhibited tumor growth with sorafenib. Mechanically, gene expression profiling and subsequent verification experiments proved that NFIB could bind with the promoter region of a complex I inhibitor NDUFA4L2 and promote its transcription. Transcriptional upregulation of NDUFA4L2 by NFIB could thus inhibit the sorafenib-induced reactive oxygen species accumulation. Finally, we found that NFIB was highly expressed in HCC tissues, and high NFIB expression level was associated with macrovascular invasion, advanced tumor stage, and poor prognosis of HCC patients (n = 156). In summary, we demonstrated that NFIB could transcriptionally upregulate NDUFA4L2 to enhance both intrinsic and acquired sorafenib resistance of HCC cells by reducing reactive oxygen species induction.
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Affiliation(s)
- Li Zhou
- Department of Gastroenterology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Lin-Hong Mao
- Department of Gastroenterology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China.,Department of Gastroenterology, Chengdu Second People's Hospital, Sichuan, China
| | - Xia Li
- Department of Gastroenterology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Qing-Liang Wang
- Department of Pathology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Si-Yuan Chen
- Department of Gastroenterology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Zhi-Ji Chen
- Department of Gastroenterology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Jing Lei
- Department of Gastroenterology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Hong-Tao Liu
- Department of Gastroenterology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Si-Qi Liao
- Department of Gastroenterology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Tao Ran
- Department of Gastroenterology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Xiao-Qin Li
- Department of Gastroenterology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Zhi-Hang Zhou
- Department of Gastroenterology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Song He
- Department of Gastroenterology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
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13
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Waldbillig F, Bormann F, Neuberger M, Ellinger J, Erben P, Kriegmair MC, Michel MS, Nuhn P, Nientiedt M. An m6A-Driven Prognostic Marker Panel for Renal Cell Carcinoma Based on the First Transcriptome-Wide m6A-seq. Diagnostics (Basel) 2023; 13:diagnostics13050823. [PMID: 36899967 PMCID: PMC10001021 DOI: 10.3390/diagnostics13050823] [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: 01/31/2023] [Revised: 02/15/2023] [Accepted: 02/20/2023] [Indexed: 02/25/2023] Open
Abstract
To date, only a single transcriptome-wide m6A sequencing study of clear cell renal cell carcinoma (ccRCC) has been reported, with no validation so far. Herein, by TCGA analysis of the KIRC cohort (n = 530 ccRCC; n = 72 normal), an external expression validation of 35 preidentified m6A targets was performed. Further in-depth expression stratification enabled assessment of m6A-driven key targets. Overall survival (OS) analysis and gene set enrichment analyses (GSEA) were conducted to assess their clinical and functional impact on ccRCC. In the hyper-up cluster significant upregulation was confirmed for NDUFA4L2, NXPH4, SAA1, and PLOD2 (40%) and in the hypo-up cluster for FCHSD1 (10%). Significant downregulation was observed for UMOD, ANK3, and CNTFR (27.3%) in the hypo-down cluster and for CHDH (25%) in the hyper-down cluster. In-depth expression stratification showed consistent dysregulation in ccRCC only for 11.67%: NDUFA4L2, NXPH4, and UMOD (NNU-panel). Patients with strong NNU panel dysregulation had significantly poorer OS (p = 0.0075). GSEA identified 13 associated and significantly upregulated gene sets (all p-values < 0.5; FDR < 0.25). External validation of the only available m6A sequencing in ccRCC consistently reduced dysregulated m6A-driven targets on the NNU panel with highly significant effects on OS. Epitranscriptomics are a promising target for developing novel therapies and for identifying prognostic markers for daily clinical practice.
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Affiliation(s)
- Frank Waldbillig
- Department of Urology & Urosurgery, University Medical Centre Mannheim, University of Heidelberg, 68167 Mannheim, Germany
| | | | - Manuel Neuberger
- Department of Urology & Urosurgery, University Medical Centre Mannheim, University of Heidelberg, 68167 Mannheim, Germany
| | - Jörg Ellinger
- Department of Urology & Pediatric Urology, University Medical Centre Bonn, University of Bonn, 53127 Bonn, Germany
| | - Philipp Erben
- Department of Urology & Urosurgery, University Medical Centre Mannheim, University of Heidelberg, 68167 Mannheim, Germany
| | - Maximilian C. Kriegmair
- Department of Urology & Urosurgery, University Medical Centre Mannheim, University of Heidelberg, 68167 Mannheim, Germany
| | - Maurice Stephan Michel
- Department of Urology & Urosurgery, University Medical Centre Mannheim, University of Heidelberg, 68167 Mannheim, Germany
| | - Philipp Nuhn
- Department of Urology & Urosurgery, University Medical Centre Mannheim, University of Heidelberg, 68167 Mannheim, Germany
| | - Malin Nientiedt
- Department of Urology & Urosurgery, University Medical Centre Mannheim, University of Heidelberg, 68167 Mannheim, Germany
- Correspondence: ; Tel.: +49-(0)621-383-2201
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14
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Metzler VM, de Brot S, Haigh DB, Woodcock CL, Lothion-Roy J, Harris AE, Nilsson EM, Ntekim A, Persson JL, Robinson BD, Khani F, Laursen KB, Gudas LJ, Toss MS, Madhusudan S, Rakha E, Heery DM, Rutland CS, Mongan NP, Jeyapalan JN. The KDM5B and KDM1A lysine demethylases cooperate in regulating androgen receptor expression and signalling in prostate cancer. Front Cell Dev Biol 2023; 11:1116424. [PMID: 37152294 PMCID: PMC10154691 DOI: 10.3389/fcell.2023.1116424] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 04/06/2023] [Indexed: 05/09/2023] Open
Abstract
Histone H3 lysine 4 (H3K4) methylation is key epigenetic mark associated with active transcription and is a substrate for the KDM1A/LSD1 and KDM5B/JARID1B lysine demethylases. Increased expression of KDM1A and KDM5B is implicated in many cancer types, including prostate cancer (PCa). Both KDM1A and KDM5B interact with AR and promote androgen regulated gene expression. For this reason, there is great interested in the development of new therapies targeting KDM1A and KDM5B, particularly in the context of castrate resistant PCa (CRPC), where conventional androgen deprivation therapies and androgen receptor signalling inhibitors are no longer effective. As there is no curative therapy for CRPC, new approaches are urgently required to suppress androgen signalling that prevent, delay or reverse progression to the castrate resistant state. While the contribution of KDM1A to PCa is well established, the exact contribution of KDM5B to PCa is less well understood. However, there is evidence that KDM5B is implicated in numerous pro-oncogenic mechanisms in many different types of cancer, including the hypoxic response, immune evasion and PI3/AKT signalling. Here we elucidate the individual and cooperative functions of KDM1A and KDM5B in PCa. We show that KDM5B mRNA and protein expression is elevated in localised and advanced PCa. We show that the KDM5 inhibitor, CPI-455, impairs androgen regulated transcription and alternative splicing. Consistent with the established role of KDM1A and KDM5B as AR coregulators, we found that individual pharmacologic inhibition of KDM1A and KDM5 by namoline and CPI-455 respectively, impairs androgen regulated transcription. Notably, combined inhibition of KDM1A and KDM5 downregulates AR expression in CRPC cells. Furthermore, combined KDM1A and KDM5 inhibition impairs PCa cell proliferation and invasion more than individual inhibition of KDM1A and KDM5B. Collectively our study has identified individual and cooperative mechanisms involving KDM1A and KDM5 in androgen signalling in PCa. Our findings support the further development of KDM1A and KDM5B inhibitors to treat advanced PCa. Further work is now required to confirm the therapeutic feasibility of combined inhibition of KDM1A and KDM5B as a novel therapeutic strategy for targeting AR positive CRPC.
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Affiliation(s)
- Veronika M. Metzler
- Biodiscovery Institute, University of Nottingham, Nottingham, United Kingdom
| | - Simone de Brot
- COMPATH, Institute of Animal Pathology, University of Bern, Bern, Switzerland
| | - Daisy B. Haigh
- Biodiscovery Institute, University of Nottingham, Nottingham, United Kingdom
| | - Corinne L. Woodcock
- Biodiscovery Institute, University of Nottingham, Nottingham, United Kingdom
| | | | - Anna E. Harris
- Biodiscovery Institute, University of Nottingham, Nottingham, United Kingdom
| | - Emeli M. Nilsson
- Biodiscovery Institute, University of Nottingham, Nottingham, United Kingdom
| | - Atara Ntekim
- Department of Oncology, University Hospital Ibadan, Ibadan, Nigeria
| | - Jenny L. Persson
- Department of Molecular Biology, Umeå University, Umeå, Sweden
- Department of Biomedical Sciences, Malmö Universitet, Malmö, Sweden
| | - Brian D. Robinson
- Department of Urology, Weill Cornell Medicine, New York, NY, United States
| | - Francesca Khani
- Department of Urology, Weill Cornell Medicine, New York, NY, United States
| | - Kristian B. Laursen
- Department of Pharmacology, Weill Cornell Medicine, New York, NY, United States
| | - Lorraine J. Gudas
- Department of Pharmacology, Weill Cornell Medicine, New York, NY, United States
| | - Michael S. Toss
- Biodiscovery Institute, University of Nottingham, Nottingham, United Kingdom
| | | | - Emad Rakha
- Biodiscovery Institute, University of Nottingham, Nottingham, United Kingdom
| | - David M. Heery
- School of Pharmacy, University of Nottingham, Nottingham, United Kingdom
| | - Catrin S. Rutland
- Biodiscovery Institute, University of Nottingham, Nottingham, United Kingdom
| | - Nigel P. Mongan
- Biodiscovery Institute, University of Nottingham, Nottingham, United Kingdom
- Department of Pharmacology, Weill Cornell Medicine, New York, NY, United States
- *Correspondence: Nigel P. Mongan, , ; Jennie N. Jeyapalan,
| | - Jennie N. Jeyapalan
- Biodiscovery Institute, University of Nottingham, Nottingham, United Kingdom
- *Correspondence: Nigel P. Mongan, , ; Jennie N. Jeyapalan,
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15
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Esmaeilzadeh AA, Kashian M, Salman HM, Alsaffar MF, Jaber MM, Soltani S, Amiri Manjili D, Ilhan A, Bahrami A, Kastelic JW. Identify Biomarkers and Design Effective Multi-Target Drugs in Ovarian Cancer: Hit Network-Target Sets Model Optimizing. BIOLOGY 2022; 11:1851. [PMID: 36552360 PMCID: PMC9776135 DOI: 10.3390/biology11121851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 12/14/2022] [Accepted: 12/16/2022] [Indexed: 12/24/2022]
Abstract
Epithelial ovarian cancer (EOC) is highly aggressive with poor patient outcomes, and a deeper understanding of ovarian cancer tumorigenesis could help guide future treatment development. We proposed an optimized hit network-target sets model to systematically characterize the underlying pathological mechanisms and intra-tumoral heterogeneity in human ovarian cancer. Using TCGA data, we constructed an epithelial ovarian cancer regulatory network in this study. We use three distinct methods to produce different HNSs for identification of the driver genes/nodes, core modules, and core genes/nodes. Following the creation of the optimized HNS (OHNS) by the integration of DN (driver nodes), CM (core module), and CN (core nodes), the effectiveness of various HNSs was assessed based on the significance of the network topology, control potential, and clinical value. Immunohistochemical (IHC), qRT-PCR, and Western blotting were adopted to measure the expression of hub genes and proteins involved in epithelial ovarian cancer (EOC). We discovered that the OHNS has two key advantages: the network's central location and controllability. It also plays a significant role in the illness network due to its wide range of capabilities. The OHNS and clinical samples revealed the endometrial cancer signaling, and the PI3K/AKT, NER, and BMP pathways. MUC16, FOXA1, FBXL2, ARID1A, COX15, COX17, SCO1, SCO2, NDUFA4L2, NDUFA, and PTEN hub genes were predicted and may serve as potential candidates for new treatments and biomarkers for EOC. This research can aid in better capturing the disease progression, the creation of potent multi-target medications, and the direction of the therapeutic community in the optimization of effective treatment regimens by various research objectives in cancer treatment.
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Affiliation(s)
| | - Mahdis Kashian
- Department of Obstetrics and Gynecology, Medical College of Iran University, Tehran 14535, Iran;
| | - Hayder Mahmood Salman
- Department of Computer Science, Al-Turath University College Al Mansour, Baghdad 10011, Iraq;
| | - Marwa Fadhil Alsaffar
- Medical Laboratory Techniques Department, AL-Mustaqbal University College, Hillah 51001, Iraq;
| | - Mustafa Musa Jaber
- Computer Techniques Engineering Department, Dijlah University College, Baghdad 00964, Iraq;
- Computer Techniques Engineering Department, Al-Farahidi University, Baghdad 10011, Iraq
| | - Siamak Soltani
- Department of Forensic Medicine, School of Medicine, Iran University of Medical Sciences, Tehran 14535, Iran;
| | - Danial Amiri Manjili
- Department of Infectious Disease, School of Medicine, Babol University of Medical Sciences, Babol 47414, Iran
| | - Ahmet Ilhan
- Department of Medical Biochemistry, Faculty of Medicine, Cukurova University, Adana 01330, Turkey
| | - Abolfazl Bahrami
- Department of Animal Science, College of Agriculture and Natural Resources, University of Tehran, Karaj 1417643184, Iran;
- Biomedical Center for Systems Biology Science Munich, Ludwig-Maximilians-University, 80333 Munich, Germany
| | - John W. Kastelic
- Department of Health, University of Calgary, Calgary, AB T2N 1N4, Canada;
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16
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van der Mijn JC, Chen Q, Laursen KB, Khani F, Wang X, Dorsaint P, Sboner A, Gross SS, Nanus DM, Gudas LJ. Transcriptional and metabolic remodeling in clear cell renal cell carcinoma caused by ATF4 activation and the integrated stress response (ISR). Mol Carcinog 2022; 61:851-864. [PMID: 35726553 PMCID: PMC9378514 DOI: 10.1002/mc.23437] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 03/14/2022] [Accepted: 04/14/2022] [Indexed: 11/10/2022]
Abstract
Research has shown extensive metabolic remodeling in clear cell renal cell carcinoma (ccRCC), with increased glutathione (GSH) levels. We hypothesized that activating transcription factor-4 (ATF4) and the integrated stress response (ISR) induce a metabolic shift, including increased GSH accumulation, and that Vitamin A deficiency (VAD), found in ccRCCs, can also activate ATF4 signaling in the kidney. To determine the role of ATF4, we used publicly available RNA sequencing (RNA-seq) data sets from The Cancer Genomics Atlas. Subsequently, we performed RNA-seq and liquid chromatography-mass spectrometry-based metabolomics analysis of the murine TRAnsgenic Cancer of the Kidney (TRACK) model for early-stage ccRCC. To validate our findings, we generated RCC4 cell lines with ATF4 gene edits (ATF4-knockout [KO]) and subjected these cells to metabolic isotope tracing. Analysis of variance, the two-sided Student's t test, and gene set enrichment analysis were used (p < 0.05) to determine statistical significance. Here we show that most human ccRCC tumors exhibit activation of the transcription factor ATF4. Activation of ATF4 is concomitant with enrichment of the ATF4 gene set and elevated expression of ATF4 target genes ASNS, ALDH1L2, MTHFD2, DDIT3 (CHOP), DDIT4, TRIB3, EIF4EBP1, SLC7A11, and PPP1R15A (GADD34). Transcript profiling and metabolomics analyses show that activated hypoxia-inducible factor-1α (HIF1α) signaling in our TRACK ccRCC murine model also induces an ATF4-mediated ISR. Notably, both normoxic HIF1α signaling in TRACK kidneys and VAD in wild-type kidneys diminish amino acid levels, increase ASNS, TRIB3, and MTHFD2 messenger RNA levels, and increase levels of lipids and GSH. By metabolic isotope tracing in human RCC4 kidney cancer parental and ATF4 gene-edited (ATF4-KO) cell lines, we show that ATF4 increases GSH accumulation in part via activation of the mitochondrial one-carbon metabolism pathway. Our results demonstrate for the first time that activation of ATF4 enhances GSH accumulation, increases purine and pyrimidine biosynthesis, and contributes to transcriptional and metabolic remodeling in ccRCC. Moreover, constitutive HIF1α expressed only in murine kidney proximal tubules activates ATF4, leading to the metabolic changes associated with the ISR. Our data indicate that HIF1α can promote ccRCC via ATF4 activation. Moreover, lack of Vitamin A in the kidney recapitulates aspects of the ISR.
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Affiliation(s)
- Johannes C. van der Mijn
- Department of Pharmacology, New York Presbyterian Hospital, Weill Cornell Medicine, New York, New York, USA
- current address: Department of Medical Oncology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Qiuying Chen
- Department of Pharmacology, New York Presbyterian Hospital, Weill Cornell Medicine, New York, New York, USA
| | - Kristian B. Laursen
- Department of Pharmacology, New York Presbyterian Hospital, Weill Cornell Medicine, New York, New York, USA
| | - Francesca Khani
- Department of Pathology and Laboratory Medicine, New York Presbyterian Hospital, Weill Cornell Medicine, New York, New York, USA
- Department of Urology; New York Presbyterian Hospital, Weill Cornell Medicine, New York, New York, USA
| | - Xiaofei Wang
- Department of Physiology and Biophysics, New York Presbyterian Hospital, Weill Cornell Medicine, New York, New York, USA
- Englander Institute for Precision Medicine, New York Presbyterian Hospital, Weill Cornell Medicine, New York, New York, USA
| | - Princesca Dorsaint
- Department of Physiology and Biophysics, New York Presbyterian Hospital, Weill Cornell Medicine, New York, New York, USA
- Englander Institute for Precision Medicine, New York Presbyterian Hospital, Weill Cornell Medicine, New York, New York, USA
| | - Andrea Sboner
- Department of Pathology and Laboratory Medicine, New York Presbyterian Hospital, Weill Cornell Medicine, New York, New York, USA
- Englander Institute for Precision Medicine, New York Presbyterian Hospital, Weill Cornell Medicine, New York, New York, USA
- HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York Presbyterian Hospital, Weill Cornell Medicine, New York, New York, USA
- Sandra and Edward Meyer Cancer Center, New York Presbyterian Hospital, Weill Cornell Medicine, New York, New York, USA
| | - Steven S. Gross
- Department of Pharmacology, New York Presbyterian Hospital, Weill Cornell Medicine, New York, New York, USA
| | - David M. Nanus
- Division of Hematology and Medical Oncology, Department of Medicine, New York Presbyterian Hospital, Weill Cornell Medicine, New York, New York, USA
- Department of Urology; New York Presbyterian Hospital, Weill Cornell Medicine, New York, New York, USA
| | - Lorraine J. Gudas
- Department of Pharmacology, New York Presbyterian Hospital, Weill Cornell Medicine, New York, New York, USA
- Department of Urology; New York Presbyterian Hospital, Weill Cornell Medicine, New York, New York, USA
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17
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Chen WJ, Cao H, Cao JW, Zuo L, Qu FJ, Xu D, Zhang H, Gong HY, Chen JX, Ye JQ, Gan SS, Zhou W, Zhu DW, Pan XW, Cui XG. Heterogeneity of tumor microenvironment is associated with clinical prognosis of non-clear cell renal cell carcinoma: a single-cell genomics study. Cell Death Dis 2022; 13:50. [PMID: 35017463 PMCID: PMC8752784 DOI: 10.1038/s41419-022-04501-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 12/08/2021] [Accepted: 01/04/2022] [Indexed: 12/18/2022]
Abstract
Non-clear renal cell carcinomas (nccRCCs) are less frequent in kidney cancer with histopathological heterogeneity. A better understanding of the tumor biology of nccRCC can provide more effective treatment paradigms for different subtypes. To reveal the heterogeneity of tumor microenvironment (TME) in nccRCC, we performed 10x sing-cell genomics on tumor and normal tissues from patients with papillary renal cell carcinoma (pRCC), chromophobe RCC (chrRCC), collecting duct carcinoma (CDRCC) and sarcomatoid RCC (sarRCC). 15 tissue samples were finally included. 34561 cells were identified as 16 major cell clusters with 34 cell subtypes. Our study presented the sing-cell landscape for four types of nccRCC, and demonstrated that CD8+ T cells exhaustion, tumor-associated macrophages (TAMs) and sarcomatoid process were the pivotal factors in immunosuppression of nccRCC tissues and were closely correlated with poor prognosis. Abnormal metabolic patterns were present in both cancer cells and tumor-infiltrating stromal cells, such as fibroblasts and endothelial cells. Combined with CIBERSORTx tool, the expression data of bulk RNA-seq from TCGA were labeled with cell types of our sing-cell data. Calculation of the relative abundance of cell types revealed that greater proportion of exhausted CD8+ T cells, TAMs and sarRCC derived cells were correlated with poor prognosis in the cohort of 274 nccRCC patients. To the best of our knowledge, this is the first study that provides a more comprehensive sight about the heterogeneity and tumor biology of nccRCC, which may potentially facilitate the development of more effective therapies for nccRCC.
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Affiliation(s)
- Wen-Jin Chen
- Department of Urology, The Third Affiliated Hospital of Second Military Medical University, 700 North Moyu Road, Shanghai, 201805, China
| | - Hao Cao
- School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, Shenyang, 110016, China.,Peking-Tsinghua Center for Life Sciences, Tsinghua University, 100084, Beijing, China
| | - Jian-Wei Cao
- Department of Urology, Xinhua Hospital, Shanghai Jiaotong University, School of Medicine, 1665 Kongjiang Road, Shanghai, 200092, China
| | - Li Zuo
- Department of Urology, The Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical University, 29 Xinglong Road, Changzhou, 213000, Jiangsu, China
| | - Fa-Jun Qu
- Department of Urology, Xinhua Hospital, Shanghai Jiaotong University, School of Medicine, 1665 Kongjiang Road, Shanghai, 200092, China
| | - Da Xu
- Department of Urology, The Third Affiliated Hospital of Second Military Medical University, 700 North Moyu Road, Shanghai, 201805, China
| | - Hao Zhang
- Department of Orthopedic Oncology, Changzheng Hospital of Second Military Medical University, 415 Fengyang Road, Shanghai, 200003, China
| | - Hai-Yi Gong
- Department of Orthopedic Oncology, Changzheng Hospital of Second Military Medical University, 415 Fengyang Road, Shanghai, 200003, China
| | - Jia-Xin Chen
- Department of Urology, The Third Affiliated Hospital of Second Military Medical University, 700 North Moyu Road, Shanghai, 201805, China
| | - Jian-Qing Ye
- Department of Urology, The Third Affiliated Hospital of Second Military Medical University, 700 North Moyu Road, Shanghai, 201805, China
| | - Si-Shun Gan
- Department of Urology, The Third Affiliated Hospital of Second Military Medical University, 700 North Moyu Road, Shanghai, 201805, China
| | - Wang Zhou
- Department of Urology, The Third Affiliated Hospital of Second Military Medical University, 700 North Moyu Road, Shanghai, 201805, China.,Department of Urology, Xinhua Hospital, Shanghai Jiaotong University, School of Medicine, 1665 Kongjiang Road, Shanghai, 200092, China
| | - Da-Wei Zhu
- Department of Urology, The Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical University, 29 Xinglong Road, Changzhou, 213000, Jiangsu, China.
| | - Xiu-Wu Pan
- Department of Urology, The Third Affiliated Hospital of Second Military Medical University, 700 North Moyu Road, Shanghai, 201805, China. .,Department of Urology, Xinhua Hospital, Shanghai Jiaotong University, School of Medicine, 1665 Kongjiang Road, Shanghai, 200092, China.
| | - Xin-Gang Cui
- Department of Urology, The Third Affiliated Hospital of Second Military Medical University, 700 North Moyu Road, Shanghai, 201805, China. .,Department of Urology, Xinhua Hospital, Shanghai Jiaotong University, School of Medicine, 1665 Kongjiang Road, Shanghai, 200092, China.
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18
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Laursen KB, Chen Q, Khani F, Attarwala N, Gross SS, Dow L, Nanus DM, Gudas LJ. Mitochondrial Ndufa4l2 Enhances Deposition of Lipids and Expression of Ca9 in the TRACK Model of Early Clear Cell Renal Cell Carcinoma. Front Oncol 2022; 11:783856. [PMID: 34970493 PMCID: PMC8712948 DOI: 10.3389/fonc.2021.783856] [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: 09/27/2021] [Accepted: 11/12/2021] [Indexed: 12/31/2022] Open
Abstract
Mitochondrial dysfunction and aberrant glycolysis are hallmarks of human clear cell renal cell carcinoma (ccRCC). Whereas glycolysis is thoroughly studied, little is known about the mitochondrial contribution to the pathology of ccRCC. Mitochondrial Ndufa4l2 is predictive of poor survival of ccRCC patients, and in kidney cancer cell lines the protein supports proliferation and colony formation. Its role in ccRCC, however, remains enigmatic. We utilized our established ccRCC model, termed Transgenic Cancer of the Kidney (TRACK), to generate a novel genetically engineered mouse model in which dox-regulated expression of an shRNA decreases Ndufa4l2 levels specifically in the renal proximal tubules (PT). This targeted knockdown of Ndufa4l2 reduced the accumulation of neutral renal lipid and was associated with decreased levels of the ccRCC markers carbonic anhydrase 9 (CA9) and Enolase 1 (ENO1). These findings suggest a link between mitochondrial dysregulation (i.e. high levels of Ndufa4l2), lipid accumulation, and the expression of ccRCC markers ENO1 and CA9, and demonstrate that lipid accumulation and ccRCC development can potentially be attenuated by inhibiting Ndufa4l2.
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Affiliation(s)
- Kristian B Laursen
- Department of Pharmacology, New York Presbyterian Hospital, Weill Cornell Medicine, New York, NY, United States
| | - Qiuying Chen
- Department of Pharmacology, New York Presbyterian Hospital, Weill Cornell Medicine, New York, NY, United States
| | - Francesca Khani
- Department of Pathology and Laboratory Medicine, New York Presbyterian Hospital, Weill Cornell Medicine, New York, NY, United States.,Department of Urology, New York Presbyterian Hospital, Weill Cornell Medicine, New York, NY, United States
| | - Nabeel Attarwala
- Department of Pharmacology, New York Presbyterian Hospital, Weill Cornell Medicine, New York, NY, United States
| | - Steve S Gross
- Department of Pharmacology, New York Presbyterian Hospital, Weill Cornell Medicine, New York, NY, United States
| | - Lukas Dow
- Department of Medicine, New York Presbyterian Hospital, Weill Cornell Medicine, New York, NY, United States.,Department of Biochemistry, New York Presbyterian Hospital, Weill Cornell Medicine, New York, NY, United States.,Graduate School of Medical Sciences, New York Presbyterian Hospital, Weill Cornell Medicine, New York, NY, United States
| | - David M Nanus
- Department of Urology, New York Presbyterian Hospital, Weill Cornell Medicine, New York, NY, United States.,Division of Hematology and Medical Oncology, Department of Medicine, New York Presbyterian Hospital, Weill Cornell Medicine, New York, NY, United States
| | - Lorraine J Gudas
- Department of Pharmacology, New York Presbyterian Hospital, Weill Cornell Medicine, New York, NY, United States.,Department of Urology, New York Presbyterian Hospital, Weill Cornell Medicine, New York, NY, United States
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19
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Alblihy A, Shoqafi A, Toss MS, Algethami M, Harris AE, Jeyapalan JN, Abdel-Fatah T, Servante J, Chan SYT, Green A, Mongan NP, Rakha EA, Madhusudan S. Untangling the clinicopathological significance of MRE11-RAD50-NBS1 complex in sporadic breast cancers. NPJ Breast Cancer 2021; 7:143. [PMID: 34782604 PMCID: PMC8593132 DOI: 10.1038/s41523-021-00350-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 10/22/2021] [Indexed: 12/27/2022] Open
Abstract
The MRE11-RAD50-NBS1 (MRN) complex is critical for genomic stability. Although germline mutations in MRN may increase breast cancer susceptibility, such mutations are extremely rare. Here, we have conducted a comprehensive clinicopathological study of MRN in sporadic breast cancers. We have protein expression profiled for MRN and a panel of DNA repair factors involved in double-strand break repair (BRCA1, BRCA2, ATM, CHK2, ATR, Chk1, pChk1, RAD51, γH2AX, RPA1, RPA2, DNA-PKcs), RECQ DNA helicases (BLM, WRN, RECQ1, RECQL4, RECQ5), nucleotide excision repair (ERCC1) and base excision repair (SMUG1, APE1, FEN1, PARP1, XRCC1, Pol β) in 1650 clinical breast cancers. The prognostic significance of MRE11, RAD50 and NBS1 transcripts and their microRNA regulators (hsa-miR-494 and hsa-miR-99b) were evaluated in large clinical datasets. Expression of MRN components was analysed in The Cancer Genome Atlas breast cancer cohort. We show that low nuclear MRN is linked to aggressive histopathological phenotypes such as high tumour grade, high mitotic index, oestrogen receptor- and high-risk Nottingham Prognostic Index. In univariate analysis, low nuclear MRE11 and low nuclear RAD50 were associated with poor survival. In multivariate analysis, low nuclear RAD50 remained independently linked with adverse clinical outcomes. Low RAD50 transcripts were also linked with reduced survival. In contrast, overexpression of hsa-miR-494 and hsa-miR-99b microRNAs was associated with poor survival. We observed large-scale genome-wide alterations in MRN-deficient tumours contributing to aggressive behaviour. We conclude that MRN status may be a useful tool to stratify tumours for precision medicine strategies.
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Affiliation(s)
- Adel Alblihy
- Nottingham Biodiscovery Institute, School of Medicine, University of Nottingham, University Park, Nottingham, NG7 3RD, UK
- Medical Center, King Fahad Security College (KFSC), Riyadh, 11461, Saudi Arabia
| | - Ahmed Shoqafi
- Nottingham Biodiscovery Institute, School of Medicine, University of Nottingham, University Park, Nottingham, NG7 3RD, UK
| | - Michael S Toss
- Nottingham Biodiscovery Institute, School of Medicine, University of Nottingham, University Park, Nottingham, NG7 3RD, UK
- Department of Pathology, Nottingham University Hospitals, City Hospital Campus, Nottingham, NG5 1PB, UK
| | - Mashael Algethami
- Nottingham Biodiscovery Institute, School of Medicine, University of Nottingham, University Park, Nottingham, NG7 3RD, UK
| | - Anna E Harris
- Nottingham Biodiscovery Institute, School of Medicine, University of Nottingham, University Park, Nottingham, NG7 3RD, UK
| | - Jennie N Jeyapalan
- Nottingham Biodiscovery Institute, School of Medicine, University of Nottingham, University Park, Nottingham, NG7 3RD, UK
| | - Tarek Abdel-Fatah
- Department of Oncology, Nottingham University Hospitals, City Hospital Campus, Nottingham, NG5 1PB, UK
| | | | - Stephen Y T Chan
- Department of Oncology, Nottingham University Hospitals, City Hospital Campus, Nottingham, NG5 1PB, UK
| | - Andrew Green
- Nottingham Biodiscovery Institute, School of Medicine, University of Nottingham, University Park, Nottingham, NG7 3RD, UK
| | - Nigel P Mongan
- Nottingham Biodiscovery Institute, School of Medicine, University of Nottingham, University Park, Nottingham, NG7 3RD, UK
| | - Emad A Rakha
- Nottingham Biodiscovery Institute, School of Medicine, University of Nottingham, University Park, Nottingham, NG7 3RD, UK
- Department of Pathology, Nottingham University Hospitals, City Hospital Campus, Nottingham, NG5 1PB, UK
| | - Srinivasan Madhusudan
- Nottingham Biodiscovery Institute, School of Medicine, University of Nottingham, University Park, Nottingham, NG7 3RD, UK.
- Department of Oncology, Nottingham University Hospitals, City Hospital Campus, Nottingham, NG5 1PB, UK.
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20
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Liu Z, Chaillou T, Santos Alves E, Mader T, Jude B, Ferreira DMS, Hynynen H, Cheng AJ, Jonsson WO, Pironti G, Andersson DC, Kenne E, Ruas JL, Tavi P, Lanner JT. Mitochondrial NDUFA4L2 is a novel regulator of skeletal muscle mass and force. FASEB J 2021; 35:e22010. [PMID: 34724256 DOI: 10.1096/fj.202100066r] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 09/24/2021] [Accepted: 10/08/2021] [Indexed: 01/07/2023]
Abstract
The hypoxia-inducible nuclear-encoded mitochondrial protein NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 4-like 2 (NDUFA4L2) has been demonstrated to decrease oxidative phosphorylation and production of reactive oxygen species in neonatal cardiomyocytes, brain tissue and hypoxic domains of cancer cells. Prolonged local hypoxia can negatively affect skeletal muscle size and tissue oxidative capacity. Although skeletal muscle is a mitochondrial rich, oxygen sensitive tissue, the role of NDUFA4L2 in skeletal muscle has not previously been investigated. Here we ectopically expressed NDUFA4L2 in mouse skeletal muscles using adenovirus-mediated expression and in vivo electroporation. Moreover, femoral artery ligation (FAL) was used as a model of peripheral vascular disease to induce hind limb ischemia and muscle damage. Ectopic NDUFA4L2 expression resulted in reduced mitochondrial respiration and reactive oxygen species followed by lowered AMP, ADP, ATP, and NAD+ levels without affecting the overall protein content of the mitochondrial electron transport chain. Furthermore, ectopically expressed NDUFA4L2 caused a ~20% reduction in muscle mass that resulted in weaker muscles. The loss of muscle mass was associated with increased gene expression of atrogenes MurF1 and Mul1, and apoptotic genes caspase 3 and Bax. Finally, we showed that NDUFA4L2 was induced by FAL and that the Ndufa4l2 mRNA expression correlated with the reduced capacity of the muscle to generate force after the ischemic insult. These results show, for the first time, that mitochondrial NDUFA4L2 is a novel regulator of skeletal muscle mass and force. Specifically, induced NDUFA4L2 reduces mitochondrial activity leading to lower levels of important intramuscular metabolites, including adenine nucleotides and NAD+ , which are hallmarks of mitochondrial dysfunction and hence shows that dysfunctional mitochondrial activity may drive muscle wasting.
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Affiliation(s)
- Zhengye Liu
- Department of Physiology and Pharmacology, Molecular Muscle Physiology and Pathophysiology, Karolinska Institutet, Stockholm, Sweden
| | - Thomas Chaillou
- Department of Physiology and Pharmacology, Molecular Muscle Physiology and Pathophysiology, Karolinska Institutet, Stockholm, Sweden
| | - Estela Santos Alves
- Department of Physiology and Pharmacology, Molecular Muscle Physiology and Pathophysiology, Karolinska Institutet, Stockholm, Sweden
| | - Theresa Mader
- Department of Physiology and Pharmacology, Molecular Muscle Physiology and Pathophysiology, Karolinska Institutet, Stockholm, Sweden
| | - Baptiste Jude
- Department of Physiology and Pharmacology, Molecular Muscle Physiology and Pathophysiology, Karolinska Institutet, Stockholm, Sweden
| | - Duarte M S Ferreira
- Department of Physiology and Pharmacology, Molecular and Cellular Exercise Physiology, Karolinska Institutet, Stockholm, Sweden
| | - Heidi Hynynen
- A.I. Virtanen Institute, University of Eastern Finland, Kuopio, Finland
| | - Arthur J Cheng
- Department of Physiology and Pharmacology, Molecular Muscle Physiology and Pathophysiology, Karolinska Institutet, Stockholm, Sweden
| | - William O Jonsson
- Department of Physiology and Pharmacology, Molecular Muscle Physiology and Pathophysiology, Karolinska Institutet, Stockholm, Sweden
| | - Gianluigi Pironti
- Department of Physiology and Pharmacology, Medical Cardiac and Skeletal Muscle Research, Karolinska Institutet, Stockholm, Sweden
| | - Daniel C Andersson
- Department of Physiology and Pharmacology, Medical Cardiac and Skeletal Muscle Research, Karolinska Institutet, Stockholm, Sweden.,Heart, Vascular and Neurology Theme, Cardiology Unit, Karolinska University Hospital, Stockholm, Sweden
| | - Ellinor Kenne
- Department of Physiology and Pharmacology, Molecular Muscle Physiology and Pathophysiology, Karolinska Institutet, Stockholm, Sweden
| | - Jorge L Ruas
- Department of Physiology and Pharmacology, Molecular and Cellular Exercise Physiology, Karolinska Institutet, Stockholm, Sweden
| | - Pasi Tavi
- A.I. Virtanen Institute, University of Eastern Finland, Kuopio, Finland
| | - Johanna T Lanner
- Department of Physiology and Pharmacology, Molecular Muscle Physiology and Pathophysiology, Karolinska Institutet, Stockholm, Sweden
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21
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Yuan X, He Y, Luo C, Wang W. Leukotriene B4 receptor 2 correlates with prognosis and immune infiltration in clear cell renal cell carcinoma. Invest New Drugs 2021; 40:232-244. [PMID: 34633577 DOI: 10.1007/s10637-021-01174-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 08/26/2021] [Indexed: 10/20/2022]
Abstract
BACKGROUND Clear cell renal cell carcinoma (ccRCC) is the most common renal cancer. According to reports, leukotriene B4 receptor 2 (LTB4R2, also known as BLT2), a chemokine receptor, is upregulated in different tumors. However, the correlation between BLT2 expression and its prognostic value in ccRCC remains to be explored. METHODS This study used the The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases to evaluate the association between BLT2 expression and the clinical outcome of ccRCC. Based on TIMER2.0, the correlation between BLT2 expression in ccRCC and tumor immune characteristics was evaluated. RESULTS The expression of BLT2 in ccRCC was higher than that in normal tissues. Kaplan-Meier survival analysis indicated that high BLT2 expression was significantly correlated with poor overall survival (HR = 1.75, p < 0.001) and disease-specific survival (HR = 1.60, p = 0.014) for patients with ccRCC. In addition, our findings revealed that there was no significant correlation between the M1 marker genes and the expression of BLT2 in ccRCC, while moderate correlations were observed between the BLT2 expression and the M2 marker genes. Tregs and T cell exhaustion marker genes were positively correlated with BLT2 expression in ccRCC (p < 0.001). CONCLUSION BLT2 may serve as a novel prognostic biomarker and is related to the shaping of tumor immune microenvironment in ccRCC. The expression of BLT2 potentially contributes to the regulation of TAMs, T cell exhaustion, and Tregs activation in ccRCC, providing new approaches to promote the development of new immunotherapeutic strategies for ccRCC.
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Affiliation(s)
- Xia Yuan
- Department of Oncology, The Affiliated Cancer Hospital of Xiangya School of Medicine, Hunan Cancer Hospital, Central South University, Changsha, Hunan, China
| | - Yi He
- Department of Oncology, The Affiliated Cancer Hospital of Xiangya School of Medicine, Hunan Cancer Hospital, Central South University, Changsha, Hunan, China
| | - Chenhui Luo
- Scientific Research Office, The Affiliated Cancer Hospital of Xiangya School of Medicine, Hunan Cancer Hospital, Central South University, Changsha, Hunan, China
| | - Wei Wang
- Department of Oncology, The Affiliated Cancer Hospital of Xiangya School of Medicine, Hunan Cancer Hospital, Central South University, Changsha, Hunan, China.
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22
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Duś-Szachniewicz K, Gdesz-Birula K, Zduniak K, Wiśniewski JR. Proteomic-Based Analysis of Hypoxia- and Physioxia-Responsive Proteins and Pathways in Diffuse Large B-Cell Lymphoma. Cells 2021; 10:cells10082025. [PMID: 34440794 PMCID: PMC8392495 DOI: 10.3390/cells10082025] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 08/05/2021] [Accepted: 08/06/2021] [Indexed: 01/17/2023] Open
Abstract
Hypoxia is a common feature in most tumors, including hematological malignancies. There is a lack of studies on hypoxia- and physioxia-induced global proteome changes in lymphoma. Here, we sought to explore how the proteome of diffuse large B-cell lymphoma (DLBCL) changes when cells are exposed to acute hypoxic stress (1% of O2) and physioxia (5% of O2) for a long-time. A total of 8239 proteins were identified by LC–MS/MS, of which 718, 513, and 486 had significant changes, in abundance, in the Ri-1, U2904, and U2932 cell lines, respectively. We observed that changes in B-NHL proteome profiles induced by hypoxia and physioxia were quantitatively similar in each cell line; however, differentially abundant proteins (DAPs) were specific to a certain cell line. A significant downregulation of several ribosome proteins indicated a translational inhibition of new ribosome protein synthesis in hypoxia, what was confirmed in a pathway enrichment analysis. In addition, downregulated proteins highlighted the altered cell cycle, metabolism, and interferon signaling. As expected, the enrichment of upregulated proteins revealed terms related to metabolism, HIF1 signaling, and response to oxidative stress. In accordance to our results, physioxia induced weaker changes in the protein abundance when compared to those induced by hypoxia. Our data provide new evidence for understanding mechanisms by which DLBCL cells respond to a variable oxygen level. Furthermore, this study reveals multiple hypoxia-responsive proteins showing an altered abundance in hypoxic and physioxic DLBCL. It remains to be investigated whether changes in the proteomes of DLBCL under normoxia and physioxia have functional consequences on lymphoma development and progression.
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Affiliation(s)
- Kamila Duś-Szachniewicz
- Department of Clinical and Experimental Pathology, Institute of General and Experimental Pathology, Wrocław Medical University, Marcinkowskiego 1, 50-368 Wrocław, Poland; (K.G.-B.); (K.Z.)
- Correspondence:
| | - Katarzyna Gdesz-Birula
- Department of Clinical and Experimental Pathology, Institute of General and Experimental Pathology, Wrocław Medical University, Marcinkowskiego 1, 50-368 Wrocław, Poland; (K.G.-B.); (K.Z.)
| | - Krzysztof Zduniak
- Department of Clinical and Experimental Pathology, Institute of General and Experimental Pathology, Wrocław Medical University, Marcinkowskiego 1, 50-368 Wrocław, Poland; (K.G.-B.); (K.Z.)
| | - Jacek R. Wiśniewski
- Biochemical Proteomics Group, Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany;
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23
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Apanovich N, Apanovich P, Mansorunov D, Kuzevanova A, Matveev V, Karpukhin A. The Choice of Candidates in Survival Markers Based on Coordinated Gene Expression in Renal Cancer. Front Oncol 2021; 11:615787. [PMID: 34046336 PMCID: PMC8144703 DOI: 10.3389/fonc.2021.615787] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 03/25/2021] [Indexed: 12/18/2022] Open
Abstract
We aimed to identify and investigate genes that are essential for the development of clear cell renal cell carcinoma (ccRCC) and sought to shed light on the mechanisms of its progression and create prognostic markers for the disease. We used real-time PCR to study the expression of 20 genes that were preliminarily selected based on their differential expression in ccRCC, in 68 paired tumor/normal samples. Upon ccRCC progression, seven genes that showed an initial increase in expression showed decreased expression. The genes whose expression levels did not significantly change during progression were associated mainly with metabolic and inflammatory processes. The first group included CA9, NDUFA4L2, EGLN3, BHLHE41, VWF, IGFBP3, and ANGPTL4, whose expression levels were coordinately decreased during tumor progression. This expression coordination and gene function is related to the needs of tumor development at different stages. Specifically, the high correlation coefficient of EGLN3 and NDUFA4L2 expression may indicate the importance of the coordinated regulation of glycolysis and mitochondrial metabolism. A panel of CA9, EGLN3, BHLHE41, and VWF enabled the prediction of survival for more than 3.5 years in patients with ccRCC, with a probability close to 90%. Therefore, a coordinated change in the expression of a gene group during ccRCC progression was detected, and a new panel of markers for individual survival prognosis was identified.
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Affiliation(s)
- Natalya Apanovich
- Laboratory of Molecular Genetics of Complex Inherited Diseases, Research Centre for Medical Genetics, Moscow, Russia
| | - Pavel Apanovich
- Laboratory of Molecular Genetics of Complex Inherited Diseases, Research Centre for Medical Genetics, Moscow, Russia
| | - Danzan Mansorunov
- Laboratory of Molecular Genetics of Complex Inherited Diseases, Research Centre for Medical Genetics, Moscow, Russia
| | - Anna Kuzevanova
- Laboratory of Molecular Genetics of Complex Inherited Diseases, Research Centre for Medical Genetics, Moscow, Russia
| | - Vsevolod Matveev
- Department of Oncourology, Federal State Budgetary Institution "N.N. Blokhin National Medical Research Center of Oncology" of the Ministry of Health of the Russian Federation, Moscow, Russia
| | - Alexander Karpukhin
- Laboratory of Molecular Genetics of Complex Inherited Diseases, Research Centre for Medical Genetics, Moscow, Russia
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24
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Chen Z, Wei X, Wang X, Zheng X, Chang B, Shen L, Zhu H, Yang M, Li S, Zheng X. NDUFA4L2 promotes glioblastoma progression, is associated with poor survival, and can be effectively targeted by apatinib. Cell Death Dis 2021; 12:377. [PMID: 33828084 PMCID: PMC8027655 DOI: 10.1038/s41419-021-03646-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Revised: 03/17/2021] [Accepted: 03/17/2021] [Indexed: 12/31/2022]
Abstract
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex, 4-like 2 (NDUFA4L2) is a subunit of Complex I of the mitochondrial respiratory chain, which is important in metabolic reprogramming and oxidative stress in multiple cancers. However, the biological role and molecular regulation of NDUFA4L2 in glioblastoma (GBM) are poorly understood. Here, we found that NDUFA4L2 was significantly upregulated in GBM; the elevated levels were correlated with reduced patient survival. Gene knockdown of NDUFA4L2 inhibited tumor cell proliferation and enhanced apoptosis, while tumor cells initiated protective mitophagy in vitro and in vivo. We used lentivirus to reduce expression levels of NDUFA4L2 protein in GBM cells exposed to mitophagy blockers, which led to a significant enhancement of tumor cell apoptosis in vitro and inhibited the development of xenografted tumors in vivo. In contrast to other tumor types, NDUFA4L2 expression in GBM may not be directly regulated by hypoxia-inducible factor (HIF)-1α, because HIF-1α inhibitors failed to inhibit NDUFA4L2 in GBM. Apatinib was able to effectively target NDUFA4L2 in GBM, presenting an alternative to the use of lentiviruses, which currently cannot be used in humans. Taken together, our data suggest the use of NDUFA4L2 as a potential therapeutic target in GBM and demonstrate a practical treatment approach.
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Affiliation(s)
- Zheng Chen
- Department of Neurosurgery, XinHua Hospital, Shanghai JiaoTong University School of Medicine, 1665 KongJiang Rd, 200092, Shanghai, China.,The Center for Diagnosis and Treatment of Cranial Nerve Diseases of Shanghai JiaoTong University, 200092, Shanghai, China
| | - Xiangyu Wei
- Department of Neurosurgery, XinHua Hospital, Shanghai JiaoTong University School of Medicine, 1665 KongJiang Rd, 200092, Shanghai, China.,The Center for Diagnosis and Treatment of Cranial Nerve Diseases of Shanghai JiaoTong University, 200092, Shanghai, China
| | - Xueyi Wang
- Department of Neurosurgery, XinHua Hospital, Shanghai JiaoTong University School of Medicine, 1665 KongJiang Rd, 200092, Shanghai, China.,The Center for Diagnosis and Treatment of Cranial Nerve Diseases of Shanghai JiaoTong University, 200092, Shanghai, China
| | - Xuan Zheng
- Department of Neurosurgery, XinHua Hospital, Shanghai JiaoTong University School of Medicine, 1665 KongJiang Rd, 200092, Shanghai, China.,The Center for Diagnosis and Treatment of Cranial Nerve Diseases of Shanghai JiaoTong University, 200092, Shanghai, China
| | - Bowen Chang
- Department of Neurosurgery, XinHua Hospital, Shanghai JiaoTong University School of Medicine, 1665 KongJiang Rd, 200092, Shanghai, China.,The Center for Diagnosis and Treatment of Cranial Nerve Diseases of Shanghai JiaoTong University, 200092, Shanghai, China
| | - Lin Shen
- Department of Neurosurgery, XinHua Hospital, Shanghai JiaoTong University School of Medicine, 1665 KongJiang Rd, 200092, Shanghai, China.,The Center for Diagnosis and Treatment of Cranial Nerve Diseases of Shanghai JiaoTong University, 200092, Shanghai, China
| | - Hanshuo Zhu
- Department of Neurosurgery, XinHua Hospital, Shanghai JiaoTong University School of Medicine, 1665 KongJiang Rd, 200092, Shanghai, China.,The Center for Diagnosis and Treatment of Cranial Nerve Diseases of Shanghai JiaoTong University, 200092, Shanghai, China
| | - Min Yang
- Department of Neurosurgery, XinHua Hospital, Shanghai JiaoTong University School of Medicine, 1665 KongJiang Rd, 200092, Shanghai, China.,The Center for Diagnosis and Treatment of Cranial Nerve Diseases of Shanghai JiaoTong University, 200092, Shanghai, China
| | - Shiting Li
- Department of Neurosurgery, XinHua Hospital, Shanghai JiaoTong University School of Medicine, 1665 KongJiang Rd, 200092, Shanghai, China. .,The Center for Diagnosis and Treatment of Cranial Nerve Diseases of Shanghai JiaoTong University, 200092, Shanghai, China.
| | - Xuesheng Zheng
- Department of Neurosurgery, XinHua Hospital, Shanghai JiaoTong University School of Medicine, 1665 KongJiang Rd, 200092, Shanghai, China. .,The Center for Diagnosis and Treatment of Cranial Nerve Diseases of Shanghai JiaoTong University, 200092, Shanghai, China.
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25
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Wei Y, Liang M, Xiong L, Su N, Gao X, Jiang Z. PD-L1 induces macrophage polarization toward the M2 phenotype via Erk/Akt/mTOR. Exp Cell Res 2021; 402:112575. [PMID: 33771483 DOI: 10.1016/j.yexcr.2021.112575] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 03/04/2021] [Accepted: 03/19/2021] [Indexed: 02/06/2023]
Abstract
PD-L1 (programmed death-ligand 1) is the ligand of PD-1 (programmed cell death protein 1) and regulates inhibitory immune responses. It is well known that PD-L1 suppresses T cell function via binding to PD-1. However, little is known about the role of the PD-1/PD-L1 axis in macrophage polarization. According to previous studies, the function of the PD-1/PD-L1 axis in macrophage polarization is controversial, and the underlying mechanism has not been fully elucidated. Thus, we treated THP-1-derived macrophages with human PD-L1 Fc to determine the role of the PD-1/PD-L1 axis in macrophage polarization. To further explore the mechanism, we performed RNA sequencing and used specific inhibitors to identify the implicated signalling pathways. In this study, we found that PD-L1 induces the upregulation of CD206 expression, which is inhibited by nivolumab, LY294002, U0126, and rapamycin. Evaluation of differentially expressed genes (DEGs) and bioinformatics analysis indicated that PD-L1 also induces the upregulation of the expression of genes that maintain mitochondrial function and mediate metabolic switching. In addition, we did not detect PD-L1-induced CD86 alterations, indicating that PD-L1 treatment has no significant influence on M1 polarization. Taken together, these results suggest that PD-L1 binds to PD-1 and promotes M2 polarization accompanied by mitochondrial function enhancement and metabolic reprogramming via Erk/Akt/mTOR. This study elucidates the role of PD-L1 in macrophage polarization and verifies the underlying mechanisms for the first time. Considering that aberrantly upregulated PD-L1 expression contributes to a wide variety of diseases, targeting PD-L1-mediated macrophage polarization is a prospective therapeutic strategy for both neoplastic and nonneoplastic diseases.
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Affiliation(s)
- Yi Wei
- Department of Nephrology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Mengjun Liang
- Department of Nephrology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Liping Xiong
- Department of Nephrology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Ning Su
- Department of Nephrology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Xiang Gao
- Department of Gastroenterology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Zongpei Jiang
- Department of Nephrology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.
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26
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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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27
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Liu Y, Nie X, Zhu J, Wang T, Li Y, Wang Q, Sun Z. NDUFA4L2 in smooth muscle promotes vascular remodeling in hypoxic pulmonary arterial hypertension. J Cell Mol Med 2021; 25:1221-1237. [PMID: 33340241 PMCID: PMC7812284 DOI: 10.1111/jcmm.16193] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 11/10/2020] [Accepted: 11/21/2020] [Indexed: 12/12/2022] Open
Abstract
Pulmonary arterial hypertension (PAH) is characterized by a progressive increase in pulmonary vascular resistance and obliterative pulmonary vascular remodelling (PVR). The imbalance between the proliferation and apoptosis of pulmonary artery smooth muscle cells (PASMCs) is an important cause of PVR leading to PAH. Mitochondria play a key role in the production of hypoxia-induced pulmonary hypertension (HPH). However, there are still many issues worth studying in depth. In this study, we demonstrated that NADH dehydrogenase (ubiquinone) 1 alpha subcomplex 4 like 2 (NDUFA4L2) was a proliferation factor and increased in vivo and in vitro through various molecular biology experiments. HIF-1α was an upstream target of NDUFA4L2. The plasma levels of 4-hydroxynonene (4-HNE) were increased both in PAH patients and hypoxic PAH model rats. Knockdown of NDUFA4L2 decreased the levels of malondialdehyde (MDA) and 4-HNE in human PASMCs in hypoxia. Elevated MDA and 4-HNE levels might be associated with excessive ROS generation and increased expression of 5-lipoxygenase (5-LO) in hypoxia, but this effect was blocked by siNDUFA4L2. Further research found that p38-5-LO was a downstream signalling pathway of PASMCs proliferation induced by NDUFA4L2. Up-regulated NDUFA4L2 plays a critical role in the development of HPH, which mediates ROS production and proliferation of PASMCs, suggesting NDUFA4L2 as a potential new therapeutic target for PAH.
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MESH Headings
- Aldehydes/metabolism
- Animals
- Arachidonate 5-Lipoxygenase/metabolism
- Cell Hypoxia
- Cell Proliferation
- Disease Models, Animal
- Electron Transport Complex I/genetics
- Electron Transport Complex I/metabolism
- Endothelial Cells/metabolism
- Gene Expression Regulation
- Gene Silencing
- Humans
- Hypoxia/complications
- Hypoxia/physiopathology
- Male
- Malondialdehyde/metabolism
- Models, Biological
- Muscle, Smooth, Vascular/pathology
- Muscle, Smooth, Vascular/physiopathology
- Myocytes, Smooth Muscle/metabolism
- Myocytes, Smooth Muscle/pathology
- Oxidation-Reduction
- Oxygen Consumption
- Pulmonary Arterial Hypertension/complications
- Pulmonary Arterial Hypertension/metabolism
- Pulmonary Arterial Hypertension/pathology
- Pulmonary Arterial Hypertension/physiopathology
- Pulmonary Artery/pathology
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Rats, Wistar
- Reactive Oxygen Species/metabolism
- Vascular Remodeling/genetics
- p38 Mitogen-Activated Protein Kinases/metabolism
- Rats
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Affiliation(s)
- Yun Liu
- Department of Pharmacy, The First People's Hospital of Lianyungang, Lianyungang, China
- Department of Pharmacy, The Affiliated Lianyungang Hospital of Xuzhou Medical University/The First People's Hospital of Lianyungang, Lianyungang, China
| | - Xiaowei Nie
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Shenzhen, China
- Lung Transplant Group, Wuxi People's Hospital Affiliated to Nanjing Medical University, Wuxi, China
| | - Jinquan Zhu
- Department of Pharmacy, The First People's Hospital of Lianyungang, Lianyungang, China
| | - Tianyan Wang
- Department of Pharmacy, The First People's Hospital of Lianyungang, Lianyungang, China
| | - Yanli Li
- Department of Pharmacy, The First People's Hospital of Lianyungang, Lianyungang, China
| | - Qian Wang
- Department of Anesthesiology, Children's Hospital of Soochow University, Suzhou, China
| | - Zengxian Sun
- Department of Pharmacy, The First People's Hospital of Lianyungang, Lianyungang, China
- Department of Pharmacy, The Affiliated Lianyungang Hospital of Xuzhou Medical University/The First People's Hospital of Lianyungang, Lianyungang, China
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28
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Sorouri M, Chang T, Jesudhasan P, Pinkham C, Elde NC, Hancks DC. Signatures of host-pathogen evolutionary conflict reveal MISTR-A conserved MItochondrial STress Response network. PLoS Biol 2020; 18:e3001045. [PMID: 33370271 PMCID: PMC7793259 DOI: 10.1371/journal.pbio.3001045] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 01/08/2021] [Accepted: 12/09/2020] [Indexed: 11/18/2022] Open
Abstract
Host-pathogen conflicts leave genetic signatures in genes that are critical for host defense functions. Using these "molecular scars" as a guide to discover gene functions, we discovered a vertebrate-specific MItochondrial STress Response (MISTR) circuit. MISTR proteins are associated with electron transport chain (ETC) factors and activated by stress signals such as interferon gamma (IFNγ) and hypoxia. Upon stress, ultraconserved microRNAs (miRNAs) down-regulate MISTR1(NDUFA4) followed by replacement with paralogs MItochondrial STress Response AntiViral (MISTRAV) and/or MItochondrial STress Response Hypoxia (MISTRH). While cells lacking MISTR1(NDUFA4) are more sensitive to chemical and viral apoptotic triggers, cells lacking MISTRAV or expressing the squirrelpox virus-encoded vMISTRAV exhibit resistance to the same insults. Rapid evolution signatures across primate genomes for MISTR1(NDUFA4) and MISTRAV indicate recent and ongoing conflicts with pathogens. MISTR homologs are also found in plants, yeasts, a fish virus, and an algal virus indicating ancient origins and suggesting diverse means of altering mitochondrial function under stress. The discovery of MISTR circuitry highlights the use of evolution-guided studies to reveal fundamental biological processes.
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Affiliation(s)
- Mahsa Sorouri
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
- Institute of Biomedical Studies, Baylor University, Waco, Texas, United States of America
| | - Tyron Chang
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
- Genetics, Development, and Disease PhD Program, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Palmy Jesudhasan
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Chelsea Pinkham
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Nels C. Elde
- Eccles Institute of Human Genetics, The University of Utah Medical School, Utah, United States of America
- * E-mail: (NCE); (DCH)
| | - Dustin C. Hancks
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
- * E-mail: (NCE); (DCH)
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29
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Alldredge J, Randall L, De Robles G, Agrawal A, Mercola D, Liu M, Randhawa P, Edwards R, McClelland M, Rahmatpanah F. Transcriptome Analysis of Ovarian and Uterine Clear Cell Malignancies. Front Oncol 2020; 10:598579. [PMID: 33415077 PMCID: PMC7784081 DOI: 10.3389/fonc.2020.598579] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 11/03/2020] [Indexed: 12/21/2022] Open
Abstract
Purpose Ovarian and uterine clear cell carcinomas (CCCs) are rare but associated with poor prognosis. This study explored RNA transcription patterns characteristic of these tumors. Experimental Design RNA sequencing (RNA-seq) of 11 ovarian CCCs and five uterine CCCs was performed and compared to publicly available data from high grade serous ovarian cancers (HGSOCs). Ingenuity Pathway Analyses were performed. CIBERSORT analyses estimated relative fractions of 22 immune cell types in each RNA-seq sample. Sequencing data was correlated with PD-L1 immunohistochemical expression. Results RNA-seq revealed 1,613 downregulated and 1,212 upregulated genes (corrected p < 0.05, |FC |≥10) in ovarian CCC versus HGSOC. Two subgroups were identified in the ovarian CCC, characterized by ethnicity and expression differences in ARID1A. There were 3,252 differentially expressed genes between PD-L1+/− ovarian CCCs, revealing immune response, cell death, and DNA repair networks, negatively correlated with PD-L1 expression, whereas cellular proliferation networks positively correlated with expression. In clear cell ovarian versus clear cell uterine cancer, 1,607 genes were significantly upregulated, and 109 genes were significantly downregulated (corrected p < 0.05, |FC|≥10). Comparative pathway analysis of late and early stage ovarian CCCs revealed unique metabolic and PTEN pathways, whereas uterine CCCs had unique Wnt/Ca+, estrogen receptor, and CCR5 signaling. CIBERSORT analysis revealed that activated mast cells and regulatory T cell populations were relatively enriched in uterine CCCs. The PD-L1+ ovarian CCCs had enriched resting NK cells and memory B cell populations, while PD-L1− had enriched CD8 T-cells, monocytes, eosinophils, and activated dendritic cells. Conclusions Unique transcriptional expression profiles distinguish clear cell uterine and ovarian cancers from each other and from other more common histologic subtypes. These insights may aid in devising novel therapeutics.
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Affiliation(s)
- Jill Alldredge
- Department of Obstetrics and Gynecology, University of Colorado, Aurora, CO, United States
| | - Leslie Randall
- Department of Obstetrics and Gynecology, Virginia Commonwealth University, Richmond, VA, United States
| | - Gabriela De Robles
- Department of Pathology and Laboratory Medicine, University of California, Irvine, CA, United States
| | - Anshu Agrawal
- Department of Immunology, University of California, Irvine, CA, United States
| | - Dan Mercola
- Department of Pathology and Laboratory Medicine, University of California, Irvine, CA, United States
| | - Marisa Liu
- Department of Obstetrics and Gynecology, University of California, Irvine, CA, United States
| | - Pavneet Randhawa
- Department of Pathology and Laboratory Medicine, University of California, Irvine, CA, United States
| | - Robert Edwards
- Department of Pathology and Laboratory Medicine, University of California, Irvine, CA, United States
| | - Michael McClelland
- Department of Pathology and Laboratory Medicine, University of California, Irvine, CA, United States.,Department of Microbiology and Molecular Genetics, University of California, Irvine, CA, United States
| | - Farah Rahmatpanah
- Department of Pathology and Laboratory Medicine, University of California, Irvine, CA, United States
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30
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Cheng CC, Wooten J, Gibbs ZA, McGlynn K, Mishra P, Whitehurst AW. Sperm-specific COX6B2 enhances oxidative phosphorylation, proliferation, and survival in human lung adenocarcinoma. eLife 2020; 9:58108. [PMID: 32990599 PMCID: PMC7556868 DOI: 10.7554/elife.58108] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 09/28/2020] [Indexed: 12/18/2022] Open
Abstract
Cancer testis antigens (CTAs) are proteins whose expression is normally restricted to the testis but anomalously activated in human cancer. In sperm, a number of CTAs support energy generation, however, whether they contribute to tumor metabolism is not understood. We describe human COX6B2, a component of cytochrome c oxidase (complex IV). COX6B2 is expressed in human lung adenocarcinoma (LUAD) and expression correlates with reduced survival time. COX6B2, but not its somatic isoform COX6B1, enhances activity of complex IV, increasing oxidative phosphorylation (OXPHOS) and NAD+ generation. Consequently, COX6B2-expressing cancer cells display a proliferative advantage, particularly in low oxygen. Conversely, depletion of COX6B2 attenuates OXPHOS and collapses mitochondrial membrane potential leading to cell death or senescence. COX6B2 is both necessary and sufficient for growth of human tumor xenografts in mice. Our findings reveal a previously unappreciated, tumor-specific metabolic pathway hijacked from one of the most ATP-intensive processes in the animal kingdom: sperm motility.
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Affiliation(s)
- Chun-Chun Cheng
- Department of Pharmacology, Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, United States
| | | | - Zane A Gibbs
- Department of Pharmacology, Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, United States
| | - Kathleen McGlynn
- Department of Pharmacology, Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, United States
| | - Prashant Mishra
- Children's Research Institute, UT Southwestern Medical Center, Dallas, United States
| | - Angelique W Whitehurst
- Department of Pharmacology, Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, United States
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31
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Novel molecular signatures and potential therapeutics in renal cell carcinomas: Insights from a comparative analysis of subtypes. Genomics 2020; 112:3166-3178. [PMID: 32512143 DOI: 10.1016/j.ygeno.2020.06.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 05/20/2020] [Accepted: 06/02/2020] [Indexed: 01/05/2023]
Abstract
Renal cell carcinomas (RCCs) are among the highest causes of cancer mortality. Although transcriptome profiling studies in the last decade have made significant molecular findings on RCCs, effective diagnosis and treatment strategies have yet to be achieved due to lack of adequate screening and comparative profiling of RCC subtypes. In this study, a comparative analysis was performed on RNA-seq based transcriptome data from each RCC subtype, namely clear cell RCC (KIRC), papillary RCC (KIRP) and kidney chromophobe (KICH), and mutual or subtype-specific reporter biomolecules were identified at RNA, protein, and metabolite levels by the integration of expression profiles with genome-scale biomolecular networks. This approach revealed already-known biomarkers in RCCs as well as novel biomarker candidates and potential therapeutic targets. Our findings also pointed out the incorporation of the molecular mechanisms of KIRC and KIRP, whereas KICH was shown to have distinct molecular signatures. Furthermore, considering the Dipeptidyl Peptidase 4 (DPP4) receptor as a potential therapeutic target specific to KICH, several drug candidates such as ZINC6745464 were identified through virtual screening of ZINC molecules. In this study, we reported valuable data for further experimental and clinical efforts, since the proposed molecules have significant potential for screening and therapeutic purposes in RCCs.
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32
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Kundu A, Nam H, Shelar S, Chandrashekar DS, Brinkley G, Karki S, Mitchell T, Livi CB, Buckhaults P, Kirkman R, Tang Y, Rowe GC, Wei S, Varambally S, Sudarshan S. PRDM16 suppresses HIF-targeted gene expression in kidney cancer. J Exp Med 2020; 217:e20191005. [PMID: 32251515 PMCID: PMC7971134 DOI: 10.1084/jem.20191005] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 12/16/2019] [Accepted: 02/21/2020] [Indexed: 11/28/2022] Open
Abstract
Analysis of transcriptomic data demonstrates extensive epigenetic gene silencing of the transcription factor PRDM16 in renal cancer. We show that restoration of PRDM16 in RCC cells suppresses in vivo tumor growth. RNaseq analysis reveals that PRDM16 imparts a predominantly repressive effect on the RCC transcriptome including suppression of the gene encoding semaphorin 5B (SEMA5B). SEMA5B is a HIF target gene highly expressed in RCC that promotes in vivo tumor growth. Functional studies demonstrate that PRDM16's repressive properties, mediated by physical interaction with the transcriptional corepressors C-terminal binding proteins (CtBP1/2), are required for suppression of both SEMA5B expression and in vivo tumor growth. Finally, we show that reconstitution of RCC cells with a PRDM16 mutant unable to bind CtBPs nullifies PRDM16's effects on both SEMA5B repression and tumor growth suppression. Collectively, our data uncover a novel epigenetic basis by which HIF target gene expression is amplified in kidney cancer and a new mechanism by which PRDM16 exerts its tumor suppressive effects.
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Affiliation(s)
- Anirban Kundu
- Department of Urology, University of Alabama at Birmingham, Birmingham, AL
| | - Hyeyoung Nam
- Department of Urology, University of Alabama at Birmingham, Birmingham, AL
| | - Sandeep Shelar
- Department of Urology, University of Alabama at Birmingham, Birmingham, AL
| | | | - Garrett Brinkley
- Department of Urology, University of Alabama at Birmingham, Birmingham, AL
| | - Suman Karki
- Department of Urology, University of Alabama at Birmingham, Birmingham, AL
| | - Tanecia Mitchell
- Department of Urology, University of Alabama at Birmingham, Birmingham, AL
| | - Carolina B. Livi
- Department of Molecular Medicine, University of Texas Health Sciences Center at San Antonio, San Antonio, TX
| | - Phillip Buckhaults
- South Carolina College of Pharmacy, University of South Carolina, Columbia, SC
| | - Richard Kirkman
- Department of Urology, University of Alabama at Birmingham, Birmingham, AL
| | - Yawen Tang
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL
| | - Glenn C. Rowe
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL
| | - Shi Wei
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL
- O’Neal Comprehensive Cancer Center, Birmingham AL
| | - Sooryanarayana Varambally
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL
- O’Neal Comprehensive Cancer Center, Birmingham AL
| | - Sunil Sudarshan
- Department of Urology, University of Alabama at Birmingham, Birmingham, AL
- O’Neal Comprehensive Cancer Center, Birmingham AL
- Birmingham Veterans Affairs Medical Center, Birmingham, AL
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33
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Simonovic S, Hinze C, Schmidt-Ott KM, Busch J, Jung M, Jung K, Rabien A. Limited utility of qPCR-based detection of tumor-specific circulating mRNAs in whole blood from clear cell renal cell carcinoma patients. BMC Urol 2020; 20:7. [PMID: 32013938 PMCID: PMC6998103 DOI: 10.1186/s12894-019-0542-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Accepted: 10/21/2019] [Indexed: 02/08/2023] Open
Abstract
Background RNA sequencing data is providing abundant information about the levels of dysregulation of genes in various tumors. These data, as well as data based on older microarray technologies have enabled the identification of many genes which are upregulated in clear cell renal cell carcinoma (ccRCC) compared to matched normal tissue. Here we use RNA sequencing data in order to construct a panel of highly overexpressed genes in ccRCC so as to evaluate their RNA levels in whole blood and determine any diagnostic potential of these levels for renal cell carcinoma patients. Methods A bioinformatics analysis with Python was performed using TCGA, GEO and other databases to identify genes which are upregulated in ccRCC while being absent in the blood of healthy individuals. Quantitative Real Time PCR (RT-qPCR) was subsequently used to measure the levels of candidate genes in whole blood (PAX gene) of 16 ccRCC patients versus 11 healthy individuals. PCR results were processed in qBase and GraphPadPrism and statistics was done with Mann-Whitney U test. Results While most analyzed genes were either undetectable or did not show any dysregulated expression, two genes, CDK18 and CCND1, were paradoxically downregulated in the blood of ccRCC patients compared to healthy controls. Furthermore, LOX showed a tendency towards upregulation in metastatic ccRCC samples compared to non-metastatic. Conclusions This analysis illustrates the difficulty of detecting tumor regulated genes in blood and the possible influence of interference from expression in blood cells even for genes conditionally absent in normal blood. Testing in plasma samples indicated that tumor specific mRNAs were not detectable. While CDK18, CCND1 and LOX mRNAs might carry biomarker potential, this would require validation in an independent, larger patient cohort.
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Affiliation(s)
- Sinisa Simonovic
- Department of Urology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany. .,Berlin Institute for Urologic Research, Berlin, Germany. .,Max-Delbrück-Center for Molecular Medicine (MDC), Berlin, Germany.
| | - Christian Hinze
- Max-Delbrück-Center for Molecular Medicine (MDC), Berlin, Germany
| | - Kai M Schmidt-Ott
- Max-Delbrück-Center for Molecular Medicine (MDC), Berlin, Germany.,Department of Nephrology and Medical Intensive Care, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Jonas Busch
- Department of Urology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Monika Jung
- Department of Urology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Klaus Jung
- Department of Urology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany.,Berlin Institute for Urologic Research, Berlin, Germany
| | - Anja Rabien
- Department of Urology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany.,Berlin Institute for Urologic Research, Berlin, Germany
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34
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Apanovich N, Peters M, Apanovich P, Mansorunov D, Markova A, Matveev V, Karpukhin A. The Genes-Candidates for Prognostic Markers of Metastasis by Expression Level in Clear Cell Renal Cell Cancer. Diagnostics (Basel) 2020; 10:diagnostics10010030. [PMID: 31936274 PMCID: PMC7168144 DOI: 10.3390/diagnostics10010030] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 12/29/2019] [Accepted: 01/07/2020] [Indexed: 02/07/2023] Open
Abstract
The molecular prognostic markers of metastasis are important for personalized approaches to clear cell renal cell carcinoma (ccRCC) treatment but markers for practical use are still missing. To address this gap we studied the expression of ten genes—CA9, NDUFA4L2, VWF, IGFBP3, BHLHE41, EGLN3, SAA1, CSF1R, C1QA, and FN1—through RT-PCR, in 56 ccRCC patients without metastases and with metastases. All of these, excluding CSF1R, showed differential and increased (besides SAA1) expression in non-metastasis tumors. The gene expression levels in metastasis tumors were decreased, besides CSF1R, FN1 (not changed), and SAA1 (increased). There were significant associations of the differentially expressed genes with ccRCC metastasis by ROC analysis and the Fisher exact test. The association of the NDUFA4L2, VWF, EGLN3, SAA1, and C1QA expression with ccRCC metastasis is shown for the first time. The CA9, NDUFA4L2, BHLHE4, and EGLN3 were distinguished as the strongest candidates for ccRCC metastasis biomarkers. We used an approach that presupposed that the metastasis marker was the expression levels of any three genes from the selected panel and received sensitivity (88%) and specificity (73%) levels with a relative risk of RR > 3. In conclusion, a panel of selected genes—the candidates in biomarkers of ccRCC metastasis—was created for the first time. The results might shed some light on the ccRCC metastasis processes.
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Affiliation(s)
- Natalya Apanovich
- Bochkov Research Centre for Medical Genetics, 1 Moskvorechye St., Moscow 115522, Russia; (N.A.); (P.A.); (D.M.)
| | - Maria Peters
- N.N. Blokhin National Medical Research Center of Oncology of the Ministry of Health of Russia, 24 Kashirskoe Shosse, Moscow 115478, Russia; (M.P.); (A.M.); (V.M.)
| | - Pavel Apanovich
- Bochkov Research Centre for Medical Genetics, 1 Moskvorechye St., Moscow 115522, Russia; (N.A.); (P.A.); (D.M.)
| | - Danzan Mansorunov
- Bochkov Research Centre for Medical Genetics, 1 Moskvorechye St., Moscow 115522, Russia; (N.A.); (P.A.); (D.M.)
| | - Anna Markova
- N.N. Blokhin National Medical Research Center of Oncology of the Ministry of Health of Russia, 24 Kashirskoe Shosse, Moscow 115478, Russia; (M.P.); (A.M.); (V.M.)
| | - Vsevolod Matveev
- N.N. Blokhin National Medical Research Center of Oncology of the Ministry of Health of Russia, 24 Kashirskoe Shosse, Moscow 115478, Russia; (M.P.); (A.M.); (V.M.)
| | - Alexander Karpukhin
- Bochkov Research Centre for Medical Genetics, 1 Moskvorechye St., Moscow 115522, Russia; (N.A.); (P.A.); (D.M.)
- Correspondence: ; Tel.: +7-499-324-12-39
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Wang C, Gao F, Giannakis GB, D'Urso G, Cai X. Efficient proximal gradient algorithm for inference of differential gene networks. BMC Bioinformatics 2019; 20:224. [PMID: 31046666 PMCID: PMC6498668 DOI: 10.1186/s12859-019-2749-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2018] [Accepted: 03/18/2019] [Indexed: 02/07/2023] Open
Abstract
Background Gene networks in living cells can change depending on various conditions such as caused by different environments, tissue types, disease states, and development stages. Identifying the differential changes in gene networks is very important to understand molecular basis of various biological process. While existing algorithms can be used to infer two gene networks separately from gene expression data under two different conditions, and then to identify network changes, such an approach does not exploit the similarity between two gene networks, and it is thus suboptimal. A desirable approach would be clearly to infer two gene networks jointly, which can yield improved estimates of network changes. Results In this paper, we developed a proximal gradient algorithm for differential network (ProGAdNet) inference, that jointly infers two gene networks under different conditions and then identifies changes in the network structure. Computer simulations demonstrated that our ProGAdNet outperformed existing algorithms in terms of inference accuracy, and was much faster than a similar approach for joint inference of gene networks. Gene expression data of breast tumors and normal tissues in the TCGA database were analyzed with our ProGAdNet, and revealed that 268 genes were involved in the changed network edges. Gene set enrichment analysis identified a significant number of gene sets related to breast cancer or other types of cancer that are enriched in this set of 268 genes. Network analysis of the kidney cancer data in the TCGA database with ProGAdNet also identified a set of genes involved in network changes, and the majority of the top genes identified have been reported in the literature to be implicated in kidney cancer. These results corroborated that the gene sets identified by ProGAdNet were very informative about the cancer disease status. A software package implementing the ProGAdNet, computer simulations, and real data analysis is available as Additional file 1. Conclusion With its superior performance over existing algorithms, ProGAdNet provides a valuable tool for finding changes in gene networks, which may aid the discovery of gene-gene interactions changed under different conditions. Electronic supplementary material The online version of this article (10.1186/s12859-019-2749-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Chen Wang
- Department of Electrical and Computer Engineering, University of Miami, 1251 Memorial Drive, Coral Gables, 33146, FL, USA
| | - Feng Gao
- Department of Electrical and Computer Engineering, University of Miami, 1251 Memorial Drive, Coral Gables, 33146, FL, USA
| | - Georgios B Giannakis
- Department of Electrical and Computer Engineering, University of Minnesota, Minneapolis, 55455, MN, USA
| | - Gennaro D'Urso
- Department of Molecular and Cellular Pharmacology, University of Miami, Miami, 33136, FL, USA
| | - Xiaodong Cai
- Department of Electrical and Computer Engineering, University of Miami, 1251 Memorial Drive, Coral Gables, 33146, FL, USA. .,Sylvester Comprehensive Cancer Center, University of Miami, Miami, 33136, FL, USA.
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Serine Catabolism by SHMT2 Is Required for Proper Mitochondrial Translation Initiation and Maintenance of Formylmethionyl-tRNAs. Mol Cell 2019; 69:610-621.e5. [PMID: 29452640 DOI: 10.1016/j.molcel.2018.01.024] [Citation(s) in RCA: 127] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Revised: 12/01/2017] [Accepted: 01/18/2018] [Indexed: 12/21/2022]
Abstract
Upon glucose restriction, eukaryotic cells upregulate oxidative metabolism to maintain homeostasis. Using genetic screens, we find that the mitochondrial serine hydroxymethyltransferase (SHMT2) is required for robust mitochondrial oxygen consumption and low glucose proliferation. SHMT2 catalyzes the first step in mitochondrial one-carbon metabolism, which, particularly in proliferating cells, produces tetrahydrofolate (THF)-conjugated one-carbon units used in cytoplasmic reactions despite the presence of a parallel cytoplasmic pathway. Impairing cytoplasmic one-carbon metabolism or blocking efflux of one-carbon units from mitochondria does not phenocopy SHMT2 loss, indicating that a mitochondrial THF cofactor is responsible for the observed phenotype. The enzyme MTFMT utilizes one such cofactor, 10-formyl THF, producing formylmethionyl-tRNAs, specialized initiator tRNAs necessary for proper translation of mitochondrially encoded proteins. Accordingly, SHMT2 null cells specifically fail to maintain formylmethionyl-tRNA pools and mitochondrially encoded proteins, phenotypes similar to those observed in MTFMT-deficient patients. These findings provide a rationale for maintaining a compartmentalized one-carbon pathway in mitochondria.
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Kawashima A, Kanazawa T, Goto K, Matsumoto M, Morimoto-Okazawa A, Iwahori K, Ujike T, Nagahara A, Fujita K, Uemura M, Nonomura N, Wada H. Immunological classification of renal cell carcinoma patients based on phenotypic analysis of immune check-point molecules. Cancer Immunol Immunother 2018; 67:113-125. [PMID: 28975380 PMCID: PMC11028191 DOI: 10.1007/s00262-017-2060-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 09/03/2017] [Indexed: 12/30/2022]
Abstract
OBJECTIVES To clarify comprehensive immunological signature patterns of tumour tissue-infiltrating lymphocytes in patients with renal cell carcinoma and show its clinical significance. MATERIALS AND METHODS We investigated the surface marker expressions of tumour tissue-infiltrating lymphocytes quantitatively and classified them based on their functional populations. We extracted 109 sets of tumour tissue-infiltrating lymphocytes from 80 patients who underwent surgical resection of renal cell carcinoma, of which 44 tumour tissue-infiltrating lymphocytes were multiply extracted from 15 patients. Each tumour tissue-infiltrating lymphocyte was characterised on the basis of functional T-cell populations using ten surface marker expressions measured by flow cytometry. RESULTS All sets of the tumour tissue-infiltrating lymphocytes were classified into three groups, which correlated significantly with Fuhrman grade (OR 0.253, 95% CI 0.094-0.678, P = 0.006). Importantly, both overall metastasis-free survival (HR 0.449, 95% CI 0.243-0.832, P = 0.011) and recurrence-free survival (HR 0.475, 95% CI 0.238-0.948, P = 0.035) of the patients with the higher marker expressions were significantly inferior to those of the patients with the lower marker expressions by multivariate analysis. Six specific genes for this classification identified by microarray analysis verified our results using the TCGA KIRC data set. In addition, we discovered the presence of intra-tumoural diversity in the classification of 3 (20%) of the 15 patients. CONCLUSIONS This study showed that the presence of classable diversity in the immunological signature of tumour tissue-infiltrating lymphocytes correlated with prognosis and tumour aggressiveness that was observed even within individual tumours in some patients with renal cell carcinoma.
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Affiliation(s)
- Atsunari Kawashima
- Department of Urology, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan.
- Department of Clinical Research in Tumour Immunology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan.
| | - Takayuki Kanazawa
- Department of Clinical Research in Tumour Immunology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan.
- Drug Discovery & Disease Research Laboratory, Shionogi & Co., Ltd., Toyonaka, Osaka, Japan.
| | - Kumiko Goto
- Department of Clinical Research in Tumour Immunology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
- Drug Discovery & Disease Research Laboratory, Shionogi & Co., Ltd., Toyonaka, Osaka, Japan
| | - Mitsunobu Matsumoto
- Department of Clinical Research in Tumour Immunology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
- Drug Discovery & Disease Research Laboratory, Shionogi & Co., Ltd., Toyonaka, Osaka, Japan
| | - Akiko Morimoto-Okazawa
- Department of Clinical Research in Tumour Immunology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
| | - Kota Iwahori
- Department of Clinical Research in Tumour Immunology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
| | - Takeshi Ujike
- Department of Urology, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Akira Nagahara
- Department of Urology, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Kazutoshi Fujita
- Department of Urology, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Motohide Uemura
- Department of Urology, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Norio Nonomura
- Department of Urology, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Hisashi Wada
- Department of Clinical Research in Tumour Immunology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
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Wang L, Peng Z, Wang K, Qi Y, Yang Y, Zhang Y, An X, Luo S, Zheng J. NDUFA4L2 is associated with clear cell renal cell carcinoma malignancy and is regulated by ELK1. PeerJ 2017; 5:e4065. [PMID: 29158991 PMCID: PMC5695248 DOI: 10.7717/peerj.4065] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 10/29/2017] [Indexed: 01/04/2023] Open
Abstract
Background Clear cell renal cell carcinoma (ccRCC) is the most common and lethal cancer of the adult kidney. However, its pathogenesis has not been fully understood till now, which hinders the therapeutic development of ccRCC. NADH dehydrogenase (ubiquinone) 1 alpha subcomplex 4-like 2 (NDUFA4L2) was found to be upregulated and play an important role in ccRCC. We aimed to further investigate the underlying mechanisms by which NDUFA4L2 exerted function and its expression level was upregulated. Methods The Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) data were mined to verify the change of NDUFA4L2 expression level in ccRCC tissues. The correlation between expression level of NDUFA4L2 and cell proliferation/apoptosis was explored by Gene Set Enrichment Analysis (GSEA). Protein-protein interaction (PPI) network of NDUFA4L2 was constructed. Biological process and involved pathways of NDUFA4L2 were analyzed by gene ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway. The transcription factors (TFs) which can induce the expression of NDUFA4L2 were explored in clinical samples by correlation analysis and its regulation on the expression of NDUFA4L2 was verified by knockdown experiment. Results NDUFA4L2 was verified to be overexpressed in ccRCC tissues and its expression level was increased accordingly as the American Joint Committee on Cancer (AJCC) stage progressed. A high NDUFA4L2 level predicted the poor prognosis of ccRCC patients and correlated with enhanced cell proliferation and anti-apoptosis. NDUFA4L2 may interact with 14 tumor-related proteins, participate in growth and death processes and be involved in ccRCC-related pathways, such as insulin-like growth factor 1 (IGF-1), mammalian target of Rapamycin (mTOR) and phosphoinositide 3 kinase serine/threonine protein kinase (PI3K/AKT). ETS domain-containing protein ELK1 level positively correlated with the level of NDUFA4L2 in ccRCC tissues and ELK1 could regulate the expression of NDUFA4L2 in ccRCC cells. Discussion NDUFA4L2 upregulation was associated with ccRCC malignancy. NDUFA4L2 expression was regulated by ELK1 in ccRCC cells. Our study provided potential mechanisms by which NDUFA4L2 affected ccRCC occurrence and progression.
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Affiliation(s)
- Lei Wang
- Department of Urology, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Zhiqiang Peng
- Department of Biochemistry and Molecular Biology, Capital Medical University, Beijing, China
| | - Kaizhen Wang
- Department of Biochemistry and Molecular Biology, Capital Medical University, Beijing, China
| | - Yijun Qi
- Department of Biochemistry and Molecular Biology, Capital Medical University, Beijing, China
| | - Ying Yang
- Core Facilities Center, Capital Medical University, Beijing, China
| | - Yue Zhang
- Department of Biochemistry and Molecular Biology, Capital Medical University, Beijing, China
| | - Xinyuan An
- Department of Biochemistry and Molecular Biology, Capital Medical University, Beijing, China
| | - Shudong Luo
- Key Laboratory of Biology of Insect-Pollinator, Ministry of Agriculture, Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Junfang Zheng
- Department of Biochemistry and Molecular Biology, Capital Medical University, Beijing, China.,Beijing Key Laboratory for Tumor Invasion and Metastasis, Cancer Institute of Capital Medical University, Beijing, China
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Kadenbach B. Regulation of Mammalian 13-Subunit Cytochrome c Oxidase and Binding of other Proteins: Role of NDUFA4. Trends Endocrinol Metab 2017; 28:761-770. [PMID: 28988874 DOI: 10.1016/j.tem.2017.09.003] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/30/2017] [Revised: 09/07/2017] [Accepted: 09/08/2017] [Indexed: 11/20/2022]
Abstract
Cytochrome c oxidase (CcO) is the final oxygen accepting enzyme complex (complex IV) of the mitochondrial respiratory chain. In contrast to the other complexes (I, II, and III), CcO is highly regulated via isoforms for six of its ten nuclear-coded subunits, which are differentially expressed in species, tissues, developmental stages, and cellular oxygen concentrations. Recent publications have claimed that NADH dehydrogenase (ubiquinone) 1 alpha subcomplex 4 (NDUFA4), originally identified as subunit of complex I, represents a 14th subunit of CcO. Results on CcO composition in tissues from adult animals and the review of data from recent literature strongly suggest that NDUFA4 is not a 14th subunit of CcO but may represent an assembly factor for CcO or supercomplexes (respirasomes) in mitochondria of growing cells and cancer tissues.
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Tissue- and Condition-Specific Isoforms of Mammalian Cytochrome c Oxidase Subunits: From Function to Human Disease. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2017; 2017:1534056. [PMID: 28593021 PMCID: PMC5448071 DOI: 10.1155/2017/1534056] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 03/29/2017] [Indexed: 01/05/2023]
Abstract
Cytochrome c oxidase (COX) is the terminal enzyme of the electron transport chain and catalyzes the transfer of electrons from cytochrome c to oxygen. COX consists of 14 subunits, three and eleven encoded, respectively, by the mitochondrial and nuclear DNA. Tissue- and condition-specific isoforms have only been reported for COX but not for the other oxidative phosphorylation complexes, suggesting a fundamental requirement to fine-tune and regulate the essentially irreversible reaction catalyzed by COX. This article briefly discusses the assembly of COX in mammals and then reviews the functions of the six nuclear-encoded COX subunits that are expressed as isoforms in specialized tissues including those of the liver, heart and skeletal muscle, lung, and testes: COX IV-1, COX IV-2, NDUFA4, NDUFA4L2, COX VIaL, COX VIaH, COX VIb-1, COX VIb-2, COX VIIaH, COX VIIaL, COX VIIaR, COX VIIIH/L, and COX VIII-3. We propose a model in which the isoforms mediate the interconnected regulation of COX by (1) adjusting basal enzyme activity to mitochondrial capacity of a given tissue; (2) allosteric regulation to adjust energy production to need; (3) altering proton pumping efficiency under certain conditions, contributing to thermogenesis; (4) providing a platform for tissue-specific signaling; (5) stabilizing the COX dimer; and (6) modulating supercomplex formation.
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Ellinger J, Poss M, Brüggemann M, Gromes A, Schmidt D, Ellinger N, Tolkach Y, Dietrich D, Kristiansen G, Müller SC. Systematic Expression Analysis of Mitochondrial Complex I Identifies NDUFS1 as a Biomarker in Clear-Cell Renal-Cell Carcinoma. Clin Genitourin Cancer 2016; 15:e551-e562. [PMID: 28063846 DOI: 10.1016/j.clgc.2016.11.010] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Revised: 11/15/2016] [Accepted: 11/20/2016] [Indexed: 01/09/2023]
Abstract
INTRODUCTION Mitochondrial dysfunction is common in cancer, and the mitochondrial electron transport chain is often affected in carcinogenesis. So far, little is known about the expression of the mitochondrial complex I (NADH:ubiquinone oxidoreductase) subunits in clear-cell renal-cell carcinoma (ccRCC). MATERIALS AND METHODS An expression profile of the mitochondrial complex I subunits was determined using the NextBio database. Subsequently, the expression of selected subunits was experimentally validated on mRNA (quantitative real-time polymerase chain reaction) and protein (Western blot analysis, immunohistochemistry) level. RESULTS We observed that 7 subunits of the complex I were down-regulated in at least 3 microarray studies. Deregulated mRNA expression was confirmed for NDUFA3, NDUFA, NDUFB1, NDUFB9, NDUFS1, NDUFS8, and NDUFV1. Low NDUFS1 mRNA expression was a significant and independent adverse predictor of a shorter overall survival in our mRNA cohort and the ccRCC cohort of The Cancer Genome Atlas project. NDUFS1 expression was furthermore analyzed on the protein level, and a distinct down-regulation was observed in ccRCC as well as in the chromophobe and the sarcomatoid subtype compared to normal renal tissue. CONCLUSION Expression alterations occur in only a few subunits of the mitochondrial complex I subunits in ccRCC, and altered mRNA and protein expression levels of NDUFS1 may be useful to distinguish between renal-cell carcinoma and normal renal tissue.
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Affiliation(s)
- Jörg Ellinger
- Department of Urology, University Hospital Bonn, Bonn, Germany.
| | - Mirjam Poss
- Department of Urology, University Hospital Bonn, Bonn, Germany
| | | | - Arabella Gromes
- Department of Urology, University Hospital Bonn, Bonn, Germany
| | - Doris Schmidt
- Department of Urology, University Hospital Bonn, Bonn, Germany
| | - Nadja Ellinger
- Department of Anesthesiology and Intensive Care, University Hospital Bonn, Bonn, Germany
| | - Yuri Tolkach
- Institute of Pathology, University Hospital Bonn, Bonn, Germany
| | - Dimo Dietrich
- Institute of Pathology, University Hospital Bonn, Bonn, Germany; Department of Otorhinolaryngology/Head and Neck Surgery, University Hospital Bonn, Bonn, Germany
| | | | - Stefan C Müller
- Department of Urology, University Hospital Bonn, Bonn, Germany
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Cabrera-Fuentes HA, Aragones J, Bernhagen J, Boening A, Boisvert WA, Bøtker HE, Bulluck H, Cook S, Di Lisa F, Engel FB, Engelmann B, Ferrazzi F, Ferdinandy P, Fong A, Fleming I, Gnaiger E, Hernández-Reséndiz S, Kalkhoran SB, Kim MH, Lecour S, Liehn EA, Marber MS, Mayr M, Miura T, Ong SB, Peter K, Sedding D, Singh MK, Suleiman MS, Schnittler HJ, Schulz R, Shim W, Tello D, Vogel CW, Walker M, Li QOY, Yellon DM, Hausenloy DJ, Preissner KT. From basic mechanisms to clinical applications in heart protection, new players in cardiovascular diseases and cardiac theranostics: meeting report from the third international symposium on "New frontiers in cardiovascular research". Basic Res Cardiol 2016; 111:69. [PMID: 27743118 PMCID: PMC5065587 DOI: 10.1007/s00395-016-0586-x] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/14/2016] [Revised: 10/02/2016] [Accepted: 10/04/2016] [Indexed: 12/12/2022]
Abstract
In this meeting report, particularly addressing the topic of protection of the cardiovascular system from ischemia/reperfusion injury, highlights are presented that relate to conditioning strategies of the heart with respect to molecular mechanisms and outcome in patients' cohorts, the influence of co-morbidities and medications, as well as the contribution of innate immune reactions in cardioprotection. Moreover, developmental or systems biology approaches bear great potential in systematically uncovering unexpected components involved in ischemia-reperfusion injury or heart regeneration. Based on the characterization of particular platelet integrins, mitochondrial redox-linked proteins, or lipid-diol compounds in cardiovascular diseases, their targeting by newly developed theranostics and technologies opens new avenues for diagnosis and therapy of myocardial infarction to improve the patients' outcome.
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Affiliation(s)
- Hector A Cabrera-Fuentes
- Institute of Biochemistry, Medical School, Justus-Liebig University, Giessen, Germany
- Cardiovascular and Metabolic Disorders Program, Duke-National University of Singapore, 8 College Road, Singapore, 169857, Singapore
- National Heart Research Institute Singapore, National Heart Centre Singapore, Singapore, Singapore
- Department of Microbiology, Kazan Federal University, Kazan, Russian Federation
- Centro de Biotecnología-FEMSA, Tecnológico de Monterrey, Monterrey, NL, Mexico
| | - Julian Aragones
- Research Unit, Hospital of Santa Cristina, Research Institute Princesa, Autonomous University of Madrid, Madrid, Spain
| | - Jürgen Bernhagen
- Department of Vascular Biology, Institute for Stroke and Dementia Research, Klinikum der Ludwig-Maximilians-Universität, Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Andreas Boening
- Department of Cardiovascular Surgery, Medical School, Justus-Liebig-University, Giessen, Germany
| | - William A Boisvert
- Department of Microbiology, Kazan Federal University, Kazan, Russian Federation
- Center for Cardiovascular Research, John A. Burns School of Medicine, University of Hawaii, Honolulu, USA
| | - Hans E Bøtker
- Department of Cardiology, Aarhus University Hospital, Skejby, Aarhus N, Denmark
| | - Heerajnarain Bulluck
- Cardiovascular and Metabolic Disorders Program, Duke-National University of Singapore, 8 College Road, Singapore, 169857, Singapore
- National Heart Research Institute Singapore, National Heart Centre Singapore, Singapore, Singapore
- The Hatter Cardiovascular Institute, University College London, London, UK
| | - Stuart Cook
- Cardiovascular and Metabolic Disorders Program, Duke-National University of Singapore, 8 College Road, Singapore, 169857, Singapore
- National Heart Research Institute Singapore, National Heart Centre Singapore, Singapore, Singapore
| | - Fabio Di Lisa
- Department of Biomedical Sciences, University of Padova, Padua, Italy
| | - Felix B Engel
- Experimental Renal and Cardiovascular Research, Department of Nephropathology, Institute of Pathology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Nuremberg, Germany
| | - Bernd Engelmann
- Institut für Laboratoriumsmedizin, Ludwig-Maximilians-Universität, Munich, Germany
| | - Fulvia Ferrazzi
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, Nuremberg, Germany
| | - Péter Ferdinandy
- Department of Pharmacology and Pharmacotherapy, Semmelweis University, Budapest, Hungary
- Pharmahungary Group, Szeged, Hungary
| | - Alan Fong
- Department of Cardiology, Sarawak Heart Centre, Sarawak, Malaysia
| | - Ingrid Fleming
- Institute for Vascular Signalling, Centre for Molecular Medicine, Goethe-University, Frankfurt, Germany
| | - Erich Gnaiger
- D. Swarovski Research Lab, Department of Visceral, Transplant Thoracic Surgery, Medical Univ Innsbruck, Innsbruck, Austria
| | - Sauri Hernández-Reséndiz
- Cardiovascular and Metabolic Disorders Program, Duke-National University of Singapore, 8 College Road, Singapore, 169857, Singapore
- National Heart Research Institute Singapore, National Heart Centre Singapore, Singapore, Singapore
- Department of Cardiovascular Medicine, National Institute of Cardiology, Ignacio Chavez, Mexico, D.F., Mexico
| | - Siavash Beikoghli Kalkhoran
- The Hatter Cardiovascular Institute, University College London, London, UK
- The National Institute of Health Research University College London Hospitals Biomedical Research Centre, London, UK
| | - Moo Hyun Kim
- Department of Cardiology, Dong-A University Hospital, Busan, Korea
| | - Sandrine Lecour
- Hatter Institute and MRC Inter-University Cape Heart Unit, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Elisa A Liehn
- Institute for Molecular Cardiovascular Research, RWTH University Hospital, Aachen, Germany
| | - Michael S Marber
- Department of Cardiology, The Rayne Institute, St Thomas' Campus, King's College London, London, UK
| | - Manuel Mayr
- The James Black Centre, King's College, University of London, London, UK
| | - Tetsuji Miura
- Department of Cardiovascular, Renal and Metabolic Medicine, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Sang-Bing Ong
- Cardiovascular and Metabolic Disorders Program, Duke-National University of Singapore, 8 College Road, Singapore, 169857, Singapore
- National Heart Research Institute Singapore, National Heart Centre Singapore, Singapore, Singapore
| | - Karlheinz Peter
- Baker IDI Heart and Diabetes Institute, Melbourne, Australia
| | - Daniel Sedding
- Department of Cardiology and Angiology, Hannover Medical School, Hannover, Germany
| | - Manvendra K Singh
- Cardiovascular and Metabolic Disorders Program, Duke-National University of Singapore, 8 College Road, Singapore, 169857, Singapore
- National Heart Research Institute Singapore, National Heart Centre Singapore, Singapore, Singapore
| | - M Saadeh Suleiman
- Bristol Heart Institute, University of Bristol, Bristol Royal Infirmary, Bristol, UK
| | - Hans J Schnittler
- Institute of Anatomy and Vascular Biology, Westfalian-Wilhelms-University, Münster, Germany
| | - Rainer Schulz
- Institute of Physiology, Justus-Liebig University, Giessen, Germany
| | - Winston Shim
- National Heart Research Institute Singapore, National Heart Centre Singapore, Singapore, Singapore
| | - Daniel Tello
- Research Unit, Hospital of Santa Cristina, Research Institute Princesa, Autonomous University of Madrid, Madrid, Spain
| | - Carl-Wilhelm Vogel
- Department of Pathology, John A. Burns School of Medicine, University of Hawaii, Honolulu, USA
| | - Malcolm Walker
- The Hatter Cardiovascular Institute, University College London, London, UK
| | - Qilong Oscar Yang Li
- Research Unit, Hospital of Santa Cristina, Research Institute Princesa, Autonomous University of Madrid, Madrid, Spain
| | - Derek M Yellon
- The Hatter Cardiovascular Institute, University College London, London, UK
- The National Institute of Health Research University College London Hospitals Biomedical Research Centre, London, UK
| | - Derek J Hausenloy
- Cardiovascular and Metabolic Disorders Program, Duke-National University of Singapore, 8 College Road, Singapore, 169857, Singapore.
- National Heart Research Institute Singapore, National Heart Centre Singapore, Singapore, Singapore.
- The Hatter Cardiovascular Institute, University College London, London, UK.
- The National Institute of Health Research University College London Hospitals Biomedical Research Centre, London, UK.
| | - Klaus T Preissner
- Institute of Biochemistry, Medical School, Justus-Liebig University, Giessen, Germany
- Department of Microbiology, Kazan Federal University, Kazan, Russian Federation
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43
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Lucarelli G, Ferro M, Battaglia M. Multi-omics approach reveals the secrets of metabolism of clear cell-renal cell carcinoma. Transl Androl Urol 2016; 5:801-803. [PMID: 27785441 PMCID: PMC5071207 DOI: 10.21037/tau.2016.06.12] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Affiliation(s)
- Giuseppe Lucarelli
- Department of Emergency and Organ Transplantation, Urology, Andrology and Kidney Transplantation Unit, University of Bari, Bari, Italy
| | - Matteo Ferro
- Department of Urology, European Institute of Oncology, Milan, Italy
| | - Michele Battaglia
- Department of Emergency and Organ Transplantation, Urology, Andrology and Kidney Transplantation Unit, University of Bari, Bari, Italy
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Liu L, Lan G, Peng L, Xie X, Peng F, Yu S, Wang Y, Tang X. NDUFA4L2 expression predicts poor prognosis in clear cell renal cell carcinoma patients. Ren Fail 2016; 38:1199-205. [DOI: 10.1080/0886022x.2016.1208517] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
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