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Wu W, Li X, Li X, Zhao J, Gui Y, Luo Y, Wang H, Wang L, Yuan C. The Role of Long Non-Coding RNF144A-AS1 in Cancer Progression. Cell Biochem Biophys 2024:10.1007/s12013-024-01411-9. [PMID: 39014185 DOI: 10.1007/s12013-024-01411-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/04/2024] [Indexed: 07/18/2024]
Abstract
RNAs transcribing more than 200 nucleotides without encoding proteins are termed long non-coding RNAs (LncRNAs). LncRNAs can be used as decoy molecules, signal molecules, scaffolds, and guide molecules. Long non-coding RNAs can interact with DNA, chromatin-modifying complexes, and transcriptional regulatory proteins, regulating gene expression in the cell nucleus. It is distributed in cytoplasm; they also participate in mRNA degradation and translational regulation via miRNAs, other transcription products, and proteins. They play a significant role in the development of various diseases, including tumors. Cancer seriously threatens human life and health. Regretfully, a great deal of newly diagnosed cancer patients found to have metastasized. RNF144A-AS1, also referred to as GRASLND, was initially recognized for its regulation of chondrogenic differentiation in MSCs. Focusing on RNF144A-AS1, this review summarizes and discusses the latest progress of RNF144A-AS1 in bladder cancer, glioblastoma, papillary renal cell carcinoma, gastric cancer, osteosarcoma, head and neck squamous cell carcinoma, and ovarian cancer. RNF144A-AS1 has good potential in tumor treatment and diagnosis.
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Affiliation(s)
- Wei Wu
- Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, China Three Gorges University, Yichang, 443002, China
- Third-grade Pharmacological Laboratory on Traditional Chinese Medicine, State Administration of Traditional Chinese Medicine, China Three Gorges University, Yichang, 443002, China
- College of Medicine and Health Science, China Three Gorges University, Yichang, 443002, China
| | - Xiaolan Li
- The Second People's Hospital of China Three Gorges University, Yichang, 443002, China
- The Second People's Hospital of Yichang, Yichang, 443002, China
| | - Xueqing Li
- Third-grade Pharmacological Laboratory on Traditional Chinese Medicine, State Administration of Traditional Chinese Medicine, China Three Gorges University, Yichang, 443002, China
- College of Medicine and Health Science, China Three Gorges University, Yichang, 443002, China
| | - Jiale Zhao
- Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, China Three Gorges University, Yichang, 443002, China
- Third-grade Pharmacological Laboratory on Traditional Chinese Medicine, State Administration of Traditional Chinese Medicine, China Three Gorges University, Yichang, 443002, China
- College of Medicine and Health Science, China Three Gorges University, Yichang, 443002, China
| | - Yibei Gui
- Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, China Three Gorges University, Yichang, 443002, China
- Third-grade Pharmacological Laboratory on Traditional Chinese Medicine, State Administration of Traditional Chinese Medicine, China Three Gorges University, Yichang, 443002, China
- College of Basic Medical Science, China Three Gorges University, Yichang, 443002, China
| | - Yiyang Luo
- Third-grade Pharmacological Laboratory on Traditional Chinese Medicine, State Administration of Traditional Chinese Medicine, China Three Gorges University, Yichang, 443002, China
- College of Medicine and Health Science, China Three Gorges University, Yichang, 443002, China
| | - Hailin Wang
- Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, China Three Gorges University, Yichang, 443002, China
- Third-grade Pharmacological Laboratory on Traditional Chinese Medicine, State Administration of Traditional Chinese Medicine, China Three Gorges University, Yichang, 443002, China
- College of Medicine and Health Science, China Three Gorges University, Yichang, 443002, China
| | - Lijun Wang
- Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, China Three Gorges University, Yichang, 443002, China
- Third-grade Pharmacological Laboratory on Traditional Chinese Medicine, State Administration of Traditional Chinese Medicine, China Three Gorges University, Yichang, 443002, China
- College of Basic Medical Science, China Three Gorges University, Yichang, 443002, China
| | - Chengfu Yuan
- Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, China Three Gorges University, Yichang, 443002, China.
- Third-grade Pharmacological Laboratory on Traditional Chinese Medicine, State Administration of Traditional Chinese Medicine, China Three Gorges University, Yichang, 443002, China.
- College of Basic Medical Science, China Three Gorges University, Yichang, 443002, China.
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2
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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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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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4
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Badoiu SC, Greabu M, Miricescu D, Stanescu-Spinu II, Ilinca R, Balan DG, Balcangiu-Stroescu AE, Mihai DA, Vacaroiu IA, Stefani C, Jinga V. PI3K/AKT/mTOR Dysregulation and Reprogramming Metabolic Pathways in Renal Cancer: Crosstalk with the VHL/HIF Axis. Int J Mol Sci 2023; 24:8391. [PMID: 37176098 PMCID: PMC10179314 DOI: 10.3390/ijms24098391] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 04/26/2023] [Accepted: 05/04/2023] [Indexed: 05/15/2023] Open
Abstract
Renal cell carcinoma (RCC) represents 85-95% of kidney cancers and is the most frequent type of renal cancer in adult patients. It accounts for 3% of all cancer cases and is in 7th place among the most frequent histological types of cancer. Clear cell renal cell carcinoma (ccRCC), accounts for 75% of RCCs and has the most kidney cancer-related deaths. One-third of the patients with ccRCC develop metastases. Renal cancer presents cellular alterations in sugars, lipids, amino acids, and nucleic acid metabolism. RCC is characterized by several metabolic dysregulations including oxygen sensing (VHL/HIF pathway), glucose transporters (GLUT 1 and GLUT 4) energy sensing, and energy nutrient sensing cascade. Metabolic reprogramming represents an important characteristic of the cancer cells to survive in nutrient and oxygen-deprived environments, to proliferate and metastasize in different body sites. The phosphoinositide 3-kinase-AKT-mammalian target of the rapamycin (PI3K/AKT/mTOR) signaling pathway is usually dysregulated in various cancer types including renal cancer. This molecular pathway is frequently correlated with tumor growth and survival. The main aim of this review is to present renal cancer types, dysregulation of PI3K/AKT/mTOR signaling pathway members, crosstalk with VHL/HIF axis, and carbohydrates, lipids, and amino acid alterations.
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Affiliation(s)
- Silviu Constantin Badoiu
- Department of Anatomy and Embryology, Faculty of Medicine, Carol Davila University of Medicine and Pharmacy, 8 Eroii Sanitari Blvd, 050474 Bucharest, Romania;
| | - Maria Greabu
- Department of Biochemistry, Faculty of Dentistry, Carol Davila University of Medicine and Pharmacy, 8 Eroii Sanitari Blvd, Sector 5, 050474 Bucharest, Romania;
| | - Daniela Miricescu
- Department of Biochemistry, Faculty of Dentistry, Carol Davila University of Medicine and Pharmacy, 8 Eroii Sanitari Blvd, Sector 5, 050474 Bucharest, Romania;
| | - Iulia-Ioana Stanescu-Spinu
- Department of Biochemistry, Faculty of Dentistry, Carol Davila University of Medicine and Pharmacy, 8 Eroii Sanitari Blvd, Sector 5, 050474 Bucharest, Romania;
| | - Radu Ilinca
- Department of Medical Informatics and Biostatistics, Faculty of Dentistry, Carol Davila University of Medicine and Pharmacy, 8 Eroii Sanitari Blvd, 050474 Bucharest, Romania;
| | - Daniela Gabriela Balan
- Department of Physiology, Faculty of Dentistry, Carol Davila University of Medicine and Pharmacy, 8 Eroii Sanitari Blvd, 050474 Bucharest, Romania; (D.G.B.); (A.-E.B.-S.)
| | - Andra-Elena Balcangiu-Stroescu
- Department of Physiology, Faculty of Dentistry, Carol Davila University of Medicine and Pharmacy, 8 Eroii Sanitari Blvd, 050474 Bucharest, Romania; (D.G.B.); (A.-E.B.-S.)
| | - Doina-Andrada Mihai
- Department of Diabetes, Nutrition and Metabolic Diseases, Faculty of Medicine, Carol Davila University of Medicine and Pharmacy, 8 Eroii Sanitari Blvd, 050474 Bucharest, Romania;
| | - Ileana Adela Vacaroiu
- Department of Nephrology, Faculty of Medicine, Carol Davila University of Medicine and Pharmacy, 020021 Bucharest, Romania;
| | - Constantin Stefani
- Department of Family Medicine and Clinical Base, Dr. Carol Davila Central Military Emergency University Hospital, 134 Calea Plevnei, 010825 Bucharest, Romania;
| | - Viorel Jinga
- Department of Urology, “Prof. Dr. Theodor Burghele” Hospital, 050653 Bucharest, Romania
- “Prof. Dr. Theodor Burghele” Clinical Hospital, University of Medicine and Pharmacy Carol Davila, 050474 Bucharest, Romania
- Medical Sciences Section, Academy of Romanian Scientists, 050085 Bucharest, Romania
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Chen X, Yong H, Chen M, Deng C, Wang P, Chu S, Li M, Hou P, Zheng J, Li Z, Bai J. TRIM21 attenuates renal carcinoma lipogenesis and malignancy by regulating SREBF1 protein stability. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2023; 42:34. [PMID: 36694250 PMCID: PMC9875457 DOI: 10.1186/s13046-022-02583-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 12/24/2022] [Indexed: 01/26/2023]
Abstract
BACKGROUND Metabolic reprogramming is a hallmark of various cancers. Targeting metabolic processes is a very attractive treatment for cancer. Renal cell carcinoma (RCC) is a type of metabolic disease, and the lipidomic profile of RCC is significantly altered compared with that of healthy tissue. However, the molecular mechanism underlying lipid metabolism regulation in RCC is not clear. METHODS The XF long-chain fatty acid oxidative stress test kits were used to assess the dependence on long-chain fatty acids and mitochondrial function after knockdown TRIM21 in RCC cells. The effect of TRIM21 on the lipid content in RCC cells was determined by metabolomics analysis, Oil Red O staining, and cellular Nile red staining. qRT-PCR and western blot were used to explore the relationship between TRIM21 and lipogenesis, and then the key molecule sterol regulatory element binding transcription factor 1 (SREBF1) was identified to interact with TRIM21 by immunoprecipitation, which was also identified in an orthotopic model. Subsequently, the relevance and clinical significance of TRIM21 and SREBF1 were analyzed by The Cancer Genome Atlas (TCGA) database, and 239 tissues were collected from RCC patients. RESULTS TRIM21 silencing attenuated the dependence of RCC cells on fatty acids, and enhanced lipid accumulation in RCC cells. TRIM21 overexpression significantly decreased lipid contents by decreasing the expression of lipogenic enzymes via ubiquitination-mediated degradation of SREBF1. SREBF1 is critical for TRIM21-mediated lipogenesis inhibition in vitro and in vivo. Moreover, TRIM21 expression is negatively correlated with SREBF1 expression, and TRIM21-SREBF1 is a reliable combinational biomarker for RCC prognosis. CONCLUSION The findings from this study reveal a novel pathway through which TRIM21 inhibits the lipid metabolism process of RCC and shed light on the development of targeted metabolic treatment and prognosis diagnosis of RCC.
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Affiliation(s)
- Xintian Chen
- grid.417303.20000 0000 9927 0537Cancer Institute, Xuzhou Medical University, 209 Tongshan Road, Jiangsu Province 221004 Xuzhou, China ,grid.413389.40000 0004 1758 1622Center of Clinical Oncology, the Affiliated Hospital of Xuzhou Medical University, Jiangsu Xuzhou, China ,grid.417303.20000 0000 9927 0537Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Cancer Institute, Xuzhou Medical University, 209 Tongshan Road, Jiangsu 221004 Xuzhou, China
| | - Hongmei Yong
- grid.417303.20000 0000 9927 0537Department of Oncology, The Second People’s Hospital of Huai’an, The Affiliated Huai’an Hospital of Xuzhou Medical University, Huaian, Jiangsu China
| | - Miaolei Chen
- grid.417303.20000 0000 9927 0537Cancer Institute, Xuzhou Medical University, 209 Tongshan Road, Jiangsu Province 221004 Xuzhou, China
| | - Chuyin Deng
- grid.417303.20000 0000 9927 0537Cancer Institute, Xuzhou Medical University, 209 Tongshan Road, Jiangsu Province 221004 Xuzhou, China
| | - Pengfei Wang
- grid.417303.20000 0000 9927 0537Cancer Institute, Xuzhou Medical University, 209 Tongshan Road, Jiangsu Province 221004 Xuzhou, China
| | - Sufang Chu
- grid.417303.20000 0000 9927 0537Cancer Institute, Xuzhou Medical University, 209 Tongshan Road, Jiangsu Province 221004 Xuzhou, China
| | - Minle Li
- grid.417303.20000 0000 9927 0537Cancer Institute, Xuzhou Medical University, 209 Tongshan Road, Jiangsu Province 221004 Xuzhou, China ,grid.413389.40000 0004 1758 1622Center of Clinical Oncology, the Affiliated Hospital of Xuzhou Medical University, Jiangsu Xuzhou, China ,grid.417303.20000 0000 9927 0537Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Cancer Institute, Xuzhou Medical University, 209 Tongshan Road, Jiangsu 221004 Xuzhou, China
| | - Pingfu Hou
- grid.417303.20000 0000 9927 0537Cancer Institute, Xuzhou Medical University, 209 Tongshan Road, Jiangsu Province 221004 Xuzhou, China ,grid.413389.40000 0004 1758 1622Center of Clinical Oncology, the Affiliated Hospital of Xuzhou Medical University, Jiangsu Xuzhou, China ,grid.417303.20000 0000 9927 0537Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Cancer Institute, Xuzhou Medical University, 209 Tongshan Road, Jiangsu 221004 Xuzhou, China
| | - Junnian Zheng
- grid.417303.20000 0000 9927 0537Cancer Institute, Xuzhou Medical University, 209 Tongshan Road, Jiangsu Province 221004 Xuzhou, China ,grid.413389.40000 0004 1758 1622Center of Clinical Oncology, the Affiliated Hospital of Xuzhou Medical University, Jiangsu Xuzhou, China ,grid.417303.20000 0000 9927 0537Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Cancer Institute, Xuzhou Medical University, 209 Tongshan Road, Jiangsu 221004 Xuzhou, China
| | - Zhongwei Li
- grid.417303.20000 0000 9927 0537Cancer Institute, Xuzhou Medical University, 209 Tongshan Road, Jiangsu Province 221004 Xuzhou, China ,grid.413389.40000 0004 1758 1622Center of Clinical Oncology, the Affiliated Hospital of Xuzhou Medical University, Jiangsu Xuzhou, China ,grid.417303.20000 0000 9927 0537Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Cancer Institute, Xuzhou Medical University, 209 Tongshan Road, Jiangsu 221004 Xuzhou, China
| | - Jin Bai
- grid.417303.20000 0000 9927 0537Cancer Institute, Xuzhou Medical University, 209 Tongshan Road, Jiangsu Province 221004 Xuzhou, China ,grid.413389.40000 0004 1758 1622Center of Clinical Oncology, the Affiliated Hospital of Xuzhou Medical University, Jiangsu Xuzhou, China ,grid.417303.20000 0000 9927 0537Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Cancer Institute, Xuzhou Medical University, 209 Tongshan Road, Jiangsu 221004 Xuzhou, China
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Zhang L, Di L, Liu J, Lei X, Gu M, Zhang W, Wang Y. The LncRNA signature associated with cuproptosis as a novel biomarker of prognosis in immunotherapy and drug screening for clear cell renal cell carcinoma. Front Genet 2023; 14:1039813. [PMID: 36755568 PMCID: PMC9899836 DOI: 10.3389/fgene.2023.1039813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 01/10/2023] [Indexed: 01/24/2023] Open
Abstract
Cuproptosis is a new form of cell death, the second form of metal ion-induced cell death defined after ferroptosis. Recently, cuproptosis has been suggested to be associated with tumorigenesis. However, the relationship between cuproptosis and patient prognosis in clear cell renal cell carcinoma (ccRCC) in the context of immunotherapy remains unknown. The aim of this study was to investigate the correlation between cuproptosis-related long non-coding RNA (lncRNA) and ccRCC in terms of immunity as well as prognosis. Clinical information on lncRNAs associated with differences in cuproptosis genes in ccRCC and normal tissues was collected from The Cancer Genome Atlas (TCGA) dataset. Univariate Cox regression was used to screen lncRNAs. A total of 11 lncRNAs closely associated with cuproptosis were further screened and established using the least absolute shrinkage and selection operator (LASSO) algorithm and multivariate Cox regression, and the samples were randomly divided into training and test groups. A risk prognostic model was constructed using the training group, and the model was validated using the test group. We investigated the predictive ability of the prognostic risk model in terms of clinical prognosis, tumor mutation, immune escape, immunotherapy, tumor microenvironment, immune infiltration levels, and tumor drug treatment of ccRCC. Using the median risk score, patients were divided into low and high-risk groups. Kaplan-Meier curves showed that the overall survival (OS) of patients in the high-risk group was significantly worse than low-risk group (p < 0.001). Receiver operating characteristic (ROC) curves further validated the reliability of our model. The model consistently and accurately predicted prognosis at 1, 3, and 5 years, with an AUC above 0.7. Tumor cell genes generally precede morphological abnormalities; therefore, the model we constructed can effectively compensate for the traditional method of evaluating the prognosis of patients with renal cancer, and our model was also clinically meaningful in predicting ccRCC staging. In addition, lower model risk scores determined by mutational load indicated a good chance of survival. The high-risk group had greater recruitment of immune cells, while the anti-immune checkpoint immunotherapy was less efficacious overall than that of the low-risk group. Tumor and immune-related pathways were enriched, and anti-tumor agents were selected to improve the survival of ccRCC. This prognostic risk model is based on the levels of cuproptosis-associated lncRNAs and provides a new perspective in the clinical assessment and precise treatment of ccRCC.
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Affiliation(s)
- Lishuo Zhang
- Department of Urology, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Longjiang Di
- College of Basic Medicine, Southern Medical University, Guangzhou, Guangdong, China
| | - Jinhui Liu
- The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Xianli Lei
- Harbin Medical University, Harbin, Heilongjiang, China
| | - Maoli Gu
- Department of Urology, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Wenjing Zhang
- The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China,*Correspondence: Yufu Wang, ; Wenjing Zhang,
| | - Yufu Wang
- The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China,*Correspondence: Yufu Wang, ; Wenjing Zhang,
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Jirásko R, Idkowiak J, Wolrab D, Kvasnička A, Friedecký D, Polański K, Študentová H, Študent V, Melichar B, Holčapek M. Altered Plasma, Urine, and Tissue Profiles of Sulfatides and Sphingomyelins in Patients with Renal Cell Carcinoma. Cancers (Basel) 2022; 14:cancers14194622. [PMID: 36230546 PMCID: PMC9563753 DOI: 10.3390/cancers14194622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 09/16/2022] [Accepted: 09/19/2022] [Indexed: 11/16/2022] Open
Abstract
Simple Summary Renal cell carcinoma (RCC) is among the most common cancer types in both men and women, and its early detection significantly improves survival. Minimally-invasive blood- or urine-based tests may increase the RCC detection rate, especially before patients develop symptoms. Here, we report significant changes in concentrations of sulfatides and sphingomyelins in plasma and urine in RCC patients compared to healthy controls. For the first time, we present findings that similar alterations appear in the lipid profiles of body fluids and tissues in patients. We observe gradual changes in sulfatide and sphingomyelin concentrations with increasing tumor stage and grade. We built binary classifiers that detect RCC based on plasma and urine lipidome dysregulations, and we show that the plasma lipidome alterations enable distinguishing between early-stage RCC and controls. Our results demonstrate the considerable potential of lipid screening in biofluids for RCC detection and monitoring in clinical settings. Abstract Purpose: RCC, the most common type of kidney cancer, is associated with high mortality. A non-invasive diagnostic test remains unavailable due to the lack of RCC-specific biomarkers in body fluids. We have previously described a significantly altered profile of sulfatides in RCC tumor tissues, motivating us to investigate whether these alterations are reflected in collectible body fluids and whether they can enable RCC detection. Methods: We collected and further analyzed 143 plasma, 100 urine, and 154 tissue samples from 155 kidney cancer patients, together with 207 plasma and 70 urine samples from 214 healthy controls. Results: For the first time, we show elevated concentrations of lactosylsulfatides and decreased levels of sulfatides with hydroxylated fatty acyls in body fluids of RCC patients compared to controls. These alterations are emphasized in patients with the advanced tumor stage. Classification models are able to distinguish between controls and patients with RCC. In the case of all plasma samples, the AUC for the testing set was 0.903 (0.844–0.954), while for urine samples it was 0.867 (0.763–0.953). The models are able to efficiently detect patients with early- and late-stage RCC based on plasma samples as well. The test set sensitivities were 80.6% and 90%, and AUC values were 0.899 (0.832–0.952) and 0.981 (0.956–0.998), respectively. Conclusion: Similar trends in body fluids and tissues indicate that RCC influences lipid metabolism, and highlight the potential of the studied lipids for minimally-invasive cancer detection, including patients with early tumor stages, as demonstrated by the predictive ability of the applied classification models.
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Affiliation(s)
- Robert Jirásko
- Department of Analytical Chemistry, Faculty of Chemical Technology, University of Pardubice, 53210 Pardubice, Czech Republic
- Correspondence:
| | - Jakub Idkowiak
- Department of Analytical Chemistry, Faculty of Chemical Technology, University of Pardubice, 53210 Pardubice, Czech Republic
| | - Denise Wolrab
- Department of Analytical Chemistry, Faculty of Chemical Technology, University of Pardubice, 53210 Pardubice, Czech Republic
| | - Aleš Kvasnička
- Laboratory for Inherited Metabolic Disorders, Department of Clinical Biochemistry, University Hospital Olomouc, Faculty of Medicine and Dentistry, Palacký University, 77900 Olomouc, Czech Republic
| | - David Friedecký
- Laboratory for Inherited Metabolic Disorders, Department of Clinical Biochemistry, University Hospital Olomouc, Faculty of Medicine and Dentistry, Palacký University, 77900 Olomouc, Czech Republic
| | - Krzysztof Polański
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
| | - Hana Študentová
- Department of Oncology, Faculty of Medicine and Dentistry, University Hospital, Palacký University, 77900 Olomouc, Czech Republic
| | - Vladimír Študent
- Department of Urology, Faculty of Medicine and Dentistry, University Hospital, Palacký University, 77900 Olomouc, Czech Republic
| | - Bohuslav Melichar
- Department of Oncology, Faculty of Medicine and Dentistry, University Hospital, Palacký University, 77900 Olomouc, Czech Republic
| | - Michal Holčapek
- Department of Analytical Chemistry, Faculty of Chemical Technology, University of Pardubice, 53210 Pardubice, Czech Republic
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8
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CD147 a direct target of miR-146a supports energy metabolism and promotes tumor growth in ALK+ ALCL. Leukemia 2022; 36:2050-2063. [PMID: 35676454 PMCID: PMC9343252 DOI: 10.1038/s41375-022-01617-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Revised: 05/23/2022] [Accepted: 05/25/2022] [Indexed: 11/30/2022]
Abstract
We recently reported that miR-146a is differentially expressed in ALK+ and ALK− anaplastic large cell lymphoma (ALCL). In this study, the downstream targets of miR-146a in ALK+ ALCL were investigated by transcriptome analysis, identifying CD147 as potential target gene. Because CD147 is differentially expressed in ALK+ ALCL versus ALK− ALCL and normal T cells, this gene emerged as a strong candidate for the pathogenesis of this tumor. Here we demonstrate that CD147 is a direct target of miR-146 and contributes to the survival and proliferation of ALK+ ALCL cells in vitro and to the engraftment and tumor growth in vivo in an ALK+ ALCL-xenotransplant mouse model. CD147 knockdown in ALK+ ALCL cells resulted in loss of monocarboxylate transporter 1 (MCT1) expression, reduced glucose consumption and tumor growth retardation, as demonstrated by [18F]FDG-PET/MRI analysis. Investigation of metabolism in vitro and in vivo supported these findings, revealing reduced aerobic glycolysis and increased basal respiration in CD147 knockdown. In conclusion, our findings indicate that CD147 is of vital importance for ALK+ ALCL to maintain the high energy demand of rapid cell proliferation, promoting lactate export, and tumor growth. Furthermore, CD147 has the potential to serve as a novel therapeutic target in ALK+ ALCL, and warrants further investigation.
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9
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Tremmel R, Nies AT, van Eijck BAC, Handin N, Haag M, Winter S, Büttner FA, Kölz C, Klein F, Mazzola P, Hofmann U, Klein K, Hoffmann P, Nöthen MM, Gaugaz FZ, Artursson P, Schwab M, Schaeffeler E. Hepatic Expression of the Na+-Taurocholate Cotransporting Polypeptide Is Independent from Genetic Variation. Int J Mol Sci 2022; 23:ijms23137468. [PMID: 35806468 PMCID: PMC9267852 DOI: 10.3390/ijms23137468] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 06/29/2022] [Accepted: 06/29/2022] [Indexed: 11/16/2022] Open
Abstract
The hepatic Na+-taurocholate cotransporting polypeptide NTCP/SLC10A1 is important for the uptake of bile salts and selected drugs. Its inhibition results in increased systemic bile salt concentrations. NTCP is also the entry receptor for the hepatitis B/D virus. We investigated interindividual hepatic SLC10A1/NTCP expression using various omics technologies. SLC10A1/NTCP mRNA expression/protein abundance was quantified in well-characterized 143 human livers by real-time PCR and LC-MS/MS-based targeted proteomics. Genome-wide SNP arrays and SLC10A1 next-generation sequencing were used for genomic analyses. SLC10A1 DNA methylation was assessed through MALDI-TOF MS. Transcriptomics and untargeted metabolomics (UHPLC-Q-TOF-MS) were correlated to identify NTCP-related metabolic pathways. SLC10A1 mRNA and NTCP protein levels varied 44-fold and 10.4-fold, respectively. Non-genetic factors (e.g., smoking, alcohol consumption) influenced significantly NTCP expression. Genetic variants in SLC10A1 or other genes do not explain expression variability which was validated in livers (n = 50) from The Cancer Genome Atlas. The identified two missense SLC10A1 variants did not impair transport function in transfectants. Specific CpG sites in SLC10A1 as well as single metabolic alterations and pathways (e.g., peroxisomal and bile acid synthesis) were significantly associated with expression. Inter-individual variability of NTCP expression is multifactorial with the contribution of clinical factors, DNA methylation, transcriptional regulation as well as hepatic metabolism, but not genetic variation.
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Affiliation(s)
- Roman Tremmel
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, 70376 Stuttgart, Germany; (R.T.); (A.T.N.); (B.A.C.v.E.); (M.H.); (S.W.); (F.A.B.); (C.K.); (F.K.); (P.M.); (U.H.); (K.K.); (E.S.)
- University of Tuebingen, 72076 Tuebingen, Germany
| | - Anne T. Nies
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, 70376 Stuttgart, Germany; (R.T.); (A.T.N.); (B.A.C.v.E.); (M.H.); (S.W.); (F.A.B.); (C.K.); (F.K.); (P.M.); (U.H.); (K.K.); (E.S.)
- University of Tuebingen, 72076 Tuebingen, Germany
- iFIT Cluster of Excellence (EXC2180) “Image Guided and Functionally Instructed Tumor Therapies”, University of Tuebingen, 72076 Tuebingen, Germany
| | - Barbara A. C. van Eijck
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, 70376 Stuttgart, Germany; (R.T.); (A.T.N.); (B.A.C.v.E.); (M.H.); (S.W.); (F.A.B.); (C.K.); (F.K.); (P.M.); (U.H.); (K.K.); (E.S.)
- University of Tuebingen, 72076 Tuebingen, Germany
| | - Niklas Handin
- Department of Pharmacy, Uppsala University, 75123 Uppsala, Sweden; (N.H.); (F.Z.G.); (P.A.)
| | - Mathias Haag
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, 70376 Stuttgart, Germany; (R.T.); (A.T.N.); (B.A.C.v.E.); (M.H.); (S.W.); (F.A.B.); (C.K.); (F.K.); (P.M.); (U.H.); (K.K.); (E.S.)
- University of Tuebingen, 72076 Tuebingen, Germany
| | - Stefan Winter
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, 70376 Stuttgart, Germany; (R.T.); (A.T.N.); (B.A.C.v.E.); (M.H.); (S.W.); (F.A.B.); (C.K.); (F.K.); (P.M.); (U.H.); (K.K.); (E.S.)
- University of Tuebingen, 72076 Tuebingen, Germany
| | - Florian A. Büttner
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, 70376 Stuttgart, Germany; (R.T.); (A.T.N.); (B.A.C.v.E.); (M.H.); (S.W.); (F.A.B.); (C.K.); (F.K.); (P.M.); (U.H.); (K.K.); (E.S.)
- University of Tuebingen, 72076 Tuebingen, Germany
| | - Charlotte Kölz
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, 70376 Stuttgart, Germany; (R.T.); (A.T.N.); (B.A.C.v.E.); (M.H.); (S.W.); (F.A.B.); (C.K.); (F.K.); (P.M.); (U.H.); (K.K.); (E.S.)
- University of Tuebingen, 72076 Tuebingen, Germany
| | - Franziska Klein
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, 70376 Stuttgart, Germany; (R.T.); (A.T.N.); (B.A.C.v.E.); (M.H.); (S.W.); (F.A.B.); (C.K.); (F.K.); (P.M.); (U.H.); (K.K.); (E.S.)
- University of Tuebingen, 72076 Tuebingen, Germany
| | - Pascale Mazzola
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, 70376 Stuttgart, Germany; (R.T.); (A.T.N.); (B.A.C.v.E.); (M.H.); (S.W.); (F.A.B.); (C.K.); (F.K.); (P.M.); (U.H.); (K.K.); (E.S.)
- University of Tuebingen, 72076 Tuebingen, Germany
| | - Ute Hofmann
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, 70376 Stuttgart, Germany; (R.T.); (A.T.N.); (B.A.C.v.E.); (M.H.); (S.W.); (F.A.B.); (C.K.); (F.K.); (P.M.); (U.H.); (K.K.); (E.S.)
- University of Tuebingen, 72076 Tuebingen, Germany
| | - Kathrin Klein
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, 70376 Stuttgart, Germany; (R.T.); (A.T.N.); (B.A.C.v.E.); (M.H.); (S.W.); (F.A.B.); (C.K.); (F.K.); (P.M.); (U.H.); (K.K.); (E.S.)
- University of Tuebingen, 72076 Tuebingen, Germany
| | - Per Hoffmann
- Institute of Human Genetics, University of Bonn, 53127 Bonn, Germany; (P.H.); (M.M.N.)
- Division of Medical Genetics, Department of Biomedicine, University of Basel, 4001 Basel, Switzerland
| | - Markus M. Nöthen
- Institute of Human Genetics, University of Bonn, 53127 Bonn, Germany; (P.H.); (M.M.N.)
- Department of Genomics, Life & Brain Center, University of Bonn, 53127 Bonn, Germany
| | - Fabienne Z. Gaugaz
- Department of Pharmacy, Uppsala University, 75123 Uppsala, Sweden; (N.H.); (F.Z.G.); (P.A.)
| | - Per Artursson
- Department of Pharmacy, Uppsala University, 75123 Uppsala, Sweden; (N.H.); (F.Z.G.); (P.A.)
| | - Matthias Schwab
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, 70376 Stuttgart, Germany; (R.T.); (A.T.N.); (B.A.C.v.E.); (M.H.); (S.W.); (F.A.B.); (C.K.); (F.K.); (P.M.); (U.H.); (K.K.); (E.S.)
- University of Tuebingen, 72076 Tuebingen, Germany
- iFIT Cluster of Excellence (EXC2180) “Image Guided and Functionally Instructed Tumor Therapies”, University of Tuebingen, 72076 Tuebingen, Germany
- Departments of Clinical Pharmacology, and of Pharmacy and Biochemistry, University of Tuebingen, 72076 Tuebingen, Germany
- Correspondence: ; Tel.: +49-711-8101-3700
| | - Elke Schaeffeler
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, 70376 Stuttgart, Germany; (R.T.); (A.T.N.); (B.A.C.v.E.); (M.H.); (S.W.); (F.A.B.); (C.K.); (F.K.); (P.M.); (U.H.); (K.K.); (E.S.)
- University of Tuebingen, 72076 Tuebingen, Germany
- iFIT Cluster of Excellence (EXC2180) “Image Guided and Functionally Instructed Tumor Therapies”, University of Tuebingen, 72076 Tuebingen, Germany
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10
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Reustle A, Menig LS, Leuthold P, Hofmann U, Stühler V, Schmees C, Becker M, Haag M, Klumpp V, Winter S, Büttner FA, Rausch S, Hennenlotter J, Fend F, Scharpf M, Stenzl A, Bedke J, Schwab M, Schaeffeler E. Nicotinamide-N-methyltransferase is a promising metabolic drug target for primary and metastatic clear cell renal cell carcinoma. Clin Transl Med 2022; 12:e883. [PMID: 35678045 PMCID: PMC9178377 DOI: 10.1002/ctm2.883] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 04/27/2022] [Accepted: 05/03/2022] [Indexed: 12/16/2022] Open
Abstract
Background The metabolic enzyme nicotinamide‐N‐methyltransferase (NNMT) is highly expressed in various cancer entities, suggesting tumour‐promoting functions. We systematically investigated NNMT expression and its metabolic interactions in clear cell renal cell carcinoma (ccRCC), a prominent RCC subtype with metabolic alterations, to elucidate its role as a drug target. Methods NNMT expression was assessed in primary ccRCC (n = 134), non‐tumour tissue and ccRCC‐derived metastases (n = 145) by microarray analysis and/or immunohistochemistry. Findings were validated in The Cancer Genome Atlas (kidney renal clear cell carcinoma [KIRC], n = 452) and by single‐cell analysis. Expression was correlated with clinicopathological data and survival. Metabolic alterations in NNMT‐depleted cells were assessed by nontargeted/targeted metabolomics and extracellular flux analysis. The NNMT inhibitor (NNMTi) alone and in combination with the inhibitor 2‐deoxy‐D‐glucose for glycolysis and BPTES (bis‐2‐(5‐phenylacetamido‐1,3,4‐thiadiazol‐2‐yl)ethyl‐sulfide) for glutamine metabolism was investigated in RCC cell lines (786‐O, A498) and in two 2D ccRCC‐derived primary cultures and three 3D ccRCC air–liquid interface models. Results NNMT protein was overexpressed in primary ccRCC (p = 1.32 × 10–16) and ccRCC‐derived metastases (p = 3.92 × 10–20), irrespective of metastatic location, versus non‐tumour tissue. Single‐cell data showed predominant NNMT expression in ccRCC and not in the tumour microenvironment. High NNMT expression in primary ccRCC correlated with worse survival in independent cohorts (primary RCC—hazard ratio [HR] = 4.3, 95% confidence interval [CI]: 1.5–12.4; KIRC—HR = 3.3, 95% CI: 2.0–5.4). NNMT depletion leads to intracellular glutamine accumulation, with negative effects on mitochondrial function and cell survival, while not affecting glycolysis or glutathione metabolism. At the gene level, NNMT‐depleted cells upregulate glycolysis, oxidative phosphorylation and apoptosis pathways. NNMTi alone or in combination with 2‐deoxy‐D‐glucose and BPTES resulted in inhibition of cell viability in ccRCC cell lines and primary tumour and metastasis‐derived models. In two out of three patient‐derived ccRCC air–liquid interface models, NNMTi treatment induced cytotoxicity. Conclusions Since efficient glutamine utilisation, which is essential for ccRCC tumours, depends on NNMT, small‐molecule NNMT inhibitors provide a novel therapeutic strategy for ccRCC and act as sensitizers for combination therapies.
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Affiliation(s)
- Anna Reustle
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany.,University of Tuebingen, Tuebingen, Germany
| | - Lena-Sophie Menig
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany.,University of Tuebingen, Tuebingen, Germany
| | - Patrick Leuthold
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany.,University of Tuebingen, Tuebingen, Germany
| | - Ute Hofmann
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany.,University of Tuebingen, Tuebingen, Germany
| | - Viktoria Stühler
- Department of Urology, University Hospital Tuebingen, Tuebingen, Germany
| | - Christian Schmees
- NMI Natural and Medical Sciences Institute at the University of Tuebingen, Reutlingen, Germany
| | - Michael Becker
- Experimental Pharmacology and Oncology GmbH, Berlin-Buch, Germany
| | - Mathias Haag
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany.,University of Tuebingen, Tuebingen, Germany
| | - Verena Klumpp
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany.,University of Tuebingen, Tuebingen, Germany
| | - Stefan Winter
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany.,University of Tuebingen, Tuebingen, Germany
| | - Florian A Büttner
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany.,University of Tuebingen, Tuebingen, Germany
| | - Steffen Rausch
- Department of Urology, University Hospital Tuebingen, Tuebingen, Germany
| | - Jörg Hennenlotter
- Department of Urology, University Hospital Tuebingen, Tuebingen, Germany
| | - Falko Fend
- Institute of Pathology and Neuropathology, University Hospital Tuebingen, Tuebingen, Germany
| | - Marcus Scharpf
- Institute of Pathology and Neuropathology, University Hospital Tuebingen, Tuebingen, Germany
| | - Arnulf Stenzl
- Department of Urology, University Hospital Tuebingen, Tuebingen, Germany
| | - Jens Bedke
- Department of Urology, University Hospital Tuebingen, Tuebingen, Germany.,German Cancer Consortium (DKTK), Partner Site Tübingen, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Matthias Schwab
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany.,University of Tuebingen, Tuebingen, Germany.,German Cancer Consortium (DKTK), Partner Site Tübingen, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Departments of Clinical Pharmacology, Pharmacy and Biochemistry, University of Tuebingen, Tuebingen, Germany.,Cluster of Excellence iFIT (EXC2180) 'Image-Guided and Functionally Instructed Tumor Therapies', University of Tuebingen, Tuebingen, Germany
| | - Elke Schaeffeler
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany.,University of Tuebingen, Tuebingen, Germany.,Cluster of Excellence iFIT (EXC2180) 'Image-Guided and Functionally Instructed Tumor Therapies', University of Tuebingen, Tuebingen, Germany
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11
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An Exploratory Analysis of Changes in Circulating Plasma Protein Profiles Following Image-Guided Ablation of Renal Tumours Provides Evidence for Effects on Multiple Biological Processes. Cancers (Basel) 2021; 13:cancers13236037. [PMID: 34885149 PMCID: PMC8656737 DOI: 10.3390/cancers13236037] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 11/20/2021] [Accepted: 11/26/2021] [Indexed: 01/20/2023] Open
Abstract
Simple Summary Ablation techniques use extremely hot or cold temperatures to kill small cancers. It is now known that in addition to killing the cancer cells, the ablation treatment may stimulate an immune response in patients against the cancer cells, acting like a vaccine. As a result, there is now interest in combining ablation together with drugs that target the immune system of patients with cancer to enhance the effects of both treatments. In order to develop such combined treatments and test them in clinical trials, we need to understand more about their effects so trials can be optimally designed to be most effective. We have analysed 164 circulating proteins in the blood from patients with small renal tumours undergoing ablation treatment to understand more about the effects of ablation on the patient, both at the level of the effects on the cancer cells and the response of the patients. Abstract Further biological understanding of the immune and inflammatory responses following ablation is critical to the rational development of combination ablation-immunotherapies. Our pilot exploratory study evaluated the circulating plasma protein profiles after image-guided ablation (IGA) of small renal masses to determine the resultant systemic effects and provide insight into impact both on the tumour and immune system. Patients undergoing cryotherapy (CRYO), radiofrequency ablation (RFA) or microwave ablation (MWA) for small renal tumours were recruited. Blood samples were obtained at four timepoints; two baselines prior to IGA and at 24 h and 1–3 months post-IGA, and a panel of 164 proteins measured. Of 55 patients recruited, 35 underwent ablation (25 CRYO, 8 RFA, 2 MWA) and biomarker measurements. The most marked changes were 24 h post-CRYO, with 29 proteins increasing and 18 decreasing significantly, principally cytokines and proteins involved in regulating inflammation, danger-associated molecular patterns (DAMPs), cell proliferation, hypoxic response, apoptosis and migration. Intra-individual variation was low but inter-individual variation was apparent, for example all patients showed increases in IL-6 (1.7 to 29-fold) but only 50% in CD27. Functional annotation analysis highlighted immune/inflammation and cell proliferation/angiogenesis-related clusters, with interaction networks around IL-6, IL-10, VEGF-A and several chemokines. Increases in IL-8, IL-6, and CCL23 correlated with cryoprobe number (p = 0.01, rs = 0.546; p = 0.009, rs = 0.5515; p = 0.005, rs = 0.5873, respectively). This initial data provide further insights into ablation-induced biological changes of relevance in informing trial design of immunotherapies combined with ablation.
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12
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Gao X, Guo R, Li Y, Kang G, Wu Y, Cheng J, Jia J, Wang W, Li Z, Wang A, Xu H, Jia Y, Li Y, Qi X, Wei Z, Wei C. Contribution of upregulated aminoacyl-tRNA biosynthesis to metabolic dysregulation in gastric cancer. J Gastroenterol Hepatol 2021; 36:3113-3126. [PMID: 34159625 PMCID: PMC9292402 DOI: 10.1111/jgh.15592] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 06/04/2021] [Accepted: 06/15/2021] [Indexed: 12/12/2022]
Abstract
BACKGROUND AND AIM Metabolic reprogramming is characterized by dysregulated levels of metabolites and metabolic enzymes. Integrated metabolomic and transcriptomic data analysis can help to elucidate changes in the levels of metabolites and metabolic enzymes, screen the core metabolic pathways, and develop novel therapeutic strategies for cancer. METHODS Here, the metabolome of gastric cancer tissues was determined using liquid chromatography-mass spectrometry. The transcriptome data from The Cancer Genome Atlas dataset were integrated with the liquid chromatography-mass spectrometry data to identify the common dysregulated gastric cancer-specific metabolic pathways. Additionally, the protein expression and clinical significance of key metabolic enzymes were examined using a gastric cancer tissue array. RESULTS Metabolomic analysis of 16 gastric cancer tissues revealed that among the 15 dysregulated metabolomic pathways, the aminoacyl-tRNA biosynthesis pathway in the gastric tissues was markedly upregulated relative to that in the adjacent noncancerous tissues, which was consistent with the results of transcriptome analysis. Bioinformatic analysis revealed that among the key regulators in the aminoacyl-tRNA biosynthesis pathway, the expression levels of threonyl-tRNA synthetase (TARS) and phenylalanyl-tRNA synthetase (FARSB) were correlated with tumor grade and poor survival, respectively. Additionally, gastric tissue array data analysis indicated that TARS and FARSB were upregulated in gastric cancer tissues and were correlated with poor prognosis and tumor metastasis. CONCLUSIONS This study demonstrated that the aminoacyl-tRNA biosynthesis pathway is upregulated in gastric cancer and both TARS and FARSB play key roles in the progression of gastric cancer. Additionally, a novel therapeutic strategy for gastric cancer was proposed that involves targeting the aminoacyl-tRNA biosynthesis pathway.
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Affiliation(s)
- Xiaoling Gao
- NHC Key Laboratory of Diagnosis and Therapy of Gastrointestinal TumorGansu Provincial HospitalLanzhouChina,The Institute of Clinical Research and Translational MedicineGansu Provincial HospitalLanzhouChina
| | - Rui Guo
- NHC Key Laboratory of Diagnosis and Therapy of Gastrointestinal TumorGansu Provincial HospitalLanzhouChina,The Institute of Clinical Research and Translational MedicineGansu Provincial HospitalLanzhouChina
| | - Yonghong Li
- NHC Key Laboratory of Diagnosis and Therapy of Gastrointestinal TumorGansu Provincial HospitalLanzhouChina,The Institute of Clinical Research and Translational MedicineGansu Provincial HospitalLanzhouChina
| | - Guolan Kang
- Department of Endoscopic Diagnosis and Treatment CenterGansu Provincial HospitalLanzhouChina
| | - Yu Wu
- NHC Key Laboratory of Diagnosis and Therapy of Gastrointestinal TumorGansu Provincial HospitalLanzhouChina
| | - Jia Cheng
- Department of Endoscopic Diagnosis and Treatment CenterGansu Provincial HospitalLanzhouChina
| | - Jing Jia
- NHC Key Laboratory of Diagnosis and Therapy of Gastrointestinal TumorGansu Provincial HospitalLanzhouChina
| | - Wanxia Wang
- NHC Key Laboratory of Diagnosis and Therapy of Gastrointestinal TumorGansu Provincial HospitalLanzhouChina
| | - Zhenhao Li
- NHC Key Laboratory of Diagnosis and Therapy of Gastrointestinal TumorGansu Provincial HospitalLanzhouChina
| | - Anqi Wang
- NHC Key Laboratory of Diagnosis and Therapy of Gastrointestinal TumorGansu Provincial HospitalLanzhouChina
| | - Hui Xu
- The Institute of Clinical Research and Translational MedicineGansu Provincial HospitalLanzhouChina
| | - Yanjuan Jia
- The Institute of Clinical Research and Translational MedicineGansu Provincial HospitalLanzhouChina
| | - Yuanting Li
- The Institute of Clinical Research and Translational MedicineGansu Provincial HospitalLanzhouChina
| | - Xiaoming Qi
- The Institute of Clinical Research and Translational MedicineGansu Provincial HospitalLanzhouChina
| | - Zhenhong Wei
- The Institute of Clinical Research and Translational MedicineGansu Provincial HospitalLanzhouChina
| | - Chaojun Wei
- NHC Key Laboratory of Diagnosis and Therapy of Gastrointestinal TumorGansu Provincial HospitalLanzhouChina,The Institute of Clinical Research and Translational MedicineGansu Provincial HospitalLanzhouChina
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13
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Guida F, Tan VY, Corbin LJ, Smith-Byrne K, Alcala K, Langenberg C, Stewart ID, Butterworth AS, Surendran P, Achaintre D, Adamski J, Amiano P, Bergmann MM, Bull CJ, Dahm CC, Gicquiau A, Giles GG, Gunter MJ, Haller T, Langhammer A, Larose TL, Ljungberg B, Metspalu A, Milne RL, Muller DC, Nøst TH, Pettersen Sørgjerd E, Prehn C, Riboli E, Rinaldi S, Rothwell JA, Scalbert A, Schmidt JA, Severi G, Sieri S, Vermeulen R, Vincent EE, Waldenberger M, Timpson NJ, Johansson M. The blood metabolome of incident kidney cancer: A case-control study nested within the MetKid consortium. PLoS Med 2021; 18:e1003786. [PMID: 34543281 PMCID: PMC8496779 DOI: 10.1371/journal.pmed.1003786] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 10/07/2021] [Accepted: 08/27/2021] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Excess bodyweight and related metabolic perturbations have been implicated in kidney cancer aetiology, but the specific molecular mechanisms underlying these relationships are poorly understood. In this study, we sought to identify circulating metabolites that predispose kidney cancer and to evaluate the extent to which they are influenced by body mass index (BMI). METHODS AND FINDINGS We assessed the association between circulating levels of 1,416 metabolites and incident kidney cancer using pre-diagnostic blood samples from up to 1,305 kidney cancer case-control pairs from 5 prospective cohort studies. Cases were diagnosed on average 8 years after blood collection. We found 25 metabolites robustly associated with kidney cancer risk. In particular, 14 glycerophospholipids (GPLs) were inversely associated with risk, including 8 phosphatidylcholines (PCs) and 2 plasmalogens. The PC with the strongest association was PC ae C34:3 with an odds ratio (OR) for 1 standard deviation (SD) increment of 0.75 (95% confidence interval [CI]: 0.68 to 0.83, p = 2.6 × 10-8). In contrast, 4 amino acids, including glutamate (OR for 1 SD = 1.39, 95% CI: 1.20 to 1.60, p = 1.6 × 10-5), were positively associated with risk. Adjusting for BMI partly attenuated the risk association for some-but not all-metabolites, whereas other known risk factors of kidney cancer, such as smoking and alcohol consumption, had minimal impact on the observed associations. A mendelian randomisation (MR) analysis of the influence of BMI on the blood metabolome highlighted that some metabolites associated with kidney cancer risk are influenced by BMI. Specifically, elevated BMI appeared to decrease levels of several GPLs that were also found inversely associated with kidney cancer risk (e.g., -0.17 SD change [ßBMI] in 1-(1-enyl-palmitoyl)-2-linoleoyl-GPC (P-16:0/18:2) levels per SD change in BMI, p = 3.4 × 10-5). BMI was also associated with increased levels of glutamate (ßBMI: 0.12, p = 1.5 × 10-3). While our results were robust across the participating studies, they were limited to study participants of European descent, and it will, therefore, be important to evaluate if our findings can be generalised to populations with different genetic backgrounds. CONCLUSIONS This study suggests a potentially important role of the blood metabolome in kidney cancer aetiology by highlighting a wide range of metabolites associated with the risk of developing kidney cancer and the extent to which changes in levels of these metabolites are driven by BMI-the principal modifiable risk factor of kidney cancer.
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Affiliation(s)
- Florence Guida
- Genomic Epidemiology Branch, International Agency for Research on Cancer (IARC/WHO), Lyon, France
| | - Vanessa Y. Tan
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, United Kingdom
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, United Kingdom
| | - Laura J. Corbin
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, United Kingdom
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, United Kingdom
| | - Karl Smith-Byrne
- Genomic Epidemiology Branch, International Agency for Research on Cancer (IARC/WHO), Lyon, France
| | - Karine Alcala
- Genomic Epidemiology Branch, International Agency for Research on Cancer (IARC/WHO), Lyon, France
| | - Claudia Langenberg
- MRC Epidemiology Unit, University of Cambridge, Cambridge, United Kingdom
| | - Isobel D. Stewart
- MRC Epidemiology Unit, University of Cambridge, Cambridge, United Kingdom
| | - Adam S. Butterworth
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
- British Heart Foundation Centre of Research Excellence, University of Cambridge, Cambridge, United Kingdom
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, United Kingdom
- National Institute for Health Research Blood and Transplant Research Unit in Donor Health and Genomics, University of Cambridge, Cambridge, United Kingdom
| | - Praveen Surendran
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
- British Heart Foundation Centre of Research Excellence, University of Cambridge, Cambridge, United Kingdom
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, United Kingdom
- Rutherford Fund Fellow, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
| | - David Achaintre
- Nutrition and Metabolism Branch, International Agency for Research on Cancer (IARC/WHO), Lyon, France
| | - Jerzy Adamski
- Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
- Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
- Chair of Experimental Genetics, School of Life Science, Weihenstephan, Technische Universität München, Freising, Germany
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Pilar Amiano
- Ministry of Health of the Basque Government, Sub Directorate for Public Health and Addictions of Gipuzkoa, San Sebastián, Spain
- Biodonostia Health Research Institute, Epidemiology of Chronic and Communicable Diseases Group, San Sebastián, Spain
- Spanish Consortium for Research on Epidemiology and Public Health (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain
| | | | - Caroline J. Bull
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, United Kingdom
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, United Kingdom
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, United Kingdom
- Bristol Renal, Translational Health Sciences, Bristol Medical School, University of Bristol, Bristol, United Kingdom
| | | | - Audrey Gicquiau
- Nutrition and Metabolism Branch, International Agency for Research on Cancer (IARC/WHO), Lyon, France
| | - Graham G. Giles
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Australia
| | - Marc J. Gunter
- Nutrition and Metabolism Branch, International Agency for Research on Cancer (IARC/WHO), Lyon, France
| | - Toomas Haller
- Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Arnulf Langhammer
- HUNT Research Centre, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Levanger, Norway
- Levanger Hospital, Nord-Trøndelag Hospital Trust, Levanger, Norway
| | - Tricia L. Larose
- Genomic Epidemiology Branch, International Agency for Research on Cancer (IARC/WHO), Lyon, France
- HUNT Research Centre, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Levanger, Norway
- Department of Community Medicine and Global Health, Institute of Health and Society, University of Oslo, Oslo, Norway
| | - Börje Ljungberg
- Department of Surgical and Perioperative Sciences, Urology and Andrology, Umeå University, Umeå, Sweden
| | | | - Roger L. Milne
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Australia
| | - David C. Muller
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, United Kingdom
| | - Therese H. Nøst
- Department of Community Medicine, Faculty of Health Sciences, UiT The Arctic University of Norway, Tromsø, Norway
| | - Elin Pettersen Sørgjerd
- HUNT Research Centre, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Levanger, Norway
| | - Cornelia Prehn
- Metabolomics and Proteomics Core (MPC), Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
| | - Elio Riboli
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, United Kingdom
| | - Sabina Rinaldi
- Nutrition and Metabolism Branch, International Agency for Research on Cancer (IARC/WHO), Lyon, France
| | - Joseph A. Rothwell
- Université Paris-Saclay, UVSQ, Inserm, Gustave Roussy, Équipe “Exposome et Hérédité”, CESP UMR1018, Inserm, Villejuif, France
| | - Augustin Scalbert
- Nutrition and Metabolism Branch, International Agency for Research on Cancer (IARC/WHO), Lyon, France
| | - Julie A. Schmidt
- Cancer Epidemiology Unit, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom
| | - Gianluca Severi
- Université Paris-Saclay, UVSQ, Inserm, Gustave Roussy, Équipe “Exposome et Hérédité”, CESP UMR1018, Inserm, Villejuif, France
- Department of Statistics, Computer Science and Applications (DISIA), University of Florence, Florence, Italy
| | - Sabina Sieri
- Epidemiology and Prevention Unit, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Milano, Italy
| | - Roel Vermeulen
- Institute for Risk Assessment Sciences (IRAS), Utrecht University, Utrecht, the Netherlands
| | - Emma E. Vincent
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, United Kingdom
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, United Kingdom
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, United Kingdom
- Bristol Renal, Translational Health Sciences, Bristol Medical School, University of Bristol, Bristol, United Kingdom
| | - Melanie Waldenberger
- Research Unit Molecular Epidemiology, Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
| | - Nicholas J. Timpson
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, United Kingdom
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, United Kingdom
| | - Mattias Johansson
- Genomic Epidemiology Branch, International Agency for Research on Cancer (IARC/WHO), Lyon, France
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14
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Marquardt A, Solimando AG, Kerscher A, Bittrich M, Kalogirou C, Kübler H, Rosenwald A, Bargou R, Kollmannsberger P, Schilling B, Meierjohann S, Krebs M. Subgroup-Independent Mapping of Renal Cell Carcinoma-Machine Learning Reveals Prognostic Mitochondrial Gene Signature Beyond Histopathologic Boundaries. Front Oncol 2021; 11:621278. [PMID: 33791209 PMCID: PMC8005734 DOI: 10.3389/fonc.2021.621278] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Accepted: 02/15/2021] [Indexed: 12/14/2022] Open
Abstract
Background: Renal cell carcinoma (RCC) is divided into three major histopathologic groups—clear cell (ccRCC), papillary (pRCC) and chromophobe RCC (chRCC). We performed a comprehensive re-analysis of publicly available RCC datasets from the TCGA (The Cancer Genome Atlas) database, thereby combining samples from all three subgroups, for an exploratory transcriptome profiling of RCC subgroups. Materials and Methods: We used FPKM (fragments per kilobase per million) files derived from the ccRCC, pRCC and chRCC cohorts of the TCGA database, representing transcriptomic data of 891 patients. Using principal component analysis, we visualized datasets as t-SNE plot for cluster detection. Clusters were characterized by machine learning, resulting gene signatures were validated by correlation analyses in the TCGA dataset and three external datasets (ICGC RECA-EU, CPTAC-3-Kidney, and GSE157256). Results: Many RCC samples co-clustered according to histopathology. However, a substantial number of samples clustered independently from histopathologic origin (mixed subgroup)—demonstrating divergence between histopathology and transcriptomic data. Further analyses of mixed subgroup via machine learning revealed a predominant mitochondrial gene signature—a trait previously known for chRCC—across all histopathologic subgroups. Additionally, ccRCC samples from mixed subgroup presented an inverse correlation of mitochondrial and angiogenesis-related genes in the TCGA and in three external validation cohorts. Moreover, mixed subgroup affiliation was associated with a highly significant shorter overall survival for patients with ccRCC—and a highly significant longer overall survival for chRCC patients. Conclusions: Pan-RCC clustering according to RNA-sequencing data revealed a distinct histology-independent subgroup characterized by strengthened mitochondrial and weakened angiogenesis-related gene signatures. Moreover, affiliation to mixed subgroup went along with a significantly shorter overall survival for ccRCC and a longer overall survival for chRCC patients. Further research could offer a therapy stratification by specifically addressing the mitochondrial metabolism of such tumors and its microenvironment.
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Affiliation(s)
- André Marquardt
- Comprehensive Cancer Center Mainfranken, University Hospital Würzburg, Würzburg, Germany.,Institute of Pathology, University of Würzburg, Würzburg, Germany.,Interdisciplinary Center for Clinical Research, University Hospital Würzburg, Würzburg, Germany
| | - Antonio Giovanni Solimando
- Guido Baccelli Unit of Internal Medicine, Department of Biomedical Sciences and Human Oncology, School of Medicine, Aldo Moro University of Bari, Bari, Italy.,IRCCS Istituto Tumori "Giovanni Paolo II" of Bari, Bari, Italy
| | - Alexander Kerscher
- Comprehensive Cancer Center Mainfranken, University Hospital Würzburg, Würzburg, Germany
| | - Max Bittrich
- Department of Internal Medicine II, University Hospital Würzburg, Würzburg, Germany
| | - Charis Kalogirou
- Department of Urology and Pediatric Urology, University Hospital Würzburg, Würzburg, Germany
| | - Hubert Kübler
- Department of Urology and Pediatric Urology, University Hospital Würzburg, Würzburg, Germany
| | | | - Ralf Bargou
- Comprehensive Cancer Center Mainfranken, University Hospital Würzburg, Würzburg, Germany
| | - Philip Kollmannsberger
- Center for Computational and Theoretical Biology, University of Würzburg, Würzburg, Germany
| | - Bastian Schilling
- Department of Dermatology, University Hospital Würzburg, Würzburg, Germany
| | - Svenja Meierjohann
- Institute of Pathology, University of Würzburg, Würzburg, Germany.,Interdisciplinary Center for Clinical Research, University Hospital Würzburg, Würzburg, Germany
| | - Markus Krebs
- Comprehensive Cancer Center Mainfranken, University Hospital Würzburg, Würzburg, Germany.,Department of Urology and Pediatric Urology, University Hospital Würzburg, Würzburg, Germany
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15
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Wang Y. Applications of Lipidomics in Tumor Diagnosis and Therapy. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1316:25-39. [PMID: 33740241 DOI: 10.1007/978-981-33-6785-2_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Lipids have many critical biological functions in cancer. There are characteristic changes of lipid metabolism and metabolites in different physiological and pathological processes. Lipidomics is an emerging discipline of metabolomics for systematic analysis of lipids in organisms, tissues, or cells and the molecules that interact with them. With the development of new analytical techniques, especially the application and development of mass spectrometry techniques, the determination of lipids can be carried out quickly and accurately and has a high throughput. A large number of studies have shown that abnormal lipid metabolism is closely related to the occurrence and development of tumors. The application of lipidomics technology can reveal changes in lipids and relative abnormal metabolic pathways associated with tumors. Moreover, it shows a wide range of application prospects in the identification of tumor lipid biomarkers, early tumor diagnosis, and the discovery of antitumor drug targets. This chapter mainly introduces the application and development direction of lipidomics in the diagnosis and therapy of different tumors.
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Affiliation(s)
- Yuping Wang
- Department of Gastroenterology, Key Laboratory for Gastrointestinal Diseases of Gansu Province, The First Hospital of Lanzhou University, Lanzhou, Gansu Province, China.
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16
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Zhan X, Liu Y, Yu CY, Wang TF, Zhang J, Ni D, Huang K. A pan-kidney cancer study identifies subtype specific perturbations on pathways with potential drivers in renal cell carcinoma. BMC Med Genomics 2020; 13:190. [PMID: 33371886 PMCID: PMC7771093 DOI: 10.1186/s12920-020-00827-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 11/17/2020] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Renal cell carcinoma (RCC) is a complex disease and is comprised of several histological subtypes, the most frequent of which are clear cell renal cell carcinoma (ccRCC), papillary renal cell carcinoma (PRCC) and chromophobe renal cell carcinoma (ChRCC). While lots of studies have been performed to investigate the molecular characterizations of different subtypes of RCC, our knowledge regarding the underlying mechanisms are still incomplete. As molecular alterations are eventually reflected on the pathway level to execute certain biological functions, characterizing the pathway perturbations is crucial for understanding tumorigenesis and development of RCC. METHODS In this study, we investigated the pathway perturbations of various RCC subtype against normal tissue based on differential expressed genes within a certain pathway. We explored the potential upstream regulators of subtype-specific pathways with Ingenuity Pathway Analysis (IPA). We also evaluated the relationships between subtype-specific pathways and clinical outcome with survival analysis. RESULTS In this study, we carried out a pathway-based analysis to explore the mechanisms of various RCC subtypes with TCGA RNA-seq data. Both commonly altered pathways and subtype-specific pathways were detected. To identify the distinctive characteristics of each subtype, we focused on subtype-specific perturbed pathways. Specifically, we observed that some of the altered pathways were regulated by several recurrent upstream regulators which presenting different expression patterns among distinct RCC subtypes. We also noticed that a large number of perturbed pathways were controlled by the subtype-specific upstream regulators. Moreover, we also evaluated the relationships between perturbed pathways and clinical outcome. Prognostic pathways were identified and their roles in tumor development and progression were inferred. CONCLUSIONS In summary, we evaluated the relationships among pathway perturbations, upstream regulators and clinical outcome for differential subtypes in RCC. We hypothesized that the alterations of common upstream regulators as well as subtype-specific upstream regulators work together to affect the downstream pathway perturbations and drive cancer initialization and prognosis. Our findings not only increase our understanding of the mechanisms of various RCC subtypes, but also provide targets for personalized therapeutic intervention.
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Affiliation(s)
- Xiaohui Zhan
- National-Regional Key Technology Engineering Laboratory for Medical Ultrasound, Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, School of Biomedical Engineering, Health Science Center, Shenzhen University, Shenzhen, 518037, China.
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, 46202, USA.
- School of Basic Medicine, Chongqing Medical University, Chongqing, 400016, China.
| | - Yusong Liu
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
- College of Automation, Harbin Engineering University, Harbin, 150001, Heilongjiang, China
| | - Christina Y Yu
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH, 43210, USA
| | - Tian-Fu Wang
- National-Regional Key Technology Engineering Laboratory for Medical Ultrasound, Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, School of Biomedical Engineering, Health Science Center, Shenzhen University, Shenzhen, 518037, China
| | - Jie Zhang
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Dong Ni
- National-Regional Key Technology Engineering Laboratory for Medical Ultrasound, Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, School of Biomedical Engineering, Health Science Center, Shenzhen University, Shenzhen, 518037, China.
| | - Kun Huang
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, 46202, USA.
- Regenstrief Institute, Indianapolis, 46202, USA.
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17
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Neef SK, Janssen N, Winter S, Wallisch SK, Hofmann U, Dahlke MH, Schwab M, Mürdter TE, Haag M. Metabolic Drug Response Phenotyping in Colorectal Cancer Organoids by LC-QTOF-MS. Metabolites 2020; 10:metabo10120494. [PMID: 33271860 PMCID: PMC7760698 DOI: 10.3390/metabo10120494] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 11/25/2020] [Accepted: 11/27/2020] [Indexed: 12/13/2022] Open
Abstract
As metabolic rewiring is crucial for cancer cell proliferation, metabolic phenotyping of patient-derived organoids is desirable to identify drug-induced changes and trace metabolic vulnerabilities of tumor subtypes. We established a novel protocol for metabolomic and lipidomic profiling of colorectal cancer organoids by liquid chromatography quadrupole time-of-flight mass spectrometry (LC-QTOF-MS) facing the challenge of capturing metabolic information from a minimal sample amount (<500 cells/injection) in the presence of an extracellular matrix (ECM). The best procedure of the tested protocols included ultrasonic metabolite extraction with acetonitrile/methanol/water (2:2:1, v/v/v) without ECM removal. To eliminate ECM-derived background signals, we implemented a data filtering procedure based on the p-value and fold change cut-offs, which retained features with signal intensities >120% compared to matrix-derived signals present in blank samples. As a proof-of-concept, the method was applied to examine the early metabolic response of colorectal cancer organoids to 5-fluorouracil treatment. Statistical analysis revealed dose-dependent changes in the metabolic profiles of treated organoids including elevated levels of 2′-deoxyuridine, 2′-O-methylcytidine, inosine and 1-methyladenosine and depletion of 2′-deoxyadenosine and specific phospholipids. In accordance with the mechanism of action of 5-fluorouracil, changed metabolites are mainly involved in purine and pyrimidine metabolism. The novel protocol provides a first basis for the assessment of metabolic drug response phenotypes in 3D organoid models.
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Affiliation(s)
- Sylvia K. Neef
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, Germany and University of Tuebingen, 70376 Tuebingen, Germany; (S.K.N.); (N.J.); (S.W.); (S.K.W.); (U.H.); (M.H.D.); (M.S.); (T.E.M.)
| | - Nicole Janssen
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, Germany and University of Tuebingen, 70376 Tuebingen, Germany; (S.K.N.); (N.J.); (S.W.); (S.K.W.); (U.H.); (M.H.D.); (M.S.); (T.E.M.)
| | - Stefan Winter
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, Germany and University of Tuebingen, 70376 Tuebingen, Germany; (S.K.N.); (N.J.); (S.W.); (S.K.W.); (U.H.); (M.H.D.); (M.S.); (T.E.M.)
| | - Svenja K. Wallisch
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, Germany and University of Tuebingen, 70376 Tuebingen, Germany; (S.K.N.); (N.J.); (S.W.); (S.K.W.); (U.H.); (M.H.D.); (M.S.); (T.E.M.)
| | - Ute Hofmann
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, Germany and University of Tuebingen, 70376 Tuebingen, Germany; (S.K.N.); (N.J.); (S.W.); (S.K.W.); (U.H.); (M.H.D.); (M.S.); (T.E.M.)
| | - Marc H. Dahlke
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, Germany and University of Tuebingen, 70376 Tuebingen, Germany; (S.K.N.); (N.J.); (S.W.); (S.K.W.); (U.H.); (M.H.D.); (M.S.); (T.E.M.)
- Department of Surgery, Robert-Bosch Hospital, 70376 Stuttgart, Germany
| | - Matthias Schwab
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, Germany and University of Tuebingen, 70376 Tuebingen, Germany; (S.K.N.); (N.J.); (S.W.); (S.K.W.); (U.H.); (M.H.D.); (M.S.); (T.E.M.)
- Departments of Clinical Pharmacology, and of Pharmacy and Biochemistry, University of Tuebingen, 72074 Tuebingen, Germany
- Cluster of Excellence iFIT (EXC 2180), Image-Guided and Functionally Instructed Tumor Therapies, University of Tuebingen, 72074 Tuebingen, Germany
| | - Thomas E. Mürdter
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, Germany and University of Tuebingen, 70376 Tuebingen, Germany; (S.K.N.); (N.J.); (S.W.); (S.K.W.); (U.H.); (M.H.D.); (M.S.); (T.E.M.)
| | - Mathias Haag
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, Germany and University of Tuebingen, 70376 Tuebingen, Germany; (S.K.N.); (N.J.); (S.W.); (S.K.W.); (U.H.); (M.H.D.); (M.S.); (T.E.M.)
- Correspondence: ; Tel.: +49-711-8101-5429
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18
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In Situ Metabolomics Expands the Spectrum of Renal Tumours Positive on 99mTc-sestamibi Single Photon Emission Computed Tomography/Computed Tomography Examination. EUR UROL SUPPL 2020; 22:88-96. [PMID: 34337482 PMCID: PMC8317898 DOI: 10.1016/j.euros.2020.11.001] [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] [Accepted: 11/03/2020] [Indexed: 02/07/2023] Open
Abstract
Background Definite noninvasive characterisation of renal tumours positive on 99mTc-sestamibi single photon emission computed tomography/computed tomography (SPECT/CT) examination including renal oncocytomas (ROs), hybrid oncocytic chromophobe tumours (HOCTs), and chromophobe renal cell carcinoma (chRCC) is currently not feasible. Objective To investigate whether combined 99mTc-sestamibi SPECT/CT and in situ metabolomic profiling can accurately characterise renal tumours exhibiting 99mTc-sestamibi uptake. Design, setting, and participants A tissue microarray analysis of 33 tumour samples from 28 patients was used to investigate whether their in situ metabolomic status correlates with their features on 99mTc-sestamibi SPECT/CT examination. In order to validate emerging data, an independent cohort comprising 117 tumours was subjected to matrix-assisted laser desorption/ionisation mass spectrometry imaging (MALDI MSI). Outcome measurements and statistical analysis MALDI MSI data analysis and image generation were facilitated by FlexImaging v. 4.2, while k-means analysis by SCiLS Lab software followed by R-package CARRoT analysis was used for assessing the highest predictive power in the differential of RO versus chRCC. Heatmap-based clustering, sparse partial least-squares discriminant analysis, and volcano plots were created with MetaboAnalyst 3.0. Results and limitations We identified a discriminatory metabolomic signature for 99mTc-sestamibi SPECT/CT–positive Birt-Hogg-Dubè–associated HOCTs versus other renal oncocytic tumours. Metabolomic differences were also evident between 99mTc-sestamibi–positive and 99mTc-sestamibi–negative chRCCs, prompting additional expert review; two of three 99mTc-sestamibi–positive chRCCs were reclassified as low-grade oncocytic tumours (LOTs). Differences were identified between distal-derived tumours from those of proximal tubule origin, including differences between ROs and chRCCs. Conclusions The current study expands the spectrum of 99mTc-sestamibi SPECT/CT–positive renal tumours, encompassing ROs, HOCTs, LOTs, and chRCCs, and supports the feasibility of in situ metabolomic profiling in the diagnostics and classification of renal tumours. Patient summary For preoperative evaluation of solid renal tumours, 99mTc-sestamibi single photon emission computed tomography/computed tomography (SPECT/CT) is a novel examination method. To increase diagnostic accuracy, we propose that 99mTc-sestamibi–positive renal tumours should be biopsied and followed by a combined histometabolomic analysis.
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19
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Manzi M, Palazzo M, Knott ME, Beauseroy P, Yankilevich P, Giménez MI, Monge ME. Coupled Mass-Spectrometry-Based Lipidomics Machine Learning Approach for Early Detection of Clear Cell Renal Cell Carcinoma. J Proteome Res 2020; 20:841-857. [PMID: 33207877 DOI: 10.1021/acs.jproteome.0c00663] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
A discovery-based lipid profiling study of serum samples from a cohort that included patients with clear cell renal cell carcinoma (ccRCC) stages I, II, III, and IV (n = 112) and controls (n = 52) was performed using ultraperformance liquid chromatography coupled to quadrupole-time-of-flight mass spectrometry and machine learning techniques. Multivariate models based on support vector machines and the LASSO variable selection method yielded two discriminant lipid panels for ccRCC detection and early diagnosis. A 16-lipid panel allowed discriminating ccRCC patients from controls with 95.7% accuracy in a training set under cross-validation and 77.1% accuracy in an independent test set. A second model trained to discriminate early (I and II) from late (III and IV) stage ccRCC yielded a panel of 26 compounds that classified stage I patients from an independent test set with 82.1% accuracy. Thirteen species, including cholic acid, undecylenic acid, lauric acid, LPC(16:0/0:0), and PC(18:2/18:2), identified with level 1 exhibited significantly lower levels in samples from ccRCC patients compared to controls. Moreover, 3α-hydroxy-5α-androstan-17-one 3-sulfate, cis-5-dodecenoic acid, arachidonic acid, cis-13-docosenoic acid, PI(16:0/18:1), PC(16:0/18:2), and PC(O-16:0/20:4) contributed to discriminate early from late ccRCC stage patients. The results are auspicious for early ccRCC diagnosis after validation of the panels in larger and different cohorts.
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Affiliation(s)
- Malena Manzi
- Centro de Investigaciones en Bionanociencias (CIBION), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2390, C1425FQD CABA, Argentina.,Departamento de Química Biológica, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires. Junín 956, C1113AAD Buenos Aires, Argentina
| | - Martín Palazzo
- LM2S, Université de Technologie de Troyes, 12 rue Marie-Curie, CS42060 Troyes, France.,Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA), CONICET, Instituto Partner de la Sociedad Max Planck, Godoy Cruz 2390, C1425FQD CABA, Argentina
| | - María Elena Knott
- Centro de Investigaciones en Bionanociencias (CIBION), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2390, C1425FQD CABA, Argentina
| | - Pierre Beauseroy
- LM2S, Université de Technologie de Troyes, 12 rue Marie-Curie, CS42060 Troyes, France
| | - Patricio Yankilevich
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA), CONICET, Instituto Partner de la Sociedad Max Planck, Godoy Cruz 2390, C1425FQD CABA, Argentina
| | - María Isabel Giménez
- Departamento de Diagnóstico y Tratamiento, Hospital Italiano de Buenos Aires, Tte. Gral. Juan Domingo Perón 4190, C1199ABB CABA, Argentina
| | - María Eugenia Monge
- Centro de Investigaciones en Bionanociencias (CIBION), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2390, C1425FQD CABA, Argentina
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20
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Neef SK, Winter S, Hofmann U, Mürdter TE, Schaeffeler E, Horn H, Buck A, Walch A, Hennenlotter J, Ott G, Fend F, Bedke J, Schwab M, Haag M. Optimized protocol for metabolomic and lipidomic profiling in formalin-fixed paraffin-embedded kidney tissue by LC-MS. Anal Chim Acta 2020; 1134:125-135. [DOI: 10.1016/j.aca.2020.08.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 07/31/2020] [Accepted: 08/02/2020] [Indexed: 12/16/2022]
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21
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de Silva S, Lockhart K, Aslan P, Nash P, Hutton A, Malouf D, Lee D, Cozzi P, Maclean F, Thompson J. Chemical shift imaging in the identification of those renal tumours that contain microscopic fat and the utility of multiparametric MRI in their differentiation. J Med Imaging Radiat Oncol 2020; 64:762-768. [PMID: 32743914 DOI: 10.1111/1754-9485.13082] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 06/18/2020] [Indexed: 11/27/2022]
Abstract
INTRODUCTION The aim of this study was to assess the qualitative and MRI findings of renal tumours, to determine which lesions contain microscopic fat, one of the potential differentiating factors between tumour types. METHODS 73 patients who underwent 3 Tesla MRI including chemical shift imaging, with subsequent biopsy or excision for histopathological diagnosis, were included in the study. The images were reviewed for a decrease in signal intensity (SI) on the opposed phase compared with the in-phase gradient echo T1 images, indicating the presence of microscopic fat. The chemical shift index was then calculated as a percentage of SI change and compared with the pathological diagnosis. RESULTS In total, 38 (52%) of lesions demonstrated a decrease in SI, consistent with microscopic fat. Microscopic fat was found in 28 (80%) clear cell renal cell carcinomas (RCCs), 6 (66.7%) angiomyolipomas, 2 (20%) papillary RCCs, 1 (20%) chromophobe RCC and 1 (9.1%) oncocytoma. Pairwise comparison of means indicated that the amount of microscopic fat was significantly larger only for angiomyolipomas compared with clear cell RCCs (P < 0.001) and other renal lesions (P < 0.001). CONCLUSIONS A decrease in SI on opposed phase compared with in-phase chemical shift imaging favours the diagnosis of either clear cell RCC or an angiomyolipoma. When combined with other parameters in mpMRI, this may aid differentiation of benign from malignant tumours and differentiation of aggressive from indolent RCC subtypes. This may be of value where biopsy is non-diagnostic, not feasible due to location or in high-risk patients.
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Affiliation(s)
- Suresh de Silva
- Faculty of Medicine, University of NSW, Sydney, New South Wales, Australia.,Department of Radiology, I-MED Radiology Network, Sydney, New South Wales, Australia
| | - Kathleen Lockhart
- Department of Urology, St George Hospital, Sydney, New South Wales, Australia
| | - Peter Aslan
- Department of Urology, St George Hospital, Sydney, New South Wales, Australia
| | - Peter Nash
- Department of Urology, St George Hospital, Sydney, New South Wales, Australia
| | - Anthony Hutton
- Faculty of Medicine, University of NSW, Sydney, New South Wales, Australia.,Department of Urology, St George Hospital, Sydney, New South Wales, Australia
| | - David Malouf
- Department of Urology, St George Hospital, Sydney, New South Wales, Australia
| | - Dominic Lee
- Department of Urology, St George Hospital, Sydney, New South Wales, Australia
| | - Paul Cozzi
- Faculty of Medicine, University of Notre Dame, Sydney, New South Wales, Australia
| | - Fiona Maclean
- Department of Anatomical Pathology, Sonic Healthcare, Sydney, New South Wales, Australia
| | - James Thompson
- Faculty of Medicine, University of NSW, Sydney, New South Wales, Australia.,Department of Urology, St George Hospital, Sydney, New South Wales, Australia
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22
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Hornigold N, Dunn KR, Craven RA, Zougman A, Trainor S, Shreeve R, Brown J, Sewell H, Shires M, Knowles M, Fukuwatari T, Maher ER, Burns J, Bhattarai S, Menon M, Brazma A, Scelo G, Feulner L, Riazalhosseini Y, Lathrop M, Harris A, Selby PJ, Banks RE, Vasudev NS. Dysregulation at multiple points of the kynurenine pathway is a ubiquitous feature of renal cancer: implications for tumour immune evasion. Br J Cancer 2020; 123:137-147. [PMID: 32390008 PMCID: PMC7341846 DOI: 10.1038/s41416-020-0874-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 04/15/2020] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Indoleamine 2,3-dioxygenase (IDO), the first step in the kynurenine pathway (KP), is upregulated in some cancers and represents an attractive therapeutic target given its role in tumour immune evasion. However, the recent failure of an IDO inhibitor in a late phase trial raises questions about this strategy. METHODS Matched renal cell carcinoma (RCC) and normal kidney tissues were subject to proteomic profiling. Tissue immunohistochemistry and gene expression data were used to validate findings. Phenotypic effects of loss/gain of expression were examined in vitro. RESULTS Quinolate phosphoribosyltransferase (QPRT), the final and rate-limiting enzyme in the KP, was identified as being downregulated in RCC. Loss of QPRT expression led to increased potential for anchorage-independent growth. Gene expression, mass spectrometry (clear cell and chromophobe RCC) and tissue immunohistochemistry (clear cell, papillary and chromophobe), confirmed loss or decreased expression of QPRT and showed downregulation of other KP enzymes, including kynurenine 3-monoxygenase (KMO) and 3-hydroxyanthranilate-3,4-dioxygenase (HAAO), with a concomitant maintenance or upregulation of nicotinamide phosphoribosyltransferase (NAMPT), the key enzyme in the NAD+ salvage pathway. CONCLUSIONS Widespread dysregulation of the KP is common in RCC and is likely to contribute to tumour immune evasion, carrying implications for effective therapeutic targeting of this critical pathway.
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Affiliation(s)
- Nick Hornigold
- Clinical and Biomedical Proteomics Group, University of Leeds, St. James's University Hospital, Beckett Street, Leeds, LS9 7TF, UK
| | - Karen R Dunn
- Clinical and Biomedical Proteomics Group, University of Leeds, St. James's University Hospital, Beckett Street, Leeds, LS9 7TF, UK
| | - Rachel A Craven
- Clinical and Biomedical Proteomics Group, University of Leeds, St. James's University Hospital, Beckett Street, Leeds, LS9 7TF, UK
| | - Alexandre Zougman
- Clinical and Biomedical Proteomics Group, University of Leeds, St. James's University Hospital, Beckett Street, Leeds, LS9 7TF, UK
- Leeds Institute of Medical Research at St James's, University of Leeds, St. James's University Hospital, Beckett Street, Leeds, LS9 7TF, UK
| | - Sebastian Trainor
- Clinical and Biomedical Proteomics Group, University of Leeds, St. James's University Hospital, Beckett Street, Leeds, LS9 7TF, UK
| | - Rebecca Shreeve
- Clinical and Biomedical Proteomics Group, University of Leeds, St. James's University Hospital, Beckett Street, Leeds, LS9 7TF, UK
| | - Joanne Brown
- Clinical and Biomedical Proteomics Group, University of Leeds, St. James's University Hospital, Beckett Street, Leeds, LS9 7TF, UK
- Leeds Institute of Medical Research at St James's, University of Leeds, St. James's University Hospital, Beckett Street, Leeds, LS9 7TF, UK
| | - Helen Sewell
- Clinical and Biomedical Proteomics Group, University of Leeds, St. James's University Hospital, Beckett Street, Leeds, LS9 7TF, UK
| | - Michael Shires
- Leeds Institute of Medical Research at St James's, University of Leeds, St. James's University Hospital, Beckett Street, Leeds, LS9 7TF, UK
| | - Margaret Knowles
- Molecular Genetics Group, University of Leeds, St. James's University Hospital, Beckett Street, Leeds, LS9 7TF, UK
| | - Tsutomu Fukuwatari
- Department of Nutrition, The University of Shiga Prefecture, 2500 Hassaka, Hikone, 5228533, Japan
| | - Eamonn R Maher
- Department of Medical Genetics, University of Cambridge and NIHR Cambridge Biomedical Research Centre, and Cancer Research UK Cambridge Centre, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, UK
| | - Julie Burns
- Molecular Genetics Group, University of Leeds, St. James's University Hospital, Beckett Street, Leeds, LS9 7TF, UK
| | - Selina Bhattarai
- Department of Pathology, St James's University Hospital, Beckett Street, Leeds, LS9 7TF, UK
| | - Mini Menon
- Department of Pathology, St James's University Hospital, Beckett Street, Leeds, LS9 7TF, UK
| | - Alvis Brazma
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, UK
| | - Ghislaine Scelo
- International Agency for Research on Cancer (IARC), Genetic Epidemiology Group, 150 cours Albert Thomas, 69372, Lyon, France
| | - Lara Feulner
- McGill University and Genome Quebec Innovation Centre, 740 Doctor Penfield Avenue, Montreal, QC, H3A 0G1, Canada
| | - Yasser Riazalhosseini
- McGill University and Genome Quebec Innovation Centre, 740 Doctor Penfield Avenue, Montreal, QC, H3A 0G1, Canada
| | - Mark Lathrop
- McGill University and Genome Quebec Innovation Centre, 740 Doctor Penfield Avenue, Montreal, QC, H3A 0G1, Canada
| | - Adrian Harris
- Cancer Research UK Clinical Centre, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Headington, Oxford, OX3 9DS, UK
| | - Peter J Selby
- Clinical and Biomedical Proteomics Group, University of Leeds, St. James's University Hospital, Beckett Street, Leeds, LS9 7TF, UK
| | - Rosamonde E Banks
- Clinical and Biomedical Proteomics Group, University of Leeds, St. James's University Hospital, Beckett Street, Leeds, LS9 7TF, UK
- Leeds Institute of Medical Research at St James's, University of Leeds, St. James's University Hospital, Beckett Street, Leeds, LS9 7TF, UK
| | - Naveen S Vasudev
- Clinical and Biomedical Proteomics Group, University of Leeds, St. James's University Hospital, Beckett Street, Leeds, LS9 7TF, UK.
- Leeds Institute of Medical Research at St James's, University of Leeds, St. James's University Hospital, Beckett Street, Leeds, LS9 7TF, UK.
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23
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Vijayalakshmi K, Shankar V, Bain RM, Nolley R, Sonn GA, Kao CS, Zhao H, Tibshirani R, Zare RN, Brooks JD. Identification of diagnostic metabolic signatures in clear cell renal cell carcinoma using mass spectrometry imaging. Int J Cancer 2020; 147:256-265. [PMID: 31863456 PMCID: PMC8571954 DOI: 10.1002/ijc.32843] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 11/14/2019] [Accepted: 12/09/2019] [Indexed: 12/31/2022]
Abstract
Clear cell renal cell carcinoma (ccRCC) is the most common and lethal subtype of kidney cancer. Intraoperative frozen section (IFS) analysis is used to confirm the diagnosis during partial nephrectomy. However, surgical margin evaluation using IFS analysis is time consuming and unreliable, leading to relatively low utilization. In our study, we demonstrated the use of desorption electrospray ionization mass spectrometry imaging (DESI-MSI) as a molecular diagnostic and prognostic tool for ccRCC. DESI-MSI was conducted on fresh-frozen 23 normal tumor paired nephrectomy specimens of ccRCC. An independent validation cohort of 17 normal tumor pairs was analyzed. DESI-MSI provides two-dimensional molecular images of tissues with mass spectra representing small metabolites, fatty acids and lipids. These tissues were subjected to histopathologic evaluation. A set of metabolites that distinguish ccRCC from normal kidney were identified by performing least absolute shrinkage and selection operator (Lasso) and log-ratio Lasso analysis. Lasso analysis with leave-one-patient-out cross-validation selected 57 peaks from over 27,000 metabolic features across 37,608 pixels obtained using DESI-MSI of ccRCC and normal tissues. Baseline Lasso of metabolites predicted the class of each tissue to be normal or cancerous tissue with an accuracy of 94 and 76%, respectively. Combining the baseline Lasso with the ratio of glucose to arachidonic acid could potentially reduce scan time and improve accuracy to identify normal (82%) and ccRCC (88%) tissue. DESI-MSI allows rapid detection of metabolites associated with normal and ccRCC with high accuracy. As this technology advances, it could be used for rapid intraoperative assessment of surgical margin status.
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Affiliation(s)
| | - Vishnu Shankar
- Department of Biomedical Data Science, and Statistics, Stanford University, Stanford, California 94305 USA
| | - Ryan M. Bain
- Department of Chemistry, Stanford University, Stanford, California 94305 USA
- Present address: Dow Chemical Co. Midland, Michigan 48674 USA
| | - Rosalie Nolley
- Department of Urology, Stanford University, Stanford, California 94305 USA
| | - Geoffrey A. Sonn
- Department of Urology, Stanford University, Stanford, California 94305 USA
| | - Chia-Sui Kao
- Department of Pathology, Stanford University, Stanford, California 94305 USA
| | - Hongjuan Zhao
- Department of Urology, Stanford University, Stanford, California 94305 USA
| | - Robert Tibshirani
- Department of Biomedical Data Science, and Statistics, Stanford University, Stanford, California 94305 USA
| | - Richard N. Zare
- Department of Chemistry, Stanford University, Stanford, California 94305 USA
| | - James D. Brooks
- Department of Urology, Stanford University, Stanford, California 94305 USA
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24
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Raimondo F, Pitto M. Prognostic significance of proteomics and multi-omics studies in renal carcinoma. Expert Rev Proteomics 2020; 17:323-334. [PMID: 32428425 DOI: 10.1080/14789450.2020.1772058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
INTRODUCTION Renal carcinoma, and in particular its most common variant, the clear cell subtype, is often diagnosed incidentally through abdominal imaging and frequently, the tumor is discovered at an early stage. However, 20% to 40% of patients undergoing nephrectomy for clinically localized renal cancer, even after accurate histological and clinical classification, will develop metastasis or recurrence, justifying the associated mortality rate. Therefore, even if renal carcinoma is not among the most frequent nor deadly cancers, a better prognostication is needed. AREAS COVERED Recently proteomics or other omics combinations have been applied to both cancer tissues, on the neoplasia itself and surrounding microenvironment, cultured cells, and biological fluids (so-called liquid biopsy) generating a list of prognostic molecular tools that will be reviewed in the present paper. EXPERT OPINION Although promising, none of the approaches listed above has been yet translated in clinics. This is likely due to the peculiar genetic and phenotypic heterogeneity of this cancer, which makes nearly each tumor different from all the others. Attempts to overcome this issue will be also revised. In particular, we will discuss how the application of omics-integrated approaches could provide the determinants of response to the different targeted drugs.
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Affiliation(s)
- Francesca Raimondo
- Clinical Proteomics and Metabolomics Unit, School of Medicine and Surgery, University of Milano - Bicocca , Vedano al Lambro, Italy
| | - Marina Pitto
- Clinical Proteomics and Metabolomics Unit, School of Medicine and Surgery, University of Milano - Bicocca , Vedano al Lambro, Italy
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25
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Zhang L, Henske EP. Chromophobe renal cell carcinoma: New genetic and metabolic insights. Urol Oncol 2020; 38:678-681. [PMID: 32444178 DOI: 10.1016/j.urolonc.2020.04.035] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 04/08/2020] [Accepted: 04/30/2020] [Indexed: 11/18/2022]
Abstract
Chromophobe renal cell carcinoma (chRCC) represents 5% of all RCC. ChRCC appears to arise from the distal nephron, in contrast to clear cell RCC that arises from the proximal nephron. ChRCC is distinctive because the tumor cells contain abundant abnormal mitochondria, and frequently have loss of one copy of multiple chromosomes, with a low rate of somatic mutations. Here, we focus on recent discoveries related to genetic and metabolic factors that may promote the progression of chRCC and summarize how these findings may relate to the prognosis and treatment of chRCC.
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Affiliation(s)
- Long Zhang
- Brigham and Women's Hospital, Boston, MA
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26
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Amaro F, Pinto J, Rocha S, Araújo AM, Miranda-Gonçalves V, Jerónimo C, Henrique R, Bastos MDL, Carvalho M, Guedes de Pinho P. Volatilomics Reveals Potential Biomarkers for Identification of Renal Cell Carcinoma: An In Vitro Approach. Metabolites 2020; 10:metabo10050174. [PMID: 32349455 PMCID: PMC7281256 DOI: 10.3390/metabo10050174] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 04/22/2020] [Accepted: 04/24/2020] [Indexed: 12/11/2022] Open
Abstract
The identification of noninvasive biomarkers able to detect renal cell carcinoma (RCC) at an early stage remains an unmet clinical need. The recognition that altered metabolism is a core hallmark of cancer boosted metabolomic studies focused in the search for cancer biomarkers. The present work aims to evaluate the performance of the volatile metabolites present in the extracellular medium to discriminate RCC cell lines with distinct histological subtypes (clear cell and papillary) and metastatic potential from non-tumorigenic renal cells. Hence, volatile organic compounds (VOCs) and volatile carbonyl compounds (VCCs) were extracted by headspace solid-phase microextraction (HS-SPME) and analyzed by gas chromatography-mass spectrometry (GC-MS). Multivariate and univariate analysis unveiled a panel of metabolites responsible for the separation between groups, mostly belonging to ketones, alcohols, alkanes and aldehydes classes. Some metabolites were found similarly altered for all RCC cell lines compared to non-tumorigenic cells, namely 2-ethylhexanol, tetradecane, formaldehyde, acetone (increased) and cyclohexanone and acetaldehyde (decreased). Furthermore, significantly altered levels of cyclohexanol, decanal, decane, dodecane and 4-methylbenzaldehyde were observed in all metastatic RCC cell lines when compared with the non-metastatic ones. Moreover, some alterations in the volatile composition were also observed between RCC histological subtypes. Overall, our results demonstrate the potential of volatile profiling for identification of noninvasive candidate biomarkers for early RCC diagnosis.
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Affiliation(s)
- Filipa Amaro
- UCIBIO, REQUIMTE, Laboratory of Toxicology, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal; (S.R.); (A.M.A.); (M.d.L.B.); (P.G.d.P.)
- Correspondence: (F.A.); (J.P.); (M.C.); Tel.: +351-220-428-500 (F.A. & J.P.); +351-225-071-300 (M.C.)
| | - Joana Pinto
- UCIBIO, REQUIMTE, Laboratory of Toxicology, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal; (S.R.); (A.M.A.); (M.d.L.B.); (P.G.d.P.)
- Correspondence: (F.A.); (J.P.); (M.C.); Tel.: +351-220-428-500 (F.A. & J.P.); +351-225-071-300 (M.C.)
| | - Sílvia Rocha
- UCIBIO, REQUIMTE, Laboratory of Toxicology, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal; (S.R.); (A.M.A.); (M.d.L.B.); (P.G.d.P.)
- Master in Oncology, Institute of Biomedical Sciences Abel Salazar–University of Porto (ICBAS-UP), 4050-313 Porto, Portugal
| | - Ana Margarida Araújo
- UCIBIO, REQUIMTE, Laboratory of Toxicology, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal; (S.R.); (A.M.A.); (M.d.L.B.); (P.G.d.P.)
| | - Vera Miranda-Gonçalves
- Cancer Biology & Epigenetics Group, Research Centre (CI-IPOP) Portuguese Oncology Institute of Porto (IPO Porto), 4200-072 Porto, Portugal; (V.M.-G.); (C.J.); (R.H.)
| | - Carmen Jerónimo
- Cancer Biology & Epigenetics Group, Research Centre (CI-IPOP) Portuguese Oncology Institute of Porto (IPO Porto), 4200-072 Porto, Portugal; (V.M.-G.); (C.J.); (R.H.)
- Department of Pathology and Molecular Immunology-Biomedical Sciences Institute (ICBAS), University of Porto, 4050-313 Porto, Portugal
| | - Rui Henrique
- Cancer Biology & Epigenetics Group, Research Centre (CI-IPOP) Portuguese Oncology Institute of Porto (IPO Porto), 4200-072 Porto, Portugal; (V.M.-G.); (C.J.); (R.H.)
- Department of Pathology and Molecular Immunology-Biomedical Sciences Institute (ICBAS), University of Porto, 4050-313 Porto, Portugal
- Department of Pathology, Portuguese Oncology Institute of Porto (IPO Porto), 4200-072 Porto, Portugal
| | - Maria de Lourdes Bastos
- UCIBIO, REQUIMTE, Laboratory of Toxicology, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal; (S.R.); (A.M.A.); (M.d.L.B.); (P.G.d.P.)
| | - Márcia Carvalho
- UCIBIO, REQUIMTE, Laboratory of Toxicology, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal; (S.R.); (A.M.A.); (M.d.L.B.); (P.G.d.P.)
- UFP Energy, Environment and Health Research Unit (FP-ENAS), University Fernando Pessoa, 349, 4249-004 Porto, Portugal
- Correspondence: (F.A.); (J.P.); (M.C.); Tel.: +351-220-428-500 (F.A. & J.P.); +351-225-071-300 (M.C.)
| | - Paula Guedes de Pinho
- UCIBIO, REQUIMTE, Laboratory of Toxicology, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal; (S.R.); (A.M.A.); (M.d.L.B.); (P.G.d.P.)
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27
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Reustle A, Di Marco M, Meyerhoff C, Nelde A, Walz JS, Winter S, Kandabarau S, Büttner F, Haag M, Backert L, Kowalewski DJ, Rausch S, Hennenlotter J, Stühler V, Scharpf M, Fend F, Stenzl A, Rammensee HG, Bedke J, Stevanović S, Schwab M, Schaeffeler E. Integrative -omics and HLA-ligandomics analysis to identify novel drug targets for ccRCC immunotherapy. Genome Med 2020; 12:32. [PMID: 32228647 PMCID: PMC7106651 DOI: 10.1186/s13073-020-00731-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 03/12/2020] [Indexed: 12/24/2022] Open
Abstract
Background Clear cell renal cell carcinoma (ccRCC) is the dominant subtype of renal cancer. With currently available therapies, cure of advanced and metastatic ccRCC is achieved only in rare cases. Here, we developed a workflow integrating different -omics technologies to identify ccRCC-specific HLA-presented peptides as potential drug targets for ccRCC immunotherapy. Methods We analyzed HLA-presented peptides by MS-based ligandomics of 55 ccRCC tumors (cohort 1), paired non-tumor renal tissues, and 158 benign tissues from other organs. Pathways enriched in ccRCC compared to its cell type of origin were identified by transcriptome and gene set enrichment analyses in 51 tumor tissues of the same cohort. To retrieve a list of candidate targets with involvement in ccRCC pathogenesis, ccRCC-specific pathway genes were intersected with the source genes of tumor-exclusive peptides. The candidates were validated in an independent cohort from The Cancer Genome Atlas (TCGA KIRC, n = 452). DNA methylation (TCGA KIRC, n = 273), somatic mutations (TCGA KIRC, n = 392), and gene ontology (GO) and correlations with tumor metabolites (cohort 1, n = 30) and immune-oncological markers (cohort 1, n = 37) were analyzed to characterize regulatory and functional involvements. CD8+ T cell priming assays were used to identify immunogenic peptides. The candidate gene EGLN3 was functionally investigated in cell culture. Results A total of 34,226 HLA class I- and 19,325 class II-presented peptides were identified in ccRCC tissue, of which 443 class I and 203 class II peptides were ccRCC-specific and presented in ≥ 3 tumors. One hundred eighty-five of the 499 corresponding source genes were involved in pathways activated by ccRCC tumors. After validation in the independent cohort from TCGA, 113 final candidate genes remained. Candidates were involved in extracellular matrix organization, hypoxic signaling, immune processes, and others. Nine of the 12 peptides assessed by immunogenicity analysis were able to activate naïve CD8+ T cells, including peptides derived from EGLN3. Functional analysis of EGLN3 revealed possible tumor-promoting functions. Conclusions Integration of HLA ligandomics, transcriptomics, genetic, and epigenetic data leads to the identification of novel functionally relevant therapeutic targets for ccRCC immunotherapy. Validation of the identified targets is recommended to expand the treatment landscape of ccRCC.
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Affiliation(s)
- Anna Reustle
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany.,University of Tuebingen, Tuebingen, Germany
| | - Moreno Di Marco
- Department of Immunology, Institute for Cell Biology, University of Tuebingen, Tuebingen, Germany
| | - Carolin Meyerhoff
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany.,University of Tuebingen, Tuebingen, Germany
| | - Annika Nelde
- Department of Immunology, Institute for Cell Biology, University of Tuebingen, Tuebingen, Germany.,Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), University Hospital Tuebingen, Tuebingen, Germany.,German Cancer Consortium (DKTK), Partner Site Tuebingen, Tuebingen, Germany
| | - Juliane S Walz
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), University Hospital Tuebingen, Tuebingen, Germany.,German Cancer Consortium (DKTK), Partner Site Tuebingen, Tuebingen, Germany.,iFIT Cluster of Excellence (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tuebingen, Tuebingen, Germany
| | - Stefan Winter
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany.,University of Tuebingen, Tuebingen, Germany
| | - Siahei Kandabarau
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany.,University of Tuebingen, Tuebingen, Germany
| | - Florian Büttner
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany.,University of Tuebingen, Tuebingen, Germany
| | - Mathias Haag
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany.,University of Tuebingen, Tuebingen, Germany
| | - Linus Backert
- Department of Immunology, Institute for Cell Biology, University of Tuebingen, Tuebingen, Germany
| | - Daniel J Kowalewski
- Department of Immunology, Institute for Cell Biology, University of Tuebingen, Tuebingen, Germany
| | - Steffen Rausch
- Department of Urology, University Hospital Tuebingen, Tuebingen, Germany
| | - Jörg Hennenlotter
- Department of Urology, University Hospital Tuebingen, Tuebingen, Germany
| | - Viktoria Stühler
- Department of Urology, University Hospital Tuebingen, Tuebingen, Germany
| | - Marcus Scharpf
- Institute of Pathology and Neuropathology, University Hospital Tuebingen, Tuebingen, Germany
| | - Falko Fend
- Institute of Pathology and Neuropathology, University Hospital Tuebingen, Tuebingen, Germany
| | - Arnulf Stenzl
- Department of Urology, University Hospital Tuebingen, Tuebingen, Germany
| | - Hans-Georg Rammensee
- Department of Immunology, Institute for Cell Biology, University of Tuebingen, Tuebingen, Germany.,German Cancer Consortium (DKTK), Partner Site Tuebingen, Tuebingen, Germany.,iFIT Cluster of Excellence (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tuebingen, Tuebingen, Germany
| | - Jens Bedke
- Department of Urology, University Hospital Tuebingen, Tuebingen, Germany
| | - Stefan Stevanović
- Department of Immunology, Institute for Cell Biology, University of Tuebingen, Tuebingen, Germany.,German Cancer Consortium (DKTK), Partner Site Tuebingen, Tuebingen, Germany.,iFIT Cluster of Excellence (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tuebingen, Tuebingen, Germany
| | - Matthias Schwab
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany. .,University of Tuebingen, Tuebingen, Germany. .,German Cancer Consortium (DKTK), Partner Site Tuebingen, Tuebingen, Germany. .,iFIT Cluster of Excellence (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tuebingen, Tuebingen, Germany. .,Departments of Clinical Pharmacology, Pharmacy and Biochemistry, University of Tuebingen, Tuebingen, Germany.
| | - Elke Schaeffeler
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany.,University of Tuebingen, Tuebingen, Germany.,iFIT Cluster of Excellence (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tuebingen, Tuebingen, Germany
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28
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Jing L, Guigonis JM, Borchiellini D, Durand M, Pourcher T, Ambrosetti D. LC-MS based metabolomic profiling for renal cell carcinoma histologic subtypes. Sci Rep 2019; 9:15635. [PMID: 31666664 PMCID: PMC6821699 DOI: 10.1038/s41598-019-52059-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 09/25/2019] [Indexed: 12/20/2022] Open
Abstract
Renal cell carcinomas (RCC) are classified according to their histological features. Accurate classification of RCC and comprehensive understanding of their metabolic dysregulation are of critical importance. Here we investigate the use of metabolomic analyses to classify the main RCC subtypes and to describe the metabolic variation for each subtype. To this end, we performed metabolomic profiling of 65 RCC frozen samples (40 clear cell, 14 papillary and 11 chromophobe) using liquid chromatography-mass spectrometry. OPLS-DA multivariate analysis based on metabolomic data showed clear discrimination of all three main subtypes of RCC (R2 = 75.0%, Q2 = 59.7%). The prognostic performance was evaluated using an independent cohort and showed an AUROC of 0.924, 0.991 and 1 for clear cell, papillary and chromophobe RCC, respectively. Further pathway analysis using the 21 top metabolites showed significant differences in amino acid and fatty acid metabolism between three RCC subtypes. In conclusion, this study shows that metabolomic profiling could serve as a tool that is complementary to histology for RCC subtype classification. An overview of metabolic dysregulation in RCC subtypes was established giving new insights into the understanding of their clinical behaviour and for the development of targeted therapeutic strategies.
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Affiliation(s)
- Lun Jing
- Laboratory Transporter in Imaging and Radiotherapy in Oncology (TIRO), Institut de biosciences et biotechnologies d'Aix-Marseille (BIAM), Commissariat à lEnergie Atomique, Nice, France.,Laboratory Transporter in Imaging and Radiotherapy in Oncology (TIRO), school of medicine, Université Nice Sophia Antipolis, Université Côte d'Azur, Nice, France
| | - Jean-Marie Guigonis
- Laboratory Transporter in Imaging and Radiotherapy in Oncology (TIRO), Institut de biosciences et biotechnologies d'Aix-Marseille (BIAM), Commissariat à lEnergie Atomique, Nice, France.,Laboratory Transporter in Imaging and Radiotherapy in Oncology (TIRO), school of medicine, Université Nice Sophia Antipolis, Université Côte d'Azur, Nice, France
| | | | - Matthieu Durand
- Urology Department, Centre Hospitalier Universitaire, Nice, France
| | - Thierry Pourcher
- Laboratory Transporter in Imaging and Radiotherapy in Oncology (TIRO), Institut de biosciences et biotechnologies d'Aix-Marseille (BIAM), Commissariat à lEnergie Atomique, Nice, France. .,Laboratory Transporter in Imaging and Radiotherapy in Oncology (TIRO), school of medicine, Université Nice Sophia Antipolis, Université Côte d'Azur, Nice, France.
| | - Damien Ambrosetti
- Central Laboratory of Anatomopathology, Centre Hospitalier Universitaire, Nice, France
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Manzi M, Riquelme G, Zabalegui N, Monge ME. Improving diagnosis of genitourinary cancers: Biomarker discovery strategies through mass spectrometry-based metabolomics. J Pharm Biomed Anal 2019; 178:112905. [PMID: 31707200 DOI: 10.1016/j.jpba.2019.112905] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2019] [Revised: 09/27/2019] [Accepted: 10/01/2019] [Indexed: 12/24/2022]
Abstract
The genitourinary oncology field needs integration of results from basic science, epidemiological studies, clinical and translational research to improve the current methods for diagnosis. MS-based metabolomics can be transformative for disease diagnosis and contribute to global health parity. Metabolite panels are promising to translate metabolomic findings into the clinics, changing the current diagnosis paradigm based on single biomarker analysis. This review article describes capabilities of the MS-based oncometabolomics field for improving kidney, prostate, and bladder cancer detection, early diagnosis, risk stratification, and outcome. Published works are critically discussed based on the study design; type and number of samples analyzed; data quality assessment through quality assurance and quality control practices; data analysis workflows; confidence levels reported for identified metabolites; validation attempts; the overlap of discriminant metabolites for the different genitourinary cancers; and the translation capability of findings into clinical settings. Ongoing challenges are discussed, and future directions are delineated.
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Affiliation(s)
- Malena Manzi
- Centro de Investigaciones en Bionanociencias (CIBION), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2390, C1425FQD, Ciudad de Buenos Aires, Argentina; Departamento de Química Biológica, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Junín 956, C1113AAD, Ciudad de Buenos Aires, Argentina
| | - Gabriel Riquelme
- Centro de Investigaciones en Bionanociencias (CIBION), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2390, C1425FQD, Ciudad de Buenos Aires, Argentina; Departamento de Química Inorgánica, Analítica y Química Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, C1428EGA, Buenos Aires, Argentina
| | - Nicolás Zabalegui
- Centro de Investigaciones en Bionanociencias (CIBION), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2390, C1425FQD, Ciudad de Buenos Aires, Argentina; Departamento de Química Inorgánica, Analítica y Química Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, C1428EGA, Buenos Aires, Argentina
| | - María Eugenia Monge
- Centro de Investigaciones en Bionanociencias (CIBION), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2390, C1425FQD, Ciudad de Buenos Aires, Argentina.
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30
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Al Ahmad A, Paffrath V, Clima R, Busch JF, Rabien A, Kilic E, Villegas S, Timmermann B, Attimonelli M, Jung K, Meierhofer D. Papillary Renal Cell Carcinomas Rewire Glutathione Metabolism and Are Deficient in Both Anabolic Glucose Synthesis and Oxidative Phosphorylation. Cancers (Basel) 2019; 11:cancers11091298. [PMID: 31484429 PMCID: PMC6770591 DOI: 10.3390/cancers11091298] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 08/29/2019] [Accepted: 08/30/2019] [Indexed: 12/12/2022] Open
Abstract
Papillary renal cell carcinoma (pRCC) is a malignant kidney cancer with a prevalence of 7–20% of all renal tumors. Proteome and metabolome profiles of 19 pRCC and patient-matched healthy kidney controls were used to elucidate the regulation of metabolic pathways and the underlying molecular mechanisms. Glutathione (GSH), a main reactive oxygen species (ROS) scavenger, was highly increased and can be regarded as a new hallmark in this malignancy. Isotope tracing of pRCC derived cell lines revealed an increased de novo synthesis rate of GSH, based on glutamine consumption. Furthermore, profound downregulation of gluconeogenesis and oxidative phosphorylation was observed at the protein level. In contrast, analysis of the The Cancer Genome Atlas (TCGA) papillary RCC cohort revealed no significant change in transcripts encoding oxidative phosphorylation compared to normal kidney tissue, highlighting the importance of proteomic profiling. The molecular characteristics of pRCC are increased GSH synthesis to cope with ROS stress, deficient anabolic glucose synthesis, and compromised oxidative phosphorylation, which could potentially be exploited in innovative anti-cancer strategies.
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Affiliation(s)
- Ayham Al Ahmad
- Max Planck Institute for Molecular Genetics, Mass Spectrometry Facility, Ihnestrasse 63-73, 14195 Berlin, Germany.
- Fachbereich Biologie, Chemie, Pharmazie, Freie Universität Berlin, Takustraße 3, 14195 Berlin, Germany.
- Berlin Institute for Urologic Research, Charitéplatz 1, 10117 Berlin, Germany.
| | - Vanessa Paffrath
- Max Planck Institute for Molecular Genetics, Mass Spectrometry Facility, Ihnestrasse 63-73, 14195 Berlin, Germany.
- Berlin Institute for Urologic Research, Charitéplatz 1, 10117 Berlin, Germany.
| | - Rosanna Clima
- Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari, Via E.Orabona, 470126 Bari, Italy.
- Department of Medical and Surgical Sciences-DIMEC, Medical Genetics Unit, University of Bologna, 40126 Bologna, Italy.
| | - Jonas Felix Busch
- Department of Urology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117 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, 10117 Berlin, Germany.
| | - Ergin Kilic
- Institut für Pathologie am Klinikum Leverkusen, Am Gesundheitspark 11, 51375 Leverkusen, Germany.
- Institute of Pathology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117 Berlin, Germany.
| | - Sonia Villegas
- Institute of Pathology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117 Berlin, Germany.
| | - Bernd Timmermann
- Max Planck Institute for Molecular Genetics, Sequencing Core Facility, Ihnestrasse 63-73, 14195 Berlin, Germany.
| | - Marcella Attimonelli
- Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari, Via E.Orabona, 470126 Bari, Italy.
| | - Klaus Jung
- Berlin Institute for Urologic Research, Charitéplatz 1, 10117 Berlin, Germany.
- Department of Urology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117 Berlin, Germany.
| | - David Meierhofer
- Max Planck Institute for Molecular Genetics, Mass Spectrometry Facility, Ihnestrasse 63-73, 14195 Berlin, Germany.
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Rathmell WK, Rathmell JC, Linehan WM. Metabolic Pathways in Kidney Cancer: Current Therapies and Future Directions. J Clin Oncol 2018; 36:JCO2018792309. [PMID: 30372395 PMCID: PMC6488445 DOI: 10.1200/jco.2018.79.2309] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Renal cell carcinoma (RCC) has become known as a metabolic disease, owing to the diverse array of metabolic defects and perturbations that occur as a result of the unique genetics that can drive these tumors. Recent attention to this feature of RCCs has fueled interest in targeting metabolism as a therapeutic strategy. METHODS We conducted a literature search to develop themes around discrete pathways or processes of cellular metabolism, provide a framework for understanding emerging therapeutic strategies, and consider future interventions. RESULTS Defects occur in metabolic pathways ranging from glycolysis to mitochondrial function and affect not only the tumor cell functionality, but also the local environment. We identified opportunities for therapeutic intervention associated with each pathway. CONCLUSION The metabolism of RCC cells presents a special environment of tumor susceptibilities, with opportunities for novel imaging applications and treatment paradigms that are being tested in monotherapy or as adjuncts to targeted or immune-based strategies.
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Affiliation(s)
- W. Kimryn Rathmell
- Vanderbilt-Ingram Cancer Center, 691 Preston Building, Nashville, TN 37232, USA
- Department of Medicine, Division of Hematology and Oncology, Vanderbilt University Medical Center, 1211 Medical Center Drive, Nashville, TN 37232, USA
| | - Jeffrey C. Rathmell
- Vanderbilt-Ingram Cancer Center, 691 Preston Building, Nashville, TN 37232, USA
- Department of Pathology, Microbiology, and Immunology; Vanderbilt Center for Immunobiology, Vanderbilt University Medical Center, 1211 Medical Center Drive, Nashville, TN 37232, USA
| | - W. Marston Linehan
- Urologic Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
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32
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Taddeo EP, Stiles L, Sereda S, Ritou E, Wolf DM, Abdullah M, Swanson Z, Wilhelm J, Bellin M, McDonald P, Caradonna K, Neilson A, Liesa M, Shirihai OS. Individual islet respirometry reveals functional diversity within the islet population of mice and human donors. Mol Metab 2018; 16:150-159. [PMID: 30098928 PMCID: PMC6157638 DOI: 10.1016/j.molmet.2018.07.003] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 06/25/2018] [Accepted: 07/01/2018] [Indexed: 11/25/2022] Open
Abstract
OBJECTIVE Islets from the same pancreas show remarkable variability in glucose sensitivity. While mitochondrial respiration is essential for glucose-stimulated insulin secretion, little is known regarding heterogeneity in mitochondrial function at the individual islet level. This is due in part to a lack of high-throughput and non-invasive methods for detecting single islet function. METHODS We have developed a novel non-invasive, high-throughput methodology capable of assessing mitochondrial respiration in large-sized individual islets using the XF96 analyzer (Agilent Technologies). RESULTS By increasing measurement sensitivity, we have reduced the minimal size of mouse and human islets needed to assess mitochondrial respiration to single large islets of >35,000 μm2 area (∼210 μm diameter). In addition, we have measured heterogeneous glucose-stimulated mitochondrial respiration among individual human and mouse islets from the same pancreas, allowing population analyses of islet mitochondrial function for the first time. CONCLUSIONS We have developed a novel methodology capable of analyzing mitochondrial function in large-sized individual islets. By highlighting islet functional heterogeneity, we hope this methodology can significantly advance islet research.
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Affiliation(s)
- Evan P Taddeo
- Department of Medicine, Division of Endocrinology, Diabetes and Hypertension, and Department of Molecular and Medical Pharmacology, David Geffen School of Medicine at UCLA, Center for Health Sciences, 650 Charles E. Young St., Los Angeles, CA 90095, USA
| | - Linsey Stiles
- Department of Medicine, Division of Endocrinology, Diabetes and Hypertension, and Department of Molecular and Medical Pharmacology, David Geffen School of Medicine at UCLA, Center for Health Sciences, 650 Charles E. Young St., Los Angeles, CA 90095, USA
| | - Samuel Sereda
- Department of Medicine, Endocrinology, Diabetes, Nutrition and Weight Management Section, Boston University School of Medicine, 650 Albany St., Room 840, Boston, MA 02118, USA
| | - Eleni Ritou
- Department of Medicine, Division of Endocrinology, Diabetes and Hypertension, and Department of Molecular and Medical Pharmacology, David Geffen School of Medicine at UCLA, Center for Health Sciences, 650 Charles E. Young St., Los Angeles, CA 90095, USA
| | - Dane M Wolf
- Department of Medicine, Division of Endocrinology, Diabetes and Hypertension, and Department of Molecular and Medical Pharmacology, David Geffen School of Medicine at UCLA, Center for Health Sciences, 650 Charles E. Young St., Los Angeles, CA 90095, USA
| | - Muhamad Abdullah
- Department of Surgery and Schulze Diabetes Institute, University of Minnesota School of Medicine, Minneapolis, MN 55455, USA
| | - Zachary Swanson
- Department of Surgery and Schulze Diabetes Institute, University of Minnesota School of Medicine, Minneapolis, MN 55455, USA
| | - Josh Wilhelm
- Department of Surgery and Schulze Diabetes Institute, University of Minnesota School of Medicine, Minneapolis, MN 55455, USA
| | - Melena Bellin
- Department of Pediatrics, Division of Pediatric Endocrinology, University of Minnesota School of Medicine, Minneapolis, MN 55455, USA
| | - Patrick McDonald
- Center for Health Research Innovation, University of Alberta, Edmonton, AB T6G 2E1, Canada
| | | | | | - Marc Liesa
- Department of Medicine, Division of Endocrinology, Diabetes and Hypertension, and Department of Molecular and Medical Pharmacology, David Geffen School of Medicine at UCLA, Center for Health Sciences, 650 Charles E. Young St., Los Angeles, CA 90095, USA.
| | - Orian S Shirihai
- Department of Medicine, Division of Endocrinology, Diabetes and Hypertension, and Department of Molecular and Medical Pharmacology, David Geffen School of Medicine at UCLA, Center for Health Sciences, 650 Charles E. Young St., Los Angeles, CA 90095, USA; Department of Medicine, Endocrinology, Diabetes, Nutrition and Weight Management Section, Boston University School of Medicine, 650 Albany St., Room 840, Boston, MA 02118, USA.
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Leuthold P, Schwab M, Hofmann U, Winter S, Rausch S, Pollak MN, Hennenlotter J, Bedke J, Schaeffeler E, Haag M. Simultaneous Extraction of RNA and Metabolites from Single Kidney Tissue Specimens for Combined Transcriptomic and Metabolomic Profiling. J Proteome Res 2018; 17:3039-3049. [PMID: 30091608 DOI: 10.1021/acs.jproteome.8b00199] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Tissue analysis represents a powerful tool for the investigation of disease pathophysiology. However, the heterogeneous nature of tissue samples, in particular of neoplastic, may affect the outcome of such analysis and hence obscure interpretation of results. Thus, comprehensive isolation and extraction of transcripts and metabolites from an identical tissue specimen would minimize variations and enable the economic use of biopsy material which is usually available in limited amounts. Here we demonstrate a fast and simple protocol for combined transcriptomics and metabolomics analysis in homogenates prepared from one single tissue sample. Metabolites were recovered by protein precipitation from lysates originally prepared for RNA isolation and were analyzed by LC-QTOF-MS after HILIC and RPLC separation, respectively. Strikingly, although ion suppression was observed, over 80% of the 2885 detected metabolic features could be extracted and analyzed with high reproducibility (CV ≤ 20%). Moreover fold changes of different tumor and nontumor kidney tissues were correlated to an established metabolomics protocol and revealed a strong correlation ( rp ≥ 0.75). In order to demonstrate the feasibility of the combined analysis of RNA and metabolites, the protocol was applied to kidney tissue of metformin treated mice to investigate drug induced alterations.
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Affiliation(s)
- Patrick Leuthold
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology , Stuttgart , Germany and University of Tübingen, Tübingen, Germany
| | - Matthias Schwab
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology , Stuttgart , Germany and University of Tübingen, Tübingen, Germany.,Department of Clinical Pharmacology , University Hospital Tübingen , Tübingen , Germany.,Department of Pharmacy and Biochemistry , University of Tübingen , Tübingen , Germany
| | - Ute Hofmann
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology , Stuttgart , Germany and University of Tübingen, Tübingen, Germany
| | - Stefan Winter
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology , Stuttgart , Germany and University of Tübingen, Tübingen, Germany
| | - Steffen Rausch
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology , Stuttgart , Germany and University of Tübingen, Tübingen, Germany.,Department of Urology , University Hospital Tübingen , Tübingen , Germany
| | | | - Jörg Hennenlotter
- Department of Urology , University Hospital Tübingen , Tübingen , Germany
| | - Jens Bedke
- Department of Urology , University Hospital Tübingen , Tübingen , Germany
| | - Elke Schaeffeler
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology , Stuttgart , Germany and University of Tübingen, Tübingen, Germany
| | - Mathias Haag
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology , Stuttgart , Germany and University of Tübingen, Tübingen, Germany
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