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Hamed MA, Wasinger V, Wang Q, Graham P, Malouf D, Bucci J, Li Y. Prostate cancer-derived extracellular vesicles metabolic biomarkers: Emerging roles for diagnosis and prognosis. J Control Release 2024; 371:126-145. [PMID: 38768661 DOI: 10.1016/j.jconrel.2024.05.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 04/23/2024] [Accepted: 05/17/2024] [Indexed: 05/22/2024]
Abstract
Prostate cancer (PCa) is a global health concern, ranking as the most common cancer among men in Western countries. Traditional diagnostic methods are invasive with adverse effects on patients. Due to the heterogeneous nature of PCa and their multifocality, tissue biopsies often yield false-negative results. To address these challenges, researchers are exploring innovative approaches, particularly in the realms of proteomics and metabolomics, to identify more reliable biomarkers and improve PCa diagnosis. Liquid biopsy (LB) has emerged as a promising non-invasive strategy for PCa early detection, biopsy selection, active surveillance for low-risk cases, and post-treatment and progression monitoring. Extracellular vesicles (EVs) are lipid-bilayer nanovesicles released by all cell types and play an important role in intercellular communication. EVs have garnered attention as a valuable biomarker resource in LB for PCa-specific biomarkers, enhancing diagnosis, prognostication, and treatment guidance. Metabolomics provides insight into the body's metabolic response to both internal and external stimuli, offering quantitative measurements of biochemical alterations. It excels at detecting non-genetic influences, aiding in the discovery of more accurate cancer biomarkers for early detection and disease progression monitoring. This review delves into the potential of EVs as a resource for LB in PCa across various clinical applications. It also explores cancer-related metabolic biomarkers, both within and outside EVs in PCa, and summarises previous metabolomic findings in PCa diagnosis and risk assessment. Finally, the article addresses the challenges and future directions in the evolving field of EV-based metabolomic analysis, offering a comprehensive overview of its potential in advancing PCa management.
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Affiliation(s)
- Mahmoud Assem Hamed
- St George and Sutherland Clinical Campuses, School of Clinical Medicine, UNSW Sydney, Kensington, NSW 2052, Australia; Cancer Care Centre, St George Hospital, Kogarah, NSW 2217, Australia
| | - Valerie Wasinger
- Bioanalytical Mass Spectrometry Facility, Mark Wainwright Analytical Centre, UNSW Sydney, Kensington, NSW 2052, Australia
| | - Qi Wang
- St George and Sutherland Clinical Campuses, School of Clinical Medicine, UNSW Sydney, Kensington, NSW 2052, Australia; Cancer Care Centre, St George Hospital, Kogarah, NSW 2217, Australia
| | - Peter Graham
- St George and Sutherland Clinical Campuses, School of Clinical Medicine, UNSW Sydney, Kensington, NSW 2052, Australia; Cancer Care Centre, St George Hospital, Kogarah, NSW 2217, Australia
| | - David Malouf
- Department of Urology, St, George Hospital, Kogarah, NSW 2217, Australia
| | - Joseph Bucci
- St George and Sutherland Clinical Campuses, School of Clinical Medicine, UNSW Sydney, Kensington, NSW 2052, Australia; Cancer Care Centre, St George Hospital, Kogarah, NSW 2217, Australia
| | - Yong Li
- St George and Sutherland Clinical Campuses, School of Clinical Medicine, UNSW Sydney, Kensington, NSW 2052, Australia; Cancer Care Centre, St George Hospital, Kogarah, NSW 2217, Australia.
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Hamed MA, Wasinger V, Wang Q, Biazik J, Graham P, Malouf D, Bucci J, Li Y. Optimising Extracellular Vesicle Metabolomic Methodology for Prostate Cancer Biomarker Discovery. Metabolites 2024; 14:367. [PMID: 39057690 PMCID: PMC11279087 DOI: 10.3390/metabo14070367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2024] [Revised: 06/21/2024] [Accepted: 06/26/2024] [Indexed: 07/28/2024] Open
Abstract
Conventional diagnostic tools for prostate cancer (PCa), such as prostate-specific antigen (PSA), transrectal ultrasound (TRUS), digital rectal examination (DRE), and tissue biopsy face, limitations in individual risk stratification due to invasiveness or reliability issues. Liquid biopsy is a less invasive and more accurate alternative. Metabolomic analysis of extracellular vesicles (EVs) holds a promise for detecting non-genetic alterations and biomarkers in PCa diagnosis and risk assessment. The current research gap in PCa lies in the lack of accurate biomarkers for early diagnosis and real-time monitoring of cancer progression or metastasis. Establishing a suitable approach for observing dynamic EV metabolic alterations that often occur earlier than being detectable by other omics technologies makes metabolomics valuable for early diagnosis and monitoring of PCa. Using four distinct metabolite extraction approaches, the metabolite cargo of PC3-derived large extracellular vesicles (lEVs) was evaluated using a combination of methanol, cell shearing using microbeads, and size exclusion filtration, as well as two fractionation chemistries (pHILIC and C18 chromatography) that are also examined. The unfiltered methanol-microbeads approach (MB-UF), followed by pHILIC LC-MS/MS for EV metabolite extraction and analysis, is effective. Identified metabolites such as L-glutamic acid, pyruvic acid, lactic acid, and methylmalonic acid have important links to PCa and are discussed. Our study, for the first time, has comprehensively evaluated the extraction and separation methods with a view to downstream sample integrity across omics platforms, and it presents an optimised protocol for EV metabolomics in PCa biomarker discovery.
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Affiliation(s)
- Mahmoud Assem Hamed
- St. George and Sutherland Clinical Campuses, School of Clinical Medicine, University of New South Wales (UNSW) Sydney, Kensington, NSW 2052, Australia; (M.A.H.); (Q.W.); (P.G.); (J.B.)
- Cancer Care Centre, St. George Hospital, Kogarah, NSW 2217, Australia
| | - Valerie Wasinger
- Bioanalytical Mass Spectrometry Facility, Mark Wainwright Analytical Centre, University of New South Wales (UNSW) Sydney, Kensington, NSW 2052, Australia;
| | - Qi Wang
- St. George and Sutherland Clinical Campuses, School of Clinical Medicine, University of New South Wales (UNSW) Sydney, Kensington, NSW 2052, Australia; (M.A.H.); (Q.W.); (P.G.); (J.B.)
- Cancer Care Centre, St. George Hospital, Kogarah, NSW 2217, Australia
| | - Joanna Biazik
- Electron Microscope Unit, Mark Wainwright Analytical Centre, University of New South Wales (UNSW) Sydney, Kensington, NSW 2052, Australia;
| | - Peter Graham
- St. George and Sutherland Clinical Campuses, School of Clinical Medicine, University of New South Wales (UNSW) Sydney, Kensington, NSW 2052, Australia; (M.A.H.); (Q.W.); (P.G.); (J.B.)
- Cancer Care Centre, St. George Hospital, Kogarah, NSW 2217, Australia
| | - David Malouf
- Department of Urology, St. George Hospital, Kogarah, NSW 2217, Australia;
| | - Joseph Bucci
- St. George and Sutherland Clinical Campuses, School of Clinical Medicine, University of New South Wales (UNSW) Sydney, Kensington, NSW 2052, Australia; (M.A.H.); (Q.W.); (P.G.); (J.B.)
- Cancer Care Centre, St. George Hospital, Kogarah, NSW 2217, Australia
| | - Yong Li
- St. George and Sutherland Clinical Campuses, School of Clinical Medicine, University of New South Wales (UNSW) Sydney, Kensington, NSW 2052, Australia; (M.A.H.); (Q.W.); (P.G.); (J.B.)
- Cancer Care Centre, St. George Hospital, Kogarah, NSW 2217, Australia
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Dong X, Qu Y, Sheng T, Fan Y, Chen S, Yuan Q, Ma G, Ge Y. HCMMD: systematic evaluation of metabolites in body fluids as liquid biopsy biomarker for human cancers. Aging (Albany NY) 2024; 16:7487-7504. [PMID: 38683118 PMCID: PMC11087094 DOI: 10.18632/aging.205779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 01/03/2024] [Indexed: 05/01/2024]
Abstract
Metabolomics is a rapidly expanding field in systems biology used to measure alterations of metabolites and identify metabolic biomarkers in response to disease processes. The discovery of metabolic biomarkers can improve early diagnosis, prognostic prediction, and therapeutic intervention for cancers. However, there are currently no databases that provide a comprehensive evaluation of the relationship between metabolites and cancer processes. In this review, we summarize reported metabolites in body fluids across pan-cancers and characterize their clinical applications in liquid biopsy. We conducted a search for metabolic biomarkers using the keywords ("metabolomics" OR "metabolite") AND "cancer" in PubMed. Of the 22,254 articles retrieved, 792 were deemed potentially relevant for further review. Ultimately, we included data from 573,300 samples and 17,083 metabolic biomarkers. We collected information on cancer types, sample size, the human metabolome database (HMDB) ID, metabolic pathway, area under the curve (AUC), sensitivity and specificity of metabolites, sample source, detection method, and clinical features were collected. Finally, we developed a user-friendly online database, the Human Cancer Metabolic Markers Database (HCMMD), which allows users to query, browse, and download metabolite information. In conclusion, HCMMD provides an important resource to assist researchers in reviewing metabolic biomarkers for diagnosis and progression of cancers.
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Affiliation(s)
- Xun Dong
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Yaoyao Qu
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Tongtong Sheng
- School of Public Health, Nanjing Medical University, Nanjing, China
| | - Yuanming Fan
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Silu Chen
- School of Public Health, Nanjing Medical University, Nanjing, China
| | - Qinbo Yuan
- Department of Urology, Wuxi Fifth People’s Hospital, Wuxi, China
| | - Gaoxiang Ma
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, China
- The Clinical Metabolomics Center, China Pharmaceutical University, Nanjing, China
- Deparment of Oncology, Pukou Hospital of Chinese Medicine affiliated to China Pharmaceutical University, Nanjing, China
| | - Yuqiu Ge
- Department of Public Health and Preventive Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, China
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Jin E, Yin Z, Zheng X, Yan C, Xu K, Eunice FY, Gao Y. Potential of Targeting TDO2 as the Lung Adenocarcinoma Treatment. J Proteome Res 2024; 23:1341-1350. [PMID: 38421152 DOI: 10.1021/acs.jproteome.3c00746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2024]
Abstract
Tryptophan catabolism plays an important role in the metabolic reconnection in cancer cells to support special demands of tumor initiation and progression. The catabolic product of the tryptophan pathway, kynurenine, has the capability of suppressing the immune reactions of tumor cells. In this study, we conducted internal and external cohort studies to reveal the importance of tryptophan 2,3-dioxygenase (TDO) for lung adenocarcinoma (LUAD). Our study further demonstrated that the TDO2 expression was associated with the proliferation, survival, and invasion of LUAD cells, and targeting TDO2 for LUAD tumors could be a potential therapeutic strategy.
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Affiliation(s)
- Er Jin
- Department of Respiratory Medicine, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou 310002 Zhejiang Province, China
| | - Zhidong Yin
- Department of Pathology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou 310009 Zhejiang Province, China
| | - Xiuxiu Zheng
- Department of Respiratory Medicine, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou 310002 Zhejiang Province, China
| | - Chenhong Yan
- Department of Respiratory Medicine, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou 310002 Zhejiang Province, China
| | - Kai Xu
- Department of Respiratory Medicine, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou 310002 Zhejiang Province, China
| | - Fouejio Yemele Eunice
- Department of Respiratory Medicine, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou 310002 Zhejiang Province, China
| | - Yue Gao
- Department of Geriatric, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou 310006 Zhejiang Province, China
- Zhejiang Provincial Key Laboratory of Traditional Chinese Medicine for the Prevention and Treatment of Major Chronic Disease in the Elderly, Hangzhou 310006 Zhejiang Province, China
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Papadopoulou MT, Panagopoulou P, Paramera E, Pechlivanis A, Virgiliou C, Papakonstantinou E, Palabougiouki M, Ioannidou M, Vasileiou E, Tragiannidis A, Papakonstantinou E, Theodoridis G, Hatzipantelis E, Evangeliou A. Metabolic Fingerprint in Childhood Acute Lymphoblastic Leukemia. Diagnostics (Basel) 2024; 14:682. [PMID: 38611595 PMCID: PMC11011894 DOI: 10.3390/diagnostics14070682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 03/11/2024] [Accepted: 03/18/2024] [Indexed: 04/14/2024] Open
Abstract
INTRODUCTION Acute lymphoblastic leukemia (ALL) is the most prevalent childhood malignancy. Despite high cure rates, several questions remain regarding predisposition, response to treatment, and prognosis of the disease. The role of intermediary metabolism in the individualized mechanistic pathways of the disease is unclear. We have hypothesized that children with any (sub)type of ALL have a distinct metabolomic fingerprint at diagnosis when compared: (i) to a control group; (ii) to children with a different (sub)type of ALL; (iii) to the end of the induction treatment. MATERIALS AND METHODS In this prospective case-control study (NCT03035344), plasma and urinary metabolites were analyzed in 34 children with ALL before the beginning (D0) and at the end of the induction treatment (D33). Their metabolic fingerprint was defined by targeted analysis of 106 metabolites and compared to that of an equal number of matched controls. Multivariate and univariate statistical analyses were performed using SIMCAP and scripts under the R programming language. RESULTS Metabolomic analysis showed distinct changes in patients with ALL compared to controls on both D0 and D33. The metabolomic fingerprint within the patient group differed significantly between common B-ALL and pre-B ALL and between D0 and D33, reflecting the effect of treatment. We have further identified the major components of this metabolic dysregulation, indicating shifts in fatty acid synthesis, transfer and oxidation, in amino acid and glycerophospholipid metabolism, and in the glutaminolysis/TCA cycle. CONCLUSIONS The disease type and time point-specific metabolic alterations observed in pediatric ALL are of particular interest as they may offer potential for the discovery of new prognostic biomarkers and therapeutic targets.
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Affiliation(s)
- Maria T. Papadopoulou
- 4th Pediatric Department, Papageorgiou General Hospital, Aristotle University of Thessaloniki, Papageorgiou General Hospital, Ring Road, Nea Efkarpia, 56403 Thessaloniki, Greece; (P.P.); (A.E.)
- Woman-Mother-Child Hospital, University Hospitals of Lyon, 69500 Bron, France
| | - Paraskevi Panagopoulou
- 4th Pediatric Department, Papageorgiou General Hospital, Aristotle University of Thessaloniki, Papageorgiou General Hospital, Ring Road, Nea Efkarpia, 56403 Thessaloniki, Greece; (P.P.); (A.E.)
| | | | - Alexandros Pechlivanis
- Department of Chemistry, Aristotle University of Thessaloniki, 54635 Thessaloniki, Greece; (A.P.)
- BIOMIC_Auth, Center for Interdisciplinary Research of the Aristotle University of Thessaloniki (CIRI), Balkan Center, 10th Km Thessaloniki-Thermi Rd, P.O. Box 8318, 57001 Thessaloniki, Greece
| | - Christina Virgiliou
- BIOMIC_Auth, Center for Interdisciplinary Research of the Aristotle University of Thessaloniki (CIRI), Balkan Center, 10th Km Thessaloniki-Thermi Rd, P.O. Box 8318, 57001 Thessaloniki, Greece
- Analytical Chemistry Laboratory, Department of Chemical Engineering, Aristotle University of Thessaloniki, 54636 Thessaloniki, Greece
| | | | - Maria Palabougiouki
- Pediatric & Adolescents Hematology-Oncology Unit, 2nd Pediatric Department, AHEPA Hospital, Aristotle University of Thessaloniki, 54636 Thessaloniki, Greece; (M.P.); (M.I.); (A.T.); (E.H.)
| | - Maria Ioannidou
- Pediatric & Adolescents Hematology-Oncology Unit, 2nd Pediatric Department, AHEPA Hospital, Aristotle University of Thessaloniki, 54636 Thessaloniki, Greece; (M.P.); (M.I.); (A.T.); (E.H.)
| | - Eleni Vasileiou
- Pediatric & Adolescents Hematology-Oncology Unit, 2nd Pediatric Department, AHEPA Hospital, Aristotle University of Thessaloniki, 54636 Thessaloniki, Greece; (M.P.); (M.I.); (A.T.); (E.H.)
| | - Athanasios Tragiannidis
- Pediatric & Adolescents Hematology-Oncology Unit, 2nd Pediatric Department, AHEPA Hospital, Aristotle University of Thessaloniki, 54636 Thessaloniki, Greece; (M.P.); (M.I.); (A.T.); (E.H.)
| | | | - Georgios Theodoridis
- Department of Chemistry, Aristotle University of Thessaloniki, 54635 Thessaloniki, Greece; (A.P.)
- BIOMIC_Auth, Center for Interdisciplinary Research of the Aristotle University of Thessaloniki (CIRI), Balkan Center, 10th Km Thessaloniki-Thermi Rd, P.O. Box 8318, 57001 Thessaloniki, Greece
| | - Emmanuel Hatzipantelis
- Pediatric & Adolescents Hematology-Oncology Unit, 2nd Pediatric Department, AHEPA Hospital, Aristotle University of Thessaloniki, 54636 Thessaloniki, Greece; (M.P.); (M.I.); (A.T.); (E.H.)
| | - Athanasios Evangeliou
- 4th Pediatric Department, Papageorgiou General Hospital, Aristotle University of Thessaloniki, Papageorgiou General Hospital, Ring Road, Nea Efkarpia, 56403 Thessaloniki, Greece; (P.P.); (A.E.)
- St Luke’s Hospital S.A., 55236 Pannorama, Greece
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Ishteyaque S, Singh G, Yadav KS, Verma S, Sharma RK, Sen S, Srivastava AK, Mitra K, Lahiri A, Bawankule DU, Rath SK, Kumar D, Mugale MN. Cooperative STAT3-NFkB signaling modulates mitochondrial dysfunction and metabolic profiling in hepatocellular carcinoma. Metabolism 2024; 152:155771. [PMID: 38184165 DOI: 10.1016/j.metabol.2023.155771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 12/12/2023] [Accepted: 12/27/2023] [Indexed: 01/08/2024]
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) continues to pose a significant health challenge and is often diagnosed at advanced stages. Metabolic reprogramming is a hallmark of many cancer types, including HCC and it involves alterations in various metabolic or nutrient-sensing pathways within liver cells to facilitate the rapid growth and progression of tumours. However, the role of STAT3-NFκB in metabolic reprogramming is still not clear. APPROACH AND RESULTS Diethylnitrosamine (DEN) administered animals showed decreased body weight and elevated level of serum enzymes. Also, Transmission electron microscopy (TEM) analysis revealed ultrastructural alterations. Increased phosphorylated signal transducer and activator of transcription-3 (p-STAT3), phosphorylated nuclear factor kappa B (p-NFκβ), dynamin related protein 1 (Drp-1) and alpha-fetoprotein (AFP) expression enhance the carcinogenicity as revealed in immunohistochemistry (IHC). The enzyme-linked immunosorbent assay (ELISA) concentration of IL-6 was found to be elevated in time dependent manner both in blood serum and liver tissue. Moreover, immunoblot analysis showed increased level of p-STAT3, p-NFκβ and IL-6 stimulated the upregulation of mitophagy proteins such as Drp-1, Phosphatase and tensin homolog (PTEN)-induced putative kinase 1 (PINK-1). Meanwhile, downregulation of Poly [ADP-ribose] polymerase 1 (PARP-1) and cleaved caspase 3 suppresses apoptosis and enhanced expression of AFP supports tumorigenesis. The mRNA level of STAT3 and Drp-1 was also found to be significantly increased. Furthermore, we performed high-field 800 MHz Nuclear Magnetic Resonance (NMR) based tissue and serum metabolomics analysis to identify metabolic signatures associated with the progression of liver cancer. The metabolomics findings revealed aberrant metabolic alterations in liver tissue and serum of 75th and 105th days of intervention groups in comparison to control, 15th and 45th days of intervention groups. Tissue metabolomics analysis revealed the accumulation of succinate in the liver tissue samples, whereas, serum metabolomics analysis revealed significantly decreased circulatory levels of ketone bodies (such as 3-hydroxybutyrate, acetate, acetone, etc.) and membrane metabolites suggesting activated ketolysis in advanced stages of liver cancer. CONCLUSION STAT3-NFκβ signaling axis has a significant role in mitochondrial dysfunction and metabolic alterations in the development of HCC.
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Affiliation(s)
- Sharmeen Ishteyaque
- Division of Cancer Biology CSIR-Central Drug Research Institute (CSIR-CDRI), Lucknow 226031, India; Division of Toxicology and Experimental Medicine, CSIR-Central Drug Research Institute (CSIR-CDRI), Lucknow 226031, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Gurvinder Singh
- Department of Advanced Spectroscopy and Imaging, Centre of Biomedical Research (CBMR), SGPGIMS Campus, Raebareli Road, Lucknow-226014, Uttar Pradesh, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Karan Singh Yadav
- Division of Cancer Biology CSIR-Central Drug Research Institute (CSIR-CDRI), Lucknow 226031, India; Division of Toxicology and Experimental Medicine, CSIR-Central Drug Research Institute (CSIR-CDRI), Lucknow 226031, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Smriti Verma
- Division of Cancer Biology CSIR-Central Drug Research Institute (CSIR-CDRI), Lucknow 226031, India; Division of Toxicology and Experimental Medicine, CSIR-Central Drug Research Institute (CSIR-CDRI), Lucknow 226031, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Rakesh Kumar Sharma
- Sophisticated Analytical Instrument Facility and Research Division CSIR-Central Drug Research Institute (CSIR-CDRI), Lucknow 226031, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Sumati Sen
- Bioprospection and Product Development Division, CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow, Uttar Pradesh 226015, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Anurag Kumar Srivastava
- Division of Toxicology and Experimental Medicine, CSIR-Central Drug Research Institute (CSIR-CDRI), Lucknow 226031, India
| | - Kalyan Mitra
- Sophisticated Analytical Instrument Facility and Research Division CSIR-Central Drug Research Institute (CSIR-CDRI), Lucknow 226031, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Amit Lahiri
- Pharmacology Division, CSIR - Central Drug Research Institute (CSIR-CDRI), Lucknow 226031, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Dnyaneshwar U Bawankule
- Bioprospection and Product Development Division, CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow, Uttar Pradesh 226015, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Srikanta Kumar Rath
- Division of Toxicology and Experimental Medicine, CSIR-Central Drug Research Institute (CSIR-CDRI), Lucknow 226031, India
| | - Dinesh Kumar
- Department of Advanced Spectroscopy and Imaging, Centre of Biomedical Research (CBMR), SGPGIMS Campus, Raebareli Road, Lucknow-226014, Uttar Pradesh, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
| | - Madhav Nilakanth Mugale
- Division of Cancer Biology CSIR-Central Drug Research Institute (CSIR-CDRI), Lucknow 226031, India; Division of Toxicology and Experimental Medicine, CSIR-Central Drug Research Institute (CSIR-CDRI), Lucknow 226031, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
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Hu JY, Lv M, Zhang KL, Qiao XY, Wang YX, Wang FY. Evaluating the causal relationship between human blood metabolites and gastroesophageal reflux disease. World J Gastrointest Oncol 2023; 15:2169-2184. [PMID: 38173433 PMCID: PMC10758654 DOI: 10.4251/wjgo.v15.i12.2169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Revised: 10/01/2023] [Accepted: 10/30/2023] [Indexed: 12/14/2023] Open
Abstract
BACKGROUND Gastroesophageal reflux disease (GERD) affects approximately 13% of the global population. However, the pathogenesis of GERD has not been fully elucidated. The development of metabolomics as a branch of systems biology in recent years has opened up new avenues for the investigation of disease processes. As a powerful statistical tool, Mendelian randomization (MR) is widely used to explore the causal relationship between exposure and outcome. AIM To analyze of the relationship between 486 blood metabolites and GERD. METHODS Two-sample MR analysis was used to assess the causal relationship between blood metabolites and GERD. A genome-wide association study (GWAS) of 486 metabolites was the exposure, and two different GWAS datasets of GERD were used as endpoints for the base analysis and replication and meta-analysis. Bonferroni correction is used to determine causal correlation features (P < 1.03 × 10-4). The results were subjected to sensitivity analysis to assess heterogeneity and pleiotropy. Using the MR Steiger filtration method to detect whether there is a reverse causal relationship between metabolites and GERD. In addition, metabolic pathway analysis was conducted using the online database based MetaboAnalyst 5.0 software. RESULTS In MR analysis, four blood metabolites are negatively correlated with GERD: Levulinate (4-oxovalerate), stearate (18:0), adrenate (22:4n6) and p-acetamidophenylglucuronide. However, we also found a positive correlation between four blood metabolites and GERD: Kynurenine, 1-linoleoylglycerophosphoethanolamine, butyrylcarnitine and guanosine. And bonferroni correction showed that butyrylcarnitine (odd ratio 1.10, 95% confidence interval: 1.05-1.16, P = 7.71 × 10-5) was the most reliable causal metabolite. In addition, one significant pathways, the "glycerophospholipid metabolism" pathway, can be involved in the pathogenesis of GERD. CONCLUSION Our study found through the integration of genomics and metabolomics that butyrylcarnitine may be a potential biomarker for GERD, which will help further elucidate the pathogenesis of GERD and better guide its treatment. At the same time, this also contributes to early screening and prevention of GERD. However, the results of this study require further confirmation from both basic and clinical real-world studies.
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Affiliation(s)
- Jia-Yan Hu
- Institute of Digestive Diseases, Xiyuan Hospital, China Academy of Chinese Medical Sciences, Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing 100091, China
| | - Mi Lv
- Institute of Digestive Diseases, Xiyuan Hospital, China Academy of Chinese Medical Sciences, Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing 100091, China
| | - Kun-Li Zhang
- Institute of Digestive Diseases, Xiyuan Hospital, China Academy of Chinese Medical Sciences, Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing 100091, China
| | - Xi-Yun Qiao
- Institute of Digestive Diseases, Xiyuan Hospital, China Academy of Chinese Medical Sciences, Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing 100091, China
| | - Yu-Xi Wang
- Institute of Digestive Diseases, Xiyuan Hospital, China Academy of Chinese Medical Sciences, Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing 100091, China
| | - Feng-Yun Wang
- Institute of Digestive Diseases, Xiyuan Hospital, China Academy of Chinese Medical Sciences, Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing 100091, China
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Ghini V, Meoni G, Vignoli A, Di Cesare F, Tenori L, Turano P, Luchinat C. Fingerprinting and profiling in metabolomics of biosamples. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2023; 138-139:105-135. [PMID: 38065666 DOI: 10.1016/j.pnmrs.2023.10.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 10/13/2023] [Accepted: 10/15/2023] [Indexed: 12/18/2023]
Abstract
This review focuses on metabolomics from an NMR point of view. It attempts to cover the broad scope of metabolomics and describes the NMR experiments that are most suitable for each sample type. It is addressed not only to NMR specialists, but to all researchers who wish to approach metabolomics with a clear idea of what they wish to achieve but not necessarily with a deep knowledge of NMR. For this reason, some technical parts may seem a bit naïve to the experts. The review starts by describing standard metabolomics procedures, which imply the use of a dedicated 600 MHz instrument and of four properly standardized 1D experiments. Standardization is a must if one wants to directly compare NMR results obtained in different labs. A brief mention is also made of standardized pre-analytical procedures, which are even more essential. Attention is paid to the distinction between fingerprinting and profiling, and the advantages and disadvantages of fingerprinting are clarified. This aspect is often not fully appreciated. Then profiling, and the associated problems of signal assignment and quantitation, are discussed. We also describe less conventional approaches, such as the use of different magnetic fields, the use of signal enhancement techniques to increase sensitivity, and the potential of field-shuttling NMR. A few examples of biomedical applications are also given, again with the focus on NMR techniques that are most suitable to achieve each particular goal, including a description of the most common heteronuclear experiments. Finally, the growing applications of metabolomics to foodstuffs are described.
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Affiliation(s)
- Veronica Ghini
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino, Italy; Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino, Italy
| | - Gaia Meoni
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino, Italy; Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino, Italy
| | - Alessia Vignoli
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino, Italy; Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino, Italy
| | - Francesca Di Cesare
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino, Italy; Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino, Italy
| | - Leonardo Tenori
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino, Italy; Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino, Italy; Consorzio Interuniversitario Risonanze Magnetiche Metallo Proteine (CIRMMP), Sesto Fiorentino, Italy
| | - Paola Turano
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino, Italy; Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino, Italy; Consorzio Interuniversitario Risonanze Magnetiche Metallo Proteine (CIRMMP), Sesto Fiorentino, Italy.
| | - Claudio Luchinat
- Consorzio Interuniversitario Risonanze Magnetiche Metallo Proteine (CIRMMP), Sesto Fiorentino, Italy; Giotto Biotech S.r.l., Sesto Fiorentino, Italy.
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9
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Navarro Ledesma S, Hamed-Hamed D, González-Muñoz A, Pruimboom L. Effectiveness of Treatments That Alter Metabolomics in Cancer Patients-A Systematic Review. Cancers (Basel) 2023; 15:4297. [PMID: 37686573 PMCID: PMC10486463 DOI: 10.3390/cancers15174297] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 08/07/2023] [Accepted: 08/25/2023] [Indexed: 09/10/2023] Open
Abstract
INTRODUCTION Cancer is the leading cause of death worldwide, with the most frequent being breast cancer in women, prostate cancer in men and colon cancer in both sexes. The use of metabolomics to find new biomarkers can provide knowledge about possible interventions based on the presence of oncometabolites in different cancer types. OBJECTIVES The primary purpose of this review is to analyze the characteristic metabolome of three of the most frequent cancer types. We further want to identify the existence and success rate of metabolomics-based intervention in patients suffering from those cancer types. Our conclusions are based on the analysis of the methodological quality of the studies. METHODS We searched for studies that investigated the metabolomic characteristics in patients suffering from breast cancer, prostate cancer or colon cancer in clinical trials. The data were analyzed, as well as the effects of specific interventions based on identified metabolomics and one or more oncometabolites. The used databases were PubMed, Virtual Health Library, Web of Science, EBSCO and Cochrane Library. Only nine studies met the selection criteria. Study bias was analyzed using the Cochrane risk of bias tool. This systematic review protocol was registered at the International Prospective Register of Systematic Reviews (PROSPERO: CRD42023401474). RESULTS Only nine studies about clinical trials were included in this review and show a moderate quality of evidence. Metabolomics-based interventions related with disease outcome were conflictive with no or small changes in the metabolic characteristics of the different cancer types. CONCLUSIONS This systematic review shows some interesting results related with metabolomics-based interventions and their effects on changes in certain cancer oncometabolites. The small number of studies we identified which fulfilled our inclusion criteria in this systematic review does not allow us to draw definitive conclusions. Nevertheless, some results can be considered as promising although further research is needed. That research must focus not only on the presence of possible oncometabolites but also on possible metabolomics-based interventions and their influence on the outcome in patients suffering from breast cancer, prostate cancer or colon cancer.
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Affiliation(s)
- Santiago Navarro Ledesma
- Department of Physiotherapy, Faculty of Health Sciences, Campus of Melilla, University of Granada, Querol Street 5, 52004 Melilla, Spain; (D.H.-H.); (A.G.-M.)
- Department of Physiotherapy, University Chair in Clinical Psychoneuroimmunology, University of Granada and PNI Europe, 52004 Melilla, Spain;
| | - Dina Hamed-Hamed
- Department of Physiotherapy, Faculty of Health Sciences, Campus of Melilla, University of Granada, Querol Street 5, 52004 Melilla, Spain; (D.H.-H.); (A.G.-M.)
| | - Ana González-Muñoz
- Department of Physiotherapy, Faculty of Health Sciences, Campus of Melilla, University of Granada, Querol Street 5, 52004 Melilla, Spain; (D.H.-H.); (A.G.-M.)
| | - Leo Pruimboom
- Department of Physiotherapy, University Chair in Clinical Psychoneuroimmunology, University of Granada and PNI Europe, 52004 Melilla, Spain;
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10
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Sunna S, Bowen CA, Ramelow CC, Santiago JV, Kumar P, Rangaraju S. Advances in proteomic phenotyping of microglia in neurodegeneration. Proteomics 2023; 23:e2200183. [PMID: 37060300 PMCID: PMC10528430 DOI: 10.1002/pmic.202200183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 04/04/2023] [Accepted: 04/05/2023] [Indexed: 04/16/2023]
Abstract
Microglia are dynamic resident immune cells of the central nervous system (CNS) that sense, survey, and respond to changes in their environment. In disease states, microglia transform from homeostatic to diverse molecular phenotypic states that play complex and causal roles in neurologic disease pathogenesis, as evidenced by the identification of microglial genes as genetic risk factors for neurodegenerative disease. While advances in transcriptomic profiling of microglia from the CNS of humans and animal models have provided transformative insights, the transcriptome is only modestly reflective of the proteome. Proteomic profiling of microglia is therefore more likely to provide functionally and therapeutically relevant targets. In this review, we discuss molecular insights gained from transcriptomic studies of microglia in the context of Alzheimer's disease as a prototypic neurodegenerative disease, and highlight existing and emerging approaches for proteomic profiling of microglia derived from in vivo model systems and human brain.
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Affiliation(s)
- Sydney Sunna
- Department of Neurology, Emory University,201 Dowman Drive Atlanta Georgia, 30322, United States of America
- Center for Neurodegenerative Diseases, Emory University, Atlanta, GA 30322, USA
| | - Christine A. Bowen
- Department of Neurology, Emory University,201 Dowman Drive Atlanta Georgia, 30322, United States of America
- Center for Neurodegenerative Diseases, Emory University, Atlanta, GA 30322, USA
- Department of Biochemistry, Emory University, Atlanta, GA 30322, USA
| | - Christina C. Ramelow
- Department of Neurology, Emory University,201 Dowman Drive Atlanta Georgia, 30322, United States of America
- Center for Neurodegenerative Diseases, Emory University, Atlanta, GA 30322, USA
| | - Juliet V. Santiago
- Department of Neurology, Emory University,201 Dowman Drive Atlanta Georgia, 30322, United States of America
- Center for Neurodegenerative Diseases, Emory University, Atlanta, GA 30322, USA
| | - Prateek Kumar
- Department of Neurology, Emory University,201 Dowman Drive Atlanta Georgia, 30322, United States of America
- Center for Neurodegenerative Diseases, Emory University, Atlanta, GA 30322, USA
| | - Srikant Rangaraju
- Department of Neurology, Emory University,201 Dowman Drive Atlanta Georgia, 30322, United States of America
- Center for Neurodegenerative Diseases, Emory University, Atlanta, GA 30322, USA
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11
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Muller Bark J, Karpe AV, Doecke JD, Leo P, Jeffree RL, Chua B, Day BW, Beale DJ, Punyadeera C. A pilot study: Metabolic profiling of plasma and saliva samples from newly diagnosed glioblastoma patients. Cancer Med 2023. [PMID: 37031458 DOI: 10.1002/cam4.5857] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 03/04/2023] [Accepted: 03/14/2023] [Indexed: 04/11/2023] Open
Abstract
BACKGROUND Despite aggressive treatment, more than 90% of glioblastoma (GBM) patients experience recurrences. GBM response to therapy is currently assessed by imaging techniques and tissue biopsy. However, difficulties with these methods may cause misinterpretation of treatment outcomes. Currently, no validated therapy response biomarkers are available for monitoring GBM progression. Metabolomics holds potential as a complementary tool to improve the interpretation of therapy responses to help in clinical interventions for GBM patients. METHODS Saliva and blood from GBM patients were collected pre and postoperatively. Patients were stratified conforming their progression-free survival (PFS) into favourable or unfavourable clinical outcomes (>9 months or PFS ≤ 9 months, respectively). Analysis of saliva (whole-mouth and oral rinse) and plasma samples was conducted utilising LC-QqQ-MS and LC-QTOF-MS to determine the metabolomic and lipidomic profiles. The data were investigated using univariate and multivariate statistical analyses and graphical LASSO-based graphic network analyses. RESULTS Altogether, 151 metabolites and 197 lipids were detected within all saliva and plasma samples. Among the patients with unfavourable outcomes, metabolites such as cyclic-AMP, 3-hydroxy-kynurenine, dihydroorotate, UDP and cis-aconitate were elevated, compared to patients with favourable outcomes during pre-and post-surgery. These metabolites showed to impact the pentose phosphate and Warburg effect pathways. The lipid profile of patients who experienced unfavourable outcomes revealed a higher heterogeneity in the abundance of lipids and fewer associations between markers in contrast to the favourable outcome group. CONCLUSION Our findings indicate that changes in salivary and plasma metabolites in GBM patients can potentially be employed as less invasive prognostic biomarkers/biomarker panel but validation with larger cohorts is required.
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Affiliation(s)
- Juliana Muller Bark
- Faculty of Health, Centre for Biomedical Technologies, School of Biomedical Sciences, Queensland University of Technology, Brisbane, Queensland, Australia
- Saliva and Liquid Biopsy Translational Laboratory, Griffith Institute for Drug Discovery - Griffith University, Brisbane, Queensland, Australia
- Faculty of Health, School of Biomedical Sciences, Queensland University of Technology, Gardens Point, Queensland, Australia
| | - Avinash V Karpe
- Environment, Commonwealth Scientific and Industrial Research Organization (CSIRO), Ecosciences Precinct, Dutton Park, Queensland, Australia
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organization (CSIRO), Acton, Australian Capital Territory, Australia
| | - James D Doecke
- Australian eHealth Research Centre, CSIRO. Level 7, Surgical Treatment and Rehabilitation Service - STARS, Royal Brisbane and Women's Hospital, Herston, Queensland, Australia
| | - Paul Leo
- Faculty of Health, School of Biomedical Sciences, Queensland University of Technology, Gardens Point, Queensland, Australia
- Faculty of Health, Translational Genomics Group, School of Biomedical Sciences, Queensland University of Technology, Woolloongabba, Australia
| | - Rosalind L Jeffree
- QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
- Faculty of Medicine, University of Queensland, Herston, Queensland, Australia
- Kenneth G. Jamieson Department of Neurosurgery, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia
- Cell and Molecular Biology Department, Sid Faithfull Brain Cancer Laboratory, QIMR Berghofer MRI, Brisbane, Queensland, Australia
| | - Benjamin Chua
- Faculty of Medicine, University of Queensland, Herston, Queensland, Australia
- Cancer Care Services, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia
| | - Bryan W Day
- Faculty of Health, School of Biomedical Sciences, Queensland University of Technology, Gardens Point, Queensland, Australia
- Faculty of Medicine, University of Queensland, Herston, Queensland, Australia
- Cell and Molecular Biology Department, Sid Faithfull Brain Cancer Laboratory, QIMR Berghofer MRI, Brisbane, Queensland, Australia
| | - David J Beale
- Environment, Commonwealth Scientific and Industrial Research Organization (CSIRO), Ecosciences Precinct, Dutton Park, Queensland, Australia
| | - Chamindie Punyadeera
- Saliva and Liquid Biopsy Translational Laboratory, Griffith Institute for Drug Discovery - Griffith University, Brisbane, Queensland, Australia
- Menzies Health Institute, Griffith University, Southport, Queensland, Australia
- Translational Research Institute, Woolloongabba, Queensland, Australia
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12
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Danzi F, Pacchiana R, Mafficini A, Scupoli MT, Scarpa A, Donadelli M, Fiore A. To metabolomics and beyond: a technological portfolio to investigate cancer metabolism. Signal Transduct Target Ther 2023; 8:137. [PMID: 36949046 PMCID: PMC10033890 DOI: 10.1038/s41392-023-01380-0] [Citation(s) in RCA: 37] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 02/08/2023] [Accepted: 02/15/2023] [Indexed: 03/24/2023] Open
Abstract
Tumour cells have exquisite flexibility in reprogramming their metabolism in order to support tumour initiation, progression, metastasis and resistance to therapies. These reprogrammed activities include a complete rewiring of the bioenergetic, biosynthetic and redox status to sustain the increased energetic demand of the cells. Over the last decades, the cancer metabolism field has seen an explosion of new biochemical technologies giving more tools than ever before to navigate this complexity. Within a cell or a tissue, the metabolites constitute the direct signature of the molecular phenotype and thus their profiling has concrete clinical applications in oncology. Metabolomics and fluxomics, are key technological approaches that mainly revolutionized the field enabling researchers to have both a qualitative and mechanistic model of the biochemical activities in cancer. Furthermore, the upgrade from bulk to single-cell analysis technologies provided unprecedented opportunity to investigate cancer biology at cellular resolution allowing an in depth quantitative analysis of complex and heterogenous diseases. More recently, the advent of functional genomic screening allowed the identification of molecular pathways, cellular processes, biomarkers and novel therapeutic targets that in concert with other technologies allow patient stratification and identification of new treatment regimens. This review is intended to be a guide for researchers to cancer metabolism, highlighting current and emerging technologies, emphasizing advantages, disadvantages and applications with the potential of leading the development of innovative anti-cancer therapies.
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Affiliation(s)
- Federica Danzi
- Department of Neurosciences, Biomedicine and Movement Sciences, Section of Biochemistry, University of Verona, Verona, Italy
| | - Raffaella Pacchiana
- Department of Neurosciences, Biomedicine and Movement Sciences, Section of Biochemistry, University of Verona, Verona, Italy
| | - Andrea Mafficini
- Department of Diagnostics and Public Health, University of Verona, Verona, Italy
| | - Maria T Scupoli
- Department of Neurosciences, Biomedicine and Movement Sciences, Biology and Genetics Section, University of Verona, Verona, Italy
| | - Aldo Scarpa
- Department of Diagnostics and Public Health, University of Verona, Verona, Italy
- ARC-NET Research Centre, University and Hospital Trust of Verona, Verona, Italy
| | - Massimo Donadelli
- Department of Neurosciences, Biomedicine and Movement Sciences, Section of Biochemistry, University of Verona, Verona, Italy.
| | - Alessandra Fiore
- Department of Neurosciences, Biomedicine and Movement Sciences, Section of Biochemistry, University of Verona, Verona, Italy
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13
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Yin C, Harms AC, Hankemeier T, Kindt A, de Lange ECM. Status of Metabolomic Measurement for Insights in Alzheimer's Disease Progression-What Is Missing? Int J Mol Sci 2023; 24:ijms24054960. [PMID: 36902391 PMCID: PMC10003384 DOI: 10.3390/ijms24054960] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 02/24/2023] [Accepted: 03/02/2023] [Indexed: 03/08/2023] Open
Abstract
Alzheimer's disease (AD) is an aging-related neurodegenerative disease, leading to the progressive loss of memory and other cognitive functions. As there is still no cure for AD, the growth in the number of susceptible individuals represents a major emerging threat to public health. Currently, the pathogenesis and etiology of AD remain poorly understood, while no efficient treatments are available to slow down the degenerative effects of AD. Metabolomics allows the study of biochemical alterations in pathological processes which may be involved in AD progression and to discover new therapeutic targets. In this review, we summarized and analyzed the results from studies on metabolomics analysis performed in biological samples of AD subjects and AD animal models. Then this information was analyzed by using MetaboAnalyst to find the disturbed pathways among different sample types in human and animal models at different disease stages. We discuss the underlying biochemical mechanisms involved, and the extent to which they could impact the specific hallmarks of AD. Then we identify gaps and challenges and provide recommendations for future metabolomics approaches to better understand AD pathogenesis.
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Affiliation(s)
- Chunyuan Yin
- Metabolomics and Analytics Centre, Leiden Academic Centre for Drug Research, Leiden University, 2333 CC Leiden, The Netherlands
- Division of Systems Pharmacology and Pharmacy, Leiden Academic Centre for Drug Research, Leiden University, 2333 CC Leiden, The Netherlands
| | - Amy C. Harms
- Metabolomics and Analytics Centre, Leiden Academic Centre for Drug Research, Leiden University, 2333 CC Leiden, The Netherlands
| | - Thomas Hankemeier
- Metabolomics and Analytics Centre, Leiden Academic Centre for Drug Research, Leiden University, 2333 CC Leiden, The Netherlands
| | - Alida Kindt
- Metabolomics and Analytics Centre, Leiden Academic Centre for Drug Research, Leiden University, 2333 CC Leiden, The Netherlands
| | - Elizabeth C. M. de Lange
- Division of Systems Pharmacology and Pharmacy, Leiden Academic Centre for Drug Research, Leiden University, 2333 CC Leiden, The Netherlands
- Correspondence:
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14
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Liu D, Shen Y, Di D, Cai S, Huang X, Lin H, Huang Y, Xue J, Liu L, Hu B. Direct mass spectrometry analysis of biological tissue for diagnosis of thyroid cancer using wooden-tip electrospray ionization. Front Chem 2023; 11:1134948. [PMID: 36846859 PMCID: PMC9947238 DOI: 10.3389/fchem.2023.1134948] [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: 12/31/2022] [Accepted: 01/20/2023] [Indexed: 02/11/2023] Open
Abstract
Direct mass spectrometry (MS) analysis of human tissue at the molecular level could gain insight into biomarker discovery and disease diagnosis. Detecting metabolite profiles of tissue sample play an important role in understanding the pathological properties of disease development. Because the complex matrices in tissue samples, complicated and time-consuming sample preparation processes are usually required by conventional biological and clinical MS methods. Direct MS with ambient ionization technique is a new analytical strategy for direct sample analysis with little sample preparation, and has been proven to be a simple, rapid, and effective analytical tools for direct analysis of biological tissues. In this work, we applied a simple, low-cost, disposable wooden tip (WT) for loading tiny thyroid tissue, and then loading organic solvents to extract biomarkers under electrospray ionization (ESI) condition. Under such WT-ESI, the extract of thyroid was directly sprayed out from wooden tip to MS inlet. In this work, thyroid tissue from normal and cancer parts were analyzed by the established WT-ESI-MS, showing lipids were mainly detectable compounds in thyroid tissue. The MS data of lipids obtained from thyroid tissues were further analyzed with MS/MS experiment and multivariate variable analysis, and the biomarkers of thyroid cancer were also investigated.
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Affiliation(s)
- Dasheng Liu
- Department of Vascular Thyroid Surgery, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Yuejian Shen
- Hangzhou Linping Hospital of Traditional Chinese Medicine, Hangzhou, China,*Correspondence: Li Liu, ; Yuejian Shen, ; Bin Hu,
| | - Dandan Di
- Institute of Mass Spectrometry and Atmospheric Environment, Guangdong Provincial Engineering Research Center for On-Line Source Apportionment System of Air Pollution, Jinan University, Guangzhou, China,Guangdong MS Institute of Scientific Instrument Innovation, Guangzhou, China
| | - Shenhui Cai
- Institute of Mass Spectrometry and Atmospheric Environment, Guangdong Provincial Engineering Research Center for On-Line Source Apportionment System of Air Pollution, Jinan University, Guangzhou, China
| | - Xueyang Huang
- Department of Vascular Thyroid Surgery, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Hongguo Lin
- Department of Vascular Thyroid Surgery, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Yalan Huang
- Department of Vascular Thyroid Surgery, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Jing Xue
- Zhejiang Province Joint Key Laboratory of Aquatic Products Processing, Collaborative Innovation Center of Seafood Deep Processing, Institute of Seafood, Zhejiang Gongshang University, Hangzhou, China
| | - Li Liu
- Health Management Center, The First Affiliated Hospital of Jinan University, Guangzhou, China,*Correspondence: Li Liu, ; Yuejian Shen, ; Bin Hu,
| | - Bin Hu
- Institute of Mass Spectrometry and Atmospheric Environment, Guangdong Provincial Engineering Research Center for On-Line Source Apportionment System of Air Pollution, Jinan University, Guangzhou, China,*Correspondence: Li Liu, ; Yuejian Shen, ; Bin Hu,
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15
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Graziani V, Garcia AR, Alcolado LS, Le Guennec A, Henriksson MA, Conte MR. Metabolic rewiring in MYC-driven medulloblastoma by BET-bromodomain inhibition. Sci Rep 2023; 13:1273. [PMID: 36690651 PMCID: PMC9870962 DOI: 10.1038/s41598-023-27375-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Accepted: 01/02/2023] [Indexed: 01/24/2023] Open
Abstract
Medulloblastoma (MB) is the most common malignant brain tumour in children. High-risk MB patients harbouring MYC amplification or overexpression exhibit a very poor prognosis. Aberrant activation of MYC markedly reprograms cell metabolism to sustain tumorigenesis, yet how metabolism is dysregulated in MYC-driven MB is not well understood. Growing evidence unveiled the potential of BET-bromodomain inhibitors (BETis) as next generation agents for treating MYC-driven MB, but whether and how BETis may affect tumour cell metabolism to exert their anticancer activities remains unknown. In this study, we explore the metabolic features characterising MYC-driven MB and examine how these are altered by BET-bromodomain inhibition. To this end, we employed an NMR-based metabolomics approach applied to the MYC-driven MB D283 and D458 cell lines before and after the treatment with the BETi OTX-015. We found that OTX-015 triggers a metabolic shift in both cell lines resulting in increased levels of myo-inositol, glycerophosphocholine, UDP-N-acetylglucosamine, glycine, serine, pantothenate and phosphocholine. Moreover, we show that OTX-015 alters ascorbate and aldarate metabolism, inositol phosphate metabolism, phosphatidylinositol signalling system, glycerophospholipid metabolism, ether lipid metabolism, aminoacyl-tRNA biosynthesis, and glycine, serine and threonine metabolism pathways in both cell lines. These insights provide a metabolic characterisation of MYC-driven childhood MB cell lines, which could pave the way for the discovery of novel druggable pathways. Importantly, these findings will also contribute to understand the downstream effects of BETis on MYC-driven MB, potentially aiding the development of new therapeutic strategies to combat medulloblastoma.
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Affiliation(s)
- Vittoria Graziani
- Department of Microbiology and Tumor Biology, Biomedicum B7, Karolinska Institutet, 171 65, Stockholm, Sweden
- Barts Cancer Institute, Queen Mary University of London, John Vane Science Building, Charterhouse Square, London, EC1M 6BQ, UK
| | - Aida Rodriguez Garcia
- Department of Microbiology and Tumor Biology, Biomedicum B7, Karolinska Institutet, 171 65, Stockholm, Sweden
| | - Lourdes Sainero Alcolado
- Department of Microbiology and Tumor Biology, Biomedicum B7, Karolinska Institutet, 171 65, Stockholm, Sweden
| | - Adrien Le Guennec
- Centre for Biomolecular Spectroscopy, King's College London, Guy's Campus, London, SE1 1UL, UK
| | - Marie Arsenian Henriksson
- Department of Microbiology and Tumor Biology, Biomedicum B7, Karolinska Institutet, 171 65, Stockholm, Sweden.
| | - Maria R Conte
- Randall Centre for Cell and Molecular Biophysics, King's College London, Guy's Campus, London, SE1 1UL, UK.
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16
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Zhi R, Wu K, Zhang J, Liu H, Niu C, Li S, Fu L. PRMT3 regulates the progression of invasive micropapillary carcinoma of the breast. Cancer Sci 2023; 114:1912-1928. [PMID: 36637351 PMCID: PMC10154826 DOI: 10.1111/cas.15724] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 12/22/2022] [Accepted: 12/27/2022] [Indexed: 01/14/2023] Open
Abstract
Invasive micropapillary carcinoma (IMPC) is a special histopathological subtype of breast cancer. Clinically, IMPC exhibits a higher incidence of lymphovascular invasion and lymph node metastasis compared with that of invasive ductal carcinoma (IDC), the most common type. However, the metabolic characteristics and related mechanisms underlying malignant IMPC biological behaviors are unknown. We performed large-scale targeted metabolomics analysis on resected tumors obtained from chemotherapy-naïve IMPC (n = 25) and IDC (n = 26) patients to investigate metabolic alterations, and we integrated mass spectrometry analysis, RNA sequencing, and ChIP-sequencing data to elucidate the potential molecular mechanisms. The metabolomics revealed distinct metabolic profiles between IMPC and IDC. For IMPC patients, the metabolomic profile was characterized by significantly high levels of arginine methylation marks, and protein arginine methyltransferase 3 (PRMT3) was identified as a critical regulator that catalyzed the formation of these arginine methylation marks. Notably, overexpression of PRMT3 was an independent risk factor for poor IMPC prognosis. Furthermore, we demonstrated that PRMT3 was a key regulator of breast cancer cell proliferation and metastasis both in vitro and in vivo, and treatment with a preclinical PRMT3 inhibitor decreased the xenograft tumorigenic capacity. Mechanistically, PRMT3 regulated the endoplasmic reticulum (ER) stress signaling pathway by facilitating histone H4 arginine 3 asymmetric dimethylation (H4R3me2a), which may endow breast cancer cells with great proliferative and metastatic capacity. Our findings highlight PRMT3 importance in regulating the malignant biological behavior of IMPC and suggest that small-molecule inhibitors of PRMT3 activity might be promising breast cancer treatments.
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Affiliation(s)
- Renyong Zhi
- Department of Breast Cancer Pathology and Research Laboratory, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China.,National Clinical Research Center of Cancer, Tianjin, China.,Key Laboratory of Cancer Prevention and Therapy, Tianjin, China.,Tianjin's Clinical Research Center for Cancer, Tianjin, China.,Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, Tianjin, China
| | - Kailiang Wu
- Department of Breast Cancer Pathology and Research Laboratory, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China.,National Clinical Research Center of Cancer, Tianjin, China.,Key Laboratory of Cancer Prevention and Therapy, Tianjin, China.,Tianjin's Clinical Research Center for Cancer, Tianjin, China.,Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, Tianjin, China
| | - Jingyue Zhang
- Department of Breast Cancer Pathology and Research Laboratory, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China.,National Clinical Research Center of Cancer, Tianjin, China.,Key Laboratory of Cancer Prevention and Therapy, Tianjin, China.,Tianjin's Clinical Research Center for Cancer, Tianjin, China.,Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, Tianjin, China
| | - Hanjiao Liu
- Department of Breast Cancer Pathology and Research Laboratory, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China.,National Clinical Research Center of Cancer, Tianjin, China.,Key Laboratory of Cancer Prevention and Therapy, Tianjin, China.,Tianjin's Clinical Research Center for Cancer, Tianjin, China.,Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, Tianjin, China
| | - Chen Niu
- Department of Breast Cancer Pathology and Research Laboratory, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China.,National Clinical Research Center of Cancer, Tianjin, China.,Key Laboratory of Cancer Prevention and Therapy, Tianjin, China.,Tianjin's Clinical Research Center for Cancer, Tianjin, China.,Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, Tianjin, China
| | - Shuai Li
- Department of Breast Cancer Pathology and Research Laboratory, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China.,National Clinical Research Center of Cancer, Tianjin, China.,Key Laboratory of Cancer Prevention and Therapy, Tianjin, China.,Tianjin's Clinical Research Center for Cancer, Tianjin, China.,Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, Tianjin, China
| | - Li Fu
- Department of Breast Cancer Pathology and Research Laboratory, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China.,National Clinical Research Center of Cancer, Tianjin, China.,Key Laboratory of Cancer Prevention and Therapy, Tianjin, China.,Tianjin's Clinical Research Center for Cancer, Tianjin, China.,Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, Tianjin, China
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17
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Skin Cancer Metabolic Profile Assessed by Different Analytical Platforms. Int J Mol Sci 2023; 24:ijms24021604. [PMID: 36675128 PMCID: PMC9866771 DOI: 10.3390/ijms24021604] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 01/03/2023] [Accepted: 01/10/2023] [Indexed: 01/17/2023] Open
Abstract
Skin cancer, including malignant melanoma (MM) and keratinocyte carcinoma (KC), historically named non-melanoma skin cancers (NMSC), represents the most common type of cancer among the white skin population. Despite decades of clinical research, the incidence rate of melanoma is increasing globally. Therefore, a better understanding of disease pathogenesis and resistance mechanisms is considered vital to accomplish early diagnosis and satisfactory control. The "Omics" field has recently gained attention, as it can help in identifying and exploring metabolites and metabolic pathways that assist cancer cells in proliferation, which can be further utilized to improve the diagnosis and treatment of skin cancer. Although skin tissues contain diverse metabolic enzymes, it remains challenging to fully characterize these metabolites. Metabolomics is a powerful omics technique that allows us to measure and compare a vast array of metabolites in a biological sample. This technology enables us to study the dermal metabolic effects and get a clear explanation of the pathogenesis of skin diseases. The purpose of this literature review is to illustrate how metabolomics technology can be used to evaluate the metabolic profile of human skin cancer, using a variety of analytical platforms including gas chromatography-mass spectrometry (GC-MS), liquid chromatography-mass spectrometry (LC-MS), and nuclear magnetic resonance (NMR). Data collection has not been based on any analytical method.
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18
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Zhang Z, Bao C, Jiang L, Wang S, Wang K, Lu C, Fang H. When cancer drug resistance meets metabolomics (bulk, single-cell and/or spatial): Progress, potential, and perspective. Front Oncol 2023; 12:1054233. [PMID: 36686803 PMCID: PMC9854130 DOI: 10.3389/fonc.2022.1054233] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 12/20/2022] [Indexed: 01/07/2023] Open
Abstract
Resistance to drug treatment is a critical barrier in cancer therapy. There is an unmet need to explore cancer hallmarks that can be targeted to overcome this resistance for therapeutic gain. Over time, metabolic reprogramming has been recognised as one hallmark that can be used to prevent therapeutic resistance. With the advent of metabolomics, targeting metabolic alterations in cancer cells and host patients represents an emerging therapeutic strategy for overcoming cancer drug resistance. Driven by technological and methodological advances in mass spectrometry imaging, spatial metabolomics involves the profiling of all the metabolites (metabolomics) so that the spatial information is captured bona fide within the sample. Spatial metabolomics offers an opportunity to demonstrate the drug-resistant tumor profile with metabolic heterogeneity, and also poses a data-mining challenge to reveal meaningful insights from high-dimensional spatial information. In this review, we discuss the latest progress, with the focus on currently available bulk, single-cell and spatial metabolomics technologies and their successful applications in pre-clinical and translational studies on cancer drug resistance. We provide a summary of metabolic mechanisms underlying cancer drug resistance from different aspects; these include the Warburg effect, altered amino acid/lipid/drug metabolism, generation of drug-resistant cancer stem cells, and immunosuppressive metabolism. Furthermore, we propose solutions describing how to overcome cancer drug resistance; these include early detection during cancer initiation, monitoring of clinical drug response, novel anticancer drug and target metabolism, immunotherapy, and the emergence of spatial metabolomics. We conclude by describing the perspectives on how spatial omics approaches (integrating spatial metabolomics) could be further developed to improve the management of drug resistance in cancer patients.
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Affiliation(s)
- Zhiqiang Zhang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China,School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Chaohui Bao
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lu Jiang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shan Wang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Kankan Wang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Chang Lu
- MRC London Institute of Medical Sciences, Imperial College London, London, United Kingdom
| | - Hai Fang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China,*Correspondence: Hai Fang,
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Zeng Z, Chen CX. Metabonomic analysis of tumor microenvironments: a mini-review. Front Oncol 2023; 13:1164266. [PMID: 37124524 PMCID: PMC10140396 DOI: 10.3389/fonc.2023.1164266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Accepted: 04/03/2023] [Indexed: 05/02/2023] Open
Abstract
Metabolomic analysis is a vital part of studying cancer progression. Metabonomic crosstalk, such as nutrient availability, physicochemical transformation, and intercellular interactions can affect tumor metabolism. Many original studies have demonstrated that metabolomics is important in some aspects of tumor metabolism. In this mini-review, we summarize the definition of metabolomics and how it can help change a tumor microenvironment, especially in pathways of three metabonomic tumors. Just as non-invasive biofluids have been identified as early biomarkers of tumor development, metabolomics can also predict differences in tumor drug response, drug resistance, and efficacy. Therefore, metabolomics is important for tumor metabolism and how it can affect oncology drugs in cancer therapy.
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Affiliation(s)
- Zeng Zeng
- Cancer Center, Department of Ultrasound Medicine, Zhejiang Provincial People’s Hospital, Affiliated People’s Hospital, Hangzhou Medical College, Hangzhou, Zhejiang, China
- Zhejiang University School of Medicine, Hangzhou, China
| | - Cong-Xian Chen
- Cancer Center, Department of Ultrasound Medicine, Zhejiang Provincial People’s Hospital, Affiliated People’s Hospital, Hangzhou Medical College, Hangzhou, Zhejiang, China
- *Correspondence: Cong-Xian Chen,
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20
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Kozioł A, Pupek M. Application of Metabolomics in Childhood Leukemia Diagnostics. Arch Immunol Ther Exp (Warsz) 2022; 70:28. [DOI: 10.1007/s00005-022-00665-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 10/04/2022] [Indexed: 11/09/2022]
Abstract
AbstractMetabolomics is a new field of science dealing with the study and analysis of metabolites formed in living cells. The biological fluids used in this test method are: blood, blood plasma, serum, cerebrospinal fluid, saliva and urine. The most popular methods of assessing the composition of metabolites include nuclear magnetic resonance spectroscopy and mass spectrometry (MS) in combination with gas chromatography–MS or liquid chromatography–MS. Metabolomics is used in many areas of medicine. The variability of biochemical processes in neoplastic cells in relation to healthy cells is the starting point for this type of research. The aim of the research currently being carried out is primarily to find biomarkers for quick diagnosis of the disease, assessment of its advancement and treatment effectiveness. The development of metabolomics may also contribute to the individualization of treatment of patients, adjusting drugs depending on the metabolic profile, and thus may improve the effectiveness of therapy, reduce side effects and help to improve the quality of life of patients. Here, we review the current and potential applications of metabolomics, focusing on its use as a biomarker method for childhood leukemia.
Graphic abstract
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21
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Adnan M, Shamsi A, Elasbali AM, Siddiqui AJ, Patel M, Alshammari N, Alharethi SH, Alhassan HH, Bardakci F, Hassan MI. Structure-Guided Approach to Discover Tuberosin as a Potent Activator of Pyruvate Kinase M2, Targeting Cancer Therapy. Int J Mol Sci 2022; 23:13172. [PMID: 36361954 PMCID: PMC9655700 DOI: 10.3390/ijms232113172] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 09/30/2022] [Accepted: 10/06/2022] [Indexed: 08/25/2023] Open
Abstract
Metabolic reprogramming is a key attribute of cancer progression. An altered expression of pyruvate kinase M2 (PKM2), a phosphotyrosine-binding protein is observed in many human cancers. PKM2 plays a vital role in metabolic reprogramming, transcription and cell cycle progression and thus is deliberated as an attractive target in anticancer drug development. The expression of PKM2 is essential for aerobic glycolysis and cell proliferation, especially in cancer cells, facilitating selective targeting of PKM2 in cell metabolism for cancer therapeutics. We have screened a virtual library of phytochemicals from the IMPPAT (Indian Medicinal Plants, Phytochemistry and Therapeutics) database of Indian medicinal plants to identify potential activators of PKM2. The initial screening was carried out for the physicochemical properties of the compounds, and then structure-based molecular docking was performed to select compounds based on their binding affinity towards PKM2. Subsequently, the ADMET (absorption, distribution, metabolism, excretion and toxicity) properties, PAINS (Pan-assay interference compounds) patterns, and PASS evaluation were carried out to find more potent hits against PKM2. Here, Tuberosin was identified from the screening process bearing appreciable binding affinity toward the PKM2-binding pocket and showed a worthy set of drug-like properties. Finally, molecular dynamics simulation for 100 ns was performed, which showed decent stability of the protein-ligand complex and relatival conformational dynamics throughout the trajectory. The study suggests that modulating PKM2 with natural compounds is an attractive approach in treating human malignancy after required validation.
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Affiliation(s)
- Mohd Adnan
- Department of Biology, College of Science, University of Ha’il, Ha’il P.O. Box 2440, Saudi Arabia
- Molecular Diagnostics and Personalized Therapeutics Unit, University of Ha’il, Ha’il P.O. Box 2440, Saudi Arabia
| | - Anas Shamsi
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Abdelbaset Mohamed Elasbali
- Department of Clinical Laboratory Science, College of Applied Medical Sciences-Qurayyat, Jouf University, Sakaka P.O. Box 72388, Saudi Arabia
| | - Arif Jamal Siddiqui
- Department of Biology, College of Science, University of Ha’il, Ha’il P.O. Box 2440, Saudi Arabia
| | - Mitesh Patel
- Department of Biotechnology, Parul Institute of Applied Sciences and Centre of Research for Development, Parul University, Vadodara 391760, India
| | - Nawaf Alshammari
- Department of Biology, College of Science, University of Ha’il, Ha’il P.O. Box 2440, Saudi Arabia
| | - Salem Hussain Alharethi
- Department of Biological Science, College of Arts and Science, Najran University, Najran P.O. Box 11001, Saudi Arabia
| | - Hassan H. Alhassan
- Department of Clinical Laboratory Science, College of Applied Medical Sciences-Sakaka, Jouf University, Sakaka P.O. Box 72388, Saudi Arabia
| | - Fevzi Bardakci
- Department of Biology, College of Science, University of Ha’il, Ha’il P.O. Box 2440, Saudi Arabia
| | - Md. Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
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22
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Bharti SK, Shannon BA, Sharma RK, Levin AS, Morris CD, Bhujwalla ZM, Fayad LM. Characterization of lipomatous tumors with high-resolution 1H MRS at 17.6T: Do benign lipomas, atypical lipomatous tumors and liposarcomas have a distinct metabolic signature? Front Oncol 2022; 12:920560. [PMID: 36158671 PMCID: PMC9500232 DOI: 10.3389/fonc.2022.920560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 08/18/2022] [Indexed: 11/30/2022] Open
Abstract
Background Distinguishing between some benign lipomas (BLs), atypical lipomatous tumors (ALTs), and dedifferentiated liposarcomas (DDLs) can be challenging due to overlapping magnetic resonance imaging characteristics, and poorly understood molecular mechanisms underlying the malignant transformation of liposarcomas. Purpose To identify metabolic biomarkers of the lipomatous tumor spectrum by examining human tissue specimens using high-resolution 1H magnetic resonance spectroscopy (MRS). Materials and methods In this prospective study, human tissue specimens were obtained from participants who underwent surgical resection for radiologically-indeterminate lipomatous tumors between November 2016 and May 2019. Tissue specimens were obtained from normal subcutaneous fat (n=9), BLs (n=10), ALTs (n=7) and DDLs (n=8). Extracts from specimens were examined with high-resolution MRS at 17.6T. Computational modeling of pattern recognition-based cluster analysis was utilized to identify significant differences in metabolic signatures between the lipomatous tumor types. Results Significant differences between BLs and ALTs were observed for multiple metabolites, including leucine, valine, branched chain amino acids, alanine, acetate, glutamine, and formate. DDLs were distinguished from ALTs by increased glucose and lactate, and increased phosphatidylcholine. Multivariate principal component analysis showed clear clustering identifying distinct metabolic signatures of the tissue types. Conclusion Metabolic signatures identified in 1H MR spectra of lipomatous tumors provide new insights into malignant progression and metabolic targeting. The metabolic patterns identified provide the foundation of developing noninvasive MRS or PET imaging biomarkers to distinguish between BLs, ALTs, and DDLs.
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Affiliation(s)
- Santosh Kumar Bharti
- Division of Cancer Imaging Research, The Russell H. Morgan Department of Radiology and Radiological Science, The Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Brett A. Shannon
- Department of Orthopaedic Surgery, The Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Raj Kumar Sharma
- Division of Cancer Imaging Research, The Russell H. Morgan Department of Radiology and Radiological Science, The Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Adam S. Levin
- Department of Orthopaedic Surgery, The Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Carol D. Morris
- Department of Orthopaedic Surgery, The Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Zaver M. Bhujwalla
- Division of Cancer Imaging Research, The Russell H. Morgan Department of Radiology and Radiological Science, The Johns Hopkins University School of Medicine, Baltimore, MD, United States
- Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, United States
- Department of Radiation Oncology and Molecular Radiation Sciences, The Johns Hopkins University School of Medicine, Baltimore, MD, United States
- *Correspondence: Laura M. Fayad, ; Zaver M. Bhujwalla,
| | - Laura M. Fayad
- Department of Orthopaedic Surgery, The Johns Hopkins University School of Medicine, Baltimore, MD, United States
- Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, United States
- Musculoskeletal Radiology, The Russell H. Morgan Department of Radiology and Radiological Science; The Johns Hopkins University School of Medicine, Baltimore, MD, United States
- *Correspondence: Laura M. Fayad, ; Zaver M. Bhujwalla,
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Dehghani F, Yousefinejad S, Walker DI, Omidi F. Metabolomics for exposure assessment and toxicity effects of occupational pollutants: current status and future perspectives. Metabolomics 2022; 18:73. [PMID: 36083566 DOI: 10.1007/s11306-022-01930-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 08/19/2022] [Indexed: 11/24/2022]
Abstract
INTRODUCTION Work-related exposures to harmful agents or factors are associated with an increase in incidence of occupational diseases. These exposures often represent a complex mixture of different stressors, challenging the ability to delineate the mechanisms and risk factors underlying exposure-disease relationships. The use of omics measurement approaches that enable characterization of biological marker patterns provide internal indicators of molecular alterations, which could be used to identify bioeffects following exposure to a toxicant. Metabolomics is the comprehensive analysis of small molecule present in biological samples, and allows identification of potential modes of action and altered pathways by systematic measurement of metabolites. OBJECTIVES The aim of this study is to review the application of metabolomics studies for use in occupational health, with a focus on applying metabolomics for exposure monitoring and its relationship to occupational diseases. METHODS PubMed, Web of Science, Embase and Scopus electronic databases were systematically searched for relevant studies published up to 2021. RESULTS Most of reviewed studies included worker populations exposed to heavy metals such as As, Cd, Pb, Cr, Ni, Mn and organic compounds such as tetrachlorodibenzo-p-dioxin, trichloroethylene, polyfluoroalkyl, acrylamide, polyvinyl chloride. Occupational exposures were associated with changes in metabolites and pathways, and provided novel insight into the relationship between exposure and disease outcomes. The reviewed studies demonstrate that metabolomics provides a powerful ability to identify metabolic phenotypes and bioeffect of occupational exposures. CONCLUSION Continued application to worker populations has the potential to enable characterization of thousands of chemical signals in biological samples, which could lead to discovery of new biomarkers of exposure for chemicals, identify possible toxicological mechanisms, and improved understanding of biological effects increasing disease risk associated with occupational exposure.
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Affiliation(s)
- Fatemeh Dehghani
- Student Research Committee, Shiraz University of Medical Sciences, Shiraz, Iran
- Research Center for Health Sciences, Research Institute for Health, Department of Occupational Health and Safety Engineering, School of Health Shiraz, University of Medical Sciences, Shiraz, Iran
| | - Saeed Yousefinejad
- Research Center for Health Sciences, Research Institute for Health, Department of Occupational Health and Safety Engineering, School of Health Shiraz, University of Medical Sciences, Shiraz, Iran.
| | - Douglas I Walker
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Fariborz Omidi
- Research Center for Environmental Determinants of Health (RCEDH), Health Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
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A Comprehensive Metabolomics Analysis of Fecal Samples from Advanced Adenoma and Colorectal Cancer Patients. Metabolites 2022; 12:metabo12060550. [PMID: 35736483 PMCID: PMC9229737 DOI: 10.3390/metabo12060550] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Revised: 06/08/2022] [Accepted: 06/14/2022] [Indexed: 12/14/2022] Open
Abstract
Accurate diagnosis of colorectal cancer (CRC) still relies on invasive colonoscopy. Noninvasive methods are less sensitive in detecting the disease, particularly in the early stage. In the current work, a metabolomics analysis of fecal samples was carried out by ultra-high-performance liquid chromatography–tandem mass spectroscopy (UPLC-MS/MS). A total of 1380 metabolites were analyzed in a cohort of 120 fecal samples from patients with normal colonoscopy, advanced adenoma (AA) and CRC. Multivariate analysis revealed that metabolic profiles of CRC and AA patients were similar and could be clearly separated from control individuals. Among the 25 significant metabolites, sphingomyelins (SM), lactosylceramides (LacCer), secondary bile acids, polypeptides, formiminoglutamate, heme and cytidine-containing pyrimidines were found to be dysregulated in CRC patients. Supervised random forest (RF) and logistic regression algorithms were employed to build a CRC accurate predicted model consisting of the combination of hemoglobin (Hgb) and bilirubin E,E, lactosyl-N-palmitoyl-sphingosine, glycocholenate sulfate and STLVT with an accuracy, sensitivity and specificity of 91.67% (95% Confidence Interval (CI) 0.7753–0.9825), 0.7 and 1, respectively.
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25
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Resurreccion EP, Fong KW. The Integration of Metabolomics with Other Omics: Insights into Understanding Prostate Cancer. Metabolites 2022; 12:metabo12060488. [PMID: 35736421 PMCID: PMC9230859 DOI: 10.3390/metabo12060488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 05/21/2022] [Accepted: 05/24/2022] [Indexed: 02/06/2023] Open
Abstract
Our understanding of prostate cancer (PCa) has shifted from solely caused by a few genetic aberrations to a combination of complex biochemical dysregulations with the prostate metabolome at its core. The role of metabolomics in analyzing the pathophysiology of PCa is indispensable. However, to fully elucidate real-time complex dysregulation in prostate cells, an integrated approach based on metabolomics and other omics is warranted. Individually, genomics, transcriptomics, and proteomics are robust, but they are not enough to achieve a holistic view of PCa tumorigenesis. This review is the first of its kind to focus solely on the integration of metabolomics with multi-omic platforms in PCa research, including a detailed emphasis on the metabolomic profile of PCa. The authors intend to provide researchers in the field with a comprehensive knowledge base in PCa metabolomics and offer perspectives on overcoming limitations of the tool to guide future point-of-care applications.
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Affiliation(s)
- Eleazer P. Resurreccion
- Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, KY 40506, USA;
| | - Ka-wing Fong
- Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, KY 40506, USA;
- Markey Cancer Center, University of Kentucky, Lexington, KY 40506, USA
- Correspondence: ; Tel.: +1-859-562-3455
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26
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Banoei MM, Mahé E, Mansoor A, Stewart D, Winston BW, Habibi HR, Shabani-Rad MT. NMR-based metabolomic profiling can differentiate follicular lymphoma from benign lymph node tissues and may be predictive of outcome. Sci Rep 2022; 12:8294. [PMID: 35585165 PMCID: PMC9117304 DOI: 10.1038/s41598-022-12445-5] [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: 02/02/2022] [Accepted: 05/10/2022] [Indexed: 11/10/2022] Open
Abstract
Follicular lymphoma (FL) is a cancer of B-cells, representing the second most common type of non-Hodgkin lymphoma and typically diagnosed at advanced stage in older adults. In contrast to the wide range of available molecular genetic data, limited data relating the metabolomic features of follicular lymphoma are known. Metabolomics is a promising analytical approach employing metabolites (molecules < 1 kDa in size) as potential biomarkers in cancer research. In this pilot study, we performed proton nuclear magnetic resonance spectroscopy (1H-NMR) on 29 cases of FL and 11 control patient specimens. The resulting spectra were assessed by both unsupervised and supervised statistical methods. We report significantly discriminant metabolomic models of common metabolites distinguishing FL from control tissues. Within our FL case series, we also report discriminant metabolomic signatures predictive of progression-free survival.
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Affiliation(s)
- Mohammad Mehdi Banoei
- Department of Critical Care Medicine, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Etienne Mahé
- Department of Pathology and Laboratory Medicine, Foothills Medical Centre, Cumming School of Medicine, University of Calgary, McCaig Tower, Room MT7523, 1403 29 St NW, Calgary, AB, T2N 2T9, Canada.
| | - Adnan Mansoor
- Department of Pathology and Laboratory Medicine, Foothills Medical Centre, Cumming School of Medicine, University of Calgary, McCaig Tower, Room MT7523, 1403 29 St NW, Calgary, AB, T2N 2T9, Canada
| | - Douglas Stewart
- Departments of Oncology and Medicine, University of Calgary and Tom Baker Cancer Centre, Calgary, AB, Canada
| | - Brent W Winston
- Departments of Critical Care Medicine, Medicine and Biochemistry and Molecular Biology, University of Calgary, Calgary, AB, Canada
| | - Hamid R Habibi
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Meer-Taher Shabani-Rad
- Department of Pathology and Laboratory Medicine, Foothills Medical Centre, Cumming School of Medicine, University of Calgary, McCaig Tower, Room MT7523, 1403 29 St NW, Calgary, AB, T2N 2T9, Canada
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27
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Emerging Role for 7T MRI and Metabolic Imaging for Pancreatic and Liver Cancer. Metabolites 2022; 12:metabo12050409. [PMID: 35629913 PMCID: PMC9145477 DOI: 10.3390/metabo12050409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 04/25/2022] [Accepted: 04/27/2022] [Indexed: 11/16/2022] Open
Abstract
Advances in magnet technologies have led to next generation 7T magnetic resonance scanners which can fit in the footprint and price point of conventional hospital scanners (1.5−3T). It is therefore worth asking if there is a role for 7T magnetic resonance imaging and spectroscopy for the treatment of solid tumor cancers. Herein, we survey the medical literature to evaluate the unmet clinical needs for patients with pancreatic and hepatic cancer, and the potential of ultra-high field proton imaging and phosphorus spectroscopy to fulfil those needs. We draw on clinical literature, preclinical data, nuclear magnetic resonance spectroscopic data of human derived samples, and the efforts to date with 7T imaging and phosphorus spectroscopy. At 7T, the imaging capabilities approach histological resolution. The spectral and spatial resolution enhancements at high field for phospholipid spectroscopy have the potential to reduce the number of exploratory surgeries due to tumor boundaries undefined at conventional field strengths. Phosphorus metabolic imaging at 7T magnetic field strength, is already a mainstay in preclinical models for molecular phenotyping, energetic status evaluation, dosimetry, and assessing treatment response for both pancreatic and liver cancers. Metabolic imaging of primary tumors and lymph nodes may provide powerful metrics to aid staging and treatment response. As tumor tissues contain extreme levels of phospholipid metabolites compared to the background signal, even spectroscopic volumes containing less than 50% tumor can be detected and/or monitored. Phosphorus spectroscopy allows non-invasive pH measurements, indicating hypoxia, as a predictor of patients likely to recur. We conclude that 7T multiparametric approaches that include metabolic imaging with phosphorus spectroscopy have the potential to meet the unmet needs of non-invasive location-specific treatment monitoring, lymph node staging, and the reduction in unnecessary surgeries for patients undergoing resections for pancreatic cancer. There is also potential for the use of 7T phosphorous spectra for the phenotyping of tumor subtypes and even early diagnosis (<2 mL). Whether or not 7T can be used for all patients within the next decade, the technology is likely to speed up the translation of new therapeutics.
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Breast cancer in the era of integrating “Omics” approaches. Oncogenesis 2022; 11:17. [PMID: 35422484 PMCID: PMC9010455 DOI: 10.1038/s41389-022-00393-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 03/27/2022] [Accepted: 03/30/2022] [Indexed: 12/24/2022] Open
Abstract
Worldwide, breast cancer is the leading cause of cancer-related deaths in women. Breast cancer is a heterogeneous disease characterized by different clinical outcomes in terms of pathological features, response to therapies, and long-term patient survival. Thus, the heterogeneity found in this cancer led to the concept that breast cancer is not a single disease, being very heterogeneous both at the molecular and clinical level, and rather represents a group of distinct neoplastic diseases of the breast and its cells. Indubitably, in the past decades we witnessed a significant development of innovative therapeutic approaches, including targeted and immunotherapies, leading to impressive results in terms of increased survival for breast cancer patients. However, these multimodal treatments fail to prevent recurrence and metastasis. Therefore, it is urgent to improve our understanding of breast tumor and metastasis biology. Over the past few years, high-throughput “omics” technologies through the identification of novel biomarkers and molecular profiling have shown their great potential in generating new insights in the study of breast cancer, also improving diagnosis, prognosis and prediction of response to treatment. In this review, we discuss how the implementation of “omics” strategies and their integration may lead to a better comprehension of the mechanisms underlying breast cancer. In particular, with the aim to investigate the correlation between different “omics” datasets and to define the new important key pathway and upstream regulators in breast cancer, we applied a new integrative meta-analysis method to combine the results obtained from genomics, proteomics and metabolomics approaches in different revised studies.
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di Meo NA, Loizzo D, Pandolfo SD, Autorino R, Ferro M, Porta C, Stella A, Bizzoca C, Vincenti L, Crocetto F, Tataru OS, Rutigliano M, Battaglia M, Ditonno P, Lucarelli G. Metabolomic Approaches for Detection and Identification of Biomarkers and Altered Pathways in Bladder Cancer. Int J Mol Sci 2022; 23:ijms23084173. [PMID: 35456991 PMCID: PMC9030452 DOI: 10.3390/ijms23084173] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 04/05/2022] [Accepted: 04/08/2022] [Indexed: 12/24/2022] Open
Abstract
Metabolomic analysis has proven to be a useful tool in biomarker discovery and the molecular classification of cancers. In order to find new biomarkers, and to better understand its pathological behavior, bladder cancer also has been studied using a metabolomics approach. In this article, we review the literature on metabolomic studies of bladder cancer, focusing on the different available samples (urine, blood, tissue samples) used to perform the studies and their relative findings. Moreover, the multi-omic approach in bladder cancer research has found novel insights into its metabolic behavior, providing excellent start-points for new diagnostic and therapeutic strategies. Metabolomics data analysis can lead to the discovery of a “signature pathway” associated with the progression of bladder cancer; this aspect could be potentially valuable in predictions of clinical outcomes and the introduction of new treatments. However, further studies are needed to give stronger evidence and to make these tools feasible for use in clinical practice.
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Affiliation(s)
- Nicola Antonio di Meo
- Department of Emergency and Organ Transplantation-Urology, Andrology and Kidney Transplantation Unit, University of Bari, 70124 Bari, Italy; (N.A.d.M.); (D.L.); (M.R.); (M.B.); (P.D.)
| | - Davide Loizzo
- Department of Emergency and Organ Transplantation-Urology, Andrology and Kidney Transplantation Unit, University of Bari, 70124 Bari, Italy; (N.A.d.M.); (D.L.); (M.R.); (M.B.); (P.D.)
- Division of Urology, Virginia Commonwealth University (VCU) Health, Richmond, VA 23298, USA; (S.D.P.); (R.A.)
| | - Savio Domenico Pandolfo
- Division of Urology, Virginia Commonwealth University (VCU) Health, Richmond, VA 23298, USA; (S.D.P.); (R.A.)
- Division of Urology, University of Naples “Federico II”, 80100 Naples, Italy
| | - Riccardo Autorino
- Division of Urology, Virginia Commonwealth University (VCU) Health, Richmond, VA 23298, USA; (S.D.P.); (R.A.)
| | - Matteo Ferro
- Division of Urology, European Institute of Oncology (IEO), IRCCS, 20141 Milan, Italy;
| | - Camillo Porta
- Department of Biomedical Sciences and Human Oncology, University of Bari, 70124 Bari, Italy; (C.P.); (A.S.)
| | - Alessandro Stella
- Department of Biomedical Sciences and Human Oncology, University of Bari, 70124 Bari, Italy; (C.P.); (A.S.)
| | - Cinzia Bizzoca
- Department of General Surgery “Ospedaliera”, Polyclinic Hospital of Bari, 70124 Bari, Italy; (C.B.); (L.V.)
| | - Leonardo Vincenti
- Department of General Surgery “Ospedaliera”, Polyclinic Hospital of Bari, 70124 Bari, Italy; (C.B.); (L.V.)
| | - Felice Crocetto
- Department of Neurosciences, Reproductive Sciences and Odontostomatology, University of Naples “Federico II”, 80131 Naples, Italy;
| | - Octavian Sabin Tataru
- I.O.S.U.D., George Emil Palade University of Medicine and Pharmacy, Science and Technology, 540142 Targu Mures, Romania;
| | - Monica Rutigliano
- Department of Emergency and Organ Transplantation-Urology, Andrology and Kidney Transplantation Unit, University of Bari, 70124 Bari, Italy; (N.A.d.M.); (D.L.); (M.R.); (M.B.); (P.D.)
| | - Michele Battaglia
- Department of Emergency and Organ Transplantation-Urology, Andrology and Kidney Transplantation Unit, University of Bari, 70124 Bari, Italy; (N.A.d.M.); (D.L.); (M.R.); (M.B.); (P.D.)
| | - Pasquale Ditonno
- Department of Emergency and Organ Transplantation-Urology, Andrology and Kidney Transplantation Unit, University of Bari, 70124 Bari, Italy; (N.A.d.M.); (D.L.); (M.R.); (M.B.); (P.D.)
| | - Giuseppe Lucarelli
- Department of Emergency and Organ Transplantation-Urology, Andrology and Kidney Transplantation Unit, University of Bari, 70124 Bari, Italy; (N.A.d.M.); (D.L.); (M.R.); (M.B.); (P.D.)
- Correspondence:
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Metabolic Profiling of Thymic Epithelial Tumors Hints to a Strong Warburg Effect, Glutaminolysis and Precarious Redox Homeostasis as Potential Therapeutic Targets. Cancers (Basel) 2022; 14:cancers14061564. [PMID: 35326714 PMCID: PMC8945961 DOI: 10.3390/cancers14061564] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 03/11/2022] [Accepted: 03/15/2022] [Indexed: 02/05/2023] Open
Abstract
Simple Summary Thymomas and thymic carcinomas (TCs) are malignant thymic epithelial tumors (TETs) with poor outcome, if non-resectable. Metabolic signatures of TETs have not yet been studied and may offer new therapeutic options. This is the first metabolomics investigation on thymic epithelial tumors employing nuclear magnetic resonance spectroscopy of tissue samples. We could detect and quantify up to 37 metabolites in the major tumor subtypes, including acetylcholine that was not previously detected in other non-endocrine cancers. A metabolite-based cluster analysis distinguished three clinically relevant tumor subgroups, namely indolent and aggressive thymomas, as well as TCs. A metabolite-based metabolic pathway analysis also gave hints to activated metabolic pathways shared between aggressive thymomas and TCs. This finding was largely backed by enrichment of these pathways at the transcriptomic level in a large, publicly available, independent TET dataset. Due to the differential expression of metabolites in thymic epithelial tumors versus normal thymus, pathways related to proline, cysteine, glutathione, lactate and glutamine appear as promising therapeutic targets. From these findings, inhibitors of glutaminolysis and of the downstream TCA cycle are anticipated to be rational therapeutic strategies. If our results can be confirmed in future, sufficiently powered studies, metabolic signatures may contribute to the identification of new therapeutic options for aggressive thymomas and TCs. Abstract Thymomas and thymic carcinomas (TC) are malignant thymic epithelial tumors (TETs) with poor outcome, if non-resectable. Metabolic signatures of TETs have not yet been studied and may offer new therapeutic options. Metabolic profiles of snap-frozen thymomas (WHO types A, AB, B1, B2, B3, n = 12) and TCs (n = 3) were determined by high resolution magic angle spinning 1H nuclear magnetic resonance (HRMAS 1H-NMR) spectroscopy. Metabolite-based prediction of active KEGG metabolic pathways was achieved with MetPA. In relation to metabolite-based metabolic pathways, gene expression signatures of TETs (n = 115) were investigated in the public “The Cancer Genome Atlas” (TCGA) dataset using gene set enrichment analysis. Overall, thirty-seven metabolites were quantified in TETs, including acetylcholine that was not previously detected in other non-endocrine cancers. Metabolite-based cluster analysis distinguished clinically indolent (A, AB, B1) and aggressive TETs (B2, B3, TCs). Using MetPA, six KEGG metabolic pathways were predicted to be activated, including proline/arginine, glycolysis and glutathione pathways. The activated pathways as predicted by metabolite-profiling were generally enriched transcriptionally in the independent TCGA dataset. Shared high lactic acid and glutamine levels, together with associated gene expression signatures suggested a strong “Warburg effect”, glutaminolysis and redox homeostasis as potential vulnerabilities that need validation in a large, independent cohort of aggressive TETs. If confirmed, targeting metabolic pathways may eventually prove as adjunct therapeutic options in TETs, since the metabolic features identified here are known to confer resistance to cisplatin-based chemotherapy, kinase inhibitors and immune checkpoint blockers, i.e., currently used therapies for non-resectable TETs.
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Singh A, Prakash V, Gupta N, Kumar A, Kant R, Kumar D. Serum Metabolic Disturbances in Lung Cancer Investigated through an Elaborative NMR-Based Serum Metabolomics Approach. ACS OMEGA 2022; 7:5510-5520. [PMID: 35187366 PMCID: PMC8851899 DOI: 10.1021/acsomega.1c06941] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 01/18/2022] [Indexed: 06/01/2023]
Abstract
Detection of metabolic disturbances in lung cancer (LC) has the potential to aid early diagnosis/prognosis and hence improve disease management strategies through reliable grading, staging, and determination of neoadjuvant status in LC. However, a majority of previous metabolomics studies compare the normalized spectral features which not only provide ambiguous information but further limit the clinical translation of this information. Various such issues can be resolved by performing the concentration profiling of various metabolites with respect to formate as an internal reference using commercial software Chenomx. Continuing our efforts in this direction, the serum metabolic profiles were measured on 39 LC patients and 42 normal controls (NCs, comparable in age/sex) using high-field 800 MHz NMR spectroscopy and compared using multivariate statistical analysis tools to identify metabolic disturbances and metabolites of diagnostic potential. Partial least-squares discriminant analysis (PLS-DA) model revealed a distinct separation between LC and NC groups and resulted in excellent discriminatory ability with the area under the receiver-operating characteristic (AUROC) = 0.97 [95% CI = 0.89-1.00]. The metabolic features contributing to the differentiation of LC from NC samples were identified first using variable importance in projection (VIP) score analysis and then checked for their statistical significance (with p-value < 0.05) and diagnostic potential using the ROC curve analysis. The analysis revealed relevant metabolic disturbances associated with LC. Among various circulatory metabolites, six metabolites, including histidine, glutamine, glycine, threonine, alanine, and valine, were found to be of apposite diagnostic potential for clinical implications. These metabolic alterations indicated altered glucose metabolism, aberrant fatty acid synthesis, and augmented utilization of various amino acids including active glutaminolysis in LC.
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Affiliation(s)
- Anjana Singh
- All
India Institute of Medical Sciences (AIIMS), Rishikesh, Uttarakhand 249201, India
- Pulmonary
& Critical Care Medicine, King George’s
Medical University, Lucknow, Uttar Pradesh 226003, India
| | - Ved Prakash
- Pulmonary
& Critical Care Medicine, King George’s
Medical University, Lucknow, Uttar Pradesh 226003, India
| | - Nikhil Gupta
- Centre
of Biomedical Research (CBMR), SGPGIMS, Lucknow, Uttar Pradesh 226014, India
- Department
of Chemistry, Banaras Hindu University, Varanasi, Uttar Pradesh 221005, India
| | - Ashish Kumar
- Department
of Chemistry, Banaras Hindu University, Varanasi, Uttar Pradesh 221005, India
| | - Ravi Kant
- All
India Institute of Medical Sciences (AIIMS), Rishikesh, Uttarakhand 249201, India
| | - Dinesh Kumar
- Centre
of Biomedical Research (CBMR), SGPGIMS, Lucknow, Uttar Pradesh 226014, India
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Wang G, Qiu M, Xing X, Zhou J, Yao H, Li M, Yin R, Hou Y, Li Y, Pan S, Huang Y, Yang F, Bai F, Nie H, Di S, Guo L, Meng Z, Wang J, Yin Y. Lung cancer scRNA-seq and lipidomics reveal aberrant lipid metabolism for early-stage diagnosis. Sci Transl Med 2022; 14:eabk2756. [PMID: 35108060 DOI: 10.1126/scitranslmed.abk2756] [Citation(s) in RCA: 67] [Impact Index Per Article: 33.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Lung cancer is the leading cause of cancer mortality, and early detection is key to improving survival. However, there are no reliable blood-based tests currently available for early-stage lung cancer diagnosis. Here, we performed single-cell RNA sequencing of different early-stage lung cancers and found that lipid metabolism was broadly dysregulated in different cell types, with glycerophospholipid metabolism as the most altered lipid metabolism-related pathway. Untargeted lipidomics was carried out in an exploratory cohort of 311 participants. Through support vector machine algorithm-based and mass spectrum-based feature selection, we identified nine lipids (lysophosphatidylcholines 16:0, 18:0, and 20:4; phosphatidylcholines 16:0-18:1, 16:0-18:2, 18:0-18:1, 18:0-18:2, and 16:0-22:6; and triglycerides 16:0-18:1-18:1) as the features most important for early-stage cancer detection. Using these nine features, we developed a liquid chromatography-mass spectrometry (MS)-based targeted assay using multiple reaction monitoring. This target assay achieved 100.00% specificity on an independent validation cohort. In a hospital-based lung cancer screening cohort of 1036 participants examined by low-dose computed tomography and a prospective clinical cohort containing 109 participants, the assay reached more than 90.00% sensitivity and 92.00% specificity. Accordingly, matrix-assisted laser desorption/ionization MS imaging confirmed that the selected lipids were differentially expressed in early-stage lung cancer tissues in situ. This method, designated as Lung Cancer Artificial Intelligence Detector, may be useful for early detection of lung cancer or large-scale screening of high-risk populations for cancer prevention.
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Affiliation(s)
- Guangxi Wang
- Institute of Systems Biomedicine, Department of Pathology, School of Basic Medical Sciences, Peking-Tsinghua Center for Life Sciences, Peking University Health Science Center and Department of Thoracic Surgery, Peking University People's Hospital, Beijing 100191, China
| | - Mantang Qiu
- Institute of Systems Biomedicine, Department of Pathology, School of Basic Medical Sciences, Peking-Tsinghua Center for Life Sciences, Peking University Health Science Center and Department of Thoracic Surgery, Peking University People's Hospital, Beijing 100191, China
| | - Xudong Xing
- Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing 100871, China
| | - Juntuo Zhou
- Institute of Systems Biomedicine, Department of Pathology, School of Basic Medical Sciences, Peking-Tsinghua Center for Life Sciences, Peking University Health Science Center and Department of Thoracic Surgery, Peking University People's Hospital, Beijing 100191, China
| | - Hantao Yao
- Institute of Automation, Chinese Academy of Sciences (CAS), Beijing 100190, China
| | - Mingru Li
- Department of Thoracic Surgery, Aerospace 731 Hospital, Beijing 100074, China
| | - Rong Yin
- Department of Thoracic Surgery, Jiangsu Cancer Hospital, Nanjing 210009, China
| | - Yan Hou
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University Health Science Center, Beijing 100191, China
| | - Yang Li
- Institute of Systems Biomedicine, Department of Pathology, School of Basic Medical Sciences, Peking-Tsinghua Center for Life Sciences, Peking University Health Science Center and Department of Thoracic Surgery, Peking University People's Hospital, Beijing 100191, China
| | - Shuli Pan
- Medical Examination Center, Aerospace 731 Hospital, Beijing 100074, China
| | - Yuqing Huang
- Department of Thoracic Surgery, Beijing Haidian Hospital, Beijing 100080, China
| | - Fan Yang
- Institute of Systems Biomedicine, Department of Pathology, School of Basic Medical Sciences, Peking-Tsinghua Center for Life Sciences, Peking University Health Science Center and Department of Thoracic Surgery, Peking University People's Hospital, Beijing 100191, China
| | - Fan Bai
- Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing 100871, China
| | - Honggang Nie
- Analytical Instrumentation Center, Peking University, Beijing 100871, China
| | - Shuangshuang Di
- Analytical Instrumentation Center, Peking University, Beijing 100871, China
| | - Limei Guo
- Department of Pathology, Peking University Third Hospital, Beijing 100191, China
| | - Zhu Meng
- Beijing University of Posts and Telecommunications, Beijing Key Laboratory of Network System and Network Culture, Beijing 100876, China
| | - Jun Wang
- Institute of Systems Biomedicine, Department of Pathology, School of Basic Medical Sciences, Peking-Tsinghua Center for Life Sciences, Peking University Health Science Center and Department of Thoracic Surgery, Peking University People's Hospital, Beijing 100191, China
| | - Yuxin Yin
- Institute of Systems Biomedicine, Department of Pathology, School of Basic Medical Sciences, Peking-Tsinghua Center for Life Sciences, Peking University Health Science Center and Department of Thoracic Surgery, Peking University People's Hospital, Beijing 100191, China
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Gautam AK, Kumar P, Raj R, Kumar D, Bhattacharya B, Rajinikanth PS, Chidambaram K, Mahata T, Maity B, Saha S. Preclinical Evaluation of Dimethyl Itaconate Against Hepatocellular Carcinoma via Activation of the e/iNOS-Mediated NF-κB-Dependent Apoptotic Pathway. Front Pharmacol 2022; 12:823285. [PMID: 35095533 PMCID: PMC8795766 DOI: 10.3389/fphar.2021.823285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Accepted: 12/13/2021] [Indexed: 11/30/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is one of the most common tumors affecting a large population worldwide, with the fifth and seventh greatest mortality rates among men and women, respectively, and the third prime cause of mortality among cancer victims. Dimethyl itaconate (DI) has been reported to be efficacious in colorectal cancer by decreasing IL-1β release from intestinal epithelial cells. In this study, diethylnitrosamine (DEN)-induced HCC in male albino Wistar rats was treated with DI as an anticancer drug. The function and molecular mechanism of DI against HCC in vivo were assessed using histopathology, enzyme-linked immunosorbent assay (ELISA), and Western blot studies. Metabolomics using 1H-NMR was used to investigate metabolic profiles. As per molecular insights, DI has the ability to trigger mitochondrial apoptosis through iNOS- and eNOS-induced activation of the NF-κB/Bcl-2 family of proteins, CytC, caspase-3, and caspase-9 signaling cascade. Serum metabolomics investigations using 1H-NMR revealed that aberrant metabolites in DEN-induced HCC rats were restored to normal following DI therapy. Furthermore, our data revealed that the DI worked as an anti-HCC agent. The anticancer activity of DI was shown to be equivalent to that of the commercial chemotherapeutic drug 5-fluorouracil.
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Affiliation(s)
- Anurag Kumar Gautam
- Department of Pharmaceutical Sciences, Babasaheb Bhimrao Ambedkar University, Lucknow, India
| | - Pranesh Kumar
- Department of Pharmaceutical Sciences, Babasaheb Bhimrao Ambedkar University, Lucknow, India.,Department of Pharmacology, Aryakul College of Pharmacy and Research, Lucknow, India
| | - Ritu Raj
- Centre of Biomedical Research, SGPGIMS Campus, Lucknow, India
| | - Dinesh Kumar
- Centre of Biomedical Research, SGPGIMS Campus, Lucknow, India
| | | | - P S Rajinikanth
- Department of Pharmaceutical Sciences, Babasaheb Bhimrao Ambedkar University, Lucknow, India
| | - Kumarappan Chidambaram
- Department of Pharmacology and Toxicology, School of Pharmacy, King Khalid University, Abha, Saudi Arabia
| | - Tarun Mahata
- Centre of Biomedical Research, SGPGIMS Campus, Lucknow, India
| | - Biswanath Maity
- Centre of Biomedical Research, SGPGIMS Campus, Lucknow, India
| | - Sudipta Saha
- Department of Pharmaceutical Sciences, Babasaheb Bhimrao Ambedkar University, Lucknow, India
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Heat Shock Proteins in Benign Prostatic Hyperplasia and Prostate Cancer. Int J Mol Sci 2022; 23:ijms23020897. [PMID: 35055079 PMCID: PMC8779911 DOI: 10.3390/ijms23020897] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Revised: 01/10/2022] [Accepted: 01/11/2022] [Indexed: 12/13/2022] Open
Abstract
Two out of three diseases of the prostate gland affect aging men worldwide. Benign prostatic hyperplasia (BPH) is a noncancerous enlargement affecting millions of men. Prostate cancer (PCa) in turn is the second leading cause of cancer death. The factors influencing the occurrence of BPH and PCa are different; however, in the course of these two diseases, the overexpression of heat shock proteins is observed. Heat shock proteins (HSPs), chaperone proteins, are known to be one of the main proteins playing a role in maintaining cell homeostasis. HSPs take part in the process of the proper folding of newly formed proteins, and participate in the renaturation of damaged proteins. In addition, they are involved in the transport of specific proteins to the appropriate cell organelles and directing damaged proteins to proteasomes or lysosomes. Their function is to protect the proteins against degradation factors that are produced during cellular stress. HSPs are also involved in modulating the immune response and the process of apoptosis. One well-known factor affecting HSPs is the androgen receptor (AR)—a main player involved in the development of BPH and the progression of prostate cancer. HSPs play a cytoprotective role and determine the survival of cancer cells. These chaperones are often upregulated in malignancies and play an indispensable role in tumor progression. Therefore, HSPs are considered as one of the therapeutic targets in anti-cancer therapies. In this review article, we discuss the role of different HSPs in prostate diseases, and their potential as therapeutic targets.
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Tasic L, Avramović N, Quintero M, Stanisic D, Martins LG, da Costa TBBC, Jadranin M, de Souza Accioly MT, Faria P, de Camargo B, de Sá Pereira BM, Maschietto M. A Metabonomic View on Wilms Tumor by High-Resolution Magic-Angle Spinning Nuclear Magnetic Resonance Spectroscopy. Diagnostics (Basel) 2022; 12:diagnostics12010157. [PMID: 35054324 PMCID: PMC8775120 DOI: 10.3390/diagnostics12010157] [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: 11/14/2021] [Revised: 12/13/2021] [Accepted: 01/01/2022] [Indexed: 11/16/2022] Open
Abstract
Pediatric cancer NMR-metabonomics might be a powerful tool to discover modified biochemical pathways in tumor development, improve cancer diagnosis, and, consequently, treatment. Wilms tumor (WT) is the most common kidney tumor in young children whose genetic and epigenetic abnormalities lead to cell metabolism alterations, but, so far, investigation of metabolic pathways in WT is scarce. We aimed to explore the high-resolution magic-angle spinning nuclear magnetic resonance (HR-MAS NMR) metabonomics of WT and normal kidney (NK) samples. For this study, 14 WT and 7 NK tissue samples were obtained from the same patients and analyzed. One-dimensional and two-dimensional HR-MAS NMR spectra were processed, and the one-dimensional NMR data were analyzed using chemometrics. Chemometrics enabled us to elucidate the most significant differences between the tumor and normal tissues and to discover intrinsic metabolite alterations in WT. The metabolic differences in WT tissues were revealed by a validated PLS-DA applied on HR-MAS T2-edited 1H-NMR and were assigned to 16 metabolites, such as lipids, glucose, and branched-chain amino acids (BCAAs), among others. The WT compared to NK samples showed 13 metabolites with increased concentrations and 3 metabolites with decreased concentrations. The relative BCAA concentrations were decreased in the WT while lipids, lactate, and glutamine/glutamate showed increased levels. Sixteen tissue metabolites distinguish the analyzed WT samples and point to altered glycolysis, glutaminolysis, TCA cycle, and lipid and BCAA metabolism in WT. Significant variation in the concentrations of metabolites, such as glutamine/glutamate, lipids, lactate, and BCAAs, was observed in WT and opened up a perspective for their further study and clinical validation.
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Affiliation(s)
- Ljubica Tasic
- Laboratory of Chemical Biology, Institute of Chemistry, University of Campinas (UNICAMP), Campinas, Sao Paulo 13083-970, Brazil; (M.Q.); (D.S.); (L.G.M.); (T.B.B.C.d.C.)
- Correspondence:
| | - Nataša Avramović
- Faculty of Medicine, Institute of Medical Chemistry, University of Belgrade, Višegradska 26, 11000 Belgrade, Serbia;
| | - Melissa Quintero
- Laboratory of Chemical Biology, Institute of Chemistry, University of Campinas (UNICAMP), Campinas, Sao Paulo 13083-970, Brazil; (M.Q.); (D.S.); (L.G.M.); (T.B.B.C.d.C.)
| | - Danijela Stanisic
- Laboratory of Chemical Biology, Institute of Chemistry, University of Campinas (UNICAMP), Campinas, Sao Paulo 13083-970, Brazil; (M.Q.); (D.S.); (L.G.M.); (T.B.B.C.d.C.)
| | - Lucas G. Martins
- Laboratory of Chemical Biology, Institute of Chemistry, University of Campinas (UNICAMP), Campinas, Sao Paulo 13083-970, Brazil; (M.Q.); (D.S.); (L.G.M.); (T.B.B.C.d.C.)
| | - Tassia Brena Barroso Carneiro da Costa
- Laboratory of Chemical Biology, Institute of Chemistry, University of Campinas (UNICAMP), Campinas, Sao Paulo 13083-970, Brazil; (M.Q.); (D.S.); (L.G.M.); (T.B.B.C.d.C.)
| | - Milka Jadranin
- Institute of Chemistry, Technology and Metallurgy, Department of Chemistry, University of Belgrade, Njegoševa 12, 11000 Belgrade, Serbia;
| | | | - Paulo Faria
- Department of Pathology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro 21941-901, Brazil;
| | - Beatriz de Camargo
- Clinical Research Department, National Cancer Institute (INCA), Rio de Janeiro 20231-091, Brazil; (B.d.C.); (B.M.d.S.P.)
| | - Bruna M. de Sá Pereira
- Clinical Research Department, National Cancer Institute (INCA), Rio de Janeiro 20231-091, Brazil; (B.d.C.); (B.M.d.S.P.)
| | - Mariana Maschietto
- National Laboratory of Biosciences (LNBio), National Center for Research in Energy and Materials (CNPEM), Campinas, Sao Paulo 13083-100, Brazil;
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Ghini V, Magherini F, Massai L, Messori L, Turano P. Comparative NMR metabolomics of the responses of A2780 human ovarian cancer cells to clinically established Pt-based drugs. Dalton Trans 2022; 51:12512-12523. [DOI: 10.1039/d2dt02068h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Pt-based drugs play a very important role in current cancer treatments; yet, their cellular and mechanistic aspects are not fully understood. NMR metabolomics provides a powerful tool to investigate the...
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37
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Dutta SD, Hexiu J, Kim J, Sarkar S, Mondal J, An JM, Lee YK, Moniruzzaman M, Lim KT. Two-photon excitable membrane targeting polyphenolic carbon dots for long-term imaging and pH-responsive chemotherapeutic drug delivery for synergistic tumor therapy. Biomater Sci 2022; 10:1680-1696. [DOI: 10.1039/d1bm01832a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Long-term dynamic tracking of cells with theranostics properties remains challenging due to difficulty in preparing and delivering drugs by the probes. Herein, we developed a highly fluorescent one- and two-photon...
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38
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Trevisan França de Lima L, Müller Bark J, Rasheduzzaman M, Ekanayake Weeramange C, Punyadeera C. Saliva as a matrix for measurement of cancer biomarkers. Cancer Biomark 2022. [DOI: 10.1016/b978-0-12-824302-2.00008-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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39
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Prabahar A. Integration of Transcriptomics Data and Metabolomic Data Using Biomedical Literature Mining and Pathway Analysis. Methods Mol Biol 2022; 2496:301-316. [PMID: 35713871 DOI: 10.1007/978-1-0716-2305-3_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Recent progress in omics technologies such as transcriptomics and metabolomics offers an unprecedented opportunity to understand the disease mechanisms and determines the associated biomedical entities using biomedical literature mining. Tremendous data available in the biomedical literature helps in addressing complex biomedical problems. Advancements in genomics and transcriptomics helps in decoding the genetic information obtained from various high throughput techniques for its use in personalized medicine and therapeutics. Integration of data from biomedical literature and data from large-scale genomic studies aids in the determination of the etiology of a disease and drug targets. This chapter addresses the perspectives of transcriptomics and metabolomics in biomedical literature mining and gives an overview of state-of-the-art techniques in this field.
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Affiliation(s)
- Archana Prabahar
- R&D Division, Eriks-Precision Components India Pvt Ltd, Mohali, Punjab, India.
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Jagannathan N, Reddy RR. Potential of nuclear magnetic resonance metabolomics in the study of prostate cancer. Indian J Urol 2022; 38:99-109. [PMID: 35400867 PMCID: PMC8992727 DOI: 10.4103/iju.iju_416_21] [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: 11/06/2021] [Revised: 12/16/2021] [Accepted: 02/09/2022] [Indexed: 12/24/2022] Open
Abstract
Nuclear magnetic resonance (NMR) metabolomics is a powerful analytical technique and a tool which has unique characteristics and capabilities for the evaluation of a number of biochemicals/metabolites of cancer and other disease processes that are present in biofluids (urine and blood) and tissues. The potential of NMR metabolomics in prostate cancer (PCa) has been explored by researchers and its usefulness has been documented. A large number of metabolites such as citrate, choline, and sarcosine were detected by NMR metabolomics from biofluids and tissues related to PCa and their levels were compared with controls and benign prostatic hyperplasia. The changes in the levels of these metabolites aid in the diagnosis and help to understand the dysregulated metabolic pathways in PCa. We review recent studies on in vitro and ex vivo NMR spectroscopy-based PCa metabolomics and its possible role as a diagnostic tool.
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Chacko S, Haseeb YB, Haseeb S. Metabolomics Work Flow and Analytics in Systems Biology. Curr Mol Med 2021; 22:870-881. [PMID: 34923941 DOI: 10.2174/1566524022666211217102105] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Revised: 08/26/2021] [Accepted: 09/24/2021] [Indexed: 11/22/2022]
Abstract
Metabolomics is an omics approach of systems biology that involves the development and assessment of large-scale, comprehensive biochemical analysis tools for metabolites in biological systems. This review describes the metabolomics workflow and provides an overview of current analytic tools used for the quantification of metabolic profiles. We explain analytic tools such as mass spectrometry (MS), nuclear magnetic resonance (NMR) spectroscopy, ionization techniques, and approaches for data extraction and analysis.
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Affiliation(s)
- Sanoj Chacko
- Division of Cardiology, Queen's University, Kingston, Ontario, Canada
| | - Yumna B Haseeb
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, Canada
| | - Sohaib Haseeb
- Division of Cardiology, Queen's University, Kingston, Ontario, Canada
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42
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Kong Y, Feng YQ, Lu YT, Feng SS, Huang Z, Wang QY, Huang HM, Ling X, Su ZH, Guo Y. Predictive serum biomarkers of patients with cerebral infarction. Neurol Res 2021; 44:331-341. [PMID: 34763612 DOI: 10.1080/01616412.2021.1987055] [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: 10/19/2022]
Abstract
OBJECTIVES Stroke is the third most common cause of death and also causes seizures and disability. Biomarkers are abnormal signal indicators at the biological level that are present before the organism is seriously affected and are more sensitive to early diagnosis than are traditional imaging methods. Early diagnosis of stroke can prevent the progression of the disease. However, there are currently no widely accepted biomarkers for stroke that have been applied clinically. METHODS A serum metabonomics method based on ultra-high-performance liquid chromatography-quadrupole-time of flight tandem mass spectrometry (UPLC-Q-TOF/MS) was used to identify potential biomarkers and metabolic pathways of cerebral infarction. The receiver-operating characteristic (ROC) curve was used to verify the diagnostic and classification abilities of the biomarkers, and a support vector machine (SVM) model was developed for the prediction of cerebral infarction. RESULTS Principal component analysis revealed a clear separation between the normal and cerebral infarction groups. A total of 13 potential serum biomarkers were identified, which were mainly involved in linoleic acid metabolism; phenylalanine, tyrosine, and tryptophan biosynthesis; tyrosine metabolism; arachidonic acid metabolism; and fatty acid biosynthesis. The ROC curve analysis showed that the potential biomarkers had high specificity and sensitivity for the diagnosis of cerebral infarction. The SVM model had good diagnostic ability and could accurately distinguish the control group from the cerebral infarction group. DISCUSSION The metabonomics approach may be a useful bioanalytical method for understanding the pathophysiology of cerebral infarction and may provide an experimental basis for the development of clinical biomarkers for stroke.
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Affiliation(s)
- Yan Kong
- College of General Medicine, Guangxi Medical University, Nanning, China
| | - Yu-Qing Feng
- RuiKang Hospital, Guangxi University of Chinese Medicine, Nanning, China
| | - Ya-Ting Lu
- Pharmaceutical College, Guangxi Medical University, Nanning, China
| | - Shi-Sui Feng
- Pharmaceutical College, Guangxi Medical University, Nanning, China
| | - Zheng Huang
- Pharmaceutical College, Guangxi Medical University, Nanning, China
| | - Qian-Yi Wang
- Pharmaceutical College, Guangxi Medical University, Nanning, China
| | - Hui-Min Huang
- Pharmaceutical College, Guangxi Medical University, Nanning, China
| | - Xue Ling
- Pharmaceutical College, Guangxi Medical University, Nanning, China
| | - Zhi-Heng Su
- Pharmaceutical College, Guangxi Medical University, Nanning, China
| | - Yue Guo
- Pharmaceutical College, Guangxi Medical University, Nanning, China
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Detection of Nail Oncometabolite SAICAR in Oral Cancer Patients and Its Molecular Interactions with PKM2 Enzyme. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:ijerph182111225. [PMID: 34769743 PMCID: PMC8583651 DOI: 10.3390/ijerph182111225] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Revised: 10/01/2021] [Accepted: 10/20/2021] [Indexed: 01/15/2023]
Abstract
Oncometabolites are known to drive metabolic adaptations in oral cancer. Several oncometabolites are known to be shared between cancer cells and non-cancer cells including microbiotas to modulate the tumor microenvironment. Among potential oncometabolites, succinylaminoimidazolecarboxamide ribose5′-phosphate (SAICAR) supports the growth and invasiveness of cancer cells by pyruvate kinase M2 (PKM2) enzyme in a glucose starved tumor microenvironment. There is a significant gap that shows the detection of SAICAR in biological samples including nails of oral cancer patients. Metabolite identification of SAICAR was investigated in the nails of oral cancer patients using novel vertical tube gel electrophoresis (VTGE) and LC-HRMS. Further molecular docking and molecular dynamics simulations (MDS) were employed to determine the nature of molecular interactions of SAICAR (CHEBI ID:18319) with PKM2 (PDB ID: 4G1N). Molecular docking of SAICAR (CHEBI ID:18319) was performed against pyruvate kinase M2 (PDB ID: 4G1N). Data suggest the presence of oncometabolite SAICAR in nails of oral cancer. Molecular docking of SAICAR with PKM2 showed appreciable binding affinity (−8.0 kcal/mol) with residues including ASP407, THR405, GLU410, ARG443, GLY321, ARG436, HIS439, LYS266, and TYR466. Furthermore, MDS confirmed the specific binding of SAICAR within the activator site of PKM2 and the stability of SAICAR and PKM2 molecular interactions. In conclusion, SAICAR is a promising oncometabolite biomarker present in the nails of oral cancer patients. A significant activation potential of SAICAR exists with the PKM2 enzyme.
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Tomacha J, Dokduang H, Padthaisong S, Namwat N, Klanrit P, Phetcharaburanin J, Wangwiwatsin A, Khampitak T, Koonmee S, Titapun A, Jarearnrat A, Khuntikeo N, Loilome W. Targeting Fatty Acid Synthase Modulates Metabolic Pathways and Inhibits Cholangiocarcinoma Cell Progression. Front Pharmacol 2021; 12:696961. [PMID: 34421595 PMCID: PMC8371458 DOI: 10.3389/fphar.2021.696961] [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] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Accepted: 07/22/2021] [Indexed: 12/21/2022] Open
Abstract
An aberrant regulation of lipid metabolism is involved in the pathogenesis and progression of cancer. Up-regulation of lipid biosynthesis enzymes, including acetyl-CoA carboxylase (ACC), fatty acid synthase (FASN) and HMG-CoA reductase (HMGCR), has been reported in many cancers. Therefore, elucidating lipid metabolism changes in cancer is essential for the development of novel therapeutic targets for various human cancers. The current study aimed to identify the abnormal expression of lipid-metabolizing enzymes in cholangiocarcinoma (CCA) and to evaluate whether they can be used as the targets for CCA treatment. Our study demonstrated that a high expression of FASN was significantly correlated with the advanced stage in CCA patients. In addition, survival analysis showed that high expression of FASN and HMGCR was correlated with shorter survival of CCA patients. Furthermore, FASN knockdown inhibited the growth, migration and invasion in CCA cell lines, KKU055 and KKU213, as well as induced cell cycle arrest and apoptosis in the CCA cell lines. In addition, metabolomics study further revealed that purine metabolism was the most relevant pathway involved in FASN knockdown. Adenosine diphosphate (ADP), glutamine and guanine levels significantly increased in KKU213 cells while guanine and xanthine levels remarkably increased in KKU055 cells showing a marked difference between the control and FASN knockdown groups. These findings provide new insights into the mechanisms associated with FASN knockdown in CCA cell lines and suggest that targeting FASN may serve as a novel CCA therapeutic strategy.
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Affiliation(s)
- Jittima Tomacha
- Department of Biochemistry, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand.,Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen, Thailand
| | - Hasaya Dokduang
- Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen, Thailand
| | - Sureerat Padthaisong
- Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen, Thailand
| | - Nisana Namwat
- Department of Biochemistry, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand.,Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen, Thailand
| | - Poramate Klanrit
- Department of Biochemistry, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand.,Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen, Thailand
| | - Jutarop Phetcharaburanin
- Department of Biochemistry, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand.,Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen, Thailand
| | - Arporn Wangwiwatsin
- Department of Biochemistry, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand.,Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen, Thailand
| | - Tueanjit Khampitak
- Department of Biochemistry, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Supinda Koonmee
- Department of Pathology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand.,Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen, Thailand
| | - Attapol Titapun
- Department of Surgery, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand.,Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen, Thailand
| | - Apiwat Jarearnrat
- Department of Surgery, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand.,Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen, Thailand
| | - Narong Khuntikeo
- Department of Surgery, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand.,Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen, Thailand
| | - Watcharin Loilome
- Department of Biochemistry, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand.,Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen, Thailand
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Lee H, Lee H, Park S, Kim M, Park JY, Jin H, Oh K, Bae J, Yang Y, Choi HK. Integrative Metabolomic and Lipidomic Profiling of Lung Squamous Cell Carcinoma for Characterization of Metabolites and Intact Lipid Species Related to the Metastatic Potential. Cancers (Basel) 2021; 13:4179. [PMID: 34439333 PMCID: PMC8391613 DOI: 10.3390/cancers13164179] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 08/12/2021] [Accepted: 08/17/2021] [Indexed: 11/29/2022] Open
Abstract
SQCC is a major type of NSCLC, which is a major cause of cancer-related deaths, and there were no reports regarding the prediction of metastatic potential of lung SQCC by metabolomic and lipidomic profiling. In this study, metabolomic and lipidomic profiling of lung SQCC were performed to predict its metastatic potential and to suggest potential therapeutic targets for the inhibition of lung SQCC metastasis. Human bronchial epithelial cells and four lung SQCC cell lines with different metastatic potentials were analyzed using gas chromatography-mass spectrometry and direct infusion-mass spectrometry. Based on the obtained metabolic and lipidomic profiles, we constructed models to predict the metastatic potential of lung SQCC; glycerol, putrescine, β-alanine, hypoxanthine, inosine, myo-inositol, phosphatidylinositol (PI) 18:1/18:1, and PI 18:1/20:4 were suggested as characteristic metabolites and intact lipid species associated with lung SQCC metastatic potential. In this study, we established predictive models for the metastatic potential of lung SQCC; furthermore, we identified metabolites and intact lipid species relevant to lung SQCC metastatic potential that may serve as potential therapeutic targets for the inhibition of lung SQCC metastasis.
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Affiliation(s)
- Heayyean Lee
- College of Pharmacy, Chung-Ang University, Seoul 06974, Korea; (H.L.); (H.L.); (M.K.); (K.O.); (J.B.)
| | - Hwanhui Lee
- College of Pharmacy, Chung-Ang University, Seoul 06974, Korea; (H.L.); (H.L.); (M.K.); (K.O.); (J.B.)
| | - Sujeong Park
- Department of Biological Sciences, Sookmyung Women’s University, Seoul 04312, Korea; (S.P.); (J.Y.P.)
| | - Myeongsun Kim
- College of Pharmacy, Chung-Ang University, Seoul 06974, Korea; (H.L.); (H.L.); (M.K.); (K.O.); (J.B.)
| | - Ji Young Park
- Department of Biological Sciences, Sookmyung Women’s University, Seoul 04312, Korea; (S.P.); (J.Y.P.)
| | - Hanyong Jin
- Department of Life Science, Chung-Ang University, Seoul 06974, Korea;
| | - Kyungsoo Oh
- College of Pharmacy, Chung-Ang University, Seoul 06974, Korea; (H.L.); (H.L.); (M.K.); (K.O.); (J.B.)
| | - Jeehyeon Bae
- College of Pharmacy, Chung-Ang University, Seoul 06974, Korea; (H.L.); (H.L.); (M.K.); (K.O.); (J.B.)
| | - Young Yang
- Department of Biological Sciences, Sookmyung Women’s University, Seoul 04312, Korea; (S.P.); (J.Y.P.)
| | - Hyung-Kyoon Choi
- College of Pharmacy, Chung-Ang University, Seoul 06974, Korea; (H.L.); (H.L.); (M.K.); (K.O.); (J.B.)
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Metabolomics in oncology – A fascinating travel into the mechanisms of metabolic disturbances during carcinogenesis. FORUM OF CLINICAL ONCOLOGY 2021. [DOI: 10.2478/fco-2021-0017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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47
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Chen Y, Li HW, Cong F, Lian YX. Metabolomics profiling for identification of potential biomarkers in chickens infected with avian leukosis virus subgroup J (ALV-J). Res Vet Sci 2021; 139:166-171. [PMID: 34332419 DOI: 10.1016/j.rvsc.2021.07.026] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 05/16/2021] [Accepted: 07/22/2021] [Indexed: 10/20/2022]
Abstract
There are currently no vaccines or effective drugs to prevent the disorders caused by avian leukosis virus subgroup J (ALV-J). Hence, it is critical to identify potential biomarkers in ALV-J-infected chickens to prevent ALV-J-induced disorders. We hypothesized that ALV-J infection alters metabolic profile in chickens. In the present study, a nontargeted metabolomics approach based on liquid chromatography coupled with mass spectrometry (LC-MS) was used to find differential metabolites in plasma samples from ALV-J-infected chickens and healthy controls. The parametric statistical test (Student's t-test) and fold change analysis were used for univariate analysis. Multivariate statistical analyses included principal component analysis (PCA) and partial least squares-discriminant analysis (PLS-DA). The levels of methyl bromide, pyraclonil, hexaflumuron, lythidathion, 3-phosphoglycerol-glutathione, bis-4-nitrophenyl phosphate, 4-ketocyclophosphamide, oxidized photinus luciferin, phenyl sulfate, and aryl sulfate significantly decreased, whereas the levels of 2-methylthiobenzothiazole, irinotecan, methadone, 3-o-ethyl-l-ascorbic acid, and o-acetylneuraminic acid markedly increased in ALV-J-infected chickens as compared to those in healthy controls. These data provide metabolic evidence and potential biomarkers for ALV-J-induced alterations in plasma metabolism.
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Affiliation(s)
- Yuan Chen
- School of Life Science, Huizhou University, Huizhou 516007, China
| | - Hong-Wei Li
- School of Life Science, Huizhou University, Huizhou 516007, China.
| | - Feng Cong
- Guangdong Laboratory Animal Monitoring Institute, Guangdong Key Laboratory of Laboratory Animals, Guangzhou 510633, China
| | - Yue-Xiao Lian
- Guangdong Laboratory Animal Monitoring Institute, Guangdong Key Laboratory of Laboratory Animals, Guangzhou 510633, China
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48
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Regulation and Functions of Protumoral Unconventional T Cells in Solid Tumors. Cancers (Basel) 2021; 13:cancers13143578. [PMID: 34298791 PMCID: PMC8304984 DOI: 10.3390/cancers13143578] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Revised: 07/02/2021] [Accepted: 07/12/2021] [Indexed: 01/03/2023] Open
Abstract
The vast majority of studies on T cell biology in tumor immunity have focused on peptide-reactive conventional T cells that are restricted to polymorphic major histocompatibility complex molecules. However, emerging evidence indicated that unconventional T cells, including γδ T cells, natural killer T (NKT) cells and mucosal-associated invariant T (MAIT) cells are also involved in tumor immunity. Unconventional T cells span the innate-adaptive continuum and possess the unique ability to rapidly react to nonpeptide antigens via their conserved T cell receptors (TCRs) and/or to activating cytokines to orchestrate many aspects of the immune response. Since unconventional T cell lineages comprise discrete functional subsets, they can mediate both anti- and protumoral activities. Here, we review the current understanding of the functions and regulatory mechanisms of protumoral unconventional T cell subsets in the tumor environment. We also discuss the therapeutic potential of these deleterious subsets in solid cancers and why further feasibility studies are warranted.
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49
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Salahshouri P, Emadi-Baygi M, Jalili M, Khan FM, Wolkenhauer O, Salehzadeh-Yazdi A. A Metabolic Model of Intestinal Secretions: The Link between Human Microbiota and Colorectal Cancer Progression. Metabolites 2021; 11:metabo11070456. [PMID: 34357350 PMCID: PMC8303431 DOI: 10.3390/metabo11070456] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 07/12/2021] [Accepted: 07/13/2021] [Indexed: 12/22/2022] Open
Abstract
The human gut microbiota plays a dual key role in maintaining human health or inducing disorders, for example, obesity, type 2 diabetes, and cancers such as colorectal cancer (CRC). High-throughput data analysis, such as metagenomics and metabolomics, have shown the diverse effects of alterations in dynamic bacterial populations on the initiation and progression of colorectal cancer. However, it is well established that microbiome and human cells constantly influence each other, so it is not appropriate to study them independently. Genome-scale metabolic modeling is a well-established mathematical framework that describes the dynamic behavior of these two axes at the system level. In this study, we created community microbiome models of three conditions during colorectal cancer progression, including carcinoma, adenoma and health status, and showed how changes in the microbial population influence intestinal secretions. Conclusively, our findings showed that alterations in the gut microbiome might provoke mutations and transform adenomas into carcinomas. These alterations include the secretion of mutagenic metabolites such as H2S, NO compounds, spermidine and TMA (trimethylamine), as well as the reduction of butyrate. Furthermore, we found that the colorectal cancer microbiome can promote inflammation, cancer progression (e.g., angiogenesis) and cancer prevention (e.g., apoptosis) by increasing and decreasing certain metabolites such as histamine, glutamine and pyruvate. Thus, modulating the gut microbiome could be a promising strategy for the prevention and treatment of CRC.
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Affiliation(s)
- Pejman Salahshouri
- Department of Genetics, Faculty of Basic Sciences, Shahrekord University, Shahrekord 8818634141, Iran; (P.S.); (M.E.-B.)
| | - Modjtaba Emadi-Baygi
- Department of Genetics, Faculty of Basic Sciences, Shahrekord University, Shahrekord 8818634141, Iran; (P.S.); (M.E.-B.)
- Biotechnology Research Institute, Shahrekord University, Shahrekord 8818634141, Iran
| | - Mahdi Jalili
- Hematology, Oncology and SCT Research Center, Tehran University of Medical Sciences, Tehran 14114, Iran;
| | - Faiz M. Khan
- Department of Systems Biology and Bioinformatics, University of Rostock, 18051 Rostock, Germany; (F.M.K.); (O.W.)
| | - Olaf Wolkenhauer
- Department of Systems Biology and Bioinformatics, University of Rostock, 18051 Rostock, Germany; (F.M.K.); (O.W.)
| | - Ali Salehzadeh-Yazdi
- Department of Systems Biology and Bioinformatics, University of Rostock, 18051 Rostock, Germany; (F.M.K.); (O.W.)
- Correspondence:
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50
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Schmidt DR, Patel R, Kirsch DG, Lewis CA, Vander Heiden MG, Locasale JW. Metabolomics in cancer research and emerging applications in clinical oncology. CA Cancer J Clin 2021; 71:333-358. [PMID: 33982817 PMCID: PMC8298088 DOI: 10.3322/caac.21670] [Citation(s) in RCA: 275] [Impact Index Per Article: 91.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 03/07/2021] [Accepted: 03/09/2021] [Indexed: 12/12/2022] Open
Abstract
Cancer has myriad effects on metabolism that include both rewiring of intracellular metabolism to enable cancer cells to proliferate inappropriately and adapt to the tumor microenvironment, and changes in normal tissue metabolism. With the recognition that fluorodeoxyglucose-positron emission tomography imaging is an important tool for the management of many cancers, other metabolites in biological samples have been in the spotlight for cancer diagnosis, monitoring, and therapy. Metabolomics is the global analysis of small molecule metabolites that like other -omics technologies can provide critical information about the cancer state that are otherwise not apparent. Here, the authors review how cancer and cancer therapies interact with metabolism at the cellular and systemic levels. An overview of metabolomics is provided with a focus on currently available technologies and how they have been applied in the clinical and translational research setting. The authors also discuss how metabolomics could be further leveraged in the future to improve the management of patients with cancer.
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Affiliation(s)
- Daniel R. Schmidt
- Koch Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Radiation Oncology, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
| | - Rutulkumar Patel
- Department of Radiation Oncology, Duke University School of Medicine, Durham, NC 27708 USA
| | - David G. Kirsch
- Department of Radiation Oncology, Duke University School of Medicine, Durham, NC 27708 USA
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC 27708 USA
| | - Caroline A. Lewis
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Matthew G. Vander Heiden
- Koch Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Jason W. Locasale
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC 27708 USA
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