1
|
Ou J, Kang Y, Medlegeh, Fu K, Zhang Y, Yang W. An analysis of the vaginal microbiota and cervicovaginal metabolomics in cervical lesions and cervical carcinoma. Heliyon 2024; 10:e33383. [PMID: 39040371 PMCID: PMC11260971 DOI: 10.1016/j.heliyon.2024.e33383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 05/16/2024] [Accepted: 06/20/2024] [Indexed: 07/24/2024] Open
Abstract
Background To explore the role of vaginal microbiota and metabolomics in the progression of cervical dysplasia. Methods The patient group consists of female patients with low-grade, high-grade cervical dysplasia, and cervical cancer. Normal cervix samples from health volunteers were used as controls. The metabolic fingerprints of cervicovaginal lavage were analyzed using liquid chromatography-mass spectrometry, while the vaginal microbiota was examined through 16S rRNA sequencing. Bioinformatic analysis was adopted to investigate the interplay between hosts and microbes. The vaginal metabolic and microbiota profiles of 90 female patients with cervical dysplasia and 10 controls were analyzed to discover the biological characteristics underlying the progression of cervical cancer. Results We found that Valyl-Glutamate, N, N'-Diacetylbenzidine, and Oxidized glutathione, which were involved in oxidative stress response, were discriminators to distinguish the normal cervix, invasive cervical carcinomas, and CIN3 from others. Cervical carcinoma was characterized by a large variety of vaginal microbes (dominated by non-Lactobacillus communities) compared to the control. These microbes affected amino acid and nucleotide metabolism, producing metabolites with cervical carcinoma and genital inflammation compared to the control group. Conclusions This study revealed that cervicovaginal metabolic profiles were determined by cervical cancer, vaginal microbiota, and their interplays. ROS metabolism can be used to discriminate normal cervix, CIN3, and invasive cervical carcinoma.
Collapse
Affiliation(s)
- Jie Ou
- Department of Gyneacology, Xiangya Hospital Central South University, Changsha, Hunan, 410008, China
| | - Yanan Kang
- Department of Gyneacology, Xiangya Hospital Central South University, Changsha, Hunan, 410008, China
| | - Medlegeh
- Department of Gyneacology, Xiangya Hospital Central South University, Changsha, Hunan, 410008, China
| | - Kun Fu
- Department of Gyneacology, Xiangya Hospital Central South University, Changsha, Hunan, 410008, China
| | - Yu Zhang
- Department of Gyneacology, Xiangya Hospital Central South University, Changsha, Hunan, 410008, China
| | - Wenqing Yang
- Department of Gyneacology, Xiangya Hospital Central South University, Changsha, Hunan, 410008, China
| |
Collapse
|
2
|
Chioccioli S, Rocchetti G, Ruzzolini J, Urciuoli S, Vitali F, Bartolucci G, Pallecchi M, Caderni G, De Filippo C, Nediani C, Lucini L. Changes in Faecal Microbiota Profile and Plasma Biomarkers following the Administration of an Antioxidant Oleuropein-Rich Leaf Extract in a Rat Model Mimicking Colorectal Cancer. Antioxidants (Basel) 2024; 13:724. [PMID: 38929163 PMCID: PMC11200411 DOI: 10.3390/antiox13060724] [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: 04/25/2024] [Revised: 06/11/2024] [Accepted: 06/12/2024] [Indexed: 06/28/2024] Open
Abstract
Oleuropein (OLE), a phenolic compound particularly abundant in the olive leaves, has been reported to have beneficial activities against colorectal cancer (CRC). In vitro studies suggested that these latter could be due to a modulation of the intestinal microbiota. Aiming to evaluate if OLE could affect the intestinal microbiota and the plasma metabolome, an antioxidant oleuropein-rich leaf extract (ORLE) was administered for one week to PIRC rats (F344/NTac-Apcam1137), a genetic model mimicking CRC. ORLE treatment significantly modulated the gut microbiota composition. Plasma metabolomic profiles revealed a significant predictive ability for amino acids, medium-chain fatty acids, and aldehydes. Pathway analysis revealed a significant decrease in phosphatidylcholine accumulation (LogFC = -1.67) in PIRC rats. These results suggest a significant effect of ORLE administration on faecal microbiota profiles and plasma metabolomes, thereby offering new omics-based insights into its protective role in CRC progression.
Collapse
Affiliation(s)
- Sofia Chioccioli
- Department of Neurosciences, Psychology, Drug Research and Child Health (NEUROFARBA), University of Florence, 50134 Florence, Italy; (S.C.); (G.B.); (G.C.)
| | - Gabriele Rocchetti
- Department of Animal Science, Food and Nutrition, Università Cattolica del Sacro Cuore, Via Emilia Parmense 84, 29122 Piacenza, Italy
| | - Jessica Ruzzolini
- Department of Experimental and Clinical Biomedical Sciences “Mario Serio”, University of Florence, 50134 Florence, Italy;
| | - Silvia Urciuoli
- PhytoLab (Pharmaceutical, Cosmetic, Food Supplement Technology and Analysis)-DiSIA, Department of Statistics, Informatics, Applications “Giuseppe Parenti”, Scientific and Technological Pole, University of Florence, 50019 Sesto Fiorentino, Italy;
| | - Francesco Vitali
- Institute of Agricultural Biology and Biotechnology, National Research Council (CNR), Via Moruzzi, 1, 56124 Pisa, Italy
- Research Centre for Agriculture and Environment, Council for Agricultural Research and Economics (CREA), Via di Lanciola 12/A, 50125 Florence, Italy
| | - Gianluca Bartolucci
- Department of Neurosciences, Psychology, Drug Research and Child Health (NEUROFARBA), University of Florence, 50134 Florence, Italy; (S.C.); (G.B.); (G.C.)
| | - Marco Pallecchi
- Department of Neurosciences, Psychology, Drug Research and Child Health (NEUROFARBA), University of Florence, 50134 Florence, Italy; (S.C.); (G.B.); (G.C.)
| | - Giovanna Caderni
- Department of Neurosciences, Psychology, Drug Research and Child Health (NEUROFARBA), University of Florence, 50134 Florence, Italy; (S.C.); (G.B.); (G.C.)
| | - Carlotta De Filippo
- Institute of Agricultural Biology and Biotechnology, National Research Council (CNR), Via Moruzzi, 1, 56124 Pisa, Italy
| | - Chiara Nediani
- Department of Experimental and Clinical Biomedical Sciences “Mario Serio”, University of Florence, 50134 Florence, Italy;
| | - Luigi Lucini
- Department for Sustainable Food Process, Università Cattolica del Sacro Cuore, Via Emilia Parmense 84, 29122 Piacenza, Italy
| |
Collapse
|
3
|
Chen CJ, Lee DY, Yu J, Lin YN, Lin TM. Recent advances in LC-MS-based metabolomics for clinical biomarker discovery. MASS SPECTROMETRY REVIEWS 2023; 42:2349-2378. [PMID: 35645144 DOI: 10.1002/mas.21785] [Citation(s) in RCA: 33] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 10/14/2021] [Accepted: 11/18/2021] [Indexed: 06/15/2023]
Abstract
The employment of liquid chromatography-mass spectrometry (LC-MS) untargeted and targeted metabolomics has led to the discovery of novel biomarkers and improved the understanding of various disease mechanisms. Numerous strategies have been reported to expand the metabolite coverage in LC-MS-untargeted and targeted metabolomics. To improve the sensitivity of low-abundance or poor-ionized metabolites for reducing the amount of clinical sample, chemical derivatization methods are used to target different functional groups. Proper sample preparation is beneficial for reducing the matrix effect, maintaining the stability of the LC-MS system, and increasing the metabolite coverage. Machine learning has recently been integrated into the workflow of LC-MS metabolomics to accelerate metabolite identification and data-processing automation, and increase the accuracy of disease classification and clinical outcome prediction. Due to the rapidly growing utility of LC-MS metabolomics in discovering disease markers, this review will address the recent advances in the field and offer perspectives on various strategies for expanding metabolite coverage, chemical derivatization, sample preparation, clinical disease markers, and machining learning for disease modeling.
Collapse
Affiliation(s)
- Chao-Jung Chen
- Graduate Institute of Integrated Medicine, College of Chinese Medicine, China Medical University, Taichung, Taiwan
- Proteomics Core Laboratory, Department of Medical Research, China Medical University Hospital, Taichung, Taiwan
| | - Der-Yen Lee
- Graduate Institute of Integrated Medicine, College of Chinese Medicine, China Medical University, Taichung, Taiwan
| | - Jiaxin Yu
- AI Innovation Center, China Medical University Hospital, Taichung, Taiwan
| | - Yu-Ning Lin
- Proteomics Core Laboratory, Department of Medical Research, China Medical University Hospital, Taichung, Taiwan
| | - Tsung-Min Lin
- Proteomics Core Laboratory, Department of Medical Research, China Medical University Hospital, Taichung, Taiwan
| |
Collapse
|
4
|
Pankevičiūtė-Bukauskienė M, Mikalayeva V, Žvikas V, Skeberdis VA, Bordel S. Multi-Omics Analysis Revealed Increased De Novo Synthesis of Serine and Lower Activity of the Methionine Cycle in Breast Cancer Cell Lines. Molecules 2023; 28:molecules28114535. [PMID: 37299011 DOI: 10.3390/molecules28114535] [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: 03/30/2023] [Revised: 05/25/2023] [Accepted: 06/01/2023] [Indexed: 06/12/2023] Open
Abstract
A pipeline for metabolomics, based on UPLC-ESI-MS, was tested on two malignant breast cancer cell lines of the sub-types ER(+), PR(+), and HER2(3+) (MCF-7 and BCC), and one non-malignant epithelial cancer cell line (MCF-10A). This allowed us to quantify 33 internal metabolites, 10 of which showed a concentration profile associated with malignancy. Whole-transcriptome RNA-seq was also carried out for the three mentioned cell lines. An integrated analysis of metabolomics and transcriptomics was carried out using a genome-scale metabolic model. Metabolomics revealed the depletion of several metabolites that have homocysteine as a precursor, which was consistent with the lower activity of the methionine cycle caused by lower expression of the AHCY gene in cancer cell lines. Increased intracellular serine pools in cancer cell lines appeared to result from the over-expression of PHGDH and PSPH, which are involved in intracellular serine biosynthesis. An increased concentration of pyroglutamic acid in malignant cells was linked to the overexpression of the gene CHAC1.
Collapse
Affiliation(s)
| | - Valeryia Mikalayeva
- Institute of Cardiology, Lithuanian University of Health Sciences, LT 50162 Kaunas, Lithuania
| | - Vaidotas Žvikas
- Institute of Pharmaceutical Technologies, Lithuanian University of Health Sciences, LT 50162 Kaunas, Lithuania
| | - V Arvydas Skeberdis
- Institute of Cardiology, Lithuanian University of Health Sciences, LT 50162 Kaunas, Lithuania
| | - Sergio Bordel
- Institute of Cardiology, Lithuanian University of Health Sciences, LT 50162 Kaunas, Lithuania
- Institute of Sustainable Processes, University of Valladolid, Dr. Mergelina s/n, 47011 Valladolid, Spain
| |
Collapse
|
5
|
Cararo Lopes E, Sawant A, Moore D, Ke H, Shi F, Laddha S, Chen Y, Sharma A, Naumann J, Guo JY, Gomez M, Ibrahim M, Smith TL, Riedlinger GM, Lattime EC, Trooskin S, Ganesan S, Su X, Pasqualini R, Arap W, De S, Chan CS, White E. Integrated metabolic and genetic analysis reveals distinct features of human differentiated thyroid cancer. Clin Transl Med 2023; 13:e1298. [PMID: 37317665 PMCID: PMC10267429 DOI: 10.1002/ctm2.1298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 05/22/2023] [Accepted: 05/27/2023] [Indexed: 06/16/2023] Open
Abstract
BACKGROUND Differentiated thyroid cancer (DTC) affects thousands of lives worldwide each year. Typically, DTC is a treatable disease with a good prognosis. Yet, some patients are subjected to partial or total thyroidectomy and radioiodine therapy to prevent local disease recurrence and metastasis. Unfortunately, thyroidectomy and/or radioiodine therapy often worsen(s) quality of life and might be unnecessary in indolent DTC cases. On the other hand, the lack of biomarkers indicating a potential metastatic thyroid cancer imposes an additional challenge to managing and treating patients with this disease. AIM The presented clinical setting highlights the unmet need for a precise molecular diagnosis of DTC and potential metastatic disease, which should dictate appropriate therapy. MATERIALS AND METHODS In this article, we present a differential multi-omics model approach, including metabolomics, genomics, and bioinformatic models, to distinguish normal glands from thyroid tumours. Additionally, we are proposing biomarkers that could indicate potential metastatic diseases in papillary thyroid cancer (PTC), a sub-class of DTC. RESULTS Normal and tumour thyroid tissue from DTC patients had a distinct yet well-defined metabolic profile with high levels of anabolic metabolites and/or other metabolites associated with the energy maintenance of tumour cells. The consistency of the DTC metabolic profile allowed us to build a bioinformatic classification model capable of clearly distinguishing normal from tumor thyroid tissues, which might help diagnose thyroid cancer. Moreover, based on PTC patient samples, our data suggest that elevated nuclear and mitochondrial DNA mutational burden, intra-tumour heterogeneity, shortened telomere length, and altered metabolic profile reflect the potential for metastatic disease. DISCUSSION Altogether, this work indicates that a differential and integrated multi-omics approach might improve DTC management, perhaps preventing unnecessary thyroid gland removal and/or radioiodine therapy. CONCLUSIONS Well-designed, prospective translational clinical trials will ultimately show the value of this integrated multi-omics approach and early diagnosis of DTC and potential metastatic PTC.
Collapse
Affiliation(s)
- Eduardo Cararo Lopes
- Rutgers Cancer Institute of New JerseyNew BrunswickNew JerseyUSA
- Department of Molecular Biology and BiochemistryRutgers UniversityPiscatawayNew JerseyUSA
| | - Akshada Sawant
- Rutgers Cancer Institute of New JerseyNew BrunswickNew JerseyUSA
| | - Dirk Moore
- Rutgers Cancer Institute of New JerseyNew BrunswickNew JerseyUSA
- Department of Biostatistics and EpidemiologyRutgers School of Public HealthPiscatawayNew JerseyUSA
| | - Hua Ke
- Rutgers Cancer Institute of New JerseyNew BrunswickNew JerseyUSA
| | - Fuqian Shi
- Rutgers Cancer Institute of New JerseyNew BrunswickNew JerseyUSA
| | - Saurabh Laddha
- Rutgers Cancer Institute of New JerseyNew BrunswickNew JerseyUSA
| | - Ying Chen
- Rutgers Cancer Institute of New JerseyNew BrunswickNew JerseyUSA
| | - Anchal Sharma
- Rutgers Cancer Institute of New JerseyNew BrunswickNew JerseyUSA
| | - Jake Naumann
- Rutgers Cancer Institute of New JerseyNew BrunswickNew JerseyUSA
| | - Jessie Yanxiang Guo
- Rutgers Cancer Institute of New JerseyNew BrunswickNew JerseyUSA
- Department of MedicineRobert Wood Johnson Medical SchoolRutgers UniversityNew BrunswickNew JerseyUSA
- Department of Chemical BiologyRutgers Ernest Mario School of PharmacyPiscatawayNew JerseyUSA
| | - Maria Gomez
- Rutgers Cancer Institute of New JerseyNew BrunswickNew JerseyUSA
| | - Maria Ibrahim
- Rutgers Cancer Institute of New JerseyNew BrunswickNew JerseyUSA
| | - Tracey L. Smith
- Rutgers Cancer Institute of New JerseyNewarkNew JerseyUSA
- Division of Cancer BiologyDepartment of Radiation OncologyRutgers New Jersey Medical SchoolNewarkNew JerseyUSA
| | | | - Edmund C. Lattime
- Rutgers Cancer Institute of New JerseyNew BrunswickNew JerseyUSA
- Department of Surgery, Robert Wood Johnson Medical SchoolRutgers UniversityNew BrunswickNew JerseyUSA
| | - Stanley Trooskin
- Department of Surgery, Robert Wood Johnson Medical SchoolRutgers UniversityNew BrunswickNew JerseyUSA
| | - Shridar Ganesan
- Rutgers Cancer Institute of New JerseyNew BrunswickNew JerseyUSA
- Department of MedicineRobert Wood Johnson Medical SchoolRutgers UniversityNew BrunswickNew JerseyUSA
| | - Xiaoyang Su
- Rutgers Cancer Institute of New JerseyNew BrunswickNew JerseyUSA
- Department of MedicineRobert Wood Johnson Medical SchoolRutgers UniversityNew BrunswickNew JerseyUSA
| | - Renata Pasqualini
- Rutgers Cancer Institute of New JerseyNewarkNew JerseyUSA
- Division of Cancer BiologyDepartment of Radiation OncologyRutgers New Jersey Medical SchoolNewarkNew JerseyUSA
| | - Wadih Arap
- Rutgers Cancer Institute of New JerseyNewarkNew JerseyUSA
- Division of Hematology/OncologyDepartment of MedicineRutgers New Jersey Medical SchoolNewarkNew JerseyUSA
| | - Subhajyoti De
- Rutgers Cancer Institute of New JerseyNew BrunswickNew JerseyUSA
| | - Chang S. Chan
- Rutgers Cancer Institute of New JerseyNew BrunswickNew JerseyUSA
- Department of MedicineRobert Wood Johnson Medical SchoolRutgers UniversityNew BrunswickNew JerseyUSA
| | - Eileen White
- Rutgers Cancer Institute of New JerseyNew BrunswickNew JerseyUSA
- Department of Molecular Biology and BiochemistryRutgers UniversityPiscatawayNew JerseyUSA
- Ludwig Princeton Branch, Ludwig Institute for Cancer ResearchPrinceton UniversityPrincetonNew JerseyUSA
| |
Collapse
|
6
|
Liu C, Yan F, Song D, Zeng Y, Qiao T, Wu D, Cheng Y, Chen H. Trans-omic analyses identified novel prognostic biomarkers for colorectal cancer survival. Clin Transl Med 2023; 13:e1304. [PMID: 37329135 PMCID: PMC10276188 DOI: 10.1002/ctm2.1304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 05/30/2023] [Accepted: 06/02/2023] [Indexed: 06/18/2023] Open
Affiliation(s)
- Chanjuan Liu
- Center for Tumor Diagnosis & Therapy, Jinshan Hospital, Fudan UniversityShanghaiChina
- Department of Pulmonary and Critical Care Medicine, Zhongshan Hospital, Fudan UniversityShanghaiChina
| | - Furong Yan
- Center for Tumor Diagnosis & Therapy, Jinshan Hospital, Fudan UniversityShanghaiChina
- Department of Pulmonary and Critical Care Medicine, Zhongshan Hospital, Fudan UniversityShanghaiChina
- Center of Molecular Diagnosis and Therapy, The Second Hospital of Fujian Medical UniversityQuanzhouFujianChina
| | - Dongli Song
- Department of Pulmonary and Critical Care Medicine, Zhongshan Hospital, Fudan UniversityShanghaiChina
- Shanghai Institute of Clinical BioinformaticsShanghaiChina
| | - Yiming Zeng
- Center of Molecular Diagnosis and Therapy, The Second Hospital of Fujian Medical UniversityQuanzhouFujianChina
| | - Tiankui Qiao
- Center for Tumor Diagnosis & Therapy, Jinshan Hospital, Fudan UniversityShanghaiChina
| | - Duojiao Wu
- Center for Tumor Diagnosis & Therapy, Jinshan Hospital, Fudan UniversityShanghaiChina
- Department of Pulmonary and Critical Care Medicine, Zhongshan Hospital, Fudan UniversityShanghaiChina
| | - Yunfeng Cheng
- Center for Tumor Diagnosis & Therapy, Jinshan Hospital, Fudan UniversityShanghaiChina
- Department of Pulmonary and Critical Care Medicine, Zhongshan Hospital, Fudan UniversityShanghaiChina
| | - Hao Chen
- Department of Thoracic SurgeryZhongshan-Xuhui Hospital, Fudan UniversityShanghaiChina
| |
Collapse
|
7
|
Sun C, Wang A, Zhou Y, Chen P, Wang X, Huang J, Gao J, Wang X, Shu L, Lu J, Dai W, Bu Z, Ji J, He J. Spatially resolved multi-omics highlights cell-specific metabolic remodeling and interactions in gastric cancer. Nat Commun 2023; 14:2692. [PMID: 37164975 PMCID: PMC10172194 DOI: 10.1038/s41467-023-38360-5] [Citation(s) in RCA: 28] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 04/27/2023] [Indexed: 05/12/2023] Open
Abstract
Mapping tumor metabolic remodeling and their spatial crosstalk with surrounding non-tumor cells can fundamentally improve our understanding of tumor biology, facilitates the designing of advanced therapeutic strategies. Here, we present an integration of mass spectrometry imaging-based spatial metabolomics and lipidomics with microarray-based spatial transcriptomics to hierarchically visualize the intratumor metabolic heterogeneity and cell metabolic interactions in same gastric cancer sample. Tumor-associated metabolic reprogramming is imaged at metabolic-transcriptional levels, and maker metabolites, lipids, genes are connected in metabolic pathways and colocalized in the heterogeneous cancer tissues. Integrated data from spatial multi-omics approaches coherently identify cell types and distributions within the complex tumor microenvironment, and an immune cell-dominated "tumor-normal interface" region where tumor cells contact adjacent tissues are characterized with distinct transcriptional signatures and significant immunometabolic alterations. Our approach for mapping tissue molecular architecture provides highly integrated picture of intratumor heterogeneity, and transform the understanding of cancer metabolism at systemic level.
Collapse
Affiliation(s)
- Chenglong Sun
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
- Key Laboratory for Applied Technology of Sophisticated Analytical Instruments of Shandong Province, Shandong Analysis and Test Center, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250014, China
- Key Laboratory for Natural Active Pharmaceutical Constituents Research in Universities of Shandong Province, School of Pharmaceutical Sciences, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250014, China
| | - Anqiang Wang
- Gastrointestinal Cancer Center, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital and Institute, Beijing, 100142, China
| | - Yanhe Zhou
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Panpan Chen
- Key Laboratory for Applied Technology of Sophisticated Analytical Instruments of Shandong Province, Shandong Analysis and Test Center, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250014, China
- Key Laboratory for Natural Active Pharmaceutical Constituents Research in Universities of Shandong Province, School of Pharmaceutical Sciences, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250014, China
| | - Xiangyi Wang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Jianpeng Huang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Jiamin Gao
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Xiao Wang
- Key Laboratory for Applied Technology of Sophisticated Analytical Instruments of Shandong Province, Shandong Analysis and Test Center, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250014, China
- Key Laboratory for Natural Active Pharmaceutical Constituents Research in Universities of Shandong Province, School of Pharmaceutical Sciences, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250014, China
| | - Liebo Shu
- Shanghai Luming Biological Technology co.Ltd, Shanghai, 201102, China
| | - Jiawei Lu
- Shanghai Luming Biological Technology co.Ltd, Shanghai, 201102, China
| | - Wentao Dai
- NHC Key Lab of Reproduction Regulation (Shanghai Institute for Biomedical and Pharmaceutical Technologies) & Shanghai Engineering Research Center of Pharmaceutical Translation, Fudan University, Shanghai, 200080, China.
- Shanghai Key Laboratory of Gastric Neoplasms, Department of General Surgery, Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Zhaode Bu
- Gastrointestinal Cancer Center, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital and Institute, Beijing, 100142, China.
| | - Jiafu Ji
- Gastrointestinal Cancer Center, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital and Institute, Beijing, 100142, China.
| | - Jiuming He
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China.
- NMPA Key Laboratory of safety research and evaluation of Innovative Drug, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China.
| |
Collapse
|
8
|
Cararo-Lopes E, Sawant A, Moore D, Ke H, Shi F, Laddha S, Chen Y, Sharma A, Naumann J, Guo JY, Gomez M, Ibrahim M, Smith TL, Riedlinger GM, Lattime EC, Trooskin S, Ganesan S, Su X, Pasqualini R, Arap W, De S, Chan CS, White E. Integrated metabolic and genetic analysis reveals distinct features of primary differentiated thyroid cancer and its metastatic potential in humans. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.03.09.23287037. [PMID: 36945575 PMCID: PMC10029066 DOI: 10.1101/2023.03.09.23287037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2023]
Abstract
Differentiated thyroid cancer (DTC) affects thousands of lives worldwide every year. Typically, DTC is a treatable disease with a good prognosis. Yet, some patients are subjected to partial or total thyroidectomy and radioiodine therapy to prevent local disease recurrence and metastasis. Unfortunately, thyroidectomy and/or radioiodine therapy often worsen(s) the quality of life and might be unnecessary in indolent DTC cases. This clinical setting highlights the unmet need for a precise molecular diagnosis of DTC, which should dictate appropriate therapy. Here we propose a differential multi-omics model approach to distinguish normal gland from thyroid tumor and to indicate potential metastatic diseases in papillary thyroid cancer (PTC), a sub-class of DTC. Based on PTC patient samples, our data suggest that elevated nuclear and mitochondrial DNA mutational burden, intratumor heterogeneity, shortened telomere length, and altered metabolic profile reflect the potential for metastatic disease. Specifically, normal and tumor thyroid tissues from these patients had a distinct yet well-defined metabolic profile with high levels of anabolic metabolites and/or other metabolites associated with the energy maintenance of tumor cells. Altogether, this work indicates that a differential and integrated multi-omics approach might improve DTC management, perhaps preventing unnecessary thyroid gland removal and/or radioiodine therapy. Well-designed, prospective translational clinical trials will ultimately show the value of this targeted molecular approach. TRANSLATIONAL RELEVANCE In this article, we propose a new integrated metabolic, genomic, and cytopathologic methods to diagnose Differentiated Thyroid Cancer when the conventional methods failed. Moreover, we suggest metabolic and genomic markers to help predict high-risk Papillary Thyroid Cancer. Both might be important tools to avoid unnecessary surgery and/or radioiodine therapy that can worsen the quality of life of the patients more than living with an indolent Thyroid nodule.
Collapse
|
9
|
Prediction of Postoperative Pathologic Risk Factors in Cervical Cancer Patients Treated with Radical Hysterectomy by Machine Learning. Curr Oncol 2022; 29:9613-9629. [PMID: 36547169 PMCID: PMC9776916 DOI: 10.3390/curroncol29120755] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 11/27/2022] [Accepted: 11/29/2022] [Indexed: 12/12/2022] Open
Abstract
Pretherapeutic serological parameters play a predictive role in pathologic risk factors (PRF), which correlate with treatment and prognosis in cervical cancer (CC). However, the method of pre-operative prediction to PRF is limited and the clinical availability of machine learning methods remains unknown in CC. Overall, 1260 early-stage CC patients treated with radical hysterectomy (RH) were randomly split into training and test cohorts. Six machine learning classifiers, including Gradient Boosting Machine, Support Vector Machine with Gaussian kernel, Random Forest, Conditional Random Forest, Naive Bayes, and Elastic Net, were used to derive diagnostic information from nine clinical factors and 75 parameters readily available from pretreatment peripheral blood tests. The best results were obtained by RF in deep stromal infiltration prediction with an accuracy of 70.8% and AUC of 0.767. The highest accuracy and AUC for predicting lymphatic metastasis with Cforest were 64.3% and 0.620, respectively. The highest accuracy of prediction for lymphavascular space invasion with EN was 59.7% and the AUC was 0.628. Blood markers, including D-dimer and uric acid, were associated with PRF. Machine learning methods can provide critical diagnostic prediction on PRF in CC before surgical intervention. The use of predictive algorithms may facilitate individualized treatment options through diagnostic stratification.
Collapse
|
10
|
Ćwilichowska N, Świderska KW, Dobrzyń A, Drąg M, Poręba M. Diagnostic and therapeutic potential of protease inhibition. Mol Aspects Med 2022; 88:101144. [PMID: 36174281 DOI: 10.1016/j.mam.2022.101144] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Revised: 07/20/2022] [Accepted: 09/09/2022] [Indexed: 12/14/2022]
Abstract
Proteases are enzymes that hydrolyze peptide bonds in proteins and peptides; thus, they control virtually all biological processes. Our understanding of protease function has advanced considerably from nonselective digestive enzymes to highly specialized molecular scissors that orchestrate complex signaling networks through a limited proteolysis. The catalytic activity of proteases is tightly regulated at several levels, ranging from gene expression through trafficking and maturation to posttranslational modifications. However, when this delicate balance is disturbed, many diseases develop, including cancer, inflammatory disorders, diabetes, and neurodegenerative diseases. This new understanding of the role of proteases in pathologic physiology indicates that these enzymes represent excellent molecular targets for the development of therapeutic inhibitors, as well as for the design of chemical probes to visualize their redundant activity. Recently, numerous platform technologies have been developed to identify and optimize protease substrates and inhibitors, which were further used as lead structures for the development of chemical probes and therapeutic drugs. Due to this considerable success, the clinical potential of proteases in therapeutics and diagnostics is rapidly growing and is still not completely explored. Therefore, small molecules that can selectively target aberrant protease activity are emerging in diseases cells. In this review, we describe modern trends in the design of protease drugs as well as small molecule activity-based probes to visualize selected proteases in clinical settings.
Collapse
Affiliation(s)
- Natalia Ćwilichowska
- Department of Chemical Biology and Bioimaging, Faculty of Chemistry, Wroclaw University of Science and Technology, Wyb, Wyspianskiego 27, 50-370, Wroclaw, Poland
| | - Karolina W Świderska
- Department of Chemical Biology and Bioimaging, Faculty of Chemistry, Wroclaw University of Science and Technology, Wyb, Wyspianskiego 27, 50-370, Wroclaw, Poland
| | - Agnieszka Dobrzyń
- Nencki Institute of Experimental Biology, Ludwika Pasteura 3, 02-093, Warsaw, Poland
| | - Marcin Drąg
- Department of Chemical Biology and Bioimaging, Faculty of Chemistry, Wroclaw University of Science and Technology, Wyb, Wyspianskiego 27, 50-370, Wroclaw, Poland.
| | - Marcin Poręba
- Department of Chemical Biology and Bioimaging, Faculty of Chemistry, Wroclaw University of Science and Technology, Wyb, Wyspianskiego 27, 50-370, Wroclaw, Poland.
| |
Collapse
|
11
|
Morine Y, Utsunomiya T, Yamanaka-Okumura H, Saito Y, Yamada S, Ikemoto T, Imura S, Kinoshita S, Hirayama A, Tanaka Y, Shimada M. Essential amino acids as diagnostic biomarkers of hepatocellular carcinoma based on metabolic analysis. Oncotarget 2022; 13:1286-1298. [PMID: 36441784 DOI: 10.18632/oncotarget.28306] [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: 11/23/2022] Open
Abstract
Metabolomics, defined as the comprehensive identification of all small metabolites in a biological sample, has the power to shed light on phenotypic changes associated with various diseases, including cancer. To discover potential metabolomic biomarkers of hepatocellular carcinoma (HCC), we investigated the metabolomes of tumor and non-tumor tissue in 20 patients with primary HCC using capillary electrophoresis-time-of-flight mass spectrometry. We also analyzed blood samples taken immediately before and 14 days after hepatectomy to identify associated changes in the serum metabolome. Marked changes were detected in the different quantity of 61 metabolites that could discriminate between HCC tumor and paired non-tumor tissue and additionally between HCC primary tumors and colorectal liver metastases. Among the 30 metabolites significantly upregulated in HCC tumors compared with non-tumor tissues, 10 were amino acids, and 7 were essential amino acids (leucine, valine, tryptophan, isoleucine, methionine, lysine, and phenylalanine). Similarly, the serum metabolomes of HCC patients before hepatectomy revealed a significant increase in 16 metabolites, including leucine, valine, and tryptophan. Our results reveal striking differences in the metabolomes of HCC tumor tissue compared with non-tumor tissue, and identify the essential amino acids leucine, valine, and tryptophan as potential metabolic biomarkers for HCC.
Collapse
Affiliation(s)
- Yuji Morine
- Department of Surgery, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima 770-8503, Japan
| | - Tohru Utsunomiya
- Department of Surgery, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima 770-8503, Japan
| | - Hisami Yamanaka-Okumura
- Department of Clinical Nutrition and Food Management, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima 770-8503, Japan
| | - Yu Saito
- Department of Surgery, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima 770-8503, Japan
| | - Shinichiro Yamada
- Department of Surgery, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima 770-8503, Japan
| | - Tetsuya Ikemoto
- Department of Surgery, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima 770-8503, Japan
| | - Satoru Imura
- Department of Surgery, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima 770-8503, Japan
| | - Shohei Kinoshita
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0052, Japan.,Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Kanagawa 252-0882, Japan
| | - Akiyoshi Hirayama
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0052, Japan.,Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Kanagawa 252-0882, Japan
| | - Yasuhito Tanaka
- Department of Gastroenterology and Hepatology, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan
| | - Mitsuo Shimada
- Department of Surgery, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima 770-8503, Japan
| |
Collapse
|
12
|
Shishkanova TV, Sinica A. Electrochemically deposited cobalt bis(dicarbollide) derivative and the detection of neuroblastoma markers on the electrode surface. J Electroanal Chem (Lausanne) 2022. [DOI: 10.1016/j.jelechem.2022.116674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
|
13
|
Parekh A, Das S, Das CK, Mandal M. Progressing Towards a Human-Centric Approach in Cancer Research. Front Oncol 2022; 12:896633. [PMID: 35928861 PMCID: PMC9343698 DOI: 10.3389/fonc.2022.896633] [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: 03/15/2022] [Accepted: 06/21/2022] [Indexed: 11/17/2022] Open
Abstract
Despite the advancement in research methodologies and technologies for cancer research, there is a high rate of anti-cancer drug attrition. In this review, we discuss different conventional and modern approaches in cancer research and how human-centric models can improve on the voids conferred by more traditional animal-centric models, thereby offering a more reliable platform for drug discovery. Advanced three-dimensional cell culture methodologies, along with in silico computational analysis form the core of human-centric cancer research. This can provide a holistic understanding of the research problems and help design specific and accurate experiments that could lead to the development of better cancer therapeutics. Here, we propose a new human-centric research roadmap that promises to provide a better platform for cancer research and drug discovery.
Collapse
Affiliation(s)
- Aditya Parekh
- School of Design, Anant National University, Ahmedabad, India
- Genetics and Development, National Centre For Biological Sciences, Bengaluru, India
- *Correspondence: Aditya Parekh,
| | - Subhayan Das
- School of Medical Science and Technology (SMST), Indian Institute of Technology, Kharagpur, India
| | - Chandan K. Das
- Cancer Biology, University of Pennsylvania, Philadelphia, PA, United States
| | - Mahitosh Mandal
- School of Medical Science and Technology (SMST), Indian Institute of Technology, Kharagpur, India
| |
Collapse
|
14
|
Wei W, Xie LZ, Xia Q, Fu Y, Liu FY, Ding DN, Han FJ. The role of vaginal microecology in the cervical cancer. J Obstet Gynaecol Res 2022; 48:2237-2254. [PMID: 35815344 DOI: 10.1111/jog.15359] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 05/24/2022] [Accepted: 06/28/2022] [Indexed: 12/24/2022]
Abstract
AIM To explore the role of vaginal microecology in cervical cancer, so as to increase the understanding of cervical cancer and lay a foundation for future large-sample clinical trials. METHODS We reviewed and summarized the literature comprehensively, and discussed the relationship between vaginal microecology and HPV infection, CIN progression and cervical cancer, as well as the potential molecular mechanism and the prospects of probiotics and prebiotics in future cancer treatments. RESULTS With the popularization of high-throughput sequencing technology and the development of bioinformatics analysis technology, many evidences show that the increase in the diversity of the bacterial community in the vaginal microecological environment and the decrease in the number of Lactobacilli are associated with the continuous infection of HPV and the further development of CIN, cervical cancer-related. CONCLUSIONS Vaginal microecological imbalance has an important impact on the occurrence and development of cervical cancer. However, the pathogenesis is not completely clear, and more high-level basic research and longitudinal clinical studies are needed to verify.
Collapse
Affiliation(s)
- Wei Wei
- Department of Obstetrics and Gynecology, Heilongjiang University of Chinese Medicine, Harbin, China
| | - Liang-Zhen Xie
- Department of Obstetrics and Gynecology, Heilongjiang University of Chinese Medicine, Harbin, China.,Department of Obstetrics and Gynecology, The First Affiliated Hospital of Heilongjiang University of Chinese Medicine, Harbin, China
| | - Qing Xia
- Department of Obstetrics and Gynecology, Heilongjiang University of Chinese Medicine, Harbin, China.,Department of Biochemistry and Molecular Biology, Harbin Medical University, Harbin, China
| | - Yang Fu
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Heilongjiang University of Chinese Medicine, Harbin, China
| | - Fang-Yuan Liu
- Department of Obstetrics and Gynecology, Heilongjiang University of Chinese Medicine, Harbin, China
| | - Dan-Ni Ding
- Department of Obstetrics and Gynecology, Heilongjiang University of Chinese Medicine, Harbin, China
| | - Feng-Juan Han
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Heilongjiang University of Chinese Medicine, Harbin, China
| |
Collapse
|
15
|
Serum and Soleus Metabolomics Signature of Klf10 Knockout Mice to Identify Potential Biomarkers. Metabolites 2022; 12:metabo12060556. [PMID: 35736488 PMCID: PMC9231117 DOI: 10.3390/metabo12060556] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 06/11/2022] [Accepted: 06/14/2022] [Indexed: 12/10/2022] Open
Abstract
The transcription factor Krüppel-like factor 10 (Klf10), also known as Tieg1 for TGFβ (Inducible Early Gene-1) is known to control numerous genes in many cell types that are involved in various key biological processes (differentiation, proliferation, apoptosis, inflammation), including cell metabolism and human disease. In skeletal muscle, particularly in the soleus, deletion of the Klf10 gene (Klf10 KO) resulted in ultrastructure fiber disorganization and mitochondrial metabolism deficiencies, characterized by muscular hypertrophy. To determine the metabolic profile related to loss of Klf10 expression, we analyzed blood and soleus tissue using UHPLC-Mass Spectrometry. Metabolomics analyses on both serum and soleus revealed profound differences between wild-type (WT) and KO animals. Klf10 deficient mice exhibited alterations in metabolites associated with energetic metabolism. Additionally, chemical classes of aromatic and amino-acid compounds were disrupted, together with Krebs cycle intermediates, lipids and phospholipids. From variable importance in projection (VIP) analyses, the Warburg effect, citric acid cycle, gluconeogenesis and transfer of acetyl groups into mitochondria appeared to be possible pathways involved in the metabolic alterations observed in Klf10 KO mice. These studies have revealed essential roles for Klf10 in regulating multiple metabolic pathways whose alterations may underlie the observed skeletal muscle defects as well as other diseases.
Collapse
|
16
|
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.
Collapse
|
17
|
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.
Collapse
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
| |
Collapse
|
18
|
Di Minno A, Gelzo M, Caterino M, Costanzo M, Ruoppolo M, Castaldo G. Challenges in Metabolomics-Based Tests, Biomarkers Revealed by Metabolomic Analysis, and the Promise of the Application of Metabolomics in Precision Medicine. Int J Mol Sci 2022; 23:5213. [PMID: 35563604 PMCID: PMC9103094 DOI: 10.3390/ijms23095213] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 04/29/2022] [Accepted: 05/05/2022] [Indexed: 12/12/2022] Open
Abstract
Metabolomics helps identify metabolites to characterize/refine perturbations of biological pathways in living organisms. Pre-analytical, analytical, and post-analytical limitations that have hampered a wide implementation of metabolomics have been addressed. Several potential biomarkers originating from current targeted metabolomics-based approaches have been discovered. Precision medicine argues for algorithms to classify individuals based on susceptibility to disease, and/or by response to specific treatments. It also argues for a prevention-based health system. Because of its ability to explore gene-environment interactions, metabolomics is expected to be critical to personalize diagnosis and treatment. Stringent guidelines have been applied from the very beginning to design studies to acquire the information currently employed in precision medicine and precision prevention approaches. Large, prospective, expensive and time-consuming studies are now mandatory to validate old, and discover new, metabolomics-based biomarkers with high chances of translation into precision medicine. Metabolites from studies on saliva, sweat, breath, semen, feces, amniotic, cerebrospinal, and broncho-alveolar fluid are predicted to be needed to refine information from plasma and serum metabolome. In addition, a multi-omics data analysis system is predicted to be needed for omics-based precision medicine approaches. Omics-based approaches for the progress of precision medicine and prevention are expected to raise ethical issues.
Collapse
Affiliation(s)
- Alessandro Di Minno
- Dipartimento di Farmacia, University of Naples Federico II, 80131 Naples, Italy
- CEINGE-Biotecnologie Avanzate, 80131 Naples, Italy; (M.G.); (M.C.); (M.C.); (M.R.); (G.C.)
| | - Monica Gelzo
- CEINGE-Biotecnologie Avanzate, 80131 Naples, Italy; (M.G.); (M.C.); (M.C.); (M.R.); (G.C.)
- Department of Molecular Medicine and Medical Biotechnology, School of Medicine, University of Naples Federico II, 80131 Naples, Italy
| | - Marianna Caterino
- CEINGE-Biotecnologie Avanzate, 80131 Naples, Italy; (M.G.); (M.C.); (M.C.); (M.R.); (G.C.)
- Department of Molecular Medicine and Medical Biotechnology, School of Medicine, University of Naples Federico II, 80131 Naples, Italy
| | - Michele Costanzo
- CEINGE-Biotecnologie Avanzate, 80131 Naples, Italy; (M.G.); (M.C.); (M.C.); (M.R.); (G.C.)
- Department of Molecular Medicine and Medical Biotechnology, School of Medicine, University of Naples Federico II, 80131 Naples, Italy
| | - Margherita Ruoppolo
- CEINGE-Biotecnologie Avanzate, 80131 Naples, Italy; (M.G.); (M.C.); (M.C.); (M.R.); (G.C.)
- Department of Molecular Medicine and Medical Biotechnology, School of Medicine, University of Naples Federico II, 80131 Naples, Italy
| | - Giuseppe Castaldo
- CEINGE-Biotecnologie Avanzate, 80131 Naples, Italy; (M.G.); (M.C.); (M.C.); (M.R.); (G.C.)
- Department of Molecular Medicine and Medical Biotechnology, School of Medicine, University of Naples Federico II, 80131 Naples, Italy
| |
Collapse
|
19
|
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.
Collapse
|
20
|
Chamaraux-Tran TN, Muller M, Pottecher J, Diemunsch PA, Tomasetto C, Namer IJ, Dali-Youcef N. Metabolomic Impact of Lidocaine on a Triple Negative Breast Cancer Cell Line. Front Pharmacol 2022; 13:821779. [PMID: 35273500 PMCID: PMC8902240 DOI: 10.3389/fphar.2022.821779] [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: 11/24/2021] [Accepted: 01/24/2022] [Indexed: 12/12/2022] Open
Abstract
Background: Metabolomics and onco-anesthesia are two emerging research fields in oncology. Metabolomics (metabolites analysis) is a new diagnostic and prognostic tool that can also be used for predicting the therapeutic or toxic responses to anticancer treatments. Onco-anesthesia studies assess the impact of anesthesia on disease-free and overall survival after cancer surgery. It has been shown that local anesthetics (LA), particularly lidocaine (LIDO), exert antitumor properties both in vitro and in vivo and may alter the biologic fingerprints of cancer cells. As LA are known to impair mitochondrial bioenergetics and byproducts, the aim of the present study was to assess the impact of LIDO on metabolomic profile of a breast cancer cell line. Methods: Breast cancer MDA-MB-231 cells were exposed for 4 h to 0.5 mM LIDO or vehicle (n = 4). The metabolomic fingerprint was characterized by high resolution magic angle spinning NMR spectroscopy (HRMAS). The multivariate technique using the Algorithm to Determine Expected Metabolite Level Alteration (ADEMA) (Cicek et al., PLoS Comput. Biol., 2013, 9, e1002859), based on mutual information to identify expected metabolite level changes with respect to a specific condition, was used to determine the metabolites variations caused by LIDO. Results: LIDO modulates cell metabolites levels. Several pathways, including glutaminolysis, choline, phosphocholine and total choline syntheses were significantly downregulated in the LIDO group. Discussion: This is the first study assessing the impact of LIDO on metabolomic fingerprint of breast cancer cells. Among pathways downregulated by LIDO, many metabolites are reported to be associated with adverse prognosis when present at a high titer in breast cancer patients. These results fit with the antitumor properties of LIDO and suggest its impact on metabolomics profile of cancer cells. These effects of LIDO are of clinical significance because it is widely used for local anesthesia with cutaneous infiltration during percutaneous tumor biopsy. Future in vitro and preclinical studies are necessary to assess whether metabolomics analysis requires modification of local anesthetic techniques during tumor biopsy.
Collapse
Affiliation(s)
- Thiên-Nga Chamaraux-Tran
- Service d'anesthésie-réanimation et Médecine Périopératoire, Hôpital de Hautepierre, Hôpitaux Universitaires de Strasbourg, Strasbourg, France.,Institut de Génétique et de Biologie Moléculaire et Cellulaire Illkirch, Illkirch, France.,Centre National de la Recherche Scientifique, UMR 7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France.,ER 3072, Mitochondrie Stress Oxydant et Protection Musculaire, Faculté de Médecine, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Strasbourg, France
| | - Marie Muller
- Service d'anesthésie-réanimation et Médecine Périopératoire, Hôpital de Hautepierre, Hôpitaux Universitaires de Strasbourg, Strasbourg, France.,Université de Strasbourg, Faculté de Médecine, Strasbourg, France
| | - Julien Pottecher
- Service d'anesthésie-réanimation et Médecine Périopératoire, Hôpital de Hautepierre, Hôpitaux Universitaires de Strasbourg, Strasbourg, France.,ER 3072, Mitochondrie Stress Oxydant et Protection Musculaire, Faculté de Médecine, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Strasbourg, France.,Université de Strasbourg, Faculté de Médecine, Strasbourg, France
| | - Pierre A Diemunsch
- Service d'anesthésie-réanimation et Médecine Périopératoire, Hôpital de Hautepierre, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Catherine Tomasetto
- Institut de Génétique et de Biologie Moléculaire et Cellulaire Illkirch, Illkirch, France.,Centre National de la Recherche Scientifique, UMR 7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France
| | - Izzie-Jacques Namer
- Université de Strasbourg, Faculté de Médecine, Strasbourg, France.,MNMS-Platform, Hôpital de Hautepierre, Hôpitaux Universitaires de Strasbourg, Strasbourg, France.,Service de Médecine Nucléaire et d'Imagerie Moléculaire, Institut de Cancérologie Strasbourg Europe, Strasbourg, France.,ICube, Université de Strasbourg/CNRS, UMR 7357, Strasbourg, France
| | - Nassim Dali-Youcef
- Institut de Génétique et de Biologie Moléculaire et Cellulaire Illkirch, Illkirch, France.,Centre National de la Recherche Scientifique, UMR 7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France.,Université de Strasbourg, Faculté de Médecine, Strasbourg, France.,Laboratoire de Biochimie et Biologie Moléculaire, Pôle de Biologie, Hôpitaux Universitaires de Strasbourg, Nouvel Hôpital Civil, 1 Place de l'hôpital, Strasbourg, France
| |
Collapse
|
21
|
Wang R, Kang H, Zhang X, Nie Q, Wang H, Wang C, Zhou S. Urinary metabolomics for discovering metabolic biomarkers of bladder cancer by UPLC-MS. BMC Cancer 2022; 22:214. [PMID: 35220945 PMCID: PMC8883652 DOI: 10.1186/s12885-022-09318-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Accepted: 02/21/2022] [Indexed: 12/24/2022] Open
Abstract
Bladder cancer (BC) is one of the most frequent cancer in the world, and its incidence is rising worldwide, especially in developed countries. Urine metabolomics is a powerful approach to discover potential biomarkers for cancer diagnosis. In this study, we applied an ultra-performance liquid chromatography coupled to mass spectrometry (UPLC-MS) method to profile the metabolites in urine from 29 bladder cancer patients and 15 healthy controls. The differential metabolites were extracted and analyzed by univariate and multivariate analysis methods. Together, 19 metabolites were discovered as differently expressed biomarkers in the two groups, which mainly related to the pathways of phenylacetate metabolism, propanoate metabolism, fatty acid metabolism, pyruvate metabolism, arginine and proline metabolism, glycine and serine metabolism, and bile acid biosynthesis. In addition, a subset of 11 metabolites of those 19 ones were further filtered as potential biomarkers for BC diagnosis by using logistic regression model. The results revealed that the area under the curve (AUC) value, sensitivity and specificity of receiving operator characteristic (ROC) curve were 0.983, 95.3% and 100%, respectively, indicating an excellent discrimination power for BC patients from healthy controls. It was the first time to reveal the potential diagnostic markers of BC by metabolomics, and this will provide a new sight for exploring the biomarkers of the other disease in the future work.
Collapse
Affiliation(s)
- Rui Wang
- Zibo Municipal Hospital, Zibo, Shandong, 255400, China
| | - Huaixing Kang
- Department of clinical laboratory, Central Hospital of Xiangtan, Xiangtan, Hunan, 411100, China
| | - Xu Zhang
- Department of Urology, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310003, China
| | - Qing Nie
- Yaneng Bioscience, Co., Ltd, Shenzhen, Guangdong, 518100, China
| | - Hongling Wang
- Zibo Municipal Hospital, Zibo, Shandong, 255400, China.
| | - Chaojun Wang
- Department of Urology, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310003, China.
| | - Shujun Zhou
- Yaneng Bioscience, Co., Ltd, Shenzhen, Guangdong, 518100, China.
| |
Collapse
|
22
|
Haince JF, Joubert P, Bach H, Ahmed Bux R, Tappia PS, Ramjiawan B. Metabolomic Fingerprinting for the Detection of Early-Stage Lung Cancer: From the Genome to the Metabolome. Int J Mol Sci 2022; 23:ijms23031215. [PMID: 35163138 PMCID: PMC8835988 DOI: 10.3390/ijms23031215] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 01/17/2022] [Accepted: 01/17/2022] [Indexed: 12/19/2022] Open
Abstract
The five-year survival rate of lung cancer patients is very low, mainly because most newly diagnosed patients present with locally advanced or metastatic disease. Therefore, early diagnosis is key to the successful treatment and management of lung cancer. Unfortunately, early detection methods of lung cancer are not ideal. In this brief review, we described early detection methods such as chest X-rays followed by bronchoscopy, sputum analysis followed by cytological analysis, and low-dose computed tomography (LDCT). In addition, we discussed the potential of metabolomic fingerprinting, compared to that of other biomarkers, including molecular targets, as a low-cost, high-throughput blood-based test that is both feasible and affordable for early-stage lung cancer screening of at-risk populations. Accordingly, we proposed a paradigm shift to metabolomics as an alternative to molecular and proteomic-based markers in lung cancer screening, which will enable blood-based routine testing and be accessible to those patients at the highest risk for lung cancer.
Collapse
Affiliation(s)
| | - Philippe Joubert
- Institut Universitaire de Cardiologie et de Pneumologie de Québec, Department of Pathology, Laval University, Quebec, QC G1V 4G5, Canada;
| | - Horacio Bach
- Department of Medicine, Division of Infectious Diseases, University of British Columbia, Vancouver, BC V6H 3Z6, Canada;
| | - Rashid Ahmed Bux
- BioMark Diagnostics Inc., Richmond, BC V6X 2W8, Canada; (J.-F.H.); (R.A.B.)
| | - Paramjit S. Tappia
- Asper Clinical Research Institute, St. Boniface Hospital, Winnipeg, MB R2H 2A6, Canada;
- Correspondence: ; Tel.: +1-204-258-1230
| | - Bram Ramjiawan
- Asper Clinical Research Institute, St. Boniface Hospital, Winnipeg, MB R2H 2A6, Canada;
- Department of Pharmacology & Therapeutics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB R3E 0T6, Canada
| |
Collapse
|
23
|
Blum BC, Lin W, Lawton ML, Liu Q, Kwan J, Turcinovic I, Hekman R, Hu P, Emili A. Multiomic Metabolic Enrichment Network Analysis Reveals Metabolite-Protein Physical Interaction Subnetworks Altered in Cancer. Mol Cell Proteomics 2022; 21:100189. [PMID: 34933084 PMCID: PMC8761777 DOI: 10.1016/j.mcpro.2021.100189] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 12/04/2021] [Accepted: 12/16/2021] [Indexed: 11/25/2022] Open
Abstract
Metabolism is recognized as an important driver of cancer progression and other complex diseases, but global metabolite profiling remains a challenge. Protein expression profiling is often a poor proxy since existing pathway enrichment models provide an incomplete mapping between the proteome and metabolism. To overcome these gaps, we introduce multiomic metabolic enrichment network analysis (MOMENTA), an integrative multiomic data analysis framework for more accurately deducing metabolic pathway changes from proteomics data alone in a gene set analysis context by leveraging protein interaction networks to extend annotated metabolic models. We apply MOMENTA to proteomic data from diverse cancer cell lines and human tumors to demonstrate its utility at revealing variation in metabolic pathway activity across cancer types, which we verify using independent metabolomics measurements. The novel metabolic networks we uncover in breast cancer and other tumors are linked to clinical outcomes, underscoring the pathophysiological relevance of the findings.
Collapse
Affiliation(s)
- Benjamin C Blum
- Center for Network Systems Biology, Boston University, Boston, Massachusetts, USA; Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Weiwei Lin
- Center for Network Systems Biology, Boston University, Boston, Massachusetts, USA; Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Matthew L Lawton
- Center for Network Systems Biology, Boston University, Boston, Massachusetts, USA; Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Qian Liu
- Departments of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Julian Kwan
- Center for Network Systems Biology, Boston University, Boston, Massachusetts, USA; Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Isabella Turcinovic
- Center for Network Systems Biology, Boston University, Boston, Massachusetts, USA
| | - Ryan Hekman
- Center for Network Systems Biology, Boston University, Boston, Massachusetts, USA; Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Pingzhao Hu
- Departments of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Andrew Emili
- Center for Network Systems Biology, Boston University, Boston, Massachusetts, USA; Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts, USA; Department of Biology, Boston University, Boston, Massachusetts, USA.
| |
Collapse
|
24
|
Zhao J, Zhang F, Xiao X, Wu Z, Hu Q, Jiang Y, Zhang W, Wei S, Ma X, Zhang X. Tripterygium hypoglaucum (Lévl.) Hutch and Its Main Bioactive Components: Recent Advances in Pharmacological Activity, Pharmacokinetics and Potential Toxicity. Front Pharmacol 2021; 12:715359. [PMID: 34887747 PMCID: PMC8650721 DOI: 10.3389/fphar.2021.715359] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 11/04/2021] [Indexed: 01/12/2023] Open
Abstract
Tripterygium hypoglaucum (Lévl.) Hutch (THH) is believed to play an important role in health care and disease treatment according to traditional Chinese medicine. Moreover, it is also the representative of medicine with both significant efficacy and potential toxicity. This characteristic causes THH hard for embracing and fearing. In order to verify its prospect for clinic, a wide variety of studies were carried out in the most recent years. However, there has not been any review about THH yet. Therefore, this review summarized its characteristic of components, pharmacological effect, pharmacokinetics and toxicity to comprehensively shed light on the potential clinical application. More than 120 secondary metabolites including terpenoids, alkaloids, glycosides, sugars, organic acids, oleanolic acid, polysaccharides and other components were found in THH based on phytochemical research. All these components might be the pharmacological bases for immunosuppression, anti-inflammatory and anti-tumour effect. In addition, recent studies found that THH and its bioactive compounds also demonstrated remarkable effect on obesity, insulin resistance, fertility and infection of virus. The main mechanism seemed to be closely related to regulation the balance of immune, inflammation, apoptosis and so on in various disease. Furthermore, the study of pharmacokinetics revealed quick elimination of the main component triptolide. The feature of celastrol was also investigated by several models. Finally, the side effect of THH was thought to be the key for its limitation in clinical application. A series of reports indicated that multiple organs or systems including liver, kidney and genital system were involved in the toxicity. Its potential serious problem in liver was paid specific attention in recent years. In summary, considering the significant effect and potential toxicity of THH as well as its components, the combined medication to inhibit the toxicity, maintain effect might be a promising method for clinical conversion. Modern advanced technology such as structure optimization might be another way to reach the efficacy and safety. Thus, THH is still a crucial plant which remains for further investigation.
Collapse
Affiliation(s)
- Junqi Zhao
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Fangling Zhang
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Xiaolin Xiao
- Hospital of Chengdu University of Traditional Chinese Medicine, School of Clinical Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Zhao Wu
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Qichao Hu
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Yinxiao Jiang
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Wenwen Zhang
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Shizhang Wei
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Xiao Ma
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Xiaomei Zhang
- Institute of Medicinal Chemistry of Chinese Medicine, Chongqing Academy of Chinese Materia Medica, Chongqing, China
| |
Collapse
|
25
|
Li J, Zheng Z, Liu M, Ren Y, Ruan Y, Li D. Relationship between the n-3 index, serum metabolites and breast cancer risk. Food Funct 2021; 12:7741-7748. [PMID: 34296713 DOI: 10.1039/d1fo01245b] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The present study aimed to investigate the relationship between the n-3 index, serum metabolites and breast cancer risk. A total of 104 newly diagnosed breast cancer patients and 70 healthy controls were recruited. The erythrocyte phospholipid fatty acid composition was determined by gas-liquid chromatography, and the n-3 index was calculated with the percentage of eicosapentaenoic acid plus docosahexaenoic acid in total fatty acids. Serum metabolomic profiles were analyzed by UHPLC-Q-Exactive Orbitrap/MS. The results showed that the erythrocyte phospholipid n-3 index was significantly lower in breast cancer patients than in healthy controls, and it was inversely associated with breast cancer risk (OR = 0.60; 95% CI: 0.36-0.84). Metabolomics analyses showed that serum 16α-hydroxy dehydroepiandrosterone (DHEA) 3-sulfate, lysophatidylethanolamines (LPE) 22:0/0:0 and hexanoylcarnitine were significantly higher, while thromboxane B3, prostaglandin E3 (PGE3) and 18β-glycyrrhetinic acid were significantly lower in breast cancer patients than those in healthy controls. In addition, serum 16α-hydroxy DHEA 3-sulfate was inversely correlated with the n-3 index (r = -0.412, p = 0.036). In conclusion, our findings suggest that the lack of n-3 PUFAs might be a potential risk factor for breast cancer, and the serum metabolite 16α-hydroxy DHEA 3-sulfate may play an important role in linking n-3 PUFA deficiency and breast disease etiology.
Collapse
Affiliation(s)
- Jiaomei Li
- Institute of Nutrition and Health, Qingdao University, 308 Ningxia Road, Qingdao 266071, China.
| | | | | | | | | | | |
Collapse
|
26
|
Metabolic Rewiring and the Characterization of Oncometabolites. Cancers (Basel) 2021; 13:cancers13122900. [PMID: 34200553 PMCID: PMC8229816 DOI: 10.3390/cancers13122900] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Revised: 05/31/2021] [Accepted: 06/08/2021] [Indexed: 02/07/2023] Open
Abstract
Simple Summary Oncometabolites are produced by cancer cells and assist the cancer to proliferate and progress. Oncometabolites occur as a result of mutated enzymes in the tumor tissue or due to hypoxia. These processes result in either the abnormal buildup of a normal metabolite or the accumulation of an unusual metabolite. Definition of the metabolic changes that occur due to these processes has been accomplished using metabolomics, which mainly uses mass spectrometry platforms to define the content of small metabolites that occur in cells, tissues, organs and organisms. The four classical oncometabolites are fumarate, succinate, (2R)-hydroxyglutarate and (2S)-hydroxyglutarate, which operate by inhibiting 2-oxoglutarate-dependent enzyme reactions that principally regulate gene expression and response to hypoxia. Metabolomics has also revealed several putative oncometabolites that include lactate, kynurenine, methylglyoxal, sarcosine, glycine, hypotaurine and (2R,3S)-dihydroxybutanoate. Metabolomics will continue to be critical for understanding the metabolic rewiring involving oncometabolite production that underpins many cancer phenotypes. Abstract The study of low-molecular-weight metabolites that exist in cells and organisms is known as metabolomics and is often conducted using mass spectrometry laboratory platforms. Definition of oncometabolites in the context of the metabolic phenotype of cancer cells has been accomplished through metabolomics. Oncometabolites result from mutations in cancer cell genes or from hypoxia-driven enzyme promiscuity. As a result, normal metabolites accumulate in cancer cells to unusually high concentrations or, alternatively, unusual metabolites are produced. The typical oncometabolites fumarate, succinate, (2R)-hydroxyglutarate and (2S)-hydroxyglutarate inhibit 2-oxoglutarate-dependent dioxygenases, such as histone demethylases and HIF prolyl-4-hydroxylases, together with DNA cytosine demethylases. As a result of the cancer cell acquiring this new metabolic phenotype, major changes in gene transcription occur and the modification of the epigenetic landscape of the cell promotes proliferation and progression of cancers. Stabilization of HIF1α through inhibition of HIF prolyl-4-hydroxylases by oncometabolites such as fumarate and succinate leads to a pseudohypoxic state that promotes inflammation, angiogenesis and metastasis. Metabolomics has additionally been employed to define the metabolic phenotype of cancer cells and patient biofluids in the search for cancer biomarkers. These efforts have led to the uncovering of the putative oncometabolites sarcosine, glycine, lactate, kynurenine, methylglyoxal, hypotaurine and (2R,3S)-dihydroxybutanoate, for which further research is required.
Collapse
|
27
|
Ye W, Lin Y, Bezabeh T, Ma C, Liang J, Zhao J, Ouyang T, Tang W, Wu R. 1 H NMR-based metabolomics of paired esophageal tumor tissues and serum samples identifies specific serum biomarkers for esophageal cancer. NMR IN BIOMEDICINE 2021; 34:e4505. [PMID: 33783927 DOI: 10.1002/nbm.4505] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Revised: 02/22/2021] [Accepted: 02/24/2021] [Indexed: 02/05/2023]
Abstract
Serum metabolites of healthy controls and esophageal cancer (EC) patients have previously been compared to predict cancer-specific profiles. However, the association between metabolic alterations in serum samples and esophageal tissues in EC patients remains unclear. Here, we analyzed 50 pairs of EC tissues and distant noncancerous tissues, together with patient-matched serum samples, using 1 H NMR spectroscopy and pattern recognition algorithms. EC patients could be differentiated from the controls based on the metabolic profiles at tissue and serum levels. Some overlapping discriminatory metabolites, including valine, alanine, glucose, acetate, citrate, succinate and glutamate, were identified in both matrices. These results suggested deregulation of metabolic pathways, and potentially revealed the links between EC and several metabolic pathways, such as the tricarboxylic acid cycle, glutaminolysis, short-chain fatty acid metabolism, lipometabolism and pyruvate metabolism. Perturbation of the pyruvate metabolism was most strongly associated with EC progression. Consequently, an optimal serum metabolite biomarker panel comprising acetate and pyruvate was developed, as these two metabolites are involved in pyruvate metabolism, and changes in their serum levels were significantly correlated with alterations in the levels of some other esophageal tissue metabolites. In comparison with individual biomarkers, this panel exhibited better diagnostic efficiency for EC, with an AUC of 0.948 in the test set, and a good predictive ability of 82.5% in the validation set. Analysis of key genes related to pyruvate metabolism in EC patients revealed patterns corresponding to the changes in serum pyruvate and acetate levels. These correlation analyses demonstrate that there were distinct metabolic characteristics and pathway aberrations in the esophageal tumor tissue and in the serum. Changes in the serum metabolic signatures could reflect the alterations in the esophageal tumor profile, thereby emphasizing the importance of distinct serum metabolic profiles as potential noninvasive biomarkers for EC.
Collapse
Affiliation(s)
- Wei Ye
- Radiology Department, Second Affiliated Hospital, Shantou University Medical College, Shantou, China
| | - Yan Lin
- Radiology Department, Second Affiliated Hospital, Shantou University Medical College, Shantou, China
| | - Tedros Bezabeh
- College of Natural & Applied Sciences, University of Guam, UOG Station, Mangilao, Guam
| | - Changchun Ma
- Radiation Oncology, Affiliated Tumor Hospital, Shantou University Medical College, Shantou, China
| | - Jiahao Liang
- Radiology Department, Second Affiliated Hospital, Shantou University Medical College, Shantou, China
| | - Jiayun Zhao
- Radiology Department, Second Affiliated Hospital, Shantou University Medical College, Shantou, China
| | - Ting Ouyang
- Radiology Department, Second Affiliated Hospital, Shantou University Medical College, Shantou, China
| | - Wan Tang
- Radiology Department, Second Affiliated Hospital, Shantou University Medical College, Shantou, China
| | - Renhua Wu
- Radiology Department, Second Affiliated Hospital, Shantou University Medical College, Shantou, China
| |
Collapse
|
28
|
Zheng Y, He Z, Kong Y, Huang X, Zhu W, Liu Z, Gong L. Combined Metabolomics with Transcriptomics Reveals Important Serum Biomarkers Correlated with Lung Cancer Proliferation through a Calcium Signaling Pathway. J Proteome Res 2021; 20:3444-3454. [PMID: 34056907 DOI: 10.1021/acs.jproteome.0c01019] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Lung cancer (LC) is one of the most malignant cancers in the world, but currently, it lacks effective noninvasive biomarkers to assist its early diagnosis. Our study aims to discover potential serum diagnostic biomarkers for LC. In our study, untargeted serum metabolomics of a discovery cohort and targeted analysis of a test cohort were performed based on gas chromatography-mass spectrometry. Both univariate and multivariate statistical analyses were employed to screen for differential metabolites between LC and healthy control (HC), followed by the selection of candidate biomarkers through multiple algorithms. The results showed that 15 metabolites were significantly dysregulated between LC and HC, and a panel, comprising cholesterol, oleic acid, myo-inositol, 2-hydroxybutyric acid, and 4-hydroxybutyric acid, was demonstrated to have excellent differentiating capability for LC based on multiple classification modelings. In addition, the molecular interaction analysis combined with transcriptomics revealed a close correlation between the candidate biomarkers and LC proliferation via a Ca2+ signaling pathway. Our study discovered that cholesterol, oleic acid, myo-inositol, 2-hydroxybutyric acid, and 4-hydroxybutyric acid in combination could be a promising diagnostic biomarker for LC, and most importantly, our results will shed some light on the pathophysiological mechanism underlying LC to understand it deeply. The data that support the findings of this study are openly available in MetaboLights at https://www.ebi.ac.uk/metabolights/, reference number MTBLS1517.
Collapse
Affiliation(s)
- Yuan Zheng
- Department of Cardiothoracic Surgery, The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong 510006, PR China
| | - Zhuoru He
- International Institute for Translational Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong 510006, PR China
| | - Yu Kong
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Plant Science Research Centre, Chinese Academy of Sciences, Shanghai Chenshan Botanical Garden, Shanghai 201602, PR China
| | - Xinjie Huang
- Department of Cardiothoracic Surgery, The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong 510006, PR China
| | - Wei Zhu
- Department of Cardiothoracic Surgery, The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong 510006, PR China
| | - Zhongqiu Liu
- International Institute for Translational Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong 510006, PR China
| | - Lingzhi Gong
- International Institute for Translational Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong 510006, PR China
| |
Collapse
|
29
|
Cakmak A, Celik MH. Personalized Metabolic Analysis of Diseases. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2021; 18:1014-1025. [PMID: 32750887 DOI: 10.1109/tcbb.2020.3008196] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The metabolic wiring of patient cells is altered drastically in many diseases, including cancer. Understanding the nature of such changes may pave the way for new therapeutic opportunities as well as the development of personalized treatment strategies for patients. In this paper, we propose an algorithm called Metabolitics, which allows systems-level analysis of changes in the biochemical network of cells in disease states. It enables the study of a disease at both reaction- and pathway-level granularities for a detailed and summarized view of disease etiology. Metabolitics employs flux variability analysis with a dynamically built objective function based on biofluid metabolomics measurements in a personalized manner. Moreover, Metabolitics builds supervised classification models to discriminate between patients and healthy subjects based on the computed metabolic network changes. The use of Metabolitics is demonstrated for three distinct diseases, namely, breast cancer, Crohn's disease, and colorectal cancer. Our results show that the constructed supervised learning models successfully differentiate patients from healthy individuals by an average f1-score of 88 percent. Besides, in addition to the confirmation of previously reported breast cancer-associated pathways, we discovered that Biotin Metabolism along with Arginine and Proline Metabolism is subject to a significant increase in flux capacity, which have not been reported before.
Collapse
|
30
|
Using proteomic and transcriptomic data to assess activation of intracellular molecular pathways. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2021; 127:1-53. [PMID: 34340765 DOI: 10.1016/bs.apcsb.2021.02.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Analysis of molecular pathway activation is the recent instrument that helps to quantize activities of various intracellular signaling, structural, DNA synthesis and repair, and biochemical processes. This may have a deep impact in fundamental research, bioindustry, and medicine. Unlike gene ontology analyses and numerous qualitative methods that can establish whether a pathway is affected in principle, the quantitative approach has the advantage of exactly measuring the extent of a pathway up/downregulation. This results in emergence of a new generation of molecular biomarkers-pathway activation levels, which reflect concentration changes of all measurable pathway components. The input data can be the high-throughput proteomic or transcriptomic profiles, and the output numbers take both positive and negative values and positively reflect overall pathway activation. Due to their nature, the pathway activation levels are more robust biomarkers compared to the individual gene products/protein levels. Here, we review the current knowledge of the quantitative gene expression interrogation methods and their applications for the molecular pathway quantization. We consider enclosed bioinformatic algorithms and their applications for solving real-world problems. Besides a plethora of applications in basic life sciences, the quantitative pathway analysis can improve molecular design and clinical investigations in pharmaceutical industry, can help finding new active biotechnological components and can significantly contribute to the progressive evolution of personalized medicine. In addition to the theoretical principles and concepts, we also propose publicly available software for the use of large-scale protein/RNA expression data to assess the human pathway activation levels.
Collapse
|
31
|
Nalbantoglu S, Karadag A. Metabolomics bridging proteomics along metabolites/oncometabolites and protein modifications: Paving the way toward integrative multiomics. J Pharm Biomed Anal 2021; 199:114031. [PMID: 33857836 DOI: 10.1016/j.jpba.2021.114031] [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: 04/22/2020] [Revised: 03/02/2021] [Accepted: 03/16/2021] [Indexed: 02/08/2023]
Abstract
Systems biology adopted functional and integrative multiomics approaches enable to discover the whole set of interacting regulatory components such as genes, transcripts, proteins, metabolites, and metabolite dependent protein modifications. This interactome build up the midpoint of protein-protein/PTM, protein-DNA/RNA, and protein-metabolite network in a cell. As the key drivers in cellular metabolism, metabolites are precursors and regulators of protein post-translational modifications [PTMs] that affect protein diversity and functionality. The precisely orchestrated core pattern of metabolic networks refer to paradigm 'metabolites regulate PTMs, PTMs regulate enzymes, and enzymes modulate metabolites' through a multitude of feedback and feed-forward pathway loops. The concept represents a flawless PTM-metabolite-enzyme(protein) regulomics underlined in reprogramming cancer metabolism. Immense interconnectivity of those biomolecules in their spectacular network of intertwined metabolic pathways makes integrated proteomics and metabolomics an excellent opportunity, and the central component of integrative multiomics framework. It will therefore be of significant interest to integrate global proteome and PTM-based proteomics with metabolomics to achieve disease related altered levels of those molecules. Thereby, present update aims to highlight role and analysis of interacting metabolites/oncometabolites, and metabolite-regulated PTMs loop which may function as translational monitoring biomarkers along the reprogramming continuum of oncometabolism.
Collapse
Affiliation(s)
- Sinem Nalbantoglu
- TUBITAK Marmara Research Center, Gene Engineering and Biotechnology Institute, Molecular, Oncology Laboratory, Gebze, Kocaeli, Turkey.
| | - Abdullah Karadag
- TUBITAK Marmara Research Center, Gene Engineering and Biotechnology Institute, Molecular, Oncology Laboratory, Gebze, Kocaeli, Turkey
| |
Collapse
|
32
|
An ion-pair free LC-MS/MS method for quantitative metabolite profiling of microbial bioproduction systems. Talanta 2021; 222:121625. [DOI: 10.1016/j.talanta.2020.121625] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 08/31/2020] [Accepted: 09/02/2020] [Indexed: 11/23/2022]
|
33
|
Gillenwater LA, Pratte KA, Hobbs BD, Cho MH, Zhuang Y, Halper-Stromberg E, Cruickshank-Quinn C, Reisdorph N, Petrache I, Labaki WW, O'Neal WK, Ortega VE, Jones DP, Uppal K, Jacobson S, Michelotti G, Wendt CH, Kechris KJ, Bowler RP. Plasma Metabolomic Signatures of Chronic Obstructive Pulmonary Disease and the Impact of Genetic Variants on Phenotype-Driven Modules. NETWORK AND SYSTEMS MEDICINE 2020; 3:159-181. [PMID: 33987620 PMCID: PMC8109053 DOI: 10.1089/nsm.2020.0009] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/05/2020] [Indexed: 02/07/2023] Open
Abstract
Background: Small studies have recently suggested that there are specific plasma metabolic signatures in chronic obstructive pulmonary disease (COPD), but there have been no large comprehensive study of metabolomic signatures in COPD that also integrate genetic variants. Materials and Methods: Fresh frozen plasma from 957 non-Hispanic white subjects in COPDGene was used to quantify 995 metabolites with Metabolon's global metabolomics platform. Metabolite associations with five COPD phenotypes (chronic bronchitis, exacerbation frequency, percent emphysema, post-bronchodilator forced expiratory volume at one second [FEV1]/forced vital capacity [FVC], and FEV1 percent predicted) were assessed. A metabolome-wide association study was performed to find genetic associations with metabolite levels. Significantly associated single-nucleotide polymorphisms were tested for replication with independent metabolomic platforms and independent cohorts. COPD phenotype-driven modules were identified in network analysis integrated with genetic associations to assess gene-metabolite-phenotype interactions. Results: Of metabolites tested, 147 (14.8%) were significantly associated with at least 1 COPD phenotype. Associations with airflow obstruction were enriched for diacylglycerols and branched chain amino acids. Genetic associations were observed with 109 (11%) metabolites, 72 (66%) of which replicated in an independent cohort. For 20 metabolites, more than 20% of variance was explained by genetics. A sparse network of COPD phenotype-driven modules was identified, often containing metabolites missed in previous testing. Of the 26 COPD phenotype-driven modules, 6 contained metabolites with significant met-QTLs, although little module variance was explained by genetics. Conclusion: A dysregulation of systemic metabolism was predominantly found in COPD phenotypes characterized by airflow obstruction, where we identified robust heritable effects on individual metabolite abundances. However, network analysis, which increased the statistical power to detect associations missed previously in classic regression analyses, revealed that the genetic influence on COPD phenotype-driven metabolomic modules was modest when compared with clinical and environmental factors.
Collapse
Affiliation(s)
| | | | - Brian D. Hobbs
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Michael H. Cho
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Yonghua Zhuang
- Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | | | | | - Nichole Reisdorph
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Irina Petrache
- National Jewish Health, Denver, Colorado, USA
- School of Medicine, University of Colorado, Aurora, Colorado, USA
| | - Wassim W. Labaki
- Division of Pulmonary and Critical Care Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Wanda K. O'Neal
- Lung Institute/Cystic Fibrosis Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Victor E. Ortega
- Department of Internal Medicine, Center for Precision Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Dean P. Jones
- Clinical Biomarkers Laboratory, Division of Pulmonary, Allergy, and Critical Care Medicine, Emory School of Medicine, Atlanta, Georgia, USA
| | - Karan Uppal
- Clinical Biomarkers Laboratory, Division of Pulmonary, Allergy, and Critical Care Medicine, Emory School of Medicine, Atlanta, Georgia, USA
| | | | | | - Christine H. Wendt
- Department of Medicine, University of Minnesota and the VAMC, Minneapolis, Minnesota, USA
| | - Katerina J. Kechris
- Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Russell P. Bowler
- National Jewish Health, Denver, Colorado, USA
- School of Medicine, University of Colorado, Aurora, Colorado, USA
| |
Collapse
|
34
|
Deng Y, Yao H, Chen W, Wei H, Li X, Zhang F, Gao S, Man H, Chen J, Tao X, Li M, Chen W. Profiling of polar urine metabolite extracts from Chinese colorectal cancer patients to screen for potential diagnostic and adverse-effect biomarkers. J Cancer 2020; 11:6925-6938. [PMID: 33123283 PMCID: PMC7592006 DOI: 10.7150/jca.47631] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 08/27/2020] [Indexed: 02/07/2023] Open
Abstract
Background: Metabolomics has demonstrated its potential in the early diagnosis, drug safety evaluation and personalized toxicology research of various cancers. Objectives: We aim to screen for potential diagnostic and capecitabine-related adverse effect (CRAE) biomarkers from urinary endogenous metabolites in Chinese colorectal cancer (CRC) patients. Methods: The metabolic profiles of 139 CRC patients and 50 non-neoplastic controls were analyzed using ultra-high-performance liquid chromatography combined with quadrupole time-of-flight mass spectrometry. Results: There were 41 metabolites identified between the CRC patients and the non-neoplastic controls, and 19 metabolites were identified between CRC patients with and without CRAE. Based on these identified metabolites, bioinformatic analysis and prediction model construction were completed. Most of these differential metabolites have important roles in cell proliferation and differentiation and the immune system. Based on binary logistic regression, a CRC prediction model, composed of 3-methylhistidine, N-heptanoylglycine, N1,N12-diacetylspermine and hippurate, was established, with an area under curve (AUC) of 0.980 (95% CI: 0.953-1.000; sensitivity: 94.3%; specificity: 92.0%) in the training set, and an AUC of 0.968 (95% CI: 0.933-1.000; sensitivity: 89.9%; specificity: 92.0%) in the testing set. In addition, methionine and 4-pyridoxic acid can be combined to predict hand foot syndrome, with an AUC of 0.884; ubiquinone-1 and 4-pyridoxic acid can be combined to predict anemia, with an AUC of 0.889; and 5-acetamidovalerate and 3,4-methylenesebacic acid can be combined to predict neutropenia, with an AUC of 0.882. Conclusion: The profiling of urine polar metabolites has great potential in the early detection of CRC and the prediction of CRAE.
Collapse
Affiliation(s)
- Yi Deng
- Department of Pharmacy, Changzheng Hospital, Secondary Military Medical University, Shanghai, China, 200003
| | - Houshan Yao
- Department of Surgery, Changzheng Hospital, Secondary Military Medical University, Shanghai, China, 200003
| | - Wei Chen
- Department of Pharmacy, Changzheng Hospital, Secondary Military Medical University, Shanghai, China, 200003
| | - Hua Wei
- Department of Pharmacy, Changzheng Hospital, Secondary Military Medical University, Shanghai, China, 200003
| | - Xinxing Li
- Department of Surgery, Changzheng Hospital, Secondary Military Medical University, Shanghai, China, 200003
| | - Feng Zhang
- Department of Pharmacy, Changzheng Hospital, Secondary Military Medical University, Shanghai, China, 200003
| | - Shouhong Gao
- Department of Pharmacy, Changzheng Hospital, Secondary Military Medical University, Shanghai, China, 200003
| | - Huan Man
- Department of Pharmacy, Changzheng Hospital, Secondary Military Medical University, Shanghai, China, 200003
- College of Chemical and Biological Engineering, Yichun University, Jiangxi Province, China, 336000
| | - Jing Chen
- Department of Pharmacy, Changzheng Hospital, Secondary Military Medical University, Shanghai, China, 200003
- College of Chemical and Biological Engineering, Yichun University, Jiangxi Province, China, 336000
| | - Xia Tao
- Department of Pharmacy, Changzheng Hospital, Secondary Military Medical University, Shanghai, China, 200003
| | - Mingming Li
- Department of Pharmacy, Changzheng Hospital, Secondary Military Medical University, Shanghai, China, 200003
| | - Wansheng Chen
- Department of Pharmacy, Changzheng Hospital, Secondary Military Medical University, Shanghai, China, 200003
- Research and Development Center of Chinese Medicine Resources and Biotechnology, Shanghai University of Traditional Chinese Medicine, Shanghai, China, 201203
| |
Collapse
|
35
|
Lu W, Xing X, Wang L, Chen L, Zhang S, McReynolds MR, Rabinowitz JD. Improved Annotation of Untargeted Metabolomics Data through Buffer Modifications That Shift Adduct Mass and Intensity. Anal Chem 2020; 92:11573-11581. [PMID: 32614575 PMCID: PMC7484094 DOI: 10.1021/acs.analchem.0c00985] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Annotation of untargeted high-resolution full-scan LC-MS metabolomics data remains challenging due to individual metabolites generating multiple LC-MS peaks arising from isotopes, adducts, and fragments. Adduct annotation is a particular challenge, as the same mass difference between peaks can arise from adduct formation, fragmentation, or different biological species. To address this, here we describe a buffer modification workflow (BMW) in which the same sample is run by LC-MS in both liquid chromatography solvent with 14NH3-acetate buffer and in solvent with the buffer modified with 15NH3-formate. Buffer switching results in characteristic mass and signal intensity changes for adduct peaks, facilitating their annotation. This relatively simple and convenient chromatography modification annotated yeast metabolomics data with similar effectiveness to growing the yeast in isotope-labeled media. Application to mouse liver data annotated both known metabolite and known adduct peaks with 95% accuracy. Overall, it identified 26% of ∼27 000 liver LC-MS features as putative metabolites, of which ∼2600 showed HMDB or KEGG database formula match. This workflow is well suited to biological samples that cannot be readily isotope labeled, including plants, mammalian tissues, and tumors.
Collapse
Affiliation(s)
- Wenyun Lu
- Lewis Sigler Institute for Integrative Genomics and Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Xi Xing
- Lewis Sigler Institute for Integrative Genomics and Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Lin Wang
- Lewis Sigler Institute for Integrative Genomics and Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Li Chen
- Lewis Sigler Institute for Integrative Genomics and Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Sisi Zhang
- Lewis Sigler Institute for Integrative Genomics and Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Melanie R McReynolds
- Lewis Sigler Institute for Integrative Genomics and Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Joshua D Rabinowitz
- Lewis Sigler Institute for Integrative Genomics and Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| |
Collapse
|
36
|
Avallone A, Piccirillo MC, Di Gennaro E, Romano C, Calabrese F, Roca MS, Tatangelo F, Granata V, Cassata A, Cavalcanti E, Maurea N, Maiolino P, Silvestro L, De Stefano A, Giuliani F, Rosati G, Tamburini E, Aprea P, Vicario V, Nappi A, Vitagliano C, Casaretti R, Leone A, Petrillo A, Botti G, Delrio P, Izzo F, Perrone F, Budillon A. Randomized phase II study of valproic acid in combination with bevacizumab and oxaliplatin/fluoropyrimidine regimens in patients with RAS-mutated metastatic colorectal cancer: the REVOLUTION study protocol. Ther Adv Med Oncol 2020; 12:1758835920929589. [PMID: 32849914 PMCID: PMC7425244 DOI: 10.1177/1758835920929589] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 05/04/2020] [Indexed: 01/30/2023] Open
Abstract
Background Despite effective treatments, metastatic colorectal cancer (mCRC) prognosis is still poor, mostly in RAS-mutated tumors, thus suggesting the need for novel combinatorial therapies. Epigenetic alterations play an important role in initiation and progression of cancers, including CRC. Histone-deacetylase inhibitors (HDACi) have shown activity in combination with chemotherapy in the treatment of solid tumors. Owing to its HDACi activity and its safe use for epileptic disorders, valproic acid (VPA) is a good candidate for anticancer therapy that we have largely explored preclinically translating our findings in currently ongoing clinical studies. We have shown in CRC models that HDACi, including VPA, induces synergistic antitumor effects in combination with fluoropyrimidines. Furthermore, unpublished results from our group demonstrated that VPA induces differentiation and sensitization of CRC stem cells to oxaliplatin. Moreover, preclinical and clinical data suggest that HDACi may prevent/reverse anti-angiogenic resistance. Methods/Design A randomized, open-label, two-arm, multicenter phase-II study will be performed to explore whether the addition of VPA to first line bevacizumab/oxaliplatin/fluoropyrimidine regimens (mFOLFOX-6/mOXXEL) might improve progression-free survival (PFS) in RAS-mutated mCRC patients. A sample size of 200 patients was calculated under the hypothesis that the addition of VPA to chemotherapy/bevacizumab can improve PFS from 9 to 12 months, with one-sided alpha of 0.20 and a power of 0.80. Secondary endpoints are overall survival, objective response rate, metastases resection rate, toxicity, and quality of life. Moreover, the study will explore several prognostic and predictive biomarkers on blood samples, primary tumors, and on resected metastases. Discussion The "Revolution" study aims to improve the treatment efficacy of RAS-mutated mCRC through an attractive strategy evaluating the combination of VPA with standard cancer treatment. Correlative studies could identify novel biomarkers and could add new insight in the mechanism of interaction between VPA, fluoropyrimidine, oxaliplatin, and bevacizumab. Trial Registration EudraCT: 2018-001414-15; ClinicalTrials.gov identifier: NCT04310176.
Collapse
Affiliation(s)
- Antonio Avallone
- Experimental Clinical Abdominal Oncology Unit, Istituto Nazionale Tumori- IRCCS-Fondazione G. Pascale, Via M. Semmola, Napoli, 80131, Italy
| | | | - Elena Di Gennaro
- Experimental Pharmacology Unit, Istituto Nazionale Tumori- IRCCS-Fondazione G. Pascale, Napoli, Italy
| | - Carmela Romano
- Experimental Clinical Abdominal Oncology Unit, Istituto Nazionale Tumori- IRCCS-Fondazione G. Pascale, Napoli, Italy
| | - Filomena Calabrese
- Experimental Clinical Abdominal Oncology Unit, Istituto Nazionale Tumori- IRCCS-Fondazione G. Pascale, Napoli, Italy
| | - Maria Serena Roca
- Experimental Pharmacology Unit, Istituto Nazionale Tumori- IRCCS-Fondazione G. Pascale, Napoli, Italy
| | - Fabiana Tatangelo
- Pathology Unit, Istituto Nazionale Tumori- IRCCS-Fondazione G. Pascale, Napoli, Italy
| | - Vincenza Granata
- Radiology Unit, Istituto Nazionale Tumori- IRCCS-Fondazione G. Pascale, Napoli, Italy
| | - Antonio Cassata
- Experimental Clinical Abdominal Oncology Unit, Istituto Nazionale Tumori- IRCCS-Fondazione G. Pascale, Napoli, Italy
| | - Ernesta Cavalcanti
- Laboratory Medicine Unit, Istituto Nazionale Tumori- IRCCS-Fondazione G. Pascale, Napoli, Italy
| | - Nicola Maurea
- Cardiology Unit, Istituto Nazionale Tumori- IRCCS-Fondazione G. Pascale, Napoli, Italy
| | - Piera Maiolino
- Pharmacy Unit, Istituto Nazionale Tumori- IRCCS-Fondazione G. Pascale, Napoli, Italy
| | - Lucrezia Silvestro
- Experimental Clinical Abdominal Oncology Unit, Istituto Nazionale Tumori- IRCCS-Fondazione G. Pascale, Napoli, Italy
| | - Alfonso De Stefano
- Experimental Clinical Abdominal Oncology Unit, Istituto Nazionale Tumori- IRCCS-Fondazione G. Pascale, Napoli, Italy
| | | | - Gerardo Rosati
- Medical Oncology Unit, S. Carlo Hospital, Potenza, Italy
| | - Emiliano Tamburini
- Dipartimento di Oncologia e Cure Palliative, Azienda Ospedaliera Cardinale G. Panico, Tricase-Lecce, Italy
| | - Pasquale Aprea
- Vascular Access Unit, Istituto Nazionale Tumori- IRCCS-Fondazione G. Pascale, Napoli, Italy
| | - Valeria Vicario
- Experimental Clinical Abdominal Oncology Unit, Istituto Nazionale Tumori- IRCCS-Fondazione G. Pascale, Napoli, Italy
| | - Anna Nappi
- Experimental Clinical Abdominal Oncology Unit, Istituto Nazionale Tumori- IRCCS-Fondazione G. Pascale, Napoli, Italy
| | - Carlo Vitagliano
- Experimental Pharmacology Unit, Istituto Nazionale Tumori- IRCCS-Fondazione G. Pascale, Napoli, Italy
| | - Rossana Casaretti
- Experimental Clinical Abdominal Oncology Unit, Istituto Nazionale Tumori- IRCCS-Fondazione G. Pascale, Napoli, Italy
| | - Alessandra Leone
- Experimental Pharmacology Unit, Istituto Nazionale Tumori- IRCCS-Fondazione G. Pascale, Napoli, Italy
| | - Antonella Petrillo
- Radiology Unit, Istituto Nazionale Tumori- IRCCS-Fondazione G. Pascale, Napoli, Italy
| | - Gerardo Botti
- Pathology Unit, Istituto Nazionale Tumori- IRCCS-Fondazione G. Pascale, Napoli, Italy
| | - Paolo Delrio
- Colorectal Oncological Surgery, Istituto Nazionale Tumori- IRCCS-Fondazione G. Pascale, Napoli, Italy
| | - Francesco Izzo
- Hepatobiliary Surgery Unit, Istituto Nazionale Tumori- IRCCS-Fondazione G. Pascale, Napoli, Italy
| | - Francesco Perrone
- Clinical Trials Unit, Istituto Nazionale Tumori- IRCCS-Fondazione G. Pascale, Napoli, Italy
| | - Alfredo Budillon
- Experimental Pharmacology Unit, Istituto Nazionale Tumori- IRCCS-Fondazione G. Pascale, Via M. Semmola, Napoli, 80131, Italy
| |
Collapse
|
37
|
Njoku K, Sutton CJ, Whetton AD, Crosbie EJ. Metabolomic Biomarkers for Detection, Prognosis and Identifying Recurrence in Endometrial Cancer. Metabolites 2020; 10:E314. [PMID: 32751940 PMCID: PMC7463916 DOI: 10.3390/metabo10080314] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 07/24/2020] [Accepted: 07/27/2020] [Indexed: 12/24/2022] Open
Abstract
Metabolic reprogramming is increasingly recognised as one of the defining hallmarks of tumorigenesis. There is compelling evidence to suggest that endometrial cancer develops and progresses in the context of profound metabolic dysfunction. Whilst the incidence of endometrial cancer continues to rise in parallel with the global epidemic of obesity, there are, as yet, no validated biomarkers that can aid risk prediction, early detection, prognostic evaluation or surveillance. Advances in high-throughput technologies have, in recent times, shown promise for biomarker discovery based on genomic, transcriptomic, proteomic and metabolomic platforms. Metabolomics, the large-scale study of metabolites, deals with the downstream products of the other omics technologies and thus best reflects the human phenotype. This review aims to provide a summary and critical synthesis of the existing literature with the ultimate goal of identifying the most promising metabolite biomarkers that can augment current endometrial cancer diagnostic, prognostic and recurrence surveillance strategies. Identified metabolites and their biochemical pathways are discussed in the context of what we know about endometrial carcinogenesis and their potential clinical utility is evaluated. Finally, we underscore the challenges inherent in metabolomic biomarker discovery and validation and provide fresh perspectives and directions for future endometrial cancer biomarker research.
Collapse
Affiliation(s)
- Kelechi Njoku
- Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, 5th Floor Research, St Mary’s Hospital, Oxford Road, Manchester M13 9WL, UK;
- Stoller Biomarker Discovery Centre, Institute of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PL, UK;
| | - Caroline J.J Sutton
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Oxford Road, Manchester M13 9WL, UK;
| | - Anthony D. Whetton
- Stoller Biomarker Discovery Centre, Institute of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PL, UK;
| | - Emma J. Crosbie
- Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, 5th Floor Research, St Mary’s Hospital, Oxford Road, Manchester M13 9WL, UK;
- Department of Obstetrics and Gynaecology, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester M13 9WL, UK
| |
Collapse
|
38
|
Tayanloo-Beik A, Sarvari M, Payab M, Gilany K, Alavi-Moghadam S, Gholami M, Goodarzi P, Larijani B, Arjmand B. OMICS insights into cancer histology; Metabolomics and proteomics approach. Clin Biochem 2020; 84:13-20. [PMID: 32589887 DOI: 10.1016/j.clinbiochem.2020.06.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 06/01/2020] [Accepted: 06/09/2020] [Indexed: 02/06/2023]
Abstract
Metabolomics as a post-genomic research area comprising different analytical methods for small molecules analysis. One of the underlying applications of metabolomics technology for better disease diagnosis and prognosis is discovering the metabolic pathway differences between healthy individuals and patients. On the other hand, the other noteworthy applications of metabolomics include its effective role in biomarker screening for cancer detection, monitoring, and prediction. In other words, emerging of the metabolomics field can be hopeful to provide a suitable alternative for the common current cancer diagnostic methods especially histopathological tests. Indeed, cancer as a major global issue places a substantial burden on the health care system. Hence, proper management can be beneficial. In this respect, formalin-fixed paraffin-embedded tissue specimens (in histopathological tests) are considered as a valuable source for metabolomics investigations. Interestingly, formalin-fixed paraffin-embedded tissue specimens can provide informative data for cancer management. In general, using these specimens, determining the cancer stage, individual response to the different therapies, personalized risk prediction are possible and high-quality clinical services are the promise of OMICS technologies for cancer disease. However, considering all of these beneficial characteristics, there are still some limitations in this area that need to be addressed in order to optimize the metabolomics utilizations and advancement.
Collapse
Affiliation(s)
- Akram Tayanloo-Beik
- Cell Therapy and Regenerative Medicine Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran.
| | - Masoumeh Sarvari
- Metabolomics and Genomics Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran.
| | - Moloud Payab
- Obesity and Eating Habits Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran.
| | - Kambiz Gilany
- Reproductive Immunology Research Center, Avicenna Research Institute, ACECR, Tehran, Iran; Integrative Oncology Department, Breast Cancer Research Center, Motamed Cancer Institute, ACECR, Tehran, Iran.
| | - Sepideh Alavi-Moghadam
- Cell Therapy and Regenerative Medicine Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran.
| | - Mahdi Gholami
- Department of Toxicology & Pharmacology, Faculty of Pharmacy; Toxicology and Poisoning Research Center, Tehran University of Medical Sciences, Tehran 1416753955, Iran.
| | - Parisa Goodarzi
- Brain and Spinal Cord Injury Research Center, Neuroscience Institute, Tehran University of Medical Sciences, Tehran, Iran.
| | - Bagher Larijani
- Endocrinology and Metabolism Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran.
| | - Babak Arjmand
- Cell Therapy and Regenerative Medicine Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran; Metabolomics and Genomics Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran.
| |
Collapse
|
39
|
Geijsen AJ, van Roekel EH, van Duijnhoven FJ, Achaintre D, Bachleitner‐Hofmann T, Baierl A, Bergmann MM, Boehm J, Bours MJ, Brenner H, Breukink SO, Brezina S, Chang‐Claude J, Herpel E, de Wilt JH, Gicquiau A, Gigic B, Gumpenberger T, Hansson BM, Hoffmeister M, Holowatyj AN, Karner‐Hanusch J, Keski‐Rahkonen P, Keulen ET, Koole JL, Leeb G, Ose J, Schirmacher P, Schneider MA, Schrotz‐King P, Stift A, Ulvik A, Vogelaar FJ, Wesselink E, van Zutphen M, Gsur A, Habermann N, Kampman E, Scalbert A, Ueland PM, Ulrich AB, Ulrich CM, Weijenberg MP, Kok DE. Plasma metabolites associated with colorectal cancer stage: Findings from an international consortium. Int J Cancer 2020; 146:3256-3266. [PMID: 31495913 PMCID: PMC7216900 DOI: 10.1002/ijc.32666] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 07/06/2019] [Accepted: 07/26/2019] [Indexed: 12/12/2022]
Abstract
Colorectal cancer is the second most common cause of cancer-related death globally, with marked differences in prognosis by disease stage at diagnosis. We studied circulating metabolites in relation to disease stage to improve the understanding of metabolic pathways related to colorectal cancer progression. We investigated plasma concentrations of 130 metabolites among 744 Stages I-IV colorectal cancer patients from ongoing cohort studies. Plasma samples, collected at diagnosis, were analyzed with liquid chromatography-mass spectrometry using the Biocrates AbsoluteIDQ™ p180 kit. We assessed associations between metabolite concentrations and stage using multinomial and multivariable logistic regression models. Analyses were adjusted for potential confounders as well as multiple testing using false discovery rate (FDR) correction. Patients presented with 23, 28, 39 and 10% of Stages I-IV disease, respectively. Concentrations of sphingomyelin C26:0 were lower in Stage III patients compared to Stage I patients (pFDR < 0.05). Concentrations of sphingomyelin C18:0 and phosphatidylcholine (diacyl) C32:0 were statistically significantly higher, while citrulline, histidine, phosphatidylcholine (diacyl) C34:4, phosphatidylcholine (acyl-alkyl) C40:1 and lysophosphatidylcholines (acyl) C16:0 and C17:0 concentrations were lower in Stage IV compared to Stage I patients (pFDR < 0.05). Our results suggest that metabolic pathways involving among others citrulline and histidine, implicated previously in colorectal cancer development, may also be linked to colorectal cancer progression.
Collapse
Affiliation(s)
- Anne J.M.R. Geijsen
- Division of Human Nutrition and HealthWageningen University & ResearchWageningenThe Netherlands
| | - Eline H. van Roekel
- Department of Epidemiology, GROW School for Oncology and Developmental BiologyMaastricht UniversityMaastrichtThe Netherlands
| | | | - David Achaintre
- Biomarkers GroupInternational Agency for Research on CancerLyonFrance
| | | | - Andreas Baierl
- Department of Statistics and Operations ResearchUniversity of ViennaViennaAustria
| | | | - Jürgen Boehm
- Huntsman Cancer InstituteSalt Lake CityUT
- Department of Population Health SciencesUniversity of UtahSalt Lake CityUT
| | - Martijn J.L. Bours
- Department of Epidemiology, GROW School for Oncology and Developmental BiologyMaastricht UniversityMaastrichtThe Netherlands
| | - Hermann Brenner
- Division of Preventive OncologyNational Center for Tumor Diseases and German Cancer Research CenterHeidelbergGermany
- Division of Clinical Epidemiology and Aging ResearchGerman Cancer Research Center (DKFZ)HeidelbergGermany
- German Cancer Consortium (DKTK)German Cancer Research Center (DKFZ)HeidelbergGermany
| | - Stéphanie O. Breukink
- Department of Surgery, GROW School for Oncology and Development BiologyMaastricht UniversityMaastrichtThe Netherlands
| | - Stefanie Brezina
- Institute of Cancer Research, Department of Medicine IMedical University of ViennaViennaAustria
| | - Jenny Chang‐Claude
- Division of Cancer EpidemiologyGerman Cancer Research CenterHeidelbergGermany
| | - Esther Herpel
- Institute of PathologyUniversity of HeidelbergHeidelbergGermany
| | - Johannes H.W. de Wilt
- Department of Surgery, Division of Surgical Oncology and Gastrointestinal SurgeryRadboud University Medical CenterNijmegenThe Netherlands
| | - Audrey Gicquiau
- Biomarkers GroupInternational Agency for Research on CancerLyonFrance
| | - Biljana Gigic
- Department of General, Visceral and Transplantation SurgeryUniversity of HeidelbergHeidelbergGermany
| | - Tanja Gumpenberger
- Institute of Cancer Research, Department of Medicine IMedical University of ViennaViennaAustria
| | - Bibi M.E. Hansson
- Department of SurgeryCanisius‐Wilhelmina HospitalNijmegenThe Netherlands
| | - Michael Hoffmeister
- Division of Clinical Epidemiology and Aging ResearchGerman Cancer Research Center (DKFZ)HeidelbergGermany
| | - Andreana N. Holowatyj
- Huntsman Cancer InstituteSalt Lake CityUT
- Department of Population Health SciencesUniversity of UtahSalt Lake CityUT
| | | | | | - Eric T.P. Keulen
- Department of Internal Medicine and GastroenterologyZuyderland Medical CenterSittardThe Netherlands
| | - Janna L. Koole
- Department of Epidemiology, GROW School for Oncology and Developmental BiologyMaastricht UniversityMaastrichtThe Netherlands
| | | | - Jennifer Ose
- Huntsman Cancer InstituteSalt Lake CityUT
- Department of Population Health SciencesUniversity of UtahSalt Lake CityUT
| | | | - Martin A. Schneider
- Department of General, Visceral and Transplantation SurgeryUniversity of HeidelbergHeidelbergGermany
| | - Petra Schrotz‐King
- Division of Preventive OncologyNational Center for Tumor Diseases and German Cancer Research CenterHeidelbergGermany
| | - Anton Stift
- Department of SurgeryMedical University ViennaViennaAustria
| | | | | | - Evertine Wesselink
- Division of Human Nutrition and HealthWageningen University & ResearchWageningenThe Netherlands
| | - Moniek van Zutphen
- Division of Human Nutrition and HealthWageningen University & ResearchWageningenThe Netherlands
| | - Andrea Gsur
- Institute of Cancer Research, Department of Medicine IMedical University of ViennaViennaAustria
| | - Nina Habermann
- Division of Preventive OncologyNational Center for Tumor Diseases and German Cancer Research CenterHeidelbergGermany
- Genome BiologyEuropean Molecular Biology Laboratory (EMBL)HeidelbergGermany
| | - Ellen Kampman
- Division of Human Nutrition and HealthWageningen University & ResearchWageningenThe Netherlands
| | - Augustin Scalbert
- Biomarkers GroupInternational Agency for Research on CancerLyonFrance
| | | | - Alexis B. Ulrich
- Department of General, Visceral and Transplantation SurgeryUniversity of HeidelbergHeidelbergGermany
| | - Cornelia M. Ulrich
- Huntsman Cancer InstituteSalt Lake CityUT
- Department of Population Health SciencesUniversity of UtahSalt Lake CityUT
| | - Matty P. Weijenberg
- Department of Epidemiology, GROW School for Oncology and Developmental BiologyMaastricht UniversityMaastrichtThe Netherlands
| | - Dieuwertje E. Kok
- Division of Human Nutrition and HealthWageningen University & ResearchWageningenThe Netherlands
| |
Collapse
|
40
|
Tolstikov V, Moser AJ, Sarangarajan R, Narain NR, Kiebish MA. Current Status of Metabolomic Biomarker Discovery: Impact of Study Design and Demographic Characteristics. Metabolites 2020; 10:metabo10060224. [PMID: 32485899 PMCID: PMC7345110 DOI: 10.3390/metabo10060224] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 05/21/2020] [Accepted: 05/27/2020] [Indexed: 12/16/2022] Open
Abstract
Widespread application of omic technologies is evolving our understanding of population health and holds promise in providing precise guidance for selection of therapeutic interventions based on patient biology. The opportunity to use hundreds of analytes for diagnostic assessment of human health compared to the current use of 10–20 analytes will provide greater accuracy in deconstructing the complexity of human biology in disease states. Conventional biochemical measurements like cholesterol, creatinine, and urea nitrogen are currently used to assess health status; however, metabolomics captures a comprehensive set of analytes characterizing the human phenotype and its complex metabolic processes in real-time. Unlike conventional clinical analytes, metabolomic profiles are dramatically influenced by demographic and environmental factors that affect the range of normal values and increase the risk of false biomarker discovery. This review addresses the challenges and opportunities created by the evolving field of clinical metabolomics and highlights features of study design and bioinformatics necessary to maximize the utility of metabolomics data across demographic groups.
Collapse
Affiliation(s)
- Vladimir Tolstikov
- BERG, Precision Medicine Division, Framingham, MA 01701, USA; (V.T.); (R.S.); (N.R.N.)
| | - A. James Moser
- Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA 02215, USA;
| | | | - Niven R. Narain
- BERG, Precision Medicine Division, Framingham, MA 01701, USA; (V.T.); (R.S.); (N.R.N.)
| | - Michael A. Kiebish
- BERG, Precision Medicine Division, Framingham, MA 01701, USA; (V.T.); (R.S.); (N.R.N.)
- Correspondence: ; Tel.: +1-617-588-2245
| |
Collapse
|
41
|
Metabolic Reprogramming in Metastatic Melanoma with Acquired Resistance to Targeted Therapies: Integrative Metabolomic and Proteomic Analysis. Cancers (Basel) 2020; 12:cancers12051323. [PMID: 32455924 PMCID: PMC7280989 DOI: 10.3390/cancers12051323] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 05/18/2020] [Accepted: 05/19/2020] [Indexed: 02/07/2023] Open
Abstract
Treatments of metastatic melanoma underwent an impressive development over the past few years, with the emergence of small molecule inhibitors targeting mutated proteins, such as BRAF, NRAS, or cKIT. However, since a significant proportion of patients acquire resistance to these therapies, new strategies are currently being considered to overcome this issue. For this purpose, melanoma cell lines with mutant BRAF, NRAS, or cKIT and with acquired resistances to BRAF, MEK, or cKIT inhibitors, respectively, were investigated using both 1H-NMR-based metabonomic and protein microarrays. The 1H-NMR profiles highlighted a similar go and return pattern in the metabolism of the BRAF, NRAS, and cKIT mutated cell lines. Indeed, melanoma cells exposed to mutation-specific inhibitors underwent metabolic disruptions following acute exposure but partially recovered their basal metabolism in long-term exposure, most likely acquiring resistance skills. The protein microarrays inquired about the potential cellular mechanisms used by the resistant cells to escape drug treatment, by showing decreased levels of proteins linked to the drug efficacy, especially in the downstream part of the MAPK signaling pathway. Integrating metabonomic and proteomic findings revealed some metabolic pathways (i.e., glutaminolysis, choline metabolism, glutathione production, glycolysis, oxidative phosphorylation) and key proteins (i.e., EPHA2, DUSP4, and HIF-1A) as potential targets to discard drug resistance.
Collapse
|
42
|
Mapping Metabolite and ICD-10 Associations. Metabolites 2020; 10:metabo10050196. [PMID: 32423141 PMCID: PMC7281140 DOI: 10.3390/metabo10050196] [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: 04/15/2020] [Revised: 05/07/2020] [Accepted: 05/13/2020] [Indexed: 12/02/2022] Open
Abstract
The search for novel metabolic biomarkers is intense but has had limited practical outcomes for medicine. Part of the problem is that we lack knowledge of how different comorbidities influence biomarkers’ performance. In this study, 49 metabolites were measured by targeted LC/MS protocols in the serum of 1011 volunteers. Their performance as potential biomarkers was evaluated by the area under the curve of receiver operator characteristics (AUC-ROC) for 105 diagnosis codes or code groups from the 10th revision of the international classification of diseases (ICD-10). Additionally, the interferences between diagnosis codes were investigated. The highest AUC-ROC values for individual metabolites and ICD-10 code combinations reached a moderate (0.7) range. Most metabolites that were found to be potential markers remained so independently of the control group composition or comorbidities. The precise value of the AUC-ROC, however, could vary depending on the comorbidities. Moreover, networks of metabolite and disease associations were built in order to map diseases, which may interfere with metabolic biomarker research on other diseases.
Collapse
|
43
|
Gupta K, Vuckovic I, Zhang S, Xiong Y, Carlson BL, Jacobs J, Olson I, Petterson XM, Macura SI, Sarkaria J, Burns TC. Radiation Induced Metabolic Alterations Associate With Tumor Aggressiveness and Poor Outcome in Glioblastoma. Front Oncol 2020; 10:535. [PMID: 32432031 PMCID: PMC7214818 DOI: 10.3389/fonc.2020.00535] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 03/25/2020] [Indexed: 12/17/2022] Open
Abstract
Glioblastoma (GBM) is uniformly fatal with a 1-year median survival, despite best available treatment, including radiotherapy (RT). Impacts of prior RT on tumor recurrence are poorly understood but may increase tumor aggressiveness. Metabolic changes have been investigated in radiation-induced brain injury; however, the tumor-promoting effect following prior radiation is lacking. Since RT is vital to GBM management, we quantified tumor-promoting effects of prior RT on patient-derived intracranial GBM xenografts and characterized metabolic alterations associated with the protumorigenic microenvironment. Human xenografts (GBM143) were implanted into nude mice 24 hrs following 20 Gy cranial radiation vs. sham animals. Tumors in pre-radiated mice were more proliferative and more infiltrative, yielding faster mortality (p < 0.0001). Histologic evaluation of tumor associated macrophage/microglia (TAMs) revealed cells with a more fully activated ameboid morphology in pre-radiated animals. Microdialyzates from radiated brain at the margin of tumor infiltration contralateral to the site of implantation were analyzed by unsupervised liquid chromatography-mass spectrometry (LC-MS). In pre-radiated animals, metabolites known to be associated with tumor progression (i.e., modified nucleotides and polyols) were identified. Whole-tissue metabolomic analysis of pre-radiated brain microenvironment for metabolic alterations in a separate cohort of nude mice using 1H-NMR revealed a significant decrease in levels of antioxidants (glutathione (GSH) and ascorbate (ASC)), NAD+, Tricarboxylic acid cycle (TCA) intermediates, and rise in energy carriers (ATP, GTP). GSH and ASC showed highest Variable Importance on Projection prediction (VIPpred) (1.65) in Orthogonal Partial least square Discriminant Analysis (OPLS-DA); Ascorbate catabolism was identified by GC-MS. To assess longevity of radiation effects, we compared survival with implantation occurring 2 months vs. 24 hrs following radiation, finding worse survival in animals implanted at 2 months. These radiation-induced alterations are consistent with a chronic disease-like microenvironment characterized by reduced levels of antioxidants and NAD+, and elevated extracellular ATP and GTP serving as chemoattractants, promoting cell motility and vesicular secretion with decreased levels of GSH and ASC exacerbating oxidative stress. Taken together, these data suggest IR induces tumor-permissive changes in the microenvironment with metabolomic alterations that may facilitate tumor aggressiveness with important implications for recurrent glioblastoma. Harnessing these metabolomic insights may provide opportunities to attenuate RT-associated aggressiveness of recurrent GBM.
Collapse
Affiliation(s)
- Kshama Gupta
- Department of Neurologic Surgery, Mayo Clinic, Rochester, MN, United States
| | - Ivan Vuckovic
- Metabolomics Core Mayo Clinic, Rochester, MN, United States
| | - Song Zhang
- Metabolomics Core Mayo Clinic, Rochester, MN, United States
| | - Yuning Xiong
- Department of Neurologic Surgery, Mayo Clinic, Rochester, MN, United States
| | - Brett L Carlson
- Department of Radiation Oncology, Mayo Clinic, Rochester, MN, United States
| | - Joshua Jacobs
- Department of Neurologic Surgery, Mayo Clinic, Rochester, MN, United States
| | - Ian Olson
- Department of Neurologic Surgery, Mayo Clinic, Rochester, MN, United States
| | | | - Slobodan I Macura
- Metabolomics Core Mayo Clinic, Rochester, MN, United States.,Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, United States
| | - Jann Sarkaria
- Department of Radiation Oncology, Mayo Clinic, Rochester, MN, United States
| | - Terry C Burns
- Department of Neurologic Surgery, Mayo Clinic, Rochester, MN, United States
| |
Collapse
|
44
|
Zhang L, Zheng J, Ahmed R, Huang G, Reid J, Mandal R, Maksymuik A, Sitar DS, Tappia PS, Ramjiawan B, Joubert P, Russo A, Rolfo CD, Wishart DS. A High-Performing Plasma Metabolite Panel for Early-Stage Lung Cancer Detection. Cancers (Basel) 2020; 12:cancers12030622. [PMID: 32156060 PMCID: PMC7139410 DOI: 10.3390/cancers12030622] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 03/02/2020] [Accepted: 03/05/2020] [Indexed: 12/19/2022] Open
Abstract
The objective of this research is to use metabolomic techniques to discover and validate plasma metabolite biomarkers for the diagnosis of early-stage non-small cell lung cancer (NSCLC). The study included plasma samples from 156 patients with biopsy-confirmed NSCLC along with age and gender-matched plasma samples from 60 healthy controls. A fully quantitative targeted mass spectrometry (MS) analysis (targeting 138 metabolites) was performed on all samples. The sample set was split into a discovery set and validation set. Metabolite concentration data, clinical data, and smoking history were used to determine optimal sets of biomarkers and optimal regression models for identifying different stages of NSCLC using the discovery sets. The same biomarkers and regression models were used and assessed on the validation models. Univariate and multivariate statistical analysis identified β-hydroxybutyric acid, LysoPC 20:3, PC ae C40:6, citric acid, and fumaric acid as being significantly different between healthy controls and stage I/II NSCLC. Robust predictive models with areas under the curve (AUC) > 0.9 were developed and validated using these metabolites and other, easily measured clinical data for detecting different stages of NSCLC. This study successfully identified and validated a simple, high-performing, metabolite-based test for detecting early stage (I/II) NSCLC patients in plasma. While promising, further validation on larger and more diverse cohorts is still required.
Collapse
Affiliation(s)
- Lun Zhang
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E8, Canada; (L.Z.); (J.Z.); (J.R.); (R.M.)
| | - Jiamin Zheng
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E8, Canada; (L.Z.); (J.Z.); (J.R.); (R.M.)
| | - Rashid Ahmed
- BioMark Diagnostics Inc., Richmond, BC V6X 2W8, Canada; (R.A.); (G.H.)
| | - Guoyu Huang
- BioMark Diagnostics Inc., Richmond, BC V6X 2W8, Canada; (R.A.); (G.H.)
| | - Jennifer Reid
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E8, Canada; (L.Z.); (J.Z.); (J.R.); (R.M.)
| | - Rupasri Mandal
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E8, Canada; (L.Z.); (J.Z.); (J.R.); (R.M.)
| | - Andrew Maksymuik
- Cancer Care Manitoba, Winnipeg, MB R3E 0V9, Canada;
- Department of Internal Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB R3A 1R9, Canada;
| | - Daniel S. Sitar
- Department of Internal Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB R3A 1R9, Canada;
- Department of Pharmacology & Therapeutics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB R3E 0T5, Canada
| | - Paramjit S. Tappia
- Asper Clinical Research Institute & Office of Clinical Research, St. Boniface Hospital, Winnipeg, MB R2H 2A6, Canada; (P.S.T.); (B.R.)
| | - Bram Ramjiawan
- Asper Clinical Research Institute & Office of Clinical Research, St. Boniface Hospital, Winnipeg, MB R2H 2A6, Canada; (P.S.T.); (B.R.)
| | - Philippe Joubert
- Department of Pathology, University of Laval, Quebec, QC G1V 4G5, Canada;
| | - Alessandro Russo
- Medical Oncology Unit A.O. Papardo & Department of Human Pathology, University of Messina, 98158 Messina, Italy;
- Thoracic Medical Oncology Program Marlene and Stewart Greenebaum Comprehensive Cancer Center, University of Maryland, Baltimore, MD 21201, USA;
| | - Christian D. Rolfo
- Thoracic Medical Oncology Program Marlene and Stewart Greenebaum Comprehensive Cancer Center, University of Maryland, Baltimore, MD 21201, USA;
| | - David S. Wishart
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E8, Canada; (L.Z.); (J.Z.); (J.R.); (R.M.)
- Correspondence:
| |
Collapse
|
45
|
Yi S, Lin K, Jiang T, Shao W, Huang C, Jiang B, Li Q, Lin D. NMR-based metabonomic analysis of HUVEC cells during replicative senescence. Aging (Albany NY) 2020; 12:3626-3646. [PMID: 32074082 PMCID: PMC7066908 DOI: 10.18632/aging.102834] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 01/27/2020] [Indexed: 01/18/2023]
Abstract
Cellular senescence is a physiological process reacting to stimuli, in which cells enter a state of irreversible growth arrest in response to adverse consequences associated with metabolic disorders. Molecular mechanisms underlying the progression of cellular senescence remain unclear. Here, we established a replicative senescence model of human umbilical vein endothelial cells (HUVEC) from passage 3 (P3) to 18 (P18), and performed biochemical characterizations and NMR-based metabolomic analyses. The cellular senescence degree advanced as the cells were sequentially passaged in vitro, and cellular metabolic profiles were gradually altered. Totally, 8, 16, 21 and 19 significant metabolites were primarily changed in the P6, P10, P14 and P18 cells compared with the P3 cells, respectively. These metabolites were mainly involved in 14 significantly altered metabolic pathways. Furthermore, we observed taurine retarded oxidative damage resulting from senescence. In the case of energy deficiency, HUVECs metabolized neutral amino acids to replenish energy, thus increased glutamine, aspartate and asparagine at the early stages of cellular senescence but decreased them at the later stages. Our results indicate that cellular replicative senescence is closely associated with promoted oxidative stress, impaired energy metabolism and blocked protein synthesis. This work may provide mechanistic understanding of the progression of cellular senescence.
Collapse
Affiliation(s)
- Shenghui Yi
- College of Chemistry and Chemical Engineering, Key Laboratory for Chemical Biology of Fujian Province, MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, Xiamen University, Xiamen 361005, China.,Department of Medical Chemistry, China Pharmaceutical University, Nanjing 210009, China
| | - Kejiang Lin
- Department of Medical Chemistry, China Pharmaceutical University, Nanjing 210009, China
| | - Ting Jiang
- College of Chemistry and Chemical Engineering, Key Laboratory for Chemical Biology of Fujian Province, MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, Xiamen University, Xiamen 361005, China
| | - Wei Shao
- College of Chemistry and Chemical Engineering, Key Laboratory for Chemical Biology of Fujian Province, MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, Xiamen University, Xiamen 361005, China
| | - Caihua Huang
- Research and Communication Center of Exercise and Health, Xiamen University of Technology, Xiamen 361024, China
| | - Bin Jiang
- State Key Laboratory of Cellular Stress Biology, School of Life Science, Xiamen University, Xiamen 361102, China
| | - Qinxi Li
- State Key Laboratory of Cellular Stress Biology, School of Life Science, Xiamen University, Xiamen 361102, China
| | - Donghai Lin
- College of Chemistry and Chemical Engineering, Key Laboratory for Chemical Biology of Fujian Province, MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, Xiamen University, Xiamen 361005, China
| |
Collapse
|
46
|
Gómez E, Salvetti P, Gatien J, Carrocera S, Martín-González D, Muñoz M. Blood Plasma Metabolomics Predicts Pregnancy in Holstein Cattle Transferred with Fresh and Vitrified/Warmed Embryos Produced in Vitro. J Proteome Res 2020; 19:1169-1182. [PMID: 31975599 DOI: 10.1021/acs.jproteome.9b00688] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Metabolomics may identify biomarkers in blood that differentiate pregnant from open embryo recipients. Fresh and vitrified/warmed, in vitro-produced embryos were transferred to Holstein recipients (discovery group). Recipient blood plasma collected on Day-0 (estrus) and Day-7 (before embryo transfer) were analyzed by nuclear magnetic resonance (N = 36 metabolites quantified). Metabolites whose concentrations differed between open and pregnant recipients were analyzed [(P < 0.05); false discovery rate (FDR) (P < 0.05)]. Biomarkers were identified in Day-7 plasma (receiver operator characteristic-area under curve (ROC-AUC) > 0.650; t-test P < 0.05; random forests, mean decrease accuracy) and cross-validated in independent Holstein, beef, and crossbred recipients (overall classification accuracy -OCA-; P < 0.05). Recipients with fresh embryos showed N = 6 biomarkers consistently on Day-40, Day-62, and at birth. Recipients with vitrified embryos showed N = 5 biomarkers on Day-40 and Day-62 but only one biomarker at birth. The most predictive biomarkers identified at birth within fresh embryos were oxoglutaric acid (ROC-AUC = 0.709; OCA = 0.812) and ornithine (ROC-AUC = 0.731; OCA = 0.727), while l-glycine was identified in vitrified embryos (ROC-AUC = 0.796; OCA = 0.667) together with other predictive biomarkers not identified at birth (Day-62: l-glutamine ROC-AUC = 0.757; OCA = 0.767) and l-lysine (Day-62: ROC-AUC = 0.680; OCA = 0.767). Pathway enrichment analysis distinguished between pregnant recipients for fresh (enriched energy oxidative metabolism from fat) and vitrified (lower lipid metabolism) embryos. Metabolomics can select individuals that will become pregnant in a defined cycle.
Collapse
Affiliation(s)
- Enrique Gómez
- Centro de Biotecnología Animal-SERIDA, Camino de Rioseco 1225, 33394 Gijón, Spain
| | - Pascal Salvetti
- ALLICE, Experimental Facilities, Le Perroi, 37380 Nouzilly, France
| | - Julie Gatien
- ALLICE, Experimental Facilities, Le Perroi, 37380 Nouzilly, France
| | - Susana Carrocera
- Centro de Biotecnología Animal-SERIDA, Camino de Rioseco 1225, 33394 Gijón, Spain
| | | | - Marta Muñoz
- Centro de Biotecnología Animal-SERIDA, Camino de Rioseco 1225, 33394 Gijón, Spain
| |
Collapse
|
47
|
van der Berg C, Venter G, van der Westhuizen FH, Erasmus E. Development and validation of LC-ESI-MS/MS methods for quantification of 27 free and conjugated estrogen-related metabolites. Anal Biochem 2019; 590:113531. [PMID: 31805274 DOI: 10.1016/j.ab.2019.113531] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 11/27/2019] [Accepted: 11/30/2019] [Indexed: 10/25/2022]
Abstract
An imbalance in the estrogen metabolism has been associated with an increased risk of breast cancer development. Evaluation of the estrogen biotransformation capacity requires monitoring of various estrogen metabolites. Up to now, only some estrogen metabolites could be measured in urine. However, in order to offer tailor made nutritional support or therapies, a complete estrogen metabolite profile is required in order to identify specific deficiencies in this pathway for each patient individually. Here, we focused on this need to quantify as many as possible of the estrogen-related metabolites excreted in urine. The method was developed to quantify 27 estrogen-related metabolites in small urine quantities. This entailed sample clean-up with a multi-step solid phase extraction procedure, derivatisation of the metabolites in the less water-soluble fraction through dansylation, and analyses using liquid chromatography-tandem mass spectrometry (LC-MS/MS). The metabolites accurately quantified by the method devised included parent estrogens, hydroxylated and methylated forms, metabolites of the 16α-hydroxyestrogen pathway, sulphate and glucuronide conjugated forms, precursors and a related steroid hormone. This method was validated and enabled quantification in the high picograms and low nanograms per millilitre range. Finally, analyses of urine samples confirmed detection and quantification of each of the metabolites.
Collapse
Affiliation(s)
- Carien van der Berg
- Human Metabolomics, North-West University (Potchefstroom Campus), Potchefstroom, 2531, South Africa.
| | - Gerda Venter
- Human Metabolomics, North-West University (Potchefstroom Campus), Potchefstroom, 2531, South Africa
| | | | - Elardus Erasmus
- Human Metabolomics, North-West University (Potchefstroom Campus), Potchefstroom, 2531, South Africa.
| |
Collapse
|
48
|
Azad RK, Shulaev V. Metabolomics technology and bioinformatics for precision medicine. Brief Bioinform 2019; 20:1957-1971. [PMID: 29304189 PMCID: PMC6954408 DOI: 10.1093/bib/bbx170] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 11/29/2017] [Indexed: 12/14/2022] Open
Abstract
Precision medicine is rapidly emerging as a strategy to tailor medical treatment to a small group or even individual patients based on their genetics, environment and lifestyle. Precision medicine relies heavily on developments in systems biology and omics disciplines, including metabolomics. Combination of metabolomics with sophisticated bioinformatics analysis and mathematical modeling has an extreme power to provide a metabolic snapshot of the patient over the course of disease and treatment or classifying patients into subpopulations and subgroups requiring individual medical treatment. Although a powerful approach, metabolomics have certain limitations in technology and bioinformatics. We will review various aspects of metabolomics technology and bioinformatics, from data generation, bioinformatics analysis, data fusion and mathematical modeling to data management, in the context of precision medicine.
Collapse
Affiliation(s)
| | - Vladimir Shulaev
- Corresponding author: Vladimir Shulaev, Department of Biological Sciences, BioDiscovery Institute, University of North Texas, Denton, TX 76210, USA. Tel.: 940-369-5368; Fax: 940-565-3821; E-mail:
| |
Collapse
|
49
|
A New Classification Method of Metastatic Cancers Using a 1H-NMR-Based Approach: A Study Case of Melanoma, Breast, and Prostate Cancer Cell Lines. Metabolites 2019; 9:metabo9110281. [PMID: 31744229 PMCID: PMC6918216 DOI: 10.3390/metabo9110281] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 11/14/2019] [Accepted: 11/15/2019] [Indexed: 01/19/2023] Open
Abstract
In this study, metastatic melanoma, breast, and prostate cancer cell lines were analyzed using a 1H-NMR-based approach in order to investigate common features and differences of aggressive cancers metabolomes. For that purpose, 1H-NMR spectra of both cellular extracts and culture media were combined with multivariate data analysis, bringing to light no less than 20 discriminant metabolites able to separate the metastatic metabolomes. The supervised approach succeeded in classifying the metastatic cell lines depending on their glucose metabolism, more glycolysis-oriented in the BRAF proto-oncogene mutated cell lines compared to the others. Other adaptive metabolic features also contributed to the classification, such as the increased total choline content (tCho), UDP-GlcNAc detection, and various changes in the glucose-related metabolites tree, giving additional information about the metastatic metabolome status and direction. Finally, common metabolic features detected via 1H-NMR in the studied cancer cell lines are discussed, identifying the glycolytic pathway, Kennedy’s pathway, and the glutaminolysis as potential and common targets in metastasis, opening up new avenues to cure cancer.
Collapse
|
50
|
Li C, Li Z, Zhang T, Wei P, Li N, Zhang W, Ding X, Li J. 1H NMR-Based Metabolomics Reveals the Antitumor Mechanisms of Triptolide in BALB/c Mice Bearing CT26 Tumors. Front Pharmacol 2019; 10:1175. [PMID: 31680959 PMCID: PMC6798008 DOI: 10.3389/fphar.2019.01175] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 09/12/2019] [Indexed: 11/13/2022] Open
Abstract
Triptolide, the main active ingredient in Tripterygium wilfordii Hook. f. (Celastraceae), has shown promising effects against a variety of tumors. However, the molecular pharmacological mechanisms explaining the action of triptolide remain unknown. In this study, the CT26 colon tumor cell line was inoculated subcutaneously into BALB/c mice, and plasma samples were subjected to 1H NMR metabolomics analysis. The metabolic signature identified five metabolites whose levels were lower and 15 whose levels were higher in CT26 tumor-bearing mice than in normal control mice. Triptolide treatment significantly reversed the levels of nine of these metabolites, including isoleucine, glutamine, methionine, proline, 3-hydroxybutyric acid, 2-hydroxyisovalerate, 2-hydroxyisobutyrate, and low-density lipoprotein/very low-density lipoprotein. Based on the identities of these potential biomarkers, we conclude that the antitumor mechanism of triptolide might rely on correcting perturbations in branched-chain amino acid metabolism, serine/glycine/methionine biosynthesis, and ketone bodies metabolism.
Collapse
Affiliation(s)
- Cheng Li
- School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, China
| | - Zhongfeng Li
- Department of Chemistry, Capital Normal University, Beijing, China
| | | | - Peihuang Wei
- School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, China
| | - Nuo Li
- School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, China
| | - Wei Zhang
- School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, China
| | - Xia Ding
- School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, China
| | - Jian Li
- School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, China
| |
Collapse
|