1
|
Pegoraro C, Domingo-Ortí I, Conejos-Sánchez I, Vicent MJ. Unlocking the Mitochondria for Nanomedicine-based Treatments: Overcoming Biological Barriers, Improving Designs, and Selecting Verification Techniques. Adv Drug Deliv Rev 2024; 207:115195. [PMID: 38325562 DOI: 10.1016/j.addr.2024.115195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 01/13/2024] [Accepted: 02/02/2024] [Indexed: 02/09/2024]
Abstract
Enhanced targeting approaches will support the treatment of diseases associated with dysfunctional mitochondria, which play critical roles in energy generation and cell survival. Obstacles to mitochondria-specific targeting include the presence of distinct biological barriers and the need to pass through (or avoid) various cell internalization mechanisms. A range of studies have reported the design of mitochondrially-targeted nanomedicines that navigate the complex routes required to influence mitochondrial function; nonetheless, a significant journey lies ahead before mitochondrially-targeted nanomedicines become suitable for clinical use. Moving swiftly forward will require safety studies, in vivo assays confirming effectiveness, and methodologies to validate mitochondria-targeted nanomedicines' subcellular location/activity. From a nanomedicine standpoint, we describe the biological routes involved (from administration to arrival within the mitochondria), the features influencing rational design, and the techniques used to identify/validate successful targeting. Overall, rationally-designed mitochondria-targeted-based nanomedicines hold great promise for precise subcellular therapeutic delivery.
Collapse
Affiliation(s)
- Camilla Pegoraro
- Polymer Therapeutics Laboratory and CIBERONC, Príncipe Felipe Research Center, Av. Eduardo Primo Yúfera 3, E-46012 Valencia, Spain.
| | - Inés Domingo-Ortí
- Polymer Therapeutics Laboratory and CIBERONC, Príncipe Felipe Research Center, Av. Eduardo Primo Yúfera 3, E-46012 Valencia, Spain.
| | - Inmaculada Conejos-Sánchez
- Polymer Therapeutics Laboratory and CIBERONC, Príncipe Felipe Research Center, Av. Eduardo Primo Yúfera 3, E-46012 Valencia, Spain.
| | - María J Vicent
- Polymer Therapeutics Laboratory and CIBERONC, Príncipe Felipe Research Center, Av. Eduardo Primo Yúfera 3, E-46012 Valencia, Spain.
| |
Collapse
|
2
|
Liu S, Ding D, Liu F, Guo Y, Xie L, Han FJ. Exploring the causal role of multiple metabolites on ovarian cancer: a two sample Mendelian randomization study. J Ovarian Res 2024; 17:22. [PMID: 38263045 PMCID: PMC10804794 DOI: 10.1186/s13048-023-01340-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Accepted: 12/30/2023] [Indexed: 01/25/2024] Open
Abstract
BACKGROUND The mechanisms and risk factors underlying ovarian cancer (OC) remain under investigation, making the identification of new prognostic biomarkers and improved predictive factors critically important. Recently, circulating metabolites have shown potential in predicting survival outcomes and may be associated with the pathogenesis of OC. However, research into their genetic determinants is limited, and there are some inadequacies in understanding the distinct subtypes of OC. In this context, we conducted a Mendelian randomization study aiming to provide evidence for the relationship between genetically determined metabolites (GDMs) and the risk of OC and its subtypes. METHODS In this study, we consolidated genetic statistical data of GDMs with OC and its subtypes through a genome-wide association study (GWAS) and conducted a two-sample Mendelian randomization (MR) analysis. The inverse variance weighted (IVW) method served as the primary approach, with MR-Egger and weighted median methods employed for cross-validation to determine whether a causal relationship exists between the metabolites and OC risk. Moreover, a range of sensitivity analyses were conducted to validate the robustness of the results. MR-Egger intercept, and Cochran's Q statistical analysis were used to evaluate possible heterogeneity and pleiotropy. False discovery rate (FDR) correction was applied to validate the findings. We also conducted a reverse MR analysis to validate whether the observed blood metabolite levels were influenced by OC risk. Additionally, metabolic pathway analysis was carried out using the MetaboAnalyst 5.0 software. RESULTS In MR analysis, we discovered 18 suggestive causal associations involving 14 known metabolites, 8 metabolites as potential risk factors, and 6 as potential cancer risk reducers. In addition, three significant pathways, "caffeine metabolism," "arginine biosynthesis," and "citrate cycle (TCA cycle)" were associated with the development of mucinous ovarian cancer (MOC). The pathways "caffeine metabolism" and "alpha-linolenic acid metabolism" were associated with the onset of endometrioid ovarian cancer (OCED). CONCLUSIONS Our MR analysis revealed both protective and risk-associated metabolites, providing insights into the potential causal relationships between GDMs and the metabolic pathways related to OC and its subtypes. The metabolites that drive OC could be potential candidates for biomarkers.
Collapse
Affiliation(s)
- Shaoxuan Liu
- First Clinical Medical College, Heilongjiang University of Chinese Medicine, Harbin, 150040, China
| | - Danni Ding
- First Clinical Medical College, Heilongjiang University of Chinese Medicine, Harbin, 150040, China
| | - Fangyuan Liu
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Heilongjiang University of Chinese Medicine, Harbin, 150040, China
| | - Ying Guo
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Heilongjiang University of Chinese Medicine, Harbin, 150040, China
| | - Liangzhen Xie
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Heilongjiang University of Chinese Medicine, Harbin, 150040, China
| | - Feng-Juan Han
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Heilongjiang University of Chinese Medicine, Harbin, 150040, China.
| |
Collapse
|
3
|
Boguszewicz Ł, Bieleń A, Ciszek M, Skorupa A, Mrochem-Kwarciak J, Składowski K, Sokół M. Metabolomic Insight into Implications of Induction Chemotherapy Followed by Concomitant Chemoradiotherapy in Locally Advanced Head and Neck Cancer. Int J Mol Sci 2023; 25:188. [PMID: 38203359 PMCID: PMC10779362 DOI: 10.3390/ijms25010188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 12/15/2023] [Accepted: 12/20/2023] [Indexed: 01/12/2024] Open
Abstract
The present study compares two groups of locally advanced patients with head and neck squamous cell carcinoma (LA-HNSCC) undergoing concurrent chemoradiotherapy (cCHRT), specifically those for whom it is a first-line treatment and those who have previously received induction chemotherapy (iCHT). The crucial question is whether iCHT is a serious burden during subsequent treatment for LA-HNSCC and how iCHT affects the tolerance to cCHRT. Of the 107 LA-HNSCC patients, 54 received cisplatin-based iCHT prior to cCHRT. The patients were clinically monitored at weekly intervals from the day before until the completion of the cCHRT. The 843 blood samples were collected and divided into two aliquots: for laboratory blood tests and for nuclear magnetic resonance (NMR) spectroscopy (a Bruker 400 MHz spectrometer). The NMR metabolites and the clinical parameters from the laboratory blood tests were analyzed using orthogonal partial least squares analysis (OPLS) and the Mann-Whitney U test (MWU). After iCHT, the patients begin cCHRT with significantly (MWU p-value < 0.05) elevated blood serum lipids, betaine, glycine, phosphocholine, and reticulocyte count, as well as significantly lowered NMR inflammatory markers, serine, hematocrit, neutrophile, monocyte, red blood cells, hemoglobin, and CRP. During cCHRT, a significant increase in albumin and psychological distress was observed, as well as a significant decrease in platelet, N-acetyl-cysteine, tyrosine, and phenylalanine, in patients who received iCHT. Importantly, all clinical symptoms (except the decreased platelets) and most metabolic alterations (except for betaine, serine, tyrosine, glucose, and phosphocholine) resolve until the completion of cCHRT. In conclusion, iCHT results in hematological toxicity, altered lipids, and one-carbon metabolism, as well as downregulated inflammation, as observed at the beginning and during cCHRT. However, these complications are temporary, and most of them resolve at the end of the treatment. This suggests that iCHT prior to cCHRT does not pose a significant burden and should be considered as a safe treatment option for LA-HNSCC.
Collapse
Affiliation(s)
- Łukasz Boguszewicz
- Department of Medical Physics, Maria Sklodowska-Curie National Research Institute of Oncology, Gliwice Branch, 44-102 Gliwice, Poland; (M.C.); (A.S.); (M.S.)
| | - Agata Bieleń
- 1st Radiation and Clinical Oncology Department, Maria Sklodowska-Curie National Research Institute of Oncology, Gliwice Branch, 44-102 Gliwice, Poland; (A.B.)
| | - Mateusz Ciszek
- Department of Medical Physics, Maria Sklodowska-Curie National Research Institute of Oncology, Gliwice Branch, 44-102 Gliwice, Poland; (M.C.); (A.S.); (M.S.)
| | - Agnieszka Skorupa
- Department of Medical Physics, Maria Sklodowska-Curie National Research Institute of Oncology, Gliwice Branch, 44-102 Gliwice, Poland; (M.C.); (A.S.); (M.S.)
| | - Jolanta Mrochem-Kwarciak
- Analytics and Clinical Biochemistry Department, Maria Sklodowska-Curie National Research Institute of Oncology, Gliwice Branch, 44-102 Gliwice, Poland;
| | - Krzysztof Składowski
- 1st Radiation and Clinical Oncology Department, Maria Sklodowska-Curie National Research Institute of Oncology, Gliwice Branch, 44-102 Gliwice, Poland; (A.B.)
| | - Maria Sokół
- Department of Medical Physics, Maria Sklodowska-Curie National Research Institute of Oncology, Gliwice Branch, 44-102 Gliwice, Poland; (M.C.); (A.S.); (M.S.)
| |
Collapse
|
4
|
van der Kemp WJM, Grinde MT, Malvik JO, van Laarhoven HWM, Prompers JJ, Klomp DWJ, Burgering B, Bathen TF, Moestue SA. Metabolic profiling of colorectal cancer organoids: A comparison between high-resolution magic angle spinning magnetic resonance spectroscopy and solution nuclear magnetic resonance spectroscopy of polar extracts. NMR IN BIOMEDICINE 2023; 36:e4882. [PMID: 36451530 DOI: 10.1002/nbm.4882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 11/18/2022] [Accepted: 11/20/2022] [Indexed: 06/17/2023]
Abstract
Patient-derived cancer cells cultured in vitro are a cornerstone of cancer metabolism research. More recently, the introduction of organoids has provided the research community with a more versatile model system. Physiological structure and organization of the cell source tissue are maintained in organoids, representing a closer link to in vivo tumor models. High-resolution magic angle spinning magnetic resonance spectroscopy (HR MAS MRS) is a commonly applied analytical approach for metabolic profiling of intact tissue, but its use has not been reported for organoids. The aim of the current work was to compare the performance of HR MAS MRS and extraction-based nuclear magnetic resonance (NMR) in metabolic profiling of wild-type and tumor progression organoids (TPOs) from human colon cancer, and further to investigate how the sequentially increased genetic alterations of the TPOs affect the metabolic profile. Sixteen metabolites were reliably identified and quantified both in spectra based on NMR of extracts and HR MAS MRS of intact organoids. The metabolite concentrations from the two approaches were highly correlated (r = 0.94), and both approaches were able to capture the systematic changes in metabolic features introduced by the genetic alterations characteristic of colorectal cancer progression (e.g., increased levels of lactate and decreased levels of myo-inositol and phosphocholine with an increasing number of mutations). The current work highlights that HR MAS MRS is a well-suited method for metabolic profiling of intact organoids, with the additional benefit that the nondestructive nature of HR MAS enables subsequent recovery of the organoids for further analyses based on nucleic acids or proteins.
Collapse
Affiliation(s)
- Wybe J M van der Kemp
- Division of Imaging and Oncology, University Medical Centre (UMC) Utrecht, Utrecht, The Netherlands
| | - Maria T Grinde
- Department of Circulation and Medical Imaging, NTNU - Norwegian University of Science and Technology, Trondheim, Norway
- Department of Radiology and Nuclear Medicine, St. Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
| | - Jon O Malvik
- Department of Circulation and Medical Imaging, NTNU - Norwegian University of Science and Technology, Trondheim, Norway
| | - Hanneke W M van Laarhoven
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
| | - Jeanine J Prompers
- Division of Imaging and Oncology, University Medical Centre (UMC) Utrecht, Utrecht, The Netherlands
| | - Dennis W J Klomp
- Division of Imaging and Oncology, University Medical Centre (UMC) Utrecht, Utrecht, The Netherlands
| | - Boudewijn Burgering
- Center for Molecular Medicine, Molecular Cancer Research, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Tone Frost Bathen
- Department of Circulation and Medical Imaging, NTNU - Norwegian University of Science and Technology, Trondheim, Norway
| | - Siver Andreas Moestue
- Department of Clinical and Molecular Medicine, NTNU - Norwegian University of Science and Technology, Trondheim, Norway
- Department of Pharmacy, Nord University, Bodø, Norway
| |
Collapse
|
5
|
Chiocchetti GDME, Lopes-Aguiar L, Miyaguti NADS, Viana LR, Salgado CDM, Orvoën OO, Florindo D, dos Santos RW, Cintra Gomes-Marcondes MC. A Time-Course Comparison of Skeletal Muscle Metabolomic Alterations in Walker-256 Tumour-Bearing Rats at Different Stages of Life. Metabolites 2021; 11:metabo11060404. [PMID: 34202988 PMCID: PMC8234487 DOI: 10.3390/metabo11060404] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 06/16/2021] [Accepted: 06/17/2021] [Indexed: 12/23/2022] Open
Abstract
Cancer cachexia is a severe wasting condition that needs further study to find ways to minimise the effects of damage and poor prognosis. Skeletal muscle is the most impacted tissue in cancer cachexia; thus, elucidation of its metabolic alterations could provide a direct clue for biomarker research and be applied to detect this syndrome earlier. In addition, concerning the significant changes in the host metabolism across life, this study aimed to compare the metabolic muscle changes in cachectic tumour-bearing hosts at different ages. We performed 1H-NMR metabolomics in the gastrocnemius muscle in weanling and young adult Walker-256 tumour-bearing rats at different stages of tumour evolution (initial, intermediate, and advanced). Among the 49 metabolites identified, 24 were significantly affected throughout tumour evolution and 21 were significantly affected regarding animal age. The altered metabolites were mainly related to increased amino acid levels and changed energetic metabolism in the skeletal muscle, suggesting an expressive catabolic process and diverted energy production, especially in advanced tumour stages in both groups. Moreover, these changes were more severe in weanling hosts throughout tumour evolution, suggesting the distinct impact of cancer cachexia regarding the host's age, highlighting the need to adopting the right animal age when studying cancer cachexia.
Collapse
Affiliation(s)
- Gabriela de Matuoka e Chiocchetti
- Laboratory of Nutrition and Cancer, Department of Structural and Functional Biology, Biology Institute, University of Campinas (UNICAMP), Rua Monteiro Lobato, 255, Campinas 13083862, SP, Brazil; (L.L.-A.); (N.A.d.S.M.); (L.R.V.); (C.d.M.S.); (O.O.O.); (D.F.); (R.W.d.S.)
- Correspondence: (G.d.M.e.C.); (M.C.C.G.-M.); Tel.: +55-19-3521-6194 (M.C.C.G.-M.)
| | - Leisa Lopes-Aguiar
- Laboratory of Nutrition and Cancer, Department of Structural and Functional Biology, Biology Institute, University of Campinas (UNICAMP), Rua Monteiro Lobato, 255, Campinas 13083862, SP, Brazil; (L.L.-A.); (N.A.d.S.M.); (L.R.V.); (C.d.M.S.); (O.O.O.); (D.F.); (R.W.d.S.)
| | - Natália Angelo da Silva Miyaguti
- Laboratory of Nutrition and Cancer, Department of Structural and Functional Biology, Biology Institute, University of Campinas (UNICAMP), Rua Monteiro Lobato, 255, Campinas 13083862, SP, Brazil; (L.L.-A.); (N.A.d.S.M.); (L.R.V.); (C.d.M.S.); (O.O.O.); (D.F.); (R.W.d.S.)
| | - Lais Rosa Viana
- Laboratory of Nutrition and Cancer, Department of Structural and Functional Biology, Biology Institute, University of Campinas (UNICAMP), Rua Monteiro Lobato, 255, Campinas 13083862, SP, Brazil; (L.L.-A.); (N.A.d.S.M.); (L.R.V.); (C.d.M.S.); (O.O.O.); (D.F.); (R.W.d.S.)
| | - Carla de Moraes Salgado
- Laboratory of Nutrition and Cancer, Department of Structural and Functional Biology, Biology Institute, University of Campinas (UNICAMP), Rua Monteiro Lobato, 255, Campinas 13083862, SP, Brazil; (L.L.-A.); (N.A.d.S.M.); (L.R.V.); (C.d.M.S.); (O.O.O.); (D.F.); (R.W.d.S.)
| | - Ophelie Ocean Orvoën
- Laboratory of Nutrition and Cancer, Department of Structural and Functional Biology, Biology Institute, University of Campinas (UNICAMP), Rua Monteiro Lobato, 255, Campinas 13083862, SP, Brazil; (L.L.-A.); (N.A.d.S.M.); (L.R.V.); (C.d.M.S.); (O.O.O.); (D.F.); (R.W.d.S.)
- Biology Department, University of Angers, 49000 Anger, France
| | - Derly Florindo
- Laboratory of Nutrition and Cancer, Department of Structural and Functional Biology, Biology Institute, University of Campinas (UNICAMP), Rua Monteiro Lobato, 255, Campinas 13083862, SP, Brazil; (L.L.-A.); (N.A.d.S.M.); (L.R.V.); (C.d.M.S.); (O.O.O.); (D.F.); (R.W.d.S.)
| | - Rogério Williams dos Santos
- Laboratory of Nutrition and Cancer, Department of Structural and Functional Biology, Biology Institute, University of Campinas (UNICAMP), Rua Monteiro Lobato, 255, Campinas 13083862, SP, Brazil; (L.L.-A.); (N.A.d.S.M.); (L.R.V.); (C.d.M.S.); (O.O.O.); (D.F.); (R.W.d.S.)
| | - Maria Cristina Cintra Gomes-Marcondes
- Laboratory of Nutrition and Cancer, Department of Structural and Functional Biology, Biology Institute, University of Campinas (UNICAMP), Rua Monteiro Lobato, 255, Campinas 13083862, SP, Brazil; (L.L.-A.); (N.A.d.S.M.); (L.R.V.); (C.d.M.S.); (O.O.O.); (D.F.); (R.W.d.S.)
- Correspondence: (G.d.M.e.C.); (M.C.C.G.-M.); Tel.: +55-19-3521-6194 (M.C.C.G.-M.)
| |
Collapse
|
6
|
Targeted 1H NMR metabolomics and immunological phenotyping of human fresh blood and serum samples discriminate between healthy individuals and inflammatory bowel disease patients treated with anti-TNF. J Mol Med (Berl) 2021; 99:1251-1264. [PMID: 34021361 PMCID: PMC8367886 DOI: 10.1007/s00109-021-02094-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 04/19/2021] [Accepted: 05/13/2021] [Indexed: 12/14/2022]
Abstract
Abstract Inflammatory bowel disease is a multifactorial etiology, associated with environmental factors that can trigger both debut and relapses. A high level of tumor necrosis factor-α in the gut is the main consequence of immune system imbalance. The aim of treatment is to restore gut homeostasis. In this study, fresh blood and serum samples were used to identify biomarkers and to discriminate between Crohn’s disease and ulcerative colitis patients under remission treated with anti-TNF. Metabolomics based on Nuclear Magnetic Resonance spectroscopy (NMR) was used to detect unique biomarkers for each class of patients. Blood T lymphocyte repertories were characterized, as well as cytokine and transcription factor profiling, to complement the metabolomics data. Higher levels of homoserine-methionine and isobutyrate were identified as biomarkers of Crohn’s disease with ileocolic localization. For ulcerative colitis, lower levels of creatine-creatinine, proline, and tryptophan were found that reflect a deficit in the absorption of essential amino acids in the gut. T lymphocyte phenotyping and its functional profiling revealed that the overall inflammation was lower in Crohn’s disease patients than in those with ulcerative colitis. These results demonstrated that NMR metabolomics could be introduced as a high-throughput evaluation method in routine clinical practice to stratify both types of patients related to their pathology. Key messages NMR metabolomics is a non-invasive tool that could be implemented in the normal clinical practice for IBD to assess beneficial effect of the treatment. NMR metabolomics is a useful tool for precision medicine, in order to sew a specific treatment to a specific group of patients. Finding predictors of response to IFX would be desirable to select patients affected by IBD. Immunological status of inflammations correlates with NMR metabolomics biomarkers.
Supplementary Information The online version contains supplementary material available at 10.1007/s00109-021-02094-y.
Collapse
|
7
|
Aru V, Khakimov B, Sørensen KM, Chikwati EM, Kortner TM, Midtlyng P, Krogdahl Å, Engelsen SB. The plasma metabolome of Atlantic salmon as studied by 1H NMR spectroscopy using standard operating procedures: effect of aquaculture location and growth stage. Metabolomics 2021; 17:50. [PMID: 33999285 DOI: 10.1007/s11306-021-01797-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 04/23/2021] [Indexed: 12/15/2022]
Abstract
INTRODUCTION Metabolomics applications to the aquaculture research are increasing steadily. The use of standardized proton nuclear magnetic resonance (1H NMR) spectroscopy can provide the aquaculture industry with an unbiased, reproducible, and high-throughput screening tool, which can help to diagnose nutritional and disease-related metabolic disorders in farmed fish. OBJECTIVE Standard operating procedures developed for analysing (human) plasma by 1H NMR were applied to fingerprint the metabolome in plasma samples collected from Atlantic salmon. The aim was to explore the metabolome of salmon plasma in relation to growth stage and sampling site. METHODS A total of 72 salmon were collected from three aquaculture sites in Norway (Lat. 65, 67, and 70 °N) and over two sampling events (December 2017 and November 2018). Plasma drawn from each salmon was measured by 1H NMR and metabolites were quantified using the SigMa software. The NMR data was analysed by principal component analysis (PCA) and ANOVA-simultaneous component analysis (ASCA). RESULTS Important metabolic differences were evidenced, with adult salmon having a much higher content of very low-density lipoproteins and cholesterol in their plasma, while smolts displayed significantly higher levels of propylene glycol. Overall, 24% of the metabolite variation was due to the growth stage, whereas 12% of the metabolite variation was related to the aquaculture site and practice (p < 0.001). CONCLUSION This study provides a baseline investigation of the plasma metabolome of the Atlantic salmon and demonstrates how 1H NMR metabolomics can be used in future investigations for comparing aquaculture practices and their influence on the fish metabolome.
Collapse
Affiliation(s)
- Violetta Aru
- Chemometrics & Analytical Technology, Department of Food Science, University of Copenhagen, Rolighedsvej 26, 1958, Frederiksberg C, Denmark.
| | - Bekzod Khakimov
- Chemometrics & Analytical Technology, Department of Food Science, University of Copenhagen, Rolighedsvej 26, 1958, Frederiksberg C, Denmark
| | - Klavs Martin Sørensen
- Chemometrics & Analytical Technology, Department of Food Science, University of Copenhagen, Rolighedsvej 26, 1958, Frederiksberg C, Denmark
| | - Elvis Mashingaidze Chikwati
- Department of Paraclinical Sciences, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Oslo, Norway
- Aquamedic AS, Gaustadallèen 21, 0349, Oslo, Norway
| | - Trond M Kortner
- Department of Paraclinical Sciences, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Oslo, Norway
| | | | - Åshild Krogdahl
- Department of Paraclinical Sciences, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Oslo, Norway
| | - Søren Balling Engelsen
- Chemometrics & Analytical Technology, Department of Food Science, University of Copenhagen, Rolighedsvej 26, 1958, Frederiksberg C, Denmark.
| |
Collapse
|
8
|
Egan JM, van Santen JA, Liu DY, Linington RG. Development of an NMR-Based Platform for the Direct Structural Annotation of Complex Natural Products Mixtures. JOURNAL OF NATURAL PRODUCTS 2021; 84:1044-1055. [PMID: 33750122 PMCID: PMC8330833 DOI: 10.1021/acs.jnatprod.0c01076] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
The development of new "omics" platforms is having a significant impact on the landscape of natural products discovery. However, despite the advantages that such platforms bring to the field, there remains no straightforward method for characterizing the chemical landscape of natural products libraries using two-dimensional nuclear magnetic resonance (2D-NMR) experiments. NMR analysis provides a powerful complement to mass spectrometric approaches, given the universal coverage of NMR experiments. However, the high degree of signal overlap, particularly in one-dimensional NMR spectra, has limited applications of this approach. To address this issue, we have developed a new data analysis platform for complex mixture analysis, termed MADByTE (Metabolomics and Dereplication by Two-Dimensional Experiments). This platform employs a combination of TOCSY and HSQC spectra to identify spin system features within complex mixtures and then matches spin system features between samples to create a chemical similarity network for a given sample set. In this report we describe the design and construction of the MADByTE platform and demonstrate the application of chemical similarity networks for both the dereplication of known compound scaffolds and the prioritization of bioactive metabolites from a bacterial prefractionated extract library.
Collapse
Affiliation(s)
- Joseph M Egan
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada
| | - Jeffrey A van Santen
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada
| | - Dennis Y Liu
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada
| | - Roger G Linington
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada
| |
Collapse
|
9
|
Clarke EJ, Anderson JR, Peffers MJ. Nuclear magnetic resonance spectroscopy of biofluids for osteoarthritis. Br Med Bull 2021; 137:28-41. [PMID: 33290503 PMCID: PMC7995852 DOI: 10.1093/bmb/ldaa037] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 10/01/2020] [Accepted: 10/24/2020] [Indexed: 12/16/2022]
Abstract
BACKGROUND Osteoarthritis is a common degenerative musculoskeletal disease of synovial joints. It is characterized by a metabolic imbalance resulting in articular cartilage degradation, reduced elastoviscosity of synovial fluid and an altered chondrocyte phenotype. This is often associated with reduced mobility, pain and poor quality of life. Subsequently, with an ageing world population, osteoarthritis is of increasing concern to public health. Nuclear magnetic resonance (NMR) spectroscopy can be applied to characterize the metabolomes of biofluids, determining changes associated with osteoarthritis pathology, identifying potential biomarkers of disease and alterations to metabolic pathways. SOURCES OF DATA A comprehensive search of PubMed and Web of Science databases using combinations of the following keywords: 'NMR Spectroscopy', 'Blood', 'Plasma', 'Serum', 'Urine', 'Synovial Fluid' and 'Osteoarthritis' for articles published from 2000 to 2020. AREAS OF AGREEMENT The number of urine metabolomics studies using NMR spectroscopy to investigate osteoarthritis is low, whereas the use of synovial fluid is significantly higher. Several differential metabolites have previously been identified and mapped to metabolic pathways involved in osteoarthritis pathophysiology. AREAS OF CONTROVERSY Conclusions are sometimes conservative or overinflated, which may reflect the variation in reporting standards. NMR metabolic experimental design may require further consideration, as do the animal models used for such studies. GROWING POINTS There are various aspects which require improvement within the field. These include stricter adherence to the Metabolomics Standards Initiative, inclusive of the standardization of metabolite identifications; increased utilization of integrating NMR metabolomics with other 'omic' disciplines; and increased deposition of raw experimental files into open access online repositories, allowing greater transparency and enabling additional future analyses. AREAS TIMELY FOR DEVELOPING RESEARCH Overall, this research area could be improved by the inclusion of more heterogeneous cohorts, reflecting varying osteoarthritis phenotypes, and larger group sizes ensuring studies are not underpowered. To correlate local and systemic environments, the use of blood for diagnostic purposes, over the collection of synovial fluid, requires increased attention. This will ultimately enable biomarkers of disease to be determined that may provide an earlier diagnosis, or provide potential therapeutic targets for osteoarthritis, ultimately improving patient prognosis.
Collapse
Affiliation(s)
- Emily J Clarke
- Institute of Life Course and Medical Sciences, Musculoskeletal and Ageing Science, William Henry Duncan Building, 6 West Derby Street, Liverpool L7 8TX, UK
| | - James R Anderson
- Institute of Life Course and Medical Sciences, Musculoskeletal and Ageing Science, William Henry Duncan Building, 6 West Derby Street, Liverpool L7 8TX, UK
| | - Mandy J Peffers
- Institute of Life Course and Medical Sciences, Musculoskeletal and Ageing Science, William Henry Duncan Building, 6 West Derby Street, Liverpool L7 8TX, UK
| |
Collapse
|
10
|
Erben V, Poschet G, Schrotz-King P, Brenner H. Comparing Metabolomics Profiles in Various Types of Liquid Biopsies among Screening Participants with and without Advanced Colorectal Neoplasms. Diagnostics (Basel) 2021; 11:561. [PMID: 33804777 PMCID: PMC8003917 DOI: 10.3390/diagnostics11030561] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 03/15/2021] [Accepted: 03/18/2021] [Indexed: 12/29/2022] Open
Abstract
Analysis of metabolomics has been suggested as a promising approach for early detection of colorectal cancer and advanced adenomas. We investigated and compared the metabolomics profile in blood, stool, and urine samples of screening colonoscopy participants and aimed to evaluate differences in metabolite concentrations between people with advanced colorectal neoplasms and those without neoplasms. Various types of bio-samples (plasma, feces, and urine) from 400 participants of screening colonoscopy were investigated using the MxP® Quant 500 kit (Biocrates, Innsbruck, Austria). We detected a broad range of metabolites in blood, stool, and urine samples (504, 331, and 131, respectively). Significant correlations were found between concentrations in blood and stool, blood and urine, and stool and urine for 93, 154, and 102 metabolites, of which 68 (73%), 126 (82%), and 39 (38%) were positive correlations. We found significant differences between participants with and without advanced colorectal neoplasms for concentrations of 123, 49, and 28 metabolites in blood, stool and urine samples, respectively. We detected mostly positive correlations between metabolite concentrations in blood samples and urine or stool samples, and mostly negative correlations between urine and stool samples. Differences between subjects with and without advanced colorectal neoplasms were found for metabolite concentrations in each of the three bio-fluids.
Collapse
Affiliation(s)
- Vanessa Erben
- Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), 69120 Heidelberg, Germany; (V.E.); (P.S.-K.)
- Medical Faculty Heidelberg, Heidelberg University, 69120 Heidelberg, Germany
| | - Gernot Poschet
- Centre for Organismal Studies (COS), Heidelberg University, 69120 Heidelberg, Germany;
| | - Petra Schrotz-King
- Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), 69120 Heidelberg, Germany; (V.E.); (P.S.-K.)
| | - Hermann Brenner
- Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), 69120 Heidelberg, Germany; (V.E.); (P.S.-K.)
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
| |
Collapse
|
11
|
Crook AA, Powers R. Quantitative NMR-Based Biomedical Metabolomics: Current Status and Applications. Molecules 2020; 25:E5128. [PMID: 33158172 PMCID: PMC7662776 DOI: 10.3390/molecules25215128] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 10/26/2020] [Accepted: 10/30/2020] [Indexed: 12/19/2022] Open
Abstract
Nuclear Magnetic Resonance (NMR) spectroscopy is a quantitative analytical tool commonly utilized for metabolomics analysis. Quantitative NMR (qNMR) is a field of NMR spectroscopy dedicated to the measurement of analytes through signal intensity and its linear relationship with analyte concentration. Metabolomics-based NMR exploits this quantitative relationship to identify and measure biomarkers within complex biological samples such as serum, plasma, and urine. In this review of quantitative NMR-based metabolomics, the advancements and limitations of current techniques for metabolite quantification will be evaluated as well as the applications of qNMR in biomedical metabolomics. While qNMR is limited by sensitivity and dynamic range, the simple method development, minimal sample derivatization, and the simultaneous qualitative and quantitative information provide a unique landscape for biomedical metabolomics, which is not available to other techniques. Furthermore, the non-destructive nature of NMR-based metabolomics allows for multidimensional analysis of biomarkers that facilitates unambiguous assignment and quantification of metabolites in complex biofluids.
Collapse
Affiliation(s)
- Alexandra A. Crook
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, USA;
| | - Robert Powers
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, USA;
- Nebraska Center for Integrated Biomolecular Communication, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, USA
| |
Collapse
|
12
|
Mili M, Panthu B, Madec AM, Berger MA, Rautureau GJP, Elena-Herrmann B. Fast and ergonomic extraction of adherent mammalian cells for NMR-based metabolomics studies. Anal Bioanal Chem 2020; 412:5453-5463. [PMID: 32556564 DOI: 10.1007/s00216-020-02764-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 05/08/2020] [Accepted: 06/08/2020] [Indexed: 11/29/2022]
Abstract
Cellular metabolomics has become key to elucidate mechanistic aspects in various fields such as cancerology or pharmacology, and is rapidly becoming a standard phenotyping tool accessible to the broad biological community. Acquisition of reliable spectroscopic datasets, such as nuclear magnetic resonance (NMR) spectra, to characterize biological systems depends on the elaboration of robust methods for cellular metabolites extraction. Previous studies have addressed many issues raised by these protocols, however with little pondering on ergonomic and practical aspects of the methods that impact their scalability, reproducibility and hence their suitability to high-throughput studies or their use by non-metabolomics experts. Here, we optimize a fast and ergonomic protocol for extraction of metabolites from adherent mammalian cells for NMR metabolomics studies. The proposed extraction protocol, including cell washing, metabolism quenching and actual extraction of intracellular metabolites, was first optimized on HeLa cells. Efficiency of the protocol, in its globality and for the different individual steps, was assessed by NMR quantification of 27 metabolites from cellular extracts. We show that a single PBS wash provides a seemly compromise between contamination from growth medium and leakage of intracellular metabolites. In HeLa cells, extraction using pure methanol, without cell scraping, recovered a higher amount of intracellular metabolites than the reference methanol/water/chloroform method with cell scraping, with yields varying across metabolite classes. Optimized and reference protocols were further tested on eight cell lines of miscellaneous nature, and inter-operator reproducibility was demonstrated. Our results stress the need for tailored extraction protocols and show that fast protocols minimizing time-consuming steps, without compromising extraction yields, are suitable for high-throughput metabolomics studies. Graphical abstract.
Collapse
Affiliation(s)
- Manhal Mili
- Institut des Sciences Analytiques UMR 5280, CRMN FRE 2034, Univ Lyon, CNRS, Université Claude Bernard Lyon 1, ENS de Lyon, 5 rue de la Doua, 69100, Villeurbanne, France
| | - Baptiste Panthu
- CarMeN laboratory, Univ Lyon, INSERM, INRA, INSA, Université Claude Bernard Lyon1, 69121, Oullins, France
| | - Anne-Marie Madec
- CarMeN laboratory, Univ Lyon, INSERM, INRA, INSA, Université Claude Bernard Lyon1, 69121, Oullins, France
| | - Marie-Agnès Berger
- CarMeN laboratory, Univ Lyon, INSERM, INRA, INSA, Université Claude Bernard Lyon1, 69121, Oullins, France
| | - Gilles J P Rautureau
- Institut des Sciences Analytiques UMR 5280, CRMN FRE 2034, Univ Lyon, CNRS, Université Claude Bernard Lyon 1, ENS de Lyon, 5 rue de la Doua, 69100, Villeurbanne, France
| | | |
Collapse
|
13
|
Nallala J, Jeynes C, Saunders S, Smart N, Lloyd G, Riley L, Salmon D, Stone N. Characterization of colorectal mucus using infrared spectroscopy: a potential target for bowel cancer screening and diagnosis. J Transl Med 2020; 100:1102-1110. [PMID: 32203151 PMCID: PMC7374084 DOI: 10.1038/s41374-020-0418-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Revised: 03/10/2020] [Accepted: 03/10/2020] [Indexed: 12/27/2022] Open
Abstract
Biological materials presenting early signs of cancer would be beneficial for cancer screening/diagnosis. In this respect, the suitability of potentially exploiting mucus in colorectal cancer was tested using infrared spectroscopy in combination with statistical modeling. Twenty-six paraffinized colon tissue biopsy sections containing mucus regions from 20 individuals (10 normal and 16 cancerous) were measured using mid-infrared spectroscopic imaging. A digital de-paraffinization, followed by cluster analysis driven digital color-coded multi-staining segmented the infrared images into various histopathological features such as epithelium, connective tissue, stroma, and mucus regions within the tissue sections. Principal component analysis followed by supervised linear discriminant analysis was carried out on pure mucus and epithelial spectra from normal and cancerous regions of the tissue. For the mucus-based classification, a sensitivity of 96%, a specificity of 83%, and an area under the curve performance of 95% was obtained. For the epithelial tissue-based classification, a sensitivity of 72%, a specificity of 88%, and an area under the curve performance of 89% was obtained. The mucus spectral profiles further showed contributions indicative of glycans including that of sialic acid changes between these pathology groups. The study demonstrates that infrared spectroscopic analysis of mucus discriminates colorectal cancers with high sensitivity. This concept could be exploited to develop screening/diagnostic approaches complementary to histopathology.
Collapse
Affiliation(s)
- Jayakrupakar Nallala
- Biomedical Physics, School of Physics and Astronomy, University of Exeter, Exeter, EX4 4QL, UK.
| | - Charles Jeynes
- 0000 0004 1936 8024grid.8391.3Living Systems Institute, University of Exeter, Exeter, EX4 4QD UK
| | - Sarah Saunders
- grid.416118.bCellular Pathology Department, Royal Devon & Exeter Hospital, Exeter, EX2 5AD UK
| | - Neil Smart
- grid.416118.bDepartment of Surgery, Royal Devon and Exeter Hospital, Exeter, EX2 5DW UK
| | - Gavin Lloyd
- 0000 0004 1936 7486grid.6572.6Phenome Centre Birmingham, University of Birmingham, Birmingham, B15 2TT UK
| | - Leah Riley
- grid.416118.bCellular Pathology Department, Royal Devon & Exeter Hospital, Exeter, EX2 5AD UK
| | - Debbie Salmon
- 0000 0004 1936 8024grid.8391.3Biocatalysis Centre, Biosciences, University of Exeter, Exeter, EX4 4QD UK
| | - Nick Stone
- 0000 0004 1936 8024grid.8391.3Biomedical Physics, School of Physics and Astronomy, University of Exeter, Exeter, EX4 4QL UK
| |
Collapse
|
14
|
Lende TH, Austdal M, Bathen TF, Varhaugvik AE, Skaland I, Gudlaugsson E, Egeland NG, Lunde S, Akslen LA, Jonsdottir K, Janssen EAM, Søiland H, Baak JPA. Metabolic consequences of perioperative oral carbohydrates in breast cancer patients - an explorative study. BMC Cancer 2019; 19:1183. [PMID: 31801490 PMCID: PMC6894229 DOI: 10.1186/s12885-019-6393-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Accepted: 11/21/2019] [Indexed: 12/21/2022] Open
Abstract
Background The metabolic consequences of preoperative carbohydrate load in breast cancer patients are not known. The present explorative study investigated the systemic and tumor metabolic changes after preoperative per-oral carbohydrate load and their influence on tumor characteristics and survival. Methods The study setting was on university hospital level with primary and secondary care functions in south-west Norway. Serum and tumor tissue were sampled from a population-based cohort of 60 patients with operable breast cancer who were randomized to either per-oral carbohydrate load (preOp™; n = 25) or standard pre-operative fasting (n = 35) before surgery. Magnetic resonance (MR) metabolomics was performed on serum samples from all patients and high-resolution magic angle spinning (HR-MAS) MR analysis on 13 tumor samples available from the fasting group and 16 tumor samples from the carbohydrate group. Results Fourteen of 28 metabolites were differently expressed between fasting and carbohydrate groups. Partial least squares discriminant analysis showed a significant difference in the metabolic profile between the fasting and carbohydrate groups, compatible with the endocrine effects of insulin (i.e., increased serum-lactate and pyruvate and decreased ketone bodies and amino acids in the carbohydrate group). Among ER-positive tumors (n = 18), glutathione was significantly elevated in the carbohydrate group compared to the fasting group (p = 0.002), with a positive correlation between preoperative S-insulin levels and the glutathione content in tumors (r = 0.680; p = 0.002). In all tumors (n = 29), glutamate was increased in tumors with high proliferation (t-test; p = 0.009), independent of intervention group. Moreover, there was a positive correlation between tumor size and proliferation markers in the carbohydrate group only. Patients with ER-positive / T2 tumors and high tumor glutathione (≥1.09), high S-lactate (≥56.9), and high S-pyruvate (≥12.5) had inferior clinical outcomes regarding relapse-free survival, breast cancer-specific survival, and overall survival. Moreover, Integrated Pathway Analysis (IPA) in serum revealed activation of five major anabolic metabolic networks contributing to proliferation and growth. Conclusions Preoperative carbohydrate load increases systemic levels of lactate and pyruvate and tumor levels of glutathione and glutamate in ER-positive patients. These biological changes may contribute to the inferior clinical outcomes observed in luminal T2 breast cancer patients. Trial of registration ClinicalTrials.gov; NCT03886389. Retrospectively registered March 22, 2019.
Collapse
Affiliation(s)
- Tone Hoel Lende
- Department of Breast & Endocrine Surgery, Stavanger University Hospital, Helse Stavanger HF, P.O. Box 8100, N-4068, Stavanger, Norway. .,Centre for Cancer Biomarkers CCBIO, Department of Clinical Medicine, Faculty of Medicine and Dentistry, University of Bergen, Jonas Lies vei 87, N-5012, Bergen, Norway.
| | - Marie Austdal
- Department of Research, Stavanger University Hospital, Helse Stavanger HF, P.O. Box 8100, N-4068, Stavanger, Norway.,Department of Pathology, Stavanger University Hospital, Helse Stavanger HF, P.O. Box 8100, N-4068, Stavanger, Norway
| | - Tone Frost Bathen
- Department of Circulation and Medical Imaging, Norwegian University of Science and Technology, Trondheim, Norway
| | - Anne Elin Varhaugvik
- Department of Pathology, Stavanger University Hospital, Helse Stavanger HF, P.O. Box 8100, N-4068, Stavanger, Norway.,Department of Pathology, Helse Møre og Romsdal, Ålesund, Norway
| | - Ivar Skaland
- Department of Pathology, Stavanger University Hospital, Helse Stavanger HF, P.O. Box 8100, N-4068, Stavanger, Norway
| | - Einar Gudlaugsson
- Department of Pathology, Stavanger University Hospital, Helse Stavanger HF, P.O. Box 8100, N-4068, Stavanger, Norway
| | - Nina G Egeland
- Department of Pathology, Stavanger University Hospital, Helse Stavanger HF, P.O. Box 8100, N-4068, Stavanger, Norway.,Department of Chemistry, Bioscience and Environmental Technology, University of Stavanger, P.O. Box 8600 Forus, N-4036, Stavanger, Norway
| | - Siri Lunde
- Department of Breast & Endocrine Surgery, Stavanger University Hospital, Helse Stavanger HF, P.O. Box 8100, N-4068, Stavanger, Norway
| | - Lars A Akslen
- Centre for Cancer Biomarkers CCBIO, Department of Clinical Medicine, Faculty of Medicine and Dentistry, University of Bergen, Jonas Lies vei 87, N-5012, Bergen, Norway
| | - Kristin Jonsdottir
- Department of Research, Stavanger University Hospital, Helse Stavanger HF, P.O. Box 8100, N-4068, Stavanger, Norway
| | - Emiel A M Janssen
- Department of Pathology, Stavanger University Hospital, Helse Stavanger HF, P.O. Box 8100, N-4068, Stavanger, Norway.,Department of Chemistry, Bioscience and Environmental Technology, University of Stavanger, P.O. Box 8600 Forus, N-4036, Stavanger, Norway
| | - Håvard Søiland
- Department of Breast & Endocrine Surgery, Stavanger University Hospital, Helse Stavanger HF, P.O. Box 8100, N-4068, Stavanger, Norway.,Department of Clinical Science, University of Bergen, Jonas Lies vei 87, N-5012, Bergen, Norway
| | - Jan P A Baak
- Department of Pathology, Stavanger University Hospital, Helse Stavanger HF, P.O. Box 8100, N-4068, Stavanger, Norway.,Dr. Med. Jan Baak AS, Risavegen 66, N-4056, Tananger, Norway
| |
Collapse
|
15
|
Debik J, Euceda LR, Lundgren S, Gythfeldt HVDL, Garred Ø, Borgen E, Engebraaten O, Bathen TF, Giskeødegård GF. Assessing Treatment Response and Prognosis by Serum and Tissue Metabolomics in Breast Cancer Patients. J Proteome Res 2019; 18:3649-3660. [DOI: 10.1021/acs.jproteome.9b00316] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
| | | | - Steinar Lundgren
- Department of Oncology, St. Olav’s University Hospital, 7006 Trondheim, Norway
| | | | - Øystein Garred
- Department of Tumor Biology, Oslo University Hospital, 0424 Oslo, Norway
| | - Elin Borgen
- Department of Tumor Biology, Oslo University Hospital, 0424 Oslo, Norway
| | - Olav Engebraaten
- Department of Oncology, Oslo University Hospital, 0424 Oslo, Norway
- Department of Tumor Biology, Oslo University Hospital, 0424 Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, 0318 Oslo, Norway
| | | | | |
Collapse
|
16
|
The effect of sampling procedures and day-to-day variations in metabolomics studies of biofluids. Anal Chim Acta 2019; 1081:93-102. [PMID: 31446969 DOI: 10.1016/j.aca.2019.07.026] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 07/11/2019] [Accepted: 07/13/2019] [Indexed: 12/26/2022]
Abstract
Metabolomics analysis of biofluids is a feasible tool for disease characterization and monitoring due to its minimally invasive nature. To reduce unwanted variation in biobanks and clinical studies, it is important to determine the effect of external factors on metabolic profiles of biofluids. In this study we examined the effect of sample collection and sample processing procedures on NMR measured serum lipoproteins and small-molecule metabolites in serum and urine, using a cohort of men diagnosed with either prostate cancer or benign prostatic hyperplasia. We determined day-to-day reliability of metabolites by systematic sample collection at two different days, in both fasting and non-fasting conditions. Study participants received prostate massage the first day to assess the differences between urine with and without prostate secretions. Further, metabolic differences between first-void and mid-stream urine samples, and the effect of centrifugation of urine samples before storage were assessed. Our results show that day-to-day reliability is highly variable between metabolites in both serum and urine, while lipoprotein subfractions possess high reliability. Further, fasting status clearly influenced the metabolite concentrations, demonstrating the importance of keeping this condition constant within a study cohort. Day-to-day reliabilities were however comparable in fasting and non-fasting samples. Urine sampling procedures such as sampling of first-void or mid-stream urine, and centrifugation or not before sample storage, were shown to only have minimal effect on the overall metabolic profile, and is thus unlikely to constitute a confounder in clinical studies utilizing NMR derived metabolomics.
Collapse
|
17
|
Vignoli A, Ghini V, Meoni G, Licari C, Takis PG, Tenori L, Turano P, Luchinat C. High-Throughput Metabolomics by 1D NMR. Angew Chem Int Ed Engl 2019; 58:968-994. [PMID: 29999221 PMCID: PMC6391965 DOI: 10.1002/anie.201804736] [Citation(s) in RCA: 204] [Impact Index Per Article: 40.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Indexed: 12/12/2022]
Abstract
Metabolomics deals with the whole ensemble of metabolites (the metabolome). As one of the -omic sciences, it relates to biology, physiology, pathology and medicine; but metabolites are chemical entities, small organic molecules or inorganic ions. Therefore, their proper identification and quantitation in complex biological matrices requires a solid chemical ground. With respect to for example, DNA, metabolites are much more prone to oxidation or enzymatic degradation: we can reconstruct large parts of a mammoth's genome from a small specimen, but we are unable to do the same with its metabolome, which was probably largely degraded a few hours after the animal's death. Thus, we need standard operating procedures, good chemical skills in sample preparation for storage and subsequent analysis, accurate analytical procedures, a broad knowledge of chemometrics and advanced statistical tools, and a good knowledge of at least one of the two metabolomic techniques, MS or NMR. All these skills are traditionally cultivated by chemists. Here we focus on metabolomics from the chemical standpoint and restrict ourselves to NMR. From the analytical point of view, NMR has pros and cons but does provide a peculiar holistic perspective that may speak for its future adoption as a population-wide health screening technique.
Collapse
Affiliation(s)
- Alessia Vignoli
- C.I.R.M.M.P.Via Luigi Sacconi 650019 Sesto FiorentinoFlorenceItaly
| | - Veronica Ghini
- CERMUniversity of FlorenceVia Luigi Sacconi 650019 Sesto FiorentinoFlorenceItaly
| | - Gaia Meoni
- CERMUniversity of FlorenceVia Luigi Sacconi 650019 Sesto FiorentinoFlorenceItaly
| | - Cristina Licari
- CERMUniversity of FlorenceVia Luigi Sacconi 650019 Sesto FiorentinoFlorenceItaly
| | | | - Leonardo Tenori
- Department of Experimental and Clinical MedicineUniversity of FlorenceLargo Brambilla 3FlorenceItaly
| | - Paola Turano
- CERMUniversity of FlorenceVia Luigi Sacconi 650019 Sesto FiorentinoFlorenceItaly
- Department of Chemistry “Ugo Schiff”University of FlorenceVia della Lastruccia 3–1350019 Sesto FiorentinoFlorenceItaly
| | - Claudio Luchinat
- CERMUniversity of FlorenceVia Luigi Sacconi 650019 Sesto FiorentinoFlorenceItaly
- Department of Chemistry “Ugo Schiff”University of FlorenceVia della Lastruccia 3–1350019 Sesto FiorentinoFlorenceItaly
| |
Collapse
|
18
|
Vignoli A, Ghini V, Meoni G, Licari C, Takis PG, Tenori L, Turano P, Luchinat C. Hochdurchsatz‐Metabolomik mit 1D‐NMR. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201804736] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Alessia Vignoli
- C.I.R.M.M.P. Via Luigi Sacconi 6 50019 Sesto Fiorentino Florence Italien
| | - Veronica Ghini
- CERMUniversity of Florence Via Luigi Sacconi 6 50019 Sesto Fiorentino Florence Italien
| | - Gaia Meoni
- CERMUniversity of Florence Via Luigi Sacconi 6 50019 Sesto Fiorentino Florence Italien
| | - Cristina Licari
- CERMUniversity of Florence Via Luigi Sacconi 6 50019 Sesto Fiorentino Florence Italien
| | | | - Leonardo Tenori
- Department of Experimental and Clinical MedicineUniversity of Florence Largo Brambilla 3 Florence Italien
| | - Paola Turano
- CERMUniversity of Florence Via Luigi Sacconi 6 50019 Sesto Fiorentino Florence Italien
- Department of Chemistry “Ugo Schiff”University of Florence Via della Lastruccia 3–13 50019 Sesto Fiorentino Florence Italien
| | - Claudio Luchinat
- CERMUniversity of Florence Via Luigi Sacconi 6 50019 Sesto Fiorentino Florence Italien
- Department of Chemistry “Ugo Schiff”University of Florence Via della Lastruccia 3–13 50019 Sesto Fiorentino Florence Italien
| |
Collapse
|
19
|
Metabolite and lipoprotein responses and prediction of weight gain during breast cancer treatment. Br J Cancer 2018; 119:1144-1154. [PMID: 30401977 PMCID: PMC6220113 DOI: 10.1038/s41416-018-0211-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2018] [Revised: 07/06/2018] [Accepted: 07/10/2018] [Indexed: 12/18/2022] Open
Abstract
Background Breast cancer treatment has metabolic side effects, potentially affecting risk of cardiovascular disease (CVD) and recurrence. We aimed to compare alterations in serum metabolites and lipoproteins during treatment between recipients and non-recipients of chemotherapy, and describe metabolite profiles associated with treatment-related weight gain. Methods This pilot study includes 60 stage I/II breast cancer patients who underwent surgery and were treated according to national guidelines. Serum sampled pre-surgery and after 6 and 12 months was analysed by MR spectroscopy and mass spectrometry. In all, 170 metabolites and 105 lipoprotein subfractions were quantified. Results The metabolite and lipoprotein profiles of chemotherapy recipients and non-recipients changed significantly 6 months after surgery (p < 0.001). Kynurenine, the lipid signal at 1.55–1.60 ppm, ADMA, 2 phosphatidylcholines (PC aa C38:3, PC ae C42:1), alpha-aminoadipic acid, hexoses and sphingolipids were increased in chemotherapy recipients after 6 months. VLDL and small dense LDL increased after 6 months, while HDL decreased, with triglyceride enrichment in HDL and LDL. At baseline, weight gainers had less acylcarnitines, phosphatidylcholines, lyso-phosphatidylcholines and sphingolipids, and showed an inflammatory lipid profile. Conclusion Chemotherapy recipients exhibit metabolic changes associated with inflammation, altered immune response and increased risk of CVD. Altered lipid metabolism may predispose for treatment-related weight gain.
Collapse
|
20
|
Rai V, Bose S, Saha S, Kumar V, Chakraborty C. Delineating metabolic dysfunction in cellular metabolism of oral submucous fibrosis using 1H nuclear magnetic resonance spectroscopy. Arch Oral Biol 2018; 97:102-108. [PMID: 30384150 DOI: 10.1016/j.archoralbio.2018.10.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 10/09/2018] [Accepted: 10/15/2018] [Indexed: 01/02/2023]
Abstract
OBJECTIVE To delineate the metabolism involved in oral submucous fibrosis progression towards carcinogenesis by 1H nuclear magnetic resonance spectroscopy. METHODS The proposed study was designed using 1H-NMR by comparing the metabolites in the serum sample of oral submucous fibrosis (n = 20) compared to the normal group (n = 20) using 1H nuclear magnetic resonance spectroscopy. Various statistical analysis like multivariate statistical analysis, Principle component analysis, Partial least squares Discriminant Analysis, Hierarchical cluster analysis was applied to analyze potential serum metabolites. RESULTS The results generated from the principle component analysis, partial least squares discriminant analysis and hierarchical cluster analysis are sufficient to distinguish between oral submucous fibrosis group and normal group. A total of 15 significant metabolites associated with main pathways were identified, which correlated with the progression of cancer. Up-regulation of glucose metabolism-related metabolites indicated the high energy demand due to enhanced cell division rate in the oral submucous fibrosis group. A significant increase in lipid metabolism-related metabolites revealed the reprogramming of the fatty acids metabolic pathway to fulfilling the need for cell membrane formation in cancer cells. On the other hand, metabolites related to choline phosphocholine, the metabolic pathway was also altered. CONCLUSION Our findings could identify the differentiating metabolites in the oral submucous fibrosis group. Significant alteration in metabolites in the oral submucous fibrosis group exhibited deregulation in metabolic events. The findings reported in the study can be beneficial to further explain the molecular aspects that lead to the progression of oral submucous fibrosis towards carcinogenesis.
Collapse
Affiliation(s)
- Vertika Rai
- School of Medical Science and Technology, IIT Kharagpur, India.
| | - Surajit Bose
- Awadh Dental College and Hospital, Jamshedpur, India
| | - Satadal Saha
- School of Medical Science and Technology, IIT Kharagpur, India
| | - Virendra Kumar
- Department of NMR, All India Institute of Medical Sciences, New Delhi, India
| | | |
Collapse
|