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Gulati K, Manukonda R, Kairamkonda M, Kaliki S, Poluri KM. Serum Metabolomics of Retinoblastoma: Assessing the Differential Serum Metabolic Signatures of Unilateral and Bilateral Patients. ACS OMEGA 2023; 8:48233-48250. [PMID: 38144138 PMCID: PMC10733957 DOI: 10.1021/acsomega.3c07424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 11/17/2023] [Accepted: 11/27/2023] [Indexed: 12/26/2023]
Abstract
Retinoblastoma (Rb) is the most common pediatric eye cancer. To identify the biomarkers for early diagnosis and monitoring the progression of Rb in patients, mapping of the alterations in their metabolic profiles is essential. The present study aims at exploring the metabolic disparity in serum from Rb patients and controls using NMR-based metabolomics. A total of 72 metabolites, including carbohydrates, amino acids, and organic acids, were quantified in serum samples from 24 Rb patients and 26 controls. Distinct clusters of Rb patients and controls were obtained using the partial least-squares discriminant analysis (PLS-DA) model. Further, univariate and multivariate analyses of unilateral and bilateral Rb patients with respect to their age-matched controls depicted their distinct metabolic fingerprints. Metabolites including 2-phosphoglycerate, 4-aminobutyrate, proline, O-phosphocholine, O-phosphoethanolamine, and Sn-glycero-3-phosphocholine (Sn-GPC) showed significant perturbation in both unilateral and bilateral Rb patients. However, metabolic differences among the bilateral Rb cases were more pronounced than those in unilateral Rb cases with respect to controls. In addition to major discriminatory metabolites for Rb, unilateral and bilateral Rb cases showed specific metabolic changes, which might be the result of their differential genetic/somatic mutational backgrounds. This further suggests that the aberrant metabolic perturbation in bilateral patients signifies the severity of the disease in Rb patients. The present study demonstrated that identified serum metabolites have potential to serve as a noninvasive method for detection of Rb, discriminate bilateral from unilateral Rb patients, and aid in better understanding of the RB tumor biology.
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Affiliation(s)
- Khushboo Gulati
- The
Operation Eyesight Universal Institute for Eye Cancer, LV Prasad Eye Institute, Hyderabad-500034, Telangana, India
- Brien
Holden Eye Research Center, L. V. Prasad
Eye Institute, Hyderabad-500034, Telangana, India
| | - Radhika Manukonda
- The
Operation Eyesight Universal Institute for Eye Cancer, LV Prasad Eye Institute, Hyderabad-500034, Telangana, India
- Brien
Holden Eye Research Center, L. V. Prasad
Eye Institute, Hyderabad-500034, Telangana, India
| | - Manikyaprabhu Kairamkonda
- Department
of Biosciences and Bioengineering, Indian
Institute of Technology Roorkee, Roorkee-247667, Uttarakhand, India
| | - Swathi Kaliki
- The
Operation Eyesight Universal Institute for Eye Cancer, LV Prasad Eye Institute, Hyderabad-500034, Telangana, India
| | - Krishna Mohan Poluri
- Department
of Biosciences and Bioengineering, Indian
Institute of Technology Roorkee, Roorkee-247667, Uttarakhand, India
- Centre
for Nanotechnology, Indian Institute of
Technology Roorkee, Roorkee-247667, Uttarakhand, India
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Kundra P, Rachmühl C, Lacroix C, Geirnaert A. Role of Dietary Micronutrients on Gut Microbial Dysbiosis and Modulation in Inflammatory Bowel Disease. Mol Nutr Food Res 2021. [DOI: 10.1002/mnfr.201901271] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Palni Kundra
- Laboratory of Food Biotechnology Institute of Food Nutrition and Health Schmelzbergstrasse 7 Zürich 8092 Switzerland
| | - Carole Rachmühl
- Laboratory of Food Biotechnology Institute of Food Nutrition and Health Schmelzbergstrasse 7 Zürich 8092 Switzerland
| | - Christophe Lacroix
- Laboratory of Food Biotechnology Institute of Food Nutrition and Health Schmelzbergstrasse 7 Zürich 8092 Switzerland
| | - Annelies Geirnaert
- Laboratory of Food Biotechnology Institute of Food Nutrition and Health Schmelzbergstrasse 7 Zürich 8092 Switzerland
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Marzec J, Ross-Adams H, Pirrò S, Wang J, Zhu Y, Mao X, Gadaleta E, Ahmad AS, North BV, Kammerer-Jacquet SF, Stankiewicz E, Kudahetti SC, Beltran L, Ren G, Berney DM, Lu YJ, Chelala C. The Transcriptomic Landscape of Prostate Cancer Development and Progression: An Integrative Analysis. Cancers (Basel) 2021; 13:345. [PMID: 33477882 PMCID: PMC7838904 DOI: 10.3390/cancers13020345] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 01/07/2021] [Accepted: 01/12/2021] [Indexed: 11/16/2022] Open
Abstract
Next-generation sequencing of primary tumors is now standard for transcriptomic studies, but microarray-based data still constitute the majority of available information on other clinically valuable samples, including archive material. Using prostate cancer (PC) as a model, we developed a robust analytical framework to integrate data across different technical platforms and disease subtypes to connect distinct disease stages and reveal potentially relevant genes not identifiable from single studies alone. We reconstructed the molecular profile of PC to yield the first comprehensive insight into its development, by tracking changes in mRNA levels from normal prostate to high-grade prostatic intraepithelial neoplasia, and metastatic disease. A total of nine previously unreported stage-specific candidate genes with prognostic significance were also found. Here, we integrate gene expression data from disparate sample types, disease stages and technical platforms into one coherent whole, to give a global view of the expression changes associated with the development and progression of PC from normal tissue through to metastatic disease. Summary and individual data are available online at the Prostate Integrative Expression Database (PIXdb), a user-friendly interface designed for clinicians and laboratory researchers to facilitate translational research.
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Affiliation(s)
- Jacek Marzec
- Bioinformatics Unit, Centre for Cancer Biomarkers and Biotherapeutics, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, UK; (J.M.); (S.P.); (J.W.); (E.G.)
| | - Helen Ross-Adams
- Bioinformatics Unit, Centre for Cancer Biomarkers and Biotherapeutics, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, UK; (J.M.); (S.P.); (J.W.); (E.G.)
| | - Stefano Pirrò
- Bioinformatics Unit, Centre for Cancer Biomarkers and Biotherapeutics, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, UK; (J.M.); (S.P.); (J.W.); (E.G.)
| | - Jun Wang
- Bioinformatics Unit, Centre for Cancer Biomarkers and Biotherapeutics, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, UK; (J.M.); (S.P.); (J.W.); (E.G.)
| | - Yanan Zhu
- Centre for Cancer Biomarkers and Biotherapeutics, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, UK; (Y.Z.); (X.M.); (S.-F.K.-J.); (E.S.); (S.C.K.); (D.M.B.); (Y.-J.L.)
| | - Xueying Mao
- Centre for Cancer Biomarkers and Biotherapeutics, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, UK; (Y.Z.); (X.M.); (S.-F.K.-J.); (E.S.); (S.C.K.); (D.M.B.); (Y.-J.L.)
| | - Emanuela Gadaleta
- Bioinformatics Unit, Centre for Cancer Biomarkers and Biotherapeutics, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, UK; (J.M.); (S.P.); (J.W.); (E.G.)
| | - Amar S. Ahmad
- Centre for Cancer Prevention, Wolfson Institute of Preventive Medicine, Barts and the London School of Medicine, Queen Mary University of London, London EC1M 6BQ, UK; (A.S.A.); (B.V.N.)
| | - Bernard V. North
- Centre for Cancer Prevention, Wolfson Institute of Preventive Medicine, Barts and the London School of Medicine, Queen Mary University of London, London EC1M 6BQ, UK; (A.S.A.); (B.V.N.)
| | - Solène-Florence Kammerer-Jacquet
- Centre for Cancer Biomarkers and Biotherapeutics, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, UK; (Y.Z.); (X.M.); (S.-F.K.-J.); (E.S.); (S.C.K.); (D.M.B.); (Y.-J.L.)
| | - Elzbieta Stankiewicz
- Centre for Cancer Biomarkers and Biotherapeutics, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, UK; (Y.Z.); (X.M.); (S.-F.K.-J.); (E.S.); (S.C.K.); (D.M.B.); (Y.-J.L.)
| | - Sakunthala C. Kudahetti
- Centre for Cancer Biomarkers and Biotherapeutics, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, UK; (Y.Z.); (X.M.); (S.-F.K.-J.); (E.S.); (S.C.K.); (D.M.B.); (Y.-J.L.)
| | - Luis Beltran
- Department of Pathology, Barts Health NHS, London E1 F1R, UK;
| | - Guoping Ren
- Department of Pathology, The First Affiliated Hospital, Zhejiang University Medical College, Hangzhou 310058, China;
| | - Daniel M. Berney
- Centre for Cancer Biomarkers and Biotherapeutics, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, UK; (Y.Z.); (X.M.); (S.-F.K.-J.); (E.S.); (S.C.K.); (D.M.B.); (Y.-J.L.)
- Department of Pathology, Barts Health NHS, London E1 F1R, UK;
| | - Yong-Jie Lu
- Centre for Cancer Biomarkers and Biotherapeutics, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, UK; (Y.Z.); (X.M.); (S.-F.K.-J.); (E.S.); (S.C.K.); (D.M.B.); (Y.-J.L.)
| | - Claude Chelala
- Bioinformatics Unit, Centre for Cancer Biomarkers and Biotherapeutics, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, UK; (J.M.); (S.P.); (J.W.); (E.G.)
- Centre for Computational Biology, Life Sciences Initiative, Queen Mary University London, London EC1M 6BQ, UK
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DeDecker L, Coppedge B, Avelar-Barragan J, Karnes W, Whiteson K. Microbiome distinctions between the CRC carcinogenic pathways. Gut Microbes 2021; 13:1854641. [PMID: 33446008 PMCID: PMC8288036 DOI: 10.1080/19490976.2020.1854641] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Revised: 10/01/2020] [Accepted: 11/10/2020] [Indexed: 02/06/2023] Open
Abstract
Colorectal cancer (CRC) is the third most commonly diagnosed cancer, the third leading cause of cancer-related deaths, and has been on the rise among young adults in the United States. Research has established that the colonic microbiome is different in patients with CRC compared to healthy controls, but few studies have investigated if and how the microbiome may relate to CRC progression through the serrated pathway versus the adenoma-carcinoma sequence.Our view is that progress in CRC microbiome research requires consideration of how the microbiome may contribute to CRC carcinogenesis through the distinct pathways that lead to CRC, which could enable the creation of novel and tailored prevention, screening, and therapeutic interventions. We first highlight the limitations in existing CRC microbiome research and offer corresponding solutions for investigating the microbiome's role in the adenoma-carcinoma sequence and serrated pathway. We then summarize the findings in the select human studies that included data points related to the two major carcinogenic pathways. These studies investigate the microbiome in CRC carcinogenesis and 1) utilize mucosal samples and 2) compare polyps or tumors by histopathologic type, molecular/genetic type, or location in the colon.Key findings from these studies include: 1) Fusobacterium is associated with right-sided, more advanced, and serrated lesions; 2) the colons of people with CRC have bacteria typically associated with normal oral flora; and 3) colons from people with CRC have more biofilms, and these biofilms are predominantly located in the proximal colon (single study).
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Affiliation(s)
- Lauren DeDecker
- School of Medicine, University of California, Irvine, California, USA
| | - Bretton Coppedge
- School of Biological Sciences, University of California, Irvine, California, USA
| | | | - William Karnes
- School of Medicine, University of California, Irvine, California, USA
| | - Katrine Whiteson
- School of Biological Sciences, University of California, Irvine, California, USA
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Zhang K, Wrzesinski K, Stephen JF, Larsen PM, Zhang X, Roepstorff P. Comparative proteome analysis of three mouse lung adenocarcinoma CMT cell lines with different metastatic potential by two-dimensional gel electrophoresis and mass spectrometry. Proteomics 2008; 8:4932-45. [DOI: 10.1002/pmic.200800299] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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Deng T, Li JS, Huan SY, Yang HF, Wang H, Shen GL, Yu RQ. Quartz crystal microbalance bioaffinity sensor for biotin based on mixed self-assembled monolayers and metastable molecular complex receptor. Biosens Bioelectron 2006; 21:1545-52. [PMID: 16085409 DOI: 10.1016/j.bios.2005.07.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2005] [Revised: 06/26/2005] [Accepted: 07/06/2005] [Indexed: 11/25/2022]
Abstract
A quartz crystal microbalance (QCM) sensor was proposed for the detection of small molecule biotin based on the mixed self-assembled monolayer (SAM) of thiols on gold substrate and the bioaffinity difference between an analyte (biotin) and an analogue compound (HABA) in binding avidin. Avidin formed a metastable complex with 2-[(4-hydroxyphenyl)azo]benzoic acid (HABA) immobilized on the crystal surface. When the sensor contacts a sample solution containing biotin, the avidin was released from the sensor surface to form a more stable complex with biotin in solution. The frequency change recorded is proportional to the desorbed mass of avidin, and there is a clear mathematic relationship between the frequency change and the biotin concentration. The use of mixed SAMs allows the stable attachment of bioreceptor molecules on the QCM, and enhances the amount of the immobilized molecules on the QCM, as a longer "space arm" in the mixed SAMs makes this monolayer membrane more accessible to capture the immobilized molecules. The proposed bioaffinity sensor has nice response to biotin in the range of 0.017-1.67 microg/mL. The sensor could be regenerated under very mild conditions simply by reimmersion of the sensor into a biotin solution to desorb the surplus avidin.
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Affiliation(s)
- Ting Deng
- State Key Laboratory of Chem/Biosensing and Chemometrics, Chemistry and Chemical Engineering College, Hunan University, Changsha, China
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Solórzano-Vargas RS, Pacheco-Alvarez D, León-Del-Río A. Holocarboxylase synthetase is an obligate participant in biotin-mediated regulation of its own expression and of biotin-dependent carboxylases mRNA levels in human cells. Proc Natl Acad Sci U S A 2002; 99:5325-30. [PMID: 11959985 PMCID: PMC122768 DOI: 10.1073/pnas.082097699] [Citation(s) in RCA: 84] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Holocarboxylase synthetase (HCS) catalyzes the covalent attachment of biotin to five biotin-dependent carboxylases in human cells. Multiple carboxylase deficiency (MCD) is a life-threatening disease characterized by the lack of carboxylase activities because of deficiency of HCS activity. Here, we report the obligatory participation of HCS in the biotin-dependent stimulation of the level of HCS mRNA and those of acetyl-CoA carboxylase and the alpha subunit of propionyl-CoA carboxylase in human cells. Fibroblasts from patients with MCD are unable to increase HCS mRNA in response to biotin unless the vitamin concentration is raised 100-fold, in keeping with mutations that cause a reduced affinity for biotin by the mutant enzyme. The outcome is deficient synthesis of biotinyl-5'-AMP, the active form of the vitamin in the biotinylation reaction. HCS and carboxylase mRNA levels in normal and MCD fibroblasts and HepG2 cells can be restored by the addition of the cGMP analogue, 8-Br-cGMP, and can be abolished by the addition of inhibitors of the soluble form of guanylate cyclase. We propose a regulatory role for biotin in the control of HCS and carboxylase mRNA levels through a signaling cascade that requires HCS, guanylate cyclase, and cGMP-dependent protein kinase.
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Affiliation(s)
- R Sergio Solórzano-Vargas
- Departamento de Biologia Molecular y Biotecnologia, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, México D.F. 04510, México
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Feltus A, Hentz NG, Daunert S. Post-capillary reaction detection in capillary electrophoresis based on the streptavidin-biotin interaction. Optimization and application to single cell analysis. J Chromatogr A 2001; 918:381-92. [PMID: 11407585 DOI: 10.1016/s0021-9673(01)00742-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
A class-selective post-capillary reaction detection method for capillary electrophoresis is described in which a streptavidin-fluorescein isothiocyanate (streptavidin-FITC) conjugate is used to detect biotin moieties. The selective binding of biotin moieties to the streptavidin-FITC conjugate causes an enhancement of fluorescence proportional to the concentration of biotin present. After capillary electrophoresis the separated analytes react with streptavidin-FITC in a coaxial reactor and are then detected either by a benchtop spectrofluorometer (2.5 microM detection limit) or by an epi-fluorescence microscope (1 x 10(-7) M detection limit). The method is used to examine biotinylated species in a crude mammalian cell lysate which was found to contain 83+/-3 fmol in 3600 cell volumes. In addition, it is used to examine the uptake of biotin by individual sea urchin oocytes. The results indicate that, in the oocytes, biocytin is the prevalent form of biotin and its concentration varies widely between cells (mean=2+/-2 microM).
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Affiliation(s)
- A Feltus
- Department of Pharmaceutical Sciences, University of Kentucky, Lexington 40506-0055, USA
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Feltus A, Grosvenor AL, Conover RC, Anderson KW, Daunert S. Detection of biotin in individual sea urchin oocytes using a bioluminescence binding assay. Anal Chem 2001; 73:1403-7. [PMID: 11321287 DOI: 10.1021/ac001258a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The ability to detect biomolecules in single cells is important in order to fully understand the processes by which many biochemical events occur. To that end, we have developed a bioluminescence binding assay capable of measuring the intracellular biotin content of individual cells. The assay depends on competition between an aequorin-biotin conjugate (AEQ-biotin) and free biotin within the oocytes for binding sites on the protein avidin. The assay is performed by microinjecting each component into the oocytes and following the resulting bioluminescence within the oocyte upon triggering of aequorin. Results obtained using sea urchin oocytes show that the assay performed within the cells behaves in a manner consistent with assay theory. Using the assay, the individual biotin content of the oocytes is an average of approximately 20 amol. To our knowledge, this is the first reported multicomponent binding assay to be performed inside an intact single cell.
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Affiliation(s)
- A Feltus
- Department of Chemistry, University of Kentucky, Lexington 40506, USA
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Livaniou E, Costopoulou D, Vassiliadou I, Leondiadis L, Nyalala JO, Ithakissios DS, Evangelatos GP. Analytical techniques for determining biotin. J Chromatogr A 2000; 881:331-43. [PMID: 10905717 DOI: 10.1016/s0021-9673(00)00118-7] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
Abstract
Biotin is a vitamin of the B-complex, which plays an important biochemical role in every living cell. In the recent years, the interest in this vitamin has been rekindled, mainly due to its association with serious human disorders, such as the inherited syndrome multiple carboxylase deficiency, which can be successfully treated with biotin administration. Diagnosis of biotin deficiency as well as monitoring of biotin levels in biological fluids of patients receiving biotin treatment is crucial. Equally important is the determination of biotin levels in pharmaceutical preparations as well as in food and food supplement products, which constitute the main source of biotin in humans. Several analytical methods for measuring biotin in various samples, e.g. human fluids, pharmaceutical formulations, food material etc., have been reported in the literature. In this review, the most representative of these methods are presented, and their characteristics are evaluated.
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Affiliation(s)
- E Livaniou
- Institute of Radioisotopes/Radiodiagnostic Products, National Center for Scientific Research Demokritos, Athens, Greece
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