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Al-Daffaie FM, Al-Mudhafar SF, Alhomsi A, Tarazi H, Almehdi AM, El-Huneidi W, Abu-Gharbieh E, Bustanji Y, Alqudah MAY, Abuhelwa AY, Guella A, Alzoubi KH, Semreen MH. Metabolomics and Proteomics in Prostate Cancer Research: Overview, Analytical Techniques, Data Analysis, and Recent Clinical Applications. Int J Mol Sci 2024; 25:5071. [PMID: 38791108 PMCID: PMC11120916 DOI: 10.3390/ijms25105071] [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: 02/12/2024] [Revised: 04/26/2024] [Accepted: 04/26/2024] [Indexed: 05/26/2024] Open
Abstract
Prostate cancer (PCa) is a significant global contributor to mortality, predominantly affecting males aged 65 and above. The field of omics has recently gained traction due to its capacity to provide profound insights into the biochemical mechanisms underlying conditions like prostate cancer. This involves the identification and quantification of low-molecular-weight metabolites and proteins acting as crucial biochemical signals for early detection, therapy assessment, and target identification. A spectrum of analytical methods is employed to discern and measure these molecules, revealing their altered biological pathways within diseased contexts. Metabolomics and proteomics generate refined data subjected to detailed statistical analysis through sophisticated software, yielding substantive insights. This review aims to underscore the major contributions of multi-omics to PCa research, covering its core principles, its role in tumor biology characterization, biomarker discovery, prognostic studies, various analytical technologies such as mass spectrometry and Nuclear Magnetic Resonance, data processing, and recent clinical applications made possible by an integrative "omics" approach. This approach seeks to address the challenges associated with current PCa treatments. Hence, our research endeavors to demonstrate the valuable applications of these potent tools in investigations, offering significant potential for understanding the complex biochemical environment of prostate cancer and advancing tailored therapeutic approaches for further development.
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Affiliation(s)
- Fatima M. Al-Daffaie
- Department of Medicinal Chemistry, College of Pharmacy, University of Sharjah, Sharjah 27272, United Arab Emirates; (F.M.A.-D.); (S.F.A.-M.); (A.A.); (H.T.); (A.M.A.)
- Research Institute of Medical and Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates; (W.E.-H.); (E.A.-G.); (A.Y.A.); (K.H.A.)
| | - Sara F. Al-Mudhafar
- Department of Medicinal Chemistry, College of Pharmacy, University of Sharjah, Sharjah 27272, United Arab Emirates; (F.M.A.-D.); (S.F.A.-M.); (A.A.); (H.T.); (A.M.A.)
| | - Aya Alhomsi
- Department of Medicinal Chemistry, College of Pharmacy, University of Sharjah, Sharjah 27272, United Arab Emirates; (F.M.A.-D.); (S.F.A.-M.); (A.A.); (H.T.); (A.M.A.)
| | - Hamadeh Tarazi
- Department of Medicinal Chemistry, College of Pharmacy, University of Sharjah, Sharjah 27272, United Arab Emirates; (F.M.A.-D.); (S.F.A.-M.); (A.A.); (H.T.); (A.M.A.)
- Research Institute of Medical and Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates; (W.E.-H.); (E.A.-G.); (A.Y.A.); (K.H.A.)
| | - Ahmed M. Almehdi
- Department of Medicinal Chemistry, College of Pharmacy, University of Sharjah, Sharjah 27272, United Arab Emirates; (F.M.A.-D.); (S.F.A.-M.); (A.A.); (H.T.); (A.M.A.)
- Research Institute of Medical and Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates; (W.E.-H.); (E.A.-G.); (A.Y.A.); (K.H.A.)
| | - Waseem El-Huneidi
- Research Institute of Medical and Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates; (W.E.-H.); (E.A.-G.); (A.Y.A.); (K.H.A.)
- Department of Basic Medical Sciences, College of Medicine, University of Sharjah, Sharjah 27272, United Arab Emirates;
| | - Eman Abu-Gharbieh
- Research Institute of Medical and Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates; (W.E.-H.); (E.A.-G.); (A.Y.A.); (K.H.A.)
- Department of Clinical Sciences, College of Medicine, University of Sharjah, Sharjah 27272, United Arab Emirates
- School of Pharmacy, The University of Jordan, Amman 11942, Jordan
| | - Yasser Bustanji
- Department of Basic Medical Sciences, College of Medicine, University of Sharjah, Sharjah 27272, United Arab Emirates;
- School of Pharmacy, The University of Jordan, Amman 11942, Jordan
| | - Mohammad A. Y. Alqudah
- Department of Pharmacy Practice and Pharmacotherapeutics, College of Pharmacy, University of Sharjah, Sharjah 27272, United Arab Emirates;
- Department of Clinical Pharmacy, Faculty of Pharmacy, Jordan University of Science and Technology, Irbid 22110, Jordan
| | - Ahmad Y. Abuhelwa
- Research Institute of Medical and Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates; (W.E.-H.); (E.A.-G.); (A.Y.A.); (K.H.A.)
- Department of Pharmacy Practice and Pharmacotherapeutics, College of Pharmacy, University of Sharjah, Sharjah 27272, United Arab Emirates;
| | - Adnane Guella
- Nephrology Department, University Hospital Sharjah, Sharjah 27272, United Arab Emirates;
| | - Karem H. Alzoubi
- Research Institute of Medical and Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates; (W.E.-H.); (E.A.-G.); (A.Y.A.); (K.H.A.)
- Department of Pharmacy Practice and Pharmacotherapeutics, College of Pharmacy, University of Sharjah, Sharjah 27272, United Arab Emirates;
| | - Mohammad H. Semreen
- Department of Medicinal Chemistry, College of Pharmacy, University of Sharjah, Sharjah 27272, United Arab Emirates; (F.M.A.-D.); (S.F.A.-M.); (A.A.); (H.T.); (A.M.A.)
- Research Institute of Medical and Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates; (W.E.-H.); (E.A.-G.); (A.Y.A.); (K.H.A.)
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Moussa A, Huygens B, Venditti C, Adrover A, Desmet G. On the contribution of the top and bottom walls in micro-pillar array columns and related high-aspect ratio chromatography systems. J Chromatogr A 2024; 1720:464825. [PMID: 38507870 DOI: 10.1016/j.chroma.2024.464825] [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: 01/31/2024] [Revised: 03/15/2024] [Accepted: 03/16/2024] [Indexed: 03/22/2024]
Abstract
We report on a steady-state based, and hence highly accurate numerical modelling study of the effect of the top and bottom wall in the current generation of micro-pillar array columns. These have a mesoporous retention layer that not only covers the pillar walls but also the bottom wall. Our results show that the performance of these columns can in general not be improved by also covering the top wall with the same layer, despite the increased column symmetry this approach would offer. The reason for this is that the local species retardation caused by a retentive layer is much stronger than the pure flow arresting effect of an uncovered wall. At least, this has a crucial impact in high aspect-ratio systems such as micro-pillar array columns because these require a small inter-pillar distance to promote mass transfer together with a large channel depth to enable a sufficiently high flow rate. On the other hand, a notable improvement could be made if micro-pillar array would be produced without having a retentive layer at the bottom. At Péclet number Pe = 50 and aspect ratio AR = 5 for flow-channels, this gain amounts up to about 4.5 h-units at a zone retention factor k'' = 2 and 1.75 h-units at k'' = 16 (gain scales almost linearly with Pe). To verify these results, we also considered another high aspect-ratio system with a simplified geometry: the open-tubular channel with a flat-rectangular cross-section. This led to very similar observations, thus confirming the findings for the micro-pillar array. The results produced in the present study also allow us to conclude that the classic modelling paradigm adopted in chromatography, which is based on the independency and hence additivity of the hCm- and hCs-contributions, can lead to large modelling errors in chromatographic systems with a high aspect-ratio, even when their geometry is so simple as that of a straight open-tubular channel with constant cross-section. Indeed, when both zones are treated independently, the analysis misses how the vertical diffusion through the retentive layer helps suppressing the vertical gradients in the mobile zone. The diffusion through this layer occurs in a ratio of k''Ds/Dm (Dm being the diffusion coefficient in mobile phase zone and Ds being the diffusion coefficient in stationary phase zone), such that at high retention factors this diffusion contribution even becomes the dominant one.
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Affiliation(s)
- Ali Moussa
- Department of Chemical Engineering, Vrije Universiteit Brussel, Brussels, Belgium
| | - Bram Huygens
- Department of Chemical Engineering, Vrije Universiteit Brussel, Brussels, Belgium
| | - Claudia Venditti
- Dipartimento di Ingegneria Chimica Materiali Ambiente, Sapienza Università di Roma, Italy
| | - Alessandra Adrover
- Dipartimento di Ingegneria Chimica Materiali Ambiente, Sapienza Università di Roma, Italy
| | - Gert Desmet
- Department of Chemical Engineering, Vrije Universiteit Brussel, Brussels, Belgium.
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Protti M, Cirrincione M, Palano S, Poeta E, Babini G, Magnifico MC, Barile SN, Balboni N, Massenzio F, Mahdavijalal M, Giorgi FM, Mandrioli R, Lasorsa FM, Monti B, Mercolini L. Targeted quantitative metabolic profiling of brain-derived cell cultures by semi-automated MEPS and LC-MS/MS. J Pharm Biomed Anal 2023; 236:115757. [PMID: 37801818 DOI: 10.1016/j.jpba.2023.115757] [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: 07/05/2023] [Revised: 09/11/2023] [Accepted: 09/26/2023] [Indexed: 10/08/2023]
Abstract
The accurate characterisation of metabolic profiles is an important prerequisite to determine the rate and the efficiency of the metabolic pathways taking place in the cells. Changes in the balance of metabolites involved in vital processes such as glycolysis, tricarboxylic acid (TCA) cycle, oxidative phosphorylation (OXPHOS), as well as in the biochemical pathways related to amino acids, lipids, nucleotides, and their precursors reflect the physiological condition of the cells and may contribute to the development of various human diseases. The feasible and reliable measurement of a wide array of metabolites and biomarkers possesses great potential to elucidate physiological and pathological mechanisms, aid preclinical drug development and highlight potential therapeutic targets. An effective, straightforward, sensitive, and selective liquid chromatography-tandem mass spectrometry (LC-MS/MS) approach was developed for the simultaneous quali-quantitative analysis of 41 compounds in both cell pellet and cell growth medium obtained from brain-derived cell cultures. Sample pretreatment miniaturisation was achieved thanks to the development and optimisation of an original extraction/purification approach based on digitally programmed microextraction by packed sorbent (eVol®-MEPS). MEPS allows satisfactory and reproducible clean-up and preconcentration of both low-volume homogenate cell pellet lysate and cell growth medium with advantages including, but not limited to, minimal sample handling and method sustainability in terms of sample, solvents, and energy consumption. The MEPS-LC-MS/MS method showed good sensitivity, selectivity, linearity, and precision. As a proof of concept, the developed method was successfully applied to the analysis of both cell pellet and cell growth medium obtained from a line of mouse immortalised oligodendrocyte precursor cells (OPCs; Oli-neu cell line), leading to the unambiguous determination of all the considered target analytes. This method is thus expected to be suitable for targeted, quantitative metabolic profiling in most brain cell models, thus allowing accurate investigations on the biochemical pathways that can be altered in central nervous system (CNS) neuropathologies, including e.g., mitochondrial respiration and glycolysis, or use of specific nutrients for growth and proliferation, or lipid, amino acid and nucleotide metabolism.
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Affiliation(s)
- Michele Protti
- Research group of Pharmaco-Toxicological Analysis (PTA Lab), Department of Pharmacy and Biotechnology (FaBiT), Alma Mater Studiorum, University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy
| | - Marco Cirrincione
- Research group of Pharmaco-Toxicological Analysis (PTA Lab), Department of Pharmacy and Biotechnology (FaBiT), Alma Mater Studiorum, University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy
| | - Sarah Palano
- Research group of Pharmaco-Toxicological Analysis (PTA Lab), Department of Pharmacy and Biotechnology (FaBiT), Alma Mater Studiorum, University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy
| | - Eleonora Poeta
- Cellular Neurobiology Lab, Department of Pharmacy and Biotechnology (FaBiT), Alma Mater Studiorum, University of Bologna, Via Selmi 3, 40126 Bologna, Italy
| | - Giorgia Babini
- Cellular Neurobiology Lab, Department of Pharmacy and Biotechnology (FaBiT), Alma Mater Studiorum, University of Bologna, Via Selmi 3, 40126 Bologna, Italy
| | - Maria Chiara Magnifico
- Department of Biosciences, Biotechnologies and Environment, University of Bari Aldo Moro, Via E. Orabona 4, 70125 Bari, Italy
| | - Simona Nicole Barile
- Department of Biosciences, Biotechnologies and Environment, University of Bari Aldo Moro, Via E. Orabona 4, 70125 Bari, Italy
| | - Nicola Balboni
- Cellular Neurobiology Lab, Department of Pharmacy and Biotechnology (FaBiT), Alma Mater Studiorum, University of Bologna, Via Selmi 3, 40126 Bologna, Italy
| | - Francesca Massenzio
- Cellular Neurobiology Lab, Department of Pharmacy and Biotechnology (FaBiT), Alma Mater Studiorum, University of Bologna, Via Selmi 3, 40126 Bologna, Italy
| | - Mohammadreza Mahdavijalal
- Research group of Pharmaco-Toxicological Analysis (PTA Lab), Department of Pharmacy and Biotechnology (FaBiT), Alma Mater Studiorum, University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy
| | - Federico M Giorgi
- Computational Genomics Lab, Department of Pharmacy and Biotechnology (FaBiT), Alma Mater Studiorum - University of Bologna, Via Selmi 3, 40126 Bologna, Italy
| | - Roberto Mandrioli
- Department for Life Quality Studies, Alma Mater Studiorum - University of Bologna, Corso d'Augusto 237, 47921 Rimini, Italy
| | - Francesco M Lasorsa
- Department of Biosciences, Biotechnologies and Environment, University of Bari Aldo Moro, Via E. Orabona 4, 70125 Bari, Italy; National Research Council (CNR) Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (IBIOM), Via Giovanni Amendola 122, 70126 Bari, Italy
| | - Barbara Monti
- Cellular Neurobiology Lab, Department of Pharmacy and Biotechnology (FaBiT), Alma Mater Studiorum, University of Bologna, Via Selmi 3, 40126 Bologna, Italy
| | - Laura Mercolini
- Research group of Pharmaco-Toxicological Analysis (PTA Lab), Department of Pharmacy and Biotechnology (FaBiT), Alma Mater Studiorum, University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy.
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Vankeerberghen B, Op de Beeck J, Desmet G. On-Chip Comparison of the Performance of First- and Second-Generation Micropillar Array Columns. Anal Chem 2023; 95:13822-13828. [PMID: 37677150 DOI: 10.1021/acs.analchem.3c01829] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/09/2023]
Abstract
Because of its dimensions, the recently introduced micropillar array columns are most suited for high-efficiency liquid chromatography separations in proteomics. Unlike the packed bed columns and capillary-based column formats, the micropillar array concept still has significant room to progress in terms of the reduction of its characteristic size (i.e., pillar diameter and interpillar distance) to open the road to even higher-efficiency separations and their applications. We report here on the on-chip comparison between first-generation (Gen 1) and second-generation (Gen 2) micropillar array columns wherein the pillar and interpillar size have been halved. Because of the on-chip measurements, the observed plate heights H represent the fundamental band broadening, devoid of any extra-column band-broadening effects. The observed reduction of H with a factor of 2 around the uopt-velocity and with a factor of 4 in the C-term dominated regime of the van Deemter-curve is in full agreement with the theoretically expected gain. This shows the pillar and interpillar size reduction could be effectuated without affecting the theoretical separation potential of the micropillar arrays. Compared to Gen 1, Gen 2 offers a 4-fold reduction of the required analysis time around the optimal velocity and about a 16-fold reduction in the C-term-dominated range.
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Affiliation(s)
- Bert Vankeerberghen
- Department of Chemical Engineering, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - Jeff Op de Beeck
- Thermo Fisher Scientific, Technologiepark-Zwijnaarde 82, 9052 Gent, Belgium
| | - Gert Desmet
- Department of Chemical Engineering, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
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Lu Q, Feng Q, Yu J, Tong L, Zhang J, Sun J, Zhao J, Xiong Z. Metabolomics and serum pharmacochemistry revealed the preventive mechanism of Gushudan in kidney-yang-deficiency-syndrome rats. Biomed Chromatogr 2023; 37:e5569. [PMID: 36527197 DOI: 10.1002/bmc.5569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 12/09/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022]
Abstract
Kidney-yang-deficiency-syndrome (KYDS) is a metabolic disease caused by neuroendocrine disorder. Gushudan (GSD) is a traditional Chinese medicine prescription with the effect of nourishing kidney and strengthening bones. In this study, the mechanism of preventive effect of GSD on KYDS was explored by integrating metabolomics and serum pharmacochemistry. Reversed-phase/hydrophilic interaction chromatography-ultra-high-performance liquid chromatography-Quadrupole-Orbitrap high-resolution mass spectrometry (RP/HILIC-UHPLC-Q-Orbitrap HRMS)-based serum metabolomics indicated metabolic disturbances of KYDS rats, and 50 potential biomarkers including l-threonine, succinic acid and phytosphingosine were obtained, which were mainly involved in alanine, aspartate and glutamate metabolism, citrate cycle (tricarboxylic acid cycle) and glycerophospholipid metabolism, among others. Serum pharmacochemistry identified 29 prototypical ingredients and 9 metabolites of GSD after administration, such as icaritin and xanthotoxol. The combination of 10 serum migration ingredients in GSD, including icaritin and osthole, with 7 important targets, including AKT serine/threonine kinase 1 (AKT1) and MAPK14, was found to be key for GSD to prevent KYDS in the network pharmacology study. This study provided a new idea for the research of pathogenesis of diseases and the pharmacodynamic mechanism of traditional Chinese medicine.
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Affiliation(s)
- Qing Lu
- School of Pharmacy, Shenyang Pharmaceutical University, Benxi, Liaoning Province, China
| | - Qisheng Feng
- School of Pharmacy, Shenyang Pharmaceutical University, Benxi, Liaoning Province, China
| | - Jiaxin Yu
- Sunwah International Business School, Liaoning University, Shenyang, Liaoning Province, China
| | - Lin Tong
- School of Pharmacy, Shenyang Pharmaceutical University, Benxi, Liaoning Province, China
| | - Jing Zhang
- School of Pharmacy, Shenyang Pharmaceutical University, Benxi, Liaoning Province, China
| | - Jinghan Sun
- School of Pharmacy, Shenyang Pharmaceutical University, Benxi, Liaoning Province, China
| | - Jing Zhao
- School of Pharmacy, Shenyang Pharmaceutical University, Benxi, Liaoning Province, China
| | - Zhili Xiong
- School of Pharmacy, Shenyang Pharmaceutical University, Benxi, Liaoning Province, China
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Affiliation(s)
- Rustam Aminov
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen AB25 2ZD, United Kingdom
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