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Gas Chromatography-Mass Spectrometry (GC-MS) Metabolites Analysis in Endometriosis Patients: A Prospective Observational Translational Study. J Clin Med 2023; 12:jcm12030922. [PMID: 36769570 PMCID: PMC9918082 DOI: 10.3390/jcm12030922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 01/04/2023] [Accepted: 01/14/2023] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND Endometriosis affects women of reproductive age, and its pathogenesis is still unclear. Typically, it overlaps other similar medical and surgical conditions, determining a delay in early diagnosis. Metabolomics allows studying metabolic changes in different physiological or pathological states to discover new potential biomarkers. We used the gas chromatography-mass spectrometer (GC-MS) to explore metabolic alterations in endometriosis to better understand its pathophysiology and find new biomarkers. METHODS Twenty-two serum samples of patients with symptomatic endometriosis and ten without it were collected and subjected to GC-MS analysis. Multivariate and univariate statistical analyses were performed, followed by pathway analysis. RESULTS Partial least squares discriminant analysis was performed to determine the differences between the two groups (p = 0.003). Threonic acid, 3-hydroxybutyric acid, and proline increased significantly in endometriosis patients, while alanine and valine decreased. ROC curves were built to test the diagnostic power of metabolites. The pathway analysis identified the synthesis and degradation of ketone bodies and the biosynthesis of phenylalanine, tyrosine, and tryptophan as the most altered pathways. CONCLUSIONS The metabolomic approach identifies metabolic alterations in women with endometriosis. These findings may improve our understanding of the pathophysiological mechanisms of disease and the discovery of new biomarkers.
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Liu Z, Xu J, Que S, Geng L, Zhou L, Mardinoglu A, Zheng S. Recent Progress and Future Direction for the Application of Multiomics Data in Clinical Liver Transplantation. J Clin Transl Hepatol 2022; 10:363-373. [PMID: 35528975 PMCID: PMC9039708 DOI: 10.14218/jcth.2021.00219] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 08/14/2021] [Accepted: 10/07/2021] [Indexed: 12/04/2022] Open
Abstract
Omics data address key issues in liver transplantation (LT) as the most effective therapeutic means for end-stage liver disease. The purpose of this study was to review the current application and future direction for omics in LT. We reviewed the use of multiomics to elucidate the pathogenesis leading to LT and prognostication. Future directions with respect to the use of omics in LT are also described based on perspectives of surgeons with experience in omics. Significant molecules were identified and summarized based on omics, with a focus on post-transplant liver fibrosis, early allograft dysfunction, tumor recurrence, and graft failure. We emphasized the importance omics for clinicians who perform LTs and prioritized the directions that should be established. We also outlined the ideal workflow for omics in LT. In step with advances in technology, the quality of omics data can be guaranteed using an improved algorithm at a lower price. Concerns should be addressed on the translational value of omics for better therapeutic effects in patients undergoing LT.
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Affiliation(s)
- Zhengtao Liu
- Shulan International Medical College, Zhejiang Shuren University, Hangzhou, Zhejiang, China
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
- NHC Key Laboratory of Combined Multi-organ Transplantation, Key Laboratory of the diagnosis and treatment of organ Transplantation, CAMS, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
- Key Laboratory of Organ Transplantation, Zhejiang Province, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Jun Xu
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Shuping Que
- DingXiang Clinics, Hangzhou, Zhejiang, China
| | - Lei Geng
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Lin Zhou
- NHC Key Laboratory of Combined Multi-organ Transplantation, Key Laboratory of the diagnosis and treatment of organ Transplantation, CAMS, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
- Key Laboratory of Organ Transplantation, Zhejiang Province, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Adil Mardinoglu
- Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King’s College London, London, UK
- Correspondence to: Adil Mardinoglu, Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden. ORCID: https://orcid.org/0000-0002-4254-6090. Tel: +46-31-772-3140, Fax: +46-31-772-3801, E-mail: ; Shusen Zheng, Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310003, China. ORCID: https://orcid.org/0000-0003-1459-8261. Tel/Fax: +86-571-87236570, E-mail:
| | - Shusen Zheng
- Shulan International Medical College, Zhejiang Shuren University, Hangzhou, Zhejiang, China
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
- NHC Key Laboratory of Combined Multi-organ Transplantation, Key Laboratory of the diagnosis and treatment of organ Transplantation, CAMS, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
- Key Laboratory of Organ Transplantation, Zhejiang Province, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
- Correspondence to: Adil Mardinoglu, Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden. ORCID: https://orcid.org/0000-0002-4254-6090. Tel: +46-31-772-3140, Fax: +46-31-772-3801, E-mail: ; Shusen Zheng, Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310003, China. ORCID: https://orcid.org/0000-0003-1459-8261. Tel/Fax: +86-571-87236570, E-mail:
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Citizens’ Literacy in Genomics: A Delphi Survey of Multidisciplinary Experts in the Field. Genes (Basel) 2022; 13:genes13030498. [PMID: 35328052 PMCID: PMC8949598 DOI: 10.3390/genes13030498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 03/03/2022] [Accepted: 03/08/2022] [Indexed: 12/04/2022] Open
Abstract
Introduction: Citizens’ literacy in the field of genomics represents one of the cornerstones of proper implementation of genomics in healthcare services. In order to identify the most effective tools by which to elevate citizens’ literacy in genomics, we conducted a survey among the group of multidisciplinary experts within the Italian Network of Genomics in Public Health (GENISAP). Methods. Two rounds of Delphi surveys were carried out in order to identify the main topics, tools, settings, and healthcare professionals’ backgrounds that might usefully be included in citizens’ training initiatives in genomics. To this end, we distributed a questionnaire with 39 items that are scored on a 5-point scale. Results. By the end of the Delphi process, 43 items were selected (19 for the topics, 6 for the tools, 9 for settings, and 9 for the healthcare professionals’ backgrounds). Genomic tests and counseling were among the main topics included, while in terms of tools, face-to-face discussion with healthcare professionals was prioritized by the experts. Among the most appropriate platforms, the group suggested internet/social media and healthcare settings. The healthcare professional considered to have the most relevant role in terms of citizens’ education was a medical doctor with a specialism in clinical genetics. Discussion. Our study attempted to identify the main characteristics that could guide the design of interventions to promote public literacy regarding the field of genomics. Specifically, we have identified the main topics to be included in an educational program for citizens, the tools and settings to consider when providing educational initiatives on genomics, and the healthcare professionals who need to be involved in these initiatives. Therefore, the results of our study provide the necessary basis for the realization of new training initiatives on genomics to be proposed and offered to citizens, these initiatives to be implemented at a national and international level for achieving the transformational change in health systems that is required by the precision health approach.
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da Silva JN, Simas DLR, Soares AR, Duarte HM, Moraes J, Conceição CC, da Silva RM, da Silva Vaz I, Logullo C. Glucose metabolomic profile during embryogenesis in the tick Rhipicephalus microplus. Metabolomics 2021; 17:79. [PMID: 34463832 DOI: 10.1007/s11306-021-01830-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 08/17/2021] [Indexed: 12/28/2022]
Abstract
INTRODUCTION Metabolomic approaches can assess the actual state of an organism's energy metabolism during a specific morphological event, providing a more accurate insight into the correlations between physiology and metabolic regulation. METHODS The study of the metabolomic profile aim to identify the largest possible number of biomolecules in a certain organism or specific structures. For this purpose, mass spectrometry (MS) and chromatography have been used in the present study. OBJECTIVES In this context, the aim of the present work is to evaluate the glucose metabolomic profile during embryogenesis in Rhipicephalus microplus tick, investigating the dynamics of nutrient utilization during tick embryo formation, as well as the control of glucose metabolism. RESULTS We show that glycogen reserves are preferentially mobilized to sustain the energy-intensive process of embryogenesis. Subsequently, the increase in concentration of specific amino acids indicates that protein degradation would provide carbons to fuel gluconeogenesis, supplying the embryo with sufficient glucose and glycogen during development. CONCLUSION Altogether, these results demonstrated the presence of a very refined catabolic and anabolic control during embryogenesis in R. microplus tick, suggesting the pronounced gluconeogenesis as a strategy to secure embryo development. Moreover, this research contributes to the understanding of the mechanisms that control glucose metabolism during tick embryogenesis and may aid the identification of putative targets for novel chemical or immunological control methods, which are essential to improve the prevention of tick infestations.
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Affiliation(s)
- Jhenifer Nascimento da Silva
- Grupo de Produtos Naturais de Organismos Aquáticos, Instituto de Biodiversidade e Sustentabilidade (NUPEM), Universidade Federal do Rio de Janeiro, Macaé, RJ, Brazil
- Laboratório Integrado de Bioquímica Hatisaburo Masuda and Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho, 373, Bloco D, Subsolo, Sala 05, Prédio do CCS. Ilha do Fundão, Rio de Janeiro, RJ, 21941-902, Brazil
| | - Daniel Luiz Reis Simas
- Fábrica de Árvores Soluções Ambientais, Sitio Anjo Gabriel, Bragança Paulista, São Paulo, SP, Brazil
| | - Angelica Ribeiro Soares
- Grupo de Produtos Naturais de Organismos Aquáticos, Instituto de Biodiversidade e Sustentabilidade (NUPEM), Universidade Federal do Rio de Janeiro, Macaé, RJ, Brazil
| | - Heitor Monteiro Duarte
- Grupo de Produtos Naturais de Organismos Aquáticos, Instituto de Biodiversidade e Sustentabilidade (NUPEM), Universidade Federal do Rio de Janeiro, Macaé, RJ, Brazil
| | - Jorge Moraes
- Laboratório Integrado de Bioquímica Hatisaburo Masuda and Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho, 373, Bloco D, Subsolo, Sala 05, Prédio do CCS. Ilha do Fundão, Rio de Janeiro, RJ, 21941-902, Brazil
| | - Christiano Calixto Conceição
- Laboratório Integrado de Bioquímica Hatisaburo Masuda and Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho, 373, Bloco D, Subsolo, Sala 05, Prédio do CCS. Ilha do Fundão, Rio de Janeiro, RJ, 21941-902, Brazil
| | - Renato Martins da Silva
- Laboratório Integrado de Bioquímica Hatisaburo Masuda and Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho, 373, Bloco D, Subsolo, Sala 05, Prédio do CCS. Ilha do Fundão, Rio de Janeiro, RJ, 21941-902, Brazil
| | - Itabajara da Silva Vaz
- Centro de Biotecnologia and Faculdade de Veterinária, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Carlos Logullo
- Laboratório Integrado de Bioquímica Hatisaburo Masuda and Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho, 373, Bloco D, Subsolo, Sala 05, Prédio do CCS. Ilha do Fundão, Rio de Janeiro, RJ, 21941-902, Brazil.
- Instituto Nacional de Ciência e Tecnologia em Entomologia Molecular, Rio de Janeiro, RJ, Brazil.
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Cho BG, Gutierrez Reyes CD, Mechref Y. N-Glycomics of Cerebrospinal Fluid: Method Comparison. Molecules 2021; 26:molecules26061712. [PMID: 33808573 PMCID: PMC8003558 DOI: 10.3390/molecules26061712] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 03/14/2021] [Accepted: 03/15/2021] [Indexed: 12/12/2022] Open
Abstract
Cerebrospinal fluid (CSF) contains valuable biological and neurological information. However, its glycomics analysis is hampered due to the low amount of protein in the biofluid, as has been demonstrated by other glycomics studies using a substantial amount of CSF. In this work, we investigated different N-glycan sample preparation approaches to develop a more sensitive method. These methods, one with an increased amount of buffer solution during the N-glycan release step with a lower amount of sample volume and the other with Filter-Aided N-Glycan Separation (FANGS), were compared with recent work to demonstrate their effectiveness. It was demonstrated that an increased amount of buffer solution showed higher intensity in comparison to the previously published method and FANGS. This suggested that digestion efficiency during the N-glycan release step was not in an optimal condition from the previously published method, and that there is a substantial loss of sample with FANGS when preparing N-glycans from CSF.
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Murgia F, Angioni S, D'Alterio MN, Pirarba S, Noto A, Santoru ML, Tronci L, Fanos V, Atzori L, Congiu F. Metabolic Profile of Patients with Severe Endometriosis: a Prospective Experimental Study. Reprod Sci 2021; 28:728-735. [PMID: 33174185 PMCID: PMC7862197 DOI: 10.1007/s43032-020-00370-9] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 10/21/2020] [Indexed: 12/12/2022]
Abstract
Endometriosis is a common disease affecting women in reproductive age. There are several hypotheses on the pathogenesis of this disease. Often, its lesions and symptoms overlap with those of many other medical and surgical conditions, causing a delay in diagnosis. Metabolomics represents a useful diagnostic tool for the study of metabolic changes during a different physiological or pathological status. We used 1H-NMR to explore metabolic alteration in a cohort of patients with endometriosis in order to contribute to a better understanding of the pathophysiology of the disease and to suggest new useful biomarkers. Thirty-seven patients were recruited for the metabolomic analysis: 22 patients affected by symptomatic endometriosis and 15 not affected by it. Their serum samples were collected and analyzed with 1H-NMR. Multivariate statistical analysis was conducted, followed by univariate and pathway analyses. Partial Least Square Discriminant Analysis (PLS-DA) was performed to determine the presence of any differences between the non-endometriosis and endometriosis samples (R2X = 0.596, R2Y = 0.713, Q2 = 0.635, and p < 0.0001). β-hydroxybutyric acid and glutamine were significantly increased, whereas tryptophan was significantly decreased in the endometriosis patients. ROC curves were built to test the diagnostic power of the metabolites (β-hydroxybutyric acid: AUC = 0.85 CI = 0.71-0.99; glutamine: AUC = 0.83 CI = 0.68-0.98; tryptophan: AUC = 0.75 CI = 0.54-0.95; β-hydroxybutyric acid + glutamine + tryptophan AUC = 0.92 CI = 0.81-1). The metabolomic approach enabled the identification of several metabolic alterations occurring in women with endometriosis. These findings may provide new bases for a better understanding of the pathophysiological mechanisms of the disease and for the discovery of new biomarkers. Trial registration number NCT02337816.
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Affiliation(s)
- Federica Murgia
- Department of Biomedical Sciences, Unit of Clinic Metabolomics, University of Cagliari, Cagliari, Italy
| | - Stefano Angioni
- Department of Surgical Sciences, Division of Gynecology and Obstetrics, University of Cagliari, Cagliari, Italy.
| | - Maurizio Nicola D'Alterio
- Department of Surgical Sciences, Division of Gynecology and Obstetrics, University of Cagliari, Cagliari, Italy
| | - Silvia Pirarba
- Obstetrics and Gynecology, ASSL Lanusei, ATS Sardinia, Lanusei, Italy
| | - Antonio Noto
- Department of Surgical Sciences, Neonatal Intensive Care Unit, Puericulture Institute and Neonatal Section, University of Cagliari, Cagliari, Italy
| | - Maria Laura Santoru
- Department of Biomedical Sciences, Unit of Clinic Metabolomics, University of Cagliari, Cagliari, Italy
| | - Laura Tronci
- Department of Biomedical Sciences, Unit of Clinic Metabolomics, University of Cagliari, Cagliari, Italy
| | - Vassilios Fanos
- Department of Surgical Sciences, Neonatal Intensive Care Unit, Puericulture Institute and Neonatal Section, University of Cagliari, Cagliari, Italy
| | - Luigi Atzori
- Department of Biomedical Sciences, Unit of Clinic Metabolomics, University of Cagliari, Cagliari, Italy
| | - Francesca Congiu
- Obstetrics and Gynecology, ASSL Lanusei, ATS Sardinia, Lanusei, Italy
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Panduro A, Roman S. Advancements in genomic medicine and the need for updated regional clinical practice guidelines in the field of hepatology. Ann Hepatol 2021; 19:1-2. [PMID: 31916948 DOI: 10.1016/j.aohep.2019.12.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 12/04/2019] [Indexed: 02/08/2023]
Affiliation(s)
- Arturo Panduro
- Department of Molecular Biology in Medicine, Civil Hospital of Guadalajara, "Fray Antonio Alcalde" and Health Sciences Center, University of Guadalajara, Guadalajara, Jalisco, Mexico.
| | - Sonia Roman
- Department of Molecular Biology in Medicine, Civil Hospital of Guadalajara, "Fray Antonio Alcalde" and Health Sciences Center, University of Guadalajara, Guadalajara, Jalisco, Mexico
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Evaluation of MDA-MB-468 Cell Culture Media Analysis in Predicting Triple-Negative Breast Cancer Patient Sera Metabolic Profiles. Metabolites 2020; 10:metabo10050173. [PMID: 32349447 PMCID: PMC7281562 DOI: 10.3390/metabo10050173] [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: 01/30/2020] [Revised: 04/07/2020] [Accepted: 04/22/2020] [Indexed: 12/12/2022] Open
Abstract
Triple-negative breast cancer (TNBC) is characterized by limited survival, poor prognosis, and high recurrence. Understanding the metabolic adaptations of TNBC could help reveal improved treatment regiments. Here we performed a comprehensive 1H NMR metabolic characterization of the MDA-MB-468 cell line, a commonly used model of TNBC, followed by an analysis of serum samples obtained from TNBC patients and healthy controls. MDA-MB-468 cells were cultured, and changes in the metabolic composition of the medium were monitored for 72 h. Based on time courses, metabolites were categorized as being consumed, being produced, or showing a mixed behavior. When comparing TNBC and control samples (HC), and by using multivariate and univariate analyses, we identified nine metabolites with differing profiles). The serum of TNBC patients was characterized by higher levels of glucose, glutamine, citrate, and acetoacetate and by lower levels of lactate, alanine, tyrosine, glutamate, and acetone. A comparative analysis between MDA-MB-468 cell culture media and TNBC patients' serum identified a potential systemic response to the carcinogenesis-associated processes, highlighting that MDA-MB-468 cells footprint does not reflect metabolic changes observed in studied TNBC serum fingerprint.
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Palma E, Tilocca B, Roncada P. Antimicrobial Resistance in Veterinary Medicine: An Overview. Int J Mol Sci 2020; 21:E1914. [PMID: 32168903 PMCID: PMC7139321 DOI: 10.3390/ijms21061914] [Citation(s) in RCA: 105] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 03/03/2020] [Accepted: 03/10/2020] [Indexed: 02/07/2023] Open
Abstract
Antimicrobial resistance (AMR) represents one of the most important human- and animal health-threatening issues worldwide. Bacterial capability to face antimicrobial compounds is an ancient feature, enabling bacterial survival over time and the dynamic surrounding. Moreover, bacteria make use of their evolutionary machinery to adapt to the selective pressure exerted by antibiotic treatments, resulting in reduced efficacy of the therapeutic intervention against human and animal infections. The mechanisms responsible for both innate and acquired AMR are thoroughly investigated. Commonly, AMR traits are included in mobilizable genetic elements enabling the homogeneous diffusion of the AMR traits pool between the ecosystems of diverse sectors, such as human medicine, veterinary medicine, and the environment. Thus, a coordinated multisectoral approach, such as One-Health, provides a detailed comprehensive picture of the AMR onset and diffusion. Following a general revision of the molecular mechanisms responsible for both innate and acquired AMR, the present manuscript focuses on reviewing the contribution of veterinary medicine to the overall issue of AMR. The main sources of AMR amenable to veterinary medicine are described, driving the attention towards the indissoluble cross-talk existing between the diverse ecosystems and sectors and their cumulative cooperation to this warning phenomenon.
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Affiliation(s)
| | | | - Paola Roncada
- Department of Health Science, University “Magna Graecia” of Catanzaro, Viale Europa, 88100 Catanzaro, Italy; (E.P.); (B.T.)
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Barbosa RH, dos Santos MLB, Silva TP, Rosa-Fernandes L, Pinto AMV, Spínola PS, Bonvicino CR, Fernandes PV, Lucena E, Palmisano G, Melo RCN, Cardoso CAA, Lemos B. Impression Cytology Is a Non-invasive and Effective Method for Ocular Cell Retrieval of Zika Infected Babies: Perspectives in OMIC Studies. Front Mol Neurosci 2019; 12:279. [PMID: 31866819 PMCID: PMC6907025 DOI: 10.3389/fnmol.2019.00279] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 11/01/2019] [Indexed: 01/08/2023] Open
Abstract
IMPORTANCE Non-invasive techniques for retrieving ocular surface cells from babies infected by zika virus (ZIKV) during the gestational period remain to be determined. OBJECTIVES The aim of this study was to describe an optimized impression cytology method for the isolation of viable cells from Zika infected babies with and without Congenital Zika Syndrome (CZS) in satisfactory amount and quality to enable easy adoption in the field and application in the context of genomic and molecular approaches. DESIGN SETTINGS AND PARTICIPANTS Ocular surface samples were obtained with a hydrophilic nitrocellulose membrane (through optimized impression cytology method) from twelve babies referred to the Pediatric Service of the Antonio Pedro Hospital, Universidade Federal Fluminense (UFF), Niteroi, Rio de Janeiro, Brazil. After an authorized written informed consent from the parents, samples were collected from both eyes of 12 babies (4 babies with maternal ZIKV exposure during gestation and presence of clinical signs which included ocular abnormalities and microcephaly; 4 babies with maternal ZIKV exposure during gestation but no clinical signs; and 4 unaffected control babies with negative PCR for Zika virus and without clinical signs). Cells were used for microscopy analyses and evaluated for their suitability for downstream molecular applications in transcriptomic and proteomic experiments. RESULTS Our optimized impression cytology protocol enabled the capture of a considerable number of viable cells. The microscopic features of the conjunctival epithelial cells were described by both direct analysis of the membrane-attached cells and analysis of cytospinned captured cells using several staining procedures. Epithelial basal, polyhedral and goblet cells were clearly identified in all groups. All cases of ZIKV infected babies showed potential morphological alterations (cell keratinization, pyknosis, karyolysis, anucleation, and vacuolization). Molecular approaches were also performed in parallel. Genomic DNA and RNA were successfully isolated from all samples to enable the establishment of transcriptomic and proteomic studies. CONCLUSIONS AND RELEVANCE Our method proved to be a suitable, fast, and non-invasive tool to obtain ocular cell preparations from babies with and without Zika infection. The method yielded sufficient cells for detailed morphological and molecular analyses of samples. We discuss perspectives for the application of impression cytology in the context of ZIKV studies in basic and clinical research.
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Affiliation(s)
- Raquel Hora Barbosa
- Molecular and Integrative Physiological Sciences Program, Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, United States
- Department of Maternal and Child, School of Medicine, Universidade Federal Fluminense, Niterói, Brazil
- Genetics Program, Instituto Nacional de Câncer, Rio de Janeiro, Brazil
| | - Maria Luiza B. dos Santos
- Department of Maternal and Child, School of Medicine, Universidade Federal Fluminense, Niterói, Brazil
| | - Thiago P. Silva
- Laboratory of Cellular Biology, Department of Biology, Universidade Federal de Juiz de Fora, Juiz de Fora, Brazil
| | - Liva Rosa-Fernandes
- Glycoproteomics Laboratory, Department of Parasitology, ICB, Universidade de São Paulo, São Paulo, Brazil
| | - Ana M. V. Pinto
- Biomedical Institute, Universidade Federal Fluminense, Niterói, Brazil
| | - Pricila S. Spínola
- Genetics Department – Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | | | | | - Evandro Lucena
- Division of Clinical Research, Instituto Nacional de Câncer, Rio de Janeiro, Brazil
| | - Giuseppe Palmisano
- Glycoproteomics Laboratory, Department of Parasitology, ICB, Universidade de São Paulo, São Paulo, Brazil
| | - Rossana C. N. Melo
- Laboratory of Cellular Biology, Department of Biology, Universidade Federal de Juiz de Fora, Juiz de Fora, Brazil
| | | | - Bernardo Lemos
- Molecular and Integrative Physiological Sciences Program, Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, United States
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Peyron PA, Lehmann S, Delaby C, Baccino E, Hirtz C. Biochemical markers of time since death in cerebrospinal fluid: A first step towards "Forensomics". Crit Rev Clin Lab Sci 2019; 56:274-286. [PMID: 31088325 DOI: 10.1080/10408363.2019.1619158] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
The accurate estimation of the time of death is a challenge in forensic medicine, as the methods routinely used to assess the postmortem interval (PMI) are far from being precise. Over the past decades, biochemical methods have been implemented on postmortem samples to improve the precision of PMI estimation. Studies have focussed on the biochemical profiles of closed compartment body fluids, as they are preserved longer than blood after death and are thus subject to confined postmortem chemical changes. Cerebrospinal fluid (CSF) has been considered a suitable fluid to investigate these changes, as it is found in large amounts and is easy to sample. Moreover, the main molecules found in CSF have known reference values in living subjects, unlike most other body fluids. In this literature review, we focus on the panel of biomarkers that have been studied in CSF based on their potential of offering information on the time of death. The interest in these biomarkers for casework and the research perspectives in this field are discussed. Integrating data from different methods, including biochemistry, for better estimation of the time of death would represent a step forward in the forensic field, paving the way for an innovative approach that we suggest to call "Forensomics."
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Affiliation(s)
- Pierre-Antoine Peyron
- a Department of Forensic Medicine , Montpellier University Hospital , Montpellier , France.,b Laboratory of Biochemistry and Clinical Proteomics, Montpellier University Hospital, Institute for Regenerative Medicine and Biotherapy , Montpellier , France
| | - Sylvain Lehmann
- b Laboratory of Biochemistry and Clinical Proteomics, Montpellier University Hospital, Institute for Regenerative Medicine and Biotherapy , Montpellier , France
| | - Constance Delaby
- b Laboratory of Biochemistry and Clinical Proteomics, Montpellier University Hospital, Institute for Regenerative Medicine and Biotherapy , Montpellier , France
| | - Eric Baccino
- a Department of Forensic Medicine , Montpellier University Hospital , Montpellier , France
| | - Christophe Hirtz
- b Laboratory of Biochemistry and Clinical Proteomics, Montpellier University Hospital, Institute for Regenerative Medicine and Biotherapy , Montpellier , France
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Adeola HA, Papagerakis S, Papagerakis P. Systems Biology Approaches and Precision Oral Health: A Circadian Clock Perspective. Front Physiol 2019; 10:399. [PMID: 31040792 PMCID: PMC6476986 DOI: 10.3389/fphys.2019.00399] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Accepted: 03/22/2019] [Indexed: 12/20/2022] Open
Abstract
A vast majority of the pathophysiological and metabolic processes in humans are temporally controlled by a master circadian clock located centrally in the hypothalamic suprachiasmatic nucleus of the brain, as well as by specialized peripheral oscillators located in other body tissues. This circadian clock system generates a rhythmical diurnal transcriptional-translational cycle in clock genes and protein expression and activities regulating numerous downstream target genes. Clock genes as key regulators of physiological function and dysfunction of the circadian clock have been linked to various diseases and multiple morbidities. Emerging omics technologies permits largescale multi-dimensional investigations of the molecular landscape of a given disease and the comprehensive characterization of its underlying cellular components (e.g., proteins, genes, lipids, metabolites), their mechanism of actions, functional networks and regulatory systems. Ultimately, they can be used to better understand disease and interpatient heterogeneity, individual profile, identify personalized targetable key molecules and pathways, discover novel biomarkers and genetic alterations, which collectively can allow for a better patient stratification into clinically relevant subgroups to improve disease prediction and prevention, early diagnostic, clinical outcomes, therapeutic benefits, patient's quality of life and survival. The use of “omics” technologies has allowed for recent breakthroughs in several scientific domains, including in the field of circadian clock biology. Although studies have explored the role of clock genes using circadiOmics (which integrates circadian omics, such as genomics, transcriptomics, proteomics and metabolomics) in human disease, no such studies have investigated the implications of circadian disruption in oral, head and neck pathologies using multi-omics approaches and linking the omics data to patient-specific circadian profiles. There is a burgeoning body of evidence that circadian clock controls the development and homeostasis of oral and maxillofacial structures, such as salivary glands, teeth and oral epithelium. Hence, in the current era of precision medicine and dentistry and patient-centered health care, it is becoming evident that a multi-omics approach is needed to improve our understanding of the role of circadian clock-controlled key players in the regulation of head and neck pathologies. This review discusses current knowledge on the role of the circadian clock and the contribution of omics-based approaches toward a novel precision health era for diagnosing and treating head and neck pathologies, with an emphasis on oral, head and neck cancer and Sjögren's syndrome.
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Affiliation(s)
- Henry A Adeola
- Hair and Skin Research Laboratory, Division of Dermatology, Department of Medicine, Faculty of Health Sciences and Groote Schuur Hospital, University of Cape Town, Cape Town, South Africa.,Department of Oral and Maxillofacial Pathology, Faculty of Dentistry, University of the Western Cape and Tygerberg Hospital, Cape Town, South Africa
| | - Silvana Papagerakis
- Laboratory of Oral, Head & Neck Cancer-Personalized Diagnostics and Therapeutics, Division of Head and Neck Surgery, Department of Surgery, University of Saskatchewan, Saskatoon, SK, Canada
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Gut metabolome meets microbiome: A methodological perspective to understand the relationship between host and microbe. Methods 2018; 149:3-12. [PMID: 29715508 DOI: 10.1016/j.ymeth.2018.04.029] [Citation(s) in RCA: 99] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Revised: 03/06/2018] [Accepted: 04/22/2018] [Indexed: 02/06/2023] Open
Abstract
It is well established that gut microbes and their metabolic products regulate host metabolism. The interactions between the host and its gut microbiota are highly dynamic and complex. In this review we present and discuss the metabolomic strategies to study the gut microbial ecosystem. We highlight the metabolic profiling approaches to study faecal samples aimed at deciphering the metabolic product derived from gut microbiota. We also discuss how metabolomics data can be integrated with metagenomics data derived from gut microbiota and how such approaches may lead to better understanding of the microbial functions. Finally, the emerging approaches of genome-scale metabolic modelling to study microbial co-metabolism and host-microbe interactions are highlighted.
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Abstract
One of the promises of multiomic analysis was to transform the clinical diagnostics to deliver much more exact phenotyping of disease states. However, despite enormous investments, the transformation of clinical routine has not taken place. There are many reasons for this lack of success but one is the failure to deliver quantitative and reproducible data. This failure is not only impeding progress in clinical phenotyping but also in the application of omic science in systems biology. The focus in this Viewpoint will be on lipidomics but the lessons learned are generally applicable.
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Affiliation(s)
- Kai Simons
- Max-Planck-Institute of Molecular Cell Biology and Genetics and Lipotype GmbH,, Dresden, Germany
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15
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Sevimoglu T, Turanli B, Bereketoglu C, Arga KY, Karadag AS. Systems biomarkers in psoriasis: Integrative evaluation of computational and experimental data at transcript and protein levels. Gene 2018; 647:157-163. [DOI: 10.1016/j.gene.2018.01.033] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Revised: 12/06/2017] [Accepted: 01/08/2018] [Indexed: 02/08/2023]
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Jones LH, Neubert H. Clinical chemoproteomics-Opportunities and obstacles. Sci Transl Med 2017; 9:9/386/eaaf7951. [PMID: 28424333 DOI: 10.1126/scitranslmed.aaf7951] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 03/06/2017] [Indexed: 12/19/2022]
Abstract
Chemoproteomics is the large-scale study of proteins using chemical methods. Although chemoproteomic techniques are becoming commonplace in preclinical research, few examples have found clinical utility. We explore the prospects for advancing chemoproteomics into the clinical setting to understand drug-target interactions and to identify new therapeutically relevant targets.
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Affiliation(s)
- Lyn H Jones
- Medicine Design, Pfizer, 610 Main Street, Cambridge, MA 02139, USA.
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Integrating Pharmacoproteomics into Early-Phase Clinical Development: State-of-the-Art, Challenges, and Recommendations. Int J Mol Sci 2017; 18:ijms18020448. [PMID: 28218733 PMCID: PMC5343982 DOI: 10.3390/ijms18020448] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Revised: 01/17/2017] [Accepted: 01/18/2017] [Indexed: 12/13/2022] Open
Abstract
Pharmacoproteomics is the study of disease-modifying and toxicity parameters associated with therapeutic drug administration, using analysis of quantitative and temporal changes to specific, predetermined, and select proteins, or to the proteome as a whole. Pharmacoproteomics is a rapidly evolving field, with progress in analytic technologies enabling processing of complex interactions of large number of unique proteins and effective use in clinical trials. Nevertheless, our analysis of clinicaltrials.gov and PubMed shows that the application of proteomics in early-phase clinical development is minimal and limited to few therapeutic areas, with oncology predominating. We review the history, technologies, current usage, challenges, and potential for future use, and conclude with recommendations for integration of pharmacoproteomic in early-phase drug development.
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Sharon T. The Googlization of health research: from disruptive innovation to disruptive ethics. Per Med 2016; 13:563-574. [PMID: 29754546 DOI: 10.2217/pme-2016-0057] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Consumer-oriented mobile technologies offer new ways of capturing multidimensional health data, and are increasingly seen as facilitators of medical research. This has opened the way for large consumer tech companies, like Apple, Google, Amazon and Facebook, to enter the space of health research, offering new methods for collecting, storing and analyzing health data. While these developments are often portrayed as 'disrupting' research in beneficial ways, they also raise many ethical issues. These can be organized into three clusters: questions concerning the quality of research; privacy/informed consent; and new power asymmetries based on access to data and control over technological infrastructures. I argue that this last cluster, insofar as it may affect future research agendas, deserves more critical attention.
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Affiliation(s)
- Tamar Sharon
- Philosophy Department, Maastricht University, Grote Gracht 90-92, 6211 SZ, Maastricht, The Netherlands
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López de Maturana E, Pineda S, Brand A, Van Steen K, Malats N. Toward the integration of Omics data in epidemiological studies: still a "long and winding road". Genet Epidemiol 2016; 40:558-569. [PMID: 27432111 DOI: 10.1002/gepi.21992] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2015] [Revised: 05/22/2016] [Accepted: 06/05/2016] [Indexed: 12/23/2022]
Abstract
Primary and secondary prevention can highly benefit a personalized medicine approach through the accurate discrimination of individuals at high risk of developing a specific disease from those at moderate and low risk. To this end precise risk prediction models need to be built. This endeavor requires a precise characterization of the individual exposome, genome, and phenome. Massive molecular omics data representing the different layers of the biological processes of the host and the nonhost will enable to build more accurate risk prediction models. Epidemiologists aim to integrate omics data along with important information coming from other sources (questionnaires, candidate markers) that has been proved to be relevant in the discrimination risk assessment of complex diseases. However, the integrative models in large-scale epidemiologic research are still in their infancy and they face numerous challenges, some of them at the analytical stage. So far, there are a small number of studies that have integrated more than two omics data sets, and the inclusion of non-omics data in the same models is still missing in most of studies. In this contribution, we aim at approaching the omics and non-omics data integration from the epidemiology scope by considering the "massive" inclusion of variables in the risk assessment and predictive models. We also provide already available examples of integrative contributions in the field, propose analytical strategies that allow considering both omics and non-omics data in the models, and finally review the challenges imbedding this type of research.
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Affiliation(s)
| | - Sílvia Pineda
- Genetic and Molecular Epidemiology Group, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Angela Brand
- Institute for Public Health Genomics, Maastricht University, Maastricht, Netherlands
| | - Kristel Van Steen
- Laboratory of Biostatistics, Biomedicine and Bioinformatics, GIGA, University of Liège, Belgium
| | - Núria Malats
- Genetic and Molecular Epidemiology Group, Spanish National Cancer Research Centre (CNIO), Madrid, Spain.
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