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Ancer-Rodríguez J, Gopar-Cuevas Y, García-Aguilar K, Chávez-Briones MDL, Miranda-Maldonado I, Ancer-Arellano A, Ortega-Martínez M, Jaramillo-Rangel G. Cell Proliferation and Apoptosis-Key Players in the Lung Aging Process. Int J Mol Sci 2024; 25:7867. [PMID: 39063108 PMCID: PMC11276691 DOI: 10.3390/ijms25147867] [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: 06/18/2024] [Revised: 07/12/2024] [Accepted: 07/15/2024] [Indexed: 07/28/2024] Open
Abstract
Currently, the global lifespan has increased, resulting in a higher proportion of the population over 65 years. Changes that occur in the lung during aging increase the risk of developing acute and chronic lung diseases, such as acute respiratory distress syndrome, chronic obstructive pulmonary disease, idiopathic pulmonary fibrosis, and lung cancer. During normal tissue homeostasis, cell proliferation and apoptosis create a dynamic balance that constitutes the physiological cell turnover. In basal conditions, the lungs have a low rate of cell turnover compared to other organs. During aging, changes in the rate of cell turnover in the lung are observed. In this work, we review the literature that evaluates the role of molecules involved in cell proliferation and apoptosis in lung aging and in the development of age-related lung diseases. The list of molecules that regulate cell proliferation, apoptosis, or both processes in lung aging includes TNC, FOXM1, DNA-PKcs, MicroRNAs, BCL-W, BCL-XL, TCF21, p16, NOX4, NRF2, MDM4, RPIA, DHEA, and MMP28. However, despite the studies carried out to date, the complete signaling pathways that regulate cell turnover in lung aging are still unknown. More research is needed to understand the changes that lead to the development of age-related lung diseases.
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Affiliation(s)
| | | | | | | | | | | | | | - Gilberto Jaramillo-Rangel
- Department of Pathology, School of Medicine, Autonomous University of Nuevo León, Monterrey 64460, Mexico; (J.A.-R.); (Y.G.-C.); (M.-d.-L.C.-B.); (I.M.-M.); (A.A.-A.); (M.O.-M.)
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2
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Filippo D, Guardone L, Listorti V, Elisabetta R. Microbiome in cancer: A comparative analysis between humans and dogs. Vet J 2024; 305:106145. [PMID: 38788999 DOI: 10.1016/j.tvjl.2024.106145] [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: 09/18/2023] [Revised: 04/22/2024] [Accepted: 05/21/2024] [Indexed: 05/26/2024]
Abstract
Cancer is a major cause of death in humans and animals worldwide. While cancer survival rates have increased over recent decades, further research to identify risk factors for the onset and progression of disease, and safe and highly efficacious treatments, is needed. Spontaneous tumours in pets represent an excellent model for neoplastic disease in humans. In this regard, dogs are an interesting species, as the divergence between the dog and human genome is low, humans and dogs have important similarities in the development and functioning of the immune system, and both species often share the same physical environment. There is also a higher homology between the canine and human microbiome than murine model. This review aims to describe and organize recently published information on canine microbiome assemblages and their relationship with the onset and progression of colorectal cancer, breast cancer and lymphoma, and to compare this with human disease. In both species, dysbiosis can induce variations in the gut microbiota that strongly influence shifts in status between health and disease. This can produce an inflammatory state, potentially leading to neoplasia, especially in the intestine, thus supporting canine studies in comparative oncology. Intestinal dysbiosis can also alter the efficacy and side effects of cancer treatments. Fewer published studies are available on changes in the relevant microbiomes in canine lymphoma and mammary cancer, and further research in this area could improve our understanding of the role of microbiota in the development of these cancers.
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Affiliation(s)
- Dell'Anno Filippo
- National Reference Center of Veterinary and Comparative Oncology (CEROVEC), Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d'Aosta, Genova 16129, Italy; Department of Public Health, Experimental and Forensic Medicine, Section of Biostatistics and Clinical Epidemiology, University of Pavia, Pavia, Italy
| | - Lisa Guardone
- National Reference Center of Veterinary and Comparative Oncology (CEROVEC), Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d'Aosta, Genova 16129, Italy
| | - Valeria Listorti
- National Reference Center of Veterinary and Comparative Oncology (CEROVEC), Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d'Aosta, Genova 16129, Italy
| | - Razzuoli Elisabetta
- National Reference Center of Veterinary and Comparative Oncology (CEROVEC), Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d'Aosta, Genova 16129, Italy.
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3
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Gallego D, Serrano M, Cordoba-Caballero J, Gámez A, Seoane P, Perkins JR, Ranea JAG, Pérez B. Transcriptomic analysis identifies dysregulated pathways and therapeutic targets in PMM2-CDG. Biochim Biophys Acta Mol Basis Dis 2024; 1870:167163. [PMID: 38599261 DOI: 10.1016/j.bbadis.2024.167163] [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: 11/22/2023] [Revised: 03/15/2024] [Accepted: 04/04/2024] [Indexed: 04/12/2024]
Abstract
PMM2-CDG (MIM # 212065), the most common congenital disorder of glycosylation, is caused by the deficiency of phosphomannomutase 2 (PMM2). It is a multisystemic disease of variable severity that particularly affects the nervous system; however, its molecular pathophysiology remains poorly understood. Currently, there is no effective treatment. We performed an RNA-seq based transcriptomic study using patient-derived fibroblasts to gain insight into the mechanisms underlying the clinical symptomatology and to identify druggable targets. Systems biology methods were used to identify cellular pathways potentially affected by PMM2 deficiency, including Senescence, Bone regulation, Cell adhesion and Extracellular Matrix (ECM) and Response to cytokines. Functional validation assays using patients' fibroblasts revealed defects related to cell proliferation, cell cycle, the composition of the ECM and cell migration, and showed a potential role of the inflammatory response in the pathophysiology of the disease. Furthermore, treatment with a previously described pharmacological chaperone reverted the differential expression of some of the dysregulated genes. The results presented from transcriptomic data might serve as a platform for identifying therapeutic targets for PMM2-CDG, as well as for monitoring the effectiveness of therapeutic strategies, including pharmacological candidates and mannose-1-P, drug repurposing.
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Affiliation(s)
- Diana Gallego
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular-SO UAM-CSIC, Universidad Autónoma de Madrid, Campus de Cantoblanco, U746- CIBER de Enfermedades Raras (CIBERER), Instituto de Investigación Sanitaria IdiPAZ, 28049 Madrid, Spain
| | - Mercedes Serrano
- Pediatric Neurology Department, Hospital Sant Joan de Déu, Institut de Recerca Sant Joan de Déu, 08950 Barcelona, Spain; U-703 Centre for Biomedical Research on Rare Diseases (CIBER-ER), Instituto de Salud Carlos III, Spain
| | - Jose Cordoba-Caballero
- Department of Molecular Biology and Biochemistry, University of Málaga, Málaga, Spain; U-741, CIBER de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Alejandra Gámez
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular-SO UAM-CSIC, Universidad Autónoma de Madrid, Campus de Cantoblanco, U746- CIBER de Enfermedades Raras (CIBERER), Instituto de Investigación Sanitaria IdiPAZ, 28049 Madrid, Spain
| | - Pedro Seoane
- Department of Molecular Biology and Biochemistry, University of Málaga, Málaga, Spain; U-741, CIBER de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - James R Perkins
- Department of Molecular Biology and Biochemistry, University of Málaga, Málaga, Spain; U-741, CIBER de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain; The Biomedical Research Institute of Málaga (IBIMA), Málaga, Spain; Spanish National Bioinformatics Institute (INB/ELIXIR-ES), Madrid, Spain
| | - Juan A G Ranea
- Department of Molecular Biology and Biochemistry, University of Málaga, Málaga, Spain; U-741, CIBER de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain; The Biomedical Research Institute of Málaga (IBIMA), Málaga, Spain; Spanish National Bioinformatics Institute (INB/ELIXIR-ES), Madrid, Spain.
| | - Belén Pérez
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular-SO UAM-CSIC, Universidad Autónoma de Madrid, Campus de Cantoblanco, U746- CIBER de Enfermedades Raras (CIBERER), Instituto de Investigación Sanitaria IdiPAZ, 28049 Madrid, Spain.
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4
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Puiu A, Gómez Tapia C, Weiss MER, Singh V, Kamen A, Siebert M. Prediction uncertainty estimates elucidate the limitation of current NSCLC subtype classification in representing mutational heterogeneity. Sci Rep 2024; 14:6779. [PMID: 38514696 PMCID: PMC10958018 DOI: 10.1038/s41598-024-57057-3] [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: 11/22/2023] [Accepted: 03/13/2024] [Indexed: 03/23/2024] Open
Abstract
The heterogeneous pathogenesis and treatment response of non-small cell lung cancer (NSCLC) has led clinical treatment decisions to be guided by NSCLC subtypes, with lung adenocarcinoma and lung squamous cell carcinoma being the most common subtypes. While histology-based subtyping remains challenging, NSCLC subtypes were found to be distinct at the transcriptomic level. However, unlike genomic alterations, gene expression is generally not assessed in clinical routine. Since subtyping of NSCLC has remained elusive using mutational data, we aimed at developing a neural network model that simultaneously learns from adenocarcinoma and squamous cell carcinoma samples of other tissue types and is regularized using a neural network model trained from gene expression data. While substructures of the expression-based manifold were captured in the mutation-based manifold, NSCLC classification accuracy did not significantly improve. However, performance was increased when rejecting inconclusive samples using an ensemble-based approach capturing prediction uncertainty. Importantly, SHAP analysis of misclassified samples identified co-occurring mutations indicative of both NSCLC subtypes, questioning the current NSCLC subtype classification to adequately represent inherent mutational heterogeneity. Since our model captures mutational patterns linked to clinical heterogeneity, we anticipate it to be suited as foundational model of genomic data for clinically relevant prognostic or predictive downstream tasks.
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Affiliation(s)
- Andrei Puiu
- Advanta, Siemens SRL, Brasov, 500007, Romania
- Automation and Information Technology, Transilvania University of Brasov, Brasov, 500174, Romania
| | - Carlos Gómez Tapia
- Digital Technology and Innovation, Siemens Healthineers, Erlangen, 91052, Germany
| | - Maximilian E R Weiss
- Digital Technology and Innovation, Siemens Healthineers, Erlangen, 91052, Germany
| | - Vivek Singh
- Digital Technology and Innovation, Siemens Healthineers, Princeton, 08540, USA
| | - Ali Kamen
- Digital Technology and Innovation, Siemens Healthineers, Princeton, 08540, USA
| | - Matthias Siebert
- Digital Technology and Innovation, Siemens Healthineers, Erlangen, 91052, Germany.
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5
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Kabbashi S, Roomaney IA, Chetty M. Bridging the gap between omics research and dental practice. BDJ Open 2024; 10:16. [PMID: 38438363 PMCID: PMC10912736 DOI: 10.1038/s41405-024-00199-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 02/11/2024] [Accepted: 02/13/2024] [Indexed: 03/06/2024] Open
Abstract
AIM The burgeoning field of omics research has witnessed exponential growth in both medicine and dentistry. However, despite more than a decade of advancements, clinical dentistry, particularly in Low- and Middle-Income Countries (LMICs), has seen limited progress in integrating omics-based approaches into routine practice. This review aims to provide a comprehensive overview of the integration of omics approaches in dentistry, focusing on the challenges and opportunities for translating research findings into clinical practice. METHODS we conducted a literature review using key databases to provide a brief overview of the history of genomics in dentistry. Additionally, we summarised recent breakthroughs in omics relevant to oral health practitioners, emphasising the inadequate translation of omics research into clinical practice. RESULTS Despite significant growth in omics research in both medicine and dentistry, its translation into routine clinical practice in dentistry remains limited. We summarise recent breakthroughs in omics and highlight the gap between research advancements and clinical implementation. DISCUSSION AND CONCLUSION The integration of omics approaches holds promise for enhancing diagnostics, personalised treatment strategies, and preventive measures in dental practice, ushering in a new era of precision oral healthcare. However, several challenges, including infrastructure limitations, cost-effectiveness, and education gaps, hinder the widespread adoption of omics-based approaches in clinical dentistry. A strong commitment to transforming dentistry is required to embrace this transition. This shift has the potential to revolutionise oral healthcare by advancing precision diagnostics and treatment strategies tailored to individual patient needs.
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Affiliation(s)
- S Kabbashi
- Department of Craniofacial Biology, Pathology, and Radiology, Faculty of Dentistry, University of Western Cape, Cape Town, South Africa.
| | - I A Roomaney
- Department of Craniofacial Biology, Pathology, and Radiology, Faculty of Dentistry, University of Western Cape, Cape Town, South Africa
| | - M Chetty
- Department of Craniofacial Biology, Pathology, and Radiology, Faculty of Dentistry, University of Western Cape, Cape Town, South Africa
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6
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Pantaleon Garcia J, Evans SE. Omics-based profiles and biomarkers of respiratory infections: are we there yet? Eur Respir J 2024; 63:2400137. [PMID: 38453245 PMCID: PMC10918315 DOI: 10.1183/13993003.00137-2024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Accepted: 01/29/2024] [Indexed: 03/09/2024]
Abstract
From the influenza pandemic of 1918–1919 to the most recent COVID-19 pandemic, respiratory infections remain a leading cause of mortality worldwide [1, 2]. Concurrently, the development of high-throughput omics technologies has revolutionised research about host responses to known and emerging respiratory pathogens [3], accelerating our understanding of highly prevalent pulmonary diseases [4]. Notably, omics technology-based characterisation of pathogens and host pathophysiology have critically supported diagnostic and therapeutic global health efforts during both the influenza A H1N1 and SARS-CoV-2 pandemics [5–7]. Nonetheless, elucidation of key immune response mechanisms and development of host-targeted therapeutics remain important unrealised research and clinical priorities in the global fight against lower respiratory tract infections (LTRIs) [8, 9]. Descriptive omics-based clinical research provides valuable early steps in understanding host immune responses to respiratory pathogens in our global efforts to mitigate the impacts of severe respiratory infections with rapidly evolving technologies https://bit.ly/4bjJsvL
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Affiliation(s)
- Jezreel Pantaleon Garcia
- Department of Pulmonary Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Scott E Evans
- Department of Pulmonary Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, USA
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7
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Tran A, Wang A, Mickaill J, Strbenac D, Larance M, Vernon ST, Grieve SM, Figtree GA, Patrick E, Yang JYH. Construction and optimization of multi-platform precision pathways for precision medicine. Sci Rep 2024; 14:4248. [PMID: 38378802 PMCID: PMC10879206 DOI: 10.1038/s41598-024-54517-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 02/13/2024] [Indexed: 02/22/2024] Open
Abstract
In the enduring challenge against disease, advancements in medical technology have empowered clinicians with novel diagnostic platforms. Whilst in some cases, a single test may provide a confident diagnosis, often additional tests are required. However, to strike a balance between diagnostic accuracy and cost-effectiveness, one must rigorously construct the clinical pathways. Here, we developed a framework to build multi-platform precision pathways in an automated, unbiased way, recommending the key steps a clinician would take to reach a diagnosis. We achieve this by developing a confidence score, used to simulate a clinical scenario, where at each stage, either a confident diagnosis is made, or another test is performed. Our framework provides a range of tools to interpret, visualize and compare the pathways, improving communication and enabling their evaluation on accuracy and cost, specific to different contexts. This framework will guide the development of novel diagnostic pathways for different diseases, accelerating the implementation of precision medicine into clinical practice.
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Affiliation(s)
- Andy Tran
- School of Mathematics and Statistics, The University of Sydney, Camperdown, NSW, Australia
- Charles Perkins Centre, The University of Sydney, Camperdown, NSW, Australia
- Sydney Precision Data Science Centre, The University of Sydney, Camperdown, NSW, Australia
| | - Andy Wang
- Westmead Medical Institute, Westmead, NSW, Australia
| | - Jamie Mickaill
- School of Mathematics and Statistics, The University of Sydney, Camperdown, NSW, Australia
- School of Computer Science, The University of Sydney, Camperdown, NSW, Australia
| | - Dario Strbenac
- School of Mathematics and Statistics, The University of Sydney, Camperdown, NSW, Australia
- Charles Perkins Centre, The University of Sydney, Camperdown, NSW, Australia
- Sydney Precision Data Science Centre, The University of Sydney, Camperdown, NSW, Australia
| | - Mark Larance
- Charles Perkins Centre, The University of Sydney, Camperdown, NSW, Australia
| | - Stephen T Vernon
- Charles Perkins Centre, The University of Sydney, Camperdown, NSW, Australia
- Kolling Institute of Medical Research, St Leonards, NSW, Australia
| | - Stuart M Grieve
- Charles Perkins Centre, The University of Sydney, Camperdown, NSW, Australia
- Department of Radiology, Royal Prince Alfred Hospital, Camperdown, Australia
| | - Gemma A Figtree
- Charles Perkins Centre, The University of Sydney, Camperdown, NSW, Australia
- Kolling Institute of Medical Research, St Leonards, NSW, Australia
| | - Ellis Patrick
- School of Mathematics and Statistics, The University of Sydney, Camperdown, NSW, Australia
- Charles Perkins Centre, The University of Sydney, Camperdown, NSW, Australia
- Sydney Precision Data Science Centre, The University of Sydney, Camperdown, NSW, Australia
- Laboratory of Data Discovery for Health Limited (D24H), Science Park, Hong Kong SAR, China
| | - Jean Yee Hwa Yang
- School of Mathematics and Statistics, The University of Sydney, Camperdown, NSW, Australia.
- Charles Perkins Centre, The University of Sydney, Camperdown, NSW, Australia.
- Sydney Precision Data Science Centre, The University of Sydney, Camperdown, NSW, Australia.
- Laboratory of Data Discovery for Health Limited (D24H), Science Park, Hong Kong SAR, China.
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8
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Iacobescu M, Pop C, Uifălean A, Mogoşan C, Cenariu D, Zdrenghea M, Tănase A, Bergthorsson JT, Greiff V, Cenariu M, Iuga CA, Tomuleasa C, Tătaru D. Unlocking protein-based biomarker potential for graft-versus-host disease following allogenic hematopoietic stem cell transplants. Front Immunol 2024; 15:1327035. [PMID: 38433830 PMCID: PMC10904603 DOI: 10.3389/fimmu.2024.1327035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 02/01/2024] [Indexed: 03/05/2024] Open
Abstract
Despite the numerous advantages of allogeneic hematopoietic stem cell transplants (allo-HSCT), there exists a notable association with risks, particularly during the preconditioning period and predominantly post-intervention, exemplified by the occurrence of graft-versus-host disease (GVHD). Risk stratification prior to symptom manifestation, along with precise diagnosis and prognosis, relies heavily on clinical features. A critical imperative is the development of tools capable of early identification and effective management of patients undergoing allo-HSCT. A promising avenue in this pursuit is the utilization of proteomics-based biomarkers obtained from non-invasive biospecimens. This review comprehensively outlines the application of proteomics and proteomics-based biomarkers in GVHD patients. It delves into both single protein markers and protein panels, offering insights into their relevance in acute and chronic GVHD. Furthermore, the review provides a detailed examination of the site-specific involvement of GVHD. In summary, this article explores the potential of proteomics as a tool for timely and accurate intervention in the context of GVHD following allo-HSCT.
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Affiliation(s)
- Maria Iacobescu
- Department of Proteomics and Metabolomics, MEDFUTURE Research Center for Advanced Medicine, “Iuliu Hatieganu” University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Cristina Pop
- Department of Pharmacology, Physiology and Pathophysiology, Faculty of Pharmacy, “Iuliu Hatieganu” University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Alina Uifălean
- Department of Pharmaceutical Analysis, Faculty of Pharmacy, “Iuliu Hatieganu” University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Cristina Mogoşan
- Department of Pharmacology, Physiology and Pathophysiology, Faculty of Pharmacy, “Iuliu Hatieganu” University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Diana Cenariu
- Department of Translational Medicine, MEDFUTURE Research Center for Advanced Medicine, “Iuliu Hatieganu” University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Mihnea Zdrenghea
- Department of Hematology, Faculty of Medicine, “Iuliu Hatieganu” University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Alina Tănase
- Department of Stem Cell Transplantation, Fundeni Clinical Institute, Bucharest, Romania
| | - Jon Thor Bergthorsson
- Department of Laboratory Hematology, Stem Cell Research Unit, Biomedical Center, School of Health Sciences, University Iceland, Reykjavik, Iceland
| | - Victor Greiff
- Department of Immunology, University of Oslo, Oslo, Norway
| | - Mihai Cenariu
- Department of Animal Reproduction, University of Agricultural Sciences and Veterinary Medicine, Cluj-Napoca, Romania
| | - Cristina Adela Iuga
- Department of Proteomics and Metabolomics, MEDFUTURE Research Center for Advanced Medicine, “Iuliu Hatieganu” University of Medicine and Pharmacy, Cluj-Napoca, Romania
- Department of Pharmaceutical Analysis, Faculty of Pharmacy, “Iuliu Hatieganu” University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Ciprian Tomuleasa
- Department of Translational Medicine, MEDFUTURE Research Center for Advanced Medicine, “Iuliu Hatieganu” University of Medicine and Pharmacy, Cluj-Napoca, Romania
- Department of Hematology, Faculty of Medicine, “Iuliu Hatieganu” University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Dan Tătaru
- Department of Internal Medicine, Faculty of Medicine, “Iuliu Hatieganu” University of Medicine and Pharmacy, Cluj-Napoca, Romania
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9
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Hügle T, Grek V. Digital transformation of an academic hospital department: A case study on strategic planning using the balanced scorecard. PLOS DIGITAL HEALTH 2023; 2:e0000385. [PMID: 37976272 PMCID: PMC10656018 DOI: 10.1371/journal.pdig.0000385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 10/10/2023] [Indexed: 11/19/2023]
Abstract
Digital transformation has a significant impact on efficiency and quality in hospitals. New solutions can support the management of data overload and the shortage of qualified staff. However, the timely and effective integration of these new digital tools in the healthcare setting poses challenges and requires guidance. The balanced scorecard (BSC) is a managerial method used to translate new strategies into action and measure their impact in an institution, going beyond financial values. This framework enables quicker operational adjustments and enhances awareness of real-time performance from multiple perspectives, including customers, internal procedures, and the learning organization. The aim of this study was to adapt the BSC to the evolving digital healthcare environment, encompassing factors like the recent pandemic, new technologies such as artificial intelligence, legislation, and user preferences. A strategic mapping with identification of corresponding key performance indicators was performed. To achieve this, we employed a qualitative research approach involving retreats, interdisciplinary working groups, and semi-structured interviews with different stakeholders (administrative, clinical, computer scientists) in a rheumatology department. These inputs served as the basis for customizing the BSC according to upcoming or already implemented solutions and to define actionable, cross-level performance indicators for all perspectives. Our defined values include quality of care, patient empowerment, employee satisfaction, sustainability and innovation. We also identified substantial changes in our internal processes, with the electronic medical record (EMR) emerging as a central element for vertical and horizontal digitalization. This includes integrating patient-reported outcomes, disease-specific digital biomarker, prediction algorithms to increase the quality of care as well as advanced language models in order save resources. Gaps in communication and collaboration between medical departments have been identified as a main target for new digital solutions, especially in patients with more than one disorder. From a learning institution's perspective, digital literacy among patients and healthcare professionals emerges as a crucial lever for successful implementation of internal processes. In conclusion, the BSC is a helpful tool for guiding digitalization in hospitals as a horizontally and vertically connected process that affects all stakeholders. Future studies should include empirical analyses and explore correlations between variables and above all input and user experience from patients.
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Affiliation(s)
- Thomas Hügle
- Department of Rheumatology, Departement Appareil Locomoteur (DAL), University Hospital Lausanne (CHUV) and University of Lausanne, Switzerland
| | - Vincent Grek
- Department of Rheumatology, Departement Appareil Locomoteur (DAL), University Hospital Lausanne (CHUV) and University of Lausanne, Switzerland
- Department of Urology,Inselspital and University of Bern,Bern, Switzerland
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10
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Viana JN, Pilbeam C, Howard M, Scholz B, Ge Z, Fisser C, Mitchell I, Raman S, Leach J. Maintaining High-Touch in High-Tech Digital Health Monitoring and Multi-Omics Prognostication: Ethical, Equity, and Societal Considerations in Precision Health for Palliative Care. OMICS : A JOURNAL OF INTEGRATIVE BIOLOGY 2023; 27:461-473. [PMID: 37861713 DOI: 10.1089/omi.2023.0120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2023]
Abstract
Advances in digital health, systems biology, environmental monitoring, and artificial intelligence (AI) continue to revolutionize health care, ushering a precision health future. More than disease treatment and prevention, precision health aims at maintaining good health throughout the lifespan. However, how can precision health impact care for people with a terminal or life-limiting condition? We examine here the ethical, equity, and societal/relational implications of two precision health modalities, (1) integrated systems biology/multi-omics analysis for disease prognostication and (2) digital health technologies for health status monitoring and communication. We focus on three main ethical and societal considerations: benefits and risks associated with integration of these modalities into the palliative care system; inclusion of underrepresented and marginalized groups in technology development and deployment; and the impact of high-tech modalities on palliative care's highly personalized and "high-touch" practice. We conclude with 10 recommendations for ensuring that precision health technologies, such as multi-omics prognostication and digital health monitoring, for palliative care are developed, tested, and implemented ethically, inclusively, and equitably.
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Affiliation(s)
- John Noel Viana
- Australian National Centre for the Public Awareness of Science, College of Science, The Australian National University, Canberra, Australia
- Responsible Innovation Future Science Platform, Commonwealth Scientific and Industrial Research Organisation, Brisbane, Australia
| | - Caitlin Pilbeam
- School of Medicine and Psychology, College of Health and Medicine, The Australian National University, Canberra, Australia
| | - Mark Howard
- Monash Data Futures Institute, Monash University, Clayton, Australia
- Department of Philosophy, School of Philosophical, Historical and International Studies, Monash University, Clayton, Australia
| | - Brett Scholz
- School of Medicine and Psychology, College of Health and Medicine, The Australian National University, Canberra, Australia
| | - Zongyuan Ge
- Monash Data Futures Institute, Monash University, Clayton, Australia
- Department of Data Science & AI, Monash University, Clayton, Australia
| | - Carys Fisser
- Australian National Centre for the Public Awareness of Science, College of Science, The Australian National University, Canberra, Australia
- School of Medicine and Psychology, College of Health and Medicine, The Australian National University, Canberra, Australia
| | - Imogen Mitchell
- School of Medicine and Psychology, College of Health and Medicine, The Australian National University, Canberra, Australia
- Intensive Care Unit, Canberra Hospital, Canberra, Australia
| | - Sujatha Raman
- Australian National Centre for the Public Awareness of Science, College of Science, The Australian National University, Canberra, Australia
| | - Joan Leach
- Australian National Centre for the Public Awareness of Science, College of Science, The Australian National University, Canberra, Australia
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11
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Rulten SL, Grose RP, Gatz SA, Jones JL, Cameron AJM. The Future of Precision Oncology. Int J Mol Sci 2023; 24:12613. [PMID: 37628794 PMCID: PMC10454858 DOI: 10.3390/ijms241612613] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 08/03/2023] [Accepted: 08/05/2023] [Indexed: 08/27/2023] Open
Abstract
Our understanding of the molecular mechanisms underlying cancer development and evolution have evolved rapidly over recent years, and the variation from one patient to another is now widely recognized. Consequently, one-size-fits-all approaches to the treatment of cancer have been superseded by precision medicines that target specific disease characteristics, promising maximum clinical efficacy, minimal safety concerns, and reduced economic burden. While precision oncology has been very successful in the treatment of some tumors with specific characteristics, a large number of patients do not yet have access to precision medicines for their disease. The success of next-generation precision oncology depends on the discovery of new actionable disease characteristics, rapid, accurate, and comprehensive diagnosis of complex phenotypes within each patient, novel clinical trial designs with improved response rates, and worldwide access to novel targeted anticancer therapies for all patients. This review outlines some of the current technological trends, and highlights some of the complex multidisciplinary efforts that are underway to ensure that many more patients with cancer will be able to benefit from precision oncology in the near future.
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Affiliation(s)
| | - Richard P. Grose
- Centre for Tumour Biology, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, UK; (R.P.G.); (J.L.J.)
| | - Susanne A. Gatz
- Cancer Research UK Clinical Trials Unit (CRCTU), Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK;
| | - J. Louise Jones
- Centre for Tumour Biology, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, UK; (R.P.G.); (J.L.J.)
| | - Angus J. M. Cameron
- Centre for Tumour Biology, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, UK; (R.P.G.); (J.L.J.)
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12
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Xing X, Chen Z, Hou Y, Yuan Y. Gradient modulated contrastive distillation of low-rank multi-modal knowledge for disease diagnosis. Med Image Anal 2023; 88:102874. [PMID: 37423056 DOI: 10.1016/j.media.2023.102874] [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: 06/15/2022] [Revised: 01/09/2023] [Accepted: 06/12/2023] [Indexed: 07/11/2023]
Abstract
The fusion of multi-modal data, e.g., medical images and genomic profiles, can provide complementary information and further benefit disease diagnosis. However, multi-modal disease diagnosis confronts two challenges: (1) how to produce discriminative multi-modal representations by exploiting complementary information while avoiding noisy features from different modalities. (2) how to obtain an accurate diagnosis when only a single modality is available in real clinical scenarios. To tackle these two issues, we present a two-stage disease diagnostic framework. In the first multi-modal learning stage, we propose a novel Momentum-enriched Multi-Modal Low-Rank (M3LR) constraint to explore the high-order correlations and complementary information among different modalities, thus yielding more accurate multi-modal diagnosis. In the second stage, the privileged knowledge of the multi-modal teacher is transferred to the unimodal student via our proposed Discrepancy Supervised Contrastive Distillation (DSCD) and Gradient-guided Knowledge Modulation (GKM) modules, which benefit the unimodal-based diagnosis. We have validated our approach on two tasks: (i) glioma grading based on pathology slides and genomic data, and (ii) skin lesion classification based on dermoscopy and clinical images. Experimental results on both tasks demonstrate that our proposed method consistently outperforms existing approaches in both multi-modal and unimodal diagnoses.
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Affiliation(s)
- Xiaohan Xing
- Department of Electronic Engineering, The Chinese University of Hong Kong, Hong Kong Special Administrative Region of China
| | - Zhen Chen
- Department of Electronic Engineering, The Chinese University of Hong Kong, Hong Kong Special Administrative Region of China
| | - Yuenan Hou
- Shanghai Artificial Intelligence Laboratory, Shanghai, China
| | - Yixuan Yuan
- Department of Electronic Engineering, The Chinese University of Hong Kong, Hong Kong Special Administrative Region of China.
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13
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Jaramillo-Rangel G, Chávez-Briones MDL, Ancer-Arellano A, Miranda-Maldonado I, Ortega-Martínez M. Back to the Basics: Usefulness of Naturally Aged Mouse Models and Immunohistochemical and Quantitative Morphologic Methods in Studying Mechanisms of Lung Aging and Associated Diseases. Biomedicines 2023; 11:2075. [PMID: 37509714 PMCID: PMC10377355 DOI: 10.3390/biomedicines11072075] [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: 04/29/2023] [Revised: 06/17/2023] [Accepted: 07/19/2023] [Indexed: 07/30/2023] Open
Abstract
Aging-related molecular and cellular alterations in the lung contribute to an increased susceptibility of the elderly to devastating diseases. Although the study of the aging process in the lung may benefit from the use of genetically modified mouse models and omics techniques, these approaches are still not available to most researchers and produce complex results. In this article, we review works that used naturally aged mouse models, together with immunohistochemistry (IHC) and quantitative morphologic (QM) methods in the study of the mechanisms of the aging process in the lung and its most commonly associated disorders: cancer, chronic obstructive pulmonary disease (COPD), and infectious diseases. The advantage of using naturally aged mice is that they present characteristics similar to those observed in human aging. The advantage of using IHC and QM methods lies in their simplicity, economic accessibility, and easy interpretation, in addition to the fact that they provide extremely important information. The study of the aging process in the lung and its associated diseases could allow the design of appropriate therapeutic strategies, which is extremely important considering that life expectancy and the number of elderly people continue to increase considerably worldwide.
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Affiliation(s)
- Gilberto Jaramillo-Rangel
- Department of Pathology, School of Medicine, Autonomous University of Nuevo León, Monterrey 64460, Mexico
| | | | - Adriana Ancer-Arellano
- Department of Pathology, School of Medicine, Autonomous University of Nuevo León, Monterrey 64460, Mexico
| | - Ivett Miranda-Maldonado
- Department of Pathology, School of Medicine, Autonomous University of Nuevo León, Monterrey 64460, Mexico
| | - Marta Ortega-Martínez
- Department of Pathology, School of Medicine, Autonomous University of Nuevo León, Monterrey 64460, Mexico
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14
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Toseef M, Olayemi Petinrin O, Wang F, Rahaman S, Liu Z, Li X, Wong KC. Deep transfer learning for clinical decision-making based on high-throughput data: comprehensive survey with benchmark results. Brief Bioinform 2023:bbad254. [PMID: 37455245 DOI: 10.1093/bib/bbad254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 06/04/2023] [Accepted: 06/20/2023] [Indexed: 07/18/2023] Open
Abstract
The rapid growth of omics-based data has revolutionized biomedical research and precision medicine, allowing machine learning models to be developed for cutting-edge performance. However, despite the wealth of high-throughput data available, the performance of these models is hindered by the lack of sufficient training data, particularly in clinical research (in vivo experiments). As a result, translating this knowledge into clinical practice, such as predicting drug responses, remains a challenging task. Transfer learning is a promising tool that bridges the gap between data domains by transferring knowledge from the source to the target domain. Researchers have proposed transfer learning to predict clinical outcomes by leveraging pre-clinical data (mouse, zebrafish), highlighting its vast potential. In this work, we present a comprehensive literature review of deep transfer learning methods for health informatics and clinical decision-making, focusing on high-throughput molecular data. Previous reviews mostly covered image-based transfer learning works, while we present a more detailed analysis of transfer learning papers. Furthermore, we evaluated original studies based on different evaluation settings across cross-validations, data splits and model architectures. The result shows that those transfer learning methods have great potential; high-throughput sequencing data and state-of-the-art deep learning models lead to significant insights and conclusions. Additionally, we explored various datasets in transfer learning papers with statistics and visualization.
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Affiliation(s)
- Muhammad Toseef
- Department of Computer Science, City University of Hong Kong, Hong Kong SAR
| | | | - Fuzhou Wang
- Department of Computer Science, City University of Hong Kong, Hong Kong SAR
| | - Saifur Rahaman
- Department of Computer Science, City University of Hong Kong, Hong Kong SAR
| | - Zhe Liu
- Department of Computer Science, City University of Hong Kong, Hong Kong SAR
| | - Xiangtao Li
- School of Artificial Intelligence, Jilin University, Jilin, China
| | - Ka-Chun Wong
- Department of Computer Science, City University of Hong Kong, Hong Kong SAR
- Hong Kong Institute for Data Science, City University of Hong Kong, Hong Kong SAR
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15
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Creydt M, Fischer M. Artefact Profiling: Panomics Approaches for Understanding the Materiality of Written Artefacts. Molecules 2023; 28:4872. [PMID: 37375427 DOI: 10.3390/molecules28124872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 06/15/2023] [Accepted: 06/18/2023] [Indexed: 06/29/2023] Open
Abstract
This review explains the strategies behind genomics, proteomics, metabolomics, metallomics and isotopolomics approaches and their applicability to written artefacts. The respective sub-chapters give an insight into the analytical procedure and the conclusions drawn from such analyses. A distinction is made between information that can be obtained from the materials used in the respective manuscript and meta-information that cannot be obtained from the manuscript itself, but from residues of organisms such as bacteria or the authors and readers. In addition, various sampling techniques are discussed in particular, which pose a special challenge in manuscripts. The focus is on high-resolution, non-targeted strategies that can be used to extract the maximum amount of information about ancient objects. The combination of the various omics disciplines (panomics) especially offers potential added value in terms of the best possible interpretations of the data received. The information obtained can be used to understand the production of ancient artefacts, to gain impressions of former living conditions, to prove their authenticity, to assess whether there is a toxic hazard in handling the manuscripts, and to be able to determine appropriate measures for their conservation and restoration.
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Affiliation(s)
- Marina Creydt
- Institute of Food Chemistry, Hamburg School of Food Science, University of Hamburg, Grindelallee 117, 20146 Hamburg, Germany
- Cluster of Excellence, Understanding Written Artefacts, University of Hamburg, Warburgstraße 26, 20354 Hamburg, Germany
| | - Markus Fischer
- Institute of Food Chemistry, Hamburg School of Food Science, University of Hamburg, Grindelallee 117, 20146 Hamburg, Germany
- Cluster of Excellence, Understanding Written Artefacts, University of Hamburg, Warburgstraße 26, 20354 Hamburg, Germany
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16
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Safarlou CW, Jongsma KR, Vermeulen R, Bredenoord AL. The ethical aspects of exposome research: a systematic review. EXPOSOME 2023; 3:osad004. [PMID: 37745046 PMCID: PMC7615114 DOI: 10.1093/exposome/osad004] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
In recent years, exposome research has been put forward as the next frontier for the study of human health and disease. Exposome research entails the analysis of the totality of environmental exposures and their corresponding biological responses within the human body. Increasingly, this is operationalized by big-data approaches to map the effects of internal as well as external exposures using smart sensors and multiomics technologies. However, the ethical implications of exposome research are still only rarely discussed in the literature. Therefore, we conducted a systematic review of the academic literature regarding both the exposome and underlying research fields and approaches, to map the ethical aspects that are relevant to exposome research. We identify five ethical themes that are prominent in ethics discussions: the goals of exposome research, its standards, its tools, how it relates to study participants, and the consequences of its products. Furthermore, we provide a number of general principles for how future ethics research can best make use of our comprehensive overview of the ethical aspects of exposome research. Lastly, we highlight three aspects of exposome research that are most in need of ethical reflection: the actionability of its findings, the epidemiological or clinical norms applicable to exposome research, and the meaning and action-implications of bias.
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Affiliation(s)
- Caspar W. Safarlou
- Department of Global Public Health and Bioethics, Julius Center for
Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, The
Netherlands
| | - Karin R. Jongsma
- Department of Global Public Health and Bioethics, Julius Center for
Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, The
Netherlands
| | - Roel Vermeulen
- Department of Global Public Health and Bioethics, Julius Center for
Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, The
Netherlands
- Department of Population Health Sciences, Utrecht University,
Utrecht, The Netherlands
| | - Annelien L. Bredenoord
- Department of Global Public Health and Bioethics, Julius Center for
Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, The
Netherlands
- Erasmus School of Philosophy, Erasmus University Rotterdam,
Rotterdam, The Netherlands
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17
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Zaid A, Hassan NH, Marriott PJ, Wong YF. Comprehensive Two-Dimensional Gas Chromatography as a Bioanalytical Platform for Drug Discovery and Analysis. Pharmaceutics 2023; 15:pharmaceutics15041121. [PMID: 37111606 PMCID: PMC10140985 DOI: 10.3390/pharmaceutics15041121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 03/26/2023] [Accepted: 03/27/2023] [Indexed: 04/05/2023] Open
Abstract
Over the last decades, comprehensive two-dimensional gas chromatography (GC×GC) has emerged as a significant separation tool for high-resolution analysis of disease-associated metabolites and pharmaceutically relevant molecules. This review highlights recent advances of GC×GC with different detection modalities for drug discovery and analysis, which ideally improve the screening and identification of disease biomarkers, as well as monitoring of therapeutic responses to treatment in complex biological matrixes. Selected recent GC×GC applications that focus on such biomarkers and metabolite profiling of the effects of drug administration are covered. In particular, the technical overview of recent GC×GC implementation with hyphenation to the key mass spectrometry (MS) technologies that provide the benefit of enhanced separation dimension analysis with MS domain differentiation is discussed. We conclude by highlighting the challenges in GC×GC for drug discovery and development with perspectives on future trends.
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Affiliation(s)
- Atiqah Zaid
- Centre for Research on Multidimensional Separation Science, School of Chemical Sciences, Universiti Sains Malaysia, Penang 11800, Malaysia
| | - Norfarizah Hanim Hassan
- Centre for Research on Multidimensional Separation Science, School of Chemical Sciences, Universiti Sains Malaysia, Penang 11800, Malaysia
| | - Philip J. Marriott
- Australian Centre for Research on Separation Science, School of Chemistry, Monash University, Wellington Road, Clayton, Melbourne, VIC 3800, Australia
| | - Yong Foo Wong
- Centre for Research on Multidimensional Separation Science, School of Chemical Sciences, Universiti Sains Malaysia, Penang 11800, Malaysia
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18
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Using Artificial Intelligence to Better Predict and Develop Biomarkers. Clin Lab Med 2023; 43:99-114. [PMID: 36764811 DOI: 10.1016/j.cll.2022.09.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
Advancements in technology have improved biomarker discovery in the field of heart failure (HF). What was once a slow and laborious process has gained efficiency through use of high-throughput omics platforms to phenotype HF at the level of genes, transcripts, proteins, and metabolites. Furthermore, improvements in artificial intelligence (AI) have made the interpretation of large omics data sets easier and improved analysis. Use of omics and AI in biomarker discovery can aid clinicians by identifying markers of risk for developing HF, monitoring care, determining prognosis, and developing druggable targets. Combined, AI has the power to improve HF patient care.
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19
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Moreno E, Ron R, Serrano-Villar S. The microbiota as a modulator of mucosal inflammation and HIV/HPV pathogenesis: From association to causation. Front Immunol 2023; 14:1072655. [PMID: 36756132 PMCID: PMC9900135 DOI: 10.3389/fimmu.2023.1072655] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 01/06/2023] [Indexed: 01/24/2023] Open
Abstract
Although the microbiota has largely been associated with the pathogenesis of viral infections, most studies using omics techniques are correlational and hypothesis-generating. The mechanisms affecting the immune responses to viral infections are still being fully understood. Here we focus on the two most important sexually transmitted persistent viruses, HPV and HIV. Sophisticated omics techniques are boosting our ability to understand microbiota-pathogen-host interactions from a functional perspective by surveying the host and bacterial protein and metabolite production using systems biology approaches. However, while these strategies have allowed describing interaction networks to identify potential novel microbiota-associated biomarkers or therapeutic targets to prevent or treat infectious diseases, the analyses are typically based on highly dimensional datasets -thousands of features in small cohorts of patients-. As a result, we are far from getting to their clinical use. Here we provide a broad overview of how the microbiota influences the immune responses to HIV and HPV disease. Furthermore, we highlight experimental approaches to understand better the microbiota-host-virus interactions that might increase our potential to identify biomarkers and therapeutic agents with clinical applications.
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Affiliation(s)
- Elena Moreno
- Department of Infectious Diseases, Hospital Universitario Ramón y Cajal, Facultad de Medicina, Universidad de Alcalá, IRYCIS, Madrid, Spain.,CIBERINFEC, Instituto de Salud Carlos III, Madrid, Spain
| | - Raquel Ron
- Department of Infectious Diseases, Hospital Universitario Ramón y Cajal, Facultad de Medicina, Universidad de Alcalá, IRYCIS, Madrid, Spain.,CIBERINFEC, Instituto de Salud Carlos III, Madrid, Spain
| | - Sergio Serrano-Villar
- Department of Infectious Diseases, Hospital Universitario Ramón y Cajal, Facultad de Medicina, Universidad de Alcalá, IRYCIS, Madrid, Spain.,CIBERINFEC, Instituto de Salud Carlos III, Madrid, Spain
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20
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Bessa LJ, Botelho J, Machado V, Alves R, Mendes JJ. Managing Oral Health in the Context of Antimicrobial Resistance. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph192416448. [PMID: 36554332 PMCID: PMC9778414 DOI: 10.3390/ijerph192416448] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 12/05/2022] [Accepted: 12/05/2022] [Indexed: 05/25/2023]
Abstract
The oral microbiome plays a major role in shaping oral health/disease state; thus, a main challenge for dental practitioners is to preserve or restore a balanced oral microbiome. Nonetheless, when pathogenic microorganisms install in the oral cavity and are incorporated into the oral biofilm, oral infections, such as gingivitis, dental caries, periodontitis, and peri-implantitis, can arise. Several prophylactic and treatment approaches are available nowadays, but most of them have been antibiotic-based. Given the actual context of antimicrobial resistance (AMR), antibiotic stewardship in dentistry would be a beneficial approach to optimize and avoid inappropriate or even unnecessary antibiotic use, representing a step towards precision medicine. Furthermore, the development of new effective treatment options to replace the need for antibiotics is being pursued, including the application of photodynamic therapy and the use of probiotics. In this review, we highlight the advances undergoing towards a better understanding of the oral microbiome and oral resistome. We also provide an updated overview of how dentists are adapting to better manage the treatment of oral infections given the problem of AMR.
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Affiliation(s)
- Lucinda J. Bessa
- Centro de Investigação Interdisciplinar Egas Moniz (CiiEM), Egas Moniz—Cooperativa de Ensino Superior, Caparica, 2829-511 Almada, Portugal
| | - João Botelho
- Centro de Investigação Interdisciplinar Egas Moniz (CiiEM), Egas Moniz—Cooperativa de Ensino Superior, Caparica, 2829-511 Almada, Portugal
- Clinical Research Unit (CRU), CiiEM, Egas Moniz—Cooperativa de Ensino Superior, Caparica, 2829-511 Almada, Portugal
- Evidence-Based Hub, CiiEM, Egas Moniz—Cooperativa de Ensino Superior, Caparica, 2829-511 Almada, Portugal
| | - Vanessa Machado
- Centro de Investigação Interdisciplinar Egas Moniz (CiiEM), Egas Moniz—Cooperativa de Ensino Superior, Caparica, 2829-511 Almada, Portugal
- Clinical Research Unit (CRU), CiiEM, Egas Moniz—Cooperativa de Ensino Superior, Caparica, 2829-511 Almada, Portugal
- Evidence-Based Hub, CiiEM, Egas Moniz—Cooperativa de Ensino Superior, Caparica, 2829-511 Almada, Portugal
| | - Ricardo Alves
- Centro de Investigação Interdisciplinar Egas Moniz (CiiEM), Egas Moniz—Cooperativa de Ensino Superior, Caparica, 2829-511 Almada, Portugal
- Clinical Research Unit (CRU), CiiEM, Egas Moniz—Cooperativa de Ensino Superior, Caparica, 2829-511 Almada, Portugal
| | - José João Mendes
- Centro de Investigação Interdisciplinar Egas Moniz (CiiEM), Egas Moniz—Cooperativa de Ensino Superior, Caparica, 2829-511 Almada, Portugal
- Clinical Research Unit (CRU), CiiEM, Egas Moniz—Cooperativa de Ensino Superior, Caparica, 2829-511 Almada, Portugal
- Evidence-Based Hub, CiiEM, Egas Moniz—Cooperativa de Ensino Superior, Caparica, 2829-511 Almada, Portugal
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21
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Shokhirev MN, Johnson AA. An integrative machine-learning meta-analysis of high-throughput omics data identifies age-specific hallmarks of Alzheimer's disease. Ageing Res Rev 2022; 81:101721. [PMID: 36029998 DOI: 10.1016/j.arr.2022.101721] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 07/15/2022] [Accepted: 08/19/2022] [Indexed: 02/06/2023]
Abstract
Alzheimer's disease (AD) is an incredibly complex and presently incurable age-related brain disorder. To better understand this debilitating disease, we collated and performed a meta-analysis on publicly available RNA-Seq, microarray, proteomics, and microRNA samples derived from AD patients and non-AD controls. 4089 samples originating from brain tissues and blood remained after applying quality filters. Since disease progression in AD correlates with age, we stratified this large dataset into three different age groups: < 75 years, 75-84 years, and ≥ 85 years. The RNA-Seq, microarray, and proteomics datasets were then combined into different integrated datasets. Ensemble machine learning was employed to identify genes and proteins that can accurately classify samples as either AD or control. These predictive inputs were then subjected to network-based enrichment analyses. The ability of genes/proteins associated with different pathways in the Molecular Signatures Database to diagnose AD was also tested. We separately identified microRNAs that can be used to make an AD diagnosis and subjected the predicted gene targets of the most predictive microRNAs to an enrichment analysis. The following key themes emerged from our machine learning and bioinformatics analyses: cell death, cellular senescence, energy metabolism, genomic integrity, glia, immune system, metal ion homeostasis, oxidative stress, proteostasis, and synaptic function. Many of the results demonstrated unique age-specificity. For example, terms highlighting cellular senescence only emerged in the earliest and intermediate age ranges while the majority of results relevant to cell death appeared in the youngest patients. Existing literature corroborates the importance of these hallmarks in AD.
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Affiliation(s)
- Maxim N Shokhirev
- Razavi Newman Integrative Genomics and Bioinformatics Core, Salk Institute for Biological Studies, La Jolla, CA, USA.
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22
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Moreira A, Jain P. Genomics and Pediatric Sepsis. Pediatr Ann 2022; 51:e387-e389. [PMID: 36215090 DOI: 10.3928/19382359-20220803-04] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/13/2023]
Abstract
Sepsis is a clinical syndrome manifested by a dysregulation of the immune system triggered by an infection. The severity of illness is variable, which can include mild symptoms with no organ dysfunction to severe symptoms and multiorgan failure, eventually leading to death. Advances in bioinformatics have elucidated distinct sepsis endotypes and have allowed for a better understanding of the pathophysiologic mechanisms. As we learn more about these sepsis endotypes, more precise therapies will emerge for use as adjuncts to antibiotics. [Pediatr Ann. 2022;51(10):e387-e389.].
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23
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Radzikowska U, Baerenfaller K, Cornejo‐Garcia JA, Karaaslan C, Barletta E, Sarac BE, Zhakparov D, Villaseñor A, Eguiluz‐Gracia I, Mayorga C, Sokolowska M, Barbas C, Barber D, Ollert M, Chivato T, Agache I, Escribese MM. Omics technologies in allergy and asthma research: An EAACI position paper. Allergy 2022; 77:2888-2908. [PMID: 35713644 PMCID: PMC9796060 DOI: 10.1111/all.15412] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 05/30/2022] [Accepted: 06/06/2022] [Indexed: 01/27/2023]
Abstract
Allergic diseases and asthma are heterogenous chronic inflammatory conditions with several distinct complex endotypes. Both environmental and genetic factors can influence the development and progression of allergy. Complex pathogenetic pathways observed in allergic disorders present a challenge in patient management and successful targeted treatment strategies. The increasing availability of high-throughput omics technologies, such as genomics, epigenomics, transcriptomics, proteomics, and metabolomics allows studying biochemical systems and pathophysiological processes underlying allergic responses. Additionally, omics techniques present clinical applicability by functional identification and validation of biomarkers. Therefore, finding molecules or patterns characteristic for distinct immune-inflammatory endotypes, can subsequently influence its development, progression, and treatment. There is a great potential to further increase the effectiveness of single omics approaches by integrating them with other omics, and nonomics data. Systems biology aims to simultaneously and longitudinally understand multiple layers of a complex and multifactorial disease, such as allergy, or asthma by integrating several, separated data sets and generating a complete molecular profile of the condition. With the use of sophisticated biostatistics and machine learning techniques, these approaches provide in-depth insight into individual biological systems and will allow efficient and customized healthcare approaches, called precision medicine. In this EAACI Position Paper, the Task Force "Omics technologies in allergic research" broadly reviewed current advances and applicability of omics techniques in allergic diseases and asthma research, with a focus on methodology and data analysis, aiming to provide researchers (basic and clinical) with a desk reference in the field. The potential of omics strategies in understanding disease pathophysiology and key tools to reach unmet needs in allergy precision medicine, such as successful patients' stratification, accurate disease prognosis, and prediction of treatment efficacy and successful prevention measures are highlighted.
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Affiliation(s)
- Urszula Radzikowska
- Swiss Institute of Allergy and Asthma Research (SIAF)University of ZurichDavosSwitzerland,Christine‐Kühne Center for Allergy Research and Education (CK‐CARE)DavosSwitzerland
| | - Katja Baerenfaller
- Swiss Institute of Allergy and Asthma Research (SIAF)University of ZurichDavosSwitzerland,Swiss Institute of Bioinformatics (SIB)DavosSwitzerland
| | - José Antonio Cornejo‐Garcia
- Research LaboratoryIBIMA, ARADyAL Instituto de Salud Carlos III, Regional University Hospital of Málaga, UMAMálagaSpain
| | - Cagatay Karaaslan
- Department of Biology, Molecular Biology SectionFaculty of ScienceHacettepe UniversityAnkaraTurkey
| | - Elena Barletta
- Swiss Institute of Allergy and Asthma Research (SIAF)University of ZurichDavosSwitzerland,Swiss Institute of Bioinformatics (SIB)DavosSwitzerland
| | - Basak Ezgi Sarac
- Department of Biology, Molecular Biology SectionFaculty of ScienceHacettepe UniversityAnkaraTurkey
| | - Damir Zhakparov
- Swiss Institute of Allergy and Asthma Research (SIAF)University of ZurichDavosSwitzerland,Swiss Institute of Bioinformatics (SIB)DavosSwitzerland
| | - Alma Villaseñor
- Centre for Metabolomics and Bioanalysis (CEMBIO)Department of Chemistry and BiochemistryFacultad de FarmaciaUniversidad San Pablo‐CEU, CEU UniversitiesMadridSpain,Institute of Applied Molecular Medicine Nemesio Diaz (IMMAND)Department of Basic Medical SciencesFacultad de MedicinaUniversidad San Pablo CEU, CEU UniversitiesMadridSpain
| | - Ibon Eguiluz‐Gracia
- Allergy UnitHospital Regional Universitario de MálagaMálagaSpain,Allergy Research GroupInstituto de Investigación Biomédica de Málaga‐IBIMAMálagaSpain
| | - Cristobalina Mayorga
- Allergy UnitHospital Regional Universitario de MálagaMálagaSpain,Allergy Research GroupInstituto de Investigación Biomédica de Málaga‐IBIMAMálagaSpain,Andalusian Centre for Nanomedicine and Biotechnology – BIONANDMálagaSpain
| | - Milena Sokolowska
- Swiss Institute of Allergy and Asthma Research (SIAF)University of ZurichDavosSwitzerland,Christine‐Kühne Center for Allergy Research and Education (CK‐CARE)DavosSwitzerland
| | - Coral Barbas
- Centre for Metabolomics and Bioanalysis (CEMBIO)Department of Chemistry and BiochemistryFacultad de FarmaciaUniversidad San Pablo‐CEU, CEU UniversitiesMadridSpain
| | - Domingo Barber
- Institute of Applied Molecular Medicine Nemesio Diaz (IMMAND)Department of Basic Medical SciencesFacultad de MedicinaUniversidad San Pablo CEU, CEU UniversitiesMadridSpain
| | - Markus Ollert
- Department of Infection and ImmunityLuxembourg Institute of HealthyEsch‐sur‐AlzetteLuxembourg,Department of Dermatology and Allergy CenterOdense Research Center for AnaphylaxisOdense University Hospital, University of Southern DenmarkOdenseDenmark
| | - Tomas Chivato
- Institute of Applied Molecular Medicine Nemesio Diaz (IMMAND)Department of Basic Medical SciencesFacultad de MedicinaUniversidad San Pablo CEU, CEU UniversitiesMadridSpain,Department of Clinic Medical SciencesFacultad de MedicinaUniversidad San Pablo CEU, CEU UniversitiesMadridSpain
| | | | - Maria M. Escribese
- Institute of Applied Molecular Medicine Nemesio Diaz (IMMAND)Department of Basic Medical SciencesFacultad de MedicinaUniversidad San Pablo CEU, CEU UniversitiesMadridSpain
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Cintron SA, Shen Q, Mahoney D, Sardiu ME, Hiebert JB, Pierce J. Obesity-Related High-Output Heart Failure: An Integrative Review. J Cardiovasc Nurs 2022; 38:00005082-990000000-00041. [PMID: 36178329 DOI: 10.1097/jcn.0000000000000939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
BACKGROUND High-output heart failure (HF) is a type of HF characterized by signs and symptoms of HF and a cardiac output of 8 L/min or greater or a cardiac index greater than 3.9 L/min/m 2 . High-output HF occurs secondary to an underlying condition that requires high cardiac output due to an increase in oxygen consumption or decreased systemic vascular resistance. Obesity is a major cause of high-output HF, yet there is limited research on obesity-related high-output HF. Thus, the pathophysiologic mechanisms of this syndrome are not fully understood. OBJECTIVE The objectives of this integrative review were to describe the current state of the research regarding obesity-related high-output HF and to recommend direction for future research. METHODS We conducted an integrative review focusing on the peer-reviewed literature on patients with obesity-related high-output HF using Whittemore and Knafl's methodology. MEDLINE, CINAHL, and EMBASE electronic databases were searched for all publications indexed in the databases as of March 9, 2022. A narrative synthesis of definitions and symptoms, obesity as an underlying condition, pathophysiology, and treatments of obesity-related high-output HF was completed. RESULTS A total of 6 articles were included in the integrative review, with 1 nonexperimental, retrospective study and 5 literature reviews. Understanding of obesity-related high-output HF is very limited because of scant empirical evidence in the existing literature. Possible pathophysiologic mechanisms include increased pressure in the upper airways, adipokine dysregulation, increased metabolic activity, and insulin resistance. CONCLUSION Additional research is needed on the pathophysiologic mechanisms of obesity-related high-output HF to begin investigations on therapeutic interventions to improve health outcomes.
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Boys EL, Liu J, Robinson PJ, Reddel RR. Clinical applications of mass spectrometry-based proteomics in cancer: where are we? Proteomics 2022; 23:e2200238. [PMID: 35968695 DOI: 10.1002/pmic.202200238] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 08/07/2022] [Accepted: 08/09/2022] [Indexed: 11/12/2022]
Abstract
Tumor tissue processing methodologies in combination with data-independent acquisition mass spectrometry (DIA-MS) have emerged that can comprehensively analyze the proteome of multiple tumor samples accurately and reproducibly. Increasing recognition and adoption of these technologies has resulted in a tranche of studies providing novel insights into cancer classification systems, functional tumor biology, cancer biomarkers, treatment response and drug targets. Despite this, with some limited exceptions, MS-based proteomics has not yet been implemented in routine cancer clinical practice. Here, we summarize the use of DIA-MS in studies that may pave the way for future clinical cancer applications, and highlight the role of alternative MS technologies and multi-omic strategies. We discuss limitations and challenges of studies in this field to date and propose steps for integrating proteomic data into the cancer clinic. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Emma L Boys
- ProCan®, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW, Australia
| | - Jia Liu
- ProCan®, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW, Australia.,The Kinghorn Cancer Centre, St Vincent's Hospital, Darlinghurst, NSW, Australia.,School of Clinical Medicine, St Vincent's Campus, University of New South Wales, Sydney, NSW, Australia
| | - Phillip J Robinson
- ProCan®, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW, Australia
| | - Roger R Reddel
- ProCan®, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW, Australia
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26
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Goossens E, Dehau T, Ducatelle R, Van Immerseel F. Omics technologies in poultry health and productivity - part 2: future applications in the poultry industry. Avian Pathol 2022; 51:418-423. [PMID: 35675218 DOI: 10.1080/03079457.2022.2085545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
The increasing global demand for poultry products, together with the growing consumer concerns related to bird health and welfare, pose a significant challenge to the poultry industry. Therefore, the poultry industry is increasingly implementing novel technologies to optimize and enhance bird welfare and productivity. This second part of a bipartite review on omics technologies in poultry health and productivity highlights the implementation of specific diagnostic biomarkers based on omics-research in the poultry industry, as well as the potential integration of multi-omics in future poultry production. A general discussion of the use of multiple omics technologies in poultry research is provided in part 1. To date, approaches focusing on one or more omics type are widely used in poultry research, but the implementation of these omics techniques in poultry production is not expected in the near future. However, great potential lays in the development of diagnostic tests based on disease- or gut health-specific biomarkers, which are identified through omics research. As the cost of omics technologies is rapidly decreasing, implementation of multi-omics measurements in routine poultry monitoring systems might be feasible in the more distant future. Therefore, the opportunities, challenges and requirements to enable the integration of multi-omics-based monitoring of bird health and productivity in future poultry production are discussed.
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Affiliation(s)
- Evy Goossens
- Livestock Gut Health Team (LiGHT) Ghent, Department of Pathobiology, Pharmacology and Zoological Medicine, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Tessa Dehau
- Livestock Gut Health Team (LiGHT) Ghent, Department of Pathobiology, Pharmacology and Zoological Medicine, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Richard Ducatelle
- Livestock Gut Health Team (LiGHT) Ghent, Department of Pathobiology, Pharmacology and Zoological Medicine, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Filip Van Immerseel
- Livestock Gut Health Team (LiGHT) Ghent, Department of Pathobiology, Pharmacology and Zoological Medicine, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
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27
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Zhao J, Li Q. Big Data-Artificial Intelligence Fusion Technology in Education in the Context of the New Crown Epidemic. BIG DATA 2022; 10:262-276. [PMID: 35605025 DOI: 10.1089/big.2021.0245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
This article presents an in-depth study and analysis of the application of big data-artificial intelligence fusion technology to the field of education in the context of the New Crown epidemic. Since the outbreak of the New Crown epidemic, there is a need to understand the channels for solving the demands of productive life during the epidemic, and the main way to solve these problems is to apply the Internet, big data, and artificial intelligence. Therefore, exploring the application of big data-artificial intelligence fusion technology in education in the context of the New Crest pneumonia epidemic is a top priority for reform and development nowadays. This study uses the paradigm narrow shift analysis framework to verify whether Computer Aided Instructional design, multimedia instructional design, and informational instructional design produce migration. For the intelligent stage of instructional design, the inevitability of the change in basic assumptions of instructional design in the context of artificial intelligence (AI) is first explained in terms of the opportunities brought by AI to education and teaching, the problems of the original information-based instructional design itself, and the many challenges it faces. On this basis, we also use the change in basic assumptions analysis framework to explain the content of intelligent instructional design by using the four elements of beliefs, values, symbols, and paradigms promised by the members of the community, verify that it has shifted, and build a change in the basic assumptions model from multimedia instructional design to information-based instructional design to intelligent instructional design. The article gives three countermeasures to solve the problem, that is, raising awareness, improving the plan, and strengthening the drill. To ensure the smooth implementation of the emergency management of national covid control program (NCCP), higher education institutions should further strengthen the construction efforts of specialized psychological counseling teams, build an early warning mechanism for psychological problems of the NCCP epidemic in higher education institutions, and a multilevel supervision system.
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Affiliation(s)
- JunJing Zhao
- School of Economics and Finance, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Qi Li
- School of Economics and Finance, Xi'an Jiaotong University, Xi'an, Shaanxi, China
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28
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Esmaeili N, Carter CG, Wilson R, Walker SP, Miller MR, Bridle AR, Symonds JE. Protein metabolism in the liver and white muscle is associated with feed efficiency in Chinook salmon (Oncorhynchus tshawytscha) reared in seawater: Evidence from proteomic analysis. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2022; 42:100994. [PMID: 35533546 DOI: 10.1016/j.cbd.2022.100994] [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: 02/03/2022] [Revised: 04/24/2022] [Accepted: 04/26/2022] [Indexed: 06/13/2023]
Abstract
Understanding the molecular mechanisms that underlie differences in feed efficiency (FE) is an important step toward optimising growth and achieving sustainable salmonid aquaculture. In this study, the liver and white muscle proteomes of feed efficient (EFF) and inefficient (INEFF) Chinook salmon (Oncorhynchus tshawytscha) reared in seawater were investigated by liquid chromatography-tandem mass spectrometry (LC-MS/MS). In total, 2746 liver and 702 white muscle proteins were quantified and compared between 21 EFF and 22 INEFF fish. GSEA showed that gene sets related to protein synthesis were enriched in the liver and white muscle of the EFF group, while conversely, pathways related to protein degradation (amino acid catabolism and proteolysis, respectively) were the most affected processes in the liver and white muscle of INEFF fish. Estimates of individual daily feed intake and share of the meal within tank were significantly higher in the INEFF than the EFF fish showing INEFF fish were likely more dominant during feeding and overfed. Overeating by the INEFF fish was associated with an increase in protein catabolism. This study found that fish with different FE values had expression differences in the gene sets related to protein turnover, and this result supports the hypothesis that protein metabolism plays a role in FE.
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Affiliation(s)
- Noah Esmaeili
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, Private Bag 49, Australia.
| | - Chris G Carter
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, Private Bag 49, Australia
| | - Richard Wilson
- Central Science Laboratory, Research Division, University of Tasmania, Hobart 7001, Australia
| | | | - Matthew R Miller
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, Private Bag 49, Australia; Cawthron Institute, Nelson 7010, New Zealand
| | - Andrew R Bridle
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, Private Bag 49, Australia
| | - Jane E Symonds
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, Private Bag 49, Australia; Cawthron Institute, Nelson 7010, New Zealand
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Hasanzad M, Sarhangi N, Ehsani Chimeh S, Ayati N, Afzali M, Khatami F, Nikfar S, Aghaei Meybodi HR. Precision medicine journey through omics approach. J Diabetes Metab Disord 2022; 21:881-888. [PMID: 35673436 DOI: 10.1007/s40200-021-00913-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 10/02/2021] [Indexed: 10/19/2022]
Abstract
It has been well established that understanding the underlying heterogeneity of numerous complex disease process needs new strategies that present in precision medicine for prediction, prevention and personalized treatment strategies. This approach must be tailored for each individual's unique omics that lead to personalized management of disease. The correlation between different omics data should be considered in precision medicine approach. The interaction provides a hypothesis which is called domino effect in the present minireview. Here we review the various potentials of omics data including genomics, transcriptomics, proteomics, metabolomics, pharmacogenomics. We comprehensively summarize the impact of omics data and its major role in precision medicine and provide a description about the domino effect on the pathophysiology of diseases. Each constituent of the omics data typically provides different information in associated with disease. Current research, although inadequate, clearly indicate that the information of omics data can be applicable in the concept of precision medicine. Integration of different omics data type in domino effect hypothesis can explain the causative changes of disease as it is discussed in the system biology too. While most existing studies investigate the omics data separately, data integration is needed on the horizon of precision medicine by using machine learning.
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Affiliation(s)
- Mandana Hasanzad
- Medical Genomics Research Center, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran.,Personalized Medicine Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Negar Sarhangi
- Personalized Medicine Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | | | - Nayereh Ayati
- Department of Pharmacoeconomics and Pharmaceutical Administration, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | - Monireh Afzali
- Department of Pharmacoeconomics and Pharmaceutical Administration, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | - Fatemeh Khatami
- Urology Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Shekoufeh Nikfar
- Endocrinology and Metabolism Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Hamid Reza Aghaei Meybodi
- Personalized Medicine Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
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30
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Srivastava N, Sarethy IP, Jeevanandam J, Danquah M. Emerging strategies for microbial screening of novel chemotherapeutics. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.132419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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31
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Kowald A, Barrantes I, Möller S, Palmer D, Murua Escobar H, Schwerk A, Fuellen G. Transfer learning of clinical outcomes from preclinical molecular data, principles and perspectives. Brief Bioinform 2022; 23:6572661. [PMID: 35453145 PMCID: PMC9116218 DOI: 10.1093/bib/bbac133] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Revised: 02/16/2022] [Accepted: 03/21/2022] [Indexed: 01/14/2023] Open
Abstract
Accurate transfer learning of clinical outcomes from one cellular context to another, between cell types, developmental stages, omics modalities or species, is considered tremendously useful. When transferring a prediction task from a source domain to a target domain, what counts is the high quality of the predictions in the target domain, requiring states or processes common to both the source and the target that can be learned by the predictor reflected by shared denominators. These may form a compendium of knowledge that is learned in the source to enable predictions in the target, usually with few, if any, labeled target training samples to learn from. Transductive transfer learning refers to the learning of the predictor in the source domain, transferring its outcome label calculations to the target domain, considering the same task. Inductive transfer learning considers cases where the target predictor is performing a different yet related task as compared with the source predictor. Often, there is also a need to first map the variables in the input/feature spaces and/or the variables in the output/outcome spaces. We here discuss and juxtapose various recently published transfer learning approaches, specifically designed (or at least adaptable) to predict clinical (human in vivo) outcomes based on preclinical (mostly animal-based) molecular data, towards finding the right tool for a given task, and paving the way for a comprehensive and systematic comparison of the suitability and accuracy of transfer learning of clinical outcomes.
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Affiliation(s)
- Axel Kowald
- Institute for Biostatistics and Informatics in Medicine and Ageing Research, Rostock University Medical Center, Rostock, Germany
| | - Israel Barrantes
- Institute for Biostatistics and Informatics in Medicine and Ageing Research, Rostock University Medical Center, Rostock, Germany
| | - Steffen Möller
- Institute for Biostatistics and Informatics in Medicine and Ageing Research, Rostock University Medical Center, Rostock, Germany
| | - Daniel Palmer
- Institute for Biostatistics and Informatics in Medicine and Ageing Research, Rostock University Medical Center, Rostock, Germany
| | - Hugo Murua Escobar
- Department of Medicine, Clinic III, Hematology, Oncology, Palliative Medicine, Rostock University Medical Center, Rostock, Germany
| | | | - Georg Fuellen
- Institute for Biostatistics and Informatics in Medicine and Ageing Research, Rostock University Medical Center, Rostock, Germany.,Centre for Transdisciplinary Neurosciences Rostock, Research Focus Oncology and Ageing of Individuals and Society, Interdisciplinary Faculty, Rostock, Germany
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32
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Michelhaugh SA, Januzzi JL. Using Artificial Intelligence to Better Predict and Develop Biomarkers. Heart Fail Clin 2022; 18:275-285. [PMID: 35341540 DOI: 10.1016/j.hfc.2021.11.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Advancements in technology have improved biomarker discovery in the field of heart failure (HF). What was once a slow and laborious process has gained efficiency through use of high-throughput omics platforms to phenotype HF at the level of genes, transcripts, proteins, and metabolites. Furthermore, improvements in artificial intelligence (AI) have made the interpretation of large omics data sets easier and improved analysis. Use of omics and AI in biomarker discovery can aid clinicians by identifying markers of risk for developing HF, monitoring care, determining prognosis, and developing druggable targets. Combined, AI has the power to improve HF patient care.
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33
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A Web Screening on Training Initiatives in Cancer Genomics for Healthcare Professionals. Genes (Basel) 2022; 13:genes13030430. [PMID: 35327984 PMCID: PMC8950486 DOI: 10.3390/genes13030430] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 02/21/2022] [Accepted: 02/23/2022] [Indexed: 02/05/2023] Open
Abstract
The disruptive advances in genomics contributed to achieve higher levels of precision in the diagnosis and treatment of cancer. This scientific advance entails the need for greater literacy for all healthcare professionals. Our study summarizes the training initiatives conducted worldwide in cancer genomics field for healthcare professionals. We conducted a web search of the training initiatives aimed at improving healthcare professionals’ literacy in cancer genomics undertaken worldwide by using two search engines (Google and Bing) in English language and conducted from 2003 to 2021. A total of 85,649 initiatives were identified. After the screening process, 36 items were included. The majority of training programs were organized in the United States (47%) and in the United Kingdom (28%). Most of the initiatives were conducted in the last five years (83%) by universities (30%) and as web-based modalities (80%). In front of the technological advances in genomics, education in cancer genomics remains fundamental. Our results may contribute to provide an update on the development of educational programs to build a skilled and appropriately trained genomics health workforce in the future.
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34
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Amaral DT, Romeiro-Brito M, Bonatelli IAS. Exploring Phylogenetic Relationships and Divergence Times of Bioluminescent Species Using Genomic and Transcriptomic Data. Methods Mol Biol 2022; 2525:409-423. [PMID: 35836087 DOI: 10.1007/978-1-0716-2473-9_32] [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] [Indexed: 06/15/2023]
Abstract
Next-generation sequencing (NGS) has dominated the scene of genomics and evolutionary biology as a great amount of genomic data have been accumulated for a diverse set of species. At the same time, phylogenetic approaches and programs are in development to allow better use of such large-size datasets. Phylogenomics appears as a promising field to accommodate and explore all the information of NGS data in phylogenetic methods, being an important approach to investigate the evolution of bioluminescence in different organisms. To guarantee accurate results in phylogenomic studies, it is mandatory to correctly identify orthologous genes in phylogenetic reconstruction. Here, we show a simplified step-by-step framework to perform phylogenetic analysis along with divergence time estimation, beginning with an orthologous search. As empirical data, we exemplify transcriptome sequences of six species of the Elateroidea superfamily (Coleoptera). We introduce several bioinformatics tools for handling genomic data, especially those available in the software OrthoFinder, IQTREE, BEAST2, and TreePL.
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Affiliation(s)
- Danilo T Amaral
- Departamento de Biologia, Centro de Ciências Humanas e Biológicas, Universidade Federal de São Carlos (UFSCar), Sorocaba, Brazil.
- Programa de Pós Graduação em Biologia Comparada, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo (USP), Ribeirão Preto, Brazil.
| | - Monique Romeiro-Brito
- Departamento de Biologia, Centro de Ciências Humanas e Biológicas, Universidade Federal de São Carlos (UFSCar), Sorocaba, Brazil
| | - Isabel A S Bonatelli
- Departamento de Ecologia e Biologia Evolutiva, Universidade Federal de São Paulo (UNIFESP), Diadema, São Paulo, Brazil
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35
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Tosadori G, Di Silvestre D, Spoto F, Mauri P, Laudanna C, Scardoni G. Analysing omics data sets with weighted nodes networks (WNNets). Sci Rep 2021; 11:14447. [PMID: 34262093 PMCID: PMC8280138 DOI: 10.1038/s41598-021-93699-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 06/16/2021] [Indexed: 11/30/2022] Open
Abstract
Current trends in biomedical research indicate data integration as a fundamental step towards precision medicine. In this context, network models allow representing and analysing complex biological processes. However, although effective in unveiling network properties, these models fail in considering the individual, biochemical variations occurring at molecular level. As a consequence, the analysis of these models partially loses its predictive power. To overcome these limitations, Weighted Nodes Networks (WNNets) were developed. WNNets allow to easily and effectively weigh nodes using experimental information from multiple conditions. In this study, the characteristics of WNNets were described and a proteomics data set was modelled and analysed. Results suggested that degree, an established centrality index, may offer a novel perspective about the functional role of nodes in WNNets. Indeed, degree allowed retrieving significant differences between experimental conditions, highlighting relevant proteins, and provided a novel interpretation for degree itself, opening new perspectives in experimental data modelling and analysis. Overall, WNNets may be used to model any high-throughput experimental data set requiring weighted nodes. Finally, improving the power of the analysis by using centralities such as betweenness may provide further biological insights and unveil novel, interesting characteristics of WNNets.
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Affiliation(s)
- Gabriele Tosadori
- Center for BioMedical Computing (CBMC), University of Verona, Strada le Grazie 8, 37134, Verona, Italy.
- Section of General Pathology, Department of Medicine, University of Verona, 37134, Verona, Italy.
| | - Dario Di Silvestre
- Institute for Biomedical Technologies, National Research Council (ITB-CNR), via F.lli Cervi 93, Segrate, 20090, Milan, Italy
| | - Fausto Spoto
- Department of Computer Science, University of Verona, Strada le Grazie 15, 37134, Verona, Italy
| | - Pierluigi Mauri
- Institute for Biomedical Technologies, National Research Council (ITB-CNR), via F.lli Cervi 93, Segrate, 20090, Milan, Italy
| | - Carlo Laudanna
- Section of General Pathology, Department of Medicine, University of Verona, 37134, Verona, Italy.
| | - Giovanni Scardoni
- Center for BioMedical Computing (CBMC), University of Verona, Strada le Grazie 8, 37134, Verona, Italy
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36
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Beck LC, Granger CL, Masi AC, Stewart CJ. Use of omic technologies in early life gastrointestinal health and disease: from bench to bedside. Expert Rev Proteomics 2021; 18:247-259. [PMID: 33896313 DOI: 10.1080/14789450.2021.1922278] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Introduction: At birth, the gastrointestinal (GI) tract is colonized by a complex community of microorganisms, forming the basis of the gut microbiome. The gut microbiome plays a fundamental role in host health, disorders of which can lead to an array of GI diseases, both short and long term. Pediatric GI diseases are responsible for significant morbidity and mortality, but many remain poorly understood. Recent advancements in high-throughput technologies have enabled deeper profiling of GI morbidities. Technologies, such as metagenomics, transcriptomics, proteomics and metabolomics, have already been used to identify associations with specific pathologies, and highlight an exciting area of research. However, since these diseases are often complex and multifactorial by nature, reliance on a single experimental approach may not capture the true biological complexity. Therefore, multi-omics aims to integrate singular omic data to further enhance our understanding of disease.Areas covered: This review will discuss and provide an overview of the main omic technologies that are used to study complex GI pathologies in early life.Expert opinion: Multi-omic technologies can help to unravel the complexities of several diseases during early life, aiding in biomarker discovery and enabling the development of novel therapeutics and augment predictive models.
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Affiliation(s)
- Lauren C Beck
- Translational and Clinical Research Institute, Newcastle University, Newcastle Upon Tyne, UK
| | - Claire L Granger
- Translational and Clinical Research Institute, Newcastle University, Newcastle Upon Tyne, UK.,Newcastle Neonatal Service, Newcastle Upon Tyne Hospitals NHS Trust, Newcastle Upon Tyne, UK
| | - Andrea C Masi
- Translational and Clinical Research Institute, Newcastle University, Newcastle Upon Tyne, UK
| | - Christopher J Stewart
- Translational and Clinical Research Institute, Newcastle University, Newcastle Upon Tyne, UK
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37
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Garcia E, Ly N, Diep JK, Rao GG. Moving From Point‐Based Analysis to Systems‐Based Modeling: Integration of Knowledge to Address Antimicrobial Resistance Against MDR Bacteria. Clin Pharmacol Ther 2021; 110:1196-1206. [DOI: 10.1002/cpt.2219] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Accepted: 02/16/2021] [Indexed: 12/28/2022]
Affiliation(s)
- Estefany Garcia
- UNC Eshelman School of Pharmacy University of North Carolina Chapel Hill North Carolina USA
| | | | - John K. Diep
- UNC Eshelman School of Pharmacy University of North Carolina Chapel Hill North Carolina USA
| | - Gauri G. Rao
- UNC Eshelman School of Pharmacy University of North Carolina Chapel Hill North Carolina USA
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Stevanovic M, Drakulic D, Lazic A, Ninkovic DS, Schwirtlich M, Mojsin M. SOX Transcription Factors as Important Regulators of Neuronal and Glial Differentiation During Nervous System Development and Adult Neurogenesis. Front Mol Neurosci 2021; 14:654031. [PMID: 33867936 PMCID: PMC8044450 DOI: 10.3389/fnmol.2021.654031] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 03/11/2021] [Indexed: 12/11/2022] Open
Abstract
The SOX proteins belong to the superfamily of transcription factors (TFs) that display properties of both classical TFs and architectural components of chromatin. Since the cloning of the Sox/SOX genes, remarkable progress has been made in illuminating their roles as key players in the regulation of multiple developmental and physiological processes. SOX TFs govern diverse cellular processes during development, such as maintaining the pluripotency of stem cells, cell proliferation, cell fate decisions/germ layer formation as well as terminal cell differentiation into tissues and organs. However, their roles are not limited to development since SOX proteins influence survival, regeneration, cell death and control homeostasis in adult tissues. This review summarized current knowledge of the roles of SOX proteins in control of central nervous system development. Some SOX TFs suspend neural progenitors in proliferative, stem-like state and prevent their differentiation. SOX proteins function as pioneer factors that occupy silenced target genes and keep them in a poised state for activation at subsequent stages of differentiation. At appropriate stage of development, SOX members that maintain stemness are down-regulated in cells that are competent to differentiate, while other SOX members take over their functions and govern the process of differentiation. Distinct SOX members determine down-stream processes of neuronal and glial differentiation. Thus, sequentially acting SOX TFs orchestrate neural lineage development defining neuronal and glial phenotypes. In line with their crucial roles in the nervous system development, deregulation of specific SOX proteins activities is associated with neurodevelopmental disorders (NDDs). The overview of the current knowledge about the link between SOX gene variants and NDDs is presented. We outline the roles of SOX TFs in adult neurogenesis and brain homeostasis and discuss whether impaired adult neurogenesis, detected in neurodegenerative diseases, could be associated with deregulation of SOX proteins activities. We present the current data regarding the interaction between SOX proteins and signaling pathways and microRNAs that play roles in nervous system development. Finally, future research directions that will improve the knowledge about distinct and various roles of SOX TFs in health and diseases are presented and discussed.
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Affiliation(s)
- Milena Stevanovic
- Laboratory for Human Molecular Genetics, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia.,Faculty of Biology, University of Belgrade, Belgrade, Serbia.,Serbian Academy of Sciences and Arts, Belgrade, Serbia
| | - Danijela Drakulic
- Laboratory for Human Molecular Genetics, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Andrijana Lazic
- Laboratory for Human Molecular Genetics, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Danijela Stanisavljevic Ninkovic
- Laboratory for Human Molecular Genetics, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Marija Schwirtlich
- Laboratory for Human Molecular Genetics, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Marija Mojsin
- Laboratory for Human Molecular Genetics, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
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Borczyk M, Piechota M, Rodriguez Parkitna J, Korostynski M. Prospects for personalization of depression treatment with genome sequencing. Br J Pharmacol 2021; 179:4220-4232. [PMID: 33786859 DOI: 10.1111/bph.15470] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 03/22/2021] [Accepted: 03/24/2021] [Indexed: 12/20/2022] Open
Abstract
The effectiveness of antidepressants in the treatment of major depressive disorder varies considerably between patients. With these interindividual differences and a number of antidepressants to choose from, the first choice of treatment often fails to produce improvement in the patient's condition. A substantial part of the variation in response to antidepressants can be explained by genetic factors. Accordingly, variants related to drug metabolism in two pharmacogenes, CYP2D6 and CYP2C19, have already been translated into guidelines for antidepressant prescriptions. The role of variants in other genes that influence antidepressant responses is not yet understood. Furthermore, rare and individual variants account for a substantial part of genetic differences in antidepressant efficacy. Recent years have brought a tremendous increase in the accessibility of genome sequencing in terms of data availability and its clinical use. In this review, we summarize recent developments and current issues in the personalization of major depressive disorder treatment through pharmacogenomics.
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Affiliation(s)
- Malgorzata Borczyk
- Laboratory of Pharmacogenomics, Department of Molecular Neuropharmacology, Maj Institute of Pharmacology, Polish Academy of Sciences, Kraków, Poland
| | - Marcin Piechota
- Laboratory of Pharmacogenomics, Department of Molecular Neuropharmacology, Maj Institute of Pharmacology, Polish Academy of Sciences, Kraków, Poland
| | - Jan Rodriguez Parkitna
- Laboratory of Pharmacogenomics, Department of Molecular Neuropharmacology, Maj Institute of Pharmacology, Polish Academy of Sciences, Kraków, Poland
| | - Michal Korostynski
- Laboratory of Pharmacogenomics, Department of Molecular Neuropharmacology, Maj Institute of Pharmacology, Polish Academy of Sciences, Kraków, Poland
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Foster S, Luciani F. Omics in immunology. Immunol Cell Biol 2021; 99:133-134. [PMID: 33569833 DOI: 10.1111/imcb.12435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Samuel Foster
- School of Medical Sciences, Kirby Institute, UNSW Sydney, Sydney, NSW, Australia.,Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC, Australia
| | - Fabio Luciani
- School of Medical Sciences, Kirby Institute, UNSW Sydney, Sydney, NSW, Australia.,Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC, Australia
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Amelio I, Bertolo R, Bove P, Buonomo OC, Candi E, Chiocchi M, Cipriani C, Di Daniele N, Ganini C, Juhl H, Mauriello A, Marani C, Marshall J, Montanaro M, Palmieri G, Piacentini M, Sica G, Tesauro M, Rovella V, Tisone G, Shi Y, Wang Y, Melino G. Liquid biopsies and cancer omics. Cell Death Discov 2020; 6:131. [PMID: 33298891 PMCID: PMC7691330 DOI: 10.1038/s41420-020-00373-0] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 11/03/2020] [Accepted: 11/05/2020] [Indexed: 02/06/2023] Open
Abstract
The development of the sequencing technologies allowed the generation of huge amounts of molecular data from a single cancer specimen, allowing the clinical oncology to enter the era of the precision medicine. This massive amount of data is highlighting new details on cancer pathogenesis but still relies on tissue biopsies, which are unable to capture the dynamic nature of cancer through its evolution. This assumption led to the exploration of non-tissue sources of tumoral material opening the field of liquid biopsies. Blood, together with body fluids such as urines, or stool, from cancer patients, are analyzed applying the techniques used for the generation of omics data. With blood, this approach would allow to take into account tumor heterogeneity (since the circulating components such as CTCs, ctDNA, or ECVs derive from each cancer clone) in a time dependent manner, resulting in a somehow "real-time" understanding of cancer evolution. Liquid biopsies are beginning nowdays to be applied in many cancer contexts and are at the basis of many clinical trials in oncology.
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Affiliation(s)
- Ivano Amelio
- Torvergata Oncoscience Research Centre of Excellence, TOR, Department of Experimental Medicine, University of Rome Tor Vergata, 00133, Rome, Italy.
- School of Life Sciences, University of Nottingham, Nottingham, UK.
| | - Riccardo Bertolo
- Torvergata Oncoscience Research Centre of Excellence, TOR, Department of Experimental Medicine, University of Rome Tor Vergata, 00133, Rome, Italy
- San Carlo di Nancy Hospital, Rome, Italy
| | - Pierluigi Bove
- Torvergata Oncoscience Research Centre of Excellence, TOR, Department of Experimental Medicine, University of Rome Tor Vergata, 00133, Rome, Italy
- San Carlo di Nancy Hospital, Rome, Italy
| | - Oreste Claudio Buonomo
- Torvergata Oncoscience Research Centre of Excellence, TOR, Department of Experimental Medicine, University of Rome Tor Vergata, 00133, Rome, Italy
| | - Eleonora Candi
- Torvergata Oncoscience Research Centre of Excellence, TOR, Department of Experimental Medicine, University of Rome Tor Vergata, 00133, Rome, Italy
| | - Marcello Chiocchi
- Torvergata Oncoscience Research Centre of Excellence, TOR, Department of Experimental Medicine, University of Rome Tor Vergata, 00133, Rome, Italy
| | - Chiara Cipriani
- Torvergata Oncoscience Research Centre of Excellence, TOR, Department of Experimental Medicine, University of Rome Tor Vergata, 00133, Rome, Italy
- San Carlo di Nancy Hospital, Rome, Italy
| | - Nicola Di Daniele
- Torvergata Oncoscience Research Centre of Excellence, TOR, Department of Experimental Medicine, University of Rome Tor Vergata, 00133, Rome, Italy
| | - Carlo Ganini
- Torvergata Oncoscience Research Centre of Excellence, TOR, Department of Experimental Medicine, University of Rome Tor Vergata, 00133, Rome, Italy
| | | | - Alessandro Mauriello
- Torvergata Oncoscience Research Centre of Excellence, TOR, Department of Experimental Medicine, University of Rome Tor Vergata, 00133, Rome, Italy
| | - Carla Marani
- Torvergata Oncoscience Research Centre of Excellence, TOR, Department of Experimental Medicine, University of Rome Tor Vergata, 00133, Rome, Italy
- San Carlo di Nancy Hospital, Rome, Italy
| | - John Marshall
- Medstar Georgetown University Hospital, Georgetown University, Washington, DC, USA
| | - Manuela Montanaro
- Torvergata Oncoscience Research Centre of Excellence, TOR, Department of Experimental Medicine, University of Rome Tor Vergata, 00133, Rome, Italy
| | - Giampiero Palmieri
- Torvergata Oncoscience Research Centre of Excellence, TOR, Department of Experimental Medicine, University of Rome Tor Vergata, 00133, Rome, Italy
| | - Mauro Piacentini
- Torvergata Oncoscience Research Centre of Excellence, TOR, Department of Experimental Medicine, University of Rome Tor Vergata, 00133, Rome, Italy
| | - Giuseppe Sica
- Torvergata Oncoscience Research Centre of Excellence, TOR, Department of Experimental Medicine, University of Rome Tor Vergata, 00133, Rome, Italy
| | - Manfredi Tesauro
- Torvergata Oncoscience Research Centre of Excellence, TOR, Department of Experimental Medicine, University of Rome Tor Vergata, 00133, Rome, Italy
| | - Valentina Rovella
- Torvergata Oncoscience Research Centre of Excellence, TOR, Department of Experimental Medicine, University of Rome Tor Vergata, 00133, Rome, Italy
| | - Giuseppe Tisone
- Torvergata Oncoscience Research Centre of Excellence, TOR, Department of Experimental Medicine, University of Rome Tor Vergata, 00133, Rome, Italy
| | - Yufang Shi
- Torvergata Oncoscience Research Centre of Excellence, TOR, Department of Experimental Medicine, University of Rome Tor Vergata, 00133, Rome, Italy
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, 200031, Shanghai, China
- The First Affiliated Hospital of Soochow University and State Key Laboratory of Radiation Medicine and Protection, Institutes for Translational Medicine, Soochow University, 199 Renai Road, 215123, Suzhou, Jiangsu, China
| | - Ying Wang
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, 200031, Shanghai, China
| | - Gerry Melino
- Torvergata Oncoscience Research Centre of Excellence, TOR, Department of Experimental Medicine, University of Rome Tor Vergata, 00133, Rome, Italy.
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