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Oppegaard KR, Armstrong TS, Anguera JA, Kober KM, Debr LK, Laister RC, Saligan LN, Ayala AP, Kuruvilla J, Alm MW, Byker WH, Miaskowski C, Mayo SJ. Blood-Based Biomarkers of Cancer-Related Cognitive Impairment in Non-Central Nervous System Cancer: A Scoping Review. Crit Rev Oncol Hematol 2022; 180:103822. [PMID: 36152911 DOI: 10.1016/j.critrevonc.2022.103822] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 09/17/2022] [Accepted: 09/19/2022] [Indexed: 11/24/2022] Open
Abstract
This scoping review was designed to synthesize the extant literature on associations between subjective and/or objective measures of cancer-related cognitive impairment (CRCI) and blood-based biomarkers in adults with non-central nervous system cancers. The literature search was done for studies published from the start of each database searched (i.e., MEDLINE, Embase, PsycINFO, Cumulative Index to Nursing and Allied Health Literature, Cochrane Central Register of Controlled Trials, grey literature) through to October 20, 2021. A total of 95 studies are included in this review. Of note, a wide variety of biomarkers were evaluated. Most studies evaluated patients with breast cancer. A variety of cognitive assessment measures were used. The most consistent significant findings were with various subjective and objective measures of CRCI and levels of interleukin-6 and tumor necrosis factor. Overall, biomarker research is in an exploratory phase. However, this review synthesizes findings and proposes directions for future research.
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Affiliation(s)
- Kate R Oppegaard
- University of California San Francisco, School of Nursing, Department of Physiological Nursing, USA
| | - Terri S Armstrong
- Neuro-Oncology Branch, National Cancer Institute, National Institutes of Health, USA
| | - Joaquin A Anguera
- University of California San Francisco, Department of Neurology and Psychiatry, USA
| | - Kord M Kober
- University of California San Francisco, School of Nursing, Department of Physiological Nursing, USA
| | - Lynch Kelly Debr
- University of Florida, College of Nursing, USA; University of Florida Health Cancer Center, USA
| | - Rob C Laister
- Princess Margaret Health Center, University Health Network, Canada
| | - Leorey N Saligan
- Symptoms Biology Unit, Division of Intramural Research, National Institutes of Health, USA
| | | | - John Kuruvilla
- Princess Margaret Health Center, University Health Network, Canada
| | - Mark W Alm
- Toronto General Hospital, University Health Network, Canada
| | | | - Christine Miaskowski
- University of California San Francisco, School of Medicine, Department of Anesthesia and Perioperative Care, USA
| | - Samantha J Mayo
- Lawrence S. Bloomberg Faculty of Nursing, University of Toronto, Canada.
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2
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Lin L, An L, Chen H, Feng L, Lu M, Liu Y, Chu C, Shan J, Xie T, Wang X, Wang S. Integrated Network Pharmacology and Lipidomics to Reveal the Inhibitory Effect of Qingfei Oral Liquid on Excessive Autophagy in RSV-Induced Lung Inflammation. Front Pharmacol 2021; 12:777689. [PMID: 34925035 PMCID: PMC8672039 DOI: 10.3389/fphar.2021.777689] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 11/12/2021] [Indexed: 01/27/2023] Open
Abstract
Background: Respiratory syncytial virus (RSV) can cause varying degrees of lung inflammation in children. Qingfei Oral Liquid (QF) is effective in treating childhood RSV-induced lung inflammation (RSV-LI) in clinics, but its pharmacological profiles and mechanisms remain unclear. Methods: This study combined network Pharmacology, lipidomics, pharmacodynamics, and pathway validation to evaluate the therapeutic mechanisms of QF. Using Cytoscape (v3.8.2) and enrichment analyses from the Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO), a global view of the putative compound-target-pathway network was created. The corresponding lipidomic profiles were then used to detect differently activated lipids, revealing the metabolic pathway, using ultra-high-performance liquid chromatography linked to hybrid Quadrupole-Exactive Orbitrap mass spectrometry (UHPLC-Q-Exactive Orbitrap MS). Meanwhile, the in vivo efficiency of QF, the enrichment pathway, and the excessive autophagy inhibition mechanisms were validated in RSV-infected mice models. Results: The network pharmacology results demonstrated 117 active compounds acted directly upon 101 core targets of QF against RSV-LI. The most significantly enriched pathway was the PI3K/Akt/mTOR signaling pathway (p < 0.05). In addition, untargeted lipidomics were performed, and it was revealed that higher lung levels of DAG 30:0, DAG 30:5, DAG 32:0, DAG 16:0_18:0, DAG 17:0_17:0, DAG 34:1, DAG 36:0, DAG 36:1 in the RSV-LI group were decreased after QF administration (FDR < 0.05, FC > 1.2). Lipin-1, a key enzyme in DAG synthesis, was increased in the RSV-LI mouse model. Animal experiments further validated that QF inhibited the PI3K/Akt/mTOR signaling pathway, with lower lung levels of phosphorylated PI3K, AKT and mTOR, as well as its related proteins of lipin-1 and VPS34 (p < 0.01). Finally, pharmacodynamic investigations indicated that QF reduced airway inflammation caused by excessive autophagy by decreasing lung levels of RSV F and G proteins, Beclin-1, Atg5, and LC3B II, IL-1 and TNF-α (p < 0.05). Conclusion: Lipidomic-based network pharmacology, along with experimental validation, may be effective approaches for illustrating the therapeutic mechanism of QF in the treatment of RSV-LI.
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Affiliation(s)
- Lili Lin
- Jiangsu Key Laboratory of Pediatric Respiratory Disease, Institute of Pediatrics, Medical Metabolomics Center, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China
| | - Li An
- Jiangsu Key Laboratory of Pediatric Respiratory Disease, Institute of Pediatrics, Medical Metabolomics Center, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China
| | - Hui Chen
- Jiangsu Key Laboratory of Pediatric Respiratory Disease, Institute of Pediatrics, Medical Metabolomics Center, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China
| | - Lu Feng
- Jiangsu Key Laboratory of Pediatric Respiratory Disease, Institute of Pediatrics, Medical Metabolomics Center, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China
| | - Mengjiang Lu
- Key Laboratory of Acupuncture and Medicine Research of Ministry of Education, Nanjing University of Chinese Medicine, Nanjing, China
| | - Yuling Liu
- Department of Pediatrics, Nanjing Pukou District Hospital of Traditional Chinese Medicine, Nanjing, China
| | - Chu Chu
- Jiangsu Key Laboratory of Pediatric Respiratory Disease, Institute of Pediatrics, Medical Metabolomics Center, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China
| | - Jinjun Shan
- Jiangsu Key Laboratory of Pediatric Respiratory Disease, Institute of Pediatrics, Medical Metabolomics Center, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China
| | - Tong Xie
- Jiangsu Key Laboratory of Pediatric Respiratory Disease, Institute of Pediatrics, Medical Metabolomics Center, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China
| | - Xiaorong Wang
- Department of Clinical Laboratory, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China
| | - Shouchuan Wang
- Jiangsu Key Laboratory of Pediatric Respiratory Disease, Institute of Pediatrics, Medical Metabolomics Center, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China
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3
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Chase Huizar C, Raphael I, Forsthuber TG. Genomic, proteomic, and systems biology approaches in biomarker discovery for multiple sclerosis. Cell Immunol 2020; 358:104219. [PMID: 33039896 PMCID: PMC7927152 DOI: 10.1016/j.cellimm.2020.104219] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 09/13/2020] [Accepted: 09/16/2020] [Indexed: 12/12/2022]
Abstract
Multiple sclerosis (MS) is a neuroinflammatory disorder characterized by autoimmune-mediated inflammatory lesions in CNS leading to myelin damage and axonal loss. MS is a heterogenous disease with variable and unpredictable disease course. Due to its complex nature, MS is difficult to diagnose and responses to specific treatments may vary between individuals. Therefore, there is an indisputable need for biomarkers for early diagnosis, prediction of disease exacerbations, monitoring the progression of disease, and for measuring responses to therapy. Genomic and proteomic studies have sought to understand the molecular basis of MS and find biomarker candidates. Advances in next-generation sequencing and mass-spectrometry techniques have yielded an unprecedented amount of genomic and proteomic data; yet, translation of the results into the clinic has been underwhelming. This has prompted the development of novel data science techniques for exploring these large datasets to identify biologically relevant relationships and ultimately point towards useful biomarkers. Herein we discuss optimization of omics study designs, advances in the generation of omics data, and systems biology approaches aimed at improving biomarker discovery and translation to the clinic for MS.
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Affiliation(s)
- Carol Chase Huizar
- Department of Biology, University of Texas at San Antonio, San Antonio, TX, USA
| | - Itay Raphael
- Department of Neurological Surgery, University of Pittsburgh, UPMC Children's Hospital, Pittsburgh, PA, USA.
| | - Thomas G Forsthuber
- Department of Biology, University of Texas at San Antonio, San Antonio, TX, USA.
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Vetma V, Guttà C, Peters N, Praetorius C, Hutt M, Seifert O, Meier F, Kontermann R, Kulms D, Rehm M. Convergence of pathway analysis and pattern recognition predicts sensitization to latest generation TRAIL therapeutics by IAP antagonism. Cell Death Differ 2020; 27:2417-2432. [PMID: 32081986 PMCID: PMC7370234 DOI: 10.1038/s41418-020-0512-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 01/30/2020] [Accepted: 01/31/2020] [Indexed: 12/28/2022] Open
Abstract
Second generation TRAIL-based therapeutics, combined with sensitising co-treatments, have recently entered clinical trials. However, reliable response predictors for optimal patient selection are not yet available. Here, we demonstrate that a novel and translationally relevant hexavalent TRAIL receptor agonist, IZI1551, in combination with Birinapant, a clinically tested IAP antagonist, efficiently induces cell death in various melanoma models, and that responsiveness can be predicted by combining pathway analysis, data-driven modelling and pattern recognition. Across a panel of 16 melanoma cell lines, responsiveness to IZI1551/Birinapant was heterogeneous, with complete resistance and pronounced synergies observed. Expression patterns of TRAIL pathway regulators allowed us to develop a combinatorial marker that predicts potent cell killing with high accuracy. IZI1551/Birinapant responsiveness could be predicted not only for cell lines, but also for 3D tumour cell spheroids and for cells directly isolated from patient melanoma metastases (80–100% prediction accuracies). Mathematical parameter reduction identified 11 proteins crucial to ensure prediction accuracy, with x-linked inhibitor of apoptosis protein (XIAP) and procaspase-3 scoring highest, and Bcl-2 family members strongly represented. Applied to expression data of a cohort of n = 365 metastatic melanoma patients in a proof of concept in silico trial, the predictor suggested that IZI1551/Birinapant responsiveness could be expected for up to 30% of patient tumours. Overall, response frequencies in melanoma models were very encouraging, and the capability to predict melanoma sensitivity to combinations of latest generation TRAIL-based therapeutics and IAP antagonists can address the need for patient selection strategies in clinical trials based on these novel drugs.
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Affiliation(s)
- Vesna Vetma
- Institute of Cell Biology and Immunology, University of Stuttgart, Stuttgart, Germany.,Department of Physiology & Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Cristiano Guttà
- Institute of Cell Biology and Immunology, University of Stuttgart, Stuttgart, Germany
| | - Nathalie Peters
- Institute of Cell Biology and Immunology, University of Stuttgart, Stuttgart, Germany
| | - Christian Praetorius
- Center for Regenerative Therapies, Technical University Dresden, Dresden, Germany.,Skin Cancer Center at the University Cancer Centre, Department of Dermatology, Faculty of Medicine, University Hospital Carl Gustav Carus, Technical University Dresden, Dresden, Germany
| | - Meike Hutt
- Institute of Cell Biology and Immunology, University of Stuttgart, Stuttgart, Germany
| | - Oliver Seifert
- Institute of Cell Biology and Immunology, University of Stuttgart, Stuttgart, Germany
| | - Friedegund Meier
- Skin Cancer Center at the University Cancer Centre, Department of Dermatology, Faculty of Medicine, University Hospital Carl Gustav Carus, Technical University Dresden, Dresden, Germany.,National Center for Tumor Diseases (NCT), Dresden, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Roland Kontermann
- Institute of Cell Biology and Immunology, University of Stuttgart, Stuttgart, Germany.,Stuttgart Research Center Systems Biology, University of Stuttgart, Stuttgart, Germany
| | - Dagmar Kulms
- Center for Regenerative Therapies, Technical University Dresden, Dresden, Germany.,Skin Cancer Center at the University Cancer Centre, Department of Dermatology, Faculty of Medicine, University Hospital Carl Gustav Carus, Technical University Dresden, Dresden, Germany.,Experimental Dermatology, Department of Dermatology, Technical University Dresden, Dresden, Germany
| | - Markus Rehm
- Institute of Cell Biology and Immunology, University of Stuttgart, Stuttgart, Germany. .,Department of Physiology & Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland. .,Stuttgart Research Center Systems Biology, University of Stuttgart, Stuttgart, Germany. .,Stuttgart Centre for Simulation Science (SC SimTech), University of Stuttgart, Stuttgart, Germany. .,Centre for Systems Medicine, Royal College of Surgeons in Ireland, Dublin, Ireland.
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5
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Prodan Žitnik I, Černe D, Mancini I, Simi L, Pazzagli M, Di Resta C, Podgornik H, Repič Lampret B, Trebušak Podkrajšek K, Sipeky C, van Schaik R, Brandslund I, Vermeersch P, Schwab M, Marc J. Personalized laboratory medicine: a patient-centered future approach. Clin Chem Lab Med 2019; 56:1981-1991. [PMID: 29990304 DOI: 10.1515/cclm-2018-0181] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Accepted: 05/11/2018] [Indexed: 12/12/2022]
Abstract
In contrast to population-based medical decision making, which emphasizes the use of evidence-based treatment strategies for groups of patients, personalized medicine is based on optimizing treatment at the level of the individual patient. The creation of molecular profiles of individual patients was made possible by the advent of "omics" technologies, based on high throughput instrumental techniques in combination with biostatistics tools and artificial intelligence. The goal of personalized laboratory medicine is to use advanced technologies in the process of preventive, curative or palliative patient management. Personalized medicine does not rely on changes in concentration of a single molecular marker to make a therapeutic decision, but rather on changes of a profile of markers characterizing an individual patient's status, taking into account not only the expected response to treatment of the disease but also the expected response of the patient. Such medical approach promises a more effective diagnostics with more effective and safer treatment, as well as faster recovery and restoration of health and improved cost effectiveness. The laboratory medicine profession is aware of its key role in personalized medicine, but to empower the laboratories, at least an enhancement in cooperation between disciplines within laboratory medicine will be necessary.
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Affiliation(s)
| | - Darko Černe
- Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia
| | - Irene Mancini
- Department of Biomedical, Experimental and Clinical Sciences, University of Florence, Florence, Italy
| | - Lisa Simi
- Department of Biomedical, Experimental and Clinical Sciences, University of Florence, Florence, Italy
| | - Mario Pazzagli
- Department of Biomedical, Experimental and Clinical Sciences, University of Florence, Florence, Italy
| | - Chiara Di Resta
- Vita-Salute San Raffaele University and Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Helena Podgornik
- Department of Hematology, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Barbka Repič Lampret
- Unit for Special Laboratory Diagnostics, University Children's Hospital, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Katarina Trebušak Podkrajšek
- Unit for Special Laboratory Diagnostics, University Children's Hospital, University Medical Centre Ljubljana, Ljubljana, Slovenia.,Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Csilla Sipeky
- Institute of Biomedicine, University of Turku, Turku, Finland
| | - Ron van Schaik
- Department of Clinical Chemistry, Erasmus Medical Center, Rotterdam, TheNetherlands
| | - Ivan Brandslund
- Biochemistry Department, University of Southern Denmark and Vejle Hospital, Vejle, Denmark
| | | | - Matthias Schwab
- Department of Clinical Pharmacology, University Hospital Tuebingen, Tuebingen, Germany.,Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, Germany.,Department of Pharmacy and Biochemistry, University of Tuebingen, Tuebingen, Germany
| | - Janja Marc
- Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia
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6
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Bocato MZ, Bianchi Ximenez JP, Hoffmann C, Barbosa F. An overview of the current progress, challenges, and prospects of human biomonitoring and exposome studies. JOURNAL OF TOXICOLOGY AND ENVIRONMENTAL HEALTH. PART B, CRITICAL REVIEWS 2019; 22:131-156. [PMID: 31543064 DOI: 10.1080/10937404.2019.1661588] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Human Biomonitoring (HB), the process for determining whether and to what extent chemical substances penetrated our bodies, serves as a useful tool to quantify human exposure to pollutants. In cases of nutrition and physiologic status, HB plays a critical role in the identification of excess or deficiency of essential nutrients. In pollutant HB studies, levels of substances measured in body fluids (blood, urine, and breast milk) or tissues (hair, nails or teeth) aid in the identification of potential health risks or associated adverse effects. However, even as a widespread practice in several countries, most HB studies reflect exposure to a single compound or mixtures which are measured at a single time point in lifecycle. On the other hand, throughout an individual's lifespan, the contact with different physical, chemical, and social stressors occurs at varying intensities, differing times and durations. Further, the interaction between stressors and body receptors leads to dynamic responses of the entire biological system including proteome, metabolome, transcriptome, and adductome. Bearing this in mind, a relatively new vision in exposure science, defined as the exposome, is postulated to expand the traditional practice of measuring a single exposure to one or few chemicals at one-time point to an approach that addresses measures of exposure to multiple stressors throughout the lifespan. With the exposome concept, the science of exposure advances to an Environment-Wide Association Perspective, which might exhibit a stronger relationship with good health or disease conditions for an individual (phenotype). Thus, this critical review focused on the current progress of HB and exposome investigations, anticipating some challenges, strategies, and future needs to be taken into account for designing future surveys.
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Affiliation(s)
- Mariana Zuccherato Bocato
- Laboratório de Toxicologia Analítica e de Sistemas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo , Ribeirão Preto , Brazil
| | - João Paulo Bianchi Ximenez
- Laboratório de Toxicologia Analítica e de Sistemas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo , Ribeirão Preto , Brazil
| | - Christian Hoffmann
- Departmento de Alimentos e Nutrição Experimental Faculdade de Ciências Farmacêuticas, Universidade de São Paulo , São Paulo , Brazil
| | - Fernando Barbosa
- Laboratório de Toxicologia Analítica e de Sistemas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo , Ribeirão Preto , Brazil
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7
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Chakravorty S, Hegde M. Inferring the effect of genomic variation in the new era of genomics. Hum Mutat 2018; 39:756-773. [PMID: 29633501 DOI: 10.1002/humu.23427] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Revised: 03/20/2018] [Accepted: 03/28/2018] [Indexed: 12/11/2022]
Abstract
Accurate and detailed understanding of the effects of variants in the coding and noncoding regions of the genome is the next big challenge in the new genomic era of personalized medicine, especially to tackle newer findings of genetic and phenotypic heterogeneity of diseases. This is necessary to resolve the gene-variant-disease relationship, the pathogenic variant spectrum of genes, pathogenic variants with variable clinical consequences, and multiloci diseases. In turn, this will facilitate patient recruitment for relevant clinical trials. In this review, we describe the trends in research at the intersection of basic and clinical genomics aiming to (a) overcome molecular diagnostic challenges and increase the clinical utility of next-generation sequencing (NGS) platforms, (b) elucidate variants associated with disease, (c) determine overall genomic complexity including epistasis, complex inheritance patterns such as "synergistic heterozygosity," digenic/multigenic inheritance, modifier effect, and rare variant load. We describe the newly emerging field of integrated functional genomics, in vivo or in vitro large-scale functional approaches, statistical bioinformatics algorithms that support NGS genomics data to interpret variants for timely clinical diagnostics and disease management. Thus, facilitating the discovery of new therapeutic or biomarker options, and their roles in the future of personalized medicine.
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Affiliation(s)
- Samya Chakravorty
- Department of Human Genetics, Emory University School of Medicine, Whitehead Biomedical Research Building Suite 301, Atlanta, Georgia
| | - Madhuri Hegde
- Department of Human Genetics, Emory University School of Medicine, Whitehead Biomedical Research Building Suite 301, Atlanta, Georgia
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8
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Fijten RRR, Smolinska A, Drent M, Dallinga JW, Mostard R, Pachen DM, van Schooten FJ, Boots AW. The necessity of external validation in exhaled breath research: a case study of sarcoidosis. J Breath Res 2017; 12:016004. [DOI: 10.1088/1752-7163/aa8409] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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9
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Chakravorty S, Hegde M. Gene and Variant Annotation for Mendelian Disorders in the Era of Advanced Sequencing Technologies. Annu Rev Genomics Hum Genet 2017; 18:229-256. [PMID: 28415856 DOI: 10.1146/annurev-genom-083115-022545] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Comprehensive annotations of genetic and noncoding regions and corresponding accurate variant classification for Mendelian diseases are the next big challenge in the new genomic era of personalized medicine. Progress in the development of faster and more accurate pipelines for genome annotation and variant classification will lead to the discovery of more novel disease associations and candidate therapeutic targets. This ultimately will facilitate better patient recruitment in clinical trials. In this review, we describe the trends in research at the intersection of basic and clinical genomics that aims to increase understanding of overall genomic complexity, complex inheritance patterns of disease, and patient-phenotype-specific genomic associations. We describe the emerging field of translational functional genomics, which integrates other functional "-omics" approaches that support next-generation sequencing genomic data in order to facilitate personalized diagnostics, disease management, biomarker discovery, and medicine. We also discuss the utility of this integrated approach for diagnostic clinics and medical databases and its role in the future of personalized medicine.
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Affiliation(s)
- Samya Chakravorty
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia 30322;
| | - Madhuri Hegde
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia 30322;
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10
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Agusti A, Bel E, Thomas M, Vogelmeier C, Brusselle G, Holgate S, Humbert M, Jones P, Gibson PG, Vestbo J, Beasley R, Pavord ID. Treatable traits: toward precision medicine of chronic airway diseases. Eur Respir J 2016; 47:410-9. [PMID: 26828055 DOI: 10.1183/13993003.01359-2015] [Citation(s) in RCA: 672] [Impact Index Per Article: 84.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Asthma and chronic obstructive pulmonary disease (COPD) are two prevalent chronic airway diseases that have a high personal and social impact. They likely represent a continuum of different diseases that may share biological mechanisms (i.e. endotypes), and present similar clinical, functional, imaging and/or biological features that can be observed (i.e. phenotypes) which require individualised treatment. Precision medicine is defined as "treatments targeted to the needs of individual patients on the basis of genetic, biomarker, phenotypic, or psychosocial characteristics that distinguish a given patient from other patients with similar clinical presentations". In this Perspective, we propose a precision medicine strategy for chronic airway diseases in general, and asthma and COPD in particular.
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Affiliation(s)
- Alvar Agusti
- Respiratory Institute, Hospital Clinic, IDIBAPS, University of Barcelona, Barcelona and CIBER Enfermedades Respiratorias (CIBERES), Spain
| | - Elisabeth Bel
- Dept of Respiratory Medicine, Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands
| | - Mike Thomas
- Primary Care and Population Sciences, University of Southampton, Southampton, UK
| | - Claus Vogelmeier
- Dept of Medicine, Pulmonary and Critical Care Medicine, University Medical Center Giessen and Marburg, Philipps-Universität Marburg, and Member of the German Center for Lung Research (DZL), Germany
| | - Guy Brusselle
- Dept of Respiratory Medicine, Ghent University Hospital, Ghent, Belgium Depts of Epidemiology and Respiratory Medicine, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Stephen Holgate
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton General Hospital, Southampton, UK
| | - Marc Humbert
- Université Paris-Sud; Service de Pneumologie, Hôpital Bicêtre (Assistance Publique-Hôpitaux de Paris); INSERM UMR_S 999, Le Kremlin-Bicêtre, France
| | - Paul Jones
- St George's University of London, London, UK
| | - Peter G Gibson
- Dept of Respiratory and Sleep Medicine, John Hunter Hospital, Hunter Medical Research Institute, and Priority Research Centre for Asthma and Respiratory Disease, The University of Newcastle, NSW, Australia
| | - Jørgen Vestbo
- Centre for Respiratory Medicine and Allergy, Manchester Academic Health Science Centre, University Hospital South Manchester NHS Foundation Trust, Manchester, UK
| | - Richard Beasley
- Medical Research Institute of New Zealand, Wellington, New Zealand
| | - Ian D Pavord
- Respiratory Medicine Unit, NDM Research Building, Nuffield Dept of Medicine, University of Oxford, Oxford, UK
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11
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Lauria M, Moyseos P, Priami C. SCUDO: a tool for signature-based clustering of expression profiles. Nucleic Acids Res 2015; 43:W188-92. [PMID: 25958391 PMCID: PMC4489218 DOI: 10.1093/nar/gkv449] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2015] [Accepted: 04/24/2015] [Indexed: 01/23/2023] Open
Abstract
SCUDO (Signature-based ClUstering for DiagnOstic purposes) is an online tool for the analysis of gene expression profiles for diagnostic and classification purposes. The tool is based on a new method for the clustering of profiles based on a subject-specific, as opposed to disease-specific, signature. Our approach relies on construction of a reference map of transcriptional signatures, from both healthy and affected subjects, derived from their respective mRNA or miRNA profiles. A diagnosis for a new individual can then be performed by determining the position of the individual's transcriptional signature on the map. The diagnostic power of our method has been convincingly demonstrated in an open scientific competition (SBV Improver Diagnostic Signature Challenge), scoring second place overall and first place in one of the sub-challenges.
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Affiliation(s)
- Mario Lauria
- The Microsoft Research-University of Trento Centre for Computational and Systems Biology (COSBI), Piazza Manifattura 1, 38068 Rovereto (TN), Italy
| | - Petros Moyseos
- The Microsoft Research-University of Trento Centre for Computational and Systems Biology (COSBI), Piazza Manifattura 1, 38068 Rovereto (TN), Italy
| | - Corrado Priami
- The Microsoft Research-University of Trento Centre for Computational and Systems Biology (COSBI), Piazza Manifattura 1, 38068 Rovereto (TN), Italy Department of Mathematics, University of Trento, via Sommarive, 14, 38123 Povo (TN), Italy
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12
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Turner RM, Park BK, Pirmohamed M. Parsing interindividual drug variability: an emerging role for systems pharmacology. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2015; 7:221-41. [PMID: 25950758 PMCID: PMC4696409 DOI: 10.1002/wsbm.1302] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Revised: 04/08/2015] [Accepted: 04/15/2015] [Indexed: 12/25/2022]
Abstract
There is notable interindividual heterogeneity in drug response, affecting both drug efficacy and toxicity, resulting in patient harm and the inefficient utilization of limited healthcare resources. Pharmacogenomics is at the forefront of research to understand interindividual drug response variability, but although many genotype-drug response associations have been identified, translation of pharmacogenomic associations into clinical practice has been hampered by inconsistent findings and inadequate predictive values. These limitations are in part due to the complex interplay between drug-specific, human body and environmental factors influencing drug response and therefore pharmacogenomics, whilst intrinsically necessary, is by itself unlikely to adequately parse drug variability. The emergent, interdisciplinary and rapidly developing field of systems pharmacology, which incorporates but goes beyond pharmacogenomics, holds significant potential to further parse interindividual drug variability. Systems pharmacology broadly encompasses two distinct research efforts, pharmacologically-orientated systems biology and pharmacometrics. Pharmacologically-orientated systems biology utilizes high throughput omics technologies, including next-generation sequencing, transcriptomics and proteomics, to identify factors associated with differential drug response within the different levels of biological organization in the hierarchical human body. Increasingly complex pharmacometric models are being developed that quantitatively integrate factors associated with drug response. Although distinct, these research areas complement one another and continual development can be facilitated by iterating between dynamic experimental and computational findings. Ultimately, quantitative data-derived models of sufficient detail will be required to help realize the goal of precision medicine.
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Affiliation(s)
- Richard M Turner
- The Wolfson Centre for Personalised Medicine, Institute for Translational Medicine, University of Liverpool, Liverpool, UK
| | - B Kevin Park
- MRC Centre for Drug Safety Science, Department of Molecular and Clinical Pharmacology, University of Liverpool, Liverpool, UK
| | - Munir Pirmohamed
- The Wolfson Centre for Personalised Medicine, Institute for Translational Medicine, University of Liverpool, Liverpool, UK
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