Omics-Based Molecular Target and Biomarker Identification

Hu, Zhang-Zhi; Huang, Hongzhan; Wu, Cathy H.; Jung, Mira; Dritschilo, Anatoly; Riegel, Anna T.; Wellstein, Anton

doi:10.1007/978-1-61779-027-0_26

Cited by 46 publications

(36 citation statements)

References 63 publications

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“…Unlike hypothesis-driven research, it has the potential to identify biomarkers of IR with no prior assumptions about underlying biological mechanisms. This is a potent tool but the analysis and interpretation of the data obtained remains challenging [48].…”

Section: Biological Classification Of Ionizing Radiation Biomarkersmentioning

confidence: 99%

Ionizing radiation biomarkers for potential use in epidemiological studies

Pernot

Hall

Baatout

et al. 2012

Mutation Research/Reviews in Mutation Research

201

153

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Ionizing radiation is a known human carcinogen that can induce a variety of biological effects depending on the physical nature, duration, doses and dose-rates of exposure. However, the magnitude of health risks at low doses and dose-rates (below 100mSv and/or 0.1mSvmin(-1)) remains controversial due to a lack of direct human evidence. It is anticipated that significant insights will emerge from the integration of epidemiological and biological research, made possible by molecular epidemiology studies incorporating biomarkers and bioassays. A number of these have been used to investigate exposure, effects and susceptibility to ionizing radiation, albeit often at higher doses and dose rates, with each reflecting time-limited cellular or physiological alterations. This review summarises the multidisciplinary work undertaken in the framework of the European project DoReMi (Low Dose Research towards Multidisciplinary Integration) to identify the most appropriate biomarkers for use in population studies. In addition to logistical and ethical considerations for conducting large-scale epidemiological studies, we discuss the relevance of their use for assessing the effects of low dose ionizing radiation exposure at the cellular and physiological level. We also propose a temporal classification of biomarkers that may be relevant for molecular epidemiology studies which need to take into account the time elapsed since exposure. Finally, the integration of biology with epidemiology requires careful planning and enhanced discussions between the epidemiology, biology and dosimetry communities in order to determine the most important questions to be addressed in light of pragmatic considerations including the appropriate population to be investigated (occupationally, environmentally or medically exposed), and study design. The consideration of the logistics of biological sample collection, processing and storing and the choice of biomarker or bioassay, as well as awareness of potential confounding factors, are also essential.

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Section: Biological Classification Of Ionizing Radiation Biomarkersmentioning

confidence: 99%

Ionizing radiation biomarkers for potential use in epidemiological studies

Pernot

Hall

Baatout

et al. 2012

Mutation Research/Reviews in Mutation Research

201

153

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“…Instead of merely considering individual up-or downregulated genes or proteins, network-or pathway-based analyses (interactomics) are increasingly applied in ophthal- mology to gain insight into disease-specific gene regulatory networks and signaling pathways. 2 …”

Section: Omics Techniquesmentioning

confidence: 99%

“…Therefore, there is a need for high-throughput analyses, so that a whole system can be evaluated in a hypothesis-free way. 2 Omics is the large-scale characterization and quantification of biological molecules, which went through rapid advancements over the last years due to technological improvements in sequencing techniques, mass spectrometry, and bioinformatic analyses. However, due to the very large scope of the datasets and disease heterogeneity, it might be challenging to extract biologically meaningful information from omics studies.…”

mentioning

confidence: 99%

Omics Biomarkers in Ophthalmology

Jong

Lefeber

et al. 2017

Invest. Ophthalmol. Vis. Sci.

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''Omics'' refers to high-throughput analyses of genes, proteins, or metabolites in a biological system, and is increasingly used for ophthalmic research. These system-based approaches can unravel disease-related processes and are valuable for biomarker discovery. Furthermore, potential therapeutic targets can be identified based on omics results, and targeted follow-up experiments can be designed to gain molecular understanding of the disease and to test new therapies. Here, we review the application of omics techniques in eye diseases, focusing on age-related macular degeneration (AMD), diabetic retinopathy (DR), retinal detachment (RD), myopia, glaucoma, Fuchs' corneal dystrophy (FCD), cataract, keratoconus, and dry eyes. We observe that genomic analyses were mainly successful in AMD research (almost half of the genomic heritability has been explained), whereas large parts of disease variability or risk remain unsolved in most of the other diseases. Other omics studies like transcriptomics, proteomics, and metabolomics provided additional candidate proteins and pathways for several eye diseases, although sample sizes in these studies were often very small and replication is lacking. In order to translate omics results into clinical biomarkers, larger sample sizes and validation across different cohorts would be essential. In conclusion, omicsbased studies are increasing in ophthalmology, and further application to the clinic might develop in the years to come. Integration of genomics with other type of omics data has the potential to improve the accuracy of predictive tests. Moreover, in the future, omics may lead to stratification of patients into subgroups based on molecular profiles, enabling the development of personalized treatments.

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“…The term ''omics'' in biological sciences widely encompasses genomics, transcriptomics, proteomics, and metabolomics which refers to the study of DNA, mRNA, proteins and metabolites, respectively. While ''omics'' is now indispensable in the search of novel biomarkers for drug and vaccine development (Hu et al, 2011;Ozdemir et al, 2011), its application to microalgae is just beginning to emerge in the last few years. Furthermore, to date, no review attempt has been undertaken to evaluate the successful integration of ''omic'' approaches in algal biofuel research.…”

mentioning

confidence: 99%

Agrigenomics for Microalgal Biofuel Production: An Overview of Various Bioinformatics Resources and Recent Studies to Link OMICS to Bioenergy and Bioeconomy

Misra

Panda²,

Parida³

2013

OMICS: A Journal of Integrative Biology

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Microalgal biofuels offer great promise in contributing to the growing global demand for alternative sources of renewable energy. However, to make algae-based fuels cost competitive with petroleum, lipid production capabilities of microalgae need to improve substantially. Recent progress in algal genomics, in conjunction with other ''omic'' approaches, has accelerated the ability to identify metabolic pathways and genes that are potential targets in the development of genetically engineered microalgal strains with optimum lipid content. In this review, we summarize the current bioeconomic status of global biofuel feedstocks with particular reference to the role of ''omics'' in optimizing sustainable biofuel production. We also provide an overview of the various databases and bioinformatics resources available to gain a more complete understanding of lipid metabolism across algal species, along with the recent contributions of ''omic'' approaches in the metabolic pathway studies for microalgal biofuel production.

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Omics-Based Molecular Target and Biomarker Identification

Cited by 46 publications

References 63 publications

Ionizing radiation biomarkers for potential use in epidemiological studies

Ionizing radiation biomarkers for potential use in epidemiological studies

Omics Biomarkers in Ophthalmology

Agrigenomics for Microalgal Biofuel Production: An Overview of Various Bioinformatics Resources and Recent Studies to Link OMICS to Bioenergy and Bioeconomy

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