Introduction to the ‘-omics’ Elliott J. Price Outline ̶What are the ‘omics’? ̶ ̶Common ‘-omics’ technologies ̶ ̶Multi-omics in environmental chemistry What is “-omics”? •Systematic and comprehensive analysis [of a cellular/ molecular layer] ̶ •i.e. a subset of [molecular] phenotyping Phenotype Phenotype = characteristics [traits] displayed by an entity [organism] Phenotype is dynamic i.e. changes over time [development] Further material: 10.1006/jtbi.1996.0335 Nature and nurture Phenotype is the results of genetics & environment GxE i.e. need to understand: •Genotype •Environment •Genotype x Environment interaction (GxE) Further material: Nature via nurture Central dogma of molecular biology Genome = all inherited genetic material [DNA] of an organism Instructions Functional product Messenger Image: Genome Research Limited Transcriptome = all the transcribed genetic material [RNA] of an organism i.e. all expressed genes Proteome = all the proteins/peptides of an organism i.e. all translated genetic material Metabolome = all the metabolites (small molecules) of an organism i.e. all small substances active in cellular processes Additional layers of molecular biology Microorganisms Microbiome = all the microorganisms [in direct contact with an organism] each with their own genes-to-functions Image: Biorender Functional genomics - driven analysis mi1 g1 met1 p1 t1 phe1 phe2 phe3 Genome Transcriptome Proteome Metabolome Microbiome Phenotype development mi2 g2 met2 p2 t2 mi3 g3 met3 p3 t3 Further material: https://youtu.be/D-Ljd5Uex0s Online course: 10.6019/TOL.FunGenI-c.2016.00001.1 What is the environment? Image: iStock by Getty images Environmental exposure and the exposome Environmental exposure: contact between an external factor (agent) and an entity. Contact occurs at an [exposure] interface. Agent includes [external] psychosocial factors. The entity is any subject experiencing contact. A single exposure event is a continuous contact (exposure period). Exposome: the totality of environmental exposures Functional exposomics •Environment-to-phenotype mapping? Further material: 10.1073/pnas.1903232116 Biodynamic interfaces & GxE measurement Further material: https://youtu.be/XeyjeZeyo4o Entity Entity Modified from: 10.1002/bies.202000017 GxE interaction – need to understand both sides equally Multi-omics analysis Further material: https://doi.org/10.5281/zenodo.5579746 “More extensive characterization of the exposome and integration with molecular multi-omics profiling is set to advance the factoring of phenotypic variance into genetic and environmental components. Studying their interplay places genotype-environment interaction at the center of integrative biology towards deepening our understanding of phenotype development and adaptation to further personal, population and ecosystem health.” Multi-omics integrated framework Consideration for ‘omics’ analysis Metabolites Microorganisms •Hypothesis or observation? • •Which layer(s)? High-throughput technologies - NGS ̶Next-generation sequencing (NGS) ̶Measure genetic material (i.e. DNA, RNA, [microbiome]) ̶Measured via physical properties (e.g. optical fluorescence / electro-conductivity) Online course: 10.6019/TOL.FunGenII-c.2016.00001.1 Image: LabManager High-throughput technologies - NGS ̶What genetic material are present? Image from DOI: 10.5772/66732 Long reads •Relatively expensive (~5 times more) •Less accurate base-pair identification •Easy to assemble / map to scaffold Short reads •Relatively affordable •Accurate base-pair identifications •Difficult to assemble / map to scaffold How much genetic material is active (expressed)? •Typically achieve relative amounts •Absolute quantification is possible, otherwise use [RT]-qPCR Further material: 10.1038/s41576-021-00367-3 High-throughput technologies - NGS High-throughput technologies - MS ̶Mass Spectrometry (MS) ̶Measure electromagnetic properties (mass-to-charge ratio [m/z]) of ions to calculate mass & elucidate structure ̶Widely applied for peptide/proteins & small molecules ̶ ̶ High-throughput technologies – MS coupling ̶MS is often preceded by chromatography ̶ ̶Major approaches are: ̶Full-scan (non-target) ̶Selective (target) ̶ ̶ High-throughput technologies - MS Further material: https://nontargetedanalysis.org/ Selective acquisition ̶Scan selected ions (m/z) specific to molecules of interest ̶How much of molecule is present? • ̶ Full-scan analysis ̶Identify what chemicals are present? ̶Quantification (even relative) is difficult https://upload.wikimedia.org/wikipedia/commons/thumb/5/57/Estron.svg/430px-Estron.svg.png Sequencing 1 million bases Low-resolution MS (100,000 scans) Mid-resolution MS (100,000 scans) High-resolution MS (100,000 scans) 1000 to 10000 x more costly Large-scale sequencing remains cheaper & easier than large-scale MS Sequencing & mass spectrometry Image: 10.1038/s41570-017-0054 ̶Sequencing is more robust than MS ̶MS methods provide finer details about phenotype due to greater inclusion of external factors ̶Sequencing shows all potential biological reactions that can occur ̶MS shows biological and non-biological reactions that occur ̶ ̶ Sequencing & mass spectrometry Further material: 10.1038/s41437-019-0209-z & 10.1038/s41570-017-0054 Network biology Image: 10.1016/B978-0-12-813762-8.00002-5 Informatics to integrate and understand big data is the major advance of ‘omics’ technologies Systems biology ‘Omics’ technologies enable more observations but more observations does not equal more understanding Benefit of the ‘-omics’ all depends on study design being correct for the hypothesis you want to test / question you wish to explore Multi-omics in environmental chemistry McCall et al. Home chemical and microbial transitions across urbanization. Nat Microbiol 5, 108–115 (2020). https://doi.org/10.1038/s41564-019-0593-4 ̶Took swab samples from inside homes and from their inhabitants across gradient of rainforest – city in Brazil ̶NGS (microbiome) & MS (chemicals) ̶Urban homes showed higher levels of irritant cleaning products / detergents ̶Urban homes had much greater fungal diversity & biomass Multi-omics in environmental chemistry https://doi.org/10.1038/s41564-019-0593-4 ̶Industrial materials cover more surfaces in urban homes & were cleaned with antimicrobials more frequently ̶Fungus inside urban homes speculated to have developed resistance ̶Allergenic load higher in urban homes Multi-omics in environmental chemistry https://doi.org/10.1038/s41564-019-0593-4 Multi-omics in environmental chemistry ‒15 people monitored for 800 days’ ‒Tracked location & air monitoring ‒Analysed airborne microbes (NGS) and chemicals (MS) Jiang et al. Dynamic Human Environmental Exposome Revealed by Longitudinal Personal Monitoring. Cell 175, 277–291 (2018). https://doi.org/10.1016/j.cell.2018.08.060 Multi-omics in environmental chemistry ‒Identified plant centric & human centric ‘exposure clouds’ with constant interaction mediated by bacteria & fungi ‒ ‒Identified many location/ lifestyle specific airborne pathogens & harmful toxins https://doi.org/10.1016/j.cell.2018.08.060 ‘omics’ takeaway messages ̶‘omics’ focus on systems/network study ̶‘omics’ techniques can easily collect lots of data ̶Theory and research questions are crucial for understanding ̶ ̶Need to study the genetic – environment interface in order to understand phenotype development, adaptation, evolution etc. • i.e. to fully investigate why anything is what it is