Omics Technologies used in Nutrition

The Science of Nutritional Genomics

▪ Most human cells contain 46 chromosomes, or pieces of
DNA (deoxyribonucleic acid)

▪ DNA sequences result in genes, and genes encode proteins

▪ The entire set of DNA found in a cell or living organism

comprises the genome

▪ Nucleotides are the building blocks of DNA

▪ Adenine (A)
▪ Guanine (G)
▪ Cytosine (C)
▪ Thymine (T)
 Common Genetic Variants in Nutrigenomics

▪ Differences in nucleotides within a gene produce genetic

polymorphisms
• Single Nucleotide Polymorphism = “SNP”
o Example: a “C” replacing an “A” !"#$%&'#$()&"*#
• Insertion/deletion = deleted segments ( “del”) or additional
inserted segments ( “ins”) !"#$%&'#((#$%&)*&+,,-,

• Copy Number Variants (CNV) = multiple functional copies of

a segment of DNA !"#$%&#'()*&%'+(*,(-./

▪ We inherit two copies of most genes, one from each parent

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different forms (e.g. A and C,
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• Therefore, three possible combinations
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(or “genotypes”):
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o Example: AA, CA, or CC "%%2#'*/#!/'+)*,)#2)8)/2!/0#%/#9.*-#0)/)#-$8):
Example: Single Nucleotide Polymorphism

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 Possible Types of SNPs !""!#$%&'"&()*(&+,&-./-0%&
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(AA) sequence
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Can still affect DNA
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may affect protein truncated – usually
or mRNA stability – may
function affects protein function
affect protein function

Image by MansiG123. Adapted from https://commons.wikimedia.org/wiki/File:Types_of_SNP_new1.png under CC BY-SA 4.0 license

 SNPs Can Affect Protein Structure & Function

https://ghr.nlm.nih.gov/primer/mutationsanddisorders/possiblemutations
 A Few Points on SNP Names and Info

There is no standard nomenclature, but generally speaking:

• Rs (Reference SNP) number: Unique identifier from dbSNP (NCBI database)
• Gene/protein name, location of variant and nucleotide or AA substitution
• Example:
• rs1801133
• MTHFR 667C>T MTHFR: Methylene tetrahydrofolate reductase
• MTHFR Ala222Val Converts dietary folate into bioactive form
• MTHFR A222V

Where to look up information on genetic variants, genes and their effects:

• PubMed (https://www.ncbi.nlm.nih.gov/pubmed/)
• dbSNP (https://www.ncbi.nlm.nih.gov/snp/)
• ClinVar (https://www.ncbi.nlm.nih.gov/clinvar/)
• OMIM (https://omim.org/)
• Ensembl (https://useast.ensembl.org/index.html)
• SNPedia (https://www.snpedia.com/index.php/SNPedia)
• Etc.
 Our Definition of Nutrigenomics

Using genetic information and genomic technologies to investigate

how nutrients interact with our genome to impact our health
and performance.

Diet Genes

Personalized Nutrition
Genomic variations can have profound effects

• Epigenome
 ‘Omics’ Technologies
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Epigenomics

Nutrients Transcriptomics

Proteomics

Lipidomics

Microbiomics
Metabolomics …etc.!
 Terminology
▪ Genome: A complete set of DNA in a cell or organism
▪ Genomics: the sequencing, assembly and analysis of structure and function of
genomes
▪ Genetics: the study of heredity and passing characteristics down from
generation to generation; it can be limited to one or a number of genes
▪ Transcriptomics: The genome-wide study of gene expression
▪ Proteomics: The study of protein structure and function
▪ Metabolomics: The study of metabolites present in a tissue, cell, organ, or
entire organism; metabolites are small molecules produced by cellular reactions
▪ Lipidomics: The study of lipid profiles and lipids present in biological cells,
tissue or fluids
 Genomics
▪ A complete set of DNA in a cell or organism is called a ‘genome’
▪ ‘Genomics’ refers to the sequencing, assembly and analysis of structure and function of
genomes
▪ The human genome has ~3 billion base pairs made up of 4 nucleotides (A,C,G,T)
▪ Genetic differences occur between individuals
▪ Common genetic differences include insertions/deletions, CNVs and SNPs
▪ Variations in genes can affect nutrient metabolism and response, eating behaviours, etc.

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 Epigenomics
▪ The study of inherited traits across a genome not caused by DNA sequence
alterations
▪ Different cell types are a product of the activation or deactivation of genes in an
individual's tissues and organs to create functionally different cell types
▪ DNA methylation and histone modification are the two major types of epigenetic
changes that can occur.
▪ Nutriepigenomics is the study of epigenomic modifications in relation to nutrition
▪ Epigenetic modifications can lead to disease through the disruption of cellular
processes
▪ Epigenomic patterns are maintained during cellular replication and passed on to
daughter cells
▪ Epigenomic imprinting takes place during embryonic development, making
perinatal nutrition an important factor for epigenomic development
 Transcriptomics
▪ The genome-wide study of gene expression
▪ Before a DNA sequence is translated into a protein it is transcribed into
messenger RNA (mRNA)
▪ mRNA molecules are present within a cell until they are processed into proteins
and degraded
▪ Genes that are highly expressed produce more mRNA copies than those that are
poorly expressed
▪ Gene expression can be influenced by factors such as cell type, genetic variations,
environmental factors, epigenetics and disease states
▪ Nutritional transcriptomics refers to the effects of diet on gene expression and its
relation to nutrition-associated chronic diseases
 Transcriptomics
Courtesy: National Human Genome Research Institute

Transcriptomics
Courtesy: National Human Genome Research Institute
 Proteomics
▪ The study of protein structure and function
▪ Proteome refers to the complete set of proteins present in a biological sample
▪ The sequence of up to 20 structurally unique amino acids determine the structure
of a protein
▪ The sequence of amino acids in a protein is determined by the sequence of base
pairs present in the corresponding gene
▪ The structure of the protein is also defined by interactions between amino acids,
as well as protein-wide interactions (3D folding), and interactions with surrounding
proteins !"#$%!&'!%()&%)*+$,%',"+$-&%."*/-&0
▪ Proteins regulate cellular processes such as the absorption, molecular transport,
cellular uptake, biotransformation, metabolism and elimination of nutrients
▪ Proteomics can use protein concentrations as a means to determine responses to
dietary exposure, and as biomarkers for disease
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Proteomics
Proteomics

Courtesy: National Human Genome Research Institute 29

Cornell, B. 2016. Proteome. [ONLINE] Available at: https://ib.bioninja.com.au/standard-level/topic-2-molecular-biology/24-proteins/proteome.html [Accessed 12 May 2020]

Courtesy: National Human Genome Research Institute 19

 Metabolomics
▪ The study of metabolites present in a tissue, cell, organ, or biological fluid
▪ Metabolites are small molecules produced by cellular reactions
▪ Sometimes referred to as metabonomics.
▪ Mass spectrometry and nuclear magnetic resonance (NMR) are the common
analytical platforms used. !"##$#%&'$(#$!)*&$&+#(,(-&$./,$+!*$(#$0/"+(,",(-&$1!"##$#%&'$(#$!)#,23$4)*$5(#')-&*36

▪Metabolites known as xenometabolites are produced through cellular reactions

when a foreign substance (drug or dietary component) is introduced
▪ The study of xenometabolites is important in identifying factors that differ
between individuals and their body's response to ingested compounds
▪ Metabolomics can involve the analysis of hundreds or thousands of molecules
and usually requires sophisticated statistical approaches.
Metabolomics
Courtesy: National Human Genome Research Institute

21
 Lipidomics
▪ The study of lipid profiles and lipids present in biological cells, tissue or fluids
▪ Lipids make up the structure of every cellular membrane and are used by the
body as signalling molecules and an important energy source
▪ Lipids derived from dietary sources (such as fatty acids) can be measured and
quantified to provide insight into physiological pathways regulated
▪ By determining changes in the cellular metabolism of lipids, abnormal lipid
profiles can be determined
▪ Abnormal lipid profiles are present in many nutrition-related disorders (such as
diabetes and cardiovascular disease) and can be used to better understand how
nutrition affects lipid metabolism and the progression of these diseases
▪ Lipidomics is often categorized as a sub-branch of metabolomics and most of the
same quantification techniques are used for both fields of study
Microbiomics
Courtesy: National Human Genome Research Institute
Diet interacts with all levels of the ‘ome’ spectrum

• Epigenome