OmicsOmics TechnologyTechnology

Trishita IssarI M.Sc.Foods, Nutrition &Dietetics

Roll no. 26

Andhra University

Contents

Introduction –Introduction –

What is OMICS technology?What is OMICS technology? History of Omics History of Omics Omes and Omics Omes and Omics Types of OmicsTypes of Omics

Omics related to Nutrition Field Omics related to Nutrition Field NutrigenomicsNutrigenomics

Genomics Genomics Proteomics Proteomics TranscriptomicsTranscriptomics Metabolomics Metabolomics

Nutrigenomics: Nutrigenomics: the effect of food on genesthe effect of food on genes

Genetic effects of FoodGenetic effects of FoodConclusion Conclusion

Contents…..

Introduction

The complete sequencing of the The complete sequencing of the human genome has ushered in a human genome has ushered in a new era of systems biology new era of systems biology referred to as referred to as Omics technologyOmics technology. .

The term omics refers to the The term omics refers to the comprehensive analysis of comprehensive analysis of biological systemsbiological systems. .

Systems biology is “biology” that Systems biology is “biology” that focuses on complex systems of focuses on complex systems of life.life.

History of OMICS

Modern uses of the term Modern uses of the term "omics""omics" derive from the term genome derive from the term genome (hence genomics), a term invented (hence genomics), a term invented by Hans Winkler in 1920, although by Hans Winkler in 1920, although the use of -ome is older, signifying the use of -ome is older, signifying the ‘‘collectivity’’ of a set of things. the ‘‘collectivity’’ of a set of things.

The word genomics is said to be appeared in the 1980s and became widely used in the 1990s. 

The first genome was completely sequenced by Sanger in Cambridge, UK, in the 1970s. Genome is the most fundamental part of many omics.

The suffix “-om-” originated as a back-formation from “genome”, a word formed in analogy with “chromosome”.

The word “chromosome” comes from the Greek stems meaning colour and body.

The word GENOMICS implies some hidden network among genetic elements. This network is regulated by many other omics such as proteomics, transcriptomics , metabolomics and physiomics.

Omes & Omics

The word The word ’omics’’omics’ refers to a  refers to a field of study in biology ending field of study in biology ending in the suffix in the suffix -omics-omics such as  such as genomics, metabolomics, or genomics, metabolomics, or proteomics. proteomics.

The related The related omeome addresses  addresses the objects of study of such the objects of study of such fields, such as the genome, fields, such as the genome, metabolome, or proteome metabolome, or proteome respectively.respectively.

Types of OMICS

Antibodyome & Antibodyomics Bacteriome Cardiogenomics Cellome & Cellomics Diseaseome & Diseaseomics Epigenome & Epigenomics Foodome &Foodomics

Genome & Genomics Glycome & Glycomics Healthome & Healthomics Herbome  & Herbomics Hygienome &Hygienomics Immunolome & Immunolomics Lipidome & Lipidomics Lipoproteome & Lipoproteomics

Types of OMICS ….

Metabolome & Metabolomics Neurogenome Nucleome Nutrigenomics Proteome & Proteomics Sequenceome Transcriptomics Virusomics AND MANY MORE…..

Types of OMICS ….

Research in…

The omics technology has driven new areas The omics technology has driven new areas of research:of research: DNA and protein micro arraysDNA and protein micro arrays Mass spectrometry Mass spectrometry A number of other instruments that enable A number of other instruments that enable

high-throughput analysis. high-throughput analysis.

Omics related to Nutrition

NUTRIGENOMICS &NUTRIGENOMICS & its related technologies : Genomics Transcriptomics Proteomics Metabolomics

The science that studies the effect of dietary bioactive compounds on gene expression is called nutrigenomics.

Nutrigenomics is a modern discipline at the interface between genetics, molecular nutrition, molecular biology, pharmacogenomics and molecular medicine.

MOLECULAR MEDICINE

PHARMOCO--GENOMICS

MOLECULAR BIOLOGY

MOLECULAR NUTRITION

GENETICS

BIOINFOMATICS

NUTRIGENOMICSNUTRIGENOMICS

Nutrigenomics

Nutrigenomics is the science that examines the response of individuals to food compounds using post-genomic and related technologies. (e.g. genomics, Transcriptomics, proteomics, metabolomics etc.).

The long-term aim of Nutrigenomics is to understand how the whole body responds to real foods .

The huge advantage in this approach is that the studies can examine people (i.e. populations, sub-populations - based on genes or disease - and individuals), food, life-stage and life-style without preconceived ideas.

Nutrigenomics focuses on the relationship between dietary nutrients and gene expression using state-of-the-art technology.

Nutrigenomics applies high –throughput molecular biology techniques including sequencing and genotyping (genomics), Transcriptomics, proteomics and metabolomics.

NUTRIGENOMICSNUTRIGENOMICS

GENOMICS TRANSCRIPTOMICS PROTEOMICS METABOLOMICS

DNA Metabolites

Analytical tools in molecular nutrition :Analytical tools in molecular nutrition :

mRNA Protein

TranscriptomicsTranscriptomics determines patterns of gene expression in response to a nutrient

ProteomicsProteomics studies the effect of nutrients on protein synthesis, protein structure and patterns of protein expression.

The profile and function of metabolites are analyzed by MetabolomicsMetabolomics techniques,

The comprehensive data handling is finally accomplished by bioinformatic bioinformatic tools

Genomics

Genomics may be described as the comprehensive analysis of DNA structure and function.

Understanding biological diversity at the whole genome level will yield insight into the origins of individual traits and disease susceptibility.

Though organisms such as humans are quite similar at the genetic level, differences exist at a frequency of about 1 in every 1000 nucleotide bases. This translates into approximately 3 million base differences between each individual. Such changes are referred to as single nucleotide polymorphisms (SNPs)

A polymorphism is distinct from a mutation. The latter is considered rare; affecting less than one percent of the species, whereas a polymorphism is relatively common and its prevalence is no different to what is considered normal.

GENETIC TESTING

Genetic testing involves the direct examination of the DNA molecule itself. A scientist scans a patient’s DNA sample for mutated sequences.

GENE THERAPY

Gene therapy may be used for treating, or even curing, genetic and acquired diseases like cancer and AIDS by using normal genes to supplement or replace defective genes or to bolster a normal function such as immunity.

APPLICATIONS OF GENOMICS: Diagnose a disease. Confirm a diagnosis. Confirm the existence of a disease in individuals. predict the risk of future disease in healthy individuals.

Genetic testing is now used for: Carrier screening, or the identification of unaffected individuals who

carry one copy of a gene for a disease that requires two copies for the disease to manifest.

Prenatal diagnostic screening Newborn screening Presymptomatic testing for predicting adult-onset disorders Presymptomatic testing for estimating the risk of developing adult-onset

cancers Confirmational diagnosis of symptomatic individuals Forensic/identity testing

GENOMICS AND PROTEOMICS

Genomics focuses on an organism's genetic makeup, while proteomics focuses on gene products. 

Both are interrelated .  

Proteomics

The focus of proteomics is a biological group called the proteome.

The proteome is dynamic, defined as the set of proteins expressed in a specific cell, given a particular set of conditions. Within a given human proteome, the number of proteins can be as large as 2 million.

Proteins themselves are macromolecules: long chains of amino acids. This amino acid chain is constructed when the cellular machinery of the ribosome translates RNA transcripts from DNA in the cell's nucleus. The transfer of information within cells commonly follows this path, from DNA to RNA to protein.

Techniques in Proteomics

Gel electrophoresis

X-ray crystallography

Nuclear Magnetic Resonance spectroscopy

Mass spectrometry etc...

Applications of Proteomics

HIV Biomarkers Eg: ELISA &

immunohistochemical staining etc.. Alzheimer's disease Heart disease Cancerous cells

Transcriptomics

The transcriptome is the set of all messenger RNA (mRNA) molecules, or "transcripts," produced in one or a population of cells. The term can be applied to the total set of transcripts in a given organism, or to the specific subset of transcripts present in a particular cell type.

The study of transcriptomics, also referred to as Expression Profiling, examines the expression level of mRNAs in a given cell population, often using high-throughput techniques based on DNA micro array technology.

The use of next-generation sequencing technology to study the transcriptome at the nucleotide level is known as RNA-Seq.

Applications of Transcriptomics

The transcriptomes of stem cells and cancer cells are of particular interest to researchers who seek to understand the processes of Cellular differentiation and carcinogenesis.

METABOLOMICS

The development of metabolomics began in 1970 by Arthur Robinson.

Metabolomics is the "systematic study of the unique chemical fingerprints that specific cellular processes leave behind" - specifically, the study of their small-molecule metabolite profiles.

Metabolome refers to the complete set of small-molecule metabolites (such as metabolic intermediates, hormones and other signaling molecules, and secondary metabolites) to be found within a biological sample, such as a single organism.

Metabolites are the intermediates and products of metabolism. The term metabolite is usually restricted to small molecules.

Techniques in metabolomics: Mass spectrometry is mostly used in

metabolomics

Applications of Metabolomics Toxicity assessment/toxicology

Urine or blood plasma samples can be used to detect the physiological changes caused by toxic insult of a chemical (or mixture of chemicals)

Functional genomics. Metabolomics can be an excellent tool for determining

the phenotype caused by a genetic manipulation, such as gene deletion or insertion. More exciting is the prospect of predicting the function of unknown genes by comparison with the metabolic perturbations caused by deletion/insertion of known genes.

Nutrigenomics

The science that studies the effect of dietary bioactive compounds on gene expression is called nutrigenomics.

Nutrigenomics—understanding how nutrients —affect genes—will enable foods to be developed that can be used to prevent and treat disease.

In 1996, Ghai and coworkers filed a seminal patent which highlighted the potential for development of foods or supplements that could alter the expression of genes associated with human diseases (Ghai et al., 1999). They demonstrated that certain flavonoids found in citrus peel enhanced expression of a gene involved in the human body’s natural defense against cancer.

Genetic Effects of Food

Chemicals found in food interact with biochemical pathways at the molecular level—for example, to elicit allergic reactions alter (potentially increase or decrease) the levels of biomarkers, such as blood/sugar, cholesterol, and various proteins.

While researchers are exploring methods to identify bioactives that alter gene expression in humans, the food we eat is already altering expression of our genes.

Nutrient Gene impact Potential Disease

Folic acid DNAmethylation

Cancer

Fatty acids Bind totranscriptionfactors

Obesity

Vitamin D mRNA stability Kidneydisease

Flavones Increase mRNAsynthesis

Cancer

Theaflavins Decrease mRNAsynthesis

Arthritis

Table 1: How nutrients regulate genes

Ordovas et al. (2002) demonstrated how a

single-point mutation in the APOA1 gene alters how an individual responds to the effect of polyunsaturated fatty acids on HDL cholesterol levels.

Several genes directly involved in inflammation include COX-2,

tumor necrosis factor:

α (TNF-α), interleukin-1 (IL-1), phospholipase A2, 5-lipoxygenase (LOX), and inducible nitric oxide synthase (iNOS).

TARGETING INFLAMMATION

Omega-3s, on the other hand, such as

EPA and DHA, are competitive inhibitors of both COX and LOX, thereby having anti-inflammatory effects.

• Another study done by V.Mohan et.al “Gene Environment interactions and the Diabetes epidemic in India” at Madras Diabetes Research Foundation & Dr. Mohan’s Diabetes Specialties Center, Chennai.(2007)

They carried out gene-diet interaction studies, which revealed that the Adiponectin Gene polymorphism contributed to insulin resistance and Diabetes.

These subjects were at an increased risk for Hypoadiponectinemia.

Similarly, the Ala54Thr polymorphism of the fatty acid-binding protein 2 gene showed a synergistic effect with a high glycemic load increasing the risk for Hypertriglceridemia.

These studies indicate that the gene-diet interactions could play a major role in increasing the risk of Diabetes.

Conclusion

Routine use of Nutrigenomics in clinical labs, in turn, will demand a new brand of dietitians, genetic counselors and nutritional scientists.