Nutrigenomics: An emerging science... Nutrition + Genomics omics study

1. NUTRIGENOMICS; AN EMERGING
TOOL IN NUTRITION
SPEAKER: Siddhartha S. Pathak

2. Introduction
• Nutrition ; induce metabolic changes in muscle,
being reflected in tissue remodeling, increased
protein turnover, and muscle atrophy.
• From a production point of view, these changes
influence efficiency of production and meat quality.
• Tremendous economic importance.

3. Contd…
• Relationship of nutrition with health and production
is long known.
• But how the components exert their effect-gradually
known.
• Expression of genes; Coding of certain protein in the
genome.

4. Contd…
• Constant switching on or off of gene; Physiological
processes and pathological events.
• Bioactive feed components; key environmental
factors regulating gene expression
(Mead, 2007)
• Nutrient- gene interaction wide spread and well
known.

5. Contd…
• Advent of molecular tools and analysis systems
revealed, mechanism by which individual senses
nutrient status and their metabolism.
• With these knowledge a new area of study called
“NUTRIGENOMICS” has emerged.
(Roche et al 2006)

6. A time for New Nutritional
Strategies
 We need to make a Change
what we think of feed
 We need to change the way
we evaluate

7. HISTORY
• 400BC : Hippocrates speculated the hypothesis that
the warm body temperature was innate
• 19th century : Liebig identified carbohydrates,
proteins, lipids, and other macronutrients that
released heat.
• 18th and 19th centuries : “Chemical and Analytical
Era of Nutrition”

8. Contd…
• 20th century :“Biological Era” studies on metabolism
and chemistry of the food.
• 21st century : “Post- Genomic Era” characterized by
the integration of three fields: biological, social, and
environmental, scientific discoveries on nutritional
metabolism are included.
• After the Human Genome Project: evolution of
bioinformatics provided advances in “omics” science
research.
• Leading to the development of
“NUTRIGENOMICS”.

9. What is a gene??...
• Functional and physical unit of
heredity passed from parent to
offspring.
• Genes are segments of DNA that
contain the information for making
a specific protein.
• Variations in the DNA; results in
the changes to the structure and
function of the protein.

10. What is Nutrigenomics??
• “Nutrigenomics” refers to study of the effects of
nutrients/bioactive food on gene expression of an
individual.
• The study of how genes and gene products interact
with dietary chemicals to alter phenotype and,
conversely, how genes and their products metabolize
nutrients is called nutritional genomics or
“nutrigenomics” (Kaput et al., 2005).

11. Contd…
• A new science seeking to understand the influence of
dietary components on the Genome, Transcriptome,
Proteome, and Metabolome (Ronteltap et al., 2009).
• Simply, “It is a science which study the effect of
nutrients on the gene expression.

12. OMICS SCIENCES

13. Why NUTRIGENOMICS ????
• Focus of most nutritional research has been on
parameters related to
 bird growth performance
 reproduction
 intestinal health or
 the utilization of specific nutrients as a mean to
reduce excess waste.

14. Contd…
“N”; individual animals/birds
statistical differences
Replication of treatments ;
statistical differences between
individual treatments
Closely interrelated measured
parameters
DIFFICULTIES
Considerable time

15. Contd…
For example, damage in the intestine as a result of
bacterial overgrowth will result in reduced nutrient
absorption and, subsequently, reduced animal
performance.
The question remains if the excess availability of
nutrients leads to more bacterial growth or if bacterial
growth leads to a lower availability of nutrients

16. Contd…
Relationship “specific nutritional intervention
and the impact on health and performance” lies in a
deeper understanding of the impact of these
nutrients on the expression of specific genes or
specific metabolic pathways.
Development of molecular tools; enable
researchers to study the effects of specific nutrients
on the whole genome
(Muller and Kersten, 2003).

17. • Selenium deficiency shown to alter protein synthesis
at transcriptional level (Rao et.al., 2001).
• Results; adverse effect like enhancement of stress
through up-regulation of specific gene expression
and signaling pathway.
• Genes responsible for detoxification mechanism and
protection from oxidative damage were hampered,
• Alteration of phenotypic expression

18. Contd…
• Hence, it is apparent that possibly “nutrigenomics”
identify the specific markers to manipulate gene
expression through use of nutrients.
• Path breaking tool through identification of pathways
responsible for dietary induced diseases.

19. NUTRIGENOMICS: HOW DOES IT WORK???
Fig. Central Dogma (Francis Crick, 1956)

20. Contd…
• These processes are controlled by the basic genetic
make-up, external factors such as
Disease
Environmental toxins or specific nutrients
• Rather than measuring the effect of a specific
nutrient on animal performance or the physiological
response at the end of the experiment, researchers
can extract “specific messenger RNA (mRNA)” from
tissue at any stage.

21. Contd…
• Amount of mRNA present relates to the relative
amount of copies of known genes, measured by
using gene chips.
• Using contrasting colour labels, it can be determined
if a gene is “up-regulated”, “down-regulated” or
“unaffected” as a result of a specific dietary
manipulation.

23. NUTRIENT REGULATION OF GENE EXPRESSION
• Feed had basically one job: get metabolized to
provide energy for the cell.
• Indeed this happens to most dietary chemicals- but
not all.
• Some don’t get metabolized at all.

24. Contd…
moment they are ingested
they are peel off
become ligands-molecules
binds to protein
Involved in turning on certain genes to one
degree or another.

25. Contd…
• Nutritional regulation of gene expression in eukaryotic
cells; considerably slower due to the
(Sanderson, 1998).
Complexity of mechanisms controlling gene
expression epithelium (IE) cells respond
Difficulty in identifying specific metabolites
to which the intestinal epithelium (IE) cells
respond

26. • Exogenous nutrients can affect gene expression directly
(A) or indirectly (B and C in Figure).

27. EFFECT OF CARBOHYDRATE ON GENE
EXPRESSION
• In the liver, glucose, in the presence of insulin,
induces expression of genes encoding glucose
transporters and glycolytic and lipogenic enzymes,
eg. acetyl-CoA carboxylase (ACC)
• Although insulin and glucagon were long known as
critical in regulating gene expression, it is only
recently that Glucose also have been shown to play a
key role in transcriptional regulation.

28. REGULATION OF GENE EXPRESSION BY DIETARY
FAT
• Plays role as an energy source and its effects on
membrane lipid composition, dietary fat has
profound effects on gene expression.
• The effects of dietary fat on gene expression reflect
an adaptive response to changes in the quantity and
type of fat ingested.
• Specific fatty acid–regulated transcription factors
have been identified in bacteria, amphibians and
mammals

29. Contd…
• PPARs (Peroxisome proliferator-activated receptors )
• Regulated either by direct binding of (oxidised) fatty
acids, fatty acyl–coenzyme A or oxidised fatty acid
(eicosanoid) regulation of cell surface receptors and
that of intracellular calcium levels as well as
activation of signaling cascades (Jump, 1999).
• At the cellular level, the physiological response to
fatty acids will depend on the quantity, chemistry
and duration of the fat ingested

30. Contd..
“Short-term (2-day) feed restriction”
 no change either in the number or the size of fat cells in
white adipose tissues
 Declined mRNA expression of PPARγ2, glucocorticoid
receptors (GR)
“Long-term (14-day) feed restriction”
 an increased number of smaller adipocytes
 Recovered expression of PPARγ2 and
glucocorticoid.

31. EFFECT OF PROTEIN ON GENE EXPRESSION
• Normal insulin secretion is influenced by level of
Protein Kinase C (PKC), K+ channel protein, calcium ion
(Ca 2+).
• Increased ATP to ADP ratio achieved through glucose
metabolism, close the K+ ATP channel, which leads to
depolarization of -cells.
• Depolarized -cells opens the voltage dependent Ca 2+
channels which results in influx of calcium leads to
exocytosis of insulin granules.

32. Contd…
• Protein-rich diets cause a shortage of mRNA
necessary for expression of the fatty acid synthase
gene in the adipocytes, resulting in the moderation
of total body fat.

33. EFFECT OF MINERALS ON GENE EXPRESSION
• As similar to other nutrients, mostly minerals are
involved in several gene expressions
• “Bivalent metals”; strong influence gene expression.
• Both parenteral and oral zinc or cadmium application
enhance the transcription rate of the metallothionein
(MT) gene in intestinal tissue.
(Ouellette et al., 1982)

34. Cadmium
• Prolongsthe half-life of MT mRNA in hepatocytes.
• This effect on the half-life prolongation of MT mRNA
tissue specific.
• Influence of cadmium is stronger than that of zinc,
and the intensity of effect in spermatocytes and
spermatids is higher than in hepatocytes and
fibroblasts (De et al., 1991)

35. Zinc
• Improvement of zinc status results in a significant
reduction of COX mRNA abundance.
(Fong et al. (2005)
• Zinc oxide supplementation: increased insulin-like
growth hormone I (IGF-I) and IGF-I receptor gene
expression in the small intestine of weanling piglets
(Li et al., 2006)

36. EFFECT OF VITAMINS ON GENE EXPRESSION
• Vitamins are micronutrients needed in very small
quantity and are involved in gene expression.
• Biotin is involved in various essential proteins
(enzymes) synthesis at gene level.
• Vitamin C is involved in hepatic gene expression

37. Vitamin A
• Vitamin A exerts its regulatory function in the form of
retinol and retinoic acid.
• The most important target tissues are in the adrenal
glands, testes, cerebellum, kidneys, prostate, cerebral
cortex, skin and the viscera.
• After retinoic acid binds to its receptor, it will stimulate
the transcription and translation of vitamin A-responsive
genes, including some involved in cell
differentiation (growth hormone, glycerolphosphate
dehydrogenase and leptin production among others.

38. Contd…
• Deficient vitamin A status was found to negatively
influence hepatic PEPCK gene expression in mice. By
the oral application of retinoic acid that expression
could be restored
(Scribner et al., 2005)

39. BIOACTIVE FEED COMPONENTS

40. RESEARCHERS EXPERIMENT
Averous et al.
2003
Amino acids by themselves or along with hormones can
play an important role in the control of gene expression
Oullette et al.
1982
Bivalent metal ions like zinc or cadmium enhances the
transcription rate of the metallothionein gene in intestinal
tissue
Bremner and
Beattie 1990
Iron influences transferrin and ferritin concentrations by
exerting an effect on mRNA stability and the translation
rate.
Yuchi et al 1996
Hyperammonaemia due to significant depression of
ornithine transcarboxylase gene expression is seen in biotin
deficient individuals

41. FUNCTIONAL GENOMICS
• Measures the level of expression of all or a selected
subset of genes.
• The most powerful tool available is DNA array
technology.
• Using one array the expression level of more than
80,000 genes can be measured in parallel, and tens
of samples can be screened per day.

42. Contd…
• In addition, high per-analysis cost seriously reduces
the number of measurements performed per study.
• Furthermore, different platforms are used, e.g.
cDNA, oligonucleotide array and printed microarrays,
on chip synthesis.

43. PROTOCOLS INVOLVED IN NUTRIGENOMICS
Transcriptomics
Proteomics
Metabolomics

44. TRANSCRIPTOMICS
• “Transcriptome” Complete set of RNA that can be
produced from the genome.
• Study of the transcriptome, i.e. gene expression at
the level of the mRNA
• Several methods to contour gene expression
RT-PCR
cDNA
Microarray

45. DNA ARRAY
• Technology (also called DNA chip technology) is
currently the most powerful.
• Tool in transcriptomics, which enables the
measurement in parallel and in tens of samples, of
the expression of up to 50,000 transcripts.
• Problems such
 Standardization of the data
 Sharing of results

46. DNA Microarray technology

47. GENE EXPRESSION PROFILING

48. PROTEOMICS
• Proteins are the ‘‘molecular robots’’ that do all the
work. (Kussmann et al 2009)
• Proteomics ; studies related to
 Structure of proteins,
 Expression levels,
 Biochemical activity
• Identify and quantifies bioactive proteins and
peptides and addresses questions of nutritional
bioefficacy (Kussmann et al 2006)

49. TECHNIQUES
• Western blot
• Immune histochemical staining
• Enzyme linked immunosorbent assay (ELISA)
• Mass spectrometry.

50. APPLICATION OF PROTEOMICS IN ANIMAL AND
FEED SCIENCES
• Assessment of the influence of dietary components
on the proteomes of selected organs, for example,
the liver.
• “Proteome” represents the protein equivalent of the
genome, which is determined by the sequence, the
type and number of its nucleotides.

51. • Evaluate the effect of dietary methionine on breast-meat
accretion and protein expression in skeletal
muscle of broiler chickens
(Corzo et al., 2006)
• “Tandem mass spectrometer” a total of 190
individual proteins were identified from Pectorali
major muscle tissue;
• Three of them were recognized which differed
distinctly between the treatment proteome;
Potential biomarkers regulated by a methionine
deficiency in broiler chickens.

52. METABOLOMICS
• Study of chemical processes involving in the
metabolites
• Examine the whole metabolism
• Reflects the behavior of different patterns of genes ,
• Investigates the metabolic regulation, in response to
specific environmental changes.

53. TECHNIQUES
• Nuclear Magnetic Resonance (NMR) spectroscopy,
• High performance liquid chromatography (HPLC)
• Gas chromatography-mass spectrometry (GC-MS).
• Main characteristics of these new technologies were
miniaturization, automation, high throughput and
computerization

54. APPLICATIONS
1. To develop feed matching to its genotype
2. To select nutrients fine-tuned with genes of bird
3. To understand role of nutritional management in
performance (production/disease) of bird
4. Immune system
5. Diseases

55. TO DEVELOP FEED MATCHING TO ITS GENOTYPE
• “Goal” develop feeds, matched to genotypes of birds
to benefit health and enhance normal physiological
processes.
• “gene chips” that contain the genetic code of bird;
measure the effects of certain nutritional
supplements, and how they alter the gene
interactions of the body.

56. TO SELECT NUTRIENTS FINE-TUNED WITH
GENES OF BIRDS
• Nutrigenomics, not alter the genetics of an animal nor
to genetically modify the animal rather altering the
activity of genes, “switching on good genes and
keeping bad ones switched down” .
• Selection of nutrients for fine-tuning genes and DNA
present in every cell and every tissue of an animal.
• Example: stress response genes

57. ROLE OF NUTRITIONAL MANAGEMENT IN
PERFORMANCE (PRODUCTION/DISEASE) OF BIRDS
• Gene expression studies will allow for the
identification of pathways responsible for
economically important traits.
• Dietary manipulations and nutritional strategies are
key tools for influencing production.
• Provides new tools; clearly understand how
nutritional management can be applied to address
disease, performance and productivity in birds.

58. NUTRIGENOMICS AND IMMUNE SYSTEM
• Nutrition is the “key element” of health maintenance,
particularly for the immune system.
• A deficiency of an essential nutrient will eventually
affect the body’s performance.
• Immune system is particularly sensitive to deficiencies,
and once the immune system is compromised,
negative consequences follows.

59. Contd…
• Deficiency is now rare in modern livestock
production systems.
• Move to the next stage rather than merely
preventing deficiency, we can strive to actually meet
the bird’s exact requirements from its diet, in order
that it can meet its genetic potential.

60. NUTRIGENOMICS AND DISEASES
• DNA microarrays; simultaneous assessment, of the
transcription of thousands of genes and of their
relative expression between normal cells and
diseased cells or before and after exposure to
different dietary components.
• Assist in the discovery of new biomarkers for disease
diagnosis and prognosis prediction and of new
therapeutic tools.

61. Contd…
• Functional integrity of gene; depends on metabolic
signals that the nucleus receives from internal
factors, e.g.
hormones, and
external factors, e.g. nutrients
• Genomes evolve in response to many types of
environmental stimuli, including nutrition.
• Therefore, the expression of genetic information can
be highly regulated by nutrients found in feed.

62. FUTURE OF NUTRIGENOMICS
• Nutrigenomics; new tool for nutritional research in
mitigating the problems related to bird’s health and
production.
• In coming year’s innovations in nutrition research with use
of various molecular technologies will indubitably update
our basic understanding of nutrient gene interrelationship
and help to define new methods for managing production.
• Finally by targeting the specific gene through nutritional
manipulation, it may be possible to get the desired
performance in terms of health as well as production.
• Discovery of “gene markers” related to economically
important traits; improved by dietary regimens

63. CONCLUSION
• Information from nutrigenomics; lot of knowledge,
understand the role of proper nutrition on
performance, health and disease in birds.
• Molecular findings with information from whole-animal
studies, such as weight gain or egg
production, we can better understand how nutrients
specifically elicit their effects on animal health and
production.

64. Contd…
• Widely utilized microarray or DNA chip technology in
nutrigenomics research enables
 Not only the screening of large numbers of genes
 Simultaneously, giving a comprehensive picture
of the variation of gene expression
 Patterns, but will also provide explanations for
complex regulatory interactions

65. Contd…
• “Nutrigenomics” is still young and emerging tool for
rapid and effective evaluation of nutritional
strategies.
• Provide a valuable tool for producers to differentiate
and identify nutritional strategies to maximize not
only animal performance but ultimately profitability.

66. THANK YOU