The Omics Revolution

Question 1

List the classic measures of toxicity (6 measures)

Answer 1

• Histopathology
• Clinical Chemistry
• Metabolism
• Physiology
• Enzymology
• Electron Microscopy

Question 2

List the new measures of toxicity (2 categories, 3 measures each)

Answer 2

• Gene expression:
  
  • RNA Microarrays
  • RT PCR
  • Deep sequencing
• Protein expression:
  
  • Western Blot
  • Eletrophoresis
  • ChIP

Question 3

Define the goal of the various “Omics”

Answer 3

To determine whether the expression of genes, RNAs, proteins or metabolites (“signatures”) can serve as markers to predict toxicity

Question 4

Define toxicogenomics and its three principle goals

Answer 4

The effects of a toxicant on all of the denes of a cell or tissue at the DNA, RNA protein, and metabolite levels.

• Understand the relationship between environmental stress and human disease susceptibility
• Identify useful biomarkers of disease and exposure to toxic substances
• Elucidate the molecular mechanisms of toxicity

Question 5

Mow many of each histone are on a nucleosome, and how many base pairs does it coil?

Answer 5

2 of each (H2A, H2B, H3, H4) octameric

147 bp

Question 6

What is the difference between Transcription and Translation in terms of gene expression?

Answer 6

Transcription: DNA -> preRNA

Translation: RNA -> protein

Question 7

True/False? Gene expression precedes protein changes and toxicity

Answer 7

True

Question 8

True/False? Changes in gene expression are not measurable at low doses

Answer 8

False

Question 9

List the route of a typical toxicogenomic flow scheme (3 steps)

Answer 9

1) Exposure
2) In vivo study (dose/response time course)
3) Gene expression
- Amount of genes perturbed by candidate in each organ
- Signalling pathways representing significantly perturbed genes
- Compare with toxicogenomic database for predicted toxicological effects based on similarities of gene expression profiles

Question 10

What are the 6 applications of a toxicogenomic flow scheme?

Answer 10

• Deciphering mechanism of action/pathway analysis of toxicant
• Response at low doses
• Revealing potentially novel health effects
• Identification of perturbed pathways -> targeted follow up
• Biomarker discovery
  Predictive toxicogenomics

Question 11

What year did affymetrix debut in?

Answer 11

1993

Question 12

List the two types of microarrays and give examples of each.

Answer 12

Spotted chips: 
    - cDNA or PCR products
    - Oligonucleotide
        Perfect match/mismatch
        Long oligonucleotide
        Short oligonucleotide

On-Chip Synthesis:
- Photolithography (affymetrix)

Question 13

What are the six advantages of microarrays?

Answer 13

• Eliminate questionable or low-quality measurements
• Remove probes in background
• Adjust the measurements to facilitate comparisons
• Select genes that are differentially expressed between samples
• Identify the biological processes and molecular functions that are alteredd
• Place data in the context of a health outcome

Question 14

Define the p-value

Answer 14

P(data|H0 is true)
Probability of getting the same results givne that there is no link

low p-value incurs statistical significance

Question 15

What are 4 reliable ways to determine significant changes in expression?

Answer 15

• Fold change
• t-test/ANOVA
• Permutation test (MANOVA or SAM)

Question 16

Define GO

Answer 16

Gene Ontology, a controlled vocabulary of terms for describing gene product characteristics and gene product annotation data (includes cellular compartment biological function, and molecular process)

Question 17

What does the KEGG pathway record?

Answer 17

everything

• metabolism
• genetic information processing
• environmental information processing
• cellular processes
• human diseases
• Drug development
• Toxicity assessment

Question 18

What are the 10 steps in designing an experiment to study mechanism of action?

Answer 18

• Adequate sample size!
• Appropriate selection of time points
• Appropriate selection of treatment conditions
• Appropriate tissue/cells sampled
• Sample collection - randomization or block design
• High Quality RNA!
• Randomization and microarray experimental design
• implementation of QA/QC
• Appropriate normalization/filtering
• Validation with alternative technologies!

Question 19

Possible reasons for discrepancies in published studies? (6)

Answer 19

• Lenient filtering methods for poor or low intensity spots
• Inclusion of saturated signals in analysis
• incorrect probe matching
• Improper data handling
• incorrect statistical analysis
• insufficient biological validation

Question 20

Limitations of toxicogenomics? (6)

Answer 20

• Difficulty in analysis of high density data
• Difficulty in integration of data obtained by different technologies
• Difficulty in linking “omics” data to specific adverse effects
• Difficulty in translating statistical assessments into biological understanding
• Limitations of incomplete functional annotation of genome databases
  Incomplete knowledge of functional pathways and networks, particularly trans-genome relationships

Question 21

Methylation of DNA histones typically _______ gene expression + name the two enzymes responsable

Answer 21

Suppresses.

SAM - S-adenosylmethionine
DNMT - SNA methyltransferase

Question 22

List the 5 histone modifications

Answer 22

Acetylation
Methylation
Ubiquitination
Sumoylation
Phosphorylation

Question 23

5 types of non coding RNAs

Answer 23

miRNAs
piRNAs
siRNAs
lncRNAs
tsRNAs