Lecture 8 - The Omics Revolution

Question 1

New vs classical “old” measures of toxicity

Answer 1

Old: hisotpathology, clinical chemistry (ions, enzymes, …), metabolism, enzymology, electron microscopy
New: geen and protein expression
Geen: DNA microarrays, gene sequencing, PCR
Protein: proteomics, western blots, electrophoresis, ChIP

Question 2

What is the goal of omics in toxicity?

Answer 2

How does the toxicant affect the taregt at the RNA, portion, geen, or metabolic level?
1. We can try to find if a particular toxicant has a certain signature (and does it apply to the entire fmaily of specific toxicants?)

2. Is the signature of a toxicant on one cell characteristic of what happens in other cells?
3. Try to determine whetehr the effectcthe toxicant has is predictovie toxicity or isi t just a refelection of the cell’s response to chemical expsoure?

Question 3

Definitions of Omics

Answer 3

Genomics: study of all genes of a cell or tissue at dna level
Epigenomics: the study of all non-sequnce effects; all epigenetiuc modifications (ex: histones that DO NOT ALTER DNA SEQUWNCE**)
Transcriptomics: the study of all gene transcripts of a tissue (RNA LEVEL) –> gene transcript=RNA, “transcription”
Proteomics: study of all the proteins of a cell or tissue; usually uses mass spec
MetabolomicsL study of all small chemicals in a cell, looking at how proteins affect metabolites in a cell
Overall: toxicogenomics is the effect of a toxicant on all of the genes at the dna, rna, protein levels

Question 4

What are the problems with -Omics studies?

Answer 4

If you are doing transcriptomics or proteomics in whole organL such an arraycthat. Can miss changes in protein or rna levels (ex: there may be a larg effect in a small % of cells)
But if u use a pure cell line, cannot see what is happening i nwhole animal, either. Still, transcriptomics and proteomics require purified cell lines/populations

Question 5

Why use toxicogenomics?

Answer 5

1. Gene expression precedes protein changes and toxicity - this is the first response to a toxicant and toxicogenomics s are extremely sensitive markers of toxicants - there is often a fold diff b/w when you see gene effects and other effects
2. Measurable at low dose

Question 6

Applications of toxicogenomics

Answer 6

1. Allow us t ideceipher mechanissm that are triggered in a cell (which genes, and therefore which pathways)
2. Can see response ar very low doses
3. No need to kill animals for toxicogenomics - can do biopsy or take blood and seee how tissue responds
4. Toxicogenomics is an unbiased way to understand mechanisms - may reveal potential movel health effects because ur looking at EVERYTHING, allows totally new mechanisms to become apparent
5. Identify perturbed pathways and follow whats happening
6. Biomarker
7. Investigate assumptions
8. Predictive Toxicology as a goal

Question 7

Microarrays: Then and now

Answer 7

Past: cDNA LINEKD to a nylon memrbane w/ radioactive probes attached to the mRNA, use 1 probe (eventually went up to 200), used spotted array
New: cDNA linked to a microscopic slide w/ fluorescent probes (no radioactivity), can now use 60,000 probes, also we use oligonucleotides instead of spotted arrays (50-60 bases=avg length of the oligo)

Question 8

TM4 cell line

Answer 8

A cell lien from immature sertoli cells that responds to fsh and cAMP (retains most sertoli cell features)
Express both androgen and estrogen Rs and secretes a factor with activism-like activities

Question 9

Non-coding mRNA size hierarchy

Answer 9

MiRNA < piRNA < siRNA < lncRNA < tsRNA

*lnc=long non-coding
Ts rna=longest (biggest size)