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16 Cards in this Set

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If a protein has increased expression in a tumor cell what can you assume? What steps could be taken? What is this protein acting as?
Activity is important to tumor cells, might be decent target for therapy, it's a marker
Tumors often result from misregulated signaling pathways that lead to uncontrolled cell growth. Using this information, how might we identify the pathway and prevent tumor formation?

What if more than one signaling pathway were involved? How would you experimentally distinguish the two?
All pathways start with receptor
Ex: RTK (hormone binds, receptor dimerizes)
Get antibody that recognizes receptor and blocks hormone from binding (will never dimerize, will never start signaling cascade)

Proteomics: look at expression fingerprints for two different tumors in two different conditions, see which are phosphorylated. (-/+ PDGF ex)
How might the tutor proteome be used in treatment monitoring?
Should get differential expression with and without drug. See what proteins are getting expressed as cells become resistant. Can determine which proteins important for co-therapies--to block proteins that give resistance).
How would you expect metabolic enzymes to change in tumor cells? Apoptotic protein levels?
Decrease in proteins responsible for apoptosis.

Increased.
How might serum be used in treatment monitoring?
Marker: monitor treatment effectiveness of tumors, find marker in the tumor and see how protein levels in blood change with it. Monitor these proteins to test effectiveness of drug.
Why do complexity of biopsies pose a challenge to clinics?
Getting tumor and non-tumor cells, need to separate using micro-dissection (with laster)
How would variability in a population pose a challenge to clinics?
Expression levels different for different individuals, normal might be abnormal for someone else. Background levels (changes with diet, etc), ranges of "normal" (via population proteomics)
How does dynamic range pose a challenge to clinics?
Low expressed proteins must be selectively enriched
How does variability in analysis pose a threat to clinics?
Different labs do things differently, which threatens reproducibility (must minimize number of sample handling steps, can standardize procedures to compare results between labs better)
How does univariant thinking pose a threat to clinics?
Proteomic marker can't just be a single protein that goes up or down, must look at many proteins to reduce chances of false positive--requires more advanced statistical analysis
How do lab costs pose a threat to clinics?
Sophisticated (delicate) instrumentation, and expensive consumables $$$$$$
Why can't we just look at changes in protein levels in differential expressions of cancer cell proteins?
Expression means more than protein levels, can be post-transltnl mod, interaction partners
What two characteristics are essential for biomarkers?
Specificity and sensitivity
How can a 2-D GE be used in diagnosis?
2-D GE followed by MALDI-TOF for both healthy and tumor tissue. Can also do chronic tissue and tumor tissue using same method (ex: can be more specific by id'ing proteins for hepatitis and liver cancer).
How does using housekeeping proteins as a biomarker pose a threat to cancer diagnostics? How can this be remedied?
Dynamic range, if testing serum and running 2D GE followed by MALDI-TOF, most likely will see highly expressed proteins (house keeping ones!) This is not very specific. So to be specific we use MANY of these proteins as markers--protein expression profiles. MUST REDUCE FALSE POSITIVES
Why is an upregulation of glycolytic enzymes and a downregulation of enzymes involved in gluoceneogenesis and TCA indicative of a rectal tumor? Why can't glycolysis be targeted against?
Tumors are growing faster than blood vessels and aren't receiving much oxygen, so they must rely heavily on glycolysis. It occurs everywhere!