Nature of Cancer
What is the difference between parenchymal cells and stromal cells?
Parenchymal cells carry out the function while stromal cells provide the structue.
What is the difference between an oncogene and a proto-oncogene?
A proto-oncogene is a normal gene involved in regulating cell growth and proliferation that can be altered or activated by a virus to promote cancer. An oncogene is the activated form of that gene.
If a gene is overamplified in a microarray is it necessarily an oncogene?
No, some genes can be in close proximity to oncogenes and just be "along for the ride".
What is Rb and what does it lead to when it is knocked out?
Rb was the first tumor suppressor discovered and leads to retinoblastoma when knocked out.
What is the most essential factor in media for tissue culture? What happens when you take it away?
Fetal Bovine Serum (FBS). Cells will turn quiescent, but can divide again once the proper growth factors are added.
What are some techniques to visualize chromosmoes and how do you label them?
Karyotype banding and FISH. Q is large arm and P is small arm, label sections out from the centromere.
Name the virus associated with each type of cancer:
Burkitts Lymphoma
Cervical Carcinoma
Hepatocellular Carcinoma
Burkitts Lymphoma = EBV
Cervical Cancer = HPV
Hepatocellular Carcinoma = HBV/C.
What are some possible ways you can get an oncogene?
Deletion or point mutation in coding sequence, regulatory mutation, gene amplification, or chromosome rearrangement.
What is LOH? Describe how this can happen as it relates to Rb.
Loss of Heterozygosity eliminates the second wild type tumor suppressor allele leading to retinoblastoma. Potential mechanisms include: mitotic recombination, gene conversion, chromosomal breakage, and mitotic nondisjunction.
What are some ways RTK's receptor firing can become dysregulated?
Site-specific mutation, truncation, or overexpression.
What are "readers and writers" and what kind of modifications do they add?
Writers add the specific PTM such as methylations and acetylations to the histone tails. Readers recognize the molecules and either carry out the function or direct another enzyme to carry out the function of the PTM.
What type of protiens do viral genomes usually encode for?
Proteins that help replicate the genome, protiens for packaging the genome, and protiens that enhance viral replication.
Why is MYC a unqiue oncogene?
MYC is a transcription factor that removes paused RNA Pol II enzymes to promote transcription of proliferative enzymes in multiple different cancers.
Why do patients with hereditary retinoblastoma more suseptible to other cancers throughout their life?
Both wild type alleles have been removed from most other tissues as well leading to increased lifetime risk.
Describe the Wnt/B-Catenin signaling pathway. What happens to B-Catenin if there is an APC mutation?
B-catenin is normally degraded without Wnt signaling via APC. Upon Wnt signaling, APC complex is inactivated, and B-catenin is stabalized to travel to the nucleas and act as a transcription factor to upregulate proliferation genes. Colon cancers often contain APC mutations that are unable to degrade B-catenin.
Describe the protocol to carry out the Ames test and possible limitations it may have.
The Ames test works by plating a mutagen with homogenized rat liver (to mimic metabolism) with His- salmonella bacteria susceptible to back mutations. The more mutagenic the compound is, the more colony formation there will be. Some limitations include the fact that it is murine liver extract and could not coorelate to human, and that many compounds may appear mutagenic that are not eg. certain foods.
What is the difference between acute transforming retroviruses and slowly transforming retroviruses?
Acutly transforming retroviruses already contain an oncogene while slowly transforming retroviruses may randomly integrate near a proto-oncogene causing it to become overly active.
What is the Philadelphia Chromosome? How is it formed and describe how it works mechanistically.
The philadelphia chromosome is a translocation between chromosome 9 and 22 giving rise to the Bcr-Abl fusion protein. This protein places the Bcr promoter behind the Abl gene to give create a constitutivley active protien in CML patients.
What is Methylation? How does this contribute to Cancer?
Methylation is a PTM that happens on CpG islands that typically leads to gene silencing. If this occurs in the promotor region of the tumor suppressor gene it can be turned off and lead to cancer development.
Describe the NF-kB pathway and its negative feedback system.
TNFa binds its receptor to activate IKK by phosphorylating it. IKK will then mark IkB for ubiquitination freeing NF-kB to travel to the nucleus and act as a coactivator for transcription of its target genes. One of NF-kB target genes is IkB thus creating a negative feedback loop.
What is the Warburg Effect and how does it work mechanistically? What are some possible ways this could be used diagnostically?
How does HPV E7 oncogene work?
HPV E7 oncogene has one of its products bind to Rb thus releasing E2F and allowing it to act as a transcription factor to help drive the cell into S phase where it creates more DNA Pol I.
Where do Oncogenic mutations in Ras occur and how does this affect cell signaling?
Ras oncogenic mutation is most often found at G12V where it is unable to hydrolize bound ATP. This makes it constitutivlly active.
What are SNPs and how can they be used to detect LOH?
Single-nucleotide polymorphisms are abundant in the non-coding regions of the genome. If LOH occurs SNPs near the gene may also be altered. By surveying the neighboring SNPs we can determine if an LOH event has occured.
What are integrins and why are they important for cell signaling? What happens if a cell loses integrin signaling? Describe outside-in activation and inside-out activation.
Integrins are receptors that bind the cytoskeleton of the cell to the ECM. If they become detatched the cell will undergo anoikis. Outside-in activation is where the integrin binds the ECM first and signals to bind the cytoskeleton. Inside-out activation binds the cytoskeleton first and sends a signal to bind to the ECM.