Lecture 28 Flashcards
What is a DNA microarray?
It is a method of using SINGLE STRANDED oligonucleotides in sequences that are complementary to sequences within every known gene. It identifies the subset of mutant candidate genes for a particular tumor by comparing them to active genes in a normal cell.
What is CGH microarray?
It is a type of microarray that detects deleted or duplicated genes.
What is CRH microarry?
It is a type of microarray used to compare the RNA production from a normal cell and a tumor cell (effectively measures the expression of genes.)
What are the indications for a CGH?
- Developmental delay or mental retardation
- Growth abnormality
- Dysmorphic features
- Multiple congenital abnormalities
- Cardiovascular malformations
On the CGH microarray, what do the Geen, Yellow, and Red colors represent?
If green is the color chosen for normal DNA taken from the patient, green indicates a deletion of a gene from a cancer cell because its DNA was labeled red, and no red showed up in that particular spot. When the normal DNA and cancer cell DNA hybridize to the same spot, it will appear yellow, which means the cancer cell has the same copies of DNA as the normal cell. When the spot is red, that means the cancer cell has a duplication, so more DNA than the normal cell for that particular gene.
What are candidate genes?
Genes that are likely to contribute to the tumorigenesis of cancer cells.
What do the different colors mean on a CRH microarry?
If the normal RNA is labeled Green, and the Cancer cell RNA is labeled Red, green represents underproduction of RNA in the cancer cell, red represents over production of RNA in the cancer cell, and yellow represents equivalent production of RNA in the Cancer cell compared to the normal cell.
What is Ion Torrent Next Generation Sequencing?
It takes sample DNA, breaks it into fragments, attaches recognizable sequences to the ends for PCR, emulsifies the DNA fragments into oil beads such that the same sequence will coat the bead, and each bead is collected in individual wells with their corresponding sequences being sequenced one NT at a time. There are 10,000,000 beads per chip with one, distinct sequence per bead used in this process.
What is the most effective vehicle for gene therapy?
Virus - the virulence factors are knocked out and the virus infects cells, bringing with it the therapeutic gene. Adenoviruses and Retroviruses are vectors of choice.
What are the disadvantages to using viruses in gene therapy?
- There’s a transient effect - the virus can’t replicate, so the therapeutic gene only lasts as long as the virus does.
- The immune system still recognizes the viral particles as a virus and leads to an immune response/inflammation.
What is the therapy of OTCase deficiency (urea cycle disorder, so think about which organ is being targeted with this therapy), and what are its advantages and disadvantages? How have we gotten around the disadvantages?
Gene therapy using adenovirus vector that targets the liver –> same disadvantages as described for viral gene therapy in general. However, adenovirus can infect non-growing OR proliferating cells, and its genome does not integrate into the host’s genome –> low risk of mutagenesis. Using Adeno-Associated Virus elicits much lesser immune and inflammatory response.
What are disadvantages of using a retroviral vehicle for gene therapy, and which subclass of retrovirus can be used to avoid one of the disadvantages?
They don’t infect non-growing cells well. Lentivirus can be used, and IS effective at infecting non-proliferating cells.
Also, because it integrates its genome into the host genome, there’s high risk of insertional mutagenesis when using retroviruses.
What is the therapy for ADA deficiency (which leads to Severe Combined Immuno Deficiency “SCID”)?
Marrow cells are taken from patient, retrovirus is added exvivo (into the cells outside of the patient), and then the infected cells are reinserted into the patient. There was incidence of insertional mutagenesis that led to lukemia.
What is the therapy for dominant disorders (disorders where you want to knock down gene function instead of restore gene function)?
shRNA - Short hairpin RNA that mimics the action of miRNA. The shRNA gene is added to retrovirus and the retrovirus infects the patient –> shRNA genes are transcribed and the shRNA is processed and acts as miRNA to silence the target gene (the aberrant dominant disorder gene.)
One of the issues with using viral gene therapy for DMD is the cDNA for the dystrophin gene is too ____. An laternative strategy is to us antisense _______ to force _____ skipping. This converts out of frame deletions to in-frame deletions, and thus a conversion from the more deleterious DMD to the less deleterious _____. Remember that the exons of the DMD gene are not all multiples of 3; it’s the combination of exons in mRNA that form a multiple of three. Think about what this means for skipping exons. There is also the possibility of upregulating ______, a dystrophin homolog.
Large
Oligonucleotide
Exon
BMD
Utrophin
