Epigenetics/Cytogenetics

Question 1

Epigenetic Characteristics (4): (Definition/characteristics)

Answer 1

1) Different gene expression pattern/phenotype, identical genome
2) Inheritance through cell division, even through generations
3) Like a Switch: ON/OFF
4) Erase-able (inter-convertible) —–>Therapeutic potential

Question 2

Waddington’s epigenetic landscape?

Answer 2

One is asked to imagine a number of marbles rolling down a hill towards a wall. The marbles will compete for the grooves on the slope, and come to rest at the lowest points. These points represent the eventual cell fates, that is, tissue types.

Question 3

What enzyme Propagates Epigenetic Marks Through Somatic Cell Division? Where does this methylation occur?

Answer 3

Maintenance Methyltransferases (DNMT); DNA methylation occurs only on 5’ C of cytosines of CpG. Does not affect base paring of 5-meC with G.

Question 4

What is DNMT? What coenzyme does it use?

Answer 4

Enzyme responsible for maintaining epigenetic marks through somatic cell replication; SAM (S-adenosyl methionine)

Question 5

Name three chemical modifications to DNA or histones that can potentially be inherited.

Answer 5

Heterochromatin domains, X-inactivaton, Imprinting

Question 6

Name a specific type of gene that, when aberrantly methylated with 5meC, can lead to cancer and an approach to therapeutic intervention in this case

Answer 6

Silencing of a tumor suppressor gene (TSG) by 5meC can lead to cancer.

Question 7

To treat aberrant methylation of TSG (Tumor Suppressor gene, the appropriate action would be to ________ DNMT and _______HDAC.

Answer 7

Inhibit; inhibit (DNA methyltransferase - silences transcription by methylation; Histone deacetylase - generally a repressor of transcription)

Question 8

The two most common leukemia translocations are:

Answer 8

t(9;22) for chronic myeloid leukemias

t(15;17) for acute myeloid leukemia

Question 9

Explain the roles of chromosomal microarray (CMA) analysis in aiding certain genetic diagnoses and why CMA testing can detect genomic deletions or duplications, but not translocations.

Answer 9

CMA uses DNA oligoprobes on microscope slide. Patient DNA=green, reference DNA =red. Patient and reference DNA are hybridized to the oligo probes. If there is an equal amount of reference and patient DNA, the spot appears yellow. If a segment of patient DNA is lost, that spot will appear red.

Question 10

How is CMA (Chromosomal microarray) used?

Answer 10

To detect chromosomal amplifications and deletions. It detects copy number variations at a higher resolution than other technologies, however; it does not detect balanced rearrangements, mosaicism or single nucleotide changes. Confirmation studies FISH, BACs, PCR and sequencing. Will replace FISH as initial diagnostic tool in the near future.

Question 11

A common finding in childhood B-cell acute lymphoblastic leukemia (ALL) is ______ revealed by _______.

Answer 11

high hyper-diploidy; chromosome and FISH analyses

Question 12

t(9;22) is diagnostic for ______, which can be treated with ____.

Answer 12

chronic myelogenous leukemia (CML), Imantinib (Gleevec), a tyrosine kinase inhibitor

Question 13

t(15;17) is diagnostic for _____, which can be treated with ______.

Answer 13

acute promyeloid leukemia (APML); retinoic acid. Will also see auer rods under light microscopy.

Question 14

Test protocol diagnosing infants, children, or adults with autism, and/or other multiple congenital anomalies (i.e. heart abnormalities):

Answer 14

1. If deletion or duplication is detected by CMA consult Database of Genomic Variants
2. Parental FISH studies
3. • Parental FISH—->test rest of family
4. If DGV, parents, family test (-), dig into literature/databases

Question 15

Regarding leukemia, which has a better prognosis, hyperdiploid or hypodiploid? Why?

Answer 15

Hypodiploid (poor prognosis); Hyperdiploid (good prognosis). Loss of tumor suppressor genes.