Notes
on gene amplification Biol.G4054y
Historically: John Littlefield (Harvard, then
Hopkins): searching for gene regulatory mutations in cultured cells
dhfr - metabolic role - folic
acid vitamin - FH4
for purine nucleotide and thymidylate
synthesis - DNA synthesis
methotrexate (amethopterin): looks like FH2 substrate, fools
enzyme, ties up enzyme
used for anti-cancer
chemotherapy via inhibition of DNA synthesis
a purine and thymidine
requirement induced in presence of MTX (HAT medium).
MTXR mutants - operational selection: MTX
-thy ®
colonies at 10-5.
= MTX-resistant. Why resistant?
(Littlefield wanted gene
activity-up mutations, to learn about control of gene activity.)
But: perhaps mutation changed
dhfr enzyme so no longer fooled by MTX
Found MTX-sensitivity of
mutant enzyme = sensitivity of normal, or "wild-type". OK.
Regulatory mutation would
result in amount of enzyme up. Measure
amount of catalytic activity: up 10x. OK.
But: could be a more active
mutant enzyme.
So: measure actual protein
directly. Had to separate dhfr protein (0.01%) from rest of cell
protein. Measured radioactivity in
immunoprecipitates or after electrophoretic separation (SDS gels) after
labeling cells with a radioactive amino acid
Found dhfr protein
up. OK.
Maybe some new factor makes translation
of dhfr mRNA ® protein more efficient in mutant.
So: isolated total
mRNA, translated it in a test tube, using protein translation machinery from
red blood cells. Mutant ® 10X more dhfr protein
here, just as in mutant cell
OK. dhfr mRNA level up, as measured by mRNA activity
So either gene is more active
in turning out mRNA, or ...perhaps more genes, of normal activity???
Meanwhile, June Biedler
(Sloan-Kettering): finding that MTX-resistant hamster cells contain chromosome
abnormalities
HSRs (homogeneously staining
regions, compared to the usual banded appearance)
Usually on the same
chromosome
Gradually lost (1-2 year
period), along with MTX-resistance.
In this (just)
pre-recombinant DNA era, then:
Bob Schimke
(Stanford): purified the dhfr mRNA from a MTXR mutant (mouse
cell line) where it was present in high levels (100X), radioactively labeled
it, used it as a probe via solution nucleic acid hybridization. Tour-de-force purification (from 1%) by a
young grad student, Fred Alt, by subtractive hybridization (one of the
first applications of this strategy):
‑ Resistant
cell mRNA ® 3H‑cDNA.
‑ High
cot hybridization to excess of WT mRNA: isolate unhybridized (single stranded)
cDNA with hydroxyapatite
‑ Low
cot hybridization to resistant cell mRNA: isolate hybridized (double‑stranded)
cDNA with hydroxyapatite.
Use this gene-specific probe
to quantify DNA per cell in normal vs. mutant cells:
Had done all the Littlefield
experiments on this mouse cell line:
MTXR mutant had
100X more enzyme, 100X more translatable mRNA and, now find: 100X more dhfr
DNA. That is, 100X more dhfr genes.
Finally, what is the
relationship of these extra genes to the HSRs (which were 100-300 times too
large to be just the extra genes).
Do the high levels of dhfr
trigger a specific chromosomal abnormality, or is the HSR actually represent
the site of dhfr gene amplification?
Jack Nunberg in the Shimke lab, with Gail Urlaub and
L. Chasin (Columbia): in situ hybridization of this radioactive dhfr
probe to metaphase chromosome spreads from an amplified Chinese hamster cell
line: hybridized to the HSRs of the chromosomes:
Size of HSR = 30X size of the
200 dhfr genes present.
[5 pg DNA/cell, or 5 X 10-12
g/cell ¸
660 g/mole = 7.6 x 10-15 moles, X 6 X 1023 molecules/mole
= 4.5 X 109 base pairs/cells, or 4.5 X 106 kb/cell. HSR = 3.5% of chromosome length, = 160,000
kb, ¸
200 amplicons = 800 kb/amplicon. Dhfr
gene is 25 kb, or only 3% of amplicon.]
So amplified region repeating
unit ("amplicon") >>> than gene itself.
Nowadays: fluorescent probes.
Two chromosomal forms of
amplified genes :
1- HSRs or ABRs (abnormally
banded regions) , stable.
2- DMs, (double
minutes) unstable
HSR DNA structure: tandem duplication
® ® ® ® ® ® ® ® ® ® ® ®
Sometimes head-to-tail
instead of head to head:
-®¬--®¬--®¬--®¬--®--¬-
Two basic ideas:
1. gene over-replication, replicon gone wild (onion‑skin). A replicon is a unit of DNA replication
(replication eye).
- must be followed by some kind of recombinational joining
to tie up loose ends.
- perhaps there is a transitory existence as a free,
circular, amplicon
- (site of HSR or amplified genes may be close to but
distinct from the orginal locus.)
2. unequal sister chromatid exchange.
Parallel slipped alignment
- one chromatid with a deletion and one with a duplication
Antiparallel (doubled back) -
Acentric fragment (lost) + fused chromatid that must break in mitosis, yielding
two unequal arms, one with the target gene duplicated.
In situ hybridization analysis of early events in
dhfr amplification support mechanism #2 (Hamlin, Trask).
Generality: Not just dhfr. Found almost whenever the selective
conditions are right:
1. a good inhibitor of gene
product, need for more of the gene product
2. a multistep selection,
to allow a multistep process (CAD, TS, pyrimidine biosynthetic enzymes,
multidrug-resistance)
This all in the lab. How about in nature?
In real normal nature:
Frog embryos: genes for
ribosomal RNA, needed for protein synthesis, amplified and present as
mini-circles in the developing egg (oocyte).
Fruit fly larvae: the gene for the chorion proteins that coat
the egg are amplified in the cells that surround the egg (follicle cells) at a
particular stage in development. In
this case there are signals in the DNA surrounding the chorion genes that
trigger the amplification.
But these are exceptional
cases, not the usual mechanism by which a cell makes a lot of a gene product
(i.e., via a high transcription rate)
Natural, but pathological: in the development of
tumors themselves:
N-myc amplification in lung
cancers and neuroblastomas. myc
seems to have a function in cell-cycle control, or commitment to a round of DNA
synthesis that is part of cell division.
DMs abound in these cells. In
lung cancer, myc amplification is associated with aggressive growth and a poor
prognosis.
In medicine: cancer chemotherapy. MTX-resistance in a tumor can occur by gene
amplification of dhfr (but not often documented).
More common: mdr1 gene (multi-drug
resistance) ® membrane protein that pumps a variety of compounds (adriamycin,
actinomycin, colcemid) out of the cell, including many of the anti-cancer
drugs. Gene amplification ® overproduction of mdr1 ® drug resistance: tumor
cells, previously killed by a drug, now resume growth.
In biotechnology industry:
To isolate a mammalian cell
line producing large amounts of a useful protein:
Select amplificants for dhfr
using MTX. Your favorite gene co‑amplifies
along with dhfr
Join dhfr gene and EPO
and transfect a cultured mammalian cell.
Isolate a transfectant. Grow it
in increasing amounts of MTX. Get a
cell line that is highly resistant to MTX, has 1000 dhfr genes, and has,
also, 1000 EPO genes. These cells will
synthesize and secrete massive amounts of EPO, normally made in small amounts
in the kidney. Manufacture EPO, inject
it into people, cure anemia, kidney disease, cancer (facilitates re-population
of blood-forming cells after aggressive radiation therapy).