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- Biology - Genetics
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- The Cystic Fibrosis Gene
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- Introduction:
- Cystic fibrosis is an inherited autosomal recessive disease
- that exerts its main effects on the digestive system and the
- lungs. This disease is the most common genetic disorder
- amongst Caucasians. Cystic fibrosis affects about one in
- 2,500 people, with one in twenty five being a heterozygote.
- With the use of antibiotics, the life span of a person
- afflicted with CF can be extended up to thirty years
- however, most die before the age of thirteen.1 Since so
- many people are affected by this disease, it's no wonder
- that CF was the first human genetic disease to be cloned by
- geneticists. In this paper, I will be focusing on how the
- cystic fibrosis gene was discovered while at the same time,
- discussing the protein defect in the CF gene, the
- bio-chemical defect associated with CF, and possible
- treatments of the disease.
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- Finding the Cystic Fibrosis Gene:
- The classical genetic approach to finding the gene that is
- responsible for causing a genetic disease has been to first
- characterize the bio-chemical defect within the gene, then
- to identify the mutated protein in the gene of interest, and
- finally to locate the actual gene. However, this classical
- approach proved to be impractical when searching for the CF
- gene. To find the gene responsible for CF, the principle of
- "reverse genetics" was applied. Scientists accomplished
- this by linking the disease to a specific chromosome. After
- this linkage, they isolated the gene of interest on the
- chromosome and then tested its product.2
- Before the disease could be linked to a specific
- chromosome, a marker needed to be found that would always
- travel with the disease. This marker is known as a
- Restriction Fragment Length Polymorphism or RFLP for short.
- RFLP's are varying base sequences of DNA in different
- individuals which are known to travel with genetic
- disorders.3 The RFLP for cystic fibrosis was discovered
- through the techniques of Somatic Cell Hybridization and
- through Southern Blot Electrophoresis (gel separation of
- DNA). By using these techniques, three RFLP's were
- discovered for CF; Doc RI, J3.11, and Met. Utilizing in
- situ hybridization, scientists discovered the CF gene to be
- located on the long arm of chromosome number seven. Soon
- after identifying these markers, another marker was
- discovered that segregated more frequently with CF than the
- other markers. This meant the new marker was closer to the
- CF gene. At this time, two scientists named Lap-Chu Tsui
- and Francis Collins were able to isolate probes from the CF
- interval. They were now able to utilize to powerful
- technique of chromosome jumping to speed up the time
- required to isolate the CF gene much faster than if they
- were to use conventional genetic techniques.3
- In order to determine the exact location of the CF gene,
- probes were taken from the nucleotide sequence obtained from
- chromosome jumping. To get these probes, DNA from a horse,
- a cow, a chicken, and a mouse were separated using Southern
- Blot electrophoresis. Four probes were found to bind to all
- of the vertebrate's DNA. This meant that the base pairs
- within the probes discovered contained important
- information, possibly even the gene. Two of the four probes
- were ruled out as possibilities because they did not contain
- open reading frames which are segments of DNA that produce
- the mRNA responsible for genes.
- The Northern Blot electrophoresis technique was then used
- to distinguish between the two probes still remaining in
- order to find out which one actually contained the CF gene.
- This could be accomplished because Northern Blot
- electrophoresis utilizes RNA instead of DNA. The RNA of
- cell types affected with CF, along with the RNA of
- unaffected cell types were placed on a gel. Probe number
- two bound to the RNA of affected cell types in the pancreas,
- colon, and nose, but did not bind to the RNA from
- non-affected cell types like those of the brain and heart.
- Probe number one did not bind exclusively to cell types from
- CF affected areas like probe number two did. From this
- evidence, it was determined that probe number two contained
- the CF gene.
- While isolating the CF gene and screening the genetic
- library made from mRNA (cDNA library), it was discovered
- that probe number two did not hybridize. The chances for
- hybridization may have been decreased because of the low
- levels of the CF gene present within the probe.
- Hybridization chances could also have been decreased because
- the cDNA used was not made from the correct cell type
- affected with CF. The solution to this lack of
- hybridization was to produce a cDNA library made exclusively
- from CF affected cells. This new library was isolated from
- cells in sweat glands. By using this new cDNA library,
- probe number two was found to hybridize excessively. It was
- theorized that this success was due to the large amount of
- the CF gene present in the sweat glands, or the gene itself
- could have been involved in a large protein family.
- Nevertheless, the binding of the probe proved the CF gene
- was present in the specific sequence of nucleotide bases
- being analyzed.
- The isolated gene was proven to be responsible for causing
- CF by comparing its base pair sequence to the base pair
- sequence of the same sequence in a non-affected cell. The
- entire CF cDNA sequence is approximately 6,000 nucleotides
- long. In those 6,000 n.t.'s, three base pairs were found to
- be missing in affected cells, all three were in exon #10.
- This deletion results in the loss of a phenylalanine residue
- and it accounts for seventy percent of the CF mutations. In
- addition to this three base pair deletion pattern, up to 200
- different mutations have been discovered in the gene
- accounting for CF, all to varying degrees.
-
- The Protein Defect:
- The Cystic Fibrosis gene is located at 7q31-32 on
- chromosome number seven and spans about 280 kilo base pairs
- of genomic DNA. It contains twenty four exons.4 This gene
- codes for a protein involved in trans-membrane ion transport
- called the Cystic Fibrosis Transmembrane Conductance
- Regulator or CFTR. The 1,480 amino acid protein structure
- of CFTR closely resembles the protein structure of the
- ABC-transporter super family. It is made up of similar
- halves, each containing a nucleotide-binding fold (NBF), or
- an ATP-binding complex, and a membrane spanning domain
- (MSD). The MSD makes up the transmembrane Cl- channels.
- There is also a Regulatory Domain (R-Domain) that is located
- mid-protein which separates both halves of the channels.
- The R-Domain is unique to CFTR and is not found in any other
- ABC-transporter. It contains multiple predicted binding
- sites for protein kinase A and protein Kinase C.4
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- Mutations in the first MDS are mainly found in exon #4 and
- exon #7. These types of mutations have been predicted to
- alter the selectivity of the chloride ion channels.4
- Mutations that are in the first NBF are predominant in
- CFTR. As previously mentioned, 70 percent of the mutations
- arising in CF cases are deletions of three base pairs in
- exon #10. These three base pairs give rise to phenylalanine
- and a mutation at this site is referred to as DF508.5 Such
- a mutation appears not to interfere with R-Domain
- phosphorylation and has even been reported to transport
- chloride ions.6&7
- There are five other frequent mutations that occur in the
- first NBF. The first is a deletion of an isoleucine
- residue, DF507. The second is a substitution of glycine or
- amino acid #551 by aspartic acid/F551D. The third involves
- stop mutations at arginine #553 and glycine #542. The
- fourth is substitutions of serine #549 by various other
- residues. The fifth is a predicted splicing mutation at the
- start of exon #11.7
- Mutations within the R-Domain are extremely rare. The only
- reason they do occur is because of frameshifts. Frameshifts
- are mutations occurring due to the starting of the reading
- frame one or two nucleotides later than in the normal gene
- translation.4
- Mutations in the second membrane spanning domain of the
- CFTR are also very rare and have only been detected in exon
- #17b. These have no relevance to mutations occurring in the
- first membrane spanning domain. They apparently do not have
- a significant impact on the Cystic Fibrosis Transmembrane
- Conductance Regulator either.4
- Mutations in the second nucleotide-binding fold occur
- frequently in exon #19 and exon #20 by the deletion of a
- stop signal at amino acid number 1282. Exon #21 is
- sometimes mutated by the substitution of asparagine #1303
- with lysine #N1303K.4
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- The Bio-Chemical Defect:
- Studies of the chloride channels on epithelial cells lining
- the lungs, sweat glands, and pancreas have shown a consensus
- in that the activation of chloride secretion in response to
- cAMP (adenosine 3', 5'-monophosphate) is impaired in cystic
- fibrosis cases. Another affected, independently regulated
- chloride channel that has been discovered is activated by
- calcium-dependent protein kinases. Sodium ions have also
- been noted to be increasingly absorbed by apical sodium
- channels.8 Therefore, the lack of regulated chloride ion
- transport across the apical membranes and apical absorption
- of sodium ions, impedes the extracellular presence of water.
- Water will diffuse osmotically into cells and will thus
- cause the dehydration of the sol (5- mm fluid layer of the
- cell membrane) and the gel (blanket of mucus) produced by
- epithelial cells.9 As a result of this diffusion of water,
- airways become blocked and pancreatic proteins turn
- inactive.
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- An Account of the Absorption and Secretion of Cl-, Na+, and
- Proteins:
- An inward, electrochemical Na+ gradient is generated by the
- Na+, K+-ATPase pump located in the basolateral membrane (the
- cell side facing the organ it is lining). A basolateral
- co-transporter then uses the Na+ gradient to transport Cl-
- into the cell against its own gradient. This is done in
- such a way that when the apical Cl- channels within the
- membrane spanning domain open, Cl- diffuse passively with
- their gradient through the cell membrane.4
- In pancreatic duct cells, a Na+, H+-ATPase pump is used and
- a bicarbonate secretion is exchanged for Cl- uptake in the
- apical membrane. Chloride ions then diffuse passively when
- the Cl- channels are opened. Such secretions also allow for
- the exocytosis of proteins in the pancreas which will later
- be taken into the small intestines for the breaking down of
- carbohydrates.4
- In addition to the pump-driven gradients and secretions,
- there exists autonomic neurotransmitter secretions from
- epithelial cells and exocrine glands. Fluid secretion,
- including Cl-, is stimulated predominately by cholinergic,
- a-adrenergic mechanisms, and the b-adrenergic actions.4
- Such chemical messengers cannot enter the cell, they can
- only bind to specific receptors on the cell surface and
- transmit messages to and through an intracellular messenger
- such as Ca2+ and cAMP by increasing their concentration.
- The intracellular message is transmitted across the cell by
- either diffusion or by a direct cascade. One example of a
- directed cascade is the following:
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- Possible Treatments For Cystic Fibrosis:
- One suggested treatment for CF has been to provide the
- missing chemicals to the epithelial cells. This can be
- accomplished by the addition of adenosine
- 3',5'-monophosphate (cAMP) or the addition of the nucleotide
- triphosphates ATP or UTP to cultures of nasal and tracheal
- epithelia. This has been proven to alter the rate of Cl-
- secretion by removing the 5-mmeter sol layer of fluid in the
- respiratory tract.9 Moreover, luminal application of the
- compound amiloride, which inhibits active Na+ absorption by
- blocking Na+ conductance in the apical membrane, reduced
- cell secretion and absorption to a steady state value.
- Another treatment that has been suggested is to squirt
- solutions of genetically engineered cold viruses in an
- aerosol form into the nasal passages and into the lungs of
- people infected with CF. This is done in hopes that the
- virus will transport corrected copies of the mutated gene
- into the affected person's airways so it can replace the
- mutated nucleotides.10 This form of treatment is known as
- gene therapy.
- A different approach taken in an attempt to cure cystic
- fibrosis involves correcting the disease while the affected
- "person" is still an embryo. Test tube fertilization (in
- vitro fertilization) and diagnosis of F508 during embryonic
- development can be accomplished through a biopsy of a
- cleavage-stage embryo, and amplification of DNA from single
- embryonic cells.5 After this treatment, only unaffected
- embryos would be selected for implantation into the uterus.
- Affected embryo's would be discarded.
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- Conclusion:
- Chloride conductance channels have dramatic potentials.
- One channel can conduct from 1x106 to 1x108 ions per
- second.8 This is particularly impressive when you consider
- the fact that there are not many channels present on cells
- to perform the required tasks. As a result of this, a
- mutation of one channel or even a partial mutation of a
- channel, that causes a decrease in the percentage of channel
- openings, can exert a major effect.
- Even the mildest of cures altering the Cystic Fibrosis
- Conductance Regulator in CF afflicted people would lead to
- significant improvements in that individuals health. Since
- cystic fibrosis is the most common genetic disorder,
- particularly amongst Caucasians, in today's society, intense
- research efforts towards its cure would be invaluable. When
- will cystic fibrosis be completely cured? No one can say
- for sure but, strong steps have already been taken towards
- reaching this goal.