Prion diseases* are a family of conditions (on both humans and animals) caused by prions, which are pathogenic agents that are transmissible and are able to induce abnormal folding of specific normal cellular proteins called prion proteins that are found primarily in the brain. [3] That abnormal folding of the prion proteins leads to brain damage which is most of the time fatal. [2]
In the paper “A naturally occuring variant of the human prion protein completely prevents prion disease” [1], Asante et al. are describing a mutation on the PRNP gene (which codes for the prion protein), G127V, which appears to instill significant resistance to prion disease (Kuru, in this particular case study), believed to be via inhibition of homotypic protein-protein interactions.
This edit is aimed at instilling prion resistance to individuals by performing a gene editing operation based on CRISPR/Cas9 targetting the same point modification of the PRNP gene.
*: Prion diseases in humans include Kuru, Creutzfeldt-Jakob disease, Fatal Familial Insomnia, and others.
The complete FASTA file is containing the PRNP gene is attached below:
NC_000020.10[4665588..4683746].fa
The particular sequence to be modified is the following:
GGCAGTGGTGGG GGG CCTTGGCGGCTA
with the point of mutation being the codon spaced out above.
The methodology for identifying the sequence went as following:
Import PRNP-201 (GRCh38.p13_EnsemblRelease_103 (Human)) in benchling.
Imported from genome: GRCh38.p13_EnsemblRelease_103 (Human (Homo sapiens))
Gene: PRNP (ENSG00000171867)
Location: chr20 4686350-4701590
Transcript: PRNP-201 (ENSG00000171867_ENST00000379440, None)
Select the bases that have been marked as exon2.
Copy the primary DNA sequence.
Use the following bit of Python code to extract the sequence:
exon2 = '...' # redacted for space reasons
n = 3 # allow for codon stepping through the sequence
# Break the string sequence in a list of codons, and fetch the one at
# location 127 (Python is 0-based indexed so in the code this is represented
# as 126)
[exon2[i:i+n] for i in range(0, len(line), n)][126]
# => 'GGG'
# build sequence code around codon of interest
codons_exon2[122] +
codons_exon2[123] +
codons_exon2[124] +
codons_exon2[125] + ' ' +
codons_exon2[126] + ' ' +
codons_exon2[127] +
codons_exon2[128] +
codons_exon2[129] +
codons_exon2[130]