– Associate Professor/Laboratory Director, Medical College of Georgia/ Augusta University, United States
Body: Differential expression of HLA genes can impact immune response and susceptibility to disease. We describe 2 novel DPA1 alleles that may have altered α chain expression of DP dimers. A third case looks at alleles that can be ambiguous, where expression of the α chain and the protein produced may differ. DNA was extracted from ACD blood samples using EZ1. HLA typing was performed using AlloseqTx17 NGS (CareDx) for the HLA classical HLA genes. Alloseq Assign software was used for analysis. The first allele had a mut at the start of exon 1 at nucleotide (nu) 1432. Temporarily named DPA1*01:NEWQ, the allele exhibits a change from start codon ATG (Met) to ACG (Thr) respect to the closer allele in sequence DPA1*01:12:01. This change could affect transcription initiation compromising protein expression. This change from T to C is found in 4 other DPA1 alleles (03:05:01:01Q, 03:05:01:02Q, 03:05:02Q and 03:20Q). A downstream start codon is located at nu 1449 for all DPA1 alleles. It is possible that this start codon can be used to translate splicing variants. The second allele, found in a patient and his related donor, had a mut at nu 1552 in intron 1. It is provisionally named DPA1*03:05:01:NEWQ since it includes the above described mut at nu 1432 that changes the start codon to Thr. Introns contain regulatory elements that can influence splicing and transcription. Of note, both alleles conserve a sequence in intron 1, spanning from nu 1572 to 1589 that is deleted in 20 of the known DPA1 alleles. This region is rich in G nu, including a quadruplex (G4s), which can interfere with replication and transcription, leading to altered expression levels. The last case concerns often ambiguous alleles DPA1*03:05:01:01Q and DPA1*03:05:01:02Q. These alleles differ at their two UTRs. Using DPA1*03:05:01:01Q as reference, DPA1*03:05:01:02Q has an insertion of 5 nu at the beginning of the 5'UTR and 3 insertions in the 3'UTR. First, is an insertion of 11 nu at 8428, second is an inserted T at nu 9222 and the third is a TA inserted at nu 9250. Insertions at both UTRs can modify allele expression. In the 5'UTR by altering the binding sites for regulatory proteins, impacting translation initiation or changing the mRNA secondary structure. In the 3'UTR by altering post-transcriptional regulation elements and/or altering the mRNA stability.
Conclusion: Studies are needed to understand allele differential expressions and their clinical implications.
