Exon sequencing of the gene encoding UCMA/GRP in healthy and clinical subjects
Independent thesis Advanced level (degree of Master (One Year)), 20 credits / 30 HE creditsStudent thesis
Mineralization of soft tissues can cause significantly increased morbidity and mortality. The mechanism for this process is still unknown; however, patients with chronic kidney disease (CKD) are at high risk of developing vascular calcifications. Coronary artery calcification occurs faster in CKD patients undergoing dialysis in comparison with the general population. The pathological process of vascular calcification is the leading cause of death in patients with CKD.
Upper zone of growth plate and cartilage matrix associated protein (UCMA) is a novel vitamin-K dependent (VKD) protein expressed in bone and the vascular system. The UCMA protein contains 15 γ-carboxyglutamic acid (Gla) residues in its 138 residue sequence which is the highest ratio between the number of Gla-residues and the size of the mature protein found in any protein so far. These Gla-residues form a domain that gives unique calcium binding properties for UCMA with high affinity for calcium phosphate crystals (i.e., hydroxyapatite). Even though the function of UCMA remains to be elucidated, it has been speculated that UCMA inhibits calcification of soft tissues and could therefore have a protective function against vascular calcification. Any mutations in the gene coding for UCMA might lead to a diminished function or defective protein.
The aim of this study was to determine whether the gene encoding UCMA in patients with the most progressed stage of CKD (stage 5 CKD) contained any mutations. This was accomplished by performing a full re-sequencing of all five exons with dideoxy sequencing in 16 patients with stage 5 CKD on heamodialysis. If any mutations were discovered, pyrosequencing would be performed on 98 healthy control individuals. This would help to determine if the mutation was exclusive for the patients or existed in the general population as well.
Genomic DNA was extracted from whole blood originating from 16 patients with CKD on haemodialysis. Each of UCMAs five exons were amplified with PCR and the results were visualized using gel electrophoresis. Each exon was re-sequenced and pyrosequencing was performed on 98 healthy control samples. The acquired results were compared with the sequence of the UCMA gene identified at NCBI-GenBank (NCBI, build 37.2, NM_145314.1, Gene ID: 221044) and the Ensemble genome browser (ENSG00000165623). In addition, the frequencies of each SNP were calculated and compared with a study at the Ensemble database originating from the 1000 genomes project (1000GENOMES:low_coverage: CEU).
Because the population of our study group was too small to yield appropriate power for statistical calculations, no definite conclusions could be drawn from the acquired results. Nevertheless, this is the first patient group with CKD ever studied and should thus be regarded as a pilot study due to the limited size. However, no indication was found that UCMA had major defects in the investigated patients. Instead, a heterozygous transversion mutation was found in SNP rs4750328, indicating that the site of this SNP is subject to other modifications. Furthermore, a novel SNP was discovered which has not been described in other populations to our knowledge. The novel SNP is non-synonymous (i.e., causes an amino acid exchange) and located at the carboxyl-terminal of the protein. A serine is incorporated instead of threonine giving a 138Thr>Ser change since the last ACC codon in exon 5 (adjacent to the stop codon) is altered to an AGC codon. The UCMA 138Thr>Ser polymorphism was submitted to the dbSNP database and has been assigned the accession number ss283927876, which will be publicly available upon the release of the next dbSNP Build, B134. In order to determine the physiological significance of the discovered SNP, functional studies are required on both the wild-type and mutated UCMA variants.
Place, publisher, year, edition, pages
2011. , 53 p.
UCMA, GRP, PCR, DNA-sequencing, dideoxy-sequencing, pyrosequencing
IdentifiersURN: urn:nbn:se:liu:diva-68647ISRN: LITH-IFM-A-EX--11/2459--SEOAI: oai:DiVA.org:liu-68647DiVA: diva2:439228
Subject / course
UppsokPhysics, Chemistry, Mathematics
Magnusson, Per, DocentOsman, Abdimajid, PhD
Carlsson, Uno, Professor