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Saudi Journal of Kidney Diseases and Transplantation
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Year : 2012  |  Volume : 23  |  Issue : 1  |  Page : 143-147
Mutation analysis of PKD1 gene in Indian population

1 Department of Medicine, Sri Venkateswara Institute of Medical Sciences, Tirupati, India
2 Department of Biotechnology, Sri Venkateswara Institute of Medical Sciences, Tirupati, India
3 Department of Nephrology, Sri Venkateswara Institute of Medical Sciences, Tirupati, India

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Date of Web Publication3-Jan-2012

How to cite this article:
Kumar B S, Sharma P, Reddy LK, Bhattaram MP, Mohan A, Kumar V S. Mutation analysis of PKD1 gene in Indian population. Saudi J Kidney Dis Transpl 2012;23:143-7

How to cite this URL:
Kumar B S, Sharma P, Reddy LK, Bhattaram MP, Mohan A, Kumar V S. Mutation analysis of PKD1 gene in Indian population. Saudi J Kidney Dis Transpl [serial online] 2012 [cited 2022 Aug 19];23:143-7. Available from: https://www.sjkdt.org/text.asp?2012/23/1/143/91406
To the Editor,

Autosomal Dominant Polycystic Kidney Disease (ADPKD) is genetically heterogeneous. About 85 - 90% of the afflicted families have mutations of PKD1 on chromosome 16. [1] This gene encodes a cell membrane protein called Polycystin - 1(PC1.)[2]

Inheritance of one mutant allele is sufficient to cause this condition. An analysis of mutations of PKD1 has revealed mainly "stop" and "frame shift" changes suggesting that the mutant allele is inactivated. Analysis of rare cases with severe ADPKD and tuberous sclerosis (TSC), which have large "deletions" disrupting (sometimes totally removing) the adjacent PKD1 and TSC2 genes indicate that a null PKD1 allele is associated with cyst development. [3] Knockout models of PKD1 support the notion that cyst development is caused by the reduction or loss of protein. In the PKD1 del34 model, older heterozygotes have occasional cyst, whereas homozygotes die in the perinatal period with enlarged and cystic kidneys. [4],[5] It has been shown that at cellular level cysts develop in a recessive manner due to the second somatic hits to the normal PKD1 allele, thus, explaining the focal nature of cyst development. [6],[7]

PC1 is thought to function as a cell surface signaling receptor at cell-cell/cell-matrix junctions and as a mechano-sensor in renal primary cilia. It activates signaling pathways involved in renal tubular differentiation. [8],[9],[10]

One unique aspect of PC1 cleavage is that it is incomplete when expressed in various cell types. PKD1-associated missense mutations in the GPS domain and the neighboring REJ domain, as well as synthetic mutations at the predicted cleavage site, were found to disrupt the cleavage. They also resulted in loss of the functional properties of PC1 to activate the JAK2-STAT pathway and induce in vitro tubulogenesis. [10],[11],[12] The PC1 proteins are diffusely expressed in the tubular epithelial cell cytoplasm in the fetal and adult kidneys. In the kidney affected with ADPKD, the PC1 proteins are heterogeneously and weakly expressed in the tubular or cyst lining epithelial cells. Data suggests that the development of the kidney may regulate the expression of PC1, and an altered PC1 expression may contribute to cyst formation.

Several investigators have proposed that PC1 and polycystin-2 (encoded by the PKD2 gene) are components of a signaling cascade, with PC1 acting as a receptor for either cell-cell or cell-matrix interactions. Immunostaining of human and mouse renal tissues have demonstrated widespread and developmentally regulated polycystin-2 expression, with the highest level of PC1 in thick ascending limb and distal convoluted tubule. [13],[14],[15] It has been shown that the two proteins interact with each other via their C-terminal regions and possibly function as flow-sensitive mechanosensors in the primary cilium of the renal epithelium cells. A failure of fluid-flow sensation of the cells may disturb tissue morphogenesis and trigger abnormal cell proliferation and cyst formation.

Trying to correlate the genotype with the phenotype within a family carrying the same mutation seems to show a wide range of variability clearly illustrating the limitations of such attempts. However, certain interdependencies have been set up in PKD1 as two mutations 5′ to the median are associated with a slightly earlier age at onset of end- stage renal disease (ESRD). Moreover, the median position of the PKD1 mutation was found to be further 5′ located in families with a vascular phenotype of intracranial aneurysms and sub-arachnoid hemorrhage. [14],[15] However, for genetic counseling and the prediction of the outcome of an individual patient, these genotype-phenotype correlations are only of limited value.

The present study is a part of a much larger study being done to detect the mutations in PKD 1 gene in this part of the globe. Our study identified two new mutations in a patient with PKD1 based renal failure and is the first of its kind from India.

We took peripheral venous blood from a patient with ESRD due to ADPKD and analyzed exons 38, 40, 45 and 46. These exons were chosen for analysis as they are the locations where mutations commonly occur. Two samples of blood were collected from normal individuals to act as controls. DNA was extracted from peripheral blood (PB) cells by standard procedure. Exons 38, 40, 45, and 46 of PKD1 gene were PCR amplified using the primers constructed from the consensus PKD1 gene sequence as found on NCBI (accession numbers FJ605456, FJ605457, FJ605458, FJ605459, FJ605460). Primer sequences and PCR conditions under which the PKD1 exon amplification was performed are mentioned in [Figure 1]. Complete PCR products (5 μL) were mixed with 5 μL 50 mM NaOH and 95% formamide and electrophoresed in 6% PAGE 1 × TBE gel with 2.5% crosslinking at 250 V for 16 h at 4°C. The gel was then stained with 0.5 mg/m/ethidium bromide and photographed under UV light. DNA samples exhibiting shifted bands were amplified and sequenced using ABI Prism™ 310 Genetic Analyzer (Applied Biosystems) according to the manufacturer's instructions at MWG (Biotech) India Ltd, Bengaluru.
Figure 1: Location of PKD-1 - Indicated by the red line (Sourced from PKD1 Gene - GeneCards at http://www.genecards.org/cgi-bin/carddisp.pl?gene=Pkd1)

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Putative missense changes in PKD1 were further analysed with human PKD1 gene sequence using BLAST and mutations in different sequences were recorded (2 and 31).

When the result of obtained sequence was compared with the existing sequence in the data base using the ClustalW2 multiple alignment tool (found at http://www.ebi.ac.uk), the exon 40 of the PKD1 gene of the patient showed the presence of an SNP at position 51032, where G from the RefSeq PKD1 sequence was observed to have been replaced by a T in the query sequence. The position 51302 was seen to be located in intron 40 of the PKD1 RefSeq sequence. This mutation was was found to be in the C-terminal domain of the protein related to the G-protein activation signal. Secondly a 6 base pair (TGGCTC) deletion was observed in the query sequence (Position 51133 - 51138 in the PKD1 RefSeq sequence). The query sequence was then compared against the human genome assembly by using BLAST from NCBI (located at http:// blast.ncbi.nlm.nih.gov/Blast.cgi) and the following observations were made: 1.) The position of the SNP was confirmed in the BLAST. 2.) The deletion was observed to have aligned differently when under the conditions of the BLAST which looks at local, rather than global alignment. Instead of a single 6bp deletion, the possibility of a single base pair deletion, a two bp deletion and a three base pair deletion was presented. All these were identified as being within the Exon 40. One of the obtained sequences were deposited in the Gene Bank at www.ncbi.nlm.nih.gov while the second is yet to be deposited (accession numbers FJ605456, FJ605457, FJ605458, FJ605459, FJ605460), [Figure 2], [Figure 3], [Figure 4] and [Figure 5].
Figure 2: PKD 1 gene sequence - Location of the deletion w.r.t the entire gene. The exons are shown in yellow. All known SNPs are also indicated in the sequence.

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Figure 3: Patient's Data (Exon 40) BLAST - The BLAST result from the patient's DNA sequence. The first two comparisons are with the human chromosome 16. DIP is a known SNP that is present in this region.

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Figure 4: The deletion in Exon 40 - the deletion w.r.t Exon 40 (indicated in yellow, blue indicates the gene) DIP here is the same as in 03.

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Figure 5: Isoform A (EAW85553) - The two amino acids that are deleted w.r.t to the protein sequence.

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Here we report a 6-base pair deletion in the middle of the exon 40 sequence. The reported mutations occurred toward the C-terminus domain G-protein activation sequence a probable coiled domain contained of the PC1, which is implicated in direct interaction with the polycystin 2, and this mutation may also directly affect the signaling pathway. This variation probably correlates with severity of the renal failure of the patient. In this study we used microsatellite containing primers [Figure 1] and the PCR products obtained indicated that PKD1 gene with such mutation probably linked in the patient's family [16] although detailed investigation of the family is required to establish the report. The utility of this data for genetic counseling and prediction of outcome in a single patient are limited, nevertheless, RNA interference may prove to be an important way to treat such patients in future.

   References Top

1.Reeders ST, Breuning MH, Davies KE, et al. A highly proliferic DNA marker linked to adult polycystic kidney disease on chromosome 16. Nature 1985;317(6037):542-4.  Back to cited text no. 1
2.The European Polycystic Kidney Disease Consortium. The polycystic kidney disease 1 gene encodes a 14 kb transcript and lies within a duplicated region on chromosome 16. Cell 1994;77(6):881-94.  Back to cited text no. 2
3.Sampson JR, Matheshwar MM, Aspinwall F, et al. Renal cystic disease in tuberous sclerosis the role of the polycystic kidney disease I gene. Am J Hum Genet 1997;61(4):843-51.  Back to cited text no. 3
4.Lu W, Peissel B, Babakhanlou H, et al. Perinatal lethality with kidney and pancreas defects in mice with a targeted pkd1 mutation. Nat Genet 1997;17:179-81.  Back to cited text no. 4
5.Lu W, Fan X, Basora N, et al. Late onset of renal and hepatic cysts in Pkd1 targeted heterozygotes. Nat Genet 1999;21(2):160-1.  Back to cited text no. 5
6.Qian F, Watnick TJ, Onuchic LF, Germino GG. The molecular basis of focal cyst formation in human autosomal dominant polycystic kidney disease type I. Cell 1996;87(6): 979-87.  Back to cited text no. 6
7.Watnick TJ, Torres VE, Gandolph MA, et al. Somatic mutation in individual liver cysts supports a two hit model of cystognesis in autosomal dominant polycystic kidney disease. Mo Cell 1998;2(2):247-51.  Back to cited text no. 7
8.Hughes J, Ward CJ, Peral B, et al. PKD1 gene encodes a novel protein with multiple cell recognition domains. Nat Genet 1995;10(2): 151-60.  Back to cited text no. 8
9.Polycystic kidney disease. The complete structure of the PKD1 gene and its protein. The International Polycystic Kidney Disease Consortium. Cell 1995;81(2):289-98.  Back to cited text no. 9
10.Hanaoka K, Qian F, Boletta A, et al Co-assembly of polycystin-1 and -2 produces unique cation-permeable currents. Nature 2000;408 (6815):990-4.  Back to cited text no. 10
11.Newby LJ, Streets AJ, Zhao Y, Harris PC, Ward CJ, Ong AC. Identification, characterization, and localization of a novel kidney polycystin-1-polycystin-2 complex. J Biol Chem 2002;277:20763-73.  Back to cited text no. 11
12.Nauta J, Goedbloed MA, van den Ouweland AM, Nellist M, Hoogeveen AT. Immunological detection of polycystin-1 in human kidney. Histochem Cell Biol 2000;113(4):303-11.  Back to cited text no. 12
13.Badenas C, Torra R, Millan JL, et al. Mutational analysis within 3' region of the PKD1 gene. Kidney Int 1999;55(4):1225-33.  Back to cited text no. 13
14.Vouk K, Strmecki L, Stekrova J, et al. PKD1 and PKD2 mutations in Slovenian families with autosomal dominant polycystic kidney disease. BMC Med Genet 2006;7:6,.  Back to cited text no. 14
15.Ritz E, Zeier M, Waldherr R. Progression to renal insufficiency. In Watson ML, Torres VE, eds: Polycystic Kidney Disease, Oxford, UK, Oxford University Press. 1996.  Back to cited text no. 15
16.Ariyurek Y, Lantinga-van Leeuwen I, Spruit L, Ravine D, Breuning MH, Peters DJ. Large deletions in the polycystic kidney disease 1 (PKD1) gene. Hum Mutat 2004;23(1):99.  Back to cited text no. 16

Correspondence Address:
B Siddhartha Kumar
Department of Medicine, Sri Venkateswara Institute of Medical Sciences, Tirupati
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Source of Support: None, Conflict of Interest: None

PMID: 22237240

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  [Figure 1], [Figure 2], [Figure 3], [Figure 4], [Figure 5]

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