Phenotypic Mutation 'Nephro'

• Allele: Nephro
• Mutation Type: missense
• Chromosome: 5
• Coordinate: 104,634,672 bp (GRCm39)
• Base Change: T ⇒ A (forward strand)
• Gene: Pkd2
• Gene Name: polycystin 2, transient receptor potential cation channel
• Synonym(s): TRPP2, polycystin-2, C030034P18Rik, PC2
• Chromosomal Location: 104,607,316-104,653,685 bp (+) (GRCm39)
• MGI Phenotype: FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a member of the polycystin protein family. The encoded protein is a multi-pass membrane protein that functions as a calcium permeable cation channel, and is involved in calcium transport and calcium signaling in renal epithelial cells. This protein interacts with polycystin 1, and they may be partners in a common signaling cascade involved in tubular morphogenesis. Mutations in this gene are associated with autosomal dominant polycystic kidney disease type 2. [provided by RefSeq, Mar 2011] ; PHENOTYPE: Homozygotes for targeted null mutations exhibit defects in cardiac septation, kidney and pancreatic cysts, impaired left-right axis determination, and late-gestation lethality. Heterozygotes show kidney and liver lesions and have reduced longevity. [provided by MGI curators]
• Mapped: No
• Amino Acid Change: Tryptophan changed to Arginine
• Institutional Source: Beutler Lab
• Gene Model: predicted gene model for protein(s): [ENSMUSP00000084041]
• AlphaFold: O35245
• SMART Domains: Protein: ENSMUSP00000084041; Gene: ENSMUSG00000034462; AA Change: W568R

Domain	Start	End	E-Value	Type
low complexity region	25	43	N/A	INTRINSIC
low complexity region	58	79	N/A	INTRINSIC
low complexity region	93	115	N/A	INTRINSIC
low complexity region	119	138	N/A	INTRINSIC
transmembrane domain	225	247	N/A	INTRINSIC
Pfam:PKD_channel	265	685	1.3e-171	PFAM
Pfam:Ion_trans	454	690	2.6e-25	PFAM
coiled coil region	765	794	N/A	INTRINSIC
PDB:3HRN|A	834	893	8e-31	PDB
low complexity region	900	915	N/A	INTRINSIC
low complexity region	949	963	N/A	INTRINSIC

• Predicted Effect: probably damaging ; PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
  (Using ENSMUST00000086831)
• Meta Mutation Damage Score: 0.9729
• Is this an essential gene?: Essential (E-score: 1.000)
• Phenotypic Category: Unknown
• Mode of Inheritance: Unknown
• Local Stock: Live Mice
• MMRRC Submission: 038225-MU
• Last Updated: 2019-09-04 9:48 PM by Anne Murray
• Record Created: 2014-10-30 11:56 AM by Lauren Prince
• Record Posted: 2016-05-16
• Science Writers: Anne Murray
• Illustrators: Peter Jurek
• Authors: Lauren Prince, Jamie Russell, and Bruce Beutler

Accession Number

NCBI RefSeq: NM_008861; MGI:1099818

Alleles Listed at MGI

All mutations/alleles(25) : Chemically induced (ENU)(1) Gene trapped(12) Targeted(11) Transgenic(1)

Phenotypic Description

Figure 1. Representation of the phenotype observed in the nephro mice. The left mouse is a depiction of the anatomy of a wild-type mouse, while the right mouse is a depiction of the kidney phenotype in the nephro mouse.

The Nephro phenotype was identified among N-nitroso-N-ethylurea (ENU)-mutagenized G3 mice of the pedigree R1907, some of which showed swollen abdomens; dissection of the affected mice revealed that the mice had polycystic kidneys (Figure 1).

Nature of Mutation

Whole exome HiSeq sequencing of the G1 grandsire identified 114 mutations. The polycystic kidney phenotype mimicked that of other mice with mutations in Pkd2 (see MGI for a list of Pkd2 alleles). The mutation in Pkd2 is a T to A transversion at base pair 56,423,352 (v38) on chromosome 7, or base pair 29,583 in the GenBank genomic region NC_000071 encoding Pkd2. The mutation corresponds to residue 1,882 in the NM_008861 mRNA sequence in exon 7 of 15 total exons. 

1867 ATGGTATTTTTGGTCTGGATTAAGCTCTTCAAA 563  -M--V--F--L--V--W--I--K--L--F--K-

The mutated nucleotide is indicated in red. The mutation results in a tryptophan (W) to arginine (G) substitution at position 568 (W568R) in the polycystin-2 (PC2) protein, and is strongly predicted by Polyphen-2 to cause loss of function (score = 1.00).

Protein Prediction

Figure 2. Domain organization and topology of PC-2. PC-2 has six transmembrane domains, an EF-hand (EF-H) and a coiled-coil (CC) motif. The Nephro mutation results in a tryptophan (W) to arginine (R) substitution at position 568 (W568R). The location of the Nephro mutation is indicated in both the domain (A) and topology (B) images.

Pkd2 encodes polycystin-2 (PC-2; alternatively, PKD2 or transient receptor potential (TRP) cation channel, subfamily P, member 2 [TRPP2]) is a member of the TRP cation channel superfamily (see the record for gingame for information about TRPV5 [TRP cation channel, subfamily V, member 5]). PC-2 has six transmembrane domains (amino acids 222-242, 467-487, 504-524, 549-569, 597-617, and 657-677) and cytoplasmic N- and C-termini [Figure 2; (1;2)]. A pore structure is formed by transmembrane domains 5 and 6 (amino acids 634-659); transmembrane domains 1-4 function as a sensor (1;3).

The N-terminus of PC-2 contains a dimerization domain that mediates formation of PC-2 tetramers (4). In addition to the N-terminus, Cys632 within the third extracellular loop is essential for PC-2 dimerization and is proposed to function in disulfide bond formation between PC-2 monomers (5). Mutation of Cys632 to alanine (C632A) reduced the calcium release function of PC-2, indicating that it is required to form functional ER tetrameric PC-2 channels (5).

Amino acids 797-820 are predicted to comprise an ER-retention motif.  An acidic cluster at the end of the ER-retention motif is essential for the interaction between PC-2 and IP₃R (6).

Within the C-terminus of PC-2, a coiled-coil region (amino acids 821-966; UniProt) is linked to a calcium-binding EF-hand (amino acids 702-797; UniProt) by a flexible acidic linker (4;7-10). The coiled-coil domain mediates heteromultimeric interactions between PC-2 and several proteins (e.g., polycystin-1 (PC-1), alpha-actinins, Hax-1, filamin, ID2, TRPC-1, TRPV4, InsP₃R, RyR2, and PDE4C), which facilitates functional diversity among several channel complexes [Table 1; (3;8;11)]; the coiled-coil domain is not necessary for PC-2 homomeric interactions (4). The EF-hand of PC-2 binds calcium and is required for channel gating (7;9;10). In response to calcium binding, discrete conformational changes in the C-terminus of PC-2 mediates gating (7;9). Mutations within the EF-hand domain prevent calcium binding and result in completely inactive PC-2, subsequently inhibiting calcium release from the endoplasmic reticulum (ER) (7).

Table 1. PC-2-interacting proteins

PC-2-interacting protein	Brief Description	PC-2-associated function	References
PC-1	Receptor-activated non-selective calcium permeable cation channel	Regulates several signaling pathways to maintain normal renal tubular structure and function; see the Background section, below, for more details	(4;10-15)
Alpha-actinins	Microfilament protein	Mediates cell adhesion, proliferation, and migration	(16)
Hax-1 and cortactin	F-actin-binding proteins	Links PC-2 to cell-matrix contacts	(17)
Filamin	Actin cross-linking protein that functions in scaffolding, membrane stabilization, and signal transduction	Inhibits the channel function of PC-2	(18)
ID2	Cell cycle regulatory protein and inhibitor of basic helix-loop-helix transcription factors (e.g., the cyclin-dependent kinase inhibitor, p21)	Sequesters ID2 in the cytoplasm to promote cell proliferation and inhibit differentiation through the ID2-p21-CDK2 pathway	(19)
TRPC1	Non-selective calcium permeable cation channel	Unknown	(3;20)
TRPV4	Non-selective calcium permeable cation channel	Cutaneous thermosensation in primary cilia; regulates cell proliferation and cyst formation in renal collecting duct cells upon epidermal growth factor (EGF; see Velvet for information about the EGF receptor) stimulation	(21-24)
TRPC1 & TRPV4	Non-selective calcium permeable cation channels	PC-2-TRPC1-TRPV4 multimer mediates flow-induced calcium increase in native vascular endothelial cells	(25)
InsP3R	Intracellular calcium channel in the ER	Stimulates PC-2 to function as an intracellular calcium release channel in the ER	(6;26;27)
RyR2	Intracellular calcium channel in the ER essential for the regulation of muscle contraction	Inhibits RyR2 function	(28-30)
PDE4C-AKAP150-Adenyl cylase 5/6-PKA complex		Modulates cyclic AMP levels and subsequent signaling in primary cilia	(31)

Abbreviations: PC-1, polycystin-1; Hax-1, HCLS1 associated X-1; ID2, inhibitor of DNA binding 2; TRPC-1, transient receptor potential cation channel, subfamily C, member 1; TRPV4, transient receptor potential cation channel, subfamily V, member 4; InsP₃R, inositol 1,4,5-trisphosphate receptor 1; RyR2, cardiac ryanodine receptor 2; PDE4C, phosphodiesterase 4C; PKA, protein kinase A; AKAP150, A-kinase anchoring protein 150

PC-2 undergoes several posttranslational modifications. PC-2 is phosphorylated at several sites including Ser76, Ser801, and Ser812 (1;32-34). Glycogen synthase kinase (GSK)-3-dependent phosphorylation of Ser76 is required for PC-2 retention at the basolateral membrane and for pronephric development in zebrafish (33). CK2-dependent phosphorylation of Ser812 is required for the retrograde trafficking of PC-2 through binding to the adaptor proteins PACS-1 and PACS-2 as well as for the cytoplasmic retention of ID2 (19;34;35). Protein kinase D (PrKD)-mediated phosphorylation of Ser801 is increased in response to serum and EGF stimulation (32). Mutation of Ser801 results in inhibition of ATP-stimulated calcium release from ER stores in Madin-Darby canine kidney (MDCK) cells and reduction in PC-2-mediated inhibition of cell proliferation (32). PC-2 has seven putative N-glycosylation sites at Asn3, 299, 305, 328, 362, 375, and 580 in humans (36). Four asparagines (Asn297, 303, 326, and 360) in mouse and five asparagines (Asn299, 305, 328, 362, and 375) in humans are located within the first extracellular loop between TM 1 and TM2 (amino acids 245-468) (36). Mutations of all of the putative glycosylated asparagines within the first extracellular loop to glycines (N299G/N305G/N328G/N362G) or glutamines (N299Q/N305Q/N328Q/N362Q) resulted in deficient synthesis of PC-2.

Alternative splicing of exons 6 (PC-2Δ6), 7 (PC-2Δ7), 9 (PC-2Δ9) and 12-13 (PC-2Δ12-13) in Pkd2 generates multiple PC-2 isoforms (37). The PC-2Δ6 transcript lacks a portion of exon 6 and results in a shift in the reading frame to generate a truncated protein of 481 amino acids. The PC-2Δ7 transcript lacks all of exon 7 and encodes an in-frame protein of 910 amino acids. The PC-2Δ7 protein is stable, but does not interact with PC-1 due to alterations of the topology of the C-terminus (37). The PC-2Δ7 protein is expressed primarily in the brain, with lower level of expression in kidney and lung (37). The PC-2Δ9 transcript lacks all of exon 9, resulting in a frameshift that would encode a protein of 644 amino acids. The PC-2Δ12-13 transcript is a minor form of PC-2, resulting in an in-frame deletion of exons 12 and 13 that encodes a protein of 872 amino acids.

The mutation in the Nephro mice is a tryptophan (W) to arginine (R) substitution at position 568 (W568R). Amino acid 568 is within TM domain 4.

Expression/Localization

PC-2 is ubiquitously expressed during development through the two-cell to compact blastocyst stage (38). As development progresses, PC-2 is expressed in the ovary, fetal craniofacial structures, fetal and adult kidney, testis, small intestine, pancreas, liver, lung, bowel, brain, thymus, reproductive organs, placenta, skeletal muscle, aortic vascular smooth muscle, and rat left ventricular myocytes (1;39-44). Within the kidney, PC-2 localizes to the plasma membrane of primary cilia of the kidney epithelium (24), the plasma membrane of cells of the ascending limb of Henle, the distal convoluted tubule, the proximal tubule, and collecting ducts (41). PC-2 also localizes to the ER membrane (29). In mouse inner medullar collecting duct cells and Madin-Darby canine kidney (MDCK) epithelial cells, endogenous PC-2 localized at the plasma membrane and the primary cilium; heterologously-expressed PC-2 exhibited predominant ER localization (45).

Background

The TRP ion channel family has seven subfamilies: TRP Canonical (TRPC), TRP Melastatin (TRPM), TRP Ankyrin (TRPA), TRP Mucolipin (TRPML), TRP Polycystin (TRPP), TRP NOPMC (TRPN), and TRP Vanilloid (TRPV) (46;47).  These receptor subfamilies respond to several external stimuli such as light (i.e. phototransduction), chemicals, and temperature as well as mechanical and osmotic pressures (48;49). TRP channels have roles in diverse processes including olfaction, nociception, speech, regulation of blood circulation, pain signal transduction, gut motility, mineral absorption, fluid balance, epithelial Ca²⁺ transport, development of airway and bladder hypersensitivities, and cell survival, growth and death (48). The TRP channels function by facilitating the transmembrane flow of cations (i.e. Na⁺ and Ca²⁺) down electrochemical gradients to depolarize the cell as well as to mediate signal transduction (50). TRP channels can be activated through the activation of phospholipase C (PLC) by G protein-coupled receptors and receptor tyrosine kinases. 

Figure 3. Function of PC-2 in Ca 2+ signaling. Store operated channels (SOC), the plasma membrane Ca 2+ -ATPase (PMCA), G-coupled protein receptor (GPCR), and polycystin-1 (PC-1) are on the plasma membrane. PC-1 and PC-2 interact via their coiled-coil domains in the primary cilia. When the cilia sense flow, PC-1 is activated through an unknown mechanism. Upon PC-1 activation, PC-1 subsequently activates PC-2, which leads to entry of Ca 2+ from the extracellular space into the cytosol. The Ca 2+ then activates the RyR in a Ca 2+ -induced Ca 2+ release (CICR) mechanism. On the plasma membrane, GPCRs activate a trimeric G-protein containing Gq; Gq then stimulates phospholipase C beta (PLCβ) to break down phosphatidylinositol-4,5-bisphosphate (PIP2) into InsP 3 and diacylglycerol. When InsP 3 binds to InsP 3 R, Ca 2+ is released from the endoplasmic reticulum (ER) into the cytosol. Ca 2+ release through the InsP 3 R can activate PC2 to potentiate Ca 2+ release from the ER stores. Figure and legend adapted from G.I. Anyatonwu and B.E. Ehrlich ( 2004 ).

PC-2 is a calcium-permeable nonselective cation channel that functions at several locations including the primary cilia, basolateral membrane, and the ER to subsequently mediate proliferation, apoptosis, tubulogenesis, and fluid secretion through the regulation of calcium transport and calcium signaling [Figure 3; (3;45)]. PC-2, often together with PC-1, respond to physical or chemical stimuli (e.g., fluid flow) to stimulate calcium influx through PC-2, subsequently resulting in calcium release from intracellular stores (14;24;29). PC-2 is activated by upon EGF stimulation (23). Activation of PLC leads to hydrolysis of PIP₂, producing diacylglycerol (DAG) and inositol (1,4,5) triphosphate (IP₃).  Strong evidence supports roles for PIP₂ hydrolysis and DAG production in modulating TRP channel activity. 

InsP₃R and RyR2 are intracellular calcium channels in the ER. RyR2 is a calcium release channel that is essential for calcium-induced calcium release, a prerequisite for excitation-contraction coupling (51). Interactions between PC-2 and InsP₃R or RyR2 stimulates PC-2 to function as an intracellular calcium release channel in the ER (26-29). In smooth muscle, PC-2 reduced the activity of store-operated calcium channels (40). Interaction between PC-2 and RyR2 resulted in functional inhibition of RyR2 by PC-2 by stabilizing RyR2 in the closed state and subsequently inhibiting the release of calcium (28). Loss of PC-2-mediated inhibition of RyR2 in PC-2-deficient cardiomyocytes results in a higher frequency of spontaneous calcium oscillations, reduced sarcoplasmic reticulum calcium stores, and reduced calcium transient amplitude compared to wild-type cells (28). In autosomal dominant polycystic kidney disease patients with PKD2 mutations, there is a high rate of idiopathic dilated cardiomyopathy compared to the general population (51).

In the embryonic node, ciliary movement generate nodal flow, an external liquid flow that determines left-right (L-R) asymmetric gene expression including Nodal and Cerl-2 (52-56). Increased levels of endodermal cell calcium is proposed to regulate the conversion of nodal flow to asymmetric gene expression (55). PC-2 acts independently of PC-1 to regulate L-R symmetry at the embryonic node (38;57;58). Field et al. propose that Pkd1l1 and PC-2 form a cilia-specific, stress-responsive channel in the node that regulates L-R asymmetry (59). PC-2 physically interacts with Pkd1l1 in the cilium to mediate L-R patterning (59). Mutations in Pkdl1l phenocopy those of Pkd2 mutants in that both develop gross situs abnormalities; Pkd1l1 mutants do not exhibit kidney development defects (59). Pkd2-deficient (Pkd2^{−/−LacZ+/+}) mice exhibit right pulmonary isomerism, randomization of embryonic turning, heart looping, and abdominal situs (38). PC-2 is proposed to act downstream or in parallel to sonic hedgehog (Shh) and upstream of the Nodal cascade. Mutations in human PKD2 have also been linked to left-right asymmetry defects (56).

PC-2 functions as a mechanoreceptor in postnatal craniofacial development and growth (44). Conditional knockout of Pkd2 in neural crest-derived cells resulted in craniofacial structural abnormalities (e.g., fractured molar roots, distorted incisors, alveolar bone loss, compressed temporomandibular joints, and skull shape abnormalities) (44).

In human syncytiotrophoblast, PC-2 functions as a nonselective cation channel with a high permeability rate to calcium (60). PC-2 (and PC-1) are required for normal placental development in both the trophoblast and fetal vascular compartments (39). Deletion of either Pkd1 or Pkd2 resulted in placental abnormality (i.e., polyhydramnios) and reduced embryonic viability (39).

Hepatocyte growth factor (HGF) and EGF stimulate cell proliferation and branching via ERK1/2 in the p42/44 MAPK pathway (61;62). Exogenous expression of PC-2 resulted in decreased HGF-induced branching morphogenesis in kidney epithelial cells, indicating that PC-2 mediates tubule maturation by negatively regulating cell growth (62).

Mutations in PKD2 are linked to autosomal dominant polycystic kidney disease 2 (ADPKD2; OMIM: #613095) (1;63-65). Patients with ADPKD2 have renal cysts, liver cysts, and intracranial aneurysm. In addition, patients often have acute and chronic pain as well as nephrolithiasis. ADPKD2 leads to progressive destruction of normal kidney tissue and approximately 50% of patients with ADPKD2 develop end-stage renal disease by 60 years of age. Patients with ADPKD2 exhibit variable phenotypes including differences in the rate of loss of glomerular filtration, the age of onset of end-stage renal disease, occurrence of hypertension, symptomatic extrarenal cysts, and subarachnoid hemorrhage.

Putative Mechanism

Pkd2-deficient (Pkd2^-/-) mice are embryonic lethal between embryonic day (E) 13.5 and birth (38;66). Mice that express mutant Pkd2 alleles (e.g., Pkd2^WS25) as well as Pkd2^-/- and Pkd2^+/- mice develop polycystic kidney similar to those observed in humans with ADPKD2 (66;67). The Pkd2^-/- mice exhibit progressive cyst formation in the nephrons and pancreatic ducts starting at E15.5 as well as defects in cardiac septation (66). Kidney development was normal up to E14.5, while pancreatic development was normal up to E13.5 in the Pkd2^-/- mice (66). After E14.5, the pancreatic ducts in the Pkd2^-/- mice exhibited progressive cystic dilation. Heterozygous Pkd2 (Pkd2^+/-) mice exhibited renal failure and premature death by approximately 65 weeks (66).  The phenotype observed in the Nephro mice indicate that PC-2^Nephro is defective.

Primers

PCR Primer
Nephro_pcr_F: GGCTCAGTAATATGGTCAGTCC
Nephro_pcr_R: TGCCATCTACATGACTGCAAAC

Sequencing Primer
Nephro_seq_F: TCAGTAATATGGTCAGTCCTCTAATC
Nephro_seq_R: CTATGCAGCAACCTCATCTGG

Genotyping

PCR program

1) 94°C 2:00
2) 94°C 0:30
3) 55°C 0:30
4) 72°C 1:00
5) repeat steps (2-4) 40x
6) 72°C 10:00
7) 4°C hold

The following sequence of 448 nucleotides is amplified (chromosome 5, + strand):

1   ggctcagtaa tatggtcagt cctctaatca gtagattaaa aataggcatt ttaaggtaga
61  gtgtctattt cttaactgat gtgataagta taactctttt tgtcttccag ttatctgtag
121 tagctatggt gattaacatt taccgaatgt caaatgcaga ggggctgcta cagtttcttg
181 aagatcaaaa ttctttcccc aactttgagc atgtggcata ctggcaaata cagttcaaca
241 atataagtgc tgtcatggta tttttggtct ggattaaggt aacttatgtc acattcttca
301 tatatagatg cattgatgat gatgatgatg atgatgatga tgatgatgat gatttacaca
361 gatcattgga agacatagat ttgccttttt aggctgattg aaatggccag atgaggttgc
421 tgcatagttt gcagtcatgt agatggca

Primer binding sites are underlined and the sequencing primers are highlighted; the mutated nucleotide is shown in red.

References

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