Monoallelic IFT140 pathogenic variants are an important cause of the autosomal dominant polycystic kidney-spectrum phenotype

Abstract

Autosomal dominant polycystic kidney disease (ADPKD), characterized by progressive cyst formation/expansion, results in enlarged kidneys and often end stage kidney disease. ADPKD is genetically heterogeneous; PKD1 and PKD2 are the common loci (∼78% and ∼15% of families) and GANAB, DNAJB11, and ALG9 are minor genes. PKD is a ciliary-associated disease, a ciliopathy, and many syndromic ciliopathies have a PKD phenotype. In a multi-cohort/-site collaboration, we screened ADPKD-diagnosed families that were naive to genetic testing (n = 834) or for whom no PKD1 and PKD2 pathogenic variants had been identified (n = 381) with a PKD targeted next-generation sequencing panel (tNGS; n = 1,186) or whole-exome sequencing (WES; n = 29). We identified monoallelic IFT140 loss-of-function (LoF) variants in 12 multiplex families and 26 singletons (1.9% of naive families). IFT140 is a core component of the intraflagellar transport-complex A, responsible for retrograde ciliary trafficking and ciliary entry of membrane proteins; bi-allelic IFT140 variants cause the syndromic ciliopathy, short-rib thoracic dysplasia (SRTD9). The distinctive monoallelic phenotype is mild PKD with large cysts, limited kidney insufficiency, and few liver cysts. Analyses of the cystic kidney disease probands of Genomics England 100K showed that 2.1% had IFT140 LoF variants. Analysis of the UK Biobank cystic kidney disease group showed probands with IFT140 LoF variants as the third most common group, after PKD1 and PKD2. The proximity of IFT140 to PKD1 (∼0.5 Mb) in 16p13.3 can cause diagnostic confusion, and PKD1 variants could modify the IFT140 phenotype. Importantly, our studies link a ciliary structural protein to the ADPKD spectrum.

Keywords: ADPKD; IFT140; cilia; ciliopathy; intraflagellar transport; monoallelic cystic disease; polycystic kidney disease; short rib thoracic dysplasia.

Graphical abstract

Figure 1

Details of the study design (A) The study is divided into screening of ADPKD spectrum families (part 1) and analysis of previously sequenced cohorts (part 2). Part 1 included subjects from ADPKD clinical trials: HALT PKD (HALT), DIPAK randomized clinical trial (RCT), and TAME; ADPKD observational studies: CRISP, DIPAC Observational (Observ), and Genkyst; genetics studies: ADPKD Modifier, Mayo PKD Center, and Irish Kidney Gene Project (IKGP); and other recruitment sites: Sheffield, Tufts, Brest, and Kuwait. Part 2 consisted of the Genomics England 100K project Cystic Kidney Disease cohort (100kG; PKD) and the UK Biobank (individuals with ICD-10 Q61). The number of analyzed individuals per study site is indicated. (B) The sequencing methods and whether participants were prescreened for PKD1 and PKD2 are indicated, the total number of screened and IFT140-positive families is shown. The number of families/probands with pathogenic IFT140 variants relative to the total number screened by each method from each study/site are shown above. Out of the 777 naive families screened at Mayo, 357 (45.9%) and 105 (13.5%) were resolved by pathogenic or likely pathogenic PKD1 or PKD2 variants, respectively, while 30 (3.9%) and six (0.8%) had a VUS to PKD1 or PKD2. Among the pathogenic variants were 19 PKD1 large deletions, one PKD1 large duplication, and three PKD2 large deletions. The relatively low number of families resolved with a PKD1 or PKD2 pathogenic variant (59.5%), reflects the broad phenotypic spectrum of the recruited individuals, including mild cystogenesis. (C) Summary of the screening showing the total number of IFT140 families identified by screening of ADPKD spectrum subjects (part 1) and identified in the 100kG, PKD cohort, and the UK Biobank (part 2).

Figure 2

Pedigree and imaging details of five IFT140 pedigrees (A–V) Pedigrees M132 (A), M199 (G), P1320 (L), EDI1005 (O), and 390044 (S); clinically affected individuals are in black, unaffected are in white, uncertain are in gray, and deceased subjects are lined through. Only affected individuals or others with a sample available are shown. (A) In M132, segregation of the IFT140 pathogenic variant and PKD1 VUS are shown; IFT140: c.2399+1G>T and PKD1: c.11017−3C>T cosegregate. (G) In M199, inheritance of IFT140: c.2767_27688+2del and a frameshifting variant in DYNC2H1 (bi-allelically causing SRTD3), which does not segregate with the disease, are shown. (L) In P1320, the IFT140 pathogenic variant segregates in four individuals with a PKD1 VUS, while a BBS2 nonsense variant does not cosegregate with disease. EDI1005 (O) just had an IFT140 pathogenic variant. Two PKD1 VUSs cosegregated with the IFT140 pathogenic variant in 390044 (S). It is not known whether these additional variants have any influence on the disease phenotype (see Table 3 for details). Abdominal coronal imaging by MRI (B–D, J, M, N, and Q) or CT (E, F, P, T, and V), axial imaging by CT (H, I, K, and U), or abdominal ultrasound (US) (R) with the age at imaging indicated shows the kidney phenotype is typically multiple, larger bilateral cysts, sometimes with marked asymmetry (K). Only M132 IV-1 (F) has liver cysts.

Figure 3

Pedigrees and imaging details of seven IFT140 families (A–S) Pedigrees of M1629 (A), PK14083 (D), M1554 (G), P1497 (J), 1470059 (M), M1169 (P), and M1266 (R); clinically affected individuals are in black, unaffected are in white, uncertain are in gray, and deceased subjects are lined through. Only affected individuals or others with a sample available are shown. The segregation of the IFT140 pathogenic variant in each family is shown (inferred in M1629 III-1), plus inheritance of variants in PKD1; in cis with the IFT140 pathogenic variant in M1629 and 1470059. A truncating variant or variant of uncertain significance to PKHD1 (M1554 and M1266), which cosegregate with disease, and WDR35 (M1554), which does not, are also noted. It is not known if these additional variants have any influence on the disease phenotype (see Table 3 for details). Abdominal coronal MRI (C, E, F, K, L, N, O, and S), coronal (B, H, and Q) or axial CT (I) with the age at imaging indicated shows the kidney and liver phenotypes. The cystic presentation varies from several large cysts bilaterally (N) to much milder cystogenesis (O and S).

Figure 4

UK Biobank data demonstrate IFT140 LoF alleles are associated with cystic kidney disease (A) Gene-level Manhattan association plot with binary trait Q61 (cystic kidney disease) and Fisher’s exact two-sided test statistics. A significance threshold of P ≤ 2 × 10⁻⁹ has been selected (see subjects and methods). Here, gene-level results are shown with a collapsing model based on protein-truncating variants with a gnomAD MAF of ≤5% (ptv5pcnt). The proportion of cases with a qualifying protein-truncating variants in the Q61 group (n = 521) was compared with the proportion in controls (n = 239,516) for each gene. Among the 521 cases, 14 (2.69%) had a monoallelic IFT140-truncating variant, compared to 506 (0.21%) among the controls. For PKD1, PKD2, and ALG9, 44 (8.45%) cases and 35 (0.015%) controls, 29 (5.57%) cases and ten (0.004%) controls, and four (0.77%) cases and 76 (0.032%) controls had a monoallelic truncating variant, respectively. The −log10 p values for enrichment in the cystic kidney disease group are shown; ALG9 did not reach the significance threshold. Graph generated from the Astra Zeneca PheWAS Portal. (B) Prevalence of kidney-related diagnoses in IFT140 high (likely pathogenic) versus low impact (likely benign) variant carriers. Of the 200,643 individuals from the UK Biobank with exome data, 481 had monoallelic high and 5,888 low impact variants to IFT140. Comparison of individuals with kidney-related diagnoses (grouped by ICD-10 terms) showed that cyst of kidney (N28.1), cystic kidney disease (Q61), and CKD stages 4 and 5 (N18.4 & N18.5) were significantly more common in individuals with high impact IFT140 variants compared to low impact (shaded; see figure for p values and odds ratios with 95% confidence intervals [CIs]). One high impact carrier was in both the N28.1 and Q61 groups. Other kidney phenotypes were not enriched for high impact IFT140 variants.

Figure 5

Comparison of eGFR and htTKV between IFT140 and PKD2 individuals (A) Plotting of eGFR values versus age demonstrates that IFT140 individuals have a slower decline in renal function compared to PKD2^, but quicker than would be expected with normal aging. Only one IFT140 subject reached ESKD and one had CKD stage 4. (B) Plot of height-adjusted TKV on the natural log scale (In htTKV) versus age for individuals with a typical and atypical MIC differentiated compared to PKD2.^, A wide range of htTKV are seen associated with ADPKD-IFT140. Shading shows the 95% confidence intervals.