Biallelic variants in TTC21B as a rare cause of early-onset arterial hypertension and tubuloglomerular kidney disease

Abstract

Monogenic disorders of the kidney typically affect either the glomerular or tubulointerstitial compartment producing a distinct set of clinical phenotypes. Primary focal segmental glomerulosclerosis (FSGS), for instance, is characterized by glomerular scarring with proteinuria and hypertension while nephronophthisis (NPHP) is associated with interstitial fibrosis and tubular atrophy, salt wasting, and low- to normal blood pressure. For both diseases, an expanding number of non-overlapping genes with roles in glomerular filtration or primary cilium homeostasis, respectively, have been identified. TTC21B, encoding IFT139, however has been associated with disorders of both the glomerular and tubulointerstitial compartment, and linked with defective podocyte cytoskeleton and ciliary transport, respectively. Starting from a case report of extreme early-onset hypertension, proteinuria, and progressive kidney disease, as well as data from the Genomics England 100,000 Genomes Project, we illustrate here the difficulties in assigning this mixed phenotype to the correct genetic diagnosis. Careful literature review supports the notion that biallelic, often hypomorph, missense variants in TTC21B are commonly associated with early-onset hypertension and histological features of both FSGS and NPHP. Increased clinical recognition of this mixed glomerular and tubulointerstitial disease with often mild or absent features of a typical ciliopathy as well as inclusion of TTC21B on gene panels for early-onset arterial hypertension might shorten the diagnostic odyssey for patients affected by this rare tubuloglomerular kidney disease.

Keywords: TTC21B; early-onset arterial hypertension; focal segmental glomerulosclerosis; molecular diagnosis; nephronophthisis.

FIGURE 1

Biallelic pathogenic TTC21B variants in sibs with early‐onset severe arterial hypertension. (a) Pedigree of investigated family. Individuals with elevated arterial blood pressure and reduced kidney function are marked in black. Circles and squares denote females and males, respectively. (b) Histological analysis of nephrectomy specimen (for II.1) stained with hematoxylin and eosin (HE) and kidney biopsy specimen (for II.2) stained with Martius Scarlet Blue (MSB). For individual II.1, widespread global glomerulosclerosis with diffuse interstitial chronic inflammation and widespread tubular atrophy are noted. In addition, marked medial hypertrophy within interlobular arteries, reflecting systemic hypertension, is observed. For individual II.2, glomerulosclerosis with widespread periglomerular fibrosis and moderate chronic non‐specific tubulo‐interstitial damage are identified. Interlobular arteries show medial hypertrophy consistent with hypertension. (c) Sanger chromatograms confirming TTC21B variants in II.1. (d) Phylogenetic conservation of Pro209. Display generated using Clustal Omega Multiple Sequence Alignment (Sievers et al., 2011). (e) The predicted three‐dimensional structural model of human IFT139, encoded by TTC21B generated using AlphaFold Protein Structure Database (https://alphafold.ebi.ac.uk) and UniProtKB (https://www.uniprot.org/uniprot/) with associated code: Q7Z4L5. Alphafold sequence AF‐Q7Z4L5‐F1 was imported to PyMOL and labeled according to available UniProtKB data due to lack of crystal structure. PyMOL Mutation Wizard was used to model the most likely structural impact of p.(Pro209Leu). The protein's 19 tetratricopeptide (TPR) domains are color coded (red representing the first TPR domain to light pink representing the 19th). Missense SNV p.(Pro209Leu) is highlighted in pink with the most probable (72.4% likelihood) rotamer demonstrated. This change is occurring at a side loop within the distal end of TPR domain 3, one of the probable interaction scaffolds of this protein. The dashed black line demonstrates likely loss of the canonical geometry between 2 atoms in this loop with overlap of 3.3 Å. The red disk represents significant pairwise overlap of atomic van der Waals radii causing a likely structural “clash.” (f) Immunofluorescence staining for ciliary marker ARL13B (green) in patient II.1 nephrectomy sample and control human kidney cortex. The inset highlights a ball‐shaped cilia more frequently observed in patient tissue. Ciliary length is assessed based on ARL13B signal (ImageJ; Schneider, Rasband, & Eliceiri, 2012) using 131 (patient) and 148 (control) cilia on four and three different visual fields, respectively. n.s., not statistically significant (two‐tailed unpaired t‐test). The percentage of ball‐shaped cilia is assessed based on ARL13B signal and scoring 113 patient and 55 control cilia on eight and 10 different visual fields, respectively, from two independent experiments. p‐value calculated using Fisher's exact test. (g) Representative immunofluorescence staining for ciliary marker ARL13B (green) and IFT‐B component IFT88 (red) in patient II.1 nephrectomy sample and control human kidney cortex. Zoom‐ins on individual cilia. The percentage of cilia with tip IFT88 accumulation is assessed based on genotype‐blinded scoring of 113 patient and 55 control cilia on eight and 10 different visual fields, respectively, from two independent experiments. p‐value calculated using Fisher's exact test

FIGURE 2

Genomics England 100,000 Genomes Project analysis for TTC21B and early‐onset hypertension. (a) Pedigree of additional family identified in the 100,000 Genomes dataset with proband II.1 carrying compound heterozygous TTC21B variants in trans. The affected individual is marked in black with phenotype description below. Information on identified TTC21B variants is provided in table. TTC21B transcript: NM_024753.5; gnomAD data (Karczewski et al., 2020) presented as allele count, total allele numbers, number of homozygotes; *In silico analysis for splicing effect: SpliceAI delta score for splice donor loss: 0.55—MaxEntScan alt: 6.1, ref: 11.0, diff: 4.9. (b) Analysis of genetic diagnoses for 100,000 Genomes Project rare disease patients recruited under “Extreme early‐onset hypertension”. Out of 188 probands, only seven probands are definitively, potentially or partially solved (including our index family with biallelic TTC21B variants). In four probands, variants in genes that explain their arterial HTN have been detected (red or black). In three other probands, variants have been reported that may explain part of their more complex phenotype but that are not known to be associated with systemic HTN (gray). Only variants in primary kidney disease genes (TTC21B, COL4A5, PKD2, and WNK4) have been detected as a cause for arterial HTN

FIGURE 3

High evidence etiologies for monogenic arterial hypertension included in the Genomics England PanelApp extreme early‐onset hypertension virtual panel (Version 1.14). Genetic etiologies are classified according to their main function and site of action relating to blood pressure regulation. TTC21B is not currently included in the extreme early‐onset hypertension virtual panel (Version 1.14) (https://panelapp.genomicsengland.co.uk/panels/314/) and would be the first representative of a new class of HTN‐associated genes with roles in the primary cilium and cytoskeleton. Figure generated using Servier Medical Art (https://smart.servier.com/)