Novel variants in the stem cell niche factor WNT2B define the disease phenotype as a congenital enteropathy with ocular dysgenesis

Abstract

WNT2B is a member of the Wnt family, a group of signal transduction proteins involved in embryologic development and stem cell renewal and maintenance. We recently reported homozygous nonsense variants in WNT2B in three individuals with severe, neonatal-onset diarrhea, and intestinal failure. Here we present a fourth case, from a separate family, with neonatal diarrhea associated with novel compound heterozygous WNT2B variants. One of the two variants was a frameshift variant (c.423del [p.Phe141fs]), while the other was a missense change (c.722 G > A [p.G241D]) that we predict through homology modeling to be deleterious, disrupting post-translational acylation. This patient presented as a neonate with severe diet-induced (osmotic) diarrhea and growth failure resulting in dependence on parenteral nutrition. Her gastrointestinal histology revealed abnormal cellular architecture particularly in the stomach and colon, including oxyntic atrophy, abnormal distribution of enteroendocrine cells, and a paucity of colonic crypt glands. In addition to her gastrointestinal findings, she had bilateral corneal clouding and atypical genital development later identified as a testicular 46,XX difference/disorder of sexual development. Upon review of the previously reported cases, two others also had anterior segment ocular anomalies though none had atypical genital development. This growing case series suggests that variants in WNT2B are associated with an oculo-intestinal (and possibly gonadal) syndrome, due to the protein's putative involvement in multiple developmental and stem cell maintenance pathways.

Fig. 1. Pedigree, growth charts, and intestinal histology.

A Pedigrees for I-4 (left) and I-2 and I-3 (right). B Growth charts showing weight (top) and height (bottom) for patient I-4. C H&E-stained tissue sections obtained from endoscopic biopsies from the body of the stomach, proximal duodenum, and right colon for patient I-4. The stomach shows full-thickness lamina propria chronic inflammation and partial oxyntic atrophy. The duodenum shows equivocally increased lamina propria chronic inflammation, and the colon shows conspicuous crypt dropout with increased lamina propria lymphoplasmacytic inflammation.

Fig. 2. Ophthalmologic and gonadal features.

A Top panel: Photo of the patient’s eyes as she is gazing at the viewer. Note the large esotropia of the right eye. Bottom left panel: Corneal clouding of the right eye that covers the visual axis and extends to the limbus. Bottom right panel: Corneal clouding of the left eye extends partially into the visual axis. B Ambiguous external genitalia in patient I-4. C Cystoscopy (left) and fluoroscopic genitogram (right) showing absent cervical os (asterisks). D H&E-stained gonadal tissue section showing testicular parenchyma containing primitive seminiferous tubules. No ovarian tissue is identified.

Fig. 3. Wnt2b tissue expression and missense variant structural analysis.

A In situ hybridization of Wnt2b mRNA (RNAscope) showing Wnt2B expression (red dots) in control (left panel), patient I-3 (middle panel) and patient I-4 (right panel) in colon biopsies. RNA expression is abolished in I-3 but intermediate in I-4. B Alignment of Wnt homologs. xWnt8: Xenopus Wnt8; mWnt3: Murine Wnt3; hWnt3: Human Wnt3; hWnt2B: Human Wnt2B. Patient I-4 G241D variant is highlighted in red. Residues of mWnt3 known to be essential for acylation are noted with red dots, nonessential for acylation are noted with green squares. Red Xs denote mWnt3 residues required for interaction with Porcupine, the mWnt3 acyltransferase. G241, the mutated residue in patient I-4, is predicted to negatively affect palmitoylation. C Homology modeling of hWnt2B based on hWnt3 structure. Left panel: hWnt2B model (red) aligned with hWnt3 structure (black) with palmitoyl group (PAM, orange) noted. Middle panel: same alignment zoomed in on palmitoylated loop. Right panel: hWnt2B model (blue sticks) with PAM moiety (orange) interaction with Frizzled (Fz, blue-gray). G241, the mutated residue in patient I-4, sits above the binding pocket and is not predicted to affect binding. D Table of variants of the four individuals in our case series and predicted synthetic defect.

Fig. 4. Wnt2b syndrome features and nutritional outcomes.

A Shared clinical features of patients with WNT2B variants. B Stomach (antrum) tissue sections stained for chromogranin (brown) showing linear (red arrow) and micronodular (black arrow) enterochromaffin-like cell hyperplasia in patients I-2, I-3, and I-4. C Parenteral nutrition requirements for adequate growth in patients I-2, I-3, and I-4. Age, weight, height and school level at last evaluation: I-2—6 years-old, 16 kg (z-score −2.92) 107 cm (z-score −2.55), elementary; I-3—3 years-old, 12.7 kg (z-score −1.10), 87 cm (z-score −2.26), pre-school; I-4—18 months-old, 9.32 kg (z-score −1.06), 82.5 cm (z-score 0.00), pre-school.