Phenotypes of Diamond Blackfan Anemia Patients with RPL35A Haploinsufficiency Due to 3q29 Deletion Compared with RPL35A Single Nucleotide Variants or Small Insertion/Deletions

Background: RPL35A, a gene encoding a large ribosomal subunit protein located at the telomeric end of chromosome 3q (3q29-qter) is essential for rRNA processing, ribosomal biogenesis, cell proliferation, and apoptosis, and accounts for a subset of patients with Diamond Blackfan anemia (DBA). Reported pathogenic RPL35A mutations include single-nucleotide variants (SNVs), small insertion/deletions (indels), and large contiguous gene deletions associated with 3q29 microdeletion syndrome. 3q29 deletion syndrome is an overlapping syndrome that consists of developmental and intellectual disability with or without dysmorphic features, and other congenital anomalies but no anemia or cytopenia. The clinical phenotype and disease severity of patients with RPL35A-related DBA may be influenced by other genes deleted within 3q29 and be different in patients with large deletions compared to those with SNVs or small indels.

Objectives: To determine whether DBA patients with large deletions of the 3q29 region have a more severe disease phenotype than those with SNVs or small indels in RPL35A, and whether other genes deleted within the 3q29 region might contribute to some of the features.

Methods and Results: We identified 40 patients in a multi-institutional, international collaborative study of patients with DBA with RPL35A haploinsufficiency: 21 had deletion of RPL35A as part of 3q29 contiguous gene deletion, ranging in size from 0.012 Mb to 11 Mb in 16 patients; the extent of the deletion beyond RPL35A in either direction was unknown in 5 patients. Nineteen patients had SNVs or small indels (7 missense, 1 nonsense, 3 splice site, 6 indels and 2 unclear pathogenicity).

Thirty-nine of 40 patients had severe anemia, 32 had neutropenia at some time and 3 had thrombocytopenia. Compared to the patients with SNVs or small indels, a significantly higher proportion of patients with RPL35A haploinsufficiency due to 3q29 deletion had steroid-resistant anemia (17 vs 7; p=0.009), severe chronic or intermittent neutropenia requiring treatment with G-CSF (7 vs 0; p=0.009), and humoral and/or cellular immunodeficiency (7 vs 1; p=0.046) diagnosed in some patients due to recurrent infections requiring hospitalizations (10 vs 2; p=0.03). Learning difficulties (12 vs 2; p=0.003), craniofacial abnormalities (11 vs 3; p=0.02), skeletal and limb defects (9 vs 2; p=0.03) or multiple physical anomalies (≥3) were also more frequent in patients with large deletions than in those with SNVs or indels (11 vs 3; p=0.02). Microcephaly (28%), short stature (33%), cardiac defects (28%) and/or urogenital abnormalities (23%) were equally distributed.

The potential genes of interest near RPL35A that may be associated with immune dysregulation and/or neutropenia are RNF168, TFRC, PAK2, PIGZ, DLG1 and LMLN. One or more of these genes were deleted in at least 6 of 7 patients with neutropenia or immunodeficiency. Eight of 9 patients with malformations involving extremities, skeleton and ribs had deletions of TCTEX1D2 which is associated with rib/thoracic dysplasia and polydactyly. The genes of interest deleted in patients with developmental delay and learning disabilities included PAK2 and DLG1 in 9 patients, as well as RNF168, PPP1R2, TNK2 and q29 KIAA0226 in 8 of 12 patients in whom the extent of the deletion was known.

Summary and Conclusion: Patients with DBA due to RPL35A contiguous gene deletions are clearly different from those with SNVs or small indels and have increased frequency of steroid-resistant transfusion-dependent anemia, severe neutropenia, immunodeficiency, learning/developmental delay, and craniofacial/skeletal/limb anomalies. Distinction of this subtype of DBA with RPL35A haploinsufficiency due to 3q29 contiguous gene deletion is relevant to their management, and evaluations should include a work-up for immunodeficiency.

Further studies are needed to determine whether the complex phenotypes and severe disease manifestations in these patients are solely due to RPL35A haploinsufficiency or to the potential effect of other genes deleted in the 3q29 region. Genotype-phenotype characterization and comparison of DBA patients with 3q29 deletion with those due to deletions in other ribosomal protein genes may determine similarities or differences in disease phenotypes related to large gene deletions versus the influence of multigenic contiguous deletions.

Supported by: AZV 16-32105A