Ribosomal protein gene RPL9 variants can differentially impair ribosome function and cellular metabolism.

Marco Lezzerini,Anne-Marie Hesse,Yohann Couté,Alexandra Nin-Velez,Marianna Penzo,Thierry Leblanc,Marie-Françoise O’Donohue,Manon Saby,Guangjun Zhang,Lorenzo Montanaro,Marc Gastou,Riekelt H Houtkooper ,Lydie Da Costa ,Pierre‐Emmanuel Gleizes ,Carolina Marques Dos Santos Vieira ,Alexandra N Olson ,Jutte Van Der Werff Ten Bosch ,Marjolijn C.j Jongmans ,Illja J Diets ,Hyung L Elfrink ,Floris Groenendaal ,Marc Bierings ,Michel Van Weeghel ,Jonathan D Dinman ,Evelien Zonneveld‐Huijssoon ,Roland P Kuiper ,Marcin W Wlodarski ,Alyson W Macinnes

doi:10.1093/nar/gkz1042

Abstract

Variants in ribosomal protein (RP) genes drive Diamond-Blackfan anemia (DBA), a bone marrow failure syndrome that can also predispose individuals to cancer. Inherited and sporadic RP gene variants are also linked to a variety of phenotypes, including malignancy, in individuals with no anemia. Here we report an individual diagnosed with DBA carrying a variant in the 5′UTR of RPL9 (uL6). Additionally, we report two individuals from a family with multiple cancer incidences carrying a RPL9 missense variant. Analysis of cells from these individuals reveals that despite the variants both driving pre-rRNA processing defects and 80S monosome reduction, the downstream effects are remarkably different. Cells carrying the 5′UTR variant stabilize TP53 and impair the growth and differentiation of erythroid cells. In contrast, ribosomes incorporating the missense variant erroneously read through UAG and UGA stop codons of mRNAs. Metabolic profiles of cells carrying the 5′UTR variant reveal an increased metabolism of amino acids and a switch from glycolysis to gluconeogenesis while those of cells carrying the missense variant reveal a depletion of nucleotide pools. These findings indicate that variants in the same RP gene can drive similar ribosome biogenesis defects yet still have markedly different downstream consequences and clinical impacts.

Highlights

Diamond-Blackfan anemia (DBA) (OMIM# 105650) is an inherited bone marrow failure disorder that typically presents in children less than one year of age
RPL9 gene allelic variation has so far been reported in one DBA-affected individual, this c.375G>C; p.Arg125Ser variation was declared to be a variant of unknown significance (VUS) since cells from this patient did not show a pre-rRNA processing defect similar to that observed upon knockdown of RPL9 with siRNAs [9]
Whole exome sequencing (WES) of patient-parent trios identified an individual within the European DBA (EuroDBA) consortium registries with the heterozygous variant c.-2+1G>C (P1) in the 5 UTR of the RPL9 gene (NM 000661.4) (Table 1 and Figure 1)

Summary

Introduction

Diamond-Blackfan anemia (DBA) (OMIM# 105650) is an inherited bone marrow failure disorder that typically presents in children less than one year of age. While the central phenotype is pure red cell aplasia and a paucity of erythroblast precursor cells in the bone marrow, a number of physical malformations are linked to DBA [1]. These include (but are not limited to) craniofacial malformations, growth retardation, abnormalities in the extremities (especially the thumb), heart defects, and urogenital defects [2,3]. RPL9 gene allelic variation has so far been reported in one DBA-affected individual, this c.375G>C; p.Arg125Ser variation was declared to be a variant of unknown significance (VUS) since cells from this patient did not show a pre-rRNA processing defect similar to that observed upon knockdown of RPL9 with siRNAs [9]. A recent study reported germinal TP53 gene activating variants in two individuals with a DBA-like phenotype that includes erythroblastopenia [26]

Methods

Results

Conclusion