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

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.

Cockayne Syndrome-Associated CSA and CSB Mutations Impair Ribosome Biogenesis, Ribosomal Protein Stability, and Global Protein Folding

“…However, the major difference between DBA and CS is the alteration or lack of the ribosomal proteins that might have extraribosomal functions suppressing cancer development [ 31 ]. Moreover, it has been shown that mutations in ribosomal proteins can lead to a reduced translational fidelity in DBA [ 32 ] but also in other developmental syndromes that resemble CS [ 33 ]. Translational fidelity is severely affected in CS, as recently shown in transfection assays by Alupei et al, and it might explain the observed loss of proteostasis with an increase of heat-sensitive proteins and the detection of misfolded proteins in the ribosomes themselves.…”

Ribosomopathies: New Therapeutic Perspectives

“…The disease is associated with growth retardation and, in 30 to 50% of cases, with congenital malformations (craniofacial, upper limb, heart, and urinary system) [ 22 ]. It has been associated with several heterozygous mutations in genes encoding for riboproteins of the 40S (RPS7-10-17-19-24-26) and 60S (RPL3-5-9-10-10A-11-15-18-19-26-34-35-35A and RPLP0) subunits [ 23 , 24 , 25 , 26 , 27 , 28 , 29 , 30 , 31 , 32 , 33 ]. The disease may also be secondary to copy number variations for some of the previously mentioned genes ( RPS17 - 19 - 24 - 26 and RPL5 - 11 - 15 - 35A ) [ 30 , 34 , 35 , 36 ].…”

Nucleolar TFIIE plays a role in ribosomal biogenesis and performance

“…The small ribosomal subunit 40S is the translation initiating and codon-decoding subunit of the ribosome. Disturbed ribosomal composition can lead to decoding-defects of the ribosome (Lezzerini, Penzo et al, 2020, Paolini, Attwood et al, 2017, Venturi & Montanaro, 2020) detectable by luciferase-based translation assays. We took advantage of a well-established luciferase transfection system (Azpurua et al, 2013) and discovered an elevated error-rate of the translation process in TTD patient cells.…”