Ribosomal proteins and human diseases: molecular mechanisms and targeted therapy

Abstract

Ribosome biogenesis and protein synthesis are fundamental rate-limiting steps for cell growth and proliferation. The ribosomal proteins (RPs), comprising the structural parts of the ribosome, are essential for ribosome assembly and function. In addition to their canonical ribosomal functions, multiple RPs have extra-ribosomal functions including activation of p53-dependent or p53-independent pathways in response to stress, resulting in cell cycle arrest and apoptosis. Defects in ribosome biogenesis, translation, and the functions of individual RPs, including mutations in RPs have been linked to a diverse range of human congenital disorders termed ribosomopathies. Ribosomopathies are characterized by tissue-specific phenotypic abnormalities and higher cancer risk later in life. Recent discoveries of somatic mutations in RPs in multiple tumor types reinforce the connections between ribosomal defects and cancer. In this article, we review the most recent advances in understanding the molecular consequences of RP mutations and ribosomal defects in ribosomopathies and cancer. We particularly discuss the molecular basis of the transition from hypo- to hyper-proliferation in ribosomopathies with elevated cancer risk, a paradox termed "Dameshek's riddle." Furthermore, we review the current treatments for ribosomopathies and prospective therapies targeting ribosomal defects. We also highlight recent advances in ribosome stress-based cancer therapeutics. Importantly, insights into the mechanisms of resistance to therapies targeting ribosome biogenesis bring new perspectives into the molecular basis of cancer susceptibility in ribosomopathies and new clinical implications for cancer therapy.

Fig. 1

A schematic representation of ribosome biogenesis in mammalian cells. a Ribosome biogenesis is a tightly coordinated process involving all three RNA polymerases (Pol I, Pol II, and Pol III). RNA Pol I transcribes the ribosomal RNA (rRNA) genes (rDNA) to produce the 47S precursor rRNA (47S pre-rRNA) transcript in the nucleolus. Pol I transcription initiation involves binding of the upstream binding factor (UBF) to the core promoter region (core) and upstream control element (UCE) of the rDNA promoters and facilitating the recruitment and binding of the selectivity factor 1 (SL-1) complex. SL-1 is composed of the TATA-box-binding protein (TBP) and five Pol I-specific TATA-box-associated factors (TAFs). This complex in turn recruits the Pol I-specific initiation factor RRN3, which associates with DNA topoisomerase IIα (TOPIIα) and Pol I to complete assembly of a transcriptionally-competent Pol I complex. Following transcription, the 47S pre-rRNA is subsequently cleaved and processed into the mature 18S, 5.8S, and 28S rRNA species. These molecules are then assembled along with ribosomal proteins and the 5S rRNA produced by Pol II and III, respectively, to form the major catalytic and architectural components of the small (40S) and the large (60S) ribosomal subunits. Once assembled, ribosomal complexes are exported from the nucleolus to the cytoplasm, where they form the mature (80S) ribosome required to initiate mRNA translation and thus protein synthesis. b A diverse range of anticancer drugs target ribosome biogenesis by inhibiting Pol I transcription and/or pre-rRNA processing

Fig. 2

p53-mediated nucleolar stress response. Cell growth and proliferation remain under constant nucleolar surveillance. Under normal growth conditions, levels of the tumor suppressor p53 are suppressed by the binding of the E3 ubiquitin ligase mouse double minute 2 (Mdm2) and its homolog Mdm4, leading to ubiquitination and degradation of p53. When ribosome biogenesis is disrupted at the level of rRNA synthesis, processing or ribosome assembly, free ribosomal proteins (RPs) (primarily RPL5 and RPL11 and RPL23) and the 5S rRNA are released from the nucleolus to the nucleoplasm where they bind and sequester Mdm2/Mdm4. This in turn prevents the poly-ubiquitination and proteasome-mediated degradation of p53, thereby mediating its stabilization. The RPs (indicated) have been shown to regulate the Mdm2/p53 axis through various mechanisms including binding Mdm2 and its homolog and binding partner Mdm4. Additional mechanisms of nucleolar stress response include ribosome stress-mediated increase in RPL11 mRNA translation, which leads to enhanced interaction between RPL11 and Mdm2 and subsequent accumulation of p53. Following nucleolar stress, p53 can also be activated by RPL26 binding to p53 mRNA and enhancing its translation. Upon activation, p53 transactivates several downstream targets, leading to cell cycle arrest, apoptosis, autophagy or senescence

Fig. 3

Altered mRNA translation in cells with ribosome biogenesis defects. a In normal cells, functional mature ribosomes (80S) comprise the small (40S) subunit and the large (60S) subunit. The small subunit interacts with the anticodon-containing ends of complementary tRNAs so as to translate the codon information contained in mRNA into its corresponding sequence of amino acids. The large subunit contains peptidyl transferase activity and is responsible for linking the amino acids into a polypeptide chain. b In ribosomopathies such as DBA (Diamond–Blackfan anemia), mutations in RPS19 can cause a decrease in the number of functional ribosomes, which may lead to a competition for ribosomes among cellular mRNAs, leading to changes in the translation efficiency of subsets of mRNAs, including reduced translation of GATA1 mRNA. Reduced levels of GATA1, a key erythroid transcription factor impairs erythroid lineage commitment and results in specific defects in erythropoiesis in DBA. c Ribosome defects due to RP mutations and variation in RP composition may generate heterogeneous ribosomes with reduced translation fidelity, resulting in altered translation patterns. In DBA patients, deficiencies in RPL11 or RPS19 due to mutations can reduce the translation of IRES-containing mRNAs BAG1 and CSDE1, which encode erythroblast proliferation and differentiation factors. In X-linked-Dyskeratosis Congenita, defects in rRNA pseudouridylation can impair the binding of ribosomes to IRES elements, resulting in reduced translational fidelity and decreased translation of several IRES-containing mRNAs, including p27, XIAP, and Bcl-xL and enhanced bone marrow failure and cancer susceptibility

Fig. 4

Inhibition of RNA polymerase I transcription by CX-5461 induces both p53-dependent and -independent responses. A schematic representation of CX-5461’s mode of action and its downstream stress response pathways. CX-5461 inhibits the initiation of Pol I-mediated transcription by disrupting the association between SL-1 and Pol I, thus preventing Pol I recruitment to the rDNA promoter. This displacement leads to “exposed” rDNA repeats devoid of Pol I and the presence of defects associated with an open chromatin structure and the recruitment and phosphorylation of RPA to single-stranded rDNA, a marker for replication stress. CX-5461-mediated alterations in rRNA synthesis and rDNA chromatin and topology in turn trigger the downstream activation of two major signaling pathways: (i) a canonical p53-dependent nucleolar stress response leading to accumulation of p53 and/or (ii) a p53-independent DNA damage response (DDR) involving the activation of ATM/ATR kinase signaling. Each pathway induces various cellular responses including G1/S and G2/M cell cycle defects, apoptosis and senescence. Pol I, RNA polymerase I; SL-1, selectivity factor 1; rDNA, ribosomal RNA gene; TBP, TATAbinding protein; UBF, upstream binding factor; UCE, upstream control element; RRN3, RNA polymerase I-specific transcription initiation factor; Mdm2, mouse double minute 2; CHK, checkpoint kinases; CDK, cyclin-dependent kinases; ATM indicates ataxia telangiectasia mutated; ATR, ataxia telangiectasia and Rad3-related

Fig. 5

A model of the transition from cellular hypo-proliferation to hyper-proliferation in ribosomopathies. Defects in ribosome biogenesis and ribosome function induce p53 activation via the nucleolar stress response, but also activate the p53-independent DNA damage response (DDR). Defects in ribosome biogenesis also result in the selective translation of subsets of mRNAs involved in the regulation of cellular metabolism. In turn, deregulation of metabolism leads to oxidative stress that further impairs ribosome biogenesis and ribosome function. These nucleolar and metabolic stresses result in hypo-proliferative responses including cell cycle arrest, senescence or apoptosis that parallel the hypo-proliferative phenotypes associated with ribosomopathies. Chronic deregulation of ribosome biogenesis and cellular metabolism promotes genomic instability and secondary mutations, leading to the outgrowth of clones harboring translationally driven elevated metabolism and pro-survival mechanisms that underpin the transition from hypo-proliferation to hyper-proliferation phenotypes and cancer predisposition in ribosomopathies