Decoding cancer‐associated ribosomal protein mutations: A new frontier in cancer and ribosome biology

For a long time, ribosomes were considered passive molecular machines that produced proteins under the direction of translation factors, but this view has changed relatively recently. ¹ Emerging evidence positions the ribosome as an active player in protein synthesis, capable of shaping translation through changes in ribosome composition, modifications, and interactions with regulatory factors. ¹ , ² This functional diversity enables ribosomes to fine‐tune protein synthesis in response to cellular demands, while altered ribosome heterogeneity has been increasingly linked to human disease. ¹ , ²

Ribosomal proteins (RPs), together with ribosomal RNA, constitute the structural and functional foundation of the ribosome and are essential for ribosome biogenesis (RiBi) and protein synthesis; accordingly, complete loss of most RP genes is incompatible with mammalian cell survival. ² In contrast, heterozygous loss‐of‐function mutations are tolerated but cause ribosomopathies, including Diamond–Blackfan anemia and 5q‐ syndrome, which are characterized by developmental abnormalities and bone marrow failure.2, 3, 4 These disorders are associated with impaired RiBi, which reduces global translational capacity and activates the 5S RNP–MDM2–p53 ribosomal stress response, along with other cellular stress pathways, while also perturbing key regulators of cell growth and proliferation, including MYC. ¹ , ⁵ These stress responses restrain cell proliferation and, when sustained, can promote apoptosis. ¹ , ⁵ Reduced ribosome abundance can also selectively alter the translation of specific mRNAs in a cell type‐ and context‐dependent manner, leading to dysregulation of lineage‐critical factors and transcriptional programs. Erythroid cells may be particularly vulnerable because erythropoiesis requires high levels of coordinated RiBi and protein synthesis. Impaired globin translation can disrupt heme–globin balance and increase oxidative stress, further compromising erythroid proliferation and differentiation. ³

FROM RIBOSOMOPATHIES TO CANCER SUSCEPTIBILITY

Paradoxically, despite reduced translational capacity and activation of robust tumor‐suppressive responses, including p53 upregulation and MYC downregulation, these disorders confer a substantial predisposition to malignancies, particularly myeloid neoplasms and selected solid tumors. ⁶ Consistent with this paradox, recurrent somatic heterozygous loss‐of‐function mutations in RP genes are found across a broad spectrum of acquired human cancers. ¹ , ⁶ In this context, TP53 inactivation is thought to represent a particularly important permissive event, enabling cells harboring heterozygous loss‐of‐function RP mutations to evade the p53‐dependent ribosomal stress checkpoint and acquire malignant potential. ⁶ These observations raise two fundamental mechanistic questions: how can heterozygous RP deletions, despite impairing a process essential for cellular growth and proliferation, contribute to malignant transformation, and how can they cooperate with TP53 loss and/or other genetic lesions to promote tumorigenesis?

Hematopoietic cancers often harbor recurrent missense mutations in RP genes, with RPS15 and RPL10 representing the best characterized examples. ⁷ , ⁸ Unlike loss‐of‐function RP mutations, which impair RiBi, activate the 5S RNP–MDM2–p53 surveillance pathway, and reduce ribosome abundance, cancer‐associated missense mutations in RPS15 and RPL10 largely evade ribosome quality‐control mechanisms and are proposed to generate “pathologically specialized” ribosomes with altered translational properties. ⁶ , ⁹ , ¹⁰ Although RP deletions and RP point mutations have fundamentally different effects on RiBi, and thus likely perturb translation through distinct mechanisms, it remains unclear if they provoke shared and/or divergent downstream responses, and how these responses converge to promote malignant phenotypes. Resolving this broader question, which extends beyond the studies discussed here, represents a central challenge in understanding ribosomopathy‐associated cancer.

REVISITING THE ROLE OF RPS15 MUTATIONS IN CHRONIC LYMPHOCYTIC LEUKEMIA PATHOGENESIS

Mechanistic studies of the RPL10 R98S mutation have established a framework for understanding how RP point mutations can alter ribosome function and contribute to malignant transformation. ⁹ Recent studies extend this framework to RPS15, a recurrently mutated driver gene in chronic lymphocytic leukemia (CLL), and suggest that these mutations generate functionally altered, potentially “specialized” ribosomes that selectively reprogram mRNA translation. ⁷ , ¹¹ , ¹² However, these conclusions were largely derived from ectopic overexpression systems, limited patient cohorts, and/or incomplete mechanistic and in vivo validation, leaving the biological consequences of RPS15 mutations insufficiently established. Recent studies in HemaSphere and Nature Communications have overcome some of these limitations of prior approaches, providing new insights into how RPS15 mutations influence ribosome function, translation programs, and CLL biology in vivo. ¹³ , ¹⁴

IMPAIRED tRNA DECODING BY RPS15 MUTANT RIBOSOMES RESHAPES TRANSLATIONAL OUTPUT

In a recent issue of HemaSphere, Astier et al. introduced RiboCancer, a systematic collection of CRISPR‐engineered RP mutant cell lines. ¹³ By faithfully recapitulating clinically relevant RP mutations in a common genetic background, these models overcome key limitations of ectopic overexpression and RNA interference approaches, providing a robust framework to dissect the functional consequences of distinct classes of RP mutations. The platform includes recurrent CLL‐associated RPS15 missense mutations (P131S and H137Y), the recurrent T‐cell acute lymphoblastic leukemia (T‐ALL)–associated RPL10‐R98S mutation, and loss‐of‐function mutations in RPL5, RPL11, and RPL22, thereby encompassing the major classes of RP alterations observed across human malignancies. Among these models, CLL‐associated RPS15 missense mutations produced the most pronounced changes in translational efficiency and were therefore characterized in greatest detail. ¹³

Previous structural studies established the highly conserved C‐terminal tail of RPS15, which is the region targeted by the mutations observed in CLL, as a key component of the ribosomal decoding center, where it stabilizes aminoacyl‐tRNA accommodation during translation elongation. ¹⁵ Building on this framework, Astier et al. integrated ribosome profiling, cryo‐electron microscopy (cryo‐EM), and functional assays to characterize translational alterations in RiboCancer cell lines harboring the CLL‐associated RPS15 mutations. ¹³ Ribosome profiling revealed codon‐specific ribosome pausing at the A site, particularly at kinetically challenging AAA lysine codons, consistent with impaired decoding efficiency and altered tRNA accommodation ¹³ , ¹⁶ (Figure 1A). These findings indicate that mutant ribosomes retain the capacity for productive translation but exhibit selective decoding defects at specific translational bottlenecks, resulting in context‐dependent elongation impairment rather than a global translational failure.

Figure 1.

Model illustrating how RPS15 mutation–induced translational stress promotes genomic instability and chronic lymphocytic leukemia (CLL) evolution. (A) RPS15 mutations alter ribosomal decoding and protein synthesis. Recurrent CLL‐associated RPS15 mutations (S138F, P131S, and H137Y) cluster within the 40S ribosomal decoding center, compromising translational accuracy and efficiency. Mutant ribosomes exhibit defective decoding of sensitive codons, including the AAA lysine codon, resulting in impaired elongation, ribosome stalling, and premature translation termination. In parallel, altered decoding increases near‐cognate tRNA incorporation at stop codons, promoting stop‐codon readthrough and the production of C‐terminally extended protein isoforms. Mechanistically, the near‐cognate tRNA competes with release factor (RF) for the A site, preventing peptide release and allowing translation to continue beyond the stop codon. (B) RPS15 mutation–induced translational stress promotes genomic instability, the key enabling event in CLL development. RPS15 mutations selectively impair translation of mRNAs involved in transcriptional regulation (including RUNX3), epigenetic control, cell‐cycle regulation, metabolism, antioxidant defense, and DNA repair. Rps15‐mutant cells exhibit increased mitochondrial ROS, potentially resulting from impaired antioxidant capacity and proteotoxic stress associated with altered protein synthesis. Elevated ROS promotes DNA damage, which may be further exacerbated by reduced translation of DNA repair factors. Accordingly, Rps15‐mutant cells display genomic instability, including increased mutation burden, copy‐number alterations, chromosomal rearrangements, and micronuclei formation, creating a permissive environment for clonal evolution and malignant transformation. Persistent translational stress may also engage adaptive proteostasis pathways, including the integrated stress response (ISR), heat‐shock response (HSR), unfolded protein response (UPR), and ribosome‐associated quality control (RQC), although these responses were not directly assessed. (C) Trp53 loss cooperates with Rps15 mutations to drive CLL progression in a mouse model. In Rps15‐mutant B cells, DNA damage and additional cellular stress signals are proposed to activate p53‐dependent checkpoint pathways, limiting proliferation and establishing a hypoproliferative but genomically unstable pre‐leukemic state. This state may favor selection of cells harboring cooperating alterations, including Trp53 loss‐of‐function mutations, although the emergence kinetics of Trp53 alterations during CLL evolution was not assessed. Loss of p53 checkpoint control in compound Rps15/Trp53‐mutant B cells enables clonal expansion, enhancing ROS accumulation, MYC activation, genomic instability, and progression to aggressive CLL and Richter syndrome–like lymphoma. These findings establish functional cooperation between Rps15 mutation and p53 pathway disruption, while leaving open the possibility that additional genetic or epigenetic alterations may similarly overcome the pre‐leukemic barrier and promote malignant progression.

Confirmed by cryo‐EM, RPS15 mutations increase ribosome conformational flexibility, destabilizing pre‐translocation (PRE) states and shifting populations toward post‐translocation (POST) states with an unoccupied A site. ¹³ Consistently, RPS15‐mutant cells exhibited increased sensitivity to anisomycin, an inhibitor that preferentially binds the peptidyl transferase center when the A site is unoccupied. Reporter assays validated that the AAA lysine codon context confers selective susceptibility to impaired translation by RPS15‐mutant ribosomes. Together, these findings support a model in which mutant ribosomes reshape the translatome based on transcript‐specific codon composition and decoding requirements.

Transcripts with reduced translational efficiency displayed a distinct 11‐codon signature and predominantly encode proteins involved in transcriptional regulation, epigenetic control, chromatin organization, histone biology, DNA repair, and cell‐cycle progression, pathways with potential relevance to malignant transformation (Figure 1B). ¹³ These findings, together with the strong overlap between gene sets enriched for the 11‐codon signature in human and mouse genomes and those translationally repressed in RPS15‐mutant cells, support codon composition as an important determinant of translational vulnerability to mutant ribosomes. However, the underlying mechanism is not fully explained by A‐site pausing. Although certain codons within the signature, such as the AAA lysine codon, exhibit increased A‐site pausing, others do not, indicating that differential codon‐specific pausing may contribute to, but does not fully account for, the translational effects of RPS15 mutant ribosomes. ¹³ . In this context, although both lysine codons (AAA and AAG) were enriched in translationally downregulated transcripts, the translational behavior of RP mRNAs in RPS15‐mutant cells was not specifically reported, despite their high lysine codon content. ¹³ , ¹⁷ Determining whether RP transcripts are also subject to translational repression in RPS15‐mutant cells could help clarify how codon composition, together with other transcript‐specific features such as GC content and ORF length, influences vulnerability to RPS15‐mutant ribosomes. ¹³ , ¹⁷ Defining these determinants will be essential for understanding how altered ribosome function rewires gene expression during tumor evolution. Indeed, the observed reduced expression of RUNX3, a key regulator of hematopoietic differentiation and tumor suppression and thus a good candidate to explain the pathology of patients possessing RPS15 mutations, seemingly occurs independently of increased A‐site occupancy at enriched CGC and AGC codons. ¹⁸

RPS15 MUTATION IS SUFFICIENT TO DRIVE CLL DEVELOPMENT IN A MOUSE MODEL

The findings of Astier et al. established mutant ribosomes as active regulators of gene expression and suggested that translational rewiring may contribute to cancer development. ¹³ Whether these defects directly drive CLL, however, remained unknown.

Missense mutations in RPS15 that cluster within the C‐terminal region occur in approximately 4%–5% of treatment‐naive CLL cases and are markedly enriched in relapsed disease, with frequencies approaching 20%. ⁷ Their consistent association with adverse clinical features and poor survival has implicated altered ribosome biology in CLL pathogenesis. Moreover, the frequent co‐occurrence of RPS15 mutations with TP53 lesions defines a particularly high‐risk subgroup with aggressive disease and grim clinical outcomes. ⁷ However, clinical associations alone cannot establish whether RPS15 mutations are bona fide drivers of leukemogenesis. These observations raise three fundamental questions: Can the translation defects of mutant ribosomes directly initiate malignant transformation? Do they promote genomic instability, enabling the selection of TP53 lesions? And finally, how does cooperation with p53 loss shape the evolution toward aggressive disease?

In a recent issue of Nature Communications, Gutierrez et al. provided compelling answers by integrating mechanistic analyses of translational dysfunction with in vivo genetic evidence of leukemogenesis. ¹⁴ They expanded the spectrum of translational defects beyond altered translational efficiency identified by Astier et al., ¹³ , ¹⁴ showing that mutant Rps15 ribosomes exhibit ribosome stalling at termination codons and increased stop‐codon readthrough, suggesting a defect in translation termination fidelity ¹⁴ (Figure 1A). Moreover, altered decoding‐center dynamics described in both studies may influence additional aspects of translation, including translational fidelity and programmed ribosomal frameshifting, underscoring the broad capacity of RPS15 mutant ribosomes to reprogram gene expression. ¹² , ¹⁴

Importantly, these translational abnormalities are sufficient to drive malignant transformation in vivo. Using a conditional Cd19‐Cre Rps15‐S138F knock‐in mouse model, the authors demonstrate that an endogenous Rps15 mutation initiates spontaneous CLL‐like disease and, in cooperation with Trp53 loss, promotes progression to aggressive CLL and Richter‐like lymphoma. ¹⁴ By showing that mutant Rps15‐containing ribosomes actively drive, rather than merely accompany, malignant evolution, this study establishes a causal link between altered ribosome function and leukemogenesis. This insight provides a mechanistic framework for resolving a longstanding paradox in ribosome biology: how ribosome dysfunction can initially produce hypoproliferative phenotypes yet ultimately promote hyperproliferative malignancies. Rps15‐mutant B cells appear to undergo this transition over time, linking early ribosomal stress to subsequent leukemic transformation. Early in life, mutant B cells exhibit impaired proliferation associated with oxidative stress, DNA damage, and activation of p53‐dependent checkpoint responses. However, with aging, a subset of these cells escapes these constraints and acquires malignant features, including activation of proliferative programs such as MYC and enhanced survival (Figure 1B,C). Thus, hypoproliferation and malignant transformation may represent sequential stages of a single evolutionary trajectory, in which chronic translational stress generates the genomic diversity and selective pressures required for leukemic progression. ¹⁴

OXIDATIVE STRESS AND GENOME INSTABILITY AS DRIVERS OF Rps15‐MUTANT LEUKEMIC EVOLUTION

The transition from a preleukemic state to overt CLL appears to be driven, at least in part, by oxidative stress and genome instability. Pre‐leukemic Rps15‐mutant B cells accumulate mitochondrial reactive oxygen species (ROS) and display impaired genome maintenance, increased DNA damage, micronuclei formation, chromosomal alterations, and a mutational signature consistent with oxidative DNA injury ¹⁴ (Figure 1B). This genomic stress would activate DNA damage response pathways that stabilize p53 and enforce the initial hypoproliferative state (Figure 1C). Consistent with this model, antioxidant treatment partially restores proliferation of Rps15‐mutant cells. Although Rps15 mutations may perturb RiBi and engage the 5S RNP–MDM2–p53 axis, current data do not support this pathway as a major mechanism underlying p53 activation in this in vivo mouse model. Over time, the accumulation of genomic alterations could provide the conditions required for clonal selection and acquisition of malignant traits, enabling progression from stress‐induced growth restraint to leukemic transformation. The genomic instability observed in this model provides a potential mechanistic explanation for the increased mutational burden observed in patients with RP‐mutant CLL compared with patients with RP‐wild‐type CLL. ¹⁹

TRANSLATIONAL DYSREGULATION AS A SOURCE OF PROTEOTOXIC AND MITOCHONDRIAL STRESS

One potential explanation for increased mitochondrial ROS generation is that translational dysregulation disrupts proteome homeostasis, resulting in chronic proteotoxic stress and impaired mitochondrial function. ²⁰ , ²¹ Notably, both Astier et al. and Gutierrez et al. identified reduced translation of GPX1 mRNA, raising the possibility of a feed‐forward circuit in which translational dysregulation simultaneously promotes ROS production while weakening antioxidant defenses. ¹³ , ¹⁴ Although these mechanisms require further validation, they provide a framework linking ribosome dysfunction to oxidative stress, genome instability, and leukemogenesis (Figure 1B).

P53 LOSS CONVERTS RIBOSOMAL STRESS INTO A SELECTIVE ADVANTAGE FOR MALIGNANT EVOLUTION

A key insight from this study is that, like many oncogenic stresses, ribosome dysfunction is governed by dosage. ¹⁴ Homozygous Rps15 mutations induce excessive (oxidative) stress that restrains tumorigenesis, whereas heterozygous mutations generate a permissive level of stress that fuels clonal evolution. Loss of p53 raises this threshold, allowing highly stressed, genomically unstable cells to survive and accelerate malignant transformation. This model explains why RPS15 mutations in human CLL are exclusively heterozygous. ⁷ Consistent with this, Gutierrez et al. generated compound Rps15‐mutant/Trp53‐deficient mice and observed that loss of Trp53 restored the proliferative capacity of severely stressed Rps15‐mutant cells without correcting the underlying translational defects; rather, it exacerbated oxidative stress and genomic instability. ¹⁴ Thus, p53 deficiency enabled cells to tolerate persistent ribosomal dysfunction and its downstream consequences, facilitating continued accumulation of genomic instability and transforming a stress‐induced barrier into a substrate for clonal evolution (Figure 1C). This model raises important questions regarding the temporal relationship between Rps15 mutation and p53 pathway disruption. In compound mice, Trp53 is deleted from the outset in all B cells, whereas in patients TP53 abnormalities typically arise during the evolution of an Rps15‐mutant clone. Thus, this model establishes the consequences of p53 loss in the context of ribosomal stress but does not determine when or how p53 pathway disruption occurs during disease progression. Longitudinal genomic analyses of evolving Rps15‐mutant clones in this mouse model will be required to address this critical gap. Compound Rps15‐mutant/Trp53‐deficient B cells showed hyperactivation of proliferative pathways, including MYC signaling, and underwent Richter‐like transformation into aggressive lymphoma in a subset of mice (Figure 1C). ⁷ , ¹⁴ , ²² Importantly, Trp53 deficiency alone can initiate CLL but is insufficient to drive Richter‐like transformation, highlighting that disruption of p53‐mediated surveillance requires cooperation with Rps15 mutation to promote advanced malignant evolution. ¹⁴ Whether other lesions affecting genome maintenance, DNA damage responses, or apoptotic checkpoints can similarly cooperate with ribosome dysfunction to drive aggressive disease remains an important question. Notably, approximately two‐thirds of RPS15‐mutant CLL cases retain wild‐type TP53, raising the possibility that alternative genetic lesions may cooperate with ribosome dysfunction to promote disease progression. ⁷ , ¹⁴ , ¹⁹

THERAPEUTIC OPPORTUNITIES ARISING FROM RPS15‐MUTANT RIBOSOME DYSFUNCTION IN CLL

Regarding therapeutic implications, the report of Gutierrez et al. reveals a network of cellular stresses and adaptive dependencies that emerge as Rps15‐mutant cells accommodate chronic translational challenges. ¹⁴ , ²⁰ , ²³ While some of these mechanisms are experimentally demonstrated, others are inferred from established knowledge of cellular stress adaptation. By adapting to persistent ribosome dysfunction, these cells may become increasingly dependent on pathways that preserve cellular homeostasis, including redox regulation, proteostasis, stress adaptation, and DNA damage tolerance (Figure 1B). Such dependencies could render RPS15‐mutant leukemia particularly vulnerable to therapeutic strategies that overwhelm these adaptive mechanisms, including approaches that exacerbate oxidative or replicative stress, inhibit compensatory DNA damage responses such as CHK1, particularly in the context of p53 deficiency, or disrupt proteostasis through chaperone, proteasome, or integrated stress response inhibition. ¹⁴ Beyond stress adaptation, the altered translational properties of mutant ribosomes may create additional therapeutic liabilities. For example, if reduced translation lowers the abundance of essential proteins to limiting levels, RPS15‐mutant CLL cells may become selectively vulnerable to inhibitors targeting these proteins. Compensatory activation of translational regulators that sustain protein synthesis despite impaired ribosome function may represent actionable dependencies, while altered decoding‐center dynamics could influence translation fidelity, programmed frameshifting, and termination, potentially generating aberrant peptides (neoantigens) that shape immune recognition and response to immunotherapy. ¹³ , ¹⁴ Importantly, the combination of RPS15 mutation with cooperating lesions such as TP53 loss may create dependencies not present in either alteration alone, providing opportunities to identify vulnerabilities specific to high‐risk CLL (Figure 1C). Defining these liabilities in relevant in vivo models, such as Rps15‐mutant mouse models, and validating them in patients with CLL will be essential for translating mutant ribosome biology into therapeutic opportunities.

OUTSTANDING QUESTIONS

Current evidence indicates that RP point mutations and deletions have distinct yet convergent consequences. Compared with RP deletions, RP point mutations have a greater impact on translational efficiency and may also compromise the fidelity of protein synthesis, as demonstrated by ribosome profiling. ¹³ This difference may reflect the incorporation of mutant RP proteins into ribosomes, which can alter ribosome function beyond the effects of reduced RP dosage and confer distinct translational properties. ¹³ In contrast, oxidative stress and the subsequent acquisition of secondary mutations emerge as a shared mechanism of transformation across RPL10 and RPS15 point mutations and may also occur in the context of RP loss‐of‐function lesions. ³ , ¹⁴ , ¹⁹ This mechanism has been proposed more broadly as a potential driver of malignant evolution in ribosomopathies. ¹⁹ An important outstanding question is how these distinct molecular consequences of RP lesions interact and converge to promote malignant evolution. ¹³ , ¹⁴ By employing genetically engineered models, Gutierrez et al. and Astier et al. established that ribosomes bearing an RPS15 point mutation actively reprogram protein synthesis and can drive CLL development in vivo. ¹³ , ¹⁴ These studies provide important mechanistic insights into this question while also highlighting several unresolved issues. How do specific translational defects trigger proteotoxic stress, and how are these effects integrated with pathways governing proteostasis, metabolism, stress adaptation, and genome stability? Which translational alterations are required for transformation and disease progression? Furthermore, the mechanisms underlying cooperation between RPS15 mutations and TP53 loss remain poorly understood. Does p53 deficiency directly reshape protein synthesis and amplify translational dysregulation in RPS15‐mutant cells, or does this cooperation instead arise from broader alterations in stress responses, metabolic adaptation, genome maintenance, and cellular fitness? Defining these mechanisms will provide critical insights into the biology of this high‐risk genetic combination. Collectively, these studies establish mutant RP‐containing ribosomes as important contributors to cancer evolution and open new avenues for understanding how altered translational control and its downstream effects shape malignancy and may be exploited as therapeutic vulnerabilities. ¹³ , ¹⁴ They also provide a conceptual framework for defining disease‐associated specialized ribosomes as functionally distinct entities that reshape mRNA translation and cellular outcomes, establishing a paradigm in which rigorous mechanistic studies and in vivo validation are required to demonstrate true ribosome specialization. ²

AUTHOR CONTRIBUTIONS

Mirsada Čaušević: Writing—review and editing. Robbie Loewith: Writing—review and editing. Siniša Volarević: Conceptualization; supervision; writing—original draft preparation.

CONFLICT OF INTEREST STATEMENT

The authors declare no conflicts of interest.

FUNDING

S.V. is supported by the Croatian Science Foundation (Grant No. IP‐2022‐10‐9967) and the University of Rijeka (Grants No. uniri‐biomed‐23‐73‐3018 and RP‐24‐23).

DATA AVAILABILITY STATEMENT

Data sharing not applicable to this article as no datasets were generated or analyzed during the current study.