Clear cell renal cell carcinoma (ccRCC) frequently exhibits transcriptional reprogramming driven by oncogenic C-Myc. Fibrillarin (FBL), a nucleolar C-Myc target, is markedly upregulated in ccRCC, correlating with poor prognosis and essential for tumor cell survival. Integrated single-cell RNA sequencing, bulk transcriptomics, and proteomics were used to identify FBL as a key target. Functional assays, immunoprecipitation-mass spectrometry, and molecular docking were performed to investigate FBL's oncogenic mechanisms and interaction with TRIM21. FBL promotes ccRCC cell proliferation, migration, and tumor growth via PI3K/AKT pathway activation. TRIM21 was identified as a novel FBL-binding E3 ubiquitin ligase that catalyzes K48-linked polyubiquitination of FBL at lysine 292, accelerating its proteasomal degradation. TRIM21 overexpression reduces FBL levels, inhibits PI3K/AKT signaling, and reverses FBL-induced oncogenic phenotypes. TRIM21 is downregulated in ccRCC tissues and associated with unfavorable prognosis. The TRIM21-FBL axis regulates ccRCC progression by modulating PI3K/AKT signaling, providing mechanistic insight and potential therapeutic targets for ribosome biogenesis and oncogenic signaling.

Chemotherapeutic agents targeting ribosome biogenesis induce profound reorganization of nucleolar architecture, yet how the tumor suppressor p53 governs these structural responses remains unclear. Here, we show that loss of p53 leads to NF-κB-dependent disappearance of nucleolar caps induced by doxorubicin (DOXO). Under these conditions, fibrillarin (FBL), which is normally confined to the nucleolus, relocates to the nucleoplasm and forms foci that partially associate with G-quadruplex (G4) structures, non-canonical nucleic acid secondary structures enriched at transcriptionally active genomic regions. To examine whether this redistribution is linked to transcriptional changes, we integrated publicly available transcriptomic datasets and identified genes that were upregulated in p53-deficient cells under DOXO treatment and downregulated upon FBL depletion. Given that casein kinase 2 alpha (CK2α) is a nuclear binding partner of FBL, we further analyzed CK2α-dependent gene programs. This analysis revealed that a fraction of FBL-responsive genes overlapped with CK2α-dependent signatures and were enriched for promoter-proximal G4 structures. Among candidate regulators, the G4-binding transcription factor MAZ emerged as a potential mediator linking nucleoplasmic FBL and CK2α to G4-associated transcriptional regulation. Together, our findings identify a mechanism linking loss of p53 to G4-associated transcriptional reprogramming through nucleolar architectural disruption mediated by an FBL-CK2α-MAZ axis during DOXO treatment.

Abstract Pancreatic ductal adenocarcinoma (PDAC) is a lethal malignancy with a poor prognosis and increasing global incidence. Although the epigenetic regulator plant homeodomain finger protein 1 (PHF1) is known for its transcriptional silencing function in cancer, its role in PDAC progression and translational regulation remains largely unexplored. Here, we report that PHF1 is significantly upregulated in PDAC and promotes the proliferation, migration, and invasion of PDAC cells. Mechanistically, PHF1 physically interacts with the fibrillarin (FBL)/NOP56/NOP58 snoRNP complex, facilitating its assembly and enhancing the internal ribosome entry site (IRES)‐dependent translation of Snail. Depletion of PHF1 reduces Snail levels, leading to ferroptosis sensitization in KRAS‐mutated PDAC cells. Additionally, PHF1 knockdown markedly reduces overall tumor burden in Kras‐mutated mice. In conclusion, our findings identify PHF1 as an oncogene that promotes PDAC progression and demonstrate that its inhibition induces ferroptosis via suppression of IRES‐dependent Snail translation. Thus, our findings reveal a previously unrecognized translational regulatory role of PHF1 and suggest its targeting as a promising therapeutic strategy for PDAC.

Reveal the regulatory role of DDX10 in diffuse large B-cell lymphoma: binding with FBL to promote cell proliferation and invasion.

Fibrillarin (FBL), a core component of the C/D box small nucleolar ribonucleoprotein (snoRNP) complex, catalyzes the 2'-O-methylation (Nm) of the ribose 2'-hydroxyl moiety in ribosomal RNA (rRNA). Distinct Nm patterns contribute to ribosome heterogeneity, which is linked to selective translation of oncogenes. FBL dysregulation generates an aberrant Nm signature in triple-negative breast cancer (TNBC), the most aggressive breast cancer subtype. This study investigated the role of FBL in TNBC via translation-driven mechanisms. Our findings show that FBL knockdown impairs oncogenic traits, triggers metabolic stress, and reduces the translation efficiency of oncogenes, such as metastasis-associated protein 1 (MTA1), interleukin-1 receptor-associated kinase 1 (IRAK1), and thymosin beta 10 (TMSB10). RiboMethSeq confirmed that the rRNA Nm sites exhibited differential sensitivity to FBL depletion. Additionally, FBL knockdown led to alterations in 18S ribosome structure confirmed by SHAPE and specifically reduced RPS28 incorporation into ribosomes. Notably, silencing RPS28 also disrupted both the oncogenic phenotype and downregulated MTA1, IRAK1, and TMSB10 expression. These findings reveal a complex interplay between FBL, rRNA Nm modifications, and RPS28 in shaping oncogenic protein pools and ribosomal composition in TNBC, offering promising insights into therapeutic approaches targeting this aggressive cancer subtype.

PTPN18 is a member of the PEST (proline-glutamic acid-serine-threonine rich sequence) protein tyrosine phosphatase subfamily that has been intensively studied in immune cells. Here, we identified a novel PTPN18-interacting protein, fibrillarin (FBL), through mass spectrometry analysis and clarified the binding sites and interaction motifs via peptide mapping. The R451 site of PTPN18 and the V187 site of FBL dominate the interaction between PTPN18 and FBL. Further studies suggest that PTPN18, but not PTPN18 R451A, can dephosphorylate the Y313 site of FBL and can reduce the protein expression level of FBL by promoting its ubiquitin proteasome degradation. In addition, PTPN18 can affect its downstream functions, including the MAPK signaling pathway and methylation of rRNA 2'-O and histone H2AQ104 sites, as well as RNA synthesis through negative regulation of FBL, whereas PTPN18 R451A cannot. As a result, the interaction between PTPN18 and FBL affects the proliferation and apoptosis of breast cancer cells, thus inhibiting tumor growth. This study reveals a novel mechanism through which PTPN18 inhibits breast cancer progression and further refines the PTPN18 protein interaction network, which is important for understanding its role in cell signaling, revealing disease mechanisms, discovering new drug targets, and developing new treatments.

Nucleolar stress has emerged as a critical regulatory mechanism linking ribosome biogenesis defects to apoptotic cell death in various pathological conditions. Fibrillarin (FBL), the catalytic component of box C/D small nucleolar ribonucleoproteins, participates in multiple forms of programmed cell death through both p53-dependent and p53-independent pathways across diverse disease contexts including cancer and neurodegeneration. In malignancies including breast cancer, colorectal cancer, and hepatocellular carcinoma, FBL overexpression promotes apoptosis resistance, whereas in Alzheimer's disease and ALS/FTD, FBL dysfunction contributes to pathological neuronal death. Dysregulation of FBL can lead to excessive apoptosis or apoptosis resistance depending on cellular context and disease state. Various cellular stressors trigger aberrant FBL function, disrupting rRNA processing and ribosome assembly, which then activates nucleolar stress responses that culminate in cell death through ribosomal protein-MDM2-p53 axis activation or selective translational control of survival factors in a context-dependent manner. Therefore, targeting FBL-mediated apoptotic pathways is considered an important avenue for the treatment of various cancers and neurodegenerative diseases. In this review, we summarize the major and recent findings focusing on the mechanisms of FBL-regulated apoptosis in disease pathogenesis and provide a systematic overview of current therapeutic strategies targeting nucleolar stress pathways, including RNA polymerase I inhibitors and precision medicine approaches based on p53 status, which may provide important therapeutic targets that merit further investigation.

IntroductionHepatocellular carcinoma (HCC) is a major cause of cancer-related mortality. While *C-myc* is known to drive hepatocarcinogenesis, the roles of its downstream targets remain unclear. NOP56, a conserved nucleolar protein and *C-myc* target, may contribute to HCC progression.MethodsWe analyzed single-cell and bulk transcriptomic datasets to determine NOP56 expression and clinical significance. Loss-of-function assays in HCC cells, along with xenograft models, were used to evaluate its biological role. Protein interaction and pathway analyses were conducted using co-immunoprecipitation and Western blotting.ResultsNOP56 was upregulated in malignant hepatocytes and associated with poor prognosis. NOP56 knockdown inhibited proliferation, colony formation, and migration, induced G0/G1 arrest and apoptosis, and reduced tumor growth in vivo. Mechanistically, NOP56 interacted with fibrillarin (FBL) and activated the PI3K/AKT/CREB pathway. Silencing NOP56 lowered FBL levels and suppressed pathway activity, whereas FBL overexpression partially rescued apoptotic effects.DiscussionNOP56 promotes HCC progression through the NOP56–FBL–PI3K/AKT/CREB axis. These findings reveal a previously unrecognized oncogenic role of nucleolar proteins in HCC and highlight this signaling axis as a promising therapeutic target.

The Mediator complex is a transcriptional co-factor for RNA polymerase II (Pol II)-dependent gene expression, with MED19 serving as an integral subunit. While MED19 overexpression has been documented in diverse cancer types to promote tumor progression, the underlying molecular mechanisms remain poorly understood. Here, we uncover a previously unrecognized function whereby MED19 localizes to the nucleolus independently of the Mediator complex. This nucleolar targeting is mediated by a conserved poly-lysine motif at the MED19 C-terminus, which enables binding to ribosomal RNA (rRNA) and fibrillarin (FBL), a catalytic component of the 2′-O-methyltransferase complex and pre-rRNA processing factor. Mechanistically, MED19 facilitates rRNA processing and 2′-O-methylation that promotes the efficiency of internal ribosome entry site-dependent translation for a number of onco-promoting genes including c-Myc. Collectively, these findings reveal a novel Mediator-independent function of MED19 in regulating ribosome-mediated translational control, thus providing mechanistic insights into its onco-promoting role.

Fibrillarin (FBL) is a key nucleolar methyltransferase involved in ribosome biogenesis through 2'-O-ribose methylation of rRNA. While its oncogenic role has been reported in several cancer types, its expression and function in human colorectal cancer (CRC) have remained largely unexplored. This study aims to investigate the expression of FBL in human CRC tissues and cell lines and to determine its functional role in tumor progression and metastasis. We examined FBL expression in paired human CRC primary tumors and liver metastases using immunohistochemistry. Functional studies were performed using SW-480 (primary tumor) and SW-620 (lymph node metastasis) CRC cell lines derived from the same patient. Cell migration, invasion, and 3D spheroid growth were analyzed following FBL downregulation. In vivo tumor growth was assessed in SCID mice xenografted with FBL-deficient cells. Molecular changes were explored through phosphorylation arrays and Western blotting. FBL expression was significantly higher in human metastatic lesions than in primary tumors. FBL downregulation impaired migration, invasion, and spheroid growth in SW-480 and SW-620 cells and reduced tumor growth in vivo. Mechanistically, FBL inhibition decreased activation of MAPK/ERK, PI3K/AKT, and JNK/p38 pathways and reduced phosphorylation of the transcription factor CREB. Our study identifies FBL as a potential contributor to colorectal cancer progression, with elevated expression associated particularly with metastatic disease. By demonstrating that FBL expression is elevated in patient-derived metastatic tissues and functionally promotes migration, invasion, and tumor growth, our findings expand the role of ribosome biogenesis factors beyond protein synthesis. The observed suppression of key oncogenic pathways and CREB phosphorylation upon FBL inhibition suggests that FBL integrates ribosomal regulation with cancer cell signaling. These insights open new avenues for targeting nucleolar activity in advanced CRC and highlight FBL as a potential biomarker and therapeutic target in metastatic disease.

Fibrillarin regulates epithelial integrity via EZH2-mediated modulation of scribble expression.

Investigating ribosome biogenesis in AML identifies MYB-binding protein 1A (MYBBP1A) as an essential regulator of leukemia cells

RNA trafficking is crucial in almost every phase of plant development. Fibrillarin (FIB), a highly conserved nucleolar protein with methyltransferase (MTase) activity, functions in methylation and rRNA processing and facilitates the transport of several RNA viruses in plants. Previously, we demonstrated that bamboo mosaic virus satellite RNA (satBaMV) traffics autonomously and systemically in a helper virus-independent but FIB-dependent manner by forming a mobile ribonucleoprotein (RNP) complex comprising satBaMV, FIB, and satBaMV-encoded P20 movement protein. Here, we show that FIB methylates the arginine-rich motif (ARM) of P20 and relies on its MTase activity for the systemic movement of satBaMV. FIB MTase-defective mutants failed to complement long-distance satBaMV transport in FIBi plants, despite still binding to satBaMV in vivo. We also demonstrate that the ARM of P20 guides its nucleolar localization for FIB-mediated methylation. P20 methylation not only contributes to its plasmodesmata (PD) targeting but also triggers nucleocytoplasmic shuttling of FIB with P20 as the RNP complex to PD. A satBaMV mutant harboring a nonmethylated P20, but not a methylation-mimic P20, exhibited disrupted PD targeting and impaired P20-assisted satBaMV trafficking. Our findings provide mechanistic insights into how FIB-mediated P20 methylation positively regulates systemic trafficking of a subviral agent in plants.

The nucleolus is a membrane‐less body present in the nucleus of the cell. The nucleolus is mainly involved in ribosomal RNA (rRNA) transcription and ribosome biogenesis for protein translation. During cancer formation, nucleolar morphology is altered, and many nucleolar proteins are expressed at a higher level, leading to enhanced ribosome biogenesis and protein translation, which supports cancer aggressiveness, proliferation, migration, and invasion. In this study, we investigated the association of two nucleolar proteins, nucleophosmin (NPM1), and fibrillarin (FBL), with prostate cancer (PCa) aggressiveness and progression. We investigated their cellular localization and expression in different PCa patient tissue specimens and their role in regulating proliferation, migration, invasion, and nucleolar morphology. Our results indicate that NPM1 and FBL are present in the nucleolus of both PCa and noncancerous prostatic cells. The expression of NPM1 and FBL was enhanced in aggressive castration‐resistant PCa (CRPC) and neuro‐endocrine PCa (NEPC) patient specimens compared to hormone‐naïve PCa (HNPC) patient specimens. The expression of NPM1 was enhanced in high‐Gleason score PCa compared to low‐Gleason score PCa. Silencing of NPM1 and FBL significantly reduced the proliferation, migration, and invasion of PCa cells without affecting noncancerous prostatic cells. Silencing of NPM1 and FBL also changed the morphology of nucleoli in both PCa and noncancerous prostatic cells, where NPM1 silencing fragmented the nucleoli and FBL silencing condensed the nucleoli. Our results suggest that NPM1 and FBL expression correlates with PCa aggressiveness and PCa cells may exhibit a unique dependence on NPM1 or FBL for PCa progression. © 2025 The Author(s). The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.

Protocol for investigating phase transition of prion-like proteins in vitro with concentration variation

Hepatocellular carcinoma (HCC) is the third leading cause of cancer-related death worldwide. Accumulating evidence suggests that epigenetic dysregulation contributes to the initiation and progression of HCC. We aimed to investigate key epigenetic regulators that contribute to tumorigenesis and progression, providing a theoretical basis for targeted therapy for HCC. We performed a comprehensive epigenetic analysis of differentially expressed genes in LIHC from the TCGA database. We identified fibrillarin (FBL), an rRNA 2′-O-methyltransferase, as an essential contributor to HCC. A series of in vitro and in vivo biological experiments were performed to investigate the potential mechanisms of FBL. FBL knockdown suppressed the proliferation of HCC cells. In vivo studies using cell-derived xenograft (CDX), patient-derived xenograft (PDX), and diethylnitrosamine (DEN)-induced HCC models in Fbl liver-specific knockout mice demonstrated the critical role of FBL in HCC carcinogenesis and progression. Mechanistically, FBL regulates the expression of CAD in HCC cells by recruiting YY1 to the CAD promoter region. We also revealed that fludarabine phosphate is a novel inhibitor of FBL and can inhibit HCC growth in vitro and in vivo. The antitumor activity of lenvatinib has been shown to be synergistically enhanced by fludarabine phosphate. Our study highlights the cancer-promoting role of the FBL-YY1-CAD axis in HCC and identifies fludarabine phosphate as a novel inhibitor of FBL.A schematic diagram depicting the FBL-YY1-CAD signaling pathway and its regulatory role in HCC progression.

Abstract Background: Ribosome biogenesis (RiBi) is a critical process underpinning cellular protein synthesis, meticulously regulated to maintain homeostasis. Dysregulated RiBi and translational control are integral to the uncontrolled proliferation of tumors, a hallmark of cancer, yet the molecular mechanisms remain poorly understood. Adenosine Deaminase Acting on RNA 1 (ADAR1), a key enzyme mediating RNA editing, has been linked to tumor transcriptomic heterogeneity and resistance to PD-1 immune checkpoint blockade. However, its precise role in tumor ribosome biogenesis and oncogenic translation remains unclear. Here, we uncover a novel connection between ADAR1 and RiBi, revealing its unrecognized role in driving tumorigenesis and therapeutic vulnerability. Methods: To identify ADAR1-regulated pathways, RNA sequencing (RNA-seq), ribosome profiling (Ribo-seq), and gene set enrichment analysis (GSEA) were performed in ADAR1-siRNA-treated tumor cells. The association between ADAR1 and RiBi was validated using single-sample GSEA (ssGSEA) in TCGA datasets and the RiBi Alu Editing Index (AEI) in the FUSCC TNBC cohort. Nucleolar morphology was evaluated using immunofluorescence and electron microscopy, while ribosome abundance and translational efficiency were assessed via sucrose density gradient centrifugation, rRNA quantification, and SUnSET assays. RNA pull-down and Sanger sequencing validated downstream targets. Functional and therapeutic potential of ADAR1 inhibition were assessed in mouse xenograft models and patient-derived organoids (PDOs) treated with CX-5461, an RNA polymerase I inhibitor. Results: ADAR1 was found to play a pivotal role in driving onco-RiBi, enhancing ribosome production and translation of oncogenic pathways such as MYC, mTOR, and DNA repair. Ribo-seq revealed that ADAR1 knockdown suppressed the translational efficiency of pro-tumorigenic genes, including MCM2 and CDC6. Mechanistically, ADAR1-mediated A-to-I RNA editing of Nucleolar Protein 14 (NOP14) stabilized fibrillarin (FBL), a key nucleolar marker, preserving nucleolar integrity and promoting ribosome assembly. High ADAR1 expression and elevated RiBi AEI scores correlated with poor prognosis in TCGA and FUSCC cohorts. CX-5461 disrupted RiBi, induced nucleolar stress, and suppressed tumor growth in preclinical models. PDOs with high ADAR1 expression demonstrated increased sensitivity to CX-5461, highlighting its therapeutic potential for targeting ADAR1-driven ribosomal dysregulation. Conclusions: Our study establishes a critical link between post-transcriptional RNA editing, tumor ribosome biogenesis, and oncogenic translation, addressing a key gap in the field. ADAR1 emerges as a pivotal regulator of onco-RiBi, and targeting ADAR1 in tumors with high expression using CX-5461 represents a promising therapeutic strategy. Citation Format: Xuliren Wang, Zhibo Shao, Qi Zhang, Han Zhu, Bingqiu Xiu, Yayun Chi, Jiong Wu. enhances ribosome biogenesis and triggers oncogenic translation [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 1411.

Antinuclear antibodies (ANAs) are central biomarkers in rheumatological conditions and can drive disease pathology. Much less is known about the role of ANAs in neurological symptoms, although a number of experimental studies have demonstrated direct effects on neuronal function, for example in neuropsychiatric lupus erythematosus. Moreover, it is unclear whether the ANAs detected in HEp-2 cell-based assays, the gold standard for ANA diagnostics, can also be recognized in modern screening assays for anti-neuronal autoimmunity, such as staining on rodent brain sections or neuronal cultures. In this study, we therefore conducted a comparative mapping of ANA-positive sera with well-characterized HEp-2 patterns to central nervous system (CNS) tissue, utilizing fixed and unfixed murine brain sections and primary murine neurons. We screened 74 ANA-positive sera classified into 14 individual patterns and combinations thereof. Majority of the samples reacted with fixed primary neurons (99%, 73/74 sera), followed by fixed brain sections (93%, 69/74), but much less to unfixed mouse brain (54%, 40/74). While the PM/SCL- and RPOI-positive sera showed no binding to unfixed brain sections, the U1RNP (U1 nuclear ribonucleoprotein particle) and FBLN (fibrillarin) ANAs reacted strongly across all assays, indicating differences in antigen accessibility. These findings suggest that the majority of ANAs can interact with neural components, which may obscure the detection of other anti-neuronal autoantibodies. The foundational mapping of ANA binding in CNS tissue provided here can also facilitate recognition of "CNS-specific ANAs," which bind to neuronal autoantigens but not to HEp-2 cells. Future studies should explore the association with certain neurological manifestations and the role of ANAs in neuronal pathology.

lncRNAs maintain the functional phase state of nucleolar prion-like protein to facilitate rRNA processing.

LncRNAs chaperoning dynamic protein condensates in cancer cells.