NUFIP1 at the crossroads of ribophagy and disease: unveiling therapeutic implications

Abstract

Background

Nuclear FMR1-interacting protein 1 (NUFIP1), originally identified as a binding partner of the fragile X mental retardation protein (FMRP), has increasingly been recognized as a pivotal factor in various pathological processes. Its recently elucidated role as a receptor in ribophagy positions it at the intersection of critical cellular pathways, suggesting broad functional significance in human disease pathogenesis.

Main body of the abstract

This review synthesizes emerging evidence underscoring the multifaceted involvement of NUFIP1 in key physiological and pathological mechanisms. It regulates fundamental processes such as tumor metabolism, immune responses during sepsis, and recovery from neural injury. Notably, recent findings indicate that impaired NUFIP1 function, particularly within the DNA damage response (DDR) pathway, can be exacerbated by external factors like low-protein diets, leading to exacerbated intestinal inflammation and the promotion of necroptosis. This compilation critically evaluates the mechanistic contributions of NUFIP1 across these diverse disease contexts and assesses its potential as a therapeutic target or biomarker.

Short conclusion

In conclusion, NUFIP1 emerges as a critical molecular player with widespread implications for human health. A comprehensive understanding of its functions provides valuable insights for developing novel therapeutic strategies. This review consolidates the current knowledge on NUFIP1, highlights its clinical relevance, and identifies promising avenues for future research to fully delineate its therapeutic potential.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12967-025-07528-6.

Introduction

Nuclear FMR1-interacting protein 1 (NUFIP1), initially identified in 1999 as a fragile X mental retardation protein (FMRP)-interacting protein [1], has been implicated in intellectual disability disorders. A pivotal 2018 study established NUFIP1 as the ribosomal receptor for ribophagy, essential for eukaryotic cellular homeostasis [2]. Subsequent investigations have demonstrated NUFIP1’s involvement in pathological processes through the mediation of ribophagy. In pancreatic ductal adenocarcinoma (PDAC), cancer-associated fibroblasts (CAFs) mediate the generation and secretion of nucleosides via ribophagy, which are subsequently internalized by PDAC cells, thereby promoting tumor metabolism [3]. During sepsis, NUFIP1-mediated ribophagy is significantly upregulated, protecting T lymphocytes from apoptosis and PANoptosis, thus contributing to immune regulation [4, 5]. NUFIP1 also plays a crucial role in neural injury repair by maintaining cellular homeostasis through ribophagy [6–8]. Furthermore, studies suggest a role for NUFIP1 in intestinal DNA damage repair [9]. Specifically, downregulation of NUFIP1, induced by low-protein diets, can lead to DNA damage accumulation, triggering necroptosis and promoting inflammatory bowel disease (IBD) development [9]. Additionally, studies have demonstrated significant roles for NUFIP1 in diseases including malaria and muscle atrophy, suggesting novel therapeutic targets [10, 11].

Given these research advancements, NUFIP1 has emerged as a significant player in various diseases, potentially serving as a biomarker or therapeutic target (Fig. 1). This presents novel opportunities for developing treatment strategies for related pathologies. This review compiles current knowledge on NUFIP1’s involvement in human diseases to provide a comprehensive resource, evaluating its potential clinical value, and identifying future research directions. The detailed literature search strategy was shown in the supplementary material (Supplementary File).

Fig. 1.

The general timeline of NUFIP1 and human diseases NUFIP1 was initially identified as an interacting protein of FMRP and is associated with intellectual disability disorders. Its roles in mediating ribophagy, forming core components of snoRNPs, participating in tumor metabolism, regulating immune responses in sepsis, facilitating DNA damage repair, and modulating cell death have been progressively elucidated. Furthermore, as the regulatory pathways of NUFIP1 become increasingly elucidated, its roles have been validated not only in neurodegenerative diseases but also in a growing number of other disorders

Biological structure and function of NUFIP1

Initial investigations revealed that NUFIP1 is predominantly localized within the nucleus. However, subsequent studies have demonstrated the presence of NUFIP1 in the cytoplasm, where it associates with ribosomes[2, 12]. In neuronal cells, NUFIP1 is observed in functional synaptic neuronal bodies and co-localizes with ribosomes[12]. The protein features a Cys2His2(C2H2) zinc finger domain, a nuclear localization signal (NLS)[1], and a Chromosome Region Maintenance 1(CRM1)-dependent nuclear export signal (NES), facilitating its nucleocytoplasmic shuttling. Moreover, it contains a cdk site at positions 292–295 and a highly conserved Proline-Enriched Peptide (PEP) domain[13–15]. Wyant et al.’s research indicates the presence of four LC3-interacting regions (LIRs) characterized by a Trp/Phe-X–X-Leu/Ile/Val sequence motif, thereby enabling its involvement in ribophagy through interaction with microtubule-associated proteins 1A/1B light chain 3B (LC3B).

In this review, we propose that NUFIP1 functions as a “homeostasis integrator”, playing a critical role at the intersection of nutrient, metabolic, and DNA damage signaling pathways by coordinating cellular resource allocation to maintain cellular homeostasis. The presence of multiple functional domains in its molecular structure, such as NLS, NES, and LIRs, enables NUFIP1 to shuttle between the nucleus and cytoplasm and participate in diverse signaling pathways, allowing it to execute context-specific functions depending on cell type, nature of the stressor, and tissue microenvironment.

Involvement in small-molecule nucleolar ribonucleoprotein (snoRNP) assembly

Box C/D snoRNPs are crucial complexes implicated in rRNA processing and modification, and their efficient assembly is a critical step for rRNA maturation[16, 17]. The assembly process of snoRNPs is intricate and involves various biogenesis factors. NUFIP1 can directly bind to the four core proteins of Box C/D snoRNPs, including 15.5 K, fibrillarin, NOP56 (Non-ribosomal protein 56), and NOP58 (Non-ribosomal protein 58), facilitating the formation of partial pre-snoRNP complexes by these core proteins in the presence of snoRNA, thereby playing a key “bridging” role in snoRNP assembly[14]. Zinc finger HIT domain-containing protein 3 (ZNHIT3) maintains the stability of NUFIP1 during this process by directly binding to NUFIP1[18]. Further investigation has explored the specific mechanism of NUFIP1’s involvement in assembly[15, 19, 20]. Moreover, Quinternet et al. validated the conservation of the snoRNP assembly mechanism through cross-species experiments[20].

Boulon et al.’s research[15] demonstrated that NUFIP1, via its PEP motif, interacts with RNA-binding proteins of the ribosomal protein L7Ae family, including 15.5 K, hNHP2 (human Non-Histone Protein 2), and SBP2 (Selenocysteine Insertion Sequence Binding Protein 2), contributing significantly to the biogenesis of various essential ribonucleoproteins. These ribonucleoproteins encompass U4 small nuclear RNPs, selenoprotein messenger RNPs, C/D box, and H/ACA small nucleolar RNPs. NUFIP1’s interaction with L7Ae family proteins, mediated by its PEP motif, and subsequent interactions with core RNP proteins through other domains, facilitate RNA-protein connectivity, acting as a scaffolding protein for RNP assembly. Furthermore, the study[15] indicated that NUFIP1 recruits assembling RNPs to the Rvb1-Rvb2-Tah1-Pih1 (R2TP) complex and the chaperone protein Heat Shock Protein 90 (Hsp90) through the conserved adapter Phosphatase 2A inhibitor 1 (Pih1). The coordinated action of assembly factors and chaperone proteins promotes the transition of proteins from an unassembled state to mature RNP complexes.

Receptor for ribophagy

Kraft et al. [21] initially posited the concept of ribophagy. Wyant et al.’s work revealed NUFIP1 in a receptor role for starvation-induced ribophagy [2], a finding corroborated by Leytens et al. [22]. The mammalian mechanistic target of rapamycin (mTOR), a serine/threonine kinase, regulates intracellular mRNA translation, protein transport, and ribosome biogenesis, and is critical for cell growth, apoptosis, and autophagy. mTOR functions through two segregated complexes in mammalian cells, mTOR complex 1 and mTOR complex 2 (mTORC1 and mTORC2). Evidence suggests that mTORC1 pathway inhibition results in increased lysosomal accumulation of NUFIP1, implying NUFIP1’s role in ribophagy initiation [23].

NUFIP1 can heterodimerize with ZNHIT3. CRISPR-Cas9-mediated knockout of the NUFIP1 gene results in the loss of ZNHIT3 [2, 20]. Neither Torin1-mediated nor amino acid starvation-induced mTORC1 inhibition reduces the total level of NUFIP1 and ZNHIT3 in cells, but induces their subcellular relocalization from the nucleus to lysosomes and autophagosomes[2]. Wyant et al. hypothesized that the NUFIP1-ZNHIT3 complex may promote the fusion of ribosome-containing autophagosomes with lysosomes by binding to the autophagosome [2], and experimentally investigated the relationship between NUFIP1-ZNHIT3 and autophagy. Ribosome transport to vacuoles requires the involvement of autophagy-related gene 1 (ATG1) and autophagy-related gene 7 (ATG7) [24]. In ATG7-deficient cell models, lysosomal localization of NUFIP1-ZNHIT3 was not observed. Following Torin1 treatment, FLAG-NUFIP1 co-localized with LC3B-positive autophagosomes, and ZNHIT3 facilitates the interaction between NUFIP1 and LC3B during this process [2]. The other study revealed that NUFIP1 possesses four LC3-interacting regions (LIRs)[2]. The introduction of LIR sequence mutations in W40A cells markedly diminished the binding affinity of NUFIP1 to LC3B, thereby impairing its capacity to facilitate ribosome degradation, even under conditions conducive to autophagy.

Subsequent investigations[2] demonstrated that NUFIP1-ZNHIT3 exhibits marked ribosomal translocation following Torin1 treatment or amino acid deprivation, with ribosomal proteins (40S and 60S) co-immunoprecipitating with NUFIP1. Upon mTORC1 inhibition, NUFIP1 interacts with LC3B via the ribosomal large subunit to facilitate ribophagy. Under amino acid starvation conditions, sucrose gradient centrifugation revealed that NUFIP1-ZNHIT3 preferentially associates with the 60S subunit. In vitro binding assays indicated that the binding strength to NUFIP1-ZNHIT3 depended on ribosomal source in vitro: only Torin1-treated cell-derived ribosomes showed high-affinity binding, while the complex’s origin had no detectable effect. This suggests that mTORC1 inhibition modulates ribosome stability, and the resultant conformational changes in ribosomes promote their interaction with the NUFIP1-ZNHIT3 complex.

In conclusion, NUFIP1 interacts with ribosomes in an mTORC1-dependent manner and requires LC3B to mediate the delivery of the complex to autophagosomes for selective ribophagy. What should be noted is that although NUFIP1 was initially identified as the sole ribophagy receptor in mammals, recent studies have identified Rpl12 (a ribosome large subunit protein) as an additional ribophagy receptor. Unlike NUFIP1, Rpl12 is conserved across a variety of organisms, including yeast and nematodes [25]. Functionally, NUFIP1 and Rpl12 are not redundant but represent an evolutionary replacement mechanism.Rpl12 is an ancient, conserved, and universally present core machinery for ribophagy, whereas NUFIP1 is a newly evolved regulatory pathway in mammals that may enable more precise control of ribosome turnover. In species lacking NUFIP1, Rpl12 independently mediates ribophagy; even in mammals possessing NUFIP1, Rpl12 remains essential as a fundamental safeguard [25].

Involvement in DNA damage response

DNA damage poses a significant threat to the fidelity of genetic information transmission and can instigate human diseases. Both endogenous factors, such as dNTP misincorporation during DNA replication and base loss following DNA depurination, and exogenous factors, including ionizing radiation, can induce DNA damage[26]. Studies have indicated that spontaneous DNA damage can result in up to 10^5 lesions per cell daily [27]. Eukaryotic cells counteract DNA damage by initiating the DNA Damage Response (DDR). The DDR is a cascade and repair mechanism activated upon DNA damage, with primary functions including damage recognition, signal transduction, and the initiation of repair processes to prevent the accumulation of DNA damage and maintain genome stability[28]. DDR is primarily orchestrated by three kinases: Ataxia-Telangiectasia Mutated (ATM), DNA-dependent Protein Kinase (DNA-PK), and Ataxia-Telangiectasia and Rad3-related (ATR) [29]. ATR is activated by replication stress and single-strand breaks, thereby ensuring replication fidelity [30]. ATM is activated by double-strand breaks (DSBs), eliciting cell cycle arrest and DNA repair pathways[31]. DNA-PK is essential for non-homologous end joining (NHEJ), a crucial double-strand break (DSB) repair pathway [32]. Recent work by Ming et al. demonstrated that NUFIP1 contributes to the DNA damage response by enhancing ATR pathway activation[9].

Replication Protein A (RPA), a heterotrimeric protein comprising RPA14, RPA32, and RPA70, functions as a critical component in DDR. RPA32 frequently scaffolds other DDR factor assembly [33, 34]. RPA recognizes and binds to single-stranded DNA (ssDNA), acting as an early sensor of DNA damage [9]. ATRIP, the binding partner of ATR, stabilizes ATR and facilitates its recruitment to DNA damage sites; DDR signaling is contingent upon the recruitment of both proteins to the damage site [9]. The initial step in the ATR-mediated DDR pathway involves RPA binding to and stabilizing ssDNA [35, 36]. Subsequently, ATR, through its interaction with ATRIP, is recruited to RPA-coated ssDNA regions. The ATR–ATRIP complex associates with the RPA–ssDNA complex, thereby initiating downstream signaling [33]. Research suggests that the recruitment of the ATR–ATRIP complex may necessitate additional factors [33, 37].

A study investigating the impact of a low-protein (LP) diet on intestinal inflammation in mice [9] revealed that NUFIP1 loss exacerbated the amino acid deficiency-induced inhibition of DNA damage repair, suggesting a role for NUFIP1 in this process. To further elucidate NUFIP1’s influence on the DDR signaling pathway, DNA damage induction in HeLa cells was achieved through hydroxyurea (HU) treatment, and NUFIP1 was knocked down. The findings indicated that NUFIP1 knockdown suppressed the DDR signaling pathway, significantly diminishing the recruitment of DDR markers BRCA1 and 53BP1 to chromatin, while the recruitment of the upstream component RPA32 was unaffected. This suggests that NUFIP1 functions within the DNA damage repair pathway downstream from RPA32 but upstream of BRCA1/53BP1 [9]. Under identical treatment conditions, the recruitment of both ATR and ATRIP to chromatin, as well as the interaction between ATRIP and RPA32, was markedly diminished, suggesting that NUFIP1 is critical for the effective recruitment of the ATR–ATRIP complex[9]. Sequence alignment revealed an RPA32-binding motif (RBM) within NUFIP1. This motif shares similarities with those found in established RPA32-interacting proteins and encompasses the phosphorylation site S292. Co-immunoprecipitation and in vitro binding assays validated that NUFIP1 directly interacts with RPA32, and this interaction is amplified subsequent to DNA damage. The introduction of an RBM deletion mutant (ΔRBM) abrogated the capacity to bind RPA32, indicating that NUFIP1 localizes to DNA damage sites via RPA32 binding[9].

Further investigation assessed the impact of NUFIP1 phosphorylation on its functionality[9]. Researchers generated a non-phosphorylatable mutant, NUFIP1S292A, and compared its function with wild-type NUFIP1. They discovered that phosphorylation enhances NUFIP1’s binding affinity to RPA32. Wild-type NUFIP1 facilitated ATRIP binding to RPA-coated ssDNA, whereas the S292A mutant did not, indicating that NUFIP1 phosphorylation is crucial for its role in the DDR. Furthermore, NUFIP1-knockout mouse models exhibited elevated levels of the DNA damage marker γH2A.X. This phenotype was rescued by reintroducing wild-type NUFIP1, but not the S292A mutant.

Breast cancer type 1 susceptibility protein (BRCA1), a pivotal tumor suppressor, is indispensable for DNA damage repair, cell cycle control, and transcriptional regulation [13, 38]. Existing literature suggests functional synergy between NUFIP1 and BRCA1, a key DNA repair factor, in modulating RNA Polymerase II transcription [39]. Moreover, a study has revealed that the NUFIP1-interacting protein FMRP participates in the DDR [40]. These findings warrant further investigation into the function of NUFIP1 in DDR; through synergistic effects with BRCA1 and FMRP, NUFIP1 may have functions in DDR beyond recruiting the ATR-ATRIP complex.

In summary, Ming et al.’s research suggests that NUFIP1 safeguards genomic integrity through DDR. NUFIP1 acts as a phosphorylation-dependent molecular bridge, and modification at its S292 site enhances its affinity for RPA32, thereby promoting the stable anchoring of the ATR–ATRIP complex onto RPA-coated single-stranded DNA, thus initiating the DDR pathway. (Fig. 2).

Fig. 2.

The biological functions of NUFIP1 is involved in diverse biological processes, including ribophagy, rRNA biogenesis, and DNA damage repair. NUFIP1 promotes the formation of the pre-snoRNP complex, which participates in pre-rRNA 2′-O-methylation. Under starvation stress or mTORC1 inhibition (e.g., Torin1), NUFIP1 translocates to the cytoplasm with ZNHIT3, where it interacts with LC3B and promotes ribophagy. Following NUFIP1 knockdown, tumor cells activate the p53/p21 and caspase pathways. Additionally, NUFIP1 is involved in DDR pathways through interactions with RPA, recruiting the ATR–ATRIP complex

Molecular mechanisms of NUFIP1 in pathological processes

Orchestrating protein homeostasis via ribophagy

Current investigations suggest that NUFIP1, via its critical function in ribophagy, participates in the development of diverse diseases. Fibrotic stromal hyperplasia constitutes a defining feature of Pancreatic ductal adenocarcinoma (PDAC), with cancer-associated fibroblasts (CAFs) representing key stromal components that promote tumor progression, metastasis, and therapeutic resistance [41]. Research [3] has revealed that, within the pancreatic tumor microenvironment, glutamine deprivation triggers the translocation of NUFIP1 to autophagosomes in CAFs, thereby mediating rRNA degradation and nucleoside generation; these nucleosides are subsequently secreted by the CAFs. Tagging of CAF-secreted nucleosides was achieved via [¹³C₆] glucose culturing. Subsequently, this conditioned medium (CM) from labeled cells was introduced to PDAC cells, demonstrating that the tracer-incorporated nucleosides were progressively internalized by the PDAC cells. The MYC (MYC proto-oncogene) pathway, a gene expression and signaling cascade regulated by the MYC protein, regulates core programs: proliferation, metabolism, and differentiation [3]. In cancer, aberrant MYC activation drives accelerated tumor cell growth and metabolic reprogramming [3, 42]. Studies indicate [3] that nucleotides internalized by PDAC cells activate the MYC pathway, upregulate the expression of glucose metabolism-related genes (e.g., Slc2a1, Solute Carrier Family 2 Member 1), and enhance the capacity of tumor cells for glucose uptake and utilization, thereby mitigating nutrient stress within the PDAC cells.

Endoplasmic reticulum (ER) dysfunction triggers misfolded protein accumulation within the ER lumen, which is called ER stress (ERS) [43]. Ischemia, hypoxia, disrupted Ca²⁺ homeostasis, ATP depletion, aberrant increases in newly synthesized proteins, and disturbances in protein processing, modification, and transport are among the factors that disrupt ER function [44]. To counteract ERS, cells transduce the unfolded protein response (UPR), a protein quality control mechanism. As a proteostatic guardian, the UPR restores ER homeostasis; however, under excessively severe or prolonged ERS, cells may initiate ER-associated apoptotic pathways leading to cell death [45–47]. The UPR is mediated by three pathways: the IRE1 (Inositol-Requiring Enzyme 1) pathway, the ATF6 (Activating Transcription Factor-6) pathway, and the PERK (PKR-Like ER Kinase) pathway. Ribosome biogenesis and protein translation are major energy-consuming processes within the cell[7]; their reduction following ischemia might prolong cell survival [48–50]. Rapamycin is an mTORC1-inhibiting drug [23], and inhibiting mTORC1 can activate NUFIP1-mediated ribophagy [2]. In the study by Carloni et al. [7], to establish a hypoxia-ischemia (HI) model, researchers performed right common carotid artery ligation on 7-day-old rats and exposed them to a hypoxic environment. In this model, all three UPR pathways were strongly activated, evidenced by significantly increased expression of downstream signaling molecules including CHOP (C/EBP Homologous Protein), GRP78 (Glucose-Regulated Protein 78), and Hsp70 (Heat Shock Protein 70), enhanced phosphorylation of eIF2α (Eukaryotic Initiation Factor 2α), and occurrence of Xbp-1 (X-Box Binding Protein 1) mRNA splicing. Treatment of rats with rapamycin increased expression of LC3–II and Beclin1, while significantly decreasing expression of CHOP, GRP78, and Hsp70, as well as reducing Xbp-1 splicing. These changes indicate enhanced autophagy accompanied by suppression of the UPR pathways and alleviation of ERS. Further studies revealed that 3-MA (an autophagy inhibitor) blocked the ameliorative effect of rapamycin on ERS, promoting a rebound in the expression of stress-related proteins like CHOP, GRP78, and Hsp70.

In alignment with existing literature, our prior investigation revealed that elevated ERS intensifies lymphocyte apoptosis in murine sepsis models, thereby representing a critical mechanism in sepsis progression [51]. We demonstrated that NUFIP1-mediated ribophagy is markedly induced through the ERS-associated PERK-ATF4-CHOP pathway (ATF4, Activating Transcription Factor 4), whereas ribophagy mitigates ERS by suppressing this pathway [5]. The PERK-ATF4-CHOP pathway is a central signaling cascade that mediates ERS-induced apoptosis. In two sepsis models, induced by cecal ligation and puncture (CLP) and lipopolysaccharide (LPS) stimulation, the PERK-ATF4-CHOP axis was markedly elevated, indicating pathway activation during sepsis. Following LPS stimulation, NUFIP1 expression peaked at 24 hours, concurrent with a reduction in ribosomal protein expression (RPL7 and RPL26), suggesting ribophagy activation [5]. To validate the relationship between autophagy and the PERK-ATF4-CHOP cascade, cells were treated with Salubrinal (Sal, an eIF2α inhibitor, used to inhibit the PERK-ATF4-CHOP axis). Experimentally, we observed that in both the NUFIP1 knockdown group and the control group, Sal significantly attenuated LPS-induced upregulation of PERK, ATF4, and CHOP, along with significantly reduced NUFIP1 expression, suggesting that upregulation of the PERK-ATF4-CHOP cascade potentiates NUFIP1 expression [5].

Given that ribophagy exhibited a protective effect on T cells, we further investigated the underlying molecular mechanism. A study [51] demonstrated that in cecal ligation and puncture(CLP) mouse models, following HMGB1 stimulation, upregulation of sestrin2 (SESN2) in dendritic cells (DCs) modulates the ERS response, reducing apoptosis in these cells. Additional studies have indicated that the PERK-ATF4-CHOP cascade is associated with the upregulation of autophagy during ERS [52–54]. In our preliminary experiments, we observed that T cells with NUFIP1 knockdown exhibited marked fragmentation and swelling of ER structures, coupled with significantly elevated expression of ERS markers GRP78, ATF4, and CHOP [5]. Based on the aforementioned research, we examined the correlation between the PERK-ATF4-CHOP pathway and NUFIP1. Western blot analysis revealed that LPS stimulation markedly upregulated the expression of PERK, ATF4, and CHOP, indicative of robust ERS activation, whereas NUFIP1 overexpression significantly downregulated these proteins. Conversely, NUFIP1 overexpression significantly suppressed the activation of this pathway. Key apoptotic proteins, for example, cleaved Caspase 3 (c-Caspase 3) and Bax(Bcl-2-associated X protein), were correspondingly downregulated. These findings suggest that NUFIP1-governed ribophagy suppresses the PERK-ATF4-CHOP cascade, thereby mitigating ERS [5].

Dendritic cells (DCs) are critical mediators of immune responses [55–59], and their dysfunction during sepsis is marked by diminished surface molecule expression and impaired T cell proliferation, ultimately promoting immunosuppression [60]. Mirroring the role of NUFIP1 in T cells, our recent data [6] demonstrate that NUFIP1-mediated ribophagy supports DCs’ function in the early phase of sepsis by mitigating endoplasmic reticulum (ER) stress. This protective effect is reflected in upregulated surface molecule expression, elevated cytokine production, and improved T cell activation. Conversely, NUFIP1 deficiency results in compromised DC function. Mechanistically, NUFIP1 binds ATF4 to regulate its nuclear translocation, thereby modulating the EIF2AK3 (eukaryotic translation initiation factor 2 alpha kinase 3)-ATF4-DDIT3 (DNA damage-inducible transcript 3) signaling pathway and attenuating excessive ER stress.

Our recent investigation reveals that NUFIP1-mediated ribophagy not only attenuates endoplasmic reticulum stress (ERS) but also ameliorates PANoptosis in septic CD4⁺ T cells dependent on the cGAS-STING(cyclic GMP-AMP synthase-stimulator of interferon genes) signaling axis, thus safeguarding T cell survival [4]. PANoptosis coalesces features of apoptosis, pyroptosis, and necroptosis, defining an integrated PCD module first identified in 2017 [61–63]. Functioning as a molecular nexus, the PANoptosome, discovered in 2020, coordinates key effectors across pyroptotic, apoptotic, and necroptotic cascades within PANoptosis [64]. Z-DNA Binding Protein 1 (ZBP1) is a cell death-associated protein. During influenza A virus (IAV) infection, ZBP1 complexes with Caspase-8, Caspase-6, and other factors to promote PANoptosis. Studies demonstrate that ZBP1 ablation completely abrogates IAV-induced PANoptosis, whereas the absence of other PCD pathway components does not yield the same effect [65], highlighting ZBP1’s crucial role in PANoptosis. Similar to ZBP1, proteins like NLRP12 (NACHT, LRR, and PYD domains-containing protein 12) are also essential for PANoptosome formation [66, 67]. The cGAS-STING pathway, an innate immune response mechanism, triggers immune responses by recognizing aberrant cytoplasmic DNA, including viral and bacterial DNA, and DNA from damaged cells. It induces type I interferons (IFN-I) and inflammatory cytokines, playing a vital role in inflammation regulation and immune defense [68–70]. Additionally, the ribosomal collisions, induced by translational stress from viral proteins, can disrupt ribosomal homeostasis and activate cGAS through double-stranded DNA sensing [71].

In our investigation, we noted a significant escalation of PANoptosis within CD4⁺ T cells derived from septic mice, correlating with heightened NUFIP1 expression and augmented ribophagy. Experimental data indicated that Jurkat T cells exhibited amplified PANoptotic pathway activation following NUFIP1 knockdown, alongside upregulated ZBP1 and NLRP12 expression, whereas NUFIP1 overexpression attenuated these effects. Proteomic profiling identified multiple cGAS fragments among the 20 most significantly altered proteins following LPS stimulation of wild-type versus NUFIP1-knockout Jurkat T cells. Integrating these findings with KEGG pathway enrichment analysis, we focused on the cGAS-STING signaling axis. Our results demonstrated that in both NUFIP1 KD Jurkat T cells and NUFIP1 conditional knockout (cKO) mouse models, the expression levels of cGAS-STING signaling components, exemplified by cGAS and phosphorylated STING (p-STING), as well as ZBP1, were significantly elevated. Conversely, NUFIP1 overexpression in Jurkat T cells resulted in a marked reduction in the expression of these proteins.

Extending prior investigations, we conducted polysome profiling, revealing significant ribosome collision events within CD4⁺ T cells amidst septic progression, coupled with heightened ribophagy and initiation of the cGAS-STING signaling axis [4]. Specifically, NUFIP1 knockdown exacerbated ribosome collisions, while its overexpression mitigated this effect. Co-immunoprecipitation (Co–IP) assays demonstrated a substantial interaction between NUFIP1 and STING in both Jurkat T cells and murine CD4⁺ T lymphocytes. SN-011, a specific inhibitor of the cGAS-STING pathway, inhibits pathway activation by competitively binding to the STING protein. Following SN-011 treatment, the expression of cGAS-STING pathway components in NUFIP1 KD Jurkat T cells was significantly reduced, accompanied by a notable decrease in the levels of PANoptosis-related proteins, including ZBP1.

Mechanically, our investigation suggests that ribosomal stasis in the CD4 + lymphocytic and the NUFIP1-STING interplay may initiate the cGAS-STING pathway via ribophagy, thereby modulating PANoptosis. Nevertheless, certain limitations persist concerning the underlying pathological mechanisms. Molecular orchestration underlying the NUFIP1-STING complex orchestrates ribophagy and cGAS-STING signaling, which requires further clarification. Furthermore, despite the established association of NUFIP1/ZBP1 with PANoptosis within CD4⁺ T cells during sepsis[4], the specific interactions and molecular mechanisms governing these proteins warrant additional investigation.

Participating in the DNA damage response

As previously indicated, NUFIP1 is an important component involved in DDR. Research by Ming and colleagues [9] revealed that in male mouse intestinal tissues, a low-protein (LP) dietary regimen decreased amino acid concentrations, thereby suppressing NUFIP1 expression and compromising the DDR.

The GCN2(General Control Nonrepressed 2) pathway, an intracellular signaling cascade, is triggered in response to amino acid deprivation. During conditions of amino acid scarcity, uncharged tRNA interacts with the HisRS-like region within the GCN2 protein, thereby activating GCN2 [72, 73]. Activated GCN2 promotes eIF2α phosphorylation-mediated translational activation of GCN4 (in yeast) or ATF4 (in mammals). These transcription factors then induce the expression of genes involved in amino acid biosynthesis, thereby enabling cellular adaptation to amino acid starvation[74–78].

In an in vitro investigation by Ming et al. [9], the researchers induced amino acid deprivation in cellular models and assessed NUFIP1 expression. They observed a downregulation of NUFIP1 expression. This suppression was reversed upon treatment with a GCN2 inhibitor (GCN2iB), indicating that amino acid deficiency downregulates NUFIP1 via the GCN2 pathway [9]. In the murine model, mice subjected to an LP diet demonstrated reduced NUFIP1 levels in colonic tissue, concomitant with elevated phosphorylation of eIF2α, indicative of GCN2 pathway activation. These results further support the hypothesis that amino acid deficiency downregulates NUFIP1 through GCN2. Building upon the findings of Wyant et al [2]., Ming et al. posited that amino acid starvation initiates NUFIP1-mediated ribophagy, thereby accelerating the degradation of the NUFIP1 protein. Nevertheless, the signal transduction mechanism coupling GCN2 activation with NUFIP1 suppression is undetermined.

Counteracting cellular senescence

High mobility group A2 (HMGA2), a nonhistone architectural protein, modulates chromatin topology and transcriptional regulation, mediating apoptosis and DDR [79]. It exhibits elevated expression across malignancies (e.g., breast cancer, PDAC, and melanoma), correlating with adverse patient prognoses [80–88]. In the context of cellular senescence, HMGA2 expression is elevated, contributing to the formation of Senescence-Associated Heterochromatin Foci (SAHF) [89, 90]. SAHF, characterized by dense heterochromatin structures within the nucleus, represents a critical hallmark of cellular senescence. SAHF-mediated sequestration of pro-proliferative genes within heterochromatin represses their expression, thereby inducing cell cycle arrest and significantly contributing to the cellular senescence program [91, 92]. HP1γ (Heterochromatin Protein 1 γ) and H3K9me3 (Histone H3 lysine 9 trimethylation) are key constituents of SAHF, collaboratively participating in its formation[92].

In a recent investigation [93], elevated NUFIP1 expression was observed in colorectal cancer (CRC) tissues, correlating with the promotion of senescence marker formation or expression. Proteomic analysis of human CRC cells revealed that NUFIP1 knockdown modulated the expression of 136 proteins and downregulated 41 proteins, thereby influencing multiple signaling pathways, including the SAHF pathway. Further exploration demonstrated that NUFIP1 knockdown activated the HMGA2/SAHF and p53/p21 signaling axis, resulting in the expression of senescence-associated marker expression (SA-β-gal/β-galactosidase, HP1γ, H3K9me3, HMGA2) and amplified p53 and its effector p21. Additionally, NUFIP1 knockdown induces apoptosis, characterized by upregulation of the pro-apoptotic protein Bax (Bcl-2-associated X protein) and downregulation of the anti-apoptotic protein Bcl-2 (B-cell lymphoma 2). These findings suggest that NUFIP1 may exhibit a pro-tumorigenic function by modulating cellular senescence. Despite evidence indicating that NUFIP1 knockdown impacts cellular senescence-related phenotypes, the precise molecular mechanisms governing the interaction between NUFIP1 and senescence factors require further investigation.

It is worth mentioning that an investigation into the lifespan of the bat species Myotis pilosus could offer insights into the mechanisms by which NUFIP1 counteracts cellular senescence [94]. Ribosomal protein Rps27l, a known regulator of the murine double minute 2 (MDM2)-p53 pathway, promotes p53 stability by inhibiting MDM2 binding to p53 [95]. Huang et al. [94] demonstrated that Rps27l stably interacts with NUFIP1 in bat fibroblasts, with this interaction enhanced under replication stress. NUFIP1 knockdown resulted in a significant accumulation of Rps27l in the nucleus and increased p53 activity under replication stress, suggesting that NUFIP1 inhibits the nuclear import of Rps27l, thereby affecting its binding to MDM2 and promoting p53 stabilization. Furthermore, NUFIP1 knockdown in human A549 cells revealed decreased nascent replication fork stability, indicating the conservation of this regulatory mechanism. This study indicates a potential link between NUFIP1 and cellular senescence, necessitating further investigation to validate its involvement in human cellular senescence. Moreover, NUFIP1 may exhibit wider interactions with cellular senescence, warranting additional research to elucidate these relationships (Fig. 3).

Fig. 3.

Molecular mechanisms of NUFIP1 in pathological processes Different colored lines represent distinct pathological processes. NUFIP1 regulates pathological processes such as unfolded protein response (UPR), ribophagy, nucleoside release, cellular senescence, PANoptosis, and DNA damage response. (Fig. 3A) Overactivation of the UPR can lead to cell apoptosis, whereas ribophagy suppresses the UPR and thereby inhibits apoptosis. Rapamycin upregulates NUFIP1 by inhibiting mTORC1, thereby suppressing the overactivated UPR. Under nutrient-deficient conditions, nucleosides generated through ribophagy are taken up by PDAC cells, thereby promoting tumor growth. (Fig. 3B) Low-protein diet conditions downregulate NUFIP1, thereby inhibiting the DDR. Downregulation of NUFIP1 activates the HMGA2/SAHF and p53/p21 pathways, thereby promoting cellular senescence. Downregulation of NUFIP1 activates the cGAS-STING (cyclic GMP-AMP synthase-stimulator of interferon genes) pathway, thereby exacerbating PANoptosis

The role of NUFIP1 in human diseases

Owing to its functional versatility and biological significance, the NUFIP1 protein is implicated in the pathogenesis of multiple human diseases (Table 1).

Table 1.

Research progress on NUFIP1 in human diseases

Diseases	Research progress	Mechanism/evidence	Related signaling pathways/genes/molecules	Reference
PDAC	NUFIP1 supports tumor growth	CAFs secrete nucleosides via ribophagy; PDAC cells uptake nucleosides to activate the MYC pathway	MYC pathway, Slc2a1, NUFIP1	[3]
CRC	NUFIP1 promotes tumor growth	NUFIP1 suppresses the HMGA2/SAHF and p53/p21 pathways	HMGA2/SAHF and p53/p21 pathways, NUFIP1	[92]
Neuroblastoma	Expression products of mutated NUFIP1 may promote neuroblastoma development	The NUFIP1 gene is mutated and highly expressed in neuroblastoma	NUFIP1, GATA, LPAR1	[96]
ALL	The ETV6-NUFIP1 fusion gene may be associated with high-risk ALL and poor prognosis	Patients carrying ETV6-NUFIP1 experienced serious adverse events and died within two months of diagnosis	ETV6-NUFIP1 fusion gene	[97]
13q14 Deletion Syndrome	NUFIP1 excluded as a candidate gene of 13q14 Deletion Syndrome	Minimal critical gene region linked to intellectual disability excludes the NUFIP1 gene locus		[98]
Neurological Injury	Neuroprotective role	Ribophagy alleviates ERS in cells	Pathways: IRE1, ATF6, PERK Molecules: CHOP, GRP78, Hsp70, eIF2α, NUFIP1	[8]
Malaria	ZNHIT3:NUFIP1 interaction exhibits strict species specificity	Overall, the 3D architecture of ZNHIT3:NUFIP1 dictates species specificity	ZNHIT3:NUFIP1	[10]
Sepsis	NUFIP1-mediated ribophagy antagonizes T lymphocyte apoptosis and PANoptosis in sepsis	NUFIP1-mediated ribophagy suppresses ERS by inhibiting the PERK pathway	PERK–ATF4–CHOP Pathway, cGAS-STING Pathway, NUFIP1, ZBP1	[4–6]
IBD	Impaired DDR due to NUFIP1 downregulation promotes inflammation	NUFIP1 facilitates the recruitment of the ATR–ATRIP complex by binding to RPA32	RPA,ATR-ATRIP,NUFIP1	[9]
Male obesity	SNP rs1706636 in the NUFIP1 gene correlates with male obesity	SNP screening results showed that rs1706636 was significantly associated with male obesity	rs1706636	[99, 100]
Glaucoma	NUFIP1 may mediate the autophagy of nuclear components damaged under CMS	Autophagy occurs without ribosomal degradation but rather facilitates the targeted degradation of mechanically damaged nuclear material.	NUFIP1, LC3	[101, 102]
Disuse muscle atrophy	NUFIP1-mediated ribophagy contributes to Disuse muscle atrophy	Cells reduce protein synthesis through ribosomal catabolism, and non-ribosomal biosynthesis is significantly reduced.	NUFIP1	[103–105]

Tumors

Tumor cells exhibit high consumption of glucose and glutamine, which significantly impacts tumor proliferation and metabolism[106–108]. NUFIP1-dependent ribophagy in CAFs promotes glucose uptake and utilization by tumor cells through activation of the MYC pathway[3]. In murine models, NUFIP1 inhibition in CAFs reduced tumor weight, suggesting NUFIP1’s pro-tumorigenic function in the TME(tumor microenvironment). Furthermore, Yuan observed high NUFIP1 expression in the stroma of 39 out of 80 PDAC patients, correlating with significantly reduced overall survival. In contrast, NUFIP1 expression in tumor cells did not affect survival. In vivo experiments revealed that the dual blockade via chloroquine (an autophagy inhibitor) plus glutaminase inhibitor markedly inhibited tumor growth, highlighting therapeutic promise. Specifically, with regard to the mechanism by which NUFIP1 supports tumor metabolism, small-molecule inhibitors could be designed to target NUFIP1 in CAFs, blocking its mediation of ribosomal RNA degradation and reducing nucleoside secretion, weakening metabolic support for pancreatic cancer cells; agents targeting the NUFIP1-dependent autophagy pathway could be developed to disrupt the interaction between NUFIP1 and proteins such as LC3, specifically inhibiting ribophagy and impairing the ability of CAFs to release nucleosides.

Notably, autophagy critically regulates TME in other cancer types. In squamous cell carcinoma, ribophagy in CAFs correlates with upregulated effector gene expression, essential for activating CAFs to sustain tumor progression[109]. Using an autophagy-dependent secretory mechanism, the cytokine HMGB1 (High Mobility Group Box-1) secreted by CAFs sustains luminal breast cancer cell stemness [110]. In summary, the critical role of NUFIP1-mediated ribophagy within the tumor microenvironment has been established. Moreover, a mouse model with fibroblast-specific knockout of NUFIP1 showed that NUFIP1 deficiency does not affect fibroblast activation or collagen deposition, suggesting that NUFIP1 could be a promising therapeutic target without compromising CAF function.

Shen’s study identified significant NUFIP1 upregulation in colorectal cancer, correlating with both tumor progression and adverse clinical outcomes[93]. Employing an integrated methodology encompassing database analysis, qPCR, and immunohistochemistry (IHC), the study validated the overexpression of NUFIP1 in CRC tissues and demonstrated a correlation between elevated NUFIP1 expression and diminished overall survival (OS), recurrence-free survival (RFS), event-free survival (EFS), and disease-free survival (DFS), as well as more advanced clinicopathological stages of CRC. Loss-of-function analysis indicated that NUFIP1 knockdown suppressed in vitro and in vivo cell growth, reduced viability/survival while inducing cell cycle arrest and apoptosis. Moreover, the study discovered that treatment with ursolic acid (UA), a natural anti-cancer triterpenoid, inhibited CRC cell proliferation, downregulated NUFIP1, and amplified knockdown effects. As previously noted, NUFIP1 knockdown elevated senescence-associated markers and concurrently upregulates the p53 pathway. Collectively, NUFIP1 promotes tumorigenesis via senescence modulation, with UA exhibiting CRC therapeutic potential through NUFIP1 downregulation [93].

In the study by Wei et al [96]., Whole-genome sequencing (WGS) and RNA sequencing (RNA-seq) were conducted on tumor samples obtained from a metastatic neuroblastoma patient at various time points (diagnosis, surgical resection, and metastasis). The analysis revealed 15 genes with consistent mutations across all three time points, thereby implicating them as potential cancer driver genes. Notably, only three genes exhibited a high expression proportion (>30%) of mutant alleles in the RNA-seq data, including NUFIP1, GATA2(GATA binding protein 2), and LPAR1 (Lysophosphatidic acid receptor 1). These findings implicate mutant NUFIP1 allele products in neuroblastoma pathogenesis, despite the underlying mechanisms remaining to be elucidated.

Furthermore, it has been documented[97] that the NUFIP1 gene can undergo fusion with the E-twenty-six variant 6 (ETV6) gene, which exhibits high variability, resulting in the formation of an ETV6-NUFIP1 fusion gene. This fusion gene may correlate with high-risk acute lymphoblastic leukemia (ALL) and its unfavorable prognosis. Patients harboring this fusion gene exhibited severe chemotherapy-induced neutropenia, septic shock, pneumonia, and multi-organ failure, culminating in mortality within two months of diagnosis confirmation. While this fusion gene may serve as a prognostic indicator, its influence on ALL pathobiology remains uncharacterized.

Neurodegenerative diseases

Fragile X Syndrome is caused by a deficiency in FMRP. NUFIP1, an interacting protein of FMRP, was initially hypothesized to be involved in Fragile X Syndrome based on early research [1]. NUFIP1 is highly expressed in neurons, specifically in functional synaptosomes, where it colocalizes with ribosomes. Bardoni implicated NUFIP1 in mRNA transport/localization and, in conjunction with FMRP, regulates local protein synthesis near synapses, thus contributing to the modulation of neuronal development and synaptic plasticity, based on its subcellular localization and nucleocytoplasmic shuttling function [12].

The NUFIP1 gene is situated within the 13q14.12 region. Research has implicated NUFIP1 as a significant candidate gene contributing to the intricate neurological phenotypes, particularly intellectual disability, observed in 13q14 deletion syndrome, with its location considered a core pathogenic region [98]. Mitter et al. reported NUFIP1 deletion in 17 of 22 patients exhibiting neurodevelopmental delay. The size of the 13q deletion correlated positively with the prevalence and severity of neurodevelopmental delay, suggesting that critical genes, such as NUFIP1, within the deleted region may impact neurodevelopmental processes [111]. Conversely, Privitera et al. conducted array-CGH analysis on seven patients with 13q deletion. Integrating these findings with existing data, they delineated a more concise minimal critical region associated with intellectual disability (ID) and global psychomotor developmental delay. Within this refined critical region, previously proposed candidate genes, including NUFIP1, were explicitly excluded [112].

Ribosomes are the primary organelles for protein synthesis, responsible for the production of a substantial fraction of cellular proteins. Ribosome degradation and the subsequent reduction in protein synthesis are critical for cell survival [113]. Baltanás et al. reported a correlation between ribophagy and neurodegenerative disorders. The researchers detected ribophagy in Purkinje cells of Purkinje cell degeneration (PCD) mice and suggested that the accumulation of DNA damage in Purkinje cells of PCD mice results in nucleolar disruption, polyribosome disassembly, and autophagic degradation of monoribosomes [114]. Carloni et al.’s research [7] demonstrated that the upregulation of ribophagy has a neuroprotective effect in animals with neonatal hypoxic-ischemia. The investigators observed that in hypoxia/ischemia (HI)-induced brain injury, hyperactivation of autophagy (rapamycin treatment) significantly diminished the activation of the UPR, indicating that ribophagy may mitigate ERS by reducing the protein synthesis load, thus decreasing apoptosis. Given the potential functional roles of ribophagy in diseases, NUFIP1 potentially mediates hypoxia/ischemia-induced brain injury via its ribosomal receptor function in ribophagy.

Of note, we have previously shown that NUFIP1 provides defense against propofol-mediated neurotoxicity[8]. We isolated hUMSC-derived NUFIP1-engineered exosomes, characterizing them via transmission electron microscopy (TEM), Flow NanoAnalyzer, qRT-PCR, and Western blot to validate their morphology, surface markers, and target gene expression. Following this, they established the optimal propofol exposure parameters to induce apoptosis in SH-SY5Y human neuroblastoma cells. Co-culturing SH-SY5Y cells with either NUFIP1 knocked down (NUFIP1-KD) or NUFIP1 overexpressed (NUFIP1-OE) exosomes revealed their impact on apoptosis. Results indicated that NUFIP1-KD exosomes significantly upregulated pro-apoptotic proteins Bax and c-Caspase 3, while downregulating the anti-apoptotic protein Bcl-2. Conversely, NUFIP1-OE exosomes exhibited the opposite trend. In vivo, NUFIP1-OE and NUFIP1-KD exosomes were administered intraperitoneally to neonatal rats with propofol-induced neurotoxicity. The NUFIP1-KD group exhibited significantly prolonged righting reflex recovery time and reduced performance in the MWM(Morris Water Maze) test, indicating exacerbated learning and memory deficits. Hematoxylin and Eosin (HE) staining and TUNEL staining results demonstrated significant hippocampal tissue atrophy and elevated apoptosis levels in this group. Conversely, the NUFIP1-OE group displayed significant behavioral improvements in the MWM test, with OE rats demonstrating enhanced spatial memory and reduced expression of apoptosis-related proteins in the hippocampus. Finally, we hypothesize that NUFIP1-engineered exosomes may exert neuroprotective effects by indirectly influencing cellular homeostasis through enhancing ribophagy, although the precise mechanism warrants further investigation.

Infectious diseases

Malaria, a prevalent and lethal disease, is induced by Plasmodium parasites, vectored to humans via Anopheles mosquitoes[115]. Chagot et al [10]. revealed that the ZNHIT3-NUFIP1 interaction displays significant cross-species specificity. Specifically, Plasmodium proteins pf-NUFIP1 and pf-ZNHIT3 do not form cross-interactions with their yeast or human homologs, which aligns with the failure of cross-species complex formation in protein co-expression experiments. Subsequent studies utilized AlphaFold for complex structure prediction and conducted structural analyses of the Plasmodium ZNHIT3:NUFIP1 complex via NMR structure determination and structural superimposition. Researchers validated the species-specific nature of the ZNHIT3:NUFIP1 interaction, and structural analyses indicated that the specificity is primarily governed by the overall tertiary structure rather than individual conserved residues.

The functional significance of the ZNHIT3-NUFIP1 interaction in stabilizing both proteins, maintaining normal snoRNA levels, and sustaining cellular growth rates has been demonstrated in both yeast and human systems[10]. Notably, it has been shown that snoRNAs in Plasmodium falciparum primarily exist as single-copy genes[116]. Consequently, any disruption to their expression or function lacks compensatory mechanisms, resulting in heightened sensitivity to perturbations in snoRNP assembly. Researchers hypothesize that this vulnerability may have driven the evolutionary acquisition of high structural stability in the ZNHIT3:NUFIP1 complex, ensuring robust snoRNP biogenesis. Supporting this hypothesis, the complex’s high stability was experimentally validated in follow-up studies[10]. The strict species specificity of the ZNHIT3-NUFIP1 interaction provides a structural basis for developing compounds that selectively target the Plasmodium NUFIP1:ZNHIT3 complex without affecting host protein functions. Furthermore, the complex’s high structural stability and critical role in Plasmodium further enhance its potential as a drug target.

Sepsis, a systemic inflammatory response syndrome (SIRS) initiated by infection, can result in multiple organ dysfunction and mortality [117–119]. Globally, despite significant efforts by the medical community, sepsis remains a life-threatening complication affecting millions of patients annually [66].T lymphocyte apoptosis is a critical mechanism of immunosuppression in sepsis [120, 121]. T cell apoptosis generally induces an immunosuppressed state, thereby increasing host susceptibility to sepsis and exacerbating disease severity [122–126]. We demonstrated that ERS-induced PERK-ATF4-CHOP activation can significantly promote NUFIP1-dependent ribophagy, reducing sepsis T cell apoptosis. As previously reported, we induced two sepsis models using LPS stimulation and CLP. For sepsis ribophagy analysis, we created NUFIP1-KD/OE human T cells (lentiviral delivery) and NUFIP1-KO mice. Our findings revealed that NUFIP1 knockdown markedly elevated T cell apoptosis but significantly decreased after Sal pretreatment, whereas NUFIP1 overexpression significantly reduced it. Consistent phenotypes occurred in CD4⁺ splenic T cells from wild-type and NUFIP1-KO mice. In NUFIP1 KO mice, T cell apoptosis was exacerbated, immunosuppression was aggravated, and the one-week mortality rate was significantly higher compared to wild-type mice, suggesting that NUFIP1-mediated ribophagy effectively protects T lymphocytes from apoptosis. Further animal experiments utilizing the CLP model showed that NUFIP1-deficient mice exhibited elevated GRP78, ATF4, and CHOP compared to wild-type mice, providing additional evidence that loss of NUFIP1 exacerbates ERS and apoptotic responses.

As previously demonstrated, NUFIP1-mediated ribophagy mitigates PANoptosis in septic CD4⁺ T cells. In alignment with observations in both the sepsis mouse model and Jurkat T cells, our clinical investigation indicated that peripheral blood CD4⁺ T cells from sepsis patients displayed increased ribophagy, significantly elevated ZBP1 expression, and heightened PANoptosis. Furthermore, the immune function of CD4⁺ T cells was compromised, as evidenced by impaired cellular activity. These clinical findings further support the hypothesis that NUFIP1-mediated ribophagy attenuates PANoptosis in CD4⁺ T cells through the cGAS-STING signaling pathway.

Sepsis-induced immunosuppression substantially increases patient mortality, underscoring the crucial need to maintain T cell function during sepsis management, given that T cell-mediated cellular immunity is vital for effective host defense [127–130]. Modulation or reversal of T lymphocyte apoptosis has been shown to effectively mitigate sepsis-induced immunosuppression [131, 132], indicating that NUFIP1 exerts a key protective function in T lymphocytes and presents significant therapeutic potential, with its clinical application likely to be a primary focus of future investigation. Furthermore, several aspects of our sepsis research require further clarification. Firstly, the observed correlation between ribosomes and ERS-related apoptotic pathways suggests novel avenues for investigating the interplay between ribosomes and the endoplasmic reticulum (ER). Secondly, while we have established that NUFIP1 protects T lymphocytes from apoptosis and PANoptosis via ribophagy, the precise mechanisms governing these two associated pathways remain to be elucidated.

mRNA-LNP therapeutics utilize lipid nanoparticles (LNPs) as carriers to deliver mRNA into cells, enabling the expression of functional proteins and achieving therapeutic goals such as protein replacement or immune modulation [133, 134]. During the immunosuppressive phase of sepsis, upregulation of NUFIP1 has been shown to effectively reduce immune cell death [4–6]. Employing mRNA-LNP therapeutics to elevate NUFIP1 expression in T cells and DCs holds promise for reducing immune cell death by modulating ribosomal homeostasis, representing a strategy worthy of exploration. In addition to reversing immunosuppression at its source, small-molecule inhibitors targeting downstream pathways, such as the PERK-ATF4-CHOP, EIF2AK3-ATF4-DDIT3, and cGAS-STING signaling axes, are also promising. Combined modulation of ribosomal homeostasis and endoplasmic reticulum stress pathways may constitute an effective therapeutic approach.

Moreover, our study still has potential biases. For example, although LPS treatment can strongly induce inflammatory responses, its effect is relatively singular and cannot fully recapitulate the complex pathophysiological processes of clinical sepsis. On the other hand, the CLP model is a more clinically relevant standard model that can mimic intra-abdominal infection and polymicrobial sepsis, but it is subject to procedural variability, which may introduce surgical bias and lead to inter-individual differences. Regarding animal selection, homozygous deficiency of NUFIP1 results in embryonic lethality; therefore, we used heterozygous mice in our experiments, which may introduce gene dosage effect bias. Future studies should validate these findings using conditional cell-specific knockout mouse models to overcome this limitation.

Inflammatory diseases

Ming et al.’s research suggests that NUFIP1 is crucial in IBD through its involvement in the DDR pathway[9]. Recently, it has been shown that intestinal cell death can initiate an inflammatory response[135], with programmed cell death driven by genomic instability in gut cells serving as a primary instigator of intestinal inflammation[136]. Subsequent investigations by Ming et al. demonstrated that compromised DDR due to NUFIP1 loss led to DNA damage accumulation. This effect promoted necroptosis of intestinal cells via activation of the ZBP1-RIPK3-MLKL pathway (RIPK3: Receptor-Interacting Serine/Threonine-Protein Kinase 3, MLKL: Mixed Lineage Kinase Domain-Like Pseudokinase), ultimately triggering intestinal inflammation. In adeno-associated virus (AAV) overexpression experiments, overexpression of wild-type NUFIP1 significantly reduced the DNA damage marker γH2A.X levels and mitigated inflammation in the IBD mouse model. However, this effect was not observed with the non-phosphorylatable mutant NUFIP1S283A. Similarly, studies revealed significantly reduced NUFIP1 in the gut of IBD patients, suggesting that NUFIP1 may hold therapeutic potential in inflammatory bowel disease.

It should be noted that this study included only 60 IBD patients, which limits the sample size. Additionally, animal experiments are typically performed under highly controlled conditions, whereas human diseases are influenced by multiple factors, including genetic diversity, environmental exposures, dietary habits, and the microbiome, resulting in greater complexity. Therefore, large-scale clinical studies are needed to further confirm the conclusions.

Based on current research, NUFIP1 functions as a homeostatic regulator in intestinal inflammation, and restoring NUFIP1 function may be a strategy to maintain intestinal integrity and mitigate inflammation. AAV is a relatively mature gene therapy vector in current clinical applications and has been used for in vivo gene delivery in multiple genetic diseases [137, 138]. Ming et al. used AAV9 to overexpress wild-type NUFIP1 in the mouse intestine, which effectively restored the DNA damage response and alleviated inflammation, suggesting potential translational prospects for gut-targeted AAV delivery of NUFIP1 in humans. Moreover, given that phosphorylation of NUFIP1 is a critical step for its function, future efforts could explore small-molecule drugs that enhance this phosphorylation process to boost NUFIP1 activity. Compared to pharmacological interventions, nutritional modulation may represent a more cost-effective strategy for IBD patients, as NUFIP1 function is regulated by amino acid levels.

Notably, while numerous studies highlight the health risks associated with high-protein diets, affecting the cardiovascular system, kidneys, gut, and lifespan[139–141], the findings of this study emphasize the need to address the dangers associated with low-protein diets.

Metabolic diseases

A research study has demonstrated that males with fragile X syndrome are more prone to developing obesity [99]. Single-nucleotide polymorphisms (SNPs) denote genetic variations at specific nucleotide positions (A, T, C, or G) within the human genome across different individuals. The SNP rs17066364 is located within the NUFIP1 gene. To assess whether bone mineral density-associated SNPs (BMD-SNPs) are correlated with phenotypes related to obesity, Cha et al. conducted comprehensive analyses [100]. They selected 18 BMD-associated SNPs identified through GWAS and performed two screening phases in a cohort of 2362 Korean adults, excluding SNPs with Hardy-Weinberg equilibrium deviation or lack of association to adiposity measures (e.g., BMI, waist circumference), and waist-to-hip ratio. Among the retained SNPs, rs17066364 demonstrated a significant association with male abdominal obesity traits, whereas none occurred in females, indicating sex-dimorphic genetic effects of this SNP. Consequently, rs17066364 may function as a genetic biomarker for predicting the risk of abdominal obesity.

Non-alcoholic fatty liver disease (NAFLD) is a condition characterized by abnormal accumulation of fat in the liver in the absence of excessive alcohol consumption. Its pathological spectrum ranges from simple steatosis to non-alcoholic steatohepatitis (NASH), fibrosis, and even cirrhosis [142]. NAFLD is closely associated with metabolic syndrome and is considered the hepatic manifestation of metabolic syndrome [142]. The pathogenesis of NAFLD involves multiple forms of autophagy, including lipophagy, mitophagy, and reticulophagy [143–146]. A thought-provoking hypothesis is whether NUFIP1, an autophagy receptor with amino acid-sensing capability, participates in the development of NAFLD. Although many aspects of the disease’s mechanisms remain unclear, NAFLD is undoubtedly closely linked to atherosclerosis and cardiovascular diseases [147]: both NAFLD and insulin resistance center on metabolic dysregulation, exhibit significant interdependence, and mutually exacerbate each other; insulin resistance promotes systemic inflammation, endothelial dysfunction, and lipid metabolism disorders, thereby accelerating the progression of atherosclerosis. Meanwhile, eosinophil chemokine levels are elevated in NAFLD patients and correlate significantly with carotid intima-media thickness [147]. NUFIP1 plays a central role in metabolic sensing and maintenance of cellular homeostasis, both of which are core mechanisms in atherosclerosis development [148]. These findings imply that NUFIP1 may occupy a particularly intriguing yet unexplored position, potentially serving as a key player in the complex and profound relationship between NAFLD and atherosclerosis. However, the causal relationships among the three require further investigation.

Other diseases

Glaucoma is characterized by optic nerve degeneration and distinct visual field deficits, with elevated intraocular pressure (IOP) serving as the primary risk factor[101, 102]. Elevated IOP exerts mechanical stress on trabecular meshwork (TM) cells, and dysfunction of TM cells constitutes a key pathogenic mechanism [149]. Prior investigations [150, 151] have documented autophagic activity in human trabecular meshwork (hTM) cells subjected to mechanical stretching conditions. Shim et al. demonstrated that under simulated elevated IOP conditions, specifically cyclic mechanical stretch (CMS), microtubule-associated protein 1 light chain 3 (LC3) accumulates within the nucleus of hTM cells and co-immunoprecipitates with the nuclear-localized factor NUFIP1. Subsequently, LC3 facilitates the translocation of NUFIP1 from the nucleus to autophagosomes and lysosomes. Experimental application of CMS to both wild-type and autophagy-deficient hTM cells (with ATG5/7 knockdown), as well as starvation-induced autophagy via HBSS treatment, validated the efficacy of ATG5/7 suppression through decreased LC3–II levels. Results indicated a reduction in ribosomal proteins RPL26 and RPS15A in starvation conditions, whereas no significant change was observed in CMS-treated groups, suggesting that ribophagy is not activated under mechanical stretch. These findings imply that NUFIP1 may function as a selective autophagy receptor for an as-yet-unidentified non-ribosomal substrate. Existing evidence indicates that nuclear LC3 monitors damaged nuclear components, which are subsequently degraded via cytoplasmic autophagy [152–155]. Based on these findings, Shim et al. posited that NUFIP1 potentially facilitates the targeting of mechanically damaged nuclear components under CMS. Nevertheless, its specific substrates and roles in the pathogenesis of glaucoma require further investigation. Future research may concentrate on elucidating the precise mechanisms and therapeutic potential of NUFIP1.

Studies have demonstrated that ribosomal catabolism occurs during disuse-induced skeletal muscle atrophy, with diminished protein biosynthesis serving as a key pathogenic factor [103, 104]. The etiology of decreased protein synthesis varies among different forms of myofiber atrophy. In cancer cachexia-associated muscle wasting, the decline in protein synthesis results from suppressed rDNA transcriptional activity [105]. Conversely, disuse atrophy is primarily characterized by enhanced ribosomal degradation rather than a significant reduction in ribosome biogenesis. Skeletal muscle unloading protocols, such as hindlimb suspension in murine models, induce disuse atrophy, as evidenced by Kotani et al., who employed hindlimb unloading combined with daily pulsed electromagnetic stimulation (pEMS) as an intervention [11]. Their findings indicated that unloading decreased ribosomal protein content and upregulated the expression of the ribophagy receptor NUFIP1. Although pEMS attenuated LC3–II accumulation, it did not significantly alter NUFIP1 expression levels. NUFIP1-mediated modulation of ribophagy represents a potential therapeutic target for specific myopathies characterized by disuse atrophy, and future investigations should evaluate the clinical therapeutic potential of NUFIP1 (Fig. 4).

Fig. 4.

NUFIP1 and human diseases NUFIP1 plays a pleiotropic role in various human diseases. The protein mediates cellular processes such as ribophagy, DNA damage response (DDR), and cellular senescence, collectively regulating cell proliferation and homeostasis. In oncology, aberrant NUFIP1 expression promotes tumor growth by enhancing tumor cell proliferation and glucose metabolism. In neurological disorders, its interaction with FMRP in mRNA transport and synaptic local protein synthesis impairs neuronal outgrowth, contributing to fragile X syndrome, while in Purkinje cells, it modulates responses to ischemic brain injury. NUFIP1 also contributes to immune dysregulation by regulating apoptosis and PANoptosis in CD4⁺ T cells during sepsis, and exacerbates inflammatory bowel disease through DDR modulation in intestinal cells. Furthermore, it is associated with glaucoma under mechanical stress and disuse muscle atrophy. Lastly, its gene coding region serves as a genetic risk marker for multiple diseases

Conclusions and perspectives

Despite advances demonstrating NUFIP1’s substantial therapeutic potential across multiple disease models, research remains predominantly at the preclinical stage, and its translational applicability in clinical settings warrants further investigation. Additionally, numerous molecular pathways involving NUFIP1 are yet to be fully elucidated. For example, in glaucoma, significant knowledge gaps persist regarding NUFIP1-associated mechanisms, including the identification of potential novel targets during cellular stress responses, such as CMS, and the mechanistic link between GCN2 activation and NUFIP1 downregulation during DNA damage response. Within the context of sepsis, the precise mechanisms governing the PERK-ATF4-CHOP pathway and the cGAS-STING pathway necessitate further investigation. Furthermore, the regulatory function of NUFIP1 in cellular senescence is not fully characterized; research into the modulation of cellular senescence by NUFIP1 may yield significant insights for cancer therapeutics. Although still in the stage of hypothesis, the potential relationship between NUFIP1 and both NAFLD and atherosclerosis warrants further investigation. Notably, Rpl12, recently identified as a ribophagy receptor, may represent an overlooked factor in previous studies; investigating Rpl12 could be pivotal for understanding NUFIP1’s involvement in human diseases.

The “homeostasis integrator” theory posits that NUFIP1, located at the intersection of nutrient, metabolic, and DNA damage signaling pathways, responds to diverse intracellular stress signals through its multifunctional molecular architecture, balances the allocation of cellular resources, and thereby maintains cellular stability. Intriguing functional crosstalk may exist among NUFIP1’s roles. Under acute nutrient stress, cells prioritize energy conservation for survival, leading to the translocation of NUFIP1 to the cytoplasm to participate in ribophagy, during which its DDR function may be suppressed. Conversely, upon DNA damage, functional priority shifts toward genome integrity, with NUFIP1 translocating to the nucleus to engage in DDR. We speculate that under such conditions, active ribophagy may be transiently inhibited to release NUFIP1 for DDR participation. Based on this, we hypothesize potential manifestations of this relationship in specific diseases. For example, in the tumor microenvironment, CAFs chronically exposed to nutrient stress may lock NUFIP1 into a pro-ribophagy state, facilitating nucleotide supply to tumor cells but at the cost of impaired DDR and increased genomic instability in CAFs. This is a hypothesis awaiting future validation. Similarly, a potential trade-off may exist between NUFIP1’s function in ribophagy and ribosome biogenesis (via snoRNP assembly), with its functional outcome dependent on stress type, nutrient status, and other contextual factors.

The therapeutic translation of NUFIP1 faces numerous challenges. For instance, NUFIP1 exhibits variable expression patterns across different tissues and cell types, making targeted delivery a key challenge. Although vectors such as AAV or mRNA-LNP can be used to deliver NUFIP1 or its regulatory factors, issues such as off-target effects, immunogenicity, and in vivo clearance must be overcome. While small-molecule compounds that promote NUFIP1 phosphorylation hold promise, drug development in this area remains difficult. Given that NUFIP1 is involved in processes such as cellular senescence and apoptosis, the long-term safety of interventions must be comprehensively evaluated, particularly with regard to oncogenic risks.

A common concern is that the research described in this paper was primarily conducted using animal models, with insufficient clinical validation in humans. There are significant differences between animals and humans in genetic background, immune system function, and metabolic characteristics, meaning that the molecular mechanisms and phenotypes observed in animal models may not fully reflect the complexity of human diseases. Therefore, further clinical studies are necessary to determine the applicability of these findings in human populations.

Despite these challenges, NUFIP1 exhibits considerable promise as a therapeutic target in oncology, infectious diseases, neurodegeneration, and inflammatory diseases. Clarifying its molecular pathways and advancing clinical translation are poised to be central themes in future research endeavors.

Supplementary Information

Below is the link to the electronic supplementary material.

Abbreviations

AAV

Adeno-associated virus

ALL

Acute lymphoblastic leukemia

ATG1

Autophagy-related gene 1

ATG7

Autophagy-related gene 7

ATF4

Activating Transcription Factor 4

ATF6

Activating Transcription Factor-6

ATM

Ataxia-Telangiectasia Mutated

ATR

Ataxia-Telangiectasia and Rad3-related

BMD-SNPs

Bone mineral density-associated SNPs

Bcl-2

B-cell lymphoma 2

Bax

Bcl-2-associated X protein

BRCA1

Breast cancer type 1 susceptibility protein

CAFs

Cancer-associated fibroblasts

CHOP

C/EBP Homologous Protein

CLP

Cecal ligation and puncture

CM

Conditioned medium

CMS

Cyclic mechanical stretch

Co-IP

Co-immunoprecipitation

CRC

Colorectal cancer

CRM1

Chromosome Region Maintenance 1

C2H2

Cys2His2

c-Caspase 3

Cleaved Caspase 3

cGAS-STING

Cyclic GMP-AMP synthase-stimulator of interferon genes

DCs

Dendritic cells

DDR

DNA damage response

DSBs

Double-strand breaks

DDIT3

DNA damage-inducible transcript 3

DFS

Disease-free survival

DNA-PK

DNA-dependent Protein Kinase

DSB

Double-strand break

EFS

Event-free survival

EIF2AK3

Eukaryotic translation initiation factor 2 alpha kinase 3

ERS

Endoplasmic reticulum stress

ETV6

E-twenty-six variant 6

eIF2α

Eukaryotic Initiation Factor 2α

FMRP

Fragile X mental retardation protein

GATA2

GATA binding protein 2

GCN2

General Control Nonrepressed 2

H3K9me3

Histone H3 lysine 9 trimethylation

HE

Hematoxylin and Eosin

HI

Hypoxia-ischemia

HMGA2

High mobility group A2

HMGB1

High Mobility Group Box-1

HP1γ

Heterochromatin Protein 1 γ

Hsp70

Heat Shock Protein 70

Hsp90

Heat Shock Protein 90

HU

Hydroxyurea

IAV

Influenza A virus

IBD

Inflammatory bowel disease

IHC

Immunohistochemistry

IFN-I

Type I interferons

IOP

Intraocular pressure

IRE1

Inositol-Requiring Enzyme 1

LC3B

Microtubule-associated protein 1A/1B light chain 3B

LIRs

LC3-interacting regions

LNPs

Lipid nanoparticles

LP

Low-protein

LPAR1

Lysophosphatidic acid receptor 1

LPS

Lipopolysaccharide

MDM2

Murine double minute 2

MLKL

Mixed Lineage Kinase Domain-Like Pseudokinase

mTOR

Mechanistic target of rapamycin

mTORC1

MTOR complex 1

mTORC2

MTOR complex 2

MYC

MYC proto-oncogene

NAFLD

Non-alcoholic fatty liver disease

NASH

Non-alcoholic steatohepatitis

NES

Nuclear export signal

NHEJ

Non-homologous end joining

hNHP2

Human Non-Histone Protein 2

NLRP12

NACHT, LRR, and PYD domains-containing protein 12

NLS

Nuclear localization signal

NOP56

Non-ribosomal protein 56

NOP58

Non-ribosomal protein 58

NUFIP1

Nuclear FMR1-interacting protein 1

OS

Overall survival

PCD

Purkinje cell degeneration

PDAC

Pancreatic ductal adenocarcinoma

PEP

Proline-Enriched Peptide

PERK

PKR-Like ER Kinase

Pih1

Phosphatase 2A inhibitor 1

pEMS

Pulsed electromagnetic stimulation

R2TP

Rvb1-Rvb2-Tah1-Pih1

RNA-seq

RNA sequencing

RPA

Replication Protein A

RBM

RPA32-binding motif

RFS

Recurrence-free survival

RIPK3

Receptor-Interacting Serine/Threonine-Protein Kinase 3

SAHF

Senescence-Associated Heterochromatin Foci

SBP2

Selenocysteine Insertion Sequence Binding Protein 2

SIRS

Systemic inflammatory response syndrome

Slc2a1

Solute Carrier Family 2 Member 1

SNPs

Single-nucleotide polymorphisms

snoRNP

Small molecule nucleolar ribonucleoprotein

ssDNA

Single-stranded DNA

TME

Tumor microenvironment

TM

Trabecular meshwork

UA

Ursolic acid

UPR

Unfolded protein response

WGS

Whole-genome sequencing

Xbp-1

X-Box Binding Protein 1

ZBP1

Z-DNA Binding Protein 1

ZNHIT3

Zinc finger HIT domain–containing protein 3

Authors’ contributions

Zhifu Li: Drafting and writing of manuscript. Yichen Bao: Drawing of tables and figures. Xingpeng Yang: Bibliographic retrieval; Yizhao Ma: Bibliographic retrieval; Lin Qi: Organization of references; Xiaohui Du: Conception and design of the work; Revision and final approval of the version to be published; Pengyue Zhao: Conception and design of the work; Revision of manuscript.

Funding

This work was supported by the National Natural Science Foundation of China (Nos. 82372158, 82502590).

Data availability

No datasets were generated or analysed during the current study.

Declarations

Ethics approval and consent to participate

Not applicable.

Consent for publication

All of the authors are aware of and agree to the content of the paper and to being listed as co-authors.

Competing interests

The authors declare no competing interests.