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NPM1

Nucleophosmin 1 (NPM1), also known as B23 or numatrin, is a highly conserved, ubiquitously expressed phosphoprotein encoded by the NPM1 gene on chromosome 5q35.1 in humans.^[1] This 294-amino-acid protein, with a molecular weight of approximately 37 kDa, primarily localizes to the nucleolus of proliferating cells, where it functions as a molecular chaperone involved in essential cellular processes such as ribosome biogenesis, histone assembly, and centrosome duplication.^[2] NPM1 shuttles dynamically between the nucleolus, nucleoplasm, and cytoplasm, enabling its multifaceted roles in maintaining cellular homeostasis and responding to stress.^[1] Structurally, NPM1 features an N-terminal oligomerization domain that facilitates its assembly into pentameric or decameric complexes, a central acidic region for binding histones and other acidic proteins, and a C-terminal domain rich in aromatic and basic residues that interacts with nucleic acids and ATP.^[2] These domains allow NPM1 to exhibit chaperone-like activity, preventing protein aggregation and aiding in the transport of ribosomal components from the nucleus to the cytoplasm.^[1] Post-translational modifications, including phosphorylation, acetylation, and sumoylation, regulate its localization and function, with phosphorylation particularly influencing its nucleolar retention during interphase.^[2] Beyond its structural roles, NPM1 participates in a wide array of cellular functions, including the regulation of p53-mediated apoptosis through interactions with tumor suppressors like ARF and MDM2, as well as contributions to DNA damage repair pathways such as homologous recombination and base excision repair.^[2] It also supports chromatin remodeling, mRNA processing, and embryogenesis, underscoring its importance in both normal development and stress responses.^[1] In proliferating cells, NPM1 is one of the most abundant proteins in the nucleolus, highlighting its pivotal role in nucleolar architecture and ribosome assembly.^[2] Dysregulation of NPM1 is strongly implicated in oncogenesis, with mutations occurring in approximately 30% of acute myeloid leukemia (AML) cases, often leading to aberrant cytoplasmic localization (NPM1c+) that disrupts its tumor-suppressive functions and promotes leukemogenesis.^[2] Overexpression of NPM1 has been observed in various solid tumors, including prostate, breast, and gastric cancers, where it acts as a proto-oncogene by enhancing cell survival and proliferation.^[2] Conversely, NPM1 can function as a tumor suppressor in certain contexts, such as by stabilizing p53; its genetic alterations, including translocations like NPM1-ALK fusions in lymphomas, further underscore its dual role in hematological and solid malignancies.^[2]

Discovery and Nomenclature

Initial Identification

NPM1 was first identified as a major nucleolar protein in 1973 through two-dimensional polyacrylamide gel electrophoresis of nucleolar extracts from normal rat liver and Novikoff hepatoma ascites cells, where it appeared as a prominent acidic spot indicative of high abundance in proliferating cells.^[3] This technique separated over 100 nucleolar proteins, highlighting NPM1 (later named B23 based on its position as the 23rd spot in the gel pattern) as one of the most abundant components, comprising up to 0.5% of total cellular protein in tumor cells.^[4] The protein was subsequently characterized as a phosphoprotein in 1974 via in vivo radiolabeling with [^{32}P]orthophosphate in Novikoff hepatoma cells, revealing its phosphorylation by nuclear kinases.^[5] In the early 1980s, further experiments using HeLa cells confirmed NPM1's high abundance and dynamic phosphorylation through radiolabeling studies and two-dimensional gel electrophoresis. NPM1 constitutes approximately 20 times more protein in exponentially growing cells compared to quiescent ones.^[6] Key experiments demonstrated cell cycle-dependent phosphorylation, with increased labeling during G2/M phases, suggesting regulatory roles in nucleolar function tied to proliferation.^[7] These findings established NPM1 as a major nucleolar phosphoprotein, initially termed B23, with its alternative name numatrin assigned in 1988 following identification as a substrate for casein kinase II.^[8] Early observations of NPM1's nucleocytoplasmic shuttling emerged in the late 1980s and early 1990s, particularly in response to cellular stress and viral infections. For instance, treatment of HeLa cells with actinomycin D induced translocation of NPM1/B23 from the nucleolus to the nucleoplasm and cytoplasm, indicating stress-responsive mobility.^[9] Similar shuttling was noted in HL-60 cells treated with iron chelators like deferoxamine, as well as during viral infections, such as with adenovirus, where NPM1 facilitated viral DNA replication by moving to the cytoplasm to interact with viral components.^[10]^[11] These initial biochemical characterizations laid the groundwork for later molecular studies on gene cloning.

Gene Cloning and Naming

The human NPM1 gene was cloned in 1989 through screening of a λgt11 cDNA expression library derived from human placenta, yielding a full-length cDNA sequence of 1.3 kb that encodes a 294-amino-acid protein.^[12] This cloning effort identified the gene as encoding nucleophosmin, a nucleolar phosphoprotein previously known from protein studies, and established early aliases such as NPM and B23.^[12] Subsequent analyses in the early 1990s further characterized related pseudogenes but confirmed the primary cDNA sequence's integrity. The official Human Genome Nomenclature Committee (HGNC) symbol for the gene, NPM1, was approved to standardize its designation, distinguishing it from related family members, with the full name nucleophosmin 1.^[13] Synonyms approved by HGNC include B23, NPM, nucleolar phosphoprotein B23, and numatrin, reflecting its historical identification as a major nucleolar protein.^[13] Early chromosomal mapping of NPM1 to 5q35 was achieved in 1994 using fluorescence in situ hybridization (FISH) on metaphase chromosomes from patients with anaplastic large cell lymphoma carrying the t(2;5)(p23;q35) translocation, which fuses NPM1 to the ALK gene on 2p23.^[14] This localization was corroborated by Southern blot analysis of somatic cell hybrids, confirming the gene's position in the 5q35 region.^[14]

Gene Characteristics

Genomic Organization

The NPM1 gene is located on the long arm of chromosome 5 at cytogenetic band 5q35.1, with genomic coordinates spanning from 171,387,116 to 171,411,810 on the GRCh38 reference assembly, encompassing approximately 24.7 kb of DNA.^[1] This gene structure includes 11 exons in its canonical transcript, with the full gene utilizing 12 exons across all isoforms as annotated in reference databases.^[1]^[15] The canonical isoform, NPM1.1 (also known as B23.1), is generated through the splicing of 11 exons (skipping exon 10), with exon lengths varying from 58 bp to 358 bp, producing a mature mRNA of about 1.3 kb that encodes a 294-amino-acid protein.^[16] Exon-intron boundaries adhere to the consensus splice site motifs, primarily GT at the 5' donor sites and AG at the 3' acceptor sites, ensuring precise removal of 10 introns during pre-mRNA processing; introns range in size from several hundred base pairs to over 5 kb, contributing to the overall genomic span.^[16] This splicing pattern defines the full-length NPM1.1 transcript (NM_002520.7), which includes untranslated regions flanking the coding sequence.^[1] NPM1 exhibits strong evolutionary conservation across mammalian species, reflecting its essential roles in cellular processes. The mouse ortholog, Npm1, shares approximately 86% amino acid sequence identity with human NPM1 in the protein-coding regions, while orthologs in other mammals such as rat and chimpanzee show even higher similarity exceeding 90% in conserved domains.^[17] This high degree of sequence identity underscores the functional importance of NPM1's genomic architecture from rodents to primates.^[18]

Expression Regulation

The NPM1 gene exhibits ubiquitous expression across various normal human tissues, reflecting its essential roles in fundamental cellular processes such as ribosome biogenesis and protein chaperoning.^[19] Expression levels are particularly elevated in proliferating tissues, including bone marrow and spleen, where NPM1 supports active cell division and growth.^[19]^[20] This pattern aligns with NPM1's higher abundance in rapidly dividing cells compared to quiescent ones, underscoring its association with cell proliferation.^[20] At the transcriptional level, NPM1 expression is governed by a TATA-less promoter lacking a canonical TATA box, which relies on alternative initiation mechanisms for basal activity.^[21] Key regulatory elements within this promoter include multiple Sp1 binding sites in the upstream region, which facilitate transcription factor recruitment and enhance promoter activity in proliferating cells.^[21] The promoter's cell cycle-dependent nature contributes to upregulated NPM1 transcription during phases of active proliferation, such as S phase, ensuring sufficient protein levels for nucleolar functions.^[20] Additional upstream elements, like AP-1 and YY1 sites, further modulate this regulation in response to growth signals.^[21] Post-transcriptional control of NPM1 involves microRNA-mediated repression, where miRNAs bind to the 3' untranslated region (3' UTR) of the mRNA to inhibit translation or promote degradation.^[22] For instance, miR-337-5p targets the NPM1 3' UTR, fine-tuning expression levels in hematopoietic cells to prevent overexpression during steady-state conditions.^[22] Such mechanisms help maintain balanced NPM1 protein availability in normal tissues. NPM1 produces multiple isoforms through alternative splicing of its 12 exons, with NPM1.1 (also known as R1 or B23.1) being the predominant variant in normal cells, accounting for the majority of transcripts and exhibiting canonical nucleolar localization.^[23] Minor isoforms, such as R2 (B23.2), arise from exclusion of exons 11 and 12, resulting in altered C-terminal domains that shift localization to the nucleoplasm or cytoplasm, potentially modulating isoform-specific functions in proliferating compartments like bone marrow.^[23] These variants are expressed at low levels in normal tissues but contribute to regulatory diversity without disrupting overall NPM1 homeostasis.^[23]

Protein Structure

Domain Composition

NPM1, also known as nucleophosmin, is a 294-amino acid protein with a calculated molecular weight of 32.6 kDa, although it typically appears at approximately 37 kDa on SDS-PAGE due to its highly phosphorylated state.^[24] The protein exhibits an overall acidic character, consistent with its domain composition rich in negatively charged residues. The N-terminal oligomerization domain spans residues 1–120 and forms the core folded region of NPM1, enabling pentamer assembly through hydrophobic interfaces that contribute to the protein's structural stability.^[25] This domain also incorporates two nuclear export signals (NES) at positions 42–49 and 94–102, which are embedded within the sequence to regulate subcellular localization.^[26] Adjacent to the N-terminal domain lies the central acidic domain, encompassing residues 118–125 (part of broader acidic tracts from 119–133 and 161–188), a negatively charged region composed primarily of aspartic and glutamic acid residues that imparts electrostatic properties suitable for histone interactions.^[27] The C-terminal nucleic acid-binding domain, covering residues 243–294, is an arginine-rich motif that adopts a three-helix bundle structure, facilitating non-specific binding to RNA and DNA.^[28] This domain includes a nucleolar localization signal (NoLS) defined by tryptophan residues at positions 288 and 290.^[29]

Oligomerization and Modifications

NPM1 primarily assembles into symmetric pentamers through interactions mediated by its N-terminal oligomerization domain, which forms a stable β-barrel structure stabilized by hydrophobic contacts and hydrogen bonds at the protomer interfaces. This pentameric configuration predominates under physiological conditions, exhibiting high-affinity assembly with dissociation constants in the nanomolar range, ensuring robust oligomerization in the nucleolar environment. The N-terminal domain's structural polymorphism allows flexibility, but the wild-type pentamer remains tightly associated, contributing to NPM1's multivalent interactions within the nucleolus. Post-translational modifications dynamically regulate NPM1's oligomerization, localization, and activity. Phosphorylation at Ser125, catalyzed by CDK1 and Aurora B during mitosis, occurs within the N-terminal domain and promotes partial dissociation of the pentamer, facilitating NPM1's redistribution from the nucleolus to the nucleoplasm and centrosomes.^[30] Acetylation at multiple lysine residues (e.g., Lys212, Lys215, Lys229, Lys230, Lys257, Lys267, Lys292) by p300 acetyltransferase enhances NPM1's association with transcriptionally active chromatin in the nucleoplasm, while unacetylated forms favor nucleolar retention through preserved oligomerization and interactions with nucleolar components.^[31] Additionally, SUMOylation at Lys263, induced under cellular stress conditions, modulates NPM1's subcellular localization and supports survival pathways by altering its binding affinities and shuttling dynamics.^[32] NPM1's nucleocytoplasmic shuttling is governed by a balance between nuclear import and export mechanisms influenced by its modifications. The N-terminal nuclear export signals (NES) interact with CRM1 (exportin-1) to mediate CRM1-dependent nuclear export, allowing NPM1 to traffic to the cytoplasm.^[26] Conversely, nuclear import is facilitated by a bipartite nuclear localization signal (NLS) in the central domain (residues 141-157), which binds importin α/β heterodimers to enable active transport into the nucleus.^[26] Phosphorylation and other modifications fine-tune this equilibrium, with mitotic phosphorylation enhancing export and nucleolar retention signals promoting import and accumulation in the nucleolus.^[33]

Cellular Functions

Chaperone Activities

Nucleophosmin (NPM1) functions as a histone chaperone, primarily interacting with core histones H3 and H4 to prevent their aggregation and facilitate the assembly of H3-H4 tetramers essential for nucleosome formation and chromatin remodeling. The central region of NPM1 contains acidic patches (AD2 and AD3) that mediate binding to the basic histone tails, shielding them from non-specific interactions and aggregation under physiological conditions. This binding is crucial during DNA replication, where NPM1 ensures the faithful inheritance of parental nucleosomes, including repressive marks like H3K27me3, by coordinating with replication factors such as MCM2 and the Polycomb repressive complex 2 (PRC2). Depletion of NPM1 leads to disrupted nucleosome assembly and altered gene expression, underscoring its role in maintaining chromatin integrity.^[34] In addition to its histone-specific functions, NPM1 exhibits general molecular chaperone activity in the nucleolus, assisting in the proper folding and stability of client proteins such as p53 and p14ARF, particularly under cellular stress conditions like heat shock. By sequestering these proteins in the nucleolus, NPM1 prevents their misfolding and degradation; for instance, it inhibits MDM2-mediated ubiquitination of p53, thereby enhancing p53 stability and promoting stress-induced responses such as apoptosis or senescence. Similarly, NPM1 acts as a nucleolar reservoir for p14ARF, regulating its release to modulate p53 activity during oncogenic stress. These interactions highlight NPM1's protective role against proteotoxic stress in the nucleolus.^[19] The chaperone mechanism of NPM1 is ATP-independent, relying on its oligomeric structure—primarily pentameric assemblies formed by the N-terminal domain—to create a hydrophobic shield via the C-terminal domain and acidic intrinsically disordered regions. This architecture traps aggregation-prone hydrophobic regions of client proteins, preventing misfolding. In vitro assays demonstrate NPM1's efficacy in retarding amyloid formation, such as delaying Aβ42 fibrillation in a dose-dependent manner, and protecting denatured proteins from aggregation, consistent with its role as a holdase chaperone. The central acidic domain, briefly referenced for enabling histone binding, contributes to this broader client recognition without requiring energy input.^[35]^[19]

Ribosome Biogenesis

Nucleophosmin 1 (NPM1), also known as B23, plays a critical role in ribosome biogenesis by facilitating multiple stages of ribosomal subunit assembly within the nucleolus. As an abundant nucleolar phosphoprotein, NPM1 acts as a chaperone that supports the maturation of pre-ribosomal ribonucleoprotein (RNP) complexes, ensuring efficient production of functional 40S and 60S subunits. Its involvement spans from pre-rRNA processing to the shuttling and integration of ribosomal proteins, ultimately contributing to the quality control of nascent ribosomes. Disruptions in NPM1 function, such as through depletion or mutation, lead to defects in ribosome assembly, highlighting its indispensable nature in cellular proliferation and homeostasis.^[36] In rRNA processing, NPM1 binds directly to pre-rRNA transcripts, associating with pre-ribosomal particles to promote their maturation. Specifically, NPM1 exhibits endoribonuclease activity that facilitates the cleavage of the 32S pre-rRNA to generate the mature 28S rRNA, a key step in 60S subunit formation. This enzymatic function is supported by its interaction with the pre-rRNA backbone, where NPM1 stabilizes intermediates and prevents degradation. Studies using small interfering RNA (siRNA) knockdown demonstrate that NPM1 inhibition impairs this cleavage event, resulting in reduced levels of mature 28S rRNA and accumulation of processing intermediates. Although NPM1 primarily acts in later nucleolar stages, its binding supports the overall fidelity of rRNA maturation by coordinating with other nucleolar factors.^[36] NPM1 is essential for the nucleocytoplasmic shuttling of ribosomal proteins, enabling their import into the nucleolus for incorporation into pre-ribosomal complexes. It directly interacts with small subunit ribosomal proteins (RPS), such as RPS9, as well as large subunit proteins like RPL5 and RPL23, facilitating their transport from the cytoplasm to the nucleolus. For instance, NPM1 chaperones the 5S rRNA-RPL5 complex, utilizing its nuclear localization signals to mediate nucleolar accumulation and subsequent assembly into pre-60S particles. This shuttling is CRM1-dependent for export but relies on NPM1's oligomeric structure for efficient import. Once in the nucleolus, NPM1 coordinates with nucleolar proteins (NOPs), including NOPP34 and PES1, to organize the hierarchical assembly of 40S and 60S subunits. These interactions ensure that ribosomal proteins are delivered in a timely manner to pre-rRNA scaffolds, preventing misassembly and supporting the maturation of both subunit types.^[36]^[37] Regarding quality control, NPM1 enforces checkpoints to prevent the export of immature or defective ribosomal subunits from the nucleolus to the cytoplasm. By binding to pre-ribosomal RNPs, NPM1 stabilizes functional complexes while inhibiting the nuclear export of aberrant particles, thereby maintaining nucleolar integrity. Depletion studies reveal that loss of NPM1 leads to the accumulation of aberrant pre-40S particles, characterized by incomplete rRNA processing and improper protein incorporation, which triggers nucleolar stress and cell cycle arrest. In NPM1 knockout mice, ribosome biogenesis is severely compromised, resulting in hematopoietic defects and embryonic lethality between E11.5 and E12.5 due to insufficient mature ribosomes.^[36]^[38]

Transcriptional Regulation

Nucleophosmin 1 (NPM1) functions as a co-activator of the NF-κB transcription factor, particularly through its interaction with the p65 (RelA) subunit. By binding to the N-terminal DNA-binding domain of p65, NPM1 enhances the recruitment of p65 to promoter regions of target genes, thereby promoting NF-κB-mediated transcriptional activation.^[39] This chaperone-like activity of NPM1 facilitates efficient DNA binding by reducing intramolecular interactions within p65, allowing better access for co-activators.^[39] In inflammatory contexts, such as TNF-α stimulation, NPM1 upregulation leads to increased expression of pro-inflammatory cytokine genes, including IL-6, IL-8, and TNF itself, with knockdown of NPM1 reducing their induction by over 1.5-fold in microarray analyses of HeLa cells.^[39] NPM1 exerts a suppressive effect on certain p53 target genes, balancing p53 activity to modulate apoptotic responses. Through direct binding to the N-terminal transactivation domain of p53, NPM1 inhibits p53's transcriptional activity, particularly on pro-apoptotic genes, thereby antagonizing stress-induced apoptosis in hematopoietic cells. This interaction prevents p53 phosphorylation at key sites like Ser15 and suppresses the expression of downstream targets such as p21, as evidenced by reduced transactivation in NPM1-overexpressing cell lines exposed to ionizing radiation. Additionally, NPM1 sequesters MDM2 in the nucleolus, inhibiting its E3 ubiquitin ligase activity toward p53 and indirectly stabilizing p53 levels, though this stabilization is contextually coupled with transcriptional inhibition to limit excessive apoptotic gene activation.^[40] As a histone chaperone, NPM1 contributes to chromatin remodeling by facilitating nucleosome disassembly and enhancing acetylation-dependent transcription. NPM1 directly binds core histones H3 and H4, promoting their acetylation by histone acetyltransferases like p300/CBP, which increases chromatin accessibility at transcription start sites.^[41] This activity supports RNA polymerase II-mediated transcription from chromatin templates in vitro, with NPM1 depletion leading to compacted heterochromatin and reduced expression of developmental genes like those in the Hox cluster.^[42] In vivo, NPM1's histone chaperone function aids in maintaining open chromatin states during cellular processes requiring transcriptional activation, without altering basal nucleosome assembly.^[41]

DNA Damage Response

Nucleophosmin (NPM1) plays a critical role in the DNA damage response by facilitating the recruitment of repair factors to sites of double-strand breaks (DSBs). Upon induction of DSBs, NPM1 is phosphorylated at threonine 199 (Thr199), enabling its accumulation at damage sites through interaction with RNF8- and RNF168-dependent ubiquitin conjugates.^[43] This recruitment occurs downstream of ATM kinase activation, integrating NPM1 into the early signaling cascade that coordinates DSB repair and chromatin remodeling.^[44] NPM1's presence at DSB foci supports the formation of repair complexes, including those involving BRCA1, thereby promoting homologous recombination and non-homologous end joining pathways.^[43] In addition to DSB repair, NPM1 contributes to translesion synthesis (TLS), a tolerance mechanism for bypassing DNA lesions that stall replication forks. NPM1 directly interacts with the catalytic domain of DNA polymerase η (Polη), stabilizing the enzyme and preventing its proteasomal degradation following UV-induced damage.^[45] This chaperone-like function enhances Polη-mediated TLS, allowing accurate bypass of cyclobutane pyrimidine dimers and reducing mutagenesis.^[46] Deficiency in NPM1 impairs TLS efficiency, leading to increased sensitivity to UV radiation and accumulation of replication stress.^[45] NPM1 also supports base excision repair (BER) by interacting with apurinic/apyrimidinic endonuclease 1 (APE1), a central enzyme in the pathway that processes oxidative and alkylative DNA lesions. The NPM1-APE1 complex enhances APE1's endonuclease activity, facilitating the removal of abasic sites and subsequent gap filling.^[47] In vivo, NPM1 knockdown sensitizes cells to BER-inducing agents like bleomycin, underscoring its role in maintaining genomic integrity against endogenous and exogenous genotoxins.^[48] Under oxidative stress, NPM1 undergoes nucleocytoplasmic shuttling, relocating to the cytoplasm where it participates in the assembly of phase-separated granules that resemble stress granules. These NPM1-enriched structures sequester and stabilize mRNAs encoding survival and repair factors, modulating translational repression to promote cell resilience.^[49] Recent studies further highlight NPM1's involvement in protecting stalled replication forks, primarily through its regulation of TLS and interactions with repair proteins, preventing fork collapse and genomic instability.^[50]

Protein Interactions

Key Binding Partners

Nucleophosmin 1 (NPM1) engages in direct interactions with several key proteins that modulate its roles in cellular homeostasis, primarily through specific domain-mediated binding. These partnerships are often characterized by multivalent or transient affinities, facilitating dynamic nucleolar assembly and function. Prominent among these are tumor suppressors like p53 and ARF, as well as regulators of protein stability and nucleic acid processing. NPM1 binds p53, stabilizing p53 and enhancing its transcriptional activity in response to stress signals.^[51] This interaction inhibits p53 ubiquitination and degradation, with binding occurring in the nucleolus under normal conditions and relocating to the nucleoplasm upon stress. Similarly, NPM1 interacts with ARF via its N-terminal oligomerization domain, where ARF's N-terminal domain engages acidic grooves on NPM1, promoting ARF's nucleolar retention and sequestration.^[52] These bindings are multivalent and of moderate affinity, typically in the micromolar range, enabling rapid disassembly during nucleolar stress.^[53] NPM1 also directly associates with MDM2, an E3 ubiquitin ligase, through interactions involving MDM2's N- and C-terminal regions, facilitating MDM2's nucleolar sequestration. This binding prevents MDM2-mediated p53 ubiquitination, thereby supporting p53 activation without altering MDM2's central domain.^[54] The interaction is enhanced under nucleolar stress, where NPM1 relocation disrupts the MDM2-p53 complex. In ribosome biogenesis, NPM1 binds ribosomal proteins such as RPS9 and RPL5, aiding their nucleolar import and assembly.^[55] These interactions were initially identified through yeast two-hybrid screens, revealing multiple binding motifs on RPS9 that mediate nucleolar targeting. For RPL5, the binding supports pre-rRNA processing and 5S rRNA incorporation into ribosomes. Additional partners include upstream binding factor (UBF), where NPM1's association enhances rRNA transcription by stabilizing UBF on rDNA promoters.^[56] NPM1 also interacts with apurinic/apyrimidinic endonuclease 1 (APE1) via APE1's N-terminal lysine-rich region (residues 1-33), stimulating APE1's endonuclease activity in base excision repair within nucleoli.^[57] Furthermore, NPM1 binds the HIV-1 Rev protein through its N-terminal and central domains (oligomerization and histone-binding regions), independent of RNA, promoting Rev's nucleolar localization with a stoichiometry of one Rev per NPM1 pentamer.^[58]

Regulatory Networks

NPM1 serves as a central node in several regulatory networks that maintain cellular homeostasis, integrating signals from nucleolar integrity, mitotic progression, and stress response pathways. Through its dynamic localization and post-translational modifications, NPM1 coordinates responses to perturbations in ribosome biogenesis and cell cycle fidelity, often converging on tumor suppressor activation to prevent aberrant proliferation. Recent studies highlight NPM1's role in phase-separated condensates that facilitate interactions with partners like ARF and ribosomal proteins, enhancing nucleolar organization.^[59] In the nucleolar stress response network, NPM1 links disruptions in ribosomal biogenesis to p53-mediated cell cycle arrest or apoptosis. Under normal conditions, NPM1 resides primarily in the nucleolus, facilitating ribosome assembly alongside factors such as ribosomal proteins (e.g., RPL5 and RPL11). Upon nucleolar stress—induced by insults like actinomycin D treatment or ribosomal protein depletion—NPM1 translocates to the nucleoplasm, where it complexes with MDM2 to inhibit p53 ubiquitination and degradation, thereby stabilizing p53 and triggering its transcriptional activity.^[60]^[61] This translocation is a hallmark of nucleolar stress and is essential for p53 activation, as nucleoplasm-restricted NPM1 mutants fail to induce p53 accumulation.^[61] Additionally, NPM1 directly interacts with c-Myc, a key regulator of ribosomal biogenesis, to control Myc-driven proliferation; NPM1 binding attenuates excessive Myc activity during unscheduled ribosome production, enforcing a checkpoint that prevents oncogenic transformation.^[62]^[63] The cell cycle checkpoint network positions NPM1 at the interface of mitotic regulation, particularly through its interaction with the Aurora-B kinase pathway to ensure chromosomal fidelity. During mitosis, Aurora-B phosphorylates NPM1 at serine 125, promoting its redistribution and supporting centrosome duplication and spindle assembly.^[64] This phosphorylation is critical for mitotic progression, as inhibition of Aurora-B disrupts NPM1 localization and leads to defects in chromosome segregation.^[64] Protein-protein interaction analyses, such as those from the STRING database, reveal that NPM1 engages over 150 high-confidence interactors, many enriched in cell cycle and mitosis modules, underscoring its role in a broader network that safeguards against aneuploidy.^[65]^[66] Feedback loops involving NPM1 further fine-tune apoptotic responses via the NPM1-MDM2-p53 circuit. NPM1 directly binds MDM2 in the nucleolus, sequestering it and preventing MDM2 from ubiquitinating p53, which stabilizes p53 levels and promotes apoptosis in response to genotoxic stress.^[40] This interaction forms a regulatory axis where NPM1 acts as a brake on MDM2 activity; disruption of NPM1-MDM2 binding, as seen with certain modulators, enhances p53-MDM2 association and accelerates p53 degradation, dampening apoptotic signaling.^[67] In UV-induced damage, NPM1's nucleoplasmic relocation amplifies this loop by further inhibiting MDM2-p53 interactions, linking nucleolar integrity to genome stability.^[40]

Pathological Roles

Somatic Mutations

Somatic mutations in the NPM1 gene are a hallmark of acute myeloid leukemia (AML), occurring primarily as heterozygous alterations that drive leukemogenesis through protein mislocalization. These mutations are detected in approximately 30% of adult de novo AML cases overall and in up to 50-60% of those with normal karyotype.^[68]^[69] The predominant somatic mutations are frameshift insertions in exon 12, accounting for over 95% of NPM1 alterations in AML. The most common variant, known as type A, involves a duplication of the TCTG sequence at nucleotides 960-963, leading to a +4 bp shift that replaces the C-terminal 7 amino acids (including the nucleolar localization signal at tryptophans 288 and 290) with 11 novel residues and creates a new nuclear export signal.^[68]^[69] This frameshift mutation, representing 70-80% of NPM1-mutated AML cases, results in a mutant protein designated NPM1c+. Less frequent exon 12 variants include type B (CATG insertion) and type D (CCTG insertion), each occurring in about 5-10% of cases.^[68]^[69] The molecular consequences of these exon 12 frameshifts profoundly alter NPM1 function. The C-terminal modification abolishes the nuclear localization signal (NLS), preventing nucleolar retention and causing aberrant cytoplasmic accumulation of NPM1c+, which is observed in nearly all leukemic blasts of affected patients.^[68] Despite retaining the N-terminal oligomerization domain, the mutant protein forms stable heteropentamers with wild-type NPM1, sequestering the latter into the cytoplasm and disrupting its normal nucleolar localization.^[68] This mislocalization impairs NPM1's chaperone and nucleolar functions, contributing to genomic instability and leukemic transformation.^[68] Other somatic NPM1 mutations are rare and include missense variants in the N-terminal oligomerization domain, which can destabilize pentamer formation and further compromise protein interactions, though they occur in less than 5% of NPM1-mutated AML. In contrast, germline NPM1 variants, distinct from somatic changes, have been associated with developmental disorders such as dysmorphism, congenital malformations, and neurodevelopmental delay due to defects in rRNA processing. NPM1 mutations frequently co-occur with other genetic alterations in AML, notably internal tandem duplications in FLT3 (FLT3-ITD), observed in approximately 40% of NPM1-mutated cases based on 2023-2024 cohort analyses. This co-occurrence enhances proliferative signaling but is mutually exclusive with certain other mutations like RUNX1 alterations.^[70]

Association with Acute Myeloid Leukemia

NPM1 mutations are a defining genetic abnormality in acute myeloid leukemia (AML), occurring in approximately 30% to 35% of adult cases overall and in 45% to 60% of those with cytogenetically normal karyotypes (CN-AML).^[71]^[72] These mutations establish NPM1-mutated AML as a distinct diagnostic entity in the 5th edition of the World Health Organization classification of hematopoietic neoplasms and the 2022 International Consensus Classification, characterized by frameshift mutations typically in exon 12 leading to cytoplasmic localization of the NPM1 protein (NPM1c+).^[73] In terms of prognosis, NPM1-mutated AML without concurrent FLT3 internal tandem duplication (FLT3-ITD) is associated with a favorable outcome, with 5-year overall survival rates approaching 60% in intensively treated adults, though this benefit diminishes in older patients or those with high FLT3-ITD allelic ratios.^[74] The pathogenic mechanism involves NPM1c+ mislocalization to the cytoplasm, which disrupts normal nucleolar sequestration of the tumor suppressor ARF, thereby inhibiting MDM2 and stabilizing p53; additionally, NPM1c+ aberrantly activates HOX cluster genes, promoting leukemic self-renewal.^[75] Recent 2024 analyses have further linked NPM1 mutations to intra-patient heterogeneity in blast maturation, driving aberrant myelopoiesis and differentiation blockade at primitive stages. Beyond AML, NPM1 mutations are rare in solid tumors, where they lack the specificity seen in myeloid neoplasms, and NPM1 overexpression has been implicated in the progression of myelodysplastic syndromes (MDS) to AML through enhanced proliferative signaling.^[26]^[76] Overexpression of NPM1 is also observed in various solid tumors, including prostate, breast, and gastric cancers, where it promotes cell survival and proliferation.^[2] In hematological malignancies beyond AML, NPM1-ALK gene fusions occur in approximately 80% of anaplastic large cell lymphomas (ALCL), resulting in constitutive activation of ALK tyrosine kinase and driving lymphomagenesis.^[77]^[78] In pediatric AML, NPM1 mutations occur at a lower frequency of about 8% to 10% and confer a generally favorable prognosis, though outcomes vary with co-mutations and age.^[79]

Therapeutic Targeting and Prognosis

Monitoring of measurable residual disease (MRD) in NPM1-mutated acute myeloid leukemia (AML) primarily relies on reverse transcription quantitative polymerase chain reaction (RT-qPCR) assays targeting NPM1 mutations, which achieve a sensitivity of 10^{-4} to 10^{-5} (0.01% to 0.001%).^[80] This method is predictive of relapse risk and overall survival, with persistent MRD post-induction associated with inferior outcomes.^[81] According to the 2025 European LeukemiaNet (ELN) MRD guidelines, RT-qPCR is recommended for NPM1-mutated AML to guide risk stratification after induction therapy, enabling decisions on consolidation strategies such as allogeneic hematopoietic stem cell transplantation (HSCT).^[82] Targeted therapies exploiting NPM1 mutations focus on disrupting aberrant localization and downstream pathways. Exportin-1 (XPO1) inhibitors, such as selinexor, promote nuclear relocalization of the mutant NPM1c protein by blocking its cytoplasmic export, leading to differentiation and reduced proliferation in NPM1-mutated AML cells.^[83] Prolonged XPO1 inhibition is required for optimal antileukemic effects, including downregulation of HOX/MEIS genes.^[84] For cases with co-occurring mutations, menin-MLL inhibitors like revumenib target the menin-MLL interaction critical for leukemogenesis in NPM1-mutated AML; phase II trials in relapsed/refractory NPM1-mutated AML have reported an overall response rate of approximately 47%, with 23% achieving complete remission (CR) or CR with partial hematologic recovery.^[85] Prognosis in NPM1-mutated AML is favorable when the mutation occurs without a co-existing FLT3 internal tandem duplication (FLT3-ITD), as defined by the ELN 2022 risk stratification, conferring intermediate to favorable risk with standard chemotherapy.^[86] High-risk subsets, such as those with high allelic ratio FLT3-ITD, benefit from allogeneic HSCT in first CR, which reduces relapse risk and improves long-term survival compared to chemotherapy alone.^[87] Emerging data from 2024 on venetoclax-based combinations, particularly with hypomethylating agents, have shown improved CR rates of around 80-85% in unfit patients with NPM1-mutated AML, enhancing accessibility for older or comorbid individuals.^[88]

References

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NPM1 nucleophosmin 1 [Homo sapiens (human)] - Gene - NCBI
### NPM1 Summary
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From a cancer perspective, elevated levels of NPM1 might promote malignant transformation by enabling cell survival. Several proteins have been identified that ...
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The Multifunctional Nucleolar Protein Nucleophosmin/NPM/B23 and ...
NPM1 was first discovered as a nucleolar protein in rat liver cells and Novikoff hepatoma ascites cells by two-dimensional polyacrylamide gel electrophoresis ( ...
[4]
The major phosphorylation site of nucleophosmin (B23) is ... - PubMed
Sep 1, 1990 · Nucleophosmin (B23) was phosphorylated in vitro with [gamma-32P]ATP and a nuclear kinase (type II) purified from HeLa cells.Missing: radiolabeling | Show results with:radiolabeling
[5]
Immunolocalization of phosphoprotein B23 in proliferating and non ...
Localization of protein B23 in HeLa cells under different growth conditions was studied using indirect immunofluorescence. Bright nucleolar fluorescence was ...Missing: phosphorylation radiolabeling
[6]
https://academicworks.cuny.edu/cgi/viewcontent.cgi?params=/context/cc_etds_theses/article/1020/&path_info=2011SpEn04.pdf
[7]
Gene symbol report | HUGO Gene Nomenclature Committee
### Summary of NPM1 Gene Information
[8]
https://pubmed.ncbi.nlm.nih.gov/3392030/
[9]
Gene: NPM1 (ENSG00000181163) - Summary - Homo_sapiens
NPM1, also known as nucleophosmin 1, is located on chromosome 5 and is a protein coding gene. It has 64 transcripts and 187 orthologues.Missing: organization | Show results with:organization
[10]
Nucleophosmin 1 Mutations in Acute Myeloid Leukemia - PMC
Human NPM1 is located on chromosome 5q35 and is composed of 12 exons with sizes ranging from 58 to 358 base pairs (bp) [42]. The regular-spliced NPM1 gene has ...
[11]
NPM1 Gene - GeneCards | NPM Protein | NPM Antibody
Complete information for NPM1 gene (Protein Coding), Nucleophosmin 1, including: function, proteins, disorders, pathways, orthologs, and expression.Missing: 1993 | Show results with:1993
[12]
https://pubmed.ncbi.nlm.nih.gov/2713355/
[13]
Nucleophosmin: from structure and function to disease development
Aug 24, 2016 · Nucleophosmin (NPM1), also known as B23, No38 or Numatrin, is an abundant nucleolar protein found in the nuclei of proliferating cells. NPM1 has ...
[14]
Nucleophosmin1 (NPM1) abnormality in hematologic malignancies ...
NPM1 is also a multifunctional phosphoprotein that plays multiple roles in ribosome biogenesis, mRNA processing, chromatin remodeling, and embryogenesis. For ...
[15]
Oncogene c‐fos and mutant R175H p53 regulate expression of ...
Aug 7, 2018 · The first study on NPM1 gene regulation showed that the NPM1 promoter has a Yin Yang 1 (YY1) binding site at −371 to −344 nucleotide position ...Missing: less | Show results with:less
[16]
untranslated region of the NPM1 gene causes illegitimate regulation ...
Together, our findings uncover a microRNA-mediated control of NPM1 expression that contributes to disease heterogeneity and suggest additional prognostic values ...Missing: post- | Show results with:post-
[17]
Analysis of NPM1 splice variants reveals differential expression ...
The NPM1 gene contains 12 exons and in humans maps to chromosome 5q35. It encodes at least three main alternatively spliced isoforms: R1 (B23.1), R2 (B23.2) ...Missing: intron boundaries canonical
[18]
NPM1 - an overview | ScienceDirect Topics
NPM1 is an oligomeric protein, with each monomer consisting of three different structural ... 2) is composed of 259 A A (Dalenc et al., 2002). Whereas NPM ...
[19]
“grappling hook” interaction connects self-assembly and chaperone ...
NPM1 has a modular structure with folded N-terminal and C-terminal domains (NTD, residues 1 to 120, and CTD, residues 240 to 294) linked by an intrinsically ...
[20]
Translocations and mutations involving the nucleophosmin (NPM1 ...
Apr 1, 2007 · The discovery of NPM1 gene alterations also represents the rationale basis for development of molecular targeted drugs. Nucleophosmin (NPM), ...Missing: 1980s | Show results with:1980s<|control11|><|separator|>
[21]
Nucleophosmin 1 (NPM1). (A) Schematic representation of its ...
The central portion of NPM1 is characterized by the presence of two acid domains (residues 119-133 and 161-188) and a basic region (residues 198-239) that are ...
[22]
Structure of Nucleophosmin DNA-binding Domain and Analysis of ...
The NPM1-C70 terminal three-helix bundle binds the G-quadruplex DNA at the interface between helices H1 and H2 through electrostatic interactions with the G- ...Missing: TATA- less Sp1
[23]
Structural investigation of nucleophosmin interaction with the tumor ...
Sep 18, 2017 · The NPM1 nucleolar localization signal is unique and consists of W288 and W290 residues near the C terminus of the protein. These tryptophans ...
[24]
https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/npm1
[25]
https://academic.oup.com/pnasnexus/article/2/2/pgac303/6973215
[26]
https://haematologica.org/article/view/4404
[27]
Inheritance of repressed chromatin domains during S phase ...
Apr 27, 2022 · The histone H3/H4 chaperone, NPM1, fosters epigenetic inheritance from parental repressed chromatin during DNA replication.
[28]
A “grappling hook” interaction connects self-assembly and ...
Full-length NPM1 and its CTD display differential chaperone activity toward amyloid formation. Previous studies have established the ability of FL NPM1 to ...Results · Full-Length Npm1 And Its Ctd... · Npm1 Pentamers Connect Via...Missing: ATP- insulin
[29]
https://www.nature.com/articles/oncsis201778
[30]
https://doi.org/10.1016/j.febslet.2014.05.014
[31]
Efficient DNA binding of NF-κB requires the chaperone-like function ...
Dec 21, 2016 · We found that NPM1 knockdown decreased NF-κB-mediated transcription of selected target genes by decreasing the recruitment of NF-κB p65 to the gene promoters.
[32]
Nucleolar protein NPM interacts with HDM2 and protects tumor ...
We find no evidence favoring subcellular trafficking of p53 to the nucleolus ... The chaperone activity of NPM could further assist p53 folding and stability.
[33]
Human Histone Chaperone Nucleophosmin Enhances Acetylation ...
Nucleophosmin (NPM1) as a human histone chaperone that becomes acetylated, resulting in the enhancement of chromatin transcription.
[34]
Histone Chaperone Nucleophosmin Regulates Transcription of Key ...
... NPM1 was less efficient in pulling down recombinant histone H3 (Fig. 4D, upper panel) or H3 in the context of reconstituted H3-H4 tetramer (Fig. 4D, lower ...
[35]
Recruitment of phosphorylated NPM1 to sites of DNA damage ...
Sep 1, 2010 · Our findings suggest that phosphorylated NPM1 is a novel component in DSB repair that is recruited by ubiquitin conjugates downstream of RNF8 and RNF168.
[36]
https://doi.org/10.1155/2011/195209
[37]
Identification of novel DNA-damage tolerance genes reveals ...
Nov 25, 2014 · We show that NPM1 (nucleophosmin) regulates TLS via interaction with the catalytic core of DNA polymerase-η (polη), and that NPM1 deficiency causes a TLS ...
[38]
Identification of novel DNA-damage tolerance genes reveals ...
We show that NPM1 (nucleophosmin) regulates TLS via interaction with the catalytic core of DNA polymerase-η (polη), and that NPM1 deficiency causes a TLS ...
[39]
Nucleophosmin interaction with APE1: Insights into DNA repair ...
NPM1 has been described to interact with APE1 (apurinic apyrimidinic endonuclease 1), a key enzyme of the base excision repair (BER) pathway.
[40]
NPM1 and APE1: nucleolar teamwork in controlling base excision ...
Apr 1, 2012 · Interestingly, NPM1 stimulated APE1 BER activity in vivo, since cells lacking NPM1 were more sensitive to bleomycin or alkylating agents and ...
[41]
High-fidelity reconstitution of stress granules and nucleoli in ...
Jan 27, 2021 · Thus, lysate granules faithfully recapitulate the RNA composition of stress granules assembled in cells. Addition of exogenous NPM1 induces a ...
[42]
Nucleophosmin Plays a Role in Repairing DNA Damage and Is a ...
NPM1 is a multifunctional oligomeric protein involved in numerous cellular functions that include participating in liquid–liquid phase separation, ribosome ...
[43]
https://pubmed.ncbi.nlm.nih.gov/20713529/
[44]
https://aacrjournals.org/cancerres/article/70/17/6746/561827/Recruitment-of-Phosphorylated-NPM1-to-Sites-of
[45]
On the relationship status for Arf and NPM1–it's complicated - NIH
Through multivalent interactions with NPM1 – a regulator of ribosome biogenesis, and Mdm2 – a regulator of cellular fate, Arf integrates within the nucleolar ...Missing: RPS9 RPL5 UBF
[46]
https://pubmed.ncbi.nlm.nih.gov/25421715/
[47]
A redox mechanism underlying nucleolar stress sensing by ... - Nature
Nov 25, 2016 · Nucleophosmin (NPM1) or B23 is an abundant nucleolar protein that can frequently shuttle between the nucleolus and the nucleoplasm or cytoplasm ...
[48]
Nucleolar Stress: hallmarks, sensing mechanism and diseases - PMC
Recently we found that common cellular insults that are able to induce p53 activation can also induce the translocation of NPM1, a hallmark of nucleolar stress, ...
[49]
Nucleophosmin interacts directly with c-Myc and controls c ... - PNAS
Dec 2, 2008 · Nucleophosmin (NPM), also termed B23, is a dynamic, multifunctional protein that is tightly regulated during proliferation. ... Because NPM is ...Missing: discovery | Show results with:discovery
[50]
MYCN-induced nucleolar stress drives an early senescence-like ...
Jul 14, 2021 · NPM1 controls the impaired ribosome biogenesis checkpoint which becomes activated upon unscheduled MYC(N) driven ribosome production. Checkpoint ...<|separator|>
[51]
Phosphorylation of multifunctional nucleolar protein nucleophosmin ...
Jun 27, 2014 · These data suggest that Aurora kinase B-mediated phosphorylation of NPM1 plays a critical role during mitosis, which could have wider ...Missing: cycle checkpoint network fidelity interactors
[52]
NPM1 protein (human) - STRING interaction network
Max number of interactors to show: 1st shell: - none / query proteins only -, no more than 5 interactors, no more than 10 interactors, no more than 20 ...
[53]
NPM1 - Nucleophosmin - Homo sapiens (Human) | UniProtKB
P06748-1. This isoform has been chosen as the canonical sequence. All positional information in this entry refers to it. This is also the sequence that ...
[54]
AKT‐dependent phosphorylation of Niban regulates nucleophosmin
Apr 17, 2012 · Niban promotes p53 downregulation and cell survival. P53 activation in response to stress signals has a central role in cell apoptosis [10].Missing: antagonizes | Show results with:antagonizes
[55]
https://pmc.ncbi.nlm.nih.gov/articles/PMC2989734/
[56]
https://doi.org/10.1128/MCB.00299-10
[57]
https://pubmed.ncbi.nlm.nih.gov/19188445/
[58]
Criteria for Diagnosis and Molecular Monitoring of NPM1-Mutated AML
NPM1-mutated AML is recognizable by molecular techniques and immunohistochemistry, which, when combined, can solve difficult diagnostic problems.
[59]
Acute Myeloid Leukemia with Normal Cytogenetics and NPM1 ... - NIH
Dec 23, 2024 · NPM1 mutation is reported in 25–35% of adults with AML and an even higher percentage of those with normal cytogenetics, 45–64% [4]. AML with ...
[60]
Criteria for Diagnosis and Molecular Monitoring of NPM1-Mutated AML
Jan 8, 2024 · NPM1-mutated AML represents a distinct entity in the 2022 International Consensus Classification and 5th edition of World Health ...
[61]
The effect of FLT3-ITD and NPM1 mutation on survival in intensively ...
Our study demonstrated a 60% OS at 5 years in FLT3−/NPM1+ patients treated with chemotherapy alone versus a 2-year OS of 62% and 47% in the US transplanted and ...
[62]
Nucleophosmin 1: from its pathogenic role to a tantalizing ...
May 27, 2022 · This review focuses on the mechanisms underlying the pathogenesis of NPM1 mut AML and the potential role of NPM1 as a therapeutic target.
[63]
Nucleophosmin1 (NPM1) abnormality in hematologic malignancies ...
Feb 3, 2020 · NPM1 overexpression is considered a prognostic marker of recurrence and progression of cancer. Thus, NPM1 abnormalities play a critical role in ...
[64]
The frequency of NPM1 mutations in childhood acute myeloid ...
Oct 27, 2010 · The NPM1 mutations were present in patients with AML M1 and M2 FAB subtypes. There was no significant difference in the prevalence of NPM1 ...
[65]
Measurable residual disease monitoring in acute myeloid leukaemia
Jun 12, 2025 · Quantitative PCR (qPCR) assays enable highly sensitive detection (10–4 to 10–5) of recurrent AML-associated mutations, most notably NPM1, RUNX1 ...
[66]
Acute myeloid leukemia management and research in 2025
Dec 10, 2024 · NPM1 MRD monitoring (RT-qPCR; sensitivity, 10−4) is predictive for relapse and OS. The persistence of NPM1 or FLT3-ITD molecular ...
[67]
Acute Myeloid Leukemia: 2025 Update on Diagnosis, Risk ... - NIH
The ELN MRD guidelines recommend using qPCR for patients with NPM1 or CBF‐mutated AML (ddPCR or NGS‐MRD may be alternatively used, though paucity of data ...
[68]
Prolonged XPO1 inhibition is essential for optimal antileukemic ...
Nov 22, 2022 · Prolonged, but not intermittent, XPO1 inhibition stably downregulates HOX/MEIS and induces differentiation in NPM1-mutated AML cells.
[69]
Menin inhibition with revumenib for NPM1-mutated relapsed or ...
Here, we report the primary efficacy analysis of revumenib in patients with R/R NPM1m AML from the phase 2 portion of the AUGMENT-101 study. Methods. Study ...
[70]
Diagnosis and management of AML in adults - ASH Publications
Sep 22, 2022 · Concurrent KIT and/or FLT3 gene mutation does not alter risk categorization. §. AML with NPM1 mutation and adverse-risk cytogenetic ...
[71]
Allogeneic hematopoietic stem cell transplantation and pre ... - Nature
Jul 4, 2023 · Patients with acute myeloid leukemia (AML) and nucleophosmin 1 gene mutations (NPM1mut) show a favorable prognosis with chemotherapy (CT) in ...
[72]
Intensive chemotherapy vs venetoclax/hypomethylating agents for ...
The differences in outcomes between patients with NPM1-mutated, favorable-risk AML who receive IC and VEN/HMA are unknown. We performed a retrospective analysis ...Statistical Analysis · Results · Impact Of Allohct On Os And...