top of page
  • Writer's pictureDr Edin Hamzić

All About The NPM1 Gene

Updated: Jan 8

What is the NPM1 gene? What does NPM1 stand for?

The NPM1 gene encodes the nucleophosmin, also known as nucleolar phosphoprotein B23 or numatrin and NO38. NPM1 is an abbreviation for nucleophosmin 1.

The NPM1 gene was discovered by Chan et al. in 1989. The NPM1 gene is involved in several cellular processes [citation] necessary for DNA-dependent activities like transcription, replication, and DNA repair [citation], but more about that in the following paragraphs.

The NPM1 gene is located on chromosome 5, roughly 24,695 MB long.

The nucleophosmin is one of the key elements in the processing and assembly of ribosomes. Nucleophosmin protein belongs to the group of nucleocytoplasmic shuttling proteins. These proteins are involved in transport between the nucleus and the cytoplasm.

Nucleophosmin also plays an important role in regulating tumor suppressor T53, which is further important in normal cellular function and protein chaperoning [citation].

Nucleophosmin is placed in the granular region of nucleoli playing a crucial role in maintaining nucleolar structure, but it can shuttle between nucleoli, nucleoplasm, and cytoplasm [citation].

Nucleophosmin has two isoforms, NPM1, and NPM1.2. The difference is in C-terminal, 35-amino acids of NPM1 are absent from NPM1.2. NPM1 is mostly nucleolar, while NPM1.2 is present in cells at low levels and is detected both in the cytoplasm and nucleoplasm [citation].

Because nucleophosmin is an essential factor in the regulation processes of eukaryotic cells, it is possible to use an approach targeting nucleophosmin to treat different types of cancers [citation], but more about that in the following paragraphs.

In what cellular processes and pathways is nucleophosmin involved?

Biochemically nucleophosmin is defined as a histone chaperone. Histone chaperones are required for the correct assembly/disassembly of nucleosomes, necessary for DNA-dependent activities like transcription, replication and repair [citation].

In addition to that, as mentioned above, nucleophosmin is involved in many other processes such as:

Nucleophosmin is also crucial for multiple other cell processes such as:

  • Regulation of ribosome biogenesis

  • Chromatin remodeling and histone assembly

  • Genomic stability

  • Apoptosis

  • mRNA transport

  • DNA repair

  • Centrosome duplication

  • Protein chaperoning

  • Histone assembly

  • Cellular proliferation

  • Regulation of tumor suppressors like TP53, and

  • Control of transcription and replication [citation].

Why is the NPM1 gene important?

As mentioned in the previous paragraph, the NPM1 gene is essential for regulating multiple cell processes, including nuclear transfer of ribosomal protein, response to stress stimuli like UV irradiation, control of centrosome duplication during mitosis, genomic stability, cellular ploidy, DNA repair, control of tumor suppressor TP53 and ARF [citation].

The best-documented role is in RNA transport and ribosome biogenesis; it is clear that NPM1 also plays a critical role in the regulation of apoptosis and the maintenance of genomic homeostasis [citation].

NPM1 possesses both proto-oncogene and tumor-suppressor functions. Overexpression of NPM protein in tumor cells is associated with increased cell growth and proliferation, the inhibition of differentiation and apoptosis, also poor prognosis [citation].

The NPM1 gene is frequently involved in chromosomal translocations or mutations, invariably restricted to the hematopoietic compartment, and associated with developing leukemias or lymphomas [citation]. NPM1 is considered one of the most common targets of genetic alterations in hematopoietic tumors [citation].

The overexpression of NPM is considered an important marker for detecting tumors.

Interestingly, high expression of NPM1 is detected in lung adenocarcinoma (LUAD), but related studies failed in more broadly or more detailed investigation of the biological function of NPM1 [citation].

The NPM gene is found to be translocated with distinct partner genes in several diseases such as acute promyelocytic leukemia (APL), anaplastic large cell lymphoma (ALCL), acute myeloid leukemia (AML), and myelodysplasia [citation].

What Happens When the NPM1 Gene Is Mutated? 

NPM1 is the most frequently mutated gene in cytogenetically normal acute myeloid leukemia. Mutations cause disruption of the transcription process, and delocalization of proteins from the cytoplasmic space and thus promote the growth of AML cells [citation]. The consequence of NPM1 mutations is the gain-of-function or loss-of-function of several different proteins, which affects several cellular pathways [citation].

Mutations in the NPM1 gene have been associated with malignant transformation and followed by diseases such as

  1. Acute promyelocytic leukemia (APL),

  2. Non-Hodgkin lymphoma,

  3. Myelodysplastic syndrome,

  4. And cytogenetically normal acute myeloid leukemia (AML) [citation].

NPM1 mutations cause aberrant expression of the NPM1 protein in the cytoplasm rather than the nucleus, inducing myeloid proliferation and the development of leukemia.

There are three common types of NPM1 mutations A, B, and D. Mutation A is the most frequent in adults and accounts for 70%-80% of mutations, while other types of mutations are detected more in children [citation].

Mutations in NPM1 result in a functionally stronger nuclear export than import signal, contrary to normal NPM1 [citation], disturbing normal shuttling and subcellular distribution. NPM1c+ represents already mutated and accumulated NPM1 in the cytoplasm [citation]. The C-terminal domain of NPM1 is unique compared to other proteins in the nucleophosmin family. It is responsible for nucleic acid binding and nucleolar localization [citation]. A mutated protein lacking a folded C-terminal domain (NPM1c+) has been found in the cytoplasm in AML patients [citation]. In addition, cytoplasmic localization is a crucial factor for leukemic transformation. The precise function of mutated NPM1 and NPM1c+ in leukemogenesis is poorly understood [citation].

The NPM1 mutation was observed to be more prevalent in females than males and in adults than children. Patients with the NPM1 mutation had significantly higher platelet counts than those without NPM1 or FLT3 mutations [citation].

What Is AML? What Are the Symptoms of AML?

Acute myeloid leukemia is the most common type of acute leukemia in adults. AML is a heterogeneous disease, meaning symptoms and physical properties vary between individuals. This disease is a blood and bone marrow cancer caused by mutations that result in the uncontrolled proliferation of immature, abnormal blast cells and uncoordinated regular function of white blood cells. A more frequent occurrence was recorded in men compared to women, with a ratio of 5/3 [citation].

In the last few years, the survival rate of 5-10 years has increased from 10% to 40-50%, thanks to the modern approach to treatment and the improvement of therapy and, in general, treatment strategies [citation].

Acute myeloid leukemia is clinically manifested in the form of

  1. Pancytopenia (anemia, thrombocytopenia, and leukopenia) 

  2. and blast proliferation [citation].

Pancytopenia is a condition in which there is a reduction in the number of all 3 major cellular elements of the blood; red blood cells, white blood cells, and platelets. As a result, it leads to anemia, leukopenia, and thrombocytopenia [citation].

Blasts are immature white blood cells. In AML, blasts fail to differentiate due to crowding out of normal hematopoietic precursors. In cancer, they form a mass of proliferative blasts [citation].

Symptoms of AML include the following:

  1. Pale skin,

  2. Fatigue,

  3. Weakness,

  4. Shortness of breath,

  5. Fever,

  6. Infection,

  7. Bleeding,

  8. and bruising [citation].

How Is NPM1 Related to AML (Acute Myeloid Leukemia)? How Does NPM1 Cause AML?

NPM1-mutated AML exhibits unique molecular, pathological, and clinical features [citation]. The World Health Organization introduced mutated NPM1 AML as an AML entity in 2017 [citation], because it is detected in 50-60% of AML patients [citation].

Mutation, translocation, and loss of function or altered gene activity of NPM1 further lead to oncogenesis or tumorigenesis. This may affect NPM1 regulatory potential [citation]. The NPM1 mutant cytoplasmic delocalization in leukemic blasts alters multiple cellular pathways through either loss or gain of function effects on different protein partners [citation].

NPM1 function in DNA repair pathways increases; it explains at least in part the genetic instability associated with cancers such as AML. Further, NPM1 deregulation or mutation will suppress the ability of that cell to respond to apoptotic stimuli, allowing for the tolerance of genetic instability [citation].

NPM1 mutations are often the only genetic abnormality detected in AML blasts. They are stable during the disease and likely represent a reliable marker for monitoring minimal residual disease [citation].

Precise mechanisms by which mutant NPM1 contributes to leukemogenesis remain under research [citation]. However, it was reported that mutated NPM1 drives leukemia by influence on different proteins, essential for several signaling pathways, through a combination of loss and gain of functions [citation; citation].

More than 50 mutations are found in the NPM1 gene, usually frameshift mutations (about 95%). Three mutations are the most common (A, B, and D):

  1. Type A mutation (c.860_863dupTCTG) accounts for 70%-80% of cases,

  2. Type B mutation (c.863_864insCATG),

  3. and type D mutation  (c.863_864insCCTG).

Type B and D mutations account for 15%–20% of disease cases. Type A mutation of NPM1 is primarily detected in adults; other mutations are more frequent in children [citation].

AML is a clinically, cytogenetically, and molecularly heterogeneous disease. NPM1 gene mutations target 50%–60% of adult AML normal karyotype (AML-NK), which is considered the most common genetic abnormality in adult de novo AML (about one-third of patients) [citation]. 

AML-NK is described, as the name suggests, with a normal karyotype, sets of chromosomes appearing normal, with a favorable overall prognosis. However, these patients have chromosomal aberrations that have not yet been well researched and described, so there is often a risk due to the timely treatment and selection of therapy [citation]. 

Patients with an abnormal karyotype belong to the minority group of AML patients with mutated NPM1 [citation]. In addition, AML-NK is the most poorly understood group [citation]. About 45–64% of AML with a normal karyotype have an NPM1 mutation [citation].

NPM1 mutated AML often presents with a high white blood cell and blast count with NPM1 mutations observed in all AML subtypes under the French-American-British (FAB) classification of AML system, except acute promyelocytic leukemia [citation].

Which Finding Is Associated With a Worse Prognosis in AML With NPM1 Mutation? 

NPM1-mutated AML is a kind of AML with a favorable prognosis [citation].

NPM1 mutations tend to be associated with a higher complete remission (CR) rate, meaning all signs of cancer disappeared due to the treatment. In multivariate analysis, FLT3‐ITD was associated with comparatively poor survival rates. Patients harboring FLT3‐ITD and no NPM1 mutation had a poorer prognosis than others  [citation]. 

In cytogenetically normal AML (AML-NK), NPM1 mutations (without FLT3-ITD) provide a more favorable or better risk prognosis, and patients do not receive allogeneic stem cell transplants. [citation].

How Is NPM1-Positive AML Treated? 

The approach of targeting oncoproteins is an effective strategy in the treatment of AML.

The primary treatment for AML has remained relatively unchanged for over 40 years, comprising the ‘7 + 3’ chemotherapy regimen involving the cytotoxic drugs cytarabine and daunorubicin infusion for 7 and 3 days, respectively [citation].

As of 2017, the approval of nine agents for different AML indications has been confirmed. These include venetoclax, FLT3 inhibitors, and IDH inhibitors [citation].

Hypomethylating agents and Venetoclax combination are the standard treatment [citation]. Furthermore, other treatments for AML include: Glasdegib, Azacitidine-oral (CC-486), Arsenic trioxide, Midostaurin, CPX-351, Gemtuzumab Ozogamicin, Enasidenib, Ivosidenib Gilteritinib, and most of them are approved by the US FDA. However, some are still not approved by the EMA [citation], i.e., Enasidenib [citation].

Hypomethylating agents such as azacitidine have been commonly used in patients unsuitable for intensive treatment since the 2000s. However, azacitidine is not recommended for older patients [citation].

NPM1-mutated AML patients in molecular relapse should be offered an Allogeneic Hematopoietic Stem Cell Transplantation (allo-HSCT). Some clinicians wait for hematological relapse, while others either proceed directly to alloHSCT or prescribe some preventive therapy. The preventive therapy involves dactinomycin, venetoclax, 5-azacitidine, and immunotherapy [citation].

Currently, NPM1-mutated AML patients with FLT3-ITD high (ratio ≥0.5) should receive conventional chemotherapy plus an FLT3 inhibitor [citation]

Some therapeutic targets include inhibitors of the nuclear exporter XPO1, such as Selinexor, intending to correct the aberrant cytoplasmic localization of NPM1 mutation [citation].

Promising future new agents in NPM1-mutated AML include XPO1 and MLL Menin  inhibitors, alone or in combination with FLT3 inhibitors or venetoclax and drugs targeting the interaction between NPM1 and its ligands [citation].

How Do We Test For NPM1  NPM1 Gene Mutations? What NPM1 Mutations Affect Midostaurin?  

PCR and fragment analysis of exon 12 of the NPM1 gene is usually done to detect small insertion mutations specific to AML. Results are reported in the percentage of abnormal DNA. NGS has the potential to identify all NPM1 mutations. Still, the commercially available panels should be implemented to include, together with exon 12, at least exon 11, 9, and 5 [citation] because mutations can sporadically affect these regions [citation].

Midostaurin is the first FLT3 inhibitor. The FLT3 is the most common mutation (~23%) from AML cases, described as an internal tandem duplication (FLT3-ITD) [citation].

Midostaurin use significantly improved overall survival in FLT3-ITD patients with NPM1 wild type but not in those presenting with a concurrent NPM1 mutation [citation].

How Is Midostaurin Related to the NPM1 Gene?

Midostaurin is used for the treatment of AML patients with FLT3 mutation. However, its prescription requires an analysis of NPM1 status. The NPM1 gene is not necessarily involved in the mechanism underlying the response to midostaurin [citation].

Testing is recommended because NPM1 mutations are a known favorable prognostic factor in AML and are associated with FLT3-ITD mutations in 50% of patients. NPM1 mutations mitigate the unfavorable prognostic effect of FLT3-ITD mutations and, when combined, define favorable- or intermediate-risk AML. Those assumptions are estimated on quantitative analysis of mutations. As previously reported, patients have a higher survival probability in the case of both mutated NPM1 and FLT3. Treatment decisions are further based on quantifying mutated NPM1 transcripts by quantitative PCR [citation]. 

How Is Venetoclax Related to the NPM1 Gene?

Venetoclax was approved in 2018 as the first selective BCL-2 inhibitor. BCL-2 stands for anti-apoptotic protein B-cell lymphoma 2 (Bcl-2), with further potential for pro-apoptotic and antineoplastic activities [citation].

Clinical studies have identified drug combinations that may be particularly effective in NPM1-mutated AML (e.g., venetoclax prescribed in combination with another drug) [citation].

One of the most promising treatments of AML for older patients is Venclexta (venetoclax). Recent research has shown it to be highly effective in treating mutated NPM1 (AML) in combination with hypomethylating agents, with patients over 65 years old showing a 69% reduction in mortality compared with those treated with intensive chemotherapy alone [citation]. 

How Venetoclax Is Tested for the NPM1 Gene, and What NPM1 Mutations Affect Venetoclax?

Venclexta (venetoclax) is indicated for daily use after the detection of 17p deletion (TP53) is confirmed through the use of the FDA-approved companion diagnostic test Vysis CLL FISH probe kit [citation]. Venclexta (venetoclax) induces rapid elimination of NPM1 mutant measurable residual disease in combination with low-intensity chemotherapy in acute myeloid leukemia [citation]. AML patients treated with venetoclax combined with HMAs or LDAC showed that patients with NPM1 or isocitrate dehydrogenase 2 (IDH2) mutations had better responsiveness to Venclexta (venetoclax). Results also show that patients with NPM1 mutations often have longer molecular remission time [citation].

PCR and fragment analysis of exon 12 of the NPM1 gene are used to detect small insertion mutations specific to AML. NPM1 mutations almost exclusively affect exon 12, and all of them cause changes at the C-terminus of NPM1 [citation].

It was reported that mutated genes can overlap with the same class of genes, for example: N-RAS, TP53, MLL-PTD, and NPM1. This scenario cooperatively can trigger the development of AML [citation].

Other mutations that affect Venetoclax are detected in BCL2 (G101V, D103Y) and may cause resistance to this drug. Mutations of BCL2 are frequent in chronic lymphocytic leukemia (CLL) [citation].


bottom of page