PNP (Purine Nucleoside Phosphorylase)
2018-03-01 Rafig Gurbanov  , Sinem Tunçer   AffiliationIdentity

Abstract
The purine nucleoside phosphorylase gene (PNP) encodes an enzyme which reversibly catalyzes the phosphorolysis of purine nucleosides. PNP is ubiquitously expressed in mammalian cells and tissues. PNP mutations cause nucleoside phosphorylase deficiency which result in defective T cell mediated immunity but can also affect B cell immunity and antibody responses.
DNA/RNA
Note
Transcription
Table 1. Transcripts of human PNP gene (Ensemble, GRCh38.p10).
| Name | Transcript ID | bp | Protein (aa) | Biotype |
| PNP-201 | ENST00000361505.9 | 1509 | 289 | Protein coding |
| PNP-203 | ENST00000553591.1 | 770 | 221 | Protein coding |
| PNP-202 | ENST00000553418.5 | 557 | 93 | Protein coding |
| PNP-205 | ENST00000554065.1 | 554 | 61 | Protein coding |
| PNP-207 | ENST00000556754.1 | 2573 | Retained intron | |
| PNP-204 | ENST00000554056.5 | 1635 | Retained intron | |
| PNP-206 | ENST00000556293.5 | 1023 | Retained intron | |
| PNP-208 | ENST00000557229.5 | 992 | Retained intron |
Pseudogene
Proteins
Note

Expression
Localisation

Function
PNP activity is crucial for cell survival and function. PNP deficiency results in the accumulation of its substrates: inosine, deoxyinosine, guanosine, and deoxyguanosine. Increased phosphorylation of deoxyguanosine leads to dGTP accumulation, a potent feedback inhibitor of human ribonucleotide reductase. dGTP accumulation can also interfere with DNA synthesis or repair directly (Arpaia et al., 2000; Ghodke-Puranik et al., 2017) (Figure 4). Abnormal activity of the enzyme is associated with different pathologies (Giuliani et al., 2016).

Homology

Mutations
Note
Table 2. Purine nucleoside phosphorylase (PNP) deficiency related mutations.
| # | Location | Mutation | Protein | Reference |
| [1] | Exon 2 | c.59A>C | p.20H>P | Yeates et al., 2017 |
| [2] | Exon 2 | c.70C>T | p.Arg24X | Walker et al., 2011 |
| [3] | Exon 2 | c.172C>T | p.Arg57X | Walker et al., 2011 |
| [4] | Exon 2 | c.181G>T | p.Tyr5AlafsX28 | Walker et al., 2011 |
| [5] | Exon 3 | c.199C>T | p.Arg67X | Walker et al., 2011 |
| [6] | Exon 3 | c.212G>A | p.71Gly>Glu | Walker et al., 2011 |
| [7] | Exon 3 | c.257A>G | p.86His>Arg | Walker et al., 2011 |
| [8] | Exon 3 | c.265G>A | p.89Glu>Lys | Walker et al., 2011 |
| [9] | Exon 4 | c.349G>A | p.117Ala>Thr | Grunebaum et al., 2004 |
| [10] | Exon 4 | c.383A>G | p.128Asp>Gly | Walker et al., 2011 |
| [11] | Exon 4 | c.385 387delATC | p.Ile129del | Walker et al., 2011 |
| [12] | Exon 4 | c.437C>T | p.146Pro>Leu | Alangari et al., 2009 |
| [13] | Exon 5 | c.467G>C | p.156Gly>Ala | Moallem et al., 2002 |
| [14] | Exon 5 | c.475T>G | p.159Phe>Val | Walker et al., 2011 |
| [15] | Exon 5 | c.487T>C | p.163Ser>Pro | Al-Saud et al., 2009 |
| [16] | Exon 5 | c.520G>C | p.174Ala>Pro | Walker et al., 2011 |
| [17] | Exon 5 | c.569G>T | p.190Gly>Val | Walker et al., 2011 |
| [18] | Exon 5 | c.575A>G | p.192Tyr>Cys | Walker et al., 2011 |
| [19] | Exon 6 | c.700C>G | p.Arg234X | Walker et al., 2011 |
| [20] | Exon 6 | c.701G>C | p.234Arg>Pro | Walker et al., 2011 |
| [21] | Exon 6 | c.729C>G | p.Asn243Lys | Brodszki et al., 2015 |
| [22] | Exon 6 | c.730delA | p.Lys244ArgfsX17 | Walker et al., 2011 |
| [23] | Exon 6 | .746A>C | p.Tyr249Cys | Brodszki et al., 2015 |
| [25] | Exon 6 | c.770A>G | p.257His>Arg | Walker et al., 2011 |
| [26] | Intron 3 | c.285+1G>A | p.Val61GlyfsX30 | Walker et al., 2011 |
Implicated in
When PNP is defective, dGTP accumulation inhibits DNA replication and mitochondrial DNA repair which cause increased sensitivity of T lymphocytes to DNA damage and apoptosis during thymus selection. In addition, the lack of DNA replication is critical especially in the immune system: PNP deficiency leads to S-phase block in 7-11% of circulating lymphocytes. Mutations leading to PNP deficiency result in an autosomal recessive disorder known as severe combined immune deficiency (SCID) characterized by a profound deficiency in T cell function with variable B cell involvement. PNP deficiency is a very rare autosomal recessive condition, accounting for approximately 4% of all SCID cases (Madkaikar et al., 2011; Ghodke-Puranik et al., 2017). Small hypoplastic thymus, reduced T lymphocytes in peripheral blood, abnormal response of T lymphocytes to stimulation, and enlarged spleen are found in most PNP-deficient patients (Toro and Grunebaum, 2006). Lymphopenia, reduced serum uric acid, and abnormal PNP enzymatic activity assist in the diagnosis of PNP deficiency. Patients with SCID lack virtually all immune protection from foreign invaders such as bacteria, viruses, and fungi, therefore they are prone to repeated and persistent infections that can be very detrimental and life threatening. About two-thirds of individuals with PNP deficiency have neurological problems, including hypertonia, spasticity, tremors, ataxia, retarded motor development, behavioral difficulties, and varying degrees of mental retardation. People with PNP deficiency are also at increased risk of developing autoimmune disorders (autoimmune hemolytic anemia, idiopathic thrombocytopenic purpura-ITP, autoimmune neutropenia, thyroiditis, and lupus). Infants with SCID typically grow much more slowly than healthy children and experience pneumonia, chronic diarrhea, and widespread skin rashes. Without successful treatment to restore immune function, children with SCID usually live only into early childhood. Lymphoma and lymphosarcoma have also been reported in children with PNP immunodeficiency (Ghodke-Puranik et al., 2017; Arpaia et al., 2000).
On the other hand, PNP levels are significantly upregulated in several tumor cells (Figure 6). In comparison with healthy individuals, PNP activity was shown to be higher in lymphocytes of patients suffering from bronchogenic carcinoma (Gierek et al., 1987; Rendeková et al., 1983). Sanfilippo et al. claimed a relationship between tissue PNP and tumor invasiveness in human colon carcinoma (Sanfilippo et al., 1994). Furthermore, Roberts et al. showed that plasma PNP activity was higher also in patients with breast, gastric, colon, lung and ovarian cancers and lymphoma (Roberts et al., 2004). From the biomarker perspective, Vareed et al. found that PNP levels were higher in sera from pancreatic adenocarcinoma patients and levels of PNP-regulated metabolites in serum, guanosine and adenosine, were suitable to determine pancreatic adenocarcinoma and distinguish pancreatic adenocarcinoma from benign tumors (Vareed et al., 2011). Plasma PNP activity was also higher in patients with asthma than in either healthy subjects or patients with gout (Yamamoto et al., 1995). However, a low level of PNP activity was found in mononuclear cells from patients with acute myeloid and lymphoblastic leukemia and with chronic lymphocytic leukemia (Morisaki et al., 1986).
Treatment
Bone marrow transplantation in PNP deficiency has been attempted with variable degree of success. However, HLA-matched donors are not readily available, and transplants using HLA incompatible donors are frequently result in procedure-related morbidity, graft-versus-host disease or graft loss (Liao et al., 2008). Myers et al. suggested umbilical cord blood, a readily available and pathogen-free source of stem cells, transplantation as a treatment option for patients with PNP deficiency who do not have a HLA-matched donor (Myers et al., 2004).
Gene therapy with autologous cells, either total bone marrow (BM) or hematopoietic stem cells (HSCs) isolated from the BM, transduced with the normal gene sequence that can express the missing protein represents an attractive option for inherited hematological and immunological defects, including PNP deficiency (Liao et al., 2008). In in vitro, Foresman et al. showed that retroviral-mediated PNP gene transfer and expression correct the metabolic defects caused by PNP deficiency in murine lymphoid cells (Foresman et al., 1992). In PNP -/- mouse model, PNP deficiency was corrected by transplanting BM cells which have been transduced with lentiviral vectors containing the human PNP gene (lentiPNP) (Liao et al., 2008). However, 12 weeks after transplant, benefit of lentiPNP transduced cells decreased, which indicates that an improved gene expression strategy is required to afford a successful gene therapy for PNP deficiency (Liao et al., 2008). Indeed, PNP enzyme replacement therapy has been evaluated in PNP -/- mice by administration of PNP fused trans-activator of transcription (TAT) protein (TAT-PNP). TAT induced rapid and efficient delivery of active PNP into many tissues, including the brain, and TAT-PNP remained effective over 24 weeks post-treatment, and corrected metabolic abnormalities and immunodeficiency, and extended survival (Toro and Grunebaum, 2006). Similarly, PNP fused with protein transduction domain (PTD) from TAT protein was found to rapidly enter PNP deficient lymphocytes and increase intracellular enzyme activity for 96 h, and correct abnormal functions of PNP deficient lymphocytes including their response to stimulation and IL-2 secretion, in vitro (Toro et al., 2006). These results show that fusion protein approach for PNP deficiency is an attractive and promising method for intracellular delivery of PNP.
Since PNP deficiency results in selective cellular immunodeficiency, PNP inhibitors are considered to be potentially effective suppressors of T cell proliferative diseases, such as T cell lymphoma and T cell related autoimmune diseases, and may also be useful for the suppression of the graft-versus-host reaction (Ting et al., 2004). In addition, PNP inhibitors have shown to be promising based on their ability to potentiate the in vivo activity of antiviral and anticancer drugs (Erion et al., 1997). As an enzyme prodrug model, Krais et al. generated a fusion protein called as PNP-AV which is composed of E. coli PNP and human annexin V (AV). AV binds to phosphatidylserine (PS) expressed externally on tumor cells and endothelial cells of tumor vasculature, but not normal vascular endothelial cells. In in vitro, the recombinant fusion protein of PNP-AV was shown to bind and kill breast cancer and endothelial cells when used in the enzyme prodrug therapy with fludarabine. Krais et al. proposed that this approach allows for systemic administration of the fusion protein, with targeted accumulation of PNP in the tumor. After clearance of PNP-AV from the bloodstream, fludarabine, the substrate of E. coli PNP, can be administered systemically, so that 2-fluoroadenine is generated at the surface of the endothelial cells lining the tumor vasculature. This freely diffusible molecule is able to enter the cell and inhibit protein, RNA, and DNA synthesis in endothelial cell of tumor blood vessel. Since fludarabine is not a substrate of human PNP, the conversion of fludarabine to 2-fluoroadenine will not occur in normal tissue. Therefore, authors suggested that this strategy can be successful as a targeted therapy for breast cancer (Krais et al., 2013). More recently, phase I dose-escalating trial of E. coli PNP-fludarabine treatment was demonstrated to be safe and effective in head and neck squamous cell carcinoma, adenoid cystic carcinoma and melanoma. Successful regression of tumors without significant toxicity was shown in this first-in-human study of an effective prodrug activation strategy using E. coli PNP (Rosenthal et al., 2015).

Article Bibliography
| Pubmed ID | Last Year | Title | Authors |
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Other Information
Locus ID:
NCBI: 4860
MIM: 164050
HGNC: 7892
Ensembl: ENSG00000198805
Variants:
dbSNP: 4860
ClinVar: 4860
TCGA: ENSG00000198805
COSMIC: PNP
RNA/Proteins
Expression (GTEx)
Pathways
Protein levels (Protein atlas)
References
| Pubmed ID | Year | Title | Citations |
|---|---|---|---|
| 36538016 | 2023 | Connecting Conformational Motions to Rapid Dynamics in Human Purine Nucleoside Phosphorylase. | 7 |
| 38431953 | 2023 | Purine Nucleoside Phosphorylase Deficiency in Two Unrelated Patients with Autoimmune Hemolytic Anemia and Eosinophilia: Two Novel Mutations. | 0 |
| 36538016 | 2023 | Connecting Conformational Motions to Rapid Dynamics in Human Purine Nucleoside Phosphorylase. | 7 |
| 38431953 | 2023 | Purine Nucleoside Phosphorylase Deficiency in Two Unrelated Patients with Autoimmune Hemolytic Anemia and Eosinophilia: Two Novel Mutations. | 0 |
| 32514656 | 2020 | A Case with Purine Nucleoside Phosphorylase Deficiency Suffering from Late-Onset Systemic Lupus Erythematosus and Lymphoma. | 4 |
| 32514656 | 2020 | A Case with Purine Nucleoside Phosphorylase Deficiency Suffering from Late-Onset Systemic Lupus Erythematosus and Lymphoma. | 4 |
| 29915028 | 2018 | Inverse enzyme isotope effects in human purine nucleoside phosphorylase with heavy asparagine labels. | 13 |
| 29915028 | 2018 | Inverse enzyme isotope effects in human purine nucleoside phosphorylase with heavy asparagine labels. | 13 |
| 27976868 | 2017 | Thermodynamics of the Purine Nucleoside Phosphorylase Reaction Revealed by Computer Simulations. | 0 |
| 28859258 | 2017 | Lupus-Associated Functional Polymorphism in PNP Causes Cell Cycle Abnormalities and Interferon Pathway Activation in Human Immune Cells. | 15 |
| 27976868 | 2017 | Thermodynamics of the Purine Nucleoside Phosphorylase Reaction Revealed by Computer Simulations. | 0 |
| 28859258 | 2017 | Lupus-Associated Functional Polymorphism in PNP Causes Cell Cycle Abnormalities and Interferon Pathway Activation in Human Immune Cells. | 15 |
| 26985580 | 2016 | Computer Simulations Reveal Substrate Specificity of Glycosidic Bond Cleavage in Native and Mutant Human Purine Nucleoside Phosphorylase. | 2 |
| 26985580 | 2016 | Computer Simulations Reveal Substrate Specificity of Glycosidic Bond Cleavage in Native and Mutant Human Purine Nucleoside Phosphorylase. | 2 |
| 25338677 | 2015 | Genetic analysis of the pathogenic molecular sub-phenotype interferon-alpha identifies multiple novel loci involved in systemic lupus erythematosus. | 38 |
Citation
Rafig Gurbanov ; Sinem Tunçer
PNP (Purine Nucleoside Phosphorylase)
Atlas Genet Cytogenet Oncol Haematol. 2018-03-01
Online version: http://atlasgeneticsoncology.org/gene/46893/new-content/helping-you
