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Carpenter KA, Altman RB. Databases of ligand-binding pockets and protein-ligand interactions. Comput Struct Biotechnol J 2024; 23:1320-1338. [PMID: 38585646 PMCID: PMC10997877 DOI: 10.1016/j.csbj.2024.03.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 03/16/2024] [Accepted: 03/17/2024] [Indexed: 04/09/2024] Open
Abstract
Many research groups and institutions have created a variety of databases curating experimental and predicted data related to protein-ligand binding. The landscape of available databases is dynamic, with new databases emerging and established databases becoming defunct. Here, we review the current state of databases that contain binding pockets and protein-ligand binding interactions. We have compiled a list of such databases, fifty-three of which are currently available for use. We discuss variation in how binding pockets are defined and summarize pocket-finding methods. We organize the fifty-three databases into subgroups based on goals and contents, and describe standard use cases. We also illustrate that pockets within the same protein are characterized differently across different databases. Finally, we assess critical issues of sustainability, accessibility and redundancy.
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Affiliation(s)
- Kristy A. Carpenter
- Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA
| | - Russ B. Altman
- Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
- Department of Medicine, Stanford University, Stanford, CA 94305, USA
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2
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Chen Y, Li Y, Gao J, Yu Q, Zhang Y, Zhang J. Perspectives and challenges in developing small molecules targeting purine nucleoside phosphorylase. Eur J Med Chem 2024; 271:116437. [PMID: 38701712 DOI: 10.1016/j.ejmech.2024.116437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 04/16/2024] [Accepted: 04/17/2024] [Indexed: 05/05/2024]
Abstract
As a cytosolic enzyme involved in the purine salvage pathway metabolism, purine nucleoside phosphorylase (PNP) plays an important role in a variety of cellular functions but also in immune system, including cell growth, apoptosis and cancer development and progression. Based on its T-cell targeting profile, PNP is a potential target for the treatment of some malignant T-cell proliferative cancers including lymphoma and leukemia, and some specific immunological diseases. Numerous small-molecule PNP inhibitors have been developed so far. However, only Peldesine, Forodesine and Ulodesine have entered clinical trials and exhibited some potential for the treatment of T-cell leukemia and gout. The most recent direction in PNP inhibitor development has been focused on PNP small-molecule inhibitors with better potency, selectivity, and pharmacokinetic property. In this perspective, considering the structure, biological functions, and disease relevance of PNP, we highlight the recent research progress in PNP small-molecule inhibitor development and discuss prospective strategies for designing additional PNP therapeutic agents.
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Affiliation(s)
- Yangyang Chen
- Department of Neurology, Laboratory of Neuro-system and Multimorbidity and State Key Laboratory of Biotherapy and Cancer Center and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Yang Li
- Department of Neurology, Laboratory of Neuro-system and Multimorbidity and State Key Laboratory of Biotherapy and Cancer Center and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Jing Gao
- Department of Neurology, Laboratory of Neuro-system and Multimorbidity and State Key Laboratory of Biotherapy and Cancer Center and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Quanwei Yu
- Department of Neurology, Laboratory of Neuro-system and Multimorbidity and State Key Laboratory of Biotherapy and Cancer Center and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China; Department of Respiratory and Critical Care Medicine, Targeted Tracer Research and Development Laboratory, Institute of Respiratory Health, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China.
| | - Yiwen Zhang
- Department of Neurology, Laboratory of Neuro-system and Multimorbidity and State Key Laboratory of Biotherapy and Cancer Center and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China.
| | - Jifa Zhang
- Department of Neurology, Laboratory of Neuro-system and Multimorbidity and State Key Laboratory of Biotherapy and Cancer Center and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China.
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3
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Nassogne MC, Marie S, Dewulf JP. Neurological presentations of inborn errors of purine and pyrimidine metabolism. Eur J Paediatr Neurol 2024; 48:69-77. [PMID: 38056117 DOI: 10.1016/j.ejpn.2023.11.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 11/25/2023] [Accepted: 11/30/2023] [Indexed: 12/08/2023]
Abstract
Purines and pyrimidines are essential components as they are the building blocks of vital molecules, such as nucleic acids, coenzymes, signalling molecules, as well as energy transfer molecules. Purine and pyrimidine metabolism defects are characterised by abnormal concentrations of purines, pyrimidines and/or their metabolites in cells or body fluids. This phenomenon is due to a decreased or an increased activity of enzymes involved in this metabolism and has been reported in humans for over 60 years. This review provides an overview of neurological presentations of inborn errors of purine and pyrimidine metabolism. These conditions can lead to psychomotor retardation, epilepsy, hypotonia, or microcephaly; sensory involvement, such as deafness and visual disturbances; multiple malformations, as well as muscular symptoms. Clinical signs are often nonspecific and thus overlooked, but some diseases are treatable and early diagnosis may improve the child's future. Although these metabolic hereditary diseases are rare, they are most probably under-diagnosed. When confronted with suggestive clinical or laboratory signs, clinicians should prescribe genetic testing in association with a biochemical screening including thorough purine and pyrimidine metabolites analysis and/or specific enzyme evaluation. This is most likely going to increase the number of confirmed patients.
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Affiliation(s)
- Marie-Cécile Nassogne
- Service de Neurologie Pédiatrique, Cliniques Universitaires Saint-Luc, UCLouvain, B-1200, Brussels, Belgium; Institut des Maladies Rares, Cliniques Universitaires Saint-Luc, UCLouvain, B-1200, Brussels, Belgium.
| | - Sandrine Marie
- Laboratoire des Maladies Métaboliques Héréditaires/Biochimie Génétique et Centre de Dépistage Néonatal, Cliniques Universitaires Saint-Luc, UCLouvain, B-1200, Brussels, Belgium.
| | - Joseph P Dewulf
- Institut des Maladies Rares, Cliniques Universitaires Saint-Luc, UCLouvain, B-1200, Brussels, Belgium; Laboratoire des Maladies Métaboliques Héréditaires/Biochimie Génétique et Centre de Dépistage Néonatal, Cliniques Universitaires Saint-Luc, UCLouvain, B-1200, Brussels, Belgium.
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4
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Alizadeh Z, Badalzadeh M, Heydarlou H, Shakerian L, Mahlooji rad M, Zandieh F, Fazlollahi MR. Purine Nucleoside Phosphorylase Deficiency in Two Unrelated Patients with Autoimmune Hemolytic Anemia and Eosinophilia: Two Novel Mutations. ARCHIVES OF IRANIAN MEDICINE 2023; 26:712-716. [PMID: 38431953 PMCID: PMC10915924 DOI: 10.34172/aim.2023.105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Accepted: 07/03/2023] [Indexed: 03/05/2024]
Abstract
Two Iranian patients with purine nucleoside phosphorylase (PNP) deficiency are described in terms of their clinical and molecular evaluations. PNP deficiency is a rare form of combined immunodeficiency with a profound cellular defect. Patients with PNP deficiency suffer from variable recurrent infections, hypouricemia, and neurological manifestations. Furthermore, patient 1 developed mild cortical atrophy, and patient 2 presented developmental delay, general muscular hypotonia, and food allergy. The two unrelated patients with developed autoimmune hemolytic anemia and T cells lymphopenia and eosinophilia were referred to Immunology, Asthma and Allergy Research Institute (IAARI) in 2019. After taking blood and DNA extraction, genetic analysis of patient 1 was performed by PCR and direct sequencing and whole exome sequencing was applied for patient 2 and the result was confirmed by direct sequencing in the patient and his parents. The genetic result showed two novel variants in exon 3 (c.246_285+9del) and exon 5 (c.569G>T) PNP (NM_000270.4) in the patients, respectively. These variants are considered likely pathogenic based on the American College of Medical Genetics and Genomics (ACMG) guideline. PNP deficiency has a poor prognosis; therefore, early diagnosis would be vital to receive hematopoietic stem cell transplantation (HSCT) as a prominent and successful treatment.
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Affiliation(s)
- Zahra Alizadeh
- Immunology, Asthma and Allergy Research Institute, Tehran University of Medical Sciences, Tehran, Iran
- Children’s Medical Center, Pediatrics Center of Excellence, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohsen Badalzadeh
- Immunology, Asthma and Allergy Research Institute, Tehran University of Medical Sciences, Tehran, Iran
- Children’s Medical Center, Pediatrics Center of Excellence, Tehran University of Medical Sciences, Tehran, Iran
| | - Hanieh Heydarlou
- Immunology, Asthma and Allergy Research Institute, Tehran University of Medical Sciences, Tehran, Iran
- Children’s Medical Center, Pediatrics Center of Excellence, Tehran University of Medical Sciences, Tehran, Iran
| | - Leila Shakerian
- Immunology, Asthma and Allergy Research Institute, Tehran University of Medical Sciences, Tehran, Iran
- Children’s Medical Center, Pediatrics Center of Excellence, Tehran University of Medical Sciences, Tehran, Iran
| | - Maryam Mahlooji rad
- Immunology, Asthma and Allergy Research Institute, Tehran University of Medical Sciences, Tehran, Iran
- Children’s Medical Center, Pediatrics Center of Excellence, Tehran University of Medical Sciences, Tehran, Iran
| | - Fariborz Zandieh
- Department of Asthma, Allergy and Immunology, Bahrami Children Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammad Reza Fazlollahi
- Immunology, Asthma and Allergy Research Institute, Tehran University of Medical Sciences, Tehran, Iran
- Children’s Medical Center, Pediatrics Center of Excellence, Tehran University of Medical Sciences, Tehran, Iran
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Xu R, Peng J, Ma Z, Xie K, Li M, Wang Q, Guo X, Nan N, Wang S, Li J, Xu J, Gong M. Prolonged administration of total glucosides of paeony improves intestinal immune imbalance and epithelial barrier damage in collagen-induced arthritis rats based on metabolomics-network pharmacology integrated analysis. Front Pharmacol 2023; 14:1187797. [PMID: 38026929 PMCID: PMC10679728 DOI: 10.3389/fphar.2023.1187797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 10/25/2023] [Indexed: 12/01/2023] Open
Abstract
Rheumatoid arthritis (RA) is a chronic systemic autoimmune disease characterized by synovial inflammation and joint damage with complex pathological mechanisms. In recent years, many studies have shown that the dysregulation of intestinal mucosal immunity and the damage of the epithelial barrier are closely related to the occurrence of RA. Total glucosides of paeony (TGP) have been used clinically for the treatment of RA in China for decades, while the pharmacological mechanism is still uncertain. The purpose of this study was to investigate the regulatory effect and mechanism of TGP on intestinal immunity and epithelial barrier in RA model rats. The results showed that TGP alleviated immune hyperfunction by regulating the ratio of CD3+, CD4+ and CD8+ in different lymphocyte synthesis sites of the small intestine, including Peyer's patches (PPs), intraepithelial lymphocytes (IELs), and lamina propria lymphocytes (LPLs). Specially, TGP first exhibited immunomodulatory effects on sites close to the intestinal lumen (IELs and LPLs), and then on PPs far away from the intestinal lumen as the administration time prolonged. Meanwhile, TGP restores the intestinal epithelial barrier by upregulating the ratio of villi height (V)/crypt depth (C) and expression of tight junction proteins (ZO-1, occludin). Finally, the integrated analysis of metabolomics-network pharmacology was also used to explore the possible regulation mechanism of TGP on the intestinal tract. Metabolomics analysis revealed that TGP reversed the intestinal metabolic profile disturbance in CIA rats, and identified 32 biomarkers and 163 corresponding targets; network pharmacology analysis identified 111 potential targets for TGP to treat RA. By intersecting the results of the two, three key targets such as ADA, PNP and TYR were determined. Pharmacological verification experiments showed that the levels of ADA and PNP in the small intestine of CIA rats were significantly increased, while TGP significantly decreased their ADA and PNP levels. In conclusion, purine metabolism may play an important role in the process of TGP improving RA-induced intestinal immune imbalance and impaired epithelial barrier.
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Affiliation(s)
- Rui Xu
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, China
- Beijing Key Laboratory of Traditional Chinese Medicine Collateral Disease Theory Research, Beijing, China
| | - Jine Peng
- Department of Pharmacy, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Zhe Ma
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, China
- Beijing Key Laboratory of Traditional Chinese Medicine Collateral Disease Theory Research, Beijing, China
| | - Kaili Xie
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, China
- Beijing Key Laboratory of Traditional Chinese Medicine Collateral Disease Theory Research, Beijing, China
| | - Meijing Li
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, China
- Beijing Key Laboratory of Traditional Chinese Medicine Collateral Disease Theory Research, Beijing, China
| | - Qi Wang
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, China
- Beijing Key Laboratory of Traditional Chinese Medicine Collateral Disease Theory Research, Beijing, China
| | - Xiaomeng Guo
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, China
- Beijing Key Laboratory of Traditional Chinese Medicine Collateral Disease Theory Research, Beijing, China
| | - Nan Nan
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, China
- Beijing Key Laboratory of Traditional Chinese Medicine Collateral Disease Theory Research, Beijing, China
| | - Sihui Wang
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, China
- Beijing Key Laboratory of Traditional Chinese Medicine Collateral Disease Theory Research, Beijing, China
| | - Jing Li
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, China
- Beijing Key Laboratory of Traditional Chinese Medicine Collateral Disease Theory Research, Beijing, China
| | - Jingjing Xu
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, China
- Beijing Key Laboratory of Traditional Chinese Medicine Collateral Disease Theory Research, Beijing, China
| | - Muxin Gong
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, China
- Beijing Key Laboratory of Traditional Chinese Medicine Collateral Disease Theory Research, Beijing, China
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Karaaslan BG, Turan I, Aydemir S, Meric ZA, Atay D, Akcay A, Sari AA, Hershfield M, Cipe F, Aksoy BA, Ersoy GZ, Bozkurt C, Demirkol YK, Ozturk G, Aydogmus C, Kiykim A, Cokugras H. Neurologic Status of Patients with Purine Nucleoside Phosphorylase Deficiency Before and After Hematopoetic Stem Cell Transplantation. J Clin Immunol 2023; 43:2062-2075. [PMID: 37726596 DOI: 10.1007/s10875-023-01585-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 09/12/2023] [Indexed: 09/21/2023]
Abstract
BACKGROUND Purine nucleoside phosphorylase (PNP) deficiency is a rare autosomal recessive combined immunodeficiency. The phenotype is profound T cell deficiency with variable B and NK cell functions and results in recurrent and persistent infections that typically begin in the first year of life. Neurologic findings occur in approximately two-thirds of patients. The mechanism of neurologic abnormalities is unclear. Hematopoietic stem cell transplantation (HSCT) is the only curative treatment for PNP deficiency. METHODS We report here six patients from five unrelated families with PNP deficiency treated in two centers in Turkey. We evaluated the neurological status of patients and compared to post-transplantation period if available. Then, we performed PubMed, Google Scholar, and Researchgate searches using the terms "PNP" and "hematopoietic stem cell transplantation" to find all reported cases of PNP transplantation and compared to our cohort. RESULTS Six patients were treated in two centers in Turkey. One patient died from post-transplant complications. The other four patients underwent successful HSCT with good immune reconstitution after transplantation (follow-up 21-48 months) and good neurological outcomes. The other patient with a new mutation is still waiting for a matching HLA donor. DISCUSSION In PNP deficiency, clinical manifestations are variable, and this disease should be considered in the presence of many different clinical findings. Despite the comorbidities that occurred before transplantation, HSCT currently appears to be the only treatment option for this disease. HSCT not only cures immunologic disorders, but probably also improves or at least stabilizes the neurologic status of patients.
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Affiliation(s)
- Betul Gemici Karaaslan
- Department of Pediatric Immunology and Allergy, School of Medicine, Istanbul University-Cerrahpaşa, Istanbul, Turkey
| | - Isilay Turan
- Department of Pediatric Immunology and Allergy, University of Health Sciences, Basaksehir Cam and Sakura City Hospital, Istanbul, Turkey
| | - Sezin Aydemir
- Department of Pediatric Immunology and Allergy, School of Medicine, Istanbul University-Cerrahpaşa, Istanbul, Turkey
| | - Zeynep Akyuncu Meric
- Department of Pediatric Immunology and Allergy, School of Medicine, Istanbul University-Cerrahpaşa, Istanbul, Turkey
| | - Didem Atay
- Department of Pediatric Hematology/Oncology, Bone Marrow Transplantation Unit, School of Medicine, Altunizade Hospital, Acibadem University, Istanbul, Turkey
| | - Arzu Akcay
- Department of Pediatric Hematology/Oncology, Bone Marrow Transplantation Unit, School of Medicine, Altunizade Hospital, Acibadem University, Istanbul, Turkey
| | - Aysun Ayaz Sari
- Department of Pediatric Neurology, School of Medicine, Istanbul University-Cerrahpaşa, Istanbul, Turkey
| | - Michael Hershfield
- Department of Medicine, Department of Biochemistry, Duke University School of Medicine, Durham, NC, Duke University School of Medicine, Durham, NC, USA
| | - Funda Cipe
- Department of Pediatric Immunology and Allergy, University of Health Sciences, Basaksehir Cam and Sakura City Hospital, Istanbul, Turkey
- Department of Pediatric Allergy-Immunology & Pediatric Bone Marrow Transplantation Unit Altınbas University, Medical Park Bahcelievler Hospital, Istanbul, Turkey
| | - Basak Adakli Aksoy
- Department of Pediatric Allergy-Immunology & Pediatric Bone Marrow Transplantation Unit Altınbas University, Medical Park Bahcelievler Hospital, Istanbul, Turkey
| | - Gizem Zengin Ersoy
- Department of Pediatric Allergy-Immunology & Pediatric Bone Marrow Transplantation Unit Altınbas University, Medical Park Bahcelievler Hospital, Istanbul, Turkey
| | - Ceyhun Bozkurt
- Department of Pediatric Allergy-Immunology & Pediatric Bone Marrow Transplantation Unit Istinye University, Medical Park Bahcelievler Hospital, Istanbul, Turkey
| | | | - Gulyuz Ozturk
- Department of Pediatric Hematology/Oncology, Bone Marrow Transplantation Unit, School of Medicine, Altunizade Hospital, Acibadem University, Istanbul, Turkey
| | - Cigdem Aydogmus
- Department of Pediatric Immunology and Allergy, University of Health Sciences, Basaksehir Cam and Sakura City Hospital, Istanbul, Turkey
| | - Ayca Kiykim
- Department of Pediatric Immunology and Allergy, School of Medicine, Istanbul University-Cerrahpaşa, Istanbul, Turkey.
| | - Haluk Cokugras
- Department of Pediatric Immunology and Allergy, School of Medicine, Istanbul University-Cerrahpaşa, Istanbul, Turkey
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Habib Dzulkarnain SM, Hashim IF, Zainudeen ZT, Taib F, Mohamad N, Nasir A, Wan Ab Rahman WS, Ariffin H, Abd Hamid IJ. Purine Nucleoside Phosphorylase Deficient Severe Combined Immunodeficiencies: A Case Report and Systematic Review (1975-2022). J Clin Immunol 2023; 43:1623-1639. [PMID: 37328647 DOI: 10.1007/s10875-023-01532-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Accepted: 06/03/2023] [Indexed: 06/18/2023]
Abstract
Purine nucleoside phosphorylase deficient severe combined immunodeficiency (PNP SCID) is one of the rare autosomal recessive primary immunodeficiency disease, and the data on epidemiology and outcome are limited. We report the successful management of a child with PNP SCID and present a systematic literature review of published case reports, case series, and cohort studies on PNP SCID listed in PubMed, Web of Science, and Scopus from 1975 until March 2022. Forty-one articles were included from the 2432 articles retrieved and included 100 PNP SCID patients worldwide. Most patients presented with recurrent infections, hypogammaglobulinaemia, autoimmune manifestations, and neurological deficits. There were six reported cases of associated malignancies, mainly lymphomas. Twenty-two patients had undergone allogeneic hematopoietic stem cell transplantation with full donor chimerism seen mainly in those receiving matched sibling donors and/or conditioning chemotherapy before the transplant. This research provides a contemporary, comprehensive overview on clinical manifestations, epidemiology, genotype mutations, and transplant outcome of PNP SCID. These data highlight the importance of screening for PNP SCID in cases presented with recurrent infections, hypogammaglobulinaemia, and neurological deficits.
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Affiliation(s)
- Syarifah Masyitah Habib Dzulkarnain
- Primary Immunodeficiency Diseases Group, Department of Clinical Medicine, Advanced Medical and Dental Institute, Universiti Sains Malaysia, Bertam 13200 Kepala Batas, Pulau Pinang, Malaysia
- Cawangan Pulau Pinang, Fakulti Sains Kesihatan, Universiti Teknologi MARA, Kampus Bertam, 13200, Kepala Batas, Pulau Pinang, Malaysia
| | - Ilie Fadzilah Hashim
- Primary Immunodeficiency Diseases Group, Department of Clinical Medicine, Advanced Medical and Dental Institute, Universiti Sains Malaysia, Bertam 13200 Kepala Batas, Pulau Pinang, Malaysia
| | - Zarina Thasneem Zainudeen
- Primary Immunodeficiency Diseases Group, Department of Clinical Medicine, Advanced Medical and Dental Institute, Universiti Sains Malaysia, Bertam 13200 Kepala Batas, Pulau Pinang, Malaysia
| | - Fahisham Taib
- Department of Paediatric, School of Medical Sciences, Universiti Sains Malaysia, 16150 Kubang Kerian, Kelantan, Malaysia
- Hospital USM, 16150 Kubang Kerian, Kelantan, Malaysia
| | - Norsarwany Mohamad
- Department of Paediatric, School of Medical Sciences, Universiti Sains Malaysia, 16150 Kubang Kerian, Kelantan, Malaysia
- Hospital USM, 16150 Kubang Kerian, Kelantan, Malaysia
| | - Ariffin Nasir
- Department of Paediatric, School of Medical Sciences, Universiti Sains Malaysia, 16150 Kubang Kerian, Kelantan, Malaysia
- Hospital USM, 16150 Kubang Kerian, Kelantan, Malaysia
| | - Wan Suriana Wan Ab Rahman
- Hospital USM, 16150 Kubang Kerian, Kelantan, Malaysia
- School of Dental Sciences, Universiti Sains Malaysia, 16150 Kubang Kerian, Kelantan, Malaysia
| | - Hany Ariffin
- Department of Paediatrics, Faculty of Medicine, Universiti Malaya, 50603, Kuala Lumpur, Malaysia
| | - Intan Juliana Abd Hamid
- Primary Immunodeficiency Diseases Group, Department of Clinical Medicine, Advanced Medical and Dental Institute, Universiti Sains Malaysia, Bertam 13200 Kepala Batas, Pulau Pinang, Malaysia.
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8
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Camici M, Garcia-Gil M, Allegrini S, Pesi R, Bernardini G, Micheli V, Tozzi MG. Inborn Errors of Purine Salvage and Catabolism. Metabolites 2023; 13:787. [PMID: 37512494 PMCID: PMC10383617 DOI: 10.3390/metabo13070787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 06/20/2023] [Accepted: 06/21/2023] [Indexed: 07/30/2023] Open
Abstract
Cellular purine nucleotides derive mainly from de novo synthesis or nucleic acid turnover and, only marginally, from dietary intake. They are subjected to catabolism, eventually forming uric acid in humans, while bases and nucleosides may be converted back to nucleotides through the salvage pathways. Inborn errors of the purine salvage pathway and catabolism have been described by several researchers and are usually referred to as rare diseases. Since purine compounds play a fundamental role, it is not surprising that their dysmetabolism is accompanied by devastating symptoms. Nevertheless, some of these manifestations are unexpected and, so far, have no explanation or therapy. Herein, we describe several known inborn errors of purine metabolism, highlighting their unexplained pathological aspects. Our intent is to offer new points of view on this topic and suggest diagnostic tools that may possibly indicate to clinicians that the inborn errors of purine metabolism may not be very rare diseases after all.
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Affiliation(s)
- Marcella Camici
- Unità di Biochimica, Dipartimento di Biologia, Università di Pisa, Via San Zeno 51, 56127 Pisa, Italy
| | - Mercedes Garcia-Gil
- Unità di Fisiologia Generale, Dipartimento di Biologia, Università di Pisa, Via San Zeno 31, 56127 Pisa, Italy
- CISUP, Centro per l'Integrazione Della Strumentazione Dell'Università di Pisa, 56127 Pisa, Italy
- Centro di Ricerca Interdipartimentale Nutrafood "Nutraceuticals and Food for Health", Università di Pisa, 56126 Pisa, Italy
| | - Simone Allegrini
- Unità di Biochimica, Dipartimento di Biologia, Università di Pisa, Via San Zeno 51, 56127 Pisa, Italy
- CISUP, Centro per l'Integrazione Della Strumentazione Dell'Università di Pisa, 56127 Pisa, Italy
- Centro di Ricerca Interdipartimentale Nutrafood "Nutraceuticals and Food for Health", Università di Pisa, 56126 Pisa, Italy
| | - Rossana Pesi
- Unità di Biochimica, Dipartimento di Biologia, Università di Pisa, Via San Zeno 51, 56127 Pisa, Italy
| | - Giulia Bernardini
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università di Siena, Via A. Moro 2, 53100 Siena, Italy
| | - Vanna Micheli
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università di Siena, Via A. Moro 2, 53100 Siena, Italy
- LND Famiglie Italiane ODV-Via Giovanetti 15-20, 16149 Genova, Italy
| | - Maria Grazia Tozzi
- Unità di Biochimica, Dipartimento di Biologia, Università di Pisa, Via San Zeno 51, 56127 Pisa, Italy
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9
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Albayrak MGB, Simsek T, Kasap M, Akpinar G, Canturk NZ, Guler SA. Tissue proteome analysis revealed an association between cancer, immune system response, and the idiopathic granulomatous mastitis. MEDICAL ONCOLOGY (NORTHWOOD, LONDON, ENGLAND) 2022; 39:238. [PMID: 36175807 DOI: 10.1007/s12032-022-01845-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 09/06/2022] [Indexed: 11/27/2022]
Abstract
Idiopathic Granulomatous Mastitis (IGM) is a disease that clinically mimics breast cancers with symptoms of pain, edema, erythema, nipple discharge, nipple retraction, and fistula. Although IGM is considered to be formed by autoimmune responses or infections, the molecular mechanism behind formation and progress is unknown. Therefore, in this study, we aimed to investigate molecular mechanisms underlying IGM formation, progress, and recurrence by monitoring the changes at the proteome level. Protein extracts prepared from IGM (n = 15) and within-control tissues (n = 15) were subjected to nHPLC followed by LC-MS/MS proteomic analysis. Label-free quantitation analysis revealed that sixty differentially regulated between the two groups. Those proteins were classified based on their role in metabolic pathways using bioinformatics tools. Based on DAVID analysis, 16 of the differently regulated proteins were associated with the immune system, while 17 proteins were involved in cancer metabolism. STRING analysis showed that five of the differentially regulated proteins were associated with combined immune deficiency which were PNP, TAP1, ITGAL, PRKDC, and PTPRC while the other proteins were involved in insulin response and neutrophil degranulation. This study is one of the very few studies that investigated the changes in protein expressions of IGM tissues compared to controls. For the first time, we have shown the relationship of IGM with the immune system at the protein level and also underlined the cancer-like behavior of the disease. Furthermore, the proteins that were pointed out as combined immune deficiency-related proteins may have value as diagnostic markers for idiopathic granulomatous mastitis although further studies are needed to shed more light on the pathogenesis of the disease.
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Affiliation(s)
| | - Turgay Simsek
- Department of General Surgery, Medical School, Kocaeli University, 41001, Kocaeli, Turkey
| | - Murat Kasap
- Department of Medical Biology, Medical School, Kocaeli University, 41001, Kocaeli, Turkey
| | - Gurler Akpinar
- Department of Medical Biology, Medical School, Kocaeli University, 41001, Kocaeli, Turkey.
| | - Nuh Zafer Canturk
- Department of General Surgery, Medical School, Kocaeli University, 41001, Kocaeli, Turkey
| | - Sertac Ata Guler
- Department of General Surgery, Medical School, Kocaeli University, 41001, Kocaeli, Turkey
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Fox DA. Immunodeficiency and autoimmunity: companions not opposites. J Clin Invest 2022; 132:162170. [PMID: 35968787 PMCID: PMC9374371 DOI: 10.1172/jci162170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Autoimmunity has long been regarded as the polar opposite of immunodeficiency, but clinical and experimental evidence refute this notion. Indeed, numerous inborn or acquired immunodeficiency syndromes are characterized by the development of autoimmune complications in the setting of deficient immune defenses against microbial pathogens. Appreciation that much of the daily business of a healthy immune system is the avoidance of potentially harmful responses to innocuous environmental antigens or components of the host organism helps provide a context for these observations. In this issue of the JCI, Abt and colleagues report on purine nucleoside phosphorylase (PNP) deficiency, exploring the basis for the autoimmune complications that develop in this particular form of T cell immune deficiency and assigning a key role for overactivation of TLR7.
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