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Bai Q, He X, Hu T. Pan‑cancer analysis of the deoxyribonuclease gene family. Mol Clin Oncol 2023; 18:19. [PMID: 36798465 PMCID: PMC9926046 DOI: 10.3892/mco.2023.2615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 01/10/2023] [Indexed: 02/05/2023] Open
Abstract
Deoxyribonuclease (DNase) is an enzyme that catalyzes the cleavage of phosphodiester bonds in the main chain of DNA to degrade DNA. DNase serves a vital role in several immune-related diseases. The present study linked the expression of DNase with overall survival (OS), performed pan-cancer co-expression analysis, and assessed the association between DNase and immune infiltration subtypes, tumor microenvironment and drug sensitivity through pan-cancer studies. Furthermore, gene expression data and clinical data were downloaded from The Cancer Genome Atlas. Next, through a series of bioinformatics analyses, DNase expression and survival, immune subtypes, tumor microenvironment and drug sensitivity in 33 tumor types were systematically studied. The expression of the DNase gene family was shown to have an apparent intratumoral heterogeneity. The expression of DNase 2, lysosomal (DNASE2) was the highest in tumors, whereas that of DNASE2 β was the lowest. DNase 1-like 3 (DNASE1L3) was mainly downregulated in tumors, whereas the rest of the DNases were mainly upregulated in tumors. The expression of DNase family members was also found to be associated with the OS rate of patients. DNase family genes may serve an essential role in the tumor microenvironment. DNase family gene expression was related to the content of cytotoxic cells, Immunescore, Stromalscore, Estimatescore and Tumorpurity. The present study also revealed that the DNase genes may be involved in the drug resistance of cancer cells. Finally, the correlation between DNase, and clinical stage and tumor microenvironment in hepatocellular carcinoma (HCC) was studied. In addition, the difference in DNASE1L3 expression between HCC and adjacent normal tissues, and the relationship between DNASE1L3 expression and clinical stage was verified by analyzing three groups in a Gene Expression Omnibus dataset and by performing immunohistochemistry. In conclusion, the present study assessed DNase gene expression, analyzed its relationship with patient OS, performed pan-cancer co-expression analysis, and assessed the association between DNase and immune infiltration subtypes, tumor microenvironment and drug sensitivity. The present study also confirmed the value of further laboratory research on DNases and their prospects in clinical cancer treatment.
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Affiliation(s)
- Qingquan Bai
- Department of Hepatology and Gastroenterology, Campus Virchow Clinic and Campus Charité Mitte, Charité University Medicine, D-13353 Berlin, Germany,Cancer Research Center, School of Medicine, Xiamen University, Xiamen, Fujian 361102, P.R. China,Correspondence to: Dr Qingquan Bai, Department of Hepatology and Gastroenterology, Campus Virchow Clinic and Campus Charité Mitte, Charité University Medicine, Augustenburger Platz 1, D-13353 Berlin, Germany
| | - Xiao He
- Department of Neurology, The First Affiliated Hospital of Shandong First Medical University, Jinan, Shandong 250014, P.R. China
| | - Tianhui Hu
- Cancer Research Center, School of Medicine, Xiamen University, Xiamen, Fujian 361102, P.R. China,Correspondence to: Dr Qingquan Bai, Department of Hepatology and Gastroenterology, Campus Virchow Clinic and Campus Charité Mitte, Charité University Medicine, Augustenburger Platz 1, D-13353 Berlin, Germany
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Verhülsdonk L, Mannherz HG, Napirei M. Comparison of the secretory murine DNase1 family members expressed in Pichia pastoris. PLoS One 2021; 16:e0253476. [PMID: 34329318 PMCID: PMC8323900 DOI: 10.1371/journal.pone.0253476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 06/07/2021] [Indexed: 11/18/2022] Open
Abstract
Soluble nucleases of the deoxyribonuclease 1 (DNase1) family facilitate DNA and chromatin disposal (chromatinolysis) during certain forms of cell differentiation and death and participate in the suppression of anti-nuclear autoimmunity as well as thrombotic microangiopathies caused by aggregated neutrophil extracellular traps. Since a systematic and direct comparison of the specific activities and properties of the secretory DNase1 family members is still missing, we expressed and purified recombinant murine DNase1 (rmDNase1), DNase1-like 2 (rmDNase1L2) and DNase1-like 3 (rmDNase1L3) using Pichia pastoris. Employing different strategies for optimizing culture and purification conditions, we achieved yields of pure protein between ~3 mg/l (rmDNase1L2 and rmDNase1L3) and ~9 mg/l (rmDNase1) expression medium. Furthermore, we established a procedure for post-expressional maturation of pre-mature DNase still bound to an unprocessed tri-N-glycosylated pro-peptide of the yeast α-mating factor. We analyzed glycosylation profiles and determined specific DNase activities by the hyperchromicity assay. Additionally, we evaluated substrate specificities under various conditions at equimolar DNase isoform concentrations by lambda DNA and chromatin digestion assays in the presence and absence of heparin and monomeric skeletal muscle α-actin. Our results suggest that due to its biochemical properties mDNase1L2 can be regarded as an evolutionary intermediate isoform of mDNase1 and mDNase1L3. Consequently, our data show that the secretory DNase1 family members complement each other to achieve optimal DNA degradation and chromatinolysis under a broad spectrum of biological conditions.
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Affiliation(s)
- Lukas Verhülsdonk
- Department of Anatomy and Molecular Embryology, Medical Faculty, Ruhr-University Bochum, Bochum, Germany
| | - Hans Georg Mannherz
- Department of Anatomy and Molecular Embryology, Medical Faculty, Ruhr-University Bochum, Bochum, Germany.,Molecular and Experimental Cardiology, St. Josef-Hospital, Clinics of the Ruhr University Bochum, Bochum, Germany
| | - Markus Napirei
- Department of Anatomy and Molecular Embryology, Medical Faculty, Ruhr-University Bochum, Bochum, Germany
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Keyel PA. Dnases in health and disease. Dev Biol 2017; 429:1-11. [PMID: 28666955 DOI: 10.1016/j.ydbio.2017.06.028] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Revised: 05/22/2017] [Accepted: 06/26/2017] [Indexed: 10/24/2022]
Abstract
DNA degradation is critical to healthy organism development and survival. Two nuclease families that play key roles in development and in disease are the Dnase1 and Dnase2 families. While these two families were initially characterized by biochemical function, it is now clear that multiple enzymes in each family perform similar, non-redundant roles in many different tissues. Most Dnase1 and Dnase2 family members are poorly characterized, yet their elimination can lead to a wide range of diseases, including lethal anemia, parakeratosis, cataracts and systemic lupus erythematosus. Therefore, understanding these enzyme families represents a critical field of emerging research. This review explores what is currently known about Dnase1 and Dnase2 family members, highlighting important questions about the structure and function of family members, and how their absence translates to disease.
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Affiliation(s)
- Peter A Keyel
- Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409, United States.
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Ueki M, Kimura-Kataoka K, Fujihara J, Takeshita H, Iida R, Yasuda T. Evaluation of all nonsynonymous single-nucleotide polymorphisms in the gene encoding human deoxyribonuclease I-like 1, possibly implicated in the blocking of endocytosis-mediated foreign gene transfer. DNA Cell Biol 2013; 33:79-87. [PMID: 24329527 DOI: 10.1089/dna.2013.2248] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Many nonsynonymous single-nucleotide polymorphisms (SNPs) in the human deoxyribonuclease I-like 1 (DNase 1L1) gene, possibly implicated in the blocking of endocytosis-mediated foreign gene transfer, have been identified, but only limited population data are available and no studies have evaluated whether such SNPs are functional. Genotyping of all 21 nonsynonymous human DNase 1L1 SNPs was performed in 16 different populations representing three ethnic groups using the PCR-restriction fragment length polymorphism technique. All of the nonsynonymous SNPs, except for SNP p.Val122Ile in Caucasian populations, exhibited a monoallelic distribution in all of the populations. On the basis of alterations in the activity levels resulting from the corresponding amino acid substitutions, two activity-abolishing and four activity-reducing SNPs were confirmed to be functional. Although all of the nonsynonymous SNPs that affected the catalytic activity showed extremely low genetic heterogeneity, it seems plausible that a minor allele of six SNPs producing a loss-of-function or extremely low-activity variant could serve directly as a genetic risk factor for diseases. Especially, the amino acid residues in activity-abolishing SNPs were conserved in animal DNases 1L1. Furthermore, results of phylogenetic analysis suggest that DNase 1L1 might have appeared latest among the DNase I family during the course of molecular evolution.
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Affiliation(s)
- Misuzu Ueki
- 1 Division of Medical Genetics and Biochemistry, Faculty of Medical Sciences, University of Fukui , Fukui, Japan
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Fujihara J, Yasuda T, Iida R, Kimura-Kataoka K, Soejima M, Koda Y, Kato H, Panduro A, Yuasa I, Takeshita H. Global analysis of single nucleotide polymorphisms in the exons of human deoxyribonuclease I-like 1 and 2 genes. Electrophoresis 2010; 31:3552-7. [PMID: 20967767 DOI: 10.1002/elps.201000319] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Several SNPs in the deoxyribonuclease I-like 1 (DNase 1L1) and DNase 1L2 were investigated. In the present study, the genotype distributions of three synonymous SNPs (V59V, rs1050095; P67P, rs1130929; A277A, rs17849495) in the DNase 1L1 gene and four non-synonymous SNPs, V122I (rs34952165), Q170H (rs6643670), and D227A (rs5987256) in the DNase 1L1 gene, as well as D197A (rs62621282) in the DNase 1L2 gene were investigated in 13 populations. In all the populations, no variation was found in four SNPs (V59V, Q170H, D227A, and A277A) in DNASE1L1 or in D197A in DNASE1L2. As for V122I, only the German population showed a low degree of polymorphism. The SNP V122I in DNASE1L1 was monoallelic for the G-allele in all of the Asian and African populations examined, with no polymorphism being evident. Since the A-allele in SNP V122I was distributed in only the Caucasian populations, not in the other ethnic groups, it was confirmed that the A-allele in SNP V122I was Caucasian-specific. On the other hand, only P67P in DNASE1L1 was polymorphic among three synonymous SNPs. The effect of nucleotide substitution corresponding to polymorphic SNP P67P on DNase 1L1 activity was examined: the corresponding nucleotide substitution in polymorphic SNP P67P has little effect on the DNase activity.
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Affiliation(s)
- Junko Fujihara
- Department of Legal Medicine, Shimane University School of Medicine, Shimane, Japan
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Ueki M, Fujihara J, Takeshita H, Kimura-Kataoka K, Iida R, Nakajima T, Kominato Y, Yuasa I, Yasuda T. Genetic and expression analysis of all non-synonymous single nucleotide polymorphisms in the human deoxyribonuclease I-like 1 and 2 genes. Electrophoresis 2010; 31:2063-9. [DOI: 10.1002/elps.201000002] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Lichtenbelt KD, Sinke RJ, Ausems MGEM, Kroos MA, Reuser AJJ, Wokke JJH. Frequency of the deletion polymorphism of DNASE1L1 in 137 patients with acid maltase deficiency (Pompe disease). Exp Mol Pathol 2006; 80:308-9; author reply 310. [PMID: 16569403 DOI: 10.1016/j.yexmp.2006.02.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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MacLea KS, Krieser RJ, Eastman A. Structural requirements of human DNase II alpha for formation of the active enzyme: the role of the signal peptide, N-glycosylation, and disulphide bridging. Biochem J 2003; 371:867-76. [PMID: 12558498 PMCID: PMC1223339 DOI: 10.1042/bj20021875] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2002] [Revised: 01/23/2003] [Accepted: 01/31/2003] [Indexed: 11/17/2022]
Abstract
DNase II alpha (EC 3.1.22.1) is an endonuclease, which is active at low pH, that cleaves double-stranded DNA to short 3'-phosphoryl oligonucleotides. Although its biochemistry is well understood, its structure-activity relationship has been largely unexamined. Recently, we demonstrated that active DNase II alpha consists of one contiguous polypeptide, heavily glycosylated, and containing at least one intrachain disulphide linkage [MacLea, Krieser and Eastman (2002) Biochem. Biophys. Res. Commun. 292, 415-421]. The present paper describes further work to examine the elements of DNase II alpha protein required for activity. Truncated forms and site-specific mutants were expressed in DNase II alpha-null mouse cells. Results indicate that the signal-peptide leader sequence is required for correct glycosylation and that N-glycosylation is important for formation of the active enzyme. Despite this, enzymic deglycosylation of wild-type protein with peptide N-glycosidase F reveals that glycosylation is not intrinsically required for DNase activity. DNase II alpha contains six evolutionarily conserved cysteine residues, and mutations in any one of these cysteines completely ablated enzymic activity, consistent with the importance of disulphide bridging in maintaining correct protein structure. We also demonstrate that a mutant form of DNase II alpha that lacks the purported active-site His(295) can still bind DNA, indicating that this histidine residue is not simply involved in DNA binding, but may have a direct role in catalysis. These results provide a more complete model of the DNase II alpha protein structure, which is important for three-dimensional structural analysis and for production of DNase II alpha as a potential protein therapeutic for cystic fibrosis or other disorders.
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Affiliation(s)
- Kyle S MacLea
- Department of Pharmacology and Toxicology, Dartmouth Medical School, 7650 Remsen, Hanover, NH 03755, USA
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Chou SF, Chen HL, Lu SC. Up-regulation of human deoxyribonuclease II gene expression during myelomonocytic differentiation of HL-60 and THP-1 cells. Biochem Biophys Res Commun 2002; 296:48-53. [PMID: 12147225 DOI: 10.1016/s0006-291x(02)00835-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Several recent studies have suggested that intracellular deoxyribonuclease II (DNase II) is responsible for the degradation of DNA from apoptotic cells that are engulfed by macrophages. In this study, we studied DNase II expression during the phorbol 12-myristate-13-acetate (PMA)-induced differentiation of HL-60 and THP-1 cells. Basal levels of DNase II mRNA and protein were low, with expression being up-regulated approximately 15- and 7-fold, respectively, in HL-60 and THP-1 cells 72 h after PMA treatment. Nuclear run-on and luciferase reporter assays showed that transcription of DNase II gene was increased in PMA-treated cells. Together, these results demonstrate that DNase II gene transcription is increased during myelomonocytic differentiation, resulting in increased levels of mRNA and protein. This increase in DNase II levels in differentiated HL-60 and THP-1 cells suggests that it may play an important role in macrophages.
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Affiliation(s)
- San Fang Chou
- Department of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, Taipei, Taiwan
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Malferrari G, Mirabella M, D'Alessandra Y, Servidei S, Biunno I. Deletion polymorphism of DNASE1L1, an X-linked DNase I-like gene, in acid maltase deficiency disorders. Exp Mol Pathol 2001; 70:173-4. [PMID: 11263960 DOI: 10.1006/exmp.2001.2374] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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