Citation: Yong Wang, Li-qun Gu. Biomedical diagnosis perspective of epigenetic detections using alpha-hemolysin nanopore[J]. AIMS Materials Science, 2015, 2(4): 448-472. doi: 10.3934/matersci.2015.4.448
[1] | MD Main Uddin, Karen P Briski . Neuroestradiol regulation of ventromedial hypothalamic nucleus 5′-AMP-activated protein kinase activity and counterregulatory hormone secretion in hypoglycemic male versus female rats. AIMS Neuroscience, 2021, 8(1): 133-147. doi: 10.3934/Neuroscience.2021006 |
[2] | Masao Ito, Naoko Nisimaru . Cerebellar Control of Defense Reactions under Orexin-mediated Neuromodulation as a Model of Cerebellohypothalamic Interaction. AIMS Neuroscience, 2014, 1(1): 89-95. doi: 10.3934/Neuroscience.2014.1.89 |
[3] | Tevzadze Gigi, Zhuravliova Elene, Barbakadze Tamar, Shanshiashvili Lali, Dzneladze Davit, Nanobashvili Zaqaria, Lordkipanidze Tamar, Mikeladze David . Gut neurotoxin p-cresol induces differential expression of GLUN2B and GLUN2A subunits of the NMDA receptor in the hippocampus and nucleus accumbens in healthy and audiogenic seizure-prone rats. AIMS Neuroscience, 2020, 7(1): 30-42. doi: 10.3934/Neuroscience.2020003 |
[4] | Hannah P Priyanka, Rahul S Nair . Neuroimmunomodulation by estrogen in health and disease. AIMS Neuroscience, 2020, 7(4): 401-417. doi: 10.3934/Neuroscience.2020025 |
[5] | Nao Fukuwada, Miki Kanno, Satomi Yoshida, Kenjiro Seki . Gαq protein signaling in the bed nucleus of the stria terminalis regulate the lipopolysaccharide-induced despair-like behavior in mice. AIMS Neuroscience, 2020, 7(4): 438-458. doi: 10.3934/Neuroscience.2020027 |
[6] | Chacchu Bhattarai, Phanindra Prasad Poudel, Arnab Ghosh, Sneha Guruprasad Kalthur . The RET gene encodes RET protein, which triggers intracellular signaling pathways for enteric neurogenesis, and RET mutation results in Hirschsprung's disease. AIMS Neuroscience, 2022, 9(1): 128-149. doi: 10.3934/Neuroscience.2022008 |
[7] | Mani Pavuluri, Kelley Volpe, Alexander Yuen . Nucleus Accumbens and Its Role in Reward and Emotional Circuitry: A Potential Hot Mess in Substance Use and Emotional Disorders. AIMS Neuroscience, 2017, 4(1): 52-70. doi: 10.3934/Neuroscience.2017.1.52 |
[8] | Mani Pavuluri, Amber May . I Feel, Therefore, I am: The Insula and Its Role in Human Emotion, Cognition and the Sensory-Motor System. AIMS Neuroscience, 2015, 2(1): 18-27. doi: 10.3934/Neuroscience.2015.1.18 |
[9] | T. Virmani, F. J. Urbano, V. Bisagno, E. Garcia-Rill . The pedunculopontine nucleus: From posture and locomotion to neuroepigenetics. AIMS Neuroscience, 2019, 6(4): 219-230. doi: 10.3934/Neuroscience.2019.4.219 |
[10] | Ziphozethu Ndlazi, Oualid Abboussi, Musa Mabandla, Willie Daniels . Memantine increases NMDA receptor level in the prefrontal cortex but fails to reverse apomorphine-induced conditioned place preference in rats. AIMS Neuroscience, 2018, 5(4): 211-220. doi: 10.3934/Neuroscience.2018.4.211 |
Asthma is a chronic inflammatory disease of the airways characterized mainly by Th2 lymphocyte-mediated immune responses and associated with bronchial hyper-responsiveness, airflow obstruction, and airway remodelling. Th2-biased inflammation is associated with leukocytes recruitment and type-2 cytokines production. However other inflammatory pathways have been identified in asthmatic patients, depending on the clinical phenotype. Previous studies demonstrated that hyperactive Th17 and Th2 immune responses and their associated cytokines were involved in the development of asthma [1,2,3].
Antigen-specific activation of naive T lymphocytes requires double signals; T cell receptor (TCR) recognition of antigen bound to MHC on antigen presenting cells (APCs), and a second signal delivered through the interaction between the co-receptor CD28 and its cognate ligands CD80 and CD86 on the same APC [4]. The magnitude of the immune response is regulated by an intricate network of co-signalling cell-surface bound receptors and their corresponding ligands. Programmed Death 1 (PD-1), Cytotoxic T Lymphocyte-associated Antigen 4 (CTLA-4) and B- and T-lymphocyte Attenuator (BTLA) are three well characterized co-inhibitory receptors, through which cell activation and proliferation can be abated. CTLA-4 competes with CD28 for interaction with the CD80 and CD86 ligands on APCs, and by interfering with co-stimulation CTLA-4 can have an attenuating effect on T cell activation [5]. PD-1 is expressed on T-cells upon activation, and has two ligands; PD-L2, which is limited to APCs, and PD-L1, which is expressed on various immune cells [6]. BTLA is broadly expressed: on B and T lymphocytes, macrophages, dendritic cells and NK cells and can be either up- or down-regulated after stimulation depending on the cell type [7]. Its ligand Herpes Virus Entry Mediator (HVEM) is also expressed on both sides of the APC-lymphocyte entity. BTLA-HVEM as well as PD-1-PD-L1/PD-L2 interactions may convey an inhibiting signal [6]. Negative co-stimulatory pathways are important both in the defence against infection and in maintaining peripheral tolerance and immune homeostasis, which is illustrated by the fact that mice deficient in PD-1, BTLA or CTLA-4 develop autoimmune and lymphoproliferative disease [8]. While increased PD-1 expression on T cells is an established marker of immune paralysis in inflammatory diseases; the roles of CTLA-4 and BTLA remain to be determined [9].
To examine the participation of these soluble isoforms in immune regulation, we aimed to measure induced sputum concentrations of the soluble isoforms of PD-1, CTLA-4 and BTLA in patients with asthma and evaluate their usefulness as biomarkers and indicators of severity of disease. We also measured IL-17 and IL-26 as inflammatory mediators and their correlations with these soluble isoforms.
Eighty patients with well-defined women asthmatic patients (20 with moderate asthma, 20 with mild asthma and 40 patients with severe asthma) were recruited from the Department of Respiratory Disease, A. Mami Hospital (Ariana, Tunisia), using the criteria set by the Global Initiative for Asthma guidelines [10]. Asthma was diagnosed with exacerbations defined as episodes of a progressive increase in shortness of breath, cough, wheezing, or chest tightness, or a combination of these symptoms, requiring a change in treatment. Detailed definitions of the inclusion and exclusion criteria for the enrolment of asthmatic subjects were reported previously [3,11].
The protocols for the study were reviewed and approved by the ethics committees of our hospital, and informed consent was obtained from all participating subjects. Patients with asthma were treated with regular inhaled glucocorticoids (ICS), but variable daily doses were required to control the symptoms (at the time of evaluation daily ICS dose ranged 200-800 µg/day). Only patients whose asthma was controlled were retained. Table 1 describes the characteristics of the asthmatic patients in the study. Thirty healthy controls (all females) were recruited (aged 45-58 years) with no respiratory nor allergic manifestations. Spirometry was carried out in the patient and the control group. FEV1% was assessed by using a spirolab II.
The sputum was induced and processed as previously described [3,11,12,13]. Cell viability was determined by trypan blue exclusion and cytospins. Cells were stained with May-Grünwald-Giemsa to assess the differential cell count by counting 500 non-squamous cells under a light microscope.
sPD-1 was analyzed with RayBio® Human SP-D ELISA Kit (RayBiotech (Norcross, GA, USA)); All samples were diluted 1:1 in phosphate-buffered saline (PBS) (pH 7.4) and 1% bovine serum antigen (BSA) supplemented with 25 µg/ml heat-inactivated normal goat IgG (DAKO A/S, Rodovre, Denmark) to ensure pre-aggregation of heterophilic antibodies in the samples examined. The minimum detection limit (cut-off) was 0.040 ng/ml, calculated as two standard deviations of the blanks. Soluble BTLA was analyzed at 1:5 dilution with Human BTLA ELISA Kit, (range detection 0.47-30 ng/ml) (Cusabio Biotech (Wuhan, China)). Sputum sCTLA-4 was analyzed at 1:2 dilution with Human sCTLA-4 Platinum ELISA, (detection range 0.16-10 ng/ml) (CTLA-4 (Soluble) Human ELISA Kit; Bender Medsystems, Milano, Italy).
IL-17 concentrations in sputum supernatants were quantified using an Enzyme-Linked Immunosorbent Assay kit (Abcam, Cambridge, United Kingdom). Concentrations below the standard range of the assay (1.6 pg/ml) were set as zero. IL-26 was quantified in induced sputum using commercially available enzyme-linked immunosorbent assay kits (LS-F4914, LifeSpan) tested for non-specific binding as previously described [14]. Sputum fluid samples were blocked for heterophilic antibodies with bovine, murine, and rabbit immunoglobulin G (Jackson Immuno Research). ELISA-Amplification System (ELAST) (NEP116001EA, PerkinElmer) was applied before adding 3,3′,5,5′-tetramethylbenzidine (TMB); otherwise, the assays were performed according to the manufacturers protocol. Samples were analyzed in duplicates, and values below the detection limit were assigned the same value as the detection limit, which in this case was 15.63 pg/ml. Optical density (OD) was measured at 450 nm with a reference value of 570 nm (Thermo Scientific, Multiskan GO). Optical densities were converted to concentrations using a four-parametric logistic regression. All ELISA analyses were performed according to the manufacturers' instructions.
Data are shown as dot plots. The one way ANOVA, independent sample t-test, Bonferroni correction, Mann-Whitney test, Wilcoxon test and Kruskal-Wallis H test were applied using the SPSS17.0 software (SPSS Inc., Chicago, Illinois, USA). A p-value less than 0.05 were considered statistically significant.
The demographic and functional characteristics of the asthmatic patients and healthy subjects are summarized in Table 1. Asthmatic patients were no smoker. Overall there was no difference in BMI between asthmatics and healthy controls.
Results are given in Table 1. The percentage of lymphocytes, eosinophils and neutrophils were higher in asthmatic groups (p = 0.001) compared to healthy subjects. The percentage of sputum macrophages tended to be higher in healthy controls compared to all asthmatic groups (p < 0.005). The percentages of macrophages were not significantly different between the 3 asthmatic groups. Severe asthmatic patients expressed low lymphocytes percentage compared to mild and moderate asthmatics (p = 0.002). Eosinophils were increased in severe asthma compared to mild and moderate asthma (p = 0.0001). Low significant differences was observed between mid and moderate asthmatics in the eosinophil percentages (p = 0.0042).
Screening cohort | Healthy subjects | Mild asthma | Moderate asthma | Severe asthma |
Number | 30 | 20 | 20 | 40 |
Demographic characteristics Age (years), median (Range) | 54.7 (27-74) | 58 (51-66) | 55.7 (55-60) | 55.87 (26-75) |
Functional characteristics | ||||
FEV1 (% pred) | 109 ± 15.3 | 97.6 ± 12.8† | 92.56 ± 11.90† | 56.72 ± 14.72† |
FEV1/FVC ratio | 80.7 ± 6.7 | 74.7 ± 6.3† | 65.4 ± 7.8† | 61.1 ± 69.8† |
Sputum characteristics | ||||
Lymphocytes | 8.2 ± 4.95 | 20.47 ± 10.5† | 20.5 ± 4.9† | 13.5 ± 7.6† |
Macrophages (%) | 58.3 ± 16.9 | 41.47 ± 19.87† | 39.7 ± 5.7† | 44.2 ± 6.7† |
Neutrophils (%) | 21.8 ± 18.9 | 31.86 ± 14.80† | 38.2 ± 10.7† | 32.2 ± 12.4† |
Eosinophils (%) | 0.0 ± 0.00 | 3.96 ± 2.3† | 2.75 ± 1.4† | 9.2 ± 2.4† |
Data are expressed as distributions (yes/no), means ± SD, or medians with range. Comparisons were done with Pearson X2 tests or the Kruskal-Wallis test, followed by the Mann-Whitney U test with the Bonferroni correction. [†]: p < 0.005 versus healthy subjects. FEV1: forced expiratory volume in 1s; FVC: forced vital capacity. FEV1 (% pred) and FEV1/FVC ratio were significantly decreased in severe asthmatic patients compared to mild (p < 0.0001) and moderate (p < 0.0005) asthmatics. The percentage of lymphocytes was decreased in severe asthmatic compared to mild and moderate (p < 0.0001) asthma patients. |
Soluble BTLA sputum concentrations were highest in the asthmatic patients (42.48 ± 26.74 ng/ml; range: 10-105 ng/ml) compared to HC (16.79 ± 4.048 ng/ml; range: 9.0-24.9 ng/ml). Significant higher sBTLA were present in severe asthmatics (64.42 ± 20.63 ng/ml; range: 30-105 ng/ml) compared to mild (16.43 ± 3.60 ng/ml; range: 10-23) and moderate (24.35 ± 3.29 ng/ml; range: 18-29.3 ng/ml) asthmatic patients. No significant differences were observed between mild asthmatics and HC (p = 0.799) (Figure1A).
In severe asthmatic patients, sputum levels of sPD-1 were increased (6.077 ± 1.59 ng/ml; range: 3.5-9.2) compared with mild asthmatics (3.27 ± 0.98 ng/ml; range: 2-6) and healthy controls (3.23 ± 0.75 ng/ml; range: 1.5-5) (Figure 1B). No significant differences were observed between severe and moderate asthmatic patients (5.44 ± 1.2 ng/ml; range: 3.0-7.0; p = 0.124). Patients with mild asthma expressed similar levels than HC (p = 0.856). Soluble PD-1 was associated to FEV1 (% pred) in asthmatic patients (r = 0.574; p = 0.0007) (Figure 1C). Soluble CTLA-4 was detectable at low level in only 10 over 30 severe asthmatics (0.7 ± 0.2 ng/ml).
Levels of sputum IL-17 were highest in asthmatic patients: severe (31.50 ± 7.78 pg/ml), moderate (22.77 ± 2.90 pg/ml) and mild (18.72 ± 2.4 pg/ml) compared to healthy controls (3.22 ± 1.92 pg/ml; p < 0.0001) (Figure 2A). Significant differences were found between the 3 asthmatic stages (p < 0.0001). Significant correlation was observed between IL-17 and the sBTLA co-inhibitors (Figure 2B). Positive correlation was found between IL-17 cytokine and sPD-1 in asthmatic patients (r = 0.627; p = 0.0004).
We quantified IL-26 by ELISA in the sputum of asthmatic patients and controls. Values are expressed as mean ± standard deviation [SD] (Figure 3A). IL-26 concentrations were higher in asthmatic patients (3.66 ± 1.77 ng/ml; p < 0.0001) than in healthy controls (1.526 ± 0.52 ng/ml) (Figure 3A). In severe asthma, IL-26 levels were overexpressed (4.94 ± 1.6 ng/ml; p < 0.0001) as compared to moderate (2.57 ± 0.34 ng/ml) and mild asthma (2.21 ± 0.69 ng/ml). The concentration of IL-26 levels was significantly associated with the asthma clinical severity from severe to mild stages (Figure 3A). Low significant difference was observed between mild and healthy controls (p = 0.0456). No correlations were observed between IL-26, and sPD-1 or sCTLA-4. However, significant correlation was observed between sBTLA and IL-26 in asthma (r = 0.885; p < 0.0001) (Figure 3B).
Significant correlations were found between IL-26 and IL-17 levels, between IL-26 and the percentage of macrophages (Table 2), between IL-26 and FEV1% and between IL-26 and PNN%. Figure 4 represents correlations observed in severe asthmatic patients.
IL-26/IL-17 | IL-26/% of macrophages | IL-26/FEV1% | IL-26/% PNN | |
Severe asthma | r = 0.569 | r = 0.656 | r = 0.872 | r = 0.552 |
(p = 0.0001) | (p = 0.0001) | (p = 0.0001) | (p = 0.0002) | |
Moderate asthma | r = 0.736 | r = 0.587 | r = 0.734 | r = 0.547 |
(p = 0.0002) | (p = 0.0003) | (p = 0.0001) | (p = 0.0002) | |
Mild asthma | r = 0.512 | r = 0.572 | r = 0. 537 | r = 0.526 |
(p = 0.0021) | (p = 0. 0004) | (p = 0.0006) | (p = 0.0003) |
In the present study we found that sputum concentrations of the soluble isoform of the co-inhibitory receptor B- and T-lymphocyte Attenuator (sBTLA) were low in healthy individuals and elevated in asthmatic patients, particularly in severe asthmatics. Evaluation of sBTLA as a dynamic marker confirmed an association to disease severity. In the same way, soluble Programmed Death 1 (sPD-1) concentrations were higher in patients with severe asthma than in healthy subjects. Level of sPD-1 was associated with the asthma clinical severity. Soluble Cytotoxic T Lymphocyte-associated Antigen 4 (sCTLA-4) concentrations were low or undetectable. Previous studies on soluble CTLA-4 show increased plasma concentrations in several autoimmune disorders, but low or undetectable levels in healthy individuals. There might be certain pathogenic mechanisms present in autoimmune disease, but not in asthma. Perhaps due to the limited sensitivity of commercially available ELISA kits, sCTLA-4 is difficult to study. IL-17 and IL-26 were highly expressed in asthma sputum and correlate with sBTLA. IL-17 and IL-26 inflammatory axis was correlated to sputum cells: macrophages and neutrophils.
This is to our knowledge the first study of soluble co-inhibitory molecules and IL-26 in induced sputum from asthmatics. Soluble BTLA was highly expressed in severe asthmatic patients. The existence of sBTLA from healthy individuals has been demonstrated by Wang et al. [15]. The BTLA-HVEM pathway is complicated by the fact that HVEM has multiple partner molecules through which cross-linking results in either a co-stimulatory (LIGHT and LTα) or a co-inhibitory (BTLA and CD160) signal [16]. Therefore BTLA might be a more fine-tuned immune regulator than CTLA-4. The origin of sBTLA remains to be elucidated. Perhaps it is generated through alternative splicing of mRNA as has been demonstrated for sPD-1 and sCTLA-4 [17,18,19]. Another potential source of the measured BTLA is proteolytic cleavage of the outer part of the membrane-bound receptor, possibly representing a means of controlling T cell inhibition. In this study, sputum sBTLA concentrations were highest in the severe stage of asthmatics suggesting that sBTLA is a marker for an activated pathway in the immune system, triggered by inflammation. sBTLA concentrations and disease severity in the asthmatic cohort were associated; sBTLA and IL-17 were correlated and IL-17 concentration had higher levels than those with mild or moderate asthmatics. IL-26 was associated with the asthma clinical severity from mild to severe and correlates significantly with the macrophages and neutrophils percentages. The most important data found was the correlation of IL-26 with FEV1 (%). By using Spearman rank test and multiple regression analysis, our research showed that sputum IL-26 in severe asthmatics was closely related to sputum macrophage and neutrophil percentages. Sputum IL-17 and IL-26 should be of clinical relevance in the pathogenesis of asthma.
Our study suggested a key role for IL-17 and IL-26 during an asthma episode by showing a gradual rise in sputum with increasing asthma severity. Furthermore, we found a significant correlation between sputum IL-26 and neutrophils. To our knowledge, the role of IL-17 and IL-26 in neutrophilic asthmatic airway inflammation is supported, mainly from mouse models of asthma and the important pathologic effects of IL-17 in neutrophilic inflammation in other diseases, such as psoriasis [20], while much less from asthma patients [21]. For the first time, we reported a significant association between sputum IL-26 and the severity of asthma, leading to the assumption that IL-17/IL-26 axis is essential in the induction of an exacerbation, of the airway inflammation. It is intriguing that we observed an association for sputum IL-26 and % FEV1. In fact, the role of IL-17/IL-26 in asthma is complex and may have different functions. IL-26 favours the generation of inflammatory cells mainly through the induction of IL-17 production. Beside its inflammatory role, IL-26 also binds to self DNA and promotes the secretion of IFN-α by pDCs, which acts as an “alarmin” to activate the innate immune system and activate a response to tissue or cell damage. These new findings suggest an intriguing mechanism of action for IL-26 in asthma pathology.
The precise functions of the soluble form of PD-1 are not well described, and sPD-1 has been reported to exhibit both functional antagonism [22,23] and agonism [24]. Although sPD-1 is known to be bioactive, and an association with disease has been proposed [18]. The correlation of sPD-1 with FEV1% in asthmatic patients could indicate an ongoing attempt to dampen the immune activity in the severe stage of disease, where protective mechanisms are overruled by the high degree of inflammation. Significant positive correlation between sPD-1 and FEV1% (r = 0.743; p < 0.0001) was observed in severe asthmatic patients. Induced sputum was depicted to have high levels of inflammatory mediators IL-17, TNF-α, IL-6 [25,26,27,28].
Levels of IL-17 were highly expressed in asthma patients [3,27,28,29,30]. Recently Ricciardolo et al. [31] investigated the role of Th17 cytokines (IL-17A and IL-17) expression in nasal/bronchial biopsies obtained from atopic/non atopic mild-to-severe asthmatics. They observed a significant increased expression of IL-17F in severe asthma which was correlated to neutrophils, airway obstruction and disease exacerbation in severe asthma. The overexpressed IL-17F was also able to recognize frequent exacerbation phenotype potentially at risk of asthma death [31].
The results of our present study indicate that the sputum concentration of IL-26 was significantly increased in asthma patients compared with controls and the elevation correlated positively with disease severity. IL-17 was significantly correlated to the new IL-26 inflammatory cytokine. IL-26 is constitutively expressed in sputum of asthmatic patients which probably indicate its intrinsic production involving inflammation and matrix inflammation. The increased IL-26 level in sputum indicates its substantial and inducible release in the lung. Griffith et al. [32] indicated that IL-26 acted on different cell types in the lungs and it would be interesting to investigate its role during inflammatory airway conditions. Ohnuma et al. [33] reported that IL-26+CD26+CD4+ T cell infiltration appears to play a significant role in the lung of obliterative bronchiolitis [33]. They also demonstrated that human IL-26 induced collagen deposition in obliterative bronchiolitis of murine allogeneic transplantation model and that IL-17 was shown to be involved in the pathogenesis of obliterative bronchiolitis associated with chronic rejection [34]. We confirmed the implication of IL-26 in the processes of exacerbation in the lung of asthmatic disease. IL-26 is involved and plays a critical role in antibacterial host defence of human lungs. Che et al. [35] reported that IL-26 is abundantly produced and released by alveolar macrophages and possibly by local helper and cytotoxic T cells [35]. We reported significant positive correlation between IL-26 and the percentage of macrophages in asthma. IL-26 produced by alveolar macrophages can recruit the neutrophils via induction of chemotaxis factors such IL-8 and leukotaxin n-formyl-methionyl-leucylphenylalanine (fMLP) [36]. Both IL-8 gene and protein expression may play a key role in asthma pathogenesis [37].
Taken together, our results suggest that, although soluble co-inhibitory receptors do not appear to be good markers to diagnose asthma, sBTLA or sPD-1 may be of interest as a prognostic indicator, perhaps in combination with classical biomarkers, and that further studies on the immune pathways involving sBTLA may be of value in clarifying the pathogenesis in human asthma. Finally, this is an observational study and no conclusions can be drawn in terms of the underlying immunological mechanisms. The interesting finding should be the correlations observed in severe asthma with IL-17 and IL-26. Future mechanistic studies are required to examine the biological activity of sBTLA, sPD-1 and why high levels are associated with disease severity. It would be interesting to more investigate the role of IL-26 during inflammatory airway conditions such as asthma, where damage to epithelial cells is more prevalent. Our data provides a valuable contribution to our knowledge of the control of pathogens in the lungs, in particular the role that IL-26 plays in antibacterial host defensiveness of asthma lungs.
The authors declare no conflicts of interest in this paper.
[1] |
Dupont C, Armant DR, Brenner CA (2009) Epigenetics: Definition, mechanisms and clinical perspective. Semin Reprod Med 27: 351-357. doi: 10.1055/s-0029-1237423
![]() |
[2] |
Dawson MA, Kouzarides T (2012) Cancer epigenetics: From mechanism to therapy. Cell 150: 12-27. doi: 10.1016/j.cell.2012.06.013
![]() |
[3] |
Esteller M (2008) Molecular origins of cancer: Epigenetics in cancer. New Engl J Med 358: 1148-1159+1096. doi: 10.1056/NEJMra072067
![]() |
[4] |
Laird PW (2005) Cancer epigenetics. Hum Mol Genet 14: R65-R76. doi: 10.1093/hmg/ddi113
![]() |
[5] |
Okugawa Y, Grady WM, Goel A (2015) Epigenetic Alterations in Colorectal Cancer: Emerging Biomarkers. Gastroenterology 149: 1204-1225e1212. doi: 10.1053/j.gastro.2015.07.011
![]() |
[6] | Deng D, Liu Z, Du Y (2010) Epigenetic Alterations as Cancer Diagnostic, Prognostic, and Predictive Biomarkers. Adv Genet 71: 126-176. |
[7] |
Herceg Z, Hainaut P (2007) Genetic and epigenetic alterations as biomarkers for cancer detection, diagnosis and prognosis. Mol Oncol 1: 26-41. doi: 10.1016/j.molonc.2007.01.004
![]() |
[8] |
Dekker C (2007) Solid-state nanopores. Nat Nanotechnol 2: 209-215. doi: 10.1038/nnano.2007.27
![]() |
[9] |
Keyser UF (2011) Controlling molecular transport through nanopores. J R Soc Interface 8: 1369-1378. doi: 10.1098/rsif.2011.0222
![]() |
[10] |
Siwy ZS, Howorka S (2010) Engineered voltage-responsive nanopores. Chem Soc Rev 39: 1115-1132. doi: 10.1039/B909105J
![]() |
[11] |
Garaj S, Hubbard W, Reina A, et al. (2010) Graphene as a subnanometre trans-electrode membrane. Nature 467: 190-193. doi: 10.1038/nature09379
![]() |
[12] |
Siwy ZS, Davenport M (2010) Nanopores: Graphene opens up to DNA. Nat Nanotechnol 5: 697-698. doi: 10.1038/nnano.2010.198
![]() |
[13] |
Tada K, Haruyama J, Yang HX, et al. (2011) Graphene magnet realized by hydrogenated graphene nanopore arrays. Appl Phys Lett 99: 183111. doi: 10.1063/1.3653286
![]() |
[14] |
Ding S, Gao C, Gu LQ (2009) Capturing single molecules of immunoglobulin and ricin with an aptamer-encoded glass nanopore. Anal Chem 81: 6649-6655. doi: 10.1021/ac9006705
![]() |
[15] |
Gu LQ, Shim JW (2010) Single molecule sensing by nanopores and nanopore devices. Analyst 135: 441-451. doi: 10.1039/B907735A
![]() |
[16] | Fertig N, Meyer C, Blick RH, et al. (2001) Microstructured glass chip for ion-channel electrophysiology. Phys Rev E Stat Nonlin Soft Matter Phys 64: 409011-409014. |
[17] |
Li J, Stein D, McMullan C, et al. (2001) Ion-beam sculpting at nanometre length scales. Nature 412: 166-169. doi: 10.1038/35084037
![]() |
[18] |
Storm AJ, Chen JH, Ling XS, et al. (2003) Fabrication of solid-state nanopores with single-nanometre precision. Nat Mater 2: 537-540. doi: 10.1038/nmat941
![]() |
[19] |
Kasianowicz JJ, Brandin E, Branton D, et al. (1996) Characterization of individual polynucleotide molecules using a membrane channel. Proc Natl Acad Sci U S A 93: 13770-13773. doi: 10.1073/pnas.93.24.13770
![]() |
[20] |
Laszlo AH, Derrington IM, Brinkerhoff H, et al. (2013) Detection and mapping of 5-methylcytosine and 5-hydroxymethylcytosine with nanopore MspA. Proc Natl Acad Sci U S A 110: 18904-18909. doi: 10.1073/pnas.1310240110
![]() |
[21] | Laszlo AH, Derrington IM, Ross BC, et al. (2014) Decoding long nanopore sequencing reads of natural DNA. Nat Biotechnol 32: 829-833. |
[22] |
Wang Y, Montana V, Grubišić V, et al. (2015) Nanopore sensing of botulinum toxin type B by discriminating an enzymatically cleaved peptide from a synaptic protein synaptobrevin 2 derivative. ACS Appl Mater Inter 7: 184-192. doi: 10.1021/am5056596
![]() |
[23] |
Liu J, Eren E, Vijayaraghavan J, et al. (2012) OccK channels from Pseudomonas aeruginosa exhibit diverse single-channel electrical signatures but conserved anion selectivity. Biochemistry 51: 2319-2330. doi: 10.1021/bi300066w
![]() |
[24] |
Mohammad MM, Iyer R, Howard KR, et al. (2012) Engineering a rigid protein tunnel for biomolecular detection. J Am Chem Soc 134: 9521-9531. doi: 10.1021/ja3043646
![]() |
[25] |
Cheneke BR, van den Berg B, Movileanu L (2015) Quasithermodynamic contributions to the fluctuations of a protein nanopore. ACS Chem Biol 10: 784-794. doi: 10.1021/cb5008025
![]() |
[26] |
Wang HY, Li Y, Qin LX, et al. (2013) Single-molecule DNA detection using a novel SP1 protein nanopore. Chem Commun (Camb) 49: 1741-1743. doi: 10.1039/c3cc38939a
![]() |
[27] |
Wang S, Haque F, Rychahou PG, et al. (2013) Engineered nanopore of phi29 dna-packaging motor for real-time detection of single colon cancer specific antibody in serum. ACS Nano 7: 9814-9822. doi: 10.1021/nn404435v
![]() |
[28] |
Wu D, Bi S, Zhang L, et al. (2014) Single-molecule study of proteins by biological nanopore sensors. Sensors (Basel) 14: 18211-18222. doi: 10.3390/s141018211
![]() |
[29] |
Venkatesan BM, Bashir R (2011) Nanopore sensors for nucleic acid analysis. Nat Nanotechnol 6: 615-624. doi: 10.1038/nnano.2011.129
![]() |
[30] |
Hall AR, Scott A, Rotem D, et al. (2010) Hybrid pore formation by directed insertion of +Ý-haemolysin into solid-state nanopores. Nat Nanotechnol 5: 874-877. doi: 10.1038/nnano.2010.237
![]() |
[31] |
Bell NA, Engst CR, Ablay M, et al. (2012) DNA origami nanopores. Nano Lett 12: 512-517. doi: 10.1021/nl204098n
![]() |
[32] |
Iqbal SM, Akin D, Bashir R (2007) Solid-state nanopore channels with DNA selectivity. Nat Nanotechnol 2: 243-248. doi: 10.1038/nnano.2007.78
![]() |
[33] |
Tinazli A, Tang J, Valiokas R, et al. (2005) High-affinity chelator thiols for switchable and oriented immobilization of histidine-tagged proteins: a generic platform for protein chip technologies. Chemistry 11: 5249-5259. doi: 10.1002/chem.200500154
![]() |
[34] |
Wei R, Pedone D, Zurner A, et al. (2010) Fabrication of metallized nanopores in silicon nitride membranes for single-molecule sensing. Small 6: 1406-1414. doi: 10.1002/smll.201000253
![]() |
[35] |
Yusko EC, Johnson JM, Majd S, et al. (2011) Controlling protein translocation through nanopores with bio-inspired fluid walls. Nat Nanotechnol 6: 253-260. doi: 10.1038/nnano.2011.12
![]() |
[36] | Wang D, Harrer S, Luan B, et al. (2014) Regulating the transport of DNA through Biofriendly Nanochannels in a thin solid membrane. Sci Rep 4: 3985. |
[37] | Branton D, Deamer DW, Marziali A, et al. (2008) The potential and challenges of nanopore sequencing. Nat Nanotechnol 26: 1146-1153. |
[38] |
Cherf GM, Lieberman KR, Rashid H, et al. (2012) Automated forward and reverse ratcheting of DNA in a nanopore at 5-A precision. Nat Biotechnol 30: 344-348. doi: 10.1038/nbt.2147
![]() |
[39] |
Kasianowicz JJ, Brandin E, Branton D, et al. (1996) Characterization of individual polynucleotide molecules using a membrane channel. Proc Natl Acad Sci U S A 93: 13770-13773. doi: 10.1073/pnas.93.24.13770
![]() |
[40] |
Manrao EA, Derrington IM, Laszlo AH, et al. (2012) Reading DNA at single-nucleotide resolution with a mutant MspA nanopore and phi29 DNA polymerase. Nat Biotechnol 30: 349-353. doi: 10.1038/nbt.2171
![]() |
[41] |
An N, Fleming AM, White HS, et al. (2012) Crown ether-electrolyte interactions permit nanopore detection of individual DNA abasic sites in single molecules. Proc Natl Acad Sci U S A 109: 11504-11509. doi: 10.1073/pnas.1201669109
![]() |
[42] |
Wallace EV, Stoddart D, Heron AJ, et al. (2010) Identification of epigenetic DNA modifications with a protein nanopore. Chem Commun(Camb) 46: 8195-8197. doi: 10.1039/c0cc02864a
![]() |
[43] |
Shim J, Kim Y, Humphreys GI, et al. (2015) Nanopore-based assay for detection of methylation in double-stranded DNA fragments. ACS Nano 9: 290-300. doi: 10.1021/nn5045596
![]() |
[44] |
Bayley H, Cremer PS (2001) Stochastic sensors inspired by biology. Nature 413: 226-230. doi: 10.1038/35093038
![]() |
[45] |
Gu LQ, Shim JW (2010) Single molecule sensing by nanopores and nanopore devices. Analyst 135: 441-451. doi: 10.1039/B907735A
![]() |
[46] |
Howorka S, Siwy Z (2009) Nanopore analytics: sensing of single molecules. Chem Soc Rev 38: 2360-2384. doi: 10.1039/b813796j
![]() |
[47] | Luan B, Peng H, Polonsky S, et al. (2010) Base-by-base ratcheting of single stranded DNA through a solid-state nanopore. Phys Rev Lett 104. |
[48] |
Asandei A, Chinappi M, Lee JK, et al. (2015) Placement of oppositely charged aminoacids at a polypeptide termini determines the voltage-controlled braking of polymer transport through nanometer-scale pores. Sci Rep 5: 10419. doi: 10.1038/srep10419
![]() |
[49] | Mereuta L, Roy M, Asandei A, et al. (2014) Slowing down single-molecule trafficking through a protein nanopore reveals intermediates for peptide translocation. Sci Rep 4: 3885. |
[50] |
Deamer D (2010) Nanopore analysis of nucleic acids bound to exonucleases and polymerases. Annu Rev Biophys 39: 79-90. doi: 10.1146/annurev.biophys.093008.131250
![]() |
[51] |
Olasagasti F, Lieberman KR, Benner S, et al. (2010) Replication of individual DNA molecules under electronic control using a protein nanopore. Nat Nanotechnol 5: 798-806. doi: 10.1038/nnano.2010.177
![]() |
[52] |
Chu J, Gonzalez-Lopez M, Cockroft SL, et al. (2010) Real-time monitoring of DNA polymerase function and stepwise single-nucleotide DNA strand translocation through a protein nanopore. Angew Chem Int Ed Engl 49: 10106-10109. doi: 10.1002/anie.201005460
![]() |
[53] |
Benner S, Chen RJ, Wilson NA, et al. (2007) Sequence-specific detection of individual DNA polymerase complexes in real time using a nanopore. Nat Nanotechnol 2: 718-724. doi: 10.1038/nnano.2007.344
![]() |
[54] |
Asandei A, Iftemi S, Mereuta L, et al. (2014) Probing of various physiologically relevant metals: Amyloid-β peptide interactions with a lipid membrane-immobilized protein nanopore. J Membrane Biol 247: 523-530. doi: 10.1007/s00232-014-9662-z
![]() |
[55] |
Asandei A, Schiopu I, Iftemi S, et al. (2013) Investigation of Cu2+ binding to human and rat amyloid fragments Aβ (1-16) with a protein nanopore. Langmuir 29: 15634-15642. doi: 10.1021/la403915t
![]() |
[56] |
Ying YL, Wang HY, Sutherland TC, et al. (2011) Monitoring of an ATP-binding aptamer and its conformational changes using an α-hemolysin nanopore. Small 7: 87-94. doi: 10.1002/smll.201001428
![]() |
[57] |
Clarke J, Wu HC, Jayasinghe L, et al. (2009) Continuous base identification for single-molecule nanopore DNA sequencing. Nat Nanotechnol 4: 265-270. doi: 10.1038/nnano.2009.12
![]() |
[58] |
Branton D, Deamer DW, Marziali A, et al. (2008) The potential and challenges of nanopore sequencing. Nat Biotechnol 26: 1146-1153. doi: 10.1038/nbt.1495
![]() |
[59] |
Bayley H (2006) Sequencing single molecules of DNA. Curr Opin Chem Biol 10: 628-637. doi: 10.1016/j.cbpa.2006.10.040
![]() |
[60] |
Bartel DP (2004) MicroRNAs: Genomics, Biogenesis, Mechanism, and Function. Cell 116: 281-297. doi: 10.1016/S0092-8674(04)00045-5
![]() |
[61] |
Carthew RW, Sontheimer EJ (2009) Origins and Mechanisms of miRNAs and siRNAs. Cell 136: 642-655. doi: 10.1016/j.cell.2009.01.035
![]() |
[62] |
Calin GA, Croce CM (2006) MicroRNA signatures in human cancers. Nat Rev Cancer 6: 857-866. doi: 10.1038/nrc1997
![]() |
[63] |
Chen X, Ba Y, Ma L, et al. (2008) Characterization of microRNAs in serum: A novel class of biomarkers for diagnosis of cancer and other diseases. Cell Res 18: 997-1006. doi: 10.1038/cr.2008.282
![]() |
[64] |
Mitchell PS, Parkin RK, Kroh EM, et al. (2008) Circulating microRNAs as stable blood-based markers for cancer detection. Proc Natl Acad Sci U S A 105: 10513-10518. doi: 10.1073/pnas.0804549105
![]() |
[65] |
Wang Y, Zheng D, Tan Q, et al. (2011) Nanopore-based detection of circulating microRNAs in lung cancer patients. Nat Nanotechnol 6: 668-674. doi: 10.1038/nnano.2011.147
![]() |
[66] |
Tian K, He Z, Wang Y, et al. (2013) Designing a polycationic probe for simultaneous enrichment and detection of microRNAs in a nanopore. ACS Nano 7: 3962-3969. doi: 10.1021/nn305789z
![]() |
[67] |
Zhang X, Wang Y, Fricke BL, et al. (2014) Programming nanopore ion flow for encoded multiplex microRNA detection. ACS Nano 8: 3444-3450. doi: 10.1021/nn406339n
![]() |
[68] |
Cao C, Ying YL, Gu Z, et al. (2014) Enhanced resolution of low molecular weight poly(ethylene glycol) in nanopore analysis. Anal Chem 86: 11946-11950. doi: 10.1021/ac504233s
![]() |
[69] |
Baral A, Kumar P, Pathak R, et al. (2013) Emerging trends in G-quadruplex biology-role in epigenetic and evolutionary events. Mol BioSyst 9: 1568-1575. doi: 10.1039/c3mb25492e
![]() |
[70] |
Frees S, Menendez C, Crum M, et al. (2014) QGRS-Conserve: A computational method for discovering evolutionarily conserved G-quadruplex motifs. Human Genomics 8: 8. doi: 10.1186/1479-7364-8-8
![]() |
[71] |
Paeschke K, Bochman ML, Daniela Garcia P, et al. (2013) Pif1 family helicases suppress genome instability at G-quadruplex motifs. Nature 497: 458-462. doi: 10.1038/nature12149
![]() |
[72] |
Qiu J, Wang M, Zhang Y, et al. (2015) Biological function and medicinal research significance of g-quadruplex interactive proteins. Curr Top Med Chem 15: 1971-1987. doi: 10.2174/1568026615666150515150803
![]() |
[73] |
Fleming AM, Burrows CJ (2013) G-quadruplex folds of the human telomere sequence alter the site reactivity and reaction pathway of guanine oxidation compared to duplex DNA. Chem Res Toxicol 26: 593-607. doi: 10.1021/tx400028y
![]() |
[74] |
An N, Fleming AM, Middleton EG, et al. (2014) Single-molecule investigation of G-quadruplex folds of the human telomere sequence in a protein nanocavity. Proc Natl Acad Sci U S A 111: 14325-14331. doi: 10.1073/pnas.1415944111
![]() |
[75] |
An N, Fleming AM, Burrows CJ (2013) Interactions of the human telomere sequence with the nanocavity of the α-hemolysin ion channel reveal structure-dependent electrical signatures for hybrid folds. J Am Chem Soc 135: 8562-8570. doi: 10.1021/ja400973m
![]() |
[76] |
Wolna AH, Fleming AM, Burrows CJ (2014) Single-molecule analysis of thymine dimer-containing G-quadruplexes formed from the human telomere sequence. Biochemistry 53: 7484-7493. doi: 10.1021/bi501072m
![]() |
[77] |
Shim JW, Gu LQ (2008) Encapsulating a single G-quadruplex aptamer in a protein nanocavity. J Phys Chem B 112: 8354-8360. doi: 10.1021/jp0775911
![]() |
[78] |
Shim JW, Tan Q, Gu LQ (2009) Single-molecule detection of folding and unfolding of the G-quadruplex aptamer in a nanopore nanocavity. Nucleic Acids Res 37: 972-982. doi: 10.1093/nar/gkn968
![]() |
[79] |
Shim J, Gu LQ (2012) Single-molecule investigation of G-quadruplex using a nanopore sensor. Methods 57: 40-46. doi: 10.1016/j.ymeth.2012.03.026
![]() |
[80] | Yang J, Xu ZP, Huang Y, et al. (2004) ATM and ATR: Sensing DNA damage. World J Gastroentero 10: 155-160. |
[81] |
Diculescu VC, Paquim AMC, Brett AMO (2005) Electrochemical DNA sensors for detection of DNA damage. Sensors 5: 377-393. doi: 10.3390/s5060377
![]() |
[82] |
Fojta M (2002) Electrochemical sensors for DNA interactions and damage. Electroanalysis 14: 1449-1463. doi: 10.1002/1521-4109(200211)14:21<1449::AID-ELAN1449>3.0.CO;2-Z
![]() |
[83] |
Paleček E, Bartošík M (2012) Electrochemistry of nucleic acids. Chem Rev 112: 3427-3481. doi: 10.1021/cr200303p
![]() |
[84] |
An N, Fleming AM, White HS, et al. (2015) Nanopore detection of 8-oxoguanine in the human telomere repeat sequence. ACS Nano 9: 4296-4307. doi: 10.1021/acsnano.5b00722
![]() |
[85] |
Boiteux S, Guillet M (2004) Abasic sites in DNA: Repair and biological consequences in Saccharomyces cerevisiae. DNA Repair 3: 1-12. doi: 10.1016/j.dnarep.2003.10.002
![]() |
[86] |
Wilson Iii DM, Barsky D (2001) The major human abasic endonuclease: Formation, consequences and repair of abasic lesions in DNA. Mutat Res-DNA Repair 485: 283-307. doi: 10.1016/S0921-8777(01)00063-5
![]() |
[87] | Reardon JT, Sancar A (2005) Nucleotide Excision Repair. In: Moldave K, editor. Progress in Nucleic Acid Research and Molecular Biology, 183-235. |
[88] |
Gates KS (2009) An overview of chemical processes that damage cellular DNA: Spontaneous hydrolysis, alkylation, and reactions with radicals. Chem Res Toxicol 22: 1747-1760. doi: 10.1021/tx900242k
![]() |
[89] |
Greco NJ, Tor Y (2005) Simple fluorescent pyrimidine analogues detect the presence of DNA abasic sites. J Am Chem Soc 127: 10784-10785. doi: 10.1021/ja052000a
![]() |
[90] |
Lucotti A, Tommasini M, Pezzoli D, et al. (2014) Molecular interactions of DNA with transfectants: A study based on infrared spectroscopy and quantum chemistry as aids to fluorescence spectroscopy and dynamic light scattering analyses. RSC Adv 4: 49620-49627. doi: 10.1039/C4RA08845J
![]() |
[91] |
Sun HB, Qian L, Yokota H (2001) Detection of abasic sites on individual DNA molecules using atomic force microscopy. Anal Chem 73: 2229-2232. doi: 10.1021/ac0013249
![]() |
[92] |
Bowler FR, Diaz-Mochon JJ, Swift MD, et al. (2010) DNA analysis by dynamic chemistry. Angew Chem Int Edit 49: 1809-1812. doi: 10.1002/anie.200905699
![]() |
[93] |
Atamna H, Cheung I, Ames BN (2000) A method for detecting abasic sites in living cells: Age-dependent changes in base excision repair. Proc Natl Acad Sci U S A 97: 686-691. doi: 10.1073/pnas.97.2.686
![]() |
[94] |
Kojima N, Takebayashi T, Mikami A, et al. (2009) Construction of highly reactive probes for abasic site detection by introduction of an aromatic and a guanidine residue into an aminooxy group. J Am Chem Soc 131: 13208-13209. doi: 10.1021/ja904767k
![]() |
[95] |
Zeglis BM, Boland JA, Barton JK (2008) Targeting abasic sites and single base bulges in DNA with metalloinsertors. J Am Chem Soc 130: 7530-7531. doi: 10.1021/ja801479y
![]() |
[96] |
Wang Y, Liu L, Wu C, et al. (2009) Direct detection and quantification of abasic sites for in vivo studies of DNA damage and repair. Nucl Med Biol 36: 975-983. doi: 10.1016/j.nucmedbio.2009.07.007
![]() |
[97] |
Hada M, Sutherland BM (2006) Spectrum of complex DNA damages depends on the incident radiation. Radiat Res 165: 223-230. doi: 10.1667/RR3498.1
![]() |
[98] |
An N, Fleming AM, White HS, et al. (2012) Crown ether-electrolyte interactions permit nanopore detection of individual DNA abasic sites in single molecules. Proc Natl Acad Sci U S A 109: 11504-11509. doi: 10.1073/pnas.1201669109
![]() |
[99] |
Jin Q, Fleming AM, Johnson RP, et al. (2013) Base-excision repair activity of uracil-DNA glycosylase monitored using the latch zone of α-hemolysin. J Am Chem Soc 135: 19347-19353. doi: 10.1021/ja410615d
![]() |
[100] |
Johnson RP, Fleming AM, Jin Q, et al. (2014) Temperature and electrolyte optimization of the α-hemolysin latch sensing zone for detection of base modification in double-stranded DNA. Biophys J 107: 924-931. doi: 10.1016/j.bpj.2014.07.006
![]() |
[101] | Lin YH, Tseng WL (2009) Highly sensitive and selective detection of silver ions and silver nanoparticles in aqueous solution using an oligonucleotide-based fluorogenic probe. Chem Commun (Camb): 6619-6621. |
[102] | Ono A, Cao S, Togashi H, et al. (2008) Specific interactions between silver(I) ions and cytosine-cytosine pairs in DNA duplexes. Chem Commun (Camb): 4825-4827. |
[103] |
Wen Y, Xing F, He S, et al. (2010) A graphene-based fluorescent nanoprobe for silver(I) ions detection by using graphene oxide and a silver-specific oligonucleotide. Chem Commun (Camb) 46: 2596-2598. doi: 10.1039/b924832c
![]() |
[104] |
Torigoe H, Okamoto I, Dairaku T, et al. (2012) Thermodynamic and structural properties of the specific binding between Ag(+) ion and C:C mismatched base pair in duplex DNA to form C-Ag-C metal-mediated base pair. Biochimie 94: 2431-2440. doi: 10.1016/j.biochi.2012.06.024
![]() |
[105] |
Miyake Y, Togashi H, Tashiro M, et al. (2006) MercuryII-mediated formation of thymine-HgII-thymine base pairs in DNA duplexes. J Am Chem Soc 128: 2172-2173. doi: 10.1021/ja056354d
![]() |
[106] |
Tanaka Y, Oda S, Yamaguchi H, et al. (2007) 15N-15N J-coupling across Hg(II): direct observation of Hg(II)-mediated T-T base pairs in a DNA duplex. J Am Chem Soc 129: 244-245. doi: 10.1021/ja065552h
![]() |
[107] |
Torigoe H, Ono A, Kozasa T (2010) Hg(II) ion specifically binds with T:T mismatched base pair in duplex DNA. Chemistry 16: 13218-13225. doi: 10.1002/chem.201001171
![]() |
[108] |
Wen S, Zeng T, Liu L, et al. (2011) Highly sensitive and selective DNA-based detection of mercury(II) with alpha-hemolysin nanopore. J Am Chem Soc 133: 18312-18317. doi: 10.1021/ja206983z
![]() |
[109] |
Ono A, Torigoe H, Tanaka Y, et al. (2011) Binding of metal ions by pyrimidine base pairs in DNA duplexes. Chem Soc Rev 40: 5855-5866. doi: 10.1039/c1cs15149e
![]() |
[110] |
Brena RM, Huang TH, Plass C (2006) Quantitative assessment of DNA methylation: Potential applications for disease diagnosis, classification, and prognosis in clinical settings. J Mol Med (Berl) 84: 365-377. doi: 10.1007/s00109-005-0034-0
![]() |
[111] |
Kriaucionis S, Heintz N (2009) The nuclear DNA base 5-hydroxymethylcytosine is present in Purkinje neurons and the brain. Science 324: 929-930. doi: 10.1126/science.1169786
![]() |
[112] |
Lister R, Pelizzola M, Dowen RH, et al. (2009) Human DNA methylomes at base resolution show widespread epigenomic differences. Nature 462: 315-322. doi: 10.1038/nature08514
![]() |
[113] | Li WW, Gong L, Bayley H (2013) Single-molecule detection of 5-hydroxymethylcytosine in DNA through chemical modification and nanopore analysis. Angew Chem Int Ed 52: 4350-4355. |
[114] | Shim J, Humphreys GI, Venkatesan BM, et al. (2013) Detection and quantification of methylation in DNA using solid-state nanopores. Sci Rep 3: 1389. |
[115] |
Wallace EV, Stoddart D, Heron AJ, et al. (2010) Identification of epigenetic DNA modifications with a protein nanopore. Chem Commun (Camb) 46: 8195-8197. doi: 10.1039/c0cc02864a
![]() |
[116] |
Wanunu M, Cohen-Karni D, Johnson RR, et al. (2011) Discrimination of methylcytosine from hydroxymethylcytosine in DNA molecules. J Am Chem Soc 133: 486-492. doi: 10.1021/ja107836t
![]() |
[117] |
Yu M, Hon GC, Szulwach KE, et al. (2012) Tet-assisted bisulfite sequencing of 5-hydroxymethylcytosine. Nat Protoc 7: 2159-2170. doi: 10.1038/nprot.2012.137
![]() |
[118] |
Yu M, Hon GC, Szulwach KE, et al. (2012) Base-resolution analysis of 5-hydroxymethylcytosine in the mammalian genome. Cell 149: 1368-1380. doi: 10.1016/j.cell.2012.04.027
![]() |
[119] |
Booth MJ, Branco MR, Ficz G, et al. (2012) Quantitative sequencing of 5-methylcytosine and 5-hydroxymethylcytosine at single-base resolution. Science 336: 934-937. doi: 10.1126/science.1220671
![]() |
[120] | Wang Y, Luan BQ, Yang Z, et al. (2014) Single Molecule Investigation of Ag+ Interactions with Single Cytosine-, Methylcytosine- and Hydroxymethylcytosine-Cytosine Mismatches in a Nanopore. Sci Rep 4: 5883. |
[121] |
Torigoe H, Miyakawa Y, Ono A, et al. (2011) Thermodynamic properties of the specific binding between Ag+ ions and C:C mismatched base pairs in duplex DNA. Nucleos Nucleot Nucl 30: 149-167. doi: 10.1080/15257770.2011.553210
![]() |
[122] |
Kistenmacher TJ, Rossi M, Marzilli LG (1979) Crystal and molecular structure of (nitrato)(1-methylcytosine)silver(I): An unusual cross-linked polymer containing a heavy metal and a modified nucleic acid constituent. Inorg Chem 18: 240-244. doi: 10.1021/ic50192a007
![]() |
[123] |
Urata H, Yamaguchi E, Nakamura Y, et al. (2011) Pyrimidine-pyrimidine base pairs stabilized by silver(I) ions. Chem Commun (Camb) 47: 941-943. doi: 10.1039/C0CC04091F
![]() |
[124] |
Wang Y, Ritzo B, Gu L-Q (2015) Silver (i) ions modulate the stability of DNA duplexes containing cytosine, methylcytosine and hydroxymethylcytosine at different salt concentrations. RSC Adv 5: 2655-2658. doi: 10.1039/C4RA14490B
![]() |
[125] |
Egger G, Liang G, Aparicio A, et al. (2004) Epigenetics in human disease and prospects for epigenetic therapy. Nature 429: 457-463. doi: 10.1038/nature02625
![]() |
[126] |
Bestor TH (2000) The DNA methyltransferases of mammals. Hum Mol Genet 9: 2395-2402. doi: 10.1093/hmg/9.16.2395
![]() |
[127] | Kang I, Wang Y, Reagan C, et al. (2013) Designing DNA interstrand lock for locus-specific methylation detection in a nanopore. Sci Rep 3: 2381. |
[128] |
Calin GA, Croce CM (2006) MicroRNA signatures in human cancers. Nat Rev Cancer 6: 857-866. doi: 10.1038/nrc1997
![]() |
[129] |
Vlassov VV, Laktionov PP, Rykova EY (2010) Circulating nucleic acids as a potential source for cancer biomarkers. Curr Mol Med 10: 142-165. doi: 10.2174/156652410790963295
![]() |
[130] |
Mitchell PS, Parkin RK, Kroh EM, et al. (2008) Circulating microRNAs as stable blood-based markers for cancer detection. Proc Natl Acad Sci U S A 105: 10513-10518. doi: 10.1073/pnas.0804549105
![]() |
[131] | Oremek GM, Sapoutzis N (2003) Pro-gastrin-releasing peptide (Pro-GRP), a tumor marker for small cell lung cancer. Anticancer Res 23: 895-898. |
[132] |
Molina R, Auge JM, Bosch X, et al. (2009) Usefulness of serum tumor markers, including progastrin-releasing peptide, in patients with lung cancer: correlation with histology. Tumour Biol 30: 121-129. doi: 10.1159/000224628
![]() |
[133] |
Albrethsen J, Moller CH, Olsen J, et al. (2006) Human neutrophil peptides 1, 2 and 3 are biochemical markers for metastatic colorectal cancer. Eur J Cancer 42: 3057-3064. doi: 10.1016/j.ejca.2006.05.039
![]() |
[134] |
Bassani-Sternberg M, Barnea E, Beer I, et al. (2010) Soluble plasma HLA peptidome as a potential source for cancer biomarkers. Proc Natl Acad Sci U S A 107: 18769-18776. doi: 10.1073/pnas.1008501107
![]() |
[135] |
Stella Tsai CS, Chen HC, Tung JN, et al. (2010) Serum cellular apoptosis susceptibility protein is a potential prognostic marker for metastatic colorectal cancer. Am J Pathol 176: 1619-1628. doi: 10.2353/ajpath.2010.090467
![]() |
[136] |
Stoeva SI, Lee JS, Smith JE, et al. (2006) Multiplexed detection of protein cancer markers with biobarcoded nanoparticle probes. J Am Chem Soc 128: 8378-8379. doi: 10.1021/ja0613106
![]() |
[137] |
Zheng W, He L (2010) Multiplexed detection of protein cancer markers on Au/Ag-barcoded nanorods using fluorescent-conjugated polymers. Anal Bioanal Chem 397: 2261-2270. doi: 10.1007/s00216-010-3834-1
![]() |
[138] | Jin H, Liu GL (2012) Fabrication and optical characterization of light trapping silicon nanopore and nanoscrew devices. Nanotechnology 23. |
[139] | Merchant CA, Drndić M (2012) Graphene nanopore devices for DNA sensing. In: Gracheva ME, editor. Methods in Molecular Biology, 211-226. |
[140] |
Park S, Lim J, Pak YE, et al. (2013) A solid state nanopore device for investigating the magnetic properties of magnetic nanoparticles. Sensors (Basel, Switzerland) 13: 6900-6909. doi: 10.3390/s130606900
![]() |
[141] |
Wu GS, Zhang Y, Si W, et al. (2014) Integrated solid-state nanopore devices for third generation DNA sequencing. Sci China Technol Sc 57: 1925-1935. doi: 10.1007/s11431-014-5644-8
![]() |
[142] | Inoue K, Kawano R, Yasuga H, et al. Logic operation in DNA nano device: Electrical input/output through biological nanopore; 2013; Freiburg. Chemical and Biological Microsystems Society. 1881-1883. |
[143] |
Lim MC, Lee MH, Kim KB, et al. (2015) A mask-free passivation process for low noise nanopore devices. J Nanosci Nanotechno 15: 5971-5977. doi: 10.1166/jnn.2015.10500
![]() |
[144] |
Mulero R, Prabhu AS, Freedman KJ, et al. (2010) Nanopore-Based Devices for Bioanalytical Applications. J Assoc Lab Automat 15: 243-252. doi: 10.1016/j.jala.2010.01.009
![]() |
[145] |
Cockroft SL, Chu J, Amorin M, et al. (2008) A single-molecule nanopore device detects DNA polymerase activity with single-nucleotide resolution. J Am Chem Soc 130: 818-820. doi: 10.1021/ja077082c
![]() |
[146] |
Kawano R, Osaki T, Sasaki H, et al. (2010) A polymer-based nanopore-integrated microfluidic device for generating stable bilayer lipid membranes. Small 6: 2100-2104. doi: 10.1002/smll.201000997
![]() |
[147] |
Shim JW, Gu LQ (2007) Stochastic sensing on a modular chip containing a single-ion channel. Anal Chem 79: 2207-2213. doi: 10.1021/ac0614285
![]() |
[148] |
Kang XF, Cheley S, Rice-Ficht AC, et al. (2007) A storable encapsulated bilayer chip containing a single protein nanopore. J Am Chem Soc 129: 4701-4705. doi: 10.1021/ja068654g
![]() |
[149] |
Eisenstein M (2012) Oxford Nanopore announcement sets sequencing sector abuzz. Nat Biotechnol 30: 295-296. doi: 10.1038/nbt0412-295
![]() |
[150] |
Quick J, Quinlan AR, Loman NJ (2014) A reference bacterial genome dataset generated on the MinIONTM portable single-molecule nanopore sequencer. GigaScience 3: 22. doi: 10.1186/2047-217X-3-22
![]() |
[151] | Ashton PM, Nair S, Dallman T, et al. (2015) MinION nanopore sequencing identifies the position and structure of a bacterial antibiotic resistance island. Nat Biotechnol 33: 296-302. |
[152] | Madoui MA, Engelen S, Cruaud C, et al. (2015) Genome assembly using Nanopore-guided long and error-free DNA reads. BMC Genomics 16. |
[153] |
Loman NJ, Quick J, Simpson JT (2015) A complete bacterial genome assembled de novo using only nanopore sequencing data. Nat Methods 12: 733-735. doi: 10.1038/nmeth.3444
![]() |
[154] | Palshikar P, Sharma A, Chauhan CS, et al. (2013) Biophotonics: A novel approach biomedical diagnosis. Int J Pharm Sci Rev Res 21: 350-354. |
[155] | Liu A, Ye B (2013) Application of gold nanoparticles in biomedical researches and diagnosis. Clin Lab 59: 23-36. |
[156] |
Nahar J, Imam T, Tickle KS, et al. (2012) Computational intelligence for microarray data and biomedical image analysis for the early diagnosis of breast cancer. Expert Syst Appl 39: 12371-12377. doi: 10.1016/j.eswa.2012.04.045
![]() |
[157] |
Kang JW, Lue N, Kong CR, et al. (2011) Combined confocal Raman and quantitative phase microscopy system for biomedical diagnosis. Biomed Opt Express 2: 2484-2492. doi: 10.1364/BOE.2.002484
![]() |
[158] |
Chen KI, Li BR, Chen YT (2011) Silicon nanowire field-effect transistor-based biosensors for biomedical diagnosis and cellular recording investigation. Nano Today 6: 131-154. doi: 10.1016/j.nantod.2011.02.001
![]() |
[159] |
Balas C (2009) Review of biomedical optical imaging - A powerful, non-invasive, non-ionizing technology for improving in vivo diagnosis. Meas Sci Technol 20: 104020. doi: 10.1088/0957-0233/20/10/104020
![]() |
[160] |
Ellis DI, Goodacre R (2006) Metabolic fingerprinting in disease diagnosis: Biomedical applications of infrared and Raman spectroscopy. Analyst 131: 875-885. doi: 10.1039/b602376m
![]() |
[161] |
Bottiroli G, Croce AC (2004) Autofluorescence spectroscopy of cells and tissues as a tool for biomedical diagnosis. Photoch Photobio Sci 3: 189-210. doi: 10.1039/b310627f
![]() |
[162] | Urbanova M, Plzak J, Strnad H, et al. (2010) Circulating nucleic acids as a new diagnostic tool. Cell Mol Biol Lett 15: 242-259. |
[163] |
Liu KJ, Brock MV, Shih Ie M, et al. (2010) Decoding circulating nucleic acids in human serum using microfluidic single molecule spectroscopy. J Am Chem Soc 132: 5793-5798. doi: 10.1021/ja100342q
![]() |
[164] |
Thompson L, Turko I, Murad F (2006) Mass spectrometry-based relative quantification of human neutrophil peptides 1, 2, and 3 from biological samples. Mol Immunol 43: 1485-1489. doi: 10.1016/j.molimm.2005.08.001
![]() |
[165] |
Wanunu M, Dadosh T, Ray V, et al. (2010) Rapid electronic detection of probe-specific microRNAs using thin nanopore sensors. Nat Nanotechnol 5: 807-814. doi: 10.1038/nnano.2010.202
![]() |
[166] |
Squires A, Meller A (2013) DNA Capture and Translocation through Nanoscale Pores-a Fine Balance of Electrophoresis and Electroosmosis. Biophys J 105: 543-544. doi: 10.1016/j.bpj.2013.06.008
![]() |
[167] |
Wanunu M, Morrison W, Rabin Y, et al. (2010) Electrostatic focusing of unlabelled DNA into nanoscale pores using a salt gradient. Nat Nanotechnol 5: 160-165. doi: 10.1038/nnano.2009.379
![]() |
[168] |
Hatlo MM, Panja D, van Roij R (2011) Translocation of DNA molecules through nanopores with salt gradients: the role of osmotic flow. Phys Rev Lett 107: 068101. doi: 10.1103/PhysRevLett.107.068101
![]() |
[169] |
He Y, Tsutsui M, Scheicher RH, et al. (2013) Mechanism of How Salt-Gradient-Induced Charges Affect the Translocation of DNA Molecules through a Nanopore. Biophys J 105: 776-782. doi: 10.1016/j.bpj.2013.05.065
![]() |
[170] |
Chou T (2009) Enhancement of charged macromolecule capture by nanopores in a salt gradient. J Chem Phys 131: 034703. doi: 10.1063/1.3170952
![]() |
1. | Nada H. Eisa, Sahar A Helmy, Dalia H. El-Kashef, Mohamed El-Sherbiny, Nehal M. Elsherbiny, Pramipexole protects against diabetic neuropathy: Effect on oxidative stress, TLR4/IRAK-1/TRAF-6/NF-κB and downstream inflammatory mediators, 2024, 128, 15675769, 111514, 10.1016/j.intimp.2024.111514 |
Screening cohort | Healthy subjects | Mild asthma | Moderate asthma | Severe asthma |
Number | 30 | 20 | 20 | 40 |
Demographic characteristics Age (years), median (Range) | 54.7 (27-74) | 58 (51-66) | 55.7 (55-60) | 55.87 (26-75) |
Functional characteristics | ||||
FEV1 (% pred) | 109 ± 15.3 | 97.6 ± 12.8† | 92.56 ± 11.90† | 56.72 ± 14.72† |
FEV1/FVC ratio | 80.7 ± 6.7 | 74.7 ± 6.3† | 65.4 ± 7.8† | 61.1 ± 69.8† |
Sputum characteristics | ||||
Lymphocytes | 8.2 ± 4.95 | 20.47 ± 10.5† | 20.5 ± 4.9† | 13.5 ± 7.6† |
Macrophages (%) | 58.3 ± 16.9 | 41.47 ± 19.87† | 39.7 ± 5.7† | 44.2 ± 6.7† |
Neutrophils (%) | 21.8 ± 18.9 | 31.86 ± 14.80† | 38.2 ± 10.7† | 32.2 ± 12.4† |
Eosinophils (%) | 0.0 ± 0.00 | 3.96 ± 2.3† | 2.75 ± 1.4† | 9.2 ± 2.4† |
Data are expressed as distributions (yes/no), means ± SD, or medians with range. Comparisons were done with Pearson X2 tests or the Kruskal-Wallis test, followed by the Mann-Whitney U test with the Bonferroni correction. [†]: p < 0.005 versus healthy subjects. FEV1: forced expiratory volume in 1s; FVC: forced vital capacity. FEV1 (% pred) and FEV1/FVC ratio were significantly decreased in severe asthmatic patients compared to mild (p < 0.0001) and moderate (p < 0.0005) asthmatics. The percentage of lymphocytes was decreased in severe asthmatic compared to mild and moderate (p < 0.0001) asthma patients. |
IL-26/IL-17 | IL-26/% of macrophages | IL-26/FEV1% | IL-26/% PNN | |
Severe asthma | r = 0.569 | r = 0.656 | r = 0.872 | r = 0.552 |
(p = 0.0001) | (p = 0.0001) | (p = 0.0001) | (p = 0.0002) | |
Moderate asthma | r = 0.736 | r = 0.587 | r = 0.734 | r = 0.547 |
(p = 0.0002) | (p = 0.0003) | (p = 0.0001) | (p = 0.0002) | |
Mild asthma | r = 0.512 | r = 0.572 | r = 0. 537 | r = 0.526 |
(p = 0.0021) | (p = 0. 0004) | (p = 0.0006) | (p = 0.0003) |
Screening cohort | Healthy subjects | Mild asthma | Moderate asthma | Severe asthma |
Number | 30 | 20 | 20 | 40 |
Demographic characteristics Age (years), median (Range) | 54.7 (27-74) | 58 (51-66) | 55.7 (55-60) | 55.87 (26-75) |
Functional characteristics | ||||
FEV1 (% pred) | 109 ± 15.3 | 97.6 ± 12.8† | 92.56 ± 11.90† | 56.72 ± 14.72† |
FEV1/FVC ratio | 80.7 ± 6.7 | 74.7 ± 6.3† | 65.4 ± 7.8† | 61.1 ± 69.8† |
Sputum characteristics | ||||
Lymphocytes | 8.2 ± 4.95 | 20.47 ± 10.5† | 20.5 ± 4.9† | 13.5 ± 7.6† |
Macrophages (%) | 58.3 ± 16.9 | 41.47 ± 19.87† | 39.7 ± 5.7† | 44.2 ± 6.7† |
Neutrophils (%) | 21.8 ± 18.9 | 31.86 ± 14.80† | 38.2 ± 10.7† | 32.2 ± 12.4† |
Eosinophils (%) | 0.0 ± 0.00 | 3.96 ± 2.3† | 2.75 ± 1.4† | 9.2 ± 2.4† |
Data are expressed as distributions (yes/no), means ± SD, or medians with range. Comparisons were done with Pearson X2 tests or the Kruskal-Wallis test, followed by the Mann-Whitney U test with the Bonferroni correction. [†]: p < 0.005 versus healthy subjects. FEV1: forced expiratory volume in 1s; FVC: forced vital capacity. FEV1 (% pred) and FEV1/FVC ratio were significantly decreased in severe asthmatic patients compared to mild (p < 0.0001) and moderate (p < 0.0005) asthmatics. The percentage of lymphocytes was decreased in severe asthmatic compared to mild and moderate (p < 0.0001) asthma patients. |
IL-26/IL-17 | IL-26/% of macrophages | IL-26/FEV1% | IL-26/% PNN | |
Severe asthma | r = 0.569 | r = 0.656 | r = 0.872 | r = 0.552 |
(p = 0.0001) | (p = 0.0001) | (p = 0.0001) | (p = 0.0002) | |
Moderate asthma | r = 0.736 | r = 0.587 | r = 0.734 | r = 0.547 |
(p = 0.0002) | (p = 0.0003) | (p = 0.0001) | (p = 0.0002) | |
Mild asthma | r = 0.512 | r = 0.572 | r = 0. 537 | r = 0.526 |
(p = 0.0021) | (p = 0. 0004) | (p = 0.0006) | (p = 0.0003) |