Alterations of 5-hydroxymethylcytosines in circulating cell-free DNA reflect retinopathy in type 2 diabetes.

Diabetic retinopathy (DR) is a common microvascular complication that may cause severe visual impairment and blindness in patients with type 2 diabetes mellitus (T2DM). Early detection of DR will expand the range of potential treatment options and enable better control of disease progression. Epigenetic dysregulation has been implicated in the pathogenesis of microvascular complications in patients with T2DM. We sought to explore the diagnostic value of 5-hydroxymethylcytosines (5hmC) in circulating cell-free DNA (cfDNA) for DR, taking advantage of a highly sensitive technique, the 5hmC-Seal. The genome-wide 5hmC profiles in cfDNA samples from 35 patients diagnosed with DR and 35 age-, gender-, diabetic duration-matched T2DM controls were obtained using the 5hmC-Seal, followed by a case-control analysis and external validation. The genomic distribution of 5hmC in cfDNA from patients with DR reflected potential gene regulatory relevance, showing co-localization with histone modification marks for active expression (e.g., H3K4me1). A three-gene signature (MESP1, LY6G6D, LINC01556) associated with DR was detected using the elastic net regularization on the multivariable logistic regression model, showing high accuracy to distinguish patients with DR from T2DM controls (AUC [area under curve] = 91.4%; 95% CI [confidence interval], 84.3- 98.5%), achieving a sensitivity of 88.6% and a specificity of 91.4%. In an external testing set, the 5hmC model detected 5 out of 6 DR patients and predicted 7 out of 8 non-DR patients with other microvascular complications. Circulating cfDNA from patients with DR contained 5hmC information that could be exploited for DR detection. As a novel non-invasive approach, the 5hmC-Seal holds the promise to be an integrated part of patient care and surveillance tool for T2DM patients.

Allosteric histidine switch for regulation of intracellular zinc(II) fluctuation.

Metalloregulators allosterically control transcriptional activity through metal binding-induced reorganization of ligand residues and/or hydrogen bonding networks, while the coordination atoms on the same ligand residues remain seldom changed. Here we show that the MarR-type zinc transcriptional regulator ZitR switches one of its histidine nitrogen atoms for zinc coordination during the allosteric control of DNA binding. The Zn(II)-coordination nitrogen on histidine 42 within ZitR's high-affinity zinc site (site 1) switches from Nε2 to Nδ1 upon Zn(II) binding to its low-affinity zinc site (site 2), which facilitates ZitR's conversion from the nonoptimal to the optimal DNA-binding conformation. This histidine switch-mediated cooperation between site 1 and site 2 enables ZitR to adjust its DNA-binding affinity in response to a broad range of zinc fluctuation, which may allow the fine tuning of transcriptional regulation.

5-Hydroxymethylcytosine profiling from genomic and cell-free DNA for colorectal cancers patients.

5-Hydroxymethylcytosine (5hmC) is a DNA modification that is generated by the oxidation of 5-methylcytosine (5mC) in a reaction catalyzed by the ten-eleven translocation (TET) family enzymes. It tends to mark gene activation and affects a spectrum of developmental and disease-related biological processes. In this manuscript, we present a 5hmC selective chemical labelling technology (hmC-Seal) to capture and sequence 5hmC-containing DNA fragments with low input. We tested 10 tumour/adjacent colon cancer tissues and 10 tumour/healthy plasma samples. Furthermore, we tested if this methodology could generate the 5hmC differential genes among cancer patients, healthy controls and precancerous adenoma patients from plasma. Robust cancer-specific epigenetic signatures were identified for colon cancers. The results show that 5hmC is mainly distributed in gene active regions. The results also indicate the potential application of 5hmC change signals in early stage of colon cancer, even show potential in the diagnosis of precancerous adenoma. We demonstrated the robustness of the 5hmC-Seal method in tissue and cell-free DNA (cfDNA) as potential biomarkers. Moreover, this study provides the potential value and feasibility of 5hmC-Seal approach on colorectal cancer (CRC) early detection. We believe this strategy could be an effective liquid biopsy-based diagnosis and a potential prognosis method for colon cancer using cfDNA.

5-Hydroxymethylcytosines in Circulating Cell-Free DNA Reveal Vascular Complications of Type 2 Diabetes.

BACKGROUND: Long-term complications of type 2 diabetes (T2D), such as macrovascular and microvascular events, are the major causes for T2D-related disability and mortality. A clinically convenient, noninvasive approach for monitoring the development of these complications would improve the overall life quality of patients with T2D and help reduce healthcare burden through preventive interventions. METHODS: A selective chemical labeling strategy for 5-hydroxymethylcytosines (5hmC-Seal) was used to profile genome-wide 5hmCs, an emerging class of epigenetic markers implicated in complex diseases including diabetes, in circulating cell-free DNA (cfDNA) from a collection of Chinese patients (n = 62). Differentially modified 5hmC markers between patients with T2D with and without macrovascular/microvascular complications were analyzed under a case-control design. RESULTS: Statistically significant changes in 5hmC markers were associated with T2D-related macrovascular/microvascular complications, involving genes and pathways relevant to vascular biology and diabetes, including insulin resistance and inflammation. A 16-gene 5hmC marker panel accurately distinguished patients with vascular complications from those without [testing set: area under the curve (AUC) = 0.85; 95% CI, 0.73-0.96], outperforming conventional clinical variables such as urinary albumin. In addition, a separate 13-gene 5hmC marker panel could distinguish patients with single complications from those with multiple complications (testing set: AUC = 0.84; 95% CI, 0.68-0.99), showing superiority over conventional clinical variables. CONCLUSIONS: The 5hmC markers in cfDNA reflected the epigenetic changes in patients with T2D who developed macrovascular/microvascular complications. The 5hmC-Seal assay has the potential to be a clinically convenient, noninvasive approach that can be applied in the clinic to monitor the presence and severity of diabetic vascular complications.

Structural characterization of the DNA-binding mechanism underlying the copper(II)-sensing MarR transcriptional regulator.

Multiple antibiotic resistance regulator (MarR) family proteins are widely conserved transcription factors that control bacterial resistance to antibiotics, environmental stresses, as well as the regulation of virulence determinants. Escherichia coli MarR, the prototype member of this family, has recently been shown to undergo copper(II)-catalyzed inter-dimer disulfide bond formation via a unique cysteine residue (Cys80) residing in its DNA-binding domain. However, despite extensive structural characterization of the MarR family proteins, the structural mechanism for DNA binding of this copper(II)-sensing MarR factor remains elusive. Here, we report the crystal structures of DNA-bound forms of MarR, which revealed a unique, concerted generation of two new helix-loop-helix motifs that facilitated MarR's DNA binding. Structural analysis and electrophoretic mobility shift assays (EMSA) show that the flexibility of Gly116 in the center of helix α5 and the extensive hydrogen-bonding interactions at the N-terminus of helix α1 together assist the reorientation of the wHTH domains and stabilize MarR's DNA-bound conformation.

Selective Fenton-like oxidation of methylene blue on modified Fe-zeolites prepared via molecular imprinting technique.

A facile strategy to increase the selectivity of heterogeneous Fenton oxidation is investigated. The increase was reached by increasing selective adsorption of heterogeneous Fenton catalyst to a target pollutant. The heterogeneous Fenton catalyst was prepared by a two-step process. First, zeolite particles were imprinted by the target pollutant, methylene blue (MB), in their aggregations, and second, iron ions were loaded on the zeolite aggregations to form the molecule imprinted Fe-zeolites (MI-FZ) Fenton catalyst. Its adsorption amount for MB reached as high as 44.6 mg g-1 while the adsorption amount of un-imprinted Fe-zeolites (FZ) is only 15.6 mg g-1. Fenton removal efficiency of MI-FZ for MB was 87.7%, being 33.9% higher than that of FZ. The selective Fenton oxidation of MI-FZ for MB was further confirmed by its removal performance for the mixed MB and bisphenol A (BPA) in solution. The removal efficiency of MB was 44.7% while that of BPA was only 14.9%. This fact shows that molecular imprinting is suitable to prepare the Fe-zeolites (FZ)-based Fenton catalyst with high selectivity for removal of target pollutants, at least MB.

Preparation and selective adsorption of organic pollutants by an inorganic molecular imprinted polymer.

A novel inorganic molecular imprinted polymer (MIP) was synthesized by adding Al(3+) to the Fe/SiO2 gel with Acid Orange II (AO II) as the template. The MIP was characterized by scanning electron microscopy, X-ray diffraction, Fourier transform infrared spectroscopy and nitrogen adsorption-desorption measurement. Compared with the non-imprinted polymer (NIP), the MIP enhanced the adsorption capacity of the target pollutants AO II. The selective adsorption capacity study indicated that the MIP adsorbed more AO II than the interferent Bisphenol A (BPA), which also has the structure of a benzene ring, thus proving the selective adsorption capacity of the MIP for template molecules AO II. In addition, the adsorption of AO II over MIP belonged to the Langmuir type and pseudo-second adsorption kinetics, and Dubinin-Radushkevich model indicates that the adsorption process of AO II over MIP and NIP are both given priority to chemical adsorption. The MIP reusability in performance was demonstrated in at least six repeated cycles.

miR­149­3p suppresses the proliferation and metastasis of glioma cells by targeting the CBX2/Wnt/ß­catenin pathway.

The present study aimed to investigate the role of miR-149-3p/chromobox 2 (CBX2)/Wnt/ß-catenin pathway in the proliferation and metastasis of glioma cells. The expression and clinical significance of miR-149-3p and CBX2 were analyzed using data from public databases. Cell Counting Kit-8 and colony formation assays were performed to measure cell proliferation. Transwell assays were used to assess cell invasion. The results showed that miR-149-3p was downregulated and CBX2 was upregulated in glioma, and that the downregulated expression of miR-149-3p promoted the proliferation and invasion of glioma cells. In addition, downregulated expression of CBX2 suppressed the proliferation and invasion of glioma cells. Dual-luciferase assay indicated that CBX2 is a target gene of miR149-3p. The possible molecular mechanism of CBX2 was probed by western blotting, which showed that it may further affect the Wnt/ß-catenin pathway. These present findings demonstrated that miR-149-3p may function as a tumor suppressor miRNA by directly regulating CBX2 and serve important roles in the malignancy of glioma.

[Effect of gefitinib on the migration of triple-negative breast cancer cell line MDA-MB-231 cells].

OBJECTIVE: To investigate the effect of gefitinib on the migration of triple-negative breast cancer cell line MDA-MB-231 cells. METHODS: Gefitinib was used in concentrations of 0 micromol/L, 0.1 micromol/L, 1 micromol/L, 10 micromol/L and 20 micromol/L, respectively. Phosphorylation levels of EGFR and Akt were analyzed by Western blot. The capability of migration was measured by scratch test and Boyden chamber assay. Microfilaments (cell skeleton ) remolding and polarization were evaluated by immunofluorescence microscopy. RESULTS: Comparing with the control group (0 micromol/L gefitinib), gefitinib effectively inhibited the phosphorylation of EGFR and its downstream key proteins, and the effect displayed an obvious dose-effect relationship. At 24 hours after wound scratch, the cell migration distance of each group with 0, 0.1, 1, 10, 20 micromol/L gefitinib was (36.3 +/- 4.0) microm, (30.3 +/- 3.8) microm, (26.8 +/- 3.3) microm, (17.0 +/- 2.6) microm, and (11.0 +/- 2.5) microm, respectively. At 3.5 hours after Boyden chamber assay, the cell count of each group with 0, 0.1, 1, 10, 20 micromol/L gefitinib was 69.2 +/- 7.0, 51.8 +/- 7.5, 43.8 +/- 8.7, 30.6 +/- 4.8, and 28.4 +/- 3.4, respectively. Compared with the control group (0 micromol/L gefitinib), gefitinib could significantly prolong the wound-healing time and decrease the migrating cell count (P < 0.05), and significantly inhibit the lamellipodium formation, cell skeleton remolding and changes of the cytoskeleton polarization. CONCLUSIONS: Gefitinib can reduce the migration capacity of triple-negative breast cancer cells through inhibiting phosphorylation of EGFR/PI3K/Akt pathway, suppressing the cell skeleton (microfilaments) remolding and changes of its polarization.

Converting a solvatochromic fluorophore into a protein-based pH indicator for extreme acidity.

Live-cell pH measurements: An environment-sensitive fluorophore (green) was site-specifically introduced on HdeA, an acid-resistant chaperone showing pH-mediated conformational changes under low pH conditions. A survey of the attachment sites led to the discovery of one position on HdeA at which the attached fluorophore showed a strong fluorescence increase upon acidification.

An integrative analysis of genome-wide 5-hydroxymethylcytosines in circulating cell-free DNA detects noninvasive diagnostic markers for gliomas.

BACKGROUND: Gliomas, especially the high-grade glioblastomas (GBM), are highly aggressive tumors in the central nervous system (CNS) with dismal clinical outcomes. Effective biomarkers, which are not currently available, may improve clinical outcomes through early detection. We sought to develop a noninvasive diagnostic approach for gliomas based on 5-hydroxymethylcytosines (5hmC) in circulating cell-free DNA (cfDNA). METHODS: We obtained genome-wide 5hmC profiles using the 5hmC-Seal technique in cfDNA samples from 111 prospectively enrolled patients with gliomas and 111 age-, gender-matched healthy individuals, which were split into a training set and a validation set. Integrated models comprised 5hmC levels summarized for gene bodies, long noncoding RNAs (lncRNAs), cis-regulatory elements, and repetitive elements were developed using the elastic net regularization under a case-control design. RESULTS: The integrated 5hmC-based models differentiated healthy individuals from gliomas (area under the curve [AUC] = 84%; 95% confidence interval [CI], 74-93%), GBM patients (AUC = 84%; 95% CI, 74-94%), WHO II-III glioma patients (AUC = 86%; 95% CI, 76-96%), regardless of IDH1 (encoding isocitrate dehydrogenase) mutation status or other glioma-related pathological features such as TERT, TP53 in the validation set. Furthermore, the 5hmC biomarkers in cfDNA showed the potential as an independent indicator from IDH1 mutation status and worked in synergy with IDH1 mutation to distinguish GBM from WHO II-III gliomas. Exploration of the 5hmC biomarkers for gliomas revealed relevance to glioma biology. CONCLUSIONS: The 5hmC-Seal in cfDNA offers the promise as a noninvasive approach for effective detection of gliomas in a screening program.

A highly selective fluorescent probe for visualization of organic hydroperoxides in living cells.

The transcriptional regulatory protein OhrR is converted into a fluorescent bioprobe capable of detecting organic hydroperoxides in living cells with high sensitivity and selectivity.

[Clinical impact of extracapsular extension of axillary lymph node metastases in breast cancer].

OBJECTIVE: To study the clinical significance of extracapsular extension (ECE) of axillary lymph node metastases in breast cancer. METHODS: The clinicopathological data of 1230 cases of nodal positive breast cancer treated in our department from 1989 to 1995 were analyzed retrospectively. RESULTS: 486 (39.5%) from the 1230 cases were ECE positive. There was a higher incidence of ECE in postmenopausal women than premenopausal ones (47.5% versus 35.5%, respectively, P < 0.001). The patients in ECE positive group had a larger tumor size (5.11 +/- 2.53 cm versus 3.90 +/- 1.80 cm, P < 0.001). 18.3% of patients with stage T1 were ECE positive, stage T2 were 36.4%, and stage T3 were 54.4%, and the difference was significant (P < 0.001). ECE was correlated with the number of positive axillary lymph nodes. The ECE positive group had more positive nodes than ECE negative group (16.96 +/- 12.16 versus 5.24 +/- 6.60, P < 0.001). 6.1% of patients with 1 positive node were ECE positive, 13.5% with 2 - 3, 35.8% with 4 - 9, 62.3% with 10 - 19, and 84.0% with more than 20 positive axillary nodes, and there was a significant difference among those groups (P < 0.001). ECE had no association with ER/PR status (P = 0.706). ECE was a risk factor of local-regional recurrence, but the relapse time had no significant difference (P = 0.559). ECE was also a risk factor of distant metastasis, and the relapse time had a significant difference (P < 0.001). The median metastasis free time was 30.0 (2 approximately 172) months in ECE positive group, while 37.5 (2 approximately 170) months in ECE negative group (P = 0.006). CE occurred in 60.4% of the patients with firstly diagnosed bone, skin and distant lymph node metastasis, but in 42.0% of the patients with firstly diagnosed visceral metastasis (P = 0.001). The metastasis-free survival rate, locoregional recurrence-free survival rate and overall survival rate of the ECE positive group were much shorter than that of the ECE negative group. COX proportional hazard regression single factor analysis and multi-factor analysis suggested that ECE is an independent factor of metastasis-free survival, locoregional free recurrence and overall survival. CONCLUSION: The presence of ECE in breast cancer is positively related with tumor size and the number of positive lymph nodes. It is also a risk factor of locoregional recurrence and distant metastasis. ECE positive group has a much shorter metastasis-free survival, locoregional recurrence-free survival and overall survival. ECE is a risk factor of those three indexes.

Author Correction: 5-Hydroxymethylcytosine signatures in circulating cell-free DNA as diagnostic biomarkers for human cancers.

In the initial published version of this article, there was a mistake in the P value for the correlation between gene-expression changes and 5 hmC changes in tumors. The correct P value should be same as the P value shown in Fig. S6A: 9.8 × 10-6 (mistakenly shown as "9.8 × 106" in the main text). This correction does not affect the description of results or the conclusions of this study, since the range of P value is between 0 and 1.

Oxidation of the antibacterial agent norfloxacin during sodium hypochlorite disinfection of marine culture water.

Chlorination disinfection and antibiotic addition are two universal processes of marine culture. The generation of disinfection byproducts (DBPs) is unavoidable. Antibiotic residue not only pollutes water but also acts as a precursor to the production of new DBPs. The fate of antibiotic norfloxacin (NOR) in chlorination disinfection was investigated. It was observed that NOR could be oxidized by disinfection agent sodium hypochlorite, but the oxidation rate varied considerably with the type of disinfected water. For fresh water, marine culture water and sea water, the reaction rate constant was 0.066 min-1, 0.466 min-1 and 1.241 min-1, respectively. The difference was primarily attributed to the promotion role of bromide ions in seawater and marine culture water. Moreover, the bromide ions could result in the generation of brominated DBPs (Br-DBPs). The kinetics, products, reaction centers and mechanisms were investigated. The active site of NOR was found to be the N4 atom on piperazinyl in fresh water. During marine culture water and sea water disinfection, the carboxyl on NOR was oxidized and two Br-DBPs were formed. This was attributed to the lowering of the reaction's required activation energy when performed in the presence of bromide ions. The Br-DBPs were also confirmed in real shrimp pond brackish water. Quantitative structure activity relationships and the total organic halogen analysis showed that the DBPs in marine culture water possessed stronger toxicological properties than the DBPs in fresh water. The toxicity increase was attributed to the production of Br-DBPs in the disinfection process of marine culture water.

5-Hydroxymethylcytosine signatures in circulating cell-free DNA as diagnostic biomarkers for human cancers.

DNA modifications such as 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) are epigenetic marks known to affect global gene expression in mammals. Given their prevalence in the human genome, close correlation with gene expression and high chemical stability, these DNA epigenetic marks could serve as ideal biomarkers for cancer diagnosis. Taking advantage of a highly sensitive and selective chemical labeling technology, we report here the genome-wide profiling of 5hmC in circulating cell-free DNA (cfDNA) and in genomic DNA (gDNA) of paired tumor and adjacent tissues collected from a cohort of 260 patients recently diagnosed with colorectal, gastric, pancreatic, liver or thyroid cancer and normal tissues from 90 healthy individuals. 5hmC was mainly distributed in transcriptionally active regions coincident with open chromatin and permissive histone modifications. Robust cancer-associated 5hmC signatures were identified in cfDNA that were characteristic for specific cancer types. 5hmC-based biomarkers of circulating cfDNA were highly predictive of colorectal and gastric cancers and were superior to conventional biomarkers and comparable to 5hmC biomarkers from tissue biopsies. Thus, this new strategy could lead to the development of effective, minimally invasive methods for diagnosis and prognosis of cancer from the analyses of blood samples.

A Genetically Encoded FRET Sensor for Intracellular Heme.

Heme plays pivotal roles in various cellular processes as well as in iron homeostasis in living systems. Here, we report a genetically encoded fluorescence resonance energy transfer (FRET) sensor for selective heme imaging by employing a pair of bacterial heme transfer chaperones as the sensory components. This heme-specific probe allows spatial-temporal visualization of intracellular heme distribution within living cells.

A readily synthesized cyclic pyrrolysine analogue for site-specific protein "click" labeling.

A concise route was developed for the facile synthesis of a cyclic pyrrolysine analogue bearing an azide handle. Directed evolution enabled the encoding of this non-natural amino acid in both prokaryotic and eukaryotic cells, which offers a highly efficient approach for the site-specific protein labeling using click chemistry.