Purification of capsular polysaccharides isolated from S. pneumoniae serotype 2 by hydrogen peroxide and endonuclease.

A high-quality and cost-effective purification procedure is one of the most important requirements for manufacturing glycoconjugate vaccines. The goal of the present work was to devise a method for removing impurities such as protein and nucleic acid from Streptococcus pneumoniae serotype 2 capsular polysaccharides (CPS). The use of hydrogen peroxide for the reduction of impurities of crude CPS was investigated. Centrifugation followed by filtration decreased protein contaminant of the hydrogen peroxide-treated CPS to meet the limit specified by WHO. The nucleic acid impurity remaining was removed by a further step of endonuclease treatment to yield the purified CPS. Characterization of purified CPS was evaluated by various analytical techniques including 1H NMR and antigenicity by competitive inhibition assay. Various hydrogen peroxide concentrations have significant impact on the antigenic property of CPS. Whereas, optimum process conditions can preserve the native characteristics of CPS.

Label-free and highly sensitive APE1 detection based on rolling circle amplification combined with G-quadruplex.

The highly sensitive detection of low-abundant apurinic/apyrimidinic endonuclease 1 (APE1) activity is of great significance for early diagnosis of disease and pathological research. Many methods for detecting APE1 based on isothermal nucleic acids amplification have been developed for improving its sensitivity. However, some of these methods have certain limitations, such as multiple reaction steps, narrow linear range, and complicated processes for fluorescent labeling. Herein, we develop a highly sensitive and label-free APE1 fluorescence detection method based on rolling circle amplification combined with G-quadruplex (RCA-G4). A hairpin probe (HP) labeled with the AP site can be recognized and cleaved by APE1, leading to the release of the primer sequence, which triggered RCA to produce long chain amplification products with a great amount of repeated sequences. The formed amplicon contains a series G-quadruplex structure, which can be combined with Thioflavin T (ThT) to produce fluorescence and achieve high sensitivity label-free detection of APE1. Benefit from the high amplification efficiency of RCA and the high fluorescence quantum yield of G-quadruplex/ThT, a detection limit as low as 1.52 × 10-6 U/mL and the linear range from 2 × 10-6 to 10 U/mL were obtained. The developed RCA-G4 method can be successfully used to detect APE1 in serum samples with a recovery from 96.3% to 105.7%. We believe that this approach is expected to play an important role in APE1-related disease research and drug development.

Nucleic acid amplification-integrated single-molecule fluorescence imaging for in vitro and in vivo biosensing.

Single-molecule fluorescence imaging is among the most advanced analytical technologies and has been widely adopted for biosensing due to its distinct advantages of simplicity, rapidity, high sensitivity, low sample consumption, and visualization capability. Recently, a variety of nucleic acid amplification approaches have been developed to provide a straightforward and highly efficient way for amplifying low abundance target signals. The integration of single-molecule fluorescence imaging with nucleic acid amplification has greatly facilitated the construction of various fluorescent biosensors for in vitro and in vivo detection of DNAs, RNAs, enzymes, and live cells with high sensitivity and good selectivity. Herein, we review the advances in the development of fluorescent biosensors by integrating single-molecule fluorescence imaging with nucleic acid amplification based on enzyme (e.g., DNA polymerase, RNA polymerase, exonuclease, and endonuclease)-assisted and enzyme-free (e.g., catalytic hairpin assembly, entropy-driven DNA amplification, ligation chain reaction, and hybridization chain reaction) strategies, and summarize the principles, features, and in vitro and in vivo applications of the emerging biosensors. Moreover, we discuss the remaining challenges and future directions in this area. This review may inspire the development of new signal-amplified single-molecule biosensors and promote their practical applications in fundamental and clinical research.

Significance of ERCC1 and Hormonal Receptor Expression in Ovarian Cancer.

Background & Objectives : Ovarian carcinoma usually has a relatively poor prognosis. A rational approach to identify patients, who are likely to benefit from therapy, is urgently needed. Excision repair cross-complementation group 1 enzyme (ERCC1) has been proposed as a molecular predictor of clinical resistance to platinum-based chemotherapy. Steroid hormone receptors are important determinants of prognosis and predictive behavior in tumor tissues of several origins. The present study aimed to investigate the expression profile of ERCC1, ER & AR in patients with Ovarian carcinoma and their association with patient outcome. Methods : This is a prospective study which included 77 patients with ovarian carcinoma who were treated with platinum based chemotherapy at the National Cancer Institute (NCI) in Egypt during the period 7/2016- 7/2018. We evaluated the expression of ER, AR, and Excision repair cross-complementation group 1 enzyme (ERCC1) by immunohistochemistry. Expression profiles were compared to clinical, histologic and prognostic factors, the clinical outcome and survival. All patients received platinum containing chemotherapy regimen. Result : Of the 77 patients with ovarian cancer, 66.2 % (51/77) were ERCC1-positive, 49.4 % (38/77) were AR positive & 75.3 % (58/77) were ER positive. Platinum resistance was found in eight of the tumors with positive ERCC1 protein expression compared with two among the patients with negative tumor staining for ERCC1 (P = 0.643). There was significant association between ER & AR expression and pathological subtypes (p = 0.004, 0.007) respectively. There were no significant association between ER, AR& ERCC1 expression and PFS (P = 0.447,P = 0.162, P = 0.508 respectively) or OS (P = 0.781, P = 0.569, P = 0.381 respectively). Based on Cox proportional hazards regression analysis ERCC1, ER &AR were not independent factors affecting the prognosis of patients with ovarian carcinoma. Conclusion : These results demonstrate that positive ERCC1 expression is not associated with clinical resistance to platinum-based chemotherapy, ERCC1, AR& ER expression are not independent factors affecting the prognosis of patients with epithelial ovarian tumors and not associated with survival benefits. J. Med. Invest. 67 : 391-398, August, 2020.

Human ANKLE1 Is a Nuclease Specific for Branched DNA.

All physical connections between sister chromatids must be broken before cells can divide, and eukaryotic cells have evolved multiple ways in which to process branchpoints connecting DNA molecules separated both spatially and temporally. A single DNA link between chromatids has the potential to disrupt cell cycle progression and genome integrity, so it is highly likely that cells require a nuclease that can process remaining unresolved and hemi-resolved DNA junctions and other branched species at the very late stages of mitosis. We argue that ANKLE1 probably serves this function in human cells (LEM-3 in Caenorhabditis elegans). LEM-3 has previously been shown to be located at the cell mid-body, and we show here that human ANKLE1 is a nuclease that cleaves a range of branched DNA species. It thus has the substrate selectivity consistent with an enzyme required to process a variety of unresolved and hemi-resolved branchpoints in DNA. Our results suggest that ANKLE1 acts as a catch-all enzyme of last resort that allows faithful chromosome segregation and cell division to occur.

Diagnostic and Prognostic Potential of Biomarkers CYFRA 21.1, ERCC1, p53, FGFR3 and TATI in Bladder Cancers.

The high occurrence of bladder cancer and its tendency to recur in combination with a lifelong surveillance make the treatment of superficial bladder cancer one of the most expensive and time-consuming. Moreover, carcinoma in situ often leads to muscle invasion with an unfavorable prognosis. Currently, invasive methods including cystoscopy and cytology remain a gold standard. The aim of this study was to explore urine-based biomarkers to find the one with the best specificity and sensitivity, which would allow optimizing the treatment plan. In this review, we sum up the current knowledge about Cytokeratin fragments (CYFRA 21.1), Excision Repair Cross-Complementation 1 (ERCC1), Tumour Protein p53 (Tp53), Fibroblast Growth Factor Receptor 3 (FGFR3), Tumor-Associated Trypsin Inhibitor (TATI) and their potential applications in clinical practice.

CRISPR-Cas9-mediated induction of heritable chromosomal translocations in Arabidopsis.

Clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein (Cas) technology has been applied in plant breeding mainly on genes for improving single or multiple traits1-4. Here we show that this technology can also be used to restructure plant chromosomes. Using the Cas9 nuclease from Staphylococcus aureus5, we were able to induce reciprocal translocations in the Mbp range between heterologous chromosomes in Arabidopsis thaliana. Of note, translocation frequency was about five times more efficient in the absence of the classical non-homologous end-joining pathway. Using egg-cell-specific expression of the Cas9 nuclease and consecutive bulk screening, we were able to isolate heritable events and establish lines homozygous for the translocation, reaching frequencies up to 2.5% for individual lines. Using molecular and cytological analysis, we confirmed that the chromosome-arm exchanges we obtained between chromosomes 1 and 2 and between chromosomes 1 and 5 of Arabidopsis were conservative and reciprocal. The induction of chromosomal translocations enables mimicking of genome evolution or modification of chromosomes in a directed manner, fixing or breaking genetic linkages between traits on different chromosomes. Controlled restructuring of plant genomes has the potential to transform plant breeding.

ERCC1 expression in advanced colorectal cancer and matched liver metastases.

BACKGROUND: Platinum-based chemotherapy is part of the standard treatment for patients with colorectal cancer. ERCC1 is a potential predictive biomarker for platinum-based chemotherapy. The aim of this study was to examine interobserver agreement on ERCC1 protein expression in primary colorectal cancer as well as corresponding liver metastasis. Furthermore, comparison of ERCC1-expression in primary tumor and the corresponding liver metastasis was performed. METHODS: Forty patients with primary colorectal cancers and corresponding liver metastases were included. One slide was stained with the anti-ERCC1 antibody, 4F9 clone (DAKO) and evaluated by two gastrointestinal pathology consultants and a pathology registrar separately. Interobserver agreement was evaluated for primary tumors and liver metastases using kappa (κ) statistics. Discordant scorings were reviewed, and consensus was obtained. The expression in primary tumor was compared with the corresponding liver metastases. RESULTS: For the primary tumors agreement was found in 85% of the tumors corresponding to an unweighted kappa value of 0,79 (95% CI 0,64-0,94). For the liver metastases agreement was found in 76% corresponding to an unweighted kappa value of 0,64 (95% CI 0,49-0,79). When comparing primary tumors to the corresponding metastases, no concordance in ERCC1-expression was observed. CONCLUSION: Interobserver agreement of ERCC1 expression was good for both primary tumors and liver metastases, which is crucial for a potential predictive biomarker. As no concordance between primary tumor and liver metastases was found it seems to be of high importance to use tissue from actual tumor burden for evaluation of ERCC1 expression. Further studies and correlation to clinical outcome are warranted.

Predictive Value of ERCC1, ERCC2, and XRCC Expression for Patients with Locally Advanced or Metastatic Gastric Cancer Treated with Neoadjuvant mFOLFOX-4 Chemotherapy.

The dismal outcome in patients with locally advanced or metastatic gastric cancer (GC) highlights the need for effective systemic neoadjuvant chemotherapy to improve clinical results. This study evaluated the correlation between the expression of three DNA repair genes, namely the excision repair cross-complementing group 1 (ERCC1), excision repair cross-complementing group 2 (ERCC2), and X-ray repair cross-complementing protein 1 (XRCC1) and the clinical outcome of patients with locally advanced or metastatic GC treated with mFOLFOX-4 neoadjuvant chemotherapy. Fifty-eight patients with histologically confirmed locally advanced or metastatic GC following neoadjuvant mFOLFOX-4 chemotherapy were enrolled between January 2009 and January 2018. We analyzed clinicopathological features and ERCC1, ERCC2, and XRCC1 expression to identify potential predictors of clinical response. Among the 58 patients, 16 (27.6%) were categorized into the response group (partial response) and 42 into the nonresponse group (stable disease in 24 patients and progressive disease in 18 patients). A multivariate analysis showed that ERCC1 overexpression (P = 0.003), ERCC2 overexpression (P = 0.049), and either ERCC1 or ERCC2 overexpression (P = 0.002) were independent predictors of response following mFOLFOX-4 neoadjuvant chemotherapy. Additionally, ERCC1 and ERCC2 overexpression did not only predict the response but also progression-free survival (both P < 0.05) and overall survival (both P < 0.05). ERCC1 and ERCC2 overexpression are promising predictive biomarkers for patients with locally advanced or metastatic GC receiving neoadjuvant mFOLFOX-4 chemotherapy and the potential clinical implication is mandatory for further investigation.

MGARP is ultrastructurally located in the inner faces of mitochondrial membranes.

Mitochondria, the centers of energy production, are highly organized with inner membranes, cristae and outer membranes. The mitochondrial architecture determines their functions in all cellular processes. Changes in the mitochondrial ultrastructure are tightly related to a wide variety of diseases. MGARP, a mitochondria-localized protein, was predicted by bioinformatics and confirmed by cellular and biochemical methods to be located in mitochondria, but there is no direct and clear evidence for its precise location. This report demonstrates the precise ultrastructural location of MGARP within mitochondria by the ascorbate peroxidase 2 (APEX2) system in combination with electron microscopy (EM). EM revealed that more MGARP is located in the inner/cristae membranes, with its C-terminus at the inner faces of the intramembrane spaces, than in the outer membranes. MGARP overexpression caused both mitochondrial remodeling and cristae shaping, leading to the collapse of the mitochondrial network. The mitochondrial morphologies in MGARP-overexpressing cells were diverse; the cells became round or short, and their cristae were deformed and became discontinuous or circular. An engineered MGARP mutant deficient in its transmembrane domain no longer localized to the mitochondria and lost its effects on mitochondrial structure, confirming that the localization of MGARP in the mitochondria depends on its structural integrity. Collectively, our findings define the location of MGARP within the mitochondria, which is associated with its functional implications for the architecture and organization of mitochondria.

The thioredoxin-mediated recycling of Arabidopsis thaliana GRXS16 relies on a conserved C-terminal cysteine.

BACKGROUND: Glutaredoxins (GRXs) are oxidoreductases involved in diverse cellular processes through their capacity to reduce glutathionylated proteins and/or to coordinate iron­sulfur (Fe-S) clusters. Among class II GRXs, the plant-specific GRXS16 is a bimodular protein formed by an N-terminal endonuclease domain fused to a GRX domain containing a 158CGFS signature. METHODS: The biochemical properties (redox activity, sensitivity to oxidation, pKa of cysteine residues, midpoint redox potential) of Arabidopsis thaliana GRXS16 were investigated by coupling oxidative treatments to alkylation shift assays, activity measurements and mass spectrometry analyses. RESULTS: Activity measurements using redox-sensitive GFP2 (roGFP2) as target protein did not reveal any significant glutathione-dependent reductase activity of A. thaliana GRXS16 whereas it was able to catalyze the oxidation of roGFP2 in the presence of glutathione disulfide. Accordingly, Arabidopsis GRXS16 reacted efficiently with oxidized forms of glutathione, leading to the formation of an intramolecular disulfide between Cys158 and the semi-conserved Cys215, which has a midpoint redox potential of - 298 mV at pH 7.0 and is reduced by plastidial thioredoxins (TRXs) but not GSH. By promoting the formation of this disulfide, Cys215 modulates GRXS16 oxidoreductase activity. CONCLUSION: The reduction of AtGRXS16, which is mandatory for its oxidoreductase activity and the binding of Fe-S clusters, depends on light through the plastidial FTR/TRX system. Hence, disulfide formation may constitute a redox switch mechanism controlling GRXS16 function in response to day/night transition or oxidizing conditions. GENERAL SIGNIFICANCE: From the in vitro data obtained with roGFP2, one can postulate that GRXS16 would mediate protein glutathionylation/oxidation in plastids but not their deglutathionylation.

A Possible Role for Long Interspersed Nuclear Elements-1 (LINE-1) in Huntington's Disease Progression.

BACKGROUND Recent studies have shown that increased mobilization of Long Interspersed Nuclear Elements-1 (L1) can promote the pathophysiology of multiple neurological diseases. However, its role in Huntington's disease (HD) remains unknown. MATERIAL AND METHODS R6/2 mice - a common mouse model of HD - were used to evaluate changes in L1 mobilization. Pyrosequencing was used to evaluate methylation content changes. L1-ORF1 and L1-ORF2 expression analysis were evaluated by RT-PCR and immunoblotting. Changes in pro-survival signaling were evaluated by L1-ORF overexpression studies and validated in the mouse model by immunohistochemistry and immunoblotting. RESULTS We found an increased mobilization of L1 elements in the caudate genome of R6/2 mice (p<0.05) - a common mouse model of HD - but not in wild-type mice. Subsequent pyrosequencing and expression analysis showed that the L1 elements were hypomethylated and their respective ORFs were overexpressed in the affected tissues. In addition, a significant decrease in the pro-survival proteins such as the phosphoproteins of AKT target proteins, mTORC1 activity, and AMPK alpha levels was observed with the increase in the expression L1-ORF2. CONCLUSIONS These findings indicate that hyperactive retrotransposition of L1 triggers a downstream signaling pathway affecting the neuronal survival pathways via downregulation of mTORC1 activity and AMPKalpha and increasing apoptosis in neurons.

Alkyne-DNA-Functionalized Alloyed Au/Ag Nanospheres for Ratiometric Surface-Enhanced Raman Scattering Imaging Assay of Endonuclease Activity in Live Cells.

A novel ratiometric surface-enhanced Raman scattering (SERS) nanosensor has been developed to probe the activity of endonuclease under in vitro and in living cells conditions. The optimized alloyed Au/Ag nanoparticles (NPs) were synthesized as the SERS substrate, which combined the superior properties of both pure Au and pure Ag nanoparticles: they exhibit excellent plasmonic property with high chemical stability and low cytotoxicity. They were then employed for quantitative detection of endonuclease through functionalization with single-stranded DNA (ssDNA) carrying 3-[4-(phenylethynyl)benzylthio]propanoic acid (PEB) as endonuclease-responsive SERS signaling molecule and 4-thiophenylacetylene (TPA) as the internal standard SERS signaling molecule. In the presence of endonuclease, the ssDNA was cleaved, releasing PEB molecules from the particle surface and decreasing the SERS signal at 2215 cm-1 from PEB. Since the SERS signal at 1983 cm-1 from alkynyl TPA remained the same, quantitative detection of endonuclease was achieved, based on the ratiometric peak intensity of I1983/ I2215, with a detection limit as low as 0.056 unit/mL. A highly biocompatible and antijamming ratiometric SERS sensor was established by combining the alloyed Au/AgNPs with two unique alkynes molecules with Raman signals in the cellular silent region. The ratiometric sensor was successfully employed to detect intracellular endonuclease activity as well as endonuclease in living cells for the first time.

DNA-templated copper nanoparticles for voltammetric analysis of endonuclease activity.

DNA endonucleases play critical roles in medicinal chemistry, which are also commonly used in molecular biology investigation. Sensitive quantification of endonuclease activity is of great significance. In this study, a reliable electrochemical approach for endonuclease activity sensing is developed with the adoption of copper nanoparticles (CuNPs) as electrochemical reporters. Firstly, a DNA duplex is designed and modified on a gold electrode, which acts as the template for the synthesis of CuNPs. Subsequently, the formed NPs are dissolved and then electrodeposited on a glassy carbon electrode for DPV measurements. With the effect of target endonuclease, the DNA duplex is specifically recognized and cleaved. Thus, CuNPs cannot be synthesized and a declined DPV peak is obtained to reveal the level of endonuclease activity. This developed sensor has a wide linear range from 10-3 to 10 U mL-1, and the limit of detection is 10-3 U mL-1, which is extremely low. High stability and excellent reproducibility are also researched. Besides, this sensor shows good selectivity, which can successfully distinguish target endonuclease from possible interferences.

Predictive value of excision repair cross- complementation group 1 expression in locoregionally advanced nasopharyngeal carcinoma receiving cisplatin-based concurrent chemoradiotherapy.

BACKGROUND: Cisplatin-based concurrent chemoradiotherapy is recommended for nasopharyngeal carcinoma (NPC) at advanced stages. Excision repair cross-complementation group 1 (ERCC1) plays an important function in the repair of DNA damage that is a critical process of chemo- and radiotherapy. OBJECTIVE: This study aimed to investigate the clinical significance of ERCC1 expression in NPC treated with cisplatin-based concurrent chemoradiotherapy in locoregionally advanced NPC. METHODS: The expression level of ERCC1 and its association with clinicopathological characteristics in 205 locoregionally advanced NPC patients receiving cisplatin-based concurrent chemoradiotherapy were analyzed retrospectively. RESULTS: The correlation analysis revealed that the treatment-sensitive patients displayed dramatically lower ERCC1 expression than treatment-resistant cases did. Furthermore, the Kaplan-Meier plots revealed lower ERCC1 expression was significantly associated with better survival. Multivariate analysis further showed that the ERCC1 expression was an independent predictor of NPC patients' survival. CONCLUSIONS: ERCC1 expression might be a useful predictive marker in patients with locoregionally advanced NPC receiving cisplatin-based concurrent chemoradiotherapy.

A novel antibody-based approach to detect the functional ERCC1-202 isoform.

ERCC1/XPF endonuclease plays an important role in multiple DNA repair pathways and stands as a potential prognostic and predictive biomarker for cisplatin-based chemotherapy. Four distinct ERCC1 isoforms arising from alternative splicing have been described (201, 202, 203 and 204) but only the 202 isoform is functional in DNA excision repair, when interacting with its obligate partner XPF. Currently, there is no tool to assess specifically the expression of ERCC1-202 due to high sequence homology between the four isoforms. Here, we generated monoclonal antibodies directed against the heterodimer of ERCC1 and its obligate interacting partner XPF by genetic immunization. We obtained three monoclonal antibodies (2C11, 7C3 and 10D10) recognizing specifically the heterodimer ERCC1-202/XPF as well as the ERCC1-204/XPF with no affinity to ERCC1 or XPF monomers. By combining one of these three heterodimer-specific antibodies with a commercial anti-ERCC1 antibody (clone 4F9) unable to recognize the 204 isoform in a proximity ligation assay (PLA), we managed to specifically detect the functional ERCC1-202 isoform. This methodological breakthrough can constitute a basis for the development of clinical tests to evaluate ERCC1 functional proficiency.

Dissection of affinity captured LINE-1 macromolecular complexes.

Long Interspersed Nuclear Element-1 (LINE-1, L1) is a mobile genetic element active in human genomes. L1-encoded ORF1 and ORF2 proteins bind L1 RNAs, forming ribonucleoproteins (RNPs). These RNPs interact with diverse host proteins, some repressive and others required for the L1 lifecycle. Using differential affinity purifications, quantitative mass spectrometry, and next generation RNA sequencing, we have characterized the proteins and nucleic acids associated with distinctive, enzymatically active L1 macromolecular complexes. Among them, we describe a cytoplasmic intermediate that we hypothesize to be the canonical ORF1p/ORF2p/L1-RNA-containing RNP, and we describe a nuclear population containing ORF2p, but lacking ORF1p, which likely contains host factors participating in target-primed reverse transcription.