Massively parallel single-cell chromatin landscapes of human immune cell development and intratumoral T cell exhaustion.

Understanding complex tissues requires single-cell deconstruction of gene regulation with precision and scale. Here, we assess the performance of a massively parallel droplet-based method for mapping transposase-accessible chromatin in single cells using sequencing (scATAC-seq). We apply scATAC-seq to obtain chromatin profiles of more than 200,000 single cells in human blood and basal cell carcinoma. In blood, application of scATAC-seq enables marker-free identification of cell type-specific cis- and trans-regulatory elements, mapping of disease-associated enhancer activity and reconstruction of trajectories of cellular differentiation. In basal cell carcinoma, application of scATAC-seq reveals regulatory networks in malignant, stromal and immune cells in the tumor microenvironment. Analysis of scATAC-seq profiles from serial tumor biopsies before and after programmed cell death protein 1 blockade identifies chromatin regulators of therapy-responsive T cell subsets and reveals a shared regulatory program that governs intratumoral CD8+ T cell exhaustion and CD4+ T follicular helper cell development. We anticipate that scATAC-seq will enable the unbiased discovery of gene regulatory factors across diverse biological systems.

Haplotyping germline and cancer genomes with high-throughput linked-read sequencing.

Haplotyping of human chromosomes is a prerequisite for cataloguing the full repertoire of genetic variation. We present a microfluidics-based, linked-read sequencing technology that can phase and haplotype germline and cancer genomes using nanograms of input DNA. This high-throughput platform prepares barcoded libraries for short-read sequencing and computationally reconstructs long-range haplotype and structural variant information. We generate haplotype blocks in a nuclear trio that are concordant with expected inheritance patterns and phase a set of structural variants. We also resolve the structure of the EML4-ALK gene fusion in the NCI-H2228 cancer cell line using phased exome sequencing. Finally, we assign genetic aberrations to specific megabase-scale haplotypes generated from whole-genome sequencing of a primary colorectal adenocarcinoma. This approach resolves haplotype information using up to 100 times less genomic DNA than some methods and enables the accurate detection of structural variants.

Multiplexed target detection using DNA-binding dye chemistry in droplet digital PCR.

Two years ago, we described the first droplet digital PCR (ddPCR) system aimed at empowering all researchers with a tool that removes the substantial uncertainties associated with using the analogue standard, quantitative real-time PCR (qPCR). This system enabled TaqMan hydrolysis probe-based assays for the absolute quantification of nucleic acids. Due to significant advancements in droplet chemistry and buoyed by the multiple benefits associated with dye-based target detection, we have created a "second generation" ddPCR system compatible with both TaqMan-probe and DNA-binding dye detection chemistries. Herein, we describe the operating characteristics of DNA-binding dye based ddPCR and offer a side-by-side comparison to TaqMan probe detection. By partitioning each sample prior to thermal cycling, we demonstrate that it is now possible to use a DNA-binding dye for the quantification of multiple target species from a single reaction. The increased resolution associated with partitioning also made it possible to visualize and account for signals arising from nonspecific amplification products. We expect that the ability to combine the precision of ddPCR with both DNA-binding dye and TaqMan probe detection chemistries will further enable the research community to answer complex and diverse genetic questions.

Chemiluminescence detection of amino acids and related compounds using acidic potassium permanganate, manganese(IV) or tris(2,2'-bipyridine)ruthenium(III).

We have explored the chemiluminescence response of amino acids and related compounds (including the tripeptide glutathione, and disulfides: cystine, homocystine and glutathione disulfide) with several new adaptations of the permanganate and tris(2,2'-bipyridine)ruthenium(III) ([Ru(bipy)(3)](3+)) reagents and a recently developed colloidal manganese(IV) system. The selectivity of the permanganate reagent can be directed towards tyrosine or thiol compounds like cysteine, homocysteine and glutathione by manipulating reaction conditions (providing limits of detection of 4 nM tyrosine and 5 nM glutathione). Colloidal Mn(IV) produced measureable responses with all analytes, but was most suitable for tryptophan, tyrosine, thiols and disulfides, including α-lipoic acid and dihydrolipoic acid, for which the limits of detection were 30 nM and 20 nM, respectively. A stabilised form of [Ru(bipy)(3)](3+), prepared by oxidising [Ru(bipy)(3)](ClO(4))(2) in acetonitrile, exhibited similar selectivity to that of the conventional aqueous reagent. The [Ru(bipy)(3)](3+) reagent was effective for the detection of secondary amino acids such as proline and hydroxyproline, as well as the disulfide, homocystine.

Direct detection of biologically significant thiols and disulfides with manganese(IV) chemiluminescence.

The quantification of low-molecular mass thiols and disulfides involved in cellular redox processes is hindered by oxidation or degradation of analytes during conventional sample preparation steps (including deproteinization and derivatization). Researchers therefore seek techniques that minimize sample handling and permit direct detection of thiols and disulfides within a single chromatographic separation. We demonstrate a new HPLC procedure for these biologically important analytes that incorporates direct chemiluminescence detection with a manganese(IV) reagent. A mixture of seven thiols and disulfides (cysteine, N-acetylcysteine, homocysteine, glutathione (GSH), glutathione disulfide (GSSG), cystine, and homocystine) in their native forms were separated using a C18 column within 20 min. Detection limits for these analytes ranged from 5 × 10(-8) to 1 × 10(-7) M, and the precision for retention times and peak areas was excellent, with relative standard deviations of less than 0.3% and 2%, respectively. This approach was employed to determine two key biomarkers of oxidative stress, GSH and GSSG, in whole blood taken from 12 healthy volunteers. Samples were deproteinized, centrifuged, and diluted prior to analysis using a simple procedure that was shown to avoid significant artificial oxidation of GSH.

Stable tris(2,2'-bipyridine)ruthenium(III) for chemiluminescence detection.

Two exceedingly stable [Ru(bipy)(3)](3+) reagents were prepared by dissolving either [Ru(bipy)(3)](ClO(4))(2) in acetonitrile (containing 0.05 M HClO(4)) or [Ru(bipy)(3)]Cl(2)·6H(2)O in 95:5 glacial acetic acid-acetic anhydride (containing 0.05 M H(2)SO(4)) followed by oxidation with PbO(2). These conveniently prepared solutions provide highly reproducible chemiluminescence detection over long periods of analysis, avoiding the need for recalibration or preparation of fresh reagent solutions and without the complications associated with online chemical or electrochemical oxidations. The reagent prepared in acetonitrile produced much greater signal intensities with a range of analytes and was deemed most suitable for high-performance liquid chromatography (HPLC) with postcolumn chemiluminescence detection.

Determination of intracellular glutathione and glutathione disulfide using high performance liquid chromatography with acidic potassium permanganate chemiluminescence detection.

Measurement of glutathione (GSH) and glutathione disulfide (GSSG) is a crucial tool to assess cellular redox state. Herein we report a direct approach to determine intracellular GSH based on a rapid chromatographic separation coupled with acidic potassium permanganate chemiluminescence detection, which was extended to GSSG by incorporating thiol blocking and disulfide bond reduction. Importantly, this simple procedure avoids derivatisation of GSH (thus minimising auto-oxidation) and overcomes problems encountered when deriving the concentration of GSSG from 'total GSH'. The linear range and limit of detection for both analytes were 7.5 × 10(-7) to 1 × 10(-5) M, and 5 × 10(-7) M, respectively. GSH and GSSG were determined in cultured muscle cells treated for 24 h with glucose oxidase (0, 15, 30, 100, 250 and 500 mU mL(-1)), which exposed them to a continuous source of reactive oxygen species (ROS). Both analyte concentrations were greater in myotubes treated with 100 or 250 mU mL(-1) glucose oxidase (compared to untreated controls), but were significantly lower in myotubes treated with 500 mU mL(-1) (p < 0.05), which was rationalised by considering measurements of H(2)O(2) and cell viability. However, the GSH/GSSG ratio in myotubes treated with 100, 250 and 500 mU mL(-1) glucose oxidase exhibited a dose-dependent decrease that reflected the increase in intracellular ROS.

Screening for antioxidants in complex matrices using high performance liquid chromatography with acidic potassium permanganate chemiluminescence detection.

The use of high performance liquid chromatography with acidic potassium permanganate chemiluminescence detection to screen for antioxidants in complex plant-derived samples was evaluated in comparison with two conventional post-column radical scavenging assays (2,2-diphenyl-1-picrylhydrazyl radical (DPPH) and 2,2'-azinobis-(3-ethylbenzothiazoline-6-sulfonic acid) radical cation (ABTS(+))). In this approach, acidic potassium permanganate can react with readily oxidisable compounds (potential antioxidants), post-column, to produce chemiluminescence. Using flow injection analysis, experimental parameters that afforded the most suitable permanganate chemiluminescence signal for a range of known antioxidants were studied in a univariate approach. Optimum conditions were found to be: 1×10(-3)M potassium permanganate solution containing 1% (w/v) sodium polyphosphates adjusted to pH 2 with sulphuric acid, delivered at a flow rate of 2.5 mL min(-1) per line. Further investigations showed some differences in detection selectivity between HPLC with the optimised post-column permanganate chemiluminescence detection and DPPH and ABTS(+) assays towards antioxidant standards. However, permanganate chemiluminescence detection was more sensitive. Moreover, screening for antioxidants in green tea, cranberry juice and thyme using potassium permanganate chemiluminescence offers several advantages over the traditional DPPH and ABTS(+) assays, such as faster reagent preparation and superior stability; simpler post-column reaction manifold; and greater compatibility with fast chromatographic separations using monolithic columns.

The analysis of café espresso using two-dimensional reversed phase-reversed phase high performance liquid chromatography with UV-absorbance and chemiluminescence detection.

In this study, an activity based screening technique combining two-dimensional liquid chromatography (2DHPLC) with UV-absorbance and chemiluminescence detection was applied to study "Ristretto", "Decaffeinatto" and "Volluto" espresso coffees. This technique, which coupled the separation power of 2DHPLC with the sensitivity and selectivity of the chemiluminescence detection, offers great potential for screening complex samples for antioxidant compounds. Detailed information regarding the complexity of the sample, and the variation between these three coffees could be obtained using this multidimensional-hyphenated method of analysis.

High-performance liquid chromatography with post-column 2,2'-diphenyl-1-picrylhydrazyl radical scavenging assay: methodological considerations and application to complex samples.

An improved post-column 2,2'-diphenyl-1-picrylhydrazyl (DPPH*) radical scavenging assay for the screening of antioxidants in complex matrices was developed. Experimental parameters believed to be influential to DPPH* response were studied in a univariate approach. Optimum conditions were found to be: 5 x 10(-5) M DPPH* reagent prepared in a 75% methanol: 25% 40 mM citric acid-sodium citrate buffer (pH 6) solution, degassed with nitrogen; reaction coil of 2 m x 0.25 mm i.d. PEEK tubing; detection at 521 nm; analysis at room temperature. The analytical utility of this protocol was evaluated by screening for antioxidants in thyme and green tea, in comparison with two commonly employed methodologies.

High performance liquid chromatography with two simultaneous on-line antioxidant assays: Evaluation and comparison of espresso coffees.

The antioxidant profiles of various espresso coffees were established using HPLC with UV-absorbance detection and two rapid, simultaneous, on-line chemical assays that enabled the relative reactivity of sample components to be screened. The assays were based on (i) the colour change associated with reduction of the 2,2'-diphenyl-1-picrylhydrazyl radical (DPPH*); and (ii) the emission of light (chemiluminescence) upon reaction with acidic potassium permanganate. Results from the two approaches were similar and reflected the complex array of antioxidant species present in the samples. However, some differences in selectivity were observed. Chromatograms generated with the chemiluminescence assay contained more peaks, which was ascribed to the greater sensitivity of the reagent towards minor, readily oxidisable sample components. The three coffee samples produced closely related profiles, signifying their fundamentally similar chemical compositions and origin. Nevertheless, the overall intensity and complexity of the samples in both UV absorption and antioxidant assay chromatograms were aligned with the manufacturers description of flavour intensity and character.

Determination of intracellular glutathione and cysteine using HPLC with a monolithic column after derivatization with monobromobimane.

An optimized high-performance liquid chromatography (HPLC) method is used to show that, as myoblasts differentiate into multinucleated muscle fibers, there is a shift to a more oxidized cell redox state. The HPLC method incorporated derivatization with monobromobimane for the determination of the reduced (GSH) and oxidized (GSSG) forms of glutathione and the reduced (Cys) and oxidized (CysSS) forms of cysteine. The derivatization was optimized to improve the sensitivity of the approach; the limits of detection for glutathione and cysteine were 3 x 10(-8) and 5 x 10(-8) M, respectively.

Evaluation of tris(4,7-diphenyl-1,10-phenanthrolinedisulfonate)ruthenium(II) as a chemiluminescence reagent.

Previous studies have suggested that tris(4,7-diphenyl-1,10-phenanthrolinedisulfonate)ruthenium(II) (Ru(BPS)(3)(4-)) has great potential as a chemiluminescence reagent in acidic aqueous solution. We have evaluated four different samples of this reagent (two commercially available and two synthesised in our laboratory) in comparison with tris(2,2'-bipyridine)ruthenium(II) (Ru(bipy)(3)(2+)) and tris(1,10-phenanthroline)ruthenium(II) (Ru(phen)(3)(2+)), using a range of structurally diverse analytes. In general, Ru(BPS)(3)(4-) produced more intense chemiluminescence, but the oxidised Ru(BPS)(3)(3-) species is less stable in aqueous solution than Ru(bipy)(3)(3+) and produced a greater blank signal than Ru(bipy)(3)(3+) or Ru(phen)(3)(3+), which had a detrimental effect on sensitivity. Although the complex is often depicted with the sulfonate groups of the BPS ligand in the para position on the phenyl rings, NMR characterisation revealed that the commercially available BPS material used in this study was predominantly the meta isomer.

Comparison of homoleptic and heteroleptic 2,2'-bipyridine and 1,10-phenanthroline ruthenium complexes as chemiluminescence and electrochemiluminescence reagents in aqueous solution.

We have conducted a comprehensive comparative study of Ru(bipy)(3)(2+), Ru(bipy)(2)(phen)(2+), Ru(bipy)(phen)(2)(2+), and Ru(phen)(3)(2+) as chemiluminescence and electrochemiluminescence (ECL) reagents, to address several previous conflicting observations and gain a greater insight into their potential for chemical analysis. Clear trends were observed in many of their spectroscopic and electrochemical properties, but the relative chemiluminescence or ECL intensity with a range of analytes/co-reactants is complicated by the contribution of numerous (sometimes opposing) factors. Significantly, the reversibility of cyclic voltammetric responses for the complexes decreased as the number of phenanthroline ligands was increased, due to the lower stability of their ruthenium(III) form in the aqueous solvent. This trend was also evident over a longer timescale when the ruthenium(III) form was spectrophotometrically monitored after chemical oxidation of the ruthenium(II) complexes. In general, the greater stability of Ru(bipy)(3)(3+) resulted in lower blank signals, although this effect was less pronounced with ECL, where the reagent is oxidised in the presence of the co-reactants. Nevertheless, this shows the need to compare signal-to-blank ratios or detection limits, rather than the more common comparisons of overall signal intensity for different ruthenium complexes. Furthermore, our results support previous observations that, compared to Ru(bipy)(3)(2+), Ru(phen)(3)(2+) provides greater ECL and chemiluminescence intensities with oxalate, which in some circumstances translates to superior detection limits, but they do not support the subsequent generalised notion that Ru(phen)(3)(2+) is a more sensitive reagent than Ru(bipy)(3)(2+) for all analytes.