Genetics of rheumatoid arthritis contributes to biology and drug discovery.

A major challenge in human genetics is to devise a systematic strategy to integrate disease-associated variants with diverse genomic and biological data sets to provide insight into disease pathogenesis and guide drug discovery for complex traits such as rheumatoid arthritis (RA). Here we performed a genome-wide association study meta-analysis in a total of >100,000 subjects of European and Asian ancestries (29,880 RA cases and 73,758 controls), by evaluating ∼10 million single-nucleotide polymorphisms. We discovered 42 novel RA risk loci at a genome-wide level of significance, bringing the total to 101 (refs 2 - 4). We devised an in silico pipeline using established bioinformatics methods based on functional annotation, cis-acting expression quantitative trait loci and pathway analyses--as well as novel methods based on genetic overlap with human primary immunodeficiency, haematological cancer somatic mutations and knockout mouse phenotypes--to identify 98 biological candidate genes at these 101 risk loci. We demonstrate that these genes are the targets of approved therapies for RA, and further suggest that drugs approved for other indications may be repurposed for the treatment of RA. Together, this comprehensive genetic study sheds light on fundamental genes, pathways and cell types that contribute to RA pathogenesis, and provides empirical evidence that the genetics of RA can provide important information for drug discovery.

Methoxsalen as an in vitro phenotyping tool in comparison with 1-aminobenzotriazole.

The objective is to evaluate methoxsalen as an in vitro phenotyping tool in comparison to ABT as a nonspecific inactivator of P450 mediated metabolism. The reversible inhibition of methoxsalen and ABT against the P450, FMO, AO, MAO-A and -B, enzymes were evaluated using standard marker probe reactions. The time-dependent inhibition of P450 enzymes was evaluated in human liver microsomes. CES1 activities were determined by monitoring the depletion of known substrate, the clopidogrel. The metabolism of P450 substrates in the presence and absence of methoxsalen or ABT was evaluated in human liver microsomes. Methoxsalen is a direct inhibitor and inhibited the activities (>90%) of all enzymes at a concentration of 300 µM except for CYP2C9. Methoxsalen is also a potent time-dependent inhibitor of all P450 enzymes except for CYP2C19 (moderate) at a concentration of 300 µM. Methoxsalen inhibited the metabolism of P450 substrates in the pre-incubation mode. ABT is a potent TDI of several P450 except for CYP2C19 (47%) and CYP2C9 (27%). The results indicate that methoxsalen is a potent pan P450 inhibitor than ABT and can be a better tool in distinguishing P450 mediated metabolism form non-P450 metabolism in human liver microsomes.

Evaluating genetic ancestry and self-reported ethnicity in the context of carrier screening.

BACKGROUND: Current professional society guidelines recommend genetic carrier screening be offered on the basis of ethnicity, or when using expanded carrier screening panels, they recommend to compute residual risk based on ethnicity. We investigated the reliability of self-reported ethnicity in 9138 subjects referred to carrier screening. Self-reported ethnicity gathered from test requisition forms and during post-test genetic counseling, and genetic ancestry predicted by a statistical model, were compared for concordance. RESULTS: We identified several discrepancies between the two sources of self-reported ethnicity and genetic ancestry. Only 30.3% of individuals who indicated Mediterranean ancestry during consultation self-reported this on requisition forms. Additionally, the proportion of individuals who reported Southeast Asian but were estimated to have a different genetic ancestry was found to depend on the source of self-report. Finally, individuals who reported Latin American demonstrated a high degree of ancestral admixture. As a result, carrier rates and residual risks provided for patient decision-making are impacted if using self-reported ethnicity. CONCLUSION: Our analysis highlights the unreliability of ethnicity classification based on patient self-reports. We recommend the routine use of pan-ethnic carrier screening panels in reproductive medicine. Furthermore, the use of an ancestry model would allow better estimation of carrier rates and residual risks.

Simplified detection of the hybridized DNA using a graphene field effect transistor.

Detection of disease-related gene expression by DNA hybridization is a useful diagnostic method. In this study a monolayer graphene field effect transistor (GFET) was fabricated for the detection of a particular single-stranded DNA (target DNA). The probe DNA, which is a single-stranded DNA with a complementary nucleotide sequence, was directly immobilized onto the graphene surface without any linker. The VDirac was shifted to the negative direction in the probe DNA immobilization. A further shift of VDirac in the negative direction was observed when the target DNA was applied to GFET, but no shift was observed upon the application of non-complementary mismatched DNA. Direct immobilization of double-stranded DNA onto the graphene surface also shifted the VDirac in the negative direction to the same extent as that of the shift induced by the immobilization of probe DNA and following target DNA application. These results suggest that the further shift of VDirac after application of the target DNA to the GFET was caused by the hybridization between the probe DNA and target DNA.

Identification of a suitable and selective inhibitor towards aldehyde oxidase catalyzed reactions.

1. Aldehyde oxidase (AO) is a liver cytosolic molybdoflavoprotein enzyme whose importance in drug metabolism is gaining in the recent. The objective of this work is to find a potent and selective inhibitor for AO activity using phthalazine oxidation as a marker reaction. 2. Among organic solvents tested, it was identified that methanol was not a suitable choice for AO activity even at concentrations less than 0.2% v/v. Acetonitrile and DMSO did not show any effect till 0.5% v/v but thereafter activites tend to decrease. 3. For selectivity, 23 compounds were selected and evaluated for their effects on AO and nine CYP450 enzymes. Among the tested compounds chlorpromazine, estradiol, hydralazine, quetiapine and raloxifene were selected based on their potency of inhibition towards AO activity. 4. Raloxifene was found to be a non-specific inhibitor of all major tested CYP450 enzymes and was excluded as a selective inhibitor for AO. Quetiapine also showed a degree of inhibition towards the major CYP450 tested. Hydralazine used as a specific inhibitor during the past for AO activity demonstrated a stimulation of AO activity at high and low concentrations respectively and the inhibition noted to be time dependent while inhibiting other enzymes like monoamine oxidase. 5. Estradiol showed no inhibition towards the tested CYP450 enzymes and thus proved to be a selective and specific inhibitor for AO activity with an uncompetitive mode of inhibition.

Recent Advances in Two-Dimensional Nanomaterials for Healthcare Monitoring.

The development of advanced technologies for the fabrication of functional nanomaterials, nanostructures, and devices has facilitated the development of biosensors for analyses. Two-dimensional (2D) nanomaterials, with unique hierarchical structures, a high surface area, and the ability to be functionalized for target detection at the surface, exhibit high potential for biosensing applications. The electronic properties, mechanical flexibility, and optical, electrochemical, and physical properties of 2D nanomaterials can be easily modulated, enabling the construction of biosensing platforms for the detection of various analytes with targeted recognition, sensitivity, and selectivity. This review provides an overview of the recent advances in 2D nanomaterials and nanostructures used for biosensor and wearable-sensor development for healthcare and health-monitoring applications. Finally, the advantages of 2D-nanomaterial-based devices and several challenges in their optimal operation have been discussed to facilitate the development of smart high-performance biosensors in the future.

Detection of Interleukin-6 Protein Using Graphene Field-Effect Transistor.

Universal platforms to analyze biomolecules using sensor devices can address critical diagnostic challenges. Sensor devices like electrical-based field-effect transistors play an essential role in sensing biomolecules by charge probing. Graphene-based devices are more suitable for these applications. It has been previously reported that Graphene Field-Effect Transistor (GFET) devices detect DNA hybridization, pH sensors, and protein molecules. Graphene became a promising material for electrical-based field-effect transistor devices in sensing biomarkers, including biomolecules and proteins. In the last decade, FET devices have detected biomolecules such as DNA molecules, pH, glucose, and protein. These studies have suggested that the reference electrode is placed externally and measures the transfer characteristics. However, the external probing method damages the samples, requiring safety measurements and a substantial amount of time. To control this problem, the graphene field-effect transistor (GFET) device is fabricated with an inbuilt gate that acts as a reference electrode to measure the biomolecules. Herein, the monolayer graphene is exfoliated, and the GFET is designed with an in-built gate to detect the Interleukin-6 (IL-6) protein. IL-6 is a multifunctional cytokine which plays a significant role in immune regulation and metabolism. Additionally, IL-6 subsidizes a variability of disease states, including many types of cancer development, and metastasis, progression, and increased levels of IL-6 are associated with a higher risk of cancer and can also serve as a prognostic marker for cancer. Here, the protein is desiccated on the GFET device and measured, and Dirac point shifting in the transfer characteristics systematically evaluates the device's performance. Our work yielded a conductive and electrical response with the IL-6 protein. This graphene-based transducer with an inbuilt gate gives a promising platform to enable low-cost, compact, facile, real-time, and sensitive amperometric sensors to detect IL-6. Targeting this pathway may help develop treatments for several other symptoms, such as neuromyelitis optica, uveitis, and, more recently, COVID-19 pneumonia.

26G endo-siRNAs regulate spermatogenic and zygotic gene expression in Caenorhabditis elegans.

Endogenous small interfering RNAs (endo-siRNAs) regulate diverse gene expression programs in eukaryotes by either binding and cleaving mRNA targets or mediating heterochromatin formation; however, the mechanisms of endo-siRNA biogenesis, sorting, and target regulation remain poorly understood. Here we report the identification and function of a specific class of germline-generated endo-siRNAs in Caenorhabditis elegans that are 26 nt in length and contain a guanine at the first nucleotide position (i.e., 26G RNAs). 26G RNAs regulate gene expression during spermatogenesis and zygotic development, and their biogenesis requires the ERI-1 exonuclease and the RRF-3 RNA-dependent RNA polymerase (RdRP). Remarkably, we identified two nonoverlapping subclasses of 26G RNAs that sort into specific RNA-induced silencing complexes (RISCs) and differentially regulate distinct mRNA targets. Class I 26G RNAs target genes are expressed during spermatogenesis, whereas class II 26G RNAs are maternally inherited and silence gene expression during zygotic development. These findings implicate a class of endo-siRNAs in the global regulation of transcriptional programs required for fertility and development.

A rapid, specific, extraction-less, and cost-effective RT-LAMP test for the detection of SARS-CoV-2 in clinical specimens.

In 2019 a newly identified coronavirus, designated as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has spread rapidly from the epicenter in Wuhan (China) to more than 150 countries around the world, causing the Coronavirus disease 2019 (COVID-19) pandemic. In this study, we describe an extraction-less method based on reverse transcriptase loop-mediated isothermal amplification (RT-LAMP) intended for the rapid qualitative detection of nucleic acid from SARS-CoV-2 in upper respiratory specimens, including oropharyngeal and nasopharyngeal swabs, anterior nasal and mid-turbinate nasal swabs, nasopharyngeal washes/aspirates or nasal aspirates as well as bronchoalveolar lavage (BAL) from individuals suspected of COVID-19 by their healthcare provider. The assay's performance was evaluated and compared to an RT quantitative PCR-based assay (FDA-approved). With high sensitivity, specificity, and bypassing the need for RNA extraction, the RT-LAMP Rapid Detection assay is a valuable and fast test for an accurate and rapid RNA detection of the SARS-CoV-2 virus and potentially other pathogens. Additionally, the versatility of this test allows its application in virtually every laboratory setting and remote location where access to expensive laboratory equipment is a limiting factor for testing during pandemic crises.

A Compact Sensory Platform Based pH Sensor Using Graphene Field Effect Transistor.

A compact sensory platform has been fabricated using a graphene field effect transistor (GFET) to identify the biomolecules by pH sensing. The monolayer GFET is driven by an in-built top-gate for detecting the pH of the contacting buffer solution. The GFET device detects the effect of hydroxide ions on a graphite surface. Electrical characteristics of the device were measured after desiccating the buffer solution on the surface of the monolayer graphene. Electrically, the VDirac point shifted toward the positive direction when the pH value of the buffer solution is varied. The transfer curve of the device also moved in the positive direction with increasing pH values, indicating charge transfer from dopant molecules to the surface of graphene. The sensitivity of the device was estimated to be ~48.5 mV/pH. The fabrication of the compact GFET device with an in-built gate provides a platform for effective pH sensing with a user-friendly interface for biosensing applications.

In vivo receptor occupancy assay of histamine H3 receptor antagonist in rats using non-radiolabeled tracer.

INTRODUCTION: Rapid and reliable preclinical receptor occupancy measurement at the target organ in relevant species is critical in accelerating the drug hunting process. The aim of this study was to develop in vivo receptor occupancy assay for histamine H3 receptors (H3R) using the non-radiolabeled GSK189254 as a tracer and to correlate the occupancy-exposure relationship for H3R antagonists in the rats. METHODS: In vivo tracer characterization studies like brain regional distribution, dose and time dependent uptake were carried out for GSK189254 in the male Wistar rats after intravenous administration. The tracer specificity was validated by pretreatment with H3 antagonists like ciproxifan, thioperamide, and GSK334429. The brain regional tracer levels and H3R antagonist concentrations in plasma and brain were quantified using liquid chromatography tandem mass spectrometry. Receptor occupancy was calculated using the ratio of total binding (striatum or frontal cortex) to the nonspecific binding (cerebellum) of the tracer in animals pretreated with H3R antagonist. RESULTS: High degree of selective distribution of GSK189254 was found in striatum, frontal cortex, and low level in the cerebellum. Regional distribution of GSK189254 in the rat brain was consistent to that of H3R distribution mapped using ³H or ¹¹C-GSK189254 in human, porcine, and rat. The calculated occupancy ED50 values in the frontal cortex were 0.14, 1.58, and 0.14 mg/kg for ciproxifan, thioperamide, and GSK334429, respectively. The plasma EC50 values (ng/mL) were found to be 2.33, 292.2, and 3.54 for ciproxifan, thioperamide and GSK334429, respectively. DISCUSSION: Results from mass spectroscopy based approach to determine H3R occupancy in rat brain is comparable with reported radiolabeled method by scintillation spectroscopy. In conclusion, non-radiolabeled GSK189254 was successfully employed as a tracer for assessing the H3R occupancy in rats and it can be used as a preclinical tool for evaluation of novel H3R ligands in the drug discovery.

The landscape of C. elegans 3'UTRs.

Three-prime untranslated regions (3'UTRs) of metazoan messenger RNAs (mRNAs) contain numerous regulatory elements, yet remain largely uncharacterized. Using polyA capture, 3' rapid amplification of complementary DNA (cDNA) ends, full-length cDNAs, and RNA-seq, we defined approximately 26,000 distinct 3'UTRs in Caenorhabditis elegans for approximately 85% of the 18,328 experimentally supported protein-coding genes and revised approximately 40% of gene models. Alternative 3'UTR isoforms are frequent, often differentially expressed during development. Average 3'UTR length decreases with animal age. Surprisingly, no polyadenylation signal (PAS) was detected for 13% of polyadenylation sites, predominantly among shorter alternative isoforms. Trans-spliced (versus non-trans-spliced) mRNAs possess longer 3'UTRs and frequently contain no PAS or variant PAS. We identified conserved 3'UTR motifs, isoform-specific predicted microRNA target sites, and polyadenylation of most histone genes. Our data reveal a rich complexity of 3'UTRs, both genome-wide and throughout development.

Conversation effects on neural mechanisms underlying reaction time to visual events while viewing a driving scene using MEG.

Magnetoencephalography (MEG) imaging examined the neural mechanisms that modulate reaction times to visual events while viewing a driving video, with and without a conversation. Twenty-four subjects ages 18-65 were monitored by whole-head MEG. The primary tasks were to monitor a driving video and to depress a foot pedal in response to a small red light presented to the left or below the driving scene at unpredictable times. The behavioral reaction time (RT) to the lights was recorded. The secondary task was a hands-free conversation. The subject pressed a button to answer a ring tone, and then covertly answered pre-recorded non-emotional questions such as "What is your birth date?" RTs for the conversation task (1043 ms, SE=65 ms) were slightly longer than for the primary task (baseline no conversation (944 ms, SE=48 ms)). During the primary task RTs were inversely related to the amount of brain activity detected by MEG in the right superior parietal lobe (Brodmann's Area 7). Brain activity was seen in the 200 to 300 ms range after the onset of the red light and in the visual cortex (BA 19) about 85 ms after the red light. Conversation reduced the strengths of these regression relationships and increased mean RT. Conversation may contribute to increased reaction times by (1) damping brain activation in specific regions during specific time windows, or (2) reducing facilitation from attention inputs into those areas or (3) increasing temporal variability of the neural response to visual events. These laboratory findings should not be interpreted as indicative of real-world driving, without on-road validation, and comparison to other in-vehicle tasks.

Comparative proteomics analysis of Barrett metaplasia and esophageal adenocarcinoma using two-dimensional liquid mass mapping.

Esophageal adenocarcinoma, currently the seventh leading cause of cancer-related death, has been associated with the presence of Barrett metaplasia. The malignant potential of Barrett metaplasia is evidenced by ultimate progression of this condition to invasive adenocarcinoma. We utilized liquid phase separation of proteins with chromatofocusing in the first dimension and nonporous reverse phase HPLC in the second dimension followed by ESI-TOF mass spectrometry to identify proteins differentially expressed in six Barrett metaplasia samples as compared with six esophageal adenocarcinoma samples; all six Barrett samples were obtained from the identical six patients from whom we obtained the esophageal adenocarcinoma tissue. Approximately 300 protein bands were detected by mass mappings, and 38 differentially expressed proteins were identified by microLC-MS/MS. The false positive rates of the peptide identifications were evaluated by reversed database searching. Among the proteins that were identified, Rho GDP dissociation inhibitor 2, alpha-enolase, Lamin A/C, and nucleoside-diphosphate kinase A were demonstrated to be up-regulated in both mRNA and protein expression in esophageal adenocarcinomas relative to Barrett metaplasia. Candidate proteins were examined at the mRNA level using high density oligonucleotide microarrays. The cellular expression patterns were verified in both esophageal adenocarcinomas and in Barrett metaplasia by immunohistochemistry. These differentially expressed proteins may have utility as useful candidate markers of esophageal adenocarcinoma.