First Dark Matter Search Results from the LUX-ZEPLIN (LZ) Experiment

The LUX-ZEPLIN experiment is a dark matter detector centered on a dual-phase xenon time projection chamber operating at the Sanford Underground Research Facility in Lead, South Dakota, USA. This Letter reports results from LUX-ZEPLIN's first search for weakly interacting massive particles (WIMPs) with an exposure of 60 live days using a fiducial mass of 5.5 t. A profile-likelihood ratio analysis shows the data to be consistent with a background-only hypothesis, setting new limits on spin-independent WIMP-nucleon, spin-dependent WIMP-neutron, and spin-dependent WIMP-proton cross sections for WIMP masses above 9  GeV/c^{2}. The most stringent limit is set for spin-independent scattering at 36  GeV/c^{2}, rejecting cross sections above 9.2×10^{-48}  cm at the 90% confidence level.

The quantum dot vs. organic dye conundrum for ratiometric FRET-based biosensors: which one would you chose?

Förster resonance energy transfer (FRET) is a widely used and ideal transduction modality for fluorescent based biosensors as it offers high signal to noise with a visibly detectable signal. While intense efforts are ongoing to improve the limit of detection and dynamic range of biosensors based on biomolecule optimization, the selection of and relative location of the dye remains understudied. Herein, we describe a combined experimental and computational study to systematically compare the nature of the dye, i.e., organic fluorophore (Cy5 or Texas Red) vs. inorganic nanoparticle (QD), and the position of the FRET donor or acceptor on the biomolecular components. Using a recently discovered transcription factor (TF)-deoxyribonucleic acid (DNA) biosensor for progesterone, we examine four different biosensor configurations and report the quantum yield, lifetime, FRET efficiency, IC50, and limit of detection. Fitting the computational models to the empirical data identifies key molecular parameters driving sensor performance in each biosensor configuration. Finally, we provide a set of design parameters to enable one to select the fluorophore system for future intermolecular biosensors using FRET-based conformational regulation in in vitro assays and new diagnostic devices.

POS1223 DIFFERENT ANTI-SARS-CoV-2 VACCINE RESPONSE UNDER B- AND T-CELL TARGETED THERAPIES VERSUS ANTI-CYTOKINE THERAPIES IN PATIENTS WITH INFLAMMATORY ARTHRITIDES

Background

Vaccination against SARS-CoV-2 is effective in preventing severe forms of COVID-19, but there remain concerns about a reduced vaccine response in patients suffering from inflammatory arthritides who are treated by immunosuppressive therapies.

Objectives

We analysed the impact of bDMARDs on the humoral anti-SARS-CoV-2 vaccine response of patients followed in day hospitals.

Methods

We studied the vaccine response after a complete vaccine regimen followed in day hospital in 5 French hospitals and treated with an intravenous bDMARD between September 2019 and August 2021. After obtaining their informed consent, we included patients with an anti-SARS-CoV-2 serology. They were considered non-responders if the antibody level detected was inferior to the threshold of positivity of the kit used.

Results

205 patients were included (148 females/57 males). The median age was 64 years (Interquartile Range [IQR] 56-71). 25 were treated with tocilizumab (TCZ), 36 with abatacept (ABA), 53 with infliximab (IFX) and 91 with rituximab (RTX). When considering both patients after a complete vaccination schema (2 doses, or 1 dose in case of prior COVID-19) and those with 1 booster dose, 34 patients (16.6%) were non-responders (2 [5.9%] treated by IFX, none treated by TCZ, 9 [26.5%] treated by ABA and 23 [67.7%] treated by RTX). In multivariate analysis, the only characteristics that significantly and independently differed between responders and non-responders were last bDMARD and corticosteroid therapy at the time of 1st vaccination (Table 1). In RTX-treated patients, the delay from last infusion to 1st vaccine dose was significantly shorter in non-responders (median 4.3 IQR [2.9-6.1] months in non-responders versus 8.4 IQR [5.7-14.5] in responders, p=0.0007). Median survival, i.e. achieving a vaccine response in 50% of RTX-treated subjects, was achieved after 277 days (95CI [209-310]) in patients vaccinated with 2 or 3 doses (Figure 1). In ABA-treated patients, the delay from last infusion to 1st vaccine dose was not different between non-responders and responders.

Table 1.

Patients’ characteristics and comparisons between responders and non-responders.

All patients (n=205)Responders (n=171)Non responders (n=34)Univariate p valueMultivariatep valueAge (median [IQR]), in years64 [56-71]64 [54-70]69 [57-75.5]0.070.40Female sex, n (%)148 (72.2)125 [73.1)23 (67.7)0.53Inflammatory arthritides, n (%)0.16**0.24 Rheumatoid Arthritis156 (78.0)128 (74.9)28 (82.4)0.51 Spondyloarthritis33 (16.1)31 (18.1)2 (5.9)0.12 Others*16 (7.8)12 (5.9)4 (1.9)0.31Last bDMARDs at time of 1st vaccination, n (%)0.0004ABA/RTX versus IFX/TCZ < 0.00010.00024 Infliximab53 (25.9)51 (29.8)2 (5.9) Tocilizumab25 (12.2)25 (14.6)0 Abatacept36 (17.6)27 (15.8)9 (26.5) Rituximab91 (44.4)68 (39.8)23 (67.7)Associated treatments at time of 1st vaccination CsDMARDs, n (%)126 (61.5)107 (62.6)19(55.9)0.56 Methotrexate91 (44.4)78 (45.6)13 (38.2)0.46 Median dose in users (mg /week) [IQR]15 [10-17.5]13.8 [10-15.6]15 [13.8-20]0.07 Corticosteroids, n (%)25 (12.2)19 (11.1)6 (17.6)0.29 Median dose (mg /day) [IQR]0 [0-0]0 [0-0]0 [0-2]0.0350.016Previous COVID-19 infection, n (%)23 (11.2)21 (12.3)2 (5.9)0.38Type of vaccine, n (%)0.62 Pfizer169 (82.4)142 (83.0)27 (79.4)0.62 Moderna14 (68.3)11 (6.4)3 (8.8)0.71 Astra-Zeneca17 (8.3)15 (8.8)2 (5.9)0.74 Janssen5 (2.4)3 (1.8)2 (5.9)0.19Vaccination, n (%) Complete167 (81.5)141 (82.5)28 (16.8)0.47 Complete + 1 booster dose56 (27.3)43 (25.1)13 (38.2)0.14Figure 1.

Cumulative seropositive rate according to the interval (days) between the last course of rituximab administration and vaccination

Conclusion

ABA and RTX alter the anti-SARS-CoV-2 vaccine response and were associated with nearly all vaccine non-responses in the present study. Corticosteroid therapy was associated with a lower vaccine response regardless of its indication or the concomitant use of bMARD.

Disclosure of Interests

None declared

POS0715 TREATMENT OF SLE PATIENTS WITH ZETOMIPZOMIB (KZR-616), A SELECTIVE INHIBITOR OF THE IMMUNOPROTEASOME, RESULTS IN CIRCULATING GENE EXPRESSION, PROTEIN LEVEL, AND IMMUNE CELL PHENOTYPIC CHANGES WITH POTENTIAL CORRELATIONS TO CLINICAL RESPONSE

Background

Systemic lupus erythematosus (SLE), a severe multiorgan autoimmune disease, involves dysfunction of multiple immune system components. In preclinical studies, KZR-616, a first-in-class small molecule selective inhibitor of the immunoproteasome, demonstrated pleiotropic immunomodulatory functions encompassing both innate and adaptive immune pathways1,2. In the recently completed MISSION Phase 1b trial in SLE patients (pts), KZR-616 exhibited encouraging safety, tolerability, and clinical improvements3. Preliminary biomarker analysis of the first two cohorts was previously reported4. Here, we present complete biomarker results from all cohorts in this study.

Objectives

1) To characterize biomarker changes (gene expression, circulating protein levels and immune cell phenotypes) following KZR-616 treatment. 2) To evaluate correlations between biomarker changes and treatment response to KZR-616.

Methods

The open-label Phase 1b MISSION Trial (NCT 03393013) was a 25-week trial of KZR- 616 administered subcutaneously once weekly at doses ranging from 30-75 mg for 13 weeks (W) with a 12 W follow-up. Forty-seven SLE pts with and without nephritis were enrolled with 35 completing all 25 W of study. Clinical response definitions at W13 or later were defined as either a >4 reduction of SLEDAI-2K or >50% drop in swollen joint counts (SJC) (baseline SJC>2). Biomarker samples included whole blood in RNA tubes (31 pts), cryopreserved PBMCs (15 pts), plasma (35 pts) and urine (2 pts). Whole blood RNA sequencing was performed using Illumina TruSeq. Differential expression was modelled using DESeq2. Fast pre-ranked gene set enrichment analysis (GSEA) was performed with gene sets derived from published literature. Cryopreserved PBMCs were analysed by flow cytometry to profile immune cell subtypes. Plasma protein was measured by Meso Scale Discovery (MSD) kits. Healthy volunteer (HV, N=12) samples were used to establish potential disease-related biomarker changes in patients at baseline (BL).

Results

Many gene modules were found to be altered at BL in SLE pts, relative to HV, including those representing interferon (IFN) response and B/plasma cells and changes were consistent with our prior report4. Comparisons of SLEDAI-2K responders (R) versus non-responders (NR) revealed enrichment of 193 gene modules (57 down and 136 up-regulated, padj,<0.1) at BL and 190 modules (105 down and 85 up) 4 weeks after treatment (W17). Expression of a 4-gene IFN module was enriched in SLEDAI-2K R vs NR at BL; expression of this module trended downward at W17 in R, whereas it increased over time in NR at W 5. Reduced numbers of circulating class-switched memory B cells and IgG-producing plasma cells were observed at W17 and/or W25. Plasma levels of BAFF were consistently increased at W5 but returned to BL levels by W17. Plasma levels of CD169/ SIGLEC-1, a monocyte activation marker, were higher at BL in SJC R vs. NR and were reduced after treatment in both groups. Two pts with active proliferative nephritis were enrolled into this study and both showed a reduction in levels of urine CD163 (uCD163), while plasma levels of this marker were stable.

Conclusion

Our integrative analysis indicates that KZR-616 elicits a potent effect on multiple immune pathways in SLE patients. Potential new biomarkers (gene, gene module, circulating protein) that may be useful for prediction of patient response were identified. Future biomarker studies in placebo-controlled trials may further our understanding of KZR-616 mechanism of action, patient selection and prediction of patient responses.

References

[1]Kirk, C.J. et al., Cells 2022, 11(1):9

[2]Muchamuel T, Arthritis Rheumatol. 2019; 71 (suppl 10).

[3]Furie R et al., Annals of the Rheumatic Diseases 2021;80:595-596,

[4]Fan R, et al., Arthritis Rheumatol. 2019; 71 (suppl 10).

Acknowledgements

Kezar Life Sciences acknowledges the support of site investigators and patient participants in the MISSION study.

Disclosure of Interests

Andrea Fan Shareholder of: Kezar, Employee of: Kezar, Brian Tuch Consultant of: Kezar, Tony Muchamuel Shareholder of: Kezar, Employee of: Kezar, Janet Anderl Shareholder of: Kezar, Employee of: Kezar, Richard Leff Consultant of: Kezar, Noreen Henig Shareholder of: Kezar, Employee of: Kezar, Christopher Kirk Shareholder of: Kezar, Employee of: Kezar

Paper-Based Progesterone Sensor Using an Allosteric Transcription Factor

Progesterone monitoring is an essential component of in vitro fertilization treatments and reproductive management of dairy cows. Gold-standard biosensors for progesterone monitoring rely on antibodies, which are expensive and difficult to procure. We have developed an alternative transcription factor-based sensor that is superior to conventional progesterone biosensors. Here, we incorporate this transcription factor-based progesterone sensor into an affordable, portable paperfluidic format to facilitate widespread implementation of progesterone monitoring at the point of care. Oligonucleotides labeled with a fluorescent dye are immobilized onto nitrocellulose via a biotin-streptavidin interaction. In the absence of progesterone, these oligonucleotides form a complex with a transcription factor that is fluorescently labeled with tdTomato. In the presence of progesterone, the fluorescent transcription factor unbinds from the immobilized DNA, resulting in a decrease in tdTomato fluorescence. The limit of detection of our system is 27 nm, which is a clinically relevant level of progesterone. We demonstrate that transcription factor-based sensors can be incorporated into paperfluidic devices, thereby making them accessible to a broader population due to the portability and affordability of paper-based devices.

Electrochemical Strategy for Low-Cost Viral Detection

Sexually transmitted infections, including the human immunodeficiency virus (HIV) and the human papillomavirus (HPV), disproportionally impact those in low-resource settings. Early diagnosis is essential for managing HIV. Similarly, HPV causes nearly all cases of cervical cancer, the majority (90%) of which occur in low-resource settings. Importantly, infection with HPV is six times more likely to progress to cervical cancer in women who are HIV-positive. An inexpensive, adaptable point-of-care test for viral infections would make screening for these viruses more accessible to a broader set of the population. Here, we report a novel, cost-effective electrochemical platform using gold leaf electrodes to detect clinically relevant viral loads. We have combined this platform with loop-mediated isothermal amplification and a CRISPR-based recognition assay to detect HPV. Lower limits of detection were demonstrated down to 10⁴ total copies of input nucleic acids, which is a clinically relevant viral load for HPV DNA. Further, proof-of-concept experiments with cervical swab samples, extracted using standard extraction protocols, demonstrated that the strategy is extendable to complex human samples. This adaptable technology could be applied to detect any viral infection rapidly and cost-effectively.

POS1475-HPR EFFECT OF ARGENTINE TANGO PRACTICE ON TOTAL PHYSICAL ACTIVITY TIME IN PATIENTS WITH CHRONIC INFLAMMATORY RHEUMATISM: A PILOT STUDY

Background:

Most patients with chronic inflammatory rheumatism (CIR) have a physical activity (PA) level below recommendations [1,2]. Currently, adapted structures offer a range of activities supervised by adapted physical activity educators. To the best of our knowledge, Argentinean tango is not yet offered in these structures.

Objectives:

The objective of this pilot study was to study the effect of 24 consecutive sessions of Argentinean tango on the total PA level in patients with CIR, including rheumatoid arthritis (RA) and spondyloarthritis (AS).

Methods:

In this controlled, randomized, open-label, clinical trial with two parallel arms, patients were required to attend two tango sessions per week, 48 sessions from 0 (M0) to 6 months (M6) for the intervention group (IG) and 24 sessions from 3 months (M3) to M6 for the control group (CG). Total PA time was measured at M3 using the Global Physical Activity Questionnaire (GPAQ) [3].

Results:

A total of 27 patients (23 women) were included, including 15 with RA and 12 with AS. Mean age was 59 ± 12 years, and median disease duration was 10 years (IQR: 3-19). The majority of patients had background treatment (conventional and/or biological). At M3, 22 patients could be evaluated (11 GC patients and 11 GI patients), as 3 patients were lost to follow-up and 2 were unable to come in due to health or professional reasons. The 11 GI patients attended a median of 16 sessions (IQR: 8-22), i.e., approximately one session per week. At M3, the total PA time was not increased, regardless of the measurement method, GPAQ questionnaire (effect size and 95% confidence interval (CI): 0.03 [-0.60; 0.67], p=0.91) or accelerometer (effect size and 95% CI: 0.43 [-0.37; 1.24], p=0.26), and regardless of the intensity of the PA. No significant change was found for sedentary time, disease activity, fatigue, or anxiety. However, improvements were found in body appreciation as assessed by the Body Appreciation Scale 2 questionnaire (p=0.016), balance (p=0.053), wrist bending angle (p=0.092), and shoulder amplitude (p=0.093). The few participants in this study is explained by the geographic distance of the classes and their homes, the lack of availability of patients in professional activity, fatigue, or not liking dance (mainly among men).

Conclusion:

The results of this pilot study suggest that one Argentinean tango session per week in CIR patients is more achievable than two sessions as originally planned. As the practice of classes in hospitals is constrained due to geographic distance, the sessions could be offered in adapted structures. Nevertheless, our pilot study shows that the Argentinean tango is beneficial for body appreciation in patients with CIR. A qualitative study is needed to better understand these effects.

References:

[1]Haute Autorité de Santé (2007). Rheumatoid arthritis: therapeutic aspects excluding drugs and surgery - medico-social and organizational aspects. Professional recommendations service - Medical-economic evaluation and public health service.

[2]Haute Autorité de Santé (2008). Spondylarthritis: guide - long-term condition. Good Professional Practices Department - Communication Department.

[3] Cleland CL, Hunter RF, Kee F, Cupples ME, Sallis JF, Tully MA. (2014 Dec). Validity of the global physical activity questionnaire (GPAQ) in assessing levels and change in moderate-vigorous physical activity and sedentary behaviour. BMC Public Health. 10;14:1255. doi: 10.1186/1471-2458-14-1255.

Disclosure of Interests:

None declared

SNAPflex: a paper-and-plastic device for instrument-free RNA and DNA extraction from whole blood

Nucleic acid amplification tests (NAATs), which amplify and detect pathogen nucleic acids, are vital methods to diagnose diseases, particularly in cases where patients exhibit low levels of infection. For many blood-borne pathogens such as HIV or Plasmodium falciparum, it is necessary to first extract pathogen RNA or DNA from patient blood prior to NAAT analysis. Traditional nucleic acid extraction methods are expensive, resource-intensive and are often difficult to deploy to resource-limited areas where many blood-borne infections are widespread. Here, we describe a portable, paper-and-plastic device, called SNAPflex, for instrument-free nucleic acid extraction from whole blood, which builds upon our previous work for RNA extraction using a pressure-driven extraction system. SNAPflex shows improved HIV RNA extraction from simulated patient samples compared to traditional extraction methods as well as long-term stability of extracted RNA without the need for cold storage. We further demonstrated successful extraction and recovery of P. falciparum DNA from cultured parasites in whole blood. SNAPflex was designed to be easily manufacturable and deployable to resource-limited settings.

Method for the elucidation of LAMP products captured on lateral flow strips in a point of care test for HPV 16

Loop-mediated amplification (LAMP) is an isothermal amplification technique favored in diagnostics and point-of-care work due to its high sensitivity and ability to run in isothermal conditions. In addition, a visual readout by lateral flow strips (LFS) can be used in conjunction with LAMP, making the assay accessible at the point-of-care. However, the amplicons resulting from a LAMP reaction varied in length and shape, making them undiscernible on a double-stranded DNA intercalating dye stained gel. Standard characterization techniques also do not identify which amplicons specifically bind to the LFS, which generate the visual readout. We aimed to standardize our characterization of LAMP products during assay development by using fluorescein amidite (FAM) and biotin-tagged loop forward and backward primers during assay development. A pvuII restriction enzyme digest is applied to the LAMP products. FAM-tagged bands are directly correlated with the LFS visual readout. We applied this assay development workflow for an HPV 16 assay using both plasmid DNA and clinical samples to demonstrate proof of concept for generalized assay development work.

A progesterone biosensor derived from microbial screening

Bacteria are an enormous and largely untapped reservoir of biosensing proteins. We describe an approach to identify and isolate bacterial allosteric transcription factors (aTFs) that recognize a target analyte and to develop these TFs into biosensor devices. Our approach utilizes a combination of genomic screens and functional assays to identify and isolate biosensing TFs, and a quantum-dot Förster Resonance Energy Transfer (FRET) strategy for transducing analyte recognition into real-time quantitative measurements. We use this approach to identify a progesterone-sensing bacterial aTF and to develop this TF into an optical sensor for progesterone. The sensor detects progesterone in artificial urine with sufficient sensitivity and specificity for clinical use, while being compatible with an inexpensive and portable electronic reader for point-of-care applications. Our results provide proof-of-concept for a paradigm of microbially-derived biosensors adaptable to inexpensive, real-time sensor devices.

The influence of age, gender and race/ethnicity on the composition of the human axillary microbiome

OBJECTIVE

The microbial community plays an important role in the generation of human axillary odour by transforming odourless natural secretions into volatile odorous molecules. A limited number of traditional culturing methods and molecular based research have been performed to characterize the human axillary microbiome in small collection sample sizes. Moreover, only a few have considered the interpersonal variations across age, gender or race/ethnicity, and none have included all three variables within one single study. The aim of this study was to characterize the axillary microbiome of healthy subjects across different age groups, genders and races/ethnicities in a large sample size.

METHODS

The underarm skin swab samples were collected from 169 healthy subjects. The axillary microbiome was analysed by IS-pro, a clinically validated high-throughput DNA fingerprinting technique.

RESULTS

The results indicate that the senior subjects (55+) tend to have a higher number of total bacterial than younger adults (of a defined age). The diversity of odour causing bacteria, e.g. corynebacteria, increases with age. Among the three races/ethnicities studied, East Asians have a unique microbial composition compared to Caucasians and Hispanics, which may contribute to the different odour profiles observed among the races/ethnicities studied.

CONCLUSION

Human axillary microbiome varies by age, gender and race/ethnicity. This study has provided an unprecedented fundamental knowledge about the axillary microbiota as a function of age, gender and race/ethnicity.

Results of a Search for Sub-GeV Dark Matter Using 2013 LUX Data

The scattering of dark matter (DM) particles with sub-GeV masses off nuclei is difficult to detect using liquid xenon-based DM search instruments because the energy transfer during nuclear recoils is smaller than the typical detector threshold. However, the tree-level DM-nucleus scattering diagram can be accompanied by simultaneous emission of a bremsstrahlung photon or a so-called "Migdal" electron. These provide an electron recoil component to the experimental signature at higher energies than the corresponding nuclear recoil. The presence of this signature allows liquid xenon detectors to use both the scintillation and the ionization signals in the analysis where the nuclear recoil signal would not be otherwise visible. We report constraints on spin-independent DM-nucleon scattering for DM particles with masses of 0.4-5  GeV/c^{2} using 1.4×10^{4}  kg day of search exposure from the 2013 data from the Large Underground Xenon (LUX) experiment for four different classes of mediators. This analysis extends the reach of liquid xenon-based DM search instruments to lower DM masses than has been achieved previously.

A novel and environmental friendly synthetic route for hydroxypyrrolidines using zeolites

A critical step in the synthesis of the hydroxypyrrolidines, 1,4-dideoxy-1,4-imino-l-lyxitol and 1,4-dideoxy-1,4-imino-d-lyxitol, from the corresponding d-sugars is the synthesis of O-methyl 2,3-O-isopropylidenepentofuranoses. Instead of applying homogeneous catalysis process with conventional inorganic acid catalysts like HCl and HClO₄, it was found that heterogeneous catalysis using zeolites could be used for the one-pot synthesis of O-methyl 2,3-O-isopropylidenepentofuranoses directly from d-sugars, MeOH and acetone at mild condition. The best catalyst was H-beta zeolite containing a Si/Al molar ratio of 150, where a yield of >83% was obtained. The overall yields of the five-step procedure to 1,4-dideoxy-1,4-imino-l-lyxitol and 1,4-dideoxy-1,4-imino-d-lyxitol were 57% and 50%, respectively. This synthetic procedure has several advantages such as competitive overall yield, reduced number of steps, and mild reaction conditions. Furthermore, the zeolite catalyst can be easily recovered from the reaction mixture and reused with no loss of activity.

Constraints on Sub-GeV Dark-Matter-Electron Scattering from the DarkSide-50 Experiment

We present new constraints on sub-GeV dark-matter particles scattering off electrons based on 6780.0 kg d of data collected with the DarkSide-50 dual-phase argon time projection chamber. This analysis uses electroluminescence signals due to ionized electrons extracted from the liquid argon target. The detector has a very high trigger probability for these signals, allowing for an analysis threshold of three extracted electrons, or approximately 0.05 keVee. We calculate the expected recoil spectra for dark matter-electron scattering in argon and, under the assumption of momentum-independent scattering, improve upon existing limits from XENON10 for dark-matter particles with masses between 30 and 100  MeV/c^{2}.

Low-Mass Dark Matter Search with the DarkSide-50 Experiment

We present the results of a search for dark matter weakly interacting massive particles (WIMPs) in the mass range below 20  GeV/c^{2} using a target of low-radioactivity argon with a 6786.0 kg d exposure. The data were obtained using the DarkSide-50 apparatus at Laboratori Nazionali del Gran Sasso. The analysis is based on the ionization signal, for which the DarkSide-50 time projection chamber is fully efficient at 0.1  keVee. The observed rate in the detector at 0.5  keVee is about 1.5  event/keVee/kg/d and is almost entirely accounted for by known background sources. We obtain a 90% C.L. exclusion limit above 1.8  GeV/c^{2} for the spin-independent cross section of dark matter WIMPs on nucleons, extending the exclusion region for dark matter below previous limits in the range 1.8-6  GeV/c^{2}.

A competitive lateral flow assay for the detection of tenofovir

Proper management of an HIV infection requires that a patient be at least 80-95% adherent to a prescribed drug regimen to avoid poor health outcomes and the development of drug-resistant HIV strains. Clinicians generally monitor adherence habits indirectly through patient self-reporting, pill counting, and electronic drug monitoring. While direct measurement of patient samples like urine for monitoring drug levels is possible, it requires specialized equipment and training that is not readily available in resource-limited settings where the need is greatest. In this work we report the development of an antibody that binds to tenofovir (TFV), a key small molecule drug for both the treatment and prevention of HIV, and a competitive lateral flow assay that uses that antibody to monitor urine samples for the presence of the drug. TFV was conjugated to an immunogenic protein and injected into rabbits to raise polyclonal antibodies sensitive to the drug. The antibodies were verified for TFV-sensitivity by immunoprecipitation and HPLC. A gold nanoparticle-based competitive assay was developed to detect the presence of TFV in urine samples with a sensitivity of 1 μg mL-1. This TFV assay could be deployed as a point-of-care device for adherence monitoring in resource-limited settings as a low-cost, accurate, and speedy alternative to current methods to better inform changes in treatment.

Low concentration DNA extraction and recovery using a silica solid phase

DNA extraction from clinical samples is commonly achieved with a silica solid phase extraction column in the presence of a chaotrope. Versions of these protocols have been adapted for point of care (POC) diagnostic devices in miniaturized platforms, but commercial kits require a high amount of input DNA. Thus, when the input clinical sample contains less than 1 μg of total DNA, the target-specific DNA recovery from most of these protocols is low without supplementing the sample with exogenous carrier DNA. In fact, many clinical samples used in the development of POC diagnostics often exhibit target DNA concentrations as low as 3 ng/mL. With the broader goal of improving the yield and efficiency of nucleic acid-based POC devices for dilute samples, we investigated both DNA adsorption and recovery from silica particles by using 1 pg- 1 μg of DNA with a set of adsorption and elution buffers ranging in pH and chaotropic presence. In terms of adsorption, we found that low pH and the presence of chaotropic guanidinium thiocyanate (GuSCN) enhanced DNA-silica adsorption. When eluting with a standard low-salt, high-pH buffer, > 70% of DNA was unrecoverable, except when DNA was initially adsorbed with 5 M GuSCN at pH 5.2. Unrecovered DNA was either not initially adsorbed or irreversibly bound on the silica surface. Recovery was improved when eluting with 95°C formamide and 1 M NaOH, which suggested that DNA-silica-chaotrope interactions are dominated by hydrophobic interactions and hydrogen bonding. While heated formamide and NaOH are non-ideal elution buffers for practical POC devices, the salient results are important for engineering a set of optimized reagents that could maximize nucleic acid recovery from a microfluidic DNA-silica-chaotrope system.

Paper-Based RNA Extraction, in Situ Isothermal Amplification, and Lateral Flow Detection for Low-Cost, Rapid Diagnosis of Influenza A (H1N1) from Clinical Specimens

The 2009 Influenza A (H1N1) pandemic disproportionately affected the developing world and highlighted the key inadequacies of traditional diagnostic methods that make them unsuitable for use in resource-limited settings, from expensive equipment and infrastructure requirements to unacceptably long turnaround times. While rapid immunoassay diagnostic tests were much less costly and more context-appropriate, they suffered from drastically low sensitivities and high false negative rates. An accurate, sensitive, and specific molecular diagnostic that is also rapid, low-cost, and independent of laboratory infrastructure is needed for effective point-of-care detection and epidemiological control in these developing regions. We developed a paper-based assay that allows for the extraction and purification of RNA directly from human clinical nasopharyngeal specimens through a poly(ether sulfone) paper matrix, H1N1-specific in situ isothermal amplification directly within the same paper matrix, and immediate visual detection on lateral flow strips. The complete sample-to-answer assay can be performed at the point-of-care in just 45 min, without the need for expensive equipment or laboratory infrastructure, and it has a clinically relevant viral load detection limit of 10(6) copies/mL, offering a 10-fold improvement over current rapid immunoassays.

Haptic characterization of human skin in vivo in response to shower gels using a magnetic levitation device

BACKGROUND/PURPOSE

Skin products such as shower gels have a direct impact on skin health and wellness. Although qualitative haptic characterization through explicit, verbal measures in consumer studies are often sufficient for general comparison on consumer perceived skin feel, a quantitative approach is desired to characterize minute changes in skin condition in response to various skin products. Prior research has sought to characterize the haptic properties of human skin in vitro and in vivo, but very few studies have compared the haptic effects of commercial skin products having relatively similar formulations. In addition, related studies have typically utilized simple, low-precision devices and fixtures. The purpose of this study was to use a precision magnetic levitation haptic device to characterize the frictional properties of human skin in vivo before, during, and after treatment with commercially available shower gels, to capture the entire cycle of consumer experience on skin feel.

METHODS

A hybrid force-position control algorithm was used to control a precision magnetic levitation haptic device with silicone tactor to stroke the human skin (on the volar forearm) in vivo. Position and force data were collected from 32 human subjects using eight different commercially available shower gels, while stroking the skin before, during, and after treatment. The data were analyzed to produce coefficients of friction and viscous damping constant, which were used as metrics for comparing the effects of each shower gel type. Other factors investigated include skin test location, order, and subject age and gender.

RESULTS

Results showed significant differences between the effects of eight various shower gels, especially after accounting for variance between subjects. Most notably, Shower Gel four with high level of petrolatum, along with Shower Gels five and six with low levels of castoryl maleate (a skin lipid analog), as well as Shower Gel two with high levels of vegetable oils yielded higher skin coefficients of friction 20 min after treatment, indicating higher levels of skin hydration than other shower gels without either high levels of skin beneficial agents or low levels of castoryl maleate. Conversely, Shower Gel eight treatment yielded the lowest skin coefficient of friction both immediately after rinsing and 20 min after treatment. In addition, when applied to the skin as un-lathered gels, Shower Gels six and seven with acrylate polymers yielded viscous damping constants twice that of other gels, while Shower Gel three yielded the lowest. When lathered into foam on skin, Shower Gel eight yielded the highest viscous damping constant, while Shower Gel three, along with Shower Gels one and five yielded lower values than others.

CONCLUSION

The results of this study show that different shower gels do have significant measurable differences in their effects on skin properties, and that using a high-precision haptic device can be a useful tool for quantifying the haptic properties of skin in vivo.

Colorimetric Detection of Azidothymidine Using an Alkyne-Modified Dextran Substrate

Monitoring the adherence of patients taking highly active antiretroviral therapy (HAART) is a key step in treating an HIV infection, especially in resource-limited settings in the developing world. For most regimens, when patients are not at least 95% adherent to their drug schedule, there is a loss of effectiveness in treatment resulting in increases in health care costs, increases in the rate of transmission, and reduction of positive patient outcomes. Currently, subjective methods such as pill counting, electronic drug monitoring, and patient self-reporting are the only ways clinicians can track adherence and intervene in cases of noncompliance. We address this issue by developing a dipstick-based point-of-care azide-alkyne click chemistry assay with colorimetric read-out that directly tests for the presence of one common HAART drug in patient urine. An alkyne-modified dextran was synthesized and characterized by NMR and then used to colorimetrically report the presence of azidothymidine, an azide-containing HAART drug, in urine samples. The assay is specific to azide-containing molecules that are not naturally present in the urine and is sensitive to physiologically relevant urine concentrations as low as 750 uM. This point-of-care device is a strong alternative in resource-limited settings over current direct measurement techniques that are expensive and require trained users such as HPLC.

Correction: Paper-based molecular diagnostic for Chlamydia trachomatis

Correction for ‘Paper-based molecular diagnostic for Chlamydia trachomatis’ by Jacqueline C. Linnes et al., RSC Adv., 2014, 4, 42245–42251.

Abstract 3494: Microfluidic platform for a protein-based thyroid cancer diagnostics

a) The current gold-standard of care in the management of patients with thyroid nodules is ultrasound-guided fine needle aspiration biopsy (FNAB) followed by microscopic examination of cell morphology by a trained cytopathologist. Due to the lack of distinguishing morphology, 10-25% of FNAs are termed “indeterminate” and required surgery. However, only 35% of them are found to have cancer. There is a need for a more accurate and minimally invasive cancer diagnostic technology. Our objective is to develop an inexpensive, point-of-care molecular diagnostic platform to isolate and detect thyroid specific proteins to enable real-world use of biomarkers to inform patient care. b) In this study, we engineer a miniature ion exchange column within a plastic (cyclic olefin polymer), disposable lab-on-a-chip platform for sample preparation and protein purification using microfluidic channels with a specialized porous polymer monolith (PPM)-based resin bed. We capitalized on the finding that cancer cells exhibit differential protein expressional patterns compared to normal thyroid cells by targeting thyroid transcription factor (TTF-1), a thyroid specific enhancer binding protein, as a biomarker for the diagnosis of thyroid cancer. The ability to capture and release TTF-1 from the papillary thyroid cancer (PTC) cell line was evaluated via western blot. We also tested various types of thyroid samples obtained from malignant and benign human thyroid nodules. c) We compared the efficiency of a small-scale protein prep using a commercial gravity column versus our lab-on-a-chip column. Our method showed TTF-1 protein was detectable from the lysate of 5x104 cultured BCPAP cancer cell line. In contrast, it was not detectable when purified by gravity ion-exchange column. We next showed that one can maximize the concentration of protein eluted from as fewer cells as possible. We found that by titrating the elution volume per fraction down to 10 µl, the final concentration of eluted protein can be increased, and hence increase the downstream LOD to 104 cells. Next, we evaluated our extraction and purification system by using 10 mg patient thyroid tissue samples. We tested 11 human thyroid specimens for TTF-1 protein capture. They were all found to be positive which correlated with the official histopathological findings. All tissue extracts had measurable levels of TTF-1 protein and the levels of the TTF-1 were variable in the tissue specimens. We also tested one negative thyroid specimen. No TTF-1 protein was found. d) Our microfluidic protein extraction and purification system is a platform technology that may allow for optimal use of low-volume sample preparation such as we see in thyroid biopsies. This manner, when combined with an on-chip ELISA assay, would be a simple, cost effective test that gives the doctor all the needed information quickly in a single test. When mature, the device can be applied to other type of cancer based on tailored assays for specific biomarkers.

Citation Format: Shichu Huang, Siddhartha Sharma, Lena Liu, Andy Fan, Catherine Klapperich, Jennifer Rosen. Microfluidic platform for a protein-based thyroid cancer diagnostics. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 3494. doi:10.1158/1538-7445.AM2014-3494

Paper-based molecular diagnostic for Chlamydia trachomatis

Herein we show the development of a minimally instrumented paper-based molecular diagnostic for point of care detection of sexually transmitted infections caused by Chlamydia trachomatis. This new diagnostic platform incorporates cell lysis, isothermal nucleic acid amplification, and lateral flow visual detection using only a pressure source and heat block, eliminating the need for expensive laboratory equipment. This paper-based test can be performed in less than one hour and has a clinically relevant limit of detection that is 100x more sensitive than current rapid immunoassays used for chlamydia diagnosis.

Sample concentration and purification for point-of-care diagnostics

The ability to increase the concentration of target analytes in a fixed sample volume can potentially lower the limit of detection for many biosensing techniques, and thus is key in sample preparation for infectious disease diagnosis. Concentration by evaporation is an effective method to achieve target enrichment. However, concentrating human samples, including blood and plasma, by evaporation-based methods is made challenging by high concentrations of proteins and electrolytes. Dehydration of the proteins causes the sample to turn into a gel, hindering further analysis. At the same time, decreasing the volume increases the overall concentration of electrolytes, causing bacterial or viral particle lysis, and making them more difficult to detect in affinity-based biosensors. Thus, we fabricated a microfluidic chip that incorporates both dialysis and concentration in a single design. The chip dialyzes the proteins from the plasma, while maintaining an appropriate concentration of electrolytes and concentrating the sample targets. The process to concentrate plasma or serum samples by a factor of 10 takes less than 30 minutes. As a proof-of-concept, we demonstrated the chip using a defective Human Immunodeficiency Virus (HIV). To distinguish patients on antiretroviral therapy who are failing therapy from those who are not, a diagnostic must be able to detect HIV in plasma down to at least 1000 particles per milliliter. For a number of technical reasons, it is difficult to get on-chip PCR reactions to reach this level of sensitivity, so concentration of HIV from lower viral load samples has the potential to improve the sensitivity of many types of molecular point-of-care viral load tests.

A Portable, Pressure Driven, Room Temperature Nucleic Acid Extraction and Storage System for Point of Care Molecular Diagnostics

Many new and exciting portable HIV viral load testing technologies are emerging for use in global medicine. While the potential to provide fast, isothermal, and quantitative molecular diagnostic information to clinicians in the field will soon be a reality, many of these technologies lack a robust front end for sample clean up and nucleic acid preparation. Such a technology would enable many different downstream molecular assays. Here, we present a portable system for centrifuge-free room temperature nucleic acid extraction from small volumes of whole blood (70 µL), using only thermally stable reagents compatible with storage and transport in low resource settings. Quantitative reverse transcriptase polymerase chain reaction (qRT-PCR) analysis of simulated samples demonstrate a lower limit of detection of 1000 copies/ml, with the ability to detect differences in viral load across four orders of magnitude. The system can also be used to store extracted RNA on detachable cartridges for up to one week at ambient temperature, and can be operated using only hand generated air pressure.

Low cost extraction and isothermal amplification of DNA for infectious diarrhea diagnosis

In order to counter the common perception that molecular diagnostics are too complicated to work in low resource settings, we have performed a difficult sample preparation and DNA amplification protocol using instrumentation designed to be operated without wall or battery power. In this work we have combined a nearly electricity-free nucleic acid extraction process with an electricity-free isothermal amplification assay to detect the presence of Clostridium difficile (C. difficile) DNA in the stool of infected patients. We used helicase-dependent isothermal amplification (HDA) to amplify the DNA in a low-cost, thermoplastic reaction chip heated with a pair of commercially available toe warmers, while using a simple Styrofoam insulator. DNA was extracted from known positive and negative stool samples. The DNA extraction protocol utilized an air pressure driven solid phase extraction device run using a standard bicycle pump. The simple heater setup required no electricity or battery and was capable of maintaining the temperature at 65°C±2°C for 55 min, suitable for repeatable HDA amplification. Experiments were performed to explore the adaptability of the system for use in a range of ambient conditions. When compared to a traditional centrifuge extraction protocol and a laboratory thermocycler, this disposable, no power platform achieved approximately the same lower limit of detection (1.25×10(-2) pg of C. difficile DNA) while requiring much less raw material and a fraction of the lab infrastructure and cost. This proof of concept study could greatly impact the accessibility of molecular assays for applications in global health.

Microfluidic chip fabrication and method to detect influenza

Fast and effective diagnostics play an important role in controlling infectious disease by enabling effective patient management and treatment. Here, we present an integrated microfluidic thermoplastic chip with the ability to amplify influenza A virus in patient nasopharyngeal (NP) swabs and aspirates. Upon loading the patient sample, the microfluidic device sequentially carries out on-chip cell lysis, RNA purification and concentration steps within the solid phase extraction (SPE), reverse transcription (RT) and polymerase chain reaction (PCR) in RT-PCR chambers, respectively. End-point detection is performed using an off-chip Bioanalyzer (Agilent Technologies, Santa Clara, CA). For peripherals, we used a single syringe pump to drive reagent and samples, while two thin film heaters were used as the heat sources for the RT and PCR chambers. The chip is designed to be single layer and suitable for high throughput manufacturing to reduce the fabrication time and cost. The microfluidic chip provides a platform to analyze a wide variety of virus and bacteria, limited only by changes in reagent design needed to detect new pathogens of interest.

Purification of DNA/RNA in a microfluidic device

Often, modern diagnostic techniques require the isolation and purification of nucleic acids directly from patient samples such as blood or stool. Many diagnostic tests are being miniaturized onto micro-sized platforms and integrated into microfluidic devices due to the economies resulting from smaller sample and reagent volumes. Often, these devices perform sample preparation in series with the diagnostic tests. The sample preparation steps are vital in order to purify the desired genetic material from potential inhibitors that can interfere with the outcome of the test. There are various techniques used to selectively capture the nucleic acids while washing away potential contamination (proteins, enzymes, lipids, etc.). Two of the most common forms of selective capture are based on nucleic acid binding to silica surface or on the precipitation of nucleic acids with or without the presence of a carrier species. Each of these methods can be performed in liquid phase or in a solid support such as an extraction column. Here we discuss both methods and address microfluidic applications.

Mec1 is one of multiple kinases that prime the Mcm2-7 helicase for phosphorylation by Cdc7

Activation of the eukaryotic replicative DNA helicase, the Mcm2-7 complex, requires phosphorylation by Cdc7/Dbf4 (Dbf4-dependent kinase or DDK), which, in turn, depends on prior phosphorylation of Mcm2-7 by an unknown kinase (or kinases). We identified DDK phosphorylation sites on Mcm4 and Mcm6 and found that phosphorylation of either subunit suffices for cell proliferation. Importantly, prior phosphorylation of either S/T-P or S/T-Q motifs on these subunits is required for DDK phosphorylation of Mcm2-7 and for normal S phase passage. Phosphomimetic mutations of DDK target sites bypass both DDK function and mutation of the priming phosphorylation sites. Mrc1 facilitates Mec1 phosphorylation of the S/T-Q motifs of chromatin-bound Mcm2-7 during S phase to activate replication. Genetic interactions between priming site mutations and MRC1 or TOF1 deletion support a role for these modifications in replication fork stability. These findings identify regulatory mechanisms that modulate origin firing and replication fork assembly during cell cycle progression.

The ovarian endometrioma: why is it so poorly managed? Indicators from an anonymous survey

As a tertiary referral centre for women with severe endometriosis we see a large number of patients who have endometriotic cysts, and many of these patients have been operated on by gynaecologists elsewhere in the UK. We have been surprised by the variety of approaches to their management. In order to establish the current clinical practices of endometrioma management amongst gynaecologists in the UK, we have carried out an anonymous survey. There appears to be an equal preference for open versus endoscopic surgery, even though there is considerable evidence suggesting that endoscopic surgery is superior. However, the management of endometriomas varies significantly between the two groups. In this article, we have presented the results of our survey and used them as the basis for a debate on the management of endometriomas.

Adapting pharmacokinetic properties of a humanized anti-interleukin-8 antibody for therapeutic applications using site-specific pegylation

A neutralizing anti-interleukin-(IL-)8 monoclonal antibody was humanized by grafting the complementary determining regions onto the human IgG framework. Subsequent alanine scanning mutagenesis and phage display enabled the production of an affinity matured antibody with a >100-fold improvement in IL-8 binding. Antibody fragments can be efficiently produced in Escherichia coli but have the limitation of rapid clearance rates in vivo. The Fab' fragment of the antibody was therefore modified with polyethylene glycol (PEG) in order to obtain a more desirable pharmacokinetic profile. PEG (5-40 kDa) was site-specifically conjugated to the Fab' via the single free cysteine residue in the hinge region. In vitro binding and bioassays showed little or no loss of activity. The pharmacokinetic profiles of the 20 kDa, 30 kDa, 40 kDa, and 40 kDa branched PEG-Fab' molecules were evaluated in rabbits. Relative to the native Fab', the clearance rates of the PEGylated molecules were decreased by 44-175-fold. In a rabbit ear model of ischemia/reperfusion injury, all PEGylated Fab' molecules were as efficacious in reducing oedema as the original monoclonal antibody. These studies demonstrate that it is possible to customize the pharmacokinetic properties of a Fab' while retaining its antigen binding activity.