Publications by authors named "James Clarke"

107 Publications

Intratumoral follicular regulatory T cells curtail anti-PD-1 treatment efficacy.

Nat Immunol 2021 08 24;22(8):1052-1063. Epub 2021 Jun 24.

La Jolla Institute for Immunology, La Jolla, CA, USA.

Immune-checkpoint blockade (ICB) has shown remarkable clinical success in boosting antitumor immunity. However, the breadth of its cellular targets and specific mode of action remain elusive. We find that tumor-infiltrating follicular regulatory T (T) cells are prevalent in tumor tissues of several cancer types. They are primarily located within tertiary lymphoid structures and exhibit superior suppressive capacity and in vivo persistence as compared with regulatory T cells, with which they share a clonal and developmental relationship. In syngeneic tumor models, anti-PD-1 treatment increases the number of tumor-infiltrating T cells. Both T cell deficiency and the depletion of T cells with anti-CTLA-4 before anti-PD-1 treatment improve tumor control in mice. Notably, in a cohort of 271 patients with melanoma, treatment with anti-CTLA-4 followed by anti-PD-1 at progression was associated with better a survival outcome than monotherapy with anti-PD-1 or anti-CTLA-4, anti-PD-1 followed by anti-CTLA-4 at progression or concomitant combination therapy.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41590-021-00958-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8434898PMC
August 2021

Human naive epiblast cells possess unrestricted lineage potential.

Cell Stem Cell 2021 06 7;28(6):1040-1056.e6. Epub 2021 Apr 7.

Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; Department of Biochemistry, University of Cambridge, Cambridge CB2 1QR, UK; Living Systems Institute, University of Exeter, Exeter EX4 4QD, UK. Electronic address:

Classic embryological experiments have established that the early mouse embryo develops via sequential lineage bifurcations. The first segregated lineage is the trophectoderm, essential for blastocyst formation. Mouse naive epiblast and derivative embryonic stem cells are restricted accordingly from producing trophectoderm. Here we show, in contrast, that human naive embryonic stem cells readily make blastocyst trophectoderm and descendant trophoblast cell types. Trophectoderm was induced rapidly and efficiently by inhibition of ERK/mitogen-activated protein kinase (MAPK) and Nodal signaling. Transcriptome comparison with the human embryo substantiated direct formation of trophectoderm with subsequent differentiation into syncytiotrophoblast, cytotrophoblast, and downstream trophoblast stem cells. During pluripotency progression lineage potential switches from trophectoderm to amnion. Live-cell tracking revealed that epiblast cells in the human blastocyst are also able to produce trophectoderm. Thus, the paradigm of developmental specification coupled to lineage restriction does not apply to humans. Instead, epiblast plasticity and the potential for blastocyst regeneration are retained until implantation.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.stem.2021.02.025DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8189439PMC
June 2021

The perceived effects of emotional labor in psychologists providing individual psychotherapy.

Psychotherapy (Chic) 2021 Sep 3;58(3):414-424. Epub 2020 Dec 3.

School of Psychology and Exercise Science.

Existing literature examining burnout in psychotherapists has not adequately considered the contributing role of emotional labor. Similarly, emotional labor research has not sufficiently explored how this construct operates in the context of psychologists who provide individual psychotherapy. To address these existing gaps in the literature, thematic analysis was conducted on interviews with 24 psychologists who provide individual psychotherapy to determine the perceived consequences of emotional labor identified by the participants. Participants discussed personal growth, feeling depleted and exhausted, and craving space free from people and work-related emotion as consequences of emotion management in the context of providing individual psychotherapy. The findings suggest that emotional labor can exert positive, negative, and neutral effects on psychologists providing psychotherapy and is worthy of attention as a variable in efforts to promote positive well-being. In the occupational group of psychologists providing individual psychotherapy, performing emotional labor can lead to personal growth, emotional exhaustion, and a need to distance oneself from work-related emotion. (PsycInfo Database Record (c) 2021 APA, all rights reserved).
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1037/pst0000351DOI Listing
September 2021

Effect of Quantum Hall Edge Strips on Valley Splitting in Silicon Quantum Wells.

Phys Rev Lett 2020 Oct;125(18):186801

QuTech and Kavli Institute of Nanoscience, Delft University of Technology, PO Box 5046, 2600 GA Delft, Netherlands.

We determine the energy splitting of the conduction-band valleys in two-dimensional electrons confined to low-disorder Si quantum wells. We probe the valley splitting dependence on both perpendicular magnetic field B and Hall density by performing activation energy measurements in the quantum Hall regime over a large range of filling factors. The mobility gap of the valley-split levels increases linearly with B and is strikingly independent of Hall density. The data are consistent with a transport model in which valley splitting depends on the incremental changes in density eB/h across quantum Hall edge strips, rather than the bulk density. Based on these results, we estimate that the valley splitting increases with density at a rate of 116  μeV/10^{11} cm^{-2}, which is consistent with theoretical predictions for near-perfect quantum well top interfaces.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1103/PhysRevLett.125.186801DOI Listing
October 2020

Determining the Impact of Roller Compaction Processing Conditions on Granule and API Properties.

AAPS PharmSciTech 2020 Aug 2;21(6):218. Epub 2020 Aug 2.

School of Chemical Engineering, University of Birmingham, Birmingham, B15 2TT, UK.

The attrition of drug particles during the process of dry granulation, which may (or may not) be incorporated into granules, could be an important factor in determining the subsequent performance of that granulation, including key factors such as sticking to punches and bio-performance of the dosage form. It has previously been demonstrated that such attrition occurs in one common dry granulation process train; however, the fate of these comminuted particles in granules was not determined. An understanding of the phenomena of attrition and incorporation into granule will improve our ability to understand the performance of granulated systems, ultimately leading to an improvement in our ability to optimize and model the process. Unique feeding mechanisms, geometry, and milling systems of roller compaction equipment mean that attrition could be more or less substantial for any given equipment train. In this work, we examined attrition of API particles and their incorporation into granule in an equipment train from Gerteis, a commonly used equipment train for dry granulation. The results demonstrate that comminuted drug particles can exist free in post-milling blends of roller compaction equipment trains. This information can help better understand the performance of the granulations, and be incorporated into mechanistic models to optimize such processes.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1208/s12249-020-01773-2DOI Listing
August 2020

Small molecule AZD4635 inhibitor of AR signaling rescues immune cell function including CD103 dendritic cells enhancing anti-tumor immunity.

J Immunother Cancer 2020 07;8(2)

Bioscience, AstraZeneca R&D Boston, Waltham, Massachusetts, USA

Accumulation of extracellular adenosine within the microenvironment is a strategy exploited by tumors to escape detection by the immune system. Adenosine signaling through the adenosine 2A receptor (AR) on immune cells elicits a range of immunosuppressive effects which promote tumor growth and limit the efficacy of immune checkpoint inhibitors. Preclinical data with AR inhibitors have demonstrated tumor regressions in mouse models by rescuing T cell function; however, the mechanism and role on other immune cells has not been fully elucidated.

Methods: We report here the development of a small molecule AR inhibitor including characterization of binding and inhibition of AR function with varying amounts of a stable version of adenosine. Functional activity was tested in both mouse and human T cells and dendritic cells (DCs) in in vitro assays to understand the intrinsic role on each cell type. The role of adenosine and AR inhibition was tested in DC differentiation assays as well as co-culture assays to access the cross-priming function of DCs. Syngeneic models were used to assess tumor growth alone and in combination with alphaprogrammed death-ligand 1 (αPD-L1). Immunophenotyping by flow cytometry was performed to examine global immune cell changes upon AR inhibition.

Results: We provide the first report of AZD4635, a novel small molecule AR antagonist which inhibits downstream signaling and increases T cell function as well as a novel mechanism of enhancing antigen presentation by CD103 DCs. The role of antigen presentation by DCs, particularly CD103 DCs, is critical to drive antitumor immunity providing rational to combine a priming agent AZD4635 with check point blockade. We find adenosine impairs the maturation and antigen presentation function of CD103 DCs. We show in multiple syngeneic mouse tumor models that treatment of AZD4635 alone and in combination with αPD-L1 led to decreased tumor volume correlating with enhanced CD103 function and T cell response. We extend these studies into human DCs to show that adenosine promotes a tolerogenic phenotype that can be reversed with AZD4635 restoring antigen-specific T cell activation. Our results support the novel role of adenosine signaling as an intrinsic negative regulator of CD103 DCs maturation and priming. We show that potent inhibition of AR with AZD4635 reduces tumor burden and enhances antitumor immunity. This unique mechanism of action in CD103 DCs may contribute to clinical responses as AZD4635 is being evaluated in clinical trials with IMFINZI (durvalumab, αPD-L1) in patients with solid malignancies.

Conclusion: We provide evidence implicating suppression of adaptive and innate immunity by adenosine as a mechanism for immune evasion by tumors. Inhibition of adenosine signaling through selective small molecule inhibition of AR using AZD4635 restores T cell function via an internal mechanism as well as tumor antigen cross-presentation by CD103 DCs resulting in antitumor immunity.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1136/jitc-2019-000417DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7394305PMC
July 2020

M1 tumor-associated macrophages boost tissue-resident memory T cells infiltration and survival in human lung cancer.

J Immunother Cancer 2020 07;8(2)

Clinical and Experimental Sciences, University of Southampton Faculty of Medicine, Southampton, UK

Background: The role of tumor-associated macrophages (TAMs) in determining the outcome between the antitumor effects of the adaptive immune system and the tumor's anti-immunity stratagems, is controversial. Macrophages modulate their activities and phenotypes by integration of signals in the tumor microenvironment. Depending on how macrophages are activated, they may adopt so-called M1-like, antitumor or M2-like, protumor profiles. In many solid tumors, a dominance of M2-like macrophages is associated with poor outcomes but in some tumor types, strong M1-like profiles are linked to better outcomes. We aimed to investigate the interrelationship of these TAM populations to establish how they modulate the efficacy of the adaptive immune system in early lung cancer.

Methods: Macrophages from matched lung (non-tumor-associated macrophages (NTAMs)) and tumor samples (TAMs) from resected lung cancers were assessed by bulk and single-cell transcriptomic analysis. Protein expression of genes characteristic of M1-like (chemokine (C-X-C motif) ligand 9) or M2-like (matrix metallopeptidase 12) functions was confirmed by confocal microscopy. Immunohistochemistry related the distribution of TAM transcriptomic signatures to density of CD8 tissue-resident memory T cells (T) in tumors and survival data from an independent cohort of 393 patients with lung cancer.

Results: TAMs have significantly different transcriptomic profiles from NTAMs with >1000 differentially expressed genes. TAMs displayed a strong M2-like signature with no significant variation between patients. However, single-cell RNA-sequencing supported by immuno-stained cells revealed that additionally, in 25% of patients the M2-like TAMs also co-expressed a strong/hot M1-like signature (M1). Importantly, there was a strong association between the density of M1 TAMs and T cells in tumors that was in turn linked to better survival. Our data suggest a mechanism by which M1 TAMs may recruit T cells via CXCL9 expression and sustain them by making available more of the essential fatty acids on which T depend.

Conclusions: We showed that in early lung cancer, expression of M1-like and M2-like gene signatures are not mutually exclusive since the same TAMs can simultaneously display both gene-expression profiles. The presence of M1 TAMs was associated with a strong T tumor-infiltrate and better outcomes. Thus, therapeutic approaches to re-program TAMs to an M1 phenotype are likely to augment the adaptive antitumor responses.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1136/jitc-2020-000778DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7375465PMC
July 2020

BACH2 drives quiescence and maintenance of resting Treg cells to promote homeostasis and cancer immunosuppression.

J Exp Med 2020 09;217(9)

Laboratory of Lymphocyte Signalling and Development, Babraham Institute, Cambridge, UK.

Regulatory T (Treg) cell populations are composed of functionally quiescent resting Treg (rTreg) cells which differentiate into activated Treg (aTreg) cells upon antigen stimulation. How rTreg cells remain quiescent despite chronic exposure to cognate self- and foreign antigens is unclear. The transcription factor BACH2 is critical for early Treg lineage specification, but its function following lineage commitment is unresolved. Here, we show that BACH2 is repurposed following Treg lineage commitment and promotes the quiescence and long-term maintenance of rTreg cells. Bach2 is highly expressed in rTreg cells but is down-regulated in aTreg cells and during inflammation. In rTreg cells, BACH2 binds to enhancers of genes involved in aTreg differentiation and represses their TCR-driven induction by competing with AP-1 factors for DNA binding. This function promotes rTreg cell quiescence and long-term maintenance and is required for immune homeostasis and durable immunosuppression in cancer. Thus, BACH2 supports a "division of labor" between quiescent rTreg cells and their activated progeny in Treg maintenance and function, respectively.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1084/jem.20190711DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7478731PMC
September 2020

Evaluation of an Assertive Management and Integrated Care Service for Frequent Emergency Department Attenders with Substance Use Disorders: The Impact Project: Evaluating an assertive management service for frequent ED attenders with substance use disorders.

Int J Integr Care 2020 Apr 23;20(2). Epub 2020 Apr 23.

The Langton Centre, Drug and Alcohol Services, South Eastern Sydney Local Health District, Surry Hills NSW, AU.

Introduction: Frequent attenders to Emergency Departments (ED) often have contributing substance use disorders (SUD), but there are few evaluations of relevant interventions. We examine one such pilot assertive management service set in Sydney, Australia (IMPACT), aimed at reducing hospital presentations and costs, and improving client outcomes.

Methods: IMPACT eligibility criteria included moderate-to-severe SUD and ED attendance on ≥5 occasions in the previous year. A pre-post intervention design examined clients' presentations and outcomes 6 months before and after participation to a comparison group of eligible clients who did not engage.

Results: Between 2014 and 2015, 34 clients engaged in IMPACT, with 12 in the comparison group. Clients demonstrated significant reductions in preventable (p < 0.05) and non-preventable (p < 0.01) ED presentations and costs, and in hospital admissions and costs (p < 0.01). IMPACT clients also reported a significant reduction in use days for primary substance (p < 0.01). The comparison group had a significant reduction (p < 0.05) in non-preventable visits only.

Conclusions: Assertive management services can be effective in preventing hospital presentations and costs for frequent ED attenders with SUDs and improving client outcomes, representing an effective integrated health approach. The IMPACT service has since been refined and integrated into routine care across a number of hospitals in Sydney, Australia.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.5334/ijic.5343DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7181945PMC
April 2020

Wnt Inhibition Facilitates RNA-Mediated Reprogramming of Human Somatic Cells to Naive Pluripotency.

Stem Cell Reports 2019 12 7;13(6):1083-1098. Epub 2019 Nov 7.

Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK. Electronic address:

In contrast to conventional human pluripotent stem cells (hPSCs) that are related to post-implantation embryo stages, naive hPSCs exhibit features of pre-implantation epiblast. Naive hPSCs are established by resetting conventional hPSCs, or are derived from dissociated embryo inner cell masses. Here we investigate conditions for transgene-free reprogramming of human somatic cells to naive pluripotency. We find that Wnt inhibition promotes RNA-mediated induction of naive pluripotency. We demonstrate application to independent human fibroblast cultures and endothelial progenitor cells. We show that induced naive hPSCs can be clonally expanded with a diploid karyotype and undergo somatic lineage differentiation following formative transition. Induced naive hPSC lines exhibit distinctive surface marker, transcriptome, and methylome properties of naive epiblast identity. This system for efficient, facile, and reliable induction of transgene-free naive hPSCs offers a robust platform, both for delineation of human reprogramming trajectories and for evaluating the attributes of isogenic naive versus conventional hPSCs.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.stemcr.2019.10.009DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6915845PMC
December 2019

Single-cell transcriptomic analysis of tissue-resident memory T cells in human lung cancer.

J Exp Med 2019 09 21;216(9):2128-2149. Epub 2019 Jun 21.

La Jolla Institute for Immunology, La Jolla, CA

High numbers of tissue-resident memory T (T) cells are associated with better clinical outcomes in cancer patients. However, the molecular characteristics that drive their efficient immune response to tumors are poorly understood. Here, single-cell and bulk transcriptomic analysis of T and non-T cells present in tumor and normal lung tissue from patients with lung cancer revealed that PD-1-expressing T cells in tumors were clonally expanded and enriched for transcripts linked to cell proliferation and cytotoxicity when compared with PD-1-expressing non-T cells. This feature was more prominent in the T cell subset coexpressing PD-1 and TIM-3, and it was validated by functional assays ex vivo and also reflected in their chromatin accessibility profile. This PD-1TIM-3 T cell subset was enriched in responders to PD-1 inhibitors and in tumors with a greater magnitude of CTL responses. These data highlight that not all CTLs expressing PD-1 are dysfunctional; on the contrary, T cells with PD-1 expression were enriched for features suggestive of superior functionality.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1084/jem.20190249DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6719422PMC
September 2019

Engineering Genetic Predisposition in Human Neuroepithelial Stem Cells Recapitulates Medulloblastoma Tumorigenesis.

Cell Stem Cell 2019 09 13;25(3):433-446.e7. Epub 2019 Jun 13.

Division of Pediatric Neurology, Department of Pediatrics, Oregon Health & Science University, Portland, OR, USA; Papé Family Pediatric Research Institute, Department of Pediatrics, Oregon Health & Science University, Portland, OR, USA; Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA.

Human neural stem cell cultures provide progenitor cells that are potential cells of origin for brain cancers. However, the extent to which genetic predisposition to tumor formation can be faithfully captured in stem cell lines is uncertain. Here, we evaluated neuroepithelial stem (NES) cells, representative of cerebellar progenitors. We transduced NES cells with MYCN, observing medulloblastoma upon orthotopic implantation in mice. Significantly, transcriptomes and patterns of DNA methylation from xenograft tumors were globally more representative of human medulloblastoma compared to a MYCN-driven genetically engineered mouse model. Orthotopic transplantation of NES cells generated from Gorlin syndrome patients, who are predisposed to medulloblastoma due to germline-mutated PTCH1, also generated medulloblastoma. We engineered candidate cooperating mutations in Gorlin NES cells, with mutation of DDX3X or loss of GSE1 both accelerating tumorigenesis. These findings demonstrate that human NES cells provide a potent experimental resource for dissecting genetic causation in medulloblastoma.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.stem.2019.05.013DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6731167PMC
September 2019

Dermal Absorption of Pesticide Residues.

Chem Res Toxicol 2018 12 6;31(12):1356-1363. Epub 2018 Dec 6.

Department of Pharmacy and Pharmacology , University of Bath , Bath BA2 7AY , United Kingdom.

Current guidance for dermal exposure assessment of plant protection products typically uses in vitro skin penetration data for the active ingredient when applied as both the concentrated product and relevant spray dilutions thereof. However, typical re-entry scenarios involve potential skin exposure to a "dried residue" of the spray dilution, from which the absorption of a pesticide may be quite different. The research reported in this paper has shown: (1) The method to assess the transfer of dried pesticide residues from a surface to the skin is reproducible for four active ingredients of diverse physicochemical properties, after their application in commercially relevant formulations. (2) Skin absorption of all four pesticides examined was significantly less from a dried residue than from a spray dilution; the difference, in general, was of the order of a factor of 2. (3) Decontamination experiments with one of the active ingredients tested (trinexapac-ethyl) showed that, post-exposure to a spray dilution, skin surface cleaning must be performed within 1 h to significantly reduce potential systemic exposure (relative to continual contact for 24 h); in contrast, after contact with a dried residue, the sooner decontamination was performed, the greater the decrease in exposure achieved, even when the time of contact was as long as 8 h.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1021/acs.chemrestox.8b00227DOI Listing
December 2018

The costs of delaying remediation on human, ecological, and eco-cultural resources: Considerations for the Department of Energy: A methodological framework.

Sci Total Environ 2019 Feb 19;649:1054-1064. Epub 2018 Aug 19.

Consortium for Risk Evaluation with Stakeholder Participation (CRESP), Vanderbilt University, Nashville, TN 37325, USA.

Remediation and restoration of the Nation's nuclear legacy of radiological and chemical contaminated areas is an ongoing and costly challenge for the U.S. Department of Energy (DOE). For large sites, such as the Hanford and Savannah River Sites, successful remediation involves complex decisions related to remedies, end-states, timing, and sequencing of cleanup of separate and related contaminated units within a site. Hanford Site cannot clean up every unit simultaneously due to limits in funding, personnel, and technology. This paper addresses one of the major considerations - the consequences of delaying remediation of a unit on different receptors (e.g. people, ecological, and eco-cultural resources), using the DOE Hanford Site as a case study. We develop a list of attributes that managers should consider for successful remediation, examine how delaying remediation could affect workers, the public and ecological resources (including water resources), and use some examples to illustrate potential effects of delays. The factors to consider when deciding whether and how long to delay remediation of a unit include personnel, information and data, funding, equipment, structural integrity, contaminant source, and resource vulnerability. Each of these factors affects receptors differently. Any remediation task may be dependent on other remediation projects, on the availability of transport, containers, interim storage and ultimate disposition decisions, or the availability of trained personnel. Delaying remediation may have consequences for people (e.g. workers, site neighbors), plants, animals, ecosystems, and eco-cultural resources (i.e. those cultural values that depend upon ecological resources). The risks, benefits, and uncertainties for evaluating the consequences of delaying remediation are described and discussed. Assessing the advantages and disadvantages of delaying remediation is important for health professionals, ecologists, resource trustees, regulators, Tribal members, recreationists, fishermen, hunters, conservationists, and a wide range of other stakeholders.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.scitotenv.2018.08.232DOI Listing
February 2019

The HARMONIC trial: study protocol for a randomised controlled feasibility trial of Shaping Healthy Minds-a modular transdiagnostic intervention for mood, stressor-related and anxiety disorders in adults.

BMJ Open 2018 08 5;8(8):e024546. Epub 2018 Aug 5.

Medical Research Council Cognition and Brain Sciences Unit, University of Cambridge, Cambridge, UK.

Introduction: Anxiety, mood and trauma-related disorders are common, affecting up to 20% of adults. Many of these individuals will experience symptoms of more than one disorder as diagnostically defined. However, most psychological treatments focus on individual disorders and are less effective for those who experience comorbid disorders. The Healthy and Resilient Mind Programme: Building Blocks for Mental Wellbeing (HARMONIC) trial introduces a novel transdiagnostic intervention (), which synthesises several evidence-based treatment techniques to address the gap in effective interventions for people with complex and comorbid difficulties. This early phase trial aims to estimate the efficacy and feasibility of the transdiagnostic intervention in preparation for a later-phase randomised controlled trial, and to explore mechanisms of change.

Methods/analysis: We outline a patient-level two-arm randomised controlled trial (HARMONIC) that compares to treatment-as-usual for individuals aged >18 years (n=50) with comorbid mood, anxiety, obsessive-compulsive or trauma/stressor disorders diagnoses, recruited from outpatient psychological services within the UK National Health Service (NHS). The co-primary outcomes will be 3-month follow-up scores on self-report measures of depressive symptoms, anxiety symptoms, and disability and functional impairment. Secondary outcomes include changes in symptoms linked to individual disorders. We will assess the feasibility and acceptability of , the utility of proposed outcome measures, and refine the treatment manuals in preparation for a later-phase trial.

Ethics And Dissemination: This trial protocol has been approved by the Health Research Authority of the NHS of the UK (East of England, Reference: 16/EE/0095). We anticipate that trial findings will inform future revisions of clinical guidelines for numerous forms of mood, anxiety and stressor-related disorders. Findings will be disseminated broadly via peer-reviewed empirical journal articles, conference presentations, clinical workshops and a trial website.

Trial Registration: NCT03143634; Pre-results.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1136/bmjopen-2018-024546DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6078277PMC
August 2018

Ethics in radiology: A case-based approach.

Can Med Educ J 2018 May 31;9(2):e79-e83. Epub 2018 May 31.

Department of Diagnostic Imaging, Dalhousie University, Nova Scotia, Canada.

Background: Ethics training is required for all radiology residents in Canada, but this may be difficult to provide as radiology departments may not have radiologists with formal ethics training, and may not have access to educational resources focussed on teaching ethics to radiologists. We describe the implementation of a case-based approach to teaching and learning ethics, designed for Canadian radiologists. This approach can be adapted for use in other specialties through development of specialty-specific ethics case scenarios.

Methods: Ethics case study rounds specific to Canadian radiologic practice were presented at two different institutions, and using two different methods within one institution. In one method, we requested that the residents read the case study and questions ahead of time; in the other, the rounds were presented without any expectation of residents doing prior preparation.

Results: The participants, as a group, agreed with all seven survey statements describing the value of the experience. The opportunity to read the case ahead of time seemed helpful for some residents, but was not found to be overall more useful than discussing the case without prior review. Indeed, more than half of the resident participants in this group indicated that they did not make use of the advance materials at all.

Conclusion: Resident feedback indicates that ethics case study rounds are a useful and valuable experience, especially when the case is specifically tailored to their medical practice. Prior preparation was not necessary for residents to benefit from these rounds.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6044307PMC
May 2018

A crossbar network for silicon quantum dot qubits.

Sci Adv 2018 07 6;4(7):eaar3960. Epub 2018 Jul 6.

QuTech, Delft University of Technology, Lorentzweg 1, 2628 CJ Delft, Netherlands.

The spin states of single electrons in gate-defined quantum dots satisfy crucial requirements for a practical quantum computer. These include extremely long coherence times, high-fidelity quantum operation, and the ability to shuttle electrons as a mechanism for on-chip flying qubits. To increase the number of qubits to the thousands or millions of qubits needed for practical quantum information, we present an architecture based on shared control and a scalable number of lines. Crucially, the control lines define the qubit grid, such that no local components are required. Our design enables qubit coupling beyond nearest neighbors, providing prospects for nonplanar quantum error correction protocols. Fabrication is based on a three-layer design to define qubit and tunnel barrier gates. We show that a double stripline on top of the structure can drive high-fidelity single-qubit rotations. Self-aligned inhomogeneous magnetic fields induced by direct currents through superconducting gates enable qubit addressability and readout. Qubit coupling is based on the exchange interaction, and we show that parallel two-qubit gates can be performed at the detuning-noise insensitive point. While the architecture requires a high level of uniformity in the materials and critical dimensions to enable shared control, it stands out for its simplicity and provides prospects for large-scale quantum computation in the near future.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1126/sciadv.aar3960DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6035036PMC
July 2018

Small-Format Drug Conjugates: A Viable Alternative to ADCs for Solid Tumours?

Antibodies (Basel) 2018 Mar 31;7(2). Epub 2018 Mar 31.

Antikor Biopharma Ltd., Stevenage Bioscience Catalyst, Gunnels Wood Road, Stevenage Herts SG12FX, UK.

Antibody-Drug Conjugates (ADCs) have been through multiple cycles of technological innovation since the concept was first practically demonstrated ~40 years ago. Current technology is focusing on large, whole immunoglobulin formats (of which there are approaching 100 in clinical development), many with site-specifically conjugated payloads numbering 2 or 4. Despite the success of trastuzumab-emtansine in breast cancer, ADCs have generally failed to have an impact in solid tumours, leading many to explore alternative, smaller formats which have better penetrating properties as well as more rapid pharmacokinetics (PK). This review describes research and development progress over the last ~10 years obtained from the primary literature or conferences covering over a dozen different smaller format-drug conjugates from 80 kDa to around 1 kDa in total size. In general, these agents are potent in vitro, particularly more recent ones incorporating ultra-potent payloads such as auristatins or maytansinoids, but this potency profile changes when testing in vivo due to the more rapid clearance. Strategies to manipulate the PK properties, whilst retaining the more effective tumour penetrating properties could at last make small-format drug conjugates viable alternative therapeutics to the more established ADCs.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3390/antib7020016DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6698822PMC
March 2018

A simulation study comparing nine mathematical models of arterial input function for dynamic contrast enhanced MRI to the Parker model.

Australas Phys Eng Sci Med 2018 Jun 23;41(2):507-518. Epub 2018 Mar 23.

Department of Radiology, The University of Chicago, 920 East 58th Street (CLSC-109), Chicago, IL, 60637, USA.

Due to large inter- and intra-patient variabilities of arterial input functions (AIFs), accurately modeling and using patient-specific AIF are very important for quantitative analysis of dynamic contrast enhanced MRI. Computer simulations were performed to evaluate and compare nine population AIF models with the Parker AIF used as 'gold standard'. The Parker AIF was calculated with a temporal resolution of 1.5 s, and then the other nine AIF models were used to fit the Parker AIF. A total of 100 randomly generated volume transfer constants (K) and distribution volumes (v) were used to calculate the contrast agent concentration curves based on the Parker AIF and the extended Tofts model with blood plasma volume (v) = 0.0, 0.01, 0.05 and 0.10. Subsequently, nine AIF models were used to fit these curves to extract physiological parameters (K, v and v). The agreements between generated and extracted K and v values were evaluated using Bland-Altman analysis. The effects of the second pass of the Parker AIF model with and without adding Rician noise on extracted physiological parameters were evaluated by 1000 simulations using one of the nine mathematical AIF models closest to the Parker model with the smallest number of parameters. The results demonstrated that a six-parameter linear function plus bi-exponential function AIF model was almost equivalent to the Parker AIF and that the corresponding generated and extracted K and v were in excellent agreements. The effects of the second pass of contrast agent circulation were small on extracted physiological parameters using the extended Tofts model, unless noise was added with signal to noise ratio less than 10 dB.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1007/s13246-018-0632-0DOI Listing
June 2018

Proteomics Profiling of CLL Versus Healthy B-cells Identifies Putative Therapeutic Targets and a Subtype-independent Signature of Spliceosome Dysregulation.

Mol Cell Proteomics 2018 04 24;17(4):776-791. Epub 2018 Jan 24.

From the ‡Antibody and Vaccine Group, Cancer Sciences Unit, Faculty of Medicine, General Hospital, University of Southampton, Southampton, UK;

Chronic lymphocytic leukemia (CLL) is a heterogeneous B-cell cancer exhibiting a wide spectrum of disease courses and treatment responses. Molecular characterization of RNA and DNA from CLL cases has led to the identification of important driver mutations and disease subtypes, but the precise mechanisms of disease progression remain elusive. To further our understanding of CLL biology we performed isobaric labeling and mass spectrometry proteomics on 14 CLL samples, comparing them with B-cells from healthy donors (HDB). Of 8694 identified proteins, ∼6000 were relatively quantitated between all samples (q<0.01). A clear CLL signature, independent of subtype, of 544 significantly overexpressed proteins relative to HDB was identified, highlighting established hallmarks of CLL ( CD5, BCL2, ROR1 and CD23 overexpression). Previously unrecognized surface markers demonstrated overexpression ( CKAP4, PIGR, TMCC3 and CD75) and three of these (LAX1, CLEC17A and ATP2B4) were implicated in B-cell receptor signaling, which plays an important role in CLL pathogenesis. Several other proteins ( Wee1, HMOX1/2, HDAC7 and INPP5F) were identified with significant overexpression that also represent potential targets. Western blotting confirmed overexpression of a selection of these proteins in an independent cohort. mRNA processing machinery were broadly upregulated across the CLL samples. Spliceosome components demonstrated consistent overexpression ( = 1.3 × 10) suggesting dysregulation in CLL, independent of SF3B1 mutations. This study highlights the potential of proteomics in the identification of putative CLL therapeutic targets and reveals a subtype-independent protein expression signature in CLL.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1074/mcp.RA117.000539DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5880099PMC
April 2018

Precursors of human CD4 cytotoxic T lymphocytes identified by single-cell transcriptome analysis.

Sci Immunol 2018 01;3(19)

Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA.

CD4 cytotoxic T lymphocytes (CD4-CTLs) have been reported to play a protective role in several viral infections. However, little is known in humans about the biology of CD4-CTL generation, their functional properties, and heterogeneity, especially in relation to other well-described CD4 memory T cell subsets. We performed single-cell RNA sequencing in more than 9000 cells to unravel CD4-CTL heterogeneity, transcriptional profile, and clonality in humans. Single-cell differential gene expression analysis revealed a spectrum of known transcripts, including several linked to cytotoxic and costimulatory function that are expressed at higher levels in the T (effector memory T cells expressing CD45RA) subset, which is highly enriched for CD4-CTLs, compared with CD4 T cells in the central memory (T) and effector memory (T) subsets. Simultaneous T cell antigen receptor (TCR) analysis in single cells and bulk subsets revealed that CD4-T cells show marked clonal expansion compared with T and T cells and that most of CD4-T were dengue virus (DENV)-specific in donors with previous DENV infection. The profile of CD4-T was highly heterogeneous across donors, with four distinct clusters identified by the single-cell analysis. We identified distinct clusters of CD4-CTL effector and precursor cells in the T subset; the precursor cells shared TCR clonotypes with CD4-CTL effectors and were distinguished by high expression of the interleukin-7 receptor. Our identification of a CD4-CTL precursor population may allow further investigation of how CD4-CTLs arise in humans and, thus, could provide insights into the mechanisms that may be used to generate durable and effective CD4-CTL immunity.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1126/sciimmunol.aan8664DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5931334PMC
January 2018

Highly parallel direct RNA sequencing on an array of nanopores.

Nat Methods 2018 03 15;15(3):201-206. Epub 2018 Jan 15.

Oxford Nanopore Technologies Ltd., Oxford, UK.

Sequencing the RNA in a biological sample can unlock a wealth of information, including the identity of bacteria and viruses, the nuances of alternative splicing or the transcriptional state of organisms. However, current methods have limitations due to short read lengths and reverse transcription or amplification biases. Here we demonstrate nanopore direct RNA-seq, a highly parallel, real-time, single-molecule method that circumvents reverse transcription or amplification steps. This method yields full-length, strand-specific RNA sequences and enables the direct detection of nucleotide analogs in RNA.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/nmeth.4577DOI Listing
March 2018

Head and Neck Squamous Cell Carcinomas Are Characterized by a Stable Immune Signature Within the Primary Tumor Over Time and Space.

Clin Cancer Res 2017 Dec 26;23(24):7641-7649. Epub 2017 Sep 26.

Cancer Sciences & NIHR and CRUK Experimental Cancer Sciences Unit, University of Southampton, Southampton, United Kingdom.

Genetic and morphologic heterogeneity is well-documented in solid cancers. Immune cells are also variably distributed within the tumor; this heterogeneity is difficult to assess in small biopsies, and may confound our understanding of the determinants of successful immunotherapy. We examined the transcriptomic variability of the immunologic signature in head and neck squamous cell carcinoma (HNSCC) within individual tumors using transcriptomic and IHC assessments. Forty-four tumor biopsies from 16 HNSCC patients, taken at diagnosis and later at resection, were analyzed using RNA-sequencing. Variance filtering was used to identify the top 4,000 most variable genes. Principal component analysis, hierarchical clustering, and correlation analysis were performed. Gene expression of was correlated to IHC analysis. Analysis of immunologic gene expression was highly consistent in replicates from the same cancer. Across the cohort, samples from the same patient were most similar to each other, both spatially (at diagnosis) and, notably, over time (diagnostic biopsy compared with resection); comparison of global gene expression by hierarchical clustering ( ≤ 0.0001) and correlation analysis [median intrapatient = 0.82; median interpatient = 0.63]. gene transcript counts were highly correlated with CD8 T-cell counts by IHC ( = 0.82). Our data demonstrate that in HNSCC the global tumor and adaptive immune signatures are stable between discrete parts of the same tumor and also at different timepoints. This suggests that immunologic heterogeneity may not be a key reason for failure of immunotherapy and underpins the use of transcriptomics for immunologic evaluation of novel agents in HNSCC patients. .
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1158/1078-0432.CCR-17-0373DOI Listing
December 2017

Cost-benefit analysis of different air change rates in an operating room environment.

Am J Infect Control 2017 Dec 12;45(12):1318-1323. Epub 2017 Oct 12.

Prism Environmental Health and Safety, Discovery Bay, CA.

Background: Hospitals face growing pressure to meet the dual but often competing goals of providing a safe environment while controlling operating costs. Evidence-based data are needed to provide insight for facility management practices to support these goals.

Methods: The quality of the air in 3 operating rooms was measured at different ventilation rates. The energy cost to provide the heating, ventilation, and air conditioning to the rooms was estimated to provide a cost-benefit comparison of the effectiveness of different ventilation rates currently used in the health care industry.

Results: Simply increasing air change rates in the operating rooms tested did not necessarily provide an overall cleaner environment, but did substantially increase energy consumption and costs. Additionally, and unexpectedly, significant differences in microbial load and air velocity were detected between the sterile fields and back instrument tables.

Conclusions: Increasing the ventilation rates in operating rooms in an effort to improve clinical outcomes and potentially reduce surgical site infections does not necessarily provide cleaner air, but does typically increase operating costs. Efficient distribution or management of the air can improve quality indicators and potentially reduce the number of air changes required. Measurable environmental quality indicators could be used in lieu of or in addition to air change rate requirements to optimize cost and quality for an operating room and other critical environments.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.ajic.2017.07.024DOI Listing
December 2017

Evaluating the effect of immune cells on the outcome of patients with mesothelioma.

Br J Cancer 2017 Oct 17;117(9):1341-1348. Epub 2017 Aug 17.

Cancer Sciences Unit, Faculty of Medicine, University of Southampton, Tremona Road, Southampton SO16 6YD, UK.

Background: We systematically assessed the prognostic and predictive value of infiltrating adaptive and innate immune cells in a large cohort of patients with advanced mesothelioma.

Methods: A tissue microarray from 302 samples was constructed. Markers of adaptive immune response in T-cells (CD8, FOXP3, CD4, CD45RO, CD3) and B-cells (CD20), and of innate immune response; neutrophils (NP57), natural killer cells (CD56) and macrophages (CD68) were evaluated.

Results: We found that in the epithelioid tumours, high CD4 and CD20 counts, and low FOXP3, CD68 and NP57 counts linked to better outcome. In the non-epithelioid group low CD8 and low FOXP3 counts were beneficial.On multivariate analysis low FOXP3 remained independently associated with survival in both groups. In the epithelioid group additionally high CD4, high CD20, and low NP57 counts were prognostic.

Conclusions: Our data demonstrate for the first time, in predominately advanced disease, the association of key markers of adaptive and innate immunity with survival and the differential effect of histology. A better understanding of the immunological drivers of the different subtypes of mesothelioma will assist prognostication and disease-specific clinical decision-making.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/bjc.2017.269DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5672927PMC
October 2017

Epigenetic resetting of human pluripotency.

Development 2017 08;144(15):2748-2763

Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 1QR, UK

Much attention has focussed on the conversion of human pluripotent stem cells (PSCs) to a more naïve developmental status. Here we provide a method for resetting via transient histone deacetylase inhibition. The protocol is effective across multiple PSC lines and can proceed without karyotype change. Reset cells can be expanded without feeders with a doubling time of around 24 h. WNT inhibition stabilises the resetting process. The transcriptome of reset cells diverges markedly from that of primed PSCs and shares features with human inner cell mass (ICM). Reset cells activate expression of primate-specific transposable elements. DNA methylation is globally reduced to a level equivalent to that in the ICM and is non-random, with gain of methylation at specific loci. Methylation imprints are mostly lost, however. Reset cells can be re-primed to undergo tri-lineage differentiation and germline specification. In female reset cells, appearance of biallelic X-linked gene transcription indicates reactivation of the silenced X chromosome. On reconversion to primed status, -induced silencing restores monoallelic gene expression. The facile and robust conversion routine with accompanying data resources will enable widespread utilisation, interrogation, and refinement of candidate naïve cells.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1242/dev.146811DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5560041PMC
August 2017

Tissue-resident memory features are linked to the magnitude of cytotoxic T cell responses in human lung cancer.

Nat Immunol 2017 Aug 19;18(8):940-950. Epub 2017 Jun 19.

Cancer Sciences Unit, Faculty of Medicine, University of Southampton, Southampton, UK.

Therapies that boost the anti-tumor responses of cytotoxic T lymphocytes (CTLs) have shown promise; however, clinical responses to the immunotherapeutic agents currently available vary considerably, and the molecular basis of this is unclear. We performed transcriptomic profiling of tumor-infiltrating CTLs from treatment-naive patients with lung cancer to define the molecular features associated with the robustness of anti-tumor immune responses. We observed considerable heterogeneity in the expression of molecules associated with activation of the T cell antigen receptor (TCR) and of immunological-checkpoint molecules such as 4-1BB, PD-1 and TIM-3. Tumors with a high density of CTLs showed enrichment for transcripts linked to tissue-resident memory cells (T cells), such as CD103, and CTLs from CD103 tumors displayed features of enhanced cytotoxicity. A greater density of T cells in tumors was predictive of a better survival outcome in lung cancer, and this effect was independent of that conferred by CTL density. Here we define the 'molecular fingerprint' of tumor-infiltrating CTLs and identify potentially new targets for immunotherapy.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/ni.3775DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6036910PMC
August 2017

Common mental disorder including psychotic experiences: Trailblazing a new recovery pathway within the Improving Access to Psychological Therapies programme in England.

Early Interv Psychiatry 2018 06 16;12(3):497-504. Epub 2017 May 16.

CAMEO Early Intervention in Psychosis Service, Cambridge and Peterborough NHS Foundation Trust, Cambridge, UK.

Psychotic experiences, depressive and anxiety symptoms may be manifestations of a latent continuum of common mental distress. The Improving Access to Psychological Therapies (IAPT) programme has increased the reach of psychological treatments to people with common mental disorders in England. However, psychotic experiences are neither measured nor considered in therapy. We aimed to confirm the presence of psychotic experiences among IAPT service-users and determine whether these experiences are associated with higher depression/anxiety levels and poorer recovery. All service-users that attended the Fenland and Peterborough IAPT teams in Cambridgeshire between November 16, 2015 and January 29, 2016 participated in a service evaluation. In addition to routine mesures, such as the Generalized Anxiety Disorder-7 questionnaire (GAD-7) and the Patient Health Questionnaire-9 (PHQ-9), we introduced a shortened version of the Community Assessment of Psychic Experiences (CAPE-P15) to measure psychotic experiences. Classes of individuals were identified with latent class analysis. Associations were reported using Pearson correlation coefficient. One hundred and seventy-three services-users were included, mostly females (N = 133; 76.9%). The mean age was 36.6 (SD = 13.3). Around 30% likely belonged to a class with psychotic experiences. CAPE-P15 frequency was significantly correlated to PHQ-9 (r = 0.44; P < .001) and GAD-7 (r = 0.32; P < .001). Similarly, CAPE-P15 distress and both PHQ-9 (r = 0.43; P < .001) and GAD-7 (r = 0.38; P < .001) were highly correlated. These associations were replicated after the initial period of the therapy, indicating poor recovery. Some IAPT service-users suffer psychotic experiences. Tailoring available evidence-based psychological therapies for these people in IAPT settings might trailblaze a new care pathway to improve recovery in this group.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1111/eip.12434DOI Listing
June 2018

Methodology for analyzing environmental quality indicators in a dynamic operating room environment.

Am J Infect Control 2017 Apr 21;45(4):354-359. Epub 2016 Dec 21.

ARTEC Environmental Monitoring, Indianapolis, IN.

Background: Sufficient quantities of quality air and controlled, unidirectional flow are important elements in providing a safe building environment for operating rooms.

Methods: To make dynamic assessments of an operating room environment, a validated method of testing the multiple factors influencing the air quality in health care settings needed to be constructed. These include the following: temperature, humidity, particle load, number of microbial contaminants, pressurization, air velocity, and air distribution. The team developed the name environmental quality indicators (EQIs) to describe the overall air quality based on the actual measurements of these properties taken during the mock surgical procedures. These indicators were measured at 3 different hospitals during mock surgical procedures to simulate actual operating room conditions. EQIs included microbial assessments at the operating table and the back instrument table and real-time analysis of particle counts at 9 different defined locations in the operating suites. Air velocities were measured at the face of the supply diffusers, at the sterile field, at the back table, and at a return grille.

Results: The testing protocol provided consistent and comparable measurements of air quality indicators between institutions. At 20 air changes per hour (ACH), and an average temperature of 66.3°F, the median of the microbial contaminants for the 3 operating room sites ranged from 3-22 colony forming units (CFU)/m at the sterile field and 5-27 CFU/m at the back table. At 20 ACH, the median levels of the 0.5-µm particles at the 3 sites were 85,079, 85,325, and 912,232 in particles per cubic meter, with a predictable increase in particle load in the non-high-efficiency particulate air-filtered operating room site. Using a comparison with cleanroom standards, the microbial and particle counts in all 3 operating rooms were equivalent to International Organization for Standardization classifications 7 and 8 during the mock surgical procedures.

Conclusions: The EQI protocol was measurable and repeatable and therefore can be safely used to evaluate air quality within the health care environment to provide guidance for operational practices and regulatory requirements.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.ajic.2016.11.001DOI Listing
April 2017
-->