Publications by authors named "Robert Holt"

310 Publications

The evolution of habitat construction with and without phenotypic plasticity.

Evolution 2021 Apr 7. Epub 2021 Apr 7.

Department of Biology, University of Florida, Gainesville, FL, 32611.

Habitat construction and phenotypic plasticity are alternative responses to variable environments. We explored evolution along an environmental gradient of habitat construction alone and in combination with phenotypic plasticity using individual-based simulations that manipulated the fitness benefit of construction and whether construction maintained or eliminated that gradient. Construction was favored when its benefits were more likely to flow to the immediate offspring of the constructing individuals. Habitat construction and phenotypic plasticity traded off against each other or plasticity was selected against, depending on how the optimum environment varied and with the fitness value of construction. When selection favored differences in the amount of construction along the environmental gradient, genetic differentiation for habitat construction increased as the fitness value of construction increased. The degree to which each adaptive response was likely to evolve also depended on the precise ordering of life history events. Adaptive habitat construction does not always occur and may be selected against. This article is protected by copyright. All rights reserved.
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http://dx.doi.org/10.1111/evo.14226DOI Listing
April 2021

Pharmacokinetics and Exposure-Response Relationship of Teprotumumab, an Insulin-Like Growth Factor-1 Receptor-Blocking Antibody, in Thyroid Eye Disease.

Clin Pharmacokinet 2021 Mar 26. Epub 2021 Mar 26.

Horizon Therapeutics plc, 150 S. Saunders Rd, Lake Forest, IL, 60045, USA.

Background And Objective: Thyroid eye disease (TED) is characterized by inflammation/expansion of orbital tissues, proptosis, and diplopia. Teprotumumab is the first US Food and Drug Administration-approved therapy for TED, administered as an initial intravenous infusion of 10 mg/kg followed by 20 mg/kg every 3 weeks for an additional seven infusions. The objective of this article is to discuss the pharmacokinetics and exposure-response profile for teprotumumab in patients with TED.

Methods: A population pharmacokinetic analysis was performed to characterize pharmacokinetics and select dosing in patients with TED. Exposure-response was evaluated for efficacy (proptosis response, clinical activity score categorical response, and diplopia response) and safety (hyperglycemia, muscle spasms, and hearing impairment) parameters.

Results: Teprotumumab pharmacokinetics was linear in patients with TED, with low systemic clearance (0.334 L/day), low volume of distribution (3.9 and 4.2 L for the central and peripheral compartment, respectively), and a long elimination half-life (19.9 days). The approved dosing regimen provided > 20 µg/mL for > 90% insulin-like growth factor 1 receptor saturation throughout the dosing interval. Model-predicted mean (± standard deviation) steady-state area under the concentration-time curve, peak, and trough concentrations in patients with TED were 131 (± 30.9) mg∙h/mL, 643 (± 130) µg/mL, and 157 (± 50.6) µg/mL, respectively. Female patients had a 15% higher steady-state peak concentration but a similar steady-state area under the concentration-time curve vs male patients. No other covariates affected teprotumumab pharmacokinetics. No meaningful correlations between teprotumumab exposures and efficacy or safety parameters were observed.

Conclusions: Teprotumumab pharmacokinetics was well characterized in patients with TED, and generally consistent with other IgG1 antibodies. Efficacy was consistent across the exposure range with a well-tolerated safety profile supporting the current dose regimen for patients with TED.
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http://dx.doi.org/10.1007/s40262-021-01003-3DOI Listing
March 2021

Hematologists' barriers and enablers to screening and recruiting patients to a chimeric antigen receptor (CAR) T cell therapy trial: a theory-informed interview study.

Trials 2021 Mar 25;22(1):230. Epub 2021 Mar 25.

Clinical Epidemiology Program, Ottawa Hospital Research Institute, 501 Smyth Road, Ottawa, Ontario, K1H 8L6, Canada.

Background: Novel therapies often fail to reach the bedside due to low trial recruitment rates. Prior to conducting one of the first chimeric antigen receptor (CAR) T cell therapy trials in Canada, we used the Theoretical Domains Framework, a novel tool for identifying barriers and enablers to behavior change, to identify physician-related barriers and enablers to screening and recruiting patients for an early phase immunotherapy trial.

Methods: We conducted interviews with hematologists across Canada and used a directed content analysis to identify relevant domains reflecting the key factors that may affect screening and recruitment.

Results: In total, we interviewed 15 hematologists. Physicians expressed "cautious hope"; while expressing safety, feasibility, and screening criteria concerns, 14 out of 15 hematologists intended to screen for the trial (domains: knowledge, goals, beliefs about consequences, intentions). Physicians underscored the "challenging contexts," identifying resources, workload, forgetting, and patient wait times to receive CAR T cells as key practical barriers to screening (domains: environmental context and resources, memory, attention and decision-making, behavioral regulation). They also highlighted "variability in roles and procedures" that may lead to missed trial candidates (domain: social and professional role). Left unaddressed, these barriers may undermine trial recruitment.

Conclusions: This study is among the first to use the Theoretical Domains Framework from the physician perspective to identify recruitment challenges to early phase trials and demonstrates the value of this approach for identifying barriers to screening and recruitment that may not otherwise have been elicited. This approach can optimize trial procedures and may serve to inform future promising early phase cancer therapy trials.

Trial Registration: ClinicalTrials.gov Identifier: NCT03765177 . Registered on December 5, 2018.
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http://dx.doi.org/10.1186/s13063-021-05121-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7995587PMC
March 2021

Navigating choice in the face of uncertainty: using a theory informed qualitative approach to identifying potential patient barriers and enablers to participating in an early phase chimeric antigen receptor T (CAR-T) cell therapy trial.

BMJ Open 2021 Mar 19;11(3):e043929. Epub 2021 Mar 19.

Blueprint Translational Research Group, Ottawa Hospital Research Institute, Ottawa, Ontario, Canada

Objectives: Bench to bedside translation of groundbreaking treatments like chimeric antigen receptor T (CAR-T) cell therapy depends on patient participation in early phase trials. Unfortunately, many novel therapies fail to be adequately evaluated due to low recruitment rates, which slows patient access to emerging treatments. Using the Theoretical Domains Framework (TDF), we sought to identify potential patient barriers and enablers to participating in an early phase CAR-T cell therapy trial.

Design: We used qualitative semistructured interviews to identify potential barriers and enablers to patients' hypothetical participation in an early phase CAR-T cell therapy trial. We used the TDF and directed content analysis to identify relevant domains based on frequency, relevance and the presence of conflicting beliefs.

Participants: Canadian adult patients diagnosed with haematological malignancies.

Results: In total, we interviewed 13 participants (8 women, 5 men). Participants ranged in age from 18 to 73 (median=56) and had been living with haematological cancer from a few months to several years. We found participants were unfamiliar with CAR-T cell therapy but wished to know more about treatment safety, efficacy and trial logistics (domains: knowledge, beliefs about consequences). They were motivated by altruistic considerations, though many prioritised personal health benefits despite recognising the goals (ie, establishing safety) of early phase clinical trials (domains: goals, intentions). Every participant valued receiving medical advice from their haematologists and oncologists, though some preferred impartial medical experts to inform their decision making (domain: social influences). Finally, participants indicated that improving access to financial and social supports would improve their trial participation experience (domain: environmental context and resources).

Conclusion: Using the TDF allowed us to identify factors that might undermine participation to a CAR-T cell therapy trial and to optimise recruitment processes by considering patient perspectives to taking part in early phase trials. NCT03765177; Pre-results.
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http://dx.doi.org/10.1136/bmjopen-2020-043929DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7986876PMC
March 2021

Environmental fluctuations dampen the effects of clonal reproduction on evolutionary rescue.

J Evol Biol 2021 Apr 19;34(4):710-722. Epub 2021 Mar 19.

Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, USA.

Evolutionary rescue occurs when genetic change allows a population to persist in response to an environmental change that would otherwise have led to extinction. Most studies of evolutionary rescue assume that species have either fully clonal or fully sexual reproduction; however, many species have partially clonal reproductive strategies in which they reproduce both clonally and sexually. Furthermore, the few evolutionary rescue studies that have evaluated partially clonal reproduction did not consider fluctuations in the environment, which are nearly ubiquitous in nature. Here, we use individual-based simulations to investigate how environmental fluctuations (either uncorrelated or positively autocorrelated) influence the effect of clonality on evolutionary rescue. We show that, for moderate magnitudes of environmental fluctuations, as was found in the absence of fluctuations, increasing the degree of clonality increases the probability of population persistence in response to an abrupt environmental change, but decreases persistence in response to a continuous, directional environmental change. However, with large magnitudes of fluctuations, both the benefits of clonality following a step change and the detrimental effects of clonality following a continuous, directional change are generally reduced; in fact, in the latter scenario, increasing clonality can even become beneficial if environmental fluctuations are autocorrelated. We also show that increased generational overlap dampens the effects of environmental fluctuations. Overall, we demonstrate that understanding the evolutionary rescue of partially clonal organisms requires not only knowledge of the species life history and the type of environmental change, but also an understanding of the magnitude and autocorrelation of environmental fluctuations.
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http://dx.doi.org/10.1111/jeb.13778DOI Listing
April 2021

Toward ecoevolutionary dynamics.

Proc Natl Acad Sci U S A 2021 Mar;118(9)

Department of Biology, University of Florida, Gainesville, FL 32611.

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http://dx.doi.org/10.1073/pnas.2100200118DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7936262PMC
March 2021

Revisiting the Role of Hyperparasitism in the Evolution of Virulence.

Am Nat 2021 02 23;197(2):216-235. Epub 2020 Dec 23.

AbstractHyperparasitism denotes the natural phenomenon where a parasite infecting a host is in turn infected by its own parasite. Hyperparasites can shape the dynamics of host-parasite interactions and often have a deleterious impact on pathogens, an important class of parasites, causing a reduction in their virulence and transmission rate. Hyperparasitism thus could be an important tool of biological control. However, host-parasite-hyperparasite systems have so far been outside the mainstream of modeling studies, especially those dealing with eco-evolutionary aspects of species interactions. Here, we theoretically explore the evolution of life-history traits in a generic host-parasite-hyperparasite system, focusing on parasite virulence and the positive impact that hyperparasitism has on the host population. We also explore the coevolution of life-history traits of the parasite and hyperparasite, using adaptive dynamics and quantitative genetics frameworks to identify evolutionarily singular strategies. We find that in the presence of hyperparasites, the evolutionarily optimal pathogen virulence generally shifts toward more virulent strains. However, even in this case the use of hyperparasites in biocontrol could be justified, since overall host mortality decreases. An intriguing possible outcome of the evolution of the hyperparasite can be its evolutionary suicide.
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http://dx.doi.org/10.1086/712351DOI Listing
February 2021

Characteristics, Comorbidities, and Potential Consequences of Uncontrolled Gout: An Insurance-Claims Database Study.

Rheumatol Ther 2021 Mar 7;8(1):183-197. Epub 2020 Dec 7.

Illinois Bone and Joint Institute, 2401 Ravine Way, Glenview, IL, 60025, USA.

Introduction: Gout is a common, progressive, systemic inflammatory arthritis caused by hyperuricemia. Current guidelines recommend that serum uric acid (sUA) levels be maintained below 6.0 mg/dl to minimize acute gout attacks, tophi development, and long-term joint and organ damage. This study examined the influence of uncontrolled gout on post-diagnosis comorbidities and medication use.

Methods: The Humana Research Database (2007-2016, commercial insurance and Medicare) was searched (PearlDiver tool) for patients who had a gout diagnosis code, claims data for at least 6 months before and after diagnosis, and at least 90 days of continuous urate-lowering therapy within 1 year of diagnosis. Patients with controlled (all sUA measurements < 6.0 mg/dl) and uncontrolled (all sUA measurements ≥ 8.0 mg/dl) gout were further examined and compared to better understand the influence of uncontrolled gout on post-diagnosis comorbidities, medication use, and reasons for seeking medical care.

Results: A total of 5473 and 1358 patients met inclusion and classification criteria for the controlled and uncontrolled groups, respectively. Identified comorbidities in both groups included hypertension, hyperlipidemia, diabetes, cardiovascular disease, and chronic kidney disease (CKD). However, the uncontrolled group was more likely to have diabetes, CKD, and cardiovascular disease (including heart failure and atrial fibrillation). Additionally, CKD tended to be more advanced in the uncontrolled gout population (Stage 4-5: 34.6 vs. 22.2%). Overall opioid use was higher in uncontrolled patients.

Conclusions: The current study identified differences between controlled and uncontrolled gout patients, including usage of medication, severity of CKD, and prevalence of CKD, diabetes, and heart disease.
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http://dx.doi.org/10.1007/s40744-020-00260-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7991061PMC
March 2021

Tumor Infiltrating Effector Memory Antigen-Specific CD8 T Cells Predict Response to Immune Checkpoint Therapy.

Front Immunol 2020 12;11:584423. Epub 2020 Nov 12.

National Centre for Asbestos Related Diseases, Institute for Respiratory Health, University of Western Australia, Nedlands, WA, Australia.

Immune checkpoint therapy (ICT) results in durable responses in individuals with some cancers, but not all patients respond to treatment. ICT improves CD8 cytotoxic T lymphocyte (CTL) function, but changes in tumor antigen-specific CTLs post-ICT that correlate with successful responses have not been well characterized. Here, we studied murine tumor models with dichotomous responses to ICT. We tracked tumor antigen-specific CTL frequencies and phenotype before and after ICT in responding and non-responding animals. Tumor antigen-specific CTLs increased within tumor and draining lymph nodes after ICT, and exhibited an effector memory-like phenotype, expressing IL-7R (CD127), KLRG1, T-bet, and granzyme B. Responding tumors exhibited higher infiltration of effector memory tumor antigen-specific CTLs, but lower frequencies of regulatory T cells compared to non-responders. Tumor antigen-specific CTLs persisted in responding animals and formed memory responses against tumor antigens. Our results suggest that increased effector memory tumor antigen-specific CTLs, in the presence of reduced immunosuppression within tumors is part of a successful ICT response. Temporal and nuanced analysis of T cell subsets provides a potential new source of immune based biomarkers for response to ICT.
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http://dx.doi.org/10.3389/fimmu.2020.584423DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7688517PMC
November 2020

Physician-Perceived Impact of Thyroid Eye Disease on Patient Quality of Life in the United States.

Ophthalmol Ther 2021 Mar 16;10(1):75-87. Epub 2020 Nov 16.

Cedars-Sinai Medical Center, Los Angeles, CA, USA.

Introduction: Thyroid eye disease (TED) is an autoimmune disease that causes retro-orbital inflammation and subsequent proptosis, corneal exposure, strabismus, and variable vision changes. European studies have shown that TED can severely impact quality of life (QOL), but little is known about the QOL of patients with TED in the USA. Given that patient QOL influences TED severity classifications and subsequent treatment, understanding physician-perceived patient QOL is extremely important.

Methods: This retrospective chart review (conducted in 2018) examined QOL in US patients with moderate-to-severe TED, as reported by treating physicians who regularly manage patients with TED (≥ 5 patients in prior 12 months). The physicians graded patients' overall QOL (7-point Likert scale; 1 = "not at all impaired", 7 = "extremely impaired"), assessing mental health, vision changes, and ocular structural signs/symptoms. Patient demographics and clinical findings were examined to understand the impact of disease presentation on physician-perceived QOL.

Results: Medical record data of 714 US patients with moderate-to-severe TED were provided by 181 physicians (73 endocrinologists, 108 ophthalmologists). Patients had a mean age of 49.4 (standard deviation [SD] 13.6) years, and 102 cases (14%) were severe. Anxiety and/or depression was reported in 36% of patients (an increase from the 18.9% prevalence reported for the USA in 2017 by the US National Institute of Mental Health; P < 0.001). The mean physician-reported QOL impact score was 4.1 (SD 1.5). Furthermore, 62 and 89% of patients with moderate and severe TED, respectively, had a high physician-perceived QOL impact (≥ 4). The higher QOL impact group had significantly higher rates of pain symptoms, visual disturbances (including diplopia), and orbito-facial structural changes. Higher disease activity and severity were associated with lower physician-perceived QOL.

Conclusion: Patients' QOL, as evaluated by US physicians, is highly impacted by the activity and severity of TED. Additionally, mental health issues were more frequently reported by patients with TED than in the general US population. Ocular pain, strabismus, and diplopia appear to be main drivers of physician-perceived QOL impairment in this sample of US patients with TED.
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http://dx.doi.org/10.1007/s40123-020-00318-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7886952PMC
March 2021

Trends in Treatment of Active, Moderate-to-Severe Thyroid Eye Disease in the United States.

J Endocr Soc 2020 Dec 25;4(12):bvaa140. Epub 2020 Sep 25.

Cedars Sinai Medical Center, Los Angeles, California.

Introduction: Limited data exist on US referral/management patterns for moderate-to-severe thyroid eye disease (TED), a disabling condition.

Methods: US ophthalmologists and endocrinologists experienced in treating TED provided medical record data of moderate-to-severe TED patients and information on referral/treatment practices. Data on signs/symptoms, medical/surgical treatments, treatment response, and referral history were collected. Moderate and severe cases were stratified to interrogate treatment/practice differences.

Results: A total of 181 physicians provided data on 714 patients (49.4 ± 13.6 years old, 65% women, 14% severe disease). Reporting physicians diagnosed 55% of patients themselves and solely managed 37% of cases, with similar referral/comanagement patterns between moderate and severe cases. Topical therapies included lubricating (79%) and glucocorticoid (39%) eye drops. Systemic therapies included oral glucocorticoids (36%), IV glucocorticoids (15%), and rituximab and/or tocilizumab (12%). Few patients underwent orbital radiation (4%) or surgical intervention (4%). IV glucocorticoids (33% vs. 12%), biologics (26% vs. 10%), orbital radiation (11% vs. 3%), and ocular surgery (12% vs. 3%) were used more often in severe versus moderate cases (all  < 0.001). However, severe disease was less responsive to therapy (very responsive to therapy: 28% vs. 49%,  < 0.001).

Conclusions: Participating physicians were primarily responsible for just over one-half of TED diagnoses, but solely treated <40% of patients. Severe TED was treated more often with surgery and systemic immunologic therapies than moderate disease, but was less likely to respond to treatment. These results reinforce that moderate-to-severe TED is difficult to treat with an unmet medical need in the United States.
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http://dx.doi.org/10.1210/jendso/bvaa140DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7645612PMC
December 2020

The interplay of movement and spatiotemporal variation in transmission degrades pandemic control.

Proc Natl Acad Sci U S A 2020 12 10;117(48):30104-30106. Epub 2020 Nov 10.

Department of Biology, University of Florida, Gainesville, FL 32611;

Successful public health regimes for COVID-19 push below unity long-term regional -the average number of secondary cases caused by an infectious individual. We use a susceptible-infectious-recovered (SIR) model for two coupled populations to make the conceptual point that asynchronous, variable local control, together with movement between populations, elevates long-term regional , and cumulative cases, and may even prevent disease eradication that is otherwise possible. For effective pandemic mitigation strategies, it is critical that models encompass both spatiotemporal heterogeneity in transmission and movement.
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http://dx.doi.org/10.1073/pnas.2018286117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7720174PMC
December 2020

Characteristics of TCR Repertoire Associated With Successful Immune Checkpoint Therapy Responses.

Front Immunol 2020 14;11:587014. Epub 2020 Oct 14.

National Centre for Asbestos Related Diseases, Institute of Respiratory Health, University of Western Australia, Perth, WA, Australia.

Immunotherapies have revolutionized cancer treatment. In particular, immune checkpoint therapy (ICT) leads to durable responses in some patients with some cancers. However, the majority of treated patients do not respond. Understanding immune mechanisms that underlie responsiveness to ICT will help identify predictive biomarkers of response and develop treatments to convert non-responding patients to responding ones. ICT primarily acts at the level of adaptive immunity. The specificity of adaptive immune cells, such as T and B cells, is determined by antigen-specific receptors. T cell repertoires can be comprehensively profiled by high-throughput sequencing at the bulk and single-cell level. T cell receptor (TCR) sequencing allows for sensitive tracking of dynamic changes in antigen-specific T cells at the clonal level, giving unprecedented insight into the mechanisms by which ICT alters T cell responses. Here, we review how the repertoire influences response to ICT and conversely how ICT affects repertoire diversity. We will also explore how changes to the repertoire in different anatomical locations can better correlate and perhaps predict treatment outcome. We discuss the advantages and limitations of current metrics used to characterize and represent TCR repertoire diversity. Discovery of predictive biomarkers could lie in novel analysis approaches, such as network analysis of amino acids similarities between TCR sequences. Single-cell sequencing is a breakthrough technology that can link phenotype with specificity, identifying T cell clones that are crucial for successful ICT. The field of immuno-sequencing is rapidly developing and cross-disciplinary efforts are required to maximize the analysis, application, and validation of sequencing data. Unravelling the dynamic behavior of the TCR repertoire during ICT will be highly valuable for tracking and understanding anti-tumor immunity, biomarker discovery, and ultimately for the development of novel strategies to improve patient outcomes.
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http://dx.doi.org/10.3389/fimmu.2020.587014DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7591700PMC
October 2020

Partnering with patients to get better outcomes with chimeric antigen receptor T-cell therapy: towards engagement of patients in early phase trials.

Res Involv Engagem 2020 14;6:61. Epub 2020 Oct 14.

Clinical Epidemiology Program, Blueprint Translational Research Group, Ottawa Hospital Research Institute, 501 Smyth Road, Ottawa, ON K1H 8L6 Canada.

Aim: Though patient engagement in clinical research is growing, recent reports suggest few clinical trials report on such activities. To address this gap, we describe our approach to patient engagement in the development of a clinical trial protocol to assess a new immunotherapy for blood cancer (chimeric antigen receptor T-cell therapy, CAR-T cell therapy).

Methods: Our team developed a clinical trial protocol by working with patient partners from inception. Two patient partners with lived blood cancer experience were identified through referrals from our team's professional network and patient organization contacts. Our patient partners were onboarded to the team and engaged in several studies conducted to develop the clinical trial protocol, including a systematic review of the existing literature on the therapy, patient interviews and a survey to obtain perspectives on barriers and enablers to participating in the trial, an early economic analysis, and a retrospective cohort study.

Results: Engaging patient partners enhanced our research in ways that would not have otherwise occurred. By selecting patient important outcomes for data collection, our partners helped flag that quality of life and health utility measures have not been reported in previous CAR-T cell therapy trials for blood cancer. Our partners also co-developed a non-technical summary of the systematic review that summarized results in an accessible manner. Our patient partners reviewed interview and survey questions, to improve the language and appropriateness; provided recruitment suggestions; and provided a patient perspective on the results, thereby confirming the importance of findings. Input was also obtained on costs for the early economic analysis. Our patient partners identified costs that may be a burden to both patients and caregivers during a trial and helped to confirm that the overall structure of the economic model reflected the patient care pathway. Our patient partners also shared their diagnosis and treatment stories, which helped to provide the research team with insight into this experience.

Conclusions: Contributions by our patient partners were invaluable to each component study, as well as the overall development of the trial protocol. We plan to use this approach in the future in order to meaningfully engage patients in the development of other clinical trials; we also hope that by reporting our methods this will help other research teams to do the same.

Trial Registration: Affiliated with the development of NCT03765177.
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http://dx.doi.org/10.1186/s40900-020-00230-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7557015PMC
October 2020

Genome and Transcriptome Biomarkers of Response to Immune Checkpoint Inhibitors in Advanced Solid Tumors.

Clin Cancer Res 2021 Jan 5;27(1):202-212. Epub 2020 Oct 5.

Department of Medical Oncology, BC Cancer, Vancouver, British Columbia, Canada.

Purpose: Immune checkpoint inhibitors (ICI) have revolutionized the treatment of solid tumors with dramatic and durable responses seen across multiple tumor types. However, identifying patients who will respond to these drugs remains challenging, particularly in the context of advanced and previously treated cancers.

Experimental Design: We characterized fresh tumor biopsies from a heterogeneous pan-cancer cohort of 98 patients with metastatic predominantly pretreated disease through the Personalized OncoGenomics program at BC Cancer (Vancouver, Canada) using whole genome and transcriptome analysis (WGTA). Baseline characteristics and follow-up data were collected retrospectively.

Results: We found that tumor mutation burden, independent of mismatch repair status, was the most predictive marker of time to progression ( = 0.007), but immune-related CD8 T-cell and M1-M2 macrophage ratio scores were more predictive for overall survival (OS; = 0.0014 and 0.0012, respectively). While [programmed death-ligand 1 (PD-L1)] gene expression is comparable with protein levels detected by IHC, we did not observe a clinical benefit for patients with this marker. We demonstrate that a combination of markers based on WGTA provides the best stratification of patients ( = 0.00071, OS), and also present a case study of possible acquired resistance to pembrolizumab in a patient with non-small cell lung cancer.

Conclusions: Interpreting the tumor-immune interface to predict ICI efficacy remains challenging. WGTA allows for identification of multiple biomarkers simultaneously that in combination may help to identify responders, particularly in the context of a heterogeneous population of advanced and previously treated cancers, thus precluding tumor type-specific testing.
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http://dx.doi.org/10.1158/1078-0432.CCR-20-1163DOI Listing
January 2021

Environmental fluctuations can promote evolutionary rescue in high-extinction-risk scenarios.

Proc Biol Sci 2020 08 5;287(1932):20201144. Epub 2020 Aug 5.

Department of Biology, University of Florida, Gainesville, FL, USA.

Substantial environmental change can force a population onto a path towards extinction, but under some conditions, adaptation by natural selection can rescue the population and allow it to persist. This process, known as evolutionary rescue, is believed to be less likely to occur with greater magnitudes of random environmental fluctuations because environmental variation decreases expected population size, increases variance in population size and increases evolutionary lag. However, previous studies of evolutionary rescue in fluctuating environments have only considered scenarios in which evolutionary rescue was likely to occur. We extend these studies to assess how baseline extinction risk (which we manipulated via changes in the initial population size, degree of environmental change or mutation rate) influences the effects of environmental variation on evolutionary rescue following an abrupt environmental change. Using a combination of analytical models and stochastic simulations, we show that autocorrelated environmental variation hinders evolutionary rescue in low-extinction-risk scenarios but facilitates rescue in high-risk scenarios. In these high-risk cases, the chance of a run of good years counteracts the otherwise negative effects of environmental variation on evolutionary demography. These findings can inform the development of effective conservation practices that consider evolutionary responses to abrupt environmental changes.
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http://dx.doi.org/10.1098/rspb.2020.1144DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7575515PMC
August 2020

Disease in Invasive Plant Populations.

Annu Rev Phytopathol 2020 08 9;58:97-117. Epub 2020 Jun 9.

Agronomy Department, University of Florida, Gainesville, Florida 32611, USA.

Non-native invasive plants can establish in natural areas, where they can be ecologically damaging and costly to manage. Like cultivated plants, invasive plants can experience a relatively disease-free period upon introduction and accumulate pathogens over time. Diseases of invasive plant populations are infrequently studied compared to diseases of agriculture, forestry, and even native plant populations. We evaluated similarities and differences in the processes that are likely to affect pathogen accumulation and disease in invasive plants compared to cultivated plants, which are the dominant focus of the field of plant pathology. Invasive plants experience more genetic, biotic, and abiotic variation across space and over time than cultivated plants, which is expected to stabilize the ecological and evolutionary dynamics of interactions with pathogens and possibly weaken the efficacy of infectious disease in their control. Although disease is expected to be context dependent, the widespread distribution of invasive plants makes them important pathogen reservoirs. Research on invasive plant diseases can both protect crops and help manage invasive plant populations.
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http://dx.doi.org/10.1146/annurev-phyto-010820-012757DOI Listing
August 2020

Intrathecal Tc-DTPA imaging of molecular passage from lumbar cerebrospinal fluid to brain and periphery in humans.

Alzheimers Dement (Amst) 2020 29;12(1):e12030. Epub 2020 Apr 29.

Cornell University Weill College of Medicine New York New York.

Introduction: Cerebrospinal fluid (CSF) molecular exchange with brain interstitial fluid (ISF) and periphery is implicated in neurological disorders but needs better quantitative clinical assessment approaches.

Methods: Following intrathecal (ITH) dosing via lumbar puncture, Technetium-99 m (Tc-) diethylenetriaminepentaacetic acid (DTPA) imaging was used to quantify neuraxial spread, CSF-brain molecular exchange, and CSF-peripheral clearance in 15 normal human volunteers. The effect of experimental convection manipulation on these processes was also assessed.

Results: Rostral cranial Tc-DTPA exposures were influenced by the volume of artificial CSF in the formulation. Signal translocation to the cranial cisterns and the brain parenchyma was observable by 3 hours. Tc-DTPA penetrated cortical ISF but showed lower signal in deeper structures. Urinary Tc-DTPA signal elimination was accelerated by higher formulation volumes and mechanical convection.

Discussion: Widely used for detecting CSF leaks, ITH Tc-DTPA imaging can also become a useful clinical biomarker for measuring molecular exchange physiology between the CSF, brain, and periphery.
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http://dx.doi.org/10.1002/dad2.12030DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7191108PMC
April 2020

Complementary Methods for de Novo Monoclonal Antibody Sequencing to Achieve Complete Sequence Coverage.

J Proteome Res 2020 07 7;19(7):2700-2707. Epub 2020 May 7.

Department of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada.

Mass spectrometry is a powerful tool for de novo sequencing of novel proteins. Recent efforts in this area have mainly focused on liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS). Here, we present an alternative method, capillary electrophoresis tandem mass spectrometry (CE-MS/MS), for sequencing novel monoclonal antibodies. Using less than 200 ng in total of tryptic digest sample in a triplicated measurement, CE-MS/MS with pH-mediated focusing successfully sequenced mAb infliximab with 100% sequence coverage and 100% accuracy for the light chain and 96% coverage and 93% accuracy for the heavy chain. It was also demonstrated that CE-MS/MS gives comparable results, and in some cases, even better results, as compared to LC-MS/MS when used as a standalone technique. A combined workflow using both CE-MS/MS and LC-MS/MS was also used to sequence a novel antibody, anti-CD-176, resulting in the first proposed sequence for this mAb.
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http://dx.doi.org/10.1021/acs.jproteome.0c00223DOI Listing
July 2020

A Rapid and Sensitive Nucleic Acid Amplification Technique for Screening of Cell Therapy Products.

Mol Ther Methods Clin Dev 2020 Jun 30;17:393-399. Epub 2020 Jan 30.

Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 1L3, Canada.

species (spp.) bacteria can infect cell cultures, posing a potential threat to recipients of cell therapy products. Conventional testing methods are highly sensitive but typically require a minimum of 28 days to produce results. This delay is problematic if rapid results are needed to inform treatment decisions. Nucleic acid amplification technique (NAT) methods have been gaining favor for testing due to their speed and specificity; however, they must first be qualified as meeting or exceeding the sensitivity of the compendial method. We present herein a NAT method for the detection of that circumvents the need for live spp. in the test procedure by instead being qualified using spp. genomic DNA. We have demonstrated a lower limit of detection that exceeds the regulatory requirements set by Health Canada. This assay is now being used to screen clinical cell therapy products manufactured at our center.
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http://dx.doi.org/10.1016/j.omtm.2020.01.009DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7044503PMC
June 2020

Identification of a CD8+ T-cell response to a predicted neoantigen in malignant mesothelioma.

Oncoimmunology 2020 3;9(1):1684713. Epub 2019 Nov 3.

National Centre for Asbestos Related Disease, School of Medicine and Pharmacology, University of Western Australia, Nedlands, Australia.

Neoantigens present unique and specific targets for personalized cancer immunotherapy strategies. Given the low mutational burden yet immunotherapy responsiveness of malignant mesothelioma (MM) when compared to other carcinogen-induced malignancies, identifying candidate neoantigens and T cells that recognize them has been a challenge. We used pleural effusions to gain access to MM tumor cells as well as immune cells in order to characterize the tumor-immune interface in MM. We characterized the landscape of potential neoantigens from SNVs identified in 27 MM patients and performed whole transcriptome sequencing of cell populations from 18 patient-matched pleural effusions. IFNγ ELISpot was performed to detect a CD8+ T cell responses to predicted neoantigens in one patient. We detected a median of 68 (range 7-258) predicted neoantigens across the samples. Wild-type non-binding to mutant binding predicted neoantigens increased risk of death in a model adjusting for age, sex, smoking status, histology and treatment (HR: 33.22, CI: 2.55-433.02, = .007). Gene expression analysis indicated a dynamic immune environment within the pleural effusions. TCR clonotypes increased with predicted neoantigen burden. A strong activated CD8+ T-cell response was identified for a predicted neoantigen produced by a spontaneous mutation in the gene. Despite the challenges associated with the identification of bonafide neoantigens, there is growing evidence that these molecular changes can provide an actionable target for personalized therapeutics in difficult to treat cancers. Our findings support the existence of candidate neoantigens in MM despite the low mutation burden of the tumor, and may present improved treatment opportunities for patients.
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http://dx.doi.org/10.1080/2162402X.2019.1684713DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6959430PMC
November 2019

The genetics of phenotypic plasticity. XVII. Response to climate change.

Evol Appl 2020 Feb 31;13(2):388-399. Epub 2019 Oct 31.

Department of Biology University of Florida Gainesville FL USA.

The world is changing at a rapid rate, threatening extinction for a large part of the world's biota. One potential response to those altered conditions is to evolve so as to be able to persist in place. Such evolution includes not just traits themselves, but also the phenotypic plasticity of those traits. We used individual-based simulations to explore the potential of an evolving phenotypic plasticity to increase the probability of persistence in the response to either a step change or continual, directional change in the environment accompanied by within-generation random environmental fluctuations. Populations could evolve by altering both their nonplastic and plastic genetic components. We found that phenotypic plasticity enhanced survival and adaptation if that plasticity was not costly. If plasticity was costly, for it to be beneficial the phenotypic magnitude of plasticity had to be great enough in the initial generations to overcome those costs. These results were not sensitive to either the magnitude of the within-generation correlation between the environment of development and the environment of selection or the magnitude of the environmental fluctuations, except for very small phenotypic magnitudes of plasticity. So, phenotypic plasticity has the potential to enhance survival; however, more data are needed on the ubiquity of trait plasticity, the extent of costs of plasticity, and the rate of mutational input of genetic variation for plasticity.
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http://dx.doi.org/10.1111/eva.12876DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6976953PMC
February 2020

Teprotumumab for the Treatment of Active Thyroid Eye Disease.

N Engl J Med 2020 01;382(4):341-352

From Cedars-Sinai Medical Center, Los Angeles (R.S.D., A.P.); Johannes Gutenberg University Medical Center, Mainz (G.J.K.), and University Hospital Essen, Essen (A.E.) - both in Germany; Horizon Therapeutics, Lake Forest, IL (S.S., E.H.Z.T., R.P., J.W.S., T.V., R.J.H.); University of Tennessee Health Science Center, Memphis (J.C.F., B.T.F.); University of Pisa, Pisa (C.M., M.M., A.A.), and Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan (M.S.) - both in Italy; Oregon Health and Sciences University, Portland (R.D.); Medical College of Wisconsin Eye Institute, Milwaukee (G.J.H.); Eye Wellness Center-Neuro-Eye Clinical Trials, Houston (J.S., R.T.); Kellogg Eye Center-Michigan Medicine (C.N., T.J.S.) and University of Michigan Medical School (T.J.S.) - both in Ann Arbor; and Bascom Palmer Eye Institute, Miami (S.W.).

Background: Thyroid eye disease is a debilitating, disfiguring, and potentially blinding periocular condition for which no Food and Drug Administration-approved medical therapy is available. Strong evidence has implicated the insulin-like growth factor I receptor (IGF-IR) in the pathogenesis of this disease.

Methods: In a randomized, double-masked, placebo-controlled, phase 3 multicenter trial, we assigned patients with active thyroid eye disease in a 1:1 ratio to receive intravenous infusions of the IGF-IR inhibitor teprotumumab (10 mg per kilogram of body weight for the first infusion and 20 mg per kilogram for subsequent infusions) or placebo once every 3 weeks for 21 weeks; the last trial visit for this analysis was at week 24. The primary outcome was a proptosis response (a reduction in proptosis of ≥2 mm) at week 24. Prespecified secondary outcomes at week 24 were an overall response (a reduction of ≥2 points in the Clinical Activity Score plus a reduction in proptosis of ≥2 mm), a Clinical Activity Score of 0 or 1 (indicating no or minimal inflammation), the mean change in proptosis across trial visits (from baseline through week 24), a diplopia response (a reduction in diplopia of ≥1 grade), and the mean change in overall score on the Graves' ophthalmopathy-specific quality-of-life (GO-QOL) questionnaire across trial visits (from baseline through week 24; a mean change of ≥6 points is considered clinically meaningful).

Results: A total of 41 patients were assigned to the teprotumumab group and 42 to the placebo group. At week 24, the percentage of patients with a proptosis response was higher with teprotumumab than with placebo (83% [34 patients] vs. 10% [4 patients], P<0.001), with a number needed to treat of 1.36. All secondary outcomes were significantly better with teprotumumab than with placebo, including overall response (78% of patients [32] vs. 7% [3]), Clinical Activity Score of 0 or 1 (59% [24] vs. 21% [9]), the mean change in proptosis (-2.82 mm vs. -0.54 mm), diplopia response (68% [19 of 28] vs. 29% [8 of 28]), and the mean change in GO-QOL overall score (13.79 points vs. 4.43 points) (P≤0.001 for all). Reductions in extraocular muscle, orbital fat volume, or both were observed in 6 patients in the teprotumumab group who underwent orbital imaging. Most adverse events were mild or moderate in severity; two serious events occurred in the teprotumumab group, of which one (an infusion reaction) led to treatment discontinuation.

Conclusions: Among patients with active thyroid eye disease, teprotumumab resulted in better outcomes with respect to proptosis, Clinical Activity Score, diplopia, and quality of life than placebo; serious adverse events were uncommon. (Funded by Horizon Therapeutics; OPTIC ClinicalTrials.gov number, NCT03298867, and EudraCT number, 2017-002763-18.).
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http://dx.doi.org/10.1056/NEJMoa1910434DOI Listing
January 2020

Sample Tracking Using Unique Sequence Controls.

J Mol Diagn 2020 02 16;22(2):141-146. Epub 2019 Dec 16.

Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada. Electronic address:

Sample tracking and identity are essential when processing multiple samples in parallel. Sequencing applications often involve high sample numbers, and the data are frequently used in a clinical setting. As such, a simple and accurate intrinsic sample tracking process through a sequencing pipeline is essential. Various solutions have been implemented to verify sample identity, including variant detection at the start and end of the pipeline using arrays or genotyping, bioinformatic comparisons, and optical barcoding of samples. None of these approaches are optimal. To establish a more effective approach using genetic barcoding, we developed a panel of unique DNA sequences cloned into a common vector. A unique DNA sequence is added to the sample when it is first received and can be detected by PCR and/or sequencing at any stage of the process. The control sequences are approximately 200 bases long with low identity to any sequence in the National Center for Biotechnology Information nonredundant database (<30 bases) and contain no long homopolymer (>7) stretches. When a spiked next-generation sequencing library is sequenced, sequence reads derived from this control sequence are generated along with the standard sequencing run and are used to confirm sample identity and determine cross-contamination levels. This approach is used in our targeted clinical diagnostic whole-genome and RNA-sequencing pipelines and is an inexpensive, flexible, and platform-agnostic solution.
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http://dx.doi.org/10.1016/j.jmoldx.2019.10.011DOI Listing
February 2020

Extinction filters mediate the global effects of habitat fragmentation on animals.

Science 2019 12;366(6470):1236-1239

Imperial College London, Silwood Park Campus, Buckhurst Road, Ascot SL5 7PY, UK.

Habitat loss is the primary driver of biodiversity decline worldwide, but the effects of fragmentation (the spatial arrangement of remaining habitat) are debated. We tested the hypothesis that forest fragmentation sensitivity-affected by avoidance of habitat edges-should be driven by historical exposure to, and therefore species' evolutionary responses to disturbance. Using a database containing 73 datasets collected worldwide (encompassing 4489 animal species), we found that the proportion of fragmentation-sensitive species was nearly three times as high in regions with low rates of historical disturbance compared with regions with high rates of disturbance (i.e., fires, glaciation, hurricanes, and deforestation). These disturbances coincide with a latitudinal gradient in which sensitivity increases sixfold at low versus high latitudes. We conclude that conservation efforts to limit edges created by fragmentation will be most important in the world's tropical forests.
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http://dx.doi.org/10.1126/science.aax9387DOI Listing
December 2019

A Prospective Clinical Study on Implant Survival at 1-Year Post-Loading of a Bone-Level Tapered Implant in Private Practice: Multicentered Study.

Compend Contin Educ Dent 2019 Nov/Dec;40(10):678-691

Private Practice limited to Periodontics and Implant Dentistry, Philadelphia, Pennsylvania.

This non-interventional study evaluated the implant survival and success of a new bone-level tapered implant design in seven private dental practices in the United States. One hundred subjects in need of implant(s) were enrolled according to all cleared indications. After implant surgery, subjects were followed for a period of 1-year post-loading. Treatment planning, implant stability, radiographic evaluation of bone levels, soft-tissue characteristics, clinician satisfaction, and adverse events were assessed. A total of 184 implants were placed, of which 172 were evaluable at 1-year follow-up. Of the 172 evaluable implants, 169 survived and were successful at 1-year post-loading. Of 152 implants with radiographs at 1 year, 90% showed no bone remodeling or <1 mm bone loss. Overall clinician satisfaction was high across all centers. Normal soft-tissue profiles were reported around the implants with improvement in color, form, and mucosal attachment at 1 year. In a "real-world" setting this observational study demonstrated high implant survival and success, stable crestal bone levels, high clinician satisfaction, and a low incidence of adverse events.
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November 2019

Relationship between conservation biology and ecology shown through machine reading of 32,000 articles.

Conserv Biol 2020 06 10;34(3):721-732. Epub 2019 Dec 10.

Department of Life Sciences, Imperial College London, Silwood Park campus, Buckhurst Road, Ascot, Berkshire, SL5 7PY, U.K.

Conservation biology was founded on the idea that efforts to save nature depend on a scientific understanding of how it works. It sought to apply ecological principles to conservation problems. We investigated whether the relationship between these fields has changed over time through machine reading the full texts of 32,000 research articles published in 16 ecology and conservation biology journals. We examined changes in research topics in both fields and how the fields have evolved from 2000 to 2014. As conservation biology matured, its focus shifted from ecology to social and political aspects of conservation. The 2 fields diverged and now occupy distinct niches in modern science. We hypothesize this pattern resulted from increasing recognition that social, economic, and political factors are critical for successful conservation and possibly from rising skepticism about the relevance of contemporary ecological theory to practical conservation.
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http://dx.doi.org/10.1111/cobi.13435DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7317371PMC
June 2020

A survey of genes modulated by host cell infection.

Microb Genom 2020 02 29;6(2). Epub 2019 Oct 29.

Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, N1G 2W1, Canada.

Here, we report comprehensive transcriptomic profiles from under conditions that mimic the first stages of bacterial infection in a highly differentiated adenocarcinoma epithelial cell line. Our transcriptomic adenocarcinoma approach allows us to measure the expression dynamics and regulation of bacterial virulence and response factors in real time, and is a novel strategy for clarifying the role of infection in colorectal cancer (CRC) progression. Our data show that: (i) infection alters metabolic and functional pathways in , allowing the bacterium to adapt to the host-imposed milieu; (ii) infection also stimulates the expression of genes required to help induce and promote a hypoxic and inflammatory microenvironment in the host; and (iii) invasion occurs by a haematogenous route of infection. Our study identifies novel gene targets from that are activated during invasion and which may aid in determining how this species invades and promotes disease within the human gastrointestinal tract. These invasion-specific genes may be useful as biomarkers for CRC progression in a host and could also assist in the development of new diagnostic tools and treatments (such as vaccines or small molecule drug targets), which will be able to combat infection and inflammation in the host while circumventing the potential problem of tolerization.
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http://dx.doi.org/10.1099/mgen.0.000300DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7067209PMC
February 2020

Brain pharmacology of intrathecal antisense oligonucleotides revealed through multimodal imaging.

JCI Insight 2019 10 17;4(20). Epub 2019 Oct 17.

Biogen, Cambridge, Masschusetts, USA.

Intrathecal (IT) delivery and pharmacology of antisense oligonucleotides (ASOs) for the CNS have been successfully developed to treat spinal muscular atrophy. However, ASO pharmacokinetic (PK) and pharmacodynamic (PD) properties remain poorly understood in the IT compartment. We applied multimodal imaging techniques to elucidate the IT PK and PD of unlabeled, radioactively labeled, or fluorescently labeled ASOs targeting ubiquitously expressed or neuron-specific RNAs. Following lumbar IT bolus injection in rats, all ASOs spread rostrally along the neuraxis, adhered to meninges, and were partially cleared to peripheral lymph nodes and kidneys. Rapid association with the pia and arterial walls preceded passage of ASOs across the glia limitans, along arterial intramural basement membranes, and along white-matter axonal bundles. Several neuronal and glial cell types accumulated ASOs over time, with evidence of probable glial accumulation preceding neuronal uptake. IT doses of anti-GluR1 and anti-Gabra1 ASOs markedly reduced the mRNA and protein levels of their respective neurotransmitter receptor protein targets by 2 weeks and anti-Gabra1 ASOs also reduced binding of the GABAA receptor PET ligand 18F-flumazenil in the brain over 4 weeks. Our multimodal imaging approaches elucidate multiple transport routes underlying the CNS distribution, clearance, and efficacy of IT-dosed ASOs.
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http://dx.doi.org/10.1172/jci.insight.129240DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6824309PMC
October 2019