Publications by authors named "Amanda J Cox"

89 Publications

Corrigendum: Probiotics, Anticipation Stress, and the Acute Immune Response to Night Shift.

Front Immunol 2021 21;12:713237. Epub 2021 Jun 21.

School of Medical Science and Menzies Health Institute QLD, Griffith University, Gold Coast, QLD, Australia.

[This corrects the article DOI: 10.3389/fimmu.2020.599547.].
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http://dx.doi.org/10.3389/fimmu.2021.713237DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8259507PMC
June 2021

Temporal changes in blood oxidative stress biomarkers across the menstrual cycle and with oral contraceptive use in active women.

Eur J Appl Physiol 2021 Sep 9;121(9):2607-2620. Epub 2021 Jun 9.

Griffith Sports Science, Griffith University, Gold Coast Campus, Gold Coast, QLD, 4222, Australia.

Purpose: To examine the temporal changes in blood oxidative stress biomarkers in recreationally-trained women that were naturally-cycling (WomenNC) or using oral contraceptives (WomenOC) across one month.

Methods: Blood samples were acquired at three timepoints of the menstrual cycle (1: early-follicular, 2: late-follicular and 3: mid-luteal) and oral contraceptive packet (1: InactiveOC, 2: Mid-activeOC and 3: Late-activeOC) for determination of estradiol, progesterone, oxidative stress, C-reactive protein (CRP) and other cardiometabolic biomarkers in plasma and serum.

Results: There was a Group by Time effect on estradiol (p < 0.001, partial η = 0.64) and progesterone (p < 0.001, partial η = 0.77). Malondialdehyde, lipid hydroperoxides and CRP concentrations were higher in WomenOC during Late-activeOC compared to InactiveOC (+ 96%, + 23% and + 104%, respectively, p < 0.05). However, there were no changes in these biomarkers across the menstrual cycle in WomenNC (p > 0.05). At all timepoints (i.e., 1, 2 and 3), WomenOC had elevated lipid hydroperoxides (+ 28, + 48% and + 50%) and CRP (+ 71%, + 117% and + 130%) compared to WomenNC (p < 0.05, partial η > 0.25). There was no Group by Time effect on non-enzymatic antioxidants or glutathione peroxidase; however, glutathione peroxidase was lower in WomenOC, i.e., main effect of group (p < 0.05, partial η > 0.20).

Conclusion: These findings demonstrate that WomenOC not only have higher oxidative stress and CRP than WomenNC, but also a transient increase across one month of habitual oral contraceptive use. Since changes in oxidative stress and CRP often relate to training stress and recovery, these outcomes may have implications to workload monitoring practices in female athletes.
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http://dx.doi.org/10.1007/s00421-021-04734-0DOI Listing
September 2021

A YOLO based software for automated detection and analysis of rodent behaviour in the open field arena.

Comput Biol Med 2021 07 15;134:104474. Epub 2021 May 15.

School of Medical Science, Griffith University, Southport, 4217, Australia.

Rodent models are important in mechanistic studies of the physiological and pathophysiological determinants of behaviour. The Open Field Test (OFT) is one of the most commonly utilised tests to assess rodent behaviour in a novel open environment. The key variables assessed in an OFT are general locomotor activity and exploratory behaviours and can be assessed manually or by automated systems. Although several automated systems exist, they are often expensive, difficult to use, or limited in the type of video that can be analysed. Here we describe a machine-learning algorithm - dubbed Cosevare - that uses a trained YOLOv3 DNN to identify and track movement of mice in the open-field arena. We validated Cosevare's capacity to accurately track locomotive and exploratory behaviour in 10 videos, comparing outputs generated by Cosevare with analysis by 5 manual scorers. Behavioural differences between control mice and those with diet-induced obesity (DIO) were also documented. We found the YOLOv3 based tracker to be accurate at identifying and tracking the mice within the open-field arena and in instances with variable backgrounds. Additionally, kinematic and spatial-based analysis demonstrated highly consistent scoring of locomotion, centre square duration (CSD) and entries (CSE) between Cosevare and manual scorers. Automated analysis was also able to distinguish behavioural differences between healthy control and DIO mice. The study found that a YOLOv3 based tracker is able to easily track mouse behaviour in the open field arena and supports machine learning as a potential future alternative for the assessment of animal behaviour in a wide range of species in differing environments and behavioural tests.
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http://dx.doi.org/10.1016/j.compbiomed.2021.104474DOI Listing
July 2021

The influence of exercise training volume alterations on the gut microbiome in highly-trained middle-distance runners.

Eur J Sport Sci 2021 Jun 13:1-9. Epub 2021 Jun 13.

Menzies Health Institute Queensland, Griffith University, Queensland, Australia.

The aim of this study was to determine the influence of training volume alterations on diversity and composition of the gut microbiome in a free-living cohort of middle-distance runners. Fourteen highly-trained middle-distance runners ( = 8 men; [Formula: see text]O = 70.1 ± 4.3 ml·kg·min;  = 6 women, [Formula: see text]O: 59.0 ± 3.2 ml·kg·min) completed three weeks of normal training (NormTr), three weeks of high-volume training (HVolTr; a 10, 20 and 30% increase in training volume during each successive week from NormTr), and a one-week taper (TaperTr; 55% exponential reduction in training volume from HVolTr week three). Faecal samples were collected before and immediately after each training phase to quantify alpha-diversity and composition of the gut microbiome. A three-day diet record was collected during each training phase and a maximal incremental running test was completed after each training phase. Results showed no significant changes in nutritional intake, alpha-diversity, or global microbial composition following HVolTr or TaperTr compared to NormTr ('s > 0.05). Following HVolTr, there was a significant decrease in Pasterellaceae ( = 0.03), ( = 0.02) ( = 0.03) ( = 0.02) and ( = 0.03), while ( = 0.03) significantly increased. These changes did not return to NormTr levels following TaperTr. This study shows that the alpha-diversity and global composition of the gut microbiome were unaffected by changes in training volume. However, an increase in training volume led to several changes at the lower taxonomy levels that did not return to pre-HVolTr levels following a taper period.
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http://dx.doi.org/10.1080/17461391.2021.1933199DOI Listing
June 2021

Probiotics, Anticipation Stress, and the Acute Immune Response to Night Shift.

Front Immunol 2020 28;11:599547. Epub 2021 Jan 28.

School of Medical Science and Menzies Health Institute QLD, Griffith University, Gold Coast, QLD, Australia.

Introduction: Sleep disturbance and sleep disruption are associated with chronic, low grade inflammation and may underpin a range of chronic diseases in night shift workers. Through modulation of the intestinal microbiota, probiotic supplements may moderate the effects of sleep disruption on the immune system. The aim of this study was to examine 14 days of daily probiotic supplementation on the acute response of acute phase proteins and immune markers to sleep disruption associated with night shift work (Australia and New Zealand Clinical Trials Registry: 12617001552370).

Methods: Individuals (mean age 41 ± 11 yrs; 74% female) performing routine night shift were randomly assigned to a probiotic group (1 × 10 colony forming units (CFU) DDS-1 or 1 × 10 CFU subsp. UABla-12) or placebo (n= 29 per group). Participants undertook a 14-day supplementation period that coincided with a period of no night shifts followed by two consecutive night shifts. Blood samples were collected prior to the start of supplementation (V1), prior to commencing the first night shift (V2), after the first night shift (V3) and after the second night shift (V4). Serum was assessed for markers of stress (cortisol), acute phase response (C reactive protein (CRP), erythrocyte sedimentation rate, pentraxin), adhesion markers (serum E-selectin, mucosal vascular addressin cell adhesion molecule 1 (MAdCAM-1), and serum cytokines (interleukin (IL)-1ra, IL-1β, IL-6, tumor necrosis factor (TNF)-α, IL-10). Sleep quality was assessed with the Pittsburgh Sleep Quality Index (PSQI) and a Fitbit activity tracker.

Results: The groups were well balanced on key markers and the probiotic strains were well tolerated. The 14-day supplementation period that coincided with typical night-day sleep-wake cycles leading up to night shift (V1 to V2) was associated with significant changes in the placebo group in the concentration of serum cortisol (p = 0.01), pentraxin (p = 0.001), MAdCAM-1 (p = 0.001), and IL-1ra (p=0.03). In contrast, probiotic supplementation moderated changes in these serum markers from V1 to V2. No significant interaction effects (time by group) were observed for the serum markers prior to and after night shift work following probiotic supplementation due to the substantial changes in the serum markers that occurred during the normal sleep period from V1 to V2.

Conclusions: Probiotics may moderate the effects of anticipatory stress on the immune system in the lead up to night shift.
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http://dx.doi.org/10.3389/fimmu.2020.599547DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7877220PMC
June 2021

Prospective validation study of prognostic biomarkers to predict adverse outcomes in patients with COVID-19: a study protocol.

BMJ Open 2021 01 6;11(1):e044497. Epub 2021 Jan 6.

Division of Primary Care, University of Nottingham, Nottingham, UK.

Introduction: Accurate triage is an important first step to effectively manage the clinical treatment of severe cases in a pandemic outbreak. In the current COVID-19 global pandemic, there is a lack of reliable clinical tools to assist clinicians to perform accurate triage. Host response biomarkers have recently shown promise in risk stratification of disease progression; however, the role of these biomarkers in predicting disease progression in patients with COVID-19 is unknown. Here, we present a protocol outlining a prospective validation study to evaluate the biomarkers' performance in predicting clinical outcomes of patients with COVID-19.

Methods And Analysis: This prospective validation study assesses patients infected with COVID-19, in whom blood samples are prospectively collected. Recruited patients include a range of infection severity from asymptomatic to critically ill patients, recruited from the community, outpatient clinics, emergency departments and hospitals. Study samples consist of peripheral blood samples collected into RNA-preserving (PAXgene/Tempus) tubes on patient presentation or immediately on study enrolment. Real-time PCR (RT-PCR) will be performed on total RNA extracted from collected blood samples using primers specific to host response gene expression biomarkers that have been previously identified in studies of respiratory viral infections. The RT-PCR data will be analysed to assess the diagnostic performance of individual biomarkers in predicting COVID-19-related outcomes, such as viral pneumonia, acute respiratory distress syndrome or bacterial pneumonia. Biomarker performance will be evaluated using sensitivity, specificity, positive and negative predictive values, likelihood ratios and area under the receiver operating characteristic curve.

Ethics And Dissemination: This research protocol aims to study the host response gene expression biomarkers in severe respiratory viral infections with a pandemic potential (COVID-19). It has been approved by the local ethics committee with approval number 2020/ETH00886. The results of this project will be disseminated in international peer-reviewed scientific journals.
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http://dx.doi.org/10.1136/bmjopen-2020-044497DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7789210PMC
January 2021

Reliability of a point-of-care device to determine oxidative stress in whole blood before and after acute exercise: A practical approach for the applied sports sciences.

J Sports Sci 2021 Mar 10;39(6):673-682. Epub 2020 Nov 10.

Griffith Sports Science, Griffith University, Gold Coast, Australia.

Measuring alterations in redox homoeostasis in athletes can provide insights into their responses to training such as adaptations or fatigued states. However, redox monitoring is impractical in athletes given the time burden of venepuncture and subsequent laboratory assays. The ability of point-of-care tests (POC): 1) Free Oxygen Radical Test (FORT) and 2) Free Oxygen Radical Defence (FORD), to reliably measure whole blood oxidative stress between days and after exercise is unknown as well as their relationship with laboratory measures (F2-isoprostanes, total antioxidant capacity; TAC). Participants completed two trials performed on separate days comprising blood sampling at rest (n=22) and after treadmill-running (n=14). Between-day CVs for FORT (4.6%) and FORD (4.8%) were acceptable at rest. There was no difference in the between-day magnitude of change in any biomarker from pre- to post-exercise (p>0.05), yet the within-trial change in FORD was variable (trial one: +4.5%, p=0.15; trial two: +6.3%, p<0.05). TAC and FORD were significantly correlated pre- and post-exercise (r=~0.53, p<0.05), whereas F2-isoprostanes and FORT had a significant correlation pre-exercise only (r=0.45, p=0.03). Overall, the POC tests are reliable and could be used for baseline longitudinal redox monitoring. More data is required on POC tests for assessing redox perturbations induced by exercise.
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http://dx.doi.org/10.1080/02640414.2020.1840755DOI Listing
March 2021

The Gut Microbiome of Adults with Allergic Rhinitis Is Characterised by Reduced Diversity and an Altered Abundance of Key Microbial Taxa Compared to Controls.

Int Arch Allergy Immunol 2021 24;182(2):94-105. Epub 2020 Sep 24.

School of Medical Science, Griffith University, Southport, Queensland, Australia.

Introduction: Unique gut microbial colonisation patterns are associated with the onset of allergic disease in infants; however, there is insufficient evidence to determine if aberrant microbial composition patterns persist in adult allergic rhinitis (AR) sufferers.

Objective: To compare the gut microbiome composition between adult AR sufferers and controls.

Methods: Gut microbial composition in stool samples was compared between 57 adult AR sufferers (39.06 ± 13.29 years) and 23 controls (CG; 36.55 ± 10.51 years) via next-generation sequencing of the V3-V4 hypervariable regions of the 16S rRNA gene. Taxonomic classification and identity assignment was performed using a reference-based approach with the NCBI database of 16S rRNA gene sequences.

Results: Species richness determined via the Shannon index was significantly reduced in the AR cohort compared to the CG (4.35 ± 0.59 in AR vs. 4.65 ± 0.55 in CG, p = 0.037); trends for reductions in operational taxonomic unit (OTU) counts, inverse Simpson, and CHAO1 diversity indices were also noted. Bacteroidetes (p = 0.014) was significantly more abundant in the AR group than in the CG. In contrast, the Firmicutes phylum was significantly less abundant in the AR group than in the CG (p = 0.006). An increased abundance of Parabacteroides (p = 0.008) and a reduced abundance of Oxalobacter (p = 0.001) and Clostridiales (p = 0.005) were also observed in the AR cohort compared to the CG.

Conclusion: Adult AR sufferers have a distinct gut microbiome profile, marked by a reduced microbial diversity and altered abundance of certain microbes compared to controls. The results of this study provide evidence that unique gut microbial patterns occur in AR sufferers in adulthood and warrant further examination in the form of mechanistic studies.
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http://dx.doi.org/10.1159/000510536DOI Listing
August 2021

Fucoidan Supplementation Restores Fecal Lysozyme Concentrations in High-Performance Athletes: A Pilot Study.

Mar Drugs 2020 Aug 4;18(8). Epub 2020 Aug 4.

School of Medical Science, Griffith University, Southport, QLD 4215, Australia.

Nutritional strategies to help promote immune competence are of particular interest for a range of population groups. This study aimed to assess the potential impacts of fucoidan, a seaweed-derived bioactive polysaccharide, on gut markers of immunity and inflammation. A group of professional team-sport athletes were selected for inclusion in the study given the recognized potential for intense physical activity to induce alterations in immune function. A retrospective analysis was performed on stored fecal samples which had been collected from professional team-sport athletes ( = 22) and healthy adults ( = 11) before and after seven days of supplementation with fucoidan (/ extract, 1 g/d). Fecal concentrations of calprotectin, secretory immunoglobulin A (sIgA) and lysozyme were determined using enzyme-linked immunosorbent assays. The supplement was well tolerated by participants with no adverse events reported. At baseline, fecal lysozyme concentrations were ~73% higher in the healthy adults compared to the professional athletes ( = 0.001). For the professional athletes, a significant (~45%) increase in fecal lysozyme was observed following the supplementation period ( = 0.001). These data suggest that fucoidan supplementation may have the potential to promote the secretion of antimicrobial peptides in specific population groups and contribute to the regulation of mucosal immune health.
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http://dx.doi.org/10.3390/md18080412DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7460205PMC
August 2020

Trimethylamine -oxide: heart of the microbiota-CVD nexus?

Nutr Res Rev 2021 06 28;34(1):125-146. Epub 2020 Jul 28.

School of Medical Science, Griffith University, Southport, QLD, Australia.

We critically review potential involvement of trimethylamine N-oxide (TMAO) as a link between diet, the gut microbiota and CVD. Generated primarily from dietary choline and carnitine by gut bacteria and hepatic flavin-containing mono-oxygenase (FMO) activity, TMAO could promote cardiometabolic disease when chronically elevated. However, control of circulating TMAO is poorly understood, and diet, age, body mass, sex hormones, renal clearance, FMO3 expression and genetic background may explain as little as 25 % of TMAO variance. The basis of elevations with obesity, diabetes, atherosclerosis or CHD is similarly ill-defined, although gut microbiota profiles/remodelling appear critical. Elevated TMAO could promote CVD via inflammation, oxidative stress, scavenger receptor up-regulation, reverse cholesterol transport (RCT) inhibition, and cardiovascular dysfunction. However, concentrations influencing inflammation, scavenger receptors and RCT (≥100 µm) are only achieved in advanced heart failure or chronic kidney disease (CKD), and greatly exceed pathogenicity of <1-5 µm levels implied in some TMAO-CVD associations. There is also evidence that CVD risk is insensitive to TMAO variance beyond these levels in omnivores and vegetarians, and that major TMAO sources are cardioprotective. Assessing available evidence suggests that modest elevations in TMAO (≤10 µm) are a non-pathogenic consequence of diverse risk factors (ageing, obesity, dyslipidaemia, insulin resistance/diabetes, renal dysfunction), indirectly reflecting CVD risk without participating mechanistically. Nonetheless, TMAO may surpass a pathogenic threshold as a consequence of CVD/CKD, secondarily promoting disease progression. TMAO might thus reflect early CVD risk while providing a prognostic biomarker or secondary target in established disease, although mechanistic contributions to CVD await confirmation.
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http://dx.doi.org/10.1017/S0954422420000177DOI Listing
June 2021

Comparison of skin biopsy sample processing and storage methods on high dimensional immune gene expression using the Nanostring nCounter system.

Diagn Pathol 2020 May 15;15(1):57. Epub 2020 May 15.

School of Medical Science and Menzies Health Institute QLD, Griffith University, Gold Coast, Queensland, 4222, Australia.

Background: Digital multiplex gene expression profiling is overcoming the limitations of many tissue-processing and RNA extraction techniques for the reproducible and quantitative molecular classification of disease. We assessed the effect of different skin biopsy collection/storage conditions on mRNA quality and quantity and the NanoString nCounter™ System's ability to reproducibly quantify the expression of 730 immune genes from skin biopsies.

Methods: Healthy human skin punch biopsies (n = 6) obtained from skin sections from four patients undergoing routine abdominoplasty were subject to one of several collection/storage protocols, including: i) snap freezing in liquid nitrogen and transportation on dry ice; ii) RNAlater (ThermoFisher) for 24 h at room temperature then stored at - 80 °C; iii) formalin fixation with further processing for FFPE blocks; iv) DNA/RNA shield (Zymo) stored and shipped at room temperature; v) placed in TRIzol then stored at - 80 °C; vi) saline without RNAse for 24 h at room temperature then stored at - 80 °C. RNA yield and integrity was assessed following extraction via NanoDrop, QuantiFluor with RNA specific dye and a Bioanalyser (LabChip24, PerkinElmer). Immune gene expression was analysed using the NanoString Pancancer Immune Profiling Panel containing 730 genes.

Results: Except for saline, all protocols yielded total RNA in quantities/qualities that could be analysed by NanoString nCounter technology, although the quality of the extracted RNA varied widely. Mean RNA integrity was highest from samples that were placed in RNALater (RQS 8.2 ± 1.15), with integrity lowest from the saline stored sample (RQS < 2). There was a high degree of reproducibility in the expression of immune genes between all samples with the exception of saline, with the number of detected genes at counts < 100, between 100 and 1000 and > 10,000 similar across extraction protocols.

Conclusions: A variety of processing methods can be used for digital immune gene expression profiling in mRNA extracted from skin that are comparable to snap frozen skin specimens, providing skin cancer clinicians greater opportunity to supply skin specimens to tissue banks. NanoString nCounter technology can determine gene expression in skin biopsy specimens with a high degree of sensitivity despite lower RNA yields and processing methods that may generate poorer quality RNA. The increased sensitivity of digital gene expression profiling continues to expand molecular pathology profiling of disease.
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http://dx.doi.org/10.1186/s13000-020-00974-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7229590PMC
May 2020

Key viral immune genes and pathways identify elite athletes with URS.

Exerc Immunol Rev 2020 ;26:56-78

School of Medical Science and Menzies Health Institute QLD, Griffith University, Southport, QLD, Australia, Griffith University, QLD, Australia.

Purpose: Habitual intense exercise may increase the incidence of upper respiratory symptoms (URS) in elite athletes. This study investigated whether immune gene expression could identify gene markers that discriminate athletes with a higher prevalence of URS.

Methods: This cross-sectional analysis of elite Australian athletes from various sports investigated whether athletes retrospectively reporting URS for two days or more in a month (n=38), had an altered immune gene expression profile compared with asymptomatic athletes (n=33). Peripheral blood samples were collected during Olympic selection events with corresponding URS data collected for the one-month period before sampling. Digital immune gene expression analysis was undertaken using the NanoString PanCancer Immune Profiling panel.

Results: Fifty immune genes were differentially expressed between the groups (p<0.05) and approximately 78% of these genes were more highly expressed in athletes reporting URS. Many of these genes were interferon-stimulated genes or genes involved in the Jak/Stat signalling pathway. Only interferon alpha inducible protein 27 (IFI27), an interferon stimulated gene involved in viral response, remained significantly higher in athletes reporting URS (log2 fold-difference=2.49, odds ratio 1.02 per unit increase; p<0.01) post-adjustment and discriminated athletes reporting URS from asymptomatic athletes with 78% accuracy.

Conclusions: Expression of IFI27 could differentiate athletes reporting URS from asymptomatic athletes, a gene that is upregulated in the immune response to viral infection. Upregulation of viral signalling pathways provides novel information on the potential aetiology of URS in elite Olympic athletes.
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March 2020

Recovery of Lactobacillus casei strain Shirota (LcS) from faeces with 14 days of fermented milk supplementation in healthy Australian adults.

Asia Pac J Clin Nutr 2019 ;28(4):734-739

School of Medical Science, Griffith University, Southport, QLD, Australia.

Background And Objectives: A key measure for classifying bacteria as a probiotic is the ability to survive gastric transport and be recoverable in faeces. The aim of this study was to determine whether Lactobacillus casei strain Shirota (LcS) could be recovered in the faeces of healthy young Australian adults following ingestion of a fermented milk drink.

Methods And Study Design: A cohort of 25 healthy individuals (male/female: 14/11; age: 29.3±6.6 years; BMI: 25.3±2.7 kg/m2, mean±SD) ingested one 65 ml bottle of fermented milk containing 6.5×109 LcS live cells daily for 14 days. Participants provided a faecal sample at day 0, day 7 (mid-supplementation), day 14 (end of supplementation) and 14 days after cessation of the supplement (day 28) for assessment of the number of viable LcS via microbial culture on selective media with confirmation using a colony-direct polymerase chain reaction and species-specific primers.

Results: The supplement was well tolerated by participants. No LcS colonies were recovered from participants prior to ingestion of the fermented milk drink. All participants had recoverable LcS colonies at day 7 and day 14, with a mean recovery of 6.5±1.1 and 6.4±1.1 log10 CFU/g of faeces (mean±SD) at each time point respectively. LcS was detectable in only one sample at 14 days following the cessation of supplementation.

Conclusions: Live LcS is recoverable in faeces from healthy Australian adults following daily ingestion of a fermented milk drink.
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http://dx.doi.org/10.6133/apjcn.201912_28(4).0009DOI Listing
May 2020

Selection of microbial biomarkers with genetic algorithm and principal component analysis.

BMC Bioinformatics 2019 Dec 10;20(Suppl 6):413. Epub 2019 Dec 10.

School of Medical Science, Griffith University, Gold Coast, Australia.

Background: Principal components analysis (PCA) is often used to find characteristic patterns associated with certain diseases by reducing variable numbers before a predictive model is built, particularly when some variables are correlated. Usually, the first two or three components from PCA are used to determine whether individuals can be clustered into two classification groups based on pre-determined criteria: control and disease group. However, a combination of other components may exist which better distinguish diseased individuals from healthy controls. Genetic algorithms (GAs) can be useful and efficient for searching the best combination of variables to build a prediction model. This study aimed to develop a prediction model that combines PCA and a genetic algorithm (GA) for identifying sets of bacterial species associated with obesity and metabolic syndrome (Mets).

Results: The prediction models built using the combination of principal components (PCs) selected by GA were compared to the models built using the top PCs that explained the most variance in the sample and to models built with selected original variables. The advantages of combining PCA with GA were demonstrated.

Conclusions: The proposed algorithm overcomes the limitation of PCA for data analysis. It offers a new way to build prediction models that may improve the prediction accuracy. The variables included in the PCs that were selected by GA can be combined with flexibility for potential clinical applications. The algorithm can be useful for many biological studies where high dimensional data are collected with highly correlated variables.
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http://dx.doi.org/10.1186/s12859-019-3001-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6904994PMC
December 2019

A correlation-based network for biomarker discovery in obesity with metabolic syndrome.

BMC Bioinformatics 2019 Dec 10;20(Suppl 6):477. Epub 2019 Dec 10.

Menzies Health Institute Queensland, Griffith University, Gold Coast, Australia.

Background: Obesity is associated with chronic activation of the immune system and an altered gut microbiome, leading to increased risk of chronic disease development. As yet, no biomarker profile has been found to distinguish individuals at greater risk of obesity-related disease. The aim of this study was to explore a correlation-based network approach to identify existing patterns of immune-microbiome interactions in obesity.

Results: The current study performed correlation-based network analysis on five different datasets obtained from 11 obese with metabolic syndrome (MetS) and 12 healthy weight men. These datasets included: anthropometric measures, metabolic measures, immune cell abundance, serum cytokine concentration, and gut microbial composition. The obese with MetS group had a denser network (total number of edges, n = 369) compared to the healthy network (n = 299). Within the obese with MetS network, biomarkers from the immune cell abundance group was found to be correlated to biomarkers from all four other datasets. Conversely in the healthy network, immune cell abundance was only correlated with serum cytokine concentration and gut microbial composition. These observations suggest high involvement of immune cells in obese with MetS individuals. There were also three key hubs found among immune cells in the obese with MetS networks involving regulatory T cells, neutrophil and cytotoxic cell abundance. No hubs were present in the healthy network.

Conclusion: These results suggest a more complex interaction of inflammatory markers in obesity, with high connectivity of immune cells in the obese with MetS network compared to the healthy network. Three key hubs were identified in the obese with MetS network, involving Treg, neutrophils and cytotoxic cell abundance. Compared to a t-test, the network approach offered more meaningful results when comparing obese with MetS and healthy weight individuals, demonstrating its superiority in exploratory analysis.
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http://dx.doi.org/10.1186/s12859-019-3064-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6905012PMC
December 2019

Digital Immune Gene Expression Profiling Discriminates Allergic Rhinitis Responders from Non-Responders to Probiotic Supplementation.

Genes (Basel) 2019 11 4;10(11). Epub 2019 Nov 4.

School of Medical Science, Griffith University, Queensland, 4215, Australia.

Probiotic supplementation for eight weeks with a multi-strain probiotic by individuals with allergic rhinitis (AR) reduced overall symptom severity, the frequency of medication use and improved quality of life. The purported mechanism of action is modulation of the immune system. This analysis examined changes in systemic and mucosal immune gene expression in a subgroup of individuals, classified as either responders or non-responders based on improvement of AR symptoms in response to the probiotic supplement. Based on established criteria of a beneficial change in the mini-rhinoconjunctivitis quality of life questionnaire (mRQLQ), individuals with AR were classified as either responders or non-responders. Systemic and mucosal immune gene expression was assessed using nCounter PanCancer Immune Profiling (Nanostring Technologies, Seattle, WA, USA) kit on blood samples and a nasal lysate. There were 414 immune genes in the blood and 312 immune genes in the mucosal samples expressed above the background threshold. Unsupervised hierarchical clustering of immune genes separated responders from non-responders in blood and mucosal samples at baseline and after supplementation, with key T-cell immune genes differentially expressed between the groups. Striking differences in biological processes and pathways were evident in nasal mucosa but not blood in responders compared to non-responders. These findings support the use of network approaches to understand probiotic-induced changes to the immune system.
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http://dx.doi.org/10.3390/genes10110889DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6896104PMC
November 2019

Modulation of Allergic Inflammation in the Nasal Mucosa of Allergic Rhinitis Sufferers With Topical Pharmaceutical Agents.

Front Pharmacol 2019 29;10:294. Epub 2019 Mar 29.

Menzies Health Institute Queensland, School of Medical Science, Griffith University, Southport, QLD, Australia.

Allergic rhinitis (AR) is a chronic upper respiratory disease estimated to affect between 10 and 40% of the worldwide population. The mechanisms underlying AR are highly complex and involve multiple immune cells, mediators, and cytokines. As such, the development of a single drug to treat allergic inflammation and/or symptoms is confounded by the complexity of the disease pathophysiology. Complete avoidance of allergens that trigger AR symptoms is not possible and without a cure, the available therapeutic options are typically focused on achieving symptomatic relief. Topical therapies offer many advantages over oral therapies, such as delivering greater concentrations of drugs to the receptor sites at the source of the allergic inflammation and the reduced risk of systemic side effects. This review describes the complex pathophysiology of AR and identifies the mechanism(s) of action of topical treatments including antihistamines, steroids, anticholinergics, decongestants and chromones in relation to AR pathophysiology. Following the literature review a discussion on the future therapeutic strategies for AR treatment is provided.
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http://dx.doi.org/10.3389/fphar.2019.00294DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6455085PMC
March 2019

Protein-coding variants implicate novel genes related to lipid homeostasis contributing to body-fat distribution.

Nat Genet 2019 03 18;51(3):452-469. Epub 2019 Feb 18.

Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA.

Body-fat distribution is a risk factor for adverse cardiovascular health consequences. We analyzed the association of body-fat distribution, assessed by waist-to-hip ratio adjusted for body mass index, with 228,985 predicted coding and splice site variants available on exome arrays in up to 344,369 individuals from five major ancestries (discovery) and 132,177 European-ancestry individuals (validation). We identified 15 common (minor allele frequency, MAF ≥5%) and nine low-frequency or rare (MAF <5%) coding novel variants. Pathway/gene set enrichment analyses identified lipid particle, adiponectin, abnormal white adipose tissue physiology and bone development and morphology as important contributors to fat distribution, while cross-trait associations highlight cardiometabolic traits. In functional follow-up analyses, specifically in Drosophila RNAi-knockdowns, we observed a significant increase in the total body triglyceride levels for two genes (DNAH10 and PLXND1). We implicate novel genes in fat distribution, stressing the importance of interrogating low-frequency and protein-coding variants.
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http://dx.doi.org/10.1038/s41588-018-0334-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6560635PMC
March 2019

GWAS and colocalization analyses implicate carotid intima-media thickness and carotid plaque loci in cardiovascular outcomes.

Nat Commun 2018 12 3;9(1):5141. Epub 2018 Dec 3.

Department of Medicine, University of Mississippi Medical Center, Jackson, MS, 39216, USA.

Carotid artery intima media thickness (cIMT) and carotid plaque are measures of subclinical atherosclerosis associated with ischemic stroke and coronary heart disease (CHD). Here, we undertake meta-analyses of genome-wide association studies (GWAS) in 71,128 individuals for cIMT, and 48,434 individuals for carotid plaque traits. We identify eight novel susceptibility loci for cIMT, one independent association at the previously-identified PINX1 locus, and one novel locus for carotid plaque. Colocalization analysis with nearby vascular expression quantitative loci (cis-eQTLs) derived from arterial wall and metabolic tissues obtained from patients with CHD identifies candidate genes at two potentially additional loci, ADAMTS9 and LOXL4. LD score regression reveals significant genetic correlations between cIMT and plaque traits, and both cIMT and plaque with CHD, any stroke subtype and ischemic stroke. Our study provides insights into genes and tissue-specific regulatory mechanisms linking atherosclerosis both to its functional genomic origins and its clinical consequences in humans.
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http://dx.doi.org/10.1038/s41467-018-07340-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6277418PMC
December 2018

The Post-Exercise Inflammatory Response to Repeated-Sprint Running in Hypoxia.

J Sports Sci Med 2018 12 20;17(4):533-538. Epub 2018 Nov 20.

Griffith Sports Physiology and Performance, School of Allied Health Sciences, Griffith University, Gold Coast, Queensland, Australia.

This study investigated the acute inflammatory response to a repeat-sprint training session in hypoxia. Eleven amateur team-sport athletes completed a repeat-sprint training in hypoxia (RSH) protocol (4 sets of 4x4-s running sprints) in both normoxia and normobaric hypoxia (FO 0.145 to simulate an altitude of 3000 m) on separate days. Participants provided venous blood samples prior to (PRE), immediately after (POST), and 3 h after (3 h) completion of the protocol, and capillary blood lactate samples were taken upon arrival, at PRE, and at POST. Distance was recorded for each sprint. Venous blood samples were analysed to determine plasma concentrations of cytokines IL-1β, IL-1ra, IL-6, IL-8, IL-10, and TNFα. There was no interaction or main effect of condition for any cytokine (p > 0.05). However, time effects indicated that IL-10 was decreased by an average of 19% across the two experimental trials at 3 h compared to POST (p = 0.04), IL-6 increased by 55% from PRE to POST (p = 0.03) then decreased by 43% from POST to 3 h (p = 0.02), and IL-8 decreased by 30% from PRE to POST (p = 0.04) and was further reduced at 3 h compared to POST (by an additional 23%; p = 0.02). A time × condition interaction (p = 0.03) indicated that lactate was higher in hypoxia. There was no interaction effect or effect of condition for sprint distance (p > 0.05). These results suggest that team-sport athletes can perform a RSH session without increasing inflammation when compared to the same training session performed in normoxia.
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6243612PMC
December 2018

Distinct Gene Expression Patterns between Nasal Mucosal Cells and Blood Collected from Allergic Rhinitis Sufferers.

Int Arch Allergy Immunol 2018 19;177(1):29-34. Epub 2018 Jun 19.

School of Medical Science, Griffith University, Southport, Queensland, Australia.

Background: Investigations of gene expression in allergic rhinitis (AR) typically rely on invasive nasal biopsies (site of inflammation) or blood samples (systemic immunity) to obtain sufficient genetic material for analysis. New methodologies to circumvent the need for invasive sample collection offer promise to further the understanding of local immune mechanisms relevant in AR.

Methods: A within-subject design was employed to compare immune gene expression profiles obtained from nasal washing/brushing and whole blood samples collected during peak pollen season. Twelve adults (age: 46.3 ± 12.3 years) with more than a 2-year history of AR and a confirmed grass pollen allergy participated in the study. Gene expression analysis was performed using a panel of 760 immune genes with the NanoString nCounter platform on nasal lavage/brushing cell lysates and compared to RNA extracted from blood.

Results: A total of 355 genes were significantly differentially expressed between sample types (9.87 to -9.71 log2 fold change). The top 3 genes significantly upregulated in nasal lysate samples were Mucin 1 (MUC1), Tight Junction Protein 1 (TJP1), and Lipocalin-2 (LCN2). The top 3 genes significantly upregulated in blood samples were cluster of differentiation 3e (CD3E), FYN Proto-Oncogene Src Family Tyrosine Kinase (FYN) and cluster of differentiation 3d (CD3D).

Conclusions: Overall, the blood and nasal lavage samples showed vastly distinct gene expression profiles and functional gene pathways which reflect their anatomical and functional origins. Evaluating immune gene expression of the nasal mucosa in addition to blood samples may be beneficial in understanding AR pathophysiology and response to allergen challenge.
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http://dx.doi.org/10.1159/000489609DOI Listing
September 2018

A Specifically Designed Multispecies Probiotic Supplement Relieves Seasonal Allergic Rhinitis Symptoms.

J Altern Complement Med 2018 Aug 21;24(8):833-840. Epub 2018 May 21.

1 Menzies Health Institute of Queensland, School of Medical Science, Griffith University , Gold Coast, Queensland, Australia .

Background: Probiotics are purported to reduce symptoms of allergic rhinitis. This study sought to determine the proportion of participants with an improvement in the mini Rhinoconjunctivitis Quality of Life Questionnaire (mRQLQ) in response to a multispecies probiotic supplement with a Simon Two-Stage design.

Methods: This study was based on a Simon Two-Stage Design for p-p = 0.18 to account for seasonal variation in symptoms. Under this design, ≥10 patients are required to exhibit an improvement in quality-of-life scores to determine that there was sufficient activity for the supplement to be considered effective. Participants consumed a probiotic supplement (Ecologic AllergyCare; probiotikpur) twice daily for 8 weeks. The primary outcome measure was based on a change in mRQLQ scores following supplementation. Secondary outcomes include assessment of change in symptoms and medication usage with a twice-weekly symptom and medication diary, nasal congestion by rhinomanometry, and total serum Immunoglobulin E (IgE) and specific IgE for Bermuda grass.

Results: A total of 40 participants completed the study. A total of 25 participants (63%, 49-76%, p < 0.001; mean, 95% confidence interval, p-value) out of 40 participants had a clinically meaningful response to treatment based on assessment of mRQLQ. On average, mRQLQ scores changed from 2.83 ± 1.51 at baseline to 1.66 ± 1.36 at week 4 and 1. 38 ± 1.13 at week 8 (p < 0.01) (mean ± SD, p-value). Sum of individual symptom scores and overall symptom scores over the course of treatment was significantly reduced (p = 0.036 and p = 0.039, respectively). A moderate reduction in frequency of allergy-related medication use in the final 4 weeks of supplementation period was observed (52.5% weeks 0-4 to 41.4% weeks 4-8; average proportion of total diary responses, p = 0.085). The supplement was largely well tolerated by participants at the dose provided.

Conclusions: The proportion of participants exhibiting improvement in quality-of-life metrics warrants continued investigation in the form of a phase III placebo-controlled trial.
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http://dx.doi.org/10.1089/acm.2017.0342DOI Listing
August 2018

Immune Response in Women during Exercise in the Heat: A Spotlight on Oral Contraception.

J Sports Sci Med 2018 06 14;17(2):229-236. Epub 2018 May 14.

Griffith Sports Physiology and Performance, School of Allied Health Sciences, Griffith University, Gold Coast, Australia.

This study compared the immune and stress response of oral contraceptive users (WomenOC; n = 9) to normally-menstruating women (WomenNM; n = 9) at rest and during exercise in temperate (TEMP; 22°C) and hot (HEAT; 35°C) conditions. Participants performed a 3-stage cycling trial in each condition at 90% (Stage 1; 30 min), 135% (Stage 2; 15 min), and 180% (Stage 3; 7.5 min) of lactate threshold 1. C-reactive protein (CRP) and immune cell counts were measured at rest, and serum cytokines (IL-1β, IL-1RA, IL-6, IL-8, IL-10, and TNF-α) and salivary cortisol were evaluated before and after exercise in both the TEMP and HEAT conditions. There were no differences in resting immune cell counts between groups, nor any differences in cortisol or any of the pro- or anti-inflammatory cytokines measured at rest or after completion of the exercise trials (p > 0.05). However, a trend for a higher resting CRP concentration was observed in WomenOC relative to WomenNM (1.102 ± 1.182 and 0.326 ± 0.228, respectively, p = 0.07). The results obtained in the current study indicate similar immunoendocrine function in WomenOC and WomenNM both at rest and after exercise in temperate and hot environments.
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5950740PMC
June 2018

Associations of coronary artery calcified plaque density with mortality in type 2 diabetes: the Diabetes Heart Study.

Cardiovasc Diabetol 2018 05 11;17(1):67. Epub 2018 May 11.

Center for Diabetes Research, Wake Forest School of Medicine, Winston-Salem, NC, USA.

Background: Coronary artery calcified plaque (CAC) is strongly predictive of cardiovascular disease (CVD) events and mortality, both in general populations and individuals with type 2 diabetes at high risk for CVD. CAC is typically reported as an Agatston score, which is weighted for increased plaque density. However, the role of CAC density in CVD risk prediction, independently and with CAC volume, remains unclear.

Methods: We examined the role of CAC density in individuals with type 2 diabetes from the family-based Diabetes Heart Study and the African American-Diabetes Heart Study. CAC density was calculated as mass divided by volume, and associations with incident all-cause and CVD mortality [median follow-up 10.2 years European Americans (n = 902, n = 286 deceased), 5.2 years African Americans (n = 552, n = 93 deceased)] were examined using Cox proportional hazards models, independently and in models adjusted for CAC volume.

Results: In European Americans, CAC density, like Agatston score and volume, was consistently associated with increased risk of all-cause and CVD mortality (p ≤ 0.002) in models adjusted for age, sex, statin use, total cholesterol, HDL, systolic blood pressure, high blood pressure medication use, and current smoking. However, these associations were no longer significant when models were additionally adjusted for CAC volume. CAC density was not significantly associated with mortality, either alone or adjusted for CAC volume, in African Americans.

Conclusions: CAC density is not associated with mortality independent from CAC volume in European Americans and African Americans with type 2 diabetes.
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http://dx.doi.org/10.1186/s12933-018-0714-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5946410PMC
May 2018

Non-typeable detection in the lower airways of patients with lung cancer and chronic obstructive pulmonary disease.

Multidiscip Respir Med 2018 9;13:11. Epub 2018 Apr 9.

2School of Medicine, Griffith University, Southport, Australia.

Background: Chronic airway inflammation and hypersensitivity to bacterial infection may contribute to lung cancer pathogenesis. Previous studies have demonstrated that nontypeable (NTHi) is the most common colonizing bacteria in the lower airways of patients with COPD. The objective of this study was to determine the presence of NTHi and immunoglobulin concentrations in patients with lung cancer, COPD and controls.

Methods: Serum and bronchial wash samples were collected from patients undergoing diagnostic bronchoscopy. Total IgE, IgG and specific NTHi IgG were measured by enzyme linked immunosorbent assay. Bronchial wash samples were examined for the presence of NTHi via PCR.

Results: Out of the 60 patients: 20 had confirmed Lung Cancer, 27 had COPD only and 13 were used as Controls. NTHi was detected in the lower airways of all three groups (Lung Cancer 20%; COPD 22% and Controls 15%). Total IgE was highest in Lung Cancer subjects followed by COPD and control subjects (mean ± SD: 870 ± 944, 381 ± 442, 159 ± 115). Likewise total IgG was higher in Lung cancer (Mean ± SD: 6.99 ± 1.8) patients compared to COPD (Mean ± SD: 5.43 ± 2).

Conclusions: The lack of difference in NTHi and specific antibodies between the three groups makes it less likely that NTHi has an important pathogenetic role in subjects with Lung Cancer. However the detection of higher IgE antibody in Lung Cancer subjects identifies a possible mechanism for carcinogenesis in these subjects and warrants further study.
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http://dx.doi.org/10.1186/s40248-018-0123-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5890355PMC
April 2018

Publisher Correction: Protein-altering variants associated with body mass index implicate pathways that control energy intake and expenditure in obesity.

Nat Genet 2018 05;50(5):766-767

Department of Genetic Epidemiology, University of Regensburg, Regensburg, Germany.

In the version of this article originally published, one of the two authors with the name Wei Zhao was omitted from the author list and the affiliations for both authors were assigned to the single Wei Zhao in the author list. In addition, the ORCID for Wei Zhao (Department of Biostatistics and Epidemiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA) was incorrectly assigned to author Wei Zhou. The errors have been corrected in the HTML and PDF versions of the article.
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http://dx.doi.org/10.1038/s41588-018-0082-3DOI Listing
May 2018

Upper Respiratory Symptoms, Gut Health and Mucosal Immunity in Athletes.

Sports Med 2018 03;48(Suppl 1):65-77

Menzies Health Institute Queensland and School of Medical Science, Griffith University, Griffith Health Gold Coast Campus, Southport, QLD, 4222, Australia.

Upper respiratory symptoms remain the most common illness in athletes. Upper respiratory symptoms during heavy training and competition may impair performance. Preventing illness is the primary reason for the use of supplements, such as probiotics and prebiotics, for maintaining or promoting gut health and immune function. While exercise-induced perturbations in the immune system may increase susceptibility to illness and infection, growing evidence indicates that upper respiratory symptoms are related to a breakdown in the homeostatic regulation of the mucosal immune system of the airways. Balancing protection of the respiratory tract with normal physiological functioning requires dynamic orchestration between a wide array of immune parameters. The intestinal microbiota regulates extra-intestinal immunity via the common mucosal immune system and new evidence implicates the microbiota of the nose, mouth and respiratory tract in upper respiratory symptoms. Omics' approaches now facilitate comprehensive profiling at the molecular and proteomic levels to reveal new pathways and molecules of immune regulation. New targets may provide for personalised nutritional and training interventions to maintain athlete health.
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http://dx.doi.org/10.1007/s40279-017-0846-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5790851PMC
March 2018

Protein-altering variants associated with body mass index implicate pathways that control energy intake and expenditure in obesity.

Nat Genet 2018 01 22;50(1):26-41. Epub 2017 Dec 22.

Department of Genetic Epidemiology, University of Regensburg, Regensburg, Germany.

Genome-wide association studies (GWAS) have identified >250 loci for body mass index (BMI), implicating pathways related to neuronal biology. Most GWAS loci represent clusters of common, noncoding variants from which pinpointing causal genes remains challenging. Here we combined data from 718,734 individuals to discover rare and low-frequency (minor allele frequency (MAF) < 5%) coding variants associated with BMI. We identified 14 coding variants in 13 genes, of which 8 variants were in genes (ZBTB7B, ACHE, RAPGEF3, RAB21, ZFHX3, ENTPD6, ZFR2 and ZNF169) newly implicated in human obesity, 2 variants were in genes (MC4R and KSR2) previously observed to be mutated in extreme obesity and 2 variants were in GIPR. The effect sizes of rare variants are ~10 times larger than those of common variants, with the largest effect observed in carriers of an MC4R mutation introducing a stop codon (p.Tyr35Ter, MAF = 0.01%), who weighed ~7 kg more than non-carriers. Pathway analyses based on the variants associated with BMI confirm enrichment of neuronal genes and provide new evidence for adipocyte and energy expenditure biology, widening the potential of genetically supported therapeutic targets in obesity.
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http://dx.doi.org/10.1038/s41588-017-0011-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5945951PMC
January 2018
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