Alan L. James’s research while affiliated with Sir Charles Gairdner Hospital and other places

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Publications (425)


Cross-sectional and longitudinal associations of DXA-measured body composition with lung function in middle-aged Australians: The Busselton Healthy Ageing Study
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May 2025

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Obesity Research & Clinical Practice

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John P. Walsh

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Spirometric diagnostic criteria for PRISm, airflow limitation and normal spirometry.
Demographic characteristics of adults ≥40 years with PRISm compared to those with airflow limitation and normal spirometry.
Comorbidities and symptoms of adults ≥40 years with PRISm compared to those with airflow limitation and normal spirometry.
Treatments reported by adults ≥40 years with PRISm compared to those with airflow limitation and normal spirometry.
Spirometry results in adults ≥40 years with PRISm compared to those with airflow limitation and normal spirometry.

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Prevalence and characteristics of adults with preserved ratio impaired spirometry (PRISm): Data from the BOLD Australia study
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January 2025

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26 Reads

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2 Citations

Background: Individuals with Preserved Ratio Impaired Spirometry (PRISm), defined as FEV1/FVC ≥0.7 and FEV1 <80% predicted, are at higher risk of developing COPD. However, data for Australian adults are limited. We aimed to describe prevalence of PRISm and its relationship with clinical characteristics in Australia. Method: Data from the Burden of Lung Disease (BOLD) Australia study of randomly selected adults aged ≥40 years from six sites was classified into airflow limitation, PRISm, or normal spirometry groups. Demographic, clinical characteristics, and lung function were compared between groups. Results: Of the study sample (n = 3518), 387 (11%) had PRISm, 549 (15.6%) had airflow limitation, and 2582 (73.4%) had normal spirometry. PRISm was more common in Indigenous Australian adults. Adults with PRISm had more frequent respiratory symptoms, more comorbidities, greater health burden and poorer quality of life than those with normal spirometry. Pre- and post-bronchodilator FEV1 and FVC were lower in adults with PRISm than those with airflow limitation. Adults with PRISm were less likely to use respiratory medicine than those with airflow limitation (OR = 0.56, 95% CI 0.38–0.81). Conclusions: PRISm was present in 11% of adults in this study and they had similar respiratory symptoms and health burden as adults with airflow limitation.

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Prenatal Origins of Obstructive Airway Disease: Starting on the Wrong Trajectory?

December 2024

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21 Reads

From the results of well‐performed population health studies, we now have excellent data demonstrating that deficits in adult lung function may be present early in life, possibly as a result of developmental disorders, incurring a lifelong risk of obstructive airway diseases such as asthma and chronic obstructive pulmonary disease. Suboptimal fetal development results in intrauterine growth restriction and low birth weight at term (an outcome distinct from preterm complications), which are associated with subsequent obstructive disease. Numerous prenatal exposures and disorders compromise fetal development and these are summarized herein. Various physiological, structural, and mechanical abnormalities may result from prenatal disruption, including changes to airway smooth muscle structure–function, goblet cell biology, airway stiffness, geometry of the bronchial tree, lung parenchymal structure and mechanics, respiratory skeletal muscle contraction, and pulmonary inflammation. The literature therefore supports the need for early life intervention to prevent or correct growth defects, which may include simple nutritional or antioxidant therapy. © 2024 American Physiological Society. Compr Physiol 14:5729‐5762, 2024.



Trends in smoking initiation and cessation over a century in two Australian cohorts

September 2024

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52 Reads

Background Historical data on smoking can enhance our comprehension of the effectiveness of past tobacco control policies and play a key role in developing targeted public health interventions. This study was undertaken to assess trends in smoking initiation and cessation in Australia for the period 1910–2005. Methods Rates of smoking initiation and cessation were calculated for participants in two population-based cohorts, the Busselton Health Study and the Tasmanian Longitudinal Health Study. The effects of time trends, gender and age group were evaluated. Results Of the 29,971 participants, 56.8% ever smoked. In males, over the period 1910–1999, the rate of smoking initiation in young adolescents remained high with a peak in the 1970s; in older adolescents it peaked in the 1940s and then declined; in young adults it showed a steady decline. In females, the rate of smoking initiation in young adolescents rose sharply in the 1960s and peaked in the 1970s, in older adolescents it increased throughout the period, and in young adults it declined after 1970. In the period 1930–2005, 27.3% of 9,605 people aged 36–50 years who smoked ceased smoking. Rates of cessation in this age group increased throughout but decreased in males after 1990 and plateaued around 2000 in females. Conclusion Our findings show substantial variation in the efficacy of tobacco control policies across age groups, with a notable lack of success among the younger population.



Genomic characteristics of airway mucosal bacteria
a Culture collection phylogeny based on average nucleotide identities between genomes with 1000 bp fragment length. Putatively novel species are highlighted in red (indicating that it is not related to any species in the TypeMat DB or NCBI Prok DB (P < 0.05) when assessed using MIGA and not assigned to a known species or incongruent species assignment using gtdbtk). Greyed-out isolates are not fully supported by MIGA and gtdbtk. Genome completeness and contamination are displayed as a bar chart. AMR finder was used to identify antimicrobial resistance genes at the protein level (red panel). Virulence factors were identified using the VFDB and Ariba databases and binned into 15 categories (heatmap). The asthma status of the host is indicated in the black asthma/control panel. Cultivation conditions are indicated in green circles for selected growth media, blue rectangles for aerobic, and white rectangles for anaerobic cultivation. Positive Gram staining for GNB, GNC, GPB, GPC, and other Gram staining is shown in black circles. The neuraminidase activity was tested if a blue star was present and was filled for the positive test and white for a negative test. b Taxonomic novelty as calculated by MIGA using TypeMat reference. The scatterplot shows support (P-value, vertical axis) for each taxon relative to complementary hypotheses that this taxon is a previously known one (red markers) or a novel one (cyan markers) at each taxonomic level (horizontal axis). Many of the isolate collections constitute novel species within known genera. c Composition of bacteria isolated and cultivated from five subjects. Counts are shown for all lineages from species level (outer circle) to phylum level (inner circle) in squared brackets. The ETE3 toolkit was used to fetch taxonomic lineages for all genera of cultured isolates¹⁰¹. The number of unique species was summed up and visualised along with their lineages using Krona tools¹⁰².
Ecology and structure of airway microbial communities
a Mapping of the 50 most abundant OTUs onto 126 novel airway isolates. Isolates are grouped into 16 clusters according to the distance and branching order of their inferred Kegg Ontology (KO) gene content. OTU/isolate nt identity is shown as 95–97% (light blue), 97–99% (medium blue), and 100% (dark blue). The complex relationship between OTUs and isolates reflects multiple copies of the 16S rRNA gene in different taxa, but in general, captures KO phylogenetic structures. b Comparison of abundance (left) and prevalence right) of bacterial OTUs in populations from northern (CELF) and southern (BUS) hemispheres. The species distribution is similar between the CELF and BUS studies. c Comparison of abundance (left) and prevalence right) of bacterial OTUs in the posterior oropharynx (ptOP) and the left lower lobe (LLL) in CELF subjects. The relative abundance of organisms in ptOP is very similar to those in the LLL, although absolute abundance is an order of magnitude lower in the LLL. Lower abundance OTUs in the CELF dataset are more prevalent in the upper than lower airways. d Spearman correlations between the abundance of organisms in the CELF ptOP samples, showing a high degree of positive and negative relationships between OTUs that is the basis of WGCNA network analysis. Common phyla are colour coded at the top of the matrix, and WGCNA modules (named for the most abundant membership) are at the bottom. Network module membership may be dominated by a single phylum (e.g., the Haemophilus or Streptococcus modules) or contain mixed phyla (e.g., the Veillonella module).
Microbial features of airway dysbiosis
a Main drivers of Dirichlet-multinomial model-based airway communities. b Beta diversity based on Bray-Curtis dissimilarity principal coordinate analysis showing separation of the two communities. c Consistency of airway community assignment between samples of the same and different donors (left) and sampling sites (right). d Alpha diversity measures and correlations. e Univariate associations of CELF 16S samples binned on phylum level to metadata. f Proportion of community assignments between ptOP samples of different study origins, sampling sites and disease groups. g relative abundance of most abundant genera based on CELF samples 16S rRNA. h Univariate metabolite associations based on binning of CELF 16S rRNA sequences onto isolate annotation.
Gene and metabolite abundance during airway epithelial development
a Global gene expression was measured 7 times over 28 days in an air-liquid model of epithelial differentiation (monolayer to ciliated epithelium). A total of 2,553 transcripts, summarised by 8 core temporal profiles, showed significant variation in abundance during mucociliary development. Hallmark functional roles are shown for each cluster. Clusters CL2, CL3, CL4 and CL5 show late peaks of expression and contain genes that can interact with the microbiome. Upregulated chemokines and immune-function genes are also noted within the clusters. b Metabolites (square) measured in the supernatant of the fully differentiated airway cells were linked to genes (circle) identified in bacterial isolates. Arrows indicate if the reactions were reversible or irreversible, with metabolites as substrates and products. These networks were built based on KEGG pathways. c Binary heatmap displaying the presence (1) or absence (0) of genes (columns) identified in the genomic sequences of bacterial isolates (rows). Bacterial isolates are organised into Kegg Ontology phylogeny clusters (see Fig. 2). Gene annotations (top) indicate the frequency of the gene: ‘frequent’ for genes in >75% of isolates, ‘intermediate’ for genes in 25–75% of isolates and ‘rare’ for those in <25% of isolates.
Genomic attributes of airway commensal bacteria and mucosa

February 2024

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228 Reads

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2 Citations

Communications Biology

Microbial communities at the airway mucosal barrier are conserved and highly ordered, in likelihood reflecting co-evolution with human host factors. Freed of selection to digest nutrients, the airway microbiome underpins cognate management of mucosal immunity and pathogen resistance. We show here the initial results of systematic culture and whole-genome sequencing of the thoracic airway bacteria, identifying 52 novel species amongst 126 organisms that constitute 75% of commensals typically present in heathy individuals. Clinically relevant genes encode antimicrobial synthesis, adhesion and biofilm formation, immune modulation, iron utilisation, nitrous oxide (NO) metabolism and sphingolipid signalling. Using whole-genome content we identify dysbiotic features that may influence asthma and chronic obstructive pulmonary disease. We match isolate gene content to transcripts and metabolites expressed late in airway epithelial differentiation, identifying pathways to sustain host interactions with microbiota. Our results provide a systematic basis for decrypting interactions between commensals, pathogens, and mucosa in lung diseases of global significance.



Quantification of smooth muscle in human airways by polarization-sensitive optical coherence tomography requires correction for perichondrium

January 2024

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2 Citations

AJP Lung Cellular and Molecular Physiology

Quantifying airway smooth muscle (ASM) in patients with asthma raises the possibility of improved and personalized disease management. Endobronchial polarization-sensitive optical coherence tomography (PS-OCT) is a promising quantitative imaging approach that is in the early stages of clinical translation. To date, only animal tissues have been used to assess the accuracy of PS-OCT to quantify absolute (rather than relative) ASM in cross-sections with directly matched histological cross-sections as validation. We report the use of whole fresh human and pig airways to perform a detailed side-by-side qualitative and quantitative validation of PS-OCT against gold standard histology. We matched and quantified 120 sections from five human and seven pig (small and large) airways and linked PS-OCT signatures of ASM to the tissue structural appearance in histology. Notably, we found that human cartilage perichondrium can share with ASM the properties of birefringence and circumferential alignment of fibers, making it a significant confounder for ASM detection. Measurements not corrected for perichondrium overestimated ASM content several-fold (p<0.001, paired t-test). After careful exclusion of perichondrium, we found a strong positive correlation (r=0.96, p<0.00001) of ASM area measured by PS-OCT and histology, supporting the method's application in human subjects. Matching human histology further indicated that PS-OCT allows conclusions on the intra-layer composition and in turn potential contractile capacity of ASM bands. Together these results form a reliable basis for future clinical studies.


Citations (67)


... Nevertheless, not all PRISm patients will acquire COPD [4,5], and the condition's reversibility highlights the importance of early intervention to manage lung function deterioration. Epidemiological data indicates that PRISm affects between 5 and 20% of the population [6][7][8][9][10][11]. Without timely intervention, the progression of these cases could significantly increase the prevalence of COPD, thus placing a greater strain on social and healthcare systems. ...

Reference:

The association between non-high-density lipoprotein cholesterol to high-density lipoprotein cholesterol ratio and preserved ratio impaired spirometry: NHANES 2007–2012
Prevalence and characteristics of adults with preserved ratio impaired spirometry (PRISm): Data from the BOLD Australia study

... En adición, el estudio informó de un aumento no significativo de organismos resistentes a la azitromicina en el esputo de los pacientes tratados con azitromicina, en comparación con placebo, pero no tuvo la potencia adecuada para evaluar plenamente este efecto. Otro estudio mostró que el agregar durante 52 semanas de Azitromicina a CSI-LABA contribuyó en alcanzar la remisión de la enfermedad, un efecto independiente del fenotipo 97 . ...

Azithromycin Induced Asthma Remission in Adults With Persistent Uncontrolled Asthma: A Secondary Analysis of a Randomized, Double-Blind, Placebo-Controlled Trial
  • Citing Article
  • February 2024

Chest

... It is less prevalent in the Western part of the world. [7,9,[17][18][19][20] In this study, 53.92% of patients were nonsmokers and 46.08% of patients were smokers, these findings are consistent with another Indian study done by Mahmood et al. [21] Among NS-COPD patients, a history of pulmonary tuberculosis and exposure to biomass smoke were the most common causes. These findings may be attributable to the high prevalence of tuberculosis in India and the use of biomass fuel in women living in rural and semi-urban regions. ...

COPD in Never-Smokers: BOLD Australia Study

... There has been increasing interest in the predictive ability of spirometry parameters and respiratory symptoms to identify those at risk of COPD [6][7][8][9], a physiological state often referred to as pre-COPD [10]. Recently, TAN et al. [6], using data from the Tasmanian Longitudinal Health Study, identified optimal z-score thresholds for spirometry parameters to predict incidence of chronic airflow obstruction. ...

Can We Use Lung Function Thresholds and Respiratory Symptoms to Identify Pre-COPD? A Prospective, Population-based Cohort Study
  • Citing Article
  • January 2024

American Journal of Respiratory and Critical Care Medicine

... While CRDs are not curable, treatments can help manage symptoms, improve breathing, and enhance overall wellbeing. In contrast, breathlessness is most commonly caused by COPD, Asthma, and chronic heart failure [5,6]. However, Women are more asthma-prone than men [7]. ...

Risk factors and clinical characteristics of breathlessness in Australian adults: Data from the BOLD Australia study

... Chronic cough exhibits varying characteristics across different age groups. In children and adolescents, it is often associated with asthma, upper airway cough syndrome, or viral infections (Zhang et al. 2024). Conversely, in adult and elderly populations, chronic cough is more frequently linked to environmental exposures, smoking, chronic bronchitis, or even medication side effects (Suresh et al. 2025). ...

Association of novel adult cough subclasses with clinical characteristics and lung function across six decades of life in a prospective, community-based cohort in Australia: an analysis of the Tasmanian Longitudinal Health Study (TAHS)
  • Citing Article
  • December 2023

The Lancet Respiratory Medicine

... We also COPD is one of the chronic diseases with a high mortality rate, whose prevalence has been increasing for decades [3][4][5]. The different outcomes of COPD, such as emphysema, chronic bronchitis, asthma, cough, expectoration, wheezing, etc., can significantly affect the patient's quality of life [73,74]. Malnutrition is one of the most important comorbidities in patients with COPD, which can worsen the above-mentioned consequences and the quality of life [2,75,76]. ...

Respiratory Symptoms, Disease Burden, and Quality of Life in Australian Adults According to GOLD Spirometry Grades: Data from the BOLD Australia Study

... In order to predict Low Birth Weight (LBW), a worldwide health concern with implications for neonatal death and morbidity, the study compares the algorithms for logistic regression and gradient boosting (Gandhi et al. 2023;Illsley and Mitchell 1984;Wang et al. 2023). In order to prevent, identify, and treat diseases that lead to LBW, prior research has shown how important data-driven approaches are in the healthcare industry (Raffa et al. 2023). ...

The airway smooth muscle layer is structurally abnormal in low birth weight infants – implications for obstructive disease
  • Citing Article
  • October 2023

European Respiratory Journal

... Although the treatment efficacy of benralizumab in obese allergic patients is conflicting, these data certainly pave a way to pursue further clinical trials evaluating the effectiveness of benralizumab in obese individuals with allergic respiratory diseases. The reduced efficacy of mepolizumab (anti-IL-5) in severe asthmatics with obesity was reported, 101,102 and the odds of achieving clinical remission decreased by 59% for those with obesity. 102 While proof has shown that mepolizumab administration effectively reduces blood eosinophil counts and asthma exacerbations in obese asthma patients, the improvement in lung function, such as pre-bronchodilator FEV 1 or FVC% predicted, is lower compared with non-obese patients. ...

Biologics (mepolizumab and omalizumab) induced remission in severe asthma patients

... Examining 56 DMCs identified from DMRs in models with maternal asthma during pregnancy and ever as the primary exposures, we found 35 unique DMCs were associated with gene expression of 4 genes. One gene of particular interest is HOXA5, which has previously been associated with organogenesis [38], lung function in adults [39,40] and mental disorder phenotypes [41] ( Table S22). The two other identified genes (KDM2B and KCTD11) were found to be involved with neurodevelopmental disorders [42] and cancer [43], respectively. ...

Multi-ancestry genome-wide association analyses improve resolution of genes and pathways influencing lung function and chronic obstructive pulmonary disease risk

Nature Genetics