Search bioRxiv⌕ Search

bioRxiv · 10.1101/193920

Systemic Markers of Adaptive and Innate Immunity Are Associated with COPD Severity and Spirometric Disease Progression

Abstract

The progression of chronic obstructive pulmonary disease (COPD) is associated with marked alterations in circulating immune cell populations, but no studies have characterized alterations in these cell types across the full spectrum of lung function impairment in current and former smokers. In 6,299 subjects from the COPDGene and ECLIPSE studies, we related Coulter blood counts and proportions to cross-sectional FEV1 adjusting for current smoking status. We also related cell count measures to three-year change in FEV1 in ECLIPSE subjects. In a subset of subjects with blood gene expression data, we used cell type deconvolution methods to infer the proportions of immune cell subpopulations, and we related these to COPD clinical status. We observed that FEV1 levels are positively correlated with lymphocytes and negatively correlated with myeloid populations such as neutrophils and monocytes. In multivariate models, absolute cell counts and proportions were associated with cross-sectional FEV1, and lymphocytes, monocytes, and eosinophil counts were predictive of three-year change in lung function. Using cell type deconvolution to study immune cell subpopulations, we observed that subjects with COPD had a lower proportion of CD4+ resting memory cells and naive B cells compared to non-COPD smokers. Alterations in circulating immune cells in COPD support a mixed pattern of lymphocyte suppression and an enhanced myeloid cell immune response. Cell counts and proportions contribute independent information to models predicting lung function suggesting a critical role for immune response in long-term COPD outcomes. Cell type deconvolution is a promising method for immunophenotyping in large cohorts.

Source connections

Explore related subjects

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Halper-Stromberg, E., Yun, J. H., Parker, M. M., Tal-Singer, R. M., Gaggar, A., Silverman, E. K., Leach, S., Bowler, R. P., Castaldi, P. J.. 2017-09-26. Systemic Markers of Adaptive and Innate Immunity Are Associated with COPD Severity and Spirometric Disease Progression. https://doi.org/10.1101/193920

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

Recurrent mitotic error and purifying selection shape chromosomal mosaicism across human tissues

Mosaic chromosomal alterations (mCAs) have been extensively studied in cancer and clonal hematopoiesis but less so in healthy solid tissues. Here, we characterized mCAs in 19 tissues across 25 donors (aged 42-89+ years) by analyzing >200x whole-genome sequencing data generated by the Somatic Mosaicism across Human Tissues (SMaHT) Network. Across 722 tissue samples, we identified 1,008 autosomal mCAs >1 Mb in length and ubiquitous losses of sex chromosomes. Surprisingly, the highest levels of Y chromosome loss in males (5-10% cell fraction in elderly donors) were observed in the lung, adrenal gland, and heart. These tissues also tended to experience more X loss in females, revealing a gradient of mitotic error burden across human tissues. Autosomal aneuploidies displayed distinct tissue-specific patterns indicative of negative selection against most events, except in the adrenal gland, in which low-level aneuploidy was pervasive. In contrast to the adrenal gland, testis rarely harbored aneuploidies but frequently experienced low-level copy-neutral loss of heterozygosity (CN-LOH), suggesting increased mitotic recombination in spermatogonial stem cells. Recurrent X chromosome losses within tissues of female donors exhibited allelic skews explained by a combination of genetic and epigenetic effects. Together, these results show that the chromosomal landscape of aging human tissues is shaped by genetics and recurrent mutations, most but not all of which are held in check by purifying selection.

genomics↗

A Chromosome Scale Genome Assembly for the Australian blue mussel Mytilus planulatus

Mussels belonging to the genus Mytilus are among the world's most ecologically and economically important bivalve molluscs. Although the genus most likely originated in the Northern Hemisphere, the evolutionary history of Southern Hemisphere lineages, including the timing and number of colonisation events leading to the extant Australian populations, remains debated. Limited genomic resources have hindered the reconstruction of these evolutionary histories. In Australia, distinguishing native Mytilus planulatus from invasive Mytilus galloprovincialis is critical for biosecurity and conservation, but previous molecular approaches lacked sufficient resolution to resolve species boundaries and hybridisation patterns. Here, we present the first chromosome-scale reference genome for M. planulatus. The assembly consists of 14 chromosomes and over 51,000 annotated protein-coding genes per haplotype. Comparative analysis revealed extensive structural variation and widespread hemizygosity despite a largely conserved chromosomal organisation relative to M. galloprovincialis. Population analyses using SNPs and gene presence-absence variation in resequenced individuals confirmed previously inferred patterns of population structure and establish this reference genome as a valuable resource for future studies of genome evolution, adaptation and population genomics in Mytilus.

genomics↗

An Isogenic iPSC Model of LMNA p.R482W Recapitulates Adipocyte Dysfunction in Familial Partial Lipodystrophy Type 2

Familial partial lipodystrophy type 2 (FPLD2) is a rare autosomal dominant disorder caused by pathogenic variants in LMNA, most commonly p.R482W, and is characterized by selective loss of subcutaneous adipose tissue, severe insulin resistance, and dyslipidemia. The cellular mechanisms underlying adipocyte dysfunction in FPLD2 remain incompletely understood, in part because existing in vitro models rely on patient-derived, non-isogenic cell lines or require non- physiologic transgene overexpression to achieve adipogenic differentiation. Here, we describe a CRISPR/Cas9-edited isogenic iPSC model of FPLD2 in which the heterozygous LMNA c.1444C>T (p.R482W) variant was introduced into a healthy donor-derived iPSC line. Using a transgene-free mesenchymal progenitor differentiation protocol, we generated LMNAp.R482W and isogenic control adipocytes and characterized their transcriptomic and functional phenotypes. Bulk RNA- sequencing demonstrated strong concordance in adipogenesis gene expression between genotypes during differentiation (Pearson {rho} = 0.968), yet LMNAp.R482W adipocytes exhibited significant downregulation of key adipogenic, lipid-handling, and extracellular matrix genes compared to isogenic controls. Functionally, LMNAp.R482W adipocytes showed markedly impaired glucose uptake under both basal and insulin-stimulated conditions, consistent with severe insulin resistance. Seahorse extracellular flux analysis revealed a globally quiescent metabolic state with significantly reduced oxygen consumption rate (126.5 vs. 261.5 pmol/min, p < 0.0001) and extracellular acidification rate (27.6 vs. 46.7 mpH/min, p < 0.0001). To validate these findings in human tissue, gene set enrichment analysis results from the iPSC model were compared to single-nucleus RNA-sequencing data from subcutaneous white adipose tissue biopsies of individuals with FPLD2 carrying the LMNA p.R482W variant. Across 37 mutually significant pathways, 59.5% were concordant between the iPSC model and human adipose tissue, including the pathways most central to FPLD2 pathophysiology: adipogenesis, fatty acid metabolism, oxidative phosphorylation, and inflammatory response. These findings establish this isogenic iPSC system as a faithful cellular model of FPLD2 adipocyte biology and a platform for functional characterization of LMNA variants of uncertain significance.

genomics↗