Biology subjects

Michaëlsson, J.

Publications and source records attributed to Michaëlsson, J..

3 recordsLinked to original sources

bioRxiv2021

Long-read whole genome analysis of human single cells

With long-read sequencing, we have entered an era where individual genomes are routinely assembled to near completion and where complex genetic variation can efficiently be resolved. Here, we demonstrate that long reads can be applied to study the genomic architecture of individual human cells. Clonally expanded CD8+ T-cells from a human donor were used as starting material for a droplet-based multiple displacement amplification (dMDA) to generate long molecules with minimal amplification bias. PacBio HiFi sequencing generated up to 20 Gb data and 40% genome coverage per single cell. The data allowed for accurate detection and haplotype phasing of single nucleotide variants (SNVs), structural variants (SVs), and tandem repeats, including in genomic regions inaccessible by short reads. Somatic SNVs were detected in the nuclear genome and mitochondrial DNA. An average of 1278 high-confidence SVs per cell were discovered in the PacBio data, nearly four times as many compared to those found in Illumina dMDA data from clonally related cells. Single-cell de novo assembly resulted in a genome size of up to 598 Mb and 1762 (12.8%) complete gene models. In summary, the work presented here demonstrates the utility of whole genome amplification combined with long-read sequencing toward the characterization of the full spectrum of genetic variation at the single-cell level.

genomics↗

bioRxiv2021

Distinct lung-homing receptor expression and activation profiles on NK cell and T cell subsets in COVID-19 and influenza

Respiratory viral infections with SARS-CoV-2 or influenza viruses commonly induce a strong infiltration of immune cells into the lung, with potential detrimental effects on the integrity of the lung tissue. Despite comprising the largest fractions of circulating lymphocytes in the lung, little is known about how blood natural killer (NK) cells and T cell subsets are equipped for lung-homing in COVID-19 and influenza. Using 28-colour flow cytometry and re-analysis of published RNA-seq datasets, we provide a detailed comparative analysis of NK cells and T cells in peripheral blood from moderately sick COVID-19 and influenza patients, focusing on the expression of chemokine receptors known to be involved in leukocyte recruitment to the lung. The results reveal a predominant role for CXCR3, CXCR6, and CCR5 in COVID-19 and influenza patients, mirrored by scRNA-seq signatures in peripheral blood and bronchoalveolar lavage from publicly available datasets. NK cells and T cells expressing lung-homing receptors displayed stronger phenotypic signs of activation as compared to cells lacking lung-homing receptors, and activation was overall stronger in influenza as compared to COVID-19. Together, our results indicate migration of functionally competent CXCR3+, CXCR6+, and/or CCR5+ NK cells and T cells to the lungs in moderate COVID-19 and influenza patients, identifying potential common targets for future therapeutic interventions in respiratory viral infections. Author summaryThe composition of in particular CXCR3+ and/or CXCR6+ NK cells and T cells is altered in peripheral blood upon infection with SARS-CoV-2 or influenza virus in patients with moderate disease. Lung-homing receptor-expression is biased towards phenotypically activated NK cells and T cells, suggesting a functional role for these cells co-expressing in particular CXCR3 and/or CXCR6 upon homing towards the lung.

immunology↗

bioRxiv2019

Cell Generation Dynamics Underlying Naïve T Cell Homeostasis in Adult Humans

Thymic involution and proliferation of naive T cells both contribute to shaping the naive T cell repertoire as humans age, but a clear understanding of the roles of each throughout a human lifespan has been difficult to determine. By measuring nuclear bomb test-derived 14C in genomic DNA we determined the turnover rates of CD4+ and CD8+ naive T cell populations and defined their dynamics in healthy individuals ranging from 20-65 years of age. We demonstrate that naive T cell generation decreases with age, and that this could be explained by a combination of declining cell loss, peripheral division and thymic production during adulthood. We investigated putative mechanisms underlying age-related changes in homeostatic regulation of naive T cell turnover using mass cytometry to profile candidate signaling pathways involved in T cell activation and proliferation in CD4+ naive T cells relative to CD31 expression, a marker of thymic proximity. We show that basal NF-{kappa}B phosphorylation inversely correlated with CD31 expression and thus is decreased in peripherally expanded naive T cell clones. Functionally we found that NF-{kappa}B signaling was essential for naive T cell proliferation to the homeostatic growth factor IL-7, and reduced NF-{kappa}B phosphorylation in CD4+CD31- naive T cells is linked to reduced homeostatic proliferation potential. Our results reveal an age-related decline in naive T cell turnover as a putative regulator of naive T cell diversity and identify a molecular pathway that restricts proliferation of peripherally expanded naive T cell clones that accumulate with age.

immunology↗