Turunen, T. | bioRxiv Science

bioRxiv2023

Cell-type-specific characterization of miRNA gene dynamics in immune cell subpopulations during aging and atherosclerosis disease development at single-cell resolution

MicroRNAs (miRNAs) are a class of regulatory non-coding RNAs that finetune cellular functions by modulating the stability and abundance of their target mRNAs, thereby contributing to regulation of tissue homeostasis. MiRNA genes are transcribed similarly to protein-coding genes and recent studies have enabled their annotation and quantification genome-wide from bulk nascent transcriptomes. Here, we developed an approach to quantify and integrate miRNA gene signatures into single-cell studies. To characterize miRNA gene expression dynamics, we first compared the suitability of droplet and plate-based single-cell RNA-sequencing (scRNA-seq) platforms using the matched datasets provided by the Tabula Muris Senis and Tabula Sapiens consortiums. We found high concordance between the platforms and with cell type-specific bulk expression data. Based on the comprehensive aging profiles, our analysis comparing spleen immune cells between young and old mice revealed a concordant regulation of miRNAs involved in senescence and inflammatory pathways in multiple immune cell types, including up-regulation of mmu-mir-146a, mmu-mir-101a and mmu-mir-30 family genes. To study the aberrant regulation of immune cell homeostasis and tissue inflammation that pre-dispose to aging-related disease development, we collected transcriptome profiles from atherosclerosis development in LDLR-/-ApoB100/100 mice. We found an elevated myeloid cell proportion in the adipose tissue and further characterized the cell subtypes based on reproducible transcriptome clusters. We then compared miRNA gene expression in early versus late disease and upon inflammatory challenge to monitor different stages during disease progression. At atherosclerotic stage, pro-inflammatory mmu-mir-511 expression increased in several macrophage subtypes, while immunosuppressive mmu-mir-23b[~]mir-24-2[~]mir-27b up-regulation was specific to Trem2+ lipid-associated macrophages. The infiltrating monocytes up-regulated mmu-mir-1938 and mmu-mir-22 expression and in classical monocytes maturation further increased mmu-mir-221[~]222, mmu-mir-511 and mmu-mir-155 expression. To validate that these changes detected from single cell profiles represent miRNA gene transcriptional regulation, we used nascent transcriptomics data from ex vivo macrophage cultures with pro-inflammatory stimulation, confirming both rapid and long-lasting transcriptional activation of the miRNA loci studied. Collectively, our work enables integrating miRNA gene analysis to current single cell genomics pipelines and facilitates characterization of miRNA regulatory networks during aging and disease development.

molecular biology↗

bioRxiv2022

Novel subthreshold retinal laser treatment with ERG-based thermal dosimetry activates hormetic heat response in pig RPE in vivo

Boosting natural mechanisms to retain cellular homeostasis and combat oxidative stress by inducing a hormetic heat shock to retinal pigment epithelium with non-damaging transpupillary laser heating, i.e., with subthreshold laser treatment (SLT), has been suggested as a promising therapeutic target for many retinal diseases, including age-related macular degeneration. However, the therapeutic temperature window for the treatments is narrow and thermal dosimetry is unavailable. Here we introduce an SLT modality where the retinal temperature is monitored with electroretinography (ERG)-based thermal dosimetry and demonstrate its feasibility with anesthetized pigs. In 60-second treatments with 810 nm laser, the ED50 peak temperature for visible lesion generation was 48{degrees}C and the relative temperature determination error was below 10% from the temperature increase. Heat shock protein expression increased, and autophagy was activated at 44.2 {degrees}C and no signs of oxidative stress or apoptosis emerged at 44.2 {degrees}C or 46.5 {degrees}C. The demonstrated method permits a controlled activation of intracellular chaperones and waste clearance in RPE cell with a clear temperature margin for adverse events. In the clinical setting, ERG-based dosimetry would allow safe and personalized SLTs for retinal diseases currently lacking effective treatments.

bioengineering↗

bioRxiv2021

Retinal OFF ganglion cells allow detection of quantal shadows at starlight

Perception of light in darkness requires no more than a handful of photons and this remarkable behavioral performance can be directly linked to a particular retinal circuit - the retinal ON pathway. However, the neural limits to shadow detection in very dim light have remained unresolved. Here, we unravel the neural mechanisms that determine the sensitivity of mice to the dimmest light decrements by measuring signals from the most sensitive ON and OFF retinal ganglion cell types and by correlating their signals with visually guided behavior. We show that mice can detect shadows when only a few photon absorptions are missing among thousands of rods. Behavioral detection of "quantal" shadows relies only on the retinal OFF pathway and is limited by noise and losses of single-photon signals in retinal processing. Thus, in the dim-light regime, light increments and decrements are encoded separately via the ON and OFF retinal pathways, respectively.

neuroscience↗