With this study, we provide a comprehensive reference dataset of detailed miRNA expression profiles from seven types of human peripheral blood cells (NK cells, B lymphocytes, cytotoxic T lymphocytes, T helper cells, monocytes, neutrophils and erythrocytes), serum, exosomes and whole blood. The peripheral blood cells from buffy coats were typed and sorted using FACS/MACS. The overall dataset was generated from 450 small RNA libraries using high-throughput sequencing. By employing a comprehensive bioinformatics and statistical analysis, we show that 3′ trimming modifications as well as composition of 3′ added non-templated nucleotides are distributed in a lineage-specific manner—the closer the hematopoietic progenitors are, the higher their similarities in sequence variation of the 3′ end. Furthermore, we define the blood cell-specific miRNA and isomiR expression patterns and identify novel cell type specific miRNA candidates. The study provides the most comprehensive contribution to date towards a complete miRNA catalogue of human peripheral blood, which can be used as a reference for future studies. The dataset has been deposited in GEO and also can be explored interactively following this link: http://134.245.63.235/ikmb-tools/bloodmiRs.

DNA methylation is an important epigenetic modification that has been repeatedly implied in organismal adaptation. However, many previous studies that have linked DNA methylation patterns to environmental parameters have been limited by confounding factors, such as cell-type heterogeneity and genetic variation. In this study, we analyzed DNA methylation variation in marbled crayfish, a clonal and invasive freshwater crayfish that is characterized by a largely tissue-invariant methylome and negligible genetic variation. Using a capture-based subgenome bisulfite sequencing approach that covers a small, variably methylated portion of the marbled crayfish genome, we identified specific and highly localized DNA methylation signatures for specimens from geographically and ecologically distinct wild populations. These results were replicated both biologically and technically by re-sampling at different time points and by using independent methodology. Finally, we show specific methylation signatures for laboratory animals and for laboratory animals that were reared at a lower temperature. Our results thus demonstrate the existence of context-dependent DNA methylation signatures in a clonal animal.

IL-2 ''virtual'' injections every 3 days, Treg cells were expected to remain stable with a delta variation of %Treg cells ranging from 3 to 4 (ie, a 60%-80% increase); with 3 MIU every 3 days, %Treg cells were predicted to increase continuously; with reinjections every 15 days, Treg cells were expected to (1) return to their baseline approximately at day 20 with 0.33 MIU; (2) be stable with a delta variation of %Treg cells ranging from 0.5 to 1.5 (ie, 10%-30% increase) with 1 MIU; and (3) to be stable with a delta variation of % of Treg cells ranging from 2.5 to 3.5 (ie, 50%-70% increase) using 3 MIU.On the basis of safety data from our previous clinical trials and our modeling, we chose the dose of 1 MIU/injection, with once-a-fortnight injections during the maintenance course to perform a novel clinical trial of ld-IL2 in patients with mild forms of various AIDs (rheumatoid arthritis, ankylosing spondylitis, systemic lupus erythematosus, psoriasis, Behcet disease, Wegener granulomatosis, Takayasu disease, Crohn disease, ulcerative colitis, autoimmune hepatitis, sclerosing cholangitis, and Gougerot-Sj€ ogren syndrome; Transreg clinical trial: NCT01988506). Treg-cell dynamics over time in the first 40 treated patients is presented in Fig 2 , B. Note that Treg-cell evaluations were always made just before an IL-2 injection, thus 14 days away from the last injection. These values therefore underestimate the overall effect during the 14-day period. As predicted from above, %Treg cells was increased during the maintenance phase in treated patients (delta of 1.12% 6 0.25%, P < .0001 at day 31, and 1.325% 6 0.33%, P < .0001 at day 91), representing a minimum 20% increase for a prediction that was between 10% and 30%.Thus, we have defined and validated a model for predicting the dynamic Treg-cell response to IL-2 that should help navigate its use in numerous therapeutic targets, from various AIDs to transplantation and allergy. Our pharmacodynamic model can predict the effects of any combination of any of the treatment parameters: dose, length of the induction phase, timing of maintenance injections. Also, our results show that the response to IL-2 is predictable across multiple AIDs and that we have validated a therapeutic scheme that provides long-term improvement in the Teff-/Treg-cell balance.We are grateful to Alice Barrateau for excellent technical assistance. We thank the animal care team members Christelle Enond, Bocar Kane, Olivier Bregerie, and Serban Morosan from the Centre d'Exploration Fonctionnelle, UPMC Paris 06. We thank the entire DF-IL2 and Transreg study groups for the performance of the clinical trials that contributed to this study (groups are listed in this article's Online Repository at www.jacionline.org).