Introduction: Human endometrium is one of peculiar tissues capable of scarless regeneration after injury during every menstrual cycle, birth, or surgery. However, it is disputable whether this feature should be attributed to specific regulatory factors of wound environment and menstrual fluid (MF) or to tissue-specific properties of endometrial mesenchymal stromal cells (eMSCs), which are pivotal participants of wound healing. We aimed to elucidate the role of eMSC tissue specificity in wound healing. Methods: We evaluated changes of eMSC transcriptomic profile in response to MF and their potency to granulation tissue formation in vitro in comparison with those of stromal cells from scar-forming organs – dermal and adipose MSC (dMSC and adMSC). Results: We have found that MF contains numerous inflammatory factors and induces a profound inflammatory response in both eMSC and dMSC, but a tissue-specific component was identified in their transcriptome profiles. Furthermore, transcriptomic tissue specificity was stable and present prior to MF treatment as well as after it, so we validated our findings against in vivo single-cell RNA-sequencing data from Human Protein Atlas. Tissue specificity traits were related to embryonic development and morphogenesis, suggesting a putative contribution of “developmental imprinting” in its establishment. Using in vitro models of fibroplasia, angiogenesis, and extracellular matrix deposition, we showed that eMSC lack the ability to induce these processes in contrast to dMSC and adMSC. Finally, we refined transcription factors (TFs) from stable tissue-specific genes that may explain the unique properties of eMSC and endometrium itself and can serve as potential targets to induce regeneration in scar-forming organs. Conclusion: eMSCs possess tissue-specific properties including stable expression of TFs that may explain the scarless regeneration of endometrium.

Recent discovery of menstruation in the Egyptian spiny mouse (Acomys cahirinus) highlighted this species as a feasible model for the study of menstrual cycle physiology. However, reports on active menstrual bleeding in this animal were contradictory, so we set out to reproduce major findings in the field. Using vaginal smear microscopy and occult blood assay, we have failed to detect menstrual bleeding in spiny mice from our colony at Lomonosov Moscow State University. Otherwise, we demonstrated appearance of well-defined decidual cells during the late secretory phase of the cycle that correlated with an increase in serum progesterone. Comparing the uteri of spiny mice from our colony vs. CD1 strain laboratory mice housed in the same animal unit, we have found several noteworthy features: (1) absence of endometrial glands, (2) higher volume of nerve fibers in the endometrium, and (3) spiral-like arteries in myometrium. Taking results of other groups into account, our results highlight putative diversity of menstrual cycles in spiny mice from different colonies and demonstrate important differences in uterus structure compared to M. musculus.

Public repositories now accumulate an unprecedented amount of metabolomics data. Despite the opportunities for large-scale meta-analyses opened by these repositories, the deposited data rarely becomes systematically re-analyzed. We conducted a systematic metadata-based re-analysis of all human blood metabolomics studies in the Metabolomics Workbench performed using Orbitrap or QTOF mass spectrometry, encompassing 44 165 samples. After harmonizing metabolites with PubChem identifiers and embedding them using SMILES representations, we generated a map of 6752 blood metabolites forming 25 structural clusters, and subsequently performed correlation analysis between these clusters, biomarkers, and drugs. Analysis of 337 120 metabolite pairs detected in at least 10 studies showed that structurally related clusters display correlated abundances (ρ up to 0.6). Correlation patterns among established clinical biomarkers revealed candidate metabolic correlates, several with ρ > 0.7. We also developed open-source software enabling similar analyses for any metabolite across the Workbench data explored. Additionally, curating drug-containing datasets enabled meta-analyses for compounds such as acetaminophen, metoprolol, and atenolol, identifying both known and novel metabolic signatures. Besides the biological insights, we have found that Orbitrap and QTOF tend to detect different metabolites, but they give quantitatively coherent results on overlapping compounds. Overall, the present study provides the methodology and software to perform large-scale mining of public metabolomics data enabling its re-analysis to obtain novel biomedical insights.

Light sheet fluorescent microscopy (LSFM) can be used to obtain large-scale (up to whole organ) 3D images; however, once one turns to lineage tracing, there is a conflict between efficacy of tissue clearing, permeabilization for immunolabeling, and tracing signal salvation. We report a methodological and analytical pipeline that would aid researchers using multi-color (Confetti) lineage tracing and utilize LSFM along with immunolabeling procedures. We used mouse cornea as a primary object and provided its detailed characteristics at a cellular level using dual-view inverted selective plane illumination (diSPIM) microscopy. We developed a protocol for a 3D image acquisition and analysis pipeline of lineage tracing data in Prrx1-expressing cells of corneal stromal and endothelial compartments. Morphometry data included calculation of cell number in epithelium, stroma, and endothelium along with measurement of corneal thickness and radius of curvature. The developed image analysis pipeline allowed calculation of Confetti marker distribution and quantitative clonal expansion estimation with adjustment imposed to correct spectral Confetti channel leakages. We believe that the presented methodology and 3D image analysis scripts should facilitate the lineage tracing studies and may be adapted to other organs.

Objective: Digit tip amputation is among few cases of injury that may result in regenerative outcome in both mice and humans, making animal model more relevant for studying the phenomenon. Nevertheless, experimental studies in the field share a significant degree of variability and contrasting approaches for injury application. A reliable and relevant model of digit tip amputation that allows to induce both—regenerative and non-regenerative outcomes with minor differences of amputation level is a pivotal condition for data consistency in comparative studies. Methods: We have tested five amputation degrees in C57/B6 mice and have identified the most suitable and reproducible among them for future application in the field. Results: Basically, obligate non-regenerative healing can be induced only by entire nail amputation. In contrast, reproducible full-scale regeneration of digit tip demanded a significant part of the nail, bone and other tissues to be retained, while intermediate amputation extent demonstrated variable results with three possible outcomes: regeneration, incomplete regeneration and non-regenerative healing. Conclusions: Overall, we believe that our findings provide a valuable methodological insight for further investigations of digit tip regeneration mechanisms and provide a feasible model that would beneficially impact data integrity in the field.