Journal: Regenerative Therapy

Article Title: Extracellular vesicles derived from adipose-derived mesenchymal stem/stromal cells prevent synovial inflammation and attenuate cartilage degeneration in rodent osteoarthritis

doi: 10.1016/j.reth.2025.101056

Figure Lengend Snippet: Single-cell RNA sequencing profiling of joint cell populations following extracellular vesicle (EVs) treatment. (a) The UMAP plot displaying the classification of joint cell populations into ten distinct clusters under three conditions: WT, PBS-treated (PBS), and EVs-treated (EVs). ( b ) Cell typing of clusters based on gene expression. Cluster 1 (NK cells), Cluster 2 (T cells), Cluster 3 (pre-B cells), Cluster 4 (Neutrophils), Cluster 5 (B cells), Cluster 6 (Chondrocyte progenitor cells), Cluster 7 (Hematopoietic progenitors), Cluster 8 (Mesenchymal cells), Cluster 9 (Plasma cells), and Cluster 10 (Erythroblasts). ( c ) Heatmap displaying the expression of representative marker genes for each cluster, including Col12a1 for the "Chondrocyte" cluster, and Col1a1 for the "Mesenchymal cell" cluster, and CD45/CD14 for the "Hematopoietic" cluster.

Article Snippet: For adipocyte differentiation, either BioMirai Lab's induction kit or PromoCell's mesenchymal stem cell adipocyte differentiation medium was used, with Oil Red O staining to assess lipid accumulation.

Techniques: RNA Sequencing, Gene Expression, Clinical Proteomics, Expressing, Marker

Journal: Regenerative Therapy

Article Title: Extracellular vesicles derived from adipose-derived mesenchymal stem/stromal cells prevent synovial inflammation and attenuate cartilage degeneration in rodent osteoarthritis

doi: 10.1016/j.reth.2025.101056

Figure Lengend Snippet: Differential gene expression besed on Single-cell RNA sequencing of joint cell clusters following extracellular vesicle (EVs) treatment . ( a-d ) Comparison of gene expression in EVs, PBS, and WT groups (a) in Cluster 6 (chondrocyte progenitors) (COL2A1, COL1A2, PRG4, MMP3, CCL2, and FGF18). ( b ) in Cluster 1 (NK cells) (CD14, MRC1, CD163, CD86, CD80, and NOS2). ( c ) in Cluster 8 (Mesenchymal cells) (COL2A1, COL1A2, PRG4, CCL2, and FGF18) ( d ) in Cluster 4 (Neutrophils) (APOE, AGPAT4, HAPLN1, CDKN1C, MET, and CEMIP2). (e) Flow cytometry analysis confirmed that the proportion of CD11b + CD163 + M2 macrophages was approximately 2.5-fold higher in the EVs-treated group compared to the PBS-treated group.

Article Snippet: For adipocyte differentiation, either BioMirai Lab's induction kit or PromoCell's mesenchymal stem cell adipocyte differentiation medium was used, with Oil Red O staining to assess lipid accumulation.

Techniques: Gene Expression, RNA Sequencing, Comparison, Flow Cytometry

Journal: bioRxiv

Article Title: Physiological re-replication during human stem cell differentiation

doi: 10.64898/2026.02.27.708451

Figure Lengend Snippet: Overview and time scale of re-replications experiments Mesenchymal stem cells were differentiated into osteoblasts, adipocytes, chondrocytes, and neurons, while myoblasts were differentiated into myotubes. Two experimental strategies were applied to detect re-replication during differentiation (A). For Rerep-seq the thymidine-analogue BrdU was added to the culture media. In the schematic representation of the re-replication bubble, yellow asterisks indicate BrdU integration. The black DNA strand represents parental DNA, the red strand corresponds to DNA from the first round of replication, the green strand to DNA from the second round, and the turquoise strand to DNA from the third round of replication. As described by Menzel et al. , UVA photolyzes incorporated BrdU converting it to Uracil. Subsequently, UDG excises the Uracil, generating an abasic site, while AP1 introduces single strand breaks at these positions. A representative agarose gel image demonstrates the effects of UVA, UDG, and AP1 treatment on DNA from chondrogenic differentiated hMSCs cultured with and without BrdU supplementation. For fiber-combing thymidine-analogues IdU and CldU were subsequently added to culture media. High molecular weight DNA was used for fiber-combing and further evaluated for fibers with simultaneous IdU and CldU incorporation. Time scale shows an overview on start and end points of all differentiation experiments (B). Yellow rectangles highlight timeframes where re-replication was detected with fiber-combing. Black arrows point on likely re-replication start points during the differentiation process. The figure was created using BioRender.

Article Snippet: The cells were seeded at a density of 100,000/25 cm 2 flask with Mesenchymal Stem cell Growth Medium (PromoCell) and expanded for 1 passage before induction of differentiation.

Techniques: Agarose Gel Electrophoresis, Cell Culture, Analogues, High Molecular Weight

Journal: bioRxiv

Article Title: Physiological re-replication during human stem cell differentiation

doi: 10.64898/2026.02.27.708451

Figure Lengend Snippet: Analysis of extranuclear DNA during differentiation Mesenchymal stem cells were grown on glass slides with corresponding differentiation media and supplemented with thymidine-analogue EdU during timeframes of re-replication determined before. EdU incorporation is detected with red fluorescence (Alexa-Fluor-594) and DNA was counterstained with Hoechst33342 in blue. An example of osteogenic differentiated hMSCs is shown and three enlarged views point to extranuclear spots and clusters of DNAs that were microdissected (A). In total 1200-1600 extranuclear DNAs were collected for further DNA isolation and sequencing for each differentiation experiment. During adipogenic differentiation extranuclear DNA was detectable after 3d and 4d and during osteogenic differentiation after 4d of differentiation. Results of sequencing analysis of extranuclear DNA were displayed using IGV with data range on the y-axis adjusted for all extranuclear DNA reads. For each differentiation extranuclear DNA sequencing (dark blue) is displayed above the corresponding Rerep-seq results (green). Representative examples for gene regions on chromosome 12 (B) and 7 (C) revealed that extranuclear DNA overlaps with re-replicated DNA regions.

Article Snippet: The cells were seeded at a density of 100,000/25 cm 2 flask with Mesenchymal Stem cell Growth Medium (PromoCell) and expanded for 1 passage before induction of differentiation.

Techniques: Fluorescence, DNA Extraction, Sequencing, DNA Sequencing

Journal: bioRxiv

Article Title: Physiological re-replication during human stem cell differentiation

doi: 10.64898/2026.02.27.708451

Figure Lengend Snippet: Asymmetric re-replication Fiber-combing experiments revealed several replication forks with varying combinations of replication and/or re-replication events. Representative examples shown, derived from neurogenic (A, B) and adipogenic (C) differentiated mesenchymal stem cells. Re-replication on two strands of the replication fork but differing in length between strands (A), re-replication only on one strand with no re-replication on the other strand of the replication fork (B) and re-replication only on one strand showing no detectable replication at the other strand of the replication fork (C). DNA is shown in blue (false color YOYO-stain) and thymidine-analogue detection is shown in red for IdU and green for CldU. Re-replicated fiber tracks appear as yellow fluorescence. Scale bars represent 20 µm = 40kb.

Article Snippet: The cells were seeded at a density of 100,000/25 cm 2 flask with Mesenchymal Stem cell Growth Medium (PromoCell) and expanded for 1 passage before induction of differentiation.

Techniques: Derivative Assay, Staining, Fluorescence