Epigenetics and Regeneration: Can Regenerative Medicine Learn From Development?

Editors

Institute of Biochemistry and Cell Biology, Department of Biomedical Sciences, National Research Council (CNR)

Institute of Transfusion Medicine and Immunology, Medical Faculty Mannheim, University Heidelberg, German Red Cross Blood Service Baden-Württemberg - Hessen, Mannheim, Germany

Elena De Falco

Department of Medical and Surgical Sciences and Biotechnology, Faculty of Pharmacy and Medicine, Sapienza University of Rome

Athar Aziz

University of Salford

Impact

Functional analysis of annotated clusters of the human PBMCs. (A) UMAP plot showing annotated clusters identified in the human PBMCs by integrating with the human PBMC scRNA-seq data. cMN, classic monocytes; h_fhT, T helper and T follicular helper cells; MAIT, mucosal-associated invariant T cells; mB, memory B cells, mDC, myeloid dendrtic cells; Naive B, naive B cells; NaiveCD4+, naive CD4+ T cells; NaiveCD8+, naïve CD8+ T cells; ncMN_interMN, non-classic monocytes and intermediate monocytes; NK, natural killer cells; pDC, plasmacytoid dendritic cells; te_emCD8_gdT, terminal effector CD8+ T cells, effector memory CD8+ T cells and γδT cells; Treg, T regulatory cells. (B) Distribution of reproducible peaks among different genomic features (promoter, intronic, exonic, and distal regions) in each cell type. (C) MA plot showing peaks preferentially accessible in intermediate and non-classic monocytes (FDR <0.01 and log2FC ≥ 1). (D) Heatmap showing 80,475 marker peaks across the 13 annotated clusters. (E) Dot plot showing top motifs enriched among marker peaks of intermediate and non-classic monocytes (ncMN_interMN). (F) Dot plot showing motifs of top variability scores across all the 13 cell types determined by ChromVAR. (G) Ridge plots showing distributions of the Z-score of motif deviation scores for SPI1_322 in each cell type. (H,I) UMAP plots showing gene scores and pseudo expression of a monocyte-specific TF, SPI1, whose motif is highly enriched in monocytes (cMN, interMN, and ncMN) and dendritic cells (mDC and pDC) and is of high deviations across clusters. (J) Heatmap showing normalized enrichment score, -log10 (adjusted p-value), of top TF motifs across the different cell types. (K) Aggregate footprints of SPI1_322 in each cell type.

Methods

27 September 2022

scATACpipe: A nextflow pipeline for comprehensive and reproducible analyses of single cell ATAC-seq data

Kai Hu

, 2 more and

Lihua Julie Zhu

Single cell ATAC-seq (scATAC-seq) has become the most widely used method for profiling open chromatin landscape of heterogeneous cell populations at a single-cell resolution. Although numerous software tools and pipelines have been developed, an easy-to-use, scalable, reproducible, and comprehensive pipeline for scATAC-seq data analyses is still lacking. To fill this gap, we developed scATACpipe, a Nextflow pipeline, for performing comprehensive analyses of scATAC-seq data including extensive quality assessment, preprocessing, dimension reduction, clustering, peak calling, differential accessibility inference, integration with scRNA-seq data, transcription factor activity and footprinting analysis, co-accessibility inference, and cell trajectory prediction. scATACpipe enables users to perform the end-to-end analysis of scATAC-seq data with three sub-workflow options for preprocessing that leverage 10x Genomics Cell Ranger ATAC software, the ultra-fast Chromap procedures, and a set of custom scripts implementing current best practices for scATAC-seq data preprocessing. The pipeline extends the R package ArchR for downstream analysis with added support to any eukaryotic species with an annotated reference genome. Importantly, scATACpipe generates an all-in-one HTML report for the entire analysis and outputs cluster-specific BAM, BED, and BigWig files for visualization in a genome browser. scATACpipe eliminates the need for users to chain different tools together and facilitates reproducible and comprehensive analyses of scATAC-seq data from raw reads to various biological insights with minimal changes of configuration settings for different computing environments or species. By applying it to public datasets, we illustrated the utility, flexibility, versatility, and reliability of our pipeline, and demonstrated that our scATACpipe outperforms other workflows.

12,385 views

6 citations

Mechanism of different histone chaperones in facilitating acquisition of pluripotency by reprogramming. Each separate box represents mechanism by which different histone chaperone facilitate reprogramming, mediated by different transcription factors, histone modifications, growth factors and histone variants (Gonzalez-Muñoz et al., 2014; Ishiuchi et al., 2015; Shakya et al., 2015; Fernández-Rivero et al., 2016; Syed et al., 2016; Shen Z et al., 2018).

Review

04 April 2022

Histone Chaperones as Cardinal Players in Development

Sruthy Manuraj Rajam

, 1 more and

Debasree Dutta

3,370 views

6 citations

Original Research

19 November 2021

Decidualization Potency and Epigenetic Changes in Human Endometrial Origin Stem Cells During Propagation

Elvina Valatkaitė

, 3 more and

Rūta Navakauskienė

Assessment of decidualization of EndSCs and MenSCs at gene expression level and protein level. 0d.—undifferentiated control cells, 3d.—cells after 3 days of decidualization, 6d.—cells after 6 days of decidualization. (A) relative gene expression of decidualization gene markers PRL, IGBFP-1, WNT4 genes was detected in early and late passages after 3 and 6 days of decidualization induction. Relative gene expression was measured using RT-qPCR and calculated using ΔΔCt method. Data were normalized to GAPDH and presented as mean ± SD (n = 6). (B) Concentrations of decidualization markers PRL and IGFBP-1 were detected in early and late passages after 6 days of decidualization induction using ELISA. Data represent mean ± SD (n = 4). * indicates p ≤ 0.05; ** indicates p ≤ 0.01; *** indicates p ≤ 0.001 compared to undifferentiated control. No statistically significant changes were detected between different passages and cell groups as evaluated by one-way ANOVA.

Human endometrium derived mesenchymal stem cells (hEndSCs) offer a great promise for regenerative medicine and reproductive system disorders treatment methods based on cell therapy due to their broad differentiation potential and highly efficient proliferation. In our study, we investigated the characteristics of hEndSCs that were isolated from two sources: endometrium and menstrual blood, which both contain endometrial origin stem cells. Changes in gene and protein expression levels during long-term cultivation and decidualization potential were examined in endometrial stem cells (EndSCs) and menstrual blood stem cells (MenSCs). The decidualization process was induced on early and late passages of hEndSCs using dibutyryl cyclic-AMP (db-cAMP) and medroxyprogesterone acetate (MPA) agents. We demonstrated that after long-term cultivation of hEndSCs the expression of typical mesenchymal stromal cell surface markers such as CD44, CD73, CD90, CD105 and perivascular marker CD146 remains at a similar level throughout long-term cultivation. Additionally, hematopoietic and endothelial markers CD34, CD45 were also tested, they were negative in all cases. Analyzed stem cells gene markers, such as OCT4, SOX2, NANOG, KLF4, showed similar expression in all passages of hEndSCs. RT-qPCR results demonstrated that the expression of cell cycle control associated genes - CDK2, CCNA2, CCNE2, p21, p53 and Rb, among all groups was very similar. Expression of genes associated with senescence (ATM, JUND, TOP2A, MYC) was maintained at a similar level throughout passaging. In addition, Western blot analysis was used to assess changes in proteins’ levels associated to epigenetics (EZH2, SUZ12, H3K27me3) and cell cycle control (cyclinE1, p53) during long-term cultivation. The levels of proteins associated with epigenetic changes were fluctuated slightly depending on the patient. Also, we demonstrated that in all induced hEndSCs the expression of decidualization markers Prolactin (PRL), IGFBP1 and WNT4 was upregulated. In conclusion, we demonstrated successful decidualization of stem cells derived from two reproductive system resources: endometrium and menstrual blood by using db-cAMP and MPA regardless of the length of the stem cell passaging. According these findings, we suppose that endometrium derived stem cells and menstrual blood derived stem cells could have a potency not only for endometrium tissue regeneration, but could also become a successful therapy for reproductive system disorders, including infertility or recurrent pregnancy loss.

5,632 views

18 citations