Journal: Cell stem cell

Article Title: Deterministic Somatic Cell Reprogramming Involves Continuous Transcriptional Changes Governed by Myc and Epigenetic-Driven Modules

doi: 10.1016/j.stem.2018.11.014

Figure Lengend Snippet: A. Experimental scheme. B. Spearman correlation between expression profiles of Mbd3f/- system Calculated over all differential genes (n=8,042), showing an average correlation of R=0.93 between consecutive samples. C. As in B, but between Mbd3flox/- and Gatad2a-/- systems. D. Overlap between targets of OSKM in promoters and enhancers. Pixel shade indicates Jaccard Index. E. Correlation between consecutive samples in Mbd3f/- system (MEF-day1, day1-day2, day2..day8-iPS), measured over all ESPGs promoters (promoters with differential chromatin pattern, n=3,593, top), or all differential enhancers (n=40,174, bottom), for each chromatin mark. Negative controls were calculated between MEF and IPS, are marked with solid border. F. Overlap between binding targets of Oct4, Sox2, Klf4 or Myc, and previously published binding data of the same factors, calculated in ES and iPS samples. Percentage out of our measured binding targets is presented, along Fisher exact test p-values. G. Global transcriptional pattern of 8,042 differential genes (FC>4 & maximal FPKM value>1), sorted by their temporal pattern in Mbd3f/-system (the same gene order was applied for the other reprogramming systems). Heatmap represents unit-transformation of FPKM values. H. PCA analysis of all samples, alongside samples from previous publications (Polo et al., 2012). PCA was calculated on the same set of genes and normalization as in G. I. GO categories enriched among the genes that are active in each day. Gene is defined to be active in samples where RPKM is above 0.5 of the gene max value. P-values were calculated with Fisher exact test, and FDR corrected. Categories with corrected p-value<0.01 in at least two-time points are presented. Gray Shades represent FDR corrected p-values

Article Snippet: Secondary mouse embryonic fibroblast (MEF) from Mbd3 flox/- cell line (A12 clone: Mbd3 flox/- cell lines that carries the GOF18-Oct4-GFP transgenic reporter (complete Oct4 enhancer region with distal and proximal enhancer elements) (Addgene plasmid #60527)) and WT-1 cell line (WT-1 clone that carries the deltaPE-GOF18-Oct4-GFP reporter (Addgene plasmid#52382) were previously described ( Rais et al., 2013 ).

Techniques: Expressing, Binding Assay, Transformation Assay

Journal: Cell stem cell

Article Title: Deterministic Somatic Cell Reprogramming Involves Continuous Transcriptional Changes Governed by Myc and Epigenetic-Driven Modules

doi: 10.1016/j.stem.2018.11.014

Figure Lengend Snippet: A. ChIP-seq landscape of two examples. Promoters are marked in red, enhancers are marked in green. Signals are normalized to sample size (RPM). B. Overlap between binding of OSKM and active enhancers, in each day of reprogramming. Enhancer is defined as active in a specific day if its ATAC-seq z-score is above 1.5 STD in that day. Gray shades indicate Fisher exact test p-value for overlap between compared samples. Note that OSKM do not bind the enhancers that are active in MEF (D0, marked in red); these enhancers are not significantly bound by OSKM at any day during reprogramming. C. Number of enhancers bound by each of OSKM factors in each day of reprogramming. Upper row: out of enhancers that are bound by the factor in late stages (day8, iPS, ESC). Bottom row: out of enhancers that are bound by the factor in early stages (day1-day3). D. Probability to observe co-localized binding of transcription factors in promoters (gray) and enhancers (black). Calculated in days 1,8 and iPS (Error bars indicate S.E.M). Right – Myc binds 32% of promoters, and 8% of active enhancers. E. Significant motifs enriched in promoters and enhancers that are bound by each of Oct4, Sox2, Klf4 and c-Myc at different days of reprogramming, as detected by Homer/4.7 software. P-values, indicated by color shade, were reported by Homer, and are FDR corrected. Motifs which are significantly enriched (corrected p<10-30) in at least one time point are presented. F. a. Motifs enriched in differential enhancers that are active in each day of reprogramming (ATAC-seq z-score >1.5). P-values, indicated by color shade, were reported by Homer, and are FDR corrected. Motifs which are significantly enriched (corrected p<10-50) in at least one-time point are presented. G. Motifs found in “closed” vs. “open” binding targets of the indicated transcription factor. Accessibility of targets was calculated based on ATAC-seq. Motifs found in OSK binding targets calculated in Mbd3f/- day1. Motifs that are different between open and closed binding targets are marked in black line. Complementary motifs to canonical motif appear in reverse order. H. Spearman correlation between ATAC-seq profiles of the two efficient reprogramming systems: Mbd3f/- MEF and C/EBPaTg B cell systems calculated over 40,174 differential enhancers.

Article Snippet: Secondary mouse embryonic fibroblast (MEF) from Mbd3 flox/- cell line (A12 clone: Mbd3 flox/- cell lines that carries the GOF18-Oct4-GFP transgenic reporter (complete Oct4 enhancer region with distal and proximal enhancer elements) (Addgene plasmid #60527)) and WT-1 cell line (WT-1 clone that carries the deltaPE-GOF18-Oct4-GFP reporter (Addgene plasmid#52382) were previously described ( Rais et al., 2013 ).

Techniques: ChIP-sequencing, Binding Assay, Software

Journal: Cell stem cell

Article Title: Deterministic Somatic Cell Reprogramming Involves Continuous Transcriptional Changes Governed by Myc and Epigenetic-Driven Modules

doi: 10.1016/j.stem.2018.11.014

Figure Lengend Snippet: A. Distribution of low (<0.02), mid (0.02-0.98) and high (>0.98) methylated CpG sites, along reprogramming. Average and SEM are indicated in red plot. B. Methylation level measured in covered enhancers (n=18,072), in Mbd3f/-, Gatad2a-/- and WT-2 systems. Enhancers are clustered into eight clusters using k-means. Cluster 8 consists of enhancers that undergo fast demethylation, compared to clusters 3 and 7. C. Average methylation measured in promoters of genes that were highly methylated (>80%) in day0. Genes that change their expression level (red) are compared to genes that do not change their expression level (gray). Wilcoxon p-value indicates places where methylation of differential genes is significantly lower than methylation of non-differential genes. D. Left: Enrichment of enhancer clusters, as shown in panel B, for OSK binding, DNA accessibility, and super enhancers, showing that cluster 8 is highly enriched for OSK binding and overlaps with super enhancers. Color shades represent FDR corrected enrichment p-value. Right: Enrichment of the same enhancer clusters to transcription factor binding, taken from hmChip database. Cluster size is indicated on the right. E. Experimental scheme summary. Reprogramming efficiency was measured by Oct4-GFP+ cells percentage in Tet1/2/3 null(Δ) and Tet1/2/3fl/fl with and without Gatad2a expression, after 8 days. **p<0.01, ***p<0.001 (Student’s t-test), n=6, error bars indicate SD. F. Secondary MEF harboring Mir290-RGM and Nanog GFP-reporter were sorted after reprogramming to 3 different populations: RGM-SE-Mir290-tdTomato positive cells (sorted at day 5), Nanog-GFP and Mir290-RGM positive cells (sorted at d10-14), and "double negative" cells (sorted at d5). The cells were seeded as single cell-per-well, and were treated with medium either supplemented with Dox or lacking Dox. On day 14 colonies were inspected for GFP and mCherry (RGM) markers.

Article Snippet: Secondary mouse embryonic fibroblast (MEF) from Mbd3 flox/- cell line (A12 clone: Mbd3 flox/- cell lines that carries the GOF18-Oct4-GFP transgenic reporter (complete Oct4 enhancer region with distal and proximal enhancer elements) (Addgene plasmid #60527)) and WT-1 cell line (WT-1 clone that carries the deltaPE-GOF18-Oct4-GFP reporter (Addgene plasmid#52382) were previously described ( Rais et al., 2013 ).

Techniques: Methylation, Expressing, Binding Assay

Journal: Cell stem cell

Article Title: Deterministic Somatic Cell Reprogramming Involves Continuous Transcriptional Changes Governed by Myc and Epigenetic-Driven Modules

doi: 10.1016/j.stem.2018.11.014

Figure Lengend Snippet: A. Experimental flow describing three experimental perturbation settings: (i) Mbd3f/- MEFs were virally infected with cMyc over-expression (OE) cassette, OSK-OE cassette or both cassettes. Gene expression was measured on day4 following infection. (ii) Mbd3f/- MEFs carrying OSK Dox-dependent cassette were treated for knockdown of c-Myc, n-Myc and l-Myc. Gene expression was measured on days 3 and 7, and colony formation was measured on day 11. (iii) Mbd3f/- MEFs carrying OSKM Dox-dependent cassette were treated with inhibitor of cMyc (10058-F4) and with Dox. Gene expression and colony formation were measured on day 3. B. Distribution of Expression fold change (FC) compared to WT MEF of up/down regulated ESPGs (down regulated ESPGs are enriched for somatic genes), and CAPGs. Presented perturbations are over-expression of OSK cassette, over-expression of c-Myc cassette, or over-expression of the two cassettes together. (*p<10-5, **p<10-20, Wilcoxon test). C-D. Reprogrammed colony formation in Myc knockdown ort small molecule inhibition, measured 11-14 days after Dox. E. Distribution of expression fold change (FC, in log2 scale) compared to MEF of up/down regulated ESPGs and CAPGs. Presented perturbations are Myc knockdown, inhibition of Myc activity with small molecular inhibitor (10058-F4). (*p<10-5, **p<10-20, Wilcoxon test). F. Experimental scheme. G. IPSC Reprogramming efficiency in different cells expressing both endogenous and/or exogenous cMyc and nMyc. H. FACS analysis for surface expression of fibroblast surface marker Thy1 on the indicated Mbd3flox/- cell types. Dotted line indicates positive threshold for detection. I. Representative pictures of Mbd3fl/- cells harboring mCherry-NLS and ΔPE-GOF18 Oct4-GFP cassettes after 13 days of reprogramming in the presence of MYCi. Scale = 100μM. J. Left panel - iPSC reprogramming efficiency by applying highly efficient mouse B cell and WT CMP reprogramming protocols by OSKM in the presence or absence of MYC small molecule inhibitor (MYCi). Right panel – Human iPSC reprogramming efficiency by applying OKS lentiviral transduction in the presence of absence of MYCi. K. Expression fold-change distribution (log2 scale) of selected GO categories in Myc over-expression or Myc knockdown, showing that upon over-expression of Myc, processes such as ribosomal biogenesis and chromosome segregation are induced. L. Fraction of Myc targets in significantly induced and repressed GO categories, compared to what is expected by random (dashed line). M. Overlap between differential genes detected in Myc perturbation experiments, and differential genes detected in previous published perturbations (Scognamiglio et al., 2016). Fisher exact test p-values are presented. N. Expression fold change of selected chromatin modifiers.

Article Snippet: Secondary mouse embryonic fibroblast (MEF) from Mbd3 flox/- cell line (A12 clone: Mbd3 flox/- cell lines that carries the GOF18-Oct4-GFP transgenic reporter (complete Oct4 enhancer region with distal and proximal enhancer elements) (Addgene plasmid #60527)) and WT-1 cell line (WT-1 clone that carries the deltaPE-GOF18-Oct4-GFP reporter (Addgene plasmid#52382) were previously described ( Rais et al., 2013 ).

Techniques: Infection, Over Expression, Expressing, Inhibition, Activity Assay, Marker, Transduction

Journal: Cell stem cell

Article Title: Deterministic Somatic Cell Reprogramming Involves Continuous Transcriptional Changes Governed by Myc and Epigenetic-Driven Modules

doi: 10.1016/j.stem.2018.11.014

Figure Lengend Snippet: Key Resources Table

Article Snippet: Secondary mouse embryonic fibroblast (MEF) from Mbd3 flox/- cell line (A12 clone: Mbd3 flox/- cell lines that carries the GOF18-Oct4-GFP transgenic reporter (complete Oct4 enhancer region with distal and proximal enhancer elements) (Addgene plasmid #60527)) and WT-1 cell line (WT-1 clone that carries the deltaPE-GOF18-Oct4-GFP reporter (Addgene plasmid#52382) were previously described ( Rais et al., 2013 ).

Techniques: Recombinant, Protease Inhibitor, Sample Prep, Methylation, Transgenic Assay, Negative Control, Software

Journal: Neurobiology of disease

Article Title: The absence of Parkin in hTau mice leads to synaptic mitochondrial dysfunction, alterations to the synaptic proteome, and increased phosphorylated tau in the Hippocampus

doi: 10.1016/j.nbd.2025.107084

Figure Lengend Snippet: The Seahorse XF Cell Mito Stress Test was performed using synaptosomes isolated from 8 to 9-month-old male hTau, hTau/PKO, and hTau/Parkin W402A mice. Oxygen consumption rate (OCR) line graphs for (A) hTau/PKO and (C) hTau/Parkin W402A compared to hTau mice. Line graph data presented as mean ± SEM. Calculated respiration profiles for (B) hTau/PKO and (D) hTau/Parkin W402A compared to hTau mice. Significance: p < 0.01**, two-way ANOVA (hTau/PKO vs hTau: interaction DF = 5, respiration profiles DF = 5, genotype DF = 1, and residual DF = 60; hTau/Parkin W402A vs hTau: interaction DF = 5, respiration profiles DF = 5, genotype DF = 1, and residual DF = 48) followed by Šidák ’ s multiple comparisons test. n = 5–6 mice per group. Extracellular acidification rate (ECAR) line graphs for (E) hTau/PKO and (G) hTau/ Parkin W402A compared to hTau mice. Calculated glycolytic profiles for (F) hTau/PKO and (H) hTau/Parkin W402A compared to hTau mice. Significance: p < 0.05*, two-way ANOVA (hTau/PKO vs hTau: interaction DF = 2, respiration profiles DF = 2, genotype DF = 1, and residual DF = 30; hTau/Parkin W402A vs hTau: interaction DF = 2, respiration profiles DF = 2, genotype DF = 1, and residual DF = 30) followed by Šidák’s multiple comparisons test. n = 5–6 mice per group. Violin plot data presented with median and quartiles indicated with dashed lines. DF = degrees of freedom; O = oligomycin, complex V inhibitor; F = FCCP, uncoupler; R/A = rotenone/antimycin A, complex I/III inhibitors.

Article Snippet: Congenic mice used for this study were generated by intercrossing human tau transgenic mice (hTau, JAX strain #005491, overexpress all six non-mutant human tau isoforms in the absence of murine tau) with either parkin knockout mice (PKO, JAX strain #006582) or mutant parkin mice (Parkin W402A , Taconic strain #15143, now available as JAX strain #029317, CRISPR/Cas9 generated mice carrying mutant Parkin W402A ), then backcrossing the progeny to the hTau strain for a minimum of ten generations.

Techniques: Isolation

Journal: Neurobiology of disease

Article Title: The absence of Parkin in hTau mice leads to synaptic mitochondrial dysfunction, alterations to the synaptic proteome, and increased phosphorylated tau in the Hippocampus

doi: 10.1016/j.nbd.2025.107084

Figure Lengend Snippet: Brain homogenate and synaptic mitochondria were isolated from 8 to 9-month-old WT, hTau, hTau/PKO, and hTau/Parkin W402A mice to assess the levels of select proteins using immunoblotting. Representative immunoblots for parkin in (A) brain and (B) synaptic mitochondria as well as (E) ubiquitin in synaptic mitochondria along with their corresponding loading controls (actin for brain, VDAC1 + 3 for synaptic mitochondria). Quantification of the levels of parkin in (C) brain homogenate (normalized to actin) and in (D) synaptic mitochondria (normalized to VDAC1 + 3) as well as (F) ubiquitin in synaptic mitochondria (normalized to VDAC1 + 3). Significance: p < 0.05*, 0.01**, one-way ANOVA (Brain (parkin): genotype DF = 2, and residual DF = 15; synaptic mitochondria (parkin): genotype DF = 2, and residual DF = 14; synaptic mitochondria (ubiquitin): genotype DF = 3, and residual DF = 19) followed by Tukey’s multiple comparisons test. n = 5–6 mice per group. Violin plot data presented with median and quartiles indicated with dashed lines. DF = degrees of freedom.

Article Snippet: Congenic mice used for this study were generated by intercrossing human tau transgenic mice (hTau, JAX strain #005491, overexpress all six non-mutant human tau isoforms in the absence of murine tau) with either parkin knockout mice (PKO, JAX strain #006582) or mutant parkin mice (Parkin W402A , Taconic strain #15143, now available as JAX strain #029317, CRISPR/Cas9 generated mice carrying mutant Parkin W402A ), then backcrossing the progeny to the hTau strain for a minimum of ten generations.

Techniques: Isolation, Western Blot, Ubiquitin Proteomics

Journal: Neurobiology of disease

Article Title: The absence of Parkin in hTau mice leads to synaptic mitochondrial dysfunction, alterations to the synaptic proteome, and increased phosphorylated tau in the Hippocampus

doi: 10.1016/j.nbd.2025.107084

Figure Lengend Snippet: Heatmap representing enriched (A) metabolic and (B) signaling pathways produced by IPA canonical pathway analysis comparing all the studied conditions. Score filter p -value cutoff = 1.3 (log10) and z-score cutoff = 1 (absolute value). Blue blocks and orange blocks represent inhibited and activated pathways, respectively. Gray dots represent pathways that did not achieve significance in the given experimental comparison. Heatmaps show the GSEA enrichment scores (NES) and adjusted p -value for the identified Gene Ontology Biological Processes (GO BP) that were significantly changed in (C) hTau vs WT, (D) hTau/PKO vs hTau, and (E) hTau/Parkin W402A vs hTau synaptosomes. n = 5 mice per group. Enrichment analysis was performed in the R software using a p -value cutoff of <0.05. The Benjamini–Hochberg postdoc test was then applied for the generation of adjusted p -values.

Article Snippet: Congenic mice used for this study were generated by intercrossing human tau transgenic mice (hTau, JAX strain #005491, overexpress all six non-mutant human tau isoforms in the absence of murine tau) with either parkin knockout mice (PKO, JAX strain #006582) or mutant parkin mice (Parkin W402A , Taconic strain #15143, now available as JAX strain #029317, CRISPR/Cas9 generated mice carrying mutant Parkin W402A ), then backcrossing the progeny to the hTau strain for a minimum of ten generations.

Techniques: Protein-Protein interactions, Produced, Comparison, Software

Journal: Neurobiology of disease

Article Title: The absence of Parkin in hTau mice leads to synaptic mitochondrial dysfunction, alterations to the synaptic proteome, and increased phosphorylated tau in the Hippocampus

doi: 10.1016/j.nbd.2025.107084

Figure Lengend Snippet: Volcano plots showing DEPs based on p -value obtained from Ms. Stats (−log 10 ) and log 2 for the 9298 identified proteins. Significance was determined by using p -value cutoff = 1.3 (log 10 ) and z-score cutoff = 1 (absolute value). Blue = significantly downregulated proteins. Red = Significantly upregulated proteins. (A) hTau vs WT synaptosome proteomic comparison showed a total of 333 DEPs, 149 upregulated and 184 downregulated. (B) hTau/PKO vs hTau synaptosome proteomic comparison showed a total of 327 DEPs, 179 upregulated and 148 downregulated. (C) hTau/Parkin W402A vs hTau synaptosome proteomic comparison showed a total of 262 DEPs, 135 upregulated and 127 downregulated. n = 5 mice per group. The five most highly enriched and depleted proteins are annotated in each comparison.

Article Snippet: Congenic mice used for this study were generated by intercrossing human tau transgenic mice (hTau, JAX strain #005491, overexpress all six non-mutant human tau isoforms in the absence of murine tau) with either parkin knockout mice (PKO, JAX strain #006582) or mutant parkin mice (Parkin W402A , Taconic strain #15143, now available as JAX strain #029317, CRISPR/Cas9 generated mice carrying mutant Parkin W402A ), then backcrossing the progeny to the hTau strain for a minimum of ten generations.

Techniques: Comparison

Journal: Neurobiology of disease

Article Title: The absence of Parkin in hTau mice leads to synaptic mitochondrial dysfunction, alterations to the synaptic proteome, and increased phosphorylated tau in the Hippocampus

doi: 10.1016/j.nbd.2025.107084

Figure Lengend Snippet: The STRING database was used for network analysis of the hTau vs WT, hTau/PKO vs hTau, and hTau/Parkin W402A vs hTau DEPs. The k-means clustering method was used under a high confidence interaction score (min. Interaction score = 0.7). (A) Network representation for the top upregulated and downregulated cluster of proteins in the hTau vs WT comparison. (B) Network representation for the top upregulated and downregulated cluster of proteins in the hTau/PKO vs hTau comparison. (C) Network representation for the top upregulated and downregulated cluster of proteins in the hTau/Parkin W402A vs hTau comparison. n = 5 mice per group. The Gene Ontology Biological Process (GO BP), KEGG, and Reactome databases were used to identify changed pathways.

Article Snippet: Congenic mice used for this study were generated by intercrossing human tau transgenic mice (hTau, JAX strain #005491, overexpress all six non-mutant human tau isoforms in the absence of murine tau) with either parkin knockout mice (PKO, JAX strain #006582) or mutant parkin mice (Parkin W402A , Taconic strain #15143, now available as JAX strain #029317, CRISPR/Cas9 generated mice carrying mutant Parkin W402A ), then backcrossing the progeny to the hTau strain for a minimum of ten generations.

Techniques: Comparison

Journal: Neurobiology of disease

Article Title: The absence of Parkin in hTau mice leads to synaptic mitochondrial dysfunction, alterations to the synaptic proteome, and increased phosphorylated tau in the Hippocampus

doi: 10.1016/j.nbd.2025.107084

Figure Lengend Snippet: (A) Representative confocal z-stack images of the DG from 8 to 9-month-old male hTau, hTau/PKO, and hTau/Parkin W402A (hTau/W402A) stained with total Tau (green), AT8 (pTauSer202 + pTauT205, red), and DAPI (blue). Objective = 60×, scale bar = 50 μm. (B) Hippocampal quantifications of the % co-localization between total Tau and AT8 in the DG and the whole hippocampus (integration of DG + CA1 + CA3). (C) Representative confocal z-stack images of the parietal cortex from 8 to 9-month-old male hTau, hTau/PKO, and hTau/Parkin W402A stained with total Tau (green), AT8 (pTauSer202 + pTauT205, red), and DAPI (blue). Objective = 60×, scale bar = 50 μm. (D) Quantification of the % co-localization between total Tau and AT8 in the parietal cortex. Significance: p < 0.05*, one-way ANOVA (DG: genotype DF = 2, and residual DF = 18. Hippocampus: genotype DF = 2, and residual DF = 16. Cortex: genotype DF = 2, and residual DF = 19) followed by Tukey’s multiple comparisons test. n = 6–8 mice per group. Violin plot data presented with median and quartiles indicated with dashed lines. DF = degrees of freedom.

Article Snippet: Congenic mice used for this study were generated by intercrossing human tau transgenic mice (hTau, JAX strain #005491, overexpress all six non-mutant human tau isoforms in the absence of murine tau) with either parkin knockout mice (PKO, JAX strain #006582) or mutant parkin mice (Parkin W402A , Taconic strain #15143, now available as JAX strain #029317, CRISPR/Cas9 generated mice carrying mutant Parkin W402A ), then backcrossing the progeny to the hTau strain for a minimum of ten generations.

Techniques: Staining

Journal: Nature Communications

Article Title: VCAM1 acts in parallel with CD69 and is required for the initiation of oligodendrocyte myelination

doi: 10.1038/ncomms13478

Figure Lengend Snippet: ( a ) Tissue lysates from 7-, 21- and 28-day-old CD69 shRNA transgenic (Tg) and control mouse brains were immunoblotted with an antibody against MBP, CNPase, CD69, VCAM1 or actin. Data are representative of three experiments. ( b ) Corpus callosum sections at postnatal day 11 were co-stained with an anti-MBP antibody (red) and DAPI (blue). Data are representative of two experiments. Scale bar, 200 μm. ( c – e ) Electron microscopic data of 9-day-old corpus callosum are shown. Data are representative. Scale bar, 2 μm. The g-ratios (200–300 myelinated fibres) are plotted for axon diameters. Average g-ratios are also shown. Data were evaluated using Student’s t -test (** P =7.13E−15; n =213–260 axons of two independent experiments).

Article Snippet: MBP promoter-driven Cre recombinase transgenic mice (RBRC No. 01461) were obtained from Riken BioResource Center (Ibaraki, Japan).

Techniques: shRNA, Transgenic Assay, Staining