Journal: Cancers

Article Title: Drug-Induced Resistance and Phenotypic Switch in Triple-Negative Breast Cancer Can Be Controlled via Resolution and Targeting of Individualized Signaling Signatures

doi: 10.3390/cancers13195009

Figure Lengend Snippet: TNBC tissues are represented by different patient-specific signaling signatures, majority of which do not include EGFR. ( A ) Fold changes in expression levels of EGFR and pEGFR in TNBC and non-TNBC tumors are shown. Y1068 and Y1173 are EGFR phosphorylation sites; ( B ) Examples for patient-specific sets of active unbalanced processes are shown. Each sample harbors a set of 1–3 active unbalanced processes (PaSSS), represented schematically by a barcode. In each barcode active unbalanced processes are represented by black or gray squares, inactive white. Negative/positive amplitude denotes how the patients are correlated with respect to a particular process. Suggested PaSSS-based therapies appear below each barcode; ( C ) Heterogeneity index of 3 subgroups, represented by a ratio between the number of distinct PaSSSs and the number of samples in each subset, is shown for the TNBC subset of tissues, the entire set (3467 samples from 11 cancer types) and the subset of non-TNBC samples. (Abbreviations: TNBC—Triple Negative Breast Cancer, PaSSS—Patient-specific signaling signature, EGFR—Epidermal Growth Factor Receptor, VEGFR2—Vascular Endothelial Growth Factor Receptor 2, Her2—Human Epidermal growth factor Receptor 2, Src—Proto-oncogene tyrosine-protein kinase Src).

Article Snippet: The following conjugated antibodies were used: anti-p-EGFR (Y1068) (R&D Systems, Minneapolis, MN, USA, cat. no. IC3570G), anti-p-ERK2 (Thr202/Tyr204) (BioLegend, San Diego, CA, USA, cat. No. 675503), anti-p-S6 (Ser235/236) (BioLegend, cat. no. 608605), and anti-GAPDH (Santa Cruz Biotechnology, Dallas, Texas, USA, cat. no. sc-47724AF594).

Techniques: Expressing, Phospho-proteomics

Journal: Nature Cell Biology

Article Title: Joint epigenome profiling reveals cell-type-specific gene regulatory programmes in human cortical organoids

doi: 10.1038/s41556-023-01296-5

Figure Lengend Snippet: (A) Gating strategy for the immunoFACS of RGC and IPC from cortical organoids. From left to right: Singlets in G 0 /G 1 based on their DNA content (DAPI) were selected first, followed by separation of nuclei positive for SOX2 or EOMES. SOX2 positive cells were further subdivided based on PAX6. Number represent mean ± SD from the parental singlet population. (B) Bar plot depicting measured methylation levels of lambda (only GpC methylated) and fully methylated puc19 DNA spike-in controls. Black dots: mean of individual biological replicates (n = 2 for each condition); Numbers: mean methylation levels. (C) DNA methylation coverage (100 bp bins) for RGC and IPC. Black dot and whiskers indicate mean ± SD (n = 2). (D-G) Pairwise correlation matrixes displaying correlation coefficient and/or scatterplot for gene expression (D; Spearman’s), DNA methylation (E; Pearson, 10 kb bins), GpC accessibility (F; Pearson, 10 kb bins) and 3D genome (G; stratum adjusted correlation coefficient, 10 kb bins). (H-I) CpG methylation (H) and GpC accessibility (I) levels at motif centered CTCF ChIP-seq peaks derived from the whole human cortex. (J) Contact probability in logarithmic bins for RGC and IPC. Lines: mean values from different methods; semi-transparent ribbons: SEM. (K) Boxplots displaying quantification of intraTAD and interTAD contact enrichment in RGC and IPC (n = 2939 TADs). Statistical significance is calculated using a two-sided paired t -test. Boxplots display median (line), 25th or 75th percentiles (box) as well as 10th or 90th percentiles (whisker). (L) Average contact strength between intraTAD pairs of GpC peaks containing convergent orientated CTCF motifs. Source numerical data are available in source data.

Article Snippet: SOX2-PE (1:20; BD Biosciences, 562195), PAX6-Alexa Fluor 488 (1:40; BD Biosciences, 561664) and EOMES-eFluor660 (1:20; Thermo Scientific, 50-4877-41) antibodies were used.

Techniques: Methylation, DNA Methylation Assay, Expressing, CpG Methylation Assay, ChIP-sequencing, Derivative Assay, Whisker Assay

Journal: Purinergic Signalling

Article Title: Up-regulation of P2X7 receptors mediating proliferation of Schwann cells after sciatic nerve injury

doi: 10.1007/s11302-015-9445-8

Figure Lengend Snippet: Expression of P2X7R ir in longitudinal sections of normal sciatic nerves. a–c show co-localization of P2X7R ir (red) and S100Aβ ir (green). Note an arrowhead showing a fibre-like structure and an arrow showing a trapezoid structure in a and b; c is the merged image of a and b. Note an arrow indicating a trapezoid structure double labelled by both P2X7R and S100β antibodies (yellow). d–f show co-localization of P2X7R ir (red) and Tuj-1 ir (green). Note an arrow showing a trapezoid structure in d and an arrow showing an axon in e. f is the merged image of d and f; note an arrow indicating a green axon passing through the middle of five trapezoid structures. g–i show co-localization of P2X7R ir (red) and p75NTR ir (green). Note an arrow showing a fibre-like structure in g and h. i is the merged image of g and h. An arrow indicates a double-labelled non-myelinating Schwann cell with P2X7R and p75NTR antibodies (yellow). j–l show co-localization of P2X7R ir (red) and MBP ir (green). Note an arrow showing a fibre-like structure with P2X7R ir, which was not labelled by MBP in l. m–o show co-localization of P2X7R ir (red) and CASPR ir (green). Note that no colocalization of P2X7R ir and CASPR ir was observed. Scale bars in a–c and g–i = 100 μm; scale bars in d–f = 50 μm

Article Snippet: The sections were washed 3–5 min in PBS, and then preincubated in a blocking solution (10 % normal bovine serum, 0.2 % Triton X-100, 0.4 % sodium azide in 0.01 mol/L PBS, pH 7.2) for 30 min followed by incubation with the primary antibodies: P2X7R (1:1000), Alomone, rabbit polyclonal, APR-004; S100β (1:400), Tuj-1 (1:200), p75NTR, PCNA (1:200), MBP (1:200), mouse monoclonal antibodies from Boster, CASPR (1:400) mouse monoclonal antibodies from Santa Cruz, at room temperature overnight.

Techniques: Expressing