Reprogrammed Cells Display Distinct Proteomic Signatures Associated with Colony Morphology Variability

Figure 5

Pathway analysis of the protein landscape between the unstable colony morphology group and the stable colony morphology group. (a) IPA-generated tables of the top predicted upstream regulators in the unstable colony morphology group. (b) A model (modified from [29, 30]) illustrating mechanistic factors involved in the EMT effect caused by TGFB signalling and the small molecules we applied in the experiment that lead to the results illustrated in (d). (c) A volcano plot showing proteins being more abundant in one of the groups (blue dots), where a selection of proteins related to EMT and TGFB signalling is highlighted in red. (d) An illustration of the experiment where cells from unstable class 1 (line 4-C) were seeded on 9 mm cover slips and treated for 7 days with the ligands ALX-270-445, A83-01, or Smurf1-i. Graphs showing quantitative immunofluorescence (surface area) of vimentin (EMT marker) and E-cadherin (colony marker) in line 4-C after treatment with the ligands ALX-270-445, A83-01, and SMURF1-i at varying concentrations. The analysis was done by using the Andor Dragonfly 505 microscope and subsequently quantified by using the Imaris software, where raw surface area measurements of vimentin and E-cadherin were normalized on nucleus count for each cover slip. Expression is given as ratio to the median of the control samples (). Statistical analysis was performed with Mann-Whitney test. Significant differences are shown as .

(a) Unstable morphology landscape

(b)

(c)

(d)