Quantitative characterization of stem cell dynamics in the hypoxic microenvironment with chemotherapy using computer vision

<p>Background: The cancer stem cell hypothesis has implicated a unique subpopulation of cancer cells as the primary drivers of tumorigenesis with capabilities of self-renewal and ability to reconstitute the full spectrum of heterogeneity within a tumour. It has been noted that the proportion of cancer stem cells is increased by hypoxia, which has been implicated as playing a key causative role in metastasis and therapeutic resistance in multiple solid tumours, including breast cancer. Recently it has been also reported that that cytotoxic chemotherapeutics may also induce a stem-like state in cancer cells. The dynamics of cancer stem cell induction by these conditions, and the possibility of synergistic effects, however, have not been accurately quantified. </p><p>Methods: In this work, we present, for the first time, an analysis pipeline for the quantification of cancer stem cell dynamics using time-lapse microscopy and computer-assisted, unbiased digital image processing. The MDA-MB-231 breast cancer cell line, transduced with a NANOG promoter driven GFP reporter gene, thereby reporting a stem-like state, was cultured under varying conditions of deferoxamine (a hypoxia chemo-mimetic) and paclitaxel (a chemotherapeutic reagent). Cellular dynamics were recorded by time-lapse microscopy capturing phase contrast and fluorescent images over a four-day period. Areas of fluorescence and confluence determined from phase images were compared to obtain the time dynamics of the proportion of stem-like cells. These dynamics were then fit to a two-state ordinary differential equation model, and the underlying distribution of parameter sets was studied.</p> <p>Results: Using the obtained dynamics, the time series of the proportion of NANOG-expressing cells was elucidated, and the parameter sets obtained by fitting experimental data to the model revealed shifts in parameter value distributions for the various cases of chemotherapy and deferoxamine concentrations. These shifts indicate that there are likely non-linear effects of these drugs on key underlying biological rates, such as the rates of differentiation and dedifferentiation. </p> <p>Conclusions: Taken together, these results are indicative of a number of relationships between the parameters governing cancer stem cell dynamics when affected by both hypoxia and chemotherapy, as occurs in the setting of a patient. This underscores the need for further characterisation of these dynamics, including a more thorough exploration of the effects of differing concentrations of chemotherapy, deferoxamine, and true hypoxia. Gaining an understanding of these dynamics may ultimately provide avenues to improve the efficacy of chemotherapy and reduce the risk of tumour recurrence, by optimizing the chemotherapy regimen together with manipulating the microenvironment.</p

Collateral Sensitivity Networks in ALK-positive Lung Cancer Reveals Dynamic Nature of Drug Resistance

<p>H3122 ALK-positive NSCLC cell line evolved, over 16 weeks, to resistance for: 4 ALK inhibitors (ceritinib, alectinib, lorlatinib, crizotinib), 3 HSP-90 inhibitors (ganetespib, IPI504, AUY922), paclitaxel, pemetrexed, and etoposide; collateral sensitivities analyzed.</p