Freeware tool for analysing numbers and sizes of cell colonies

Brzozowska, B.; Gałecki, Maciej; Tartas, Adrianna; Ginter, J.; Kaźmierczak, Urszula; Lundholm, Lovisa

doi:10.1007/s00411-018-00772-z

Cited by 36 publications

(29 citation statements)

References 20 publications

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“…Following incubation, cells were fixed in methanol and stained using 0.5% crystal violet in PBS, rinsed with water, and air-dried overnight. Colonies containing >~50 cells were counted using inverted light microscope manually or from captured images using countPHICS (count and Plot HIstograms of Colony Size) software, a macro written for ImageJ ( Brzozowska et al, 2019 ).…”

Section: Methodsmentioning

confidence: 99%

Co-regulation and function of FOXM1/RHNO1 bidirectional genes in cancer

Barger

Chee

Albahrani

et al. 2021

eLife

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The FOXM1 transcription factor is an oncoprotein and a top biomarker of poor prognosis in human cancer. Overexpression and activation of FOXM1 is frequent in high-grade serous carcinoma (HGSC), the most common and lethal form of human ovarian cancer, and is linked to copy number gains at chromosome 12p13.33. We show that FOXM1 is co-amplified and co-expressed with RHNO1, a gene involved in the ATR-Chk1 signaling pathway that functions in the DNA replication stress response. We demonstrate that FOXM1 and RHNO1 are head-to-head (i.e., bidirectional) genes (BDG) regulated by a bidirectional promoter (BDP) (named F/R-BDP). FOXM1 and RHNO1 each promote oncogenic phenotypes in HGSC cells, including clonogenic growth, DNA homologous recombination repair, and poly-ADP ribosylase inhibitor resistance. FOXM1 and RHNO1 are one of the first examples of oncogenic BDG, and therapeutic targeting of FOXM1/RHNO1 BDG is a potential therapeutic approach for ovarian and other cancers.

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Section: Methodsmentioning

confidence: 99%

Co-regulation and function of FOXM1/RHNO1 bidirectional genes in cancer

Barger

Chee

Albahrani

et al. 2021

eLife

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show abstract

“…The colonies in 24-well plates were counted manually, only including those that count at least 50 cells. Colonies in the 12-well plate were additionally counted and measured using countPHICS [ 58 ].…”

Section: Methodsmentioning

confidence: 99%

CCAAT/Enhancer-Binding Protein Delta (C/EBPδ): A Previously Unrecognized Tumor Suppressor that Limits the Oncogenic Potential of Pancreatic Ductal Adenocarcinoma Cells

Hartl

Duitman

Aberson

et al. 2020

Cancers

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CCAAT/enhancer-binding protein δ (C/EBPδ) is a transcription factor involved in growth arrest and differentiation, which has consequently been suggested to harbor tumor suppressive activities. However, C/EBPδ over-expression correlates with poor prognosis in glioblastoma and promotes genomic instability in cervical cancer, hinting at an oncogenic role of C/EBPδ in these contexts. Here, we explore the role of C/EBPδ in pancreatic cancer. We determined C/EBPδ expression in biopsies from pancreatic cancer patients using public gene-expression datasets and in-house tissue microarrays. We found that C/EBPδ is highly expressed in healthy pancreatic ductal cells but lost in pancreatic ductal adenocarcinoma. Furthermore, loss of C/EBPδ correlated with increased lymph node involvement and shorter overall survival in pancreatic ductal adenocarcinoma patients. In accordance with this, in vitro experiments showed reduced clonogenic capacity and proliferation of pancreatic ductal adenocarcinoma cells following C/EBPδ re-expression, concurrent with decreased sphere formation capacity in soft agar assays. We thus report a previously unrecognized but important tumor suppressor role of C/EBPδ in pancreatic ductal adenocarcinoma. This is of particular interest since only few tumor suppressors have been identified in the context of pancreatic cancer. Moreover, our findings suggest that restoration of C/EBPδ activity could hold therapeutic value in pancreatic ductal adenocarcinoma, although the latter claim needs to be substantiated in future studies.

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“…The experiment was performed in triplicates and repeated three times. Additionally, the number of cell colonies, their area, and the distribution of their size was calculated and plotted with the help of ImageJ macro PHICS (Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Warsaw, Poland) [33].…”

Section: Colony Formation Assaymentioning

confidence: 99%

Triple Combination of Ascorbate, Menadione and the Inhibition of Peroxiredoxin-1 Produces Synergistic Cytotoxic Effects in Triple-Negative Breast Cancer Cells

et al. 2020

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Triple-negative breast cancer (TNBC) is an aggressive form of mammary malignancy currently without satisfactory systemic treatment options. Agents generating reactive oxygen species (ROS), such as ascorbate (Asc) and menadione (Men), especially applied in combination, have been proposed as an alternative anticancer modality. However, their effectiveness can be hampered by the cytoprotective effects of elevated antioxidant enzymes (e.g., peroxiredoxins, PRDX) in cancer. In this study, PRDX1 mRNA and protein expression were assessed in TNBC tissues by analysis of the online RNA-seq datasets and immunohistochemical staining of tissue microarray, respectively. We demonstrated that PRDX1 mRNA expression was markedly elevated in primary TNBC tumors as compared to non-malignant controls, with PRDX1 protein staining intensity correlating with favorable survival parameters. Subsequently, PRDX1 functionality in TNBC cell lines or non-malignant mammary cells was targeted by genetic silencing or chemically by auranofin (AUR). The PRDX1-knockdown or AUR treatment resulted in inhibition of the growth of TNBC cells in vitro. These cytotoxic effects were further synergistically potentiated by the incubation with a combination of the prooxidant agents, Asc and Men. In conclusion, we report that the PRDX1-related antioxidant system is essential for maintaining redox homeostasis in TNBC cells and can be an attractive therapeutic target in combination with ROS-generating agents.

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Freeware tool for analysing numbers and sizes of cell colonies

Cited by 36 publications

References 20 publications

Co-regulation and function of FOXM1/RHNO1 bidirectional genes in cancer

Co-regulation and function of FOXM1/RHNO1 bidirectional genes in cancer

CCAAT/Enhancer-Binding Protein Delta (C/EBPδ): A Previously Unrecognized Tumor Suppressor that Limits the Oncogenic Potential of Pancreatic Ductal Adenocarcinoma Cells

Triple Combination of Ascorbate, Menadione and the Inhibition of Peroxiredoxin-1 Produces Synergistic Cytotoxic Effects in Triple-Negative Breast Cancer Cells

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