Toxicity of Combinations of Kinase Pathway Inhibitors to Normal Human Cells in a Three-Dimensional Culture

Nejad, Pouria Rafsanjani; Thakuri, Pradip Shahi; Singh, Sunil; Lamichhane, Astha; Heiss, Jacob; Tavana, Hossein

doi:10.1177/24726303211008858

Cited by 5 publications

(5 citation statements)

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“…In such a strategy, modulating signaling pathways would be used prior to the addition of the main targeted therapy to drive heterogeneous populations of cells into a drug susceptible state. This is in contrast to dosing with a combination of inhibitors at the same time, which is not always tolerated due to toxicity and side effects (Park et al 2013; Rafsanjani Nejad et al 2021; Jardim et al 2020).…”

Section: Discussionmentioning

confidence: 99%

Disrupting cellular memory to overcome drug resistance

Harmange

Hueros

Schaff

et al. 2022

Preprint

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Cellular memory describes the length of time a particular transcriptional state exists at the single-cell level. Transcriptional states with memory can underlie important processes in biology, including therapy resistance in cancer. Here we present a new experimental and computational approach for identifying gene expression states with memory at single-cell resolution by combining single-cell RNA sequencing (scRNA-seq) with cellular barcoding. With this technique, we can systematically quantify the full expression profile of these memory states as well as their population dynamics including the relative growth rates of cells within different states and the rates of switching between states. We applied this approach to human melanoma cells and uncovered memory gene expression states that are predictive of which cells will be resistant to combination BRAF and MEK inhibition. While these cells have not been treated with targeted therapies, they already express markers of resistance, and thus are referred to here as “primed” for resistance. From the scRNA-seq data alone, the drug-susceptible and primed cells appear as two distinct and unrelated cell populations. From the lineage barcodes, we found that most cells remain within the same state, demonstrating memory of gene expression. However, we also directly observe state switching as we find that about 18% of lineages contain cells that have switched states. While the molecular drivers of state switching are not immediately apparent from scRNA-seq data alone, we specifically analyzed lineages that undergo state switching and identified TGF-β and PI3K as drivers of state switching at the single-cell level. Through functional validation and single-cell RNA-sequencing, we show mechanistic single-cell manipulation of state switching that ultimately yields changes in cellular phenotype. We leverage these mechanisms of state switching to delay resistance by demonstrating that reducing the number of primed cells with a PI3K inhibitor prior to BRAF and MEK inhibition ultimately leads to fewer resistant colonies. Our results show that modulation of cellular signaling can globally regulate gene expression programs to overcome therapy resistance.

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Section: Discussionmentioning

confidence: 99%

Disrupting cellular memory to overcome drug resistance

Harmange

Hueros

Schaff

et al. 2022

Preprint

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“…59 Beyond investigating efficacy of drug combinations against cancer cells, it is critical to study their potential toxic effects. While we recently used a 3D model of normal cells to study toxicities of combinations of MAPK and PI3K/Akt inhibitors to normal bone marrow and colon cells, 60 more complex models such as organs-on-a-chip are developed to address this important question. 61 ■ MATERIALS AND METHODS Cell Culture and Spheroid Formation.…”

Section: ■ Discussionmentioning

confidence: 99%

Therapeutic Targeting of Cancer Stem Cells Prevents Resistance of Colorectal Cancer Cells to MEK Inhibition

Lamichhane

Thakuri

Singh

et al. 2022

ACS Pharmacol. Transl. Sci.

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Drug resistance is a leading cause for the failure of cancer treatments. Plasticity of cancer cells to acquire stem cell-like properties enables them to escape drug toxicity through different adaptive mechanisms. Eliminating cancer stem cells (CSCs) can potentially improve treatment outcomes for patients. To determine the role of CSCs in resistance of colorectal cancer cells to targeted therapies and identify treatment strategies, we treated spheroids of BRAFmut and KRASmut colorectal cancer cells with inhibitors of the mitogen-activated protein kinase pathway and studied resistance mechanisms through gene and protein expression analyses. We found that treatments activated several oncogenic pathways and expression of CSC markers CD166 and ALDH1A3. We identified a specific combination treatment using trametinib and mithramycin A to simultaneously inhibit the CSC phenotype and activities of several pathways in cancer cells. This study demonstrates the feasibility of therapeutic targeting of CSCs as a strategy to block tumorigenic activities of cancer cells.

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“…In such a strategy, modulating signaling pathways would be used before the addition of the main targeted therapy to drive heterogeneous populations of cells into a drug-susceptible state. This is in contrast to dosing with a combination of inhibitors at the same time, which is not always tolerated due to toxicity and side effects [60][61][62] .…”

Section: Primed Cells Survive Continued Treatment Brafi Mekimentioning

confidence: 99%

Disrupting cellular memory to overcome drug resistance

Harmange,

Hueros,

Schaff

et al. 2023

Nat Commun

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Gene expression states persist for varying lengths of time at the single-cell level, a phenomenon known as gene expression memory. When cells switch states, losing memory of their prior state, this transition can occur in the absence of genetic changes. However, we lack robust methods to find regulators of memory or track state switching. Here, we develop a lineage tracing-based technique to quantify memory and identify cells that switch states. Applied to melanoma cells without therapy, we quantify long-lived fluctuations in gene expression that are predictive of later resistance to targeted therapy. We also identify the PI3K and TGF-β pathways as state switching modulators. We propose a pretreatment model, first applying a PI3K inhibitor to modulate gene expression states, then applying targeted therapy, which leads to less resistance than targeted therapy alone. Together, we present a method for finding modulators of gene expression memory and their associated cell fates.

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Toxicity of Combinations of Kinase Pathway Inhibitors to Normal Human Cells in a Three-Dimensional Culture

Cited by 5 publications

References 51 publications

Disrupting cellular memory to overcome drug resistance

Disrupting cellular memory to overcome drug resistance

Therapeutic Targeting of Cancer Stem Cells Prevents Resistance of Colorectal Cancer Cells to MEK Inhibition

Disrupting cellular memory to overcome drug resistance

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