Differential unfolded protein response regulation in KRAS silencing sensitive versus innately resistant colorectal cancer cells [LS174T]
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ABSTRACT:
PROVIDER: PRJNA1072041 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR27833119.fastq.gz | Fastqsanger.gz | |||
| SRR27833120.fastq.gz | Fastqsanger.gz | |||
| SRR27833121.fastq.gz | Fastqsanger.gz | |||
| SRR27833122.fastq.gz | Fastqsanger.gz |
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Project description:Colorectal cancer (CRC) responses to mutant-selective KRAS inhibitors remain modest, with stable disease and rapid recurrence as the most common outcomes. The molecular mechanisms enabling CRC cells to tolerate KRAS inhibition and ultimately develop resistance remain poorly understood. Here, we investigated early transcriptional and proteomic responses to KRAS silencing in 3D CRC cell line spheroid models, aiming to identify pathways associated with sensitivity or resistance to KRAS blockade. Cell lines were stratified into KRAS silencing-sensitive (HCT116 and SW480) and -resistant (LS174T and SW837) groups based on spheroid growth, cell cycle progression, and apoptosis induction. Transcriptional profiling revealed the unfolded protein response (UPR) and WNT/β-catenin signaling as pathways specifically upregulated in KRAS silencing-sensitive cells and downregulated in resistant cells. Proteomic analysis of membrane-enriched fractions further supported UPR deregulation, showing a pronounced downregulation of translation-related proteins in sensitive cells. Functional assays validated that the sensitive cell line HCT116 exhibits reduced protein aggregation and lower translational capacity upon KRAS knockdown, consistent with UPR activation. Pharmacological inhibition of IRE1α-mediated UPR signaling did not revert KRAS silencing-induced cell cycle arrest or apoptosis in this cell line. Collectively, our results highlight the UPR activation as an early adaptive response of KRAS-dependent CRC cells tolerant to KRAS silencing.
2024-02-06 | GSE254833 | GEO
Project description:Colorectal cancer (CRC) responses to mutant-selective KRAS inhibitors remain modest, with stable disease and rapid recurrence as the most common outcomes. The molecular mechanisms enabling CRC cells to tolerate KRAS inhibition and ultimately develop resistance remain poorly understood. Here, we investigated early transcriptional and proteomic responses to KRAS silencing in 3D CRC cell line spheroid models, aiming to identify pathways associated with sensitivity or resistance to KRAS blockade. Cell lines were stratified into KRAS silencing-sensitive (HCT116 and SW480) and -resistant (LS174T and SW837) groups based on spheroid growth, cell cycle progression, and apoptosis induction. Transcriptional profiling revealed the unfolded protein response (UPR) and WNT/β-catenin signaling as pathways specifically upregulated in KRAS silencing-sensitive cells and downregulated in resistant cells. Proteomic analysis of membrane-enriched fractions further supported UPR deregulation, showing a pronounced downregulation of translation-related proteins in sensitive cells. Functional assays validated that the sensitive cell line HCT116 exhibits reduced protein aggregation and lower translational capacity upon KRAS knockdown, consistent with UPR activation. Pharmacological inhibition of IRE1α-mediated UPR signaling did not revert KRAS silencing-induced cell cycle arrest or apoptosis in this cell line. Collectively, our results highlight the UPR activation as an early adaptive response of KRAS-dependent CRC cells tolerant to KRAS silencing.
2024-02-06 | GSE254832 | GEO
Project description:Colorectal cancer (CRC) responses to mutant-selective KRAS inhibitors remain modest, with stable disease and rapid recurrence as the most common outcomes. The molecular mechanisms enabling CRC cells to tolerate KRAS inhibition and ultimately develop resistance remain poorly understood. Here, we investigated early transcriptional and proteomic responses to KRAS silencing in 3D CRC cell line spheroid models, aiming to identify pathways associated with sensitivity or resistance to KRAS blockade. Cell lines were stratified into KRAS silencing-sensitive (HCT116 and SW480) and -resistant (LS174T and SW837) groups based on spheroid growth, cell cycle progression, and apoptosis induction. Transcriptional profiling revealed the unfolded protein response (UPR) and WNT/β-catenin signaling as pathways specifically upregulated in KRAS silencing-sensitive cells and downregulated in resistant cells. Proteomic analysis of membrane-enriched fractions further supported UPR deregulation, showing a pronounced downregulation of translation-related proteins in sensitive cells. Functional assays validated that the sensitive cell line HCT116 exhibits reduced protein aggregation and lower translational capacity upon KRAS knockdown, consistent with UPR activation. Pharmacological inhibition of IRE1α-mediated UPR signaling did not revert KRAS silencing-induced cell cycle arrest or apoptosis in this cell line. Collectively, our results highlight the UPR activation as an early adaptive response of KRAS-dependent CRC cells tolerant to KRAS silencing.
2024-12-12 | GSE283752 | GEO
Project description:Differential unfolded protein response regulation in KRAS silencing sensitive versus innately resistant colorectal cancer cells [HCT116]
| PRJNA1072042 | ENA
Project description:Differential unfolded protein response regulation in KRAS silencing sensitive versus innately resistant colorectal cancer cells [SW480 and SW837]
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Project description:Preclinical and clinical data revealed that targeting KRAS mutant tumors is more challenging than expected. While initially sensitive to the treatment, cancer cells have the capability to rapidly bypass dependence on this oncogene to acquire a drug-tolerant phenotype. Gaining a comprehensive understanding of the mechanisms underlying the transition from a drug-sensitive to a drug-tolerant state holds the key to invaluable insights. Such insights will inform the development of therapeutic strategies aimed at disrupting intrinsic or adaptive resilience, ultimately enhancing therapeutic outcomes. Building upon this rationale, we established three-dimensional culture models of mutant KRAS CRC cell lines with distinct KRAS dependencies to investigate the cellular response to KRAS silencing. Our approach revealed a unique response in KRAS-dependent cells, characterized by G0/G1 cell cycle arrest and entry into a quiescent-like state. Proteomics analysis identified nucleosome assembly, regulation of gene expression, mRNA splicing, and mRNA processing as the top biologic processes specifically up-regulated in KRAS-dependent CRC cell lines upon KRAS silencing. Additionally, alterations in histone 3 post-translational modifications and chromatin compaction were also observed, along with enhanced transcriptional performance revealed by longitudinal RNA-Seq analysis. Our discoveries substantiate the existence of an epigenetic mechanism responsible for inducing tolerance to KRAS loss. This mechanism relies on both chromatin reorganization and transcriptional upregulation, illuminating the cancer cells' remarkable capacity to swiftly adapt, survive, and sustain malignancy even in the absence of oncogenic KRAS.
2023-12-15 | GSE250117 | GEO
Project description:KRAS inhibition impacts chromatin organization and transcriptional performance in colorectal cancer cells [LS174T RNA-seq]
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Project description:The goal of this experiment was to determine the expression signature in colon cancer LS174T cell line after selamectin treatment. The current study of selamectin is continuation of our previous work, PMID: 25143352.
2017-02-22 | GSE87873 | GEO
Project description:KRAS signaling has been extensively studied, yet the clarification between KRAS-autonomous and non-autonomous mechanisms are still less explored. Understanding how KRAS signaling and effects are affected by exogenous stimuli can provide valuable insights not only to understand resistance mechanisms that justify pathway inhibition failure, but also to uncover novel therapeutic targets for mutant KRAS patients. Hence, aiming at understanding KRAS-autonomous versus non autonomous mechanisms, we studied the response of two mutant KRAS colorectal cancer cell lines (HCT116 and LS174T) - control and KRAS silenced- to TGFβ1-activated fibroblasts secretome. By performing a total proteome analysis, we observed that TGFβ1-activated fibroblast-secreted factors triggered cell-line specific proteome alterations and that mutant KRAS governs approximately 1/3 of those alterations. Moreover, the analysis of the impact of exogenous factors on the modulation of KRAS proteome revealed that more than 2/3 of the KRAS-associated proteome is controlled in a KRAS-non-autonomous manner, dependent on the exogeneous factors, in both cell lines. This work highlights the context-dependency of KRAS-associated signaling and reinforces the importance of establishing more integrative models resembling the complexity of the tumor microenvironment to study KRAS-associated signals.
2022-04-06 | PXD030551 | Pride
Project description:Inositol-Requiring Enzyme (IRE)1 is an evolutionarily conserved sensor protein of the unfolded protein response (UPR). Vertebrates express two distinct paralogues: IRE1α (gene name ERN1) and IRE1β (gene name ERN2). Both proteins have a similar overall structure, with a sensor domain positioned in the endoplasmic reticulum (ER) lumen, and cytoplasmic kinase and endonuclease domains. For IRE1α, it is well-established that a protein folding chaperone called HSPA5 binds to the ER-luminal domain in conditions when the folding load and capacity are balanced. When unfolded proteins accumulate, HSPA5 is recruited to these unfolded proteins to aid in folding, thereby releasing IRE1α. This initiates a chain reaction of dimerization, trans-autophosphorylation and further oligomerization, resulting in an endonuclease-active IRE1α. Activated IRE1α cleaves an intron from the X-box binding protein 1 mRNA in an unusual cytoplasmic splicing reaction, and the resulting frameshift leads to production of a central UPR transcription factor, XBP1S. In contrast to this, IRE1β is far less extensively characterized. It is expressed solely in mucus-producing cells, more specifically goblet cells. Ectopic expression in other cell types such as Hela cells causes rapid cell death, most likely due to unregulated endonuclease activity. Upon aligning the two IRE1 paralogues, it becomes clear that the luminal domain has the lowest homology between the two paralogues, suggesting differences in how activity of either paralogue is tuned in the ER. In this project, we aimed to characterize and compare the IRE1β and IRE1α interactomes in LS174T cells, a cell line that has retained many goblet cell characteristics, to gain more insights into the regulation and downstream activity of IRE1β in a more relevant cellular background.
2023-11-21 | PXD042756 | Pride