Measuring and Modelling the Epithelial- Mesenchymal Hybrid State in Cancer: Clinical Implications

The epithelial-mesenchymal (E/M) hybrid state has emerged as an important mediator of elements of cancer progression, facilitated by epithelial mesenchymal plasticity (EMP). We review here evidence for the presence, prognostic significance, and therapeutic potential of the E/M hybrid state in carcinoma. We further assess modelling predictions and validation studies to demonstrate stabilised E/M hybrid states along the spectrum of EMP, as well as computational approaches for characterising and quantifying EMP phenotypes, with particular attention to the emerging realm of single-cell approaches through RNA sequencing and protein-based techniques.

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Measuring and Modelling the Epithelial Mesenchymal Hybrid State in Cancer: Clinical Implications

10.20944/preprints202008.0023.v1 ◽

2020 ◽

Cited By ~ 1

Author(s):

Mohit Kumar Jolly ◽

Ryan J. Murphy ◽

Sugandha Bhatia ◽

Holly J. Whitfield ◽

Melissa J. Davis ◽

...

Keyword(s):

Single Cell ◽

Rna Sequencing ◽

Cancer Progression ◽

Clinical Implications ◽

Computational Approaches ◽

Hybrid State ◽

Important Mediator

The epithelial-mesenchymal (E/M) hybrid state has emerged as an important mediator of the elements of cancer progression facilitated by epithelial mesenchymal plasticity (EMP). We review here the evidence for the presence and prognostic potential of E/M hybrid state in carcinoma, modelling predictions and validations studies to demonstrate stabilised E/M hybrid intermediates along the spectrum of EMP, and computational approaches for characterising and quantifying EMP phenotypes, with particular attention to the emerging realm of single-cell approaches through RNA sequencing and protein-based approaches.

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Identification of EMT signaling cross-talk and gene regulatory networks by single-cell RNA sequencing

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.2102050118 ◽

2021 ◽

Vol 118 (19) ◽

pp. e2102050118

Author(s):

Abhijeet P. Deshmukh ◽

Suhas V. Vasaikar ◽

Katarzyna Tomczak ◽

Shubham Tripathi ◽

Petra den Hollander ◽

...

Keyword(s):

Single Cell ◽

Signaling Pathways ◽

Rna Sequencing ◽

Cancer Progression ◽

Tyrosine Kinases ◽

Regulatory Networks ◽

Expression Profiles ◽

Critical Role ◽

Mesenchymal Transition ◽

Single Cell Rna Sequencing

The epithelial-to-mesenchymal transition (EMT) plays a critical role during normal development and in cancer progression. EMT is induced by various signaling pathways, including TGF-β, BMP, Wnt–β-catenin, NOTCH, Shh, and receptor tyrosine kinases. In this study, we performed single-cell RNA sequencing on MCF10A cells undergoing EMT by TGF-β1 stimulation. Our comprehensive analysis revealed that cells progress through EMT at different paces. Using pseudotime clustering reconstruction of gene-expression profiles during EMT, we found sequential and parallel activation of EMT signaling pathways. We also observed various transitional cellular states during EMT. We identified regulatory signaling nodes that drive EMT with the expression of important microRNAs and transcription factors. Using a random circuit perturbation methodology, we demonstrate that the NOTCH signaling pathway acts as a key driver of TGF-β–induced EMT. Furthermore, we demonstrate that the gene signatures of pseudotime clusters corresponding to the intermediate hybrid EMT state are associated with poor patient outcome. Overall, this study provides insight into context-specific drivers of cancer progression and highlights the complexities of the EMT process.

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The Unfolded Protein Response as a Compensatory Mechanism and Potential Therapeutic Target in PLN R14del Cardiomyopathy

Circulation ◽

10.1161/circulationaha.120.049844 ◽

2021 ◽

Author(s):

Dries A.M. Feyen ◽

Isaac Perea-Gil ◽

Renee G.C. Maas ◽

Magdalena Harakalova ◽

Alexandra A. Gavidia ◽

...

Keyword(s):

Single Cell ◽

Unfolded Protein Response ◽

Rna Sequencing ◽

Therapeutic Potential ◽

Compensatory Mechanism ◽

Unfolded Protein ◽

Single Cell Rna Sequencing ◽

The Unfolded Protein Response ◽

Protein Response ◽

The Impact

Background: Phospholamban (PLN) is a critical regulator of calcium cycling and contractility in the heart. The loss of arginine at position 14 in PLN (R14del) is associated with dilated cardiomyopathy (DCM) with a high prevalence of ventricular arrhythmias. How the R14 deletion causes DCM is poorly understood and there are no disease-specific therapies. Methods: We used single-cell RNA sequencing to uncover PLN R14del disease-mechanisms in human induced pluripotent stem cells (hiPSC-CMs). We utilized both 2D and 3D functional contractility assays to evaluate the impact of modulating disease relevant pathways in PLN R14del hiPSC-CMs. Results: Modeling of the PLN R14del cardiomyopathy with isogenic pairs of hiPSC-CMs recapitulated the contractile deficit associated with the disease in vitro . Single-cell RNA sequencing revealed the induction of the unfolded protein response pathway (UPR) in PLN R14del compared to isogenic control hiPSC-CMs. The activation of UPR was also evident in the hearts from PLN R14del patients. Silencing of each of the three main UPR signaling branches (IRE1, ATF6, or PERK) by siRNA exacerbated the contractile dysfunction of PLN R14del hiPSC-CMs. We explored the therapeutic potential of activating the UPR with a small molecule activator, BiP protein Inducer X (BiX). PLN R14del hiPSC-CMs treated with BiX showed a dose-dependent amelioration of the contractility deficit of in both 2D cultures and 3D engineered heart tissues without affecting calcium homeostasis. Conclusions: Together, these findings suggest that the UPR exerts a protective effect in the setting of PLN R14del cardiomyopathy and that modulation of the UPR might be exploited therapeutically.

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Single-Cell RNA Sequencing Reveals Enteric Glial Subpopulations with Therapeutic Potential in Hirschsprung Disease

Journal of the American College of Surgeons ◽

10.1016/j.jamcollsurg.2020.07.775 ◽

2020 ◽

Vol 231 (4) ◽

pp. S213

Author(s):

Richard A. Guyer ◽

Sukhada Bhave ◽

Rhian Stavely ◽

Ryo Hotta ◽

Allan Moises Goldstein

Keyword(s):

Single Cell ◽

Rna Sequencing ◽

Therapeutic Potential ◽

Hirschsprung Disease ◽

Single Cell Rna Sequencing

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Single-cell analyses identify circulating anti-tumor CD8 T cells and markers for their enrichment

10.1101/2020.09.30.294959 ◽

2020 ◽

Author(s):

Kristen E. Pauken ◽

Osmaan Shahid ◽

Kaitlyn A. Lagattuta ◽

Kelly M. Mahuron ◽

Jacob M. Luber ◽

...

Keyword(s):

T Cells ◽

T Cell ◽

Single Cell ◽

Rna Sequencing ◽

Therapeutic Potential ◽

Cell Receptor ◽

Cell Responses ◽

Cell Clones ◽

Single Cell Rna Sequencing ◽

Melanoma Patients

AbstractThe ability to monitor anti-tumor CD8+ T cell responses in the blood has tremendous therapeutic potential. Here, we used paired single-cell RNA sequencing and T cell receptor (TCR) sequencing to detect and characterize “tumor matching” (TM) CD8+ T cells in the blood of mice with MC38 tumors and melanoma patients using the TCR as a molecular barcode. TM cells showed increased activation compared to non-matching T cells in blood, and appeared less exhausted than matching counterparts in tumor. Importantly, PD-1, which has been used to identify putative circulating anti-tumor CD8+ T cells, showed poor sensitivity for identifying TM cells. By leveraging the transcriptome we identified candidate cell surface marker panels for TM cells in mice and melanoma patients, and validated NKG2D, CD39, and CX3CR1 in mice. These data demonstrate that the TCR can be used to identify tumor-relevant populations for comprehensive characterization, reveal unique transcriptional properties of TM cells, and develop marker panels for tracking and analysis of these cells.SummaryUsing single-cell RNA-sequencing coupled with TCR sequencing, we detected CD8+ T cell clones shared between blood and tumor in mice and melanoma patients, characterized these matching clones in blood and tumor, and identified potential biomarkers for their isolation in blood.

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