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Interleukin-11-expressing fibroblasts have a unique gene signature correlated with poor prognosis of colorectal cancer.

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TLDR
In this paper, the origin and functions of IL-11-producing (IL-11+) cells are not fully understood, but they appear in the colon in murine tumor and acute colitis models and express fibroblast markers and genes associated with cell proliferation and tissue repair.
Abstract
Interleukin (IL)-11 is a member of the IL-6 family of cytokines and is involved in multiple cellular responses, including tumor development. However, the origin and functions of IL-11-producing (IL-11+) cells are not fully understood. To characterize IL-11+ cells in vivo, we generate Il11 reporter mice. IL-11+ cells appear in the colon in murine tumor and acute colitis models. Il11ra1 or Il11 deletion attenuates the development of colitis-associated colorectal cancer. IL-11+ cells express fibroblast markers and genes associated with cell proliferation and tissue repair. IL-11 induces the activation of colonic fibroblasts and epithelial cells through phosphorylation of STAT3. Human cancer database analysis reveals that the expression of genes enriched in IL-11+ fibroblasts is elevated in human colorectal cancer and correlated with reduced recurrence-free survival. IL-11+ fibroblasts activate both tumor cells and fibroblasts via secretion of IL-11, thereby constituting a feed-forward loop between tumor cells and fibroblasts in the tumor microenvironment.

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Colon stroma mediates an inflammation-driven fibroblastic response controlling matrix remodeling and healing

TL;DR: A critical role for the metalloprotease Adamdec1 at the interface between tissue remodeling and healing during colitis is supported, demonstrating its requirement for colon epithelial integrity.
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The Versatile Roles of Cancer-Associated Fibroblasts in Colorectal Cancer and Therapeutic Implications.

TL;DR: In this paper, the authors outline the emerging concept of cancer-associated fibroblasts in colorectal cancer, with an emphasis on their origins, biomarkers, prognostic significance, as well as their functional roles and underlying mechanisms in CRC biology.
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Interleukin-11 signaling promotes cellular reprogramming and limits fibrotic scarring during tissue regeneration

TL;DR: In contrast, species like zebrafish can regenerate damaged tissues without excessive fibribr... as mentioned in this paper, which is a leading cause of morbidity in mammals and is the most common cause of fibrotic scarring.
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The Analysis of Inflammation-Related Proteins in a Cargo of Exosomes Derived from the Serum of Uveal Melanoma Patients Reveals Potential Biomarkers of Disease Progression.

TL;DR: In this article, a panel of exosomal proteins for early detection of uveal melanoma progression into metastatic disease was proposed based on the obtained results, which showed a significant correlation between the disease stage and the concentration of these inflammation-related proteins from exosome cargo.
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IL11 Stimulates IL33 Expression and Proinflammatory Fibroblast Activation across Tissues

TL;DR: RNA sequencing over a time course of IL11 stimulation revealed a robust short-lived transcriptional response, which was enriched for gene set hallmarks of inflammation and characterized by upregulation of SERPINB2, TNFRSF18, IL33, CCL20, IL1RL1, CXCL3/5/8, ICAM1 and IL11 itself.
References
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Journal ArticleDOI

Fast gapped-read alignment with Bowtie 2

TL;DR: Bowtie 2 combines the strengths of the full-text minute index with the flexibility and speed of hardware-accelerated dynamic programming algorithms to achieve a combination of high speed, sensitivity and accuracy.
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edgeR: a Bioconductor package for differential expression analysis of digital gene expression data.

TL;DR: EdgeR as mentioned in this paper is a Bioconductor software package for examining differential expression of replicated count data, which uses an overdispersed Poisson model to account for both biological and technical variability and empirical Bayes methods are used to moderate the degree of overdispersion across transcripts, improving the reliability of inference.
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Cutadapt removes adapter sequences from high-throughput sequencing reads

TL;DR: The command-line tool cutadapt is developed, which supports 454, Illumina and SOLiD (color space) data, offers two adapter trimming algorithms, and has other useful features.
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