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Open AccessJournal ArticleDOI

Tumor Cell-Intrinsic Factors Underlie Heterogeneity of Immune Cell Infiltration and Response to Immunotherapy

TLDR
A library of congenic tumor cell clones from an autochthonous mouse model of pancreatic adenocarcinoma is established, identifying heterogeneous and multifactorial pathways regulating tumor‐cell‐intrinsic mechanisms that dictate the immune microenvironment and thereby responses to immunotherapy.
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This article is published in Immunity.The article was published on 2018-07-17 and is currently open access. It has received 453 citations till now. The article focuses on the topics: Tumor microenvironment & Immunotherapy.

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Cancer immunoediting and resistance to T cell-based immunotherapy

TL;DR: How a deeper understanding of the mechanisms underlying the cancer immunoediting process can provide insight into the development of resistance to immunotherapies and the strategies that can be used to overcome such resistance is discussed.
Journal ArticleDOI

Clonal replacement of tumor-specific T cells following PD-1 blockade.

TL;DR: Paired single-cell RNA and T cell receptor sequencing on 79,046 cells from site-matched tumors from patients with basal or squamous cell carcinoma before and after anti-PD-1 therapy demonstrates that pre-existing tumor-specific T cells may have limited reinvigoration capacity, and that the T cell response to checkpoint blockade derives from a distinct repertoire of T cell clones that may have just recently entered the tumor.
Journal ArticleDOI

IL1-Induced JAK/STAT Signaling Is Antagonized by TGFβ to Shape CAF Heterogeneity in Pancreatic Ductal Adenocarcinoma.

TL;DR: An IL1-induced signaling cascade that leads to JAK/STAT activation and promotes an inflammatory CAF state is identified, suggesting multiple strategies to target these cells in vivo and illuminating strategies to selectively target CAFs that support tumor growth.
References
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Journal ArticleDOI

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2

TL;DR: This work presents DESeq2, a method for differential analysis of count data, using shrinkage estimation for dispersions and fold changes to improve stability and interpretability of estimates, which enables a more quantitative analysis focused on the strength rather than the mere presence of differential expression.
Journal ArticleDOI

Fast and accurate short read alignment with Burrows–Wheeler transform

TL;DR: Burrows-Wheeler Alignment tool (BWA) is implemented, a new read alignment package that is based on backward search with Burrows–Wheeler Transform (BWT), to efficiently align short sequencing reads against a large reference sequence such as the human genome, allowing mismatches and gaps.
Journal ArticleDOI

featureCounts: an efficient general-purpose program for assigning sequence reads to genomic features

TL;DR: FeatureCounts as discussed by the authors is a read summarization program suitable for counting reads generated from either RNA or genomic DNA sequencing experiments, which implements highly efficient chromosome hashing and feature blocking techniques.
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