WorldCat Identities

Aran, Dvir

Overview
Works: 15 works in 15 publications in 1 language and 21 library holdings
Genres: Academic theses 
Roles: Author
Publication Timeline
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Most widely held works by Dvir Aran
Comprehensive analysis of normal adjacent to tumor transcriptomes by Dvir Aran( )

1 edition published in 2017 in English and held by 2 WorldCat member libraries worldwide

DNA methylation of distal regulatory sites characterizes dysregulation of cancer genes by Dvir Aran( )

1 edition published in 2013 in English and held by 2 WorldCat member libraries worldwide

Heterogeneity in HIV and cellular transcription profiles in cell line models of latent and productive infection: implications for HIV latency by Sushama Telwatte( )

1 edition published in 2019 in English and held by 2 WorldCat member libraries worldwide

Digitally deconvolving the tumor microenvironment by Dvir Aran( )

1 edition published in 2016 in English and held by 2 WorldCat member libraries worldwide

Reference-based analysis of lung single-cell sequencing reveals a transitional profibrotic macrophage by Dvir Aran( )

1 edition published in 2019 in English and held by 2 WorldCat member libraries worldwide

XCell: digitally portraying the tissue cellular heterogeneity landscape by Dvir Aran( )

1 edition published in 2017 in English and held by 2 WorldCat member libraries worldwide

Reference-based analysis of lung single-cell sequencing reveals a transitional profibrotic macrophage by Dvir Aran( )

1 edition published in 2019 in Undetermined and held by 1 WorldCat member library worldwide

Tissue fibrosis is a major cause of mortality that results from the deposition of matrix proteins by an activated mesenchyme. Macrophages accumulate in fibrosis, but the role of specific subgroups in supporting fibrogenesis has not been investigated in vivo. Here, we used single-cell RNA sequencing (scRNA-seq) to characterize the heterogeneity of macrophages in bleomycin-induced lung fibrosis in mice. A novel computational framework for the annotation of scRNA-seq by reference to bulk transcriptomes (SingleR) enabled the subclustering of macrophages and revealed a disease-associated subgroup with a transitional gene expression profile intermediate between monocyte-derived and alveolar macrophages. These CX3CR1+SiglecF+ transitional macrophages localized to the fibrotic niche and had a profibrotic effect in vivo. Human orthologs of genes expressed by the transitional macrophages were upregulated in samples from patients with idiopathic pulmonary fibrosis. Thus, we have identified a pathological subgroup of transitional macrophages that are required for the fibrotic response to injury
Widespread parainflammation in human cancer by Dvir Aran( )

1 edition published in 2016 in Undetermined and held by 1 WorldCat member library worldwide

Chronic inflammation has been recognized as one of the hallmarks of cancer. We recently showed that parainflammation, a unique variant of inflammation between homeostasis and chronic inflammation, strongly promotes mouse gut tumorigenesis upon p53 loss. Here we explore the prevalence of parainflammation in human cancer and determine its relationship to certain molecular and clinical parameters affecting treatment and prognosis.We generated a transcriptome signature to identify parainflammation in many primary human tumors and carcinoma cell lines as distinct from their normal tissue counterparts and the tumor microenvironment and show that parainflammation-positive tumors are enriched for p53 mutations and associated with poor prognosis. Non-steroidal anti-inflammatory drug (NSAID) treatment suppresses parainflammation in both murine and human cancers, possibly explaining a protective effect of NSAIDs against cancer.We conclude that parainflammation, a low-grade form of inflammation, is widely prevalent in human cancer, particularly in cancer types commonly harboring p53 mutations. Our data suggest that parainflammation may be a driver for p53 mutagenesis and a guide for cancer prevention by NSAID treatment
xCell: digitally portraying the tissue cellular heterogeneity landscape by Dvir Aran( )

1 edition published in 2017 in Undetermined and held by 1 WorldCat member library worldwide

Tissues are complex milieus consisting of numerous cell types. Several recent methods have attempted to enumerate cell subsets from transcriptomes. However, the available methods have used limited sources for training and give only a partial portrayal of the full cellular landscape. Here we present xCell, a novel gene signature-based method, and use it to infer 64 immune and stromal cell types. We harmonized 1822 pure human cell type transcriptomes from various sources and employed a curve fitting approach for linear comparison of cell types and introduced a novel spillover compensation technique for separating them. Using extensive in silico analyses and comparison to cytometry immunophenotyping, we show that xCell outperforms other methods. xCell is available at http://xCell.ucsf.edu/
Widespread parainflammation in human cancer by Dvir Aran( )

1 edition published in 2016 in Undetermined and held by 1 WorldCat member library worldwide

BackgroundChronic inflammation has been recognized as one of the hallmarks of cancer. We recently showed that parainflammation, a unique variant of inflammation between homeostasis and chronic inflammation, strongly promotes mouse gut tumorigenesis upon p53 loss. Here we explore the prevalence of parainflammation in human cancer and determine its relationship to certain molecular and clinical parameters affecting treatment and prognosis.ResultsWe generated a transcriptome signature to identify parainflammation in many primary human tumors and carcinoma cell lines as distinct from their normal tissue counterparts and the tumor microenvironment and show that parainflammation-positive tumors are enriched for p53 mutations and associated with poor prognosis. Non-steroidal anti-inflammatory drug (NSAID) treatment suppresses parainflammation in both murine and human cancers, possibly explaining a protective effect of NSAIDs against cancer.ConclusionsWe conclude that parainflammation, a low-grade form of inflammation, is widely prevalent in human cancer, particularly in cancer types commonly harboring p53 mutations. Our data suggest that parainflammation may be a driver for p53 mutagenesis and a guide for cancer prevention by NSAID treatment
Reference-based analysis of lung single-cell sequencing reveals a transitional profibrotic macrophage by Dvir Aran( )

1 edition published in 2019 in Undetermined and held by 1 WorldCat member library worldwide

Tissue fibrosis is a major cause of mortality that results from the deposition of matrix proteins by an activated mesenchyme. Macrophages accumulate in fibrosis, but the role of specific subgroups in supporting fibrogenesis has not been investigated in vivo. Here, we used single-cell RNA sequencing (scRNA-seq) to characterize the heterogeneity of macrophages in bleomycin-induced lung fibrosis in mice. A novel computational framework for the annotation of scRNA-seq by reference to bulk transcriptomes (SingleR) enabled the subclustering of macrophages and revealed a disease-associated subgroup with a transitional gene expression profile intermediate between monocyte-derived and alveolar macrophages. These CX3CR1+SiglecF+ transitional macrophages localized to the fibrotic niche and had a profibrotic effect in vivo. Human orthologs of genes expressed by the transitional macrophages were upregulated in samples from patients with idiopathic pulmonary fibrosis. Thus, we have identified a pathological subgroup of transitional macrophages that are required for the fibrotic response to injury
Comprehensive analysis of normal adjacent to tumor transcriptomes by Dvir Aran( )

1 edition published in 2017 in Undetermined and held by 1 WorldCat member library worldwide

Histologically normal tissue adjacent to the tumor (NAT) is commonly used as a control in cancer studies. However, little is known about the transcriptomic profile of NAT, how it is influenced by the tumor, and how the profile compares with non-tumor-bearing tissues. Here, we integrate data from the Genotype-Tissue Expression project and The Cancer Genome Atlas to comprehensively analyze the transcriptomes of healthy, NAT, and tumor tissues in 6506 samples across eight tissues and corresponding tumor types. Our analysis shows that NAT presents a unique intermediate state between healthy and tumor. Differential gene expression and protein-protein interaction analyses reveal altered pathways shared among NATs across tissue types. We characterize a set of 18 genes that are specifically activated in NATs. By applying pathway and tissue composition analyses, we suggest a pan-cancer mechanism of pro-inflammatory signals from the tumor stimulates an inflammatory response in the adjacent endothelium
xCell: digitally portraying the tissue cellular heterogeneity landscape by Dvir Aran( )

1 edition published in 2017 in Undetermined and held by 1 WorldCat member library worldwide

Tissues are complex milieus consisting of numerous cell types. Several recent methods have attempted to enumerate cell subsets from transcriptomes. However, the available methods have used limited sources for training and give only a partial portrayal of the full cellular landscape. Here we present xCell, a novel gene signature-based method, and use it to infer 64 immune and stromal cell types. We harmonized 1822 pure human cell type transcriptomes from various sources and employed a curve fitting approach for linear comparison of cell types and introduced a novel spillover compensation technique for separating them. Using extensive in silico analyses and comparison to cytometry immunophenotyping, we show that xCell outperforms other methods. xCell is available at http://xCell.ucsf.edu/
Contribution of epigenetic variations at distant control elements to the etiology of common human diseases by Dvir Aran( Book )

1 edition published in 2014 in English and held by 1 WorldCat member library worldwide

Comprehensive analysis of normal adjacent to tumor transcriptomes by Dvir Aran( )

1 edition published in 2017 in Undetermined and held by 1 WorldCat member library worldwide

Histologically normal tissue adjacent to the tumor (NAT) is commonly used as a control in cancer studies. However, little is known about the transcriptomic profile of NAT, how it is influenced by the tumor, and how the profile compares with non-tumor-bearing tissues. Here, we integrate data from the Genotype-Tissue Expression project and The Cancer Genome Atlas to comprehensively analyze the transcriptomes of healthy, NAT, and tumor tissues in 6506 samples across eight tissues and corresponding tumor types. Our analysis shows that NAT presents a unique intermediate state between healthy and tumor. Differential gene expression and protein-protein interaction analyses reveal altered pathways shared among NATs across tissue types. We characterize a set of 18 genes that are specifically activated in NATs. By applying pathway and tissue composition analyses, we suggest a pan-cancer mechanism of pro-inflammatory signals from the tumor stimulates an inflammatory response in the adjacent endothelium
 
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