BBrowser: Making single-cell data easily accessible

Le, Tao; Phan, Tri Giang; Pham, Minh; Tran, Duc; Lam, Loretta; Nguyen, Thuy Duong; Truong, Thuy; Vuong, Hy; T, Luu; Phung, Nam; Pham, O; Nguyen, Andrew V.; Nguyen, Hien; Tran, Hoa; Tran, Loc; Hà, Nguyễn Hải; Tran, Tony; Nguyen, Nam; Tran, Nhat; Boysen, Cecilie; Nguyen, Uyen; Pham,; Theodore, K; Pham, Nhung; Gill, T. Grandon; Pham, Son

doi:10.1101/2020.12.11.414136

Cited by 60 publications

(47 citation statements)

References 27 publications

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“…Clustering was performed using a resolution of 0.4. For data visualization and figure preparation of scRNA-seq data BBrowser version 2.7.5 was used (42).…”

Section: Single-cell Rnaseq Analysismentioning

confidence: 99%

Heterogeneity of meningeal B cells reveals a lymphopoietic niche at the CNS borders

Brioschi

Wang

Peng

et al. 2021

Science

301

332

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The meninges contain adaptive immune cells that provide immunosurveillance of the CNS. These cells are thought to derive from the systemic circulation. Through single-cell analyses, confocal imaging, bone marrow chimeras, and parabiosis experiments, we show that meningeal B cells derive locally from the calvaria, which harbors a bone marrow niche for hematopoiesis. B cells reach the meninges from the calvaria through specialized vascular connections. This calvarial–meningeal path of B cell development may provide the CNS with a constant supply of B cells educated by CNS antigens. Conversely, we show that a subset of antigen-experienced B cells that populate the meninges in aging mice are blood-borne. These results identify a private source for meningeal B cells. which may help maintain immune privilege within the CNS.

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“…Clustering was performed using a resolution of 0.4. For data visualization and figure preparation of scRNA-seq data BBrowser version 2.7.5 was used (42).…”

Section: Single-cell Rnaseq Analysismentioning

confidence: 99%

Heterogeneity of meningeal B cells reveals a lymphopoietic niche at the CNS borders

Brioschi

Wang

Peng

et al. 2021

Science

301

332

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“…Single cell RNAseq analysis were performed in the BioTuring Browser Software (v2.8.42) developed by BioTuring, using a dataset made available by Liao et al (43) (ID: GSE145926). All processing steps were done by BioTuring Browser (71). Cells with less than 200 genes and mitochondrial genes higher than 10% were excluded from the analysis.…”

Section: Flow Cytometrymentioning

confidence: 99%

Identification of DAXX As A Restriction Factor Of SARS-CoV-2 Through A CRISPR/Cas9 Screen

Kain

Maarifi

Aicher

et al. 2021

Preprint

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While interferon restricts SARS-CoV-2 replication in cell culture, only a handful of Interferon Stimulated Genes with antiviral activity against SARS-CoV-2 have been identified. Here, we describe a functional CRISPR/Cas9 screen aiming at identifying SARS-CoV-2 restriction factors. We identified DAXX, a scaffold protein residing in PML nuclear bodies known to limit the replication of DNA viruses and retroviruses, as a potent inhibitor of SARS-CoV-2 replication in human cells. Basal expression of DAXX was sufficient to limit the replication of the virus, and DAXX over-expression further restricted infection. In contrast with most of its previously described antiviral activities, DAXX-mediated restriction of SARS-CoV-2 was independent of the SUMOylation pathway. SARS-CoV-2 infection triggered the re-localization of DAXX to cytoplasmic sites of viral replication and led to its degradation. Together, these results demonstrate that DAXX is a potent restriction factor for SARS-CoV-2 and that the virus has evolved a mechanism to counteract its action.

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“…Consistent with the analysis of the TNBC specimen from WFBMC, this study also utilized the 10X Genomics Chromium system for single cell library production, followed by Illumina sequencing (NextSeq 500 and NovaSeq 6000 platforms), and utilized Cell Ranger data processing workflows and similar quality control filters for cell selection (38). Analysis of the Bassez et al dataset was facilitated by the BioTuring BBrowser and associated analytical tools (39) and the Seurat v3 R toolkit (40).…”

Section: Single-cell Rnaseq Analysismentioning

confidence: 99%

Bulk and Single-Cell Profiling of Breast Tumors Identifies TREM-1 as a Dominant Immune Suppressive Marker Associated With Poor Outcomes

Pullikuth¹,

Routh²,

Zimmerman³

et al. 2021

Front. Oncol.

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BackgroundTriggering receptor expressed on myeloid cells (TREM)-1 is a key mediator of innate immunity previously associated with the severity of inflammatory disorders, and more recently, the inferior survival of lung and liver cancer patients. Here, we investigated the prognostic impact and immunological correlates of TREM1 expression in breast tumors.MethodsBreast tumor microarray and RNAseq expression profiles (n=4,364 tumors) were analyzed for associations between gene expression, tumor immune subtypes, distant metastasis-free survival (DMFS) and clinical response to neoadjuvant chemotherapy (NAC). Single-cell (sc)RNAseq was performed using the 10X Genomics platform. Statistical associations were assessed by logistic regression, Cox regression, Kaplan-Meier analysis, Spearman correlation, Student’s t-test and Chi-square test.ResultsIn pre-treatment biopsies, TREM1 and known TREM-1 inducible cytokines (IL1B, IL8) were discovered by a statistical ranking procedure as top genes for which high expression was associated with reduced response to NAC, but only in the context of immunologically “hot” tumors otherwise associated with a high NAC response rate. In surgical specimens, TREM1 expression varied among tumor molecular subtypes, with highest expression in the more aggressive subtypes (Basal-like, HER2-E). High TREM1 significantly and reproducibly associated with inferior distant metastasis-free survival (DMFS), independent of conventional prognostic markers. Notably, the association between high TREM1 and inferior DMFS was most prominent in the subset of immunogenic tumors that exhibited the immunologically hot phenotype and otherwise associated with superior DMFS. Further observations from bulk and single-cell RNAseq analyses indicated that TREM1 expression was significantly enriched in polymorphonuclear myeloid-derived suppressor cells (PMN-MDSCs) and M2-like macrophages, and correlated with downstream transcriptional targets of TREM-1 (IL8, IL-1B, IL6, MCP-1, SPP1, IL1RN, INHBA) which have been previously associated with pro-tumorigenic and immunosuppressive functions.ConclusionsTogether, these findings indicate that increased TREM1 expression is prognostic of inferior breast cancer outcomes and may contribute to myeloid-mediated breast cancer progression and immune suppression.

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BBrowser: Making single-cell data easily accessible

Cited by 60 publications

References 27 publications

Heterogeneity of meningeal B cells reveals a lymphopoietic niche at the CNS borders

Heterogeneity of meningeal B cells reveals a lymphopoietic niche at the CNS borders

Identification of DAXX As A Restriction Factor Of SARS-CoV-2 Through A CRISPR/Cas9 Screen

Bulk and Single-Cell Profiling of Breast Tumors Identifies TREM-1 as a Dominant Immune Suppressive Marker Associated With Poor Outcomes

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