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Article: Accelerating Single-Cell Sequencing Data Analysis with SciDAP: A User-Friendly Approach.

Kotliar, Michael / Kartashov, Andrey / Barski, Artem

bioRxiv : the preprint server for biology

2024

Abstract: Single-cell (sc) RNA, ATAC and Multiome sequencing became powerful tools for uncovering biological and disease mechanisms. Unfortunately, manual analysis of sc data presents multiple challenges due to large data volumes and complexity of configuration ... ...

Abstract	Single-cell (sc) RNA, ATAC and Multiome sequencing became powerful tools for uncovering biological and disease mechanisms. Unfortunately, manual analysis of sc data presents multiple challenges due to large data volumes and complexity of configuration parameters. This complexity, as well as not being able to reproduce a computational environment, affects the reproducibility of analysis results. The Scientific Data Analysis Platform (https://SciDAP.com) allows biologists without computational expertise to analyze sequencing-based data using portable and reproducible pipelines written in Common Workflow Language (CWL). Our suite of computational pipelines addresses the most common needs in scRNA-Seq, scATAC-Seq and scMultiome data analysis. When executed on SciDAP, it offers a user-friendly alternative to manual data processing, eliminating the need for coding expertise. In this protocol, we describe the use of SciDAP to analyze scMultiome data. Similar approaches can be used for analysis of scRNA-Seq, scATAC-Seq and scVDJ-Seq datasets.
Language	English
Publishing date	2024-02-29
Publishing country	United States
Document type	Preprint
DOI	10.1101/2024.02.28.582604
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Article ; Online: TSLP shapes the pathogenic responses of memory CD4

Rochman, Yrina / Kotliar, Michael / Ben-Baruch Morgenstern, Netali / Barski, Artem / Wen, Ting / Rothenberg, Marc E

Science signaling

2023 Volume 16, Issue 802, Page(s) eadg6360

Abstract: The cytokine thymic stromal lymphopoietin (TSLP) mediates type 2 immune responses, and treatments that interfere with TSLP activity are in clinical use for asthma. Here, we investigated whether TSLP contributes to allergic inflammation by directly ... ...

Abstract	The cytokine thymic stromal lymphopoietin (TSLP) mediates type 2 immune responses, and treatments that interfere with TSLP activity are in clinical use for asthma. Here, we investigated whether TSLP contributes to allergic inflammation by directly stimulating human CD4
MeSH term(s)	Humans ; CD4-Positive T-Lymphocytes ; Cytokines ; Eosinophilic Esophagitis ; STAT5 Transcription Factor/genetics ; T-Lymphocytes ; Thymic Stromal Lymphopoietin
Chemical Substances	Cytokines ; STAT5 Transcription Factor ; Thymic Stromal Lymphopoietin (GT0IL38SP4)
Language	English
Publishing date	2023-09-12
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
ZDB-ID	2417226-1
ISSN	1937-9145 ; 1945-0877
ISSN (online)	1937-9145
ISSN	1945-0877
DOI	10.1126/scisignal.adg6360
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Article ; Online: CWL-Airflow: a lightweight pipeline manager supporting Common Workflow Language.

Kotliar, Michael / Kartashov, Andrey V / Barski, Artem

GigaScience

2019 Volume 8, Issue 7

Abstract: Background: Massive growth in the amount of research data and computational analysis has led to increased use of pipeline managers in biomedical computational research. However, each of the >100 such managers uses its own way to describe pipelines, ... ...

Abstract	Background: Massive growth in the amount of research data and computational analysis has led to increased use of pipeline managers in biomedical computational research. However, each of the >100 such managers uses its own way to describe pipelines, leading to difficulty porting workflows to different environments and therefore poor reproducibility of computational studies. For this reason, the Common Workflow Language (CWL) was recently introduced as a specification for platform-independent workflow description, and work began to transition existing pipelines and workflow managers to CWL. Findings: Herein, we present CWL-Airflow, a package that adds support for CWL to the Apache Airflow pipeline manager. CWL-Airflow uses CWL version 1.0 specification and can run workflows on stand-alone MacOS/Linux servers, on clusters, or on a variety of cloud platforms. A sample CWL pipeline for processing of chromatin immunoprecipitation sequencing data is provided. Conclusions: CWL-Airflow will provide users with the features of a fully fledged pipeline manager and the ability to execute CWL workflows anywhere Airflow can run-from a laptop to a cluster or cloud environment. CWL-Airflow is available under Apache License, version 2.0 (Apache-2.0), and can be downloaded from https://barski-lab.github.io/cwl-airflow, https://scicrunch.org/resolver/RRID:SCR_017196.
MeSH term(s)	Animals ; Big Data ; Chromatin Immunoprecipitation Sequencing/methods ; Genomics/methods ; Humans ; Software ; Workflow
Language	English
Publishing date	2019-07-18
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	2708999-X
ISSN	2047-217X ; 2047-217X
ISSN (online)	2047-217X
ISSN	2047-217X
DOI	10.1093/gigascience/giz084
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Article ; Online: Aryl hydrocarbon receptor and IL-13 signaling crosstalk in human keratinocytes and atopic dermatitis.

Proper, Steven P / Dwyer, Alexander T / Appiagyei, Andrews / Felton, Jennifer M / Ben-Baruch Morgenstern, Netali / Marlman, Justin M / Kotliar, Michael / Barski, Artem / Troutman, Ty D / Rothenberg, Marc E / Mersha, Tesfaye B / Azouz, Nurit P

Frontiers in allergy

2024 Volume 5, Page(s) 1323405

Abstract: Introduction: Atopic dermatitis (AD) is an allergic skin disease mediated by skin barrier impairment and IL-13-driven immune response. Activation of the aryl hydrocarbon receptor (AHR) has shown promise in early clinical trials for AD; however, the ... ...

Abstract	Introduction: Atopic dermatitis (AD) is an allergic skin disease mediated by skin barrier impairment and IL-13-driven immune response. Activation of the aryl hydrocarbon receptor (AHR) has shown promise in early clinical trials for AD; however, the mechanism by which AHR partially ameliorates AD is not well known. Methods: Gene expression data from human biopsies were analyzed, and compared to gene expression from RNA-sequencing in our Results: The AHR target gene Discussion: Together, these data suggest that the AHR pathway is dysregulated in AD and that AHR modulates IL-13 downstream signaling in keratinocytes through genome-wide, transcriptional regulatory effects.
Language	English
Publishing date	2024-01-26
Publishing country	Switzerland
Document type	Journal Article
ISSN	2673-6101
ISSN (online)	2673-6101
DOI	10.3389/falgy.2024.1323405
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Article ; Online: Single-cell RNA-Seq of human esophageal epithelium in homeostasis and allergic inflammation.

Rochman, Mark / Wen, Ting / Kotliar, Michael / Dexheimer, Phillip J / Ben-Baruch Morgenstern, Netali / Caldwell, Julie M / Lim, Hee-Woong / Rothenberg, Marc E

JCI insight

2022 Volume 7, Issue 11

Abstract: Inflammation of the esophageal epithelium is a hallmark of eosinophilic esophagitis (EoE), an emerging chronic allergic disease. Herein, we probed human esophageal epithelial cells at single-cell resolution during homeostasis and EoE. During allergic ... ...

Abstract	Inflammation of the esophageal epithelium is a hallmark of eosinophilic esophagitis (EoE), an emerging chronic allergic disease. Herein, we probed human esophageal epithelial cells at single-cell resolution during homeostasis and EoE. During allergic inflammation, the epithelial differentiation program was blocked, leading to loss of KRT6hi differentiated populations and expansion of TOP2hi proliferating, DSPhi transitioning, and SERPINB3hi transitioning populations; however, there was stability of the stem cell-enriched PDPNhi basal epithelial compartment. This differentiation program blockade was associated with dysregulation of transcription factors, including nuclear receptor signalers, in the most differentiated epithelial cells and altered NOTCH-related cell-to-cell communication. Each epithelial population expressed genes with allergic disease risk variants, supporting their functional interplay. The esophageal epithelium differed notably between EoE in histologic remission and controls, indicating that remission is a transitory state poised to relapse. Collectively, our data uncover the dynamic nature of the inflamed human esophageal epithelium and provide a framework to better understand esophageal health and disease.
MeSH term(s)	Eosinophilic Esophagitis/genetics ; Eosinophilic Esophagitis/pathology ; Epithelium/pathology ; Homeostasis ; Humans ; Inflammation/genetics ; RNA-Seq
Language	English
Publishing date	2022-06-08
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
ISSN	2379-3708
ISSN (online)	2379-3708
DOI	10.1172/jci.insight.159093
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Article ; Online: Preparation of mouse pancreatic tumor for single-cell RNA sequencing and analysis of the data.

Surumbayeva, Aizhan / Kotliar, Michael / Gabitova-Cornell, Linara / Kartashov, Andrey / Peri, Suraj / Salomonis, Nathan / Barski, Artem / Astsaturov, Igor

STAR protocols

2021 Volume 2, Issue 4, Page(s) 100989

Abstract: Preparation of single-cell suspension from primary tumor tissue can provide a valuable resource for functional, genetic, proteomic, and tumor microenvironment studies. Here, we describe an effective protocol for mouse pancreatic tumor dissociation with ... ...

Abstract	Preparation of single-cell suspension from primary tumor tissue can provide a valuable resource for functional, genetic, proteomic, and tumor microenvironment studies. Here, we describe an effective protocol for mouse pancreatic tumor dissociation with further processing of tumor suspension for single-cell RNA sequencing analysis of cellular populations. We further provide an outline of the bioinformatics processing of the data and clustering of heterogeneous cellular populations comprising pancreatic tumors using Common Workflow Language (CWL) pipelines within user-friendly Scientific Data Analysis Platform (https://SciDAP.com). For complete details on the use and execution of this protocol, please refer to Gabitova-Cornell et al. (2020).
MeSH term(s)	Animals ; Computational Biology/methods ; Female ; Male ; Mice ; Pancreas/cytology ; Pancreas/pathology ; Pancreatic Neoplasms/genetics ; Pancreatic Neoplasms/metabolism ; Pancreatic Neoplasms/pathology ; Sequence Analysis, RNA/methods ; Single-Cell Analysis/methods ; Software
Language	English
Publishing date	2021-12-04
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ISSN	2666-1667
ISSN (online)	2666-1667
DOI	10.1016/j.xpro.2021.100989
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Article ; Online: maxATAC: Genome-scale transcription-factor binding prediction from ATAC-seq with deep neural networks.

Cazares, Tareian A / Rizvi, Faiz W / Iyer, Balaji / Chen, Xiaoting / Kotliar, Michael / Bejjani, Anthony T / Wayman, Joseph A / Donmez, Omer / Wronowski, Benjamin / Parameswaran, Sreeja / Kottyan, Leah C / Barski, Artem / Weirauch, Matthew T / Prasath, V B Surya / Miraldi, Emily R

PLoS computational biology

2023 Volume 19, Issue 1, Page(s) e1010863

Abstract: Transcription factors read the genome, fundamentally connecting DNA sequence to gene expression across diverse cell types. Determining how, where, and when TFs bind chromatin will advance our understanding of gene regulatory networks and cellular ... ...

Abstract	Transcription factors read the genome, fundamentally connecting DNA sequence to gene expression across diverse cell types. Determining how, where, and when TFs bind chromatin will advance our understanding of gene regulatory networks and cellular behavior. The 2017 ENCODE-DREAM in vivo Transcription-Factor Binding Site (TFBS) Prediction Challenge highlighted the value of chromatin accessibility data to TFBS prediction, establishing state-of-the-art methods for TFBS prediction from DNase-seq. However, the more recent Assay-for-Transposase-Accessible-Chromatin (ATAC)-seq has surpassed DNase-seq as the most widely-used chromatin accessibility profiling method. Furthermore, ATAC-seq is the only such technique available at single-cell resolution from standard commercial platforms. While ATAC-seq datasets grow exponentially, suboptimal motif scanning is unfortunately the most common method for TFBS prediction from ATAC-seq. To enable community access to state-of-the-art TFBS prediction from ATAC-seq, we (1) curated an extensive benchmark dataset (127 TFs) for ATAC-seq model training and (2) built "maxATAC", a suite of user-friendly, deep neural network models for genome-wide TFBS prediction from ATAC-seq in any cell type. With models available for 127 human TFs, maxATAC is the largest collection of high-performance TFBS prediction models for ATAC-seq. maxATAC performance extends to primary cells and single-cell ATAC-seq, enabling improved TFBS prediction in vivo. We demonstrate maxATAC's capabilities by identifying TFBS associated with allele-dependent chromatin accessibility at atopic dermatitis genetic risk loci.
MeSH term(s)	Humans ; Chromatin/genetics ; Chromatin Immunoprecipitation Sequencing ; Deoxyribonucleases/genetics ; High-Throughput Nucleotide Sequencing/methods ; Sequence Analysis, DNA/methods ; Nerve Net
Chemical Substances	Chromatin ; Deoxyribonucleases (EC 3.1.-)
Language	English
Publishing date	2023-01-31
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2193340-6
ISSN	1553-7358 ; 1553-734X
ISSN (online)	1553-7358
ISSN	1553-734X
DOI	10.1371/journal.pcbi.1010863
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Article ; Online: Vitamin D receptor and STAT6 interactome governs oesophageal epithelial barrier responses to IL-13 signalling.

Brusilovsky, Michael / Rochman, Mark / Shoda, Tetsuo / Kotliar, Michael / Caldwell, Julie M / Mack, Lydia E / Besse, John A / Chen, Xiaoting / Weirauch, Matthew T / Barski, Artem / Rothenberg, Marc E

Gut

2022 Volume 72, Issue 5, Page(s) 834–845

Abstract: Objective: The contribution of vitamin D (VD) deficiency to the pathogenesis of allergic diseases remains elusive. We aimed to define the impact of VD on oesophageal allergic inflammation.: Design: We assessed the genomic distribution and function of ...

Abstract	Objective: The contribution of vitamin D (VD) deficiency to the pathogenesis of allergic diseases remains elusive. We aimed to define the impact of VD on oesophageal allergic inflammation. Design: We assessed the genomic distribution and function of VD receptor (VDR) and STAT6 using histology, molecular imaging, motif discovery and metagenomic analysis. We examined the role of VD supplementation in oesophageal epithelial cells, in a preclinical model of IL-13-induced oesophageal allergic inflammation and in human subjects with eosinophilic oesophagitis (EoE). Results: VDR response elements were enriched in oesophageal epithelium, suggesting enhanced VDR binding to functional gene enhancer and promoter regions. Metagenomic analysis showed that VD supplementation reversed dysregulation of up to 70% of the transcriptome and epigenetic modifications (H3K27Ac) induced by IL-13 in VD-deficient cells, including genes encoding the transcription factors Conclusions: Collectively, these findings identify VD as a natural IL-13 antagonist with capacity to regulate the oesophageal epithelial barrier functions, providing a novel therapeutic entry point for type 2 immunity-related diseases.
MeSH term(s)	Humans ; Eosinophilic Esophagitis ; Inflammation/metabolism ; Interleukin-13/pharmacology ; Interleukin-13/metabolism ; Nerve Tissue Proteins/metabolism ; Receptors, Calcitriol/genetics ; Receptors, Immunologic/metabolism ; STAT6 Transcription Factor/genetics ; STAT6 Transcription Factor/metabolism ; Vitamin D
Chemical Substances	Interleukin-13 ; Nerve Tissue Proteins ; Receptors, Calcitriol ; Receptors, Immunologic ; STAT6 protein, human ; STAT6 Transcription Factor ; Vitamin D (1406-16-2) ; VDR protein, human ; IL13 protein, human
Language	English
Publishing date	2022-08-02
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
ZDB-ID	80128-8
ISSN	1468-3288 ; 0017-5749
ISSN (online)	1468-3288
ISSN	0017-5749
DOI	10.1136/gutjnl-2022-327276
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Article ; Online: Epigenetic Analysis of the Chromatin Landscape Identifies a Repertoire of Murine Eosinophil-Specific PU.1-Bound Enhancers.

Felton, Jennifer M / Vallabh, Sushmitha / Parameswaran, Sreeja / Edsall, Lee E / Ernst, Kevin / Wronowski, Benjamin / Malik, Astha / Kotliar, Michael / Weirauch, Matthew T / Barski, Artem / Fulkerson, Patricia C / Rothenberg, Marc E

Journal of immunology (Baltimore, Md. : 1950)

2021 Volume 207, Issue 4, Page(s) 1044–1054

Abstract: Eosinophils develop in the bone marrow from hematopoietic progenitors into mature cells capable of a plethora of immunomodulatory roles via the choreographed process of eosinophilopoiesis. However, the gene regulatory elements and transcription factors ( ... ...

Abstract	Eosinophils develop in the bone marrow from hematopoietic progenitors into mature cells capable of a plethora of immunomodulatory roles via the choreographed process of eosinophilopoiesis. However, the gene regulatory elements and transcription factors (TFs) orchestrating this process remain largely unknown. The potency and resulting diversity fundamental to an eosinophil's complex immunomodulatory functions and tissue specialization likely result from dynamic epigenetic regulation of the eosinophil genome, a dynamic eosinophil regulome. In this study, we applied a global approach using broad-range, next-generation sequencing to identify a repertoire of eosinophil-specific enhancers. We identified over 8200 active enhancers located within 1-20 kB of expressed eosinophil genes. TF binding motif analysis revealed PU.1 (
MeSH term(s)	Animals ; Cells, Cultured ; Chromatin/genetics ; Eosinophils/metabolism ; Epigenesis, Genetic/genetics ; Mice ; Mice, Inbred BALB C ; Myeloid Cells ; Protein Binding/genetics ; Proto-Oncogene Proteins/genetics ; Regulatory Sequences, Nucleic Acid/genetics ; Trans-Activators/genetics ; Transcription Factors/genetics
Chemical Substances	Chromatin ; Proto-Oncogene Proteins ; Trans-Activators ; Transcription Factors ; proto-oncogene protein Spi-1
Language	English
Publishing date	2021-07-30
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	3056-9
ISSN	1550-6606 ; 0022-1767 ; 1048-3233 ; 1047-7381
ISSN (online)	1550-6606
ISSN	0022-1767 ; 1048-3233 ; 1047-7381
DOI	10.4049/jimmunol.2000207
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Article ; Online: Microbiota-sensitive epigenetic signature predicts inflammation in Crohn's disease.

JCI insight

2018 Volume 3, Issue 18

Abstract: Altered response to the intestinal microbiota strongly associates with inflammatory bowel disease (IBD); however, how commensal microbial cues are integrated by the host during the pathogenesis of IBD is not understood. Epigenetics represents a potential ...

Abstract	Altered response to the intestinal microbiota strongly associates with inflammatory bowel disease (IBD); however, how commensal microbial cues are integrated by the host during the pathogenesis of IBD is not understood. Epigenetics represents a potential mechanism that could enable intestinal microbes to modulate transcriptional output during the development of IBD. Here, we reveal a histone methylation signature of intestinal epithelial cells isolated from the terminal ilea of newly diagnosed pediatric IBD patients. Genes characterized by significant alterations in histone H3-lysine 4 trimethylation (H3K4me3) showed differential enrichment in pathways involving immunoregulation, cell survival and signaling, and metabolism. Interestingly, a large subset of these genes was epigenetically regulated by microbiota in mice and several microbiota-sensitive epigenetic targets demonstrated altered expression in IBD patients. Remarkably though, a substantial proportion of these genes exhibited H3K4me3 levels that correlated with the severity of intestinal inflammation in IBD, despite lacking significant differential expression. Collectively, these data uncover a previously unrecognized epigenetic profile of IBD that can be primed by commensal microbes and indicate sensitive targets in the epithelium that may underlie how microbiota predispose to subsequent intestinal inflammation and disease.
MeSH term(s)	Adolescent ; Animals ; Child ; Crohn Disease/metabolism ; Epigenesis, Genetic ; Epithelial Cells/metabolism ; Female ; Gastrointestinal Microbiome/physiology ; Histones/metabolism ; Humans ; Ileum ; Inflammation ; Male ; Methylation ; Mice ; Mice, Inbred C57BL
Chemical Substances	Histones ; histone H3 trimethyl Lys4
Language	English
Publishing date	2018-09-20
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ISSN	2379-3708
ISSN (online)	2379-3708
DOI	10.1172/jci.insight.122104
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