Dataset Roundup - Noteworthy datasets on autoimmune diseases
FAIR Data

Dataset Roundup - Noteworthy datasets on autoimmune diseases

Shraddha Dumawat, Harsh Malavia, Deepthi Das
August 4, 2022

This month’s roundup features datasets that capture the molecular landscape of autoimmune diseases. Transcriptome analysis enables us to compare gene expression in different immune cell types in patients and healthy individuals, thereby improving our understanding of the pathological roles of immune cells in autoimmune diseases. It can also capture the dynamic genome-wide gene expression changes in immune cells, reflecting genetic and environmental stimulations. Therefore, it is a valuable tool for investigating disease mechanisms and direct clinical application in future precision medicine.

Here, we showcase important transcriptomic datasets on autoimmune diseases that cover datasets on systemic lupus erythematosus, rheumatoid arthritis, studies that compare the transcriptomic data of different autoimmune diseases; Guillain-Barre Syndrome patient and her healthy twin, and many more! You can find many more highly curated datasets on autoimmune diseases (see figure below) from different repositories that can be visualized and analyzed using our DataOps platform, Polly.

Summary of Autoimmune disease related datasets on Polly

Dataset 1

RNA sequencing of B cell subsets (CD11chi IgD+ B cells, CD11chi IgD- B cells, memory B cells, and Native B cells) from healthy subjects and subjects with Systemic Lupus Erythematosus (SLE) or Rheumatoid Arthritis (RA)


Dataset ID: GSE110999_GPL11154

Year of Publication: 2018

Total Samples: 25

Experiment type: Transcriptomics

Organism: Homo sapiens

Reference link: Publication, Raw data

The dataset compares the transcriptomes of B cell of cell subsets isolated from healthy controls and patients of Autoimmune

Summary:

CD11c+ B cells (IgD+ and IgD-) are pathogenic B cells expanded in autoimmune disease. This study aims to identify the pathways unique to IgD+ CD11c B cells and IgD- CD11c B cells. Although the etiology of SLE is unclear, dysregulated B cell responses have been implicated. Here, the researchers show that an unusual CD11chiT-bet+ B cell subset, with a unique expression profile including chemokine receptors consistent with migration to target tissues, is expanded in SLE patients, present in nephrotic kidneys, enriched for autoreactive specificities, and correlates with defined clinical manifestations.

IL-21 can potently induce CD11chiT-bet+ B cells and promote the differentiation of these cells into Ig-secreting autoreactive plasma cells. While murine studies have identified a role for T-bet-expressing B cells in autoimmunity, this study describes and exemplifies the importance of CD11chiT-bet+ B cells in human SLE.

PCA plot for distribution of disease

PCA plot for types of Bcell distribution

Heat map describing gene expression across different B cell types

Dataset 2

Transcriptomic, epigenetic, and functional analyses implicate neutrophil diversity in the pathogenesis of SLE.


Dataset ID: GSE139358_GPL21290

Year of Publication: 2019

Total Samples: 50

Experiment type: Transcriptomics

Organism: Homo sapiens

Reference link: Publication, Raw data

The sunburst chart depicts the distribution of disease type along with the cell type distribution.

Summary:

This study provides insights into the mechanism of immune dysregulation and the vascular damage characteristic of Lupus by studying transcriptomes of low-density granulocytes. The authors have identified a proinflammatory neutrophil subset known as low-density granulocytes (LDGs) that differs functionally from autologous Lupus normal density neutrophils (NDNs).

LDGs induce increased endothelial damage and vascular dysfunction in vitro through their enhanced ability to synthesize and extrude neutrophil extracellular traps (NETs). In SLE, NETs stimulate the production of proinflammatory cytokines and type-I interferons (IFNs), promote immune cell maturation, and contribute to tissue damage. SLE LDG numbers are associated with in vivo vascular inflammation and coronary atherosclerosis, independent of other cardiovascular (CV) risk factors and the promotion of T-cell activation. These observations suggest that specifically targeting LDGs could abrogate certain aspects of immune dysregulation, organ damage, and premature atherosclerosis characteristic of SLE.

Heat map describing the comparison between NDN and LDG

Dataset 3

Next-generation sequencing of human immune cell subsets across diseases

Dataset ID: GSE60424_GPL15456

Year of Publication: 2015

Total Samples: 134

Experiment type: Transcriptomics

Organism: Homo sapiens

Reference link: Publication, Raw data


Summary:

This study describes a novel method to monitor levels of immune cells and pathways in expression data from solid tumors using pre-defined groups or modules of co-regulated immune genes. The authors performed whole genome RNAseq profiling of immune cell subsets and whole blood from subjects with an array of immune-associated diseases. The authors demonstrated the link between type-I interferon action and immune cell levels in melanomas and suggest that therapeutic approaches augmenting both activities may be most beneficial.

PCA plot describes the distribution of samples across a particular disease to display the variation between them.

Dataset 4

Transcriptomes of peripheral blood mononuclear cells from a Guillain-Barre Syndrome (GBS) patient and her healthy twin were sampled at three different points of the disease evolution.

Dataset ID: GSE72748_GPL10999

Year of Publication: 2015

Total Samples: 6

Experiment type: Transcriptomics

Organism: Homo sapiens

Reference link:  Publication, Raw data


Sample characteristics : Comparative samples taken at different time points between the healthy twin and the twin with the disease.

Summary:

Guillain-Barré syndrome (GBS) is an immune-mediated peripheral neuropathy. The goal of this research was the identification of biomarkers associated with recovery from GBS. In this study, the authors compared the transcriptome of PBMCs from a GBS patient and her healthy twin to discover possible correlates of disease progression and recovery. Blood samples were collected simultaneously from the Guillain-Barré patient and her control healthy twin at three different time points during disease progression from hospitalization in the intensive care unit, passing to intermediate care, and at the conclusion of locomotion rehabilitation program when the patient was close to getting discharged from the hospital.

During disease recovery, the early growth response gene-2 (EGR2) was upregulated in GBS patients. The results provided evidence for the implication of EGR2 in GBS and suggested a role for EGR2 in the regulation of IL-17, IL-22, IL-28A, and TNF-β cytokines in GBS patients. The study identified biomarkers associated with GBS recovery and suggested that EGR2 overexpression has a pivotal role in the downregulation of cytokines implicated in the pathophysiology of this acute neuropathy.

Expression looked at through the discover application on Polly

Dataset 5

Abnormal neutrophil signature in the blood and pancreas of pre-symptomatic and symptomatic type-1 diabetes patients

Dataset ID: GSE110914_GPL16791

Year of Publication: 2018

Total Samples: 21

Experiment type: Transcriptomics

Organism: Homo sapiens

Reference link: Publication, Raw data

Sample characteristics - The study dives into at risk and healthy control patients and compares them with patients diagnosed with diabetes.

This study aimed to identify possible changes in circulating and pancreas-residing neutrophils throughout the disease course to better elucidate neutrophil involvement in human T1D.

Heat map to display the gene IFN related gene expression across the 3 groups.

This research shows that the decline in β-cell function is greatest in individuals with the lowest peripheral neutrophil numbers. Neutrophils infiltrate the pancreas prior to the onset of symptoms, and they continue to do so as the disease progresses. A fraction of these pancreas-infiltrating neutrophils also extrudes neutrophil extracellular traps (NETs), suggesting a tissue-specific pathogenic role. Whole-transcriptome analysis of purified blood neutrophils revealed a unique molecular signature distinguished by an overabundance of Interferon (IFN)-associated genes; despite being healthy, said signature is already present in T1D-autoantibody-negative at-risk subjects.

Dataset 6

Gene expression studies of lupus and healthy B-cell subsets through RNA sequencing


Dataset ID: GSE92387_GPL11154

Year of Publication: 2018

Total Samples: 24

Experiment type: Transcriptomics

Organism: Homo sapiens

Reference link: Publication, Raw data

Summary:

Based on the expression of IgD, CD27, and CXCR5, four different B-cell subsets were isolated from 3 healthy control donors and 3 SLE patients. Gene expression was compared between SLE and HCD B cells within each subset and between B cell subsets.

Sample characteristics - The sample level metadata looks into different types of Bcells in order to explore them through RNASeq for both case and control.

Dramatic expansions of class-switched B-cells lacking IgD and CD27 (double negative; DN) are characteristic of SLE. However, their origin, clinical and immunological significance, and relationship to CD27+ memory B cells remain unclear. The authors demonstrate that SLE DN expansions are dominated by a CXCR5- CD21- subset with a pre-plasma cell phenotype and distinctive transcriptional and functional properties. SLE patients with an expansion of CXCR5- DN are predominantly African-American with higher disease activity and anti-Smith/RNP autoantibodies. CXCR5- DN cells display a distinct transcriptome characterized by differential expression of cytokine receptors, transcription factors, and signaling molecules. DN expresses high levels of the key INFg effector factor, T-bet, and associated transcription factor Zeb2 and uniquely among B-cell subsets, do not express TRAF5, a negative regulator of TLR signaling. Consistent with this pattern, gene expression SLE DN has enhanced responsiveness to TLR7 and can differentiate into autoantibody-secreting plasma cells.


The given PCA plot displays the distribution across the two disease condition (case vs control)

The given PCA Plot determines the distribution across different B cells subset types.

Dataset 7

RNAseq study of synovial biopsies after triple disease-modifying anti-rheumatic drugs (tDMARD) treatment

Dataset ID: GSE97165_GPL11154

Year of Publication: 2017

Total Samples: 38

Experiment type: Transcriptomics

Organism: Homo sapiens

Reference link:   Publication , Raw data

Summary:

This study sought to investigate the genome-wide transcriptional effects of a combination of DMARD, methotrexate, sulfasalazine, and hydroxychloroquine in synovial tissues obtained from early RA patients. Total RNA sequencing was performed on samples isolated from joint synovial biopsies from subjects with RA before and after six months of tDMARD treatment. The research identified transcriptomic signatures that characterize synovial tissue from RA patients with early disease. Analysis after six months of tDMARD treatment highlight consistent alterations in the expression of genes related to T-cell activation and plasmablast/plasma cell differentiation. These results provided a novel insight into the biology of early RA and the mechanism of tDMARD action. They may help identify novel drug targets to improve rates of treatment-induced disease remission.

The PCA plot shows the distribution within the two groups, i.e pre and post tDMARD treatment.

Dataset 8

Treatment of RA patients with chaperonin 10

Dataset ID: GSE112809_GPL570

Year of Publication: 2018

Total Samples: 8

Experiment type: Transcriptomics

Organism: Homo sapiens

Reference link:  Publication, Raw data

Summary:

Chaperonin 10 (heat shock protein 10, XToll) has anti-inflammatory properties related to inhibiting Toll-like receptor signaling pathways. The authors aim to establish whether chaperonin 10 is safe and effective in treating RA. RA patients were treated with chaperonin 10, twice weekly, for 56 days. Blood samples were collected before and after treatment. The results indicated that chaperonin 10 is well tolerated and efficacious in treating the symptoms of RA, at least in the short term.

The PCA plot describes the difference between the two cohorts, i.e before and after treatment of Chaperonin 10.

The study showcases the reduction of cytokine production at a significant rate, including TNFα, interleukin 1β, interleukin 6, and interleukin 10.

Box plot showcasing the difference in gene expression before and after treatment.


Polly’s OmixAtlases provide FAIR biomolecular data on the Polly platform enabling researchers to carry out robust data analysis and effective consumption of omics data. Reach out to us at info@elucidata.io for more details.

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