Publications
Genome-wide Transcriptional Changes are Associated with Disease Phenotype and Course
Figure 1
a) Gene expression is increased (red) and decreased (blue) in sarcoidosis (red vs. control (blue) subjects.
b) Gene expression is increased (dark blue) and decreased (light blue) in progressive sarcoidosis vs. non-progressive sarcoidosis.
Genome-wide DNA Methylation Changes are Associated with Disease Phenotypes and Gene Expression
Figure 2 Differentially methylated single-CpG probes in BAL cells associated with progressive sarcoidosis.
a) A volcano plot for disease status (P/NP). Probes with statistically significant change q<0.05 and methylation change .5% are highlighted in red.
b) Methlyation-expression plot for genes with P-associated DNA methylation changes with q<0.05.
Single-cell RNA Sequencing Identifies Macrophage Transcriptional Heterogeneities in Granulomatous Diseases
Figure 3
a) Uniform manifold approximation and projection (UMAP) analysis of cell identities of all samples demonstrates the subpopulations of macrophages, including recruited macrophages and resident macrophages. Cluster markers for main cell populations were identified in Seurat, and additional markers were used to distinguish recruited (FCN1) from resident (FABP4) macrophages.
b) Analysis of the 82 differentially expressed (DE) genes (using healthy control) in common to chronic beryllium disease (CBD) and sarcoidosis in all macrophages. Heatmap of log fold change for each disease comparison is shown.
c) Analysis of the 53 DE genes (using beryllium-sensitised non-diseased subjects (BeS) controls) in common to CBD and sarcoidosis in all macrophages. Heatmap of log fold change for each disease comparison is shown. #: genes that are also DE between progressive sarcoidosis (SarcP) and remitting sarcoidosis (SarcR).
d) Network of the overlap DE genes (using healthy control) between sarcoidosis and CBD. Green means stimulate, red means inhibit, and grey means uncertain.
Liao SY, Atif SM, Mould K, Konigsberg IR, Fu R, Davidson E, Li L, Fontenot AP, Maier LA, Yang IV. Single-cell RNA sequencing identifies macrophage transcriptional heterogeneities in granulomatous diseases. Eur Respir J. 2021 Jun;57(6). doi: 10.1183/13993003.03794-2020. Print 2021 Jun. PubMed PMID: 33602861; PubMed Central PMCID: PMC8247459.
Epigenetics Serves as a Link Between Environmental Stimuli and Gene Expression
Figure 4
Konigsberg IR, Maier LA, Yang I v. Epigenetics and sarcoidosis. European Respiratory Review. 2021;30(160):210076. doi:10.1183/16000617.0076-2021