Journal: Nature Communications

Article Title: Transcriptional regulation of the postnatal cardiac conduction system heterogeneity

doi: 10.1038/s41467-024-50849-1

Figure Lengend Snippet: a (Top) Integrated heatmap/dotplot of CCS regulons, as inferred by the SCENIC algorithm. The heatmap color represents regular activities for each CCS component based on the area under the curve (AUC) scores. Dot size represents transcription factor expression in each CCS component. (Bottom) Motifs of representative transcription factors in the CCS regions. b Tbx3 and Irx3 show unique and overlapping expression patterns exclusively within the CCS. c SAN and cAVN show enrichment of Tbx3 with atrial genes ( Myl4 and Myl7 ); LNB, HIS, and PBB show enrichment of both Tbx3 and Irx3 with ventricular genes ( Myl2 and Myl3 ); and DBB and PF show enrichment of Irx3 with ventricular genes. d Schematic showing unique and overlapping expression patterns of Tbx3 and Irx3 throughout the CCS. Created with BioRender.com. e Genome browser views of chromatin accessibilities in the right atria, SA node, ventricle, and Tbx3-positive atrioventricular junction (Tbx3 + AVJ) as well as Tbx3 ChIP-seq, and the presence of Iroquois homeobox (Irx) transcription factor motifs, for the CCS component and regional marker genes. SAN sinoatrial node, cAVN compact atrioventricular node, LNB lower nodal bundle, HIS His bundle, PBB proximal bundle branch, DBB distal bundle branch, PF Purkinje fibers, Prolif. CCS proliferative CCS, CM contractile myocyte, VCS ventricular conduction system.

Article Snippet: The sections were then incubated overnight at 4 °C with the following primary antibodies: chicken anti-RFP (Rockland Immunochemicals, 600-901-379, lot #42649, 1:100), goat anti-Cntn2 (R&D Systems, AF4439, lot #CDSO0219101, 1:50), rabbit anti-Gnao1 (Thermo Fisher Scientific, PA5-30044, lot #YH4027897A, 1:100), rabbit anti-Scn10a (Alomone Labs, ASC-016, lot #, ASC016AN2550, 1:50), rabbit anti-Igfbp7 (Abcam, ab74169, lot #GR242021-1, 1:50), rabbit anti-S100a6 (Abcam, ab181975, lot #GR3438351-1, 1:100), rabbit anti-Nppa (EMD Millipore, ab5490, lot #Q3015715, 1:250), mouse anti-Shox2 IgG2a (Santa Cruz Biotechnology, sc-81955, lot #B2822, 1:50) or rabbit anti-Vsnl1 (GeneTex, GTX115039, lot #40247, 1:100), rabbit anti-Ppp1r17 (Thermo Fisher Scientific, PA5-61599, lot #YH4028316B, 1:200).

Techniques: Expressing, ChIP-sequencing, Marker, Chromatin Immunoprecipitation, Single Cell RNA-Seq

Journal: Clinical cancer research : an official journal of the American Association for Cancer Research

Article Title: Characterization of an Immunogenic Mutation in a Patient with Metastatic Triple-Negative Breast Cancer

doi: 10.1158/1078-0432.CCR-16-1423

Figure Lengend Snippet: Identification of RBPJ mutation-reactive TCR. A, 4062-TILs were cocultured with autologous APCs presenting RBPJA611T peptide and sorted on the basis of expression of CD4+/4–1BB+ by FACS. Data are gated on live CD3+ cells. B and C, TCR analysis revealed an oligoclonal population of TCR-α (B) and TCR-β (C) chains. Of note, 42.9% of the TCR-α chains were unresolved. On the basis of the frequency, the two most frequent TCR-α and TCR-β chains were used to synthesize the four possible TCR combinations. PBL transduced with TCRAV05 (the second most frequent alpha chain) and TCRBV07 (the most frequent beta chain) recognized APCs specifically presenting mutRBPJ based on IFNγ ELISPOT (D) and upregulation of 4–1BB (E) in the CD4+ T-cell population (▲, mutRBPJ; △, wtRBPJ; ○, irrelevant peptide). Data are representative of three separate patient TCR-transduced PBL.

Article Snippet: Alternatively, 4–1BB + – sorted cells were subjected to single-cell RNA sequencing (RNA-seq) on the Fluidigm C1, according to the manufacturer’s protocol and paired TCR-alpha and beta sequences were identified and synthesized (Genscript).

Techniques: Mutagenesis, Expressing, Transduction, Enzyme-linked Immunospot

Journal: Frontiers in Immunology

Article Title: Endothelial Immunity Trained by Coronavirus Infections, DAMP Stimulations and Regulated by Anti-Oxidant NRF2 May Contribute to Inflammations, Myelopoiesis, COVID-19 Cytokine Storms and Thromboembolism

doi: 10.3389/fimmu.2021.653110

Figure Lengend Snippet: (A–E) The mRNA transcripts of four types of coronavirus receptors such as membrane alanyl aminopeptidase (ANPEP, CD13, receptor for human coronavirus-229E), carcinoembryonic antigen family cell adhesion molecule 1 (CEACAM1, receptor for mouse hepatitis virus), angiotensin-converting enzyme 2 (ACE, receptor for SARS-CoV, SARS-CoV2), and dipeptidyl peptidase-4 (DPP4, receptor for MERS-CoV) as well as TMPRSS2 are found in two clusters of human heart endothelial cells. The data mining analyses were performed on the Single Cell RNA-Seq database of the Broad Institute of MIT and Harvard (Single CellBeta Portal; https://singlecell.broadinstitute.org/single_cell/study/SCP498/transcriptional-and-cellular-diversity-of-the-human-heart#study-summary ). (F–J) The mRNA transcripts of four types of coronavirus receptors such as ANPEP, CEACAM1, ACE, and DPP4 are found in mouse aortic endothelial cell clusters. The data mining analyses were performed on the Single Cell RNA-Seq database of the Broad Institute of MIT and Harvard (Single CellBeta Portal; https://singlecell.broadinstitute.org/single_cell/study/SCP289/single-cell-analysis-of-the-normal-mouse-aorta-reveals-functionally-distinct-endothelial-cell-populations#study-summay , PMID: 31146585). (F) ANPEP expressions in three endothelial cell clusters were circled in red in the Scatter; (G) ANPEP expressions in three endothelial cell clusters were boxed in red in the Distribution; (H) CEACAM1 expressions in three endothelial cell clusters were also boxed in read in the Distribution; (I) ACE expressions in three endothelial cell clusters were also boxed in read in the Distribution; (J) DPP4 expressions in three endothelial cell clusters were also boxed in read in the Distribution. (K) A new working model: Infection of vascular endothelial cells by SARS-CoV2/MERS-CoV causes innate immune responses in endothelial cells, which may induces cytokine storm, and triggers thromboembolism. The part of figure was created with BioRender.com .

Article Snippet: To test this hypothesis, we searched the expression of these four receptors and coronavirus S protein priming serine protease TMPRSS2 ( ) in human EC in the MIT-Harvard Broad Institute Single Cell Beta Porter single-cell RNA-Seq database, Study: Transcriptional and Cellular Diversity of the Human Heart ( https://singlecell.broadinstitute.org/single_cell/study/SCP498 ).

Techniques: Membrane, Virus, RNA Sequencing, Single-cell Analysis, Infection