Journal: American Journal of Respiratory and Critical Care Medicine

Article Title: A Tracheal Aspirate-derived Airway Basal Cell Model Reveals a Proinflammatory Epithelial Defect in Congenital Diaphragmatic Hernia

doi: 10.1164/rccm.202205-0953OC

Figure Lengend Snippet: Congenital diaphragmatic hernia (CDH) basal stem cells (BSCs) have a disease-associated transcriptome and exhibit a proinflammatory signature. (A) Representative images of antibody staining for KRT5, TP63, and NKX2.1 in BSCs derived from TA of newborns with CDH. (B) Principal component analysis of bulk RNA sequencing datasets of BSC samples from CDH newborns (n = 12) and control, term (n = 6), and preterm (n = 6) newborns. Patients with CDH are labeled with A, B, C, and D according to their reported type of defect size during surgical repair. Arrow indicates one control case with prenatal oligohydramnios-associated lung hypoplasia. (C) Volcano plot highlighting differentially expressed genes between CDH and control BSCs with an adjusted P < 0.05. (D) Pathway analysis for bulk RNA sequencing results of CDH and control BSCs. (E) Heatmap of interferon signaling pathway genes that are differentially expressed between CDH and control BSCs. (F) Representative Western blot for concentrations of Ser536 phosphorylation of the p65 subunit of nuclear factor kappa B (pNF-ΚB) in CDH (n = 4) and control (n = 4) BSCs. β-actin was a loading control. (G) Activity of nuclear NF-kB measured by ELISA in CDH BSCs (n = 4) and control BSCs (n = 3). *P < 0.05 by Mann-Whitney U test. Scale bar, 25 μm. Ctrl = control; DN = downregulated; NS = not significant; pNF-ΚB = phosphorylated nuclear factor kappa B; TA = tracheal aspirate; UP = upregulated.

Article Snippet: Bulk RNA sequencing and assay for transposase accessible chromatin with (ATAC) sequencing of BSCs were performed by ActiveMotif.inc.

Techniques: Staining, Derivative Assay, RNA Sequencing, Control, Labeling, Western Blot, Phospho-proteomics, Activity Assay, Enzyme-linked Immunosorbent Assay, MANN-WHITNEY

Journal: American Journal of Respiratory and Critical Care Medicine

Article Title: A Tracheal Aspirate-derived Airway Basal Cell Model Reveals a Proinflammatory Epithelial Defect in Congenital Diaphragmatic Hernia

doi: 10.1164/rccm.202205-0953OC

Figure Lengend Snippet: Basal stem cells (BSCs) from newborns with congenital diaphragmatic hernia (CDH) exhibit changes in chromatin accessibility. (A) Enrichment of target genes of epigenetic regulation among differentially expressed genes by bulk RNA sequencing between CDH and control BSCs. (B) Principal component analysis of assay for transposase accessible chromatin with sequencing datasets comparing CDH BSCs (n = 2) and control BSCs (n = 6). (C) Volcano plot highlighting significantly altered chromatin accessibility between CDH and control BSCs. (D) Summary of peak intensity within 1 kb surrounding the transcription start site of genes with at least one enriched peak between CDH and control BSCs. (E) Detailed examination of changes in peak signals within regulatory sequences of select genes. (F) HOMER motif analysis of chromatin accessibility. **P < 0.01 by Student’s t test. Ctrl = control; DN = downregulated; HOMER = hypergeometric optimization of motif enrichment; NS = not significant; NES = normalized enrichment score; NF-kB = nuclear factor kappa B; PC1 = principal component 1; PC2 = principal component 2; PWN = position weight matrix; UP = upregulated.

Article Snippet: Bulk RNA sequencing and assay for transposase accessible chromatin with (ATAC) sequencing of BSCs were performed by ActiveMotif.inc.

Techniques: RNA Sequencing, Control, Sequencing

Journal: Materials Today Bio

Article Title: Replenishment of mitochondrial Na + and H + by ionophores potentiates cutaneous wound healing in diabetes

doi: 10.1016/j.mtbio.2024.101056

Figure Lengend Snippet: Monensin An up-regulates mitochondrially encoded genes. (A) Overview of the monensin A mediated alteration of gene expression on HACAT cells using bulk RNA-seq. (B) Pathway enrichment analysis arranging the top up-regulated pathways according to the adjusted p-value (left). The altered information on the top-ranking pathway was further excavated (right). (C) Heatmap shows monensin A-triggered actively expressed genes involved in the top-ranking pathway. Data are color-coded to reflect the relative expression level of mitochondrially encoded genes. All data are normalized to their matched control. (D) PCR-based validation of the mRNA expression of mitochondrial genes in HACAT cells treated with or without monensin A (125 nM) for 3 h. Data are represented as mean ± SD. Two-tailed Student's unpaired t -test (D). (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)

Article Snippet: RNA samples were submitted to LC Sciences (Hangzhou, China) for bulk RNA sequencing using the Illumina platform.

Techniques: Gene Expression, RNA Sequencing, Expressing, Control, Biomarker Discovery, Two Tailed Test

Journal: Cell Death & Disease

Article Title: The TRPM7 channel reprograms cellular glycolysis to drive tumorigenesis and angiogenesis

doi: 10.1038/s41419-023-05701-7

Figure Lengend Snippet: A Volcano plots of glucose metabolism-related genes that are induced in WT versus TRPM7KO cells. Genes with a fold-change ≥2 and P value of < 0.05 are shown. B RT-qPCR analysis validating the decreased expression of glucose catabolic genes from RNA-seq in TRPM7KO cells. C Immunofluorescent staining of TRPM7, SLC2A3 and DAPI in the xenograft tumor (scale bars, 100 μm). D Immunohistochemical staining for TRPM7, SLC2A1 and SLC2A3 in tumor tissue (scale bars, 100 μm). E , F Increased SLC2A3 in naltriben-induced (25 μM, 24 h) WT cells but not TRPM7KO cells. Quantification of protein was below. Two groups of samples were compared by unpaired two-tailed Student’s t -test. Multiple groups were compared by ANOVA.

Article Snippet: The bulk RNA sequencing was performed by Metware Co., LTD.

Techniques: Quantitative RT-PCR, Expressing, RNA Sequencing, Staining, Immunohistochemical staining, Two Tailed Test

Journal: Osteoarthritis and Cartilage Open

Article Title: Transcriptomics and metabolomics: Challenges of studying obesity in osteoarthritis

doi: 10.1016/j.ocarto.2024.100479

Figure Lengend Snippet: Summary of 15 studies identified investigating obesity as a variable related to human or animal model osteoarthritis using transcriptomics or metabolomics. Publications with associated Gene Expression Omnibus dataset accession numbers (GSE) are indicated.

Article Snippet: Schott et al. (2018) [ ] (GSE98287) , Mouse diet-induced obesity , • Low-fat diet-fed mice • high-fat diet-fed mice , Not Reported , Transcriptomics , Bulk RNA sequencing , Colon.

Techniques: Animal Model, Gene Expression, Comparison, RNA Sequencing, Mouse Assay, Microarray, Clinical Proteomics, Structural Proteomics, Control, Gas Chromatography