Journal: Cell stem cell

Article Title: MicroRNAs Induce a Permissive Chromatin Environment That Enables Neuronal Subtype-specific Reprogramming of Adult Human Fibroblasts

doi: 10.1016/j.stem.2017.08.002

Figure Lengend Snippet: (A) Genome wide expression analysis of miNs and starting fibroblasts by RNA-seq at day 30 of reprogramming. Plot shows the relationship between average gene expression (logCPM) and log fold-change of miNs compared to fibroblasts. A selection of pan-neuronal and fibroblast-specific genes are highlighted in black text. Blue = fold change < −2 log2 p < 0.01 (more abundant in fibroblasts), grey = fold change > −2 log2 < 2 log2 p > 0.01, and red = fold change > 2 log2 p < 0.01 (more abundant in miNs). FDR < 0.01.

Article Snippet: Primary fibroblasts utilized in this study: 1-year-old male (PCS-201-010, ATCC), 22-year-old female (GM02171, NIGMS Human Genetic Cell Repository at the Coriell Institute for Medical Research), 42-year-old female (F09-238, Washington University in St. Louis School of Medicine iPSC core facility), 56-year-old male (AG04148, NIA Aging Cell Repository at the Coriell Institute for Medical Research), and 68-year-old female (ND34769, NINDS Cell Line Repository at the Coriell Institute for Medical Research).

Techniques: Genome Wide, Expressing, RNA Sequencing, Gene Expression, Selection

Journal: Cell stem cell

Article Title: MicroRNAs Induce a Permissive Chromatin Environment That Enables Neuronal Subtype-specific Reprogramming of Adult Human Fibroblasts

doi: 10.1016/j.stem.2017.08.002

Figure Lengend Snippet: (A) Schematic of sample collection during miR-9/9*-124-mediated neuronal reprogramming for DNA methylation studies. Human fibroblasts were transduced with virus expressing miR-9/9*-124 or a non-specific (NS) control (Ctrl) virus at day 0. Samples were collected at day 10, day 20, and day 30.

Article Snippet: Primary fibroblasts utilized in this study: 1-year-old male (PCS-201-010, ATCC), 22-year-old female (GM02171, NIGMS Human Genetic Cell Repository at the Coriell Institute for Medical Research), 42-year-old female (F09-238, Washington University in St. Louis School of Medicine iPSC core facility), 56-year-old male (AG04148, NIA Aging Cell Repository at the Coriell Institute for Medical Research), and 68-year-old female (ND34769, NINDS Cell Line Repository at the Coriell Institute for Medical Research).

Techniques: DNA Methylation Assay, Transduction, Virus, Expressing, Control

Journal: Epigenetics

Article Title: Expression of human NAA11 ( ARD1B ) gene is tissue-specific and is regulated by DNA methylation

doi: 10.4161/epi.6.11.18125

Figure Lengend Snippet: Identification of CpG islands in proximal promoter regions of NAA10 and NAA11 genes and analysis of their methylation status. (A) Genomic organization of NAA10 and NAA11 genes at their 5′ ends. Black bars represent the locations of CpG islands in both genes. The arrow pairs denote the positions of primers used for MS-PCR. Grey bar refers to the genomic fragment cloned for NAA11 promoter assay. TSS, transcription start site. The genomic positions of CpG islands and NAA11 promoter fragment are annotated with respect to the start codon (ATG) of the respective gene, with A denoted as +1. (B) Analysis of methylation status of NAA10 and NAA11 gene proximal promoters in human tissues and cell lines by MS-PCR. Sizes of amplicons: for NAA10 gene: M primers (178 bp), U primers (183 bp); for NAA11 gene: M primers (129 bp), U primers (126 bp). Duplicate sets of genomic DNA samples from HeLa (H-1 and H-2) and HEK 293 (3-1 and 3-2) cells, which were harvested from the same preparations of cells for NAA10 and NAA11 expression analysis in Figure 1D, were examined. TE, testis; LV, liver; KD, kidney; LG, lung; PL, placenta; NTC, no-template control reaction. Forty cycles of amplification were performed. (C) Bisulfite sequencing analysis of the CpG island in NAA11 gene. Vertical lines on horizontal bar refer to the position of CpG dinucleotides (1–13) in the CpG island. Annotations are defined as in (A). Owing to the constraints in primer design, the 13th CpG dinucleotide was not analyzed in this experiment. For HeLa and HEK 293 cells, only one genomic DNA sample from each cell line was analyzed. Black circle, methylated CpG dinucleotide; white circle, non-methylated CpG dinucleotide.

Article Snippet: Genomic DNA samples from human tissues (testis: D1234260; liver: D1234149; kidney: D1234142; lung: D1234152; placenta: D1234200) were obtained from Biochain; those from human cell lines were extracted with Puregene Cell kit (Gentra D-5010A).

Techniques: Methylation, Clone Assay, Promoter Assay, Expressing, Amplification, Methylation Sequencing

Journal: Experimental and Therapeutic Medicine

Article Title: Comprehensive analysis and immunohistochemistry localization of NRP1 expression in pancancer and normal individual tissues in relation to SARS‑CoV‑2 susceptibility

doi: 10.3892/etm.2023.12340

Figure Lengend Snippet: NRP1 expression comparison between cancer tissues and matched healthy tissues. (A) NRP1 expression comparison between human tumor tissues and matched healthy tissues among different cancer types. Red colors indicate increase of expression while green colors indicate decrease of expression in tumor tissues in The Cancer Genome Atlas database. (B) NRP1 expression increases significantly in cancer tissues compared with that in matched healthy tissues among different cancer types. (C) NRP1 expression is significantly decreased in cancer tissues compared with that in matched healthy tissues among different cancer types. * P<0.01. N, normal; T, tumor; NRP1, neuropilin 1; TPM, transcripts per million. ACC, adrenocortical carcinoma; BLCA, bladder urothelial carcinoma; BRCA, breast invasive carcinoma; CESC, cervical squamous cell carcinoma and endocervical adenocarcinoma; CHOL, cholangiocarcinoma; COAD, colon adenocarcinoma; DLBC, lymphoid neoplasm diffuse large B-cell lymphoma; ESCA, esophageal carcinoma; GBM, glioblastoma multiforme; HNSC, head and neck squamous cell carcinoma; KICH, kidney chromophobe; KIRC, kidney renal clear cell carcinoma; KIRP, kidney renal papillary cell carcinoma; LAML, acute myeloid leukemia; LGG, brain lower grade glioma; LIHC, liver hepatocellular carcinoma; LUAD, lung adenocarcinoma; LUSC, lung squamous cell carcinoma; MESO, mesothelioma; OV, ovarian serous cystadenocarcinoma; PAAD, pancreatic adenocarcinoma; PCPG, pheochromocytoma and paraganglioma; PRAD, prostate adenocarcinoma; READ, rectum adenocarcinoma; SARC, sarcoma; SKCM, skin cutaneous melanoma; STAD, stomach adenocarcinoma; TGCT, testicular germ cell tumors; THCA, thyroid carcinoma; THYM, thymoma; UCEC, uterine corpus endometrial carcinoma; UCS, uterine carcinosarcoma; UVM, uveal melanoma.

Article Snippet: Human NRP1 gene expression in normal tissues and cancer was analyzed in The Cancer Genome Atlas (TCGA) database of the Human Protein Atlas (HPA) ( https://www.proteinatlas.org/ENSG00000099250-NRP1/tissue and ( https://www.proteinatlas.org/ENSG00000099250-NRP1/pathology ) ( , ), and the association between NRP 1 gene expression and survival in patients with cancer was analyzed by Gene Expression Profiling Interactive Analysis (GEPIA 2; http://gepia2.cancer-pku.cn/#analysis ) ( , ) in TCGA and GTEx data.

Techniques: Expressing, Comparison

Journal: Experimental and Therapeutic Medicine

Article Title: Comprehensive analysis and immunohistochemistry localization of NRP1 expression in pancancer and normal individual tissues in relation to SARS‑CoV‑2 susceptibility

doi: 10.3892/etm.2023.12340

Figure Lengend Snippet: Mutations in the NRP1 gene across multiple cancer types. (A) Mutation frequency of NRP1 across multiple cancer types. (B) Mutation locations of NRP1 across multiple cancer types. (C) Overall survival for wild-type and mutant NRP1 cases. NRP1, neuropilin 1; TCGA, The Cancer Genome Atlas; CNA, copy number alteration; SV, structured variant; VUS, variant of uncertain significance.

Article Snippet: Human NRP1 gene expression in normal tissues and cancer was analyzed in The Cancer Genome Atlas (TCGA) database of the Human Protein Atlas (HPA) ( https://www.proteinatlas.org/ENSG00000099250-NRP1/tissue and ( https://www.proteinatlas.org/ENSG00000099250-NRP1/pathology ) ( , ), and the association between NRP 1 gene expression and survival in patients with cancer was analyzed by Gene Expression Profiling Interactive Analysis (GEPIA 2; http://gepia2.cancer-pku.cn/#analysis ) ( , ) in TCGA and GTEx data.

Techniques: Mutagenesis, Variant Assay

Journal: Non-coding RNA Research

Article Title: Long non-coding RNA AK023617 orchestrates atherosclerosis by regulating the circadian rhythm of immunity-related GTPase family M protein in macrophages

doi: 10.1016/j.ncrna.2024.12.008

Figure Lengend Snippet: LncRNA-AK023617 interacts with Bmal1 to regulate circadian expression of IRGM. A Cytoplasmic and nuclear levels of lncRNA-AK023617 in THP-1 cells. B Silver staining of protein mixtures following an RNA pull-down assay in THP-1 cells. C Western blotting analysis of the interaction of Bmal1 with AK023617 probe following RNA pull-down assay. D RNA immunoprecipitation assay showing an interaction between Bmal1 and AK023617. E–G Representative blots and quantification of cytoplasmic and nuclear Bmal1 levels in THP-1 cells transfected with scrambled siRNA or siRNA targeting lncAK023617 and treated with oxidized low-density lipoprotein (ox-LDL; 50 μg/mL). H Potential binding sites for the Bmal1/Clock heterodimer in the IRGM promoter were analyzed using the JASPAR database. I Fastq data for ChIP-seq samples from Gene Expression Omnibus (GEO) series GSE95712 were analyzed using Genome-wide Event finding and Motif discovery (GEM) and visualized with the UCSC genome browser. J ChIP assays showing recruitment of Bmal1 protein to the promoter of IRGM in synchronized THP-1 cells stimulated with ox-LDL (50 μg/mL) at ZT0 and ZT12, n = 3. NS, not significant, ∗ P < 0.05, ∗∗ P < 0.005, ∗∗∗ P < 0.0005, ∗∗∗∗ P < 0.0001.

Article Snippet: Cell lysates were isolated from THP-1 which was stimulated with oxidized low-density lipoprotein (ox-LDL; 50 μg/mL) and treated with RNase inhibitor and protease inhibitor, followed by incubation with human anti -Bmal1 antibody (14,020, Cell Signaling Technology [CST], USA) or normal rabbit IgG (2729, CST, USA) antibody at 4 °C overnight.

Techniques: Expressing, Silver Staining, Pull Down Assay, Western Blot, RNA Immunoprecipitation, Transfection, Binding Assay, ChIP-sequencing, Gene Expression, Genome Wide