Journal: International Journal of Molecular Sciences

Article Title: Bioactive-Glass-Based Materials with Possible Application in Diabetic Wound Healing: A Systematic Review

doi: 10.3390/ijms25021152

Figure Lengend Snippet: Wound healing stages. ( a ) Processes that occur during the different wound healing stages. I. Hemostasis: occurs immediately after tissue damage to stop bleeding by platelet aggregation and the coagulation cascade. II. Inflammation: removal of the bacteria and dead cells in wound bed by inflammatory cells (neutrophils and macrophages). Triggers the proliferation stage. III. Proliferation: proliferation and migration of fibroblasts, keratinocytes, and endothelial cells. Re-epithelialization, angiogenesis, and granulation tissue formation. IV. Remodeling: reorganization of ECM, where collagen type III is replaced by collagen type I. This can last one year or more . ECM: extracellular matrix; MP: metalloproteinases; TIMP: tissue inhibitors of metalloproteinases . ( b ) Four phases of wound healing. Each stage is key in order to ensure a proper wound healing response .

Article Snippet: The remaining studies used one of the following cells: endothelial cells, endothelial progenitor cells (EPCs), human acute monocytes leukemia THP-1 cells (THP-1 cells), mouse aortic endothelial cells (MAECs), human neonatal foreskin epidermal keratinocytes, and mouse macrophages (RAW 264.7 cells, ATCC, USA).

Techniques: Coagulation, Bacteria, Migration

Journal: International Journal of Molecular Sciences

Article Title: Bioactive-Glass-Based Materials with Possible Application in Diabetic Wound Healing: A Systematic Review

doi: 10.3390/ijms25021152

Figure Lengend Snippet: Methodological and study outcome characteristics of articles included in this systematic review.

Article Snippet: The remaining studies used one of the following cells: endothelial cells, endothelial progenitor cells (EPCs), human acute monocytes leukemia THP-1 cells (THP-1 cells), mouse aortic endothelial cells (MAECs), human neonatal foreskin epidermal keratinocytes, and mouse macrophages (RAW 264.7 cells, ATCC, USA).

Techniques: Staining, Gene Expression, In Vitro, Animal Model, In Vivo, Derivative Assay

Journal: bioRxiv

Article Title: Two non-coding variants associated with isolated orofacial cleft promote binding of transcriptional repressors FOXE1 or ETS2 and reduce expression of IRF6

doi: 10.1101/2024.06.01.596914

Figure Lengend Snippet: FOXE1 KO GMSM-K: Browser view of the human genome, GRCh37/hg19, focused on FOXE1 gene. First track represents a pair of guide RNAs (marked with a block) and primers (marked with arrows) used to generate FOXE1 KO cells. Primer sequences are provided in Table S5. Following color coded bars represent chromatin status revealed by ChIP-Seq to various chromatin marks from the ENCODE Project cell lines and facial explants from human embryos at Carnegie stage (CS) 13-20, encompassing the time when palatal shelves fuse, where yellow bars represent the enhancer element, bright red, active promoter; light red, weak promoter; purple, inactive/poised promoter; grey, Polycomb repressed; dark purple in facial explants dataset, bivalent promoter; GM12878, B-cell derived cell line; ESC, embryonic stem cells; K562, myelogenous leukemia; HepG2, liver cancer; HUVEC, human umbilical vein endothelial cells; HMEC, human mammary epithelial cells; HSMM, human skeletal muscle myoblasts; NHEK, normal human epidermal keratinocytes; NHLF, normal human lung fibroblasts, CS13-CS20 are facial explants from human embryos. The blue region highlights the deleted fragment after CRISPR/Cas9 targeting.

Article Snippet: Primary Epidermal Keratinocytes: Normal, Human, Neonatal Foreskin (HEKn) purchased from ATCC (ATCC Catalog no. PCS-200-010) were maintained and cultured as per manufacturer’s instruction in dermal cell basal medium (ATCC Catalog no. PCS-200-030) supplemented with keratinocyte growth kit (ATCC Catalog no. PCS-200-040).

Techniques: Blocking Assay, ChIP-sequencing, Derivative Assay, CRISPR

Journal: bioRxiv

Article Title: Two non-coding variants associated with isolated orofacial cleft promote binding of transcriptional repressors FOXE1 or ETS2 and reduce expression of IRF6

doi: 10.1101/2024.06.01.596914

Figure Lengend Snippet: A) Browser view of the human genome, GRCh37/hg19, focused on the GWAS-identified SNPs at IRF6 associated with orofacial cleft. First two tracks represent the total SNPs (608) identified by GWAS at IRF6 and MPRA-identified SNPs (46) at IRF6 respectively. Next track represents IRF6 enhancers revealed by the ABC (Activity by Contact) method. B) Browser view (zoomed in from ) of the human genome, GRCh37/hg19, focused on the SNPs at IRF6 (rs11119348 and rs661849) that lie in active elements. First three tracks represent the same as in . Next two tracks represent open chromatin elements detected by ATAC-Seq and active chromatin revealed by H3K27Ac in HIOEC, respectively, illustrating rs11119348 and rs661849 lie within IRF6 enhancers. Following color coded bars represent chromatin status revealed by ChIP-Seq to various chromatin marks from the ENCODE Project cell lines and facial explants from human embryos at Carnegie stage (CS) 13-20, encompassing the time when palatal shelves fuse, where orange and yellow bars represent the active and weak enhancer element, respectively; bright red, active promoter; light red, weak promoter; purple, inactive/poised promoter; blue, insulator; light green, weak transcribed; grey, Polycomb repressed; light grey, heterochromatin/repetitive; green and dark purple in facial explants dataset, transcription and bivalent promoter respectively; GM12878, B-cell derived cell line; ESC, embryonic stem cells; K562, myelogenous leukemia cell line; HepG2, liver cancer cell line; HUVEC, human umbilical vein endothelial cells; HMEC, human mammary epithelial cells; HSMM, human skeletal muscle myoblasts; NHEK, normal human epidermal keratinocytes; NHLF, normal human lung fibroblasts, CS13-CS20 are facial explants from human embryos. C) Bar chart of MPRA and luciferase reporter activities for the indicated SNPs at various loci in GMSM-K. For luciferase reporter activities, data are represented as mean values +/- s. d. from four independent experiments. Statistical significance is determined by Student’s t-test, two-tailed P value (* P <0.05, ** P <0.01, *** P <0.001, **** P <0.0001) and NS, non-significant; Luc, luciferase. D and E) Scattered dot plot of relative luciferase activity for non-risk and risk alleles of rs11119348 and rs661849 respectively in HEKn. Data are represented as mean values +/- s. d. from four independent experiments. Statistical significance is determined by Student’s t -test. P value (two-tailed) is indicated on the plot.

Article Snippet: Primary Epidermal Keratinocytes: Normal, Human, Neonatal Foreskin (HEKn) purchased from ATCC (ATCC Catalog no. PCS-200-010) were maintained and cultured as per manufacturer’s instruction in dermal cell basal medium (ATCC Catalog no. PCS-200-030) supplemented with keratinocyte growth kit (ATCC Catalog no. PCS-200-040).

Techniques: Activity Assay, ChIP-sequencing, Derivative Assay, Luciferase, Two Tailed Test

Journal: bioRxiv

Article Title: Two non-coding variants associated with isolated orofacial cleft promote binding of transcriptional repressors FOXE1 or ETS2 and reduce expression of IRF6

doi: 10.1101/2024.06.01.596914

Figure Lengend Snippet: A ) Browser view of the human genome, GRCh37/hg19, focused on the GWAS-identified SNPs at FOXE1. First two tracks represent the OFC associated SNPs at FOXE1 and MPRA-identified SNPs at FOXE1 respectively. Next track represents the ABC (Activity by Contact) elements scored using HiC data from NHEK. Next two tracks represent open chromatin peaks detected by ATAC-Seq and H3K27Ac marks in HIOEC respectively. Following color coded bars represent chromatin status revealed by ChIP-Seq to various chromatin marks from the ENCODE Project cell lines and facial explants from human embryos at Carnegie stage (CS) 13-20, encompassing the time when palatal shelves fuse, where orange and yellow bars represent the active and weak enhancer element, respectively; bright red, active promoter; light red, weak promoter; purple, inactive/poised promoter; blue, insulator; light green, weak transcribed; grey, Polycomb repressed; light grey, heterochromatin/repetitive; pale turquoise, light purple and dark purple in facial explants dataset, heterochromatin poised promoter and bivalent promoter respectively; GM12878, B-cell derived cell line; ESC, embryonic stem cells; K562, myelogenous leukemia; HepG2, liver cancer; HUVEC, human umbilical vein endothelial cells; HMEC, human mammary epithelial cells; HSMM, human skeletal muscle myoblasts; NHEK, normal human epidermal keratinocytes; NHLF, normal human lung fibroblasts, CS13-CS20 are facial explants from human embryos. Box in A , a SNP (rs10984103) with significant effect in MPRA lying within an enhancer for FOXE1 in HEKn by the ABC method, and within chromatin marked as an active enhancer in human embryonic faces. B) Browser view of the human genome, GRCh37/hg19, focused on the GWAS-identified SNPs at MAFB associated with orofacial cleft. Tracks and color code are similar as in . Box in B , a SNP (rs4812449) with significant effect in MPRA lying within chromatin marked as an active enhancer in human embryonic faces.

Article Snippet: Primary Epidermal Keratinocytes: Normal, Human, Neonatal Foreskin (HEKn) purchased from ATCC (ATCC Catalog no. PCS-200-010) were maintained and cultured as per manufacturer’s instruction in dermal cell basal medium (ATCC Catalog no. PCS-200-030) supplemented with keratinocyte growth kit (ATCC Catalog no. PCS-200-040).

Techniques: Activity Assay, ChIP-sequencing, Derivative Assay

Journal: bioRxiv

Article Title: Two non-coding variants associated with isolated orofacial cleft promote binding of transcriptional repressors FOXE1 or ETS2 and reduce expression of IRF6

doi: 10.1101/2024.06.01.596914

Figure Lengend Snippet: A) RNA expression levels of different epithelial markers and IRF6 gene plotted from RNA-Seq data. For NHEK two different publicly available RNA-seq profiles were used (GSM6050574: NHEK-Alpha and GSM6050576: NHEK-Hotel). B) Immunofluorescence staining for E-cadherin, Keratin 14, and P63 (green) of human GMSM-K and normal human skin keratinocytes (NHSK). White arrows indicate positive staining in NHSK absent in GMSM-K. Nuclear DNA is labeled with DAPI (blue). Scale bar = 20 µm.

Article Snippet: Primary Epidermal Keratinocytes: Normal, Human, Neonatal Foreskin (HEKn) purchased from ATCC (ATCC Catalog no. PCS-200-010) were maintained and cultured as per manufacturer’s instruction in dermal cell basal medium (ATCC Catalog no. PCS-200-030) supplemented with keratinocyte growth kit (ATCC Catalog no. PCS-200-040).

Techniques: RNA Expression, RNA Sequencing, Immunofluorescence, Staining, Labeling

Journal: PLoS ONE

Article Title: Generation of Human Melanocytes from Induced Pluripotent Stem Cells

doi: 10.1371/journal.pone.0016182

Figure Lengend Snippet: Either 3F- (3F-iPS MEL, A–E) or 4F- (4F-iPS MEL, F–J) iPS cells derived melanocytes were positive for an array of melanocyte markers: SILV (silver protein), TYRP1 (tyrosinase-related protein-1), TYR (tyrosinase), MITF (microphthalmia-associated transcription factor) , and S100. Normal human epidermal melanocytes (NHEM) were also stained with the same antibodies (K–O). Transmission electron microscopy images of either 3F (P), 4F (Q)-iPS cells derived melanocytes, or NHEM (R) showed that those melanocytes have many melanosomes in the cytoplasm. Scale bar, 20 µm (A–O), 0.5 µm (P, Q, and R). (S) Quantitative real-time PCR analysis of MITF-M and c-Kit in 3F-iPS, 3F-iPS MEL, and NHEM. The data are normalized to GAPDH and represented as fold change relative to RNA levels in 3F-iPS. The graphs show the average of two independent experiments. Error bar indicates mean±S.E.M. (T) Quantitation of SILV-positive cells induced from 3F and 4F-iPS cells. Percentage of SILV positive cells upon total differentiation of EBs cells 7 weeks after differentiation under melanocyte differentiation medium. Error bar indicates mean±S.E.M (3F-iPS, n = 3; 4F-iPS, n = 2). (U) The global gene-expression patterns were compared between human 3F-iPS cells and 3F-iPS derived-MEL (3F-iPS MEL), and between NHEM and 3F-iPS MEL. The lines indicate the linear equivalent and 5-fold differences on either side in gene expression levels between the two samples.

Article Snippet: Cultured normal human foreskin-derived epidermal melanocyte (NHEM) cells were obtained from Kurabo (Osaka, Japan).

Techniques: Derivative Assay, Staining, Transmission Assay, Electron Microscopy, Real-time Polymerase Chain Reaction, Quantitation Assay, Gene Expression

Journal: International Journal of Molecular Sciences

Article Title: Stem Cells in Skin Regeneration, Wound Healing, and Their Clinical Applications

doi: 10.3390/ijms161025476

Figure Lengend Snippet: Some examples of skin scaffolds: epidermal substitutes ( A ); dermal substitutes ( B ); composite substitutes ( C ) [ 95 ].

Article Snippet: Trancyte , Advanced BioHealing, Inc., Westport, CT, USA , Nylon mesh coated with porcine collagen with non-viable cultured neonatal foreskin-derived fibroblasts attached to silicone membrane as temporary epidermis , Partial-thickness and full-thickness wounds; burn wounds.

Techniques: Cell Culture, Suspension, Membrane, Clinical Proteomics, Polymer, Derivative Assay