Journal: Frontiers in Cell and Developmental Biology

Article Title: Establishment of human periodontal ligament cell lines with ALPL mutations to mimic dental aspects of hypophosphatasia

doi: 10.3389/fcell.2025.1572571

Figure Lengend Snippet: Potential consequences of genetic changes in clone 1.5. and investigation of mRNA products via RT-PCR. (A) Sequencing of clone 1.5 gDNA showed a huge genetic alteration within the ALPL exon 6 locus, including a 48 bp duplication and a 48 bp deletion. Clonal cDNA sequencing further clarified that the deletion results in an in-frame loss of 48 bp, thereby subsequently should result in loss of 16 aa within the corresponding TNAP protein domain. The corresponding insertion is not detected in the cDNA sequencing. (B) A potential gain of a novel splice acceptor site was predicted by different algorithms (Alamut Visual Plus splice summary is shown, blue box marks ALPL exon 6 locus, red box indicates gained sequence, green box marks novel splice site). (C) The in silico predicted novel splice product was detectable via RT-PCR by electrophoresis. The analyses indicate an additional PCR product in clone 1.5. While the larger product (marked with white arrowhead) is also present in clone 1.3, the smaller band was only detected in clone 1.5 (marked with green arrowhead). (D) Sequencing of the smaller RT-PCR products shows deletion of 48 bp and the active usage of the new splice site. (E) Schematic presentation of sequence aberration and splice prediction for the wildtype and the aberrant sequence on gDNA (upper panel) and mRNA level (lower panel). PCR primer binding sites and expected RT-PCR product sites (in grey) are in addition sketched below. The CRISPR target region is marked in red. The green box marks 48 bp duplication in clone 1.5, while the crossed white box indicates deletion of 48 bp. Black asterisk marks position of potential novel splice site.

Article Snippet: Prediction of splice site consequences after the 48 bp duplication via Alamut Visual Plus software (combining four different splice algorithms) resulted in identification of a high-scoring novel splice acceptor site in this region ( ; SpliceSite Finder score: 81.9; MaxEntScan score: 7.2; NNSPLICE score: 0.9; GeneSplicer score: 8.4).

Techniques: Reverse Transcription Polymerase Chain Reaction, Sequencing, In Silico, Electrophoresis, Binding Assay, CRISPR

Journal: British Journal of Pharmacology

Article Title: Next-generation sequencing for mitochondrial disorders

doi: 10.1111/bph.12469

Figure Lengend Snippet: (A) Novel mutations or novel phenotypes in known mitochondrial disease genes affecting oxidative phosphorylation identified using NGS methods. (B) Novel mutations or novel phenotypes in known mitochondrial disease genes not affecting oxidative phosphorylation identified using NGS methods

Article Snippet: C19orf12 (Horvath et al ., 2012 ) , Mitochondrial protein of unknown function , WES-SureSelct Illumina , Brain iron accumulation with dystonia, optic atrophy and peripheral neuropathy.

Techniques: Phospho-proteomics, Sequencing, Binding Assay, Membrane

Journal: eLife

Article Title: Transcriptional profiling of Hutchinson-Gilford Progeria syndrome fibroblasts reveals deficits in mesenchymal stem cell commitment to differentiation related to early events in endochondral ossification

doi: 10.7554/eLife.81290

Figure Lengend Snippet: RNA-seq datasets from progeria patients used in this study.

Article Snippet: AG03199 , 10 yr , F , White , polyA (Illumina SureSelect Strand Specific RNA library Prep) , Arufe , GSE113648.

Techniques: Sample Prep

Journal: eLife

Article Title: Transcriptional profiling of Hutchinson-Gilford Progeria syndrome fibroblasts reveals deficits in mesenchymal stem cell commitment to differentiation related to early events in endochondral ossification

doi: 10.7554/eLife.81290

Figure Lengend Snippet: RNA-seq datasets from adult controls used in this study.

Article Snippet: AG03199 , 10 yr , F , White , polyA (Illumina SureSelect Strand Specific RNA library Prep) , Arufe , GSE113648.

Techniques:

Journal: eLife

Article Title: Transcriptional profiling of Hutchinson-Gilford Progeria syndrome fibroblasts reveals deficits in mesenchymal stem cell commitment to differentiation related to early events in endochondral ossification

doi: 10.7554/eLife.81290

Figure Lengend Snippet: RNA-seq datasets from children controls used in this study.

Article Snippet: AG03199 , 10 yr , F , White , polyA (Illumina SureSelect Strand Specific RNA library Prep) , Arufe , GSE113648.

Techniques: Sample Prep