Journal: Oncotarget

Article Title: PLCB4 copy gain and PLCß4 overexpression in primary gastrointestinal stromal tumors: Integrative characterization of a lipid-catabolizing enzyme associated with worse disease-free survival

doi: 10.18632/oncotarget.15306

Figure Lengend Snippet: A . In one each representative GISTs classified as very low- (A 1 ), low- (A 2 ), intermediate- (A 3 ), and high-risk (A 4 ) levels, tumor cells exhibit no (A 5 ), weak (A 6 ), moderate (A 7 ) to diffuse strong (A 8 ) cytoplasmic reactivity to PLCß4, respectively. B . Using the probe directed against the centromeric sequence ( green ) as the reference, a locus-specific FISH probe targeting PLCB4 gene ( red ) demonstrated normal status (B 1 ), polysomy (B 2 ), and amplification (B 3 ) in one each representative GIST.

Article Snippet: The Chromosome 20 Control probe targeting the centromeric region (#041015, Empire Genomics) was labeled with Green 5-Fluorescein dUTP essentially following the previously described method [ ].

Techniques: Sequencing, Amplification

Journal: Neuron

Article Title: Rewiring of human neurodevelopmental gene regulatory programs by Human Accelerated Regions (HARs)

doi: 10.1016/j.neuron.2021.08.005

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: CaptureMPRA library design, cloning, and transfection Molecular Inversion Probes (MIPs) targeting flanking regions of all HAR sequences were designed using the MIPgen program ( Boyle et al., 2014 ) and manufactured as a pool by CustomArray (Bothell, WA).

Techniques: Virus, Recombinant, Electron Microscopy, Modification, Lysis, Sonication, Plasmid Preparation, Software

Journal: Neuron

Article Title: Rewiring of human neurodevelopmental gene regulatory programs by Human Accelerated Regions (HARs)

doi: 10.1016/j.neuron.2021.08.005

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: CaptureMPRA library design, cloning, and transfection Molecular Inversion Probes (MIPs) targeting flanking regions of all HAR sequences were designed using the MIPgen program ( Boyle et al., 2014 ) and manufactured as a pool by CustomArray (Bothell, WA).

Techniques: Virus, Recombinant, Electron Microscopy, Modification, Lysis, Sonication, Plasmid Preparation, Software

Journal: Frontiers in Neuroscience

Article Title: DYRK1A roles in human neural progenitors

doi: 10.3389/fnins.2025.1533253

Figure Lengend Snippet: List of DYRK1A interactors identified by Mass-Spectrometry in human neural stem cells

Article Snippet: Proteins extracted from untreated hNSC were immunoprecipitated with DYRK1A antibodies targeting the N-terminal and C-terminal regions of the protein, respectively (Cohesion Biosciences #CPA1357, Immunogen sequence aa 39-51 and Abnova H00001859-M01, aa 674–763).

Techniques: Expressing

Journal: Frontiers in Neuroscience

Article Title: DYRK1A roles in human neural progenitors

doi: 10.3389/fnins.2025.1533253

Figure Lengend Snippet: Representation of DYRK1A protein interactome in human neural stem cells. (A) Protein interactome of DYRK1A: boxes are filled with a yellow to dark red gradient corresponding to the number of peptide-spectrum matching (PSM) values (see ); proteins found using the anti-DYRK1A antibody directed against the C-terminal part of the protein are circled in green, those found using the one directed against the N-terminal part in pink, and those found with both antibodies in gray; “P” indicates that phosphorylation events have been identified. (B) Significant enrichment in GO terms among DYRK1A interactors. (C) Number of Human Phenotype Ontology (HPO) terms of DYRK1A syndrome reported in the diseases associated with DYRK1A’s partners.

Article Snippet: Proteins extracted from untreated hNSC were immunoprecipitated with DYRK1A antibodies targeting the N-terminal and C-terminal regions of the protein, respectively (Cohesion Biosciences #CPA1357, Immunogen sequence aa 39-51 and Abnova H00001859-M01, aa 674–763).

Techniques: Phospho-proteomics

Journal: Frontiers in Neuroscience

Article Title: DYRK1A roles in human neural progenitors

doi: 10.3389/fnins.2025.1533253

Figure Lengend Snippet: Transcriptomic changes induced by DYRK1A knockdown in human neural stem cells. (A) Volcano plot showing RNA sequencing data (control vs. si DYRK1A treated hNSC 1 ) with the significance (−log10 of the p -value) as a function of the log2 fold change. Genes not significantly deregulated are shown in black; genes significantly deregulated (DEG) with an adjusted p-value between 0.05 and 0.1 are shown in orange, while genes with an adjusted p -value <0.05 are shown in red. (B) Pathways analysis using Uniprot and Gene Ontology terms revealed significant enrichment in proteins from the extracellular matrix (ECM), involved in cell adhesion and binding calcium; CC, cellular component; MF, molecular function, BP, biological process; PTM, posttranslational modification. (C) Representation of RNA-Seq results for a subset of DEG: RNAseq results including adjusted p -value (* p -value<0.1, ** p -value<0.05, and *** p -value<0.01) and log2 fold change (color intensity), RT-qPCR analysis performed in a third series of hNSC 1 ( n = 3) and in three series of hNSC 2 ( n = 9; normalized on GAPDH and YWHAZ ); significant change in gene expression confirmed in hNSC 1 (1), hNSC 2 (2), or both (1 + 2). Genes involved in neurodevelopmental disorders (NDD) are retrieved from the “Definitive” ( D ) and “Limited” ( L ) gene lists of SysNDD database. b , gene not already associated with an NDD but having a high intolerance to loss-of-function in the gnomAD database (pLI > 0.9).

Article Snippet: Proteins extracted from untreated hNSC were immunoprecipitated with DYRK1A antibodies targeting the N-terminal and C-terminal regions of the protein, respectively (Cohesion Biosciences #CPA1357, Immunogen sequence aa 39-51 and Abnova H00001859-M01, aa 674–763).

Techniques: Knockdown, RNA Sequencing, Control, Binding Assay, Modification, Quantitative RT-PCR, Gene Expression

Journal: Frontiers in Neuroscience

Article Title: DYRK1A roles in human neural progenitors

doi: 10.3389/fnins.2025.1533253

Figure Lengend Snippet: DYRK1A knockdown affects human neural stem cell proliferation. (A) Western blot analysis on total protein extract from hNSC 1 treated with lipofectant alone (Control) or transfected with Scramble or DYRK1A siRNA for 48 h. The level of p21 protein ( n = 3) and ERK and phosphoERK (pERK; n = 3) was normalized to the GAPDH level. Multiple comparison tests were performed using a one-way ANOVA test with Dunnett’s correction: ns: not significant; **: adjusted p -value<0.01; *: adjusted p -value<0.05; errors bar represent standard error of the mean (SEM); (B) proliferation assay performed on hNSC 1 treated with lipofectant alone (Control), transfected with Scramble siRNA, DYRK1A siRNA (si DYRK1A ). A treatment with PLK1 siRNA (si PLK1 ) was used as a positive control, leading to cell apoptosis. At each time point (days 0, 1, 2, 3, and 4), cells were counted and data normalized with day 0 ( n = 3 per line). Student’s t -test comparison was done comparing to Control condition: * p -value<0.05; error bars represent SEM.

Article Snippet: Proteins extracted from untreated hNSC were immunoprecipitated with DYRK1A antibodies targeting the N-terminal and C-terminal regions of the protein, respectively (Cohesion Biosciences #CPA1357, Immunogen sequence aa 39-51 and Abnova H00001859-M01, aa 674–763).

Techniques: Knockdown, Western Blot, Control, Transfection, Comparison, Proliferation Assay, Positive Control