Journal: bioRxiv

Article Title: Allelic imbalance reveals widespread germline-somatic regulatory differences and prioritizes risk loci in Renal Cell Carcinoma

doi: 10.1101/631150

Figure Lengend Snippet: ( a ) Manhattan plots for SCARB1 locus (top to bottom): (1) GWAS association significance; (2) eQTL in all tumors; (3) eQTL in subset of 66 tumors with matched normals; (4) eQTL in 66 matched normals. Risk SNP is a nominally significant eQTL in the subset of tumors but not in the matched normals. ( b ) Manhattan plots for GRAMD4 locus as described in ( a ). Risk SNP is a highly significant eQTL in the subset of tumors but not in the matched normals. ( c ) Per-individual distribution of allelic imbalance for GRAMD4 in heterozygous GWAS risk variant carriers. Each point represents an individual allelic-fraction (x-axis, log scale) in tumor (left) and normal (right). Point size corresponds to number of reads at that heterozygous haplotype. Gray line shows approximate standard error estimated likelihood ratio test. ( d ) Per-individual absolute tumor allelic imbalance at exonic SNP stratified by homozygous risk carriers (left) and heterozygous risk carriers (right). Homozygous risk SNP carriers are typically not significantly imbalanced, consistent with no secondary imbalance signal. Heterozygous risk SNP carriers are typically imbalanced, consistent with being the causal regulatory variant.

Article Snippet: RNA expression levels were quantified after reverse transcription with MMLV H-(Promega) using the TaqMan gene expression system (Thermo Fisher, probe numbers Hs00411719 and Hs00969821).

Techniques: Variant Assay

Journal: Cell reports

Article Title: Quantitative trait loci mapping provides insights into the genetic regulation of dendritic cell numbers in mouse tissues

doi: 10.1016/j.celrep.2024.114296

Figure Lengend Snippet: (A) Manhattan plot showing all splice variant SNPs across the 49 phenotypes. For each splice variant, the best p value observed among all assessed traits is plotted on a –log10 scale (y axis), according to its genomic coordinates (x axis). Gramd4 splice variant chosen for validation is highlighted in red. (B) Variation in frequency of BM pre-cDCs in C57BL/6J (gray; n = 3), 129 (pink; n = 3), NOD (blue; n = 3), NZO (cyan; n = 3), A/J (yellow; n = 3), WSB (purple; n = 3), DO (black; n = 170), and CC-RI (open; n = 47) mice. (C) A QTL driving the frequency of BM pre-cDCs found within chromosome 15 (chr15:86,581,607, LOD = 10.7) that appears to be driven by an A/J and NZO founder effect. (D) Gramd4 gene structure and schematic representation of alternative splicing (UCSC Genome Browser). SNP localization is shown in red. (E) Western blot on total splenocytes from Gramd4 w/w and Gramd4 sp/sp mice showing alternative splicing. (F) Schematic representation of mixed BM chimera experiment. (G) Representative flow cytometry plot for mixed BM experiment. (H) Frequencies of DC progenitors and subsets in mixed BM chimera mice due to differential expression of Gramd4 SNP variant in BM, spleen, and inguinal LN. Chimerism is expressed as the ratio between the number of CD45.2 and CD45.1/CD45.2 cells for each cell population. Representative of 2 independent experiments; each dot represents one mouse, n = 6 per group, Gramd4 w/w (red) and Gramd4 sp/sp (blue), and horizontal lines represent means. (I) Schematic representation of the experimental setup in (J) and (K). (J) Representative flow cytometry plot for OT-II CD4 + T cell activation (CTV dilution after immunization with OVA 328–339 peptide in alum) in popliteal LN of Gramd4 w/w and Gramd4 sp/sp recipient mice. Graph shows the absolute numbers of OT-II cells in popliteal lymph nodes and the x axis the number of divisions after immunization. (K) CD69 and CD43 expression of divided OT-II T cells in popliteal LN of Gramd4 w/w and Gramd4 sp/sp recipient mice. Each dot represents one mouse, n = 6 per group, Gramd4 w/w (orange) and Gramd4 sp/sp (green), and horizontal lines represent means (J and K). Student’s t test, * p < 0.05, ** p < 0.01, *** p < 0.001, **** p < 0.0001. iLN (inguinal LN).

Article Snippet: After being blocked, the western blot membrane was subsequently incubated with anti-Gramd4 antibody (Clone C-8, Santa-Cruz).

Techniques: Variant Assay, Biomarker Discovery, Alternative Splicing, Western Blot, Flow Cytometry, Quantitative Proteomics, Activation Assay, Expressing

Journal: Cell reports

Article Title: Quantitative trait loci mapping provides insights into the genetic regulation of dendritic cell numbers in mouse tissues

doi: 10.1016/j.celrep.2024.114296

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: After being blocked, the western blot membrane was subsequently incubated with anti-Gramd4 antibody (Clone C-8, Santa-Cruz).

Techniques: Marker, Staining, Recombinant, Red Blood Cell Lysis, Software

Journal: Cell Death Discovery

Article Title: Knockdown of SUCLG2 inhibits glioblastoma proliferation and promotes apoptosis through LMNA acetylation and the mediation of H4K16la lactylation

doi: 10.1038/s41420-025-02856-4

Figure Lengend Snippet: A H4K16la and L-Lac expression patterns in shNC and shSUCLG2 cells of U251 and LN229 were determined using western blotting. B Cell precipitates were collected for cleavage under targets and tagmentation (CUT&Tag) assay to identify H4K16la binding peaks, and the heatmap shows the distribution of H4K16la peaks near the translation start site (TSS). C Comparison of shNC and shSUCLG2 peaks in LN229 cells. D Genomic distribution of H4K16la, which was annotated for its localisation (promoter, exon, intron, or intergenic) and quantified in relative and absolute amounts. E Volcano plots of upregulated versus downregulated genes after CUT&Tag assay for H4K16la binding. F The heat map shows genes downregulated around TSS in LN229 cells containing shNC and shSUCLG2 as detected by the CUT&Tag assay. G KEGG analysis of CUT&Tag-detected downregulated genes at H4K16la. H GO analysis of CUT&Tag-detected downregulated genes. I Volcano plot of differential gene expression in RNA-seq. J KEGG analysis of downregulated genes in shSUCLG2 versus shNC using RNA-seq. K GO analysis of shSUCLG2 versus shNC downregulated genes using RNA-seq. L Combined CUT&Tag and RNA-seq analyses were performed to identify potential downstream target intersections of H4K16la. M Integrated genomics viewer trajectory track of CUT&Tag data showing enrichment of H4K16la at BEST1, GRAMD4H, and MBD6 promoter regions. N LN229 and U251 cells were treated with shNC or shRNA, and DNA fragments were immunoprecipitated with H4K16la antibody and analysed by qPCR. O Representative western blotting images show the quantification of BEST1, MBD6, and GRAMD4 protein levels. P Western blotting of IL-6 and IL-8 in shNC or shRNA lines of LN229 and U251. * P < 0.05, ** P < 0.01, *** P < 0.001; ns, not significant.

Article Snippet: The following antibodies were used: SUCLG2 (A8976, 1:1 200, ABclonal, Wobum, MA), Bax (60267-1-Ig, 1:1000, Proteintech, Rosemont, IL), PCNA (HRP-60097, 1:1 000, Proteintech), Caspase-3 (68773-1-Ig, 1:1000, Proteintech), Bcl-2 (12789-1-AP, 1:1000, Proteintech), β-actin (11313-2-AP, 1:1 500, Proteintech), Cyclin D1 (60186-1-Ig, 1:1500, Proteintech), DLAT (ab172617, 1:1000, Abcam, Cambridge, UK), LMNA (ab172617, 1:1000, Abcam), L-Lac (PTM-1401RM, 1:1000, Jingjie Bio, Nanjing, China), D-Lac (PTM-1429RM, 1:1000, Jingjie Bio), HIF-1α (H1alpha67, 1:1000, Abcam), H4K16la (PTM-122, 1:1000, Jingjie Bio), H4 (PTM-1015RM, Jingjie Bio), Total oxidative phosphorylation Rodent Antibody Cocktail (ab110413, 1:1000, Abcam), BEST1 (1:1000, ab259836, Abcam); GRAMD4 (1:1000, 24299-1-AP9, Proteintech), MBD6 (1:1000, ab204403, Abcam); MFN1 (A21293, 1:1200, ABclonal); MFN2 (A19678, 1:1200, ABclonal); DR1 (A13298,1:1200, ABclonal); IL-6 (A26791, 1:1000, ABclonal); IL-8 (RP00052, 1:1000, ABclonal); anti-rabbit IgG (H + L) (ab205718, 1:5000, Abcam), and anti-mouse IgG (H + L) (ab205719, 1:5000, Proteintech).

Techniques: Expressing, Western Blot, Binding Assay, Comparison, Gene Expression, RNA Sequencing, shRNA, Immunoprecipitation