Journal: medRxiv

Article Title: Severus: accurate detection and characterization of somatic structural variation in tumor genomes using long reads

doi: 10.1101/2024.03.22.24304756

Figure Lengend Snippet: (A) Examples of simple and complex SVs from each junction type; Head-to-tail (deletion-like), Tail-to-head (duplication-like), Head-to-head/Tail-to-tail (inversion-like), and Interchromosomal (translocation-like). Each colored arrow is a genomic segment, and the direction of the arrows represents the direction of the segment. Red dashed lines represent junctions. Simple SVs are indicated with a gray box and are not included in breakpoint graph construction. (B) Number of junctions in simple SVs and complex SVs in each cell line. (C) The distribution of complex cluster size in each cell line is colored by technology. (D) Number of junctions in each category involved in a complex SV. (E) A chromothripsis-like event in chr21 in HCC1954 and (F) in chr3 in HCC1395. (G) The distribution of junctions as unphased, a single phased junction within a phase block, and multiple junctions within a block; cis and trans refer to the same or different phases of two adjacent variants, respectively.

Article Snippet: Normal cell lines: HCC1954 BL (ATCC, CRL-2339), BL2009 (ATCC, CRL-5961), HCC1937, BL1437 (ATCC, CRL-5958), and HCC1395 BL (ATCC, CRL-2325).

Techniques: Translocation Assay, Blocking Assay

Journal: Nature Communications

Article Title: High-throughput identification of functional regulatory SNPs in systemic lupus erythematosus

doi: 10.1038/s41467-024-50710-5

Figure Lengend Snippet: A Flow chart illustrating the identification of functional candidate SNPs from SLE GWAS data. B SNP-seq: To generate the SNP-seq construct (top), a 31 bp sequence centered on the SNP is positioned between two type IIS restriction enzyme (IIS RE) binding sites. SNPs that fail to bind regulatory proteins such as transcription factors (TF) are negatively selected (bottom), allowing enrichment of protected constructs by PCR. The whole construct can be amplified using primers as per Supplementary Data . Bio biotin. Figure 1B was created with BioRender.com released under a Creative Commons Attribution-NonCommerical-NoDerivs 4.0 International license. C The experimental procedure for SNP-seq; NE nuclear extract, Bio biotin. D Spearman’s correlation with a two-tailed test of SNP-seq allele counts normalized to control between PBMC and BL2 samples (ρ = 0.89, P < 1 \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\times$$\end{document} × 10 −15 ). E We selected 248 SNPs that passed next-generation sequencing quality control (NGS-QC) and demonstrated progressive allele-specific protection (Suppl. Fig. 1C). Source data are provided as a Source Data file.

Article Snippet: Human B cell line BL2 was from DSMZ (catalog number ACC 625) and human B cell line Daudi was kindly provided by Dr. Baglaenko Yuriy.

Techniques: Functional Assay, Construct, Sequencing, Binding Assay, Amplification, Two Tailed Test, Control, Next-Generation Sequencing

Journal: Nature Communications

Article Title: High-throughput identification of functional regulatory SNPs in systemic lupus erythematosus

doi: 10.1038/s41467-024-50710-5

Figure Lengend Snippet: A Seven biallelic and two triallelic (rs2297550 and rs936394) SNPs showed consistent allele-imbalanced binding for nuclear by EMSA. Allele-specific gel shift/binding marked with red circles. Experiments were repeated three times using distinct nuclear extracts. Representative blots from PBMCs are shown here; BL2 data and negative SNPs are provided in Supplementary Fig. and Supplementary Data . B Luciferase reporter assay between the reference (red) and alternative (blue) alleles of nine candidate regulatory SNPs from A in Daudi B cells (mean \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\pm$$\end{document} ± s.d, n = 8 biological replicates, Mann–Whitney two-tailed U -test with two-stage step-up correction for multiple hypothesis testing: rs2297550 p = 0.00047, rs906868 p = 0.0013, rs936394 p = 0.00047, rs9907966 p = 0.0071, rs13213604 p = 0.0085). C Diagram displaying the position of 5 SNPs that showed consistent significant differences between alleles through EMSA and luciferase reporter assay; rs2297550 in promoter of IKBKE , rs906868 in intergenic region between YPEL5 and LBH , rs936394 in intron of WBP2 , rs9907966 in intron of IKZF3 , rs13213604 in intron of BLTP3A . The unit of chromosome position is in kilobases (Kb). A diagram of gene features including exon, intron, and UTR was generated using GSDS 2.0 ( http://gsds.gao-lab.org/index.php ). Source data are provided as a Source Data file.

Article Snippet: Human B cell line BL2 was from DSMZ (catalog number ACC 625) and human B cell line Daudi was kindly provided by Dr. Baglaenko Yuriy.

Techniques: Binding Assay, Gel Shift, Luciferase, Reporter Assay, MANN-WHITNEY, Two Tailed Test, Generated

Journal: Scientific reports

Article Title: Circular ZDHHC11 supports Burkitt lymphoma growth independent of its miR-150 binding capacity.

doi: 10.1038/s41598-024-59443-3

Figure Lengend Snippet: Figure 2. CircZDHHC11 knockdown inhibits Burkitt lymphoma cell growth. ST486, DG75, CA46 and BL41 cells were transfected with lentivirus carrying shRNAs targeting circZDHHC11 or control vectors (NT1: black, NT2: grey, sh1: light red, sh2: dark red). Relative cell growth was assessed by following the percentage of GFP+ cells over three weeks post-transfection (n = 3), with the GFP percentage normalized to day 4 after transfection. Mean ± SD of three independent experiments is shown. Significance was determined by mixed model analysis; *p < 0.05, ***p < 0.001, ****p < 0.0001.

Article Snippet: Burkitt lymphoma cell lines ST486, BL41, CA46 and DG75 and the HEK293T cell line were purchased from ATCC and DSMZ.

Techniques: Knockdown, Transfection, Control

Journal: Biomedicines

Article Title: Reversal of Myofibroblast Apoptosis Resistance and Collagen Deposition by Phaseoloidin-Induced Autophagy Attenuates Pulmonary Fibrosis

doi: 10.3390/biomedicines13112679

Figure Lengend Snippet: PTPN13 mediated by phaseoloidin links autophagy and apoptosis. ( A ) Western blot analysis of PTPN13 levels in FasL and different dose phaseoloidin co-treated myofibroblasts ( left ) and quantification of the PTPN13 band intensity ( right ). ( B ) Western blotting reflects the CO-IP assay of PTPN13 binding to p62 under co-treatment with FasL and phaseoloidin or CQ. ( C ) Western blot analysis of PTPN13 levels in FasL and 100 μM phaseoloidin co-treated primary mouse myofibroblasts in the presence or absence of CQ ( top ) and quantification of the PTPN13 band intensity ( bottom ). ( D ) Flow cytometry was used to detect the percentage of apoptosis in the above experimental groups. ( E ) Flow cytometry was used to detect the percentage of apoptosis in groups with or without vector-PTPN13. Data in this figure represent the means ± S.D. (* p < 0.05, ** p < 0.01, **** p < 0.0001).

Article Snippet: A total of 10% of the proteins electrophoresed on sodium dodecyl sulfate-polyacrylamide gel electrophoresis gels were transferred to PVDF membranes (Bio-Rad) and 5% ( w / v ) skim milk with TBS buffer containing 0.1% ( v / v ) Tween 20 (TBST) TBS buffer for blocking. β-ACTIN monoclonal antibody (1:5000, Proteintech, Wuhan, China), α-SMA monoclonal antibody (1:1000, CST, USA), Caspase3 polyclonal antibody (1:1000, Proteintech, China), collagen I polyclonal antibody (1:1000, Millipore, USA), Bcl-2 polyclonal antibody (1:1000, Proteintech, China), BAX polyclonal antibody (1:1000, Proteintech, China), PTPN13 polyclonal antibody (1:1000, RD, Minneapolis, MN, USA), p70S6K polyclonal antibody (1:1000, CST, USA), elf-4B polyclonal antibody (1:500, ABclonal, Wuhan, China), mTOR monoclonal antibody (1:1000, CST, USA), Pho-mTOR monoclonal antibody (1:1000, CST, USA), AMPK monoclonal antibody (1:1000, CST, USA) and Pho-AMPK monoclonal antibody (1:1000, CST, USA) were incubated overnight at 4 °C.

Techniques: Western Blot, Co-Immunoprecipitation Assay, Binding Assay, Flow Cytometry, Plasmid Preparation