Journal: British Journal of Cancer

Article Title: A human cancer-associated truncation of MBD4 causes dominant negative impairment of DNA repair in colon cancer cells

doi: 10.1038/sj.bjc.6603592

Figure Lengend Snippet: Dominant negative inhibition of glycosylase activities in cell-free glycosylase assays. ( A ) Oligo substrate BH:BHrev containing T.G mismatch, and FL-MBD4 competed with MBD4 tru . ( B ) Oligo substrate MM2:MM3revU containing U.G mismatch, and FL-MBD4 competed with MBD4 tru . ( C ) Oligo substrate BH:BHrevU containing U.G mismatch, and UDG competed with MBD4 tru . In each case, ‘+’ indicates presence and ‘−’ absence of protein, and the wedge indicates relative concentration of MBD4 tru in roughly two-fold increments from 1 to 10 ( A ) or from 1 to 20 ( B , C ). Vertical lines indicate where lanes have been juxtaposed owing to removal of an intervening, non-two-fold incremental lane.

Article Snippet: The role of MBD4 as a methyl-CpG-focused DNA mismatch glycosylase was subsequently supported by increases in mutation frequency at CpG sites in mouse models lacking Mbd4 ( Millar et al , 2002 ; Wong et al , 2002 ).

Techniques: Dominant Negative Mutation, Inhibition, Concentration Assay

Journal: Annals of Translational Medicine

Article Title: Circulating tumour DNA analysis for early detection of lung cancer: a systematic review

doi: 10.21037/atm-23-1572

Figure Lengend Snippet: Studies on the use of ctDNA analysis for early detection of lung cancer

Article Snippet: 36175411 , Stackpole et al. , 2022 ( ) , Pan-cancer , cfDNA methylation markers , 23,748 cancer-specific hypermethylation markers, 28,197 cancer-specific hypomethylation markers, 7,547 tissue-specific hypermethylation markers, 7,212 tissue-specific hypomethylation markers , Lung cancer (N=126), other cancers (N=150); stage I/II/III/IV =33/23/30/40, histological subtype (LUAD/LUSC) =77/49 , Non-cancer (healthy individuals and patients of various noncancer diseases (e.g., cirrhosis, pancreatitis, hepatitis, diabetes, etc.), N=203) , Integrating four marker types (all cancer types (n=217) vs. noncancer (n=191): sen./spec.=80.7%/97.9%, AUC =0.974.

Techniques: Biomarker Discovery, Concentration Assay, Amplification, Mutagenesis, Control, Clinical Proteomics, Methylation, DNA Methylation Assay, Computed Tomography, In Situ, Marker, Comparison, Diagnostic Assay, Genome Wide, RNA Expression

Journal: Cell Reports Medicine

Article Title: Haploinsufficiency of NFKBIA reshapes the epigenome antipodal to the IDH mutation and imparts disease fate in diffuse gliomas

doi: 10.1016/j.xcrm.2023.101082

Figure Lengend Snippet:

Article Snippet: For near-complete knockdown of NFKBIA , G418-resistant primary human astrocytes transduced to stably express wildtype IDH1 or mutant IDH1- ( R132H ) were transfected with Accell human NFKBIA small interfering (si)RNA or non-targeting control siRNA (Dharmacon), at 20nM concentration using lipofectamine 2000 reagent (Invitrogen) at 1:1 ratio for 48 h. For complete clustered regularly interspaced short palindromic repeats (CRISPR) knockout of NFKBIA , astrocytes were transfected with IκBα Double Nickase Plasmid (h) (sc-400034-NIC, Santa Cruz)—consisting of a pair of plasmids each encoding a D10A mutated Cas9 nuclease and a target-specific 20-nucleotide (nt) guide RNA (gRNA)—using plasmid transfection medium (sc-108062) and Ultra-Cruz transfection reagent (sc-395739) at 1:1.5 ratio and were incubated for 72 h. After incubation, cells were screened for GFP-positivity to select for successfully transfected cells.

Techniques: Plasmid Preparation, Recombinant, Transfection, Activation Assay, Methylation, Marker, DNA Methylation Assay, Sequencing, Empire Assay, Software

Journal: Cell reports

Article Title: Chromatin dysregulation associated with NSD1 mutation in head and neck squamous cell carcinoma

doi: 10.1016/j.celrep.2021.108769

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: Total RNA was extracted from cell pellets of approximatively 1 million cells, washed with PBS, spun down and preserved at −80, using the AllPrep DNA/RNA/miRNA Universal Kit (QIAGEN) according to the manufacturer’s instructions including DNase treatment option.

Techniques: Recombinant, CRISPR, Methylation, Purification, Software