Journal: Genome biology

Article Title: Acute expression of human APOBEC3B in mice results in RNA editing and lethality.

doi: 10.1186/s13059-023-03115-4

Figure Lengend Snippet: Fig. 3 Local preference of APOBEC3B-driven RNA editing. A Schematic of the pipeline used to call RNA-editing sites in the A3B livers and pancreas. We used Mutect2 to identify DNA mutations and RNA edits. We pooled the WES and RNA-seq of the two control animals (no dox), and used them as a reference to identify variants of the A3B expressing tissues. This step was performed separately for DNA and RNA sequences, leading to the identification of DNA variants or RNA variants that were detected in at least one A3B expressing tissues but not in any of the other two control tissues. After that, we compared the RNA variants with the DNA variants from each sample to identify the RNA edits that are not DNA SNPs. B Trinucleotide mutation profiles for all base substitutions in the RNA from liver and pancreatic tissues of A3B mice (n = 6 in each group). Relative contribution refers to the contribution that each single base substitution has to the overall base substitution spectrum in A3B mice. C-D Lollipop plots indicating the percentage of mice showing C-to-U editing after experimental validation by RT-PCR in selected targets (n = 6 tissues in each group). E–F Heatmap plot showing the editing ratios of each sanger sequence validated position in each individual sample (liver shown in E and pancreas in F)

Article Snippet: Primary antibodies used were anti-pH3 Ser10 (1:200, Cell Signalling, 9701), cleaved caspase 3 (1:200, Cell Signalling, 9661), γH2AX (1:200, Bethyl Labs 00059), APOBEC3B (5210–87-13 mAb, 1:200) [63], tGFP (1:200 Origene, TA150041), Ki67 (Medac 275R-18).

Techniques: RNA Sequencing, Control, Expressing, Mutagenesis, Biomarker Discovery, Reverse Transcription Polymerase Chain Reaction, Sequencing

Journal: Translational oncology

Article Title: MiR-138-5p inhibits prostate cancer cell proliferation and chemoresistance by targeting APOBEC3B.

doi: 10.1016/j.tranon.2023.101723

Figure Lengend Snippet: Fig. 1. Differential expression and prognostic analysis of APOBEC3B. A. The mRNA expression of APOBEC3B in different tumour tissues and adjacent normal tissues based on the TCGA database. B. APOBEC3B expression in 52 pairs of PCa tissues and adjacent normal tissues in the TCGA database. C. APOBEC3B expression with Gleason Score in PCa patients based on TCGA database. D. PCa patients’ DFS for individuals in the TCGA database was assessed in terms of quartile via the Kaplan-Meier method (Log-rank test) using GEPIA2. E. APOBEC3B expression in docetaxel-resistant PCa cells (DU145/DR and PC-3/DR) and corresponding parental sensitive cells (DU145 and PC-3) measured by qRT-PCR and Western blot. U6 was used as a normalization reference at the mRNA level, and GAPDH was used as a loading control at the protein level. *, P<0.05; **, P<0.01; ***, P<0.001; ****, P<0.0001.

Article Snippet: The membranes were blocked for 2 h at room temperature in media supplemented with 5% skim milk, followed by overnight incubation with primary antibodies of APOBEC3B (1/1000, Novus, Colorado, USA) and GAPDH (1/ 10,000, Abcam, Cambridge, UK) at 4°C.

Techniques: Quantitative Proteomics, Expressing, Quantitative RT-PCR, Western Blot, Control

Journal: Translational oncology

Article Title: MiR-138-5p inhibits prostate cancer cell proliferation and chemoresistance by targeting APOBEC3B.

doi: 10.1016/j.tranon.2023.101723

Figure Lengend Snippet: Fig. 2. Silencing of APOBEC3B inhibited PCa cell proliferation and chemoresistance. A. The APOBEC3B expression in docetaxel-resistant cells DU145/DR and PC-3/DR transfected with siNC or siAPOBEC3B for 48 h was determined by qRT-PCR and Western blot. Expression of APOBEC3B at the mRNA level was normalized by U6. GAPDH was used as a loading control at the protein level. B. Cell viability of DU145/DR and PC-3/DR cells transfected with siNC or siAPOBEC3B determined by CCK-8 assay. C. Colony formation assay of DU145/DR and PC-3/DR cells transfected with siNC or siAPOBEC3B. D. Chemosensitivity analysis of DU145/DR and PC-3/DR cells to docetaxel after APOBEC3B knockdown. Docetaxel-resistant cells (DU145/DR and PC-3/DR) transfected with siRNA for 24 h in 6-well plates were digested and then seeded into 96-well plates, respectively. Adherent cells were treated with docetaxel diluted in a gradient for another 48 h before performing CCK-8 analysis. Then, calculate the IC50 of siAPOBEC group and siNC group. The IC50s of DU145/DR: siNC, 62.17; siAPOBEC3B#2, 32.87; siAPOBEC3B#3, 28.60; The IC50s of PC-3/DR: siNC, 37.14; siAPOBEC3B#2, 18.50; siAPOBEC3B#3: 17.43. *, P<0.05; **, P<0.01; ***, P<0.001, ****, P<0.0001.

Article Snippet: The membranes were blocked for 2 h at room temperature in media supplemented with 5% skim milk, followed by overnight incubation with primary antibodies of APOBEC3B (1/1000, Novus, Colorado, USA) and GAPDH (1/ 10,000, Abcam, Cambridge, UK) at 4°C.

Techniques: Expressing, Transfection, Quantitative RT-PCR, Western Blot, Control, CCK-8 Assay, Colony Assay, Knockdown

Journal: Translational oncology

Article Title: MiR-138-5p inhibits prostate cancer cell proliferation and chemoresistance by targeting APOBEC3B.

doi: 10.1016/j.tranon.2023.101723

Figure Lengend Snippet: Fig. 3. miR-138–5p directly targeted APOBEC3B. A. The upstream target genes of APOBEC3B were predicted and screened by the database. B. The expression level of miR-138–5p in docetaxel-sensitive cells (DU145 and PC-3) and docetaxel-resistant cells (DU145/DR And PC-3/DR) was evaluated by qRT-PCR. C. The expression efficiency of miR-138–5p in docetaxel-resistant PCa cells transfected with mimics or inhibitors detected by qRT-PCR. d-E. Effect of miR-138–5p mimics and inhibitor on APOBEC3B expression in docetaxel-resistant PCa cells by qRT-PCR (D) and Western blot (E). U6 was used as the internal reference for miR-138–5p and APOBEC3B at the mRNA level. GAPDH was used as the loading control at the protein level. F. Schematic depiction of the interaction between miR-138–5p and APOBEC3B mRNA 3′-UTR. G. The wild-type and mutant-type plasmids of APOBEC3B mRNA 3′-UTR were constructed on the putative binding sites of miR-138–5p and APOBEC3B mRNA. H. Dual luciferase activity assay confirmed that miR-138–5p mimics negatively regulates APOBEC3B expression by binding to wild-type APOBEC3B mRNA 3′-UTR instead of mutant-type. I. Dual luciferase activity assay confirmed that miR-138–5p inhibitor upregulated APOBEC3B expression by binding wild-type APOBEC3B mRNA 3′-UTR instead of mutant-type. ns, no sig nificance; *, P<0.05; **, P<0.01; ***, P<0.001; ****, P<0.0001.

Article Snippet: The membranes were blocked for 2 h at room temperature in media supplemented with 5% skim milk, followed by overnight incubation with primary antibodies of APOBEC3B (1/1000, Novus, Colorado, USA) and GAPDH (1/ 10,000, Abcam, Cambridge, UK) at 4°C.

Techniques: Expressing, Quantitative RT-PCR, Transfection, Western Blot, Control, Mutagenesis, Construct, Binding Assay, Luciferase, Activity Assay

Journal: Translational oncology

Article Title: MiR-138-5p inhibits prostate cancer cell proliferation and chemoresistance by targeting APOBEC3B.

doi: 10.1016/j.tranon.2023.101723

Figure Lengend Snippet: Fig. 5. APOBEC3B overexpression blocked the function of miR-138–5p on cell proliferation and docetaxel resistance. A. The overexpression efficiency of miR-138–5p in docetaxel-resistant PCa cells transfected with mimics detected by qRT-PCR. B. APOBEC3B overexpression level of docetaxel-resistant PCa cells transfected with miR-138–5p and APOBEC3B overexpression plasmid determined by Western blot. C. Cell viability of docetaxel-resistant PCa cells transfected with miR-138–5p and APOBEC3B overexpression plasmid determined by CCK-8 assay. D. Colony formation assay of docetaxel-resistant PCa cells transfected with miR-138–5p and APOBEC3B overexpression plasmid. E. The chemosensitivity of docetaxel-resistant PCa cells transfected with miR-138–5p and APOBEC3B overexpression plasmid to docetaxel was determined by CCK-8 assay. After docetaxel-resistant PCa cells were transfected with mimic NC plus OE-NC (control vector), miR-138–5p mimics plus OE-NC, mimic NC plus APOBEC3B-OE, or miR-138–5p mimics plus APOBEC3B-OE (mimic NC plus OE-NC vs miR- 138–5p mimics plus OE-NC, and miR-138–5p mimics plus OE-NC vs miR-138–5p mimics plus APOBEC3B-OE-NC, respectively), CCK-8 viability assay was performed at 0, 24, 48, 72 and 96 h (B) and chemosensitivity was measured after incubation with docetaxel diluted in a gradient for another 48 h (E). The IC50s of DU145/DR: mimic NC + OE-NC, 63.77; miR-138–5p mimics + OE-NC, 31.20; miR-138–5p mimics + APOBEC3B-OE, 50.17. The IC50s of PC-3/DR: mimic NC + OE-NC, 38.43; miR-138–5p mimics + OE-NC, 18.74; miR-138–5p mimics + APOBEC3B-OE, 29.80. ns, no significance; *, P<0.05; **, P<0.01; ***, P<0.001; ****, P<0.0001, mimic NC plus OE-NC transfection group vs miR-138–5p mimics plus OE-NC transfection group. #, P<0.05; ###, P<0.001, miR-138–5p mimics plus OE-NC transfection group vs miR-138–5p mimics plus APOBEC3B-OE transfection group.

Article Snippet: The membranes were blocked for 2 h at room temperature in media supplemented with 5% skim milk, followed by overnight incubation with primary antibodies of APOBEC3B (1/1000, Novus, Colorado, USA) and GAPDH (1/ 10,000, Abcam, Cambridge, UK) at 4°C.

Techniques: Over Expression, Transfection, Quantitative RT-PCR, Plasmid Preparation, Western Blot, CCK-8 Assay, Colony Assay, Control, Viability Assay, Incubation

Journal: Journal of molecular biology

Article Title: Characterization of the Catalytic Domain of Human APOBEC3B and the Critical Structural Role for a Conserved Methionine.

doi: 10.1016/j.jmb.2015.08.006

Figure Lengend Snippet: Fig. 1. Structure and activity of APOBEC3B constructs. (A) Align- ment between parts of A3G and A3B sequences is shown. The sec- ondary structural elements within A3G [21] are shown as boxes above the sequences. The amino-terminal ends of 193-CTD, 195-CTD and 187-CTD are indicated by arrows. (B) Results of KanR reversion assay for 195-CTDintheabsenceofIPTG in the host BH214. The horizontal lines within the data points represent the median values. (C) KanR revertants due to 195-CTD following induction of its transcription using 50 μM or 100 μM IPTG. ** represents P value of b0.01. (D) The results of KanR

Article Snippet: The full length of APOBEC3B was amplified from the human APOBEC3B cDNA purchased from OriGene Technologies (Rockville, MD) and cloned into vector plasmid pSU24 as HindIII-KpnI fragments.

Techniques: Activity Assay, Construct

Journal: Journal of molecular biology

Article Title: Characterization of the Catalytic Domain of Human APOBEC3B and the Critical Structural Role for a Conserved Methionine.

doi: 10.1016/j.jmb.2015.08.006

Figure Lengend Snippet: Fig. 2. KanR reversion and RifR mutation assay for APOBEC3B mutants. (A) Effect of D194A mutation on KanR

Article Snippet: The full length of APOBEC3B was amplified from the human APOBEC3B cDNA purchased from OriGene Technologies (Rockville, MD) and cloned into vector plasmid pSU24 as HindIII-KpnI fragments.

Techniques: Mutagenesis

Journal: Journal of molecular biology

Article Title: Characterization of the Catalytic Domain of Human APOBEC3B and the Critical Structural Role for a Conserved Methionine.

doi: 10.1016/j.jmb.2015.08.006

Figure Lengend Snippet: Fig. 4. Preliminary characterization of purified APOBEC3B 193-CTD. (A) Stability of 193-CTD during reaction incubations. The ability of 193-CTD protein to convert cytosine into uracil is quantified following pre-incubations for different lengths of time. (B) Ability of 193-CTD to turn over. The amount of product generated by the enzyme is shown under two different ratios of substrate to enzyme.

Article Snippet: The full length of APOBEC3B was amplified from the human APOBEC3B cDNA purchased from OriGene Technologies (Rockville, MD) and cloned into vector plasmid pSU24 as HindIII-KpnI fragments.

Techniques: Purification, Generated

Journal: Journal of molecular biology

Article Title: Characterization of the Catalytic Domain of Human APOBEC3B and the Critical Structural Role for a Conserved Methionine.

doi: 10.1016/j.jmb.2015.08.006

Figure Lengend Snippet: Fig. 5. Inability of APOBEC3B NTD to deaminate cytosines. (A) KanR reversion assay for A3B NTD. The revertant frequencies due to the NTD are compared to full-length A3B and the empty vector. (B) Lack of cytosine deamination activity for partially purified NTD. The TCGA-40 substrate (2 pmol) was incubated with different amounts of the NTD alone (lanes 4, 6 and 8, respectively) or together with 10 pmol of 193-CTD (lanes 5, 7 and 9).

Article Snippet: The full length of APOBEC3B was amplified from the human APOBEC3B cDNA purchased from OriGene Technologies (Rockville, MD) and cloned into vector plasmid pSU24 as HindIII-KpnI fragments.

Techniques: Plasmid Preparation, Activity Assay, Purification, Incubation

Journal: Journal of molecular biology

Article Title: Characterization of the Catalytic Domain of Human APOBEC3B and the Critical Structural Role for a Conserved Methionine.

doi: 10.1016/j.jmb.2015.08.006

Figure Lengend Snippet: Fig. 6. Ability of APOBEC3B to deaminate 5mCs. (A) Comparison of KanR revertant frequencies due to conversion of 5mC into T. The abilities of 193-CTD, 187-CTD and full-length A3B to deaminate 5mC are compared with empty vector and A3A. ** represents P value of b0.01 and *** represents P value of b0.001. (B) Comparison of kinetics of cytosine and 5mC deamination by 193-CTD. DNA oligomers containing a single C or 5mC in the indicated sequence context were treated with increasing concentrations of purified 193-CTD and the products were quantified. (C) Kinetics of cytosine and 5mC deamination by partially purified A3A.

Article Snippet: The full length of APOBEC3B was amplified from the human APOBEC3B cDNA purchased from OriGene Technologies (Rockville, MD) and cloned into vector plasmid pSU24 as HindIII-KpnI fragments.

Techniques: Comparison, Plasmid Preparation, Sequencing, Purification

Journal: Journal of molecular biology

Article Title: Characterization of the Catalytic Domain of Human APOBEC3B and the Critical Structural Role for a Conserved Methionine.

doi: 10.1016/j.jmb.2015.08.006

Figure Lengend Snippet: Fig. 7. Sequence alignment of APOBEC3B CTD and APOBEC3 proteins with known structures. Clustal Omega alignment of APOBEC3 single-domain proteins (A3A and A3C) and CTD of two-domain proteins (A3F and A3G) with A3B CTD are shown. The structural motifs are shown according the structure of A3G CTD [21]. The conserved methionine at the junction of NTD and CTD is marked with a green arrow. All the conserved residues between the five proteins are shown in blue and marked by asterisks. The residues that line the hydrophobic pocket in which the conserved methionine resides are shown in red and are marked with a dot.

Article Snippet: The full length of APOBEC3B was amplified from the human APOBEC3B cDNA purchased from OriGene Technologies (Rockville, MD) and cloned into vector plasmid pSU24 as HindIII-KpnI fragments.

Techniques: Sequencing

Journal: iScience

Article Title: Exploring ABOBEC3A and APOBEC3B substrate specificity and their role in HPV positive head and neck cancer

doi: 10.1016/j.isci.2022.105077

Figure Lengend Snippet: Preclinical and clinical trial specimens showing 5-AzaC upregulates A3B in HPV+ HNSCC (A) A3B is upregulated in HPV+, but not in HPV− head and neck cancer cells after 5-AzaC treatment. Relative to GPDH mRNA, levels of A3B in cells after 5-AzaC treatment. (B) A3B protein levels in HPV+ UMSCC47 and UMSCC47 A3B CRISPR cells (UMSCC47 A3B-7) after 5-AzaC treatment, GPDH shown as loading control. (C) Relative mRNA levels of A3B in tumors before and after 5 or 7 days of 5-AzaC treatment from HNSCC patients enrolled in a window clinical trial. 1–5 represent tumors from five different HPV HNSCC patients; “post” indicates a tumor sample after 5-AzaC treatment. (D) Clonogenic survival after 5-AzaC treatment of HPV+ UMSCC47 and APOBEC3B CRISPR (A3B-7) cells. Data are represented as mean ± SD.

Article Snippet: For UMSCC47 cells, co-transfection of A3B CRISPR/Cas KO (Santa Cruz # sc-401700) and A3B HDR (Santa Cruz # sc-401700-HDR) plasmids were used per manufacture’s protocol to establish A3B knockout UMSCC47 cells.

Techniques: CRISPR, Control

Journal: iScience

Article Title: Exploring ABOBEC3A and APOBEC3B substrate specificity and their role in HPV positive head and neck cancer

doi: 10.1016/j.isci.2022.105077

Figure Lengend Snippet: Effect of Oligonucleotide Length on A3B-FL, A3A, and A3B-CTD Cytosine Deaminase Activity (A)Time course single-turnover kinetics of A3B-FL, A3A, and A3B-CTD against ssDNA substrates of varying lengths: 10mer, 25mer, 43mer, and 70mer. (B) Graphical comparison of the deamination rates of the substrates for A3B-FL, A3A, and A3B-CTD. Data are represented as mean ± SD.

Article Snippet: For UMSCC47 cells, co-transfection of A3B CRISPR/Cas KO (Santa Cruz # sc-401700) and A3B HDR (Santa Cruz # sc-401700-HDR) plasmids were used per manufacture’s protocol to establish A3B knockout UMSCC47 cells.

Techniques: Activity Assay, Comparison

Journal: iScience

Article Title: Exploring ABOBEC3A and APOBEC3B substrate specificity and their role in HPV positive head and neck cancer

doi: 10.1016/j.isci.2022.105077

Figure Lengend Snippet: Deamination rates of A3B-FL, A3A and A3B-CTD on substrates of varying lengths

Article Snippet: For UMSCC47 cells, co-transfection of A3B CRISPR/Cas KO (Santa Cruz # sc-401700) and A3B HDR (Santa Cruz # sc-401700-HDR) plasmids were used per manufacture’s protocol to establish A3B knockout UMSCC47 cells.

Techniques:

Journal: iScience

Article Title: Exploring ABOBEC3A and APOBEC3B substrate specificity and their role in HPV positive head and neck cancer

doi: 10.1016/j.isci.2022.105077

Figure Lengend Snippet: Effect of ssDNA Primary Sequence on A3B-FL Cytidine Deaminase Activity (A) Effect of the identity of the nucleotide in the −2 position on the rate of A3B cytidine deaminase activity. (B) Effect of the identity of the nucleotide in the −1 position on the rate of A3B cytidine deaminase activity. Constructs with a pyrimidine in the −1 position are deaminated more completely than those with a purine in the −1 position. Constructs with a thymine in the −1 position undergo complete product formation. (C) Effect of the identity of the nucleotide in the +1 position on the rate of A3B deaminase activity. (D) Effect of the identity of the nucleotide in the +2 position on the rate of A3B deaminase activity. Data are represented as mean ± SD.

Article Snippet: For UMSCC47 cells, co-transfection of A3B CRISPR/Cas KO (Santa Cruz # sc-401700) and A3B HDR (Santa Cruz # sc-401700-HDR) plasmids were used per manufacture’s protocol to establish A3B knockout UMSCC47 cells.

Techniques: Sequencing, Activity Assay, Construct

Journal: iScience

Article Title: Exploring ABOBEC3A and APOBEC3B substrate specificity and their role in HPV positive head and neck cancer

doi: 10.1016/j.isci.2022.105077

Figure Lengend Snippet: Deamination rates of A3B on substrates varying the identity of the nucleotide in the −2, −1, +1, and +2 positions

Article Snippet: For UMSCC47 cells, co-transfection of A3B CRISPR/Cas KO (Santa Cruz # sc-401700) and A3B HDR (Santa Cruz # sc-401700-HDR) plasmids were used per manufacture’s protocol to establish A3B knockout UMSCC47 cells.

Techniques:

Journal: iScience

Article Title: Exploring ABOBEC3A and APOBEC3B substrate specificity and their role in HPV positive head and neck cancer

doi: 10.1016/j.isci.2022.105077

Figure Lengend Snippet: Effect of the identity of the nucleoside at the -2 position on A3A and A3B-CTD cytidine deaminase activity (A) Effect of the identity of the nucleotide in the −2 position on the rate of A3A cytidine deaminase activity. (B) Effect of the identity of the nucleotide in the −2 position on the rate of A3B-CTD cytidine deaminase activity. Data are represented as mean ± SD.

Article Snippet: For UMSCC47 cells, co-transfection of A3B CRISPR/Cas KO (Santa Cruz # sc-401700) and A3B HDR (Santa Cruz # sc-401700-HDR) plasmids were used per manufacture’s protocol to establish A3B knockout UMSCC47 cells.

Techniques: Activity Assay

Journal: iScience

Article Title: Exploring ABOBEC3A and APOBEC3B substrate specificity and their role in HPV positive head and neck cancer

doi: 10.1016/j.isci.2022.105077

Figure Lengend Snippet: Deamination rates of A3A and A3B-CTD on substrates varying the identity of the nucleotide in the −2 position

Article Snippet: For UMSCC47 cells, co-transfection of A3B CRISPR/Cas KO (Santa Cruz # sc-401700) and A3B HDR (Santa Cruz # sc-401700-HDR) plasmids were used per manufacture’s protocol to establish A3B knockout UMSCC47 cells.

Techniques:

Journal: iScience

Article Title: Exploring ABOBEC3A and APOBEC3B substrate specificity and their role in HPV positive head and neck cancer

doi: 10.1016/j.isci.2022.105077

Figure Lengend Snippet: Endogenous A3B from HNSCC cell lines confirms preference for purine at -2 position (A) Whole cell lysates from five out of six HNSCC cell lines prefer a guanine at −2 position over a thymine, except for SCC35 cell lysate, whose cytidine deaminase activity is undetectable. Nucleotides at −2 position and the cytidine that is deaminated are indicated by underscore. Red box designates substrate (S) and blue box product (P). (B) Western blot showing the expression level of A3B in all six HNSCC cell lines. A3B expression in SCC35 cells is below the detection limit, and HPV-positive cells (UMSCC47, UDSCC2, and YSCC94) have higher A3B expression compared to HPV-negative cells (SCC35, UNC521, and WSCC283). (C) Correlation of APOBEC3B expression with mutational profiles in HNSCC tumors. Tumors were classified by HPV status and substrate specificity for A3A and A3B. Xt[c]a > t/g polymorphisms were considered APOBEC related. Mutational signatures from individual tumors with >=50% A/Gt[c]a > t/g mutations were considered A3B like; and conversely tumors with >50% T/Ct[c]a > t/g designated A3A like, see also . Wilcoxon rank sum test. ns – not significant. ∗∗∗ p-value < 5∗10ˆ-3. TPM – transcripts per million. (D) Western blot showing A3B expression in A3B CRISPR and A3B siRNA clones. A3A expression is not significantly altered. C = siRNA control. (E) A3B knockout and knockdown decrease the cytidine deaminase activity to below the detection level with the DNA substrate having a guanine at −2 position. DNA substrates (S) and products (P) are indicated in red and blue boxes, respectively. C = siRNA control. (F) A3B knockout and knockdown also decrease the turnover of the DNA substrate with a thymine at −2 position to below the detection level. DNA substrates (S) and products (P) are indicated in red and blue boxes, respectively. C, siRNA control.

Article Snippet: For UMSCC47 cells, co-transfection of A3B CRISPR/Cas KO (Santa Cruz # sc-401700) and A3B HDR (Santa Cruz # sc-401700-HDR) plasmids were used per manufacture’s protocol to establish A3B knockout UMSCC47 cells.

Techniques: Activity Assay, Western Blot, Expressing, CRISPR, Clone Assay, Control, Knock-Out, Knockdown

Journal: iScience

Article Title: Exploring ABOBEC3A and APOBEC3B substrate specificity and their role in HPV positive head and neck cancer

doi: 10.1016/j.isci.2022.105077

Figure Lengend Snippet: Analysis of A3A and A3B mutational signatures in TCGA HNSCC Tumors were classified by HPV status and substrate specificity for A3A and A3B. Xt[c]a > t/g polymorphisms were considered APOBEC related. Mutational signatures from individual tumors with >=50% A/Gt[c]a > t/g mutations were considered A3B like; and conversely tumors with >50% T/Ct[c]a > t/g designated A3A like, see also . (A) APOBEC mutations per HNSCC tumor in the TCGA, stratified by HPV status and A3A vs. A3B mutational signature. Log10(n APOBEC mutations + 1) is plotted for clarity. Wilcoxon rank sum test. ∗∗∗ p-value < 5∗10ˆ-3. (B and C) Progression-free Survival of HPV-negative (B) and HPV-positive (C) HNSCC by APOBEC mutation profile. HPV+ HNSCC included oropharyngeal cancers in patients with up to 30 pack year tobacco smoke exposure, see .

Article Snippet: For UMSCC47 cells, co-transfection of A3B CRISPR/Cas KO (Santa Cruz # sc-401700) and A3B HDR (Santa Cruz # sc-401700-HDR) plasmids were used per manufacture’s protocol to establish A3B knockout UMSCC47 cells.

Techniques: Mutagenesis

Journal: iScience

Article Title: Exploring ABOBEC3A and APOBEC3B substrate specificity and their role in HPV positive head and neck cancer

doi: 10.1016/j.isci.2022.105077

Figure Lengend Snippet:

Article Snippet: For UMSCC47 cells, co-transfection of A3B CRISPR/Cas KO (Santa Cruz # sc-401700) and A3B HDR (Santa Cruz # sc-401700-HDR) plasmids were used per manufacture’s protocol to establish A3B knockout UMSCC47 cells.

Techniques: Virus, Recombinant, Modification, Sterility, Transfection, Protease Inhibitor, Fractionation, Cell Culture, RNA Extraction, Purification, cDNA Synthesis, SYBR Green Assay, Labeling, CRISPR, Plasmid Preparation, Software