apobec3b  (Cell Signaling Technology Inc)


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    Cell Signaling Technology Inc apobec3b
    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 <t>APOBEC3B</t> CRISPR (A3B-7) cells. Data are represented as mean ± SD.
    Apobec3b, supplied by Cell Signaling Technology Inc, used in various techniques. Bioz Stars score: 94/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/apobec3b/product/Cell Signaling Technology Inc
    Average 94 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    apobec3b - by Bioz Stars, 2023-01
    94/100 stars

    Images

    1) Product Images from "Exploring ABOBEC3A and APOBEC3B substrate specificity and their role in HPV positive head and neck cancer"

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

    Journal: iScience

    doi: 10.1016/j.isci.2022.105077

    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.
    Figure Legend 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.

    Techniques Used: CRISPR

    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.
    Figure Legend 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.

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


    Figure Legend Snippet:

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

    apobec3b  (Cell Signaling Technology Inc)


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    Cell Signaling Technology Inc apobec3b
    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 <t>APOBEC3B</t> CRISPR (A3B-7) cells. Data are represented as mean ± SD.
    Apobec3b, supplied by Cell Signaling Technology Inc, used in various techniques. Bioz Stars score: 94/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/apobec3b/product/Cell Signaling Technology Inc
    Average 94 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    apobec3b - by Bioz Stars, 2023-01
    94/100 stars

    Images

    1) Product Images from "Exploring ABOBEC3A and APOBEC3B substrate specificity and their role in HPV positive head and neck cancer"

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

    Journal: iScience

    doi: 10.1016/j.isci.2022.105077

    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.
    Figure Legend 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.

    Techniques Used: CRISPR

    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.
    Figure Legend 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.

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


    Figure Legend Snippet:

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

    rabbit monoclonal apobec3b antibody  (Cell Signaling Technology Inc)


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    Cell Signaling Technology Inc rabbit monoclonal apobec3b antibody
    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 <t>APOBEC3B</t> CRISPR (A3B-7) cells. Data are represented as mean ± SD.
    Rabbit Monoclonal Apobec3b Antibody, supplied by Cell Signaling Technology Inc, used in various techniques. Bioz Stars score: 94/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/rabbit monoclonal apobec3b antibody/product/Cell Signaling Technology Inc
    Average 94 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    rabbit monoclonal apobec3b antibody - by Bioz Stars, 2023-01
    94/100 stars

    Images

    1) Product Images from "Exploring ABOBEC3A and APOBEC3B substrate specificity and their role in HPV positive head and neck cancer"

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

    Journal: iScience

    doi: 10.1016/j.isci.2022.105077

    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.
    Figure Legend 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.

    Techniques Used: CRISPR

    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.
    Figure Legend 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.

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


    Figure Legend Snippet:

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

    apobec3b  (Cell Signaling Technology Inc)


    Bioz Verified Symbol Cell Signaling Technology Inc is a verified supplier
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    Cell Signaling Technology Inc apobec3b
    a, Tumourigenesis in E and EA3B mice was induced using the indicated viral titer (2.5×10 7 viral particles/mouse). Tumour growth was assessed by microCT analysis. b, Total tumour volume per mouse at 3 months post-induction quantified by microCT analysis ( E = 15, EA3B = 24, mean with SD, two-sided Mann-Whitney Test, P = 0.0163, each dot represents a mouse). c , Total tumour number per mouse at 3 months post-induction quantified by microCT analysis ( E = 15, EA3B = 24, mean with SD, two-sided Mann-Whitney Test, P = 0.0236, each dot represents a mouse). d, Quantification of EGFR L858R -positive cells per lung area (mm 2 ) by immunohistochemical (IHC) staining at 3 months post-induction ( E = 9, EA3B = 10, mean with SD, two-sided Mann-Whitney Test, P =0.0435, each dot represents a mouse). e, Quantification of caspase-3-positive cells per mm 2 of tumour at 3 months post-induction ( E = 9, EA3B = 10, mean with SD, two-sided Mann-Whitney Test, P<0.0001, each dot represents a tumour). f, Representative IHC stainings of EGFR L858R , <t>APOBEC3B,</t> and caspase-3 (scale bar = 20 µm, arrow indicates positive cell). g , Percent chromosome missegregation errors at 3 months post-induction (two-sided Fisher’s exact test, p = 0.016, E = 9, EA3B =10). h ,Quantification of p53 positive cells per lung area by IHC staining at 3 months post-induction ( E = 5, EA3B = 5, mean with SD, two-sided Mann-Whitney Test, p = 0.0159). i , Survival curve of E versus EA3B mice ( E =15, EA3B = 24, each dot represents a mouse). j , Quantification of p53 positive cells per lung area by IHC staining at late timepoint (termination) ( E = 8, EA3B = 8, mean with SD).
    Apobec3b, supplied by Cell Signaling Technology Inc, used in various techniques. Bioz Stars score: 94/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/apobec3b/product/Cell Signaling Technology Inc
    Average 94 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    apobec3b - by Bioz Stars, 2023-01
    94/100 stars

    Images

    1) Product Images from "The role of APOBEC3B in lung tumour evolution and targeted therapy resistance"

    Article Title: The role of APOBEC3B in lung tumour evolution and targeted therapy resistance

    Journal: bioRxiv

    doi: 10.1101/2020.12.18.423280

    a, Tumourigenesis in E and EA3B mice was induced using the indicated viral titer (2.5×10 7 viral particles/mouse). Tumour growth was assessed by microCT analysis. b, Total tumour volume per mouse at 3 months post-induction quantified by microCT analysis ( E = 15, EA3B = 24, mean with SD, two-sided Mann-Whitney Test, P = 0.0163, each dot represents a mouse). c , Total tumour number per mouse at 3 months post-induction quantified by microCT analysis ( E = 15, EA3B = 24, mean with SD, two-sided Mann-Whitney Test, P = 0.0236, each dot represents a mouse). d, Quantification of EGFR L858R -positive cells per lung area (mm 2 ) by immunohistochemical (IHC) staining at 3 months post-induction ( E = 9, EA3B = 10, mean with SD, two-sided Mann-Whitney Test, P =0.0435, each dot represents a mouse). e, Quantification of caspase-3-positive cells per mm 2 of tumour at 3 months post-induction ( E = 9, EA3B = 10, mean with SD, two-sided Mann-Whitney Test, P<0.0001, each dot represents a tumour). f, Representative IHC stainings of EGFR L858R , APOBEC3B, and caspase-3 (scale bar = 20 µm, arrow indicates positive cell). g , Percent chromosome missegregation errors at 3 months post-induction (two-sided Fisher’s exact test, p = 0.016, E = 9, EA3B =10). h ,Quantification of p53 positive cells per lung area by IHC staining at 3 months post-induction ( E = 5, EA3B = 5, mean with SD, two-sided Mann-Whitney Test, p = 0.0159). i , Survival curve of E versus EA3B mice ( E =15, EA3B = 24, each dot represents a mouse). j , Quantification of p53 positive cells per lung area by IHC staining at late timepoint (termination) ( E = 8, EA3B = 8, mean with SD).
    Figure Legend Snippet: a, Tumourigenesis in E and EA3B mice was induced using the indicated viral titer (2.5×10 7 viral particles/mouse). Tumour growth was assessed by microCT analysis. b, Total tumour volume per mouse at 3 months post-induction quantified by microCT analysis ( E = 15, EA3B = 24, mean with SD, two-sided Mann-Whitney Test, P = 0.0163, each dot represents a mouse). c , Total tumour number per mouse at 3 months post-induction quantified by microCT analysis ( E = 15, EA3B = 24, mean with SD, two-sided Mann-Whitney Test, P = 0.0236, each dot represents a mouse). d, Quantification of EGFR L858R -positive cells per lung area (mm 2 ) by immunohistochemical (IHC) staining at 3 months post-induction ( E = 9, EA3B = 10, mean with SD, two-sided Mann-Whitney Test, P =0.0435, each dot represents a mouse). e, Quantification of caspase-3-positive cells per mm 2 of tumour at 3 months post-induction ( E = 9, EA3B = 10, mean with SD, two-sided Mann-Whitney Test, P<0.0001, each dot represents a tumour). f, Representative IHC stainings of EGFR L858R , APOBEC3B, and caspase-3 (scale bar = 20 µm, arrow indicates positive cell). g , Percent chromosome missegregation errors at 3 months post-induction (two-sided Fisher’s exact test, p = 0.016, E = 9, EA3B =10). h ,Quantification of p53 positive cells per lung area by IHC staining at 3 months post-induction ( E = 5, EA3B = 5, mean with SD, two-sided Mann-Whitney Test, p = 0.0159). i , Survival curve of E versus EA3B mice ( E =15, EA3B = 24, each dot represents a mouse). j , Quantification of p53 positive cells per lung area by IHC staining at late timepoint (termination) ( E = 8, EA3B = 8, mean with SD).

    Techniques Used: MANN-WHITNEY, Immunohistochemical staining, Immunohistochemistry

    a, Two by two contingency table of the number of mice with visible tumours (VT) or no visible tumours (NVT) by microCT at 3 months post-induction (two-sided Fisher’s exact test, P<0.05). b , Representative images of p53 nuclear immunohistochemical staining. Scale bar = 10 µm, arrows indicates positive cells. c , Quantification of Ki67-positive cells per mm 2 of tumour at 3 months post-induction ( E = 9, EA3B = 10, each dot represents a tumour). d , Quantification of γH2AX-positive cells per mm 2 of tumour at 3 months post-induction ( E = 9, EA3B = 10, each dot represents a tumour). e , Quantification of CD4+ cells per mm 2 of tumour at 3 months post-induction (Mice E =8 EA3B = 7, each dot represents a tumour, mean with SD, two-sided Mann-Whitney Test, P = 0.0086). f , Quantification of CD8+ cells per mm 2 of tumour at 3 months post-induction (Mice E =8 EA3B = 8, each dot represents a tumour, mean with SD, two-sided Mann-Whitney Test, P = 0.0003). g , Representative IHC stainings of EGFR L858R , APOBEC3B, and CD4 and CD8 T cells (scale bar = 50 µm). h , Quantification of CD4+ cells per mm 2 of tumour at late timepoint (termination) (Mice E =8 EA3B = 7, each dot represents a tumour, mean with SD, two-sided Mann-Whitney Test, P < 0.0001). i, Quantification of CD8+ cells per mm 2 of tumour at late timepoint (termination)(Mice E =6 EA3B = 6, each dot represents a tumour, mean with SD).
    Figure Legend Snippet: a, Two by two contingency table of the number of mice with visible tumours (VT) or no visible tumours (NVT) by microCT at 3 months post-induction (two-sided Fisher’s exact test, P<0.05). b , Representative images of p53 nuclear immunohistochemical staining. Scale bar = 10 µm, arrows indicates positive cells. c , Quantification of Ki67-positive cells per mm 2 of tumour at 3 months post-induction ( E = 9, EA3B = 10, each dot represents a tumour). d , Quantification of γH2AX-positive cells per mm 2 of tumour at 3 months post-induction ( E = 9, EA3B = 10, each dot represents a tumour). e , Quantification of CD4+ cells per mm 2 of tumour at 3 months post-induction (Mice E =8 EA3B = 7, each dot represents a tumour, mean with SD, two-sided Mann-Whitney Test, P = 0.0086). f , Quantification of CD8+ cells per mm 2 of tumour at 3 months post-induction (Mice E =8 EA3B = 8, each dot represents a tumour, mean with SD, two-sided Mann-Whitney Test, P = 0.0003). g , Representative IHC stainings of EGFR L858R , APOBEC3B, and CD4 and CD8 T cells (scale bar = 50 µm). h , Quantification of CD4+ cells per mm 2 of tumour at late timepoint (termination) (Mice E =8 EA3B = 7, each dot represents a tumour, mean with SD, two-sided Mann-Whitney Test, P < 0.0001). i, Quantification of CD8+ cells per mm 2 of tumour at late timepoint (termination)(Mice E =6 EA3B = 6, each dot represents a tumour, mean with SD).

    Techniques Used: Immunohistochemical staining, Staining, MANN-WHITNEY

    a, Fraction of tumours positive for A3B at early and late timepoints measured by IHC staining (Early E = 3, EA3B = 3, Late E = 8, EA3B = 8). b , Representative IHC staining of EGFR L858R , and APOBEC3B. Scale bar = 50 µm. c , PCR analysis of recombination efficiency of LoxP-Stop-LoxP site upstream of human APOBEC3B transgene. Primer 1 (P1) in LoxP, Primer 2 (P2) in stop codon, Primer 3 (P3) in human APOBEC3B transgene. P1+P2 = LSL 500 bp, P1+P3 = 598 bp. EA3B tumours at a late timepoint (termination). LSL = unrecombined tail DNA, Loxp = fully recombined cell line DNA. Ratios represent fraction of unrecombined tail DNA to fully recombined cell line DNA.
    Figure Legend Snippet: a, Fraction of tumours positive for A3B at early and late timepoints measured by IHC staining (Early E = 3, EA3B = 3, Late E = 8, EA3B = 8). b , Representative IHC staining of EGFR L858R , and APOBEC3B. Scale bar = 50 µm. c , PCR analysis of recombination efficiency of LoxP-Stop-LoxP site upstream of human APOBEC3B transgene. Primer 1 (P1) in LoxP, Primer 2 (P2) in stop codon, Primer 3 (P3) in human APOBEC3B transgene. P1+P2 = LSL 500 bp, P1+P3 = 598 bp. EA3B tumours at a late timepoint (termination). LSL = unrecombined tail DNA, Loxp = fully recombined cell line DNA. Ratios represent fraction of unrecombined tail DNA to fully recombined cell line DNA.

    Techniques Used: Immunohistochemistry

    a , Experimental set up of induction of subclonal APOBEC3B using TetO-EGFR L858R ;CCSP-rtTA;R26 LSL-APOBEC3B/Cre-ER(T2) (EA3Bi) or TetO-EGFR L858R ;CCSP-rtTA;R26 Cre-ER(T2)/+ (CCSP_Ei) mice. b , Average A3B positive cells/mm 2 of tumour per mouse ( Ei = 9, CCSP_EA3Bi = 10, median = dashed line, 1st and 3rd quartiles = dotted lines, two sided Mann-Whitney Test, **P = 0.0041, each dot represents a mouse, dots below A3B neg line are A3B negative). c ,Tumour nodules per lung section per mouse at termination ( Ei =10, CCSP_EA3Bi = 10, median = dashed line, 1st and 3rd quartiles = dotted lines, two-sided Mann-Whitney Test, *P = 0.0494). d , Tumour area per lung area at termination ( Ei =10, EA3Bi = 10, median = dashed line, 1st and 3rd quartiles = dotted lines, two-sided Mann-Whitney Test, *P = 0.0216). e , EGFR L858R positive cells per lung area per mouse in Ei and EA3Bi mice at termination. f, Lung weight in Ei vs EA3Bi mice at termination Ei = 13, EA3Bi = 12, median = dashed line, 1st and 3rd quartiles = dotted lines, each dot represents a mouse). g, Survival curve of Ei versus EA3Bi mice ( Ei = 14, EA3Bi = 17, each dot represents a mouse, Log-rank (Mantel-Cox) test, *P = 0.0358).
    Figure Legend Snippet: a , Experimental set up of induction of subclonal APOBEC3B using TetO-EGFR L858R ;CCSP-rtTA;R26 LSL-APOBEC3B/Cre-ER(T2) (EA3Bi) or TetO-EGFR L858R ;CCSP-rtTA;R26 Cre-ER(T2)/+ (CCSP_Ei) mice. b , Average A3B positive cells/mm 2 of tumour per mouse ( Ei = 9, CCSP_EA3Bi = 10, median = dashed line, 1st and 3rd quartiles = dotted lines, two sided Mann-Whitney Test, **P = 0.0041, each dot represents a mouse, dots below A3B neg line are A3B negative). c ,Tumour nodules per lung section per mouse at termination ( Ei =10, CCSP_EA3Bi = 10, median = dashed line, 1st and 3rd quartiles = dotted lines, two-sided Mann-Whitney Test, *P = 0.0494). d , Tumour area per lung area at termination ( Ei =10, EA3Bi = 10, median = dashed line, 1st and 3rd quartiles = dotted lines, two-sided Mann-Whitney Test, *P = 0.0216). e , EGFR L858R positive cells per lung area per mouse in Ei and EA3Bi mice at termination. f, Lung weight in Ei vs EA3Bi mice at termination Ei = 13, EA3Bi = 12, median = dashed line, 1st and 3rd quartiles = dotted lines, each dot represents a mouse). g, Survival curve of Ei versus EA3Bi mice ( Ei = 14, EA3Bi = 17, each dot represents a mouse, Log-rank (Mantel-Cox) test, *P = 0.0358).

    Techniques Used: MANN-WHITNEY

    a, Experimental set up of A3B induction post-initiation of TKI therapy using TetO-EGFR L858R ;CCSP-rtTA;R26 LSL-APOBEC3B/Cre-ER(T2) (EA3Bi) mice. b, Fraction of tumour grade, divided into no tumours present (not present) or hyperplasia only and bronchioloalveolar adenoma or carcinoma, in Ei and EA3Bi mice at 5 months post-induction post-TKI treatment ( Ei = 19, EA3Bi = 19, two sided Fisher’s exact test, **P= 0.0044). c, Tumour nodules per lung section per mouse at 5 months post induction post-TKI treatment ( Ei =19, EA3Bi = 19,median = dashed line, 1st and 3rd quartiles = dotted lines, two-sided Mann-Whitney Test, *P =0.0443). d, Tumour area per lung area per mouse at 5 months post-induction post-TKI treatment ( Ei =19, EA3Bi = 19, median = dashed line, 1st and 3rd quartiles = dotted lines, two-sided Mann-Whitney Test, *P =0.0212). e, Representative immunohistochemical staining of EGFR L858R and A3B. Scale bar = 100 µm and 20 µm. f, A3B positive cells/mm 2 of tumour per mouse ( EA3Bi - TKI = 151, EA3Bi + TKI = 52, median = dashed line, 1st and 3rd quartiles = dotted lines, two sided Mann Whitney Test, **** P = <0.0001) g , Experimental set up of induction of subclonal APOBEC3B using TetO-EGFR L858R ;CCSP-rtTA;R26 LSL-APOBEC3B/Cre-ER(T2) (EA3Bi) or TetO-EGFR L858R ;CCSP-rtTA;R26 Cre-ER(T2)/+ (Ei) mice with continuous TKI therapy (erlotinib). h , Tumour nodules per lung section per mouse ( Ei = 13, EA3Bi = 17, median = dashed line, 1st and 3rd quartiles = dotted lines, two sided Mann Whitney Test, ** P = 0.0086). i , Fraction of tumour grade in Ei and EA3Bi mice ( E =13, EA3Bi = 17, NP = not present, H = hyperplasia, A =bronchioloalveolar adenoma, WDC = bronchioloalveolar carcinoma, well differentiated, Fisher’s exact test).
    Figure Legend Snippet: a, Experimental set up of A3B induction post-initiation of TKI therapy using TetO-EGFR L858R ;CCSP-rtTA;R26 LSL-APOBEC3B/Cre-ER(T2) (EA3Bi) mice. b, Fraction of tumour grade, divided into no tumours present (not present) or hyperplasia only and bronchioloalveolar adenoma or carcinoma, in Ei and EA3Bi mice at 5 months post-induction post-TKI treatment ( Ei = 19, EA3Bi = 19, two sided Fisher’s exact test, **P= 0.0044). c, Tumour nodules per lung section per mouse at 5 months post induction post-TKI treatment ( Ei =19, EA3Bi = 19,median = dashed line, 1st and 3rd quartiles = dotted lines, two-sided Mann-Whitney Test, *P =0.0443). d, Tumour area per lung area per mouse at 5 months post-induction post-TKI treatment ( Ei =19, EA3Bi = 19, median = dashed line, 1st and 3rd quartiles = dotted lines, two-sided Mann-Whitney Test, *P =0.0212). e, Representative immunohistochemical staining of EGFR L858R and A3B. Scale bar = 100 µm and 20 µm. f, A3B positive cells/mm 2 of tumour per mouse ( EA3Bi - TKI = 151, EA3Bi + TKI = 52, median = dashed line, 1st and 3rd quartiles = dotted lines, two sided Mann Whitney Test, **** P = <0.0001) g , Experimental set up of induction of subclonal APOBEC3B using TetO-EGFR L858R ;CCSP-rtTA;R26 LSL-APOBEC3B/Cre-ER(T2) (EA3Bi) or TetO-EGFR L858R ;CCSP-rtTA;R26 Cre-ER(T2)/+ (Ei) mice with continuous TKI therapy (erlotinib). h , Tumour nodules per lung section per mouse ( Ei = 13, EA3Bi = 17, median = dashed line, 1st and 3rd quartiles = dotted lines, two sided Mann Whitney Test, ** P = 0.0086). i , Fraction of tumour grade in Ei and EA3Bi mice ( E =13, EA3Bi = 17, NP = not present, H = hyperplasia, A =bronchioloalveolar adenoma, WDC = bronchioloalveolar carcinoma, well differentiated, Fisher’s exact test).

    Techniques Used: MANN-WHITNEY, Immunohistochemical staining, Staining

    a , Whole exome sequencing analysis of mutation burden and APOBEC-associated mutations (TCN, C>T/C>G) acquired during osimertinib treatment of A3B proficient or deficient PC9 cells (Knockout verified in Ext. Data. Fig18a, unpaired t-test, ***P < 0.0005). b, Whole genome sequencing analysis of mutation burden and APOBEC-associated mutations (TCN, C>T/C>G) acquired with DMSO or osimertinib treatment of A3B proficient or deficient PC9 cells (Knockout verified in , DMSO 1 month, osimertinib 2.5 months). c , Comparison of APOBEC3B expression levels (Exp: batch corrected TPM) measured using RNA-Seq analysis in human NSCLC specimens obtained before treatment (treatment naïve, TN), or on-treatment at residual disease (RD) or at progressive disease (PD) stages from lung cancer patients undergoing treatment with tyrosine kinase inhibitors (all data points shown; ANOVA test, mixed effects model, *P = 0.0318). d , Representative images of IHC analysis of A3B protein levels in patients with NSCLC at TN, RD and PD stages, red arrows indicate positive stained cells (scale bar: 30 µM). e , IHC quantification of human NSCLC samples obtained before treatment (Pre-TKI) or after treatment (Post-TKI) (all data points shown, unpaired t-test, *P = 0.0113, patients treated with single agent TKI). f, Quantification of total mutation burden (SNV count) in human NSCLC samples obtained before (Pre-TKI) or after (Post-TKI) treatment (Wilcoxon matched-pairs signed rank test, two tailed, ** P = 0.0023). g, Quantification of APOBEC-associated mutation count in human NSCLC samples obtained before treatment (Pre-TKI) or after treatment (Post-TKI) (Wilcoxon matched-pairs signed rank test, two tailed, ** P = 0.0152). h , Mutation signature associated with each putative de novo TKI resistance mutation detected in clinical patient samples analyzed post-TKI at progressive disease. *Denotes sample from patient having received prior chemotherapy.
    Figure Legend Snippet: a , Whole exome sequencing analysis of mutation burden and APOBEC-associated mutations (TCN, C>T/C>G) acquired during osimertinib treatment of A3B proficient or deficient PC9 cells (Knockout verified in Ext. Data. Fig18a, unpaired t-test, ***P < 0.0005). b, Whole genome sequencing analysis of mutation burden and APOBEC-associated mutations (TCN, C>T/C>G) acquired with DMSO or osimertinib treatment of A3B proficient or deficient PC9 cells (Knockout verified in , DMSO 1 month, osimertinib 2.5 months). c , Comparison of APOBEC3B expression levels (Exp: batch corrected TPM) measured using RNA-Seq analysis in human NSCLC specimens obtained before treatment (treatment naïve, TN), or on-treatment at residual disease (RD) or at progressive disease (PD) stages from lung cancer patients undergoing treatment with tyrosine kinase inhibitors (all data points shown; ANOVA test, mixed effects model, *P = 0.0318). d , Representative images of IHC analysis of A3B protein levels in patients with NSCLC at TN, RD and PD stages, red arrows indicate positive stained cells (scale bar: 30 µM). e , IHC quantification of human NSCLC samples obtained before treatment (Pre-TKI) or after treatment (Post-TKI) (all data points shown, unpaired t-test, *P = 0.0113, patients treated with single agent TKI). f, Quantification of total mutation burden (SNV count) in human NSCLC samples obtained before (Pre-TKI) or after (Post-TKI) treatment (Wilcoxon matched-pairs signed rank test, two tailed, ** P = 0.0023). g, Quantification of APOBEC-associated mutation count in human NSCLC samples obtained before treatment (Pre-TKI) or after treatment (Post-TKI) (Wilcoxon matched-pairs signed rank test, two tailed, ** P = 0.0152). h , Mutation signature associated with each putative de novo TKI resistance mutation detected in clinical patient samples analyzed post-TKI at progressive disease. *Denotes sample from patient having received prior chemotherapy.

    Techniques Used: Sequencing, Mutagenesis, Knock-Out, Expressing, RNA Sequencing Assay, Staining, Two Tailed Test

    a, Comparison of APOBEC3B expression levels (Exp: Batch corrected TPM) measured using RNA-Seq analysis in human NSCLC specimens obtained before treatment (TN), or on-treatment at residual disease (RD) or at progressive disease (PD) stages from lung cancer patients undergoing treatment with single agent tyrosine kinase inhibitors (TKI) or a combination of chemo- and TKI therapy (all data points shown).
    Figure Legend Snippet: a, Comparison of APOBEC3B expression levels (Exp: Batch corrected TPM) measured using RNA-Seq analysis in human NSCLC specimens obtained before treatment (TN), or on-treatment at residual disease (RD) or at progressive disease (PD) stages from lung cancer patients undergoing treatment with single agent tyrosine kinase inhibitors (TKI) or a combination of chemo- and TKI therapy (all data points shown).

    Techniques Used: Expressing, RNA Sequencing Assay

    a , At tumour initiation continous APOBEC3B expression induces, chromosomal instability and p53 pathway activation, resulting in cell death. b , With targeted therapy, APOBEC3B expression is induced in an NF-κB dependent manner, and UNG2 expression is lost driving genetic diversity and TKI resistance.
    Figure Legend Snippet: a , At tumour initiation continous APOBEC3B expression induces, chromosomal instability and p53 pathway activation, resulting in cell death. b , With targeted therapy, APOBEC3B expression is induced in an NF-κB dependent manner, and UNG2 expression is lost driving genetic diversity and TKI resistance.

    Techniques Used: Expressing, Activation Assay

    rabbit anti apobec3b  (Cell Signaling Technology Inc)


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    Cell Signaling Technology Inc rabbit anti apobec3b
    Expression of other genes with known roles in resistance to gemcitabine in GR cells compared with C cells
    Rabbit Anti Apobec3b, supplied by Cell Signaling Technology Inc, used in various techniques. Bioz Stars score: 94/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    1) Product Images from "Acquired chemoresistance can lead to increased resistance of pancreatic cancer cells to oncolytic vesicular stomatitis virus"

    Article Title: Acquired chemoresistance can lead to increased resistance of pancreatic cancer cells to oncolytic vesicular stomatitis virus

    Journal: Molecular Therapy Oncolytics

    doi: 10.1016/j.omto.2021.11.019

    Expression of other genes with known roles in resistance to gemcitabine in GR cells compared with C cells
    Figure Legend Snippet: Expression of other genes with known roles in resistance to gemcitabine in GR cells compared with C cells

    Techniques Used: Expressing

    rabbit anti apobec3b  (Cell Signaling Technology Inc)


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    Cell Signaling Technology Inc rabbit anti apobec3b
    Rabbit Anti Apobec3b, supplied by Cell Signaling Technology Inc, used in various techniques. Bioz Stars score: 94/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/rabbit anti apobec3b/product/Cell Signaling Technology Inc
    Average 94 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
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    rabbit anti apobec3b  (Cell Signaling Technology Inc)


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    Cell Signaling Technology Inc rabbit anti apobec3b
    Rabbit Anti Apobec3b, supplied by Cell Signaling Technology Inc, used in various techniques. Bioz Stars score: 94/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/rabbit anti apobec3b/product/Cell Signaling Technology Inc
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    rabbit anti apobec3b monoclonal antibody 5210 87 13  (Cell Signaling Technology Inc)


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    Cell Signaling Technology Inc rabbit anti apobec3b monoclonal antibody 5210 87 13
    APOBEC3 activity and replication stress in breast cancer cell lines. a <t>APOBEC3B</t> ( black ), APOBEC3G ( grey ) and APOBEC3A ( white ) mRNA expression in 15 breast cancer cell lines as determined by quantitative PCR. HER2+ cell lines ( red ), basal cell lines ( black ), luminal cell lines ( green ). SKBR3 cells have a null mutation for APOBEC3B . Error bars represent standard deviation. b APOBEC3 activity in the 15 breast cancer cell lines used in a . Cells were lysed and subjected to oligonucleotide-based cytidine deamination assay followed by electrophoresis on 15 % TBE-urea gels. c Cells were grown for two population doublings on glass coverslips followed by fixation and staining with 53BP1 and cyclin A antibodies. The fractions of cyclin A-negative cells displaying more than five 53BP1 nuclear foci were scored. APOBEC3B mRNA expression was determined by quantitative PCR from parallel cell lysates. A Spearman’s rank correlation test was performed to correlate the fraction of 53BP1 nuclear bodies in cell lines with the level of APOBEC3B (r = 0.62, p = 0.0284). Error bars represent standard deviation. d BT474 cells were treated with 12.5–300 μM nucleosides for 72 h prior to lysis. Western blots were probed with the indicated antibodies. e BT474 cells were treated as in d followed by lysis and an APOBEC3 cytidine deamination assay
    Rabbit Anti Apobec3b Monoclonal Antibody 5210 87 13, supplied by Cell Signaling Technology Inc, used in various techniques. Bioz Stars score: 94/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/rabbit anti apobec3b monoclonal antibody 5210 87 13/product/Cell Signaling Technology Inc
    Average 94 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    rabbit anti apobec3b monoclonal antibody 5210 87 13 - by Bioz Stars, 2023-01
    94/100 stars

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    1) Product Images from "DNA replication stress mediates APOBEC3 family mutagenesis in breast cancer"

    Article Title: DNA replication stress mediates APOBEC3 family mutagenesis in breast cancer

    Journal: Genome Biology

    doi: 10.1186/s13059-016-1042-9

    APOBEC3 activity and replication stress in breast cancer cell lines. a APOBEC3B ( black ), APOBEC3G ( grey ) and APOBEC3A ( white ) mRNA expression in 15 breast cancer cell lines as determined by quantitative PCR. HER2+ cell lines ( red ), basal cell lines ( black ), luminal cell lines ( green ). SKBR3 cells have a null mutation for APOBEC3B . Error bars represent standard deviation. b APOBEC3 activity in the 15 breast cancer cell lines used in a . Cells were lysed and subjected to oligonucleotide-based cytidine deamination assay followed by electrophoresis on 15 % TBE-urea gels. c Cells were grown for two population doublings on glass coverslips followed by fixation and staining with 53BP1 and cyclin A antibodies. The fractions of cyclin A-negative cells displaying more than five 53BP1 nuclear foci were scored. APOBEC3B mRNA expression was determined by quantitative PCR from parallel cell lysates. A Spearman’s rank correlation test was performed to correlate the fraction of 53BP1 nuclear bodies in cell lines with the level of APOBEC3B (r = 0.62, p = 0.0284). Error bars represent standard deviation. d BT474 cells were treated with 12.5–300 μM nucleosides for 72 h prior to lysis. Western blots were probed with the indicated antibodies. e BT474 cells were treated as in d followed by lysis and an APOBEC3 cytidine deamination assay
    Figure Legend Snippet: APOBEC3 activity and replication stress in breast cancer cell lines. a APOBEC3B ( black ), APOBEC3G ( grey ) and APOBEC3A ( white ) mRNA expression in 15 breast cancer cell lines as determined by quantitative PCR. HER2+ cell lines ( red ), basal cell lines ( black ), luminal cell lines ( green ). SKBR3 cells have a null mutation for APOBEC3B . Error bars represent standard deviation. b APOBEC3 activity in the 15 breast cancer cell lines used in a . Cells were lysed and subjected to oligonucleotide-based cytidine deamination assay followed by electrophoresis on 15 % TBE-urea gels. c Cells were grown for two population doublings on glass coverslips followed by fixation and staining with 53BP1 and cyclin A antibodies. The fractions of cyclin A-negative cells displaying more than five 53BP1 nuclear foci were scored. APOBEC3B mRNA expression was determined by quantitative PCR from parallel cell lysates. A Spearman’s rank correlation test was performed to correlate the fraction of 53BP1 nuclear bodies in cell lines with the level of APOBEC3B (r = 0.62, p = 0.0284). Error bars represent standard deviation. d BT474 cells were treated with 12.5–300 μM nucleosides for 72 h prior to lysis. Western blots were probed with the indicated antibodies. e BT474 cells were treated as in d followed by lysis and an APOBEC3 cytidine deamination assay

    Techniques Used: Activity Assay, Expressing, Real-time Polymerase Chain Reaction, Mutagenesis, Standard Deviation, Electrophoresis, Staining, Lysis, Western Blot

    Induction of replication stress and APOBEC3 activity in breast cancer cell lines. a MCF10A cells were treated with the indicated drugs for 48 h followed by mRNA extraction, cDNA synthesis and quantitative PCR for APOBEC3B and APOBEC3G expression levels. b MCF10A cells were treated as in a followed by western blotting with the indicated antibodies. c MCF10A cells were treated as in a prior to lysis and a cytidine deamination assay for APOBEC3 activity using probe 2. d MCF10A cells were treated as in a followed by fixation and immunofluorescence for Ser139 γH2AX and S4/8 replication protein A phosphorylation ( pRPA ). Red asterisks indicate treatments inducing APOBEC3B mRNA, protein expression, activity levels and S4/8 RPA phosphorylation. e MCF10A cells were pre-treated with 300 μM exogenous nucleosides followed by incubation with the indicated drugs for an additional 24 h. Following lysis, APOBEC3 activity was measured by a cytidine deamination assay. f Ribonucleotide reductase subunits RRM1 , RRM2 and RRM2B were depleted from MCF10A cells by RNA interference and, after 72 h, cells were lysed and subjected to an APOBEC3 cytidine deamination assay. 5FU 5-fluorouracil, MMS methyl methanesulfonate, siNT non-targeting control siRNA
    Figure Legend Snippet: Induction of replication stress and APOBEC3 activity in breast cancer cell lines. a MCF10A cells were treated with the indicated drugs for 48 h followed by mRNA extraction, cDNA synthesis and quantitative PCR for APOBEC3B and APOBEC3G expression levels. b MCF10A cells were treated as in a followed by western blotting with the indicated antibodies. c MCF10A cells were treated as in a prior to lysis and a cytidine deamination assay for APOBEC3 activity using probe 2. d MCF10A cells were treated as in a followed by fixation and immunofluorescence for Ser139 γH2AX and S4/8 replication protein A phosphorylation ( pRPA ). Red asterisks indicate treatments inducing APOBEC3B mRNA, protein expression, activity levels and S4/8 RPA phosphorylation. e MCF10A cells were pre-treated with 300 μM exogenous nucleosides followed by incubation with the indicated drugs for an additional 24 h. Following lysis, APOBEC3 activity was measured by a cytidine deamination assay. f Ribonucleotide reductase subunits RRM1 , RRM2 and RRM2B were depleted from MCF10A cells by RNA interference and, after 72 h, cells were lysed and subjected to an APOBEC3 cytidine deamination assay. 5FU 5-fluorouracil, MMS methyl methanesulfonate, siNT non-targeting control siRNA

    Techniques Used: Activity Assay, Real-time Polymerase Chain Reaction, Expressing, Western Blot, Lysis, Immunofluorescence, Incubation

    HER2 expression and PTEN contribute to APOBEC3 activity. a APOBEC3B mRNA expression following silencing of HER2 expression in BT474 cells by RNAi. HER2 levels were depleted by RNAi and, after 72 h, cells were harvested and mRNA extracted. Following cDNA synthesis, APOBEC3B mRNA levels were determined by quantitative PCR; * p < 0.01 ( t -test). siNT non-targeting control siRNA. b BT474 cells were treated as in a and, following lysis, western blots were probed with the indicated antibodies. c BT474 and MDA-MB-361 cells were treated as in a and, following lysis, samples were subjected to cytidine deamination assay to determine levels of APOBEC3 activity. d BT474 cells were treated with 10 nM afatinib or 30 nM lapatinib for 24 h followed by mRNA isolation and quantitative PCR to determine APOBEC3B mRNA expression levels; * p < 0.01, *** p < 0.005 ( t -test). e BT474 cells were treated as in d and, following lysis, western blots were probed with the indicated antibodies. f BT474 cells were treated as in d and, following lysis, samples were subjected to cytidine-based deamination assay to determine levels of APOBEC3 activity. g MCF10A cells were treated with or without 2 mM hydroxyurea ( HU ) and exposed to the indicated drugs for 48 h followed by APOBEC3 cytidine deamination assay. h MDA-MB-453 cells were treated with the indicated drugs for 48 h followed by APOBEC3 cytidine deamination assay. i PTEN levels were depleted from MCF7 cells growing on glass coverslips by RNAi. Cells were fixed and stained with 53BP1 and cyclin A antibodies. The fraction of cyclin A-negative cells displaying more than five 53BP1 nuclear foci were scored; * p < 0.05 ( t -test). j PTEN levels were depleted from MCF7 cells by RNAi. After 72 h cells were harvested and samples were subjected to cytidine deamination assay to determine APOBEC3 activity. k APOBEC3 activity in response to RAS induction and hydroxyurea ( HU ) treatment. MCF10A-ER:HRAS V12 cells were induced with tamoxifen (4-hydroxytamoxifen; 4- OHT ) in either the presence or absence of hydroxyurea for 48 h, followed by mRNA isolation, cDNA synthesis and quantitative PCR to determine APOBEC3B expression levels. l MCF10A-ER:HRAS V12 cells were treated as in k . Cells were subsequently lysed and subjected to APOBEC3 cytidine deamination assay. LY LY294002, MK MK2206, NT non-targeting, RAPA rapamycin, UNT untreated
    Figure Legend Snippet: HER2 expression and PTEN contribute to APOBEC3 activity. a APOBEC3B mRNA expression following silencing of HER2 expression in BT474 cells by RNAi. HER2 levels were depleted by RNAi and, after 72 h, cells were harvested and mRNA extracted. Following cDNA synthesis, APOBEC3B mRNA levels were determined by quantitative PCR; * p < 0.01 ( t -test). siNT non-targeting control siRNA. b BT474 cells were treated as in a and, following lysis, western blots were probed with the indicated antibodies. c BT474 and MDA-MB-361 cells were treated as in a and, following lysis, samples were subjected to cytidine deamination assay to determine levels of APOBEC3 activity. d BT474 cells were treated with 10 nM afatinib or 30 nM lapatinib for 24 h followed by mRNA isolation and quantitative PCR to determine APOBEC3B mRNA expression levels; * p < 0.01, *** p < 0.005 ( t -test). e BT474 cells were treated as in d and, following lysis, western blots were probed with the indicated antibodies. f BT474 cells were treated as in d and, following lysis, samples were subjected to cytidine-based deamination assay to determine levels of APOBEC3 activity. g MCF10A cells were treated with or without 2 mM hydroxyurea ( HU ) and exposed to the indicated drugs for 48 h followed by APOBEC3 cytidine deamination assay. h MDA-MB-453 cells were treated with the indicated drugs for 48 h followed by APOBEC3 cytidine deamination assay. i PTEN levels were depleted from MCF7 cells growing on glass coverslips by RNAi. Cells were fixed and stained with 53BP1 and cyclin A antibodies. The fraction of cyclin A-negative cells displaying more than five 53BP1 nuclear foci were scored; * p < 0.05 ( t -test). j PTEN levels were depleted from MCF7 cells by RNAi. After 72 h cells were harvested and samples were subjected to cytidine deamination assay to determine APOBEC3 activity. k APOBEC3 activity in response to RAS induction and hydroxyurea ( HU ) treatment. MCF10A-ER:HRAS V12 cells were induced with tamoxifen (4-hydroxytamoxifen; 4- OHT ) in either the presence or absence of hydroxyurea for 48 h, followed by mRNA isolation, cDNA synthesis and quantitative PCR to determine APOBEC3B expression levels. l MCF10A-ER:HRAS V12 cells were treated as in k . Cells were subsequently lysed and subjected to APOBEC3 cytidine deamination assay. LY LY294002, MK MK2206, NT non-targeting, RAPA rapamycin, UNT untreated

    Techniques Used: Expressing, Activity Assay, Real-time Polymerase Chain Reaction, Lysis, Western Blot, Isolation, Staining

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    Cell Signaling Technology Inc apobec3b
    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 <t>APOBEC3B</t> CRISPR (A3B-7) cells. Data are represented as mean ± SD.
    Apobec3b, supplied by Cell Signaling Technology Inc, used in various techniques. Bioz Stars score: 94/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Cell Signaling Technology Inc rabbit monoclonal apobec3b antibody
    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 <t>APOBEC3B</t> CRISPR (A3B-7) cells. Data are represented as mean ± SD.
    Rabbit Monoclonal Apobec3b Antibody, supplied by Cell Signaling Technology Inc, used in various techniques. Bioz Stars score: 94/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Cell Signaling Technology Inc rabbit anti apobec3b
    Expression of other genes with known roles in resistance to gemcitabine in GR cells compared with C cells
    Rabbit Anti Apobec3b, supplied by Cell Signaling Technology Inc, used in various techniques. Bioz Stars score: 94/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Cell Signaling Technology Inc rabbit anti apobec3b monoclonal antibody 5210 87 13
    APOBEC3 activity and replication stress in breast cancer cell lines. a <t>APOBEC3B</t> ( black ), APOBEC3G ( grey ) and APOBEC3A ( white ) mRNA expression in 15 breast cancer cell lines as determined by quantitative PCR. HER2+ cell lines ( red ), basal cell lines ( black ), luminal cell lines ( green ). SKBR3 cells have a null mutation for APOBEC3B . Error bars represent standard deviation. b APOBEC3 activity in the 15 breast cancer cell lines used in a . Cells were lysed and subjected to oligonucleotide-based cytidine deamination assay followed by electrophoresis on 15 % TBE-urea gels. c Cells were grown for two population doublings on glass coverslips followed by fixation and staining with 53BP1 and cyclin A antibodies. The fractions of cyclin A-negative cells displaying more than five 53BP1 nuclear foci were scored. APOBEC3B mRNA expression was determined by quantitative PCR from parallel cell lysates. A Spearman’s rank correlation test was performed to correlate the fraction of 53BP1 nuclear bodies in cell lines with the level of APOBEC3B (r = 0.62, p = 0.0284). Error bars represent standard deviation. d BT474 cells were treated with 12.5–300 μM nucleosides for 72 h prior to lysis. Western blots were probed with the indicated antibodies. e BT474 cells were treated as in d followed by lysis and an APOBEC3 cytidine deamination assay
    Rabbit Anti Apobec3b Monoclonal Antibody 5210 87 13, supplied by Cell Signaling Technology Inc, used in various techniques. Bioz Stars score: 94/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/rabbit anti apobec3b monoclonal antibody 5210 87 13/product/Cell Signaling Technology Inc
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    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.

    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: Membranes were blocked with 3% BSA in PBS and incubated with primary antibodies against APOBEC3A (PA5-78800 from Thermo Fisher) and/or APOBEC3B (E9A2G, Cell Signaling), as well as GAPDH (D4C6R, Cell Signaling).

    Techniques: CRISPR

    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.

    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: Membranes were blocked with 3% BSA in PBS and incubated with primary antibodies against APOBEC3A (PA5-78800 from Thermo Fisher) and/or APOBEC3B (E9A2G, Cell Signaling), as well as GAPDH (D4C6R, Cell Signaling).

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

    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: Membranes were blocked with 3% BSA in PBS and incubated with primary antibodies against APOBEC3A (PA5-78800 from Thermo Fisher) and/or APOBEC3B (E9A2G, Cell Signaling), as well as GAPDH (D4C6R, Cell Signaling).

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

    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.

    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: Rabbit monoclonal APOBEC3B antibody (clone E9A2G) , Cell Signaling Technology , Cat# 41494, RRID: AB_2799203.

    Techniques: CRISPR

    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.

    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: Rabbit monoclonal APOBEC3B antibody (clone E9A2G) , Cell Signaling Technology , Cat# 41494, RRID: AB_2799203.

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

    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: Rabbit monoclonal APOBEC3B antibody (clone E9A2G) , Cell Signaling Technology , Cat# 41494, RRID: AB_2799203.

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

    Expression of other genes with known roles in resistance to gemcitabine in GR cells compared with C cells

    Journal: Molecular Therapy Oncolytics

    Article Title: Acquired chemoresistance can lead to increased resistance of pancreatic cancer cells to oncolytic vesicular stomatitis virus

    doi: 10.1016/j.omto.2021.11.019

    Figure Lengend Snippet: Expression of other genes with known roles in resistance to gemcitabine in GR cells compared with C cells

    Article Snippet: Membranes were then incubated in TBS-T with 5% BSA or milk with 0.02% sodium azide and a 1:5,000 dilution of rabbit polyclonal anti-VSV antibodies (raised against VSV virions), a 1:1,000 dilution of rabbit anti-phospho-STAT1 (catalog number 9177S, clone p-S727, Cell Signaling), a 1:1,000 dilution of rabbit anti-STAT1 (catalog number 14994T, clone D1K9Y, Cell Signaling), a 1:1,000 dilution of rabbit anti-phospho-STAT2 (catalog number 600-401-A93S, clone p-Y689, Rockland), a 1:1,000 dilution of rabbit anti-STAT2 (catalog number 4594, Cell Signaling), a 1:1,000 dilution of rabbit anti-phospho-STAT3 (catalog number 9134P, clone Y705, Cell Signaling), a 1:1,000 dilution of mouse anti-STAT3 (catalog number 9139P, clone 124H6, Cell Signaling), a 1:1,000 dilution of rabbit anti-MX1 (catalog number 13750-1-AP, Proteintech), a 1:1,000 dilution of rabbit anti-MX2 (catalog number 43924S, clone E7Y8H, Cell Signaling), a 1:1,000 dilution of rabbit anti-IFI16 (catalog number 14970S, clone D8B5T, Cell Signaling), a 1:1,000 dilution of rabbit anti-APOBEC3B (catalog number 41494S, clone E9A2G, Cell Signaling), a 1:1,000 dilution of rabbit anti-ISG15 (catalog number 2758S, clone 22D2, Cell Signaling), a 1:1,000 dilution of rabbit anti-CDK14-PFTK1 (catalog number 21612-1-AP, Proteintech), a 1:1,000 dilution of rabbit anti-LARGE2/GYLTL1B (catalog number PA5-63331, Invitrogen), a 1:1,000 dilution of rabbit anti-STING (catalog number 13647S, clone D2P2F, Cell Signaling), a 1:1,000 dilution of rabbit anti-phsopho-TBK1/NAK (catalog number 5483P, clone S172, Cell Signaling), a 1:1,000 dilution of rabbit anti-cGAS (catalog number 79978, clone E5V3W, Cell Signaling), or a 1:1,000 dilution of rabbit anti-cyclin B1 (catalog number 12231T, clone D5C10, Cell Signaling).

    Techniques: Expressing

    APOBEC3 activity and replication stress in breast cancer cell lines. a APOBEC3B ( black ), APOBEC3G ( grey ) and APOBEC3A ( white ) mRNA expression in 15 breast cancer cell lines as determined by quantitative PCR. HER2+ cell lines ( red ), basal cell lines ( black ), luminal cell lines ( green ). SKBR3 cells have a null mutation for APOBEC3B . Error bars represent standard deviation. b APOBEC3 activity in the 15 breast cancer cell lines used in a . Cells were lysed and subjected to oligonucleotide-based cytidine deamination assay followed by electrophoresis on 15 % TBE-urea gels. c Cells were grown for two population doublings on glass coverslips followed by fixation and staining with 53BP1 and cyclin A antibodies. The fractions of cyclin A-negative cells displaying more than five 53BP1 nuclear foci were scored. APOBEC3B mRNA expression was determined by quantitative PCR from parallel cell lysates. A Spearman’s rank correlation test was performed to correlate the fraction of 53BP1 nuclear bodies in cell lines with the level of APOBEC3B (r = 0.62, p = 0.0284). Error bars represent standard deviation. d BT474 cells were treated with 12.5–300 μM nucleosides for 72 h prior to lysis. Western blots were probed with the indicated antibodies. e BT474 cells were treated as in d followed by lysis and an APOBEC3 cytidine deamination assay

    Journal: Genome Biology

    Article Title: DNA replication stress mediates APOBEC3 family mutagenesis in breast cancer

    doi: 10.1186/s13059-016-1042-9

    Figure Lengend Snippet: APOBEC3 activity and replication stress in breast cancer cell lines. a APOBEC3B ( black ), APOBEC3G ( grey ) and APOBEC3A ( white ) mRNA expression in 15 breast cancer cell lines as determined by quantitative PCR. HER2+ cell lines ( red ), basal cell lines ( black ), luminal cell lines ( green ). SKBR3 cells have a null mutation for APOBEC3B . Error bars represent standard deviation. b APOBEC3 activity in the 15 breast cancer cell lines used in a . Cells were lysed and subjected to oligonucleotide-based cytidine deamination assay followed by electrophoresis on 15 % TBE-urea gels. c Cells were grown for two population doublings on glass coverslips followed by fixation and staining with 53BP1 and cyclin A antibodies. The fractions of cyclin A-negative cells displaying more than five 53BP1 nuclear foci were scored. APOBEC3B mRNA expression was determined by quantitative PCR from parallel cell lysates. A Spearman’s rank correlation test was performed to correlate the fraction of 53BP1 nuclear bodies in cell lines with the level of APOBEC3B (r = 0.62, p = 0.0284). Error bars represent standard deviation. d BT474 cells were treated with 12.5–300 μM nucleosides for 72 h prior to lysis. Western blots were probed with the indicated antibodies. e BT474 cells were treated as in d followed by lysis and an APOBEC3 cytidine deamination assay

    Article Snippet: Antibodies: HER2 (Cell Signaling #2248), pSer473 AKT (Cell Signaling #4060), total AKT (Cell Signaling #2920), rabbit anti-APOBEC3B monoclonal antibody 5210-87-13 [ ], HRP-conjugated anti-β-GAPDH antibody (Abcam ab9482) and HRP-conjugated goat anti-mouse/rabbit immunoglobulins (Dako).

    Techniques: Activity Assay, Expressing, Real-time Polymerase Chain Reaction, Mutagenesis, Standard Deviation, Electrophoresis, Staining, Lysis, Western Blot

    Induction of replication stress and APOBEC3 activity in breast cancer cell lines. a MCF10A cells were treated with the indicated drugs for 48 h followed by mRNA extraction, cDNA synthesis and quantitative PCR for APOBEC3B and APOBEC3G expression levels. b MCF10A cells were treated as in a followed by western blotting with the indicated antibodies. c MCF10A cells were treated as in a prior to lysis and a cytidine deamination assay for APOBEC3 activity using probe 2. d MCF10A cells were treated as in a followed by fixation and immunofluorescence for Ser139 γH2AX and S4/8 replication protein A phosphorylation ( pRPA ). Red asterisks indicate treatments inducing APOBEC3B mRNA, protein expression, activity levels and S4/8 RPA phosphorylation. e MCF10A cells were pre-treated with 300 μM exogenous nucleosides followed by incubation with the indicated drugs for an additional 24 h. Following lysis, APOBEC3 activity was measured by a cytidine deamination assay. f Ribonucleotide reductase subunits RRM1 , RRM2 and RRM2B were depleted from MCF10A cells by RNA interference and, after 72 h, cells were lysed and subjected to an APOBEC3 cytidine deamination assay. 5FU 5-fluorouracil, MMS methyl methanesulfonate, siNT non-targeting control siRNA

    Journal: Genome Biology

    Article Title: DNA replication stress mediates APOBEC3 family mutagenesis in breast cancer

    doi: 10.1186/s13059-016-1042-9

    Figure Lengend Snippet: Induction of replication stress and APOBEC3 activity in breast cancer cell lines. a MCF10A cells were treated with the indicated drugs for 48 h followed by mRNA extraction, cDNA synthesis and quantitative PCR for APOBEC3B and APOBEC3G expression levels. b MCF10A cells were treated as in a followed by western blotting with the indicated antibodies. c MCF10A cells were treated as in a prior to lysis and a cytidine deamination assay for APOBEC3 activity using probe 2. d MCF10A cells were treated as in a followed by fixation and immunofluorescence for Ser139 γH2AX and S4/8 replication protein A phosphorylation ( pRPA ). Red asterisks indicate treatments inducing APOBEC3B mRNA, protein expression, activity levels and S4/8 RPA phosphorylation. e MCF10A cells were pre-treated with 300 μM exogenous nucleosides followed by incubation with the indicated drugs for an additional 24 h. Following lysis, APOBEC3 activity was measured by a cytidine deamination assay. f Ribonucleotide reductase subunits RRM1 , RRM2 and RRM2B were depleted from MCF10A cells by RNA interference and, after 72 h, cells were lysed and subjected to an APOBEC3 cytidine deamination assay. 5FU 5-fluorouracil, MMS methyl methanesulfonate, siNT non-targeting control siRNA

    Article Snippet: Antibodies: HER2 (Cell Signaling #2248), pSer473 AKT (Cell Signaling #4060), total AKT (Cell Signaling #2920), rabbit anti-APOBEC3B monoclonal antibody 5210-87-13 [ ], HRP-conjugated anti-β-GAPDH antibody (Abcam ab9482) and HRP-conjugated goat anti-mouse/rabbit immunoglobulins (Dako).

    Techniques: Activity Assay, Real-time Polymerase Chain Reaction, Expressing, Western Blot, Lysis, Immunofluorescence, Incubation

    HER2 expression and PTEN contribute to APOBEC3 activity. a APOBEC3B mRNA expression following silencing of HER2 expression in BT474 cells by RNAi. HER2 levels were depleted by RNAi and, after 72 h, cells were harvested and mRNA extracted. Following cDNA synthesis, APOBEC3B mRNA levels were determined by quantitative PCR; * p < 0.01 ( t -test). siNT non-targeting control siRNA. b BT474 cells were treated as in a and, following lysis, western blots were probed with the indicated antibodies. c BT474 and MDA-MB-361 cells were treated as in a and, following lysis, samples were subjected to cytidine deamination assay to determine levels of APOBEC3 activity. d BT474 cells were treated with 10 nM afatinib or 30 nM lapatinib for 24 h followed by mRNA isolation and quantitative PCR to determine APOBEC3B mRNA expression levels; * p < 0.01, *** p < 0.005 ( t -test). e BT474 cells were treated as in d and, following lysis, western blots were probed with the indicated antibodies. f BT474 cells were treated as in d and, following lysis, samples were subjected to cytidine-based deamination assay to determine levels of APOBEC3 activity. g MCF10A cells were treated with or without 2 mM hydroxyurea ( HU ) and exposed to the indicated drugs for 48 h followed by APOBEC3 cytidine deamination assay. h MDA-MB-453 cells were treated with the indicated drugs for 48 h followed by APOBEC3 cytidine deamination assay. i PTEN levels were depleted from MCF7 cells growing on glass coverslips by RNAi. Cells were fixed and stained with 53BP1 and cyclin A antibodies. The fraction of cyclin A-negative cells displaying more than five 53BP1 nuclear foci were scored; * p < 0.05 ( t -test). j PTEN levels were depleted from MCF7 cells by RNAi. After 72 h cells were harvested and samples were subjected to cytidine deamination assay to determine APOBEC3 activity. k APOBEC3 activity in response to RAS induction and hydroxyurea ( HU ) treatment. MCF10A-ER:HRAS V12 cells were induced with tamoxifen (4-hydroxytamoxifen; 4- OHT ) in either the presence or absence of hydroxyurea for 48 h, followed by mRNA isolation, cDNA synthesis and quantitative PCR to determine APOBEC3B expression levels. l MCF10A-ER:HRAS V12 cells were treated as in k . Cells were subsequently lysed and subjected to APOBEC3 cytidine deamination assay. LY LY294002, MK MK2206, NT non-targeting, RAPA rapamycin, UNT untreated

    Journal: Genome Biology

    Article Title: DNA replication stress mediates APOBEC3 family mutagenesis in breast cancer

    doi: 10.1186/s13059-016-1042-9

    Figure Lengend Snippet: HER2 expression and PTEN contribute to APOBEC3 activity. a APOBEC3B mRNA expression following silencing of HER2 expression in BT474 cells by RNAi. HER2 levels were depleted by RNAi and, after 72 h, cells were harvested and mRNA extracted. Following cDNA synthesis, APOBEC3B mRNA levels were determined by quantitative PCR; * p < 0.01 ( t -test). siNT non-targeting control siRNA. b BT474 cells were treated as in a and, following lysis, western blots were probed with the indicated antibodies. c BT474 and MDA-MB-361 cells were treated as in a and, following lysis, samples were subjected to cytidine deamination assay to determine levels of APOBEC3 activity. d BT474 cells were treated with 10 nM afatinib or 30 nM lapatinib for 24 h followed by mRNA isolation and quantitative PCR to determine APOBEC3B mRNA expression levels; * p < 0.01, *** p < 0.005 ( t -test). e BT474 cells were treated as in d and, following lysis, western blots were probed with the indicated antibodies. f BT474 cells were treated as in d and, following lysis, samples were subjected to cytidine-based deamination assay to determine levels of APOBEC3 activity. g MCF10A cells were treated with or without 2 mM hydroxyurea ( HU ) and exposed to the indicated drugs for 48 h followed by APOBEC3 cytidine deamination assay. h MDA-MB-453 cells were treated with the indicated drugs for 48 h followed by APOBEC3 cytidine deamination assay. i PTEN levels were depleted from MCF7 cells growing on glass coverslips by RNAi. Cells were fixed and stained with 53BP1 and cyclin A antibodies. The fraction of cyclin A-negative cells displaying more than five 53BP1 nuclear foci were scored; * p < 0.05 ( t -test). j PTEN levels were depleted from MCF7 cells by RNAi. After 72 h cells were harvested and samples were subjected to cytidine deamination assay to determine APOBEC3 activity. k APOBEC3 activity in response to RAS induction and hydroxyurea ( HU ) treatment. MCF10A-ER:HRAS V12 cells were induced with tamoxifen (4-hydroxytamoxifen; 4- OHT ) in either the presence or absence of hydroxyurea for 48 h, followed by mRNA isolation, cDNA synthesis and quantitative PCR to determine APOBEC3B expression levels. l MCF10A-ER:HRAS V12 cells were treated as in k . Cells were subsequently lysed and subjected to APOBEC3 cytidine deamination assay. LY LY294002, MK MK2206, NT non-targeting, RAPA rapamycin, UNT untreated

    Article Snippet: Antibodies: HER2 (Cell Signaling #2248), pSer473 AKT (Cell Signaling #4060), total AKT (Cell Signaling #2920), rabbit anti-APOBEC3B monoclonal antibody 5210-87-13 [ ], HRP-conjugated anti-β-GAPDH antibody (Abcam ab9482) and HRP-conjugated goat anti-mouse/rabbit immunoglobulins (Dako).

    Techniques: Expressing, Activity Assay, Real-time Polymerase Chain Reaction, Lysis, Western Blot, Isolation, Staining