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coding sequences  (Twist Bioscience)


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    Structured Review

    Twist Bioscience coding sequences
    Coding Sequences, supplied by Twist Bioscience, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/coding+sequence/coding+sequences+synthetic/bio_rxiv__64898__2026__05__17__725801-378-1-30
    Average 86 stars, based on 1 article reviews
    coding sequences - by Bioz Stars, 2026-10
    86/100 stars

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    Related Articles

    Sequencing:

    Article Title: Metabolic engineering of stomatal precursor cells enhances photosynthetic water‐use efficiency and vegetative growth under water‐deficit conditions in Arabidopsis thaliana
    Article Snippet: .. Appropriate flanking regions compatible with Golden Gate Assembly (Marillonnet and Engler, ) were added to the 5' and 3' regions, and the resulting coding sequence was commercially synthesized (TWIST Bioscience, South San Francisco, CA, USA). ..

    Article Title: Systematic investigation of Epstein-Barr virus transcriptional regulator interactions with the human genome
    Article Snippet: The pcDNA5/FRT/TO backbone and DNA sequences for EBV vTRs from strain B95-8 were supplied to Twist Bioscience to generate untagged, N-terminally GFP tagged and C-terminally GFP tagged plasmids. .. The coding sequence was codon optimized if necessary for production by Twist Bioscience. .. Some of the vTR constructs could not be generated by Twist Bioscience, so they were made through restriction digest or TOPO cloning into the same plasmid backbone instead (labeled in the resource table as “This paper”).

    Article Title: Advancing Vibrio genetics: A platform for efficient genomic manipulation
    Article Snippet: To add chloramphenicol resistance, the selectable marker used during genomic integration and counter-selection, a DNA fragment was synthesized consisting of the cat sequence from pBACe3.6 with a single FRT site upstream of the coding sequence (Twist Biosciences)( ). .. To add chloramphenicol resistance, the selectable marker used during genomic integration and counter-selection, a DNA fragment was synthesized consisting of the cat sequence from pBACe3.6 with a single FRT site upstream of the coding sequence (Twist Biosciences)( ). ..

    Article Title: Site-specific deacylation by ABHD17a controls BK channel splice variant activity
    Article Snippet: .. A catalytically inactive version of ABHD17a was made by mutating amino acids Ser 170 and Asp 255 in the catalytic triad to alanine by synthesizing the entire coding sequence (Twist Bioscience) containing the mutated amino acid codons and incorporating the FLAG tag and restriction sites EcoRI and NotI flanking the coding sequence and subcloned into pcDNA3.1. ..

    Article Title: A CRISPRi Gene Regulation System for Bifidobacteria
    Article Snippet: A 500 bp fragment of the integrated erythromycin resistance marker present in B. breve dCas9 strains was amplified by PCR and cloned into pFREM29‐CAT using NotI and XbaI (New England Biolabs) to generate pFREM29‐CAT‐E500. .. The coding sequence of nanoluciferase was codon optimized for expression in B. breve and designed to exclude restriction modification motifs present in B. breve UCC2003 (Bottacini et al. ) prior to being chemically synthesized (Twist Biosciences) and cloned into pFREM29‐CAT‐E500 with EcoRI and NotI to generate pFREM29‐CAT‐E500‐nanoluciferase. .. This plasmid was transformed into B. breve ‐dCas9 strains by electroporation and the presence of integrated nanoluciferase in resulting clones was verified by PCR and by DNA sequencing of the PCR products to confirm the genome‐insertion boundaries (Genewiz).

    Article Title: Development of a Biosafety Level 1 Cellular Assay for Identifying Small-Molecule Antivirals Targeting the Main Protease of SARS-CoV-2: Evaluation of Cellular Activity of GC376, Boceprevir, Carmofur, Ebselen, and Selenoneine
    Article Snippet: .. For Mpro expression, the coding sequence (YP_009725301.1) corresponding to bases 10055-10972 of the SARS-CoV-2 (NC_045512) genome was synthesized (Twist Bioscience, South San Francisco, CA, USA) and cloned downstream of a GST tag with a preceding Mpro cleavage sequence (TSAVLQ↓SGFRK) (arrow indicates the cleavage site). ..

    Article Title: Chromosome-level assembly of basil genome unveils the genetic variation driving Genovese and Thai aroma types.
    Article Snippet: Jing Zhang, Mohamad Abu-Abied, Renana Milavski, Chen Adler, Alona Shachter, Tali Kahane-Achinoam, Hadas Melnik-Ben-Gera, Rachel Davidovich-Rikanati, Adrian F. Powell , David Chaimovitsh, Gon Carmi, Nativ Dudai, Susan R. Strickler and Itay Gonda Boyce Thompson Institute, Ithaca, New York, USA, Unit of Aromatic and Medicinal Plants, Newe Ya’ar Research Center, Volcani Institute, Ramat-Yishay, Israel, Faculty of Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel, Bioinformatics Unit, Newe Ya’ar Research Center, Agricultural Research Organization, Volcani Institute, Ramat-Yishay, Israel, Chicago Botanic Garden, Plant Science and Conservation, 1000 Lake Cook Rd., Glencoe, Illinois 60022, USA, and Plant Biology and Conservation Program, Northwestern University, 2145 Sheridan Rd., Evanston, Illinois 60208, USA

    Synthesized:

    Article Title: Metabolic engineering of stomatal precursor cells enhances photosynthetic water‐use efficiency and vegetative growth under water‐deficit conditions in Arabidopsis thaliana
    Article Snippet: .. Appropriate flanking regions compatible with Golden Gate Assembly (Marillonnet and Engler, ) were added to the 5' and 3' regions, and the resulting coding sequence was commercially synthesized (TWIST Bioscience, South San Francisco, CA, USA). ..

    Article Title: Advancing Vibrio genetics: A platform for efficient genomic manipulation
    Article Snippet: To add chloramphenicol resistance, the selectable marker used during genomic integration and counter-selection, a DNA fragment was synthesized consisting of the cat sequence from pBACe3.6 with a single FRT site upstream of the coding sequence (Twist Biosciences)( ). .. To add chloramphenicol resistance, the selectable marker used during genomic integration and counter-selection, a DNA fragment was synthesized consisting of the cat sequence from pBACe3.6 with a single FRT site upstream of the coding sequence (Twist Biosciences)( ). ..

    Article Title: A CRISPRi Gene Regulation System for Bifidobacteria
    Article Snippet: A 500 bp fragment of the integrated erythromycin resistance marker present in B. breve dCas9 strains was amplified by PCR and cloned into pFREM29‐CAT using NotI and XbaI (New England Biolabs) to generate pFREM29‐CAT‐E500. .. The coding sequence of nanoluciferase was codon optimized for expression in B. breve and designed to exclude restriction modification motifs present in B. breve UCC2003 (Bottacini et al. ) prior to being chemically synthesized (Twist Biosciences) and cloned into pFREM29‐CAT‐E500 with EcoRI and NotI to generate pFREM29‐CAT‐E500‐nanoluciferase. .. This plasmid was transformed into B. breve ‐dCas9 strains by electroporation and the presence of integrated nanoluciferase in resulting clones was verified by PCR and by DNA sequencing of the PCR products to confirm the genome‐insertion boundaries (Genewiz).

    Article Title: Development of a Biosafety Level 1 Cellular Assay for Identifying Small-Molecule Antivirals Targeting the Main Protease of SARS-CoV-2: Evaluation of Cellular Activity of GC376, Boceprevir, Carmofur, Ebselen, and Selenoneine
    Article Snippet: .. For Mpro expression, the coding sequence (YP_009725301.1) corresponding to bases 10055-10972 of the SARS-CoV-2 (NC_045512) genome was synthesized (Twist Bioscience, South San Francisco, CA, USA) and cloned downstream of a GST tag with a preceding Mpro cleavage sequence (TSAVLQ↓SGFRK) (arrow indicates the cleavage site). ..

    Article Title: Chromosome-level assembly of basil genome unveils the genetic variation driving Genovese and Thai aroma types.
    Article Snippet: Jing Zhang, Mohamad Abu-Abied, Renana Milavski, Chen Adler, Alona Shachter, Tali Kahane-Achinoam, Hadas Melnik-Ben-Gera, Rachel Davidovich-Rikanati, Adrian F. Powell , David Chaimovitsh, Gon Carmi, Nativ Dudai, Susan R. Strickler and Itay Gonda Boyce Thompson Institute, Ithaca, New York, USA, Unit of Aromatic and Medicinal Plants, Newe Ya’ar Research Center, Volcani Institute, Ramat-Yishay, Israel, Faculty of Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel, Bioinformatics Unit, Newe Ya’ar Research Center, Agricultural Research Organization, Volcani Institute, Ramat-Yishay, Israel, Chicago Botanic Garden, Plant Science and Conservation, 1000 Lake Cook Rd., Glencoe, Illinois 60022, USA, and Plant Biology and Conservation Program, Northwestern University, 2145 Sheridan Rd., Evanston, Illinois 60208, USA

    Marker:

    Article Title: Advancing Vibrio genetics: A platform for efficient genomic manipulation
    Article Snippet: To add chloramphenicol resistance, the selectable marker used during genomic integration and counter-selection, a DNA fragment was synthesized consisting of the cat sequence from pBACe3.6 with a single FRT site upstream of the coding sequence (Twist Biosciences)( ). .. To add chloramphenicol resistance, the selectable marker used during genomic integration and counter-selection, a DNA fragment was synthesized consisting of the cat sequence from pBACe3.6 with a single FRT site upstream of the coding sequence (Twist Biosciences)( ). ..

    FLAG-tag:

    Article Title: Site-specific deacylation by ABHD17a controls BK channel splice variant activity
    Article Snippet: .. A catalytically inactive version of ABHD17a was made by mutating amino acids Ser 170 and Asp 255 in the catalytic triad to alanine by synthesizing the entire coding sequence (Twist Bioscience) containing the mutated amino acid codons and incorporating the FLAG tag and restriction sites EcoRI and NotI flanking the coding sequence and subcloned into pcDNA3.1. ..

    Expressing:

    Article Title: A CRISPRi Gene Regulation System for Bifidobacteria
    Article Snippet: A 500 bp fragment of the integrated erythromycin resistance marker present in B. breve dCas9 strains was amplified by PCR and cloned into pFREM29‐CAT using NotI and XbaI (New England Biolabs) to generate pFREM29‐CAT‐E500. .. The coding sequence of nanoluciferase was codon optimized for expression in B. breve and designed to exclude restriction modification motifs present in B. breve UCC2003 (Bottacini et al. ) prior to being chemically synthesized (Twist Biosciences) and cloned into pFREM29‐CAT‐E500 with EcoRI and NotI to generate pFREM29‐CAT‐E500‐nanoluciferase. .. This plasmid was transformed into B. breve ‐dCas9 strains by electroporation and the presence of integrated nanoluciferase in resulting clones was verified by PCR and by DNA sequencing of the PCR products to confirm the genome‐insertion boundaries (Genewiz).

    Article Title: Development of a Biosafety Level 1 Cellular Assay for Identifying Small-Molecule Antivirals Targeting the Main Protease of SARS-CoV-2: Evaluation of Cellular Activity of GC376, Boceprevir, Carmofur, Ebselen, and Selenoneine
    Article Snippet: .. For Mpro expression, the coding sequence (YP_009725301.1) corresponding to bases 10055-10972 of the SARS-CoV-2 (NC_045512) genome was synthesized (Twist Bioscience, South San Francisco, CA, USA) and cloned downstream of a GST tag with a preceding Mpro cleavage sequence (TSAVLQ↓SGFRK) (arrow indicates the cleavage site). ..

    Article Title: Chromosome-level assembly of basil genome unveils the genetic variation driving Genovese and Thai aroma types.
    Article Snippet: Jing Zhang, Mohamad Abu-Abied, Renana Milavski, Chen Adler, Alona Shachter, Tali Kahane-Achinoam, Hadas Melnik-Ben-Gera, Rachel Davidovich-Rikanati, Adrian F. Powell , David Chaimovitsh, Gon Carmi, Nativ Dudai, Susan R. Strickler and Itay Gonda Boyce Thompson Institute, Ithaca, New York, USA, Unit of Aromatic and Medicinal Plants, Newe Ya’ar Research Center, Volcani Institute, Ramat-Yishay, Israel, Faculty of Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel, Bioinformatics Unit, Newe Ya’ar Research Center, Agricultural Research Organization, Volcani Institute, Ramat-Yishay, Israel, Chicago Botanic Garden, Plant Science and Conservation, 1000 Lake Cook Rd., Glencoe, Illinois 60022, USA, and Plant Biology and Conservation Program, Northwestern University, 2145 Sheridan Rd., Evanston, Illinois 60208, USA

    Modification:

    Article Title: A CRISPRi Gene Regulation System for Bifidobacteria
    Article Snippet: A 500 bp fragment of the integrated erythromycin resistance marker present in B. breve dCas9 strains was amplified by PCR and cloned into pFREM29‐CAT using NotI and XbaI (New England Biolabs) to generate pFREM29‐CAT‐E500. .. The coding sequence of nanoluciferase was codon optimized for expression in B. breve and designed to exclude restriction modification motifs present in B. breve UCC2003 (Bottacini et al. ) prior to being chemically synthesized (Twist Biosciences) and cloned into pFREM29‐CAT‐E500 with EcoRI and NotI to generate pFREM29‐CAT‐E500‐nanoluciferase. .. This plasmid was transformed into B. breve ‐dCas9 strains by electroporation and the presence of integrated nanoluciferase in resulting clones was verified by PCR and by DNA sequencing of the PCR products to confirm the genome‐insertion boundaries (Genewiz).

    Clone Assay:

    Article Title: A CRISPRi Gene Regulation System for Bifidobacteria
    Article Snippet: A 500 bp fragment of the integrated erythromycin resistance marker present in B. breve dCas9 strains was amplified by PCR and cloned into pFREM29‐CAT using NotI and XbaI (New England Biolabs) to generate pFREM29‐CAT‐E500. .. The coding sequence of nanoluciferase was codon optimized for expression in B. breve and designed to exclude restriction modification motifs present in B. breve UCC2003 (Bottacini et al. ) prior to being chemically synthesized (Twist Biosciences) and cloned into pFREM29‐CAT‐E500 with EcoRI and NotI to generate pFREM29‐CAT‐E500‐nanoluciferase. .. This plasmid was transformed into B. breve ‐dCas9 strains by electroporation and the presence of integrated nanoluciferase in resulting clones was verified by PCR and by DNA sequencing of the PCR products to confirm the genome‐insertion boundaries (Genewiz).

    Article Title: Development of a Biosafety Level 1 Cellular Assay for Identifying Small-Molecule Antivirals Targeting the Main Protease of SARS-CoV-2: Evaluation of Cellular Activity of GC376, Boceprevir, Carmofur, Ebselen, and Selenoneine
    Article Snippet: .. For Mpro expression, the coding sequence (YP_009725301.1) corresponding to bases 10055-10972 of the SARS-CoV-2 (NC_045512) genome was synthesized (Twist Bioscience, South San Francisco, CA, USA) and cloned downstream of a GST tag with a preceding Mpro cleavage sequence (TSAVLQ↓SGFRK) (arrow indicates the cleavage site). ..

    Article Title: Chromosome-level assembly of basil genome unveils the genetic variation driving Genovese and Thai aroma types.
    Article Snippet: Jing Zhang, Mohamad Abu-Abied, Renana Milavski, Chen Adler, Alona Shachter, Tali Kahane-Achinoam, Hadas Melnik-Ben-Gera, Rachel Davidovich-Rikanati, Adrian F. Powell , David Chaimovitsh, Gon Carmi, Nativ Dudai, Susan R. Strickler and Itay Gonda Boyce Thompson Institute, Ithaca, New York, USA, Unit of Aromatic and Medicinal Plants, Newe Ya’ar Research Center, Volcani Institute, Ramat-Yishay, Israel, Faculty of Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel, Bioinformatics Unit, Newe Ya’ar Research Center, Agricultural Research Organization, Volcani Institute, Ramat-Yishay, Israel, Chicago Botanic Garden, Plant Science and Conservation, 1000 Lake Cook Rd., Glencoe, Illinois 60022, USA, and Plant Biology and Conservation Program, Northwestern University, 2145 Sheridan Rd., Evanston, Illinois 60208, USA

    Functional Assay:

    Article Title: Chromosome-level assembly of basil genome unveils the genetic variation driving Genovese and Thai aroma types.
    Article Snippet: Jing Zhang, Mohamad Abu-Abied, Renana Milavski, Chen Adler, Alona Shachter, Tali Kahane-Achinoam, Hadas Melnik-Ben-Gera, Rachel Davidovich-Rikanati, Adrian F. Powell , David Chaimovitsh, Gon Carmi, Nativ Dudai, Susan R. Strickler and Itay Gonda Boyce Thompson Institute, Ithaca, New York, USA, Unit of Aromatic and Medicinal Plants, Newe Ya’ar Research Center, Volcani Institute, Ramat-Yishay, Israel, Faculty of Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel, Bioinformatics Unit, Newe Ya’ar Research Center, Agricultural Research Organization, Volcani Institute, Ramat-Yishay, Israel, Chicago Botanic Garden, Plant Science and Conservation, 1000 Lake Cook Rd., Glencoe, Illinois 60022, USA, and Plant Biology and Conservation Program, Northwestern University, 2145 Sheridan Rd., Evanston, Illinois 60208, USA

    Activity Assay:

    Article Title: Chromosome-level assembly of basil genome unveils the genetic variation driving Genovese and Thai aroma types.
    Article Snippet: Jing Zhang, Mohamad Abu-Abied, Renana Milavski, Chen Adler, Alona Shachter, Tali Kahane-Achinoam, Hadas Melnik-Ben-Gera, Rachel Davidovich-Rikanati, Adrian F. Powell , David Chaimovitsh, Gon Carmi, Nativ Dudai, Susan R. Strickler and Itay Gonda Boyce Thompson Institute, Ithaca, New York, USA, Unit of Aromatic and Medicinal Plants, Newe Ya’ar Research Center, Volcani Institute, Ramat-Yishay, Israel, Faculty of Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel, Bioinformatics Unit, Newe Ya’ar Research Center, Agricultural Research Organization, Volcani Institute, Ramat-Yishay, Israel, Chicago Botanic Garden, Plant Science and Conservation, 1000 Lake Cook Rd., Glencoe, Illinois 60022, USA, and Plant Biology and Conservation Program, Northwestern University, 2145 Sheridan Rd., Evanston, Illinois 60208, USA



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    Image Search Results


    TRAF3 is positively correlated with favorable prognosis in breast cancer. ( a ) High TRAF3 mRNA expression levels are associated with better OS (Living vs. Diseased, Mann–Whitney U test), lower disease stage (Bonferroni correction), lower lymph node stage (N) (N0 vs. N1: p = 0.004, Bonferroni correction) and lower tumor stage (T) (T1 vs. T3: p = 0.019, Bonferroni correction) in the TCGA-BRCA cohort. ( b ) High TRAF3 mRNA expression presents with a statistically significant better OS ( p = 0.00405) and DMFS ( p = 0.00729) in the ER-negative breast cancer cohort employed by GOBO, with ER-positive disease presenting a similar association despite not reaching statistical significance.

    Journal: International Journal of Molecular Sciences

    Article Title: Dual Role of Cancer Epithelial-Specific TRAF3 in Regulating Breast Cancer Cell Survival and Lymphocyte Activity

    doi: 10.3390/ijms27104414

    Figure Lengend Snippet: TRAF3 is positively correlated with favorable prognosis in breast cancer. ( a ) High TRAF3 mRNA expression levels are associated with better OS (Living vs. Diseased, Mann–Whitney U test), lower disease stage (Bonferroni correction), lower lymph node stage (N) (N0 vs. N1: p = 0.004, Bonferroni correction) and lower tumor stage (T) (T1 vs. T3: p = 0.019, Bonferroni correction) in the TCGA-BRCA cohort. ( b ) High TRAF3 mRNA expression presents with a statistically significant better OS ( p = 0.00405) and DMFS ( p = 0.00729) in the ER-negative breast cancer cohort employed by GOBO, with ER-positive disease presenting a similar association despite not reaching statistical significance.

    Article Snippet: The TRAF3 coding sequence was amplified from a pCMV6-TRAF3-GFP (RG210417, Origene, Rockville, MD, USA) vector and cloned into pLenti-EF1a-GFP-2A-Puro (LV067, ABM Inc, Richmond, BC, Canada).

    Techniques: Expressing, MANN-WHITNEY

    Forced TRAF3 expression in breast cancer cell lines induces partial EMT and affects cell proliferation. ( a ) Invasion, migration and colony formation assays depicting an opposing phenotype between migratory and proliferative states of MCF7-TRAF3 cells. ( b ) Western blot analyses for the indicated proteins in MDA-MB-231 and MCF-7 cells (control and TRAF3 expressing). ( c ) ICC for the indicated proteins in MCF-7 cells, indicating significant downregulation of key molecules upon TRAF3 expression (ns: no significance; *** p < 0.001 Student’s t -test).

    Journal: International Journal of Molecular Sciences

    Article Title: Dual Role of Cancer Epithelial-Specific TRAF3 in Regulating Breast Cancer Cell Survival and Lymphocyte Activity

    doi: 10.3390/ijms27104414

    Figure Lengend Snippet: Forced TRAF3 expression in breast cancer cell lines induces partial EMT and affects cell proliferation. ( a ) Invasion, migration and colony formation assays depicting an opposing phenotype between migratory and proliferative states of MCF7-TRAF3 cells. ( b ) Western blot analyses for the indicated proteins in MDA-MB-231 and MCF-7 cells (control and TRAF3 expressing). ( c ) ICC for the indicated proteins in MCF-7 cells, indicating significant downregulation of key molecules upon TRAF3 expression (ns: no significance; *** p < 0.001 Student’s t -test).

    Article Snippet: The TRAF3 coding sequence was amplified from a pCMV6-TRAF3-GFP (RG210417, Origene, Rockville, MD, USA) vector and cloned into pLenti-EF1a-GFP-2A-Puro (LV067, ABM Inc, Richmond, BC, Canada).

    Techniques: Expressing, Migration, Western Blot, Control

    Identification of interactors, pathways and processes of TRAF3 in breast cancer. ( a ) Volcano plot of significant TRAF3 interactions in MCF-7 cells (FDR < 0.05). ( b ) Top 20 enriched pathways (Metascape) among proteins that interact with TRAF3 in MCF-7 cells with −log10(Padj) > 10 −20 . ( c ) Significantly enriched pathways among genes co-expressed with TRAF3 in the TCGA BRCA cohort. ( d ) Representative BRCA cases from the TCGA cohort presenting with High and Low TILs (upper panel). High TRAF3 mRNA expression is correlated ( p = 0.02, Mann–Whitney U Test) with High stromal TILs in the TCGA BRCA cohort ( n = 200).

    Journal: International Journal of Molecular Sciences

    Article Title: Dual Role of Cancer Epithelial-Specific TRAF3 in Regulating Breast Cancer Cell Survival and Lymphocyte Activity

    doi: 10.3390/ijms27104414

    Figure Lengend Snippet: Identification of interactors, pathways and processes of TRAF3 in breast cancer. ( a ) Volcano plot of significant TRAF3 interactions in MCF-7 cells (FDR < 0.05). ( b ) Top 20 enriched pathways (Metascape) among proteins that interact with TRAF3 in MCF-7 cells with −log10(Padj) > 10 −20 . ( c ) Significantly enriched pathways among genes co-expressed with TRAF3 in the TCGA BRCA cohort. ( d ) Representative BRCA cases from the TCGA cohort presenting with High and Low TILs (upper panel). High TRAF3 mRNA expression is correlated ( p = 0.02, Mann–Whitney U Test) with High stromal TILs in the TCGA BRCA cohort ( n = 200).

    Article Snippet: The TRAF3 coding sequence was amplified from a pCMV6-TRAF3-GFP (RG210417, Origene, Rockville, MD, USA) vector and cloned into pLenti-EF1a-GFP-2A-Puro (LV067, ABM Inc, Richmond, BC, Canada).

    Techniques: Expressing, MANN-WHITNEY

    TRAF3 expression across cell populations in the scRNA human breast cancer dataset. ( a ) UMAP visualization of 81,389 quality-filtered single cells derived from the Breast Cancer Atlas, colored by cell type annotation. ( b ) Feature plot showing log-normalized TRAF3 expression projected onto the UMAP embedding. ( c ) Violin plots depicting log-normalized TRAF3 expression across each of the cell types. Statistical comparisons were performed using Wilcoxon rank-sum tests, comparing each cell type against all remaining cells, followed by Benjamini–Hochberg correction for multiple testing. Asterisks (*) indicate adj p -values < 0.05. ( d ) Volcano Plot of Differential expression of TRAF3 -positive ( TRAF3 +) vs. negative ( TRAF3 -) Cancer Epithelial (CE) cells. The x-axis represents the log 2 fold change of expression in TRAF3 -positive versus TRAF3 -negative cells, and the y-axis shows the −log 10 adjusted p -value (FDR). Points are colored according to FDR significance, while labels highlight specific immunologically relevant genes, colored according to the following categories: (i) Immunogenicity—Immunogenicity/Antigen Presentation; (ii) MHC-I—MHC class I pathway (CD8 + T-cell recognition); (iii) MHC-II—MHC class II (tumor-intrinsic or antigen-presenting cell mediated); (iv) Checkpoint—Checkpoint blockade/Immune Modulation; (v) Infiltration—Increase immune infiltration into tumors; and (vi) Non-self—Promote tumor cell recognition as “non-self”. Selected genes of interest not in the above categories are colored black (‘Other’ category). ( e ) Gene Ontology (GO) Enrichment Analysis of the filtered top DE genes (FDR < 0.05 & |log2FC| > 0.1) identified via differential expression analysis between TRAF3 + and TRAF3 -cancer epithelial (CE) cells. X-axis represents the Fold Enrichment, and y-axis represents the immune-related Biological Process and Molecular Function GO terms, grouped into clusters based on functional similarity (for the full GO term graph with all the immune and non-immune related GO terms, see ). Dot size is analogous to the number of specific genes associated with each GO term, while their color gradient corresponds to the FDR-adjusted p -value (Q value). Abbreviations used include the following: CE (Cancer Epithelial cells), NE (Normal Epithelial cells), PVL (PeriVascular-Like cells), CAFs (Cancer-Associated Fibroblasts), PR (Positive Regulation), R (Regulation), prd (production), MM (Molecular Mediator), MBP (Macromolecule Biosynthetic Process), MMP (Macromolecule Metabolic Process), CR (Cellular Response), env/tal (environmental), RSP (receptor signaling pathway), SP (signaling pathway), resp. (response), ext. (external), and If-M (interferon-mediated).

    Journal: International Journal of Molecular Sciences

    Article Title: Dual Role of Cancer Epithelial-Specific TRAF3 in Regulating Breast Cancer Cell Survival and Lymphocyte Activity

    doi: 10.3390/ijms27104414

    Figure Lengend Snippet: TRAF3 expression across cell populations in the scRNA human breast cancer dataset. ( a ) UMAP visualization of 81,389 quality-filtered single cells derived from the Breast Cancer Atlas, colored by cell type annotation. ( b ) Feature plot showing log-normalized TRAF3 expression projected onto the UMAP embedding. ( c ) Violin plots depicting log-normalized TRAF3 expression across each of the cell types. Statistical comparisons were performed using Wilcoxon rank-sum tests, comparing each cell type against all remaining cells, followed by Benjamini–Hochberg correction for multiple testing. Asterisks (*) indicate adj p -values < 0.05. ( d ) Volcano Plot of Differential expression of TRAF3 -positive ( TRAF3 +) vs. negative ( TRAF3 -) Cancer Epithelial (CE) cells. The x-axis represents the log 2 fold change of expression in TRAF3 -positive versus TRAF3 -negative cells, and the y-axis shows the −log 10 adjusted p -value (FDR). Points are colored according to FDR significance, while labels highlight specific immunologically relevant genes, colored according to the following categories: (i) Immunogenicity—Immunogenicity/Antigen Presentation; (ii) MHC-I—MHC class I pathway (CD8 + T-cell recognition); (iii) MHC-II—MHC class II (tumor-intrinsic or antigen-presenting cell mediated); (iv) Checkpoint—Checkpoint blockade/Immune Modulation; (v) Infiltration—Increase immune infiltration into tumors; and (vi) Non-self—Promote tumor cell recognition as “non-self”. Selected genes of interest not in the above categories are colored black (‘Other’ category). ( e ) Gene Ontology (GO) Enrichment Analysis of the filtered top DE genes (FDR < 0.05 & |log2FC| > 0.1) identified via differential expression analysis between TRAF3 + and TRAF3 -cancer epithelial (CE) cells. X-axis represents the Fold Enrichment, and y-axis represents the immune-related Biological Process and Molecular Function GO terms, grouped into clusters based on functional similarity (for the full GO term graph with all the immune and non-immune related GO terms, see ). Dot size is analogous to the number of specific genes associated with each GO term, while their color gradient corresponds to the FDR-adjusted p -value (Q value). Abbreviations used include the following: CE (Cancer Epithelial cells), NE (Normal Epithelial cells), PVL (PeriVascular-Like cells), CAFs (Cancer-Associated Fibroblasts), PR (Positive Regulation), R (Regulation), prd (production), MM (Molecular Mediator), MBP (Macromolecule Biosynthetic Process), MMP (Macromolecule Metabolic Process), CR (Cellular Response), env/tal (environmental), RSP (receptor signaling pathway), SP (signaling pathway), resp. (response), ext. (external), and If-M (interferon-mediated).

    Article Snippet: The TRAF3 coding sequence was amplified from a pCMV6-TRAF3-GFP (RG210417, Origene, Rockville, MD, USA) vector and cloned into pLenti-EF1a-GFP-2A-Puro (LV067, ABM Inc, Richmond, BC, Canada).

    Techniques: Expressing, Derivative Assay, Quantitative Proteomics, Immunopeptidomics, Functional Assay

    TRAF3 expression in cancer cells affects PBMC subpopulations and cytokine expression. ( a ) FACs analysis of PBMCs co-cultured with MCF7-TRAF3 cells indicates the downregulation of the CD25+CD127low (Tregs) subpopulation of CD4+ T cells. ( b ) FACS analysis of PBMCs co-cultured with MCF7-TRAF3 cells indicates the upregulation of the CD56+CD16- subpopulation of NK-cells. ( c ) Diagrams depicting absolute quantification of IFN-γ, TNF-α and IL-10 in the supernatants of co-cultured PBMCs/MCF7-TRAF3 cells. ( d ) FACs analysis for live/dead MCF-7 breast cancer cells co-cultured with PBMCs depicting a shift from alive to dead cells in the MCF7-TRAF3 cell population in comparison to MCF7-control cells. ( e ) IHC stain for PD-L1 (CD274) on MCF7-control and MCF7-TRAF3. Arrowheads depict PD-L1 expression only on MCF7-control cells. ( f ) Schematic illustration of a proposed model of TRAF3 action in breast cancer epithelial cells and on the surrounding tumor microenvironmental cells.

    Journal: International Journal of Molecular Sciences

    Article Title: Dual Role of Cancer Epithelial-Specific TRAF3 in Regulating Breast Cancer Cell Survival and Lymphocyte Activity

    doi: 10.3390/ijms27104414

    Figure Lengend Snippet: TRAF3 expression in cancer cells affects PBMC subpopulations and cytokine expression. ( a ) FACs analysis of PBMCs co-cultured with MCF7-TRAF3 cells indicates the downregulation of the CD25+CD127low (Tregs) subpopulation of CD4+ T cells. ( b ) FACS analysis of PBMCs co-cultured with MCF7-TRAF3 cells indicates the upregulation of the CD56+CD16- subpopulation of NK-cells. ( c ) Diagrams depicting absolute quantification of IFN-γ, TNF-α and IL-10 in the supernatants of co-cultured PBMCs/MCF7-TRAF3 cells. ( d ) FACs analysis for live/dead MCF-7 breast cancer cells co-cultured with PBMCs depicting a shift from alive to dead cells in the MCF7-TRAF3 cell population in comparison to MCF7-control cells. ( e ) IHC stain for PD-L1 (CD274) on MCF7-control and MCF7-TRAF3. Arrowheads depict PD-L1 expression only on MCF7-control cells. ( f ) Schematic illustration of a proposed model of TRAF3 action in breast cancer epithelial cells and on the surrounding tumor microenvironmental cells.

    Article Snippet: The TRAF3 coding sequence was amplified from a pCMV6-TRAF3-GFP (RG210417, Origene, Rockville, MD, USA) vector and cloned into pLenti-EF1a-GFP-2A-Puro (LV067, ABM Inc, Richmond, BC, Canada).

    Techniques: Expressing, Cell Culture, Quantitative Proteomics, Comparison, Control, Staining