Review



romrgfp his6 synthetic coding sequences  (Twist Bioscience)


Bioz Verified Symbol Twist Bioscience is a verified supplier
Bioz Manufacturer Symbol Twist Bioscience manufactures this product  
  • Logo
  • About
  • News
  • Press Release
  • Team
  • Advisors
  • Partners
  • Contact
  • Bioz Stars
  • Bioz vStars
  • 86

    Structured Review

    Twist Bioscience romrgfp his6 synthetic coding sequences
    Romrgfp His6 Synthetic 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/pet28a/pm42297786-293-7-18
    Average 86 stars, based on 1 article reviews
    romrgfp his6 synthetic coding sequences - by Bioz Stars, 2026-10
    86/100 stars

    Images

    Related Articles

    Isolation:

    Article Title: Machine learning-driven optimization of specific, compact, and efficient base editors via single-round diversification.
    Article Snippet: .. The digests were then pooled and fragments from 75 to 300 bp, representing approximately half of all the digestion products with no fragment being > 65% of the size of the initial synthesis product, were isolated via gel electrophoresis and assembled via polymerase chain reaction (PCR) into full-length deaminase constructs, which were isolated via gel electrophoresis and cloned into acceptor pET28 vectors synthesized by Twist Biosciences. .. These starting pools then individually underwent DNA shuffling [ 34 ] by being separately digested with eight different four-base-pair restriction enzymes (AluI, HaeIII, HhaI, HinfI, HpaII, MboI, RsaI, and TaqI) from New England Biolabs according to the manufacturer’s specifications ( Supplementary Fig. S6 ).

    Nucleic Acid Electrophoresis:

    Article Title: Machine learning-driven optimization of specific, compact, and efficient base editors via single-round diversification.
    Article Snippet: .. The digests were then pooled and fragments from 75 to 300 bp, representing approximately half of all the digestion products with no fragment being > 65% of the size of the initial synthesis product, were isolated via gel electrophoresis and assembled via polymerase chain reaction (PCR) into full-length deaminase constructs, which were isolated via gel electrophoresis and cloned into acceptor pET28 vectors synthesized by Twist Biosciences. .. These starting pools then individually underwent DNA shuffling [ 34 ] by being separately digested with eight different four-base-pair restriction enzymes (AluI, HaeIII, HhaI, HinfI, HpaII, MboI, RsaI, and TaqI) from New England Biolabs according to the manufacturer’s specifications ( Supplementary Fig. S6 ).

    Polymerase Chain Reaction:

    Article Title: Machine learning-driven optimization of specific, compact, and efficient base editors via single-round diversification.
    Article Snippet: .. The digests were then pooled and fragments from 75 to 300 bp, representing approximately half of all the digestion products with no fragment being > 65% of the size of the initial synthesis product, were isolated via gel electrophoresis and assembled via polymerase chain reaction (PCR) into full-length deaminase constructs, which were isolated via gel electrophoresis and cloned into acceptor pET28 vectors synthesized by Twist Biosciences. .. These starting pools then individually underwent DNA shuffling [ 34 ] by being separately digested with eight different four-base-pair restriction enzymes (AluI, HaeIII, HhaI, HinfI, HpaII, MboI, RsaI, and TaqI) from New England Biolabs according to the manufacturer’s specifications ( Supplementary Fig. S6 ).

    Construct:

    Article Title: Machine learning-driven optimization of specific, compact, and efficient base editors via single-round diversification.
    Article Snippet: .. The digests were then pooled and fragments from 75 to 300 bp, representing approximately half of all the digestion products with no fragment being > 65% of the size of the initial synthesis product, were isolated via gel electrophoresis and assembled via polymerase chain reaction (PCR) into full-length deaminase constructs, which were isolated via gel electrophoresis and cloned into acceptor pET28 vectors synthesized by Twist Biosciences. .. These starting pools then individually underwent DNA shuffling [ 34 ] by being separately digested with eight different four-base-pair restriction enzymes (AluI, HaeIII, HhaI, HinfI, HpaII, MboI, RsaI, and TaqI) from New England Biolabs according to the manufacturer’s specifications ( Supplementary Fig. S6 ).

    Clone Assay:

    Article Title: Machine learning-driven optimization of specific, compact, and efficient base editors via single-round diversification.
    Article Snippet: .. The digests were then pooled and fragments from 75 to 300 bp, representing approximately half of all the digestion products with no fragment being > 65% of the size of the initial synthesis product, were isolated via gel electrophoresis and assembled via polymerase chain reaction (PCR) into full-length deaminase constructs, which were isolated via gel electrophoresis and cloned into acceptor pET28 vectors synthesized by Twist Biosciences. .. These starting pools then individually underwent DNA shuffling [ 34 ] by being separately digested with eight different four-base-pair restriction enzymes (AluI, HaeIII, HhaI, HinfI, HpaII, MboI, RsaI, and TaqI) from New England Biolabs according to the manufacturer’s specifications ( Supplementary Fig. S6 ).

    Article Title: Cell polarity control by an unconventional G-protein complex in bacteria.
    Article Snippet: Fractions containing the protein were pooled, concentrated, dialysed overnight in Buffer D (Buffer A without imidazole) and stored at -80°C in Buffer D. Protein purity was analyzed by SDS-PAGE, and protein concentrations were quantified using NanoDrop (Thermo Scientific). .. - Expression and purification of RomR-His6 and RomRGFP-His6 Synthetic coding sequences of RomR and RomRGFP were obtained from Twist Bioscience, cloned in a modified pET28 vector for expression of C-terminal hexa-histidine tagged proteins. .. - Expression and purification of RomR-His6 and RomRGFP-His6 Synthetic coding sequences of RomR and RomRGFP were obtained from Twist Bioscience, cloned in a modified pET28 vector for expression of C-terminal hexa-histidine tagged proteins.

    Article Title: Large-scale discovery, analysis and design of protein energy landscapes.
    Article Snippet: .. The DNA sequences were codon-optimized for E. coli and cloned into pET-28a(+) (thrombin cleavage site) from Twist Biosciences or pET-28a(+)-TEV from GenScript. ..

    Article Title: Nucleoprotein and glycoprotein based serological assays for detection of Marburg virus infections
    Article Snippet: .. These sequences were codon-optimised for bacterial expression and cloned into pET28a by Twist Bioscience. ..

    Synthesized:

    Article Title: Machine learning-driven optimization of specific, compact, and efficient base editors via single-round diversification.
    Article Snippet: .. The digests were then pooled and fragments from 75 to 300 bp, representing approximately half of all the digestion products with no fragment being > 65% of the size of the initial synthesis product, were isolated via gel electrophoresis and assembled via polymerase chain reaction (PCR) into full-length deaminase constructs, which were isolated via gel electrophoresis and cloned into acceptor pET28 vectors synthesized by Twist Biosciences. .. These starting pools then individually underwent DNA shuffling [ 34 ] by being separately digested with eight different four-base-pair restriction enzymes (AluI, HaeIII, HhaI, HinfI, HpaII, MboI, RsaI, and TaqI) from New England Biolabs according to the manufacturer’s specifications ( Supplementary Fig. S6 ).

    Article Title: Structural basis of iron piracy by human gut Bacteroides
    Article Snippet: .. Similarly, the nucleotide sequence encoding amino acid residues 29-491 of B. viscericola DSM 18177 XusB ( BARVI_05925 ) was synthesized by Twist Bioscience and subcloned into pET28b using NcoI and XhoI restriction sites. ..

    Article Title: Structural analysis of de novo designed binders targeting the closed state of HSP90
    Article Snippet: .. For the 31 selected binders, genes were synthesized in pET28a vector by TwistBioscience. .. For the 31 selected binders, genes were synthesized in pET28a vector by TwistBioscience.

    other:

    Article Title: De novo and scaffold-based design of GDF15 binders for cancer cachexia diagnostics and therapeutics.
    Article Snippet: The gene encoding mature human GDF15 (residues 198–308; GenBank accession no. 9518) was inserted into the NotI and XhoI sites of a modified pcDNA3.4 vector (#A14697, Invitrogen) containing an N-terminal Twin-Strep tag followed by a thrombin cleavage sequence.

    Expressing:

    Article Title: Cell polarity control by an unconventional G-protein complex in bacteria.
    Article Snippet: Fractions containing the protein were pooled, concentrated, dialysed overnight in Buffer D (Buffer A without imidazole) and stored at -80°C in Buffer D. Protein purity was analyzed by SDS-PAGE, and protein concentrations were quantified using NanoDrop (Thermo Scientific). .. - Expression and purification of RomR-His6 and RomRGFP-His6 Synthetic coding sequences of RomR and RomRGFP were obtained from Twist Bioscience, cloned in a modified pET28 vector for expression of C-terminal hexa-histidine tagged proteins. .. - Expression and purification of RomR-His6 and RomRGFP-His6 Synthetic coding sequences of RomR and RomRGFP were obtained from Twist Bioscience, cloned in a modified pET28 vector for expression of C-terminal hexa-histidine tagged proteins.

    Article Title: Nucleoprotein and glycoprotein based serological assays for detection of Marburg virus infections
    Article Snippet: .. These sequences were codon-optimised for bacterial expression and cloned into pET28a by Twist Bioscience. ..

    Purification:

    Article Title: Cell polarity control by an unconventional G-protein complex in bacteria.
    Article Snippet: Fractions containing the protein were pooled, concentrated, dialysed overnight in Buffer D (Buffer A without imidazole) and stored at -80°C in Buffer D. Protein purity was analyzed by SDS-PAGE, and protein concentrations were quantified using NanoDrop (Thermo Scientific). .. - Expression and purification of RomR-His6 and RomRGFP-His6 Synthetic coding sequences of RomR and RomRGFP were obtained from Twist Bioscience, cloned in a modified pET28 vector for expression of C-terminal hexa-histidine tagged proteins. .. - Expression and purification of RomR-His6 and RomRGFP-His6 Synthetic coding sequences of RomR and RomRGFP were obtained from Twist Bioscience, cloned in a modified pET28 vector for expression of C-terminal hexa-histidine tagged proteins.

    Modification:

    Article Title: Cell polarity control by an unconventional G-protein complex in bacteria.
    Article Snippet: Fractions containing the protein were pooled, concentrated, dialysed overnight in Buffer D (Buffer A without imidazole) and stored at -80°C in Buffer D. Protein purity was analyzed by SDS-PAGE, and protein concentrations were quantified using NanoDrop (Thermo Scientific). .. - Expression and purification of RomR-His6 and RomRGFP-His6 Synthetic coding sequences of RomR and RomRGFP were obtained from Twist Bioscience, cloned in a modified pET28 vector for expression of C-terminal hexa-histidine tagged proteins. .. - Expression and purification of RomR-His6 and RomRGFP-His6 Synthetic coding sequences of RomR and RomRGFP were obtained from Twist Bioscience, cloned in a modified pET28 vector for expression of C-terminal hexa-histidine tagged proteins.

    Sequencing:

    Article Title: Structural basis of iron piracy by human gut Bacteroides
    Article Snippet: .. Similarly, the nucleotide sequence encoding amino acid residues 29-491 of B. viscericola DSM 18177 XusB ( BARVI_05925 ) was synthesized by Twist Bioscience and subcloned into pET28b using NcoI and XhoI restriction sites. ..

    Plasmid Preparation:

    Article Title: Structural analysis of de novo designed binders targeting the closed state of HSP90
    Article Snippet: .. For the 31 selected binders, genes were synthesized in pET28a vector by TwistBioscience. .. For the 31 selected binders, genes were synthesized in pET28a vector by TwistBioscience.



    Similar Products

    86
    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
      Buy from Supplier

    90
    Addgene inc mouse lin28a coding sequence
    Mouse Lin28a Coding Sequence, supplied by Addgene inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/coding+sequence/pCI+H2B-GFP+(Plasmid+%2392399)/bio_rxiv__64898__2026__10__02__755877-330-8-21
    Average 90 stars, based on 1 article reviews
    mouse lin28a coding sequence - by Bioz Stars, 2026-10
    90/100 stars
      Buy from Supplier

    96
    Addgene inc amino acid coding sequence
    Amino Acid Coding Sequence, supplied by Addgene inc, used in various techniques. Bioz Stars score: 96/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/coding+sequence/lentiCRISPR+v2+(Plasmid+%2352961)/10__1007_slash_s00018___026___06432___6-261-8-19
    Average 96 stars, based on 1 article reviews
    amino acid coding sequence - by Bioz Stars, 2026-10
    96/100 stars
      Buy from Supplier

    86
    Gene Universal Inc full length hip3r 2 coding sequence
    Full Length Hip3r 2 Coding Sequence, supplied by Gene Universal Inc, 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/2+coding+full+hip3r+length+sequence/pm42315508-277-14-33
    Average 86 stars, based on 1 article reviews
    full length hip3r 2 coding sequence - by Bioz Stars, 2026-10
    86/100 stars
      Buy from Supplier

    86
    Twist Bioscience romrgfp his6 synthetic coding sequences
    Romrgfp His6 Synthetic 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/pet28a/pm42297786-293-7-18
    Average 86 stars, based on 1 article reviews
    romrgfp his6 synthetic coding sequences - by Bioz Stars, 2026-10
    86/100 stars
      Buy from Supplier

    94
    OriGene traf3 coding sequence
    <t>TRAF3</t> 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.
    Traf3 Coding Sequence, supplied by OriGene, 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/product/coding+sequence/TRAF3+(NM_145725)+Human+Tagged+ORF+Clone/pmc13207503-129-1-10
    Average 94 stars, based on 1 article reviews
    traf3 coding sequence - by Bioz Stars, 2026-10
    94/100 stars
      Buy from Supplier

    86
    Synthego Inc coding sequence targeting guide rna
    <t>TRAF3</t> 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.
    Coding Sequence Targeting Guide Rna, supplied by Synthego Inc, 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/guide+rna+sequence/bio_rxiv__64898__2026__05__05__723075-352-4-8
    Average 86 stars, based on 1 article reviews
    coding sequence targeting guide rna - by Bioz Stars, 2026-10
    86/100 stars
      Buy from Supplier

    86
    Biotechnology Information mitochondrial protein coding gene sequences
    <t>TRAF3</t> 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.
    Mitochondrial Protein Coding Gene Sequences, supplied by Biotechnology Information, 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+protein/pmc13143415-113-6-26
    Average 86 stars, based on 1 article reviews
    mitochondrial protein coding gene sequences - by Bioz Stars, 2026-10
    86/100 stars
      Buy from Supplier

    86
    Biotechnology Information coding sequence
    <t>TRAF3</t> 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.
    Coding Sequence, supplied by Biotechnology Information, 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/cds+coding+gene+irf1+sequence/pm42055158-133-2-14
    Average 86 stars, based on 1 article reviews
    coding sequence - by Bioz Stars, 2026-10
    86/100 stars
      Buy from Supplier

    86
    Azenta hnrnpk coding sequences
    <t>TRAF3</t> 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.
    Hnrnpk Coding Sequences, supplied by Azenta, 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+hnrnpk+sequences/pm42045261-377-5-17
    Average 86 stars, based on 1 article reviews
    hnrnpk coding sequences - by Bioz Stars, 2026-10
    86/100 stars
      Buy from Supplier

    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