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fasta files with translated cds annotated protein sequences for brugia malayi (Broad Institute Inc)

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Broad Institute Inc fasta files with translated cds annotated protein sequences for brugia malayi

The percent identity levels between human proteins (x-axis) a representative helminth ( B. <t>malayi</t> , A ), protozoan ( P. falciparum , B ) and fungus ( C. albicans , C ) protein (y-axis). Correlations were evaluated by Spearman rank test. Each dot represents one allergen and the squared-dot at the origin of the axis represents allergens that had neither homologues in humans nor in the microbes: (A) n = 222, (B) n = 247 and (C) n = 210 allergens.

Fasta Files With Translated Cds Annotated Protein Sequences For Brugia Malayi, supplied by Broad Institute Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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Average 90 stars, based on 1 article reviews

fasta files with translated cds annotated protein sequences for brugia malayi - by Bioz Stars, 2026-11

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1) Product Images from "Structural Differences between Human Proteins and Aero- and Microbial Allergens Define Allergenicity"

Article Title: Structural Differences between Human Proteins and Aero- and Microbial Allergens Define Allergenicity

Journal: PLoS ONE

doi: 10.1371/journal.pone.0040552

The percent identity levels between human proteins (x-axis) a representative helminth ( B. malayi , A ), protozoan ( P. falciparum , B ) and fungus ( C. albicans , C ) protein (y-axis). Correlations were evaluated by Spearman rank test. Each dot represents one allergen and the squared-dot at the origin of the axis represents allergens that had neither homologues in humans nor in the microbes: (A) n = 222, (B) n = 247 and (C) n = 210 allergens.

Figure Legend Snippet: The percent identity levels between human proteins (x-axis) a representative helminth ( B. malayi , A ), protozoan ( P. falciparum , B ) and fungus ( C. albicans , C ) protein (y-axis). Correlations were evaluated by Spearman rank test. Each dot represents one allergen and the squared-dot at the origin of the axis represents allergens that had neither homologues in humans nor in the microbes: (A) n = 222, (B) n = 247 and (C) n = 210 allergens.

Techniques Used:

other:

Article Title: Structural Differences between Human Proteins and Aero- and Microbial Allergens Define Allergenicity
Article Snippet: Fasta files with translated CDS annotated protein sequences for Brugia malayi , Loa loa and Wuchereria bancrofti (all version 1) were the Broad Institute ( http://www.broadinstitute.org/annotation/genome/filarial_worms/MultiDownloads.html ), Schistosoma mansoni fasta file (version GeneDB v 4.0 h) was Sanger Institute ( ftp://ftp.sanger.ac.uk/pub/pathogens/ ), Plasmodium falciparum (PlasmoDB 6.4) from Plasmodb ( http://plasmodb.org/common/downloads/ ), Trypanosoma cruzi CL Brener (TriTrypDB-2.2) and Leishmania major Friedlin (TriTrypDB-2.2) from Tritrypdb ( http://tritrypdb.org/common/downloads/ ), Toxoplasma gondii ME-49 (ToxoDB 6.0) from Toxobd ( http://toxodb.org/common/downloads/ )

Image Search Results

Mechanism and melting temperature analysis of repressive probes. (A) Schematic of the repressive probe mechanism: qPCR amplification is coupled with a proprietary probe to selectively enrich mutant alleles by blocking wild‐type (WT) DNA amplification. (B) Mutation types covered by the switch region of the ESR1 L536H probe. (C, D) Melting curve analysis of the L536H probe shows clear peak differentiation between mutant (61°C, orange) and WT templates (65°C, green). Mut, mutation. (E) Iterative optimization of the E380Q probe design. Version 1: 46°C versus 51°C; Version 2: 48°C versus 53°C; Version 3: 64°C versus 66°C; Version 4: 56°C versus 60°C for mutant versus WT. (F, G) Increasing the proportion of E380Q and L536H probes in the PCR system enhanced the relative amplification of the corresponding mutant sequences. F, forward primer; R, reverse primer; S, switch‐blocker.

Journal: Cancer Innovation

Article Title: A Novel Sensitive Technique to Detect ESR1 Hotspot Mutations in Liquid Biopsy Using Switch‐Blocker–Enhanced Targeted Amplification Coupled With Pyrosequencing

doi: 10.1002/cai2.70054

Figure Lengend Snippet: Mechanism and melting temperature analysis of repressive probes. (A) Schematic of the repressive probe mechanism: qPCR amplification is coupled with a proprietary probe to selectively enrich mutant alleles by blocking wild‐type (WT) DNA amplification. (B) Mutation types covered by the switch region of the ESR1 L536H probe. (C, D) Melting curve analysis of the L536H probe shows clear peak differentiation between mutant (61°C, orange) and WT templates (65°C, green). Mut, mutation. (E) Iterative optimization of the E380Q probe design. Version 1: 46°C versus 51°C; Version 2: 48°C versus 53°C; Version 3: 64°C versus 66°C; Version 4: 56°C versus 60°C for mutant versus WT. (F, G) Increasing the proportion of E380Q and L536H probes in the PCR system enhanced the relative amplification of the corresponding mutant sequences. F, forward primer; R, reverse primer; S, switch‐blocker.

Article Snippet: The wild‐type ESR1 CDS sequence and the 1607T>A mutant sequence were synthesized by GENEWIZ (Suzhou, China).

Techniques: Amplification, Mutagenesis, Blocking Assay, DNA Amplification

The repressive probe targeting ESR1 CDS 1607 shows strong amplification capability for low‐abundance mutations. (A) Amplification performance of the repressive probe in samples with high mutant allele frequency. (B) Amplification performance of the repressive probe in detecting low‐level, rare mutations.

Journal: Cancer Innovation

Article Title: A Novel Sensitive Technique to Detect ESR1 Hotspot Mutations in Liquid Biopsy Using Switch‐Blocker–Enhanced Targeted Amplification Coupled With Pyrosequencing

doi: 10.1002/cai2.70054

Figure Lengend Snippet: The repressive probe targeting ESR1 CDS 1607 shows strong amplification capability for low‐abundance mutations. (A) Amplification performance of the repressive probe in samples with high mutant allele frequency. (B) Amplification performance of the repressive probe in detecting low‐level, rare mutations.

Article Snippet: The wild‐type ESR1 CDS sequence and the 1607T>A mutant sequence were synthesized by GENEWIZ (Suzhou, China).

Techniques: Amplification, Mutagenesis

A . Feature fusion process. Amino acid (AA) vectors and codon vectors are extracted from protein and CDS sequences using the protein language model ESM2 (650M) and the RNA language model mRNA-FM, respectively. The two sets of vectors are combined by weighted summation to generate merged vectors representing integrated protein and CDS features. B . Training of the CodonNAT module. CDSs ranked in the top 10% by the codon similarity index (CSI) within the host genome are first selected. A masked language modeling task is then constructed by labeling 15% of codons to learn host-specific codon context features. A Naturalness score is defined as the geometric mean of the predicted probabilities for the labeled codons and is used to quantify the compatibility between the input CDS and the codon context of the host genome. C . Training of the CodonEXP module. Each CDS is assigned a binary label indicating High or Low protein expression. CodonEXP predicts the probability of high protein expression given a CDS. A Fitness score is defined as the product of the Naturalness score and the predicted probability of high protein expression and is used to select the optimal CDS. D . Two-step generation of optimized CDSs. In the CDS initialization step, the CDS corresponding to the input protein sequence is fully masked at the codon level, after which CodonNAT predicts the most probable synonymous codon for each AA. This step, termed CodonIni, produces an initial CDS for further optimization. In the second step, the CDS is optimized using either a genetic algorithm (CodonGa) or hallucination design (CodonHa). Optimization proceeds through multiple iterations until the Fitness score reaches a plateau, resulting in a final CDS that balances compatibility with host codon usage and a high probability of protein expression.

Journal: bioRxiv

Article Title: HalluCodon enables species-specific codon optimization using multimodal language models

doi: 10.64898/2026.03.31.715573

Figure Lengend Snippet: A . Feature fusion process. Amino acid (AA) vectors and codon vectors are extracted from protein and CDS sequences using the protein language model ESM2 (650M) and the RNA language model mRNA-FM, respectively. The two sets of vectors are combined by weighted summation to generate merged vectors representing integrated protein and CDS features. B . Training of the CodonNAT module. CDSs ranked in the top 10% by the codon similarity index (CSI) within the host genome are first selected. A masked language modeling task is then constructed by labeling 15% of codons to learn host-specific codon context features. A Naturalness score is defined as the geometric mean of the predicted probabilities for the labeled codons and is used to quantify the compatibility between the input CDS and the codon context of the host genome. C . Training of the CodonEXP module. Each CDS is assigned a binary label indicating High or Low protein expression. CodonEXP predicts the probability of high protein expression given a CDS. A Fitness score is defined as the product of the Naturalness score and the predicted probability of high protein expression and is used to select the optimal CDS. D . Two-step generation of optimized CDSs. In the CDS initialization step, the CDS corresponding to the input protein sequence is fully masked at the codon level, after which CodonNAT predicts the most probable synonymous codon for each AA. This step, termed CodonIni, produces an initial CDS for further optimization. In the second step, the CDS is optimized using either a genetic algorithm (CodonGa) or hallucination design (CodonHa). Optimization proceeds through multiple iterations until the Fitness score reaches a plateau, resulting in a final CDS that balances compatibility with host codon usage and a high probability of protein expression.

Article Snippet: Genewiz produced CDS sequences with an average CAI of 0.98, indicating that its algorithm also relies largely on codon usage frequency.

Techniques: Construct, Labeling, Expressing, Sequencing

a, b . Fitness scores increase and reach plateaus during iterative optimization of the DsRed2 CDS using the CodonGa (a) and CodonHa (b) algorithms. c, d . GC3 content increases and reaches plateaus during iterative optimization of the DsRed2 CDS using the CodonGa (c) and CodonHa (d) algorithms. Green dots represent the Fitness score or GC3 content of each optimized CDS throughout the iterative process. The red line shows the overall trend of Fitness score or GC3 content, fitted using locally weighted scatterplot smoothing (LOESS). e, f . Clustered patterns of CAI (e) and GC3 content (f) calculated from the optimized CDSs of the fifteen benchmark proteins generated by the six methods. CodonTrans denotes the CodonTransformer method. g, h . Mean Jaccard index (g) and mean sequence similarity (h) among optimized CDSs of the fifteen benchmark proteins generated by different methods.

Journal: bioRxiv

Article Title: HalluCodon enables species-specific codon optimization using multimodal language models

doi: 10.64898/2026.03.31.715573

Figure Lengend Snippet: a, b . Fitness scores increase and reach plateaus during iterative optimization of the DsRed2 CDS using the CodonGa (a) and CodonHa (b) algorithms. c, d . GC3 content increases and reaches plateaus during iterative optimization of the DsRed2 CDS using the CodonGa (c) and CodonHa (d) algorithms. Green dots represent the Fitness score or GC3 content of each optimized CDS throughout the iterative process. The red line shows the overall trend of Fitness score or GC3 content, fitted using locally weighted scatterplot smoothing (LOESS). e, f . Clustered patterns of CAI (e) and GC3 content (f) calculated from the optimized CDSs of the fifteen benchmark proteins generated by the six methods. CodonTrans denotes the CodonTransformer method. g, h . Mean Jaccard index (g) and mean sequence similarity (h) among optimized CDSs of the fifteen benchmark proteins generated by different methods.

Article Snippet: Genewiz produced CDS sequences with an average CAI of 0.98, indicating that its algorithm also relies largely on codon usage frequency.

Techniques: Generated, Sequencing

Poxin transgene inhibits DNA sensing-induced innate immune response. A. Schematic of cloning process. B-G. Cells were transfected with plasmid DNA (pDNA) using TransIT-2020. B. 2.5 μg and 7.5 μg of pDNA encoding Poxin or mutant Poxin (mtPoxin) were transfected into 293T cells, respectively, and FLAG-tagged proteins were detected. C. Activation of STING, TBK1, and IRF3 was analyzed by western blotting. Quantitative analysis of p-IRF3 expression level is shown. D. H151 was pre-treated 1 h before pDNA transfection, and protein expression levels were assessed after 24 h. E. Cells were transfected with pEGFP-N1, and protein expression levels were detected. F. mRNA levels of IFNB1 and ISG15 were analyzed by RT-qPCR (n = 3). G. IFN-β secretion levels were quantitatively analyzed using ELISA. (Representative western blots are shown.).

Journal: Journal of Advanced Research

Article Title: Enhancement of NK cell activity via DNA-sensing inhibition by Poxin transgene

doi: 10.1016/j.jare.2025.05.058

Figure Lengend Snippet: Poxin transgene inhibits DNA sensing-induced innate immune response. A. Schematic of cloning process. B-G. Cells were transfected with plasmid DNA (pDNA) using TransIT-2020. B. 2.5 μg and 7.5 μg of pDNA encoding Poxin or mutant Poxin (mtPoxin) were transfected into 293T cells, respectively, and FLAG-tagged proteins were detected. C. Activation of STING, TBK1, and IRF3 was analyzed by western blotting. Quantitative analysis of p-IRF3 expression level is shown. D. H151 was pre-treated 1 h before pDNA transfection, and protein expression levels were assessed after 24 h. E. Cells were transfected with pEGFP-N1, and protein expression levels were detected. F. mRNA levels of IFNB1 and ISG15 were analyzed by RT-qPCR (n = 3). G. IFN-β secretion levels were quantitatively analyzed using ELISA. (Representative western blots are shown.).

Article Snippet: The Poxin coding sequence (CDS) fragment was synthesized by Bioneer, and the H17A mutant Poxin (mtPoxin) fragment was generated via overlapping PCR.

Techniques: Cloning, Transfection, Plasmid Preparation, Mutagenesis, Activation Assay, Western Blot, Expressing, Quantitative RT-PCR, Enzyme-linked Immunosorbent Assay

Poxin protects NK-92 cells from pDNA transfection-induced innate immunity. A. Cells were transfected by electroporation with 10 μg pDNA, and mRNA dynamics were analyzed by RT-qPCR (n = 3). B. IFN-β secretion levels were quantitatively analyzed using ELISA. C. Expression levels of innate immune signaling proteins were detected by western blotting. (Representative data shown). D. Quantitative analysis of p-STING and p-TBK1 expression levels.

Journal: Journal of Advanced Research

Article Title: Enhancement of NK cell activity via DNA-sensing inhibition by Poxin transgene

doi: 10.1016/j.jare.2025.05.058

Figure Lengend Snippet: Poxin protects NK-92 cells from pDNA transfection-induced innate immunity. A. Cells were transfected by electroporation with 10 μg pDNA, and mRNA dynamics were analyzed by RT-qPCR (n = 3). B. IFN-β secretion levels were quantitatively analyzed using ELISA. C. Expression levels of innate immune signaling proteins were detected by western blotting. (Representative data shown). D. Quantitative analysis of p-STING and p-TBK1 expression levels.

Article Snippet: The Poxin coding sequence (CDS) fragment was synthesized by Bioneer, and the H17A mutant Poxin (mtPoxin) fragment was generated via overlapping PCR.

Techniques: Transfection, Electroporation, Quantitative RT-PCR, Enzyme-linked Immunosorbent Assay, Expressing, Western Blot

Poxin prolongs NK-92 cell survival and activity by reducing irradiation-induced innate immune activation. A. Cell survival rate was measured by FACS at specified times after irradiation. B. Cell proliferation rate was quantified by counting live cells. C. Cytotoxicity of effector cells against K562 cells was measured 1- and 2-days post-irradiation over a 4-hour period. D. Protein expression levels were detected by western blotting. (Representative data shown). E. Quantitative analysis of p-IRF3 expression level.

Journal: Journal of Advanced Research

Article Title: Enhancement of NK cell activity via DNA-sensing inhibition by Poxin transgene

doi: 10.1016/j.jare.2025.05.058

Figure Lengend Snippet: Poxin prolongs NK-92 cell survival and activity by reducing irradiation-induced innate immune activation. A. Cell survival rate was measured by FACS at specified times after irradiation. B. Cell proliferation rate was quantified by counting live cells. C. Cytotoxicity of effector cells against K562 cells was measured 1- and 2-days post-irradiation over a 4-hour period. D. Protein expression levels were detected by western blotting. (Representative data shown). E. Quantitative analysis of p-IRF3 expression level.

Article Snippet: The Poxin coding sequence (CDS) fragment was synthesized by Bioneer, and the H17A mutant Poxin (mtPoxin) fragment was generated via overlapping PCR.

Techniques: Activity Assay, Irradiation, Activation Assay, Expressing, Western Blot

Poxin transgene enhances the cytotoxic activity of NK-92 cells. A. Cytotoxicity of NK-92 cells with and without Poxin expression against K562 cells was measured over 4 h. B-C. Cells were co-cultured with target K562 cells for indicated times. B. Apoptosis levels in effector cells were assessed by FACS. C. Protein expression levels were detected by western blotting. (Representative data shown). D-G. Cells were harvested after 24 h in culture, and extracted total RNA was analyzed by RNA sequencing. (C = mock cells; P = Pox-NK-92 cells; n = 3). D. Heatmap. E. GO analysis. F. Differentially expressed genes in NK-92 and Pox-NK-92 groups were categorized by function. G. Top 10 upstream transcription factors and target genes were analyzed by network analysis. H. NK cell activation pathway was analyzed by western blotting. (Representative data shown). I. Quantitative analysis of Perforin expression level. J. mRNA levels of cytotoxic factors were analyzed by RT-qPCR (n = 3).

Journal: Journal of Advanced Research

Article Title: Enhancement of NK cell activity via DNA-sensing inhibition by Poxin transgene

doi: 10.1016/j.jare.2025.05.058

Figure Lengend Snippet: Poxin transgene enhances the cytotoxic activity of NK-92 cells. A. Cytotoxicity of NK-92 cells with and without Poxin expression against K562 cells was measured over 4 h. B-C. Cells were co-cultured with target K562 cells for indicated times. B. Apoptosis levels in effector cells were assessed by FACS. C. Protein expression levels were detected by western blotting. (Representative data shown). D-G. Cells were harvested after 24 h in culture, and extracted total RNA was analyzed by RNA sequencing. (C = mock cells; P = Pox-NK-92 cells; n = 3). D. Heatmap. E. GO analysis. F. Differentially expressed genes in NK-92 and Pox-NK-92 groups were categorized by function. G. Top 10 upstream transcription factors and target genes were analyzed by network analysis. H. NK cell activation pathway was analyzed by western blotting. (Representative data shown). I. Quantitative analysis of Perforin expression level. J. mRNA levels of cytotoxic factors were analyzed by RT-qPCR (n = 3).

Article Snippet: The Poxin coding sequence (CDS) fragment was synthesized by Bioneer, and the H17A mutant Poxin (mtPoxin) fragment was generated via overlapping PCR.

Techniques: Activity Assay, Expressing, Cell Culture, Western Blot, RNA Sequencing, Activation Assay, Quantitative RT-PCR

Poxin enhances the anti-tumor capacity of NK-92 cells. A. Experimental scheme for mouse study (n = 4). B. Ventral bioluminescence (BLI) images following injection of NK92 or Pox-NK-92 cells. C. Quantification and statistical analysis (n = 4). D. Survival curves post-injection of K562-Luc cells. Data are presented as mean ± SEM. Mouse experiments were conducted independently twice, yielding consistent results.

Journal: Journal of Advanced Research

Article Title: Enhancement of NK cell activity via DNA-sensing inhibition by Poxin transgene

doi: 10.1016/j.jare.2025.05.058

Figure Lengend Snippet: Poxin enhances the anti-tumor capacity of NK-92 cells. A. Experimental scheme for mouse study (n = 4). B. Ventral bioluminescence (BLI) images following injection of NK92 or Pox-NK-92 cells. C. Quantification and statistical analysis (n = 4). D. Survival curves post-injection of K562-Luc cells. Data are presented as mean ± SEM. Mouse experiments were conducted independently twice, yielding consistent results.

Article Snippet: The Poxin coding sequence (CDS) fragment was synthesized by Bioneer, and the H17A mutant Poxin (mtPoxin) fragment was generated via overlapping PCR.

Techniques: Injection

Poxin improves the anti-tumor efficacy of PD-L1-CAR-NK cells against H460 lung cancer. A. PD-L1-CAR expression levels in NK-92 cells. Abbreviations: TM = Transmembrane; Co-stim=Co-stimulatory; SD=Signaling domain. B. Cytotoxicity of CAR-NK-92 cells with or without Poxin expression against K562 and H460 cells, measured over 2 h. C. Experimental scheme for the H460 xenograft mouse model (n = 8). D. Tumor sizes were measured using digital calipers at the indicated time points. E. Representative tumor images from both groups at 28 days post-H460 inoculation. F. Tumor volumes were calculated. Error bars in panels B and D represent mean ± SEM. Mouse experiments were independently repeated twice with similar outcomes. Statistical significance was assessed using Two-way ANOVA (D) or Student's t -test (F).

Journal: Journal of Advanced Research

Article Title: Enhancement of NK cell activity via DNA-sensing inhibition by Poxin transgene

doi: 10.1016/j.jare.2025.05.058

Figure Lengend Snippet: Poxin improves the anti-tumor efficacy of PD-L1-CAR-NK cells against H460 lung cancer. A. PD-L1-CAR expression levels in NK-92 cells. Abbreviations: TM = Transmembrane; Co-stim=Co-stimulatory; SD=Signaling domain. B. Cytotoxicity of CAR-NK-92 cells with or without Poxin expression against K562 and H460 cells, measured over 2 h. C. Experimental scheme for the H460 xenograft mouse model (n = 8). D. Tumor sizes were measured using digital calipers at the indicated time points. E. Representative tumor images from both groups at 28 days post-H460 inoculation. F. Tumor volumes were calculated. Error bars in panels B and D represent mean ± SEM. Mouse experiments were independently repeated twice with similar outcomes. Statistical significance was assessed using Two-way ANOVA (D) or Student's t -test (F).

Article Snippet: The Poxin coding sequence (CDS) fragment was synthesized by Bioneer, and the H17A mutant Poxin (mtPoxin) fragment was generated via overlapping PCR.

Techniques: Expressing

Expression of IRF1 and Type I interferon pathway-related proteins in gastric cancer cells. A : Simulation of type I interferon response in gastric cancer cells by incubating with interferon, showing increased expression of interferon pathway protein IRF1. B : Protein expression in gastric cancer cells after transfection with pcDNA3.1(+) -IRF1-HA.1 C : Protein expression in gastric cancer cells after transfection with siRNA-IRF1. D : Changes in the expression of interferon pathway proteins after overexpression or inhibition of IRF1 in gastric cancer cells

Journal: Cellular Oncology (Dordrecht, Netherlands)

Article Title: IRF1 suppresses gastric tumorigenesis via dual PI3K/AKT-ERK pathway modulation and functional antagonism of oncogenic MX2

doi: 10.1007/s13402-025-01134-w

Figure Lengend Snippet: Expression of IRF1 and Type I interferon pathway-related proteins in gastric cancer cells. A : Simulation of type I interferon response in gastric cancer cells by incubating with interferon, showing increased expression of interferon pathway protein IRF1. B : Protein expression in gastric cancer cells after transfection with pcDNA3.1(+) -IRF1-HA.1 C : Protein expression in gastric cancer cells after transfection with siRNA-IRF1. D : Changes in the expression of interferon pathway proteins after overexpression or inhibition of IRF1 in gastric cancer cells

Article Snippet: The IRF1 gene coding sequence (CDS) was retrieved from the National Center for Biotechnology Information (NCBI), selecting the longest transcript.

Techniques: Expressing, Transfection, Over Expression, Inhibition

Expression characteristics and clinical relevance of IRF1 in gastric cancer tissues. A : IRF1 expression is significantly higher in gastric cancer tissues compared to adjacent normal tissues ( P < 0.001). B : Paired analysis shows that IRF1 expression is significantly upregulated in gastric cancer tissues compared to matched adjacent tissues ( P = 0.002). C : Survival analysis indicates that high IRF1 expression is associated with a relatively better prognosis in gastric cancer patients (Log-rank P = 0.030). D : Representative immunohistochemistry (IHC) images showing high and low IRF1 expression in tumor tissues. E : Differential expression analysis confirms that IRF1 is significantly upregulated in tumor tissues ( P = 0.021). F : Paired analysis of tumor and adjacent normal tissues demonstrates significantly higher IRF1 expression in tumors ( P < 0.001). G : Survival analysis further supports that high IRF1 expression correlates with a better prognosis in gastric cancer patients (Log-rank P = 0.010). * P < 0.05, ** P < 0.01, *** P < 0.001, *** P < 0.0001

Journal: Cellular Oncology (Dordrecht, Netherlands)

Article Title: IRF1 suppresses gastric tumorigenesis via dual PI3K/AKT-ERK pathway modulation and functional antagonism of oncogenic MX2

doi: 10.1007/s13402-025-01134-w

Figure Lengend Snippet: Expression characteristics and clinical relevance of IRF1 in gastric cancer tissues. A : IRF1 expression is significantly higher in gastric cancer tissues compared to adjacent normal tissues ( P < 0.001). B : Paired analysis shows that IRF1 expression is significantly upregulated in gastric cancer tissues compared to matched adjacent tissues ( P = 0.002). C : Survival analysis indicates that high IRF1 expression is associated with a relatively better prognosis in gastric cancer patients (Log-rank P = 0.030). D : Representative immunohistochemistry (IHC) images showing high and low IRF1 expression in tumor tissues. E : Differential expression analysis confirms that IRF1 is significantly upregulated in tumor tissues ( P = 0.021). F : Paired analysis of tumor and adjacent normal tissues demonstrates significantly higher IRF1 expression in tumors ( P < 0.001). G : Survival analysis further supports that high IRF1 expression correlates with a better prognosis in gastric cancer patients (Log-rank P = 0.010). * P < 0.05, ** P < 0.01, *** P < 0.001, *** P < 0.0001

Article Snippet: The IRF1 gene coding sequence (CDS) was retrieved from the National Center for Biotechnology Information (NCBI), selecting the longest transcript.

Techniques: Expressing, Immunohistochemistry, Quantitative Proteomics

Effects of IRF1 expression on gastric cancer cell function. A - B : CCK8 cytotoxicity assay showing inhibition of AGS and BGC-823 cell proliferation after transfection with IRF1-HA overexpression plasmid. C - D : Transwell migration and invasion assay showing suppression of AGS and BGC-823 cell migration and invasion 48 h after transfection with IRF1-HA overexpression plasmid. E - F : CCK8 cytotoxicity assay showing promotion of AGS and BGC-823 cell proliferation after transfection with siRNA-IRF1. G - H : Transwell migration and invasion assay showing enhanced migration and invasion of AGS and BGC-823 cells 48 h after transfection with siRNA-IRF1. I : Flow cytometry apoptosis assay showing increased apoptosis in gastric cancer cells 48 h after Dox-induced IRF1 overexpression in stable cell lines. J : Changes in apoptosis-related protein expression 48 h after Dox-induced IRF1 overexpression in gastric cancer cell stable lines. K : Immunofluorescence localization experiment confirming nuclear localization of IRF1 in gastric cancer cells. Scale bar: 10 μm. * P < 0.05, ** P < 0.01, ** P < 0.001

Journal: Cellular Oncology (Dordrecht, Netherlands)

Article Title: IRF1 suppresses gastric tumorigenesis via dual PI3K/AKT-ERK pathway modulation and functional antagonism of oncogenic MX2

doi: 10.1007/s13402-025-01134-w

Figure Lengend Snippet: Effects of IRF1 expression on gastric cancer cell function. A - B : CCK8 cytotoxicity assay showing inhibition of AGS and BGC-823 cell proliferation after transfection with IRF1-HA overexpression plasmid. C - D : Transwell migration and invasion assay showing suppression of AGS and BGC-823 cell migration and invasion 48 h after transfection with IRF1-HA overexpression plasmid. E - F : CCK8 cytotoxicity assay showing promotion of AGS and BGC-823 cell proliferation after transfection with siRNA-IRF1. G - H : Transwell migration and invasion assay showing enhanced migration and invasion of AGS and BGC-823 cells 48 h after transfection with siRNA-IRF1. I : Flow cytometry apoptosis assay showing increased apoptosis in gastric cancer cells 48 h after Dox-induced IRF1 overexpression in stable cell lines. J : Changes in apoptosis-related protein expression 48 h after Dox-induced IRF1 overexpression in gastric cancer cell stable lines. K : Immunofluorescence localization experiment confirming nuclear localization of IRF1 in gastric cancer cells. Scale bar: 10 μm. * P < 0.05, ** P < 0.01, ** P < 0.001

Article Snippet: The IRF1 gene coding sequence (CDS) was retrieved from the National Center for Biotechnology Information (NCBI), selecting the longest transcript.

Techniques: Expressing, Cell Function Assay, Cytotoxicity Assay, Inhibition, Transfection, Over Expression, Plasmid Preparation, Migration, Invasion Assay, Flow Cytometry, Apoptosis Assay, Stable Transfection, Immunofluorescence

Establishment of an Inducible IRF1 expression nude mouse subcutaneous xenograft and lung metastasis model. A : In vivo experiments show that the tumor volume of the IRF1 overexpression group in nude mouse subcutaneous xenografts is significantly smaller than that of the control group (Mean ± SEM). B : Gross anatomy of subcutaneous xenograft tumors in nude mice. C : HE staining of subcutaneous xenograft tumors (tumor tissues from mouse #1 and #2). D : Immunohistochemistry (IHC) analysis of IRF1 expression in subcutaneous xenograft tumors, showing significant IRF1 overexpression in the Dox (+) group. E : Bioluminescence imaging of nude mice injected via the tail vein with BGC-IRF1-LUC cells at 0, 2, 3, and 4 weeks post-injection. F : Quantification of lung fluorescence intensity in both groups, demonstrating significantly lower fluorescence intensity in the IRF1 overexpression group compared to the control group. G : Gross anatomy of lung tissues in nude mice, showing more metastatic nodules in the control group than in the IRF1 overexpression group. H : HE staining and IRF1-specific IHC staining of lung tissues in nude mice, confirming IRF1 overexpression in the Dox-induced group. Scale bar: 100 μm. * P < 0.05, ** P < 0.01, *** P < 0.001

Journal: Cellular Oncology (Dordrecht, Netherlands)

Article Title: IRF1 suppresses gastric tumorigenesis via dual PI3K/AKT-ERK pathway modulation and functional antagonism of oncogenic MX2

doi: 10.1007/s13402-025-01134-w

Figure Lengend Snippet: Establishment of an Inducible IRF1 expression nude mouse subcutaneous xenograft and lung metastasis model. A : In vivo experiments show that the tumor volume of the IRF1 overexpression group in nude mouse subcutaneous xenografts is significantly smaller than that of the control group (Mean ± SEM). B : Gross anatomy of subcutaneous xenograft tumors in nude mice. C : HE staining of subcutaneous xenograft tumors (tumor tissues from mouse #1 and #2). D : Immunohistochemistry (IHC) analysis of IRF1 expression in subcutaneous xenograft tumors, showing significant IRF1 overexpression in the Dox (+) group. E : Bioluminescence imaging of nude mice injected via the tail vein with BGC-IRF1-LUC cells at 0, 2, 3, and 4 weeks post-injection. F : Quantification of lung fluorescence intensity in both groups, demonstrating significantly lower fluorescence intensity in the IRF1 overexpression group compared to the control group. G : Gross anatomy of lung tissues in nude mice, showing more metastatic nodules in the control group than in the IRF1 overexpression group. H : HE staining and IRF1-specific IHC staining of lung tissues in nude mice, confirming IRF1 overexpression in the Dox-induced group. Scale bar: 100 μm. * P < 0.05, ** P < 0.01, *** P < 0.001

Article Snippet: The IRF1 gene coding sequence (CDS) was retrieved from the National Center for Biotechnology Information (NCBI), selecting the longest transcript.

Techniques: Expressing, In Vivo, Over Expression, Control, Staining, Immunohistochemistry, Imaging, Injection, Fluorescence

Exploration of IRF1-related mechanisms. A : Schematic diagram of the IRF1 protein structure; DBD: DNA binding domain; IAD: IRF-association domain. B : Validation of successful expression of the pcDNA3.1(+)-IRF1Δ1 recombinant plasmid. C : No significant changes in apoptosis-related protein expression after IRF1Δ1 overexpression. D : Overexpression of IRF1 significantly affects PI3K pathway-related proteins, whereas IRF1Δ1 overexpression shows no apparent changes. E : Bidirectional validation of the interaction between IRF1 and MX2 using HA and Flag magnetic beads. F : Immunofluorescence co-localization analysis confirming the nuclear co-expression of IRF1 and MX2

Journal: Cellular Oncology (Dordrecht, Netherlands)

Article Title: IRF1 suppresses gastric tumorigenesis via dual PI3K/AKT-ERK pathway modulation and functional antagonism of oncogenic MX2

doi: 10.1007/s13402-025-01134-w

Figure Lengend Snippet: Exploration of IRF1-related mechanisms. A : Schematic diagram of the IRF1 protein structure; DBD: DNA binding domain; IAD: IRF-association domain. B : Validation of successful expression of the pcDNA3.1(+)-IRF1Δ1 recombinant plasmid. C : No significant changes in apoptosis-related protein expression after IRF1Δ1 overexpression. D : Overexpression of IRF1 significantly affects PI3K pathway-related proteins, whereas IRF1Δ1 overexpression shows no apparent changes. E : Bidirectional validation of the interaction between IRF1 and MX2 using HA and Flag magnetic beads. F : Immunofluorescence co-localization analysis confirming the nuclear co-expression of IRF1 and MX2

Article Snippet: The IRF1 gene coding sequence (CDS) was retrieved from the National Center for Biotechnology Information (NCBI), selecting the longest transcript.

Techniques: Binding Assay, Biomarker Discovery, Expressing, Recombinant, Plasmid Preparation, Over Expression, Magnetic Beads, Immunofluorescence

MX2-related functions in gastric cancer. A : Schematic diagram of MX2 functional domain fragments. B : Co-IP assay validating the interaction between IRF1-HA and MX2-Flag, showing that IRF1 loses interaction with MX2-FlagΔ1. C : Schematic of MX2 site-directed mutations. K131A: GTP-binding defective, unable to enter the nucleus; NLS: nuclear localization signal; BSE: bundle signaling element. D : WB validation of MX2 site-directed mutant overexpression plasmids. E : MX2 overexpression promotes AGS cell migration and invasion. F : MX2 overexpression promotes BGC-823 cell migration and invasion. G : After transfecting MX2 and its mutants into BGC-823 cells and incubating for 48 h, nuclear localization site mutations in MX2 result in the loss of its pro-migratory and pro-invasive effects. H : Immunofluorescence localization of MX2 and its mutants in gastric cancer cells. After transfection with MX2-ΔN or MX2-K131A, MX2 is retained in the cytoplasm, losing its nuclear localization ability. I : WB validation of MX2’s pro-migratory function through EMT pathway analysis. Scale bar: 10 μm. * P < 0.05, ** P < 0.01, *** P < 0.001

Journal: Cellular Oncology (Dordrecht, Netherlands)

Article Title: IRF1 suppresses gastric tumorigenesis via dual PI3K/AKT-ERK pathway modulation and functional antagonism of oncogenic MX2

doi: 10.1007/s13402-025-01134-w

Figure Lengend Snippet: MX2-related functions in gastric cancer. A : Schematic diagram of MX2 functional domain fragments. B : Co-IP assay validating the interaction between IRF1-HA and MX2-Flag, showing that IRF1 loses interaction with MX2-FlagΔ1. C : Schematic of MX2 site-directed mutations. K131A: GTP-binding defective, unable to enter the nucleus; NLS: nuclear localization signal; BSE: bundle signaling element. D : WB validation of MX2 site-directed mutant overexpression plasmids. E : MX2 overexpression promotes AGS cell migration and invasion. F : MX2 overexpression promotes BGC-823 cell migration and invasion. G : After transfecting MX2 and its mutants into BGC-823 cells and incubating for 48 h, nuclear localization site mutations in MX2 result in the loss of its pro-migratory and pro-invasive effects. H : Immunofluorescence localization of MX2 and its mutants in gastric cancer cells. After transfection with MX2-ΔN or MX2-K131A, MX2 is retained in the cytoplasm, losing its nuclear localization ability. I : WB validation of MX2’s pro-migratory function through EMT pathway analysis. Scale bar: 10 μm. * P < 0.05, ** P < 0.01, *** P < 0.001

Article Snippet: The IRF1 gene coding sequence (CDS) was retrieved from the National Center for Biotechnology Information (NCBI), selecting the longest transcript.

Techniques: Functional Assay, Co-Immunoprecipitation Assay, Binding Assay, Biomarker Discovery, Mutagenesis, Over Expression, Migration, Immunofluorescence, Transfection

Functional model of the IRF1-MX2 protein complex

Journal: Cellular Oncology (Dordrecht, Netherlands)

Article Title: IRF1 suppresses gastric tumorigenesis via dual PI3K/AKT-ERK pathway modulation and functional antagonism of oncogenic MX2

doi: 10.1007/s13402-025-01134-w

Figure Lengend Snippet: Functional model of the IRF1-MX2 protein complex

Article Snippet: The IRF1 gene coding sequence (CDS) was retrieved from the National Center for Biotechnology Information (NCBI), selecting the longest transcript.

Techniques: Functional Assay

Review

fasta files with translated cds annotated protein sequences for brugia malayi (Broad Institute Inc)

Structured Review

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