Journal: Discover oncology

Article Title: Increased nuclear expression of DNA damage inducible transcript 4 can serve as a potential prognostic biomarker in patients with gliomas: a study based on data mining and experimental tools.

doi: 10.1007/s12672-025-01865-0

Figure Lengend Snippet: Fig. 1 Genetic alteration analysis of DDIT4 in glioma patients using cBioPortal. The analysis indicates that the DDIT4 gene is altered in less than 1% of patients. Alterations include copy number variations (CNV) such as deep deletions and somatic mutations, with no significant representation of other genetic changes

Article Snippet: Subsequently, the sections were incubated with a primary antibody specific for DDIT4 (1:80 dilution, Biorbyt, Cambridge, MA, UK) for an overnight at 4◦C.

Techniques:

Journal: Discover oncology

Article Title: Increased nuclear expression of DNA damage inducible transcript 4 can serve as a potential prognostic biomarker in patients with gliomas: a study based on data mining and experimental tools.

doi: 10.1007/s12672-025-01865-0

Figure Lengend Snippet: Fig. 4 GeneMANIA network analysis for DDIT4 and associated genes. The analysis identifies gene sets enriched in the DDIT4 network, rep- resented by various edge colors indicating different types of interactions: Physical Interactions, Co-expression, Predicted, Co-localization, Genetic Interactions, Pathway, and Shared protein domains. Node colors correspond to the biological functions of the enriched gene sets, such as TOR signaling and response to oxygen levels

Article Snippet: Subsequently, the sections were incubated with a primary antibody specific for DDIT4 (1:80 dilution, Biorbyt, Cambridge, MA, UK) for an overnight at 4◦C.

Techniques: Expressing

Journal: Discover oncology

Article Title: Increased nuclear expression of DNA damage inducible transcript 4 can serve as a potential prognostic biomarker in patients with gliomas: a study based on data mining and experimental tools.

doi: 10.1007/s12672-025-01865-0

Figure Lengend Snippet: Fig. 3 Prognostic analysis of DDIT4 mRNA expression in glioma patients using the GEPIA2 tool. High DDIT4 expression is significantly asso- ciated with worse prognosis in gliomas, including glioblastoma multiforme (GBM) and low-grade gliomas (LGG). A Kaplan–Meier curve for overall survival (OS) shows that patients with high DDIT4 expression have reduced survival compared to those with low expression. B Kaplan–Meier curve for recurrence-free survival (RFS) demonstrates a similar trend, with high DDIT4 expression correlating with shorter recurrence-free periods. Statistical significance is indicated with log-rank P-values

Article Snippet: Subsequently, the sections were incubated with a primary antibody specific for DDIT4 (1:80 dilution, Biorbyt, Cambridge, MA, UK) for an overnight at 4◦C.

Techniques: Expressing

Journal: Discover oncology

Article Title: Increased nuclear expression of DNA damage inducible transcript 4 can serve as a potential prognostic biomarker in patients with gliomas: a study based on data mining and experimental tools.

doi: 10.1007/s12672-025-01865-0

Figure Lengend Snippet: Fig. 5 Immunohistochemical (IHC) analysis of DDIT4 protein expression in glial tumors and controls. A, A-1, A-2 Positive nuclear expression of DDIT4 in glial tumor tissues at different magnifications (100×, 200×, and 400×). B, B-1, B-2 Positive cytoplasmic expression of DDIT4 in glial tumor tissues at corresponding magnifications. C IHC staining of normal glial tissue. D Human normal kidney tissue as a positive con- trol. E Human normal kidney tissue as a negative control. F Isotype control for validation. Magnifications are indicated for each panel

Article Snippet: Subsequently, the sections were incubated with a primary antibody specific for DDIT4 (1:80 dilution, Biorbyt, Cambridge, MA, UK) for an overnight at 4◦C.

Techniques: Immunohistochemical staining, Expressing, Immunohistochemistry, Negative Control, Control, Biomarker Discovery

Journal: Discover oncology

Article Title: Increased nuclear expression of DNA damage inducible transcript 4 can serve as a potential prognostic biomarker in patients with gliomas: a study based on data mining and experimental tools.

doi: 10.1007/s12672-025-01865-0

Figure Lengend Snippet: Fig. 6 Kaplan–Meier survival curves for disease-specific survival (DSS) and recurrence- free survival (RFS) based on nuclear DDIT4 protein expres- sion levels in glial tumors. A Kaplan–Meier analysis for DSS indicates that tumors with positive nuclear DDIT4 expression are associated with significantly worse survival compared to those with negative expression (Log-rank test, P = 0.013). B Kaplan–Meier analysis for RFS reveals a significant associa- tion between positive nuclear DDIT4 expression and shorter recurrence-free periods (Log- rank test, P = 0.024). Survival statistics include mean and median values with 95% con- fidence intervals, as shown in the accompanying tables

Article Snippet: Subsequently, the sections were incubated with a primary antibody specific for DDIT4 (1:80 dilution, Biorbyt, Cambridge, MA, UK) for an overnight at 4◦C.

Techniques: Expressing

Journal: Discover oncology

Article Title: Increased nuclear expression of DNA damage inducible transcript 4 can serve as a potential prognostic biomarker in patients with gliomas: a study based on data mining and experimental tools.

doi: 10.1007/s12672-025-01865-0

Figure Lengend Snippet: Fig. 7 Kaplan–Meier survival curves for disease-specific survival (DSS) (A) and recur- rence-free survival (RFS) (B) in patients with glial tumors treated with temozolomide (TMZ). The analysis indicates no significant differences in DSS or RFS between patients with positive and nega- tive nuclear DDIT4 expres- sion under TMZ treatment (Log-rank test: P = 0.129 and P = 0.299, respectively)

Article Snippet: Subsequently, the sections were incubated with a primary antibody specific for DDIT4 (1:80 dilution, Biorbyt, Cambridge, MA, UK) for an overnight at 4◦C.

Techniques:

Journal: Discover oncology

Article Title: Increased nuclear expression of DNA damage inducible transcript 4 can serve as a potential prognostic biomarker in patients with gliomas: a study based on data mining and experimental tools.

doi: 10.1007/s12672-025-01865-0

Figure Lengend Snippet: Fig. 8 Kaplan–Meier survival curves for disease-specific sur- vival (DSS) (A) and recurrence- free survival (RFS) (B) based on cytoplasmic DDIT4 protein expression levels in glial tumors. Kaplan–Meier analysis reveals no significant differ- ences in DSS or RFS between patients with positive and negative cytoplasmic DDIT4 expression (Log-rank test: P = 0.884 for DSS and P = 0.974 for RFS). Survival statistics, including mean and median values with 95% confidence intervals, are displayed in the accompanying tables

Article Snippet: Subsequently, the sections were incubated with a primary antibody specific for DDIT4 (1:80 dilution, Biorbyt, Cambridge, MA, UK) for an overnight at 4◦C.

Techniques: Expressing

Journal: Cell Reports

Article Title: Oxidative Stress Triggers Selective tRNA Retrograde Transport in Human Cells during the Integrated Stress Response

doi: 10.1016/j.celrep.2019.02.077

Figure Lengend Snippet:

Article Snippet: Rabbit Antibody against REDD1/DDIT4 , Novus Biologicals , Cat# NBP1-77321SS; RRID: AB_11036185.

Techniques: Recombinant, Cell Isolation, Reverse Transcription, SYBR Green Assay, Isolation, Sequencing, Software

Journal: Cell cycle (Georgetown, Tex.)

Article Title: REDD1 is required for RAS-mediated transformation of human ovarian epithelial cells.

doi: 10.4161/cc.8.5.7887

Figure Lengend Snippet: Figure 1. Effect of REDD1 on tumor cell growth in vitro. (A) REDD1 expression was detected by Western blotting in T80, T80K, T80H, T29, T29K and T29H cell lines. (B) Western blot analysis showed increased REDD1 expression after introduction of REDD1 cDNA into immortalized ovarian epithelial cell lines T80 and T29 and decreased REDD1 expression after REDD1 siRNA knockdown in RAS-transformed ovarian epithelial T29H cells. (C and D) T80-REDD1 and T29-REDD1 cells displayed statistically significant increases in cell proliferation and colony formation compared with findings in parental T80 and T29 cells, whereas cells expressing REDD1 siRNA showed reduced cell proliferation and colony formation compared with parental cells infected with scrambled siRNA. (C) Cell proliferation rate following overexpression of REDD1 or siRNA knockdown for all three groups. (D) Number of colonies of anchorage-independent cell growth on soft agar in the presence of REDD1 overexpression or knockdown. (p < 0.05).

Article Snippet: The following antibodies were used: 1:500 dilution for rabbit polyclonal REDD1 antibody (Proteintech Group, Inc., Chicago, IL), 1:500 dilution for mouse monoclonal Bcl-2 antibody (Santa Cruz Biotechnology, Inc., Santa Cruz, CA), 1 μg/mlofmouse monoclonal Anti-Bcl-xL (Calbiochem, San Diego, CA), 1:2000 dilution of mouse monoclonal Bax antibody (Santa Cruz iotechnology, Inc.,), 2.5 μg/ml of rabbit polyclonal Bcl-xs antibody (Calbiochem), 1 μg/ml of mouse monoclonal Caspase-8 antibody (Biolegend, San Diego, CA), 1:2000 dilution of mouse monoclonal Caspase-9 antibody (Biolegend), 1:1000 dilution of mouse monoclonal Caspase-10 antibody (Biolegend), 1:1000 dilution of rabbit polyclonal Caspase-1 antibody (Cell Signaling Technology, Danvers, MA), and 1:1000 dilution of rabbit polyclonal fat-associated protein with death domain (FADD) antibody (Cell Signaling Technologies) followed by incubation with secondary antibodies NA931 anti-mouse immunoglobulin or NA9340 anti-rabbit immunoglobulin horseradish peroxidase-linked F(ab)2 fragment (Amersham Biosciences, UK Limited, Little Chalfont HP7 9NA, UK).

Techniques: In Vitro, Expressing, Western Blot, Knockdown, Transformation Assay, Infection, Over Expression

Journal: Cell cycle (Georgetown, Tex.)

Article Title: REDD1 is required for RAS-mediated transformation of human ovarian epithelial cells.

doi: 10.4161/cc.8.5.7887

Figure Lengend Snippet: Figure 2. Effect of REDD1 on tumor growth in nude mice. (A and B) Tumor growth curve following s.c. injection of T80-REDD1 (p < 0.01, n = 4) and T29- REDD1 cells (p < 0.05, n = 4). (C) Tumor growth curve for s.c. tumors in nude mice inoculated with T29H and T29H-REDD11i cells (p < 0.01, n = 5). (D) Histopathologic analysis of xenograft tumors produced by i.p. injection of T29-REDD1 cells showed morphology of high-grade papillary serous carcinoma. Immunohistochemical positive staining of SV40, p53, CA125 and MUC2. (x400).

Article Snippet: The following antibodies were used: 1:500 dilution for rabbit polyclonal REDD1 antibody (Proteintech Group, Inc., Chicago, IL), 1:500 dilution for mouse monoclonal Bcl-2 antibody (Santa Cruz Biotechnology, Inc., Santa Cruz, CA), 1 μg/mlofmouse monoclonal Anti-Bcl-xL (Calbiochem, San Diego, CA), 1:2000 dilution of mouse monoclonal Bax antibody (Santa Cruz iotechnology, Inc.,), 2.5 μg/ml of rabbit polyclonal Bcl-xs antibody (Calbiochem), 1 μg/ml of mouse monoclonal Caspase-8 antibody (Biolegend, San Diego, CA), 1:2000 dilution of mouse monoclonal Caspase-9 antibody (Biolegend), 1:1000 dilution of mouse monoclonal Caspase-10 antibody (Biolegend), 1:1000 dilution of rabbit polyclonal Caspase-1 antibody (Cell Signaling Technology, Danvers, MA), and 1:1000 dilution of rabbit polyclonal fat-associated protein with death domain (FADD) antibody (Cell Signaling Technologies) followed by incubation with secondary antibodies NA931 anti-mouse immunoglobulin or NA9340 anti-rabbit immunoglobulin horseradish peroxidase-linked F(ab)2 fragment (Amersham Biosciences, UK Limited, Little Chalfont HP7 9NA, UK).

Techniques: Injection, Produced, Immunohistochemical staining, Staining

Journal: Cell cycle (Georgetown, Tex.)

Article Title: REDD1 is required for RAS-mediated transformation of human ovarian epithelial cells.

doi: 10.4161/cc.8.5.7887

Figure Lengend Snippet: Figure 3. Level of apoptosis in ovarian cancer cells following REDD1 expression or knockdown. (A) Level of apoptosis as measured by flow cytometry. (B) Expression of key signaling molecules regulating the apoptotic pathway in T80-REDD1 and T29-REDD1 cells. (C) Model describing REDD1-mediated ovarian tumorigenesis. RAS activates expression of REDD1, which in turn inhibits apoptosis and promotes proliferation; both mechanisms synergistically promote ovarian malignant progression.

Article Snippet: The following antibodies were used: 1:500 dilution for rabbit polyclonal REDD1 antibody (Proteintech Group, Inc., Chicago, IL), 1:500 dilution for mouse monoclonal Bcl-2 antibody (Santa Cruz Biotechnology, Inc., Santa Cruz, CA), 1 μg/mlofmouse monoclonal Anti-Bcl-xL (Calbiochem, San Diego, CA), 1:2000 dilution of mouse monoclonal Bax antibody (Santa Cruz iotechnology, Inc.,), 2.5 μg/ml of rabbit polyclonal Bcl-xs antibody (Calbiochem), 1 μg/ml of mouse monoclonal Caspase-8 antibody (Biolegend, San Diego, CA), 1:2000 dilution of mouse monoclonal Caspase-9 antibody (Biolegend), 1:1000 dilution of mouse monoclonal Caspase-10 antibody (Biolegend), 1:1000 dilution of rabbit polyclonal Caspase-1 antibody (Cell Signaling Technology, Danvers, MA), and 1:1000 dilution of rabbit polyclonal fat-associated protein with death domain (FADD) antibody (Cell Signaling Technologies) followed by incubation with secondary antibodies NA931 anti-mouse immunoglobulin or NA9340 anti-rabbit immunoglobulin horseradish peroxidase-linked F(ab)2 fragment (Amersham Biosciences, UK Limited, Little Chalfont HP7 9NA, UK).

Techniques: Expressing, Knockdown, Flow Cytometry

Journal: PLoS Pathogens

Article Title: Influenza virus differentially activates mTORC1 and mTORC2 signaling to maximize late stage replication

doi: 10.1371/journal.ppat.1006635

Figure Lengend Snippet: ( A-C ) A549 cells were infected with WSN at MOI of 2 PFU/cell for the indicated times. Cell extracts were subjected to ( A ) western blot analysis to detect the depicted proteins and quantified as shown in or ( B ) RNA was purified for qRT-PCR to determine REDD1 mRNA levels. Mean and standard deviation are shown for qRT-PCR, n = 4 independent experiments done in triplicates. ** p <0.000004, Student's t -test. ( C ) A549 cells were transfected with siRNAs (pool of three each) targeting viral mRNAs and then infected for 7 h at MOI of 2 PFU/cell. Immunoblot analysis was performed to detect the depicted proteins, n = 3. ( D ) A549 cells were transfected with plasmids encoding the indicated virus proteins. At 48 h post-transfection, total RNA was purified and REDD1 mRNA levels were determined by qRT-PCR as in B . The bottom panel in D shows viral polymerase activity upon tranfection of the depicted viral proteins and/or minigenome as control. Minigenome mRNA was measured by qRT-PCR. In cells transfected with the complete set of plasmids that encode the viral polymerase we detect the minigenome RNA transcribed by pol I directly from the plasmid in addition to the minigenme RNA amplified by the influenza proteins, indicating protein activity. In cells transfected with the same plasmids except for PA, we only detect the minigenome RNA transcribed by pol I directly from the plasmid, and the average values was set to 1. The minigenome RNA level is higher when all plasmids were transfected ( n = 3). ( E, F ) MDCK cells were transfected with control plasmid of plasmid enconding the M2 protein. In E, RNA was purified for qRT-PCR to determine REDD1 mRNA levels as in B , n = 3, ***p<0.001. In F, cell extracts were subjected to western blot analysis to detect the depicted proteins ( n = 3). ( G ) U2OS-REDD1 cells were treated with vehicle or 1μg/ml tetracycline for 2 h prior to and during infection to induce REDD1 expression. Cells were infected at MOI of 2 PFU/cell for 6 h. Immunoblot analyses were performed to detect the depicted proteins. Total S6K serves as the loading control. The upper band in the S6K/p-S6K blots is p85 S6K, whereas the lower band is p70 S6K ( n = 3).

Article Snippet: Additional antibodies used for western blot analysis were against Rictor (Millipore 05–1471), IFITM3 (R&D Systems AF3377), MAVS (generated by Z. Chen laboratory), β-actin (Sigma A5441), REDD1 (Novus Biologicals NBP1-22966), ATG5 (Novus Biologicals NB110-53818), ATG7 (Sigma A2856), and LC3 (Novus Biologicals NB100-2220).

Techniques: Infection, Western Blot, Purification, Quantitative RT-PCR, Standard Deviation, Transfection, Virus, Activity Assay, Control, Plasmid Preparation, Amplification, Expressing

Journal: PLoS Pathogens

Article Title: Influenza virus differentially activates mTORC1 and mTORC2 signaling to maximize late stage replication

doi: 10.1371/journal.ppat.1006635

Figure Lengend Snippet: The viral protein HA and virus replication promote mTORC1 activation through PDPK1-mediated phosphorylation of AKT at T308. In addition, down-regulation of REDD1 by the viral M2 protein amplifies or support mTORC1 activation downstream of AKT. NS1 promotes AKT phosphorylation at S473 via mTORC2 and this process is known to regulate apoptosis. Differential AKT phosphorylation dictates downstream effects.

Article Snippet: Additional antibodies used for western blot analysis were against Rictor (Millipore 05–1471), IFITM3 (R&D Systems AF3377), MAVS (generated by Z. Chen laboratory), β-actin (Sigma A5441), REDD1 (Novus Biologicals NBP1-22966), ATG5 (Novus Biologicals NB110-53818), ATG7 (Sigma A2856), and LC3 (Novus Biologicals NB100-2220).

Techniques: Virus, Activation Assay, Phospho-proteomics

Journal: International journal of molecular medicine

Article Title: Identification of an intermediate signature that marks the initial phases of the colorectal adenoma-carcinoma transition.

doi: 10.3892/ijmm_00000508

Figure Lengend Snippet: Figure 4. IHC analysis of the 4-gene set in NOR, CRA and CRC. Left, IHC images of the cytoplasm-positive (DDIT4 and CXCL10) and nuclei-positive (FOXQ1 and FOXM1) genes in the NOR, CRA and CRC samples at 200x and 400x magnifications. Right, bar graph representation of the percentage of samples in which a positive signal (IHC scores of 5-12) was observed in NOR, CRA and CRC. An ‘a’ indicates the statistical significance (P<0.05) of differential expression in CRA vs. NOR, as well as in CRC vs. NOR, and a ‘b’ indicates the statistical significance (P<0.05) of differential expression in CRC vs. CRA.

Article Snippet: The primary antibodies, rabbit polyclonal DDIT4 (Abcam, ab63059), rabbit polyclonal IP10/CXCL10 (Abcam, ab9807), rabbit polyclonal FOXQ1 (Abcam, ab51340) and mouse monoclonal FOXM1 (Abcam, ab5506), were each diluted 1:100 and incubated in a humidified chamber overnight at 4 ̊C.

Techniques: Quantitative Proteomics