Journal: Reports of Biochemistry & Molecular Biology

Article Title: The Prognostic Significance of P16 Immunohistochemical Expression Pattern in Women with Invasive Ductal Breast Carcinoma

doi: 10.52547/rbmb.12.1.83

Figure Lengend Snippet: Immunohistochemical staining for p16 protein in invasive ductal breast tumors. A. p16 negative, B. p16 low positive, C. High-positive.

Article Snippet: Parameters P16 Protein Expression Level P-value(Chi-Square) Negative (n = 29) Low-Positive (n = 44) High-Positive (n = 27) ER receptor Positive 22 (75.9%) 41 (93.2%) 17 (63%) 0.007* Negative 7 (24.1%) 3 (6.8%) 10 (37%) PR receptor Positive 14 (48.3%) 33 (75%) 16 (59.3%) 0.061 Negative 15 (51.7%) 11 (25%) 11 (40.7%) HER2 Positive 4 (13.8%) 15 (34.1%) 11 (40.7%) 0.065 Negative 25 (86.2%) 29 (65.9%) 16 (59.3%) Ki67 Positive (> 14%) 7 (24.1%) 16 (36.4%) 5 (18.5%) 0.229 Negative (≤ 14%) 22 (75.9%) 28 (63.6%) 22 (81.5%) Cancer Grade I 2 (6.9%) 2 (4.5%) 4 (14.8%) 0.252 II 20 (69%) 37 (84.1%) 17 (6%) III 7 (24.1%) 5 (11.4%) 6 (22.2%) Tumor Size ≤ 20 mm 11 (37.9%) 18 (40.9%) 13 (48.1%) 0.754 21-50 mm 18 (62.1%) 25 (56.8%) 14 (51.9%) > 50 mm 0 (0%) 1 (2.3%) 0 (0%) Cancer Type Luminal A 7 (29.16%) 13 (54.16%) 4 (16.66%) 0.144 Luminal B 15 (26.31%) 28 (49.12%) 14 (24.56%) HER2 positive 2 (28.57%) 1 (14.28%) 4 (57.14%) Triple Negative 5 (41.66%) 2 (16.66%) 5 (41.66%) Age ≤ 40 years 7 (24.1%) 11 (25%) 10 (37%) 0.471 > 40 yea 22 (75.9%) 33 (75%) 17 (63%) Family History Yes 5 (17.2%) 11 (25%) 5 (18.5%) 0.68 No 24 (82.8%) 33 (75%) 22 (81.5%) Open in a separate window The data are shown as mean ± SD.

Techniques: Immunohistochemical staining, Staining

Journal: Reports of Biochemistry & Molecular Biology

Article Title: The Prognostic Significance of P16 Immunohistochemical Expression Pattern in Women with Invasive Ductal Breast Carcinoma

doi: 10.52547/rbmb.12.1.83

Figure Lengend Snippet: Correlation between clinicopathological characteristics and p16 protein expression in women with invasive ductal breast carcinoma.

Article Snippet: Parameters P16 Protein Expression Level P-value(Chi-Square) Negative (n = 29) Low-Positive (n = 44) High-Positive (n = 27) ER receptor Positive 22 (75.9%) 41 (93.2%) 17 (63%) 0.007* Negative 7 (24.1%) 3 (6.8%) 10 (37%) PR receptor Positive 14 (48.3%) 33 (75%) 16 (59.3%) 0.061 Negative 15 (51.7%) 11 (25%) 11 (40.7%) HER2 Positive 4 (13.8%) 15 (34.1%) 11 (40.7%) 0.065 Negative 25 (86.2%) 29 (65.9%) 16 (59.3%) Ki67 Positive (> 14%) 7 (24.1%) 16 (36.4%) 5 (18.5%) 0.229 Negative (≤ 14%) 22 (75.9%) 28 (63.6%) 22 (81.5%) Cancer Grade I 2 (6.9%) 2 (4.5%) 4 (14.8%) 0.252 II 20 (69%) 37 (84.1%) 17 (6%) III 7 (24.1%) 5 (11.4%) 6 (22.2%) Tumor Size ≤ 20 mm 11 (37.9%) 18 (40.9%) 13 (48.1%) 0.754 21-50 mm 18 (62.1%) 25 (56.8%) 14 (51.9%) > 50 mm 0 (0%) 1 (2.3%) 0 (0%) Cancer Type Luminal A 7 (29.16%) 13 (54.16%) 4 (16.66%) 0.144 Luminal B 15 (26.31%) 28 (49.12%) 14 (24.56%) HER2 positive 2 (28.57%) 1 (14.28%) 4 (57.14%) Triple Negative 5 (41.66%) 2 (16.66%) 5 (41.66%) Age ≤ 40 years 7 (24.1%) 11 (25%) 10 (37%) 0.471 > 40 yea 22 (75.9%) 33 (75%) 17 (63%) Family History Yes 5 (17.2%) 11 (25%) 5 (18.5%) 0.68 No 24 (82.8%) 33 (75%) 22 (81.5%) Open in a separate window The data are shown as mean ± SD.

Techniques: Expressing

Journal: Reports of Biochemistry & Molecular Biology

Article Title: The Prognostic Significance of P16 Immunohistochemical Expression Pattern in Women with Invasive Ductal Breast Carcinoma

doi: 10.52547/rbmb.12.1.83

Figure Lengend Snippet: Correlation of p16 expression with tumor grade and age of patients with invasive ductal breast carcinoma. The data are shown as mean ± SD.

Article Snippet: Parameters P16 Protein Expression Level P-value(Chi-Square) Negative (n = 29) Low-Positive (n = 44) High-Positive (n = 27) ER receptor Positive 22 (75.9%) 41 (93.2%) 17 (63%) 0.007* Negative 7 (24.1%) 3 (6.8%) 10 (37%) PR receptor Positive 14 (48.3%) 33 (75%) 16 (59.3%) 0.061 Negative 15 (51.7%) 11 (25%) 11 (40.7%) HER2 Positive 4 (13.8%) 15 (34.1%) 11 (40.7%) 0.065 Negative 25 (86.2%) 29 (65.9%) 16 (59.3%) Ki67 Positive (> 14%) 7 (24.1%) 16 (36.4%) 5 (18.5%) 0.229 Negative (≤ 14%) 22 (75.9%) 28 (63.6%) 22 (81.5%) Cancer Grade I 2 (6.9%) 2 (4.5%) 4 (14.8%) 0.252 II 20 (69%) 37 (84.1%) 17 (6%) III 7 (24.1%) 5 (11.4%) 6 (22.2%) Tumor Size ≤ 20 mm 11 (37.9%) 18 (40.9%) 13 (48.1%) 0.754 21-50 mm 18 (62.1%) 25 (56.8%) 14 (51.9%) > 50 mm 0 (0%) 1 (2.3%) 0 (0%) Cancer Type Luminal A 7 (29.16%) 13 (54.16%) 4 (16.66%) 0.144 Luminal B 15 (26.31%) 28 (49.12%) 14 (24.56%) HER2 positive 2 (28.57%) 1 (14.28%) 4 (57.14%) Triple Negative 5 (41.66%) 2 (16.66%) 5 (41.66%) Age ≤ 40 years 7 (24.1%) 11 (25%) 10 (37%) 0.471 > 40 yea 22 (75.9%) 33 (75%) 17 (63%) Family History Yes 5 (17.2%) 11 (25%) 5 (18.5%) 0.68 No 24 (82.8%) 33 (75%) 22 (81.5%) Open in a separate window The data are shown as mean ± SD.

Techniques: Expressing

Journal: Breast Cancer Research : BCR

Article Title: Evaluating the predictive value of biomarkers for efficacy outcomes in response to pertuzumab- and trastuzumab-based therapy: an exploratory analysis of the TRYPHAENA study

doi: 10.1186/bcr3690

Figure Lengend Snippet: The relationship between biomarker levels and whether a pathologic complete response (pCR) was achieved, adjusted for estrogen receptor status (all arms pooled)

Article Snippet: Targos Molecular Pathology GmbH, Kassel, Germany conducted analysis of: mRNA expression levels of HER2 , HER3, EGFR, amphiregulin, and betacellulin ; protein expression levels of HER3, EGFR, IGF-1R, and PTEN and of c-myc and TOP2A gene amplification.

Techniques: Biomarker Discovery, Membrane, Mutagenesis

Journal: Breast Cancer Research : BCR

Article Title: Evaluating the predictive value of biomarkers for efficacy outcomes in response to pertuzumab- and trastuzumab-based therapy: an exploratory analysis of the TRYPHAENA study

doi: 10.1186/bcr3690

Figure Lengend Snippet: Comparison of baseline levels of biomarkers derived from tissue samples with the levels detected at surgery. (A) PTEN nuc, (B) HER2-CR, ( C ) EGFR-CR, (D) HER2-mem. (In the box plot, the horizontal line represents the median value, the diamond represents the mean, the upper and lower bounds of the box represent the 75th and 25th quartiles, respectively, and whiskers represent 95% confidence limits). CR, concentration ratio; EGFR, epidermal growth factor receptor; HER2, human epidermal growth factor receptor 2; mem, membrane; nuc, nuclear; PTEN, phosphatase and tensin homolog.

Article Snippet: Targos Molecular Pathology GmbH, Kassel, Germany conducted analysis of: mRNA expression levels of HER2 , HER3, EGFR, amphiregulin, and betacellulin ; protein expression levels of HER3, EGFR, IGF-1R, and PTEN and of c-myc and TOP2A gene amplification.

Techniques: Comparison, Derivative Assay, Concentration Assay, Membrane

Journal: Biomolecules

Article Title: Differential MicroRNA Expression Involved in Endometrial Receptivity of Goats

doi: 10.3390/biom11030472

Figure Lengend Snippet: Chi-miR-483 targets the 3′-untranslated region (UTR) of deltex E3 ubiquitin ligase 3L (DTX3L). ( A ) The predicted binding site of chi-miR-483 in the 3′UTR of DTX3L according to bioinformatics analysis. ( B ) Design of the luciferase reporter. WT, the wildtype sequence of DTX3L-3′UTR contains the chi-miR-483 binding site; Mut, the sequence of DTX3L-3′UTR with a mutation in the chi-miR-483 binding site. ( C ) 293T cells were co-transfected with wildtype (WT) or mutant (Mut) luciferase reports of DTX3L 3′UTR with chi-miR-483 mimics or negative control (NC) mimics. The luciferase reporter assay demonstrated that chi-miR-483 significantly decreased the luciferase activity of DTX3L WT in 293T cells. Data are shown as the mean ± SEM values ( n = 3, ** p < 0.01, Student’s t -test).

Article Snippet: Differences in wildtype (WT) or mutant (Mut) DTX3L 3′UTR luciferase reports and the expression level of DTX3L protein under two conditions were compared using Student’s t -test (GraphPad Prism version 8.0, San Diego, CA, USA).

Techniques: Ubiquitin Proteomics, Binding Assay, Luciferase, Sequencing, Mutagenesis, Transfection, Negative Control, Reporter Assay, Activity Assay

Journal: Biomolecules

Article Title: Differential MicroRNA Expression Involved in Endometrial Receptivity of Goats

doi: 10.3390/biom11030472

Figure Lengend Snippet: Immunohistochemical analysis of DTX3L in the C16 and P16 uterus. ( A ) Images stained with DTX3L antibodies. The positive signal of DTX3L was distinctly detected in the uterine luminal epithelium or glandular epithelium in P16. The section stained with nonrelevant immunoglobulin G served as the negative control (NC). ( B ) Quantitative analysis of DTX3L by measuring the average integrated optical density (IOD) in the endometrium. Asterisks indicate significant differences (mean ± SEM) between C16 and P16 (*** p < 0.001); the p -value was determined by Student’s t -test. Legend: LE, endometrial luminal epithelium; GE, glandular epithelium. Scale bar = 100 μm.

Article Snippet: Differences in wildtype (WT) or mutant (Mut) DTX3L 3′UTR luciferase reports and the expression level of DTX3L protein under two conditions were compared using Student’s t -test (GraphPad Prism version 8.0, San Diego, CA, USA).

Techniques: Immunohistochemical staining, Staining, Negative Control

Journal: Cell Death & Disease

Article Title: TMBIM6 enhances dopaminergic neuron survival by modulating the IRE1a pathway in Parkinson’s disease

doi: 10.1038/s41419-025-08391-5

Figure Lengend Snippet: A In silico TMBIM6 mRNA expression in human CNS from THPA database. B Tmbim6 mRNA expression on N2a cells after 18 h of exposure to 25 μM 6-OHDA or 50 μM rotenone. C Tmbim6 mRNA levels over time in PCNs exposed to aSyn for 96 h. D Changes of expression of Tmbim6 , BcL2 , and Bax over time in PCNs exposed to aSyn for 96 h. E Representative Western blots of total protein extracts from postmortem human SN from neurologically healthy controls and PD patients, probed for TMBIM6 and GAPDH (loading control). Full, uncropped blots are provided in Supplementary Material. F Densitometric quantification of TMBIM6 from blots in ( E ). Band intensities were normalized to GAPDH for each lane; individual data points are shown with mean ± SEM (n = 9–10 per group). For experiments involving more than two groups, a two-way ANOVA followed by Tukey’s multiple comparison test was performed. Pairwise comparisons between two groups were analyzed using unpaired t-test ( B ) or the Mann–Whitney U test ( F ). All bars represent mean ± SEM. Statistical significance (p < 0.05) between samples is indicated in the figures as follows: *=p < 0.05; **=p < 0.01; ***=p < 0.001; ****=p < 0.0001.

Article Snippet: Using data on TMBIM6 mRNA expression levels from The Human Protein Atlas database (THPA) [ ], we confirmed through in silico analysis that TMBIM6 is expressed in various cortical regions of the human brain, with notably high expression in the midbrain and retina, two areas rich in DAergic cells [ , ] (Fig. ).

Techniques: In Silico, Expressing, Western Blot, Control, Comparison, MANN-WHITNEY

Journal: Cell Death & Disease

Article Title: TMBIM6 enhances dopaminergic neuron survival by modulating the IRE1a pathway in Parkinson’s disease

doi: 10.1038/s41419-025-08391-5

Figure Lengend Snippet: A Graph shows validation of decreased Tmbim6 mRNA levels after 48 h of siRNA transfection in SN4741. B , C Representative immunoblots and quantification show mTmbim6 KD cells after 48 h. D Cytotoxicity assay shows cell death induced by 10 μM Tunicamycin after 24 h in KD cells. Results are expressed as % of LDH release. E Cytotoxicity assay shows cell death induced by 50 μM 6-OHDA after 24 h in KD cells. F Retention of DiOC6(3) assay shows the effect of aSyn on ΔΨm in KD cells after 18 h. Results are expressed as % of DiOC6(3) retention. G MTT assay shows mitochondrial-dependent cell death induced by aSyn in KD cells after 24 h. Results are expressed as % of MTT. H DEVD-AMC fluorescent assay shows the effect of aSyn on Caspase-3 activity in Tmbim6 KD cells after 24 h. Results are expressed as fold change of DEVD-AMC fluorescence intensity relative to vehicle. I Cytotoxicity assay shows the KD cell death induced by aSyn after 24 h. J Representative immunoblot of high–molecular-weight (HMW) aSyn species in SN4741 cells transfected with si Cntrl or si Tmbim6 and treated with 10 µM aSyn PFFs for 24 h; Tubulin was used as a loading control. K Densitometric quantification of HMW aSyn bands from the experiment described in ( J ) (integrated density normalized to Tubulin). All bars represent mean ± SEM. For experiments involving more than two groups, a two-way ANOVA followed by Tukey’s multiple comparison test was performed. Pairwise comparisons between two groups were analyzed using unpaired t-test ( A , C ) or the Mann–Whitney U test ( K ). Statistical significance (p < 0.05) between samples is indicated in the figures as follows: *=p < 0.05; **=p < 0.01; ***=p < 0.001.

Article Snippet: Using data on TMBIM6 mRNA expression levels from The Human Protein Atlas database (THPA) [ ], we confirmed through in silico analysis that TMBIM6 is expressed in various cortical regions of the human brain, with notably high expression in the midbrain and retina, two areas rich in DAergic cells [ , ] (Fig. ).

Techniques: Biomarker Discovery, Transfection, Western Blot, Cytotoxicity Assay, MTT Assay, Fluorescence, Activity Assay, High Molecular Weight, Control, Comparison, MANN-WHITNEY

Journal: Cell Death & Disease

Article Title: TMBIM6 enhances dopaminergic neuron survival by modulating the IRE1a pathway in Parkinson’s disease

doi: 10.1038/s41419-025-08391-5

Figure Lengend Snippet: A d Tmbim6 mRNA expression on homogenized flies’ heads. Results are expressed as fold change of mRNA expression. The bars represent mean ± SEM. B Optic image of eye integrity in RNAi-dTmbim6 flies incubated at 25 °C. C Quantification of eye integrity score in RNAi- dTmbim6 flies incubated at 25 °C (n = 25 per group). D Immunostaining of TH+ neurons in the lamina of RNAi-dTmbim6 flies incubated at 25 °C (n = 6 per group). E Quantification of the number of TH+ neurons in the lamina of RNAi-dTmbim6 flies incubated at 25 °C (n = 6 per group). F Schematic representation of rotenone-induced PD model in D. mel . G Spontaneous activity in DAergic RNAi-dTmbim6 flies after exposition to rotenone 300 μM for 7 days (n = 6 populations of 12 flies). H Climbing assay showed the motor ability of DAergic RNAi-dTmbim6 flies exposed to rotenone 300 μM for 7 days (n = 12 per group). I Representative confocal images of IF assay showed TH+ cells from DAergic RNAi-dTmbim6 flies exposed to rotenone 300 μM for 7 days. J The numbers of TH+ cells were quantified in each DAergic cluster, and K the somal size was analyzed (n = 7 per group). All bars represent mean ± SEM. For experiments involving more than two groups, a two-way ANOVA followed by Tukey’s multiple comparison test was performed. Pairwise comparisons between two groups were analyzed using unpaired t-test ( A , C ) or the Mann–Whitney U test ( E ). Statistical significance (p < 0.05) between samples is indicated in the figures as follows: *=p < 0.05; ** = p < 0.01; ***= p < 0.001; ****= p < 0.0001.

Article Snippet: Using data on TMBIM6 mRNA expression levels from The Human Protein Atlas database (THPA) [ ], we confirmed through in silico analysis that TMBIM6 is expressed in various cortical regions of the human brain, with notably high expression in the midbrain and retina, two areas rich in DAergic cells [ , ] (Fig. ).

Techniques: Expressing, Incubation, Immunostaining, Activity Assay, Climbing Assay, Comparison, MANN-WHITNEY

Journal: Cell Death & Disease

Article Title: TMBIM6 enhances dopaminergic neuron survival by modulating the IRE1a pathway in Parkinson’s disease

doi: 10.1038/s41419-025-08391-5

Figure Lengend Snippet: A Representative immunoblot shows a stable expression of TMBIM6 HA in SN4741 cells. B Cytotoxicity assay shows the cell death induced by Tunicamycin in SN4741 TMBIM6 HA cells after 24 h. C , D MTT assay shows cell death induced by 6-OHDA or rotenone in SN4741 TMBIM6 HA cells after 24 h. Results are expressed as % of MTT. E Retention of DiOC6(3) assay shows the effect of aSyn on ΔΨm in SN4741 hTMBIM6 HA cells after 18 h. Results are expressed as % of DiOC6(3) retention. F MTT assay shows cell death induced by aSyn in SN4741 TMBIM6 HA cells after 24 h. G DEVD-AMC fluorescent assay shows the effect of aSyn on Caspase-3 activity in SN4741 TMBIM6 HA cells after 24 h. H Cytotoxicity assay shows the cell death induced by aSyn in SN4741 TMBIM6 HA cells after 24 h. I Representative immunoblot of HMW aSyn species in Mock or TMBIM6 HA cells treated with aSyn PFFs for 24 h; TCE staining was used as a loading control. J Densitometric quantification of HMW aSyn bands from the experiment described in J (integrated density normalized to TCE). K Representative immunoblot shows expression of TMBIM6 HA and TMBIM6 D213A/HA in SN4741 cells. L MTT assay shows cell death induced by Tunicamycin and Thapsigargin in SN4741 Mock, TMBIM6 HA , and TMBIM6 D213A/HA cells after 24 h. Results are expressed as % of MTT. M Cytotoxicity assay shows the cell death induced by aSyn in SN4741 TMBIM6 HA and TMBIM6 D213A/HA cells after 24 h. N Cytotoxicity assay shows the cell death induced by aSyn after 10 days in PCNs transfected with Mock, TMBIM6 HA and TMBIM6 D213A/HA constructs. All bars represent mean ± SEM. For experiments involving more than two groups, a two-way ANOVA followed by Tukey’s multiple comparison test was performed. Pairwise comparisons between two groups were analyzed using the Mann–Whitney U test. Statistical significance (p < 0.05) between samples is indicated in the figures as follows: *=p < 0.05; **=p < 0.01; ***=p < 0.001; ****=p < 0.0001.

Article Snippet: Using data on TMBIM6 mRNA expression levels from The Human Protein Atlas database (THPA) [ ], we confirmed through in silico analysis that TMBIM6 is expressed in various cortical regions of the human brain, with notably high expression in the midbrain and retina, two areas rich in DAergic cells [ , ] (Fig. ).

Techniques: Western Blot, Expressing, Cytotoxicity Assay, MTT Assay, Fluorescence, Activity Assay, Staining, Control, Transfection, Construct, Comparison, MANN-WHITNEY

Journal: Cell Death & Disease

Article Title: TMBIM6 enhances dopaminergic neuron survival by modulating the IRE1a pathway in Parkinson’s disease

doi: 10.1038/s41419-025-08391-5

Figure Lengend Snippet: A An in-silico assay using Ingenuity Pathway Analysis (IPA) software shows the canonical pathways significantly associated with TMBIM6 interactors. B , C UMAP visualizations of the snRNA-seq dataset (GEO: GSE178265 ) from human postmortem substantia nigra. B shows TMBIM6 expression across all nuclei, while C distinguishes nuclei from healthy and PD donors. D Dot plot comparing the expression of TMBIM6 and UPR-related genes ( HSPA5, ERN1, XBP1, BLOC1S1 ) between healthy and PD conditions across all nuclei. E UMAP plot identifying resistant and vulnerable DAergic neuron populations within the dataset. F Dot plot comparing gene expression between resistant and vulnerable DAergic neurons within the PD cohort. For dot plots ( D , F ), dot size represents the percentage of cells expressing the gene, and color intensity indicates the mean expression level. Statistical significance for the differential expression shown in ( D , F ) was determined using the Model-based Analysis of Single-cell Transcriptomics (MAST) test. Full statistical details, including FDR-adjusted p-values, are provided in Supplementary Fig. .

Article Snippet: Using data on TMBIM6 mRNA expression levels from The Human Protein Atlas database (THPA) [ ], we confirmed through in silico analysis that TMBIM6 is expressed in various cortical regions of the human brain, with notably high expression in the midbrain and retina, two areas rich in DAergic cells [ , ] (Fig. ).

Techniques: In Silico, Software, Expressing, Gene Expression, Quantitative Proteomics, Single-cell Transcriptomics

Journal: Cell Death & Disease

Article Title: TMBIM6 enhances dopaminergic neuron survival by modulating the IRE1a pathway in Parkinson’s disease

doi: 10.1038/s41419-025-08391-5

Figure Lengend Snippet: A Representative images show red fluorescent dots of PLA assay to TMBIM6 HA /IRE1a in stable SN4741 TMBIM6 HA cells exposed to aSyn. B Quantification of PLA dots per cell. Kruskal-Wallis followed by Dunn’s multiple comparison test. C In SN4741 siRNA- mTMBIM6 cells, an RT-qPCR assay shows the effect of aSyn on mRNA levels of mouse XBP1s ( mXbp1s ), D mouse BLOCS1 (mBlocs1) , and E mouse BIP (mBip) . F In SN4741 TMBIM6 HA cells, RT-qPCR assay shows the effect of aSyn in mXbp1s , G mBlocs1 , and H mBip , mRNA levels. Results are expressed as fold change, and bars represent mean ± SEM. All bars represent mean ± SEM. In ( B ), a Kruskal–Wallis test was performed followed by Dunn’s multiple comparison test. For experiments involving more than two groups, a two-way ANOVA followed by Tukey’s multiple comparison test was performed ( C – H ). Statistical significance (p < 0.05) between samples is indicated in the figures as follows: *=p < 0.05; ***=p < 0.001; ****=p < 0.0001.

Article Snippet: Using data on TMBIM6 mRNA expression levels from The Human Protein Atlas database (THPA) [ ], we confirmed through in silico analysis that TMBIM6 is expressed in various cortical regions of the human brain, with notably high expression in the midbrain and retina, two areas rich in DAergic cells [ , ] (Fig. ).

Techniques: Comparison, Quantitative RT-PCR

Journal: Cell Death & Disease

Article Title: TMBIM6 enhances dopaminergic neuron survival by modulating the IRE1a pathway in Parkinson’s disease

doi: 10.1038/s41419-025-08391-5

Figure Lengend Snippet: A , B Cytotoxicity assay shows the effect of IRE1a inhibition using MKC or 4 μ 8c on cell death induced by aSyn in Tmbim6 KD cells after 24 h. Results are expressed as % of LDH release. C Cytotoxicity assay shows the effect of PERK inhibitor on cell death induced by aSyn in mTmbim6 KD cells after 24 h. D A RT-qPCR assay shows effective double knockdown of both mTmbim6 (left panel) and mIre1 a (right panel) in SN4741 cells. Results are expressed as fold change, and bars represent mean ± SEM. One way ANOVA, Dunnett´s multiple comparation test. E Cytotoxicity assay shows downregulation of mIRE1a over cell death induced by aSyn in mTmbim6 KD cells after 24 h. Results are expressed as % of LDH release. F Cytotoxicity assay shows the JNK inhibitor AS60125 over cell death induced by aSyn in mTmbim6 KD cells after 24 h. G Cytotoxicity assay shows the BAX inhibitor BAI-1 over cell death induced by aSyn in mTmbim6 KD cells after 24 h. H Cytotoxicity assay shows the pan-caspase inhibitor ZVAD-FMK (casp-inh) over cell death induced by aSyn in mTmbim6 KD cells after 24 h. All bars represent mean ± SEM. In ( D ), a one-way ANOVA followed by Dunnett’s multiple comparison test was performed, whereas in ( E , F , G , H ), a two-way ANOVA with Tukey’s multiple comparisons test was conducted. Statistical significance (p < 0.05) between samples is indicated in the figures as follows: *=p < 0.05; **=p < 0.01; ***=p < 0.001; ****=p < 0.0001.

Article Snippet: Using data on TMBIM6 mRNA expression levels from The Human Protein Atlas database (THPA) [ ], we confirmed through in silico analysis that TMBIM6 is expressed in various cortical regions of the human brain, with notably high expression in the midbrain and retina, two areas rich in DAergic cells [ , ] (Fig. ).

Techniques: Cytotoxicity Assay, Inhibition, Quantitative RT-PCR, Knockdown, Comparison

Journal: Cell Death & Disease

Article Title: TMBIM6 enhances dopaminergic neuron survival by modulating the IRE1a pathway in Parkinson’s disease

doi: 10.1038/s41419-025-08391-5

Figure Lengend Snippet: A Effect of two 6-OHDA doses on motor performance of mice, as a pharmacologic in vivo PD model (n = 4 per condition). Results are expressed as a percentage of contralateral forelimb use. B Timeline of in vivo transduction of the AAV-TMBIM6 HA/GFP and AAV-Mock GFP in SN and motor performance measurements in mice wild-type lesioned with 6-OHDA in CPu. C Cylinder test shows the effect of AAV-TMBIM6 HA/GFP and AAV-Mock GFP expression in SN over forelimb use after 2-, 3-, 4-, and 5-weeks post-injection (wpi). The colored area shows treatment with 6-OHDA injuries in the CPu. Results are expressed as a percentage of contralateral forelimb use (n Mockl = 4 and n TMBIM6 = 5). D Beam test shows the effect of the AAV-TMBIM6 HA/GFP and AAV-Mock GFP expression in SN on balance and coordination after 2, 3, 4, and 5 weeks after injection. The colored area shows treatment with 6-OHDA injury in the CPu. Results are expressed as the number of paws slips (n Mockl = 4 and n TMBIM6 = 5). E Effect of the AAV-TMBIM6 HA/GFP and AAV-Mock GFP expression over time, animals used to complete the Beam test during 2-, 3-, 4-, and 5-wpi. The colored area shows treatment with 6-OHDA injury in the CPu. Results are expressed as the time in seconds to complete the test (n Mockl = 4 and n TMBIM6 = 5). All bars represent mean ± SEM. In all tests, two-way ANOVA followed by Tukey’s multiple comparison test was performed. Statistical significance (p < 0.05) between samples is indicated in the figures as follows: *=p < 0.05; **=p < 0.01; ***=p < 0.001; ****=p < 0.0001.

Article Snippet: Using data on TMBIM6 mRNA expression levels from The Human Protein Atlas database (THPA) [ ], we confirmed through in silico analysis that TMBIM6 is expressed in various cortical regions of the human brain, with notably high expression in the midbrain and retina, two areas rich in DAergic cells [ , ] (Fig. ).

Techniques: In Vivo, Transduction, Expressing, Injection, Comparison

Journal: Biology Direct

Article Title: Comprehensive pan-cancer analysis reveals SH3GLB1 is a novel prognostic biomarker with immunomodulatory potential

doi: 10.1186/s13062-026-00728-0

Figure Lengend Snippet: The expression patterns of SH3GLB1 across pan-cancer tissues and its subcellular localization. ( A ) SH3GLB1 expression levels based on the Human Protein Atlas (HPA) database. ( B ) Subcellular localization of SH3GLB1 as derived from the UniProt database. ( C ) Violin plots illustrating variations in SH3GLB1 mRNA expression levels across TCGA-GTEx pan-cancer datasets. ( D ) Paired differential analysis comparing SH3GLB1 mRNA expression levels between tumor and adjacent normal tissues within the TCGA pan-cancer dataset. ( E ) SH3GLB1 gene expression profiles across multiple cancer types: TIMER 3.0 database analysis. ( F ) Boxplots depicting differences in SH3GLB1 protein expression levels using proteomics pan-cancer datasets. ( G ) A heatmap demonstrating SH3GLB1 mRNA expression levels across pan-cancer datasets at the spatial transcriptomic level. * P < 0.05, ** P < 0.01, *** P < 0.001, **** P < 0.0001. HPA, Human Protein Atlas

Article Snippet: Fig. 2 The expression patterns of SH3GLB1 across pan-cancer tissues and its subcellular localization. ( A ) SH3GLB1 expression levels based on the Human Protein Atlas (HPA) database. ( B ) Subcellular localization of SH3GLB1 as derived from the UniProt database. ( C ) Violin plots illustrating variations in SH3GLB1 mRNA expression levels across TCGA-GTEx pan-cancer datasets. ( D ) Paired differential analysis comparing SH3GLB1 mRNA expression levels between tumor and adjacent normal tissues within the TCGA pan-cancer dataset. ( E ) SH3GLB1 gene expression profiles across multiple cancer types: TIMER 3.0 database analysis. ( F ) Boxplots depicting differences in SH3GLB1 protein expression levels using proteomics pan-cancer datasets. ( G ) A heatmap demonstrating SH3GLB1 mRNA expression levels across pan-cancer datasets at the spatial transcriptomic level.

Techniques: Expressing, Derivative Assay, Gene Expression

Journal: Biology Direct

Article Title: Comprehensive pan-cancer analysis reveals SH3GLB1 is a novel prognostic biomarker with immunomodulatory potential

doi: 10.1186/s13062-026-00728-0

Figure Lengend Snippet: SH3GLB1 in HPA - pathology. ( A ) A statistical analysis was conducted on the immunohistochemical staining results of the SH3GLB1 gene across various tumor types. ( B ) Immunohistochemical sections revealed distinct differences in the protein expression levels of SH3GLB1 among different tissues. The intensity and distribution patterns observed in these immunohistochemical sections reflect both the expression level and subcellular localization of the target protein within cells

Article Snippet: Fig. 2 The expression patterns of SH3GLB1 across pan-cancer tissues and its subcellular localization. ( A ) SH3GLB1 expression levels based on the Human Protein Atlas (HPA) database. ( B ) Subcellular localization of SH3GLB1 as derived from the UniProt database. ( C ) Violin plots illustrating variations in SH3GLB1 mRNA expression levels across TCGA-GTEx pan-cancer datasets. ( D ) Paired differential analysis comparing SH3GLB1 mRNA expression levels between tumor and adjacent normal tissues within the TCGA pan-cancer dataset. ( E ) SH3GLB1 gene expression profiles across multiple cancer types: TIMER 3.0 database analysis. ( F ) Boxplots depicting differences in SH3GLB1 protein expression levels using proteomics pan-cancer datasets. ( G ) A heatmap demonstrating SH3GLB1 mRNA expression levels across pan-cancer datasets at the spatial transcriptomic level.

Techniques: Immunohistochemical staining, Staining, Expressing

Journal: Biology Direct

Article Title: Comprehensive pan-cancer analysis reveals SH3GLB1 is a novel prognostic biomarker with immunomodulatory potential

doi: 10.1186/s13062-026-00728-0

Figure Lengend Snippet: SH3GLB1 demonstrates both diagnostic and prognostic value across various types of cancer. ( A ) Bar plots illustrate the AUC values used to assess the diagnostic performance of SH3GLB1 expression in tumor versus normal tissues. ( B ) A heatmap depicts the association between SH3GLB1 mRNA expression levels and diverse survival outcomes in pan-cancer analysis. ( C – F ) Forest plots present the results of pan-cancer analyses evaluating the relationship between SH3GLB1 expression and overall survival (OS) ( C ), disease-free survival (DFS) ( D ), progression-free interval (PFI) ( E ), and distant metastasis-free interval (DFI) ( F )

Article Snippet: Fig. 2 The expression patterns of SH3GLB1 across pan-cancer tissues and its subcellular localization. ( A ) SH3GLB1 expression levels based on the Human Protein Atlas (HPA) database. ( B ) Subcellular localization of SH3GLB1 as derived from the UniProt database. ( C ) Violin plots illustrating variations in SH3GLB1 mRNA expression levels across TCGA-GTEx pan-cancer datasets. ( D ) Paired differential analysis comparing SH3GLB1 mRNA expression levels between tumor and adjacent normal tissues within the TCGA pan-cancer dataset. ( E ) SH3GLB1 gene expression profiles across multiple cancer types: TIMER 3.0 database analysis. ( F ) Boxplots depicting differences in SH3GLB1 protein expression levels using proteomics pan-cancer datasets. ( G ) A heatmap demonstrating SH3GLB1 mRNA expression levels across pan-cancer datasets at the spatial transcriptomic level.

Techniques: Diagnostic Assay, Expressing

Journal: Biology Direct

Article Title: Comprehensive pan-cancer analysis reveals SH3GLB1 is a novel prognostic biomarker with immunomodulatory potential

doi: 10.1186/s13062-026-00728-0

Figure Lengend Snippet: Analyses of SH3GLB1 genomic alterations. ( A ) Stacked bar plots showing mutation frequencies of SH3GLB1 in pan-cancer. ( B ) Lollipop map of SH3GLB1 mutation sites in pan-cancer. ( C ) Spearman correlation between copy number variation score and SH3GLB1 mRNA expression level. ( D ) Heatmap showing mutation of SH3GLB1 and several classical carcinogenic signaling pathways in pan-cancer. ( E ) Oncoplot of the mutation distribution of SH3GLB1 in pan-cancer

Article Snippet: Fig. 2 The expression patterns of SH3GLB1 across pan-cancer tissues and its subcellular localization. ( A ) SH3GLB1 expression levels based on the Human Protein Atlas (HPA) database. ( B ) Subcellular localization of SH3GLB1 as derived from the UniProt database. ( C ) Violin plots illustrating variations in SH3GLB1 mRNA expression levels across TCGA-GTEx pan-cancer datasets. ( D ) Paired differential analysis comparing SH3GLB1 mRNA expression levels between tumor and adjacent normal tissues within the TCGA pan-cancer dataset. ( E ) SH3GLB1 gene expression profiles across multiple cancer types: TIMER 3.0 database analysis. ( F ) Boxplots depicting differences in SH3GLB1 protein expression levels using proteomics pan-cancer datasets. ( G ) A heatmap demonstrating SH3GLB1 mRNA expression levels across pan-cancer datasets at the spatial transcriptomic level.

Techniques: Mutagenesis, Expressing, Protein-Protein interactions

Journal: Biology Direct

Article Title: Comprehensive pan-cancer analysis reveals SH3GLB1 is a novel prognostic biomarker with immunomodulatory potential

doi: 10.1186/s13062-026-00728-0

Figure Lengend Snippet: SH3GLB1 is implicated in multiple oncogenic pathways and exhibits a significant association with immune activity. ( A ) Bubble plots illustrating the correlation between SH3GLB1 mRNA expression levels and each hallmark gene set activity across the TCGA pan-cancer dataset. NES denotes the normalized enrichment score. ( B ) Comparative analysis of pathway activity scores between the high-expression and low-expression groups of SH3GLB1 based on data from the TCPA database. ( C ) Variations in immune subtypes among pan-cancer samples stratified by high and low SH3GLB1 mRNA expression levels. ( D ) A heatmap depicting the Pearson correlation between SH3GLB1 expression and immune-related genes across pan-cancer types

Article Snippet: Fig. 2 The expression patterns of SH3GLB1 across pan-cancer tissues and its subcellular localization. ( A ) SH3GLB1 expression levels based on the Human Protein Atlas (HPA) database. ( B ) Subcellular localization of SH3GLB1 as derived from the UniProt database. ( C ) Violin plots illustrating variations in SH3GLB1 mRNA expression levels across TCGA-GTEx pan-cancer datasets. ( D ) Paired differential analysis comparing SH3GLB1 mRNA expression levels between tumor and adjacent normal tissues within the TCGA pan-cancer dataset. ( E ) SH3GLB1 gene expression profiles across multiple cancer types: TIMER 3.0 database analysis. ( F ) Boxplots depicting differences in SH3GLB1 protein expression levels using proteomics pan-cancer datasets. ( G ) A heatmap demonstrating SH3GLB1 mRNA expression levels across pan-cancer datasets at the spatial transcriptomic level.

Techniques: Activity Assay, Expressing

Journal: Biology Direct

Article Title: Comprehensive pan-cancer analysis reveals SH3GLB1 is a novel prognostic biomarker with immunomodulatory potential

doi: 10.1186/s13062-026-00728-0

Figure Lengend Snippet: SH3GLB1 in colorectal cancer: expression levels, survival analysis, and pathway enrichment. ( A ) The Beeswarm plots illustrate the correlation between the distribution of SH3GLB1 mRNA expression in normal and tumor tissues. ( B ) The forest plot presents the findings of a univariate Cox survival meta-analysis for the SH3GLB1 gene in colorectal cancer, incorporating data from the TCGA database as well as other external datasets. ( C ) The box diagram displays the results of comparing pathway activity scores between two groups of SH3GLB1 samples (Low group and High group), based on the Wilcoxon rank sum test

Article Snippet: Fig. 2 The expression patterns of SH3GLB1 across pan-cancer tissues and its subcellular localization. ( A ) SH3GLB1 expression levels based on the Human Protein Atlas (HPA) database. ( B ) Subcellular localization of SH3GLB1 as derived from the UniProt database. ( C ) Violin plots illustrating variations in SH3GLB1 mRNA expression levels across TCGA-GTEx pan-cancer datasets. ( D ) Paired differential analysis comparing SH3GLB1 mRNA expression levels between tumor and adjacent normal tissues within the TCGA pan-cancer dataset. ( E ) SH3GLB1 gene expression profiles across multiple cancer types: TIMER 3.0 database analysis. ( F ) Boxplots depicting differences in SH3GLB1 protein expression levels using proteomics pan-cancer datasets. ( G ) A heatmap demonstrating SH3GLB1 mRNA expression levels across pan-cancer datasets at the spatial transcriptomic level.

Techniques: Expressing, Activity Assay

Journal: Biology Direct

Article Title: Comprehensive pan-cancer analysis reveals SH3GLB1 is a novel prognostic biomarker with immunomodulatory potential

doi: 10.1186/s13062-026-00728-0

Figure Lengend Snippet: Analysis of Immune Infiltration and Correlation of SH3GLB1 in CRC. ( A ) The heatmap illustrates disparities in microenvironmental components between SH3GLB1 high - and low - expression groups, as evaluated by seven distinct algorithms. ( B ) The heatmap displays variations in the expression of immune - stimulating genes, immunosuppressive genes, chemokines, and human leukocyte antigens between SH3GLB1 high - and low - expression groups. ( C ) The lollipop plot depicts the correlation between SH3GLB1 expression and microenvironment components as assessed by seven algorithms. ( D ) The Spearman correlation between TIP scores and SH3GLB1 gene expression levels, as well as the autocorrelation among TIP scores, is presented. ( E ) The scatter plot reveals the correlation between SH3GLB1 expression levels in immune - infiltrated cells and the abundance of various immune cells

Article Snippet: Fig. 2 The expression patterns of SH3GLB1 across pan-cancer tissues and its subcellular localization. ( A ) SH3GLB1 expression levels based on the Human Protein Atlas (HPA) database. ( B ) Subcellular localization of SH3GLB1 as derived from the UniProt database. ( C ) Violin plots illustrating variations in SH3GLB1 mRNA expression levels across TCGA-GTEx pan-cancer datasets. ( D ) Paired differential analysis comparing SH3GLB1 mRNA expression levels between tumor and adjacent normal tissues within the TCGA pan-cancer dataset. ( E ) SH3GLB1 gene expression profiles across multiple cancer types: TIMER 3.0 database analysis. ( F ) Boxplots depicting differences in SH3GLB1 protein expression levels using proteomics pan-cancer datasets. ( G ) A heatmap demonstrating SH3GLB1 mRNA expression levels across pan-cancer datasets at the spatial transcriptomic level.

Techniques: Expressing, Gene Expression

Journal: Biology Direct

Article Title: Comprehensive pan-cancer analysis reveals SH3GLB1 is a novel prognostic biomarker with immunomodulatory potential

doi: 10.1186/s13062-026-00728-0

Figure Lengend Snippet: ( A ) Relative expression levels of SH3GLB1 in various CRC cell lines as determined by qRT-PCR. ( B ) Western blot analysis confirming SH3GLB1 protein expression in CRC cell lines. ( C - D ) HT-29 cells were transfected with shRNA targeting SH3GLB1 or a negative control, LOVO cells were transfected with OE-RNA targeting SH3GLB1 or a negative control, and SH3GLB1 protein expression was assessed by Western blot. ( E ) CCK-8 assays evaluated cellular growth curves across groups. ( F ) Wound healing assays evaluated the efficacy of migration across groups. ( G ) Colony formation assays evaluated the efficacy of proliferation and stemness across groups. ( H ) Transwell assays evaluated the efficacy of migration across groups. ( I ) Representative images of xenogeneic subcutaneous tumors in HT-29 cells and LOVO cells of BALB/C mice, and comparison of subcutaneous tumor volumes in BALB/C mice inoculated with HT-29 cells and LOVO cells

Article Snippet: Fig. 2 The expression patterns of SH3GLB1 across pan-cancer tissues and its subcellular localization. ( A ) SH3GLB1 expression levels based on the Human Protein Atlas (HPA) database. ( B ) Subcellular localization of SH3GLB1 as derived from the UniProt database. ( C ) Violin plots illustrating variations in SH3GLB1 mRNA expression levels across TCGA-GTEx pan-cancer datasets. ( D ) Paired differential analysis comparing SH3GLB1 mRNA expression levels between tumor and adjacent normal tissues within the TCGA pan-cancer dataset. ( E ) SH3GLB1 gene expression profiles across multiple cancer types: TIMER 3.0 database analysis. ( F ) Boxplots depicting differences in SH3GLB1 protein expression levels using proteomics pan-cancer datasets. ( G ) A heatmap demonstrating SH3GLB1 mRNA expression levels across pan-cancer datasets at the spatial transcriptomic level.

Techniques: Expressing, Quantitative RT-PCR, Western Blot, Transfection, shRNA, Negative Control, CCK-8 Assay, Migration, Comparison