Journal: Cell reports

Article Title: Activity-assembled nBAF complex mediates rapid immediate early gene transcription by regulating RNA polymerase II productive elongation

doi: 10.1016/j.celrep.2024.114877

Figure Lengend Snippet: (A) Schematic representation of three biochemically distinct BAF complexes: nBAF (neuronal cBAF), GBAF, and PBAF. Complex-defining unique subunits are represented in colors. Subunits shared by all three complexes are not indicated. Degraders and small-molecule inhibitors to target each complex are noted below. Schematic was created using BioRender. (B) Neurons were treated with DMSO (control) or the indicated concentrations of ACBI1 or cis -ACBI1 (inactive isomer of ACBI1) for 3 h. Whole-cell lysates were electrophoresed, western blotted, and probed for the indicated BAF subunits. (C–E) Neuronal lysates were used to immunoprecipitate SMARCA4 (C), ARID1A (D), and ARID1B (E). Five percent of the cell lysate was used as input. Histone 3 and IgG are depicted as loading controls. (F and G) Transcriptional assays in which Arc pre-mRNA normalized by GAPDH pre-mRNA levels is illustrated. (F) Neurons were treated with ACBI1 or cis -ACBI1 for 3 h followed by bicuculline and 4AP treatment for 15 min (Bic + 4AP). (G) Neurons were treated with BAF ATPase domain inhibitors BRM014 and FHT for 30 min, followed by Bic + 4AP treatment to induce neuronal activity. Gray dots represent biological replicates, error bars show SE of the mean. * p < 0.05 and ** p < 0.01. One-way ANOVA was followed by Tukey’s post hoc test. Approximate position of the nearest molecular weight marker is depicted against each band.

Article Snippet: To inhibit BAF ATPase function, BRM014 (compound 14, MedChemExpress; catalog no. HY-119374) and FHT-1015 (MedChemExpress; catalogue no. HY-144896) were used at concentrations described in figure legends.

Techniques: Control, Western Blot, Activity Assay, Molecular Weight, Marker

Journal: Cell reports

Article Title: Activity-assembled nBAF complex mediates rapid immediate early gene transcription by regulating RNA polymerase II productive elongation

doi: 10.1016/j.celrep.2024.114877

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: To inhibit BAF ATPase function, BRM014 (compound 14, MedChemExpress; catalog no. HY-119374) and FHT-1015 (MedChemExpress; catalogue no. HY-144896) were used at concentrations described in figure legends.

Techniques: Recombinant, Plasmid Preparation, Magnetic Beads, One Step RT-PCR, SYBR Green Assay, Mass Spectrometry, Software

Journal: BioMed Research International

Article Title: PLP2 Expression as a Prognostic and Therapeutic Indicator in High-Risk Multiple Myeloma

doi: 10.1155/2020/4286101

Figure Lengend Snippet: PLP2 was a high-risk myeloma gene. (a) PLP2 expression of NPC ( n = 22), MGUS ( n = 44), SMM ( n = 12), and MM (TT2, n = 351; TT3, n = 208) in GSE5900 and GSE2658 datasets ( ∗∗ p < 0.01, ∗∗∗ p < 0.001). (b) A scatter plot showing the PLP2 expression in eight MM subgroups (CD1 and CD2 subgroups with spiked expression of CCND1 and CCND3; PR: proliferation; LB: low-bone disease; HY: hyperdiploid; MS: MMSET; MF: MAFB; MY: myeloid). (c) CD138 and PLP2 expressions in the bone marrow of NDMM patients. Representative case with a lack of PLP2 expression: H&E stain, CD138 immunostain, and PLP2 immunostain (upper row). Representative case with stable PLP2 expression: H&E stain, CD138 immunostain, and PLP2 immunostain (lower row).

Article Snippet: Formalin-fixed, paraffin-embedded sections were utilized for IHC with the following antibodies: CD138 (Proteintech, USA) and PLP2 (Proteintech, USA), according to the manufacturer's protocol [ ].

Techniques: Expressing, Staining

Journal: BioMed Research International

Article Title: PLP2 Expression as a Prognostic and Therapeutic Indicator in High-Risk Multiple Myeloma

doi: 10.1155/2020/4286101

Figure Lengend Snippet: PLP2 was linked to myeloma progression. (a–d) β 2-MG, LDH, bone marrow infiltration, and ISS stages were expressed the highest in the high PLP2 expression subgroup, while the lowest in the low PLP2 expression subgroup ( ∗ p < 0.05). (e–g) β 2-MG and CRP were expressed the highest in the PLP2 high subgroup, while ALB was expressed the lowest in the PLP2 high subgroup ( ∗∗ p < 0.01, ∗∗∗ p < 0.001).

Article Snippet: Formalin-fixed, paraffin-embedded sections were utilized for IHC with the following antibodies: CD138 (Proteintech, USA) and PLP2 (Proteintech, USA), according to the manufacturer's protocol [ ].

Techniques: Expressing

Journal: BioMed Research International

Article Title: PLP2 Expression as a Prognostic and Therapeutic Indicator in High-Risk Multiple Myeloma

doi: 10.1155/2020/4286101

Figure Lengend Snippet: High PLP2 expression was linked to a poor prognosis in two independent datasets. (a, b) Kaplan-Meier analyses of OS and PFS revealed that strong PLP2 staining intensity conferred inferior clinical outcomes in our cohort. (c, d) Kaplan-Meier analyses of OS and PFS revealed that high PLP2 gene expression conferred inferior clinical outcomes in GSE24080.

Article Snippet: Formalin-fixed, paraffin-embedded sections were utilized for IHC with the following antibodies: CD138 (Proteintech, USA) and PLP2 (Proteintech, USA), according to the manufacturer's protocol [ ].

Techniques: Expressing, Staining, Gene Expression

Journal: BioMed Research International

Article Title: PLP2 Expression as a Prognostic and Therapeutic Indicator in High-Risk Multiple Myeloma

doi: 10.1155/2020/4286101

Figure Lengend Snippet: Univariate and multivariate Cox regression analyses for OS in 87 NDMM patients.

Article Snippet: Formalin-fixed, paraffin-embedded sections were utilized for IHC with the following antibodies: CD138 (Proteintech, USA) and PLP2 (Proteintech, USA), according to the manufacturer's protocol [ ].

Techniques:

Journal: BioMed Research International

Article Title: PLP2 Expression as a Prognostic and Therapeutic Indicator in High-Risk Multiple Myeloma

doi: 10.1155/2020/4286101

Figure Lengend Snippet: Univariate and multivariate Cox regression analyses for PFS in 87 NDMM patients.

Article Snippet: Formalin-fixed, paraffin-embedded sections were utilized for IHC with the following antibodies: CD138 (Proteintech, USA) and PLP2 (Proteintech, USA), according to the manufacturer's protocol [ ].

Techniques:

Journal: BioMed Research International

Article Title: PLP2 Expression as a Prognostic and Therapeutic Indicator in High-Risk Multiple Myeloma

doi: 10.1155/2020/4286101

Figure Lengend Snippet: PLP2 was related to treatment response. The correlations between drug responses with PLP2 levels were analyzed by chi-square test. Patients with low PLP2 expression significantly responded to chemotherapies evidenced by increased ORR, ≥VGPR, ≥CR, and ≥sCR.

Article Snippet: Formalin-fixed, paraffin-embedded sections were utilized for IHC with the following antibodies: CD138 (Proteintech, USA) and PLP2 (Proteintech, USA), according to the manufacturer's protocol [ ].

Techniques: Expressing

Journal: BMC musculoskeletal disorders

Article Title: Construction and evaluation of a prognostic model based on the expression of the metabolism-related signatures in patients with osteosarcoma.

doi: 10.1186/s12891-025-08439-9

Figure Lengend Snippet: Fig. 6 Validation of signature genes in osteosarcoma cells. A The expression levels of three lncRNAs (LINC00545, FOXC2-AS1, and LINC01537) were determined by qRT-PCR. B The expression levels of six mRNAs (CYP27B1, PFKFB4, PHKG1, PHYKPL, PXMP2, and XYLB) were measured by qRT-PCR. C The protein expression levels of PFKFB4, PHYKPL, PXMP2, and XYLB in osteosarcoma cells were detected by western blotting. * p < 0.05, ** p < 0.01, compared with the osteoblasts hFOB1.19

Article Snippet: After blocked with 5% skim milk at 37 °C for 2 h, the membranes were respectively incubated with the anti-PFKFB4 antibody (1:1000, Proteintech, Wuhan, China), anti-PHYKPL antibody (1:1000, Proteintech), anti-PXMP2 antibody (1:1000, Abcam, Cambridge, UK), anti-XYLB antibody (1: 1000, Thermo Fisher Scientific), and anti-GAPDH antibody (1:1000, Proteintech) at 4 °C overnight.

Techniques: Biomarker Discovery, Expressing, Quantitative RT-PCR, Western Blot

Journal: Cell Death & Disease

Article Title: RACK1 depletion in the ribosome induces selective translation for non-canonical autophagy

doi: 10.1038/cddis.2017.204

Figure Lengend Snippet: RACK1 depletion-induced autophagy is non-canonical. ( a ) HT1080 cells transfected with control or RACK1 siRNAs (50 pmol) were incubated for 48 h, followed by immunoblot analysis using the indicated antibodies (left panel). Intensities of Atg5/12 and Beclin1 proteins were normalized against that of tubulin proteins, and the relative expressions in RACK1 siRNA-treated cells compared with that in control cells were plotted (right panel). ( b ) HT1080 cells were transfected with siRNAs against control or RACK1 in combination with or without Beclin1 siRNA (100 pmol). After 48 h, these cells were analyzed by immunoblotting using the indicated antibodies. ( c ) HT1080 cells were transfected with control or Atg5 siRNA (100 pmol). After 24 h, the cells were re-transfected with control or RACK1 siRNA. After a further 48 h incubation, the cell extracts were subjected to immunoblot analysis using the indicated antibodies. ( d ) HT1080 cells transfected with control or RACK1 siRNAs (50 pmol) were incubated for 48 h, followed by immunoblot analysis using the indicated antibodies. ( e ) HT1080 cells transfected with control or RACK1 siRNAs (50 pmol) were incubated for 24 h. Extracts of siRNA-transfected cells were pretreated with rapamycin 1 μM for 24 h, followed by immunoblot analysis using the indicated antibodies. Intensities of LAMP1 and LAMP2 proteins were normalized against that of tubulin proteins, and the relative expressions in RACK1 siRNA-treated cells compared with that in control cells were plotted. * P <0.05, ** P <0.01 (Student’s t -test)

Article Snippet: Antibodies against Atg5, Atg9A, Atg4B, Atg16, LAMP1 and LAMP2 were obtained from ProSci (Poway, CA, USA), and the anti-rpS3 antibody was from HAEL (Seoul, Korea).

Techniques: Transfection, Control, Incubation, Western Blot