Journal: Frontiers in Immunology

Article Title: Effect of the m6ARNA gene on the prognosis of thyroid cancer, immune infiltration, and promising immunotherapy

doi: 10.3389/fimmu.2022.995645

Figure Lengend Snippet: Expression of 17 m6A RNA modification genes in thyroid cancer tissues vs. cancer adjacent tissues and their correlation. (A) Vioplot visualizing the 17 m6A RNA methylation genes differentially in thyroid cancer. (B) Expression levels of 17 m6A RNA methylation genes (METTL3/14, RBM15,RBM15B, WTAP, KIAA1429, ZC3H13, YTHDC1/2, YTHDF1/2, HNRNPC, ELF3, IGF2BP2, CBLL1, FTO and ALKBH5)in thyroid cancer tissues vs. cancer adjacent tissues (blue bar represents cancer adjacent and red represents thyroid cancer). The higher or lower the expression, the darker the color (red is up-regulated and green is down-regulated). (C) The Spearman correlation analysis was used to determine the relationships between each individual 17 m6A RNA methylation genes in thyroid cancer. (D) The PPI diagram of 17 m6A RNA methylation genes. (E) The cytohubba software analysis yielded the hub genes in the 17 genes. (*p<0.05, **p<0.01, ***p<0.001, ****p<0.0001 was considered significant.)

Article Snippet: Rabbit antihuman antibodies (FTO antibody (No. DF8421, Affinity Biosciences, Cincinnati, OH, USA), RBM15 antibody (No. DF12061, Affinity Biosciences USA), KIAA1429 antibody (No. 25712-1-AP, Proteintech, Rosemont, IL, USA), were used at 1:500 dilutions.

Techniques: Expressing, RNA modification, Methylation, Software

Journal: Frontiers in Immunology

Article Title: Effect of the m6ARNA gene on the prognosis of thyroid cancer, immune infiltration, and promising immunotherapy

doi: 10.3389/fimmu.2022.995645

Figure Lengend Snippet: Risk signature with three m6A RNA methylation modulators. (A) Univariate Cox regression analysis of the 17 m6A RNA methylation genes in TCGA dataset; the hazard ratios (HR), p value, 3 genes (KIAA1429, FTO, RBM15) are identified (p<0.05, HR>1). (B, C) 3 genes (KIAA1429, FTO, RBM15) with p value<0.05 and HR>1 were selected according to the criteria to construct the best predictive gene signatures, and the risk score of the TCGA dataset was calculated using the coefficients obtained by LASSO algorithm. (D) Chart of clinical significance-prognostication-risk factors. Compared with the low-risk group, the high-risk group had higher expression levels of 3 genes and higher mortality rate. (E) The ROC curve (AUC) of high-risk and low-risk group, the risk signature is credible (AUC=0.744). (F) The survival curve of high-risk and low-risk group, the overall survival of patients with thyroid cancer was poor in the high-risk subgroup.

Article Snippet: Rabbit antihuman antibodies (FTO antibody (No. DF8421, Affinity Biosciences, Cincinnati, OH, USA), RBM15 antibody (No. DF12061, Affinity Biosciences USA), KIAA1429 antibody (No. 25712-1-AP, Proteintech, Rosemont, IL, USA), were used at 1:500 dilutions.

Techniques: Methylation, Construct, Expressing

Journal: Frontiers in Immunology

Article Title: Effect of the m6ARNA gene on the prognosis of thyroid cancer, immune infiltration, and promising immunotherapy

doi: 10.3389/fimmu.2022.995645

Figure Lengend Snippet: Representative immunohistochemical staining of RBM15, KIAA1429, FTO in benign thyroid nodule tissue and thyroid cancer tissue. (A) Immunohistochemical image of FTO in thyroid cancer tissue. (B) Immunohistochemical image of FTO in benign thyroid nodule tissue. (C) Immunohistochemical image of RBM15 in PTC tissue. (D) Immunohistochemical staining image of RBM15 in benign thyroid nodule tissue. (E) Immunohistochemical image of KIAA1429 in PTC tissue. (F) Immunohistochemical image of KIAA1429 in benign thyroid nodule tissue.

Article Snippet: Rabbit antihuman antibodies (FTO antibody (No. DF8421, Affinity Biosciences, Cincinnati, OH, USA), RBM15 antibody (No. DF12061, Affinity Biosciences USA), KIAA1429 antibody (No. 25712-1-AP, Proteintech, Rosemont, IL, USA), were used at 1:500 dilutions.

Techniques: Immunohistochemical staining, Staining

Journal: bioRxiv

Article Title: DUX4-induced HSATII RNA accumulation drives protein aggregation impacting RNA processing pathways

doi: 10.1101/2024.12.17.628988

Figure Lengend Snippet: ( A ) Biological process pathway analysis of DUX4-induced stable EU-RNA associated RNPs (EU-RNPs) proteomics filtered protein hits (>2 unique peptide matches and >1.5 difference) ran through Enrichr. EU-RNP complexes were isolated from - DOX+EU, +DOX+EU or +DOX-EU iDUX4 cells harvested at the 48-hour time point using the “RICK” approach . Protein was purified from isolated EU-RNP complexes and was subjected to mass-spectrometry. Proteomics was performed in experimental duplicates. ( B ) Validation of selected proteins identified through EU-RNP proteomics: Known DUX4-induced protein aggregates SC35 and TDP-43, and m 5 C-related factors NSUN2 and YBX-1. Proteins were isolated as stated in . GAPDH and beta-tubulin were used as loading controls for inputs and negative controls for pulldown samples. Blot shows singletons, but representative of experimental triplicates. -D+E, -DOX+EU samples; +D+E, +DOX+EU samples; +D-E, +DOX-EU samples. ( C ) Immunofluorescence of EU-RNA (green) and SC35 (magenta) in -DOX+EU or +DOX+EU iDUX4 cells fixed at 48-hour time point. Scale bar = 20μm. Images are representative of two independent experimental replicates performed. ( D ) Mean signal intensity of SC35 within specified regions of interest (ROI) in the nucleus: either within EU-RNA foci or the remainder of the nucleoplasm in +DOX EU-RNA+ nuclei in iDUX4 cells. Dots are each individual ROI. N ≥ 35 ROI. ROI within the nucleoplasm is drawn with relatively the same circumference as EU-RNA foci ROI. Data are representative of two independent experimental replicates. Data represent means. Statistical differences between groups were analyzed employing Mann Whitney test. ( E ) Combined immunofluorescence and HSATII RNA-FISH of HSATII (green) and SC35 (magenta) in -DOX or +DOX iDUX4 cells fixed at 24-hour time point. Scale bar = 20μm. Images are representative of two independent experimental replicates performed. ( F ) Mean signal intensity of SC35 within specified ROI in the nucleus: either within HSATII RNA foci or the remainder of the nucleoplasm in +DOX HSATII+ nuclei in iDUX4 cells. Dots are each individual ROI. N ≥ 35 ROI. ROI within the nucleoplasm is drawn with relatively the same circumference as HSATII RNA foci ROI. Data are representative of two independent experimental replicates. Data represent means. ( G ) Immunofluorescence of EU-RNA (green) and TDP-43 (magenta) in -DOX+EU or +DOX+EU iDUX4 cells fixed at 48-hour time point. Scale bar = 20μm. Images are representative of two independent experimental replicates performed. ( H ) Mean signal intensity of TDP-43 within specified ROI in the nucleus: either within EU-RNA foci or the remainder of the nucleoplasm in +DOX EU-RNA+ nuclei in iDUX4 cells. Dots are each individual ROI. N ≥ 30 ROI. ROI within the nucleoplasm is drawn with relatively the same circumference as EU-RNA foci ROI. Data are representative of two independent experimental replicates. Data represent means. Statistical differences between groups were analyzed employing Mann Whitney test. ( I ) Combined immunofluorescence and HSATII RNA-FISH of HSATII (green) and TDP-43 (magenta) in -DOX or +DOX iDUX4 cells with CTRL KD or HSATII KD fixed at 24-hour time point. Scale bar = 20μm. Images are representative of three independent experimental replicates performed. ( J ) Mean signal intensity of TDP-43 within specified ROI in the nucleus: either within HSATII RNA foci or the remainder of the nucleoplasm in +DOX HSATII+ nuclei in iDUX4 cells. Dots are each individual ROI. N ≥ 90 ROI. ROI within the nucleoplasm is drawn with relatively the same circumference as HSATII RNA foci ROI. Data are representative of three independent experimental replicates. Data represent means. Statistical differences between groups were analyzed employing Mann Whitney test. ( K ) Percent of cells with TDP-43 nuclear aggregates in +DOX iDUX4 cells with CTRL KD or HSATII KD. N ≥ 200 nuclei. Dots represent averages of three experimental replicates graphed. Data represent means ± SD. Statistical differences between groups were analyzed employing two-tailed Unpaired t-test.

Article Snippet: SC35 (Abcam Cat# ab204916, RRID:AB_2909393), TDP-43 (Proteintech Cat# 10782-2-AP, RRID:AB_615042), MeCP2 (Abcam Cat#ab137357), NSUN2 (Proteintech Cat# 20854-1-AP, RRID:AB_10693629), NSUN2 (Cell Signaling Techonology Cat#52901), MVP (Proteintech Cat# 16478-1-AP, RRID:AB_2147597), YBX-1 (Abcam Cat# ab76149, RRID:AB_2219276), NPM1 (Proteintech Cat# 60096-1-Ig, RRID:AB_2155162), FBL (Proteintech Cat# 16021-1-AP, RRID:AB_2105788), m 5 C (Cell Signaling Technology Cat# 28692, RRID:AB_2798962), K1 (SCICONS Cat# 10020200, RRID:AB_2756865), GAPDH (GeneTex Cat# GTX28245, RRID:AB_370675), eIF4A3 (Abcam Cat#ab180573), H3.X/Y (Active Motif Cat# 61161, RRID:AB_2793533), Beta Tubulin (Proteintech Cat# 10094-1-AP, RRID:AB_2210695), VIRMA (Proteintech Cat# 25712-1-AP, RRID:AB_2880204), WTAP (Cell Signaling Technology Cat# 56501, RRID:AB_2799512), YTHDC1 (Cell Signaling Technology Cat# 77422, RRID:AB_2799899), m 6 A (Synaptic Systems Cat# 202 003, RRID:AB_2279214), DUX4 (E14-3) , eIF4ENIF1 (Thermo Fisher Scientific Cat# PA5-115169, RRID:AB_2899805), TRIM21 (Thermo Fisher Scientific Cat# PA5-22294, RRID:AB_11153206), Goat Anti-Rabbit IgG (H+L) Superclonal Recombinant Secondary Antibody, HRP (Thermo Fisher Scientific Cat# A27036, RRID:AB_2536099), Goat Anti-Mouse IgG (H+L) Superclonal Recombinant Secondary Antibody, HRP (Thermo Fisher Scientific Cat# A28177, RRID:AB_2536163), Goat anti-Rat IgG (H+L) Secondary Antibody, HRP (Thermo Fisher Scientific Cat# 31470, RRID:AB_228356), Rhodamine (TRITC)-AffiniPure Donkey Anti-Rabbit IgG (H+L) (Jackson ImmunoResearch Labs Cat# 711-025-152, RRID:AB_2340588), Rhodamine (TRITC)-AffiniPure Donkey Anti-Mouse IgG (H+L) (Jackson ImmunoResearch Labs Cat# 715-025-151, RRID:AB_2340767), Fluorescein (FITC)-AffiniPure Donkey Anti-Mouse IgG (H+L) (Jackson ImmunoResearch Labs Cat# 715-095-151, RRID:AB_2335588), Fluorescein (FITC)-AffiniPure Donkey Anti-Rabbit IgG (H+L) (Jackson ImmunoResearch Labs Cat# 711-095-152, RRID:AB_2315776), Streptavidin, Alexa Fluor 555 conjugate antibody (ThermoFisher Scientific Cat# S21381), Donkey anti-Rabbit IgG (H+L) Highly Cross-Adsorbed Secondary Antibody, Alexa Fluor 488 (Thermo Fisher Scientific Cat# A-21206, RRID:AB_2535792), Donkey anti-Mouse IgG (H+L) Highly Cross-Adsorbed Secondary Antibody, Alexa Fluor 488 (Thermo Fisher Scientific Cat# A-21202, RRID:AB_141607), Donkey anti-Rabbit IgG (H+L) Highly Cross-Adsorbed Secondary Antibody, Alexa Fluor 555 (Thermo Fisher Scientific Cat# A-31572, RRID:AB_162543), Donkey anti-Mouse IgG (H+L) Highly Cross-Adsorbed Secondary Antibody, Alexa Fluor 555 (Thermo Fisher Scientific Cat# A-31570, RRID:AB_2536180).

Techniques: Isolation, Purification, Mass Spectrometry, Immunofluorescence, MANN-WHITNEY, Two Tailed Test

Journal: iScience

Article Title: KIAA1429 promotes clear cell renal cell carcinoma progression by regulating MYC mRNA stability

doi: 10.1016/j.isci.2026.115198

Figure Lengend Snippet: Comprehensive analysis of the KIAA1429 in the TCGA and GEO database (A) The expression of KIAA1429 in the TCGA-KIRCC database (tumor samples n = 523, normal samples n = 100). (B–D) The expression levels of KIAA1429 in ccRCC tissues and adjacent normal tissues (23 pairs of paired samples) in (B) GSE36895 dataset, (C) GSE53757 dataset (72 pairs of paired samples), and (D) GSE40435 dataset (101 pairs of paired samples). (E) The GEPIA database analyzed the expression of KIAA1429 in patients with ccRCC of different clinical stages. (F and G) The GEPIA database analyzed the effect of KIAA1429 mRNA expression on the OS and DFS of patients with ccRCC. Data are presented as the means ± SEM. ∗ p < 0.05, ∗∗∗ p < 0.001 by Student’s two-tailed t test.

Article Snippet: KIAA1429 Rabbit Polyclonal antibody , Proteintech , Cat#24761-1-AP.

Techniques: Expressing, Two Tailed Test

Journal: iScience

Article Title: KIAA1429 promotes clear cell renal cell carcinoma progression by regulating MYC mRNA stability

doi: 10.1016/j.isci.2026.115198

Figure Lengend Snippet: KIAA1429 mRNA and protein expression was significantly upregulated in ccRCC tissues and cell lines and its relationship to clinicopathological parameters (A and B) The protein and mRNA levels of KIAA1429 in ccRCC and normal kidney tissues. (C and D) KIAA1429 mRNA and protein expression in ccRCC cell lines and normal epithelium cell of renal tubule (HK2) cells. (E and F) The expression level of KIAA1429 in ccRCC tissue and surrounding normal renal tissue was detected using IHC. Scale bars, 100 μm. (G) The expression level of KIAA1429 in patients with ccRCC with different clinical stages and Fuhrman’s grade. (H) Effect of KIAA1429 expression on the overall survival of patients with ccRCC. T, tumor; N, normal. Data are presented as the means ± SEM. ∗ p < 0.05, ∗∗ p < 0.01, ∗∗∗ p < 0.001 by Student’s two-tailed t test.

Article Snippet: KIAA1429 Rabbit Polyclonal antibody , Proteintech , Cat#24761-1-AP.

Techniques: Expressing, Two Tailed Test

Journal: iScience

Article Title: KIAA1429 promotes clear cell renal cell carcinoma progression by regulating MYC mRNA stability

doi: 10.1016/j.isci.2026.115198

Figure Lengend Snippet: KIAA1429 promoted ccRCC cell proliferation in vitro (A) Knockdown efficiencies of KIAA1429 mRNA in ACHN and Caki-1 cells were detected using RT-qPCR; KIAA1429 protein expression decreased significantly in groups of shKIAA1429 in western blot analysis. (B and C) The effect of KIAA1429 knockdown on the proliferation of ccRCC cells was detected using a CCK-8 assay (B) and colony formation assay (C). (D) The effect of KIAA1429 on the cell cycle of ccRCC cells was detected using flow cytometry. Data are presented as the means ± SEM ∗ p < 0.05, ∗∗ p < 0.01 by Student’s two-tailed t test.

Article Snippet: KIAA1429 Rabbit Polyclonal antibody , Proteintech , Cat#24761-1-AP.

Techniques: In Vitro, Knockdown, Quantitative RT-PCR, Expressing, Western Blot, CCK-8 Assay, Colony Assay, Flow Cytometry, Two Tailed Test

Journal: iScience

Article Title: KIAA1429 promotes clear cell renal cell carcinoma progression by regulating MYC mRNA stability

doi: 10.1016/j.isci.2026.115198

Figure Lengend Snippet: KIAA1429 promoted ccRCC cell migration and invasion in vitro (A and B) The effect of KIAA1429 knockdown on the migration and invasion of Caki-1 and ACHN cells were detected using a cell wound-healing assay (A) and transwell assay (B). (C) Western blot analysis of vimentin, N-cadherin, and E-cadherin protein expression in Caki-1 and ACHN cells with KIAA1429 knockdown. Data are presented as the means ± SEM. ∗ p < 0.05 by Student’s two-tailed t test.

Article Snippet: KIAA1429 Rabbit Polyclonal antibody , Proteintech , Cat#24761-1-AP.

Techniques: Migration, In Vitro, Knockdown, Wound Healing Assay, Transwell Assay, Western Blot, Expressing, Two Tailed Test

Journal: iScience

Article Title: KIAA1429 promotes clear cell renal cell carcinoma progression by regulating MYC mRNA stability

doi: 10.1016/j.isci.2026.115198

Figure Lengend Snippet: KIAA1429 promoted tumorigenesis of ccRCC cells in vivo (A) Subcutaneous tumor model of ACHN cells with KIAA1429 knockdown. KIAA1429 knockdown led to decreased tumor volume. (B and C) The changes in volume and weight were measured at the indicated weeks after mice were transplanted with the relevant cells. (D) IHC of vimentin, Ki-67, and E-cadherin protein expression in tumors with KIAA1429 knockdown. Data are presented as the means ± SEM. ∗ p < 0.05, ∗∗∗ p < 0.001 by Student’s two-tailed t test.

Article Snippet: KIAA1429 Rabbit Polyclonal antibody , Proteintech , Cat#24761-1-AP.

Techniques: In Vivo, Knockdown, Expressing, Two Tailed Test

Journal: iScience

Article Title: KIAA1429 promotes clear cell renal cell carcinoma progression by regulating MYC mRNA stability

doi: 10.1016/j.isci.2026.115198

Figure Lengend Snippet: MYC might be a potential target for regulation by KIAA1429 in ccRCC (A) KIAA1429 has a significant effect on most RNA-specific processes, cell cycle, cell death, apoptosis, and intracellular signaling pathways, as revealed by GO and KEGG analyses. (B) Heatmap illustrating the downregulated genes in ACHN cells after KIAA1429 knockdown. (C) The expression level of MYC in ccRCC, obtained from the TCGA database. (D) Correlation analysis between the expression of MYC and KIAA1429. Data are presented as the means ± SEM. ∗∗∗ p < 0.001 by Student’s two-tailed t test.

Article Snippet: KIAA1429 Rabbit Polyclonal antibody , Proteintech , Cat#24761-1-AP.

Techniques: Protein-Protein interactions, Knockdown, Expressing, Two Tailed Test

Journal: iScience

Article Title: KIAA1429 promotes clear cell renal cell carcinoma progression by regulating MYC mRNA stability

doi: 10.1016/j.isci.2026.115198

Figure Lengend Snippet: KIAA1429 regulated the expression of MYC mRNA and its stability in an m6A-dependent manner (A and C) KIAA1429 knockdown inhibits the protein and mRNA expression of MYC in ccRCC cells. (B) KIAA1429 knockdown decreased the stability of MYC mRNA. (D) RIP assay showed that KIAA1429 interacts with MYC mRNA in Caki-1 and ACHN cells. (E) KIAA1429 knockdown reduced overall m6A levels in Caki-1 and ACHN cells. (F) KIAA1429 knockdown reduced m6A levels in MYC. (G) m6A methylation sites on MYC were predicted using the SRAMP database. (H) The pmirGLO-MYC-WT or pmirGLO-MYC-MUT luciferase reporter was transfected into KIAA1429-knockdown and control Caki-1 and ACHN cells, and relative luciferase activity was measured. Data are presented as the ratio of firefly to Renilla luciferase activity. Data are presented as the means ± SEM. ∗ p < 0.05, ∗∗ p < 0.01, ∗∗∗ p < 0.001 by Student’s two-tailed t test.

Article Snippet: KIAA1429 Rabbit Polyclonal antibody , Proteintech , Cat#24761-1-AP.

Techniques: Expressing, Knockdown, Methylation, Luciferase, Transfection, Control, Activity Assay, Two Tailed Test