Journal: Molecular Cancer

Article Title: Analysis of colorectal cancers in British Bangladeshi identifies early onset, frequent mucinous histotype and a high prevalence of RBFOX1 deletion

doi: 10.1186/1476-4598-12-1

Figure Lengend Snippet: Genomic alterations and expression changes of RBFOX1 in CRC. (A) Analysis of relative copy number (blue) gain and (red) loss across all cancers (CIN, MACS and BAN) shows recurrent deletions on chromosome 16p13 affecting the RBFOX1 gene. (B) Scatter plot showing RBFOX1 gene expression level as detected by quantitative real time PCR. Nineteen tumour / normal sample pairs were tested and mRNA level is expressed as ratio of RBFOX1 and HPRT concentration, [ RBFOX1 ] / [ HPRT ].

Article Snippet: Quantitative Real-time polymerase chain reaction (QPCR) was performed using TaqMan assays (Applied Biosystems) against RBFOX1 (Hs00251554_m1) and thecontrol housekeeping gene HPRT (hypoxanthine phosphoribosyltransferase 1;HuHPRT_0604009).

Techniques: Expressing, Gene Expression, Real-time Polymerase Chain Reaction, Concentration Assay

Journal: Molecular Cancer

Article Title: Analysis of colorectal cancers in British Bangladeshi identifies early onset, frequent mucinous histotype and a high prevalence of RBFOX1 deletion

doi: 10.1186/1476-4598-12-1

Figure Lengend Snippet: Immunohistochemical detection of RBFOX1. (A) Normal appearing colonic mucosa with diffuse cytoplasmic staining of most epithelium (x100). (B) Normal colon with diffuse staining of the epithelium and some stromal cells and inflammatory cells; the pericryptal sheath fibroblasts appear unstained (x200). (C) Adenocarcinoma showing absence of RBFOX1 staining in the majority of the cells lining the two-neoplastic glands in the lower half of the picture (x200). (D) Neighbouring glands show persistence (left) or reduction/ loss (right) of RBFOX1 immunoreactivity on epithelial cell cytoplasm (x200).

Article Snippet: Quantitative Real-time polymerase chain reaction (QPCR) was performed using TaqMan assays (Applied Biosystems) against RBFOX1 (Hs00251554_m1) and thecontrol housekeeping gene HPRT (hypoxanthine phosphoribosyltransferase 1;HuHPRT_0604009).

Techniques: Immunohistochemical staining, Staining

Journal: Molecular Cancer

Article Title: Analysis of colorectal cancers in British Bangladeshi identifies early onset, frequent mucinous histotype and a high prevalence of RBFOX1 deletion

doi: 10.1186/1476-4598-12-1

Figure Lengend Snippet: RBFOX1 mutations and single nucleotide polymorphisms found in CRC cell lines and patient tumour samples

Article Snippet: Quantitative Real-time polymerase chain reaction (QPCR) was performed using TaqMan assays (Applied Biosystems) against RBFOX1 (Hs00251554_m1) and thecontrol housekeeping gene HPRT (hypoxanthine phosphoribosyltransferase 1;HuHPRT_0604009).

Techniques:

Journal: Technology in Cancer Research & Treatment

Article Title: The Expression Characteristics of the RBFOX1 Gene in Colorectal Cancer

doi: 10.1177/15330338251333695

Figure Lengend Snippet: Copy Number Variation of RBFOX1 and Its Correlation with DFS and OS. A. Online Data from Cbioportal shows that RBFOX1 has the Highest Frequency of Copy Number Deletions in Colorectal Cancer. B And C. Analysis of RBFOX1 Copy Number Situation in Colorectal Adenocarcinoma (TCGA, Firehose Legacy) and Colon Cancer (CPTAC-2 Prospective, Cell 2019) Data. D. KM Survival Curve of Progression-Free Survival and Overall Survival Among the Four Groups.

Article Snippet: A2BP1 Polyclonal antibody (Proteintech, USA, 22647-1-AP) was added dropwise and incubated at 37 °C for 1 h. The liquid was poured off, and the sections were rinsed with PBS three times.

Techniques:

Journal: Technology in Cancer Research & Treatment

Article Title: The Expression Characteristics of the RBFOX1 Gene in Colorectal Cancer

doi: 10.1177/15330338251333695

Figure Lengend Snippet: Characteristics of RBFOX1 mRNA in Colorectal Cancer. A. Correlation Analysis of Total RBFOX1 Copy Number Variation and RBFOX1 mRNA Expression. B. Differences in RBFOX1 mRNA Expression Among the Four Groups, with Significant Differences Between Groups A And C (**** Represent P < 0.0001), and Significant Differences Between Groups C And D (*** Denotes P < 0.001). C-F. Correlation Analysis of Copy Number Variation and Corresponding mRNA Expression in Each Group Among the Four Groups., C: (Group A–High–Level Copy Number Deletions Group), D(Group B– Represent Low-Level Deletion Group), E(Group C– Normal Group), F(Group D –Copy Number Amplification Group). G. Relative mRNA Expression of RBFOX1 in Colon Adenocarcinoma and Rectal Adenocarcinoma, Indicating that RBFOX1 mRNA Expression in Colorectal Cancer is Lower than in Normal Tissues. H. Correlation between BRAF Gene Mutation and RBFOX1 mRNA in Colon Cancer and Rectal Cancer Tissues. I. Correlation Between PIK3CA Gene Mutation and RBFOX1 mRNA in Colon Cancer and Rectal Cancer Tissues.

Article Snippet: A2BP1 Polyclonal antibody (Proteintech, USA, 22647-1-AP) was added dropwise and incubated at 37 °C for 1 h. The liquid was poured off, and the sections were rinsed with PBS three times.

Techniques: Expressing, Amplification, Mutagenesis

Journal: Technology in Cancer Research & Treatment

Article Title: The Expression Characteristics of the RBFOX1 Gene in Colorectal Cancer

doi: 10.1177/15330338251333695

Figure Lengend Snippet: Immunofluorescence Analysis of RBFOX1 Protein in Tumor Cells. A. Immunofluorescence from the Human Protein Atlas Database shows that RBFOX1 has Different Nuclear-Cytoplasmic Distribution Characteristics in Cancer Cells of Three Different Tissues. ( https://www.proteinatlas.org/search/RBFOX1 ) B. COSMIC Cancer Cell Engineering shows Copy Number Deletions in Multiple Colorectal Cancer Cells. C. Immunofluorescence shows that RBFOX1 Protein is Mainly Distributed in the Nucleus of Well-Differentiated Tumor Cells HT-29 and SW480, While in Poorly Differentiated HCT116, The Protein shows Nuclear-Cytoplasmic Distribution Characteristics.

Article Snippet: A2BP1 Polyclonal antibody (Proteintech, USA, 22647-1-AP) was added dropwise and incubated at 37 °C for 1 h. The liquid was poured off, and the sections were rinsed with PBS three times.

Techniques: Immunofluorescence

Journal: Technology in Cancer Research & Treatment

Article Title: The Expression Characteristics of the RBFOX1 Gene in Colorectal Cancer

doi: 10.1177/15330338251333695

Figure Lengend Snippet: Immunohistochemical Analysis of RBFOX1 Expression Level in Normal and Cancerous Colorectal Tissues. A. Immunohistochemical Results from The Human Protein Atlas Database Show that the Protein is Mainly Distributed in the Glandular Cells of the Normal Intestine and shows Low Cytoplasmic Distribution Characteristics, But the Expression of this Protein is not Detected in Colorectal Cancer Tissues, Here are Two Representative Tissues. N1958 Representative an Immunohistochemical Results of RBFOX1 of 84 Years Old Female Patient in Normal Colon Tissue, 1958 is the Patient ID, N1857 Representative an Immunohistochemical Results of RBFOX1 of 47 Years Old Male Patient in Normal Colon Tissue, C4724 Representative an Immunohistochemical Results of RBFOX1 of 70 Years Old Female Patient in Adenocarcinoma Tissue, C4724 Representative an Immunohistochemical Results of RBFOX1 of 82 Years Old Female Patient in Colon Adenocarcinoma Tissue. ( https://www.proteinatlas.org/search/RBFOX1 ). B. Immunohistochemical Results of RBFOX1 in Two High-Throughput Pathological Tissue Chips (Consisting of 69 Colorectal Cancer Tissues). C. A Normal Brain Sample was Used as a Positive Control., On the Left is a 100x Microscopic Image of the Brain, And on the Right is a 200x Magnified Image of a Localized Area on the Left. D. Immunohistochemical Results of RBFOX1 in Intestinal Tissue from a Case of slow Transit Constipation Undergoing Total Colectomy. E. Immunohistochemical Results of RBFOX1 in Three Right-Sided Colorectal Cancers and Adjacent Tissues. N Means Normal, C Means Cancer.

Article Snippet: A2BP1 Polyclonal antibody (Proteintech, USA, 22647-1-AP) was added dropwise and incubated at 37 °C for 1 h. The liquid was poured off, and the sections were rinsed with PBS three times.

Techniques: Immunohistochemical staining, Expressing, High Throughput Screening Assay, Positive Control

Journal: Nature structural & molecular biology

Article Title: Concentration-dependent splicing is enabled by Rbfox motifs of intermediate affinity.

doi: 10.1038/s41594-020-0475-8

Figure Lengend Snippet: Fig. 2 | Rbfox proteins reproducibly bind a class of secondary motifs with moderate affinity. a, Ribbon structure of RBFOX1 (teal) bound to UGCAUG (gold). Generated with data from Auweter et al.41 (PDB 2ERR). Protein–RNA hydrogen bonds are indicated in black. b, Relative per-base conservation, as represented by phyloP score, for each position of GCAUG at all instances of the motif in 3′ UTRs (dark teal; n = 26,707) and introns (light teal; n = 91,791). c, Primary motif (gold), secondary motif (teal), poly(A) and poly(C) (light gray), and GCAGG, GUAAG and GUCCG (dark gray) R values are shown across nsRBNS experiments with four different concentrations of RBFOX2. d, Analysis of the fraction of oligonucleotides bound in nsRBNS at three concentrations of RBFOX2 for primary (gold (GCAUG and GCACG); nGCAUG-1 = 5,435, nGCAUG-2 = 384, nGCACG-1 = 1,246, nGCACG-2 = 30) and secondary (teal; nSecondary-1 = 15,676, nSecondary-2 = 6,722, nSecondary-6 = 64) motifs. An oligonucleotide was considered bound if it had an R value of at least 1.1. e, nsRBNS R values at a RBFOX2 concentration of 1.1 µM for all pentamers diverging from GCAUG or GCACG by one or two bases. Secondary motifs identified here are outlined in black.

Article Snippet: The EGFP sequence in a pEGFP-rbFOX1 plasmid (Addgene, 63085) expressing human RBFOX1 was replaced with the coding sequence for Cerulean (Cerulean-N1; Addgene, 54742) to produce a Cerulean-RBFOX1 vector.

Techniques: Generated, Concentration Assay

Journal: Nature structural & molecular biology

Article Title: Concentration-dependent splicing is enabled by Rbfox motifs of intermediate affinity.

doi: 10.1038/s41594-020-0475-8

Figure Lengend Snippet: Fig. 6 | Secondary motifs are active in neuronal cell types with high Rbfox expression. a, Differentiated neuronal cell types from Weyn-Vanhentenryck et al.4 (SRA, SRP055008), arranged by combined Rbfox1, Rbfox2 and Rbfox3 expression (log10 of the sum of TPM values). Cell types were grouped into those with the lowest, low, medium, high and highest Rbfox expression. Cells analyzed included olfactory sensory neurons (OSN; OMP+), enterochromaffin cells (EC), taste receptor cells (TRC), rod or cone photoreceptors, jugular or nodose visceral sensory ganglia, dopaminergic neurons (DN), motor neurons (MN), dorsal root ganglia sensory neurons (DRG; Nav1.8+ or Avil+), trigeminal ganglia, Purkinje neurons (PN) and cerebellar granule neurons (CGN). b, Linear regression of 1,909 alternatively spliced exons comparing the Rbfox expression groups from a. Horizontal bars represent the Pearson r value (left) and uncorrected significance (right) of the correlation between the number of occurrences of primary or secondary (GCUUG, GAAUG, GUUUG and GUAUG) motifs and ΔPSI values between the medium and low (1), high and low (2) or highest and low (3) Rbfox expression regimes. Gray dotted and dashed lines indicate significance thresholds of 0.05 and 0.01, respectively. c, An equilibrium model for Rbfox binding to intronic sequences in the nucleus at various expression levels of Rbfox (gray area, low expression; teal area, high expression). GCAUG is indicated by gold and GCACG is indicated by yellow; secondary motifs are indicated in teal; nonspecific 5-mers are indicated in gray. d, Graphical summary of how Rbfox proteins (gold ellipses) regulate distinct splicing events at different expression levels (teal shading). Secondary motifs are functionally relevant only at higher Rbfox levels, occurring at later stages of neuronal differentiation or in cell types with high Rbfox expression, while primary motifs are functionally relevant at earlier stages and in cell types with medium as well as high Rbfox levels.

Article Snippet: The EGFP sequence in a pEGFP-rbFOX1 plasmid (Addgene, 63085) expressing human RBFOX1 was replaced with the coding sequence for Cerulean (Cerulean-N1; Addgene, 54742) to produce a Cerulean-RBFOX1 vector.

Techniques: Expressing, Binding Assay

Journal: Diabetes

Article Title: Evaluation of A2BP1 as an Obesity Gene

doi: 10.2337/db09-1604

Figure Lengend Snippet: Linkage disequilibrium plots (D′ and r 2 ) for the region around rs10500331 and rs12924838. D′ is indicated by the intensity of the shading, and the numbers in the boxes indicate r 2 . A : Schematic showing A2BP1 gene structures. Black box indicates the location of the region shown in ( B ) and ( C ). B : Linkage disequilibrium pattern for Pima Indians. C : Linkage disequilibrium pattern for Caucasians.

Article Snippet: Gene expression levels for mouse A2bp1 , Atxn2 , Insr , Mc4r , Lepr , and Npy1r were quantified by real-time PCR using predesigned gene expression assays (assay IDs: A2bp1 , Mm00480615_m1; Atxn2 , Mm00485932_m1; Insr , Mm00439693_m1; Mc4r , Mm00457483_s; Lepr , Mm00440181_m1; and Npy1r , Mm00650798_g1; Applied Biosystems, Foster City, CA).

Techniques:

Journal: Diabetes

Article Title: Evaluation of A2BP1 as an Obesity Gene

doi: 10.2337/db09-1604

Figure Lengend Snippet: Association analyses between BMI/obesity and variants spanning 1.2 Mb of A2BP1 . Black diamonds, association results for BMI in the population-based sample of full-heritage Pima Indians. Open triangles, association results for obesity in the French children case/control subjects. Gray circles, association results for obesity in the French adult case/control subjects.

Article Snippet: Gene expression levels for mouse A2bp1 , Atxn2 , Insr , Mc4r , Lepr , and Npy1r were quantified by real-time PCR using predesigned gene expression assays (assay IDs: A2bp1 , Mm00480615_m1; Atxn2 , Mm00485932_m1; Insr , Mm00439693_m1; Mc4r , Mm00457483_s; Lepr , Mm00440181_m1; and Npy1r , Mm00650798_g1; Applied Biosystems, Foster City, CA).

Techniques: Control

Journal: Diabetes

Article Title: Evaluation of A2BP1 as an Obesity Gene

doi: 10.2337/db09-1604

Figure Lengend Snippet: Expression profile for A2BP1 in different human tissues.

Article Snippet: Gene expression levels for mouse A2bp1 , Atxn2 , Insr , Mc4r , Lepr , and Npy1r were quantified by real-time PCR using predesigned gene expression assays (assay IDs: A2bp1 , Mm00480615_m1; Atxn2 , Mm00485932_m1; Insr , Mm00439693_m1; Mc4r , Mm00457483_s; Lepr , Mm00440181_m1; and Npy1r , Mm00650798_g1; Applied Biosystems, Foster City, CA).

Techniques: Expressing

Journal: Diabetes

Article Title: Evaluation of A2BP1 as an Obesity Gene

doi: 10.2337/db09-1604

Figure Lengend Snippet: Relative gene expression for A2bp1 , Atxn2 , Insr , Mc4r , Lepr , and Npy1r in A2bp1 knockdown N-41 mouse embryonic hypothalamus cells. Gray shaded bars, N-41 cells transfected with a negative control (scrambled) siRNA. Open bars, N-41 cells transfected with A2bp1 siRNA. Negative control siRNA was a scrambled, randomly selected nonspecific siRNA sequence.

Article Snippet: Gene expression levels for mouse A2bp1 , Atxn2 , Insr , Mc4r , Lepr , and Npy1r were quantified by real-time PCR using predesigned gene expression assays (assay IDs: A2bp1 , Mm00480615_m1; Atxn2 , Mm00485932_m1; Insr , Mm00439693_m1; Mc4r , Mm00457483_s; Lepr , Mm00440181_m1; and Npy1r , Mm00650798_g1; Applied Biosystems, Foster City, CA).

Techniques: Gene Expression, Knockdown, Transfection, Negative Control, Sequencing

Journal: Frontiers in Psychiatry

Article Title: Variants of the Aggression-Related RBFOX1 Gene in a Population Representative Birth Cohort Study: Aggressiveness, Personality, and Alcohol Use Disorder

doi: 10.3389/fpsyt.2020.501847

Figure Lengend Snippet: RBFOX1 genotype frequencies in the ECPBHS sample.

Article Snippet: For rs809682, the Assay C___8926788_10 was utilized; for rs8062784, rs12921846, and rs6500744 polymorphisms, the Assays C__29081048_20, C__32104163_10, and C___3008571_10 were used, respectively.

Techniques:

Journal: Frontiers in Psychiatry

Article Title: Variants of the Aggression-Related RBFOX1 Gene in a Population Representative Birth Cohort Study: Aggressiveness, Personality, and Alcohol Use Disorder

doi: 10.3389/fpsyt.2020.501847

Figure Lengend Snippet: RBFOX1 genotypes and the Buss-Perry Aggression Questionnaire at age 25.

Article Snippet: For rs809682, the Assay C___8926788_10 was utilized; for rs8062784, rs12921846, and rs6500744 polymorphisms, the Assays C__29081048_20, C__32104163_10, and C___3008571_10 were used, respectively.

Techniques:

Journal: Frontiers in Psychiatry

Article Title: Variants of the Aggression-Related RBFOX1 Gene in a Population Representative Birth Cohort Study: Aggressiveness, Personality, and Alcohol Use Disorder

doi: 10.3389/fpsyt.2020.501847

Figure Lengend Snippet: RBFOX1 genotypes and the life history of aggression interview at age 25.

Article Snippet: For rs809682, the Assay C___8926788_10 was utilized; for rs8062784, rs12921846, and rs6500744 polymorphisms, the Assays C__29081048_20, C__32104163_10, and C___3008571_10 were used, respectively.

Techniques:

Journal: Frontiers in Psychiatry

Article Title: Variants of the Aggression-Related RBFOX1 Gene in a Population Representative Birth Cohort Study: Aggressiveness, Personality, and Alcohol Use Disorder

doi: 10.3389/fpsyt.2020.501847

Figure Lengend Snippet: The effects of RBFOX1 genotypes on neuroticism and extraversion at age 25.

Article Snippet: For rs809682, the Assay C___8926788_10 was utilized; for rs8062784, rs12921846, and rs6500744 polymorphisms, the Assays C__29081048_20, C__32104163_10, and C___3008571_10 were used, respectively.

Techniques:

Journal: Frontiers in Psychiatry

Article Title: Variants of the Aggression-Related RBFOX1 Gene in a Population Representative Birth Cohort Study: Aggressiveness, Personality, and Alcohol Use Disorder

doi: 10.3389/fpsyt.2020.501847

Figure Lengend Snippet: Association of RBFOX1 rs8062784 with alcohol use disorder in males. Males, χ 2 = 7.01; p = 0.008 ( n = 411); females, χ 2 = 0.45; p = 0.509 ( n = 520). Lifetime diagnosis is based on MINI interview at age 25. AUD in 158 males out of 413 and 54 females out of 523 (in total, 212 out of 936).

Article Snippet: For rs809682, the Assay C___8926788_10 was utilized; for rs8062784, rs12921846, and rs6500744 polymorphisms, the Assays C__29081048_20, C__32104163_10, and C___3008571_10 were used, respectively.

Techniques: Biomarker Discovery

Journal: Frontiers in Psychiatry

Article Title: Variants of the Aggression-Related RBFOX1 Gene in a Population Representative Birth Cohort Study: Aggressiveness, Personality, and Alcohol Use Disorder

doi: 10.3389/fpsyt.2020.501847

Figure Lengend Snippet: Association of RBFOX1 rs12921846 with alcohol use disorder in females. Males, χ 2 = 0.41; p = 0.815 ( n = 411); females, χ 2 = 6.22; p = 0.045 ( n = 520). Lifetime diagnosis is based on MINI interview at age 25. AUD in 158 males out of 413 and 54 females out of 523 (in total, 212 out of 936).

Article Snippet: For rs809682, the Assay C___8926788_10 was utilized; for rs8062784, rs12921846, and rs6500744 polymorphisms, the Assays C__29081048_20, C__32104163_10, and C___3008571_10 were used, respectively.

Techniques: Biomarker Discovery

Journal: Frontiers in Psychiatry

Article Title: Variants of the Aggression-Related RBFOX1 Gene in a Population Representative Birth Cohort Study: Aggressiveness, Personality, and Alcohol Use Disorder

doi: 10.3389/fpsyt.2020.501847

Figure Lengend Snippet: Mediation by neuroticism of the association of RBFOX1 rs8062784 and alcohol use disorder. Regression weights with credible intervals (95%) are shown.

Article Snippet: For rs809682, the Assay C___8926788_10 was utilized; for rs8062784, rs12921846, and rs6500744 polymorphisms, the Assays C__29081048_20, C__32104163_10, and C___3008571_10 were used, respectively.

Techniques: