Journal: Cancer immunology research

Article Title: Using Quantitative Seroproteomics to Identify Antibody Biomarkers in Pancreatic Cancer

doi: 10.1158/2326-6066.CIR-15-0200-T

Figure Lengend Snippet: List of proteins of interest identified by the SASI approach.

Article Snippet: Purified recombinant proteins, PSMC5 (TP301251), MYPT1 (TP323540) and TFRC (TP300980) expressed in human HEK293 cells were purchased from Origene.

Techniques:

Journal: Cancer immunology research

Article Title: Using Quantitative Seroproteomics to Identify Antibody Biomarkers in Pancreatic Cancer

doi: 10.1158/2326-6066.CIR-15-0200-T

Figure Lengend Snippet: Correlation of increased antibody response to PSMC5, MYPT1 and TFRC post-vaccination with response to vaccine.

Article Snippet: Purified recombinant proteins, PSMC5 (TP301251), MYPT1 (TP323540) and TFRC (TP300980) expressed in human HEK293 cells were purchased from Origene.

Techniques:

Journal: Cancer immunology research

Article Title: Using Quantitative Seroproteomics to Identify Antibody Biomarkers in Pancreatic Cancer

doi: 10.1158/2326-6066.CIR-15-0200-T

Figure Lengend Snippet: Representative tissue sections from the J9988 study stained for (A) PSMC5, MYPT1 and TFRC are shown. Normal non-neoplastic duct cells (indicated with an N) and cancer cells (indicated with a C). Scale bars = 50 μm. Staining summary for (B) PSMC5 (n = 45), (C) MYPT1 (n = 44) and (D) TFRC (n = 42). PDA glands (black bars) express PSMC5, MYPT1 and TFRC in both cytoplasm and nucleus/membrane. However, minimal staining is evident in non-neoplastic (white bars) pancreatic ducts. *P < 0.01 Fisher exact test.

Article Snippet: Purified recombinant proteins, PSMC5 (TP301251), MYPT1 (TP323540) and TFRC (TP300980) expressed in human HEK293 cells were purchased from Origene.

Techniques: Staining, Membrane

Journal: Cancer immunology research

Article Title: Using Quantitative Seroproteomics to Identify Antibody Biomarkers in Pancreatic Cancer

doi: 10.1158/2326-6066.CIR-15-0200-T

Figure Lengend Snippet: (A) Comparing cytoplasmic and membranous MYPT1 staining in PDA (n = 44) versus biliary (n = 90), lung (n = 91), liver (n = 36), colon (n = 72) and breast (n = 54) cancers. Both cytoplasmic as well as membranous expression of MYPT1 is PDA-specific (P < 0.01). (B) Comparing cytoplasmic and nuclear PSMC5 staining in PDA (n = 45) versus biliary (n = 82), lung (n = 83), liver (n = 36), colon (n = 57) and breast cancers (n = 54). Nuclear expression of PSMC5 is PDA-specific (P < 0.01). However, cytoplasmic expression of PSMC5 is significant expressed in PDA compared to 72% lung, 59% liver and 48% colon but not 88% breast cancer.

Article Snippet: Purified recombinant proteins, PSMC5 (TP301251), MYPT1 (TP323540) and TFRC (TP300980) expressed in human HEK293 cells were purchased from Origene.

Techniques: Staining, Expressing

Journal: medRxiv

Article Title: Unveiling the crucial neuronal role of the proteasomal ATPase subunit gene PSMC5 in neurodevelopmental proteasomopathies

doi: 10.1101/2024.01.13.24301174

Figure Lengend Snippet: Clinical phenotypes associated with PSMC5 variants. A. To visually represent the phenotypic data from tables S2b-2c, we organized the HPO terms into categories and ranked the top categories based on their prevalence within the cohort. Within each category, circles illustrate the number of phenotypes assessed and documented for each individual. The size of a circle corresponds to the number of phenotypes evaluated for a particular subject. If no phenotypes were assessed, there is no circle present. The color of each circle indicates the proportion of these confirmed phenotypes in a subject, with a spectrum ranging from dark blue (indicating the lowest fraction) to red (indicating the highest fraction). The top categories are arranged in descending order according to the highest average fraction observed among subjects. Notably, the most commonly observed categories among these are nervous system and head and neck anomalies. Intriguingly, there was no apparent correlation between genotype and phenotype, as significant variability in phenotypic expression was observed even among individuals with the same genetic variant. B . Dysmorphic facial features included notably abnormal ear morphology as seen in subjects S3/9/10/13/19/30/32-34 (this feature is present in 19/31 (61%) subjects in the whole cohort), abnormal palpebral fissures (13/35; 37% in the whole cohort) including downslanted ones as in subjects S3/10/13/30, thin upper lip vermilion as in subjects S3/34 (7/35; 20%), abnormal palate as in subject S10 (7/35; 20%), tall or broad forehead as in S3/33/34 (9/35; 26%), epicanthus as in S4/38 (5/35; 14%), and orofacial clefts as in subject S10 (2/35; 6%). C. Facial image analysis using GestaltMatcher. The pairwise rank matrix and hierarchical clustering of 13 PSMC5 subjects. Each column is the result of testing one subject in the column and ranking of the remaining 12 photos in each row. For example, by testing the similarities between S10 and the 7,459 images of affected individuals from GMDB, S31 was ranked 1st and S19 was ranked 7th as being most similar to S10. The red box is the cluster of subjects with at least one match below the rank 50, which indicates this cluster shares a similar facial phenotype.

Article Snippet: 24 hours after plating, Psmc5 - Rat shRNA lentiviral particles (TL711271V, Origene) were introduced into the culture medium at a multiplicity of Infection rate of 5 and incubated for 18 hours before a complete medium change was carried out.

Techniques: Expressing, Variant Assay

Journal: medRxiv

Article Title: Unveiling the crucial neuronal role of the proteasomal ATPase subunit gene PSMC5 in neurodevelopmental proteasomopathies

doi: 10.1101/2024.01.13.24301174

Figure Lengend Snippet: Structural analysis of PSMC5 variants reveals most missense variants are located in the AAA+ ATPase domain of PSMC5/Rpt6, and affect proteasome dynamics or subunit interactions. A . Schematic representation of the PSMC5 (i.e. RPT6) protein on which the 23 alterations identified in patients with NDD are designated. Approximately half of these mutations fall into three distinct hotspot regions within the AAA+ ATPase domain of PSMC5/RPT6, as indicated. Numbers refer to the sums of unrelated NDD subjects in which the highlighted variant has been identified. Missense variants are colored in blue, frameshift variants in red and splice site variants in purple. B . Basing on the structures 6MSK from RCSB Protein Data Bank, we localized the missense variants identified in the AAA+ ATPase subunit PSMC5/Rpt6 within the 26S proteasomal complex. The variants of interest (spheres) are primarily located in the lower ATPase domain. Part of the 26S proteasome was hidden for better visibility; Rpt6 is shown in cartoon representation.

Article Snippet: 24 hours after plating, Psmc5 - Rat shRNA lentiviral particles (TL711271V, Origene) were introduced into the culture medium at a multiplicity of Infection rate of 5 and incubated for 18 hours before a complete medium change was carried out.

Techniques: Variant Assay

Journal: medRxiv

Article Title: Unveiling the crucial neuronal role of the proteasomal ATPase subunit gene PSMC5 in neurodevelopmental proteasomopathies

doi: 10.1101/2024.01.13.24301174

Figure Lengend Snippet: Suppression of Psmc5 leads to changes in reversal learning in flies and disrupts the balance between excitatory and inhibitory signals in rat hippocampal neurons. A. Pan-neuronal knockdown of Rpt6 in Drosophila did not significantly affect normal olfactory learning (p=0.3059, n=4). B. When faced with the more difficult task of reversal olfactory learning, knocking down Rpt6 pan-neuronally in Drosophila resulted in a significant decrease in performance (p<0.0001, n=4). (C-J) Primary rat hippocampal neurons infected DIV1-DIV14 with scrambled shRNA or PMSC5 knockdown (KD) shRNA delivering lenti-particles that co-express GFP. C. Assessment of PMSC5 fluorescent signal intensity in neurons at DIV14 shows a significant reduction in cells infected (GFP positive) with PMSC5 knockdown (KD) compared to cells infected with scrambled shRNA (n=10, Mann Whitney test, p = 0.0002). D. Exemplary images of neurons infected with scrambled shRNA (left) or PMSC5 shRNA (right) lenti-particles. PMSC5 labeling (arrow) is significantly reduced, confirming the KD of PMSC5. E-F. Infected neurons stained for MAP2 to visualize neuronal morphology. E. No significant difference in dendritic branching measured by the mean number of primary, secondary, and tertiary dendrites per neuron at DIV14 was found comparing scrambled Ctrl and PMSC5 KD conditions (n=6). F. Exemplary images of neurons infected with scrambled shRNA (left) or PMSC5 shRNA (right) lenti-particles. MAP2 labeling is shown in red. G-J. Infected neurons stained for vGlut to visualize excitatory presynaptic compartments or vGat to visualize inhibitory presynapses. G. The number of vGlut positive puncta along the primary dendrites was measured at DIV14. In Psmc5 KD conditions, a significant reduction was observed compared to scrambled Ctrls (n=5, Mann Whitney test, p = 0.0045). H. The number of vGat positive puncta along the primary dendrites was not significantly altered (n=5, Mann Whitney test, p = 0.2988). I-J. Exemplary images of primary dendrites of neurons infected with scrambled shRNA (left) or Psmc5 shRNA (right) lenti- particles. VGlut (full arrow) positive signals per dendrite length are significantly reduced, while VGat (open arrow) positive signals per dendrite length are not altered after Psmc5 KD.

Article Snippet: 24 hours after plating, Psmc5 - Rat shRNA lentiviral particles (TL711271V, Origene) were introduced into the culture medium at a multiplicity of Infection rate of 5 and incubated for 18 hours before a complete medium change was carried out.

Techniques: Knockdown, Infection, shRNA, MANN-WHITNEY, Labeling, Staining

Journal: medRxiv

Article Title: Unveiling the crucial neuronal role of the proteasomal ATPase subunit gene PSMC5 in neurodevelopmental proteasomopathies

doi: 10.1101/2024.01.13.24301174

Figure Lengend Snippet: Overexpression of PSMC5 affects neuronal morphology. A. Representative images of primary hippocampal neurons transfected with the empty vector control (EV), PSMC5 -WT or the different PSMC5 variants. Red indicates the tdTomato blue indicat MAP2. B. Analysis of the total neurite length in the different conditions reveal: (i) a significant increase induced by overexpression of PSMC5-WT compared to empty vector control (One-way ANOVA, F=3.296, p= 0.0014; empty vector versus PSMC5-WT, p=0.0046, Dunnet’s multiple comparison test); (ii) a similar effect as PSMC5-WT induced by overexpression of variants p.(Arg201Trp), p.(Pro320His) and p.(Arg325Trp) (PSMC5-WT versus p.(Arg201Trp), p=0.8; PSMC5-WT versus p.(Pro320His), p=0.8; PSMC5-WT versus p.(Arg325Trp), p=0.5, Dunnet’s multiple comparison test); (iii) a decrease induced by overexpression of variants p.(Ala202Val), p.(Thr207Met), p.(Pro320Arg) and PSMC5-Δex10, compared to PSMC5-WT (PSMC5-WT versus p.(Ala202Val), p=0.0031; PSMC5-WT versus p.(Thr207Met), p=0.02; PSMC5-WT versus p.(Pro320Arg), p=0.006; PSMC5-WT versus PSMC5-Δex10, p=0.03, Dunnet’s multiple comparison test). The effects of these variants were indistinguishable from the empty vector control (empty vector versus p.(Ala202Val), p=0.4; empty vector versus p.(Thr207Met), p=0.9; empty vector versus p.(Pro320Arg), p=0.9; empty vector versus PSMC5-Δex10, p=0.9, Dunnet’s multiple comparison test). C. Analysis of the arborization showed no differences between conditions compared to the empty vector control (One-way ANOVA, F=2.179, p= 0.03; empty vector versus PSMC5-WT, p=0.9, PSMC5-WT versus p.(Arg201Trp), p=0.9; PSMC5-WT versus p.(Ala202Val), p=0.9; PSMC5- WT versus p.(Thr207Met), p=0.6; PSMC5-WT versus p.(Pro320His), p=0.3; PSMC5-WT versus p.(Pro320Arg), p=0.9; PSMC5-WT versus p.(Arg 325Trp), p=0.9; PSMC5-WT versus PSMC5-Δex10, p=0.9, Dunnet’s multiple comparison test). Error bars indicate SEM, n (number of neurons traced): EV=40, PSMC5-WT=30, p.(Arg201Trp)=18 p.(Ala202Val)=20, p.(Thr207Met)=27, p.(Pro320Arg)=29, p.(Pro320Arg)=19, p.(Arg325Trp)=20 and PSMC5-Δex10=20. *p<0.05; **p<0.01. Scale bar: 100μm.

Article Snippet: 24 hours after plating, Psmc5 - Rat shRNA lentiviral particles (TL711271V, Origene) were introduced into the culture medium at a multiplicity of Infection rate of 5 and incubated for 18 hours before a complete medium change was carried out.

Techniques: Over Expression, Transfection, Plasmid Preparation, Control, Comparison

Journal: medRxiv

Article Title: Unveiling the crucial neuronal role of the proteasomal ATPase subunit gene PSMC5 in neurodevelopmental proteasomopathies

doi: 10.1101/2024.01.13.24301174

Figure Lengend Snippet: T cells from NDD subjects carrying PSMC5 heterozygous variants exhibit abnormalities in their proteasome expression and/or activity profiles. A . T cells expanded from PBMC isolated from NDD subjects S6/11/12/21/32 as well as related controls (father and/or mother) and heathy donors (noted ‘un. control’ for unrelated controls) were lysed in RIPA buffer prior to SDS-PAGE/western-blotting analysis using antibodies specific PSMC5/RPT6 and GAPDH (loading control). Arrow indicates full-length endogenous PSMC5/RPT6 at the expected size of approximately 45 kDa detected in all samples. PSMC5/Rpt6 staining of T cell lysates from subjects 6/11/21/32 uncovered a further shorter PSMC5/Rpt6 immunoreactive band migrating at ∼30kDa (denoted as a low-molecular mass (LMM) species by the square brackets) following prolonged exposure times, whereas T cells from subject S12 exhibited an extra PSMC5/Rpt6 signal running a little bit lighter than PSMC5/Rpt6 expected size just below 40 kDa (indicated by an asterisk). Lower panel: the RPT6 and GAPDH immunoreactive bands were quantified by densitometry. Data are presented as RPT6 full-length and low molecular weight (LMW) species on GAPDH ratio mean values ± SD for the control (n=9) and patients (PSMC5 lesions, n=5) groups, as indicated. Statistical analysis was performed using the Mann-Whitney U test where *** indicates p <0.001. B . Resting T cells from NDD subjects S6/11/12/21/32/33 as well as related (subject’s father and/or mother, as indicated) and unrelated (healthy donor) control T cells were analyzed for proteasome function and abundance. They were subjected to non- denaturing protein extraction using TSDG buffer prior to native-PAGE/western-blotting analysis using monoclonal antibodies specific for the α6 and PSMC5/RPT6 subunits, as indicated. Proteasome complexes (20S and 26S) were also visualized by in-gel activity assay using the Suc-LLVY-AMC fluorogenic peptide reflecting chymotrypsin-like activity. Lower panel: the LLVY-AMC fluorescent signals as well as the α6 and RPT6 immunoreactive bands in 30S and/or 26S proteasome complexes were quantified by densitometry and presented as fold change values in patients S6, S11, S12, S21, S32 and S33 versus the control group for each gel whose densitometry measurements were set to 1 (grid line). Columns indicate foldchange mean values ± SD of the patient group (n=6) for LLVY-AMC, α6 and RPT6 in 30S and/or 26S complexes, as indicated. Statistical analysis was performed using the Mann-Whitney U test where * indicates p<0.05.

Article Snippet: 24 hours after plating, Psmc5 - Rat shRNA lentiviral particles (TL711271V, Origene) were introduced into the culture medium at a multiplicity of Infection rate of 5 and incubated for 18 hours before a complete medium change was carried out.

Techniques: Expressing, Activity Assay, Isolation, Control, SDS Page, Western Blot, Staining, Molecular Weight, MANN-WHITNEY, Protein Extraction, Clear Native PAGE, Bioprocessing

Journal: medRxiv

Article Title: Unveiling the crucial neuronal role of the proteasomal ATPase subunit gene PSMC5 in neurodevelopmental proteasomopathies

doi: 10.1101/2024.01.13.24301174

Figure Lengend Snippet: T cells from NDD subjects with PSMC5 heterozygous variants are characterized by disrupted protein homeostasis, increased mitophagy rates and a specific lipid signature. A . T cells expanded from PBMC isolated from NDD subjects S6/11/12/21/32 were stained with 1 µM of the PROTEOSTAT® dye prior to flow cytometry analysis using the B3 (PerCP-Vio 700) channel. PROTEOSTAT®, a dye that specifically intercalates into the cross-beta spine of quaternary protein structures typically found in misfolded and aggregated proteins. All T cells with PSMC5 variants exhibited increased aggresome formation, as evidenced by increased PROTEOSTAT® fluorescence intensity detected using flow cytometry. Shown are one representative histogram overlay plot of the five T cell NDD subject samples over a control one (left panel), the individual mean fluorescence intensity (MFI) values of the patient ( PSMC5 lesions, n=5) and control (n=5) groups (middle panel) (* p <0.05, Mann-Whitney U test) and the foldchange of the. aggresome propensity factor (APF) for each NDD subject sample compared to the mean value of the five controls (right panel). B . T cells from NDD subjects S1/6/11/12/21/32, relatives (subject’s father, mother and/or brother) and unrelated controls (healthy donors) were subjected to RIPA-mediated protein extraction and subsequent SDS-PAGE/western-blotting using antibodies directed against ubiquitin, β-actin (loading control) and GAPDH (loading control), as indicated. Right panel: the ubiquitin, β-actin immunoreactive bands were quantified by densitometry and data are presented as ubiquitin/loading control mean values ±SD for both control (n=6) and patient (PSMC5 lesion, n=6) groups, as indicated. Statistical analysis was performed using the Mann-Whitney test with ** indicating p<0.01. C. In an attempt to deepen our understanding of the involvement of proteasomes in the regulation of lipid metabolism, we undertook an untargeted lipidomic analysis of T cells from seven unrelated PSMC5 Subjects (S1, S6, S11, S12, S19, S21 and S33) together with their six relative controls (probands’ brother, father and/or mother). Principal component analysis (PCA) plots were first generated to visualize lipid distribution and identify specific patterns across control and patient samples with positive (left panel) and negative (right panel) ion modes. The control and patient groups are presented in red and blue, respectively. D . Fold change analysis showing the lipid classes undergoing significant changes in T cells derived from NDD patients when compared to those from healthy donors. E . T cells expanded from PBMC isolated from the six NDD subjects S1/6/11/12/21/33 as well as from related and unrelated healthy donors (n=7) were incubated overnight with 100 nM of the Mtphagy dye prior to flow cytometry analysis using the B4 (PE-Vio 770) channel. Shown are the percentage values of the patient (PSMC5 lesions) and control groups (** p <0.01, Mann-Whitney U test).

Article Snippet: 24 hours after plating, Psmc5 - Rat shRNA lentiviral particles (TL711271V, Origene) were introduced into the culture medium at a multiplicity of Infection rate of 5 and incubated for 18 hours before a complete medium change was carried out.

Techniques: Isolation, Staining, Flow Cytometry, Fluorescence, Control, MANN-WHITNEY, Protein Extraction, SDS Page, Western Blot, Ubiquitin Proteomics, Generated, Derivative Assay, Incubation

Journal: medRxiv

Article Title: Unveiling the crucial neuronal role of the proteasomal ATPase subunit gene PSMC5 in neurodevelopmental proteasomopathies

doi: 10.1101/2024.01.13.24301174

Figure Lengend Snippet: Gene expression analysis reveals a specific gene signature and a spontaneous type I IFN response in T cells from NDD subjects with PSMC5 heterozygous variants. A. The heat map indicates the fold-change of expression of immune-related genes between T cell samples from five subjects with NDD (S1/11/12/21/32) and five heathy individuals (probands’ fathers and unrelated donors). Our profiling was based on a panel of 700 immune system genes, using the previously described NanoString nCounter® technology . Differentially expressed genes are hierarchically clustered. Upregulated and downregulated genes are represented in red and green, respectively. Forty genes were differentially expressed, almost all upregulated. The vast majority of them belonged to the large family of type I interferon (IFN)-stimulated genes (ISGs), including in particular the signal transducers STAT1 and STAT2 and members of the ISG15 conjugation machinery (e.g. UBE2L6 and HERC5). D . A comparative expression analysis of seven ISG ( IFIT1 , IFI27 , IFI44 , IFI44L , ISG15 , MX1 and RSAD2 ) was done by quantitative real-time PCR (see Materials & Methods), as previously described between T cells from PSMC5 subjects S1/11/12/21/32/33, unrelated healthy donors (HD) and subjects’ parents. Type I IFN score was determined for each sample by calculating the median of the normalized fold-change values of the seven ISG relative to one control calibrator. Shown are the IFN scores of each group of donor and parental controls (n=8; left panel) and affected individuals (n=6; right panel). (*p<0.05, Mann-Whitney U test). E . We evaluated the potential contribution of PKR to the initiation of type I IFN responses in NDD patients with PSMC5 variants. To this end, T cell from subjects S1/11/12/21/32/33 were exposed to PKR specific inhibitor C16 for 12 h prior to quantification of ISG transcripts by qPCR. T cells expanded from PBMC isolated from NDD subjects were subjected were subjected to an 8-hr treatment with DMSO (vehicle) or the PKR specific inhibitor C16 (3 µM), 4µ8C (100 µM), H-151 (2 µM), baricitinib (1 µM) or A92 (10 µM). Then RNAs were extracted and submitted to RT-qPCR for ISG gene expression analysis. Shown are the median values of the IFN scores calculated for each T cell patient sample (n=6) under different treatment conditions (* p <0.05, Mann-Whitney U test).

Article Snippet: 24 hours after plating, Psmc5 - Rat shRNA lentiviral particles (TL711271V, Origene) were introduced into the culture medium at a multiplicity of Infection rate of 5 and incubated for 18 hours before a complete medium change was carried out.

Techniques: Gene Expression, Expressing, Conjugation Assay, Real-time Polymerase Chain Reaction, Control, MANN-WHITNEY, Isolation, Quantitative RT-PCR

Journal: PLoS ONE

Article Title: 25-hydroxyvitamin D3 and 1,25-dihydroxyvitamin D3 exert distinct effects on human skeletal muscle function and gene expression

doi: 10.1371/journal.pone.0170665

Figure Lengend Snippet: Bivariate correlations between expression of Vitamin D Receptor ( VDR ) and other skeletal muscle target genes. Data are Spearman correlation coefficients (rho)), with 95% confidence intervals (CI) and p values in brackets).

Article Snippet: Gene targets and assay IDs were as follows: VDR (Hs00172113_m1), CYP27B1 Hs01096154_m1, CYP24A1 Hs00167999_m1, mTOR (Hs00234508_m1), MAFbx/Atrogin-1 (Hs01041408_m1), p300 (Hs00914223_m1), MuRF1 (Hs00261590_m1), Calpain-1 (Hs00559804_m1), Calpain-2 (Hs00965097_m1), USP19 (Hs00324123_m1), ATF4 (Hs00909569_g1), Caspase 3 (Hs00234387_m1), eIF4BP1 (Hs00607050_m1), FOXO1 (Hs01054576_m1), FOXO3 (Hs00818121_m1), MYH1 (Hs00428600_m1), MYH2 (Hs00430042_m1), MYH4 ( Hs00757977_m1 ), myogenin (Hs01072232_m1), SIRT1 (Hs01009005_m1), SIRT3 (Hs00202030_m1), myostatin (Hs00976237_m1), SMAD2 (Hs00183425_m1), SMAD3 (Hs00969210_m1), SMAD4 (Hs00929647_m1), SMAD7 (Hs00998193_m1), ACVR2A (Hs00155658_m1), ACVR2B (Hs00609603_m1), RELA (Hs00153294_m1), RELB (Hs00232399_m1), IL6 (Hs00985639_m1), IL1B (Hs01555410_m1), NFKB1 (Hs00765730_m1), INSR (Hs00961554_m1), IRS1 (Hs00178563_m1), AKT1 (Hs00178289_m1), GSK3B (Hs01047719_m1), DDIT4 (Hs01111686_g1), HSD11B1 (Hs01547870_m1), HSD11B2 (Hs00388669_m1), H6PD ( Hs00188728_m1 ), HSP90AA1 (Hs00743767_sH), HSP90B1 (Hs00427665_g1), GHR (Hs00174872_m1), GHSR (Hs00269780_s1), IGF1 (Hs01547656_m1), HIF1A (Hs00153153_m1), EIF6 (Hs00158272_m1), EIF2B (Hs00426752_m1), PDK4 (Hs01037712_m1), IGF1R (Hs00609566_m1), GADD45A (Hs00169255_m1), ACACA (Hs01046047), AR (Hs00171172_m1), CD36 (Hs00169627_m1), CDNK1 (Hs00355782_m1), CEBP1 (Hs00270923_s1), CRYAB (Hs00157107_m1), CYSC (Hs01588974_g1), GLUL (Hs00365928_g1), HSL (Hs00193510_m1), LPL (Hs00173425_m1), MYCL1 (Hs00420495_m1), MYF5 (Hs00929416_g1), NRC31 (Hs00354508_m1), PPARD (Hs04187066_g1), PPARG (Hs00234592_m1), PPARGC1A (Hs01016719_m1), PPP3R2 (Hs00931245_s1), PSMA2 (Hs00746751_s1), PSMC1 (Hs02386942_g1), PSMC2 (Hs00739800_m1), PSMC4 (Hs00197826_m1), PSMC5 ( Hs01029472_g1), PSMC6 (Hs01652481_g1), PSMD1 (Hs00160631_m1), PSMD2 (Hs01092076_g1), PSMD3 (Hs00160646_m1), PSMD4 (Hs01937833_s1), PSMD6 (Hs00207850_m1), PSMD7 (Hs00427396_m1), PSMD11 (Hs00160660_m1), PSMD12 (Hs00356667_m1), PSMD14 (Hs01113429_m1), RPS6KB1 (Hs00177357_m1), RXRG (Hs00199455_m1), SLC2A4 (Hs00168966_m1), SOCSS3 (Hs00168966_m1), SOD1 (Hs00533490_m1), SREBF1 (Hs01088691_m1), TGFB1 (Hs00998133_m1), TNFA (Hs01113624_g1), TRIM54 (Hs00936695_m1).

Techniques: Expressing

Journal: PLoS ONE

Article Title: 25-hydroxyvitamin D3 and 1,25-dihydroxyvitamin D3 exert distinct effects on human skeletal muscle function and gene expression

doi: 10.1371/journal.pone.0170665

Figure Lengend Snippet: Bivariate correlations between serum 25OHD3, 1α,25(OH) 2 D3 and gene expression in skeletal muscle. Data are Spearman correlation coefficients (rho)), with 95% confidence intervals (CI) and p values in brackets).

Article Snippet: Gene targets and assay IDs were as follows: VDR (Hs00172113_m1), CYP27B1 Hs01096154_m1, CYP24A1 Hs00167999_m1, mTOR (Hs00234508_m1), MAFbx/Atrogin-1 (Hs01041408_m1), p300 (Hs00914223_m1), MuRF1 (Hs00261590_m1), Calpain-1 (Hs00559804_m1), Calpain-2 (Hs00965097_m1), USP19 (Hs00324123_m1), ATF4 (Hs00909569_g1), Caspase 3 (Hs00234387_m1), eIF4BP1 (Hs00607050_m1), FOXO1 (Hs01054576_m1), FOXO3 (Hs00818121_m1), MYH1 (Hs00428600_m1), MYH2 (Hs00430042_m1), MYH4 ( Hs00757977_m1 ), myogenin (Hs01072232_m1), SIRT1 (Hs01009005_m1), SIRT3 (Hs00202030_m1), myostatin (Hs00976237_m1), SMAD2 (Hs00183425_m1), SMAD3 (Hs00969210_m1), SMAD4 (Hs00929647_m1), SMAD7 (Hs00998193_m1), ACVR2A (Hs00155658_m1), ACVR2B (Hs00609603_m1), RELA (Hs00153294_m1), RELB (Hs00232399_m1), IL6 (Hs00985639_m1), IL1B (Hs01555410_m1), NFKB1 (Hs00765730_m1), INSR (Hs00961554_m1), IRS1 (Hs00178563_m1), AKT1 (Hs00178289_m1), GSK3B (Hs01047719_m1), DDIT4 (Hs01111686_g1), HSD11B1 (Hs01547870_m1), HSD11B2 (Hs00388669_m1), H6PD ( Hs00188728_m1 ), HSP90AA1 (Hs00743767_sH), HSP90B1 (Hs00427665_g1), GHR (Hs00174872_m1), GHSR (Hs00269780_s1), IGF1 (Hs01547656_m1), HIF1A (Hs00153153_m1), EIF6 (Hs00158272_m1), EIF2B (Hs00426752_m1), PDK4 (Hs01037712_m1), IGF1R (Hs00609566_m1), GADD45A (Hs00169255_m1), ACACA (Hs01046047), AR (Hs00171172_m1), CD36 (Hs00169627_m1), CDNK1 (Hs00355782_m1), CEBP1 (Hs00270923_s1), CRYAB (Hs00157107_m1), CYSC (Hs01588974_g1), GLUL (Hs00365928_g1), HSL (Hs00193510_m1), LPL (Hs00173425_m1), MYCL1 (Hs00420495_m1), MYF5 (Hs00929416_g1), NRC31 (Hs00354508_m1), PPARD (Hs04187066_g1), PPARG (Hs00234592_m1), PPARGC1A (Hs01016719_m1), PPP3R2 (Hs00931245_s1), PSMA2 (Hs00746751_s1), PSMC1 (Hs02386942_g1), PSMC2 (Hs00739800_m1), PSMC4 (Hs00197826_m1), PSMC5 ( Hs01029472_g1), PSMC6 (Hs01652481_g1), PSMD1 (Hs00160631_m1), PSMD2 (Hs01092076_g1), PSMD3 (Hs00160646_m1), PSMD4 (Hs01937833_s1), PSMD6 (Hs00207850_m1), PSMD7 (Hs00427396_m1), PSMD11 (Hs00160660_m1), PSMD12 (Hs00356667_m1), PSMD14 (Hs01113429_m1), RPS6KB1 (Hs00177357_m1), RXRG (Hs00199455_m1), SLC2A4 (Hs00168966_m1), SOCSS3 (Hs00168966_m1), SOD1 (Hs00533490_m1), SREBF1 (Hs01088691_m1), TGFB1 (Hs00998133_m1), TNFA (Hs01113624_g1), TRIM54 (Hs00936695_m1).

Techniques: Gene Expression