scholarly journals Quantitative proteomics reveals key roles for post-transcriptional gene regulation in the molecular pathology of FSHD

2018 ◽  
Author(s):  
Sujatha Jagannathan ◽  
Yuko Ogata ◽  
Philip R. Gafken ◽  
Stephen J. Tapscott ◽  
Robert K. Bradley

AbstractDUX4 is a transcription factor whose misexpression in skeletal muscle causes facioscapulohumeral muscular dystrophy (FSHD). While DUX4’s transcriptional activity has been extensively characterized, the DUX4-induced proteome remains undescribed. Here, we report concurrent measurement of RNA and protein levels in DUX4-expressing cells via RNA-seq and quantitative mass spectrometry. DUX4 transcriptional targets were robustly translated, confirming the likely clinical relevance of proposed FSHD biomarkers. However, a multitude of mRNAs and proteins exhibited discordant expression changes upon DUX4 expression. Our dataset revealed unexpected proteomic, but not transcriptomic, dysregulation of diverse molecular pathways, including Golgi apparatus fragmentation, as well as extensive post-transcriptional buffering of stress response genes. Key components of RNA degradation machineries, including UPF1, UPF3B, and XRN1, exhibited suppressed protein, but not mRNA, levels, explaining the build-up of aberrant RNAs that characterizes DUX4-expressing cells. Our results provide a resource for the FSHD community and illustrate the importance of post-transcriptional processes to DUX4-induced pathology.

eLife ◽  
2019 ◽  
Vol 8 ◽  
Author(s):  
Sujatha Jagannathan ◽  
Yuko Ogata ◽  
Philip R Gafken ◽  
Stephen J Tapscott ◽  
Robert K Bradley

DUX4 is a transcription factor whose misexpression in skeletal muscle causes facioscapulohumeral muscular dystrophy (FSHD). DUX4’s transcriptional activity has been extensively characterized, but the DUX4-induced proteome remains undescribed. Here, we report concurrent measurement of RNA and protein levels in DUX4-expressing cells via RNA-seq and quantitative mass spectrometry. DUX4 transcriptional targets were robustly translated, confirming the likely clinical relevance of proposed FSHD biomarkers. However, a multitude of mRNAs and proteins exhibited discordant expression changes upon DUX4 expression. Our dataset revealed unexpected proteomic, but not transcriptomic, dysregulation of diverse molecular pathways, including Golgi apparatus fragmentation, as well as extensive post-transcriptional buffering of stress-response genes. Key components of RNA degradation machineries, including UPF1, UPF3B, and XRN1, exhibited suppressed protein, but not mRNA, levels, explaining the build-up of aberrant RNAs that characterizes DUX4-expressing cells. Our results provide a resource for the FSHD community and illustrate the importance of post-transcriptional processes in DUX4-induced pathology.


Cells ◽  
2020 ◽  
Vol 9 (11) ◽  
pp. 2440
Author(s):  
Ioanna-Maria Gkotinakou ◽  
Eleni Kechagia ◽  
Kalliopi Pazaitou-Panayiotou ◽  
Ilias Mylonis ◽  
Panagiotis Liakos ◽  
...  

Hypoxia-inducible transcription factors 1 and 2 (HIFs) are major mediators of cancer development and progression and validated targets for cancer therapy. Although calcitriol, the biologically active metabolite of vitamin D, was attributed with anticancer properties, there is little information on the effect of calcitriol on HIFs and the mechanism underling this activity. Here, we demonstrate the negative effect of calcitriol on HIF-1/2α protein levels and HIF-1/2 transcriptional activity and elucidate the molecular mechanism of calcitriol action. We also reveal that the suppression of vitamin D receptor (VDR) expression by siRNA does not abrogate the negative regulation of HIF-1α and HIF-2α protein levels and HIF-1/2 transcriptional activity by calcitriol, thus testifying that the mechanism of these actions is VDR independent. At the same time, calcitriol significantly reduces the phosphorylation of Akt protein kinase and its downstream targets and suppresses HIF-1/2α protein synthesis by inhibiting HIF1A and EPAS1 (Endothelial PAS domain-containing protein 1) mRNA translation, without affecting their mRNA levels. On the basis of the acquired data, it can be proposed that calcitriol reduces HIF-1α and HIF-2α protein levels and inhibits HIF-1 and HIF-2 transcriptional activity by a VDR-independent, nongenomic mechanism that involves inhibition of PI3K/Akt signaling pathway and suppression of HIF1A and EPAS1 mRNA translation.


1993 ◽  
Vol 293 (1) ◽  
pp. 137-142 ◽  
Author(s):  
S J Lee ◽  
T D Boyer

The effect of hepatic regeneration on expression of four glutathione S-transferase (GST) subunits (Ya, Yc, Yb1, Yb2) was examined in rats following partial hepatectomy (PH). mRNA levels of the Ya and Yc subunits (Alpha class) decreased and were 13% and 42% of levels in sham-operated animals respectively 12 h after surgery. mRNA levels for the Yb1 subunit (Mu class) also decreased but were not maximally reduced until 24 h after PH (22% of sham-treated level). mRNA levels of the Yb2 subunit were affected little by PH. Changes in levels of mRNA appeared to reflect a decrease in both transcriptional activity and mRNA stability. The decrease in mRNA levels was associated with a fall in enzymic activity and in protein levels of Alpha-class GSTs. Within 48 h of surgery, levels of mRNA, protein enzymic activity and transcriptional activity had all fully recovered. GSH levels also decreased in the first 6 h after PH. However, 24 h after surgery GSH levels in animals having undergone PH exceeded those in sham-treated animals by 2-fold and this difference persisted for 72 h. These findings suggest that during the early phases of hepatic regeneration, because of decreased GST and GSH levels, the liver may be unusually susceptible to injury by toxic compounds. However, by the first round of cell division (36-48 h post-surgery) the liver has fully recovered its ability to metabolize toxic electrophiles.


Blood ◽  
2010 ◽  
Vol 116 (21) ◽  
pp. 2982-2982
Author(s):  
Ya-Wei Qiang ◽  
Peter Stewart ◽  
Yu Chen ◽  
Bo Hu ◽  
John Shaughnessy ◽  
...  

Abstract Abstract 2982 Gene expression profiling (GEP) of normal and malignant plasma cells and B-cells, revealed that MM is uniquely characterized by elevated expression of E- or N-cadherin. Classical cadherins are integral plasma membrane proteins, that together with a- and b-catenin form calcium-dependent adherent junctions. Homotypic interaction of N-cadherin+ hematopoietic stem cells and N-cadherin+ bone lining cells in the endosteal niche regulates HSC function. Adherent junctions contribute to the regulation of Wnt/b-catenin signaling by modulating the balance between membrane-bound and free cytosolic b-catenin, the latter of which is required for TCF transcriptional activity. Overexpression of DKK1 and suppression of Wnt/b-catenin osteoblasts causes a loss in self-renewal of HSC and only stromal cells with active nuclear b-catenin can support hematopoiesis in-vitro. On the other hand, disruption of adherent junctions and release of b-catenin contributes to epithelial-to-mesenchymal transition and solid tumor metastases. We, and others, have demonstrated that Wnt/β-catenin signaling is active in MM. However, emerging evidence suggests that loss of Wnt/b-catenin activity, rather than its activation, is central to MM pathogenesis. Nearly 90% of primary MM cells express and secrete DKK1 and/or SFRP3 or SFRP2, potent inhibitors of Wnt/b-catenin signaling. Moreover, loss-of-function mutations of APC or axin genes or gain-of-function mutations in the β-catenin gene common in colon cancer have not been found in MM. We therefore hypothesized that elevated expression of N/E-cadherin in MM cells contributes to the abnormally increase of b-catenin in MM. We first assessed the steady-state levels of β-catenin protein in MMCL with immunoblotting analysis. β-Catenin protein was expressed in all tested MMCL, with variable levels in individual lines. Interestingly, relative levels of β-catenin protein were comparable to N-cadherin expression in all eight tested myeloma cell lines. CD138-enriched plasma cells from the BM of 72 patients newly diagnosed MM revealed β-catenin protein levels are highly variable. After normalization of β-catenin with β-tubulin levels we segregated cases into three groups: 39% had low, 23% moderate, and 38% high levels of β-catenin. Analysis of correlation of b-catenin protein levels with U133Plus microarray data revealed there are striking positive correlations between N- or E-cadherin mRNA levels with levels of b-catenin protein. Importantly, b-catenin levels were not correlated with known Wnt/b-catenin target genes. To evaluate the role of N-cadherin in regulating β-catenin signaling in MM, we used a lentiviral expression system to express wild-type N-cadherin (NCadW/MMS1) or empty vector (EV/MMS1) in MMS1 cells. Significant increases in total and free b-catenin correlated with N-cadherin protein expression. These results indicate that N-cadherin protein modulates b-catenin levels MM cells. Results of experiments to determine whether N-cadherin-mediated regulation of b-catenin translates into altered TCF/b-catenin transcriptional activity in MM cells will be reported. Disclosures: Shaughnessy: Myeloma Health LLC: Consultancy, Equity Ownership, Patents & Royalties; Novartis: Membership on an entity's Board of Directors or advisory committees, Patents & Royalties; Genzyme: Patents & Royalties; Millennium: Honoraria; Celgene: Honoraria; OrthoBiotech: Honoraria; Array BioPharma: Honoraria.


Circulation ◽  
2014 ◽  
Vol 130 (suppl_2) ◽  
Author(s):  
David Barefield ◽  
Mohit Kumar ◽  
Joshua Gorham ◽  
Jonathan Seidman ◽  
Christine Seidman ◽  
...  

Introduction: Mutations in MYBPC3, encoding cardiac myosin binding protein-C (cMyBP-C), account for ~40% of hypertrophic cardiomyopathy (HCM) cases. MYBPC3 mutations are usually encode truncated proteins and are not found in tissue and are typically heterozygous (Het) in humans. Reduced protein levels occur in human HCM patients with these mutations, suggesting haploinsufficiency. However, it is unknown if cMyBP-C reduction causes or results from hypertrophy. Hypothesis: To test whether haploinsufficiency occurs following cardiac stress and if heterozygous MYBPC3 mice had worsened disease progression. Methods & Results: Transverse aortic constriction (TAC) was performed on 3 month old wild type (WT) and Het MYBPC3 truncation mutant mice which were allowed to hypertrophy for 4 or 12 weeks. Het TAC mice showed increased hypertrophy 12 weeks post-TAC compared to WT TAC controls. Het TAC hearts showed reduced ejection fraction compared to WT TAC at 4 and 12 weeks. MYBPC3 transcript levels were significantly reduced in sham and TAC Het hearts. cMyBP-C levels decreased in Het sham and TAC at 4 weeks but returned to baseline levels at 12 weeks. Het TAC myocytes showed higher Ca2+ sensitivity at 4 weeks, and impaired maximal force development. Het sham and TAC skinned cardiomyocytes showed reduced length dependent increases in Ca2+ sensitivity and maximal force development. RNA-Seq shows no alterations in proteasome of RNA-degradation pathways which have been suggested to play a role in the pathology of these mutations. Overexpression of WT cMyBP-C in the presence of truncated MYBPC3 rescued the decline in force observed in Het myocytes in the absence of stress. Conclusions: Heterozygous MYBPC3 truncation mutant carriers develop more profound hypertrophy and dysfunction following stress. Also, increased MYBPC3 expression reverses myocyte deficits in force generation in the presence of truncated alleles.


2007 ◽  
Vol 27 (10) ◽  
pp. 3758-3768 ◽  
Author(s):  
Sandra Barth ◽  
Jutta Nesper ◽  
Philippe A. Hasgall ◽  
Renato Wirthner ◽  
Katarzyna J. Nytko ◽  
...  

ABSTRACT The heterodimeric hypoxia-inducible transcription factors (HIFs) are central regulators of the response to low oxygenation. HIF-α subunits are constitutively expressed but rapidly degraded under normoxic conditions. Oxygen-dependent hydroxylation of two conserved prolyl residues by prolyl-4-hydroxylase domain-containing enzymes (PHDs) targets HIF-α for proteasomal destruction. We identified the peptidyl prolyl cis/trans isomerase FK506-binding protein 38 (FKBP38) as a novel interactor of PHD2. Yeast two-hybrid, glutathione S-transferase pull-down, coimmunoprecipitation, colocalization, and mammalian two-hybrid studies confirmed specific FKBP38 interaction with PHD2, but not with PHD1 or PHD3. PHD2 and FKBP38 associated with their N-terminal regions, which contain no known interaction motifs. Neither FKBP38 mRNA nor protein levels were regulated under hypoxic conditions or after PHD inhibition, suggesting that FKBP38 is not a HIF/PHD target. Stable RNA interference-mediated depletion of FKBP38 resulted in increased PHD hydroxylation activity and decreased HIF protein levels and transcriptional activity. Reconstitution of FKBP38 expression abolished these effects, which were independent of the peptidyl prolyl cis/trans isomerase activity. Downregulation of FKBP38 did not affect PHD2 mRNA levels but prolonged PHD2 protein stability, suggesting that FKBP38 is involved in PHD2 protein regulation.


2021 ◽  
Vol 2021 ◽  
pp. 1-12
Author(s):  
Lei Liu ◽  
Guangyuan Xia ◽  
Peifan Li ◽  
Yiming Wang ◽  
Qian Zhao

Background. Recent studies suggest a correlation between the reduced Sirt-1 expression with Alzheimer’s diseases (AD) and depression, respectively, suggesting a possible pathogenic role of the altered Sirt-1 expression in neuronal degenerative diseases, such as AD and depression. However, the molecular mechanisms underlying how Sirt-1 reduction impairs neuronal functions remain unknown. Methods. We used the SK-N-SH neuroblastoma cells to study the role of Sirt-1 expression on physiological roles in neuronal cells. Gain of Sirt-1 was achieved by transiently transfecting Sirt-1 expression plasmid. Sirt-1-specific shRNA was used to elucidate the role of Sirt-1 loss of function. CCK-8 (Cell Counting Kit-8) assay and flow cytometry were used to evaluate cell proliferation. Semiquantitative western blotting was used to detect relative protein levels. A further luciferase reporter gene assay was employed to examine the effect of Sirt-1 expression on the transcriptional activity of p53. RT-qPCR was used to determine the mRNA levels of p21, Bax, and Bcl-2, which were the downstream target genes of p53. Results. Sirt-1 suppressed the p53 downstream gene p21 transcription, while shRNA-mediated Sirt-1 knockdown resulted in a significant increase in p21 expression, implying a possibility that Sirt-1 promotes neuron proliferation through suppressing p53 transcriptional activity. The mRNA and protein levels of p53 were not affected by the altered Sirt-1 expression, suggesting that Sirt-1 regulates the transcriptional regulatory activity of p53 rather than p53 expression. Indeed, we further confirmed that Sirt-1 appeared to inhibit p53 transcriptional activity by attenuating its acetylation and resulted in a decrease of p53’s binding to the p21 promoter. Overexpressed Sirt-1 scavenged reactive oxygen species (ROS) production in SK-N-SH with H2O2. Knockdown of Sirt-1 presented opposite effect; the addition of EX527 (Sirt-1 inhibitor) increased ROS accumulation. Conclusions. Oxidative stress induces Sirt-1 in neuron cells, and Sirt-1 promotes proliferation in SK-N-SH cells, which protects them from oxidative stress-induced cell death, potentially via suppressing the transcriptional activity of p53. These results provide a molecular explanation underlying how the reduced Sirt-1 potentially causes the AD and depression-related diseases, supporting the idea that Sirt-1 can possibly be used as a diagnostic biomarker and/or therapeutic drug target for the AD and depression-related diseases.


2021 ◽  
Vol 22 (20) ◽  
pp. 10962
Author(s):  
Kouji Niidome ◽  
Ruri Taniguchi ◽  
Takeshi Yamazaki ◽  
Mayumi Tsuji ◽  
Kouichi Itoh ◽  
...  

We previously showed that the antiepileptic drug levetiracetam (LEV) inhibits microglial activation, but the mechanism remains unclear. The purpose of this study was to identify the target of LEV in microglial activity suppression. The mouse microglial BV-2 cell line, cultured in a ramified form, was pretreated with LEV and then treated with lipopolysaccharide (LPS). A comprehensive analysis of LEV targets was performed by cap analysis gene expression sequencing using BV-2 cells, indicating the transcription factors BATF, Nrf-2, FosL1 (Fra1), MAFF, and Spic as candidates. LPS increased AP-1 and Spic transcriptional activity, and LEV only suppressed AP-1 activity. FosL1, MAFF, and Spic mRNA levels were increased by LPS, and LEV only attenuated FosL1 mRNA expression, suggesting FosL1 as an LEV target. FosL1 protein levels were increased by LPS treatment and decreased by LEV pretreatment, similar to FosL1 mRNA levels. The FosL1 siRNA clearly suppressed the expression of TNFα and IL-1β. Pilocarpine-induced status epilepticus increased hippocampus FosL1 expression, along with inflammation. LEV treatment significantly suppressed FosL1 expression. Together, LEV reduces FosL1 expression and AP-1 activity in activated microglia, thereby suppressing neuroinflammation. LEV might be a candidate for the treatment of several neurological diseases involving microglial activation.


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