scholarly journals Quantifying the Protein Levels of All Nuclear Hormone Receptors by Mass Spectrometry

2021 ◽  
Vol 5 (Supplement_1) ◽  
pp. A815-A815
Author(s):  
Michael Fadi Saikali ◽  
Carolyn L Cummins
Keyword(s):  
Mass Spectrometry ◽  
Protein Expression ◽  
Hormone Receptors ◽  
Target Genes ◽  
Mrna Level ◽  
Fold Increase ◽  
Hek293 Cells ◽  
Endogenous Expression ◽  
Mouse Tissues ◽  
Wide Range

Abstract Nuclear Receptors (NRs) are a family of ligand-activated transcription factors that control the expression of genes involved in a wide range of physiological processes. An atlas detailing the expression of all NRs at the mRNA level was completed in 2006 using quantitative PCR [Bookout et al. Cell 2006]. The comparative measurement of NRs at the protein level, however, has been hindered by the poor quality of commercially available antibodies, as well as the absence of a high throughput method for quantitation. To address this need, we are developing a mass spectrometry-based targeted proteomic assay to quantify the absolute amounts of NR protein in a panel of mouse tissues. NRs were overexpressed in HEK293 cells by transient transfection and protein was isolated. The cell lysates were digested with a combination of trypsin and Lys-C following the Multi-Enzyme Digestion Filter Aided Sample Preparation protocol. The peptides were desalted using an in-house made C18 tip, separated on an EASY-Spray C18 column (75 um x 50 cm, 3Å), and analyzed on a Thermo QExactive HF in Top20 data-dependent acquisition mode. Protein identifications were made using MaxQuant software, and the identifications were mined for members of the NR family. The NR peptides detected were searched against an in silico generated list of optimal NR peptides (filtered for uniqueness, length, absence of post translational modifications, and conservation between human and mouse). The matching peptides were validated by parallel reaction monitoring (PRM) and purchased as synthetic isotopes with a heavy terminal arginine or lysine. Peptide linearity, and lower limits of detection (LLOD) were estimated by spiking digests from a C57Bl/6 mouse liver lysate with increasing amounts of the labeled peptides and analyzing by PRM. Peptides that displayed non-linear behavior were excluded for quantitation. The LLOD were between 100 amol and 1.5 fmol on column. A test panel of tissues (cerebrum, hippocampus, cerebellum, liver, spleen, brown/white adipose, and kidney) showed that we could detect endogenous expression of NRs. To date, we have purchased and validated peptides for 44 of the 49 receptors. We used this assay to quantify the changes in NR protein expression in mouse livers in response to 16 hours of fasting. We found significant changes in the nuclear expression of CAR (3.1-fold increase), RXRβ (1.8-fold increase), SHP (3.9-fold decrease) and RARβ (2.0-fold decrease) in the fasted vs. fed state. Increased CAR activity with fasting was further supported by label-free quantitative proteomics on the same lysates which revealed 210 differentially expressed proteins (2-fold change, p<0.05), with 61 (29%) identified as known CAR target genes. Once complete, this assay will provide researchers with a robust quantitative tool to investigate changes in NR protein expression that will be widely applicable to endocrine research.

scholarly journals Adipogenesis is differentially impaired by thyroid hormone receptor mutant isoforms

2010 ◽  
Vol 44 (4) ◽  
pp. 247-255 ◽  
Author(s):  
Alok Mishra ◽  
Xu-guang Zhu ◽  
Kai Ge ◽  
Sheue-Yann Cheng
Keyword(s):  
Thyroid Hormone ◽  
Hormone Receptors ◽  
Target Genes ◽  
Thyroid Hormone Receptor ◽  
Fold Increase ◽  
Dominant Negative ◽  
Peroxisome Proliferator ◽  
Loss Of Function ◽  
Peroxisome Proliferator Activated Receptor ◽  
Protein Levels

To understand the roles of thyroid hormone receptors (TRs) in adipogenesis, we adopted a loss-of-function approach. We generated 3T3-L1 cells stably expressing either TRα1 mutant (TRα1PV) or TRβ1 mutant (TRβ1PV). TRα1PV and TRβ1PV are dominant negative mutations with a frameshift in the C-terminal amino acids. In control cells, the thyroid hormone, tri-iodothyronine (T3), induced a 2.5-fold increase in adipogenesis in 3T3-L1 cells, as demonstrated by increased lipid droplets. This increase was mediated by T3-induced expression of the peroxisome proliferator-activated receptor γ (PPARγ) and CCAAT/enhancer-binding protein α (C/EBPα), which are master regulators of adipogenesis at both the mRNA and protein levels. In 3T3-L1 cells stably expressing TRα1PV (L1-α1PV cells) or TRβ1PV (L1-β1PV cells), adipogenesis was reduced 94 or 54% respectively, indicative of differential inhibitory activity of mutant TR isoforms. Concordantly, the expression of PPARγ and C/EBPα at the mRNA and protein levels was more repressed in L1-α1PV cells than in L1-β1PV cells. In addition, the expression of PPARγ downstream target genes involved in fatty acid synthesis – the lipoprotein lipase (Lpl) and aP2 involved in adipogenesis – was more inhibited by TRα1PV than by TRβ1PV. Chromatin immunoprecipitation assays showed that TRα1PV was more avidly recruited than TRβ1PV to the promoter to preferentially block the expression of the C/ebpα gene. Taken together, these data indicate that impaired adipogenesis by mutant TR is isoform dependent. The finding that induction of adipogenesis is differentially regulated by TR isoforms suggests that TR isoform-specific ligands could be designed for therapeutic intervention for lipid abnormalities.

Eph-A4 Plays a Important Role in Metastasis and Invasive Activity of Myeloid Leukemia Cells

Blood ◽  
2012 ◽  
Vol 120 (21) ◽  
pp. 4819-4819
Author(s):  
Liu Xiaoli ◽  
Xuan Zhou ◽  
Yuan Zuo ◽  
Lulu Xu ◽  
Jinfang Zhang ◽  
...  
Keyword(s):  
Protein Expression ◽  
Cell Line ◽  
Myeloid Leukemia ◽  
Mrna Level ◽  
K562 Cells ◽  
Leukemia Cell Line ◽  
Leukemia Cells ◽  
Migration Assay ◽  
Wide Range ◽  
Myeloid Leukemias

Abstract Abstract 4819 The Eph receptors are found in a wide range of cancers and correlate with metastasis. However, their precise role in cancer has only started to be addressed. In this study, we investigated the role of Eph-A4 receptor in metastasis and invasive activity of myeloid leukemia cells. We fisr tested the expression of Eph-A4 in eight primary myeloid leukemias imclulding four with extramedullary metastasis and four without it, and leukemia cell line K562 by Real-time PCR and western blotting, then found that Eph- A4 was wildly expressed in myeloid Leukemia cells, especially in myeloid leukemia cells with high invasive activity. To further clarified the question, the stable over-expressing Eph-A4 cell line (K562-EphA4) based the wild K562 cell and pGC lentivirus vector were established to declare the metastasis and invasive activity in myeloid leukemia cells in vitro by trans-well migration assay. The results indicated that the mRNA level and protein expression of Eph-A4 were significantly increased in myeloid leukemias with extramedullary metastasis and K562 cells compared to those without it (P<0.05).After we successfully established the stable over-expressing Eph-A4 cell line, we verified its mRNA level and protein expression were both significantly increased ((P<0.05).Furthermore, RhoA and Rac1/cdc42, which are important adhesion molecules and related to metastasis and invasive activity were both highly expressed in K562-EphA4 cells compared to wild K562 cells (P<0.05). Moreover, the trans-well migration assay showed that cells that migrated to lower chambers and matrigel hydrogel were both increased in K562-EphA4 cells compared to wild K562 cells (5.22±2.11*104/ml vs 13.56±2.70*104 /ml P<0.000;18.07±3.15/cm2 vs 28.53±2.50/cm2P<0.000 respectively). Our findings suggest that Eph- A4 is likely to play an important role in the regulation the of myeloid Leukemia through the control of RhoA and Rac1/cdc42 associated signaling, migration and invasive activity, and therefore may represent a novel target for cancer treatment. Disclosures: No relevant conflicts of interest to declare.

P2560Metalloprotease nardilysin controls heart rate through the transcriptional regulation of ion channels critical for sinus automaticity

2019 ◽  
Vol 40 (Supplement_1) ◽  
Author(s):  
M Ohno ◽  
H Matsuura ◽  
T Makiyama ◽  
K Nishi ◽  
H Iwasaki ◽  
...  
Keyword(s):  
Heart Rate ◽  
Transcriptional Regulation ◽  
Ion Channels ◽  
Target Genes ◽  
Sinus Node ◽  
Mrna Level ◽  
Pcr Analysis ◽  
Mrna Levels ◽  
Wide Range ◽  
Transcriptional Coregulator

Abstract Nardilysin (NRDC; N-arginine dibasic convertase) is a metalloprotease of the M16 family. We have demonstrated that NRDC in the extracellular space enhances ectodomain cleavage of multiple membrane proteins. We also reported that nuclear NRDC regulates transcription of several target genes as a transcriptional coregulator. These results indicated that NRDC is a protease having localization-dependent multiple functions. NRDC-deficient mice (Nrdc−/−) showed wide range of phenotypes such as hypomyelination, hypothermia, and bradycardia. In this study, we have explored a role of NRDC in the regulation of heart rate. (1) Pharmacological blocking of autonomic nervous system revealed that an intrinsic heart rate of Nrdc−/− was significantly reduced compared with that of wild-type mice. (2) In Nrdc−/− hearts, mRNA levels of Cav3.1 and HCN1/4, ion channels responsible for sinus automaticity, were significantly reduced. (3) Funny (If) current and T-type Ca current measured in the sinus node cells were markedly reduced in Nrdc−/− cells, indicating that the functions of Cav3.1 and HCN4 are impaired. (4) Gene knockdown of NRDC in primary rat ventricular myocyte led to the reduction of mRNA level of HCN4. (5) Chromatin immunoprecipitation-PCR analysis showed that NRDC binds to the promoter region of Cav3.1 and HCN4, suggesting the direct involvement of NRDC in transcriptional regulation of these ion channels. (6) Atrium-specific Nrdc−/− (Sarcolipin-Cre) showed mild bradycardia and reduced Cav3.1 mRNA expression. Together, our results indicated that NRDC in cardiomyocyte controls heart rate through the transcriptional regulation of ion channels critical for sinus automaticity. Acknowledgement/Funding KAKENHI (17K09575)

scholarly journals Indirect Regulation of Human Dehydroepiandrosterone Sulfotransferase Family 1A Member 2 by Thyroid Hormones

Endocrinology ◽  
2006 ◽  
Vol 147 (5) ◽  
pp. 2481-2489 ◽  
Author(s):  
Ya-Hui Huang ◽  
Chih-Yi Lee ◽  
Pei-Ju Tai ◽  
Chun-Che Yen ◽  
Chu-Yu Liao ◽  
...  
Keyword(s):  
Thyroid Hormone ◽  
Binding Site ◽  
Protein Level ◽  
Target Genes ◽  
Thyroid Hormone Receptor ◽  
Cell Metabolism ◽  
Hepatoma Cell ◽  
Mrna Level ◽  
Fold Increase ◽  
Hepatoma Cell Line

Thyroid hormone, T3, regulates cell metabolism, differentiation, and development. cDNA microarrays were performed to study the mechanism of target gene regulation after T3 treatment in a thyroid hormone receptor-α (TRα)-overexpressing hepatoma cell line (HepG2-TRα). The differentially expressed target genes are several metabolic enzymes, including dehydroepiandrosterone-sulfotransferase family 1A member 2 (SULT2A1). Enzyme SULT2A1 was elevated roughly 5-fold at the protein level and 9-fold increase at the mRNA level after 48 h T3 treatment in HepG2-TRα cells. Cycloheximide inhibited T3-induced SULT2A1 expression, suggesting that regulation was indirect. SULT2A1 has been reported to be regulated by the two transcription factors, steroidogenic factor 1 (SF1) and GATA, in the human adrenal gland. T3 induced a 2.5- to 3.5-fold elevation of SF1 at the protein level and a 6.2-fold increase at the RNA level in HepG2-TRα cells. About seven SF1 binding sites exist on the SULT2A1 gene. To identify and localize the critical SF1 binding site, series of deletion mutants of SULT2A1 promoter fragments in pGL2 plasmid were constructed. The promoter activity of the SULT2A1 gene was enhanced about 2.8- to 7.1-fold by T3. The −228 SF1 binding site was identified as the most critical site because deleting this region reduced T3-induced expression. Transcription factor SF1 application enhanced the −228 but not −117 reporter plasmid activities. SULT2A1 and SF1 up-regulation at protein and RNA levels in thyroidectomized rats occurred after T3 application. In summary, this work demonstrated that the SULT2A1 gene was mediated by SF1 and indirectly regulated by T3. Further study is required to elucidate the physiological importance of SULT2A1 induction mediated by T3.

scholarly journals Ets-1 expression and gemcitabine chemoresistance in pancreatic cancer cells

2011 ◽  
Vol 16 (1) ◽  
Author(s):  
Amit Khanna ◽  
Kulandaivelu Mahalingam ◽  
Debarshi Chakrabarti ◽  
Giridharan Periyasamy
Keyword(s):  
Pancreatic Cancer ◽  
Protein Expression ◽  
Western Blot ◽  
Cancer Cells ◽  
Blot Analysis ◽  
Western Blot Analysis ◽  
Time Course ◽  
Target Genes ◽  
Fold Increase ◽  
Pancreatic Cancer Cells

AbstractGemcitabine, a novel pyrimidine nucleoside analog, has become the standard chemotherapeutic agent for pancreatic cancer patients. The clinical impact of gemcitabine remains modest owing to the high degree of inherent and acquired resistance. There are various lines of evidence that confirm the role of Ets-1, a proto-oncoprotein, in tumor invasion, progression, and chemoresistance. This study examines a hypothesis that implicates Ets-1 in the development of gemcitabine-resistance in pancreatic cancer cells. Ets-1 protein expression was assessed in parental pancreatic cancer cells and their gemcitabine-resistant clones. Western blot analysis revealed elevated levels of Ets-1 protein expression in gemcitabine-resistant PANC1GemRes (4.8-fold increase; P < 0.05), MIA PaCa2GemRes (3.2-fold increase; P < 0.05), and Capan2GemRes (2.1-fold increase; P < 0.05) cells as compared to their parental counterparts. A time course analysis was conducted to determine the change in Ets-1 expression in the parental cells after incubation with gemcitabine. Reverse transcriptase quantitative real-time PCR (RT-qPCR) and Western blot analysis revealed a significant increase in Ets-1 expression. All the three parental cells incubated with gemcitabine showed elevated Ets-1 protein expression at 6 h. By 24 h, the expression level had decreased. Using small interfering RNA (siRNA) against Ets-1 in gemcitabine-resistant cells, we demonstrated a reversal in gemcitabine chemosensitivity and also detected a marked reduction in the expression of the Ets-1 target genes MMP1 and uPA. Our novel finding demonstrates the significance of Ets-1 in the development of gemcitabine chemoresistance in pancreatic cancer cells. Based on these results, a new siRNA-based therapeutic strategy targeting the Ets-1 genes can be designed to overcome chemoresistance.

scholarly journals Comparative Analysis of CREB3 and CREB3L2 Protein Expression in HEK293 Cells

2021 ◽  
Vol 22 (5) ◽  
pp. 2767
Author(s):  
Kentaro Oh-hashi ◽  
Ayumi Yamamoto ◽  
Ryoichi Murase ◽  
Yoko Hirata
Keyword(s):  
Molecular Weight ◽  
Comparative Analysis ◽  
Protein Expression ◽  
Protein Degradation ◽  
Target Genes ◽  
Brefeldin A ◽  
Cellular Responses ◽  
Full Length ◽  
The Other ◽  
Hek293 Cells

We performed a comparative analysis of two ER-resident CREB3 family proteins, CREB3 and CREB3L2, in HEK293 cells using pharmacological and genome editing approaches and identified several differences between the two. Treatment with brefeldin A (BFA) and monensin induced the cleavage of full-length CREB3 and CREB3L2; however, the level of the full-length CREB3 protein, but not CREB3L2 protein, was not noticeably reduced by the monensin treatment. On the other hand, treatment with tunicamycin (Tm) shifted the molecular weight of the full-length CREB3L2 protein downward but abolished CREB3 protein expression. Thapsigargin (Tg) significantly increased the expression of only full-length CREB3L2 protein concomitant with a slight increase in the level of its cleaved form. Treatment with cycloheximide and MG132 revealed that both endogenous CREB3 and CREB3L2 are proteasome substrates. In addition, kifunensine, an α-mannosidase inhibitor, significantly increased the levels of both full-length forms. Consistent with these findings, cells lacking SEL1L, a crucial ER-associated protein degradation (ERAD) component, showed increased expression of both full-length CREB3 and CREB3L2; however, cycloheximide treatment downregulated full-length CREB3L2 protein expression more rapidly in SEL1L-deficient cells than the full-length CREB3 protein. Finally, we investigated the induction of the expression of several CREB3 and CREB3L2 target genes by Tg and BFA treatments and SEL1L deficiency. In conclusion, this study suggests that both endogenous full-length CREB3 and CREB3L2 are substrates for ER-associated protein degradation but are partially regulated by distinct mechanisms, each of which contributes to unique cellular responses that are distinct from canonical ER signals.

Current Trends in Biotherapeutic Higher Order Structure Characterization by Irreversible Covalent Footprinting Mass Spectrometry

2019 ◽  
Vol 26 (1) ◽  
pp. 35-43 ◽  
Author(s):  
Natalie K. Garcia ◽  
Galahad Deperalta ◽  
Aaron T. Wecksler
Keyword(s):  
Mass Spectrometry ◽  
Protein Structure ◽  
Protein Interactions ◽  
Quaternary Structure ◽  
Solvent Accessibility ◽  
Higher Order ◽  
Structure Characterization ◽  
Order Structure ◽  
Protein Footprinting ◽  
Wide Range

Background: Biotherapeutics, particularly monoclonal antibodies (mAbs), are a maturing class of drugs capable of treating a wide range of diseases. Therapeutic function and solutionstability are linked to the proper three-dimensional organization of the primary sequence into Higher Order Structure (HOS) as well as the timescales of protein motions (dynamics). Methods that directly monitor protein HOS and dynamics are important for mapping therapeutically relevant protein-protein interactions and assessing properly folded structures. Irreversible covalent protein footprinting Mass Spectrometry (MS) tools, such as site-specific amino acid labeling and hydroxyl radical footprinting are analytical techniques capable of monitoring the side chain solvent accessibility influenced by tertiary and quaternary structure. Here we discuss the methodology, examples of biotherapeutic applications, and the future directions of irreversible covalent protein footprinting MS in biotherapeutic research and development. Conclusion: Bottom-up mass spectrometry using irreversible labeling techniques provide valuable information for characterizing solution-phase protein structure. Examples range from epitope mapping and protein-ligand interactions, to probing challenging structures of membrane proteins. By paring these techniques with hydrogen-deuterium exchange, spectroscopic analysis, or static-phase structural data such as crystallography or electron microscopy, a comprehensive understanding of protein structure can be obtained.

Osteopontin expressed by renal tubular epithelium mediates interstitial monocyte infiltration in rats

2000 ◽  
Vol 278 (1) ◽  
pp. F110-F121 ◽  
Author(s):  
Hirokazu Okada ◽  
Kenshi Moriwaki ◽  
Raghuram Kalluri ◽  
Tsuneo Takenaka ◽  
Hiroe Imai ◽  
...  
Keyword(s):  
Target Genes ◽  
Renal Plasma Flow ◽  
Mrna Level ◽  
Antisense Oligodeoxynucleotide ◽  
Tubular Epithelium ◽  
Rt Pcr ◽  
Goodpasture Syndrome ◽  
Renal Tubular Epithelium ◽  
Protein Excretion ◽  
Renal Tubular

In this study, we have shown that intravenously administered antisense oligodeoxynucleotide (ODN) was demonstrated to be taken up by tubular epithelium, after which it blocked mRNA expression of target genes in normal and nephritic rats. Therefore, we injected osteopontin (OPN) antisense ODN to Goodpasture syndrome (GPS) rats every second day between days 27 and 35, the time when renal OPN expression increased and interstitial monocyte infiltration was aggravated. In parallel to blockade of tubular OPN expression, this treatment significantly attenuated monocyte infiltration and preserved renal plasma flow in GPS rats at day 37, compared with sense ODN-treated and untreated GPS rats. No significant changes were observed in OPN mRNA level by RT-PCR and histopathology of the glomeruli after ODN treatment, which was compatible with an absence of differences in the urinary protein excretion rate. In conclusion, OPN expressed by tubular epithelium played a pivotal role in mediating peritubular monocyte infiltration consequent to glomerular disease.

scholarly journals Ways into Understanding HIF Inhibition

Cancers ◽  
2021 ◽  
Vol 13 (1) ◽  
pp. 159
Author(s):  
Tina Schönberger ◽  
Joachim Fandrey ◽  
Katrin Prost-Fingerle
Keyword(s):  
Protein Interactions ◽  
Target Genes ◽  
Protein Protein Interactions ◽  
Low Oxygen ◽  
Drug Candidates ◽  
Open Questions ◽  
Wide Range ◽  
Hif Pathway

Hypoxia is a key characteristic of tumor tissue. Cancer cells adapt to low oxygen by activating hypoxia-inducible factors (HIFs), ensuring their survival and continued growth despite this hostile environment. Therefore, the inhibition of HIFs and their target genes is a promising and emerging field of cancer research. Several drug candidates target protein–protein interactions or transcription mechanisms of the HIF pathway in order to interfere with activation of this pathway, which is deregulated in a wide range of solid and liquid cancers. Although some inhibitors are already in clinical trials, open questions remain with respect to their modes of action. New imaging technologies using luminescent and fluorescent methods or nanobodies to complement widely used approaches such as chromatin immunoprecipitation may help to answer some of these questions. In this review, we aim to summarize current inhibitor classes targeting the HIF pathway and to provide an overview of in vitro and in vivo techniques that could improve the understanding of inhibitor mechanisms. Unravelling the distinct principles regarding how inhibitors work is an indispensable step for efficient clinical applications and safety of anticancer compounds.

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