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1.
Nucleic Acids Res ; 51(13): 6754-6769, 2023 07 21.
Artigo em Inglês | MEDLINE | ID: mdl-37309898

RESUMO

The Sirtuin family of NAD+-dependent enzymes plays an important role in maintaining genome stability upon stress. Several mammalian Sirtuins have been linked directly or indirectly to the regulation of DNA damage during replication through Homologous recombination (HR). The role of one of them, SIRT1, is intriguing as it seems to have a general regulatory role in the DNA damage response (DDR) that has not yet been addressed. SIRT1-deficient cells show impaired DDR reflected in a decrease in repair capacity, increased genome instability and decreased levels of γH2AX. Here we unveil a close functional antagonism between SIRT1 and the PP4 phosphatase multiprotein complex in the regulation of the DDR. Upon DNA damage, SIRT1 interacts specifically with the catalytical subunit PP4c and promotes its inhibition by deacetylating the WH1 domain of the regulatory subunits PP4R3α/ß. This in turn regulates γH2AX and RPA2 phosphorylation, two key events in the signaling of DNA damage and repair by HR. We propose a mechanism whereby during stress, SIRT1 signaling ensures a global control of DNA damage signaling through PP4.


Assuntos
Dano ao DNA , Sirtuína 1 , Animais , Humanos , Mamíferos/metabolismo , Monoéster Fosfórico Hidrolases , Fosforilação , Transdução de Sinais , Sirtuína 1/metabolismo
3.
Cancers (Basel) ; 10(3)2018 Mar 07.
Artigo em Inglês | MEDLINE | ID: mdl-29518918

RESUMO

Approximately 75% of patients with pancreatic ductal adenocarcinoma are diagnosed with advanced cancer, which cannot be safely resected. The most commonly used biomarker CA19-9 has inadequate sensitivity and specificity for early detection, which we define as Stage I/II cancers. Therefore, progress in next-generation biomarkers is greatly needed. Recent reports have validated a number of biomarkers, including combination assays of proteins and DNA mutations; however, the history of translating promising biomarkers to clinical utility suggests that several major hurdles require careful consideration by the medical community. The first set of challenges involves nominating and verifying biomarkers. Candidate biomarkers need to discriminate disease from benign controls with high sensitivity and specificity for an intended use, which we describe as a two-tiered strategy of identifying and screening high-risk patients. Community-wide efforts to share samples, data, and analysis methods have been beneficial and progress meeting this challenge has been achieved. The second set of challenges is assay optimization and validating biomarkers. After initial candidate validation, assays need to be refined into accurate, cost-effective, highly reproducible, and multiplexed targeted panels and then validated in large cohorts. To move the most promising candidates forward, ideally, biomarker panels, head-to-head comparisons, meta-analysis, and assessment in independent data sets might mitigate risk of failure. Much more investment is needed to overcome these challenges. The third challenge is achieving clinical translation. To moonshot an early detection test to the clinic requires a large clinical trial and organizational, regulatory, and entrepreneurial know-how. Additional factors, such as imaging technologies, will likely need to improve concomitant with molecular biomarker development. The magnitude of the clinical translational challenge is uncertain, but interdisciplinary cooperation within the PDAC community is poised to confront it.

4.
Nat Commun ; 8(1): 2035, 2017 12 11.
Artigo em Inglês | MEDLINE | ID: mdl-29229958

RESUMO

Transport of macromolecules through the nuclear pore by importins and exportins plays a critical role in the spatial regulation of protein activity. How cancer cells co-opt this process to promote tumorigenesis remains unclear. The epidermal growth factor receptor (EGFR) plays a critical role in normal development and in human cancer. Here we describe a mechanism of EGFR regulation through the importin ß family member RAN-binding protein 6 (RanBP6), a protein of hitherto unknown functions. We show that RanBP6 silencing impairs nuclear translocation of signal transducer and activator of transcription 3 (STAT3), reduces STAT3 binding to the EGFR promoter, results in transcriptional derepression of EGFR, and increased EGFR pathway output. Focal deletions of the RanBP6 locus on chromosome 9p were found in a subset of glioblastoma (GBM) and silencing of RanBP6 promoted glioma growth in vivo. Our results provide an example of EGFR deregulation in cancer through silencing of components of the nuclear import pathway.


Assuntos
Receptores ErbB/genética , Regulação Neoplásica da Expressão Gênica , Glioma/genética , beta Carioferinas/genética , Proteína ran de Ligação ao GTP/genética , Transporte Ativo do Núcleo Celular/genética , Animais , Antibióticos Antineoplásicos/farmacologia , Linhagem Celular Tumoral , Células Cultivadas , Doxorrubicina/farmacologia , Receptores ErbB/metabolismo , Retroalimentação Fisiológica , Feminino , Técnicas de Silenciamento de Genes , Glioma/tratamento farmacológico , Glioma/metabolismo , Células HEK293 , Humanos , Camundongos Knockout , Camundongos SCID , Fator de Transcrição STAT3/genética , Fator de Transcrição STAT3/metabolismo , Ensaios Antitumorais Modelo de Xenoenxerto , beta Carioferinas/metabolismo , Proteína ran de Ligação ao GTP/metabolismo
5.
J Proteome Res ; 16(3): 1121-1132, 2017 03 03.
Artigo em Inglês | MEDLINE | ID: mdl-28102081

RESUMO

Labeling peptides with isobaric tags is a popular strategy in quantitative bottom-up proteomics. In this study, we labeled six breast tumor cell lysates (1.34 mg proteins per channel) using 10-plex tandem mass tag reagents and analyzed the samples on a Q Exactive HF Quadrupole-Orbitrap mass spectrometer. We identified a total of 8,706 proteins and 28,186 phosphopeptides, including 7,394 proteins and 23,739 phosphosites common to all channels. The majority of technical replicates correlated with a R2 ≥ 0.98, indicating minimum variability was introduced after labeling. Unsupervised hierarchical clustering of phosphopeptide data sets successfully classified the breast tumor samples into Her2 (epidermal growth factor receptor 2) positive and Her2 negative groups, whereas mRNA abundance did not. The tyrosine phosphorylation levels of receptor tyrosine kinases, phosphoinositide-3-kinase, protein kinase C delta, and Src homology 2, among others, were significantly higher in the Her2 positive than the Her2 negative group. Despite ratio compression in MS2-based experiments, we demonstrated the ratios calculated using an MS2 method are highly correlated (R2 > 0.65) with ratios obtained using MS3-based quantitation (using a Thermo Orbitrap Fusion mass spectrometer) with reduced ratio suppression. Given the deep coverage of global and phosphoproteomes, our data show that MS2-based quantitation using TMT can be successfully used for large-scale multiplexed quantitative proteomics.


Assuntos
Neoplasias da Mama/patologia , Proteômica/métodos , Coloração e Rotulagem , Linhagem Celular Tumoral , Análise por Conglomerados , Feminino , Humanos , Espectrometria de Massas/métodos , Fosfopeptídeos/análise , Fosforilação , Receptor ErbB-2/análise , Tirosina/metabolismo
6.
J Am Soc Nephrol ; 28(6): 1729-1740, 2017 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-28028135

RESUMO

Two metrics, a rise in serum creatinine concentration and a decrease in urine output, are considered tantamount to the injury of the kidney tubule and the epithelial cells thereof (AKI). Yet neither criterion emphasizes the etiology or the pathogenetic heterogeneity of acute decreases in kidney excretory function. In fact, whether decreased excretory function due to contraction of the extracellular fluid volume (vAKI) or due to intrinsic kidney injury (iAKI) actually share pathogenesis and should be aggregated in the same diagnostic group remains an open question. To examine this possibility, we created mouse models of iAKI and vAKI that induced a similar increase in serum creatinine concentration. Using laser microdissection to isolate specific domains of the kidney, followed by RNA sequencing, we found that thousands of genes responded specifically to iAKI or to vAKI, but very few responded to both stimuli. In fact, the activated gene sets comprised different, functionally unrelated signal transduction pathways and were expressed in different regions of the kidney. Moreover, we identified distinctive gene expression patterns in human urine as potential biomarkers of either iAKI or vAKI, but not both. Hence, iAKI and vAKI are biologically unrelated, suggesting that molecular analysis should clarify our current definitions of acute changes in kidney excretory function.


Assuntos
Injúria Renal Aguda/classificação , Injúria Renal Aguda/genética , Transcriptoma , Animais , Feminino , Expressão Gênica , Humanos , Camundongos , Camundongos Endogâmicos C57BL
7.
Mol Cell Proteomics ; 14(9): 2357-74, 2015 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-25693799

RESUMO

There is an increasing need in biology and clinical medicine to robustly and reliably measure tens to hundreds of peptides and proteins in clinical and biological samples with high sensitivity, specificity, reproducibility, and repeatability. Previously, we demonstrated that LC-MRM-MS with isotope dilution has suitable performance for quantitative measurements of small numbers of relatively abundant proteins in human plasma and that the resulting assays can be transferred across laboratories while maintaining high reproducibility and quantitative precision. Here, we significantly extend that earlier work, demonstrating that 11 laboratories using 14 LC-MS systems can develop, determine analytical figures of merit, and apply highly multiplexed MRM-MS assays targeting 125 peptides derived from 27 cancer-relevant proteins and seven control proteins to precisely and reproducibly measure the analytes in human plasma. To ensure consistent generation of high quality data, we incorporated a system suitability protocol (SSP) into our experimental design. The SSP enabled real-time monitoring of LC-MRM-MS performance during assay development and implementation, facilitating early detection and correction of chromatographic and instrumental problems. Low to subnanogram/ml sensitivity for proteins in plasma was achieved by one-step immunoaffinity depletion of 14 abundant plasma proteins prior to analysis. Median intra- and interlaboratory reproducibility was <20%, sufficient for most biological studies and candidate protein biomarker verification. Digestion recovery of peptides was assessed and quantitative accuracy improved using heavy-isotope-labeled versions of the proteins as internal standards. Using the highly multiplexed assay, participating laboratories were able to precisely and reproducibly determine the levels of a series of analytes in blinded samples used to simulate an interlaboratory clinical study of patient samples. Our study further establishes that LC-MRM-MS using stable isotope dilution, with appropriate attention to analytical validation and appropriate quality control measures, enables sensitive, specific, reproducible, and quantitative measurements of proteins and peptides in complex biological matrices such as plasma.


Assuntos
Proteínas de Neoplasias/sangue , Neoplasias/metabolismo , Peptídeos/análise , Proteômica/métodos , Cromatografia Líquida/métodos , Humanos , Marcação por Isótopo , Espectrometria de Massas/métodos , Proteínas de Neoplasias/química , Proteínas de Neoplasias/isolamento & purificação , Neoplasias/sangue , Peptídeos/química , Reprodutibilidade dos Testes
8.
Mol Cell Proteomics ; 13(11): 3082-96, 2014 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-25056937

RESUMO

Cancer is responsible for many deaths and is a major source of healthcare expenditures. The identification of new, non-invasive biomarkers might allow improvement of the direct diagnostic or prognostic ability of already available tools. Here, we took the innovative approach of interrogating the activity of exopeptidases in the serum of cancer patients with the aim of establishing a distinction based on enzymatic function, instead of simple protein levels, as a means to biomarker discovery. We first analyzed two well-characterized mouse models of prostate cancer, each with a distinct genetic lesion, and established that broad exopeptidase and targeted aminopeptidase activity tests reveal proteolytic changes associated with tumor development. We also describe new peptide-based freeze-frame reagents uniquely suited to probe the altered balance of selected aminopeptidases, as opposed to the full array of exopeptidases, and/or their modulators in patient serum or plasma. One particular proteolytic activity was impaired in animals with aggressive disease relative to cancer-free littermates. We identified the protease in question as dipeptidyl peptidase 4 (DPP4) by analyzing selected knockout mice and evaluating the effect of specific inhibitors. DPP4 activity was also reduced in the sera of patients with metastatic prostate cancer relative to patients with localized disease or healthy controls. However, no significant differences in DPP4 serum levels were observed, which established the loss of activity as the result of impaired enzymatic function. Biochemical analysis indicated that reduced activity was the result not of post-translational modifications or allosteric changes, but instead of a low-molecular-weight inhibitor. After we adjusted for age and total prostate-specific antigen, reduced DPP4 activity remained a significant predictor of cancer status. The results of this proof-of-principle study suggest that DPP4 activity might be a potential blood-based indicator of the presence of metastatic cancer of prostatic origin, either by itself or, more likely, as a means to improve the sensitivity and specificity of existing markers.


Assuntos
Biomarcadores Tumorais/sangue , Dipeptidil Peptidase 4/sangue , Dipeptidil Peptidase 4/metabolismo , Neoplasias da Próstata/sangue , Aminopeptidases/sangue , Aminopeptidases/genética , Aminopeptidases/metabolismo , Animais , Biomarcadores Tumorais/genética , Biomarcadores Tumorais/metabolismo , Dipeptidil Peptidase 4/genética , Humanos , Masculino , Camundongos , Camundongos Knockout , Neoplasias Experimentais/sangue , Neoplasias Experimentais/diagnóstico , PTEN Fosfo-Hidrolase/genética , Neoplasias da Próstata/diagnóstico , Neoplasias da Próstata/genética , Proteínas Proto-Oncogênicas c-myc/biossíntese , Proteína Supressora de Tumor p53/genética
9.
Mol Cell Biol ; 34(13): 2437-49, 2014 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-24752897

RESUMO

MacroH2A1 is a histone variant harboring an ∼25-kDa carboxyl-terminal macrodomain. Due to its enrichment on the inactive X chromosome, macroH2A1 was thought to play a role in transcriptional repression. However, recent studies have shown that macroH2A1 occupies autosomal chromatin and regulates genes in a context-specific manner. The macrodomain may play a role in the modulation of gene expression outcomes via physical interactions with effector proteins, which may depend on the ability of the macrodomain to bind NAD(+) metabolite ligands. Here, we identify proline, glutamic acid, and leucine-rich protein 1 (PELP1), a chromatin-associated factor and transcriptional coregulator, as a ligand-independent macrodomain-interacting factor. We used chromatin immunoprecipitation coupled with tiling microarrays (ChIP-chip) to determine the genomic localization of PELP1 in MCF-7 human breast cancer cells. We find that PELP1 genomic localization is highly correlated with that of macroH2A1. Additionally, PELP1 positively correlates with heterochromatic chromatin marks and negatively correlates with active transcription marks, much like macroH2A1. MacroH2A1 specifically recruits PELP1 to the promoters of macroH2A1 target genes, but macroH2A1 occupancy occurs independent of PELP1. This recruitment allows macroH2A1 and PELP1 to cooperatively regulate gene expression outcomes.


Assuntos
Proteínas Correpressoras/genética , Regulação da Expressão Gênica/genética , Histonas/metabolismo , Fatores de Transcrição/genética , Transcrição Gênica , Antibacterianos/farmacologia , Linhagem Celular Tumoral , Cromatina/química , Cromatina/genética , Imunoprecipitação da Cromatina , Proteínas Correpressoras/biossíntese , Doxiciclina/farmacologia , Histonas/genética , Humanos , Células MCF-7 , Análise de Sequência com Séries de Oligonucleotídeos , Regiões Promotoras Genéticas , Estrutura Terciária de Proteína , Interferência de RNA , RNA Interferente Pequeno , Receptores de Estrogênio/genética , Transdução de Sinais/genética , Fatores de Transcrição/biossíntese
10.
Proteomics Clin Appl ; 8(5-6): 317-26, 2014 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-24591208

RESUMO

PURPOSE: Proteases have been implicated in cancer progression and invasiveness. We have investigated the activities, as opposed to simple protein levels, of selected aminopeptidases in urine specimens to serve as potential novel biomarkers for urothelial cancer. EXPERIMENTAL DESIGN: The unique urinary proteomes of males and females were profiled to establish the presence of a gender-independent set of aminopeptidases. Samples were also collected from patients with urothelial cancer and matched controls. A SOP for urine processing was developed taking into account hydration variation. Five specific aminopeptidase activity assays, using fluorophoric substrates, were optimized for evaluation of marker potential. RESULTS: Nineteen exopeptidases and 21 other proteases were identified in urine and the top-five most abundant aminopeptidases, identical in both genders, selected for functional studies. Depending on the enzyme, activities were consistently lower (p ≤ 0.05), higher or unchanged in the cancer samples as compared to controls. Two selected aminopeptidase activities used as a binary classifier resulted in a ROC curve with an AUC = 0.898. CONCLUSION AND CLINICAL RELEVANCE: We have developed functional assays that characterize aminopeptidase activities in urine specimens with adequate technical and intraindividual reproducibility. With further testing, it could yield a reliable biomarker test for bladder cancer detection or prognostication.


Assuntos
Aminopeptidases/urina , Biomarcadores Tumorais/urina , Proteômica/métodos , Neoplasias da Bexiga Urinária/enzimologia , Neoplasias da Bexiga Urinária/urina , Feminino , Humanos , Masculino , Prognóstico , Estudos Prospectivos , Neoplasias da Bexiga Urinária/diagnóstico
11.
Cell Rep ; 5(6): 1625-38, 2013 Dec 26.
Artigo em Inglês | MEDLINE | ID: mdl-24332853

RESUMO

Defining the role of epigenetic regulators in hematopoiesis has become critically important, because recurrent mutations or aberrant expression of these genes has been identified in both myeloid and lymphoid hematological malignancies. We found that PRMT4, a type I arginine methyltransferase whose function in normal and malignant hematopoiesis is unknown, is overexpressed in acute myelogenous leukemia patient samples. Overexpression of PRMT4 blocks the myeloid differentiation of human stem/progenitor cells (HSPCs), whereas its knockdown is sufficient to induce myeloid differentiation of HSPCs. We demonstrated that PRMT4 represses the expression of miR-223 in HSPCs via the methylation of RUNX1, which triggers the assembly of a multiprotein repressor complex that includes DPF2. As part of the feedback loop, PRMT4 expression is repressed posttranscriptionally by miR-223. Depletion of PRMT4 results in differentiation of myeloid leukemia cells in vitro and their decreased proliferation in vivo. Thus, targeting PRMT4 holds potential as a novel therapy for acute myelogenous leukemia.


Assuntos
Subunidade alfa 2 de Fator de Ligação ao Core/metabolismo , Repressão Epigenética , Hematopoese , Células Progenitoras Mieloides/metabolismo , Proteína-Arginina N-Metiltransferases/metabolismo , Animais , Linhagem Celular Tumoral , Proteínas de Ligação a DNA/metabolismo , Humanos , Metilação , Camundongos , MicroRNAs/genética , MicroRNAs/metabolismo , Células Progenitoras Mieloides/citologia , Ligação Proteica , Proteína-Arginina N-Metiltransferases/genética , Processamento Pós-Transcricional do RNA , Fatores de Transcrição
12.
Cell ; 154(5): 983-995, 2013 Aug 29.
Artigo em Inglês | MEDLINE | ID: mdl-23993092

RESUMO

DNA damage triggers polyubiquitylation and degradation of the largest subunit of RNA polymerase II (RNAPII), a "mechanism of last resort" employed during transcription stress. In yeast, this process is dependent on Def1 through a previously unresolved mechanism. Here, we report that Def1 becomes activated through ubiquitylation- and proteasome-dependent processing. Def1 processing results in the removal of a domain promoting cytoplasmic localization, resulting in nuclear accumulation of the clipped protein. Nuclear Def1 then binds RNAPII, utilizing a ubiquitin-binding domain to recruit the Elongin-Cullin E3 ligase complex via a ubiquitin-homology domain in the Ela1 protein. This facilitates polyubiquitylation of Rpb1, triggering its proteasome-mediated degradation. Together, these results outline the multistep mechanism of Rpb1 polyubiquitylation triggered by transcription stress and uncover the key role played by Def1 as a facilitator of Elongin-Cullin ubiquitin ligase function.


Assuntos
Proteínas Cromossômicas não Histona/metabolismo , Proteínas de Saccharomyces cerevisiae/metabolismo , Saccharomyces cerevisiae/fisiologia , Transcrição Gênica , Sequência de Aminoácidos , Proteínas Cromossômicas não Histona/química , Dados de Sequência Molecular , Complexo de Endopeptidases do Proteassoma/metabolismo , Estrutura Terciária de Proteína , RNA Polimerase II/metabolismo , Proteínas de Saccharomyces cerevisiae/química , Alinhamento de Sequência , Estresse Fisiológico , Complexos Ubiquitina-Proteína Ligase/metabolismo
13.
Genes Dev ; 27(14): 1581-95, 2013 Jul 15.
Artigo em Inglês | MEDLINE | ID: mdl-23824326

RESUMO

Post-translational histone modifications play important roles in regulating chromatin structure and function. Histone H2B ubiquitination and deubiquitination have been implicated in transcriptional regulation, but the function of H2B deubiquitination is not well defined, particularly in higher eukaryotes. Here we report the purification of ubiquitin-specific peptidase 49 (USP49) as a histone H2B-specific deubiquitinase and demonstrate that H2B deubiquitination by USP49 is required for efficient cotranscriptional splicing of a large set of exons. USP49 forms a complex with RuvB-like1 (RVB1) and SUG1 and specifically deubiquitinates histone H2B in vitro and in vivo. USP49 knockdown results in small changes in gene expression but affects the abundance of >9000 isoforms. Exons down-regulated in USP49 knockdown cells show both elevated levels of alternative splicing and a general decrease in splicing efficiency. Importantly, USP49 is relatively enriched at this set of exons. USP49 knockdown increased H2B ubiquitination (uH2B) levels at these exons as well as upstream 3' and downstream 5' intronic splicing elements. Change in H2B ubiquitination level, as modulated by USP49, regulates U1A and U2B association with chromatin and binding to nascent pre-mRNA. Although H3 levels are relatively stable after USP49 depletion, H2B levels at these exons are dramatically increased, suggesting that uH2B may enhance nucleosome stability. Therefore, this study identifies USP49 as a histone H2B-specific deubiquitinase and uncovers a critical role for H2B deubiquitination in cotranscriptional pre-mRNA processing events.


Assuntos
Histonas/metabolismo , Precursores de RNA/metabolismo , Splicing de RNA , Ubiquitina Tiolesterase/genética , Ubiquitina Tiolesterase/metabolismo , ATPases Associadas a Diversas Atividades Celulares , Proteínas Adaptadoras de Transdução de Sinal/metabolismo , Proteínas de Transporte/metabolismo , Linhagem Celular Tumoral , DNA Helicases/metabolismo , Regulação da Expressão Gênica , Técnicas de Silenciamento de Genes , Células HeLa , Humanos , Proteínas com Domínio LIM/metabolismo , Complexo de Endopeptidases do Proteassoma , Fatores de Transcrição/metabolismo , Ubiquitina Tiolesterase/isolamento & purificação , Ubiquitinação
15.
Mol Cell Proteomics ; 12(9): 2623-39, 2013 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-23689285

RESUMO

Multiple reaction monitoring (MRM) mass spectrometry coupled with stable isotope dilution (SID) and liquid chromatography (LC) is increasingly used in biological and clinical studies for precise and reproducible quantification of peptides and proteins in complex sample matrices. Robust LC-SID-MRM-MS-based assays that can be replicated across laboratories and ultimately in clinical laboratory settings require standardized protocols to demonstrate that the analysis platforms are performing adequately. We developed a system suitability protocol (SSP), which employs a predigested mixture of six proteins, to facilitate performance evaluation of LC-SID-MRM-MS instrument platforms, configured with nanoflow-LC systems interfaced to triple quadrupole mass spectrometers. The SSP was designed for use with low multiplex analyses as well as high multiplex approaches when software-driven scheduling of data acquisition is required. Performance was assessed by monitoring of a range of chromatographic and mass spectrometric metrics including peak width, chromatographic resolution, peak capacity, and the variability in peak area and analyte retention time (RT) stability. The SSP, which was evaluated in 11 laboratories on a total of 15 different instruments, enabled early diagnoses of LC and MS anomalies that indicated suboptimal LC-MRM-MS performance. The observed range in variation of each of the metrics scrutinized serves to define the criteria for optimized LC-SID-MRM-MS platforms for routine use, with pass/fail criteria for system suitability performance measures defined as peak area coefficient of variation <0.15, peak width coefficient of variation <0.15, standard deviation of RT <0.15 min (9 s), and the RT drift <0.5min (30 s). The deleterious effect of a marginally performing LC-SID-MRM-MS system on the limit of quantification (LOQ) in targeted quantitative assays illustrates the use and need for a SSP to establish robust and reliable system performance. Use of a SSP helps to ensure that analyte quantification measurements can be replicated with good precision within and across multiple laboratories and should facilitate more widespread use of MRM-MS technology by the basic biomedical and clinical laboratory research communities.


Assuntos
Cromatografia Líquida/instrumentação , Cromatografia Líquida/métodos , Espectrometria de Massas/instrumentação , Espectrometria de Massas/métodos , Sequência de Aminoácidos , Animais , Bovinos , Limite de Detecção , Dados de Sequência Molecular , Peptídeos/química , Peptídeos/metabolismo , Padrões de Referência , Software , Fatores de Tempo
16.
Mol Cell Biol ; 33(8): 1546-60, 2013 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-23401860

RESUMO

Nucleocytoplasmic shuttling of class IIa of histone deacetylases (HDACs) is a key mechanism that controls cell fate and animal development. We have identified the filamin B (FLNB) as a novel HDAC7-interacting protein that is required for temporal and spatial regulation of vascular endothelial growth factor (VEGF)-mediated HDAC7 cytoplasmic sequestration. This interaction occurs in the cytoplasm and requires monoubiquitination of an evolutionarily conserved lysine 1147 (K1147) in the immunoglobulin (Ig)-like repeat 10 (R10) of FLNB and the nuclear localization sequence of HDAC7. Inhibition of protein kinase C (PKC) blocks VEGF-induced ubiquitination of FLNB and its interaction with HDAC7. Small interfering RNA (siRNA) knockdown of FLNB or ubiquitin (Ub) in human primary endothelial cells blocks VEGF-mediated cytoplasmic accumulation of HDAC7, reduces VEGF-induced expression of the HDAC7 target genes Mmp-10 and Nur77, and inhibits VEGF-induced vascular permeability. Using dominant negative mutants and rescue experiments, we demonstrate the functional significance of FLNB K1147 to interfere with the ability of phorbol myristate acetate (PMA) to promote FLNB-mediated cytoplasmic accumulation of HDAC7. Taken together, our data show that VEGF and PKC promote degradation-independent protein ubiquitination of FLNB to control intracellular trafficking of HDAC7.


Assuntos
Proteínas Contráteis/metabolismo , Histona Desacetilases/metabolismo , Proteínas dos Microfilamentos/metabolismo , Proteína Quinase C/metabolismo , Fatores de Crescimento do Endotélio Vascular/metabolismo , Sequência de Aminoácidos , Carbazóis/farmacologia , Linhagem Celular Tumoral , Movimento Celular , Proteínas Contráteis/genética , Células Endoteliais/metabolismo , Filaminas , Células HeLa , Humanos , Indóis/farmacologia , Maleimidas/farmacologia , Metaloproteinase 10 da Matriz/biossíntese , Proteínas dos Microfilamentos/genética , Neovascularização Fisiológica , Membro 1 do Grupo A da Subfamília 4 de Receptores Nucleares/biossíntese , Proteína Quinase C/antagonistas & inibidores , Estrutura Terciária de Proteína , Transporte Proteico , Interferência de RNA , RNA Interferente Pequeno , Acetato de Tetradecanoilforbol/farmacologia , Ubiquitina/genética , Ubiquitinação , Fatores de Crescimento do Endotélio Vascular/genética
17.
Kidney Int ; 82(6): 718-22, 2012 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-22695331

RESUMO

The type and the extent of tissue damage inform the prognosis of chronic kidney disease (CKD), but kidney biopsy is not a routine test. Urinary tests that correlate with specific histological findings might serve as surrogates for the kidney biopsy. We used immunoblots and ARCHITECT-NGAL assays to define the immunoreactivity of urinary neutrophil gelatinase-associated lipocalin (NGAL) in CKD, and we used mass spectroscopy to identify associated proteins. We analyzed kidney biopsies to determine whether specific pathological characteristics associated with the monomeric NGAL species. Advanced CKD urine contained the NGAL monomer as well as novel complexes of NGAL. When these species were separated, we found a significant correlation between the NGAL monomer and glomerular filtration rate (r=-0.53, P<0.001), interstitial fibrosis (mild vs. severe disease; mean 54 vs. 167 µg uNGAL/g Cr, P<0.01), and tubular atrophy (mild vs. severe disease; mean 54 vs. 164 µg uNGAL/g Cr, P<0.01). Monospecific assays of the NGAL monomer demonstrated a correlation with histology that typifies progressive, severe CKD.


Assuntos
Proteínas de Fase Aguda/urina , Rim/patologia , Lipocalinas/urina , Proteínas Proto-Oncogênicas/urina , Insuficiência Renal Crônica/diagnóstico , Adulto , Idoso , Atrofia , Biomarcadores/urina , Biópsia , Western Blotting , Resinas de Troca de Cátion , Distribuição de Qui-Quadrado , Cromatografia em Gel , Cromatografia por Troca Iônica , Progressão da Doença , Ensaio de Imunoadsorção Enzimática , Feminino , Fibrose , Taxa de Filtração Glomerular , Humanos , Rim/fisiopatologia , Lipocalina-2 , Masculino , Espectrometria de Massas , Pessoa de Meia-Idade , Valor Preditivo dos Testes , Prognóstico , Proteinúria/diagnóstico , Proteinúria/patologia , Proteinúria/urina , Insuficiência Renal Crônica/patologia , Insuficiência Renal Crônica/fisiopatologia , Insuficiência Renal Crônica/urina , Índice de Gravidade de Doença , Urinálise
18.
J Exp Med ; 209(5): 955-63, 2012 May 07.
Artigo em Inglês | MEDLINE | ID: mdl-22529269

RESUMO

Artemis is an endonuclease that opens coding hairpin ends during V(D)J recombination and has critical roles in postirradiation cell survival. A direct role for the C-terminal region of Artemis in V(D)J recombination has not been defined, despite the presence of immunodeficiency and lymphoma development in patients with deletions in this region. Here, we report that the Artemis C-terminal region directly interacts with the DNA-binding domain of Ligase IV, a DNA Ligase which plays essential roles in DNA repair and V(D)J recombination. The Artemis-Ligase IV interaction is specific and occurs independently of the presence of DNA and DNA-protein kinase catalytic subunit (DNA-PKcs), another protein known to interact with the Artemis C-terminal region. Point mutations in Artemis that disrupt its interaction with Ligase IV or DNA-PKcs reduce V(D)J recombination, and Artemis mutations that affect interactions with Ligase IV and DNA-PKcs show additive detrimental effects on coding joint formation. Signal joint formation remains unaffected. Our data reveal that the C-terminal region of Artemis influences V(D)J recombination through its interaction with both Ligase IV and DNA-PKcs.


Assuntos
DNA Ligases/metabolismo , Proteína Quinase Ativada por DNA/metabolismo , Proteínas Nucleares/metabolismo , Recombinação V(D)J/fisiologia , Sequência de Aminoácidos , Sequência de Bases , DNA Ligase Dependente de ATP , Primers do DNA/genética , Reparo do DNA/genética , Proteínas de Ligação a DNA/metabolismo , Endonucleases , Polarização de Fluorescência , Vetores Genéticos/genética , Células HeLa , Humanos , Imunoprecipitação , Dados de Sequência Molecular , Proteínas Nucleares/genética , Fosforilação , Mutação Puntual/genética , Análise de Sequência de DNA , Transfecção
19.
EMBO J ; 31(2): 443-56, 2012 Jan 18.
Artigo em Inglês | MEDLINE | ID: mdl-22045337

RESUMO

Regulation of mtDNA expression is critical for maintaining cellular energy homeostasis and may, in principle, occur at many different levels. The leucine-rich pentatricopeptide repeat containing (LRPPRC) protein regulates mitochondrial mRNA stability and an amino-acid substitution of this protein causes the French-Canadian type of Leigh syndrome (LSFC), a neurodegenerative disorder characterized by complex IV deficiency. We have generated conditional Lrpprc knockout mice and show here that the gene is essential for embryonic development. Tissue-specific disruption of Lrpprc in heart causes mitochondrial cardiomyopathy with drastic reduction in steady-state levels of most mitochondrial mRNAs. LRPPRC forms an RNA-dependent protein complex that is necessary for maintaining a pool of non-translated mRNAs in mammalian mitochondria. Loss of LRPPRC does not only decrease mRNA stability, but also leads to loss of mRNA polyadenylation and the appearance of aberrant mitochondrial translation. The translation pattern without the presence of LRPPRC is misregulated with excessive translation of some transcripts and no translation of others. Our findings point to the existence of an elaborate machinery that regulates mammalian mtDNA expression at the post-transcriptional level.


Assuntos
Deficiência de Citocromo-c Oxidase/genética , Doença de Leigh/genética , Mitocôndrias Cardíacas/fisiologia , Proteínas de Neoplasias/fisiologia , Poliadenilação/fisiologia , Biossíntese de Proteínas/fisiologia , Animais , DNA Mitocondrial/genética , Complexo IV da Cadeia de Transporte de Elétrons/análise , Células HeLa , Humanos , Substâncias Macromoleculares , Camundongos , Camundongos Knockout , Proteínas de Neoplasias/deficiência , Proteínas de Neoplasias/genética , Especificidade de Órgãos , Polinucleotídeo Adenililtransferase , Estabilidade de RNA , RNA Mensageiro , Proteínas de Ligação a RNA/metabolismo
20.
Sci Signal ; 4(188): pt6, 2011 Aug 23.
Artigo em Inglês | MEDLINE | ID: mdl-21878678

RESUMO

Integrin-mediated activation of PAK (p21-activated kinase) causes phosphorylation and inactivation of the FERM (4.1, ezrin, radixin, moesin) domain-containing protein Merlin, which is encoded by the NF2 (neurofibromatosis type 2) tumor suppressor gene. Conversely, cadherin engagement inactivates PAK, thus leading to accumulation of unphosphorylated Merlin. Current models imply that Merlin inhibits cell proliferation by inhibiting mitogenic signaling at or near the plasma membrane. We have recently shown that the unphosphorylated, growth-inhibiting form of Merlin accumulates in the nucleus and binds to the E3 ubiquitin ligase CRL4(DCAF1) to suppress its activity. Depletion of DCAF1 blocks the hyperproliferation caused by inactivation of Merlin. Conversely, expression of a Merlin-insensitive DCAF1 mutant counteracts the antimitogenic effect of Merlin. Expression of Merlin or silencing of DCAF1 in Nf2-deficient cells induce an overlapping, tumor-suppressive program of gene expression. Mutations present in some tumors from NF2 patients disrupt Merlin's ability to interact with or inhibit CRL4(DCAF1). Lastly, depletion of DCAF1 inhibits the hyperproliferation of Schwannoma cells isolated from NF2 patients and suppresses the oncogenic potential of Merlin-deficient tumor cell lines. Current studies are aimed at identifying the substrates and mechanism of action of CRL4(DCAF1) and examining its role in NF2-dependent tumorigenesis in mouse models. We propose that Merlin mediates contact inhibition and suppresses tumorigenesis by translocating to the nucleus to inhibit CRL4(DCAF1).


Assuntos
Núcleo Celular/enzimologia , Regulação da Expressão Gênica/fisiologia , Neurofibromina 2/fisiologia , Oncogenes , Ubiquitina-Proteína Ligases/fisiologia , Animais , Camundongos , Fosforilação , Transdução de Sinais
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