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1.
Genes Dis ; 11(4): 101079, 2024 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-38560501

RESUMO

CYP3A5 is a cytochrome P450 (CYP) enzyme that metabolizes drugs and contributes to drug resistance in cancer. However, it remains unclear whether CYP3A5 directly influences cancer progression. In this report, we demonstrate that CYP3A5 regulates glucose metabolism in pancreatic ductal adenocarcinoma. Multi-omics analysis showed that CYP3A5 knockdown results in a decrease in various glucose-related metabolites through its effect on glucose transport. A mechanistic study revealed that CYP3A5 enriches the glucose transporter GLUT1 at the plasma membrane by restricting the translation of TXNIP, a negative regulator of GLUT1. Notably, CYP3A5-generated reactive oxygen species were proved to be responsible for attenuating the AKT-4EBP1-TXNIP signaling pathway. CYP3A5 contributes to cell migration by maintaining high glucose uptake in pancreatic cancer. Taken together, our results, for the first time, reveal a role of CYP3A5 in glucose metabolism in pancreatic ductal adenocarcinoma and identify a novel mechanism that is a potential therapeutic target.

2.
Elife ; 122024 Mar 15.
Artigo em Inglês | MEDLINE | ID: mdl-38488852

RESUMO

Dysregulated pre-mRNA splicing and metabolism are two hallmarks of MYC-driven cancers. Pharmacological inhibition of both processes has been extensively investigated as potential therapeutic avenues in preclinical and clinical studies. However, how pre-mRNA splicing and metabolism are orchestrated in response to oncogenic stress and therapies is poorly understood. Here, we demonstrate that jumonji domain containing 6, arginine demethylase, and lysine hydroxylase, JMJD6, acts as a hub connecting splicing and metabolism in MYC-driven human neuroblastoma. JMJD6 cooperates with MYC in cellular transformation of murine neural crest cells by physically interacting with RNA binding proteins involved in pre-mRNA splicing and protein homeostasis. Notably, JMJD6 controls the alternative splicing of two isoforms of glutaminase (GLS), namely kidney-type glutaminase (KGA) and glutaminase C (GAC), which are rate-limiting enzymes of glutaminolysis in the central carbon metabolism in neuroblastoma. Further, we show that JMJD6 is correlated with the anti-cancer activity of indisulam, a 'molecular glue' that degrades splicing factor RBM39, which complexes with JMJD6. The indisulam-mediated cancer cell killing is at least partly dependent on the glutamine-related metabolic pathway mediated by JMJD6. Our findings reveal a cancer-promoting metabolic program is associated with alternative pre-mRNA splicing through JMJD6, providing a rationale to target JMJD6 as a therapeutic avenue for treating MYC-driven cancers.


Assuntos
Neuroblastoma , Precursores de RNA , Sulfonamidas , Humanos , Animais , Camundongos , Precursores de RNA/genética , Precursores de RNA/metabolismo , Glutaminase/genética , Reprogramação Metabólica , Histona Desmetilases com o Domínio Jumonji/metabolismo
3.
bioRxiv ; 2023 Nov 20.
Artigo em Inglês | MEDLINE | ID: mdl-37425900

RESUMO

Dysregulated pre-mRNA splicing and metabolism are two hallmarks of MYC-driven cancers. Pharmacological inhibition of both processes has been extensively investigated as potential therapeutic avenues in preclinical and clinical studies. However, how pre-mRNA splicing and metabolism are orchestrated in response to oncogenic stress and therapies is poorly understood. Here, we demonstrate that Jumonji Domain Containing 6, Arginine Demethylase and Lysine Hydroxylase, JMJD6, acts as a hub connecting splicing and metabolism in MYC-driven neuroblastoma. JMJD6 cooperates with MYC in cellular transformation by physically interacting with RNA binding proteins involved in pre-mRNA splicing and protein homeostasis. Notably, JMJD6 controls the alternative splicing of two isoforms of glutaminase (GLS), namely kidney-type glutaminase (KGA) and glutaminase C (GAC), which are rate-limiting enzymes of glutaminolysis in the central carbon metabolism in neuroblastoma. Further, we show that JMJD6 is correlated with the anti-cancer activity of indisulam, a "molecular glue" that degrades splicing factor RBM39, which complexes with JMJD6. The indisulam-mediated cancer cell killing is at least partly dependent on the glutamine-related metabolic pathway mediated by JMJD6. Our findings reveal a cancer-promoting metabolic program is associated with alternative pre-mRNA splicing through JMJD6, providing a rationale to target JMJD6 as a therapeutic avenue for treating MYC-driven cancers.

5.
Nat Commun ; 14(1): 809, 2023 02 13.
Artigo em Inglês | MEDLINE | ID: mdl-36781850

RESUMO

Rearrangments in Histone-lysine-N-methyltransferase 2A (KMT2Ar) are associated with pediatric, adult and therapy-induced acute leukemias. Infants with KMT2Ar acute lymphoblastic leukemia (ALL) have a poor prognosis with an event-free-survival of 38%. Herein we evaluate 1116 FDA approved compounds in primary KMT2Ar infant ALL specimens and identify a sensitivity to proteasome inhibition. Upon exposure to this class of agents, cells demonstrate a depletion of histone H2B monoubiquitination (H2Bub1) and histone H3 lysine 79 dimethylation (H3K79me2) at KMT2A target genes in addition to a downregulation of the KMT2A gene expression signature, providing evidence that it targets the KMT2A transcriptional complex and alters the epigenome. A cohort of relapsed/refractory KMT2Ar patients treated with this approach on a compassionate basis had an overall response rate of 90%. In conclusion, we report on a high throughput drug screen in primary pediatric leukemia specimens whose results translate into clinically meaningful responses. This innovative treatment approach is now being evaluated in a multi-institutional upfront trial for infants with newly diagnosed ALL.


Assuntos
Leucemia-Linfoma Linfoblástico de Células Precursoras , Complexo de Endopeptidases do Proteassoma , Lactente , Adulto , Humanos , Criança , Complexo de Endopeptidases do Proteassoma/genética , Lisina/genética , Proteína de Leucina Linfoide-Mieloide/genética , Leucemia-Linfoma Linfoblástico de Células Precursoras/tratamento farmacológico , Leucemia-Linfoma Linfoblástico de Células Precursoras/genética , Transcriptoma
6.
Anal Chem ; 94(13): 5325-5334, 2022 04 05.
Artigo em Inglês | MEDLINE | ID: mdl-35315655

RESUMO

Proteome profiling is a powerful tool in biological and biomedical studies, starting with samples at bulk, single-cell, or single-cell-type levels. Reliable methods for extracting specific cell-type proteomes are in need, especially for the cells (e.g., neurons) that cannot be readily isolated. Here, we present an innovative proximity labeling (PL) strategy for single-cell-type proteomics of mouse brain, in which TurboID (an engineered biotin ligase) is used to label almost all proteins in a specific cell type. This strategy bypasses the requirement of cell isolation and includes five major steps: (i) constructing recombinant adeno-associated viruses (AAVs) to express TurboID driven by cell-type-specific promoters, (ii) delivering the AAV to mouse brains by direct intravenous injection, (iii) enhancing PL labeling by biotin administration, (iv) purifying biotinylated proteins, followed by on-bead protein digestion, and (v) quantitative tandem-mass-tag (TMT) labeling. We first confirmed that TurboID can label a wide range of cellular proteins in human HEK293 cells and optimized the single-cell-type proteomic pipeline. To analyze specific brain cell types, we generated recombinant AAVs to coexpress TurboID and mCherry proteins, driven by neuron- or astrocyte-specific promoters and validated the expected cell expression by coimmunostaining of mCherry and cellular markers. Subsequent biotin purification and TMT analysis identified ∼10,000 unique proteins from a few micrograms of protein samples with excellent reproducibility. Comparative and statistical analyses indicated that these PL proteomes contain cell-type-specific cellular pathways. Although PL was originally developed for studying protein-protein interactions and subcellular proteomes, we extended it to efficiently tag the entire proteomes of specific cell types in the mouse brain using TurboID biotin ligase. This simple, effective in vivo approach should be broadly applicable to single-cell-type proteomics.


Assuntos
Proteoma , Proteômica , Animais , Biotinilação , Encéfalo/metabolismo , Células HEK293 , Humanos , Camundongos , Proteoma/análise , Proteômica/métodos , Reprodutibilidade dos Testes
7.
Nat Aging ; 2(10): 923-940, 2022 10.
Artigo em Inglês | MEDLINE | ID: mdl-36636325

RESUMO

Recent proteome and transcriptome profiling of Alzheimer's disease (AD) brains reveals RNA splicing dysfunction and U1 small nuclear ribonucleoprotein (snRNP) pathology containing U1-70K and its N-terminal 40-KDa fragment (N40K). Here we present a causative role of U1 snRNP dysfunction to neurodegeneration in primary neurons and transgenic mice (N40K-Tg), in which N40K expression exerts a dominant-negative effect to downregulate full-length U1-70K. N40K-Tg recapitulates N40K insolubility, erroneous splicing events, neuronal degeneration and cognitive impairment. Specifically, N40K-Tg shows the reduction of GABAergic synapse components (e.g., the GABA receptor subunit of GABRA2), and concomitant postsynaptic hyperexcitability that is rescued by a GABA receptor agonist. Crossing of N40K-Tg and the 5xFAD amyloidosis model indicates that the RNA splicing defect synergizes with the amyloid cascade to remodel the brain transcriptome and proteome, deregulate synaptic proteins, and accelerate cognitive decline. Thus, our results support the contribution of U1 snRNP-mediated splicing dysfunction to AD pathogenesis.


Assuntos
Doença de Alzheimer , Disfunção Cognitiva , Animais , Camundongos , Ribonucleoproteína Nuclear Pequena U1/genética , Doença de Alzheimer/genética , Proteoma/genética , Splicing de RNA/genética , Disfunção Cognitiva/genética
8.
Mol Neurodegener ; 15(1): 43, 2020 07 25.
Artigo em Inglês | MEDLINE | ID: mdl-32711556

RESUMO

BACKGROUND: Based on amyloid cascade and tau hypotheses, protein biomarkers of different Aß and tau species in cerebrospinal fluid (CSF) and blood/plasma/serum have been examined to correlate with brain pathology. Recently, unbiased proteomic profiling of these human samples has been initiated to identify a large number of novel AD biomarker candidates, but it is challenging to define reliable candidates for subsequent large-scale validation. METHODS: We present a comprehensive strategy to identify biomarker candidates of high confidence by integrating multiple proteomes in AD, including cortex, CSF and serum. The proteomes were analyzed by the multiplexed tandem-mass-tag (TMT) method, extensive liquid chromatography (LC) fractionation and high-resolution tandem mass spectrometry (MS/MS) for ultra-deep coverage. A systems biology approach was used to prioritize the most promising AD signature proteins from all proteomic datasets. Finally, candidate biomarkers identified by the MS discovery were validated by the enzyme-linked immunosorbent (ELISA) and TOMAHAQ targeted MS assays. RESULTS: We quantified 13,833, 5941, and 4826 proteins from human cortex, CSF and serum, respectively. Compared to other studies, we analyzed a total of 10 proteomic datasets, covering 17,541 proteins (13,216 genes) in 365 AD, mild cognitive impairment (MCI) and control cases. Our ultra-deep CSF profiling of 20 cases uncovered the majority of previously reported AD biomarker candidates, most of which, however, displayed no statistical significance except SMOC1 and TGFB2. Interestingly, the AD CSF showed evident decrease of a large number of mitochondria proteins that were only detectable in our ultra-deep analysis. Further integration of 4 cortex and 4 CSF cohort proteomes highlighted 6 CSF biomarkers (SMOC1, C1QTNF5, OLFML3, SLIT2, SPON1, and GPNMB) that were consistently identified in at least 2 independent datasets. We also profiled CSF in the 5xFAD mouse model to validate amyloidosis-induced changes, and found consistent mitochondrial decreases (SOD2, PRDX3, ALDH6A1, ETFB, HADHA, and CYB5R3) in both human and mouse samples. In addition, comparison of cortex and serum led to an AD-correlated protein panel of CTHRC1, GFAP and OLFM3. In summary, 37 proteins emerged as potential AD signatures across cortex, CSF and serum, and strikingly, 59% of these were mitochondria proteins, emphasizing mitochondrial dysfunction in AD. Selected biomarker candidates were further validated by ELISA and TOMAHAQ assays. Finally, we prioritized the most promising AD signature proteins including SMOC1, TAU, GFAP, SUCLG2, PRDX3, and NTN1 by integrating all proteomic datasets. CONCLUSIONS: Our results demonstrate that novel AD biomarker candidates are identified and confirmed by proteomic studies of brain tissue and biofluids, providing a rich resource for large-scale biomarker validation for the AD community.


Assuntos
Doença de Alzheimer , Biomarcadores , Córtex Cerebral/metabolismo , Mitocôndrias/metabolismo , Doença de Alzheimer/sangue , Doença de Alzheimer/líquido cefalorraquidiano , Peptídeos beta-Amiloides/metabolismo , Biomarcadores/sangue , Biomarcadores/líquido cefalorraquidiano , Disfunção Cognitiva/sangue , Disfunção Cognitiva/líquido cefalorraquidiano , Disfunção Cognitiva/metabolismo , Humanos , Fragmentos de Peptídeos/metabolismo , Proteômica/métodos , Proteínas tau/metabolismo
9.
Anal Chem ; 92(10): 7162-7170, 2020 05 19.
Artigo em Inglês | MEDLINE | ID: mdl-32343560

RESUMO

Multiplexed isobaric labeling methods, such as tandem mass tags (TMT), remarkably improve the throughput of quantitative mass spectrometry. Here, we present a 27-plex TMT method coupled with two-dimensional liquid chromatography (LC/LC) for extensive peptide fractionation and high-resolution tandem mass spectrometry (MS/MS) for peptide quantification and then apply the method to profile the complex human brain proteome of Alzheimer's disease (AD). The 27-plex method combines multiplexed capacities of the 11-plex and the 16-plex TMT, as the peptides labeled by the two TMT sets display different mass and hydrophobicity, which can be well separated in LC-MS/MS. We first systematically optimized the protocol for the newly developed 16-plex TMT, including labeling reaction, desalting, and MS conditions, and then directly compared the 11-plex and 16-plex methods by analyzing the same human AD samples. Both methods yielded similar proteome coverage, analyzing >100 000 peptides in >10 000 human proteins. Furthermore, the 11-plex and 16-plex samples were mixed for a 27-plex assay, resulting in more than 8000 protein measurements within the same MS time. The 27-plex results are highly consistent with those of the individual 11-plex and 16-plex TMT analyses. We also used these proteomics data sets to compare the AD brain with the nondementia controls, discovering major AD-related proteins and revealing numerous novel protein alterations enriched in the pathways of amyloidosis, immunity, mitochondrial, and synaptic functions. Overall, our data strongly demonstrate that this new 27-plex strategy is highly feasible for routine large-scale proteomic analysis.


Assuntos
Doença de Alzheimer/diagnóstico , Lobo Frontal/química , Proteoma/análise , Cromatografia Líquida , Humanos , Peptídeos/análise , Espectrometria de Massas em Tandem
10.
Nat Commun ; 10(1): 3718, 2019 08 16.
Artigo em Inglês | MEDLINE | ID: mdl-31420543

RESUMO

High throughput omics approaches provide an unprecedented opportunity for dissecting molecular mechanisms in cancer biology. Here we present deep profiling of whole proteome, phosphoproteome and transcriptome in two high-grade glioma (HGG) mouse models driven by mutated RTK oncogenes, PDGFRA and NTRK1, analyzing 13,860 proteins and 30,431 phosphosites by mass spectrometry. Systems biology approaches identify numerous master regulators, including 41 kinases and 23 transcription factors. Pathway activity computation and mouse survival indicate the NTRK1 mutation induces a higher activation of AKT downstream targets including MYC and JUN, drives a positive feedback loop to up-regulate multiple other RTKs, and confers higher oncogenic potency than the PDGFRA mutation. A mini-gRNA library CRISPR-Cas9 validation screening shows 56% of tested master regulators are important for the viability of NTRK-driven HGG cells, including TFs (Myc and Jun) and metabolic kinases (AMPKa1 and AMPKa2), confirming the validity of the multiomics integrative approaches, and providing novel tumor vulnerabilities.


Assuntos
Neoplasias Encefálicas/genética , Perfilação da Expressão Gênica , Glioma/genética , Proteômica , Proteínas Quinases Ativadas por AMP/metabolismo , Animais , Neoplasias Encefálicas/metabolismo , Modelos Animais de Doenças , Retroalimentação Fisiológica , Glioma/metabolismo , Camundongos , Mutação , Proteína Oncogênica p65(gag-jun)/metabolismo , Fosfopeptídeos/metabolismo , Fosfoproteínas/metabolismo , Proteínas Proto-Oncogênicas c-akt/metabolismo , Proteínas Proto-Oncogênicas c-myc/metabolismo , Receptor alfa de Fator de Crescimento Derivado de Plaquetas/genética , Receptor trkA/genética , Transdução de Sinais , Biologia de Sistemas , Regulação para Cima
11.
Exp Cell Res ; 379(1): 55-64, 2019 06 01.
Artigo em Inglês | MEDLINE | ID: mdl-30922922

RESUMO

Metabolic studies of human pluripotent stem cells (hPSCs) have focused on how the cells produce energy through the catabolic pathway. The less-studied anabolic pathway, by which hPSCs expend energy in the form of adenosine triphosphate (ATP), is not yet fully understood. Compared to fully differentiated somatic cells, hPSCs undergo significant changes not only in their gene expression but also in their production and/or expenditure of ATP. Here, we investigate how hPSCs tightly control their energy homeostasis by studying the main energy-consuming process, mRNA translation. In addition, change of subcellular organelles regarding energy homeostasis has been investigated. Lysosomes are organelles that play an important role in the elimination of unnecessary cellular materials by digestion and in the recycling system of the cell. We have found that hPSCs control their lysosome numbers in part by regulating lysosomal gene/protein expression. Thus, because the levels of mRNA translation rate are lower in hPSCs than in somatic cells, not only the global translational machinery but also the lysosomal recycling machinery is suppressed in hPSCs. Overall, the results of our study suggest that hPSCs reprogram gene expression and signaling to regulate energy-consuming processes and energy-controlling organelles.


Assuntos
Metabolismo Energético/fisiologia , Organelas/metabolismo , Células-Tronco Pluripotentes/metabolismo , Trifosfato de Adenosina/metabolismo , Diferenciação Celular/fisiologia , Células Cultivadas , Expressão Gênica/fisiologia , Homeostase/fisiologia , Humanos , Lisossomos/metabolismo , Biossíntese de Proteínas/fisiologia , RNA Mensageiro/metabolismo , Transdução de Sinais/fisiologia
12.
Cancer Cell ; 34(3): 411-426.e19, 2018 09 10.
Artigo em Inglês | MEDLINE | ID: mdl-30146332

RESUMO

Personalized cancer therapy targeting somatic mutations in patient tumors is increasingly being incorporated into practice. Other therapeutic vulnerabilities resulting from changes in gene expression due to tumor specific epigenetic perturbations are progressively being recognized. These genomic and epigenomic changes are ultimately manifest in the tumor proteome and phosphoproteome. We integrated transcriptomic, epigenomic, and proteomic/phosphoproteomic data to elucidate the cellular origins and therapeutic vulnerabilities of rhabdomyosarcoma (RMS). We discovered that alveolar RMS occurs further along the developmental program than embryonal RMS. We also identified deregulation of the RAS/MEK/ERK/CDK4/6, G2/M, and unfolded protein response pathways through our integrated analysis. Comprehensive preclinical testing revealed that targeting the WEE1 kinase in the G2/M pathway is the most effective approach in vivo for high-risk RMS.


Assuntos
Antineoplásicos/farmacologia , Biomarcadores Tumorais/antagonistas & inibidores , Proteínas de Ciclo Celular/antagonistas & inibidores , Neoplasias Musculares/tratamento farmacológico , Proteínas Nucleares/antagonistas & inibidores , Proteínas Tirosina Quinases/antagonistas & inibidores , Rabdomiossarcoma/tratamento farmacológico , Animais , Antineoplásicos/uso terapêutico , Biomarcadores Tumorais/genética , Biomarcadores Tumorais/metabolismo , Proteínas de Ciclo Celular/genética , Proteínas de Ciclo Celular/metabolismo , Linhagem Celular Tumoral , Criança , Epigenômica , Feminino , Pontos de Checagem da Fase G2 do Ciclo Celular/efeitos dos fármacos , Perfilação da Expressão Gênica , Regulação Neoplásica da Expressão Gênica/efeitos dos fármacos , Regulação Neoplásica da Expressão Gênica/genética , Genômica , Humanos , Masculino , Camundongos , Terapia de Alvo Molecular/métodos , Neoplasias Musculares/genética , Neoplasias Musculares/patologia , Proteínas Nucleares/genética , Proteínas Nucleares/metabolismo , Medicina de Precisão/métodos , Proteínas Tirosina Quinases/genética , Proteínas Tirosina Quinases/metabolismo , Proteômica , Rabdomiossarcoma/genética , Rabdomiossarcoma/patologia , Transdução de Sinais/efeitos dos fármacos , Transdução de Sinais/genética , Resposta a Proteínas não Dobradas/genética , Ensaios Antitumorais Modelo de Xenoenxerto
13.
Anal Chem ; 89(5): 2956-2963, 2017 03 07.
Artigo em Inglês | MEDLINE | ID: mdl-28194965

RESUMO

Isobaric labeling quantification by mass spectrometry (MS) has emerged as a powerful technology for multiplexed large-scale protein profiling, but measurement accuracy in complex mixtures is confounded by the interference from coisolated ions, resulting in ratio compression. Here we report that the ratio compression can be essentially resolved by the combination of pre-MS peptide fractionation, MS2-based interference detection, and post-MS computational interference correction. To recapitulate the complexity of biological samples, we pooled tandem mass tag (TMT)-labeled Escherichia coli peptides at 1:3:10 ratios and added in ∼20-fold more rat peptides as background, followed by the analysis of two-dimensional liquid chromatography (LC)-MS/MS. Systematic investigation shows that quantitative interference was impacted by LC fractionation depth, MS isolation window, and peptide loading amount. Exhaustive fractionation (320 × 4 h) can nearly eliminate the interference and achieve results comparable to the MS3-based method. Importantly, the interference in MS2 scans can be estimated by the intensity of contaminated y1 product ions, and we thus developed an algorithm to correct reporter ion ratios of tryptic peptides. Our data indicate that intermediate fractionation (40 × 2 h) and y1 ion-based correction allow accurate and deep TMT profiling of more than 10 000 proteins, which represents a straightforward and affordable strategy in isobaric labeling proteomics.


Assuntos
Cromatografia Líquida de Alta Pressão/métodos , Peptídeos/análise , Espectrometria de Massas em Tandem/métodos , Algoritmos , Animais , Encéfalo/metabolismo , Escherichia coli/metabolismo , Proteínas de Escherichia coli/metabolismo , Concentração de Íons de Hidrogênio , Íons/química , Peptídeos/metabolismo , Ratos
14.
J Proteome Res ; 15(7): 2309-20, 2016 07 01.
Artigo em Inglês | MEDLINE | ID: mdl-27225868

RESUMO

Proteogenomics is an emerging approach to improve gene annotation and interpretation of proteomics data. Here we present JUMPg, an integrative proteogenomics pipeline including customized database construction, tag-based database search, peptide-spectrum match filtering, and data visualization. JUMPg creates multiple databases of DNA polymorphisms, mutations, splice junctions, partially trypticity, as well as protein fragments translated from the whole transcriptome in all six frames upon RNA-seq de novo assembly. We use a multistage strategy to search these databases sequentially, in which the performance is optimized by re-searching only unmatched high-quality spectra and reusing amino acid tags generated by the JUMP search engine. The identified peptides/proteins are displayed with gene loci using the UCSC genome browser. Then, the JUMPg program is applied to process a label-free mass spectrometry data set of Alzheimer's disease postmortem brain, uncovering 496 new peptides of amino acid substitutions, alternative splicing, frame shift, and "non-coding gene" translation. The novel protein PNMA6BL specifically expressed in the brain is highlighted. We also tested JUMPg to analyze a stable-isotope labeled data set of multiple myeloma cells, revealing 991 sample-specific peptides that include protein sequences in the immunoglobulin light chain variable region. Thus, the JUMPg program is an effective proteogenomics tool for multiomics data integration.


Assuntos
Química Encefálica , Proteínas de Neoplasias/análise , Proteínas/análise , Proteogenômica/métodos , Fluxo de Trabalho , Doença de Alzheimer/patologia , Mineração de Dados , Humanos , Mieloma Múltiplo/patologia , Neoplasias/química , Peptídeos/análise , Ferramenta de Busca , Software
15.
PLoS One ; 7(7): e41561, 2012.
Artigo em Inglês | MEDLINE | ID: mdl-22859996

RESUMO

MicroRNAs (miRNAs) are small, non-coding RNAs that regulate various biological processes, primarily through interaction with messenger RNAs. The levels of specific, circulating miRNAs in blood have been shown to associate with various pathological conditions including cancers. These miRNAs have great potential as biomarkers for various pathophysiological conditions. In this study we focused on different sample types' effects on the spectrum of circulating miRNA in blood. Using serum and corresponding plasma samples from the same individuals, we observed higher miRNA concentrations in serum samples compared to the corresponding plasma samples. The difference between serum and plasma miRNA concentration showed some associations with miRNA from platelets, which may indicate that the coagulation process may affect the spectrum of extracellular miRNA in blood. Several miRNAs also showed platform dependent variations in measurements. Our results suggest that there are a number of factors that might affect the measurement of circulating miRNA concentration. Caution must be taken when comparing miRNA data generated from different sample types or measurement platforms.


Assuntos
MicroRNAs/sangue , Adulto , Plaquetas/metabolismo , Eritrócitos/metabolismo , Feminino , Humanos , Leucócitos/metabolismo , Masculino , MicroRNAs/isolamento & purificação , Plasma , Soro , Adulto Jovem
16.
J Clin Invest ; 122(9): 3248-59, 2012 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-22863622

RESUMO

Crosstalk between the Notch and wingless-type MMTV integration site (WNT) signaling pathways has been investigated for many developmental processes. However, this negative correlation between Notch and WNT/ß-catenin signaling activity has been studied primarily in normal developmental and physiological processes in which negative feedback loops for both signaling pathways are intact. We found that Notch1 signaling retained the capability of suppressing the expression of WNT target genes in colorectal cancers even when ß-catenin destruction by the adenomatous polyposis coli (APC) complex was disabled. Activation of Notch1 converted high-grade adenoma into low-grade adenoma in an Apcmin mouse colon cancer model and suppressed the expression of WNT target genes in human colorectal cancer cells through epigenetic modification recruiting histone methyltransferase SET domain bifurcated 1 (SETDB1). Extensive microarray analysis of human colorectal cancers also showed a negative correlation between the Notch1 target gene, Notch-regulated ankyrin repeat protein 1 (NRARP), and WNT target genes. Notch is known to be a strong promoter of tumor initiation, but here we uncovered an unexpected suppressive role of Notch1 on WNT/ß-catenin target genes involved in colorectal cancer.


Assuntos
Adenocarcinoma/metabolismo , Adenoma/metabolismo , Cromatina/metabolismo , Neoplasias Colorretais/metabolismo , Receptor Notch1/metabolismo , Proteínas Wnt/metabolismo , beta Catenina/metabolismo , Adenocarcinoma/mortalidade , Adenocarcinoma/patologia , Adenoma/patologia , Proteína da Polipose Adenomatosa do Colo/deficiência , Proteína da Polipose Adenomatosa do Colo/genética , Análise de Variância , Animais , Fator de Transcrição CDX2 , Linhagem Celular Tumoral , Neoplasias Colorretais/mortalidade , Neoplasias Colorretais/patologia , Regulação Neoplásica da Expressão Gênica , Histona-Lisina N-Metiltransferase , Proteínas de Homeodomínio/genética , Proteínas de Homeodomínio/metabolismo , Humanos , Peptídeos e Proteínas de Sinalização Intracelular/metabolismo , Estimativa de Kaplan-Meier , Camundongos , Camundongos Transgênicos , Análise de Sequência com Séries de Oligonucleotídeos , Regiões Promotoras Genéticas , Proteínas Metiltransferases/metabolismo , Proteínas Serina-Treonina Quinases/metabolismo , Transcriptoma , Proteínas Supressoras de Tumor/genética , Proteínas Supressoras de Tumor/metabolismo , Vimentina/genética , Vimentina/metabolismo , Via de Sinalização Wnt
17.
Thorax ; 67(2): 122-31, 2012 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-21940491

RESUMO

BACKGROUND: The mechanisms underlying chronic obstructive pulmonary disease (COPD) remain unclear. MicroRNAs (miRNAs or miRs) are small non-coding RNA molecules that modulate the levels of specific genes and proteins. Identifying expression patterns of miRNAs in COPD may enhance our understanding of the mechanisms of disease. A study was undertaken to determine if miRNAs are differentially expressed in the lungs of smokers with and without COPD. miRNA and mRNA expression were compared to enrich for biological networks relevant to the pathogenesis of COPD. METHODS: Lung tissue from smokers with no evidence of obstructive lung disease (n=9) and smokers with COPD (n=26) was examined for miRNA and mRNA expression followed by validation. We then examined both miRNA and mRNA expression to enrich for relevant biological pathways. RESULTS: 70 miRNAs and 2667 mRNAs were differentially expressed between lung tissue from subjects with COPD and smokers without COPD. miRNA and mRNA expression profiles enriched for biological pathways that may be relevant to the pathogenesis of COPD including the transforming growth factor ß, Wnt and focal adhesion pathways. miR-223 and miR-1274a were the most affected miRNAs in subjects with COPD compared with smokers without obstruction. miR-15b was increased in COPD samples compared with smokers without obstruction and localised to both areas of emphysema and fibrosis. miR-15b was differentially expressed within GOLD classes of COPD. Expression of SMAD7, which was validated as a target for miR-15b, was decreased in bronchial epithelial cells in COPD. CONCLUSIONS: miRNA and mRNA are differentially expressed in individuals with COPD compared with smokers without obstruction. Investigating these relationships may further our understanding of the mechanisms of disease.


Assuntos
Regulação da Expressão Gênica/genética , Redes Reguladoras de Genes/genética , MicroRNAs/genética , Doença Pulmonar Obstrutiva Crônica/genética , Idoso , Brônquios/metabolismo , Análise por Conglomerados , Células Epiteliais/metabolismo , Feminino , Perfilação da Expressão Gênica/métodos , Humanos , Pulmão/metabolismo , Masculino , MicroRNAs/biossíntese , Pessoa de Meia-Idade , Análise de Sequência com Séries de Oligonucleotídeos/métodos , Doença Pulmonar Obstrutiva Crônica/metabolismo , RNA Mensageiro/genética , Reação em Cadeia da Polimerase Via Transcriptase Reversa/métodos , Proteína Smad7/biossíntese , Proteína Smad7/genética , Fumar/genética , Fumar/metabolismo , Fator de Crescimento Transformador beta/biossíntese , Fator de Crescimento Transformador beta/genética , Via de Sinalização Wnt/genética
18.
Exp Neurol ; 235(2): 464-8, 2012 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-22075182

RESUMO

Neurofibromatosis type 1 (NF1) is one of the most common inherited neurological disorders with a wide range of clinical manifestations. The causative gene for NF1 encodes a multi-domain protein, neurofibromin, which interacts with RAS through its RAS-GAP domain. Dysfunction of neurofibromin results in abnormal RAS activation in the cells which has been thought to be the main process in the initiation and progression of NF1. Based on this hypothesis, inhibitors for various RAS mediated signaling pathways are in different stages of clinical trials to treat NF1 or NF1-associated symptoms. While the molecular genetics of NF1 has made significant progress in recent years, the underlying etiology and progression of NF1 are yet to be fully understood. Besides review and summarization of the latest results of genetic, transcriptomic and microRNA studies associated with NF1, we conducted limited post-hoc analysis to illustrate the importance of using integrated systems biology approach to study complex diseases like NF1.


Assuntos
Redes Reguladoras de Genes/fisiologia , MicroRNAs/fisiologia , Neurofibromatose 1/genética , Neurofibromatose 1/metabolismo , Biologia de Sistemas/métodos , Animais , Humanos , Neurofibromatose 1/patologia , Transdução de Sinais/genética
19.
Proc Natl Acad Sci U S A ; 108(16): 6573-8, 2011 Apr 19.
Artigo em Inglês | MEDLINE | ID: mdl-21460253

RESUMO

Early cancer detection and disease stratification or classification are critical to successful treatment. Accessible, reliable, and informative cancer biomarkers can be medically valuable and can provide some relevant insights into cancer biology. Recent studies have suggested improvements in detecting malignancies by the use of specific extracellular microRNAs (miRNAs) in plasma. In chronic lymphocytic leukemia (CLL), an incurable hematologic disorder, sensitive, early, and noninvasive diagnosis and better disease classification would be very useful for more effective therapies. We show here that circulating miRNAs can be sensitive biomarkers for CLL, because certain extracellular miRNAs are present in CLL patient plasma at levels significantly different from healthy controls and from patients affected by other hematologic malignancies. The levels of several of these circulating miRNAs also displayed significant differences between zeta-associated protein 70 (ZAP-70)(+) and ZAP-70(-) CLL. We also determined that the level of circulating miR-20a correlates reliably with diagnosis-to-treatment time. Network analysis of our data, suggests a regulatory network associated with BCL2 and ZAP-70 expression in CLL. This hypothesis suggests the possibility of using the levels of specific miRNAs in plasma to detect CLL and to determine the ZAP-70 status.


Assuntos
Biomarcadores Tumorais/sangue , Leucemia Linfocítica Crônica de Células B/sangue , MicroRNAs/sangue , RNA Neoplásico/sangue , Idoso , Feminino , Humanos , Leucemia Linfocítica Crônica de Células B/mortalidade , Leucemia Linfocítica Crônica de Células B/terapia , Masculino , Pessoa de Meia-Idade , Proteínas de Neoplasias/sangue , Proteína-Tirosina Quinase ZAP-70/sangue
20.
J Biol Chem ; 285(12): 9262-72, 2010 Mar 19.
Artigo em Inglês | MEDLINE | ID: mdl-20071342

RESUMO

Abnormal neuronal aggregation of alpha-synuclein is implicated in the development of many neurological disorders, including Parkinson disease and dementia with Lewy bodies. Glial cells also show extensive alpha-synuclein pathology and may contribute to disease progression. However, the mechanism that produces the glial alpha-synuclein pathology and the interaction between neurons and glia in the disease-inflicted microenvironment remain unknown. Here, we show that alpha-synuclein proteins released from neuronal cells are taken up by astrocytes through endocytosis and form inclusion bodies. The glial accumulation of alpha-synuclein through the transmission of the neuronal protein was also demonstrated in a transgenic mouse model expressing human alpha-synuclein. Furthermore, astrocytes that were exposed to neuronal alpha-synuclein underwent changes in the gene expression profile reflecting an inflammatory response. Induction of pro-inflammatory cytokines and chemokines correlated with the extent of glial accumulation of alpha-synuclein. Together, these results suggest that astroglial alpha-synuclein pathology is produced by direct transmission of neuronal alpha-synuclein aggregates, causing inflammatory responses. This transmission step is thus an important mediator of pathogenic glial responses and could qualify as a new therapeutic target.


Assuntos
Astrócitos/metabolismo , Neurônios/metabolismo , alfa-Sinucleína/metabolismo , Animais , Diferenciação Celular , Linhagem Celular Tumoral , Meios de Cultivo Condicionados/farmacologia , Humanos , Inflamação , Masculino , Camundongos , Camundongos Transgênicos , Modelos Biológicos , Doenças Neurodegenerativas/metabolismo , Ratos , Ratos Sprague-Dawley
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