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1.
Cell ; 187(1): 184-203.e28, 2024 01 04.
Artigo em Inglês | MEDLINE | ID: mdl-38181741

RESUMO

We performed comprehensive proteogenomic characterization of small cell lung cancer (SCLC) using paired tumors and adjacent lung tissues from 112 treatment-naive patients who underwent surgical resection. Integrated multi-omics analysis illustrated cancer biology downstream of genetic aberrations and highlighted oncogenic roles of FAT1 mutation, RB1 deletion, and chromosome 5q loss. Two prognostic biomarkers, HMGB3 and CASP10, were identified. Overexpression of HMGB3 promoted SCLC cell migration via transcriptional regulation of cell junction-related genes. Immune landscape characterization revealed an association between ZFHX3 mutation and high immune infiltration and underscored a potential immunosuppressive role of elevated DNA damage response activity via inhibition of the cGAS-STING pathway. Multi-omics clustering identified four subtypes with subtype-specific therapeutic vulnerabilities. Cell line and patient-derived xenograft-based drug tests validated the specific therapeutic responses predicted by multi-omics subtyping. This study provides a valuable resource as well as insights to better understand SCLC biology and improve clinical practice.


Assuntos
Neoplasias Pulmonares , Proteogenômica , Carcinoma de Pequenas Células do Pulmão , Humanos , Linhagem Celular , Neoplasias Pulmonares/química , Neoplasias Pulmonares/genética , Carcinoma de Pequenas Células do Pulmão/química , Carcinoma de Pequenas Células do Pulmão/genética , Xenoenxertos , Biomarcadores Tumorais/análise
2.
Cell ; 179(2): 561-577.e22, 2019 10 03.
Artigo em Inglês | MEDLINE | ID: mdl-31585088

RESUMO

We performed the first proteogenomic characterization of hepatitis B virus (HBV)-related hepatocellular carcinoma (HCC) using paired tumor and adjacent liver tissues from 159 patients. Integrated proteogenomic analyses revealed consistency and discordance among multi-omics, activation status of key signaling pathways, and liver-specific metabolic reprogramming in HBV-related HCC. Proteomic profiling identified three subgroups associated with clinical and molecular attributes including patient survival, tumor thrombus, genetic profile, and the liver-specific proteome. These proteomic subgroups have distinct features in metabolic reprogramming, microenvironment dysregulation, cell proliferation, and potential therapeutics. Two prognostic biomarkers, PYCR2 and ADH1A, related to proteomic subgrouping and involved in HCC metabolic reprogramming, were identified. CTNNB1 and TP53 mutation-associated signaling and metabolic profiles were revealed, among which mutated CTNNB1-associated ALDOA phosphorylation was validated to promote glycolysis and cell proliferation. Our study provides a valuable resource that significantly expands the knowledge of HBV-related HCC and may eventually benefit clinical practice.


Assuntos
Carcinoma Hepatocelular/genética , Carcinoma Hepatocelular/virologia , Frutose-Bifosfato Aldolase/genética , Vírus da Hepatite B , Hepatite B Crônica/complicações , Neoplasias Hepáticas/genética , Neoplasias Hepáticas/virologia , Proteogenômica/métodos , beta Catenina/genética , Animais , Proliferação de Células , Estudos de Coortes , Feminino , Perfilação da Expressão Gênica , Regulação Neoplásica da Expressão Gênica , Células Hep G2 , Humanos , Masculino , Camundongos , Camundongos Endogâmicos BALB C , Pessoa de Meia-Idade , Microambiente Tumoral/genética
3.
Cell ; 161(5): 1175-1186, 2015 May 21.
Artigo em Inglês | MEDLINE | ID: mdl-26000486

RESUMO

The scarcity of tissue-specific stem cells and the complexity of their surrounding environment have made molecular characterization of these cells particularly challenging. Through single-cell transcriptome and weighted gene co-expression network analysis (WGCNA), we uncovered molecular properties of CD133(+)/GFAP(-) ependymal (E) cells in the adult mouse forebrain neurogenic zone. Surprisingly, prominent hub genes of the gene network unique to ependymal CD133(+)/GFAP(-) quiescent cells were enriched for immune-responsive genes, as well as genes encoding receptors for angiogenic factors. Administration of vascular endothelial growth factor (VEGF) activated CD133(+) ependymal neural stem cells (NSCs), lining not only the lateral but also the fourth ventricles and, together with basic fibroblast growth factor (bFGF), elicited subsequent neural lineage differentiation and migration. This study revealed the existence of dormant ependymal NSCs throughout the ventricular surface of the CNS, as well as signals abundant after injury for their activation.


Assuntos
Epêndima/citologia , Células-Tronco Neurais/metabolismo , Antígeno AC133 , Animais , Antígenos CD/metabolismo , Diferenciação Celular , Movimento Celular , Epêndima/metabolismo , Fatores de Crescimento de Fibroblastos/metabolismo , Perfilação da Expressão Gênica , Redes Reguladoras de Genes , Glicoproteínas/metabolismo , Camundongos , Células-Tronco Neurais/citologia , Peptídeos/metabolismo , Análise de Sequência de RNA , Análise de Célula Única , Fator A de Crescimento do Endotélio Vascular/metabolismo
5.
EMBO J ; 42(12): e112675, 2023 06 15.
Artigo em Inglês | MEDLINE | ID: mdl-37092319

RESUMO

Tumor cells surviving hypoxic stress acquire the ability to drive cancer progression. To explore the contribution of dehydrogenases to the low oxygen concentration response, we used siRNAs targeting 163 dehydrogenase-coding genes and discovered that glutamate dehydrogenase 1 (GDH1) plays a critical role in regulating colorectal cancer (CRC) cell survival under hypoxia. We observed that GDH1 deficiency had an inhibitory effect on CRC occurrence and impaired hypoxia-inducible factor 1-alpha (HIF-1α) stability even under hypoxia. Mechanistically, hypoxia triggered p300 recruitment to GDH1, promoting its acetylation at K503 and K527. GDH1 acetylation at K527 induced the formation of a GDH1 complex with EGLN1/HIF-1α; in contrast, GDH1 acetylation at K503 reinforced its affinity for α-ketoglutarate (αKG), and glutamate production. In line with this view, αKG is a product of GDH1 under normoxia, but hypoxia stimulation reversed GDH1 enzyme activity and αKG consumption by the EGLN1/HIF-1α complex, increasing HIF-1α stability and promoting CRC progression. Clinically, hypoxia-modulated GDH1 AcK503/527 can be used as a biomarker of CRC progression and is a potential target for CRC treatment.


Assuntos
Neoplasias Colorretais , Ácido Glutâmico , Humanos , Ácido Glutâmico/metabolismo , Hipóxia , Hipóxia Celular/genética , Transformação Celular Neoplásica , Carcinogênese , Neoplasias Colorretais/metabolismo , Subunidade alfa do Fator 1 Induzível por Hipóxia/genética , Subunidade alfa do Fator 1 Induzível por Hipóxia/metabolismo , Linhagem Celular Tumoral
6.
Nature ; 571(7763): 127-131, 2019 07.
Artigo em Inglês | MEDLINE | ID: mdl-31243371

RESUMO

Cancer metastasis is the primary cause of morbidity and mortality, and accounts for up to 95% of cancer-related deaths1. Cancer cells often reprogram their metabolism to efficiently support cell proliferation and survival2,3. However, whether and how those metabolic alterations contribute to the migration of tumour cells remain largely unknown. UDP-glucose 6-dehydrogenase (UGDH) is a key enzyme in the uronic acid pathway, and converts UDP-glucose to UDP-glucuronic acid4. Here we show that, after activation of EGFR, UGDH is phosphorylated at tyrosine 473 in human lung cancer cells. Phosphorylated UGDH interacts with Hu antigen R (HuR) and converts UDP-glucose to UDP-glucuronic acid, which attenuates the UDP-glucose-mediated inhibition of the association of HuR with SNAI1 mRNA and therefore enhances the stability of SNAI1 mRNA. Increased production of SNAIL initiates the epithelial-mesenchymal transition, thus promoting the migration of tumour cells and lung cancer metastasis. In addition, phosphorylation of UGDH at tyrosine 473 correlates with metastatic recurrence and poor prognosis of patients with lung cancer. Our findings reveal a tumour-suppressive role of UDP-glucose in lung cancer metastasis and uncover a mechanism by which UGDH promotes tumour metastasis by increasing the stability of SNAI1 mRNA.


Assuntos
Neoplasias Pulmonares/genética , Neoplasias Pulmonares/patologia , Metástase Neoplásica/genética , Metástase Neoplásica/prevenção & controle , Estabilidade de RNA , Fatores de Transcrição da Família Snail/genética , Uridina Difosfato Glucose/metabolismo , Animais , Linhagem Celular Tumoral , Movimento Celular , Proteína Semelhante a ELAV 1/deficiência , Proteína Semelhante a ELAV 1/genética , Proteína Semelhante a ELAV 1/metabolismo , Transição Epitelial-Mesenquimal , Feminino , Humanos , Neoplasias Pulmonares/enzimologia , Neoplasias Pulmonares/metabolismo , Camundongos , Camundongos Nus , Fosfotirosina/metabolismo , Prognóstico , RNA Mensageiro/genética , RNA Mensageiro/metabolismo , RNA Neoplásico/genética , RNA Neoplásico/metabolismo , Fatores de Transcrição da Família Snail/biossíntese , Uridina Difosfato Glucose Desidrogenase/química , Uridina Difosfato Glucose Desidrogenase/genética , Uridina Difosfato Glucose Desidrogenase/metabolismo , Uridina Difosfato Ácido Glucurônico/metabolismo
7.
Proteomics ; 23(3-4): e2100407, 2023 02.
Artigo em Inglês | MEDLINE | ID: mdl-35689503

RESUMO

Phosphorylation is one of the most common post-translational modifications (PTMs) and is closely related to protein activity and function, playing a critical role during cancer development. Quantitative phosphoproteomic strategies have been widely used to study the underlying mechanisms of cancer progression or drug resistance. In this report, we analyzed the association of phosphosite levels originated from our previously reported proteogenomic study in hepatocellular carcinoma (HCC) with clinical parameters, including prognosis, recurrence, and Tumor-Node-Metastasis (TNM) stages. By using both the log-rank test and univariate Cox proportional hazards regression analysis, we found that the abundance levels of 1712 phosphosites were associated with prognosis and those of 393 phosphosites associated with recurrence. Besides, 692 phosphosites had different abundance levels among TNM stages (I, II, III+IV) by Analysis of Variance (ANOVA) test. Gene ontology (GO) biological process and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed using proteins with these statistically significant phosphosites. In conclusion, we provided a dataset resource for clinically associated phosphosites in HCC, which may be beneficial to liver cancer related basic research.


Assuntos
Carcinoma Hepatocelular , Neoplasias Hepáticas , Humanos , Carcinoma Hepatocelular/patologia , Neoplasias Hepáticas/patologia , Prognóstico
8.
J Proteome Res ; 22(5): 1446-1454, 2023 05 05.
Artigo em Inglês | MEDLINE | ID: mdl-36751022

RESUMO

The global proteome analysis was limited by the identification of peptides with low abundance or specific physiochemical properties. Here, a one-dimensional online alkaline-pH reverse phase nanoelectrospray-tandem mass spectrometry (alkaline-pH-MS/MS) method was developed and optimized for global proteomic analysis. In this method, peptides were separated on a nanoflow C18 column with an alkaline-pH mobile phase (pH = 8.0) and directly injected into the mass spectrometer. The unique peptides overlapped between alkaline-pH-MS/MS and conventional online low-pH reverse phase nanoelectrospray-tandem mass spectrometry (low-pH-MS/MS) were as low as 45%, strongly indicating that these two methods were complementary to each other. In addition, alkaline-pH-MS/MS showed identification capacity for a higher proportion of peptides with negative grand average of hydropathy (GRAVY) or high isoelectric point (pI). Compared to low-pH-MS/MS, alkaline-pH-MS/MS enabled enrichment preference toward histidine-, lysine-, methionine-, and proline-containing peptides. The complementarity of alkaline-pH-MS/MS and low-pH-MS/MS was further demonstrated for the analysis of tryptic digests from 15 intrahepatic cholangiocarcinoma (iCCA) cell lines. The alternating 60 min alkaline-pH-MS/MS plus 60 min low-pH-MS/MS method outperformed the conventional 120 min low-pH-MS/MS method in both the identification of amino acid variants and protein groups. Therefore, we established the alkaline-pH-MS/MS method as a simple, competitive, alternative method to low-pH-MS/MS for global proteomic analysis.


Assuntos
Proteômica , Espectrometria de Massas em Tandem , Espectrometria de Massas em Tandem/métodos , Cromatografia Líquida de Alta Pressão , Proteômica/métodos , Peptídeos/análise , Proteínas do Sistema Complemento , Proteoma/análise , Concentração de Íons de Hidrogênio
9.
Neurol Sci ; 43(6): 3949-3956, 2022 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-35043357

RESUMO

OBJECTIVE: We investigated the efficacy of low-dose prednisolone (PSL) regimen in patients with generalized myasthenia gravis (MG) post-thymectomy and its correlation with long-term outcome. METHODS: This is a 2-year observational study. The subjects were aged 16-75 years, a Myasthenia Gravis Foundation of America (MGFA) clinical classification of II to IV, generalized MG after thymectomy. We selected a low-dose (5 mg/day) initiation and slowly incrementing (10 mg every 4 weeks) PSL therapy regimen. We collected the clinical characteristics, treatment-related data, and 2-year clinical outcomes of MG patients, and analyzed the effect of various factors on the achievement of the treatment target. RESULTS: Sixty-three generalized MG were recruited in our study. After 2 years of observation, 52 patients (82.5%) of generalized MG achieved treatment goal. Based on the maximum daily dose of PSL received, the MG patients were divided into 20 mg, 30 mg, and ≥ 40 mg groups. Subgroup analysis showed that the 20 mg group had the highest rate of achieving the treatment target (94.9%), followed by the 30 mg group (73.3%) and the lowest rate was among the ≥ 40 mg group (44.4%). Using a multivariate logistic regression analysis, we identified that the maximum daily dose of PSL 20 mg was the only positive, independent predictor of treatment goal achievement after 2 years. CONCLUSION: Low-dose initiation, slowly incrementing PSL therapy is feasible for generalized MG patients after thymectomy. Early response to low-dose PSL therapy may predict better long-term outcomes.


Assuntos
Miastenia Gravis , Timectomia , Corticosteroides/uso terapêutico , Humanos , Miastenia Gravis/tratamento farmacológico , Miastenia Gravis/cirurgia , Prednisolona/uso terapêutico , Prognóstico , Estudos Retrospectivos , Timectomia/efeitos adversos , Resultado do Tratamento
10.
Mol Syst Biol ; 16(3): e9170, 2020 03.
Artigo em Inglês | MEDLINE | ID: mdl-32175694

RESUMO

Profiling of biological relationships between different molecular layers dissects regulatory mechanisms that ultimately determine cellular function. To thoroughly assess the role of protein post-translational turnover, we devised a strategy combining pulse stable isotope-labeled amino acids in cells (pSILAC), data-independent acquisition mass spectrometry (DIA-MS), and a novel data analysis framework that resolves protein degradation rate on the level of mRNA alternative splicing isoforms and isoform groups. We demonstrated our approach by the genome-wide correlation analysis between mRNA amounts and protein degradation across different strains of HeLa cells that harbor a high grade of gene dosage variation. The dataset revealed that specific biological processes, cellular organelles, spatial compartments of organelles, and individual protein isoforms of the same genes could have distinctive degradation rate. The protein degradation diversity thus dissects the corresponding buffering or concerting protein turnover control across cancer cell lines. The data further indicate that specific mRNA splicing events such as intron retention significantly impact the protein abundance levels. Our findings support the tight association between transcriptome variability and proteostasis and provide a methodological foundation for studying functional protein degradation.


Assuntos
Isoformas de Proteínas/análise , Proteínas/análise , Isoformas de RNA/metabolismo , RNA Mensageiro/metabolismo , Processamento Alternativo , Regulação Neoplásica da Expressão Gênica , Células HeLa , Humanos , Marcação por Isótopo/métodos , Espectrometria de Massas , Isoformas de Proteínas/metabolismo , Proteínas/metabolismo , Proteólise , Proteômica/métodos , Isoformas de RNA/genética , RNA Mensageiro/genética , Fluxo de Trabalho
11.
Pharmacol Res ; 169: 105678, 2021 07.
Artigo em Inglês | MEDLINE | ID: mdl-34015449

RESUMO

Triptolide has shown a good immunosuppressive effect on autoimmune diseases. However, the toxicity limited its widely clinical practice. In this study, we investigated the effects and underlying mechanisms of (5R)-5-hydroxytriptolide (LLDT-8), a novel triptolide derivative, on a murine psoriasis-like dermatitis model and related cell lines. Here, we showed that LLDT-8 significantly attenuated symptoms of psoriasis-like dermatitis induced by imiquimod (IMQ, a TLR7 agonist) by reducing the psoriasis area and severity index (PASI) score and inflammatory parameters. The action of LLDT-8 was involved in down-regulated interleukin (IL)-36α expression and blocked IL-36α pathway by LC-MS-based label-free quantitative (LFQ) proteomic approach and further experiments. Meanwhile, we observed that LLDT-8 significantly inhibited the expression of IL-36α in R837-treated bone marrow-derived dendritic cells (BMDCs). In conclusion, LLDT-8 notably alleviated IMQ-induced psoriasis-like skin inflammation via suppressing the IL-36α signaling pathway, suggesting LLDT-8 might be a potential drug for the treatment of psoriasis.


Assuntos
Dermatite/tratamento farmacológico , Fármacos Dermatológicos/uso terapêutico , Diterpenos/uso terapêutico , Interleucina-1/antagonistas & inibidores , Psoríase/tratamento farmacológico , Transdução de Sinais/efeitos dos fármacos , Animais , Western Blotting , Linhagem Celular , Dermatite/metabolismo , Modelos Animais de Doenças , Feminino , Citometria de Fluxo , Humanos , Interleucina-1/metabolismo , Camundongos , Camundongos Endogâmicos BALB C , Psoríase/metabolismo , Pele/efeitos dos fármacos , Pele/metabolismo
12.
BMC Bioinformatics ; 21(1): 439, 2020 Oct 07.
Artigo em Inglês | MEDLINE | ID: mdl-33028193

RESUMO

BACKGROUND: Mass spectrometry (MS) has become a promising analytical technique to acquire proteomics information for the characterization of biological samples. Nevertheless, most studies focus on the final proteins identified through a suite of algorithms by using partial MS spectra to compare with the sequence database, while the pattern recognition and classification of raw mass-spectrometric data remain unresolved. RESULTS: We developed an open-source and comprehensive platform, named MSpectraAI, for analyzing large-scale MS data through deep neural networks (DNNs); this system involves spectral-feature swath extraction, classification, and visualization. Moreover, this platform allows users to create their own DNN model by using Keras. To evaluate this tool, we collected the publicly available proteomics datasets of six tumor types (a total of 7,997,805 mass spectra) from the ProteomeXchange consortium and classified the samples based on the spectra profiling. The results suggest that MSpectraAI can distinguish different types of samples based on the fingerprint spectrum and achieve better prediction accuracy in MS1 level (average 0.967). CONCLUSION: This study deciphers proteome profiling of raw mass spectrometry data and broadens the promising application of the classification and prediction of proteomics data from multi-tumor samples using deep learning methods. MSpectraAI also shows a better performance compared to the other classical machine learning approaches.


Assuntos
Neoplasias/metabolismo , Redes Neurais de Computação , Proteoma/metabolismo , Proteômica/métodos , Interface Usuário-Computador , Algoritmos , Cromatografia Líquida de Alta Pressão , Humanos , Espectrometria de Massas , Neoplasias/patologia
13.
J Hepatol ; 72(5): 896-908, 2020 05.
Artigo em Inglês | MEDLINE | ID: mdl-31887370

RESUMO

BACKGROUND & AIMS: The presence of multifocal tumors, developed either from intrahepatic metastasis (IM) or multicentric occurrence (MO), is a distinct feature of hepatocellular carcinoma (HCC). Immunogenomic characterization of multifocal HCC is important for understanding immune escape in different lesions and developing immunotherapy. METHODS: We combined whole-exome/transcriptome sequencing, multiplex immunostaining, immunopeptidomes, T cell receptor (TCR) sequencing and bioinformatic analyses of 47 tumors from 15 patients with HCC and multifocal lesions. RESULTS: IM and MO demonstrated distinct clonal architecture, mutational spectrum and genetic susceptibility. The immune microenvironment also displayed spatiotemporal heterogeneity, such as less T cell and more M2 macrophage infiltration in IM and higher expression of inhibitory immune checkpoints in MO. Similar to mutational profiles, shared neoantigens and TCR repertoires among tumors from the same patients were abundant in IM but scarce in MO. Combining neoantigen prediction and immunopeptidomes identified T cell-specific neoepitopes and achieved a high verification rate in vitro. Immunoediting mainly occurred in MO but not IM, due to the relatively low immune infiltration. Loss of heterozygosity of human leukocyte antigen (HLA) alleles, identified in 17% of multifocal HCC, hampered the ability of major histocompatibility complex to present neoantigens, especially in IM. An integrated analysis of Immunoscore, immunoediting, TCR clonality and HLA loss of heterozygosity in each tumor could stratify patients into 2 groups based on whether they have a high or low risk of recurrence (p = 0.038). CONCLUSION: Our study comprehensively characterized the genetic structure, neoepitope landscape, T cell profile and immunoediting status that collectively shape tumor evolution and could be used to optimize personalized immunotherapies for multifocal HCC. LAY SUMMARY: Immunogenomic features of multifocal hepatocellular carcinoma (HCC) are important for understanding immune-escape mechanisms and developing more effective immunotherapy. Herein, comprehensive immunogenomic characterization showed that diverse genomic structures within multifocal HCC would leave footprints on the immune landscape. Only a few tumors were under the control of immunosurveillance, while others evaded the immune system through multiple mechanisms that led to poor prognosis. Our study revealed heterogeneous immunogenomic landscapes and immune-constrained tumor evolution, the understanding of which could be used to optimize personalized immunotherapies for multifocal HCC.


Assuntos
Carcinoma Hepatocelular/genética , Carcinoma Hepatocelular/imunologia , Neoplasias Hepáticas/genética , Neoplasias Hepáticas/imunologia , Neoplasias Primárias Múltiplas/genética , Neoplasias Primárias Múltiplas/imunologia , Evasão Tumoral , Adulto , Idoso , Idoso de 80 Anos ou mais , Antígenos de Neoplasias/genética , Biomarcadores Tumorais/genética , Linfócitos T CD8-Positivos/imunologia , Feminino , Predisposição Genética para Doença , Antígenos HLA/genética , Humanos , Linfócitos do Interstício Tumoral/imunologia , Masculino , Pessoa de Meia-Idade , Mutação , Recidiva Local de Neoplasia , Receptores de Antígenos de Linfócitos T/genética , Transcriptoma , Sequenciamento do Exoma
14.
J Proteome Res ; 18(6): 2654-2665, 2019 06 07.
Artigo em Inglês | MEDLINE | ID: mdl-31059266

RESUMO

The deubiquitinase USP9X is involved in multiple diseases including neurodegeneration, epilepsy, and various types of tumors by targeting different substrates. In the present study, we aimed to explore the potential substrates of USP9X and performed SILAC-based quantitative proteomics to compare these substrates in USP9X-knockdown and wild-type HeLa cells. We consequently carried out Flag-NFX1-123 tag affinity-based mass spectrometry and confirmed that the X-box binding nuclear factor NFX1-123 interacted with USP9X. Moreover, immunoprecipitation assays verified a direct interaction between USP9X and NFX1-123. Further experiments confirmed that NFX1-123 could be modified by ubiquitination and that USP9X stabilized NFX1-123 via efficient deubiquitination of NFX1-123. Knockdown of USP9X resulted in decreased NFX1-123 protein levels compared with their unchanged corresponding mRNA levels in different cell lines. In summary, we found that NFX1-123 was a bona fide substrate of the deubiquitinase USP9X and that it could be degraded by the ubiquitin-proteasome system. The present study provided new insight into understanding the biological function of USP9X by targeting its substrate NFX1-123.


Assuntos
Degeneração Neural/genética , Proteômica , Proteínas Repressoras/genética , Ubiquitina Tiolesterase/genética , Apoptose/genética , Proliferação de Células/genética , Regulação da Expressão Gênica/genética , Técnicas de Silenciamento de Genes , Células HeLa , Humanos , Degeneração Neural/patologia , Complexo de Endopeptidases do Proteassoma/genética , Complexo de Endopeptidases do Proteassoma/metabolismo , Ubiquitina/genética , Ubiquitinação/genética
15.
J Biol Chem ; 293(18): 6693-6706, 2018 05 04.
Artigo em Inglês | MEDLINE | ID: mdl-29549123

RESUMO

Once urinary bladder cancer (UBC) develops into muscle-invasive bladder cancer, its mortality rate increases dramatically. However, the molecular mechanisms of UBC invasion and metastasis remain largely unknown. Herein, using 5637 UBC cells, we generated two sublines with low (5637 NMI) and high (5637 HMI) invasive capabilities. Mass spectrum analyses revealed that the Wnt family protein Wnt7a is more highly expressed in 5637 HMI cells than in 5637 NMI cells. We also found that increased Wnt7a expression is associated with UBC metastasis and predicted worse clinical outcome in UBC patients. Wnt7a depletion in 5637 HMI and T24 cells reduced UBC cell invasion and decreased levels of active ß-catenin and its downstream target genes involved in the epithelial-to-mesenchymal transition (EMT) and extracellular matrix (ECM) degradation. Consistently, treating 5637 NMI and J82 cells with recombinant Wnt7a induced cell invasion, EMT, and expression of ECM degradation-associated genes. Moreover, TOP/FOPflash luciferase assays indicated that Wnt7a activated canonical ß-catenin signaling in UBC cells, and increased Wnt7a expression was associated with nuclear ß-catenin in UBC samples. Wnt7a ablation suppressed matrix metalloproteinase 10 (MMP10) expression, and Wnt7a overexpression increased MMP10 promoter activity through two TCF/LEF promoter sites, confirming that Wnt7a-mediated MMP10 activation is mediated by the canonical Wnt/ß-catenin pathway. Of note, the microRNA miR-370-3p directly repressed Wnt7a expression and thereby suppressed UBC cell invasion, which was partially restored by Wnt7a overexpression. Our results have identified an miR-370-3p/Wnt7a axis that controls UBC invasion through canonical Wnt/ß-catenin signaling, which may offer prognostic and therapeutic opportunities.


Assuntos
MicroRNAs/fisiologia , Neoplasias da Bexiga Urinária/patologia , Proteínas Wnt/fisiologia , Via de Sinalização Wnt , Linhagem Celular Tumoral , Transição Epitelial-Mesenquimal , Regulação Neoplásica da Expressão Gênica , Genes Supressores de Tumor , Humanos , Espectrometria de Massas , Metaloproteinase 10 da Matriz/biossíntese , Invasividade Neoplásica , Metástase Neoplásica , Oncogenes , Prognóstico , Neoplasias da Bexiga Urinária/metabolismo , Proteínas Wnt/genética , beta Catenina/metabolismo
16.
Biochem Biophys Res Commun ; 516(1): 320-326, 2019 08 13.
Artigo em Inglês | MEDLINE | ID: mdl-31256935

RESUMO

Kappa-opioid receptor (KOR) is a member of G-protein coupled receptors (GPCRs) expressed in serotonergic neurons and neuronal terminals. The involvement of KOR ligands in nociception, diuresis, emotion, cognition, and immune system has been extensively studied. Omics-based methods are preferable to understand the signaling cascade after KOR activation in a systematic manner. In this study, an in-depth quantitative phosphoproteomic analysis resulted in 305 phosphosites, which were significantly changed in three KOR-overexpressed cells upon treatment with two KOR agonists. The subsequent substrate-kinase prediction analysis revealed that 18 potential kinases might be activated under stimulation of the agonists. We found that phosphorylation of PAK1/2 (p21-activated kinase 1/2) was induced by KOR agonists, resulting in reduced actin stress fibers and cytoskeletal reorganization. In summary, this quantitative phosphoproteomics-based research studied the downstream phosphorylation events upon KOR activation, which may shed light on the investigations of KOR signaling pathway and targeted therapy for KOR-related diseases.


Assuntos
Ativadores de Enzimas/farmacologia , Fosforilação/efeitos dos fármacos , Receptores Opioides kappa/agonistas , Quinases Ativadas por p21/metabolismo , Ativação Enzimática/efeitos dos fármacos , Células HEK293 , Humanos , Proteômica , Receptores Opioides kappa/metabolismo
17.
Stem Cells ; 36(12): 1839-1850, 2018 12.
Artigo em Inglês | MEDLINE | ID: mdl-30247783

RESUMO

Recessive dystrophic epidermolysis bullosa (RDEB) is a severe skin fragility disorder caused by mutations in the Col7a1 gene. Patients with RDEB suffer from recurrent erosions in skin and mucous membranes and have a high risk for developing cutaneous squamous cell carcinoma (cSCCs). TGFß signaling has been associated with fibrosis and malignancy in RDEB. In this study, the activation of TGFß signaling was demonstrated in col7a1-/- mice as early as a week after birth starting in the interdigital folds of the paws, accompanied by increased deposition of collagen fibrils and elevated dermal expression of matrix metalloproteinase (MMP)-9 and MMP-13. Furthermore, human cord blood-derived unrestricted somatic stem cells (USSCs) that we previously demonstrated to significantly improve wound healing and prolong the survival of col7a1-/- mice showed the ability to suppress TGFß signaling and MMP-9 and MMP-13 expression meanwhile upregulating anti-fibrotic TGFß3 and decorin. In parallel, we cocultured USSCs in a transwell with RDEB patient-derived fibroblasts, keratinocytes, and cSCC, respectively. The patient-derived cells were constitutively active for STAT, but not TGFß signaling. Moreover, the levels of MMP-9 and MMP-13 were significantly elevated in the patient derived-keratinocytes and cSCCs. Although USSC coculture did not inhibit STAT signaling, it significantly suppressed the secretion of MMP-9 and MMP-13, and interferon (IFN)-γ from RDEB patient-derived cells. Since epithelial expression of these MMPs is a biomarker of malignant transformation and correlates with the degree of tumor invasion, these results suggest a potential role for USSCs in mitigating epithelial malignancy, in addition to their anti-inflammatory and anti-fibrotic functions. Stem Cells 2018;36:1839-12.


Assuntos
Epidermólise Bolhosa Distrófica/genética , Sangue Fetal/metabolismo , Fibroblastos/metabolismo , Fibrose/metabolismo , Animais , Diferenciação Celular , Progressão da Doença , Epidermólise Bolhosa Distrófica/metabolismo , Humanos , Camundongos
18.
Anal Chem ; 90(4): 2434-2439, 2018 02 20.
Artigo em Inglês | MEDLINE | ID: mdl-29376338

RESUMO

Membrane proteins may act as transporters, receptors, enzymes, and adhesion-anchors, accounting for nearly 70% of pharmaceutical drug targets. Difficulties in efficient enrichment, extraction, and solubilization still exist because of their relatively low abundance and poor solubility. A simplified membrane protein extraction approach with advantages of user-friendly sample processing procedures, good repeatability and significant effectiveness was developed in the current research for enhancing enrichment and identification of membrane proteins. This approach combining centrifugation and detergent along with LC-MS/MS successfully identified higher proportion of membrane proteins, integral proteins and transmembrane proteins in membrane fraction (76.6%, 48.1%, and 40.6%) than in total cell lysate (41.6%, 16.4%, and 13.5%), respectively. Moreover, our method tended to capture membrane proteins with high degree of hydrophobicity and number of transmembrane domains as 486 out of 2106 (23.0%) had GRAVY > 0 in membrane fraction, 488 out of 2106 (23.1%) had TMs ≥ 2. It also provided for improved identification of membrane proteins as more than 60.6% of the commonly identified membrane proteins in two cell samples were better identified in membrane fraction with higher sequence coverage. Data are available via ProteomeXchange with identifier PXD008456.

19.
Biochem Biophys Res Commun ; 505(4): 1112-1120, 2018 11 10.
Artigo em Inglês | MEDLINE | ID: mdl-30336977

RESUMO

Dermal fibroblast is one of the major constitutive cells of skin and plays a central role in skin senescence. The replicative senescence of fibroblasts may cause skin aging, bad wound healing, skin diseases and even cancer. In this study, a label-free quantitative proteomic approach was employed to analyzing the serial passaged human skin fibroblast (CCD-1079Sk) cells, resulting in 3371 proteins identified. Of which, 280 proteins were significantly changed in early passage (6 passages, P6), middle passage (12 passages, P12) and late passage (21 passages, P21), with a time-dependent decrease or increase tendency. Bioinformatic analysis demonstrated that the chromosome condensin complex, including structural maintenance of chromosomes protein 2 (SMC2) and structural maintenance of chromosomes protein 4 (SMC4), were down-regulated in the serially passaged fibroblast cells. The qRT-PCR and Western Blot experiments confirmed that the expression of these two proteins were significantly down-regulated in a time-dependent manner in the subculture of human skin fibroblasts (HSFb cells). In summary, we used serially passaged human skin fibroblast cells coupled with quantitative proteomic approach to profile the protein expression pattern in the temporal progress of replicative senescence in HSFb cells and revealed that the down-regulation of the chromosome condensin complex subunits, such as SMC2 and SMC4, may play an important role in the fibroblast senescence.


Assuntos
Adenosina Trifosfatases/metabolismo , Proteínas de Ligação a DNA/metabolismo , Regulação para Baixo , Fibroblastos/metabolismo , Complexos Multiproteicos/metabolismo , Proteômica , Pele/metabolismo , Células Cultivadas , Senescência Celular , Cromossomos/metabolismo , Biologia Computacional , Humanos , Envelhecimento da Pele
20.
Cell Physiol Biochem ; 42(6): 2242-2254, 2017.
Artigo em Inglês | MEDLINE | ID: mdl-28817816

RESUMO

BACKGROUND/AIMS: Mesenchymal stem/stromal cells (MSCs) are known to home to sites of tumor microenvironments where they participate in the formation of the tumor microenvironment and to interplay with tumor cells. However, the potential functional effects of MSCs on tumor cell growth are controversial. Here, we, from the view of bone marrow MSC-derived exosomes, study the molecular mechanism of MSCs on the growth of human osteosarcoma and human gastric cancer cells. METHODS: MSCs derived from human bone marrow (hBMSCs) were isolated and cultured in complete DMEM/F12 supplemented with 10% exosome-depleted fetal bovine serum and 1% penicillin-streptomycin, cell culture supernatants containing exosomes were harvested and exosome purification was performed by ultracentrifugation. Osteosarcoma (MG63) and gastric cancer (SGC7901) cells, respectively, were treated with hBMSC-derived exosomes in the presence or absence of a small molecule inhibitor of Hedgehog pathway. Cell viability was measured by transwell invasion assay, scratch migration assay and CCK-8 test. The expression of the signaling molecules Smoothened, Patched-1, Gli1 and the ligand Shh were tested by western blot and RT-PCR. RESULTS: In this study, we found that hBMSC-derived exosomes promoted MG63 and SGC7901 cell growth through the activation of Hedgehog signaling pathway. Inhibition of Hedgehog signaling pathway significantly suppressed the process of hBMSC-derived exosomes on tumor growth. CONCLUSION: Our findings demonstrated the new roles of hedgehog signaling pathway in the hBMSCs-derived exosomes induced tumor progression.


Assuntos
Exossomos/metabolismo , Proteínas Hedgehog/metabolismo , Western Blotting , Células da Medula Óssea/citologia , Movimento Celular/efeitos dos fármacos , Sobrevivência Celular/efeitos dos fármacos , Células Cultivadas , Exossomos/transplante , Proteínas Hedgehog/antagonistas & inibidores , Humanos , Células-Tronco Mesenquimais/citologia , Células-Tronco Mesenquimais/metabolismo , Microscopia Confocal , Microscopia Eletrônica de Transmissão , Osteossarcoma/metabolismo , Osteossarcoma/patologia , Receptor Patched-1/genética , Receptor Patched-1/metabolismo , Piridinas/farmacologia , Pirimidinas/farmacologia , Reação em Cadeia da Polimerase em Tempo Real , Transdução de Sinais/efeitos dos fármacos , Receptor Smoothened/genética , Receptor Smoothened/metabolismo , Neoplasias Gástricas/metabolismo , Neoplasias Gástricas/patologia , Microambiente Tumoral/efeitos dos fármacos , Proteína GLI1 em Dedos de Zinco/genética , Proteína GLI1 em Dedos de Zinco/metabolismo
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