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BACKGROUND: The present study aimed to investigate the changes in volatile components and metabolites of Dendrobium officinale (D. officinale) juice fermented with starter cultures containing Saccharomycopsis fibuligera and Lactobacillus paracasei at 28 â for 15 days and post-ripened at 4 â for 30 days using untargeted metabolomics of liquid chromatography-mass spectrometry (LC-MS) and headspace solid-phase microextraction-gas chromatography (HS-SPME-GC-MS) before and after fermentation. RESULTS: The results showed that the alcohol contents in the S. fibuligera group before fermentation and after fermentation were 444.806 ± 10.310 µg/mL and 510.999 ± 38.431 µg/mL, respectively. Furthermore, the alcohol content in the fermentation broth group inoculated with the co-culture of L. paracasei + S. fibuligera was 504.758 ± 77.914 µg/mL, containing a significant amount of 3-Methyl-1-butanol, Linalool, Phenylethyl alcohol, and 2-Methyl-1-propanol. Moreover, the Ethyl L (-)-lactate content was higher in the co-culture of L. paracasei + S. fibuligera group (7.718 ± 6.668 µg/mL) than in the L. paracasei (2.798 ± 0.443 µg/mL) and S. fibuligera monoculture groups (0 µg/mL). The co-culture of L. paracasei + S. fibuligera significantly promoted the metabolic production of ethyl L (-)-lactate in D. officinale juice. The differential metabolites screened after fermentation mainly included alcohols, organic acids, amino acids, nucleic acids, and their derivatives. Twenty-three metabolites, including 11 types of acids, were significantly up-regulated in the ten key metabolic pathways of the co-culture group. Furthermore, the metabolic pathways, such as pentose and glucuronate interconversions, the biosynthesis of alkaloids derived from terpenoid and polyketide, and aminobenzoate degradation were significantly up-regulated in the co-culture group. These three metabolic pathways facilitate the synthesis of bioactive substances, such as terpenoids, polyketides, and phenols, and enrich the flavor composition of D. officinale juice. CONCLUSIONS: These results demonstrate that the co-culture of L. paracasei + S. fibuligera can promote the flavor harmonization of fermented products. Therefore, this study provides a theoretical basis for analyzing the flavor of D. officinale juice and the functional investigation of fermentation metabolites.
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Dendrobium , Lacticaseibacillus paracasei , Saccharomycopsis , Saccharomycopsis/metabolismo , Terpenos , Ácidos/metabolismo , Lactatos/metabolismo , FermentaciónRESUMEN
This meta-analysis examined the post-operative wound effect of both obese and non-obese in total hip arthroplasty (THA) patients. To gather as complete an overview as possible, the researchers took advantage of 4 databases-PubMed, Embase, Cochrane Library and Web of Science-to conduct a critical assessment. Following the development of inclusion and exclusion criteria, the researchers evaluated the quality of each document. A total of 9 related trials were conducted to determine the 95% CI (CI) and OR using a fixed-effect model. The final meta-analyses were conducted with RevMan 5.3. Our findings indicate that there is no statistically significant benefit in terms of post-operative wound complications among obese and non-obese patients. Obese subjects had a significantly higher risk of injury than those without obesity (OR, 1.43; 95% CI, 1.04, 1.95, p = 0.03); obesity was also associated with a significantly higher risk of operative site infection than in non-obese subjects (OR, 1.96; 95% CI, 1.76, 2.18, p < 0.0001); and after surgery, there was also a significant increase in the risk of post-operative wound infections among obese subjects than in non-obese subjects (OR, 1.57; 95% CI, 1.34, 1.84, p < 0.0001). However, due to the small size of the cohort study in this meta-study, caution is required in the analysis. More randomized, controlled studies will be needed to validate these results.
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Artroplastia de Reemplazo de Cadera , Herida Quirúrgica , Humanos , Artroplastia de Reemplazo de Cadera/efectos adversos , Artroplastia de Reemplazo de Cadera/métodos , Estudios de Cohortes , Obesidad/complicaciones , Infección de la Herida Quirúrgica/etiología , Herida Quirúrgica/etiología , Complicaciones Posoperatorias/etiologíaRESUMEN
BACKGROUND: Limited studies have focused on the associated clinicopathologic features and short-term prognostic impacts of metastatic patterns at initial diagnosis in differentiated thyroid cancer (DTC). METHODS: Overall, 530 individuals with distant DTC diagnosed between 2010 and 2014 were identified from Surveillance, Epidemiology, and End Results (SEER) database. Multinomial logistic regression model was used to assess the clinicopathologic factors influencing the pattern of distant metastasis. Kaplan-Meier method and multivariable Cox regression were used to estimate the short-term effects of metastatic patterns on overall (OS) and thyroid cancer-specific survival (TCSS). RESULTS: Fifty, 111, 263, 59 and 47 patients presented with distant lymph node (LN)-only, bone-only, lung-only, bone plus lung, and liver and/or brain metastases (Mets), respectively. Regional lymph node metastasis (LNM) and follicular histotype were the only confirmed risk factors for distant LN-only Mets and bone-only Mets, respectively. Larger tumour size, extrathyroidal extension (ETE) and papillary histotype were associated with lung-only Mets. Synchronous bone and lung Mets were more likely to occur in older patients. In addition, patients with distant LN-only Mets had hardly any negative effect on OS and TCSS, whereas those with synchronous bone and lung or liver/brain Mets predicted unfavourable short-term outcomes, regardless of whether they received total thyroidectomy and radioisotopes. CONCLUSIONS: Different clinicopathologic factors predispose to different patterns of metastases with profound short-term survival differences among DTC patients. Our findings may help to determine effective pretreatment screening for aggressive metastatic patterns at initial diagnosis, and thus to provide additional treatment or access of clinical trials for these patients.
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Neoplasias Pulmonares , Neoplasias de la Tiroides , Anciano , Humanos , Metástasis Linfática , Pronóstico , Estudios Retrospectivos , Neoplasias de la Tiroides/patología , Tiroidectomía/métodosRESUMEN
OPINION STATEMENT: Melanoma is caused by a variety of somatic mutations, and among these mutations, BRAF mutation occurs most frequently and has routinely been evaluated as a critical diagnostic biomarker in clinical practice. The introduction of targeted agents for BRAF-mutant melanoma has significantly improved overall survival in a large proportion of patients. However, there is BRAF inhibitor resistance in most patients, and its mechanisms are complicated and need further clarification. Additionally, treatment approaches to overcome resistance have evolved rapidly, shifting from monotherapy to multimodality treatment, which has dramatically improved patient outcomes in clinical trials and practice. This review highlights the mechanisms of BRAF inhibitor resistance in melanoma and discusses the current state of its therapeutic approaches that can be further explored in clinical practice.
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Melanoma , Proteínas Proto-Oncogénicas B-raf , Humanos , Proteínas Proto-Oncogénicas B-raf/genética , Resistencia a Antineoplásicos/genética , Melanoma/etiología , Melanoma/genética , Inhibidores de Proteínas Quinasas/farmacología , Inhibidores de Proteínas Quinasas/uso terapéutico , Mutación , BiomarcadoresRESUMEN
OBJECTIVES: MicroRNAs (miRNAs) have been considered as a new class of novel diagnostic and predictive biomarker in many diseases. However, there are few studies on miRNA in osteosarcoma (OS). This study aimed to investigate the roles of miR-30 on OS occurrence and development. METHODS: PCR was used to detect mRNA levels of miR-30 and MTA1 in cancer tissues, adjacent non-cancerous tissues from OS patients. Western blot was used to detect MTA1 protein expression in all tissues and cell lines (hFOb1.19,Saos-2, MG63, and U2OS). The correlation between miR-30 and MTA1 was predicted through bioinformatics software, and identified by a luciferase reporting experiment. In vitro, functional test detected the specific effects of miR-30 and MTA1 on the development of OS. RESULTS: miR-30 expression was significantly reduced, while the expression of MTA1 was increased in OS tissues and cells. Luciferase reporting experiment showed that miR-30 sponged MTA1 which was negatively correlated with miR-30 expression. Furthermore, rescue tests revealed that MTA1 restrained the functions of miR-30 on cell proliferation and migration of OS. CONCLUSION: Our finding showed that miR-30 modulated the proliferation and migration by targeting MTA1 in OS.
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Neoplasias Óseas , MicroARNs , Osteosarcoma , Proteínas Represoras , Transactivadores , Neoplasias Óseas/genética , Neoplasias Óseas/metabolismo , Línea Celular Tumoral , Regulación Neoplásica de la Expresión Génica , Humanos , MicroARNs/genética , MicroARNs/metabolismo , Osteosarcoma/genética , Proteínas Represoras/genética , Proteínas Represoras/metabolismo , Transactivadores/genética , Transactivadores/metabolismoRESUMEN
DNA methyltransferases (DNMTs) including DNMT1 are a conserved family of cytosine methylases that play crucial roles in epigenetic regulation. The versatile functions of DNMT1 rely on allosteric networks between its different interacting partners, emerging as novel therapeutic targets. In this work, based on the modeling structures of DNMT1-ubiquitylated H3 (H3Ub)/ubiquitin specific peptidase 7 (USP7) complexes, we have used a combination of elastic network models, molecular dynamics simulations, structural residue perturbation, network modeling, and pocket pathway analysis to examine their molecular mechanisms of allosteric regulation. The comparative intrinsic and conformational dynamics analysis of three DNMT1 systems has highlighted the pivotal role of the RFTS domain as the dynamics hub in both intra- and inter-molecular interactions. The site perturbation and network modeling approaches have revealed the different and more complex allosteric interaction landscape in both DNMT1 complexes, involving the events caused by mutational hotspots and post-translation modification sites through protein-protein interactions (PPIs). Furthermore, communication pathway analysis and pocket detection have provided new mechanistic insights into molecular mechanisms underlying quaternary structures of DNMT1 complexes, suggesting potential targeting pockets for PPI-based allosteric drug design.
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Regulación Alostérica/genética , ADN (Citosina-5-)-Metiltransferasa 1/metabolismo , Histonas/metabolismo , Peptidasa Específica de Ubiquitina 7/metabolismo , ADN (Citosina-5-)-Metiltransferasa 1/genética , Metilación de ADN/genética , Epigénesis Genética/genética , Histonas/genética , Humanos , Simulación de Dinámica Molecular , Unión Proteica/genética , Conformación Proteica , Dominios y Motivos de Interacción de Proteínas/genética , Peptidasa Específica de Ubiquitina 7/genéticaRESUMEN
BACKGROUND Thyroid cancer, which is the most common endocrine cancer, has shown a drastic increase in incidence globally over the past decade. The present study investigated the thyroid cancer-inhibitory potential of jatrorrhizine-platinum(II) complex (JR-P(II) in vitro and in vivo. MATERIAL AND METHODS The JR-P(II)-mediated cytotoxicity in thyroid carcinoma cells was determined by using MTT assay. Assessment of acetylated histones, tubulin, and DNA repair proteins was made by Western blot assays. Flow cytometry was used for apoptosis and ROS accumulation measurement. RESULTS The JR-P(II) suppressed proliferative capacity of SW1736, BHP7-13, and 8305C cells. JR-P(II) treatment markedly promoted expression of acetylated histone H3, H4, and tubulin in a dose-dependent manner. Treatment with JR-P(II) significantly elevated the proportion of cells in sub-G1 and promoted cleaved caspase-3 and -9. In JR-P(II)-treated cells, DCFH-DA fluorescence was much higher relative to control cells. The JR-P(II) treatment consistently suppressed expression of pS6, p-ERK1/2, p-4E-BP1, and p-AKT, and increased p-H2AX expression and suppressed KU70 and KU80 protein levels. The level of RAD51 was repressed in JR-P(II)-treated cells. JR-P(II) administration in mice caused no significant change in body weight, and it inhibited SW1736 tumor growth in mice. CONCLUSIONS The JR-P(II) induced cytotoxicity in thyroid cancer cells by inhibiting the mechanism responsible for repair of double-stranded DNA. The in vivo data also revealed that JR-P(II) effectively inhibits thyroid tumor growth by inducing DNA damage. Thus, our results suggest that further evaluation of JR-P(II) as a therapeutic candidate for thyroid cancer is warranted.
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Apoptosis/efectos de los fármacos , Berberina/análogos & derivados , Neoplasias de la Tiroides/metabolismo , Animales , Autofagia/efectos de los fármacos , Berberina/farmacología , Línea Celular Tumoral , Proliferación Celular/efectos de los fármacos , China , Femenino , Humanos , Ratones , Ratones Desnudos , Fosfatidilinositol 3-Quinasas/metabolismo , Platino (Metal)/metabolismo , Platino (Metal)/farmacología , Proteínas Proto-Oncogénicas c-akt/metabolismo , Transducción de Señal/efectos de los fármacos , Serina-Treonina Quinasas TOR/metabolismo , Glándula Tiroides/patología , Neoplasias de la Tiroides/tratamiento farmacológico , Ensayos Antitumor por Modelo de XenoinjertoRESUMEN
Motivation: Mass spectrometry (MS) based quantification of proteins/peptides has become a powerful tool in biological research with high sensitivity and throughput. The accuracy of quantification, however, has been problematic as not all peptides are suitable for quantification. Several methods and tools have been developed to identify peptides that response well in mass spectrometry and they are mainly based on predictive models, and rarely consider the linearity of the response curve, limiting the accuracy and applicability of the methods. An alternative solution is to select empirically superior peptides that offer satisfactory MS response intensity and linearity in a wide dynamic range of peptide concentration. Results: We constructed a reference database for proteome quantification based on experimental mass spectrum response curves. The intensity and dynamic range of over 2 647 773 transitions from 121 318 peptides were obtained from a set of dilution experiments, covering 11 040 gene products. These transitions and peptides were evaluated and presented in a database named SCRIPT-MAP. We showed that the best-responder (BR) peptide approach for quantification based on SCRIPT-MAP database is robust, repeatable and accurate in proteome-scale protein quantification. This study provides a reference database as well as a peptides/transitions selection method for quantitative proteomics. Availability and implementation: SCRIPT-MAP database is available at http://www.firmiana.org/responders/. Supplementary information: Supplementary data are available at Bioinformatics online.
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Bases de Datos de Proteínas , Espectrometría de Masas/métodos , Péptidos/química , Proteómica/métodos , Células HEK293 , Células HeLa , Humanos , Péptidos/análisisRESUMEN
OBJECTS: To evaluate prognostic factors and treatment outcomes of primary squamous cell carcinoma in thyroid (PSCCTh) over the past decades using a large national database. METHODS: All patients diagnosed with PSCCTh between 1973 and 2015 were identified with the Surveillance, Epidemiology, and End Results Program (SEER) 18-registry database. Relevant clinical data were collected, and prognostic factors of overall survival (OS) and disease-specific survival (DSS) were analyzed. RESULTS: This cohort study included 242 patients, accounting for 0.12% of all primary thyroid carcinomas from 1973 to 2015 nationwide. Of the patients with PSCCTh, 75% were older than 60 years at diagnosis. Patient age older than 60 years (HR 2.242, 95% CI 1.367-3.676, P = 0.001) and a tumor size larger than or equal to 50 mm (HR 1.479, 95% CI 1.011-2.165, P = 0.044) were independent negative prognostic factors. The univariate analysis suggested that the morphological subtype (OS, P = 0.033; DSS, P = 0.048), clinical treatment modality (OS, P < 0.0001; DSS, P < 0.0001), and T stage (OS, P = 0.004; DSS, P = 0.001) were important predictive factors for OS and DSS. In contrast, gender, race, year of diagnosis, geographic location, N stage, and M stage were not prognostic factors. CONCLUSIONS: PSCCTh is a rare malignancy with an aggressive nature and poor prognosis. Survival is predicted by the treatment modality, patient age, T stage, tumor size, and morphological subtypes. This study showed that early diagnosis and complete surgical resection plus adjuvant radiation therapy were associated with a better outcome.
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Carcinoma de Células Escamosas/diagnóstico , Carcinoma de Células Escamosas/terapia , Neoplasias de la Tiroides/diagnóstico , Neoplasias de la Tiroides/terapia , Adulto , Anciano , Carcinoma de Células Escamosas/mortalidad , Carcinoma de Células Escamosas/patología , Estudios de Cohortes , Femenino , Humanos , Estimación de Kaplan-Meier , Masculino , Persona de Mediana Edad , Estadificación de Neoplasias , Pronóstico , Sistema de Registros , Factores de Riesgo , Programa de VERF , Neoplasias de la Tiroides/mortalidad , Neoplasias de la Tiroides/patología , Resultado del Tratamiento , Estados Unidos/epidemiología , Adulto JovenRESUMEN
Parenchymatous organs consist of multiple cell types, primarily defined as parenchymal cells (PCs) and nonparenchymal cells (NPCs). The cellular characteristics of these organs are not well understood. Proteomic studies facilitate the resolution of the molecular details of different cell types in organs. These studies have significantly extended our knowledge about organogenesis and organ cellular composition. Here, we present an atlas of the cell-type-resolved liver proteome. In-depth proteomics identified 6000 to 8000 gene products (GPs) for each cell type and a total of 10,075 GPs for four cell types. This data set revealed features of the cellular composition of the liver: (1) hepatocytes (PCs) express the least GPs, have a unique but highly homogenous proteome pattern, and execute fundamental liver functions; (2) the division of labor among PCs and NPCs follows a model in which PCs make the main components of pathways, but NPCs trigger the pathways; and (3) crosstalk among NPCs and PCs maintains the PC phenotype. This study presents the liver proteome at cell resolution, serving as a research model for dissecting the cell type constitution and organ features at the molecular level.
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Hígado/citología , Proteoma/análisis , Análisis de la Célula Individual/métodos , Animales , Ontología de Genes , Hígado/metabolismo , Ratones , Proteómica/métodosRESUMEN
Eukaryotic cells store neutral lipids in cytoplasmic lipid droplets (LDs) enclosed in a monolayer of phospholipids and associated proteins [LD proteins (LDPs)]. Growing evidence has demonstrated that LDPs play important roles in the pathogenesis of liver diseases. However, the composition of liver LDPs and the role of their alterations in hepatosteatosis are not well-understood. In this study, we performed liver proteome and LD sub-proteome profiling to identify enriched proteins in LDs as LDPs, and quantified their changes in a high-fat diet (HFD)-induced fatty liver model. Among 5,000 quantified liver proteins, 101 were enriched by greater than 10-fold in the LD sub-proteome and were classified as LDPs. Differential profiling of LDPs in HFD-induced fatty liver provided a list of candidate LDPs for functional investigation. We tested the function of an upregulated LDP, S100a10, in vivo with adenovirus-mediated gene silencing and found, unexpectedly, that knockdown of S100a10 accelerated progression of HFD-induced liver steatosis. The S100A10 interactome revealed a connection between S100A10 and lipid transporting proteins, suggesting that S100A10 regulates the development and formation of LDs by transporting and trafficking. This study identified LD-enriched sub-proteome in homeostatic as well as HFD-induced fatty livers, providing a rich resource for the LDP research field.
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Hígado Graso/genética , Gotas Lipídicas/metabolismo , Hígado/metabolismo , Proteoma/genética , Animales , Dieta Alta en Grasa/efectos adversos , Hígado Graso/metabolismo , Hígado Graso/patología , Perfilación de la Expresión Génica , Células Hep G2 , Humanos , Gotas Lipídicas/patología , Metabolismo de los Lípidos/genética , Ratones , Fosfolípidos/genética , Biosíntesis de Proteínas/genética , Proteoma/metabolismo , ProteómicaRESUMEN
The ability to map endogenous transcription factors (TFs) DNA binding activity at the proteome scale will greatly enhance our understanding of various biological processes. Here we report a highly sensitive, rapid, and high-throughput approach, transcription factor response elements on tip-mass spectrometry (TOT-MS), that allows for quantitative measurement of endogenous TFs. A total of 150 TFs from 1 µg of nuclear extracts can be quantified with single shot mass spectrometry detection in 1 h of machine time. Up to 755 TFs, which is comparable to the depth of RNA-seq, were identified by TOT coupled with on-tip small size reverse-phase liquid chromatography. We further demonstrated the capability of TOT-MS by interrogating the dynamic change of TFs in the epidermal growth factor (EGF) signaling pathway. This approach should find broad applications in elucidating the TF landscape from limited amounts of biological materials.
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Espectrometría de Masas/métodos , Elementos de Respuesta/genética , Factores de Transcripción/análisis , Núcleo Celular/metabolismo , Cromatografía de Fase Inversa , Células HEK293 , Células HeLa , Humanos , Factores de Transcripción/metabolismoRESUMEN
Transcription factors (TFs) are families of proteins that bind to specific DNA sequences, or TF response elements (TFREs), and function as regulators of many cellular processes. Because of the low abundance of TFs, direct quantitative measurement of TFs on a proteome scale remains a challenge. In this study, we report the development of an affinity reagent that permits identification of endogenous TFs at the proteome scale. The affinity reagent is composed of a synthetic DNA containing a concatenated tandem array of the consensus TFREs (catTFRE) for the majority of TF families. By using catTFRE to enrich TFs from cells, we were able to identify as many as 400 TFs from a single cell line and a total of 878 TFs from 11 cell types, covering more than 50% of the gene products that code for the DNA-binding TFs in the genome. We further demonstrated that catTFRE pull-downs could quantitatively measure proteome-wide changes in DNA binding activity of TFs in response to exogenous stimulation by using a label-free MS-based quantification approach. Applying catTFRE on the evaluation of drug effects, we described a panoramic view of TF activations and provided candidates for the elucidation of molecular mechanisms of drug actions. We anticipate that the catTFRE affinity strategy will find widespread applications in biomedical research.
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ADN/metabolismo , Regulación de la Expresión Génica/genética , Análisis por Matrices de Proteínas/métodos , Proteoma/genética , Elementos de Respuesta/genética , Factores de Transcripción/genética , Factores de Transcripción/aislamiento & purificación , Línea Celular , Cromatografía Liquida , Biología Computacional , Cartilla de ADN/genética , Regulación de la Expresión Génica/efectos de los fármacos , Humanos , Espectrometría de Masas en Tándem , Factores de Transcripción/metabolismoRESUMEN
BACKGROUND: Decreased serum levels of uncarboxylated matrix Gla-protein (ucMGP) have been detected in Ankylosing Spondylitis (AS) patients. The current study was to investigate the expression of MGP in AS tissues as well as the relationship between serum ucMGP (an inactive form of MGP) levels and radiographic severity in AS patients. METHODS: Local MGP expression were assessed by Western blot and RT-PCR in hip synovial tissues from patients with AS and control subjects. In addition, the serum level of ucMGP was assessed by enzyme-linked immunosorbent assay in 68 healthy subjects and 62 patients with AS. The radiographic progression of AS was classified according to the radiographic events of modified New York Criteria for sacroiliac joint evaluation and modified Stoke Ankylosing Spondylitis Spine Score (mSASSS) system for spine assessment. RESULTS: MGP expression was downregulated in AS patients compared to controls in hip tissues. Decreased levels of ucMGP in serum were found in AS patients compared with healthy controls. ucMGP levels in serum of AS patients were significantly negatively correlated with the disease radiographic severity evaluated by modified New York grading criteria (r = -0.293, p = 0.045) and mSASSS system (r = -0.361, p = 0.03). CONCLUSIONS: MGP expression is impaired in patients with AS. A low serum level of ucMGP in the setting of AS is linked to increased structural damage, emphasizing the role of MGP in the suppression of new bone formation.
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Proteínas de Unión al Calcio/sangre , Proteínas de la Matriz Extracelular/sangre , Espondilitis Anquilosante/sangre , Espondilitis Anquilosante/diagnóstico por imagen , Adulto , Biomarcadores/sangre , Huesos/diagnóstico por imagen , Subunidad alfa 1 del Factor de Unión al Sitio Principal/sangre , Progresión de la Enfermedad , Regulación hacia Abajo , Ensayo de Inmunoadsorción Enzimática , Femenino , Cadera/diagnóstico por imagen , Cadera/patología , Humanos , Masculino , Persona de Mediana Edad , ARN/análisis , Radiografía , Reacción en Cadena en Tiempo Real de la Polimerasa , Factor de Transcripción SOX9/sangre , Índice de Severidad de la Enfermedad , Columna Vertebral/diagnóstico por imagen , Membrana Sinovial/patología , Proteína Gla de la MatrizRESUMEN
Nuclear receptors (NRs) are a superfamily of transcription factors that, upon binding to ligands, bind specific DNA sequences and regulate a transcriptional program governing cell proliferation, differentiation, and metabolism. In the liver, by sensing lipid-soluble hormones and dietary lipids and governing the expression of key liver metabolic genes, NR proteins direct a large array of key hepatic functions that include lipid and glucose metabolism, bile secretion, and bile acid homeostasis. Although much has been learned about the physiology of NRs, little is known about their protein expression and DNA binding activity in the liver because of their low abundance and the lack of high-throughput methods for detection at the protein level. Here we report a method for profiling the DNA binding activity of the NR transcription factor superfamily in mouse liver. We use DNA constructs of hormone response elements (HREs) as affinity reagents to enrich NR proteins from nuclear extracts of mouse liver and then identify them using mass spectrometry. We evaluated 20 DNA constructs containing various combinations of HREs for their ability to enrich endogenous NR proteins and found that two different HREs are sufficient to achieve isolation and identification of nearly all endogenous NR proteins from one mouse liver. We have detected proteins for 35 members of the NR family out of 41 that are expressed in mouse liver at mRNA level. Thus, this method allows coverage of most of the whole NR proteome and establishes a practical assay for the investigation of NR actions in mouse liver. We anticipate that this method will find widespread use in future investigations of NR actions in liver biology and pathology. Furthermore, this workflow is a useful tool for NR biologists interested in measuring NR expression, DNA binding, post-translational modifications, cellular localization, and other functional aspects of NRs in organs under normal physiological and pathological conditions, as well as during pharmacological intervention.
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ADN/química , Hígado/metabolismo , Procesamiento Proteico-Postraduccional , ARN Mensajero/química , Receptores Citoplasmáticos y Nucleares/química , Receptores Citoplasmáticos y Nucleares/metabolismo , Secuencia de Aminoácidos , Animales , Secuencia de Bases , ADN/genética , ADN/metabolismo , Femenino , Regulación de la Expresión Génica , Ligandos , Hígado/química , Hígado/citología , Masculino , Espectrometría de Masas , Ratones , Ratones Endogámicos C57BL , Datos de Secuencia Molecular , Proteómica , ARN Mensajero/genética , ARN Mensajero/metabolismo , Receptores Citoplasmáticos y Nucleares/genética , Elementos de Respuesta , Factores SexualesRESUMEN
The current in-depth proteomics makes use of long chromatography gradient to get access to more peptides for protein identification, resulting in covering of as many as 8000 mammalian gene products in 3 days of mass spectrometer running time. Here we report a fast sequencing (Fast-seq) workflow of the use of dual reverse phase high performance liquid chromatography - mass spectrometry (HPLC-MS) with a short gradient to achieve the same proteome coverage in 0.5 day. We adapted this workflow to a quantitative version (Fast quantification, Fast-quan) that was compatible to large-scale protein quantification. We subjected two identical samples to the Fast-quan workflow, which allowed us to systematically evaluate different parameters that impact the sensitivity and accuracy of the workflow. Using the statistics of significant test, we unraveled the existence of substantial falsely quantified differential proteins and estimated correlation of false quantification rate and parameters that are applied in label-free quantification. We optimized the setting of parameters that may substantially minimize the rate of falsely quantified differential proteins, and further applied them on a real biological process. With improved efficiency and throughput, we expect that the Fast-seq/Fast-quan workflow, allowing pair wise comparison of two proteomes in 1 day may make MS available to the masses and impact biomedical research in a positive way.
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Proteoma/análisis , Proteómica/métodos , Cromatografía Líquida de Alta Presión , Ciclopentanos/farmacología , Células HeLa , Células Hep G2 , Células Endoteliales de la Vena Umbilical Humana/metabolismo , Humanos , Pirimidinas/farmacología , Espectrometría de Masas en TándemRESUMEN
Acquisition of drug-resistant phenotypes is often associated with chemotherapy in osteosarcoma. Studies show that high-mobility group box 1 (HMGB1) plays an important role in facilitating autophagy and promotes drug resistance in osteosarcoma cells. In this study, we determined the targeting role of miR-22 to HMGB1 and the regulation of miR-22 on the HMGB1-mediated cell autophagy and on the cell proliferation, migration, and invasion of osteosarcoma cells. Results demonstrated that miR-22 well paired with the 3'-UTR of HMGB1 downregulated the HMGB1 expression and blocked the HMGB1-mediated autophagy during chemotherapy in osteosarcoma cells in vitro. Further study showed that the blockage of autophagy by miR-22 inhibited the osteosarcoma cell proliferation, migration, and invasion. In summary, this study implied the negative regulation of miR-22 on the HMGB1-mediated autophagy in osteosarcoma cells.
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Neoplasias Óseas/genética , Proteína HMGB1/biosíntesis , MicroARNs/genética , Osteosarcoma/genética , Regiones no Traducidas 3' , Autofagia/genética , Neoplasias Óseas/patología , Movimiento Celular/genética , Proliferación Celular , Resistencia a Antineoplásicos/genética , Proteína HMGB1/genética , Humanos , Osteosarcoma/patologíaRESUMEN
Objective: To investigate the application of modified elastic intramedullary nail and the outcomes between modified elastic stable intramedullary nailing and traditional elastic stable intramedullary nailing in children with distal tibial metaphyseal junction fracture. Methods: A retrospective study was conducted. From January 2018 to January 2021, a total of 36 children with distal tibial metaphyseal junction fracture were treated in our hospital. All of them were treated with closed reduction and elastic stable intramedullary nailing internal fixation. A total of 18 children were treated by modified elastic stable intramedullary nailing and 18 children were treated by traditional elastic stable intramedullary nailing. Postoperative imaging, clinical efficacy, and complications were analyzed. Results: The mean follow-up time was 20 (15-36) months in modified group and 22 (16-33) months in traditional group. There were no complications such as infection, loss of reduction, and unequal length of lower limbs in modified group while loss of reduction occurred in two cases in traditional group. In these two cases of loss of reduction, we preformed manual reduction and replacement of long leg casts, and there was no loss of reduction, and the patient achieved a good prognosis. In the last follow-up, American Orthopaedic Foot & Ankle Society score was used. In modified group, excellent outcome achieved in 17 cases, good outcome achieved in 1 case, and satisfactory therapeutic effect was achieved. In traditional elastic stable intramedullary nailing group, excellent outcome achieved in 14 cases, and good outcome achieved in 4 cases. There was no statistical difference in the scores between the two groups. Conclusion: It was concluded that modified elastic stable intramedullary nailing fixation is a safe and effective treatment.
RESUMEN
Background: Elastic stable intramedullary nailing (ESIN) and plates are currently the main internal fixation for treating Pediatric Diaphyseal Femur Fractures (PDFF), and the optimal choice of internal fixation is controversial. The purpose of this meta-analysis is to compare the surgical outcomes and complications of the two fixation methods. Materials and Methods: MEDLINE, Embase, and the Cochrane Library were systematically searched for studies published up to March, 2023, that compared ESIN and plate fixation techniques for treating PDFF. Pooled analysis identified differences in surgical outcomes between ESIN and plate, mainly regarding surgical outcomes and postoperative complications, such as time at surgery, fracture healing time, blood loss and related complications. Results: We included 10 studies with 775 patients with PDFF in our review. Of these, 428 and 347 were treated with ESIN and Plate, respectively. In terms of postoperative complications, ESIN led to a shorter surgery time [MD = - 28.93, 95% CI (- 52.88 to - 4.98), P < 0.05], less blood loss [MD = - 66.94, 95% CI (- 87.79 to - 46.10), P < 0.001] and more fracture healing time [MD = 2.65, 95% CI (1.22-4.07), P < 0.001]. In terms of postoperative complications, ESIN led to fewer fections (RR = 0.77, 95% CI 0.37, 1.60, P = 0.48), fewer angulation deformities (RR = 0.80, 95% CI 0.35, 1.83, P = 0.60) and more prominent implants (RR = 3.36, 95% CI 1.88, 6.01, P < 0.001), more delayed unions (RR = 4.06, 95% CI 0.71, 23.06, P = 0.11). Conclusions: ESIN and Plate have similar rates of complications besides a prominent implant rate, while ESIN has a shorter period of operation and less intraoperative bleeding. Although both options are suitable, the results of this study support the use of ESIN rather than plates in the treatment of PDFF in terms of complication rates. In clinical applications, surgeons should choose the appropriate treatment method according to the actual situation.