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1.
Brief Bioinform ; 2021 Nov 13.
Artigo em Inglês | MEDLINE | ID: mdl-34791010

RESUMO

The application of next-generation sequencing in research and particularly in clinical routine requires highly accurate variant calling. Here we describe UVC, a method for calling small variants of germline or somatic origin. By unifying opposite assumptions with sublation, we discovered the following two empirical laws to improve variant calling: allele fraction at high sequencing depth is inversely proportional to the cubic root of variant-calling error rate, and odds ratios adjusted with Bayes factors can model various sequencing biases. UVC outperformed other variant callers on the GIAB germline truth sets, 192 scenarios of in silico mixtures simulating 192 combinations of tumor/normal sequencing depths and tumor/normal purities, the GIAB somatic truth sets derived from physical mixture, and the SEQC2 somatic reference sets derived from the breast-cancer cell-line HCC1395. UVC achieved 100% concordance with the manual review conducted by multiple independent researchers on a Qiagen 71-gene-panel dataset derived from 16 patients with colon adenoma. UVC outperformed other unique molecular identifier (UMI)-aware variant callers on the datasets used for publishing these variant callers. Performance was measured with sensitivity-specificity trade off for called variants. The improved variant calls generated by UVC from previously published UMI-based sequencing data provided additional insight about DNA damage repair. UVC is open-sourced under the BSD 3-Clause license at https://github.com/genetronhealth/uvc and quay.io/genetronhealth/gcc-6-3-0-uvc-0-6-0-441a694.

2.
Front Pharmacol ; 12: 743086, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34675809

RESUMO

As a traditional Chinese medicine-originated disease-modifying anti-rheumatic drug prescription, Baihu-Guizhi decoction (BHGZD) is extensively used for the treatment of rheumatoid arthritis (RA) with a satisfying therapeutic efficacy. Mechanically, our previous data indicated that BHGZD may ameliorate RA partially by restoring the balance of the "inflammation-immune" system through regulating the TLR4-c-Fos-IL2-TNF-alpha axis. Toll-like receptor 4 (TLR4) has been revealed to be involved in the activation of the NLR family pyrin domain containing 3 (NLRP3) inflammasome complex. Thus, the aim of the current study was to determine the regulatory effects of BHGZD on the TLR4-mediated inflammasome activation during RA progression based on the modified adjuvant-induced arthritis model (AIA-M) and the lipopolysaccharide/adenosine triphosphate (LPS/ATP)-induced pyroptosis cellular models. As a result, oral administration of BHGZD exhibited prominent improvement in the disease severity of AIA-M rats, such as reducing the redness and swelling of joints, arthritis incidence, arthritic scores, and diameter of the limb and increasing pain thresholds. In line with the in vivo findings, BHGZD treatment effectively inhibited the LPS/ATP-induced pyroptosis of both Raw264.7 macrophage and MH7A cells in vitro by reducing pyroptotic cell death morphology (swollen cells) and decreasing propidium iodide-positive and terminal deoxynucleotidyl transferase-mediated dUTP-fluorescein nick end labeling (TUNEL)-positive cells. Notably, the increased expression levels of TLR4, NLRP3, interleukin 1ß, and interleukin 18 proteins and the elevated activities of caspase-1 and lactic dehydrogenase in in vivo and in vitro disease models were markedly reversed by the treatment with BHGZD. In conclusion, the above findings proved the immunomodulatory and anti-inflammatory activities of BHGZD, especially in pyroptosis, which may be attributed to the activation of TLR4-mediated NLRP3 inflammasome signaling.

3.
BMJ Open ; 11(10): e043790, 2021 10 01.
Artigo em Inglês | MEDLINE | ID: mdl-34598979

RESUMO

OBJECTIVES: As early prediction of severe illness and death for patients with coronavirus disease 2019 (COVID-19) is important, we aim to explore the clinical value of laboratory indicators in evaluating the progression and prognosis of patients with COVID-19. DESIGN: Retrospective cohort study. SETTING: Hospital-based study in China. PARTICIPANTS: Adult patients with COVID-19 from December 15, 2019 to March 15, 2020. END POINT: Disease severity and mortality. METHODS: Clinical data of 638 patients with COVID-19 were collected and compared between severe and non-severe groups. The predictive ability of laboratory indicators in disease progression and prognosis of COVID-19 was analysed using the receiver operating characteristic curve. The survival differences of COVID-19 patients with different levels of laboratory indicators were analysed utilising Kaplan-Meier analysis. RESULTS: 29.8% (190/638) of patients with COVID-19 progressed to severe. Compared with patients with no adverse events, C reactive protein (CRP), neutrophil-to-lymphocyte ratio (NLR) and D-dimer were significantly higher in severe patients with adverse events, such as acute myocardial injury, respiratory failure, acute kidney injury, mechanical ventilation, intensive care unit admission, multiple organ dysfunction syndromes and death (all p<0.05). The multivariate logistic analysis suggested that CRP, NLR and D-dimer were independent risk factors for the disease progression of COVID-19 (all p<0.05). The model combining all of them owned the highest area under the receiver operating characteristic curve (AUC) predicting disease progression and death of COVID-19, with AUC of 0.894 (95% CI 0.857 to 0.931) and 0.918 (95% CI 0.873 to 0.962), respectively. Survival analysis suggested that the patients with a high level of CRP, NLR or D-dimer performed shorter overall survival time (all p<0.05). CONCLUSIONS: The combination of CRP, NLR and D-dimer could be an effective predictor for the aggravation and death in patients with COVID-19. The abnormal expression of these indicators might suggest a strong inflammatory response and multiple adverse events in patients with severe COVID-19.


Assuntos
COVID-19 , Laboratórios , Adulto , Progressão da Doença , Humanos , Neutrófilos , Prognóstico , Curva ROC , Estudos Retrospectivos , SARS-CoV-2
4.
Cell Res ; 2021 Oct 26.
Artigo em Inglês | MEDLINE | ID: mdl-34702946

RESUMO

The infusion of coronavirus disease 2019 (COVID-19) patients with mesenchymal stem cells (MSCs) potentially improves clinical symptoms, but the underlying mechanism remains unclear. We conducted a randomized, single-blind, placebo-controlled (29 patients/group) phase II clinical trial to validate previous findings and explore the potential mechanisms. Patients treated with umbilical cord-derived MSCs exhibited a shorter hospital stay (P = 0.0198) and less time required for symptoms remission (P = 0.0194) than those who received placebo. Based on chest images, both severe and critical patients treated with MSCs showed improvement by day 7 (P = 0.0099) and day 21 (P = 0.0084). MSC-treated patients had fewer adverse events. MSC infusion reduced the levels of C-reactive protein, proinflammatory cytokines, and neutrophil extracellular traps (NETs) and promoted the maintenance of SARS-CoV-2-specific antibodies. To explore how MSCs modulate the immune system, we employed single-cell RNA sequencing analysis on peripheral blood. Our analysis identified a novel subpopulation of VNN2+ hematopoietic stem/progenitor-like (HSPC-like) cells expressing CSF3R and PTPRE that were mobilized following MSC infusion. Genes encoding chemotaxis factors - CX3CR1 and L-selectin - were upregulated in various immune cells. MSC treatment also regulated B cell subsets and increased the expression of costimulatory CD28 in T cells in vivo and in vitro. In addition, an in vivo mouse study confirmed that MSCs suppressed NET release and reduced venous thrombosis by upregulating kindlin-3 signaling. Together, our results underscore the role of MSCs in improving COVID-19 patient outcomes via maintenance of immune homeostasis.

5.
Dalton Trans ; 50(32): 11180-11188, 2021 Aug 28.
Artigo em Inglês | MEDLINE | ID: mdl-34338267

RESUMO

Pt(iv) prodrugs have gained tremendous attention due to their indisputable advantages compared to cisplatin. Herein, new Pt(iv) derivatives with cinnamic acid at the first axial position, and inhibitor of matrix metalloproteinases-2 and -9, histone deacetylase, cyclooxygenase or pyruvate dehydrogenase at the second axial position are constructed to develop multi-action prodrugs. We demonstrate that Pt(iv) prodrugs are reducible and have superior antiproliferative activity with IC50 values at submicromolar concentrations. Notably, Pt(iv) prodrugs exhibit highly potent anti-tumour activity in an in vivo breast cancer model. Our results support the view that a triple-action Pt(iv) prodrug acts via a synergistic mechanism, which involves the effects of CDDP and the effects of axial moieties, thus jointly leading to the death of tumour cells. These findings provide a practical strategy for the rational design of more effective Pt(iv) prodrugs to efficiently kill tumour cells by enhancing their cellular accumulation and tuning their canonical mechanism.

6.
Brief Bioinform ; 22(6)2021 Nov 05.
Artigo em Inglês | MEDLINE | ID: mdl-34368852

RESUMO

The identification of structural variations (SVs) and viral integrations in circulating tumor DNA (ctDNA) is a key step in precision oncology that may assist clinicians in treatment selection and monitoring. However, due to the short fragment size of ctDNA, it is challenging to accurately detect low-frequency SVs or SVs involving complex junctions in ctDNA sequencing data. Here, we describe Aperture, a new fast SV caller that applies a unique strategy of $k$-mer-based searching, binary label-based breakpoint detection and candidate clustering to detect SVs and viral integrations with high sensitivity, especially when junctions span repetitive regions. Aperture also employs a barcode-based filter to ensure specificity. Compared with existing methods, Aperture exhibits superior sensitivity and specificity in simulated, reference and real data tests, especially at low dilutions. Additionally, Aperture is able to predict sites of viral integration and identify complex SVs involving novel insertions and repetitive sequences in real patient data. Aperture is freely available at https://github.com/liuhc8/Aperture.

7.
Clin Transl Gastroenterol ; 12(8): e00385, 2021 08 03.
Artigo em Inglês | MEDLINE | ID: mdl-34342293

RESUMO

INTRODUCTION: Patients with atrophic gastritis (AG) or gastric intestinal metaplasia (GIM) have elevated risk of gastric adenocarcinoma. Endoscopic screening and surveillance have been implemented in high incidence countries. The study aimed to evaluate the accuracy of a deep convolutional neural network (CNN) for simultaneous recognition of AG and GIM. METHODS: Archived endoscopic white light images with corresponding gastric biopsies were collected from 14 hospitals located in different regions of China. Corresponding images by anatomic sites containing AG, GIM, and chronic non-AG were categorized using pathology reports. The participants were randomly assigned (8:1:1) to the training cohort for developing the CNN model (TResNet), the validation cohort for fine-tuning, and the test cohort for evaluating the diagnostic accuracy. The area under the curve (AUC), sensitivity, specificity, and accuracy with 95% confidence interval (CI) were calculated. RESULTS: A total of 7,037 endoscopic images from 2,741 participants were used to develop the CNN for recognition of AG and/or GIM. The AUC for recognizing AG was 0.98 (95% CI 0.97-0.99) with sensitivity, specificity, and accuracy of 96.2% (95% CI 94.2%-97.6%), 96.4% (95% CI 94.8%-97.9%), and 96.4% (95% CI 94.4%-97.8%), respectively. The AUC for recognizing GIM was 0.99 (95% CI 0.98-1.00) with sensitivity, specificity, and accuracy of 97.9% (95% CI 96.2%-98.9%), 97.5% (95% CI 95.8%-98.6%), and 97.6% (95% CI 95.8%-98.6%), respectively. DISCUSSION: CNN using endoscopic white light images achieved high diagnostic accuracy in recognizing AG and GIM.

8.
Bioengineered ; 12(1): 3947-3956, 2021 12.
Artigo em Inglês | MEDLINE | ID: mdl-34281454

RESUMO

Diabetic retinopathy (DR) represents the most typical complication of type 2 diabetes mellitus and one of the most primary oculopathy causing blindness. However, the mechanism of DR remains unknown. RIPK1/RIPK3, as homologous serine/threonine kinases, are key elements in mediating necroptosis and may have functions in DR development. To clarify the relationship between DR and RIPK1/RIPK3, this study established a model of apoptosis using high-glucose induced RGCs, which were treated with 7.5, 19.5, and 35 mM D-glucose for 12, 24, and 48 h, respectively. Subsequently, the expression of RIPK1/RIPK3 was determined and the protective effect of necrostatin-1 on RGCs injury induced by high glucose was explored. The results demonstrated that the expression of RIPK1 and RIPK3 in the cells was increased markedly following 12 h treatment with 19.5 mM D-glucose. Additionally, following an addition of 100 µM necrostatin-1 in 19.5 mM D-glucose medium for RGCs treatment 12 h, the protein expression of RIPK1 and RIPK3 was decreased markedly, and the number of Nissl bodies in cells was increased substantially. The findings of the present study indicated that high glucose could induce the expression of RIPK1/RIPK3, and necrostatin-1 could effectively protect RGCs from D-glucose-induced cell necrosis.


Assuntos
Regulação Enzimológica da Expressão Gênica , Glucose/toxicidade , Proteína Serina-Treonina Quinases de Interação com Receptores/metabolismo , Células Ganglionares da Retina/enzimologia , Animais , Separação Celular , Imidazóis/farmacologia , Indóis/farmacologia , Camundongos Endogâmicos C57BL , Células Ganglionares da Retina/efeitos dos fármacos
9.
Ecotoxicol Environ Saf ; 220: 112404, 2021 Sep 01.
Artigo em Inglês | MEDLINE | ID: mdl-34111660

RESUMO

Cadmium (Cd), chromium (Cr), lead (Pb), mercury (Hg) and arsenic (As) are potent toxicants to human health via dietary intake. It is imperative to establish accurate soil thresholds based on soil-plant transfer models and food safety standards for safe agricultural production. This study takes rice genotypes and soil properties into account to derive soil thresholds for five heavy metal(loid)s using the bioconcentration factors (BCF) and species sensitivity distribution (SSD) based on the food safety standard. The BCF generated from two paddy soils was calculated to investigate the sensitivity of heavy metal accumulation in nine rice cultivars in a greenhouse pot experiment. Then, empirical soil-plant transfer models were developed from a middle-sensitivity rice cultivar (Denong 2000, one selected from nine rice) grown in nineteen paddy soils with various soil properties under a proper exogenously metal(loid)s concentration gradient. After normalization, hazardous concentrations from the fifth percentile (HC5) were calculated from the SSD curves, and the derived soil thresholds were obtained from HC5 prediction models that based on the combination of pH and organic carbon (OC) or cation exchange capacity (CEC). The soil Cd threshold derived based on pH and organic carbon (pH < 7.5, OC ≥ 20 g kg-1) was 1.3-fold of those only considering pH, whereas the Pb threshold (pH > 6, CEC ≥ 20 cmolc kg-1) was 3.1 times lower than the current threshold. The derived thresholds for five elements were validated to be reliable through literature data and field experiments. The results suggested that deriving soil heavy metal(loid)s threshold using SSD method and local food safety standards is feasible and also applicable to other crops as well as other regions with potential health risks of toxic elements contamination in agricultural production.


Assuntos
Metais Pesados/normas , Oryza/crescimento & desenvolvimento , Poluentes do Solo/normas , Solo/normas , Arsênio/análise , Arsênio/normas , Cádmio/análise , Cádmio/normas , Cromo/análise , Cromo/normas , Produtos Agrícolas/crescimento & desenvolvimento , Produtos Agrícolas/normas , Inocuidade dos Alimentos , Humanos , Chumbo/análise , Chumbo/normas , Mercúrio/análise , Mercúrio/normas , Metais Pesados/análise , Oryza/química , Oryza/genética , Solo/química , Poluentes do Solo/análise
10.
Cereb Cortex ; 31(11): 4945-4957, 2021 Oct 01.
Artigo em Inglês | MEDLINE | ID: mdl-34023872

RESUMO

Attention-deficit/hyperactivity disorder (ADHD) has been reported exist abnormal topology structure in the brain network. However, these studies often treated the brain as a static monolithic structure, and dynamic characteristics were ignored. Here, we investigated how the dynamic network reconfiguration in ADHD patients differs from that in healthy people. Specifically, we acquired resting-state functional magnetic resonance imaging data from a public dataset including 40 ADHD patients and 50 healthy people. A novel model of a "time-varying multilayer network" and metrics of recruitment and integration were applied to describe group differences. The results showed that the integration scores of ADHD patients were significantly lower than those of controls at every level. The recruitment scores were lower than healthy people except for the whole-brain level. It is worth noting that the subcortical network and the thalamus in ADHD patients exhibited reduced alliance preference both within and between functional networks. In addition, we also found that recruitment and integration coefficients showed a significant correlation with symptom severity in some regions. Our results demonstrate that the capability to communicate within or between some functional networks is impaired in ADHD patients. These evidences provide a new opportunity for studying the characteristics of ADHD brain networks.

11.
Artigo em Inglês | MEDLINE | ID: mdl-33790549

RESUMO

Background: Home noninvasive positive pressure ventilation (NPPV) can be considered not only as an evidence-based treatment for stable hypercapnic chronic obstructive pulmonary disease (COPD) patients, but also as a predictor for detecting severe acute exacerbations of chronic obstructive pulmonary disease (AECOPD). Methods: In this retrospective observational study, we collected clinical exacerbations information and daily NPPV-related data in a cohort of COPD patients with home NPPV for 6 months. Daily changes in NPPV-related parameters' variability prior to AECOPD were examined using two-way repeated measures ANOVA and individual abnormal values (>75th or <25th percentile of individual baseline parameters) were calculated during 7-day pre-AECOPD period. Multivariate logistic regression was used to identify the independent risk factors associated with AECOPD that then were incorporated into the nomogram. Results: Between January 1, 2018, and January 1, 2020, a total of 102 patients were included and 31 (30.4%) participants experienced hospitalization (AECOPD group) within 6 months. Respiratory rate changed significantly from baseline at 1, 2 or 3 days prior to admission (p<0.001, respectively) in the AECOPD group. The number of days with abnormal values of daily usage, leaks, or tidal volume during the 7-day pre-AECOPD period in the AECOPD group was higher than in the stable group (p<0.001, respectively). On multivariate analysis, 7-day mean respiratory rate (OR 1.756, 95% CI 1.249-2.469), abnormal values of daily use (OR 1.918, 95% CI 1.253-2.934) and tidal volume (OR 2.081, 95% CI 1.380-3.140) within 7 days were independently associated with the risk of AECOPD. Incorporating these factors, the nomogram achieved good concordance indexes of 0.962. Conclusion: Seven-day mean respiratory rate, abnormal values of daily usage, leaks, and tidal volume within the 7-day pre-AECOPD period may be biomarkers for detection of AECOPD.


Assuntos
Ventilação não Invasiva , Doença Pulmonar Obstrutiva Crônica , Hospitalização , Humanos , Hipercapnia , Respiração com Pressão Positiva , Doença Pulmonar Obstrutiva Crônica/diagnóstico , Doença Pulmonar Obstrutiva Crônica/terapia
12.
Diabetes Care ; 44(6): 1324-1333, 2021 06.
Artigo em Inglês | MEDLINE | ID: mdl-33832957

RESUMO

OBJECTIVE: This study aimed to evaluate the efficacy and safety of mulberry twig alkaloids (Sangzhi alkaloids [SZ-A]) in the treatment of type 2 diabetes (T2D). RESEARCH DESIGN AND METHODS: This was a multicenter, randomized, double-blind, double-dummy, and parallel controlled noninferiority clinical trial that was conducted for 24 weeks. A total of 600 patients were randomly allocated to the SZ-A group (n = 360) or acarbose group (n = 240). The primary efficacy end point was the change of glycosylated hemoglobin (HbA1c) compared with baseline. In addition, adverse events (AEs), severe AEs (SAEs), treatment-related AEs (TAEs), and gastrointestinal disorders (GDs) were monitored. RESULTS: After treatment for 24 weeks, the change in HbA1c was -0.93% (95% CI -1.03 to -0.83) (-10.2 mmol/mol [-11.3 to -9.1]) and -0.87% (-0.99 to -0.76) (-9.5 mmol/mol [-10.8 to -8.3]) in the SZ-A and acarbose groups, respectively, and the least squares mean difference was -0.05% (95% CI -0.18 to 0.07) (-0.5 mmol/mol [-2.0 to 0.8]) between the two groups, with no significant difference on the basis of covariance analysis (P > 0.05). The incidence of TAEs and GDs was significantly lower in the SZ-A group than the acarbose group (P < 0.01), but no differences for AEs or SAEs between the two groups were observed (P > 0.05). CONCLUSIONS: SZ-A exhibited equivalent hypoglycemic effects to acarbose in patients with T2D. Nevertheless, the incidence of TAEs and GDs was lower following SZ-A treatment than acarbose treatment, suggesting good safety.


Assuntos
Alcaloides , Diabetes Mellitus Tipo 2 , Morus , Alcaloides/uso terapêutico , Glicemia , Diabetes Mellitus Tipo 2/tratamento farmacológico , Método Duplo-Cego , Quimioterapia Combinada , Hemoglobina A Glicada/análise , Humanos , Hipoglicemiantes , Morus/química , Comprimidos , Resultado do Tratamento
13.
Proc Natl Acad Sci U S A ; 118(16)2021 04 20.
Artigo em Inglês | MEDLINE | ID: mdl-33846246

RESUMO

The high northern latitudes (>50°) experienced a pronounced surface stilling (i.e., decline in winds) with climate change. As a drying factor, the influences of changes in winds on the date of autumn foliar senescence (DFS) remain largely unknown and are potentially important as a mechanism explaining the interannual variability of autumn phenology. Using 183,448 phenological observations at 2,405 sites, long-term site-scale water vapor and carbon dioxide flux measurements, and 34 y of satellite greenness data, here we show that the decline in winds is significantly associated with extended DFS and could have a relative importance comparable with temperature and precipitation effects in contributing to the DFS trends. We further demonstrate that decline in winds reduces evapotranspiration, which results in less soil water losses and consequently more favorable growth conditions in late autumn. In addition, declining winds also lead to less leaf abscission damage which could delay leaf senescence and to a decreased cooling effect and therefore less frost damage. Our results are potentially useful for carbon flux modeling because an improved algorithm based on these findings projected overall widespread earlier DFS than currently expected by the end of this century, contributing potentially to a positive feedback to climate.

14.
Genome Biol ; 22(1): 80, 2021 03 10.
Artigo em Inglês | MEDLINE | ID: mdl-33691754

RESUMO

BACKGROUND: Millions of nucleotide variants are identified through cancer genome sequencing and it is clinically important to identify the pathogenic variants among them. By introducing base substitutions at guide RNA target regions in the genome, CRISPR-Cas9-based base editors provide the possibility for evaluating a large number of variants in their genomic context. However, the variability in editing efficiency and the complexity of outcome mapping are two existing problems for assigning guide RNA effects to variants in base editing screens. RESULTS: To improve the identification of pathogenic variants, we develop a framework to combine base editing screens with sgRNA efficiency and outcome mapping. We apply the method to evaluate more than 9000 variants across all the exons of BRCA1 and BRCA2 genes. Our efficiency-corrected scoring model identifies 910 loss-of-function variants for BRCA1/2, including 151 variants in the noncoding part of the genes such as the 5' untranslated regions. Many of them are identified in cancer patients and are reported as "benign/likely benign" or "variants of uncertain significance" by clinicians. Our data suggest a need to re-evaluate their clinical significance, which may be helpful for risk assessment and treatment of breast and ovarian cancer. CONCLUSIONS: Our results suggest that base editing screens with efficiency correction is a powerful strategy to identify pathogenic variants in a high-throughput manner. Applying this strategy to assess variants in both coding and noncoding regions of the genome could have a direct impact on the interpretation of cancer variants.

15.
ISME J ; 15(9): 2561-2573, 2021 09.
Artigo em Inglês | MEDLINE | ID: mdl-33712697

RESUMO

Understanding the effects of changing climate and long-term human activities on soil organic carbon (SOC) and the mediating roles of microorganisms is critical to maintain soil C stability in agricultural ecosystem. Here, we took samples from a long-term soil transplantation experiment, in which large transects of Mollisol soil in a cold temperate region were translocated to warm temperate and mid-subtropical regions to simulate different climate conditions, with a fertilization treatment on top. This study aimed to understand fertilization effect on SOC and the role of soil microorganisms featured after long-term community incubation in warm climates. After 12 years of soil transplantation, fertilization led to less reduction of SOC, in which aromatic C increased and the consumption of O-alkyl C and carbonyl C decreased. Soil live microbes were analyzed using propidium monoazide to remove DNAs from dead cells, and their network modulization explained 60.4% of variations in soil labile C. Single-cell Raman spectroscopy combined with D2O isotope labeling indicated a higher metabolic activity of live microbes to use easily degradable C after soil transplantation. Compared with non-fertilization, there was a significant decrease in soil α- and ß-glucosidase and delay on microbial growth with fertilization in warmer climate. Moreover, fertilization significantly increased microbial necromass as indicated by amino sugar content, and its contribution to soil resistant C reached 22.3%. This study evidentially highlights the substantial contribution of soil microbial metabolism and necromass to refractory C of SOC with addition of nutrients in the long-term.


Assuntos
Carbono , Solo , Ecossistema , Fertilização , Fertilizantes , Humanos , Microbiologia do Solo
16.
Theranostics ; 11(10): 4585-4598, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-33754015

RESUMO

Background: The genomic spectrum of biliary tract carcinoma (BTC) has been characterized and is associated with distinct anatomic and etiologic subtypes, yet limited studies have linked genomic alterations with personalized therapies in BTC patients. Methods: This study analyzed 803 patients with BTC:164 with gallbladder cancer, 475 with intrahepatic cholangiocarcinoma (ICC) and 164 with extrahepatic cholangiocarcinoma. We determined genomic alterations, mutational signatures related to etiology and histopathology and prognostic biomarkers. Personalized targeted therapies for patients harboring potentially actionable targets (PATs) were investigated. Results: The median tumor mutation burden (TMB) was 1.23 Mut/Mb, with 4.1% of patients having hypermutated BTCs. Unlike the results obtained from the Western population, the most frequently altered cancer-related genes in our cohort included TP53 (53%), KRAS (26%), ARID1A (18%), LRP1B (14%) and CDKN2A (14%). Germline mutations occurred mostly in DNA damage repair genes. Notably, 35.8% of the ICCs harbored aristolochic acid related signatures and an elevated TMB. TP53 and KRAS mutations and amplified 7q31.2 were demonstrated to negatively affect patient prognosis. Moreover, 19 genes were proposed to be PATs in BTCs, with 25.4% of patients harboring these PATs. Forty-six patients received PAT-matched targeted therapies, achieving a 26.1% objective response rate; the median progression-free survival (PFS) was 5.0 months, with 56.8% of patients obtaining PFS benefits. Conclusions: Extensive genomic diversity and heterogeneity were observed among BTC patients, with contributions according to potential etiology exposures, anatomical subtypes and clinicopathological characteristics. We also demonstrated that patients with refractory BTCs who have PATs can derive considerable benefit from receiving a matched therapy, initiating further prospective clinical trials guided by molecular profiling among this aggressive cancer.


Assuntos
Neoplasias dos Ductos Biliares/genética , Ductos Biliares Intra-Hepáticos , Carcinoma/genética , Colangiocarcinoma/genética , Neoplasias da Vesícula Biliar/genética , Idoso , Neoplasias dos Ductos Biliares/patologia , Carcinoma/patologia , Colangiocarcinoma/patologia , Inibidor p16 de Quinase Dependente de Ciclina/genética , Variações do Número de Cópias de DNA , Proteínas de Ligação a DNA/genética , Feminino , Neoplasias da Vesícula Biliar/patologia , Genômica , Humanos , Mutação INDEL , Masculino , Pessoa de Meia-Idade , Terapia de Alvo Molecular , Mutação , Estadiamento de Neoplasias , Polimorfismo de Nucleotídeo Único , Medicina de Precisão , Proteínas Proto-Oncogênicas p21(ras)/genética , Receptores de LDL/genética , Fatores de Transcrição/genética , Proteína Supressora de Tumor p53/genética , Sequenciamento Completo do Exoma
17.
Genomics Proteomics Bioinformatics ; 19(1): 64-79, 2021 02.
Artigo em Inglês | MEDLINE | ID: mdl-33716151

RESUMO

Although DNA 5-hydroxymethylcytosine (5hmC) is recognized as an important epigenetic mark in cancer, its precise role in lymph node metastasis remains elusive. In this study, we investigated how 5hmC associates with lymph node metastasis in breast cancer. Accompanying with high expression of TET1 and TET2 proteins, large numbers of genes in the metastasis-positive primary tumors exhibit higher 5hmC levels than those in the metastasis-negative primary tumors. In contrast, the TET protein expression and DNA 5hmC decrease significantly within the metastatic lesions in the lymph nodes compared to those in their matched primary tumors. Through genome-wide analysis of 8 sets of primary tumors, we identified 100 high-confidence metastasis-associated 5hmC signatures, and it is found that increased levels of DNA 5hmC and gene expression of MAP7D1 associate with high risk of lymph node metastasis. Furthermore, we demonstrate that MAP7D1, regulated by TET1, promotes tumor growth and metastasis. In conclusion, the dynamic 5hmC profiles during lymph node metastasis suggest a link between DNA 5hmC and lymph node metastasis. Meanwhile, the role of MAP7D1 in breast cancer progression suggests that the metastasis-associated 5hmC signatures are potential biomarkers to predict the risk for lymph node metastasis, which may serve as diagnostic and therapeutic targets for metastatic breast cancer.


Assuntos
Neoplasias da Mama , Proteínas Associadas aos Microtúbulos/genética , 5-Metilcitosina/análogos & derivados , Neoplasias da Mama/genética , Epigenômica , Feminino , Humanos , Metástase Linfática , Oxigenases de Função Mista , Proteínas Proto-Oncogênicas/genética
19.
J Mol Recognit ; 34(7): e2890, 2021 07.
Artigo em Inglês | MEDLINE | ID: mdl-33620127

RESUMO

The specific regulation of PTPN18 protein to three HER2 phospho-peptides has been studied by molecular dynamics simulations and free energy calculations. The results revealed that the three HER2 phospho-peptides binding to the PTPN18 catalytic domain is energetically favorable due to substrate specificity of PTPN18, and moreover, the PTPN18 protein have significantly higher affinity to pY1248 peptide (-45.22 kcal/mol) than that of pY1112 (-25.3 kcal/mol) and pY1196 (-31.86 kcal/mol) peptides. Further, the binding of HER2 phospho-peptides to PTPN18 have also caused the closure of WPD-loop with the decrease of the centroid distances between the P-loop and the WPD loop. The WPD-loop closure of PTPN18 relates directly to the new hydrogen bond and hydrophobic interaction formations between the residues Tyr62, Asp64, Val65, Ala231, Arg235, and Ala273 in PTPN18 and Tyr(PO3) in the HER2 phospho-peptides, which suggests that these key residues would contribute to the specific regulation of PTPN18 to the substrates. The correlation analysis revealed the allosteric communication networks from the pY binding loop to the WPD loop through the structural change and the residue interactions in PTPN18. These results will be helpful to understand the specific regulation through the allosteric communication network in the PTPN18 catalytic domain.

20.
Food Chem ; 347: 129013, 2021 Jun 15.
Artigo em Inglês | MEDLINE | ID: mdl-33482481

RESUMO

The effective analysis of cephalosporin antibiotics in food animals has attracted considerable attention. Herein, a high-performance liquid chromatograph equipped with a UV method based on molecularly imprinted-solid phase extraction (MISPE-HPLC-UV) was developed for preconcentration, cleanup and determination of ceftiofur sodium (CTFS) in food samples. In this method, an eco-friendly molecularly imprinted polymer (MIP) was synthesized and employed as an adsorbent, which exhibited excellent selectivity towards CTFS in water, and adsorption equilibrium could be reached within 1 h. Under the optimized conditions, good linearity was obtained for CTFS in the range of 0.005-1.0 mg L-1 with a lower LOD of 0.0015 mg L-1, and the average recoveries were higher than 91.9% (RSD less than 8.5%) at three spiked levels in milk, chicken, pork and beef samples. After 20 cycles, the recovery of the MISPE cartridge for CTFS was still higher than 95%, which proved that the MISPE-HPLC-UV method was highly sensitive and selective for the analysis of CTFS in food samples.


Assuntos
Cefalosporinas/análise , Cromatografia Líquida de Alta Pressão/métodos , Análise de Alimentos , Extração em Fase Sólida/métodos , Animais , Carne/análise , Leite/química
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