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1.
Cell ; 183(6): 1479-1495.e20, 2020 12 10.
Artigo em Inglês | MEDLINE | ID: mdl-33171100

RESUMO

We present an integrated analysis of the clinical measurements, immune cells, and plasma multi-omics of 139 COVID-19 patients representing all levels of disease severity, from serial blood draws collected during the first week of infection following diagnosis. We identify a major shift between mild and moderate disease, at which point elevated inflammatory signaling is accompanied by the loss of specific classes of metabolites and metabolic processes. Within this stressed plasma environment at moderate disease, multiple unusual immune cell phenotypes emerge and amplify with increasing disease severity. We condensed over 120,000 immune features into a single axis to capture how different immune cell classes coordinate in response to SARS-CoV-2. This immune-response axis independently aligns with the major plasma composition changes, with clinical metrics of blood clotting, and with the sharp transition between mild and moderate disease. This study suggests that moderate disease may provide the most effective setting for therapeutic intervention.


Assuntos
COVID-19 , Genômica , RNA-Seq , SARS-CoV-2 , Análise de Célula Única , Adolescente , Adulto , Idoso , Idoso de 80 Anos ou mais , COVID-19/sangue , COVID-19/imunologia , Feminino , Humanos , Masculino , Pessoa de Meia-Idade , SARS-CoV-2/imunologia , SARS-CoV-2/metabolismo , Índice de Gravidade de Doença
2.
Nature ; 567(7747): 257-261, 2019 03.
Artigo em Inglês | MEDLINE | ID: mdl-30814741

RESUMO

Hepatocellular carcinoma is the third leading cause of deaths from cancer worldwide. Infection with the hepatitis B virus is one of the leading risk factors for developing hepatocellular carcinoma, particularly in East Asia1. Although surgical treatment may be effective in the early stages, the five-year overall rate of survival after developing this cancer is only 50-70%2. Here, using proteomic and phospho-proteomic profiling, we characterize 110 paired tumour and non-tumour tissues of clinical early-stage hepatocellular carcinoma related to hepatitis B virus infection. Our quantitative proteomic data highlight heterogeneity in early-stage hepatocellular carcinoma: we used this to stratify the cohort into the subtypes S-I, S-II and S-III, each of which has a different clinical outcome. S-III, which is characterized by disrupted cholesterol homeostasis, is associated with the lowest overall rate of survival and the greatest risk of a poor prognosis after first-line surgery. The knockdown of sterol O-acyltransferase 1 (SOAT1)-high expression of which is a signature specific to the S-III subtype-alters the distribution of cellular cholesterol, and effectively suppresses the proliferation and migration of hepatocellular carcinoma. Finally, on the basis of a patient-derived tumour xenograft mouse model of hepatocellular carcinoma, we found that treatment with avasimibe, an inhibitor of SOAT1, markedly reduced the size of tumours that had high levels of SOAT1 expression. The proteomic stratification of early-stage hepatocellular carcinoma presented in this study provides insight into the tumour biology of this cancer, and suggests opportunities for personalized therapies that target it.


Assuntos
Carcinoma Hepatocelular/tratamento farmacológico , Carcinoma Hepatocelular/metabolismo , Neoplasias Hepáticas/tratamento farmacológico , Neoplasias Hepáticas/metabolismo , Terapia de Alvo Molecular/tendências , Proteômica , Animais , Carcinoma Hepatocelular/patologia , Carcinoma Hepatocelular/virologia , Processos de Crescimento Celular , Movimento Celular , Vírus da Hepatite B/patogenicidade , Humanos , Neoplasias Hepáticas/patologia , Neoplasias Hepáticas/virologia , Masculino , Camundongos , Camundongos Endogâmicos NOD , Camundongos SCID , Estadiamento de Neoplasias , Prognóstico , Esterol O-Aciltransferase/genética
3.
BMC Bioinformatics ; 20(Suppl 7): 195, 2019 May 01.
Artigo em Inglês | MEDLINE | ID: mdl-31074374

RESUMO

BACKGROUND: Lipid metabolism reprogramming is a hallmark for tumor which contributes to tumorigenesis and progression, but the commonality and difference of lipid metabolism among pan-cancer is not fully investigated. Increasing evidences suggest that the alterations in tumor metabolism, including metabolite abundance and accumulation of metabolic products, lead to local immunosuppression in the tumor microenvironment. An integrated analysis of lipid metabolism in cancers from different tissues using multiple omics data may provide novel insight into the understanding of tumorigenesis and progression. RESULTS: Through systematic analysis of the multiple omics data from TCGA, we found that the most-widely altered lipid metabolism pathways in pan-cancer are fatty acid metabolism, arachidonic acid metabolism, cholesterol metabolism and PPAR signaling. Gene expression profiles of fatty acid metabolism show commonalities across pan-cancer, while the alteration in cholesterol metabolism and arachidonic acid metabolism differ with tissue origin, suggesting tissue specific lipid metabolism features in different tumor types. An integrated analysis of gene expression, DNA methylation and mutations revealed factors that regulate gene expression, including the differentially methylated sites and mutations of the lipid genes, as well as mutation and differential expression of the up-stream transcription factors for the lipid metabolism pathways. Correlation analysis of the proportion of immune cells in the tumor microenvironment and the expression of lipid metabolism genes revealed immune-related differentially expressed lipid metabolic genes, indicating the potential crosstalk between lipid metabolism and immune response. Genes related to lipid metabolism and immune response that are associated with poor prognosis were discovered including HMGCS2, GPX2 and CD36, which may provide clues for tumor biomarkers or therapeutic targets. CONCLUSIONS: Our study provides an integrated analysis of lipid metabolism in pan-cancer, highlights the perturbation of key metabolism processes in tumorigenesis and clarificates the regulation mechanism of abnormal lipid metabolism and effects of lipid metabolism on tumor immune microenvironment. This study also provides new clues for biomarkers or therapeutic targets of lipid metabolism in tumors.


Assuntos
Biomarcadores Tumorais/genética , Metilação de DNA , Regulação Neoplásica da Expressão Gênica , Metabolismo dos Lipídeos/genética , Neoplasias/genética , Neoplasias/metabolismo , Microambiente Tumoral/imunologia , Biologia Computacional/métodos , Perfilação da Expressão Gênica , Humanos , Mutação , Neoplasias/imunologia , Neoplasias/patologia , Transcriptoma , Microambiente Tumoral/genética
4.
Neurosignals ; 22(2): 65-78, 2014.
Artigo em Inglês | MEDLINE | ID: mdl-25300231

RESUMO

The small- and intermediate-conductance Ca(2+)-activated potassium (SK/IK) channels play important roles in the regulation of excitable cells in both the central nervous and cardiovascular systems. Evidence from animal models has implicated SK/IK channels in neurological conditions such as ataxia and alcohol use disorders. Further, genome-wide association studies have suggested that cardiovascular abnormalities such as arrhythmias and hypertension are associated with single nucleotide polymorphisms that occur within the genes encoding the SK/IK channels. The Ca(2+) sensitivity of the SK/IK channels stems from a constitutively bound Ca(2+)-binding protein: calmodulin. Small-molecule positive modulators of SK/IK channels have been developed over the past decade, and recent structural studies have revealed that the binding pocket of these positive modulators is located at the interface between the channel and calmodulin. SK/IK channel positive modulators can potentiate channel activity by enhancing the coupling between Ca(2+) sensing via calmodulin and mechanical opening of the channel. Here, we review binding pocket studies that have provided structural insight into the mechanism of action for SK/IK channel positive modulators. These studies lay the foundation for structure-based drug discovery efforts that can identify novel SK/IK channel positive modulators.


Assuntos
Calmodulina/metabolismo , Sistema Cardiovascular/metabolismo , Sistema Nervoso Central/metabolismo , Descoberta de Drogas , Canais de Potássio Ativados por Cálcio de Condutância Intermediária/metabolismo , Canais de Potássio Ativados por Cálcio de Condutância Baixa/metabolismo , Animais , Humanos
5.
iScience ; 27(9): 110755, 2024 Sep 20.
Artigo em Inglês | MEDLINE | ID: mdl-39280607

RESUMO

Acute myeloid leukemia (AML) is a highly aggressive and heterogeneous disease, underscoring the need for improved therapeutic options and methods to optimally predict responses. With the wealth of available data resources, including clinical features, multiomics analysis, and ex vivo drug screening from AML patients, development of drug response prediction models has become feasible. Knowledge graphs (KGs) embed the relationships between different entities or features, allowing for explanation of a wide breadth of drug sensitivity and resistance mechanisms. We designed AML drug response prediction models guided by KGs. Our models included engineered features, relative gene expression between marker genes for each drug and regulators (e.g., transcription factors). We identified relative gene expression of FGD4-MIR4519, NPC2-GATA2, and BCL2-NFKB2 as predictive features for venetoclax ex vivo drug response. The KG-guided models provided high accuracy in independent test sets, overcame potential platform batch effects, and provided candidate drug sensitivity biomarkers for further validation.

6.
bioRxiv ; 2024 Sep 19.
Artigo em Inglês | MEDLINE | ID: mdl-39345612

RESUMO

Gene regulatory network (GRNs) models provide mechanistic understanding of the gene regulations and interactions that control various aspects of cellular behaviors. While researchers have constructed GRNs to model specific sets of gene regulations or interactions, little work has been made to integrate or merge these models into larger, more comprehensive ones that could encompass more genes, and improve the accuracy of predicting biological processes. Here, we present a workflow for merging logical GRN models, which requires sequential steps including model standardization, reproducing, merging and evaluations, and demonstrate its application in acute myeloid leukemia (AML) study. We demonstrate the feasibility and benefits of model merging by integrating two pairs of published models. Our integrated models were able to retain similar accuracy of the original publications, while increasing the coverage and explainability of the biological system. This approach highlights the integration of logical models in advancing system biology and enhancing the understanding of complex diseases.

7.
Front Digit Health ; 6: 1336050, 2024.
Artigo em Inglês | MEDLINE | ID: mdl-38343907

RESUMO

Introduction: A digital twin is a virtual representation of a patient's disease, facilitating real-time monitoring, analysis, and simulation. This enables the prediction of disease progression, optimization of care delivery, and improvement of outcomes. Methods: Here, we introduce a digital twin framework for type 2 diabetes (T2D) that integrates machine learning with multiomic data, knowledge graphs, and mechanistic models. By analyzing a substantial multiomic and clinical dataset, we constructed predictive machine learning models to forecast disease progression. Furthermore, knowledge graphs were employed to elucidate and contextualize multiomic-disease relationships. Results and discussion: Our findings not only reaffirm known targetable disease components but also spotlight novel ones, unveiled through this integrated approach. The versatile components presented in this study can be incorporated into a digital twin system, enhancing our grasp of diseases and propelling the advancement of precision medicine.

8.
Clin Cancer Res ; 30(12): 2659-2671, 2024 Jun 14.
Artigo em Inglês | MEDLINE | ID: mdl-38619278

RESUMO

PURPOSE: The inherent genetic heterogeneity of acute myeloid leukemia (AML) has challenged the development of precise and effective therapies. The objective of this study was to elucidate the genomic basis of drug resistance or sensitivity, identify signatures for drug response prediction, and provide resources to the research community. EXPERIMENTAL DESIGN: We performed targeted sequencing, high-throughput drug screening, and single-cell genomic profiling on leukemia cell samples derived from patients with AML. Statistical approaches and machine learning models were applied to identify signatures for drug response prediction. We also integrated large public datasets to understand the co-occurring mutation patterns and further investigated the mutation profiles in the single cells. The features revealed in the co-occurring or mutual exclusivity pattern were further subjected to machine learning models. RESULTS: We detected genetic signatures associated with sensitivity or resistance to specific agents, and identified five co-occurring mutation groups. The application of single-cell genomic sequencing unveiled the co-occurrence of variants at the individual cell level, highlighting the presence of distinct subclones within patients with AML. Using the mutation pattern for drug response prediction demonstrates high accuracy in predicting sensitivity to some drug classes, such as MEK inhibitors for RAS-mutated leukemia. CONCLUSIONS: Our study highlights the importance of considering the gene mutation patterns for the prediction of drug response in AML. It provides a framework for categorizing patients with AML by mutations that enable drug sensitivity prediction.


Assuntos
Resistencia a Medicamentos Antineoplásicos , Leucemia Mieloide Aguda , Mutação , Humanos , Leucemia Mieloide Aguda/genética , Leucemia Mieloide Aguda/tratamento farmacológico , Resistencia a Medicamentos Antineoplásicos/genética , Antineoplásicos/uso terapêutico , Antineoplásicos/farmacologia , Análise de Célula Única/métodos , Aprendizado de Máquina , Sequenciamento de Nucleotídeos em Larga Escala , Masculino
9.
J Am Chem Soc ; 134(15): 6720-31, 2012 Apr 18.
Artigo em Inglês | MEDLINE | ID: mdl-22316159

RESUMO

ErbB4, a receptor tyrosine kinase of the ErbB family, plays crucial roles in cell growth and differentiation, especially in the development of the heart and nervous system. Ligand binding to its extracellular region could modulate the activation process. To understand the mechanism of ErbB4 activation induced by ligand binding, we performed one microsecond molecular dynamics (MD) simulations on the ErbB4 extracellular region (ECR) with and without its endogenous ligand neuregulin1ß (NRG1ß). The conformational transition of the ECR-ErbB4/NRG1ß complex from a tethered inactive conformation to an extended active-like form has been observed, while such large and function-related conformational change has not been seen in the simulation on the ECR-ErbB4, suggesting that ligand binding is indeed the active inducing force for the conformational transition and further dimerization. On the basis of MD simulations and principal component analysis, we constructed a rough energy landscape for the conformational transition of ECR-ErbB4/NRG1ß complex, suggesting that the conformational change from the inactive state to active-like state involves a stable conformation. The energy barrier for the tether opening was estimated as ~2.7 kcal/mol, which is very close to the experimental value (1-2 kcal/mol) reported for ErbB1. On the basis of the simulation results, an atomic mechanism for the ligand-induced activation of ErbB4 was postulated. The present MD simulations provide a new insight into the conformational changes underlying the activation of ErbB4.


Assuntos
Receptores ErbB/química , Simulação de Dinâmica Molecular , Neuregulina-1/química , Transição de Fase , Ligantes , Conformação Proteica , Receptor ErbB-4 , Termodinâmica
10.
iScience ; 25(5): 104190, 2022 May 20.
Artigo em Inglês | MEDLINE | ID: mdl-35479398

RESUMO

Patients with cancer with different molecular characterization and subtypes result in different response to anticancer therapeutics and survival. To identify features that are associated with prognosis is essential to precision medicine by providing clues for target identification, drug discovery. Here, we developed a tumor online prognostic analysis platform (ToPP) which integrated eight multi-omics features and clinical data from 68 cancer projects. It provides multiple approaches for customized prognostic studies, including 1) Prognostic analysis based on multi-omics features and clinical characteristics; 2) Automatic construction of prognostic model; 3) Pancancer prognostic analysis in multi-omics data; 4) Explore the impact of different levels of feature combinations on patient prognosis; 5) More sophisticated prognostic analysis according to regulatory network. ToPP provides a comprehensive source and easy-to-use interface for tumor prognosis research, with one-stop service of multi-omics, subtyping, and online prognostic modeling. The web server is freely available at http://www.biostatistics.online/topp/index.php.

11.
Cell Rep ; 38(3): 110269, 2022 01 18.
Artigo em Inglês | MEDLINE | ID: mdl-35045296

RESUMO

Cells are complex systems in which many functions are performed by different genetically defined and encoded functional modules. To systematically understand how these modules respond to drug or genetic perturbations, we develop a functional module states framework. Using this framework, we (1) define the drug-induced transcriptional state space for breast cancer cell lines using large public gene expression datasets and reveal that the transcriptional states are associated with drug concentration and drug targets, (2) identify potential targetable vulnerabilities through integrative analysis of transcriptional states after drug treatment and gene knockdown-associated cancer dependency, and (3) use functional module states to predict transcriptional state-dependent drug sensitivity and build prediction models for drug response. This approach demonstrates a similar prediction performance as approaches using high-dimensional gene expression values, with the added advantage of more clearly revealing biologically relevant transcriptional states and key regulators.


Assuntos
Neoplasias da Mama , Perfilação da Expressão Gênica/métodos , Aprendizado de Máquina , Terapia de Alvo Molecular , Transcriptoma , Feminino , Humanos
12.
F1000Res ; 11: 493, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-36761837

RESUMO

Synthetic lethal interactions (SLIs), genetic interactions in which the simultaneous inactivation of two genes leads to a lethal phenotype, are promising targets for therapeutic intervention in cancer, as exemplified by the recent success of PARP inhibitors in treating BRCA1/2-deficient tumors. We present SL-Cloud, a new component of the Institute for Systems Biology Cancer Gateway in the Cloud (ISB-CGC), that provides an integrated framework of cloud-hosted data resources and curated workflows to enable facile prediction of SLIs. This resource addresses two main challenges related to SLI inference: the need to wrangle and preprocess large multi-omic datasets and the availability of multiple comparable prediction approaches. SL-Cloud enables customizable computational inference of SLIs and testing of prediction approaches across multiple datasets. We anticipate that cancer researchers will find utility in this tool for discovery of SLIs to support further investigation into potential drug targets for anticancer therapies.


Assuntos
Computação em Nuvem , Neoplasias , Humanos , Neoplasias/genética , Biologia de Sistemas , Multiômica
13.
Oncogene ; 41(24): 3355-3369, 2022 06.
Artigo em Inglês | MEDLINE | ID: mdl-35538224

RESUMO

The oncogene Ras and the tumor suppressor gene p53 are frequently co-mutated in human cancer and mutations in Ras and p53 can cooperate to generate a more malignant cell state. To discover novel druggable targets for cancers carrying co-mutations in Ras and p53, we performed arrayed, kinome focused siRNA and oncology drug phenotypic screening utilizing a set of syngeneic Ras mutant squamous cell carcinoma (SCC) cell lines that also carried co-mutations in selected p53 pathway genes. These cell lines were derived from SCCs from carcinogen-treated inbred mice which harbored germline deletions or mutations in Trp53, p19Arf, Atm, or Prkdc. Both siRNA and drug phenotypic screening converge to implicate the phosphoinositol kinases, receptor tyrosine kinases, MAP kinases, as well as cell cycle and DNA damage response genes as targetable dependencies in SCC. Differences in functional kinome profiles between Ras mutant cell lines reflect incomplete penetrance of Ras synthetic lethal kinases and indicate that co-mutations cause a rewiring of survival pathways in Ras mutant tumors. This study describes the functional kinomic landscape of Ras/p53 mutant chemically-induced squamous cell carcinoma in both the baseline unperturbed state and following DNA damage and nominates candidate therapeutic targets, including the Nek4 kinase, for further development.


Assuntos
Carcinoma de Células Escamosas , Proteína Supressora de Tumor p53 , Proteínas ras , Animais , Carcinoma de Células Escamosas/enzimologia , Carcinoma de Células Escamosas/genética , Carcinoma de Células Escamosas/patologia , Linhagem Celular Tumoral , Inibidor p16 de Quinase Dependente de Ciclina/genética , Humanos , Camundongos , Mutação , RNA Interferente Pequeno , Proteína Supressora de Tumor p53/genética , Proteína Supressora de Tumor p53/metabolismo , Proteínas ras/genética
14.
Clin Transl Sci ; 15(8): 1848-1855, 2022 08.
Artigo em Inglês | MEDLINE | ID: mdl-36125173

RESUMO

Within clinical, biomedical, and translational science, an increasing number of projects are adopting graphs for knowledge representation. Graph-based data models elucidate the interconnectedness among core biomedical concepts, enable data structures to be easily updated, and support intuitive queries, visualizations, and inference algorithms. However, knowledge discovery across these "knowledge graphs" (KGs) has remained difficult. Data set heterogeneity and complexity; the proliferation of ad hoc data formats; poor compliance with guidelines on findability, accessibility, interoperability, and reusability; and, in particular, the lack of a universally accepted, open-access model for standardization across biomedical KGs has left the task of reconciling data sources to downstream consumers. Biolink Model is an open-source data model that can be used to formalize the relationships between data structures in translational science. It incorporates object-oriented classification and graph-oriented features. The core of the model is a set of hierarchical, interconnected classes (or categories) and relationships between them (or predicates) representing biomedical entities such as gene, disease, chemical, anatomic structure, and phenotype. The model provides class and edge attributes and associations that guide how entities should relate to one another. Here, we highlight the need for a standardized data model for KGs, describe Biolink Model, and compare it with other models. We demonstrate the utility of Biolink Model in various initiatives, including the Biomedical Data Translator Consortium and the Monarch Initiative, and show how it has supported easier integration and interoperability of biomedical KGs, bringing together knowledge from multiple sources and helping to realize the goals of translational science.


Assuntos
Reconhecimento Automatizado de Padrão , Ciência Translacional Biomédica , Conhecimento
15.
Clin Transl Sci ; 2022 May 25.
Artigo em Inglês | MEDLINE | ID: mdl-35611543

RESUMO

Clinical, biomedical, and translational science has reached an inflection point in the breadth and diversity of available data and the potential impact of such data to improve human health and well-being. However, the data are often siloed, disorganized, and not broadly accessible due to discipline-specific differences in terminology and representation. To address these challenges, the Biomedical Data Translator Consortium has developed and tested a pilot knowledge graph-based "Translator" system capable of integrating existing biomedical data sets and "translating" those data into insights intended to augment human reasoning and accelerate translational science. Having demonstrated feasibility of the Translator system, the Translator program has since moved into development, and the Translator Consortium has made significant progress in the research, design, and implementation of an operational system. Herein, we describe the current system's architecture, performance, and quality of results. We apply Translator to several real-world use cases developed in collaboration with subject-matter experts. Finally, we discuss the scientific and technical features of Translator and compare those features to other state-of-the-art, biomedical graph-based question-answering systems.

16.
Biophys J ; 99(12): 4003-11, 2010 Dec 15.
Artigo em Inglês | MEDLINE | ID: mdl-21156143

RESUMO

The principal role of acetylcholinesterase is termination of nerve impulse transmission at cholinergic synapses, by rapid hydrolysis of the neurotransmitter acetylcholine to acetate and choline. Its active site is buried at the bottom of a deep and narrow gorge, at the rim of which is found a second anionic site, the peripheral anionic site. The fact that the active site is so deeply buried has raised cogent questions as to how rapid traffic of substrate and products occurs in such a confined environment. Various theoretical and experimental approaches have been used to solve this problem. Here, multiple conventional molecular dynamics simulations have been performed to investigate the clearance of the product, thiocholine, from the active-site gorge of acetylcholinesterase. Our results indicate that thiocholine is released from the peripheral anionic site via random pathways, while three exit routes appear to be favored for its release from the active site, namely, along the axis of the active-site gorge, and through putative back- and side-doors. The back-door pathway is that via which thiocholine exits most frequently. Our results are in good agreement with kinetic and kinetic-crystallography studies. We propose the use of multiple molecular dynamics simulations as a fast yet accurate complementary tool in structural studies of enzymatic trafficking.


Assuntos
Acetilcolinesterase/química , Acetilcolinesterase/metabolismo , Domínio Catalítico , Simulação de Dinâmica Molecular , Tiocolina/metabolismo , Torpedo/metabolismo , Animais , Ânions , Biocatálise , Transporte Biológico , Proteínas Mutantes/química , Proteínas Mutantes/metabolismo , Fenilalanina/metabolismo , Maleabilidade , Eletricidade Estática , Fatores de Tempo , Triptofano/metabolismo
17.
Microbiology (Reading) ; 156(Pt 10): 3194-3202, 2010 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-20656778

RESUMO

The emergence of multi-drug-resistant strains of Staphylococcus epidermidis emphasizes the need to develop new antibiotics. The unique and essential role of the peptide deformylase (PDF) in catalysing the removal of the N-terminal formyl group from newly synthesized polypeptides in eubacteria makes it an attractive antibacterial drug target. In the present study, both deformylase homologues from S. epidermidis (SePDF-1 and SePDF-2) were cloned and expressed, and their enzymic activities were characterized. Co(2+)-substituted SePDF-1 exhibited much higher enzymic activity (k(cat)/K(m) 6.3 × 10(4) M(-1) s(-1)) than those of Ni(2+)- and Zn(2+)-substituted SePDF-1, and SePDF-1 showed much weaker binding ability towards Ni(2+) than towards Co(2+) and Zn(2+), which is different from PDF in Staphylococcus aureus (SaPDF), although they share 80 % amino-acid sequence identity. The determined crystal structure of SePDF-1 was similar to that of (SaPDF), except for differences in the metal-binding sites. The other deformylase homologue, SePDF-2, was shown to have no peptide deformylase activity; the function of SePDF-2 needs to be further investigated.


Assuntos
Amidoidrolases/metabolismo , Proteínas de Bactérias/metabolismo , Staphylococcus epidermidis/enzimologia , Amidoidrolases/genética , Motivos de Aminoácidos , Proteínas de Bactérias/genética , Sítios de Ligação , Clonagem Molecular , Cobalto/metabolismo , Modelos Moleculares , Mutagênese Sítio-Dirigida , Níquel/metabolismo , Homologia de Sequência de Aminoácidos , Staphylococcus epidermidis/genética , Zinco/metabolismo
18.
Front Mol Biosci ; 7: 53, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32391377

RESUMO

The classification of immune subtypes was based on immune signatures highlighting the tumor immuno-microenvironment. It was found that immune subtypes associated with mutation and expression patterns in the tumor. How the intrinsic genetic and transcriptomic alterations contribute to the immune subtypes and how to select drug combinations from both targeted drugs and immune therapeutic drugs according to different immune subtypes are still not clear. Through statistical analysis of genetic alterations and transcriptional profiles of breast invasive carcinoma (BRCA) samples, we found significant differences in the number of somatic missense mutations and frameshift deletions among the different immune subtypes. The high mutation load for somatic missense mutations and frameshift deletions may be explained by the high frequency of mutations and high expression of DNA double-strand break repair pathway genes. Extensive analysis of signaling pathways in both the genetic and transcriptomic levels reveals significantly altered pathways such as tumor protein Tumor Protein P53 (TP53) and receptor tyrosine kinase (RTK)/RAS signaling pathways among different subtypes. Drug targets in the signaling pathways such as mitogen-activated protein kinase kinase kinase 1 (MAP3K1) and Phosphatidylinositol-4,5-Bisphosphate 3-Kinase Catalytic Subunit Alpha (PIK3CA) show genetic alteration in specific subtypes, which may be potential targets for patients of a specific subtype. More drug targets which show transcriptional difference among immune subtypes were discovered, such as cyclin-dependent kinase (CDK)4, CDK6, Erb-B2 receptor tyrosine kinase 2 (ERBB2), etc. Moreover, differences in functional activity between tumor growth and immune-related pathways also elucidate the extrinsic factors of differences in prognosis and suggest potential drug combinations for different immune subtypes. These results help to explain how intrinsic alterations are associated with the immune subtypes and provide clues for possible combination therapy for different immune subtypes.

19.
Cancer Biol Med ; 17(4): 953-969, 2020 11 15.
Artigo em Inglês | MEDLINE | ID: mdl-33299646

RESUMO

Objective: Pancreatic ductal adenocarcinoma (PDAC) is a disease with high mortality. Many so-called "junk" noncoding RNAs need to be discovered in PDAC. The purpose of this study was therefore to investigate the function and regulatory mechanism of the long noncoding RNA MEG3 in PDAC. Methods: The Gene Expression Omnibus database (GEO database) was used to determine the differential expression of long noncoding RNAs in PDAC, and MEG3 was selected for subsequent verification. Tissue and cell samples were used to verify MEG3 expression, followed by functional detection in vitro and in vivo. Microarrays were used to characterize long noncoding RNA and mRNA expression profiles. Competing endogenous RNA analyses were used to detect differential MEG3 and relational miRNA expression in PDAC. Finally, promoter analyses were conducted to explain the downregulation of MEG3 PDAC. Results: We generated a catalogue of PDAC-associated long noncoding RNAs in the GEO database. The ectopic expression of MEG3 inhibited PDAC growth and metastasis in vitro and in vivo, which was statistically significant (P < 0.05). Microarray analysis showed that multiple microRNAs interacted with MEG3. We also showed that MEG3, as a competing endogenous RNA, directly sponged miR-374a-5p to regulate PTEN expression. The transcription factor, Sp1, recruited EZH2 and HDAC3 to the promoter and transcriptionally repressed MEG3 expression. Finally, clinical data showed that MEG3 and miR-374a-5p expressions were correlated with clinicopathological features. Statistically, Sp1, EZH2, HDAC3, and miR-374a-5p were negatively correlated with MEG3 (P < 0.05). Conclusions: Reduced MEG3 levels played a crucial role in the PDAC malignant phenotype, which provided insight into novel and effective molecular targets of MEG3 for pancreatic cancer treatment.


Assuntos
Carcinoma Ductal Pancreático/genética , Proteína Potenciadora do Homólogo 2 de Zeste/genética , Histona Desacetilases/genética , Neoplasias Pancreáticas/genética , RNA Longo não Codificante/genética , Animais , Carcinoma Ductal Pancreático/patologia , Proliferação de Células , Regulação para Baixo , Feminino , Regulação Neoplásica da Expressão Gênica , Humanos , Masculino , Camundongos Endogâmicos BALB C , Camundongos Nus , Pessoa de Meia-Idade , Neoplasias Pancreáticas/patologia , Prognóstico , Regiões Promotoras Genéticas , Ensaios Antitumorais Modelo de Xenoenxerto
20.
bioRxiv ; 2020 Jul 31.
Artigo em Inglês | MEDLINE | ID: mdl-32766585

RESUMO

Host immune responses play central roles in controlling SARS-CoV2 infection, yet remain incompletely characterized and understood. Here, we present a comprehensive immune response map spanning 454 proteins and 847 metabolites in plasma integrated with single-cell multi-omic assays of PBMCs in which whole transcriptome, 192 surface proteins, and T and B cell receptor sequence were co-analyzed within the context of clinical measures from 50 COVID19 patient samples. Our study reveals novel cellular subpopulations, such as proliferative exhausted CD8 + and CD4 + T cells, and cytotoxic CD4 + T cells, that may be features of severe COVID-19 infection. We condensed over 1 million immune features into a single immune response axis that independently aligns with many clinical features and is also strongly associated with disease severity. Our study represents an important resource towards understanding the heterogeneous immune responses of COVID-19 patients and may provide key information for informing therapeutic development.

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