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Biomarcadores Tumorais , Inflamação , Melanoma , Neoplasias Cutâneas , Humanos , Melanoma/patologia , Melanoma/genética , Melanoma/metabolismo , Melanoma/diagnóstico , Neoplasias Cutâneas/patologia , Neoplasias Cutâneas/metabolismo , Neoplasias Cutâneas/genética , Neoplasias Cutâneas/diagnóstico , Biomarcadores Tumorais/metabolismo , Prognóstico , Inflamação/patologia , Melanoma Maligno Cutâneo , MultiômicaRESUMO
BACKGROUND: Using epigenetic markers and fragmentomics of cell-free DNA for cancer detection has been proven applicable. METHODS: We further investigated the diagnostic potential of combining two features (epigenetic markers and fragmentomic information) of cell-free DNA for detecting various types of cancers. To do this, we extracted cfDNA fragmentomic features from 191 whole-genome sequencing data and studied them in 396 low-pass 5hmC sequencing data, which included four common cancer types and control samples. RESULTS: In our analysis of 5hmC sequencing data from cancer samples, we observed aberrant ultra-long fragments (220-500 bp) that differed from normal samples in terms of both size and coverage profile. These fragments played a significant role in predicting cancer. Leveraging the ability to detect cfDNA hydroxymethylation and fragmentomic markers simultaneously in low-pass 5hmC sequencing data, we developed an integrated model that incorporated 63 features representing both fragmentomic features and hydroxymethylation signatures. This model achieved high sensitivity and specificity for pan-cancer detection (88.52% and 82.35%, respectively). CONCLUSION: We showed that fragmentomic information in 5hmC sequencing data is an ideal marker for cancer detection and that it shows high performance in low-pass sequencing data.
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Liquid biopsy techniques based on deep sequencing of plasma cell-free DNA (cfDNA) could detect the low-frequency somatic mutations and provide an accurate diagnosis for many cancers. However, for brain gliomas, reliable performance of these techniques currently requires obtaining cfDNA from patients' cerebral spinal fluid, which is cumbersome and risky. Here we report a liquid biopsy method based on sequencing of plasma cfDNA fragments carrying 5-hydroxymethylcytosine (5hmC) using selective chemical labeling (hMe-Seal). We first constructed a dataset including 180 glioma patients and 229 non-glioma controls. We found marked concordance between cfDNA hydroxymethylome and the aberrant transcriptome of the underlying gliomas. Functional analysis also revealed overrepresentation of the differentially hydroxymethylated genes (DhmGs) in oncogenic and neural pathways. After splitting our dataset into training and test cohort, we showed that a penalized logistic model constructed with training set DhmGs could distinguish glioma patients from healthy controls in both our test set (AUC = 0.962) and an independent dataset (AUC = 0.930) consisting of 111 gliomas and 111 controls. Additionally, the DhmGs between gliomas with mutant and wild-type isocitrate dehydrogenase (IDH) could be used to train a cfDNA predictor of the IDH mutation status of the underlying tumor (AUC = 0.816), and patients with predicted IDH mutant gliomas had significantly better outcome (P = .01). These results indicate that our plasma cfDNA 5hmC sequencing method could obtain glioma-specific signals, which may be used to noninvasively detect these patients and predict the aggressiveness of their tumors.
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Neoplasias Encefálicas , Glioma , Humanos , Neoplasias Encefálicas/diagnóstico , Neoplasias Encefálicas/genética , Neoplasias Encefálicas/metabolismo , Glioma/diagnóstico , Glioma/genética , Glioma/metabolismo , 5-Metilcitosina , Mutação , Encéfalo/patologia , Isocitrato Desidrogenase/genética , Isocitrato Desidrogenase/metabolismoRESUMO
This paper aims to develop a chloride transport model of engineered cementitious composites (ECC) that can consider the influence of both exposure time and crack width. ECC specimens with crack widths of 0.1 mm, 0.2 mm and 0.3 mm were soaked into NaCl solution with periods of 30, 60, 90 and 120 days. The free chloride content profile was measured and used for the development of the transport model. Regression analysis was applied to build the time and crack width dependent models of apparent diffusion coefficient and surface chloride content. The results show that the crack width has significant influence on the free chloride concentration profile when it is above 0.2 mm and the time-dependent constant n decreases linearly with the crack width. The chloride transport model was obtained by subscribing the models of apparent diffusion coefficient and surface chloride content into the analytical solution of Fick's second law. The model was further validated with the experimental results, showing a deviation within 20%. The findings of the presented study can enhance the current understanding on the chloride transportation in ECC.
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The V-region immunoglobulin-containing suppressor of T cell activation (VISTA), a unique B7 family member, is an attractive immunotherapeutic target for cancer, autoimmune and inflammatory diseases. In 2016, a patent demonstrated V-Set and Immunoglobulin domain containing 8 (VSIG-8) was the putative VISTA receptor. Antagonistic or agonistic agents can conceivably modulate VISTA and its interacting partners, which will greatly benefit the treatment of many diseases. The interaction of VISTA and VSIG-8 were measured by Enzyme-linked Immuno Sorbent Assay (ELISA), Microscale Thermophoresis (MST) and coimmunoprecipitation (Co-IP) experiments. The bioactivity of VSIG-8 inhibitor L557-0155 was evaluated in vitro and in vivo. Kd value of human VISTA binding to human VSIG-8 was 1.58 ± 0.44 µM by MST. When the related amino acid binding site of VISTA was mutated to alanine, the interaction between VISTA and VSIG-8 disappeared. VSIG-8 protein induced an decrease in the level of IL-2 in VISTA-overexpressing cells but a increase in VISTA-/- cells. Furthermore, VSIG-8 inhibitor L557-0155 promoted cytokine production and cell proliferation in PBMCs and suppressed melanoma growth. VSIG-8/VISTA coinhibitory pathway may provide a novel strategy for the treatment of human cancers, and VSIG-8 blockade may increase antitumor immunity. This study was the first time to report that VSIG-8 interacts with VISTA, and inhibited T cell function.
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Antígenos B7 , Neoplasias , Proliferação de Células , Humanos , Ativação Linfocitária , Linfócitos TRESUMO
Functional near-infrared spectroscopy (fNIRS) is a non-invasive and promising method for continuously monitoring hemodynamic and metabolic changes in tissues. However, the existing fNIRS equipment uses optical fiber, which is bulky, expensive, and time-consuming. We present a miniaturized, modular, novel silicon photomultiplier (SiPM) detector and develop a fNIRS instrument aimed at investigating the cerebral hemodynamic response for patients with epilepsy. Light emitting probe is a circle with a diameter of 5 mm. Independent and modular light source and detector are more flexible in placement. The system can be expanded to high-density measurement with 16 light sources, 16 detectors, and 52 channels. The sampling rate of each channel is 25 Hz. Instrument performance was evaluated using brain tissue phantom and in vivo experiments. High signal-to-noise ratio (60 dB) in source detector separation (SDS) of 30 mm, good stability (0.1%), noise equivalent power (0.89 pW), and system drift (0.56%) were achieved in the phantom experiment. Forearm blood-flow occlusion experiments were performed on the forearm of three healthy volunteers to demonstrate the ability to track rapid hemodynamic changes. Breath holding experiments on the forehead of healthy volunteers demonstrated the system can well detect brain function activity. The computer software was developed to display the original light signal intensity and the concentration changes of oxygenated hemoglobin (HbO2) and deoxygenated hemoglobin (HbR) in real time. This system paves the way for our further diagnosis of epilepsy.
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Oxiemoglobinas , Espectroscopia de Luz Próxima ao Infravermelho , Encéfalo , Hemodinâmica , Humanos , Imagens de FantasmasRESUMO
BACKGROUND: Lung cancer is one of most common cancers worldwide, with a 5-year survival rate of less than 20%, which is mainly due to late-stage diagnosis. Noninvasive methods using 5-hydroxymethylation of cytosine (5hmC) modifications and fragmentation profiles from 5hmC cell-free DNA (cfDNA) sequencing provide an opportunity for lung cancer detection and management. RESULTS: A total of 157 lung cancer patients were recruited to generate the largest lung cancer cfDNA 5hmC dataset, which mainly consisted of 62 lung adenocarcinoma (LUAD), 48 lung squamous cell carcinoma (LUSC) and 25 small cell lung cancer (SCLC) patients, with most patients (131, 83.44%) at advanced tumor stages. A 37-feature 5hmC model was constructed and validated to distinguish lung cancer patients from healthy controls, with areas under the curve (AUCs) of 0.8938 and 0.8476 (sensitivity = 87.50% and 72.73%, specificity = 83.87% and 80.60%) in two distinct validation sets. Furthermore, fragment profiles of cfDNA 5hmC datasets were first explored to develop a 48-feature fragmentation model with good performance (AUC = 0.9257 and 0.822, sensitivity = 87.50% and 78.79%, specificity = 80.65% and 76.12%) in the two validation sets. Another diagnostic model integrating 5hmC signals and fragment profiles improved AUC to 0.9432 and 0.8639 (sensitivity = 87.50% and 83.33%, specificity = 90.30% and 77.61%) in the two validation sets, better than models based on either of them alone and performing well in different stages and lung cancer subtypes. Several 5hmC markers were found to be associated with overall survival (OS) and disease-free survival (DFS) based on gene expression data from The Cancer Genome Atlas (TCGA). CONCLUSIONS: Both the 5hmC signal and fragmentation profiles in 5hmC cfDNA data are sensitive and effective in lung cancer detection and could be incorporated into the diagnostic model to achieve good performance, promoting research focused on clinical diagnostic models based on cfDNA 5hmC data.
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5-Metilcitosina/análogos & derivados , Fragmentação do DNA/efeitos dos fármacos , Neoplasias Pulmonares/genética , 5-Metilcitosina/análise , Adulto , Idoso , Idoso de 80 Anos ou mais , Biomarcadores Tumorais/análise , Biomarcadores Tumorais/genética , China/epidemiologia , Metilação de DNA/efeitos dos fármacos , Metilação de DNA/genética , Feminino , Humanos , Neoplasias Pulmonares/epidemiologia , Neoplasias Pulmonares/fisiopatologia , Masculino , Pessoa de Meia-IdadeRESUMO
Multi-drug resistance (MDR) is the major hindrance towards the successful treatment of malignant lung cancer. The aim of this study was to develop a novel nanoparticle co-loaded with docetaxel (DTX) and si-colon cancer-associated transcript-2 (siCCAT2) (NP-DTX/siCCAT2) for overcoming the DTX-resistant non-small cell lung cancer (NSCLC). The NP-DTX/siCCAT2, developed by DTX-conjugated poly (D,L-lactic-co-glycolic acid) (PLGA) copolymers, has an average size of t 87.26 nm. Further modification of Transferrin (Tf) peptides on the surface of NP-DTX/siCCAT2 did not significantly change the particle size with an average diameter of 96.81 nm. The present study demonstrated that TfNP-DTX/siCCAT2 has excellent tumour targeting ability and resulted in an enhanced anti-tumour effect both in vitro and in vivo experiments. Not unexpectedly, a more excellent anti-tumour effect of NP-DTX/siCCAT2 was obtained than the NP-DTX because the silencing of CCAT2 levels in lung cancer cells resulted in down-regulated expressions of P-glycoprotein (P-gp) and multidrug-resistance-associated proteins 1 (MRP1). Further investigation revealed that inhibition of CCAT2 expression dramatically increased the activity of miR-204-3p and thereby signally suppressed the IGFBP2/AKT/Bcl2 pathway.
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Antineoplásicos , Carcinoma Pulmonar de Células não Pequenas , Neoplasias do Colo , Neoplasias Pulmonares , MicroRNAs , Nanopartículas , Antineoplásicos/farmacologia , Antineoplásicos/uso terapêutico , Carcinoma Pulmonar de Células não Pequenas/tratamento farmacológico , Linhagem Celular Tumoral , Neoplasias do Colo/tratamento farmacológico , Docetaxel/farmacologia , Portadores de Fármacos/uso terapêutico , Humanos , Ácido Láctico , Neoplasias Pulmonares/tratamento farmacológico , Polímeros/uso terapêuticoRESUMO
Chronic wounds have become an increasing medical and economic problem of aging societies because they are difficult to manage. Tissue engineering provides new perspectives for the clinically applicable skin substitutes. Epidermal keratinocytes play an important role in wound epithelization and construction of tissue-engineered skin substitutes. How to obtain a large number of autologous epidermal keratinocytes in a short time is the main problem that limits the application of tissue-engineered skin and epidermal cell membranes. Developing an appropriate method for reproducing the biological potential of cell-cell interactions and simulating the three-dimensional structure between cells has great significance for epidermal keratinocytes expansion and full-thickness skin regeneration. In this article, we propose the concept of tissue-engineered skin regeneration units (TESRUs) as the smallest unit with complete full-thickness skin regeneration ability. First, autologous dermal fibroblasts are cultured in biodegradable macroporous microcarriers to provide the mesenchyme support. Second, autologous epidermal keratinocytes and autologous melanocytes are incubated with the fibroblasts-loaded microcarriers and expand in vitro. Incorporating the above co-culture method into the macroporous microcarriers is reasonable for maintaining cell-cell interactions in spatial and temporal context and providing a suitable growth niche for epidermal keratinocytes. Moreover, TESRUs are composed of fibroblasts, keratinocytes, and melanocytes and have complete full-thickness skin regeneration ability. We suggest that TESRUs could be a promising strategy to repair full-thickness skin defects for clinical applications if the hypothesis proves to be practical.
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Epiderme/crescimento & desenvolvimento , Queratinócitos/fisiologia , Regeneração/fisiologia , Engenharia Tecidual/métodos , Cicatrização , Epiderme/fisiologia , Humanos , Modelos BiológicosRESUMO
Non-small cell lung carcinoma (NSCLC), the most common form of lung cancer, is the leading cause of cancer-related death worldwide. We perform whole-genome sequencing (WGS) on samples from 43 primary patients with NSCLC and matched normal samples and analyze their matched open chromatin data and transcriptome data. Our results indicate that next-generation sequencing (NGS) and the Bionano Genomics (BNG) platform should be viewed as complementary technologies in terms of structural variations detection. By creating a framework integrating these two platforms, we detect high-technical-confidence somatic structural variations (SVs) in NSCLC cases, which could aid in the efficient investigation of new candidate oncogenes, such as TRIO and SESTD1. Our findings highlight the impact of somatic SVs on NSCLC oncogenesis and lay a foundation for exploring associations among somatic SVs, gene expression, and regulatory networks in patients with NSCLC.
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Carcinoma Pulmonar de Células não Pequenas/genética , Carcinoma Pulmonar de Células não Pequenas/patologia , Neoplasias Pulmonares/genética , Neoplasias Pulmonares/metabolismo , Genoma Humano/genética , Genômica/métodos , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Humanos , Mutação/genética , Oncogenes/genética , Sequenciamento Completo do Genoma/métodosRESUMO
BACKGROUND: Cancer immunotherapy has gained increasing popularity as a novel approach to treat cancer. A member of the B7 family, V-domain immunoglobulin suppressor of T-cell activation (VISTA) is a novel immune checkpoint that regulates a broad spectrum of immune responses. VISTA is an acidic pH-selective ligand for P-selectin glycoprotein ligand-1(PSGL-1). CA-170, a first-in-class small-molecule dual antagonist of VISTA/PD-L1, was collaboratively developed by Aurigene Discovery Technologies Limited and Curis, Inc. It is currently in Phase I clinical trial. RESULTS: In this study, we develop homology modeling for the VISTA 3D structure and subsequent virtual screening for VISTA small-molecule hit ligands. Visualization of the binding postures of docked ligands with the VISTA protein indicates that some small molecular compounds target VISTA. The ability of antagonist to disrupt immune checkpoint VISTA pathways was investigated though functional studies in vitro. CONCLUSIONS: Affinity active molecule for VISTA was obtained through virtual screening, and the antagonist compound activity to VISTA was assayed in cellular level. We reported a small molecule with high VISTA affinity as antagonist, providing ideas for development VISTA-targeted small molecule compound in cancer immunotherapy.
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Inibidores de Checkpoint Imunológico/farmacologia , Fatores Imunológicos/farmacologia , Glicoproteínas de Membrana/agonistas , Proteínas de Membrana/antagonistas & inibidores , Neoplasias/terapia , Animais , Antígeno B7-H1/antagonistas & inibidores , Humanos , Inibidores de Checkpoint Imunológico/química , Fatores Imunológicos/química , Imunoterapia , Ligantes , Camundongos , Camundongos Endogâmicos C57BL , Simulação de Acoplamento Molecular , Neoplasias/imunologia , Ligação Proteica , Homologia Estrutural de ProteínaRESUMO
BACKGROUND AND PURPOSE: The protein V-domain immunoglobulin suppressor of T-cell activation (VISTA) is a novel immune-checkpoint molecule that belongs to the B7 family and regulates a broad spectrum of immune responses. So far, low MW compounds targeting VISTA for the treatment of autoimmune diseases or inflammation, have not been identified. EXPERIMENTAL APPROACH: We developed a homology modelling for VISTA 3D structure and subsequent virtual screening for low MW ligands binding to VISTA. Visualization of the binding postures of docked ligands with protein VISTA indicated that compound M351-0056 targeted VISTA. The biological activities of compound M351-0056 targeting VISTA were investigated in vitro using monocytes and T cells and in vivo, using mice with imiquimod-induced dermatitis. KEY RESULTS: The KD value of M351-0056 for human VISTA-extracellular domain was 12.60 ± 3.84 µM as assessed by microscale thermophoresis. M351-0056 decreased cytokine secretion from PBMCs or human CD4+ T cells, suppressed proliferation of PBMCs and enhanced expression of Foxp3+ T cells. These effects of M351-0056 modulating VISTA involved the JAK2-STAT2 pathway. Daily administration of M351-0056 ameliorated imiquimod-induced psoriasis-like dermatitis. Expression of mRNA and protein of inflammatory cytokines in psoriatic lesions was decreased after M351-0056 treatment. CONCLUSION AND IMPLICATIONS: The compound M351-0056 showed high affinity for VISTA and may modulate its immune function in vitro and in vivo. Our finding provides a lead compound for therapeutically enhancing VISTA-mediated pathways to benefit the treatment of autoimmune diseases or inflammation.
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Dermatite/genética , Proteínas de Checkpoint Imunológico , Ativação Linfocitária , Proteínas de Membrana/antagonistas & inibidores , Animais , Citocinas , Imiquimode , Inflamação , Ligantes , CamundongosRESUMO
Background: Immunotherapies targeting CTLA-4 and PD-1 have elicited promising responses in a variety of cancers. However, the relatively low response rates warrant the identification of additional immunosuppressive pathways. V domain immunoglobulin suppressor of T cell activation (VISTA) plays a critical role in antitumor immunity and is a valuable target in cancer immunotherapy. Methods: Here, we used single-cell RNA-seq to analyze the gene expression levels of 14897 cells from a breast cancer sample and its paired 7,320 normal cells. Then, we validated the protein expression of immune checkpoint molecules (VISTA, PD-1, PD-L1, TIGIT, TIM3, and LAG3) in 324 human breast cancer samples by immunohistochemistry and quantitative immunofluorescence (QIF) approaches. Results: Single cell RNA-seq results show a higher level of immune checkpoint VISTA expression in breast cancer tissue compared to adjacent normal tissue. We also found that VISTA expressed highest in breast cancer tissue than other immune-checkpoints. Immunohistochemical results showed that VISTA was detected with a membranous/cytoplasmic staining pattern in intratumoral immune cells and breast cancer cells. Additionally, VISTA was positively correlated with pathological grade, lymph node status and the levels of PD-1 according to the chi-square test or Fisher's test. Furthermore, VISTA expression was higher in CD68+ tumor-associated macrophages (TAMs) than in CD4+ T cells, CD8+ cytotoxic T cells or CD20+ B cells. Conclusions: These findings therefore support the immunoregulatory role of VISTA in breast cancer and indicate that targeting VISTA may benefit breast cancer immunotherapy.
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Antígenos B7/genética , Antígenos B7/metabolismo , Neoplasias da Mama/imunologia , Proteínas de Checkpoint Imunológico/genética , Proteínas de Checkpoint Imunológico/metabolismo , Adulto , Idoso , Idoso de 80 Anos ou mais , Biomarcadores Tumorais/genética , Biomarcadores Tumorais/metabolismo , Neoplasias da Mama/patologia , Feminino , Expressão Gênica , Regulação Neoplásica da Expressão Gênica , Humanos , Imuno-Histoquímica , Pessoa de Meia-Idade , RNA-Seq , Análise de Célula Única , Evasão Tumoral , Microambiente Tumoral/imunologia , Macrófagos Associados a Tumor/imunologiaRESUMO
Rationale: V-domain immunoglobulin suppressor of T cell activation (VISTA) is a novel inhibitory immune checkpoint molecule. Vsir-/- mice have exacerbated psoriasis-like skin inflammation. The immune cell subsets involved in inflammation in Vsir-/- psoriatic mice are largely unknown. We have used scRNA-seq as an unbiased profiling strategy to study the heterogeneity of immune cells at a single cell level in the skin of Vsir-/- psoriatic mice. Methods: In the present study, the right ear and shaved back skin of wild type and Vsir-/- mice were treated with IMQ for 5 consecutive days to induce psoriasis-like dermatitis. Then, the single-cell RNA sequencing analysis of mouse back skin lesions was performed using 10 × Genomics technique. Results: We identified 12 major cell subtypes among 23,258 cells. The major populations of the skin cells included macrophages, dendritic cells and fibroblasts. Macrophages constituted the main immune cell population in the WT (61.29%) and Vsir-/- groups (77.7%). It should be noted that DCs and fibroblasts were expanded in the Vsir-/- psoriatic mice. Furthermore, the gene expression signatures were assessed. We observed that Hspb1 and Cebpb were significantly upregulated in the Vsir-/- psoriatic mice. Differential gene expression and gene ontology enrichment analyses revealed specific gene expression patterns distinguishing these subsets and uncovered putative functions of each cell type. Date analysis resulted in the discovery of a number of novel psoriasis-associated genes in Vsir-/- mice. Conclusion: We present a comprehensive single-cell landscape of the skin immune cells in Vsir-/- psoriatic mice. These unprecedented data uncovered the transcriptional landscape and phenotypic heterogeneity of skin macrophages in psoriasis and identified their gene expression signature suggesting specialized functions in Vsir-/- mice. Our findings will open novel opportunities to investigate the role of VISTA in driving psoriasis.
Assuntos
Macrófagos/metabolismo , Proteínas de Membrana/genética , Psoríase/genética , Transcriptoma/imunologia , Animais , Células Dendríticas/imunologia , Células Dendríticas/metabolismo , Modelos Animais de Doenças , Feminino , Fibroblastos/imunologia , Fibroblastos/metabolismo , Humanos , Imiquimode/administração & dosagem , Imiquimode/imunologia , Macrófagos/imunologia , Camundongos , Camundongos Knockout , Psoríase/imunologia , Psoríase/patologia , RNA-Seq , Análise de Célula Única , Pele/citologia , Pele/imunologia , Pele/patologia , Transcrição Gênica/imunologia , Transcriptoma/genéticaRESUMO
BACKGROUND: The high lethal rate of pancreatic cancer is partly due to a lack of efficient biomarkers for screening and early diagnosis. We attempted to develop effective and noninvasive methods using 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) markers from circulating cell-free DNA (cfDNA) for the detection of pancreatic ductal adenocarcinoma (PDAC). RESULTS: A 24-feature 5mC model that can accurately discriminate PDAC from healthy controls (area under the curve (AUC) = 0.977, sensitivity = 0.824, specificity = 1) and a 5hmC prediction model with 27 features demonstrated excellent detection power in two distinct validation sets (AUC = 0.992 and 0.960, sensitivity = 0.786 and 0.857, specificity = 1 and 0.993). The 51-feature model combining 5mC and 5hmC markers outperformed both of the individual models, with an AUC of 0.997 (sensitivity = 0.938, specificity = 0.955) and particularly an improvement in the prediction sensitivity of PDAC. In addition, the weighted diagnosis score (wd-score) calculated with the 5hmC model can distinguish stage I patients from stage II-IV patients. CONCLUSIONS: Both 5mC and 5hmC biomarkers in cfDNA are effective in PDAC detection, and the 5mC-5hmC integrated model significantly improve the detection sensitivity.
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Adenocarcinoma/sangue , Biomarcadores Tumorais/sangue , Carcinoma Ductal Pancreático/sangue , Ácidos Nucleicos Livres/sangue , Epigênese Genética/fisiologia , Neoplasias Pancreáticas/sangue , 5-Metilcitosina/análogos & derivados , 5-Metilcitosina/sangue , Feminino , Humanos , Masculino , Pessoa de Meia-Idade , Reprodutibilidade dos Testes , Sensibilidade e EspecificidadeRESUMO
The rhesus macaque is a prime model animal in neuroscience. A comprehensive transcriptomic and open chromatin atlas of the rhesus macaque brain is key to a deeper understanding of the brain. Here we characterize the transcriptome of 416 brain samples from 52 regions of 8 rhesus macaque brains. We identify gene modules associated with specific brain regions like the cerebral cortex, pituitary, and thalamus. In addition, we discover 9703 novel intergenic transcripts, including 1701 coding transcripts and 2845 lncRNAs. Most of the novel transcripts are only expressed in specific brain regions or cortical regions of specific individuals. We further survey the open chromatin regions in the hippocampal CA1 and several cerebral cortical regions of the rhesus macaque brain using ATAC-seq, revealing CA1- and cortex-specific open chromatin regions. Our results add to the growing body of knowledge regarding the baseline transcriptomic and open chromatin profiles in the brain of the rhesus macaque.
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Encéfalo/anatomia & histologia , Encéfalo/metabolismo , Macaca mulatta/anatomia & histologia , Macaca mulatta/genética , Animais , Cromatina/genética , Cromatina/metabolismo , Feminino , Perfilação da Expressão Gênica , Redes Reguladoras de Genes , Humanos , Macaca mulatta/metabolismo , Masculino , Modelos Animais , RNA Longo não Codificante/genética , RNA Longo não Codificante/metabolismo , RNA-Seq , Especificidade da Espécie , Distribuição TecidualRESUMO
Non-small cell lung carcinoma (NSCLC) is a major cancer type whose epigenetic alteration remains unclear. We analyzed open chromatin data with matched whole-genome sequencing and RNA-seq data of 50 primary NSCLC cases. We observed high interpatient heterogeneity of open chromatin profiles and the degree of heterogeneity correlated to several clinical parameters. Lung adenocarcinoma and lung squamous cell carcinoma (LUSC) exhibited distinct open chromatin patterns. Beyond this, we uncovered that the broadest open chromatin peaks indicated key NSCLC genes and led to less stable expression. Furthermore, we found that the open chromatin peaks were gained or lost together with somatic copy number alterations and affected the expression of important NSCLC genes. In addition, we identified 21 joint-quantitative trait loci (joint-QTL) that correlated to both assay for transposase accessible chromatin sequencing peak intensity and gene expression levels. Finally, we identified 87 regulatory risk loci associated with lung cancer-related phenotypes by intersecting the QTLs with genome-wide association study significant loci. In summary, this compendium of multiomics data provides valuable insights and a resource to understand the landscape of open chromatin features and regulatory networks in NSCLC. SIGNIFICANCE: This study utilizes state of the art genomic methods to differentiate lung cancer subtypes.See related commentary by Bowcock, p. 4808.
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Carcinoma Pulmonar de Células não Pequenas , Carcinoma de Células Escamosas , Neoplasias Pulmonares , Cromatina , Estudo de Associação Genômica Ampla , HumanosRESUMO
Immunotherapy is considered as a promising therapeutic approach for cancer treatment. This therapy focuses on the specificity and memory of the immune system against malignant cells to achieve a sustained cure with minimal toxicity. However, the effectiveness of immunotherapy is often limited by the insufficient delivery and low accumulation of therapeutic molecules in tumors. Ultrasound exposures with the presence of microbubbles can be used as an effective method to greatly increase cell membrane permeability and enhance tissue accessibility to drugs or genes, thereby improving the access of therapeutic molecules into non-permeable tissues and enhancing the therapeutic outcomes. In this review, we discuss challenges in current tumor immunotherapy and feasible approaches that could potentially overcome these obstacles with the help of ultrasound; thereafter, we elaborate on the recent advantages of ultrasound-mediated delivery approach in tumor immunotherapy.
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Imunoterapia , Neoplasias/terapia , Pesquisa Translacional Biomédica , Terapia por Ultrassom , Animais , Terapia Combinada , Humanos , Imunoterapia/efeitos adversos , Neoplasias/imunologia , Neoplasias/patologia , Fatores de Risco , Microambiente Tumoral , Terapia por Ultrassom/efeitos adversosRESUMO
Cardiac hypertrophy is a risk factor which can intrigue heart failure. In the present study, we explored whether AdipoRon attenuates isoprenaline (ISO) or l-thyroxine-induced cardiac hypertrophy in Sprague-Dawley (SD) rats and whether the anti-hypertrophy effect is mediated by AMPK-related pathway. Here, cardiac hypertrophy was induced by injection of l-thyroxine or ISO in SD rats. In the treatment group, AdipoRon was co-administered. We examined the effects of AdipoRon on cardiac hypertrophy and hypertrophy signaling pathway. The weight of SD rats was recorded every day. Rats were killed for collection of blood and heart under anesthesia. The left heart weight and heart weight were weighed. Paraffin-embedded heart tissue regions (4 µm) were stained with hematoxylin and eosin or Masson to detect left heart hypertrophy and myocardial fibrosis. The serum BNP levels were determined by using an enzyme-linked immunosorbent assay. The mRNA levels of ANP, BNP, PGC-1α, and ERRα were evaluated by real-time PCR analysis. The protein expression levels of PGC-1α, ERRα, and pAMPK/AMPK were determined by western blot analysis. The results showed that AdipoRon significantly reversed heart weight (HW)/body weight (BW) ratio, left ventricular (LV)/BW ratio, serum BNP level and the mRNA level of ANP and BNP induced by ISO or l-thyroxine. ISO or l-thyroxine reduced both the mRNA level and protein level of ERRα and PGC-1α, and also reduced the protein level of pAMPK/AMPK. However, AdipoRon reversed ISO or l-thyroxine-induced changes of pAMPK/AMPK, ERRα, and PGC-1α. Our data indicated that the effects of AdipoRon are mediated partly by activating AMPK-related pathway, and AdipoRon plays a potential role in the prevention of cardiac hypertrophy.
Assuntos
Proteínas Quinases Ativadas por AMP/metabolismo , Cardiomegalia/prevenção & controle , Piperidinas/farmacologia , Transdução de Sinais/efeitos dos fármacos , Animais , Fator Natriurético Atrial/genética , Fator Natriurético Atrial/metabolismo , Peso Corporal/efeitos dos fármacos , Cardiomegalia/induzido quimicamente , Cardiomegalia/metabolismo , Expressão Gênica/efeitos dos fármacos , Isoproterenol , Masculino , Peptídeo Natriurético Encefálico/genética , Peptídeo Natriurético Encefálico/metabolismo , Tamanho do Órgão/efeitos dos fármacos , Coativador 1-alfa do Receptor gama Ativado por Proliferador de Peroxissomo/genética , Coativador 1-alfa do Receptor gama Ativado por Proliferador de Peroxissomo/metabolismo , Ratos Sprague-Dawley , TiroxinaRESUMO
Photoplethysmography (PPG) has been widely used in noninvasive blood volume and blood flow detection since its first appearance. However, its noninvasiveness also makes the PPG signals vulnerable to noise interference and thus exhibits nonlinear and nonstationary characteristics, which have brought difficulties for the denoising of PPG signals. Ensemble empirical mode decomposition known as EEMD, which has made great progress in noise processing, is a noise-assisted nonlinear and nonstationary time series analysis method based on empirical mode decomposition (EMD). The EEMD method solves the "mode mixing" problem in EMD effectively, but it can do nothing about the "end effect," another problem in the decomposition process. In response to this problem, an improved EEMD method based on support vector regression extension (SVR-EEMD) is proposed and verified by simulated data and real-world PPG data. Experiments show that the SVR-EEMD method can solve the "end effect" efficiently to get a better decomposition performance than the traditional EEMD method and bring more benefits to the noise processing of PPG signals.