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1.
J Fluoresc ; 2024 Mar 27.
Artigo em Inglês | MEDLINE | ID: mdl-38536610

RESUMO

In this work, a simple and sensitive N-acetyl-L-cysteine (NAC)-covered CdTe quantum dots (NAC-CdTe QDs) fluorescence probe for continuous detection of Co2+ and pyrophosphate ions (PPi, P2O74-) was synthesized. The fluorescence of the quantum dots was significantly quenched by Co2+ through the coordination of Co2+ and the carboxyl groups on the NAC-CdTe quantum dots. Interestingly, the combination of NAC-CdTe quantum dots with Co2+ yields a new fluorescence probe of Co2+-modified NAC-CdTe QDs (Co2+@NAC-CdTe). The addition of PPi restored the fluorescence due to the competition between PPi and carboxyl groups with Co2+ causing Co2+ to detach from the surface of Co2+@NAC-CdTe quantum dots. Thus, a sensitive and reversible detection of Co2+ and PPi had been successfully established. The Co2+@NAC-CdTe quantum dots fluorescence probe exhibits excellent selectivity and high sensitivity toward PPi detection with low detection limit of 0.28 µM. In addition, the novel fluorescence probe was successfully applied to detect the concentration of PPi in environmental water samples and in-vitro cells imaging.

2.
Int J Mol Sci ; 25(7)2024 Mar 29.
Artigo em Inglês | MEDLINE | ID: mdl-38612653

RESUMO

To understand chemoresistance in the context of cancer stem cells (CSC), a cisplatin resistance model was developed using a high-grade serous ovarian cancer patient-derived, cisplatin-sensitive sample, PDX4. As a molecular subtype-specific stem-like cell line, PDX4 was selected for its representative features, including its histopathological and BRCA2 mutation status, and exposed to cisplatin in vitro. In the cisplatin-resistant cells, transcriptomics were carried out, and cell morphology, protein expression, and functional status were characterized. Additionally, potential signaling pathways involved in cisplatin resistance were explored. Our findings reveal the presence of distinct molecular signatures and phenotypic changes in cisplatin-resistant PDX4 compared to their sensitive counterparts. Surprisingly, we observed that chemoresistance was not inherently linked with increased stemness. In fact, although resistant cells expressed a combination of EMT and stemness markers, functional assays revealed that they were less proliferative, migratory, and clonogenic-features indicative of an underlying complex mechanism for cell survival. Furthermore, DNA damage tolerance and cellular stress management pathways were enriched. This novel, syngeneic model provides a valuable platform for investigating the underlying mechanisms of cisplatin resistance in a clinically relevant context, contributing to the development of targeted therapies tailored to combat resistance in stem-like ovarian cancer.


Assuntos
Neoplasias Ovarianas , Platina , Humanos , Feminino , Platina/farmacologia , Cisplatino/farmacologia , Cisplatino/uso terapêutico , Neoplasias Ovarianas/tratamento farmacológico , Neoplasias Ovarianas/genética , Carcinoma Epitelial do Ovário
3.
Biochem Biophys Res Commun ; 547: 65-68, 2021 04 02.
Artigo em Inglês | MEDLINE | ID: mdl-33596482

RESUMO

Single-molecule real-time DNA sequencing revealed that 4-methylcytosine (m4C) commonly exists in bacterial genomes. In this work, samples with different m4C methylation patterns were studied. Results reveal that m4C modification is a biochemical reaction with distance effect, and its distribution follows the power function in the positive, negative, and double strands of genomic DNA sequences of Geobacter sulfurreducens. Furthermore, the value of regression coefficient in the fitting formula for double strands was the sum of those in the fitting formulae for positive and negative strands. Meanwhile, the value of exponent coefficient was the average, implicating an interesting mathematical phenomenon about power function. Considering the potent role of m4C in gene expression and the present results being obtained from the same genomic DNA sequence, this work suggests that the patterns of m4C distribution may be served as a signal for G. sulfurreducens to rapidly identify the genes to respond to environmental stresses or signals. This study opens a new avenue to extend our knowledge about the modification mechanisms and the epigenetic information of m4C modification in prokaryotes.


Assuntos
Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , Citosina/metabolismo , Metilação de DNA , Geobacter/genética , Geobacter/metabolismo , Citosina/análogos & derivados , Citosina/química , Genoma Bacteriano , Filogenia , Análise de Sequência de DNA/métodos
4.
Nucleic Acids Res ; 46(19): 10195-10215, 2018 11 02.
Artigo em Inglês | MEDLINE | ID: mdl-30239926

RESUMO

Genome editing of human induced pluripotent stem cells (iPSCs) is instrumental for functional genomics, disease modeling, and regenerative medicine. However, low editing efficiency has hampered the applications of CRISPR-Cas9 technology in creating knockin (KI) or knockout (KO) iPSC lines, which is largely due to massive cell death after electroporation with editing plasmids. Here, we report that the transient delivery of BCL-XL increases iPSC survival by ∼10-fold after plasmid transfection, leading to a 20- to 100-fold increase in homology-directed repair (HDR) KI efficiency and a 5-fold increase in non-homologous end joining (NHEJ) KO efficiency. Treatment with a BCL inhibitor ABT-263 further improves HDR efficiency by 70% and KO efficiency by 40%. The increased genome editing efficiency is attributed to higher expressions of Cas9 and sgRNA in surviving cells after electroporation. HDR or NHEJ efficiency reaches 95% with dual editing followed by selection of cells with HDR insertion of a selective gene. Moreover, KO efficiency of 100% can be achieved in a bulk population of cells with biallelic HDR KO followed by double selection, abrogating the necessity for single cell cloning. Taken together, these simple yet highly efficient editing strategies provide useful tools for applications ranging from manipulating human iPSC genomes to creating gene-modified animal models.


Assuntos
Sistemas CRISPR-Cas/fisiologia , Edição de Genes/métodos , Células-Tronco Pluripotentes Induzidas/metabolismo , Proteína bcl-X/genética , Animais , Células Cultivadas , Genoma Humano/genética , Células HEK293 , Humanos , Células Jurkat , Células K562 , Camundongos , Transfecção , Regulação para Cima/genética
5.
Stroke ; 49(5): 1232-1240, 2018 05.
Artigo em Inglês | MEDLINE | ID: mdl-29593101

RESUMO

BACKGROUND AND PURPOSE: Brain arteriovenous malformation (bAVM) is an important risk factor for intracranial hemorrhage. Current treatments for bAVM are all associated with considerable risks. There is no safe method to prevent bAVM hemorrhage. Thalidomide reduces nose bleeding in patients with hereditary hemorrhagic telangiectasia, an inherited disorder characterized by vascular malformations. In this study, we tested whether thalidomide and its less toxic analog, lenalidomide, reduce bAVM hemorrhage using a mouse model. METHODS: bAVMs were induced through induction of brain focal activin-like kinase 1 (Alk1, an AVM causative gene) gene deletion and angiogenesis in adult Alk1-floxed mice. Thalidomide was injected intraperitoneally twice per week for 6 weeks, starting either 2 or 8 weeks after AVM induction. Lenalidomide was injected intraperitoneally daily starting 8 weeks after AVM induction for 6 weeks. Brain samples were collected at the end of the treatments for morphology, mRNA, and protein analyses. The influence of Alk1 downregulation on PDGFB (platelet-derived growth factor B) expression was also studied on cultured human brain microvascular endothelial cells. The effect of PDGFB in mural cell recruitment in bAVM was explored by injection of a PDGFB overexpressing lentiviral vector to the mouse brain. RESULTS: Thalidomide or lenalidomide treatment reduced the number of dysplastic vessels and hemorrhage and increased mural cell (vascular smooth muscle cells and pericytes) coverage in the bAVM lesion. Thalidomide reduced the burden of CD68+ cells and the expression of inflammatory cytokines in the bAVM lesions. PDGFB expression was reduced in ALK1-knockdown human brain microvascular endothelial cells and in mouse bAVM lesion. Thalidomide increased Pdgfb expression in bAVM lesion. Overexpression of PDGFB mimicked the effect of thalidomide. CONCLUSIONS: Thalidomide and lenalidomide improve mural cell coverage of bAVM vessels and reduce bAVM hemorrhage, which is likely through upregulation of Pdgfb expression.


Assuntos
Inibidores da Angiogênese/farmacologia , Vasos Sanguíneos/efeitos dos fármacos , Malformações Arteriovenosas Intracranianas/prevenção & controle , Hemorragias Intracranianas/prevenção & controle , Lenalidomida/farmacologia , Miócitos de Músculo Liso/efeitos dos fármacos , Pericitos/efeitos dos fármacos , Talidomida/farmacologia , Receptores de Ativinas Tipo I/genética , Receptores de Activinas Tipo II/genética , Animais , Vasos Sanguíneos/patologia , Modelos Animais de Doenças , Regulação para Baixo , Células Endoteliais , Humanos , Inflamação , Malformações Arteriovenosas Intracranianas/genética , Malformações Arteriovenosas Intracranianas/metabolismo , Linfocinas/metabolismo , Camundongos , Microvasos/metabolismo , Músculo Liso Vascular/efeitos dos fármacos , Músculo Liso Vascular/patologia , Miócitos de Músculo Liso/patologia , Pericitos/patologia , Fator de Crescimento Derivado de Plaquetas/metabolismo , Proteínas Proto-Oncogênicas c-sis/metabolismo , RNA Mensageiro/metabolismo , Receptor beta de Fator de Crescimento Derivado de Plaquetas/efeitos dos fármacos , Receptor beta de Fator de Crescimento Derivado de Plaquetas/metabolismo
6.
Proc Natl Acad Sci U S A ; 112(29): E3893-900, 2015 Jul 21.
Artigo em Inglês | MEDLINE | ID: mdl-26150503

RESUMO

Substantial advances have been made in the past two decades in the management of osteoporosis. However, none of the current medications can eliminate the risk of fracture and rejuvenate the skeleton. To this end, we recently reported that transplantation of hematopoietic stem/progenitor cells (HSCs) or Sca1(+) cells engineered to overexpress FGF2 results in a significant increase in lamellar bone matrix formation at the endosteum; but this increase was attended by the development of secondary hyperparathyroidism and severe osteomalacia. Here we switch the therapeutic gene to PDGFB, another potent mitogen for mesenchymal stem cells (MSCs) but potentially safer than FGF2. We found that modest overexpression of PDGFB using a relatively weak phosphoglycerate kinase (PGK) promoter completely avoided osteomalacia and secondary hyperparathyroidism, and simultaneously increased trabecular bone formation and trabecular connectivity, and decreased cortical porosity. These effects led to a 45% increase in the bone strength. Transplantation of PGK-PDGFB-transduced Sca1(+) cells increased MSC proliferation, raising the possibility that PDGF-BB enhances expansion of MSC in the vicinity of the hematopoietic niche where the osteogenic milieu propels the differentiation of MSCs toward an osteogenic destination. Our therapy should have potential clinical applications for patients undergoing HSC transplantation, who are at high risk for osteoporosis and bone fractures after total body irradiation preconditioning. It could eventually have wider application once the therapy can be applied without the preconditioning.


Assuntos
Osso e Ossos/fisiopatologia , Terapia Genética , Transplante de Células-Tronco Hematopoéticas , Proteínas Proto-Oncogênicas c-sis/genética , Proteínas Proto-Oncogênicas c-sis/uso terapêutico , Fosfatase Alcalina/sangue , Animais , Antígenos Ly/metabolismo , Peso Corporal , Remodelação Óssea , Diferenciação Celular , Proliferação de Células , Hiperparatireoidismo/complicações , Hiperparatireoidismo/metabolismo , Hiperparatireoidismo/fisiopatologia , Hiperparatireoidismo/terapia , Antígeno Ki-67/metabolismo , Lentivirus/metabolismo , Proteínas de Membrana/metabolismo , Células-Tronco Mesenquimais/citologia , Camundongos , Modelos Biológicos , Neovascularização Fisiológica , Osteoblastos/metabolismo , Osteoblastos/patologia , Osteocalcina/sangue , Osteogênese , Osteomalacia/complicações , Osteomalacia/fisiopatologia , Fosfoglicerato Quinase/genética , Fosfoglicerato Quinase/metabolismo , Regiões Promotoras Genéticas/genética , Vírus Formadores de Foco no Baço/metabolismo , Transdução Genética , Transgenes , Suporte de Carga
7.
Stroke ; 45(3): 900-2, 2014 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-24457293

RESUMO

BACKGROUND AND PURPOSE: In humans, activin receptor-like kinase 1 (Alk1) deficiency causes arteriovenous malformations (AVMs) in multiple organs, including the brain. Focal Alk1 pan-cellular deletion plus vascular endothelial growth factor stimulation induces brain AVMs in the adult mouse. We hypothesized that deletion of Alk1 in endothelial cell (EC) alone plus focal vascular endothelial growth factor stimulation is sufficient to induce brain AVM in the adult mouse. METHODS: Focal angiogenesis was induced in the brain of 8-week-old Pdgfb-iCreER;Alk1(2f/2f) mice by injection of adeno-associated viral vectors expressing vascular endothelial growth factor. Two weeks later, EC-Alk1 deletion was induced by tamoxifen treatment. Vascular morphology was analyzed, and EC proliferation and dysplasia index (number of vessels with diameter>15 µm per 200 vessels) were quantified 10 days after tamoxifen administration. RESULTS: Tangles of enlarged vessels resembling AVMs were present in the brain angiogenic region of tamoxifen-treated Pdgfb-iCreER;Alk1(2f/2f) mice. Induced brain AVMs were marked by increased dysplasia index (P<0.001) and EC proliferation clustered within the dysplastic vessels. AVMs were also detected around the ear tag-wound and in other organs. CONCLUSIONS: Deletion of Alk1 in EC in adult mice leads to an increased local EC proliferation during brain angiogenesis and de novo brain AVM.


Assuntos
Receptores de Ativinas Tipo I/genética , Receptores de Ativinas Tipo I/fisiologia , Indutores da Angiogênese/farmacologia , Malformações Vasculares do Sistema Nervoso Central/genética , Malformações Vasculares do Sistema Nervoso Central/fisiopatologia , Receptores de Activinas Tipo II , Adenoviridae , Animais , Antimetabólitos/farmacologia , Antineoplásicos Hormonais/farmacologia , Bromodesoxiuridina/farmacologia , Proliferação de Células , Células Endoteliais/fisiologia , Éxons/genética , Deleção de Genes , Camundongos , Organismos Geneticamente Modificados , Tamoxifeno/farmacologia , Telangiectasia Hemorrágica Hereditária/genética , Telangiectasia Hemorrágica Hereditária/patologia , Fator A de Crescimento do Endotélio Vascular/metabolismo
8.
Arterioscler Thromb Vasc Biol ; 33(2): 305-10, 2013 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-23241407

RESUMO

OBJECTIVE: Vessels in brain arteriovenous malformations are prone to rupture. The underlying pathogenesis is not clear. Hereditary hemorrhagic telangiectasia type 2 patients with activin receptor-like kinase 1 (Alk1) mutation have a higher incidence of brain arteriovenous malformation than the general population. We tested the hypothesis that vascular endothelial growth factor impairs vascular integrity in the Alk1-deficient brain through reduction of mural cell coverage. METHODS AND RESULTS: Adult Alk1(1f/2f) mice (loxP sites flanking exons 4-6) and wild-type mice were injected with 2×10(7) PFU adenovious-cre recombinase and 2×10(9) genome copies of adeno-associated virus-vascular endothelial growth factor to induce focal homozygous Alk1 deletion (in Alk1(1f/2f) mice) and angiogenesis. Brain vessels were analyzed 8 weeks later. Compared with wild-type mice, the Alk1-deficient brain had more fibrin (99±30×10(3) pixels/mm(2) versus 40±13×10(3); P=0.001), iron deposition (508±506 pixels/mm(2) versus 6±49; P=0.04), and Iba1(+) microglia/macrophage infiltration (888±420 Iba1(+) cells/mm(2) versus 240±104 Iba1(+); P=0.001) after vascular endothelial growth factor stimulation. In the angiogenic foci, the Alk1-deficient brain had more α-smooth muscle actin negative vessels (52±9% versus 12±7%, P<0.001), fewer vascular-associated pericytes (503±179/mm(2) versus 931±115, P<0.001), and reduced platelet-derived growth factor receptor-ß expression. CONCLUSIONS: Reduction of mural cell coverage in response to vascular endothelial growth factor stimulation is a potential mechanism for the impairment of vessel wall integrity in hereditary hemorrhagic telangiectasia type 2-associated brain arteriovenous malformation.


Assuntos
Receptores de Ativinas Tipo I/deficiência , Vasos Sanguíneos/enzimologia , Encéfalo/irrigação sanguínea , Neovascularização Patológica , Pericitos/enzimologia , Telangiectasia Hemorrágica Hereditária/enzimologia , Fator A de Crescimento do Endotélio Vascular/metabolismo , Actinas/metabolismo , Receptores de Ativinas Tipo I/genética , Receptores de Activinas Tipo II , Animais , Becaplermina , Vasos Sanguíneos/patologia , Dependovirus/genética , Modelos Animais de Doenças , Fibrina/metabolismo , Técnicas de Transferência de Genes , Vetores Genéticos , Ferro/metabolismo , Macrófagos/metabolismo , Macrófagos/patologia , Camundongos , Camundongos Endogâmicos C57BL , Camundongos Knockout , Microglia/metabolismo , Microglia/patologia , Pericitos/patologia , Proteínas Proto-Oncogênicas c-sis/metabolismo , Receptor beta de Fator de Crescimento Derivado de Plaquetas/metabolismo , Telangiectasia Hemorrágica Hereditária/genética , Telangiectasia Hemorrágica Hereditária/patologia , Fator A de Crescimento do Endotélio Vascular/genética
9.
J Nutr Sci Vitaminol (Tokyo) ; 70(2): 98-105, 2024.
Artigo em Inglês | MEDLINE | ID: mdl-38684391

RESUMO

Chronic kidney disease (CKD) poses a major global public health challenge. The World Health Organization's data shows that CKD affects about 10% of the world's population, particularly in low- and middle-income countries. Due to limited access to diagnosis and treatment, CKD has become the 12th leading cause of death worldwide. The advanced stage of CKD can lead to kidney failure, which is clinically referred to as end-stage renal disease (ESRD). In such cases, patients can only sustain life through dialysis or kidney transplantation. However, the long-term affordability of these treatments remains low. Moreover, the effectiveness of kidney transplantation is modest, posing a significant treatment barrier in resource-limited settings, and significantly impacting patient survival. To address this issue, we suggest using dietary supplementation of the trace element zinc to impede CKD development and prolong patient survival.


Assuntos
Suplementos Nutricionais , Insuficiência Renal Crônica , Zinco , Humanos , Zinco/uso terapêutico , Zinco/deficiência , Zinco/administração & dosagem , Insuficiência Renal Crônica/terapia , Insuficiência Renal Crônica/complicações , Falência Renal Crônica/complicações , Falência Renal Crônica/terapia , Oligoelementos/administração & dosagem , Oligoelementos/uso terapêutico , Transplante de Rim , Diálise Renal
10.
Genome Biol ; 25(1): 163, 2024 06 20.
Artigo em Inglês | MEDLINE | ID: mdl-38902799

RESUMO

BACKGROUND: Copy number variation (CNV) is a key genetic characteristic for cancer diagnostics and can be used as a biomarker for the selection of therapeutic treatments. Using data sets established in our previous study, we benchmark the performance of cancer CNV calling by six most recent and commonly used software tools on their detection accuracy, sensitivity, and reproducibility. In comparison to other orthogonal methods, such as microarray and Bionano, we also explore the consistency of CNV calling across different technologies on a challenging genome. RESULTS: While consistent results are observed for copy gain, loss, and loss of heterozygosity (LOH) calls across sequencing centers, CNV callers, and different technologies, variation of CNV calls are mostly affected by the determination of genome ploidy. Using consensus results from six CNV callers and confirmation from three orthogonal methods, we establish a high confident CNV call set for the reference cancer cell line (HCC1395). CONCLUSIONS: NGS technologies and current bioinformatics tools can offer reliable results for detection of copy gain, loss, and LOH. However, when working with a hyper-diploid genome, some software tools can call excessive copy gain or loss due to inaccurate assessment of genome ploidy. With performance matrices on various experimental conditions, this study raises awareness within the cancer research community for the selection of sequencing platforms, sample preparation, sequencing coverage, and the choice of CNV detection tools.


Assuntos
Biologia Computacional , Variações do Número de Cópias de DNA , Sequenciamento de Nucleotídeos em Larga Escala , Perda de Heterozigosidade , Neoplasias , Software , Humanos , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Neoplasias/genética , Biologia Computacional/métodos , Diploide , Genoma Humano , Linhagem Celular Tumoral , Reprodutibilidade dos Testes , Análise de Sequência de DNA/métodos
11.
Sci Total Environ ; 870: 161939, 2023 Apr 20.
Artigo em Inglês | MEDLINE | ID: mdl-36731572

RESUMO

Numerous works have reported that extremely low frequency electromagnetic fields (ELF-EMFs) were associated with human health; however, little is known about their effects on the occurrence of agricultural diseases. In this study, Magnaporthe oryzae was used as a model organism, and its pathogenicity under 50 Hz, 3 mT ELF-EMF was studied. Our results showed that the pathogenicity, growth rate, and conidia generation of M. oryzae were enhanced under ELF-EMF exposure. In addition, M. oryzae exposed to ELF-EMF showed enhanced tolerance to cell wall-perturbing agents sodium lauryl sulphate, and increased expression of cell wall integrity-related genes, including RAC1, CDC42, RHO2, and NOX2. In addition, the level of reactive oxygen species (ROS) and the expression level of ROS scavenger system-related gene MoAP1 increased in ELF-EMF-exposed samples, whereas the total antioxidant capacity and the activities of superoxide dismutase and catalase did not change. Results of our study demonstrated that exposure to 50 Hz, 3 mT ELF-EMF enhanced the infection ability of M. oryzae, which present new important challenges for understanding the effect of ELF-EMF exposure on farmland ecology, especially on agricultural diseases.


Assuntos
Antioxidantes , Campos Eletromagnéticos , Humanos , Espécies Reativas de Oxigênio/metabolismo , Virulência , Antioxidantes/metabolismo , Proteínas Adaptadoras de Transdução de Sinal/metabolismo , Proteínas Reguladoras de Apoptose/metabolismo
12.
Commun Biol ; 6(1): 393, 2023 04 11.
Artigo em Inglês | MEDLINE | ID: mdl-37041280

RESUMO

Mesenchymal stromal cells (MSCs) have great value in cell therapies. The MSC therapies have many challenges due to its inconsistent potency and limited quantity. Here, we report a strategy to generate induced MSCs (iMSCs) by directly reprogramming human peripheral blood mononuclear cells (PBMCs) with OCT4, SOX9, MYC, KLF4, and BCL-XL using a nonintegrating episomal vector system. While OCT4 was not required to reprogram PBMCs into iMSCs, omission of OCT4 significantly impaired iMSC functionality. The omission of OCT4 resulted in significantly downregulating MSC lineage specific and mesoderm-regulating genes, including SRPX, COL5A1, SOX4, SALL4, TWIST1. When reprogramming PBMCs in the absence of OCT4, 67 genes were significantly hypermethylated with reduced transcriptional expression. These data indicate that transient expression of OCT4 may serve as a universal reprogramming factor by increasing chromatin accessibility and promoting demethylation. Our findings represent an approach to produce functional MSCs, and aid in identifying putative function associated MSC markers.


Assuntos
Leucócitos Mononucleares , Células-Tronco Mesenquimais , Humanos , Diferenciação Celular/genética , Leucócitos Mononucleares/metabolismo , Plasmídeos , Células-Tronco Mesenquimais/metabolismo , Fator 3 de Transcrição de Octâmero/genética , Fatores de Transcrição SOXC/genética , Fatores de Transcrição SOXC/metabolismo
13.
Precis Clin Med ; 6(1): pbad004, 2023 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-37007745

RESUMO

The desmoplastic and complex tumor microenvironment of pancreatic ductal adenocarcinoma (PDAC) has presented tremendous challenges for developing effective therapeutic strategies. Strategies targeting tumor stroma, albeit with great potential, have met with limited success due to the lack of knowledge on the molecular dynamics within the tumor microenvironment (TME). In pursuit of a better understanding of the influence of miRNAs on TME reprogramming and to explore circulating miRNAs as diagnostic and prognostic biomarkers for PDAC, using RNA-seq, miRNA-seq, and single-cell RNA-seq (scRNA-seq), we investigated the dysregulated signaling pathways in PDAC TME modulated by miRNAs from plasma and tumor tissue. Our bulk RNA-seq in PDAC tumor tissue identified 1445 significantly differentially expressed genes with extracellular matrix and structure organization as the top enriched pathways. Our miRNA-seq identified 322 and 49 abnormally expressed miRNAs in PDAC patient plasma and tumor tissue, respectively. We found many of the TME signaling pathways were targeted by those dysregulated miRNAs in PDAC plasma. Combined with scRNA-seq from patient PDAC tumor, our results revealed that these dysregulated miRNAs were closely associated with extracellular matrix (ECM) remodeling, cell-ECM communication, epithelial-mesenchymal transition, as well as immunosuppression orchestrated by different cellular components of TME. The findings of this study could assist the development of miRNA-based stromal targeting biomarkers or therapy for PDAC patients.

14.
Ann Neurol ; 69(6): 954-62, 2011 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-21437931

RESUMO

OBJECTIVE: Brain arteriovenous malformations (bAVMs) are an important cause of hemorrhagic stroke. The underlying mechanisms are not clear. No animal model for adult bAVM is available for mechanistic exploration. Patients with hereditary hemorrhagic telangiectasia type 2 (HHT2) with activin receptor-like kinase 1 (ALK1; ACVRL1) mutations have a higher incidence of bAVM than the general population. We tested the hypothesis that vascular endothelial growth factor (VEGF) stimulation with regional homozygous deletion of Alk1 induces severe dysplasia in the adult mouse brain, akin to human bAVM. METHODS: Alk1(2f/2f) (exons 4-6 flanked by loxP sites) and wild-type (WT) mice (8-10 weeks old) were injected with adenoviral vector expressing Cre recombinase (Ad-Cre; 2 × 10(7) plaque forming units [PFU]) and adeno-associated viral vectors expressing VEGF (AAV-VEGF; 2 × 10(9) genome copies) into the basal ganglia. At 8 weeks, blood vessels were analyzed. RESULTS: Gross vascular irregularities were seen in Alk1(2f/2f) mouse brain injected with Ad-Cre and AAV-VEGF. The vessels were markedly enlarged with abnormal patterning resembling aspects of the human bAVM phenotype, displayed altered expression of the arterial and venous markers (EphB4 and Jagged-1), and showed evidence of arteriovenous shunting. Vascular irregularities were not seen in similarly treated WT mice. INTERPRETATION: Our data indicate that postnatal, adult formation of the human disease, bAVM, is possible, and that both genetic mutation and angiogenic stimulation are necessary for lesion development. Our work not only provides a testable adult mouse bAVM model for the first time, but also suggests that specific medical therapy can be developed to slow bAVM growth and potentially stabilize the rupture-prone abnormal vasculature.


Assuntos
Malformações Arteriovenosas/patologia , Encéfalo/patologia , Modelos Animais de Doenças , Receptores de Activinas Tipo II/genética , Animais , Malformações Arteriovenosas/induzido quimicamente , Malformações Arteriovenosas/genética , Encéfalo/efeitos dos fármacos , Encéfalo/metabolismo , Proteínas de Ligação ao Cálcio/genética , Proteínas de Ligação ao Cálcio/metabolismo , Endotélio Vascular/efeitos dos fármacos , Endotélio Vascular/metabolismo , Endotélio Vascular/patologia , Regulação da Expressão Gênica/genética , Proteínas de Fluorescência Verde/genética , Humanos , Peptídeos e Proteínas de Sinalização Intercelular/genética , Peptídeos e Proteínas de Sinalização Intercelular/metabolismo , Proteína Jagged-1 , Proteínas de Membrana/genética , Proteínas de Membrana/metabolismo , Camundongos , Camundongos Transgênicos , Mutação/genética , Neovascularização Patológica/induzido quimicamente , Receptor EphB4/genética , Receptor EphB4/metabolismo , Proteínas Serrate-Jagged , Transdução Genética/métodos , Fator A de Crescimento do Endotélio Vascular/efeitos adversos
15.
iScience ; 25(8): 104686, 2022 Aug 19.
Artigo em Inglês | MEDLINE | ID: mdl-35874099

RESUMO

Although emerging evidence reveals that vaping alters the function of the central nervous system, the effects of maternal vaping on offspring brain development remain elusive. Using a well-established in utero exposure model, we performed single-nucleus ATAC-seq (snATAC-seq) and RNA sequencing (snRNA-seq) on prenatally e-cigarette-exposed rat brains. We found that maternal vaping distorted neuronal lineage differentiation in the neonatal brain by promoting excitatory neurons and inhibiting lateral ganglionic eminence-derived inhibitory neuronal differentiation. Moreover, maternal vaping disrupted calcium homeostasis, induced microglia cell death, and elevated susceptibility to cerebral ischemic injury in the developing brain of offspring. Our results suggest that the aberrant calcium signaling, diminished microglial population, and impaired microglia-neuron interaction may all contribute to the underlying mechanisms by which prenatal e-cigarette exposure impairs neonatal rat brain development. Our findings raise the concern that maternal vaping may cause adverse long-term brain damage to the offspring.

16.
Genome Biol ; 23(1): 237, 2022 11 09.
Artigo em Inglês | MEDLINE | ID: mdl-36352452

RESUMO

BACKGROUND: The use of a personalized haplotype-specific genome assembly, rather than an unrelated, mosaic genome like GRCh38, as a reference for detecting the full spectrum of somatic events from cancers has long been advocated but has never been explored in tumor-normal paired samples. Here, we provide the first demonstrated use of de novo assembled personalized genome as a reference for cancer mutation detection and quantifying the effects of the reference genomes on the accuracy of somatic mutation detection. RESULTS: We generate de novo assemblies of the first tumor-normal paired genomes, both nuclear and mitochondrial, derived from the same individual with triple negative breast cancer. The personalized genome was chromosomal scale, haplotype phased, and annotated. We demonstrate that it provides individual specific haplotypes for complex regions and medically relevant genes. We illustrate that the personalized genome reference not only improves read alignments for both short-read and long-read sequencing data but also ameliorates the detection accuracy of somatic SNVs and SVs. We identify the equivalent somatic mutation calls between two genome references and uncover novel somatic mutations only when personalized genome assembly is used as a reference. CONCLUSIONS: Our findings demonstrate that use of a personalized genome with individual-specific haplotypes is essential for accurate detection of the full spectrum of somatic mutations in the paired tumor-normal samples. The unique resource and methodology established in this study will be beneficial to the development of precision oncology medicine not only for breast cancer, but also for other cancers.


Assuntos
Neoplasias , Humanos , Neoplasias/genética , Medicina de Precisão , Genoma , Software , Haplótipos , Mutação , Análise de Sequência de DNA , Sequenciamento de Nucleotídeos em Larga Escala/métodos
17.
Genome Biol ; 23(1): 255, 2022 12 13.
Artigo em Inglês | MEDLINE | ID: mdl-36514120

RESUMO

BACKGROUND: The cancer genome is commonly altered with thousands of structural rearrangements including insertions, deletions, translocation, inversions, duplications, and copy number variations. Thus, structural variant (SV) characterization plays a paramount role in cancer target identification, oncology diagnostics, and personalized medicine. As part of the SEQC2 Consortium effort, the present study established and evaluated a consensus SV call set using a breast cancer reference cell line and matched normal control derived from the same donor, which were used in our companion benchmarking studies as reference samples. RESULTS: We systematically investigated somatic SVs in the reference cancer cell line by comparing to a matched normal cell line using multiple NGS platforms including Illumina short-read, 10X Genomics linked reads, PacBio long reads, Oxford Nanopore long reads, and high-throughput chromosome conformation capture (Hi-C). We established a consensus SV call set of a total of 1788 SVs including 717 deletions, 230 duplications, 551 insertions, 133 inversions, 146 translocations, and 11 breakends for the reference cancer cell line. To independently evaluate and cross-validate the accuracy of our consensus SV call set, we used orthogonal methods including PCR-based validation, Affymetrix arrays, Bionano optical mapping, and identification of fusion genes detected from RNA-seq. We evaluated the strengths and weaknesses of each NGS technology for SV determination, and our findings provide an actionable guide to improve cancer genome SV detection sensitivity and accuracy. CONCLUSIONS: A high-confidence consensus SV call set was established for the reference cancer cell line. A large subset of the variants identified was validated by multiple orthogonal methods.


Assuntos
Variações do Número de Cópias de DNA , Neoplasias , Humanos , Análise de Sequência de DNA/métodos , Variação Estrutural do Genoma , Tecnologia , Linhagem Celular , Sequenciamento de Nucleotídeos em Larga Escala , Genoma Humano , Neoplasias/genética
18.
Stroke ; 42(3): 764-9, 2011 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-21273567

RESUMO

BACKGROUND AND PURPOSE: Osteopontin (OPN) is neuroprotective in ischemic brain injuries in adult experimental models; therefore, we hypothesized that OPN would provide neuroprotection and improve long-term neurological function in the immature brain after hypoxic-ischemic (HI) injury. METHODS: HI was induced by unilateral ligation of the right carotid artery followed by hypoxia (8% O(2) for 2 hours) in postnatal Day 7 rats. OPN (0.03 µg or 0.1 µg) was injected intracerebroventricularly at 1 hour post-HI. Temporal expression of endogenous OPN was evaluated in the normal rat brain at the age of 0, 4, 7, 11, 14, and 21 days and in the ipsilateral hemisphere after HI. The effects of OPN were evaluated using 2-3-5-triphenyl tetrazolium chloride staining, apoptotic cell death assay, and cleaved caspase-3 expression. Neurological function was assessed by the Morris water maze test. RESULTS: Endogenous OPN expression in the brain was the highest at the age of 0 day with continuous reduction until the age of 21 days during development. After HI injury, endogenous OPN expression was increased and peaked at 48 hours. Exogenous OPN decreased infarct volume and improved neurological outcomes 7 weeks after HI injury. OPN-induced neuroprotection was blocked by an integrin antagonist. CONCLUSIONS: OPN-induced neuroprotection was associated with cleaved-caspase-3 inhibition and antiapoptotic cell death. OPN treatment improved long-term neurological function against neonatal HI brain injury.


Assuntos
Proteínas Reguladoras de Apoptose/fisiologia , Apoptose/fisiologia , Modelos Animais de Doenças , Hipóxia-Isquemia Encefálica/patologia , Hipóxia-Isquemia Encefálica/prevenção & controle , Osteopontina/fisiologia , Animais , Animais Recém-Nascidos , Proteínas Reguladoras de Apoptose/administração & dosagem , Proteínas Reguladoras de Apoptose/uso terapêutico , Caspase 3/metabolismo , Caspase 3/fisiologia , Inibidores de Caspase , Morte Celular/efeitos dos fármacos , Morte Celular/fisiologia , Osteopontina/administração & dosagem , Osteopontina/uso terapêutico , Ratos
19.
Ann Neurol ; 68(5): 650-60, 2010 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-21031580

RESUMO

OBJECTIVE: Osteopontin (OPN), a pleiotropic extracellular matrix glycoprotein, has been reported to be protective against ischemic lesions, but effects of OPN on vascular functions have not been investigated. The aim of this study was to assess whether recombinant OPN (r-OPN) could prevent cerebral vasospasm after subarachnoid hemorrhage (SAH) in rats. METHODS: r-OPN was administered intraventricularly to rats undergoing SAH by endovascular perforation, and its protective effects were evaluated by measuring the diameter of cerebral arteries and neurobehavioral testing. Western blotting and immunofluorescence were performed to explore the underlying mechanisms. An integrin receptor antagonist GRGDSP or mitogen-activated protein kinase (MAPK) phosphatase (MKP)-1 small interfering RNA (siRNA) was also administered to r-OPN-treated SAH rats, and those effects were evaluated. RESULTS: Pre-SAH administration of r-OPN prevented vasospasm and neurological impairments at 24-72 hours post-SAH. r-OPN enhanced an endogenous MAPK inhibitor, MKP-1, and suppressed the phosphorylation of MAPKs, caldesmon, and heat shock protein 27 in the spastic cerebral arteries at 24 hours post-SAH. Immunofluorescence revealed that MKP-1 was induced in the arterial smooth muscle layer. GRGDSP prevented r-OPN-induced MKP-1 upregulation, and MKP-1 siRNA abolished both MAPK inactivation and anti-vasospastic effects by r-OPN. Post-SAH r-OPN treatment also prevented vasospasm. INTERPRETATION: r-OPN induced MKP-1 in the spastic cerebral arteries via binding to L-arginyl-glycyl-L-aspartate-dependent integrin receptors and prevented vasospasm after SAH. Therapeutic induction of MKP-1 may be a novel approach for the prevention and treatment of cerebral vasospasm.


Assuntos
Osteopontina/administração & dosagem , Proteínas Recombinantes/administração & dosagem , Hemorragia Subaracnóidea/metabolismo , Vasoespasmo Intracraniano/prevenção & controle , Animais , Comportamento Animal/efeitos dos fármacos , Artérias Cerebrais/efeitos dos fármacos , Artérias Cerebrais/metabolismo , Artérias Cerebrais/patologia , Modelos Animais de Doenças , Interações Medicamentosas , Fosfatase 1 de Especificidade Dupla/metabolismo , Injeções Intraventriculares , Masculino , Oligopeptídeos/administração & dosagem , Osteopontina/antagonistas & inibidores , RNA Interferente Pequeno/administração & dosagem , Ratos , Ratos Sprague-Dawley , Proteínas Recombinantes/antagonistas & inibidores , Hemorragia Subaracnóidea/complicações , Hemorragia Subaracnóidea/patologia , Regulação para Cima , Vasoespasmo Intracraniano/complicações , Vasoespasmo Intracraniano/metabolismo
20.
Acta Neurochir Suppl ; 111: 243-51, 2011.
Artigo em Inglês | MEDLINE | ID: mdl-21725763

RESUMO

BACKGROUND: Hyperbaric oxygenation is a readily available treatment modality, and its ability to improve neurological outcomes in a variety of animal models has been demonstrated. This study was designed to investigate the use of a single pretreatment regimen of either hyperbaric oxygenation or normobaric oxygenation to determine its effects in a murine model of surgically induced brain injury (SBI). MATERIALS AND METHODS: Hyperbaric oxygen (2.5ATM, 1 h), normobaric oxygen (100% FIO2, 1 h) or room air (21% FIO2, 1 h) was applied on CD-1 mice immediately, or at 1, 2 or 3 h followed by SBI or sham surgical operation. Neurological assessment of the animals was done by a blinded observer at 24 and 72 h using a 21-point modified Garcia scale, wire hanging test, and beam balance test. The brain edema was evaluated using brain water content at 24 and 72 h after SBI. RESULTS: There was no statistically significant difference in the mortality rate after treatment compared with the SBI group. The brain water content after SBI was significantly increased in the right (ipsilateral) frontal lobe surrounding the site of surgical resection compared with the sham group. Both hyperbaric and normobaric oxygen treatment significantly increased the brain edema and worsened the neurological outcomes using a 21-point Garcia score compared with the SBI group. The brain edema at 24 h after injury was most pronounced in the group treated with normobaric oxygenation 2 h prior to surgery. These differences disappeared at 72 h after SBI. CONCLUSION: Immediate pretreatment with either hyperbaric (2.5ATM, 1 h) or normobaric oxygen (100% FIO2, 1 h) increased brain edema and worsened neurological function at 24 h following SBI.


Assuntos
Edema Encefálico/etiologia , Lesões Encefálicas/complicações , Oxigenoterapia Hiperbárica/efeitos adversos , Doenças do Sistema Nervoso/terapia , Análise de Variância , Animais , Edema Encefálico/patologia , Lesões Encefálicas/etiologia , Córtex Cerebral/fisiopatologia , Modelos Animais de Doenças , Lateralidade Funcional , Camundongos , Doenças do Sistema Nervoso/etiologia , Exame Neurológico , Procedimentos Neurocirúrgicos/efeitos adversos , Fatores de Tempo , Resultado do Tratamento
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