Your browser doesn't support javascript.
loading
Mostrar: 20 | 50 | 100
Resultados 1 - 20 de 68
Filtrar
1.
Ecotoxicol Environ Saf ; 285: 117059, 2024 Sep 19.
Artículo en Inglés | MEDLINE | ID: mdl-39303636

RESUMEN

Microcystin-LR (MC-LR), a common hepatotoxin produced by bloom-forming cyanobacteria, presents a serious threat to the health of aquatic animals. In this study, we studied the impact of MC-LR on hepatopancreas histopathology, enzyme activity, transcriptome, and apoptosis of Litopenaeus vannamei. Thus, shrimp postlarvae (1.63 ± 0.5 g) exposed to MC-LR at 500 µg/kg caused morphological lesions in the histology of the shrimp hepatopancreas, which exhibited swollen, lighter coloration and unclear edges. Moreover, MC-LR significantly altered the hepatopancreas enzyme activities such as the levels of glutathione peroxidase (GSH-Px), superoxide dismutase (SOD), acid phosphatase (ACP), alkaline phosphatase (AKP) and lysozyme (LZM), including the state of apoptosis in hepatopancreas. From the RNA-seq analysis of the hepatopancreas, a total of 728 differentially expressed genes (DEGs) were identified, and their functions in MC-LR treatment group were involved in cellular processes, metabolic processes, biological regulation, cellular components, catalytic activity and binding. The metabolic pathways primarily associated with the DEGs included reactive oxygen species, glycerophospholipid metabolism and the phospholipase D signaling pathway. Overall, q-PCR results indicated that MC-LR led to significant changes in multiple apoptosis genes of shrimp hepatopancreas. This study expand the understanding of the effect of microcystin-LR on commercially farmed crustaceans.

2.
Microb Ecol ; 87(1): 82, 2024 Jun 03.
Artículo en Inglés | MEDLINE | ID: mdl-38831142

RESUMEN

Denitrification and anaerobic ammonium oxidation (anammox) are key processes for nitrogen removal in aquaculture, reducing the accumulated nitrogen nutrients to nitrogen gas or nitrous oxide gas. Complete removal of nitrogen from aquaculture systems is an important measure to solve environmental pollution. In order to evaluate the nitrogen removal potential of marine aquaculture ponds, this study investigated the denitrification and anammox rates, the flux of nitrous oxide (N2O) at the water-air interface, the sediment microbial community structure, and the gene expression associated with the nitrogen removal process in integrated multi-trophic aquaculture (IMTA) ponds (Apostistius japonicus-Penaeus japonicus-Ulva) with different culture periods. The results showed that the denitrification and anammox rates in sediments increased with the increase of cultivation periods and depth, and there was no significant difference in nitrous oxide gas flux at the water-air interface between different cultivation periods (p > 0.05). At the genus and phylum levels, the abundance of microorganisms related to nitrogen removal reactions in sediments changed significantly with the increase of cultivation period and depth, and was most significantly affected by the concentration of particulate organic nitrogen (PON) in sediments. The expression of denitrification gene (narG, nirS, nosZ) in surface sediments was significantly higher than that in deep sediments (p < 0.05), and was negatively correlated with denitrification rate. All samples had a certain anammox capacity, but no known anammox bacteria were found in the microbial diversity detection, and the expression of gene (hzsB) related to the anammox process was extremely low, which may indicate the existence of an unknown anammox bacterium. The data of this study showed that the IMTA culture pond had a certain potential for nitrogen removal, and whether it could make a contribution to reducing the pollution of culture wastewater still needed additional practice and evaluation, and also provided a theoretical basis for the nitrogen removal research of coastal mariculture ponds.


Asunto(s)
Acuicultura , Bacterias , Desnitrificación , Microbiota , Nitrógeno , Óxido Nitroso , Penaeidae , Estanques , Nitrógeno/metabolismo , Bacterias/clasificación , Bacterias/genética , Bacterias/metabolismo , Bacterias/aislamiento & purificación , Estanques/microbiología , Animales , Penaeidae/microbiología , Óxido Nitroso/metabolismo , Óxido Nitroso/análisis , Sedimentos Geológicos/microbiología , Oxidación-Reducción , Compuestos de Amonio/metabolismo
3.
ACS Nano ; 18(26): 16853-16866, 2024 Jul 02.
Artículo en Inglés | MEDLINE | ID: mdl-38896491

RESUMEN

The precise modulation of electrical activity in specific neuronal populations is paramount for rectifying abnormal neurological functions and is a critical element in the therapeutic arsenal for neurological disorders. However, achieving a balance between minimal invasiveness and robust neuroprotection poses a considerable challenge. Herein, we present a nanoneuromodulation strategy integrating neuroprotective features to effectively address epilepsy with minimal invasiveness and enable wireless functionality. Strategically engineered nanotransducer, adorned with platinum (Pt) decoration with titanium disulfide (TiS2) (TiS2/Pt), enables precise modulation of neuronal electrical activity in vitro and in vivo, ensuring exceptional temporal fidelity under millisecond-precision near-infrared (NIR) light pulses irradiation. Concurrently, TiS2/Pt showcase a pronounced enhancement in enzyme-mimicking activity, offering a robust defense against oxidative neurological injury in vitro. Nanotransducer-enabled wireless neuromodulation with biocatalytic neuroprotective capacity is highly effective in alleviating epileptic high-frequency neural activity and diminishing oxidative stress levels, thereby restoring redox equilibrium. This integrated therapeutic approach reduces the severity of epilepsy, demonstrating minimal invasiveness and obviating the requirements for genetic manipulation and optical fiber implantation, while providing an alternative avenue for neurological disorder treatment.


Asunto(s)
Epilepsia , Epilepsia/terapia , Animales , Titanio/química , Titanio/farmacología , Platino (Metal)/química , Platino (Metal)/farmacología , Fármacos Neuroprotectores/farmacología , Fármacos Neuroprotectores/química , Neuroprotección/efectos de los fármacos , Ratones , Disulfuros/química , Disulfuros/farmacología , Estrés Oxidativo/efectos de los fármacos , Humanos , Neuronas/efectos de los fármacos , Neuronas/metabolismo , Rayos Infrarrojos , Ratas
4.
Biosens Bioelectron ; 261: 116453, 2024 Oct 01.
Artículo en Inglés | MEDLINE | ID: mdl-38850739

RESUMEN

Implantable cardiac pacemakers are crucial therapeutic tools for managing various cardiac conditions. For effective pacing, electrodes should exhibit flexibility, deformability, biocompatibility, and high conductivity/capacitance. Laser-induced graphene (LIG) shows promise due to its exceptional electrical and electrochemical properties. However, the fragility of LIG and the non-stretchability of polyimide substrates pose challenges when interfacing with the beating heart. Here, we present a simple method for fabricating robust, flexible, and stretchable bioelectronic interfaces by transferring LIG via water-responsive, nonswellable polyvinyl alcohol (PVA) gels. PVA solution penetrates the porous structure of LIG and solidifies into PVA xerogel as the solvent evaporates. The robust PVA xerogel enables the smooth transfer of LIG and prevents stretching of the LIG network during this process, which helps maintain its conductivity. When hydrated, the xerogel becomes a stable, nonswellable hydrogel. This gives the LIG-PVA hydrogel (LIG-PVA-H) composites with excellent conductivity (119.7 ± 4.3Ω sq-1), high stretchability (up to 420%), reliability (cyclic stretch under 15% strain, with ∼ 1-time resistance increase), and good stability in phosphate buffered saline. The LIG-PVA-H composites were used as biointerfaces for electrocardiogram signal recording and electrical pacing on rat hearts ex vivo and in vivo, using commercial setups and a custom-built implantable wireless device. This work expands the application of LIG in bioelectronic interfaces and facilitates the development of electrotherapy for cardiac diseases.


Asunto(s)
Técnicas Biosensibles , Grafito , Rayos Láser , Alcohol Polivinílico , Grafito/química , Alcohol Polivinílico/química , Animales , Ratas , Conductividad Eléctrica , Agua/química , Marcapaso Artificial , Estimulación Cardíaca Artificial , Geles/química , Ratas Sprague-Dawley
5.
Biosens Bioelectron ; 255: 116229, 2024 Jul 01.
Artículo en Inglés | MEDLINE | ID: mdl-38554574

RESUMEN

Quantifying trace glycoproteins in biofluids requires ultrasensitive components, but feedback is not available in the current portable platforms of point-of-care (POC) diagnosis technologies. A compact and ultrasensitive bioelectrochemical patch was based on boronate-affinity amplified organic electrochemical transistors (BAAOECTs) for POC use was developed to overcome this dilemma. Benefit from the cascading signal enhancement deriving from boronate-affinity targeting multiple regions of glycoprotein and OECTs' inherent signal amplification capability, the BAAOECTs achieved a detection limit of 300 aM within 25 min, displaying about 3 orders of magnitude improvement in sensitivity compared with the commercial electrochemical luminescence (ECL) kit. By using a microfluidic chip, a microcontroller module, and a wireless sensing system, the testing workflows of the above patch was automated, allowing for running the sample-to-answer pipeline even in a resource-limited environment. The reliability of such portable biosensing platform is well recognized in clinical diagnostic applications of heart failure. Overall, the remarkable enhanced sensitivity and automated workflow of BAAOECTs biosensing platform provide a prospective and generalized design policy for expanding the POC diagnosis capabilities of glycoproteins.


Asunto(s)
Técnicas Biosensibles , Sistemas de Atención de Punto , Estudios Prospectivos , Reproducibilidad de los Resultados , Glicoproteínas , Técnicas Electroquímicas
6.
Appl Microbiol Biotechnol ; 108(1): 225, 2024 Feb 20.
Artículo en Inglés | MEDLINE | ID: mdl-38376561

RESUMEN

The gut microbial communities interact with the host immunity and physiological functions. In this study, we investigated the bacterial composition in Litopenaeus vannamei shrimp's gut and rearing water under different host (developmental stage: juvenile and adult; health status: healthy and diseased) and environmental factors (temperature 25 °C and 28 °C; and light intensity: low and high). The PCoA analysis showed that all water samples were clustered together in a quarter, whereas the gut samples spread among three quarters. In terms of functional bacteria, gut samples of adult shrimp, healthy adult shrimp, adult shrimp raised at 28 °C, and juvenile shrimp under high light intensity exhibited a higher abundance of Vibrionaceae compared to each other opposite group. Gut samples of juvenile shrimp, infected adult shrimp, juvenile shrimp with low light intensity, and adult shrimp with a water temperature of 25 °C showed a higher abundance of Pseudoaltromonadaceae bacteria compared to each other opposite group. Gut samples of juvenile shrimp, healthy adult shrimp, adult shrimp raised at a water temperature of 28 °C, and juvenile shrimp with high light intensity showed the higher abundance of Firmicutes/Bacteroidota ratio compared to each other opposite group. Our results showed that L. vannamei juveniles are more sensitive to bacterial infections; besides, water temperature of 28 °C and high light intensity groups were both important conditions improving the shrimp gut bacterial composition under industrial indoor farming systems. KEY POINTS: • Bacteria diversity was higher among shrimp intestinal microbiota compared to the rearing water. • Shrimp juveniles are more sensitive to bacterial infection compared to adults. • Water temperature of 28 °C and high light intensity are recommended conditions for white shrimp aquaculture.


Asunto(s)
Microbioma Gastrointestinal , Microbiota , Penaeidae , Animales , Agricultura , Granjas , Agua
7.
Adv Healthc Mater ; 13(17): e2303219, 2024 Jul.
Artículo en Inglés | MEDLINE | ID: mdl-38198617

RESUMEN

Irregular electrical impulses in atrium are the leading cause of atrial fibrillation (AF), resulting in fatal arrhythmia and sudden cardiac death. Traditional medication and physical therapies are widely used, but generally suffer problems in serious physical damage and high surgical risks. Flexible and soft implants have great potential to be a novel approach for heart diseases therapy. A conductive hydrogel-based mesh cardiac patch is developed for application in AF elimination. The designed mesh patch with rhombic-shaped structure exhibits excellent flexibility, surface conformability, and deformation compliance, making it fit well with heart surface and accommodate to the deformation during heart beating. Moreover, the mechanical elastic and shape-memory properties of the mesh patch enable a minimally invasive injection of the patch into living animals. The mesh patch is implanted on the atrium surface for one month, indicating good biocompatibility and stability. Furthermore, the conductive patch can effectively eliminate AF owing to the conductivity and high charge storage capability (CSC) of the hydrogel. The proposed scheme of cardiac bioelectric signal modulation using conductive hydrogel brings new possibility for the treatment of arrhythmia diseases.


Asunto(s)
Fibrilación Atrial , Conductividad Eléctrica , Hidrogeles , Fibrilación Atrial/terapia , Animales , Hidrogeles/química , Hidrogeles/farmacología , Ratas , Ratas Sprague-Dawley , Masculino
8.
Nano Lett ; 24(4): 1052-1061, 2024 Jan 31.
Artículo en Inglés | MEDLINE | ID: mdl-37955335

RESUMEN

Epilepsy is a prevalent and severe neurological disorder and generally requires prolonged electrode implantation and tether brain stimulation in refractory cases. However, implants may cause potential chronic immune inflammation and permanent tissue damage due to material property mismatches with soft brain tissue. Here, we demonstrated a nanomaterial-enabled near-infrared (NIR) neuromodulation approach to provide nongenetic and nonimplantable therapeutic benefits in epilepsy mouse models. Our study showed that crystal-exfoliated photothermal black phosphorus (BP) flakes could enhance neural activity by altering the membrane capacitive currents in hippocampus neurons through NIR photothermal neuromodulation. Optical stimulation facilitated by BP flakes in hippocampal slices evoked action potentials with a high spatiotemporal resolution. Furthermore, BP flake-enabled NIR neuromodulation of hippocampus neural circuits can suppress epileptic signals in epilepsy model mice with minimal invasiveness and high biocompatibility. Consequently, nanomaterial-enabled NIR neuromodulation may open up opportunities for nonimplantable optical therapy of epilepsy in nontransgenic organisms.


Asunto(s)
Epilepsia , Nanoestructuras , Ratones , Animales , Fósforo/uso terapéutico , Epilepsia/terapia , Hipocampo , Modelos Animales de Enfermedad
9.
Eur J Med Res ; 28(1): 533, 2023 Nov 20.
Artículo en Inglés | MEDLINE | ID: mdl-37986009

RESUMEN

BACKGROUND: The incidence and mortality of early-onset colorectal cancer (EOCRC; < 50 years old) is increasing worldwide, with a high recurrence rate. The inherent heterogeneity of EOCRC makes its treatment challenging. Hence, to further understand the biology and reveal the molecular mechanisms of EOCRC, a recurrence risk signature is needed to guide clinical management. METHODS: Based on the relative expression orderings (REOs) of genes in each sample, a prognostic signature was developed and validated utilizing multiple independent datasets. The underlying molecular mechanisms between distinct prognostic groups were explored via integrative analysis of multi-omics data. RESULTS: The prognostic signature consisting of 6 gene pairs (6-GPS) could predict the recurrence risk for EOCRC at the individual level. High-risk EOCRC classified by 6-GPS showed a poor prognosis but a good response to adjuvant chemotherapy. Moreover, high-risk EOCRC was characterized by epithelial-mesenchymal transition (EMT) and enriched angiogenesis, and had higher mutation burden, immune cell infiltration, and PD-1/PD-L1 expression. Furthermore, we identified four genes associated with relapse-free survival in EOCRC, including SERPINE1, PECAM1, CDH1, and ANXA1. They were consistently differentially expressed at the transcriptome and proteome levels between high-risk and low-risk EOCRCs. They were also involved in regulating cancer progression and immune microenvironment in EOCRC. Notably, the expression of SERPINE1 and ANXA1 positively correlated with M2-like macrophage infiltration. CONCLUSION: Our results indicate that 6-GPS can robustly predict the recurrence risk of EOCRC, and that SERPINE1, PECAM1, CDH1, and ANXA1 may serve as potential therapeutic targets. This study provides valuable information for the precision treatment of EOCRC.


Asunto(s)
Neoplasias Colorrectales , Transcriptoma , Humanos , Persona de Mediana Edad , Pronóstico , Neoplasias Colorrectales/genética , Neoplasias Colorrectales/metabolismo , Microambiente Tumoral
10.
Fish Shellfish Immunol ; 132: 108458, 2023 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-36455777

RESUMEN

The Penaeus vannamei is an important shrimp species with enormous commercial and ecological values. In production process, the air exposure resistance is vital for live transportation without water. We tested the air exposure resistant ability of P. vannamei, and carried out gill histological observation and gene expression analysis. The physiology and molecular response to the air exposure stress of P. vannamei was revealed. We found that body weight could affect the air exposure tolerance. Air exposure caused epithelial cell of gill filament shrinking and tissue fluid exudation within half of hour, and triggered oxidative stress response. After retrieved to water, epithelial cell shrinking and tissue fluid exudation recovered gradually, but oxidative and antioxidant response is still going on. Organisms reduced oxidative stress by regulating levels of antioxidants and antioxidant enzymes that remove reactive oxygen species (ROS) and RNA and DNA processing to repair tissue damage, and expression of apoptosis associated-genes altered. Furthermore, the survive shrimps could live steadily more than 5 days, and their gill filament recovered to normal state, proving that the damage of air exposure is reversible. These findings could be considered in the waterless live transportation of P. vannamei.


Asunto(s)
Antioxidantes , Penaeidae , Animales , Antioxidantes/metabolismo , Penaeidae/fisiología , Branquias/metabolismo , Estrés Oxidativo , Oxidación-Reducción
11.
Antibiotics (Basel) ; 11(12)2022 Dec 09.
Artículo en Inglés | MEDLINE | ID: mdl-36551441

RESUMEN

This study aimed to determine the immunity, survival rate, and disease resistance of Litopenaeus vannamei treated using quercetin and florfenicol alone or in combination, after infection with acute hepatopancreatic necrosis syndrome caused by Vibrio parahaemolyticus (VPAHPND). After infection with VPAHPND, different types of feed were given to the shrimp for 5 days, including a control diet (drug-free), florfenicol only diet (15 mg/kg), quercetin only diet (400 mg/kg), a low-dose florfenicol/quercetin combined diet (200 mg/kg quercetin + 7.0 mg/kg florfenicol), a moderate-dose florfenicol/quercetin combined diet (400 mg/kg quercetin + 15 mg/kg florfenicol), and a high-dose florfenicol/quercetin combined diet (800 mg/kg quercetin + 30 mg/kg florfenicol). The cumulative mortality of shrimp was significantly reduced in the drug combination groups compared with either drug used alone (p < 0.05). The density of Vibrio was significantly lower and the immune parameters were significantly increased in the drug combination groups compared with either drug used alone (p < 0.05). Moreover, in the drug combination groups, the hepatopancreas tubules showed better integrity and structure compared with those when either drug was used alone. Therefore, compared with single drug treatment, the florfenicol and quercetin combination enhanced disease resistance, survival, and immune activity of VPAHPND-infected shrimp. When the combination treatment is used, the dosage of florfenicol can be reduced and a better therapeutic effect is obtained.

12.
Micromachines (Basel) ; 13(11)2022 Nov 21.
Artículo en Inglés | MEDLINE | ID: mdl-36422463

RESUMEN

We designed, fabricated and measured full-color, reflective electrowetting displays (EWDs). The display system is composed of three-layer cyan, magenta and yellow EWD elements fabricated with standard photolithographic techniques. The EWDs were driven successfully by the proposed control system and the measurement results show that the electro-optical performance was improved. The aperture ratio of the EWD element can be tuned from 0 to ∼80% as the applied voltage is changed from 0 to 30 V. The response time and the color gamut were measured to be ∼18 ms and ∼58% NTSC, respectively. This paper makes it possible for large numbers of reflective full-color EWDs to be fabricated directly, with advantages of saving power significantly by 85% and no eye irritation compared with LED displays.

13.
Genes (Basel) ; 13(10)2022 10 21.
Artículo en Inglés | MEDLINE | ID: mdl-36292798

RESUMEN

Pancreatic adenocarcinoma (PAAD) has a poor prognosis with high individual variation in the treatment response among patients; however, there is no standard molecular typing method for PAAD prognosis in clinical practice. We analyzed DNA methylation data from The Cancer Genome Atlas database, which identified 1235 differentially methylated DNA genes between PAAD and adjacent tissue samples. Among these, 78 methylation markers independently affecting PAAD prognosis were identified after adjusting for significant clinical factors. Based on these genes, two subtypes of PAAD were identified through consistent clustering. Fourteen specifically methylated genes were further identified to be associated with survival. Further analyses of the transcriptome data identified 301 differentially expressed cancer driver genes between the two PAAD subtypes and the degree of immune cell infiltration differed significantly between the subtypes. The 14 specific genes characterizing the unique methylation patterns of the subtypes were used to construct a Bayesian network-based prognostic prediction model for typing that showed good predictive value (area under the curve value of 0.937). This study provides new insight into the heterogeneity of pancreatic tumors from an epigenetic perspective, offering new strategies and targets for personalized treatment plan evaluation and precision medicine for patients with PAAD.


Asunto(s)
Adenocarcinoma , Neoplasias Pancreáticas , Humanos , Neoplasias Pancreáticas/patología , Adenocarcinoma/genética , Metilación de ADN/genética , Teorema de Bayes , Regulación Neoplásica de la Expresión Génica/genética , Biomarcadores de Tumor/genética , Biomarcadores de Tumor/análisis , Pronóstico , ADN , Neoplasias Pancreáticas
14.
Matter ; 5(12): 4347-4362, 2022 Dec 07.
Artículo en Inglés | MEDLINE | ID: mdl-36157685

RESUMEN

Respiratory infectious diseases (H1N1, H5N1, COVID-19, etc.) are pandemics that can continually spread in the air through micro-droplets or aerosols. However, the detection of samples in gaseous media is hampered by the requirement for trace amounts and low concentrations. Here, we develop a wearable bioelectronic mask device integrated with ion-gated transistors. Based on the sensitive gating effect of ion gels, our aptamer-functionalized transistors can measure trace-level liquid samples (0.3 µL) and even gaseous media samples at an ultra-low concentration (0.1 fg/mL). The ion-gated transistor with multi-channel analysis can respond to multiple targets simultaneously within as fast as 10 min, especially without sample pretreatment. Integrating a wireless internet of things system enables the wearable mask to achieve real-time and on-site detection of the surrounding air, providing an alert before infection. The wearable bioelectronic masks hold promise to serve as an early warning system to prevent outbreaks of respiratory infectious diseases.

15.
Sci Rep ; 12(1): 6163, 2022 04 13.
Artículo en Inglés | MEDLINE | ID: mdl-35418129

RESUMEN

The study of the selective feeding of bivalves is necessary in order to improve our understanding of bivalve growth and development, which helps to better define the roles of bivalves in their ecosystems. Little information is currently available on the feeding preferences of bivalves in natural waters, since all diets are provided as single or mixed algae in experiments. In this study, high-throughput sequencing of the 23S rRNA gene was performed to explore differences in the feeding selectivity of Mercenaria mercenaria, Meretrix meretrix and Ruditapes philippinarum during different stages of their culturing to reveal their feeding preferences in natural waters. We found that the three bivalve species had different preferential selection of phytoplankton genera, indicating specific selection and avoidance of particular types of algae during their development in aquaculture. M. mercenaria was the most selective of the bivalves, followed by M. meretrix and then R. philippinarum. With the growth of M. mercenaria and M. meretrix, more kinds of phytoplankton could be ingested. In addition, high-throughput sequencing showed that some picophytoplankton including Synechococcus, Microchloropsis, and Chrysochromulina were dominant in the hepatopancreas samples obtained from these three bivalves. Therefore, the importance of these pico-sized algae in bivalve diets should be reassessed.


Asunto(s)
Bivalvos , Fitoplancton , Animales , Bivalvos/genética , Ecosistema , Secuenciación de Nucleótidos de Alto Rendimiento , Fitoplancton/genética , Estanques
16.
Brief Bioinform ; 23(2)2022 03 10.
Artículo en Inglés | MEDLINE | ID: mdl-35152286

RESUMEN

Individual pathway analysis can dissect heterogeneities among different cancer patients and provide efficient guidelines for individualized therapy. However, the existence of the batch effect brings extensive limitations for the application of many individual methods for pathway analysis. Previously, researchers proposed that methods based on within-sample relative expression ordering (REO) of the genes are notably insensitive to 'batch effects'. In this article, we focus on the Gene Ontology (GO) database and propose an individual qualitative GO term analysis method (IndGOterm) based on the REO of genes. Compared with some current widely used single-sample enrichment analysis methods, such as ssGSEA and GSVA, IndGOterm has a predominance of ignoring the batch effects caused by diverse technologies. Through the survival and drug responses analysis, we found IndGOterm could capture more terms connected to cancer than other single-sample enrichment analysis methods. Furthermore, through the application of IndGOterm, we found some terms that present different dysregulation models that manifest heterogenetic in homologous patients. Collectively, these results attested that IndGOterm could capture useful information from patients and be a useful tool to reveal the intrinsic characteristic of cancer. An open-source R statistical analysis package 'IndGOterm' is available at https://github.com/robert19960424/IndGOterm.


Asunto(s)
Perfilación de la Expresión Génica , Neoplasias , Perfilación de la Expresión Génica/métodos , Ontología de Genes , Humanos , Neoplasias/genética
17.
Mol Ther Nucleic Acids ; 26: 1014-1026, 2021 Dec 03.
Artículo en Inglés | MEDLINE | ID: mdl-34786207

RESUMEN

Pancreatic cancer (PC) with homologous recombination deficiency (HRD) has been reported to benefit from poly ADP-ribose polymerase (PARP) inhibitors. However, accurate identification of HRD status for PC patients from the transcriptional level is still a great challenge. Here, based on a relative expression ordering (REO)-based algorithm, we developed an HRD signature including 24 gene pairs (24-GPS) using PC transcriptional profiles from The Cancer Genome Atlas (TCGA). HRD samples classified by 24-GPS showed worse overall survival (p = 4.4E-3 for TCGA; p = 1.2E-3 for International Cancer Genome Consortium-Australia cohort; p = 6.4E-2 for GSE17891; p = 7.5E-2 for GSE57495) and higher HRD scores than non-HRD samples (p = 1.4E-4). HRD samples showed highly unstable genomic characteristics and also displayed HRD-related alterations at the epigenomic and proteomic levels. Moreover, HRD cell lines identified by 24-GPS tended to be sensitive to PARP inhibitors (p = 6.6E-2 for olaparib; p = 2.6E-3 for niraparib). Compared with the non-HRD group, the HRD group presented lower immune scores and CD4/CD8 T cell infiltration proportion. Interestingly, PC tumor cells with co-inhibition of PARP-related genes and ATR showed reduced survival ability. In conclusion, 24-GPS can robustly identify PC patients with HRD status at the individualized level.

18.
J Bioinform Comput Biol ; 19(3): 2140004, 2021 06.
Artículo en Inglés | MEDLINE | ID: mdl-33971799

RESUMEN

Glioma is one particular type of brain malignancy which is highly complex and usually has a poor prognosis. Despite the limited diagnostic level of glioma, the survival time of affected patients broadly varies. Here, we conducted a detailed analysis, regarding the differences in patient survival time, to discover potential survival-related genes in glioma as well as their putative regulatory mechanisms. To contextualize the acquisition of these potential prognosis markers in large populations, particularly in China, we combined CGGA and The Cancer Genome Atlas (TCGA) databases to properly identify genes that are significantly related to survival. Our workflow combined a series of analytical approaches, including differential analysis, survival time, co-expression, clinical correlation analysis, ROC curve evaluation and prediction ability. Our results indicate that the four particular genes - PLAT, IGFBP2, BCAT1, SERPINH1 could be used as independent prognostic marker genes. These genes have also shown good prognostic ability in distinct populations, reiterating the robustness and value of these prognostic markers.


Asunto(s)
Neoplasias Encefálicas , Glioma , Neoplasias Encefálicas/genética , China , Análisis de Datos , Glioma/genética , Humanos , Transaminasas
19.
Mol Ther Methods Clin Dev ; 18: 501-510, 2020 Sep 11.
Artículo en Inglés | MEDLINE | ID: mdl-32775488

RESUMEN

Dosage effect is one of the common mechanisms of somatic copy number alteration in the development of colorectal cancer, yet the roles of dosage-sensitive genes (DSGs) in colorectal cancer (CRC) remain to be characterized more deeply. In this study, we developed a five-step pipeline to identify DSGs and analyzed their characterization in CRC. Results showed that our pipeline performed better than existing methods, and the result was significantly overlapped between solid tumor and cell line. We also found that the top five DSGs (PSMF1, RAF1, PTPRA, MKRN2, and ELP3) were associated with the progression of CRC. By analyzing the characterization, DSGs were enriched in driver genes and they drove sub-pathways of CRC. In addition, immune-related DSGs are associated with CRC progression. Our results also showed that the CRC samples affected by high microsatellites have fewer DSGs, but a higher overlap with DSGs in microsatellite low instability and microsatellite stable samples. In addition, we applied DSGs to identify potential drug targets, with the results showing that 22 amplified DSGs were more sensitive to four drugs. In conclusion, DSGs play an important role in CRC, and our pipeline is effective to identify them.

20.
Clin Infect Dis ; 71(8): 1943-1946, 2020 11 05.
Artículo en Inglés | MEDLINE | ID: mdl-32301964

RESUMEN

BACKGROUND: Since December 2019, SARS-CoV-2 has extended to most parts of China with >80 000 cases and to at least 100 countries with >60 000 international cases as of 15 March 2020. Here we used a household cohort study to determine the features of household transmission of COVID-19. METHODS: A total of 105 index patients and 392 household contacts were enrolled. Both index patients and household members were tested by SARS-CoV-2 RT-PCR. Information on all recruited individuals was extracted from medical records and confirmed or supplemented by telephone interviews. The baseline characteristics of index cases and contact patients were described. Secondary attack rates of SARS-CoV-2 to contact members were computed and the risk factors for transmission within the household were estimated. RESULTS: Secondary transmission of SARS-CoV-2 developed in 64 of 392 household contacts (16.3%). The secondary attack rate to children was 4% compared with 17.1% for adults. The secondary attack rate to the contacts within the households with index patients quarantined by themselves since onset of symptoms was 0% compared with 16.9% for contacts without quarantined index patients. The secondary attack rate to contacts who were spouses of index cases was 27.8% compared with 17.3% for other adult members in the households. CONCLUSIONS: The secondary attack rate of SARS-CoV-2 in household is 16.3%. Age of household contacts and spousal relationship to the index case are risk factors for transmission of SARS-CoV-2 within a household. Quarantine of index patients at home since onset of symptoms is useful to prevent the transmission of SARS-Co-2 within a household.


Asunto(s)
Infecciones por Coronavirus/transmisión , Composición Familiar , Neumonía Viral/transmisión , Adolescente , Adulto , Betacoronavirus , COVID-19 , Niño , Preescolar , Estudios de Cohortes , Infecciones Comunitarias Adquiridas/transmisión , Trazado de Contacto/estadística & datos numéricos , Femenino , Humanos , Masculino , Persona de Mediana Edad , Pandemias , SARS-CoV-2 , Factores de Tiempo , Adulto Joven
SELECCIÓN DE REFERENCIAS
DETALLE DE LA BÚSQUEDA