Next‐Generation Sequencing Reveals Differential Responses to Acute versus Long‐Term Exposures to Graphene Oxide in Human Lung Cells

ABSTRACTOur understanding of adenovirus (Ad) biology is largely extrapolated from human species C Ad5. Most humans are immune to Ad5, so lower-seroprevalence viruses like human Ad6 and Ad26 are being tested as therapeutic vectors. Ad6 and Ad26 differ at the DNA level by 34%. To better understand how this might impact their biology, we examined the life cycle of the two viruses in human lung cellsin vitro. Both viruses infected A549 cells with similar efficiencies, executed DNA replication with identical kinetics within 12 h, and began killing cells within 72 h. While Ad6-infected cells remained adherent until death, Ad26-infected cells detached within 12 h of infection but remained viable. Next-generation sequencing (NGS) of mRNA from infected cells demonstrated that viral transcripts constituted 1% of cellular mRNAs within 6 h and 8 to 16% within 12 h. Quantitative PCR and NGS revealed the activation of key early genes at 6 h and transition to late gene activation by 12 h by both viruses. There were marked differences in the balance of E1A and E1B activation by the two viruses and in the expression of E3 immune evasion mRNAs. Ad6 was markedly more effective at suppressing major histocompatibility complex class I (MHC I) display on the cell surface and in evading TRAIL-mediated apoptosis than was Ad26. These data demonstrate shared as well as divergent life cycles in these genetically distant human adenoviruses. An understanding of these differences expands the knowledge of alternative Ad species and may inform the selection of related Ads for therapeutic development.IMPORTANCEA burgeoning number of adenoviruses (Ads) are being harnessed as therapeutics, yet the biology of these viruses is generally extrapolated from Ad2 and Ad5. Here, we are the first to compare the transcriptional programs of two genetically distant Ads by mRNA next-generation sequencing (NGS). Species C Ad6 and Ad26 are being pursued as lower-seroprevalence Ad vectors but differ at the DNA level by 34%. Head-to-head comparison in human lung cells by NGS revealed that the two viruses generally conform to our general understanding of the Ad transcriptional program. However, fine mapping revealed subtle and strong differences in how these two viruses execute these programs, including differences in the balance of E1A and E1B mRNAs and in E3 immune evasion genes. This suggests that not all adenoviruses behave like Ad2 and Ad5 and that they may have unique strategies to infect cells and evade the immune system.

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Next Generation Sequencing Discoveries of the Nitrate-Responsive Oral Microbiome and Its Effect on Vascular Responses

Journal of Clinical Medicine ◽

10.3390/jcm8081110 ◽

2019 ◽

Vol 8 (8) ◽

pp. 1110 ◽

Cited By ~ 3

Author(s):

Melissa M. Grant ◽

Daniel Jönsson

Keyword(s):

Nitric Oxide ◽

Next Generation Sequencing ◽

Human Condition ◽

Oral Microbiome ◽

Oral Microbiota ◽

Next Generation ◽

Contributing Factors ◽

Future Directions ◽

Generation Sequencing

Cardiovascular disease is a worldwide human condition which has multiple underlying contributing factors: one of these is long-term increased blood pressure—hypertension. Nitric oxide (NO) is a small nitrogenous radical species that has a number of physiological functions including vasodilation. It can be produced enzymatically through host nitric oxide synthases and by an alternative nitrate–nitrite–NO pathway from ingested inorganic nitrate. It was discovered that this route relies on the ability of the oral microbiota to reduce nitrate to nitrite and NO. Next generation sequencing has been used over the past two decades to gain deeper insight into the microbes involved, their location and the effect of their removal from the oral cavity. This review article presents this research and comments briefly on future directions.

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Correlation of Long-term Results of Imatinib in Advanced Gastrointestinal Stromal Tumors With Next-Generation Sequencing Results

JAMA Oncology ◽

10.1001/jamaoncol.2016.6728 ◽

2017 ◽

Vol 3 (7) ◽

pp. 944 ◽

Cited By ~ 25

Author(s):

Michael C. Heinrich ◽

Cathryn Rankin ◽

Charles D. Blanke ◽

George D. Demetri ◽

Ernest C. Borden ◽

...

Keyword(s):

Next Generation Sequencing ◽

Gastrointestinal Stromal Tumors ◽

Long Term Results ◽

Next Generation ◽

Stromal Tumors ◽

Generation Sequencing

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Expression of lung resistance-related protein, LRP, and multidrug resistance-related protein, MRP1, in normal human lung cells in long-term cultures

Archives of Toxicology ◽

10.1007/s00204-005-0669-1 ◽

2005 ◽

Vol 79 (10) ◽

pp. 600-609 ◽

Cited By ~ 7

Author(s):

Thomas Lehmann ◽

Abdel-Rahman Wageeh Torky ◽

Ekkehard Stehfest ◽

Stefan Hofmann ◽

Heidi Foth

Keyword(s):

Multidrug Resistance ◽

Human Lung ◽

Lung Cells ◽

Related Protein ◽

Human Lung Cells ◽

Lung Resistance ◽

Normal Human ◽

Multidrug Resistance Related Protein

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Graphene oxide is degraded by neutrophils and the degradation products are non-genotoxic

Nanoscale ◽

10.1039/c7nr03552g ◽

2018 ◽

Vol 10 (3) ◽

pp. 1180-1188 ◽

Cited By ~ 63

Author(s):

Sourav P. Mukherjee ◽

Anda R. Gliga ◽

Beatrice Lazzaretto ◽

Birgit Brandner ◽

Matthew Fielden ◽

...

Keyword(s):

Graphene Oxide ◽

Human Lung ◽

Degradation Products ◽

Lung Cells ◽

Human Lung Cells

Graphene oxide (GO) undergoes neutrophil myeloperoxidase (MPO) dependent degradation and the degradation products are non-genotoxic for human lung cells.

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Case Report: Metagenomics Next-Generation Sequencing Can Help Define the Best Therapeutic Strategy for Brain Abscesses Caused by Oral Pathogens

Frontiers in Medicine ◽

10.3389/fmed.2021.644130 ◽

2021 ◽

Vol 8 ◽

Author(s):

Zhonghui Ma ◽

Su Yan ◽

Haoxin Dong ◽

Huifen Wang ◽

Yonggang Luo ◽

...

Keyword(s):

Next Generation Sequencing ◽

Brain Abscess ◽

Genomic Analysis ◽

Critical Factor ◽

Oral Microbiome ◽

Next Generation ◽

Gram Staining ◽

Brain Abscesses ◽

Generation Sequencing

Brain abscesses are associated with an increased long-term risk of new seizures and increased mortality within several years after infection. Common microorganisms that cause brain abscesses include bacteria, fungi, and mycoplasma. We report a 75-year-old man with a brain abscess caused by Prevotella denticola, an oral pathogen. Based on the clinical condition, we suspected that the patient had a blood-borne brain abscess, and he received antibiotics and systemic supportive treatment. The patient developed shock for the second time after negative Gram-staining results. Metagenomics next-generation sequencing showed one strain from the oral microbiome, confirming our hypothesis, and targeted antibiotic treatment was administered quickly. Thus, we report a case in which genomic analysis was the critical factor in determining the best antimicrobial therapy for administration.

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Rapid succession drives spring community dynamics of small protists at Helgoland Roads, North Sea

Journal of Plankton Research ◽

10.1093/plankt/fbaa017 ◽

2020 ◽

Vol 42 (3) ◽

pp. 305-319 ◽

Cited By ~ 1

Author(s):

Laura Käse ◽

Alexandra C Kraberg ◽

Katja Metfies ◽

Stefan Neuhaus ◽

Pim A A Sprong ◽

...

Keyword(s):

Next Generation Sequencing ◽

Community Dynamics ◽

Sampling Period ◽

Next Generation ◽

Helgoland Roads ◽

Long Term Ecological Research ◽

Eukaryotic Microbes ◽

Five Phases ◽

Generation Sequencing

Abstract The dynamics of diatoms and dinoflagellates have been monitored for many decades at the Helgoland Roads Long-Term Ecological Research site and are relatively well understood. In contrast, small-sized eukaryotic microbes and their community changes are still much more elusive, mainly due to their small size and uniform morphology, which makes them difficult to identify microscopically. By using next-generation sequencing, we wanted to shed light on the Helgoland planktonic community dynamics, including nano- and picoplankton, during a spring bloom. We took samples from March to May 2016 and sequenced the V4 region of the 18S rDNA. Our results showed that mixotrophic and heterotrophic taxa were more abundant than autotrophic diatoms. Dinoflagellates dominated the sequence assemblage, and several small-sized eukaryotic microbes like Haptophyta, Choanoflagellata, Marine Stramenopiles and Syndiniales were identified. A diverse background community including taxa from all size classes was present during the whole sampling period. Five phases with several communities were distinguished. The fastest changes in community composition took place in phase 3, while the communities from phases 1 to 5 were more similar to each other despite contrasting environmental conditions. Synergy effects of next-generation sequencing and traditional methods may be exploited in future long-term observations.

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