Understanding virus–host interactions in tissues

Speranza, Emily

doi:10.1038/s41564-023-01434-7

Cited by 11 publications

(3 citation statements)

References 116 publications

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“…The development of high-throughput sequencing technologies has made it possible to determine the transcriptomic landscape at a single cell level. As for viral infection studies, single-cell RNA sequencing (scRNA-seq) does not only allow for discrimination between infected and non-infected bystander cells, but it also provides insight into cell typespecific responses in tissue culture as well as complex organs and immune systems [1][2][3]. However, the more stringent biosafety requirements using highly pathogenic viruses have hindered scRNA-seq analysis in studies involving viruses handled at the highest specific responses in tissue culture as well as complex organs and immune systems [1][2][3].…”

Section: Introductionmentioning

confidence: 99%

“…As for viral infection studies, single-cell RNA sequencing (scRNA-seq) does not only allow for discrimination between infected and non-infected bystander cells, but it also provides insight into cell typespecific responses in tissue culture as well as complex organs and immune systems [1][2][3]. However, the more stringent biosafety requirements using highly pathogenic viruses have hindered scRNA-seq analysis in studies involving viruses handled at the highest specific responses in tissue culture as well as complex organs and immune systems [1][2][3]. However, the more stringent biosafety requirements using highly pathogenic viruses have hindered scRNA-seq analysis in studies involving viruses handled at the highest biosafety level, BSL-4.…”

Section: Introductionmentioning

confidence: 99%

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Heat Inactivation of Nipah Virus for Downstream Single-Cell RNA Sequencing Does Not Interfere with Sample Quality

Hume,

Olejnik,

White

et al. 2024

Pathogens

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Single-cell RNA sequencing (scRNA-seq) technologies are instrumental to improving our understanding of virus–host interactions in cell culture infection studies and complex biological systems because they allow separating the transcriptional signatures of infected versus non-infected bystander cells. A drawback of using biosafety level (BSL) 4 pathogens is that protocols are typically developed without consideration of virus inactivation during the procedure. To ensure complete inactivation of virus-containing samples for downstream analyses, an adaptation of the workflow is needed. Focusing on a commercially available microfluidic partitioning scRNA-seq platform to prepare samples for scRNA-seq, we tested various chemical and physical components of the platform for their ability to inactivate Nipah virus (NiV), a BSL-4 pathogen that belongs to the group of nonsegmented negative-sense RNA viruses. The only step of the standard protocol that led to NiV inactivation was a 5 min incubation at 85 °C. To comply with the more stringent biosafety requirements for BSL-4-derived samples, we included an additional heat step after cDNA synthesis. This step alone was sufficient to inactivate NiV-containing samples, adding to the necessary inactivation redundancy. Importantly, the additional heat step did not affect sample quality or downstream scRNA-seq results.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Heat Inactivation of Nipah Virus for Downstream Single-Cell RNA Sequencing Does Not Interfere with Sample Quality

Hume,

Olejnik,

White

et al. 2024

Pathogens

View full text Add to dashboard Cite

show abstract

“…The study of emerging infectious diseases is greatly aided by the availability of single-cell RNA sequencing technologies. With the power to deeply profile individual cellular responses to infection, we can now generate a deeper understanding of how the host response to infections is coordinated [ 1 ]. One challenge faced when working with many pathogens of high public health impact is the need for work in high containment laboratories under the biosafety level 3 and biosafety level 4 (BSL-4) conditions [ 2 ].…”

Section: Introductionmentioning

confidence: 99%

Preservation of scRNA-Seq Libraries Using Existing Inactivation Protocols

Sturdevant,

Meade-White,

Best

et al. 2024

Pathogens

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Single-cell RNA sequencing has soared in popularity in recent years. The ability to deeply profile the states of individual cells during the course of disease or infection has helped to expand our knowledge of coordinated responses. However, significant challenges arise when performing this analysis in high containment settings such as biosafety level 3 (BSL-3), BSL-3+ and BSL-4. Working in containment is necessary for many important pathogens, such as Ebola virus, Marburg virus, Lassa virus, Nipah and Hendra viruses. Since standard operating procedures (SOPs) for inactivation are extensive and may compromise sample integrity, we tested whether the removal of single-cell sequencing libraries from containment laboratories using existing inactivation protocols for nucleic acid extraction (Trizol, RLT buffer, or AVL buffer) was feasible. We have demonstrated that the inactivation does not affect sample quality and can work with existing methods for inactivation.

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Simultaneously Controlling Inflammation and Infection by Smart Nanomedicine Responding to the Inflammatory Microenvironment

Lv,

Min,

Huang

et al. 2024

Advanced Science

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The overactivated immune cells in the infectious lesion may lead to irreversible organ damages under severe infections. However, clinically used immunosuppressive anti‐inflammatory drugs will usually disturb immune homeostasis and conversely increase the risk of infections. Regulating the balance between anti‐inflammation and anti‐infection is thus critical in treating certain infectious diseases. Herein, considering that hydrogen peroxide (H2O2), myeloperoxidase (MPO), and neutrophils are upregulated in the inflammatory microenvironment and closely related to the severity of appendectomy patients, an inflammatory‐microenvironment‐responsive nanomedicine is designed by using poly(lactic‐co‐glycolic) acid (PLGA) nanoparticles to load chlorine E6 (Ce6), a photosensitizer, and luminal (Lum), a chemiluminescent agent. The obtained Lum/Ce6@PLGA nanoparticles, being non‐toxic within normal physiological environment, can generate cytotoxic single oxygen via bioluminescence resonance energy transfer (BRET) in the inflammatory microenvironment with upregulated H2O2 and MPO, simultaneously killing pathogens and excessive inflammatory immune cells in the lesion, without disturbing immune homeostasis. As evidenced in various clinically relevant bacterial infection models and virus‐induced pneumonia, Lum/Ce6@PLGA nanoparticles appeared to be rather effective in controlling both infection and inflammation, resulting in significantly improved animal survival. Therefore, the BRET‐based nanoparticles by simultaneously controlling infections and inflammation may be promising nano‐therapeutics for treatment of severe infectious diseases.

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Understanding virus–host interactions in tissues

Cited by 11 publications

References 116 publications

Heat Inactivation of Nipah Virus for Downstream Single-Cell RNA Sequencing Does Not Interfere with Sample Quality

Heat Inactivation of Nipah Virus for Downstream Single-Cell RNA Sequencing Does Not Interfere with Sample Quality

Preservation of scRNA-Seq Libraries Using Existing Inactivation Protocols

Simultaneously Controlling Inflammation and Infection by Smart Nanomedicine Responding to the Inflammatory Microenvironment

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