Literature highlights – 11/02/2022

First wanted to shout out to the cover of Cell last week. Inspired by one of my favourite pieces of art The Great Wave by Japanese artist Hokusai. Love it! It references a study of a COVID outbreak in a vaccinated community published by Siddle et al.

On the cover: In July 2021, an outbreak of over 1,000 COVID-19 cases in Provincetown,
Massachusetts, was the first large outbreak mostly in vaccinated individuals in the
US, which raised questions about infection and transmission among vaccinated individuals.
In this issue, Siddle et al. (485–492) use viral genomic sequencing to learn from
the first wave of the Delta variant in Massachusetts, which resulted in a large outbreak
in the coastal tourist town of Provincetown. The cover is a reference to Hokusai’s
“The Great Wave off Kanagawa,” in this case illustrating instead the SARS-CoV-2 Delta
wave in Provincetown. The waves represent waves of the Delta variant, and the lighthouse
represent Provincetown, the site of the outbreak studied. The light emanating from
the lighthouse represents genomic sequencing. Image credit: Eric Diotte and Thought

The gut microbiota of environmentally enriched mice regulates visual cortical plasticity – Cell Reports

Fascinating study on how experiences in your environment shape the gut microbiota.

  • Housing mice in an enriched environment changes the gut microbiota
  • An intact gut microbiota is necessary for enrichment-driven cortical plasticity
  • Short-chain fatty acids modulate microglia morphology and visual cortical plasticity
  • The pro-plasticity phenotype of enriched mice is transferred by fecal transplant
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Long-term cardiovascular outcomes of COVID-19 – Nature Medicine.

Fascinating study. A little outside my expertise but will be very interested to see if this is reproduced by others. It’s could be a potent argument to get vaccinated.

Here we used national healthcare databases from the US Department of Veterans Affairs to build a cohort of 153,760 individuals with COVID-19, as well as two sets of control cohorts with 5,637,647 (contemporary controls) and 5,859,411 (historical controls) individuals, to estimate risks and 1-year burdens of a set of pre-specified incident cardiovascular outcomes

We show that, beyond the first 30 d after infection, individuals with COVID-19 are at increased risk of incident cardiovascular disease spanning several categories, including cerebrovascular disorders, dysrhythmias, ischemic and non-ischemic heart disease, pericarditis, myocarditis, heart failure and thromboembolic disease. These risks and burdens were evident even among individuals who were not hospitalized

Respiratory mucosal delivery of next-generation COVID-19 vaccine provides robust protection against both ancestral and variant strains of SARS-CoV-2 – Cell

The vaccine technology being developed due to the pandemic is very exciting this is prime example!

We show that single-dose intranasal immunization, particularly with chimpanzee Ad-vectored vaccine, is superior to intramuscular immunization in induction of the tripartite protective immunity consisting of local and systemic antibody responses, mucosal tissue-resident memory T cells and mucosal trained innate immunity. We further show that intranasal immunization provides protection against both the ancestral SARS-CoV-2 and two VOC, B.1.1.7 and B.1.351

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Spatial-CUT&Tag: Spatially resolved chromatin modification profiling at the cellular level – Science

Sounds like a major advacement in spatial omics tech! Very excited to see where this goes. Combining this with something like spatial 10X RNASeq and spatial mass spec would have some great applications in studying host-microbe interactions.

This method resolved spatially distinct and cell-type-specific chromatin modifications

Spatial-CUT&Tag adds a new dimension to spatial biology by enabling the mapping of epigenetic regulations broadly implicated in development and disease

Host-pathogen genetic interactions underlie tuberculosis susceptibility in genetically diverse mice – eLife

Very cool resource for studying host-pathogen interactions. I’m not sure I’ve ever heard of a collaborative cross mouse panel before, but that says more about me I think.

We leveraged the genetically diverse Collaborative Cross (CC) mouse panel in conjunction with a library of Mtb mutants to create a resource for associating bacterial genetic requirements with host genetics and immunity. We report that CC strains vary dramatically in their susceptibility to infection

many virulence pathways are only required in specific host microenvironments, identifying a large fraction of the pathogen’s genome that has been maintained to ensure fitness in a diverse population

Using Community Ecology Theory and Computational Microbiome Methods To Study Human Milk as a Biological System – mSystems

” In this review, we advocate for longitudinal multiomics data collection and demonstrate how incorporating knowledge gleaned from microbial community ecology and computational methods developed for microbiome research can serve as an anchor to advance the study of human milk and its many components as a “system within a system.”

Marginal zone B cells acquire dendritic cell functions by trogocytosis – Science

Dendritic cells are my favourite cell type so I couldn’t not highlight this article finding that a subset of B cells copy DCs

Transcriptome-wide changes in gene expression, splicing, and lncRNAs in response to a live attenuated dengue virus vaccine – Cell Reports

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Genome-wide transcriptome analysis of dengue vaccine-elicited immune responses
• A temporality of changes in lncRNA, splicing, and gene expression patterns
• Genes strongly enriched for pathways involved in antiviral innate immunity
• Cell-type-related modules exhibit a significant correlation with antibody titers

“These data provide insights into the early determinants of the variable immune response to the vaccine, highlighting the significance of splicing and isoform-level gene regulatory mechanisms in defining vaccine immunogenicity.”

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