@charliejpyle.bsky.social
150 followers 320 following 30 posts
Duke University | Tobin Lab Postdoc | PharmD, PhD Translational Scientist interested in Cell Biology — Genetics — Microbiology — Pharmacy — Innate Immunity — Zebrafish — Tuberculosis Opinions are my own & don't represent those of my employer.
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charliejpyle.bsky.social
You can now explore the mRNA expression of your favorite TB gene of interest in our recently published human pulmonary M.tb granuloma single-cell dataset at the Broad Single Cell PORTAL!

@broadinstitute.org
@wallacewly.bsky.social

singlecell.broadinstitute.org/single_cell/...
Paired single-cell and spatial transcriptional profiling reveals a central osteopontin macrophage response mediating tuberculous granuloma formation - Single Cell Portal
Granulomas are classic manifestations of tuberculosis pathogenesis. They result from an ensemble of immune responses to Mycobacterium tuberculosis infection, but the identities, arrangement, cellular interactions, and regulation of the cells that comprise them have thus far been incompletely understood. To better understand the composition of granulomas, we conducted spatial and single-cell RNA sequencing of granulomas in biopsy specimens from patients with tuberculosis. We found that granulomas consist of concentric transcriptional laminae surrounding areas of central necrosis. We identified distinct populations of granuloma-associated stromal cells, fibroblasts, lymphocytes, mast cells, dendritic cells, neutrophils, and macrophages. Furthermore, gene expression among these cell populations differed by location within granulomas. We used inferential analysis to predict dominant granuloma cell-cell interactions, the activity of major signaling pathways, and transcription factor activities. Using spatial deconvolution, we mapped a conserved pattern of cellular organization dominated by macrophages rich in SPP1/osteopontin expression. Trajectory analysis of macrophage subtypes mapped their differentiation and supported the importance of SPP1 to granuloma macrophage polarization. Using the Mycobacterium marinum-zebrafish model, we found that mycobacterial infection induces spp1 expression in macrophages and that spp1 ablation results in granuloma formation defects and reduced survival in adult animals. Cumulatively, we have identified a dominant macrophage granuloma population as well as its central regulatory gene in human samples and confirmed the importance of spp1 to granuloma biology in vivo.
singlecell.broadinstitute.org
charliejpyle.bsky.social
An image I took for my osteopontin macrophage project is featured on the cover of this months issue of mBio!

"A multinucleated giant cell and epithelioid macrophages stained for osteopontin in the myeloid cuff of a human tuberculosis granuloma."
journals.asm.org/toc/mbio/16/10
mBio Table of Contents Volume 16, Issue 10
mBio Table of Contents 16 10
journals.asm.org
Reposted
jcb.org
@kirstin-rollins.bsky.social, @mmorrissey.bsky.social et al show that #macrophages attack adherent cells using #trogocytosis instead of #phagocytosis. Reducing adhesion increased phagocytosis. Mitotic cells, which disassemble adhesions, are more vulnerable to phagocytosis rupress.org/jcb/article/...
charliejpyle.bsky.social
We need to act now or all of Portland will be lost beyond the Powell's singularity event horizon!
Reposted
theramseylab.bsky.social
New Element in the Philosophy of Biology series—free to download until October 6! Walter Veit examines the role of models in evolutionary biology: their types, testability, and interrelations 👇📕 www.cambridge.org/core/element... #philsci #HPBio #evobio
Book cover of “Modelling Evolution” by Walter Veit, in the Cambridge Elements: The Philosophy of Biology series. Against a black background, the title is surrounded by Ernst Haeckel’s illustrations of marine organisms—radial, symmetrical forms in vivid blues, oranges, reds, and greens.
Reposted
tobinlab.bsky.social
Really interesting work from our neighbor Clare Smith @dukemedschool.bsky.social starting from CC mice and linking Ctsz to TB infection outcome as well as functional variation in human populations (UW, Case Western, Uganda) and expression in human granulomas (@charliejpyle.bsky.social)
plosbiology.org
#Tuberculosis severity varies widely between people; why is this? This study uses the #CollaborativeCross mouse panel to identify the protease #cathepsin Z (CTSZ) as a conserved regulator of #TB outcomes via its influence on CXCL1 in mice & in humans @plosbiology.org 🧪 plos.io/4phwRA8
Human CTSZ variants are associated with TB severity, and CTSZ is present at the host-pathogen interface within human pulmonary Mtb granulomas. Top left: A manually annotated UMAP generated by unsupervised clustering of data from single-cell mRNA-Seq of human biopsy tissue, containing Mtb granulomas from three patients with TB. Top right: Analysis of normalized expression values reveals that CTSZ is specifically induced in granuloma macrophages, particularly in lipid-associated macrophages. Bottom: Brightfield (BF) images and immunofluorescent staining of CTSZ and CD68 within a granuloma biopsy from an individual with pulmonary TB. Goat (Gt) and mouse (Ms) IgG isotype control staining is depicted in the top row. DAPI staining indicates cell nuclei. Scale bar is 60 µM in length.
Reposted
crick.ac.uk
Watch @maxgg.bsky.social, Group Leader at the Crick, as he explains what happens to cells that are infected with tuberculosis and how his lab is studying our bodies’ response to this infection.
www.youtube.com/watch?v=VWCt...
Researching the World’s Deadliest Infectious Disease – with Maximiliano Gutierrez
YouTube video by Francis Crick Institute
www.youtube.com
charliejpyle.bsky.social
You can now explore the mRNA expression of your favorite TB gene of interest in our recently published human pulmonary M.tb granuloma single-cell dataset at the Broad Single Cell PORTAL!

@broadinstitute.org
@wallacewly.bsky.social

singlecell.broadinstitute.org/single_cell/...
Paired single-cell and spatial transcriptional profiling reveals a central osteopontin macrophage response mediating tuberculous granuloma formation - Single Cell Portal
Granulomas are classic manifestations of tuberculosis pathogenesis. They result from an ensemble of immune responses to Mycobacterium tuberculosis infection, but the identities, arrangement, cellular interactions, and regulation of the cells that comprise them have thus far been incompletely understood. To better understand the composition of granulomas, we conducted spatial and single-cell RNA sequencing of granulomas in biopsy specimens from patients with tuberculosis. We found that granulomas consist of concentric transcriptional laminae surrounding areas of central necrosis. We identified distinct populations of granuloma-associated stromal cells, fibroblasts, lymphocytes, mast cells, dendritic cells, neutrophils, and macrophages. Furthermore, gene expression among these cell populations differed by location within granulomas. We used inferential analysis to predict dominant granuloma cell-cell interactions, the activity of major signaling pathways, and transcription factor activities. Using spatial deconvolution, we mapped a conserved pattern of cellular organization dominated by macrophages rich in SPP1/osteopontin expression. Trajectory analysis of macrophage subtypes mapped their differentiation and supported the importance of SPP1 to granuloma macrophage polarization. Using the Mycobacterium marinum-zebrafish model, we found that mycobacterial infection induces spp1 expression in macrophages and that spp1 ablation results in granuloma formation defects and reduced survival in adult animals. Cumulatively, we have identified a dominant macrophage granuloma population as well as its central regulatory gene in human samples and confirmed the importance of spp1 to granuloma biology in vivo.
singlecell.broadinstitute.org
charliejpyle.bsky.social
Data rich for your enjoyment!

3 RNAseq datasets. Spatial and single-cell from clinical biopsies of human M.tuberculosis granulomas plus flow sorted macrophage bulk RNAseq from M.marinum-infected zebrafish larvae. Bonus functional validations in the adult zebrafish model.
Reposted
labwaggoner.bsky.social
Symptomatic primary EBV infection generates B cell subsets that gain access to the CNS, attract T cells and thereby initiate multiple sclerosis @nature.com
www.nature.com/articles/s41...
charliejpyle.bsky.social
“Generative AI designs high-specificity pMHC-binding artificial TCRs for more precise targeting of tumor antigen”?
charliejpyle.bsky.social
Treat it as an opportunity to expound on your scientific philosophy within the context of your dissertations central question. This is assuming you're working towards a doctorate of philosophy in your chosen field. Write it as a synthesis essay.
charliejpyle.bsky.social
Why is the Northern Irish line green? That border was established in 1921.
Reposted
ec.europa.eu
Choose Science. Choose Europe.

A new Marie Skłodowska-Curie Actions Postdoctoral Fellowships 2025 call is now open.

With a budget of €404.3 million, it will support around 1,650 researchers from Europe and beyond.

Apply by 10 September → europa.eu/!fBTMgF
A graphic for the Marie Skłodowska-Curie Actions (MSCA), showing a historical portrait of Marie Skłodowska-Curie overlaid with an image of four young researchers walking down a hallway. The European Commission logo is in the top left. Text reads: "Marie Skłodowska-Curie Actions – €404.3 million to support postdoctoral researchers”
Reposted
thelancet.com
When a person is diagnosed with #tuberculosis, one of their first questions is often, “Why did I get tuberculosis? Why me?” 💬

Explore a Seminar which aims to help healthcare providers identify those at risk of TB & address patient concerns: tinyurl.com/zb2bwces #MedSky
Image based on a figure in the paper illustrating risk factors and main clinical characteristics of tuberculosis infection and disease. Image based on a figure in the paper illustrating risk factors and main clinical characteristics of tuberculosis infection and disease. Image based on a figure in the paper illustrating risk factors and main clinical characteristics of tuberculosis infection and disease.
charliejpyle.bsky.social
Those are some pretty big atoms.
Reposted
kaiamattioli.bsky.social
born too late to get a two Western blot Nature paper, born too early to be a science TikTokker, born just in time to start a postdoc during a global pandemic and look for faculty positions during a historic hiring freeze
charliejpyle.bsky.social
Post original content here but only reference it there.
Reposted
tobinlab.bsky.social
Inspiring speakers highlighting the importance to our collective health as well as economic return on investment of basic, curiosity-driven research at yesterday’s @standupforscience.bsky.social

Frightening to see active dismantling of decades of public investments in our health and futures.
Itai Yanai speaking in front of thousands of participants at the Stand Up for Science event in front of the Lincoln Memorial in Washington, D.C.