𝐂𝚑𝚊𝚛𝚕𝚒𝚎 𝐏𝚢𝚕𝚎
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charliejpyle.bsky.social
𝐂𝚑𝚊𝚛𝚕𝚒𝚎 𝐏𝚢𝚕𝚎
@charliejpyle.bsky.social
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.
Pinned
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
Reposted by 𝐂𝚑𝚊𝚛𝚕𝚒𝚎 𝐏𝚢𝚕𝚎
A new study led by Harvard Chan School and @busph.bsky.social projects that U.S. funding cuts to global health aid will have a catastrophic effect on pediatric #tuberculosis.
U.S. funding cuts could result in nearly 9 million child tuberculosis cases, 1.5 million child deaths | Harvard T.H. Chan School of Public Health
A new Harvard Chan School and BUSPH study projects that U.S. funding cuts to global health aid will have a catastrophic effect on pediatric TB.
hsph.harvard.edu
October 21, 2025 at 8:19 PM
Reposted by 𝐂𝚑𝚊𝚛𝚕𝚒𝚎 𝐏𝚢𝚕𝚎
Fibronectin, a key component of the vessel wall, triggers smooth muscle cells to release collagen-rich extracellular vesicles that guide their movement during vessel repair and atherosclerosis.
buff.ly/YOkDI4a
October 12, 2025 at 10:02 AM
Reposted by 𝐂𝚑𝚊𝚛𝚕𝚒𝚎 𝐏𝚢𝚕𝚎
Important piece from Sarah Stanley at Berkeley on new NIH definitions that can be construed to arbitrarily halt research that is both safe and important to public health and future cures www.statnews.com/2025/10/06/g... via @statnews.com
The NIH ordered me to stop my ‘dangerous’ gain-of-function research. It isn’t dangerous at all
Safe gain-of-function research is necessary to identify new treatments for diseases like for tuberculosis — but the NIH has imposed unfounded stops.
www.statnews.com
October 6, 2025 at 12:15 PM
Reposted by 𝐂𝚑𝚊𝚛𝚕𝚒𝚎 𝐏𝚢𝚕𝚎
@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/...
October 3, 2025 at 5:34 PM
Reposted by 𝐂𝚑𝚊𝚛𝚕𝚒𝚎 𝐏𝚢𝚕𝚎
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
September 24, 2025 at 12:48 PM
Reposted by 𝐂𝚑𝚊𝚛𝚕𝚒𝚎 𝐏𝚢𝚕𝚎
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)
#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
September 10, 2025 at 5:32 PM
Reposted by 𝐂𝚑𝚊𝚛𝚕𝚒𝚎 𝐏𝚢𝚕𝚎
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
September 10, 2025 at 3:32 PM
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
September 4, 2025 at 1:38 PM
Proud to present our latest work!
@tobinlab.bsky.social
@wallacewly.bsky.social
@gregorylab.bskyverified.social

Human TB granuloma transcriptional blueprints show they are dominated by SPP1 macrophages. spp1 is essential for granuloma formation in zebrafish.

journals.asm.org/doi/10.1128/...
Paired single-cell and spatial transcriptional profiling reveals a central osteopontin macrophage response mediating tuberculous granuloma formation | mBio
Tuberculosis is the world’s most deadly single-pathogen infection. Its causative bacterium, Mycobacterium tuberculosis, sickens over 10 million people annually. Mycobacterial granulomas are the pathol...
journals.asm.org
August 7, 2025 at 7:11 PM
Reposted by 𝐂𝚑𝚊𝚛𝚕𝚒𝚎 𝐏𝚢𝚕𝚎
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...
August 6, 2025 at 5:34 PM
Reposted by 𝐂𝚑𝚊𝚛𝚕𝚒𝚎 𝐏𝚢𝚕𝚎
A review emphasizes the advantages of using zebrafish in research, outlines key differences in experimental approaches, and offers guidelines for designing studies in a way that enhances experimental rigor and reproducibility. www.nature.com/articles/s42...
Zebrafishology, study design guidelines for rigorous and reproducible data using zebrafish - Communications Biology
A review emphasizes the advantages of using zebrafish in research, outlines key differences in experimental approaches, and offers guidelines for designing studies in a way that enhances experimental ...
www.nature.com
May 15, 2025 at 7:06 PM
Reposted by 𝐂𝚑𝚊𝚛𝚕𝚒𝚎 𝐏𝚢𝚕𝚎
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
May 8, 2025 at 10:12 AM
Reposted by 𝐂𝚑𝚊𝚛𝚕𝚒𝚎 𝐏𝚢𝚕𝚎
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
May 12, 2025 at 2:30 PM
Reposted by 𝐂𝚑𝚊𝚛𝚕𝚒𝚎 𝐏𝚢𝚕𝚎
Researchers pinpoint the genes responsible for the final three pea traits studied by Gregor Mendel more than 160 years ago

https://go.nature.com/3EC3eqT
Century-old genetics mystery of Mendel’s peas finally solved
Researchers pinpoint the genes responsible for the final three pea traits studied by the famed citizen scientist.
go.nature.com
April 23, 2025 at 4:28 PM
Reposted by 𝐂𝚑𝚊𝚛𝚕𝚒𝚎 𝐏𝚢𝚕𝚎
Today is a great day to highlight what an incredible, extensive, and diverse learning resource MIT OpenCourseWare is! 🧪 #AcademicSky

🔗 ocw.mit.edu
MIT OpenCourseWare | Free Online Course Materials
MIT OpenCourseWare is a web based publication of virtually all MIT course content. OCW is open and available to the world and is a permanent MIT activity
ocw.mit.edu
March 15, 2025 at 8:26 AM
Reposted by 𝐂𝚑𝚊𝚛𝚕𝚒𝚎 𝐏𝚢𝚕𝚎
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
March 10, 2025 at 4:32 PM
Reposted by 𝐂𝚑𝚊𝚛𝚕𝚒𝚎 𝐏𝚢𝚕𝚎
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.
March 8, 2025 at 2:51 PM
Reposted by 𝐂𝚑𝚊𝚛𝚕𝚒𝚎 𝐏𝚢𝚕𝚎
Nancy By Ernie Bushmiller
February 26,1954
February 27, 2025 at 3:04 AM
Reposted by 𝐂𝚑𝚊𝚛𝚕𝚒𝚎 𝐏𝚢𝚕𝚎
Different flavors of #zebrafish. Credit to Renee Daigle & @margaritapk.bsky.social. #ZebrafishZunday 🧪
February 23, 2025 at 2:22 PM
Potent & very personal insights from my graduate school mentor Larry Schlesinger on the absurdity of "taking a break" from infectious disease research to focus on chronic diseases.

www.statnews.com/2024/12/16/c...
My oral cancer shows the deep connections between chronic and infectious disease
The new administration wants “a break” from infectious disease research to focus on chronic disease. That’s impossible, writes Larry Schlesinger, an infectious disease doctor whose cancer was caused b...
www.statnews.com
February 21, 2025 at 8:26 PM
The US public health infrastructure was instituted as a mechanism to control TB, & it worked! Now in a time when the public goods of science and health services are under corporate raid we have a rash of TB outbreaks, this one in my local community.

www.independent.co.uk/news/health/...
North Carolina tuberculosis cases are on the rise for the first time in decades
Cases of the world’s deadliest infectious disease have been increasing in the U.S. in recent years
www.independent.co.uk
February 8, 2025 at 5:46 AM
Designer Jeans by Tobin218
December 28, 2024 at 12:01 AM