Ralph Stadhouders

In @jem.org, Metzemaekers et al review how memory T cells fight infections & cancer by retaining epigenetic “memories” that enable rapid reactivation of inflammatory genes, & how such epigenetic mechanisms may fuel T cell dysfunction in disease rupress.org/jem/article/...
@r-stadhouders.bsky.social

Epigenetic priming as a driver of memory recall and dysfunction in T cells. A new review from Mieke Metzemaekers, Niels Rinzema, and Ralph Stadhouders @r-stadhouders.bsky.social: rupress.org/jem/article/...

#LymphocyteBiology #MucosalImmunology #TumorImmunology #Epigenetics #Cancer

BPL-inactivated SARS-CoV-2 vaccines exist e.g., CoronaVac. The challenge with most means to inactivate microbes is that you want to do this in a manner that does not meaningfully change the structural information being provided to the immune system so that when it encounters the real thing...

Transcription factor networks disproportionately enrich for heritability of blood cell phenotypes Most phenotype-associated genetic variants map to noncoding regulatory regions of the human genome, but their mechanisms remain elusive in most cases. We developed a highly efficient strategy, Perturb...

Sounds interesting! www.science.org/doi/10.1126/...

Who funds biomedical research? @nature.com
www.nature.com/articles/d41...

RNA xkcd.com/3056

FFS, these appear to be studies that try to determine, for example, if feminizing hormone therapy is associated with asthma (the largest grant) to determine if estrogen is causal in the higher asthma rates seen in women. Idiots.

As the #measles outbreak continues, and has now unfortunately resulted in the death of a child, I see a lot of posts along the lines of: "I had measles as a child and I'm fine". Let me tell you a different version of that story:
🧵1/11 🧪 #medsky

The analogy of omics data normalization and cooking:
some processing is usually necessary, overcooking makes it bland, highly over-processed foods are unhealthy, and the quality of the ingredients matters.

Disease diagnostics using machine learning of B cell and T cell receptor sequences Clinical diagnosis typically incorporates physical examination, patient history, various laboratory tests, and imaging studies but makes limited use of the human immune system’s own record of antigen ...

Disease diagnostics using machine learning of B cell and T cell receptor sequences

www.science.org/doi/10.1126/...

TL;DR: BCRs ARE ALL YOU NEED!

(Well actually .... keep reading) 1/

Anonymous messages! Anonymous messages!

Seems like people are dealing with a lot.
If you go to this link, you can ask me anything anonymously. I will try to give my best answers for all questions

ngl.link/deplatformdi...

#Immunology out now @science.org

Machine learning, using the sequences of an individual's B and T cell receptors, has the potential to diagnose immune-related diseases.

https://buff.ly/3QvxSVf

By Maxim Zaslavsky, Erin Craig, @anshulkundaje.bsky.social , @scottboydlab.bsky.social et al.

Long-term outcomes of GD2-directed CAR-T cell therapy in patients with neuroblastoma - Nature Medicine In an extended follow-up of a phase 1 trial evaluating a first-generation GD2-directed CAR-T cell therapy in patients with neuroblastoma, one patient has had a sustained clinical response for over 18 ...

Very promising news and an honor to be a part of this report! @bcmhouston.bsky.social @texaschildrens.bsky.social

www.nature.com/articles/s41...

Coffee Boosts Beneficial Gut Bacterium Researchers found a strong connection between coffee and the gut microbiome

Large epidemiologic studies have consistently shown an association between coffee and improved health outcomes. This may be one of the reasons: favorable changes to the gut microbiome 🏢🏢

www.scientificamerican.com/article/coff...

I love this.... there doesn't even need to be point 2 or more (which there are, and they're also great). The insanity of this proposal is mind-boggling.

Functional memory T cells are derived from exhausted clones and expanded by checkpoint blockade https://www.biorxiv.org/content/10.1101/2025.02.10.637523v1

KLF2 maintains lineage fidelity and suppresses CD8 T cell exhaustion during acute LCMV infection
www.science.org/doi/10.1126/...
@science.org @nikjoshilabyale.bsky.social

Nice work, congrats!

#CellPlasticity—the ability of cells to change their identity—is vital for tissue growth and repair. But when it goes unchecked, it can fuel #cancer. Our latest study examines how to block #LiverCancer by actively suppressing plasticity. www.nature.com/articles/s41... #CancerBiology

A clam with a spring attached to the shell. The spring has a magnet placed above a sensor.

Hardly new info, but BSky should know:

Warsaw's water quality is monitored by eight clams with magnets attached to their shells. If contamination in the water causes the clams to close, the magnets trigger an alarm and shut off the city's water supply.
Thank you, little guardian molluscs.

🧪🌏🚰

Spatial transcriptomics identifies molecular niche dysregulation associated with distal lung remodeling in pulmonary fibrosis - Nature Genetics Xenium spatial transcriptomic profiling of pulmonary fibrosis characterizes cell composition dynamics and histopathological features associated with the disease.

Excited to post my first #skySplain about our recent work published yesterday in Nature Genetics! www.nature.com/articles/s41.... One of the first authors of this study - Annika Vannan – actually wrote this breakdown, but she's not yet over here on bluesky and asked me to post!

Multiscale footprints reveal the organization of cis-regulatory elements - Nature We developed PRINT, a computational method that identifies footprints of DNA–protein interactions from bulk and single-cell chromatin accessibility data across multiple scales of protein size.

Congrats to the @jbuenrostro.bsky.social lab on this recent paper.

www.nature.com/articles/s41...

Unfortunately, it makes several misleading claims that we disagree with. We will address these technical & other issues with this work over the next few months.

One thing that does not get enough attention I think in all these dialogues is the persistent attempt to dichotomize infectious diseases and chronic illnesses.

- HPV and Hepatitis B are major causes of cancer.
- Many viruses can trigger dilated cardiomyopathy in genetically susceptible people.

I am really enjoying the surge of people to bluesky but still kind of missing the VERY early career group of people! (Aging in academia is a funny thing) - I went ahead and made this starter pack go.bsky.app/Jq8YaQM - if you would like to be removed/added please let me know

Today the Trump admin abruptly and indefinitely terminated many of the activities of the National Institutes of Health, the $50B/year collection of agencies that power the US biotech and health ecosystems. Even if these orders were lifted tomorrow, the disruption would be enormous.

Why care? 🧵

RELMβ sets the threshold for microbiome-dependent oral tolerance - Nature RELMβ mediates a gut immune–epithelial circuit regulating tolerance to food antigens, offering targetable candidates for the prevention and treatment of food allergies.

So very cool! An epithelial-microbiota-immune axis controls the susceptibility to food allergy! #gastrosky #innateimmunity
congrats to the Chatila and Rakoff-nahoum lab @bostonchildrens.bsky.social

doi.org/10.1038/s415...

GZMK-expressing CD8+ T cells promote recurrent airway inflammatory diseases - Nature Comparing T cells in nasal polyps from repeated surgeries shows that effector memory-like persistent clones colonize the mucosal tissue during disease recurrence and promote inflammation by producing ...

Sometimes you can have too much of a good thing - granzyme K in CD8 T cells can kill infected host cells, but may also drive pathology.... (e.g. chronic rhinosinusitis / asthma)
#ImmunoSky 🧪 @nature.com
www.nature.com/articles/s41...

If there's something we don't understand I assume transposons are responsible unless proven otherwise

Long somatic DNA-repeat expansion drives neurodegeneration in Huntington’s disease Single-cell measurement of the Huntington’s disease-causing CAG repeat reveals that somatic expansion of this repeat drives pathological changes in neurons, providing insights into disease progression...

I started working on genetic therapies for Mendelian disease in 2000 - and in the subsequent 25 years have never seen a disease where the molecular aetiology has undergone as giant an "OH WOW" moment as this.
www.cell.com/cell/fulltex...

@anusri.bsky.social first author & developer of ChromBPNet is looking for opportunities in industry in ML for bio/genomics. She is an excellent rigorous scientist (as u can see from the paper). Very strongly recommend her. Plz reach out to her if u have openings. Plz forward.