Lightnews — Scholar-powered news

Lucia Ramirez-Navarro @luciaramirez.bsky.social · Jul 15

The final pre-print of the IBDverse project is out now ✨ - looking at the genetics of IBD 🧬 Led by the amazing @tobioinformatics.bsky.social and @bradleyomics.bsky.social

Tobi Alegbe @tobioinformatics.bsky.social · Jul 8

🚨New preprint just dropped 🚨
medrxiv.org/content/10.1101/2025.06.24.25330216
The main output from my PhD is finally public and we’re SUPER excited about the findings! If you’re interested in what we learnt about IBD with a massive 700+ sample sc-eQTL dataset of the gut, read on!

4

Lucia Ramirez-Navarro @luciaramirez.bsky.social · Jun 4

🙏 Huge thanks to our patients, collaborators, and funders @crohnscolitisfdn.bsky.social — this work wouldn’t be possible without you.
Special thanks to my PhD supervisors @carlanderson.bsky.social and Tim Raine for their incredible support and guidance.

🧵 10/10

1 1

Lucia Ramirez-Navarro @luciaramirez.bsky.social · Jun 4

TL;DR:

📘 We provide a single-cell resource of mucosal and blood immune cells in Crohn’s disease
🔥 Reveal the unique role of circulating ex-Trms
📍 Show that inflammation is largely gut-restricted
🧭 Open up new paths for biomarker & therapeutic discovery

🧵 9/10

1

Lucia Ramirez-Navarro @luciaramirez.bsky.social · Jun 4

🧪 We also saw gut-specific transcriptional remodeling in Naive B cells and Tregs with upregulation of IFN-γ, chemokine, and T cell migration pathways.

Again, none of these were present in the blood 🥲

🧵 8/10

1

Lucia Ramirez-Navarro @luciaramirez.bsky.social · Jun 4

🔬 In terms of cell type abundance, circulating classical monocytes were negatively associated with inflammation, while all the other inflammation-related changes were gut-restricted.

🧬 Reinforcing the tissue-restricted nature of Crohn's inflammation.

🧵 7/10

1

Lucia Ramirez-Navarro @luciaramirez.bsky.social · Jun 4

🧠 CD4⁺ ex-Trms were enriched for IFN-γ signaling, while the pro-inflammatory CD4⁺ subset was enriched for TNFR2 and interleukin signaling.

Many of these inflammation-associated genes were also found in intestinal Tregs and macrophages — two key IBD players.

🧵 6/10

1

Lucia Ramirez-Navarro @luciaramirez.bsky.social · Jun 4

📈 More importantly ex-Trms were the only blood population whose gene expression correlated with gut inflammation, as measured by the TI-SES-CD scores.

👉These signatures were also shared with their intestinal counterparts.

🧵 5/10

1

Lucia Ramirez-Navarro @luciaramirez.bsky.social · Jun 4

👀 These ex-Trms were also present in public PBMC scRNA-seq datasets - across IBD, healthy donors, and other inflammatory conditions.

🧵 4/10

1

Lucia Ramirez-Navarro @luciaramirez.bsky.social · Jun 4

🔥 We discovered a rare subset of circulating T cells with Trm-like features (aka ex-Trms).

This included CD8⁺, CD4⁺, and a pro-inflammatory CD4⁺ subset expressing KLRB1 and CCR5, previously seen in the gut.

🧵 3/10

1

Lucia Ramirez-Navarro @luciaramirez.bsky.social · Jun 4

🧬 We performed single-cell RNA-seq on paired ileum and blood samples from 125 CD patients with matched endoscopy scores (TI-SES-CD), capturing shared and tissue-specific immune states.

🧵 2/10

1 1

Lucia Ramirez-Navarro @luciaramirez.bsky.social · Jun 4

🚨 SUPER EXCITED to share our new preprint on the mucosal and circulatory immune landscape of Crohn’s disease!

🩸 Blood is commonly used in biomarker discovery and drug development, but how well does it reflect what's actually happening in the gut? 👀

🧵 1/10
🔗 www.medrxiv.org/content/10.1...

Tissue-specific and circulatory immune signatures of mucosal inflammation in Crohn's disease

Crohn's disease (CD) is a heterogeneous disease characterized by chronic inflammation of the gastrointestinal tract driven by an aberrant immune response. To understand the immune mechanisms underlyin...

www.medrxiv.org

1 4 5

Lucia Ramirez-Navarro @luciaramirez.bsky.social · Feb 19

All these measures will not only affect US-based science but worldwide (eg. developing countries).
Guess so much about equity in genomics?
Hopefully, other (maybe non-US) alternatives arise from this 🙏🏻

Alejandra Medina-Rivera @alemedinarivera.bsky.social · Feb 19

Within the very few international mechanisms that had grant schemes for developing countries were the CZI grants... seams that that door is closing.
I'm sad cause I felt it was a safe community

Crystal Rogers, PhD @rogerslabucd.bsky.social · Feb 19

Pretty sad. Just got the email that CZI is canceling the second round of Diversity Leadership Awards. Private industry will definitely not fill the hole that NIH and NSF are leaving. 😢💔

1 2

Reposted by Lucia Ramirez-Navarro

Petter Brodin @petterbrodin.bsky.social · Jan 21

New paper alert 📢! (Cell) @cp-cell.bsky.social
- How does immune responses to solid tumors vary by age and tumor characteristics in children?! www.cell.com/cell/fulltex... 🧵1/8

3 33 76

Reposted by Lucia Ramirez-Navarro

Shannon Mattern @shannonmattern.bsky.social · Dec 9

"Women full professors are 19% more likely than men at the same career stage to leave academia, as compared with 6% for women assistant professors and 10% for associates."

Women faculty feel ‘pushed’ from academia by poor workplace climate

The gender gap in faculty attrition worsens after tenure, according to a new study

www.science.org

15 290 580

Reposted by Lucia Ramirez-Navarro

Anshul Kundaje @anshulkundaje.bsky.social · Dec 4

This is really horrific. These single cell reference atlases are widely used as is to train all kinds of models! This is one of the reasons I've constantly harping about uniform reprocessing & extremely careful QC of large atlases. 1/

Tomàs Montserrat Ayuso @tmontsay.bsky.social · Dec 3

scRNA-seq has revolutionized biology, but it’s not without challenges. We uncovered significant quality issues in widely used reference cell atlases like the Human Cell Atlas and Tabula Sapiens. Up to 85% of cells in some datasets are low-quality or misidentified!
2/8

9 41 140

Lucia Ramirez-Navarro @luciaramirez.bsky.social · Nov 14

Today, I got the opportunity to present at #ISCBLA2024 about how we are using single-cell to identify circulating and tissue specific signatures in Crohn's disease 👩🏻‍💻

1 1 7

Reposted by Lucia Ramirez-Navarro

🇲🇽 Leonardo Collado-Torres @lcolladotor.bsky.social · Nov 8

Hi everyone!

Here's a starter pack of genomics scientists trained in Mexico 🇲🇽 including from #LCG-UNAM #LCG-EJ-UNAM undergrads, #RMB / #NNB-UNAM / @cdsbmexico.bsky.social workshops, and more

It's in an early stage and I'm trying to get more to join us here at #AcademicSky

go.bsky.app/5bWBN5V

2 23 39