Happy to end 2025 by sharing a review we wrote on a dichotomy that fascinates me: are cryptic proteins mostly rapidly degraded to generate MHC antigens, or do they give rise to evolutionarily recent proteins testing new functions? The answer: probably both. onlinelibrary.wiley.com/doi/10.1002/...

Decoding the Cryptic Proteome Between Antigens and Novel Functional Proteins

Unannotated splicing and translation of non-canonical open reading frames generate a diverse repertoire of cryptic proteins. Most are rapidly degraded, rendering them possible MHC-I substrates. Yet, ....

onlinelibrary.wiley.com

@biorxivpreprint.bsky.social Endogenous retroelements promote tolerance to dietary antigens @belkaidlab.bsky.social www.biorxiv.org/content/10.1...

🚨🚨🚨 New review article on #microexons from the lab! A comprehensive recap of the current state of the field by @tahneema.bsky.social. www.annualreviews.org/content/jour...

@tahneema.bsky.social · 11mo ago

🚀 Check out our new review article “From Tiny Exons to Big Insights: The Expanding Field of #Microexons” now out in Annual Review of Genomics and Human Genetics! doi.org/10.1146/annu... Special thanks to @mirimiam.bsky.social, @crg.eu and @upf.edu!

Many transcriptome regions are translated but not known to encode proteins. They remain poorly annotated and thus under studied, partly due to the lack of terminology for these features. In @natmethods.nature.com we propose using "Translon" for any region decoded by the ribosome

🧬🚨PREPRINT🚨- The first placental isoform reference from long-read seq & supporting data! We demonstrate how tissue-specific assembly improves transcript quantification with short-read data from multi-ancestry birth studies & reveals placenta-mediated effects of gestational diabetes on birth weight🫄

Long-read transcriptome assembly reveals vast isoform diversity in the placenta associated with metabolic and endocrine function

The placenta plays a critical role in fetal development and mediates maternal metabolic effects on offspring health outcomes. Despite its importance, the placenta remains understudied in large-scale g...

doi.org

Excited to see this out in @science.org today!! www.science.org/doi/10.1126/...

Intracellular protein editing enables incorporation of noncanonical residues in endogenous proteins

The ability to study proteins in their native cellular context is crucial to our understanding of biology. In this work, we report a technology for intracellular protein editing, drawing from split in...

science.org

George Burslem@gburslem.bsky.social · 2y ago

Ever wanted to edit a protein sequence inside a living mammalian cell? Maybe to site specifically incorporate a non-canonical residue? Perhaps you’d like to do a pull down without an antibody? Or use a small molecule fluorophore to image an endogenous protein? 1/4

"The main fates after gene duplication are gene loss, redundancy, subfunctionalization and neofunctionalization". In our new review, @fedemantica.bsky.social and I argue we are missing the most prevalent one: specialization. And the same applies to alternative splicing! 1/7 tinyurl.com/45k7kbmp

Excited to share my first post & see the second part of my PhD work published! Our study on mTNBC highlights that baseline clonal expansion of dysfunctional CD8 cells is linked to better response to chemoimmunotherapy. More here: www.sciencedirect.com/science/arti... #CD8 #TCellExhaustion #TNBC

Continuous replenishment of the dysfunctional CD8 T cell axis is associated with response to chemoimmunotherapy in advanced breast cancer

Chemotherapy combined with immune checkpoint blockade has shown clinical activity in breast cancer. Response, however, occurs in only a low proportion…

sciencedirect.com

Nuevo número de la Revista de la @sebbm.bsky.social dedicado al “Genoma no codificante” coordinado por Crisanto Gutiérrez @cbm-csic-uam.bsky.social entrevista a Jordi Camí, @prbb.org y presidente del #CEEI con artículos+contenido interesante Editora: @inmayruela.bsky.social sebbm.es/revista/nume...

El genoma no codificante

sebbm.es

🌸Happy Women's Day! 💪👩‍🔬 As we wrap up our campaign, we celebrate the incredible contributions of women in science and beyond. 🌟 A big shoutout to the amazing women of the #yefis Task Force! ✨ Let’s keep inspiring and empowering each other. 💜 #WomensDay #WomenInScience #WomenInStem

1/ We saw an update on the PDAC neoantigen vaccine (Sethna et al., 2025). A remarkable effort in showing long-lived T cell protection in PDAC + an exhaustive look at the T cells. One question intrigued me: Were the selected neoantigens different between the 8 responder and 8 non-responder patients?

Merck & Co. digs into 'junk DNA' for cancer clues in new Epitopea deal firstwordpharma.com/story/5936238

FirstWord

firstwordpharma.com

I am very happy to share that last week, I had the opportunity to present my research at the Winter Meeting of the Catalan Society of Immunology. But I feel even more honored to have presented in a session chaired by my first mentor in immunology, Dolores Jaraquemada.

Registration is now open for the next ImmunoSchool! This year’s theme: "10 Years of Discovery in Immunotherapy." We’ve put together a stellar lineup of speakers—don’t miss it! Free registration @ bit.ly/3WFj0Hc #ImmunoSchool #Immunotherapy #CancerResearch

Thrilled to introduce our Cell Reports @cellreports.bsky.social article, showing how the iconic 'Hallmarks of Cancer' are located in the space of real human primary tumors. A team effort co-led by Eduard Porta, Matthew H. Bailey, and yours truly #SpatialBiology #Visium www.cell.com/cell-reports...

Top 4 things to know about doing science: 1. You need to have someone you can talk to 2. One-on-one discussions are the best 3. Think about discussions as improvisations and use the ‘yes, and’ rule 4. Create a safe space so both of you feel open to saying seemingly silly things

The last Cell issue of the year is online. This one is a doozy if you like interferons (as I do!) or transposons and ERVs (and who doesn't?!) There's also cool stem cell and dev bio in this issue, immune responses to Zika during pregnancy... cancer, plants... cool stuff! www.cell.com/cell/issue?p...

The final chapter of my PhD thesis is now out! 🎉 We compared the latest gene regulatory network (#GRN) inference methods for #single-cell multimodal datasets and evaluated their performance across various tasks. Hard to believe this journey started in March 2021 and has finally reached this point 😅🥳

Saez-Rodriguez Group@saezlab.bsky.social · 2y ago

We present Gene Regulatory nETwork Analsyis (GRETA), a framework to infer, compare and evaluate gene regulatory networks #GRNs. With it, we have benchmarked multimodal and unimodal GRN inference methods. Check the results here 👇 Paper: doi.org/10.1101/2024.12.20.629764 Code: github.com/saezlab/greta

MAETi: Mild acid elution in a tip enables quantitative immunopeptidome profiling from 25,000 cells https://www.biorxiv.org/content/10.1101/2024.12.20.628848v1

WeekendRead! @cicacanesso.bsky.social @danmucida.bsky.social @victora.bsky.social &co show @science.org that cDC1s & Rorgt APCs drive peripheral Tregs to dietary antigens, & that helminth infections increase the ratio of inflammatory cDC2 preventing tolerance induction!

Identification of antigen-presenting cell–T cell interactions driving immune responses to food

The intestinal immune system must concomitantly tolerate food and commensals and protect against pathogens. Antigen-presenting cells (APCs) orchestrate these immune responses by presenting luminal ant...

science.org

🔬 New insights into protein diversity published in @cellpress.bsky.social: researchers led by Dr. Amigorena have identified over 1,000 unannotated protein isoforms derived from transposable element exonization. Read full publication ⤵️ www.cell.com/cell/fulltext/S0092-8674%2824%2901328-X

To generate HLA-restricted, TAA-binding TCRs (normally eliminated by central tolerance), Abdelfattah et al. (1) mutated a TAA peptide of interest by a single amino acid, (2) used the mutant peptide to expand and identify endogenous reactive [...] acir.org/journal-art...  @harvardmed.bsky.social

Al 1990 va néixer l'ACCC (llavors l'Associació Catalana de Periodisme Científic), com anuncia la nota de premsa compartida aquí per @xavierduran.bsky.social, membre de la 1a Junta Directiva. 📖 Descobreix tota la història de l'ACCC a accc.cat/lassociacio/#historia

@xavierduran.bsky.social · 2y ago

Coses que trobes fent endreça @comunicacioaccc.bsky.social

How does the immune system make "decisions" at mucosal barriers? My new perspective explores how seeing strategic cell interactions through the lens of game theory could reveal fresh insights into mucosal immune homeostasis and disease. 🧵 1/7 www.sciencedirect.com/science/arti...

Organismal mucosal immunology: A perspective through the eyes of game theory

In complex organisms, functional units must interact cohesively to maintain homeostasis, especially within mucosal barriers that house diverse, specia…

sciencedirect.com

#NotOnlyParasites! 2 Cell papers by @edchuong.bsky.social lab & Amigorena lab demonstrate that transposable elements #TEs can exonize giving rise to functional (often shorter) proteins with distinct functions: eg a decoy short IFNAR2 that inhibits #interferon signaling! www.cell.com/cell/fulltex...

Transposable element exonization generates a reservoir of evolving and functional protein isoforms

Transposable element exonization by unannotated splicing events produces stable protein isoforms with acquired functions that are subject to evolutionary selection.

cell.com

And more TEs! Exciting to see this field growing! 😊

Ed Chuong@edchuong.bsky.social · 2y ago

I’m excited to share our latest study led by @giuliapasquesi.bsky.social out today in @cellpress.bsky.social , uncovering a new way transposons have been repurposed for human interferon signaling! Read on for a thread on cryptic splice variants, decoy receptors, and viruses (1/N) 👇🧵 #TESky 🧪

Not easy to describe the emotions of seeing our work published in @cellpress.bsky.social ! We explored how novel isoforms emerge during evolution through the exonization of Transposable Elements. Exonized TEs modify the functions and structures of host proteins. www.cell.com/cell/fulltex...

Transposable element exonization generates a reservoir of evolving and functional protein isoforms

Transposable element exonization by unannotated splicing events produces stable protein isoforms with acquired functions that are subject to evolutionary selection.

cell.com