Thanks to Emma and Sebastian for the interesting discussions while preparing the manuscript! Hope all of you enjoy reading it as much as I did. 🤓

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, ....

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/...

@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...

Snapshot of the Correspondence titled 'Translon: a single term for translated regions'

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

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...

🧬🚨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🫄

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

"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

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…

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

El genoma no codificante

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...

🌸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

7/ ii) Binding affinity predictions don’t always correlate with actual presentation at the cell surface. More immunopeptidomics is essential—not just to rely on binding predictions but to better assess HLA presentation.

6/ Two additional (and not-so-original) thoughts:
i) Mutations generate the best neoantigens, but each patient may require more antigens for an effective vaccine. --> additional sources (cryptic proteome or alternative splicing) may help?

5/ Both findings suggest that, beyond lower binding affinity, non-responder peptides are also less likely to be presented.

4/ Also, Müller et al.(PMID:29104575) proposed that if the WT peptide is presented, the mutated version is more likely to be presented. We searched for WT counterpart peptides in an in-house dataset of 1000s of immunopept. samples and found a higher proportion of presented peptides in responders.

3/ However, HLA-I binding affinity doesn’t guarantee real peptide presentation. I explored PDAC neoantigen presentation using two approaches.
First, Cysteines are generally depleted in the immunopeptidome. Notably, non-responder peptides had a 3-fold increase in cysteine-containing peptides.

2/ Responder peptides had a higher HLA-I affinity than those in non-responders (as expected). ~50% of the non-immunogenic peptides weren’t binders (by NetMHC). This suggests that one distinction between responders and non-responders lies in the quality of the neoantigens included in the vaccine.

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?

FirstWord

Merck & Co. digs into 'junk DNA' for cancer clues in new Epitopea deal

firstwordpharma.com/story/5936238

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

Cover art for the December 26, 2024 issue of the journal Cell. The artwork resembles spilled and swirled paint, with bright colors of pink, yellow, green, white, and black on a deep blue background. The "Cell" logo appears in bold white text in the upper left corner and the Cell Press 50th anniversary logo appears in light blue text in the bottom right corner. Taken from the published cover description: "The cover image features an artistic representation of how the fetal tripotent pancreatic stem cell (pink, yellow, and white smaller circle) gives rise to the three main cell lineages of the pancreas (pink, yellow, and green fluid lines), which together make up the pancreas organ (yellow, green, and pink larger oval). Image resources: Simona Jole Anna Lafirenze."

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 😅🥳

MAETi: Mild acid elution in a tip enables quantitative immunopeptidome profiling from 25,000 cells www.biorxiv.org/content/10.1101/2024.12....

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...

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!

🔬 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