Elisa Rosati Scalchi

Challenges for the Immunoglobulin and T cell receptor gene nomenclatures in the modern genomics era For over thirty years, an approach to the nomenclatures of human immunoglobulin (IG) and T cell receptor (TR) genes has operated successfully and has …

6/6 📄 Read the full commentary:
“Challenges for the Immunoglobulin and T cell receptor gene nomenclatures in the modern genomics era”
👉 www.sciencedirect.com/science/arti...
✍️ By Andrew Collins, @cdubsig.bsky.social, Luc Teyton, Henk-Jan van den Ham, Elisa Rosati, @yanasafonova.bsky.social

T-cell Receptor and Immunoglobulin Nomenclature Sub-Committee » IUIS Since this Sub-Committee has not addressed MHC/HLA nomenclature for several decades, the name of the Sub-Committee has been changed to “T-cell Receptor and Immunoglobulin Nomenclature Sub-Committee”…

5/6 What can we do now?
We outline strategies in the paper:
✔️ Clear, provisional reporting formats
✔️ Transparent criteria for future naming
✔️ Global dialogue to shape consensus
Let’s build something better—together.
🧠🌍

iuis.org/committees/n...

4/6 Look up the work of the @iuis-online.bsky.social IG/TR Nomenclature Sub-Committee.
They’re urging caution and precision:
➡️ Don’t rush to name
➡️ Wait for sufficient genomic context
➡️ Use consistent interim strategies for gene reporting
#IUIS #GenomicsPolicy

3/6 The problem?
Old naming rules assumed gene order and structure were mostly conserved.
Now we know that’s not always true.
Assigning permanent names too soon could mislead downstream research.
#NomenclatureMatters #IGTR

2/6 For 30+ years, the IG/TR gene naming system worked well—standardized, community-supported, and extended across species.
But things have changed…
Genomic sequencing is exposing extreme structural variation across individuals and species.
🧬🔍

1/6 🧬 NEW COMMENTARY 🧬
Let’s talk about the challenges in immunoglobulin (IG) & T cell receptor (TR) gene nomenclature in the era of modern genomics.
A 🧵 on why it’s time to rethink how we name these genes—and what it means for immunogenetics.
#IGTR #Genomics #Immunology

This fantastic work by @emilyaunins.bsky.social, Anthony Phan, @drewweissmanlab.bsky.social, @kingofpathogens.bsky.social, & colleagues is featured on this month's cover of #Science #Immunology!

And the second day of #ATCR25 also came to an end. Felt the meeting was a real fresh air of ideas. Super glad I joined. The best part is always to meet with old friends, and the #goodscience of course 😉
I love the location in Antwerp too 😍

First day of #ATCR25 in Antwerp: done ☑️ 🤩
Picture of Antwerp city station
#immunology #TCRrepertoire #Tcells #research

Four images to illustrate some prominent single-gene myths. Top left shows a photograph of a person deftly rolling their tongue into a U-shape. Top right shows a photograph of a person’s ear, highlighting the shape and features of the earlobe and cartilage. Bottom left shows a close-up photograph of a person’s eye, with a vivid blue colouration. Bottom right shows a photograph of a person poised to write with their left hand on the blank white page of a spiral-bound notebook.

Remember when you first learned about genetics at school? All those fascinating examples of human traits that are each apparently determined by just a single gene? Time to check in on some of your favourites to see how they’re doing. 🧬🧵🧪 1/n

'Unparalleled' snake antivenom made from man bitten 200 times Scientists hope to make a universal antivenom from the extraordinary blood of a man exposed to snake venom for decades.

'Unparalleled' snake antivenom made from man bitten 200 times

The blood of a US man who deliberately injected himself with snake venom for nearly two decades has led to an "unparalleled" antivenom, say scientists.

www.bbc.com/news/art...
1/8

New @science.org
An innovative way to deliver drugs to the gut at low doses to suppress inflammation
www.science.org/doi/10.1126/...

Differential T cell receptor gene expression analysis using the Wilcoxon test with similarity-based weighting To better understand immune responses, comparing the abundance of T cell receptors (TCRs) between conditions can provide insights into which T cells have proliferated or were involved in immune activa...

Cool pre-print in my feeds this morning, using a neat trick weighting TCRs by similarity prior to DGE better resolve differential usage. Seems to be a clever trick to make TCRseq behave a little more like regular RNAseq data and better use regular stats/tools:

www.biorxiv.org/content/10.1...

A natural experiment on the effect of herpes zoster vaccination on dementia - Nature Using a natural experiment that avoids common bias concerns, this study finds that the live-attenuated shingles vaccine reduced the probability of a new dementia diagnosis within a follow-up period of...

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

Ultra long-lived plasma cells in the human small intestine produce microbiota-reactive IgA antibodies A large fraction of the intestinal microbiota is highly coated with secretory IgA, and bacteria-specific IgA is believed to shape the composition of the microbiota. A hallmark of the adaptive immune s...

This looks super interesting www.biorxiv.org/content/10.1...

Direct presentation of endogenous antigen on MHC II is crucial to mRNA-LNP vaccine-induced immune responses
doi.org/10.1101/2025...

42-Parameter (40-Color) Spectral Flow Cytometry Panel for Comprehensive Immunophenotyping of Human Peripheral Blood Leukocytes
doi.org/10.1002/cyto...

T-bet+ CXCR3+ B cells drive hyperreactive B-T cell interactions in multiple sclerosis Multiple sclerosis (MS) is an autoimmune disease of the central nervous system (CNS). Self-peptide-dependent autoproliferation (AP) of B and T cells i…

T-bet+ CXCR3+ B cells drive hyperreactive B-T cell interactions in multiple sclerosis

www.sciencedirect.com/science/arti...

check out our new manuscript (led by Gian Marco Visani):

structure-based machine learning model for TCR-pMHC complexes, predicting T-cell affinity to peptide-MHC complexes, quantifying T-cell receptor specificity, and designing de-novo immunogenic peptides:
arxiv.org/abs/2503.00648

Excited to see our new single cell immunology tool out now in @naturecomms.bsky.social. We made "Single cell suppression profiling of human regulatory T cells" to generate a human model to screen for cell-type specific effects on all immune cells simultaneously.
www.nature.com/articles/s41...

Mass firings decimate U.S. science agencies White House dismissals and rationale challenged by dismissed scientists and lawsuits

More and more scientists are joining the ranks of fired federal workers—and fighting back through protests, appeals, and legal challenges.

Lung CD4+ resident memory T cells use airway secretory cells to stimulate and regulate onset of allergic airway neutrophilic disease @cp-cellreports.bsky.social
www.cell.com/cell-reports... @anukulshenoy.bsky.social

SEED-Selection enables high-efficiency enrichment of primary T cells edited at multiple loci - Nature Biotechnology Primary T cells with multiple genetic modifications are rapidly isolated by negative selection.

Excited to share our latest work, now out in
@NatureBiotech
! We introduce SEED-Selection, a powerful method that enables high-efficiency enrichment of T cells edited at multiple loci in a single step 🧵👇

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

KLF2 maintains lineage fidelity and suppresses CD8 T cell exhaustion during acute LCMV infection Naïve CD8 T cells have the potential to differentiate into a spectrum of functional states during an immune response. How these developmental decisions are made and what mechanisms exist to suppress d...

To read: www.science.org/doi/10.1126/...

The Problem With Vaccines When a public health intervention is literally too good.

The problem with vaccines.

When a public health intervention becomes a victim of its own success.

gidmk.substack.com/p/the-proble...

Understanding the therapeutic toolkit for inflammatory bowel disease Nature Reviews Gastroenterology & Hepatology, Published online: 31 January 2025; doi:10.1038/s41575-024-01035-7The management of inflammatory bowel disease (IBD) continues to evolve. This Review is a practical guide on the therapeutic toolkit for IBD,…

New online! Understanding the therapeutic toolkit for inflammatory bowel disease

Integrating single-cell RNA and T cell/B cell receptor sequencing with mass cytometry reveals dynamic trajectories of human peripheral immune cells from birth to old age - Nature Immunology In this Resource, authors profile peripheral immune cells from a total of 220 healthy volunteers from birth to over 90 years. This revealed that T cells were most affected by aging with divergent agin...

Dynamic trajectories of human peripheral immune cells from birth to old age
@natimmunol.bsky.social
www.nature.com/articles/s41...
www.nature.com/articles/s41...

Predicting adaptive immune receptor specificities by machine learning is a data generation problem Predicting immune receptor specificity is crucial to progress in developing immunotherapies. Despite the advent of AI tools for protein structure prediction, challenges remain in accurately modeling i...

Yet another piece on immune receptor specificity predictions.
More and more papers on tje topic, it feels like little small pieces of a very big puzzle 🧩, will we ever complete it?
#immunerepetoire #machinelearning

www.cell.com/cell-systems...

"'evidence suggests that they are specifically tasked with controlling self-reactive T cells that have been activated by infection.

How Ly49+/KIR+ CD8 regulatory cells can identify which cells are self-reactive? this interpretation seems unrealistic.

#immunology