Matteo Gentili

Super excited about first Shendure/Baker Lab collaboration & preprint on a multiplex sequencing-based strategy for screening de novo proteome editors in mammalian cells. Kudos to the brilliant Chase Suiter (not here) & @greenahn.bsky.social on the work! Preprint here:
www.biorxiv.org/content/10.1...

Virus driven Disruption of Transcription Termination (DoTT) generated cellular Z-RNAs are bona fide ZBP1 ligands driving cell death as a host response to counter viral disruption of the cellular transcriptional machinery @nature.com @foxchasecancer.bsky.social
www.nature.com/articles/s41...

Progression to rheumatoid arthritis in at-risk individuals is defined by systemic inflammation and by T and B cell dysregulation Individuals at risk for rheumatoid arthritis exhibit inflammation and immune dysregulation before and during transition to active disease.

Progression to rheumatoid arthritis in at-risk individuals is defined by systemic inflammation and by T and B cell dysregulation www.science.org/doi/10.1126/...

What an amazing work @iannaconelab.bsky.social &friends just out @natimmunol.nature.com, it was really cool to have a preview of this fantastic work at the 2025 ENII EFIS EJI Summer School! Many congrats Matteo &co! Check it out here 👉 www.nature.com/articles/s41... & here 😉 👇👇👇

A reference model of circulating hematopoietic stem cells across the lifespan with applications to diagnostics Nature Medicine - A large single-cell transcriptomic-based reference model for hematopoietic stem and progenitor cells from 148 age- and sex-diverse individuals identifies physiological and...

🧬🖥️ scAtlas of CD34+ cells from 148 people reveals how circulating hematopoietic stem/progenitor cells (cHSPCs) shift with age, sex & disease. Reference model enables myelodysplastic syndrome (MDS) diagnosis. From great Liran Shlush & Amos Tanay ‪@natmed.nature.com‬: doi.org/10.1038/s415... 🧪

A checklist for designing and improving the visualization of scientific data Nature Cell Biology - Creating clear and engaging scientific figures is crucial to communicate complex data. In this Comment, I condense principles from design, visual perception and data...

I gave in! After students asking for it, I now made a simple figure design checklist.
To help all scientists w/o graphic skills create clear, accessible, and truthful charts!
-> Out in @nature Cell Biology: rdcu.be/erwl4

#DataVisualization #PhD #SciComm

Thx for review @bethcimini.bsky.social + 2

Perturb-Multimodal: A platform for pooled genetic screens with imaging and sequencing in intact mammalian tissue @cellcellpress.bsky.social @jswlab.bsky.social @weallen1.bsky.social
www.cell.com/cell/fulltex...

ENPP1 governs the metabolic regulation of effector T cells in autoimmunity by detecting cytosolic mitochondrial DNA @cp-cellreports.bsky.social
www.cell.com/cell-reports...

If you love #viruses, #ribosomes, and genomic #darkmatter, this thread is for you!! 💫
We're excited to share our new publication developing Massively Parallel Ribosome Profiling (MPRP), which uncovered ~4,000 hidden proteins in ~700 viral genomes. www.science.org/doi/10.1126/...

Transcript-specific enrichment enables profiling of rare cell states via single-cell RNA sequencing - Nature Genetics Programmable Enrichment via RNA FlowFISH by sequencing (PERFF-seq) isolates rare cells based on RNA marker transcripts for single-cell RNA sequencing profiling of complex tissues, with applicability t...

Out today in @naturegenet.bsky.social -- PERFF-seq! With @tsionabay.bsky.social , @ronanchaligne.bsky.social, Bob Stickels, Meril Takizawa, + Ansu Satpathy, we describe this new assay to study rare populations with programmable nucleic acid cytometry. 1/n
www.nature.com/articles/s41...

Congrats Nicolas and team! 🍾

Centromeric DNA amplification triggered by viral proteins activates nuclear cGAS Herpesvirus proteins disrupt centromeres, triggering centromeric DNA amplification and local nuclear activation of the nucleic acid sensor cGAS. This reveals an immune surveillance mechanism in the nu...

Thrilled to share our latest @cp-cell.bsky.social.
We present VICAR (VIral-induced Centromeric DNA Amplification and Recognition), a new defense system to detect viruses in the nucleus based on nuclear cGAS.
www.cell.com/cell/abstrac...

Caspase-11 drives macrophage hyperinflammation in models of Polg-related mitochondrial disease - Nature Communications Mitochondrial diseases lead to chronic health impairment, aggravated by infections and other environmental exposures. Here authors show, in a mouse model of polymerase gamma (Polg)-related mitochondri...

Delighted to share our paper describing how type I interferon promotes caspase-11 hyperactivity in models of PolG-related mitochondrial disease. Thanks to all co-authors and the POLG Foundation for for their support. www.nature.com/articles/s41...

Systemic inflammation impairs myelopoiesis and interferon type I responses in humans - Nature Immunology Stunnenberg et al. use a model of lipopolysaccharide injection in humans to characterize the transcriptomic landscape of bone marrow and blood immune cells during the hyperinflammatory and immunosuppr...

#WeekendRead! #InterferonPower! Stunnenberg Pickkers Kox, Keramati &co show @natimmunol.bsky.org that 2 LPS injections in volunteers mimic the proinflammatory & immunosuppressive phases of #sepsis & found that IFNb treatment restores immune responsiveness in the suppressive phase!

Gomez-Diaz, @v-hornung.bsky.social et al. show that RNase T2 restricts TLR13-mediated #autoinflammation in vivo. rupress.org/jem/article/...

📘 In JEM #Immunology Collection: rupress.org/jem/collecti...
#AAI2025

Base-modified nucleotides mediate immune signaling in bacteria Signaling from pathogen sensing to effector activation is a fundamental principle of cellular immunity. Whereas cyclic (oligo)nucleotides have emerged as key signaling molecules, the existence of othe...

"Immune signaling through nucleotide-based second messengers is a widespread defense mechanism observed across organisms, from bacteria to animals. Zeng et al. discovered a base-modified nucleotide, deoxyinosine 5′-triphosphate (dITP), that acts as an antiviral immune signal in bacteria"
#Immunology

Base-modified nucleotides mediate immune signaling in bacteria Signaling from pathogen sensing to effector activation is a fundamental principle of cellular immunity. Whereas cyclic (oligo)nucleotides have emerged as key signaling molecules, the existence of othe...

#weekendreading📑🔬

Base-modified nucleotides mediate immune signaling in bacteria

@science.org #microsky

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

ZBP1 senses splicing aberration through Z-RNA to promote cell death
www.cell.com/molecular-ce...
www.cell.com/molecular-ce...

AAV vectors trigger DNA damage response-dependent pro-inflammatory signaling in human iPSC-derived CNS models and mouse brain @natcomms.nature.com @kajastelab.bsky.social
www.nature.com/articles/s41...

Integrator loss leads to dsRNA formation that triggers the integrated stress response Integrator (INT) prevents the escape of immature RNAPII to ensure full-length mRNA production. INT deficiency causes defects in RNAPII maturation that lead to premature termination, accumulation of immunogenic dsRNA, and activation of the integrated stress response (ISR) observed in patient cells.

Now online! Integrator loss leads to dsRNA formation that triggers the integrated stress response

Setdb2 regulates trained immunity by 2 complementary mechanisms:
1: increase glycolytic & inflammatory pathway genes via enhancer-promoter looping
2: increased promoter associated H3K9 methylation & repressed interferon response papers.ssrn.com/sol3/papers....

STING mediates lysosomal quality control and recovery through its proton channel function and TFEB activation in lysosomal storage disorders STING signaling in the innate immune system is well known for its role in the antiviral type I interferon response. Tang et al. find that STING acts as an immune sensor of lysosomal activity. When the...

#WeekendRead! #NotOnlyInterferons! @nanyanlab.bsky.social &co show @cp-molecularcell.bsky.social that other than inducing pathogenic IFNs in lysosomal storage disorders, STING also play protective functions as a proton channel activating TFEB & inducing lysosomal repair www.cell.com/molecular-ce...

An atlas of single-cell eQTLs dissects autoimmune disease genes and identifies novel drug classes for treatment
www.cell.com/cell-genomic...

Butterflies on a blue sky

THREAD

The numbers are in. @bsky.app research sharing volumes vs X Formerly Twitter

In March 2024, on most days, Bluesky hosts more posts linked to research published in 2025 than X.

By quite a lot.

Release the Kraken...

#AcademicSky #HigherEd #Altmetrics
1/11

Functional and antigenic landscape of the Nipah virus receptor binding protein bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution

In new study led by Brendan Larsen in collab w Veesler & Crowe labs, we map functional & antigenic landscape of Nipah virus receptor binding protein (RBP)
www.biorxiv.org/content/10.1...
 
Results elucidate constraints on RBP function & provide insight into protein’s evolutionary potential

Wonder which #innate responses in your animal models are shared with or distinct from humans? We did too! To answer, we teamed up with @mcampomd.bsky.social and the Hawn lab to compare human and murine alveolar and monocyte-derived #macrophage responses to #Mtb. (1/4)

#TBSky #ImmunoSky #NewPI x 2

Epidermal ZBP1 stabilizes mitochondrial Z-DNA to drive UV-induced IFN signaling in autoimmune photosensitivity ZBP1 and mitochondrial Z-DNA drive autoimmune photosensitivity via cGAS-STING activation.

#InterferonFriendOrFoe?! Klein @kahlenberglab.bsky.social &co show Science Immunology that UV drives mitochondrial Z-DNA to induce type I & III IFNs in keratinocytes. IFN-I upregulates ZBP1 that binds Z-DNA activating cGAS-STING to boost IFNs, photosensitivity & inflammation in #Lupus skin!

Sign the Petition Petition to Reverse the NIH Indirect Cost Cap (NOT-OD-25-068)

Petition to Reverse the NIH Indirect Cost Cap initiated by Tom Maniatis. Please amplify
Sign the Petition: chng.it/kK2HMP5pGk
"Share with Leadership & Faculty. Reach out to professional societies, biotech and pharma leaders, and philanthropic organizations to raise awareness and mobilize support."

The TLR7/9 adaptors TASL and TASL2 mediate IRF5-dependent antiviral responses and autoimmunity in mouse - Nature Communications TASL is an adaptor molecule bridging Toll-like receptor signalling and transcription activation by IRF5. Here the authors show that TASL deficiency impacts TLR7/9 responses, and that a TASL paralogue,...

Excited to share our latest paper out today in @naturecomms.bsky.social !

Great work led by postdoc Ales Drobek showing for the first time the critical role in vivo of the SLC15A4/TASL/IRF5 pathway that we discovered few years ago.

#ImmunoSky #InterferoSky

5,562 proteins were found to have tissue-specific enrichment across 32 human tissues.

The majority of them (3,088) are enriched at the protein but not RNA level.

The brain hosts the largest number of proteins that are only enriched at the protein level but not RNA level.