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nipagh.bsky.social

@nipagh.bsky.social
88 followers 231 following 25 posts

Ph.d. in immunolgy. T cells, tetramers, DNA barcodes, Espresso Martini, and the Tank/Healer in my local DnD group. 🇩🇰🏳️‍🌈.

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Reposted by @nipagh.bsky.social
Redwan Farooq @redwanfarooq.bsky.social · 3h
Fantastic preprint showing how circulating EBV-specific CD8+ T cells in MS adopt a GZMK+ effector–memory state that is primed to migrate to the CNS & may drive neuroinflammation through non-cytolytic interactions with B cells & myeloid cells. 🧵👇 1/
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Kilian Schober @kischober.bsky.social · 6h
New preprint from our lab, now on bioRxiv! We are VERY excited about this one! www.biorxiv.org/content/10.6... How does Epstein–Barr virus (EBV) immunity become linked to multiple sclerosis (MS)? (1/8)
biorxiv.org
A pro-inflammatory effector-memory T cell program links peripheral EBV priming to CNS autoimmunity
T and B cell-mediated immunosurveillance of the central nervous system (CNS) can become maladaptive in multiple sclerosis (MS). Epstein-Barr virus (EBV) is a likely driver of MS, yet how exactly EBV-s...
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Joe Sabatino @jsabatino37.bsky.social · 06/04/2026
Why Is MS a More Frequent Complication of EBV Infection in Females? onlinelibrary.wiley.com/doi/10.1111/...
onlinelibrary.wiley.com
Why Is MS a More Frequent Complication of EBV Infection in Females?
Multiple sclerosis (MS) is a T helper (Th) cell-mediated disease that targets central nervous system (CNS) white matter. This disease affects three times more females than males. For many years, the ...
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Cameron Blevins @cblevins.bsky.social · 03/04/2026
This is so, so well-articulated.
People call this friction "grunt work." Schwartz uses exactly that phrase, and he's right that LLMs can remove it. What he doesn't say, because he already has decades of hard-won intuition and doesn't need the grunt work anymore, is that for someone who doesn't yet have that intuition, the grunt work is the work. The boring parts and the important parts are tangled together in a way that you can't separate in advance. You don't know which afternoon of debugging was the one that taught you something fundamental about your data until three years later, when you're working on a completely different problem and the insight surfaces. Serendipity doesn't come from efficiency. It comes from spending time in the space where the problem lives, getting your hands dirty, making mistakes that nobody asked you to make and learning things nobody assigned you to learn.
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Waggoner Lab @labwaggoner.bsky.social · 03/04/2026
Preprint: B-cell depletion therapy in multiple sclerosis reduced EBV viral load and was coupled to a pronounced reduction in CD8+ T cell responses to all lytic EBV antigens www.researchsquare.com/article/rs-9...
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Immunity @cp-immunity.bsky.social · 31/03/2026
Online now: Memory T cell aging and rejuvenation
dlvr.it
Memory T cell aging and rejuvenation
Aging profoundly alters memory T cell immunity, reshaping diversity, differentiation, and function. Adamo et al. review how intrinsic aging programs, antigenic experience, and tissue context shape T cell responses and discuss emerging strategies to recalibrate memory T cell immunity in later life without compromising immune balance.
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Adrian Liston @labliston.bsky.social · 31/03/2026
A one minute primer on how #AutoSpectral improves spectral flow cytometry unmixing by using per-cell calculation of autofluroscence spectra. Use our R package and get higher quality spectral data, easy as that! www.biorxiv.org/content/10.1...
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Waggoner Lab @labwaggoner.bsky.social · 19/03/2026
Unique and interactive effects of race/ethnicity, genetics, herpesviruses, age, and gender on immunophenotypes @cp-cellrepmed.bsky.social @fredhutch.org @pgtimmune.bsky.social www.cell.com/cell-reports...
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Waggoner Lab @labwaggoner.bsky.social · 19/03/2026
Review @natrevimmunol.nature.com Renaissance of antiviral CD8+ T cell immunity in vaccination and disease www.nature.com/articles/s41...
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Rippling Ideas @ripplingideas.bsky.social · 27/02/2026
This is one of the most interesting developments as it appears that authors are now submitting preprints earlier in the process. A reminder that our data suggests that the best time to post is approx 1 month prior to journal submission (which ~30% now are).
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Waggoner Lab @labwaggoner.bsky.social · 24/02/2026
Metabolic quiescence of naive-like memory T cells precedes and maintains antigen-specific T cell memory @natimmunol.nature.com www.nature.com/articles/s41...
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Ule Lab @ulelab.bsky.social · 24/01/2026
A great read! link.springer.com/article/10.1...
link.springer.com
What is the question? - Genome Biology
Genome Biology -
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nipagh.bsky.social @nipagh.bsky.social · 05/01/2026
💀wtf!? "" .. the last time they paid the annual maintenance fee on it was 2018! You can even find a letter where their lawyers send a refund request for the 2017 maintenance fee ($250) because Novo apparently wanted some more time to see if they wanted to pay it... "" www.science.org/content/blog...
science.org
Novo Nordisk's Canadian Mistake
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Albert Vilella, PhD. @albertvilella.bsky.social · 17/12/2025
.@slavov-n.bsky.social on cell size vs cell count in the human body. Lots of white blood cells in number, lots of adipocytes (fat) in volume.
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Waggoner Lab @labwaggoner.bsky.social · 12/12/2025
Single-cell transcriptomics resolves mononuclear phagocyte diversity in the human intestine in health and inflammatory bowel disease @sciimmunology.bsky.social www.science.org/doi/10.1126/...
science.org
Heterogeneity of the intestinal mononuclear phagocyte compartment in health and inflammatory bowel disease
Single-cell transcriptomics resolves mononuclear phagocyte diversity in the human intestine in health and inflammatory bowel disease.
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Ksenia Matlawska @kseniam.bsky.social · 24/10/2025
Our fresh and still-steaming Journal of Clinical Investigation preprint is out! 🚀 We explore how T-cell acute lymphoblastic leukemia (T-ALL) exploits inflammatory CXCR3–CXCL10 signaling within the meninges to drive CNS infiltration. www.jci.org/articles/vie...
jci.org
JCI - T-cell acute lymphoblastic leukemia exploits a neural proinflammatory pathway to colonize the meninges
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nipagh.bsky.social @nipagh.bsky.social · 29/11/2025
A very interesting read. I wonder how one could replicate this in other autoimmune disorders. www.nature.com/articles/s41...
nature.com
A microenvironment-driven HLA-II-associated insulin neoantigen elicits persistent memory T cell activation in diabetes - Nature Immunology
The authors identify a Cys→Ser transformation (C19S) in insulin leading to neoepitope presentation and CD4⁺ T cell autoreactivity in type 1 diabetes. Inflammation and oxidative stress enhanced C19S tr...
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saligramalab.bsky.social @saligramalab.bsky.social · 26/11/2025
We are #absolutely #thrilled to #present @cp-immunity.bsky.social - Deep profiling of human T cells defines compartmentalized clones and phenotypic trajectories across blood and tonsils: Immunity www.cell.com/immunity/ful...
cell.com
Deep profiling of human T cells defines compartmentalized clones and phenotypic trajectories across blood and tonsils
Human T cell responses are often studied using blood, yet most T cells reside in tissues. By comparing T cell receptor repertoires from millions of T cells from autologous tonsils and blood, Sureshcha...
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Daniel Peeper Lab @peeperlab.bsky.social · 19/11/2025
Our new paper is out in Nature - online today! Huge congrats to shared first authors Sofía Ibáñez-Molero & Johanna Veldman, the whole team & all collaborators. 📄 Open-access paper: www.nature.com/articles/s41...
nature.com
Tumour-reactive heterotypic CD8 T cell clusters from clinical samples - Nature
Tumour-reactive CD8+ T cells are enriched in functional clusters with tumour cells and/or antigen-presenting cells and can be isolated and expanded from clinical samples.
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nipagh.bsky.social @nipagh.bsky.social · 16/11/2025
Sunday reading. I aspire to write something like this for T cells one day. www.cell.com/immunity/ful...
cell.com
A roadmap for defining “extrafollicular” B cell responses
The term “extrafollicular” is now being used expansively to describe a variety of B cell processes beyond the original use of the term, potentially obscuring important distinct immunological processes...
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Waggoner Lab @labwaggoner.bsky.social · 12/11/2025
Epstein-Barr virus–mediated B cell reprogramming may initiate systemic lupus erythematosus www.science.org/doi/10.1126/... www.science.org/doi/10.1126/... @stanfordmedicine.bsky.social @shady-myounis.bsky.social
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Kilian Schober @kischober.bsky.social · 03/11/2025
Dear single-cell bluesky community: We’re running Cell Ranger (5’ scRNA-seq) on sorted human CD8+ T cells with a custom library. Custom seqs (27–133 bp) appear in FASTQs + BAM but aren’t mapped. They are filtered out by STAR for being too short—any way to lower the length limit or workaround?
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nipagh.bsky.social @nipagh.bsky.social · 30/10/2025
Me as a PhD student:"I hate how useful this is". Me as a Postdoc: "I LOVE HOW USEFUL THIS IS".
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bioRxiv Immunology @biorxiv-immuno.bsky.social · 24/10/2025
Mapping of CD8 T-cell recognition to latent EBV infection and neuroantigens reveals HLA-specific depletion of T-cell responses in multiple sclerosis www.biorxiv.org/content/10.1101/202…
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Kilian Schober @kischober.bsky.social · 03/10/2025
If the immune system is an army... ... would you rather rely on one “super warrior” — or on a diverse team of fighters, even if none of them is the single strongest? I’d go with the team. Why? Check out our new study, just published in Science Immunology: www.science.org/doi/10.1126/...
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Kilian Schober @kischober.bsky.social · 08/10/2025
When a T cell carries both its natural TCR and an engineered CAR, do these two receptors cooperate - or compete? Our new preprint on bioRxiv shows that TCR activation can enhance CAR-T activation but impairs CAR-mediated killing when targets are on separate cells. www.biorxiv.org/content/10.1...
biorxiv.org
TCR activation impairs CAR-T cytotoxicity against separate target cells
Chimeric antigen receptor T cells (CAR-T) are effective therapeutics against cancer and autoimmunity, but whether the endogenous T cell receptor (TCR) is beneficial, detrimental or irrelevant for CAR ...
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Griffiths Lab @griffithslab.bsky.social · 04/08/2025
Sometimes, knocking out a gene isn't a good way to figure out the function of that gene ... In our new @jcellsci.bsky.social paper, we report potent transcriptional adaptation by cytotoxic T lymphocytes (CTLs) in response to CRISPR/Cas9-mediated deletion of the important polarity protein CDC42 🧵⬇️
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bioRxiv Immunology @biorxiv-immuno.bsky.social · 05/08/2025
De novo identification of the specificities of recurrent human T cell receptors www.biorxiv.org/content/10.1101/202…
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Stephen Turner @stephenturner.us · 25/01/2025
Writing a technical blog improves your writing, forces you to learn new things, helps others and yourself, and helps your career. In this essay: (1) why blog, (2) what to blog about, (3) how to get started, and (4) using AI. doi.org/10.59350/bqnfd-7p249 🧪
doi.org
Technical blogging for growth and learning
Writing a technical blog improves your writing, forces you to learn new things, helps others and yourself, and helps your career. This post: why blog, what to blog about, how to start, and using AI.
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nipagh.bsky.social @nipagh.bsky.social · 02/08/2025
Double negative T cells can act as professional APCs capable of tolerance induction? How fascinating - I'm picturing a western stand-off between two T cells (both equipped with granzymes btw) unwilling to let go of the other!
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Waggoner Lab @labwaggoner.bsky.social · 02/08/2025
Intestinal CD4−CD8αβ−TCRαβ+ T cells function as tolerogenic antigen presenting cells in mice @natcomms.nature.com www.nature.com/articles/s41...
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Waggoner Lab @labwaggoner.bsky.social · 23/07/2025
Autoantibodies against cytokines, growth factors, immunoreceptors, & tumor surface proteins robustly modulate immune checkpoint inhibition therapy response @aaronmring.bsky.social @nature.com www.nature.com/articles/s41...
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Caleb Lareau @caleblareau.bsky.social · 22/07/2025
Excited to share a new preprint from the lab with @ryandhindsa.bsky.social ! www.biorxiv.org/content/10.1... Led by @sherrynyeo.bsky.social, @erinmayc.bsky.social, and friends, we continue our journey to find viral DNA in our favorite place-- the overlooked and discarded reads in existing data! 1/
the treasure trove of all sequencing datasets
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nipagh.bsky.social @nipagh.bsky.social · 21/07/2025
My last history lesson in school was in 2012. Today I realized that my memory is blank on certain events outside biology, many probably. Fx. I had no idea the EU includes illegal activities in calculating GDP. The amount of colorful assumptions as to how much this contributes to GDP must be wild!
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Waggoner Lab @labwaggoner.bsky.social · 14/07/2025
Early identification of individuals at risk for multiple sclerosis by quantification of EBNA-1381-452-specific antibody titers @natcomms.nature.com www.nature.com/articles/s41...
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Ruth Montgomery @rrmsky.bsky.social · 27/06/2025
Wow, when lower IFN in aging is a good thing! Congratulations Chaz L and team. #ImmuneProfiling #Aging Epigenetic attenuation of interferon signaling is associated with aging-related improvements in systemic lupus erythematosus | Science Translational Medicine www.science.org/doi/10.1126/...
science.org
Epigenetic attenuation of interferon signaling is associated with aging-related improvements in systemic lupus erythematosus
Patients with systemic lupus erythematosus exhibit aging-related decreases in interferon signaling that correlate with improved disease activity.
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Ivan Zanoni @lozanzi.bsky.social · 26/06/2025
#ToStressOrNotToStress! @christinviral.bsky.social @cadwelllab.bsky.social show @naturemicrobiol.nature.com that stress drives #interferon stimulated genes to protect against an enteric virus! After immune suppression by stress-induced glucorticoids, CD8 T cells get activated protecting the host!
nature.com
Environmental stress drives clearance of a persistent enteric virus in mice - Nature Microbiology
Cage change of mice with persistent murine astrovirus infection triggers stress responses marked by corticosterone fluctuation, which is followed by CD8 T cell activation and induction of epithelial a...
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nipagh.bsky.social @nipagh.bsky.social · 22/06/2025
Outright banning ChatGPT? Like a commenter said, chess robots have been instrumental in teaching chess, so why can't AI be a way to teach better scientific writing? "ChatGPT is fun, but not an author" | Science www.science.org/doi/10.1126/...
science.org
ChatGPT is fun, but not an author
In less than 2 months, the artificial intelligence (AI) program ChatGPT has become a cultural sensation. It is freely accessible through a web portal created by the tool’s developer, OpenAI. The progr...
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nipagh.bsky.social @nipagh.bsky.social · 19/06/2025
A perfect date in Erlangen for me really is June 19th. Summer, green parks, a long weekend ahead, and nobody in sight!
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nipagh.bsky.social @nipagh.bsky.social · 13/06/2025
Absolutely fascinating work. ""In this vein, we contend that future incorporation of physiological microbial exposure into animal models may offer translational value to the study of brain health and disease."" (most? any? some?) Infections create a T cell memory in the brain.
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Waggoner Lab @labwaggoner.bsky.social · 13/06/2025
Physiological microbial exposure normalizes memory T cell surveillance of the brain and modifies host seizure outcomes @natimmunol.nature.com www.nature.com/articles/s41...
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Joe Sabatino @jsabatino37.bsky.social · 11/06/2025
Really interesting new study on CD8+ T cells in MS from @ali-syedaliraza.bsky.social and Danny Reich
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bioRxiv Immunology @biorxiv-immuno.bsky.social · 23/05/2025
CSF single-cell RNA sequencing reveals clonally expanded CD4+ stem cell-like memory T cells in GAD65-antibody associated neurological syndromes www.biorxiv.org/content/10.1101/202…
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Janos Groh @janos-groh.bsky.social · 22/05/2025
Pleased to share our latest work on neural-immune interactions in aging white matter. It was a long journey, made possible by incredible support and persistent efforts of many colleagues across various locations. Many thanks to everyone involved. www.nature.com/articles/s41...
nature.com
Microglia activation orchestrates CXCL10-mediated CD8+ T cell recruitment to promote aging-related white matter degeneration - Nature Neuroscience
White matter aging leads to degenerative and inflammatory changes. Here the authors show that microglial dysfunction exacerbates glial CXCL10 expression, harmful CD8+ T cell recruitment, myelinated ax...
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Sandro Da Mesquita @da-mesquita.bsky.social · 21/05/2025
Read our latest review article out in @thelancetneuro.bsky.social if you want to know more about CSF transport across the different compartments of the brain-meningeal border and its importance for neurological diseases with strong neuroimmune components 😉 authors.elsevier.com/a/1l7l75FFzL...
authors.elsevier.com
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Waggoner Lab @labwaggoner.bsky.social · 19/05/2025
Epstein–Barr virus induces aberrant B cell migration and diapedesis via FAK-dependent chemotaxis pathways www.nature.com/articles/s41...
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nipagh.bsky.social @nipagh.bsky.social · 19/05/2025
A reminder to myself that chemokines are likely not exerting their effects via soluble concentration gradients due to their binding to GAGs. At least they weren't in 2011, when this well written review was made! www.sciencedirect.com/science/arti...
sciencedirect.com
The blood–brain barrier, chemokines and multiple sclerosis
The infiltration of leukocytes into the central nervous system (CNS) is an essential step in the neuropathogenesis of multiple sclerosis (MS). Leukocy…
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Waggoner Lab @labwaggoner.bsky.social · 17/05/2025
Mechanism by IL-15 stimulates bystander memory CD8+ T-cells to enter the CNS and contribute to injury independent of antigen-specific stimulation www.biorxiv.org/content/10.1...
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Waggoner Lab @labwaggoner.bsky.social · 09/05/2025
Immunosequencing identifies signatures of T cell responses for early detection of nasopharyngeal carcinoma @cp-cancercell.bsky.social www.cell.com/cancer-cell/...
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Schumacher Lab @schumacher-lab.bsky.social · 02/05/2025
It's not the models, it's the data! We show that a substantial proportion of a widely used TCR-pMHC database does not functionally validate, causing underestimation of performance of TCR-pMHC prediction models. www.biorxiv.org/content/10.1...
biorxiv.org
A functionally validated TCR-pMHC database for TCR specificity model development
Accurate prediction of TCR specificity forms a holy grail in immunology and large language models and computational structure predictions provide a path to achieve this. Importantly, current TCR-pMHC ...
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