Lightnews — Scholar-powered news

Jamie Blundell @jamie-blundell.bsky.social · Jul 3

Delighted to share our latest on longitudinal methylation dynamics preceding cancer. Epigenetic signs of AML appear in blood DECADES before Dx.
👉 Early cancer detection
👉 Methylation drivers
👉 Epimutation rates
👉 CpG lineage tracing

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

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Reposted by Jamie Blundell

Dmitri Petrov @petrovadmitri.bsky.social · Jun 3

Flybase lost all of the NIH support overnight - it is a disaster for the community. Please consider donating. I just did! www.philanthropy.cam.ac.uk/give-to-camb...

Drosophila Genetic Database

The Drosophila Genetic Database, FlyBase, is on the brink of collapse due to the sudden termination of the FlyBase NIH grant, which includes salaries for 5 literature curators based at the University ...

www.philanthropy.cam.ac.uk

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Reposted by Jamie Blundell

Charlie Pugh @cwjpugh.bsky.social · May 26

New preprint in collaboration with @paulinanunezv.bsky.social supervised by @jonnyfrazer.bsky.social and Mafalda Dias – we propose a simple approach to improving zero-shot variant effect prediction in pre-existing protein and genome language models: 🧶 1/n

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

From Likelihood to Fitness: Improving Variant Effect Prediction in Protein and Genome Language Models

Generative models trained on natural sequences are increasingly used to predict the effects of genetic variation, enabling progress in therapeutic design, disease risk prediction, and synthetic biolog...

www.biorxiv.org

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Reposted by Jamie Blundell

EvoMG Program @evomg-bcn.bsky.social · May 23

🚨With some delay, we're excited to announce that our proposal for a MSCA Doctoral Network on Evolutionary Medical Genomics (EvoMG-DN) got funded! 🎉

🧬 14 labs and 2 companies across 7 European countries will be coordinated by the EvoMG Joint Program at @crg.eu & @upf.edu.

europa.eu/!NNq63m

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Reposted by Jamie Blundell

Mohamed A. El-Erian @elerianm.bsky.social · Apr 24

I just wanted to let you know that, having been encouraged by many and received over four times the number of nominations required, I announced today that I am throwing my hat into the ring for the election of the next Chancellor of the University of Cambridge...
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Jamie Blundell @jamie-blundell.bsky.social · Mar 6

Delighted to share a major update on our work investigating age-related deceleration in clonal haematopoiesis.

Takehome: Widespread and substantial deceleration in fitness with age!

Amazing effort by PhD student Hamish MacGregor 💪

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

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Jamie Blundell @jamie-blundell.bsky.social · Mar 5

This is beautiful work — congrats to all the authors 👏

Klaus Okkenhaug @klausokken.bsky.social · Mar 5

Brilliant new paper from Jie Yang @jieyang437.bsky.social and Rahul Roychoudhuri @roychoudhurilab.bsky.social linking aspirin to immune-mediated prevention of cancer metastasis.
www.nature.com/articles/s41...

Aspirin prevents metastasis by limiting platelet TXA2 suppression of T cell immunity - Nature

Inhibition of cyclooxygenase 1 releases T cells from immunosuppression by platelet-derived thromboxane A2, thereby enhancing the immune response against metastasis.

www.nature.com

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Reposted by Jamie Blundell

Cancer Research UK Cambridge Centre @crukcamcentre.bsky.social · Mar 4

Join the Early Cancer Institute for talks from Professor Jamie Blundell and Dr Daniel Muñoz Espín, on their research into cancer evolution and aging! @cambridgefestival.bsky.social

📅 Tues 25 March
⏰ 6-8pm
📍 St John's College Old Divinity School, CB2 1TP
Register ➡️ zurl.co/7NTWz

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Reposted by Jamie Blundell

Alejo Rodriguez-Fraticelli @alejofraticelli.bsky.social · Feb 25

🔥 New Fraticelli lab publication🔥

“Pre-existing stem cell heterogeneity dictates clonal responses to the acquisition of leukemia driver mutations”

Now at Cell Stem Cell, with two new figures, in vivo, and sequential mutagenesis data.

Performed with the support of Cris Cancer and @erc.europa.eu

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Reposted by Jamie Blundell

Aylwyn Scally @aylwyn-scally.bsky.social · Feb 21

We are excited to announce a new faculty position here in Cambridge, for researchers in computational and/or theoretical biology, based jointly in Genetics and Mathematics. Come and join us! Happy to answer questions about research, teaching and working here. www.jobs.cam.ac.uk/job/50414/

Assistant/Associate Professor in Computational Biology - Job Opportunities - University of Cambridge

Assistant/Associate Professor in Computational Biology in the Department of Applied Mathematics and Theoretical Physics at the University of Cambridge.

www.jobs.cam.ac.uk

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Reposted by Jamie Blundell

Michael Baym @baym.lol · Feb 21

Legitmately thrilled to share our latest work, in which @fernpizza.bsky.social solved an experimental challenge in plasmid biology as old as the field: measuring how plasmids compete and evolve within individual cells!

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Reposted by Jamie Blundell

Ewan Birney @ewanbirney.bsky.social · Feb 21

Want to work in one of the most dynamic places in mathematical biology - in one of the oldest universities in the world - great colleagues, great science.

Aylwyn Scally @aylwyn-scally.bsky.social · Feb 21

We are excited to announce a new faculty position here in Cambridge, for researchers in computational and/or theoretical biology, based jointly in Genetics and Mathematics. Come and join us! Happy to answer questions about research, teaching and working here. www.jobs.cam.ac.uk/job/50414/

Assistant/Associate Professor in Computational Biology - Job Opportunities - University of Cambridge

Assistant/Associate Professor in Computational Biology in the Department of Applied Mathematics and Theoretical Physics at the University of Cambridge.

www.jobs.cam.ac.uk

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Jamie Blundell @jamie-blundell.bsky.social · Jan 21

Thank you Vijay!

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Jamie Blundell @jamie-blundell.bsky.social · Jan 21

Delighted to share our latest work exploring levels of selection operating during pre-cancerous evolution usng single-cell DNA sequencing of HSCs led by the outstanding Gladys Poon
www.cell.com/cell-genomic...

Single-cell DNA sequencing reveals pervasive positive selection throughout preleukemic evolution

The representation of driver mutations in preleukemic HSCs provides a window into the somatic evolution that precedes AML. Here, Poon et al. isolate pHSCs from the bone marrow of 16 patients with AML ...

www.cell.com

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Jamie Blundell @jamie-blundell.bsky.social · Dec 27

This idea -- Somatic variants as an in vivo saturation mutagenesis screen — opens up so many opportunities too. # cells >> # people, so you get more statistical power and you preserve cell context (i.e. specific to T-cells here). They have opened up the world of somatic, tissue specific GWAS…

Jamie Blundell @jamie-blundell.bsky.social · Dec 27

For me it is "Naturally occurring T cell mutations enhance engineered T cell therapies"

The idea is so simple: use naturally occurring somatic mutations as an in vivo screen. Evolution finds mutations that improve T-cell persistence and survival which would not have been discovered with CRISPR.

Naturally occurring T cell mutations enhance engineered T cell therapies - Nature

A study examines the effects of mutations that occur naturally in T cell cancers, reporting that such mutations can potentially be exploited to increase the potency of T cell therapies.

www.nature.com

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Reposted by Jamie Blundell

Greifflab @victorgreiff.bsky.social · Dec 15

Extremely pleased to share our new work in collaboration with the @bruskolab.bsky.social lab, where we leveraged one of the largest TCRbeta sequencing datasets to identify T1D-associated TCR-based signatures. Paper link and 🧵 are below. Incredible work led by @puneet021192.bsky.social.

Puneet Rawat, PhD @puneet021192.bsky.social · Dec 14

Happy to share our new collaborative work! 🚨 We analyzed 2250 TCR repertoires to uncover how HLA risk alleles shape immune autoreactivity in T1D. T1D-specific HLA-motifs were also validated in pancreatic lymph nodes (pLN) & spleen. 🧬🧵 #T1D #Immunology #TCR 1/9

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Reposted by Jamie Blundell

Leopold Parts @leopoldparts.bsky.social · Dec 2

Does my mutation have the same impact as yours? Population genetics 🤠 🥸 🤓 🤡 meets single cell CRISPRi ⚡ ! www.biorxiv.org/content/10.1... Led by Claudia Feng, Oliver Stegle, Britta Velten, @sangerinstitute.bsky.social .

This link will take you to a page that’s not on LinkedIn

lnkd.in

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Reposted by Jamie Blundell

Simone Zaccaria @zaccasimo.bsky.social · Nov 29

🚨So proud to present the first study from our @ccg-ucl.bsky.social group together with @charlesswanton.bsky.social @NnennayaKanu and led by @ojlucas.bsky.social with key collaboration @sophie-ward.bsky.social and fundamental support @rijazaidi.bsky.social @abibunkum.bsky.social & others

Out now👇
🧵👇

Characterizing the evolutionary dynamics of cancer proliferation in single-cell clones with SPRINTER - Nature Genetics

Single-cell Proliferation Rate Inference in Non-homogeneous Tumors through Evolutionary Routes (SPRINTER) allows users to infer proliferation rates of individual clones within a tumor from single-cell...

doi.org

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Jamie Blundell @jamie-blundell.bsky.social · Nov 29

Landmark moment for early cancer detection 🤩👏👏👏

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Jamie Blundell @jamie-blundell.bsky.social · Nov 28

V interesting idea 👇

Adam MacLean @adamlmaclean.bsky.social · Nov 28

Just in time for thanksgiving our paper is out ☄️

using fluctuating methylation clocks as barcodes we show that the variation in the hematopoietic stem cell pool that (in most of us) leads to clonal hematopoiesis in later life is likely present *before birth*

👉🏼 www.nature.com/articles/s41...

Developmental hematopoietic stem cell variation explains clonal hematopoiesis later in life - Nature Communications

Clonal hematopoiesis becomes increasingly common with age. Here the authors track stem cell dynamics in monozygotic twins and provide evidence that clonal hematopoiesis in later life reflects weak sel...

www.nature.com

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Reposted by Jamie Blundell

Paul Thomas @pgtimmune.bsky.social · Nov 26

We keep improving TIRTL-seq, see the updated preprint (www.biorxiv.org/content/10.1...)! New additions include: a manual 96-well protocol, code and raw data now available, and successful in vitro validation of EBV and SARS-CoV-2 TCRs.

TIRTL-seq: Deep, quantitative, and affordable paired TCR repertoire sequencing

α/β T cells are key players in adaptive immunity. The specificity of T cells is determined by the sequences of the hypervariable T cell receptor (TCR) α and β chains. Although bulk TCR sequencing offe...

www.biorxiv.org

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Reposted by Jamie Blundell

Centre de Regulació Genòmica (CRG) @crg.eu · Nov 23

Big 🧬 news this week: we have launched the first Joint Program on Evolutionary Medical Genomics. Spearheaded by @mirimiam.bsky.social, Barcelona researchers will study and exploit the vast genomic diversity of life on Earth to enhance precision medicine. Full story in @elpais.com

The dawn of a new medicine: Researchers use the theory of evolution to fight cancer

The world’s first joint research program in evolutionary medical genomics has been launched in Barcelona, under the direction of biologist Manuel Irimia

english.elpais.com

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Jamie Blundell @jamie-blundell.bsky.social · Nov 20

Amazing work and a technology which opens up so many research directions. Congratulations @imartincorena.bsky.social and team!

Inigo Martincorena @imartincorena.bsky.social · Nov 20

Resharing here a recent X post. In this preprint, we introduce an improved version of NanoSeq, a duplex sequencing protocol with <5 errors per billion bp in single DNA molecules, and use it to study the somatic mutation landscape of oral epithelium in >1000 people. 1/ www.medrxiv.org/content/10.1...

Somatic mutation and selection at epidemiological scale

As we age, many tissues become colonised by microscopic clones carrying somatic driver mutations ([1][1]–[10][2]. Some of these clones represent a first step towards cancer whereas others may contribu...

www.medrxiv.org

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Reposted by Jamie Blundell

Sten Linnarsson @sten.linnarsson.org · Nov 17

Before I go to bed let me post an amazing paper by Filipe Pereira’s group (Ervin Ascic et al) for your enjoyment. I think this is a likely fundamental breakthrough in cancer immunotherapy: personalized, yet generic and probably pan-cancer. www.science.org/doi/10.1126/...

In vivo dendritic cell reprogramming for cancer immunotherapy

Immunotherapy can lead to long-term survival for some cancer patients, yet generalized success has been hampered by insufficient antigen presentation and exclusion of immunogenic cells from the tumor ...

www.science.org

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