Simon Baker

Somatic genomics as a discovery engine for biomedicine Somatic mutations, or genetic changes occurring in cells after conception, are widespread in healthy tissues but are conventionally viewed as signs of…

Somatic genomics as a discovery engine for biomedicine - a Perspective in Cell
www.sciencedirect.com/science/arti...

Cells that communicate may help hinder bladder cancer from spreading Researchers at University of York’s Jack Birch Unit have revealed how direct communication between cells can help maintain healthy human tissue - potentially paving the way for new treatments for blad...

Researchers at the Jack Birch Unit @biologyatyork.bsky.social @ybri-uoy.bsky.social revealed how direct communication between cells can help maintain healthy tissue, potentially paving the way for new bladder cancer treatments 🔬

Open access paper in Life Science Alliance doi.org/10.26508/lsa... 🔓 📄

Pleased to see Jenny’s first author work on Connexin communication in the urothelium published. It’s a great story.

New results suggest that bladder cancer could be caused by the body’s response to common childhood virus - Kidney Research UK New data from Dr Simon Baker suggests BK virus can drive bladder cancer development, which kidney transplant recipients are at more risk of.

For World Cancer Day, we're shining a spotlight on Dr Simon Baker and his team at the University of York, and their research into BK virus and bladder cancer.

Read more the research here: https://bit.ly/4pjXEvr

Sounds interesting. Shame it’s not open access.

Virus-induced APOBEC3 transmutagenesis in bladder cancer initiation A model for hit-and-run viral carcinogenesis in the bladder.

The relevant recent paper 🔬🔗:
www.science.org/doi/10.1126/...

Our work is supported by @kidneyresearchuk.org and @yorkagainstcancer.bsky.social, and is hosted by the @biologyatyork.bsky.social and @ybri-uoy.bsky.social.

I chatted with @philiprlang.bsky.social on his podcast about how a virus might be involved in bladder cancer. Since "Phil Lang is Not a Scientist", we made this really accessible. If you're interested in how small sneaky DNA viruses might contribute to the origins of cancers, give it a listen.

I had a lovely chat with Phil Lang on his podcast "Phil Lang is Not a Scientist" where I talk a lot about dreams and sleep! Phil interviews researchers from across the University of York about their work in all sorts of fascinating areas. (creators.spotify.com/pod/profile/...).

Another virus which causes ‘just a cold’ or ‘cold like symptoms’ is actually causing cancer. Tip of the iceberg?

This work was hosted @biologyatyork.bsky.social, @ybri-uoy.bsky.social and @yorkbioscience.bsky.social. With collaborators at @universityofleeds.bsky.social, @lthtresearchcomms.bsky.social, @leedsth.nhs.uk, University of Texas at San Antonio and the National Cancer Institute at Bethesda.

The fantastic authors on Bluesky are @sallyjamesyork.bsky.social, @asmasonomics.bsky.social, @karen-hogg.bsky.social, @imartincorena.bsky.social, @starrett.bsky.social

With thanks to our funders @kidneyresearchuk.org and @yorkagainstcancer.bsky.social for supporting #bladdercancer research which is so often neglected. #cancer #cancerresearch #APOBEC

A model for bladder cancer initiation where persistent BK virus infections of the kidney reactivate and shed decoy cells into the urine infecting the urothelium. In late-stage infections, the urothelium isolates and apically extrudes infected cells (marked by expression of the Viral capsid major Protein 1 “VP1”). In the viral extrusion microenvironment, bystander cells express interferon-regulated APOBEC3A, which damages the host genome. This is a hypothesis for how bladder cancers become defined by APOBEC3A/B mutagenesis without any virus present in the final tumour.

These findings suggest a model of bladder carcinogenesis where the urothelial response to BK virus infections drives the initiating APOBEC mutations, but the virus is not required in the arising tumour.

Flow cytometry was used to sort a population that was high in antiviral APOBEC3 cytidine deaminase expression but had no detectable viral protein expression. Nanorate sequencing (NanoSeq) was then used to capture the APOBEC mutational signature forming in these cells. Could these cells be the progenitors of bladder cancers with APOBEC mutations in their genome but no trace of viruses?

"Transmutagenesis" describes the observation of bystander cells that were negative for viral proteins and proximal to infected neighbours acquiring APOBEC3A mediated potentially cancer initiating mutations.

Histology images showing coordinated apical extrusion of BK virus infected cells by the healthy tissue. APOBEC3 cytidine deaminases were upregulated in bystander cells (without detectable viral proteins) involved in the apical extrusion process.

Chronic (>21 day) BK virus infections of normal human urothelium led to robust inductions of APOBEC3 mutational signatures. APOBEC3A was induced by bystander cells (negative for viral proteins) and in association with apical extrusion of infected cells by interferon signalling.

Mutograph image showing that mutational signatures characteristic of antiviral APOBECs form in the genomes of urothelial cells when cultures are infected with BK virus.

Our evidence suggests there could be a route to bladder cancer prevention by stopping/controlling the reactivation of persistent BK virus infections.

Virus-induced APOBEC3 transmutagenesis in bladder cancer initiation A model for hit-and-run viral carcinogenesis in the bladder.

What causes bladder cancer initiating mutations?
Our paper in Science Advances asks the question: can BK virus infections of normal urothelium lead to the APOBEC3 mutational signatures found in bladder cancers?
We found that they can!

newsGP - Australia set for world-first cervical cancer elimination Vaccination programs have played a key role, and GPs remain ‘instrumental’ in boosting screening rates to reach the 2035 target.

Australia recorded ZERO cases of cervical cancer in women under 25 for the first time since they started tracking the cancer in the 80s.

This is the power of vaccines.

The HPV vaccine is extremely effective at preventing cancer.

Viruses can be oncogenic. Get your vaccines and protect yourself!

Research webinar - Kidney Research UK A webinar to hear directly from Kidney Research UK funded researchers as they share the latest updates on projects tackling BK virus and cytomegalovirus.

Are you a kidney transplant recipient who would like to learn more about post-transplant viral infections?

Join @kidneyresearchuk.org funded researchers to hear updates on their research. This online seminar will take place 1-2pm on Friday 28th November 2025, register for free below.

New PhD opportunity! Can skin inflammation protect us from mosquito-borne viruses like Zika?
Join our MRC PhD project at York exploring how psoriasis and eczema change skin immunity to virus.
Our grads thrive in academia, biotech & beyond.
Apply now 👉 tinyurl.com/bfmd2rf4

Poster for the 2nd Course on Urothelial Cancers on January 14th-16th 2026 at the Institut Curie in Paris. Theme: Understanding molecular basis of urothelial tumors to improve diagnosis and treatments. Contact: c.uro2026@curie.fr

I'm really excited to be teaching about mutational signatures and viral aetiologies in #bladdercancer at the "Course on Urothelial Malignancies" in Paris 14-16 January 2026. There are so many great speakers, I'm sure I'll learn lots. Hope to see you there!
Contact: c.uro2026@curie.fr

Collectively common, rare kidney disease report - Kidney Research UK A report about the impact of rare kidney diseases in the UK including diagnosis delays and waits for new treatments.

“Rare” kidney diseases leave a deep and widespread impact. 160,000+ people in the UK are affected — driving 25% of dialysis demand and costing the NHS £263m a year.
As a @kidneyresearchuk.org Trustee, I’m calling for faster diagnosis and fairer access to care.
🔗 bit.ly/47Wdp5Z

#KidneyHealth

We all know vaccines target the pathogen, but can you also target the vector?
📢 in a new paper out today in Vaccines,
we show that a vaccine targeting mosquito salivary peptides, AGSv-PLUS, enhances human skin immune response to biting.
Open access: www.mdpi.com/2076-393X/13...
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Image of a fluorescently labeled adult mouse kidney showing AQP2 staining of collecting ducts and connecting segment in green and alpha SMA staining of the arterial tree in magenta. The collecting ducts look like squiggly branches.

For this #FluorescenceFriday, a gorgeous image of an adult mouse kidney labeled with AQP2 and alpha SMA antibodies. AQP2 (green) marks the collecting duct and distal connecting segment while SMA marks the arterial tree. Courtesy of talented postdoc Sarah McLarnon.

Having a fantastic time listening to all the progress in kidney research in the UK @kidneyresearchuk.org driving discoveries. Fantastic talk @willkidney.bsky.social about how large well designed trials have changed our practice in nephrology

QUOD's National Operational Coordinator, Sarah Cross, is at the Kidney Research UK #DrivingDiscoveries conference today in Bristol and is ready to talk to you about how the QUOD biobank can support your kidney research.

Come and say hello! 👋

@nhsbt.bsky.social @ndsurgicalsci.bsky.social @ox.ac.uk

€1.5 million to uncover disease risk hiding in non-coding DNA Greg Findlay, Group Leader of the Genome Function Laboratory at the Francis Crick Institute, has been awarded a Starting Grant from the European Research Council for €1.5 million to take a deep dive i...

Congratulations to @gregfindlay.bsky.social on being awarded a €1.5 million Starting Grant from the @erc.europa.eu to take a closer look at possible disease variants hiding in the dark genome.

www.crick.ac.uk/news/2025-09...

The Leeds Transplant teams are amazing humans. Great to see this celebration.

If you're a kidney transplant recipient who has been diagnosed with BK virus infection, please consider reading our evidence-based patient information leaflet that was co-developed alongside BK nephropathy patients. We hope it helps and welcome any feedback to develop it.
www.kidney.org.uk/bk-virus

A highly potent human antibody neutralizing all serotypes of BK polyomavirus Author summary BK polyomavirus (BKPyV) is a common virus that infects most people during childhood and typically remains dormant in the kidneys without causing harm. However, in kidney transplant pati...

"A highly potent human antibody neutralizing all serotypes of BK polyomavirus"

journals.plos.org/plospathogen...