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Floris Barthel @florisbarthel.bsky.social · 21h

Read the original work here academic.oup.com/neuro-oncolo...

Clinical, radiological, and molecular insights into extracranial metastases from adult gliomas

AbstractBackground. Extracranial metastases from adult gliomas cause diagnostic and therapeutic challenges and are generally poorly investigated. The aim o

academic.oup.com

Floris Barthel @florisbarthel.bsky.social · 21h

I had the opportunity to write an editorial for a piece in Neuro-Oncology (@neuroonc.bsky.social) executing a genomic analysis on perhaps the largest cohort of extracranial metastases of adult gliomas to date. Congratulations to the authors on this terrific piece of work! bit.ly/494Pz8s

Uncommon Territory: The Clinical and Molecular Profile of Metastatic Gliomas

Floris P Barthel; Uncommon Territory: The Clinical and Molecular Profile of Metastatic Gliomas, Neuro-Oncology, , noaf244, https://doi.org/10.1093/neuonc/n

bit.ly

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Reposted by Floris Barthel

Mike Schatz @mikeschatz.bsky.social · 1d

Getting excited for #ASHG25. The must see talk is tomorrow at 1:30 by Qiuhui (Iris) Li presenting the first large-scale integration of long-read genome sequencing with electronic health record data across >1000 All of Us participants meetings.ashg.org/event/ASHG25...

PheedLoop

PheedLoop: Hybrid, In-Person & Virtual Event Software

meetings.ashg.org

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Floris Barthel @florisbarthel.bsky.social · 2d

Why does the telomere interact with these distant repeats? We speculate that this is key for maintaining nuclear organization or chromosome territories and may involve nuclear orphan receptors. Many questions remain. Read the paper to dive into the data 👇 #TelomereC #Genomics #Chromatin #Epigenetics

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Floris Barthel @florisbarthel.bsky.social · 2d

We validated these contacts with classic 3C/PCR and confirmed the 3D proximity using Southern Blotting and stunning 3D FISH data, proving these are real, higher-order chromatin structures.

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Floris Barthel @florisbarthel.bsky.social · 2d

Specifically, we found strong enrichment at three classes of repetitive elements: Interstitial Telomeric Sequences (ITS), Telomere-Associated Repeat 1 (TAR1), and D20S16 elements.

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Floris Barthel @florisbarthel.bsky.social · 2d

The telomeric interactome spans the entire genome! While contacts are enriched near telomeres (<100 Kb), over 80% of all interactions occurred >5 Mb away from chromosome ends. This isn't just about the subtelomere.

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Floris Barthel @florisbarthel.bsky.social · 2d

Our initial goal was to map telomeric regulation of key genes, like TERT. The reality? Gene-level interactions were massively outnumbered by contacts with repetitive elements! 🤯

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Floris Barthel @florisbarthel.bsky.social · 2d

To map the telomeric interactome, we developed Telomere-C (Telomere Conformation Capture). This novel, ligation-free method uses a biotinylated PNA probe to capture telomeric DNA, allowing us to measure nuclear contacts efficiently using short-read sequencing.

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Floris Barthel @florisbarthel.bsky.social · 2d

This 7-year journey has reached a first milestone! 🥳 Excited to share our preprint (3rd of 2025) on the 3D telomeric interactome, a project that started with a K99 in 2018. Thanks to Yi-An Chen, first postdoc in our lab and first author who worked tirelessly to realize this dream. bit.ly/3W3wuMk

Mapping the Telomeric 3D Interactome with Telomere-C Reveals Repetitive Element Hubs Associated with Telomere Maintenance

Telomeres are essential for genome integrity, but the accurate, high-resolution mapping of their three-dimensional (3D) chromatin interactions, a process thought to mediate gene regulation and telomer...

bit.ly

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Floris Barthel @florisbarthel.bsky.social · 2d

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Reposted by Floris Barthel

bioRxiv Genomics @biorxiv-genomic.bsky.social · 5d

Mapping the Telomeric 3D Interactome with Telomere-C Reveals Repetitive Element Hubs Associated with Telomere Maintenance https://www.biorxiv.org/content/10.1101/2025.10.09.681516v1

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Reposted by Floris Barthel

Andre Kahles @akkah21.bsky.social · 7d

After years of research and continuous refinement, we’re thrilled to share that our paper on the MetaGraph framework — enabling Petabase-scale search across sequencing data — has been published today in Nature (www.nature.com/articles/s41...)

Efficient and accurate search in petabase-scale sequence repositories - Nature

MetaGraph enables scalable indexing of large sets of DNA, RNA or protein sequences using annotated de Bruijn graphs.

www.nature.com

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Floris Barthel @florisbarthel.bsky.social · Aug 7

Fully on board with this as you know and happy to contribute my 2 cents. Coordinates/position, be gone!

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Floris Barthel @florisbarthel.bsky.social · Jul 14

P.s. this is a repost of a deleted post from earlier today, where the link to the pre-print was not working. An update to BlueSky allowing post editing would be welcomed :)

Floris Barthel @florisbarthel.bsky.social · Jul 14

This was pre-print number two of 2025 from our lab. Several more scheduled for public release later this year... Stay tuned!!

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Floris Barthel @florisbarthel.bsky.social · Jul 14

We're actively developing a novel high-sensitive method for #cfDNA analysis and anticipate a preprint on that approach very soon. Exciting times ahead for #LiquidBiopsy in #GBM research! Kudo's to @tgenresearch.bsky.social for supporting this work and #PrecisionMedicine in general!

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Floris Barthel @florisbarthel.bsky.social · Jul 14

This preprint marks a significant milestone for our lab and especially for Sharvari. Her dedication and scientific rigor shine through in this comprehensive study. Incredibly proud of her accomplishments and grateful for the opportunity to mentor her! 👩‍🔬

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Floris Barthel @florisbarthel.bsky.social · Jul 14

What's next? @sharvarimankame.bsky.social is currently evaluating cfDNA in plasma and CSF samples from #Glioblastoma patients, translating these exciting in vitro findings to the clinic.

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Floris Barthel @florisbarthel.bsky.social · Jul 14

We observed specific cfDNA fragmentation signatures associated with TMZ sensitivity and resistance. These patterns could serve as valuable biomarkers for predicting treatment response.

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Floris Barthel @florisbarthel.bsky.social · Jul 14

@sharvarimankame.bsky.social's work leverages cfDNA as a non-invasive window into the complex interplay between treatment, tumor evolution, and the host. This brings us closer to developing more effective monitoring strategies for #GBM patients.

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Floris Barthel @florisbarthel.bsky.social · Jul 14

Some key findings: co-culturing glioblastoma cells with host cells significantly alters cfDNA fragmentation patterns. This highlights the vital role of the tumor microenvironment in shaping cfDNA characteristics.

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Floris Barthel @florisbarthel.bsky.social · Jul 14

Our study reveals how TMZ treatment drives dynamic changes in cfDNA profiles, reflecting tumor response and resistance mechanisms. This is crucial for understanding how #GBM adapts to therapy over time.

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Floris Barthel @florisbarthel.bsky.social · Jul 14

Thrilled to share our preprint led by the lab's incredible first PhD student, @sharvarimankame.bsky.social! 🎉 We've explored the longitudinal consequences of temozolomide (TMZ) treatment & host co-culture in #Glioblastoma using cell-free DNA (cfDNA) sequencing. A deep dive into therapeutic impact..

Cell-Free DNA Reveals the Longitudinal Effects of Temozolomide Treatment and Host Co-Culture in Glioblastoma Models

Glioblastoma (GBM) is a highly aggressive brain tumor with limited options for longitudinal monitoring. We evaluated the potential of cell-free DNA (cfDNA) as a real-time biomarker of tumor burden und...

doi.org

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Floris Barthel @florisbarthel.bsky.social · Jul 14

This preprint marks a significant milestone for our lab and especially for Sharvari. Her dedication and scientific rigor shine through in this comprehensive study. Incredibly proud to have the opportunity to mentor her in our lab! 👩‍🔬