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Karsten Rippe @karsten-rippe.bsky.social · Aug 21

Happy to report that the Xenium system for spatial transcriptomics in the Single Cell Open Lab www.dkfz.de/en/single-ce... @dkfz.bsky.social was the first one worldwide to pass the mark of 100 runs according to @10xgenomics.bsky.social. And it keeps on running with another one, so stay tuned...

Single-cell Open Lab - German Cancer Research Center

www.dkfz.de

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Karsten Rippe @karsten-rippe.bsky.social · Aug 21

"In our view, it [hexanediol] should thus be avoided and not be used as evidence for the formation of an assembly via phase separation or the fluid-like nature of a condensate in vitro or in vivo." doi.org/10.1038/s414...

Current practices in the study of biomolecular condensates: a community comment - Nature Communications

The realization that the cell is abundantly compartmentalized into biomolecular condensates has opened new opportunities for understanding the physics and chemistry underlying many cellular processes1...

doi.org

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Karsten Rippe @karsten-rippe.bsky.social · Aug 13

These features allow it to predict immunotherapy response and point to potential universal T cell based therapies. Great multi-group effort led by Mirco Friedrich together with @michael-platten.bsky.social, @raabms.bsky.social, @stefaneichmueller.bsky.social, and many more collaborators.

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Karsten Rippe @karsten-rippe.bsky.social · Aug 13

Glad that the preprint on identifying and characterizing rare tumor-reactive T cells in multiple myeloma & AML patients is out now doi.org/10.1101/2025.... Single-cell TCR and transcriptome profiling & immunopeptidomics revealed conserved programs and shared non-canonical antigens.

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Karsten Rippe @karsten-rippe.bsky.social · Jul 11

Liquid-liquid phase separation of HP1? Not in our mouse fibroblasts… This paper by the Fabian Erdel group offers a fresh perspective on how this can be reconciled with seemingly conflicting reports: The phase separation propensity of HP1 decreases from yeast → fly → mouse. doi.org/10.1038/s414...

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Karsten Rippe @karsten-rippe.bsky.social · Jun 20

3/ Great joint effort with Philipp Mallm and the Single Cell Open Lab @dkfz.bsky.social, led by Anne Rademacher, Alik Huseynov, and Michele Bortolomeazzi, with key contributions from our colleagues at KiTZ Heidelberg, supported by the @mspacealliance.bsky.social program of @hlsalliance.bsky.social.

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Karsten Rippe @karsten-rippe.bsky.social · Jun 20

2/ Using medulloblastoma cryosections, we analyzed sensitivity, specificity, and spatial signal patterns to distinguish background from rare-cell signals. We also show how reimaging slides improves cell segmentation—and enables additional transcript and protein readouts from the same section.

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Karsten Rippe @karsten-rippe.bsky.social · Jun 20

1/ Spatial transcriptomics technologies are rapidly evolving. We compared five methods—Visium, RNAscope HiPlex, Molecular Cartography, Merscope, and Xenium—and developed technology-agnostic quality control metrics to guide their use: doi.org/10.1186/s130...

Comparison of spatial transcriptomics technologies using tumor cryosections - Genome Biology

Background Spatial transcriptomics technologies are revolutionizing our understanding of intra-tumor heterogeneity and the tumor microenvironment by revealing single-cell molecular profiles within the...

doi.org

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Karsten Rippe @karsten-rippe.bsky.social · Jun 19

How do transcription compartments form — and does phase separation drive gene expression? I enjoyed discussing these questions with @akispapantonis.bsky.social a lot, and we put our thoughts together for @naturerevgenet.bsky.social, now out at rdcu.be/erP1u

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Karsten Rippe @karsten-rippe.bsky.social · Apr 12

From enhancer hijacking to ecDNA and onco-condensates – we review how changes in nuclear architecture drive oncogenic gene expression by disrupting enhancer–promoter communication. doi.org/10.1002/ijc..... Kudos to Isabelle Seufert, @claire-vrgs.bsky.social and Sina Wille 👏

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Karsten Rippe @karsten-rippe.bsky.social · Apr 9

Thanks to the Wissenschaftsrat @wissrat.bsky.social — the German Science and Humanities Council — for their clear statement expressing solidarity with US research institutions and scientists and defending academic freedom. www.wissenschaftsrat.de/SharedDocs/P...

Pressemitteilungen - Solidarität mit Einrichtungen und Forschenden in den USA

Der Wissenschaftsrat (WR) und die Hochschulrektorenkonferenz (HRK) kritisieren Angriffe auf die Wissenschaftsfreiheit und erklären ihre Solidarität mit US-amerikanischen Einrichtungen, Wissenschaftlerinnen und Wissenschaftlern.

www.wissenschaftsrat.de

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Karsten Rippe @karsten-rippe.bsky.social · Mar 31

“We all rely on science.” U.S. scientists are speaking out for scientific integrity and academic freedom. What they’re doing matters. We owe them our solidarity and a clear stand beside them.
www.nytimes.com/2025/03/31/s...

Trump Administration Has Begun a War on Science, Researchers Say (Gift Article)

Nearly 2,000 scientists urged that Congress restore funding to federal agencies decimated by recent cuts.

www.nytimes.com

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Karsten Rippe @karsten-rippe.bsky.social · Jan 25

A mechanism for maintaining and spreading H3K9me3 in heterochromatin from the Fejes Toth and Aravin labs that depends on the local H3K9me3 density: HP1 dimers recruit SetDB1 to chromatin by simultaneously binding H3K9me3 on histone H3 and auto-methylated SetDB1. www.biorxiv.org/content/10.1...

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Karsten Rippe @karsten-rippe.bsky.social · Jan 22

Fakten sind das Rückgrat unserer Demokratie
Facts are the backbone of our democracy
When facts are treated as opinions and replaced by rhetoric or propaganda, meaningful discourse suffers, threatening democracy and leaving it vulnerable to manipulation.
www.openpetition.de/!ychtb

Fakten sind das Rückgrat unserer Demokratie - Online-Petition

Liebe Mitbürgerinnen und Mitbürger, als Wissenschaftlerinnen und Wissenschaftler arbeiten wir täglich daran, die Grundlagen für fundierte Entscheidungen und Innovationen zu schaffen – basierend auf üb...

www.openpetition.de

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Karsten Rippe @karsten-rippe.bsky.social · Jan 13

www.uni-heidelberg.de/en/newsroom/...

Universität Heidelberg Discontinues Communication Activities on Central X Account

www.uni-heidelberg.de

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Karsten Rippe @karsten-rippe.bsky.social · Dec 13

🙏 9/ Kudos to lead author Robin Weinmann, @udupaarjun.bsky.social and @janfabio.bsky.social for shaking up heterochromatin and cracking this puzzle! Thanks to @dfgpublic.bsky.social for funding us in the SPP2191 program.

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Karsten Rippe @karsten-rippe.bsky.social · Dec 13

💡 8/ Time to think different: HP1α isn't a global chromatin compaction machine, but a local transcriptional gatekeeper that strong activators can bypass. A new view on how heterochromatin does its job.

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Karsten Rippe @karsten-rippe.bsky.social · Dec 13

💻 7/ Our mathematical modeling showed it could be beautifully simple: Each repeat unit independently switches between silent/active states. No fancy mechanisms needed - basic ligand binding math explains everything we see, with no evidence for HP1α phase separation in our mouse fibroblasts.

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Karsten Rippe @karsten-rippe.bsky.social · Dec 13

🔍 6/ Looking up close with super-resolution microscopy revealed: HP1α sits in small ~50 nm clusters that persist during activation. Just good old chromatin binding at work, with additional HP1α molecules recruited through protein-protein interactions.

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Karsten Rippe @karsten-rippe.bsky.social · Dec 13

💭 5/ Another surprise: Chromatin can unpack without histone acetylation! In cells lacking HP1α/H3K9me3, VP16 can decondense chromatin and activate genes without enriching H3K27ac - revealing an alternative paths to open up chromatin.

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Karsten Rippe @karsten-rippe.bsky.social · Dec 13

🚫 4/ HP1α acts as a local transcriptional brake in two ways: complete silencing or partial attenuation of transcription. Weak activators like VP16 are blocked, while strong ones like VPR can overcome this barrier - shown both at chromocenters and using a reporter system.

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Karsten Rippe @karsten-rippe.bsky.social · Dec 13

💥 3/ The big surprise: Even when the strongest activator VPR decondenses chromatin and drives transcription, HP1α and H3K9me3 stay put! This challenges the dogma that these repressive chromatin features must be removed for gene activation.

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Karsten Rippe @karsten-rippe.bsky.social · Dec 13

🔬 2/ We systematically analyzed how chromocenter structure, HP1α binding, histone marks and transcription respond to the recruitment of transcriptional activators with different strengths (VP16, p65, VPR).

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Karsten Rippe @karsten-rippe.bsky.social · Dec 13

🧬 1/ Heterochromatin protein 1 (HP1) still surprises us after all these years: It simply sticks to chromatin when pericentric heterochromatin domains – the chromocenters – are activated in mouse fibroblasts and acts as a local rather than global repressor. New preprint: doi.org/10.1101/2024...

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Reposted by Karsten Rippe

Rob Schneider @robertife.bsky.social · Dec 8

Please RS/RT. #GordonConference on "Histone and DNA Modifications" #epigenetics #chromatin 20-25. July 2025. Il Ciocco, Italy. Great speaker lineup.
➡️Register now www.grc.org/histone-and-...

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