Sign in

Axel Künstner

@knstnr.bsky.social
485 followers 781 following 153 posts

Bioinformatician. Statistician. Data squeezer. Omics-addicted with strong focus on #microbiome and #cancer.

PostsRepliesMedia
Axel Künstner @knstnr.bsky.social · 14/09/2026
Great teamwork with @uniluebeck.bsky.social & UKSH (ENT, Infectious Diseases/Microbiology & Systems Biology). Open access, data at EGA (PRJEB104438), code included. #Microbiome #Mycobiome #OtitisMedia #NetworkAnalysis #OpenAccess
000
Axel Künstner @knstnr.bsky.social · 14/09/2026
7/8 Bottom line: diversity indices alone can miss real ecological restructuring. Network analysis uncovers hidden shifts in host-associated microbiomes and points to new therapeutic/biomarker targets for COM.
100
Axel Künstner @knstnr.bsky.social · 14/09/2026
6/8 Responders vs. non-responders already differed at baseline: high Pseudomonas abundance predicted response, while Corynebacterium species were enriched in non-responders. Are these candidate biomarkers for therapy outcome?
100
Axel Künstner @knstnr.bsky.social · 14/09/2026
5/8 Cross-domain (bacteria↔fungi) network density rose by ~50%, domain specialization declined by 46%. This is a more balanced, interconnected community after treatment. Keystone taxa were almost completely replaced.
100
Axel Künstner @knstnr.bsky.social · 14/09/2026
4/8 But co-occurrence network analysis told an entirely different story. Fungal networks exploded: 10 genera/16 connections → 33 genera/257 connections. Bacterial networks stayed comparatively stable.
100
Axel Künstner @knstnr.bsky.social · 14/09/2026
3/8 Surprise #1: Classic diversity metrics (alpha & beta diversity) showed NO significant shift after treatment neither for bacteria nor fungi. On the surface, nothing changed.
100
Axel Künstner @knstnr.bsky.social · 14/09/2026
2/8 We swabbed the ear canals of 22 antibiotic-resistant COM patients before & after 14 days of oral 1,8-Cineol (Soledum®) and profiled bacterial + fungal (!) communities by shotgun sequencing.
100
Axel Künstner @knstnr.bsky.social · 14/09/2026
1/8 🦠🍃 New paper in npj Systems Biology and Applications! Chronic otitis media (COM) is a leading cause of preventable hearing loss. We asked: can the natural anti-inflammatory compound 1,8-Cineol reshape the ear microbiome beyond antibiotics? 🧵 www.nature.com/articles/s41...
nature.com
Bacterial and fungal communities and network dynamics in Otitis media patients upon 1,8-Cineol treatment - npj Systems Biology and Applications
npj Systems Biology and Applications - Bacterial and fungal communities and network dynamics in Otitis media patients upon 1,8-Cineol treatment
100
Axel Künstner @knstnr.bsky.social · 14/09/2026
🧬 New paper! Within #InstandNGS4P we developed MRD prototypes detecting ctDNA in blood plasma to support diagnosis of pancreatic & ovarian cancer — UMI-based error correction + ultra-deep sequencing. 📄 Open Research Europe: open-research-europe.ec.europa.eu/articles/6-87 #LiquidBiopsy #ctDNA
open-research-europe.ec.europa.eu
000
Reposted by Axel Künstner
Helmholtz Institute Würzburg @helmholtz-hiri.bsky.social · 24/08/2026
🚨 The #HIRI & the Faculty of Medicine of the @uni-wuerzburg.de invite applications for 2️⃣ JUNIOR PROFESSORSHIPS in: 🔵 RNA-BASED INFECTION RESEARCH 🔵 MICROBIAL RNA BIOLOGY 🔵 RNA-BASED MEDICINE Apply by September 21: www.helmholtz-hiri.de/en/jobs-tale... Find an overview in this thread. 🧵👇 (1/5)
helmholtz-hiri.de
W1 Groups
The Faculty of Medicine of the Julius-Maximilians-University of Würzburgand theHelmholtz Institute for RNA-based Infection Research (HIRI, Würzburg)jointly open a call for
21019
Axel Künstner @knstnr.bsky.social · 24/08/2026
A gene expression classifier built accurately flags FOXF1/FENDRR cases in independent cohorts (GRAALL, St. Jude), so this subtype can now be systematically identified in routine diagnostics. Grateful to the whole UKSH Kiel team and collaborators! 📄
000
Axel Künstner @knstnr.bsky.social · 24/08/2026
Clinically, this subtype responds poorly to standard chemo: most patients had induction failure or MRD persistence. But intensification with blinatumomab and/or allo-HSCT rescued the majority — pointing to early immunotherapy as a promising strategy.
100
Axel Künstner @knstnr.bsky.social · 24/08/2026
The rearrangement drives massive overexpression of FOXF1 and the lncRNA FENDRR, with distinct gene expression and DNA methylation signatures — proud to have led the methylation analysis showing this is a truly independent subtype, not just a BCR::ABL1-like variant.
100
Axel Künstner @knstnr.bsky.social · 24/08/2026
🧬 New in Blood: we describe FOXF1/FENDRR — a novel molecular subtype of B-cell precursor ALL in adults, found in 20/4857 patients across 3 cohorts. Defined by a previously unknown IGH::FENDRR rearrangement + recurrent KRAS mutations (p.A146V/T/P). 🧵 doi.org/10.1182/bloo...
doi.org
IGH::FENDRR and specific KRAS mutations define a novel B-ALL molecular subtype with poor chemotherapy response
Key PointsFOXF1/FENDRR is a molecular B-ALL subtype in adults defined by IGH::FENDRR, specific KRAS mutations, and FOXF1 overexpression.Patients with FOXF1
100
Axel Künstner @knstnr.bsky.social · 14/08/2026
See the commentary as well doi.org/10.1182/bloo...
doi.org
IKAROS descent and rise of lenalidomide-associated B-ALL
In this issue of Blood, Horns et al1 report a multimodal molecular characterization of 57 patients with lenalidomide-associated B-cell acute lymphoblastic
000
Axel Künstner @knstnr.bsky.social · 14/08/2026
DNA methylation profiling revealed IDH2mt LenB-ALL has its own hypermeth. phenotype, distinct from primary B-ALL. Epigenetic evidence backing up the mutational story. IDH2 mutations were even detectable in remission, pointing to a preleukemic origin.
120
Axel Künstner @knstnr.bsky.social · 14/08/2026
New in Blood @bloodjournals.hematology.org lenalidomide (maintenance tx in myeloma) raises B-ALL risk. We show WHY in a subset of cases IDH2 R140Q clonal hematopoiesis + lenalidomide-driven IKAROS loss cooperate to arrest B-cell dev., seeding a distinct leukemia subtype. 🧵 doi.org/10.1182/bloo...
doi.org
IDH2 clonal hematopoiesis and IKAROS loss cooperate in a B-ALL subtype after lenalidomide therapy for multiple myeloma
Key PointsIDH2 R140Q mutations define a distinct B-ALL subtype that is highly enriched in LenB-ALL.IDH2mt LenB-ALL emerges from IDH2-mutant clonal hematopo
121
Axel Künstner @knstnr.bsky.social · 06/07/2026
This "fortress model" offers a new lens on PD-L1–driven immune evasion in EBV+ DLBCL, and may help explain variable responses to checkpoint blockade in this subtype. Preprint + full methods + data 5/5
000
Axel Künstner @knstnr.bsky.social · 06/07/2026
Even T cells that do get close are functionally silenced (exhaustion markers up, metabolic suppression signatures enriched, effector programs down). It's a two-layer fortress: physical exclusion + functional suppression working together. 4/5
100
Axel Künstner @knstnr.bsky.social · 06/07/2026
CAFs physically intercalate between T cells and tumour cells. A structural micro-barrier, not immune exclusion at a distance. This resolves an apparent contradiction between platforms: Visium sees suppression at tissue-scale, CosMx sees the contact block at single-cell scale. 3/5
100
Axel Künstner @knstnr.bsky.social · 06/07/2026
The paradox: PD-L1 Gain tumours actually show BETTER T cell infiltration by proximity — 84% of T cells within 50µm of tumour cells, vs 69% in PD-L1 Normal. But direct contact? 0% in Gain tumours. Getting close ≠ getting in. 2/5
100
Axel Künstner @knstnr.bsky.social · 06/07/2026
Preprint: In PD-L1-gain EBV+ DLBCL, T cells get close to tumour cells but rarely touch them; a spatial "decoupling" of proximity and engagement. Fibroblast barriers, metabolic suppression, and T cell exhaustion together block anti-tumour immunity. 🧵1/5 doi.org/10.64898/202...
100
Reposted by Axel Künstner
Stephen Turner @stephenturner.us · 23/06/2026
Really nice interactive here. Also, tax these killing machines into obscurity. www.nytimes.com/interactive/...
nytimes.com
The Deadly Rise of Giant Trucks and S.U.V.s (Gift Article)
The vehicles on American roads have grown larger — and they are killing thousands more pedestrians, a Times investigation found.
1227
Axel Künstner @knstnr.bsky.social · 22/06/2026
🧬 EaCoN v0.5.0 "Parallel Universe" is out! A modernized fork of Bastien Job's (@gustaveroussy.fr) copy number analysis package for Affymetrix arrays: → foreach/doParallel fully replaced with furrr/future + purrr/dplyr → R ≥ 4.2.0 compatible → OncoScan, CytoScan, SNP6 github.com/kunstner/EaCoN
github.com
GitHub - kunstner/EaCoN: Easy Copy Number !
Easy Copy Number ! Contribute to kunstner/EaCoN development by creating an account on GitHub.
000
Reposted by Axel Künstner
Molly Przeworski @mollyprz.bsky.social · 09/06/2026
Now published: journals.plos.org/plosbiology/...
journals.plos.org
What sets the mutation rate of a cell type in an animal species?
Mutation rates per generation are strikingly similar across germlines of animals and across at least one somatic cell type, suggesting a key role for natural selection in shaping mutation rates. This ...
08643
Axel Künstner @knstnr.bsky.social · 09/06/2026
Thanks @ignaciorubiosomoza.bsky.social :)
000
Axel Künstner @knstnr.bsky.social · 09/06/2026
💡 Fully open-source, containeriation is in progress (nextflow), and freely available — built for reproducible deployment in routine MTB workflows. 🔗 Code: github.com/kunstner/UKSH_liquidbiopsy
github.com
GitHub - kunstner/UKSH_liquidbiopsy
Contribute to kunstner/UKSH_liquidbiopsy development by creating an account on GitHub.
000
Axel Künstner @knstnr.bsky.social · 09/06/2026
🏥 Clinical utility shown in 3 longitudinal case studies (breast cancer, melanoma, rectal cancer): ctDNA dynamics tracked disease progression & revealed additional targetable variants missed by single-gene ddPCR or static tissue WES.
100
Axel Künstner @knstnr.bsky.social · 09/06/2026
📊 Performance (n=87 samples, 9 tumor entities):✅ 92% sensitivity, 99% specificity ✅ VAF detection down to 0.05% (tumor-informed) ✅ r = 0.99 concordance with ddPCR ✅ 82% concordance with blood-based ddPCR, 75% with WES
100
Axel Künstner @knstnr.bsky.social · 09/06/2026
🔬 What it does: Pan-cancer ctDNA profiling from plasma SNVs, indels, gene fusions & CNVs in one workflow CHIP-aware: discriminates tumor variants from clonal hematopoiesis UMI-based error correction + panel of normals filtering Dual variant calling with VarDict & Mutect2
100
Axel Künstner @knstnr.bsky.social · 09/06/2026
🦁 New preprint! We developed LION — a manufacturer-independent, 109-gene liquid biopsy panel for pan-cancer ctDNA analysis to support clinical decision-making. 📄 Preprint on medRxiv: www.medrxiv.org/content/10.6... #LiquidBiopsy #ctDNA #CancerGenomics #NGS #Oncology #Bioinformatics
medrxiv.org
A liquid biopsy-centered, pan-cancer, open next generation sequencing panel to support clinical decision-making (LION panel)
Cancer treatment has shifted toward personalized therapy based on molecular profiling, particularly in advanced disease. Existing circulating tumor DNA panels are often broad, generating many non-acti...
241
Axel Künstner @knstnr.bsky.social · 29/04/2026
PD-L1 alone is not enough to capture immune suppression in brain mets. Time to look beyond checkpoint inhibition.
000
Axel Künstner @knstnr.bsky.social · 29/04/2026
Key findings: 🔬 KRAS mutations linked to tumor-intrinsic CD39/CD73 expression 🧬 APC & PIK3CA correlate with immune-compartment adenosine signaling 🎯 A distinct "adenosine-high / PD-L1-low" subtype = rational target for CD39/CD73-directed therapy
110
Axel Künstner @knstnr.bsky.social · 29/04/2026
🧠 New paper out in Cancers! We profiled 49 solid tumor brain metastases and found that the adenosine pathway (CD39/CD73) is a frequent immune escape mechanism - often operating independently of PD-L1. #BrainMetastases #CancerGenomics #Oncology #OpenAccess www.mdpi.com/2072-6694/18...
mdpi.com
100
Axel Künstner @knstnr.bsky.social · 29/04/2026
🧬 New paper out in @Cancers_MDPI! We show that Regnase-1 is a prognostic biomarker in high-grade soft tissue sarcoma — favorable in UPS, but flipped in adjuvantly irradiated patients. Context matters! 👉 www.mdpi.com/2072-6694/18... #SarcomaResearch #CancerBiomarkers #Immunology
mdpi.com
030
Axel Künstner @knstnr.bsky.social · 24/03/2026
Interestingly, the beneficial effect of Regnase-1 may be lost after radiotherapy. Regnase-1 could serve as a biomarker for an immunologically active TME in UPS—and potentially guide treatment strategies.
000
Axel Künstner @knstnr.bsky.social · 24/03/2026
Key findings: • Regnase-1-high → longer OS & lower mortality • CD68+ TAM-high → shorter OS & higher mortality • Results validated in TCGA-SARC • Regnase-1-high tumours show IFN/inflammatory enrichment & reduced TGF-β signalling
100
Axel Künstner @knstnr.bsky.social · 24/03/2026
We show that Regnase-1 (ZC3H12A) marks a pro-inflammatory tumour microenvironment and predicts improved overall survival in undifferentiated pleomorphic sarcoma (UPS). In contrast, high CD68+ TAMs associate with worse outcomes.
100
Axel Künstner @knstnr.bsky.social · 24/03/2026
Preprint alert! 🚨 www.preprints.org/manuscript/2... High-grade soft tissue sarcomas (STS) lack robust biomarkers—but we may have a new signal. #Sarcoma #Immunology #CancerResearch #TumorMicroenvironment #Biomarkers #Oncology
preprints.org
110
Axel Künstner @knstnr.bsky.social · 17/02/2026
Fresh from the press www.nature.com/articles/s41...
nature.com
Exploring the underlying gene expression profiles of differences of sex development phenotypes through transcriptome analysis - Scientific Reports
Scientific Reports - Exploring the underlying gene expression profiles of differences of sex development phenotypes through transcriptome analysis
000
Axel Künstner @knstnr.bsky.social · 12/02/2026
Some news from the press www.nature.com/articles/s41...
nature.com
Colonic spatial single-cell proteomics and murine models link mitochondrial dysfunction to dimeric IgA-secreting plasma cell deficiency in Crohn’s disease - Nature Communications
Crohn’s disease is associated with disturbances in the B-cell compartment and secreted antibodies. Here, the authors reveal impaired colonic dimeric IgA responses in patients with Crohn’s disease and ...
000
Axel Künstner @knstnr.bsky.social · 17/10/2025
Fresh from the press with some minor contribution from our group onlinelibrary.wiley.com/doi/10.1111/...
onlinelibrary.wiley.com
Immune Training of the Interleukin 6 Gene in Airway Epithelial Cells is Central to Asthma Exacerbations
This study aims to investigate how immune activation influences the epigenetic regulation and expression of the Interleukin-6 (IL-6) gene during asthma exacerbations. By examining molecular mechanism...
011
Axel Künstner @knstnr.bsky.social · 30/07/2025
@daanspeth.bsky.social
020
Axel Künstner @knstnr.bsky.social · 19/06/2025
9/ This rare lymphoma may require organ-aware treatment strategies and could benefit from targeted approaches like STAT3 inhibition. 🎓 Big thanks to all co-authors & funders!
000
Axel Künstner @knstnr.bsky.social · 19/06/2025
8/ 💡 What does this mean clinically? prDLBCL is: • Genomically distinct from nodal DLBCL • Closely aligned with immune-privileged lymphomas • Marked by deep immune evasion strategies Implication: Better diagnostic distinction & CNS-risk stratification needed.
100
Axel Künstner @knstnr.bsky.social · 19/06/2025
7/ 📈 RNA-seq revealed transcriptional programs enriched in: • Interferon response (α/γ) • MYC target genes • STAT1/3 and NF-κB target genes → This further supports immune evasion and stress-adapted survival.
110
Axel Künstner @knstnr.bsky.social · 19/06/2025
6/ We also detected structural fusions like ETV6::IGH and ETV6::PAX5, adding to the uniqueness of prDLBCL biology. This hints at transcriptional deregulation as an additional driver.
100
Axel Künstner @knstnr.bsky.social · 19/06/2025
5/ Despite some overlap, prDLBCL isn’t just CNS/testicular DLBCL in the kidney. Only 3 cases met MCD subtype criteria (LymphGen). Most fell into EZB (32%) or remained unclassified.
100
Axel Künstner @knstnr.bsky.social · 19/06/2025
4/ Mutational landscape: • Frequent mutations in STAT3, MYD88, TNFAIP3, CDKN2A, PIM1, PRDM1 • Deregulated signaling: JAK/STAT, NF-κB, MYC targets • Large 6q deletions (PRDM1, ARID1B) in ~50% of cases
100
Axel Künstner @knstnr.bsky.social · 19/06/2025
3/ Key findings: • MHC class I loss: 69% • MHC class II disruption: 62% • Biallelic CDKN2A deletions: 38% → These changes mimic CNS/testicular DLBCL more than nodal forms.
100