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Articles by Christian Beisel
Combined high-quality metagenomics reveals off-target effects of albendazole, ivermectin-albendazole and moxidectin-albendazole on the human gut bacteria
Abstract Human whipworm infections caused by Trichuris trichiura and Trichuris incognita remain a major public health problem, affecting over 400 million people globally and responding poorly to standard benzimidazole chemotherapy. Ivermectin-albendazole and moxidectin-albendazole have emerged as promising combination therapies, but recent in vitro evidence suggests that ivermectin and moxidectin may also affect gut bacteria.
LysG-driven transcriptional network rewiring underlies lineage-specific phenotypes in Mycobacterium tuberculosis
Abstract The Mycobacterium tuberculosis complex (MTBC) includes ten human-adapted lineages with varying geography and pathogenicity. Lineage 1 (L1) shows low virulence while Lineage 2 (L2) is hyper-virulent, more transmissible, and associated with drug-resistance. We performed comparative analyses integrating whole-genome sequencing with transcriptomic and proteomic profiling of L1 and L2 clinical strains under two in vitro growth conditions.
Ovarian cancer metastasis to the human omentum disrupts organ homeostasis and induces fundamental tissue reprogramming - Nature Communications
Abstract The omentum, a visceral adipose tissue with critical metabolic, immunological, and stem cell functions is the preferred site for ovarian cancer metastasis. However, its role in maintaining homeostasis and its responses to metastatic colonization remain incompletely understood. Using single-cell transcriptomics, we profile different anatomical regions of the omentum in patients with benign conditions and metastasis.
Publisher Correction: Feasibility of multiomics tumor profiling for guiding treatment of melanoma - Nature Medicine
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Correction to: Nature Medicine https://doi.org/10.1038/s41591-025-03715-6, published online 27 May 2025. In the version of the article initially published, the far-right column of the lower panel in Fig. 2c was missing and has now been added, as seen in Fig. 1, below.
By Nora C Toussaint, Ximena Bonilla, Tarun Mehra, Francis Jacob, Parisa Rahimzadeh, Natalia Chicherova, Rebekka Wegmann, Julien Mena, Sandra Goetze, Franziska Singer, Anne Bertolini, Michael Prummer, Rudolf Aebersold, Holger Moch, Michael Weller, Markus G. Manz, Niko Beerenwinkel, Christian Beisel, Bernd Bodenmiller, Mitchell Levesque, Viktor H. Koelzer, Reinhard Dummer
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Nature
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Feasibility of multiomics tumor profiling for guiding treatment of melanoma - Nature Medicine
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Abstract There is limited evidence supporting the feasibility of using omics and functional technologies to inform treatment decisions. Here we present results from a cohort of 116 melanoma patients in the prospective, multicentric observational Tumor Profiler (TuPro) precision oncology project. Nine independent technologies, mostly at single-cell level, were used to analyze 126 patient samples, generating up to 500 Gb of data per sample (40,000 potential markers) within 4 weeks.
By Nora C Toussaint, Ximena Bonilla, Tarun Mehra, Francis Jacob, Rebekka Wegmann, Julien Mena, Sandra Goetze, Franziska Singer, Anne Bertolini, Michael Prummer, Rudolf Aebersold, Holger Moch, Michael Weller, Markus G. Manz, Niko Beerenwinkel, Christian Beisel, Bernd Bodenmiller, Mitchell Levesque, Viktor H. Koelzer, Reinhard Dummer, Parisa Rahimzadeh, Natalia Chicherova
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Nature
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Single-cell landscape of innate and acquired drug resistance in acute myeloid leukemia - Nature Communications
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Abstract Deep single-cell multi-omic profiling offers a promising approach to understand and overcome drug resistance in relapsed or refractory (rr) acute myeloid leukemia (AML). Here, we combine single-cell ex vivo drug profiling (pharmacoscopy) with single-cell and bulk DNA, RNA, and protein analyses, alongside clinical data from 21 rrAML patients.
By Rebekka Wegmann, Ximena Bonilla, Ricardo Coelho, Sandra Goetze, Francis Jacob, Jack Kuipers, Ulrike Lischetti, Julien Mena, Michael Prummer, Franziska Singer, Nora C Toussaint, Rudolf Aebersold, Niko Beerenwinkel, Christian Beisel, Bernd Bodenmiller, Viktor H. Koelzer, Mitchell Levesque, Holger Moch, Lucas Pelkmans, Andreas Wicki, Bernd Wollscheid, Markus G. Manz, Berend Snijder
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Nature
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Detection of isoforms and genomic alterations by high-throughput full-length single-cell RNA sequencing in ovarian cancer - Nature Communications
Abstract Understanding the complex background of cancer requires genotype-phenotype information in single-cell resolution. Here, we perform long-read single-cell RNA sequencing (scRNA-seq) on clinical samples from three ovarian cancer patients presenting with omental metastasis and increase the PacBio sequencing depth to 12,000 reads per cell. Our approach captures 152,000 isoforms, of which over 52,000 were not previously reported.
Dynamic thresholding and tissue dissociation optimization for CITE-seq identifies differential surface protein abundance in metastatic melanoma - Communications Biology
Human primary tissue and live-cell biobanking Human healthy skin, primary and melanoma metastasis samples, as well as PBMCs from consenting patients treated with immunotherapy were obtained from the Dermatology Biobank, University Hospital Zurich (BASEC Nr.2017-00494). Experimental and clinical information are summarized in Supplementary Data 2. After collection, tissue sample biopsies and surgical material were live-cell biobanked.
The relative transmission fitness of multidrug-resistant Mycobacterium tuberculosis in a drug resistance hotspot - Nature Communications
Abstract Multidrug-resistant tuberculosis (MDR-TB) is among the most frequent causes of death due to antimicrobial resistance. Although only 3% of global TB cases are MDR, geographical hotspots with up to 40% of MDR-TB have been observed in countries of the former Soviet Union. While the quality of TB control and patient-related factors are known contributors to such hotspots, the role of the pathogen remains unclear.
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