Biology subjects

Kirchner, P.

Publications and source records attributed to Kirchner, P..

8 recordsLinked to original sources

bioRxiv2026

Cross-Cohort Optimal Transport Maps Macrophage Plasticity and Competing Routes to Inflammation and Fibrosis in Human Atherosclerotic Plaques

Single-cell transcriptomics has revealed extensive macrophage heterogeneity in atherosclerotic plaques, but how macrophages move between states, and whether transition mechanisms depend on cellular origin, remain unclear. Here we develop a computational framework that reconstructs directed cell-state transition networks from cross-sectional single-cell RNA-sequencing data by combining optimal transport with RNA velocity and systematic cross-cohort validation. Applying this approach to seven human atherosclerotic plaque cohorts, we generate an integrated atlas of 81,633 monocytes and macrophages and identify 15 statistically significant pairwise transitions, of which 11 directed transitions organize into three biological axes: monocyte fate diversification, inflammatory reactivation, and fibrotic remodeling. The strongest transition links scavenging macrophages to inflammatory macrophages, suggesting that plaque inflammation is driven predominantly by reactivation of tissue-adapted macrophages rather than by direct differentiation of newly recruited monocytes. By tracking gene expression changes along the OT target-association gradient, we find that macrophage plasticity follows an origin-dependent spectrum. Tissue-resident macrophages, in particular scavenging macrophages, acquire inflammatory programs while preserving and reinforcing their resident scavenging identity, a mechanism we term transcriptional layering, whereas monocyte-derived transitions proceed through selective loss of source-identity modules. Despite these distinct routes, transitions converging on the same fate activate shared destination-specific regulatory circuits, with inflammatory and fibrotic programs governed by mutually antagonistic transcription factor networks. These findings identify inflammatory reactivation of scavenging macrophages as a dominant transition axis in human atherosclerosis and suggest that macrophage origin constrains how disease-associated programs are acquired. More broadly, this framework provides a general strategy for quantifying cell-state transitions and dissecting plasticity mechanisms in chronic inflammatory disease.

bioinformatics↗

bioRxiv2025

Aberrant brain-type neuronal programs in large-cell pancreatic neuroendocrine carcinoma

High-grade pancreatic neuroendocrine carcinoma (panNEC) is a rare, aggressive cancer with limited tissue availability. Single-nucleus transcriptomics of five large-cell panNECs revealed two clinically relevant neuroendocrine cell states: one highly proliferative with an aberrant brain-specific neuronal differentiation program and another stress-responsive state enriched for heat stress, hypoxia, and glycolysis. Our findings suggest potentially new therapeutic vulnerabilities, highlighting the need to evaluate the efficacy of combination therapies.

cancer biology↗

bioRxiv2025

Exonuclease ISG20 inhibits human cytomegalovirus replication by inducing an innate immune defense signature

ISG20 is an interferon-regulated protein that exhibits RNase activity thereby inhibiting the replication of a broad spectrum of RNA viruses. By single cell RNA sequencing, we identified ISG20 as an antiviral factor for human cytomegalovirus (HCMV) as it was upregulated in a population of HCMV-resistant cells. In accordance with an antiviral role on herpesviruses, overexpression of ISG20 in primary human fibroblasts led to reduced HCMV and HSV-1 replication, while knockdown of ISG20 enhanced virus growth. In Western blot kinetics, we observed that inhibition of HCMV replication by ISG20 occurs at the early stage of infection which correlated with reduced amounts of viral early and late transcripts. However, neither the half-life of viral and cellular RNAs nor of viral DNA was decreased in ISG20-expressing cells, indicating that ISG20 does not exert its antiviral effect via a degradation of RNAs or DNA. Instead, RNA-seq analysis revealed an innate immune defense signature upon ISG20 expression that comprised the upregulation of a distinct set of interferon stimulated genes (ISGs), zinc finger proteins (ZNFs) and of transposable elements (TEs). Our data indicate that this gene signature augments both IFN production and response of the host cell. Consistently, the JAK-STAT inhibitor ruxolitinib rescued HCMV gene expression in ISG20-expressing cells. We conclude that ISG20 induces a so far unprecedented immune defense signature that serves to amplify the IFN-mediated host cell defense thus explaining its broad antiviral activity.

microbiology↗

bioRxiv2024

IgA displays site- and subclass-specific glycoform differences despite equal glycoenzyme expression

BackgroundGlycosylation is an important posttranslational modification of proteins and in most cases indispensable for proper protein function. Like most soluble proteins, IgA, the second most prevalent antibody in human serum, contains several N- and O-glycosylation sites. While for IgG the impact of Fc glycosylation on effector functions and inflammatory potential has been intensively studied, only little is known for IgA. In addition, only glimpses exist regarding the regulation of IgA glycosylation. We have previously shown that IgA1 and IgA2 differ functionally and also show differences in their glycosylation pattern. The more pro-inflammatory IgA2 which is linked to autoimmune diseases displays decreased sialylation, galactosylation, fucosylation and bisection as compared to IgA1. In the present study, we aimed to investigate these differences in glycosylation in detail and to explore the mechanisms underlying them. MethodsIgA1 and IgA2 was isolated from serum of 12 healthy donors. Site specific glycosylation was analyzed by mass spectrometry. In addition, human bone marrow plasma cells were investigated using single cell mRNA sequencing, flow cytometry and ELISpot. ResultsWe found that certain glycoforms greatly differ in their abundance between IgA1 and IgA2 while others are equally abundant. Overall, the IgA2 glycans displayed a more immature phenotype with a higher prevalence of oligomannose and fewer fully processed glycans. Of note, these differences cant be explained by differences in the glycosylation enzyme machinery as mRNA sequencing and flow cytometry analysis showed equal enzyme expression in IgA1 and IgA2 producing plasma cells. ELISpot analysis suggested a slightly increased antibody production rate in IgA2 producing plasma cells which might contribute to its lower glycan processing rates. But this difference was only minor, suggesting that further factors such as steric accessibility determine glycan processing. This is supported by the fact that glycans at different positions on the same IgA chain differ dramatically in fucosylation, sialylation and bisection. ConclusionIn summary, our detailed overview of IgA1 and IgA2 glycosylation shows a class, subclass, and site-specific glycosylation fingerprint, most likely due to structural differences of the protein backbones.

immunology↗

bioRxiv2024

Morpho-molecular features of Epithelial Mesenchymal Transition associate with clinical outcome in patients with rectal cancer

In rectal cancer, where part of the patients undergoes chemoradiotherapy, there is a need for improved pretreatment biomarkers applicable to biopsies. Tumor budding (TB) is a biomarker used in colon cancer, and due to its link to epithelial-mesenchymal transition (EMT), is hypothesized to be a potential marker for therapy resistance. Assessment of the utility of tumor buds in rectal biopsies is challenging due to their rarity. As EMT-related processes are also seen in other morphological features beyond tumor buds, we investigated EMT in tumor tissue including morphological features such as tumor cluster size and fibril-like structures. To do so, we leveraged a cohort of colon cancer whole-slide images and another cohort consisting of rectal cancer biopsies, visualized using hyperplex immunofluorescence to identify tumor and EMT-associated proteins. We built a custom image analysis pipeline to detect and segment tumor buds and other morphological features and correlated them with molecular expression intensities. We found strong correlations of EMT up-regulation and morphological transition states, both at the invasive margin and the tumor center. We furthermore observed a link between morpho-molecular transitions and histological growth patterns, which in turn can inform novel biomarkers. Finally, quantification of these morpho-molecular transition states in rectal biopsies showed their impact on survival after neoadjuvant chemoradiotherapy.

cancer biology↗

bioRxiv2022

Patient-derived tumoroids of advanced high-grade neuroendocrine neoplasms mimic patient chemotherapy responses and guide the design of personalized combination therapies

There are no therapeutic predictive biomarkers or representative preclinical models for high-grade gastroenteropancreatic neuroendocrine neoplasms (GEP-NEN), a highly aggressive, fatal, and heterogeneous epithelial malignancy. We established patient-derived (PD) tumoroids from biobanked tissue samples of advanced high-grade GEP-NEN patients and applied this model for targeted rapid ex vivo pharmacotyping, next-generation sequencing, and perturbational profiling. We used tissue-matched PD tumoroids to profile individual patients, compared ex vivo drug response to patients clinical response to chemotherapy, and investigated treatment-induced adaptive stress responses. PD tumoroids recapitulated biological key features of high-grade GEP-NEN and mimicked clinical response to cisplatin and temozolomide ex vivo. When we investigated treatment-induced adaptive stress responses in PD tumoroids in silico, we discovered and functionally validated Lysine demethylase 5A and interferon-beta, which act synergistically in combination with cisplatin. Since ex vivo drug response in PD tumoroids matched clinical patient responses to standard-of-care chemotherapeutics for GEP-NEN, our rapid and functional precision oncology approach could expand personalized therapeutic options for patients with advanced high-grade GEP-NEN.

cancer biology↗

bioRxiv2020

scRNA-Sequencing uncovers a TCF-4-dependent transcription factor network regulating commissure development

Intercortical connectivity is important for higher cognitive brain functions by providing the basis for integrating information from both hemispheres. We show that ablation of the neurodevelopmental disorder associated bHLH factor Tcf4 results in complete loss of forebrain commissural systems in mice. Applying a new bioinformatic strategy integrating transcription factor expression levels and regulon activities from single cell RNA-sequencing data predicted a TCF-4 interacting transcription factor network in intercortical projection neurons regulating commissure formation. This network comprises a number of regulators previously linked to the pathogenesis of intellectual disability, autism-spectrum disorders and schizophrenia, e.g. Foxg1, Sox11 and Brg1. Furthermore, we demonstrate that TCF-4 and SOX11 biochemically interact and cooperatively control commissure formation in vivo, and regulate the transcription of genes implied in this process. Our study provides a regulatory transcriptional network for the development of interhemispheric connectivity with potential pathophysiological relevance in neurodevelopmental disorders.

genomics↗

bioRxiv2020

CRNKL1 is a highly selective regulator of intron-retaining HIV-1 and cellular mRNAs

The HIV-1 Rev protein is a nuclear export factor for unspliced and incompletely-spliced HIV-1 RNAs. Without Rev, these intron-retaining RNAs are trapped in the nucleus. A genome-wide screen identified nine proteins of the spliceosome which all enhanced expression from the HIV-1 unspliced RNA after CRISPR/Cas knock-down. Depletion of DHX38, WDR70 and four proteins of the Prp19-associated complex (ISY1, BUD31, XAB2, CRNKL1) resulted in a more than 20-fold enhancement of unspliced HIV-1 RNA levels in the cytoplasm. Targeting of CRNKL1, DHX38, and BUD31 affected nuclear export efficiencies of the HIV-1 unspliced RNA to a much larger extent than splicing. Transcriptomic analyses further revealed that CRNKL1 also suppresses cytoplasmic levels of cellular mRNAs with selectively retained introns. Thus, CRNKL1 dependent nuclear retention seems to be a novel mechanism for the regulation of cytoplasmic levels of intron-retaining cellular mRNAs that is harnessed by HIV-1 to direct its complex splicing pattern.

molecular biology↗