Biology subjects

Tschandl, P.

Publications and source records attributed to Tschandl, P..

4 recordsLinked to original sources

bioRxiv2026

Independent benchmark of H&E-based gene expression prediction in skin

Given the widespread availability of H&E slides, there is considerable interest in determining whether molecular information can be inferred directly from tissue morphology, potentially reducing the need for costly spatial transcriptomic profiling. We assessed three state-of-the-art methods for predicting single-cell gene expression from H&E images across three skin disease contexts and two Xenium panels. As controls, we included simple linear regression models trained on embeddings from multiple foundation models, totalling 16 models evaluated in this study. We show that all models performed poorly: for most genes, prediction accuracy was near zero, and reliable predictions were largely restricted to keratinocyte-associated genes. Predicted expression failed to preserve cell-type identity and spatial organisation, with only keratinocytes forming coherent clusters, while immune, fibroblast, and other dermal populations were extensively mixed. Notably, simple ridge regression on pretrained embeddings matched or outperformed the more complex published architectures, indicating that the predictive signal originates primarily from image representations rather than model design. Our results demonstrate that current H&E-based gene expression prediction methods are not yet suitable for single-cell-level interpretation of spatial transcriptomics in skin tissue.

bioinformatics↗

bioRxiv2026

Spatially organized cancer-associated fibroblast subtypes partition cutaneous carcinomas into immune-active and contracted, immune-repressed niches

Basal cell carcinoma (BCC) and cutaneous squamous cell carcinoma (SCC) are the most common keratinocyte-derived malignancies, yet they differ markedly in invasiveness, metastatic potential, and immune contexture. Although cancer-associated fibroblasts (CAFs) are increasingly recognized as key regulators of tumor architecture and tumor immunity, the spatial organization of distinct CAF subtypes in cutaneous carcinomas and their functional relationship with immune cells remains incompletely understood. Using a 33-plex imaging mass cytometry (IMC) panel, we profiled 28 regions of interest (ROIs) from 17 human BCC and SCC specimens, encompassing more than 739,000 single cells, and integrated these data with RNA fluorescence in situ hybridization (RNA-FISH), immunohistochemistry (IHC), multiplex immunofluorescence, and in vitro functional assays. We identified four fibroblast populations, including immunomodulatory CAFs (iCAFs), matrix CAFs (mCAFs), myofibroblast-like CAFs (myoCAFs), and reticular fibroblasts (retFIBs), and found that aggressive tumor subtypes were characterized by increased stromal area, extracellular matrix deposition, and altered CAF composition. CAF composition differed most prominently across BCC subtypes, with nodular BCC enriched for mCAFs and infiltrative BCC showing increased myoCAF density, consistent with a shift toward a contractile stromal program. Spatial analyses revealed distinct CAF-immune niches: iCAFs localized to immune-cell-rich, inflamed niches enriched for activated and/or exhaustion-associated immune-cell marker programs, whereas myoCAFs occupied fibroblast-dense, immune-poor niches with globally reduced immune activation. mCAFs were preferentially associated with immune cell accumulation in the stroma and spatial immune compartmentalization, with limited immune cell presence within tumor nests. At the invasive front, CAF-immune coupling was highly subset-dependent, with iCAFs linked to antigen-experienced T-cell states and myoCAFs linked to immune exclusion. In vitro, patient-derived CAF cultures from myoCAF-rich biopsies showed enhanced collagen-gel contraction, with cultures enriched for MCAM+ CAFs displaying increased contractile capacity. Aggressive tumor variants displayed increased stromal nuclear YAP/TAZ, while complementary single-cell pathway analysis supported a mechanically remodeled stromal microenvironment in which mCAFs contribute ECM/matrix-remodeling programs and RGS5/myoCAF-like populations show enhanced mechanotransduction-associated signaling, rather than a uniform CAF-wide increase in canonical YAP/TAZ transcriptional output. Together, these findings define spatially organized CAF programs in cutaneous carcinomas and identify myoCAF-rich stromal niches as a recurrent feature of aggressive, immune-repressed tumor architecture. These results nominate CAF composition as a biomarker of immune architecture and a potential determinant of therapeutic response.

cancer biology↗

bioRxiv2026

A scRNA-seq atlas of chronic inflammatory skin diseases

Inflammatory skin diseases (ISDs) affect up to 25% of the global population. Yet, large-scale comparative single-cell RNA-sequencing (scRNA-seq) analyses between ISDs are still missing. Here, we integrated scRNA-seq datasets spanning 27 skin diseases from 50 studies, comprising over 2 million cells from 441 samples. Using the healthy skin cell atlas as reference, we could build a robust ISD atlas that enabled us to differentiate universal inflammatory signatures and disease-specific ones. This highlighted, for example, a shared gene program between keratinocytes in atopic dermatitis and parapsoriasis, not present in cutaneous T-cell lymphoma, confirms the plasticity of Th17 cells throughout ISDs, defines specific macrophage signatures in acne, and reveals a yet undescribed role of mural cells in ISDs. This demonstrates the power of the ISD atlas as a resource to resolve disease-specific immune mechanisms. The complete atlas is available through an interactive online portal at https://isd-atlas.derma.meduniwien.ac.at.

immunology↗

bioRxiv2024

Stiffness-dependent LOX regulation via HIF-1 drives extracellular matrix modifications in psoriasis

Psoriasis is a common chronic inflammatory skin disease characterized by a thickened epidermis with elongated rete ridges and massive inflammatory immune cell infiltration. It is currently unclear what impact mechanoregulatory aspects in the dermis may have on disease progression. Using multiphoton second harmonic generation microscopy we found that the extracellular matrix (ECM) was profoundly reorganized within the dermis in psoriasis compared to healthy skin. Collagen fibers were highly aligned and assembled into thick, long collagen bundles, whereas the overall fiber density was reduced in psoriasis. This was particularly pronounced within dermal papillae extending into the epidermis. Further, the enzyme LOX, a crucial posttranslational modifier of ECM molecules, was highly upregulated in the dermis of psoriasis patients. In vitro functional and knock-down experiments identified a novel link between HIF-1 stabilization and LOX protein regulation in mechanosensitive skin fibroblasts. LOX secretion and activity directly correlated with substrate stiffness, and was independent of hypoxia and IL-17. Finally, scRNA-seq analysis identified skin fibroblasts expressing high amounts of LOX and other ECM-relevant genes and confirmed elevated HIF-1 expression in psoriasis. Our findings suggest a potential yet undescribed mechanical aspect of psoriasis stemming from disordered ECM architecture in the papillary dermis, which could initiate a positive feedback loop in fibroblasts driven by mechanical forces. This mechanism may contribute to tissue stiffening and diminished skin elasticity in psoriasis, potentially exacerbating its pathogenesis.

cell biology↗