high-throughput-imaging-analysis-workflow-for-evaluating-skin-cell

High-throughput Imaging and Analysis Workflow for Evaluating Skin Cell Phenotypes and Proliferation States in Tissue Samples

Skin injuries initiate a complex regenerative cascade that engages various cell types. Amongst those, peripheral glial cells play a critical role in ...

University of Zurich

Melanoma cells rely on developmental programs during tumor initiation and progression. Here we show that the embryonic stem cell (ESC) factor Sall4 is re-expressed in the Tyr::Nras; Cdkn2a melanoma model and that its expression is necessary for primary melanoma formation. Surprisingly, while Sall4 loss prevents tumor formation, it promotes micrometastases to distant organs in this melanoma-prone mouse model. Transcriptional profiling and in vitro assays using human melanoma cells demonstrate that SALL4 loss induces a phenotype switch and the acquisition of an invasive phenotype. We show that SALL4 negatively regulates invasiveness through interaction with the histone deacetylase (HDAC) 2 and direct co-binding to a set of invasiveness genes. Consequently, SALL4 knock down, as well as HDAC inhibition, promote the expression of an invasive signature, while inhibition of histone acetylation partially reverts the invasiveness program induced by SALL4 loss. Thus, SALL4 appears to regulate phenotype switching in melanoma through an HDAC2-mediated mechanism.

Epigenetic control of melanoma cell invasiveness by the stem cell factor SALL4.

Schwann cell precursors (SCPs) are transient glial progenitors that are important for the formation of late neural crest derivatives, yet their heterogeneity and developmental potential remain incompletely understood. In this issue, Kastriti, Faure, von Ahsen et al (2022) use comprehensive single-cell RNA sequencing analyses to identify a transient "hub" state common to SCPs and neural crest cells (NCCs), revealing a striking similarity of SCPs to late migrating NCCs. These results raise important questions about the potential role of such a state in adult tissue regeneration and tumourigenesis.

Schwann cell precursors: a hub of neural crest development.

Neural crest cells arise in the neurectoderm of vertebrate embryos, but their developmental potential goes way beyond neurectodermal derivatives. In this issue of Developmental Cell, Hovland et al. reveal that neural crest cells re-employ embryonic stem cell factors in combination with specific transcription factors to enable their broad potential.

Neural crest cells hijack pluripotent stem cell factors to realize their developmental potential.

Metastatic disease is a major cause of death for patients with melanoma. Melanoma cells can become metastatic not only due to cell-intrinsic plasticity but also due to cancer-induced protumorigenic remodeling of the immune microenvironment. Here, we report that innate immune surveillance by natural killer (NK) cells is bypassed by human melanoma cells expressing the stem cell marker NGFR. Using in vitro and in vivo cytotoxic assays, we show that NGFR protects melanoma cells from NK cell-mediated killing and, furthermore, boosts metastasis formation in a mouse model with adoptively transferred human NK cells. Mechanistically, NGFR leads to down-regulation of NK cell activating ligands and simultaneous up-regulation of the fatty acid stearoyl-coenzyme A desaturase (SCD) in melanoma cells. Notably, pharmacological and small interfering RNA-mediated inhibition of SCD reverted NGFR-induced NK cell evasion in vitro and in vivo. Hence, NGFR orchestrates immune control antagonizing pathways to protect melanoma cells from NK cell clearance, which ultimately favors metastatic disease.

Escape from NK cell tumor surveillance by NGFR-induced lipid remodeling in melanoma.

Iterative Bleaching Extends multipleXity (IBEX) is a versatile method for highly multiplexed imaging of diverse tissues. Based on open science principles, we created the IBEX Knowledge-Base, a resource for reagents, protocols and more, to empower innovation.

The IBEX Knowledge-Base: Achieving more together with open science.

The TGFβ signaling pathway is known for its pleiotropic functions in a plethora of biological processes. In melanoma, TGFβ signaling promotes invasiveness and metastasis formation. However, its involvement in the response to therapy is controversial. While several studies have linked TGFβ signaling to elevated resistance to targeted therapy in melanoma, separate findings have indicated a favorable treatment response through TGFβ-mediated increase of cell death. We now found that the outcome of TGFβ signaling in the context of targeted therapy is dose dependent. Unlike low doses, high levels of TGFβ signal activation induce apoptosis upon simultaneous MAPK pathway inhibition, even in targeted therapy resistant melanoma cell lines. Using transcriptomic analyses, combined with genomic target identification of the critical TGFβ signaling effector SMAD4, we demonstrate that parallel activation of TGFβ signaling and MAPK pathway inhibition causes a complete switch of TGFβ target genes from promoting pro-invasive processes to fueling pro-apoptotic pathways. Investigations of underlying mechanisms identified a novel apoptosis-inducing gene signature. Functional validation of signature members highlighted a central role of the pro-apoptotic BCL2 family member BCL2L11 (BIM) in mediating apoptosis in this condition. Using a modified, synthetic version of the TGFB1 mRNA for intra-tumoral injections, we additionally showcase a potential therapeutic application of this treatment combination.

TGFβ signaling sensitizes MEKi-resistant human melanoma to targeted therapy-induced apoptosis.

The iterative bleaching extends multiplexity (IBEX) Knowledge-Base is a central portal for researchers adopting IBEX and related 2D and 3D immunofluorescence imaging methods. The design of the Knowledge-Base is modeled after efforts in the open-source software community and includes three facets: a development platform (GitHub), static website, and service for data archiving. The Knowledge-Base facilitates the practice of open science throughout the research life cycle by providing validation data for recommended and non-recommended reagents, e.g., primary and secondary antibodies. In addition to reporting negative data, the Knowledge-Base empowers method adoption and evolution by providing a venue for sharing protocols, videos, datasets, software, and publications. A dedicated discussion forum fosters a sense of community among researchers while addressing questions not covered in published manuscripts. Together, scientists from around the world are advancing scientific discovery at a faster pace, reducing wasted time and effort, and instilling greater confidence in the resulting data.

The IBEX Imaging Knowledge-Base: A Community Resource Enabling Adoption and Development of Immunofluoresence Imaging Methods.

Multiplexed imaging is a powerful approach in spatial biology, although it is complex, expensive and labor-intensive. Here, we present the IBEX Knowledge-Base, a central resource for reagents, protocols and more, to enhance knowledge sharing, optimization and innovation of spatial proteomics techniques.

Article	Year
Epigenetic control of melanoma cell invasiveness by the stem cell factor SALL4. Nature communications\| PubMed ID: 34417458	2021
Schwann cell precursors: a hub of neural crest development. The EMBO journal\| PubMed ID: 35894449	2022
Neural crest cells hijack pluripotent stem cell factors to realize their developmental potential. Developmental cell\| PubMed ID: 36220078	2022
Escape from NK cell tumor surveillance by NGFR-induced lipid remodeling in melanoma. Science advances\| PubMed ID: 36638181	2023
The IBEX Knowledge-Base: Achieving more together with open science. ArXiv\| PubMed ID: 39398203	2024
TGFβ signaling sensitizes MEKi-resistant human melanoma to targeted therapy-induced apoptosis. Cell death & disease\| PubMed ID: 39709491	2024
The IBEX Imaging Knowledge-Base: A Community Resource Enabling Adoption and Development of Immunofluoresence Imaging Methods. ArXiv\| PubMed ID: 39764400	2024
The IBEX Knowledge-Base: A central resource for multiplexed imaging techniques. PLoS biology\| PubMed ID: 40106489	2025

Salome Stierli

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