At Nexco, our mission is to accelerate scientific discovery by providing robust, cutting-edge bioinformatics solutions. We love understanding your data and your needs, and partnering with researchers to tackle their complex biological questions by transforming raw data into clear insights.

We routinely show you how we stay at the forefront of bioinformatics, to bring to our clients the latest in terms of tools, datasets, methods and technologies. Today, we bring you something different, but that also illustrates how we work: Nexco in action, driving forward discoveries as published in two recent papers coauthored by our experts together with two separate research labs that hired our services. We are very excited to showcase how our expertise contributed to two recent studies published in the prestigious PNAS and EMBO Molecular Medicine journals.

1. Forey et al, PNAS 2025: Cancer cells subvert the primate-specific KRAB zinc finger protein ZNF93 to control APOBEC3B

In this paper, researchers from the Trono lab at EPFL uncovered a fascinating dual role for the protein ZNF93, revealing how cancer cells hijack it to survive self-induced DNA damage.

Scientists have long-known that the primate-specific protein ZNF93 acts as a guardian of the genome by silencing ancient viral DNA (specifically certain L1 transposable elements) embedded in our chromosomes. This new study, where our experts participated, revealed a surprising second job: ZNF93 also tightly controls apotent enzyme called APOBEC3B. While APOBEC3B helps tumors evolve, its activity can cause catastrophic DNA damage, leading to cell death. The research team discovered that cancer cells exploit ZNF93 to stop APOBEC3B’s activity, thus reaching a balance that allows them to benefit from mutagenesis without succumbing to its lethal effects. This quite sophisticated survival mechanism could be a target for future cancer therapies.

This research required a multi-omics approach to connect ZNF93’s binding on DNA, epigenetic changes, and downstream gene expression. The analysis was particularly complex due to ZNF93’s affinity for repetitive L1 elements, which are notoriously difficult to analyze with standard tools. Our team provided the advanced bioinformatics support necessary to navigate these challenges. We delivered end-to-end analysis of multiple next-generation sequencing (NGS) datasets, including RNA-seq and CUT&Tag analysis, to precisely quantify how ZNF93 affects gene expression and the deposition of repressive epigenetic marks across the genome; and we also had to analyze repetitive elements mapping ZNF93’s binding sites and epigenetic influence over thousands of L1 transposable elements. This work relied on integrating large amounts of public data from The Cancer Genome Atlas, to demonstrate that ZNF93 expression is correlated with proliferation across many human cancers, underscoring the clinical relevance of the findings. Finally, and key in all bioinformatics studies, we had to generate clear plots that would allow us and our collaborators to draw solid conclusions, and we had to create publication-quality visualizations that could properly illustrate the complex interplay between ZNF93, L1 elements, and APOBEC3B.

Direct link to full paper: https://www.pnas.org/doi/10.1073/pnas.2505021122

2. Bracq et al, EMBO Molecular Medicine 2025: Injury-induced intestinal stem cell renewal requires capillary morphogenesis gene 2

This study from the van der Goot lab at EPFL, published this year in EMBO Molecular Medicine, provides a molecular explanation for the severe symptoms of a rare genetic disorder called Hyaline Fibromatosis Syndrome. And in doing so, the study also reveals a critical protein for intestinal repair.

The most severe form of Hyaline Fibromatosis Syndrome is fatal in infancy due to intractable diarrhea, but the reason has been a mystery. This study used a mouse model to show that the protein behind this syndrome, CMG2, is essential for the gut to regenerate after injury. It turns out that while the gut functions normally day-to-day without CMG2, it completely fails to heal after damage like that from chemically induced colitis. In this work involving our experts, we found that CMG2 is required for the crucial transition of fetal-like regenerative cells back into adult intestinal stem cells. Without this step, the pool of these cells is not replenished, and the intestinal lining cannot be repaired.

To prove this, we needed to quantify subtle changes in different cell populations and molecular markers directly within tissue samples. This required moving beyond bulk measurements to sophisticated, spatially-aware image analysis. One of our main contributions was then to provide highly specialized bioimage analysis and support for analyzing public genomics datasets. For this we developed custom workflows using QuPath to automatically and accurately quantify microscopy images, which then allowed us to measure the number of proliferating cells, detect rare intestinal stem cells via RNAscope, and analyze the localization of key signaling proteins within the complex gut tissue architecture. Besides, we analyzed public spatial transcriptomics and single-cell RNA-seq datasets to pinpoint exactly which cell types in the gut express CMG2, providing crucial context for the experimental results. Finally, by combining the results from image analysis, qPCR, and public datasets, we helped the team build a cohesive and compelling story about CMG2’s context-specific role in Wnt signaling and stem cell renewal, allowing to frame a quite complete story linking molecular details to physiology.

Direct link to full paper: https://www.embopress.org/doi/full/10.1038/s44321-025-00295-3

How Nexco can be your partner in research and development

These two studies, both published this year, demonstrate the breadth of Nexco’s capabilities: from large-scale omics and public data analysis to specialized bioimage informatics. Whether you are exploring the frontiers of the genome or quantifying cellular changes in tissue, our team is ready to partner with you. Check out Nexco’s full breadth of services here.

Contact us today to discuss how we can help accelerate your next breakthrough.