Biology subjects

Anagho-Mattanovich, M.

Publications and source records attributed to Anagho-Mattanovich, M..

2 recordsLinked to original sources

bioRxiv2025

ProteoBench: the community-curated platform for comparing proteomics data analysis workflows

Mass spectrometry (MS)-based proteomics is a well-established strategy for analyzing complex biological mixtures. Many MS instruments and data acquisition strategies are available, and the data they acquire differ substantially, thus requiring tailored analysis algorithms. Hence, many dedicated bioinformatics workflows are developed. These are in constant evolution, and the community lacks a centralized platform for comparing their performance. Here, we propose ProteoBench, a single platform that brings together software developers and software users to provide an ever-evolving comparison of state-of-the-art proteomics data processing tools. ProteoBench is an open-source resource that enables the community to evaluate data analysis workflows, develop benchmarking modules dedicated to specific comparisons, and discuss the best methods to compare software tools. The platform ensures that the benchmark evolves alongside advances in proteomics data analysis workflows. ProteoBench guides researchers towards the best-suited tool and parameters for their specific project and data according to their needs, and developers can test their newly developed tools or workflows privately, before adding them as public references. This community-driven effort will increase transparency and reproducibility between MS data analysis workflows, as well as facilitate the development and publication of software workflows in the field.

bioinformatics↗

bioRxiv2025

TCA cycle rewiring underpins implantation and histone acetylation programming

Metabolism has emerged as a key regulator of stem cell differentiation and their epigenomes. This coupling is particularly evident during the exit from naive pluripotency in vitro. However, our understanding of the dynamics of the metabolic rewiring especially at implantation remains rudimentary. In this study, we reconstruct the intracellular metabolite routings in pre- and post-implantation mouse embryos and during dynamic pluripotency transitions of cultured stem cells. Our findings reveal that, instead of a simple TCA cycle shutdown, there is a spatio-temporally programmed rewiring of the TCA cycle at implantation. Focusing on the spectrum of pluripotent cells, we identify pyruvate as a key metabolic nexus. Indeed, pyruvate carboxylase and malic enzyme activity establish cyclical carbon flow, which is essential for maintaining a balanced metabolic and transcriptional state and timely exit from naive pluripotency. Additionally, we discover that formative and primed pluripotent cells exhibit increased glutamine contribution to the TCA cycle, reduced oxidative TCA activity, and reciprocal reductive glutamine metabolism. This metabolic rewiring supports increased histone acetylation turnover, primarily using glutamine as a carbon source, supplemented by pyruvate cycling. Thus, we uncover diverse nutrient strategies that are functionally coupled to epigenome programming and dynamic pluripotency cell state transitions at the time of implantation.

developmental biology↗