• The funded initiatives aim to improve our understanding of the microbiome’s role in reproductive health and advance research in epitranscriptomics.
• I2SysBio will collaborate with Endorenew and Longseq in the development of these projects

Two projects from the Institute of Integrative Systems Biology (I2SysBio, UV–CSIC) have been selected in the third call of the CSIC COCREA 2025 programme, which aims to promote collaboration between research groups and companies in areas of high technological impact. Among the ten proposals approved at the national level, two correspond to the Gene Expression Genomics group, led by researcher Ana Conesa.

This programme, which is part of the CSIC Converge open innovation hub, funds open innovation projects that stand out for their novelty, potential to generate industrial property and their potential for application. In this edition, the selection focused on two strategic lines within the field of disruptive technologies: on the one hand, solutions based on artificial intelligence and quantum technologies; on the other, the development of advanced materials with high added value and lower environmental impact.

The two projects awarded to I2SysBio fall within the first of these lines and address two issues of great clinical interest in the field of biomedicine: female reproductive health and the study of epitranscriptomics through advanced sequencing technologies.

Both projects are expected to run for two years and have been awarded €100,000 each.

The role of the microbiome in reproductive health, with Endorenew

The first project, developed in collaboration with the company Endorenew, will investigate the role of the microbiome and endometrial gene expression in fertility through the integration of multi-omic data. The team will combine single-cell transcriptomics (scRNA seq) and metagenomics (WMS) to obtain a comprehensive multi-omic profile of the endometrium under physiological and pathological conditions.

The study will analyse endometrial aspirate samples collected during the implantation window and faecal samples from fertile and infertile women, including patients with Asherman's syndrome, chronic endometritis or endometriosis/adenomyosis. The research will map transcriptional changes across different endometrial cell types and correlate them with microbial composition, with the aim of identifying biomarkers that can improve diagnosis and personalised treatments in reproductive medicine.

Development of tools for epitranscriptomics, with LongSeq

The second project, in collaboration with Longseq, focuses on the development of an innovative bioinformatics tool designed to harness the full potential of nanopore sequencing for the joint analysis of transcriptomics and epitranscriptomics. Based on SQANTI3, a platform previously created by Conesa's laboratory for the comprehensive characterisation of isoforms from long-read data, the team will adapt and expand its functionality to interpret raw dRNA seq signals, detect patterns of epitranscriptomic modifications, and integrate the identification of point mutations in transcripts.

The aim is to develop a robust and versatile tool that will advance our understanding of epitranscriptomics in health and disease, opening up new opportunities for precision medicine and the development of early diagnosis strategies and potential therapeutic targets.