This funded PhD position at the University of Udine, Italy, focuses on investigating the role of Cyclophilin D (CypD), a mitochondrial matrix protein, in mitochondrial RNA (mtRNA) metabolism. While CypD is traditionally known for its role in regulating the mitochondrial permeability transition pore (mPTP), recent findings from Dr. Carlo Vascotto’s laboratory suggest it may also be involved in post-transcriptional regulation of mitochondrial gene expression. The project aims to elucidate the functional interactions between CypD and mtRNAs, potentially revealing new mechanisms in mitochondrial biology and identifying therapeutic targets for diseases linked to mitochondrial dysfunction. The research will involve developing a novel protocol for immunoprecipitating CypD–RNA complexes from mitochondrial fractions, followed by high-throughput RNA sequencing to identify and classify bound mtRNA species. Bioinformatic analyses will characterize RNA families and regulatory motifs associated with CypD binding. Functional relevance will be assessed by modulating CypD expression in cell models using shRNA knockdown and overexpression systems, with subsequent analyses including qPCR, Western blotting, and mitochondrial functional assays to measure changes in mtRNA abundance, stability, and organelle physiology. The host laboratory, led by Dr. Vascotto, specializes in DNA repair mechanisms, mitochondrial RNA processes, and the role of mitochondria in tumor progression and resistance. The lab is well-equipped with facilities for mammalian cell culture, flow cytometry, advanced microscopy, and instruments for monitoring cell viability, apoptosis, and mitochondrial respiration. The project includes secondments to collaborating groups in Poland (Prof. Barbara Uszczynska-Ratajczak, Institute of Bioorganic Chemistry, Polish Academy of Sciences) and the UK (Dr. Alexander Jackson, Nanovery Ltd.), so candidates must be willing to travel and spend time abroad. Eligibility requires a Master’s degree in Biology, Biotechnology, or a related field, and compliance with the mobility rule (not residing in Italy for more than 12 months in the past 36 months). Research experience in cellular and molecular biology is required, with mitochondrial and/or RNA biology experience as a strong advantage. Proficiency in English is mandatory, demonstrated by a recognized test unless exempted. Applicants must submit a statement of interest, CV, university examination certificate with marks, and a final degree certificate translated into English (if not available, can be submitted later), all merged into a single PDF. Selected candidates will be invited for an interview and must provide referee contact details. The application deadline is January 31, 2026. For more information, visit the INT2ACT recruitment page or contact Dr. Carlo Vascotto.

This PhD project, hosted at the University of Udine and Flomics Biotech SL in Barcelona, focuses on the identification and implementation of novel cell-free RNA (cfRNA) biomarkers for early cancer detection using liquid biopsy. Flomics Biotech is pioneering a multi-purpose blood test that leverages optimized cfRNA profiling via Next-generation sequencing (NGS) and advanced machine learning analysis to detect cancer and other complex diseases before symptoms arise. Unlike traditional liquid biopsy approaches that target circulating tumor DNA (ctDNA), this project emphasizes cfRNA, which is more abundant and informative in early disease stages, as it is released from both cancerous and non-cancerous cells, including those from the immune system and stroma. The candidate will utilize proprietary RNA sequencing protocols and analyze a large in-house dataset (~1,100 samples) covering five cancer types and healthy controls. Research will involve developing bioinformatics pipelines to explore RNA-based signals beyond gene expression, such as mitochondria-derived RNAs, circular RNAs, single nucleotide variants, and novel transcripts. The project includes advanced data normalization and removal of unwanted variation, addressing key challenges in cfRNA research. Machine learning models will be developed to classify cancer patients versus healthy controls with high accuracy, integrating novel biomarker types and global gene expression signatures. The position is part of the INT2ACT Doctoral Network, offering strong collaboration and secondments with leading European research groups, including the Institute of Bioorganic Chemistry (Polish Academy of Science) and University of Udine. The host laboratory at Flomics Biotech provides a dynamic environment with cutting-edge genomics and bioinformatics resources. Applicants must have a Master’s degree in a relevant field, proficiency in English, and willingness to travel for collaborative research. Funding is provided, and the application deadline is January 31, 2026.