Jacopo Ronchi

Dr. Jacopo Ronchi is a young PhD student in the field of neurosciences at the University of Milano-Bicocca. He works under the mentorship of Prof. Maria Foti, and his research is mainly focused on the analysis of omics data. In particular, his project consists in the development of an integrative multi-omics framework for modeling the molecular interactions in complex diseases. This novel approach enabled him to propose mechanistic hypotheses that could potentially explain some uncharacterized features of several autoimmune diseases, including multiple sclerosis, type 1 diabetes, and myasthenia gravis. He obtained his Bachelor’s degree in Biotechnology in 2021, followed by a Master’s degree in Medical Biotechnologies in 2023. During his education, in addition to the study of biology, he further deepened his knowledge of mathematics, computer science, and statistics, enabling him to approach the field of omics science, network modeling, and complex multivariate analysis. Prominent among his diverse skills are his proficiency in programming in various languages, including R, python, and C++, his ability to approach problems algorithmically, and his ability to interpret the biological relevance of results. In addition, his knowledge of molecular biology and its techniques enables him to reason about the various regulatory aspects of molecular events inside the cell, and to carefully evaluate the pathological implications that any deregulations may have. In this regard, he is particularly interested in the study of epigenetic phenomena and how modeling of miRNA-mRNA-lncRNA regulatory networks can help explain the fine regulatory mechanisms that coordinate gene expression, both in the physiological and pathological state. His objective is to identify the pathological mechanisms underlying pathogenesis, progression, or resistance to treatments, with the ultimate goal of developing new, innovative therapeutic strategies that can improve patient outcomes.

PhD research project

Integrative Multi-Omics Analysis to identify miRNA Regulatory Networks in Multiple Sclerosis: towards the comprehension of molecular mechanisms driving disease progression

Multiple Sclerosis (MS) is an autoimmune disease that affects the central nervous system (CNS), and is caused by an interplay of multiple immune populations that promote neurodegeneration. MS is characterized by acute and chronic inflammation throughout the disease course, with acute inflammation being particularly prominent during the relapsing phase of the disease. Both innate and adaptive immune responses have been shown to be involved. However, the precise molecular events that contribute to the initiation and exacerbation of MS are not yet fully understood. In this context, microRNAs have been shown to play a critical role in regulating both innate and adaptive immune gene expression. Nevertheless, the exact contribution of impaired miRNA networks to MS has not been thoroughly investigated. To address this limit, the current project aims to develop an integrative multi-omic analysis to elucidate the impaired miRNA networks in MS. In particular, novel computational methods will be developed for joint multi-omic analyses that correlate dysregulated miRNAs to target protein regulation, epigenomic marks, SNP variants, gene expression, and lncRNA modulation. Several experimental data will be used, including microarrays, bulk and single-cell RNA-Seq, bisulfite sequencing, mass spectrometry and spatial transcriptomics. Moreover, the identified miRNA networks will be further characterized to infer the functional consequences of the impairment. Finally, in vitro and in vivo models will be used to extensively validate the compromised molecular networks.