Dissertation committee:
Αλέξανδρος Κόκκινος, Καθηγητής, Ιατρική Σχολή, ΕΚΠΑ
Νικόλαος Τεντολούρης, Καθηγητής, Ιατρική Σχολή, ΕΚΠΑ
Χριστίνα Πιπέρη, Καθηγήτρια, Ιατρική Σχολή, ΕΚΠΑ
Ευάγγελος Λυμπερόπουλος, Καθηγητής, Ιατρική Σχολή, ΕΚΠΑ
Ραφαήλ Σανδαλτζόπουλος, Καθηγητής, Τμήμα Μοριακής Βιολογίας και Γενετικής, ΔΠΘ
Απόστολος Κλινάκης, Ερευνητής Α’ βαθμίδας, Κέντρο Βασικής Έρευνας, Ι.ΙΒ.Ε.Α.Α
Γεώργιος Παναγιώτου, Ερευνητής Α’ βαθμίδας, Πρόεδρος Δ.Σ., Ερευνητικό Κέντρο Βιοϊατρικών Επιστημών (Ε.Κ.Ε.Β.Ε.) «Αλέξανδρος Φλέμιγκ»
Summary:
Viral infections are major causes of morbidity and mortality worldwide, causing significant impacts on human health and often leading to pandemics. Viruses play a critical role in the development of multifactorial diseases, which arise from the interaction of environmental factors and microbial load. The entrance of viral genetic information into host cells often causes molecular disorders, leading to the appearance of complex pathological phenotypes. Examples of diseases associated with viral infections include Type 1 Diabetes Mellitus (T1DM), Ebola disease, Acquired Immunodeficiency Syndrome (AIDS), Hepatitis B and C, as well as other autoimmune diseases. The recent COVID-19 pandemic, caused by the SARS-CoV-2 virus, has highlighted the potential of viruses to destabilize the homeostasis of the human body, causing significant impacts on health and longevity. In modern biomedical research, understanding the relationship between environmental factors—such as microorganisms, chemicals, radiation, nutrition, and stress—and genetic parameters, i.e. mutations in the human genome, is considered crucial for understanding the emergence, evolution, and spread of diseases in human populations.
At the molecular level, the entrance of the viruses causes reprogramming of the transcriptional profile of cells, disrupting the gene expression programs that support homeostatic mechanisms. This often leads to the appearance of pathological phenotypes, accompanied by a disruption of the defense/immune response, which facilitates the development of diseases. The ability of cells to mount complex defense responses against microbial pathogens, such as viruses, is fundamental to maintaining human health. However, the (epi)genomic mechanisms involved in the adaptation of these responses are not fully understood. A key limitation in understanding these mechanisms is the insufficient mapping of functional cis-Regulatory Modules (CRMs) in the human genome, which regulate gene expression in vivo. The investigation of these regulatory mechanisms is essential for elucidating the molecular basis of the human body’s defense responses and for the development of new therapeutic approaches for the effective treatment of viral infections.
T1DM is characterized as one of the most damaging autoimmune diseases of the pancreas, causing the destruction of pancreatic β cells and affecting millions of people worldwide. Over the past three decades, the incidence of the disease has increased significantly. However, despite advances in research, the molecular mechanisms underlying the development of T1DM remain unclear, and the precise association between the presence of viruses in the human body and the development of the disease has not been determined. Studies involving patients with T1DM indicate that viral infections, and in particular enteroviruses, are important environmental risk factors for the development of the disease. In addition, genes that are activated or induced by viruses, such as IRF7 and IFIH1, have been strongly associated with the development of the autoimmune phenotype of T1DM. At the same time, Genome-Wide Association Studies (GWAS) have identified genetic regions with Single Nucleotide Polymorphisms (SNPs), which increase the genetic predisposition to the development of the disease. Based on the above, the scientific hypothesis arises that specific regions of regulatory DNA, which function as “regulators” of gene expression during the antiviral cellular response, may contribute to the pathogenesis of T1DM. This hypothesis is strengthened by the fact that mutations in these regions may alter their activity, causing an abnormal antiviral response and, ultimately, the manifestation of the disease. Further investigation of these mechanisms is necessary to understand the interaction between environmental and genetic factors, as well as to develop new therapeutic approaches for T1DM.
The aim of this PhD Thesis, entitled “The Role of Functional Elements of the Genome in the Evolution of Gene Expression Programs during the Cellular Response to Viral Infections”, is to decode and understand the molecular mechanisms that regulate gene expression in mammalian cells during viral infections. The PhD Thesis focuses on identifying functional elements of the genome, which regulate gene expression under conditions of viral infection and examines how these regions change in the organism’s response, through a comprehensive experimental approach at the genome-wide level. The experimental strategy of the PhD Thesis combines the most advanced methods of Cell Biology, Molecular Biology, Biochemistry, Genomics, Bioinformatics and Computational Biology, to acquire new knowledge for understanding the effect of viral infections on gene regulation.
The results of this PhD Thesis contributed significantly to the in-depth understanding of the molecular mechanism underlying the establishment of virus-induced gene expression programs in human epithelial HeLa cells, Namalwa B lymphocytes, human and mouse pancreatic β cells.
The findings of the PhD Thesis highlighted critical elements regarding the regulation of antiviral gene induction and the functional organization of the (epi)genome, revealing extensive chromatin regions/gene coordinates/gene coordinates, which are specialized in gene expression related to defense and antimicrobial responses. In particular, the findings of the PhD Thesis revealed key elements regarding the regulation of antiviral gene induction and the functional organization of the (epi)genome, revealing extensive chromatin regions/gene coordinates/gene coordinates specialized in the regulation of gene expression related to defense and antimicrobial responses. At the same time, novel virus-induced CRMs, such as typical enhancers (tEs), super-enhancers (SEs) and repetitive DNA enhancers (rDEs), were identified. These regulatory elements proved to be crucial for the activation of innate immunity during infection and the maintenance of cellular homeostasis under physiological conditions. Particular importance was given to the investigation of the DNA “Grammar” and “Syntax” of sequences, with the aim of better understanding the organizational architecture of the genome, which affects the antiviral responses of the organism. In addition, the evolutionary conservation of these regulatory elements from humans to microbes was studied, revealing how mammalian (epi)genomes have evolved to respond to exogenous challenges, such as viral infections, by activating adaptive defense transcriptional responses. Furthermore, it was discovered that after viral infection, certain transposable elements (TEs) are activated, producing RNA molecules that affect the function of neighboring antiviral genes and their regulatory regions, thus identifying new aspects of gene regulation during viral infection. Finally, a significant discovery was the identification of single nucleotide polymorphisms (SNPs), which are associated with autoimmune diseases and are located in regions of the genome that are in cis proximity and/or within critical regulatory elements. These SNPs may determine the individual genetic predisposition to the development of autoimmune diseases, the differentiated response of the organism to viral infections. Overall, this PhD Thesis offers valuable insights into the function, architecture and evolutionary origin of the human and mouse (epi)genome. These findings open new perspectives for understanding the importance of the genome in maintaining homeostasis, as well as in addressing the challenges caused by microbial and viral agents, contributing to the development of innovative therapeutic strategies for the treatment of autoimmune and viral diseases.
