This is part of my master thesis.
In the complex world of a healthy brain, T cells make themselves at home in the parenchyma, closely interacting with microglia. The resident T cells aren't just passive guards; they play a versatile role. They not only keep an eye on the brain's health but also have specific jobs related to essential tissue activities. They help regulate synaptic transmission and influence the creation of new neurons, shaping the connectivity of the neural network. The fact that brain T cells impact both the immune system and neural processes highlights their crucial role in shaping normal brain function and responding to diseases. Despite their importance, we still don't fully understand how brain-resident T cells and microglia interact and how this interaction affects overall brain function and pathology. In this master thesis, I aim to uncover these mysteries, using various tools and systematic approaches to explore cell-cell interactions. The focus is on understanding the intricacies of the T cells-microglia axis, where immune surveillance and neural regulation intersect. For my thesis, I will be looking at LIANA+ and DIALOGUE, tools designed to decode the molecular interaction between brain T cells and microglia. My research plan involves a thorough examination of how the dynamic interactions between these cells change during both normal and inflammatory conditions. To achieve this, including the single-cell transcriptome of brain CD4 T cells and microglia, will be analyzed, and explored. The research landscape benefits from advanced analysis tools and pipelines, using the capabilities of LIANA+ and DIALOGUE for in-depth exploration of the vast amount of data. Ultimately, the goal is to contribute to our understanding of brain immunology and neurobiology, providing insights into the intricate relationship between immunity and neural function in both health and disease.