Employing CRISPR-Cas9 to identify nuclear mechano-sensing pathways tailoring macrophage function in cancer

• Grant number: 25/24517-0
• Support Opportunities: Scholarships abroad - Research Internship - Doctorate
• Start date: March 20, 2026
• End date: March 19, 2027
• Field of knowledge: Biological Sciences - Immunology - Cellular Immunology
• Principal Investigator: Rodrigo Nalio Ramos
• Grantee: Carla Sanzochi Fogolin
• Supervisor: Guilherme Pedreira de Freitas Nader
• Host Institution: Hospital das Clínicas da Faculdade de Medicina da USP (HCFMUSP). Secretaria da Saúde (São Paulo - Estado). São Paulo , SP, Brazil
• Institution abroad: University of Pennsylvania, United States
• Associated to the scholarship: 23/15440-8 - Reprogramming Macrophages through CRISPR-Cas9: an alternative to treating tumors, BP.DR

Abstract

Macrophages, essential for tissue homeostasis and immune regulation, exist as tissue-resident cells and monocyte-derived cells recruited during inflammation. Tumor-associated macrophages (TAMs), primarily derived from circulating monocytes, constitute a major myeloid component in tumors and are implicated in tumor progression through immunosuppressive functions, promotion of angiogenesis, and facilitation of metastasis. Mechanical stress inherent from dense 3D microenvironments such as the TME cause nuclear deformations. The cell nucleus is the largest and stiffest organelle in the cell and often constitutes a limiting mechanical factor when cells explore dense and confining spaces. Importantly, the traditional view of the nucleus as a passive object that cells must drag along has become obsolete. High magnitude physical inputs can cause nuclear deformations and changes in nuclear envelope (NE) state (wrinkled versus fully stretched versus ruptured, as the mechanical stress/confinement increases). The nucleus is a critical mechano-sensory organelle that senses environmental strains and compressive forces. As such, it orchestrates a variety of signaling events that modulate cell migratory strategies and other cell functions ranging from increased cortical contractility to cancer progression and immune responses. Mechanical stress and nuclear deformations are frequently experienced by macrophages as they infiltrate dense and complex 3D landscapes, undergo extravasation in immune responses (which involves squeezing of their bulky nuclei through tight endothelial barriers), and patrol peripheral lymphoid organs. Also, compression events have also been seen in dense compartments like the tumor microenvironment. However, the impact of physical forces on their function has been overlooked. This project aims to define how nuclear mechano-sensing affects the transcriptional and epigenetic landscape of monocyte-derived macrophages in homeostasis and in tumoral contexts using bulk RNA-sequencing and ATAC-sequencing. It also seeks to assess the consequences of nuclear deformation on macrophage activation, phagocytosis, cytokine production, and antigen presentation. Ultimately, this study will identify mechanoresponsive factors and validate their roles via CRISPR-cas9 gene knockouts to unveil novel mechano-sensing pathways regulating macrophage phenotypes in the TME, with critical implications to designing macrophage-targeted cancer therapies.