Dissecting the host-pathogen interaction of Histoplasma capsulatum through an integrative genomics approach

• Grant number: 24/13497-5
• Support Opportunities: Scholarships in Brazil - Post-Doctoral
• Start date: December 01, 2024
• End date: November 30, 2026
• Field of knowledge: Health Sciences - Pharmacy
• Principal Investigator: Ana Marisa Fusco Almeida
• Grantee: Samanta de Matos Silva
• Host Institution: Faculdade de Ciências Farmacêuticas (FCFAR). Universidade Estadual Paulista (UNESP). Campus de Araraquara. Araraquara , SP, Brazil

Abstract

Dimorphic fungi, including the genus Histoplasma, have a unique ability to undergo morphological changes, assuming a mycelial form in the soil and a yeast-like form in the host. This facultative intracellular pathogen is known for initiating respiratory infections in mammals that can progress to systemic infections. Additionally, its ability to form biofilms is a concern due to the inherent difficulty in controlling biofilm-related infections in clinical practice. While research efforts have predominantly focused on studying pathogen-host interactions using two-dimensional (2D) cell models, the literature extensively covers the application of three-dimensional (3D) models to elucidate pathogen-host interactions in various microorganisms, including bacteria, viruses, and fungi such as Candida albicans and Aspergillus spp. However, research related to dimorphic fungi remains limited in this context.Among the molecular biology techniques employed to advance studies of pathogen-host interactions, multi-omic approaches have evolved as robust molecular tools in the research of differentiation and integration among genomics, epigenomics, transcriptomics, proteomics, and metabolomics, deepening our understanding of infectious processes. In this context, this research project aims to use an integrative multi-omic approach combining transcriptomic data generated by Single-Cell RNA-Seq (scRNAseq) and epigenomic data to dissect the pathogen-host interaction of H. capsulatum biofilms during the infection of a 3D human small airway tissue model. To achieve this, the tissue formed by the co-culture of differentiated pulmonary epithelial cells (Calu-3) in an Air-Liquid Interface (ALI), pulmonary fibroblasts (MRC-5), and macrophage-like cells (THP-1) (3:3:1) in type I collagen hydrogel scaffolds (developed during the Regular FAPESP project Process No. 2022/1582-6) will be infected with planktonic and biofilm forms of H. capsulatum strains G186A and EH-315 for 24 hours. Subsequently, scRNAseq analysis will be performed using the CHROMIUM single-cell technology platform, which allows for dual analysis of transcripts from both the pathogen and host cells, divided into populations of fungi, epithelial cells, fibroblasts, and macrophages, followed by Illumina transcripts sequencing. For the analysis of epigenetic markers, sequencing of both the pathogen and host will be conducted using Oxford Nanopore Technology and the Nanopore MinION r9.4.1 sequencer. Finally, bioinformatics pipelines will be constructed to integrate the obtained data. Consequently, it is believed that the questions generated from our group's previous study will be better elucidated and answered based on an integrative multi-omic approach. (AU)