A metatranscriptomics pipeline to investigate host-microbe interactions in low-biomass samples: a case study in liquid biopsies from prostate cancer patients

• Grant number: 23/03951-8
• Support Opportunities: Scholarships abroad - Research Internship - Doctorate (Direct)
• Start date: September 01, 2023
• End date: June 29, 2024
• Field of knowledge: Interdisciplinary Subjects
• Principal Investigator: Helder Takashi Imoto Nakaya
• Grantee: Ícaro Maia Santos de Castro
• Supervisor: Nicola Segata
• Host Institution: Centro de Inovação da USP (INOVA). Universidade de São Paulo (USP). São Paulo , SP, Brazil
• Institution abroad: Universitá degli Studi di Trento, Italy
• Associated to the scholarship: 20/05284-0 - Interaction of microorganisms and human hosts associated with the clinical outcome of patients with infectious diseases, BP.DD

Abstract

The human microbiome has gained attention in recent years due to its involvement in both health and disease. Recent studies have found that some microbes may play an important role in the occurrence, progression, and prognosis of prostate cancer (PCa). Nonetheless, the impact of microbes on disease development remains complex and requires further investigation. Nowadays, RNA-Seq has become the leading high-throughput sequencing technology for understanding the immune response in human diseases. Although most human transcriptomic studies focus exclusively on human gene expression, resulting in the exclusion of reads not aligned to the human genome during the read alignment process. Nevertheless, these unaligned reads contain valuable information regarding microbial presence within the tissue without the need for additional targeted sequencing approaches. In this project, we introduce a novel bioinformatics workflow that simultaneously assesses the host transcriptome and microbial composition. This will allow the characterization of host-microbe interactions in PCa. We will then benchmark our method with state-of-the-art tools and apply it to liquid biopsy samples of prostate cancer patients. Our approach may contribute to identifying potential microbes related to disease progression and generating new insights into microbe-host interactions in the context of prostate cancer research. (AU)