Cell free RNA liquid biopsies

摘要

ABSTRACT The ultimate goal of this proposal is to verify an RNA liquid biopsy platform and transition it to have specific utility for the study, and non-invasive assessment, of the hematopoietic bone marrow (BM) niche. In addition to their reliance of material excreted from dying, diseased cells, cell-free DNA (cfDNA) platforms are limited to primarily detecting changes in somatic genomic sequence, copy number, or methylation status. Many biological and clinical events, such as hematopoiesis, fibrosis, and tumorigenesis, are executed via global changes in transcriptional regulation. My PhD advisor Dr. Daniel Kim and I have established a platform for exRNA liquid biopsy in human blood-plasma that has demonstrated significant diagnostic and monitoring potential in both Pancreatic cancer and COVID-19 patients. I propose to continue this research to complete my PhD by assessing diagnostic performance of the exRNA platform in a new cohort of 60 lung adenocarcinoma (LUAD) patients with matched controls. Furthermore, I will apply my expertise in exRNA liquid biopsies to assay the transcriptional dynamics of hematopoiesis and hematopoietic stem cells (HSCs) in the bone marrow (BM) niche. Currently, bone marrow biopsies or aspirations are used to determine bone marrow health and production. These techniques are costly and require sedation and/or pain relief for the subject and have the potential to lead to long term discomfort, infection, excessive bleeding, and other side-effects. BM aspirations remain a critical diagnostic and monitoring tool for HSC transplant recovery, leukemias and lymphomas, blood cell pathologies, and infections of unknown origin but the primary readout remains identification and counting of cell types. I hypothesize that hematopoietic lineages within the BM secrete exRNA that reflect cell state and identity that can be used in a non-invasive RNA liquid biopsy for detailed study of transcription and populations within the BM. I propose to identify exRNA expressed and secreted by HSCs and the remaining hematopoietic lineage in order to develop a platform to deconvolute peripheral blood into constituent hematopoietic cell types without the need for HSC mobilization.