Document text
Principal Investigator: Megan Evelyn Barefoot
Organization: GEORGETOWN UNIVERSITY
Fiscal Year: 2024
Award: $53,974
Funding agency: National Cancer Institute
ABSTRACT
Liquid biopsy applications are rapidly emerging as a minimally invasive approach to collect system-wide
representative analytes for genomic monitoring of physiologic and disease-related changes. Dying cells release
fragmented DNA into the circulation, referred to as cell-free DNA (cfDNA). Decoding the cellular origins of cfDNA
over time can reveal altered cellular contributions reflective of dynamic changes to tissue damages in longitudinal
studies. Here, I will focus on the changes in cellular and tissue homeostasis post liver transplant using molecular
analyses of cfDNA. Cell-type specific methylation patterns will be used to trace the cellular origins of cfDNA
molecules. In addition, solid organ transplant place a separate DNA set with the donor organ into the body
of the host, allowing cfDNA molecules from the allograft to be identified and validated through genotyping
using donor-derived SNPs. In this proposal, I aim to track the changing composition of cellular damage post-
liver transplant and use this information to improve diagnosis and management of graft dysfunction (Aim 1).
During transplant there is simultaneous transfer of tissue-resident immune cells along with the donor organ
tissue. I will use immune cell-specific DNA methylation patterns together with the donor SNP analysis to
distinguish the host and donor tissue-resident immune cell changes after transplant and during
immunosuppressive treatment (Aim 2).
The proposed research will evaluate an innovative approach to gain insights into the reaction of host cells,
donor organ cells, plus host and donor-immune cells relative to different transplant outcomes. A series of proof-
of-principle studies are outlined using liver transplantation as an ideal setup that introduces an organ with a
distinct genome at a specific timepoint where there will be induced changes in cell homeostasis to a range of
cells in the allografts as well as the host. Beyond the transplant outcome analysis, the cfDNA approach
established under this proposal can be expanded to determine the cellular contributions to tissue damages in
any setting. Cell type-specific methylation patterns are universal markers that can be used to trace the damaged
cell origin of cfDNA irrespective of the cause of damage. Cellular damage in the liver can be due to targeted
therapy, chemotherapy, immunosuppression or other interventions, initiation or recurrence of primary liver
malignancy, cancer metastatic seeding or organ damage observed during the COVID-19 pandemic. We propose
that distinct cellular cfDNA signatures will be observed from different types of injury. Also, there is an unmet
need to gain insights into tissue damage during the development of new treatments and understand the
cellular basis of adverse events relative to therapeutic efficacy. The global impact of this proposal will be to
link cfDNAs in the circulation to their cellular origins and thus reveal drivers of pathophysiology.
Terms: <Acute><Adverse Experience><Adverse event><Allografting><Apoptosis><Apoptosis Pathway><Area><Autoregulation><Biliary><Biological><Biopsy><Blood Sample><Blood Serum><Blood Vessels><Blood specimen><Body Tissues><COVID crisis><COVID epidemic><COVID pandemic><COVID-19 crisis><COVID-19 epidemic><COVID-19 era><COVID-19 global health crisis><COVID-19 global pandemic><COVID-19 health crisis><COVID-19 pandemic><COVID-19 period><COVID-19 public health crisis><COVID-19 years><Cancers><Cell Body><Cell Death><Cells><Cellular injury><Cessation of life><Characteristics><Chimerism><Circulation><Clinical><DNA><DNA Methylation><Data><Death><Death Rate><Decision Making><Deoxyribonucleic Acid><Detection><Development><Diagnosis><Diagnostic><Disease><Disorder><Disseminated Malignant Neoplasm><Dysfunction><Endothelium><Engraftment><Enzyme Gene><Enzymes><Exhibits><Frequencies><Functional disorder><Genetic><Genome><Genomics><Genotype><Goals><Grafting Procedure><Hepatic><Hepatic Cancer><Hepatic Cells><Hepatic Circulation><Hepatic Parenchymal Cell><Hepatic Transplantation><Hepatocyte><Heterogeneity><Homeostasis><Human><Human Figure><Human body><Immune><Immunes><Immunosuppressants><Immunosuppression><Immunosuppression Effect><Immunosuppressive Agents><Immunosuppressive Effect><Immunosuppressive drug><Immunosuppressive treatment><Infection><Injury><Injury to Liver><Intervention><Intervention Strategies><Ischemia-Reperfusion Injury><Link><Liver><Liver Cells><Liver Circulation><Liver Function Tests><Liver Grafting><Liver Transplant><Liver lesion biopsy><Longitudinal Studies><Malignant Neoplasms><Malignant Tumor><Malignant neoplasm of liver><Measures><Medicine><Metastatic Cancer><Metastatic Malignant Neoplasm><Methylation><Modern Man><Molecular><Molecular Analysis><Monitor><Morphology><Necrosis><Necrotic><Organ><Organ Donor><Organ Transplantation><Organ Transplants><Outcome><Pathologic><Physiologic><Physiologic Monitoring><Physiological><Physiological Homeostasis><Physiological Monitoring><Physiopathology><Population><Process><Programmed Cell Death><Proteins><RNA Seq><RNA sequencing><RNAseq><Reaction><Recurrence><Recurrent><Reperfusion Damage><Reperfusion Injury><Research><Research Resources><Resources><Role><SARS-CoV-2 epidemic><SARS-CoV-2 global health crisis><SARS-CoV-2 global pandemic><SARS-CoV-2 pandemic><SARS-coronavirus-2 epidemic><SARS-coronavirus-2 pandemic><Sampling><Series><Serum><Severe Acute Respiratory Syndrome CoV 2 epidemic><Severe Acute Respiratory Syndrome CoV 2 pandemic><Severe acute respiratory syndrome coronavirus 2 epidemic><Severe acute respiratory syndrome coronavirus 2 pandemic><Solid><Surgical complication><System><Therapeutic><Therapeutic Intervention><Time><Tissue Donors><Tissues><Transplant Recipients><Transplantation><Treatment Efficacy><analyzing longitudinal><biologic><cell damage><cell free DNA><cell free circulating DNA><cell injury><cell type><cellular damage><chemotherapy><cholangiocyte><clinical decision-making><clinical significance><clinically significant><coronavirus disease 2019 crisis><coronavirus disease 2019 epidemic><coronavirus disease 2019 global health crisis><coronavirus disease 2019 global pandemic><coronavirus disease 2019 health crisis><coronavirus disease 2019 pandemic><coronavirus disease 2019 public health crisis><coronavirus disease crisis><coronavirus disease epidemic><coronavirus disease pandemic><coronavirus disease-19 global pandemic><coronavirus disease-19 pandemic><damage to cells><developmental><entire genome><full genome><genome sequencing><graft dysfunction><hepatic body system><hepatic damage><hepatic injury><hepatic organ system><immune suppression><immune suppressive activity><immune suppressive agent><immune suppressive function><immune suppressor><immunosuppressive activity><immunosuppressive function><immunosuppressive response><immunosuppressive substance><immunosuppressor><improved><injuries><injury to cells><innovate><innovation><innovative><insight><intervention efficacy><intervention therapy><interventional strategy><liquid biopsy><liver biopsy><liver cancer><liver damage><liver injury><liver malignancy><liver transplantation><long-term study><longitudinal analysis><longitudinal outcome studies><longterm study><malignancy><malignant liver tumor><methylation biomarker><methylation marker><methylation pattern><methylome><minimally invasive><mortality rate><mortality ratio><necrocytosis><neoplasm/cancer><novel><organ allograft><organ graft><organ xenograft><pathophysiology><prenatal screening><prenatal testing><residence><residential building><residential site><severe acute respiratory syndrome coronavirus 2 global health crisis><severe acute respiratory syndrome coronavirus 2 global pandemic><social role><surgery complication><targeted drug therapy><targeted drug treatments><targeted therapeutic><targeted therapeutic agents><targeted therapy><targeted treatment><therapeutic efficacy><therapy efficacy><tool><transcriptome sequencing><transcriptomic sequencing><transplant><transplant patient><vascular><whole genome>