Biology subjects

Sharkia, I.

Publications and source records attributed to Sharkia, I..

4 recordsLinked to original sources

bioRxiv2024

ChIP-seq of Urinary Cell-Free Chromatin Infers Tissue Origin and Detects Tumor-Derived Cell-Free DNA in Bladder Cancer

Urine contains fragments of cell-free DNA, which hold valuable molecular insights into the processes occurring within the urinary system and the whole body. It is unknown whether these fragments are in the form of chromatin, as in the cell of origin, and whether they maintain the cell of origin chromatin modifications. Here, we examine these questions using cell-free chromatin immunoprecipitation followed by sequencing (cfChIP-seq) on human urine. We demonstrate that we can capture cell-free nucleosomes (cf-nucleosomes) from urine and that these preserve multiple histone post-translational modifications indicative of activation and repression. By analyzing these modifications, we identified the primary tissues contributing to cf-nucleosomes in a cohort of healthy individuals. Notably, we observe distinct populations of circulating cf-nucleosomes in urine samples from healthy donors with a contribution from the kidney, which are not detected in matched urine exfoliated cells or matching plasma samples. We further show that, at most, a negligible amount of urine cf-nucleosomes originates from plasma, suggesting that kidney filtration excludes plasma-circulating nucleosomes from urine. Additionally, we show that urine cf nucleosomes can report pathologically driven changes in the urine of bladder cancer patients, reflecting tumor-associated transcriptional programs and immune responses. Our findings highlight the potential of urine cf nucleosomes as accessible, noninvasive biomarkers for both basic research in renal physiology and monitoring urinary pathologies. Key FindingsO_LIUrine cell-free nucleosomes exist and retain multiple histone marks that are informative of gene promoters and enhancers. C_LIO_LIUrine cfChIP-seq identifies bladder, kidney, and immune cells as the major contributing organs to the pool of urine cell-free nucleosomes. C_LIO_LIThe populations of cell-free nucleosomes in urine and blood are distinct and primarily disjoint, suggesting that few, if any, nucleosomes cross the blood-urine interface. C_LIO_LIUrine cell-free nucleosomes reflect pathologically driven changes in tumors and immune cells responding to the tumor. C_LI

genomics↗

bioRxiv2023

Epigenetic liquid biopsies reveal elevated vascular endothelial cell turnover and erythropoiesis in asymptomatic COVID-19 patients

The full spectrum of tissues affected by SARS-CoV-2 infection is crucial for deciphering the heterogenous clinical course of COVID-19. Here, we analyzed DNA methylation and histone modification patterns in circulating chromatin to assess cell type-specific turnover in severe and asymptomatic COVID-19 patients, in relation to clinical outcome. Patients with severe COVID-19 had a massive elevation of circulating cell-free DNA (cfDNA) levels, which originated in lung epithelial cells, cardiomyocytes, vascular endothelial cells and erythroblasts, suggesting increased cell death or turnover in these tissues. The immune response to infection was reflected by elevated B cell and monocyte/macrophage cfDNA levels, and by evidence of an interferon response in cells prior to cfDNA release. Strikingly, monocyte/macrophage cfDNA levels (but not monocyte counts), as well as lung epithelium cfDNA and vascular endothelial cfDNA, predicted clinical deterioration and duration of hospitalization. Asymptomatic patients had elevated levels of immune-derived cfDNA but did not show evidence of pulmonary or cardiac damage. Surprisingly, these patients showed elevated levels of vascular endothelial cell and erythroblast cfDNA, suggesting that sub-clinical vascular and erythrocyte turnover are universal features of COVID-19, independent of disease severity. Epigenetic liquid biopsies provide non-invasive means of monitoring COVID-19 patients, and reveal sub-clinical vascular damage and red blood cell turnover.

microbiology↗

bioRxiv2022

Subtyping of Small Cell Lung Cancer using plasma cell-free nucleosomes

Emerging data on small cell lung cancer (SCLC), an aggressive malignancy with exceptionally poor prognosis, support subtypes driven by distinct transcription regulators, which engender unique therapeutic vulnerabilities. However, the translational potential of these observations is limited by access to tumor biopsies. Here, we leverage chromatin immunoprecipitation of cell-free nucleosomes carrying active chromatin modifications followed by sequencing (cfChIP-seq) on 442 plasma samples from individuals with advanced SCLC, neuroendocrine carcinomas (NEC), non-SCLC cancers, and healthy adults. Beyond providing reliable estimates of SCLC circulating free DNA tumor fraction, cfChIP-seq captures the unique epigenetic states of SCLC tissue- and cell-of-origin. Comparison of cfChIP-seq signals to matched tumor transcriptomes reveals genome-wide concordance, establishing a direct link between gene expression in the tumor and plasma cell-free nucleosomes. Exploiting this link, we develop a classifier that discriminates between SCLC lineage-defining transcription factor subtypes based on cfChIP-seq data. This work sets the stage to non-invasively profile SCLC transcriptomes using plasma cfDNA histone modifications.

cancer biology↗

bioRxiv2019

ChIP-seq of plasma cell-free nucleosomes identifies cell-of-origin gene expression programs

AbstractGenomic DNA is packed by histone proteins that carry a multitude of post-translational modifications that reflect cellular transcriptional state. Cell-free DNA (cfDNA) is derived from fragmented chromatin in dying cells, and as such it retains the histones markings present in the cells of origin. Here, we pioneer chromatin immunoprecipitation followed by sequencing of cell-free nucleosomes (cfChIP-seq) carrying active chromatin marks. Our results show that cfChIP-seq provides multidimensional epigenetic information that recapitulates the epigenetic and transcriptional landscape in the cells of origin. We applied cfChIP-seq to 268 samples including samples from patients with heart and liver pathologies, and 135 samples from 56 metastatic CRC patients. We show that cfChIP-seq can detect pathology-related transcriptional changes at the site of the disease, beyond the information on tissue of origin. In CRC patients we detect clinically-relevant, and patient-specific information, including transcriptionally active HER2 amplifications. cfChIP-seq provides genome-wide information and requires low sequencing depth. Altogether, we establish cell-free chromatin immunoprecipitation as an exciting modality with potential for diagnosis and interrogation of physiological and pathological processes using a simple blood test. One Sentence SummaryChIP-seq of plasma-circulating nucleosomes (cfChIP-seq) from a simple blood test provides detailed information about gene expression programs in human organs, and cancer.

molecular biology↗