Plasma DNA Profile Associated with DNASE1L3 Gene Mutations: Clinical Observations, Relationships to Nuclease Substrate Preference, and In Vivo Correction

Abstract

Summary Plasma DNA fragmentomics is an emerging area in cell-free DNA diagnostics and research. In murine models, it has been shown that the extracellular DNase, DNASE1L3, plays a role in the fragmentation of plasma DNA. In humans, DNASE1L3 deficiency causes familial monogenic systemic lupus erythematosus with childhood onset and anti- ds DNA reactivity. In this study, we found that human patients with DNASE1L3 disease-associated gene variations showed aberrations in size and a reduction of a “CC” end motif of plasma DNA. Furthermore, we demonstrated that DNA from DNASE1L3-digested cell nuclei showed a median length of 153 bp with CC motif frequencies resembling plasma DNA from healthy individuals. Adeno-associated virus-based transduction of Dnase1l3 into Dnase1l3 -deficient mice restored the end motif profiles to those seen in the plasma DNA of wild-type mice. Our findings demonstrate that DNASE1L3 is an important player in the fragmentation of plasma DNA, which appears to act in a cell-extrinsic manner to regulate plasma DNA size and motif frequency.

DNASE1L3 arrests tumor angiogenesis by impairing the senescence-associated secretory phenotype in response to stress

“…Since DNASE1L3 is also an extracellular secreted protein [ 18 ], furthermore, we analyzed plasma DNASE1L3 protein levels in another cohort of 95 cases encompassing 50 inoperable HCC patients, 27 patients with hepatitis only and 18 healthy individuals. HCC patients exhibited a significantly lower DNASE1L3 levels compared to the normal group, but higher than patients with hepatitis only ( Figure 1H ).…”

“…In our experiments, DNASE1L3 translocates from the cytoplasm to the nucleus in response to UV or H 2 O 2 induced DNA damage. As an intracellular endonuclease, it has been investigated that DNASE1L3 associates with DFFB to digest DNA and fragment it into internucleosomal repeats of 153-200 bp [ 18 , 30 – 32 ]. The DFFB is involved in the initial cleavage of DNA into 50kb fragments, but not sufficient for acetaminophen-induced internucleosomal DNA fragmentation [ 32 ].…”

“…In contrast, overexpression of DNASE1L3 provokes more cellular apoptosis than senescence during DNA damage. This must be relevant to its function in processing DNA fragmentation from ~50kb into mononucleosome of 153 bp [ 18 ]. Low expression of DNASE1L3 decrease the degradation efficiency of unsuccessful repaired DNA to some extent.…”

A literature-derived knowledge graph augments the interpretation of single cell RNA-seq datasets

“…Given recent evidence for structural conservation between CLIC6 and other CLIC family proteins [90], we suggest that directed studies to analyze CLIC6 function in RPE cells are warranted. DNASE1L3 is an extracellular DNase which is historically reported to be released specifically by macrophages and dendritic cells [74,75,80]. Our analysis challenges this canon, insteading highlighting this gene as an uncharacterized marker of endothelial cells (in addition to myeloid cells) in tissues including liver, kidney, lung, nasal cavity, thyroid, and adrenal cortex.…”

“…While 24 of the top 50 genes were strongly associated with ECs (e.g., PECAM1, VWF, ICAM1), several other genes were poorly characterized or previously uncharacterized endothelial markers (Figure 7B). For example, DNASE1L3 was identified as an EC marker whereas it is canonically reported to be expressed by macrophages and dendritic cells [74][75][76]. While its expression in liver sinusoidal ECs, non-sinusoidal hepatic ECs, and renal ECs of the ascending vasa recta has been recently reported [57,[77][78][79], we not only confirmed expression in these populations (Supplemental Figure 9) but also identified several other tissues in which ECs were the predominant DNASE1L3-expressing cell type, including the adrenal gland, lung, and nasal cavity (Supplemental Figure 10).…”