Biology subjects

Pisareva, E.

Publications and source records attributed to Pisareva, E..

4 recordsLinked to original sources

bioRxiv2026

Extracellular DNASE1L3 dysfunction fuels obesity-driven inflammation and metabolic syndrome

Obesity, a global health crisis affecting 16% of the world population, is characterized by chronic inflammation that contributes to health complications such as type 2 diabetes and metabolic dysfunction-associated steatotic liver disease (MASLD). Emerging evidence suggests that self-DNA released from dying cells aberrantly activates inflammatory responses during obesity. However, the role of extracellular deoxyribonucleases (DNASEs), which at steady state regulate abundance of extracellular self-DNA, remains poorly understood in this context. Here, we show that individuals with obesity exhibit elevated levels of circulating cell-free DNA (cfDNA) with a distinctive end-motif signature, anti-DNASE1L3 autoantibodies and a reduction in circulating DNASE activity. These cfDNA alterations correlate with the severity of obesity and can be corrected by therapeutic intervention such as bariatric surgery. Similarly, mice fed a high-fat diet (HFD) displayed increased cfDNA levels and decreased DNASE activity. Genetic deficiency of the extracellular nuclease DNASE1L3 in mice worsened HFD-induced metabolic complications, including glucose intolerance, insulin resistance, MASLD, and metabolic tissue inflammation. Conversely, targeted supplementation of DNASE1L3 in the liver using adeno-associated viral vectors protected obese mice from developing MASLD and liver inflammation. These findings uncover a novel role of DNASE1L3 in controlling obesity-associated inflammation and its potential therapeutic use for preventing metabolic disease.

pathology↗

bioRxiv2025

Circulating DNA reveals nucleosome occupancy patterns that are associated with nucleosome-DNA affinity and are affected in cancer

The study of cell-free circulating DNA (cirDNA) fragments (fragmentomics) from liquid biopsies has received increasing attention. By constructing an atlas of these well-positioned nucleosomes, which we called WPNA, we found that their occupancy was associated with histone-DNA affinity, as evidenced by codon usage bias and differences in cirDNA fragment sizes. Moreover, WPNA nucleosome occupancy was different in healthy and cancer samples, thus allowing developing a high-performance machine learning approach for cancer detection (specificity and sensitivity >0.95 for seven cancer types). Cancer influenced WPNA nucleosome occupancy in a global manner, although distinct cancer types retained specific features. WPNA nucleosome occupancy at transcription factor binding sites revealed shared, pan-cancer regulation of transcriptional programs involved in hematopoietic cell differentiation and neutrophil biology, the main cirDNA sources. This work provides new fundamental insights into cirDNA and DNA sequence using cirDNA as a physical readout. It also bares translational significance by disclosing a new high-performance strategy for cancer detection from liquid biopsies.

genomics↗

bioRxiv2025

Single- and double-strand circulating DNA fragmentomics for enhanced cancer detection performance

In early detection of cancer, the use of circulating cell-free DNA (cirDNA) obtained from blood samples is notable for its minimally invasive nature. We have developed an algorithm designed to discriminate cancer patients and healthy individuals based on cirDNA fragment end motif analysis assisted by machine learning, using data obtained from shallow whole genome sequencing (a method we call EMA). We applied EMA to cirDNA from the plasma of patients with stage II-III breast cancer, stage I-III non-small cell lung cancer, and metastatic colorectal cancer (mCRC). CirDNA from 158 individuals was prepared following the conventional double-stranded DNA library preparation (DSP). Using 3 bp end motifs, each tumor type was detected with a sensitivity of 0.87-1.00, a specificity of 0.95, and an AUC above 0.96. The three selected cancer types could be differentiated with an accuracy (ACC) above 0.94. Multi-cancer detection by pooling samples from the three cancer types showed ACC, AUC and sensitivity of 0.98, 0.99 and 0.98, respectively. Comparisons with 4 and 2 bp end motifs were conducted, and our main observations were confirmed using an external public dataset (N=366). We also performed a single-stranded DNA library preparation (SSP) using mCRC patients and healthy control cirDNA, which allowed us to make the first ever end motif analysis in the literature which compares the use of DSP and SSP. As compared to EMAD (use of DSP), EMAS (use of SSP) produced a very significant difference in end motif frequency and an improved cancer detection performance (ACC, AUC and sensitivity of 0.97, 1.00 and 0.99, respectively). Furthermore, optimal performance was produced when the full-size range was used for EMAS, whereas when the dataset was restricted to fragments of 115 - 220 bp for EMAD. EMAS strong performance, coupled with its compatibility with cost-effective shallow cirDNA sequencing, positions this methodology as a potentially transformative tool in early cancer screening.

genomics↗

bioRxiv2021

Plasma derived cell-free mitochondrial DNA originates mainly from circulating cell-free mitochondria

Circulating mitochondrial DNA (cir-mtDNA) could have a potential comparable to circulating nuclear DNA (cir-nDNA), with numerous applications. However, research and development in this area have fallen behind, particularly considering its origin and structural features. To tackle this, we initially combined Q-PCR and low-pass whole genome sequencing in the same analytical strategy previously and successfully used for cir-nDNA. This revealed unexplained structural patterns and led us to correlate these data with observations made during physical examinations such as filtration, and differential centrifugation in various plasma preparations. Both the integrity index and number of reads revealed a very minor proportion of low size-ranged fragments (<1000 bp) in plasma obtained with a standard preparation (0.06%). Filtration and high speed second step centrifugation revealed that 98.7 and 99.4% corresponded to extracellular mitochondria either free or in large extracellular vesicles. When avoiding platelet activation during plasma preparation, the proportion of both types of entities was still preponderant (76-80%), but the amount of detected mitochondrial DNA decreased 67-fold. In correlation with our previous study on the presence of circulating cell-free mitochondria in blood, our differential centrifugation procedure suggested that cir-mtDNA is also associated with approximately 18% small extracellular vesicles, 1.7% exosomes and 4% protein complexes.

genomics↗