DNA Patterns Research Articles

The Characteristic of Biofilm Formation in ESBL-Producing K. pneumoniae Isolates.

Klebsiella pneumoniae is a pathogen that commonly causes hospital-acquired infections. Bacterial biofilms are structured bacterial communities that adhere to the surface of objects or biological tissues. In this study, we investigated the genome homology and biofilm formation capacity of ESBL-producing K. pneumoniae. Thirty ESBL-producing K. pneumoniae isolates from 25 inpatients at Ruijin Hospital, Shanghai, were subjected to pulsed-field gel electrophoresis (PFGE) to estimate genomic relatedness. Based on the chromosomal DNA patterns we obtained, we identified 21 PFGE profiles from the 30 isolates, eight of which had high homology indicating that they may have genetic relationships and/or potential clonal advantages within the hospital. Approximately 84% (21/25) of the clinical patients had a history of surgery, urinary tract catheterization, and/or arteriovenous intubation, all of which may have increased the risk for nosocomial infections. Biofilms were observed in 73% (22/30) of the isolates and that strains did not express type 3 fimbriae did not have biofilm formation capacity. Above findings indicated that a high percentage of ESBL-producing K. pneumoniae isolates formed biofilms in vitro and even though two strains with cut-off of PFGE reached 100% similarity, they generated biofilms differently. Besides, the variability in biofilm formation ability may be correlated with the expression of type 3 fimbriae. Thus, we next screened four ESBL-producing K. pneumoniae isolates (Kpn5, Kpn7, Kpn11, and Kpn16) with high homology and significant differences in biofilm formation using PFGE molecular typing, colony morphology, and crystal violet tests. Kpn7 and Kpn16 had stronger biofilm formation abilities compared with Kpn5 and Kpn11. The ability of above four ESBL-producing K. pneumoniae isolates to agglutinate in a mannose-resistant manner or in a mannose-sensitive manner, as well as RNA sequencing-based transcriptome results, showed that type 3 fimbriae play a significant role in biofilm formation. In contrast, type 1 fimbriae were downregulated during biofilm formation. Further research is needed to fully understand the regulatory mechanisms which underlie these processes.

Eco‐physiological arguments on the functional impact of Lepus timidus mitochondrial DNA introgression in Iberian hares (Lepus granatensis)

AbstractGenetic exchanges between species provide valuable opportunities to dissect the relative importance of neutral and selective processes driving introgression events and to test their functional relevance. In the northern half of the Iberian Peninsula, the Iberian hare, Lepus granatensis, presents extensive patterns of mitochondrial DNA (mtDNA) introgression from the mountain hare, L. timidus, a species that disappeared from the region after the Last Glacial Maximum. Here, we test whether mtDNA introgression affects reproductive success and body condition of Iberian hare individuals. For that end, hares (n = 149) were sampled from populations along the mtDNA introgression gradient during the 2013–2014 and 2014–2015 hunting seasons. Reproductive performance indicators, including pregnancy status and testicular weight, were recorded, while body condition was measured as kidney fat (our response variables). Predictors included individual traits (sex and age), sampling period (month and hunting season), mtDNA introgression, occurrence or burden of different endoparasites and environmental factors. Our results showed that mtDNA introgression was negatively associated with pregnancy in females and body condition in males, while a positive association was found with body condition in females. These results suggest that carrying the mountain hare mtDNA has physiological effects in Iberian hares, but that the allospecific mtDNA type may not always be beneficial for the individual. This study shows that the patterns of mtDNA introgression seen in the Iberian hare today may result from a complex balance between deleterious and beneficial individual effects.

Cell-Free Nucleic Acids for Early Prediction of Preeclampsia.

This review summarizes the potential of cell-free nucleic acids for predicting preeclampsia, contrasts them with other methods, and discusses these findings' relevance to preeclampsia's pathogenesis and care. Recent studies have demonstrated the utility of cell-free nucleic acids in early preeclampsia risk prediction. Encouragingly, nucleic acid measurement exhibits similar or better sensitivity as compared to standard screening assays and furthermore sheds light on preeclampsia's underlying placental biology. Over the past decade, liquid biopsies measuring cell-free nucleic acids have found diverse applications, including in prenatal care. Recent advances have extended their utility to predict preeclampsia, a major cause of maternal mortality. These assays assess methylation patterns in cell-free DNA (cfDNA) or gene levels in cell-free RNA (cfRNA). Currently, preeclampsia care focuses on blood pressure control, seizure prevention, and delivery. If validated, early prediction of preeclampsia through liquid biopsies can improve maternal health and deepen our understanding of its causes.

Karyotype stasis but species-specific repetitive DNA patterns in Anguis lizards (Squamata: Anguidae), in the evolutionary framework of Anguiformes

Abstract Karyotype divergence may strongly affect the degree of hybridization between species. Western Palearctic slow worms (Anguis) are legless lizards forming different types of secondary contact zones. To identify the level of chromosomal variation in slow worms, we examined karyotype in multiple populations of all species except one and Pseudopus apodus as an outgroup. We applied conventional and molecular cytogenetic methods and whole-chromosome painting using macrochromosome probes from Varanus komodoensis to interpret results within the evolutionary framework of the common clade Anguiformes. All Anguis species and P. apodus have conserved karyotype structures composed of 44 chromosomes. Despite the conserved chromosome morphology, the phylogenetically oldest Anguis cephallonica living in partial sympatry with Anguis graeca, and parapatric Anguis colchica vs. Anguis fragilis exhibit distinct patterns of constitutive heterochromatin distribution and telomeric repeat accumulation. In contrast, the sister species A. colchica and A. graeca living in allopatry display highly similar karyotype features. Our findings thus indicate karyotype stasis in Anguis and Pseudopus for > 20 Myr, with fixed species-specific differences present in sympatric and parapatric species. These differences in repetitive DNA patterns may play a role as intrinsic factors co-maintaining species divergence. They may also be used as cytotaxonomic markers to identify slow worm species in practice.

Induction of double-strand breaks with the non-steroidal androgen receptor ligand flutamide in patients on androgen suppression: a study protocol for a randomized, double-blind prospective trial

BackgroundProstate cancer remains the most prevalent malignancy and the second-leading cause of cancer-related death in men in the USA. Radiation therapy, typically with androgen suppression, remains a mainstay in the treatment of intermediate- and high-risk, potentially lethal prostate cancers. However, local recurrence and treatment failure remain common. Basic and translational research has determined the potential for using androgen receptor (AR) ligands (e.g., dihydrotestosterone and flutamide) in the context of androgen-deprived prostate cancer to induce AR- and TOP2B-mediated DNA double-strand breaks (DSBs) and thereby synergistically enhance the effect of radiation therapy (RT). The primary aim of this study is to carry out pharmacodynamic translation of these findings to humans.MethodsPatients with newly diagnosed, biopsy-confirmed localized prostatic adenocarcinoma will be recruited. Flutamide, an oral non-steroidal androgen receptor ligand, will be administered orally 6–12 h prior to prostate biopsy (performed under anesthesia prior to brachytherapy seed implantation). Key study parameters will include the assessment of DNA double-strand breaks by γH2A.x foci and AR localization to the nucleus. The initial 6 patients will be treated in a single-arm run-in phase to assess futility by establishing whether at least 2 subjects from this group develop γH2A.x foci in prostate cancer cells. If this criterion is met, the study will advance to a two-arm, randomized controlled phase in which 24 participants will be randomized 2:1 to either flutamide intervention or placebo standard-of-care (with all patients receiving definitive brachytherapy). The key pharmacodynamic endpoint will be to assess whether the extent of γH2A.x foci (proportion of cancer cells positive and number of foci per cancer cell) is greater in patients receiving flutamide versus placebo. Secondary outcomes of this study include an optional, exploratory analysis that will (a) describe cancer-specific methylation patterns of cell-free DNA in plasma and urine and (b) assess the utility of serum and urine samples as a DNA-based biomarker for tracking therapeutic response.DiscussionThis study will confirm in humans the pharmacodynamic effect of AR ligands to induce transient double-strand breaks when administered in the context of androgen deprivation as a novel therapy for prostate cancer. The findings of this study will permit the development of a larger trial evaluating flutamide pulsed-dose sequencing in association with fractionated external beam RT (+/− brachytherapy). The study is ongoing, and preliminary data collection and recruitment are underway; analysis has yet to be performed.Trial registrationClinicalTrials.gov NCT03507608. Prospectively registered on 25 April 2018.

Increasing the productive potential of large and small cattle breed resources in the South of Russia based on modern breeding methods

The results of the genetic characteristics research of large and small cattle populations grown in the Southern Russia are stated. Breed-specific DNA patterns have been identified in three of the most common cattle breeds of meat productivity in arid conditions. The milk productivity of Holstein cows of different breeding lines has been studied. It was found that increasing the frequency of animals of Vis Back Ideal and Reflection Sovering lines in the parent pairs could be able to increase the level of milk productivity of offspring and improve the quality indicators of dairy raw materials. The adaptive abilities and milk productivity of imported foreign Holstein cows depending on their origin were estimated. In comparison with Australian and Danish Holstein cows, American and German analogues have a higher level of milk productivity. However Australian and Danish animals have a more flexible adaptive capacity. As a result of the comparative study of the economic and biological characteristics of two generations of Aberdeen-Angus cattle (parental foreign generation, and the first generation - obtained under breeding conditions in Southern Russia), tendencies to increase productive values are revealed. The features of the meat productivity formation in Kalmyk steers different exterior and constitutional types are investigated. It was found that the Kalmyk steers of the tall body type have a higher meat productivity compared with their analogues of medium and compact body types. However, the beef of compact steers has a higher fat percentage, more attractive taste characteristics, culinary and technological indices. The features of polymorphism of CAST, GH, GDF9, CLPG, FABP4 and MC4R genes in populations of sheep of different breeds grown in the Republic of Kalmykia, Volgograd and Rostov regions, Kabardino-Balkaria Republic were also studied. As a promising method of early diagnosis of presence economically useful traits in sheep during ontogenesis, the effectiveness of DNA analysis in young lambs and the further selection of animals with desirable genotypes according to these genes were justified.

Are kuravirus capsid diameters quantized? The first all-atom genome tracing method for double-stranded DNA viruses.

The revolution in cryo-electron microscopy has resulted in unprecedented power to resolve large macromolecular complexes including viruses. Many methods exist to explain density corresponding to proteins and thus entire protein capsids have been solved at the all-atom level. However methods for nucleic acids lag behind, and no all-atom viral double-stranded DNA genomes have been published at all. We here present a method which exploits the spiral winding patterns of DNA in icosahedral capsids. The method quickly generates shells of DNA wound in user-specified, idealized spherical or cylindrical spirals. For transition regions, the method allows guided semiflexible fitting. For the kuravirus SU10, our method explains most of the density in a semiautomated fashion. The results suggest rules for DNA turns in the end caps under which two discrete parameters determine the capsid inner diameter. We suggest that other kuraviruses viruses may follow the same winding scheme, producing a discrete rather than continuous spectrum of capsid inner diameters. Our software may be used to explain the published density maps of other double-stranded DNA viruses and uncover their genome packaging principles.

Epigenetic phenotype of plasma cell-free DNA in the prediction of early-onset preeclampsia

Background In the current study, we sought to characterise the methylation haplotypes and nucleosome positioning patterns of placental DNA and plasma cell-free DNA of pregnant women with early-onset preeclampsia using whole genome bisulphite sequencing (WGBS) and methylation capture bisulphite sequencing (MCBS) and further develop and examine the diagnostic performance of a generalised linear model (GLM) by incorporating the epigenetic features for early-onset preeclampsia. Methods This case-control study recruited pregnant women aged at least 18 years who delivered their babies at our Hospital. In addition, non-pregnant women with no previous history of diseases were included. Placental samples of the villous parenchyma were taken at the time of delivery and venous blood was drawn from pregnant women during non-invasive prenatal testing at 12–15 weeks of pregnancy and nonpregnant women during the physical check-up. WGBS and MCBS were carried out of extracted genomic DNA. Then, we established the GLM by incorporating preeclampsia-specific methylation haplotypes and nucleosome positioning patterns and examined the diagnostic performance of the model by receiver operating characteristic (ROC) curve analysis. Results The study included 135 pregnant women and 50 non-pregnant women. Our high-depth MCBS revealed notably different DNA methylation and nucleosome positioning patterns between women with and without preeclampsia. Preeclampsia-specific hypermethylated sites were found predominantly in the promoter regions and particularly enriched in CTCF on the X chromosome. Totally, 2379 preeclampsia-specific methylation haplotypes were found across the entire genome. ROC analysis showed that the area under the ROC curve (AUC) was 0.938 (95%CI 0.877, 1.000). At a GLM cut-off of 0.341, the AUC was the maximum, with a sensitivity of 95.6% and a specificity of 89.7%. Conclusion Pregnant women with early-onset preeclampsia exhibit DNA methylation and nucleosome positioning patterns in placental and plasma DNA.

A Novel Approach to Epigenetic Profiling in Acute Myeloid Leukemia: Mapping Methylation and Hydroxymethylation in Genomic and Cell-Free DNA

Introduction: Acute Myeloid Leukemia (AML) is marked by uncontrolled growth of undifferentiated myeloid cells. DNA methylation patterns in AML have been thoroughly researched, however, studies on hydroxy methylation patterns, indicating active DNA methylation erasure, are still evolving. Our principal goal was to detect differential methylation and hydroxy methylation regions between AML and non-malignant samples. We proposed that simultaneous profiling of blood cells and circulating cell-free DNA would offer more insights into the disease mechanism. Therefore, we combined these data sources to provide a comprehensive epigenetic picture, assuming that this dual approach could reveal new AML biomarkers and enhance our understanding regarding AML pathobiology. Methods: We collected peripheral blood samples from 16 newly diagnosed AML patients (median age 64, age range 36-85) treated at Tel Aviv Sourasky Medical Center, Israel, and 33 age-matched healthy volunteers (NCT05735704). We utilized novel microarray technology to examine methylation and hydroxy methylation patterns in both genomic and cell-free DNA. Following differential methylation region extraction, we used DAVID functional annotation tool to interpret our results' biological significance. Results: This report presents the preliminary methylation data results. Methylation analysis unveiled 474 and 475 differentially methylated regions between AML and controls in genomic and cell-free DNA analysis, respectively, with only 18 common regions. The clear AML-control distinction is displayed in hierarchical clustering heatmaps (Figure 1a, 1b). Further DAVID tool analysis revealed enrichment in biological processes such as aging, cell cycle regulation, cell morphogenesis, and MAP kinase activity - processes closely linked with AML. Notably, genomic data analysis showed significant enrichment of the ‘transcriptional misregulation in cancer’ pathway, involving genes encoding vital transcription factors for cell development and differentiation. Figure 2 demonstrates the biological pathways for genomic and cell free data analysis. Conclusions: This research underscores the importance of combined epigenetic data from malignant tissue and its microenvironment, obtained by examining genomic and cell-free DNA. Both datasets exhibit striking differences between AML and control samples. We detected enrichment of AML-related biological pathways within differential regions. Our findings of enriched biological pathways align with existing literature, reinforce our analysis validity, and support our combined view of methylation patterns in genomic and cell-free DNA. By suggesting a combined view of these two types of DNA, we provide a more comprehensive perspective on AML's complex epigenetic landscape. It underscores the value of such integrative epigenetic profiling in shedding new light on the intricacies of AML development and progression, which may eventually guide the discovery of novel therapeutic targets.

Megakaryocyte- and erythroblast-specific cell-free DNA patterns in plasma and platelets reflect thrombopoiesis and erythropoiesis levels

Circulating cell-free DNA (cfDNA) fragments are a biological analyte with extensive utility in diagnostic medicine. Understanding the source of cfDNA and mechanisms of release is crucial for designing and interpreting cfDNA-based liquid biopsy assays. Using cell type-specific methylation markers as well as genome-wide methylation analysis, we determine that megakaryocytes, the precursors of anuclear platelets, are major contributors to cfDNA (~26%), while erythroblasts contribute 1–4% of cfDNA in healthy individuals. Surprisingly, we discover that platelets contain genomic DNA fragments originating in megakaryocytes, contrary to the general understanding that platelets lack genomic DNA. Megakaryocyte-derived cfDNA is increased in pathologies involving increased platelet production (Essential Thrombocythemia, Idiopathic Thrombocytopenic Purpura) and decreased upon reduced platelet production due to chemotherapy-induced bone marrow suppression. Similarly, erythroblast cfDNA is reflective of erythrocyte production and is elevated in patients with thalassemia. Megakaryocyte- and erythroblast-specific DNA methylation patterns can thus serve as biomarkers for pathologies involving increased or decreased thrombopoiesis and erythropoiesis, which can aid in determining the etiology of aberrant levels of erythrocytes and platelets.

Mucosal DNA methylome alteration in Crohn's disease: surgical and non-surgical groups.

Crohn's disease (CD) is characterized as a chronic, relapsing, and progressive disorder with a complex etiology involving interactions between host, microbiome, and the external environment. Genome wide association studies (GWAS) suggest several genetic variations in the diseased individuals but that explains only a small proportion of susceptibility to disease conditions. This indicates the possible role of epigenome which links environmental factors to the genetic variation in the disease etiology. The current study is focused on the DNA methylome evolution with disease progression. We performed Reduced Representation Bisulfite Sequencing (RRBS) to analyze differential DNA methylation in the diseased and healthy mucosal tissues of 2 different groups of CD patients: non-surgical and surgical, categorized based on the severity of disease and standard of care needed. Patients in both groups have unique DNA methylation signature compared to the healthy tissue. After removing single nucleotide polymorphisms (SNPs), 1,671 differentially methylated loci were found in the non-surgical and 3,334 in the surgical group of which only 206 were found overlapping in both groups. Furthermore, differential DNA methylation was noted in some of the GWAS associated genes implicated in CD. Also, functional enrichment analysis showed high representation of several key pathways where differential methylations were observed, and these can be implicated in CD pathogenesis. We identified specific DNA methylation patterns in the mucosal DNA of surgical and non-surgical CD patients which indicates evolution of the methylome as the disease progresses from initial to the advance stage. These unique patterns can be used as DNA methylation signatures to identify different stages of the disease.

The entanglement of DNA damage and pattern recognition receptor signaling

Cells are under constant pressure to suppress DNA damage originating from both exogenous and endogenous sources. Cellular responses to DNA damage help to prevent mutagenesis and cell death that arises when DNA damage is either left unrepaired or repaired inaccurately. During the “acute phase” of DNA damage signaling, lesions are recognized, processed, and repaired to restore the primary DNA sequence whilst cell cycle checkpoints delay mitotic progression, cell death and the propagation of errors to daughter cells. Increasingly, there is recognition of a “chronic phase” of DNA damage signaling, exemplified by the secretion of dozens of cytokines days after the inciting damage event. In this review, we focus on the cellular origin of these chronic responses, the molecular pathways that control them and the increasing appreciation for the interconnection between acute and chronic DNA damage responses.

BIOM-08. SINGLE-MOLECULE SYSTEMS FOR DETECTION OF PLASMA CIRCULATING ONCOPROTEINS IN DIFFUSE MIDLINE GLIOMA

Abstract Diffuse midline glioma (DMG) is a high-risk pediatric brain tumor that has primarily been diagnosed and monitored via medical imaging (MRI) due to risks associated with re-biopsying midline brain structures. Recent advances in molecular diagnostics have improved classification and molecular characterization of DMG; these tumors are in dire need of non-invasive, molecular-based diagnostic tools to supplement serial assessments of radiographic response. Our group recently developed a single-molecule imaging platform, Epigenetics of Plasma Isolated Nucleosomes (EPINUC), to profile histone modification patterns in cell-free tumor DNA (ctDNA) from plasma of cancer patients. We developed a novel strategy for single-molecule detection of the histone mutation H3K27M, a key DMG genetic driver, by capturing mutant nucleosomes on a PEG-streptavidin coated surface and detecting them with fluorescently labeled antibodies targeting histone modifications enriched on these mutant nucleosomes. We applied this method to 46 H3K27M and 10 H3 wildtype DMG samples and found significantly higher signal in K27M samples. Using this data, we generated a predictive model of H3 status with an AUC of 0.81, sensitivity 90%, specificity 71%, and precision 73%. This test was found to be highly reproducible and rapid (60 minutes) and required less than 100 uL of plasma. We also analyzed mutant p53 protein in plasma samples from 11 p53-mutant and 4 p53-wildtype DMG patients, seeing significant separation between the two groups. We overlayed H3K27M and p53 cell-free protein results with H3.3K27M and TP53 ctDNA variant allele fraction (VAF) by digital droplet PCR (ddPCR) in serial plasma samples from n = 3 DMG patients undergoing experimental therapy. These data highlighted unique patterns of disease response by (1) MRI, (2) plasma tumor protein, and (3) plasma ctDNA. Overall, these results demonstrate the clinical potential of our platform for non-invasive and accurate detection and monitoring of levels of key oncoproteins in plasma of DMG patients.

Murine cartilage microbial DNA deposition occurs rapidly following the introduction of a gut microbiome and changes with obesity, aging, and knee osteoarthritis

Cartilage microbial DNA patterns have been recently characterized in osteoarthritis (OA). The objectives of this study were to evaluate the gut origins of cartilage microbial DNA, to characterize cartilage microbial changes with age, obesity, and OA in mice, and correlate these to gut microbiome changes. We used 16S rRNA sequencing performed longitudinally on articular knee cartilage from germ-free (GF) mice following oral microbiome inoculation and cartilage and cecal samples from young and old wild-type mice with/without high-fat diet-induced obesity (HFD) and with/without OA induced by destabilization of the medial meniscus (DMM) to evaluate gut and cartilage microbiota. Microbial diversity was assessed, groups compared, and functional metagenomic profiles reconstructed. Findings were confirmed in an independent cohort by clade-specific qPCR. We found that cartilage microbial patterns developed at 48 h and later timepoints following oral microbiome inoculation of GF mice. Alpha diversity was increased in SPF mouse cartilage samples with age (P = 0.013), HFD (P = 5.6E-4), and OA (P = 0.029) but decreased in cecal samples with age (P = 0.014) and HFD (P = 1.5E-9). Numerous clades were altered with aging, HFD, and OA, including increases in Verrucomicrobia in both cartilage and cecal samples. Functional analysis suggested changes in dihydroorotase, glutamate-5-semialdehyde dehydrogenase, glutamate-5-kinase, and phosphoribosylamine-glycine ligase, in both cecum and cartilage, with aging, HFD, and OA. In conclusion, cartilage microbial DNA patterns develop rapidly after the introduction of a gut microbiome and change in concert with the gut microbiome during aging, HFD, and OA in mice. DMM-induced OA causes shifts in both cartilage and cecal microbiome patterns independent of other factors.

FISH painting for chromosome identification of aneuploid cauliflower (Brassica oleracea L. var. botrytis)

A common problem in the cultivation and breeding of cauliflower (Brassica oleracea L. var. botrytis) is the occurrence of aneuploids in offspring families. To reveal the chromosomal cause of such numerical variants, it was necessary to develop karyotype tools with which chromosomes can be easily identified. Since mitotic chromosomes in this crop are morphologically similar and lack differentiating banding patterns, we tested two Fluorescent in situ Hybridization (FISH) procedures for chromosome identification: (1) FISH painting with diagnostic repetitive DNA patterns and (2) cross-species chromosome painting. The first method consists of a five-colour FISH with 5s rDNA, 45S rDNA, and two Brassica rapa centromere-specific repeats, and a B. rapa BAC (KBrH092N02) containing a dispersed repeat of an unknown class. The second method is an advanced FISH technology based on hybridising DNA probes of a related species under adapted stringency conditions to identify their homoeologous loci. To this end, we applied four pools of BACs from Arabidopsis thaliana in a multicolour FISH for a banding pattern on the chromosomes of cauliflower (Brassica oleracea L. var. botrytis). Due to the genome triplication and various chromosome rearrangements of Brassica oleracea compared to Arabidopsis, we used MUMmer whole-genome alignment plot information to select Arabidopsis BAC pools with which all cauliflower chromosomes could be identified. In a sample of 21 plants with aberrant phenotypes, we demonstrated primary trisomy for chromosomes 1–6 and 8, and telo-trisomy for chromosomes 7 and 9. Finally, we discuss the advantages and drawbacks of the two painting methods and eventual alternatives for demonstrating numerical aberrations in the cauliflower populations.Graphical

DNMT3A R882H Exhibits Greater Inflammatory Potential Than R882C in Primary Hematopoietic Stem and Progenitor Cell Knock-in Model and Population Data

Clonal hematopoiesis (CH) is an age-associated phenomenon which is known to increase the risk for hematologic malignancy and cardiovascular disease. The most commonly mutated gene in CH is de novo DNA methyltransferase DNMT3A. R882H and R882C are the most common hotspot mutations in this gene, and these mutations are commonly grouped together in interpretation of clinical data even though in vitro experiments suggest divergence in their biochemical consequences. Here, we used CRISPR knock-in of primary hematopoietic stem and progenitor cells (HSPCs) along with population data from the UK Biobank (UKB) to evaluate the extent to which R882H and R882C differentially predispose to inflammatory phenotypes. Using two homology donor (HD) templates with distinct self-cleaving fluorescent tags, we used FACS to isolate homozygous R882H- or R882C-mutant cells from six unique samples of cord blood HSPCs. We subsequently cultured these isogeneic mutant cells and their mock-electroporated wild-type (WT) controls in monocyte differentiation media and evaluated their transcriptomes via bulk RNA sequencing (RNAseq) and production of secreted cytokines in a Luminex-based assay. Analysis of transcripts using differential expression for repeated measures (Dream) revealed that, when compared to WT, the mutants demonstrated many shared differentially expressed genes (DEGs) but also exhibited many DEGs unique to each variant. Furthermore, gene set enrichment analysis (GSEA) of Hallmark pathways revealed common enrichment of cell cycle related pathways in both variants, but found that R882H displayed greater enrichment of inflammation-related pathways than either WT or R882C (Figure 1A). Rank-order GO and KEGG pathway enrichment comparison of R882H vs R882C showed further evidence of bias in inflammation-related pathways among the most upregulated gene sets (e.g., GO:0019882, Antigen Processing & Presentation and KEGG:hsa04145, Phagosome). IL-6 is significantly regulated by R882 genotype in our model; levels of IL-6 for R882H (13,065 ± 2,446; mean ± s.e. in pg/mL) but not R882C (10,340 ± 2,446) were significantly different than WT (6,281 ± 1,730; p = 0.014). We next sought to better understand if this biased inflammatory priming would also be observed for heterozygous mutations and across different cell types, so using mutant and WT HD templates we performed single cell RNAseq on CRISPR'd heterozygous mutants and knock-in WT controls. Comparing R882H to R882C in this context demonstrated upregulation of numerous inflammation-related genes, including CXCL8 (IL-8), S100A8, and S100A9. GSEA of Hallmark pathways revealed enrichment of inflammatory pathways (e.g., Inflammatory Response & TNFA Signaling via NFKB) in monocytic cells but also in progenitor cells. We then investigated whether these transcriptional differences between R882H and R882C might be due to divergent patterns of DNA (hypo)methylation. Employing 5-letter next-generation sequencing (A, C, G, T, methyl-C), we compared the methylation landscape of three isogeneic donors with homozygous R882H, R882C, or mock-electroporated WT genotypes. As expected, comparison of either mutant to WT showed a global hypomethylation. Comparison of R882H to R882C revealed no systematic bias in methylation of gene promoters but a pervasive hypomethylation of gene bodies. A gene set of the 50 most upregulated genes from our single cell RNAseq experiment was significantly enriched in rank order analysis of R882H vs R882C hypomethylation of gene bodies (NES = 1.47, p = 0.036) but not promoters (NES = -0.86, p = 0.71). Finally, we asked if there were differences in patient phenotypes for those with R882H or R882C clonal hematopoiesis. Here, we used our previously published UKB clonal hematopoiesis cohort (Vlasschaert et al. 2023, Blood). In Cox proportional hazards models controlling for basic demographics (N = 451K) or demographics plus cardiovascular-relevant covariates (N = 390K), we found that R882H but not R882C was associated with significantly greater incidence of heart failure and of a composite measure consisting of death or coronary artery disease (Figure 1B). In conclusion, our study found evidence in experimental models and patient data that DNMT3A R882H may pose a greater risk for inflammatory phenotypes than R882C.

Chronic graft-versus-host disease is characterized by high levels and distinctive tissue-of-origin patterns of cell-free DNA

Chronic graft-versus-host disease (cGvHD) is a devastating complication of hematopoietic stem cell transplantation (HSCT). Effective early detection may improve the outcome of cGvHD. The potential utility of circulating cell-free DNA (cfDNA), a sensitive marker for tissue injury, in HSCT and cGvHD remains to be established. Here, cfDNA of prospectively collected plasma samples from HSCT recipients (including both cGvHD and non-cGvHD) and healthy control (HC) subjects were evaluated. Deconvolution methods utilizing tissue-specific DNA methylation signatures were used to determine cfDNA tissue-of-origin. cfDNA levels were significantly higher in HSCT recipients than HC and significantly higher in cGvHD than non-cGvHD. cGvHD was characterized by a high level of cfDNA from innate immune cells, heart, and liver. Non-hematologic tissue-derived cfDNA was significantly higher in cGvHD than non-cGvHD. cfDNA temporal dynamics and tissue-of-origin composition have distinctive features in patients with cGvHD, supporting further exploration of the utility of cfDNA in the study of cGvHD.

Application of Finite State Automaton in a Random DNA Sequence and Pattern Analysis

Application of Finite State Automaton in a Random DNA Sequence and Pattern Analysis

Multidimensional fragmentomic profiling of cell-free DNA released from patient-derived organoids

BackgroundFragmentomics, the investigation of fragmentation patterns of cell-free DNA (cfDNA), has emerged as a promising strategy for the early detection of multiple cancers in the field of liquid biopsy. However, the clinical application of this approach has been hindered by a limited understanding of cfDNA biology. Furthermore, the prevalence of hematopoietic cell-derived cfDNA in plasma complicates the in vivo investigation of tissue-specific cfDNA other than that of hematopoietic origin. While conventional two-dimensional cell lines have contributed to research on cfDNA biology, their limited representation of in vivo tissue contexts underscores the need for more robust models. In this study, we propose three-dimensional organoids as a novel in vitro model for studying cfDNA biology, focusing on multifaceted fragmentomic analyses.ResultsWe established nine patient-derived organoid lines from normal lung airway, normal gastric, and gastric cancer tissues. We then extracted cfDNA from the culture medium of these organoids in both proliferative and apoptotic states. Using whole-genome sequencing data from cfDNA, we analyzed various fragmentomic features, including fragment size, footprints, end motifs, and repeat types at the end. The distribution of cfDNA fragment sizes in organoids, especially in apoptosis samples, was similar to that found in plasma, implying occupancy by mononucleosomes. The footprints determined by sequencing depth exhibited distinct patterns depending on fragment sizes, reflecting occupancy by a variety of DNA-binding proteins. Notably, we discovered that short fragments (< 118 bp) were exclusively enriched in the proliferative state and exhibited distinct fragmentomic profiles, characterized by 3 bp palindromic end motifs and specific repeats.ConclusionsIn conclusion, our results highlight the utility of in vitro organoid models as a valuable tool for studying cfDNA biology and its associated fragmentation patterns. This, in turn, will pave the way for further enhancements in noninvasive cancer detection methodologies based on fragmentomics.

Unravelling the sexual developmental biology of Cystoisospora suis, a model for comparative coccidian parasite studies.

The apicomplexan parasite Cystoisospora suis has global significance as an enteropathogen of suckling piglets. Its intricate life cycle entails a transition from an asexual phase to sexual development, ultimately leading to the formation of transmissible oocysts. To advance our understanding of the parasite's cellular development, we complemented previous transcriptome studies by delving into the proteome profiles at five distinct time points of in vitro cultivation through LC/MS-MS analysis. A total of 1,324 proteins were identified in the in vitro developmental stages of C. suis, and 1,082 proteins were identified as significantly differentially expressed. Data are available via ProteomeXchange with identifier PXD045050. We performed BLAST, GO enrichment, and KEGG pathway analyses on the up- and downregulated proteins to elucidate correlated events in the C. suis life cycle. Our analyses revealed intriguing metabolic patterns in macromolecule metabolism, DNA- and RNA-related processes, proteins associated with sexual stages, and those involved in cell invasion, reflecting the adaptation of sexual stages to a nutrient-poor and potentially stressful extracellular environment, with a focus on enzymes involved in metabolism and energy production. These findings have important implications for understanding the developmental biology of C. suis as well as other, related coccidian parasites, such as Eimeria spp. and Toxoplasma gondii. They also support the role of C. suis as a new model for the comparative biology of coccidian tissue cyst stages.