Epigenomics

Proliferation of cytotrophoblasts (CTBs) and their differentiation into invasive extravillous trophoblasts (EVTs) are critical processes in early placental development. Defects in these processes are associated with adverse pregnancy outcomes, including recurrent pregnancy loss (RPL). There is evidence that reduced expression of the maintenance DNA methyltransferase DNMT1 in the placenta occurs in pregnancy loss and that RPL is associated with aberrant DNA methylation patterns. Therefore, we investigated the role of DNMT1 in human trophoblast growth and differentiation. Using human trophoblast stem cells (hTSCs), an in vitro analog to CTBs, we found that shRNA-mediated knockdown of DNMT1 led to decreased hTSC proliferation, genome-wide reductions in methylation, broad changes in gene expression, and impaired EVT differentiation. Transcriptome profiling of DNMT1-deficient hTSCs and hTSC-derived EVTs highlighted aberrant cytokine expression, drawing a connection to prior reports of immunological dysfunction in RPL. Finally, using a catalytic DNMT1 chemical inhibitor, we demonstrate the canonical methyltransferase activity of DNMT1 is essential for EVT differentiation and invasion. This study identifies new roles for DNMT1 in trophoblasts and addresses the molecular basis of the associations between DNMT1 expression, altered DNA methylation profiles, and RPL.

BACKGROUNDSpontaneous preterm birth (sPTB) remains the foremost cause of neonatal morbidity and mortality worldwide. Although histologic chorioamnionitis (HCA) and placental vascular abnormalities are frequently observed in sPTB, the molecular cascades linking these lesions to labor initiation remain poorly understood. Emerging evidence implicates circadian dysregulation and trophoblast dysfunction as additional drivers of sPTB. OBJECTIVEThis study aims to map placental pathology to distinct transcriptomic functional signatures that may precipitate sPTB, delineate the contribution of circadian regulation - both core-clock genes and circadian transcription-factor target sets (TFTs) - to sPTB, and identify placental cell-type-enriched and developmental pathway signatures that differ between sPTB and term deliveries. STUDY DESIGNWe performed bulk RNA sequencing on 32 formalin fixed, paraffin embedded placental specimens from 12 selected women (9 sPTB and 3 Term) in the POUCH Study cohort. Samples were selected for white ethnicity, maternal age 23-33years, and parity 1-4 to reduce heterogeneity within groups. An extraction-free HTG transcriptome panel assayed 19,398 protein-coding genes. Log2-fold changes of all genes were computed with limma adjusted for maternal age, gestational age, parity, placental region, placental pathology, and POUCHID (a clustering variable) for sPTB vs. Term and HCA/vascular lesion vs. no pathology (no placental pathology adjustment). Gene-set enrichment used 50 Hallmark sets (MSigDB) plus curated placental circadian, circadian TFT, cell-type, and developmental pathways or gene sets. RESULTSsPTB placentas displayed a global suppression of metabolic, secretory, and immune pathways (e.g., protein secretion, oxidative phosphorylation, Interferon responses, Complement, ROS, MYC Targets, TGF {beta}, mTORC1, and Coagulation) while KRAS Signaling Down and EMT were up-regulated. HCA-enriched sets (TNF/NF-{kappa}B, ROS, KRAS Up, IL-2/STAT5, Hypoxia, Interferon-{gamma}) were up-regulated, with EMT and Notch remaining down. Vascular abnormalities alone showed up-regulation of 12 Hallmark sets - including TGF-{beta}, TNF/NF-{kappa}B, ROS, pancreatic {beta}-cell stress, Hypoxia, Oxidative Phosphorylation, EMT, and mTORC1 - while Notch was down-regulated. When HCA co-exists with vascular abnormalities, the Hallmark profile becomes more inflammatory highlighting a synergistic exacerbation of innate immunity, oxidative stress, and programmed cell death with the 12 up-regulated sets (Complement, Interferon /{gamma}, TNF, ROS, Apoptosis, and Heme Metabolism). The exclusive downregulation of DNA Repair suggests compromised genomic integrity. Circadian gene-sets analysis revealed an up-regulated Regulation of Circadian Sleep Wake Cycle in sPTB but down-regulation of core clock pathway and suppressed circadian TF targets. Cell-type enrichment reveals increased trophoblast giant cells and IGFBP1-DKK1 positive fetal cells, with marked suppression of extravillous trophoblasts, syncytiotrophoblasts, villous cytotrophoblasts, and fetal myeloid cells. Placental developmental pathways were downregulated, indicating arrested trophoblast maturation. CONCLUSIONOur pilot analysis demonstrates sPTB placentas exhibit a global suppression of metabolic, secretory, and immune-modulatory programs and maladaptive trophoblast remodeling, whereas HCA and vascular abnormalities drove distinct inflammatory or hypoxic signatures. The shared and opposing Hallmark pathways across phenotypes highlight distinct yet overlapping pathogenic mechanisms. Dysregulated circadian pathways, consistent downregulated transcription factor target gene sets, and trophoblast-specific signatures implicate circadian misalignment and impaired placental maturation as key contributors to preterm parturition. These findings provide a mechanistic atlas linking placental pathology to sPTB and highlight potential targets for chronotherapeutic and cell-type-specific interventions. AJOG at a GlanceO_ST_ABSWhy was this study conducted?C_ST_ABSSpontaneous preterm birth remains a leading cause of neonatal morbidity. Histopathologic lesions of the placenta, particularly chorioamnionitis and vascular abnormalities, are common in preterm deliveries, yet the underlying molecular pathways are poorly understood. We sought to integrate functioning pathway profiles of placental histology, circadian biology, and cell types to identify mechanistic drivers of sPTB. Key findingsO_LIsPTB placentas showed widespread down-regulation of oxidative phosphorylation, mTORC1, hypoxia, interferon, and TNF/NF-{kappa}B pathways. C_LIO_LIHCA placentas up-regulated the same pathways (except androgen response), revealing a reciprocal inflammatory-hypoxic signature. C_LIO_LIVascular abnormalities displayed a distinct mix of up- and down-regulated pathways, suggesting divergent reparative responses. C_LIO_LIPlacentas with co-existing HCA and vascular abnormalities enriched more inflammatory Hallmark pathways: the 12 up-regulated sets (Complement, Interferon /{gamma}, TNF, ROS, Apoptosis, and Heme Metabolism) highlight a synergistic exacerbation of innate immunity, oxidative stress, and programmed cell death and the exclusive down-regulation of DNA Repair suggests compromised genomic integrity, which can contribute to premature placental senescence and preterm labor. C_LIO_LICircadian clock and multiple transcription-factor targets were enriched in sPTB, and trophoblast-specific signatures (giant, extravillous, syncytiotrophoblast) were prominent. C_LI What does this add to what is known?The study demonstrates a clear dichotomy between inflammatory and hypoxic molecular programs in sPTB and HCA, identifies circadian dysregulation as a potential contributor, and highlights trophoblast subpopulations as key players. These insights open avenues for targeted biomarkers and chronotherapy in preterm birth prevention.

ObjectiveTo develop and validate a cell-free DNA (cfDNA) fragmentomic classifier for the early prediction of spontaneous preterm birth (PTB) using routine first-trimester non-invasive prenatal testing (NIPT) data. MethodsA nested case-control study was conducted within a prospective multicenter Vietnamese cohort comprising 286 pregnancies, including 82 spontaneous PTB cases and 204 term controls. Maternal plasma cfDNA collected during routine first-trimester NIPT (median gestational age, 12 weeks) was sequenced to a depth of approximately 20 million reads per sample. Five fragmentomic feature categories including copy number alterations, end-motif composition, nucleosome distance, fragment length, and joint fragment-lengthxend-motif were evaluated for PTB prediction. Machine learning classifiers were developed in a training cohort (n = 228, 65 PTB vs 163TB) and tested in a validation cohort (n = 58, 17 PTB vs 41 TB). ResultsAmong the five fragmentomic feature classes evaluated, 4-mer end-motif (EM) profiles exhibited the most pronounced differences between PTB and term control samples. Consistent with these findings, the EM-based classifier demonstrated the highest discriminative performance in the validation cohort, achieving an AUC of 0.970 (95% CI, 0.912-1.000). At a specificity >90%, the model achieved a sensitivity of 94% (95% CI, 78-100%). ConclusionThese findings demonstrate that cfDNA EM signatures derived from routine first-trimester NIPT can accurately identify pregnancies at risk of spontaneous preterm birth, without additional blood collection or sequencing, thereby extending the clinical utility of existing prenatal screening infrastructure. KEY POINTSO_ST_ABSWhat is already known about this topic?C_ST_ABSO_LICurrent first-trimester prediction strategies based on maternal characteristics, cervical length, and biochemical markers have limited predictive accuracy, particularly in nulliparous women. C_LIO_LIExisting cfDNA-based approaches have shown only modest performance or require additional assays, limiting clinical applicability. C_LI What does this study add?O_LIExisting NIPT sequencing data can be repurposed (without additional blood sampling or sequencing) for accurate prediction of spontaneous preterm birth (AUC=0.970). C_LIO_LIA classifier employing 4-mer end-motif (EM) profiles achieved an AUC of 0.970. At a specificity >90%, the model achieved a sensitivity of 94%. C_LI

Background: Sequence-to-function (S2F) deep learning models are increasingly used to prioritize non-coding regulatory variants, but their behavior across ancestrally diverse populations remains unclear. Because both training data and reference resources are heavily European-centered, multi-ancestry benchmarks are needed to determine whether S2F scores capture regulatory effects consistently across populations with different allele-frequency and LD patterns. Methods: We evaluated Borzoi and AlphaGenome using whole blood eQTL data from the MAGENTA cohort, including African American (AA; N=224), Caribbean Hispanic (CH; N=209), and Non-Hispanic White (NHW; N=235) participants. Model predictions were benchmarked against sampled nominal eQTLs and ancestry-stratified SuSiE fine-mapped variants using Spearman correlation, direction concordance, inter-model convergence, and distance-matched AUROC, with sensitivity analyses for minor allele frequency and comparison-set definition. We also compared FILER functional annotation overlap among high-Posterior Inclusion Probability (PIP) variants across ancestries. Results: Both models showed weak agreement with nominal eQTL effect sizes across ancestries and TSS-distance bins ({rho}[&le;]0.138), with direction concordance only marginally above chance. Agreement and discrimination improved for high-confidence fine-mapped variants, and Borzoi and AlphaGenome showed stronger inter-model convergence on fine-mapped variants than on nominal eQTLs, consistent with enrichment for regulatory variants whose effects are more apparent to sequence-based models. In distance-matched AUROC analyses at PIP [&ge;]0.9 using PIP <0.01 variants as low-PIP comparison variants, the AA high-PIP variant set yielded the highest discrimination for both Borzoi (0.837 [95% CI: 0.790-0.870]) and AlphaGenome (0.820 [0.793-0.845]). The CH-versus-NHW ordering was model-dependent: Borzoi yielded higher AUROC in NHW than CH, whereas AlphaGenome produced nearly identical CH and NHW estimates. AUROC values were lower when intermediate-PIP variants were used as comparison variants, but the AA set retained the highest discrimination. MAF-stratified sensitivity analyses attenuated some ancestry contrasts but did not eliminate the higher AA discrimination pattern. Functional annotation analysis showed that AA high-PIP variants more often overlapped chromatin accessibility and chromatin-contact annotations than NHW variants, despite lower overlap with prior eQTL and sQTL annotation catalogs. Conclusions: Borzoi and AlphaGenome showed limited agreement with nominal eQTL effect sizes, but better distinguished high-confidence fine-mapped eQTLs from low-PIP variants. These results support using S2F scores as prioritization evidence for fine-mapped regulatory variants, especially promoter-proximal high-PIP variants, rather than as standalone predictors of eQTL effect size. The strongest discrimination was observed for the AA high-PIP variant set. Overall, the AA result is best interpreted as stronger separation of high-PIP variants from lower-PIP comparison variants, shaped by fine-mapping resolution, LD, the choice of comparison variants, and annotation composition.

Pulmonary hypertension (BPD-PH) associated with bronchopulmonary dysplasia (BPD) in preterm infants associates with high morbidity and mortality within the first two years of life. In a previous unbiased study, we identified a panel miRNAs in tracheal aspirates (TA) that were differentially expressed in extremely low gestational age newborns (ELGANs) with BPD-PH compared to those with BPD but no PH. To explore the predictive potential of these miRNAs, we studied TA exosomes from 7 days old ELGANs and analysed a curated panel of 16 miRNAs through logistic regression and calculated the predictive AUROC to diagnose BPD-PH at 36 weeks PMA. AUROC of TA miRNAs was 0.76 with sensitivity and specificity of 53% and 93%, respectively. Adding sex and gestational age to the variables improved the AUROC to 0.78 with sensitivity and specificity of 61 and 87% respectively. Due to challenges of obtaining TA in non-invasively ventilated infants, we collected saliva samples from ELGANs at 7 days of age and compared the log expression of these 16 miRNAs in both biofluids and found significant correlation in their expression (pearson r=0.92, p<0.001). We calculated the predictive AUROC of the same miRNAs to diagnose BPD-PH at 36 weeks PMA. AUROC of these miRNAs in saliva was = 0.85 with sensitivity and specificity of 82% and 72%, respectively; addition of biological sex and gestational age improved AUROC to 0.86 with sensitivity and specificity of 79% and 76% respectively. Leave-one-sample-out sensitivity analysis demonstrated stable training performance with reduced performance in testing samples, supporting the need for validation in larger independent cohorts. In conclusion, early salivary miRNAs have great potential for risk stratification of ELGANs to develop BPD-PH, while also providing the opportunity to identify target molecules and mechanisms that modulate molecular function.

BackgroundPrenatal cannabis use is becoming increasingly more commonplace. However, cannabis exposure is linked to adverse pregnancy outcomes, including gestational hypertension, preeclampsia, and preterm birth. The aim of this study was to determine the morphological and molecular effects of prenatal cannabinoid exposure on the placenta. MethodsPregnant Sprague-Dawley rats were exposed daily to vaporized THC (100 mg/mL) starting at gestational day (GD)5 until GD19 when dams were sacrificed and fetuses and placentas collected. Fetuses were genotyped for genetic sex and transcriptomic analysis was performed on male and female THC-exposed and control placentas. ResultsOn GD19, both the fetuses and placentas from the THC group were significantly larger than the control. When separated by sex, both male and female THC fetuses were significantly larger; however, only male THC placentas were significantly larger than male control placentas with no significant difference in placental weight between female control and THC placentas. RNA-sequencing revealed enriched biological processes related to nutrient transport and lipid catabolism, protein-lipid complex formation, and lipoprotein particle remodeling and organization. Further transcriptomic analysis determined that the differentially expressed genes and enriched biological processes related to lipid metabolism were preferentially enriched in the female THC placentas compared to the male, suggesting a sex-specific effect. DiscussionCollectively, these data present sex-specific effects of prenatal cannabinoid exposure on placental growth and global gene expression. These data also suggest that sex influences gene expression of genes related to lipid metabolism in the THC-exposed placentas.

IDH1 R132 mutations are among the most frequent hotspot mutations in cancer, but their mutational origins have remained unclear. Here, we provide evidence that IDH1 R132C, the predominant IDH1 mutation in cholangiocarcinoma, acute myeloid leukemia, and melanoma, likely arises through APOBEC3-mediated mutagenesis. IDH1 R132C is a TpC>TpT substitution on the lagging-strand DNA template within a hairpin-forming sequence context, consistent with APOBEC3 susceptibility. In vitro assays showed that APOBEC3A can deaminate the relevant cytosine, and APOBEC3A and APOBEC3B were relatively highly expressed in tumor types with recurrent IDH1 R132C mutations. IDH1 R132G, a TpC>TpG substitution at the same site, may similarly result from APOBEC3 activity. By contrast, IDH1 R132H, the predominant IDH1 mutation in lower grade glioma and glioblastoma, is a CpG>TpG substitution at a methylated cytosine on the leading-strand DNA template, a pattern more consistent with DNA polymerase epsilon replication error. Concordantly, tumor types enriched for IDH1 R132H showed relatively low POLE expression. Together, these in vitro and bioinformatic analyses provide insight into the distinct mutational mechanisms that likely underlie recurrent IDH1 hotspot mutations in cancer.

Trimethylamine n-oxide (TMAO) is a plasma metabolite linked to adverse cardiometabolic health with complex regulation involving diet, sex, and host genetics. We explored the role of these factors in the genetic regulation of TMAO by performing a primary-level meta-analysis in 1,482 female and male Diversity Outbred (DO) mice from five distinct studies conducted in various regions of the United States. We identified a quantitative trait locus (QTL) associated with TMAO concentration at [~]86 megabase pairs on mouse chromosome 12 with a highly significant LOD score of 67.67. Alleles at the chromosome 12 QTL inherited from the Cast/EiJ (CAST) and PWK/PhJ (PWK) mouse strains primarily drove the association with reduced TMAO concentrations. The chromosome 12 QTL remained significant in sex-stratified analyses and the mode of inheritance appeared additive; furthermore, the QTL was regulated by sex-by-genotype and sex-by-diet interactions. Using a CAST/EiJ X C57BL/6J F2 cross, positional candidates were prioritized by eQTL analysis. Further analysis in a study utilizing the eight DO founding strains identified that Acyp1 was differentially expressed in hepatic tissue from CAST mice, prompting investigation into its genetic regulation. Acyp1 demonstrated relevant cis- and trans-regulation and was significantly correlated with TMAO and hepatic Fmo3. However, no significant relationships between Acyp1 and TMAO were identified in mice inactivated for Acyp1 or with AAV overexpression of Acyp1 in the liver. Genes within the chromosome 12 QTL have synteny with humans and may translate to the genetic regulation of human plasma TMAO concentrations and atherosclerosis. Author SummaryWe explored the roles of diet, sex, and genetics on the regulation of fasting plasma trimethylamine n-oxide (TMAO) concentration by performing a meta-analysis in 1,482 female and male Diversity Outbred (DO) mice from five unique studies. We identified a QTL associated with TMAO concentration on chromosome 12 at [~]86 mega base pair (Mb) with a highly significant LOD score of 67.67. The locus is modified by both sex and diet.

Background Complex traits are influenced by numerous variants, most of which have regulatory effects on gene expression that can be mediated by DNA methylation. Molecular QTL mapping is an approach that aims to dissect these effects. However, obtaining molecular phenotypes on a large scale is challenging, particularly in livestock species. In cattle, an epigenotyping array called EpiChip has recently been developed in the European RUMIGEN project. The EpiChip, which contains 43,317 CpG sites distributed all over the bovine genome, enables large-scale measurement of DNA methylation. This study aims to characterize the genetic determinism of blood DNA methylation in cows by estimating heritability and mapping cis- and trans-methylation QTLs (meQTLs). Results Whole blood samples from 4,457 genotyped Holstein cows were epigenotyped. Across all CpG sites, the heritability estimates averaged 24.6%. The local meQTL mapping at sequence-level for variable CpG sites (SD > 2.5%; n = 28,806) detected cis-meQTLs for 80.1% of the CpG sites, with sentinel SNPs located close to their associated CpGs. A two-step analysis was also conducted to identify long-range associations, with a particular focus on trans-meQTL hotspots. First, we identified CpG-SNP trans-associations using medium-density genotypes (50k SNPs) that revealed 31,846 SNPs with significant effects on 1 to 530 trans-CpG sites. Then, regions associated with at least 34 independent trans-CpGs were retained defining 31 hotpots. For each hotspot, a local sequence-level GWAS was conducted using the first principal component derived from the associated trans-CpGs. Out of the 31 detected hotspots, three were located close to transcription factor genes (RUNX1, NFIC and FOXA3) for which the associated trans-CpGs were enriched for the corresponding binding motif. Two other hotspots were located within KDM5A and KDM5B, and their corresponding trans-CpGs were strongly overrepresented in H3K4me3 narrow peaks in blood as well as in other tissues. Conclusions By identifying functional candidate genes associated with blood DNA methylation in cattle, these findings provide new insights into the regulatory architecture of DNA methylation in mammals, highlighting the value of large-scale molecular data from livestock populations.

PURPOSE Colorectal cancer (CRC) incidence and mortality rates differ by population, and evidence suggests that genetic differences may affect cancer biology. However, studies investigating CRC variants in genetically heterogeneous populations are limited. Using somatic tumor mutation profiling of CRCs diagnosed in African Americans (AAs), Ghanaians, Ethiopians, and NHWs, we explore correlations between population group and population-specific tumor variants. PATIENTS AND METHODS Somatic DNA from CRC tumors resected from 150 individuals, including 43 AAs (27%), 53 NHWs (35%), 21 Ghanaians (14.2%), and 33 Ethiopians (22.3%), was sequenced on the Illumina NovaSeq platform, targeting 290 genes. We compared mutations in AAs, Ghanaians, and Ethiopians to those in NHWs to identify variants enriched in historically underrepresented groups. RESULTS US cohort tumors were diagnosed at significantly younger ages with more early-onset cases (<50 years old) than African cohorts (p <0.05). Significant differences were observed in primary tumor location, MMR phenotypes, KRAS mutations, and distribution of tumor mutational burden by population. BRAF V600E mutations were rare across all groups, while non-V600E BRAF mutation rates were higher in AA and NHW (43-44%) than Ethiopian and Ghanaian (14-33%) samples. Population-specific differences were identified in mutation rates of APC, CTNNB1, RNF43, PIK3CA, and TP53, as well as in pathogenic variant occurrence.

Long non-coding RNAs (lncRNAs) and single nucleotide polymorphisms (SNPs) within them play crucial role in cancer susceptibility and disease outcomes. Breast and ovarian cancers, characterized by genetic heterogeneity, present significant challenges for precise diagnosis and treatment. Despite recent advancements in personalized medicine, inclusion of lncRNA-SNP (LSNP) markers into cancer risk detection panels remains limited. In this work, we put forward lncRNA-SNP regulated gene expression-based breast and ovarian cancer risk prediction model LsGCRPred (LSNP-Gene Interaction Based Cancer Risk Prediction Model). Notably, our approach accounts for the tissue-specificity of lncRNAs as well the benefit for individuals with predisposing conditions. Additionally, pathway analysis revealed the involvement of the LSNP interacting genes in key cancer regulating pathways. TaqMan genotyping and qPCR were performed to confirm the presence of selected LSNPs in ovarian and breast cancer cell lines along with the significant expression of the lncRNA and associated gene transcripts. These findings highlight previously overlooked genetic variants within lncRNA loci and their regulatory impact on disease outcomes, providing insights into personalized cancer diagnosis and treatment strategies. The tool LsGCRPred can be accessed as a standalone version on GitHub. Github Link: https://github.com/zglabDIB/LsGCRPred

Autism development involves multiple genetic and early-life environmental factors. Studying the placenta's gene expression profile may reveal key mechanistic pathways in autism development. Here, using a nested case-cohort design within an Australian population-derived prebirth cohort study (n=1074), we identified 1,644 differentially expressed genes (DEGs; FDR<0.05) in the placenta of children with autism diagnosis (n=43), compared to those without (n=120). The top enriched pathways related to mitochondrial translation, oxidative stress, RNA processing and transcription regulation. CYP1A1, the most important xenobiotic-metabolising enzyme of the placenta, was the top downregulated DEG in the placenta of children with autism, while immuno-regulatory human leukocyte antigen (HLA)-related genes were among the top upregulated DEGs. A machine learning-based approach predicted autism from the transcriptomic data with a median sensitivity of 0.57 (2.5th-97.5th centiles: 0.29, 0.76) and median specificity of 0.92 (2.5th-97.5th centiles: 0.78, 0.98). Weighted Gene Correlation Network Analysis identified eight affected placental gene modules, with the largest five modules being enriched primarily for mitochondrial bioenergetics, oxidative phosphorylation and RNA processing pathways. This placental transcriptomic signature of impaired mitochondrial function and gene transcription regulation among infants subsequently diagnosed with autism has profound implications for understanding both risk factors and prediction, suggesting the possibility of identifying modifiable prenatal pathways to improve autism outcomes.

Background The relationship between total cell-free DNA (cfDNA) concentration and multi-cancer early detection (MCED) sensitivity is non-obvious on account of competing considerations. On the one hand, this concentration is elevated in cancer and increases in advanced disease, suggesting higher concentrations may be associated with more biologically active tumors that are easier to detect. On the other hand, this elevation is known to be largely leukocyte-derived, which may dilute tumor-derived DNA (ctDNA) and make detection harder. The net direction of these competing effects on detection sensitivity has not been systematically examined. Methods EMERGE is an observational case-control study conducted at 43 Indian sites from June 2022-February 2025. It prospectively enrolled and analyzed 1,030 treatment-naive participants with malignant or benign conditions, most presenting symptomatically, along with 450 controls aged [&ge;]50 years without prior malignancy. Plasma cfDNA underwent targeted hybrid-capture enzymatic methylation sequencing. Classifiers were trained for cancer detection and tissue-of-origin prediction, and tested on the independent validation set. Primary outcomes were the associations between total cfDNA concentration and (i) detection sensitivity and (ii) tissue-of-origin accuracy, evaluated in an independent validation cohort. Results After adjustment for cancer type, stage, demographic and technical covariates, cfDNA concentration was significantly associated with detection sensitivity (p=6x10-4) but not with tissue-of-origin accuracy (p=0.67). At 0.986 specificity (95% CI: 0.968-1.000), stage I sensitivity rose monotonically from 0.52 (95% CI: 0.34-0.69) in the lowest cfDNA concentration tertile to 0.85 (95% CI: 0.73-0.97) in the highest. This association was mechanistically supported by a region-specific increase in hypermethylation scores within regions identified as differentially hypermethylated in TCGA tumor tissue, while panel-wide scores declined. The dissociation between the concentration-sensitivity and concentration-tissue-of-origin associations, together with inverse or insignificant correlations between ctDNA fraction and cfDNA concentration at early stages in published datasets, suggests that the concentration-sensitivity association is partly independent of ctDNA fraction. Conclusions Total cfDNA concentration is a routinely measured determinant of MCED assay sensitivity, reflecting enrichment of tumor-associated aberrant methylation partly independent of ctDNA fraction, an association likely most pronounced in symptomatic cohorts. Standardized reporting of cfDNA concentration could improve cross-study benchmarking. Study Registration Clinical Trials Registry, India: CTRI2022/05/042936 Keywords Cell-free DNA (cfDNA), Tumor Fraction, Circulating Tumor DNA (ctDNA), Circulating Mutant Allele Frequency (cMAF), Multi-cancer early detection (MCED), cfDNA Concentration, Tissue-of-Origin (TOO), Methylation, Epigenomics

Cigarette smoking induces complex signaling disruptions that contribute to diseases such as COPD and lung cancer, yet the molecular mechanisms underlying these effects remain incompletely understood. To address this gap, we analyzed peripheral blood from 3190 COPDGene participants using LIONESS and PUMA and constructed miRNA-mRNA regulatory networks associated with smoking status. Comparing networks for active versus former smokers uncovered a striking shift in regulatory architecture: active smokers exhibited elevated miRNA targeting of the mitochondrial complex I protein NDUFA12. This finding was validated in lung tissue expression data from the Lung Genomics Research Consortium (LGRC), where we observed that ever-smokers showed consistent dysregulation of Ndufa12-targeting miRNAs compared to never-smokers. This allowed us to identify a set of smoking-defined circulating and tissue-associated miRNAs. To investigate the specific cellular compartment, we analyzed cell-type deconvoluted expression data from COPDGene blood and LTRC (Lung Tissue Research Consortium) lung tissue, as well as lung transcriptomics data from cigarette smoke-exposed mice, and identified the monocyte/macrophage compartment as a principal site of NDUFA12/Ndufa12 expression. Human THP-1 macrophages treated with cigarette smoke extract demonstrated selective inhibition of NDUFA12 by network-defined miRNAs. These distinct, NDUFA12-targeting, smoking-associated miRNA signatures, revealed through network analysis, describe new smoking-mitochondrial interactions that may serve as novel targets for therapeutic intervention.

Chromatin-based genomics data are essential for understanding genome regulation and the mechanisms underlying epigenetic memory. Recent methods such as ChOR-seq and SCAR-seq assess histone modifications and chromatin-associated proteins during and after replication, capturing chromatin states that contribute to memory across cell divisions. Current tools for chromatin data analysis lack scalability and reproducibility across computing infrastructures, offer limited parameters, and are applicable only to a few sequencing techniques, ignoring the information from nascent chromatin assays. To address these challenges, we developed CREPAS, a Nextflow pipeline for analyzing nascent and parental chromatin sequencing data, including ChIP-seq, ChOR-seq, SCAR-seq, OK-seq, ATAC-seq, CUT&RUN, and CUT&Tag, and derivative protocols. CREPAS provides an end-to-end solution, from quality control to advanced analyses, including downsampling, peak calling, annotation, and visualization. By harnessing quantitative assays such as qChIP-seq and qChOR-seq, the normalization methods in CREPAS allow to compare the restoration kinetics of individual marks or proteins across replication timepoints. Moreover, the pipeline includes calculations such as fork directionality and partitioning using OK-seq and SCAR-seq data, linking replication dynamics to epigenetic inheritance. CREPAS is a valuable resource that enhances the efficiency and reproducibility of nascent chromatin sequencing data analyses, enabling the study of chromatin replication and propagation of epigenetic states. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=80 SRC="FIGDIR/small/732899v1_ufig1.gif" ALT="Figure 1"> View larger version (24K): org.highwire.dtl.DTLVardef@29ad26org.highwire.dtl.DTLVardef@26b9acorg.highwire.dtl.DTLVardef@67dcb8org.highwire.dtl.DTLVardef@cbc299_HPS_FORMAT_FIGEXP M_FIG C_FIG

MYC oncoprotein binding at promoters and enhancers influences RNA polymerase II (RNAPII)-driven gene expression. Numerous genes also bind MYC near their transcriptional end sites (TESs). This often allows direct promoter-TES contact via looping and further regulates total and 'read-through' transcription that extends beyond standard termination sites. We aimed here to better clarify the rules governing TES associated MYC and/or RNAPII binding cross-talk in human and murine cells. Using ChIPseq and RNAseq datasets from the ENCODE portal and elsewhere, MYC and RNAPII binding profiles were found to differ around TESs and transcriptional start sites (TSSs). Variations in E box flanking sequences likely accounted for the somewhat lower affinities of MYC for TES-associated sites. Motifs for numerous other transcription factors were also observed to cluster non-randomly and in close proximity to MYC and RNAPII binding site peak summits. On average, genes with TES-proximal MYC or RNAPII sites were more highly expressed than those without, although co-binding tended to be suppressive. Both normal and neoplastic proliferative stimuli altered the MYC and RNAPII binding patterns of many genes, indicating that 'category switching' was common, subject to disparate external signals and often reversible. Functionally related gene sets with high levels of read-through transcription were uniformly marked by significant amounts of TES-associated MYC and/or RNAPII binding. These findings indicate that, both independently and together, MYC and RNAPII binding near TESs dynamically impact total and read-through transcription while also coordinating the expression of many common purpose gene sets.

Whole-genome sequencing identifies focal DNA amplifications with base-pair resolution but cannot determine whether amplified sequences reside on extrachromosomal DNA (ecDNA, also known as double minutes) or within chromosomally integrated homogeneously staining regions (HSRs). DNA fluorescence in situ hybridization (DNA-FISH) metaphase spreads remain the gold standard for distinguishing these amplification states at single-cell resolution. Here, we present a detailed protocol for DNA-FISH metaphase spreads using human cancer cell lines, encompassing cell culture, metaphase arrest, hypotonic treatment, fixation, chromosome spreading, fluorescent probe hybridization, and fluorescence imaging. The protocol incorporates intermediate quality-control steps to verify successful chromosome dispersion and optimize metaphase spread quality, making the workflow accessible to laboratories without specialized cytogenetics expertise. Results demonstrate clear visualization of ecDNA and HSR amplification states using locus-specific probes and illustrate common technical artifacts that can affect interpretation. This protocol provides a robust and reproducible approach for studying the structural organization of oncogene amplification in cancer cells.

The Developmental Origins of Health and Disease (DOHaD) hypothesis proposes that the perinatal environment shapes susceptibility to complex traits across life [1]. The placenta, a transient organ mediating maternal-fetal exchange, plays a central role in this process and has emerged as a key molecular archive in utero [2-4]. Placental DNA methylation (DNAm) is a unique mediator between prenatal exposures, fetal genetics and later-life outcomes [5-9]. DNAm quantitative trait loci (mQTL) have helped disentangling causal mechanisms underlying GWAS loci for complex diseases [10-15]. Despite growing evidence that placental genomic regulation has broad and profound effects on the developmental programming of early- and later-life health outcomes [17], existing placental studies remain limited in scale and largely focused on growth- and neuro-related traits [12-16]. Here, we construct a high-resolution placental mQTL resource and systematically investigate how placental DNAm relates to early- and later-life traits, and to shared vulnerability and complex interactions among them.

Aberrant changes in circulating cell-free mitochondrial DNA (ccf-mtDNA) across gestation are associated with adverse pregnancy outcomes. Given the inflammatory properties of ccf-mtDNA via pattern recognition receptors such as Toll-like receptor 9 (TLR9), we hypothesized that extracellular mtDNA induces placental inflammation via TLR9 signaling and that this response differs by fetal sex. Pregnant Sprague-Dawley rats were treated intravenously with purified mtDNA (300 g/kg), nuclear DNA (nDNA), saline, and/or the TLR9 antagonist ODN2088 across five studies. Placental responses were evaluated 4 h (Studies 1-3) and 24 h (Study 4) post-treatment; pregnancy and neonatal outcomes were assessed at delivery (Study 5). Exposure to mtDNA, but not nDNA, increased placental il1{beta}, tnf, and il10 mRNA (p < 0.05), establishing response specificity. mtDNA-induced placental inflammation was fetal sex-dependent: mtDNA increased il6 and il1{beta} mRNA in male placentas (p [&le;] 0.0004) but not female placentas, whereas ifn{gamma} was selectively induced in female placentas (p = 0.0004). TLR9 and MyD88 abundance increased in female but not male placentas, and TLR9 antagonism modified selected inflammatory responses with sex-specific patterns. The 4 h inflammatory transcriptional signature resolved by 24 h, whereas mtDNA exposure was associated with a sex-specific shift in antioxidant enzyme expression persisting to 24 h. Despite no effects on gestational length or neonatal biometrics, mtDNA exposure was associated with a higher estimated stillbirth count per litter (IRR = 4.23, 95% CI [0.89, 20.1], p = 0.069). These findings establish extracellular mtDNA as an acute, sex-differentiated placental inflammatory stimulus with partial TLR9 dependence and a potential impact on fetal viability. New & NoteworthyThis study demonstrates that acute exposure to extracellular mtDNA induces placental inflammatory responses in vivo. This response is specific to mtDNA, fetal-sex dependent, and partially mediated by TLR9, with male and female placentas engaging distinct inflammatory signals within hours of exposure. The biological effects extend beyond the initial inflammatory window, with mtDNA exposure producing lasting, sex-specific changes in antioxidant enzyme expression. mtDNA-exposed dams had higher expected stillbirth counts, suggesting extracellular mtDNA may affect fetal viability.

The early onset of labour increases mortality and developmental risks for a human newborn. Key genes in human labour have been investigated using multiple modalities, but their regulation by non-coding RNA (e.g. lncRNA and miRNA) remains incomplete. This study explores the three-way relationship between labour-associated transcription factors (TFs), miRNA and lncRNA suggested by the competing endogenous RNA (ceRNA) hypothesis, to understand the underlying regulatory framework. Experimentally validated miRNA-lncRNA interactions are modelled using five distinct machine learning (ML) architectures to predict 20469 labour-linked miRNA-lncRNA interactions. Known mRNA-ncRNA interactions from databases were included to construct a tripartite network, and a subset of 9989 labour-linked network motifs containing TFs were isolated and analysed. Gene enrichment of nodes in TF-lncRNA-miRNA network, as well as validation from public myometrial datasets indicate high significance in contractile pathways including immune signalling. Experimentally unconfirmed tripartite network motifs have been found, and we elaborate on their potential regulation in labour using 8 TF-lncRNA-miRNA network motifs. A unified ncRNA-TF regulatory atlas in labour has been synthesized, and a complete summary of the tripartite network motifs can be accessed and visualised using the user-friendly, public database.