Epigenomics

Background: Preeclampsia (PE) is a hypertensive pregnancy disorder with contributions from both maternal and fetal genetic factors, but how both genomes regulate placental transcription remains incompletely understood. Results: We analyzed placental 5'-end RNA sequencing data from 59 pregnancies in the FINNPEC cohort and performed separate maternal and fetal cis-eQTL analyses using gene-level expression and promoter-level expression defined as Transcript Far 5' Ends (TFE). Genotype-by-PE interaction models were used to identify genetic effects that differ according to PE status. No gene-level interaction eQTLs remained significant after multiple-testing correction, although suggestive signals included LILRB2 in the maternal and LPCAT3 in the fetal analyses. In contrast, we identified two significant syntenic promoter-level interaction eQTLs: rs12504642-TFE61820 at the FHDC1 locus in the maternal analysis and rs1557150-TFE9032 at the PPIAP31 locus in the fetal analysis. Conclusion: These findings suggest that PE-dependent genetic interaction effects may be detectable at specific transcript promoter regions even when they are not captured at annotated gene levels.

Prenatal alcohol exposure (PAE) can produce persistent alterations in mammary development and increase susceptibility to mammary tumorigenesis, but the early molecular events underlying these effects remain poorly understood. Here, we examined whether PAE alters the molecular program of the mammary gland at birth. Pregnant MMTV-ErbB2 mice received control or ethanol-containing liquid diets during gestation, and mammary tissues were collected from newborn female offspring. RNA sequencing revealed exposure-level-dependent transcriptional reprogramming, with substantially broader alterations following moderate compared with lower ethanol exposure. Pathway analyses identified prominent changes in metabolic and growth-regulatory networks, including insulin signaling, with coordinated alterations in components of the insulin/IGF-IRS-PI3K/AKT pathway. Biochemical analyses further demonstrated exposure-dependent changes in IGFBP expression and IRS1 abundance and phosphorylation, supporting remodeling of insulin/IGF-associated signaling. Transcriptomic analyses also revealed enrichment of RNA metabolic and translational processes and, particularly following moderate exposure, enhanced DNA-replication, cell-cycle, and mitotic programs. These molecular signatures were accompanied by increased proliferative features in newborn mammary tissue. Together, these findings demonstrate that PAE establishes substantial molecular reprogramming of the mammary gland by birth and identify altered insulin/metabolic signaling and proliferative programming as prominent features of this early developmental response.

Background: Infants <30 weeks gestational age (very preterm (VPT)), are at risk of experiencing multiple serious neonatal morbidities. These morbidities impart serious biological stress, which may be reflected in dysregulated protein expression even after the morbidities have resolved. Recent studies suggest that DNA methylation-based predictors of circulating proteins may reflect the molecular effects of neonatal adversity. The objective of this study is to examine associations between DNA methylation-derived EpiScores, which are externally trained methylation signatures that proxy circulating protein levels, and neonatal morbidity burden in children born VPT. Buccal DNA methylation was obtained at NICU discharge in 537 infants from the NOVI cohort. A total of 111 EpiScores were calculated and tested for association with multimorbidity (0-1 vs. [&ge;] 2 morbidities) using adjusted linear regression models. Cross-tissue analyses in an external paired blood-buccal dataset (n=21) were used to identify EpiScores with moderate-to-strong correlations across tissues. Results: Eighteen EpiScores were nominally associated with multimorbidity (p < 0.05), with Melanoma-derived growth regulatory protein (MIA) with FDR < 0.05 (beta = 0.0023, p = 0.0004). In cross-tissue analyses, 35 EpiScores yielded r > 0.50 (p<0.05), 11 of which showed nominal associations with multimorbidity, including MIA. Overall, the morbidity-associated EpiScores reflected immune, inflammatory, metabolic, and growth-related pathways. Conclusions: Buccal DNA methylation-derived EpiScores capture biological signatures associated with neonatal morbidity burden in very preterm infants.

Minor introns are rare but evolutionarily conserved introns in the human genome. Defects in minor spliceosome components have been reported to cause several human diseases. Mutations in ZRSR2 are frequently observed in myelodysplastic syndrome (MDS) patients. However, the precise molecular mechanism by which these mutations cause a loss of ZRSR2 function in minor intron splicing remain elusive. In this study, we characterized the impact of MDS-causing missense mutations in ZRSR2. Most of the mutant ZRSR2 proteins we tested showed different subnuclear localization pattern from that of wild-type ZRSR2 protein. Co-immunoprecipitation (co-IP) analysis revealed that UHM missense mutations disrupted the interaction between ZRSR2 and SF3B complex. We also demonstrated that ZRSR2 preferentially immunoprecipitated minor spliceosome components over major spliceosome components and it directly interacts with SF3B1. Furthermore, co-IP analysis utilizing a variety of ZRSR2 mutants revealed that mutations in the UHM and Zn2 domains significantly attenuated the interaction with SF3B complex. Finally, UHM and Zn2 mutations markedly disrupted the supporting activity of ZRSR2 for minor intron splicing. Our results indicate that disruption of the physical interaction with SF3B complex is one of the hallmarks of MDS-causing mutations of ZRSR2, which results in aberrant splicing of minor introns.

Fetal development is highly sensitive to environmental influences, including maternal smoking during pregnancy (MSDP) and air pollution. The placenta may play a central role in mediating these effects through epigenetic mechanisms, including small non-coding RNAs (sncRNAs). While most studies have focused on microRNAs (miRNAs), other sncRNA classes remain poorly characterized. Here, we characterized the placental sncRNA landscape and investigated its associations with prenatal exposure to MSDP and air pollution. The sncRNA expression profile of 390 chorionic villi samples from the Barcelona Life Study Cohort (BiSC) was measured using small RNA sequencing and the seqBuster/seqCluster pipeline. MSDP was assessed via questionnaire, and prenatal exposure to black carbon (BC), particulate matter [&le;]2.5 m (PM2.5), and nitrogen dioxide (NO2) was estimated using hybrid dispersion-land-use regression (LUR) spatiotemporal models. Associations were evaluated using linear regressions adjusted for relevant covariates. We identified 979 placental sncRNA clusters, assigned primarily to miRNAs (33.2%), piRNAs (26.4%), snoRNAs (12.2%), tRFs (7.8%), and others (20.4%). MSDP was associated with the downregulation of miR-421 and the upregulation of multiple snoRNAs from the imprinted DLK1-DIO3 locus (SNORD113-4, SNORD114-2, SNORD114-3, and SNORD114-17), as well as the piR-26394. No sncRNAs remained significantly associated with air pollution after multiple-testing correction, although several miRNAs showed suggestive associations. Overall, this study provides a comprehensive characterization of placental sncRNAs and identifies previously unreported smoking-associated sncRNAs within the imprinted DLK1-DIO3 locus, expanding our understanding of placental epigenetic responses to prenatal environmental exposures.

In utero alcohol exposure (IUE) can alter mammary development and increase mammary tumor susceptibility in experimental models. However, most previous studies have relied on carcinogen-induced or genetically tumor-prone models, leaving it unresolved whether prenatal alcohol exposure produces mammary developmental and molecular changes before the introduction of an oncogenic challenge. Here, we addressed this question using non-tumorigenic C57BL/6 mice. Pregnant dams received a Lieber-DeCarli liquid diet containing 1.7% (v/v) ethanol or an isocaloric control diet from gestational day 11 to 19, and mammary glands from female offspring were examined during puberty (postnatal day 40, PND40) and young adulthood (PND70). At PND40, IUE enhanced mammary ductal morphogenesis, increased terminal end bud numbers, and elevated epithelial proliferation. These developmental alterations persisted at PND70, with increased lateral branching and proliferative activity. IUE also altered mammary epithelial composition, expanding the basal/myoepithelial compartment and the CD24highCD49fhigh mammary repopulating unit/stem cell-enriched population. Mammary epithelial cells from IUE-exposed offspring exhibited increased colony-forming cells (CFCs), mammosphere formation, and 3D Matrigel growth, indicating enhanced stem/progenitor-associated activity. At the molecular level, IUE increased ER; expression and phosphorylation together with Cyclin D1, c-Myc, E2F1, and Bcl-2, and enhanced AKT, ERK, and STAT3 phosphorylation, IL-6 expression, and SOX2 at PND40. Importantly, major components of this signaling phenotype remained altered at PND70, including ER;-associated signaling, AKT/ERK activation, and IL-6/STAT3 signaling, whereas the pubertal increase in SOX2 was not sustained. Together, these findings demonstrate that prenatal alcohol exposure induces profound and persistent histomorphological, cellular, and signaling alterations in the mammary gland in the absence of a carcinogenic challenge or genetically introduced oncogenic driver. These results identify intrinsic developmental reprogramming of normal mammary tissue as a potential basis through which prenatal alcohol exposure may modify subsequent responses to tumor-promoting or other environmental challenges.

Recurrent pregnancy loss (RPL) affects 5% of couples worldwide. Over half of cases remain unexplained (uRPL), in part because paternal factors are rarely evaluated beyond paternal karyotype. Sperm DNA methylation is a putative paternal contributor to RPL. Using ONT direct whole methylome sequencing, we generated the first and largest cohort of locus-resolved, single-molecule sperm methylome maps from men with uRPL to date (n=39). We identified 294 differentially methylated regions (DMRs), of which 158 (53.7%) overlapped AluY repetitive elements, representing significant enrichment (z=40.9); most were hypomethylated in uRPL sperm and spanned the full length of individual AluY insertions. Because of single-molecule resolution, we show that the methylation differences found in uRPL sperm occur in a subpopulation of sperm rather than a uniform DNA methylation change across all sperm. Affected loci were underrepresented for imprinting-associated chromatin marks and instead overrepresented for H2A.Z. Although DMR-associated genes were enriched for neuronal GO terms, many converge on reported roles in implantation, placentation, and early embryonic development. AluY epimutation represents a previously unrecognized, predominant signature of paternal epigenetic perturbation in uRPL, establishing repetitive elements as a new axis of sperm epigenetic risk.

Pregnancy involves profound changes to maternal immunity throughout gestation to simultaneously tolerate the fetus and protect both mother and baby from infection. Dysregulation of this process can lead to pregnancy complications and adverse outcomes. However, how the maternal peripheral immune system adapts throughout an uncomplicated pregnancy remains poorly understood, limiting our ability to identify and interpret alterations associated with pregnancy complications. Here, we longitudinally profiled maternal whole-blood transcriptomes of 1,305 nulliparous women at 12, 20, 28 and 36 weeks of gestation (n=3,776 samples) from the Pregnancy Outcome Prediction Study 2 (POPs2). Differential expression analysis revealed that the maternal immune system underwent its most pronounced remodeling in early pregnancy (between 12 and 20 weeks gestation). Co-expressed gene modules demonstrated immune-dominant programs were highly active in early stages, shifting towards increased cellular and metabolic activity in later pregnancy, reflecting maternal adaptation to increasing physiological demands. Through cis-eQTL mapping we found that genetic regulatory effects increasingly diverged from the non-pregnant state as pregnancy advanced. Colocalising with GWAS revealed putative mechanisms underlying genetic predisposition to pregnancy complications, with 58% of these colocalizations detectable only in the context of pregnancy. Finally, we identified eQTL that exhibit significant interactions with gestational age, implicating dynamic regulation of innate immune and metabolic pathways. These findings show that pregnancy is not only a state of changing gene expression, but also a dynamic regulatory environment that reshapes the effects of genetic variation. By characterizing these adaptations across gestation, this work provides a reference for interpreting maternal immune variation and genetic risk across gestation.

Functionally linking enhancers to gene promoters at high resolution often entails analysis of 3C datasets, including viewpoint-based methods such as Capture-(Hi)C. Quantitative comparison across samples and experiments, together with visualization and integration of promoter interactions with other datasets are of critical importance. While existing statistical tools identify significant interactions and quantify underlying signal, systematically comparing the shape and extent of this signal across large sets of intervals remains challenging. Moreover, experimental artefacts, such as inefficient crosslinking, can affect downstream interpretation, but are difficult to detect systematically. Here we introduce PostChicago, an R/Bioconductor package that fills this gap. Building upon the widely used interaction-calling package Chicago, PostChicago provides a complete workflow for quality control, visualization, integration and quantitative analysis of promoter interactions between multiple samples, including annotation and quantification of genomic regions based on external datasets. PostChicago extends visual quantitative comparisons beyond individual viewpoints by computing normalized metaprofiles around large sets of intervals that visualize the distribution of interaction signal, enabling comparison between narrow and broad interaction patterns. We further demonstrate how PostChicago can identify experimental crosslinking artefacts. Together, PostChicago enables integrative, shape-sensitive analysis and quality control of promoter Capture-(Hi)C datasets at a scale that would otherwise require extensive custom scripting.

Research shows that genetic variation directly influences DNA methylation, and this association has generally been explored on germline SNPs and at a population level. The presence of genomic variation and base modification on sequence reads generated from a technology like nanopore sequencing offers an opportunity to link disease-specific variants to methylation changes in individual genomes. Here, we present unduliner, a framework with an embedded pretrained convolutional neural network model, that predicts somatic variants, single-nucleotide (SNVs) and structural (SVs), associated with methylation pattern changes in cancer genomes. We trained the model (accuracy = 0.803 on validation; 0.897 on held-out test) using phased sequence reads, single-nucleotide germline variants, per-base methylation probability, and variant proximity or presence in haplotype-specific differentially methylated regions (DMRs). Unduliner was applied to subline-specific variants from MCF7 breast cancer cell lines as proof-of-concept, and we demonstrated its ability to identify variant-stratified methylation differences independent of haplotype-based methylation differences. In a pancreatic ductal adenocarcinoma (PDAC) sample, we identified coding and non-coding SNVs and SVs associated with tumour-normal DMRs, allele-specific methylation, and intratumour DMRs. These observations demonstrate that integrating long-read methylation and variant information can provide additional interpretative context for both coding and non-coding genomic variation beyond the conventional variant impact prediction tools. The results from unduliner include variant information, size and direction of methylation change with respect to the variant (increase or decrease), and genomic location of methylation change. Unduliner is publicly available on GitHub at https://github.com/Chisomgold/unduliner.

Aldehyde dehydrogenase 1a3 (Aldh1a3) is an enzyme involved in retinoic acid synthesis with dynamic expression patterns during development, including in the urogenital system. Here, we generated a bicistronic Aldh1a3-P2A-TagBFP knock-in mouse using CRISPR/Cas9 genome editing, inserting TagBFP immediately upstream of the endogenous Aldh1a3 stop codon. Correct targeting was confirmed by Oxford Nanopore long-read sequencing, and heterozygous and homozygous mice were viable and fertile without overt morphological abnormalities. TagBFP fluorescence faithfully overlapped with endogenous Aldh1a3 immunoreactivity and reproduced established expression domains in the developing craniofacial region, intestine, kidney, and broader urogenital system. Extensive characterization of the urogenital system revealed dynamic, spatially restricted BFP reporter activity in Aldh1a3-expressing domains across several key structures, including the ureteric bud and collecting duct lineage, seminal vesicles, caput epididymis, and developing uterine horns. The Aldh1a3-P2A-TagBFP mouse provides a fluorescent resource for visualizing Aldh1a3 expression across development and in adult tissues, including for the characterization of Aldh1a3-expressing domains in the urogenital system. The relatively low fluorescence intensity of TagBFP should be considered when assessing low-level reporter expression.

Background and Aims: As a microbiome/diet-derived vitamin, queuine (q) is a micronutrient that eukaryotes acquire from microbiota or diet. Vitamin q, the free base form of queuosine (Q), is used for Q-modification of transfer RNA (tRNA). Although tRNA-Q-modification in regulating eukaryotic cell physiology is recognized, the relationship between Q-tRNA-modification and the human microbiome in health and inflammatory bowel diseases (IBD) remains unknown. Which bacteria produce q and how the q-producing bacteria contributing to human health and IBD are not explored. Here, we hypothesize that disrupted microbial Q-biosynthesis contributes to the dysbiosis of human IBD. We performed comprehensive multi-omics integrative analyses using publicly available datasets. Specifically, we re-analyzed publicly available shotgun metagenomic, single-cell RNA sequencing (scRNA-seq), metabolic datasets, and completed meta-analysis. Methods: To systematically investigate microbial Q-biosynthesis in healthy individuals and IBD patients, we performed a systematic secondary analysis by integrating 9 publicly available metagenomic datasets, 15 scRNA-seq datasets and one metabolic dataset published prior to 2026. We present a novel secondary bioinformatic reanalysis of sequence outputs mapped to the latest microbial taxonomy, functional pathways and microbial Q-related genes. Longitudinal study of shotgun metagenomics across the human lifespan (3146 samples) enabled taxonomic and functional profiling. Results: We first identified key q-producing bacteria (e.g., Bacteroides and Alistipes) in healthy populations. We then found that patients with IBD had significantly reducation of q-producing bacteria and a coordinated downregulation of the Q-related pathways, including Q, preQ0, de novo guanosine ribonucleotide biosynthesis and de novo guanosine deoxyribonucleotide biosynthesis pathways. This functional impairment was primarily driven by reduced contributions from Bacteroides, Alistipes and Akkermansia. The longitudinal stability of the q-producing bacteria community across the human lifespan (1638 samples). We observed a significant negative correlation between host age and the abundance of q-producing bacteria in patients with UC. Moreover, Queuine tRNA-ribosyltransferase 1 (QTRT1) expression in human intestinal epithelial cells was significantly reduced in patients with IBD compared to healthy controls. Conclusions: Our study used multi-omics datasets to define a novel functional dysbiosis characterized by a reduction of microbial Q-biosynthesis in patients with IBD. Vitamin q and its tRNA modification is lesser-recognized in human IBD. Understanding the cellular and organismal mechanisms of this microbiome-dependent micronutrient will advance the prevention of IBD and improve the quality of life of patients with IBD.

Palmitate-associated lipotoxic stress activates the endoplasmic-reticulum stress sensor protein IRE1, but how IRE1 signaling influences genotoxic-stress responses in triple-negative breast cancer remains unclear. Here, we investigated IRE1 and XBP1 signaling in MDA-MB-231 cells exposed to palmitate and etoposide. Under combined lipotoxic and genotoxic stress, XBP1 depletion increased DNA-damage accumulation in IRE1 wild-type cells but not in IRE1-deficient cells, whereas IRE1 re-expression reduced DNA damage. Pharmacologic IRE1 RNase inhibition also increased etoposide-associated DNA damage, supporting a protective role for IRE1 RNase-dependent signaling. IRE1 status and XBP1 manipulation differentially affected H2A.X and {gamma}H2A.X abundance, indicating context-dependent regulation of chromatin-associated DNA-damage signaling. At the RNA level, H2A.X was enriched in IRE1 immunoprecipitates, and the H2A.X-linked DNA-damage-response transcripts HUWE1 and BRCA2 also associated with IRE1 under combined stress. These findings link palmitate-activated IRE1-XBP1 signaling to genome-protective responses during genotoxic stress and identify a network of IRE1-associated DNA-damage-response transcripts in triple-negative breast cancer cells. Direct IRE1-mediated cleavage of these transcripts remains to be established.

Background: Maternal cigarette smoking is associated with adverse birth outcomes, but low birthweight may reflect preterm delivery, restricted fetal growth, or both. Contemporary evidence distinguishing smoking trajectories is limited. Objectives: To examine associations between maternal cigarette-smoking trajectories and low birthweight among U.S.-resident singleton live births in 2023 to 2024. Methods: We analyzed 5,861,166 U.S.-resident singleton live births in the 2023 to 2024 National Vital Statistics System natality files. Low birthweight was defined as birthweight <2,500 g. Trajectories were never smoking, quitting before pregnancy, quitting during pregnancy, persistent smoking, or other/intermittent smoking. Modified Poisson regression estimated adjusted risk ratios (aRRs) and 95% confidence intervals controlling for birth year and maternal, pregnancy, and infant characteristics. Results: Low-birthweight prevalence was 6.4% among never smokers, 7.7% among mothers who quit before pregnancy, 11.2% among those who quit during pregnancy, 14.6% among persistent smokers, and 10.2% among those with other/intermittent smoking. Compared with never smoking, adjusted risks were higher for quitting before pregnancy (aRR 1.06, 95% CI 1.03, 1.09), quitting during pregnancy (aRR 1.46, 95% CI 1.42, 1.51), persistent smoking (aRR 1.95, 95% CI 1.93, 1.98), and other/intermittent smoking (aRR 1.36, 95% CI 1.25, 1.49). Associations varied little by year (joint interaction P = 0.102). Conclusions: Persistent smoking showed the strongest association with low birthweight. Because the outcome combines preterm delivery and impaired fetal growth, the estimates should not be interpreted as associations with fetal growth restriction alone. Keywords Cigarette Smoking; Smoking Cessation; Pregnancy; Low Birthweight; Birthweight; United States

Background: Circadian syndrome (CircS) comprises metabolic abnormalities, short sleep, and depressive symptoms, and is associated with cardiovascular, liver, and lung diseases and mortality; evidence on digestive disease is scarce. We assessed its association with incident non-neoplastic digestive disease in Chinese adults. Methods: In this prospective analysis of the China Health and Retirement Longitudinal Study (CHARLS), we included 2011 baseline participants aged >=45 years free of digestive disease, with follow-up to 2018. CircS (>=4 of 7 components) was analysed as a continuous score and as a binary exposure. Cox models estimated hazard ratios (HRs) adjusting for demographic factors, BMI, smoking, and alcohol use. We did dose-response, component, subgroup, and sensitivity analyses; hs-CRP mediation was explored. Findings: 907 (19.0%) of 4 771 participants developed digestive disease over a median 84 months. Each additional CircS component raised the risk by 9.1% (HR 1.091, 95% CI 1.041-1.144, P<0.001); CircS positivity (36.1%) was associated with a 25.7% higher risk (HR 1.257, 1.084-1.456, P=0.002). Risk rose approximately linearly to about 70% higher at 5-7 components. Short sleep (HR 1.178, 1.017-1.365) and depressive symptoms (HR 1.570, 1.367-1.803) were the only independently associated components; no metabolic component was associated. Results were robust across sensitivity analyses; hs-CRP did not mediate the association. Interpretation: CircS is associated with incident non-neoplastic digestive disease, driven by its circadian-emotional rather than metabolic components. Sleep and mood may be targets for prevention. Funding: This research received no specific grant from any funding agency in the public, commercial, or not-for-profit sectors. Keywords: circadian syndrome; digestive diseases; cohort study; sleep; depression; brain-gut axis

Chromatin profiling methods, such as ChIP-seq (chromatin immunoprecipitation followed by sequencing), are used to characterize the genomic localization of DNA-associated proteins. While ChIP and ChIP-seq have been used for decades, an orthogonal approach, CUT&Tag (Cleavage Under Targets and Tagmentation), is gaining popularity as an efficient and cost-effective alternative. Although previous comparative studies note discrepancies in signal-to-noise ratios and detection bias at certain genomic regions, many differences between ChIP-seq and CUT&Tag results remain largely unreconciled. Here, we systematically investigate the disagreeing signals captured by these two methods across well annotated genomic regions. We assess multiple histone mark profiles generated by different groups in two cell lines (K562 and MCF-7). Overall, our analysis indicates that compared to ChIP-seq, CUT&Tag may have limited sensitivity in low-GC environments and, as previously observed, increased signal in hyper-accessible chromatin. Notably, within GC-poor regions of active gene bodies and Polycomb-repressed domains, CUT&Tag exhibits a loss of H3K36me3 and H3K27me3 signal, respectively, where occupancy of these histone marks is otherwise expected. Further, active promoters with discrepant H3K4me3 and H3K27ac signal between the two assays differ systematically in GC content and chromatin accessibility. Promoters differentially enriched for CUT&Tag signal relative to ChIP-seq generally show higher, broader GC-content profiles and higher DNase-seq and ATAC-seq signal, while promoters enriched for ChIP-seq signal harbor the opposite characteristics. A local bias for high GC content and/or chromatin accessibility in CUT&Tag may also explain its differing signal patterns at nucleosome-depleted regions (NDRs) compared to ChIP-seq and MNase-seq promoter profiles. Altogether, our results highlight that studies focused on profiling the intensity and structure of histone modification occupancy can be sensitive to potential biases of CUT&Tag to GC content and chromatin accessibility. These characteristics should be accounted for when selecting a chromatin profiling approach, analyzing and interpreting data as well as drawing biological conclusions.

Objective: To investigate sex-specific associations between DNA methylation (DNAm) of neurodevelopmental, stress-response, and dopaminergic pathway genes and need for pharmacological treatment for Neonatal Opioid Withdrawal Syndrome (NOWS) among opioid-exposed newborns. Study Design: Buccal swabs were collected at birth from 181 infants in the multi-site Child and Family Study (CAFS). DNAm was measured via pyrosequencing at CpG sites within promoter regions of neurodevelopmental (BDNF), stress-response (AVP, NR3C1, OXTR, FKBP5, SLC6A4), dopaminergic (DRD2, DRD4), and opioid signaling (OPRM1) genes. Need for pharmacological treatment for NOWS was obtained from medical records. We estimated robust linear regression models to investigate sex-specific associations of DNAm and need for NOWS treatment. Estimated marginal means quantified sex-specific DNAm differences by treatment status. Results: After correction for multiple testing, five CpG sites within DRD4 were significantly associated with need for pharmacological treatment, with four sites showing higher DNAm in treated infants and one showing lower DNAm. Significant sex-specific associations were identified within DRD4 and AVP. Conclusions: Epigenetic variation across multiple biological pathways contributes to variability in NOWS severity among infants with prenatal opioid exposure. The relationship between epigenetic variation and need for NOWS treatment may vary depending on infant sex.

Abstract Background: Placental insufficiency (PI), characterized by impaired placental function, is a leading cause of stillbirth. Although rare coding variants are known to cause a subset of stillbirths, their contribution to PI is poorly understood. Methods: We conducted a secondary analysis of stillbirth cases (N=292) of the Stillbirth Collaborative Research Network study with exome sequencing available on postmortem placental or fetal samples. PI was defined by standardized placental pathological lesions (e.g., maternal vascular malperfusion) and prespecified clinical criteria for placental dysfunction. Candidate gene-based rare-variant burden analysis was performed using the Sequence Kernel Association Test-Optimal framework, focusing on evolutionarily constrained developmental and placental-function genes. Primary analysis compared stillbirths with and without placental vascular malperfusion. Similar comparisons by clinical PI and other placental pathological lesions were conducted in secondary analysis. Results: Stillbirths with PI phenotypes demonstrated different patterns of genetic variation than stillbirths without PI. Specifically, we observed nominal differential enrichment of constrained variants in biologically prioritized placental-function genes, regulating extravillous trophoblast invasion and spiral artery remodeling (CTNND2, PHACTR1, SLIT1, VEGFA), placental angiogenesis (IGF2R, TEK), mitochondrial homeostasis (OPA1), and fetal growth (DLK1, GNAS). Secondary analyses on specific placental pathological lesions suggested recurrent enrichment of genes within similar placental developmental pathways. Conclusions: We observed nominal differential enrichment of constrained developmental and placental-function genes in stillbirths with PI compared to stillbirths without PI. The observed genetic signals across PI phenotypes suggest shared biological pathways underlie placental dysfunction. Our findings advance genotype-phenotype characterization and help prioritize candidate pathways for larger collaborative genomic and functional studies to improve stillbirth risk stratification and prevention.

Objectives: To investigate whether genetic predisposition to hypertensive disorders of pregnancy (HDP), measured using polygenic risk scores (PRS), is associated with subsequent cardiovascular disease (CVD) outcomes in analyses stratified by HDP history. Study design and main outcome measures: This population-based cohort included 1,284 women from the 1994-95 Busselton Health Study with genotype data, pregnancy history, cardiovascular risk factors, and linked hospitalisation and death records to 2022. Four HDP-related PRS were assessed: two for preeclampsia, one for gestational hypertension, and one for broad HDP phenotype. Outcomes were incident first CVD events classified into categories. Fine-Gray competing-risk models adjusted for age, cardiovascular risk factors, and genetic principal components estimated subdistribution hazard ratios (sHR) per standard deviation increase in PRS. Results: Of 1,284 women, 309 reported a history of HDP and 651 experienced an incident CVD event during follow-up. In analyses stratified by HDP history, the largest estimates were observed for first cerebrovascular disease, although event numbers were small. The PGS003586 preeclampsia PRS showed the largest estimate (sHR 3.41, 95% confidence interval (CI) 1.54-7.58, p = 0.003), while PGS004593, another preeclampsia-related score, was also positively associated with cerebrovascular disease (sHR 1.86, 95% CI 1.05-3.30, p = 0.035). The gestational hypertension and broad HDP scores also showed positive estimates, but CI included 1.0, indicating inconclusive evidence. Conclusions: Among women with a history of HDP, preeclampsia-related PRS showed preliminary evidence of an association with incident cerebrovascular disease. Given the small number of events, findings should be interpreted cautiously and validated in larger, multi-ancestry cohorts.

Pancreatic ductal adenocarcinoma (PDAC) arises within an extensively remodeled microenvironment, yet tissue markers that distinguish invasive carcinoma from precursor lesions remain limited. Integrating four single cell RNA sequencing atlases comprising 324,662 cells from 26 patients, we identified cancer associated fibroblast expansion, accumulation of C1QA+ immunoregulatory macrophages, and depletion of a dendritic cell compartment expressing plasmacytoid markers. Fibroblasts were enriched for extracellular matrix and PI3K AKT programs and macrophages for an antigen-presentation program. We then examined the protein level correlates of these populations in a tissue proteomic reference framework of 356 samples spanning non diseased pancreas, normal-adjacent tissue, low and high grade intraductal papillary mucinous neoplasms (IPMNs), IPMN associated invasive carcinoma, and PDAC, prioritizing proteins that changed monotonically across the six histopathologic reference groups or marked tumor enriched cell types. Despite depletion of plasmacytoid dendritic cells, the principal source of type I interferon, the interferon stimulated protein ISG15, expressed by both fibroblasts and macrophages, increased monotonically toward PDAC. In exploratory cross-validated benchmarking of PDAC versus low and high grade IPMN, excluding IPMN-associated invasive carcinoma (145 versus 56 samples), CATB+EPIPL achieved an AUC of 0.98, with a sensitivity of 92% at an achieved specificity of 92%, exceeding protein abundance models of diagnostic IHC-associated markers (S100P+IMP3+maspin+MSLN, 0.79) and refitted published IPMN progression combinations (<0.91). Against non diseased pancreas, candidate and comparator panels performed similarly (AUC 0.99 1.00). These biologically informed tissue protein panels warrant independent validation, including immunohistochemical evaluation of EUS guided fine needle biopsy specimens and measurement in blood.