Epigenomics

Maternal pancreatic {beta}-cells undergo functional and structural changes to adapt to increased metabolic demands during pregnancy. Lactogen signaling via the prolactin receptor (PRLR) contributes to these adaptations by increasing {beta}-cell mass, insulin transcription and glucose-stimulated insulin secretion[1-4]. In other lactogen-responsive tissues such as the mammary glands and specific hypothalamic nuclei, gestation induces epigenetic changes, some of which persist long after birth[5, 6]. We have previously found that prolactin treatment in islets regulates the expression of epigenetic modifiers[7, 8]. However, whether lactogen signaling in {beta}-cells mediates epigenetic changes to regulate chromatin accessibility has not been examined. Therefore, our objective was to determine whether PRLR signaling alters chromatin accessibility of {beta}-cells to facilitate transcriptional regulation. Using single-cell ATAC-sequencing, we identified differentially accessible regions (DARs) in {beta}-cells which had 718 overrepresented motifs following prolactin treatment of murine islets. Validating this approach, these included motifs bound by established PRLR signaling effectors such as the STAT family of transcription factors (TFs). Using RNA-sequencing we identified transcriptional changes in 41 TFs whose motifs were overrepresented in DARs, including several previously linked to PRLR signaling within {beta}-cells, including Myc, Mafb and Esr1. Importantly, we also identified TFs not previously associated with PRLR signaling, including OVOL2 an established regulator of epigenetic landscape within cells. OVOL2 is a transcription factor involved in EMT inhibition and energy homeostasis with unknown roles in pancreatic {beta}-cells. Here, we establish that OVOL2 acts as a negative regulator of lactogen-dependent effects on {beta}-cell proliferation, establishing a novel regulator of PRLR signaling.

Pregnancy results in profound physiological changes driven by dynamic and precisely programmed molecular processes. Maternal peripheral blood is generally the specimen of choice for studying these processes, as it is easily accessible and essential for many aspects of maintaining a healthy pregnancy. Here, we present a high-resolution atlas of the dynamic temporal changes in the transcriptome of maternal peripheral blood in healthy human pregnancy. We generated comprehensive RNA sequencing data in 802 weekly samples from 31 healthy pregnant women from the first trimester until after delivery. Using a strict discovery and replication setup, our longitudinal analysis of gene expression identified 720 genes with robust pregnancy-specific expression patterns. Using weighted graph correlation network analysis, we identified nine pregnancy-associated transcriptional modules that reveal a strong, coordinated enrichment of innate/neutrophil and antiviral immune programs, alongside changes in adaptive immunity (T cell differentiation and signaling), erythropoiesis and hemoglobin metabolism. Cell-type deconvolution revealed that these transcriptomic shifts were accompanied by increased relative neutrophil proportions and reduced naive CD4 and CD8 T cells in pregnancy. We provide a comprehensive characterization of dynamic changes across pregnancy, highlighting maternal blood as a key systemic regulator in healthy gestation. Together, our findings establish a reference atlas of healthy pregnancy, which can be used to identify dysregulated processes and mechanisms in women with pregnancy complications. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=168 SRC="FIGDIR/small/715300v1_ufig1.gif" ALT="Figure 1"> View larger version (34K): org.highwire.dtl.DTLVardef@2a4b28org.highwire.dtl.DTLVardef@ac49d9org.highwire.dtl.DTLVardef@12468c8org.highwire.dtl.DTLVardef@15b282f_HPS_FORMAT_FIGEXP M_FIG C_FIG O_LI720 genes showed robust pregnancy specific expression patterns. C_LIO_LICo-expression analysis clustered the genes into nine modules with distinct dynamics. C_LIO_LIEnrichment in pathways involved in innate and neutrophil-mediated immunity, antiviral responses, T cell differentiation and signaling, erythropoiesis and hemoglobin metabolism. C_LIO_LICell-type deconvolution showed increases in neutrophils and decreases in naive CD4 and CD8 T cells. C_LIO_LIThe atlas of detailed longitudinal transcriptional changes provides a baseline reference for healthy pregnancy. C_LIO_LIResults for all genes and protein-protein interaction networks are made available for interactive exploration. C_LI

Introduction: Nonsyndromic cleft lip with or without cleft palate (NSCL/P) is a common congenital malformation with complex etiology involving both genetic and environmental factors. Epigenetic mechanisms may mediate environmental contributions, but separating genetic from environmental effects remains challenging. Methods: We present an epigenome-wide association study with 32 monozygotic and 22 dizygotic twin pairs discordant for NSCL/P on blood and saliva samples. Differential methylation analysis was conducted using linear models to identify CpG sites showing significant methylation differences between affected and unaffected twins followed by functional annotation and pathway enrichment analysis. Results: The top-ranked finding is a differentially methylated region comprising two CpG sites at the CYP26A1 locus, cg12110262 (P = 3.21x10-7) and cg15055355 (P = 1.39x10-3). CYP26A1 is essential for retinoic acid catabolism and craniofacial patterning. The chromatin regulator ANKRD11, which causes KBG syndrome featuring cleft palate was the second best hit. Differentially methylated CpG sites showed significant enrichment in craniofacial enhancers and overlap with multiple GWAS-validated cleft genes including VAX1, PVRL1, SMAD3, and PRDM16. Conclusions: Our findings implicate retinoic acid signaling and chromatin regulation in NSCL/P etiology and demonstrate the value of discordant twin designs for distinguishing environmental from genetic epigenetic contributions to complex malformations.

Ehmt2 is a key H3K9 methyltransferase that regulates genome silencing and structural integrity during animal development. In addition to this canonical function, Ehmt2 has also been implicated in neural tissues mediating both direct and indirect transcriptional activation, and exon splicing, to facilitate proper neural cell differentiation and survival. Several germline loss-of-function animal models have been developed showing both conserved and divergent phenotypes that range from embryonic lethality to behavioural deficits in adult, fertile animals. Here, we generated the first maternal-zygotic ehmt2 loss of function mutant in zebrafish using CRISPR-Cas9 mutagenesis. An assessment of the pattern of H3K9 methylation in mutant embryos by ChIP-seq indicates that there are aberrant levels of this repressive mark, including reduction in discrete 5 non-coding regions of genes, but with no significant change in the overall pattern distribution of these marks across the genome. Global transcriptome and morphological analyses demonstrated that mutant embryos displayed greater variation in the timing of developmental progression that is, on average, slower compared to controls. Despite this, mutant embryos ultimately survive and are fertile. Through examination of progenitor cell dynamics and gene expression profiles, we found that the delay in embryonic development was associated with longer rates of S-M phases of the progenitor cell cycle in mutants leading to deficits in tissue growth. Finally, our data suggest a robust network of epigenetic regulators can potentially compensate for Ehmt2 loss of function and permit embryonic development and survival in ehmt2 mutant zebrafish. Our work establishes a zebrafish ehmt2 loss of function model that will facilitate examination of the complex and varied roles of Ehmt2 in vertebrate development.

BackgroundPolycystic ovary syndrome (PCOS) is a prevalent endocrine disorder and a leading cause of female infertility, with complex genetic, metabolic, and hormonal etiologies. Long non-coding RNAs (lncRNAs) have emerged as important regulators of diverse biological processes, yet their roles in PCOS remain underexplored. Here, we identified and characterized PCOS differentially expressed gene-associated lncRNAs (PDEGAL) with an integrative approach combining expression data, genetic association, and evolutionary analysis. MethodsThirty-three PCOS-associated protein-coding genes were obtained from our prior study, and all their nearby and overlapping lncRNAs were annotated. These candidates were analyzed using UCSC Genome Browser-mapped annotations and datasets, including NCBI RefSeq, GENCODE, GTEx, GWAS SNPs, and conservation, as well as the FANTOM5 cap analysis of gene expression (CAGE) promoter data, to assess their expression, regulatory potential, genetic variant overlaps, and evolutionary conservation. ResultsTwenty-three PDEGALs (18 antisense to, and 5 sharing bidirectional promoters with, known PCOS-associated protein-coding genes) were identified. 17 PDEGALs contained GWAS SNPs with statistically significant disease associations, 9 of which were associated with PCOS-related traits. 5 PDEGALs demonstrated expression in the KGN granulosa cell model of PCOS. Key gene structure element (KGSE) analysis revealed that most PDEGALs are primate-specific. Integrating four criteria--GTEx expression, GWAS SNPs, FANTOM promoterome, and KGSE conservation--highlighted HELLPAR as the only lncRNA fulfilling all four, while five others--PGR-AS1, MTOR-AS1, ENSG00000265179, ENSG00000256218, and LOC105377276--fulfilled three of the four criteria. ConclusionsWe have systematically identified candidate PCOS regulatory lncRNAs with convergent genetic, expression, and evolutionary evidence. These results provide a framework for functional validation and highlight lncRNAs as potential biomarkers and therapeutic targets in PCOS that function by regulating their nearby and overlapping protein-coding genes.

Long-chain n-3 polyunsaturated fatty acids (n-3 PUFAs) are candidate preventive agents for breast cancer. With emerging evidence of epigenetic regulation of the tumor microenvironment, tissue-level epigenetic effects may represent an important target for cancer prevention. In a randomized Phase II sub-study (high-dose 5 g/day vs low-dose 1 g/day for 12 months; n = 17; Clinicaltrials.gov: NCT02295059), DNA methylation (DNAm) of the breast environment was profiled by reduced-representation bisulfite sequencing (RRBS). DNAm was assessed genome-wide, at individual gene promoters, and for locus-level heterogeneity which has been linked to epigenetic dysregulation that can precede breast cancer. Both doses induced promoter DNAm changes, but their responses diverged: low-dose samples showed increased CpG variance and more differentially methylated promoters without pathway enrichment, whereas high-dose samples had reduced DNAm heterogeneity and promoter enrichment in inflammation signaling pathways. Many overlapping differentially methylated promoters changed in opposite directions between doses. The finding that high-dose n-3 PUFA affects DNAm fidelity in the breast adipose suggests a new potential mechanism for n-3 PUFA-mediated prevention of breast cancer development. Together with the dose-specific, directionally discordant DNAm responses in breast adipose, this study has important implications for both advancing n-3 PUFA for breast cancer prevention and dose selection in future n-3 PUFA supplementation trials.

BackgroundGene expression changes in response to developmental and environmental cues rely on cis-regulatory sequence elements (cREs). BRG1/BRM-Associated Factors (BAF) chromatin remodeling complexes maintain chromatin accessibility at many cREs, enabling binding by transcription factors (TFs). However, cREs exhibit a broad range of sensitivity to loss of BAF function, and the basis of this variability remains unknown. ResultsTo identify the characteristics of BAF-dependent cREs, we mapped chromatin accessibility changes following acute pharmacologic BAF inhibition in GM12878 lymphoblastoid cells. We integrated these results with over 100 TF and histone modification ChIP-seq datasets and used machine learning to identify features that predict chromatin accessibility changes. We found that Activator Protein 1 (AP-1) factors and lymphoid lineage-defining TFs including RUNX3 and PU.1 predicted BAF-dependence. Strikingly, we found that cREs bearing the chromatin signature of "primed" enhancers - enriched for H3K4me1 but lacking H3K27ac - were significantly more sensitive to BAF inhibition than typical active enhancers. As primed enhancers are known to facilitate transcriptional responses to stimuli, we tested the requirement of BAF activity in these responses. Acute BAF inhibition was sufficient to prevent both chromatin and transcriptional responses to interferon gamma and dexamethasone. cREs which normally gained accessibility in response to stimulation failed to do so with BAF inhibition, and these cREs were linked to genes with suppressed transcriptional induction. ConclusionsCollectively, our results demonstrate a requirement for continuous BAF activity to enable stimulus response and suggest that defective signal responsiveness may be a pathogenic mechanism in disease states caused by loss-of-function mutations in BAF subunits.

Terminal erythroid differentiation involves dramatic cellular remodeling that culminates in the expulsion of the nucleus, a process known as enucleation. While enucleation is conserved across mammals and is crucial for the generation of fully functional erythrocytes, the mechanisms governing this process have remained largely unknown, in part because the absence of genetic material in mature, enucleated red blood cells hinders genetic experimentation. Here, we performed a pooled, forward-genetic CRISPR-Cas9 screen in enucleated red blood cells derived from primary human hematopoietic stem cells to identify genes required for enucleation. We found that Chloride Intracellular Channel 3 (CLIC3) and Vesicle-associated membrane protein 8 (VAMP8) are both necessary for terminal erythroid differentiation, yet likely act through different mechanisms. Knockdown of CLIC3 led to a delay in erythroblast differentiation, culminating in impaired enucleation. We found that the knockdown cells had increased p53 and p21 and exhibited cell cycle alterations, suggesting CLIC3 plays a crucial role in coordinating cell cycle progression during erythropoiesis. In comparison, VAMP8-depleted cells initially appear to undergo accelerated differentiation but then display a specific defect in enucleation. Transcriptional analysis of the VAMP8-knockdown cells suggested dysregulation of pathways for vesicle trafficking and actin binding, and imaging of late-stage erythroblasts revealed impaired nuclear polarization and disorganized actin. This work provides a new approach for functional genomics in enucleated cells and reveals novel factors important for terminal erythroid differentiation and enucleation. Key pointsO_LIA CROPseq-based CRISPR-Cas9 screen enables functional genomics in enucleated primary human red blood cells. C_LIO_LIChloride Intracellular Channel 3 (CLIC3) and Vesicle Associated Membrane Protein 8 (VAMP8) were identified as critical for terminal erythroid differentiation and enucleation, likely acting through two distinct mechanisms. C_LI

Preeclampsia (PE), or gestational hypertension, affects around 5% of pregnancies and leads to approximately 70,000 maternal and 500,000 fetal deaths per year worldwide, with increased cardiovascular and metabolic disease in survivors. PE is associated with elevated circulating levels of the alternative splice isoform of VEGF receptor 1 (sFlt1), defects in placental vasculature, kidney damage and, in severe disease, fetal growth restriction. Current mouse models induce PE via direct expression of sFlt1 or elevation of blood pressure, which bypass the natural risk factors for human disease, such as age, obesity, hypertension and diabetes. These risk factors have in common reduced expression of Kruppel-like factors 2 and 4 (KLF2/4), the endothelial transcription factors that protect against cardiovascular disease. We now report that inducible deletion of KLF4 in maternal endothelium (KLF4iECKO) results in gestational hypertension, elevated sFlt1, defective placental vasculature, kidney damage and fetal growth restriction. KLF4iECKO may thus serve as a mouse PE model suitable for mechanistic analysis and screening of treatments that address upstream risk factors.

Background: APOL1 risk alleles are prevalent in individuals of West African ancestry and associated with increased risk of kidney disease. Although preeclampsia disproportionately affects women of Black ethnic backgrounds, evidence linking APOL1 alleles to preeclampsia remains conflicting. Objectives: The purpose of this study was to explore whether maternal APOL1 alleles contribute to preeclampsia risk and associated adverse pregnancy outcomes. Study design: We conducted a nested case-control study of 5210 pregnant women, including 745 preeclampsia cases and 949 controls of Black self-reported ethnicity, 1385 preeclampsia cases and 2131 controls of White self-reported ethnicity. APOL1 G1 and G2 risk alleles were directly genotyped on the Illumina Infinium Global Screening Array. Associations with preeclampsia, early preeclampsia, recurrent preeclampsia, birthweight centiles and gestational age at delivery were examined using regression models assuming a recessive mode of inheritance with adjustment for established risk factors and stratification by self-reported ethnicity and genetically-determined ancestry. Results: Presence of APOL1 risk alleles was almost exclusively observed in women of Black self-reported ethnicity. 168/949 controls (17.7%) and 133/745 cases (17.9%) carried two APOL1 risk alleles, and these women did not have a significantly increased risk of preeclampsia compared to those with zero or one APOL1 risk alleles in adjusted analyses (OR 1.00, 95% CI 0.76-1.29, p=0.972). When restricting analysis to women of Black self-reported ethnicity only, no association was observed between APOL1 genotype and preeclampsia risk (adjusted OR 0.94, 95% CI 0.61-1.25, p=0.673). When restricting analysis to women of pan-African genetically-determined ancestry only, also no association was observed between APOL1 genotype and preeclampsia risk (adjusted OR 1.00, 95% CI 0.76-1.32). No associations were found between number of APOL1 risk alleles and early preeclampsia, recurrent preeclampsia, birthweight centile or gestational age at delivery after adjustment for established risk factors and stratification by self-reported ethnicity or genetically-determined ancestry. Conclusions: Maternal APOL1 risk alleles do not independently influence preeclampsia risk or related adverse outcomes in a multi-ethnic pregnancy study. Future studies should examine whether fetal APOL1 genotypes, alone or in interaction with maternal genotypes, contribute to preeclampsia risk.

ABSTRACT/SUMMARYVascular remodeling within the developing fetus and placenta is essential for supporting the growth and function of emerging tissues and organs. Pericytes (PCs) play a central role in stabilizing and maturing microvascular networks by extending along endothelial cells (ECs) and reinforcing vessel integrity. In the placenta, as in other organs, PC-EC communication is mediated in part by platelet-derived growth factor-BB (PDGF-BB) signaling, which governs PC differentiation, proliferation, migration, and survival, ultimately enabling their recruitment and retention along capillaries. In this study, we identified progressive PC investment along feto-placental capillaries in both murine and human tissues across gestation, supported by morphological and molecular evidence. Placental PCs displayed phenotypic heterogeneity comparable to that observed in the brain and heart, suggesting conserved diversity across organ systems. In addition to characterizing PC dynamics, we examined the expression of recently identified soluble PDGF Receptor-{beta} (sPDGFR{beta}) isoforms. These variants were detected at the protein and transcript levels in mouse and human placentas, as well as in a murine trophoblast-embryonic stem cell (TESC) differentiation model that recapitulates aspects of early placental vascular development. Within this model, sPDGFR{beta} expression was independent of ADAM10 activity and exogenous growth factors during early vessel formation but was markedly upregulated during hypoxia. To assess how elevated sPDGFR{beta} might influence PDGF-BB signaling, we exposed TESCl-derived vascular networks to excess PDGF-BB with or without a sPDGFR{beta} mimetic. PDGF-BB alone reduced full-length PDGFR{beta} levels while increasing receptor phosphorylation, consistent with known ligand-induced regulatory mechanisms. Inclusion of the sPDGFR{beta} mimetic shifted these responses toward baseline, suggesting a potential modulatory or feedback role for soluble receptor variants. Together, these findings demonstrate that PCs are progressively recruited to placental capillaries and exhibit diverse phenotypes during development, and that soluble PDGFR{beta} isoforms may modulate PDGF-BB signaling in a manner sensitive to oxygen tension. Understanding these mechanisms provides insight into the regulation of placental vascular maturation and may inform strategies to improve human health by targeting disorders rooted in impaired placental development.

ObjectivesCD4+ T cells play key roles in regulating immune responses during pregnancy, therefore we aimed to understand the CD4+ T cell surface proteome and transcriptome during pregnancy. MethodsCD4+ T cells were analysed in blood and decidua from term-pregnancies (>37 weeks), and non-pregnant blood. >350 surface proteins were screened via flow cytometry, and transcriptomes were analysed using single-cell RNA sequencing with >130 CITE-seq barcoded antibodies. ResultsSurface protein screening identified changes to ILT4/CD85d, CD9, IFN-{gamma} receptor {beta}-chain, CX3CR1 and CCR5 in the pregnant blood and decidual CD4+ T cells. CX3CR1 and CCR5 had the highest expression on the effector-memory T cell (TEM) subset in the blood, with expression consistent across subsets in decidua. CD126/IL-6R was lower in pregnant blood and decidual CD4+ T cells, while scRNAseq identified enrichment in the IL-6R signalling pathway in naive CD4+ T cells in pregnant blood. Both sIL-6R and IL-6 concentrations were increased in plasma during pregnancy, suggesting perturbations to the IL-6/IL-6R signalling axis. Meanwhile, decidual CD4+ T cells had increased expression of transcription factor RUNX3 in the CD69+ tissue-resident-like subset. ConclusionsOur findings demonstrate altered molecular expression in CD4+ T cells during pregnancy. This provides important mechanistic insight of their adaptation and regulation during placental development, which may drive placental dysfunction or pregnancy complications including preeclampsia, fetal growth restriction and stillbirth. These new data may inform future studies that focus on determining the significance of differentially- expressed immune features in pregnancy to identify potential targets for immune modulation to treat pregnancy complications and infections.

Mitochondria undergo significant structural and functional changes during human pre-implantation embryogenesis, yet the transcriptional activity of both nuclear-encoded mitochondria-associated genes and mitochondrially transcribed genes across this developmental window remains poorly characterized. While mitochondria are established as the primary energy source for the early embryo, emerging evidence suggests they may also influence lineage specification through epigenetic regulation and metabolite availability. To investigate this, we reanalyzed two publicly available human single-cell RNA sequencing datasets filtered for mitochondria-associated genes using the MitoCarta 3.0 reference database, with separate analyses conducted on the nuclear-encoded and mitochondrially transcribed subsets. The first dataset spanned individual blastomeres from the oocyte through blastocyst stage, and the second compared trophectoderm and inner cell mass cells isolated from blastocysts. Mitochondria-associated gene expression was sufficient to cluster human blastomeres by developmental stage, with morula and blastocyst stage cells forming well-defined clusters. Mitochondrially transcribed genes were found to be the primary drivers of clustering in earlier developmental stages, while nuclear-encoded mitochondria-associated genes drove clustering at the blastocyst stage. A pronounced shift in the expression of both gene sets was identified at the transition from the 4-cell to the 8-cell stage, with 115 unique differentially expressed genes identified across the two stages immediately following this transition, compared to only 5 across the two prior stages. The timing of this transcriptional upregulation, preceding the known onset of oxidative phosphorylation at approximately the 32-cell stage, suggests a mitochondrial role in early embryogenesis beyond energy production. Analysis of trophectoderm and inner cell mass cells showed that mitochondrial gene expression profiles partially distinguished these two lineages, consistent with known differences in mitochondrial activity between them. These findings suggest that both nuclear-encoded and mitochondrially transcribed gene expression is upregulated prior to the first lineage specification event in the human embryo, potentially contributing to epigenetic regulation and cell fate determination through altered metabolite availability. A limitation of this study is its reliance on transcriptomic data alone; future work incorporating functional metabolite measurements will be needed to establish causality. Nonetheless, these data reframe mitochondria as active participants in early human developmental programming rather than passive energy suppliers.

Systemic inflammation is implicated in various diseases, yet its upstream determinants remain poorly examined. We conducted a large scale two-sample Mendelian randomisation (MR) study to systematically evaluate the potential causal effects of 3,213 molecular (metabolomic, proteomic), physiological and disease traits on circulating interleukin-6 (IL-6) and C-reactive protein (CRP) levels. Genetic instruments were derived from genome wide association studies and analysed using inverse variance weighted (IVW), weighted median, and MR-Egger methods with multiple testing correction. Bidirectional MR was performed to assess reverse causation. After Bonferroni correction, evidence of potential causal effects was observed for 72 traits on CRP and 9 traits on IL-6. CRP was predominantly influenced by metabolomic traits, especially lipid and fatty acid measures. Genetically proxied adiposity (body mass index and obesity), triglyceride rich lipoproteins, glycoprotein acetyls (GlycA), and apolipoprotein E increased CRP levels, whereas HDL-related cholesterols, polyunsaturated fatty acids, and glutamine decreased CRP. Most associations were consistent across MR methods, supporting the robustness of these results. As expected, IL-6 had a large effect on CRP. IL-6 was influenced by primarily adiposity and HDL-related lipid measures, with generally smaller effect sizes and limited support across sensitivity analyses. Bidirectional analyses indicated little evidence that CRP directly drives metabolic traits when restricting to cis-acting instruments, whereas genetically proxied IL-6 signalling showed consistent downstream effects on HDL particle concentration and composition. Adiposity is a shared upstream determinant of both inflammatory biomarkers, with stronger and broader effects on CRP. These findings suggest that CRP acts as an integrated downstream readout of systemic inflammatory burden, whereas IL-6 reflects a more tightly regulated and context-dependent process. Our work clarifies traits that may causally influence systemic inflammation and highlights biological pathways linking inflammation to cardiometabolic and inflammatory diseases. By mapping upstream determinants of IL-6 and CRP, we also provide a resource to prioritise key drivers for mechanistic study and therapeutic targeting.

Cancer-related genomic instability (GI) may cause genetic alterations in spermatozoa, implying health issues not only in cancer survivors, but also in their children [1, 2]. We therefore studied Loss of Y chromosome (LOY), considered as hallmark of GI [3-15], in spermatozoa and blood from survivors of childhood and testicular cancer (CC, TC), and controls (CTRL). We found that LOY was statistically significantly more frequent in spermatozoa from cancer survivors than in controls (Odds Ratio [OR]=2.2 for CC vs. CTRL and OR=2.4 for TC vs. CTRL). Furthermore, LOY was about an order of magnitude more prevalent in spermatozoa than in blood among 18-53-year-old males within all cohorts. Our findings suggest that LOY in spermatozoa might be a clinically useful marker of GI, reduced fertility and disease predisposition in males. Introducing LOY in spermatozoa as a biomarker opens a new research avenue into disease prevention and the causes and consequences of LOY.

BackgroundConventional models of human ribosomal DNA (rDNA) array organization have historically depended on transcription-centric boundaries, partitioning the unit into a [~]13 kb rDNA transcription region and a monolithic [~]31 kb intergenic spacer (IGS). While our previous identification of Duplication Segment Units (DSUs) mapped these arrays based on an intuitive analysis of the microsatellite density landscape of the complete reference human genome, our present deep mining of this landscape has revealed a more accurate rDNA Gene Unit Pattern. Methods & ResultsIn this study, we conducted a deep mining analysis of our previously established microsatellite density landscape of the T2T-CHM13 assembly, focusing specifically on nucleolar organizing regions (NORs). We suggest a more accurate rDNA Gene Unit Pattern containing a (CTTT)n microsatellite aggregation ahead of the rDNA gene and a (CT)n microsatellite aggregation behind the gene, rather than a pattern featuring an IGS region inserted between two rDNA genes. ConclusionsA correct rDNA gene pattern of the human genome probably includes a (CTTT)n microsatellite aggregation ahead of the gene and a (CT)n microsatellite aggregation behind it, which possibly constitute cis- and trans-regulating regions; the (CTTT)n and (CT)n microsatellite aggregations may provide two different local stable DNA structures for regulatory protein binding.

Long noncoding RNAs (LncRNAs) have emerged as a class of important regulatory ncRNAs and are known to fine-tune numerous cellular processes including proliferation, differentiation and development; however, their role in quiescence still remains largely unexplored. A miRNA host gene lncRNA, MIR503HG, has been reported to play important role in cancer development. Here, we demonstrate the role of MIR503HG lncRNA in regulating cellular quiescence. MIR503HG displays elevated levels in human diploid fibroblasts induced to undergo quiescence. Depletion of MIR503HG in HDFs affects the entry of cells into quiescence but has no effect on cell cycle progression, suggesting its role in quiescence attainment and/or maintenance. Additionally, MIR503HG depletion led to a drastic decrease in the levels of miR508 target, PTEN with a concomitant increase in pAkt levels, indicating its role in negative regulation of miR508. Further, we demonstrate that the lncRNA MIR503HG regulates PTEN levels by acting as a ceRNA for miR508 to maintain cellular quiescence. Our studies illustrate that MIR503HG can function synergistically with miR503 to maintain cells under quiescence and both the miRNA-HG and the miRNA encoded by its gene locus synergistically control the same biological process in different ways by regulating different downstream genes.

La-related protein 1 (LARP1) is an RNA-binding protein that post-transcriptionally regulates mRNA with potential oncogenic role in multiple cancers; however, its function in endometrial cancer remains unknown. An analysis of the TCGA endometrial cancer cohort showed that overexpression of LARP1 is associated with shorter overall survival (OS) and progression-free interval (PFI) as indicated by Kaplan-Meier analysis. Functional in vitro studies revealed that LARP1 knockdown by two different siRNAs markedly suppressed cell viability and triggered apoptosis, as confirmed by increased protein levels of cleaved PARP1 and cleaved caspase-3. Mechanistically, LARP1 knockdown remarkably reduced E2F1 protein levels as confirmed by immunofluorescence and Western blotting. Clinically, co-overexpression of LARP1 and E2F1 further decreased OS and PFI, suggesting a co-operative oncogenic axis. Importantly, LARP1 knockdown enhanced the sensitivity of ISHI and HEC-1A endometrial cancer cell lines to carboplatin treatment. These findings suggest that LARP1 promotes endometrial cancer survival and resistance to chemotherapy, at least in part, through the regulation of E2F1 and suppression of apoptosis. Targeting LARP1 could represent a promising therapeutic strategy to suppress tumor growth and enhance sensitivity to platinum-based chemotherapy.

Background and purpose: Excessive sitting and genetic liability to obesity are associated with risk of obesity and hypertension, two significant risk factors for cardiovascular disease. This study aimed to investigate the interactive effects of genetic liability to obesity and excessive sitting on prevalence of hypertension. Methods: Obesity genetic liability was estimated in unrelated individuals of European ancestry (n=208,594) using previously identified genetic variants and their effect sizes for adiposity related traits. Hypertension was defined as systolic blood pressure ? 140 mmHg, diastolic blood pressure ? 90 mmHg, or the use of anti-hypertensive medications. Logistic regression was used to examine the association between obesity genetic liability and across different levels of self-reported sitting time. Results: excessive sitting and increased genetic liability were independently associated with higher odds of hypertension. The greatest odds of hypertension was observed in participants with high sitting time combined with increased genetic liability to obesity (OR=1.29; 95% CI = 1.25, 1.33, P <2 x10-16) compared to individuals with low genetic liability and low sitting time. Interaction analysis identified that in individuals with excessive sitting, the effect of genetic liability of waist circumference on hypertension was greater compared to individuals with low sitting time (P interaction=0.03). Conclusion: Combined excessive sitting and high genetic susceptibility to obesity is associated with greatest odds of hypertension. These findings highlight the importance of lifestyle in offsetting risk imposed by genetic factors.

Importance: Assessment of cardiovascular health (CVH) during may unmask latent metabolic vulnerability and indicate long-term disease risk. However, the prognostic value of the AHA's Life's Essential 8 (LE8) framework during pregnancy remains uncertain. Objective: To evaluate CVH during using a modified Life's Essential 8 (mLE8) score in association with time to incident cardiometabolic disease. Design: Prospective cohort study with electronic medical record (EMR) surveillance for 7 years postpartum (August 2018-March 2026). Adjusted accelerated time-to-failure models estimated mLE8 associations with incident conditions. Setting: A population-based prenatal cohort recruited from a large academic medical system in South Carolina. Participants: Singleton pregnancies in individuals aged 18 to 44 years without pre-existing diabetes or cardiovascular disease (CVD) Exposures: A 7-component mLE8 score assessed during pregnancy, incorporating hypertensive disorders of pregnancy (HDP), 50-g glucose tolerance test results, pre-pregnancy body mass index, smoking status, sleep adequacy, diet quality, and physical activity. Scores ranged from 0 to 100, with higher scores indicating more favorable CVH. Main Outcomes and Measures: Post-delivery incident cardiometabolic conditions captured through EMRs and classified as chronic hypertensive conditions, chronic metabolic conditions (e.g., dyslipidemia, impaired glucose regulation), and CVD (e.g. cardiac arrest, cardiomyopathy). Time to incident diagnosis was measured in days from delivery. Results: Among 1,225 pregnancies (mean age, 25.0 [5.3] years), 499 incident cardiometabolic events occurred over a median follow-up of 6.2 (2.8) years. Each 10-point higher mLE8 score was associated with a longer time to incident diagnosis of chronic hypertensive conditions (time ratio [TR], 1.26; 95% CI, 1.11, 1.42) and chronic metabolic conditions (TR, 1.20; 95% CI, 1.11, 1.29). Healthier HDP, glucose, BMI, and sleep scores were most strongly associated with longer time to diagnosis of chronic metabolic disease. Results were robust to sensitivity analyses excluding individuals who developed gestational diabetes or HDP. Conclusions and Relevance: In this racially diverse, low-income cohort study of 1,225 pregnancies, better CVH during pregnancy was associated with a longer time to incident post-delivery diagnosis of cardiometabolic conditions. Pregnancy-based CVH assessment may help identify individuals with elevated and emerging cardiometabolic risk who could benefit from early, targeted intervention and enhanced longitudinal surveillance.