Epigenetic Variation Research Articles

Abstract 3491: Tumor subtype classification of HPV-associated head and neck cancers is central to key clinically relevant variables

Abstract Cancer types are typically categorized according to the cell of origin, but within these groupings there exists vast heterogeneity. Thus, subtypes based on molecular features are often defined that have clinical utility as prognostic biomarkers, aid in selection of therapeutic strategies, or are associated with treatment response. Head and neck cancer (HNC) is the seventh most common cancer globally and projected to have 54,540 new cases in the U.S. in 2023. Within the US, HPV(+) HNC is now more prevalent than HPV(+) cervical cancer, and it is expected to continue to rise. Although there is wide morphologic and epigenetic diversity within HPV(+) HNC, tumor subtyping is not yet widely used for this cancer population, largely because of HPV(+) HNC’s unique tumorigenesis process. Unlike other cancers that are driven by specific genetic signatures, HNC is driven by viral gene mechanisms. Given the large degree of heterogeneity among HPV(+) HNC cases and the lack of key mutations to define subtypes, the classification of HPV(+) HNSC subtypes requires a more sophisticated approach. In this study, we introduce a robust, ensemble machine learning (ML) classifier for subtyping HPV(+) HNC that was trained on multiple cohorts and gene feature sets from RNA-seq data, and rigorously tested to ensure high reproducibility. The results classify HPV(+) HNC into the two main recognized subtypes: IMU (immune strong) and KRT(highly keratinized). Using a cohort of 227 patients, we show that the IMU/KRT classification is highly correlated with key clinically relevant variables in HNC. Of 41 molecular, clinical, and epidemiologic variables tested, 24 significantly associated with subtype. The IMU subtype was significantly associated with CD8 T-cells (p-value = 4.21 × 10−9), Dendritic cells (p-value = 1.65 × 10−8), B-cells (p-value = 2.20E−8), and epithelial to mesenchymal transition (p-value = 0.00013146). The KRT subtype is significantly associated with keratinization (p-value = 7.11 × 10−9), HPV integration (p-value = 3.14 × 10−6), radiation resistance (p-value = 0.00307), female sex (p-value = 0.00641), and high T stage (p-value = 0.0324). Genetic, epigenetic, and HPV gene-related variables were also among those significantly associated with subtype. HPV(+) HNC subtypes have been shown to be associated with survival, with KRT-like patients having worse clinical outcomes than IMU. Given the different carcinogenic processes underlying IMU and KRT tumors, our ensemble ML subtype classifier web tool will help inform future studies of HPV(+) HNC. Future work to assess how HPV(+) subtypes can be incorporated into precision treatment strategies is well-motivated by our findings. Citation Format: Bailey F. Garb, Shiting Li, Tingting Qin, Elizabeth Lopez, Sarah Soppe, Snehal Patil, Laura Rozek, Nisha D'Silva, Maureen Sartor. Tumor subtype classification of HPV-associated head and neck cancers is central to key clinically relevant variables [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 3491.

Abstract 3666: Multi-cancer early detection using metrics of DNA methylation based epigenetic instability

Abstract Cancers present significant changes in DNA methylation, which has proven to be highly useful in cell-free DNA (cfDNA) based cancer detection. Cancer epigenomes are marked by a high degree of intra- and inter-tumor epigenetic variation, indicative of the high level of epigenetic instability. However, the nature of the regions with high epigenetic instability and its utility as biomarker has not been explored. Here we developed a novel methodology and metric to measure the degree of epigenetic perturbation, termed the Epigenetic Instability Index (EII), for multiple cancer screening through cfDNA. Our novel methodology provides a sample specific score of epigenetic perturbation in relation to the expected normal state as opposed to only looking at CpG sites that change between samples. Through machine learning, we have elucidated 269 CpG-island regions which sufficiently capture the epigenetic instability in cancers. We have built classifier models using the EII metrics of these 269 regions and demonstrate that they can efficiently identify breast and lung cancer cases from cfDNA methylation data. Particularly, the models can differentiate even Stage IA of NSCLC with ~75% sensitivity at 95% specificity and early-stage breast cancer at ~68% sensitivity and 95% specificity. The EII metrics perform significantly better than metrics that measure absolute DNA methylation levels. Our studies highlight the potential of measuring epigenetic instability from cfDNA in any given sample in addition to traditional methods of methylation measurement for non-invasive screenings via liquid biopsies. Citation Format: Sara-Jayne Thursby, Zhicheng Jin, Steve B. Baylin, Malcolm Brock, Thomas Pisanic, Hariharan Easwaran. Multi-cancer early detection using metrics of DNA methylation based epigenetic instability [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 3666.

Abstract 1711: Rearranged active enhancers and promoter-enhancer contacts promote lipid metabolic reprogramming during secondary trastuzumab adaptation of HER2 positive breast cancer

Abstract Background: The development of secondary trastuzumab resistance signifies an evolutionary adaptation within HER2-positive breast cancer during anti-HER2 treatment. Our research reveals a comprehensive metabolic reprogramming, with a particular emphasis on the synthesis of unsaturated fatty acids and the degradation of arachidonic acid, accompanying this adaptation. Non-mutational epigenetic variations, particularly alterations in active enhancers, coupled with the rearrangement of enhancer-promoter contacts, demonstrate robust correlations with lipid metabolic reprogramming. These findings suggest that non-mutational epigenetic variations play a crucial role in driving the adaptation to trastuzumab. Materials and Methods: In a prior investigation, we successfully generated secondary trastuzumab-resistant SKBR3_HR cells. In our current study, total RNA was extracted from both trastuzumab-resistant SKBR3_HR and trastuzumab-sensitive SKBR3 cells for transcriptome analysis. Additionally, mass spectrometry was employed to analyze cellular metabolism in both resistant and sensitive cell populations. Simultaneously, we utilized the CUT&Tag kit with an anti-H3K27ac antibody to create a sequencing library for active enhancer measurement. Furthermore, the Micro-C kit was applied to generate a sequencing library for genome contact measurement. Results: In our study, secondary trastuzumab-adaptive SKBR3_HR cells demonstrated a reduction in cellular unsaturated fatty acids, with more than 110 UFAs or UFA-containing lipids showing decreases, while only 36 exhibited increases. This phenomenon may be attributed to the downregulation of SCD, FADS2, and HACD2. Simultaneously, the upregulation of PTGS1 and PTGES may contribute to a higher conversion of arachidonic acid to prostaglandin E2 (PGE2), resulting in immune inhibition. In SKBR3 and SKBR3_HR cells, 10,955 and 10,889 non-promoter H3K27me3 peaks, respectively, were identified as active enhancer regions. Among them, 379 enhancers became silent, and 313 transitioned into an active state during the formation of trastuzumab adaptation. Trastuzumab adaptation led to an increase in intra-chromosomal interactions, particularly short-distance contacts (< 1MB). By employing the activity-by-contact (ABC) algorithm, we observed significant variant contacts between PTGES and SCD promoters and enhancers within 1MB genomic regions in SKBR3_HR cells compared to SKBR3 cells. Conclusion: The formation of secondary trastuzumab adaptation involves the rearrangement of active enhancers and promoter-enhancer contacts, serving as an effective force to drive lipid metabolic reprogramming, especially the synthesis of unsaturated fatty acids and PGE2 production, reshaping the cellular fatty acid composition and anti-tumor immunity. Citation Format: Ningjun Duan, Yijia Hua, Yongmei Yin. Rearranged active enhancers and promoter-enhancer contacts promote lipid metabolic reprogramming during secondary trastuzumab adaptation of HER2 positive breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 1711.

A pocket companion to cell-free DNA (cfDNA) preanalytics.

The cumulative pool of cell-free DNA (cfDNA) molecules within bodily fluids represents a highly dense and multidimensional information repository. This "biological mirror" provides real-time insights into the composition, function, and dynamics of the diverse genomes within the body, enabling significant advancements in personalized molecular medicine. However, effective use of this information necessitates meticulous classification of distinct cfDNA subtypes with exceptional precision. While cfDNA molecules originating from different sources exhibit numerous genetic, epigenetic, and physico-chemical variations, they also share common features that complicate analyses. Considerable progress has been achieved in mapping the landscape of cfDNA features, their clinical correlations, and optimizing extraction procedures, analytical approaches, bioinformatics pipelines, and machine learning algorithms. Nevertheless, preanalytical workflows, despite their profound impact on cfDNA measurements, have not progressed at a corresponding pace. In this perspective article, we emphasize the pivotal role of robust preanalytical procedures in the development and clinical integration of cfDNA assays, highlighting persistent obstacles and emerging challenges.

Comparative and functional analysis unveils the contribution of photoperiod to DNA methylation, sRNA accumulation, and gene expression variations in short-day and long-day grasses.

Photoperiod employs complicated networks to regulate various developmental processes in plants, including flowering transition. However, the specific mechanisms by which photoperiod affects epigenetic modifications and gene expression variations in plants remain elusive. In this study, we conducted a comprehensive analysis of DNA methylation, small RNA (sRNA) accumulation, and gene expressions under different daylengths in facultative long-day (LD) grass Brachypodium distachyon and short-day (SD) grass rice. Our results showed that while overall DNA methylation levels were minimally affected by different photoperiods, CHH methylation levels were repressed under their favorable light conditions, particularly in rice. We identified numerous differentially methylated regions (DMRs) that were influenced by photoperiod in both plant species. Apart from differential sRNA clusters, we observed alterations in the expression of key components of the RNA-directed DNA methylation pathway, DNA methyltransferases, and demethylases, which may contribute to the identified photoperiod-influenced CHH DMRs. Furthermore, we identified many differentially expressed genes in response to different daylengths, some of which were associated with the DMRs. Notably, we discovered a photoperiod-responsive gene MYB11 in the transcriptome of B.distachyon, and further demonstrated its role as a flowering inhibitor by repressing FT1 transcription. Together, our comparative and functional analysis sheds light on the effects of daylength on DNA methylation, sRNA accumulation, and gene expression variations in LD and SD plants, thereby facilitating better designing breeding programs aimed at developing high-yield crops that can adapt to local growing seasons.

A dog's life: Early life histories influence methylation of glucocorticoid (NR3C1) and oxytocin (OXTR) receptor genes, cortisol levels, and attachment styles.

Early life deprivation and stress can contribute to life-long, problematic consequences, including epigenetic variations related to behavior and health. Domestic dogs share human environments and social-cognitive traits, making them a promising comparative model to examine developmental plasticity. We examined 47 owner-dog dyads, including dogs rescued from abusive or neglectful environments, and matched control dogs for changes in DNA methylation of glucocorticoid (NR3C1) and oxytocin (OXTR) receptor genes previously shown to be affected by early life stress in other species including humans. We used an attachment paradigm, which included a separation event to examine cortisol levels and owner-dog attachment styles. Overall, dogs with adverse histories had different NR3C1 methylation patterns as a function of age and less OXTR methylation than comparison dogs. Dogs with adverse histories did not differ in their cortisol change from baseline to poststressor from comparison dogs, but the change in cortisol was associated with NR3C1 methylation. In addition, dogs with a history of early life stress had more insecure attachment styles; for every unit increase of OXTR methylation, the odds increased for insecure attachment style. This study demonstrates that adverse life histories lead to methylation differences, resulting in the hypothalamic-pituitary-adrenal (HPA) axis's dysregulation and differences in behavioral phenotypes.

Spatial covariation between genetic and epigenetic diversity in wild plant and animal populations: a meta-analysis.

Epigenetic variation may be crucial in understanding the structure of wild populations, thereby aiding in their management and conservation. However, the relationship between epigenetic and genetic variation remains poorly understood, especially in wild populations. To address this, we conducted a meta-analysis of studies that examined the genetic and epigenetic structures of wild plant and animal populations. We aimed to determine whether epigenetic variation is spatially independent of genetic variation in the wild and to highlight the conditions under which epigenetic variation might be informative. We show a significant positive correlation between genetic and epigenetic pairwise differentiation, indicating that in wild populations, epigenetic diversity is closely linked to genetic differentiation. The correlation was weaker for population pairs that were weakly differentiated genetically, suggesting that in such cases, epigenetic marks might be independent of genetic marks. Additionally, we found that global levels of genetic and epigenetic differentiation were similar across plant and animal populations, except when populations were weakly differentiated genetically. In such cases, epigenetic differentiation was either higher or lower than genetic differentiation. Our results suggest that epigenetic information is particularly relevant in populations that have recently diverged genetically or are connected by gene flow. Future studies should consider the genetic structure of populations when inferring the role of epigenetic diversity in local adaptation in wild populations. Furthermore, there is a need to identify the factors that sustain the links between genetic and epigenetic diversity to improve our understanding of the interplay between these two forms of variation in wild populations.

(060) Epigenetic and Gene Expression Profiles in Non-Plaque Tissues from Men with Peyronie’s Disease

Abstract Introduction Peyronie’s Disease (PD) can significantly impact sexual function. A hereditary predisposition to PD suggests that genetic variants may exist, and gene expression may modulate the penetrance of the disease. Identification of changes in epigenetic and gene expression profiles will facilitate a deeper understanding of the disease and provide insight for more targeted therapies. Objective Our objective is to determine if PD is correlated with epigenetic variations and/or gene expression changes, as indicated by DNA methylation assessment and RNA sequencing. Methods Penile tunica albuginea samples (not from fibrotic plaques) were obtained from men with PD undergoing penile prosthesis placement. Control samples were collected from men with erectile dysfunction (ED) without PD undergoing penile prosthesis placement. DNA methylation analyses were performed on homogenized penile tissue samples via an Illumina Human MethylationEPIC BeadChip v2 array. Using the minfi package in R, beta values were produced for all 936,990 CpG sites for each sample and SWAN normalization was applied. Differentially methylated regions (DMR) were found via USEQ with a threshold Wilcoxon FDR score of 40. Gene expression levels were examined in PD and ED samples via RNA-sequencing. Gene expression data was compared against epigenetic data to determine if any epigenetics changes identified affected gene expression profiles. Results A total of 24 tissue samples were collected: 12 ED and 12 PD. USEQ yielded 36 total DMRs with an FDR score of 40 or greater (p-value<0.0001). Of these 36 DMRs, a Stanford GREAT analysis revealed 60 total gene-region associations and five implicated biological processes: anterior/posterior pattern specification, chordate embryonic development, embryo development (ending in birth or egg hatching), somitogenesis, and pattern specification process. Furthermore, differential gene expression analysis identified 76 genes with significant expression changes between PD and ED groups, of which 17 genes were upregulated while 59 were downregulated. Long noncoding RNAs and the keratocan gene showed notable expression differences between PD and ED groups. GO enrichment analysis revealed significant terms related to DNA binding and protein binding. None of the differentially regulated genes overlapped with identified DMRs. Conclusions This study identified distinct gene expression and DNA methylation patterns between PD and ED groups, despite PD samples not being taken from plaque regions, suggesting that more systemic changes may be present. Upregulated genes in PD included long noncoding RNAs and the keratocan gene, suggesting their involvement in disease pathogenesis. Long noncoding RNA overexpression may serve a regulatory function in gene expression or cell processes while overexpression of the keratocan gene may promote collagen accumulation and remodeling, leading to fibrous plaque formation. Likewise, DMRs and their region-gene associations suggest a role in early embryonic development for pathogenesis. Although RNA-seq did not indicate any significant differentially expressed genes that matched with gene-region associations correlated with DMRs, the significance and quantity of DMRs between ED and PD sample groups is indicative of affected biological processes that manifest in distinct pathophysiologies. Further research is needed to investigate if differentially regulated genes exist in DMRs that exhibited changes but did not meet the criteria threshold for inclusion here. Disclosure Any of the authors act as a consultant, employee or shareholder of an industry for: Contraline, Techfields Inc, Alto Neurosciences, Curebase.

Three near-complete genome assemblies reveal substantial centromere dynamics from diploid to tetraploid in Brachypodium genus

BackgroundCentromeres are critical for maintaining genomic stability in eukaryotes, and their turnover shapes genome architectures and drives karyotype evolution. However, the co-evolution of centromeres from different species in allopolyploids over millions of years remains largely unknown.ResultsHere, we generate three near-complete genome assemblies, a tetraploid Brachypodium hybridum and its two diploid ancestors, Brachypodium distachyon and Brachypodium stacei. We detect high degrees of sequence, structural, and epigenetic variations of centromeres at base-pair resolution between closely related Brachypodium genomes, indicating the appearance and accumulation of species-specific centromere repeats from a common origin during evolution. We also find that centromere homogenization is accompanied by local satellite repeats bursting and retrotransposon purging, and the frequency of retrotransposon invasions drives the degree of interspecies centromere diversification. We further investigate the dynamics of centromeres during alloploidization process, and find that dramatic genetics and epigenetics architecture variations are associated with the turnover of centromeres between homologous chromosomal pairs from diploid to tetraploid. Additionally, our pangenomes analysis reveals the ongoing variations of satellite repeats and stable evolutionary homeostasis within centromeres among individuals of each Brachypodium genome with different polyploidy levels.ConclusionsOur results provide unprecedented information on the genomic, epigenomic, and functional diversity of highly repetitive DNA between closely related species and their allopolyploid genomes at both coarse and fine scale.

Contributions of transcriptional noise to leukaemia evolution: KAT2A as a case-study.

Transcriptional noise is proposed to participate in cell fate changes, but contributions to mammalian cell differentiation systems, including cancer, remain associative. Cancer evolution is driven by genetic variability, with modulatory or contributory participation of epigenetic variants. Accumulation of epigenetic variants enhances transcriptional noise, which can facilitate cancer cell fate transitions. Acute myeloid leukaemia (AML) is an aggressive cancer with strong epigenetic dependencies, characterized by blocked differentiation. It constitutes an attractive model to probe links between transcriptional noise and malignant cell fate regulation. Gcn5/KAT2A is a classical epigenetic transcriptional noise regulator. Its loss increases transcriptional noise and modifies cell fates in stem and AML cells. By reviewing the analysis of KAT2A-depleted pre-leukaemia and leukaemia models, I discuss that the net result of transcriptional noise is diversification of cell fates secondary to alternative transcriptional programmes. Cellular diversification can enable or hinder AML progression, respectively, by differentiation of cell types responsive to mutations, or by maladaptation of leukaemia stem cells. KAT2A-dependent noise-responsive genes participate in ribosome biogenesis and KAT2A loss destabilizes translational activity. I discuss putative contributions of perturbed translation to AML biology, and propose KAT2A loss as a model for mechanistic integration of transcriptional and translational control of noise and fate decisions. This article is part of a discussion meeting issue 'Causes and consequences of stochastic processes in development and disease'.

Cardiovascular Characteristics in Patients with Prader-Willi Syndrome

Abstract The most prevalent type of syndromic obesity is referred to as Prader-Willi Syndrome (PWS), being determined by the lack of expression of paternal genes on chromosome 15q11.2-q13 due to genomic or epigenetic variations, such as DNA and histone methylation or acetylation. The syndrome is frequently associated with behavioral disorders, intellectual deficiencies, short stature, polyphagia, hypogonadism and muscular hypotonia, all stemming from the multiple endocrine dysfunctions characterizing this condition. Cardiovascular (CV) anomalies can manifest even in the early stages of life, and those with PWS have an elevated risk of early onset cardiovascular diseases. The somatic and behavioral aspects of the syndrome interact intricately to cause this increased risk for CV pathologies. Changes in the GH-IGF axis are seen in most Prader-Willi Syndrome (PWS) patients, irrespective of obesity. Specific cardiovascular features of GHD in adult PWS patients include reduced cardiac mass, decreased ejection fraction, and diminished chronotropic response to dobutamine.

Identification of lineage-specific epigenetic regulators FOXA1 and GRHL2 through chromatin accessibility profiling in breast cancer cell lines.

Breast cancer is a heterogeneous disease, and breast cancer cell lines are invaluable for studying this heterogeneity. However, the epigenetic diversity across these cell lines remains poorly understood. In this study, we performed genome-wide chromatin accessibility analysis on 23 breast cancer cell lines, including 2 estrogen receptor (ER)-positive/human epidermal growth factor receptor 2 (HER2)-negative (ER+/HER2-), 3 ER+/HER2+, 3 HER2+, and 15 triple-negative breast cancer (TNBC) lines. These cell lines were classified into three groups based on their chromatin accessibility: the receptor-positive group (Group-P), TNBC basal group (Group-B), and TNBC mesenchymal group (Group-M). Motif enrichment analysis revealed that only Group-P exhibited coenrichment of forkhead box A1 (FOXA1) and grainyhead-like 2 (GRHL2) motifs, whereas Group-B was characterized by the presence of the GRHL2 motif without FOXA1. Notably, Group-M did not show enrichment of either FOXA1 or GRHL2 motifs. Furthermore, gene ontology analysis suggested that group-specific accessible regions were associated with their unique lineage characteristics. To investigate the epigenetic landscape regulatory roles of FOXA1 and GRHL2, we performed knockdown experiments targeting FOXA1 and GRHL2, followed by assay for transposase-accessible chromatin sequencing analysis. The findings revealed that FOXA1 maintains Group-P-specific regions while suppressing Group-B-specific regions in Group-P cells. In contrast, GRHL2 preserves commonly accessible regions shared between Group-P and Group-B in Group-B cells, suggesting that FOXA1 and GRHL2 play a pivotal role in preserving distinct chromatin accessibility patterns for each group. Specifically, FOXA1 distinguishes between receptor-positive and TNBC cell lines, whereas GRHL2 distinguishes between basal-like and mesenchymal subtypes in TNBC lines.

Is developmental plasticity triggered by DNA methylation changes in the invasive cane toad (Rhinella marina)?

Many organisms can adjust their development according to environmental conditions, including the presence of conspecifics. Although this developmental plasticity is common in amphibians, its underlying molecular mechanisms remain largely unknown. Exposure during development to either 'cannibal cues' from older conspecifics, or 'alarm cues' from injured conspecifics, causes reduced growth and survival in cane toad (Rhinella marina) tadpoles. Epigenetic modifications, such as changes in DNA methylation patterns, are a plausible mechanism underlying these developmental plastic responses. Here we tested this hypothesis, and asked whether cannibal cues and alarm cues trigger the same DNA methylation changes in developing cane toads. We found that exposure to both cannibal cues and alarm cues was associated with local changes in DNA methylation patterns. These DNA methylation changes affected genes putatively involved in developmental processes, but in different genomic regions for different conspecific-derived cues. Genetic background explains most of the epigenetic variation among individuals. Overall, the molecular mechanisms triggered by exposure to cannibal cues seem to differ from those triggered by alarm cues. Studies linking epigenetic modifications to transcriptional activity are needed to clarify the proximate mechanisms that regulate developmental plasticity in cane toads.

Former smoking associated with epigenetic modifications in human granulosa cells among women undergoing assisted reproduction

Smoking exposure during adulthood can disrupt oocyte development in women, contributing to infertility and possibly adverse birth outcomes. Some of these effects may be reflected in epigenome profiles in granulosa cells (GCs) in human follicular fluid. We compared the epigenetic modifications throughout the genome in GCs from women who were former (N = 15) versus never smokers (N = 44) undergoing assisted reproductive technologies (ART). This study included 59 women undergoing ART. Smoking history including time since quitting was determined by questionnaire. GCs were collected during oocyte retrieval and DNA methylation (DNAm) levels were profiled using the Infinium MethylationEPIC BeadChip. We performed an epigenome-wide association study with robust linear models, regressing DNAm level at individual loci on smoking status, adjusting for age, ovarian stimulation protocol, and three surrogate variables. We performed differentially methylated regions (DMRs) analysis and over-representation analysis of the identified CpGs and corresponding gene set. 81 CpGs were differentially methylated among former smokers compared to never smokers (FDR < 0.05). We identified 2 significant DMRs (KCNQ1 and RHBDD2). The former smoking-associated genes were enriched in oxytocin signaling, adrenergic signaling in cardiomyocytes, platelet activation, axon guidance, and chemokine signaling pathway. These epigenetic variations have been associated with inflammatory responses, reproductive outcomes, cancer development, neurodevelopmental disorder, and cardiometabolic health. Secondarily, we examined the relationships between time since quitting and DNAm at significant CpGs. We observed three CpGs in negative associations with the length of quitting smoking (p < 0.05), which were cg04254052 (KCNIP1), cg22875371 (OGDHL), and cg27289628 (LOC148145), while one in positive association, which was cg13487862 (PLXNB1). As a pilot study, we demonstrated epigenetic modifications associated with former smoking in GCs. The study is informative to potential biological pathways underlying the documented association between smoking and female infertility and biomarker discovery for smoking-associated reproductive outcomes.

Epigenetic variation impacts individual differences in the transcriptional response to influenza infection.

Humans display remarkable interindividual variation in their immune response to identical challenges. Yet, our understanding of the genetic and epigenetic factors contributing to such variation remains limited. Here we performed in-depth genetic, epigenetic and transcriptional profiling on primary macrophages derived from individuals of European and African ancestry before and after infection with influenza A virus. We show that baseline epigenetic profiles are strongly predictive of the transcriptional response to influenza A virus across individuals. Quantitative trait locus (QTL) mapping revealed highly coordinated genetic effects on gene regulation, with many cis-acting genetic variants impacting concomitantly gene expression and multiple epigenetic marks. These data reveal that ancestry-associated differences in the epigenetic landscape can be genetically controlled, even more than gene expression. Lastly, among QTL variants that colocalized with immune-disease loci, only 7% were gene expression QTL, while the remaining genetic variants impact epigenetic marks, stressing the importance of considering molecular phenotypes beyond gene expression in disease-focused studies.

Epigenetic modifications in solid tumor metastasis in people of African ancestry.

This review focuses on the critical role of epigenetic modifications in solid tumor metastasis, particularly in people of African ancestry. Epigenetic alterations, such as DNA methylation, histone modifications, alterations in non-coding RNAs, and mRNA methylation, significantly influence gene expression, contributing to cancer development and progression. Despite the primary focus on populations of European, American, and Asian descent in most cancer research, this work emphasizes the importance of studying the unique genetic and epigenetic landscapes of African populations for a more inclusive approach in understanding and treating cancer. Insights from this review have the potential to pave the way for the development of effective, tailored treatments, and provide a richer resource for understanding cancer progression and metastasis. Specific focus was placed on the role of DNA methylation, histone modifications, non-coding RNAs, and mRNA methylation in solid tumor metastasis, including how these modifications contribute to the regulation of tumor suppressor genes and oncogenes, influence cellular pathways and signaling, and interact with the immune system. Moreover, this review elaborates on the development of epigenetic-targeted therapeutic strategies and the current advances in this field, highlighting the promising applications of these therapies in improving outcomes for African ancestry populations disproportionately affected by certain types of cancer. Nevertheless, this work acknowledges the challenges that lie ahead, particularly the under-representation of African populations in cancer genomic and epigenomic studies and the technical complications associated with detecting subtle epigenetic modifications. Emphasis is placed on the necessity for more inclusive research practices, the development of more robust and sensitive methods for detecting and interpreting epigenetic changes, and the understanding of the interplay between genetic and epigenetic variations. The review concludes with an optimistic outlook on the future of epigenetic research in People of African ancestry, urging the concerted efforts of researchers, clinicians, funding agencies, and policymakers to extend the benefits of this research to all populations.

Epigenetic variation in early and late flowering plants of the rubber-producing Russian dandelion Taraxacum koksaghyz provides insights into the regulation of flowering time

The Russian dandelion (Taraxacum koksaghyz) grows in temperate zones and produces large amounts of poly(cis-1,4-isoprene) in its roots, making it an attractive alternative source of natural rubber. Most T. koksaghyz plants require vernalization to trigger flower development, whereas early flowering varieties that have lost their vernalization dependence are more suitable for breeding and domestication. To provide insight into the regulation of flowering time in T. koksaghyz, we induced epigenetic variation by in vitro cultivation and applied epigenomic and transcriptomic analysis to the resulting early flowering plants and late flowering controls, allowing us to identify differences in methylation patterns and gene expression that correlated with flowering. This led to the identification of candidate genes homologous to vernalization and photoperiodism response genes in other plants, as well as epigenetic modifications that may contribute to the control of flower development. Some of the candidate genes were homologous to known floral regulators, including those that directly or indirectly regulate the major flowering control gene FT. Our atlas of genes can be used as a starting point to investigate mechanisms that control flowering time in T. koksaghyz in greater detail and to develop new breeding varieties that are more suited to domestication.

DNA methylation: an emerging paradigm of gene regulation under drought stress in plants.

Drought is an enormous threat to global crop production. In order to ensure food security for the burgeoning population, we must develop drought tolerant crop varieties. This necessitates the identification of drought-responsive genes and understanding the mechanisms involved in their regulation. DNA methylation is a widely studied mechanism of epigenetic regulation of gene expression, which is known to play vital role in conferring tolerance to various biotic and abiotic stress factors. The recent advances in next-generation sequencing (NGS) technologies, has allowed unprecedented access to genome-wide methylation marks, with single base resolution. The most important roles of DNA methylation have been studied in terms of gene body methylation (gbM), which is associated with regulation of both transcript abundance and its stability. The availability of mutants for the various genes encoding enzymes involved in methylation of DNA has allowed ascertainment of the biological significance of methylation. Even though a vast number of reports have emerged in the recent past, where both genome-wide methylation landscape and locus specific changes in DNA methylation have been studied, a conclusive picture with regards to the biological role of DNA methylation is still lacking. Compounding this, is the lack of sufficient evidence supporting the heritability of these epigenetic changes. Amongst the various epigenetic variations, the DNA methylation changes are observed to be the most stable. This review describes the drought-induced changes in DNA methylation identified across different plant species. We also briefly describe the stress memory contributed by these changes. The identification of heritable, drought-induced methylation marks would broaden the scope of crop improvement in the future.

Epiallelic variation of non-coding RNA genes and their phenotypic consequences

Epigenetic variations contribute greatly to the phenotypic plasticity and diversity. Current functional studies on epialleles have predominantly focused on protein-coding genes, leaving the epialleles of non-coding RNA (ncRNA) genes largely understudied. Here, we uncover abundant DNA methylation variations of ncRNA genes and their significant correlations with plant adaptation among 1001 natural Arabidopsis accessions. Through genome-wide association study (GWAS), we identify large numbers of methylation QTL (methylQTL) that are independent of known DNA methyltransferases and enriched in specific chromatin states. Proximal methylQTL closely located to ncRNA genes have a larger effect on DNA methylation than distal methylQTL. We ectopically tether a DNA methyltransferase MQ1v to miR157a by CRISPR-dCas9 and show de novo establishment of DNA methylation accompanied with decreased miR157a abundance and early flowering. These findings provide important insights into the genetic basis of epigenetic variations and highlight the contribution of epigenetic variations of ncRNA genes to plant phenotypes and diversity.

(059) Epigenetic Profiles of Men with Peyronie’s Disease

Abstract Introduction Peyronie’s Disease (PD) can significantly impact sexual function. A hereditary predisposition to PD suggests that genetic variants may exist, and gene expression may modulate the penetrance of the disease. Identification of changes in epigenetic or gene expression profiles would facilitate a deeper understanding of the disease and provide insight for more targeted therapies. Objective Our objective is to determine if predisposition to PD is correlated with epigenetic variations and/or gene expression changes, as indicated by DNA methylation assessment and RNA sequencing. Methods Penile tunica albuginea samples were obtained from men with PD undergoing penile prosthesis placement. Penile sample from these men were not from fibrotic plaques. Control samples were collected from men with erectile dysfunction (ED) without PD undergoing penile prosthesis placement. DNA methylation analyses were performed on homogenized penile tissue samples via an Illumina Human MethylationEPIC BeadChip v2 array. Using the minfi package in R, beta values were produced for all 936,990 CpG sites for each sample and SWAN normalization was applied. Differentially methylated regions (DMR) were found via USEQ with a threshold Wilcoxon FDR score of 40. Gene expression levels were examined in PD and ED samples via RNA-sequencing. Gene expression data was compared against epigenetic data to determine if any epigenetics changes identified affected gene expression profiles. Results A total of 24 tissue samples were collected: 12 ED and 12 PD. USEQ yielded 36 total DMRs with a FDR score of 40 or greater (p-value&amp;lt;0.0001). Of these 36 DMRs, a Stanford GREAT analysis revealed 60 total gene-region associations and five implicated biological processes: anterior/posterior pattern specification, chordate embryonic development, embryo development (ending in birth or egg hatching), somitogenesis, and pattern specification process. Furthermore, differential gene expression analysis identified 76 genes with significant expression changes between PD and ED groups, of which 17 genes were upregulated while 59 were downregulated. Long noncoding RNAs and the keratocan gene showed notable expression differences between PD and ED groups. GO enrichment analysis revealed significant terms related to DNA binding and protein binding. None of the differentially regulated genes overlapped with identified DMRs. Conclusions This study identified distinct gene expression and DNA methylation patterns between PD and ED groups, despite PD samples not being taken from plaque regions. Upregulated genes in PD included long noncoding RNAs and the keratocan gene, suggesting their involvement in disease pathogenesis. Long noncoding RNA overexpression may serve a regulatory function in gene expression or cell processes while overexpression of the keratocan gene may promote collagen accumulation and remodeling, leading to fibrous plaque formation in the affected area. Likewise, DMRs and their region-gene associations suggest a role in early embryonic development for pathogenesis. Although RNA-seq did not indicate any significant differentially expressed genes that matched with gene-region associations correlated with DMRs, the significance and quantity of DMRs between ED and PD sample groups is indicative of affected biological processes that manifest in distinct pathophysiologies. Further research is needed to investigate if differentially regulated genes exist in DMRs that exhibited changes but did not meet the criteria threshold for inclusion here. Disclosure Any of the authors act as a consultant, employee or shareholder of an industry for: Paterna bio, Firmtech, Turtle health, Maximus, Carrot, Contraline, endo pharmaceuticals, inherent biosciences, techfields inc, macro trials, alto neurosciences, curebase, vivify medical.