'; ?> geneimprint : Hot off the Press http://www.geneimprint.com/site/hot-off-the-press Daily listing of the most recent articles in epigenetics and imprinting, collected from the PubMed database. en-us Wed, 27 Aug 2025 13:23:20 EDT Wed, 27 Aug 2025 13:23:20 EDT jirtle@radonc.duke.edu james001@jirtle.com Epigenetic and genetic profiling of comorbidity patterns among substance dependence diagnoses. Pathak GA, Pietrzak RH, Lacobelle A, Overstreet C, Wendt FR, Deak JD, Friligkou E, Nunez YZ, Montalvo-Ortiz JL, Levey DF, Kranzler HR, Gelernter J, Polimanti R
Mol Psychiatry (Sep 2025)

This study investigated the genetic and epigenetic mechanisms underlying the comorbidity of five substance dependence diagnoses (SDs; alcohol, AD; cannabis, CaD; cocaine, CoD; opioid, OD; tobacco, TD). A latent class analysis (LCA) was performed on 22,668 individuals from six cohorts to identify comorbid DSM-IV SD patterns. In subsets of this sample, we tested SD-latent classes with respect to polygenic overlap of psychiatric and psychosocial traits in 7659 individuals of European descent and epigenome-wide changes in 886 individuals of African, European, and Admixed-American descents. The LCA identified four latent classes related to SD comorbidities: AD + TD, CoD + TD, AD + CoD + OD + TD (i.e., polysubstance addiction, PSU), and TD. In the epigenome-wide association analysis, SPATA4 cg02833127 was associated with CoD + TD, AD + TD, and PSU latent classes. AD + TD latent class was also associated with CpG sites located on ARID1B, NOTCH1, SERTAD4, and SIN3B, while additional epigenome-wide significant associations with CoD + TD latent class were observed in ANO6 and MOV10 genes. PSU-latent class was also associated with a differentially methylated region in LDB1. We also observed shared polygenic score (PGS) associations for PSU, AD + TD, and CoD + TD latent classes (i.e., attention-deficit hyperactivity disorder, anxiety, educational attainment, and schizophrenia PGS). In contrast, TD-latent class was exclusively associated with posttraumatic stress disorder-PGS. Other specific associations were observed for PSU-latent class (subjective wellbeing-PGS and neuroticism-PGS) and AD + TD-latent class (bipolar disorder-PGS). In conclusion, we identified shared and unique genetic and epigenetic mechanisms underlying SD comorbidity patterns. These findings highlight the importance of modeling the co-occurrence of SD diagnoses when investigating the molecular basis of addiction-related traits.]]> Wed, 31 Dec 1969 19:00:00 EST Deciphering sarcoidosis immunopathogenesis through systems biology. Jbeli AH, Crouser ED, Bhargava M
Curr Opin Pulm Med (Sep 2025)

Sarcoidosis is a complex, multisystem disease characterized by granulomatous inflammation and variable clinical outcomes. Its pathogenesis and progression are driven by intricate biological interactions, involving a complex interplay between patient-specific factors such as genetic background, sex, and environmental exposures, as well as epigenetic modifications that regulate gene expression and protein levels. These interconnected layers ultimately drive immune response to yet unidentified trigger(s), culminating in granuloma formation and, in some cases, with an aberrant repair response leading to irreversible organ dysfunction in some cases. In this review, we aim to synthesize recent multiomics research that unravels the underlying biological networks, offering a systems-level understanding of sarcoidosis.]]> Wed, 31 Dec 1969 19:00:00 EST and are human placenta-specific imprinted genes associated with germline-inherited maternal DNA methylation. Daskeviciute D, Sainty B, Chappell-Maor L, Bone C, Russell S, Iglesias-Platas I, Arnaud P, Monteagudo-Sánchez A, Greenberg MVC, Chen K, Manerao-Azua A, Perez de Nanclares G, Lartey J, Monk D
Epigenetics (Dec 2025)

Genomic imprinting is the parent-of-origin specific monoallelic expression of genes that result from complex epigenetic interactions. It is often achieved by monoallelic 5-methylcytosine, resulting in the formation of differentially methylated regions (DMRs). These show a bias towards oocyte-derived methylation and survive reprogramming in the pre-implantation embryo. Imprinting is widespread in the human placenta. We have recently performed whole-genome screens for novel imprinted placenta-specific germline DMRs (gDMRs) by comparing methylomes of gametes, blastocysts and various somatic tissues, including placenta. We observe that, unlike conventional imprinting, for which methylation at gDMRs is observed in all tissues, placenta-specific imprinting is associated with transient gDMRs, present only in the pre-implantation embryo and extra-embryonic lineages. To expand the list of imprinted genes subject to placenta-specific imprinting, we reinvestigated our list of candidate loci and characterized two novel imprinted genes, and , both of which display polymorphic imprinting. Interrogation of placenta single-cell RNA-seq datasets, as well as cell-type methylation profiles, revealed complex cell-type specificity. We further interrogated their methylation and expression in placental samples from complicated pregnancies, but failed to identify differences between intrauterine growth restricted or pre-eclamptic samples and controls, suggesting they are not involved in these conditions.]]> Wed, 31 Dec 1969 19:00:00 EST [Example of a genetic condition caused by an imprinting disorder: Angelman syndrome]. Coquisart C, Skouri S, Delplancq G, Spentchian M, Maneglier B, Guberto M, Brisset S
Ann Biol Clin (Paris) (Aug 2025)

An 18-months old boy was seen in a clinical genetics consultation with both his parents for a global developmental delay, hypotonia, post-natal microcephaly, as well as cognitive impairment including an absence of language acquisition. High throughput exome sequencing identified a pathogenic variant in the UBE3A gene that was inherited from his asymptomatic mother. This variant causes the child to lose the contribution of the maternal allele, through loss of UBE3A genetic expression. UBE3A is localized into a genomic imprinting region which undergoes transcriptional regulation based on parental origin, an epigenetic phenomenon described in certain specific regions of the human genome. Its expression is repressed on the paternal chromosome at locus 15q11-13. The truncating variant on the maternal allele then leads to a complete loss of UBE3A expression. This results in Angelman syndrome. Angelman syndrome is a genetic neurodevelopmental disorder whose transmission mode depends on the causative molecular mechanism, which consists of a lack of contribution from the maternal 15q11-q13 region. Angelman's phenotype and evolution varies according to causative molecular mechanism. Precise laboratory diagnosis is especially important for genetic counselling: in our patient's family, the recurrence risk amounts to 50 % in the event of a future pregnancy, and the family's relatives must me informed and offered medical counsel.]]> Wed, 31 Dec 1969 19:00:00 EST The myoblast methylome: multiple types of associations with chromatin and transcription. Sen S, Lacey M, Baribault C, Ponnaluri VKC, Esteve PO, Ehrlich KC, Meletta M, Pradhan S, Ehrlich M
Epigenetics (Dec 2025)

Epigenetic changes are implicated in development, repair, and physiology of postnatal skeletal muscle (SkM). We generated methylomes for human myoblasts (SkM progenitor cells) and determined myoblast differentially methylated regions (DMRs) for comparison to the epigenomics and transcriptomics of diverse cell types. Analyses were from global genomic and single-gene perspectives and included reporter gene assays. One atypical finding was the association of promoter-adjacent hypermethylation in myoblasts with transcription turn-on, but at downmodulated levels, for certain genes (., and ). In contrast, brain-specific was in repressed chromatin and silent in most cell types but linked to hypermethylated DMRs specifically in myoblasts. The -linked DMRs might be needed because of the overlapping or nearby binding of myogenic differentiation protein 1 (MYOD). We found genome-wide overlap of DMRs with MYOD or CCCTC-binding factor (CTCF) binding sites in myoblasts that is consistent with the importance of MYOD, as well as CTCF, in organizing myoblast transcription-enhancing chromatin interactions. We also observed some gene upregulation correlated with a special association of regional DNA hypomethylation with H3K36me3, H3K27ac, and H3K4me1 enrichment. Our study highlights unusual relationships between epigenetics and gene expression that illustrate the interplay between DNA methylation and chromatin epigenetics in the regulation of transcription.]]> Wed, 31 Dec 1969 19:00:00 EST Accounting for differences between Infinium MethylationEPIC v2 and v1 in DNA methylation-based tools. Zhuang BC, Jude MS, Konwar C, Yusupov N, Ryan CP, Engelbrecht HR, Whitehead J, Halberstam AA, MacIsaac JL, Dever K, Tran TK, Korinek K, Zimmer Z, Lee NR, McDade TW, Kuzawa CW, Huffman KM, Belsky DW, Binder EB, Czamara D, Korthauer K, Kobor MS
Life Sci Alliance (Sep 2025)

The recently launched Illumina Infinium MethylationEPIC v2.0 (EPICv2), successor of MethylationEPIC v1.0 (EPICv1), retains most of the probes in EPICv1, while expanding coverage of regulatory elements. The concordance between the two EPIC versions in DNA methylation-based tools has not yet been investigated. To address this, DNA methylation was profiled on both versions using matched blood samples across four cohorts spanning early to late adulthood. High concordance between versions at the array level but variable agreement at the individual probe level was noted. A significant contribution of the EPIC version to DNA methylation variation was observed, though it was to a smaller extent compared with sample relatedness and cell-type composition. Modest but significant differences in DNA methylation-based estimates between versions were observed, irrespective of the data preprocessing method used. Adjustments for EPIC version or calculation of estimates separately for each version largely mitigated these version-specific discordances. This work emphasizes the importance of accounting for EPIC version differences in research scenarios, especially in meta-analyses and longitudinal studies that require data harmonization across versions.]]> Wed, 31 Dec 1969 19:00:00 EST Differential methylation patterns in cord blood associated with prenatal exposure to neighborhood crime: an epigenome-wide association study and regional analysis. Martin CL, Chen J, D'Alessio AS, Ward-Caviness CK, Ye A, Lodge EK, Ghastine L, Dhingra R, Jima DD, Murphy SK, Hoyo C
Epigenetics (Dec 2025)

Exposure to prenatal social stressors during pregnancy is associated with adverse birth outcomes and has been linked to epigenetic changes in DNA methylation (DNAm); however, less understood is the effect of neighborhood-level stressors like crime during pregnancy on offspring DNAm. Using data from the Newborn Epigenetic Study, we conducted epigenome-wide and regional analyses of the association between exposure to neighborhood crime and DNAm in offspring cord blood using Illumina's HumanMethylation450k BeadChip among 185 mother-offspring pairs. Prenatal exposure to neighborhood crime at the census block group level was mapped to participants' residential addresses during the gestational window from the date of last menstrual period to delivery. Models for the epigenome-wide and regional analyses were adjusted for maternal age, race/ethnicity, education, smoking, cell-type composition, and offspring sex. Genetic influence and gene expression enrichment were assessed using methylation quantitative trait loci (mQTLs) and expression quantitative trait methylation (eQTMs) analyses. Functional enrichment was determined using Gene Ontology and KEGG databases. We did not find evidence of epigenome-wide associations between prenatal neighborhood crime exposure and DNAm; however, we identified nine differentially methylated regions (DMRs) comprising 51 CpG sites associated with neighborhood crime. CpG sites within significant differentially methylated regions were associated with mQTLs at birth and eQTMs upon further examination. KEGG analysis identified a significant Th1 and Th2 cell differentiation pathway. Our results suggest potential links between prenatal neighborhood crime exposure and offspring DNAm; however, additional research is needed in larger cohorts across wider geographic areas to confirm our results.]]> Wed, 31 Dec 1969 19:00:00 EST Progress on Multiomics Research on Acne Vulgaris: A Literature Review. Lai Y, Fan M, Fan X, Chen J, Xiang LF, Ma Y
J Invest Dermatol (Sep 2025)

Acne vulgaris, a prevalent chronic inflammatory disease of the pilosebaceous unit, continues to present with a complex pathogenesis that is not fully understood. The advent of high-throughput sequencing technologies has revolutionized biomedical research, enabling the comprehensive use of multiomics analyses to study diseases with intricate mechanisms, such as acne. This review summarizes the progress in genomics, epigenomics, transcriptomics, proteomics, and metabolomics research on acne. By providing a comprehensive overview, we aim to enhance our understanding of acne pathogenesis and identify potential therapeutic targets that could inspire the prevention and treatment of acne.]]> Wed, 31 Dec 1969 19:00:00 EST use capsules, transporters, mobile genetic elements, and other evolutionary adaptations to survive antibiotics exposure in the absence of resistance genes. Mmatli M, Mbelle NM, Fourie B, Osei Sekyere J
Virulence (Dec 2025)

Whole-genome sequencing, transcriptomic profiling, and epigenomic analyses were performed. Phenotypic assays were used to evaluate the effects of various inhibitors on antibiotic susceptibility, while bioinformatic pipelines were used to characterize resistance determinants, virulence factors, and mobile genetic elements (MGEs).]]> Wed, 31 Dec 1969 19:00:00 EST Sex-stratified piRNA expression analysis reveals shared functional impacts of perinatal lead (Pb) exposure in murine hearts. Sala-Hamrick KE, Wang K, Perera BPU, Sartor MA, Svoboda LK, Dolinoy DC
Epigenetics (Dec 2025)

The landscape of PIWI-interacting RNA (piRNA) expression in the heart is poorly understood, particularly regarding sex differences. Altered piRNA expression has been reported in cardiovascular disease (CVD), and although exposure to the metal lead (Pb) is strongly associated with CVD risk, no studies have investigated Pb's effects on cardiac piRNAs. This study aimed to characterize piRNA expression in the murine heart and assess sex-specific effects of human-relevant maternal Pb exposure on adult offspring cardiac piRNA expression. piRNAs were identified from whole mouse hearts using sodium periodate exclusion of small RNA and subsequent sequencing. Control mice expressed 18,956 piRNAs in combined-sex analysis; sex-specific analyses revealed 9,231 piRNAs in female hearts and 5,972 piRNAs in male hearts. Genomic mapping showed 28-41% aligned to introns, while 12-28% mapped to exons. Comparing control and Pb-exposed hearts, we found more potential Pb-induced expression changes in females (847) compared to males (187) (p-value < 0.05 and |logFC| > 1). These piRNAs were significantly enriched near genes involved in biological processes related to heart function and CVD development, including mitochondrial function, energy metabolism, and cardiac muscle structure (FDR < 0.05). Overall, we characterized combined and sex-stratified piRNA expression in both control and Pb-exposed murine hearts. In addition to providing a foundation for sex-specific piRNA expression in the heart, these findings suggest a novel epigenetic mechanism by which developmental Pb exposure may impact CVD risk later in life. Future studies will link these sex-specific molecular changes to Pb-induced alterations in cardiac function.]]> Wed, 31 Dec 1969 19:00:00 EST Host-microbe multi-omics and succinotype profiling have prognostic value for future relapse in patients with inflammatory bowel disease. O'Sullivan J, Patel S, Leventhal GE, Fitzgerald RS, Laserna-Mendieta EJ, Huseyin CE, Konstantinidou N, Rutherford E, Lavelle A, Dabbagh K, DeSantis TZ, Shanahan F, Temko A, Iwai S, Claesson MJ
Gut Microbes (Dec 2025)

Crohn's disease (CD) and ulcerative colitis (UC) are chronic relapsing inflammatory bowel disorders (IBD), the pathogenesis of which is uncertain but includes genetic susceptibility factors, immune-mediated tissue injury and environmental influences, most of which appear to act via the gut microbiome. We hypothesized that host-microbe alterations could be used to prognostically stratify patients experiencing relapses up to four years after endoscopy. We therefore examined multiple omics data, including published and new datasets, generated from paired inflamed and non-inflamed mucosal biopsies from 142 patients with IBD (54 CD; 88 UC) and from 34 control (non-diseased) biopsies. The relapse-predictive potential of 16S rRNA gene and transcript amplicons (standing and active microbiota) were investigated along with host transcriptomics, epigenomics and genetics. While standard single-omics analysis could not distinguish between patients who relapsed and those that remained in remission within four years of colonoscopy, we did find an association between the number of flares and a patient's succinotype. Our multi-omics machine learning approach was also able to predict relapse when combining features from the microbiome and human host. Therefore multi-omics, rather than single omics, better predicts relapse within 4 years of colonoscopy, while a patient's succinotype is associated with a higher frequency of relapses.]]> Wed, 31 Dec 1969 19:00:00 EST Placental DNA methylation key topics: sex- and cell-type specificity, mediation, multi-omics, and biomarker discovery. Cohen NJ, Lesseur C, Cardenas A, Ward-Caviness CK, Spring AC, Rager JE, Fry RC, Eaves LA
Epigenomics (Sep 2025)

The placenta is a dynamic organ that serves numerous purposes for fostering a successful pregnancy and the delivery of a healthy infant in humans. It performs critical functions in nutrient and oxygen transport, immune modulation, and hormonal regulation. DNA methylation, a key epigenetic mechanism of transcriptional regulation, plays a key role in the underlying etiologies of placenta-related health complications. Therefore, assessing placental DNA methylation is essential for understanding how adverse prenatal exposures may impact both short-term and long-term health outcomes in women and children. In this review, we summarize current knowledge on the effects of prenatal exposures on placental DNA methylation and their implications for maternal and child health, focused on human population studies. We also outline five critical directions for human placental DNA methylation research: (1) Investigating sex-specific DNA methylation patterns, (2) Assessing cell type-specific DNA methylation signatures, (3) Applying causal inference methods, (4) Integrating multi-omics approaches, and (5) Using DNA methylation as a biomarker for environmental exposures and developmental outcomes. Advancing research in these areas will enhance our understanding of the biological underpinnings of the developmental origins of health and disease (DOHaD) hypothesis and maximize the potential of placental samples to inform DOHaD-related research.]]> Wed, 31 Dec 1969 19:00:00 EST Perfluoroalkyl substance pollutants disrupt microglia function and trigger transcriptional and epigenomic changes. Cheng Y, Li JR, Yu H, Li S, Tychhon B, Cheng C, Weng YL
Toxicology (Nov 2025)

Per- and polyfluoroalkyl substances (PFAS), commonly referred to as "forever chemicals", are widely utilized in various industries and consumer products worldwide. Their exposure has been associated with numerous diseases and malignancies, including neurodevelopmental and neurodegenerative disorders. However, the molecular mechanisms underlying PFAS-induced adverse effects on the central nervous system (CNS) remain poorly understood. In this study, we investigated the transcriptomic and epigenetic changes in microglia exposed to perfluorooctane sulfonate (PFOS), a prevalent PFAS compound. Our findings demonstrate that 24-hour PFOS exposure (25 and 50 µM) disrupts the microglial transcriptome and compromises their homeostatic state, marked by increased inflammation and impaired actin cytoskeleton remodeling. Comparative analysis with in vivo transcriptional states revealed that PFOS-exposed microglia exhibit gene expression profiles resembling those of aged microglia. Additionally, profiling of active chromatin regions uncovered significant alterations in the H3K27ac landscape in PFOS-exposed microglia. Notably, these epigenetic disruptions persisted even after PFOS withdrawal, with a subset of H3K27ac-enriched regions remaining altered, suggesting the presence of lasting epigenetic scars. Furthermore, transcription factor analysis implicated the AP-1 and TEAD families as potential upstream regulators connecting the altered chromatin landscape to transcriptomic changes. Collectively, these findings provide mechanistic insights into how PFOS exposure disrupts microglial function and highlight its potential role in exacerbating neurodegenerative processes.]]> Wed, 31 Dec 1969 19:00:00 EST Mosaicism for Genome Wide Homozygosity Identified as an Incidental Finding in Two Apparently Healthy Pregnant Women. Haskell GT, Askree SH, Kline L, Hasadsri L, Cabral H, Gadi I, Schwartz S
Am J Med Genet A (Sep 2025)

Uniparental Disomy (UPD) occurs when both copies of a chromosome or chromosomal segment originate from only one parent. Mosaic genome-wide UPD (mos gwUPD) is typically identified in cases of fetal demise and placental dysplasia or in prenatal cases, where imprinting effects are associated with abnormal ultrasound findings. Children with mos gwUPD and clinical features due to UPD-associated imprinting effects (especially Beckwith-Wiedemann syndrome) have been reported; however, reports of adults with mos gwUPD are rare. Here we describe mos gwUPD in two apparently healthy pregnant adult women. Carrier testing noted variants with skewed allelic ratios outside of the normal heterozygous range, prompting further testing. Single nucleotide polymorphism (SNP) microarray identified mosaicism for gwUPD in both individuals, present at 85% and 90%, respectively, in blood, with varying percentages in other tissues. Neither woman displayed clinical features that would be expected with gwUPD at the time of testing, although retrospective careful personal history was consistent. Both women had uneventful pregnancies and delivered full-term healthy infants. These two cases demonstrate that mos gwUPD can be an incidental finding identified in apparently healthy adult women. Clinical follow-up is important for tumor monitoring, genetic counseling, and monitoring of future pregnancies due to mos gwUPD in the maternal endometrial tissue.]]> Wed, 31 Dec 1969 19:00:00 EST Vigorous But Not Moderate Physical Activity Is Associated With Reduced Cardiovascular Disease Risk In Young Hispanic Men. Gattoni C, Bebe K, Bross R, Wang C, Swerdloff RS, Oudiz RJ, Kraus WE, Rossiter HB
Am J Cardiol (Sep 2025)

Physical Activity Guidelines for Americans recommend at least 150 min/week of moderate (MPA) to vigorous (VPA) physical activity to maintain health, regardless of cardiovascular disease (CVD) risk. This study assessed whether physical activity (PA) intensity distinguishes between low and high CVD risk in 196 lean and obese Hispanic men aged 18-40 from the Study of Male Reproductive Epigenomics. PA was measured for 7 days using triaxial accelerometry. The 30-year "full" Framingham Risk Score (FRS) was calculated. Diet quality was assessed using the Healthy Eating Index (HEI-2020). Mean age was 30 ± 5 years with a median FRS of 14% (range: 3% to 85%). The high-risk group (n = 89) had a mean full FRS of 20.3% ± 11.1%, compared to 7.0% ± 3.6% in the low-risk group (n = 107; p <0.001). Both groups met guideline-recommended PA levels. However, the low-risk group performed more VPA (25 ± 20 vs 12 ± 12 min/day; p <0.001). Logistic regressions showed that each additional 1 min/day of VPA reduced the odds of high CVD risk by 4.4% (p = 0.007), adjusted for smoking, diet, age and Body Mass Index (BMI), while MPA did not significantly predict CVD risk (p = 0.823). Stepwise regressions showed that smoking status, BMI, VPA, and diet explained 47.8% of FRS variance (p <0.001), while MPA was excluded. In conclusion, VPA, but not MPA, significantly distinguished low from high CVD risk in young Hispanic men, highlighting the potential role of higher-intensity exercise to reduce CVD risk in this population.]]> Wed, 31 Dec 1969 19:00:00 EST Computational analysis of DNA methylation from long-read sequencing. Fu Y, Timp W, Sedlazeck FJ
Nat Rev Genet (Sep 2025)

DNA methylation is a critical epigenetic mechanism in numerous biological processes, including gene regulation, development, ageing and the onset of various diseases such as cancer. Studies of methylation are increasingly using single-molecule long-read sequencing technologies to simultaneously measure epigenetic states such as DNA methylation with genomic variation. These long-read data sets have spurred the continuous development of advanced computational methods to gain insights into the roles of methylation in regulating chromatin structure and gene regulation. In this Review, we discuss the computational methods for calling methylation signals, contrasting methylation between samples, analysing cell-type diversity and gaining additional genomic insights, and then further discuss the challenges and future perspectives of tool development for DNA methylation research.]]> Wed, 31 Dec 1969 19:00:00 EST High-throughput assessment of and methylation-based newborn screening using IsoPure and QIAcube HT systems. Cartagena C, Alshawsh M, Bui MQ, Gamage D, Thakor RP, Pitt J, Greaves RF, Wall M, Saffery R, Amor DJ, Godler DE
Epigenomics (Sep 2025)

This study compared methylation-specific quantitative melt analysis of FMR1 and SNRPN methylation (mDNA) using automated bisulfite conversion by the magnetic-bead-based IsoPure and column-based QIAcube HT systems.]]> Wed, 31 Dec 1969 19:00:00 EST Germline variants in are associated with multilocus imprinting disturbance in humans and mice. Ochoa E, Zvetkova I, Liv Lee S, Takahashi N, Lan-Leung B, Hobson E, Issa M, Yngvadottir B, Docquier F, Rodger F, Foster-Hall D, Clark G, Toribio A, Martin E, Bottolo L, Ferguson-Smith AC, Fischle W, Constancia M, Maher ER
Proc Natl Acad Sci U S A (Aug 2025)

The investigation of congenital imprinting disorders (CIDs) provides opportunities to elucidate the molecular mechanisms and role of genomic imprinting in development and human disease. Beckwith-Wiedemann spectrum (BWSp) is a prototypic CID resulting from genetic and epigenetic alterations of imprinted genes at chromosome 11p15.5. In up to a quarter of individuals with BWSp, the epigenetic alterations are not confined to 11p15.5 imprinting control regions but also involve other imprinted gene clusters (multilocus imprinting disturbance; MLID). In a consanguineous family with two children diagnosed with BWSp and MLID, the affected individuals were homozygous for a missense variant in , a gene previously implicated in the maintenance of DNA methylation. To investigate whether the c. 2001G>C, p.(Lys667Asn) missense substitution predisposes to abnormal establishment/maintenance of genomic imprinting patterns, a genetically engineered mouse model with a p.(Lys661Asn) variant was developed. Mice homozygous for the variant born to heterozygous mothers did not display an abnormal phenotype, but homozygotes born to healthy homozygous mothers displayed a range of phenotypes including prenatal lethality. Also, MLID was observed in affected mouse embryos. These findings are consistent with biallelic variants in affected individuals resulting in an autosomal recessively inherited cause of MLID in humans and expand the range of epigenetic disorders associated with ]]> Wed, 31 Dec 1969 19:00:00 EST The emerging role of multiomics in aging research. Ruden DM
Epigenomics (Sep 2025)

Aging is a complex biological process involving coordinated changes across multiple molecular systems. Traditional reductionist approaches, while valuable, are insufficient to capture the full scope of aging's systemic nature. Multiomics - integrating data from genomics, transcriptomics, epigenomics, proteomics, and metabolomics - provides a comprehensive framework to study aging as an interconnected network. In this Perspective, I explore how multiomic strategies, particularly those leveraging epigenomic and single-cell data, are reshaping our understanding of aging biology. Epigenetic alterations, including DNA methylation and histone modifications, are not only hallmarks but also powerful biomarkers of biological age. I discuss advances in multiomic aging clocks, cross-tissue atlases, and single-cell spatial technologies that decode aging at unprecedented resolution. I also build on a prior review I wrote with colleagues, Epigenomics. 2023;15(14):741-754, which introduced the concept of pathological epigenetic events that are reversible (PEERs) - epigenetic alterations linked to early-life exposures that predispose to aging and disease but may be therapeutically modifiable. This Perspective examines how PEERs and multiomics intersect to inform biomarkers, geroprotective interventions, and personalized aging medicine. Finally, I highlight integration challenges, ethical concerns, and the need for standardization to accelerate clinical translation. Together, these insights position multiomics as a central pillar in the future of aging research.]]> Wed, 31 Dec 1969 19:00:00 EST Single-cell multi-omics in cancer immunotherapy: from tumor heterogeneity to personalized precision treatment. Le J, Dian Y, Zhao D, Guo Z, Luo Z, Chen X, Zeng F, Deng G
Mol Cancer (Aug 2025)

Cancer immunotherapy has revolutionized clinical oncology; however, the inherent complexity and heterogeneity of cancer present substantial challenges to achieving broad therapeutic efficacy. Tumor heterogeneity manifests not only among different patients but also within individual tumors, further complicating personalized treatment approaches. Single-cell sequencing technologies encompassing genomics, transcriptomics, epigenomics, proteomics, and spatial omics have significantly enhanced our ability to dissect tumor heterogeneity at single-cell resolution with multi-layered depth. These approaches have illuminated tumor biology, immune escape mechanisms, treatment resistance, and patient-specific immune response mechanisms, thereby substantially advancing precision oncology strategies. This review systematically examines recent advances in single-cell multi-omics technologies across various cancer research areas, emphasizing their transformative impacts on understanding tumor heterogeneity, immunotherapy, minimal residual disease monitoring, and neoantigen discovery. Additionally, we discuss current technical and analytical limitations and unresolved questions associated with single-cell technologies. We anticipate single-cell multi-omics technologies will become central to precision oncology, facilitating truly personalized therapeutic interventions.]]> Wed, 31 Dec 1969 19:00:00 EST