Sperm Mitochondrial DNA Copy Number and Nuclear DNA Methylation Across Clinical and Non-Clinical Preconception Cohorts.

Epigenomics in severe male infertility: sperm-derived cell-free DNA methylation for prediction of sperm retrieval.

PURPOSE OF REVIEW Severe male factor infertility is increasingly managed with surgical sperm retrieval, yet current noninvasive predictors cannot reliably distinguish men with retrievable focal spermatogenesis from those with global spermatogenic failure. This review evaluates epigenomic approaches, with emphasis on seminal plasma cell-free DNA methylation, for prediction of sperm retrieval in nonobstructive azoospermia. RECENT FINDINGS Recent literature reinforces a persistent clinical limitation: conventional markers and multivariable models can inform risk, but they do not reliably distinguish focal spermatogenesis from global failure before surgery. At the same time, DNA methylation-based tissue-of-origin analysis and seminal plasma cell-free DNA (cfDNA) studies have created a new opportunity to measure sperm-associated molecular signal directly from the reproductive tract. Preliminary multisite clinical data suggest that sperm-derived cfDNA is best understood as a conditional biomarker whose meaning depends on endocrine and etiologic context. SUMMARY Epigenomic liquid biopsy analysis of cfDNA in seminal plasma may add a biologically direct, noninvasive layer to NOA counseling. The key insight is not simply that sperm-derived cfDNA can be measured, but that its interpretation changes with FSH, genetics, histology and the differential diagnosis of azoospermia. Prospective validation is needed to determine whether this approach improves treatment counseling and surgical planning.

Circulating Cell-Free Mitochondrial DNA as a Redox-Associated Marker of Mitochondrial Homeostasis Disruption during Gastric Carcinogenesis.

Circulating cell-free mitochondrial DNA (ccf-mtDNA) is an emerging non-invasive marker across cancers. Yet, in gastric cancer (GC), its relationship to tissue mtDNA content, oxidative remodeling and somatic mtDNA variants, and thus its basis in mitochondrial homeostasis, remains poorly defined. We analyzed 169 individuals: 70 GC patients, 29 with precancerous gastric lesions and 70 healthy controls. MtDNA copy number was measured by quantitative PCR, and plasma biomarkers of oxidative damage (8-hydroxy-2'-deoxyguanosine, 8OH-dG; 4-hydroxynonenal, 4HNE) and of antioxidant capacity (glutathione peroxidase-1, GPX-1) were measured by ELISA. MtDNA variants were identified by next-generation sequencing. In MKN-28 GC cells, mitochondrial transcription factor A (TFAM) was manipulated with lentiviral vectors to alter mtDNA content. The results showed that GC progression was accompanied by higher ccf-mtDNA, shifts in plasma oxidative damage and antioxidant markers, and accumulation of mtDNA variants, alongside lower mtDNA content in cancers than in adjacent tissues. In GC cells, lowering mtDNA content by TFAM silencing promoted the malignant phenotype and increased intracellular superoxide-related fluorescence. By multiplex immunohistochemistry, tissue markers of mitochondrial maintenance and mtDNA release declined without a rise in caspase-3. D-loop variants already present at the precancerous stage suggest early mitochondrial changes, whereas predicted deleterious coding variants affecting respiratory chain components were observed in GC tissues. These findings support a redox-associated model of mitochondrial homeostasis that links impaired mitochondrial maintenance, mtDNA instability, and ccf-mtDNA accumulation, and provide a tissue-anchored mechanistic basis for the circulating mtDNA changes detected by plasma-based approaches in GC.

High sperm DNA fragmentation is associated with increased embryonic chromosomal abnormality: a retrospective study of 8 years involving 5637 couples undergoing ART

Does sperm DNA fragmentation impair blastocyst chromosomal integrity? A high sperm DNA fragmentation index (DFI) is associated with an increased risk of blastocyst aneuploidy, particularly when the man has poor semen quality or when the female partner is aged ≥35 years. Evidence linking sperm DFI to embryo development and blastocyst chromosomal integrity remains inconsistent, and controversy persists regarding its association with blastocyst aneuploidy detected by preimplantation genetic testing for aneuploidy (PGT-A). Existing studies have often been limited by small sample sizes, inconsistent DFI assays, and insufficient controls of key confounders. This retrospective cohort study was conducted at a tertiary reproductive centre. A total of 5637 infertile couples undergoing assisted reproduction between January 2016 and March 2023 were screened, and 3948 couples with complete data were included after applying standardized exclusion criteria. All male partners who underwent sperm DNA fragmentation assessment using the Sperm Chromatin Structure Assay were included. Infertile couples were stratified by treatment modality, age of both partners, and male semen quality parameters. The primary outcome was blastocyst aneuploidy rate. Beta-binomial regression and zero-inflated beta-binomial regression were used to analyze embryonic outcomes, with model selection guided by the Akaike Information Criterion. Generalized linear mixed models were applied to account for clustering of multiple embryos within the same ovarian stimulation cycle. Higher DFI was associated with a higher rate of blastocyst aneuploidy. Compared to the low DFI group, the high DFI group had a significantly higher adjusted odds ratio (aOR) of aneuploidy (38.19% vs. 24.42%, aOR=1.35, 95% CI: 1.10–1.81, P=0.042), while there was no substantial difference between the medium and low DFI group (25.78% vs. 24.42%, aOR=0.93, 95% CI: 0.76–1.13, P=0.465). Particularly, when women were aged ≥35 years, the embryonic aneuploidy rate in the high DFI group was significantly higher than low DFI subgroup (52.02% vs. 38.75%, aOR=1.61, 95% CI: 1.12–2.32, P=0.010). Also, among men with severe oligoasthenoteratozoospermia (SOAT), high DFI significantly increased aneuploidy risk (36.81% vs. 18.03%, aOR=1.99, 95% CI: 1.11–3.57, P=0.022). For all men aged <40 years, high DFI was associated with a reduced likelihood of high-quality blastocyst formation (aOR=0.79, 95% CI: 0.64–0.99, P=0.044). Given the single-centre retrospective design, residual confounding cannot be excluded despite rigorous statistical adjustment. Routine sperm DFI assessment may provide clinically meaningful information for infertile couples, particularly those with advanced maternal age or compromised male fertility. These findings support the integration of DFI into embryo risk stratification and individualized treatment planning, potentially improving reproductive outcomes and resource allocation. This work was supported by the National Natural Science Foundation for Young Scientists (72504291), Hunan Provincial Natural Science Foundation of China (2025JJ50703), and the Scientific Research Foundation of Reproductive and Genetic Hospital of CITIC-Xiangya (YNXM-202411). None of the authors have any conflict of interest to disclose. N/A

Mitochondrial DNA copy number in neurodegenerative diseases: a global meta-analysis of 156 comparisons across 76 studies

Circadian Disruption Is Associated with Elevated Whole-Semen mtDNA Copy Number and Implicates CRY1 as a Candidate Regulator in Humans and Mice

This study is the first to identify whole-semen mtDNAcn as a circadian-disruption-associated molecular phenotype and supports CRY1 as a candidate regulator and supports CRY1 as a candidate regulator.

The applicability of DNA methylation-based tools in a low-income, sub-Saharan African population: Malawi longitudinal study of families and health

Summary DNA methylation (DNAm)-based tools are predominantly developed in European ancestry, high-income populations, raising questions on their applicability in diverse and rural settings. To evaluate these tools in a sub-Saharan African low-income context, we analyzed genome-wide DNAm data from 49 dried blood spot samples from adults aged 45+ years in the Malawi Longitudinal Study of Families and Health (MLSFH). Leveraging varying field and storage conditions inherent to this rural setting, we examined their impact on DNAm and found no significant contribution to genome-wide DNAm or predictive sites used in these tools. DNAm-derived estimates of epigenetic clocks and lifestyle biomarkers showed modest to high correlations with self-reported measures. Known associations of epigenetic age acceleration with adverse health behaviors were validated. DNAm-based immune cell type proportions aligned with expected cell-type changes in aging and human immunodeficiency virus. Our findings lay the groundwork for broader use of DNAm-based tools in sub-Saharan African populations.