Paternal Origin Research Articles

The Importance of Pathogenesis: A Molecular Investigation on A Solitary Choriocarcinoma Lung Lesion with No Primary Lesion

Abstract Introduction/Objective We present an exceedingly rare case of metastatic choriocarcinoma to the lung with no primary lesion. Notably, this is the only case where STR molecular studies have been conducted. Methods/Case Report A 43-year-old G1P1001 female with no past medical history presents with severe shortness of breath, left-sided back, and chest pain for severe shortness of breath, left sided back and chest pain. Patients pregnancy test was positive with a B-hCG of 17944 u/L. Transvaginal ultrasound was negative for IUP. CTAP showed no masses in the uterine cavity or ovaries. D-dimer was elevated at 623 ng/ml. However, CTA chest was negative for pulmonary emboli but revealed a RLL mass measuring 2.6 x 2.5 cm x 2.9 cm with lobulated areas suspicious for vascular structures and connection to the right pulmonary vein. Patient was treated with a complete right lower lobectomy. An endometrial biopsy was performed and was negative for malignancy with no significant findings. Grossly, the mass was well-circumscribe, hemorrhagic, and necrotic, measuring 3.5 cm. Microscopically, the malignant cells had highly pleomorphic and hyperchromatic nuclei. There were also multiple multinucleated cells and mitotic figures present. Some of the cells had nested architecture leading to us to suspect a pleomorphic lung adenocarcinoma with choriocarcinomatous differentiation. We performed IHC staining that demonstrated strong positivity of AE1/AE3, CK7, hCG and a high Ki-67 index. The neoplastic cells also had focal p63 and p40 positivity. Furthermore, TTF1 and SALL4 were both negative. This staining pattern as well as patient’s clinical history of no gynecological lesion, lead us to favor lung adenocarcinoma with choriocarcinomatous differentiation. However, due to the abundance of syncytiotrophoblastic and trophoblastic cells, metastatic choriocarcinoma could not be ruled out. Therefore, the case was sent out for external consultation and Short Tandem Repeat (STR) molecular testing. Surprisingly, the STR testing results showed some STR of paternal origin indicating a metastatic gestational choriocarcinoma. The patient’s surgery was highly successful and lead to a down trending of b-hCG from 17944 to 1768 after removal. Results (if a Case Study enter NA) NA Conclusion Performing STR testing was pivotal in this case as it revealed the presence of DNA of paternal origin, providing crucial evidence that the tumor was of gestational origin, guiding the diagnosis towards metastatic gestational choriocarcinoma.

Archaeogenetic analysis revealed East Eurasian paternal origin to the Aba royal family of Hungary

Archaeogenetic analysis revealed East Eurasian paternal origin to the Aba royal family of Hungary

In Planta Androgenesis (Paternal Origin) in Saacharum X Erianthus Intergeneric Hybrid

The present investigation was carried in crosses made between Saccharum species hybrid clones i.e. Co 419, Co 7201 and Co 7224 (2n = 108-112) and Erianthus arundinaceus viz. IK 76-91 (2n = 60) and IK 76-99 (2n = 60) for introducing better ratoon ability, vigour, wide ecological adaptability, extensive root system, drought and water logging resistance, high biomass and disease resistance into modern sugarcane cultivars during 2020-23 at VSI-Sugarcane Breeding Centre, Amboli. Parental apomixis (paternal origin) has been recently noticed and it is unique in Saccharum X Erianthus intergeneric cross seedlings. A total of fifty-one seedlings were obtained from above three intergeneric crosses and out of these eighteen seedlings were reported as androgenetic seedlings as the female act as a surrogate mother. At the early stages, seed germination of seedlings was found two types i.e., one type resembling Saccharum and other resembling Erianthus with deep purple coloration. Morphologically androgenetic seedlings were similar to the male parents IK 76-91 and IK 76-99 with tall large tufted grass like clumps, vegetative stem with thick reproductive buds, root zone narrow and only one row of root eyes, the lamina gradually passes into leaf sheath with no auricle and dewlaps. Cytological studies were made in these seedlings and during metaphase the somatic chromosome number was observed to be 2n = 60 rather than expected 2n = 84-90. This paternal origin may be due to the ability of Erianthus male gametes to produce an embryo within the seed tissues of Saccharum species hybrids but without genetic contribution of the seed. Thus, in planta androgenesis is achieved through the combination of embryogenic behavior of male gametes which has entered in the ovule and the ability of ovules to act as a surrogate mother. They could derive either from the fusion of two male gametes or from the early natural diplodization of the haploid embryo. Such homozygous true breeding seedlings of Saccharum X Erianthus with hybrid vigour are extremely important in crop improvement. This system provides an unparalleled opportunity to shorten the breeding cycle and fix agronomic traits in the homozygous state. These androgenetic plants with Saccharum cytoplasm and Erianthus genome are male sterile making them highly useful for further hybridization and sugarcane improvement programme.

SMAD4 mutations causing Myhre syndrome are under positive selection in the male germline

While it is widely thought that de novo mutations (DNMs) occur randomly, we previously showed that some DNMs are enriched because they are positively selected in the testes of aging men. These "selfish" mutations cause disorders with a shared presentation of features, including exclusive paternal origin, significant increase of the father's age, and high apparent germline mutation rate. To date, all known selfish mutations cluster within the components of the RTK-RAS-MAPK signaling pathway, a critical modulator of testicular homeostasis. Here, we demonstrate the selfish nature of the SMAD4 DNMs causing Myhre syndrome (MYHRS). By analyzing 16 informative trios, we show that MYHRS-causing DNMs originated on the paternally derived allele in all cases. We document a statistically significant epidemiological paternal age effect of 6.3 years excess for fathers of MYHRS probands. We developed an ultra-sensitive assay to quantify spontaneous MYHRS-causing SMAD4 variants in sperm and show that pathogenic variants at codon 500 are found at elevated level in sperm of most men and exhibit a strong positive correlation with donor's age, indicative of a high apparent germline mutation rate. Finally, we performed invitro assays to validate the peculiar functional behavior of the clonally selected DNMs and explored the basis of the pathophysiology of the different SMAD4 sperm-enriched variants. Taken together, these data provide compelling evidence that SMAD4, a gene operating outside the canonical RAS-MAPK signaling pathway, is associated with selfish spermatogonial selection and raises the possibility that other genes/pathways are under positive selection in the aging human testis.

P-249 Morphokinetic parameters comparison between balanced and unbalanced embryos from patients with structural chromosome abnormalities

Abstract Study question Are there morphokinetic differences between balanced and unbalanced embryos after PGT-SR? Summary answer The total time embryos remain at the morula stage (TiCAV- TM) could be a morphokinetic marker to consider in PGT-SR cycles. What is known already Due to the preimplantation genetic testing for structural rearrangements (PGT-SR) it is possible to identify embryos with an excess or defect of genetic material associated with a parental structural rearrangement. This technique is suitable for patients with a normal phenotype but a balanced chromosomal rearrangement. These patients have a higher risk of spontaneous abortion, as well as higher aneuploidy rates. Within structural chromosomal alterations, translocations are the most common presentation of chromosomal rearrangement. Study design, size, duration Within this multicentre retrospective study, we evaluated 133 embryos, from 39 cycles in which one of the partners had a karyotype with balanced reciprocal or Robertsonian translocations, from January 2021 to September 2023. After PGT-SR was carried out, we obtained 40 balanced embryos and 93 unbalanced embryos. Participants/materials, setting, methods We compared the conventional morphokinetic parameters and the duration of each state between two groups after PGT-SR samples were analysed. All embryos were cultured in Geri® time-lapse incubators, and underwent embryo biopsy on day 5-7. Statistical analysis was conducted using R software (v.4.3.1), including the following confounding variables: origin of karyotype alteration (maternal or paternal), type of translocation (Robertsonian or reciprocal), female and male gamete age, type of oocyte (fresh or frozen) and oocyte origin. Main results and the role of chance We observed that the mean age of the oocyte was significantly higher in the unbalanced embryos compared to the balanced ones (32.85±5.32 years vs.30.45±5.01 years). In terms of the altered karyotype, the paternal origin is more prevalent than the maternal one (60.9% vs. 39.1%). Regarding the type of translocation, reciprocal translocation is more predominant than Robertsonian translocation (83.5% vs. 16.5%) in our study population. When comparing morphokinetic parameters between both groups, we observed that unbalanced embryos tend to reach an expanded blastocyst stage later than balanced embryos (107.62±10.02h vs. 102.48±8.87h, respectively; p = 0.008, corrected p-value=0.186). We observed the same tendency with hatching initiation time (110.64±10.49h vs. 105.91±9.38h; p = 0.013, corrected p-value=0.296). We observed that unbalanced embryos have a slower development than balanced embryos (TiCAV-TFB 10.10±4.46h vs. 8.35±3.79h; p = 0.006, corrected p-value=0.437; TiH-TiCAV 13.03±5.98h vs. 11.79±5.50h; p = 0.017, corrected p-value=0.816). We did observe significant differences in total time at morula stage (TiCAV – TM) when comparing unbalanced and balanced embryos (12.60±6.94 vs. 8.88±5.65; p = 0.003, corrected p-value=0.001). Limitations, reasons for caution A higher number of embryos should be evaluated in order to enhance the statistical power of this study, as there is an important difference in sample size between balanced and unbalanced embryos in the PGT-SR cycles included in this study. Wider implications of the findings Further morphokinetic study of embryos from patients with structural chromosomal abnormalities can open up new lines of research and can help us to predict the final outcome of the cycle, accompanied by a genetic study. Trial registration number Not applicable

P-271 Deep sequencing of spermatozoal accessible chromatin reveals complex arrangements underlying spermatozoal chromatin packaging and fertilization

Abstract Study question Could structural aspects of sperm DNA packaging contribute to fertilization and early embryo development? Summary answer Structural aspects of sperm DNA include complex patterns of repetitive-DNA and developmental gene packaging that could delineate a paternal impact on fertilization and early development. What is known already Genetics, epigenetics and transcriptomics of ejaculate human spermatozoa could have important effects on the establishment of embryonic chromatin architecture that may impact early fetal development. Spermatozoa are transcriptionally silent; however, a small fraction (∼5%-15%) of their chromatin escapes repackaging by protamines and remains in a more open nucleosomal conformation that may be poised for transcription. The sensitivity of this fraction to progressive salt/detergent disruption is likely assayed in sperm chromatin dispersion (SCD) or halo tests that are commonly used in assessments of sperm DNA fragmentation. Study design, size, duration Eleven healthy male donors and 9 women undergoing IVF treatment agreed to participate in this study. Eleven normozoospermic semen samples were donated by male donors, aged 25-39 years, who abstained from sexual activity for 3 days. Seven MII oocytes and 5 pronuclear zygotes were donated from 5 and 4 women, respectively, undergoing IVF treatment. The samples were collected within a time frame of 6 months. Female donors provided either MII oocytes or pronuclear zygotes. Participants/materials, setting, methods Sperm chromatin was processed by differential salt extraction tailored with endonuclease or micrococcal nuclease treatment and RNA isolated using established protocols. Oocytes and pronuclear zygotes were analyzed at the single cell level. DNA library construction employed the NEBNext Ultra approach (NEB) and RNA libraries the Ovation Single Cell (NuGEN) for Illumina. Bioinformatics analysis included FastQC, HISAT2, StringTie, GREAT, edgeR and other source-software. Public datasets were employed to further increase the statistical power. Main results and the role of chance The aim of our approach was to dissect the accessible sperm chromatin fraction, identifying regions of great importance that could contribute towards the formation of the zygote and/or early embryonic development. Differing extraction methods revealed complementary accessible and resistant fractions in sperm, with accessible regions being significantly enriched for chromatin important in very early embryonic development. These chromatin fractions contained various genomic features including promoter sequences, CpG-islands and CTCF-binding sites that could attract transcription binding factors in the paternally-derived chromatin. Accessible sperm chromatin also contains high levels of specific DNA repeat classes of retroviral origin, known to impact early gene expression and gene expression programs. Accessible sperm chromatin was strongly associated with developmental and regulatory signatures with Bonferroni P values ranging between 2.07x10-4 and 1.03x10-20, potentially revealing a role for paternal chromatin in the initial start-up of early zygotic development. We further investigated paternally- and maternally- derived transcripts and identified mono-allelically transcribed genes present in the zygotes, that were entirely absent from all seven oocyte transcriptomes, suggesting a paternal origin, and potentially important roles following oocyte fertilization. Limitations, reasons for caution Due to the restraints of obtaining human material, the study relied on a relatively small sample size. However, sequencing results showed quite homogeneous clustering in both DNA/RNA samples, with at least 5 biological replicates from at least 4 donors per group, potentially reducing the impact of low sample size. Wider implications of the findings A better understanding of differentially accessible sperm chromatin and residual RNA, could help support the discovery of biomarkers that can be used to select more competent spermatozoa for IVF cycles, resulting in higher success rates in couples undergoing ART. Trial registration number not applicable

P-560 Characterization of ploidy level and parental genome inheritance abnormalities in preimplantation human embryos

Abstract Study question Can preimplantation genetic testing (PGT) platforms with integrated genotyping aid the characterization of genome-wide chromosomal abnormalities in human embryos and factors contributing to their occurrence? Summary answer Signatures detected by genotype-criteria-based models in PGT pinpoint origin of haploidy, triploidy and genome-wide uniparental disomy (gwUPD), highlighting recombination deficiencies potentially underpinning these phenomena. What is known already While there is a growing body of knowledge on the frequency and origin of individual chromosome abnormalities, very little is known about genome-wide chromosomal abnormalities in human development. Indeed, genome-wide abnormalities are incompatible with normal human development, making the preimplantation stage the ideal time to characterize them. Novel PGT technologies provide the research and clinical opportunity to characterize both known ploidy-level abnormalities (triploid/haploid) and identify theoretical genome-wide abnormalities undetectable at later stages of development. Study design, size, duration PGT genotyping data from 96660 embryos were used to assess incidence of ploidy-level abnormalities and correlation with potential predisposing clinical factors. Parental origin of putative haploidy and triploidy was assessed on 14 and 41 embryos with parental genotypes available (trios), respectively. For the 41 triploid trios, meiotic origin and recombination rates were also evaluated. A novel genotype-criteria based model to detect theoretical gwUPD and meiotic origin was developed on a semi-contemporaneous 74009 female embryo dataset. Participants/materials, setting, methods PGT was performed with targeted next-generation sequencing, including 5000 genome-wide SNPs. Informative SNPs from trios were used to identify parental origin of haploidy/triploidy. Informative SNPs within 5cM of the centromere were used to evaluate meiotic origin and extended beyond 5cM to identify maternal recombination observing shifts between single (SPH) and biparental (BPH) homologs. gwUPD was predicted when low genome-wide heterozygosity, increased homozygosity in the centromeric region, and decreased similarity to sibling embryos were observed. Main results and the role of chance Genome wide ploidy abnormalities were detected in 1.1% (n = 1.063/96.660; CI 95%: 1-1,2%) of embryos. Haploidy was mainly of paternal origin (n = 12/14), whereas triploidy was exclusively maternal in origin (n = 41/41) and prominently due to meiosis II errors (n = 30/41; 73.2%; 95% CI:57.1-85.8%). Advanced maternal age was positively associated with an increased risk of triploid conceptions (OR = 1.059 per year; p < 0.001). Investigation of maternal recombination rates detected by three consecutive SNPs shifting between SPH and BPH (with a calculated genotyping error of 0.16%) in triploid embryos revealed an outlier group of 7 embryos with statistically lower (P < 0.001) identified crossover events (0-2 events genome-wide) compared to the average 23.7 detectable events genome-wide (SD:4.3). Recombinant gwUPD was predicted in 41 out of 74009 human embryos (0.05%; 95% CI:0.04-0.07%). These embryos showed a high homozygosity in pericentromeric regions, as a proof of each pair of chromosomes being the same parental homolog resulting from a faulty meiosis II, but with detectable heterozygosity regions throughout the rest of the genome, indicating that crossovers occurred between the two parental homologs during prophase I. Multifocal biopsies from the same embryos confirmed the reproducibility of identification of the number of recombination events in triploid embryos and the gwUPD prediction. Limitations, reasons for caution This assay genotypes only a portion of the genome and underestimation of recombination events is possible. Our current detection of gwUPD is limited to recombinant uniparental isodisomy of MII origin only. Therefore, the exact prevalence of these abnormal gwUPD configurations requires further understanding and analysis. Wider implications of the findings Genotyping in routine PGT can identify severe genome-wide abnormalities with associated gestational complications that would otherwise go undiagnosed. Comprehensive characterization of these abnormalities is not possible at later stages of development. Therefore, PGT offers a unique opportunity to delve into their biological origin and identify novel biomarkers for embryo competence. Trial registration number not applicable

Confirmation and pathogenicity of small copy number variations incidentally detected via a targeted next-generation sequencing–based preimplantation genetic testing for aneuploidy platform

ObjectiveTo evaluate the technical accuracy, inheritance, and pathogenicity of small copy number variants (CNVs) detected by a targeted next-generation sequencing (NGS)-based PGT-A platform. DesignRetrospective observational study performed between 2020-2022. Subjects12,157 patients who underwent clinical PGT-A performed by targeted NGS for whole chromosome and large segmental aneuploidies. ExposureAn incidental finding was reported when a CNV gain/loss of at least three consecutive amplicons appeared in at least two embryos from the same IVF cycle. Main Outcome MeasuresThe primary outcome measures were the specificity, incidence, inheritance, and pathogenicity of small CNVs detected by the PGT-A platform. Accuracy of the PGT-A platform CNV calls was assessed via concordance with the CNV calls (size and genomic location) on chromosomal microarray of the gamete provider(s). Parental origin of the CNV and pathogenicity classifications were also reported. ResultsIn 75 of 12,157 unique PGT-A patients (0.62%;95%CI:0.5-0.8%), an incidental finding that met reporting criteria was identified. Chromosomal microarray follow-up was requested for all cases and results were received for one or both members of 65 reproductive couples. In all cases, one of the gamete providers was confirmed to have the CNV identified in the embryos (100.0%: N=65/65 95%CI:94.5-100). The identified CNV was of maternal origin in 34 cases (52.3%) and of paternal origin in 31 cases (47.7%). A significant correlation was identified between PGT-A-predicted CNV sizes and chromosomal microarray detected sizes (r=0.81) and genomic coordinates on parental DNA. Twenty-six (40%) of the CNVs were classified as benign/likely benign, 30 (46.2%) as a variant of uncertain significance (VUS), and 9 (13.8%) as pathogenic/likely pathogenic. ConclusionCertain PGT-A platforms may enable the detection of inherited, small CNVs with extremely high specificity without prior knowledge of parental status. The majority of CNVs in this data set were confirmed to be benign/likely benign or a VUS; however, pathogenic/likely pathogenic CNVs associated with a broad range of phenotypic features may also be detected, although a reliable negative predictive value for small CNVs with current PGT-A technologies is unknown due to the many technical challenges.

First Trimester Hemorrhage Revealing A Partial Molar Pregnancy: About A Case

Partial molar pregnancy is a triploid conception with a chromosomal lot of paternal origin. Progression to persistent trophoblastic disease, invasive mole or choriocarcinoma remains exceptional. We report the case of a 45-year-old woman who presented with heavy bleeding of genital origin and a partial molar pregnancy on ultrasound with no visible embryonic structure. Careful ultrasound-guided aspiration was performed under antibiotic and uterotonic cover, and the aspirate was sent for histological examination. The patient underwent monthly b-hCG monitoring for 6 months, with a final negativation.

Machine learning-enhanced noninvasive prenatal testing of monogenic disorders.

Single-nucleotide variants (SNVs) are of great significance in prenatal diagnosis as they are the leading cause of inherited single-gene disorders (SGDs). Identifying SNVs in a non-invasive prenatal screening (NIPS) scenario is particularly challenging for maternally inherited SNVs. We present an improved method to predict inherited SNVs from maternal or paternal origin in a genome-wide manner. We performed SNV-NIPS based on the combination of fragments of cell free DNA (cfDNA) features, Bayesian inference and a machine-learning (ML) prediction refinement step using random forest (RF) classifiers trained on millions of non-pathogenic variants. We next evaluate the real-world performance of our refined method in a clinical setting by testing our models on 16 families with singleton pregnancies and varying fetal fraction (FF) levels, and validate the results over millions of inherited variants in each fetus. The average area under the ROC curve (AUC) values are 0.996 over all families for paternally inherited variants, 0.81 for the challenging maternally inherited variants, 0.86 for homozygous biallelic variants and 0.95 for compound heterozygous variants. Discriminative AUCs were achieved even in families with a low FF. We further investigate the performance of our method in correctly predicting SNVs in coding regions of clinically relevant genes and demonstrate significantly improved AUCs in these regions. Finally, we focus on the pathogenic variants in our cohort and show that our method correctly predicts if the fetus is unaffected or affected in all (10/10, 100%) of the families containing a pathogenic SNV. Overall, we demonstrate our ability to perform genome-wide NIPS for maternal and homozygous biallelic variants and showcase the utility of our method in a clinical setting.

22q11.2 Deletion Syndrome: Influence of Parental Origin on Clinical Heterogeneity.

22q11.2 deletion syndrome (22q11.2DS) shows significant clinical heterogeneity. This study aimed to explore the association between clinical heterogeneity in 22q11.2DS and the parental origin of the deletion. The parental origin of the deletion was determined for 61 individuals with 22q11.2DS by genotyping DNA microsatellite markers and single-nucleotide polymorphisms (SNPs). Among the 61 individuals, 29 (47.5%) had a maternal origin of the deletion, and 32 (52.5%) a paternal origin. Comparison of the frequency of the main clinical features between individuals with deletions of maternal or paternal origin showed no statistically significant difference. However, Truncus arteriosus, pulmonary atresia, seizures, and scoliosis were only found in patients with deletions of maternal origin. Also, a slight difference in the frequency of other clinical features between groups of maternal or paternal origin was noted, including congenital heart disease, endocrinological alterations, and genitourinary abnormalities, all of them more common in patients with deletions of maternal origin. Although parental origin of the deletion does not seem to contribute to the phenotypic variability of most clinical signs observed in 22q11.2DS, these findings suggest that patients with deletions of maternal origin could have a more severe phenotype. Further studies with larger samples focusing on these specific features could corroborate these findings.

Genetic Variation and Composition of Two Commercial Estonian Dairy Cattle Breeds Assessed by SNP Data.

The aims of this study were to assess the genomic relatedness of Estonian and selected European dairy cattle breeds and to examine the within-breed diversity of two Estonian dairy breeds using genome-wide SNP data. This study was based on a genotyped heifer population of the Estonian Red (ER) and Estonian Holstein (EH) breeds, including about 10% of all female cattle born in 2017-2020 (sample sizes n = 215 and n = 2265, respectively). The within-breed variation study focused on the level of inbreeding using the ROH-based inbreeding coefficient. The genomic relatedness analyses were carried out among two Estonian and nine European breeds from the WIDDE database. Admixture analysis revealed the heterogeneity of ER cattle with a mixed pattern showing several ancestral populations containing a relatively low proportion (1.5-37.0%) of each of the reference populations used. There was a higher FROH in EH (FROH = 0.115) than in ER (FROH = 0.044). Compared to ER, the long ROHs of EH indicated more closely related parents. The paternal origin of the genetic material used in breeding had a low effect on the inbreeding level. However, among EH, the highest genomic inbreeding was estimated in daughters of USA-born sires.

Abstract 7026: Multi-omic genomic mapping with long read sequencing

Abstract Gene transcription is regulated by the complex interplay between histone post-translational modifications (PTMs), chromatin associated proteins (CAPs), and DNA methylation (DNAme). Mapping their genomic locations and examining the relationships between these chromatin elements is a powerful approach to decipher mechanisms of disease, thereby enabling discovery of novel biomarkers and therapeutics. Leading epigenomic mapping technologies (e.g., ChIP-seq, CUT&RUN) rely upon DNA fragmentation to isolate regions of interest for sequencing on short read platforms (e.g., Illumina). This strategy leads to substantial loss of contextual information regarding the surrounding DNA, precluding the identification of multiple co-occurring epigenomic features on a single DNA molecule. By contrast, long-read sequencing (LRS) platforms are capable of sequencing very long reads from a single molecule (typically >10kb), allowing relationships between features on a single molecule to be used to resolve heterogeneity within mixed populations. Here we report a robust multi-omic method that leverages LRS to simultaneously profile histone PTMs (or CAPs), DNAme, and parental haplotype in a single assay. This nondestructive, epigenomic mapping approach leverages a novel DNA methyltransferase fusion protein (pAG-M.EcoGII) to label DNA underneath antibody-targeted chromatin features, thereby marking sites of interest while preserving DNA molecules intact for LRS. Inspired by our work with state-of-the-art immunotethering-based approaches (CUT&RUN/CUT&Tag), nuclei are bound to magnetic beads to streamline and automate sample processing. Next, adenosines nearby antibody-targeted chromatin features are methylated with pAG-M.EcoGII, which are then directly read from genomic DNA using Oxford Nanopore Technologies or Pacific Biosciences LRS platforms. To determine the capabilities and limitations of this assay, we tested multiple chromatin targets in various cell lines. Importantly, this method is highly reproducible across biological replicates, and highly concordant with orthogonal SRS assays (e.g., CUT&RUN). Further, we showed that this method is a true multi-omic approach by simultaneously profiling histone PTMs, native DNAme (5mC), and parental single-nucleotide variants from single DNA molecules within a single reaction. Finally, this workflow preserves chromatin integrity for LRS, revealing heterogeneity (e.g., haplotype or paternal origin) within/between data types and providing access to previously unmappable genomic regions (e.g., centromeres). Citation Format: Bryan J. Venters, Paul W. Hook, Vishnu S. Kumary, Alli R. Hickman, James T. Anderson, Anup Vaidya, Ryan J. Ezell, Jonathan M. Burg, Zu-Wen Sun, Martis W. Cowles, Winston Timp, Michael-Christopher Keogh. Multi-omic genomic mapping with long read sequencing [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 7026.

Associations between a paternal healthy lifestyle score and its individual components with childhood overweight and obesity.

Maternal healthy lifestyle behaviors during pregnancy have been associated with reduced risk of offspring overweight and obesity (OWOB). However, there has been little investigation, in the context of the Paternal Origins of Health and Disease (POHaD) paradigm, of the potential influence of the paternal lifestyle on offspring OWOB. To describe paternal healthy lifestyle factors around pregnancy and investigate their associations, individually and combined, with offspring risk of OWOB during childhood. Participants included 295 father-child pairs from the Lifeways Cross-Generation Cohort Study. A composite paternal healthy lifestyle score (HLS) based on having a high dietary quality (top 40% of the Healthy Eating Index-2015), meeting physical activity guidelines (≥450 MET-min/week of moderate-to-vigorous physical activity), having a healthy body mass index (BMI) (18.5-24.9kg/m2 ), being a non-smoker, and having no/moderate alcohol intake, was calculated (range 0-5). Paternal HLS (and individual components) associations with child BMI and waist-to-height ratio (WHtR) at age 5 and 9 years were assessed using linear (BMI z-scores and WHtR) and logistic (IOTF categories) regression analyses, adjusted for sociodemographic characteristics. At age 5 and 9 years, 23.5% and 16.9% of children were classified as living with OWOB, respectively. Of the 160 pairs with a complete HLS, 45.0% of the fathers had unfavorable lifestyle factors, determined by a low HLS between 0 and 2 points. Although a low paternal HLS was not significantly associated with a higher risk of childhood OWOB measured using either BMI z-scores and IOTF categories, it was associated with a greater child WHtR, an indicator of central adiposity, at 9 years of age (β [95% CI]=0.04 [0.01,0.07]). Almost half of the fathers had unfavorable lifestyle factors around pregnancy. A low paternal HLS was associated with a greater child WHtR at 9 years but not with a higher risk of childhood OWOB when measured by BMI z-scores or IOTF categories.

Future in the past: paternal reprogramming of offspring phenotype and the epigenetic mechanisms.

That certain preconceptual paternal exposures reprogram the developmental phenotypic plasticity in future generation(s) has conceptualized the "paternal programming of offspring health" hypothesis. This transgenerational effect is transmitted primarily through sperm epigenetic mechanisms-DNA methylation, non-coding RNAs (ncRNAs) and associated RNA modifications, and histone modifications-and potentially through non-sperm-specific mechanisms-seminal plasma and circulating factors-that create 'imprinted' memory of ancestral information. The epigenetic landscape in sperm is highly responsive to environmental cues, due to, in part, the soma-to-germline communication mediated by epididymosomes. While human epidemiological studies and experimental animal studies have provided solid evidences in support of transgenerational epigenetic inheritance, how ancestral information is memorized as epigenetic codes for germline transmission is poorly understood. Particular elusive is what the downstream effector pathways that decode those epigenetic codes into persistent phenotypes. In this review, we discuss the paternal reprogramming of offspring phenotype and the possible underlying epigenetic mechanisms. Cracking these epigenetic mechanisms will lead to a better appreciation of "Paternal Origins of Health and Disease" and guide innovation of intervention algorithms to achieve 'healthier' outcomes in future generations. All this will revolutionize our understanding of human disease etiology.

ALDH18A1‐related hereditary spastic paraplegia and developmental and epileptic encephalopathy with spike‐wave activation in sleep: Expanding the clinical phenotype

AbstractObjectiveWe present the cases of two sisters, both harboring the same ALDH18A1 gene mutations, who presented with a complex clinical phenotype characterized by spastic paraparesis with ataxia, epileptic encephalopathy, severe psychomotor deficits, and behavioral abnormalities.MethodsCase description of two sisters with ALDH18A1 gene mutations.ResultsThe older patient, a 12‐year‐old girl, exhibited spastic paraparesis with ataxia, microcephaly, facial dysmorphisms, and severe intellectual disability, with an absence of verbal language. An electroencephalogram (EEG) revealed marked spike‐and‐wave activation during sleep (SWAS), although no clinically documented seizures were observed. The younger sister, who was 9 years old, displayed a similar clinical presentation, including spastic paraparesis with ataxia, microcephaly, dysmorphisms, however, she displayed slightly more severe intellectual deficits and polymorphic seizures. EEG revealed a SWAS pattern in this case. Magnetic resonance imaging scans in both cases showed only a thin corpus callosum. Whole exome sequencing unveiled the presence of two likely pathogenic variants in compound heterozygosity within the ALDH18A1 gene. Specifically, these variants included the splice site variant c.88 + 1c.88+1G>A of paternal origin and the variant c.1364c.1364T>C (p.Leu455Ser) of maternal origin. Both sisters displayed normal blood levels of ammonia, ornithine, citrulline, arginine, and other amino acids.InterpretationThese findings were compatible with ALDH18A1‐related HSP complicated with a clinical and EEG pattern reminiscent of DEE‐SWAS. We present the first report of DEE‐SWAS in ALDH18A1‐related HSP, expanding the clinical manifestations of this complex neurodevelopmental condition.

Maternal thyroid function and free beta human chorionic gonadotrophin level in triploid pregnancies of paternal origin

Maternal thyroid function and free beta human chorionic gonadotrophin level in triploid pregnancies of paternal origin

Paternal p,p′-DDE exposure and pre-pubertal high-fat diet increases the susceptibility to fertility impairment and sperm Igf2 DMR2 hypo-methylation in male offspring

The hypothesis of paternal origins of health and disease (POHaD) indicates that paternal exposure to adverse environment could alter the epigenetic modification in germ line, increasing the disease susceptibility in offspring or even in subsequent generations. p,p′-Dichlorodiphenyldichloroethylene (p,p′-DDE) is an anti-androgenic chemical and male reproductive toxicant. Gestational p,p′-DDE exposure could impair reproductive development and fertility in male offspring. However, the effect of paternal p,p′-DDE exposure on fertility in male offspring remains uncovered. From postnatal day (PND) 35 to 119, male rats (F0) were given 10 mg/body weight (b.w.) p,p′-DDE or corn oil by gavage. Male rats were then mated with the control females to generate male offspring. On PND35, the male offspring were divided into 4 groups according whether to be given the high-fat diet (HF): corn oil treatment with control diet (C-C), p,p′-DDE treatment with control diet (DDE-C), corn oil treatment with high-fat diet (C-HF) or p,p′-DDE treatment with high-fat diet (DDE-HF) for 35 days. Our results indicated that paternal p,p′-DDE exposure did not affect the male fertility of male offspring directly, but decreased sperm quality and induced testicular apoptosis after the high-fat diet treatment. Further analysis demonstrated that paternal exposure to p,p′-DDE and pre-pubertal high-fat diet decreased sperm Igf2 DMR2 methylation and gene expression in male offspring. Hence, paternal exposure to p,p′-DDE and pre-pubertal high-fat diet increases the susceptibility to male fertility impairment and sperm Igf2 DMR2 hypo-methylation in male offspring, posing a significant implication in the disease etiology.

Parent-of-origin effects for the number of oocytes and embryos in Gir cattle

Imprinting is a phenomenon that alters the expression of genes according to the parental origin of their alleles. A quantitative form to evaluate the imprinting effect is known as parent-of-origin effect. Our aim with this work is to identify parent-of-origin effects that influence the number of oocytes and embryos in Gir dairy cattle. A dataset with 17,526 Ovum Pick Up observations from 1641 Gir donors was used to estimate parent-of-origin effects for the traits number of total oocytes (TO), number of viable oocytes (VO) and number of embryos (EM). To identify parent-of-origin effects, dam and sire gametic effects were included, individually or together, in an animal model for TO, VO and EM traits. For TO, inclusion of paternal origin effects in the model was significant (P < 0.05), and explained 6 % of the total phenotypic variance. For VO and EM no significant parent-of-origin effects were found for either parental line. In conclusion, paternal effects appear to influence the total oocyte production in the Gir cattle breed.

Novel compound heterozygous ABCA2 variants cause IDPOGSA, a variable phenotypic syndrome with intellectual disability.

The gene for ATP binding cassette subfamily A member 2 (ABCA2) is located at chromosome 9q34.3. Biallelic ABCA2 variants lead to intellectual developmental disorder with poor growth and with or without seizures or ataxia (IDPOGSA). In this study, we identified novel compound heterozygous ABCA2 variants (NM_001606.5:c.[5300-17C>A];[6379C>T]) by whole exome sequencing in a 28-year-old Korean female patient with intellectual disability. These variants included intronic and nonsense variants of paternal and maternal origin, respectively, and are absent from gnomAD. SpliceAI predicted that the intron variant creates a cryptic acceptor site. Reverse transcription-PCR using RNA extracted from a lymphoblastoid cell line of the patient confirmed two aberrant transcripts. Her clinical features are compatible with those of IDPOGSA.