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Endocrine Journal Jun 2024Fibroblast growth factor (FGF) 21, a hormone produced by the liver, improves glucose and lipid metabolism. We recently demonstrated that the FGF21 gene (Fgf21) underwent...
Fibroblast growth factor (FGF) 21, a hormone produced by the liver, improves glucose and lipid metabolism. We recently demonstrated that the FGF21 gene (Fgf21) underwent DNA demethylation in the mouse liver via peroxisome proliferator-activated receptor (PPAR) α during the fetal to lactation periods. Furthermore, we found that the DNA methylation state of Fgf21 was involved in obesity in adult animals. In the present study, we analyzed the DNA methylation state of the FGF21 gene (FGF21) in obese patients using genomic DNA extracted from human monocytes and macrophages and investigated the pathophysiological significance of the FGF21 expression response to pemafibrate (PM), a PPARα ligand. We examined 67 patients with obesity stratified into in- and outpatient cohorts. A positive correlation was observed between serum FGF21 levels and triglyceride (TG) levels before PM administration. However, changes in serum FGF21 levels following PM administration did not correlate with the FGF21 DNA methylation rate, except at one CpG site. The body mass index (BMI) and serum TG levels positively correlated with the FGF21 DNA methylation rate, particularly at different CpG positions. A negative correlation was observed between absolute changes in serum FGF21 levels and the ratio of change in serum TG levels after PM administration. Collectively, these results indicate the potential of FGF21 DNA methylation as a surrogate indicator of BMI and serum TG levels, while absolute changes in serum FGF21 levels after PM administration may offer prognostic insights into the efficacy of reducing serum TG levels through PM administration.
PubMed: 38910123
DOI: 10.1507/endocrj.EJ23-0570 -
Clinica Chimica Acta; International... Jun 2024Vitreoretinal lymphoma (VRL) is a rare malignant lymphoproliferative tumor. Our study aimed to investigate the mutational profile of VRL distinguishing from uveitis...
BACKGROUND
Vitreoretinal lymphoma (VRL) is a rare malignant lymphoproliferative tumor. Our study aimed to investigate the mutational profile of VRL distinguishing from uveitis using next-generation sequencing (NGS) analysis on small amounts of vitreous fluid.
METHODS
Vitreous samples from twenty-six eyes of twenty VRL patients and six eyes of five uveitis patients were enrolled. All vitreous samples underwent cytology, immunocytochemistry for B-cell markers, cytokines analysis of IL-10 and IL-6, and flow cytometry. NGS was performed in vitreous specimens from the 25 patients using 82 DLBCL-targeted mutation panels. Vitreous fluids from 8 cases were performed paired NGS-based mutation analysis on both cell-free DNA (cfDNA) and genomic DNA.
RESULTS
The sensitivity and accuracy rates for vitreous cytology were 70 % and 76 %, and for cytokine analysis (IL-10/IL-6 > 1) were 65 % and 72 %, respectively. Overall, the common mutations in VRL were PIM1 (88.5 %), IGLL5 (88.5 %), KMT2C (73 %), MYD88 (77 %), CD79B (50 %) and TBL1XR1 (46.2 %). In addition, the genetic mutation in cfDNA was consistent with that in genomic DNA in eight VRL cases.
CONCLUSIONS
The mutation analysis of 82 DLBCL-targeted spectrum mutation panels by NGS on the vitreous samples is a sensitive and specific tool for distinguishing VRL from uveitis. Utilizing cfDNA for NGS analysis may serve as a liquid biopsy to aid in the diagnosis of VRL, particularly when using small-volume aspirate.
PubMed: 38909978
DOI: 10.1016/j.cca.2024.119827 -
Molecular Phylogenetics and Evolution Jun 2024In the present study, first generation DNA sequencing (mitochondrial cytochrome c oxidase subunit one, COI) and reduced-representative genomic RADseq data were used to...
Congruent patterns of cryptic cladogenesis revealed using RADseq and Sanger sequencing in a velvet worm species complex (Onychophora: Peripatopsidae: Peripatopsis sedgwicki).
In the present study, first generation DNA sequencing (mitochondrial cytochrome c oxidase subunit one, COI) and reduced-representative genomic RADseq data were used to understand the patterns and processes of diversification of the velvet worm, Peripatopsis sedgwicki species complex across its distribution range in South Africa. For the RADseq data, three datasets (two primary and one supplementary) were generated corresponding to 1,259-11,468 SNPs, in order to assess the diversity and phylogeography of the species complex. Tree topologies for the two primary datasets were inferred using maximum likelihood and Bayesian inferences methods. Phylogenetic analyses using the COI datasets retrieved four distinct, well-supported clades within the species complex. Five species delimitation methods applied to the COI data (ASAP, bPTP, bGMYC, STACEY and iBPP) all showed support for the distinction of the Fort Fordyce Nature Reserve specimens. In the main P. sedgwicki species complex, the species delimitation methods revealed a variable number of operational taxonomic units and overestimated the number of putative taxa. Divergence time estimates coupled with the geographic exclusivity of species and phylogeographic results suggest recent cladogenesis during the Plio/Pleistocene. The RADseq data were subjected to a principal components analysis and a discriminant analysis of principal components, under a maximum-likelihood framework. The latter results corroborate the four main clades observed using the COI data, however, applying additional filtering revealed additional diversity. The high overall congruence observed between the RADseq data and COI data suggest that first generation sequence data remain a cheap and effective method for evolutionary studies, although RADseq does provide a far greater resolution of contemporary temporo-spatial patterns.
PubMed: 38909874
DOI: 10.1016/j.ympev.2024.108132 -
Reproductive Toxicology (Elmsford, N.Y.) Jun 2024Previous retrospective cohort studies have found that, compared with oxygen tension in the uterus and fallopian tubes (2%-8%), exposure of pre-implantation embryos to...
Previous retrospective cohort studies have found that, compared with oxygen tension in the uterus and fallopian tubes (2%-8%), exposure of pre-implantation embryos to atmospheric oxygen tension (AtmO, 20%) during assisted reproductive technology(ART) can affect embryo quality, pregnancy outcomes and offspring health. However, current research on the effects and mechanisms of AtmO on the development of embryos and offspring is mainly limited to animal experiments. Human embryonic stem cells (hESCs) play a special and irreplaceable role in the study of early human embryonic development. In this study, we used hESCs as a model to elucidate the possible effects and mechanisms of AtmO exposure on human embryonic development. We found that exposure to AtmO can reduce cell viability, produce oxidative stress, increase DNA damage, initiate DNA repair, activate autophagy, and increase cell apoptosis. We also noticed that approximately 50% of hESCs survived, adapted and proliferated through high expression of self-renewal and pluripotency regulatory factors, and affected embryoid body differentiation. These data indicate that hESCs experience oxidative stress, accumulation of DNA damage, and activate DNA damage response under the selective pressure of AtmO.Some hESCs undergo cell death, whereas other hESCs adapt and proliferate through increased expression of self-renewal genes. The current findings provide in vitro evidence that exposure to AtmO during the early preimplantation stage negatively affects hESCs.
PubMed: 38909692
DOI: 10.1016/j.reprotox.2024.108648 -
Journal of Gynecologic Oncology Jun 2024Biomarkers reflecting real-time response to therapy and recurrence are lacking. We assessed the clinical value of detecting cell-free circulating tumor DNA (ctDNA)...
OBJECTIVE
Biomarkers reflecting real-time response to therapy and recurrence are lacking. We assessed the clinical value of detecting cell-free circulating tumor DNA (ctDNA) mutations in endometrial cancer (EC) and ovarian cancer (OC) patients.
METHODS
EC/OC patients undergoing primary surgery were consented for tissue banking and 2-year serial blood draws. Tumor tissue DNA and plasma ctDNA underwent next generation sequencing using a targeted gene panel to identify somatic mutations.
RESULTS
Of 44 patients (24 EC, 17 OC, 2 synchronous endometrial and ovarian carcinomas [SEOC] and 1 endocervical adenocarcinoma [EA]) at least one somatic mutation was identified in tumor tissue in 40 (91%, 20/24 EC, all OC/SEOC/EA), and in preoperative plasma ctDNA in 12 (27%) patients (6/24 [25%] EC and 6/17 [35%] OC). Detection of preoperative ctDNA mutations was associated with advanced stage, higher preoperative CA125, and disease recurrence. In 5/12 (42%) patients with preoperative ctDNA mutations, examination/imaging suggested clinical stage I however final pathology revealed stage II/III. In 11 patients where serial timepoints were assessed during treatment for ctDNA and CA125, ctDNA clearance preceded normalization of CA125. Thirteen patients developed recurrent disease (4 EC, 8 OC, 1 EA); 8 in whom ctDNA mutations were detected postoperatively, and 4 followed through time of recurrence with ctDNA mutations identified 2-5 months prior to clinical/radiologic/biomarker progression in 3.
CONCLUSION
ctDNA can reflect larger tumor volume/metastases, treatment response and recurrence in EC and OC. Careful patient selection is critical to direct resources to patients most likely to benefit, considering disease burden and risk group.
PubMed: 38909641
DOI: 10.3802/jgo.2025.36.e5 -
Journal of Chromatography. A Jun 2024Slalom chromatography (SC) was discovered in 1988 for analyzing double-stranded (ds) DNA. However, its progress was impeded by practical issues such as low-purity...
Slalom chromatography (SC) was discovered in 1988 for analyzing double-stranded (ds) DNA. However, its progress was impeded by practical issues such as low-purity particles, sample loss, and lack of a clear retention mechanism. With the rise of cell and gene therapies and the availability today of bio-inert ultra-high-pressure liquid chromatography (UHPLC) columns and systems, SC has regained interest. In SC, the elution order is opposite to that observed in hydrodynamic chromatography (HDC): larger DNA molecules are more retained than small ones. Yet, the underlying SC retention mechanism remains elusive. We provide the physicochemical background necessary to explain, at a microscopic scale, the full transition from a HDC to a SC retention mechanism. This includes the persistence length of the DNA macromolecule (representing DNA stiffness), their relaxation time (τ) from the non-equilibrium contour length to the equilibrium entropic configuration, and the relationship between the mobile phase shear rate (〈γ̇〉) in packed columns and the DNA extended length. We propose a relevant retention model to account for the simultaneous impact of hydrodynamic chromatography (HDC) and SC on the retention factors of a series of large and linear dsDNAs (ranging from 2 to 48 kbp). SC data were acquired using bio-inert MaxPeak Columns packed with 1.7μm BEH 45 Å, 1.8μm BEH 125 Å, 2.4μm BEH 125 Å, 5.3μm BEH 125 Å, and 11.3μm BEH 125 Å Particles, an ACQUITY UPLC I-class PLUS System, and either 1 × PBS (pH 7.4) or 100 mM phosphate buffer (pH 8) as the mobile phase. SC is a non-equilibrium retention mode that is dominant when the Weissenberg number (Wi=〈γ̇〉τ) is much larger than 10 and the average extended length of DNA exceeds the particle diameter. HDC, on the other hand, is an equilibrium retention mode that dominates when Wi<1 (DNA chains remaining in their non-extended configuration). Maximum dsDNA resolution is observed in a mixed HDC-SC retention mode when the extended length of the DNA is approximately half the particle diameter. This work facilitates the development of methods for characterizing various plasmid DNA mixtures, containing linear, supercoiled, and relaxed circular dsDNAs which all have different degree of molecular stiffness.
PubMed: 38909519
DOI: 10.1016/j.chroma.2024.465075 -
International Immunopharmacology Jun 2024The occurrence and progression of hepatocellular carcinoma (HCC) are significantly affected by DNA damage response (DDR). Exploring DDR-related biomarkers can help...
BACKGROUND
The occurrence and progression of hepatocellular carcinoma (HCC) are significantly affected by DNA damage response (DDR). Exploring DDR-related biomarkers can help predict the prognosis and immune characteristics of HCC.
METHODS
First, the single-cell RNA sequencing (scRNA-seq) dataset GSE242889 was processed and performed manual annotation. Then we found the marker genes of DDR-active subgroups based on "AUCell" algorithm. The "Limma" R package was used to identify differentially expressed genes (DEGs) between tumor and normal samples of HCC. The risk prognostic model was constructed by filtering genes using univariate Cox and LASSO regression analyses. Finally, the signatures were analyzed for immune infiltration, gene mutation, and drug sensitivity. Last but not least, KPNA2, which had the largest coefficient in our model was validated by experiments including western blot, MTT, colony formation and γ-H2AX assays.
RESULTS
We constructed a prognostic model based on 5 DDR marker genes including KIF2C, CDC20, KPNA2, UBE2S and ADH1B for HCC. We also proved that the model had an excellent performance in both training and validation cohorts. Patients in the high-risk group had a poorer prognosis, different immune features, gene mutation frequency, immunotherapy response and drug sensitivity compared with the low-risk group. Besides, our experimental results proved that KPNA2 was up-regulated in liver cancer cells than in hepatocytes. More importantly, the knockdown of KPNA2 significantly inhibited cell variability, proliferation and promoted DNA damage.
CONCLUSIONS
We innovatively integrated scRNA-seq and bulk RNA sequencing to construct the DDR-related prognostic model. Our model could effectively predict the prognosis, immune landscape and therapy response of HCC.
PubMed: 38909498
DOI: 10.1016/j.intimp.2024.112475 -
Forensic Science International Jun 2024In cases of sexual assault, the interpretation of biological traces on clothing, and particularly undergarments, may be complex. This is especially so when the...
In cases of sexual assault, the interpretation of biological traces on clothing, and particularly undergarments, may be complex. This is especially so when the complainant and defendant interact socially, for instance as (ex-)partners or by co-habitation. Here we present the results from a study where latent male DNA on female worn undergarments is recovered in four groups with different levels of male-female social interaction. The results conform to prior expectation, in that less interaction tend to result in less male DNA on undergarments. We explore the use of these experimental data for evaluative reporting given activity level propositions in a mock case scenario. We show how the selection of different populations to represent the social interaction between complainant and defendant may affect the strength of the evidence. We further show how datasets of limited size can be used for robust activity level evaluative reporting.
PubMed: 38909409
DOI: 10.1016/j.forsciint.2024.112097 -
Clinical Epigenetics Jun 2024Genetic and environmental factors are implicated in many developmental processes. Recent evidence, however, has suggested that epigenetic changes may also influence the...
BACKGROUND
Genetic and environmental factors are implicated in many developmental processes. Recent evidence, however, has suggested that epigenetic changes may also influence the onset of puberty or the susceptibility to a wide range of diseases later in life. The present study aims to investigate changes in genomic DNA methylation profiles associated with pubertal onset analyzing human peripheral blood leukocytes from three different groups of subjects: 19 girls with central precocious puberty (CPP), 14 healthy prepubertal girls matched by age and 13 healthy pubertal girls matched by pubertal stage. For this purpose, the comparisons were performed between pre- and pubertal controls to identify changes in normal pubertal transition and CPP versus pre- and pubertal controls.
RESULTS
Analysis of methylation changes associated with normal pubertal transition identified 1006 differentially methylated CpG sites, 86% of them were found to be hypermethylated in prepubertal controls. Some of these CpG sites reside in genes associated with the age of menarche or transcription factors involved in the process of pubertal development. Analysis of methylome profiles in CPP patients showed 65% and 55% hypomethylated CpG sites compared with prepubertal and pubertal controls, respectively. In addition, interestingly, our results revealed the presence of 43 differentially methylated genes coding for zinc finger (ZNF) proteins. Gene ontology and IPA analysis performed in the three groups studied revealed significant enrichment of them in some pathways related to neuronal communication (semaphorin and gustation pathways), estrogens action, some cancers (particularly breast and ovarian) or metabolism (particularly sirtuin).
CONCLUSIONS
The different methylation profiles of girls with normal and precocious puberty indicate that regulation of the pubertal process in humans is associated with specific epigenetic changes. Differentially methylated genes include ZNF genes that may play a role in developmental control. In addition, our data highlight changes in the methylation status of genes involved in signaling pathways that determine the migration and function of GnRH neurons and the onset of metabolic and neoplastic diseases that may be associated with CPP in later life.
Topics: Humans; Puberty, Precocious; Female; DNA Methylation; Child; CpG Islands; Epigenesis, Genetic; Epigenome; Case-Control Studies
PubMed: 38909248
DOI: 10.1186/s13148-024-01683-1 -
Communications Biology Jun 2024Although the chloroplast genome (cpDNA) of higher plants is known to exist as a large protein-DNA complex called 'plastid nucleoid', researches on its DNA state and...
Although the chloroplast genome (cpDNA) of higher plants is known to exist as a large protein-DNA complex called 'plastid nucleoid', researches on its DNA state and regulatory elements are limited. In this study, we performed the assay for transposase-accessible chromatin sequencing (ATAC-seq) on five common tissues across five grasses, and found that the accessibility of different regions in cpDNA varied widely, with the transcribed regions being highly accessible and accessibility patterns around gene start and end sites varying depending on the level of gene expression. Further analysis identified a total of 3970 putative protein binding footprints on cpDNAs of five grasses. These footprints were enriched in intergenic regions and co-localized with known functional elements. Footprints and their flanking accessibility varied dynamically among tissues. Cross-species analysis showed that footprints in coding regions tended to overlap non-degenerate sites and contain a high proportion of highly conserved sites, indicating that they are subject to evolutionary constraints. Taken together, our results suggest that the accessibility of cpDNA has biological implications and provide new insights into the transcriptional regulation of chloroplasts.
Topics: Genome, Chloroplast; Poaceae; DNA, Chloroplast; Gene Expression Regulation, Plant; Chloroplasts
PubMed: 38909165
DOI: 10.1038/s42003-024-06374-4