Innovative insights into extrachromosomal circular DNAs in gynecologic tumors and reproduction

Originating but free from chromosomal DNA,extrachromosomal circular DNAs(eccDNAs)are organized in circular form and have long been found in unicellular and multicellular eukaryotes.Their biogenesis and function are poorly understood as they are characterized by sequence homology with linear DNA,for which few detection methods are available.Recent advances in high-throughput sequencing technologies have revealed that eccDNAs play crucial roles in tumor formation,evolution,and drug resistance as well as aging,genomic diversity,and other biological processes,bringing it back to the research hotspot.Several mechanisms of eccDNA formation have been proposed,including the breakage-fusion-bridge(BFB)and translocation-deletion-amplification models.Gynecologic tumors and disorders of embryonic and fetal development are major threats to human reproductive health.The roles of eccDNAs in these pathological processes have been partially elucidated since the first discovery of eccDNA in pig sperm and the double minutes in ovarian cancer ascites.The present review summarized the research history,biogenesis,and currently available detection and analytical methods for eccDNAs and clarified their functions in gynecologic tumors and reproduction.We also proposed the application of eccDNAs as drug targets and liquid biopsy markers for prenatal diagnosis and the early detection,prognosis,and treatment of gynecologic tumors.This review lays theoretical foundations for future investigations into the complex regulatory networks of eccDNAs in vital physiological and pathological processes.

Cell–cell communication:new insights and clinical implications

Multicellular organisms are composed of diverse cell types that must coordinate their behaviors through communication.Cell–cell communication(CCC)is essential for growth,development,differentiation,tissue and organ formation,maintenance,and physiological regulation.Cells communicate through direct contact or at a distance using ligand–receptor interactions.So cellular communication encompasses two essential processes:cell signal conduction for generation and intercellular transmission of signals,and cell signal transduction for reception and procession of signals.Deciphering intercellular communication networks is critical for understanding cell differentiation,development,and metabolism.First,we comprehensively review the historical milestones in CCC studies,followed by a detailed description of the mechanisms of signal molecule transmission and the importance of the main signaling pathways they mediate in maintaining biological functions.Then we systematically introduce a series of human diseases caused by abnormalities in cell communication and their progress in clinical applications.Finally,we summarize various methods for monitoring cell interactions,including cell imaging,proximity-based chemical labeling,mechanical force analysis,downstream analysis strategies,and single-cell technologies.These methods aim to illustrate how biological functions depend on these interactions and the complexity of their regulatory signaling pathways to regulate crucial physiological processes,including tissue homeostasis,cell development,and immune responses in diseases.In addition,this review enhances our understanding of the biological processes that occur after cell–cell binding,highlighting its application in discovering new therapeutic targets and biomarkers related to precision medicine.This collective understanding provides a foundation for developing new targeted drugs and personalized treatments.

Targeting RIP3 inhibits osteoarthritis development by restoring anabolic-catabolic balance in the bone-cartilage unit

Background:Osteoarthritis(OA)is a debilitating joint disorder characterized by pro-gressive cartilage degeneration.During OA,subchondral bone undergoes micro-structural and molecular changes that precede cartilage degradation.However,spe-cific mechanisms underlying metabolic dysregulation of the bone-cartilage unit remain unclear.This study aims to investigate the role of receptor-interacting protein kinase-3(RIP3)in OA progression,focusing on bone-cartilage metabolic homeostasis.Methods:RIP3-mediated pathological and metabolic alterations in chondrocytes,os-teoblasts,and bone marrow-derived macrophages(BMMs)were evaluated.RIP3-mediated OA manifestations in cartilage and,more importantly,subchondral bone were determined by intra-articular overexpression of RIP3 in rats.The protective effect of RIP3 deficiency on the bone-cartilage unit during OA was systematically investigated using Rip3 knockout mice.The CMap database was used to screen for compounds that abrogate RIP3-induced OA pathological changes.Results:RIP3 was upregulated in the cartilage and subchondral bone of OA patients and post-traumatic OA mouse model.RIP3 overexpression not only inhibited extra-cellular matrix(ECM)anabolism in chondrocytes but also attenuated osteoblast differentiation,whereas RIP3 deficiency blunted receptor activator of NF-kappaB ligand-mediated osteoclastogenesis of BMMs.Intra-articular RIP3 overexpression induced the imbalance of SP7+osteoblasts/tartrate-resistant acid phosphatase(TRAP)+osteoclasts within the subchondral bone in addition to cartilage degen-eration in rats,while Rip3 deletion significantly improved structural outcomes of the bone-cartilage unit,and achieved pain relief as well as functional improvement in surgery-induced and spontaneous OA mouse models.Mechanistically,RIP3 initiates OA by perturbing critical events,including cartilage metabolism,inflammatory re-sponses,senescence,and osteoclast differentiation.Clofibrate,a hypolipidemic drug,was identified as a novel RIP3 inhibitor that reverses ECM catabolism in OA.Conclusions:RIP3 is an essential governor of whole joint metabolic homeostasis by regulating both cartilage metabolism and subchondral bone remodeling.Reconstruction of the bone-cartilage unit by targeting RIP3 might provide a two-birds-one-stone approach for the development of future OA therapies.

Identification and analysis of intermediate-size noncoding RNAs in the rhesus macaque fetal brain

Although only about 2%of the human genome has proved to be protein-coding genes,recent advances in genome wide analysis have revealed that the majority of the genome is transcribed,mainly from noncoding segments that were once considered＂junk sequences＂or＂dark matters＂（Liu et al.,2011a;Zhang et al.,2014b）. In addition to the well-characterized housekeeping non- coding RNAs （ncRNAs） （tRNA, rRNA, small nuclear RNA and small nucleolar RNAs） and some small regulatory ncRNAs （microRNAs and small interfering RNAs）, the transcriptome of mammals could also pervasively have been transcribed long noncoding RNAs （lncRNAs, at least 200 nt） （Rinn and Chang, 2012; Xie et al., 2012）.

The effect of pore size on the mechanical properties, biodegradation and osteogenic effects of additively manufactured magnesium scaffolds after high temperature oxidation: An in vitro and in vivo study

The effects of pore size in additively manufactured biodegradable porous magnesium on the mechanical properties and biodegradation of the scaffolds as well as new bone formation have rarely been reported. In this work, we found that high temperature oxidation improves the corrosion resistance of magnesium scaffold. And the effects of pore size on the mechanical characteristics and biodegradation of scaffolds, as well as new bone formation, were investigated using magnesium scaffolds with three different pore sizes, namely, 500, 800, and 1400 μm (P500, P800, and P1400). We discovered that the mechanical characteristics of the P500 group were much better than those of the other two groups. In vitro and in vivo investigations showed that WE43 magnesium alloy scaffolds supported the survival of mesenchymal stem cells and did not cause any local toxicity. Due to their larger specific surface area, the scaffolds in the P500 group released more magnesium ions within reasonable range and improved the osteogenic differentiation of bone mesenchymal stem cells compared with the other two scaffolds. In a rabbit femoral condyle defect model, the P500 group demonstrated unique performance in promoting new bone formation, indicating its great potential for use in bone defect regeneration therapy.

Functional analysis of the methyltransferase SMYD in the single-cell model organism Tetrahymena thermophila

Lysine methylation of histones and non-histones plays a pivotal role in diverse cellular processes.The SMYD(SET and MYND domain)family methyltransferases can methylate various histone and non-histone substrates in mammalian systems,implicated in HSP90 methylation,myofilament organization,cancer inhibition,and gene transcription regulation.To resolve controversies concerning SMYD's substrates and functions,we studied SMYD1(TTHERM_00578660),the only homologue of SMYD in the unicellular eukaryote Tetrahymena thermophila.We epitope-tagged SMYD1,and analyzed its localization and interactome.We also characterized △SMYD1 cells,focusing on the replication and transcription phenotype.Our results show that:(1)SMYD1 is present in both cytoplasm and transcriptionally active macronucleus and shuttles between cytoplasm and macronucleus,suggesting its potential association with both histone and non-histone substrates;(2)SMYD1 is involved in DNA replication and regulates transcription of metabolism-related genes;(3)HSP90 is a potential substrate for SMYD1 and it may regulate target selection of HSP90,leading to pleiotropic effects in both the cytoplasm and the nucleus.

MBRidge: an accurate and cost-effective method for profiling DNA methylome at single-base resolution

Organisms and cells,in response to environmental influences or during development,undergo considerable changes in DNA methylation on a genome-wide scale,which are linked to a variety of biological processes.Using MethylC-seq to decipher DNA methylome at single-base resolution is prohibitively costly.In this study,we develop a novel approach,named MBRidge,to detect the methylation levels of repertoire CpGs,by innovatively introducing C-hydroxylmethylated adapters and bisulfate treatment into the MeDIP-seq protocol and employing ridge regression in data analysis.A systematic evaluation of DNA methylome in a human ovarian cell line T29 showed that MBRidge achieved high correlation(R>0.90)with much less cost(∼10%)in comparison with MethylC-seq.We further applied MBRidge to profiling DNA methylome in T29H,an oncogenic counterpart of T29’s.By comparing methylomes of T29H and T29,we identified 131790 differential methylation regions(DMRs),which are mainly enriched in carcinogenesis-related pathways.These are substantially different from7567 DMRs that were obtained by RRBS and related with cell development or differentiation.The integrated analysis ofDMRsin the promoterand expression of DMR-corresponding genes revealed thatDNAmethylation enforced reverse regulation of gene expression,depending on the distance fromthe proximalDMRto transcription starting sites in both mRNA and lncRNA.Taken together,our results demonstrate that MBRidge is an efficient and cost-effective method that can be widely applied to profiling DNA methylomes.