Single-cell RNA-Seq profiling of human preimplantation embryos and embryonic stem cells. Nat Struct Mol Biol. 2013;20:1131-1139. [PMID: 23934149 DOI: 10.1038/nsmb.2660]

Guanylate-binding proteins protect the sea cucumbers Apostichopus japonicus against infection of Vibrio splendidus

Guanylate-binding proteins (GBPs) are interferon-induced innate immune effector molecules belonging to the GTPase superfamily and are crucial components of cell-autonomous immunity. To date, most research on GBPs has focused on mammals, with limited studies in marine invertebrates. In this study, we identified three GBP genes from the sea cucumber Apostichopus japonicus, designated as AjGBP1, AjGBP2, and AjGBP3. Phylogenetic analysis revealed that AjGBPs cluster with GBPs from other invertebrates. Multiple sequence alignment and protein structural analysis indicated that the AjGBPs possess a conserved GTPase-binding domain at the N-terminus and an effector domain composed of α-helices at the C-terminus. These AjGBPs are ubiquitously expressed in the body wall, muscle, intestine, respiratory tree, and coelomocytes of A. japonicus, although their expression levels vary among different tissues. Under Vibrio splendidus challenge, the expression of all three AjGBPs was significantly upregulated in coelomocytes. Recombinant AjGBP proteins with GTPase activity were produced through prokaryotic expression, and bacterial binding assays demonstrated that they could bind V. splendidus in vitro in a GTP hydrolysis-dependent manner. Interference with AjGBPs expression suppressed the antibacterial capacity of coelomocytes. These findings suggest that AjGBPs target V. splendidus and play an important role in the antibacterial immune response of A. japonicus.

SHMT2 is essential for mammalian preimplantation embryonic development through de novo biosynthesis of nucleotide metabolites

Assisted reproductive technology (ART) is used widely and efficiently to treat infertility. During the ART procedure, one of the main factors affecting the success rate is abnormal development of preimplantation embryos. The establishment and maintenance of developmental competence are precisely regulated at different levels, while minor errors at early stages may result in adverse outcomes, including developmental arrest and implantation failure. As one of the major inputs, the regulatory mechanisms of metabolites in embryonic development are less known. In this study, we investigated the functional relevance of the metabolic enzyme serine hydroxymethyltransferase 2 (SHMT2) and deoxyribonucleotide (dNTP) metabolites in mouse preimplantation embryonic development. By using a well-characterized SHMT2 inhibitor, SHMT-IN-2, we effectively inhibited the catalytic activity of the SHMT2 enzyme, which led to developmental arrest at the pronuclear stage of the embryo. A low-input liquid chromatography-tandem mass spectrometry (LC-MS/MS) method was developed and applied for detecting dNTP content in embryos. We found that SHMT2 inhibition led to an insufficient dTTP supply and replication stress during the first mitotic cleavage, thereby causing failure of pronuclear fusion and developmental arrest. Our findings demonstrate a specific mechanism where, apart from building blocks of DNA, the availability of dNTPs contributes to the control of mouse preimplantation embryonic development.

New Evidence for the Mechanisms of Nanoplastics Amplifying Cadmium Cytotoxicity: Trojan Horse Effect, Inflammatory Response, and Calcium Imbalance

Nanoplastics (NPs) are emerging pollutants worldwide. Particularly worrisome is that although studies have reported that NPs can amplify the biotoxicity of environmental pollutants, the specific mechanism remains unclear. Here, we found that NPs, even without significant toxicity (cell survival: 99.11%), amplified the hepatocyte toxicity of Cd2+. Mechanistically, higher Cd2+ uptake (Δ = 23.80%) combined with crucial intracellular desorption behavior of Cd2+ loaded in NPs (desorption rate: 82.70%) were identified as prerequisites for NPs amplifying Cd2+ cytotoxicity. As for toxigenic pathways, the inflammatory response and calcium (Ca) signaling pathway were identified as the primary molecular events leading to the amplification of Cd2+ cytotoxicity. Further phenotypic monitoring revealed that NPs synergized with Cd2+ to induce more severe pyroptosis and apoptosis by activating the inflammatory caspase-1-dependent and Ca2+-mitochondrial-caspase-3 pathways to a greater extent, respectively. This study reveals and proves for the first time the "Trojan horse" effects of NPs, thus elucidating the actual mechanisms by which NPs act as toxicity amplifiers of pollutants, providing significant insights into accurate risk assessment of NPs in composite pollution.

Whole-genome transcriptome and DNA methylome analyses reveal molecular abnormalities during the oocyte-to-embryo transition in preimplantation embryos derived from prepubertal lamb oocytes†

The juvenile in vitro embryo transfer technology holds the potential to accelerate livestock breeding. However, its application is limited due to the weak in vitro development of oocytes and embryos from prepubertal lambs. To dissect the regulatory networks of gene expression of sheep embryos and identify the defects in gene expression in prepubertal lamb embryos during the oocyte-to-embryo transition, full-length RNA sequencing and whole-genome bisulfite sequencing based on trace cells were conducted on in vitro-derived embryos generated from adult sheep and prepubertal lamb oocytes. We found that the maternal transcript degradation occurred selectively in adult sheep embryos in multiple waves and was most completed until the morula stage. Major embryonic genome activation was found to occur at the morula stage. By comparing with the patterns of adult embryos, we observed incomplete maternal transcript degradation and abnormal embryonic genome activation in lamb embryos and analyzed their potential molecular mechanisms. Furthermore, we explored dynamic DNA methylation concerning the paternal and maternal genomes during the preimplantation development of sheep embryos, revealing the negative regulatory role of promoter DNA methylation on embryonic genome activation process. Lamb embryos generally displayed higher DNA methylation levels than adults, potentially repressing the embryonic genome activation gene expression, especially the genes associated with ribosomal and mitochondrial organization. We also found abnormalities in the methylation status of imprinted genes in lamb embryos. Our findings advance the understanding of sheep in vitro embryo development and offer insights for improving the juvenile in vitro embryo transfer technology in livestock.

Profiling and functional characterization of long noncoding RNAs during human tooth development

The regulatory processes in developmental biology research are significantly influenced by long non-coding RNAs (lncRNAs). However, the dynamics of lncRNA expression during human tooth development remain poorly understood. In this research, we examined the lncRNAs present in the dental epithelium (DE) and dental mesenchyme (DM) at the late bud, cap, and early bell stages of human fetal tooth development through bulk RNA sequencing. Developmental regulators co-expressed with neighboring lncRNAs were significantly enriched in odontogenesis. Specific lncRNAs expressed in the DE and DM, such as PANCR, MIR205HG, DLX6-AS1, and DNM3OS, were identified through a combination of bulk RNA sequencing and single-cell analysis. Further subcluster analysis revealed lncRNAs specifically expressed in important regions of the tooth germ, such as the inner enamel epithelium and coronal dental papilla (CDP). Functionally, we demonstrated that CDP-specific DLX6-AS1 enhanced odontoblastic differentiation in human tooth germ mesenchymal cells and dental pulp stem cells. These findings suggest that lncRNAs could serve as valuable cell markers for tooth development and potential therapeutic targets for tooth regeneration.

DUX4 activates common and context-specific intergenic transcripts and isoforms

DUX4 regulates the expression of genic and nongenic elements and modulates chromatin accessibility during zygotic genome activation in cleavage stage embryos. Its misexpression in skeletal muscle causes facioscapulohumeral dystrophy (FSHD). By leveraging full-length RNA isoform sequencing with short-read RNA sequencing of DUX4-inducible myoblasts, we elucidate an isoform-resolved transcriptome featuring numerous unannotated isoforms from known loci and novel intergenic loci. While DUX4 activates similar programs in early embryos and FSHD muscle, the isoform usage of known DUX4 targets is notably distinct between the two contexts. DUX4 also activates hundreds of previously unannotated intergenic loci dominated by repetitive elements. The transcriptional and epigenetic profiles of these loci in myogenic and embryonic contexts indicate that the usage of DUX4-binding sites at these intergenic loci is influenced by the cellular environment. These findings demonstrate that DUX4 induces context-specific transcriptomic programs, enriching our understanding of DUX4-induced muscle pathology.

Proteogenomic reprogramming to a functional human blastomere-like stem cell state via a PARP-DUX4 regulatory axis

Here, we show that conventional human pluripotent stem cells cultured with non-specific tankyrase-PARP1-inhibited conditions underwent proteogenomic reprogramming to functional blastomere-like tankyrase/PARP inhibitor-regulated naive stem cells (TIRN-SC). TIRN-SCs concurrently expressed hundreds of pioneer factors in hybrid 2C-8C-morula-ICM programs that were augmented by induced expression of DUX4. Injection of TIRN-SCs into 8C-staged murine embryos equipotently differentiated human cells to the extra-embryonic and embryonic compartments of chimeric blastocysts and fetuses. Ectopic expression of murine-E-Cadherin in TIRN-SCs further enhanced interspecific chimeric tissue targeting. TIRN-SC-derived trophoblast stem cells efficiently generated placental chimeras. Proteome-ubiquitinome analyses revealed increased TNKS and reduced PARP1 levels and an ADP-ribosylation-deficient, hyper-ubiquitinated proteome that impacted expression of both tankyrase and PARP1 substrates. ChIP-seq of NANOG-SOX2-OCT4 and PARP1 (NSOP) revealed genome-wide NSOP co-binding at DUX4-accessible enhancers of embryonic lineage factors; suggesting a DUX4-NSOP axis regulated TIRN-SC lineage plasticity. TIRN-SCs may serve as valuable models for studying the proteogenomic regulation of pre-lineage human embryogenesis. VIDEO ABSTRACT.

Transcriptome Analysis of Individual Ovine Oocytes and Preimplantation Embryos From In Vitro Fertilization Source

In this study, we examine the transcriptional profiles of eight stages of preimplantation embryo development, from germinal vesicle (GV) oocytes to blastocysts, in in vitro fertilized sheep embryos using RNA sequencing. Between 12,744 and 15,539 genes were detected from the GV moving forward to blastocyst, with cluster analysis revealing two distinct clusters related to developmental stage. The largest change for differentially expressed genes (DEGs) numbers took place between 2- to 4-cell comparison and 4- to 8-cell comparison, with a c. 35-fold increase from 19 to 670 DEGs. This suggests that zygotic genome activation occurred at 8-cell stage in sheep. All the DEGs had gene ontology annotations in three classes, and these comprised 53 subclasses. Most of the pathways (89 of 93) were enriched through KEGG analysis of the DEGs, and the most enriched pathway was oxidative phosphorylation. The 2- and 16-cell stage embryos possessed the highest and lowest numbers, respectively, of single nucleotide polymorphisms and insertion-deletion markers. Five major types of alternative splicing were found. A total of 2361 transcription factor genes were mutually expressed among the eight developmental stages. The top five differential transcription factor protein families were Zf-C2H2, bHLH, Homeobox, Others, and HMG. This is the first study to investigate the transcriptional profiling of sheep preimplantation embryos at different developmental stages, and it displays a comprehensive transcriptome landscape in sheep oocytes and embryos.

Krüppel-like factors play essential roles in regulating pluripotency and the formation of neural crest stem cells

The evolution of complex vertebrate body plans was driven by the acquisition of the neural crest, a stem cell population that retains broad, multi-germ layer potential after most embryonic cells have become lineage restricted. We have previously shown that neural crest cells share significant gene regulatory architecture with pluripotent blastula stem cells. Here, we examine the roles that two Krüppel-like Family (Klf) transcription factors, Klf2 and Klf17, play in these cell populations. We found that inhibition of either klf2 or klf17 expanded expression of pluripotency, neural plate border and neural crest factors in neurula stage Xenopus embryos, suggesting that Klf factors regulate the exit from pluripotency and proper establishment of the boundary of the neural crest domain. To gain further insights into the role of Klf factors in the evolution of the neural crest, we examined their expression in sea lamprey, a jawless vertebrate, and show that ectopic expression of lamprey klf17 in Xenopus embryos phenocopies Xenopus klf17. These data suggest that klf17 may have been the ancestral Klf factor that functioned in these gene regulatory networks in stem vertebrates.

Improving Bovine Embryo Development and Quality Using Bovine Oviductal Epithelial Cell-Derived Conditioned Medium (bOEC-CM)

BACKGROUND

The embryo co-culture systems with the monolayer cultured cells are complex, unreproducible, and have a high probability of biological contamination. Therefore, nowadays, using conditioned media is a suitable alternative to these methods.

OBJECTIVES

This study aimed to investigate the impact of utilizing bovine oviductal epithelial cell-derived conditioned medium (bOEC-CM) on subsequent embryo development and quality.

METHODS

Bovine embryos produced in vitro were cultured in a specific medium supplemented with either 5% charcoal-stripped FBS (Charcoled Strip Serum [CSS]) or 10% bOEC-CM from either Days 1 or 3 post-fertilization. Various parameters, such as cleavage rate, blastocyst formation, hatching rate and blastocyst quality, were assessed.

RESULTS

The results indicated that adding 10% CM from Day 1 significantly reduced the cleavage rate compared to using CSS on the same day (p < 0.05). Furthermore, the CSS and CM from both Days 1 and 3 increased blastocyst formation rates (p < 0.05). Notably, the addition of 10% CM on Day 3 significantly improved the hatching rate compared to the other groups (p < 0.05). Both CM and CSS were found to enhance the inner cell mass (ICM), trophectoderm (TE) and total cell numbers in blastocysts when used on both Days 1 and 3 (p < 0.05). Additionally, CM from Day 3 positively influenced the expression levels of development-specific genes in cultured embryos (p < 0.05).

CONCLUSION

Overall, the findings suggest that using bOEC-CM at a 10% concentration may provide a promising supplement even better than serum and traditional co-culture methods during the last 5 days of embryo culture.

α-Ketoglutarate promotes trophectoderm induction and maturation from naive human embryonic stem cells

Development and lineage choice are driven by interconnected transcriptional, epigenetic and metabolic changes. Specific metabolites, such as α-ketoglutarate (αKG), function as signalling molecules affecting the activity of chromatin-modifying enzymes. However, how metabolism coordinates cell-state changes, especially in human pre-implantation development, remains unclear. Here we uncover that inducing naive human embryonic stem cells towards the trophectoderm lineage results in considerable metabolic rewiring, characterized by αKG accumulation. Elevated αKG levels potentiate the capacity of naive embryonic stem cells to specify towards the trophectoderm lineage. Moreover, increased αKG levels promote blastoid polarization and trophectoderm maturation. αKG supplementation does not affect global histone methylation levels; rather, it decreases acetyl-CoA availability, reduces histone acetyltransferase activity and weakens the pluripotency network. We propose that metabolism functions as a positive feedback loop aiding in trophectoderm fate induction and maturation, highlighting that global metabolic rewiring can promote specificity in cell fate decisions through intricate regulation of signalling and chromatin.

pH-responsive nanoparticles for oral delivery of RNAi for sustained protection against Spodoptera exigua

To enhance the RNAi efficiency of dsRNA against the Spodoptera exigua through a feeding method, we developed a pH-responsive nanoparticle, chitosan-polyethylene glycol-carboxyl (CS-PEG-COOH). This nanoparticle enhances RNAi efficiency by improving dsRNA stability in the midgut of S. exigua and can intelligently release dsRNA under alkaline conditions. Firstly, the CS-PEG-COOH carrier was prepared via cross-linking reactions, and the mass ratio of dsRNA to CS-PEG-COOH was obtained using electrophoretic mobility. The carrier composite materials were then characterized using isothermal titration calorimetry (ITC), transmission electron microscopy (TEM), atomic force microscopy (AFM), and Zeta potential analysis. The stability and delivery efficiency of the dsRNA/CS-PEG-COOH complex were then verified using electrophoretic mobility and fluorescence labeling methods. Finally, the RNAi efficiency and synergistic mechanism of the complex were analyzed using feeding methods and RNA-seq. The results show that CS-PEG-COOH (40.16 nm size, + 6.44 mV charge) forms a clustered complex with dsRNA through hydrogen bonding and hydrophobic interactions. CS-PEG-COOH significantly enhancing the stability and delivery efficiency of dsRNA in the midgut of S. exigua. Additionally, at pH > 8, dsRNA could be released from dsRNA/CS-PEG-COOH. The RNAi results showed that, dsRNA/CS-PEG-COOH could effectively inhibit the expression of the Acetylcholinesterase (Ace1 + Ace2) gene (65 %), and led to significantly increase mortality (51.82 %), a prolonged developmental period (25 %) and reduced egg production (22.02 %). The physiological and molecular synergistic mechanisms were revealed by RNA-seq analysis. The CS-PEG-COOH-loaded dsACE1 + dsACE2 led to down-regulation of genes related to drug metabolism, hormone synthesis, and stratum corneum biosynthesis, which inhibited insect growth and development. Overall, We developed an appropriate delivery method for dsRNA application in Lepidoptera, providing a basis for developing RNA pesticides with high efficiency and environmental safety.

NKX2-5/LHX1 and UHRF1 Establishing a Positive Feedback Regulatory Circuitry Drives Esophageal Squamous Cell Carcinoma through Epigenetic Dysregulation

DNA methylation regulators play critical roles in modulating oncogenic driver genes in cancers. However, the precise mechanisms through which these DNA methylation regulators influence oncogenesis and clinical therapy have yet to be fully elucidated. This study reveals that hypermethylation of under-methylated regions (UMRs) within gene bodies is involved in the activation of oncogenic homeobox genes, particularly NKX2-5 and LHX1, in esophageal squamous cell carcinoma (ESCC). Mechanistically, NKX2-5 and LHX1 synergistically bind to the promoter region of UHRF1, thereby augmenting its transcription. In turn, UHRF1 orchestrates the recruitment of DNMT1/DNMT3A, alongside NKX2-5 and LHX1, to the UMRs of these genes, thereby increasing DNA methylation levels and their expression. This intricate interplay forms a positive transcriptional feedback loop between NKX2-5/LHX1 and UHRF1, thus promoting the overexpression of all three genes and ultimately facilitating tumor growth. Notably, concurrent inhibition of UHRF1 and DNMTs impedes tumor growth by suppressing NKX2-5 and LHX1 expression. Overall, this study identifies a positive feedback regulatory circuitry underlying the UMR hypermethylation-mediated activation of oncogenic drivers in ESCC and proposes a promising therapeutic strategy for ESCC patients.

Establishment of human expanded potential stem cell lines via preimplantation embryo cultivation and somatic cell reprogramming

We previously reported the derivation of expanded potential stem cells (EPSCs) by modulating signaling pathways involved in preimplantation embryogenesis. These cells exhibit expanded developmental potential into embryonic and extraembryonic lineages, and we have shown that human EPSCs (hEPSCs) possess trophoblast differentiation potency for generating human trophoblast stem cells. Here we report protocols for deriving stable hEPSC lines directly from morula or early blastocyst stages of human preimplantation embryos (hEPSC-em) and by reprogramming human dermal fibroblasts (human induced EPSCs) using six exogenous factors, as an extension to our previous protocols on deriving porcine EPSCs from preimplantation embryos and by reprogramming somatic cells. These hEPSC lines proliferate robustly over long-term passaging and are amenable to both simple indels and precision genome editing. We provide guidance for characterizing these newly established hEPSCs, including cell-cycle analysis, pluripotency validation and karyotyping. The hEPSCs form teratomas with embryonic and extraembryonic cell lineages and readily differentiate into human trophoblast stem cells in vitro. At the molecular level, hEPSCs have unique features such as high expression of core histone genes and low H3K27me3 levels resembling eight-cell/morula stage embryos. These properties make hEPSCs a valuable tool not only for studying early human development but also for potential applications in regenerative medicine. The protocols presented in this manuscript can be readily performed by postgraduate students or postdoctoral fellows and completed within around 2 months.

A Cross-Linked Cyclosiloxane Polymer Matrix as a Platform Enabling Long-Term Culture of Human Induced Pluripotent Stem Cells with Naïve-Like Features

Culture platforms for human induced pluripotent stem cells (hiPSCs) that rely on feeder cells or extracellular matrices (ECMs) face substantial limitations for practical regenerative medicine applications, including undefined components, high costs, and a tendency to maintain hiPSCs in the primed pluripotent state, which has lower differentiation potential than the naïve state. To overcome these challenges, we developed a long-term hiPSC culture platform based on a cross-linked cyclosiloxane polymer matrix that preserves pluripotency with naïve-like characteristics. Through optimization, we identified an ideal cyclosiloxane polymer matrix, designated as poly-Z, which supported the growth of hiPSCs as spheroids. Even after 60 d of continuous culture, hiPSC spheroids maintained on poly-Z retained pluripotency markers and normal karyotypes at levels comparable to those of hiPSC colonies cultured on conventional vitronectin (VN)-coated plates. Furthermore, mRNA sequencing revealed that hiPSC spheroids cultured on poly-Z not only exhibited up-regulation of typical pluripotency-related genes but also showed increased expression of genes associated with the naïve pluripotent state, in contrast to the primed state observed in hiPSCs cultured on VN-coated plates or in suspension culture. Gene ontology (GO) analysis and gene set enrichment analysis (GSEA) further suggested that the down-regulation of genes involved in cell-ECM interactions contributed to the induction of naïve-like features in poly-Z-cultured hiPSC spheroids. These findings highlight the potential of cross-linked cyclosiloxane-based polymer matrices as an innovative platform for human pluripotent stem cell research and regenerative medicine.

High-resolution single-cell RNA-seq data and heterogeneity analysis of human ESCs and ffEPSCs

This study presents a comprehensive transcriptomic analysis of feeder-free extended pluripotent stem cells (ffEPSCs) and their parental human embryonic stem cells (ESCs), providing new insights into understanding human early development and cellular heterogeneity of pluripotency. Leveraging Smart-seq2-based single-cell RNA sequencing (scRNA-seq), we have compared gene expression profiles between ESCs and ffEPSCs and uncovered distinct subpopulations within both groups. Through pseudotime analysis, we have mapped the transition process from ESCs to ffEPSCs, revealing critical molecular pathways involved in the shift from a primed pluripotency to an extended pluripotent state. Additionally, we have employed repeat sequence analysis based on the latest T2T database and identified the stage-specific repeat elements contributing to regulating pluripotency and developmental transitions. This dataset deepens our understanding on early pluripotency and highlights the role of repeat sequences in early embryonic development. Our findings thus offer valuable resources for researchers in stem cell biology, pluripotency, early embryonic development, and potential cell therapy and regenerative medical applications.

Human oocyte quality and reproductive health

Declining female fertility is a health issue that has received broad global attention. Oocyte quality is the key limiting factor of female fertility, and key processes affecting oocyte quality involve the secretion of and response to hormones, ovarian function, oogenesis, oocyte maturation, and meiosis. However, compared with other species, the research and understanding of human oocyte quality and human reproductive health is limited. This review highlights our current understanding of the physiological factors and pathological factors related to human oocyte quality and discusses potential treatments. In terms of physiology, we discuss the regulation of the hypothalamic-pituitary-gonadal axis, granulosa cells, key subcellular structures, maternal mRNA homeostasis, the extracellular matrix, the maternal microenvironment, and multi-omics resources related to human oocyte quality. In terms of pathology, we review hypothalamic-pituitary-gonadal defects, ovarian dysfunction (including premature ovarian insufficiency and polycystic ovary syndrome), human oocyte development defects, and aging. In terms of the pathological aspects of human oocyte development and quality defects, nearly half of the reported pathogenic genes are involved in meiosis, while the remainder are involved in maternal mRNA regulation, the subcortical maternal complex, zona pellucida formation, ion channels, protein transport, and mitochondrial function. Furthermore, we outline the emerging scientific prospects and challenges for future explorations of the biological mechanisms behind infertility and the development of clinical treatments. This review seeks to deepen our understanding of the mechanisms regulating human oocyte quality and to provide novel insights into clinical female infertility characterized by defects in oocyte quality and oocyte development.

CeiTEA: Adaptive Hierarchy of Single Cells with Topological Entropy

Advances in single-cell RNA sequencing (scRNA-seq) enable detailed analysis of cellular heterogeneity, but existing clustering methods often fail to capture the complex hierarchical structures of cell types and subtypes. CeiTEA is introduced, a novel algorithm for adaptive hierarchical clustering based on topological entropy (TE), designed to address this challenge. CeiTEA constructs a multi-nary partition tree that optimally represents relationships and diversity among cell types by minimizing TE. This method combines a bottom-up strategy for hierarchy construction with a top-down strategy for local diversification, facilitating the identification of smaller hierarchical structures within subtrees. CeiTEA is evaluated on both simulated and real-world scRNA-seq datasets, demonstrating superior clustering performance compared to state-of-the-art tools like Louvain, Leiden, K-means, and SEAT. In simulated multi-layer datasets, CeiTEA demonstrated superior performance in retrieving hierarchies with a lower average clustering information distance of 0.15, compared to 0.39 from SEAT and 0.67 from traditional hierarchical clustering methods. On real datasets, the CeiTEA hierarchy reflects the developmental potency of various cell populations, validated by gene ontology enrichment, cell-cell interaction, and pseudo-time analysis. These findings highlight CeiTEA's potential as a powerful tool for understanding complex relationships in single-cell data, with applications in tumor heterogeneity and tissue specification.

scPRINT: pre-training on 50 million cells allows robust gene network predictions

A cell is governed by the interaction of myriads of macromolecules. Inferring such a network of interactions has remained an elusive milestone in cellular biology. Building on recent advances in large foundation models and their ability to learn without supervision, we present scPRINT, a large cell model for the inference of gene networks pre-trained on more than 50 million cells from the cellxgene database. Using innovative pretraining tasks and model architecture, scPRINT pushes large transformer models towards more interpretability and usability when uncovering the complex biology of the cell. Based on our atlas-level benchmarks, scPRINT demonstrates superior performance in gene network inference to the state of the art, as well as competitive zero-shot abilities in denoising, batch effect correction, and cell label prediction. On an atlas of benign prostatic hyperplasia, scPRINT highlights the profound connections between ion exchange, senescence, and chronic inflammation.

Heterogeneity-preserving discriminative feature selection for disease-specific subtype discovery

Disease-specific subtype identification can deepen our understanding of disease progression and pave the way for personalized therapies, given the complexity of disease heterogeneity. Large-scale transcriptomic, proteomic, and imaging datasets create opportunities for discovering subtypes but also pose challenges due to their high dimensionality. To mitigate this, many feature selection methods focus on selecting features that distinguish known diseases or cell states, yet often miss features that preserve heterogeneity and reveal new subtypes. To overcome this gap, we develop Preserving Heterogeneity (PHet), a statistical methodology that employs iterative subsampling and differential analysis of interquartile range, in conjunction with Fisher's method, to identify a small set of features that enhance subtype clustering quality. Here, we show that this method can maintain sample heterogeneity while distinguishing known disease/cell states, with a tendency to outperform previous differential expression and outlier-based methods, indicating its potential to advance our understanding of disease mechanisms and cell differentiation.

Single-cell metabolomics reveals that bisphosphoglycerate mutase influences oocyte maturation through glucose metabolism

The spatiotemporal turnover of metabolites is essential for oocyte maturation, embryonic development, and cell lineage differentiation. Here, we analyzed the metabolic profiles of individual living mouse oocytes and studied how bisphosphoglycerate mutase (BPGM), an important maternal factor, influences metabolite regulation during oocyte maturation. We found that BPGM is expressed in mouse follicles, oocytes, and embryos, as well as in human embryos. Notably, deletion of Bpgm significantly reduced the rate of oocyte maturation and reduced mouse fertility, which was observed as reduced pups per litter. Also, the expression levels for meiosis-related genes and genes related to glucose metabolic pathways (glycolysis, tricarboxylic acid cycle, and pentose phosphate pathway) were altered in BPGM-deficient mouse oocytes. We used a highly sensitive, live-cell sampling approach to carry out metabolite assays using induced nanoelectrospray-ionization mass spectrometry technology on 1 picolitre of aspirated cytoplasm from oocytes. BPGM gene disruption impaired glucose metabolism pathways, tyrosine metabolism, and amino acid biosynthesis. Together, our findings indicate that Bpgm participates in oocyte and embryo development, and we demonstrate the feasibility of studying metabolite composition and other phenotypic features of single oocytes.

ZNHIT3 Regulates Translation to Ensure Cell Lineage Differentiation in Mouse Preimplantation Development

Upon fertilization, the mouse zygotic genome is activated and maternal RNAs as well as proteins are degraded. Early developmental programs are built on proteins encoded by zygotic mouse genes that are needed to guide early cell fate commitment. The box C/D snoRNA ribonucleoprotein (snoRNP) complex is required for rRNA biogenesis, ribosome assembly and pre-mRNA splicing essential for protein translation. Zinc finger, HIT type 3 (encoded by Znhit3) is previously identified as a component in the assembly of the box C/D snoRNP complex. Using gene-edited mice, it identifies Znhit3 as an early embryonic gene whose ablation reduces protein translation and prevents mouse embryos development beyond the morula stage. The absence of ZNHIT3 leads to decreased snoRNA and rRNA abundance which causes defects of ribosomes and mRNA splicing. Microinjection of Znhit3 cRNA partially rescues the phenotype and confirms that ZNHIT3 is required for mRNA translation during preimplantation development.

Pluripotent cell states and fates in human embryo models

Pluripotency, the capacity to generate all cells of the body, is a defining property of a transient population of epiblast cells found in pre-, peri- and post-implantation mammalian embryos. As development progresses, the epiblast cells undergo dynamic transitions in pluripotency states, concurrent with the specification of extra-embryonic and embryonic lineages. Recently, stem cell-based models of pre- and post-implantation human embryonic development have been developed using stem cells that capture key properties of the epiblast at different developmental stages. Here, we review early primate development, comparing pluripotency states of the epiblast in vivo with cultured pluripotent cells representative of these states. We consider how the pluripotency status of the starting cells influences the development of human embryo models and, in turn, what we can learn about the human pluripotent epiblast. Finally, we discuss the limitations of these models and questions arising from the pioneering studies in this emerging field.

RN7SL1 overexpression promotes cell proliferation in cutaneous T-cell lymphoma via miR-34a-5p/MYCN axis

BACKGROUND

Cutaneous T-cell lymphoma (CTCL) is a type of lymphoma that presents in skin tissue without evidence of extracutaneous disease. Emerging evidence indicates that long noncoding RNA-RN7SL1 serves as crucial effectors in modulating progression of different malignancies, including breast cancer, liver cancer, and other neoplasms.

OBJECTIVE

To figure out the role of RN7SL1 in the pathogenesis of CTCL.

METHODS

We detected RN7SL1 expression of CTCL patients by quantitative real-time polymerase chain reaction and fluorescent in situ hybridization. CTCL cell lines were transfected with lentiviral-based RN7SL1 gene knockdown vectors. Whole transcriptome sequencing was conducted to investigate differentially expressed miRNA and mRNA in CTCL, and we used qRT-PCR, RNA immunoprecipitation, dual-luciferase assay, RNA pull down and Western Blotting to further detect the relation of miRNA and mRNA. Also, we have verified above results in mice and clinical samples.

RESULTS

LncRNA-RN7SL1 was overexpressed in CTCL compared with benign inflammatory dermatosis and was related to the TNMB stage of mycosis fungoides and Sézary syndrome (higher expression in IIB-IVB stage than IA-IIA stage). Additionally, the proliferation of CTCL cell lines HH and Hut78 was weakened, but apoptosis was facilitated by RN7SL1 downregulation, resulting in a reduced tumorigenic capacity in vivo. Subsequently, Whole transcriptome sequencing and target validation indicated that the RN7SL1/miR-34a-5p/MYCN axis may promoted malignant behavior in CTCL.

CONCLUSION

Our study suggested that RN7SL1 promoted malignant behavior by targeting miR-34a-5p/MYCN signaling. This finding might facilitate the discovery of novel biomarkers for CTCL diagnosis and treatment.

ERVcancer: a web resource designed for querying activation of human endogenous retroviruses across major cancer types

Human endogenous retroviruses (HERVs) comprise approximately 8% of the human genome, integrated into the dynamic regulatory network of cellular potency during early embryonic development. In recent studies, resurgent the transcriptional activity of HERVs has been frequently observed in many types of human cancers, suggesting their potential functions in the occurrence and progression of malignancy. However, a dedicated web resource for querying the relationship between the activation of HERVs and cancer development is lacking. Here, we construct a database to explore the sequence information, expression profiles, survival prognosis, and genetic interactions of HERVs in diverse cancer types. Our database currently contains RNA sequencing data of 580 HERVs across 16,246 samples, including that of 6478 tumoral and 634 normal tissues, 932 cancer cell lines, as well as 151 early embryonic and 8051 human adult tissues. The primary goal is to provide an easily accessible and user-friendly database for professionals in the fields of bioinformatics, pathology, pharmacology, and related areas, enabling them to efficiently screen the activity of HERVs of interest in normal and cancerous tissues and evaluate the clinical relevance. The ERVcancer database is available at http://kyuanlab.com/ervcancer/.

X-scPAE: An explainable deep learning model for embryonic lineage allocation prediction based on single-cell transcriptomics revealing key genes in embryonic cell development

In single-cell transcriptomics research, accurately predicting cell lineage allocation and identifying differences between lineages are crucial for understanding cell differentiation processes and reducing early pregnancy miscarriages in humans. This paper introduces an explainable PCA-based deep learning attention autoencoder model, X-scPAE (eXplained Single Cell PCA - Attention Auto Encoder), which is built on the Counterfactual Gradient Attribution (CGA) algorithm. The model is designed to predict lineage allocation in human and mouse single-cell transcriptomic data, while identifying and interpreting gene expression differences across lineages to extract key genes. It first reduces dimensionality using Principal Component Analysis (PCA) and ranks the importance of principal components. An autoencoder is then employed for feature extraction, integrating an attention mechanism to capture interactions between features. Finally, the Counterfactual Gradient Attribution algorithm calculates the importance of each feature. The model achieved an accuracy of 0.945 on the test set and 0.977 on the validation set, with other metrics such as F1-score, Precision, and Recall all reaching 0.94. It significantly outperformed both baseline algorithms (XGBoost, SVM, RF, and LR) and advanced approaches like F-Score-SVM, CV2-LR, scChrBin, and TripletCell. Notably, the explainability analysis uncovered key lineage predictor genes for both humans and mice and identified crucial genes distinguishing between developmental stages and lineages. A logistic regression model built using the extracted key genes still achieved an AUROC of 0.92, surpassing the performance of other feature extraction methods, including F-Score, CV2, PCA, random feature selection, and the interpretability method Shapley. Lastly, ablation studies demonstrated the effectiveness of each model component.

Transient chemical-mediated epigenetic modulation confers unrestricted lineage potential on human primed pluripotent stem cells

Human primed pluripotent stem cells are capable of generating all the embryonic lineages. However, their extraembryonic trophectoderm potentials are limited. It remains unclear how to expand their developmental potential to trophectoderm lineages. Here we show that transient treatment with a cocktail of small molecule epigenetic modulators imparts trophectoderm lineage potentials to human primed pluripotent stem cells while preserving their embryonic potential. These chemically treated cells can generate trophectoderm-like cells and downstream trophoblast stem cells, diverging into syncytiotrophoblast and extravillous trophoblast lineages. Transcriptomic and CUT&Tag analyses reveal that these induced cells share transcriptional profiles with in vivo trophectoderm and cytotrophoblast, and exhibit reduced H3K27me3 modification at gene loci specific to trophoblast lineages compared with primed pluripotent cells. Mechanistic exploration highlighted the critical roles of epigenetic modulators HDAC2, EZH1/2, and KDM5s in the activation of trophoblast lineage potential. Our findings demonstrate that transient epigenetic resetting activates unrestricted lineage potential in human primed pluripotent stem cells, and offer new mechanistic insights into human trophoblast lineage specification and in vitro models for studying placental development and related disorders.

Early Embryo Development: What Does Daddy Do?

Infertility represents a major global health challenge, with male infertility accounting for a significant proportion of cases, yet its underlying causes remain elusive in many instances. Traditionally, spermatozoa were viewed merely as DNA carriers, with little consideration given to their role beyond fertilization. Recent research, however, is challenging this view, revealing that spermatozoa are far more than passive delivery vehicles. They carry a complex array of molecules, particularly RNAs, which actively influence fertilization, early embryo development, and the transmission of paternal traits. These sperm-carried RNAs, including mRNAs, small RNAs, and noncoding RNAs, regulate gene expression in both spermatozoa and embryo, with profound implications for offspring development. Additionally, environmental factors, such as lifestyle choices and exposure to toxins, have been shown to affect sperm RNA composition, highlighting the dynamic interplay between genetics and the environment in shaping fertility. This emerging and evolving understanding of sperm function challenges traditional reproductive biology and offers new insights into male infertility, particularly in cases that remain unexplained by current diagnostic methods. Although the exact molecular mechanisms underlying these processes are still being investigated, this paradigm shift opens the door to innovative diagnostic tools and therapeutic strategies for treating male infertility. By uncovering the critical role of sperm RNAs, these findings not only enhance our understanding of reproductive biology but also hold the promise to improve assisted reproductive technologies and outcomes for infertile couples.

K-Volume Clustering Algorithms for scRNA-Seq Data Analysis

Clustering high-dimensional and structural data remains a key challenge in computational biology, especially for complex single-cell and multi-omics datasets. In this study, we present K-volume clustering, a novel algorithm that uses the total convex volume defined by points within a cluster as a biologically relevant and geometrically interpretable criterion. This method simultaneously optimizes both the hierarchical structure and the number of clusters at each level through nonlinear optimization. Validation on real datasets shows that K-volume clustering outperforms traditional methods across a range of biological applications. With its theoretical foundation and broad applicability, K-volume clustering holds great promise as a core tool for diverse data analysis tasks.

Heterogeneity-Preserving Discriminative Feature Selection for Disease-Specific Subtype Discovery

The identification of disease-specific subtypes can provide valuable insights into disease progression and potential individualized therapies, important aspects of precision medicine given the complex nature of disease heterogeneity. The advent of high-throughput technologies has enabled the generation and analysis of various molecular data types, such as single-cell RNA-seq, proteomic, and imaging datasets, on a large scale. While these datasets offer opportunities for subtype discovery, they also pose challenges in finding subtype signatures due to their high dimensionality. Feature selection, a key step in the machine learning pipeline, involves selecting signatures that reduce feature size for more efficient downstream computational analysis. Although many existing methods focus on selecting features that differentiate known diseases or cell states, they often struggle to identify features that both preserve heterogeneity and reveal subtypes. To address this, we utilized deep metric learning-based feature embedding to explore the statistical properties of features crucial for preserving heterogeneity. Our analysis indicated that features with a notable difference in interquartile range (IQR) between classes hold important subtype information. Guided by this insight, we developed a statistical method called PHet (Preserving Heterogeneity), which employs iterative subsampling and differential analysis of IQR combined with Fisher's method to identify a small set of features that preserve heterogeneity and enhance subtype clustering quality. Validation on public single-cell RNA-seq and microarray datasets demonstrated PHet's ability to maintain sample heterogeneity while distinguishing known disease/cell states, with a tendency to outperform previous differential expression and outlier-based methods. Furthermore, an analysis of a single-cell RNA-seq dataset from mouse tracheal epithelial cells identified two distinct basal cell subtypes differentiating towards a luminal secretory phenotype using PHet-based features, demonstrating promising results in a real-data application. These results highlight PHet's potential to enhance our understanding of disease mechanisms and cell differentiation, contributing significantly to the field of personalized medicine.

scMUG: deep clustering analysis of single-cell RNA-seq data on multiple gene functional modules

Single-cell RNA sequencing (scRNA-seq) has revolutionized our understanding of cellular heterogeneity by providing gene expression data at the single-cell level. Unlike bulk RNA-seq, scRNA-seq allows identification of different cell types within a given tissue, leading to a more nuanced comprehension of cell functions. However, the analysis of scRNA-seq data presents challenges due to its sparsity and high dimensionality. Since bioinformatics plays an important role in the analysis of big data and its utility for the welfare of living beings, it has been widely applied in analyzing scRNA-seq data. To address these challenges, we introduce the scMUG computational pipeline, which incorporates gene functional module information to enhance scRNA-seq clustering analysis. The pipeline includes data preprocessing, cell representation generation, cell-cell similarity matrix construction, and clustering analysis. The scMUG pipeline also introduces a novel similarity measure that combines local density and global distribution in the latent cell representation space. As far as we can tell, this is the first attempt to integrate gene functional associations into scRNA-seq clustering analysis. We curated nine human scRNA-seq datasets to evaluate our scMUG pipeline. With the help of gene functional information and the novel similarity measure, the clustering results from scMUG pipeline present deep insights into functional relationships between gene expression patterns and cellular heterogeneity. In addition, our scMUG pipeline also presents comparable or better clustering performances than other state-of-the-art methods. All source codes of scMUG have been deposited in a GitHub repository with instructions for reproducing all results (https://github.com/degiminnal/scMUG).

Genomic insights and metabolic pathways of an enriched bacterial community capable of degrading polyethylene

In the face of mounting global plastic pollution, especially concerning microplastics, biodegradation must be a sustainable solution. The key factor driving this technology is to explore efficient plastic-biodegraders from different habitats, among which activated sludge (AS) may be an important option since it holds diverse microorganisms occupying various ecological niches. Here we intend to enrich the plastic-degrading microorganisms from AS by using polyethylene (PE) plastic as the carbon and energy source. After a 28-day incubation, the weight loss of PE films reached 3% and the hydrophobicity decreased, indicating physical biodegradation. Moreover, Fourier-transform infrared spectroscopy (FTIR) results showed the formation of several new oxygen-containing functional groups on PE. Microbial analysis extracted 26 metagenome-assembled genomes (MAGs) from the enriched microbial communities. Among them MAG10, MAG21 and MAG26 displayed the increased abundance upon PE addition and harbored abundant genes related to carbohydrate transport and metabolism, suggesting their potential to degrade PE. Additionally, functional analysis revealed 14 plastic degradation-related genes, including oxidase, laccase, and lipase, indicating the significant potential in plastic degradation. Furthermore, a pathway for synergistic biodegradation of PE was proposed based on the potential PE degradation genes retrieved from MAGs. This work offers a promising and sustainable solution to plastic pollution by enriching the potential biodegraders from AS.

Transcriptomic analysis of Virescentia guangxiensis (Rhodophyta: Batrachospermales) revealed differential expression of genes in gametophyte and chantransia life phases

BACKGROUND

The genus Virescentia is a significant member of the Batrachospermaceae, exhibiting distinctive life history characteristics defined by alternating generations. This group of taxa has specific environmental requirements for growth. This paper investigates Virescentia, which primarily thrives in freshwater environments, such as streams and springs, characterized by low light, low temperatures, and high dissolved oxygen levels. Currently, no laboratory simulations of their growth conditions have been reported in culture studies. Additionally, previous studies indicate that comparisons of photosynthetic strength across different life-history stages of the same species have not been conducted, mainly due to the challenges of simultaneously collecting algal strains at both life-history stages.

RESULTS

During the gametophyte stage, the chloroplast and mitochondrial genomes were measured at 184,899 bp and 26,867 bp, respectively. In the chantransia stage, the lengths of these genomes were 184,887 bp and 27,014 bp, respectively. A comparison of organellar genome covariation and phylogenetic reconstruction revealed that the chloroplast and mitochondrial genomes across different life history stages were highly conserved, with genetic distances of 0 and nucleotide variants of only 9-15 bp. The mitochondrial genome of gametophyte SXU-YN24005 was found to lack two tRNA-Leu (tag) genes compared to that of the chantransia strain. Additionally, a comparative analysis of KEGG pathway transcriptome data from the two life history stages showed that 33 genes related to the ribosomal pathway and 53 genes associated with the photosynthesis pathway exhibited a significant decline in expression during the gametophyte stage compared to the chantransia stage.

CONCLUSION

In this study, two samples of the same species at different life-history stages were collected from the same location for the first time. The analysis revealed a high degree of conservation between their organelle genomes. Additionally, transcriptome sequencing results indicated substantial differences in gene expression patterns between the two life-history stages. This research will provide reliable data to support the future histological database of freshwater red algae and will establish a theoretical basis for conserving rare and endangered species.

Brems1 mutation induced tapetum deficiency leading to male sterility in Chinese cabbage (Brassica rapa L. ssp. pekinensis)

KEY MESSAGE

The mutation in Brems1 resulting in male sterility in Chinese cabbage were validated through two allelic mutations. Male sterile lines are ideal for hybrid seed production in Chinese cabbage. Herein, the complete male sterile mutants M5026 and M5073 were obtained through ethyl methanesulfonate (EMS) mutagenesis in the Chinese cabbage double haploid line 'FT'. Cytological observations revealed that M5026 exhibited an absence of the tapetum, an overabundance of microsporocytes, and abnormal exine formation in pollen. The male sterility phenotype of M5026 was controlled by a single recessive nuclear gene. Using mutmap sequencing and kompetitive allele-specific PCR (KASP) identification and gene cloning, two distinct SNPs in BraA10g029920.3.5C, encoding EMS1 (excess microsporocytes 1), were identified to be associated with the male sterility of M5026 and M5073. The gene was named as Brems1. M5026 and M5073 were determined to be allelic variants. Both BrEMS1 and Brems1 were subcellularly localized at the cell membrane. Brems1 exhibited the highest expression level in buds, while no expression was detected in roots. Transcriptomic analysis revealed that Brems1 mutations reduced the expression levels of genes associated with the tapetum, pollen tube, and LRR-RLK family. These results suggested that Brems1 played a critical role in pollen development and contributes to elucidating the molecular mechanisms underlying tapetum development and male sterility in Chinese cabbage.

Single-Cell RNA Sequencing in Unraveling Acquired Resistance to EGFR-TKIs in Non-Small Cell Lung Cancer: New Perspectives

Epidermal growth factor receptor tyrosine kinase inhibitors (EGFR-TKIs) have demonstrated remarkable efficacy in treating non-small cell lung cancer (NSCLC), but acquired resistance greatly reduces efficacy and poses a significant challenge to patients. While numerous studies have investigated the mechanisms underlying EGFR-TKI resistance, its complexity and diversity make the existing understanding still incomplete. Traditional approaches frequently struggle to adequately reveal the process of drug resistance development through mean value analysis at the overall cellular level. In recent years, the rapid development of single-cell RNA sequencing technology has introduced a transformative method for analyzing gene expression changes within tumor cells at a single-cell resolution. It not only deepens our understanding of the tumor microenvironment and cellular heterogeneity associated with EGFR-TKI resistance but also identifies potential biomarkers of resistance. In this review, we highlight the critical role of single-cell RNA sequencing in lung cancer research, with a particular focus on its application to exploring the mechanisms of EGFR-TKI-acquired resistance in NSCLC. We emphasize its potential for elucidating the complexity of drug resistance mechanism and its promise in informing more precise and personalized treatment strategies. Ultimately, this approach aims to advance NSCLC treatment toward a new era of precision medicine.

Ectopic expression of DNMT3L in human trophoblast stem cells restores features of the placental methylome

The placental DNA methylation landscape is unique, with widespread partially methylated domains (PMDs). The placental "methylome" is conserved across mammals, a shared feature of many cancers, and extensively studied for links with pregnancy complications. Human trophoblast stem cells (hTSCs) offer exciting potential for functional studies to better understand this epigenetic feature; however, whether the hTSC epigenome recapitulates primary trophoblast remains unclear. We find that hTSCs exhibit an atypical methylome compared with trophectoderm and 1st trimester cytotrophoblast. Regardless of cell origin, oxygen levels, or culture conditions, hTSCs show localized DNA methylation within transcribed gene bodies and a complete loss of PMDs. Unlike early human trophoblasts, hTSCs display a notable absence of DNMT3L expression, which is necessary for PMD establishment in mouse trophoblasts. Remarkably, we demonstrate that ectopic expression of DNMT3L in hTSCs restores placental PMDs, supporting a conserved role for DNMT3L in de novo methylation in trophoblast development in human embryogenesis.

Comparative proteomic landscapes elucidate human preimplantation development and failure

Understanding mammalian preimplantation development, particularly in humans, at the proteomic level remains limited. Here, we applied our comprehensive solution of ultrasensitive proteomic technology to measure the proteomic profiles of oocytes and early embryos and identified nearly 8,000 proteins in humans and over 6,300 proteins in mice. We observed distinct proteomic dynamics before and around zygotic genome activation (ZGA) between the two species. Integrative analysis with translatomic data revealed extensive divergence between translation activation and protein accumulation. Multi-omic analysis indicated that ZGA transcripts often contribute to protein accumulation in blastocysts. Using mouse embryos, we identified several transcriptional regulators critical for early development, thereby linking ZGA to the first lineage specification. Furthermore, single-embryo proteomics of poor-quality embryos from over 100 patient couples provided insights into preimplantation development failure. Our study may contribute to reshaping the framework of mammalian preimplantation development and opening avenues for addressing human infertility.

Advancements in single-cell RNA sequencing and spatial transcriptomics: transforming biomedical research

In recent years, significant advancements in biochemistry, materials science, engineering, and computer-aided testing have driven the development of high-throughput tools for profiling genetic information. Single-cell RNA sequencing (scRNA-seq) technologies have established themselves as key tools for dissecting genetic sequences at the level of single cells. These technologies reveal cellular diversity and allow for the exploration of cell states and transformations with exceptional resolution. Unlike bulk sequencing, which provides population-averaged data, scRNA-seq can detect cell subtypes or gene expression variations that would otherwise be overlooked. However, a key limitation of scRNA-seq is its inability to preserve spatial information about the RNA transcriptome, as the process requires tissue dissociation and cell isolation. Spatial transcriptomics is a pivotal advancement in medical biotechnology, facilitating the identification of molecules such as RNA in their original spatial context within tissue sections at the single-cell level. This capability offers a substantial advantage over traditional single-cell sequencing techniques. Spatial transcriptomics offers valuable insights into a wide range of biomedical fields, including neurology, embryology, cancer research, immunology, and histology. This review highlights single-cell sequencing approaches, recent technological developments, associated challenges, various techniques for expression data analysis, and their applications in disciplines such as cancer research, microbiology, neuroscience, reproductive biology, and immunology. It highlights the critical role of single-cell sequencing tools in characterizing the dynamic nature of individual cells.

LINE1 elements at distal junctions of rDNA repeats regulate nucleolar organization in human embryonic stem cells

The nucleolus is a major subnuclear compartment where ribosomal DNA (rDNA) is transcribed and ribosomes are assembled. In addition, recent studies have shown that the nucleolus is a dynamic organizer of chromatin architecture that modulates developmental gene expression. rDNA gene units are assembled into arrays located in the p-arms of five human acrocentric chromosomes. Distal junctions (DJs) are ∼400 kb sequences adjacent to rDNA arrays that are thought to anchor them at the nucleolus, although the underlying regulatory elements remain unclear. Here we show that DJs display a dynamic chromosome conformation profile in human embryonic stem cells (hESCs). We identified a primate-specific, full-length insertion of the retrotransposon long interspersed nuclear element 1 (LINE1) in a conserved position across all human DJs. This DJ-LINE1 locus interacts with specific regions of the DJ and is upregulated in naïve hESCs. CRISPR-based deletion and interference approaches revealed that DJ-LINE1 contributes to nucleolar positioning of the DJs. Moreover, we found that the expression of DJ-LINE1 is required for maintenance of the structure and transcriptional output of the nucleolus in hESCs. Silencing of DJ-LINE1 leads to loss of self-renewal, disruption of the landscape of chromatin accessibility, and derepression of earlier developmental programs in naïve hESCs. This work uncovers specific LINE1 elements with a fundamental role in nucleolar organization in hESCs and provides new insights into how the nucleolus functions as a key genome-organizing hub.

A pilot study of transcriptomic preimplantation genetic testing (PGT-T): towards a new step in embryo selection?

STUDY QUESTION

Is it possible to predict an euploid chromosomal constitution and identify a transcriptomic profile compatible with extended embryonic development from RNA sequencing (RNA-Seq) data?

SUMMARY ANSWER

It has been possible to obtain a karyotype comparable to preimplantation genetic testing for aneuploidy (PGT-A), in addition to a transcriptomic signature of embryos which might be suggestive of improved implantation capacity.

WHAT IS KNOWN ALREADY

Conventional assessment of embryo competence, based on morphology and morphokinetic, lacks knowledge of molecular aspects and faces controversy in predicting ploidy status. Understanding the embryonic transcriptome is crucial, as gene expression influences development and implantation. PGT has improved pregnancy rates, but problems persist when high-quality euploid embryos do not reach term. In fact, only around 50-60% implant, of which 10% result in miscarriage. Comprehensive approaches, including RNA-Seq, offer the potential to discover molecular markers of reproductive competence, and could theoretically be combined with extended-embryo culture platforms up to Day 14 that can be utilized as a proxy to study embryo development at post-implantation stages.

STUDY DESIGN, SIZE, DURATION

This prospective pilot cohort study was conducted from March 2023 to August 2023. A total of 30 vitrified human blastocysts with previous PGT-A diagnosis on Day 5 (D5) or Day 6 (D6) of development were analysed: n = 15 euploid and n = 15 aneuploid. Finally, 21 embryo samples were included in the study; the rest (n = 9) were excluded due to poor quality pre-sequencing data (n = 7) or highly discordant data (n = 2).

PARTICIPANTS/MATERIALS, SETTING, METHODS

Following warming and re-expansion, embryos underwent a second trophectoderm (TE) biopsy. The embryos were then cultured until day 11 to assess their development. Biopsy analysis by RNA-Seq, studied the differential expressed genes (DEG) to compare embryos which did not or did attach to the plate: unattached embryos (n = 12) versus attached embryos (n = 9). Thus, we also obtained a specific transcriptomic signature of embryos with a "theoretical" capacity for sustained implantation, based on plate attachment on day 11.

MAIN RESULTS AND THE ROLE OF CHANCE

The digital karyotype obtained by RNA-Seq showed good concordance with the earlier PGT-A data, with a sensitivity of 0.81, a specificity of 0.83, a Cohen's Kappa of 0.66, and an area under the ROC of 0.9. At the gene level, 76 statistically significant DEGs were found in the comparison unattached versus attached embryos (Padj < 0.05; FC > 1). To address the functional implications of these differences, significantly deregulated pathways according to GO and KEGG categories were identified. The mural trophectoderm (TE) of the unattached blastocysts showed 63 significantly deregulated terms, displaying upregulation in autophagy, apoptosis, protein kinase and ubiquitin-like protein ligase activity, and downregulation of ribosome, spliceosome, kinetochore, segregation, and chromosome condensation processes. The overall transcriptomic signature specific to embryos still attached to the plate on day 11 (with a theoretically higher implantation capacity) consists of 501 genes, including: EMP2, AURKB, FOLR1, NOTCH3, LRP2, FZD5, MDH1, APOD, GPX8, COLEC12, HSPA1A, CMTM7, BEX3, which are related to implantation and embryonic development (raw P-value < 0.05; shrunk LFC > 1.1). These findings indicate that it might be possible to identify euploid embryos with a greater capacity for implantation and development, after excluding those embryos that present chromosomal alterations.

LIMITATIONS, REASONS FOR CAUTION

This study included a small sample size, remarkable variability between samples, and low success rate of RNA amplification. Also, structural chromosomal abnormalities were not included, and it was not possible to diagnose mosaic embryos. TE biopsy does not assure the chromosomal status of the whole embryo. The maximum day for in vitro development was Day 11, and attachment to the plate on this day does not provide a clear indication of implantation capacity and viability, which was not tested in this study.

WIDER IMPLICATIONS OF THE FINDINGS

The short-term goals following on from this pilot study is to expand the sample size with embryos of more complex abnormalities, and to perform a prospective in vitro preclinical validation. In a more distant future and with optimal results, this technique could have clinical application, thus increasing clinical outcomes by assessing both chromosomal content and transcriptomic profiling.

STUDY FUNDING/COMPETING INTEREST(S)

The Institut Valencià de Competitivitat Empresarial (IVACE) (IMIDCA/2022/39) and Generalitat Valenciana (CIACIF/2021/11) supported the present study. A.C. is an employee of JUNO Genetics. He has received honoraria for an IBSA lecture and a Merck lecture. He is also a minor shareholder of IVIRMA Global. The other authors have no conflicts of interest to declare.

TRIAL REGISTRATION NUMBER

N/A.

scSFCL:Deep clustering of scRNA-seq data with subspace feature confidence learning

The rapid development of single-cell RNA sequencing(scRNA-seq) technology has spawned a variety of single-cell clustering methods. These methods combine statistics and bioinformatics to reveal differences in gene expression between cells and the diversity of cell types. Deep exploration of single-cell data is more challenging due to the high dimensionality, sparsity and noise of scRNA-seq data. Discriminative attribute information is often difficult to be fully utilised, while traditional clustering methods may not accurately capture the diversity of cell types. Therefore, a deep clustering method is proposed for scRNA-seq data based on subspace feature confidence learning called scSFCL. By dividing the subspace based on kernel density, discriminative feature subsets are filtered. The feature confidence of the subset is learned by combining the graph convolutional network (GCN) with weighting. Also, scSFCL facilitates the complementary fusion of generic structural and idiosyncratic information through a mutually supervised clustering that integrates GCN and a denoising variational autoencoder based on zero-inflated negative binomials (DVAE-ZINB). By validation on multiple scRNA-seq datasets, it is shown that the clustering performance of scSFCL is significantly improved compared with traditional methods, providing an effective solution for deep clustering of scRNA-seq data.

Mechanisms of immune responses in Acanthopagrus latus to Streptococcus agalactiae infection revealed by transcriptomic analysis

Acanthopagrus latus (yellowfin seabream) is an economically important fish in the southeast coastal sea of China. Its slower growth rate makes it more prone to diseases in the cultivation period, leading to substantial economic losses. Epidemiological investigations have indicated that Streptococcus agalactiae is one of the most common Gram-positive pathogens, which have garnered increasing attention due to its high contagion and lethality rates in A. latus. In this work, an infection model of yellowfin seabream was established with an intraperitoneal injection of S. agalactiae. Clinical sign observations and various analyses, including histological examination, serum biochemical index assessment, immune-related enzyme level measurement, and transcriptome analysis of tissues (liver and intestine) with obvious clinical signs, were conducted for revealing the effects of S. agalactiae infection and immune response mechanisms in yellowfin seabream. The results indicate that evident clinical signs and multi-tissue damages with the notable changes in indices and significant increase in immune-related enzyme levels in the serum occurred in infected fish. RNA sequencing analysis identified 1130 differentially expressed genes (DEGs) in the liver and 1218 DEGs in the intestine, which were involved in multiple immune- and metabolism-related pathways via KEGG enrichment analysis. The transcriptomic results were further corroborated by quantitative real-time RT-PCR (qRT-PCR) tests of some specific immune-related genes. These findings provide new insights into the molecular immune mechanisms in yellowfin seabream following S. agalactiae infection and offer valuable reference data for disease prevention and molecular breeding (i.e., selective breeding through developing molecular markers of key genes).

Predicting ART outcomes: The role of ovarian RAS and VEGF in follicular fluid of dominant follicles

As tissue and intracellular RAS have been reported in different organs and systems. there is local RAS in the ovary, called the ovarian renin-angiotensin system (OVRAS). In this study, we investigated the correlation between RAS (total renin, AngII, Ang1-7), vascular endothelial growth factor (VEGF) and E2 in dominant follicular fluid and ovarian reserve capacity and patient age. Moreover, we analyzed its predictive value for assisted reproductive technology (ART) related outcomes. We observed that the concentrations of VEGF in the follicular fluid of dominant follicles in the ≥ 38 year old group were markedly higher than those in the < 30 year old group (P < 0.05). Total renin and AngII levels were positively correlated with normal fertilization rate (P < 0.05). Ang1-7 levels were positively correlated with the number of mature oocytes, oocyte maturation rate and number of 2PN fertilized cells (P < 0.05). Expressions of VEGF were negatively correlated with number of 2PN fertilized cells, number of D3 embryos for blastocyst culture, number of blastocysts formed, number of available embryos and number of high-quality embryos (P < 0.05). Thus, the expressions of OVRAS (total renin, AngII, Ang1-7 and VEGF) in dominant follicular fluid are correlated with ART outcomes.

WDR36 Regulates Trophectoderm Differentiation During Human Preimplantation Embryonic Development Through Glycolytic Metabolism

Mammalian pre-implantation development is a complex process involving sophisticated regulatory dynamics. WD repeat domain 36 (WDR36) is known to play a critical role in mouse early embryonic development, but its regulatory function in human embryogenesis is still elusive due to limited access to human embryos. The human pluripotent stem cell-derived blastocyst-like structure, termed a blastoid, offers an alternative means to study human development in a dish. In this study, after verifying that WDR36 inhibition disrupted polarization in mouse early embryos, it is further demonstrated that WDR36 interference can block human blastoid formation, dominantly hindering the trophectoderm lineage commitment. Both transcriptomics and targeted metabolomics analyses revealed that WDR36 interference downregulated glucose metabolism. WDR36 can interact with glycolytic metabolic protein lactate dehydrogenase A (LDHA), thereby positively regulating glycolysis during the late stage of human blastoid formation. Taken together, the study has established a mechanistic connection between WDR36, glucose metabolism, and cell fate determination during early embryonic lineage commitment, which may provide potential insights into novel therapeutic targets for early adverse pregnancy interventions.

Chromosome-Level Genome Assembly and Comparative Genomic Analysis of Planiliza haematocheilus: Insights into Environmental Adaptation and Hypoxia Tolerance Mechanisms

Planiliza haematocheilus, a teleostan species noted for its ecological adaptability and economic significance, thrives in both freshwater and marine environments. This study presents a novel chromosome-level genome assembly through Hi-C, PacBio CCS, and Illumina sequencing methods. The assembled genome has a final size of 651.58 Mb, with 24 chromosomes anchoring 91.94% of contigs. Contig N50 and scaffold N50 are respectively measured at 25.52 Mb and 28.59 Mb. Of the 22,476 protein-coding genes identified in the genome, 21,834 have functional annotations. BUSCO (Benchmarking Universal Single-Copy Orthologs) genome and gene annotation assessments yielded scores of 96% and 96.6%, respectively. The genome of P. haematocheilus revealed 228 expanded and 1433 contracted gene families. Comparative genomic analyses highlight adaptations and hypoxia tolerance, linked to protein synthesis, immune response, and metabolic regulation. The high-quality genome assembly supports advanced studies on gene expression patterns under different environmental stressors, contributing to genetic enhancement efforts for this economically important aquaculture species.

Deciphering transcription activity of mammalian early embryos unveils on/off of zygotic genome activation by protein translation/degradation

Quantification of transcription activities in mammalian preimplantation embryos is challenging due to a huge amount of maternally stored transcripts and paucity of research materials. Here, we investigate genome-wide transcription activities of mouse and human preimplantation embryos by quantifying elongating RNA polymerase II. Two transcriptional waves are identified in early mouse embryos, with summits at the 2-cell and 8-cell stages. Gene collections with different expression patterns are obtained, with genes mainly transcribed at the mouse early/late 2-cell stage designated as zygotic genome activation-early/late 2-cell (ZGA-E2C/L2C). ZGA-E2C genes are short and have low promoter CpG density. Protein translation/degradation not only regulates transcription activity through stepwise orchestration of histone modifications, transcriptional initiation, and elongation in early mouse embryos but also controls on/off switching of ZGA-E2C/L2C genes in maternal aged mouse embryos. Genes mainly transcribed at the mouse 2-cell stage can also be transcribed as early as the human 2-cell stage.

LINE1 and PRC2 control nucleolar organization and repression of the 8C state in human ESCs

The mechanisms that ensure developmental progression in the early human embryo remain largely unknown. Here, we show that the family of long interspersed nuclear element 1 (LINE1) transposons prevents the reversion of naive human embryonic stem cells (hESCs) to 8-cell-like cells (8CLCs). LINE1 RNA contributes to maintenance of H3K27me3 levels, particularly at chromosome 19 (Chr19). Chr19 is enriched for key 8C regulators, H3K27me3, and genes derepressed upon LINE1 knockdown or PRC2 inhibition. Moreover, Chr19 is strongly associated with the nucleolus in hESCs but less in 8CLCs. Direct inhibition of PRC2 activity induces the 8C program and leads to a relocalization of Chr19 away from the nucleolus. LINE1 KD or PRC2 inhibition induces nucleolar stress, and disruption of nucleolar architecture is sufficient to de-repress the 8C program. These results indicate that LINE1 RNA and PRC2 maintain H3K27me3-mediated gene repression and 3D nuclear organization to prevent developmental reversion of hESCs.

Herpesviruses mimic zygotic genome activation to promote viral replication

Zygotic genome activation (ZGA) is crucial for maternal to zygotic transition at the 2-8-cell stage in order to overcome silencing of genes and enable transcription from the zygotic genome. In humans, ZGA is induced by DUX4, a pioneer factor that drives expression of downstream germline-specific genes and retroelements. Here we show that herpesviruses from all subfamilies, papillomaviruses and Merkel cell polyomavirus actively induce DUX4 expression to promote viral transcription and replication. Analysis of single-cell sequencing data sets from patients shows that viral DUX4 activation is of relevance in vivo. Herpes-simplex virus 1 (HSV-1) immediate early proteins directly induce expression of DUX4 and its target genes, which mimics zygotic genome activation. Upon HSV-1 infection, DUX4 directly binds to the viral genome and promotes viral transcription. DUX4 is functionally required for infection, since genetic depletion by CRISPR/Cas9 as well as degradation of DUX4 by nanobody constructs abrogates HSV-1 replication. Our results show that DNA viruses including herpesviruses mimic an embryonic-like transcriptional program that prevents epigenetic silencing of the viral genome and facilitates herpesviral gene expression.

Circadian rhythm disruptions exacerbate inner ear damage in a murine endolymphatic hydrops model

Meniere's disease (MD) is an inner ear disease characterized by endolymphatic hydrops (EH). Maintaining a regular daily routine is crucial for MD patients. However, the relationship between circadian rhythms and MD remains unclear. Therefore, we investigated the effect of circadian rhythm on endolymphatic hydrops and its underlying mechanisms. Mice with endolymphatic hydrops were subjected to chronic jet lag (CJL) conditions to simulate the MD patients under circadian rhythm disruptions. We assessed whether this disruption would exacerbate inner ear damage with endolymphatic hydrops. RNA-seq of the inner ear and bioinformatic analysis were performed. Then, the expression of PER2, AQP2, AQP4, AQP5, and BDNF were assessed, and the morphological changes were evaluated in the inner ear. Our findings showed circadian rhythm disruption affected the cochlear internal clock genes in the inner ear, particularly in mice with EH. EH mice under CJL conditions exhibited exacerbated hearing impairment and an increased severity of EH. GO enrichment analysis revealed that the regulation of fluid homeostasis and neurotransmitter release at synapses were significantly enriched. Disruption of circadian rhythms disturbed the expression pattern of PER2, reduced BDNF levels, and affected the expression of aquaporins in the cochlea. Moreover, the disruption of circadian rhythm compromised inner hair cell synapses and auditory nerve fibers. This study indicated that disruption of circadian rhythms may exacerbate inner ear damage in endolymphatic hydrops mice by affecting the aquaporins and compromising synapses and auditory nerves in the inner ear. BDNF and PER2 may play a central role in these pathophysiological processes.

Krüppel-like Factors Play Essential Roles in Regulating Pluripotency and the Formation of Neural Crest Stem Cells

The evolutionary transition from simple chordate body plans to complex vertebrate body plans was driven by the acquisition of the neural crest, a stem cell population that retains broad, multi-germ layer developmental potential long after most embryonic cells have become lineage restricted. We have previously shown that neural crest cells share significant gene regulatory architecture with pluripotent blastula stem cells. Here we examine the roles that Krüppel-like Family (Klf) transcription factors play in these stem cell populations. Although Klf4 has established roles in regulating pluripotency in mammalian stem cells cultures, we find that in Xenopus it is klf2 that is highly expressed in pluripotent blastula stem cells. klf2 expression is down-regulated as cells transition to a neural crest state while a related klf factor, klf17, is significantly up regulated in response to neural crest induction. We used gain and loss of function studies to compare the activities of these closely related factors and found that they have both shared and distinct activities. Inhibition of either klf2 or klf17 activity led to significantly expanded expression of pluripotency, neural plate border and neural crest factors in neurula stage embryos, leading us to hypothesize that klf factors regulate the exit from pluripotency and proper establishment of the boundary of the neural crest domain. To gain further insights into the role of klf factors in the evolution of the neural crest, we examined their expression in the jawless vertebrate, Petromyzon marinus ( sea lamprey). We find that lamprey have a klf2/4 and a klf17 gene, but that only klf17 is expressed in blastula and neural crest stem cells. Moreover, ectopic expression of lamprey klf17 in Xenopus embryos phenocopies Xenopus klf17 activity. These data suggest that klf17, rather than klf4, may have been the ancestral klf factor that functioned in these GRNs in stem vertebrates.