Chromatin modifications are fundamental epigenetic marks that determine genome functions, but it remains challenging to profile those of repetitive elements and complex genomic regions. Here, we develop scNanoSeq-CUT&Tag, a streamlined method, by adapting modified cleavage under targets and tagmentation (CUT&Tag) to the nanopore sequencing platform for genome-wide chromatin modification profiling within individual cells. We show that scNanoSeq-CUT&Tag can accurately profile histone marks and transcription factor occupancy patterns at single-cell resolution as well as distinguish different cell types. scNanoSeq-CUT&Tag efficiently maps the allele-specific chromatin modifications and allows analysis of their neighboring region co-occupancy patterns within individual cells. Moreover, scNanoSeq-CUT&Tag can accurately detect chromatin modifications for individual copies of repetitive elements in both human and mouse genomes. Overall, we prove that scNanoSeq-CUT&Tag is a valuable single-cell tool for efficiently profiling histone marks and transcription factor occupancies, especially for previously poorly studied complex genomic regions and blacklist genomic regions. This work presents scNanoSeq-CUT&Tag, using long-read sequencing to profile histone modifications and DNA-binding proteins at the single-cell level.

Mitochondrial DNA (mtDNA) mutations are often associated with incurable diseases and lead to detectable pathogenic variants in 1 out of 200 babies. Uncoupling of the inheritance of mtDNA and the nuclear genome by spindle transfer (ST) can potentially prevent the transmission of mtDNA mutations from mother to offspring. However, no well-established studies have critically assessed the safety of this technique. Here, using single-cell triple omics sequencing method, we systematically analyzed the genome (copy number variation), DNA methylome, and transcriptome of ST and control blastocysts. The results showed that, compared to that in control embryos, the percentage of aneuploid cells in ST embryos did not significantly change. The epiblast, primitive endoderm, and trophectoderm (TE) of ST blastocysts presented RNA expression profiles that were comparable to those of control blastocysts. However, the DNA demethylation process in TE cells of ST blastocysts was slightly slower than that in the control blastocysts. Collectively, our results suggest that ST seems generally safe for embryonic development, with a relatively minor delay in the DNA demethylation process at the blastocyst stage.

Although chromosomal mosaic embryos detected by trophectoderm (TE) biopsy offer healthy embryos available for transfer, high-resolution postnatal karyotyping and chromosome testing of the transferred embryos are insufficient. Here, we applied single-cell multi-omics sequencing for seven infants with blastula chromosomal mosaicism detected by TE biopsy. The chromosome ploidy was examined by single-cell genome analysis, with the cellular identity being identified by single-cell transcriptome analysis. A total of 1616 peripheral leukocytes from seven infants with embryonic chromosomal mosaicism and three control ones with euploid TE biopsy were analyzed. A small number of blood cells showed copy number alterations (CNAs) on seemingly random locations at a frequency of 0%-2.5% per infant. However, none of the cells showed CNAs that were the same as those of the corresponding TE biopsies. The blastula chromosomal mosaicism may be fully self-corrected, probably through the selective loss of the aneuploid cells during development, and the transferred embryos can be born as euploid infants without mosaic CNAs corresponding to the TE biopsies. The results provide a new reference for the evaluations of transferring chromosomal mosaic embryos in certain situations.

OBJECTIVE:Human gastric epithelial stem/progenitor cells are important for stomach homeostasis; however, the in vitro culture system of these cells remains immature. Although three-dimensional (3D) organoid culture has fundamentally changed the in vitro study of gastrointestinal tract, its use is limited by inaccessible luminal compartment, and difficulties of imaging and manipulation. To overcome these limitations of 3D organoid culture system, we established adult human gastric epithelial progenitor-like (hGEPL) cell lines using a novel robust monolayer cell culture system.MATERIALS AND METHODS:We established an in vitro gel-based monolayer culture system for normal human adult gastric epithelium, and compared it with traditional two-dimensional (2D) and 3D organoid culture systems using transcriptomics, immunofluorescence and cell viability experiments. At the same time, we used single-cell transcriptomics to compare the differences of the hGEPL cells in conditioned medium (Cond.) and in chemically defined medium (Chem.), the two most common media for organoid culture, in maintaining the stemness and proliferative activity of hGEPL cells. Finally, we explored the role of key niche factors in inducing hGEPL cell differentiation.RESULTS:The hGEPL cells were similar to the in vivo gastric epithelial stem/progenitor cells, which could stably proliferate in culture for a long time. Based on the established culture system, we explored signalling pathways that were important for the homeostasis of hGEPL cells. We found that after blocking the WNT signalling pathway or activating the BMP signalling pathway, hGEPL cells could differentiate into mucous surface cells.CONCLUSION:Our culture system of hGEPL cells from adults is robust and easy to operate, and has the transformative potential of personalized and precision medicine, laying a solid foundation for studying the self-renewal and differentiation potentials of gastric epithelial stem/progenitor cells as well as modelling of related gastric diseases.

Incorporating poly(lactic-co-glycolic) acid (PLGA) microparticles into human mesenchymal stem cells (hMSC) aggregates has shown promising application prospects. However, the acidic degradation products and burst release of PLGA microparticles still need to be ameliorated. In this study, the PLGA/chitosan-heparin (P/C-h) composite microparticles were successfully fabricated by integrating the double emulsion and microfluidic technology through the precise manipulation of the emulsion composition and flow rate of the two-phase in a flow-focusing chip. The P/C-h microparticles were highly monodispersed with a diameter of 23.45 ± 0.25 μm and shell-core structure of the PLGA encapsulated C-h complex, which were suitable for the fabrication of hMSC aggregates. When the mass ratio of PLGA to the C-h complex was optimized to 2 : 1, the pH of the leach liquor of P/C-h microparticles remained neutral. Compared with those of PLGA microparticles, the cytotoxicity and the initial burst release (loaded FGF-2 and VEGF) were both significantly reduced in P/C-h microparticles. Furthermore, the survival, stemness, as well as secretion and migration abilities of cells in hMSC aggregates incorporating P/C-h microparticles were also enhanced. In summary, the P/C-h composite microparticles prepared by the droplet microfluidic technique support the optimal biological and functional profile of the hMSC aggregates, which may facilitate the clinical applications of MSC-based therapy.