Cell Biology

ScRNA-seq and scATAC-seq reveal that sertoli cell mediate spermatogenesis disorders through stage-specific communications in non-obstructive azoospermia

Shimin Wang author has email address
Hongxian Wang
Bicheng Jin
Hongli Yan
Qingliang Zheng author has email address
Dong Zhao author has email address

Prenatal Diagnosis Center, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
Department of Gynaecology and Obstetrics, Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
Department of Urology and Andrology, School of Medicine, Renji Hospital, Shanghai Jiao Tong University, Shanghai, China
Department of Surgical Subject, Guizhou Electric Staff Hospital, Guiyang, China
Reproductive medicine center, the Navy Medical University, Shanghai, China

https://doi.org/10.7554/eLife.97958.2

Open access
Copyright information

Figures and data

Patient characteristics in this study.

Patient characteristics in this study.

Overview of major cell types and cellular attributes of testes of OA and NOA patients.
(A) Representative images of HE staining of testicular tissues of OA and NOA patients. (B) Schematic of the experimental design for scRNA-seq and scATAC-seq. (C) UMAP analysis of human testicular cells in scRNA-seq results. (D) UMAP analysis of human testicular cells in scATAC-seq results. (E) Heatmap of expression of markers for the 12 cell types. (F) UMAP analysis of testicular cell population.

Identification of germ cell subtypes.
(A) UMAP analysis of 12 germ cell subsets in scRNA-seq results. (B) Pseudotime analysis of 12 germ cell subpopulations. (C) Gene expression patterns of marker genes on UMAP plots. (D) State of germ cell subsets using pseudotime analysis. (E) Immunofluorescence double staining of markers of newly identified spermatocyte subpopulations with the classical marker DDX4. (F) Accessibility peak plots of markers for newly identified germ cell subpopulations.

Analysis of germ cells at different stages.
(A) Germ cell subsets at different stages of the cell cycle. (B) Heatmap of cell cycle in germ cells. (C) Transcriptional dynamics of driver genes of germ cell subtypes. (D) The main stage of spermatogenesis. (E) Beam analysis of differentially expressed genes at different stages of SSC.

Identification of Sertoli cell subtypes and epigenetic analysis.
(A) UMAP analysis showed 8 Sertoli cell subsets in scRNA-seq results. (B) Heatmap of markers of differentially expressed genes in eight Sertoli cell subsets. (C) Gene expression patterns of Sertoli cell subtype marker genes on violin plots. (D) Accessibility peak plots of markers for newly identified Sertoli cell subpopulations.

The development of Sertoli cells.
(A) State of Sertoli cells using pseudotime analysis. (B) Distribution of Sertoli cell subtypes in different states. (C) Potential temporal differentiation of SC subgroups using RNA velocity. (D) Sertoli cells division diagram and representative markers. (E) Immunofluorescence of Sertoli cell subtype markers in testicular tissues from OA patients. The scale bar represents 20 μm.

Correlation analysis of germ and Sertoli cell expression in different groups.
(A) Cell proportion of germ cell subtypes in different groups. (B) Cell proportion of Sertoli cell subtypes in different groups. (B) Pseudotime analysis of germ cell subtypes in different groups. (D) Pseudotime analysis of Sertoli cell subtypes in different groups. (E) Distribution map of germ cell subtypes in different samples. (F) Distribution map of Sertoli cell subtypes in different samples. (G) The interaction between germ cells and other cells. (H) Spearman correlation between germ and Sertoli cells.

Co-localization of subpopulations of Sertoli cells and germ cells.
(A) Representative images of HE staining of testicular tissues of OA and NOA patients. (B) Immunofluorescence analysis of germ cell and Sertoli cell subtype markers in testicular tissues. Blue DAPI indicates nuclei. The colors of the markers and cells indicate the fluorescent color of the corresponding antibody. The scale bar represents 20 μm.

Schematic diagram of spermatogenesis and stage specificity of sertoli cell subtypes.

scATAC-seq analysis of the entire cell subpopulation.
(A) UMAP analysis of 10 cell subsets in scATAC-seq results. (B) Accessibility peak plots of markers for cell subpopulations.

Integrating scRNA-seq and scATAC-seq analysis.
(A-C) Integrating all cell types (A), germ cell types (B), Sertoli cell types (C) from scRNA-seq and scATAC-seq by UMAP plot.

Analysis of germ cell markers in spermatogenesis.
(A) Heatmap showed marker gene expression of germ cell subtypes. (B) Gene expression patterns of germ cell markers on violin plots. (C) Distribution diagram of germ cell subsets using pseudotime analysis.

scATAC-Seq Clustering.
(A) Heatmap of germ cell markers in scATAC-seq results. (B) Heatmap of motifs in scATAC-seq results.

Germ cell function analysis and epigenetic analysis.
(A-C) Analysis of beam cluster transcription factors and its GO term. (D) Heatmap of transcription factors in germ cells. (E) GO analysis of different states of Sertoli cells. (F) Qusage analysis of different states of Sertoli cells.

GO analysis of germ cells.

GO analysis of Sertoli cells.

Correlation analysis of germ and Sertoli cell expression.
(A) The interaction between germ cells and Sertoli cells through Notch signaling pathway. (B) Accessibility peak plots of NOTCH1/2/3.

Identification of Leydig cell types in the testis.
(A) Clustering on the Leydig cells revealed 12 different cell types. (B) Heatmap showed Leydig cell subtype specific maker genes. (C) The distribution of Leydig cells in different samples. (D) Proportion of Leydig cell subtypes in each sample.

Identification of PMCs types in the testis.
(A) Clustering on the PMCs revealed 8 different cell types. (B) Heatmap showed PMCs subtype specific maker genes. (C) The distribution of PMCs in different samples. (D) Proportion of PMCs subtypes in each sample.

Identification of macrophage types in the testis.
(A) Clustering on the macrophage revealed 6 different cell types. (B) Heatmap showed macrophage subtype specific maker genes. (C) The distribution of macrophage in different samples. (D) Proportion of macrophage subtypes in each sample.

Sign up for email alerts