Identification of Differentially Expressed Genes in Human Testis Biopsies with Defective Spermatogenesis
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ABSTRACT:
PROVIDER: PRJNA933130 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR23381326.fastq.gz | Fastqsanger.gz | |||
| SRR23381327.fastq.gz | Fastqsanger.gz | |||
| SRR23381328.fastq.gz | Fastqsanger.gz | |||
| SRR23381329.fastq.gz | Fastqsanger.gz | |||
| SRR23381330.fastq.gz | Fastqsanger.gz |
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Project description:The study was designed to identify differences in the expressed transcriptome of the two pathological human testis sample groups compared to normal spermatogenesis samples, with the objective of discovering genes related to the pathological condition. Transcriptional differences in human testis biopsies collected from men with normal spermatogenesis (NSP, n=3; intact germ cells, clinical score - 10), spermatid arrest (SDA, n=2; contains somatic cells and germ cells up to round spermatids, clinical score – 4-5) and Sertoli cell-only (SCO, n=2; complete absence of germ cells, clinical score - 0) phenotypes were assessed by RNA sequencing. A total of over 49 million reads were generated in NSP samples, over 24 million reads in SDA samples, and over 13 million reads in SCO samples. Differentially expressed genes (DEG) were identified based on a mean minimum count => 5, FDR <= 0.05 and log2FC fold change of >0.585 or <-0.585. Genes differentially expressed in pathological groups SDA and SCO compared to NSP, and genes differentially expressed in between the two pathological groups SDA and SCO were filtered. The study discovered a number of significantly differentially expressed genes (DEG) between groups as follows: NSP vs SDA n=1,873; SDA vs SCO n= 4,017; and NSP vs SCO n=10,253. A number of genes (n=10) were selected for further analysis by qRT-PCR and the detection of the protein (n=2) localization in testis by immunohistochemistry.
2024-12-05 | GSE224929 | GEO
Project description:PurposeSperm morphology and motility are major contributors to male-factor infertility, with many genes predicted to be involved. This study aimed to elucidate differentially expressed transcripts in human testis tissues of normal and abnormal spermatogenesis that could reveal new genes that may regulate sperm morphology and function.MethodsHuman testis biopsies were collected from men with well-characterized phenotypes of normal spermatogenesis, spermatid arrest, and Sertoli cell-only phenotype, and transcriptional differences were quantified by RNA-sequencing (RNA-Seq). Differentially expressed genes (DEGs) were filtered based on predominant expression in spermatids and gene functional annotations relevant to sperm morphology and motility. Selected 10 DEGs were validated by qRT-PCR and the localization of two proteins was determined in testis biopsies.ResultsThe analysis revealed 6 genes (SPATA31E1, TEKT3, SLC9C1, PDE4A, CFAP47, and TNC) that are excellent candidates for novel genes enriched in developing human sperm. The immunohistochemical localization of two proteins, ORAI1 and SPATA31E1, in testis biopsies, verified that both are expressed in developing human germ cells, with SPATA31E1 enriched in late spermatocytes and spermatids.ConclusionThis study identified human germ cell-enriched genes that could play functional roles in spermiogenesis and could thus be important in the development of morphologically normal, motile sperm.
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Project description:Conditional inactivation of DIS3 in spermatocytes impairs meiotic progression and causes defective spermatogenesis in mice. scRNA-seq analysis indicates that DIS3 mutation significantly impairs spermatocytes meiotic progression and dysregulates transcriptome in spermatocytes. We show that DIS3 ribonuclease plays critical roles in male meiotic progression and spermatogenesis in mice.
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Project description:Our experimental design includes samples at different time points during the first wave of spermatogenesis. Each time point corresponds to specific cell content in the testis. First time point is post natal day (PND) 7, when only somatic cells and spermatogonia are present in the testis. Thereafter additional cell types are present in selected samples in chronological order: PND 14 contains early spermatocytes, PND 17 late spermatocytes, PND 21 round spermatids and finally PND 28 elongating spermatids. Our results highlight differentially expressed genes and gene isoforms, which are important for correct sperm development and male fertility. In addition, functional analysis suggests a highly controlled gene expression pattern during the first wave of spermatogenesis. Transcriptome sequencing of the mouse testes at PND 7, 14, 17, 21 and 28 for analysis of differences in gene expression pattern during the first wave of spermatogenesis. In total 10 samples were analysed, replicates for each time point.
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Project description:Our experimental design includes samples at different time points during the first wave of spermatogenesis. Each time point corresponds to specific cell content in the testis. First time point is post natal day (PND) 7, when only somatic cells and spermatogonia are present in the testis. Thereafter additional cell types are present in selected samples in chronological order: PND 14 contains early spermatocytes, PND 17 late spermatocytes, PND 21 round spermatids and finally PND 28 elongating spermatids. Our results highlight differentially expressed genes and gene isoforms, which are important for correct sperm development and male fertility. In addition, functional analysis suggests a highly controlled gene expression pattern during the first wave of spermatogenesis.
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Project description:Continuous sperm production is not necessary for the survival of the organism, but is essential to maintain a species. The process of spermatogenesis is comprised of three phases: mitotic proliferation, meiosis, and spermiogenesis. To illuminate germline intrinsic and extrinsic programs, we performed single-cell RNA sequencing on ~35K cells from the adult mouse testis. This analysis provides a comprehensive molecular atlas of the testis, identifying both known and novel cell types. We demonstrate for the first time the continuous nature of germ cell differentiation, provide molecular signatures and subtype-specific molecular markers, and identify several novel candidate regulators of spermatogenesis. Finally, we demonstrate in vivo using spatial mapping that germ and somatic cell molecular subtypes correspond to previously defined histological cell types residing at different stages of seminiferous epithelial cycle. Taken together, our results unveil the complexity of the testis, and provide a global, unbiased roadmap of the in vivo gametogenesis program.
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