Spatio-temporal landscape of mouse epididymal cells and specific mitochondria-rich segments defined by large-scale single-cell RNA-seq
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ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE159713 | GEO | 2021/04/12
REPOSITORIES: GEO
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Project description:Purpose: To compare the transcriptome profiles (RNA-seq) of cultured human epididymis cells and tissue from the caput, corpus and cauda regions of the human epididymis. Methods: Human epididymis tissue was obtained with Institutional Review Board approval from 3 patients (UC05, UC06, UC09, range: 22 - 36 years) undergoing inguinal radical orchiectomy for a clinical diagnosis of testicular cancer. None of the epididymides had extension of the testicular cancer. The three anatomical regions: caput, corpus and cauda, were separated and segments of each snap frozen. Adult human epididymis epithelial (HEE) cultures were also established from tissue. RNA was extracted from both tissue and cultured HEE cells and RNA-seq libraries prepared (TruSeq RNA Sample Preparation Kit v2, Low-Throughput protocol, Illumina). Libraries were sequenced on Illumina HiSeq2500 machines. Data were analyzed using TopHat and Cufflinks. Results: Libraries generated ~19-39 million reads per library from the cells (95-99% mapping to the human genome) and ~14-39 million reads from the tissue samples (84-99% mapped). Raw reads were aligned to the genome with Tophat and gene expression values were processed using Cufflinks as Fragments Per Kilobase per Million mapped fragments (FPKM). FPKM values were subject to principle component analysis, which revealed that though caput, corpus and cauda cell samples respectively from UC05, UC06 and UC09 clustered together. RNA-seq data from the 3 biological replicas (UC05, UC06 and UC09) of caput, corpus and cauda were pooled for further analysis. Cufflinks was used to determine differentially expressed genes (DEGs) between caput, corpus and cauda cells, combined from the 3 donors. The gene expression profiles of corpus and cauda are remarkably similar and both differ from the caput to a similar degree. We identified ~40 genes differentially expressed between corpus and cauda and more than 1600 DEGs between caput and cauda. The DEGs for each comparison (caput and corpus/cauda) were analysed using a gene ontology process enrichment analysis (DAVID, Huang et al., NAR 2009;37:1-13, Huang et al., 2009 Nat Prot 4:44-57). Conclusions: Here we describe an in depth analysis of the gene expression repertoire of primary cultures of epithelial cells and intact tissues from each region of the adult human epididymis. These data will be valuable to decipher pathways of normal epididymis function and aspects of epididymis disease that cause male infertility. RNA-seq was performed on libraries generated from caput, corpus and cauda-derived cultured cells (passage 2 or 3) from 3 donors and on caput, corpus and cauda tissue from 2 of the same donors. Donor age range: 22 - 36 years.
2016-01-04 | E-GEOD-72986 | biostudies-arrayexpress
Project description:Mammalian spermatozoa acquire their fertilizing ability during epididymal transit. Gene expression patterns along the epididymis are established by specific transcription factor networks that coordinate region-specific functions. The epididymis is usually divided into 3 segments: caput, corpus, and cauda. The human epididymis anatomy does not allow clear distinction between these three segments. To determine to which extent gene expression is segmented along the human epididymis, transcriptome profiling was performed on 8 distinct epididymal regions from 3 donors. Microarray analysis was performed on a Gene Chip Human Clariom S (Affymetrix®) array representing 337 100 transcriptional variants encoded by 20 800 genes. Proximal segments 1 to 3 were distinguishable from the distal epididymal segments (4 to 8) as shown by unsupervised Principal Component Analysis. Transcripts from each segment with differentially expressed genes (DEGs) > 2-fold change and FDR < 0.05 were clustered in relation to their intensity profiles. While no DEGs were detected between segments 1–3 corresponding to the efferent ducts, 1140 DEGs were detected between efferent ducts (1–3) and the epididymis (4–8), 400 between caput (4–6) vs. corpus/cauda (7–8) and none between corpus (7) and cauda (8). Gene Ontology annotation revealed that up-regulated DEGs in the efferent ducts (1–3) were predominantly related to cilium assembly/movement and cell differentiation. The biological process terms fertilization, defense and immune responses were associated with caput epididymis (4–6) while spermatogenesis and protein binding were found all along the epididymis (4–8). In conclusion, the proximal human epididymis is exclusively occupied by efferent ducts with a distinct DEG profile compared with the downstream epididymal segments. Moreover, gene expression profiling revealed two regions in the human epididymis; the caput and the distal corpus/cauda region. Taken together, analysis of the human epididymal transcriptome reveals a limited DEG profile.
2020-11-06 | GSE141568 | GEO
Project description:Purpose: To compare the transcriptome profiles (RNA-seq) of cultured human epididymis cells and tissue from the caput, corpus and cauda regions of the human epididymis. Methods: Human epididymis tissue was obtained with Institutional Review Board approval from 3 patients (UC05, UC06, UC09, range: 22 - 36 years) undergoing inguinal radical orchiectomy for a clinical diagnosis of testicular cancer. None of the epididymides had extension of the testicular cancer. The three anatomical regions: caput, corpus and cauda, were separated and segments of each snap frozen. Adult human epididymis epithelial (HEE) cultures were also established from tissue. RNA was extracted from both tissue and cultured HEE cells and RNA-seq libraries prepared (TruSeq RNA Sample Preparation Kit v2, Low-Throughput protocol, Illumina). Libraries were sequenced on Illumina HiSeq2500 machines. Data were analyzed using TopHat and Cufflinks. Results: Libraries generated ~19-39 million reads per library from the cells (95-99% mapping to the human genome) and ~14-39 million reads from the tissue samples (84-99% mapped). Raw reads were aligned to the genome with Tophat and gene expression values were processed using Cufflinks as Fragments Per Kilobase per Million mapped fragments (FPKM). FPKM values were subject to principle component analysis, which revealed that though caput, corpus and cauda cell samples respectively from UC05, UC06 and UC09 clustered together. RNA-seq data from the 3 biological replicas (UC05, UC06 and UC09) of caput, corpus and cauda were pooled for further analysis. Cufflinks was used to determine differentially expressed genes (DEGs) between caput, corpus and cauda cells, combined from the 3 donors. The gene expression profiles of corpus and cauda are remarkably similar and both differ from the caput to a similar degree. We identified ~40 genes differentially expressed between corpus and cauda and more than 1600 DEGs between caput and cauda. The DEGs for each comparison (caput and corpus/cauda) were analysed using a gene ontology process enrichment analysis (DAVID, Huang et al., NAR 2009;37:1-13, Huang et al., 2009 Nat Prot 4:44-57). Conclusions: Here we describe an in depth analysis of the gene expression repertoire of primary cultures of epithelial cells and intact tissues from each region of the adult human epididymis. These data will be valuable to decipher pathways of normal epididymis function and aspects of epididymis disease that cause male infertility.
2016-01-04 | GSE72986 | GEO
Project description:Purpose: The goal of this study is to detect differentially expressed genes, among Wild type caput, corpus, and cauda epididymis by RNA sequencing Methods: Caput, corpus, and cauda epidiymal mRNA profiles of 9-month-old wild-type mice were generated by deep sequencing, in triplicate, using Illumina GAIIx. Results: RNA-seq data identified transcripts differentially expressed in caput, corpus, and cauda epididymis. Conclusions: Our results show that the expression of many genes were differentially regulated in caput, corpus, and cauda epididymis.
2020-06-05 | GSE138517 | GEO
Project description:BACKGROUND: The molecular mechanisms resulting in the establishment of regionalized gene expression in the human epididymis involve numerous and complex regulatory elements that have not yet been fully elucidated. Interestingly, more than 200 microRNAs (miRNAs) have been identified in the human epididymis that could be involved in the regulation of mRNA stability and post-transcriptionnal expression in this organ. METHODS: Using a global miRNA microarray approach, we investigated the correlation between the miRNA signature and the gene expression profile found in three distinct regions (caput, corpus and cauda) of human epididymides from 3 donors. In silico prediction of transcript miRNA targets was performed in silico using TargetScan and Miranda software’s. To experimentally verify some of these data, FHCE1 immortalized epididymal cell lines were cotransfected with mimics microRNAs and plasmid constructs containing the 3’UTR of target genes downstream of the luciferase gene. RESULTS: We identified 35 miRNAs differentially expressed between the different segments of the epididymis (fold change > 2, P < 0.01). Among these miRNAs, miR-890, miR-892a, miR-892b, miR-891a, miR-891b belonging to the same cluster located on the X chromosome and specifically expressed in epididymal tissues, are significantly more expressed in the corpus and cauda regions compared to the caput. Interestingly, a strong negative correlation (r= -0,89, P <0.001) was found between the pattern of expression of miR-892b and its potential mRNA target Esrrg (Estrogen Related Receptor Gamma), with miR-145 and Cldn10 mRNA (r= -0,92, P<0.001) and with miR-145 and Cftr mRNA (r= -0,69, P<0.05). We confirmed that miR-145 and miR-892b inhibit the expression of the luciferase reporter via Cldn10 and Esrrg 3’ UTRs respectively, whereas miR-145 does not affect the expression of luciferase after its co-transfection with the plasmid containing the Cftr 3’UTR. CONCLUSION: Overall, our study shows that the expression of miRNAs is segmented along the different regions of the human epididymal duct and correlates with the pattern of target gene expression in these regions. Therefore, epididymal miRNAs may be in charge of the maintenance of gene expression profile in the epididymis that dictate segment-specific secretion of proteins and establish physiological compartments that directly or indirectly affect sperm maturation and fertility. Normal human epididymides from three donors of 26–50 years of age, were collected and dissected into 3 anatomical regions (caput, corpus and cauda).A cross-comparison between the miRNA signature found in different segments was performed using GeneChip miRNA Array 1.0 (Affimetrix, Santa Clara, CA).
2012-06-30 | E-GEOD-35522 | biostudies-arrayexpress
Project description:We reported the cell composition and segmental expression differences in three epididymis segments using single-cell RNA sequencing. A total of 13,949 cells were detected, which were further clustered into eight cell populations identified with all known constituent cells of mouse epididymis including principle cell, basal cell, clear/narrow cell and immune cells. Through the study of 35 known epididymal proteins linking to sperm function phenotypes (EPSFPs), we found they were mainly expressed in principle cells and also revealed their segmental specific expression patterns. Notably, a part of EPSFPs was associated with sperm protection and predominantly localized in caput principal cells, whereas some EPSFPs, highly expressed in corpus and cauda, were served as the regulating molecular for the sperm functions such as motility, capacitation or acrosome reactions.In addition, focused analyses uncovered 5 subtypes of the principal cell. Intriguingly, Prc5, the subpopulation of principle cells, was almost only existed in the caput epididymis.
2021-06-02 | GSE151998 | GEO
Project description:Viral infections of the epididymis are associated with epididymitis, which damages the epithelium and impairs fertility. We showed previously that innate immune response genes were differentially expressed in the corpus and cauda region of the human epididymis in comparison to the caput. Here we investigate the antiviral defense response mechanisms of human epididymis epithelial (HEE) cells. Toll-like receptor (TLR) 3 and retinoic acid-inducible gene I (RIG-I)- like receptors (RLRs) are enriched in HEE cells from the corpus and cauda region. Furthermore, corpus and cauda HEE cells show an enhanced response to antiviral ligands (poly(I:C) and HSV-60), as shown by increased IFN-β mRNA expression and secretion of IFN-β. We also show that paired box 2 (PAX2), which was implicated in regulating antiviral response pathways is required for basal expression of the DNA sensor, Z-DNA binding protein (ZBP1) and type I interferon, in caput but not in cauda cells.
2019-10-11 | GSE104944 | GEO
Project description:Dicer1 is an endoribonuclease involved in the biogenesis of functional microRNAs (miRNAs). These small non-coding RNAs are important regulators of the posttranscriptional gene expression and participate to the control of male fertility. Knowing that 1) Dicer1-dependent factors are needed for proper sperm maturation in the epididymis, and that 2) miRNAs are potent mediators of intercellular communication in most biological systems, we investigated the role of Dicer1 dependent-miRNAs produced from the proximal epididymis (initial segment/caput) on the paracrine regulation of epididymal gene expression in the distal epididymis regions (i.e. corpus and cauda). To this aim, we performed comparative microarray and ANOVA analyses on control vs. Defb41iCre/wt;Dicer1fl/fl mice in which functional Dicer1 is absent from the principal cells of the proximal epididymis. We identified 21 and 16 transcripts, including Prostate And Testis Expressed 4 protein and the Zn-alpha 2-glycoprotein, that display significant expression level changes in the corpus and cauda regions, respectively (Fold change >2 or <-2; p<0.001). In addition, 154 miRNAs, including miR- 210, miR-672, miR-191 and miR-204, show a significantly impaired biogenesis in the absence of Dicer1 from the proximal epididymis (Fold change>2 or <-2; p<0.01). These miRNAs are secreted via extracellular vesicles derived from DC2 epididymal principal cell line, and their expression correlates with target transcripts involved in important biological pathways, as evidenced by in silico analysis. These observations suggest that Dicer1-dependent miRNAs could act as potent paracrine regulators of epididymal functions (i.e. control of sperm motility, ciliogenesis) and may contribute to the infertility phenotype observed in the Defb41iCre/wt;Dicer1fl/fl mouse model. These findings open new avenues for the identification of molecular targets important to male fertility control.
2016-09-19 | GSE77139 | GEO
Project description:BACKGROUND: The molecular mechanisms resulting in the establishment of regionalized gene expression in the human epididymis involve numerous and complex regulatory elements that have not yet been fully elucidated. Interestingly, more than 200 microRNAs (miRNAs) have been identified in the human epididymis that could be involved in the regulation of mRNA stability and post-transcriptionnal expression in this organ. METHODS: Using a global miRNA microarray approach, we investigated the correlation between the miRNA signature and the gene expression profile found in three distinct regions (caput, corpus and cauda) of human epididymides from 3 donors. In silico prediction of transcript miRNA targets was performed in silico using TargetScan and Miranda software’s. To experimentally verify some of these data, FHCE1 immortalized epididymal cell lines were cotransfected with mimics microRNAs and plasmid constructs containing the 3’UTR of target genes downstream of the luciferase gene. RESULTS: We identified 35 miRNAs differentially expressed between the different segments of the epididymis (fold change > 2, P < 0.01). Among these miRNAs, miR-890, miR-892a, miR-892b, miR-891a, miR-891b belonging to the same cluster located on the X chromosome and specifically expressed in epididymal tissues, are significantly more expressed in the corpus and cauda regions compared to the caput. Interestingly, a strong negative correlation (r= -0,89, P <0.001) was found between the pattern of expression of miR-892b and its potential mRNA target Esrrg (Estrogen Related Receptor Gamma), with miR-145 and Cldn10 mRNA (r= -0,92, P<0.001) and with miR-145 and Cftr mRNA (r= -0,69, P<0.05). We confirmed that miR-145 and miR-892b inhibit the expression of the luciferase reporter via Cldn10 and Esrrg 3’ UTRs respectively, whereas miR-145 does not affect the expression of luciferase after its co-transfection with the plasmid containing the Cftr 3’UTR. CONCLUSION: Overall, our study shows that the expression of miRNAs is segmented along the different regions of the human epididymal duct and correlates with the pattern of target gene expression in these regions. Therefore, epididymal miRNAs may be in charge of the maintenance of gene expression profile in the epididymis that dictate segment-specific secretion of proteins and establish physiological compartments that directly or indirectly affect sperm maturation and fertility.
2012-07-01 | GSE35522 | GEO
Project description:The epididymis can be subdivided into three regions, the caput, corpus and cauda epididymidis, that have different characteristics and functions. Goal was to determine the differential pattern of gene expression along the regions of the human epididymis. Two-condition experiment, region 1 vs region 2. Replicates: 4 biological replicates from each epididymal region.
2010-08-25 | E-GEOD-23812 | biostudies-arrayexpress