| Literature DB >> 31703718 |
Yu-Xiang Zheng1,2, Xiu-Xiang Zhang3, Jorge A Hernandez4, Yasser S Mahmmod5,6, Wan-Yi Huang1,2, Gui-Feng Li1,2, Ya-Pei Wang1,2, Xue Zhou1,2, Xiu-Ming Li7, Zi-Guo Yuan8,9.
Abstract
BACKGROUND: Some researchers have reported that Toxoplasma gondii can cause serious reproductive impairment in male animals. Specifically, T. gondii destroy the quality of sperm in the epididymis, which affects their sexual ability. However, among such studies, none have investigated the male reproductive transcriptome. Therefore, to investigate the relationship between T. gondii and sperm maturation, we infected mice with T. gondii prugniaud (PRU) strain and performed transcriptome sequencing of the epididymis.Entities:
Keywords: Chronic infection; DEGs; RNA-seq; Reproductive impairment; Toxoplasma gondii
Mesh:
Year: 2019 PMID: 31703718 PMCID: PMC6839085 DOI: 10.1186/s13071-019-3783-2
Source DB: PubMed Journal: Parasit Vectors ISSN: 1756-3305 Impact factor: 3.876
Procedures for transcriptome sequencing, data analysis and validation
| Experimental procedure | Experimental method or threshold considered |
|---|---|
| Extraction of total RNA | Trizol reagent (Invitrogen, CA, USA) |
| Quality and purity detection of total RNA | RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number > 7.0 |
| cDNA library construction | The cleaved mRNA fragments were reverse-transcribed to create the final cDNA library by the instructions of the mRNA-Seq sample preparation kit (Illumina, San Diego, USA) |
| Sample library construction | Illumina Hiseq 2500 sequencing platform |
| Transcript abundance estimation | The RPKM of each gene were calculated by the MARS model in DEGseq program, when the RPKM greater than 1000, it is considered to be a highly expressed gene |
| Threshold of differentially expressed genes | FDR (false discovery rate) < 0.001 and |log2fold change| ≥ 1 |
| Bioinformatics analysis | GO and KEGG enrichment |
| Verification of mRNA expression level | Real-time fluorescence quantitative PCR |
| Verification of protein expression level | Western blot |
Quality analysis of RNA
| Sample | Concentration (µg/µl) | O.D. 260/280 | O.D. 260/230 | Amount (µg) | rRNA | RIN | QC evaluation |
|---|---|---|---|---|---|---|---|
| PRU-1 | 1.46 | 2.07 | 2.3 | 65.83 | 0.8 | 7 | A |
| PRU-2 | 1.16 | 2.09 | 2.25 | 52.24 | 1.8 | 7.2 | A |
| PRU-3 | 1.38 | 2.08 | 2.28 | 62.34 | 1.5 | 7.5 | A |
| Control-1 | 0.87 | 2.07 | 2.35 | 39.35 | 0.8 | 7 | A |
| Control-2 | 1.69 | 2.1 | 2.32 | 76.25 | 1.7 | 7.9 | A |
| Control-3 | 1.26 | 2.03 | 2.29 | 56.65 | 1.8 | 8.1 | A |
Pre-treatment results of data quality in the high throughput sequencing
| Sample | Raw data reads | Base | Valid data reads | Base | Valid reads % | Q20% | Q30% | GC% |
|---|---|---|---|---|---|---|---|---|
| PRU-1 | 42,640,370 | 6.4G | 41,484,632 | 6.22G | 97.29 | 98.77 | 90.81 | 46.5 |
| PRU-2 | 49,368,291 | 7.4G | 48,326,910 | 7.25G | 97.89 | 98.47 | 90.93 | 48.0 |
| PRU-3 | 43,890,326 | 6.58G | 42,897,451 | 6.44G | 97.74 | 98.93 | 90.25 | 47.7 |
| Control-1 | 62,208,188 | 9.33G | 60,729,140 | 9.11G | 97.62 | 98.86 | 91.00 | 47.5 |
| Control-2 | 58,037,289 | 8.7G | 57,291,719 | 8.6G | 98.71 | 98.72 | 90.35 | 50.0 |
| Control-3 | 65,038,924 | 9.76G | 63,902,392 | 9.59G | 98.25 | 99.04 | 91.37 | 46.5 |
Notes: Q20%, error rate is 1%, or the correct rate is 99%; Q30%, error rate is 0.1%, or the correct rate is 99.9%
Fig. 1Statistics of gene expression distribution. Infection group: the maximum, upper quartile, median, lower quartile and the minimum values are 92252.6, 1.84, 0.03, 0 and 0, respectively. Control group: the maximum, upper quartile, median, lower quartile and minimum values are 107446, 1.7, 0.02, 0 and 0, respectively
Fig. 2Distribution map of significant differentially expressed genes. Bright red dots indicate significantly upregulated genes, while blue dots indicate significantly downregulated genes
Partial of upregulated DEGs in the high throughput sequencing data
| Symbol | Name | log2(FC) | Function |
|---|---|---|---|
| Iigp1 | Interferon-inducible GTPase 1 | 6.5608 | Required for disruption of the parasitophorous vacuole formed following |
| Klrb1c | Killer cell lectin-like receptor subfamily B member 1C | 6.17868 | Plays a stimulatory role on natural killer (NK) cells cytotoxicity, activation by cross-linking of the receptor induces Ca2+ mobilization and interferon-gamma production |
| Tgtp1 | T cell-specific GTPase 1 | 5.61362 | Involved in innate cell-autonomous resistance to intracellular pathogens, such as |
| Tnfsf10 | Tumor necrosis factor (ligand) superfamily, member 10 | 1.53097 | Involved in male gonad development and regulation of the apoptotic process |
| Spata18 | Spermatogenesis associated 18 | 1.29567 | A key regulator of mitochondrial quality that mediates the repairing or degradation of unhealthy mitochondria in response to mitochondrial damage |
| Pgk2 | Phosphoglycerate kinase 2 | 1.11099 | Essential for sperm motility and male fertility but is not required for the completion of spermatogenesis |
| Piwil2 | Piwi-like RNA-mediated gene silencing 2 | 1.1907 | Essential role in meiotic differentiation of spermatocytes and self-renewal of spermatogonial stem cells |
Partial of downregulated DEGs in the high throughput sequencing data
| Symbol | Name | log2(FC) | Function |
|---|---|---|---|
| Lipf | Gastric triacylglycerol lipase | − 3.40022 | Involved in lipid catabolic process and mitochondria when classification of cellular component |
| Nrk | Nik-related protein kinase | − 3.41519 | Involved in the TNF-alpha-induced signaling pathway |
| Nwd1 | NACHT and WD repeat domain containing 1 | − 1.60721 | Play a role in the control of androgen receptor (AR) protein steady-state levels |
| Slc14a2 | Solute carrier family 14 (urea transporter), member 2 | − 1.11457 | Mediates rapid transepithelial urea transport across the inner medullary collecting duct and plays a major role in the urinary concentrating mechanism |
| Spink2 | Serine protease inhibitor Kazal type 2 | − 1.02159 | Required for maintenance of normal spermatogenesis, involved in regulating serine protease-dependent germ cell apoptosis |
Fig. 3GO analysis of the significant DEGs
Fig. 4The most enriched pathways of DEGs
Design of primers used for qPCR analysis
| Gene ID | Gene | Forward primer | Reverse primer | Product length (bp) |
|---|---|---|---|---|
| 57746 | piwil2 | GGCAGAGGCCTTGTGTTTAG | CGTTTTGAAGGAGGCCGGAA | 134 |
| 73472 | Spata18 | TTATCACGTGTGGCCTGCTC | TTAAGCTCCTGCTACGGCAC | 125 |
| 22035 | Tnfsf10 | ACGCTTCCAAGATGGTCTCA | ACAGTCCGTACTCGGCATCT | 147 |
| 21822 | Tgtp1 | CGCCACGTCTTCTCACTGTC | CACCAAGTGGAATGGTGGCT | 130 |
| 60440 | Iigp1 | TCACTATGACTTCCCCGTCCT | TGCTTCAGAAATTGCCGCTT | 132 |
| 18663 | Pgk2 | GCCTGTGCCAACCCAGATAA | ACAGTGATGCTTGGAAGGCT | 145 |
| 319555 | Nwd1 | CTCTTTGGACCACCAGGCAT | AGGCTCAGCTTTGATGTCCC | 125 |
| 69982 | Spink2 | GCATGCCCTAGGAACCTCAA | ATATGGCTACCGTCCTCCCT | 101 |
| 11461 | β-actin | AGAGAAGCTGTGCTATGTTGCT | GGAACCGCTCGTTGCCAATA | 128 |
Fig. 5Results of qPCR and compared with RNA-seq
Fig. 6Results of Western blot compared with RNA-seq. Lane 1: control group; Lane 2: infection group; from top to bottom, represent the β-actin internal reference, spata18, tnfsf10 and piwil2 protein
The testis-specific gene was highly expressed in the epididymis
| Symbol | log2 (FC) | Tissue specificity | Function |
|---|---|---|---|
| Piwil2 | 1.1907 | Expressed in adult testis, specifically in spermatocytes and in spermatogonia | Plays an essential role in meiotic differentiation of spermatocytes and self-renewal of spermatogonial stem cells |
| Rgs22 | 2.18187 | Expressed in testis, including in Leydig cells and spermatogenic cells from the spermatogonia to spermatid stages | Negative regulation of signal transduction |
| Shcbp1l | 1.78449 | Testis-specific. Expressed in pachytene spermatocytes and elongating spermatids inside the seminiferous tubules | Testis-specific spindle-associated factor that plays a role in spermatogenesis |
| Spz1 | 1.08852 | Expressed specifically in the testis (Sertoli and Leydig cells) and epididymis | Play an important role in the regulation of cell proliferation and differentiation during spermatogenesis |
| Spata18 | 1.29567 | In testis, expressed primarily in spermatids | Key regulator of mitochondrial quality that mediates the repairing or degradation of unhealthy mitochondria in response to mitochondrial damage |