Selection of optimal reference genes for quantitative RT-PCR studies of boar spermatozoa cryopreservation

Insights into crucial molecules and protein channels involved in pig sperm cryopreservation

Cryopreservation is the most efficient procedure for long-term preservation of mammalian sperm; however, its use is not currently dominant for boar sperm before its use for artificial insemination. In fact, freezing and thawing have an extensive detrimental effect on sperm function and lead to impaired fertility. The present work summarises the basis of the structural and functional impact of cryopreservation on pig sperm that have been extensively studied in recent decades, as well as the molecular alterations in sperm that are related to this damage. The wide variety of mechanisms underlying the consequences of alterations in expression levels and structural modifications of sperm proteins with diverse functions is detailed. Moreover, the use of cryotolerance biomarkers as predictors of the potential resilience of a sperm sample to the cryopreservation process is also discussed. Regarding the proteins that have been identified to be relevant during the cryopreservation process, they are classified according to the functions they carry out in sperm, including antioxidant function, plasma membrane protection, sperm motility regulation, chromatin structure, metabolism and mitochondrial function, heat-shock response, premature capacitation and sperm-oocyte binding and fusion. Special reference is made to the relevance of sperm membrane channels, as their function is crucial for boar sperm to withstand osmotic shock during cryopreservation. Finally, potential aims for future research on cryodamage and cryotolerance are proposed, which might be crucial to minimise the side-effects of cryopreservation and to make it a more advantageous strategy for boar sperm preservation.

Development of a biomolecular approach to identify sperm functions and fertility using sperm RNAs

Infertility affects a significant percentage of couples worldwide, and male factors contribute significantly to this problem. Traditional assessments of male fertility rely primarily on parameters such as sperm motility, morphology, viability, and concentration. However, these metrics often do not provide a comprehensive understanding of sperm function, which is critical not only for fertilization but also for successful embryo development. Herein, we used porcine spermatozoa as a model to investigate the potential of sperm RNA markers in assessing various aspects of sperm function from motility to fertility. Using artificial insemination, we evaluated male fertility based on the litter size of sows inseminated with sperm from 20 boars. In addition, we measured parameters such as weaning rate, death births, live births, and mummy births. Sperm functional parameters, including motility and kinematics, were assessed before and after in vitro capacitation. Finally, correlations between various sperm functional parameters and sperm RNA markers were explored. Our results revealed interesting relationships between sperm functional parameters. While motility and kinematics were correlated, they were not correlated with sperm capacitation status. Surprisingly, no significant correlations were found between these parameters and male fertility. However, specific parameters of sperm capacitation status after in vitro capacitation were correlated with weaning rate and live births, highlighting their importance in predicting successful fertilization. Further analysis of sperm RNA markers identified genes related to male fertility, including IZUMO1, known for its role in sperm-egg fusion. These genes showed correlations with motility, capacitation, and fertilization parameters, shedding light on their potential roles in sperm function. In conclusion, our study demonstrates that sperm RNA markers hold promise for the diagnosis and prognosis of various aspects of sperm function, providing valuable insights into male infertility. These markers may serve as diagnostic tools to improve our understanding of male fertility problems, ultimately benefiting couples struggling with infertility.

Identification and functional analysis of differentially expressed proteins in high and low freezing tolerance sheep sperm

The purpose of this study was to identify proteins associated with differences in the freezing tolerance of sheep sperm and to analyze their functions. Qualified fresh semen from four breeds of rams, the Australian White, white-head Dorper, Black-head Dorper, and Hu sheep breeds, were selected for cryopreservation. The sperm freezing tolerance was investigated by evaluation of the overall vitality, progressive vitality, and rapidly advance vitality of the sperm. A differential model of sperm freezing tolerance was constructed for sheep breeds showing significant differences. Differentially expressed proteins associated with sperm freezing tolerance were identified using iTRAQ and the protein functions were analyzed. It was found that sperm freezing tolerance was best in Hu sheep and worst in white-head Dorper sheep. These two breeds were used for the construction of a model based on differences in freezing tolerance and the identification of sperm proteins expressed differentially before freezing and after thawing. A total of 128 differentially expressed proteins (88 up-regulated and 40 down-regulated) were identified before freezing and after thawing in Hu sheep sperm (fresh/frozen Hu sheep sperm referred to as HL vs. HF), while 219 differentially expressed proteins (106 up-regulated and 113 down-regulated) were identified in white-head Dorper sheep (fresh/frozen white-head Dorper sheep sperm referred to as WL vs. WF). A comparison of these differentially expressed proteins showed that 57 proteins overlapped between the two breeds while 71 were only expressed in Hu sheep and 162 were only expressed in white-head Dorper sheep. Functional annotation and enrichment analyses of differentially expressed proteins down-regulated in Hu sheep involved in phosphorylation of phosphatidylinositol phosphate kinases, regulation of GTPase activity and glycolysis/gluconeogenesis signaling pathway. Up-regulated proteins of Hu sheep participated in oxidoreductase activity and oxidative phosphorylation process of sperm freezing. Furthermore, down-regulated in white-head Dorper sheep involved in the metabolic regulation of carbohydrate and nuclear sugar metabolism. Up-regulated proteins of white-head Dorper sheep involved in the ferroptosis and oxidative phosphorylation pathways. Collectively, These proteins were found to participate mainly in oxidative phosphorylation as well as phosphorylation and metabolic processes in the mitochondria to affect the freezing tolerance of sheep sperm.

Density Gradient Centrifugation Alone or the Combination of DGC with Annexin V Magnetic-Activated Cell Sorting Prior to Cryopreservation Enhances the Postthaw Quality of Sperm from Infertile Male Patients with Poor Sperm Quality

Objective. To examine whether density gradient centrifugation (DGC) alone or its combination with annexin V magnetic-activated cell sorting (DGC-MACS) can be used to process semen samples from infertile male patients with poor sperm quality prior to subjecting these to freeze/thaw process in order to optimize the outcomes of sperm freezing. Methods. This study enrolled sixteen patients with sperm $\text{concentration}\ge 20\times {10}^6/\text{mL}$ , sperm $\text{motility}<30$ %, and/or <4% normal sperm morphology. Sperms were processed by DGC or DGC-MACS prior to the freeze/thaw process. Sperm motility, hyperosmotic swelling test (HOS), TUNEL test, and morphological analysis were performed before and after the freeze/thaw process. Results. The freeze/thaw process had a detrimental effect on sperm motility, viability, morphology, and DNA integrity in all three groups (RAW, DGC, and DGC + MACS groups). The DGC and DGC + MACS groups showed increased sperm motility, viability, and normal morphology following freeze/thaw than untreated frozen controls. The motility and viability were not significantly different between DGC-MACS-CPT (cryopreservation-thawing) and DGC-CPT groups. Moreover, almost no grade A or grade B sperm was observed in the DGC-MACS-CPT groups. The sperm selected by DGC or DGC + MACS showed decreased levels of sperm DNA fragmentation than RAW samples following freeze/thaw. Moreover, the sperm DNA fragmentation following freeze/thaw in the DGC-MACS-CPT group was significantly lower than that in the DGC-CPT group. Conclusions. Sperm preparation by DGC before cryopreservation improved the quality of sperm postthaw in infertile males with poor sperm quality. If the sperm quality following freeze/thaw is foreseen to be insufficient for artificial insemination with husband’s sperm or in vitro fertilization, or if there is high DNA fragmentation in RAW sperm, DGC + MACS should be used prior to cryopreservation to reduce sperm DNA fragmentation and improve the quality of sperm available for intracytoplasmic sperm injection.

Identification and validation of reference genes for normalization of gene expression analysis using qRT-PCR in Megalurothrips usitatus (thysanoptera: thripidae)

Introduction: Gene expression analysis by reverse transcription quantitative polymerase chain reaction (qRT-PCR) has been widely used in research including insects. The selection of appropriate reference genes is the key to obtaining accurate and reliable results from qRT-PCR. However, studies on the expression stability of reference genes in Megalurothrips usitatus remain lacking. Methods: In this study, qRT-PCR was used to analyze the expression stability of candidate reference genes in M. usitatus. The expression levels of six candidate reference gene transcription of M. usitatus were analyzed. GeNorm, NormFinder, BestKeeper, and ΔCt were used to analyze the expression stability of M. usitatus treated with biological factors (developmental period treatment) and abiotic factors (light, temperature, insecticide treatment, respectively). Comprehensive stability ranking of candidate reference genes was recommended by RefFinder. Results and Discussion: Results showed that ribosomal protein S (RPS) was the most suitable expression in insecticide treatment. Ribosomal protein L (RPL) was the most suitable expression at developmental stage and light treatment, whereas elongation factor was the most suitable expression in temperature treatment. RefFinder was used to comprehensively analyze the above four treatments, and the results showed that RPL and actin (ACT) showed high stability in each treatment. Therefore, this study identified these two genes as reference genes in the qRT-PCR analysis of different treatment conditions of M. usitatus. Ourfindings will be beneficial for improving the accuracy of qRT-PCR analysis for future functional analysis of the target gene expression in M. usitatus.

Expression of TXNRD1, HSPA4L and ATP1B1 Genes Associated with the Freezability of Boar Sperm

Cryopreservation is associated with increased oxidative stress, which is responsible for sperm damage. We analyzed the effect of cryopreservation on mRNA and protein expression of thioredoxin reductase 1 (TXNRD1), heat shock protein family A (HSP 70) member 4 like (HSPA4L) and sodium/potassium-transporting ATPase subunit beta-1 (ATP1B1) genes in boar sperm with different freezability. Boars were classified as having good and poor semen freezability (GSF and PSF, respectively), according to the assessment of post-thaw sperm motility. Total RNA was isolated from fresh pre-freeze (PF) and frozen-thawed (FT) sperm from five boars of the GSF and PSF groups, respectively. Quantification of TXNRD1, HSPA4L and ATP1B1 gene expression was performed by RT-qPCR analysis. Proteins extracted from sperm were subjected to Western blotting and SDS-PAGE analyses. Poor freezability ejaculates were characterized by significantly higher relative mRNA expression levels of TXNRD1 and HSPA4L in FT sperm compared with the fresh PF sperm. Furthermore, the relative mRNA expression level of ATP1B1 was significantly higher in the fresh PF sperm of the GSF group. Western blotting analysis revealed significantly higher relative expression of TXNRD1 protein in the fresh PF sperm of the GSF group, while HSPA4L protein expression was markedly increased in FT sperm of the PSF group. Electrophoretic and densitometric analyses revealed a higher number of proteins in the fresh PF and FT sperm of the PSF and GSF groups, respectively. The results of this study indicate that ATP1B1 mRNA expression in the fresh PF sperm is a promising cryotolerance marker, while the variations of TXNRD1 and HSPA4L protein expression in the fresh PF or FT sperm provide useful information that may help to elucidate their biological significance in cryo-damage.

Further Insights on RNA Expression and Sperm Motility

Asthenozoospermia is one of the main causes of male infertility and it is characterized by reduced sperm motility. Several mutations in genes that code for structural or functional constituents of the sperm have already been identified as known causes of asthenozoospermia. In contrast, the role of sperm RNA in regulating sperm motility is still not fully understood. Consequently, here we aim to contribute to the knowledge regarding the expression of sperm RNA, and ultimately, to provide further insights into its relationship with sperm motility. We investigated the expression of a group of mRNAs by using real-time PCR (CATSPER3, CFAP44, CRHR1, HIP1, IQCG KRT34, LRRC6, QRICH2, RSPH6A, SPATA33 and TEKT2) and the highest score corresponding to the target miRNA for each mRNA in asthenozoospermic and normozoospermic individuals. We observed a reduced expression of all mRNAs and miRNAs in asthenozoospermic patients compared to controls, with a more accentuated reduction in patients with progressive sperm motility lower than 15%. Our work provides further insights regarding the role of RNA in regulating sperm motility. Further studies are required to determine how these genes and their corresponding miRNA act regarding sperm motility, particularly KRT34 and CRHR1, which have not previously been seen to play a significant role in regulating sperm motility.

Heat shock protein family D member 1 in boar spermatozoa is strongly related to the litter size of inseminated sows

Background

Sperm quality evaluation is the logical first step in increasing field fertility. Spermatozoa contain cytoplasmic organelles and biomolecules known as sperm-intrinsic factors, which play key roles in sperm maturation, sperm-oocyte fusion, and embryo development. In particular, sperm membrane proteins [e.g., arginine vasopressin receptor 2, beta-actin, prohibitin, and heat shock protein family D member 1 (HSPD1)] and RNA could be used as functional indicators of male fertility. We sought to clarify the effects of differential mRNA expression of selected genes on several fertilisation parameters, including sperm motility, motion kinematics, capacitation, and litter size, in a porcine model.

Results

Our results demonstrated that HSPD1 expression was significantly correlated with male fertility, as measured by the litter size of inseminated sows. The expression of HSPD1 mRNA was linked to sperm motility and other motion kinematic characteristics. Furthermore, HSPD1 had a 66.7% overall accuracy in detecting male fertility, and the high-litter size group which was selected with the HSPD1 marker had a 1.34 greater litter size than the low-litter size group.

Conclusions

Our findings indicate that HSPD1 might be a helpful biomarker for superior boar selection for artificial insemination, which could boost field fertility.

Supplementary Information

The online version contains supplementary material available at 10.1186/s40104-022-00689-0.

Comparative Effect of Photobiomodulation on Human Semen Samples Pre- and Post-Cryopreservation

The primary objective of this study is to evaluate and to compare the effects of photobiomodulation (PBM) on sperm parameters both before and after cryopreservation. In this regard, 24 freshly ejaculated semen samples from normozoospermic men were included in this study. Each semen sample was randomly divided into three groups (1 ml aliquot for each group): the control group (group one) underwent conventional sperm cryopreservation (n = 24), group two underwent pre-freezing PBM exposure (810 nm, diode laser, and 0.6 J/cm²) (n = 24), and group three underwent post freezing and thawing PBM exposure (n = 24). Indicators of sperm quality, including total sperm motility (TSM), progressive sperm motility (PSM), DNA fragmentation, lipid peroxidation levels, apoptosis-like changes, and gene expression levels of protamine (PRM) 1, PRM2, and adducin 1 alpha (ADD1), were investigated in a blinded style. Due to the beneficial effect of pre-freezing PBM therapy, group 2 exhibited the highest TSM and PSM levels compared to groups 1 and 3. At the same time, DNA fragmentation and lipid peroxidation were significantly reduced in the group 2 compared to the group 1 (p = 0.024 p = 0.016, respectively). Evaluation of apoptotic/necrotic changes revealed that parameters including early apoptosis, dead, and necrotic cells decreased in the group 2 compared to the either groups 1 (p = 0. 008, p = 0. 032, p = 0. 02, respectively) or group 3 (p = 0.037, p = 0.108, p = 0.083). There were no significant differences in the expression levels of PRM1, PRM2, and ADD1 among the study groups. Based on our results, PBM therapy prior to cryopreservation, even in the normal semen samples, plays a significant protective role against cryo-damage by preserving the functional parameters of spermatozoa.

Transcriptome-wide m6A profiling reveals mRNA post-transcriptional modification of boar sperm during cryopreservation

Background

Cryopreservation induces transcriptomic and epigenetic modifications that strongly impairs sperm quality and function, and thus decrease reproductive performance. N⁶-methyladenosine (m⁶A) RNA methylation varies in response to stress and has been implicated in multiple important biological processes, including post-transcriptional fate of mRNA, metabolism, and apoptosis. This study aimed to explore whether cryopreservation induces m⁶A modification of mRNAs associated with sperm energy metabolism, cryoinjuries, and freezability.

Results

The mRNA and protein expression of m⁶A modification enzymes were significantly dysregulated in sperm after cryopreservation. Furthermore, m⁶A peaks were mainly enriched in coding regions and near stop codons with classical RRACH motifs. The mRNAs containing highly methylated m⁶A peaks (fts vs. fs) were significantly associated with metabolism and gene expression, while the genes with less methylated m⁶A peaks were primarily involved in processes regulating RNA metabolism and transcription. Furthermore, the joint analysis of DMMGs and differentially expressed genes indicated that both of these play a vital role in sperm energy metabolism and apoptosis.

Conclusions

Our study is the first to reveal the dynamic m⁶A modification of mRNAs in boar sperm during cryopreservation. These epigenetic modifications may affect mRNA expression and are closely related to sperm motility, apoptosis, and metabolism, which will provide novel insights into understanding of the cryoinjuries or freezability of boar sperm during cryopreservation.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-07904-8.

Social sperm freezing

Increased paternal age has been associated with lower fertility and higher genetic risk for the offspring. One way to prevent these consequences is to freeze sperm at a young age. Social sperm freezing could be developed in a way similar to social oocyte freezing. The main difference between freezing oocytes and sperm is that social sperm freezing is much less focussed on fertility preservation and much more on avoiding increased genetic risk. Contrary to what some people seem to believe, sperm freezing is more complicated than it looks at first sight. This article considers three practical aspects: freezing, storage and testing. It is concluded that the remedy (cryopreservation) may itself cause damage to the quality of the spermatozoon and to its genetic integrity, thus undoing the possible benefits in terms of fertility and health of offspring.

Mathematical Modeling and Optimization of Cryopreservation in Single Cells

Cryobiology is a multiscale and interdisciplinary field. The scope and scale of interactions limit the gains that can be made by one theory or experiment alone. Because of this, modeling has played a critical role in both explaining cryobiological phenomena and predicting improved protocols. Modeling facilitates understanding of the biophysical and some of the biochemical mechanisms of damage during all phases of cryopreservation including CPA equilibration and cooling and warming. Moreover, as a tool for optimization of cryopreservation protocols, modeling has yielded many successes. Modern cryobiological modeling includes very detailed descriptions of the physical phenomena that occur during freezing, including ice growth kinetics and spatial gradients that define heat and mass transport models. Here we reduce the complexity and approach only a small but classic subset of these problems. Namely, here we describe the process of building and using a mathematical model of a cell in suspension where spatial homogeneity is assumed for all quantities. We define the models that describe the critical cell quantities used to describe optimal and suboptimal protocols and then give an overview of classical methods of how to determine optimal protocols using these models. We include practical considerations of modeling in cryobiology, including fitting transport models to cell volume data, performing optimization with cell volume constraints, and a look at expanding cost functions to cooling regimes.

Regulatory Potential of Long Non-Coding RNAs (lncRNAs) in Boar Spermatozoa with Good and Poor Freezability

Long non-coding RNAs (lncRNAs) are suggested to play an important role in the sperm biological processes. We performed de novo transcriptome assembly to characterize lncRNAs in spermatozoa, and to investigate the role of the potential target genes of the differentially expressed lncRNAs (DElncRNAs) in sperm freezability. We detected approximately 4007 DElncRNAs, which were differentially expressed in spermatozoa from boars classified as having good and poor semen freezability (GSF and PSF, respectively). Most of the DElncRNAs were upregulated in boars of the PSF group and appeared to significantly affect the sperm's response to the cryopreservation conditions. Furthermore, we predicted that the potential target genes were regulated by DElncRNAs in cis or trans. It was found that DElncRNAs of both freezability groups had potential cis- and trans-regulatory effects on different protein-coding genes, such as COX7A2L, TXNDC8 and SOX-7. Gene Ontology (GO) enrichment revealed that the DElncRNA target genes are associated with numerous biological processes, including signal transduction, response to stress, cell death (apoptosis), motility and embryo development. Significant differences in the de novo assembled transcriptome expression profiles of the DElncRNAs between the freezability groups were confirmed by quantitative real-time PCR analysis. This study reveals the potential effects of protein-coding genes of DElncRNAs on sperm functions, which could contribute to further research on their relevance in semen freezability.

Investigation of molecular cryopreservation, fertility potential and microRNA-mediated apoptosis in Oligoasthenoteratozoospermia men

Investigation of the cryo-injury mechanism can provide novel insight into cryopreservation. The objective of this study is to assess the effect of cryopreservation on fertility potential, motility, oxidative stress (OS), DNA fragmentation, microRNAs (miRNAs), and apoptotic target genes in the infertile men compared to the fertile men. All 40 samples were divided into two leading groups of fresh and cryopreserved sperms. Each main group was subdivided into three groups including, Normozoospermia, and Mild, and Severe Oligoasthenoteratozoospermia (OAT). In all collected samples the following were assessed: microRNA-34c (miR-34c) and miR-184, P53 and Caspase9 using Quantitative real-time polymerase chain reaction (RT-PCR), malondialdehyde (MDA), Superoxide dismutase (SOD) using imaging multi-mode reader, and DNA fragmentation using Sperm DNA Fragmentation Assay Test (SDFA). Within the studied groups, immotile spermatozoa were increased due to cryopreservation. We observed an increasing levels of SOD, MDA, and DNA fragmentation. Also, cryopreservation was associated with decreasing the expression of P53, mir-43c, and miR-184 while capase9 was showed enhancing expression after freeze-thawing of sperm cells. During cryopreservation, sperm fertility and motility were influenced via apoptosis cascade-mediated mitochondrial dysfunctions such as caspase9. Also, we found that miR-34c, miR184, and P53 could impact fertility potential. In Addition, there was a meaningful correlations between microRNAs and motility post freeze-thawing process in Severe Oligoasthenoteratozoospermia men.

Optimization of sperm RNA processing for developmental research

Recent studies have demonstrated the significance of sperm RNA function as a transporter of important information directing the course of life. To determine the message contained in sperm RNA, it is necessary to optimize transcriptomic research tools. The current study was performed to optimize the processing of sperm RNA from sample storage to quantitative real-time PCR and assess the corresponding method with to evaluate male fertility and its representative markers, equatorin (EQTN) and peroxiredoxin (PRDX). Following successive steps of the Minimum Information for Publication of Quantitative Real-Time PCR Experiments guidelines, several options were compared using boar spermatozoa. To evaluate the optimized procedures, the relationship between mRNA expression of EQTN and PRDX in spermatozoa and the fertility (litter size) of 20 individual boars was assessed. Unexpectedly, DNase treatment during RNA isolation had the deleterious effect by decreasing the RNA concentration by 56% and eliminating the correlation between EQTN and PRDX4 mRNA expression and male fertility. Moreover, when sperm RNA was processed using the corresponding method, the results showed the highest exon sequence expression, male fertility prediction power, and consistency. This optimized protocol for predicting male fertility can be used to study the transport of messages directing the life course from spermatozoon to offspring.

Transcriptome analysis of boar spermatozoa with different freezability using RNA-Seq

Semen freezability is associated with genetic markers, and there is a diverse set of sperm transcripts that have been attributed to various cellular functions. RNA-Seq was performed to compare the transcript profiles of spermatozoa from boars with different semen freezability. We examined ejaculates from the Polish large white (PLW) boars that were classified as having good and poor semen freezability (GSF and PSF, respectively; n = 3 boars per group) by assessing post-thaw motility characteristics, mitochondrial membrane potential, plasma membrane and acrosome integrity. Total RNA was isolated from fresh spermatozoa from boars of the GSF and PSF groups and subjected to RNA-Seq (Illumina NextSeq 500 platform). Transcript abundance was assessed with the DESeq2, DESeq, and EdgeR Bioconductor R packages, and varying numbers of differentially expressed gene (DEG) transcripts were detected in the spermatozoa of each boar. Using RNA-Seq, we identified several genes associated with inflammation and apoptosis (FOS, NFATC3, ITGAL, EAF2 and ZDHHC14), spermatogenesis (FGF-14 and BAMBI), autophagy (RAB33B), protein phosphorylation (PTPRU and PTPN2) and energy metabolism (ND6 and ACADM) that were predominantly up-regulated in poor freezability ejaculates. Quantitative reverse transcription polymerase chain reaction (RT-qPCR) validated the transcript expression levels detected by RNA-Seq and thus confirmed the reliability of this technique. Subsequent validation with western blotting showed that the expression of three proteins was in accordance with the transcript abundance. Overall, we demonstrated that the up-regulation of the DEG transcripts in spermatozoa was associated with poor semen freezability. We suggest that spermatozoa transcriptome profiling provides a foundation to further elucidate the relevance of sperm-related transcripts on cryo-survival. The sperm-related transcripts, namely FOS, NFATC3, EAF2, BAMBI, PTPRU, PTPN2, ND6 and ACADM, are potential markers for predicting the freezability of boar semen.

Comparative Analysis of MicroRNA and mRNA Profiles of Sperm with Different Freeze Tolerance Capacities in Boar (Sus scrofa) and Giant Panda (Ailuropoda melanoleuca)

Post-thawed sperm quality parameters vary across different species after cryopreservation. To date, the molecular mechanism of sperm cryoinjury, freeze-tolerance and other influential factors are largely unknown. In this study, significantly dysregulated microRNAs (miRNAs) and mRNAs in boar and giant panda sperm with different cryo-resistance capacity were evaluated. From the result of miRNA profile of fresh and frozen-thawed giant panda sperm, a total of 899 mature, novel miRNAs were identified, and 284 miRNAs were found to be significantly dysregulated (195 up-regulated and 89 down-regulated). Combined analysis of miRNA profiling of giant panda sperm and our previously published data on boar sperm, 46, 21 and 4 differentially expressed (DE) mRNAs in boar sperm were believed to be related to apoptosis, glycolysis and oxidative phosphorylation, respectively. Meanwhile, 87, 17 and 7 DE mRNAs in giant panda were associated with apoptosis, glycolysis and oxidative phosphorylation, respectively. Gene ontology (GO) analysis of the targets of DE miRNAs showed that they were mainly distributed on membrane related pathway in giant panda sperm, while cell components and cell processes were tied to the targets of DE miRNAs in boar sperm. Finally, Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of DE mRNAs indicated that most of these DE mRNAs were distributed in membrane signal transduction-related pathways in giant panda sperm, while those in boar sperm were mainly distributed in the cytokine-cytokine receptor interaction pathway and inflammatory related pathways. In conclusion, although the different freezing extenders and programs were used, the DE miRNAs and mRNAs involved in apoptosis, energy metabolism, olfactory transduction pathway, inflammatory response and cytokine-cytokine interactions, could be the possible molecular mechanism of sperm cryoinjury and freeze tolerance.

Validation of Reference Genes for Gene Expression Normalization in RAW264.7 Cells under Different Conditions

RAW264.7 is a macrophage strain derived from mice tumour and shows a significant ability in antigen uptake. Real-time quantitative PCR (RT-qPCR) is one of the most commonly used methods in gene studies and requires suitable reference genes to normalize and quantitate the expression of gene of interest with sensitivity and specificity. However, suitable reference genes in RAW264.7 cells have not yet been identified for accurate gene expression quantification. In the current study, we evaluated expression levels of ten candidate reference genes in RAW264.7 cells under different conditions. RT-qPCR results indicated significant differences in the expression levels among the ten reference genes. Statistical analyses were carried out using geNorm, NormFinder, and BestKeeper software to further investigate the stability of the reference genes. Integrating the results from the three analytical methods, cytochrome c-1 and hydroxymethylbilane synthase were found to be the most stable and therefore more suitable reference genes, while ribosomal protein L4 and cyclophilin A were the least stable. This study emphasises the importance of identifying and selecting the most stable reference genes for normalization and provides a basis for future gene expression studies using RAW264.7 cells.

Exploration of miRNA and mRNA Profiles in Fresh and Frozen-Thawed Boar Sperm by Transcriptome and Small RNA Sequencing

Due to lower farrowing rate and reduced litter size with frozen-thawed semen, over 90% of artificial insemination (AI) is conducted using liquid stored boar semen. Although substantial progress has been made towards optimizing the cryopreservation protocols for boar sperm, the influencing factors and underlying mechanisms related to cryoinjury and freeze tolerance of boar sperm remain largely unknown. In this study, we report the differential expression of mRNAs and miRNAs between fresh and frozen-thawed boar sperm using high-throughput RNA sequencing. Our results showed that 567 mRNAs and 135 miRNAs were differentially expressed (DE) in fresh and frozen-thawed boar sperm. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses revealed that the majority of DE mRNAs were enriched in environmental information processing such as cytokine-cytokine receptor interactions, PI3K-Akt signaling, cell adhesion, MAPK, and calcium signaling pathways. Moreover, the targets of DE miRNAs were enriched in significant GO terms such as cell process, protein binding, and response to stimuli. In conclusion, we speculate that DE mRNAs and miRNAs are heavily involved in boar sperm response to environment stimuli, apoptosis, and metabolic activities. The differences in expression also reflect the various structural and functional changes in sperm during cryopreservation.

High throughput small RNA and transcriptome sequencing reveal capacitation-related microRNAs and mRNA in boar sperm

Background

Capacitation, a prerequisite for oocyte fertilization, is a complex process involving series of structural and functional changes in sperms such as membrane modifications, modulation of enzyme activities, and protein phosphorylation. In order to penetrate and fertilize an oocyte, mammalian sperms must undergo capacitation. Nevertheless, the process of sperm capacitation remains poorly understood and requires further elucidation. In the current study, via high throughput sequencing, we identified and explored the differentially expressed microRNAs (miRNAs) and mRNAs involved in boar sperm capacitation.

Results

We identified a total of 5342 mRNAs and 204 miRNAs that were differentially expressed in fresh and capacitated boar sperms. From these, 12 miRNAs (8 known and 4 newly identified miRNAs) and their differentially expressed target mRNAs were found to be involved in sperm capacitation-related PI3K-Akt, MAPK, cAMP-PKA and Ca²⁺signaling pathways.

Conclusions

Our study is first to provide the complete miRNA and transcriptome profiles of boar sperm. Our findings provide important insights for the understanding of the RNA profile in boar sperm and future elucidation of the underlying molecular mechanism relevant to mammalian sperm capacitation.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-5132-9) contains supplementary material, which is available to authorized users.

Transcriptome Sequencing Reveals the Differentially Expressed lncRNAs and mRNAs Involved in Cryoinjuries in Frozen-Thawed Giant Panda (Ailuropoda melanoleuca) Sperm

Sperm cryopreservation and artificial insemination are important methods for giant panda breeding and preservation of extant genetic diversity. Lower conception rates limit the use of artificial insemination with frozen-thawed giant panda sperm, due to the lack of understanding of the cryodamaging or cryoinjuring mechanisms in cryopreservation. Long non-coding RNAs (lncRNAs) are involved in regulating spermatogenesis. However, their roles during cryopreservation remain largely unexplored. Therefore, this study aimed to identify differentially expressed lncRNAs and mRNAs associated with cryodamage or freeze tolerance in frozen-thawed sperm through high throughput sequencing. A total of 61.05 Gb clean reads and 22,774 lncRNA transcripts were obtained. From the sequencing results, 1477 significantly up-regulated and 1,396 significantly down-regulated lncRNA transcripts from fresh and frozen-thawed sperm of giant panda were identified. GO and KEGG showed that the significantly dysregulated lncRNAs and mRNAs were mainly involved in regulating responses to cold stress and apoptosis, such as the integral component of membrane, calcium transport, and various signaling pathways including PI3K-Akt, p53 and cAMP. Our work is the first systematic profiling of lncRNA and mRNA in fresh and frozen-thawed giant panda sperm, and provides valuableinsights into the potential mechanism of cryodamage in sperm.

Sperm cryopreservation: A review on current molecular cryobiology and advanced approaches

The cryopreservation of spermatozoa was introduced in the 1960s as a route to fertility preservation. Despite the extensive progress that has been made in this field, the biological and biochemical mechanisms involved in cryopreservation have not been thoroughly elucidated to date. Various factors during the freezing process, including sudden temperature changes, ice formation and osmotic stress, have been proposed as reasons for poor sperm quality post-thaw. Little is known regarding the new aspects of sperm cryobiology, such as epigenetic and proteomic modulation of sperm and trans-generational effects of sperm freezing. This article reviews recent reports on molecular and cellular modifications of spermatozoa during cryopreservation in order to collate the existing understanding in this field. The aim is to discuss current freezing techniques and novel strategies that have been developed for sperm protection against cryo-damage, as well as evaluating the probable effects of sperm freezing on offspring health.

Artificial insemination with frozen-thawed boar sperm

Artificial insemination with frozen-thawed semen in pigs is not a routine technique; its use is restricted to specific cases, such as preservation of valuable genetic material (germplasm banks), safety strategies in case of natural disasters, long-distance transport of sperm, and in combination with sex-sorting. Cryoinjuries resulting from freeze-thawing protocols are a major concern with regard to the fertilization capacity of the treated sperm, which is lower than that of liquid-stored semen. Here, we provide an overview of artificial insemination using cryopreserved sperm, and summarize the factors that influence cryopreservation success before, during, and after freeze-thaw (i.e., sperm selection before starting the cryopreservation process, holding time, use of cryoprotectants, and rates of freezing and thawing) and that are driving the identification of biomarkers to predict sensitivity to cryodamage. Three different artificial insemination techniques (conventional or intracervical; intrauterine; and deep intrauterine) are also discussed with regards to their relevance when using frozen-thawed semen. Finally, we review the use of additives to freezing and thawing media, given reports that they may maintain and improve the quality and fertilizing capacity of frozen-thawed sperm. In sum, artificial insemination with frozen-thawed boar sperm can provide reasonable fertility outcomes, if freezable ejaculates, specific additives, and appropriate insemination techniques are used.

Insights on Cryopreserved Sheep Fibroblasts by Cryomicroscopy and Gene Expression Analysis

Cryopreservation includes a set of techniques aimed at storing biological samples and preserving their biochemical and functional features without any significant alterations. This study set out to investigate the effects induced by cryopreservation on cultured sheepskin fibroblasts (CSSF) through cryomicroscopy and gene expression analysis after subsequent in vitro culture. CSSF cells were cryopreserved in a cryomicroscope (CM) or in a straw programmable freezer (SPF) using a similar thermal profile (cooling rate -5°C/min to -120°C, then -150°C/min to -196°C). CSSF volume and intracellular ice formation (IIF) were monitored by a CM, while gene expression levels were investigated by real-time polymerase chain reaction in SPF-cryopreserved cells immediately after thawing (T0) and after 24 or 48 hours (T24, T48) of post-thaw in vitro culture. No significant difference in cell viability was observed at T0 between CM and SPF samples, while both CM and SPF groups showed lower viability (p < 0.05) compared to the untreated control group. Gene expression analysis of cryopreserved CSSF 24 and 48 hours post-thawing showed a significant upregulation of the genes involved in protein folding and antioxidant mechanisms (HPS90b and SOD1), while a transient increase (p < 0.05) in the expression levels of OCT4, BCL2, and GAPDH was detected 24 hours post-thawing. Overall, our data suggest that cryostored CSSF need at least 24 hours to activate specific networks to promote cell readaptation.

Identification and evaluation of reference genes for accurate gene expression normalization of fresh and frozen-thawed spermatozoa of water buffalo (Bubalus bubalis)

The quantitative real time PCR (qRT-PCR) has become an important tool for gene-expression analysis for a selected number of genes in life science. Although large dynamic range, sensitivity and reproducibility of qRT-PCR is good, the reliability majorly depend on the selection of proper reference genes (RGs) employed for normalization. Although, RGs expression has been reported to vary considerably within same cell type with different experimental treatments. No systematic study has been conducted to identify and evaluate the appropriate RGs in spermatozoa of domestic animals. Therefore, this study was conducted to analyze suitable stable RGs in fresh and frozen-thawed spermatozoa. We have assessed 13 candidate RGs (BACT, RPS18s, RPS15A, ATP5F1, HMBS, ATP2B4, RPL13, EEF2, TBP, EIF2B2, MDH1, B2M and GLUT5) of different functions and pathways using five algorithms. Regardless of the approach, the ranking of the most and the least candidate RGs remained almost same. The comprehensive ranking by RefFinder showed GLUT5, ATP2B4 and B2M, MDH1 as the top two stable and least stable RGs, respectively. The expression levels of four heat shock proteins (HSP) were employed as a target gene to evaluate RGs efficiency for normalization. The results demonstrated an exponential difference in expression levels of the four HSP genes upon normalization of the data with the most stable and the least stable RGs. Our study, provides a convenient RGs for normalization of gene-expression of key metabolic pathways effected during freezing and thawing of spermatozoa of buffalo and other closely related bovines.

Selection of Suitable Reference Genes for Quantitative Real-Time PCR Normalization in Three Types of Rat Adipose Tissue

Quantitative real-time PCR (qRT-PCR) is the most classical technique in the field of gene expression study. This method requires an appropriate reference gene to normalize mRNA levels. In this study, the expression stability of four frequently-used reference genes in epididymal white adipose tissue (eWAT), inguinal beige adipose tissue (iBeAT) and brown adipose tissue (BAT) from obese and lean rats were evaluated by geNorm, NormFinder and BestKeeper. Based on the Minimum Information for Publication of Quantitative Real-Time PCR Experiments (MIQE) guidelines, the two most stable reference genes were recommended in each type of adipose tissue. Two target genes were applied to test the stability of the reference genes. The geNorm and NormFinder results revealed that GAPDH and 36B4 exhibited the highest expression stabilities in eWAT, while 36B4 and β-actin had the highest expression stabilities in iBeAT and BAT. According to the results of the BestKeeper analysis, 36B4 was the most stable gene in eWAT, iBeAT and BAT, in terms of the coefficient of variance. In terms of the coefficient of correlation, GAPDH, 36B4 and β-actin were the most stable genes in eWAT, iBeAT and BAT, respectively. Additionally, expected results and statistical significance were obtained using a combination of two suitable reference genes for data normalization. In conclusion, 36B4 and GAPDH, in combination, are the best reference genes for eWAT, while 36B4 and β-actin are two most suitable reference genes for both iBeAT and BAT. We recommend using these reference genes accordingly.

Sperm cryopreservation update: Cryodamage, markers, and factors affecting the sperm freezability in pigs

Cryopreservation is the most efficient method for long-term preservation of mammalian sperm. However, freeze-thawing procedures may strongly impair the sperm function and survival and thus decrease the reproductive performance. In addition, the sperm resilience to withstand cryopreservation, also known as freezability, presents a high individual variability. The present work summarizes the principles of cryoinjury and the relevance of permeating and nonpermeating cryoprotective agents. Descriptions about sperm cryodamage are mainly focused on boar sperm, but reference to other mammalian species is also made when relevant. Main cryoinjuries not only regard to sperm motility and membrane integrity, but also to the degradation effect exerted by freeze-thawing on other important components for sperm fertilizing ability, such as mRNAs. After delving into the main differences between good and poor freezability boar ejaculates, those protein markers predicting the sperm ability to sustain cryopreservation are also mentioned. Moreover, factors that may influence sperm freezability, such as season, diet, breed, or ejaculate fractions are discussed, together with the effects of different additives, like seminal plasma and antioxidants. After briefly referring to the effects of long-term sperm preservation in frozen state and the reproductive performance of frozen-thawed boar sperm, this work speculates with new research horizons on the preservation of boar sperm, such as vitrification and freeze-drying.

Modeling and optimization of cryopreservation

Modeling plays a critical role in understanding the biophysical processes behind cryopreservation. It facilitates understanding of the biophysical and some of the biochemical mechanisms of damage during all phases of cryopreservation including CPA equilibration, cooling, and warming. Modeling also provides a tool for optimization of cryopreservation protocols and has yielded a number of successes in this regard. While modern cryobiological modeling includes very detailed descriptions of the physical phenomena that occur during freezing, including ice growth kinetics and spatial gradients that define heat and mass transport models, here we reduce the complexity and approach only a small but classic subset of these problems. Namely, here we describe the process of building and using a mathematical model of a cell in suspension where spatial homogeneity is assumed for all quantities. We define the models that describe the critical cell quantities used to describe optimal and suboptimal protocols and then give an overview of classical methods of how to determine optimal protocols using these models.

Tissue-specific selection of optimal reference genes for expression analysis of anti-cancer drug-related genes in tumor samples using quantitative real-time RT-PCR

Gene transcription analysis in clinical tumor samples can help with diagnosis, prognosis, and treatment of cancers. We aimed to identify the optimal reference genes for reliable expression analysis in various tumor samples by quantitative real-time reverse transcription polymerase chain reaction (qRT-PCR). Using a one-step TaqMan-based qRT-PCR, 5 commonly used reference genes (ACTB, GAPDH, RPLPO, GUSB, and TFRC) and 10 anticancer drug-related genes (TYMS, RRM1, TUBB3, STMN1, TOP2A, EGFR, VEGFR2, HER2, ERCC1, and BRCA1) were analyzed in 327 tissue samples from lung, rectal, colon, gastric, esophageal, and breast tumors. According to the expression stability assessments obtained by using three programs (geNorm, NormFinder, and BestKeeper) and a comprehensive ranking method, the optimal reference genes for lung, gastric, esophageal, and breast tumors were RPLPO, GAPDH, ACTB, and ACTB, respectively. For rectal tumors, a combination of the 3 most stable genes (GUSB, ACTB, and RPLPO) was suitable for qRT-PCR, whereas for colon tumors, a combination of the 4 most stable genes (GAPDH, ACTB, GUSB, and RPLPO) was optimal for qRT-PCR. Based on the expression data of target genes normalized against selected reference genes, the principal component analysis revealed 4 expression patterns in 6 different tissues. One pattern was observed in gastric, rectal, and colon tumor tissues, which are gastrointestinal tumors. Expressions in the breast, lung, and esophageal tissues were separately represented as one pattern. Our results could facilitate the practice of personalized cancer medicine based on the gene expression profile of the patients.

Reliable reference gene selection for Cordyceps militaris gene expression studies under different developmental stages and media

Cordyceps militaris is considered a model organism for the study of Cordyceps species, which are highly prized in traditional Chinese medicine. Gene expression analysis has become more popular and important in studies of this fungus. Reference gene validation under different experimental conditions is crucial for RT-qPCR analysis. In this study, eight candidate reference genes, actin, cox5, gpd, rpb1, tef1, try, tub, and ubi, were selected and their expression stability was evaluated in C. militaris samples using four algorithms, genorm, normfinder, bestkeeper, and the comparative ∆Ct method. Three sets of samples, five different developmental stages cultured in wheat medium and pupae, and all the samples pool were included. The results showed that rpb1 was the best reference gene during all developmental stages examined, while the most common reference genes, actin and tub, were not suitable internal controls. Cox5 also performed poorly and was less stable in our analysis. The ranks of ubi and gpd were inconsistent in different sample sets by different methods. Our results provide guidelines for reference gene selection at different developmental stages and also represent a foundation for more accurate and widespread use of RT-qPCR in C. militaris gene expression analysis.