RNA-sequencing and bioinformatics analysis of long noncoding RNAs and mRNAs in the asthenozoospermia

Lü, Hui; Xu, Dongchuan; Wang, Ping; Sun, Wenye; Xue, Xinhuai; Hu, Yuxin; Xie, Chunli; Ma, Yanlin

doi:10.1042/bsr20194041

Cited by 21 publications

(34 citation statements)

References 39 publications

(44 reference statements)

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“…Human spermatogenesis is a carefully coordinated and precisely regulated biological process that includes rigorous regulation of gene expression at specific phases 3 . Noncoding RNAs such as circular RNAs (circRNAs), long noncoding RNAs (lncRNAs) and microRNAs (miRNAs) are critical regulators of gene expression in multiple phases of spermatogenesis [16][17][18] . piRNAs are a recently discovered class of small RNAs that are mainly expressed in germ cells.…”

Section: Discussionmentioning

confidence: 99%

Seminal Plasma piRNA Array Analysis Identifies Possible Biomarker piRNAs for the Diagnosis of Asthenozoospermia

He¹,

Wu²,

wu³

et al. 2021

Preprint

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Asthenozoospermia (AZS) is characterized by reduced sperm motility, and its pathogenesis remains poorly understood. Piwi-interacting RNAs (piRNAs) have been recognized to play important roles in spermatogenesis. However, little is known about the correlation of piRNAs with AZS. In this study, small RNA sequencing was performed on samples from AZS patients and fertile controls. Real-time quantitative reverse transcription polymerase chain reaction (qRT-PCR) was used to validate the small RNA-seq results. Bioinformatics analyses were performed to predict the functions of differentially expressed piRNAs. Logistic regression models were constructed, and receiver operating characteristic curve (ROC) analysis was used to evaluate their diagnostic performance. A total of 114 upregulated and 169 downregulated piRNAs were detected in AZS patients. GO and KEGG analyses showed that the differentially expressed piRNAs were mainly associated with transcription, signal transduction, cell differentiation, metal ion binding and focal adhesion. These results were verified by qRT-PCR of 8 selected piRNAs. Among the differentially expressed piRNAs tested, piR-hsa-32694, piR-hsa-26591, piR-hsa-18725, piR-hsa-18586 and piR-hsa-2912 produced qRT-PCR results consistent with the sequencing results in AZS compared with controls in the first cohort, whereas the other three genes did not show significant differences in expression. piR-hsa-32694, piR-hsa-26591, piR-hsa-18725, and piR-hsa-18586 were significantly upregulated in AZS. The diagnostic power of the four piRNAs was further analysed using ROC analysis; piR-hsa-26591 exhibited an area under the ROC curve (AUC) of 0.913 (95% CI: 0.795-0.994). Logistic regression modelling and subsequent ROC analysis indicated that the combination of the 4 piRNAs reached good diagnostic efficacy (AUC: 0.935).

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Section: Discussionmentioning

confidence: 99%

Seminal Plasma piRNA Array Analysis Identifies Possible Biomarker piRNAs for the Diagnosis of Asthenozoospermia

He¹,

Wu²,

wu³

et al. 2021

Preprint

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“…The predicted lncRNAs in the last step were screened according to lncRNAs associated with male infertility that have been identified by Joshi and Lu [32,33]. |Log FC| > 3 and p value < 0.05 were considered statistically significant to identify differentially expressed lncRNAs.…”

Section: Filtering the Lncrnas Associated With Male Infertilitymentioning

confidence: 99%

“…In addition, we identified the interactions between these miRNAs and differentially expressed lncRNAs in infertile men identified by Joshi and Lu [32,33]. In addition, we identified the interactions between these miRNAs and differentially expressed lncRNAs in infertile men identified by Joshi and Lu [32,33].…”

Section: Filtering the Lncrnas Associated With Male Infertilitymentioning

confidence: 99%

In Silico Identification of miRNA–lncRNA Interactions in Male Reproductive Disorder Associated with COVID-19 Infection

Sabetian

Castiglioni

Jahromi

et al. 2021

Cells

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Coronavirus disease 2019 (COVID-19), a global pandemic, is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Angiotensin-converting enzyme 2 (ACE2) is the receptor for SARS-CoV-2 and transmembrane serine protease 2 (TMPRSS2) facilitates ACE2-mediated virus entry. Moreover, the expression of ACE2 in the testes of infertile men is higher than normal, which indicates that infertile men may be susceptible to be infected and SARS-CoV-2 may cause reproductive disorder through the pathway induced by ACE2 and TMPRSS2. Little is known about the pathway regulation of ACE2 and TMPRSS2 expression in male reproductive disorder. Since the regulation of gene expression is mediated by microRNAs (miRNAs) and long non-coding RNAs (lncRNAs) at the post-transcriptional level, the aim of this study was to analyze the dysregulated miRNA–lncRNA interactions of ACE2 and TMPRSS2 in male reproductive disorder. Using bioinformatics analysis, we speculate that the predicted miRNAs including miR-125a-5p, miR-125b-5p, miR-574-5p, and miR-936 as regulators of ACE2 and miR-204-5p as a modulator of TMPRSS2 are associated with male infertility. The lncRNAs with a tissue-specific expression for testis including GRM7-AS3, ARHGAP26-AS1, BSN-AS1, KRBOX1-AS1, CACNA1C-IT3, AC012361.1, FGF14-IT1, AC012494.1, and GS1-24F4.2 were predicted. The identified miRNAs and lncRNAs are proposed as potential biomarkers to study the possible association between COVID-19 and male infertility. This study encourages further studies of miRNA–lncRNA interactions to explain the molecular mechanisms of male infertility in COVID-19 patients.

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“…Long non-coding RNAs (lncRNAs) are a class of RNAs with a length longer than 200 nucleotides, acting as gene expression regulators from both transcription and post-transcription aspects [ 76 , 77 ]. RNA-sequencing of seminal plasma exosomes revealed the existence of lncRNAs, some of which differentially expressed in asthenozoospermia compared with a normal group, indicating a pivotal role of lncRNAs as molecular mechanisms of asthenozoospermia [ 78 ]. In addition, the expression profile of extracellular vesicle lncRNAs in nonobstructive azoospermia (NOA) patients is significantly altered, of which a set of differentially expressed testis-specific lncRNAs displayed valuable prediction potential to assess the presence of testicular spermatozoa in NOA patients [ 79 ].…”

Section: Cell-free Nucleic Acids In Spmentioning

confidence: 99%

The Vehicle Determines the Destination: The Significance of Seminal Plasma Factors for Male Fertility

Wang

Yang

Ouyang

et al. 2020

IJMS

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Of all human infertility cases, up to 50% show contributing factors leading to defects in the male reproductive physiology. Seminal plasma (SP) is the biological fluid derived from the male accessory sex gland which carries spermatozoa passing throughout the male and female reproductive tract during ejaculation. It contains a complicated set of heterogeneous molecular structures, including proteins, cell-free nucleic acid (DNA, microRNA and LncRNA), and small-molecule metabolites as well as inorganic chemicals (ions). For a long time, the substantial significance of seminal plasma factors’ functions has been underestimated, which is restricted to spermatozoa transport and protection. Notably, significant advancements have been made in dissecting seminal plasma components, revealing new insights into multiple aspects of sperm function, as well as fertilization and pregnancy outcomes in recent years. In this review, we summarize the state-of-art discoveries regarding SP compositions and their implications in male fertility, particularly describing the novel understanding of seminal plasma components and related modifications using “omics” approaches and mainly focusing on proteome and RNA-seq data in the latest decade. Meanwhile, we highlighted the proposed mechanism of the regulation of SP molecules on immunomodulation in the female reproductive tract. Moreover, we also discussed the proteins investigated as non-invasive diagnosis biomarkers for male infertility in the clinic.

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RNA-sequencing and bioinformatics analysis of long noncoding RNAs and mRNAs in the asthenozoospermia

Cited by 21 publications

References 39 publications

Seminal Plasma piRNA Array Analysis Identifies Possible Biomarker piRNAs for the Diagnosis of Asthenozoospermia

Seminal Plasma piRNA Array Analysis Identifies Possible Biomarker piRNAs for the Diagnosis of Asthenozoospermia

In Silico Identification of miRNA–lncRNA Interactions in Male Reproductive Disorder Associated with COVID-19 Infection

The Vehicle Determines the Destination: The Significance of Seminal Plasma Factors for Male Fertility

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