Transcriptome-wide association study revealed two novel genes associated with nonobstructive azoospermia in a Chinese population

Deciphering the Molecular Characteristics of Human Idiopathic Nonobstructive Azoospermia from the Perspective of Germ Cells

Nonobstructive azoospermia (NOA) is one of the most important causes of male infertility, accounting for 10-15% of infertile men worldwide. Among these, more than 70% of cases are idiopathic NOA (iNOA), whose pathogenesis and molecular basis remain unknown. This work profiles 3696 human testicular single-cell transcriptomes from 17 iNOA patients, which are classified into four classes with different arrest periods and variable cell proportions based on the gene expression patterns and pathological features. Genes related to the cell cycle, energy production, and gamete generation show obvious abnormalities in iNOA germ cells. This work identifies several candidate causal genes for iNOA, including CD164, LELP1, and TEX38, which are significantly downregulated in iNOA germ cells. Notably, CD164 knockdown promotes apoptosis in spermatogonia. Cellular communications between spermatogonial stem cells and Sertoli cells are disturbed in iNOA patients. Moreover, BOD1L2, C1orf194, and KRTCAP2 are found to indicate testicular spermatogenic capacity in a variety of testicular diseases, such as Y-chromosome microdeletions and Klinefelter syndrome. In general, this study analyzes the pathogenesis of iNOA from the perspective of germ cell development, transcription factor (TF) regulatory networks, as well as germ cell and somatic cell interactions, which provides new ideas for clinical diagnosis.

Transcriptome-wide association study identifies novel genes associated with bone mineral density and lean body mass in children

OBJECTIVE

To identify novel candidate genes whose expression is associated with bone mineral density (BMD) and body lean mass (LM) in children.

METHODS

A tissue-specific transcriptome-wide association study (TWAS) was conducted utilizing a large-scale genome-wide association study (GWAS) dataset associated with BMD and LM and involving 10,414 participants. The measurement of BMD and LM phenotypes was made based on total-body dual-energy X-ray absorptiometry (TB-DXA) scans. TWAS was conducted by using FUSION software. Reference panels for muscle skeleton (MS), peripheral blood (NBL) and whole blood (YBL) were used for TWAS analysis. Functional enrichment and protein-protein interaction (PPI) analyses of the genes identified by TWAS were performed by using the online tool Metascape ( http://metascape.org ).

RESULTS

For BMD, we identified 174 genes with P < 0.05, such as IKZF1 (P = 1.46 × 10^-9) and CHKB (P = 8.31 × 10^-7). For LM, we identified 208 genes with P < 0.05, such as COPS5 (P = 3.03 × 10^-12) and MRPS33 (P = 5.45 × 10^-10). Gene ontology (GO) enrichment analysis of the BMD-associated genes revealed 200 GO terms, such as protein catabolic process (Log P = -5.09) and steroid hormone-mediated signaling pathway (Log P = -3.13). GO enrichment analysis of the LM-associated genes detected 287 GO terms, such as the apoptotic signaling pathway (Log P = -8.08) and lipid storage (Log P = -3.55).

CONCLUSION

This study identified several candidate genes for BMD and LM in children, providing novel clues to the genetic mechanisms underlying the development of childhood BMD and LM.

Transcriptome-wide association study identifies PSMB9 as a susceptibility gene for coal workers' pneumoconiosis

Coal workers' pneumoconiosis (CWP) is a type of typical occupational lung disease caused by prolonged inhalation of coal mine dust. The individuals' different genetic background may underlie their different susceptibility to develop pneumoconiosis, even under the same exposure level. This study aimed to identify susceptibility genes associated with CWP. Based on our previous genome-wide association study (GWAS, 202 CWP cases vs. 198 controls) and gene expression data obtained by analyzing human lungs and whole blood from the Genotype-Tissue Expression (GTEx) Portal, a transcriptome-wide association study (TWAS) was applied to identify CWP risk-related genes. Luciferase report gene assay, qRT-PCR, Western blot, immunofluorescence assay, and TUNEL assay were conducted to explore the potential role of the candidate gene in CWP. Proteasome 20S subunit beta 9 (PSMB9) was identified as a strong risk-related gene of CWP in both lungs and whole blood (Lungs: P_TWAS  = 4.22 × 10^-4 ; Whole blood: P_TWAS  = 2.11 × 10^-4 ). Single nucleotide polymorphisms (SNPs) rs2071480 and rs1351383, which locate in the promoter region and the first intron of the PSMB9 gene, were in high linkage disequilibrium (LD, r²  = 0.98) with the best GWAS SNP rs4713600 (G>T, OR = 0.55, 95% CI: 0.42-0.74, P = 6.86 × 10^-5 ). Both rs2071480 and rs1351383 significantly enhanced the transcriptional activity of PSMB9. Functional experiments revealed that silica exposure remarkably reduced the PSMB9 expression and caused cell apoptosis, while overexpression of PSMB9 markedly abolished silica-induced cell apoptosis. We here identified PSMB9 as a novel susceptibility gene for CWP and provided important insights into the further exploration of the CWP pathogenesis.

Human obstructive (postvasectomy) and nonobstructive azoospermia - Insights from scRNA-Seq and transcriptome analysis

A substantial number of male infertility is caused by azoospermia. However, the underlying etiology and the molecular basis remain largely unknown. Through single-cell (sc)RNA sequencing, we had analyzed testis biopsy samples from two patients with obstructive azoospermia (OA) and nonobstructive azoospermia (NOA). We found only somatic cells in the NOA samples and explored the transcriptional changes in Sertoli cells in response to a loss of interactions with germ cells. Moreover, we observed a germ cell population discrepancy between an OA (postvasectomy) patient and a healthy individual. We confirmed this observation in a secondary study with two datasets at GSM3526588 and GSE124263 for detailed analysis wherein the regulatory mechanisms at the transcriptional level were identified. These findings thus provide valuable information on human spermatogenesis, and we also identified insightful information for further research on reproduction-related diseases.

KRAB zinc finger protein ZNF676 controls the transcriptional influence of LTR12-related endogenous retrovirus sequences

BACKGROUND

Transposable element-embedded regulatory sequences (TEeRS) and their KRAB-containing zinc finger protein (KZFP) controllers are increasingly recognized as modulators of gene expression. We aim to characterize the contribution of this system to gene regulation in early human development and germ cells.

RESULTS

Here, after studying genes driven by the long terminal repeat (LTR) of endogenous retroviruses, we identify the ape-restricted ZNF676 as the sequence-specific repressor of a subset of contemporary LTR12 integrants responsible for a large fraction of transpochimeric gene transcripts (TcGTs) generated during human early embryogenesis. We go on to reveal that the binding of this KZFP correlates with the epigenetic marking of these TEeRS in the germline, and is crucial to the control of genes involved in ciliogenesis/flagellogenesis, a biological process that dates back to the last common ancestor of eukaryotes.

CONCLUSION

These results illustrate how KZFPs and their TE targets contribute to the evolutionary turnover of transcription networks and participate in the transgenerational inheritance of epigenetic traits.

Telomere Length and Male Fertility

Over the past decade, telomeres have attracted increasing attention due to the role they play in human fertility. However, conflicting results have been reported on the possible association between sperm telomere length (STL) and leukocyte telomere length (LTL) and the quality of the sperm parameters. The aim of this study was to run a comprehensive study to investigate the role of STL and LTL in male spermatogenesis and infertility. Moreover, the association between the sperm parameters and 11 candidate single nucleotide polymorphisms (SNPs), identified in the literature for their association with telomere length (TL), was investigated. We observed no associations between sperm parameters and STL nor LTL. For the individual SNPs, we observed five statistically significant associations with sperm parameters: considering a p < 0.05. Namely, ACYP2˗rs11125529 and decreased sperm motility (p = 0.03); PXK˗rs6772228 with a lower sperm count (p = 0.02); NAF1˗rs7675998 with increased probability of having abnormal acrosomes (p = 0.03) and abnormal flagellum (p = 0.04); ZNF208˗rs8105767 and reduction of sperms with normal heads (p = 0.009). This study suggests a moderate involvement of telomere length in male fertility; however, in our analyses four SNPs were weakly associated with sperm variables, suggesting the SNPs to be pleiotropic and involved in other regulatory mechanisms independent of telomere homeostasis, but involved in the spermatogenic process.

Transcriptome-wide association study identifies susceptibility genes for rheumatoid arthritis

Objective

To identify rheumatoid arthritis (RA)-associated susceptibility genes and pathways through integrating genome-wide association study (GWAS) and gene expression profile data.

Methods

A transcriptome-wide association study (TWAS) was conducted by the FUSION software for RA considering EBV-transformed lymphocytes (EL), transformed fibroblasts (TF), peripheral blood (NBL), and whole blood (YBL). GWAS summary data was driven from a large-scale GWAS, involving 5539 autoantibody-positive RA patients and 20,169 controls. The TWAS-identified genes were further validated using the mRNA expression profiles and made a functional exploration.

Results

TWAS identified 692 genes with P_TWAS values < 0.05 for RA. CRIPAK (P^EL = 0.01293, P^TF = 0.00038, P^NBL = 0.02839, P^YBL = 0.0978), MUT (P^EL = 0.00377, P^TF = 0.00076, P^NBL = 0.00778, P^YBL = 0.00096), FOXRED1 (P^EL = 0.03834, P^TF = 0.01120, P^NBL = 0.01280, P^YBL = 0.00583), and EBPL (P^EL = 0.00806, P^TF = 0.03761, P^NBL = 0.03540, P^YBL = 0.04254) were collectively expressed in all the four tissues/cells. Eighteen genes, including ANXA5, AP4B1, ATIC (P_TWAS = 0.0113, downregulated expression), C12orf65, CMAH, PDHB, RUNX3 (P_TWAS = 0.0346, downregulated expression), SBF1, SH2B3, STK38, TMEM43, XPNPEP1, KIAA1530, NUFIP2, PPP2R3C, RAB24, STX6, and TLR5 (P_TWAS = 0.04665, upregulated expression), were validated with integrative analysis of TWAS and mRNA expression profiles. TWAS-identified genes functionally involved in endoplasmic reticulum organization, regulation of cytokine production, TNF signaling pathway, immune response-regulating signaling pathway, regulation of autophagy, etc.

Conclusion

We identified multiple candidate genes and pathways, providing novel clues for the genetic mechanism of RA.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13075-021-02419-9.

Quantile regression for challenging cases of eQTL mapping

Mapping of expression quantitative trait loci (eQTLs) facilitates interpretation of the regulatory path from genetic variants to their associated disease or traits. High-throughput sequencing of RNA (RNA-seq) has expedited the exploration of these regulatory variants. However, eQTL mapping is usually confronted with the analysis challenges caused by overdispersion and excessive dropouts in RNA-seq. The heavy-tailed distribution of gene expression violates the assumption of Gaussian distributed errors in linear regression for eQTL detection, which results in increased Type I or Type II errors. Applying rank-based inverse normal transformation (INT) can make the expression values more normally distributed. However, INT causes information loss and leads to uninterpretable effect size estimation. After comprehensive examination of the impact from overdispersion and excessive dropouts, we propose to apply a robust model, quantile regression, to map eQTLs for genes with high degree of overdispersion or large number of dropouts. Simulation studies show that quantile regression has the desired robustness to outliers and dropouts, and it significantly improves eQTL mapping. From a real data analysis, the most significant eQTL discoveries differ between quantile regression and the conventional linear model. Such discrepancy becomes more prominent when the dropout effect or the overdispersion effect is large. All the results suggest that quantile regression provides more reliable and accurate eQTL mapping than conventional linear models. It deserves more attention for the large-scale eQTL mapping.

Integrative Genomic Enrichment Analysis Identified the Brain Regions and Development Stages Related to Anorexia Nervosa and Obsessive-Compulsive Disorder

Our aim is to explore the spatial and temporal features of anorexia nervosa (AN) and obsessive-compulsive disorder (OCD) considering different brain regions and development stages. The gene sets related to 16 brain regions and nine development stages were obtained from a brain spatial and temporal transcriptomic dataset. Using the genome-wide association study data, transcriptome-wide association study (TWAS) was conducted to identify the genes whose imputed expressions were associated with AN and OCD, respectively. The mRNA expression profiles were analyzed by GEO2R to obtain differentially expressed genes. Gene set enrichment analysis was conducted to detect the spatial and temporal features related to AN and OCD using the TWAS and mRNA expression analysis results. We observed multiple common association signals shared by TWAS and mRNA expression analysis of AN, such as the primary auditory cortex vs. cerebellar cortex in fetal development and earlier vs. later fetal development in the somatosensory cortex. For OCD, we also detected multiple common association signals, such as medial prefrontal cortex vs. amygdala in adulthood and fetal development vs. infancy in mediodorsal nucleus of thalamus. Our study provides novel clues for describing the spatial and temporal features of brain development in the pathogenesis of AN and OCD.

Evaluating the Genetic Correlations Between Left-Handedness and Mental Disorder Using Linkage Disequilibrium Score Regression and Transcriptome-Wide Association Study

Handedness is an elusive human behavioral phenotypes and the genetic basis of it remains unclear until now. The aim of this study is to evaluate the genetic correlations between left-handedness and multiple mental disorders, and explored the genes detected by genetic correlations. In this study, linkage disequilibrium score regression (LDSC) analysis was conducted to evaluate the genetic correlations between left-handedness and multiple mental disorders. The significant genetic correlation was only observed between left-handedness and schizophrenia (SCZ). For the observed genetic correlation, transcriptome-wide association study (TWAS) was performed to identify the genes associated with left-handedness and SCZ, including brain RNA-seq (CBR) and brain RNA-seq splicing (CBRS). We detected several common genes associated with both left-handedness and SCZ, such as YWHAH, MAPT and ANO10. The common genes shared by left-handedness and SCZ were subjected to gene set enrichment analysis. Our study provides a novel clue for understanding the genetic correlation between left-handedness and SCZ.

Unraveling epigenomic abnormality in azoospermic human males by WGBS, RNA-Seq, and transcriptome profiling analyses

PURPOSE

To determine associations between genomic DNA methylation in testicular cells and azoospermia in human males.

METHODS

This was a case-control study investigating the differences and conservations in DNA methylation, genome-wide DNA methylation, and bulk RNA-Seq for transcriptome profiling using testicular biopsy tissues from NOA and OA patients. Differential methylation and different conserved methylation regions associated with azoospermia were identified by comparing genomic DNA methylation of testicular seminiferous cells derived from NOA and OA patients.

RESULTS

The genome methylation modification of testicular cells from NOA patients was disordered, and the reproductive-related gene expression was significantly different.

CONCLUSION

Our findings not only provide valuable knowledge of human spermatogenesis but also paved the way for the identification of genes/proteins involved in male germ cell development. The approach presented in this report provides a powerful tool to identify responsible biomolecules, and/or cellular changes (e.g., epigenetic abnormality) that induce male reproductive dysfunction such as OA and NOA.

Genetic Landscape of Nonobstructive Azoospermia and New Perspectives for the Clinic

Nonobstructive azoospermia (NOA) represents the most severe expression of male infertility, involving around 1% of the male population and 10% of infertile men. This condition is characterised by the inability of the testis to produce sperm cells, and it is considered to have an important genetic component. During the last two decades, different genetic anomalies, including microdeletions of the Y chromosome, karyotype defects, and missense mutations in genes involved in the reproductive function, have been described as the primary cause of NOA in many infertile men. However, these alterations only explain around 25% of azoospermic cases, with the remaining patients showing an idiopathic origin. Recent studies clearly suggest that the so-called idiopathic NOA has a complex aetiology with a polygenic inheritance, which may alter the spermatogenic process. Although we are far from a complete understanding of the molecular mechanisms underlying NOA, the use of the new technologies for genetic analysis has enabled a considerable increase in knowledge during the last years. In this review, we will provide a comprehensive and updated overview of the genetic basis of NOA, with a special focus on the possible application of the recent insights in clinical practice.

An integrative analysis of transcriptome-wide association study and mRNA expression profile identified candidate genes for attention-deficit/hyperactivity disorder

BACKGROUND

Attention-deficit/hyperactivity disorder (ADHD) is a common neurodevelopmental disorder, but the genetic mechanism of ADHD remains elusive now.

METHODS

Tissue specific transcriptome-wide association study (TWAS) of ADHD was performed by FUSION utilizing a genome-wide association study (GWAS) dataset of ADHD (including 20,183 ADHD cases and 35,191 healthy controls) and gene expression reference from brain and blood. Furthermore, the genes identified by TWAS were compared with the differently expressed genes detected by mRNA expression profiles of ADHD rat model and autism spectrum disorders (ASD) patients. Functional enrichment and annotation analysis of the identified genes were performed by DAVID and FUMAGWAS tool.

RESULTS

For brain tissue, TWAS identified 148 genes with P value < 0.05, such as TDO2 (P_TWAS=4.01×10^-2), CHD1L (P_TWAS=9.64×10^-3) and KIAA0319L (P_TWAS=4.05×10^-4). Further 11 common genes were examined in the mRNA expression datasets, such as ACSM5 (P_TWAS=3.62×10^-2, P_mRNA=0.005), CCDC24 (P_TWAS=1.49×10^-2, P_mRNA=2.35×10^-3) and MVP (P_TWAS=5.55×10^-3, P_mRNA=5.40×10^-3). Pathway enrichment analysis of the genes identified by TWAS detected 3 pathways for ADHD, including Other glycan degradation (P value=0.021), Viral myocarditis (P value=0.034) and Endocytosis (P value=0.041).

CONCLUSIONS

Through integrating GWAS and mRNA expression data, we identified a group of ADHD-associated genes and pathways, providing novel clues for understanding the genetic mechanism of ADHD.