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Infertility Network and Hub Genes for Nonobstructive Azoospermia Utilizing Integrative Analysis

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Infertility Network and Hub Genes for Nonobstructive Azoospermia Utilizing Integrative Analysis www.aging-us.com AGING 2021, Vol. 13, No. 5 Research Paper Infertility network and hub genes for nonobstructive azoospermia utilizing integrative analysis Baoquan Han1,*, Zihui Yan2,*, Shuai Yu1,*, Wei Ge2, Yaqi Li3, Yan Wang1, Bo Yang4, Wei Shen1,2, Hui Jiang5, Zhongyi Sun1 1Department of Urology, Peking University Shenzhen Hospital, Shenzhen Peking University, The Hong Kong University of Science and Technology Medical Center, Shenzhen 518036, China 2College of Life Sciences, Institute of Reproductive Sciences, Qingdao Agricultural University, Qingdao 266109, China 3Department of Urology, Zaozhuang Hospital of Zaozhuang Mining Group, Zaozhuang 277100, China 4Guangdong and Shenzhen Key Laboratory of Male Reproductive Medicine and Genetics, Institute of Urology, Peking University Shenzhen Hospital, Shenzhen PKU-HKUST Medical Center, Shenzhen 518036, China 5Department of Urology, Department of Andrology, Department of Human Sperm Bank, Peking University Third Hospital, Beijing 100191, China *Equal contribution Correspondence to: Zhongyi Sun, Wei Shen, Hui Jiang; email: [email protected], https://orcid.org/0000-0002- 2013-7827; [email protected]; [email protected] Keywords: nonobstructive azoospermia, integrative analysis, scRNA-seq, male infertility, biomarkers Received: November 5, 2020 Accepted: December 29, 2020 Published: February 17, 2021 Copyright: © 2021 Han et al. This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. ABSTRACT Non-obstructive azoospermia (NOA) is the most severe form of male infertility owing to the absence of sperm during ejaculation as a result of failed spermatogenesis. The molecular mechanisms of NOA have not been well studied. Here, we revealed the dysregulated differentially expressed genes in NOA and related signaling pathways or biological processes. Cluster features of biological processes include spermatogenesis, fertilization, cilium movement, penetration of zona pellucida, sperm chromatin condensation, and being significantly enriched metabolic pathways in proximal tubule bicarbonate reclamation, aldosterone synthesis and secretion, glycolysis and glycogenesis pathways in NOA using Gene Ontology analysis and pathway enrichment analysis. The NOA gene co-expression network was constructed by weighted gene co-expression network analysis to identify the hub genes (CHD5 and SPTBN2). In addition, we used another Gene Expression Omnibus dataset (GSE45887) to validate these hub genes. Furthermore, we used the Seurat package to classify testicular tissue cells from NOA patients and to characterize the differential expression of hub genes in different cell types from different adult males based on the scRNA-seq dataset (GSE106487). These results provide new insights into the pathogenesis of NOA. Of particular note, CHD5 and SPTBN2 may be potential biomarkers for the diagnosis and treatment of NOA. INTRODUCTION is multifactorial and accounts for approximately half of all infertility cases [2]. However, the genetic basis Infertility is a serious health problem that may be of male infertility has not been extensively studied associated with aging [1]. It is one of the most [3]. A significant portion of male infertility is commonly diagnosed conditions associated with associated with idiopathic azoospermia, usually either reproductive health or male-related problems; it manifested as non-obstructive azoospermia (NOA), www.aging-us.com 7052 AGING which affects about 1% of all adult males [4]. that has been extensively developed and applied to Currently, NOA remains the most clinically severe biological and pathological research [20–22]. It can be form of male infertility due to the absence of sperm in used to study the functional status of individual cells, the ejaculate as a result of failed spermatogenesis [5]. to infer and discover new cell types in an unbiased Several studies have reported the involvement of manner, and can also be used to construct genetic factors in the occurrence of NOA, such as differentiation trajectories for cell lineages, as well as defective chromosome number, microdeletions of the molecular maps of cell developmental profiles. Since Y-chromosome, and autosomal mutations or its development, single-cell transcriptome sequencing polymorphisms in multiple biological pathways [6, 7]. has been widely used in cancer and bio-developmental While there has been some progress regarding the fields with excellent results. Although two studies etiology of the disease (involving either intrinsic performed single-cell transcriptome sequencing on testicular impairment or insufficient gonadotropin testicular tissue from NOA patients [16, 17], no study production), the molecular defects responsible for has yet applied these open resources to an integrated NOA that are associated with male sterility are largely analysis of NOA; this omission lays the foundation unknown. for our study. An adequate diagnosis of NOA is currently far from In the current study, WGCNA and scRNA-seq were satisfactory, especially in terms of identifying combined to analyze hub gene profiling of NOA molecular causes, which can be complex [8]. samples extracted from the Sequence Read Archive Therefore, the identification of potential biomarkers (SRA) database, while two additional GEO databases involved in NOA appears to be crucial. With the rise were used to validate the results. After integrative of high-throughput sequencing technology, several analysis, two hub genes, CHD5 and SPTBN2, were key NOA-related genes have been identified. In 2008, screened in the NOA group of patients. The results of using genome-wide gene expression analysis, this study will be informative for basic research on Hiroyuki et al. identified ART3 as a susceptibility NOA and provide a theoretical basis for the clinical gene for NOA [9]. Subsequent study found that diagnosis and treatment of NOA. deletion or under-expression of the Y-chromosome genes CDY2 and HSFY is associated with the blocking RESULTS of sperm maturation in American men with NOA [10]. More recent studies have indicated that there are Overview of the transcriptomes of NOA and GO several potential NOA-related biomarkers (such as enrichment analysis IL1-RA, AKAP4, UBQLN3, CAPN11, GGN, SPACA4, SPATA3, and FAM71F1) [8, 11]. Moreover, other In order to elucidate the molecular pathogenesis of researchers have identified ENTPD6 and STX2 as NOA, we firstly screened the DEGs between normal potential NOA pathogenic genes [12, 13]. testicular biopsies and NOA cases using the limma package and then built the volcano map and heat map Currently, except for traditional microarray analysis, using the ggplot2 and pheatmap packages. The heat several studies have used weighted gene co- map of all mRNAs is shown in Supplementary Figure expression network analysis (WGCNA) analysis [14], 1A, where significant differences in gene expression whole-exome sequencing [15], and single-cell between the two groups can be seen. Subsequently, the transcriptome sequencing (scRNA-seq) [16, 17] to volcano map was constructed using differentially screen for novel infertility causative genes in NOA. expressed mRNAs (|log2fold change|≥2, p-value < 0.05) The resulting data provide a basis for further studies as shown in Supplementary Figure 1B. In total, 214 on the pathogenesis of NOA, but these existing mRNAs displayed the differential expressions in NOA, studies do not integrate multiple sequencing data, including two upregulated and 212 downregulated which makes the results obtained by a single mRNAs (|log2fold change|≥2, p-value < 0.05) analytical approach less convincing. Correlation (Supplementary Table 1). In addition, from the heat networks are increasingly being used in bio- map and the cluster dendrogram (Supplementary Figure informatics applications, especially using WGCNA. 3A), it can be seen that the normal testicular biopsies This technique has been widely used to explore the and NOA cases were allocated into two distinct main large and complex relationships between microarray clusters (control and NOA). and RNA sequence data, which provides a convenient and effective solution for screening potential After Metascape analysis, the Top 10 clusters with their biomarkers for clinical prognosis and therapy [18, representative enriched terms are shown in Figure 1A 19]. Single-cell transcriptome sequencing is an and Supplementary Table 2. GO analysis results were optimized second-generation sequencing technology enriched in Biological Process, Cellular Components, www.aging-us.com 7053 AGING Figure 1. GO enrichment and Gene Set Enrichment Analysis of NOA, and validation of hub genes. (A) Top 10 clusters with their representative enriched term based on GO enrichment analysis of DEGs. (B) NOA samples were correlated positively with gene signatures www.aging-us.com 7054 AGING related to Steroid Hormone Biosynthesis and Ubiquitin Mediated Proteolysis pathways. (C) NOA samples were correlated negatively with gene signatures related to Glycerophospholipid Metabolism and Proximal Tubule Bicarbonate Reclamation pathway. (D) The normalized expression validation of hub genes using the GSE45887 dataset. The Y‐axis expressions were normalized by log2 (TPM/10+1). (E) The normalized expression validation of hub genes using the GSE106487 dataset. The Y‐axis expressions were normalized by log2 (TPM/10+1). and Molecular
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