CN113584042A - ODNAH gene new mutation and application thereof in severe hypospadias detection - Google Patents
ODNAH gene new mutation and application thereof in severe hypospadias detection Download PDFInfo
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Abstract
The application provides a mutant DNAH8 gene, the nucleotide of which at position 4690 of NM-001206927.1 is T, and also provides a corresponding mutant protein, a kit and a corresponding detection method. The newly discovered mutations of the application provide new tools and ways for genetic detection of hypospadias and male infertility.
Description
Technical Field
The application belongs to the field of urinary system diseases and the field of molecular biology, and particularly provides a mutant DNAH8 gene, wherein the nucleotide of the mutant DNAH8 gene at 4690 position of NM-001206927.1 is T, and the application also provides a corresponding mutant protein, a kit and a corresponding detection method.
Background
Hypospadias is one of the most common congenital diseases in the male reproductive system. The incidence of the disease is about two thousandths, and recent studies have shown an increasing incidence during the years 1980 and 2010. Hypospadias is a complex congenital disease caused by the interaction of a variety of genetic and environmental factors, with a heritability of about 57% -77%. Low paternal fertility is one of the many risk factors that cause hypospadias, and double-blind case-control studies have shown that 24% of low paternal fertility may cause hypospadias. However, the genetic cause of hypospadias, particularly the genetic contribution associated with low fertility, remains unclear.
The development of the penis is regulated by the Androgen Receptor (AR) and estrogen receptor alpha (ESR 1). Recent studies have further demonstrated that the AR and ESR1 signaling pathways play an important role in the development of light and severe hypospadias. The etiology of the hypospadias relates to a plurality of signal pathways and a plurality of genes, including a WNT signal pathway, a BMP signal pathway, an FGF signal pathway, an HH (Hedgehog) signal pathway and a Homeobox gene. In addition, previous studies have also shown that 79% (22/28) of the known genes associated with the risk of hypospadias interact directly or indirectly with AR and ESR 1. Risk polymorphic sites associated with hypospadias are also found in the AR, ESR1, ESR2, DGKK, SRD5a2, CYP1a1, SD17B3, FGF8, FGFR2, HMID1, ATF3, MAMLD1, GSTM1, and GSTT110 genes. In addition, about 24 susceptible sites were found in two large Genome Wide Association Studies (GWAS) cohorts directed to hypospadias. Subsequently, Kojima et al also verified a risk site for the HAAO and IRX6 genes in Japanese population in relation to hypospadias. Chen et al found that rs11170516 site in SP1/SP7 was associated with moderate and severe hypospadias. However, GWASs only account for 9.4% of the genetic variance, and the genetic cause of hypospadias is still unknown.
For human hypospadias studies, most genetic studies are either based on GWAS studies or search for key genes in a broad sub-urethral fissure patient cohort. Recently, the Kalfa team attempted to solve the problem of "genetic deletion" of hypospadia by using Next Generation Sequencing (NGS) technology including 336 candidate genes. Although this study is valuable, these variations still result in genetic loss of the hypospadia and do not prove pathogenic. Previous studies have shown that rare, destructive variations in protein function [ including loss of function variations (LoF) and missense variations predicted by software to be detrimental ] can significantly alter protein sequences, can account for "genetic deletions" resulting from GWAS analysis, and are used to identify the cause of birth defects diseases, such as neural tube defects and congenital heart disease. These studies suggest that this rare, destructive variation may be the cause of human hypospadias; however, the data relating to hypospadias is quite lacking. The genetic cause of hypospadias also requires extensive genetic research and statistical evidence.
Disclosure of Invention
Unlike previous hypospadias studies focused primarily on common variations and candidate genes, we performed whole exome sequencing and RNA sequencing analysis on large queues of hypospadias. We identified a significant enrichment of the extra-dynamic arm heavy chain (ODNAH) genes (including DNAH5, DNAH8, DNAH9, DNAH11, and DNAH17) in severe hypospadia and found a new DNAH8 mutation. This study complemented the known common hypospadias risk-related variations and indicated the role of rare protein destructive variations in the development of the hypospadias.
In one aspect, the present application provides a mutant DNAH8 gene, the nucleotide at position 4690 of NM _001206927.1 being T.
In another aspect, the present application provides a mutant DNAH8 protein having the amino acid Ser at position 1564.
In another aspect, the present application provides use of a reagent for detecting the mutated DNAH8 gene or the mutated DNAH8 protein as described above in preparing a kit for predicting a risk of a hypospadias.
Further, the hypospadias are severe hypospadias.
Further, the reagent is a PCR reagent or an ELISA reagent.
In another aspect, the present application provides a kit for predicting the risk of a hypospadias, comprising reagents for detecting the mutated DNAH8 gene or the mutated DNAH8 protein described above.
Further, the hypospadias are severe hypospadias.
Further, the reagent is a PCR reagent or an ELISA reagent.
In another aspect, the present application provides a non-diagnostic method of detecting the above-described mutated DNAH8 gene or mutated DNAH8 protein, wherein the above-described kit is used.
The kits of the present application may be used for diagnostic or non-diagnostic uses including, but not limited to, scientific research, macro-survey of population, and the like.
Reagents and methods for detecting mutations those skilled in the art can select reagents, kits and methods existing and under development in the art according to the general knowledge of molecular biology; such reagents, kits and methods include, but are not limited to, detection reagents, kits and methods based on various sequencing, hybridization, PCR, chromatography, antigen/antibody interactions, including, but not limited to, primers, probes, chips, ELISA reagents, and the like.
Drawings
FIG. 1 is a graph of sequencing depth, coverage, and average number of causative mutations carried per hypospadias individual;
FIG. 2 shows the relevant sites verified with a one-generation sequencing screen.
FIG. 3 shows a network regulatory analysis of known hypospadias risk-associated genes in the group of individuals with AR, DNAH8, and DNAH17 mutations. (A) Unsupervised hierarchical cluster analysis of known risk genes in AR, DNAH8, and DNAH17 mutant individuals. (B) Networks of protein-protein interactions (PPIs) mediated by AR and, in AR mutant individuals, direct or indirect interactions based on the PPIs of the AR network. (C) Protein-protein interaction (PPIs) networks mediated by DNAH8 and, in DNAH8 mutant individuals, direct or indirect interactions of DNAH 8-network PPIs. (D) Protein-protein interaction (PPIs) networks mediated by DNAH17 and, in DNAH17 mutant individuals, direct or indirect interactions of DNAH 17-network PPIs.
FIG. 4 shows expression analysis of ODNAH gene in different tissues and phylogenetic analysis of hypospadias. (A) DNAH5, DNAH8, DNAH9, DNAH11 and DNAH17 were highly expressed in testis tissue. (B) A pedigree comprising genetic variation of DNAH 8.
Detailed Description
Research sample
We included 194 patients who underwent severe hypospadias repair surgery at the shanghai children hospital at shanghai university of transportation in 2011 to 2019 (table S1). We performed Whole Exome Sequencing (WES) on 200 samples (including three trios) and RNA sequencing on 18 samples. In the RNA sequencing analysis, 18 children who received continuous circumcision due to phimosis (control group; n ═ 6; mean age 2.84 ± 0.22 years) or samples repaired by hypospadias were included in the study (including 4 samples of AR-mutated hypospadias, 4 samples of DNAH8 mutations, and 4 samples of DNAH17 mutations).
All patients with hypospadias were diagnosed by urology surgery. Patients with congenital penile curvature without hypospadias were excluded from the study. Each patient was informed of the purpose of the study and had a written consent form from all participants or their parents/legal guardians.
TABLE 1 background characteristics of hypospadias samples
age at diagnosis of case or control enrollment; b severity of hypospadias divided into mild (glandular), moderate (penile) or severe (scrotum or perineum) according to abnormal position of urethral meatus
Example 1 analysis of genetic variation and functional analysis
Systematic genetic variation analysis was performed on the 191 hypospadia populations and the 208 rare variations of the chinese han-nationality population in the thousand human genome (1000 genes Project,1KGP) in this study. We performed analysis and functional annotation of the whole exome using our earlier method (Chen, Z.et al.Threshold for neural tube defect lost-of-function variants. cell Res 28,1039-1041 (2018)). The method further classifies coding variation into loss-of-function (LoF), missense, and the like. Missense mutations in the results were further predicted by SIFT (scanning endogenous From Tolerant) and PolyPhon-2 (Polymorphism phosphorylation version 2) software, and mutations predicted to be deleterious by both software were annotated as deleterious missense mutations (D-mis). The predicted genetic variation was also screened for allele frequency (MAF). For the hypospadia or control group, we filtered out genetic loci with MAF > 1%. Rare functional disruptive variants with a MAF < 0.1% (LoF and D-mis) were further selected as candidate genetic variants in the 1KGP and ExAC databases (http:// ExAC. Broadaptitum. org). In the results, we also performed Sanger sequencing validation on 27 DNAH8, DNAH9, and DNAH17 gene mutations that we identified and predicted to be potentially destructive. In addition, we also identified DNAH gene family members (http:// www.treefam.org/family/TF316836) in the EMBL-EBI phylogenetic database, which include DNAH1, DNAH2, DNAH3, DNAH5, DNAH6, DNAH7, DNAH8, DNAH9, DNAH10, DNAH11, DNAH12, DNAH14, and DNAH 17.
Example 2 RNA sequencing and Gene expression analysis
RNA was extracted from human tissues using TRIzol reagent and paired-end sequencing using Illumina NovaSeq 6000 platform. The original fastq file for RNA-Seq was generated by Illumina NovaSeq 6000 sequencer. Then using Skewer software21Removing the linker contaminating sequences as well as the low quality sequences. The results obtained were further evaluated for quality using the FastQC tool (www.bioinformatics.babraham.ac.uk/projects/FastQC /). Then use STAR22The trimmed clean reads were mapped to the human reference genome (GRCh 38). Then, through StringTie software23Transcriptomes were assembled on the basis of the Ensembl database. Differentially expressed genes were evaluated using the FPKM (fragments Per Kibase of transcript Per Million mapped reads) method. Differential expression analysis of genes, p, Using the two-tailed Student's t test<0.05 is the significance level. Using the heatmap function25Visual analysis of the differential genes was performed. GeneSense and STRING (https:// www.string-db.org) were used to identify interactions (PPIs) between proteins encoded by human genes associated with the risk of developing hypospadias. All statistical analyses were performed using R software (http:// www.R-project. org). We also analyzed the expression of the relevant genes in 27 different tissues of 95 individuals, and this data was obtained from Human Protein Atlas (www.proteinatlas.org) (BioProject: PRJEB 4337).
Example 3 results and analysis
1 ODNAH gene is obviously enriched in hypospadias
We performed Whole Exome Sequencing (WES) on 191 severe hypospadias individuals using Illumina sequencing platform, with an average depth of 142 ×, coverage of target nucleotides of 99.9% (fig. 1). The mean number of rare pathogenic mutations per hypospadias individual (fig. 1) was close to the number of pathogenic mutations per individual at the previous time based on the uk biosystems.
Based on the sequencing data, we further analyzed the association of rare functionally disruptive mutations at the gene level with the risk of severe hypospadias using a burden test. We found for the first time that rare, functionally disruptive mutations were significantly enriched in the exokinetin arm heavy chain (ODNAH) genes, including DNAH5, DNAH8, DNAH9, DNAH11, and DNAH 17. FIG. 2, Table 2 and Table 3 are the relevant sites and primer information verified by one generation sequencing screen for random screening. After removing the false positive sites, there were 51 mutation sites in total (table 4), and based on the burden test analysis of the binomial distribution, it was found that the significant level of the rare functional destructive variation of the ODNAH gene in the severe hypospadias reached p ═ 4.8 × 10-17Level of (d) (table 1). Among them, DNAH5, DNAH9 and DNAH11 were considered as the motile cilia-specific expression genes29These genes were significantly enriched for rare pathogenic variants (table 5). In addition to the ODNAH gene, we further investigated genetic variations of the intein dynein arm heavy chain (IDNAH) gene from the DNAH family (TF316836) (table 6). Among them, DNAH1 and DNAH2 were significantly enriched for rare functional disruptive variants (p)<0.01), whereas DNAH3, DNAH6, DNAH7, DNAH10, and DNAH12 did not find significant enrichment of rare functional disruptive variations. Rare functional disruptive variations in the ODNAH gene were significantly enriched in the severe hypospadias group compared to the control group. These data show rare ODNAH genetic variation, accounting for 22.5% of cases with (43/191) sporadic hypospadias, and are expected to be the major genetic cause of hypospadias.
Table 2 sites based in part on one generation sequencing validation
TABLE 3 first generation sequencing-based verification of site PCR primer information
TABLE 4 information on 51-site mutations in the ODNAH family
TABLE 5 enrichment analysis based on rare pathogenic mutations of ODNAH gene in severe hypospadias and control group
aThe P value calculation is based on a binomial distribution.
TABLE 6 enrichment analysis based on rare pathogenic mutations of the IDNAH gene in severe hypospadias and controls
aP value calculation is based on binomial distribution
Abnormal network regulation due to genetic variation of AR and ODNAH genes
Rare functionally disruptive mutations often interfere with the transcription of their associated genes and lead to aberrant expression of the protein, which in turn leads to loss of protein function or gain of a functional effect. To explore the AR and ODNAH genes and understand how rare, functionally disruptive changes lead to hypospadias, we performed transcriptome sequencing analysis on 12 of 191 patients (4 AR mutations, 4 DNAH8 mutations, and 4 DNAH7 mutations) and 6 controls. Unsupervised hierarchical cluster analysis showed that 15 of the 30 hypospadias risk-associated genes previously reported were significantly different between the hypospadias and the control group (fig. 3A). We then performed network interaction analysis to understand the effect of rare variations in AR, DNAH8, and DNAH17 on signal pathway regulation. In AR mutant individuals, DNAH17, SHH genes (GLI1 and GLI2), estrogen regulatory gene ATF3, and gonadal development-associated gene CHD7 were significantly differentially expressed (p <0.05) compared to the control group (fig. 3B). We studied the protein-protein network interactions (PPIs) relationship between AR genes and known hypospadias risk-associated genes, and found that rare destructive variations in AR might directly alter the expression of GLI1, GLI2, ATF3 and CHD7, and indirectly affect the expression of DNAH17 (fig. 3B). Compared with the control group, the DNAH8 mutant individuals were significantly differentially expressed (p <0.05) in AR, DNAH17, ATF3, CHD7, and homeobox genes (HOXA4 and HOXB6) (fig. 3C). The PPI network interacting with DNAH17 showed that expression of AR, DNAH17, ATF3, and CHD7 may be directly affected by DNAH8, while HOXA4 and HOXB6 may be indirectly affected by DNAH8 (fig. 3C). In DNAH17 mutant individuals, AR, SRD5a2, GLI1, GLI2, GLI3, BMP4, ATF3, CHD7, HSD17B3, HOXA4, HOXB6, MAMLD1, COL6A3 were all significantly differentially expressed in severe sub-urethral fissure (p <0.05) (fig. 3D). The PPI network consisting of DNAH17 suggests that all genes may be indirectly affected by pathogenic variations in DNAH17 (fig. 3D). In addition, AR, ATF3, CHD7 and DNAH17 are the most connected key nodes in the three networks, and may be closely related to the occurrence and development of hypospadias.
Possible regulatory mechanisms and genetic patterns mediated by the 3 ODNAH gene
The abnormal expression pattern of the genes indicates that AR, ATF3, and CHD7 are abnormally expressed in patients carrying DNAH8 and DNAH17 mutations. Previous studies have shown that ATF3 and CHD7 may interact with AR, a pivotal gene, playing a key role in the etiology of hypospadias. Furthermore, the expression of SRD5a2 involved in the conversion of testosterone (T) to Dihydrotestosterone (DHT) was significantly reduced in DNAH17 variant patients. T-DHT-AR signaling is critical in the development of the external genitalia. Based on differential gene expression and network analysis, we believe that the ODNAH gene may cause the occurrence of hypospadias by affecting T-DHT-AR signaling. In addition, the average expression level of the ODNAH genes, including DNAH5, DNAH8, DNAH9, DNAH11, and DNAH17, in the testis tissue transcriptome was higher than that of the other 26 tissues (fig. 4A). Among these genes, DNAH8 and DNAH17 were specifically highly expressed only in testis tissues. The ODNAH gene is expressed in human testis and specific sex, thus facilitating differentiation selection. To investigate the possible genetic patterns of this gene, we recruited three families to understand the genetic preference of this gene family. In these three families, we found a new genetic variation in the DNAH8 gene (fig. 4B). The DNAH8 gene variant p.Pro1564Ser or p.P1564S (NM-001206927.1: c.4690C > T) was not present in the thousand human genome (1KGP) database. The proline residue at position 1564 of DNAH8 is highly conserved across species, and the variation is inherited from mother.
4. To summarize:
hypospadias are associated with low fertility and their main genetic cause remains unclear. We explore the genetic causes of hypospadias for the first time in Chinese hypospadias queue based on WES technology. In addition to confirming that the early-stage hypospadias risk gene can account for about 27.2% of severe hypospadias, this study provides new findings in several respects as follows.
A very significant finding of this study is that there is a genetic variation of the ODNAH gene in 22.5% of severe hypospadia, suggesting that pathogenic variation of the ODNAH gene may be an important cause for the occurrence of human hypospadia. The axon consists of a microtubule cytoskeleton and is a key extracellular component of the cilia and flagella of eukaryotes. The existing research shows that the infertility and the hypospadias have strong correlation, but the contribution of related genes is not clear. Dynein is one of the motor proteins, which produces force and motion on microtubules. The motor protein of axon is composed of an inner part and an outer part, and plays an important role in the oscillation of cilia and sperms by the ATPase activity of its heavy chain. In this study, all 5 ODNAH genes were testis-specific genes, and their expression in testis tissues was higher in transcript levels than in other tissues. Mutations in male testis-specific genes are more likely to confer a disease phenotype, particularly in relation to diseases associated with the male reproductive process, than in other genes. Among five ODNAH genes, DNAH17 and DNAH8 mutations have recently been reported to be associated with male infertility caused by asthenospermia, which indicates that rare functionally destructive variations in ODNAH genes often lead to infertility. We next examined whether rare functional disruptive variations of the IDNAH gene or the intein arm (IDA) lead to hypospadias. Although there was no association between the other IDAH genes (DNAH3, DNAH6, DNAH7, DNAH10 and DNAH12) and the severe hypospadias, DNAH1 and DNAH2 showed significant enrichment in the severe hypospadias (p < 0.01).
Furthermore, our findings suggest that genetic variation of the ODNAH gene may be inherited from unaffected mothers and may lead to the development of hypospadias by affecting T-DHT-AR signaling. A previously published study showed that the AR and ESR1 signaling pathways play a key role in the development of mild and severe hypospadias. The expression disturbance of AR and ATF3 in the hypospadias individuals mutated DNAH8 and DNAH17 further supported this view. The main function of the testes is to produce sperm and androgen, testosterone being the androgen in the testes. Compared to other tissues, the ODNAH gene was highly expressed in human testis (fig. 4A). Thus genetic variation of the ODNAH gene may influence testosterone production. In combination with the core regulation role played by AR in PPI network regulation consisting of proteins encoded by genes related to the risk of hypospadias reported earlier, we speculate that the ODNAH gene may cause the occurrence of hypospadias by interfering T-DHT-AR signals. The ODNAH gene may have undergone sex evolutionary selection. Because of deleterious mutations, neither viability nor fertility prior to reproduction will be passed on to offspring, as they will reduce fertility3. To explore gender-restricted selection, we examined three families and identified a pathogenic mutation of DNAH8 inherited from the mother (fig. 4B). Consistent with the inheritance of male infertility-induced mutations, this study showed that urineThe subthalamic mutations may be inherited by unaffected women, requiring further investigation in the future.
It should be understood that the above-described embodiments of the present invention are merely examples for clearly illustrating the present invention, and are not intended to limit the embodiments of the present invention. Other variations and modifications will be apparent to persons skilled in the art in light of the above description. And are neither required nor exhaustive of all embodiments. And such obvious variations or modifications which fall within the spirit of the invention are intended to be covered by the scope of the present invention.
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Claims (9)
1. A mutant DNAH8 gene, wherein the nucleotide at position 4690 of NM — 001206927.1 is T.
2.A mutant DNAH8 protein, wherein the amino acid at position 1564 is Ser.
3. Use of a reagent to detect the mutated DNAH8 gene or the mutated DNAH8 protein according to claim 1 or 2 in the preparation of a kit for predicting the risk of a hypospadias.
4. The use of claim 3, wherein the hypospadias is severe hypospadias.
5. The use of claim 3 or 4, wherein the reagent is a PCR reagent or an ELISA reagent.
6. A kit for predicting a risk of a hypospadias comprising a reagent for detecting the mutated DNAH8 gene or the mutated DNAH8 protein according to claim 1 or 2.
7. The kit of claim 6, wherein the hypospadias is severe hypospadias.
8. The kit of claim 6 or 7, wherein the reagents are PCR reagents or ELISA reagents.
9. The non-diagnostic method of a mutated DNAH8 gene or a mutated DNAH8 protein according to claim 1 or 2, wherein a kit according to any one of claims 6 to 8 is used.
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US20100292088A1 (en) * | 2009-05-15 | 2010-11-18 | The University Of North Carolina At Chapel Hill | Methods and compositions for detecting genetic markers associated with primary ciliary dyskinesia |
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ZHONGZHONG CHEN ET AL.: "Whole-exome Sequencing Study of Hypospadia", 《MEDRXIV》 * |
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