1
|
Xie S, Ma Y, Liu Y, Tao D, Wang Z, Yang Y. Primary azoospermia factor C duplication associated with spermatogenic impariment: a case-control study based on Y-chromosome haplogrouping in a Han Chinese population. Andrology 2024; 12:561-569. [PMID: 37594248 DOI: 10.1111/andr.13510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 06/22/2023] [Accepted: 08/06/2023] [Indexed: 08/19/2023]
Abstract
BACKGROUND Azoospermia factor C (AZFc) in the male-specific region of Y-chromosome (MSY) presents wide structure variation mainly due to frequent non-allele homologous recombination, leading to significant copy number variation of the AZFc-linked coding sequences involving in spermatogenesis. A large number of studies had been conducted to investigate the association between AZFc deletions and male infertility in certain Y chromosome genetic backgrounds, however, the influence of primary AZFc duplication on spermatogenesis remained controversial and the cause of the discrepant outcomes is unknown. METHODS In the present study, a total of 1,102 unrelated Han Chinese males without any detectable AZF deletions were recruited from 2014 to 2019, including 411 controls with normozoospermia and 691 patients with idiopathic spermatogenic failure. Using multiple paralog ratio tests (PRTs), the structure duplications were classified by the copy number of the AZFc-linked amplicons and genes. The Y-chromosome haplogroup (Y-hg) was categorized by genetyping of MSY-linked polymorphism loci. The association of primary AZFc duplication with spermatogenic phenotype was investigated in males with the same Y-hg. RESULTS Within Y-hg O3* group, the frequency of the gr/gr duplication in patients is significantly higher than that of controls (P = 1.29×10-3 , odds ratio (OR) 7.64, 95% confidence interval (CI) 1.79-32.57). Moreover, Y-hg O3* males with the gr/gr duplication presented a significantly lower sperm production compared with non-AZFc duplicated ones (sperm concentration: P = 1.46×10-3 ; total sperm count: P = 1.82 ×10-3 ). The b2/b3 duplication were identified clustered in Y-hg Cα2*, and the significant difference in the distribution was not observed between patients with spermatogenic failure and controls. CONCLUSION The results suggest that, in the Han Chinese population, the gr/gr duplication is a predisposing genetic factor for spermatogenic impairment in males harboring Y-hg O3* . Meanwhile, the b2/b3 duplication may be fixed on a yet-unidentified subbranch of Y-hg Cα2* without significantly deleterious effect on spermatogenesis. Our findings provide evidence that the difference in the Y-hg composition may cause the discrepancy on the association of AZFc duplication with spermatogenic failure among the studied populations.
Collapse
Affiliation(s)
- Shengyu Xie
- Department of Medical Genetics, State Key Laboratory of Biotherapy, West China Hospital, West China School of medicine, Sichuan University, Chengdu, China
| | - Yongyi Ma
- Department of Medical Genetics, State Key Laboratory of Biotherapy, West China Hospital, West China School of medicine, Sichuan University, Chengdu, China
- Precision Medicine Center, Precision Medicine Key Laboratory of Sichuan Province, West China Hospital, Sichuan University, Chengdu, China
| | - Yunqiang Liu
- Department of Medical Genetics, State Key Laboratory of Biotherapy, West China Hospital, West China School of medicine, Sichuan University, Chengdu, China
| | - Dachang Tao
- Department of Medical Genetics, State Key Laboratory of Biotherapy, West China Hospital, West China School of medicine, Sichuan University, Chengdu, China
| | - Zhaokun Wang
- Department of Medical Genetics, State Key Laboratory of Biotherapy, West China Hospital, West China School of medicine, Sichuan University, Chengdu, China
| | - Yuan Yang
- Department of Medical Genetics, State Key Laboratory of Biotherapy, West China Hospital, West China School of medicine, Sichuan University, Chengdu, China
| |
Collapse
|
2
|
Bukayev A, Aidarov B, Fesenko D, Saidamarova V, Ivanovsky I, Maltseva E, Naizabayeva D, Bukayeva A, Faizov B, Pylev V, Darmenov A, Skiba Y, Balanovska E, Zhabagin M. Genotype data for 60 SNP genetic markers associated with eye, hair, skin color, ABO blood group, sex, core Y-chromosome haplogroups in Kazakh population. BMC Res Notes 2024; 17:51. [PMID: 38369539 PMCID: PMC10874529 DOI: 10.1186/s13104-024-06712-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 02/01/2024] [Indexed: 02/20/2024] Open
Abstract
OBJECTIVES The collection of genotype data was conducted as an essential part of a pivotal research project with the goal of examining the genetic variability of skin, hair, and iris color among the Kazakh population. The data has practical application in the field of forensic DNA phenotyping (FDA). Due to the limited size of forensic databases from Central Asia (Kazakhstan), it is practically impossible to obtain an individual identification result based on forensic profiling of short tandem repeats (STRs). However, the pervasive use of the FDA necessitates validation of the currently employed set of genetic markers in a variety of global populations. No such data existed for the Kazakhs. The Phenotype Expert kit (DNA Research Center, LLC, Russia) was used for the first time in this study to collect data. DATA DESCRIPTION The present study provides genotype data for a total of 60 SNP genetic markers, which were analyzed in a sample of 515 ethnic Kazakhs. The dataset comprises a total of 41 single nucleotide polymorphisms (SNPs) obtained from the HIrisPlex-S panel. Additionally, there are 4 SNPs specifically related to the AB0 gene, 1 marker associated with the AMELX/Y genes, and 14 SNPs corresponding to the primary haplogroups of the Y chromosome. The aforementioned data could prove valuable to researchers with an interest in investigating genetic variability and making predictions about phenotype based on eye color, hair color, skin color, AB0 blood group, gender, and biogeographic origin within the male lineage.
Collapse
Affiliation(s)
- Alizhan Bukayev
- National Center for Biotechnology, Astana, 010000, Republic of Kazakhstan
| | - Baglan Aidarov
- National Center for Biotechnology, Astana, 010000, Republic of Kazakhstan
| | - Denis Fesenko
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia
| | - Viktoriya Saidamarova
- Karaganda Academy of the Ministry of Internal Affairs of the Republic of Kazakhstan Named After Barimbek Beisenov, Karaganda, 100000, Republic of Kazakhstan
| | | | - Elina Maltseva
- Almaty Branch of the National Center for Biotechnology, Almaty, 050054, Kazakhstan
- Tethys Scientific Society, Almaty, 050063, Kazakhstan
| | - Dinara Naizabayeva
- Almaty Branch of the National Center for Biotechnology, Almaty, 050054, Kazakhstan
| | - Ayagoz Bukayeva
- National Center for Biotechnology, Astana, 010000, Republic of Kazakhstan
| | - Bekzhan Faizov
- National Center for Biotechnology, Astana, 010000, Republic of Kazakhstan
| | - Vladimir Pylev
- Bochkov Research Centre of Medical Genetics, Moscow, 115522, Russia
| | - Akynkali Darmenov
- Karaganda Academy of the Ministry of Internal Affairs of the Republic of Kazakhstan Named After Barimbek Beisenov, Karaganda, 100000, Republic of Kazakhstan
| | - Yuriy Skiba
- Almaty Branch of the National Center for Biotechnology, Almaty, 050054, Kazakhstan
| | - Elena Balanovska
- Bochkov Research Centre of Medical Genetics, Moscow, 115522, Russia
| | - Maxat Zhabagin
- National Center for Biotechnology, Astana, 010000, Republic of Kazakhstan.
| |
Collapse
|
3
|
Fesenko DO, Aramova OY, Vdovchenkov EV, Ivanovsky ID, Fesenko OE, Polyakov SA, Faleeva TG, Filippova MA, Florinskaya VS, Kornienko IV. [DNA Phenotyping of Remains from Elite Burials of the Khazar Period of Southern Russia]. Mol Biol (Mosk) 2023; 57:597-608. [PMID: 37528780 DOI: 10.31857/s0026898423040055, edn: qkucek] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 12/28/2022] [Indexed: 08/03/2023]
Abstract
Ancient DNA analyses help to solve the problems related to the genogeographic origin and migration patterns of populations. The Khazar Khaganate is a subject of controversy among researchers. Its complex historical development, lack of a sufficient number of artistic and written sources, the disappearance of representatives of Khazar culture leaves open the question of the appearance of the Khazars. DNA phenotyping of bone remains from elite burials of the Khazar period of Southern Russia was carried out with respect to eye color, hair color, skin color, and AB0 blood groups. Eight out of 10 individuals had brown eyes, dark hair (to varying degrees), and a predominantly dark skin during their lifetime. Individuals from two burials had gray-blue eyes, and one individual had blond hair. The most probable AB0 blood group was identified in eight people, of which five blood group 0 (I) group, four had blood group A (II), and one had blood group B (III). The allele frequency distribution was assessed for ten population-specific autosomal markers and suggested high heterogeneity for the ethnogeographic origin of the Khazars examined. The results are evidence for ethnocultural, genetic, and phenotypic diversity of the Khazar Khaganate.
Collapse
Affiliation(s)
- D O Fesenko
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991 Russia
| | - O Yu Aramova
- Southern Research Center, Russian Academy of Sciences, Rostov-on-Don, 344006 Russia
- Ivanovsky Academy of Biology and Biotechnology, Southern Federal University, Rostov-on-Don, 344090 Russia
| | - E V Vdovchenkov
- Ivanovsky Academy of Biology and Biotechnology, Southern Federal University, Rostov-on-Don, 344090 Russia
| | - I D Ivanovsky
- DNA Research Center, LLC, Hkimki, Moscow Oblast, 141402 Russia
| | - O E Fesenko
- Institute of Physics, Southern Federal University, Rostov-on-Don, 344090 Russia
| | - S A Polyakov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991 Russia
| | - T G Faleeva
- St. Petersburg Forensic Bureau, St. Petersburg, 195067 Russia
- Mechnikov North-Western State Medical University, St. Petersburg, 191015 Russia
| | - M A Filippova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991 Russia
| | - V S Florinskaya
- Ivanovsky Academy of Biology and Biotechnology, Southern Federal University, Rostov-on-Don, 344090 Russia
| | - I V Kornienko
- Southern Research Center, Russian Academy of Sciences, Rostov-on-Don, 344006 Russia
- Ivanovsky Academy of Biology and Biotechnology, Southern Federal University, Rostov-on-Don, 344090 Russia
| |
Collapse
|
4
|
Westra WM, Rygiel AM, Mostafavi N, de Wit GMJ, Roes AL, Moons LMG, Peppelenbosch MP, Ouburg S, Morré SA, Jacobs M, Siersema PD, Repping S, Wang KK, Krishnadath KK. The Y-chromosome F haplogroup contributes to the development of Barrett's esophagus-associated esophageal adenocarcinoma in a white male population. Dis Esophagus 2020; 33:5780184. [PMID: 32129453 PMCID: PMC7471775 DOI: 10.1093/dote/doaa011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 02/03/2020] [Accepted: 02/06/2020] [Indexed: 12/11/2022]
Abstract
Barrett's esophagus (BE) is a metaplastic condition of the distal esophagus, resulting from longstanding gastroesophageal reflux disease (GERD). BE predisposes for the highly malignant esophageal adenocarcinoma (EAC). Both BE and EAC have the highest frequencies in white males. Only a subset of patients with GERD develop BE, while <0.5% of BE will progress to EAC. Therefore, it is most likely that the development of BE and EAC is associated with underlying genetic factors. We hypothesized that in white males, Y-chromosomal haplogroups are associated with BE and EAC. To investigate this we conducted a multicenter study studying the frequencies of the Y-chromosomal haplogroups in GERD, BE, and EAC patients. We used genomic analysis by polymerase chain reaction and restriction fragment length polymorphism to determine the frequency of six Y-chromosomal haplogroups (DE, F(xJ,xK), K(xP), J, P(xR1a), and R1a) between GERD, BE, and EAC in a cohort of 1,365 white males, including 612 GERD, 753 BE patients, while 178 of the BE patients also had BE-associated EAC. Univariate logistic regression analysis was used to compare the outcomes. In this study, we found the R1a (6% vs. 9%, P = 0.04) and K (3% vs. 6%, P = 0.035) to be significantly underrepresented in BE patients as compared to GERD patients with an odds ratio (OR) of 0.63 (95% CI 0.42-0.95, P = 0.03) and of 0.56 (95% CI 0.33-0.96, P = 0.03), respectively, while the K haplogroup was protective against EAC (OR 0.30; 95% CI 0.07-0.86, P = 0.05). A significant overrepresentation of the F haplogroup was found in EAC compared to BE and GERD patients (34% vs. 27% and 23%, respectively). The F haplogroup was found to be a risk factor for EAC with an OR of 1.5 (95% CI 1.03-2.19, P = 0.03). We identified the R1a and K haplogroups as protective factors against development of BE. These haplogroups have low frequencies in white male populations. Of importance is that we could link the presence of the predominantly occurring F haplogroup in white males to EAC. It is possible that this F haplogroup is associated to genetic variants that predispose for the EAC development. In future, the haplogroups could be applied to improve stratification of BE and GERD patients with increased risk to develop BE and/or EAC.
Collapse
Affiliation(s)
- W M Westra
- CEMM, Amsterdam UMC-AMC, Amsterdam, The Netherlands,Department of Gastroenterology and Hepatology, Mayo Foundation, Rochester, MN, USA,Department of Gastroenterology and Hepatology, Amsterdam UMC-AMC, Amsterdam, The Netherlands
| | - A M Rygiel
- CEMM, Amsterdam UMC-AMC, Amsterdam, The Netherlands,Department of Medical Genetics, Institute of Mother and Child, Warsaw, Poland
| | - N Mostafavi
- Biostatistical Unit, Department of Gastroenterology, Amsterdam UMC, Amsterdam, The Netherlands
| | - G M J de Wit
- CEMM, Amsterdam UMC-AMC, Amsterdam, The Netherlands
| | - A L Roes
- CEMM, Amsterdam UMC-AMC, Amsterdam, The Netherlands
| | - L M G Moons
- Department of Gastroenterology and Hepatology, UMC Utrecht, The Netherlands
| | - M P Peppelenbosch
- Department of Gastroenterology and Hepatology, Erasmus MC, Rotterdam, The Netherlands
| | - S Ouburg
- Department of Medical Microbiology and Infection Control, Amsterdam UMC-VUMC, Amsterdam, The Netherlands
| | - S A Morré
- Department of Medical Microbiology and Infection Control, Amsterdam UMC-VUMC, Amsterdam, The Netherlands,Department of Genetics and Cell Biology, Maastricht University, Maastricht, The Netherlands
| | - M Jacobs
- Department of Gastroenterology and Hepatology, Amsterdam UMC-VUMC, Amsterdam, The Netherlands
| | - P D Siersema
- Department of Gastroenterology and Hepatology, Radboud UMC, Nijmegen, The Netherlands
| | - S Repping
- Department of Reproductive Medicine, Amsterdam UMC-AMC, Amsterdam, The Netherlands
| | - K K Wang
- Department of Gastroenterology and Hepatology, Mayo Foundation, Rochester, MN, USA
| | - K K Krishnadath
- Department of Gastroenterology and Hepatology, Amsterdam UMC-AMC, Amsterdam, The Netherlands,Address correspondence to: Professor Kausilia K. Krishnadath, MD, PhD, Gastroenterology and Hepatology, Amsterdam UMC-AMC, Amsterdam, C2-321, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands.
| |
Collapse
|
5
|
Yan Y, Yang X, Liu Y, Shen Y, Tu W, Dong Q, Yang D, Ma Y, Yang Y. Copy number variation of functional RBMY1 is associated with sperm motility: an azoospermia factor-linked candidate for asthenozoospermia. Hum Reprod 2018; 32:1521-1531. [PMID: 28498920 DOI: 10.1093/humrep/dex100] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Accepted: 04/28/2017] [Indexed: 02/05/2023] Open
Abstract
STUDY QUESTION What is the influence of copy number variation (CNV) in functional RNA binding motif protein Y-linked family 1 (RBMY1) on spermatogenic phenotypes? SUMMARY ANSWER The RBMY1 functional copy dosage is positively correlated with sperm motility, and dosage insufficiency is an independent risk factor for asthenozoospermia. WHAT IS KNOWN ALREADY RBMY1, a multi-copy gene expressed exclusively in the adult testis, is one of the most important candidates for male infertility in the azoospermia factor (AZF) region of the Y-chromosome. RBMY1 encodes an RNA-binding protein that serves as a pre-mRNA splicing regulator during spermatogenesis, and male mice deficient in Rbmy are sterile. STUDY DESIGN, SIZE, DURATION A total of 3127 adult males were recruited from 2009 to 2016; of this group, the dosage of RBMY1 functional copy were investigated in 486 fertile males. In the remaining 2641 males with known spermatogenesis status, 1070 Y-chromosome haplogroup (Y-hg) O3* or O3e carriers without chromosomal aberration or known AZF structure mutations responsible for spermatogenic impairment, including 506 men with normozoospermia and 564 men with oligozoospermia or/and asthenozoospermia, were screened, and the RBMY1 functional copy dosage and copy conversion were determined to explore their associations with sperm phenotypes. The correlation between RBMY1 dosage and its mRNA level or RBMY1 protein level and the correlation between sperm RBMY1 level and motility were analysed in 15 testis tissue samples and eight semen samples. Ten additional semen samples were used to confirm the subcellular localization of RBMY1 in individual sperm. PARTICIPANTS/MATERIALS, SETTING, METHODS All the Han volunteers donating whole blood, semen and testis tissue were from southwest China. RBMY1 copy number, copy conversion, mRNA/protein amount and protein location in sperm were detected using the AccuCopy® assay method, paralog ratio test, quantitative PCR, western blotting and immunofluorescence staining methods, respectively. MAIN RESULTS AND THE ROLE OF CHANCE This study identified Y-hg-independent CNV of functional RBMY1 in the enrolled population. A difference in the distribution of RBMY1 copy number was observed between the group with normal sperm motility and the group with asthenozoospermia. A positive correlation between the RBMY1 copy dosage and sperm motility was identified, and the males with fewer than six copies of RBMY1 showed an elevated risk for asthenozoospermia relative to those with six RBMY1 copies, the most common dosage in the population. The RBMY1 copy dosage was positively correlated with its mRNA and protein level in the testis. Sperm with high motility were found to carry more RBMY1 protein than those with relatively low motility. The RBMY1 protein was confirmed to predominantly localize in the neck and mid-piece region of sperm as well as the principal piece of the sperm tail. Our population study completes a chain of evidence suggesting that RBMY1 influences the susceptibility of males to asthenozoospermia by modulating sperm motility. LIMITATIONS REASONS FOR CAUTION High sequence similarity between the RBMY1 functional copies and a large number of pseudogenes potentially reduces the accuracy of the copy number detection. The mechanism underlying the CNV in RBMY1 is still unclear, and the effect of the structural variations in the RBMY1 copy cluster on the copy dosage of other protein-coding genes located in the region cannot be excluded, which may potentially bias our observations. WIDER IMPLICATIONS OF THE FINDINGS Asthenozoospermia is a multi-factor complex disease with a limited number of proven susceptibility genes. This study identified a novel genomic candidate independently contributing to the condition, enriching our understanding of the role of AZF-linked genes in male reproduction. Our finding provides insight into the physiological and pathological characteristics of RBMY1 in terms of sperm motility, supplies persuasive evidence of the significance of RBMY1 copy number analysis in the clinical counselling of male infertility resulting from asthenozoospermia. STUDY FUNDING/COMPETING INTEREST(S) This work was funded by the National Natural Science Foundation of China (Nos. 81370748 and 30971598). The authors have no conflicts of interest.
Collapse
Affiliation(s)
- Yuanlong Yan
- Department of Medical Genetics, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, No. 1, Keyuan Road 4, Gaopeng Street, Chengdu, Sichuan 610041, China
| | - Xiling Yang
- Department of Medical Genetics, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, No. 1, Keyuan Road 4, Gaopeng Street, Chengdu, Sichuan 610041, China
| | - Yunqiang Liu
- Department of Medical Genetics, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, No. 1, Keyuan Road 4, Gaopeng Street, Chengdu, Sichuan 610041, China
| | - Ying Shen
- Department of Medical Genetics, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, No. 1, Keyuan Road 4, Gaopeng Street, Chengdu, Sichuan 610041, China
| | - Wenling Tu
- Department of Medical Genetics, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, No. 1, Keyuan Road 4, Gaopeng Street, Chengdu, Sichuan 610041, China
| | - Qiang Dong
- Department of Urology, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Dong Yang
- Reproductive Medicine Institute, Chengdu Women's and Children's Central Hospital, Chengdu, Sichuan 610031, China
| | - Yongyi Ma
- Jinjiang Maternal and Child Health Hospital, Chengdu, Sichuan 610016, China
| | - Yuan Yang
- Department of Medical Genetics, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, No. 1, Keyuan Road 4, Gaopeng Street, Chengdu, Sichuan 610041, China
| |
Collapse
|