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Anjali K, Kumar T, Kar AG, Kumar P, Narayan G, Singh S. Association of haplotype and linkage disequilibrium of PARP1 polymorphisms rs1136410, rs1805405 and rs3219088 with gallbladder cancer. Dig Liver Dis 2022; 55:807-814. [PMID: 36581511 DOI: 10.1016/j.dld.2022.12.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 10/05/2022] [Accepted: 12/07/2022] [Indexed: 12/31/2022]
Abstract
BACKGROUND Previously, we have reported that PARP1 rs1136410 is significantly associated with increased the risk of gallbladder cancer. AIM We aimed to investigate the association of PARP1 rs1805405 and rs3219088 polymorphisms with risk of GBC and also association of the haplotype and combined effect of PARP1 SNPs (rs1805405 G/A, rs3219088 G/T and rs1136410 A/G). We have also investigated the expression profile of PARP1 and its correlation with polymorphisms, clinical parameters and overall survival. METHODS PARP1 polymorphisms were genotyped by PCR-RFLP and the expression profile of PARP1 at mRNA level was analyzed by semi-quantitative PCR. Overall survival was analyzed using Kaplan-Meier plot and Cox-regression analysis. RESULTS Haplotype analysis of the PARP1 polymorphisms revealed that AGG, AAG and GGT haplotypes are significantly associated with decreased risk of GBC, while AAT, AGT, GGG and GAG haplotypes are significantly associated with increased risk of GBC. Patients with T1+T2 and treated with chemotherapy having risk genotypes of rs1805405 have decreased overall survival. Upregulation of PARP1 is significantly associated with longer overall survival in patients with GBC with different clinical parameters. SNPs rs1136410 and rs1805405 genotypes are significantly associated with PARP1 expression. CONCLUSION Haplotype analysis suggests that PARP1 may have a potential role in gallbladder carcinogenesis.
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Affiliation(s)
- Kumari Anjali
- Department of Zoology, Mahila Mahavidyalaya, Banaras Hindu University, Varanasi 221005, Uttar Pradesh
| | - Tarun Kumar
- Department of Surgical Oncology, Institute of Medical Sciences, Banaras Hindu University, Varanasi 221005, Uttar Pradesh
| | - Amrita Ghosh Kar
- Department of Pathology, Institute of Medical Sciences, Banaras Hindu University, Varanasi 221005, Uttar Pradesh
| | - Puneet Kumar
- Department of General Surgery, Institute of Medical Sciences, Banaras Hindu University, Varanasi 221005, Uttar Pradesh
| | - Gopeshwar Narayan
- Cancer Genetics Laboratory, Department of Molecular and Human Genetics, Institute of Science, Banaras Hindu University, Varanasi 221005, Uttar Pradesh
| | - Sunita Singh
- Department of Zoology, Mahila Mahavidyalaya, Banaras Hindu University, Varanasi 221005, Uttar Pradesh.
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Ferreira CER, Campos GS, Schmidt PI, Sollero BP, Goularte KL, Corcini CD, Gasperin BG, Lucia T, Boligon AA, Cardoso FF. Genome-wide association and genomic prediction for scrotal circumference in Hereford and Braford bulls. Theriogenology 2021; 172:268-280. [PMID: 34303226 DOI: 10.1016/j.theriogenology.2021.07.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 07/12/2021] [Accepted: 07/14/2021] [Indexed: 11/19/2022]
Abstract
Scrotal circumference (SC) is widely used as a selection criterion for bulls in breeding programs, since it is easily assessed and correlated with several desirable reproductive traits. The objectives of this study were: to perform a genome-wide association study (GWAS) to identify genomic regions associated with SC adjusted for age (SCa) and for both age and weight (SCaw); to select Tag SNPs from GWAS to construct low-density panel for genomic prediction; and to compare the prediction accuracy of the SC through different methods for Braford and Hereford bulls from the same genetic breeding program. Data of SC from 18,172 bulls (30.4 ± 3.7 cm) and of genotypes from 131 sires and 3,545 animals were used. From GWAS, the top 1% of 1-Mb windows were observed on chromosome (BTA) 2, 20, 7, 8, 15, 3, 16, 27, 6 and 8 for SCa and on BTA 8, 15, 16, 21, 19, 2, 6, 5 and 10 for SCaw, representing 17.4% and 18.8% of the additive genetic variance of SCa and SCaw, respectively. The MeSH analysis was able to translate genomic information providing biological meanings of more specific gene functions related to the SCa and SCaw. The genomic enhancement methods, especially single step GBLUP, that combined phenotype and pedigree data with direct genomic values generated gains in accuracy in relation to pedigree BLUP, suggesting that genomic predictions should be applied to improve genetic gain and to narrow the generation interval compared to traditional methods. The proposed Tag-SNP panels may be useful for lower-cost commercial genomic prediction applications in the future, when the number of bulls in the reference population increases for SC in Hereford and Braford breeds.
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Affiliation(s)
- Carlos E R Ferreira
- ReproPel, Faculdade de Veterinária, Universidade Federal de Pelotas, Pelotas, RS, Brazil.
| | - Gabriel S Campos
- Departamento de Zootecnia, Faculdade de Agronomia Eliseu Maciel, Universidade Federal de Pelotas, Pelotas, RS, Brazil
| | - Patricia I Schmidt
- Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual de São Paulo, Jaboticabal, SP, Brazil
| | | | - Karina L Goularte
- ReproPel, Faculdade de Veterinária, Universidade Federal de Pelotas, Pelotas, RS, Brazil
| | - Carine D Corcini
- ReproPel, Faculdade de Veterinária, Universidade Federal de Pelotas, Pelotas, RS, Brazil
| | - Bernardo G Gasperin
- ReproPel, Faculdade de Veterinária, Universidade Federal de Pelotas, Pelotas, RS, Brazil
| | - Thomaz Lucia
- ReproPel, Faculdade de Veterinária, Universidade Federal de Pelotas, Pelotas, RS, Brazil
| | - Arione A Boligon
- Departamento de Zootecnia, Faculdade de Agronomia Eliseu Maciel, Universidade Federal de Pelotas, Pelotas, RS, Brazil
| | - Fernando F Cardoso
- Departamento de Zootecnia, Faculdade de Agronomia Eliseu Maciel, Universidade Federal de Pelotas, Pelotas, RS, Brazil; Embrapa Pecuária Sul, Bagé, RS, Brazil
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LncRNAs induce oxidative stress and spermatogenesis by regulating endoplasmic reticulum genes and pathways. Aging (Albany NY) 2021; 13:13764-13787. [PMID: 34001678 PMCID: PMC8202879 DOI: 10.18632/aging.202971] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 11/08/2020] [Indexed: 12/17/2022]
Abstract
Oligozoospermia or low sperm count is a leading cause of male infertility worldwide. Despite decades of work on non-coding RNAs (ncRNAs) as regulators of spermatogenesis, fertilization, and male fertility, the literature on the function of long non-coding RNAs (lncRNAs) in human oligozoospermia is scarce. We integrated lncRNA and mRNA sequencing data from 12 human normozoospermic and oligozoospermic samples and comprehensively analyzed the function of differentially expressed lncRNAs (DE lncRNAs) and mRNAs (DE mRNAs) in male infertility. The target genes of DE lncRNAs were identified using a Gaussian graphical model. Gene ontology terms and Kyoto Encyclopedia of Genes and Genomes pathways were primarily enriched in protein transport and localization to the endoplasmic reticulum (ER). The lncRNA–mRNA co-expression network revealed cis- and trans-regulated target genes of lncRNAs. The transcriptome data implicated DE lncRNAs and DE mRNAs and their target genes in the accumulation of unfolded proteins in sperm ER, PERK-EIF2 pathway-induced ER stress, oxidative stress, and sperm cell apoptosis in individuals with oligozoospermia. These findings suggest that the identified lncRNAs and pathways could serve as effective therapeutic targets for male infertility.
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A novel protein biochip screening serum anti-sperm antibody expression and natural pregnancy rate in a follow-up study in Chinese infertility. Biosci Rep 2021; 40:221951. [PMID: 31985014 PMCID: PMC7012658 DOI: 10.1042/bsr20191769] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 01/06/2020] [Accepted: 01/24/2020] [Indexed: 01/17/2023] Open
Abstract
Production of anti-sperm antibody (ASA) often suffers from autoimmune reaction against sperms in human infertility. The antibodies are measured in both blood and seminal plasma of males. Here, we reported a simple protein biochip methodology that takes advantage of a functionalized self-assembled monolayer modified by N-hydroxysuccinimide (NHS) and enables identification of anti-sperm antibody in Chinese male infertility. To validate this biochip platform, we immobilized purified sperm protein on the biochip surface and tested a variety of parameters in quality controls for the protein assay, respectively. Then, we analyzed serum samples from 368 patients with infertility and 116 healthy donors by means of this biochip simultaneously. We found that positive rate of serum ASA was 20.92% (77/368) in the cases and 1.72% (2/116) in the controls, respectively. Furthermore, we further corroborated the biochip assay in comparison with ELISA method. We found that both methods were compatible for the detection of serum ASA in the patients. In addition, a follow-up study for natural conception in ASA-positive and ASA-negative patients was conducted. The result showed a significant correlation between serum ASA expression and natural pregnancy rate 6.5% in ASA-positive patients while 18.9% in ASA-negative patients, indicating the potential roles of ASA in naturally reproductive processes.
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Batnasan E, Xie S, Zhang Q, Li Y. Observation of Parthanatos Involvement in Diminished Ovarian Reserve Patients and Melatonin's Protective Function Through Inhibiting ADP-Ribose (PAR) Expression and Preventing AIF Translocation into the Nucleus. Reprod Sci 2020; 27:75-86. [PMID: 32046374 DOI: 10.1007/s43032-019-00005-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Accepted: 02/25/2019] [Indexed: 01/09/2023]
Abstract
Diminished ovarian reserve (DOR) is characterized by the depletion of the ovarian pool, which leads to reductions in oocyte quality and quantity. Studies have suggested that ovarian reserve or ovarian aging is tightly related to apoptosis. However, the cell death mechanism is not comprehensively understood. Parthanatos, a type of poly [ADP-ribose] polymerase 1(PARP1)-dependent and apoptosis-inducing factor (AIF)-mediated cell death, plays a crucial role in various disorders. In the present study, we aimed to investigate whether parthanatos is involved in the pathogenesis of DOR. We recruited 40 patients (20 DOR patients and 20 normal ovarian reserve (NOR) patients) and examined PAR expression and AIF translocation in their isolated cumulus GCs (granulosa cells) by fluorescence microscopy. Our results demonstrated that PAR expression and AIF nuclear translocation were significantly higher in cumulus GCs of DOR patients, suggesting that PARP1-dependent cell death may be associated with DOR pathophysiology. Moreover, we tested the protective function of melatonin on hydrogen peroxide (H2O2)-induced parthanatos in human ovarian cancer (IGROV1) cells. Our results demonstrated that H2O2 treatment of IGROV1 cells led to excessive protein PARylation and AIF translocation into the nuclei. Melatonin effectively inhibits PARylation, blocks translocation of AIF into the nucleus, and consequently decreases the risk of parthanatos in cumulus GCs.
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Affiliation(s)
- Enkhzaya Batnasan
- Center for Reproductive Medicine, Xiang-Ya Hospital, Central South University, Changsha, Hunan Province, People's Republic of China.,Clinical Research Center for Women's Reproductive Health in Hunan Province, Changsha, Hunan Province, People's Republic of China
| | - Shi Xie
- Center for Reproductive Medicine, Xiang-Ya Hospital, Central South University, Changsha, Hunan Province, People's Republic of China.,Clinical Research Center for Women's Reproductive Health in Hunan Province, Changsha, Hunan Province, People's Republic of China
| | - Qiong Zhang
- Center for Reproductive Medicine, Xiang-Ya Hospital, Central South University, Changsha, Hunan Province, People's Republic of China.,Clinical Research Center for Women's Reproductive Health in Hunan Province, Changsha, Hunan Province, People's Republic of China
| | - Yanping Li
- Center for Reproductive Medicine, Xiang-Ya Hospital, Central South University, Changsha, Hunan Province, People's Republic of China. .,Clinical Research Center for Women's Reproductive Health in Hunan Province, Changsha, Hunan Province, People's Republic of China.
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Kui F, Ye H, Chen XL, Zhang J. Microarray meta-analysis identifies candidate genes for human spermatogenic arrest. Andrologia 2019; 51:e13301. [PMID: 31037746 DOI: 10.1111/and.13301] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 03/28/2019] [Accepted: 03/29/2019] [Indexed: 02/06/2023] Open
Abstract
Male infertility affects approximately half of couples who have difficulty becoming pregnant, and its prevalence is continuously rising. Many studies have been performed using animal testes to reveal the mechanisms of male infertility, but few studies have investigated human testes due to various limitations. The aim of this study was to investigate the gene expression profile of impaired human testes through a meta-analysis of microarray data sets, which was accomplished by using 178 human testis samples and 7 microarray data sets. Impaired testes were categorised into four pathological phenotypes or the normal phenotype based on their Johnsen score. Then, a meta-analysis was performed to screen out the differentially expressed genes (DEGs) in each phenotype. The DEGs were used in a subsequent bioinformatics analysis. Our results identified several novel hub genes and pathways and suggested that G1 mitotic cell cycle arrest was a remarkable feature in pre-meiotic arrest. Furthermore, fifteen p53-interacting proteins, such as ABL1 and HDAC2, whose roles in spermatogenesis have not been well characterised, were selected from the DEGs through a strict screening procedure.
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Affiliation(s)
- Fang Kui
- Clinical Laboratory, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Clinical Laboratory, The Third Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, China
| | - Hui Ye
- Clinical Laboratory, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xi-Ling Chen
- Clinical Laboratory, The Third Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, China
| | - Jun Zhang
- Clinical Laboratory, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
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Krupa R, Czarny P, Wigner P, Wozny J, Jablkowski M, Kordek R, Szemraj J, Sliwinski T. The Relationship Between Single-Nucleotide Polymorphisms, the Expression of DNA Damage Response Genes, and Hepatocellular Carcinoma in a Polish Population. DNA Cell Biol 2017; 36:693-708. [PMID: 28598207 DOI: 10.1089/dna.2017.3664] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The molecular mechanism of hepatocellular carcinoma (HCC) is related to DNA damage caused by oxidative stress products induced by hepatitis B virus (HBV) or C (HCV) infection and exposure to environmental pollutants. Single-nucleotide polymorphisms (SNPs) of DNA damage response (DDR) genes may influence individual susceptibility to environmental risk factors and affect DNA repair efficacy, which, in turn, can influence the risk of HCC. The study evaluates a panel of 15 SNPs in 11 DDR genes (XRCC1, XRCC3, XPD, MUTYH, LIG1, LIG3, hOGG1, PARP1, NFIL1, FEN1, and APEX1) in 65 HCC patients, 50 HBV- and 50 HCV-infected non-cancerous patients, and 50 healthy controls. It also estimates the mRNA expression of nine DDR genes in cancerous and adjacent healthy liver tissues. Two of the investigated polymorphisms (rs1052133 and rs13181) were associated with HCC risk. For all investigated genes, the level of mRNA was significantly lower in HCC cancer tissue than in non-cancerous liver tissue. Seven of the investigated polymorphisms were statistically related to gene expression in cancer tissues. The disruption of DDR genes may be responsible for hepatocellular transformation in HCV-infected patients.
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Affiliation(s)
- Renata Krupa
- 1 Department of Molecular Genetics, University of Lodz , Lodz, Poland
| | - Piotr Czarny
- 2 Department of Medical Biochemistry, Medical University of Lodz , Lodz, Poland
| | - Paulina Wigner
- 1 Department of Molecular Genetics, University of Lodz , Lodz, Poland
| | - Joanna Wozny
- 3 Department of Infectious and Liver Diseases, Medical University of Lodz , Lodz, Poland
| | - Maciej Jablkowski
- 3 Department of Infectious and Liver Diseases, Medical University of Lodz , Lodz, Poland
| | - Radzislaw Kordek
- 4 Department of Pathology, Medical University of Lodz , Lodz, Poland
| | - Janusz Szemraj
- 2 Department of Medical Biochemistry, Medical University of Lodz , Lodz, Poland
| | - Tomasz Sliwinski
- 1 Department of Molecular Genetics, University of Lodz , Lodz, Poland
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Lack of association between genetic polymorphisms in three folate-related enzyme genes and male infertility in the Chinese population. J Assist Reprod Genet 2015; 32:369-74. [PMID: 25578539 DOI: 10.1007/s10815-014-0423-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Accepted: 12/26/2014] [Indexed: 12/15/2022] Open
Abstract
PURPOSE This study explored the possible association of four single nucleotide polymorphisms (SNPs) of the three folate-related enzyme genes: MTHFR C677T and A1298C, MTR A2756G and MTRR A66G, with male infertility in the Chinese population. METHODS The polymorphic distributions of the four SNPs (MTHFR C677T and A1298C, MTR A2756G and MTRR A66G) were investigated by the method of SNaPshot in a Chinese cohort including 296 idiopathic infertile males with azoospermia or oligozoospermia and 204 fertile males. RESULTS We found no evidence for an association between any of these variants (MTHFR C677T and A1298C, MTR A2756G and MTRR A66G) and male infertility. CONCLUSIONS There is no evidence for an association between male infertility and polymorphism of the three folate-related enzyme genes in the Chinese population.
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