1
|
Tan WLA, Hudson NJ, Porto Neto LR, Reverter A, Afonso J, Fortes MRS. An association weight matrix identified biological pathways associated with bull fertility traits in a multi-breed population. Anim Genet 2024. [PMID: 38692842 DOI: 10.1111/age.13431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 02/26/2024] [Accepted: 04/01/2024] [Indexed: 05/03/2024]
Abstract
Using seven indicator traits, we investigated the genetic basis of bull fertility and predicted gene interactions from SNP associations. We used percent normal sperm as the key phenotype for the association weight matrix-partial correlation information theory (AWM-PCIT) approach. Beyond a simple list of candidate genes, AWM-PCIT predicts significant gene interactions and associations for the selected traits. These interactions formed a network of 537 genes: 38 genes were transcription cofactors, and 41 genes were transcription factors. The network displayed two distinct clusters, one with 294 genes and another with 243 genes. The network is enriched in fertility-associated pathways: steroid biosynthesis, p53 signalling, and the pentose phosphate pathway. Enrichment analysis also highlighted gene ontology terms associated with 'regulation of neurotransmitter secretion' and 'chromatin formation'. Our network recapitulates some genes previously implicated in another network built with lower-density genotypes. Sequence-level data also highlights additional candidate genes relevant to bull fertility, such as FOXO4, FOXP3, GATA1, CYP27B1, and EBP. A trio of regulatory genes-KDM5C, LRRK2, and PME-was deemed core to the network because of their overarching connections. This trio probably influences bull fertility through their interaction with genes, both known and unknown as to their role in male fertility. Future studies may target the trio and their target genes to enrich our understanding of male fertility further.
Collapse
Affiliation(s)
- Wei Liang Andre Tan
- School of Chemistry and Molecular Bioscience, The University of Queensland, St Lucia, Queensland, Australia
| | - Nicholas James Hudson
- School of Agriculture and Food Sustainability, The University of Queensland, Gatton, Queensland, Australia
| | | | | | - Juliano Afonso
- School of Chemistry and Molecular Bioscience, The University of Queensland, St Lucia, Queensland, Australia
- Empresa Brasileira de Pesquisa Agropecuária, Pecuária Sudeste, São Carlos, São Paulo, Brazil
| | | |
Collapse
|
2
|
Schon SB, Moritz L, Rabbani M, Meguid J, Juliano BR, Ruotolo BT, Aston K, Hammoud SS. Proteomic analysis of human sperm reveals changes in protamine 1 phosphorylation in men with infertility. F&S SCIENCE 2024; 5:121-129. [PMID: 38065301 PMCID: PMC11116066 DOI: 10.1016/j.xfss.2023.12.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 11/21/2023] [Accepted: 12/01/2023] [Indexed: 01/03/2024]
Abstract
OBJECTIVE To perform a comprehensive assessment of protamine (P) isoforms and modifications in human sperm with the aim of identifying how P modifications and isoforms are altered in men with reduced sperm motility and low sperm count. DESIGN Cross-sectional. SETTING Academic medical center. PATIENTS A total of 18 men with prior reported pregnancy and normozoospermia (normal sperm), 14 men from couples with infertility and asthenozoospermia (reduced sperm motility), and 24 men from couples with infertility and oligoasthenoteratozoospermia (low sperm count and motility and abnormal sperm morphology). INTERVENTION(S) Not applicable. MAIN OUTCOME MEASURE(S) Proteomic assessment using both top-down and bottom-up liquid chromatography mass spectrometry (MS) analysis. RESULTS A total of 13 posttranslational modifications were identified on P1 and P2 using bottom-up MS, including both phosphorylation and methylation. Top-down MS revealed an unmodified and phosphorylated isoform of P1 and the 3 major isoforms of P2, HP2, HP3, and HP4. Protamine 1 phosphorylation was overall higher in men with male factor infertility compared with those with normal semen analysis (40.5% vs. 32.6). There was no difference in P posttranslational modifications or isoforms of P2 in men with normal vs. abnormal fertility. CONCLUSION Human protamines bear a number of posttranslational modifications, with alterations in P1 phosphorylation noted in the setting of male factor infertility.
Collapse
Affiliation(s)
- Samantha B Schon
- Division of Reproductive Endocrinology and Infertility, Department of Obstetrics and Gynecology, University of Michigan, Ann Arbor, Michigan.
| | - Lindsay Moritz
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan
| | - Mashiat Rabbani
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan
| | - Julia Meguid
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan
| | - Brock R Juliano
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan
| | - Brandon T Ruotolo
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan
| | - Kenneth Aston
- Department of Surgery, University of Utah, Salt Lake City, Utah
| | - Saher Sue Hammoud
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan; Department of Obstetrics and Gynecology, University of Michigan, Ann Arbor, Michigan; Department of Urology, University of Michigan, Ann Arbor, Michigan
| |
Collapse
|
3
|
Oikeh E, Ziebarth J, Dinar MAM, Kirchhoff D, Aronova A, Dziubla TD, Wang Y, DeRouchey JE. DNA Packaging and Polycation Length Determine DNA Susceptibility to Free Radical Damage in Condensed DNA. J Phys Chem B 2024; 128:3329-3339. [PMID: 38557033 DOI: 10.1021/acs.jpcb.3c06116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
In nature, DNA exists primarily in a highly compacted form. The compaction of DNA in vivo is mediated by cationic proteins: histones in somatic nuclei and protamines in sperm chromatin. The extreme, nearly crystalline packaging of DNA by protamines in spermatozoa is thought to be essential for both efficient genetic delivery as well as DNA protection against damage by mutagens and oxidative species. The protective role of protamines is required in sperm, as they are sensitive to ROS damage due to the progressive loss of DNA repair mechanisms during maturation. The degree to which DNA packaging directly relates to DNA protection in the condensed state, however, is poorly understood. Here, we utilized different polycation condensing agents to achieve varying DNA packaging densities and quantify DNA damage by free radical oxidation within the condensates. Although we see that tighter DNA packaging generally leads to better protection, the length of the polycation also plays a significant role. Molecular dynamics simulations suggest that longer polyarginine chains offer increased protection by occupying more space on the DNA surface and forming more stable interactions. Taken together, our results suggest a complex interplay among polycation properties, DNA packaging density, and DNA protection against free radical damage within condensed states.
Collapse
Affiliation(s)
- Ehigbai Oikeh
- Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506, United States
| | - Jesse Ziebarth
- Department of Chemistry, University of Memphis, Memphis, Tennessee 38152, United States
| | - Md Abu Monsur Dinar
- Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506, United States
| | - Daniel Kirchhoff
- Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506, United States
| | - Anastasiia Aronova
- Chemical and Materials Engineering Department, University of Kentucky, Lexington, Kentucky 40506, United States
| | - Thomas D Dziubla
- Chemical and Materials Engineering Department, University of Kentucky, Lexington, Kentucky 40506, United States
| | - Yongmei Wang
- Department of Chemistry, University of Memphis, Memphis, Tennessee 38152, United States
| | - Jason E DeRouchey
- Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506, United States
| |
Collapse
|
4
|
Castillo J, de la Iglesia A, Leiva M, Jodar M, Oliva R. Proteomics of human spermatozoa. Hum Reprod 2023; 38:2312-2320. [PMID: 37632247 DOI: 10.1093/humrep/dead170] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 07/12/2023] [Indexed: 08/27/2023] Open
Abstract
Proteomic methodologies offer a robust approach to identify and quantify thousands of proteins from semen components in both fertile donors and infertile patients. These strategies provide an unprecedented discovery potential, which many research teams are currently exploiting. However, it is essential to follow a suitable experimental design to generate robust data, including proper purification of samples, appropriate technical procedures to increase identification throughput, and data analysis following quality criteria. More than 6000 proteins have been described so far through proteomic analyses in the mature sperm cell, increasing our knowledge on processes involved in sperm function, intercommunication between spermatozoa and seminal fluid, and the transcriptional origin of the proteins. These data have been complemented with comparative studies to ascertain the potential role of the identified proteins on sperm maturation and functionality, and its impact on infertility. By comparing sperm protein profiles, many proteins involved in the acquisition of fertilizing ability have been identified. Furthermore, altered abundance of specific protein groups has been observed in a wide range of infertile phenotypes, including asthenozoospermia, oligozoospermia, and normozoospermia with unsuccessful assisted reproductive techniques outcomes, leading to the identification of potential clinically useful protein biomarkers. Finally, proteomics has been used to evaluate alterations derived from semen sample processing, which might have an impact on fertility treatments. However, the intrinsic heterogeneity and inter-individual variability of the semen samples have resulted in a relatively low overlap among proteomic reports, highlighting the relevance of combining strategies for data validation and applying strict criteria for proteomic data analysis to obtain reliable results. This mini-review provides an overview of the most critical steps to conduct robust sperm proteomic studies, the most relevant results obtained so far, and potential next steps to increase the impact of sperm proteomic data.
Collapse
Affiliation(s)
- Judit Castillo
- Molecular Biology of Reproduction and Development Research Group, Departament de Biomedicina, Facultat de Medicina i Ciències de la Salut, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Fundació Clínic per a la Recerca Biomèdica, Universitat de Barcelona (UB), Barcelona, Spain
| | - Alberto de la Iglesia
- Molecular Biology of Reproduction and Development Research Group, Departament de Biomedicina, Facultat de Medicina i Ciències de la Salut, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Fundació Clínic per a la Recerca Biomèdica, Universitat de Barcelona (UB), Barcelona, Spain
| | - Marina Leiva
- Molecular Biology of Reproduction and Development Research Group, Departament de Biomedicina, Facultat de Medicina i Ciències de la Salut, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Fundació Clínic per a la Recerca Biomèdica, Universitat de Barcelona (UB), Barcelona, Spain
| | - Meritxell Jodar
- Molecular Biology of Reproduction and Development Research Group, Departament de Biomedicina, Facultat de Medicina i Ciències de la Salut, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Fundació Clínic per a la Recerca Biomèdica, Universitat de Barcelona (UB), Barcelona, Spain
- Biochemistry and Molecular Genetics Service, Biomedical Diagnostic Center (CDB), Hospital Clínic de Barcelona, Barcelona, Spain
| | - Rafael Oliva
- Molecular Biology of Reproduction and Development Research Group, Departament de Biomedicina, Facultat de Medicina i Ciències de la Salut, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Fundació Clínic per a la Recerca Biomèdica, Universitat de Barcelona (UB), Barcelona, Spain
- Biochemistry and Molecular Genetics Service, Biomedical Diagnostic Center (CDB), Hospital Clínic de Barcelona, Barcelona, Spain
| |
Collapse
|
5
|
Odroniec A, Olszewska M, Kurpisz M. Epigenetic markers in the embryonal germ cell development and spermatogenesis. Basic Clin Androl 2023; 33:6. [PMID: 36814207 PMCID: PMC9948345 DOI: 10.1186/s12610-022-00179-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Accepted: 11/25/2022] [Indexed: 02/24/2023] Open
Abstract
Spermatogenesis is the process of generation of male reproductive cells from spermatogonial stem cells in the seminiferous epithelium of the testis. During spermatogenesis, key spermatogenic events such as stem cell self-renewal and commitment to meiosis, meiotic recombination, meiotic sex chromosome inactivation, followed by cellular and chromatin remodeling of elongating spermatids occur, leading to sperm cell production. All the mentioned events are at least partially controlled by the epigenetic modifications of DNA and histones. Additionally, during embryonal development in primordial germ cells, global epigenetic reprogramming of DNA occurs. In this review, we summarized the most important epigenetic modifications in the particular stages of germ cell development, in DNA and histone proteins, starting from primordial germ cells, during embryonal development, and ending with histone-to-protamine transition during spermiogenesis.
Collapse
Affiliation(s)
- Amadeusz Odroniec
- grid.413454.30000 0001 1958 0162Institute of Human Genetics, Polish Academy of Sciences, Strzeszynska 32, 60–479 Poznan, Poland
| | - Marta Olszewska
- Institute of Human Genetics, Polish Academy of Sciences, Strzeszynska 32, 60-479, Poznan, Poland.
| | - Maciej Kurpisz
- grid.413454.30000 0001 1958 0162Institute of Human Genetics, Polish Academy of Sciences, Strzeszynska 32, 60–479 Poznan, Poland
| |
Collapse
|
6
|
Bukhari I, Thorne RF, Shi Q. Editorial: Molecular and cytogenetic research advances in human reproduction. Front Endocrinol (Lausanne) 2022; 13:1107903. [PMID: 36568095 PMCID: PMC9780652 DOI: 10.3389/fendo.2022.1107903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 11/30/2022] [Indexed: 12/14/2022] Open
Affiliation(s)
- Ihtisham Bukhari
- Henan Key Laboratory of Helicobacter pylori, Microbiota and Gastrointestinal Cancers, Marshall Medical Research Center, Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Rick Francis Thorne
- Translational Research Institute, Henan Provincial and Zhengzhou City Key Laboratory of Non-coding RNA and Cancer Metabolism, Henan International Join Laboratory of Non-coding RNA and Metabolism in Cancer, Henan Provincial People’s Hospital, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan, China
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, NSW, Australia
- *Correspondence: Qinghua Shi, ; Rick Francis Thorne,
| | - Qinghua Shi
- Division of Reproduction and Genetics, First Affiliated Hospital of USTC, Hefei National Laboratory for Physical Sciences at Microscale, School of Basic Medical Sciences, Division of Life Sciences and Medicine, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei, China
- *Correspondence: Qinghua Shi, ; Rick Francis Thorne,
| |
Collapse
|