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RESEARCH ARTICLE (Open Access)
Contents Vol 36(13)

ShinySperm: navigating the sperm proteome landscape

David A. Skerrett-Byrne https://orcid.org/0000-0002-1804-1826 A B C D * , Raffaele Teperino https://orcid.org/0000-0001-8815-1409 C D and Brett Nixon https://orcid.org/0000-0003-2745-8188 A B
+ Author Affiliations
- Author Affiliations

A Priority Research Centre for Reproductive Science, School of Environmental and Life Sciences, College of Engineering, Science and Environment, The University of Newcastle, Callaghan, NSW 2308, Australia.

B Infertility and Reproduction Research Program, Hunter Medical Research Institute, New Lambton Heights, NSW 2305, Australia.

C Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany.

D German Center for Diabetes Research (DZD), Neuherberg, Germany.

* Correspondence to: David.Skerrett-Byrne@helmholtz-munich.de

Handling Editor: Ana Villaverde

Reproduction, Fertility and Development 36, RD24079 https://doi.org/10.1071/RD24079
Submitted: 28 May 2024  Accepted: 11 July 2024  Published online: 1 August 2024

© 2024 The Author(s) (or their employer(s)). Published by CSIRO Publishing. This is an open access article distributed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License (CC BY-NC-ND)

Abstract

Context

Integrated omics studies hold a crucial role in improving our understanding of reproductive biology. However, the complex datasets so generated are often only accessible via supplementary data files, which lack the capacity for interactive features to allow users to readily interrogate and visualise data of interest.

Aims

The intent of this technical note was to develop an interactive web-based application that enables detailed interrogation of a representative sperm proteome, facilitating a deeper understanding of the proteins identified, their relative abundance, classifications, functions, and associated phenotypes.

Methods

We developed a Shiny web application, ShinySperm (https://reproproteomics.shinyapps.io/ShinySperm/), utilising R and several complementary libraries for data manipulation (dplyr), interactive tables (DT), and visualisation (ggplot2, plotly). ShinySperm features a responsive user interface, dynamic filtering options, interactive charts, and data export capabilities.

Key results

ShinySperm allows users to interactively search, filter, and visualise sperm proteomics data based on key features (e.g. protein classification, sperm cell domain, presence, or absence at different maturation stages). This application responds live to filtering options and enables the generation of interactive plots and tables, thus enhancing user engagement and understanding of the data.

Conclusions

ShinySperm provides a robust platform for the dynamic exploration of epididymal sperm proteome data. It significantly improves accessibility and interpretability of complex datasets, allowing for effective data-driven insights.

Implications

This technical note highlights the potential of interactive web applications in reproductive biology and provides a plug and play script for the field to produce applications for meaningful researcher interaction with complex omic datasets.

Keywords: epididymis, fertility, male fertility, proteomics, publicly accessible data, ShinySperm app, sperm, sperm maturation, sperm proteome.

References

Battistone MA, Spallanzani RG, Mendelsohn AC, Capen D, Nair AV, Brown D, Breton S (2019) Novel role of proton-secreting epithelial cells in sperm maturation and mucosal immunity. Journal of Cell Science 133(5), jcs233239.
| Crossref | Google Scholar |

Bedford JM (2015) The epididymis re-visited: a personal view. Asian Journal of Andrology 17(5), 693-698.
| Crossref | Google Scholar | PubMed |

Deutsch EW, Bandeira N, Sharma V, Perez-Riverol Y, Carver JJ, Kundu DJ, García-Seisdedos D, Jarnuczak AF, Hewapathirana S, Pullman BS, Wertz J, Sun Z, Kawano S, Okuda S, Watanabe Y, Hermjakob H, MacLean B, MacCoss MJ, Zhu Y, Ishihama Y, Vizcaíno JA (2019) The ProteomeXchange consortium in 2020: enabling ‘big data’ approaches in proteomics. Nucleic Acids Research 48(D1), D1145-D1152.
| Crossref | Google Scholar |

Fuentes-Albero MC, González-Brusi L, Cots P, Luongo C, Abril-Sánchez S, Ros-Santaella JL, Pintus E, Ruiz-Díaz S, Barros-García C, Sánchez-Calabuig MJ, García-Párraga D, Avilés M, Izquierdo Rico MJ, García-Vázquez FA (2021) Protein identification of spermatozoa and seminal plasma in bottlenose dolphin. Frontiers in Cell Developmental Biology 9, 673961.
| Crossref | Google Scholar |

Garlovsky MD, Sandler JA, Karr TL (2022) Functional diversity and evolution of the drosophila sperm proteome. Molecular & Cellular Proteomics 21(10), 100281.
| Crossref | Google Scholar | PubMed |

Hermo L, Pelletier R-M, Cyr DG, Smith CE (2010) Surfing the wave, cycle, life history, and genes/proteins expressed by testicular germ cells. Part 2: changes in spermatid organelles associated with development of spermatozoa. Microscopy Research and Technique 73(4), 279-319.
| Crossref | Google Scholar | PubMed |

Krämer A, Green J, Pollard J, Jr, Tugendreich S (2013) Causal analysis approaches in ingenuity pathway analysis. Bioinformatics 30(4), 523-530.
| Crossref | Google Scholar | PubMed |

Nixon B, Johnston SD, Skerrett-Byrne DA, Anderson AL, Stanger SJ, Bromfield EG, Martin JH, Hansbro PM, Dun MD (2019a) Modification of crocodile spermatozoa refutes the tenet that post-testicular sperm maturation is restricted to mammals. Molecular & Cellular Proteomics 18(Suppl 1), S58-S76.
| Crossref | Google Scholar | PubMed |

Nixon B, De Iuliis GN, Hart HM, Zhou W, Mathe A, Bernstein IR, Anderson AL, Stanger SJ, Skerrett-Byrne DA, Jamaluddin MFB, Almazi JG, Bromfield EG, Larsen MR, Dun MD (2019b) Proteomic profiling of mouse epididymosomes reveals their contributions to post-testicular sperm maturation. Molecular & Cellular Proteomics 18(Suppl 1), S91-S108.
| Crossref | Google Scholar | PubMed |

Nixon B, Cafe SL, Eamens AL, De Iuliis GN, Bromfield EG, Martin JH, Skerrett-Byrne DA, Dun MD (2020) Molecular insights into the divergence and diversity of post-testicular maturation strategies. Molecular and Cellular Endocrinology 517, 110955.
| Crossref | Google Scholar | PubMed |

Pini T, Rickard JP, Leahy T, Crossett B, Druart X, de Graaf SP (2018) Cryopreservation and egg yolk medium alter the proteome of ram spermatozoa. Journal of Proteomics 181, 73-82.
| Crossref | Google Scholar | PubMed |

Skerrett-Byrne DA, Anderson AL, Hulse L, Wass C, Dun MD, Bromfield EG, De Iuliis GN, Pyne M, Nicolson V, Johnston SD, Nixon B (2021) Proteomic analysis of koala (Phascolarctos cinereus) spermatozoa and prostatic bodies. Proteomics 21(19), e2100067.
| Crossref | Google Scholar | PubMed |

Skerrett-Byrne DA, Anderson AL, Bromfield EG, Bernstein IR, Mulhall JE, Schjenken JE, Dun MD, Humphrey SJ, Nixon B (2022) Global profiling of the proteomic changes associated with the post-testicular maturation of mouse spermatozoa. Cell Reports 41(7), 111655.
| Crossref | Google Scholar | PubMed |

Trigg NA, Stanger SJ, Zhou W, Skerrett-Byrne DA, Sipilä P, Dun MD, Eamens AL, De Iuliis GN, Bromfield EG, Roman SD, Nixon B (2021) A novel role for milk fat globule-EGF factor 8 protein (MFGE8) in the mediation of mouse sperm-extracellular vesicle interactions. Proteomics 21(13–14), e2000079.
| Crossref | Google Scholar | PubMed |

Vandenbrouck Y, Lane L, Carapito C, Duek P, Rondel K, Bruley C, Macron C, Gonzalez de Peredo A, Couté Y, Chaoui K, Com E, Gateau A, Hesse A-M, Marcellin M, Méar L, Mouton-Barbosa E, Robin T, Burlet-Schiltz O, Cianferani S, Ferro M, Fréour T, Lindskog C, Garin J, Pineau C (2016) Looking for missing proteins in the proteome of human spermatozoa: an update. Journal of Proteome Research 15(11), 3998-4019.
| Crossref | Google Scholar | PubMed |

Zhang M, Chiozzi RZ, Skerrett-Byrne DA, Veenendaal T, Klumperman J, Heck AJR, Nixon B, Helms JB, Gadella BM, Bromfield EG (2022) High resolution proteomic analysis of subcellular fractionated boar spermatozoa provides comprehensive insights into perinuclear theca-residing proteins. Frontiers in Cell and Developmental Biology 10, 836208.
| Crossref | Google Scholar | PubMed |

Zhou W, De Iuliis GN, Dun MD, Nixon B (2018) Characteristics of the epididymal luminal environment responsible for sperm maturation and storage. Frontiers in Endocrinology 9, 59.
| Crossref | Google Scholar |