Prediction and Validation of Mouse Meiosis-Essential Genes Based on Spermatogenesis Proteome Dynamics

Abstract

The molecular mechanism associated with mammalian meiosis has yet to be fully explored, and one of the main reasons for this lack of exploration is that some meiosis-essential genes are still unknown. The profiling of gene expression during spermatogenesis has been performed in previous studies, yet few studies have aimed to find new functional genes. Since there is a huge gap between the number of genes that are able to be quantified and the number of genes that can be characterized by phenotype screening in one assay, an efficient method to rank quantified genes according to phenotypic relevance is of great importance. We proposed to rank genes by the probability of their function in mammalian meiosis based on global protein abundance using machine learning. Here, nine types of germ cells focusing on continual substages of meiosis prophase I were isolated, and the corresponding proteomes were quantified by high-resolution mass spectrometry. By combining meiotic labels annotated from the MGI mouse knockout database and the spermatogenesis proteomics dataset, a supervised machine learning package, FuncProFinder, was developed to rank meiosis-essential candidates. Of the candidates whose functions were unannotated, four of ten genes with the top prediction scores, Zcwpw1, Tesmin, 1700102P08Rik and Kctd19, were validated as meiosis-essential genes by knockout mouse models. Therefore, mammalian meiosis-essential genes could be efficiently predicted based on the protein abundance dataset, which provides a paradigm for other functional gene mining from a related abundance dataset.

KCTD19 and its associated protein ZFP541 are independently essential for meiosis in male mice

“…In the present study, we identified Kctd19 as a male fertility-related factor by CRISPR/Cas9-mediated screening of testis enriched genes and validated our result with transgenic rescue experiments. Recently, Fang et al also reported metaphase I arrest in Kctd19 KO male mice [30], corroborating our results. In detailed phenotypic analyses, we found that Kctd19 KO spermatocytes failed to complete meiotic division with defects in metaphase I organization.…”

“…Recently, Fang et al . also reported metaphase I arrest in Kctd19 KO male mice [ 30 ], corroborating our results. In detailed phenotypic analyses, we found that Kctd19 KO spermatocytes failed to complete meiotic division with defects in metaphase I organization.…”

A drastic shift in the energetic landscape of toothed whale sperm cells

“…Unlike most mammals, the dismantling of sperm glycolysis and shift toward mitochondrial-enclosed metabolic pathways allowed the maintenance of normal sperm functions in Odontoceti. For instance, the inactivation of glycolytic genes, in humans and mice, induces defects in sperm structure and motility, leading to infertility in humans and mice (figshare link in Key resources table); 7,18,20,23,[31][32][33][34][35][36][37][38][39][40][41] while in the eusocial naked mole rat, with a dominant male mating strategy, sperm is abnormal. 17 Yet in dolphins, sperm quality is generally very high, with few abnormal sperm, in agreement with their promiscuous mating system based on sperm competition.…”

Diverse Monogenic Subforms of Human Spermatogenic Failure

“…We elected to remove cases who were heterozygous for a single well-acknowledged pathogenic CFTR variant as a conservative measure. Due to the limitations of WES to detect variants in non-exonic regions, we are not able to exclude the presence of other non-coding pathogenic variants in the CFTR gene in trans with the coding variants 19, 20 . Additionally, identity by descent (IBD) analysis was performed using SNPRelate R package 21 to identify and remove one counterpart of each accidental sample duplicate or twin pairs and cases with cryptic relatedness to avoid ascertainment bias of rare variation.…”