Unified single-cell analysis of testis gene regulation and pathology in 5 mouse strains

Abstract

By removing the confounding factor of cellular heterogeneity, single cell genomics can revolutionize the study of development and disease, but methods are needed to simplify comparison among individuals. To develop such a framework, we assayed the transcriptome in 62,600 single cells from the testes of wildtype mice, and mice with gonadal defects due to disruption of the genes Mlh3, Hormad1, Cul4a or Cnp. The resulting expression atlas of distinct cell clusters revealed novel markers and new insights into testis gene regulation. By jointly analysing mutant and wildtype cells using a model-based factor analysis method, SDA, we decomposed our data into 46 components that identify novel meiotic gene regulatory programmes, mutant-specific pathological processes, and technical effects. Moreover, we identify, de novo, DNA sequence motifs associated with each component, and show that SDA

Dynamic transcriptome profiles within spermatogonial and spermatocyte populations during postnatal testis maturation revealed by single-cell sequencing

“…Adult samples were minimally processed with a single-step magnetic cell sort to provide representation of all germ cell types in the adult testis. Previously, single-cell-sequencing studies on sorted cells have provided valuable information about specific, and marker-defined cell types [15,70]. The study presented here, however, focuses on profiling the germline during postnatal testis maturation, importantly capturing the first-wave of spermatogonia and spermatocytes which exhibit differences from later, steady-state spermatogenesis.…”

“…Cell types were manually identified by characteristic marker genes [18,94,95], and confirmed by SingleR (Single-cell Recognition) package. Differential expression analysis was performed based on the MAST (Model-based Analysis of Single Cell Transcriptomics) [36].…”

“…While the developmental transitions which underlie germ cell differentiation and maturation have been broadly defined, the gene regulatory underpinnings of these transitions remain largely uncharacterized. Concurrent with our work presented herein, many groups have also investigated developmental transitions within the testis using single-cell sequencing, and have begun to shed some light upon genetic regulatory mechanisms of these processes [14–18]. Intriguingly, several new cell types have been identified, including previously unidentified somatic cells [14], and murine spermatogenesis has been extensively compared to human spermatogenesis [15], emphasizing the translational impact of these types of studies.…”

Testis single-cell RNA-seq reveals the dynamics of de novo gene transcription and germline mutational bias in Drosophila

“…Spermatogenesis is a highly conserved process in many animal taxa and is well-understood from an anatomical and histological perspective, but its molecular foundations are still poorly understood (Birkhead et al, 2008; Demarco et al, 2014; Russell et al, 1993; White-Cooper, 2010). New analytical methods in genomics allow the quantification of expression biases of gene groups involved in various cellular processes (Jung et al, 2018; Lukassen et al, 2018; Stévant et al, 2018). From the prevalence of their transcripts, one can make inferences about the developmental timing of translation, DNA repair, nuclear export, and other processes.…”

Staged profiling of sperm development in sync

“…The outcomes from other similar ongoing studies would also be important for the field, especially as elongating spermatids and the surrounding niche of somatic subtypes were not profiled in this study. 10,11 In summary, the study shows a careful application of scRNA-seq together with synchronization of developing cells that enriches rare cellular sub-populations. Such an approach can be used to identify and validate novel players during differentiation in other contexts.…”