The Human Infertility Single-cell Testis Atlas (HISTA): An interactive molecular scRNA-Seq reference of the human testis

Abstract

Background: The Human Infertility Single-cell Testis Atlas (HISTA) is an interactive web tool and a reference for navigating the transcriptome of the human testis. It was developed using joint analyses of scRNA-Seq datasets derived from a dozen donors, including healthy adult controls, juveniles, and several infertility cases. HISTA is very different than other websites of testis scRNA-seq data, providing visualization and hypothesis testing tools on a batch-removed and integrated dataset of 23429 genes measured across 26093 cells. Objective: The main goal of this manuscript is to describe HISTA in detail and highlight its unique and novel features. Methods: Therefore, we used HISTA as a guide for its application and demonstrated HISTA's translational capacity to follow up on two observations of biological relevance. Results: Our first analytical vignette identifies novel groupings of tightly regulated long non-coding RNA (lncRNA) molecules throughout spermatogenesis, suggesting specific functional genomics of these groupings. This analysis also found highly controlled expression of pairs of sense and antisense transcripts, suggesting conjoined regulatory mechanisms. In the next investigative vignette, we examined gene patterns in undifferentiated spermatogonia (USgs). We found the NANOS family of genes function as key drivers of transcriptomic signatures involved in human spermatogonial self-renewal programming; for the first time, demonstrating the relationship of NANOS1/2/3 transcripts in humans with scRNA-seq. Discussion and Conclusions: Using HISTA, we found new observations that contribute to unraveling the mechanisms behind transcriptional regulation and maintenance germ cells across spermatogenesis. Furthermore, our findings provide guidance on future validation studies and experimental direction. Overall, HISTA continues to be utilized in testis-related research, and thus is updated regularly with new analytical methods, visualizations, and data. We aim to have it serve as a research environment for a broad range of investigators looking to explore the testis tissue and male infertility. Availability and Implementation: HISTA is available as an interactive web tool: https://conradlab.shinyapps.io/HISTA Source code and documentation for HISTA are provided on GitHub: https://github.com/eisascience/HISTA

A naturally occurring variant ofMBD4causes maternal germline hypermutation in primates

“…Notably, our finding of a maternal germline hypermutator phenotype appears to be the first clear evidence of genetic variants affecting germline mutation in a female mammal. It seems plausible that, as the male germline is subject to extensive methylation and as MBD4 is strongly expressed in male germ cells ( Mahyari et al 2023 ), zygotic MBD4 loss of function in a male would also lead to an increased rate of germline mutation. Indeed, all of the paternal hypermutator alleles reported to date affect genes that show robust expression in human oocytes ( Menezo et al 2007 ) and, as such, would be expected to lead to hypermutation of the female germline as well.…”

X-chromosome loss rescues Sertoli cell maturation and spermatogenesis in Klinefelter syndrome

“…To investigate if Sertoli cells in type A tubules are mature as their nuclei morphology and localization along the basement membrane in the tubules suggest, we stained with antibodies against three Sertoli cell maturity markers, the androgen receptor (AR) (Sharpe et al, 2003;Wang et al, 2022), Clusterin (CLU, also known as SGP-2), which is secreted from mature Sertoli cells (Sharpe et al, 2003;Sylvester et al, 1984), and defensin beta 119 (DEFB119), a newly identified marker (Mahyari et al, 2023;Zhao et al, 2020). All three markers were highly expressed in type A Sertoli cells which was in contrast to type B Sertoli cells showing low expression levels (Fig.…”

The human infertility single‐cell testis atlas (HISTA): an interactive molecular scRNA‐Seq reference of the human testis

“…HISTA is developed using the "shinydashboard" package 48 on the Shiny framework 49 written in R 50 with the help of several key packages, including ggplot 51 , dplyr 52,53 , and data.table 54 as well as Seurat 52 , which was used in parallel processing of this data as described previously 1 . The code is available on Github (https://github.com/eisascience/HISTA) 55 .…”