Application of single-cell RNA sequencing on human testicular samples: a comprehensive review

Fan, Daiming; Ping, Ping; Ma, Yi; Chen, Xiang-Feng

doi:10.7150/ijbs.82191

Cited by 4 publications

(2 citation statements)

References 245 publications

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“…Recently, novel molecular and computational methods were also adopted, such as the metabolic and multi‐Omics employed in spermatogonial stem cell maturation and niche studies (Voigt et al., 2022; Voigt et al., 2023) and comprehensive machine learning for the identification of key genes and molecular pathways for azoospermia (He et al., 2023). Testicular scRNA‐seq data could be further extensively analysed (Dong et al., 2023), which could provide novel insights and resources for mammalian spermatogenesis research.…”

Section: Discussionmentioning

confidence: 99%

“…Single‐cell transcriptome sequencing (scRNA‐seq) is proven to be efficient and effective in disentangling the complex molecular, mechanistic, and evolutionary network of mammalian spermatogenesis in the testis (Dong et al., 2023; Hermann et al., 2018; Murat et al., 2023; Staub & Johnson, 2018; Suzuki, 2023). In humans, the first testicular scRNA‐seq study defined the cell types of spermatogonia (3), spermatocyte (7), and spermatid (4), and discovered altered gene expression patterns of testicular somatic cells for one nonobstructive azoospermia (NOA) patient (Wang et al., 2018).…”

Section: Introductionmentioning

confidence: 99%

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Integrated single cell transcriptome sequencing analysis reveals species‐specific genes and molecular pathways for pig spermiogenesis

Zhao,

Yang,

2023

Reprod Domestic Animals

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Mammalian spermatogenesis is a highly complicated and intricately organized process involving spermatogonia propagation (mitosis) and meiotic differentiation into mature sperm cells (spermiogenesis). In pigs, spermatogonia development and the role of somatic cells in spermatogenesis were previously investigated in detail. However, the characterization of key molecules fundamental to pig spermiogenesis remains less explored. Here we compared spermatogenesis between humans and pigs, focusing on spermiogenesis, by integrative testicular single‐cell RNA sequencing (scRNA‐seq) analysis. Human and pig testicular cells were clustered into 26 different groups, with cell‐type‐specific markers and signalling pathways. For spermiogenesis, pseudo‐time analysis classified the lineage differentiation routes for round, elongated spermatids and spermatozoa. Moreover, markers and molecular pathways specific to each type of spermatids were examined for humans and pigs, respectively. Furthermore, high‐dimensional weighted gene co‐expression network analysis (hdWGCNA) identified gene modules specific for each type of human and pig spermatids. Hub genes (pig: SNRPD2.1 related to alternative splicing; human: CATSPERZ, Ca[2+] ion channel) potentially involved in spermiogenesis were also revealed. Taken together, our integrative analysis found that human and pig spermiogeneses involve specific genes and molecular pathways and provided resources and insights for further functional investigation on spermatid maturation and male reproductive ability.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Integrated single cell transcriptome sequencing analysis reveals species‐specific genes and molecular pathways for pig spermiogenesis

Zhao,

Yang,

2023

Reprod Domestic Animals

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Adverse effects of microplastics and nanoplastics on the reproductive system: A comprehensive review of fertility and potential harmful interactions

Hong

Wei

2023

Science of The Total Environment

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

Mahyari,

Vigh-Conrad,

Daube

et al. 2023

Preprint

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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

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Application of single-cell RNA sequencing on human testicular samples: a comprehensive review

Cited by 4 publications

References 245 publications

Integrated single cell transcriptome sequencing analysis reveals species‐specific genes and molecular pathways for pig spermiogenesis

Integrated single cell transcriptome sequencing analysis reveals species‐specific genes and molecular pathways for pig spermiogenesis

Adverse effects of microplastics and nanoplastics on the reproductive system: A comprehensive review of fertility and potential harmful interactions

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

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