Analysis of <scp>lncRNA</scp> and <scp>mRNA</scp> expression profiling in immature and mature <scp>DeZhou</scp> donkey (<i>equine Taurus</i>) testes

Yu, Jie; Wang, Zhaofei; Wang, Fuwen; Ge, Yang; Cheng, Jie; Ji, Chuanliang; Li, Min; Liu, Bing; Wang, Yantao; Dang, Ruihua

doi:10.1111/rda.14330

Cited by 3 publications

(1 citation statement)

References 65 publications

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“…Several others have specifically focused on the testis [19][20][21][22] , including studies in domesticated animals linking fertility robustness to several lncRNAs [23][24][25] . In a study with mice using microarrays, the testis was shown to have the highest number of expressed and specific lncRNAs 22 .…”

Section: Vignette 1: Novel Sets Of Lncrna Molecules Identified As Key...mentioning

confidence: 99%

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

Mahyari,

Vigh‐Conrad,

Daube

et al. 2024

Andrology

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BackgroundSingle‐cell RNA‐seq (scRNA‐Seq) has been widely adopted to study gene expression of the human testis. Several datasets of scRNA‐Seq from human testis have been generated from different groups processed with different informatics pipelines. An integrated atlas of scRNA‐Seq expression constructed from multiple donors, developmental ages, and fertility states would be widely useful for the testis research community.ObjectiveTo describe the generation and use of the human infertility single‐cell testis atlas (HISTA), an interactive web tool for understanding human spermatogenesis through scRNA‐Seq analysis.MethodsWe obtained scRNA‐Seq datasets derived from 12 donors, including healthy adult controls, juveniles, and several infertility cases, and reprocessed these data using methods to remove batch effects. Using Shiny, an open‐source environment for data visualization, we created numerous interactive tools for exploring the data, some of which support simple statistical hypothesis testing. We used the resulting HISTA browser and its underlying data to demonstrate HISTA's value for testis researchers.ResultsA primary application of HISTA is to search by a single gene or a set of genes; thus, we present various analyses that quantify and visualize gene expression across the testis cells and pathology. HISTA also contains machine‐learning‐derived gene modules (“components”) that capture the entire transcriptional landscape of the testis tissue. We show how the use of these components can simplify the highly complex data in HISTA and assist with the interpretation of genes with unknown functions. Finally, we demonstrate the diverse ways HISTA can be used for new data analysis, including hypothesis testing.Discussion and conclusionsHISTA is a research environment that can help scientists organize and understand the high‐dimensional transcriptional landscape of the human testis. HISTA has already contributed to published testis research and can be updated as needed with input from the research community or downloaded and modified for individual needs.

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Section: Vignette 1: Novel Sets Of Lncrna Molecules Identified As Key...mentioning

confidence: 99%

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

Mahyari,

Vigh‐Conrad,

Daube

et al. 2024

Andrology

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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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A review of genetic resources and trends of omics applications in donkey research: focus on China

Khan,

Chen,

Wang

et al. 2024

Front. Vet. Sci.

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Omics methodologies, such as genomics, transcriptomics, proteomics, metabolomics, lipidomics and microbiomics, have revolutionized biological research by allowing comprehensive molecular analysis in livestock animals. However, despite being widely used in various animal species, research on donkeys has been notably scarce. China, renowned for its rich history in donkey husbandry, plays a pivotal role in their conservation and utilization. China boasts 24 distinct donkey breeds, necessitating conservation efforts, especially for smaller breeds facing extinction threats. So far, omics approaches have been employed in studies of donkey milk and meat, shedding light on their composition and quality. Similarly, omics methods have been utilized to explore the molecular basis associated with donkey growth, meat production, and quality traits. Omics analysis has also unraveled the critical role of donkey microbiota in health and nutrition, with gut microbiome studies revealing associations with factors such as pregnancy, age, transportation stress, and altitude. Furthermore, omics applications have addressed donkey health issues, including infectious diseases and reproductive problems. In addition, these applications have also provided insights into the improvement of donkey reproductive efficiency research. In conclusion, omics methodologies are essential for advancing knowledge about donkeys, their genetic diversity, and their applications across various domains. However, omics research in donkeys is still in its infancy, and there is a need for continued research to enhance donkey breeding, production, and welfare in China and beyond.

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Analysis of lncRNA and mRNA expression profiling in immature and mature DeZhou donkey (equine Taurus) testes

Cited by 3 publications

References 65 publications

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

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

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

A review of genetic resources and trends of omics applications in donkey research: focus on China

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