In Silico Identification of lncRNAs Regulating Sperm Motility in the Turkey (Meleagris gallopavo L.)

Jastrzebski, J; Lipka, Aleksandra; Majewska, Marta; Makowczenko, Karol G; Paukszto, Łukasz; Bukowska, Joanna; Dorocki, Sławomir; Kozłowski, Krzysztof; Słowińska, Mariola

doi:10.3390/ijms23147642

Cited by 4 publications

(1 citation statement)

References 96 publications

(117 reference statements)

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“…More recently, using public microarray data, Joshi et al identified fifteen functionally conserved lncRNAs across multiple studies in humans and mice 25 , which with HISTA, we explore deeply. Broadly, in the testis, lncRNA could A) regulate the expression of protein-coding genes involved in sperm production or function 26 . B) Directly interact with sperm cells or other cells in the testis 27 , potentially binding to receptors on the surface of sperm cells, altering their motility or ability to fertilize an egg or interact with the Sertoli cells or Leydig cells.…”

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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IncRna: The R Package for Optimizing lncRNA Identification Processes

Jastrzebski,

Pascarella,

Lipka

et al. 2023

Journal of Computational Biology

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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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In Silico Identification of lncRNAs Regulating Sperm Motility in the Turkey (Meleagris gallopavo L.)

Cited by 4 publications

References 96 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

IncRna: The R Package for Optimizing lncRNA Identification Processes

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

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