GonadSAGE: a comprehensive SAGE database for transcript discovery on male embryonic gonad development

ASER: Animal Sex Reversal Database

Sex reversal, representing extraordinary sexual plasticity during the life cycle, not only triggers reproduction in animals but also affects reproductive and endocrine system-related diseases and cancers in humans. Sex reversal has been broadly reported in animals; however, an integrated resource hub of sex reversal information is still lacking. Here, we constructed a comprehensive database named ASER (Animal Sex Reversal) by integrating sex reversal-related data of 18 species from teleostei to mammalia. We systematically collected 40,018 published papers and mined the sex reversal-associated genes (SRGs), including their regulatory networks, from 1611 core papers. We annotated homologous genes and computed conservation scores for whole genomes across the 18 species. Furthermore, we collected available RNA-seq datasets and investigated the expression dynamics of SRGs during sex reversal or sex determination processes. In addition, we manually annotated 550 in situ hybridization (ISH), fluorescence in situ hybridization (FISH), and immunohistochemistry (IHC) images of SRGs from the literature and described their spatial expression in the gonads. Collectively, ASER provides a unique and integrated resource for researchers to query and reuse organized data to explore the mechanisms and applications of SRGs in animal breeding and human health. The ASER database is publicly available at http://aser.ihb.ac.cn/.

Hi-C deconvolution of a textile dye-related microbiome reveals novel taxonomic landscapes and links phenotypic potential to individual genomes

Microbial biodiversity is represented by a variety of genomic landscapes adapted to dissimilar environments on Earth. These genomic landscapes contain functional signatures connected with the community phenotypes. Here, we assess the genomic microbial diversity landscape at a high-resolution level of a polluted river-associated microbiome (Morelos, México), cultured in a medium enriched with anthraquinone Deep Blue 35 dye. We explore the resultant textile dye microbiome to infer links between predicted biodegradative functions, and metagenomic and metabolic potential, especially using the information obtained from individual reconstructed genomes. By using Hi-C proximity-ligation deconvolution method, we deconvoluted 97 genome composites (80% potentially novel species). The main taxonomic determinants were Methanobacterium, Clostridium, and Cupriavidus genera constituting 50, 22, and 11% of the total community profile. Also, we observed a rare biosphere of novel taxa without clear taxonomic standing. Removal of 50% chemical oxygen demand with 23% decolorization was observed after 30 days of dye enrichment. Genes related to catalase-peroxidase, polyphenol oxidase, and laccase enzymes were predicted as associated with textile dye biodegradation phenotype under our study conditions, highlighting the potential of metagenome-wide analysis to predict biodegradative determinants. This study prompts high-resolution screening of individual genomes within textile dye river sediment microbiomes or complex communities under environmental pressures.

Assessment of the impact of mitochondrial genotype upon drug-induced mitochondrial dysfunction in platelets derived from healthy volunteers

Mitochondrial DNA (mtDNA) is highly polymorphic and encodes 13 proteins which are critical to the production of ATP via oxidative phosphorylation. As mtDNA is maternally inherited and undergoes negligible recombination, acquired mutations have subdivided the human population into several discrete haplogroups. Mitochondrial haplogroup has been found to significantly alter mitochondrial function and impact susceptibility to adverse drug reactions. Despite these findings, there are currently limited models to assess the effect of mtDNA variation upon susceptibility to adverse drug reactions. Platelets offer a potential personalised model of this variation, as their anucleate nature offers a source of mtDNA without interference from the nuclear genome. This study, therefore, aimed to determine the effect of mtDNA variation upon mitochondrial function and drug-induced mitochondrial dysfunction in a platelet model. The mtDNA haplogroup of 383 healthy volunteers was determined using next-generation mtDNA sequencing (Illumina MiSeq). Subsequently, 30 of these volunteers from mitochondrial haplogroups H, J, T and U were recalled to donate fresh, whole blood from which platelets were isolated. Platelet mitochondrial function was tested at basal state and upon treatment with compounds associated with both mitochondrial dysfunction and adverse drug reactions, flutamide, 2-hydroxyflutamide and tolcapone (10–250 μM) using extracellular flux analysis. This study has demonstrated that freshly-isolated platelets are a practical, primary cell model, which is amenable to the study of drug-induced mitochondrial dysfunction. Specifically, platelets from donors of haplogroup J have been found to have increased susceptibility to the inhibition of complex I-driven respiration by 2-hydroxyflutamide. At a time when individual susceptibility to adverse drug reactions is not fully understood, this study provides evidence that inter-individual variation in mitochondrial genotype could be a factor in determining sensitivity to mitochondrial toxicants associated with costly adverse drug reactions.

Impact of concurrency on the performance of a whole exome sequencing pipeline

Background

Current high-throughput technologies—i.e. whole genome sequencing, RNA-Seq, ChIP-Seq, etc.—generate huge amounts of data and their usage gets more widespread with each passing year. Complex analysis pipelines involving several computationally-intensive steps have to be applied on an increasing number of samples. Workflow management systems allow parallelization and a more efficient usage of computational power. Nevertheless, this mostly happens by assigning the available cores to a single or few samples’ pipeline at a time. We refer to this approach as naive parallel strategy (NPS). Here, we discuss an alternative approach, which we refer to as concurrent execution strategy (CES), which equally distributes the available processors across every sample’s pipeline.

Results

Theoretically, we show that the CES results, under loose conditions, in a substantial speedup, with an ideal gain range spanning from 1 to the number of samples. Also, we observe that the CES yields even faster executions since parallelly computable tasks scale sub-linearly. Practically, we tested both strategies on a whole exome sequencing pipeline applied to three publicly available matched tumour-normal sample pairs of gastrointestinal stromal tumour. The CES achieved speedups in latency up to 2–2.4 compared to the NPS.

Conclusions

Our results hint that if resources distribution is further tailored to fit specific situations, an even greater gain in performance of multiple samples pipelines execution could be achieved. For this to be feasible, a benchmarking of the tools included in the pipeline would be necessary. It is our opinion these benchmarks should be consistently performed by the tools’ developers. Finally, these results suggest that concurrent strategies might also lead to energy and cost savings by making feasible the usage of low power machine clusters.

Epigenomic, genomic, and transcriptomic landscape of schwannomatosis

Schwannomatosis (SWNTS) is a genetic cancer predisposition syndrome that manifests as multiple and often painful neuronal tumors called schwannomas (SWNs). While germline mutations in SMARCB1 or LZTR1, plus somatic mutations in NF2 and loss of heterozygosity in chromosome 22q have been identified in a subset of patients, little is known about the epigenomic and genomic alterations that drive SWNTS-related SWNs (SWNTS-SWNs) in a majority of the cases. We performed multiplatform genomic analysis and established the molecular signature of SWNTS-SWNs. We show that SWNTS-SWNs harbor distinct genomic features relative to the histologically identical non-syndromic sporadic SWNs (NS-SWNS). We demonstrate the existence of four distinct DNA methylation subgroups of SWNTS-SWNs that are associated with specific transcriptional programs and tumor location. We show several novel recurrent non-22q deletions and structural rearrangements. We detected the SH3PXD2A-HTRA1 gene fusion in SWNTS-SWNs, with predominance in LZTR1-mutant tumors. In addition, we identified specific genetic, epigenetic, and actionable transcriptional programs associated with painful SWNTS-SWNs including PIGF, VEGF, MEK, and MTOR pathways, which may be harnessed for management of this syndrome.

Germline variants of Brazilian women with breast cancer and detection of a novel pathogenic ATM deletion in early-onset breast cancer

BACKGROUND

It is estimated that 5-10% of breast cancer cases are hereditary. The identification of pathogenic germline variants allows individualized preventive health care, improvement of clinical management and genetic counseling. Studies in ethnically admixed Latin American populations have identified regions with increased frequency of deleterious variants in breast cancer predisposing genes. In this context, the Brazilian population exhibits great genetic heterogeneity, and is not well represented in international databases, which makes it difficult to interpret the clinical relevance of germline variants.

METHODS

We evaluated the frequency of pathogenic/likely pathogenic (P/LP) germline variants in up to 37 breast cancer predisposing genes, in a cohort of 105 breast and/or ovarian cancer Brazilian women referred to two research centers between 2014 and 2019.

RESULTS

A total of 22 patients (21%) were found to carry P/LP variants, and 16 VUS were detected in 15 patients (14.3%). Additionally, a novel pathogenic ATM intragenic deletion was identified in an early-onset breast cancer. We also detected a BRCA1 pathogenic variant (c.5074+2T>C) in higher frequency (10×) than in other studies with similar cohorts.

CONCLUSIONS

Our findings contribute to the characterization of the genetic background of breast cancer predisposition in the Brazilian population as a useful resource to discriminate between deleterious variants and VUS, thus enabling improvement in the preventive health care and clinical management of carriers.

The ReproGenomics Viewer: a multi-omics and cross-species resource compatible with single-cell studies for the reproductive science community

MOTIVATION

Recent advances in transcriptomics have enabled unprecedented insight into gene expression analysis at a single-cell resolution. While it is anticipated that the number of publications based on such technologies will increase in the next decade, there is currently no public resource to centralize and enable scientists to explore single-cell datasets published in the field of reproductive biology.

RESULTS

Here, we present a major update of the ReproGenomics Viewer, a cross-species and cross-technology web-based resource of manually-curated sequencing datasets related to reproduction. The redesign of the ReproGenomics Viewer's architecture is accompanied by significant growth of the database content including several landmark single-cell RNA-sequencing datasets. The implementation of additional tools enables users to visualize and browse the complex, high-dimensional data now being generated in the reproductive field.

AVAILABILITY AND IMPLEMENTATION

The ReproGenomics Viewer resource is freely accessible at http://rgv.genouest.org. The website is implemented in Python, JavaScript and MongoDB, and is compatible with all major browsers. Source codes can be downloaded from https://github.com/fchalmel/RGV.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Methods for the Study of Gonadal Development

Current knowledge on gonadal development and sex determination is the product of many decades of research involving a variety of scientific methods from different biological disciplines such as histology, genetics, biochemistry, and molecular biology. The earliest embryological investigations, followed by the invention of microscopy and staining methods, were based on histological examinations. The most robust development of histological staining techniques occurred in the second half of the nineteenth century and resulted in structural descriptions of gonadogenesis. These first studies on gonadal development were conducted on domesticated animals; however, currently the mouse is the most extensively studied species. The next key point in the study of gonadogenesis was the advancement of methods allowing for the in vitro culture of fetal gonads. For instance, this led to the description of the origin of cell lines forming the gonads. Protein detection using antibodies and immunolabeling methods and the use of reporter genes were also invaluable for developmental studies, enabling the visualization of the formation of gonadal structure. Recently, genetic and molecular biology techniques, especially gene expression analysis, have revolutionized studies on gonadogenesis and have provided insight into the molecular mechanisms that govern this process. The successive invention of new methods is reflected in the progress of research on gonadal development.

GermlncRNA: a unique catalogue of long non-coding RNAs and associated regulations in male germ cell development

Spermatogenic failure is a major cause of male infertility, which affects millions of couples worldwide. Recent discovery of long non-coding RNAs (lncRNAs) as critical regulators in normal and disease development provides new clues for delineating the molecular regulation in male germ cell development. However, few functional lncRNAs have been characterized to date. A major limitation in studying lncRNA in male germ cell development is the absence of germ cell-specific lncRNA annotation. Current lncRNA annotations are assembled by transcriptome data from heterogeneous tissue sources; specific germ cell transcript information of various developmental stages is therefore under-represented, which may lead to biased prediction or fail to identity important germ cell-specific lncRNAs. GermlncRNA provides the first comprehensive web-based and open-access lncRNA catalogue for three key male germ cell stages, including type A spermatogonia, pachytene spermatocytes and round spermatids. This information has been developed by integrating male germ transcriptome resources derived from RNA-Seq, tiling microarray and GermSAGE. Characterizations on lncRNA-associated regulatory features, potential coding gene and microRNA targets are also provided. Search results from GermlncRNA can be exported to Galaxy for downstream analysis or downloaded locally. Taken together, GermlncRNA offers a new avenue to better understand the role of lncRNAs and associated targets during spermatogenesis.

Database URL: http://germlncrna.cbiit.cuhk.edu.hk/

The ReproGenomics Viewer: an integrative cross-species toolbox for the reproductive science community

We report the development of the ReproGenomics Viewer (RGV), a multi- and cross-species working environment for the visualization, mining and comparison of published omics data sets for the reproductive science community. The system currently embeds 15 published data sets related to gametogenesis from nine model organisms. Data sets have been curated and conveniently organized into broad categories including biological topics, technologies, species and publications. RGV's modular design for both organisms and genomic tools enables users to upload and compare their data with that from the data sets embedded in the system in a cross-species manner. The RGV is freely available at http://rgv.genouest.org.

Characterization of gonadal transcriptomes from Nile tilapia (Oreochromis niloticus) reveals differentially expressed genes

Four pairs of XX and XY gonads from Nile tilapia were sequenced at four developmental stages, 5, 30, 90, and 180 days after hatching (dah) using Illumina Hiseq(TM) technology. This produced 28 Gb sequences, which were mapped to 21,334 genes. Of these, 259 genes were found to be specifically expressed in XY gonads, and 69 were found to be specific to XX gonads. Totally, 187 XX- and 1,358 XY-enhanced genes were identified, and 2,978 genes were found to be co-expressed in XX and XY gonads. Almost all steroidogenic enzymes, including cyp19a1a, were up-regulated in XX gonads at 5 dah; but in XY gonads these enzymes, including cyp11b2, were significantly up-regulated at 90 dah, indicating that, at a time critical to sex determination, the XX fish produced estrogen and the XY fish did not produce androgens. The most pronounced expression of steroidogenic enzyme genes was observed at 30 and 90 dah for XX and XY gonads, corresponding to the initiation of germ cell meiosis in the female and male gonads, respectively. Both estrogen and androgen receptors were found to be expressed in XX gonads, but only estrogen receptors were expressed in XY gonads at 5 dah. This could explain why exogenous steroid treatment induced XX and XY sex reversal. The XX-enhanced expression of cyp19a1a and cyp19a1b at all stages suggests an important role for estrogen in female sex determination and maintenance of phenotypic sex. This work is the largest collection of gonadal transcriptome data in tilapia and lays the foundation for future studies into the molecular mechanisms of sex determination and maintenance of phenotypic sex in non-model teleosts.

The bioinformatics tool box for reproductive biology

Genetics and molecular biology have been instrumental for a better understanding of heritable defects causing human infertility over the past decades. More recently, the field of reproductive biology has harnessed genome biological approaches to gain insight into molecular processes underlying normal and pathological gametogenesis and gamete function. We are currently witnessing yet another quantum leap in our ability to monitor the flow of information from the genome via the transcriptome to the proteome: tiling arrays that cover both strands of a given target genome and RNA-Seq, a method based on ultra-high throughput DNA sequencing, enable us to study noncoding and protein-coding transcripts with unprecedented precision and depth at a reasonable cost. These technologies have spawned a thriving discipline within the bioinformatics field that employs information technology for managing and interpreting biological high-throughput data. This review outlines database projects and online analysis tools useful for life scientists in general and discusses in detail selected projects that have specifically been developed for researchers and clinicians in the field of reproductive biology. This article is part of a Special Issue entitled: Molecular Genetics of Human Reproductive Failure.

Revealing the transcriptome landscape of mouse spermatogonial cells by tiling microarray

In the past decade, the advent of microarray technologies has allowed functional genomic studies of male germ cell development, resulting in the identification of genes governing various processes. A major limitation with conventional gene expression microarray is that results obtained are biased due to gene probe design. The gene probes for expression microarrays are usually represented by a small number of probes located at the 3' end of a transcript. Tiling microarrays eliminate such issue by interrogating the genome in an unbiased fashion through probes tiled across the entire genome. These arrays provide higher genomic resolution and allow the identification of novel transcripts. To reveal the complexity of the genomic landscape of developing male germ cells, we applied tiling microarray to evaluate the transcriptome in spermatogonial cells. Over 50% of all known mouse genes are expressed during testicular development. More than 47% of the transcripts are uncharacterized. The results suggested that the transcription machinery in spermaotogonial cells is more complex than previously envisioned.

Identification of novel long noncoding RNA transcripts in male germ cells

Emerging evidence from these studies suggested that the male germ cell transcriptome is more complex than previously envisioned. In addition to protein-coding genes, the transcriptome also encodes a significant number of nonprotein-coding transcripts. These noncoding (nc) RNAs appear to be involved in a variety of cellular activities, ranging from simple housekeeping to complex regulatory functions. A class of ncRNAs known as long ncRNAs (lncRNAs) were recently shown to be expressed in a developmentally regulated manner during brain and embryonic stem cell development. This protocol aims to predict and identify potential lncRNA candidates using Serial Analysis of Gene Expression (SAGE) data. We also illustrate how to validate the potential lncRNAs by expression analyses using real-time PCR and Northern Blot. Potential lncRNA candidates in male germ cells are identified using our previously established male germ cell SAGE database (GermSAGE).

Building pathways for ovary organogenesis in the mouse embryo

Despite its significant role in oocyte generation and hormone production in adulthood, the ovary, with regard to its formation, has received little attention compared to its male counterpart, the testis. With the exception of germ cells, which undergo a female-specific pattern of meiosis, morphological changes in the fetal ovary are subtle. Over the past 40 years, a number of hypotheses have been proposed for the organogenesis of the mammalian ovary. It was not until the turn of the millennium, thanks to the advancement of genetic and genomic approaches, that pathways for ovary organogenesis that consist of positive and negative regulators have started to emerge. Through the action of secreted factors (R-spondin1, WNT4, and follistatin) and transcription regulators (beta-catenin and FOXL2), the developmental fate of the somatic cells is directed toward ovarian, while testicular components are suppressed. In this chapter, we review the history of studying ovary organogenesis in mammals and present the most recent discoveries using the mouse as the model organism.