Identification of genital tract markers in the human seminal plasma using an integrative genomics approach

Rolland, Antoine; Lavigne, Régis; Dauly, Claire; Calvel, Pierre; Kervarrec, Christine; Fréour, Thomas; Evrard, Bertrand; Rioux‐Leclercq, Nathalie; Auger, Jacques; Pineau, Charles

doi:10.1093/humrep/des360

Cited by 112 publications

(109 citation statements)

References 42 publications

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“…The strategy employed for the visualization of missing proteins expressed in the testis/germ cells was similar to that previously described by our team 27 …”

Section: Immunohistochemistrymentioning

confidence: 99%

Human Spermatozoa as a Model for Detecting Missing Proteins in the Context of the Chromosome-Centric Human Proteome Project

et al. 2015

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The Chromosome-Centric Human Proteome Project (C-HPP) aims at cataloguing the proteins as gene products encoded by the human genome in a chromosome-centric manner. The existence of products of about 82% of the genes has been confirmed at the protein level. However, the number of so-called "missing proteins" remains significant. It was recently suggested that the expression of proteins that have been systematically missed might be restricted to particular organs or cell types, for example, the testis. Testicular function, and spermatogenesis in particular, is conditioned by the successive activation or repression of thousands of genes and proteins including numerous germ cell- and testis-specific products. Both the testis and postmeiotic germ cells are thus promising sites at which to search for missing proteins, and ejaculated spermatozoa are a potential source of proteins whose expression is restricted to the germ cell lineage. A trans-chromosome-based data analysis was performed to catalog missing proteins in total protein extracts from isolated human spermatozoa. We have identified and manually validated peptide matches to 89 missing proteins in human spermatozoa. In addition, we carefully validated three proteins that were scored as uncertain in the latest neXtProt release (09.19.2014). A focus was then given to the 12 missing proteins encoded on chromosomes 2 and 14, some of which may putatively play roles in ciliation and flagellum mechanistics. The expression pattern of C2orf57 and TEX37 was confirmed in the adult testis by immunohistochemistry. On the basis of transcript expression during human spermatogenesis, we further consider the potential for discovering additional missing proteins in the testicular postmeiotic germ cell lineage and in ejaculated spermatozoa. This project was conducted as part of the C-HPP initiatives on chromosomes 14 (France) and 2 (Switzerland). The mass spectrometry proteomics data have been deposited with the ProteomeXchange Consortium under the data set identifier PXD002367.

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“…The strategy employed for the visualization of missing proteins expressed in the testis/germ cells was similar to that previously described by our team 27 …”

Section: Immunohistochemistrymentioning

confidence: 99%

Human Spermatozoa as a Model for Detecting Missing Proteins in the Context of the Chromosome-Centric Human Proteome Project

et al. 2015

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“…For instance, Rolland et al (2013) compiled several human seminal plasma proteomic studies and compared the resulting proteome to gene expression data for the organs contributing to this biological fluid, i.e. the testis, epididymis, seminal vesicle, and prostate.…”

Section: Integrative Omics Strategies To Study Spermatogenesismentioning

confidence: 99%

Linking transcriptomics and proteomics in spermatogenesis

Chalmel¹,

Rolland²

2015

Reproduction

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Spermatogenesis is a complex and tightly regulated process leading to the continuous production of male gametes, the spermatozoa. This developmental process requires the sequential and coordinated expression of thousands of genes, including many that are testisspecific. The molecular networks underlying normal and pathological spermatogenesis have been widely investigated in recent decades, and many high-throughput expression studies have studied genes and proteins involved in male fertility. In this review, we focus on studies that have attempted to correlate transcription and translation during spermatogenesis by comparing the testicular transcriptome and proteome. We also discuss the recent development and use of new transcriptomic approaches that provide a better proxy for the proteome, from both qualitative and quantitative perspectives. Finally, we provide illustrations of how testis-derived transcriptomic and proteomic data can be integrated to address new questions and how the 'proteomics informed by transcriptomics' technique, by combining RNA-seq and MS-based proteomics, can contribute significantly to the discovery of new protein-coding genes or new protein isoforms expressed during spermatogenesis.Reproduction (2015) 150 R149-R157

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“…Rudomin et al [19] were also able to identify 49% more unique proteins using this strategy. IE has been applied to LC/MS approaches with both LTQ-Orbitrap [20] and qTOF platforms [18] and has been shown to be advantageous for proteomic applications. Examples employing this approach include using IE to study post-translational modifications of proteins [21], discover previously unknown human embryonic growth promoters [18], identify genital track markers [20], characterize Matrigel marketed as a basement membrane matrix for stem cell growth [22], and track pH induced protein changes [23].…”

Section: Introductionmentioning

confidence: 99%

Expanding Lipidome Coverage Using LC-MS/MS Data-Dependent Acquisition with Automated Exclusion List Generation

Koelmel

Kroeger

Gill

et al. 2017

J. Am. Soc. Mass Spectrom.

185

154

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Untargeted omics analyses aim to comprehensively characterize biomolecules within a biological system. Changes in the presence or quantity of these biomolecules can indicate important biological perturbations, such as those caused by disease. With current technological advancements, the entire genome can now be sequenced; however, in the burgeoning fields of lipidomics, only a subset of lipids can be identified. The recent emergence of high resolution tandem mass spectrometry (HR-MS/MS), in combination with ultra-high performance liquid chromatography, has resulted in an increased coverage of the lipidome. Nevertheless, identifications from MS/MS are generally limited by the number of precursors which can be selected for fragmentation during chromatographic elution. Therefore, we developed the software IE-Omics to automate iterative exclusion (IE), where selected precursors using data-dependent topN analyses are excluded in sequential injections. In each sequential injection, unique precursors are fragmented until HR-MS/MS spectra of all ions above a user-defined intensity threshold are acquired. IE-Omics was applied to lipidomic analyses in Red Cross plasma and substantia nigra tissue. Coverage of the lipidome was drastically improved using IE. When applying IE-Omics to Red Cross plasma and substantia nigra lipid extracts in positive ion mode, 69 % and 40 % more molecular identifications were obtained, respectively. In addition, applying IE-Omics to a lipidomics workflow increased the coverage of trace species, including odd-chained and short-chained diacylglycerides and oxidized lipid species. By increasing the coverage of the lipidome, applying IE to a lipidomics workflow increases the probability of finding biomarkers and provides additional information for determining etiology of disease.

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Identification of genital tract markers in the human seminal plasma using an integrative genomics approach

Cited by 112 publications

References 42 publications

Human Spermatozoa as a Model for Detecting Missing Proteins in the Context of the Chromosome-Centric Human Proteome Project

Human Spermatozoa as a Model for Detecting Missing Proteins in the Context of the Chromosome-Centric Human Proteome Project

Linking transcriptomics and proteomics in spermatogenesis

Expanding Lipidome Coverage Using LC-MS/MS Data-Dependent Acquisition with Automated Exclusion List Generation

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