Deciphering the Dark Proteome: Use of the Testis and Characterization of Two Dark Proteins

Melaine, Nathalie; Com, Emmanuelle; Bellaud, Pascale; Guillot, Laetitia; Lagarrigue, Mélanie; Morrice, Nick; Guével, Blandine; Lavigne, Régis; Calle, Juan-Felipe Velez de la; Dojahn, Jörg; Pineau, Charles

doi:10.1021/acs.jproteome.8b00387

Cited by 10 publications

(16 citation statements)

References 38 publications

(88 reference statements)

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“…Feature detection was also performed using DataAnalysis 5.1 software and the results were exported in .mgf format. Peptide identification was then performed with Mascot version 2.5.1, applying the previously described search parameters and using its automatic decoy database search to calculate the false discovery rate (FDR) [ 43 , 44 ]. MS/MS spectra were searched against the UniProt Homo sapiens reference proteome database (UP000005640, release 20 June 2018; 21,044 sequences which contain canonicals).…”

Section: Methodsmentioning

confidence: 99%

The Eutopic Endometrium Proteome in Endometriosis Reveals Candidate Markers and Molecular Mechanisms of Physiopathology

et al. 2022

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Endometriosis is a common chronic gynaecological disease causing various symptoms, such as infertility and chronic pain. The gold standard for its diagnosis is still laparoscopy and the biopsy of endometriotic lesions. Here, we aimed to compare the eutopic endometrium from women with or without endometriosis to identify proteins that may be considered as potential biomarker candidates. Eutopic endometrium was collected from patients with endometriosis (n = 4) and women without endometriosis (n = 5) during a laparoscopy surgery during the mid-secretory phase of their menstrual cycle. Total proteins from tissues were extracted and digested before LC-MS-MS analysis. Among the 5301 proteins identified, 543 were differentially expressed and enriched in two specific KEGG pathways: focal adhesion and PI3K/AKT signaling. Integration of our data with a large-scale proteomics dataset allowed us to highlight 11 proteins that share the same trend of dysregulation in eutopic endometrium, regardless of the phase of the menstrual cycle. Our results constitute the first step towards the identification of potential promising endometrial diagnostic biomarkers. They provide new insights into the mechanisms underlying endometriosis and its etiology. Our results await further confirmation on a larger sample cohort.

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Section: Methodsmentioning

confidence: 99%

The Eutopic Endometrium Proteome in Endometriosis Reveals Candidate Markers and Molecular Mechanisms of Physiopathology

et al. 2022

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“…There remain many under-investigated types of specimens, including unusual tissue types, embryonic and fetal stages of life, and responses to oxidative or inflammatory stress. The Chr 2/14 French/Swiss consortium has exploited the knowledge of exclusive expression of hundreds of transcripts in male reproductive tract by performing deep studies of sperm 14, 26–27 , complemented by studies of testis by the Chinese team 15, 28, 29–30 . Other examples are dental pulp 31 , male fetal cardiac development 17 , kidney and bladder 16 , and beta-defensins 32 .…”

Section: Seeking Pe234 Missing Proteins In Major Protein Familiesmentioning

confidence: 99%

Progress on Identifying and Characterizing the Human Proteome: 2018 Metrics from the HUPO Human Proteome Project

et al. 2018

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The Human Proteome Project (HPP) annually reports on progress throughout the field in credibly identifying and characterizing the human protein parts list and making proteomics an integral part of multiomics studies in medicine and the life sciences. NeXtProt release 2018-01-17, the baseline for this sixth annual HPP special issue of the Journal of Proteome Research, contains 17 470 PE1 proteins, 89% of all neXtProt predicted PE1-4 proteins, up from 17 008 in release 2017-01-23 and 13 975 in release 2012-02-24. Conversely, the number of neXtProt PE2,3,4 missing proteins has been reduced from 2949 to 2579 to 2186 over the past two years. Of the PE1 proteins, 16 092 are based on mass spectrometry results, and 1378 on other kinds of protein studies, notably protein-protein interaction findings. PeptideAtlas has 15 798 canonical proteins, up 625 over the past year, including 269 from SUMOylation studies. The largest reason for missing proteins is low abundance. Meanwhile, the Human Protein Atlas has released its Cell Atlas, Pathology Atlas, and updated Tissue Atlas, and is applying recommendations from the International Working Group on Antibody Validation. Finally, there is progress using the quantitative multiplex organ-specific popular proteins targeted proteomics approach in various disease categories.

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“…We hope that the current study will stimulate experimental studies on C6orf118, CXorf58 and TMEM232 in cilia-related functions and on TMEM53 and SMLR1 in lipid metabolism by the HPP teams who have demonstrated their expertise in characterizing human proteins involved in male reproduction ( 79 ), ciliogenesis ( 80 ) or liver metabolism ( 81 ). Researchers from the RNA biology community are welcome to join HPP and test the putative role of C7orf25 and RSRP1 in RNA metabolism and gene expression.…”

Section: Discussionmentioning

confidence: 98%

Functionathon: a manual data mining workflow to generate functional hypotheses for uncharacterized human proteins and its application by undergraduate students

et al. 2021

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About 10% of human proteins have no annotated function in protein knowledge bases. A workflow to generate hypotheses for the function of these uncharacterized proteins has been developed, based on predicted and experimental information on protein properties, interactions, tissular expression, subcellular localization, conservation in other organisms, as well as phenotypic data in mutant model organisms. This workflow has been applied to seven uncharacterized human proteins (C6orf118, C7orf25, CXorf58, RSRP1, SMLR1, TMEM53 and TMEM232) in the frame of a course-based undergraduate research experience named Functionathon organized at the University of Geneva to teach undergraduate students how to use biological databases and bioinformatics tools and interpret the results. C6orf118, CXorf58 and TMEM232 were proposed to be involved in cilia-related functions; TMEM53 and SMLR1 were proposed to be involved in lipid metabolism and C7orf25 and RSRP1 were proposed to be involved in RNA metabolism and gene expression. Experimental strategies to test these hypotheses were also discussed. The results of this manual data mining study may contribute to the project recently launched by the Human Proteome Organization (HUPO) Human Proteome Project aiming to fill gaps in the functional annotation of human proteins. Database URL: http://www.nextprot.org

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Deciphering the Dark Proteome: Use of the Testis and Characterization of Two Dark Proteins

Cited by 10 publications

References 38 publications

The Eutopic Endometrium Proteome in Endometriosis Reveals Candidate Markers and Molecular Mechanisms of Physiopathology

The Eutopic Endometrium Proteome in Endometriosis Reveals Candidate Markers and Molecular Mechanisms of Physiopathology

Progress on Identifying and Characterizing the Human Proteome: 2018 Metrics from the HUPO Human Proteome Project

Functionathon: a manual data mining workflow to generate functional hypotheses for uncharacterized human proteins and its application by undergraduate students

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