Proteome-wide and matrisome-specific atlas of the human ovary from prepuberty to menopause
Description
The data describes the evolution of the human ovarian matrisome from prepuberty til menopause, demonstrating that follicle survival and development, and ultimately fertility, would not be possible without its involvement. We confidently identified and quantified 98 matrisome proteins present in the three ovary groups. Among them, 26 were expressed differently among age groups (n=5/group), delineating a peculiar matrisomal fingerprint at each stage. Such proteins could be potential biomarkers phenotyping ovarian ECM at each age phase of female reproductive life. Beyond proteomics, our study presents a unique approach to understanding the data and depicting the ECM-intracellular signaling networks and remodeling with age through advanced text-mining based on NLP technology, machine learning, and data sonification. Our findings provide essential context for healthy ovarian physiology, and recapitulating physiological tissues or development in vitro. This comprehensive proteomics analysis represents the ovarian proteomic codex and contributes to an improved understanding of the critical roles that ECM plays throughout the ovarian life span. o Sup fig 1. Interactive network of ovarian matrisome proteins with Hippo pathway as illustrated by Pathway Studio. o Sup fig 2. Interactive network of ovarian matrisome proteins with mTOR pathway as illustrated by Pathway Studio. o Sup fig 3. A. Reproducibility of DC-MaP pipeline and TMT-16pro plex strategy in characterizing matrisome and cellular proteins. o Sup fig 4. Positive and negative controls for the validation of antibodies used in 3D immunostaining. o Sup Tab 1. Raw data of detected hydroxylation and advanced glycation end intensities in modified proteins among all samples. o Sup Tab 2. Involvement of ovarian matrisome proteins with Hippo and mTOR pathways as depicted by Pathway Studio. o Sup Tab 3. Raw data of the intensity of confidently detected matrisome and cellular proteins among all samples. o Supe Tab 4. References used by Pathway Studio to create the relationships displayed in Fig.6-7. o Table 2. Matrisome biomarkers interaction with mTOR and Hippo pathways. o Neural Network. Modelisation of matrisome protein changes with age accesible through two available files in html or jrp format. While html format enables to see the modelisation, html format enables to interact with the model and evaluate different possible theoretical ovarian profiles (e.g., pathological conditions) through modifying the protein intensities. This can be achieved by downloading the source data (.jrp format) and opening the jrp file using JMP software. o Hydroxylation report. Statistical interactive reports detailing each hydroxylation position at every data point of Fig.3A. o AGE report. Statistical interactive reports detailing each advanced glycation end position at every data point of Fig.3B. o Data sonification. Videos of the 26 matrisome biomarkers and their turnover with age expressed as sonified data.
Files
Steps to reproduce
The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE [94] partner repository with the dataset identifier PXD (Username: reviewer_pxd025940@ebi.ac.uk; Password: 0K9w3nwz ). The data sonification Matlab code can be accessed at the GitHub page: https://github.com/inatamara/Sonificator.