Periodic Reporting for period 3 - EVOMENS (The evolution of menstruation in primates)
Berichtszeitraum: 2023-07-01 bis 2024-12-31
A woman will, on average, menstruate 450 times during her lifetime. Menstruation corresponds to the shedding of the uterine lining (endometrium) when fecundation has not occurred. This physiological process affects half of the human species and is associated with severe gynecological conditions. Yet, the molecular pathways responsible for menstruation remain relatively understudied despite its tremendous importance for human health and reproduction. Menstruation is a recent evolutionary innovation in primates: the trait is present in humans, apes and some monkeys (macaques, baboons, capuchins), but not in closely related others (marmosets, saimiris). Female non-menstruating primates experience a similar hormonal cycle to humans, but their endometrium is reabsorbed by the uterine wall at the end of the cycle, as is the case in most other mammals. In this project, we leverage these differences in uterine endometrium function between primate species to understand the molecular mechanisms of menstruation, and to illuminate how menstruation evolved during the diversification of the primate clade. The objectives of the project are to (i) profile how gene expression has changed in the different cell types that compose the endometrium along the evolution of primates, to identify functional transitions associated with the acquisition of menstruation; (ii) detect new gene regulatory elements associated with those changes in gene expression, to characterize the regulatory networks that control this new phenotype in primates; (iii) understand how these regulatory changes became embedded in the primate genome when menstruation was acquired; and (iv) compare the evolutionary dynamics of the uterine endometrium to other organs and tissues in primates, to test whether reproductive tissues evolve faster than other organs. Overall, this project utilizes comparative signatures detected in the uterus and in the genome across related primate species to illuminate how menstruation works at the functional level in humans, and how such reproductive traits appear during evolution. This project has far-reaching implications for human reproductive health and evolutionary genomics, and will significantly advance our understanding of uterine functions and the evolution of the female genital tract in the human lineage.
During the first reporting period (24 months), we approached the project from two different angles: a wet-lab front, where we worked on the human and primate uterine tissue collection, gene expression profiling and regulatory elements discovery pipeline; and a bioinformatics front, where we investigated the evolution of genomes and menstrual phenotypes across primate species and made crucial methodological advances.
We curated phenotypic and genomic resources for 27 primate species, and rigorously assessed which key ancestors were menstruating or not. We triangulated that menstruation likely evolved between the Simiiformes and the Catarrhine ancestors, and are currently investigating which gene families expressed in the uterus have evolved unexpectedly fast during that time period.
We obtained ethical agreements to collect uterine tissue samples from human donors and four primate species of interest. Seven human samples have already been collected. In collaboration with primate research facilities, we developed tailored, non-lethal experimental procedures to follow the hormonal cycles and collect uterine tissue in female individuals from each of these species. So far, we have tracked hormonal modifications in 15 baboons, 11 macaques, 4 saimiris and 2 marmosets, and uterine tissue samples have been collected at controlled cycle time-points from about half of these individuals, with more collections planned. We are working to obtain complementary samples through collaborations with a primate biobank and a lemur research center.
We developed the experimental pipeline to profile gene expression and active regulatory elements from these tissue samples. We have obtained thousands of individual cellular transcriptomes and regulatory profiles in three species (baboon, macaque and mouse), confirming that we are able to recover all major uterine cell types and to profile their gene expression and regulation. We are working to improve protocols yield and performance, as first results revealed quality issues that we hope to resolve.
We have developed a new method to test whether local regulatory activity has significantly changed in any tree of the species tree (manuscript in progress). We are also extending on methods to compare single-cell transcriptomes between different species, as results from us and others show that methods for whole-tissue data are inappropriate. These methodological advances are currently being benchmarked and proofed on separate datasets.
We curated phenotypic and genomic resources for 27 primate species, and rigorously assessed which key ancestors were menstruating or not. We triangulated that menstruation likely evolved between the Simiiformes and the Catarrhine ancestors, and are currently investigating which gene families expressed in the uterus have evolved unexpectedly fast during that time period.
We obtained ethical agreements to collect uterine tissue samples from human donors and four primate species of interest. Seven human samples have already been collected. In collaboration with primate research facilities, we developed tailored, non-lethal experimental procedures to follow the hormonal cycles and collect uterine tissue in female individuals from each of these species. So far, we have tracked hormonal modifications in 15 baboons, 11 macaques, 4 saimiris and 2 marmosets, and uterine tissue samples have been collected at controlled cycle time-points from about half of these individuals, with more collections planned. We are working to obtain complementary samples through collaborations with a primate biobank and a lemur research center.
We developed the experimental pipeline to profile gene expression and active regulatory elements from these tissue samples. We have obtained thousands of individual cellular transcriptomes and regulatory profiles in three species (baboon, macaque and mouse), confirming that we are able to recover all major uterine cell types and to profile their gene expression and regulation. We are working to improve protocols yield and performance, as first results revealed quality issues that we hope to resolve.
We have developed a new method to test whether local regulatory activity has significantly changed in any tree of the species tree (manuscript in progress). We are also extending on methods to compare single-cell transcriptomes between different species, as results from us and others show that methods for whole-tissue data are inappropriate. These methodological advances are currently being benchmarked and proofed on separate datasets.
We have made significant progress beyond the state of the art on several aspects:
1. Non-human primate tissue collections: we have developed new, minimally invasive methods to obtain uterine biopsies at accurate time-points in the hormonal cycles of different species of non-human primates and are continuously building a unique collection of such samples.
2. Single-cell transcriptomics and regulatory genomics: we obtained what is, to our knowledge, the first cellular maps of gene expression and regulation of non-pregnant uteruses of non-human primates. We expect that by the end of the project, we will have obtained the first comparison of single-cell transcriptomes and regulatory profiles of the uterus across primates and some of their close mammalian relatives, and identified changes in gene regulation that resulted in the evolution of menstruation.
3. Ancestral menstrual traits in primates: we performed the first rigorous reconstruction of the ancestral phenotypes of primates as regard to menstruation, using state-of-the-art phylogenetic methods. We expect that by the end of the project, we will have integrated these ancestral phenotypes with comparative analyses of their genomes to understand how menstrual traits evolved at the sequence level.
4. Methodological advances: as described above, we extended computational frameworks to compare gene expression across species along two axes: (i) to adapt for regulatory activity information instead of gene expression; and (ii) to integrate gene expression data obtained at the single-cell level, which present different computational challenges compared to bulk tissue data. We are currently proof-testing those methodologies and expect that they will be crucial to interpret the data obtained in this project.
Until the end of the project, we expect to address other key questions beyond the state-of-the-art, including how quickly the uterine transcriptome changes compared to other primate tissues; how the human uterine transcriptome differs from other related primates and model species; and how selection shaped the evolution of the primate uterine transcriptome.
1. Non-human primate tissue collections: we have developed new, minimally invasive methods to obtain uterine biopsies at accurate time-points in the hormonal cycles of different species of non-human primates and are continuously building a unique collection of such samples.
2. Single-cell transcriptomics and regulatory genomics: we obtained what is, to our knowledge, the first cellular maps of gene expression and regulation of non-pregnant uteruses of non-human primates. We expect that by the end of the project, we will have obtained the first comparison of single-cell transcriptomes and regulatory profiles of the uterus across primates and some of their close mammalian relatives, and identified changes in gene regulation that resulted in the evolution of menstruation.
3. Ancestral menstrual traits in primates: we performed the first rigorous reconstruction of the ancestral phenotypes of primates as regard to menstruation, using state-of-the-art phylogenetic methods. We expect that by the end of the project, we will have integrated these ancestral phenotypes with comparative analyses of their genomes to understand how menstrual traits evolved at the sequence level.
4. Methodological advances: as described above, we extended computational frameworks to compare gene expression across species along two axes: (i) to adapt for regulatory activity information instead of gene expression; and (ii) to integrate gene expression data obtained at the single-cell level, which present different computational challenges compared to bulk tissue data. We are currently proof-testing those methodologies and expect that they will be crucial to interpret the data obtained in this project.
Until the end of the project, we expect to address other key questions beyond the state-of-the-art, including how quickly the uterine transcriptome changes compared to other primate tissues; how the human uterine transcriptome differs from other related primates and model species; and how selection shaped the evolution of the primate uterine transcriptome.