Biology subjects

Wagner, G. P.

Publications and source records attributed to Wagner, G. P..

14 recordsLinked to original sources

bioRxiv2025

Precocial ancestry of placental mammals

1Mammals exhibit two distinct reproductive strategies: altriciality, where neonates are highly underdeveloped, and precociality, where neonates are well-developed. The neonatal developmental state of deep nodes in mammalian phylogeny remains unresolved. Here, we use phylogenetic comparative methods to reconstruct the evolutionary history of neonatal maturity in mammals and demonstrate that the eutherian ancestor likely gave birth to precocial neonates. This finding contradicts the prevailing view that precociality evolved multiple times within the eutherian lineage. We contextualize this result with three lines of evidence. First, recent fossil evidence suggests that precocial life history traits arose early in therian evolution. Second, altricial eutherian neonates are markedly more developed at birth compared to altricial non-eutherians, suggesting a precocial ancestry in eutherian evolution. Third, reproductive traits that enable prolonged pregnancy originated in the stem lineage prior to the eutherian ancestor. Based on these findings, we propose an alternative model for the evolutionary history of precociality in mammals.

evolutionary biology↗

bioRxiv2024

High fitness paths can connect proteins with low sequence overlap

The structure and function of a protein are determined by its amino acid sequence. While random mutations change a proteins sequence, evolutionary forces shape its structural fold and biological activity. Studies have shown that neutral networks can connect a local region of sequence space by single residue mutations that preserve viability. However, the larger-scale connectedness of protein morphospace remains poorly understood. Recent advances in artificial intelligence have enabled us to computationally predict a proteins structure and quantify its functional plausibility. Here we build on these tools to develop an algorithm that generates viable paths between distantly related extant protein pairs. The intermediate sequences in these paths differ by single residue changes over subsequent steps - substitutions, insertions and deletions are admissible moves. Their fitness is evaluated using the protein language model ESM2, and maintained as high as possible subject to the constraints of the traversal. We document the qualitative variation across paths generated between progressively divergent protein pairs, some of which do not even acquire the same structural fold. The ease of interpolating between two sequences could be used as a proxy for the likelihood of homology between them.

bioinformatics↗

bioRxiv2024

Hallmarks of uterine receptivity predate placental mammals

Embryo implantation is essential to pregnancy in eutherian (placental) mammals. The cellular changes that enabled invasive implantation to evolve from superficial embryo apposition, the ancestral condition still retained in marsupials, have remained unclear. We generated and compared single-cell transcriptomes from the peri-implantation and non-pregnant uterus of two rodents with invasive implantation, the mouse and the guinea pig, and the opossum, a marsupial lacking invasive implantation. Cross-species analysis of endometrial cell types and ligand-receptor signaling revealed that the opossum blastocyst-stage uterus, despite lacking fetal-maternal contact, shares key features with the eutherian window of receptivity. These include a window in which the epithelial-stromal IHH-PTCH1 axis is active, but the downstream BMP2-mediated signaling that enables decidualization in eutherians is antagonized through a temporary spike in glandular GREM2. We propose that a homologous progesterone-responsive endometrial remodeling reaction preceded the evolution of eutherian and marsupial modes of implantation in their respective lineages. Complementary analysis of pre- and post-implantation embryonic transcriptomes from the same species revealed broad conservation of implantation-related functional genes in the blastocyst, as well as a remarkable similarity in ligand production between the mature trophoblast and the luminal epithelium. We suggest that this redundancy between trophectoderm and luminal epithelial signaling was an enabling factor for the evolution of invasive placentation. Together, these findings suggest that eutherian implantation evolved by maternal rewiring of the output of an ancestral window of receptivity-like epithelial-stromal signaling axis toward decidualization, stabilized epithelial loss, and invasion. Significance StatementPregnancy in placental mammals begins with implantation and invasion of the embryo, whereas marsupials retain a superficial mode of embryo apposition. How this major evolutionary transition occurred is unknown. Comparing uterine and embryonic single-cell transcriptomes between model rodents and the opossum reveals that the marsupial uterus activates an epithelial-stromal signaling axis canonically associated with receptivity to implantation. In the marsupial uterus, its outputs are opposed by inhibitory signals, whereas in placental mammals, this program promotes uterine decidual transformation and invasion. Early-embryo implantation-related gene expression, in contrast, shows little change across species. These results challenge the view that implantation evolved through the gain of invasive properties by the embryo, and reveal a common developmental foundation from which placentals evolved their novel mode of gestation.

evolutionary biology↗

bioRxiv2024

Comparative single cell analysis reveals complex patterns of cell type and cell signaling innovations at the fetal-maternal interface

How fetal and maternal cell types have co-evolved to enable mammalian placentation poses a unique evolutionary puzzle. Here, we present a multi-species atlas integrating single-cell transcriptomes from six species bracketing therian mammal diversity. We find that invasive trophoblasts share a gene-expression signature across eutherians, and evidence that endocrine decidual cells evolved stepwise from an immunomodulatory cell type retained in Tenrec with affinity to human decidua of menstruation. We recover evolutionary patterns in ligand-receptor signaling: fetal and maternal cells show a pronounced tendency towards disambiguation, but a predicted arms race dynamic between them is limited. We reconstruct cell communication networks of extinct mammalian ancestors, finding strong integration of fetal trophoblast into maternal networks. Together, our results reveal a dynamic history of cell type and signaling evolution. SynopsisThe fetal-maternal interface is one of the most intense loci of cell-cell signaling in the human body. Invasion of cells from the fetal placenta into the uterus, and the corresponding transformation of maternal tissues called decidualization, first evolved in the stem lineage of eutherian mammals(1, 2). Single-cell studies of the human fetal-maternal interface have provided new insight into the cell type diversity and cell-cell interactions governing this chimeric organ(3-5). However, the fetal-maternal interface is also one of the most rapidly evolving, and hence most diverse, characters among mammals(6), and an evolutionary analysis is missing. Here, we present and compare single-cell data from the fetal-maternal interface of species bracketing key events in mammal phylogeny: a marsupial (opossum, Monodelphis domestica), the afrotherian Tenrec ecaudatus, and four Euarchontoglires - guinea pig and mouse (Rodentia) together with recent macaque and human data (primates) (4, 5, 7). We infer cell type homologies, identify a gene-expression signature of eutherian invasive trophoblast conserved over 99 million years, and discover a predecidual cell in the tenrec which suggests stepwise evolution of the decidual stromal cell. We reconstruct ancestral cell signaling networks, revealing the integration of fetal cell types into the interface. Finally, we test two long-standing theoretical predictions, the disambiguation hypothesis(8) and escalation hypothesis(9), at transcriptome-wide scale, finding divergence between fetal and maternal signaling repertoires but arms race dynamics restricted to a small subset of ligand-receptor pairs. In so doing, we trace the co-evolutionary history of cell types and their signaling across mammalian viviparity.

evolutionary biology↗

bioRxiv2023

Experimental and Phylogenetic Evidence for Correlated Gene Expression Evolution between Dermal and Endometrial Fibroblasts: implications for the evolution of cancer malignancy

Changes in transcriptional gene expression is a dominant mode of evolution, mostly driven by mutations at cis-regulatory regions. Mutations can affect gene expression in multiple cell types if the same cis-regulatory elements are used by different cell types. As a consequence, changes in gene expression in one cell type may be associated with similar gene expression changes in another cell type. Correlated gene expression change can explain correlated character evolution, as for instance the correlation between placental invasion and vulnerability to cancer malignancy. Here we test this hypothesis using a comparative and an experimental data set. Specifically, we investigate gene expression in dermal skin fibroblasts (SF) and uterine endometrial stomal fibroblasts (ESF). The comparative dataset consists of transcriptomes from cultured SF and ESF from 9 mammalian species. We calculated the independent phylogenetic contrasts (PIC) for each gene and cell type. We find that evolutionary changes in gene expression in SF and ESF are highly correlated, supporting the hypothesis that the correlated gene expression changes are a prevalent feature of gene expression evolution. The experimental data set derives from a SCID mouse strain that was selected for slow cancer growth which led to substantial changes in the SF compared to wild type SCID mice. We isolated SF and ESF from wild type and evolved SCID mice and compared their gene expression profiles. We find a significant correlation between the gene expression contrasts of SF and ESF, which supports the hypothesis that gene expression variation in SF and ESF is correlated. We discuss the implications of these findings for the hypothesized correlation between placental invasiveness and vulnerability to metastatic cancer.

evolutionary biology↗

bioRxiv2023

The extension of mammalian pregnancy required taming inflammation; independent evolution of extended placentation in the tammar wallaby

In the first live bearing mammals, it is assumed that pregnancy was short and ended with a brief period of inflammatory maternal-fetal interaction. This mode of reproduction has been retained in many marsupials. While inflammation is key to successful implantation in eutherians, a key innovation in eutherians is the ability to switch off this inflammation after it has been initiated. This extended period, in which inflammation is suppressed, likely allowed for an extended period of placentation. One lineage of marsupials, the macropodids (wallabies and kangaroos), have extended placentation beyond the 2-4 days seen in other marsupial taxa, which allows us to test whether a moderated inflammation response after attachment is a general pattern associated with the extension of placentation in mammals. We show that during tammar wallaby pregnancy, some inflammatory genes are expressed at key time points of gestation, including IL6, before attachment, IL12A and LIF throughout the period of placentation and prostaglandins before birth. However, we did not see evidence of a complete inflammatory response at any time point. We argue that genes involved in a moderated inflammation reaction may have been co-opted into roles for placentation, facilitating the establishment and maintenance of extended fetal-maternal contact. Whilst the absence of other key mediators of inflammation may prevent prolonged damage to the uterus. We argue the moderation of inflammation following maternal-fetal contact is a convergently evolved key innovation that allowed for the extension of placentation in different mammalian lineages. Significance statementOur data suggest that moderation of the inflammatory reaction to embryo attachment allows for extension of pregnancy in mammals. The ancestor of all mammals likely experienced an ancestral inflammatory reaction in response to embryo attachment. In contrast, eutherians and some marsupials, such as macropodids, have an extended period of fetal-maternal contact. During this period of placentation many inflammatory genes are silenced while a few others are still expressed. This moderated expression of inflammatory genes suggests that some genes of inflammation were coopted into establishing and maintaining the placenta. This challenges the perspective of inflammation as being detrimental to pregnancy, instead suggesting that fetal-maternal interactions are based on a modified inflammation response necessary for maintaining pregnancy over an extensive period of time.

evolutionary biology↗

bioRxiv2021

Mapping the Promiscuous Binding Interface of HOX-A11 with KIX by Experimentally Guided in-silico docking

Transcription factors (TFs) regulate levels of transcription through a complex array of protein-protein interactions, thereby controlling key physiological processes such as development, stress response and cell growth. The transcription factor HOXA11 contains an intrinsically disordered regions (IDR) through which it interacts with CREB binding protein (CBP) and regulates endometrial development and function in eutherian mammals. The interaction between the IDR of HOXA11 and CBP was analyzed using computational docking guided by experimental constraints. HOXA11 IDR interacts with the KIX domain of CBP at two discrete sites - MLL and cMyb, mediated by sticky hydrophobic grooves on the surface of KIX. A five residue motif FDQFF on HOXA11 can interact both at cMyb and MLL site of KIX resulting in a promiscuous binding. Author SummaryWe demonstrate how the intrinsically disordered region (IDR) of transcription factor HOXA11 interacts at two distinct sites of the transcription coactivator CREB binding protein (CBP). By combining computational docking with limited experimental data we construct models of the complex of the KIX domain within CBP and a short helical segment within the IDR of HOXA11. The interaction between HOXA11 and CBP is believed to trigger the downstream expression of genes important in embryonic development.

biophysics↗

bioRxiv2020

Single-cell analysis of prostaglandin E2-induced decidual cell differentiation: does extracellular 8-Br-cAMP cause artifacts?

Development of the uterine decidua, the transient maternal tissue contacting the fetus during extended gestation, is the hallmark of reproduction in many placental mammals. Differentiation of decidual stromal cells is known to be induced by stimuli that activate the nuclear progesterone receptor and the cyclic AMP/protein kinase A (cAMP/PKA) pathways. The nature of the stimulus upstream of PKA has not been clearly defined, although a number of candidates have been proposed. To bypass this uncertainty for in vitro experiments, direct addition of membrane-permeable cAMP along with progestin has been the prevailing method. Phylogenetic inference suggests that the inflammatory eicosanoid prostaglandin E2 (PGE2) was the stimulus that ancestrally induced decidualization. Accordingly, we developed a protocol to decidualize human endometrial stromal fibroblasts using progestin and PGE2 and analyzed the response in comparison with a cAMP-based protocol. Transcriptomic comparison reveals a common activation of core decidual cell genes between both treatments, and a set of senescence-related genes exaggerated under cAMP treatment. Single-cell transcriptomic analysis of PGE2-mediated decidualization revealed a major transcriptomic transition between an early activated cell state and a differentiated decidual state, but notably did not identify a developmental trajectory representing a distinct senescent decidual state as reported in recent literature. Furthermore, investigation of the signal transduction process underlying PGE2-mediated decidualization showed that it depends upon progestin-dependent induction of PGE2 receptor 2 (PTGER2 aka EP2) and PKA, the kinase activated by PTGER2. This progesterone-dependent induction of PTGER2 is absent in the opossum, a species incapable of decidualization. Together, these findings suggest that the origin of the decidual cell type involved the evolution of progesterone-dependent activation of the PGE2/EP2/PKA axis. We propose the use of PGE2 for in vitro decidualization studies as a potentially more physiological model than 8-Br-cAMP.

systems biology↗

bioRxiv2019

Transcriptomic responses to hypoxia in endometrial and decidual stromal cells

Human reproductive success depends on a properly decidualized uterine endometrium that allows implantation and the formation of the placenta. At the core of the decidualization process are endometrial stromal fibroblasts (ESF) that differentiate to decidual stromal cells (DSC). As variations in oxygen levels are functionally relevant in endometrium both upon menstruation and during placentation, we assessed the transcriptomic responses to hypoxia in ESF and DSC. In both cell types hypoxia upregulated genes in classical hypoxia pathways such as glycolysis and the epithelial mesenchymal transition. In DSC hypoxia restored an ESF like transcriptional state for a subset of transcription factors that are known targets of the progesterone receptor, suggesting that hypoxia partially interferes with progesterone signaling. In both cell types hypoxia modified transcription of several inflammatory transcription factors that are known regulators of decidualization, including decreased transcription of STATs and increased transcription of CEBPs. We observed that hypoxia upregulated genes had a significant overlap with genes previously detected to be upregulated in endometriotic stromal cells. Promoter analysis of the genes in this overlap suggested the hypoxia upregulated Jun/Fos and CEBP transcription factors as potential drivers of endometriosis-associated transcription. Using immunohistochemistry we observed increased expression of JUND and CEBPD in endometriosis lesions compared to healthy endometria. Overall the findings suggest that hypoxic stress establishes distinct transcriptional states in ESF and DSC, and that hypoxia influences the expression of genes that contribute to the core gene regulation of endometriotic stromal cells.

physiology↗

bioRxiv2019

The Evolution of Placental Invasion and Cancer Metastasis are Causally Linked

Among mammals, the extent of placental invasion is correlated with vulnerability to malignancy. Animals with more invasive placentation (e.g. humans) are more vulnerable to malignancy, whereas animals with a non-invasive placenta (e.g. ruminants) are less likely to develop malignant cancer. To explain this correlation, we propose the hypothesis of Evolved Levels of Invasibility (ELI) positing that the permissiveness of stromal tissue to invasion is a unitary character affecting both placental and cancer invasion. We provide evidence for this hypothesis by contrasting invasion of human and bovine cancer and placental cells into a lawn of stromal cells from different species. We find that both bovine endometrial and skin fibroblasts are more resistant to invasion of placental and cancer cells than their human counterparts. Gene expression profiling identified genes with high expression in human but not bovine fibroblasts. Knocking down of a subset of them in human fibroblasts leads to significantly stronger resistance to cancer cell invasion. Comparative analysis of gene expression among mammals suggests that humans evolved higher vulnerability to malignancy than the eutherian ancestor, possibly as a correlate of more invasive placentation, and boroeutherians evolved to decrease stromal invasibility. Identifying the evolutionary determinants of stromal invasibility can provide significant insights to develop rational anti-metastatic therapeutics.

cancer biology↗

bioRxiv2018

Evolution of embryo implantation was enabled by the origin of decidual cells in eutherian mammals

Embryo implantation is the first step in the establishment of pregnancy in eutherian (Placental) mammals. Although viviparity evolved prior to the common ancestor of marsupials and eutherian mammals (therian ancestor), implantation is unique to eutherians. The ancestral therian pregnancy likely involved a short phase of attachment between the fetal and maternal tissues followed by parturition rather than implantation, similar to the mode of pregnancy found in marsupials such as the opossum. Embryo implantation in eutherian mammals as well as embryo attachment in opossum, induce a homologous inflammatory response in the uterus. Here, we elucidate the evolutionary mechanism by which the ancestral inflammatory fetal-maternal attachment was transformed into the process of implantation. We performed a comparative transcriptomic and immunohistochemical study of the gravid and non-gravid uteri of two eutherian mammals, armadillo (Dasypus novemcinctus) and hyrax (Procavia capensis); a marsupial outgroup, opossum (Monodelphis domestica); and compared it to previously published data on rabbit (Oryctolagus cuniculus). This taxon sampling allows inference of the eutherian ancestral state. Our results show that in the eutherian lineage, the ancestral inflammatory response was domesticated by suppressing a detrimental component viz. signaling by the cytokine IL17A, while retaining components that are beneficial to placentation, viz. angiogenesis, vascular permeability, remodeling of extracellular matrix. IL17A mediates recruitment of neutrophils to inflamed mucosal tissues, which, if unchecked, can damage the uterus as well as the embryo and lead to expulsion of the fetus. We hypothesized that the uterine decidual stromal cells, which evolved coincidentally with embryo implantation, evolved, in part, to prevent IL17A-mediated neutrophil infiltration. We tested a prediction of this hypothesis in vitro, and showed that decidual stromal cells can suppress differentiation of human naive T cells into IL17A-producing Th17 cells. Together, these results provide a mechanistic understanding of early stages of the evolution of the eutherian mode of pregnancy, and also identify a potentially ancestral function of an evolutionary novelty, the decidual stromal cell-type.

evolutionary biology↗

bioRxiv2018

Subdivision of ancestral scale genetic program underlies origin of feathers and avian scutate scales

Birds and other reptiles possess a diversity of feather and scale-like skin appendages. Feathers are commonly assumed to have originated from ancestral scales in theropod dinosaurs. However, most birds also have scaled feet, indicating birds evolved the capacity to grow both ancestral and derived morphologies. This suggests a more complex evolutionary history than a simple linear transition between feathers and scales. We set out to investigate the evolution of feathers via the comparison of transcriptomes assembled from diverse skin appendages in chicken, emu, and alligator. Our data reveal that feathers and the overlapping scutate scales of birds share more similar gene expression to each other, and to two types of alligator scales, than they do to the tuberculate reticulate scales on bird footpads. Accordingly, we propose a history of skin appendage diversification, in which feathers and bird scutate scales arose from ancestral archosaur body scales, whereas reticulate scales arose earlier in tetrapod evolution. We also show that many \"feather-specific genes\" are also expressed in alligator scales. In-situ hybridization results in feather buds suggest that these genes represent ancestral scale genes that acquired novel roles in feather morphogenesis and were repressed in bird scales. Our findings suggest that the differential reuse, in feathers, and suppression, in bird scales, of genes ancestrally expressed in archosaur scales has been a key factor in the origin of feathers - and may represent an important mechanism for the origin of evolutionary novelties.

evolutionary biology↗

bioRxiv2018

The mammalian decidual cell evolved from a cellular stress response

Among animal species, cell types vary greatly in terms of number and kind. The broad range of number of cell types among species suggests that cell type origination is a significant source of evolutionary novelty. The molecular mechanisms giving rise to novel cell types, however, are poorly understood. Here we show that a novel cell type of eutherian mammals, the decidual stromal cell (DSC), evolved by rewiring an ancestral cellular stress response. We isolated the precursor cell type of DSCs, endometrial stromal fibroblasts (ESFs), from the opossum Monodelphis domestica. We show that, in opossum ESF, the majority of decidual core regulatory genes respond to decidualizing signals, but do not regulate decidual effector genes. Rather, in opossum ESF, decidual transcription factors function in apoptotic and oxidative stress response. We propose that the rewiring of cellular stress responses could be a general mechanism for the evolution of novel cell types.

evolutionary biology↗

bioRxiv2017

The Core Transcriptome Of Mammalian Placentas And The Divergence Of Expression With Placental Shape

IntroductionThe placenta is arguably the most anatomically variable organ in mammals even though its primary function is conserved.\n\nMethodUsing RNA-Seq, we measured the expression profiles of 55 term placentas of 14 species of mammals representing all major eutherian superordinal clades and marsupials, and compared the evolution of expression across clades.\n\nResultsWe identified a set of 115 core genes which is expressed (FPKM[≥] 10) in all eutherian placentas, including genes with immune-modulating properties (ANXA2, ANXA1, S100A11, S100A10, and LGALS1), cell-cell interactions (LAMC1, LUM, and LGALS1), invasion (GRB2 and RALB) and syncytialization (ANXA5 and ANXA1). We also identified multiple pre-eclampsia associated genes which are differentially expressed in Homo sapiens when compared to the other 13 species. Multiple genes are significantly associated with placenta morphology, including EREG and WNT5A which are both associated with placental shape.\n\nDiscussion115 genes are important for the core functions of the placenta in all eutherian species analyzed. The molecular functions and pathways enriched in the core placenta align with the evolutionarily conserved functionality of the placenta.

genomics↗