Biology subjects

Wimberger, P.

Publications and source records attributed to Wimberger, P..

11 recordsLinked to original sources

bioRxiv2025

Human-specific morphoregulatory signatures in basal radial glia characterize neocortex evolution

As the seat of our cognition, the human neocortex is an object of immense fascination. Human neocortex expansion during evolution has been attributed to an increase in the proliferative capacity of neural progenitor cells during development, particularly basal radial glia (bRG). Despite their evolutionary relevance, the genomic changes driving human-specific bRG biology remain uncharacterized. We used comparative chromatin and transcriptional profiling of neural progenitor cells isolated from gorilla, chimpanzee and human cerebral organoids to identify cis-regulatory elements that have gained activity in humans. Focusing specifically on bRG, we discovered that morphoregulatory enhancer activity and gene expression signatures distinguish human bRG from other great apes. Functional analysis of the morphoregulatory genes FAM107A and CNGA3 in human organoids revealed that these genes are required for the morphological complexity of human bRG. Taken together, our interspecies comparison of basal radial glia suggests that human-specific morphoregulatory signatures characterize neocortex evolution.

neuroscience↗

bioRxiv2024

Epigenome profiling identifies H3K27me3 regulation of extra-cellular matrix composition in human corticogenesis

Epigenetic mechanisms regulate gene expression programs during neurogenesis, but the extent of epigenetic remodelling during human cortical development remains unknown. Here, we characterize the epigenetic landscape of the human developing neocortex by leveraging Epi-CyTOF, a mass cytometry-based approach for the simultaneous single cell analysis of more than 30 epigenetic marks. We identify H3K27me3, deposited by Polycomb Repressive Complex 2 (PRC2), as the modification with the strongest cell type-specific enrichment. Inhibition of PRC2 in human cortical organoids resulted in a shift of neural progenitor cell (NPC) proliferation towards differentiation. Cell type- specific profiling of H3K27me3 not only identified neuronal differentiation genes in the human neocortex, but also extra-cellular matrix (ECM) genes. PRC2 inhibition resulted in increased production of the proteoglycan Syndecan 1. Overall, this study comprehensively characterizes the epigenetic state of specific neural cell types and highlights a novel role for H3K27me3 in regulating the ECM composition in the human developing neocortex.

developmental biology↗

bioRxiv2024

Canonical and non-canonical PRC1 differentially contribute to the regulation of neural stem cell fate

Neocortex development is characterized by sequential phases of neural progenitor cell (NPC) expansion, neurogenesis and gliogenesis. Polycomb-mediated epigenetic mechanisms are known to play important roles in regulating the lineage potential of NPCs during development. The composition of Polycomb Repressive Complex 1 (PRC1) is highly diverse in mammals and was hypothesized to contribute to context-specific regulation of cell fate. Here, we have performed side-by-side comparison of the role of canonical PRC1.2/1.4 and non-canonical PRC1.3/1.5, all of which are expressed in the developing neocortex, in NSC proliferation and differentiation. We found that the deletion of Pcgf2/4 in NSCs led to a strong reduction in proliferation and to altered lineage fate, both during the neurogenic and gliogenic phase, whereas Pcgf3/5 played a minor role. Mechanistically, genes encoding stem cell and neurogenic factors were bound by PRC1 and differentially expressed upon Pcgf2/4 deletion. Thus, rather than different PRC1 sub-complexes contributing to different phases of neural development, we found that canonical PRC1 played a more significant role in NSC regulation during proliferative, neurogenic and gliogenic phases compared to non-canonical PRC1.

developmental biology↗

bioRxiv2023

Primate-expressed EPIREGULIN promotes basal progenitor proliferation in the developing neocortex

Neocortex expansion during evolution is linked to higher numbers of neurons thought to result from increased proliferative capacity and neurogenic potential of basal progenitor cells (BPs) during development. Here we show that EREG, encoding the growth factor EPIREGULIN, is expressed in the human developing neocortex and in gorilla organoids, but not in the mouse neocortex. Addition of EPIREGULIN to the mouse neocortex increases proliferation of BPs via EGFR-mediated signaling, whereas ablation of EREG in human cortical organoids reduces BP proliferation. Addition of EPIREGULIN to cortical organoids promotes a further increase in proliferation of gorilla but not human BPs. Finally, we identify putative cis-regulatory elements that may contribute to inter-species differences in EREG expression. Overall, our results suggest that species-specific expression of EPIREGULIN may contribute to increased neocortex size in primates by providing a pro-proliferative signal to BPs in the subventricular zone progenitor niche.

developmental biology↗

bioRxiv2022

Cerebral organoids expressing mutant actin genes reveal cellular mechanism underlying microcephalic cortical malformation

Actins are structural cytoskeletal proteins playing crucial roles in multiple cellular processes. Mutations in the ACTB and ACTG1 genes, encoding the ubiquitous beta- and gamma- cytoskeletal actin isoforms, respectively, cause a broad spectrum of neurodevelopmental disorders, with microcephaly as the most frequent one. Here we used patient-derived cerebral organoids to gain insight into the pathogenesis underlying this cortical malformation. Cerebral organoids from induced pluripotent stem cells (iPSCs) of patients with the Baraitser-Winter- CerebroFrontoFacial syndrome (BWCFF-S), expressing either an ACTB or an ACTG1 missense mutation, are reduced in size, showing a thinner ventricular zone (VZ). This decrease in VZ progenitors is in turn associated with a striking change in the orientation of their cleavage plane from predominantly vertical (control) to predominantly horizontal (BWCFF-S), which is incompatible with increasing VZ progenitor abundance. Various cytoskeletal and morphological irregularities of BWCFF-S VZ progenitors, notably in the apical region of these cells, seemingly contribute to their predominantly horizontal cleavage plane orientation. Our results provide insight into the cell biological basis of the microcephaly associated with BWCFF-S caused by actin mutations.

neuroscience↗

bioRxiv2022

Community science for enigmatic ecosystems: Using eBird to assess avian biodiversity on glaciers and snowfields

AimTo quantify avian biodiversity and habitat preference and describe behavior in an enigmatic, understudied ecosystem: mountain glaciers and snowfields. LocationMountains in the Pacific Northwest of western North America: British Columbia (CA), Washington and Oregon (USA). TaxonBirds observed within our study area and focal habitat. MethodsWe used community science data from eBird--an online database of bird observations from around the world--to estimate bird biodiversity and abundance in glacier and snowfield ecosystems as well as nearby, ice-adjacent habitats. We used field notes from eBird users and breeding codes to extend our data set to include insight into habitat usage and behavior. Finally, we compared our community-science approach to previous studies that used traditional survey methods. ResultsWe identified considerable avian biodiversity in glacier and snowfield habitat (46 species) with four specialists that appeared to prefer glaciers and snowfields over nearby, ice-adjacent habitat. Combined with field notes by eBird users, our efforts increased the known global total of avian species associated with ice and snow habitats by 14%. When community science data was compared to traditional methods, we found similar species diversity but differences in abundance. Main conclusionsDespite the imminent threat of glacier and snowfield melt due to climate change, species living in these habitats remain poorly studied, likely due to the remoteness and ruggedness of their terrain. Glaciers and snowfields hold notable bird diversity, however, with a specialized set of species appearing to preferentially forage in these habitats. Our results show that community science data can provide a valuable starting point for studying difficult to access areas, but traditional surveys are still useful for more rigorous quantification of avian biodiversity.

ecology↗

bioRxiv2022

Longer metaphase and fewer chromosome segregation errors in modern human than Neandertal brain development

Since the ancestors of modern humans separated from those of Neandertals, around one hundred amino acid substitutions spread to essentially all modern humans. The biological significance of these changes is largely unknown. Here, we examine all six such amino acid substitutions in the three proteins known to have key roles in kinetochore function and chromosome segregation and to be highly expressed in the stem cells of the developing neocortex. When we introduce these modern human-specific substitutions in the mouse, three substitutions in two of these proteins, KIF18a and KNL1, cause a prolongation of metaphase and a reduction in chromosome segregation errors in apical progenitors of the developing neocortex. Conversely, the ancestral substitutions cause a reduction in metaphase length and an increase in chromosome segregation errors in human brain organoids. Our data also show that, in these aspects, Neandertals were more similar to chimpanzees than to modern humans. Thus, the fidelity of chromosome segregation during neocortex development improved in modern humans after their divergence from Neandertals.

neuroscience↗

bioRxiv2021

Human and wildlife use of mountain glacier habitat in western North America

ContextThe global recession of glaciers and perennial snowfields is reshaping mountain ecosystems. Beyond physical changes to the landscape and altered downstream hydrology, the implications of glacier decline for biodiversity are poorly known. Before predictions can be made about how climate change will affect wildlife in glacier-associated ecosystems, a more thorough accounting of the role that glaciers play in species life histories is needed. However, typical approaches for documenting wildlife presence and behavior--remote camera traps--are difficult to use in glaciated terrain due to limited options for securing them (e.g., no trees) and dramatic seasonal changes in snowpack. AimsIn this study, we sought to test a novel camera trap designed for glaciated mountain ecosystems. We also aimed to use this approach to gain insight into wildlife and human usage of a mountain glacier in western North America. MethodsWe deployed an elevational transect of uniquely designed camera traps along the western margin of the Paradise Glacier, a rapidly receding mountain glacier on the south side of Mount Rainier, WA, USA. Our simple camera trap design consisted of a wildlife camera attached to a camouflaged cylindrical cooler filled with snow and rocks. Key resultsOur camera design proved ideal for a mountain glacier ecosystem and from June to September 2021, we detected at least 16 vertebrate species (seven birds, nine mammals) over 770 trap nights using glacier-associated habitats. Humans, primarily skiers, were the most common species detected, but we also recorded 99 observations of wildlife (birds and mammals). These included three species of conservation concern in Washington: wolverine (Gulo gulo), Cascade red fox (Vulpes vulpes cascadensis), and white-tailed ptarmigan (Lagopus leucura). ConclusionsCollectively, our results provide proof-of-concept for a novel camera trap design that is ideal for treeless, perennially snow-covered landscapes and revealed a rich diversity of wildlife using mountain glacier habitat in the Pacific Northwest. We highlight the global need for similar studies to better understand the true scale of biodiversity that will be impacted by glacier recession in mountain ecosystems.

ecology↗

bioRxiv2018

Hypoxia-induced epigenetic silencing of polo-like kinase 2 promotes fibrosis in atrial fibrillation

Fibrosis and inflammation promote atrial fibrillation (AF) and worsen its clinical outcome. The underlying molecular mechanisms, that are relevant for effective antifibrotic drug development, are still under debate. This study deciphers a novel mechanistic interplay between polo-like kinase 2 (PLK2) and the pro-inflammatory cytokine osteopontin (OPN) in the pathogenesis of atrial fibrosis. Compared to sinus rhythm (SR) controls, right atrial appendages and isolated right atrial fibroblasts from AF patients showed downregulation of PLK2 mRNA and protein levels, which were accompanied by remarkable hypoxia-sensitive DNA-methylation of the PLK2 promotor. In an experimental setting, both, genetic deletion and pharmacological inhibition of PLK2 induced myofibroblast differentiation and reduced fibroblast proliferation. Notably, proteomics from PLK2-deleted fibroblasts revealed de novo secretion of OPN. Accordingly, we observed higher OPN plasma levels in AF patients with atrial fibrosis compared to non-fibrosis AF patients. Hence, we provide evidence for PLK2 reactivation and/or OPN inhibition as potential novel targets to prevent fibrosis progression in AF.

pharmacology and toxicology↗

bioRxiv2018

YAP activity is necessary and sufficient for basal progenitor abundance and proliferation in the developing neocortex

The expansion of the neocortex during mammalian evolution has been linked to an enlargement of the subventricular zone during cortical development and an increase in the proliferation of the basal progenitors residing therein. Here, we explored a potential role of YAP, the major downstream effector of the Hippo signaling pathway, in proliferation of basal progenitors. We show that YAP expression and activity are high in ferret and human basal progenitors, which are known to exhibit high proliferative capacity, but low in mouse basal progenitors, which lack such capacity. To induce YAP activity in mouse basal progenitors, we expressed a constitutively active YAP (CA-YAP). This resulted in an increase in proliferation of basal progenitor. In addition, CA-YAP expressing mouse basal progenitors promoted the production of upper-layer neurons. To investigate if YAP is required for the proliferation of basal progenitors, we pharmacologically interfered with the function of YAP in the developing ferret and human neocortex. This resulted in a decrease of cycling basal progenitors. In concert, genetical interference with the function of YAP in ferret developing neocortex resulted in decreased abundance of basal progenitors. Together, our data indicate that YAP promotes the proliferation of basal progenitors and suggest that changes in YAP activity levels contributed to the evolutionary expansion of the neocortex.

neuroscience↗

bioRxiv2017

Evolution and cell-type specificity of human-specific genes preferentially expressed in progenitors of fetal neocortex

To understand the molecular basis underlying the expansion of the neocortex during primate, and notably human, evolution, it is essential to identify the genes that are particularly active in the neural stem and progenitor cells of developing neocortex. Here, we have used existing transcriptome datasets to carry out a comprehensive screen for protein-coding genes preferentially expressed in progenitors of fetal human neocortex. In addition to the previously studied gene ARHGAP11B, we show that ten known and two newly identified human-specific genes exhibit such expression, however with distinct neural progenitor cell-type specificity compared to their ancestral paralogs. Furthermore, we identify 41 additional human genes with progenitor-enriched expression which have orthologs only in primates. Our study not only provides a resource of genes that are candidates to exert specific, and novel, roles in neocortical development, but also reveals that distinct mechanisms gave rise to these genes during primate, and notably human, evolution.

developmental biology↗