Biology subjects

Kaessmann, H.

Publications and source records attributed to Kaessmann, H..

At least 19 recordsLinked to original sources

bioRxiv2026

Reconstructing human gene regulatory evolution using deep learning

Understanding the genetic changes that drove the evolution of human-specific traits is a central goal in biology. Changes in gene expression are thought to be a major source of phenotypic innovations, but identifying the underlying changes in cis-regulatory elements (CREs) along the human lineage has been difficult: functional data from great apes are scarce and unobtainable for extinct hominins, and pinpointing causal substitutions requires knowing which sequences determine CRE activity. Here, we used AlphaGenome, a sequence-to-function deep-learning model, to predict the cis-regulatory effects of ~17 million single-nucleotide substitutions specific to the human lineage and traced their consequences for gene expression evolution across 305 tissues and cell types. The 71,345 predicted cis-regulatory gains lie mostly outside human accelerated regions and arose either through creation of new CREs or, more often, through co-option of CREs ancestrally accessible in other tissues. They are also enriched for distal enhancers and for target gene functions characteristic of the corresponding tissues, suggesting that they contributed to the evolution of tissue-specific biology in humans. Genes linked to more gains were more likely to be upregulated in humans, and in silico reversion to ancestral alleles traced such upregulations to individual substitutions creating transcription factor binding motifs. Comparison with Neandertal and Denisovan genomes revealed that nearly all gains now fixed in humans predate the split from archaic hominins, yet a few modern-human-specific gains contribute substantially to gene upregulation. Our study provides a genome-wide, tissue-resolved map of cis-regulatory changes and their contribution to gene expression evolution along the human lineage.

evolutionary biology↗

bioRxiv2026

Conserved cerebellar rhombic lip compartmentalization and Eomes regulatory networks govern unipolar brush cell development

The rhombic lip (RL) gives rise to all cerebellar glutamatergic cell types, including unipolar brush cells (UBCs). Disruptions to UBC development can lead to the neurodevelopmental disorder Dandy-Walker Syndrome and the pediatric brain tumor medulloblastoma, but these diseases have not been adequately modeled in mice. To evaluate conservation of UBC development in mouse and human, we examined UBC localization, lineage decisions, and the underlying molecular mechanisms of UBC differentiation using multiplex immunofluorescence and single-cell RNA-seq of wild-type and conditional knockout animals of the primary UBC transcription factor Eomes. Similar to the human RL, the murine RL is molecularly compartmentalized, cycling EOMES+ UBC progenitors are highly abundant, and persist after birth. Eomes regulates the transcriptional networks important for UBC differentiation and migration, but not UBC fate. Overall, our findings suggest that murine UBC development recapitulates many features of human UBC development, with EOMES playing a central role in UBC maturation.

developmental biology↗

bioRxiv2026

A multi-omics atlas of human hindbrain development

The human hindbrain controls essential motor and autonomic functions and is the site of neurodevelopmental diseases. Yet, its cellular diversity, developmental trajectories and underlying regulatory logic remain poorly understood. We present a comprehensive multi-omics atlas of human hindbrain development spanning embryonic to adult stages, encompassing 594,817 transcriptomic and 422,568 chromatin-accessibility single-nucleus profiles. This dataset resolved the cellular architecture of hindbrain cellular lineages, and delineated coordinated gene expression, cis-regulatory programs and regulatory grammar guiding their developmental trajectories. By integrating multi-omics data, we discovered context-specific roles of transcription factors across cell types and deciphered the role of HOX genes in driving divergent cellular identity in related lineages. We further leveraged the atlas to contextualize pediatric gliomas to decode how subtle yet coordinated shifts in gene expression context can define oncogenic transformation. Together, this atlas provides a foundational resource for hindbrain biology and establishes a gene-regulatory framework linking development and disease.

neuroscience↗

bioRxiv2025

A dual genetic constraint underlies the conservation of early brains in vertebrates.

As the body plan, the embryonic brain bauplan reflects the shared features of vertebrate brains. Yet, disagreements among sparse histogenetic frameworks have undermined the bauplans power to trace homologies. Here, we generate and integrate five vertebrate single-cell multi-omic atlases of early embryonic brains, revealing a conserved cellular blueprint that defines equivalent progenitor domains across species. Our cellular neuromeric model provides an unified and unbiased framework for the vertebrate brain bauplan and revises the regionalisation of the prosencephalon, refining its molecular boundaries and developmental relationships. Furthermore, cross-species gene-network analyses expose regulatory complexity beyond classical neuromeric patterning, resolving networks into modules aligned with regional cell types or cell class (progenitor/neuron). Evolutionarily, two main developmental constraints emerge: brain bauplan genes, early essential for regional identity, and pleiotropic stemness gene modules, indispensable across all proliferating cells. In turn, later development displays tissue-specific and less essential modules, explaining its rapid divergence into species-specific features. Together, these findings reveal a dual evolutionary constraint--neuromeric identity and pleiotropic stemness--that underlies the conservation of early vertebrate brains. This duality explains how deeply conserved regulatory architectures coexist with evolutionary flexibility to develop into the immense diversity of vertebrate nervous systems. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=77 SRC="FIGDIR/small/684766v1_ufig1.gif" ALT="Figure 1"> View larger version (32K): org.highwire.dtl.DTLVardef@a337a2org.highwire.dtl.DTLVardef@19987adorg.highwire.dtl.DTLVardef@9a9394org.highwire.dtl.DTLVardef@4ef279_HPS_FORMAT_FIGEXP M_FIG C_FIG

evolutionary biology↗

bioRxiv2025

Gene regulatory innovations from transposable elements in mammalian cerebellum development

Transposable elements (TEs) are hypothesized to have driven gene regulatory innovation, yet their contributions to primate brain development at the cell type level remain largely unexplored. Using single-cell multiomics data for the cerebellum from human, macaque, marmoset, and mouse, we revealed that TE contributions to different cell types are shaped by differences in evolutionary constraint across cell types, as well as the preferential co-option of certain TEs in specific cell states. Using a sequence-based deep-learning model predicting cell-type-specific chromatin accessibility, we systematically assessed the co-option potential of TEs into cerebellar gene regulatory networks, identifying seventeen TE fragments with complex regulatory sequences in their ancestral states that facilitate their co-option as cell-type-specific cis-regulatory elements. Primate-specific HERVL (human endogenous retrovirus L) is predominantly accessible in differentiating granule cells and other rhombic-lip-derived neuroblasts during hindbrain development, and contributes to species-specific gene expression patterns. Our study uncovers a pivotal role for TEs in the evolution of the cerebellum. More generally, it demonstrates how TEs can be directly co-opted into the gene regulatory networks of specific cell types and introduces a generalizable analytical framework for dissecting their contribution to mammalian regulatory evolution.

genetics↗

bioRxiv2025

The origin and molecular evolution of the mammalian liver cell architecture

The liver is a central organ with essential roles in processes such as nutritional metabolism, detoxification, and immune defense1-6. It has been instrumental in the adaptation of mammalian species to diverse environments, as reflected by its rapid molecular evolution7,8. However, the origins and evolutionary dynamics of liver cell types and their structural organization remain largely unexplored. Here we report evolutionary analyses of transcriptome and chromatin accessibility data for liver cells from 17 species, spanning all major feeding strategies (herbivory, omnivory, carnivory, insectivory), great apes (including humans), placental clades (Afrotheria, Xenarthra, Laurasiatheria, Euarchontoglires), major mammalian lineages (placentals, marsupials, monotremes), and a bird as outgroup. Integrated with spatial transcriptomics, our data reveal that liver zonation--the compartmentalization of hepatocyte functions along the lobule, the livers fundamental anatomical and functional unit--is conserved across mammals but absent in other vertebrates. We find that zonation originated in the mammalian ancestor, driven by the emergence of WNT and R-spondin signaling from central vein endothelial cells, which activate central hepatocyte gene expression via the transcription factor TCF7L2. Despite this conserved architecture and signaling, genes with zonated expression exhibit rapid evolutionary turnover. Consistently, hepatocytes evolve fast, likely due to reduced selective constraints, enabling adaptive changes under positive selection. Alongside immune cells, hepatocytes are therefore key drivers of the livers rapid evolution and functional innovations. In great apes, we identify human-specific shifts in zonation and cell-type-specific expression linked to recent cis-regulatory changes, particularly in genes involved in lipid metabolism, likely contributing to human-specific metabolic traits. Our study uncovers the origins of a mammal-specific liver cell architecture, within which reduced constraints facilitated molecular changes underlying ecological adaptations.

evolutionary biology↗

bioRxiv2025

The evolution of gene regulatory programs controlling gonadal development in primates

Sex-determining pathways produce dimorphic gonads (ovaries and testes), yet the gene regulatory programs governing gonadogenesis and their evolution in primates remain little explored. Here we report evolutionary analyses of transcriptome and chromatin accessibility data of male and female human, marmoset (New World monkey), and mouse gonadal cells spanning key prenatal stages. We find that the two primates and mouse share similar X chromosome expression dynamics, including X chromosome reactivation (XCR), and that in Klinefelter syndrome (XXY) testes, germ cells undergo female-like XCR and escape of X inactivation. New male-specific regulatory regions have emerged progressively during mammalian evolution, especially on the X following sex chromosome origination. Further analyses revealed that male-specific regulatory regions evolved faster than female-specific ones in both supporting and pre-meiotic germ cells. However, female meiotic germ cells show even higher rates of molecular evolution and exhibit a permissive chromatin state that facilitates the birth of new genes, thus resembling their adult spermatogenic counterparts. Finally, we traced both conserved and species-specific gene expression trajectories across the three mammals, uncovering candidate genes for disorders of sex development that are typically central to cell-type-specific regulatory networks. Together, our study unveils both ancestral mammalian and recently evolved gene regulatory programs that control human- and primate-specific aspects of gonadal development in both sexes.

evolutionary biology↗

bioRxiv2025

Developmental landscape of shark telencephalon sheds light on the evolution of telencephalic cell types and the ancient origin of Cajal-Retzius cells

The emergence of predation and associated complex behaviors in jawed vertebrates (gnathostomes) were major driving forces in brain evolution. To gain insight into the neuronal complexity of the last common gnathostome ancestor, we studied the development of the shark telencephalon by combining single-cell and spatial transcriptomics. Our findings suggest an ancient origin of pallial neurogenesis, including basal progenitors, which were previously only identified in tetrapods. We find evidence for migrating gabaergic neurons populating the dorsal pallium, where we observe incipient layering. Finally, we provide evidence for the existence of Cajal-Retzius cells in the developing shark telencephalon, with a conserved molecular profile and tissue localization relative to mammals. Our analyses revealed that major features of the vertebrate pallium arose much earlier than previously thought, in the gnathostome lineage.

developmental biology↗

bioRxiv2025

A simple, fast and cost-efficient protocol for ultra-sensitive ribosome profiling

Ribosome profiling has become an essential tool for studying mRNA translation in cells with codon-level resolution. However, its widespread application remains hindered by the labour-intensive workflow, low efficiency and high costs associated with sequencing sample preparation. Here, we present a new cost-effective and ultra-sensitive library preparation method that significantly advances the applicability of ribosome profiling. By implementing bead-coupled enzymatic reactions and product purifications, our approach increases both yield and throughput while maintaining high reproducibility. Demonstrating the sensitivity of the protocol we prepared libraries from as little as 12 fmol of RNA, which expands the feasibility of ribosome profiling from minimal input samples, such as derived from small populations, stressed cells, or patient-derived specimens. Additionally, we validate the versatility of the protocol across multiple species and demonstrate its applicability for RNA-seq library preparation. Altogether, this protocol provides a highly accessible and efficient alternative to existing ribosome profiling workflows, facilitating research in previously challenging experimental contexts.

systems biology↗

bioRxiv2025

The evolution of gene regulation in mammalian cerebellum development

Gene regulatory changes are considered major drivers of evolutionary innovations, including the cerebellums expansion during human evolution, yet they remain largely unexplored. In this study, we combined single-nucleus measurements of gene expression and chromatin accessibility from six mammals (human, bonobo, macaque, marmoset, mouse, and opossum) to uncover conserved and diverged regulatory networks in cerebellum development. We identified core regulators of cell identity and developed sequence-based models that revealed conserved regulatory codes. By predicting chromatin accessibility across 240 mammalian species, we reconstructed the evolutionary histories of human cis-regulatory elements, identifying sets associated with positive selection and gene expression changes, including the recent gain of THRB expression in cerebellar progenitor cells. Collectively, our work reveals the shared and mammalian lineage-specific regulatory programs governing cerebellum development.

evolutionary biology↗

bioRxiv2024

Developmental origins and evolution of pallial cell types and structures in birds

The advanced cognitive abilities of birds rival those of mammals and have been attributed to evolutionary innovations in the pallium. However, a comprehensive cellular characterization of this brain region in birds has been lacking. We scrutinized the structures, cell types and evolutionary origins of the avian pallium based on single-cell and spatial transcriptomics atlases for the adult and developing chicken, and comparisons to corresponding data from mammals and non-avian reptiles. We found that the avian pallium shares most inhibitory neuron types with other amniotes. While excitatory neuron repertoires in the (medial) hippocampal formation show high conservation, they substantially diverged in other pallial regions during avian evolution, defining novel structures like the avian-specific (dorsal) hyperpallium, whose neuronal gene expression identities partly converge during late development with those of the (ventral) nidopallium. Our work also unveils the evolutionary relationships of pallial structures across amniotes, like the previously unknown homology between avian (lateral) mesopallial and mammalian deep layer cortical neurons. One-Sentence SummaryAn avian neural cell type atlas illuminates the developmental origins and evolution of the amniote pallium.

evolutionary biology↗

bioRxiv2024

A single-nucleus RNA sequencing atlas of the postnatal retina of the shark Scyliorhinus canicula

The retina, whose basic cellular structure is highly conserved across vertebrates, constitutes an accessible system for studying the central nervous system. In recent years, single-cell RNA-sequencing studies have uncovered cellular diversity in the retina of a variety of species, providing new insights on retinal evolution and development. However, similar data in cartilaginous fishes, the sister group to all other extant jawed vertebrates, are still lacking. Here, we present a single-nucleus RNA-sequencing atlas of the postnatal retina of the catshark Scyliorhinus canicula, consisting of the expression profiles for 17,438 individual cells from three female, juvenile catshark specimens. Unsupervised clustering revealed 22 distinct cell types comprising all major retinal cell classes, as well as retinal progenitor cells (whose presence reflects the persistence of proliferative activity in postnatal stages in sharks) and oligodendrocytes. Thus, our dataset serves as a foundation for further studies on the development and function of the catshark retina. Moreover, integration of our atlas with data from other species will allow for a better understanding of vertebrate retinal evolution.

neuroscience↗

bioRxiv2024

A male-essential microRNA is key for avian sex chromosome dosage compensation

Birds have a sex chromosome system in which females are heterogametic (ZW) and males are homogametic (ZZ). The differentiation of avian sex chromosomes from ancestral autosomes entailed the loss of most genes from the W chromosome during evolution. However, to what extent mechanisms evolved that counterbalance the consequences of this extensive gene dosage reduction in female birds has remained unclear. Here we report functional in vivo and evolutionary analyses of a Z-chromosome-linked microRNA (miR-2954) with strongly male-biased expression that was previously proposed to play a key role in sex chromosome dosage compensation1. We knocked out miR-2954 in chicken, which resulted in early embryonic lethality of homozygous knockout males, likely due to the highly specific upregulation of dosage-sensitive Z-linked target genes of miR-2954. Our evolutionary gene expression analyses further revealed that these dosage-sensitive target genes have become upregulated on the single Z in female birds during evolution. Altogether, our work unveils a scenario where evolutionary pressures on females following W gene loss led to the evolution of transcriptional upregulation of dosage-sensitive genes on the Z not only in female but also in male birds. The resulting overabundance of transcripts in males resulting from the combined activity of two dosage-sensitive Z gene copies was in turn offset by the emergence of a highly targeted miR-2954-mediated transcript degradation mechanism during avian evolution. Our findings demonstrate that birds have evolved a unique sex chromosome dosage compensation system in which a microRNA has become essential for male survival.

evolutionary biology↗

bioRxiv2024

Medulloblastoma oncogene aberrations are not involved in tumor initiation, but essential for disease progression and therapy resistance

Despite recent advances in understanding disease biology, treatment of Group 3/4 medulloblastoma remains a therapeutic challenge in pediatric neuro-oncology. Bulk-omics approaches have identified considerable intertumoral heterogeneity in Group 3/4 medulloblastoma, including the presence of clear single-gene oncogenic drivers in only a subset of cases, whereas in the majority of cases, large-scale copy-number aberrations prevail. However, intratumoral heterogeneity, the role of oncogene aberrations, and broad CNVs in tumor evolution and treatment resistance remain poorly understood. To dissect this interplay, we used single-cell technologies (snRNA-seq, snATAC-seq, spatial transcriptomics) on a cohort of Group 3/4 medulloblastoma with known alterations in the oncogenes MYC, MYCN, and PRDM6. We show that large-scale chromosomal aberrations are early tumor initiating events, while the single-gene oncogenic events arise late and are typically sub-clonal, but MYC can become clonal upon disease progression to drive further tumor development and therapy resistance. We identify that the subclones are mostly interspersed across tumor tissue using spatial transcriptomics, but clear segregation is also present. Using a population genetics model, we estimate medulloblastoma initiation in the cerebellar unipolar brush cell-lineage starting from the first gestational trimester. Our findings demonstrate how single-cell technologies can be applied for early detection and diagnosis of this fatal disease.

cancer biology↗

bioRxiv2024

Gene regulatory network landscape of Group 3/4 medulloblastoma

Cellular heterogeneity in Group 3 and Group 4 medulloblastomas is a major driver of therapeutic intractability. Here, we describe transcription factor-driven mechanisms underlying cellular diversity in these tumors using a comprehensive single-nucleus multi-omics atlas. Our analysis reveals that rather than fixed entities, these tumors exist along a continuum of cell states defined by four molecular identity axes. We show that perturbing transcription factor activity drives cellular plasticity, a key contributor to tumor heterogeneity. Strikingly, modulation of the lineage determinant PAX6 redirects tumor cells along both Group 3- and Group 4-like differentiation trajectories, modeling a bi-lineage medulloblastoma, and reduces aggressiveness of MYC-driven tumor models. Together, our findings reveal how oncogenic signals co-opt cerebellar unipolar brush cell programs to rewire tumor cell states and identify cellular plasticity as a potential targetable vulnerability in medulloblastoma.

cancer biology↗

bioRxiv2022

Reconstructing the ancestral vertebrate brain using a lamprey neural cell type atlas

The vertebrate brain emerged more than [~]500 million years ago in common evolutionary ancestors. To systematically trace its cellular and molecular origins, we established a spatially resolved cell type atlas of the entire brain of the sea lamprey - a jawless species whose phylogenetic position affords the reconstruction of ancestral vertebrate traits - based on extensive single-cell RNA-seq and in situ sequencing data. Comparisons of this atlas to neural data from the mouse and other jawed vertebrates unveiled various shared features that enabled the reconstruction of the core cell type composition, tissue structures, and gene expression programs of the ancestral brain. However, our analyses also revealed key tissues and cell types that arose later in evolution. For example, the ancestral vertebrate brain was likely devoid of cerebellar cell types and oligodendrocytes (myelinating cells); our data suggest that the latter emerged from astrocyte-like evolutionary precursors on the jawed vertebrate lineage. Our work illuminates the cellular and molecular architecture of the ancestral vertebrate brain and provides a foundation for exploring its diversification during evolution.

evolutionary biology↗

bioRxiv2021

Cellular development and evolution of the mammalian cerebellum

The expansion of the neocortex, one of the hallmarks of mammalian evolution1,2, was accompanied by an increase in the number of cerebellar neurons3. However, little is known about the evolution of the cellular programs underlying cerebellum development in mammals. In this study, we generated single-nucleus RNA-sequencing data for [~]400,000 cells to trace the development of the cerebellum from early neurogenesis to adulthood in human, mouse, and the marsupial opossum. Our cross-species analyses revealed that the cellular composition and differentiation dynamics throughout cerebellum development are largely conserved, except for human Purkinje cells. Global transcriptome profiles, conserved cell state markers, and gene expression trajectories across neuronal differentiation show that the cerebellar cell type-defining programs have been overall preserved for at least 160 million years. However, we also discovered differences. We identified 3,586 genes that either gained or lost expression in cerebellar cells in one of the species, and 541 genes that evolved new expression trajectories during neuronal differentiation. The potential functional relevance of these cross-species differences is highlighted by the diverged expression patterns of several human disease-associated genes. Altogether, our study reveals shared and lineage-specific programs governing the cellular development of the mammalian cerebellum, and expands our understanding of the evolution of mammalian organ development.

evolutionary biology↗

bioRxiv2021

Mapping pediatric brain tumors to their origins in the developing cerebellum

Understanding the cellular origins of childhood brain tumors is key for discovering novel tumor-specific therapeutic targets. Previous strategies mapping cellular origins typically involved comparing human tumors to murine embryonal tissues1,2, a potentially imperfect approach due to spatio-temporal gene expression differences between species3. Here we use an unprecedented single-nucleus atlas of the developing human cerebellum (Sepp, Leiss, et al) and extensive bulk and single-cell transcriptome tumor data to map their cellular origins with focus on three most common pediatric brain tumors - pilocytic astrocytoma, ependymoma, and medulloblastoma. Using custom bioinformatics approaches, we postulate the astroglial and glial lineages as the origins for posterior fossa ependymomas and radiation-induced gliomas (secondary tumors after medulloblastoma treatment), respectively. Moreover, we confirm that SHH, Group3 and Group4 medulloblastomas stem from granule cell/unipolar brush cell lineages, whereas we propose pilocytic astrocytoma to originate from the oligodendrocyte lineage. We also identify genes shared between the cerebellar lineage of origin and corresponding tumors, and genes that are tumor specific; both gene sets represent promising therapeutic targets. As a common feature among most cerebellar tumors, we observed compositional heterogeneity in terms of similarity to normal cells, suggesting that tumors arise from or differentiate into multiple points along the cerebellar "lineage of origin".

cancer biology↗