Biology subjects

Klein, P.

Publications and source records attributed to Klein, P..

11 recordsLinked to original sources

bioRxiv2026

Prior experience dynamically determines differential cue weighting in the medial entorhinal cortex

Spatial navigation depends on integrating multiple cue sets whose influence is determined primarily by their inferred reliability. Here we investigated how cue weighting in the medial entorhinal cortex is updated based on previous experience at different time scales (minutes vs. days). In mice recorded in light and darkness while manipulating coherence between distal room cues and local arena cues, grid cells displayed stable firing fields in darkness only when prior light experience maintained coherent cue relationships. Grid activity remained anchored to local cues, and stability continuously increased by repeated exposure. In contrast, mice that experienced cue mismatch in light showed markedly reduced grid stability in darkness. Strikingly, re-establishing cue coherence produced only partial recovery, whereas a single exposure to cue mismatch abolished reliance on local cues. The reference frame shift at different time scales reflects a dynamic balance between flexibility and stability determined by a conservative cue weighting strategy.

neuroscience↗

bioRxiv2026

Specific killing of Ewing sarcoma by TCR-T cells targeting public neogene-encoded antigens

EWSR1::FLI1, the oncogenic chimeric transcription factor driving Ewing sarcoma (EwS)induces expression of exquisitely EwS-specific neogenes (Ew_NGs) through neomorphic binding and transcription activation at GGAA microsatellites in genomic regions that are silent in normal tissues. We show that peptides encoded by Ew_NGs are presented on HLA-I complexes on EwS cells. The cytokine secretion of CD8+ T cells specific for Ew_NG-encoded HLA-I-bound peptides is activated by all HLA-I-matched EwS cells but not by non-EwS cells. These T cells kill EwS cells in an HLA-I restricted manner. This cytotoxicity is dependent on the expression of EWSR1::FLI1 and of the corresponding Ew_NG. It can be reproduced by transduction of the TCR into donor T cells (TCR-T) which kill EwS cells in vivo. Moreover, we show that neither off target nor allogeneic activation are observed with TCR-T thus paving the way for cell therapy in relapsed/resistant EwS patients for which therapeutic options are very limited. Statement of significanceThe chimeric transcription factor EWSR1::FLI1 generates tumor-specific neogenes encoding neoantigen presented by the HLA-I molecules of Ewing cells. Neoantigen-specific CD8+ T-cell clones and engineered TCR-T cells can selectively recognize and kill EwS tumor cells in vitro and in vivo.

immunology↗

bioRxiv2026

Single-nucleotide resolution profiling reveals dynamic and site-specific m⁶A regulation during human myogenesis

BackgroundMyogenic differentiation of muscle stem cells required for skeletal muscle growth and regeneration relies on the precise spatiotemporal coordination of multiple gene-expression programs. Over the past decades, considerable progress has been made in defining the transcriptional networks that govern myogenesis. In particular, myogenic transcription factors integrate extrinsic and intrinsic cues to drive skeletal muscle development and regeneration. In contrast, post-transcriptional layers of regulation have remained comparatively underexplored. Among these, the epitranscriptome - comprising more than 170 chemical RNA modifications - has recently emerged as a major regulatory axis in cellular differentiation. N-methyladenosine (mA), the most abundant internal modification of mRNA, is now recognized as a key regulator of stem-cell fate decisions across multiple biological systems. By dynamically modulating RNA stability, translation, and other processing steps, mA enables precise fine-tuning of gene-expression programs in response to physiological cues. These effects are mediated through mA-binding RNA-binding proteins (RBPs), also referred to as "readers", which selectively recognize methylated transcripts and translate the modification into functional cellular outcomes. Despite its central role in other tissue contexts, the contribution of mA to skeletal muscle physiology - and particularly to human muscle stem cell biology - remains poorly characterized. This gap represents a critical and largely unexplored frontier in muscle biology. MethodsTo define the epitranscriptome landscape during the myogenic differentiation of human skeletal muscle cells, we performed GLORI on proliferating and differentiated human primary myoblasts. This recently developed approach enables detection of mA at single-nucleotide resolution together with quantitative measurement of methylation stoichiometry at individual sites. mA-modified positions were mapped across the transcriptome in both cellular states and integrated with matched RNA-seq datasets data to contextualise mA features relative to transcript abundance. To place these findings in a broader context, we compared our human mA maps with previously published mouse muscle cell datasets and overlaid them with available CLIP-seq datasets of mA RNA-binding proteins. ResultsWe identified tens of thousands of high-confidence mA sites in proliferating and differentiated human myogenic cells. While many sites were shared between states, myogenic differentiation was accompanied by epitranscriptomic remodeling, affecting both the distribution and stoichiometry of mA marks. Transcripts exhibiting differential mA regulation were enriched for pathways related to myogenic development, cytoskeletal remodeling, signalling, nucleic-acid-associated processes and energy metabolism. Joint analysis of mA site number, methylation stoichiometry, and expression levels indicated the presence of distinct mA regulatory frameworks at the transcript level. Genes associated with myogenesis and regulatory pathways were distributed across these categories, consistent with the coexistence of multiple regulatory programs during myogenic differentiation. In addition, cross-species comparisons revealed the presence of human-specific methylation patterns. Integration with published mA RNA-binding protein datasets uncovered distinct subsets of mA sites with varying binding profiles, suggesting state-dependent interpretation of mA marks. Together, these data constitute, to our knowledge, the first single-nucleotide-resolution atlas of mA methylation in human skeletal muscle, revealing a previously uncharacterized epitranscriptomic landscape and providing a foundational resource for studies of human myogenesis.

molecular biology↗

bioRxiv2025

Leveraging species-wide variation and patterns of adaptation to inform pecan crop improvement efforts

The genetic basis of adaptation is a fundamental question in evolutionary biology, and understanding how species will be able to adapt to changing conditions across their range has important implications for conservation and agriculture. To accurately interrogate the genetics of adaptation and assess the adaptive capacity of a species requires also characterizing the ways other mechanisms, including geographic distance and population dynamics, shape genetic variation. Pecan is an ecologically, culturally, and economically important North American tree, and a broader understanding of the genetics of environment adaptation will aid pecan conservation, breeding, and commercial management. Here, we use an expansive set of more than 700 pecan genotypes in combination with the first haplotype-resolved genome assembly for pecan to assess species-wide genetic variation and evaluate environmental adaptation across the native distribution. We identify five gene pools in pecan, with the lowest diversity in southern gene pools, and present evidence that gene pools began differentiating during multiple glacial cycles. Using complementary genotype-environment association approaches, we infer species-wide patterns of environmental adaptation. With these results, we predict mismatches in adaptation for pecan genotypes to different environments, including future environment scenarios. We see that in all locations, present-day genotypes incur some level of predicted maladaptation to simulated future environments, but current genetic diversity may provide a valuable source of resilience to future conditions through assisted migration. These results expand the understanding of environmental adaptation in pecan and provide insight into how long-lived species will be able to adapt to future conditions.

evolutionary biology↗

bioRxiv2025

Disrupted transcriptional networks regulated by CHD1L during neurodevelopment underlie the mirrored neuroanatomical and growth phenotypes of the 1q21.1 copy number variant

Distal 1q21.1 deletions and duplications are associated with variable phenotypes including autism, head circumference and height defects. To elucidate which gene(s) are responsible for the 1q21.1 duplication/deletion-associated phenotypes, we performed gene manipulation in zebrafish and mice. We modeled 1q21.1 duplication by overexpressing the eight human protein-coding genes in zebrafish. We found that overexpression of CHD1L only led to macrocephaly and increased larval body length, whereas chd1l deletion caused opposite phenotypes. These mirrored phenotypes were also observed in mouse embryos. Transcriptomic, cistromic, and chromatin accessibility analyses of CHD1L knock-out hiPSC-derived neuronal progenitor cells revealed that CHD1L regulates the expression levels and chromatin accessibility of genes involved in neuronal differentiation and synaptogenesis, including autism genes. Moreover, we found that CHD1L favors telencephalon development during forebrain regionalization by facilitating chromatin accessibility to pioneer transcription factors including SOX2 and OTX2 while simultaneously compacting chromatin through its interaction with the repressor NuRD complex. Last, atypical 1q21.1 CNV encompassing CHD1L and pathogenic missense and truncating CHD1L variants were found in individuals with autism. Overall, our data reveal a novel role for CHD1L as a master regulator of cell fate and its dosage imbalance contributes to the neuroanatomical and growth phenotypes associated with the 1q21.1 distal CNV. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=71 SRC="FIGDIR/small/638841v1_ufig1.gif" ALT="Figure 1"> View larger version (32K): org.highwire.dtl.DTLVardef@7dd5borg.highwire.dtl.DTLVardef@55a12dorg.highwire.dtl.DTLVardef@1c8ce0corg.highwire.dtl.DTLVardef@4faf29_HPS_FORMAT_FIGEXP M_FIG C_FIG

genomics↗

bioRxiv2024

Birds affected by a 2021 avian mortality event are strongly associated with supplemental feeding and ground foraging behaviors

In 2021, news outlets and state natural resources agencies reported a large number of avian deaths across several states in the eastern and midwestern USA. This event fomented a rapid and robust response from animal health experts from across the country. Given the clustered pattern of disease and death, an infectious etiology was rigorously investigated. No single causative pathogen was identified, leaving the cause and thus epidemiology of the mortality event unex-plained. In this study, we attempted to hone in on potential causes or contributors to this event by constructing a dataset on affected birds life history, phylogeny, and ecology. After a preliminary analysis of these features, we developed a statistical pipeline to test two hypotheses regarding features of birds associated with the mortality event: (1) that a significant proportion of affected birds in the total sample are members of the Cornell Feederwatch list (i.e., birds that consume supplemental feed, and their predators), and that (2) ground-feeding species would be significantly represented in the sample. While logistic regression models support the plausibility of the two hypotheses, they are statistically indistinguishable. We discuss the implications of these findings, propose future work, and highlight the importance of ecological and behavioral expertise in understanding epidemiological phenomena.

ecology↗

bioRxiv2023

m6a methylation orchestrates IMP1 regulation of microtubules during human neuronal differentiation

Neuronal differentiation requires building a complex intracellular architecture, and therefore the coordinated regulation of defined sets of genes. RNA-binding proteins (RBPs) play a key role in this regulation. However, while their action on individual mRNAs has been explored in depth, the mechanisms used to coordinate expression of the gene programs shaping neuronal morphology are poorly understood. To address this, we analysed how the paradigmatic RBP IMP1 (IGF2BP1), an essential developmental factor, selects and regulates its RNA targets during the differentiation of human neurons. We performed a combination of system-wide and molecular analyses, revealing that IMP1 developmentally transitions to and directly regulates the expression of mRNAs encoding essential regulators of the microtubule network, a key component of neuronal morphology. Furthermore, we showed that m6A methylation drives the selection of specific IMP1 mRNA targets and their protein expression during the developmental transition from neural precursors to neurons, providing a molecular principle for the onset of target selectivity.

molecular biology↗

bioRxiv2022

Temporal control of the integrated stress response by a stochastic molecular switch

Stress granules (SGs) are formed in the cytosol as an acute response to environmental cues and activation of the integrated stress response (ISR), a central signaling pathway controlling protein synthesis. Using chronic virus infection as stress model, we previously uncovered a unique temporal control of the ISR resulting in recurrent phases of SG assembly and disassembly. Here, we elucidate the molecular network generating this fluctuating stress response, by integrating quantitative experiments with mathematical modeling, and find that the ISR operates as a stochastic switch. Key elements controlling this switch are the cooperative activation of the stress-sensing kinase PKR, the ultrasensitive response of SG formation to the phosphorylation of the translation initiation factor eIF2, and negative feedback via GADD34, a stress-induced subunit of protein phosphatase 1. We identify GADD34 mRNA levels as the molecular memory of the ISR that plays a central role in cell adaptation to acute and chronic stress.

cell biology↗

bioRxiv2020

An aberrant cytoplasmic intron retention programme is a blueprint for ALS-related RBP mislocalization

We recently described aberrant cytoplasmic SFPQ intron-retaining transcripts (IRTs) and concurrent SFPQ protein mislocalization as a new hallmark of amyotrophic lateral sclerosis (ALS). However the generalizability and potential roles of cytoplasmic IRTs in health and disease remain unclear. Here, using time-resolved deep-sequencing of nuclear and cytoplasmic fractions of hiPSCs undergoing motor neurogenesis, we reveal that ALS-causing VCP gene mutations lead to compartment-specific aberrant accumulation of IRTs. Specifically, we identify >100 IRTs with increased cytoplasmic (but not nuclear) abundance in ALS samples. Furthermore, these aberrant cytoplasmic IRTs possess sequence-specific attributes and differential predicted binding affinity to RNA binding proteins (RBPs). Remarkably, TDP-43, SFPQ and FUS - RBPs known for nuclear-to-cytoplasmic mislocalization in ALS - avidly and specifically bind to this aberrant cytoplasmic pool of IRTs, as opposed to any individual IRT. Our data are therefore consistent with a novel role for cytoplasmic IRTs in regulating compartment-specific protein abundance. This study provides new molecular insight into potential pathomechanisms underlying ALS and highlights aberrant cytoplasmic IRTs as potential therapeutic targets. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=181 SRC="FIGDIR/small/211557v2_ufig1.gif" ALT="Figure 1"> View larger version (68K): org.highwire.dtl.DTLVardef@153fc1eorg.highwire.dtl.DTLVardef@cd3506org.highwire.dtl.DTLVardef@544868org.highwire.dtl.DTLVardef@15ddb68_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2019

A gold standard method for human cell quantification after xenotransplantation

Xenotransplantation of human cells into immunodeficient mouse models is a very powerful tool and an essential step for the pre-clinical evaluation of therapeutic cell-and gene-based strategies. Here we describe an optimized protocol combining immunofluorescence and real-time quantitative PCR to both quantify and visualize the fate and localization of human myogenic cells after injection in regenerating muscles of immunodeficient mice. Whereas real-time quantitative PCR-based method provides an accurate quantification of human cells, it does not document their specific localization. The addition of an immunofluorescence approach using human-specific antibodies recognizing engrafted human cells gives information on the localization of the human cells within the host muscle fibres, in the stem cell niche or in the interstitial space.\n\nThese two combined approaches offer an accurate evaluation of human engraftment including cell number and localization and should provide a gold standard to compare results obtained either using different types of human stem cells or comparing healthy and pathological muscle stem cells between different research laboratories worldwide.

cell biology↗

bioRxiv2018

Norovirus infection results in assembly of virus-specific G3BP1 granules and evasion of eIF2α signaling.

During viral infection, the accumulation of RNA replication intermediates or viral proteins imposes major stress on the host cell. In response, cellular stress pathways can rapidly impose defence mechanisms by shutting off the protein synthesis machinery, which viruses depend on, and triggering the accumulation of mRNAs into stress granules to limit the use of energy and nutrients. Because this threatens viral gene expression, viruses need to evade these pathways to propagate. Human norovirus is responsible for gastroenteritis outbreaks worldwide. Previously we showed that murine norovirus (MNV) regulates the activity of eukaryotic initiation factors (eIFs). Here we examined how MNV interacts with the eIF2a signaling axis controlling translation and stress granules accumulation. We show that while MNV infection represses host cell translation, it results in the assembly of virus-specific granules rather than stress granules. Further mechanistic analyses revealed that eIF2a signaling is uncoupled from translational stalling. Moreover the interaction of the RNA-binding protein G3BP1 with viral factors together with a redistribution of its cellular interacting partners could explain norovirus evasion of stress granules assembly. These results identify novel strategies by which norovirus ensure efficient replication propagation by manipulating the host stress response.

microbiology↗