Biology subjects

Luisier, R.

Publications and source records attributed to Luisier, R..

13 recordsLinked to original sources

bioRxiv2026

Resolving context-specific protein-protein interactomes forbiological discovery and therapeutic target prioritisation

Protein function is shaped by cellular context, yet most protein representations and interaction maps remain context-agnostic. Here we present ProtScape, a multiscale graph-learning framework integrating global protein interactions, cell-type gene expression and protein language models to learn context-specific representations and infer interactomes across more than 200 cell types. ProtScape substantially outperforms existing approaches in interaction reconstruction, increasing the area under the precision-recall curve by 40 percentage points. Its predicted interactions were supported by held-out continuous STRING global evidence, while its representations recovered higher-order protein organisation. In patient-derived amyotrophic lateral sclerosis motor neurons, ProtScape revealed stage-specific network changes implicating RAB-dependent trafficking as a candidate early disease mechanism. In Parkinson's disease, it recovered clinically supported therapeutic targets from a proteome-wide search space 16-fold smaller than that required by competing representations. Together, ProtScape provides a scalable framework for translating context-specific interactome organisation into experimentally testable disease mechanisms and therapeutic hypotheses.

bioinformatics↗

bioRxiv2026

Topology-aware reconstruction of cellular state landscapes from microscopy using self-supervised learning

Morphology and spatial organisation provide complementary readouts of cellular state. However, reconstructing continuous cellular state landscapes from imaging data remains challenging, particularly in dense biological cultures. Here we present SI-SimCLR, a spatially informed self-supervised learning framework that learns biologically informative representations directly from fluorescence microscopy images without requiring segmentation or manual annotation. Combined with a graph-based partial optimal transport framework, SI-SimCLR enables reconstruction of cellular phenotypic landscapes from static imaging data, revealing how phenotypic substates are organised and connected. To establish and validate this framework, we generated a multimodal dataset of human iPSC-derived astrocytes using high-content imaging and matched bulk transcriptomics. SI-SimCLR resolved distinct interconnected astrocyte substates associated with disease and inflammatory states. ALS astrocytes occupied constrained regions of the morphological landscape. Strikingly, morphology and transcriptomics captured distinct and complementary aspects of astrocyte state variation.Together, our framework establishes a scalable and annotation-free strategy for reconstructing cellular phenotypic landscapes from microscopy data, enabling analysis of cellular heterogeneity, landscape connectivity and phenotypic responses across biological systems.

bioinformatics↗

bioRxiv2025

Extended pre-training of histopathology foundation models uncovers co-existing breast cancer archetypes characterized by RNA splicing or TGF-β dysregulation

In recent years, histopathology foundation models (hFM) have rapidly advanced in size and complexity, achieving excellent performance in tasks such as cancer diagnosis and biomarker discovery. Here, we reveal novel capabilities of these models by specializing hFMs, originally trained on diverse tissue types, specifically to invasive tumor tissue. It enables unprecedented discrimination of visually similar yet molecularly distinct tumor regions, that were previously indistinguishable by baseline models, which eventually leads to uncovering new biological insights into breast cancer. Our contributions are threefold. First, to the best of our knowledge, this is the first study to systematically evaluate the biological concepts encoded within hFM representations across multiple scales. Second, we explore extended pre-training to identify optimal conditions that enhance the models ability to encode richer, tumor tissue-specific biological concepts. We show that this refinement strategy transforms generalist models into a specialist one capable of resolving subtle, recurrent tumor regions with distinct morphological and molecular identities, called tumor archetypes. Finally, leveraging this specialized model, we uncover two dominant tumor archetypes in invasive breast cancer characterized by distinct aberrant gene expression signatures, notably RNA metabolism dysregulation and TGF-{beta} signaling. Strikingly, these archetypes coexist within the same tumors as spatially distinct regions with varying densities and patterns, and are recurrent across patients, highlighting their universality and potential clinical relevance for patient stratification. Altogether our study demonstrates how extended pre-training of state-of-the-art hFM with specific tumor tissues can unlock rich molecular and morphological information encoded in H&E images. By providing a more accessible approach to investigating tumor heterogeneity, this work opens new avenues for precision oncology, using routine histopathology slides and low computational resources. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=128 SRC="FIGDIR/small/645192v1_ufig1.gif" ALT="Figure 1"> View larger version (30K): org.highwire.dtl.DTLVardef@38e660org.highwire.dtl.DTLVardef@19ce335org.highwire.dtl.DTLVardef@108e8e6org.highwire.dtl.DTLVardef@1f25bc0_HPS_FORMAT_FIGEXP M_FIG Graphical abstract C_FIG

cancer biology↗

bioRxiv2024

Generation of morphologically distinct astrocyte subtypes from human iPSCs reveals a link between glial shape, function and reactivity

Astrocyte morphology in vivo is heterogeneous across different subtypes and dynamically changes in response to various stimuli. However, several questions on the mechanistic links between shape and function remain unanswered. Here, we developed an efficient protocol to generate pure populations of morphologically distinct human astrocytes in vitro, which we used for a systematic analysis of shape-function relationships. We performed a structural, molecular, and functional characterization of these populations and highlighted how their distinct morphologies mirror distinct functional and transcriptional patterns at the population level. We were also able to both correlate gene expression profiles of these morphologically distinct astrocyte subtypes with in vivo astrocytes in the human brain, and to validate our findings with primary isolated murine astrocytes in vitro. Moreover, we show that the observed morphological differences are correlated with changes in key cytoskeletal proteins, which offers a potential link to the observed functional differences. Finally, we demonstrated that different morphological subtypes of astrocytes have distinct reactivity responses to a common stimulus. This study offers a glimpse into the shape-function dynamics of human astrocytes, highlighting potential mechanistic links between cytoskeletal usage and astrocyte function, while also providing tools and datasets that will be useful for further studies into human glial biology in health and disease.

neuroscience↗

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

The RNA Binding proteome of axonal mRNAs in sympathetic neurons

BackgroundNeurons are morphologically complex cells that rely on the compartmentalization of protein expression to develop and maintain their cytoarchitecture. Targeting of RNA transcripts to axons is one of the mechanisms that allows rapid local translation of proteins in response to extracellular signals. 3 untranslated regions (UTRs) of mRNA are non-coding sequences that play a critical role in determining transcript localisation and translation by interacting with specific RNA binding proteins (RBPs). However, how 3UTRs contribute to mRNA metabolism and the nature of RBP complexes responsible for these functions remain elusive. ResultsWe performed 3 end sequencing of RNA isolated from axons and cell bodies of sympathetic neurons exposed to either Nerve Growth factor (NGF) or Neurotrophin 3 (NT3). NGF and NT3 are growth factors essential for sympathetic neuron development that act through distinct signalling mechanisms. Whereas NT3 is thought to act only locally, NGF signals back from axons to the cell bodies. We discovered that both NGF and NT3 affect transcription and alternative polyadenylation and induce the localisation of specific 3UTR isoforms to axons. The finding that many transcripts with short 3UTR were detected only in axons suggest that these may undergo local post-transcriptional remodelling. The integration of our data with CLIP-sequencing data revealed that long 3UTR isoforms associate with RBP complexes in the nucleus, and once in axons, regulate cytoplasmic 3 UTR isoform cleavage into shorter isoform. ConclusionsOur findings shed new light on the complex interplay between nuclear polyadenylation, mRNA localisation and local 3UTR remodelling in developing neurons. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=106 SRC="FIGDIR/small/517728v1_ufig1.gif" ALT="Figure 1"> View larger version (36K): org.highwire.dtl.DTLVardef@17196eforg.highwire.dtl.DTLVardef@6c26adorg.highwire.dtl.DTLVardef@5f335borg.highwire.dtl.DTLVardef@24a6d6_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2021

Image-based deep learning reveals the responses of human motor neurons to stress and ALS

Although morphological attributes of cells and their substructures are recognized readouts of physiological or pathophysiological states, these have been relatively understudied in amyotrophic lateral sclerosis (ALS) research. In this study we integrate multichannel fluorescence high-content microscopy data with deep-learning imaging methods to reveal - directly from unsegmented images - novel neurite-associated morphological perturbations associated with (ALS-causing) VCP-mutant human motor neurons (MNs). Surprisingly, we reveal that previously unrecognized disease-relevant information is withheld in broadly used and often considered generic biological markers of nuclei (DAPI) and neurons ({beta}III-tubulin). Additionally, we identify changes within the information content of ALS-related RNA binding protein (RBP) immunofluorescence imaging that is captured in VCP-mutant MN cultures. Furthermore, by analyzing MN cultures exposed to different extrinsic stressors, we show that heat stress recapitulates key aspects of ALS. Our study therefore reveals disease-relevant information contained in a range of both generic and more specific fluorescent markers, and establishes the use of image-based deep learning methods for rapid, automated and unbiased testing of biological hypotheses.

neuroscience↗

bioRxiv2021

Diminished miRNA activity is associated with aberrant cytoplasmic intron retention in ALS pathogenesis

Intron retention (IR) is now recognized as a dominant splicing event during motor neuron (MN) development, however the role and regulation of intron-retaining transcripts (IRTs) localized to the cytoplasm remain particularly understudied. By resolving the spatiotemporal dynamics of IR underlying distinct stages of MN lineage restriction, we identify a cytoplasmic group of IRTs that is not associated with reduced expression of their own genes but instead with an upregulation of predicted target genes of specific miRNAs, the motifs of which are enriched within the intronic sequences of this group. Next, we show that ALS-causing VCP mutations lead to a selective increase in IR of this particular class of introns. This in turn temporally coincides with an increase in the expression level of predicted target genes of these miRNAs, providing a potential mechanistic insight into ALS pathogenesis. Altogether, we propose a novel role for the cytoplasmic intronic sequences in regulating miRNA activity through miRNA sequestration, which potentially contributes to ALS pathogenesis.

neuroscience↗

bioRxiv2020

Automated and unbiased classification of motor neuron phenotypes with single cell resolution in ALS tissue.

Histopathological analysis of tissue sections is an invaluable resource in neurodegeneration research. Importantly, cell-to-cell variation in both the presence and severity of a given phenotype is however a key limitation of this approach, reducing the signal to noise ratio and leaving unresolved the potential of single-cell scoring for a given disease attribute. Here, we developed an image processing pipeline for automated identification and profiling of motor neurons (MNs) in amyotrophic lateral sclerosis (ALS) pathological tissue sections. This approach enabled unbiased analysis of hundreds of cells, from which hundreds of features were readily extracted. Next by testing different machine learning methods, we automated the identification of phenotypically distinct MN subpopulations in VCP- and SOD1-mutant transgenic mice, revealing common aberrant phenotypes in cellular shape. Additionally we established scoring metrics to rank cells and tissue samples for both disease probability and severity. Finally, by adapting this methodology to human post-mortem tissue analysis, we validated our core finding that morphological descriptors strongly discriminate ALS from control healthy tissue at the single cell level. In summary, we show that combining automated image processing with machine learning methods substantially improves the speed and reliability of identifying phenotypically diverse MN populations. Determining disease presence, severity and unbiased phenotypes at single cell resolution might prove transformational in our understanding of ALS and neurodegenerative diseases more broadly.

neuroscience↗

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

Widespread FUS mislocalization is a molecular hallmark of ALS

Amyotrophic lateral sclerosis (ALS)-causing mutations clearly implicate ubiquitously expressed and predominantly nuclear RNA binding proteins (RBPs), which form pathological cytoplasmic inclusions in this context. However, the possibility that wild-type RBPs mislocalize without necessarily becoming constituents of ALS cytoplasmic inclusions themselves remains unexplored. We hypothesized that nuclear-to-cytoplasmic mislocalization of the RBP Fused in Sarcoma (FUS), in an unaggregated state, may occur more widely in ALS that previously recognized. To address this hypothesis, we analysed motor neurons (MNs) from an human ALS induced-pluripotent stem cells (iPSC) model caused by the VCP mutation. Additionally, we examined mouse transgenic models and post-mortem tissue from human sporadic ALS cases. We report nuclear-to-cytoplasmic mislocalization of FUS in both VCP-mutation related ALS and, crucially, in sporadic ALS spinal cord tissue from multiple cases. Furthermore, we provide evidence that FUS protein binds to an aberrantly retained intron within the SFPQ transcript, which is exported from the nucleus into the cytoplasm. Collectively, these data support a model for ALS pathogenesis whereby aberrant intron-retention in SFPQ transcripts contributes to FUS mislocalization through their direct interaction and nuclear export. In summary, we report widespread mislocalization of the FUS protein in ALS and propose a putative underlying mechanism for this process.

neuroscience↗

bioRxiv2017

Post-transcriptional remodelling is temporally deregulated during motor neurogenesis in human ALS models

Mutations causing amyotrophic lateral sclerosis (ALS) strongly implicate regulators of RNA-processing that are ubiquitously expressed throughout development. To understand the molecular impact of ALS-causing mutations on early neuronal development and disease, we performed transcriptomic analysis of differentiated human control and VCP-mutant induced pluripotent stem cells (iPSCs) during motor neurogenesis. We identify intron retention (IR) as the predominant splicing change affecting early stages of wild-type neural differentiation, targeting key genes involved in the splicing machinery. Importantly, IR occurs prematurely in VCP-mutant cultures compared with control counterparts; these events are also observed in independent RNAseq datasets from SOD1- and FUS-mutant motor neurons (MNs). Together with related effects on 3UTR length variation, these findings implicate alternative RNA-processing in regulating distinct stages of lineage restriction from iPSCs to MNs, and reveal a temporal deregulation of such processing by ALS mutations. Thus, ALS-causing mutations perturb the same post-transcriptional mechanisms that underlie human motor neurogenesis.\n\nHIGHLIGHTSO_LIIntron retention is the main mode of alternative splicing in early differentiation.\nC_LIO_LIThe ALS-causing VCP mutation leads to premature intron retention.\nC_LIO_LIIncreased intron retention is seen with multiple ALS-causing mutations.\nC_LIO_LITranscriptional programs are unperturbed despite post-transcriptional defects.\nC_LI\n\neTOC BLURBLuisier et al. identify post-transcriptional changes underlying human motor neurogenesis: extensive variation in 3 UTR length and intron retention (IR) are the early predominant modes of splicing. The VCP mutation causes IR to occur prematurely during motor neurogenesis and these events are validated in other ALS-causing mutations, SOD1 and FUS.

neuroscience↗

bioRxiv2017

3’UTR Remodelling of Axonal Transcripts in Sympathetic Neurons

The 3 untranslated regions (3UTRs) of messenger RNAs (mRNA) are non-coding sequences that regulate several aspects of mRNA metabolism, including intracellular localisation and translation. Here, we show that in sympathetic neuron axons, the 3UTRs of many transcripts undergo cleavage, generating both translatable isoforms expressing a shorter 3UTR, and 3UTR fragments. 3end RNA sequencing indicated that 3UTR cleavage is a potentially widespread event in axons, which is mediated by a protein complex containing the endonuclease Ago2 and the RNA binding protein HuD. Analysis of the Inositol monophosphatase 1 (Impa1) mRNA revealed that a stem loop structure within the 3UTR is necessary for Ago2 cleavage. Thus, remodeling of the 3UTR provides an alternative mechanism that simultaneously regulates local protein synthesis and generates a new class of 3UTR RNAs with yet unknown functions.

neuroscience↗