Biology subjects

Paul, A.

Publications and source records attributed to Paul, A..

At least 37 records · Page 2Linked to original sources

bioRxiv2026

Assessing the impact of mono- and bi-allelic deletions in NRXN1 on synaptic function

Neurexin 1 (NRXN1) is an adhesion protein involved in synapse development and function. Mutations in NRXN1 are strongly linked with neurodevelopmental and psychiatric conditions. Mono-allelic NRXN1 mutations are associated with autistic traits, with increased likelihood of co-occurring intellectual disability. However, mono-allelic mutations have variable penetrance and occur in individuals without neurodevelopmental phenotypes. Conversely, bi-allelic mutations, though rarer, are associated with more stable penetrance and severe neurodevelopmental phenotypes. Human induced pluripotent stem cells (iPSC) have been used to study how mutations in NRXN1 impacts its function, with most studies focusing on monoallelic mutations. In this study, we systematically compared monoallelic and biallelic mutations in NRXN1, characterising their effects on molecular, synaptic, and functional phenotypes. Using CRISPR-Cas9, we introduced indels in NRXN1 exon 19, in an iPSC line containing inducible NGN2. These edits caused either mono-allelic or compound bi-allelic frameshift mutations. iPSCs containing either mutation robustly generated glutamatergic neurons, but these neurons displayed reduced expression of major NRXN1 isoforms. Transcriptomic profiling revealed modest gene expression changes in mono-allelic mutant neurons, whereas bi-allelic mutants exhibited extensive dysregulation of gene networks associated with neuronal maturation and synaptic function. Furthermore, synaptic phenotypes were mild in mono-allelic mutants but pronounced in bi-allelic mutant neurons. Both mono-allelic and bi-allelic mutant neurons displayed alterations in neuronal network activity and reduced peak depolarisation responses to KCl stimulation. Together, these data demonstrate that NRXN1 exhibits gene-dosage sensitivity, with bi-allelic disruption of exon 19 unmasking molecular, synaptic, and functional phenotypes that are only modest in mono-allelic mutant neurons.

neuroscience↗

bioRxiv2025

SMAD4 loss drives cancer chromosomal instability through transcription-replication conflict-induced replication stress

Cancer chromosomal instability (CIN) drives tumor evolution through generating structural and numerical chromosome aberrations. However, its molecular determinants remain poorly characterized. Here, we uncover a yet unrecognized role for the tumor suppressor SMAD4 as a key regulator of genome stability. Mechanistically, loss of SMAD4 induces replication stress by promoting transcription-replication conflicts (TRCs), which induces chromosomal breaks and subsequent mitotic errors, leading to the concomitant emergence of structural and numerical CIN. While the tumor suppressor function of SMAD4 has been predominantly attributed to TGF-{beta} signaling, we find that its role in genome maintenance operates via BMP signaling and its transcriptional target gene ID3. Consequently, inhibition of BMP signaling mimics the loss of SMAD4 whereas re-expression of SMAD4 or ID3 suppresses TRCs, replication stress and mitotic errors in SMAD4-deficient cancer cells. Our findings reveal a TRC- and replication stress-driven mechanism by which loss of BMP-SMAD4 signaling causes cancer chromosomal instability.

cancer biology↗

bioRxiv2025

Phase separation as a concentrating mechanism of protein/peptide hormones for the secretory granule storage

Protein/peptide hormones in the regulated secretory pathway are stored within secretory granules (SGs) as densely packed aggregates for extended periods of time until their stimulated release. These aggregated dense cores are reported as functional amyloids for several pituitary hormones. However, the molecular events initiating hormone aggregation and SG biogenesis remain poorly understood. Using a diverse set of protein/peptide hormones with different sizes and structures, we demonstrated that all these hormones undergo phase separation in trans-Golgi network (TGN)-relevant conditions (including low pH, the presence of glycosaminoglycans, etc.), which rapidly transitioned into solid-like structures and eventually form amyloid fibrils. Further, the cellular model expressing two protein hormones (GH-EGFP and PRL-EGFP) showed the highly dynamic, liquid-like condensate formation at the TGN volume, which was transported via microtubule to the cellular periphery/tips and formed a ready pool of mature SGs containing amyloid-rich hormone aggregates. Importantly, both in vitro and cellular studies confirmed that solid-like amyloid aggregates are reversible and can release bioactive monomeric hormones, recapitulating regulated exocytosis. Together, our findings suggest hormone phase separation at the TGN as a common molecular principle for concentrating cargo, driving rapid functional aggregation, and ensuring efficient storage within SGs.

biochemistry↗

bioRxiv2025

PD-1 regulates CD4+ T cell-mediated CD8+ T cell responses in the brain to balance viral control and neuroinflammation

Programmed cell death protein 1 (PD-1) is expressed by T cells during progressive multifocal leukoencephalopathy (PML), a life-threatening brain disease caused by the human-only JC polyomavirus. Why PD-1 blockade finds variable success in PML patients is unclear. Brain CD4+ and CD8+ T cells are PD-1high during mouse polyomavirus (MuPyV) encephalitis. Here, we show that PD-1 loss during MuPyV infection acts in a brain-autonomous manner to increase the magnitude of brain-infiltrating CD4+ and CD8+ T cells and the function of virus-specific CD8+ T cells; in concert, brain virus levels decline and neuroinflammation increases. Deletion of PD-1 in CD4+ T cells, but not CD8+ T cells, recapitulates effects of global PD-1 loss. Single-cell RNA sequencing shows that PD-1-deficient CD8+ T cells cluster as effectors while transcripts associated with proliferation and function are upregulated with loss of PD-1. Thus, CD4+ T cell-intrinsic PD-1 signaling balances antiviral defense against neural injury during polyomavirus CNS infection.

immunology↗

bioRxiv2025

The anti-retroviral therapy emtricitabine affects skeletal muscle DNA methylation and transcriptome patterns in a male HIV mouse model

BackgroundAlthough antiretroviral therapies (ART) have substantially reduced HIV-associated mortality, the increased lifespan achieved by widespread ART deployment has revealed that HIV infection is linked to an unexplained earlier onset and increased incidence of aging-associated conditions like sarcopenia. Complex syndromes, like sarcopenia, often arise from a combination of genetic and environmental factors, so in this study, we investigated effects of short-term treatment with emtricitabine (2,3-dideoxy-5-fluoro-3-thiacytidine; FTC), an FDA approved ART, on skeletal muscle DNA methylation patterns and transcriptome-wide responses in a male murine model of HIV phenotypic biology (Tg26 mice). MethodsWe treated 6 month old male Tg26 (+/-) mice or wildtype (WT) littermates on a C57BL/6 genetic background with FTC in the drinking water for one month; control groups received drinking water vehicle alone (VEH). Muscle function and body composition were measured longitudinally. Skeletal muscle methylation patterns, transcriptional changes, and histological features were quantified at sacrifice. ResultsAlthough neither gross structural nor functional muscle deficits were observed in this short-term study with ART usage, relative decreases in muscle endurance measured by hang time over the study were 2-fold more severe in the Tg26 as compared to WT mice (p=0.0453), and markers of myogenic cell maturation (Myf5, Myf6) were disrupted in the Tg26 HIV model as compared to WT littermates in a manner exacerbated by FTC treatment. Fat mass, measured by DXA, also tended (p=0.085) to be uniquely increased by FTC treatment in the Tg26 mice over the study. Differential methylation patterns and pathway enrichment data suggested that the presence of an HIV phenotype and exposure to an ART regimen altered the methylation status in skeletal muscle genes such as Camk2B, Pcolce2 and Lima1 in a manner consistent with promoting eventual functional impairment in muscle. Additionally, RNAseq revealed differential gene expression profiles and key regulatory pathways including cellular differentiation, regulation of lipid metabolism, and neuroactive ligand-receptor interactions. Lipodystrophy-related genes including LEP, ADIPOQ and PPAR involved in fat distribution and metabolism along with skeletal genes related to regulation of muscle strength were affected by the presence of an HIV phenotype and ART treatment. ConclusionsThe current study provides insights into mechanisms by which a clinically relevant ART may influence DNA methylation and transcriptome changes in skeletal muscle in the context of HIV biology. The differentially regulated pathways suggest novel targets for understanding, and eventually abrogating, the harmful effects of long-term ART use in PLWH on skeletal muscle mass and function.

cell biology↗

bioRxiv2025

Density-dependence and territorial competitors can modulate parrotfish social foraging and herbivory on coral reefs

Social context can modify the behaviour of animals, influencing how they interact with their environment - potentially cascading to effects on ecosystem functions. However, typical proxies for functions, such as biomass or densities, may not completely capture this behavioural variation. We examined how grouping behaviour of an abundant parrotfish species, Chlorurus sordidus, influences the critical function of herbivory on coral reefs in the Lakshadweep Archipelago and evaluated the role of density-dependence and territorial aggression from competitors in driving group formation in the entire herbivorous fish assemblage. Feeding rates increased with group size and decreased with aggressive encounters, with parrotfish in larger groups consuming about 80% more algae per capita than solitary individuals. Group foragers also benefitted marginally from reduced territorial aggression from competing herbivores. The propensities of herbivores to form groups, and their group sizes were positively density dependent, and, to a lesser extent, were driven by access to resources defended by territorial competitors. Our study highlights the importance of incorporating behavioural variation in assessments and predictive frameworks of ecosystem functioning. As our results indicate, for social animals, key ecosystem functions are particularly sensitive to animal densities and interspecific interactions, especially when individual function varies with social context.

ecology↗

bioRxiv2025

Clock Modulation by Naringenin via RORα Suppresses Lipogenesis and Promotes Adipose Tissue Browning

The circadian clock orchestrates adipocyte development and lipid remodeling, with its disruption leading to the development of obesity and insulin resistance. Here we demonstrate that the flavonoid compound naringenin displays clock modulatory activity via ROR that suppresses adipocyte lipid storage while promoting browning. In adipogenic progenitors, naringenin activates ROR with induction of clock gene expression to promote circadian clock oscillation with protective effect against cytokine-induced dampening. The clock-enhancing properties of naringenin suppressed lipogenesis in mature adipocytes together with induction of browning characteristics. The inhibitory effect of naringenin on lipogenesis was dependent on clock modulation as it was abolished in ROR-deficient adipocytes. We further show that naringenin administration in vivo up-regulated ROR expression with clock gene induction together with browning of subcutaneous beige fat depot, resulting reduced fat mass and body weight. Naringenin treatment in vivo also lowered plasma glucose and free fatty acid levels, with markedly enhanced insulin signaling in adipose depots and skeletal muscle. Collectively, our findings uncover a new clock-activating mechanism of action in mediating the metabolic benefits of naringenin, suggesting its potential as a natural supplement for anti-obesity and metabolic disease interventions.

cell biology↗

bioRxiv2025

Individual differences in learning and decision-making: the role of COMT Val158Met polymorphism in transitive inference

Understanding the ordinal relationships between items requires constructing a rank order supporting decision-making between options. This process depends on the ability to learn reciprocal relationships and to select the best option available when making a choice. In such forms of decision-making, the prefrontal cortex (PFC) plays a crucial role in encoding the relative value of alternatives as a decision is formed. Higher-order cognitive abilities are influenced by genetic factors that affect dopamine availability in the PFC, potentially contributing to individual differences. Here, we examined the performance of 83 participants in a transitive inference task (TI), grouped by genotype based on the Val158Met single-nucleotide polymorphism in the Catechol-O-Methyltransferase (COMT) gene. The task included a learning phase in which participants acquired the reciprocal relationships among a set of hierarchically ranked items (A>B>C>D>E>F), followed by a test phase in which they were required to compare all possible item pairs and select the higher-ranked one. While genotype did not significantly influence test-phase performance, it did affect learning efficiency. Specifically, Val homozygotes took a longer learning procedure than both heterozygotes and Met homozygotes during the learning phase. Drift diffusion modelling (DDM) revealed that task performance was explained by the efficiency of evidence accumulation, which was lower in Val homozygotes, accounting for their poorer performance not only during initial learning but also when required to switch to a reversed hierarchical structure (A<B<C<D<E<F). These findings suggest that individual differences in inferential decision-making and cognitive flexibility may be partially driven by genetically determined variations in prefrontal dopamine availability.

neuroscience↗

bioRxiv2025

The difficulty in numerical computation impacts motor decisions in a Stop Signal task

The proper interpretation of environmental information is necessary for effective decision-making. The resulting cognitive burden may affect the entire process if interpretation is not instantaneous. In this study, we investigated how numerical distance (ND), a measure of cognitive demand in numerical comparisons, influences movement initiation and inhibition. To this end, 32 participants completed a novel numerical comparison Stop-Signal Task (NC-SST), in which the cognitive demand of each trial was manipulated by varying the ND between pairs of numbers in both Go and Stop signals. Participants were required to initiate or stop a movement if an upcoming number was higher or smaller than the one presented previously. Results showed that larger NDs (i.e., easier comparisons) facilitated faster and more accurate responses during movement initiation and enhanced stopping performance. Using a generalized drift-diffusion model, we found that drift rates increased with ND and were modulated by the spatial location of numerical stimuli, consistent with a left-to-right space number association. A generalized linear mixed-effects model further revealed that Go process parameters, particularly the drift rate, strongly predicted successful stopping and interacted with Stop ND and Stop signal delay (SSD). These findings demonstrate that higher cognitive load impairs both movement initiation and inhibition, and that motor decisions result from the integration of cognitive information onto perceptual features, extending the classical race model framework.

neuroscience↗

bioRxiv2025

The RNA splicing factor Prp45 directs histone H2B ubiquitination through its C-terminal domain

While chromatins influence on co-transcriptional splicing is well established, the reciprocal model, that spliceosomal components actively shape chromatin, has lacked mechanistic support. Here we show that the C-terminal intrinsically disordered region (IDR) of the yeast splicing factor Prp45 (mammalian SKIP) promotes histone H2B ubiquitination, a hallmark of active transcription. The Prp45 IDR binds and stabilizes Lge1, the scaffold of the H2B ubiquitin ligase complex, enabling its function with the ubiquitin ligase Bre1. When this interaction is disrupted, Lge1 is degraded by the SUMO-targeted ubiquitin ligase Slx5, Bre1 is mislocalized, H2B ubiquitination is lost, and cells become enlarged. Deleting SLX5 restores Lge1 stability, H2B ubiquitination, and normal cell morphology. Although its sequence diverges across eukaryotes, the IDRs structural properties are conserved, and the disordered regions of Arabidopsis and human SKIP functionally replace the yeast domain. These findings reveal a conserved IDR-mediated mechanism by which a splicing factor directs chromatin modification.

molecular biology↗

bioRxiv2025

STARTER : A Stand-Alone Reconfigurable and TranslationalOoC Platorm based on Modularity and Open Design Principles

Organ-on-Chips (OoC) have the potential to revolutionize drug testing. However, the fragmented ecosystem of available OoC systems leads to wasted resources and collaboration barriers, slowing uptake. To address this, there is a need for OoC platforms based on interoperability standards, modularity, and reconfigurability. Technology platforms based on open designs would enable seamless integration of diverse OoC models and components, facilitating translation. Our study introduces a modular microfluidic platform that integrates swappable modules for pumping, sensing, and OoCs, all within the ANSI/SLAS microplate footprint. Sub-components operate as microfluidic building blocks (MFBBs) and can interface with the demonstrated Fluidic Circuit Board (FCB) universally as long as the designs adhere to ISO standards. The platform architecture allows tube-less inter-module interactions via arbitrary and reconfigurable fluidic circuits. We demonstrate two possible fluidic configurations which include in-line sensors and furthermore demonstrate biological functionality by running both in-vitro and ex-vivo OoC models for multiple days. This platform is designed to support automated multi-organ experiments, independent of OoC type or material. All designs shown are made open source to encourage broader compatibility and collaboration.

bioengineering↗

bioRxiv2025

Targeting non-canonical NF-κB signalling in CYLD cutaneous syndrome by selective inhibition of IκB kinase alpha.

CYLD cutaneous syndrome (CCS) skin tumors develop from puberty onwards, can number in the hundreds and progressively grow over time. CCS patients lack medical therapies and require repeated surgery to control tumor burden. CYLD loss of heterozygosity (LOH) drives tumor growth, and CCS tumors have previously been shown to demonstrate increased canonical NF-{kappa}B and Wnt signalling. Here, we demonstrate evidence of non-canonical NF-{kappa}B signalling in CCS tumor keratinocytes, with increased p100 to p52 processing and RelB protein expression compared to normal skin. Utilizing complementary transcriptomics and proteomics on patient derived CCS tumor cell fractions, we identify I{kappa}B kinase alpha (IKK) as a candidate target in the non-canonical NF-{kappa}B signalling pathway. A novel, highly selective, IKK inhibitor (SU1644) used in patient derived CCS tumor spheroid cultures demonstrated that IKK inhibition reduced tumor spheroid viability. These data provide the pre-clinical rationale for the assessment of topical IKK inhibitors as a novel preventative treatment for CCS. TeaserTopical IKK inhibition emerges as a potential therapy for CYLD cutaneous syndrome by targeting non-canonical NF-{kappa}B signalling Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=125 SRC="FIGDIR/small/635629v1_ufig1.gif" ALT="Figure 1"> View larger version (39K): org.highwire.dtl.DTLVardef@829218org.highwire.dtl.DTLVardef@459f5dorg.highwire.dtl.DTLVardef@e198f6org.highwire.dtl.DTLVardef@1015685_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2024

Cited4a limits cardiomyocyte dedifferentiation and proliferation during zebrafish heart regeneration

Cardiac regeneration involves the interplay of complex interactions between many different cell types, including cardiomyocytes. The exact mechanism that enables cardiomyocytes to undergo dedifferentiation and proliferation to replace lost cells has been intensely studied. Here we report a single nuclear RNA sequencing profile of the injured zebrafish heart and identify distinct cardiomyocyte populations in the injured heart. These cardiomyocyte populations have diverse functions, including stress response, myofibril assembly, proliferation and contraction. The contracting cardiomyocyte population also involves the activation of maturation pathways as an early response to injury. This intriguing finding suggests that constant maintenance of a distinctive terminally differentiated cardiomyocyte population is important for cardiac function during regeneration. To test this hypothesis, we determined that cited4a, a p300/CBP transcriptional coactivator, is induced after injury in the mature cardiomyocyte population. Moreover, loss-of-cited4a mutants presented increased dedifferentiation, proliferation and accelerated heart regeneration. Thus, suppressing cardiomyocyte maturation pathway activity in injured hearts could be an approach to promote heart regeneration.

developmental biology↗

bioRxiv2024

Brain-wide connectivity and novelty response of the dorsal endopiriform nucleus in mice

The dorsal endopiriform nucleus (EPd) is an enigmatic cortical subplate structure located inside the piriform cortex that shares a similar developmental origin with the claustrum. Although the EPd has been previously implicated in epilepsy and olfactory processing, its anatomical organization, connectivity patterns, and function remain largely unclear due to a lack of specific molecular markers. Our previous mapping study serendipitously identified that the Oxt receptor (Oxtr) is densely expressed in the EPd. Subsequent immunohistochemical and spatial transcriptomic analyses confirmed that Oxtr expression is enriched in the EPd, revealing distinct molecular organization compared to the neighboring claustrum. Whole brain input-output mapping of EPd Oxtr-positive neurons unveils extensive bidirectional connections to the ventral half of the brain, orchestrating functional circuits regulating olfaction, internal state, and emotion. Furthermore, our in-vivo miniscope recordings show that EPd Oxtr neurons exhibit high baseline activity during exploratory behavior, with a sharp decrease in activity in response to novel stimuli. This suggests that the EPd regulates interoceptive states and likely plays a role in adapting to novel exteroceptive cues.

neuroscience↗

bioRxiv2024

Impact of intragenic NRXN1 deletions on early cortical development

BackgroundDeletions in NRXN1 are strongly associated with neurodevelopmental and psychiatric conditions. While exonic deletions are well-studied, intragenic deletions, particularly in intron 5, are less understood and generally consider benign. Recent studies show exonic deletions impact isoform diversity during neurodevelopment, affecting neurogenesis and neuronal function. However, whether intragenic deletions impact isoform expression and neurodevelopment remains underexplored. MethodsWe used hiPSCs from typically developing individuals (control) and those with NRXN1 intron 5 deletions to study neurodevelopment. HiPSCs were differentiated towards a cortical fate, with NRXN1 isoform expression, molecular differences, and neuronal morphology examined. ResultsWe observed distinct NRXN1 isoform expression dynamics during early neurodevelopment, with two expression peaks post-neuronal induction and NRXN1{beta} being most highly expressed. Both NRXN1 deletion and control lines showed similar acquisition of regional and cell fate identity, but significant differences in NRXN1 isoform expression were observed between deletion and control lines, and between deletion lines. RNA sequencing revealed genotype-dependent alterations, particularly in pathways related to synaptic function and neuronal morphology. Consistent with these findings, NRXN1 deletion lines exhibited altered dendrite outgrowth, with variations between deletion lines. ConclusionsOur results indicate a potential role for intron 5 in controlling NRXN1 isoform expression during neurodevelopment. Alterations in gene expression profiles, correlated with morphological changes, suggest a role for NRXN1 isoforms in shaping dendritic morphology. Molecular and cellular differences observed between lines with identical intronic deletions suggest that additional factors, such as genetic background or biological sex, may also play an important role in these phenotypes. Collectively, these findings indicate that NRXN1 intronic deletions are not benign, influencing isoform expression, cellular phenotypes, and neurodevelopment.

neuroscience↗

bioRxiv2024

Distinct Proline residues in hinge-regions of SYMRK generates a phosphocode for releasing Malectin-like-Domain to allow progress of rhizobia-legume symbiosis at epidermal-cortical barrier.

Symbiosis Receptor Kinase (SYMRK), a malectin-like-domain/leucine-rich-repeat receptor-like-kinase (MLD-LRR-RLK), is the upstream most component in Common-Symbiosis-Signalling-Pathway. We highlight two Proline residues that were distinctly acquired by SYMRK orthologues in its hinge-regions to evolve a signalling module for allowing progress of symbionts across transcellular barriers during rhizobia-legume symbiosis. Within the Ectodomain hinge (EctoD-hinge) all MLD-LRR-RLKs have a conserved W1xnGDPCxnW2x4C motif, where SYMRK orthologues within legumes have a distinct signature with a Proline preceding W2 enabling cleavage of SYMRK-EctoD for releasing MLD. Within the kinase hinge (KD-hinge) at gatekeeper+1 position, a conserved Glutamate in MLD-LRR-RLKs is replaced by Proline in all SYMRK orthologues that enabled its dual-specific kinase activity for ensuring EctoD-cleavage. Substitution of either Proline restricted symbionts at the transcellular epidermal-cortical barrier forming infection patches in the nodule apex without affecting epidermal invasion and nodule organogenesis. This halt was entirely overcome by ectopic expression of free MLD demonstrating the released MLD to have an active role in progress of symbionts. Overall, we show that adaptations of distinct Prolines in hinge-regions of SYMRK orthologues in legumes have evolved a signalling module involving dimerization and optimal phosphorylation of SYMRK for releasing MLD as an active transducer of symbiosis signalling.

plant biology↗

bioRxiv2024

From solo to collaborative: the global increase in neuroscience authors over two decades

The increase in the number of authors per article is a well-documented phenomenon across various academic disciplines. While prior studies have examined this trend in specific fields and countries, they in most cases did not compare the increase in the number of authors between countries. While it has previously shown that the number of authors in neuroscience publications has risen in the G10 countries, no study has yet addressed whether it reflects a global trend in the field. To address this gap, we quantified the global trend in the number of authors in neuroscience publications from 2001 to 2022. Our findings reveal a consistent increase in authorship across nearly all the countries examined. Italy ranks highest in terms of average authorship per article, while Ukraine ranks the lowest. On the other hand, China shows the largest increase in authorship over the years, followed by Norway and Egypt. South Korea is the only country showing a slight decreasing trend rather than growth. These results contribute to a better understanding of authorship patterns in neuroscience, and can stimulate further investigations on the reasons behind such an increase in terms of socio-economic factors, the need for collaborative efforts in some fields, or, on the negative side, the effect of utilitarian reasons to meet career evaluation criteria.

neuroscience↗

bioRxiv2024

FUSION: A web-based application for in-depth exploration of multi-omics data with brightfield histology

Spatial -OMICS technologies facilitate the interrogation of molecular profiles in the context of the underlying histopathology and tissue microenvironment. Paired analysis of histopathology and molecular data can provide pathologists with otherwise unobtainable insights into biological mechanisms. To connect the disparate molecular and histopathologic features into a single workspace, we developed FUSION (Functional Unit State IdentificatiON in WSIs [Whole Slide Images]), a web-based tool that provides users with a broad array of visualization and analytical tools including deep learning-based algorithms for in-depth interrogation of spatial -OMICS datasets and their associated high-resolution histology images. FUSION enables end-to-end analysis of functional tissue units (FTUs), automatically aggregating underlying molecular data to provide a histopathology-based medium for analyzing healthy and altered cell states and driving new discoveries using "pathomic" features. We demonstrate FUSION using 10x Visium spatial transcriptomics (ST) data from both formalin-fixed paraffin embedded (FFPE) and frozen prepared datasets consisting of healthy and diseased tissue. Through several use-cases, we demonstrate how users can identify spatial linkages between quantitative pathomics, qualitative image characteristics, and spatial --omics

pathology↗