Biology subjects

Shin, J. H.

Publications and source records attributed to Shin, J. H..

At least 19 recordsLinked to original sources

bioRxiv2026

Single-cell full-length transcriptome of human lung reveals genetic effects on isoform regulation beyond gene-level expression

Genetic regulation of splicing uniquely contributes to trait-associated genome-wide association studies (GWAS) signals. However, quantitative trait loci (QTL) analysis using short-read sequencing of bulk tissues fails to capture full-length and cell-type-specific isoforms. Here, we present an isoform-level lung cell atlas from 129 never-smoking Korean women using single-cell long-read RNA-sequencing, identifying abundant unannotated and cell-type-specific isoforms. Isoform-level signatures of 37 lung cell types display a larger difference and therefore improve cell-type classification compared to gene-level expression. Notably, isoform-QTLs (isoQTLs) detect unannotated and/or cell-type-specific isoforms with independent genetic regulation from expression-QTL (eQTL), supported by enriched splicing functional elements. IsoQTLs nominate susceptibility isoforms from previously unexplained lung function and cancer GWAS loci, via eQTL-independent signals. We highlight a potentially functional novel variant of PPIL6 in multiciliated cells underlying lung cancer risk through alternative splicing. This isoform-level resource advances our understanding of cell-type-specific isoform regulation and its contribution to lung traits and diseases.

genetics↗

bioRxiv2026

Single-cell lung eQTL dataset of Asian never-smokers highlights the roles of alveolar cells in lung cancer etiology

Single-cell expression quantitative trait loci (sc-eQTL) analyses are powerful in identifying context-specific susceptibility genes from genome-wide association studies (GWAS) loci. However, few studies have comprehensively investigated cells of lung cancer origin in non-European populations. Here, we built a lung sc-eQTL dataset from 129 Korean women never-smokers with epithelial cell enrichment. eQTL mapping identified 2,229 genes with an eQTL in 33 cell types, including East Asian-specific findings when compared to predominantly European datasets. Integration with single-cell chromatin accessibility data demonstrated an enrichment of cell-type specific eQTLs in cell-type matched candidate enhancers, while shared eQTLs were more frequently found near promoters. Colocalization and transcriptome-wide association study unveiled 36 susceptibility genes from 22 cell types in 22 lung cancer loci, including 10 loci not achieving genome-wide significance in prior GWAS. Around 47% of these genes were from cells of the alveoli, underscoring their importance, especially in lung adenocarcinoma (LUAD) susceptibility. Focusing on the trajectory of alveolar epithelial cell regeneration, we detected 785 cell-state-interacting QTLs, which overlapped with 28% (10) of the identified susceptibility genes. Finally, we experimentally validated East Asian-and alveolar type 2 cell-specific eQTL of TCF7L2 underlying East Asian LUAD locus, 10q25.2. Consistent with its role as a Wnt/{beta}-catenin effector, TCF7L2 displayed significant effect on lung adenocarcinoma cell growth. Our data highlighted context-specific susceptibility genes, especially from alveolar cells of lung, contributing to lung cancer etiology.

genetics↗

bioRxiv2026

Distinct cellular DNA methylation mechanisms underlie common and rare genetic risk for brain disorders

Noncoding genetic variation contributes to brain disorder risk, but the mechanisms through which it acts in specific brain cell types remain unclear. DNA methylation (DNAm), a highly cell type-specific regulatory layer in the brain, may mediate noncoding genetic risk, yet whether methylation at CG (mCG) and neuron-enriched non-CG (mCH) dinucleotides contribute differently to that risk remains unknown. Here we develop a deep learning framework that predicts DNAm from DNA sequence and estimates variant effects across 186 brain cell subtypes in both mCG and mCH, leveraging single-nucleus DNAm profiles from 46 brain regions. The models reveal distinct transcription factor (TF) programs underlying the two methylation contexts, with mCH-associated TFs showing stronger evolutionary constraint. Predicted variant effects agree closely with cell type-matched mQTLs in both direction and magnitude. Common variants predicted to affect mCG, particularly in excitatory neurons, show substantially greater heritability enrichment for brain-related traits than variants affecting mCH. By contrast, noncoding de novo mutations in autism preferentially perturb mCH, but not mCG, at conserved neuronal regulatory regions. This pattern is replicated across two independent cohorts totaling 5,782 probands and 4,053 unaffected siblings. Together, these findings indicate that common and rare noncoding variants contribute to brain disorders through distinct DNA methylation mechanisms.

genetics↗

bioRxiv2026

D2 autoreceptors gate vulnerability to cocaine use disorder

A defining feature of substance use disorder is that repeated drug use does not always lead to addiction, motivating the search for biomarkers of vulnerability1. Reduced striatal dopamine D2/3 receptor availability is a robust PET correlate of problematic stimulant use2-5, but the signal may reflect high endogenous dopamine level, and it conflates presynaptic D2 autoreceptors on dopamine axons with postsynaptic D2/3 heteroreceptors on striatal projection neurons. We dissociated these contributions using cell type-specific Drd2 haploinsufficiency in dopamine neurons (autoD2KD), D2-expressing medium spiny neurons (MSN-D2KD), or both. Autoreceptor haploinsufficiency (autoD2KD) weakened presynaptic control of dopamine release, enhanced phasic gain, and prolonged cocaine-evoked dopamine elevations. This was accompanied by a hyper-exploratory trait and altered cocaine adaptation. Specifically, autoD2KD mice showed greater cocaine-seeking behavior, despite intact responses to sucrose reward and punishment. Although all genotypes showed graded reductions in striatal D2/3 binding, D1-like compensations diverged, resulting in different D1:D2/3 ratio in the striatum. The clinical implication is that striatal D1 density and D1:D2/3 balance may emerge as critical biomarkers for distinguishing cell-type-specific D2 reductions relevant to addiction vulnerability.

neuroscience↗

bioRxiv2026

Scn4b Modulates Huntington's Disease Phenotype Severity in vivo

Although it has been known for over 30 years that CAG trinucleotide repeat expansions in the HTT gene are the cause of Huntingtons disease (HD), it is still not understood how these mutations lead to the loss of striatal spiny projection neurons (SPNs) and other vulnerable neuronal cell types in HD. Here we show that SCN4B, a gene that is enriched in neurons that influence motor function, including striatal SPNs, modulates HD-associated phenotypes in vivo. Loss of Scn4b in wild-type mice mimics and Scn4b overexpression in an HD mouse model rescues several HD-associated phenotypes, including motor and cognitive deficits. Single nucleus RNA sequencing (snRNA-seq) analysis reveals that loss of Scn4b replicates several HD-associated gene expression signatures in the striatum. Conversely, overexpression of Scn4b rescues HD gene expression signatures and improves various SPN electrophysiological properties in HD model mice. Taken together, our results implicate loss of Scn4b expression as an important contributor to HD pathogenesis and therapeutic target in HD.

neuroscience↗

bioRxiv2026

Volumetric mechanosensing of CAF in 3D hydrogels drive altered drug response in breast cancer

Altered mechanical properties of the tumor microenvironment (TME) influence cancer progression, yet the mechanistic basis by which 3D mechanics shape CAF heterogeneity and downstream tumor drug response remains poorly understood. Here, we engineered a modulus-tunable gelatin methacryloyl (GelMA) hydrogel platform spanning a normal-like (soft [~]2 kPa) to desmoplastic-like (stiff[~]40 kPa) range to culture primary breast CAFs under 3D confinement. CAFs exhibited pronounced volumetric morphoadaptation across matrices, with soft 3D matrices supporting larger, more protrusive morphologies and stiff gels constraining cell geometry. In contrast to canonical 2D paradigms, nuclear YAP localization was reduced in stiff 3D matrices and varied substantially across cells, consistent with a dominant role for 3D geometric/volumetric state in regulating mechanotransduction. Functionally, in transwell co-culture with MCF-7 spheroids under paclitaxel treatment, CAFs cultured in stiff 3D matrices induced a broader chemoresistance-associated transcriptional program, whereas soft 3D matrices CAFs favored stress/checkpoint-like responses. A 2D monolayer comparator indicated that coordinated resistance-associated programs emerge most clearly in 3D tumor architecture. Together, these results establish a GelMA-based biomaterials framework in which CAF volumetric state provides a quantifiable intermediate linking 3D matrix mechanics to mechanotransduction and tumor drug-response programs, motivating future strategies to modulate stromal function through mechanically controlled cell-state regulation.

bioengineering↗

bioRxiv2026

Deep Plasma Proteomics Coupled with Functional Genomics Reveals Drivers of Parkinson's Disease Progression and Levodopa Response

Parkinsons disease (PD) is a progressive neurodegenerative disorder lacking disease-modifying therapies, and its clinical management is limited by the absence of accessible biomarkers for tracking disease progression and treatment response. To map these complex disease trajectories, we implemented an ultra-deep plasma proteomics workflow integrating Mag-Net extracellular vesicle enrichment with Orbitrap Astral mass spectrometry to profile longitudinal samples from PD patients. This approach quantified 6,481 plasma proteins at unprecedented depth in PD studies, revealing distinct signatures directly associated with disease duration and dopaminergic therapy exposure. Candidate biomarkers were subsequently validated in an independent cohort using ELISA, demonstrating robust predictive utility in AI-driven prediction models. To uncover the mechanistic drivers underlying these systemic changes, we intersected our proteomic data with novel proteome-wide gene overexpression perturbation screens designed to identify regulators of alpha-synuclein pre-formed fibril (PFF) uptake and PFF-induced neuronal toxicity. Finally, an integrative network analysis combining three independent proteome-wide assays revealed that key pathological hubs, such as CD14, IFNG, and PLAT, are targets of currently approved pharmacological agents. Collectively, these findings provide a comprehensive, systems-level map for PD biomarker discovery and highlight druggable pathways to advance precision medicine strategies.

neuroscience↗

bioRxiv2026

Genetic architecture of miRNA expression in human brain and its contribution to brain disorders

MicroRNAs (miRNAs) regulate nearly all protein-coding genes and play critical roles in gene regulation, yet the mechanisms governing miRNA regulation remain poorly understood. Here, we examined the genetic architecture of miRNA expression in 995 human brain tissues spanning four regions and two ancestries (African and European) from neurotypical controls and individuals with three psychiatric disorders (schizophrenia, major depressive disorder, and bipolar disorder). We found that miRNA expression is highly dynamic across brain regions, with region-specific differences exceeding those attributable to ancestry or psychiatric diagnosis. Through miRNA expression quantitative trait loci (miR-eQTL) analyses, we identified genetic variants associated with miRNA expression in a region- and ancestry-dependent manner. Overall, miRNAs exhibited heritability levels comparable to protein-coding genes and were positively co-regulated with their host transcripts. Notably, miRNA-regulating genetic variants were enriched in enhancers active in oligodendrocytes and in binding sites of the transcription factor OLIG2, suggesting miRNA-mediated gene regulation in oligodendrocyte lineage. Finally, we identified 15 miRNAs as likely causative factors for psychiatric and neurodegenerative disorders such as major depressive disorder and Alzheimers disease. Together, our results reveal the genetic underpinnings of miRNA regulation in the human brain and suggest that miRNAs serve as key intermediaries linking genetic variation to complex neuropsychiatric and neurological phenotypes.

genomics↗

bioRxiv2025

Cholinergic-dependent dopamine signals in mouse dorsal striatum are regulated by frontal but not sensory cortices

Everyday decisions depend on linking sensory stimuli with actions and outcomes. The striatum supports these sensorimotor associations through dopamine-dependent plasticity. Thus, the timing and magnitude of dopamine release is critical for learning. Recent work has characterized a local striatal microcircuit in which cholinergic interneurons (CINs) modulate dopamine release via acetylcholine activation of nicotinic receptors on dopamine axons. Here, we show that visual stimuli evoke dopamine responses in the dorsomedial striatum through this cholinergic-dependent mechanism. Using anatomical and functional methods to identify which pathways elicit these signals, we found that visual and auditory cortices that project to the dorsomedial striatum lack robust connectivity to CINs and were unable to drive cholinergic-dependent dopamine release. In contrast, frontal cortical regions, including the prelimbic and anterior cingulate cortices, strongly recruited CINs and acetylcholine, producing robust dopamine release both ex vivo and in vivo. These frontal corticostriatal projections are activated by visual stimuli, representing a possible pathway by which visual information reaches the dorsomedial striatum to evoke dopamine. These findings reveal a fundamental distinction between sensory and frontal cortical inputs to the striatum, demonstrating that only the latter evoke cholinergic-dependent dopamine signaling. This work establishes a framework for understanding how cortical circuits shape striatal dopamine to support reinforcement learning.

neuroscience↗

bioRxiv2025

Low-intensity focused ultrasound enables temporal modulation of human midbrain organoid differentiation

Controlling the precise timing of biosignaling cues in complex 3D models such as organoids is critical for guiding cellular differentiation and functional maturation. Ultrasound stimulation, a next-generation neuromodulation modality, offers unique advantages due to its target specificity, ability to elicit mechanosensitive responses, and high spatial resolution. However, there is still a lack of precision stimulation platforms and comprehensive biomarker assays for selective control of organoid development. Here, we introduce a modular piezoelectric ultrasound stimulation platform that integrates seamlessly with conventional multi-well plates, enabling selective neuromodulation of midbrain organoids (mBOs). We demonstrate that ultrasound can specifically modulate cellular differentiation by promoting dopaminergic progenitor markers while delaying terminal differentiation. Importantly, ultrasound stimulation did not induce cellular damage, as confirmed by the absence of apoptosis and DNA damage markers. This work demonstrates the potential of focused ultrasound as a safe, non-invasive, and tunable biophysical cue for temporal regulation of organoid differentiation and maturation. Significance StatementOrganoids are three dimensional in vitro models derived from human tissue that recapitulate the complex features of organs. However, precise modulation of organoid differentiation relies on biochemical factors, which are limited in their temporal controllability. In this study, we demonstrate that low-intensity ultrasound stimulation enables temporal modulation of midbrain organoid differentiation using a modular multi-well stimulation platform. In particular, we show that ultrasound promotes the proliferation of dopaminergic progenitor cells. These findings suggest that ultrasound can serve as a supplementary mechanical cue to regulate midbrain organoid development.

developmental biology↗

bioRxiv2025

Slow synaptic plasticity from the hippocampus underlies gradual mapping and fragmentation of novel spaces by grid cells

Animals construct internal "cognitive maps" of the world during navigation in spatial and non-spatial domains, with grid cells in the medial entorhinal cortex (MEC) playing a key role. This requires associating internal position estimates with external cues to reduce spatial uncertainty over time. However, how grid cell representations evolve in novel spaces to support map formation is unclear. To address this question, we longitudinally imaged calcium dynamics of grid cells over 10 days as mice learn operant tasks in novel virtual linear tracks. We observe that spatial tuning of grid cells is present immediately in novel tracks but evolves as a significant fraction of spatial fields shift backward on a run-by-run basis, within and across days. Backward shifts are more prevalent and persistent in successful learners. The fields gradually stabilize across days, anchored by landmarks, suggesting slow plasticity. The backward shifts partially reset daily, reflecting a slower consolidation timescale. While individual fields of a cell shift differentially, co-active fields of co-modular grid cells shift together, indicating their coupled dynamics on the same two-dimensional torus. Spatial learning leads to systematic changes and stabilization of their population phase trajectory, including lateral shift, rotation, and phase resets at landmarks, forming a landmark-fragmented representation for the environment. Next, we build an entorhinal-hippocampal model that provides a mechanistic explanation of the diverse phenomena - grid field shifts, increasing fidelity, and fragmentation of the spatial map - and predicts slow Hebbian plasticity in the hippocampus-to-entorhinal pathway. Supporting this, electrophysiology demonstrates that learning-performance-correlated weakening of local inhibition facilitates potentiation of indirect hippocampal inputs to superficial MEC. Together, our study provides multifaceted evidence of slow hippocampus-to-MEC plasticity, elucidating the formation of stable and fragmented cognitive maps that combine internal and cue-driven positional estimates in rich environments during learning. This mechanism may extend to broader memory processes involving this circuit.

neuroscience↗

bioRxiv2025

A Cross-Species Atlas of the Dorsal Vagal Complex Reveals Neural Mediators of Cagrilintide's Effects on Energy Balance

Amylin analogs, including potential anti-obesity therapies like cagrilintide, act on neurons in the brainstem dorsal vagal complex (DVC) that express calcitonin receptors (CALCR). These receptors, often combined with receptor activity-modifying proteins (RAMPs), mediate the suppression of food intake and body weight. To understand the molecular and neural mechanisms of cagrilintide action, we used single-nucleus RNA sequencing to define 89 cell populations across the rat, mouse, and non-human primate caudal brainstem. We then integrated spatial profiling to reveal neuron distribution in the rat DVC. Furthermore, we compared the acute and long-term transcriptional responses to cagrilintide across DVC neurons of rats, which exhibit strong cagrilintide responsiveness, and mice, which respond poorly to cagrilintide over the long term. We found that cagrilintide promoted long-term transcriptional changes, including increased prolactin releasing hormone (Prlh) expression, in the nucleus of the solitary tract (NTS) Calcr/Prlh cells in rats, but not in mice, suggesting the importance of NTS Calcr/Prlh cells for sustained weight loss. Indeed, activating rat area postrema Calcr cells briefly reduced food intake but failed to decrease food intake or body weight over the long term. Overall, these results not only provide a cross-species and spatial atlas of DVC cell populations but also define the molecular and neural mediators of acute and long-term cagrilintide action.

bioinformatics↗

bioRxiv2024

Erbin interacts with NHERF1 and Ezrin to stabilize a membrane ErbB2 signaling complex in HER2-positive breast cancer

Approximately 20% of breast cancers overexpress ErbB2/HER2/Neu, a receptor tyrosine kinase. Our previous studies demonstrated that HER2 interacts with the calcium pump, PMCA2, and the scaffolding molecules, NHERF1 and Ezrin to stabilize HER2/HSP90 interactions and contribute to the retention of active HER2 at the plasma membrane. In the normal mammary epithelium where apical/basal polarity is tightly regulated by junctional proteins, HER2 is expressed at the basolateral membrane and interacts with the LAP family member, Erbin, whereas PMCA2, NHERF1, and Ezrin localize to the apical membrane. Here, we show that loss of apical membrane polarity in hyperplastic lesions of MMTV-Neu mammary glands or in human DCIS leads to intermixing of these molecules and allows Erbin to interact with NHERF1, Ezrin and HER2 initially within the basolateral membrane and then more diffusely within the plasma membrane. In SKBR3 cells, Erbin physically interacts with NHERF1, Ezrin and HER2 in actin-rich membrane protrusions that we have previously described to be sites of active HER2 signaling. Knockdown of Erbin in these cells reduced HER2 signaling by disrupting the formation of a HER2/NHERF1/Ezrin/HSP90 protein complex in the membrane protrusions. Furthermore, inhibition of Ezrin or knock-down of NHERF1 expression disrupted the ability of Erbin to interact with HER2. Taken together, our data suggest that Erbin supports HER2 stability, HER2 membrane retention and HER2 transforming ability by interacting with Ezrin and NHERF1 to maintain a multi-protein signaling complex necessary for HER2-mediated transformation.

cancer biology↗

bioRxiv2024

EMT Induction In Normal Breast Epithelial Cells By COX2-Expressing Fibroblasts

BackgroundThe tumor microenvironment (TME) plays a pivotal role in cancer progression, with cancer-associated fibroblasts (CAFs) significantly influencing tumor behavior. Especially, elevated COX2 expressing fibroblasts within the TME, notably in collagen-dense tumors like breast cancer, has been recently emphasized in the literature. However, the specific effect of COX2-expressing CAFs (COX2+ CAFs) on neighboring cells and their consequent role in cancer progression is not fully elucidated. MethodsWe induced COX2+ fibroblasts by forcing the fibroblasts forming aggregates to undergo Nemosis as a proxy for COX2+ CAFs. This approach enabled us to simulate the paracrine interactions between COX2+ CAFs and normal breast epithelial cells via conditioned media from COX2+ fibroblasts. We developed an innovative in vitro platform that combines cell mechanics-based analysis and biomolecular assays to study the interactions between COX2+ fibroblasts and normal breast epithelial cells. By focusing on the mechanical characteristics of the cells and the EMT marker expressions, we aimed to elucidate the paracrine mechanisms through which COX2+ CAFs influence the tumor microenvironment. ResultsOur in vitro findings reveal that COX2+ fibroblasts, through conditioned media, induce significant changes in the mechanical behavior of normal breast epithelial cells, facilitating their transition towards mesenchymal types. This transition was corroborated by increased expression of mesenchymal markers. By drawing parallels between COX2+ fibroblasts and COX2+ CAFs, we established a positive feedback loop involving COX2+ CAFs, prostaglandin E2 (PGE2), and the EP4-SNAI1 axes. ConclusionThis study advances our understanding of the potential mechanisms by which COX2+ CAFs influence tumor progression within the breast tumor microenvironment (TME) through controlled in vitro investigations. By integrating cell mechanics-based analysis, biomolecular assays, and innovative in vitro cell-based modeling of COX2+ CAFs, we have delineated the contributory role of these cells in a controlled setting. These insights lay a groundwork for future studies that could explore the implications of these findings in vivo, potentially guiding targeted therapeutic strategies.

cell biology↗

bioRxiv2024

An enhancer-AAV toolbox to target and manipulate distinct interneuron subtypes

In recent years, we and others have identified a number of enhancers that, when incorporated into rAAV vectors, can restrict the transgene expression to particular neuronal populations. Yet, viral tools to access and manipulate specific neuronal subtypes are still limited. Here, we performed systematic analysis of single cell genomic data to identify enhancer candidates for each of the telencephalic interneuron subtypes. We established a set of enhancer-AAV tools that are highly specific for distinct cortical interneuron populations and striatal cholinergic interneurons. These enhancers, when used in the context of different effectors, can target (fluorescent proteins), observe activity (GCaMP) and manipulate (opto-genetics) specific neuronal subtypes. We also validated our enhancer-AAV tools across species. Thus, we provide the field with a powerful set of tools to study neural circuits and functions and to develop precise and targeted therapy.

neuroscience↗

bioRxiv2024

Exploring the energetic and conformational properties of the sequence space connecting naturally occurring RNA tetraloop receptor motifs

Folded RNAs contain tertiary contact motifs whose structures and energetics are conserved across different RNAs. The transferable properties of RNA motifs simplify the RNA folding problem, but measuring energetic and conformational properties of many motifs remains a challenge. Here, we use a high-throughput thermodynamic approach to investigate how sequence changes alter the binding properties of naturally-occurring motifs, the GAAA tetraloop * tetraloop receptor (TLR) interactions. We measured the binding energies and conformational preferences of TLR sequences that span mutational pathways from the canonical 11ntR to two other natural TLRs, the IC3R and Vc2R. While the IC3R and Vc2R share highly similar energetic and conformational properties, the landscapes that map the sequence changes for their conversion from the 11ntR to changes in these properties differ dramatically. Differences in the energetic landscapes stem from the mutations needed to convert the 11ntR to the IC3R and Vc2R rather than a difference in the intrinsic energetic architectures of these TLRs. The conformational landscapes feature several non-native TLR variants with conformational preferences that differ from both the initial and final TLRs; these species represent potential branching points along the multidimensional sequence space to sequences with greater fitness in other RNA contexts with alternative conformational preferences. Our high-throughput, quantitative approach reveals the complex nature of sequence-fitness landscapes and leads to models for their molecular origins. Systematic and quantitative molecular approaches provide critical insights into understanding the evolution of natural RNAs as they traverse complex landscapes in response to selective pressures.

biophysics↗

bioRxiv2024

Metastasis of colon cancer requires Dickkopf-2 to generate cancer cells with Paneth cell properties

Metastasis is the leading cause of cancer-related mortality. Paneth cells provide stem cell niche factors in homeostatic conditions, but the underlying mechanisms of cancer stem cell niche development are unclear. Here we report that Dickkopf-2 (DKK2) is essential for the generation of cancer cells with Paneth cell properties during colon cancer metastasis. Splenic injection of Dkk2-knockout (KO) cancer organoids into C57BL/6 mice resulted in a significant reduction of liver metastases. Transcriptome analysis showed reduction of Paneth cell markers such as lysozymes in KO organoids. Single cell RNA sequencing analyses of murine metastasized colon cancer cells and patient samples identified the presence of lysozyme positive cells with Paneth cell properties including enhanced glycolysis. Further analyses of transcriptome and chromatin accessibility suggested Hepatocyte nuclear factor 4-alpha (HNF4A) as a downstream target of DKK2. Chromatin immunoprecipitation followed by sequencing analysis revealed that HNF4A binds to the promoter region of Sox9, a well-known transcription factor for Paneth cell differentiation. In the liver metastatic foci, DKK2 knockout rescued HNF4A protein levels followed by reduction of lysozyme positive cancer cells. Taken together, DKK2-mediated reduction of HNF4A protein promotes the generation of lysozyme positive cancer cells with Paneth cell properties in the metastasized colon cancers.

cancer biology↗

bioRxiv2024

AI-driven Classification of Cancer-Associated Fibroblasts Using Morphodynamic and Motile Features

The heterogeneous natures of cancer-associated fibroblasts (CAFs) play critical roles in cancer progression, with some promoting tumor growth while others inhibit it. To utilize CAFs as a target for cancer treatment, issues with subtypes of CAFs must be resolved such that specific pro-tumorigenic subtypes can be suppressed or reprogrammed into anti-tumorigenic ones. Currently, single-cell RNA sequencing (scRNA-Seq) is a prevalent strategy for classifying CAFs, primarily based on their biomolecular features. Alternatively, this study proposes assessing CAFs on a larger biophysical scale, focusing on cell morphological and motile features. Since these features are downstream effectors of differential gene expression combinations, they can serve as holistic descriptors for CAFs, offering a complementary strategy for classifying CAF subtypes. Here, we propose an artificial intelligence (AI) classification framework to comprehensively characterize CAF subtypes using morphodynamic and motile features. This framework extracts these features from label-free live-cell imaging data of CAFs employing advanced deep learning and machine learning algorithms. The results of this study highlight the ability of morphodynamic and motile features to complement biomolecular features in accurately reflecting CAF subtype characteristics. In essence, our AI-based classification framework not only provides valuable insights into CAF biology but also introduces a novel approach for comprehensively describing and targeting heterogeneous CAF subtypes based on biophysical features.

cancer biology↗