Biology subjects

Chen, L.

Publications and source records attributed to Chen, L..

At least 397 records · Page 22Linked to original sources

bioRxiv2024

A Refined Analysis of Neanderthal-Introgressed Sequences in Modern Humans with a Complete Reference Genome

BackgroundLeveraging long-read sequencing technologies, the first complete human reference genome, T2T-CHM13, corrects the assembly errors in prior references and addresses the remaining 8% of the genome. While the studies on archaic admixture in modern humans so far have been relying on the GRCh37 reference due to the archaic genome data, the impact of T2T-CHM13 in this field remains unknown. ResultsWe remapped the sequencing reads of the high-quality Altai Neanderthal and Denisovan genomes onto GRCh38 and T2T-CHM13 respectively. Compared with GRCh37, we found T2T-CHM13 has a significant improvement of read mapping quality in archaic samples. We then applied IBDmix to identify Neanderthal introgressed sequences in 2,504 individuals from 26 geographically diverse populations in different references. We observed different pre-phasing filtering strategies prevalently used in public data can largely impact determination of archaic ancestry, calling for consideration on the choice of filters. We discovered ~51Mb T2T-CHM13 unique Neanderthal sequences, which are predominantly located in regions where the variants distinct between the GRCh38 and T2T-CHM13 assemblies emerge. Besides, we unfolded new instances of population-specific archaic introgression in diverse populations, covering genes involved in metabolism, olfactory-related, and icon-channel. Finally, we integrated the introgressed sequences and adaptive signals with all references into a visualization database website, called ASH (www.arcseqhub.com), to facilitate the utilization of archaic alleles and adaptive signals in human genomics and evolutionary research. ConclusionsOur study refines the detection of archaic variations in modern humans, highlights the importance of T2T-CHM13 reference utility, and provides novel insights into functional consequences of archaic hominin admixture.

evolutionary biology↗

bioRxiv2024

Efficient clustering of large molecular libraries

The widespread use of Machine Learning (ML) techniques in chemical applications has come with the pressing need to analyze extremely large molecular libraries. In particular, clustering remains one of the most common tools to dissect the chemical space. Unfortunately, most current approaches present unfavorable time and memory scaling, which makes them unsuitable to handle million- and billion-sized sets. Here, we propose to bypass these problems with a time- and memory-efficient clustering algorithm, BitBIRCH. This method uses a tree structure similar to the one found in the Balanced Iterative Reducing and Clustering using Hierarchies (BIRCH) algorithm to ensure O(N) time scaling. BitBIRCH leverages the instant similarity (iSIM) formalism to process binary fingerprints, allowing the use of Tanimoto similarity, and reducing memory requirements. Our tests show that BitBIRCH is already > 1,000 times faster than standard implementations of the Taylor-Butina clustering for libraries with 1,500,000 molecules. BitBIRCH increases efficiency without compromising the quality of the resulting clusters. We explore strategies to handle large sets, which we applied in the clustering of one billion molecules under 5 hours using a parallel/iterative BitBIRCH approximation.

bioinformatics↗

bioRxiv2024

The study on the impact of indoleacetic acid on enhancing the ability of the rumen's original microecology to degrade aflatoxin B1.

Aflatoxin B1 (AFB1) poses a serious threat to the health of cattle and is strictly monitored in their diets. Rumen microorganisms in cattle have the ability to degrade AFB1, but this capability is limited. Enhancing the degradation capacity of the original rumen microecology for AFB1 is a novel approach. From a molecular perspective,indoleacetic-3-acid (IAA) promotes the expression of cytochromes, which can improve the degradation of AFB1. Therefore, this study aims to investigate the impact of different concentrations of IAA on the degradation of AFB1 by the rumen microecology. Experiments used rumen fluid from three adult cows as donors, and the cows were all fed the same total mixed ration. Rumen fluid was collected from these three cannulated cows before morning feeding to prepare in vitro fermentation fluid. The experiments used a completely randomized design, with each treatment repeated four times. The results showed that as the fermentation time increased, the content of AFB1 gradually decreased, with a degradation rate of up to 75.73% after 24 h. AFB1 altered the rumen fermentation pattern, with a significant reduction in the content of acetic acid (P<0.05) and a significant decrease in the acetic acid to propionic acid ratio (P<0.05). It also affected the rumen microecology, causing a significant reduction in the abundance of Ruminococcus amylophilus, Prevotella ruminicola, and Fusobacterium succinogenes (P<0.05). In addition, this study found that with the increase in the amount of IAA added, the content of AFB1 in the rumen gradually decreased. IAA enhances the degradation capacity of the original rumen microecology for AFB1, and the addition of IAA alleviates the impact of AFB1 on Ruminococcus amylophilus, Prevotella ruminicola, and Fusobacterium succinogenes in the rumen (P<0.05). Moreover, the addition of IAA can promote the stability of the rumen microecology, with significantly higher acetic acid and acetic acid to propionic acid ratios in the fermentation fluid compared to the non-added group (P<0.05). In summary, the addition of IAA can improve the degradation capacity of the rumen microecology for AFB1, providing a new solution for alleviating the impact of AFB1 on animal health.

microbiology↗

bioRxiv2024

Enhanced and idiosyncratic neural representations of personally typical scenes

Previous research shows that the typicality of visual scenes (i.e., if they are good examples of a category) determines how easily they can be perceived and represented in the brain. However, the unique visual diets individuals are exposed to across their lifetimes should sculpt very personal notions of typicality. Here, we thus investigated whether scenes that are more typical to individual observers are more accurately perceived and represented in the brain. We used drawings to enable participants to describe typical scenes (e.g., a kitchen) and converted these drawings into 3D renders. These renders were used as stimuli in a scene categorization task, during which we recorded EEG. In line with previous findings, categorization was most accurate for renders resembling the typical scene drawings of individual participants. Our EEG analyses reveal two critical insights on how these individual differences emerge on the neural level: First, personally typical scenes yielded enhanced neural representations from around 200 ms after onset. Second, personally typical scenes were represented in idiosyncratic ways, with reduced dependence on high-level visual features. We interpret these findings in a predictive processing framework, where individual differences in internal models of scene categories formed through experience shape visual analysis in idiosyncratic ways.

neuroscience↗

bioRxiv2024

Towards a new standard in genomic data privacy: a realization of owner-governance

With the rapid developments in sequencing technologies, individuals now have unprecedented access to their genomic data. However, existing data management systems or protocols are inadequate for protecting privacy, limiting individuals control over their genomic information, hindering data sharing, and posing a challenge for biomedical research. To fill the gap, an owner-governed system that fulfills owner authority, lifecycle data encryption, and verifiability at the same time is prompted. In this paper, we realized Governome, an owner-governed data management system designed to empower individuals with absolute control over their genomic data during data sharing. Governome uses a blockchain to manage all transactions and permissions, enabling data owners with dynamic permission management and to be fully informed about every data usage. It uses homomorphic encryption and zero-knowledge proofs to enable genomic data storage and computation in an encrypted and verifiable form for its whole lifecycle. Governome supports genomic analysis tasks, including individual variant query, cohort study, GWAS analysis, and forensics. Query of a variants genotype distribution among 2,504 1kGP individuals in Governome can be efficiently completed in under 18 hours on an ordinary server. Governome is an open-source project available at https://github.com/HKU-BAL/Governome.

bioinformatics↗

bioRxiv2024

Genetic evolution of keratinocytes to cutaneous squamous cell carcinoma

We performed multi-omic profiling of epidermal keratinocytes, precancerous actinic keratoses, and squamous cell carcinomas to understand the molecular transitions during skin carcinogenesis. Single-cell mutational analyses of normal skin cells showed that most keratinocytes have remarkably low mutation burdens, despite decades of sun exposure, however keratinocytes with TP53 or NOTCH1 mutations had substantially higher mutation burdens. These observations suggest that wild-type keratinocytes (i.e. without pathogenic mutations) are able to withstand high dosages of cumulative UV radiation, but certain pathogenic mutations break these adaptive mechanisms, priming keratinocytes for transformation by increasing their mutation rate. Mutational profiling of squamous cell carcinomas adjacent to actinic keratoses revealed TERT promoter and CDKN2A mutations emerging in actinic keratoses, whereas additional mutations inactivating ARID2 and activating the MAPK-pathway delineated the transition to squamous cell carcinomas. Surprisingly, actinic keratoses were often not related to their neighboring squamous cell carcinoma, indicating that collisions of unrelated neoplasms are common in the skin. Spatial variation in gene expression patterns was common in both tumor and immune cells, with high expression of checkpoint molecules at the invasive front of tumors. In conclusion, this study catalogues the key events during the evolution of cutaneous squamous cell carcinoma.

genomics↗

bioRxiv2024

Nuclear FAK aggravates CD8+ T cell exhaustion via the SP1-IL-6 axis in colorectal cancer

Nuclear abnormalities such as nuclear deformation are hallmarks of many diseases, including cancer. Accumulating evidence suggests that the dense and mechanically stiff tumor microenvironment promotes nuclear deformation in cancer cells. However, little is known about how nuclear deformation in neoplastic cells regulates immune exhaustion in the tumor microenvironment. Here, we found that lamin A/C-mediated nuclear stiffening in neoplastic cells promotes the nuclear translocation of phosphorylated focal adhesion kinase (pFAK), which is strongly correlated with the heterogeneity and exhaustion of CD8+ T cells within the spatial context of the tumor microenvironment in human colorectal cancer. Mechanistically, we revealed that increased nuclear tension within tumor cells promotes pFAK nuclear translocation, where nuclear pFAK was found to regulate SP1/IL-6-mediated T-cell exhaustion and the transcription of proinflammatory cytokines/chemokines. Pharmacological inhibition or disruption of pFAK nuclear translocation enhanced antitumor immune responses and synergistically potentiated PD-1 and TIM-3 immunotherapy by increasing CD8+ T-cell cytotoxicity and restoring exhaustion in preclinical models of colorectal cancer. These findings highlight the pivotal role of nuclear tension-mediated pFAK translocation into the tumor cell nucleus in regulating CD8+ T-cell exhaustion, suggesting that pFAK is a promising target for advancing cancer immunotherapy.

immunology↗

bioRxiv2024

Motor Cortical Neuronal Hyperexcitability Associated with α-Synuclein Aggregation

Dysfunction of the cerebral cortex is thought to underlie motor and cognitive impairments in Parkinson disease (PD). While cortical function is known to be suppressed by abnormal basal ganglia output following dopaminergic degeneration, it remains to be determined how the deposition of Lewy pathology disrupts cortical circuit integrity and function. Moreover, it is also unknown whether cortical Lewy pathology and midbrain dopaminergic degeneration interact to disrupt cortical function in late-stage. To begin to address these questions, we injected -synuclein (Syn) preformed fibrils (PFFs) into the dorsolateral striatum of mice to seed Syn pathology in the cortical cortex and induce degeneration of midbrain dopaminergic neurons. Using this model system, we reported that Syn aggregates accumulate in the motor cortex in a layer- and cell-subtype-specific pattern. Particularly, intratelencephalic neurons (ITNs) showed earlier accumulation and greater extent of Syn aggregates relative to corticospinal neurons (CSNs). Moreover, we demonstrated that the intrinsic excitability and inputs resistance of Syn aggregates-bearing ITNs in the secondary motor cortex (M2) are increased, along with a noticeable shrinkage of cell bodies and loss of dendritic spines. Last, neither the intrinsic excitability of CSNs nor their thalamocortical input was altered by a partial striatal dopamine depletion associated with Syn pathology. Our results documented motor cortical neuronal hyperexcitability associated with Syn aggregation and provided a novel mechanistic understanding of cortical circuit dysfunction in PD.

neuroscience↗

bioRxiv2024

Conditioned immunological memory: implication for cognition of immune cells

Associative learning refers to the process by which animals or human beings build the new relationship between two stimuli or events, which has been found throughout the animal kingdom. However, no studies have reported the associative learning in cells in the body to date. In the study, we focused on immune cells, as immunological memory is considered as one of the cardinal features of the immune system. As for a classical conditioning procedure, we designed the analogues of ginsenoside Rh1 (e.g., protopanaxadiol and panaxadiol) as the conditioned stimulus (CS) and the mcKLH-Rh1 conjugate as the unconditioned stimulus (US) and determined the CS-US association by detecting the dynamics of anti-Rh1 antibody production in serum. To test the hypothesis that immune cells also have the same associative learning ability as animals or human beings, mice were divided into control and CS group. Based on above CS and US, two groups of mice were subjected to conditioned learning, conditional memory recall, and deconditioning. When we used protopanaxadiol as the CS, the antibody response to Rh1 in the mice of CS group was slower and weaker than the control mice during conditional memory recall. Interestingly, the difference between two groups in antibody response to the immunogen disappeared during deconditioning. When we used panaxadiol as the CS, the antibody response to Rh1 in the mice of two groups was similar with that in studies regarding protopanaxadiol as the CS throughout three experimental phases. These results suggested that immune cells could acquire new association between a hapten analogue and a hapten-protein conjugate after undergoing a classical conditioning. Moreover, the conditioned immunological memory enables immune cells to make a conditioned response of humoral immunosuppression to prevent US induced immune damage. Our findings open a new frontier to explore cognitive functions of cells in the body and contribute to a novel understanding of cellular bioactivities.

immunology↗

bioRxiv2024

Unremodeled plasma membrane GPI-anchored proteins trigger aberrant clathrin-mediated endocytosis

The plasma membrane has a complex organization that includes the polarized distribution of membrane proteins as well as lipids. Glycosylphosphatidylinositol-anchored proteins (GPI-AP) are ubiquitously expressed in eukaryotes and represent a functionally diverse group of proteins some of which are critical for the organization and function of the plasma membrane. Here we investigated how the plasma membrane of yeast cells responded to the accumulation of GPI-APs in which phosphoethanolamine (EtNP) had not been removed from mannose 2 (Man2) of the GPI moiety. The persistence of EtNP on Man2 prevented cleavage of a subset of GPI-APs, but the proteins were not endocytosed. Man2 unremodeled GPI-APs increased lipid disorder and generated a stress response whereby abnormal ubiquitin- and clathrin-dependent endocytosis was triggered. The resulting stress-induced endocytosis disrupted the trafficking repertoire of a subset of plasma membrane proteins. These proteins were redirected, via the multivesicular body, to numerous small vacuoles for degradation. Our findings highlight the critical importance GPI-AP Man2 remodeling for maintaining the integrity and homeostasis of the plasma membrane.

cell biology↗

bioRxiv2024

Multi-omic profiling of intraductal papillary neoplasms of the pancreas reveals distinct expression patterns and potential markers of progression

In order to advance our understanding of precancers in the pancreas, 69 pancreatic intraductal papillary neoplasms (IPNs), including 64 intraductal papillary mucinous neoplasms (IPMNs) and 5 intraductal oncocytic papillary neoplasms (IOPNs), 32 pancreatic cyst fluid samples, 104 invasive pancreatic ductal adenocarcinomas (PDACs), 43 normal adjacent tissues (NATs), and 76 macro-dissected normal pancreatic ducts (NDs) were analyzed by mass spectrometry. A total of 10,246 proteins and 22,284 glycopeptides were identified in all tissue samples, and 756 proteins with more than 1.5-fold increase in abundance in IPMNs relative to NDs were identified, 45% of which were also identified in cyst fluids. The over-expression of selected proteins was validated by immunolabeling. Proteins and glycoproteins overexpressed in IPMNs included those involved in glycan biosynthesis and the immune system. In addition, multiomics clustering identified two subtypes of IPMNs. This study provides a foundation for understanding tumor progression and targets for earlier detection and therapies. SignificanceThis multilevel characterization of intraductal papillary neoplasms of the pancreas provides a foundation for understanding the changes in protein and glycoprotein expression during the progression from normal duct to intraductal papillary neoplasm, and to invasive pancreatic carcinoma, providing a foundation for informed approaches to earlier detection and treatment.

cancer biology↗

bioRxiv2024

EstroGene2.0: A multi-omic database of response to estrogens, ER-modulators, and resistance to endocrine therapies in breast cancer

Endocrine therapies targeting the estrogen receptor (ER/ESR1) are the cornerstone to treat ER-positive breast cancers patients, but resistance often limits their effectiveness. Understanding the molecular mechanisms is thus key to optimize the existing drugs and to develop new ER-modulators. Notable progress has been made although the fragmented way data is reported has reduced their potential impact. Here, we introduce EstroGene2.0, an expanded database of its precursor 1.0 version. EstroGene2.0 focusses on response and resistance to endocrine therapies in breast cancer models. Incorporating multi-omic profiling of 361 experiments from 212 studies across 28 cell lines, a user-friendly browser offers comprehensive data visualization and metadata mining capabilities (https://estrogeneii.web.app/). Taking advantage of the harmonized data collection, our follow-up meta-analysis revealed substantial diversity in response to different classes of ER-modulators including SERMs, SERDs, SERCA and LDD/PROTAC. Notably, endocrine resistant models exhibit a spectrum of transcriptomic alterations including a contra-directional shift in ER and interferon signaling, which is recapitulated clinically. Furthermore, dissecting multiple ESR1-mutant cell models revealed the different clinical relevance of genome-edited versus ectopic overexpression model engineering and identified high-confidence mutant-ER targets, such as NPY1R. These examples demonstrate how EstroGene2.0 helps investigate breast cancers response to endocrine therapies and explore resistance mechanisms.

cancer biology↗

bioRxiv2024

Down regulation of Engase in Caenorhabditis elegans may improve its stresses adaptivity

Endo-beta-N-acetylglucosaminidase (ENGASE) is one of the key enzymes involved in the regulation of structure and function of glycoproteins. It is conserved from prokaryotic to eukaryotic cells. Although their activities in vitro and applications have been well studied, the biological function of ENGASE remains to be illustrated. In this study, we analyzed the molecular and physiological function of Engase from Caenorhabditis elegans homolog eng-1(CeEngase). We found that CeEngase knockout or knockdown increased the environmental stresses adaptability, such as heat stress and osmotic stress. Preliminary glycomics analysis showed that the basement membrane proteins of extracellular matrix may be the main targets of CeENGASE. In addition, CeENGASE may selectively prefer to N2H7 glycans on glycoproteins. In conclusion, our data illustrated that the defection and/or down regulation of CeEngase may provide a beneficially adaptation for stresses.

biochemistry↗

bioRxiv2024

In silico generation and augmentation of regulatory variants from massively parallel reporter assay using conditional variational autoencoder

Predicting the functional consequences of genetic variants in non-coding regions is a challenging problem. Massively parallel reporter assays (MPRAs), which are an in vitro high-throughput method, can simultaneously test thousands of variants by evaluating the existence of allele specific regulatory activity. Nevertheless, the identified labelled variants by MPRAs, which shows differential allelic regulatory effects on the gene expression are usually limited to the scale of hundreds, limiting their potential to be used as the training set for achieving a robust genome-wide prediction. To address the limitation, we propose a deep generative model, MpraVAE, to in silico generate and augment the training sample size of labelled variants. By benchmarking on several MPRA datasets, we demonstrate that MpraVAE significantly improves the prediction performance for MPRA regulatory variants compared to the baseline method, conventional data augmentation approaches as well as existing variant scoring methods. Taking autoimmune diseases as one example, we apply MpraVAE to perform a genome-wide prediction of regulatory variants and find that predicted regulatory variants are more enriched than background variants in enhancers, active histone marks, open chromatin regions in immune-related cell types, and chromatin states associated with promoter, enhancer activity and binding sites of cMyC and Pol II that regulate gene expression. Importantly, predicted regulatory variants are found to link immune-related genes by leveraging chromatin loop and accessible chromatin, demonstrating the importance of MpraVAE in genetic and gene discovery for complex traits.

bioinformatics↗

bioRxiv2024

Faster and more accurate assessment of differential transcript expression with Gibbs sampling and edgeR 4.0

Differential transcript expression analysis of RNA-seq data is an increasingly popular tool to assess changes in expression of individual transcripts between biological conditions. Software designed for transcript-level differential expression analyses account for the uncertainty of transcript quantification, the read-to-transcript ambiguity (RTA), in statistical analyses via resampling methods. Bootstrap sampling is a popular resampling method that is implemented in the RNA-seq quantification tools kallisto and Salmon. However, bootstrapping is computationally intensive and provides replicate counts with low resolution when the number of sequence reads originating from a gene is low. For lowly expressed genes, bootstrap sampling results in noisy replicate counts for the associated transcripts, which in turn leads to non reproducible and unrealistically high RTA-dispersion for those transcripts. Gibbs sampling is a more efficient and high resolution algorithm implemented in Salmon. Here we leverage the developments of edgeR v4 to present an improved differential transcript expression analysis pipeline with Salmons Gibbs sampling algorithm. The new bias-corrected quasi-likelihood method with adjusted deviances for small counts from edgeR, combined with the efficient Gibbs sampling algorithm from Salmon, provides faster and more accurate DTE analyses of RNA-seq data. Comprehensive simulations and test data show that the presented analysis pipeline is more powerful and efficient than previous differential transcript expression pipelines while providing correct control of the false discovery rate.

bioinformatics↗

bioRxiv2024

Identification of key residues in water channel formation in the Bacillus subtilis germinant receptor protein GerAB

Some Bacillales and Clostridiales bacteria form spores in unfavorable environments. These spores are dormant but can rapidly resume metabolism in response to certain small molecule nutrients. This process is termed germination and can be initiated by a variety of low molecular wt nutrients termed germinants. Structural modeling and mutagenesis studies showed that GerAB, an inner membrane (IM) protein of the Bacillus subtilis spore germinant receptor (GR) GerA, is involved in L-alanine-initiated spore germination. A previous molecular simulation study also suggested there is a water channel in GerAB. In the current work, Steered Molecular Dynamics (SMD) simulations were employed to force a single water molecule through GerAB, identifying three key amino acid residues, Y97, L199 and F342, that interfere with water passage. When these residues were altered to alanine, L-alanine germination was minimal in spores with L199A, F342A and triA (Y97A, L199A and F342A triple mutant), while Y97A mutant spores germinated [~]61%. And besides Y97A, all other mutants showed compromised germination triggered by AGFK mixture. Western blotting found reduced levels of the GerA GR in the Y97A mutant, and an absence of the GerA GR in all other mutants. This proved that all three identified residues are crucial to the structural integrity of the GerAB protein and therefore probably the formation of the GR complex, the germinosome.

microbiology↗

bioRxiv2024

Mature and migratory dendritic cells promote immune infiltration and response to anti-PD-1 checkpoint blockade in metastatic melanoma

Immune checkpoint inhibitors (ICIs) have heralded a remarkable shift in cancer care, significantly extending survival for advanced cancer patients. However, despite their remarkable clinical successes, a substantial majority of patients fail to achieve a lasting response to ICIs. To address this challenge and gain insights into the complex landscape of the tumor microenvironment (TME), we conducted an extensive analysis using single-cell RNA sequencing (scRNA; [~]216K cells across 39 samples) and single-nucleus transposase-accessible chromatin sequencing (snATAC; [~]43K cells from 15 samples) in a metastatic melanoma cohort. This systematic approach delineates 14 distinct cell types and 55 cell subtypes, including the identification of 15 transcriptional hallmarks of malignant cells. Through correlation analysis of cell subtype proportions, we unveiled six distinct clusters associated with varying tumor responses. Particularly intriguing was the identification of the mature DC enriched in immunoregulatory molecules (mregDC) subtype exhibiting correlations with naive T and B cells, forming an anti-tumor program that underscores the importance of multiple immune cell types in mediating anti-tumor immunity. Notably, we found that mregDC abundance represents a good prognostic predictor of progression-free survival (PFS) in the context of ICI treatment, and when combined with the TCF7+/- CD8 T cell ratio, it reliably predicts patient PFS across treatments beyond ICI. We validated our findings using an independent cohort of 274 ICI-treated melanoma samples analyzed using tissue-level expression. We next compared mregDCs and conventional dendritic cell types 1 and 2 (cDC1 and cDC2) using transcriptome signature, differentiation trajectory, interactome, cytokine milieu, and epigenome landscape analyses. This comparative analysis shed light on the unique attributes of mregDCs within the TME. Finally, we investigated cell type/subtype-specific genes, pathways, immune response enrichment, and ligand-receptor interactions closely associated with the proportions of mregDCs within the TME. These molecular and cellular insights, with their critical roles in enhancing the immune response against cancer, offer valuable prospects for predicting the efficacy of ICI regimens, and potentially guiding the selection of rational combinatorial therapies.

cancer biology↗

bioRxiv2024

Loss of cell junctional components and matrix alterations drive cell desquamation and fibrotic changes in Idiopathic Pulmonary Fibrosis

The distal bronchioles in Idiopathic Pulmonary Fibrosis (IPF) exhibit histopathological abnormalities such as bronchiolization, peribronchiolar fibrosis and honeycomb cysts that contribute to the overall architectural remodeling of lung tissue seen in the disease. Here we describe an additional histopathologic finding of epithelial desquamation in patients with IPF, wherein epithelial cells detach from the basement membrane of the distal bronchioles. To understand the mechanism driving this pathology, we performed spatial transcriptomics of the epithelial cells and spatial proteomics of the basement membrane of the distal bronchioles from IPF patients and patients with no prior history of lung disease. Our findings reveal a downregulation of cell junctional components, upregulation of epithelial-mesenchymal transition signatures and dysregulated basement membrane matrix in IPF distal bronchioles, facilitating epithelial desquamation. Further, functional assays identified regulation between Collagen IV in the matrix, and the junctional genes JUP and PLEC, that is crucial for maintaining distal bronchiolar homeostasis. In IPF, this balanced regulation between matrix and cell-junctions is disrupted, leading to loss of epithelial adhesion, peribronchiolar fibrosis and epithelial desquamation. Overall, our study suggests that in IPF the interplay between the loss of cell junctions and a dysregulated matrix results in desquamation of distal bronchiolar epithelium and lung remodeling, exacerbating the disease. One Sentence SummaryTwo-way regulation of cell junctional proteins and matrix proteins drives cellular desquamation and fibrosis in the distal bronchioles of patients with Idiopathic Pulmonary Fibrosis.

pathology↗