Biology subjects

Lim, J.

Publications and source records attributed to Lim, J..

At least 55 records · Page 3Linked to original sources

bioRxiv2024

Glycosomal phosphoenolpyruvate carboxykinase CRISPR/Cas9-deletion and its role in Trypanosoma cruzi metacyclogenesis and infectivity in mammalian host

Trypanosoma cruzi, the causative agent of Chagas disease, possesses glycosomes - unique organelles that house key metabolic enzymes, several of which are promising therapeutic targets. Among them, phosphoenolpyruvate carboxykinase (PEPCK) plays a central role in succinic fermentation, the main pathway for NAD+ regeneration within the organelle. Using CRISPR/Cas9 editing, PEPCK gene was disrupted in T. cruzi, producing single- allele knockout epimastigotes (TcPEPCK-sKO) with reduced enzyme activity. This disruption impaired glucose consumption and mitochondrial respiration, particularly oxidative phosphorylation, reducing dependence on mitochondrial ATP production. To compensate, pyruvate phosphate dikinase was upregulated, increasing alanine production, possibly to maintain redox balance. Although TcPEPCK-sKO epimastigotes exhibited a minor reduction in growth, their differentiation (metacyclogenesis) and invasion were severely compromised. However, once inside the host cell, TcPEPCK-sKO amastigotes increased their replication, leading to enhanced trypomastigote production. The same was observed in in vivo infection, where TcPEPCK-sKO infection in IFN{gamma}-deficient mice caused uncontrolled parasitemia and severe pathology, highlighting the PEPCK critical role in host-pathogen interactions. However, an intact immune system effectively contained TcPEPCK-sKO infection. Taken together, our findings demonstrate that PEPCK is crucial for T. cruzi energy metabolism, enabling the parasite differentiation within the insect vector and controlling the infection of mammalian host cells.

microbiology↗

bioRxiv2024

Antibiotics that Kill Gram-negative Bacteria by Restructuring the Outer Membrane Protein BamA

The essential outer membrane protein insertase BamA has recently emerged as a valid target for killing Gram-negative bacteria. Bamabactins, competitive inhibitors targeting the lateral gate of BamA, disrupt the substrate folding process, compromise the outer membrane integrity, and lead to bacterial cell death. Despite their promise, the full pharmacological potential of bamabactins remains underexploited. We applied phylogenetic genome mining and synthetic biology to identify xenorceptides which selectively kill Enterobacteriaceae. Mode of action studies show that xenorceptide A2 integrates itself into BamA as an additional {beta}-strand between {beta}1 and {beta}16 at the lateral gate, inducing a conformation of BamA that has not been observed before. Biological evaluation of xenorceptide A2 shows promising activity in vitro and in vivo, and limited resistance which differentiates it from other bamabactin antibiotics. Our data show that the chemical diversity of bamabactins is far greater than previously recognized and thus an attractive source for antibiotic discovery.

microbiology↗

bioRxiv2024

APOBEC3A, not APOBEC3B, drives deaminase mutagenesis in human gastric epithelium

Cancer genomes frequently carry APOBEC (apolipoprotein B mRNA editing catalytic polypeptide-like)-associated DNA mutations, suggesting APOBEC enzymes as innate mutagens during cancer initiation and evolution. However, the pure mutagenic impacts of the specific enzymes among this family that are responsible for APOBEC-associated mutagenesis remain unclear in human normal cell lineage, particularly the comparative mutagenic activities of APOBEC3A and APOBEC3B. Here, we investigated the mutagenic contributions of these enzymes through whole-genome sequencing of human normal gastric organoid lines carrying doxycycline-inducible APOBEC3A or APOBEC3B cassettes. Our findings demonstrated that transcriptional APOBEC3A upregulation led to the acquisition of a massive number of genomic mutations in a few cell cycles. By contrast, APOBEC3B upregulation did not generate a substantial number of mutations in gastric epithelium. APOBEC3B-associated mutagenesis remained insignificant even after a combined inactivation of TP53. Based on the spectrum of acquired mutations after APOBEC3A upregulation, we further analyzed APOBEC3A-associated mutational signatures, encompassing indels mainly composed of 1bp deletions, characteristics of clustered mutations, and selective pressures operative on cells carrying the mutations. Our observations provide a clear foundation for understanding the mutational impact of APOBEC enzymes in human cells.

genomics↗

bioRxiv2024

Lactoferrin-Derived Peptide Chimera Induces Caspase-independent Cell Death in Multiple Myeloma

Lactoferrin-derived peptide chimera is a synthetic peptide that mimics the functional unit of lactoferrin with antibacterial activity. Antimicrobial peptides are promising candidates for cancer treatment. Although LF is known to have anticancer effects, to the best of our knowledge, its effects on multiple myeloma have not yet been studied. In this study, we explored the potential of lactoferrin-derived chimera for the treatment of multiple myeloma, a malignant clonal plasma cell disease of the bone marrow. Lactoferrin-derived chimera effectively inhibited MM1S, MM1R, and RPMI8226 multiple myeloma cell growth and induced the early and late phases of apoptosis, but not in normal peripheral blood mononuclear cells. Furthermore, lactoferrin-derived chimera modulates the relative expression of genes involved in survival, apoptosis, and mitochondrial dysfunction at the transcriptional level. Mitochondrial analysis revealed that lactoferrin-derived chimera triggered oxidative stress in multiple myeloma cells, leading to the generation of reactive oxygen species and a decline in mitochondrial membrane potential, resulting in mitochondrial dysfunction. Although lactoferrin-derived chimera did not cause caspase-dependent cell death, it induced nuclear translocation of apoptosis-inducing factor and endonuclease G, indicating the initiation of caspase-independent apoptosis. Overall, our data suggest that lactoferrin-derived chimera induces caspase-independent programmed cell death in multiple myeloma cell lines by increasing the nuclear translocation of apoptosis-inducing factor/endonuclease G. Therefore, lactoferrin-derived chimera has potential in multiple myeloma cancer therapies.

cancer biology↗

bioRxiv2024

Detection of intra-tumoral microbiota from transcriptomic sequencing of Asian breast cancer

The human microbiome has garnered significant interest in recent years as an important driver of human health and disease. Likewise, it has been suggested that the intra-tumoral microbiome may be associated with specific features of cancer such as tumour progression and metastasis. However, additional research is needed to validate these findings in diverse populations. In this study, we characterized the intra-tumoral microbiota of 883 Malaysian breast cancer patients using transcriptomic data from bulk tumours and investigated their association with clinical variables and immune scores. We found that the tumour microbiome was not associated with breast cancer molecular subtype, cancer stage, tumour grade, or patient age, but was weakly associated with immune scores. We also found that the tumour microbiome was able to predict immune scores in our cohort using random forest models, suggesting the possibility of an interaction between the tumour microbiome and the tumour immune microenvironment in Asian breast cancer.

microbiology↗

bioRxiv2024

Unsaturated lipids as key control points for caveola formation and disassembly

Caveolae are specialized plasma membrane domains with a unique lipid composition. Recent work has implicated lipid peroxidation in triggering caveola disassembly, releasing caveolar proteins to regulate the cellular response to oxidative stress. Here we investigated the role of specific lipid species in caveola formation and response to oxidative stress. Systematic screening of lipid enzymes identified ACSL4, a critical enzyme in the synthesis of polyunsaturated fatty acid-containing lipids, and enzymes involved in the biosynthesis of pro-ferroptotic ether lipids, as key regulators of caveola formation. Omega-6 fatty acids promoted efficient caveola formation, while their oxidation or displacement by omega-3 or monounsaturated fatty acids disrupted this process. Moreover, we found that omega-6 fatty acid-containing membrane lipids were required for oxidative stress-induced caveola disassembly. These findings unveil a new model for caveola formation, highlighting specific unsaturated lipids as essential caveolar components and key control points for caveola disassembly in response to an oxidizing environment.

cell biology↗

bioRxiv2024

Acetylation of lysine 82 initiates TDP-43 nuclear loss of function by disrupting its nuclear import

The hallmark of a spectrum of age-dependent neurodegenerative diseases, including Amyotrophic Lateral Sclerosis (ALS), is a TDP-43 proteinopathy that includes nuclear loss of function and cytoplasmic aggregation. Here, reduced proteasome activity, as naturally occurs during aging, is shown to inhibit nuclear import of TDP-43. Quantitative mass spectrometry is used to determine that TDP-43 is the protein whose nuclear localization is most perturbed upon reduction in proteasome activity, culminating in elevated cytoplasmic TDP-43. Interaction of importin-1 with the bipartite classical nuclear localization sequence (cNLS) of TDP-43 is shown to be disrupted by partial proteasome inhibition but maintained by replacement with a PY-NLS that is recognized by importin-{beta}2. Mechanistically, this nuclear depletion of TDP-43 is shown to be driven by ubiquitination or acetylation of lysines 79, 82, and 84 within the cNLS when proteasome activity is reduced in human neurons. Specifically, acetylation at lysine 82 is sufficient to abolish TDP-43 binding to importin-1 and subsequent nuclear import of TDP-43. Moreover, using acetylation-specific TDP-43 antibodies, we detected acetylation of lysine 82 in the motor cortex of sporadic ALS patients but not control subjects. Our findings demonstrate that post-translational acetylation at lysine 82 of TDP-43 drives disruption of its importin-1-mediated nuclear import and is sufficient to initiate TDP-43 nuclear loss of function and cytoplasmic accumulation, evidence supporting acetylation as a plausible initiator of TDP-43 proteinopathies.

neuroscience↗

bioRxiv2024

Accurate antibody loop structure prediction enables zero-shot design of target-specific antibodies

Protein loops, characterized by their versatile structures with varying sizes and shapes, can recognize a wide range of targets with high specificity and affinity. The variable loops of the antibody complementarity-determining region (CDR) are particularly crucial for immune responses and therapeutic applications due to their effective target recognition capabilities. Accurate structure prediction of these antibody loops is essential for the efficient in silico design of target-binding antibodies for therapeutic or industrial use. However, predicting antibody loop structures is challenging due to the lack of evolutionary information from related proteins. Thus, a successful ab initio structure prediction method, which operates without structural templates or related sequences, is crucial for the effective design of antibody loop-mediated interactions. This study demonstrates that highly accurate antibody loop structure prediction enables the effective zero-shot design of target-binding antibody loops. The performance of loop design has been shown to depend on the accuracy of ab initio loop structure prediction, as tested with two versions of our design model. The high affinity, diversity, novelty, and specificity of the antibody loops designed with these new methods were validated experimentally on four target proteins.

bioengineering↗

bioRxiv2024

Conservation of gene expression patterns between the amniotic epithelium at birth and a newborn's nasal epithelium

BackgroundAmniotic epithelial cells are foetal-derived stem cells, capable of differentiating into all three germ layers, including mature epithelial cell populations. However, the conservation between amniotic epithelium and other epithelial tissues has not been sufficiently explored. We hypothesised that the amniotic epithelium might serve as a surrogate tissue source for investigating transcriptional profiles in the respiratory epithelium of the newborn. We compared gene expression profiles and weighted gene co-expression network structure in paired amniotic and newborn nasal epithelial samples from 85 participants in the Airway Epithelium Respiratory Illnesses and Allergy (AERIAL) birth cohort. ResultsIn total, 11,867 genes (79.7%) were commonly expressed in both amniotic and nasal epithelium, with uniquely expressed genes (2,563 and 458, respectively) enriched for biological functions related to each tissues specialist functions (e.g. developmental programs and ciliated cells, respectively). We observed a strong overlap in weighted gene co-expression network structure between both tissues, with ten co-expression modules identified in consensus network analysis. Genes commonly expressed in both tissues and/or found in the consensus network modules were enriched for biologically relevant gene signatures and pathway terms related to airway function. We also observed significant overlap in gene expression and network structure between the amniotic epithelium and published datasets of epithelial samples from the lower airway and other epithelial tissues including skin and oesophagus, suggesting a global epithelial signature. ConclusionsOverall, we observed significant overlap in gene expression and network structure between paired amniotic and nasal epithelial samples, supporting the potential of the amnion as a non-invasive and abundant tissue surrogate. Observed differences between tissues were related to each tissues specialist functions, which remains an important consideration when assessing their overlap. Future studies aimed at investigating amnion-based biomarkers for respiratory exposures in utero and disease outcomes in childhood are needed to extend these results towards clinical translation.

molecular biology↗

bioRxiv2024

Evidence for belief updating in decision-variable space: past decisions with finer granularity attract future ones more strongly

When engaged in decision-making tasks, humans are known to create decision variables. Much effort has focused on the cognitive processes involved in forming decision variables. However, there is limited understanding of how decision variables, once formed, are utilized to adapt to the environment. We reason that decision-makers would benefit from updating the belief of decision-variable. As one such belief updating, we hypothesize that a decision commitment restricts the probabilistic belief distribution of decision variable to a range corresponding to that decision. This implies that past decisions not only attract future ones but also exert a greater pull when those decisions are made with finer granularity-- dubbed the granularity effect. Here, we present the findings of seven psychophysical experiments that confirm these implications. Further, as a unified account of the granularity effect, we offer a Bayesian model. Our work demonstrates how humans leverage the decision-variable to effectively adapt to their surroundings.

neuroscience↗

bioRxiv2024

A comparison of super-resolution microscopy techniques for imaging tightly packed microcolonies of an obligate intracellular bacterium

Conventional optical microscopy imaging of obligate intracellular bacteria is hampered by the small size of bacterial cells, tight clustering exhibited by some bacterial species and challenges relating to labelling such as background from host cells, a lack of validated reagents, and a lack of tools for genetic manipulation. In this study we imaged intracellular bacteria from the species Orientia tsutsugamushi (Ot) using five different fluorescence microscopy techniques: standard confocal, Airyscan confocal, instant Structured Illumination Microscopy (iSIM), three-dimensional Structured Illumination Microscopy (3D-SIM) and Stimulated Emission Depletion Microscopy (STED). We compared the ability of each to resolve bacterial cells in intracellular clumps in the lateral (xy) axis, using full width half maximum (FWHM) measurements of a labelled outer membrane protein (ScaA) and the ability to detect small, outer membrane vesicles external to the cells. We next compared the ability of each technique to sufficiently resolve bacteria in the axial (z) direction and found 3D-STED to be the most successful method for this. We then combined this approach with a custom 3D cell segmentation and analysis pipeline using the open-source, deep learning software, Cellpose to segment the cells and subsequently the commercial software Imaris to analyze their 3D shape and size. Using this combination, we demonstrated differences in bacterial shape, but not their size, when grown in different mammalian cell lines. Overall, we compare the advantages and disadvantages of different super-resolution microscopy techniques for imaging this cytoplasmic obligate intracellular bacterium based on the specific research question being addressed.

microbiology↗

bioRxiv2024

Hierarchical structural organization in bioinspired peptide coacervate microdroplets

This study explores the dynamic and hierarchical structural organization of peptide coacervate microdroplets at the meso-to atomic-scale resolution using a combination of Transferred Nuclear Overhauser Effect Spectroscopy (TrNOESY), Small Angle Neutron Scattering (SANS), and confocal microscopy. Dynamic interactions driving the self-association of peptide clusters are revealed, highlighting the critical roles of interacting residues. These phase-separating model peptides form small oligomers at low pH, which aggregate into larger clusters at neutral pH. These clusters organize into a porous network within the droplets, facilitating size-selective cargo sequestration. The findings underscore the significance of the dynamic spatio-temporal properties of peptide-based coacervates, contributing to our understanding of phase separation at the atomic and molecular levels. Critically, this approach enables the investigation of coacervate structures in their native state, offering insights into the physical and dynamic interactions governing droplet formation and cargo encapsulation. TOC O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=106 SRC="FIGDIR/small/602323v4_ufig1.gif" ALT="Figure 1"> View larger version (43K): org.highwire.dtl.DTLVardef@15aadb2org.highwire.dtl.DTLVardef@41be55org.highwire.dtl.DTLVardef@36f0d8org.highwire.dtl.DTLVardef@fe1af8_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2024

Single-cell analysis of human diversity in circulating immune cells

Lack of diversity and proportionate representation in genomics datasets and databases contributes to inequity in healthcare outcomes globally1,2. The relationships of human diversity with biological and biomedical phenotypes are pervasive3, yet remain understudied, particularly in a single-cell genomics context. Here we present the Asian Immune Diversity Atlas (AIDA), a multi-national single-cell RNA-sequencing (scRNA-seq) healthy reference atlas of human immune cells. AIDA comprises 1,265,624 circulating immune cells from 619 healthy donors and 6 controls, spanning 7 population groups across 5 countries. AIDA is one of the largest healthy blood datasets in terms of number of cells, and also the most diverse in terms of number of population groups. Though population groups are frequently compared at the continental level, we identified a pervasive impact of sub-continental diversity on cellular and molecular properties of immune cells. These included cell populations and genes implicated in disease risk and pathogenesis as well as those relevant for diagnostics. We detected single-cell signatures of human diversity not apparent at the level of cell types, as well as modulation of the effects of age and sex by self-reported ethnicity. We discovered functional genetic variants influencing cell type-specific gene expression, including context-dependent effects, which were under-represented in analyses of non-Asian population groups, and which helped contextualise disease-associated variants. We validated our findings using multiple independent datasets and cohorts. AIDA provides fundamental insights into the relationships of human diversity with immune cell phenotypes, enables analyses of multi-ancestry disease datasets, and facilitates the development of precision medicine efforts in Asia and beyond.

genomics↗

bioRxiv2024

Cellular dsRNA interactome reveals the regulatory map of exogenous RNA sensing

RNA-binding proteins (RBPs) provide a critical post-transcriptional regulatory layer in determining RNA fate. Currently, UV crosslinking followed by oligo-dT pull-down is the golden standard in identifying the RBP repertoire, but such method is ineffective in capturing RBPs that recognize double-stranded RNAs (dsRNAs). Here, we utilize anti-dsRNA antibody immunoprecipitation followed by quantitative mass spectrometry to comprehensively identify RBPs bound to cellular dsRNAs without any external stimulus. Notably, our dsRNA interactome contains proteins involved in sensing N6-methyladenosine RNAs and stress granule components. We further perform targeted CRISPR-Cas9 knockout functional screening and discover proteins that can regulate the interferon (IFN) response during exogenous RNA sensing. Interestingly, depleting dsRBPs mostly attenuate the IFN response, and they act as antiviral factors during human {beta}-coronavirus HCoV-OC43 infection. Our dsRNA interactome capture provides an unbiased and comprehensive characterization of putative dsRBPs and will facilitate our understanding of dsRNA sensing in both physiological and pathological contexts.

molecular biology↗

bioRxiv2024

Gut microbial metabolite imidazole propionate impairs endothelial cell function and promotes the development of atherosclerosis

BackgroundThe microbially generated amino acid-derived metabolite imidazole propionate (ImP) contributes to the pathogenesis of type 2 diabetes. However, the effect of ImP on endothelial cell physiology and its role in atherosclerotic coronary artery disease (CAD) is unknown. Using both human and animal model studies, we investigated the potential contributory role of ImP in the development of atherosclerosis. MethodsPlasma levels of ImP were measured in patients undergoing elective cardiac angiography (n = 831) by means of ultra high-performance liquid chromatography coupled to tandem mass spectrometry. Odds ratios (ORs) and corresponding 95% confidence intervals for CAD were calculated based on the ImP quartiles using both univariable and multivariable logistic regression models. Atheroprone apolipoprotein E-/- (Apoe-/-) mice fed a high-fat diet were additionally treated with ImP (800 {micro}g) or vehicle and aortic atherosclerotic lesion area was evaluated after 12 weeks. In a mouse model of carotid artery injury, the effect of ImP on vascular regeneration was examined. Using human aortic endothelial cells (HAECs) the effect of ImP on functional properties of endothelial cells were assessed. Next-generation sequencing, western blot analysis, siRNA-based gene knockdown and tamoxifen-inducible Cre-loxP experiments were performed to investigate ImP-mediated molecular mechanisms. ResultsPlasma ImP levels in subjects undergoing cardiac evaluation were associated with increased risk for prevalent CAD. In atheroprone Apoe-/- mice ImP increased atherosclerotic lesion size. We found that ImP dose-dependently impaired migratory and angiogenic properties of human endothelial cells, and promoted an increased inflammatory response. Long-term exposure to ImP impaired the repair potential of the endothelium after an arterial insult. Mechanistically, ImP attenuated insulin receptor signaling by suppressing PI3K/AKT pathway leading to the sustained activation of the forkhead box protein O1 (FOXO1) transcription factor. Genetic inactivation of endothelial FOXO1 signaling in ImP-treated mice enhanced the angiogenic activity and preserved the vascular repair capacity of endothelial cells after carotid injury. ConclusionsOur findings reveal a hitherto unknown role of the microbially produced histidine-derived metabolite ImP in endothelial dysfunction and atherosclerosis, suggesting that ImP metabolism is a potential therapeutic target in atherosclerotic cardiovascular disease.

systems biology↗

bioRxiv2024

Astrocytic hemoglobin is an H2O2-decomposing peroxidase and therapeutic target for Alzheimer's disease

Summary paragraphHemoglobin (Hb) is well-known for transporting oxygen in red blood cells within blood vessels1. Although Hb is also present in the brain2, its role remains poorly understood. Here, we show that Hb, found in astrocytes of neurodegenerative animal models and patients, displays significant antioxidant effects through its H2O2-decomposing peroxidase activity, and a small molecule enhancer boosts this activity, reducing aberrant H2O2 and mitigating H2O2-induced neurodegeneration. To counteract the harmful effects of aberrant H2O2-production in Alzheimers disease (AD), we developed KDS12025, a blood-brain barrier (BBB)-permeable small molecule that effectively enhances the peroxidase activity of Hb by a hundredfold, especially at a low level of Hb. KDS12025 and its analogs achieve this enhancement through its electron-donating amine group. KDS12025 reduces H2O2 levels in astrocytes, exhibits neuroprotective effects, and reverses memory impairment in AD models. Gene-silencing of Hb{beta} abrogates KDS12025s impact in both culture and animal models of AD. Moreover, KDS12025 prevented the death of dopaminergic neurons in a Parkinsons disease (PD) model without altering the oxygen-transporting function of Hb. KDS12025 extended survival and improved motor function even in the severe amyotrophic lateral sclerosis (ALS) mouse model. Our findings propose Hb as a new therapeutic target for neurodegenerative diseases, with KDS12025 emerging as a first-in-class drug candidate that enhances Hbs peroxidase activity to reduce H2O2. Boosting Hbs peroxidase activity with KDS12025 mitigates oxidative stress and alleviates neurodegeneration in AD, PD, and ALS with broad applicability for numerous oxidative-stress-driven diseases.

neuroscience↗

bioRxiv2024

FOXA1 is required for ErbB2 expression and luminal differentiation in HER2-positive breast cancer

The function of the pioneer factor forkhead box A1 (FOXA1) in estrogen receptor (ER)-negative, human epidermal growth factor receptor 2 (HER2, encoded by the ERBB2 gene)-positive breast cancer represents a critical gap in our understanding of lineage identity in tumorigenesis. Here, we solve this enigma by addressing this question through the identification of an indispensable, co-dependent regulatory circuit formed between FOXA1 and the SAM pointed domain containing ETS-family transcription factor (SPDEF). Using integrative multi-omics analyses of patient tumors and experimental models, we demonstrate that this circuit functions as the master guardian of the HER2-positive luminal state. It executes this role via two distinct, essential mechanisms: it directly binds regulatory elements to drive high-level expression of the ERBB2 oncogene, and it simultaneously preserves epithelial identity by suppressing a latent program of epithelial-to-mesenchymal transition (EMT). Mechanistically, the FOXA1/SPDEF circuit promotes the expression of the transcriptional repressor TRPS1, which in turn antagonizes the pro-mesenchymal activity of the TEAD/YAP complex. Our findings define a central regulatory node that couples lineage fidelity to oncogenic output in HER2-positive cancer, revealing the FOXA1/SPDEF-TRPS1 axis as a critical determinant of tumor plasticity and a potential therapeutic target for overcoming resistance in HER2-positive breast cancer.

cancer biology↗

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↗