Biology subjects

Ng, N.

Publications and source records attributed to Ng, N..

11 recordsLinked to original sources

bioRxiv2026

Inositol Polyphosphate-4-Phosphatase Type II promotes gemcitabine resistance in pancreatic ductal adenocarcinoma cells via lysosomal exocytosis

Chemotherapy resistance is a major challenge in pancreatic ductal adenocarcinoma (PDAC). While high Inositol Polyphosphate-4-Phosphatase Type II (INPP4B) expression correlates with poor outcomes, its function in chemotherapy response is unclear. We show that INPP4B promotes gemcitabine resistance by enhancing lysosomal exocytosis. Across PDAC models, high INPP4B linked to reduced gemcitabine sensitivity, while knockdown restored it. INPP4B also conferred cross-resistance to agents including irinotecan, oxaliplatin, paclitaxel, and daunorubicin. Mechanistically, INPP4B increased cell-surface LAMP1, enhanced extracellular gemcitabine release, and mitigated DNA damage. Pharmacological targeting of lysosomes with chloroquine (CQ), Bafilomycin A (BafA), or specific PIKfyve or TRPML1 inhibitors blocked exocytosis and reversed resistance in vitro. Moreover, chloroquine co-treatment restored gemcitabine sensitivity in INPP4B-overexpressing xenografts. These results establish INPP4B-driven lysosomal exocytosis as a key mechanism of gemcitabine resistance, highlighting a therapeutic target for PDAC resensitization.

cancer biology↗

bioRxiv2025

Structural and functional brain asymmetry in relation to heterogeneous causes of situs inversus totalis

Various aspects of brain organization differ between the left and right hemispheres. Clues to the developmental origins of these asymmetries may be gained through associations with situs inversus totalis (SIT), a rare condition in which visceral organs are reversed on the left-right axis. In the largest previous brain imaging analyses of SIT (38 cases, 38 controls from Belgium), typical functional asymmetries such as left-hemisphere language dominance were mostly unaltered, but various aspects of asymmetrical cerebral structure - petalia, bending, and posterior venous anatomy - were often reversed in this condition. SIT can be a monogenic trait that arises from rare genetic variants, usually affecting motile cilia which help to create the embryonic left-right body axis. However, most SIT cases do not have obvious genetic causes and may arise from environmental or random effects during embryogenesis. We sequenced the genomes of 23 SIT cases and 23 controls from the Belgian brain imaging dataset and pooled with prior data from 15 cases and 15 controls. We aimed to discover whether there are altered brain asymmetries in SIT cases with disruptive DNA variants in ciliary genes, or in other types of genes, as compared to genetically unsolved cases. In total, 19 cases had likely causal variants affecting ciliary function, while 19 cases remained genetically unsolved. Functional and structural brain asymmetries were not significantly different in genetically solved versus unsolved SIT cases. Therefore, functional brain asymmetries seem largely independent of known mechanisms of visceral situs formation, while structural brain torque is altered in SIT regardless of the presence or absence of overt genetic causes.

neuroscience↗

bioRxiv2025

The mutational landscape defines the proteome and spatial organization of tumor, stroma and immune cells in ovarian cancer

High-grade serous ovarian cancer (HGSOC) is a highly aggressive and lethal form of ovarian cancer. Challenges to diagnosis and treatment include a lack of effective screening methods for early detection, the absence of cancer-specific symptoms, and the development of chemoresistance. The genomic instability of HGSOC, further complicated by homologous recombination deficiency (HRD), leads to heterogeneity in HGSOC tumors and patient response to treatment. This makes it challenging to develop a single, effective diagnostic and treatment approach for this disease. Proteogenomic studies have provided some insight into HGSOC biology, but a deeper understanding of the tumor proteome through chemotherapy and disease recurrence is needed. Here we have profiled the proteome of tumors from 29 HGSOC patients before and after multiple rounds of chemotherapy. The proteome of HGSOC tumors remained unchanged for individual patients even after numerous rounds of chemotherapy. Differential expression analysis revealed known and novel proteins associated with chemoresistance and HRD status, further supported by similar changes at the genetic and epigenetic levels. We found that HRD affected proteins related to immune pathways. HRD was also associated with more shared T cell receptor (TCR) CDR3 repertoires of tumor-infiltrating T cells and increased neoantigen counts. ERAP1, a protein involved in peptide trimming before antigen presentation to immune cells via MHC-class I, was overexpressed in homologous recombination proficient (HRP) tumors and negatively correlated to neoantigen count. Its potential role in immune suppression in HRP tumors makes it an attractive therapeutic target that may be effective in combination with immunotherapy, particularly for HRP tumors. 26-plex immunostaining of HGSOC whole tissues further revealed significant differences in the spatial proximities of immune cells to each other and to tumor cells based on HRD status. Through proteomic and imaging analysis, this work has shown that the immune landscape of HGSOC tumors is influenced by homologous recombination status and identified candidate drivers of HGSOC biology.

cancer biology↗

bioRxiv2024

Sphingosine-1-phosphate signaling inhibition suppresses Th1-like Treg generation by reversing mitochondrial uncoupling

Inflammatory environments induce the generation of dysfunctional IFN{gamma}+T-bet+FOXP3+ Th1-like Tregs, which show defective function and are found in autoimmune conditions including multiple sclerosis (MS). The pathways that control the generation of Th1-like Tregs are not well understood. Sphingosine-1-phosphate (S1P) signaling molecules are upregulated in Th1-like Tregs, and in vivo S1P inhibition with Fingolimod (FTY720) inhibits the expression of genes responsible for Treg plasticity in MS patients. However, the underlying mechanisms are unknown. Here we show that S1P signaling inhibition by FTY720 inhibits the generation of Th1-like Tregs and rescues their suppressive function. These effects are mediated by a decrease in mTORC1 signaling and reversal of the mitochondrial uncoupling that Tregs undergo during their reprogramming into Th1-like Tregs in vitro. Finally, these results are validated in in vivo generated Th1-like Tregs, as the Tregs from MS patients treated with FTY720 display decreased Th1-like Treg frequency, increased suppressive function, and mitochondrial metabolism rebalance. These results highlight the involvement of mitochondrial uncoupling in Treg reprogramming and identify S1P signaling inhibition as a target to suppress the generation of dysfunctional Th1-like Tregs.

immunology↗

bioRxiv2024

Clonal sharing of CD8+ T-cells links skin and joint inflammation in psoriatic arthritis

We hypothesised that skin and joint inflammation in psoriatic arthritis (PsA) is linked in terms of CD8+ T-cell phenotype and clonality. We employed scRNAseq to directly compare the transcriptional signature and T-cell receptor repertoire of memory T-cells from paired skin and synovial tissue and/or fluid from patients with PsA. We identified an enrichment of type-17 CD8+ tissue-resident memory (TRM) T-cells in both skin and joint, with a stronger IL-17 signature in the skin than the joint. Several T-cell clones were shared between the skin and joint and these shared clones tended to have the same signature at both sites, characterised by increased expression of genes associated with a cytotoxic, tissue-resident phenotype. Our findings support the hypothesis that skin and joint inflammation in PsA is linked in terms of T-cell clonality and raises the possibility that specific T-cells migrate between these compartments to propagate inflammation across both sites.

immunology↗

bioRxiv2024

REST and RCOR genes display distinct expression profiles in neurons and astrocytes using 2D and 3D human pluripotent stem cell models

Repressor element-1 silencing transcription factor (REST) is a transcriptional repressor involved in neurodevelopment and neuroprotection. REST forms a complex with the REST corepressors, CoREST1, CoREST2, or CoREST3 (encoded by RCOR1, RCOR2, and RCOR3, respectively). Emerging evidence suggests that the CoREST family can target unique genes independently of REST, in various neural and glial cell types during different developmental stages. However, there is limited knowledge regarding the expression and function of the CoREST family in human neurodevelopment. To address this gap, we employed 2D and 3D human pluripotent stem cell (hPSC) models to investigate REST and RCOR gene expression levels. Our study revealed a significant increase in RCOR3 expression in glutamatergic cortical and GABAergic ventral forebrain neurons, as well as mature functional NGN2-induced neurons. Additionally, a simplified astrocyte transdifferentiation protocol resulted in a significant decrease in RCOR2 expression following differentiation. REST expression was notably reduced in mature neurons and cerebral organoids, along with RCOR2 in the latter. In summary, our findings provide the first insights into the cell-type-specific expression patterns of RCOR genes in human neuronal and glial differentiation. Specifically, RCOR3 expression increases in neurons, while RCOR2 levels decrease in astrocytes. The dynamic expression patterns of REST and RCOR genes during hPSC neuronal and glial differentiation underscore the potential distinct roles played by REST and CoREST proteins in regulating the development of these cell types in humans. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=138 SRC="FIGDIR/small/584254v1_ufig1.gif" ALT="Figure 1"> View larger version (19K): org.highwire.dtl.DTLVardef@7be30borg.highwire.dtl.DTLVardef@1771388org.highwire.dtl.DTLVardef@a376aforg.highwire.dtl.DTLVardef@1c4dc83_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIREST and RCOR genes display cell-type specific expression patterns in neural cells C_LIO_LIRCOR3 (encodes CoREST3) is upregulated during neuronal and astrocyte differentiation C_LIO_LIRCOR2 (encodes CoREST2) is downregulated during differentiation of astrocytes C_LIO_LIEvidence of potential cell-type specific functions of the CoREST family C_LI

neuroscience↗

bioRxiv2024

Toxic eburicol accumulation drives the antifungal activity of azoles against Aspergillus fumigatus

Azole antifungals inhibit the sterol C14-demethylase (CYP51/Erg11), a key enzyme in the ergosterol biosynthesis pathway. They have fungistatic effects against yeasts but fungicidal effects against molds. The molecular basis for this difference remained unknown. The sequence of enzymatic steps required for ergosterol biosynthesis is different in yeasts and molds. Here we show that the azole-induced synthesis of fungicidal cell wall carbohydrate patches in the pathogenic mold Aspergillus fumigatus strictly correlates with the accumulation of the CYP51 substrate eburicol. A lack of other essential ergosterol biosynthesis enzymes, such as sterol C24-methyltransferase (Erg6A), squalene synthase (Erg9) or squalene epoxidase (Erg1) does not result in comparable cell wall alterations. Partial repression of Erg6A, which converts lanosterol into eburicol, increases azole resistance. The sterol C5-desaturase (ERG3)-dependent conversion of eburicol into 14-methylergosta-8,24(28)-dien-3{beta},6-diol, the "toxic diol" responsible for the antifungal effects of azoles in yeasts, is not required for the fungicidal effects in A. fumigatus. In contrast to yeast, where a lack of ERG3 functionality causes azole resistance, A. fumigatus lacking ERG3 becomes more azole susceptible. Mutants lacking mitochondrial complex III functionality, which are less susceptible to the fungicidal effects of azoles, but get strongly inhibited in growth, convert eburicol much more efficiently into the supposedly "toxic diol". Our results support a mechanistic model where the mode of action of azoles against the pathogenic mold A. fumigatus, other than in yeast, relies on the accumulation of eburicol which exerts fungicidal effects by triggering the formation of cell wall carbohydrate patches.

microbiology↗

bioRxiv2020

Identification of repurposable cytoprotective drugs for Vanishing White Matter Disease

Vanishing white matter disease (VWMD) is a rare leukodystrophy involving loss of function mutations of the guanine exchange factor eIF2B and typically presenting with juvenile onset. We aimed to identify repurposable FDA approved drugs in an in vitro drug screen using patient-derived fibroblasts and induced pluripotent stem cell (iPSC)-derived astrocytes. Dysregulated GADD34 and CHOP were identified in patient fibroblasts and iPSC-derived astrocytes under proteasomal stress conditions. A drug screen from a 2400 FDA approved drug library with EIF2B5 disease patient fibroblasts identified 113 anti-inflammatory drugs as a major class of hits with cytoprotective effects. A panel of potential candidate drugs including berberine, deflazacort, ursodiol, zileuton, guanabenz and Anavex 2-73, and preclinical ISRIB, increased cell survival of MG132-stressed EIF2B2 and EIF2B5 disease VWMD astrocytes, and were further investigated for their effect on the integrated stress response and mitochondrial stress. ISRIB but not other drugs significantly affected eIF2 phosphorylation and GADD34 expression. Ursodiol demonstrated capacity to reduce complex I subunit upregulation, ameliorate oxidative stress, loss of mitochondrial membrane potential and upregulation of eIF2B subunits in VWMD astrocytes, highlighting its potential as a cytoprotective compound for VWMD.

neuroscience↗

bioRxiv2020

Hypoxia-induced SETX links replication stress with the unfolded protein response

The levels of hypoxia associated with resistance to radiotherapy significantly impact cancer patient prognosis. These levels of hypoxia initiate a unique transcriptional response with the rapid activation of numerous transcription factors in a background of global repression of transcription. Here, we show that the biological response to radiobiological hypoxia includes the induction of the DNA/RNA helicase SETX. In the absence of hypoxia-induced SETX, R-loop levels increase, DNA damage accumulates, and DNA replication rates decrease. SETX plays a key role in protecting cells from DNA damage induced during transcription in hypoxia. Importantly, we show that the mechanism of SETX induction is reliant on the PERK/ATF4 arm of the unfolded protein response. These data not only highlight the unique cellular response to radiobiological hypoxia, which includes both a replication stress dependent DNA damage response and an unfolded protein response but uncover a novel link between these two distinct pathways.

cancer biology↗

bioRxiv2019

Predicting the effects of SNPs on transcription factor binding affinity

GWAS have revealed that 88% of disease associated SNPs reside in noncoding regions. However, noncoding SNPs remain understudied, partly because they are challenging to prioritize for experimental validation. To address this deficiency, we developed the SNP effect matrix pipeline (SEMpl). SEMpl estimates transcription factor binding affinity by observing differences in ChIP-seq signal intensity for SNPs within functional transcription factor binding sites genome-wide. By cataloging the effects of every possible mutation within the transcription factor binding site motif, SEMpl can predict the consequences of SNPs to transcription factor binding. This knowledge can be used to identify potential disease-causing regulatory loci.

bioinformatics↗

bioRxiv2018

Conservation of conformational dynamics across prokaryotic actins

The actin family of cytoskeletal proteins is essential to the physiology of virtually all archaea, bacteria, and eukaryotes. While X-ray crystallography and electron microscopy have revealed structural homologies among actin-family proteins, these techniques cannot probe molecular-scale conformational dynamics. Here, we use all-atom molecular dynamic simulations to reveal conserved dynamical behaviors in four prokaryotic actin homologs: MreB, FtsA, ParM, and crenactin. We demonstrate that the majority of the conformational dynamics of prokaryotic actins can be explained by treating the four subdomains as rigid bodies. MreB, ParM, and FtsA monomers exhibited nucleotide-dependent dihedral and opening angles, while crenactin monomer dynamics were nucleotide-independent. We further determine that the opening angle of ParM is sensitive to a specific interaction between subdomains. Steered molecular dynamics simulations of MreB, FtsA, and crenactin dimers revealed that changes in subunit dihedral angle lead to intersubunit bending or twist, suggesting a conserved mechanism for regulating filament structure. Taken together, our results provide molecular-scale insights into the nucleotide and polymerization dependencies of the structure of prokaryotic actins, suggesting mechanisms for how these structural features are linked to their diverse functions.\n\nSignificance StatementSimulations are a critical tool for uncovering the molecular mechanisms underlying biological form and function. Here, we use molecular-dynamics simulations to identify common and specific dynamical behaviors in four prokaryotic homologs of actin, a cytoskeletal protein that plays important roles in cellular structure and division in eukaryotes. Dihedral angles and opening angles in monomers of bacterial MreB, FtsA, and ParM were all sensitive to whether the subunit was bound to ATP or ADP, unlike in the archaeal homolog crenactin. In simulations of MreB, FtsA, and crenactin dimers, changes in subunit dihedral angle led to bending or twisting in filaments of these proteins, suggesting a mechanism for regulating the properties of large filaments. Taken together, our simulations set the stage for understanding and exploiting structure- function relationships of bacterial cytoskeletons.

biophysics↗