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Biology subjects

Humphries, M. J.

Publications and source records attributed to Humphries, M. J..

14 recordsLinked to original sources

Co-translational O-glycosylation driven by GALNTs spatial reprogramming fosters pancreatic cancer growth

Signal-driven relocation of GalNAc-transferases (GALNTs) from the Golgi to the ER, termed GALA, promotes tumour growth, but its effects on glycosylation are unclear. Unlike N-glycosylation, which is co-translational, O-glycosylation initiates post-translationally in the Golgi. Here we show that GALA subverts this arrangement in pancreatic ductal adenocarcinomas (PDAC) and in murine pancreatic tumours, where it stimulates growth. Quantitative glycoproteomics on a cellular model reveals a substantial expansion of the O-glycoproteome, consisting in thousands of sites across hundreds of proteins, ER-resident proteins, cell-surface receptors, secreted factors, and extracellular matrix components. Profiling of murine tumours and patient-derived xenografts confirms widespread activation and cross-species conservation of glycosylation patterns. Structural analysis reveals that GALA-specific residues have solvent accessibility as low as N-glycosylation sites, and below Golgi O-glycosylation or phosphorylation sites, indicating that ER O-glycosylation occurs co-translationally. By inverting the normal temporal sequence of folding and glycosylation, cancer cells generate alternative glycoforms that foster tumour growth.

cancer biology↗

Regulation of reticular adhesions by KANK2 and talin2 in two melanoma cell lines

Integrins bind to extracellular matrix proteins and, upon clustering, form multimolecular integrin adhesion complexes (IACs) that connect to and regulate the cell cytoskeleton, influencing various aspects of normal and tumour cell behaviour. Alongside well-characterized nascent adhesions, focal adhesions (FAs), fibrillar adhesions (FBs) and hemidesmosomes, a new class of IACs, reticular adhesions (RAs), have been identified. RAs, initially described as flat clathrin lattices formed by integrin V{beta}5, lack association with actin and are devoid of FAs markers. The physiological role of RAs in normal and tumor cells is still incompletely understood and requires further investigation. Previously, we analysed IACs of two melanoma cell lines, MDA-MB-435S and RPMI-7951, grown under long term culture conditions, and demonstrated that both cell lines preferentially use integrin V{beta}5 for adhesion. Here we present a comprehensive analysis of RAs in these two melanoma cell lines that differ in their ability to form FBs. To determine RAs composition, we treated cells with actin polymerisation inhibitor cytochalasin D (CytoD) which disrupts FAs, allowing isolation of RAs, which were analysed by MS-based proteomics, Western blotting and immunofluorescence. Known RA-associated proteins, including the AP-2 adaptor complex, disabled homolog 2 (DAB2) and Numb were identified in both lines, along with talin2. Notably, we also detected the presence of KN motif and ankyrin repeat domains protein (KANK2) in RA isolates. Proximity ligation analysis following CytoD-induced actin disruption confirmed the proximity of KANK2 and talin2 in RAs. We then investigated the effect of talin2 or KANK2 knockdown on RAs composition. While both talin2 and KANK2 are located in RAs, neither is essential for RA formation. Talin2 knockdown led to a reduction in RA components abundance in both cell lines. In MDA-MB-435S cell line, KANK2 produced a similar effect, mirroring the functional interaction of talin2 and KANK2 in FAs. However, in RPMI-7951 cells, KANK2 knockdown had no significant effect on RA components abundance. This discrepancy likely reflects the preferential localization of KANK2 in FBs and underscores the differing roles of talin2 and KANK2 in V{beta}5-mediated FAs across the two cell lines. These findings underscore the complexity of adhesion signalling and highlight the importance of adhesion crosstalk in regulating cellular function.

cell biology↗

The RNA splicing factor PRPF8 is required for left-right organiser cilia function and determination of cardiac left-right asymmetry via regulation of Arl13b splicing

Cilia function in the left-right organizer (LRO) is critical for determining internal organ asymmetry in vertebrates. To further understand the genetics of left-right asymmetry, we isolated a mouse mutant with laterality defects, l11Jus27, from a random mutagenesis screen. l11Jus27 mutants carry a missense mutation in the pre-mRNA processing factor, Prpf8. cephaloph[o]nus (cph) mutant zebrafish, carrying a protein truncating mutation in prpf8, phenocopy the laterality defects of l11Jus27 mutants. Prpf8 mutant mouse and fish embryos have increased expression of an alternative transcript encoding the cilium-associated protein, ARL13B, that lacks exon 9. In zebrafish, over-expression of the arl13b transcript lacking exon 9 perturbed cilium formation and caused laterality defects. The shorter ARL13B protein isoform lacked interactions with intraflagellar transport proteins. Our data suggest that PRPF8 plays a prominent role in LRO cilia by through the regulation of alternative splicing of ARL13B, thus uncovering a new mechanism for cilia-linked developmental defects.

developmental biology↗

Inhibitory TIGIT signalling is dependent on T cell receptor activation

TIGIT is an immune checkpoint receptor that can signal via cytoplasmic ITT-like and ITIM motifs to regulate T cell function. The signalling molecules that mediate inhibitory TIGIT signalling in T cells remain poorly defined, and it is not clear how TIGIT activation is regulated. Here, proximity proteomics was employed in Jurkat T cells to identify TIGIT-associating proteins upon engagement with its ligand CD155. This identified several ligation-specific TIGIT interactors, including proteins involved in signalling (Grb2 and SOS1), cytoskeletal regulation (CD2AP and SdcBP), and endocytosis (IST1 and SNX3). A TIGIT mutant (Y225A/Y231A) incapable of signalling via its inhibitory motifs prevented the recruitment of these proteins, indicating inhibitory signalling-specific engagement of these pathways. Strikingly, T cell receptor (TCR) stimulation was also needed for TIGIT to engage with these pathways. Mechanistically, phosphorylation of TIGIT required both CD155 ligation and TCR activation, which resulted in signalling and internalisation. These findings demonstrate that TIGIT signalling is context-dependent and restricted to T cells receiving simultaneous TCR activation. This establishes a regulatory mechanism that limits checkpoint control to when functionally required.

immunology↗

A TRPV4-dependent calcium signaling axis governs lamellipodial actin architecture to promote cell migration

Cell migration is crucial for development and tissue homeostasis, while its dysregulation leads to severe pathologies. Cell migration is driven by the extension of actin-based lamellipodia protrusions, powered by actin polymerization, which is tightly regulated by signaling pathways, including Rho GTPases and Ca2+ signaling. While the importance of Ca2+ signaling in lamellipodia protrusions has been established, the molecular mechanisms linking Ca2+ to lamellipodia assembly are unknown. Here, we identify a novel Ca2+ signaling axis involving the mechano-gated channel TRPV4, which regulates lamellipodia protrusions in various cell types. Using Ca2+ and FRET imaging, we demonstrate that TRPV4-mediated Ca2+ influx upregulates RhoA activity within lamellipodia, which then facilitates formin-mediated actin assembly. Mechanistically, we identify CaMKII and TEM4 as key mediators relaying the TRPV4-mediated Ca2+ signal to RhoA. These data define a molecular pathway by which Ca2+ influx regulates small GTPase activity within a specific cellular domain - lamellipodia - and demonstrate the critical role in organizing the actin machinery and promoting cell migration in diverse biological contexts.

cell biology↗

Localization of KANK2 to Focal or Fibrillar Adhesions Influences Migration in Melanoma Cell Lines

BackgroundIntegrins form focal adhesions (FAs) at the cell edge and fibrillar adhesions (FBs) located centrally. Talin 1 is essential to FAs, while talin2 is found in FAs and FBs. KANK (kidney ankyrin repeat-containing) family proteins regulate adhesion dynamics and are recruited to adhesions through interaction with talins. Previously, we showed in MDA-MB-435S melanoma cells that KANK2 is part of integrin V{beta}5 FAs, that its interaction with talin2 regulates actin-microtubule (MT) crosstalk and that KANK2 knockdown mimics the effect of integrin V or {beta}5 knockdown by reducing cell migration. Here, in another melanoma cell line RPMI-7951 we observed that KANK2 is part of FAs and FBs and that KANK2 knockdown increases cell migration. Therefore, we analyse integrin adhesion complexes in RPMI-7951 cells, explore the localization and role of KANK2 in FAs and FBs. MethodsKnockdown in human melanoma RPMI-7951 cells was achieved by transfection with gene-specific siRNAs. Integrin adhesion complexes were isolated and analysed by mass spectrometry. Immunofluorescence analysis, live cell imaging and the proximity ligation assays were done using confocal microscopy. Cell migration was assessed using Transwell Cell Culture Inserts. MTT assays were performed to determine cell sensitivity to paclitaxel. Data were statistically evaluated using one-way or two-way ANOVA or unpaired Students t-tests in GraphPad Software. ResultsWe demonstrate that RPMI-7951 melanoma cells use integrin V{beta}5 FAs and integrin 5{beta}1 FBs for adhesion, and that KANK2 is part of both structures. KANK2 is predominantly in proximity to talin1 at the cell edge (FAs) and in proximity to talin2 in the cell center (FBs). KANK2 in FAs functionally interacts with talin1 to maintain FAs, and with talin2 to regulate their dynamics. KANK2 is a component of FBs, and its knockdown mimics integrin 5 knockdown by increasing MT-dependent cell migration. ConclusionsOur study reveals the distinct roles of KANK2 in FAs and FBs. We show that KANK2 is a component of FBs, linking them to MTs and promoting their stabilisation. Loss of integrin 5 or KANK2 from FBs increases cell migration, a process that relies on the MT cytoskeleton. Plain English summaryCells adhere to their surroundings using specialized structures called adhesions, which are formed by different types of integrins and have different cell localisations: focal adhesions at the cell edge and fibrillar adhesions in the cell center. Talin1 is essential for focal adhesions, while talin2 is present in focal and fibrillar adhesions. KANK (kidney ankyrin repeat-containing) family proteins regulate adhesion dynamics by connecting talins to the microtubule cytoskeleton. Our study explored the different roles of KANK2 in focal or fibrillar adhesions, by focusing on its interactions with integrins and talins. We show that in RPMI-7951 cells, which form V{beta}5 focal and 5{beta}1 fibrillar adhesions, KANK2 is present in both of these adhesions. KANK2 supports V{beta}5 focal adhesion maintenance via talin1 and regulates their dynamics via talin2. KANK2 is also a component of 5{beta}1 fibrillar adhesions, and its depletion mimics integrin 5 knockdown and enhances cell migration, a process dependent on the microtubule cytoskeleton. In conclusion, our study demonstrates that KANK2 plays distinct roles in different adhesion structures, contributing to both focal and fibrillar adhesion function.

cell biology↗

Extracellular vesicles stimulate smooth muscle cell migration by presenting collagen VI.

The extracellular matrix (ECM) supports blood vessel architecture and functionality and undergoes active remodelling during vascular repair and atherogenesis. Vascular smooth muscle cells (VSMCs) are essential for vessel repair and, via their secretome, can invade from the vessel media into the intima to mediate ECM remodelling. Accumulation of fibronectin (FN) is a hallmark of early vascular repair and atherosclerosis. Here we show that FN stimulates VSMCs to secrete small extracellular vesicles (sEVs) by activating the {beta}1 integrin/FAK/Src pathway as well as Arp2/3-dependent branching of the actin cytoskeleton. We found that sEVs are trapped by the ECM in vitro and colocalise with FN in symptomatic atherosclerotic plaques in vivo. Functionally, ECM-trapped sEVs induced the formation of focal adhesions (FA) with enhanced pulling forces at the cellular periphery preventing cellular spreading and adhesion. Proteomic and GO pathway analysis revealed that VSMC-derived sEVs display a cell adhesion signature and are specifically enriched with collagen VI on the sEV surface. In vitro assays identified collagen VI as playing a key role in cell adhesion and invasion directionality. Taken together our data suggests that the accumulation of FN is a key early event in vessel repair acting to promote secretion of collage VI enriched sEVs by VSMCs. These sEVs stimulate directional invasion, most likely by triggering peripheral focal adhesion formation and actomyosin contraction to exert sufficient traction force to enable VSMC movement within the complex vascular ECM network. Figure AbstractVascular smooth muscle cells sense fibronectin via {beta}1 integrin and secrete small extracellular vesicles loaded with collagen VI. These extracellular vesicles are entrapped in the extracellular matrix and induce formation of peripheral focal adhesions presenting adhesion complex ECM proteins including collagen VI, LGALS3BP, EDIL3 and TGFBI. Focal adhesions anchor the extracellular matrix to actin fibrils in the cell. Contraction of the actin fibrils generates the mechanical force for directional cell invasion through the matrix. This figure was created with BioRender (https://biorender.com/). O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=132 SRC="FIGDIR/small/551257v3_ufig1.gif" ALT="Figure 1"> View larger version (43K): org.highwire.dtl.DTLVardef@1355004org.highwire.dtl.DTLVardef@1186e9forg.highwire.dtl.DTLVardef@106ad30org.highwire.dtl.DTLVardef@1543518_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

Lineage plasticity in SCLC generates non-neuroendocrine cells primed for vasculogenic mimicry

IntroductionVasculogenic mimicry (VM), the process of tumor cell trans-differentiation to endow endothelial-like characteristics supporting de novo vessel formation, is associated with poor prognosis in several tumor types, including small cell lung cancer (SCLC). In genetically engineered mouse models (GEMMs) of SCLC, NOTCH and MYC co-operate to drive a neuroendocrine (NE) to non-NE phenotypic switch and co-operation between NE and non-NE cells is required for metastasis. Here, we define the phenotype of VM-competent cells and molecular mechanisms underpinning SCLC VM using circulating tumor cell-derived explant (CDX) models and GEMMs. MethodsWe analysed perfusion within VM vessels and their association with NE and non-NE phenotypes using multiplex immunohistochemistry in CDX and GEMMs. VM-proficient cell subpopulations in ex vivo cultures were molecularly profiled by RNA sequencing and mass spectrometry. We evaluated their 3D structure and defined collagen-integrin interactions. ResultsWe show that VM vessels are present in 23/25 CDX models and in 2 GEMMs. Perfused VM vessels support tumor growth and only Notch-active non-NE cells are VM-competent in vivo and ex vivo, expressing pseudohypoxia, blood vessel development and extracellular matrix (ECM) organization signatures. On Matrigel, VM-primed non-NE cells re-model ECM into hollow tubules in an integrin {beta}1-dependent process. ConclusionsWe identify VM as an exemplar of functional heterogeneity and plasticity in SCLC and these findings take significant steps towards understanding the molecular events that enable VM. These results support therapeutic co-targeting of both NE and non-NE cells to curtail SCLC progression and to improve SCLC patient outcomes in future.

cancer biology↗

Pancreatic ductal adenocarcinoma cells employ integrin α6β4 to form hemidesmosomes and regulate cell proliferation

Pancreatic ductal adenocarcinoma (PDAC) has a dismal prognosis due to its aggressive progression, late detection and lack of druggable driver mutations, which often combine to result in unsuitability for surgical intervention. Together with activating mutations of the small GTPase KRas, which are found in over 90% of PDAC tumours, a contributory factor for PDAC tumour progression is formation of a rigid extracellular matrix (ECM) and associated desmoplasia. This response leads to aberrant integrin signalling, and accelerated proliferation and invasion. To identify the integrin adhesion systems that operate in PDAC, we analysed a range of pancreatic ductal epithelial cell models using 2D, 3D and organoid culture systems. Proteomic analysis of isolated integrin receptor complexes from human pancreatic ductal epithelial (HPDE) cells predominantly identified integrin 6{beta}4 and hemidesmosome components, rather than classical focal adhesion components. Electron microscopy, together with immunofluorescence, confirmed the formation of hemidesmosomes by HPDE cells, both in 2D and 3D culture systems. Similar results were obtained for the human PDAC cell line, SUIT-2. Analysis of HPDE cell secreted proteins and cell-derived matrices (CDM) demonstrated that HPDE cells secrete a range of laminin subunits and form a hemidesmosome-specific, laminin 332-enriched ECM. Expression of mutant KRas (G12V) did not affect hemidesmosome composition or formation by HPDE cells. Cell-ECM contacts formed by mouse and human PDAC organoids were also assessed by electron microscopy. Organoids generated from both the PDAC KPC mouse model and human patient-derived PDAC tissue displayed features of acinar-ductal cell polarity, and hemidesmosomes were visible proximal to prominent basement membranes. Furthermore, electron microscopy identified hemidesmosomes in normal human pancreas. Depletion of integrin {beta}4 using siRNA reduced cell proliferation in both SUIT-2 and HPDE cells, reduced the number of SUIT-2 cells in S-phase, and induced G1 cell cycle arrest, indicating a requirement for 6{beta}4-mediated adhesion for cell cycle progression and growth. Taken together, these data suggest that laminin-binding adhesion mechanisms in general, and hemidesmosome-mediated adhesion in particular, may be under-appreciated in the context of PDAC. Proteomic data are available via ProteomeXchange with the identifiers PXD027803, PXD027823 and PXD027827.

cancer biology↗

A SNAI2-PEAK1 stromal axis drives progression and lapatinib resistance in HER2-positive breast cancer by supporting a cytokine expression profile that converges on PI3K/Akt signaling

Intercellular mechanisms by which the stromal microenvironment contributes to solid tumor progression and targeted therapy resistance remain poorly understood, presenting significant clinical hurdles. PEAK1 (Pseudopodium-Enriched Atypical Kinase One) is an actin cytoskeleton- and focal adhesion-associated pseudokinase that promotes cell state plasticity and cancer metastasis by mediating growth factor-integrin signaling crosstalk. Here, we determined that stromal PEAK1 expression predicts poor outcomes in HER2-positive breast cancers high in SNAI2 expression and enriched for MSC content. Notably, we identified that mesenchymal stem cells (MSCs) and cancer-associated fibroblasts (CAFs) express high PEAK1 protein levels and MSCs require PEAK1 to potentiate tumorigenesis, lapatinib resistance and metastasis of HER2-positive breast cancer cells. Analysis of PEAK1-dependent secreted factors from MSCs revealed a CCL4-, INHBA- and GDF5-focused network that converged on PI3K/Akt signaling. In this regard, we observed that MSC expression of PEAK1 is required for sustained Akt phosphorylation in neighboring HER2-positive breast cancer cells following lapatinib treatment. Finally, we uncovered a significant correlation between INHBA and PEAK1 expression levels in breast cancer, and that INHBA is an excellent predictor of disease relapse and decreased survival in HER2-positive tumors enriched for PEAK1 expression and MSC content. Importantly, we provide the first evidence that PEAK1 promotes tumorigenic phenotypes through a previously unrecognized SNAI2-PEAK1-INHBA-PI3K/Akt stromal to tumor cell signaling axis. These results establish a new, targetable intercellular mechanism that may be leveraged to improve targeted therapy responses and patient outcomes in breast cancer and other stroma-rich malignancies.

cancer biology↗

Definition of the fibroblast adhesome using multiplexed proximity biotinylation

Integrin adhesion complexes (IACs) bridge the extracellular matrix to the actin cytoskeleton and transduce signals in response to both chemical and mechanical cues. The composition, interactions, stoichiometry and topological organisation of proteins within IACs are not fully understood. To address this gap, we used multiplexed proximity biotinylation (BioID) to generate an in situ, proximity-dependent adhesome in mouse pancreatic fibroblasts. Integration of the interactomes of 16 IAC-associated baits revealed a network of 147 proteins with 361 proximity interactions. Candidates with underappreciated roles in adhesion were identified, in addition to established IAC components. Bioinformatic analysis revealed five clusters of IAC baits that link to common groups of prey, and which therefore may represent functional modules. The five clusters, and their spatial associations, are consistent with current models of IAC interaction networks and stratification. This study provides a resource to examine proximal relationships within IACs at a global level.

cell biology↗

A pivotal role for Nrf2 in endothelial detachment- implications for endothelial erosion of stenotic plaques

Endothelial erosion of atherosclerotic plaques and resulting thrombosis causes approximately 30% of acute coronary syndromes (ACS). As changes in the haemodynamic environment strongly influence endothelial function and contribute to plaque development, we reconstructed the coronary artery geometries of plaques with thrombi overlying intact fibrous caps from 17 ACS patients and performed computational fluid dynamic analysis. The results demonstrated that erosions frequently occur within areas of stenosis exposed to elevated flow. We recapitulated this flow environment in vitro, exposing human coronary artery endothelial cells to elevated flow and modelled smoking (a risk factor for erosion) by exposure to a combination of aqueous cigarette smoke extract and TNF. This treatment induced endothelial detachment, which increased with pharmacological activation of the antioxidant system controlled by transcription factor Nrf2 (encoded by NFE2L2). The expression of Oxidative Stress Growth INhibitor genes OSGIN1 and OSGIN2 increased under these conditions and also in the aortas of mice exposed to cigarette smoke. Sustained high level expression of OSGIN1+2 resulted in cell cycle arrest, induction of senescence, loss of focal adhesions and actin stress fibres, and dysregulation of autophagy. Overexpression of either Nrf2 or OSGIN1+2 induced cell detachment, which did not depend on apoptosis, and could be partially rescued by inhibition of HSP70 using VER-155008, or AMP kinase activation using metformin. These findings demonstrate that under elevated flow, smoking-induced hyperactivation of Nrf2 can trigger endothelial cell detachment, highlighting a novel mechanism that could contribute to ACS involving endothelial erosion overlying stenotic plaques.

cell biology↗

Reticular adhesions: A new class of adhesion complex that mediates cell-matrix attachment during mitosis

Adhesion to the extracellular matrix (ECM) persists during mitosis in most cell types. Yet, classical adhesion complexes (ACs), such as focal adhesions and focal complexes, do and must disassemble to enable cytoskeletal rearrangements associated with mitotic rounding. Given this paradox, mechanisms of mitotic cell-ECM adhesion remain undefined. Here, we identify reticular adhesions, a new class of AC that is mediated by integrin v{beta}5, formed during interphase and preserved at cell-ECM attachment sites throughout cell division. Consistent with this role, integrin {beta}5 depletion perturbs mitosis and disrupts spatial memory transmission between cell generations. Quantitative imaging reveals reticular adhesions to be both morphologically and dynamically distinct from classic focal adhesions, while mass spectrometry defines their unique composition; lacking virtually all consensus adhesome components. Indeed, remarkably, reticular adhesions are functionally independent of both talin and F-actin, yet are promoted by phosphatidylinositol-4,5-bisphosphate (PI-4,5-P2). Overall, the distinct characteristics of reticular adhesions provide a unique solution to the problem of maintaining cell-ECM attachment during mitotic rounding and division.

cell biology↗

Improved LC-MS chromatographic alignment increases the accuracy of label-free quantitative proteomics: Comparison of spectral counting versus ion intensity-based proteomic quantification strategies.

The ability to provide an unbiased qualitative and quantitative description of the global changes to proteins in a cell or an organism would permit the systems-wide study of complex biological systems. Label-free quantitative shotgun proteomic strategies (including LC-MS ion intensity quantification and spectral counting) are attractive because of their relatively low cost, ease of implementation, and the lack of multiplexing restrictions when comparing multiple samples. Owing to improvements in the resolution and sensitivity of mass spectrometers, and the availability of analytical software packages, protein quantification by LC-MS ion intensity has increased in popularity. Here, we have addressed the importance of chromatographic alignment on protein quantification, and then assessed how spectral counting compares to ion intensity-based proteomic quantification. Using a spiked-in protein strategy, we analysed two situations that commonly arise in the application of proteomics to cell biology: (i) samples with a small number of proteins of differential abundance in a larger non-changing background, and (ii) samples with a larger number of proteins of differential abundance. To perform these assessments on biologically relevant samples, we used isolated integrin adhesion complexes (IACs). Technical replicate analysis of isolated IACs resulted in a range of alignment scores using the Progenesis QI software package and demonstrated that higher LC-MS chromatographic alignment scores increased the precision of protein quantification. Furthermore, implementation of a simple sample batch-running strategy enabled good chromatographic alignment for hundreds of samples over multiple batches. Finally, we applied the sample batch-running strategy and compared quantification by LC-MS ion intensity to spectral counting and found that quantification by LC-MS ion intensity was more accurate and precise. In summary, these results demonstrate that chromatographic alignment is important for precise and accurate protein quantification based on LC-MS ion intensity and accordingly we present a simple sample re-ordering strategy to facilitate improved alignment. These findings are not only relevant to label-free quantification using Progenesis QI but may be useful to the wide range of MS-based quantification strategies that rely on chromatographic alignment.

bioinformatics↗