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Joshi, P.

Publications and source records attributed to Joshi, P..

At least 19 recordsLinked to original sources

Multistage AI Crop Inspection and Segmentation Framework (MACISF)

Crop quality assessment is one of the most critical components of modern agriculture, which directly influences yield optimization, post-harvest management, and food security. Conventional evaluation of field crops relies on manual inspection, which is time-consuming, subjective, and unscalable. This paper proposes the Multistage AI Crop Inspection and Segmentation Framework (MACISF), an automated multistage deep learning pipeline for fruit quality evaluation from visual features. The pipeline is comprised of three stages: (i) an EfficientNetV2-L backbone, fine-tuned with a three-stage progressive strategy, for crop type classification; (ii) seven species-specific EfficientNetV2-S classifiers for healthy-versusdefective detection; and (iii) a YOLOv8m module for defect localization. Trained and evaluated on a composite dataset spanning seven fruit species, MACISF achieves 99.23% crop type accuracy (macro F1-score 99.23%, macro AUC-ROC 0.993), 99.39% mean health state accuracy with 99.51% mean defective-class recall, and a projected grading mAP@0.5 of 92.3%. On crop type classification, the Stage 1 classifier is second only to InceptionV3 (by 0.15 percentage points) among seven models trained on the same data, and outperforms ResNet-50, Xception, EfficientNetB3, DenseNet-121, and MobileNetV2. Unlike these singletask baseline models, MACISF additionally delivers health-state assessment, defect severity grading, and a per-unit economic and nutritional evaluation. Results are reported on heldout test data from a controlled dataset, and field validation is left for future work.

plant biology↗

Conserved cerebellar rhombic lip compartmentalization and Eomes regulatory networks govern unipolar brush cell development

The rhombic lip (RL) gives rise to all cerebellar glutamatergic cell types, including unipolar brush cells (UBCs). Disruptions to UBC development can lead to the neurodevelopmental disorder Dandy-Walker Syndrome and the pediatric brain tumor medulloblastoma, but these diseases have not been adequately modeled in mice. To evaluate conservation of UBC development in mouse and human, we examined UBC localization, lineage decisions, and the underlying molecular mechanisms of UBC differentiation using multiplex immunofluorescence and single-cell RNA-seq of wild-type and conditional knockout animals of the primary UBC transcription factor Eomes. Similar to the human RL, the murine RL is molecularly compartmentalized, cycling EOMES+ UBC progenitors are highly abundant, and persist after birth. Eomes regulates the transcriptional networks important for UBC differentiation and migration, but not UBC fate. Overall, our findings suggest that murine UBC development recapitulates many features of human UBC development, with EOMES playing a central role in UBC maturation.

developmental biology↗

High-speed volumetric single-molecule imaging using dual-wavelength light sheets and PSF-engineered enhanced biplane detection

Single-molecule localization microscopy (SMLM) enables nanoscale imaging but remains limited in three-dimensional (3D), high-speed, and high-density applications due to background fluorescence, photon inefficiency, and large point-spread function (PSF) footprints. Here, we present single-objective light-sheet microscopy with PSF-engineering enhanced biplane detection (SoLiD-3D), a versatile imaging platform that integrates dual-wavelength light-sheet illumination with dual-color, multi-configuration biplane imaging for parallel acquisition with PSF engineered detection for high-speed volumetric SMLM. Parallelized single-objective light-sheet excitation combined with PSF engineering overcomes key limitations of conventional wide-field and biplane approaches. Independent control of two excitation wavelengths for optical sectioning enables simultaneous dual-target imaging and single-target dual-color imaging with improved contrast and temporal resolution utilizing dynamically displaced light sheets for volumetric coverage. Using SoLiD-3D, we demonstrate high-speed single- and dual-target dual-color imaging that doubles localization density without sacrificing photon efficiency and continuous volumetric imaging via PSF-engineering enhanced biplane detection for whole-cell 3D imaging with improved axial localization performance over extended depth ranges. We further demonstrate improved speed by utilizing the Hummus PSF, a compact engineered PSF that enables high-precision 3D localization with a substantially reduced spatial footprint, for the first time for super-resolution imaging applications. Taken together, SoLiD-3D mitigates the trade-off between axial range and localization precision and offers improved speed compared to conventional 3D SMLM approaches.

biophysics↗

On the state of protein function prediction: a report on the fourth CAFA challenge

BackgroundThe Critical Assessment of Functional Annotation (CAFA) is a community effort held to understand the field of computational protein function prediction. Every three years, since 2010, the organizers initiate an experiment to collect function predictions on a large set of proteins and then evaluate the performance of predicting methods on a subset of proteins that have accumulated experimental annotations between the submission deadline and the evaluation time. CAFA provides an independent and rigorous assessment of the current state of the art, thus leveling the playing field, highlighting successes, revealing bottlenecks, and offering a forum for the exchange of ideas in protein science. Here, we report the results of the fourth CAFA experiment (CAFA4). ResultsCAFA4 featured the participation of 148 methods from 70 research groups on a total of 46,205 unique proteins over a 5-year annotation accumulation phase, the longest in any CAFA. In a comparison across CAFA2-CAFA4 methods, the prediction of Gene Ontology (GO) terms has clearly improved across all three GO aspects and traditional evaluation settings. While not achieving the first rank, several CAFA2 and CAFA3 methods featured in the top ten methods in many evaluations, suggesting that earlier methods still hold relevance. The performance is weaker in the newly introduced "partial knowledge" evaluation category (proteins with experimental annotations before submission deadline that gained additional annotations in the same GO aspect during the annotation accumulation phase), highlighting the need for a new class of methods. The rankings of the methods were stable over the years in traditional evaluation settings, but less so in the new partial knowledge evaluation. Overall, the field continues to progress with some influx of new participants. Sustained efforts will be necessary to substantially advance it.

bioinformatics↗

Advances in protein function prediction from the fifth CAFA challenge

The Critical Assessment of Functional Annotation (CAFA) is a long-standing community effort to independently assess computational methods for protein function prediction, to highlight well-performing methodologies, to identify bottlenecks in the field, and to provide a forum for the dissemination of results and exchange of ideas. In its fifth round (CAFA5) of triennial challenges, a partnership with Kaggle Inc. facilitated participation from a large community of data scientists and computational biologists through a competitive prospective challenge on the crowdsourcing platform. In this work, we present an in-depth analysis of the submitted predictions and report improvements in accuracy over all methods from the previous CAFA challenges. We further introduce a new evaluation setting for proteins with pre-existing (incomplete) annotations and identify the need for methods that better leverage existing annotations to predict those that will be discovered later. Finally, we characterize the prospective evaluation framework by examining performance on a strict set of unpublished annotations and across intermediate database releases. Our results indicate that recent developments in the field, such as the availability of protein language models and accurately predicted 3D structures, as well as the growth of experimental annotations through biocuration, have all contributed to performance improvements. 1

bioinformatics↗

Versatile and scalable reflective micromirrors for single-objective light sheet microscopy

We present a tunable microfabrication pipeline for creating robust, reflective inserts that adapt conventional commercial imaging chambers for single-objective light sheet (LS) illumination. This system reduces the complexity associated with dual-objective LS setups and specialized LS chambers while retaining the native functionality and biocompatibility of the original chambers. The fabricated insert features a metalized, 3D nanoprinted micromirror with an angled reflective surface, enabling alignment of a thin LS for sectioning and imaging throughout mammalian cells. Using this pipeline, we demonstrate that single-objective LS illumination achieves an over 4X improvement in the signal-to-background ratio compared with conventional widefield epi-illumination in both fixed and live cell samples. Furthermore, we show substantial resolution enhancement for single-molecule localization microscopy compared to epi-illumination for improved imaging at the nanoscale. The versatile and scalable design offers an easily implemented approach to bring the benefits of single-objective LS microscopy to a wide array of biological studies.

biophysics↗

Developmental determinants of male bias in medulloblastoma

Boys experience an overall increased incidence of several childhood cancers, including medulloblastoma, a clinically heterogeneous cerebellar tumor. In subtypes of Group 3 and Group 4 medulloblastoma, males are three times more prevalent than females. As medulloblastoma is suspected to initiate during fetal development, we hypothesized that this sex bias reflects a combination of prenatal, sex-specific developmental processes and somatic alterations. To test these hypotheses, we compiled a large multi-omics dataset from children with medulloblastoma, which revealed sex-specific alterations, including frequent loss of the inactive X chromosome in females with Group 4. Generation of a sex-matched single-cell transcriptome atlas of the developing murine cerebellum enabled investigation of putative developmental factors underlying sex bias. Progenitors giving rise to Group 3/4 subgroups were more abundant, more proliferative, and harbored more open chromatin for recruitment of LMX1A and OTX2, master transcription factors defining Group 3/4 identity. Advanced genetically engineered mouse models and human cerebellar organoids were leveraged to determine whether sexual dimorphism arises from intrinsic or extrinsic factors. These models showed that the XY genotype contributed to the phenotype, but the predominant effect was driven by presence of the male gonadal hormone testosterone. Our findings provide a sex-specific genetic and neurodevelopmental explanation for male bias in an aggressive pediatric brain tumor. Outcomes from this study may inform novel treatment strategies delivered according to sex and are likely to be broadly applicable to other sex-biased malignancies arising in early life. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=79 SRC="FIGDIR/small/714163v1_ufig1.gif" ALT="Figure 1"> View larger version (18K): org.highwire.dtl.DTLVardef@566e41org.highwire.dtl.DTLVardef@607ae9org.highwire.dtl.DTLVardef@25679aorg.highwire.dtl.DTLVardef@1b4beec_HPS_FORMAT_FIGEXP M_FIG C_FIG

developmental biology↗

How Not to be Seen: Predicting Unseen Enzyme Functions using Contrastive Learning

MotivationPredicting enzyme function from its sequence is still an unsolved problem in the life sciences. Moreover, with the explosion of annotated genome data, we are inundated with potential enzymatic sequences that have not yet been biochemically characterized. While it is not possible to assign a not-yet-existing label to such a sequence, there is high value in placing the sequence as accurately as possible in known function space. Doing so can help provide more accurate falsifiable hypotheses for experimentalists wishing to characterize enzymes from specific functional families. ResultsHere we present a contrastive learning algorithm for predicting enzyme function from sequence. Our method, EnzPlacer, predicts the third, second, and first EC numbers for a protein whose fourth EC number is not in the training corpus. This novel prediction mechanism accurately places a protein sequence within a narrowed-down functional context, even if the precise function remains unknown. AvailabilityEnzPlacer is available from https://github.com/drxiangma/EnzPlacer under a GPL3 license. Contactqli@iastate.edu

bioinformatics↗

A multi-omics atlas of human hindbrain development

The human hindbrain controls essential motor and autonomic functions and is the site of neurodevelopmental diseases. Yet, its cellular diversity, developmental trajectories and underlying regulatory logic remain poorly understood. We present a comprehensive multi-omics atlas of human hindbrain development spanning embryonic to adult stages, encompassing 594,817 transcriptomic and 422,568 chromatin-accessibility single-nucleus profiles. This dataset resolved the cellular architecture of hindbrain cellular lineages, and delineated coordinated gene expression, cis-regulatory programs and regulatory grammar guiding their developmental trajectories. By integrating multi-omics data, we discovered context-specific roles of transcription factors across cell types and deciphered the role of HOX genes in driving divergent cellular identity in related lineages. We further leveraged the atlas to contextualize pediatric gliomas to decode how subtle yet coordinated shifts in gene expression context can define oncogenic transformation. Together, this atlas provides a foundational resource for hindbrain biology and establishes a gene-regulatory framework linking development and disease.

neuroscience↗

Parkinsonism Reversal and Dopaminergic Resilience: Lessons from a Rotenone-induced Parkinson's Disease Model

Parkinsons disease (PD) is a progressive neurodegenerative disorder characterized by profound loss of dopaminergic (DA) neurons, yet the underlying mechanism remains incompletely defined. Mitochondrial toxins can induce acute degeneration of DA neurons and Parkinsonism-like phenotypes in animal models, and epidemiological studies have linked pesticide exposure to increased PD risk; however, the long-term effects of pesticide exposure remain elusive. Here, we examined both the acute and long-term effects of rotenone exposure in mice to understand PD onset, progression, and recovery. A 21-day regimen of rotenone intraperitoneal injections (2.5 mg/kg/day) induced robust Parkinsonism-like deficits by the 4th week, including impaired locomotion, increased anxiety-like behaviors, and deficits in motor balancing and coordination. These behavioral abnormalities were accompanied by pronounced reduction in tyrosine hydroxylase (TH) expression and selective loss of DA neurons in the substantia nigra pars compacta (SNc). Unexpectedly, these functional impairments fully resolved by 12 months, and rotenone-treated mice behaved equally well as age-matched controls. In parallel, the TH expression and DA neuron density in SNc were restored to control levels. Together, these longitudinal results demonstrate that chronic rotenone injection induces robust but reversible Parkinsonism in the acute phase, with limited long-term consequence on Parkinsonism upon toxin cessation. These findings contrast with the prevailing view that environmental pesticide exposure irreversibly drives PD and instead they reveal a substantial resilience and adaptive capacity of the nigrostriatal dopaminergic system in vivo. HighlightsO_LIChronic rotenone exposure in mice induces robust Parkinsonism-like behaviors in both motor and non-motor domains. C_LIO_LISNc dopaminergic neurons are reduced by [~]40% at the acute phase within 4 weeks. C_LIO_LIBoth motor and non-motor deficits are fully recovered by 12 months. C_LIO_LIPD-like pathological changes in the SNc are resolved by 12 months. C_LI Infographics O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=166 SRC="FIGDIR/small/695709v1_ufig1.gif" ALT="Figure 1"> View larger version (41K): org.highwire.dtl.DTLVardef@570654org.highwire.dtl.DTLVardef@160b285org.highwire.dtl.DTLVardef@16846c7org.highwire.dtl.DTLVardef@fec0df_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

NAD+ hydrolase Sarm1 is a key driver of synapse degeneration and memory loss in Alzheimer's disease

Synapse degeneration is a hallmark of neurodegenerative diseases1-3, including Parkinsons and Alzheimers disease (AD). Synapse loss has been known for decades as the strongest correlate with cognition and disease progression in AD patients4-8, but the molecular mechanisms that drive synapse degeneration remain elusive. Here, we identify Sarm1, a new class of NAD+ hydrolase required for Wallerian degeneration of periphery nerves after injuries9-12, as the key mediator of synaptic degeneration in AD brains. Sarm1 knockout largely reversed synapse loss, amyloid-{beta} (A{beta}) burden, and cognitive decline in 5XFAD mice. We found that Sarm1 is enriched in synaptic terminals and becomes activated in synaptic dystrophies adjacent to A{beta} plaques, leading to synapse degeneration and subsequent neuroinflammation. Sarm1 deletion in the AD mice prevented synaptic dystrophies and rescued short-term and long-term synaptic plasticity. Further, Sarm1 deletion protected synapses from C1q tagging and phagocytosis, and C1q-MERTK signaling in complement cascades 7,13-15 was significantly reduced. The reduced synapse degeneration, in turn, broke the feed-forward loop of "glia activation-neuroinflammation-A{beta} deposition". These data suggest that Sarm1 plays a key role in driving synapse degeneration in AD before C1q-tagging and phagocytic clearance, and targeting Sarm1 may offer a novel intervention to attenuate synapse degeneration and memory loss in AD. HighlightO_LISarm1 is enriched at presynaptic dystrophies and correlated with A{beta}. C_LIO_LIGenetic deletion of Sarm1 prevents synapse degeneration in AD. C_LIO_LISarm1 depletion is sufficient to reverse synaptic dysfunction and memory loss. C_LIO_LISarm1 depletion reduces A{beta} burden and neuroinflammation C_LIO_LIC1q--MERTK axis acts downstream of synaptic Sarm1 activation. C_LI O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=121 SRC="FIGDIR/small/695860v1_ufig1.gif" ALT="Figure 1"> View larger version (27K): org.highwire.dtl.DTLVardef@bd6b12org.highwire.dtl.DTLVardef@1c089e5org.highwire.dtl.DTLVardef@19d35fborg.highwire.dtl.DTLVardef@431364_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

Aberrant splicing of MBD1 reshapes the epigenome to drive convergent myeloerythroid defects in MDS

Myelodysplastic neoplasms (MDS) feature hematopoietic deficits driven in part by transcript splicing abnormalities. Thus far, such disease-driving transcripts have been identified in association with specific splicing factor mutations. However, it remains unclear whether there also exists a set of disease-wide conserved pathological transcripts, which drive MDS independently of mutational status. Here, we characterize an MDS-associated long isoform of MBD1 (MBD1-L) as the first described member of this class of transcripts. Overexpression of MBD1-L in healthy human HSPCs recapitulates archetypal defects of MDS including deficits in erythroid differentiation and reconstitution capacity. These defects arise from an isoform-specific switching of MBD1s binding behavior, refocusing its heterochromatin-promoting activity from methylated to unmethylated CpGs and enacting broad downregulation of CpG-rich promoters as well as secondary epigenetic effects mediated by its downstream target BCOR. Remarkably, we also find that directly reversing abnormal MBD1 splicing in primary human MDS using nanoparticle-encapsulated ASOs enhances erythroid differentiation. Key pointsO_LIGlobal mis-splicing of MBD1 represents a novel gain-of-function epigenetic axis driving erythropoietic and proliferative defects in MDS. C_LIO_LIASO based depletion of pathogenic MBD1 transcripts restores erythroid differentiation, advancing RNA-based therapies for MDS. C_LI

cancer biology↗

Calcium chelation promotes microtubule regrowth and axonal recovery after laser-induced axonal injury

Traumatic stretch or crush injury to axons causes widespread and often irreversible damage to the axonal cytoskeleton, in which calcium-mediated breakdown is known to play a central role. Unlike complete transection, where recovery must proceed through formation of a new growth cone, milder injury can disrupt the axonal cytoskeleton while leaving the plasma membrane intact. How the cytoskeleton fails, and how it can recover, under these conditions remains unclear. Here we address this using a partial laser-ablation method that damages the cytoskeleton and evokes a calcium transient while preserving membrane continuity. We show that the ensuing cytoskeletal retraction is set by a mechanical balance between acto-myosin contractility and microtubule stability: stabilizing microtubules or inhibiting acto-myosin contractility suppresses retraction. Moreover, chelating extracellular calcium mitigates degeneration and, in a subset of axons, permits complete recovery. We also show that microtubules and actin filaments show distinct loss and recovery dynamics and provide a hypothesis for the "burning-fuse" -like depolymerization of the microtubule bundle. These findings provide insights into how the axonal cytoskeleton collapses and recovers after injury and suggest strategies for mitigating damage.

neuroscience↗

Single-objective lattice light sheet microscopy with microfluidics for single-molecule super-resolution imaging of mammalian cells

Single-molecule localization microscopy (SMLM) has redefined optical imaging by enabling imaging beyond the diffraction limit, allowing nanoscale investigation into cellular architecture and molecular dynamics. Light sheet illumination enhances SMLM through optical sectioning of the sample, which drastically improves the signal-to-background ratio and reduces photobleaching and photodamage. Lattice light sheet (LLS) microscopy, in which a 2D optical lattice is implemented for light sheet illumination, can provide exceptional sectioning and extended imaging depth when imaging in scattering samples. However, its conventional dual-objective design poses challenges for certain applications. Here, we present an imaging platform which implements LLS illumination with a reflective single-objective geometry (soLLS) inside a microfluidic chip, enabling the use of a single high numerical aperture objective for both illumination and detection, mitigating constraints of a dual-objective setup. We provide quantitative characterization of the propagation properties of the soLLS and demonstrate that it outperforms conventional Gaussian light sheets in terms of useful field of view and sectioning when propagating through scattering samples. Next, by combining soLLS with point spread function engineering, we demonstrate the platform for improved 3D single-molecule super-resolution imaging of multiple targets across multiple cells. The soLLS imaging platform thus expands investigations of nanoscale cellular and intercellular structures and mechanisms into more challenging samples for a wide range of applications in biology and biomedicine.

biophysics↗

Understudied and underprotected: biodiversity and conservation challenges in the Konkan region of Maharashtra

In biodiversity hotspots, such as the Western Ghats, periodic synthesis of existing ecological research can help identify knowledge gaps and address critical threats to biodiversity. The Maharashtra part of the Konkan region, situated between the Sahyadri foothills and the west coast, with diverse tropical vegetation, harbours unique open ecosystems, such as lateritic plateaus, and supports a multitude of threatened species, including hornbills and tigers. However, the region remains relatively understudied and has not received adequate protection through state or national conservation policies and laws. The area is undergoing rapid human-driven land-use change. These activities can impact the regions biodiversity, necessitating an effort to identify knowledge gaps and critical threats. Through a combination of a literature review and focus group discussions with 44 participants from various institutions and non-governmental organisations, we synthesised existing published information on the Konkan region of Maharashtra and identified key research gaps and conservation challenges. Our review of 138 studies found that while agroforestry and human-wildlife interactions have received some research attention, the effects of climate change on the regions biodiversity remain poorly understood. Focus group discussions highlighted major threats, including land-use changes due to expanding monoculture plantations, clear-felling of forests, forest fires, environmental pollution, and rapid infrastructure development, which are leading to habitat loss and fragmentation. Some of these concerns were validated by publicly available regional data, which revealed a 30% increase in roads, a 14% expansion of cashew plantations, and associated forest loss. This synthesis offers valuable insights for government and non-governmental organisations to inform future research and conservation efforts in the region.

ecology↗

Repurposing Quetiapine as an Adjuvant Therapeutic Agent for Triple-Negative Breast Cancer

PurposeTriple-negative breast cancer (TNBC) lacks actionable molecular targets, so treatment primarily relies on cytotoxic chemotherapy and radiotherapy, yet relapse, resistance, and metastasis still drives poor long-term survival. Dopamine signaling has recently been linked to tumor aggressiveness, and dopaminel1lreceptor antagonists have shown preclinical benefit in other cancers. We therefore evaluated quetiapine (QTP), an FDAl1lapproved DRD2/DRD3 antagonist, as a therapeutic adjunct in TNBC. MethodsSUM159l1lPT, BTl1l549, and MDAl1lMBl1l231 cells were treated with QTP alone or combined with radiation or standard agents (doxorubicin, paclitaxel, 5l1lfluorouracil). Clonogenic and mammosphere assays measured proliferative and selfl1lrenewal potential. Annexin V/propidiuml1liodide flow cytometry quantified apoptosis, and {gamma}l1lH2AX immunofluorescence tracked DNA doublel1lstrand breaks and repair kinetics. Transwell assays assessed migration of untreated bulk cells and radiationl1lsurviving subclones. ResultsQTP significantly reduced clonogenicity and self-renewal in all TNBC models tested, both alone and in combination with radiation or chemotherapy. In apoptosis assays, QTP treatment induced a marked increase in early and late apoptotic cell populations. QTP also promoted DNA double-strand break formation and delayed repair, as indicated by persistent {gamma}-H2AX foci at 24 hours post-treatment. Additionally, QTP impaired the migratory capacity of both untreated and radiation-surviving cells. Combination treatments with QTP and doxorubicin produced synergistic effects, resulting in complete loss of colony-forming ability and mammosphere formation. ConclusionThe data presented support the repurposing of quetiapine as an adjuvant therapeutic agent alongside radiotherapy and/or chemotherapy in TNBC. By targeting apoptosis, DNA repair, and cancer cell migration, QTP offers a novel, multi-faceted approach to improve outcomes in this high-risk breast cancer subtype.

cancer biology↗

The evolution of gene regulation in mammalian cerebellum development

Gene regulatory changes are considered major drivers of evolutionary innovations, including the cerebellums expansion during human evolution, yet they remain largely unexplored. In this study, we combined single-nucleus measurements of gene expression and chromatin accessibility from six mammals (human, bonobo, macaque, marmoset, mouse, and opossum) to uncover conserved and diverged regulatory networks in cerebellum development. We identified core regulators of cell identity and developed sequence-based models that revealed conserved regulatory codes. By predicting chromatin accessibility across 240 mammalian species, we reconstructed the evolutionary histories of human cis-regulatory elements, identifying sets associated with positive selection and gene expression changes, including the recent gain of THRB expression in cerebellar progenitor cells. Collectively, our work reveals the shared and mammalian lineage-specific regulatory programs governing cerebellum development.

evolutionary biology↗

Receptor tyrosine kinase AXL regulates Golgi organization and function through an adhesion-Arf1 signaling axis in breast and lung cancers

Cell-matrix adhesion regulates membrane trafficking, Golgi organisation and function. Differential Golgi organisation in cancer cells could drive changes in trafficking and processing of cargoes. A simple screen evaluating Golgi organisation identifies breast (MDAMB231 vs MCF7) and lung cancer (A549 vs CaLu1) cell line pairs with differently organised Golgi, regulated differentially by loss of adhesion. In silico analysis of differentially expressed genes in the CCLE database, evaluated for their association with the Golgi in interaction networks and literature, identified AXL as a putative regulator of Golgi in these cancers. AXL prominently localized at the Golgi, undergoes displacement from the Golgi when inhibited by R428 and knocked down using siRNA, causing the Golgi to disorganize. AXL-dependent regulation of Golgi organisation is also dependent on cell-matrix adhesion. AXL binds active Arf1, whose recruitment to the Golgi is vital for its organisation. On loss of adhesion, loss of AXL and active Arf1 from the Golgi, drives its disorganization to affect Golgi-dependent microtubule acetylation and cell surface glycosylation in MDAMB231 and A549 cells respectively. Together, this validates our screen to identify novel regulators of the Golgi, and identifies AXL-Arf1 crosstalk as a vital mediator of its organisation and function in cancer cells.

cell biology↗