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A Human Brain Map of Mitochondrial Respiratory Capacity and Diversity

Mitochondrial oxidative phosphorylation (OxPhos) powers brain activity1,2, and mitochondrial defects are linked to neurodegenerative and neuropsychiatric disorders3,4, underscoring the need to define the brains molecular energetic landscape5-10. To bridge the cognitive neuroscience and cell biology scale gap, we developed a physical voxelization approach to partition a frozen human coronal hemisphere section into 703 voxels comparable to neuroimaging resolution (3x3x3 mm). In each cortical and subcortical brain voxel, we profiled mitochondrial phenotypes including OxPhos enzyme activities, mitochondrial DNA and volume density, and mitochondria-specific respiratory capacity. We show that the human brain contains a diversity of mitochondrial phenotypes driven by both topology and cell types. Compared to white matter, grey matter contains >50% more mitochondria. We show that the more abundant grey matter mitochondria also are biochemically optimized for energy transformation, particularly among recently evolved cortical brain regions. Scaling these data to the whole brain, we created a backward linear regression model integrating several neuroimaging modalities11, thereby generating a brain-wide map of mitochondrial distribution and specialization that predicts mitochondrial characteristics in an independent brain region of the same donor brain. This new approach and the resulting MitoBrainMap of mitochondrial phenotypes provide a foundation for exploring the molecular energetic landscape that enables normal brain functions, relating it to neuroimaging data, and defining the subcellular basis for regionalized brain processes relevant to neuropsychiatric and neurodegenerative disorders.

neuroscience↗

Pancreatic tumor organoids for modeling in vivo drug response and discovering clinically-actionable biomarkers

Patient-derived models are transforming translational cancer research. It is not clear if the emergence of patient-derived organoid (PDO) models can extend the utility of the widely used patient-derived xenograft (PDX). In addition, the utility of PDO models for serum biomarker discovery is not known. Here, we demonstrate that PDO models recapitulate the genomics, cell biology, glycomics and drug responses observed in PDX models. Furthermore, we demonstrate the applicability of PDO models for identification of N-glycans that are enriched in the glycome of pancreatic ductal adenocarcinoma (PDAC). Surprisingly, among all the glycans observed in PDX and PDOs, a core set of 57 N-glycans represent 50-94% of the relative abundance of all N-glycans detected, suggesting that only a subset of glycans dominate the cell surface landscape in PDAC. In addition, we outline a tumor organoid-based pipeline to identify surface proteins in extracellular vesicles (EV) from media supernatant of PDO cultures. When combined with the affinity-based validation platform, the EV surface proteins discovered in PDOs are effective in differentiating patients with PDAC from those with benign pancreatitis in the clinic, identifying PDO as powerful discovery platform for serum biomarkers. Thus, PDOs extend the utility of the archival collections of PDX models for translational research and function as a powerful platform for identification of clinically-actionable biomarkers in patients blood. Significance statementTumor organoids extend the utility of PDX models as platforms for investigating drug response, glycosylation changes and function as new platforms for discovering blood-based biomarkers

cancer biology↗

High-Affinity, Structure-Validated and Selective Macrocyclic Peptide Tools for Chemical Biology Studies of Huntingtin

Huntingtons disease (HD) is a fatal neurodegenerative disorder caused by a CAG repeat expansion in the Huntingtin (HTT) gene, with no disease-modifying therapies currently available. The precise molecular function of the HTT protein is unclear, and the lack of selective chemical tools has limited functional studies. We have identified and characterized macrocyclic peptide binders targeting HTT. These binders exhibit low-nanomolar affinity in vitro and engage distinct HTT and HTT-HAP40 interfaces, as revealed by hydrogen-deuterium exchange mass spectrometry and cryo-electron microscopy. Chemoproteomics confirmed selective binding in cell extracts from wildtype but not HTT-null cell lines. HAP40 consistently and stoichiometrically co-purified with HTT across cell lines, including with HTT variants containing different CAG repeat lengths, highlighting the broad presence of the HTT-HAP40 complex. Significance StatementHuntingtin (HTT) is a large, essential protein with conserved roles in development, intracellular trafficking, and protein homeostasis, yet its precise molecular functions remain incompletely defined. Here, we report the first high-affinity, selective, and structurally validated macrocyclic peptide ligands for HTT. These chemical tools bind HTT and its complex with HAP40 across polyglutamine repeat lengths, enabling direct interrogation of HTT structure and function in health and disease contexts. By overcoming longstanding barriers to studying HTT at the molecular level, these ligands open new avenues for discovery in neurobiology, cell biology, and offer opportunities for therapeutic development. This study delivers urgently needed tools to both the Huntingtons disease field and the broader scientific community seeking to understand this elusive and biologically fundamental protein.

biochemistry↗

The AGC protein kinase UNICORN controls planar growth by attenuating PDK1 in Arabidopsis thaliana

Tissue morphogenesis critically depends on the coordination of cellular growth patterns. In plants, many organs consist of clonally distinct cell layers, such as the epidermis, whose cells undergo divisions that are oriented along the plane of the layer. The developmental control of such planar growth is poorly understood. We have previously identified the Arabidopsis AGCVIII-class protein kinase UNICORN (UCN) as a central regulator of this process. Plants lacking UCN activity show spontaneous formation of ectopic multicellular protrusions in integuments and malformed petals indicating that UCN suppresses uncontrolled growth in those tissues. In the current model UCN regulates planar growth of integuments in part by directly repressing the putative transcription factor ABERRANT TESTA SHAPE (ATS). Here we report on the identification of 3-PHOSPHOINOSITIDE-DEPENDENT PROTEIN KINASE 1 (PDK1) as a novel factor involved in UCN-mediated growth control. PDK1 constitutes a basic component of signaling mediated by AGC protein kinases throughout eukaryotes. Arabidopsis PDK1 is implied in stress responses and growth promotion. Here we show that loss-of-function mutations in PDK1 suppress aberrant growth in integuments and petals of ucn mutants. Additional genetic, in vitro, and cell biological data support the view that UCN functions by repressing PDK1. Furthermore, our data indicate that PDK1 is indirectly required for deregulated growth caused by ATS overexpression. Our findings support a model proposing that UCN suppresses ectopic growth in integuments through two independent processes: the attenuation of the protein kinase PDK1 in the cytoplasm and the repression of the transcription factor ATS in the nucleus.\n\nAuthor SummaryPlant organs, such as petals or roots, are composites of distinct cell layers. As a rule, cells making up a layer, for example the epidermis, the outermost layer of a tissue, divide \"within the plane\" of the layer. This cellular behavior results in the two-dimensional sheet-like or planar growth of the cell layer. The mechanism orchestrating such a growth pattern is poorly understood. In particular, it is unclear how uncontrolled and \"out-of-plane\" growth is avoided. Here we provide insight into this process. Our data indicate that higher than normal activity of a central regulator of growth and stress responses results in wavy and malformed petals and in protrusion-like aberrant outgrowths in the tissue that will develop into the seed coat. It is therefore important to keep this factor in check to allow proper formation of those tissues. We further show that a protein called UNICORN attenuates the activity of this regulator thereby ensuring the sheet-like growth of young petals or the developing seed coat.

plant biology↗

Reconstructing and Analysing The Genome of The Last Eukaryote Common Ancestor to Better Understand the Transition from FECA to LECA.

It is still a matter of debate whether the First Eukaryote Common Ancestor (FECA) arose from the merger of an archaeal host with an alphaproteobacterium, or was a proto-eukaryote with significant eukaryotic characteristics way before endosymbiosis occurred. The Last Eukaryote Common Ancestor (LECA) as its descendant is thought to be an entity that possessed functional and cellular complexity comparable to modern organisms. The precise nature and physiology of both of these organisms has been a long-standing, unanswered question in evolutionary and cell biology. Recently, a much broader diversity of eukaryotic genomes has become available and this means we can reconstruct early eukaryote evolution with a greater deal of precision. Here, we reconstruct a hypothetical genome for LECA from modern eukaryote genomes. The constituent genes were mapped onto 454 pathways from the KEGG database covering cellular, genetic, and metabolic processes across six model species to provide functional insights into its capabilities. We reconstruct a LECA that was a facultatively anaerobic, single-celled organism, similar to a modern Protist possessing complex predatory and sexual behaviour. We go on to examine how much of these capabilities arose along the FECA-to-LECA transition period. We see a at least 1,554 genes gained by FECA during this evolutionary period with extensive remodelling of pathways relating to lipid metabolism, cellular processes, genetic information processing, protein processing, and signalling. We extracted the BRITE classifications for the genes from the KEGG database, which arose during the transition from FECA-to-LECA and examine the types of genes that saw the most gains and what novel classifications were introduced. Two-thirds of our reconstructed LECA genome appears to be prokaryote in origin and the remaining third consists of genes with functional classifications that originate from prokaryote homologs in our LECA genome. Signal transduction and Post Translational Modification elements stand out as the primary novel classes of genes developed during this period. These results suggest that largely the eukaryote common ancestors achieved the defining characteristics of modern eukaryotes by primarily expanding on prokaryote biology and gene families.

evolutionary biology↗

GenePert: Leveraging GenePT Embeddings for Gene Perturbation Prediction

Predicting how perturbation of a target gene affects the expression of other genes is a critical component of understanding cell biology. This is a challenging prediction problem as the model must capture complex gene-gene relationships and the output is high-dimensional and sparse. To address this challenge, we present GenePert, a simple approach that leverages GenePT embeddings, which are derived using ChatGPT from text descriptions of individual genes, to predict gene expression changes due to perturbations via regularized regression models. Benchmarked on eight CRISPR perturbation screen datasets across multiple cell types and five different pretrained gene embedding models, GenePert consistently outperforms all the state-of-the-art prediction models measured in both Pearson correlation and mean squared error metrics. Even with limited training data, our model generalizes effectively, offering a scalable solution for predicting perturbation outcomes. These findings underscore the power of informative gene embeddings in predicting the outcomes of unseen genetic perturbation experiments in silico. GenePert is available at https://github.com/zou-group/GenePert.

bioinformatics↗

Oviduct epithelial cells constitute two developmentally distinct lineages that are spatially separated along the distal-proximal axis

Owing to technical advances in single cell biology, the appreciation of cellular heterogeneity has increased, which has aided our understanding of organ function, homeostasis and disease progression. The oviduct (also known as the fallopian tube in humans) is the distal-most portion of the female reproductive tract. It is essential for reproduction and the proposed origin of high grade serous ovarian carcinoma (HGSOC). In mammals, the oviduct is morphologically segmented along the ovary-uterus axis into four evolutionally conserved regions. It is unknown however if there is a diversification of epithelial cell characteristics between these regions. In this study, we identified transcriptionally distinct populations of secretory and multiciliated cells restricted to the distal and proximal regions of the oviduct. We demonstrated that these distal and proximal populations are distinct lineages specified early in Mullerian duct development and are maintained separately. These results aid our understanding of epithelial development, homeostasis and initiation of disease from the oviduct.

developmental biology↗

The Spirogyra genome: signatures of shared and divergent division and differentiation

Zygnematophytes emerged as the unexpected closest algal relatives of land plants despite their simple body plans, raising questions about the morphogenetic toolkit present in the last common ancestor of land plants and algae. Genomic analyses have revealed that zygnematophytes are cellular giants, sharing homologous frameworks for several phytohormones, secondary metabolites, and key morphogenetic and transcriptional regulatory processes. Zygnematophytes fall into five orders, each of which has charted its own evolutionary path. Here, we have sequenced a contiguous genome of Spirogyra pratensis, the eponymous representative of Spirogyrales and a classical model system for evolutionary cell biology in the green lineage. Building on this genome, we transcriptionally profiled the tractable life cycle of Spirogyra and its responses to a bifactorial gradient of light and temperature. Our data highlight the activation of quiescence and homeostatic programs. Yet what stands out most in Spirogyra is its spiral chloroplast--undulating intracellularly and abscising during mixed phragmoplast formation and furrowing. Leveraging the genome in tandem with co-expression network analyses, we describe the molecular underpinnings of the unique cytokinetic processes that govern both cell and plastid division. We find that Spirogyra deploys a molecular program characteristic of Phragmoplastophyta, yet lacks the deeply conserved plastid division machinery found in other archaeplastid plastids.

plant biology↗

McaA and McaB control the dynamic positioning of a bacterial magnetic organelle

Magnetotactic bacteria (MTB) are a diverse group of microorganisms that use intracellular chains of ferrimagnetic nanocrystals, produced within their magnetosome organelles, to align and navigate along the geomagnetic field. The cell biological and biochemical properties of magnetosomes make them a powerful model for studying the molecular mechanisms of biomineralization and compartmentalization in bacteria. While several conserved magnetosome formation genes have been described, the evolutionary strategies for their species-specific diversification remain unknown. Here, we demonstrate that the fragmented nature of magnetosome chains in Magnetospirillum magneticum AMB-1 is controlled by two genes named mcaA and mcaB. McaA recognizes the positive curvature of the inner cell membrane while McaB localises to magnetosomes. Along with the MamK actin-like cytoskeleton, they create space for addition of new magnetosomes in between pre-existing magnetosomes. Phylogenetic analyses suggest that McaAB homologs are widespread and may represent an ancient strategy for organelle positioning in MTB.

microbiology↗

Tumor suppressor miR-317 and lncRNA Peony are expressed from a polycistronic non-coding RNA locus that regulates germline differentiation and testis morphology

The impact of non-coding RNAs on stem cell biology and differentiation processes is an important and incompletely understood area of research. Using the testes of Drosophila melanogaster as a valuable system for investigating these processes, we identified a polycistronic locus from which two non-coding transcripts, miR-317 and the long non-coding RNA (lncRNA) Peony, are produced, with alternative polyadenylation implicated in regulation of their differential expression levels. We report here that each transcript has a distinct role in Drosophila testes; the increased expression of Peony results in the disruption of the muscle sheath covering the testis, and the absence of miR-317 leads to the emergence of germ-cell tumors in developing flies. The deficiency of miR-317 increases Notch signaling activity in somatic cyst cells, upregulates multiple predicted targets of miR-317, and drives germline tumorigenesis. Our findings establish miR-317 as a tumor suppressor controlling Notch signaling strength and uncover alternative polyadenylation as an unrecognized mechanism governing miRNA expression.

molecular biology↗

Zebrafish Drug Screening Identifies Erlotinib as an Inhibitor of Wnt/β-Catenin Signaling and Self-Renewal in T-cell Acute Lymphoblastic Leukemia

The Wnt/{beta}-catenin pathways significance in cancer initiation, progression, and stem cell biology underscores its therapeutic potential, yet clinical application of Wnt inhibitors remains limited due to challenges posed by off-target effects and complex crosstalk with other pathways. In this study, we leveraged the zebrafish model to perform a robust and rapid drug screening of 773 FDA-approved compounds to identify Wnt/{beta}-catenin inhibitors with minimal toxicity. Utilizing zebrafish expressing a Wnt reporter, we identified several drugs that suppressed Wnt signaling without compromising zebrafish development. The efficacy of the top hit, Erlotinib, extended to human cells, where it blocked Wnt/{beta}-catenin signaling downstream of the destruction complex. Notably, Erlotinib treatment reduced self-renewal in human T-cell Acute Lymphoblastic Leukemia cells, which are known to rely on active {beta}-catenin signaling for maintenance of leukemia-initiating cells. Erlotinib also reduced leukemia-initiating cell frequency and delayed disease formation in zebrafish models. This study underscores zebrafishs translational potential in drug discovery and repurposing, and highlights a new use for Erlotinib as a Wnt inhibitor for cancers driven by aberrant Wnt/{beta}-catenin signaling. HighlightsO_LIZebrafish-based drug screening offers an inexpensive and robust platform for identifying compounds with high efficacy and low toxicity in vivo. C_LIO_LIErlotinib, an Epidermal Growth Factor Receptor (EGFR) inhibitor, emerged as a potent and promising Wnt inhibitor with effects in both zebrafish and human cell-based Wnt reporter assays. C_LIO_LIThe identification of Erlotinib as a Wnt inhibitor underscores the value of repurposed drugs in developing targeted therapies to disrupt cancer stemness and improve clinical outcomes C_LI Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=42 SRC="FIGDIR/small/555200v1_ufig1.gif" ALT="Figure 1"> View larger version (14K): org.highwire.dtl.DTLVardef@150e0a0org.highwire.dtl.DTLVardef@cb3455org.highwire.dtl.DTLVardef@d8d8a8org.highwire.dtl.DTLVardef@780535_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

Venom vesicles from the parasitoid Ganaspis hookeri facilitate venom protein entry into host immune cells

The parasitoid wasp Ganaspis hookeri infects Drosophila melanogaster larvae, laying an egg and injecting venom directly into the host body cavity. While infected hosts mount an immune response in an attempt to eliminate the parasitoid egg, parasitoid venom proteins act to inhibit these host immune responses and manipulate host physiology to ensure infection success. A key immune suppressive venom protein in G. hookeri is a venom- specific isoform of the SERCA (Sarco/endoplasmic reticulum Ca2+-ATPase) calcium pump. However, SERCA is a large hydrophobic protein, and the mechanism by which it and other venom proteins are transported into the host is not well understood. We used a variety of biophysical, biochemical, and cell biological approaches to assess the properties of G. hookeri venom. Electronic microscopy and nanoparticle tracking analysis revealed the presence of venom vesicles as a putative transport mechanism. We used tunable resistive pulse sensing (TRPS) to biophysically characterize these vesicles, and our TRPS data suggest G. hookeri venom is composed of multiple vesicle types that are distinguishable by size, zeta potential, and density. Finally, we fluorescently labeled venom vesicles to test for entry into host immune cells. We observed that these vesicles interact with immune cells membranes and are internalized into the cell. Our data support a model in which G. hookeri venom proteins, including SERCA, are packaged into an array of venom vesicles, and transported into host cells for immune suppression.

biochemistry↗

Disruption of natural killer cell homing as a biomarker in persons aging with or without HIV

Natural killer (NK) cells are critical modulators of HIV transmission and disease. While recent evidence suggests a loss of NK cell cytotoxicity during aging, a compound analysis of NK cell biology and aging in persons with HIV (PWH) is lacking. We set out to perform one of the first large comprehensive analyses of people aging with and without HIV to determine NK phenotypic changes during aging and how these changes are modulated while aging with HIV. Utilizing high-dimensional polychromatic flow cytometry we analyzed 30 immune-related proteins spanning broad functions such as trafficking, activation/inhibition, NK specific receptors, and memory/checkpoint receptors on peripheral NK cells from health donors, PWH with viral suppression, and viremic PWH. NK cell phenotypes are dynamic across the age span but are significantly altered in HIV and ART and with co-factors such as CMV. Specifically, NK cells in healthy aging show increasing levels of 4{beta}7 and decreasing CCR7 expression during aging, a phenomenon nearly perfectly reversed in PWH. These HIV-associated trafficking changes could be in part due to NK cell recruitment to HIV reservoir formation in lymphoid tissue or failed mucosal signaling in the HIV-infected gut, but regardless appear to be tight biomarkers of age-related NK cell changes.

immunology↗

Volume and surface methods for microparticle traction force microscopy: a computational and experimental comparison

It is an essential element of mechanobiology to measure the forces of biological cells. In microparticle traction force microscopy, they are inferred from the deformation of elastic microparticles. Two complementary variants have been introduced before: the volume method, which reconstructs surface stresses from the displacements of fiducial markers embedded inside the particles, and the surface method, which infers stresses directly from the deformation of the particle surface. However, a systematic comparison of the two methods has been lacking. Here, we quantitatively compare both approaches using simulated traction fields representing biologically relevant loading scenarios. We find that the surface method consistently reconstructs traction profiles with substantially lower errors than the volume method, which suffers from displacement tracking and stress calculation at the surface. At high noise levels, however, the performance gap becomes smaller. To compare the performance of the two methods in a realistic experimental setting, we developed DNA-based hydrogel microparticles equipped with both fluorescent surface labels and embedded fluorescent nanoparticles, enabling the direct comparison of the two methods within the same system. Compression experiments produced traction profiles consistent with Hertzian contact mechanics and confirmed the trends observed in the simulations. We also show that despite large experimental deformations and strains (both up to 20 percent), linear elasticity theory should still be valid. While our computational workflow establishes a framework to apply both methods, our experimental workflow establishes DNA microparticles as versatile and biocompatible probes for measuring cellular forces.

biophysics↗

A fast and robust gene knockout method for Salpingoeca rosetta clarifies the genetics of choanoflagellate multicellular development

As the closest living relatives of animals, choanoflagellates offer crucial insights into the evolutionary origin of animals. Notably, certain choanoflagellate species engage in facultative multicellular development that resembles the early stages of embryogenesis. In the past few years, Salpingoeca rosetta has emerged as a tractable model for choanoflagellate cell biology and multicellular development, in particular through mutant screens and CRISPR/Cas9-mediated gene knockout (KO). However, existing KO pipelines have variable and sometimes low efficiency, frequently requiring isolation and genotyping of hundreds of clones without guarantee to obtain a KO strain. Here, we present a robust method for gene inactivation in S. rosetta that relies on insertion by CRISPR/Cas9 of a single 1.9 kb cassette encoding both a premature termination sequence and an antibiotic resistance gene. We show that this approach allows robust, fast and efficient isolation of KO clones after antibiotic selection. As a proof of principle, we first knocked out all three genes previously reported to regulate S. rosetta multicellular development in a published mutant screen (rosetteless, couscous and jumble), and confirmed that all three KOs abolished multicellular development. To showcase the potential of this method for de novo characterization of candidate developmental genes, we then inactivated three homologs of genes in the Hippo pathway: hippo, warts and yorkie, which together control cell proliferation and multicellular size in animals. Interestingly, warts KO rosettes were consistently about twice as large as their wild-type counterparts, showing our KO pipeline can reveal novel loss-of-function phenotypes of biological interest. Thus, this method has the potential to accelerate choanoflagellate functional genetics.

evolutionary biology↗

Amino Acid and Glucose Fermentation Maintain ATP Content in Mouse and Human Malignant Glioma Cells

Energy is necessary for tumor cell viability and growth. Aerobic glucose-driven lactic acid fermentation is a common metabolic phenotype seen in most cancers including malignant gliomas. This metabolic phenotype is linked to abnormalities in mitochondrial structure and function. A luciferin-luciferase bioluminescence ATP assay was used to measure the influence of amino acids, glucose, and oxygen on ATP content and viability in mouse (VM-M3 and CT-2A) and human (U-87MG) glioma cells that differed in cell biology, genetic background, and species origin. Oxygen consumption was measured using the Resipher system. Extracellular lactate and succinate were measured as end products of the glycolysis and glutaminolysis pathways, respectively. The results showed that: 1) glutamine was a source of ATP content irrespective of oxygen. No other amino acid could replace glutamine in sustaining ATP content and viability; 2) ATP content persisted in the absence of glucose and under hypoxia, ruling out substantial contribution through either glycolysis or oxidative phosphorylation (OxPhos) under these conditions; 3) Mitochondrial complex IV inhibition showed that oxygen consumption was not an accurate measure for ATP production through OxPhos. The glutaminase inhibitor, 6-diazo-5-oxo-L-norleucine (DON), reduced ATP content and succinate export in cells grown in glutamine. The data suggests that mitochondrial substrate level phosphorylation in the glutamine-driven glutaminolysis pathway contributes to ATP content in these glioma cells. A new model is presented highlighting the synergistic interaction between the high-throughput glycolysis and glutaminolysis pathways that drive malignant glioma growth and maintain ATP content through the aerobic fermentation of both glucose and glutamine. Summary statementMalignant gliomas, regardless of cell of origin or species, rely on fermentation mechanisms for ATP production due to OxPhos insufficiency. Glucose and glutamine together are necessary and sufficient for dysregulated tumor cell growth, whereas OxPhos is neither necessary nor sufficient.

cancer biology↗

TRPM7-dependent electrical signals drive phagocytic clearance for effective anti-fungal defense

Sentinel phagocytes of the innate immune system have a critical role in detecting and eliminating fungal pathogens. We used patch clamp electrophysiology to explore the electrical signals elicited when macrophages engulf Candida albicans. In the perforated patch configuration, which is least disruptive to intracellular signaling, we detected a composite outwardly rectifying current during the engulfment of C. albicans or zymosan. FTY720, a known inhibitor of ion channel TRPM7, suppressed the current. We then tested the hypothesis that TRPM7 regulates the engulfment and clearance of C. albicans. We found that Trpm7-/- macrophages are highly deficient in the engulfment of C. albicans. Trpm7-/- macrophages initiate phagocytosis of yeast but are defective in sealing the phagocytic cups. While the precise mechanism through which TRPM7 regulates phagosome sealing is not clear, we tested the immunological significance of this discovery using a mouse model of systemic candidiasis. We show that in mice, wherein TRPM7 is deleted selectively in the myeloid cells, infection by C. albicans results in significantly higher lethality, increased colonization of vital organs and increased inflammatory cytokines in the blood. Our study establishes TRPM7 as an ion channel critical for the innate immune responses against fungal pathogens and sets the stage for cell biological studies that define the mechanisms through which TRPM7 regulates phagosome sealing. Significance statementThe worldwide increase in deadly or persistent fungal infections has prompted the research for alternative ways of treatment. We applied the specialized, perforated patch clamp technique to track and identify electrical currents elicited during the detection and engulfment of fungi by macrophages. The ion channel TRPM7 emerged as an important determinant of anti-fungal host defense as its deletion in the murine myeloid cells made the host mice highly susceptible to lethal candidiasis. Ion channels are attractive drug targets whose activation and inhibition can be manipulated with pharmacological therapeutics. This study raises the possibility of enhancing fungal clearance using activators of TRPM7. Such pharmacological strategy may benefit patients of persistent fungal infections that are recalcitrant to anti-fungal drugs.

immunology↗

Robust virtual staining of landmark organelles

Correlative dynamic imaging of cellular landmarks, such as nuclei and nucleoli, cell membranes, nuclear envelope and lipid droplets is critical for systems cell biology and drug discovery, but challenging to achieve with molecular labels. Virtual staining of label-free images with deep neural networks is an emerging solution for correlative dynamic imaging. Multiplexed imaging of cellular landmarks from scattered light and subsequent demultiplexing with virtual staining leaves the light spectrum for imaging additional molecular reporters, photomanipulation, or other tasks. Current approaches for virtual staining of landmark organelles are fragile in the presence of nuisance variations in imaging, culture conditions, and cell types. We report training protocols for virtual staining of nuclei and membranes robust to variations in imaging parameters, cell states, and cell types. We describe a flexible and scalable convolutional architecture, UNeXt2, for supervised training and self-supervised pre-training. The strategies we report here enable robust virtual staining of nuclei and cell membranes in multiple cell types, including human cell lines, neuromasts of zebrafish and stem cell (iPSC)-derived neurons, across a range of imaging conditions. We assess the models by comparing the intensity, segmentations, and application-specific measurements obtained from virtually stained and experimentally stained nuclei and cell membranes. The models rescue missing labels, non-uniform expression of labels, and photobleaching. We share three pre-trained models (VSCyto3D, VSNeuromast, and VSCyto2D) and a PyTorch-based pipeline (VisCy) for training, inference, and deployment that leverages current community standards for image data and metadata.

bioinformatics↗