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Rao, R.

Publications and source records attributed to Rao, R..

At least 19 recordsLinked to original sources

Distinct Orbitofrontal Feedback Signals Shape Sensory Behavioral Strategies during Flexible Learning

Animals adapt their behavior by integrating sensory evidence with prior experience and contextual information. Understanding how animals employ specific behavioral strategies to integrate these variables and how neural mechanisms support such strategies remains unclear. We trained mice on a tactile reversal learning task and used a trial-by-trial computational model to infer latent decision strategies. Early in learning, mice relied on action-based ("choice-driven") policies but progressively transitioned to stimulus-guided choices ("cue-driven") as they learned the task. Following a rule reversal, mice flexibly reinstated this policy to adapt their behavior. Chemogenetic silencing of the lateral orbitofrontal cortex (lOFC) delayed this transition and impaired reversal learning. To identify the neural basis of strategy learning, we developed a novel approach combining low-dimensional analysis of neural activity with decoding of behavioral strategies from longitudinal two-photon imaging. We revealed reward- and error-strategy representations in excitatory layer 2/3 neurons in the primary somatosensory cortex (S1) that were differentially modulated by OFC instructive signals. Within S1, distinct subpopulations of positive and negative-valence-coding neurons tracked evolving decision strategies through trial-history integration. Together, these findings revealed how mice flexibly deploy distinct exploratory strategies during adaptive behavior, highlighting OFCs role in supporting reward and error-guided learning through distinct corticocortical interactions.

neuroscience↗

Myofibroblast- specific autophagy drives cyst growth in autosomal dominant polycystic kidney disease

BackgroundAutosomal dominant polycystic kidney disease (ADPKD) is characterized by progressive cyst expansion, fibrosis and inflammation, leading to kidney failure. Myofibroblasts (MFs) often accumulate around cysts and promote fibrosis and cyst growth, but the cellular mechanisms enabling their pro-cystogenic activity remain unclear. Here we examined the role of autophagy within MFs, on their paracrine stimulation of cyst expansion in ADPKD. MethodsAutophagy was assessed in human ADPKD nephrectomy tissue, primary human ADPKD renal myofibroblasts (ADPKD-MFs) and male RC/RC mouse model of ADPKD using immunostaining, LC3/p62 analyses, and transmission electron microscopy. Autophagy in MFs was inhibited pharmacologically in ADPKD-MFs, or by conditional Atg5 deletion in PDGFR{beta}-expressing renal stromal cells in RC/RC (RC/RC;Atg5KO) and wild type (WT;Atg5KO) mice. ResultsIn human and mouse ADPKD kidneys, we detected LC3 puncta and autophagic organelles within SMA-expressing MFs. Inhibition of autophagy in ADPKD-MFs blocked their paracrine stimulation of cyst epithelial cell proliferation in vitro. RC/RC;Atg5KO mice showed significantly reduced cystic growth, fibrosis, MF abundance, and improved kidney function. WT;Atg5KO mice showed no abnormalities in kidney structure or function. Targeted metabolomics performed on ADPKD cyst epithelial-cell conditioned media (ADPKD-ECs CM) revealed moderate increase in lactate levels compared to normal human kidney epithelial-cell conditioned media. Furthermore, lactate treatment stabilized hypoxia-inducible factor-1 (HIF1) in myofibroblasts, while pharmacological inhibition of HIF1 reduced the expression of autophagy-related genes and impaired autophagic flux. ConclusionThese findings reveal that autophagy in MFs is a previously unrecognized driver of cyst expansion and fibrosis in ADPKD. Lactate-mediated HIF1 stabilization in MFs promotes autophagy that is required for their paracrine stimulation of cyst epithelial growth. Targeting MF-specific autophagy or its upstream regulators may represent a therapeutic strategy to limit cyst growth and fibrosis in ADPKD.

molecular biology↗

Language Modeling Materializes a World Model of Protein Biology

Proteins are fundamental to life. The full extent of their biology is beyond our ability to characterize with experimental approaches in the physical laboratory. Accurate digital representations could accelerate the discovery of protein biology through virtual experiments. We propose language modeling to learn unified and general representations that can be scaled to all of protein biology. Building on these representations, we develop a structure prediction model that exceeds the performance of established methods for biomolecular complex prediction across benchmarks, including for the interactions of antibodies with their targets. A simple search procedure yields high experimental success rates for the discovery of proteins with nanomolar binding affinities for both miniproteins and single-chain antibodies, a modality critical for therapeutic design. Study of the concepts in the language models representation space reveals a systematic organization aligned with the reductionist understanding of proteins developed through empirical science. Leveraging this organization, we generate a comprehensive map of protein biology encompassing over 6.8 billion sequences and 1.1 billion predicted structures, identifying connections across known and unknown biology. As a whole, this shows language modeling as a powerful substrate for representing the biology of proteins, operating across scales from the prediction and design of protein interactions at the atomic level, to identifying properties of proteins at different levels of granularity and abstraction, to the scale of mapping connections between proteins across billions of years of evolution.

bioinformatics↗

Urban Environments Reshape Reproductive Phenology in Plants Across the Tropics

Plant phenological responses to global change phenomena like urbanization remain understudied in the tropics, hindering predictions regarding the dynamics of tropical ecosystems amid rapid land use changes. Studies of tropical phenology are limited by complexities, like the limited availability of phenological data, especially in urbanized landscapes. Observations recorded on citizen science platforms can overcome this limitation by providing vast, spatially distributed data. In this study, we utilize iNaturalist data to evaluate plant reproductive phenology in tropical urban vs. rural habitats. We first compare iNaturalist data (111533 records) to herbarium collections (217991 records) in order to validate their use, and we then investigate urban-rural phenology differences within 25-km spatial grids for 238 species. Data from iNaturalist and herbaria yield complementary insights, with the former being uniformly distributed between urban and rural settings, and the latter biased towards rural observations. On average, we found species to have significantly longer reproductive duration ({beta} = 11.79 {+/-} 2.83 SE, t = 4.16, p < 10^4), and correspondingly weaker strength of seasonality in urban settings than in nearby rural localities. We also find trait-mediated variation, with seasonal, annual, and herbaceous plants showing more pronounced differences in reproductive duration and seasonality strength. These results suggest that urbanization in tropical landscapes might have important implications for plant demography, with potential consequences for community and ecosystem dynamics. Our work also points to the value of integrating insights from natural history collections with data from citizen science platforms for enabling broad-scale insights into ecological dynamics in tropical urban landscapes.

ecology↗

Insulin-Regulated Actin Dynamics is Disrupted in a Human Keratinocyte Model of Hailey Hailey Disease

Hailey Hailey Disease (HHD) is an autosomal dominant cutaneous disorder caused by mutations in ATP2C1, the gene encoding the Golgi/secretory pathway Ca2+-ATPase SPCA1. Characterized by suprabasal acantholysis and intertriginous blistering of the skin, HHD treatment focuses on managing symptoms as there is no cure. Challenges to targeted therapy are due to the lack of facile and reliable models, both human and rodent, for mechanistic studies. Here we validate and characterize CRISPR/Cas9 mediated single and bi-allelic ATP2C1 knockouts in immortalized human hTERT keratinocytes. Whereas SPCA1 expression, Golgi morphology and Golgi Ca2+ accumulation were proportionately affected in heterozygous and homozygous ATP2C1 null mutants as expected, both single and double allelic mutants showed near complete loss of cadherins associated with desmosomal and adherens junctions. HHD is characterized by poor wound healing and impaired keratinocyte migration. We show that SPCA1 is required for dynamic reorganization of actin cytoskeleton in keratinocyte spreading. We identified an insulin activated PI3K-AKT-Rac1 signaling pathway required for lamellipodia formation and keratinocyte spreading, defective in SPCA1 mutants. Transgenic expression of hSPCA1 or treatment with CDN1163, a small molecule Ca2+-ATPase agonist, restored defective phenotypes in the HHD model, paving the way for future therapeutic approaches to treat this disorder.

cell biology↗

Androgens Drive SOX9 Upregulation in Injured Proximal Tubular Cells

IntroductionSex influences susceptibility, recovery, and long-term outcomes after acute kidney injury (AKI) in humans. Rodent models have been invaluable for elucidating AKI mechanisms; however, most studies have focused on males, assuming direct applicability to females, an assumption that remains largely untested. In males, the transcription factor SOX9 regulates injury-associated proximal tubule cell states, supporting survival during injury but also contributing to maladaptive repair. Given the well-described role of SOX9 in sex determination during development and its emerging importance in AKI, we investigated whether it mediates sex-specific tubular responses in the adult kidney. MethodsWe first optimized differential ischemic and cisplatin conditions in males and females to generate injury-matched models. We then used these models to ask whether proximal tubular cell responses, particularly Sox9 upregulation, are sex dependent. Tubule-specific knockout models of Sox9, Sox4, Sox11, Vgf, Zfp24, and the androgen receptor (Ar), along with gonadectomy and hormone replacement studies, combined with gene and protein analyses, were used to define regulatory networks. ResultsIn both ischemic and nephrotoxic AKI, SOX9 expression was markedly blunted in females, with levels more than fivefold lower than in males. While injury biomarkers such as NGAL and KIM1 were equally induced in both sexes, Sox9 and its downstream target Vgf showed markedly reduced induction in females, whereas the upstream regulator Zfp24 was functionally relevant only in males. Deletion of Sox9, Zfp24, or Vgf worsened injury in males but not in females. In contrast, Sox4 and Sox11 were equally upregulated and protective in both sexes. Castration or proximal tubule-specific deletion of Ar in males abolished Sox9 induction, establishing a testosterone-dependent regulatory axis. ConclusionsThese findings define a hormone-driven, male-specific tubular repair program and demonstrate that injury and recovery pathways differ fundamentally between sexes, underscoring the need for sex-inclusive therapeutic strategies for AKI. Translational StatementSex influences susceptibility and outcomes after AKI, but the molecular basis remains unclear. SOX9, a transcription factor recently identified as one of the most highly upregulated genes in proximal tubular cells during AKI in both mice and humans, has been presumed to mediate a universal protective program. Using injury-matched murine models of AKI, we now demonstrate that this response is restricted to males, driven by testosterone and androgen receptor signaling, while SOX9 induction is markedly blunted and functionally dispensable in females. These findings reveal that tubular protective pathways differ fundamentally between sexes despite equivalent injury severity. Because SOX9 activation confers epithelial protection in males, therapeutic targeting of this pathway may have clinical relevance primarily in male patients. These data underscore the importance of incorporating biological sex into mechanistic, translational, and clinical studies of kidney injury and recovery.

cell biology↗

Single-cell and Spatial Omics Reveals Region-Specific Plasticity and Therapeutic Vulnerabilities in Metastatic High-Risk Neuroblastoma

Neuroblastoma, a deadly pediatric cancer derived from sympathetic ganglia of the peripheral nervous system, frequently metastasizes, driving poor outcomes. Primary neuroblastomas are well-characterized, but the mechanisms underlying metastasis remain poorly understood. Here, by applying single-cell and spatial multi-omics analyses to primary and metastatic tumors, we found that lymph-node metastases in high-risk neuroblastomas display distinctive cellular heterogeneity and plasticity, marked by mesenchymal-like and stem-like states and heightened epithelial-to-mesenchymal transition activity compared to primary adrenal tumors. Additionally, compared to primary adrenal masses, the metastatic niche display increased immunosuppressive myeloid programs, heightened immune checkpoint signaling, and lymphocyte exhaustion, which are indicative of immune evasion and dysfunction. Notably, metastatic neuroblastomas show elevated eIF4F translation machinery and XPO1 levels. Dual inhibition of eIF4A and XPO1 synergistically halted tumor growth and prolonged survival in xenograft models. Together, our multi-omics studies reveal the molecular and cellular plasticity that contributes to therapy resistance and highlight exploitable therapeutic vulnerabilities in high-risk metastatic neuroblastomas.

cancer biology↗

METTL3 Uncouples Chromatin Accessibility from Transcription during Retinal Development

METTL3 is a key regulator of RNA metabolism, yet its genomic and epitranscriptomic roles in tissue development are largely unexplored. Using embryonic stem cell-derived 3D retinal organoids to model retinal progenitor cell (RPC) differentiation, we integrated transcriptome-wide m6A profiling (GLORI), protein-DNA (ChIP-seq and CUT&RUN) and chromatin accessibility (ATAC-seq) mapping, and targeted m6A engineering (dCas13b-FTO) to dissect METTL3 function. Loss of METTL3 nuclear m6A activity disrupted Rx+ retinal anlage formation in vitro, with dCas13b-FTO epitranscriptome engineering revealing that m6A at the Six3 3UTR governs its stability. Surprisingly, while METTL3 loss altered histone modifications and chromatin accessibility, its direct chromatin targets showed little transcriptional correlation. A degron-based METTL3 degradation strategy, paired with protein-RNA interaction profiling, exposed rapid regulatory shifts in RPCs, revealing a METTL3-Ythdf1 protein-RNA axis. Our multi-omics approach establishes METTL3-dependent m6A as a critical epitranscriptomic layer in retinal development, unveiling a genomic paradigm in which chromatin accessibility diverges from transcriptional output.

developmental biology↗

Single-Cell Atlas of CD4+ T-Helper 2 Cells Reveals Distinct Cytokine Functions Across Diseases

Despite the prevalence of autoimmune diseases, treatment options for specific conditions remain limited. These diseases are driven by three types of inflammatory pathways, each orchestrated by different T-helper cell subsets; however, a comprehensive atlas capturing their diverse functions across conditions and tissues is lacking. One of these subsets, CD4+ T-helper type 2 (Th2) cells, is a relatively infrequent immune cell population that plays a central role in orchestrating type 2 inflammation. In this study, we developed the first comprehensive CD4+Th2 single-cell atlas by analyzing the BioTuring database, which has data from over 300 million cells. This atlas integrates data from 52 studies, comprising a total of 39,243 cells derived from 9 major tissues, representing over 30 distinct diseases. Leveraging this atlas, we confirmed a rarely recognized CD4+Th2 cell population co-expressing IL22 and IL13 observed exclusively in atopic dermatitis and not in other allergic conditions. By integrating single-cell data with other "omics" technologies, our analysis suggests distinct downstream effects of IL22 and IL13, highlighting the potential for combination therapy to enhance treatment outcomes for AD patients. Additionally, by utilizing data derived from the wide range of diseases, tissues, and time points included in this atlas, we re-confirmed the unique connection between IL9 expression and conditions related to allergen exposure. Pseudotime analysis detailed CD4+Th2 cytokine dynamics upon allergen stimulation, showing a shift from early IL2 and IL4 expression to later IL9 and IL5, with IL13 consistently expressed, and further revealed that IL9 production was transient. Collectively, these findings reveal distinct, context-dependent CD4+Th2 cytokine functions, opening the potential for identifying novel therapeutic strategies for allergic and inflammatory diseases.

immunology↗

Pirfenidone treatment attenuates fibrosis in autosomal dominant polycystic kidney disease

Autosomal dominant polycystic kidney disease (ADPKD) is a leading genetic cause of kidney failure, marked by progressive cyst expansion, inflammation and fibrosis. Renal fibrosis, characterized by myofibroblast activation and excessive extracellular matrix (ECM) deposition is a central driver of disease progression in ADPKD, yet targeted anti-fibrotic therapies remain limited. Here, we evaluated the therapeutic potential of pirfenidone to suppress fibrosis and disease progression in ADPKD. To define the ECM in human ADPKD kidneys, we analyzed snRNA-seq data and found that fibroblasts are the principal source of fibrous and adhesive ECM in ADPKD kidneys, exhibiting higher ECM gene expression than normal controls. In vitro, primary culture human ADPKD renal myofibroblasts showed a similar profibrotic gene expression profile, and pirfenidone treatment suppressed ECM gene expression, cell proliferation, migration and contractility. In the Pkd1RC/RC mouse model of ADPKD, pirfenidone treatment significantly reduced renal fibrosis, myofibroblast accumulation, ECM deposition, pro-fibrotic gene expression and associated cell signaling pathways. Pirfenidone also decreased kidney-to-body weight ratio and improved kidney function in Pkd1RC/RC mice, without altering cyst burden. Collectively, these findings demonstrate that pirfenidone attenuates renal fibrosis and improves kidney function in ADPKD by targeting myofibroblast activation and ECM production, supporting a complementary therapeutic approach to cyst-directed therapies.

molecular biology↗

Multimodal Validation of the Existence of Transitional Cerebellar Progenitors in the Human Fetal Cerebellum

The developing human cerebellum comprises a series of transient progenitor states that are essential for generating diverse neural subtypes, yet the identity and validation of intermediate cell populations bridging stem-like and lineage-committed neuronal precursors remain limited. In our previous single-cell transcriptomic study, we identified a distinct transitional cerebellar progenitor (TCP) population enriched in specific progenitor zones such as the rhombic lip during human fetal cerebellar development. To address the concerns raised in the Matters Arising regarding the existence of the TCP cells, we provide additional multimodal validations of this population. Rigorous reanalysis of our single-cell transcriptomic data, applying stringent quality control measures, validated the quality of TCP cells and their classification as a transcriptionally distinct population. Multiple orthogonal validations of TCP signature genes (SOX11 and HNRNPH1) using RNAscope in situ hybridization, Xenium-based spatial transcriptomics, and immunohistochemistry on additional fetal cerebellar samples across different stages demonstrated the consistent presence of TCPs in the rhombic lip, transitioning from PRTG+ stem-like zones in the ventricular zone at early developmental stages to the subventricular zone overlapping with EOMES+ unipolar brush cell precursors at later stages. TCP-like populations were also independently identified in two fetal cerebellar single-nucleus transcriptomic atlases, and their gene signature was enriched in a cell population associated with aggressive medulloblastomas. Collectively, these multimodal validations confirm the existence of a transitional progenitor population in the human fetal cerebellum, with implications for cerebellar lineage progression and medulloblastoma origin.

developmental biology↗

Prosystemin-derived signals: bridging leaf microbiome dynamics and defense activation

AbstractThe use of plant-derived peptides as resistance inducers provides innovative and potentially environmentally friendly methods to safeguard crop health. Although their use is increasing rapidly, their broader impact, particularly on plant-associated microbiomes, remains underexplored. This study investigated the influence of a promising immunomodulatory peptide derived from the tomato defense protein prosystemin on the tomato phyllosphere microbiome. We applied the peptide via foliar spray biweekly to simulate common agricultural practices from the planting stage to two months post-germination. Using a shotgun metagenomics approach combined with qPCR, we identified bacterial communities of high abundance (up to 4.6 log10 bacterial 16S rRNA copies) and high diversity, mainly comprising Actino-, Alphaproteo- and Gammaproteobacteria, on all tomato leaves. The peptide treatment led to a significant and targeted shift in the bacterial community, characterized by reduced diversity and network complexity and species loss, i.e., Streptomyces. The enrichment was predominantly observed in bacterial genera such as Acinetobacter, Sphingobium, Sphingomonas, Brevundimonas, and Massilia, which are typically associated with improved plant growth and stress resilience. Intriguingly, shifts in both taxonomic and functional profile upon peptide application aligned with patterns typically observed during plant defense activation, involving jasmonic acid and related secondary metabolites. Members of the Sphingomonadaceae family, particularly Sphingobium yanoikuyae, have emerged as potential drivers of such microbial dynamics, likely adapting to plant upregulated defenses and potentially supporting its resilient phenotype. Overall, in addition to its well-established role in combating tomato pests and necrotrophic fungi, the prosystemin-derived peptide paves the way for disentangling peptide-induced resistance and its interplay with the plant microbiota.

plant biology↗

Circadian clock disruption and growth of kidney cysts in autosomal dominant polycystic kidney disease

BackgroundAutosomal dominant polycystic kidney disease (ADPKD) is caused by mutations in the PKD1 and PKD2 genes, and often progresses to kidney failure. ADPKD progression is not uniform among patients, suggesting that factors secondary to the PKD1/2 gene mutation could regulate the rate of disease progression. Here we tested the effect of circadian clock disruption on ADPKD progression. Circadian rhythms are regulated by cell-autonomous circadian clocks composed of clock proteins. BMAL1 is a core constituent of the circadian clock. MethodsTo disrupt the circadian clock, we deleted Bmal1 gene in the renal collecting ducts of the Pkd1RC/RC (RC/RC) mouse model of ADPKD (RC/RC;Bmal1f/f;Pkhd1cre, called DKO mice), and in Pkd1 knockout mouse inner medullary collecting duct cells (Pkd1Bmal1KO mIMCD3 cells). Only male mice were used. ResultsHuman nephrectomy ADPKD kidneys and Pkd1KO mIMCD3 cells showed reduced Bmal1 gene expression compared to normal controls. When compared to RC/RC kidneys, DKO kidneys showed significantly altered clock gene expression, increased cyst growth, cell proliferation, apoptosis and fibrosis. DKO kidneys also showed increased lipogenesis and cholesterol synthesis-related gene expression, and increased tissue triglyceride levels compared to RC/RC kidneys. Similarly, in vitro, Pkd1Bmal1KO cells showed altered clock genes, increased lipogenesis and cholesterol synthesis-related genes, and reduced fatty-acid oxidation-related gene expression compared to Pkd1KO cells. The Pkd1Bmal1KO cells showed increased cell proliferation compared to Pkd1KO cells, which was rescued by pharmacological inhibition of lipogenesis. ConclusionRenal collecting duct specific Bmal1 gene deletion disrupts the circadian clock and triggers accelerated ADPKD progression by altering lipid metabolism-related gene expression. Key pointsO_LILack of BMAL1, a circadian clock protein in renal collecting ducts disrupted the clock and increased cyst growth and fibrosis in an ADPKD mouse model. C_LIO_LIBMAL1 gene deletion increased cell proliferation by increasing lipogenesis in kidney cells. C_LIO_LIThus, circadian clock disruption could be a risk factor for accelerated disease progression in patients with ADPKD. C_LI

molecular biology↗

Simulating 500 million years of evolution with a language model

More than three billion years of evolution have produced an image of biology encoded into the space of natural proteins. Here we show that language models trained on tokens generated by evolution can act as evolutionary simulators to generate functional proteins that are far away from known proteins. We present ESM3, a frontier multimodal generative language model that reasons over the sequence, structure, and function of proteins. ESM3 can follow complex prompts combining its modalities and is highly responsive to biological alignment. We have prompted ESM3 to generate fluorescent proteins with a chain of thought. Among the generations that we synthesized, we found a bright fluorescent protein at far distance (58% identity) from known fluorescent proteins. Similarly distant natural fluorescent proteins are separated by over five hundred million years of evolution.

synthetic biology↗

Inhibition of the UFD-1-NPL-4 complex triggers an inflammation-like response in Caenorhabditis elegans

The UFD-1 (ubiquitin fusion degradation 1)-NPL-4 (nuclear protein localization homolog 4) heterodimer is involved in extracting ubiquitinated proteins from several plasma membrane locations, including the endoplasmic reticulum. This heterodimer complex helps in the degradation of ubiquitinated proteins via the proteasome with the help of the AAA+ ATPase CDC-48. While the ubiquitin-proteasome system is known to have important roles in maintaining innate immune responses, the role of the UFD-1-NPL-4 complex in regulating immunity remains elusive. In this study, we investigate the role of the UFD-1-NPL-4 complex in maintaining Caenorhabditis elegans innate immune responses. Inhibition of the UFD-1-NPL-4 complex activates an aberrant immune response that reduces the survival of the wild-type worms on the pathogenic bacterium Pseudomonas aeruginosa despite diminishing colonization of the gut with the bacterium. This aberrant immune response improves the survival of severely immunocompromised worms on pathogenic bacteria but is detrimental on nonpathogenic bacteria. Transcriptomics studies reveal that the GATA transcription factor ELT-2 mediates the aberrant immune response upon inhibition of the UFD-1-NPL-4 complex. Collectively, our findings show that inhibition of the UFD-1-NPL-4 complex triggers an aberrant immune response that is detrimental to immunocompetent worms under infection conditions but can be advantageous for immunocompromised worms.

immunology↗

The Endosomal pH Regulator NHE6 is Required for Insulin-Stimulated Glucose Uptake in Adipocytes

ObjectiveTrafficking of GLUcose Transporter isoform 4 (GLUT4) from the adipocyte vesicular pool to the cell surface is tightly regulated by insulin to maintain glucose homeostasis in response to changing demands in energy consumption. Previously, endosomal Na+/H+ exchanger 6 (NHE6, gene name SLC9A6) was identified in adipocyte plasma membranes and shown to associate with GLUT4-positive vesicles. However, the functional contribution of NHE6 to GLUT4 trafficking and glucose uptake remained uncharacterized. MethodsNHE6 was knocked down in 3T3L1 cells either before or after differentiation into adipocytes using lentiviral delivery of shRNA. Uptake of [3H] 2-deoxyglucose into adipocytes was quantified in response to insulin. We used epitope tagged constructs to distinguish between localization of vesicular and surface levels of NHE6 and GLUT4 proteins. Protein and transcript levels of components of the glucose signaling pathway were monitored by qPCR and Western analysis, respectively, in response to NHE6 knockdown and/or treatment with chemical modulators of endosomal pH. ResultsWe show that insulin-stimulated glucose uptake in adipocytes is severely impaired upon NHE6 depletion. Correspondingly, insulin-stimulated surface expression of GLUT4 at the adipocyte plasma membrane was diminished in NHE6 knockdown cells due to a post-transcriptional decrease in basal GLUT4. Metformin response of GLUT4 was also muted in the absence of NHE6. Further, we demonstrate diminished activation of the GLUT4 translocation pathway in the absence of NHE6 via reduced expression of the insulin receptor and reduced phosphorylation of the downstream effector kinase Akt. Components of GLUT4 storage vesicles, including GLUT4, LRP1 and sortilin were downregulated in NHE6-knockdown adipocytes under basal conditions. Proteostatic control of key components of the insulin signaling pathway (insulin receptor, GLUT4) could be restored by chemical bypass of NHE6 using the V-ATPase inhibitor bafilomycin or the Na+/H+ exchanger mimetic monensin. ConclusionsThus, NHE6 is critical for proper expression and trafficking of GLUT4. Basal expression of both insulin receptor and GLUT4 in NHE6 knockdown cells could be restored by bafilomycin-inhibition of the H+-ATPase or the H+ ionophore monensin pointing to pH dysregulation as the underlying defect. We suggest that NHE6 is a component of GLUT4 storage vesicles where it regulates proteostasis. These findings establish NHE6 as a novel contributor to glucose homeostasis and energy metabolism with implications for Christianson syndrome patients who carry loss of function mutations in the SLC9A6 gene. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=147 SRC="FIGDIR/small/551163v1_ufig1.gif" ALT="Figure 1"> View larger version (38K): org.highwire.dtl.DTLVardef@f6fc88org.highwire.dtl.DTLVardef@13d7faforg.highwire.dtl.DTLVardef@89d577org.highwire.dtl.DTLVardef@11da50a_HPS_FORMAT_FIGEXP M_FIG C_FIG

physiology↗

A high-level programming language for generative protein design

Combining a basic set of building blocks into more complex forms is a universal design principle. Most protein designs have proceeded from a manual bottom-up approach using parts created by nature, but top-down design of proteins is fundamentally hard due to biological complexity. We demonstrate how the modularity and programmability long sought for protein design can be realized through generative artificial intelligence. Advanced protein language models demonstrate emergent learning of atomic resolution structure and protein design principles. We leverage these developments to enable the programmable design of de novo protein sequences and structures of high complexity. First, we describe a high-level programming language based on modular building blocks that allows a designer to easily compose a set of desired properties. We then develop an energy-based generative model, built on atomic resolution structure prediction with a language model, that realizes all-atom structure designs that have the programmed properties. Designing a diverse set of specifications, including constraints on atomic coordinates, secondary structure, symmetry, and multimerization, demonstrates the generality and controllability of the approach. Enumerating constraints at increasing levels of hierarchical complexity shows that the approach can access a combinatorially large design space.

synthetic biology↗

Single-cell Atlas of Human Fetal Cerebellum Decoding Medulloblastoma Origin and Oncogenesis

Medulloblastoma (MB) is the most common malignant childhood brain tumor1,2, yet the origin of the most aggressive subgroup-3 form remains elusive, impeding development of effective targeted treatments. Previous analyses of mouse cerebella3,4 or human counterparts from frozen tissue nuclei5 have not fully defined the compositional heterogeneity of MBs. Here, we undertook an unprecedented single-cell profiling of freshly-isolated human fetal cerebella to establish a reference map delineating hierarchical cellular states in MBs. We identified a unique transitional cerebellar progenitor connecting neural stem cells to neuronal lineages in developing fetal cerebella. Intersectional analysis revealed that the transitional progenitors were enriched in aggressive MB subgroups, including group-3 and metastatic tumors. Single-cell multi-omics revealed underlying regulatory networks in the transitional progenitor populations, including transcriptional determinants HNRNPH1 and SOX11, which are correlated with clinical prognosis in group-3 MBs. Genomic and Hi-C profiling identified de novo long-range chromatin-loops juxtaposing HNRNPH1/SOX11-targeted super-enhancers to cis-regulatory elements of MYC, an oncogenic driver for group-3 MBs. Targeting the transitional progenitor regulators inhibited MYC expression and MYC-driven group-3 MB growth. Our integrated single-cell atlases of human fetal cerebella and MBs reveal potential cell populations predisposed to transformation and regulatory circuitries underlying tumor cell states and oncogenesis, highlighting hitherto unrecognized transitional progenitor intermediates predictive of disease prognosis and potential therapeutic vulnerabilities.

cancer biology↗