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Robinson, B.

Publications and source records attributed to Robinson, B..

9 recordsLinked to original sources

Multiscale, Survey-and-Target Optical Super-Resolution Histology

Super-resolution microscopy reveals fine subcellular tissue architecture, yet extending this capability to histological screening requires balancing spatial resolution with imaging area, axial access, throughput, and instrumental complexity. Here we present multiscale optical super-resolution histology (MOSH), an integrated optical-computational platform that combines tissue-scale, extended-depth-of-focus super-resolution surveys with coordinate-guided three-dimensional interrogation of selected targets. MOSH leverages stationary multifocal excitation, continuous sample translation, tunable axial refocusing, and parallelized reconstruction within a shared spatial-coordinate framework in a conventional epi-fluorescence setting. This survey-and-target strategy preserves tissue-scale context, directs volumetric acquisition to selected subcellular structures, and generates virtual H&E images that retain resolution-enhanced structural information. Across cultured cells, cytological preparations, conventional tissue sections, and intact unsectioned biopsies, MOSH achieved approximately twofold resolution enhancement, continuous lateral coverage beyond the native field of view, and tunable axial survey ranges up to 20 m. Bridging tissue-scale histological screening and targeted, quantitative nanoscale interrogation, MOSH establishes a scalable framework for multiscale analysis of biological and clinical specimens.

bioengineering↗

Endolysosomal acidification regulates intestinal injury and repair in Drosophila by augmenting JNK activation and innate immune signaling pathways

Vacuolar ATPases (V-ATPases) are highly conserved multi-subunit proton pumps that drive the acidification of intracellular vesicles, especially endosomes and lysosomes. Beyond enabling cargo degradation, endolysosomal acidification shapes signal transduction, acting both positively through receptor processing in endosomes and negatively through lysosomal turnover of pathway mediators. Whether endolysosomal acidification shapes the intestinal epithelial response to oxidative injury remains unclear. Here we use Drosophila to define the role of V-ATPases in intestinal injury driven by excessive oxidative stress. Consistent with lysosomal biogenesis programs induced by oxidant in other systems, we find that oxidant exposure increases V-ATPase subunit expression and abundance of acidified vesicles in the midgut. Yet this response is not protective. RNAi depletion of multiple V-ATPase subunits suppresses lethality induced by either hydrogen peroxide or paraquat exposure. These effects map to mature absorptive enterocytes rather than to intestinal progenitors. Enterocyte-specific depletion of Vha44 (subunit C of the V1 domain) preserves intestinal barrier function and suppresses the cell death, JNK pathway activation, and IMD/NF-{kappa}B reporter activity induced by oxidant exposure. Overexpression of the MAP3K Tak1 sensitizes animals to oxidative stress and drives JNK and IMD signaling, both of which require Vha44. Together, these findings identify endolysosomal acidification as an amplifier of pro-apoptotic JNK and IMD/NF-{kappa}B signaling, such that attenuating V-ATPase levels in mature enterocytes protects the intestinal epithelium from excessive oxidant burden.

cell biology↗

The Spatial Atlas of Human Anatomy (SAHA): A Multimodal Subcellular-Resolution Reference Across Human Organs

The Spatial Atlas of Human Anatomy (SAHA) represents the first multimodal, subcellular- resolution reference of healthy adult human tissues across multiple organ systems. Integrating spatial transcriptomics, proteomics, and histological features across over 15 million cells from more than 100 donors, SAHA maps conserved and organ-specific cellular niches in gastrointestinal and immune tissues. High-resolution profiling using CosMx SMI, 10x Xenium, RNAscope, GeoMx DSP, and single-nucleus RNA-seq reveals spatially organized cell states, rare adaptive immune populations, and tissue-specific cell-cell interactions and ligand-receptor pairs. Comparative analyses with colorectal cancer and inflammatory bowel disease demonstrate the power of SAHA to detect disease-associated spatial disruptions, including crypt dedifferentiation, perineural invasion, and therapy-resistant immune remodeling. All data are openly accessible through a FAIR-compliant interactive portal to support exploration, benchmarking, and machine learning model training. Through SAHA, we provide a foundational framework for spatial diagnostics and next-generation precision medicine grounded in a comprehensive human tissue atlas, enabling the development of context-aware models that simulate tissue behavior, decode complex pathologies, and accelerate therapeutic innovation at unprecedented scale.

systems biology↗

Recurrent connections enable point attractor dynamics and dimensionality reduction in a connectome-constrained model of the insect learning center

The learning center in the insect, the mushroom body (MB) with its predominant population of Kenyon Cells (KCs), is a widely studied model system to investigate neural processing principles, both experimentally and theoretically. While many computational models of the MB have been studied, the computational role of recurrent connectivity between KCs remains inadequately understood. Dynamical point attractors are a candidate theoretical framework where recurrent connections in a neural network can enable a discrete set of stable activation patterns. However, given that detailed, full recurrent connectivity patterns in biological neuron populations are mostly unknown, how theoretical models are substantiated by specific networks found in biology has not been clear. Leveraging the recent release of the full synapse-level connectivity of the MB in the fly, we performed a series of analyses and network model simulations to investigate the computational role of the recurrent KC connections, especially their significance in attractor dynamics. Structurally, the recurrent excitation (RE) connections are highly symmetric and balanced with feedforward input. In simulations, RE facilitates dimensionality reduction and allows a small set of self-sustaining point attractor states to emerge. To further quantify the possible range of network properties mediated by RE, we systematically explored the dynamical regimes enabled by changing recurrent connectivity strength. Finally, we establish connections between our findings and potential functional or behavioral implications. Overall, our work provides quantitative insights into the possible functional role of the recurrent excitatory connections in the MB by quantifying the point attractor network dynamics within a full synapse-level connectome-constrained highly recurrent network model. These findings advance our understanding of how biological neural networks may utilize point attractor dynamics. Author summaryPoint attractor neural networks are widely used theoretical models of associative memory, where recurrent connections between neurons enable a discrete set of stable activation patterns that can recover a full pattern based on partial cues. The detailed full recurrent connectivity patterns in biological neuron populations are largely unknown, however, raising questions about the precise correspondence between theoretical point attractor models and neural networks found in biology. Recent breakthroughs have unveiled the synapse-level connectivity of all neurons within the learning center of an insect, including recurrent connections between the primary neuron type--a crucial component with an elusive computational role. In this work, we perform analyses of these recurrent connectivity patterns and simulate neural network models that have these biologically constrained neural network patterns. We find that these recurrent connections are highly symmetric and balanced with input to the memory center. In simulations, we find that these recurrent connections perform dimensionality reduction and enable a small set of point attractor states. We additionally characterize how the strength of these recurrent connections affects network properties and downstream behavioral consequences. Overall, this work advances an understanding of the insect learning center as well as the relationship between theoretical and biological recurrent networks.

neuroscience↗

Population Dynamics and Resource Availability Drive Seasonal Shifts in the Consumptive and Competitive Impacts of Introduced House Mice (Mus musculus) on an Island Ecosystem

BackgroundHouse mice (Mus musculus) are widespread and invasive on many islands where they can have both direct and indirect ecological impacts on native ecological communities. Given their opportunistic, omnivorous nature the consumptive and competitive impacts of house mice on islands have the potential to vary over time in concert with resource availability and mouse population dynamics. MethodsWe examined the ecological niche of invasive house mice on Southeast Farallon Island, California, USA using a combination of mouse trapping, food resource surveys, and stable isotope analysis to better understand their trophic interactions with native flora and fauna. ResultsWe found that plants were the important resource for house mice during the spring months when vegetation is abundant and mouse populations are low. However, plants decline in dietary importance throughout the summer and fall as mouse populations increase, and seabird and insect resources become relatively more available and consumed by house mice. Mouse abundance peaks and other resource availability are low in the fall months when the isotopic niches of house mice and salamanders overlap significantly indicating the potential for competition, most likely for insect prey. DiscussionThese results indicate how seasonal shifts in both the mouse abundance and resource availability are key factors that mediate the consumptive and competitive impacts of introduced house mice on this island ecosystem.

ecology↗

The evolution of genomic, transcriptomic, and single-cell protein markers of metastatic upper tract urothelial carcinoma

The molecular characteristics of metastatic upper tract urothelial carcinoma (UTUC) are unknown. The genomic and transcriptomic differences between primary and metastatic UTUC is not well described either. We combined whole-exome sequencing, RNA-sequencing, and Imaging Mass Cytometry (IMC) of 44 tumor samples from 28 patients with high-grade primary and metastatic UTUC. IMC enables spatially resolved single-cell analyses to examine the evolution of cancer cell, immune cell, and stromal cell markers using mass cytometry with lanthanide metal-conjugated antibodies. We discovered that actionable genomic alterations are frequently discordant between primary and metastatic UTUC tumors in the same patient. In contrast, molecular subtype membership and immune depletion signature were stable across primary and matched metastatic UTUC. Molecular and immune subtypes were consistent between bulk RNA-sequencing and mass cytometry of protein markers from 340,798 single-cells. Molecular subtyping at the single cell level was highly conserved between primary and metastatic UTUC tumors within the same patient.

cancer biology↗

A septin GTPase scaffold of dynein-dynactin motors triggers retrograde lysosome transport

The metabolic and signaling functions of lysosomes depend on their intracellular positioning and trafficking, but the underlying mechanisms are little understood. Here, we have discovered a novel septin GTPase-based mechanism for retrograde lysosome transport. We found that septin 9 (SEPT9) associates with lysosomes, promoting the perinuclear localization of lysosomes in a Rab7-independent manner. SEPT9 targeting to mitochondria and peroxisomes is sufficient to recruit dynein and cause perinuclear clustering. We show that SEPT9 interacts with both dynein and dynactin through its GTPase domain and N-terminal extension, respectively. Strikingly, SEPT9 associates preferentially with the dynein intermediate chain (DIC) in its GDP-bound state, which favors dimerization and assembly into septin multimers. In response to oxidative cell stress induced by arsenite, SEPT9 localization to lysosomes is enhanced, promoting the perinuclear clustering of lysosomes. We posit that septins function as GDP-activated scaffolds for the cooperative assembly of dynein-dynactin, providing an alternative mechanism of retrograde lysosome transport at steady state and during cellular adaptation to stress. SummaryThe intracellular position of lysosomes is critical for cell metabolism and signaling. Kesisova et al discovered a membrane-associated septin GTPase scaffold of dynein-dynactin that promotes retrograde traffic and perinuclear lysosome clustering at steady state and in response to oxidative stress.

cell biology↗

Phosphoprotein-based Biomarkers as Predictors for Cancer Therapy

Disparities in cancer patient responses have prompted widespread searches to identify differences in sensitive vs. non-sensitive populations and form the basis of personalized medicine. This customized approach is dependent upon the development of pathway-specific therapeutics in conjunction with biomarkers that predict patient responses. Here, we show that Cdk5 drives growth in subgroups of human patients with multiple types of neuroendocrine neoplasms. Phosphoproteomics and high throughput screening identified novel phosphorylation sites downstream of Cdk5. These phosphorylation events serve as biomarkers of Cdk5 activity and effectively pinpoint Cdk5-driven tumors. Toward achieving targeted therapy, we demonstrate that mouse models of neuroendocrine cancer are responsive to selective Cdk5 inhibitors and biomimetic nanoparticles are effective vehicles for enhanced tumor targeting and reduction of drug toxicity. Finally, we show that biomarkers of Cdk5-dependent tumors effectively predict response to anti-Cdk5 therapy in patient-derived xenografts. Thus, a phosphoprotein-based diagnostic assay combined with Cdk5-targeted therapy is a rational treatment approach for neuroendocrine malignancies.

cancer biology↗

Recurrent loss of heterozygosity correlates with clinical outcome in pancreatic neuroendocrine cancer

Pancreatic neuroendocrine tumors (pNETs) are uncommon cancers arising from pancreatic islet cells. Analysis of gene mutation, copy number and RNA expression of 57 sporadic pNETs showed that pNET genomes are dominated by aneuploidy. Remarkably, ~25% of pNETs had genomes characterized by recurrent loss of heterozygosity (LoH) of the same 10 chromosomes, accompanied by bi-allelic MEN1 inactivation, and these cases had generally poor clinical outcome. Another ~25% of all pNETs had chromosome 11 LoH and bi-allelic MEN1 inactivation, lacking the recurrent LoH pattern - these had universally good clinical outcome. Some level of aneuploidy was common, and overall ~80% of pNETs had LoH of [≥]1 chromosome. This aneuploidy led to changes in RNA expression at the level of whole chromosomes and allowed pathogenic germline variants (e.g. ATM) to be expressed unopposed, inactivating downstream tumor suppressor pathways. Some pNETs appear to utilize VHL gene methylation or mutation to activate pseudo-hypoxia. Contrary to expectation neither tumor morphology within well-differentiated pNETs nor single gene mutation had significant associations with clinical outcome, nor did expression of RNAs reflecting the activity of immune, differentiation, proliferative or tumor suppressor pathways. MEN1 was the only statistically significant recurrently mutated driver gene in pNETs. Only one pNET had clearly oncogenic and actionable SNVs (in PTEN and FLCN) confirmed by corroborating RNA expression changes. The two distinct patterns of aneuploidy described here, associated with markedly poor and good clinical outcome respectively, define a novel oncogenic mechanism and the first route to genomic precision oncology for this tumor type.

cancer biology↗