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Creators/Authors contains: "Krishnaswamy, Smita"

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  1. Free, publicly-accessible full text available June 30, 2024
  2. Abstract Due to commonalities in pathophysiology, age-related macular degeneration (AMD) represents a uniquely accessible model to investigate therapies for neurodegenerative diseases, leading us to examine whether pathways of disease progression are shared across neurodegenerative conditions. Here we use single-nucleus RNA sequencing to profile lesions from 11 postmortem human retinas with age-related macular degeneration and 6 control retinas with no history of retinal disease. We create a machine-learning pipeline based on recent advances in data geometry and topology and identify activated glial populations enriched in the early phase of disease. Examining single-cell data from Alzheimer’s disease and progressive multiple sclerosis with our pipeline, we find a similar glial activation profile enriched in the early phase of these neurodegenerative diseases. In late-stage age-related macular degeneration, we identify a microglia-to-astrocyte signaling axis mediated by interleukin-1 β which drives angiogenesis characteristic of disease pathogenesis. We validated this mechanism using in vitro and in vivo assays in mouse, identifying a possible new therapeutic target for AMD and possibly other neurodegenerative conditions. Thus, due to shared glial states, the retina provides a potential system for investigating therapeutic approaches in neurodegenerative diseases. 
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    Free, publicly-accessible full text available December 1, 2024
  3. In modern relational machine learning it is common to encounter large graphs that arise via interactions or similarities between observations in many domains. Further, in many cases the target entities for analysis are actually signals on such graphs. We propose to compare and organize such datasets of graph signals by using an earth mover’s distance (EMD) with a geodesic cost over the underlying graph. Typically, EMD is computed by optimizing over the cost of transporting one probability distribution to another over an underlying metric space. However, this is inefficient when computing the EMD between many signals. Here, we propose an unbalanced graph EMD that efficiently embeds the unbalanced EMD on an underlying graph into an L1 space, whose metric we call unbalanced diffusion earth mover’s distance (UDEMD). Next, we show how this gives distances between graph signals that are robust to noise. Finally, we apply this to organizing patients based on clinical notes, embedding cells modeled as signals on a gene graph, and organizing genes modeled as signals over a large cell graph. In each case, we show that UDEMD-based embeddings find accurate distances that are highly efficient compared to other methods. 
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  4. We propose a method called integrated diffusion for combining multimodal data, gathered via different sensors on the same system, to create a integrated data diffusion operator. As real world data suffers from both local and global noise, we introduce mechanisms to optimally calculate a diffusion operator that reflects the combined information in data by maintaining low frequency eigenvectors of each modality both globally and locally. We show the utility of this integrated operator in denoising and visualizing multimodal toy data as well as multi-omic data generated from blood cells, measuring both gene expression and chromatin accessibility. Our approach better visualizes the geometry of the integrated data and captures known cross-modality associations. More generally, integrated diffusion is broadly applicable to multimodal datasets generated by noisy sensors collected in a variety of fields. 
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  5. Skin homeostasis is maintained by stem cells, which must communicate to balance their regenerative behaviors. Yet, how adult stem cells signal across regenerative tissue remains unknown due to challenges in studying signaling dynamics in live mice. We combined live imaging in the mouse basal stem cell layer with machine learning tools to analyze patterns of Ca2+ signaling. We show that basal cells display dynamic intercellular Ca2+ signaling among local neighborhoods. We find that these Ca2+ signals are coordinated across thousands of cells and that this coordination is an emergent property of the stem cell layer. We demonstrate that G2 cells are required to initiate normal levels of Ca2+ signaling, while connexin43 connects basal cells to orchestrate tissue-wide coordination of Ca2+ signaling. Lastly, we find that Ca2+ signaling drives cell cycle progression, revealing a communication feedback loop. This work provides resolution into how stem cells at different cell cycle stages coordinate tissue-wide signaling during epidermal regeneration.

     
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  6. We propose a new graph neural network (GNN) module, based on relaxations of recently proposed geometric scattering transforms, which consist of a cascade of graph wavelet filters. Our learnable geometric scattering (LEGS) module enables adaptive tuning of the wavelets to encourage band-pass features to emerge in learned representations. The incorporation of our LEGS-module in GNNs enables the learning of longer-range graph relations compared to many popular GNNs, which often rely on encoding graph structure via smoothness or similarity between neighbors. Further, its wavelet priors result in simplified architectures with significantly fewer learned parameters compared to competing GNNs. We demonstrate the predictive performance of LEGS-based networks on graph classification benchmarks, as well as the descriptive quality of their learned features in biochemical graph data exploration tasks. 
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  7. Abstract

    The evolution of uniquely human traits likely entailed changes in developmental gene regulation. Human Accelerated Regions (HARs), which include transcriptional enhancers harboring a significant excess of human-specific sequence changes, are leading candidates for driving gene regulatory modifications in human development. However, insight into whether HARs alter the level, distribution, and timing of endogenous gene expression remains limited. We examined the role of the HARHACNS1(HAR2) in human evolution by interrogating its molecular functions in a genetically humanized mouse model. We find thatHACNS1maintains its human-specific enhancer activity in the mouse embryo and modifies expression ofGbx2, which encodes a transcription factor, during limb development. Using single-cell RNA-sequencing, we demonstrate thatGbx2is upregulated in the limb chondrogenic mesenchyme ofHACNS1homozygous embryos, supporting thatHACNS1alters gene expression in cell types involved in skeletal patterning. Our findings illustrate that humanized mouse models provide mechanistic insight into how HARs modified gene expression in human evolution.

     
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  8. null (Ed.)