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Afshar, M.

Publications and source records attributed to Afshar, M..

2 recordsLinked to original sources

Thrombo-inflammation analyzed in a validated seven-layer platelet decision model: cellular decisions are tough problems fast and heuristically solved

Decisions in biology happen fast and are driven by evolution to optimize survival chances. In platelets, this is achieved by organizing signaling cascades into rapid decision-funnels with modulatory crosstalk. We show that network decision processes underlying cellular decisions are tough to solve (equivalent to classical satisfiability problems, SAT). Hence, heuristics, modular decision-making, and decision funnels are required for efficient decisions. We establish this using a seven-layer platelet decision network that agrees well with all available genetic and functional experimental data. Platelet decision cascades are robust to perturbations: For example, receptors such as TRPM7 modulate platelet activity. However, knockouts of the receptors still leave platelets reactive overall. Dynamic control resolves relaying functions from kinases to cytoskeleton alterations. This allows fast execution of platelet shape change or aggregation. Stress conditions can shift platelet decision funnels towards constant activation of aggregation or immune signaling, causing thrombosis or thrombo-inflammation. Based on the network dynamics, we conclude that platelets pragmatically resolve the complex (non-polynomial (NP)) cellular decision problems by using a similar relaxation to those proposed in mathematics - many different configurations end up in similar states. Metamathematical considerations (no mathematical proof) suggest that NP problems are more complex then P problems. One sentence abstractWe show that cellular decision problems like the platelet signaling cascade may need unexpectedly long to solve but in general, they are efficiently solved using heuristics ("decision funnels"), implying fast decisions but the risk of chronic stress and inflammation.

bioinformatics↗

A single cell spatial temporal atlas of skeletal muscle reveals cellular neighborhoods that orchestrate regeneration and become disrupted in aging

Our mobility requires muscle regeneration throughout life. Yet our knowledge of the interplay of cell types required to rebuild injured muscle is lacking, because most single cell assays require tissue dissociation. Here we use multiplexed spatial proteomics and neural network analyses to resolve a single cell spatiotemporal atlas of 34 cell types during muscle regeneration and aging. This atlas maps interactions of immune, fibrogenic, vascular, nerve, and myogenic cells at sites of injury in relation to tissue architecture and extracellular matrix. Spatial pseudotime mapping reveals sequential cellular neighborhoods that mediate repair and a nodal role for immune cells. We confirm this role by macrophage depletion, which triggers formation of aberrant neighborhoods that obstruct repair. In aging, immune dysregulation is chronic, cellular neighborhoods are disrupted, and an autoimmune response is evident at sites of denervation. Our findings highlight the spatial cellular ecosystem that orchestrates muscle regeneration, and is altered in aging. HighlightsO_LISingle cell resolution spatial atlas resolves a cellular ecosystem of 34 cell types in multicellular neighborhoods that mediate efficient skeletal muscle repair C_LIO_LIHighly multiplexed spatial proteomics, neural network and machine learning uncovers temporal dynamics in the spatial crosstalk between immune, fibrogenic, vascular, nerve, and muscle stem cells and myofibers during regeneration C_LIO_LISpatial pseudotime mapping reveals coherent formation of multicellular neighborhoods during efficacious repair and the nodal role of immune cells in coordinating muscle repair C_LIO_LIIn aged muscle, cellular neighborhoods are disrupted by a chronically inflamed state and autoimmunity C_LI

cell biology↗