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Githaka, J. M.

Publications and source records attributed to Githaka, J. M..

2 recordsLinked to original sources

ClusToRa: A niche-centric framework for identifying structural recruitment and infiltration in spatial omics

Spatial omics maps cellular landscapes, yet current tools might conflate stochastic proximity with organized niches. We present ClusToRa (Cluster-to-Randomization), a framework that identifies high-density cellular territories and quantifies cell-type recruitment using a fixed-position null model. Benchmarked against graph-based neighborhood-enrichment and point-pattern statistics, ClusToRa reduced false-positive enrichment in simulations and resolved core-vs-boundary interactions. Applied to cirrhotic MASH liver, ClusToRa identifies stellate-cell territories with immune/endothelial infiltration and stress-, Notch-, and PPAR-associated programs, providing a niche-centric framework for distinguishing structural cellular infiltration from boundary adjacency or density-driven colocalization.

bioinformatics↗

A glucose-dependent spatial patterning of exocytosis inhuman β-cells is disrupted in type 2 diabetes

Impaired insulin secretion in type 2 diabetes (T2D) is linked to reduced insulin granule docking, disorganization of the exocytotic site, and an impaired glucose-dependent facilitation of insulin exocytosis. We show in {beta}-cells from 80 human donors that the glucose-dependent amplification of exocytosis is disrupted in T2D. Spatial analyses of granule fusion events, visualized by total internal reflection fluorescence (TIRF) microscopy, demonstrate that these are non-random across the surface of {beta}-cells from donors with no diabetes (ND). The compartmentalization of events occurs within regions defined by concurrent or recent membrane-resident secretory granules. This organization, and the number of membrane-associated granules, is glucose-dependent and notably impaired in T2D {beta}-cells. Mechanistically, multi-channel Kv2.1 clusters contribute to maintaining the density of membrane-resident granules and the number of fusion hot spots, while SUMOylation sites at the channel N-(K145) and C-terminus (K470) determine the relative proportion of fusion events occurring within these regions. Thus, a glucose-dependent compartmentalization of fusion, regulated in part by a structural role for Kv2.1, is disrupted in {beta}-cells from donors with type 2 diabetes. HIGHLIGHTSO_LIExocytosis of secretory granules is non-random across the surface of human {beta}-cells, and this organization is disrupted in type 2 diabetes. C_LIO_LIIncreasing glucose facilitates the spatial compartmentalization of fusion, independent of an overall increase in event frequency. C_LIO_LICompartmentalized hot spots occur at sites marked by membrane-associated granules, the density of which is regulated in part by a clustered K+ channel (Kv2.1). C_LIO_LISUMOylation status of the channel controls the proportion of events that occur within these local regions. C_LI

cell biology↗