Biology subjects

Udager, A. M.

Publications and source records attributed to Udager, A. M..

4 recordsLinked to original sources

bioRxiv2026

Multi-resolution Spatial Graphical Regression Models for Hierarchical Spatial Transcriptomics Data

Advances in spatial transcriptomics (ST) technologies enable systematic molecular characterization of tumor microenvironment, tumor gradients and gene regulatory networks. Cancer progression is known to vary along pathological gradients, yet existing network approaches for gene network inference typically ignore hierarchical spatial organization across the tumor. We develop a Bayesian multi-resolution spatial graphical regression (mSGR) framework to infer spatially varying gene networks from multi-resolution ST data. The proposed model allows precision matrices to vary across hierarchically structured spatial domains, capturing both local and global organization within the tumor. To identify spatially varying regulatory relationships, we introduce a spatially structured edge selection strategy that borrows strength across regions according to spatial proximity and pathological gradients, while Gaussian-process priors flexibly model spatial variation in edge strengths. Scalable inference is achieved through an augmented mean-field variational Bayes algorithm with node-wise parallel regressions, enabling efficient estimation in high-dimensional settings. Simulation studies demonstrate improved recovery of network structures compared with competing approaches. Applying mSGR to multi-resolution ST data from kidney cancer reveals stronger regulatory connectivity in transitional regions of epithelial-mesenchymal transition pathway and identifies hub genes along the tumor gradient, illustrating how spatially resolved network analysis can provide key insights into tumor microenvironment organization.

genomics↗

bioRxiv2025

Spatial analysis reveals a novel inflammatory tumor transition state which promotes a macrophage-driven induction of sarcomatoid renal cell carcinoma

Sarcomatoid renal cell carcinoma (sRCC) is an aggressive transdifferentiation of epithelioid clear cell RCC (ccRCC) tumors that shows heightened response to immunotherapy. The underlying biology leading to sarcomatoid transformation and mechanisms contributing to immunotherapy response are not well understood. Novel single cell spatial techniques were used in ccRCC and sRCC tumors from 40 patients to understand the spatial sRCC transformation and corresponding immune changes. A transcriptional transition state in epithelioid ccRCC cells along a continuum to mesenchymal sRCC was identified which expresses high levels of pro-inflammatory cytokines and an immune infiltrate. In vitro studies demonstrated that M2-like macrophages, recruited to the tumor by the transition state, induce full transition to the sarcomatoid state. A combination of increased PD-L1 expression and T-cells recruited by the transition state was observed, consistent with the increased immunotherapy response. This study enriches our understanding of the mechanisms leading to development and immune responsiveness of sRCC paving the way for novel approaches to diminish RCC progression.

cancer biology↗

bioRxiv2024

Somatic Mutations in MCOLN3 in Aldosterone-Producing Adenomas cause Primary Aldosteronism.

Primary aldosteronism is characterized by renin-independent hyperaldosteronism that originates from aldosterone-producing lesions in the adrenal glands. Under physiological conditions, aldosterone synthase (CYP11B2) expression is confined to the adrenal zona glomerulosa where it catalyzes the final reaction yielding aldosterone. The regulation of CYP11B2 transcription depends on the control of cellular membrane potential and cytosolic calcium activity. In primary aldosteronism, aldosterone-producing adenomas (APAs) are characterized by disrupted regulation of CYP11B2 expression resulting in autonomous biosynthesis of aldosterone. These lesions often harbor aldosterone-driver somatic mutations in genes encoding ion transporters/channels/pumps that increase cytosolic calcium activity causing increased CYP11B2 expression and aldosterone biosynthesis. We investigated APAs devoid of known somatic mutations and detected a missense mutation and a deletion-insertion variant in MCOLN3 which encodes for mucolipin-3 (TRPML3) -- a highly conserved inwardly-rectifying, cation-permeable channel. These MCOLN3 mutations were identified in three APAs derived from male patients with primary aldosteronism: p. Y391D and p.N411_V412delinsI. Both mutations are located near the ion pore and selectivity filter of TRPML3. This is the first report of disease-causing MCOLN3 mutations in humans. Functional studies suggest MCOLN3Y391D might directly or indirectly via membrane depolarization alter calcium influx of transfected adrenocortical cells, resulting in increased CYP11B2 transcription and aldosterone production. This study implicates mutated MCOLN3 as a driver of aldosterone excess in primary aldosteronism. Significance StatementPrimary aldosteronism is a common but under-diagnosed endocrine disease that contributes to global hypertension burden and cardiovascular mortality and morbidity. Hyperaldosteronism in primary aldosteronism is mainly caused by adrenal lesions harboring somatic mutations that disrupt intracellular calcium levels and consequently aldosterone synthase expression and aldosterone production. Majority of these mutations have been identified in genes encoding ion transporters/channels/pumps. Herein, we report the first disease-causing somatic mutations in human MCOLN3 in aldosterone-producing adenomas (APAs) devoid of known mutations. In vitro investigations showed the MCOLN3 variant (p.Y391D) caused an influx of cytosolic calcium in adrenocortical cells and the subsequent increase in aldosterone synthase and aldosterone biosynthesis.

genetics↗

bioRxiv2022

Zinc transporter somatic gene mutations cause primary aldosteronism

Primary aldosteronism (PA) is the most common form of endocrine hypertension and effects one in 50 adults. PA is characterized by inappropriately elevated aldosterone production via renin-independent mechanisms. Driver somatic mutations for aldosterone excess have been found in approximately 90% of aldosterone-producing adenomas (APAs). Using next-generation sequencing, we identified recurrent in-frame deletions in SLC30A1 in five APAs (p.L51_A57del, n=3; p.L49_L55del, n=2). SLC30A1 encodes the ubiquitous zinc efflux transporter ZnT1 (zinc transporter 1). The identified SLC30A1 variants are situated in close proximity of the zincbinding site (H43 and D47) in transmembrane domain II and likely cause abnormal ion transport. PA cases with the unique SLC30A1 mutations showed male dominance and demonstrated increased aldosterone and 18-oxo-cortisol concentrations. Functional studies of the mutant SLC30A151_57del variant in a doxycycline-inducible adrenal cell system revealed abnormal Na+ conductivity caused by the mutant, which in turn led to the depolarization of the resting membrane potential, and thus to the opening of voltage-gated calcium channels. This resulted in an increase in cytosolic Ca2+ activity, which stimulated CYP11B2 mRNA expression and aldosterone production. Collectively, these data implicate the first-in-field zinc transporter mutations as a dominant driver of aldosterone excess in PA.

genetics↗