Biology subjects

Aldea, D.

Publications and source records attributed to Aldea, D..

7 recordsLinked to original sources

bioRxiv2026

Spatially resolved diversity in molecular states underlies congenital melanocytic nevi and associated tumors

The congenital melanocytic nevus (CMN) is a developmental skin disorder characterized by prenatal melanocyte overgrowth, exhibiting heterogeneity in surface size, depth, and clinical behavior. Large/giant CMN carry an elevated, anticipatory melanoma risk relative to more common, small CMN. However, deeper insights into melanocytic states, genomic and epigenomic alterations, and microenvironmental cues governing disease progression are needed to predict lesions disposed to transformation. Although large/giant CMN melanocyte heterogeneity was recently established, spatial organization of these states and their niche interactions are unknown. Using advanced spatial and single-cell transcriptomics and bulk methylomics, we characterized ten CMN, seven CMN-associated proliferative nodules and three clinically diagnosed melanomas arising in CMN from children, integrating data from healthy skin references to contextualize melanocyte states in situ. CMN-specific melanocytic states, distinct in differentiation and proliferation, were spatially stratified, with immature melanocytes in deep dermis and more differentiated melanocytes approaching the epidermis. We then constructed a robust atlas of CMN cellular states by integrating single-cell transcriptomic data from five new large/giant CMN with published datasets, using it to deconvolute the spatial information. Cell-cell communication inference uncovered enhanced signaling (e.g. pleiotrophin, IGF1, periostin, semaphorin pathways) between CMN melanocytes, fibroblasts, and hair follicle-associated cells. Analysis of CMN-derived tumors, including longitudinal cases with [≥]2 samples, revealed divergent spatial melanocytic transcription distinguishing immune-enriched lesions from tumors with oncogenic/pro-invasive signatures. Collectively, these findings establish a spatially resolved framework linking melanocyte heterogeneity, signaling, and genomic instability in CMN, providing mechanistic insights to refine risk stratification and prognosis for CMN-associated tumors.

genetics↗

bioRxiv2024

Deconvoluted methylation profiles discriminate between closely related melanocytic nevi

Congenital melanocytic nevi (CMN) and common acquired melanocytic nevi (AMN) are melanoma-predisposing skin conditions presenting excessive numbers of melanocytes but arising at different times in life. Appropriately weighted whole-genome methylation analysis can be used as a basis for further research in dermatopathology and as applied here provides new insights into nevus biology.

cancer biology↗

bioRxiv2023

A transient dermal niche and dual epidermal programs underlie sweat gland development

Eccrine glands are mammalian skin appendages indispensable for human thermoregulation. Like all skin-derived appendages, eccrine glands form from multipotent progenitors in the basal skin epidermis. It remains unclear how epidermal progenitors progressively specialize to specifically form eccrine glands, precluding efforts to regenerate these vital organs. Herein, we applied single nucleus transcriptomics to compare the expression content of wildtype, eccrine-forming mouse skin to that of mice harboring a skin-specific disruption of Engrailed 1 (En1), a transcription factor that promotes the formation of eccrine glands in both humans and mice. We identify two concurrent epidermal transcriptomes in the earliest eccrine anlagen: a predominant transcriptome that is shared with hair follicles, and a vastly underrepresented transcriptome that is En1-dependent and eccrine-specific. We demonstrate that differentiation of the eccrine anlage requires the induction of a transient and transcriptionally unique dermal niche that forms around each developing gland in humans and mice. Our study defines the transcriptional determinants underlying eccrine identity in the epidermis and uncovers the dermal niche required for eccrine developmental progression. By identifying these defining components of the eccrine developmental program, our findings set the stage for directed efforts to regenerate eccrine glands for comprehensive skin repair.

developmental biology↗

bioRxiv2022

Differential modularity of the mammalian Engrailed 1 enhancer network directs eccrine sweat gland development

Enhancers are context-specific regulators of expression that drive biological complexity and variation through the redeployment of conserved genes. An example of this is the enhancer-mediated control of the transcription of Engrailed 1 (EN1), a pleiotropic gene whose expression is required for the specification of eccrine sweat glands in mammals. We have previously identified an enhancer, ECE18 that has been highly and repeatedly derived on the human lineage to potentiate ectodermal EN1 and induce our species uniquely high eccrine gland density. Intriguingly, ECE18 quantitative activity is negligible outside of primates and ECE18 is not required for En1 regulation and eccrine gland specification in mice, raising the possibility that distinct enhancers have evolved to modulate the same trait. Here we report the identification of the ECE20 enhancer and show it has conserved functionality in mouse and human developing skin ectoderm. Unlike ECE18, knock-out of ECE20 in mice reduces ectodermal En1 and eccrine gland number. Notably, we find ECE20, but not ECE18, is also required for En1 expression in the embryonic mouse brain, demonstrating that ECE20 is a pleiotropic En1 enhancer. Finally, that ECE18 deletion does not potentiate the eccrine phenotype of ECE20 knockout mice supports the secondary incorporation of ECE18 into the regulation of this trait in primates. Our findings reveal that the mammalian En1 regulatory machinery diversified to incorporate both shared and lineage-restricted enhancers to regulate the same phenotype, and also have implications for understanding the forces that shape the robustness and evolvability of developmental traits.

evolutionary biology↗

bioRxiv2022

Ectodysplasin signaling via Xedar is required for mammary gland morphogenesis

The Ectodysplasin A2 receptor (XEDAR), is a member of the tumor necrosis factor receptor subfamily and is a mediator of the Ectodysplasin (EDA) signaling pathway. EDA signaling plays evolutionarily conserved roles in the development of the ectodermal appendage organ class that includes hair, eccrine sweat glands, and mammary glands. Loss of function mutations in Eda, which encodes the two major ligand isoforms, EDA-A1 and EDA-A2, result in X-linked hypohidrotic ectodermal dysplasia (XLHED), which is characterized by defects in two or more ectodermal appendage types. EDA-A1 and EDA-A2 signal through the receptors EDAR and XEDAR, respectively. While the contributions of the EDA-A1/EDAR signaling pathway to ectodermal appendage phenotypes have been extensively characterized, the significance of the EDA-A2/XEDAR branch of the pathway has remained obscure. Herein, we report the phenotypic consequences of disrupting the EDA-A2/XEDAR pathway on mammary gland differentiation and growth. Using a mouse Xedar knock-out model, we show that Xedar has a specific and temporally restricted role in promoting post-pubertal growth and branching of the mammary epithelium that can be influenced by genetic background. Our findings are the first to implicate Xedar in ectodermal appendage development and suggest that the EDA-A2/XEDAR signaling axis contributes to the etiology of EDA-dependent mammary phenotypes.

developmental biology↗

bioRxiv2020

An Engrailed1 enhancer underlies human thermoregulatory evolution

Humans rely on sweating to cool off and have the highest eccrine sweat gland density among mammals. We investigated whether altered regulation of the Engrailed 1 (EN1) gene, the levels of which are critical for patterning eccrine glands during development, could underlie the evolution of this defining human trait. First, we identify five EN1 candidate enhancers (ECEs) using comparative genomics and validation of enhancer activity in mouse skin. The human ortholog of one ECE, hECE18, contains multiple derived substitutions that together dramatically increase the activity of this enhancer in keratinocytes. Targeted repression of hECE18 reduces EN1 expression in human keratinocytes, indicating hECE18 upregulates EN1 in this context. Finally, we find that hECE18 increases ectodermal En1 in a humanized knock-in mouse to increase eccrine gland number. Our study uncovers a genetic basis for the evolution of one of the most singular human adaptations and implicates the recurrent mutation of a single enhancer as a novel mechanism for evolutionary change.

evolutionary biology↗

bioRxiv2018

FDA-ARGOS: A Public Quality-Controlled Genome Database Resource for Infectious Disease Sequencing Diagnostics and Regulatory Science Research

Infectious disease next generation sequencing (ID-NGS) diagnostics are on the cusp of revolutionizing the clinical market. To facilitate this transition, FDA proactively invested in tools to support innovation of emerging technologies. FDA and collaborators established a publicly available database, FDA dAtabase for Regulatory-Grade micrObial Sequences (FDA-ARGOS), as a tool to fill reference database gaps with quality-controlled genomes. This manuscript discusses quality control metrics for the proposed FDA-ARGOS genomic resource and outlines the need for quality-controlled genome gap filling in the public domain. Here, we also present three case studies showcasing potential applications for FDA-ARGOS in infectious disease diagnostics, specifically: assay design, reference database and in silico sequence comparison in combination with representative microbial organism wet lab testing; a novel composite validation strategy for ID-NGS diagnostics. The use of FDA-ARGOS as an in silico comparator tool could reduce the burden for completing ID-NGS clinical trials. In addition, use cases identifying Enterococcus avium and Ebola virus (Zaire ebolavirus variant Makona) demonstrate the utility of FDA-ARGOS as a reference database for independent performance validation of new tests and for documenting how one would use this database as an in silico sequence target comparator tool for ID-NGS validation, respectively.

microbiology↗